[Biopython-dev] Working with the new SearchIO API
Kai Blin
kai.blin at biotech.uni-tuebingen.de
Tue Oct 30 15:54:50 UTC 2012
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On 2012-10-30 08:35, Kai Blin wrote:
Hi Bow,
> I'm mainly wondering why at this position, I can't just create the
> Hit object already, and then later set the HSPs. You could do this
> via a setter function that validates the IDs are identical if you
> want to make sure you're not shooting yourself in the foot there.
I've just stumbled over a case where not being able to pre-create Hit
objects really bites me.
See the attached hmmpfam output. You'll notice that the domain table
is not in the order of the hit table. As I'd like to preserve the
order of the hit table, the current setup of the API forces me to
either repeatedly parse the domain annotations until I find the
correct domain annotations for my hit, or to create the hits in the
order of the domain annotation table and then reshuffle them to make
sure they're in the order of the hit table.
If I could just create "empty" hit objects when parsing the hit table,
I could easily preserve the order of the hits but still add the hsps
as I parse them.
Cheers,
Kai
- --
Dipl.-Inform. Kai Blin kai.blin at biotech.uni-tuebingen.de
Institute for Microbiology and Infection Medicine
Division of Microbiology/Biotechnology
Eberhard-Karls-Universität Tübingen
Auf der Morgenstelle 28 Phone : ++49 7071 29-78841
D-72076 Tübingen Fax : ++49 7071 29-5979
Germany
Homepage: http://www.mikrobio.uni-tuebingen.de/ag_wohlleben
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hmmpfam - search one or more sequences against HMM database
HMMER 2.3.2 (Oct 2003)
Copyright (C) 1992-2003 HHMI/Washington University School of Medicine
Freely distributed under the GNU General Public License (GPL)
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HMM file: ../Shared/Pfam_fs
Sequence file: single_porphyra_AA.fa
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Query sequence: gi|90819130|dbj|BAE92499.1|
Accession: [none]
Description: glutamate synthase [Porphyra yezoensis]
Scores for sequence family classification (score includes all domains):
Model Description Score E-value N
-------- ----------- ----- ------- ---
Glu_synthase Conserved region in glutamate synthas 858.6 3.6e-255 2
GATase_2 Glutamine amidotransferases class-II 731.8 3.9e-226 1
Glu_syn_central Glutamate synthase central domain 649.1 7.9e-213 1
GXGXG GXGXG motif 367.3 2.7e-107 1
HdeA hns-dependent expression protein A (H 9.6 0.015 1
GDC-P Glycine cleavage system P-protein 7.1 0.086 1
Cache_1 Cache domain 7.0 0.14 1
IBN_N Importin-beta N-terminal domain 8.2 0.17 1
DUF1200 Protein of unknown function (DUF1200) 6.7 0.42 1
cobW CobW/HypB/UreG, nucleotide-binding do 5.1 0.45 1
PUF Pumilio-family RNA binding repeat 6.5 0.47 1
Arch_flagellin Archaebacterial flagellin 4.1 0.66 1
FMN_dh FMN-dependent dehydrogenase 3.2 0.89 1
RNA_pol_Rpb2_4 RNA polymerase Rpb2, domain 4 4.6 1.4 1
DUF477 Domain of unknown function (DUF477) 3.8 1.7 1
FRG1 FRG1-like family 0.2 1.7 1
DUF1393 Protein of unknown function (DUF1393) 3.1 2 1
tRNA_anti OB-fold nucleic acid binding domain 4.9 2 1
SelT Selenoprotein T 3.1 2.2 1
RNase_PH_C 3' exoribonuclease family, domain 2 4.2 2.3 1
Pencillinase_R Penicillinase repressor 3.9 2.5 1
Hormone_4 Neurohypophysial hormones, N-terminal 4.4 2.5 1
DSRB Dextransucrase DSRB 2.7 2.7 1
FtsK_SpoIIIE FtsK/SpoIIIE family 2.6 3.1 1
UBA UBA/TS-N domain 4.2 3.1 1
DUF1981 Domain of unknown function (DUF1981) 3.6 3.3 1
Gla Vitamin K-dependent carboxylation/gam 4.0 3.5 1
Scm3 Centromere protein Scm3 2.2 3.5 1
Ribosomal_S6 Ribosomal protein S6 3.3 3.7 1
Cystatin Cystatin domain 2.4 3.9 1
Phage_prot_Gp6 Phage portal protein, SPP1 Gp6-like 1.0 4 1
DUF1976 Domain of unknown function (DUF1976) -1.5 4.3 1
DUF37 Domain of unknown function DUF37 3.0 4.5 1
Flavodoxin_NdrI NrdI Flavodoxin like 2.1 4.6 1
Bac_rhodopsin Bacteriorhodopsin 0.9 4.9 1
Nitro_FeMo-Co Dinitrogenase iron-molybdenum cofacto 2.1 5.3 1
MoCF_biosynth Probable molybdopterin binding domain 1.3 5.6 1
PaaA_PaaC Phenylacetic acid catabolic protein 0.4 5.6 1
Albicidin_res Albicidin resistance domain 1.7 5.7 1
DUF1514 Protein of unknown function (DUF1514) 3.5 5.7 1
T5orf172 T5orf172 domain 2.0 6.1 1
Nup133_N Nup133 N terminal like -0.6 6.5 1
BicD Microtubule-associated protein Bicaud -1.6 6.8 1
Sel1 Sel1 repeat 2.5 7 1
CAP_C DE Adenylate cyclase associated (CA 1.3 7.4 1
Colicin Colicin pore forming domain 1.4 7.5 1
MADF_DNA_bdg Alcohol dehydrogenase transcription f 1.8 8.2 1
DUF258 Protein of unknown function, DUF258 0.3 8.3 1
PspB Phage shock protein B 0.4 8.4 1
GspM General secretion pathway, M protein 1.0 8.6 1
Coq4 Coenzyme Q (ubiquinone) biosynthesis -0.3 9.1 1
P22_AR_N P22_AR N-terminal domain -0.2 9.5 1
C1_2 C1 domain 1.1 9.6 1
Phage_Mu_P Bacteriophage Mu P protein -0.4 10 1
Parsed for domains:
Model Domain seq-f seq-t hmm-f hmm-t score E-value
-------- ------- ----- ----- ----- ----- ----- -------
GATase_2 1/1 34 404 .. 1 385 [] 731.8 3.9e-226
FRG1 1/1 88 107 .. 151 173 .. 0.2 1.7
C1_2 1/1 191 210 .. 9 27 .. 1.1 9.6
MADF_DNA_bdg 1/1 235 261 .. 57 95 .] 1.8 8.2
PaaA_PaaC 1/1 258 269 .. 1 13 [. 0.4 5.6
Albicidin_res 1/1 274 289 .. 50 65 .. 1.7 5.7
UBA 1/1 311 331 .. 18 38 .] 4.2 3.1
Gla 1/1 342 357 .. 27 42 .] 4.0 3.5
RNA_pol_Rpb2_4 1/1 369 381 .. 1 13 [. 4.6 1.4
MoCF_biosynth 1/1 371 396 .. 23 49 .. 1.3 5.6
DUF1200 1/1 389 401 .. 1 13 [. 6.7 0.42
Nup133_N 1/1 397 419 .. 475 498 .] -0.6 6.5
DUF1976 1/1 428 448 .. 1296 1319 .] -1.5 4.3
Bac_rhodopsin 1/1 445 472 .. 219 250 .] 0.9 4.9
Coq4 1/1 459 481 .. 60 82 .. -0.3 9.1
Glu_syn_central 1/1 478 773 .. 1 301 [] 649.1 7.9e-213
Flavodoxin_NdrI 1/1 488 497 .. 122 131 .] 2.1 4.6
P22_AR_N 1/1 524 541 .. 110 126 .] -0.2 9.5
Cache_1 1/1 537 557 .. 1 23 [. 7.0 0.14
Glu_synthase 1/2 650 676 .. 297 323 .. 1.3 3
HdeA 1/1 727 749 .. 58 79 .] 9.6 0.015
Sel1 1/1 729 745 .. 32 49 .] 2.5 7
DUF1981 1/1 765 787 .. 62 88 .] 3.6 3.3
tRNA_anti 1/1 818 839 .. 54 85 .] 4.9 2
Cystatin 1/1 826 859 .. 1 38 [. 2.4 3.9
RNase_PH_C 1/1 827 846 .. 64 84 .] 4.2 2.3
Glu_synthase 2/2 830 1216 .. 1 412 [] 857.3 9e-255
DUF258 1/1 839 860 .. 282 305 .] 0.3 8.3
Pencillinase_R 1/1 856 894 .. 84 118 .] 3.9 2.5
SelT 1/1 872 885 .. 96 111 .] 3.1 2.2
Nitro_FeMo-Co 1/1 879 897 .. 87 105 .] 2.1 5.3
DUF37 1/1 927 934 .. 61 68 .] 3.0 4.5
Scm3 1/1 953 963 .. 103 113 .] 2.2 3.5
cobW 1/1 1038 1058 .. 202 222 .] 5.1 0.45
Arch_flagellin 1/1 1050 1072 .. 197 219 .] 4.1 0.66
DUF1393 1/1 1055 1068 .. 1 14 [. 3.1 2
FtsK_SpoIIIE 1/1 1107 1143 .. 163 198 .. 2.6 3.1
FMN_dh 1/1 1109 1148 .. 291 330 .. 3.2 0.89
DSRB 1/1 1120 1134 .. 1 16 [. 2.7 2.7
Phage_Mu_P 1/1 1122 1131 .. 1 10 [. -0.4 10
Hormone_4 1/1 1168 1176 .. 1 9 [] 4.4 2.5
GDC-P 1/1 1205 1225 .. 10 30 .. 7.1 0.086
PspB 1/1 1268 1276 .. 1 9 [. 0.4 8.4
T5orf172 1/1 1271 1293 .. 35 58 .. 2.0 6.1
CAP_C 1/1 1283 1292 .. 161 170 .] 1.3 7.4
GXGXG 1/1 1290 1485 .. 1 228 [] 367.3 2.7e-107
DUF1514 1/1 1453 1469 .. 50 66 .] 3.5 5.7
Colicin 1/1 1456 1467 .. 192 203 .] 1.4 7.5
Ribosomal_S6 1/1 1461 1481 .. 16 36 .. 3.3 3.7
BicD 1/1 1465 1481 .. 1 17 [. -1.6 6.8
PUF 1/1 1470 1486 .. 19 35 .] 6.5 0.47
DUF477 1/1 1472 1495 .. 1 24 [. 3.8 1.7
Phage_prot_Gp6 1/1 1479 1492 .. 1 14 [. 1.0 4
IBN_N 1/1 1498 1516 .. 1 20 [. 8.2 0.17
GspM 1/1 1506 1520 .. 1 15 [. 1.0 8.6
Alignments of top-scoring domains:
GATase_2: domain 1 of 1, from 34 to 404: score 731.8, E = 3.9e-226
CS EEEEEEEEETSSHSBHHHHHHHHHHHHHGGGGSSCSTTSSCECEEEE
*->CGvlGfiAhikgkpshkivedaleaLerLeHRGavgADgktGDGAGI
CGv GfiA+ ++ ++hkiv +aleaL+++eHRGa++AD ++GDGAGI
gi|9081913 34 CGV-GFIADVNNVANHKIVVQALEALTCMEHRGACSADRDSGDGAGI 79
CS EEECTCCCHHHHHHHCT----S GC-EEEEEEE-SSHHHHHHHHHHHHHH
ltqiPdgFFrevakelGieLpe.gqYAVGmvFLPqdelaraearkifEki
t+iP+++F++ ++++i++ ++ +VGm+FLP l+ + i+E +
gi|9081913 80 TTAIPWNLFQKSLQNQNIKFEQnDSVGVGMLFLPAHKLKES--KLIIETV 127
CS HHHTT-EEEEEEE--B-GGGS-HHHHHC--EEEEEEEE-TT--HHHHHHC
aeeeGLeVLGWReVPvnnsvLGetAlatePvIeQvFvgapsgdgedfErr
++ee+Le++GWR VP+ +vLG++A + P++eQvF+ +++ +++ +E++
gi|9081913 128 LKEENLEIIGWRLVPTVQEVLGKQAYLNKPHVEQVFCKSSNLSKDRLEQQ 177
CS EEEEECHSCHHHHTHHH. BEEEEEESSEEEEEECC-GGGHHHHBHG
LyviRkrieksivaenvn....fYiCSLSsrTIVYKGMLtseQLgqFYpD
L+++Rk+iek+i+ + + ++fYiCSLS++TIVYKGM++s++LgqFY+D
gi|9081913 178 LFLVRKKIEKYIGINGKDwaheFYICSLSCYTIVYKGMMRSAVLGQFYQD 227
CS GGSTTEEBSEEEEEECESSSSSCTGGGSSCEEECCCTTCEEEEEEEEETT
LqderfeSalAivHsRFSTNTfPsWplAQPfRVnslwgggivlAHNGEIN
L++++++S++Ai+H+RFSTNT+P+WplAQP+R ++ HNGEIN
gi|9081913 228 LYHSEYTSSFAIYHRRFSTNTMPKWPLAQPMR---------FVSHNGEIN 268
CS THHHHHHHHHHTSCCCSSTTCGHHHHCC-SSS-TTSCHHHHHHHHHHHHH
TlrgNrnwMraRegvlksplFgddldkLkPIvneggSDSaalDnvlEllv
Tl gN nwM++Re +l+s++++d++++LkPI n+++SDSa+lD ++Ell+
gi|9081913 269 TLLGNLNWMQSREPLLQSKVWKDRIHELKPITNKDNSDSANLDAAVELLI 318
CS HTT--HHHHHHHHS----TT-GGGTST-HHHHHHHHHHHHHHCCHCCEEE
raGRslpeAlMMlIPEAWqnnpdmdkdrpekraFYeylsglmEPWDGPAa
++GRs++eAlM+l+PEA+qn+pd +++e+ +FYey+sgl+EPWDGPA+
gi|9081913 319 ASGRSPEEALMILVPEAFQNQPDFA-NNTEISDFYEYYSGLQEPWDGPAL 367
CS EEEETSSEEEEEEETTTSCESEEEEEEEEEE.TTEEEEEESSC
lvftDGryavgAtLDRNGLTRPaRygiTrdldkDglvvvaSEa<-*
+vft+G++ +gAtLDRNGL RPaRy+iT kD+lv+v+SE+
gi|9081913 368 VVFTNGKV-IGATLDRNGL-RPARYVIT----KDNLVIVSSES 404
FRG1: domain 1 of 1, from 88 to 107: score 0.2, E = 1.7
*->FQkfKvDLqdrklrinekDkkel<-*
FQk+ Lq+ + +++D+ ++
gi|9081913 88 FQKS---LQNQNIKFEQNDSVGV 107
C1_2: domain 1 of 1, from 191 to 210: score 1.1, E = 9.6
*->idgfyg...fYsCkkccddftl<-*
i+g+++ ++fY C+ c +t+
gi|9081913 191 INGKDWaheFYICSLSC--YTI 210
MADF_DNA_bdg: domain 1 of 1, from 235 to 261: score 1.8, E = 8.2
*->drYrrelrkirqgnsegsstgsgesykskWryyeelsFL<-*
+++ ++r+ ++ +kW+++ ++F
gi|9081913 235 SSFAIYHRRFS------------TNTMPKWPLAQPMRFV 261
PaaA_PaaC: domain 1 of 1, from 258 to 269: score 0.4, E = 5.6
CS X............
*->MYnFvEHGGvint<-*
M Fv H G int
gi|9081913 258 M-RFVSHNGEINT 269
Albicidin_res: domain 1 of 1, from 274 to 289: score 1.7, E = 5.7
*->LrlmharEPsLrkgtG<-*
L+ m+ rEP L+ +++
gi|9081913 274 LNWMQSREPLLQSKVW 289
UBA: domain 1 of 1, from 311 to 331: score 4.2, E = 3.1
CS HHHHHHHHHTTT-HHHHHHHH
*->eeakkALeatngnverAvewL<-*
++a++ L a++ ++e+A+++L
gi|9081913 311 DAAVELLIASGRSPEEALMIL 331
Gla: domain 1 of 1, from 342 to 357: score 4.0, E = 3.5
CS CSSHHHHHHHHHHCTC
*->fednegtkefwrkYfg<-*
f++n+++ f++ Y g
gi|9081913 342 FANNTEISDFYEYYSG 357
RNA_pol_Rpb2_4: domain 1 of 1, from 369 to 381: score 4.6, E = 1.4
CS EEETTEEEEEESS
*->VYvNGklvGthrn<-*
V+ NGk++G + +
gi|9081913 369 VFTNGKVIGATLD 381
MoCF_biosynth: domain 1 of 1, from 371 to 396: score 1.3, E = 5.6
CS CHHHHHHHHHHHTTTCEEEEEEEE-SS
*->tNgpmLaalLresaGaevirygiVpDd<-*
tNg+ + a L + G ++ry+i +D+
gi|9081913 371 TNGKVIGATLDR-NGLRPARYVITKDN 396
DUF1200: domain 1 of 1, from 389 to 401: score 6.7, E = 0.42
*->kYvltedtLlIks<-*
+Yv+t+d L+I+s
gi|9081913 389 RYVITKDNLVIVS 401
Nup133_N: domain 1 of 1, from 397 to 419: score -0.6, E = 6.5
*->lylltrnsGvvrIeHaleedstne<-*
l++ + +sGvv++e + + s +
gi|9081913 397 LVIVSSESGVVQVE-PGNVKSKGR 419
DUF1976: domain 1 of 1, from 428 to 448: score -1.5, E = 4.3
*->VsvYiyFkevtdnksLsEysVtyk<-*
V++++ ++++nk ++ sVt k
gi|9081913 428 VDIFS--HKILNNKEIK-TSVTTK 448
Bac_rhodopsin: domain 1 of 1, from 445 to 472: score 0.9, E = 4.9
CS HHHHHHHHHHHHHHHHHCHHHTC---------
*->vvAKVgFgfilLrsravlertvavgsalaage<-*
v++K+++g +l ++r++le + + l+++
gi|9081913 445 VTTKIPYGELLTDARQILE--HK--PFLSDQQ 472
Coq4: domain 1 of 1, from 459 to 481: score -0.3, E = 9.1
*->rrILkEkPRissetldlkkLrkL<-*
r+IL kP s ++d kkL +L
gi|9081913 459 RQILEHKPFLSDQQVDIKKLMQL 481
Glu_syn_central: domain 1 of 1, from 478 to 773: score 649.1, E = 7.9e-213
CS HHHHHHCTT--HHHHHCTCHHHHHHSS--EE-S---S--CCC-SS--
*->llrrQkAFGYTyEdvelvllPMAetGkEalGSMGdDtPLAVLSekpr
l+++Q+AFGYT+Edvelv+++MA+++kE++++MGdD+PL +LSek++
gi|9081913 478 LMQLQTAFGYTNEDVELVIEHMASQAKEPTFCMGDDIPLSILSEKSH 524
CS -GGGCEEE----SSS----TTTTGGG-B--EEES--S-TTS-SGGGC-CE
lLYdYFKQlFAQVTNPPIDPIREelVMSLetylGpegNlLeptpeqarrl
+LYdYFKQ+FAQVTNP+IDP+RE+lVMSL+ ++G+++NlL+ p+ a+++
gi|9081913 525 ILYDYFKQRFAQVTNPAIDPLRESLVMSLAIQIGHKSNLLDDQPTLAKHI 574
CS EESSSB--HHHHHH.HHHH....CCCCEEEEESEEESTTSTTCHHHHHHH
kLesPILsnselekmlknidairegfkaatIditFdveeGvdgLeaaLdr
kLesP+++++el++ + + +++++ I+++F e+G++ ++ + +
gi|9081913 575 KLESPVINEGELNA-IFE-----SKLSCIRINTLFQLEDGPKNFKQQIQQ 618
CS HHHHHHHHHHCT-SEEEEESTCG--CTTEEE--HHHHHHHHHHHHHCTT-
lceeAeeAirsGaniivLSDRndildeervaIPaLLAvGAVHhHLIrkgL
lce A++Ai +G ni+vLSD+n+ ld+e+v+IP+LLAvGAVHhHLI kgL
gi|9081913 619 LCENASQAILDGNNILVLSDKNNSLDSEKVSIPPLLAVGAVHHHLINKGL 668
CS CCC-EEEEEESS--SHHHHHHHHCTT-SEEEEHCCHHHHHHHHCCCCCCC
RtkvslvVETGEaREvHHFAvLiGYGAsAInPYLAyETirdWWlirrGll
R+ +s+ VET++++++HHFA+LiGYGAsAI+PYLA+ET r+WW + ++++
gi|9081913 669 RQEASILVETAQCWSTHHFACLIGYGASAICPYLAFETARHWWSNPKTKM 718
CS CHTTTS- T--HHHHHHHHHHHHHHHHHHHHHCTT--BHHHHCCS--EEE
lmskGkl.elsleeavkNYrkAiekGlLKIMSKMGISTlqSYrGAQIFEA
lmskG+l++++++ea++NY+kA+e+GlLKI+SKMGIS+l+SY+GAQIFE+
gi|9081913 719 LMSKGRLpACNIQEAQANYKKAVEAGLLKILSKMGISLLSSYHGAQIFEI 768
CS SSB-H
vGLsk<-*
+GL++
gi|9081913 769 LGLGS 773
Flavodoxin_NdrI: domain 1 of 1, from 488 to 497: score 2.1, E = 4.6
CS -HHHHHHHHH
*->TneDVerVrk<-*
TneDVe V +
gi|9081913 488 TNEDVELVIE 497
P22_AR_N: domain 1 of 1, from 524 to 541: score -0.2, E = 9.5
*->dVLydYWtrkGkAv..NPR<-*
++LydY+ + +A +NP+
gi|9081913 524 HILYDYFK-QRFAQvtNPA 541
Cache_1: domain 1 of 1, from 537 to 557: score 7.0, E = 0.14
*->wTePYvdaalktgdlViTiaqPv<-*
+T+P++d + +++lV ++a+++
gi|9081913 537 VTNPAIDPL--RESLVMSLAIQI 557
Glu_synthase: domain 1 of 2, from 650 to 676: score 1.3, E = 3
CS --HHHHHHHHHHHHHCTT-CCCSEEEE
*->lPwelgLaevhqtLvengLRdrVsLia<-*
+P l++ +vh L++ gLR + s+ +
gi|9081913 650 IPPLLAVGAVHHHLINKGLRQEASILV 676
HdeA: domain 1 of 1, from 727 to 749: score 9.6, E = 0.015
*->ACk.QdkkAsFkdKvkaEldKvk<-*
AC Q+ +A++k+ v+a l K+
gi|9081913 727 ACNiQEAQANYKKAVEAGLLKIL 749
Sel1: domain 1 of 1, from 729 to 745: score 2.5, E = 7
CS .HHH.HHHHHHHHHHTT-
*->DyekeAlkwyekAAeqGn<-*
++++ A + y+kA e+G
gi|9081913 729 NIQE-AQANYKKAVEAGL 745
DUF1981: domain 1 of 1, from 765 to 787: score 3.6, E = 3.3
*->iFgvltlaakeesesivklAfqiid.qi<-*
iF++l+l++ v+lAf+ +++qi
gi|9081913 765 IFEILGLGSEV-----VNLAFKGTTsQI 787
tRNA_anti: domain 1 of 1, from 818 to 839: score 4.9, E = 2
CS EEEEEEETTSSTSTCTCTT..EEEEEEEEEEE
*->tGkvkkrpggeqNnlkTGeKAlelvveeievl<-*
+G v+ rpgge ++++ +e+
gi|9081913 818 YGFVQYRPGGE----------YHINNPEMSKA 839
Cystatin: domain 1 of 1, from 826 to 859: score 2.4, E = 3.9
CS ECEEEEET.STSHHHHHHHHHHHHHHHHHSSSSEEEEE
*->GglspvdpNendpevqealdfAlakyNeksndnylfel<-*
Gg +++ pe +al+ A+ yN + +ny++ l
gi|9081913 826 GGEYHINN----PEMSKALHQAVRGYNPEYYNNYQSLL 859
RNase_PH_C: domain 1 of 1, from 827 to 846: score 4.2, E = 2.3
CS SSSS.B.HHHHHHHHHHHHHH
*->GkgnglteelleealelAkeg<-*
G +++++ +++ +al++A+ g
gi|9081913 827 G-EYHINNPEMSKALHQAVRG 846
