[Bioperl-l] problems running Bio::SearchIO on the FASTA results

Christie Robertson cpr at geospiza.com
Mon Dec 27 18:53:35 EST 2004


Hi folks,

I'm wondering if anybody here is currently parsing the results of
the FASTA program with Bio::SearchIO.  I'm running into a problem very
early on in the process, right at the moment of trying to parse a result.
Here is a pared-down example program:

>>>>>>

use Bio::SearchIO;

my $fastaFile = 'chWnt3_hg_Gnomon_prots_E0.001.out';
my $searchIO = new Bio::SearchIO(-format => 'fasta',
                                 -file => $fastaFile);

my $result = $searchIO->next_result;

<<<<<<<

This program dies on the call to $searchIO->next_result() with this
message:

>>>>>>>

1039 cpr at napa:~/fastaTest > ./bioperlFastaParseTest.pl
Use of uninitialized value in concatenation (.) or string at
/usr/lib/perl5/site_perl/5.8.0/Bio/Search/HSP/GenericHSP.pm line 231,
<GEN1> line 131.

------------- EXCEPTION  -------------
MSG: Did not specify a Query End or Query Begin -verbose 0 -algorithm
FASTP -hit_seq
CRNYIEIMPSVAEGVKLGIQECQHQFRGRRWNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNKHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDFLKDKYDSASEMVVEKHRESRGWVETLRAKYSLFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRIYDVHTCK
-hit_length 297 -query_length 297 -query_frame 0 -rank 1 -hit_name hmm6623
-query_name gi|18091804|gb|AAL58093.1| -evalue 0 -score 4361.0 -hit_frame
0 -hsp_length 297 -swscore 3215 -query_seq
WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
-homology_seq
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::::::::::::::::.::::::::::::::::::::::::::::::
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::.:::::::
-bits 815.4 (qs='
STACK Bio::Search::HSP::GenericHSP::new
/usr/lib/perl5/site_perl/5.8.0/Bio/Search/HSP/GenericHSP.pm:231
STACK Bio::Search::HSP::FastaHSP::new
/usr/lib/perl5/site_perl/5.8.0/Bio/Search/HSP/FastaHSP.pm:97
STACK Bio::Factory::ObjectFactory::create_object
/usr/lib/perl5/site_perl/5.8.0/Bio/Factory/ObjectFactory.pm:150
STACK Bio::SearchIO::SearchResultEventBuilder::end_hsp
/usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/SearchResultEventBuilder.pm:275
STACK Bio::SearchIO::fasta::end_element
/usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/fasta.pm:872
STACK Bio::SearchIO::fasta::next_result
/usr/lib/perl5/site_perl/5.8.0/Bio/SearchIO/fasta.pm:403
STACK toplevel ./bioperlFastaParseTest.pl:9

--------------------------------------
1040 cpr at napa:~/fastaTest >

<<<<<<<

Apparently, Bio::Search::HSP::GenericHSP.pm expects Query End and Query
Begin to be set, and isn't getting them.  Out of curiosity, I commented
the die line (231) from GenericHSP.pm, and then the module dies on the
next line, looking for Hit Begin and Hit End.  Did the FASTA output format
get out of sync with SearchIO?  Am I missing something?

I am attaching my output file.

Thanks for any help!

Christie


~~~~~~~~~~~~~~~~~~~~~~~~~
Christie P Robertson, PhD
Research Associate
Geospiza, Inc.

cpr at geospiza.com
(206)633-4403
~~~~~~~~~~~~~~~~~~~~~~~~~
-------------- next part --------------
# fasta chWnt3.fasta /usr/local/data/hg_Gnomon_prots.fsa 1 -E 0.001 -Q -s P20
FASTA searches a protein or DNA sequence data bank
 version 3.4t24 July 21, 2004
Please cite:
 W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448

Query library chWnt3.fasta vs /usr/local/data/hg_Gnomon_prots.fsa library
searching /usr/local/data/hg_Gnomon_prots.fsa library

  1>>>gi|18091804|gb|AAL58093.1| Wnt3 [Gallus gallus] - 267 aa
 vs  /usr/local/data/hg_Gnomon_prots.fsa library

       opt      E()
< 20     1     0:=
  22     2     0:=          one = represents 62 library sequences
  24     8     0:=
  26    43     1:*
  28    94     9:*=
  30   295    52:*====
  32   526   200:===*=====
  34   791   543:========*====
  36   844  1115:==============   *
  38  1300  1843:=====================        *
  40  2554  2571:=========================================*
  42  3522  3142:==================================================*======
  44  3683  3466:=======================================================*====
  46  3282  3530:=====================================================   *
  48  3115  3380:===================================================   *
  50  2902  3084:===============================================  *
  52  2509  2711:=========================================  *
  54  2338  2316:=====================================*
  56  2088  1935:===============================*==
  58  1837  1588:=========================*====
  60  1427  1287:====================*===
  62   998  1031:================*
  64   809   820:=============*
  66   546   648:========= *
  68   434   510:======= *
  70   370   400:======*
  72   303   312:=====*
  74   266   243:===*=
  76   183   190:===*
  78    95   147:==*
  80    83   114:=*
  82    62    87:=*
  84    71    69:=*
  86    56    54:*
  88    52    41:*          inset = represents 1 library sequences
  90    28    32:*
  92    14    25:*         :==============          *
  94    10    19:*         :==========        *
  96    12    15:*         :============  *
  98     6    12:*         :======     *
 100    10     9:*         :========*=
 102     3     7:*         :===   *
 104     5     5:*         :====*
 106     5     4:*         :===*=
 108     1     3:*         := *
 110     0     2:*         : *
 112     0     2:*         : *
 114     0     1:*         :*
 116     0     1:*         :*
 118     0     1:*         :*
>120    22     1:*         :*=====================
17173199 residues in 37605 sequences
  Expectation_n fit: rho(ln(x))= 1.9310+/-0.000241; mu= 29.4800+/- 0.014
 mean_var=54.1966+/-10.424, 0's: 0 Z-trim: 22  B-trim: 0 in 0/45
 Lambda= 0.174216
 Kolmogorov-Smirnov  statistic: 0.0254 (N=29) at  34

FASTA (3.47 Mar 2004) function [optimized, MD20 matrix (18:-29)] ktup: 1
 join: 42, opt: 30, gap-pen: -26/-4, width:  32
 Scan time:  6.780
The best scores are:                                      opt bits E(37605)
hmm6623 Gene predicted by Gnomon on Homo sapiens   ( 453) 3215 815.4       0
hmm10855 Gene predicted by Gnomon on Homo sapiens  ( 352) 2746 697.3 4.4e-201
hmm9156 Gene predicted by Gnomon on Homo sapiens   ( 351)  899 233.0 2.5e-61
hmm2415 Gene predicted by Gnomon on Homo sapiens   ( 370)  814 211.7 6.8e-55
hmm19724 Gene predicted by Gnomon on Homo sapiens  ( 360)  711 185.8 4.2e-47
hmm18663 Gene predicted by Gnomon on Homo sapiens  ( 360)  711 185.8 4.2e-47
hmm12279 Gene predicted by Gnomon on Homo sapiens  ( 865)  703 184.7 2.3e-46
hmm13855 Gene predicted by Gnomon on Homo sapiens  ( 349)  652 171.0 1.2e-42
hmm9892 Gene predicted by Gnomon on Homo sapiens   ( 391)  610 160.5 1.9e-39
hmm14214 Gene predicted by Gnomon on Homo sapiens  ( 380)  606 159.5 3.7e-39
hmm2064 Gene predicted by Gnomon on Homo sapiens   ( 411)  526 139.5 4.3e-33
hmm627 Gene predicted by Gnomon on Homo sapiens r  ( 351)  518 137.3 1.7e-32
hmm2414 Gene predicted by Gnomon on Homo sapiens   ( 389)  514 136.4 3.4e-32
hmm19734 Gene predicted by Gnomon on Homo sapiens  ( 365)  469 125.0 8.6e-29
hmm18673 Gene predicted by Gnomon on Homo sapiens  ( 365)  469 125.0 8.6e-29
hmm16428 Gene predicted by Gnomon on Homo sapiens  ( 355)  446 119.2 4.7e-27
hmm13573 Gene predicted by Gnomon on Homo sapiens  ( 587)  391 105.9   8e-23
hmm13572 Gene predicted by Gnomon on Homo sapiens  ( 709)  378 102.8 8.2e-22
hmm1658 Gene predicted by Gnomon on Homo sapiens   ( 354)  363  98.3 8.9e-21
hmm10853 Gene predicted by Gnomon on Homo sapiens  ( 365)  170  49.9 3.6e-06
hmm6624 Gene predicted by Gnomon on Homo sapiens   ( 357)  165  48.6 8.5e-06

>>hmm6623 Gene predicted by Gnomon on Homo sapiens refer  (453 aa)
 initn: 3215 init1: 3215 opt: 3215  Z-score: 4361.0  bits: 815.4 E():    0
Smith-Waterman score: 3215;  98.502% identity (99.625% similar) in 267 aa overlap (1-267:187-453)

                                             10        20        30
gi|180                               WNCTTIDDSLAIFGPVLDKATRESAFVHAI
                                     ::::::::::::::::::::::::::::::
hmm662 CRNYIEIMPSVAEGVKLGIQECQHQFRGRRWNCTTIDDSLAIFGPVLDKATRESAFVHAI
        160       170       180       190       200       210      

               40        50        60        70        80        90
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADAREN
       ::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
hmm662 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADAREN
        220       230       240       250       260       270      

              100       110       120       130       140       150
gi|180 RPDARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKY
       :::::::::.::::::::::::::::::::::::::::::::::::::::::::.:::::
hmm662 RPDARSAMNKHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDFLKDKY
        280       290       300       310       320       330      

              160       170       180       190       200       210
gi|180 DSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDR
       ::::::::::::::::::::::::: ::::::::::::::::::::::::::::::::::
hmm662 DSASEMVVEKHRESRGWVETLRAKYSLFKPPTERDLVYYENSPNFCEPNPETGSFGTRDR
        340       350       360       370       380       390      

              220       230       240       250       260       
gi|180 TCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
       :::::::::::::::::::::::::::::::::::::::::::::::::.:::::::
hmm662 TCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRIYDVHTCK
        400       410       420       430       440       450   

>>hmm10855 Gene predicted by Gnomon on Homo sapiens refe  (352 aa)
 initn: 2746 init1: 2746 opt: 2746  Z-score: 3724.6  bits: 697.3 E(): 4.4e-201
Smith-Waterman score: 2746;  87.640% identity (90.262% similar) in 267 aa overlap (1-267:86-352)

                                             10        20        30
gi|180                               WNCTTIDDSLAIFGPVLDKATRESAFVHAI
                                     :::::. :::::::::::::::::::::::
hmm108 CRNYVEIMPSVAEGIKIGIQECQHQFRGRRWNCTTVHDSLAIFGPVLDKATRESAFVHAI
          60        70        80        90       100       110     

               40        50        60        70        80        90
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADAREN
       :::::::::::::::::  :::: : : : :: :::::::::: .::  :::::::::::
hmm108 ASAGVAFAVTRSCAEGTAAICGCSSRHQGSPGKGWKWGGCSEDIEFGGMVSREFADAREN
         120       130       140       150       160       170     

              100       110       120       130       140       150
gi|180 RPDARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKY
       :::::::::::::::::  :  :::::::::::::::::::::: :::::::::.:::::
hmm108 RPDARSAMNRHNNEAGRQAIASHMHLKCKCHGLSGSCEVKTCWWSQPDFRAIGDFLKDKY
         180       190       200       210       220       230     

              160       170       180       190       200       210
gi|180 DSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDR
       :::::::::::::::::::::: .:  :: :::::::::: :::::::::::::::::::
hmm108 DSASEMVVEKHRESRGWVETLRPRYTYFKVPTERDLVYYEASPNFCEPNPETGSFGTRDR
         240       250       260       270       280       290     

              220       230       240       250       260       
gi|180 TCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
       :::: ::::::::::::::::: : :.:.::: :.:::::::::::: :::::::::
hmm108 TCNVSSHGIDGCDLLCCGRGHNARAERRREKCRCVFHWCCYVSCQECTRVYDVHTCK
         300       310       320       330       340       350  

>>hmm9156 Gene predicted by Gnomon on Homo sapiens refer  (351 aa)
 initn: 954 init1: 393 opt: 899  Z-score: 1215.7  bits: 233.0 E(): 2.5e-61
Smith-Waterman score: 899;  53.676% identity (58.456% similar) in 272 aa overlap (1-266:87-350)

                                             10        20        30
gi|180                               WNCTTIDDSLAIFGPVLDKATRESAFVHAI
                                     ::: : : :: .:: :    ::: :::.::
hmm915 CKRNLEVMDSVRRGAQLAIEECQYQFRNRRWNCSTLD-SLPVFGKVVTQGTREAAFVYAI
         60        70        80        90        100       110     

               40        50        60        70        80        90
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADAREN
        :::::::::: :  :    ::::    :    :  : :::.   .::  :  : : :: 
hmm915 SSAGVAFAVTRACSSGELEKCGCDRTVHGVSPQGFQWSGCSDNIAYGVAFSQSFVDVRER
         120       130       140       150       160       170     

                 100       110       120       130       140       
gi|180 RPDARSA---MNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLK
          : :    :: :::::::  :: ::   ::::: :::::::::: : : :: .:  ::
hmm915 SKGASSSRALMNLHNNEAGRKAILTHMRVECKCHGVSGSCEVKTCWRAVPPFRQVGHALK
         180       190       200       210       220       230     

       150       160       170          180       190       200    
gi|180 DKYDSASEMVVEKHRESRGWVETLRA---KYALFKPPTERDLVYYENSPNFCEPNPETGS
       .:.: : :  ::  :     :   ::   . : ::: :. :::: : :: :::     : 
hmm915 EKFDGATE--VEPRR-----VGSSRALVPRNAQFKPHTDEDLVYLEPSPDFCEQDMRSGV
         240              250       260       270       280        

          210       220       230       240       250       260    
gi|180 FGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVH
        ::: :::: ::  ::::.:::::::  :      :.: : :::::.: :  : :  . :
hmm915 LGTRGRTCNKTSKAIDGCELLCCGRGFHTAQVELAERCSCKFHWCCFVKCRQCQRLVELH
      290       300       310       320       330       340        

          
gi|180 TCK
       :: 
hmm915 TCR
      350 

>>hmm2415 Gene predicted by Gnomon on Homo sapiens refer  (370 aa)
 initn: 927 init1: 554 opt: 814  Z-score: 1100.1  bits: 211.7 E(): 6.8e-55
Smith-Waterman score: 814;  52.282% identity (58.091% similar) in 241 aa overlap (22-257:122-360)

                        10        20        30        40        50 
gi|180          WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTIC
                                     :: ::. :: ::::   : ::: ::    :
hmm241 ECKWQFRNRRWNCPTAPGPHLFGKIVNRGCRETAFIFAITSAGVTHSVARSCSEGSIESC
             100       110       120       130       140       150 

              60        70        80        90       100       110 
gi|180 GCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRTTIL
        ::   .:: :  : :::::.  ::: :  ::: :  :   : :  :: :::::::::. 
hmm241 TCDYRRRGPGGPDWHWGGCSDNIDFGRLFGREFVDSGEKGRDLRFLMNLHNNEAGRTTVF
             160       170       180       190       200       210 

             120       130       140       150       160           
gi|180 DHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEK---HRESRGWV
         :   ::::: :::: :.:::   :  ::.:: :.:..: ::          : ::   
hmm241 SEMRQECKCHGMSGSCTVRTCWMRLPTLRAVGDVLRDRFDGASRVLYGNRGSNRASR--A
             220       230       240       250       260           

      170         180       190       200       210       220      
gi|180 ETLR--AKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLC
       : ::        :::   ::::.: :::::      :  ::  : ::  :   :::.:::
hmm241 ELLRLEPEDPAHKPPSPHDLVYFEKSPNFCTYSGRLGTAGTAGRACNSSSPALDGCELLC
     270       280       290       300       310       320         

        230       240       250       260       
gi|180 CGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
       ::::: ::: .  :.: : :::::.:::  :          
hmm241 CGRGHRTRTQRVTERCNCTFHWCCHVSCRNCTHTRVLHECL
     330       340       350       360       370

>>hmm19724 Gene predicted by Gnomon on Homo sapiens HSC_  (360 aa)
 initn: 892 init1: 418 opt: 711  Z-score: 960.3  bits: 185.8 E(): 4.2e-47
Smith-Waterman score: 711;  48.718% identity (54.945% similar) in 273 aa overlap (1-267:85-349)

                                             10        20        30
gi|180                               WNCTTIDDSLAIFGPVLDKATRESAFVHAI
                                     ::: : :     :: :: .  ::::::.::
hmm197 CHRHPDVMRAISQGVAEWTAECQHQFRQHRWNCNTLDRDHSLFGRVLLRSSRESAFVYAI
           60        70        80        90       100       110    

               40        50        60            70        80      
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWK----WGGCSEDADFGVLVSREFAD
        :::: ::.:: :  :    : ::    :   .  :    :::::.  :.:.   : : :
hmm197 SSAGVVFAITRACSQGEVKSCSCDPKKMGSAKDS-KGIFDWGGCSDNIDYGIKFARAFVD
          120       130       140        150       160       170   

         90        100       110       120       130       140     
gi|180 ARENRP-DARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDY
       :.: .  :::  :: ::: :::  .       ::::: ::::  .::: :  :::  :::
hmm197 AKERKGKDARALMNLHNNRAGRKAVKRFLKQECKCHGVSGSCTLRTCWLAMADFRKTGDY
           180       190       200       210       220       230   

         150       160        170       180       190       200    
gi|180 LKDKYDSASEMVVEKHRESRGW-VETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGS
       :  ::  :   :     .  :  :   :     :: ::  ::::.:::: .:    : ::
hmm197 LWRKYNGAIQVVM--NQDGTGFTVANER-----FKKPTKNDLVYFENSPDYCIRDREAGS
           240         250            260       270       280      

          210       220       230       240       250       260    
gi|180 FGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVH
        ::  : :: :: : : :.  :::::. :    :  :: : ::::: : ::.:    :::
hmm197 LGTAGRVCNLTSRGMDSCEVMCCGRGYDTSHVTRMTKCGCKFHWCCAVRCQDCLEALDVH
        290       300       310       320       330       340      

                     
gi|180 TCK           
       :::           
hmm197 TCKAPKNADWTTAT
        350       360

>>hmm18663 Gene predicted by Gnomon on Homo sapiens refe  (360 aa)
 initn: 892 init1: 418 opt: 711  Z-score: 960.3  bits: 185.8 E(): 4.2e-47
Smith-Waterman score: 711;  48.718% identity (54.945% similar) in 273 aa overlap (1-267:85-349)

                                             10        20        30
gi|180                               WNCTTIDDSLAIFGPVLDKATRESAFVHAI
                                     ::: : :     :: :: .  ::::::.::
hmm186 CHRHPDVMRAISQGVAEWTAECQHQFRQHRWNCNTLDRDHSLFGRVLLRSSRESAFVYAI
           60        70        80        90       100       110    

               40        50        60            70        80      
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKGPPGEGWK----WGGCSEDADFGVLVSREFAD
        :::: ::.:: :  :    : ::    :   .  :    :::::.  :.:.   : : :
hmm186 SSAGVVFAITRACSQGEVKSCSCDPKKMGSAKDS-KGIFDWGGCSDNIDYGIKFARAFVD
          120       130       140        150       160       170   

         90        100       110       120       130       140     
gi|180 ARENRP-DARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDY
       :.: .  :::  :: ::: :::  .       ::::: ::::  .::: :  :::  :::
hmm186 AKERKGKDARALMNLHNNRAGRKAVKRFLKQECKCHGVSGSCTLRTCWLAMADFRKTGDY
           180       190       200       210       220       230   

         150       160        170       180       190       200    
gi|180 LKDKYDSASEMVVEKHRESRGW-VETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGS
       :  ::  :   :     .  :  :   :     :: ::  ::::.:::: .:    : ::
hmm186 LWRKYNGAIQVVM--NQDGTGFTVANER-----FKKPTKNDLVYFENSPDYCIRDREAGS
           240         250            260       270       280      

          210       220       230       240       250       260    
gi|180 FGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVH
        ::  : :: :: : : :.  :::::. :    :  :: : ::::: : ::.:    :::
hmm186 LGTAGRVCNLTSRGMDSCEVMCCGRGYDTSHVTRMTKCGCKFHWCCAVRCQDCLEALDVH
        290       300       310       320       330       340      

                     
gi|180 TCK           
       :::           
hmm186 TCKAPKNADWTTAT
        350       360

>>hmm12279 Gene predicted by Gnomon on Homo sapiens refe  (865 aa)
 initn: 675 init1: 544 opt: 703  Z-score: 947.1  bits: 184.7 E(): 2.3e-46
Smith-Waterman score: 703;  53.361% identity (58.403% similar) in 238 aa overlap (22-254:618-852)

                        10        20        30        40        50 
gi|180          WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTIC
                                     :: :: .::  :::: :::  :  :    :
hmm122 ECQYQFRFGRWNCSALGEKTVFGQELRVGSREAAFTYAITAAGVAHAVTAACSQGNLSNC
       590       600       610       620       630       640       

                60        70        80        90       100         
gi|180 GCDSHHKG--PPGEGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRTT
       :::    :     ::::::::: :  .:.  :: : :::: .  ::  :: :::::::  
hmm122 GCDREKQGYYNQAEGWKWGGCSADVRYGIDFSRRFVDAREIKKNARRLMNLHNNEAGRKV
       650       660       670       680       690       700       

     110       120       130       140       150       160         
gi|180 ILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKHRESRGWVE
         : :.: ::::: ::::  ::::   : :: .:  ::.::  :    ::  : ::    
hmm122 LEDRMQLECKCHGVSGSCTTKTCWTTLPKFREVGHLLKEKYNAAVQ--VEVVRASRLRQP
       710       720       730       740       750         760     

     170          180       190       200       210       220      
gi|180 T-LRAKYAL--FKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLC
       : :: :  :  .  : : :::: : :::.::    ::: ::  : :: :: : ::::  :
hmm122 TFLRIK-QLRSYQKPMETDLVYIEKSPNYCEEDAATGSVGTQGRLCNRTSPGADGCDTMC
         770        780       790       800       810       820    

        230       240       250       260       
gi|180 CGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
       ::::.::    .   : : :::::.: :             
hmm122 CGRGYNTHQYTKVWQCNCKFHWCCFVKCNTCSERTEVFTCK
          830       840       850       860     

>>hmm13855 Gene predicted by Gnomon on Homo sapiens refe  (349 aa)
 initn: 592 init1: 483 opt: 652  Z-score: 880.2  bits: 171.0 E(): 1.2e-42
Smith-Waterman score: 652;  52.101% identity (57.563% similar) in 238 aa overlap (22-254:102-336)

                        10        20        30        40        50 
gi|180          WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTIC
                                     :: :: .::  :::: :.:  :  :    :
hmm138 ECQFQFRNGRWNCSALGERTVFGKELKVGSREAAFTYAIIAAGVAHAITAACTQGNLSDC
              80        90       100       110       120       130 

              60          70        80        90       100         
gi|180 GCDSHHKGP--PGEGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRTT
       :::    :     ::::::::: :  .:.   . : :::: .  ::  :: :::::::  
hmm138 GCDKEKQGQYHRDEGWKWGGCSADIRYGIGFAKVFVDAREIKQNARTLMNLHNNEAGRKI
             140       150       160       170       180       190 

     110       120       130       140       150        160        
gi|180 ILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMV-VEKHRESRGWV
         . : : ::::: ::::  ::::   : ::  :  :::::    : : ::  : ::   
hmm138 LEENMKLECKCHGVSGSCTTKTCWTTLPQFRELGYVLKDKYN---EAVHVEPVRASRNKR
             200       210       220       230          240        

