Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_077243518.1 B1A74_RS01060 3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::Q83E11 (438 letters) >NCBI__GCF_001995255.1:WP_077243518.1 Length = 434 Score = 464 bits (1193), Expect = e-135 Identities = 244/433 (56%), Positives = 310/433 (71%), Gaps = 4/433 (0%) Query: 1 MDYQTIPSQG-LSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQM 59 MD T+ G LSG + V GDKSISHRA++L A+AEG T V GFL G D LA + A + M Sbjct: 1 MDTLTVQPGGVLSGTLRVAGDKSISHRAIMLGALAEGTTHVTGFLEGEDCLATLEAFRAM 60 Query: 60 GASIQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSS 119 G I+ E +++EGVGM GL+AP LD GNSGTA+RLL G+LAGQ F++ LTGD+S Sbjct: 61 GVPIRR-EGPGEVIIEGVGMHGLRAPEGPLDMGNSGTAMRLLCGVLAGQAFDSELTGDTS 119 Query: 120 LQRRPMKRIIDPLTLMGAKIDST-GNVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAG 178 L RRPM+R+ +PLT MGA+ID+ G PPL++ G L G Y L +ASAQVKS LLLAG Sbjct: 120 LSRRPMRRVTEPLTRMGAQIDTAEGGTPPLRVRGGQPLQGTEYALEVASAQVKSALLLAG 179 Query: 179 LYARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAA 238 L+A G+TC+TEPAP+RDHTER+L+ F +++D + CV+GGG+L+ D+ +P DISSAA Sbjct: 180 LWAEGRTCVTEPAPTRDHTERMLEGFGVEVERDGATACVAGGGRLRGGDVDVPADISSAA 239 Query: 239 FFIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHA 298 FF+V A+I PGS + L VGVNPTR GVI +L+ MGADI + E + EP ADI V Sbjct: 240 FFMVGASIAPGSHVILRHVGVNPTRTGVIEILRRMGADIRLLDLREVSGEPVADIEVLSH 299 Query: 299 RLKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLG 358 L+GI+IP DQVPL IDEFP + IAAA A G+TVL A ELRVKE+DRI M DGL LG Sbjct: 300 ELRGIEIPEDQVPLAIDEFPAIFIAAACAHGETVLTGAEELRVKESDRIQVMADGLAALG 359 Query: 359 IAAESLPDGVIIQGGT-LEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPN 417 + E PDG+ IQGG +GGE+ S+ DHRIAMAFA+A A PV I +C NV TSFP+ Sbjct: 360 VDCEVRPDGIRIQGGDGFQGGEIQSHGDHRIAMAFAMAALRADAPVTIHDCRNVATSFPD 419 Query: 418 FVELANEVGMNVK 430 F +LA + G++++ Sbjct: 420 FADLARQTGLHLE 432 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: 685 Number of extensions: 35 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: 434 Length adjustment: 32 Effective length of query: 406 Effective length of database: 402 Effective search space: 163212 Effective search space used: 163212 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: 51 (24.3 bits)
Align candidate WP_077243518.1 B1A74_RS01060 (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.21624.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-133 428.9 0.0 1.1e-132 428.8 0.0 1.0 1 lcl|NCBI__GCF_001995255.1:WP_077243518.1 B1A74_RS01060 3-phosphoshikimate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001995255.1:WP_077243518.1 B1A74_RS01060 3-phosphoshikimate 1-carboxyvinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.8 0.0 1.1e-132 1.1e-132 1 412 [. 14 427 .. 14 430 .. 0.96 Alignments for each domain: == domain 1 score: 428.8 bits; conditional E-value: 1.1e-132 TIGR01356 1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 g ++++g+KSishRa++l+aLaeg+t vt++L++eD+latlea+r++G+ +++e +e++iegvg+ l lcl|NCBI__GCF_001995255.1:WP_077243518.1 14 GTLRVAGDKSISHRAIMLGALAEGTTHVTGFLEGEDCLATLEAFRAMGVPIRREgPGEVIIEGVGMhgL 82 6799************************************************77699********999* PP TIGR01356 67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135 + pe ld+gnsGt++Rll gvla ++++++ltgd sl++RP++r++e+L ++ga+i+ +e g++Pl+ lcl|NCBI__GCF_001995255.1:WP_077243518.1 83 RAPEGPLDMGNSGTAMRLLCGVLAGQAFDSELTGDTSLSRRPMRRVTEPLTRMGAQIDTAE-GGTPPLR 150 **********************************************************988.69***** PP TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203 ++g++++ g+ + aS+Q+ksallla+ l a++ + v+e+ +r+++e++L+ fgveve++ lcl|NCBI__GCF_001995255.1:WP_077243518.1 151 VRGGQPLqGTEYALEVASAQVKSALLLAG---LWAEGRTCVTEPAPTRDHTERMLEG---FGVEVERDG 213 ****9998*********************...7899*****************9875...5688***98 PP TIGR01356 204 erkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadve 271 + v gg+ + +v+v++D+SsAaff++ a i+++ +v ++++g n+t+++ +i++L++mGad++ lcl|NCBI__GCF_001995255.1:WP_077243518.1 214 A-TACVAGGGRLRGGDVDVPADISSAAFFMVGASIAPGsHVILRHVGVNPTRTG--VIEILRRMGADIR 279 7.99999999988888**********************9***************..888********** PP TIGR01356 272 veeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdR 331 + + r d+ev +++l+g+++ + +v+ +iDe+p++ ++aa+A get+++++eelRvkEsdR lcl|NCBI__GCF_001995255.1:WP_077243518.1 280 LLDLRevsgepvaDIEVL-SHELRGIEIpEDQVPLAIDEFPAIFIAAACAHGETVLTGAEELRVKESDR 347 *99999999999999999.679******99*************************************** PP TIGR01356 332 iaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvak 400 i+++a+ L++lGv++e+++dg+ i+G+ ++g+++++++DHRiama+a+++l+a+++v+i+d va+ lcl|NCBI__GCF_001995255.1:WP_077243518.1 348 IQVMADGLAALGVDCEVRPDGIRIQGG-DGFQGGEIQSHGDHRIAMAFAMAALRADAPVTIHDCRNVAT 415 ***************************.5**************************************** PP TIGR01356 401 sfPeFfevleql 412 sfP+F ++++q lcl|NCBI__GCF_001995255.1:WP_077243518.1 416 SFPDFADLARQT 427 *******99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (434 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: 7.71 // [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