Glu_synthase: domain 2 of 2, from 830 to 1216: score 857.3, E = 9e-255
CS -SS-HHHHHHHHHHHHC--T-HHHHHHHHHHHHTS.-S-SGGGGEEE
*->hrnepeviktlqkavqvpveskpsydkYreplnertpigalrdlLef
h n+pe++k l++av+ + y +Y+ +l +r p++alrdlL++
gi|9081913 830 HINNPEMSKALHQAVRG--YNPEYYNNYQSLLQNR-PPTALRDLLKL 873
CS --SS--......--GGGS--HHHHHTTEEEEEB-CTTC-HHHHHHHHHHH
kyaeepldtdkiipieevepaleikkrfctgaMSyGALSeeAheALAiAm
++++p i+i+eve+++ i + fctg+MS+GALS+e+he+LAiAm
gi|9081913 874 QSNRAP------ISIDEVESIEDILQKFCTGGMSLGALSRETHETLAIAM 917
CS HHCT-EEEETTT---GGGCSB-TTS-T S BTTSTT--S--TT-B---SE
nriGtksNtGEGGedperlkpaadlds.G.SpTlpHLkGLqnednarSAI
nriG+ksN+GEGGedp r+k + d++s+G+Sp lpHLkGL+n+d+a+SAI
gi|9081913 918 NRIGGKSNSGEGGEDPVRFKILNDVNSsGtSPLLPHLKGLKNGDTASSAI 967
CS EEE-TT-TT--............HHHHCC-SEEEEE---TTSTTT--EE-
kQvASGRFGVtkRnGefWeefkRseYLvnAdalEIKiAQGAKPGeGGhLP
kQ+ASGRFGVt +eYL+nA++lEIKiAQGAKPGeGG+LP
gi|9081913 968 KQIASGRFGVT------------PEYLMNAKQLEIKIAQGAKPGEGGQLP 1005
CS GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-.TTS
GeKVspeIAriRnstPGvgliSPpPHHDIysiEDLaqLIydLkeindpkA
G+K+sp+IA +R ++PGv liSPpPHHDIysiEDL+qLI+dL++in pkA
gi|9081913 1006 GKKISPYIATLRKCKPGVPLISPPPHHDIYSIEDLSQLIFDLHQIN-PKA 1054
CS EEEEEEE-STTHHHHHHH...HHHTT-SEEEEE-TT---SSEECCHHHHC
pisVKLVsehgvgtiaaGhmqvakAnADiIlIdGhdGGTGASpktsikha
+isVKLVse g+gtiaaG vak+nADiI+I+GhdGGTGASp++sikha
gi|9081913 1055 KISVKLVSEIGIGTIAAG---VAKGNADIIQISGHDGGTGASPLSSIKHA 1101
CS ---HHHHHHHHHHHHHCTT-CCCSEEEEESS--SHHHHHHHHHCT-SEEE
GlPwelgLaevhqtLvengLRdrVsLiadGGLrTGaDVakAaaLGAdavg
G PwelgL+evhq+L en+LRdrV+L++dGGLrTG D+++Aa++GA+++g
gi|9081913 1102 GSPWELGLSEVHQLLAENQLRDRVTLRVDGGLRTGSDIVLAAIMGAEEFG 1151
CS -SHHHHHHCT--S---CCCT--TTSSS---CCHH..CT----HHHHHHHH
iGTaaLiAlGCimaRvCHtntCPvGvATQDPeLrKrlkfegaperVvNyf
+GT+a+iA+GCimaR+CHtn+CPvGvATQ++eLr +f g+pe +vN+f
gi|9081913 1152 FGTVAMIATGCIMARICHTNKCPVGVATQREELR--ARFSGVPEALVNFF 1199
CS HHHHHHHHHHHHHHT-S
iflaeEvrellaqlGfr<-*
+f+ Evre+la+lG++
gi|9081913 1200 LFIGNEVREILASLGYK 1216
DUF258: domain 1 of 1, from 839 to 860: score 0.3, E = 8.3
CS HHHHHHHCTSS-HHHHHHHHHHHH
*->AVkaAveeGeIseeRYesYlklle<-*
A+ +Av +++e Y++Y+ ll+
gi|9081913 839 ALHQAVR--GYNPEYYNNYQSLLQ 860
Pencillinase_R: domain 1 of 1, from 856 to 894: score 3.9, E = 2.5
CS XXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXX
*->drlfggsvgalvanfleee....klSeddieeLrelLde<-*
+ l++++++ ++ ++l+ ++++ ++S d++e ++++L++
gi|9081913 856 QSLLQNRPPTALRDLLKLQsnraPISIDEVESIEDILQK 894
SelT: domain 1 of 1, from 872 to 885: score 3.1, E = 2.2
*->KLqtGrvYAPPtpqEL<-*
KLq++r P++++E+
gi|9081913 872 KLQSNRA--PISIDEV 885
Nitro_FeMo-Co: domain 1 of 1, from 879 to 897: score 2.1, E = 5.3
CS EEE-TTSSBHHHHHHHHHC
*->pikagegetieeaiealqe<-*
pi e e+ie+ + ++ +
gi|9081913 879 PISIDEVESIEDILQKFCT 897
DUF37: domain 1 of 1, from 927 to 934: score 3.0, E = 4.5
*->hpGGyDPV<-*
++GG DPV
gi|9081913 927 GEGGEDPV 934
Scm3: domain 1 of 1, from 953 to 963: score 2.2, E = 3.5
*->HLraLeteddi<-*
HL++L+++d++
gi|9081913 953 HLKGLKNGDTA 963
cobW: domain 1 of 1, from 1038 to 1058: score 5.1, E = 0.45
CS ...HHHHHHHHHH-SSS-EEE
*->adlekleadlrrlnpeapiip<-*
+dl++l+ dl+++np+a+i
gi|9081913 1038 EDLSQLIFDLHQINPKAKISV 1058
Arch_flagellin: domain 1 of 1, from 1050 to 1072: score 4.1, E = 0.66
*->inpstkvrgeVvpenGapgtief<-*
inp k+++++v+e+G+ ++
gi|9081913 1050 INPKAKISVKLVSEIGIGTIAAG 1072
DUF1393: domain 1 of 1, from 1055 to 1068: score 3.1, E = 2
*->klSvKtVVAiGIGA<-*
k+SvK V iGIG+
gi|9081913 1055 KISVKLVSEIGIGT 1068
FtsK_SpoIIIE: domain 1 of 1, from 1107 to 1143: score 2.6, E = 3.1
*->lviDnydeLaeenlL.ervtsLknqGlsygvhvmata<-*
l++ + ++L +en+L++rvt+ + +Gl +g +++++a
gi|9081913 1107 LGLSEVHQLLAENQLrDRVTLRVDGGLRTGSDIVLAA 1143
FMN_dh: domain 1 of 1, from 1109 to 1148: score 3.2, E = 0.89
CS HHHHHHHHHCHHTTTSSEEEEESS-SSHHHHHHHHHHTSS
*->LpeVvPIlkeaAvkgdieVllDgGvRRGtDVlKALALGAr<-*
L eV +l e + +++ +DgG R+G+D++ A +GA+
gi|9081913 1109 LSEVHQLLAENQLRDRVTLRVDGGLRTGSDIVLAAIMGAE 1148
DSRB: domain 1 of 1, from 1120 to 1134: score 2.7, E = 2.7
*->mKvndrvtvKtDGgpR<-*
++ drvt + DGg R
gi|9081913 1120 -QLRDRVTLRVDGGLR 1134
Phage_Mu_P: domain 1 of 1, from 1122 to 1131: score -0.4, E = 10
*->sntVtLrvgG<-*
++VtLrv+G
gi|9081913 1122 RDRVTLRVDG 1131
Hormone_4: domain 1 of 1, from 1168 to 1176: score 4.4, E = 2.5
CS X-TT--TT-
*->CyirnCPrG<-*
C + CP+G
gi|9081913 1168 CHTNKCPVG 1176
GDC-P: domain 1 of 1, from 1205 to 1225: score 7.1, E = 0.086
*->eqqeMLstiGlssLddLidat<-*
e++e+L+++G++sLdd ++++
gi|9081913 1205 EVREILASLGYKSLDDITGQN 1225
PspB: domain 1 of 1, from 1268 to 1276: score 0.4, E = 8.4
*->MsaffLagP<-*
M+ ++La+P
gi|9081913 1268 MDDDILAIP 1276
T5orf172: domain 1 of 1, from 1271 to 1293: score 2.0, E = 6.1
*->dvvalievedaraklEklLHkrFk<-*
d+ a+ ev++a klE+++ k+Fk
gi|9081913 1271 DILAIPEVSNAI-KLETEITKHFK 1293
CAP_C: domain 1 of 1, from 1283 to 1292: score 1.3, E = 7.4
CS EEEEEE----
*->KLvTevveha<-*
KL+Te++ h
gi|9081913 1283 KLETEITKHF 1292
GXGXG: domain 1 of 1, from 1290 to 1485: score 367.3, E = 2.7e-107