      170         180       190       200       210       220      
gi|180 ET-LRAKYAL-FKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLC
        : :. :  : .. : . :::: : :::.::  : ::: ::  : :: :     :::: :
hmm138 PTFLKIKKPLSYRKPMDTDLVYIEKSPNYCEEDPVTGSVGTQGRACNKTAPQASGCDLMC
      250       260       270       280       290       300        

        230       240       250       260       
gi|180 CGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
       ::::.::    :   : : ::::::: :             
hmm138 CGRGYNTHQYARVWQCNCKFHWCCYVKCNTCSERTEMYTCK
      310       320       330       340         

>>hmm9892 Gene predicted by Gnomon on Homo sapiens refer  (391 aa)
 initn: 821 init1: 316 opt: 610  Z-score: 822.9  bits: 160.5 E(): 1.9e-39
Smith-Waterman score: 610;  45.588% identity (53.676% similar) in 272 aa overlap (1-267:116-380)

                                             10        20        30
gi|180                               WNCTTIDDSLAIFGPVLDKATRESAFVHAI
                                     ::::: :    .:: :  .  :: :::.::
hmm989 CQRYPDIMRSVGEGAREWIRECQHQFRHHRWNCTTLDRDHTVFGRVMLRSSREAAFVYAI
          90       100       110       120       130       140     

               40        50            60        70        80      
gi|180 ASAGVAFAVTRSCAEGTSTICGCDSHHKG----PPGEGWKWGGCSEDADFGVLVSREFAD
        ::::  :.:: :  :   .: :: . .:      :.   :::::.   .::   . : :
hmm989 SSAGVVHAITRACSQGELSVCSCDPYTRGRHHDQRGD-FDWGGCSDNIHYGVRFAKAFVD
         150       160       170       180        190       200    

         90        100       110       120       130       140     
gi|180 ARENRP-DARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDY
       :.: :  :::  :: :::  ::: .     : ::::: ::::  .::: :  :::  :::
hmm989 AKEKRLKDARALMNLHNNRCGRTAVRRFLKLECKCHGVSGSCTLRTCWRALSDFRRTGDY
          210       220       230       240       250       260    

         150       160       170       180       190       200     
gi|180 LKDKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSF
       :. .:: :                  :  :   .  :  ::::..::: .:      :: 
hmm989 LRRRYDGAVQVMATQDGAN---FTAARQGY---RRATRTDLVYFDNSPDYCVLDKAAGSL
          270       280          290          300       310        

         210       220       230       240       250       260     
gi|180 GTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHT
       ::  : :  :: : :::.  :::::. :    :   : : ::::: : : ::    ::::
hmm989 GTAGRVCSKTSKGTDGCEIMCCGRGYDTTRVTRVTQCECKFHWCCAVRCKECRNTVDVHT
      320       330       340       350       360       370        

                    
gi|180 CK           
       ::           
hmm989 CKAPKKAEWLDQT
      380       390 

>>hmm14214 Gene predicted by Gnomon on Homo sapiens refe  (380 aa)
 initn: 753 init1: 327 opt: 606  Z-score: 817.5  bits: 159.5 E(): 3.7e-39
Smith-Waterman score: 606;  47.761% identity (54.478% similar) in 268 aa overlap (1-257:113-370)

                                             10        20        30
gi|180                               WNCTTIDDSLAIFGPVLDKATRESAFVHAI
                                     ::: :.:    .:: :     :: :: .:.
hmm142 CHLYQDHMQYIGEGAKTGIKECQYQFRHRRWNCSTVDNT-SVFGRVMQIGSRETAFTYAV
             90       100       110       120        130       140 

               40        50          60        70        80        
gi|180 ASAGVAFAVTRSCAEGTSTICGC--DSHHKGPPGEGWKWGGCSEDADFGVLVSREFADAR
         :::  :  : : ::    :::      :  : . : :::: .  :.:    .:: :::
hmm142 SAAGVVNAMSRACREGELSTCGCSRAARPKDLPRD-WLWGGCGDNIDYGYRFAKEFVDAR
             150       160       170        180       190       200

        90              100       110       120       130       140
gi|180 E-NRPDAR----SA---MNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFR
       :  :  :.    ::   :: ::::::: :.       ::::: ::::  ::::    :::
hmm142 ERERIHAKGSYESARILMNLHNNEAGRRTVYNLADVACKCHGVSGSCSLKTCWLQLADFR
              210       220       230       240       250       260

              150       160       170       180       190       200
gi|180 AIGDYLKDKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNP
        .:: ::.:::::  :       :::    :      :  ::  :::: . :: .:  : 
hmm142 KVGDALKEKYDSAAAM----RLNSRG---KLVQVNSRFNSPTTQDLVYIDPSPDYCVRNE
              270           280          290       300       310   

              210       220       230        240       250         
gi|180 ETGSFGTRDRTCNVTSHGIDGCDLLCCGRGHNT-RTEKRKEKCHCIFHWCCYVSCQECIR
        ::: ::  : :: :: : :::.: :::::.   .:    :.::: ::::::: :  :  
hmm142 STGSLGTQGRLCNKTSEGMDGCELMCCGRGYDQFKTVQ-TERCHCKFHWCCYVKCKKCTE
           320       330       340       350        360       370  

     260       
gi|180 VYDVHTCK
               
hmm142 IVDQFVCK
            380

>>hmm2064 Gene predicted by Gnomon on Homo sapiens refer  (411 aa)
 initn: 691 init1: 299 opt: 526  Z-score: 708.7  bits: 139.5 E(): 4.3e-33
Smith-Waterman score: 526;  44.944% identity (53.558% similar) in 267 aa overlap (1-257:144-401)

                                             10        20        30
gi|180                               WNCTTIDDSLAIFGPVLDKATRESAFVHAI
                                     ::: : :    .:: :     :: :: ::.
hmm206 CQLYQEHMAYIGEGAKTGIKECQHQFRQRRWNCSTADNA-SVFGRVMQIGSRETAFTHAV
           120       130       140       150        160       170  

               40        50          60        70        80        
gi|180 ASAGVAFAVTRSCAEGTSTICGCD--SHHKGPPGEGWKWGGCSEDADFGVLVSREFADAR
         :::  :. : : ::    :::      :  : . : :::: .  ..:    .:: :::
hmm206 SAAGVVNAISRACREGELSTCGCSRTARPKDLPRD-WLWGGCGDNVEYGYRFAKEFVDAR
            180       190       200        210       220       230 

             90         100       110       120       130       140
gi|180 E------NRPD--ARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFR
       :         .   :  :: .::::::  .       ::::: ::::  ::::    .::
hmm206 EREKNFAKGSEEQGRVLMNLQNNEAGRRAVYKMADVACKCHGVSGSCSLKTCWLQLAEFR
             240       250       260       270       280       290 

              150       160       170       180       190       200
gi|180 AIGDYLKDKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNP
        .:: ::.:::::  : : .    .:  :    .   :  ::  :::: . :: .:  : 
hmm206 KVGDRLKEKYDSAAAMRVTR----KGRLELVNSR---FTQPTPEDLVYVDPSPDYCLRNE
             300       310           320          330       340    

              210       220       230       240       250       260
gi|180 ETGSFGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRV
        ::: ::  : :: :: : :::.: :::::.:       :.::: :::::.: :  :   
hmm206 STGSLGTQGRLCNKTSEGMDGCELMCCGRGYNQFKSVQVERCHCKFHWCCFVRCKKCTEI
          350       360       370       380       390       400    

              
gi|180 YDVHTCK
              
hmm206 VDQYICK
          410 

>>hmm627 Gene predicted by Gnomon on Homo sapiens refere  (351 aa)
 initn: 662 init1: 398 opt: 518  Z-score: 698.2  bits: 137.3 E(): 1.7e-32
Smith-Waterman score: 518;  53.333% identity (60.000% similar) in 135 aa overlap (20-153:81-215)

                          10        20        30        40         
gi|180            WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTST
                                     : :: :::::: :::: .  :: :  :   
hmm627 IEECKYQFAWDRWNCPERALQLSSHGGLRSANRETAFVHAISSAGVMYTLTRNCSLGDFD
               60        70        80        90       100       110

      50        60         70        80        90       100        
gi|180 ICGCDSHHKGPPG-EGWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRT
        ::::    :  :  :: :::::.   ::  .:. : :: :   ::: ::: ::::::: 
hmm627 NCGCDDSRNGQLGGQGWLWGGCSDNVGFGEAISKQFVDALETGQDARAAMNLHNNEAGRK
              120       130       140       150       160       170

      110       120       130       140       150       160        
gi|180 TILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKHRESRGWV
        .   :   ::::: ::::   :::   :.:: .: .::.::  :               
hmm627 AVKGTMKRTCKCHGVSGSCTTQTCWLQLPEFREVGAHLKEKYHAALKVDLLQGAGNSAAG
              180       190       200       210       220       230

      170       180       190       200       210       220        
gi|180 ETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLCCG
                                                                   
hmm627 RGAIADTFRSISTRELVHLEDSPDYCLENKTLGLLGTEGRECLRRGRALGRWERRSCRRL
              240       250       260       270       280       290

>>hmm2414 Gene predicted by Gnomon on Homo sapiens refer  (389 aa)
 initn: 702 init1: 415 opt: 514  Z-score: 692.5  bits: 136.4 E(): 3.4e-32
Smith-Waterman score: 514;  49.485% identity (56.701% similar) in 194 aa overlap (65-257:194-379)

           40        50        60        70        80        90    
gi|180 VAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRPDA
                                     : ::::  : :::   ::.: : ::   : 
hmm241 LQALSRGKSFPHSLPSPGPGSSPSPGPQDTWEWGGCNHDMDFGEKFSRDFLDSREAPRDI
           170       180       190       200       210       220   

          100       110       120       130       140       150    
gi|180 RSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSAS
          :  :::  ::  . .    :::::: ::::  :::: : :.:::.:  :...   : 
hmm241 QARMRIHNNRVGRQVVTENLKRKCKCHGTSGSCQFKTCWRAAPEFRAVGAALRERLGRA-
           230       240       250       260       270       280   

          160        170       180       190       200       210   
gi|180 EMVVEKH-RESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCN
          .. : : :      :: .    .   :  :::.: :: :::  :  :: ::: : ::
hmm241 -IFIDTHNRNSGAFQPRLRPR----RLSGE--LVYFEKSPDFCERDPTMGSPGTRGRACN
             290       300             310       320       330     

           220       230       240       250       260       
gi|180 VTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
        ::   :::  ::::::::     : :.::: ::::::: : ::          
hmm241 KTSRLLDGCGSLCCGRGHNVLRQTRVERCHCRFHWCCYVLCDECKVTEWVNVCK
         340       350       360       370       380         

>>hmm19734 Gene predicted by Gnomon on Homo sapiens HSC_  (365 aa)
 initn: 606 init1: 297 opt: 469  Z-score: 631.5  bits: 125.0 E(): 8.6e-29
Smith-Waterman score: 469;  45.136% identity (51.751% similar) in 257 aa overlap (21-267:117-365)

                         10        20        30        40        50
gi|180           WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTI
                                     :.: ::..:.  ::    :::::  :  : 
hmm197 HERWNCMITAAATTAPMGASPLFGYELSSGTKETAFIYAVMAAGLVHSVTRSCSAGNMTE
         90       100       110       120       130       140      

                 60        70        80               90       100 
gi|180 CGCDS--HHKGPPGEGWKWGGCSEDADFGVLVSREFAD-------ARENRPDARSAMNRH
       : ::   .  :   ::: :::::.:  .:   :: : :        .::.     ::: :
hmm197 CSCDTTLQNGGSASEGWHWGGCSDDVQYGMWFSRKFLDFPIGNTTGKENK--VLLAMNLH
        150       160       170       180       190         200    

             110       120       130       140       150       160 
gi|180 NNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKH
       ::::::  .   :   :.::: :::: :::::     :  ::  :::::.          
hmm197 NNEAGRQAVAKLMSVDCRCHGVSGSCAVKTCWKTMSSFEKIGHLLKDKYENSIQISDKTK
          210       220       230       240       250       260    

             170       180        190       200       210       220
gi|180 RESRGWVETLRAKYALFKPPTERD-LVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGID
       :  :      :      : :  .: : :   :::.:      :  ::  : :: :: : :
hmm197 RKMRRREKDQR------KIPIHKDDLLYVNKSPNYCVEDKKLGIPGTQGRECNRTSEGAD
          270             280       290       300       310        

