Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_028486633.1 B076_RS0106685 3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::Q83E11 (438 letters) >NCBI__GCF_000483485.1:WP_028486633.1 Length = 446 Score = 438 bits (1126), Expect = e-127 Identities = 235/433 (54%), Positives = 301/433 (69%), Gaps = 10/433 (2%) Query: 7 PSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVI 66 P + G I VPGDKSISHR+++L AI+EG T V GFL GAD LA + A + MG I+ Sbjct: 10 PGGRIHGRIRVPGDKSISHRSIMLGAISEGTTTVTGFLEGADALATLQAFKDMGVQIEGP 69 Query: 67 EDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMK 126 + N+ + GVG+ GL+ P + +D GNSGT+ RLL+G+LAGQ F+ L GD+SL +RPMK Sbjct: 70 DKGNV-TIHGVGLRGLKKPEKPMDMGNSGTSTRLLAGILAGQDFDCELVGDASLSKRPMK 128 Query: 127 RIIDPLTLMGAKIDST-GNVPPLKIYGNPR-LTGIHYQLPMASAQVKSCLLLAGLYARGK 184 R+ DPL +MGAKI++ G P+KI G+ + L I Y LPMASAQVKSC+LLAGLYA+GK Sbjct: 129 RVTDPLAMMGAKIETAEGGTLPMKICGHGQTLKAIDYVLPMASAQVKSCVLLAGLYAQGK 188 Query: 185 TCITEPAPSRDHTERLLKHFHYT-----LQKDKQSICVSGGGKLKANDISIPGDISSAAF 239 TC EPAP+RDHTER+L F Y L + C+ GGG LKA I +P DISSAAF Sbjct: 189 TCAEEPAPTRDHTERMLNGFGYEVVSTRLDNSRTRACLQGGGSLKARHIDVPSDISSAAF 248 Query: 240 FIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHAR 299 F+VAA ++ GS + + VG+NPTR GVI++LK+MGA+I + + E EP AD+ +R+A Sbjct: 249 FMVAAAVSEGSDLVIEHVGMNPTRTGVIDILKLMGANIVLENAHEVGGEPVADVHIRYAP 308 Query: 300 LKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGI 359 L+GI+IP VPL IDEFPVL +AAA A G+TVL A ELRVKE+DRI M D LQ +GI Sbjct: 309 LQGIEIPESLVPLAIDEFPVLFVAAASATGQTVLSGAEELRVKESDRIQVMADALQAVGI 368 Query: 360 AAESLPDGVIIQGG--TLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPN 417 A PDG++I GG + + E+ S+ DHRI+MA VAG A V I +C NV TSFP Sbjct: 369 DAVPTPDGMVINGGQQSPQAAEIQSHHDHRISMAMTVAGLNAVSEVVIDDCANVNTSFPT 428 Query: 418 FVELANEVGMNVK 430 FV L NEVGM ++ Sbjct: 429 FVSLMNEVGMQIE 441 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: 612 Number of extensions: 32 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: 446 Length adjustment: 32 Effective length of query: 406 Effective length of database: 414 Effective search space: 168084 Effective search space used: 168084 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_028486633.1 B076_RS0106685 (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.16301.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-128 413.8 0.6 4.1e-128 413.6 0.6 1.0 1 lcl|NCBI__GCF_000483485.1:WP_028486633.1 B076_RS0106685 3-phosphoshikimat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000483485.1:WP_028486633.1 B076_RS0106685 3-phosphoshikimate 1-carboxyvinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 413.6 0.6 4.1e-128 4.1e-128 1 414 [. 16 438 .. 16 439 .. 0.96 Alignments for each domain: == domain 1 score: 413.6 bits; conditional E-value: 4.1e-128 TIGR01356 1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 g+i++pg+KSishR+++l+a++eg+t+vt++L+++D latl+a++++G+++e +k++++i+gvg l lcl|NCBI__GCF_000483485.1:WP_028486633.1 16 GRIRVPGDKSISHRSIMLGAISEGTTTVTGFLEGADALATLQAFKDMGVQIEgPDKGNVTIHGVGLrgL 84 79**************************************************767********99888* PP TIGR01356 67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135 k pe+ +d+gnsGt++Rll g+la ++++++l gd sl+kRP++r++++L ++ga+ie +e g+lP++ lcl|NCBI__GCF_000483485.1:WP_028486633.1 85 KKPEKPMDMGNSGTSTRLLAGILAGQDFDCELVGDASLSKRPMKRVTDPLAMMGAKIETAE-GGTLPMK 152 **********************************************************988.69***** PP TIGR01356 136 isgp.lkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveee 202 i g+ +++ +i ++ ++aS+Q+ks++lla+ l a++ + +e+ +r+++e++L+ ++ + v+ + + lcl|NCBI__GCF_000483485.1:WP_028486633.1 153 ICGHgQTLkAIDYVLPMASAQVKSCVLLAG---LYAQGKTCAEEPAPTRDHTERMLNGFGYEVVSTRLD 218 ***987778*********************...677888999999******************999988 PP TIGR01356 203 de.rkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGad 269 ++ ++ ++gg++ k ++++v++D+SsAaff++aaa++++ ++++e++g+n+t+++ +i++L+ mGa+ lcl|NCBI__GCF_000483485.1:WP_028486633.1 219 NSrTRACLQGGGSLKARHIDVPSDISSAAFFMVAAAVSEGsDLVIEHVGMNPTRTG--VIDILKLMGAN 285 886788899999999999*********************99***************..788******** PP TIGR01356 270 veveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEs 329 + +e+ + dv ++ l+g+++ + v+ +iDe+p+l v+aa A g+t++ ++eelRvkEs lcl|NCBI__GCF_000483485.1:WP_028486633.1 286 IVLENAHevggepvaDVHIR-YAPLQGIEIpESLVPLAIDEFPVLFVAAASATGQTVLSGAEELRVKES 353 ******99************.568******99************************************* PP TIGR01356 330 dRiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecv 398 dRi+++a++L+++G+++ +++dg++i+G++++ + a++++++DHRi ma++v+gl a +ev i+d + v lcl|NCBI__GCF_000483485.1:WP_028486633.1 354 DRIQVMADALQAVGIDAVPTPDGMVINGGQQSPQAAEIQSHHDHRISMAMTVAGLNAVSEVVIDDCANV 422 ********************************************************************* PP TIGR01356 399 aksfPeFfevleqlga 414 ++sfP F+ +++++g+ lcl|NCBI__GCF_000483485.1:WP_028486633.1 423 NTSFPTFVSLMNEVGM 438 ************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (446 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 9.38 // [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