Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_084687487.1 OLEAN_RS07045 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::Q83E11 (438 letters) >NCBI__GCF_000967895.1:WP_084687487.1 Length = 748 Score = 459 bits (1182), Expect = e-133 Identities = 244/434 (56%), Positives = 306/434 (70%), Gaps = 6/434 (1%) Query: 1 MDYQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMG 60 ++Y P LSGE VPGDKSISHR+++L ++AEG T++ GFL G D+LA + + + MG Sbjct: 311 VNYVAKPGGKLSGEFRVPGDKSISHRSIMLGSLAEGTTEITGFLEGEDSLATLQSFRDMG 370 Query: 61 ASIQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSL 120 I+ + V GVG+ GL+ PP AL GNSGT++RLLSGL++ Q F+ +TGD SL Sbjct: 371 VVIEGPHRGRV-TVHGVGLHGLKTPPNALYLGNSGTSMRLLSGLMSAQSFDVEMTGDVSL 429 Query: 121 QRRPMKRIIDPLTLMGAKIDSTGNV-PPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGL 179 +RPM R+ +PL MGA I+S PPLKI G L GIHY LPMASAQVKSCLLLAGL Sbjct: 430 SKRPMDRVANPLREMGAVIESADKGRPPLKIKGGQPLKGIHYVLPMASAQVKSCLLLAGL 489 Query: 180 YARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAF 239 YA G+T + EPAP+RDHTER+LK F Y + D + V GGKL A I +P DISSAAF Sbjct: 490 YAEGETTVIEPAPTRDHTERMLKGFGYPVDVDGPKVTVRPGGKLTATAIDVPSDISSAAF 549 Query: 240 FIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHAR 299 F+VAA+I S I L VG+NPTR+GVIN+L+ MGA+IE+ + +E EP AD+ +R A+ Sbjct: 550 FMVAASIAKDSDITLQHVGINPTRVGVINILRQMGANIEMLNESEVGGEPVADLRIRSAQ 609 Query: 300 LKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGI 359 LKGI IP DQVPL IDEFP + IAAA A+G TVL A ELRVKE+DRI AMV+G+Q LG+ Sbjct: 610 LKGIQIPEDQVPLAIDEFPAIFIAAACAEGTTVLTGAEELRVKESDRIQAMVEGMQALGV 669 Query: 360 AAESLPDGVIIQG----GTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSF 415 A DG II G G+ GGEV+S DDHRIAM+F +A A P+ I++C NV TSF Sbjct: 670 DAVGTEDGAIINGFGSEGSFNGGEVDSVDDHRIAMSFTIASLRANAPILIKDCANVATSF 729 Query: 416 PNFVELANEVGMNV 429 P FVELA+E G+ V Sbjct: 730 PGFVELASESGIQV 743 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: 900 Number of extensions: 43 Number of successful extensions: 5 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: 748 Length adjustment: 36 Effective length of query: 402 Effective length of database: 712 Effective search space: 286224 Effective search space used: 286224 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 WP_084687487.1 OLEAN_RS07045 (bifunctional prephenate dehydrogenase/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.11465.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.6e-131 422.9 0.0 8.4e-131 422.5 0.0 1.1 1 lcl|NCBI__GCF_000967895.1:WP_084687487.1 OLEAN_RS07045 bifunctional preph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000967895.1:WP_084687487.1 OLEAN_RS07045 bifunctional prephenate dehydrogenase/3-phosphoshikimate 1-ca # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.5 0.0 8.4e-131 8.4e-131 1 413 [. 323 740 .. 323 742 .. 0.96 Alignments for each domain: == domain 1 score: 422.5 bits; conditional E-value: 8.4e-131 TIGR01356 1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 ge+++pg+KSishR+++l++Laeg+t++t++L++eD latl+++r++G+ +e ++++++++gvg l lcl|NCBI__GCF_000967895.1:WP_084687487.1 323 GEFRVPGDKSISHRSIMLGSLAEGTTEITGFLEGEDSLATLQSFRDMGVVIEgPHRGRVTVHGVGLhgL 391 799*************************************************666*********98889 PP TIGR01356 67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135 k+p ++l+lgnsGt++Rll+g+++++s++v++tgd sl+kRP++r+ ++Lre+ga ies++ +g++Pl+ lcl|NCBI__GCF_000967895.1:WP_084687487.1 392 KTPPNALYLGNSGTSMRLLSGLMSAQSFDVEMTGDVSLSKRPMDRVANPLREMGAVIESAD-KGRPPLK 459 **********************************************************999.59***** PP TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203 i+g++++ gi+++ ++aS+Q+ks+llla+ l a+++++v+e+ +r+++e++Lk ++ v+++ lcl|NCBI__GCF_000967895.1:WP_084687487.1 460 IKGGQPLkGIHYVLPMASAQVKSCLLLAG---LYAEGETTVIEPAPTRDHTERMLKGFGYP---VDVDG 522 ****9999*********************...77789999999************999877...88876 PP TIGR01356 204 erkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadve 271 k++v++g+k + + ++v++D+SsAaff++aa i++ ++t++++g+n+t+ + +i++L++mGa++e lcl|NCBI__GCF_000967895.1:WP_084687487.1 523 P-KVTVRPGGKLTATAIDVPSDISSAAFFMVAASIAKDsDITLQHVGINPTRVG--VINILRQMGANIE 588 5.9********88888**********************9***************..888********** PP TIGR01356 272 veeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdR 331 + +++ d++++ + +lkg+++ + +v+ +iDe+p++ ++aa+Aeg+t+++++eelRvkEsdR lcl|NCBI__GCF_000967895.1:WP_084687487.1 589 MLNESevggepvaDLRIR-SAQLKGIQIpEDQVPLAIDEFPAIFIAAACAEGTTVLTGAEELRVKESDR 656 ***999************.578******99*************************************** PP TIGR01356 332 iaaiaeeLeklGveveeledgllieGkk..kelkgavvdtydDHRiamalavlglaaegeveiedaecv 398 i+a++e +++lGv++ +edg +i+G +++g++vd+ dDHRiam++++++l+a++++ i+d + v lcl|NCBI__GCF_000967895.1:WP_084687487.1 657 IQAMVEGMQALGVDAVGTEDGAIINGFGseGSFNGGEVDSVDDHRIAMSFTIASLRANAPILIKDCANV 725 ************************9977779************************************** PP TIGR01356 399 aksfPeFfevleqlg 413 a+sfP F+e++ + g lcl|NCBI__GCF_000967895.1:WP_084687487.1 726 ATSFPGFVELASESG 740 *********988765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (748 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: 14.47 // [ok]
This GapMind analysis is from Apr 10 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