              230       240       250       260       
gi|180 GCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
       :: :::::::.::   .  :.: : : ::::: :  :    ::::::
hmm197 GCNLLCCGRGYNTHVVRHVERCECKFIWCCYVRCRRCESMTDVHTCK
      320       330       340       350       360     

>>hmm18673 Gene predicted by Gnomon on Homo sapiens refe  (365 aa)
 initn: 606 init1: 297 opt: 469  Z-score: 631.5  bits: 125.0 E(): 8.6e-29
Smith-Waterman score: 469;  45.136% identity (51.751% similar) in 257 aa overlap (21-267:117-365)

                         10        20        30        40        50
gi|180           WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTSTI
                                     :.: ::..:.  ::    :::::  :  : 
hmm186 HERWNCMITAAATTAPMGASPLFGYELSSGTKETAFIYAVMAAGLVHSVTRSCSAGNMTE
         90       100       110       120       130       140      

                 60        70        80               90       100 
gi|180 CGCDS--HHKGPPGEGWKWGGCSEDADFGVLVSREFAD-------ARENRPDARSAMNRH
       : ::   .  :   ::: :::::.:  .:   :: : :        .::.     ::: :
hmm186 CSCDTTLQNGGSASEGWHWGGCSDDVQYGMWFSRKFLDFPIGNTTGKENK--VLLAMNLH
        150       160       170       180       190         200    

             110       120       130       140       150       160 
gi|180 NNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKH
       ::::::  .   :   :.::: :::: :::::     :  ::  :::::.          
hmm186 NNEAGRQAVAKLMSVDCRCHGVSGSCAVKTCWKTMSSFEKIGHLLKDKYENSIQISDKTK
          210       220       230       240       250       260    

             170       180        190       200       210       220
gi|180 RESRGWVETLRAKYALFKPPTERD-LVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGID
       :  :      :      : :  .: : :   :::.:      :  ::  : :: :: : :
hmm186 RKMRRREKDQR------KIPIHKDDLLYVNKSPNYCVEDKKLGIPGTQGRECNRTSEGAD
          270             280       290       300       310        

              230       240       250       260       
gi|180 GCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
       :: :::::::.::   .  :.: : : ::::: :  :    ::::::
hmm186 GCNLLCCGRGYNTHVVRHVERCECKFIWCCYVRCRRCESMTDVHTCK
      320       330       340       350       360     

>>hmm16428 Gene predicted by Gnomon on Homo sapiens refe  (355 aa)
 initn: 549 init1: 344 opt: 446  Z-score: 600.4  bits: 119.2 E(): 4.7e-27
Smith-Waterman score: 446;  51.128% identity (59.398% similar) in 133 aa overlap (20-151:81-213)

                          10        20        30        40         
gi|180            WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEGTST
                                     ::::  :.::: :::: . .:. :  :   
hmm164 IEECKFQFAWERWNCPENALQLSTHNRLRSATRETSFIHAISSAGVMYIITKNCSMGDFE
               60        70        80        90       100       110

      50        60         70        80        90       100        
gi|180 ICGCDSHHKGPPGE-GWKWGGCSEDADFGVLVSREFADARENRPDARSAMNRHNNEAGRT
        ::::    :  :  :: :::::.  .::  .:. : :  :   :::  :: ::: ::: 
hmm164 NCGCDGSNNGKTGGHGWIWGGCSDNVEFGERISKLFVDSLEKGKDARALMNLHNNRAGRL
              120       130       140       150       160       170

      110       120       130       140       150       160        
gi|180 TILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKHRESRGWV
        .   :   ::::: :::: . :::    .::  ::::: :::                 
hmm164 AVRATMKRTCKCHGISGSCSIQTCWLQLAEFREMGDYLKAKYDQALKIEMDKRQLRAGNS
              180       190       200       210       220       230

      170       180       190       200       210       220        
gi|180 ETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGCDLLCCG
                                                                   
hmm164 AEGHWVPAEAFLPSAEAELIFLEESPDYCTCNSSLGIYGTEGRECLQNSHNTSRWERRSC
              240       250       260       270       280       290

>>hmm13573 Gene predicted by Gnomon on Homo sapiens refe  (587 aa)
 initn: 726 init1: 344 opt: 391  Z-score: 524.4  bits: 105.9 E(): 8e-23
Smith-Waterman score: 391;  43.541% identity (49.761% similar) in 209 aa overlap (65-257:379-577)

           40        50        60        70        80        90    
gi|180 VAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRPDA
                                     : ::::: :  ::   :..: : ::   : 
hmm135 LDALQRGKGLSHGVPEHPALPTASPGLQDSWEWGGCSPDMGFGERFSKDFLDSREPHRDI
      350       360       370       380       390       400        

          100       110       120       130       140       150    
gi|180 RSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSAS
          :  :::  ::  . . :  :::::: ::::  ::::   :.:: .:  :. ..  : 
hmm135 HARMRLHNNRVGRQAVMENMRRKCKCHGTSGSCQLKTCWQVTPEFRTVGALLRSRFHRAT
      410       420       430       440       450       460        

          160       170                       180       190        
gi|180 EMVVEKHRESRGWVET----------------LRAKYALFKPPTERDLVYYENSPNFCEP
          .  :    :  :                  ::       :   ::::.: :: ::: 
hmm135 --LIRPHNRNGGQLEPGPAGAPSPAPGAPGPRRRA------SPA--DLVYFEKSPDFCER
        470       480       490       500               510        

      200       210       220       230       240       250        
gi|180 NPETGSFGTRDRTCNVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECI
        :   : ::  : ::  : : :::   :::::::     : :.::: :::::.: : :: 
hmm135 EPRLDSAGTVGRLCNKSSAGSDGCGSMCCGRGHNILRQTRSERCHCRFHWCCFVVCEECR
      520       530       540       550       560       570        

      260       
gi|180 RVYDVHTCK
                
hmm135 ITEWVSVCK
      580       

>>hmm13572 Gene predicted by Gnomon on Homo sapiens refe  (709 aa)
 initn: 641 init1: 295 opt: 378  Z-score: 506.2  bits: 102.8 E(): 8.2e-22
Smith-Waterman score: 378;  46.667% identity (51.795% similar) in 195 aa overlap (65-257:511-699)

