Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate GFF1397 HP15_1364 3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::Q83E11 (438 letters) >FitnessBrowser__Marino:GFF1397 Length = 742 Score = 483 bits (1243), Expect = e-141 Identities = 251/425 (59%), Positives = 312/425 (73%), Gaps = 3/425 (0%) Query: 7 PSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVI 66 P ++G+I VPGDKS+SHR+++L A+A+G T+V GFL G D+LA + A + MG +I+ Sbjct: 313 PGGAITGDIRVPGDKSMSHRSIMLGALADGVTEVKGFLEGEDSLATLQAFRDMGVTIEG- 371 Query: 67 EDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMK 126 D+ + + GVGM GLQAP L GNSGTA+RL +GLLA QPF++ LTGD+SL RPM Sbjct: 372 PDDGFVRIHGVGMHGLQAPRGPLYLGNSGTAMRLFAGLLAAQPFDSELTGDASLSGRPMG 431 Query: 127 RIIDPLTLMGAKIDST-GNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLYARGKT 185 R+ DPL MGA ID+ G PPLKI G +L+GIHY++P+ASAQVKSCLLLAGLYA G T Sbjct: 432 RVADPLRAMGAVIDTAEGGRPPLKIRGGQKLSGIHYEMPVASAQVKSCLLLAGLYAEGST 491 Query: 186 CITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFIVAAT 245 +TEPAP+RDHTER+L F Y + +D + VSGGGKL A +I +P DISS+AFF+VAA+ Sbjct: 492 SVTEPAPTRDHTERMLAGFGYHVHRDGATASVSGGGKLTATNIDVPADISSSAFFLVAAS 551 Query: 246 ITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLKGIDI 305 I PGS + L VG+NPTR+GVIN+L MGA+IE+ E EP AD+ VR A L+GIDI Sbjct: 552 IAPGSNLILRHVGMNPTRVGVINILNQMGANIEILDEREIGGEPVADLRVRSAELQGIDI 611 Query: 306 PPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAAESLP 365 P DQVPL IDEFPVL IAAA A G+TVLR A ELRVKE+DRI M DGL LG+ P Sbjct: 612 PEDQVPLAIDEFPVLFIAAACANGRTVLRGAEELRVKESDRIQVMADGLAALGVETTVTP 671 Query: 366 DGVIIQGG-TLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFVELANE 424 DG+II GG T+ GG VNS+ DHRIAM+FAVA A G + + +C NV TSFP FVELA Sbjct: 672 DGIIIDGGQTIGGGTVNSHGDHRIAMSFAVASLRAAGDITVNDCANVATSFPGFVELAQG 731 Query: 425 VGMNV 429 G+N+ Sbjct: 732 TGINI 736 Lambda K H 0.318 0.137 0.392 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 968 Number of extensions: 42 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 438 Length of database: 742 Length adjustment: 36 Effective length of query: 402 Effective length of database: 706 Effective search space: 283812 Effective search space used: 283812 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 53 (25.0 bits)
Align candidate GFF1397 HP15_1364 (3-phosphoshikimate 1-carboxyvinyltransferase)
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01356.hmm # target sequence database: /tmp/gapView.20524.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01356 [M=415] Accession: TIGR01356 Description: aroA: 3-phosphoshikimate 1-carboxyvinyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-130 419.7 0.0 8.6e-130 419.2 0.0 1.2 1 lcl|FitnessBrowser__Marino:GFF1397 HP15_1364 3-phosphoshikimate 1-c Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF1397 HP15_1364 3-phosphoshikimate 1-carboxyvinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 419.2 0.0 8.6e-130 8.6e-130 1 413 [. 319 733 .. 319 735 .. 0.96 Alignments for each domain: == domain 1 score: 419.2 bits; conditional E-value: 8.6e-130 TIGR01356 1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..lkepeae 72 g+i++pg+KS+shR+++l+aLa+g t+v+++L++eD latl+a+r++G+++e +++ + i+gvg+ l+ p lcl|FitnessBrowser__Marino:GFF1397 319 GDIRVPGDKSMSHRSIMLGALADGVTEVKGFLEGEDSLATLQAFRDMGVTIEgPDDGFVRIHGVGMhgLQAPRGP 393 79**************************************************6669999*****9999******* PP TIGR01356 73 ldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlaisgplkg.give 146 l+lgnsGt++Rl g+la+++++++ltgd sl+ RP++r+ ++Lr++ga i+ +e g++Pl+i+g++k+ gi++ lcl|FitnessBrowser__Marino:GFF1397 394 LYLGNSGTAMRLFAGLLAAQPFDSELTGDASLSGRPMGRVADPLRAMGAVIDTAE-GGRPPLKIRGGQKLsGIHY 467 ****************************************************988.69*********7777**** PP TIGR01356 147 lsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeederkivvkggqkykqkeve 221 + aS+Q+ks+llla+ l a++ + v+e+ +r+++e++L+ ++ + v+++ + +v gg+k + ++++ lcl|FitnessBrowser__Marino:GFF1397 468 EMPVASAQVKSCLLLAG---LYAEGSTSVTEPAPTRDHTERMLAGFGYH---VHRDGA-TASVSGGGKLTATNID 535 *****************...67789999999***********9998877...999887.*********88888** PP TIGR01356 222 vegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveveeqr........dvevegasklk 287 v++D+Ss affl+aa i+++ ++ ++++g+n+t+ + +i++L++mGa++e+ ++r d++v+ + +l+ lcl|FitnessBrowser__Marino:GFF1397 536 VPADISSSAFFLVAASIAPGsNLILRHVGMNPTRVG--VINILNQMGANIEILDEReiggepvaDLRVR-SAELQ 607 ********************9***************..888**************99************.578** PP TIGR01356 288 gvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRiaaiaeeLeklGveveeledgllieGkkke 361 g+++ + +v+ +iDe+p+l ++aa+A+g t+++++eelRvkEsdRi+++a+ L++lGve+++++dg++i G+ ++ lcl|FitnessBrowser__Marino:GFF1397 608 GIDIpEDQVPLAIDEFPVLFIAAACANGRTVLRGAEELRVKESDRIQVMADGLAALGVETTVTPDGIIIDGG-QT 681 ****99******************************************************************.6* PP TIGR01356 362 lkgavvdtydDHRiamalavlglaaegeveiedaecvaksfPeFfevleqlg 413 + g++v++++DHRiam++av++l+a+g ++++d + va+sfP F+e+++ g lcl|FitnessBrowser__Marino:GFF1397 682 IGGGTVNSHGDHRIAMSFAVASLRAAGDITVNDCANVATSFPGFVELAQGTG 733 **********************************************998765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (742 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 15.08 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory