Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_028489167.1 Q394_RS0109965 3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::Q83E11 (438 letters) >NCBI__GCF_000621325.1:WP_028489167.1 Length = 440 Score = 451 bits (1160), Expect = e-131 Identities = 229/430 (53%), Positives = 302/430 (70%), Gaps = 1/430 (0%) Query: 1 MDYQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMG 60 + + P L G + VPGDKSISHR+++L ++AEG T V GFL G D L ++A + MG Sbjct: 8 LQFNVQPGGSLHGTVRVPGDKSISHRSIMLGSLAEGTTHVSGFLQGEDCLCTLNAFRSMG 67 Query: 61 ASIQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSL 120 +I D+ + + GVG+ GLQAP L+ GNSGT++RL+SGL++GQ F+ +TGD+SL Sbjct: 68 VAIDGPTDDGKVTIHGVGLHGLQAPAGDLEMGNSGTSMRLMSGLMSGQAFDVRMTGDASL 127 Query: 121 QRRPMKRIIDPLTLMGAKIDSTG-NVPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGL 179 +RPMKR+ PL MGA ID+T PPL ++G +L GIHY +P+ASAQVKS LLLAGL Sbjct: 128 SKRPMKRVTVPLASMGAVIDATEIGTPPLLVHGGSKLQGIHYDMPVASAQVKSSLLLAGL 187 Query: 180 YARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAF 239 YA+G+T + EPAP+RDHTER+L+ F Y ++ D I + GGGKL A DI +P DISSAAF Sbjct: 188 YAQGETSVIEPAPTRDHTERMLRGFGYAVKTDGNHISLQGGGKLTATDIDVPSDISSAAF 247 Query: 240 FIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHAR 299 F+V A+I GS + + VG+NPTR GVI++L++MGA++E+ + E EP AD+ VR A Sbjct: 248 FMVGASIAAGSDLTIEHVGMNPTRTGVIDILRLMGANLEILNEREVGGEPVADVRVRAAP 307 Query: 300 LKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGI 359 LKGI IP VPL IDEFP L IAAA A+G+TVL A ELRVKE+DRI M DGL G+ Sbjct: 308 LKGIQIPEALVPLAIDEFPALFIAAAFAEGQTVLTGAEELRVKESDRIQVMADGLIACGV 367 Query: 360 AAESLPDGVIIQGGTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFV 419 A+ PDG+II+ G GG ++S+ DHRIAM+FA+A A P+ I +C NV TSFP FV Sbjct: 368 DAQPTPDGIIIKPGNFTGGTIDSHGDHRIAMSFAMAALRATQPITINDCANVNTSFPGFV 427 Query: 420 ELANEVGMNV 429 LA G+ + Sbjct: 428 GLAAGAGVRI 437 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: 629 Number of extensions: 25 Number of successful extensions: 2 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: 440 Length adjustment: 32 Effective length of query: 406 Effective length of database: 408 Effective search space: 165648 Effective search space used: 165648 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_028489167.1 Q394_RS0109965 (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.17827.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-128 413.6 0.0 4.9e-128 413.4 0.0 1.0 1 lcl|NCBI__GCF_000621325.1:WP_028489167.1 Q394_RS0109965 3-phosphoshikimat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000621325.1:WP_028489167.1 Q394_RS0109965 3-phosphoshikimate 1-carboxyvinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 413.4 0.0 4.9e-128 4.9e-128 1 410 [. 20 431 .. 20 436 .. 0.96 Alignments for each domain: == domain 1 score: 413.4 bits; conditional E-value: 4.9e-128 TIGR01356 1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.ee.keelviegvgg.. 65 g +++pg+KSishR+++l++Laeg+t v ++L++eD+l tl+a+r++G+ + + +++++i+gvg lcl|NCBI__GCF_000621325.1:WP_028489167.1 20 GTVRVPGDKSISHRSIMLGSLAEGTTHVSGFLQGEDCLCTLNAFRSMGVAIDgPTdDGKVTIHGVGLhg 88 789*************************************************844599******99888 PP TIGR01356 66 lkepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPl 134 l+ p l++gnsGt++Rl++g+++ ++++v +tgd sl+kRP++r++ +L ++ga i+++e g++Pl lcl|NCBI__GCF_000621325.1:WP_028489167.1 89 LQAPAGDLEMGNSGTSMRLMSGLMSGQAFDVRMTGDASLSKRPMKRVTVPLASMGAVIDATE-IGTPPL 156 9**********************************************************988.69**** PP TIGR01356 135 aisgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveee 202 ++g++k+ gi++ + aS+Q+ks+llla+ l a++++ v+e+ +r+++e++L ++ + v+ + lcl|NCBI__GCF_000621325.1:WP_028489167.1 157 LVHGGSKLqGIHYDMPVASAQVKSSLLLAG---LYAQGETSVIEPAPTRDHTERMLRGFGYA---VKTD 219 *****8888*********************...77889999999************999877...8887 PP TIGR01356 203 derkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadv 270 ++i+++gg+k + ++++v++D+SsAaff++ a i+ + ++t+e++g+n+t+++ +i++L+ mGa++ lcl|NCBI__GCF_000621325.1:WP_028489167.1 220 G-NHISLQGGGKLTATDIDVPSDISSAAFFMVGASIAAGsDLTIEHVGMNPTRTG--VIDILRLMGANL 285 6.5*********88888********************999***************..788********* PP TIGR01356 271 eveeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsd 330 e+ ++r dv+v+ a lkg+++ ++ v+ +iDe+p+l ++aafAeg+t+++++eelRvkEsd lcl|NCBI__GCF_000621325.1:WP_028489167.1 286 EILNERevggepvaDVRVR-AAPLKGIQIpEALVPLAIDEFPALFIAAAFAEGQTVLTGAEELRVKESD 353 *******************.779******99************************************** PP TIGR01356 331 RiaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecva 399 Ri+++a+ L + Gv++++++dg++i++++ + g+++d+++DHRiam++a+++l+a ++++i+d + v+ lcl|NCBI__GCF_000621325.1:WP_028489167.1 354 RIQVMADGLIACGVDAQPTPDGIIIKPGN--FTGGTIDSHGDHRIAMSFAMAALRATQPITINDCANVN 420 ****************************5..************************************** PP TIGR01356 400 ksfPeFfevle 410 +sfP F+ +++ lcl|NCBI__GCF_000621325.1:WP_028489167.1 421 TSFPGFVGLAA 431 ******98766 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (440 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: 00:00:00.01 # Mc/sec: 9.86 // [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