Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_004513010.1 GMET_RS04325 3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::Q31RQ5 (448 letters) >NCBI__GCF_000012925.1:WP_004513010.1 Length = 429 Score = 445 bits (1145), Expect = e-129 Identities = 235/421 (55%), Positives = 304/421 (72%), Gaps = 6/421 (1%) Query: 27 GLRGRIRVPGDKSISHRALMLGAIASGETTIEGLLLGEDPLSTAACFRAMGAEISELNSE 86 G+RG I VPGDKSISHR++MLG+IA GETT+ G L GED ++T FRAMG I + + E Sbjct: 11 GIRGEITVPGDKSISHRSIMLGSIARGETTVRGFLRGEDNIATLNAFRAMGVVIDD-DGE 69 Query: 87 LVRVKGIGLQNLQEPLDVLNAGNSGTTIRLMMGLLAGQRDRFFCV-TGDESLRSRPMARV 145 +R+ G GL+ L EP DVL+ GNSGT++RL+ GLLA QR F+ V +GD+ LR RPM RV Sbjct: 70 TLRIAGKGLRGLAEPTDVLDCGNSGTSMRLLTGLLAPQR--FYSVLSGDQYLRRRPMRRV 127 Query: 146 IQPLSQMGAEIRGRQGNTRAPLAISGRSLQPIRYVSPIASAQVKSSILLAGLTCEGQTTV 205 ++PLS+MGA I GR+G +APLAI GR L+ I Y S +ASAQVKS+++LAGL EG+T V Sbjct: 128 VEPLSRMGACIHGREGGEKAPLAIVGRDLKGISYTSSVASAQVKSALMLAGLYAEGETRV 187 Query: 206 VEPALSRDHSERMFRAFGAKLTVNPEEISVTVEGPAELTGQPVVVPGDISSAAFWLVAAA 265 EP LSRDHSERMFR FGA + P V V G EL G+ ++VPGDISSAAF++VAA Sbjct: 188 TEPHLSRDHSERMFRHFGADIENGPA--GVVVRGGRELEGRDIIVPGDISSAAFFMVAAL 245 Query: 266 IVPDSDLLIENVGVNPTRTGILEALQQMEAQITLENERIVAGEPVADLRVRSSNLQAIEI 325 IVP S+LLI VGVNPTRTGI++ L M + L ++R V+GEPVAD+ VRSS L+ IEI Sbjct: 246 IVPGSELLIRGVGVNPTRTGIIDILTAMGGSLELLDQREVSGEPVADILVRSSRLKGIEI 305 Query: 326 GGSLIPRLIDEVPILAVAAAFAKGTTIIRDAEELRVKESDRIAVMASELGRMGATISERP 385 G ++PR IDE P++ VAAA A+G T++R+A ELRVKE+DRIA MA+ L +G T++E Sbjct: 306 AGEVVPRAIDEFPVICVAAAVAEGRTVVREARELRVKETDRIAAMATNLRAVGVTVTESE 365 Query: 386 DGLEITGGAALTGATVDSYTDHRIAMSLAIAALQAKGQTQIQQAEAAAVSYPDFVPTLQQ 445 DG++I G + TV+S+ DHRIAMS+ IA L A G + E S+P F P L++ Sbjct: 366 DGMDIEGAEQIAAGTVESFGDHRIAMSMLIAGLTAGGDITVTDTECIGTSFPTFFPLLEK 425 Query: 446 L 446 + Sbjct: 426 V 426 Lambda K H 0.317 0.133 0.366 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: 611 Number of extensions: 26 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: 448 Length of database: 429 Length adjustment: 32 Effective length of query: 416 Effective length of database: 397 Effective search space: 165152 Effective search space used: 165152 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
Align candidate WP_004513010.1 GMET_RS04325 (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.14145.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-133 431.2 0.1 2.2e-133 431.0 0.1 1.0 1 lcl|NCBI__GCF_000012925.1:WP_004513010.1 GMET_RS04325 3-phosphoshikimate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012925.1:WP_004513010.1 GMET_RS04325 3-phosphoshikimate 1-carboxyvinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 431.0 0.1 2.2e-133 2.2e-133 1 414 [. 14 428 .. 14 429 .] 0.97 Alignments for each domain: == domain 1 score: 431.0 bits; conditional E-value: 2.2e-133 TIGR01356 1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg..lk 67 gei++pg+KSishR+++l+++a+get+v+++L++eD +atl+a+r++G+ + +++e+l i g+g l+ lcl|NCBI__GCF_000012925.1:WP_004513010.1 14 GEITVPGDKSISHRSIMLGSIARGETTVRGFLRGEDNIATLNAFRAMGVVIDDDGETLRIAGKGLrgLA 82 89**************************************************99*******998788** PP TIGR01356 68 epeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlai 136 ep+++ld+gnsGt++Rlltg+la +++ +vl+gd+ l++RP++r+ve+L+++ga i+ +e+ +++Plai lcl|NCBI__GCF_000012925.1:WP_004513010.1 83 EPTDVLDCGNSGTSMRLLTGLLAPQRFYSVLSGDQYLRRRPMRRVVEPLSRMGACIHGREGGEKAPLAI 151 ********************************************************************* PP TIGR01356 137 sgplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeeder 205 g gi++ s aS+Q+ksal+la+ l a++++ v+e+ +sr++ e++ ++++ +e+ lcl|NCBI__GCF_000012925.1:WP_004513010.1 152 VGRDLKGISYTSSVASAQVKSALMLAG---LYAEGETRVTEPHLSRDHSERMFRHFGAD---IENGPA- 213 **6555*********************...77889999999**********98777766...999776. PP TIGR01356 206 kivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveve 273 +vv+gg + + +++ v+gD+SsAaff++aa+i ++ e+ ++++g n+t+++ ii++L +mG+++e+ lcl|NCBI__GCF_000012925.1:WP_004513010.1 214 GVVVRGGRELEGRDIIVPGDISSAAFFMVAALIVPGsELLIRGVGVNPTRTG--IIDILTAMGGSLELL 280 ********988888**********************9***************..888************ PP TIGR01356 274 eqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRia 333 +qr d+ v+ +s lkg+++ + v+++iDe+p++ v+aa+Aeg t++++++elRvkE+dRia lcl|NCBI__GCF_000012925.1:WP_004513010.1 281 DQRevsgepvaDILVR-SSRLKGIEIaGEVVPRAIDEFPVICVAAAVAEGRTVVREARELRVKETDRIA 348 ***9************.789******99***************************************** PP TIGR01356 334 aiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksf 402 a+a++L+++Gv+v+e edg+ ieG+ +++ ++v++++DHRiam++ ++gl a g ++++d+ec+ +sf lcl|NCBI__GCF_000012925.1:WP_004513010.1 349 AMATNLRAVGVTVTESEDGMDIEGA-EQIAAGTVESFGDHRIAMSMLIAGLTAGGDITVTDTECIGTSF 416 *************************.6****************************************** PP TIGR01356 403 PeFfevleqlga 414 P Ff +le++ a lcl|NCBI__GCF_000012925.1:WP_004513010.1 417 PTFFPLLEKVAA 428 ********9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (429 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: 10.34 // [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