           40        50        60        70        80        90    
gi|180 VAFAVTRSCAEGTSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADARENRP--
                                     : :::: .: :::   :: : :::  :   
hmm135 PRGRAPPRPSGLPGTPGPPGPAGSPEGSAAWEWGGCGDDVDFGDEKSRLFMDARHKRGRG
              490       500       510       520       530       540

            100       110       120       130       140       150  
gi|180 DARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDS
       : :     :::::::  .  :    ::::::::::  .:::   : :: .:  : ...  
hmm135 DIRALVQLHNNEAGRLAVRSHTRTECKCHGLSGSCALRTCWQKLPPFREVGARLLERFHG
              550       560       570       580       590       600

            160       170       180       190       200       210  
gi|180 ASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTC
       ::  :     . .      :      :::   :: :   :: :: ::  ::: ::: : :
hmm135 ASR-VMGTN-DGKALLPAVRT----LKPPGRADLLYAADSPDFCAPNRRTGSPGTRGRAC
                610           620       630       640       650    

            220       230       240       250       260       
gi|180 NVTSHGIDGCDLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
       :       :::::::::::        : : : ::::: : :. :          
hmm135 NSSAPDLSGCDLLCCGRGHRQESVQLEENCLCRFHWCCVVQCHRCRVRKELSLCL
          660       670       680       690       700         

>>hmm1658 Gene predicted by Gnomon on Homo sapiens refer  (354 aa)
 initn: 497 init1: 351 opt: 363  Z-score: 487.6  bits: 98.3 E(): 8.9e-21
Smith-Waterman score: 363;  42.041% identity (51.020% similar) in 245 aa overlap (17-257:104-344)

                             10        20        30        40      
gi|180               WNCTTIDDSLAIFGPVLDKATRESAFVHAIASAGVAFAVTRSCAEG
                                     :.. :::::::.:   : .  :. : :  :
hmm165 REVMKACRRAFADMRWNCSSIELAPNYLLDLERGTRESAFVYALSAAAISHAIARACTSG
            80        90       100       110       120       130   

         50        60        70        80            90       100  
gi|180 TSTICGCDSHHKGPPGEGWKWGGCSEDADFGVLVSREFADA----RENRPDARSAMNRHN
           : :      ::: : .:::: .   .: :    : ::    .     :   :  ::
hmm165 DLPGCSCGPVPGEPPGPGNRWGGCADNLSYGLLMGAKFSDAPMKVKKTGSQANKLMRLHN
           140       150       160       170       180       190   

            110       120       130       140       150       160  
gi|180 NEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLKDKYDSASEMVVEKHR
        : ::         :::::: :::: ..:::    .   .   :: .: ::   :   ::
hmm165 SEVGRQALRASLEMKCKCHGVSGSCSIRTCWKGLQELQDVAADLKTRYLSATKVV---HR
           200       210       220       230       240          250

            170       180       190       200       210       220  
gi|180 ESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGTRDRTCNVTSHGIDGC
          :    :  :    .:  . .:::   :: ::  :   :: :: :: :: :: : : :
hmm165 -PMGTRKHLVPKDLDIRPVKDSELVYLQSSPDFCMKNEKVGSHGTQDRQCNKTSNGSDSC
               260       270       280       290       300         

            230       240       250       260       
gi|180 DLLCCGRGHNTRTEKRKEKCHCIFHWCCYVSCQECIRVYDVHTCK
       :: :::::.:  :..  :.::: .:::::: :  :          
hmm165 DLMCCGRGYNPYTDRVVERCHCKYHWCCYVTCRRCERTVERYVCK
     310       320       330       340       350    

>>hmm10853 Gene predicted by Gnomon on Homo sapiens refe  (365 aa)
 initn: 283 init1: 170 opt: 170  Z-score: 225.4  bits: 49.9 E(): 3.6e-06
Smith-Waterman score: 170;  55.556% identity (66.667% similar) in 36 aa overlap (118-153:215-250)

        90       100       110       120       130       140       
gi|180 RENRPDARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLK
                                     ::::: :::: :.:::     :  .: .::
hmm108 RRSSKDLRARVDFHNNLVGVKVIKAGVETTCKCHGVSGSCTVRTCWRQLAPFHEVGKHLK
          190       200       210       220       230       240    

       150       160       170       180       190       200       
gi|180 DKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGT
        ::. :                                                      
hmm108 HKYETALKVGSTTNEAAGEAGAISPPRGRASGAGGSDPLPRTPELVHLDDSPSFCLAGRF
          250       260       270       280       290       300    

>>hmm6624 Gene predicted by Gnomon on Homo sapiens refer  (357 aa)
 initn: 339 init1: 165 opt: 165  Z-score: 218.7  bits: 48.6 E(): 8.5e-06
Smith-Waterman score: 165;  81.250% identity (87.500% similar) in 16 aa overlap (118-133:210-225)

        90       100       110       120       130       140       
gi|180 RENRPDARSAMNRHNNEAGRTTILDHMHLKCKCHGLSGSCEVKTCWWAQPDFRAIGDYLK
                                     ::::: :::: :.:::              
hmm662 KRGNKDLRARADAHNTHVGIKAVKSGLRTTCKCHGVSGSCAVRTCWKQLSPFRETGQVLK
     180       190       200       210       220       230         

       150       160       170       180       190       200       
gi|180 DKYDSASEMVVEKHRESRGWVETLRAKYALFKPPTERDLVYYENSPNFCEPNPETGSFGT
                                                                   
hmm662 LRYDSAVKVSSATNEALGRLELWAPARQGSLTKGLAPRSGDLVYMEDSPSFCRPSKYSPG
     240       250       260       270       280       290         



267 residues in 1 query   sequences
17173199 residues in 37605 library sequences
 Scomplib [34t24]
 start: Mon Dec 27 15:38:25 2004 done: Mon Dec 27 15:38:32 2004
 Total Scan time:  6.780 Total Display time:  0.030

Function used was FASTA [version 3.4t24 July 21, 2004]


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