CS EEEEE-TT--STTHHHHHHHHHHCTTTS.S-TTCEEEEEEEEE-TTT
*->keeaiiNtdrlvgtrlsgeiakkygeegalpkdtgkivfnGsAGqsf
k+++i Nt+r+vgtrlsg iak yg+ g + k+ +k++f+GsAGqsf
gi|9081913 1290 KHFKIANTNRTVGTRLSGIIAKNYGNTG-F-KGLIKLNFYGSAGQSF 1334
CS TTT-BTTEEEEEEEEE-S.TTTTT-ECCEEEEE--TT-.......SS-GG
GafmagGvtLeleGdAnddyvGkgmsGGeIvikgnagdpvGnnMdageyv
Gaf+a+G++L l+G+And yvGkgm+GG+Ivi+++ag +e +
gi|9081913 1335 GAFLASGINLKLMGEAND-YVGKGMNGGSIVIVPPAGT-------IYEDN 1376
CS GSEEC-SSTTTT--CEEEEESSEE-TTTTTT-.....CCEEEEESEB.-S
gnviaGNtclyGatGGkifiaGdAGerfgvrnkayKdsgatiVveGvaGd
++vi+GNtclyGatGG++f++G+AGerf+vrn s a+ VveGv Gd
gi|9081913 1377 NQVIIGNTCLYGATGGYLFAQGQAGERFAVRN-----SLAESVVEGV-GD 1420
CS STTTT-EEEEEEESS-B-SSBTTT--CCEEEEE-TTS.......THHHHB
hggEYMtGGtivVlGdaGrnvGagMtGGiaYvlgeiedfsyMiatlpgkv
h++EYMtGG+ivVlG+aGrnvGagMtGG+aY+l+e+e + ++v
gi|9081913 1421 HACEYMTGGVIVVLGKAGRNVGAGMTGGLAYFLDEDE-------NFIDRV 1463
CS -CCCEEEE...ES-S......CCHHHHHHHH
nleiVeledlkrievkrkklLpegekqlkel<-*
n+eiV+ + r+ + ++ge+qlk+l
gi|9081913 1464 NSEIVKIQ---RVIT------KAGEEQLKNL 1485
DUF1514: domain 1 of 1, from 1453 to 1469: score 3.5, E = 5.7
*->LeeyrieveRikkevkk<-*
L e+++ ++R++ e+ k
gi|9081913 1453 LDEDENFIDRVNSEIVK 1469
Colicin: domain 1 of 1, from 1456 to 1467: score 1.4, E = 7.5
CS SHHHHHHHHHCH
*->DdkfveklNkli<-*
D++f++ +N +i
gi|9081913 1456 DENFIDRVNSEI 1467
Ribosomal_S6: domain 1 of 1, from 1461 to 1481: score 3.3, E = 3.7
CS CCHHHHHHHHHHHHHCTT-EE
*->EqvkqeiekYqkvLtnngAei<-*
++v++ei k+q+v+t++g+e+
gi|9081913 1461 DRVNSEIVKIQRVITKAGEEQ 1481
BicD: domain 1 of 1, from 1465 to 1481: score -1.6, E = 6.8
*->gqaysnqrkvAkdGeer<-*
+ +++qr+ +k Gee+
gi|9081913 1465 SEIVKIQRVITKAGEEQ 1481
PUF: domain 1 of 1, from 1470 to 1486: score 6.5, E = 0.47
*->lQkllevateeqkqlil<-*
+Q+++++a+eeq ++++
gi|9081913 1470 IQRVITKAGEEQLKNLI 1486
DUF477: domain 1 of 1, from 1472 to 1495: score 3.8, E = 1.7
*->gtLspserarLeqalaalEqktga<-*
++++++ ++L ++ ++ktg+
gi|9081913 1472 RVITKAGEEQLKNLIENHAAKTGS 1495
Phage_prot_Gp6: domain 1 of 1, from 1479 to 1492: score 1.0, E = 4
*->eEmikkFidkHklr<-*
eE +k++i+ H+++
gi|9081913 1479 EEQLKNLIENHAAK 1492
IBN_N: domain 1 of 1, from 1498 to 1516: score 8.2, E = 0.17
CS HHHHHHHHHCCTHHCHHHHH
*->AEkqLeqlekqklPgfllaL<-*
A++ Le+++++ lP+f++ +
gi|9081913 1498 AHTILEKWNSY-LPQFWQVV 1516
GspM: domain 1 of 1, from 1506 to 1520: score 1.0, E = 8.6
CS XXXXXXXXXXXXXXX
*->mneLqawWqgrspRE<-*
++ L ++Wq ++p+E
gi|9081913 1506 NSYLPQFWQVVPPSE 1520
//
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