Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_057506776.1 ABB28_RS00670 3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::Q83E11 (438 letters) >NCBI__GCF_001431535.1:WP_057506776.1 Length = 437 Score = 418 bits (1074), Expect = e-121 Identities = 219/423 (51%), Positives = 287/423 (67%), Gaps = 3/423 (0%) Query: 9 QGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMGASIQVIED 68 Q L G + +PGDKS+SHRAV+ AA+A+G + +DGFL G D A QMGA ++ Sbjct: 13 QPLQGSLVIPGDKSVSHRAVMFAALADGTSTIDGFLEGEDTRATARIFSQMGARMETPSP 72 Query: 69 ENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSLQRRPMKRI 128 VV GVG+ GLQAP LDCGN+GT +RL++G+LAGQ F++VL GD SL RRPM+R+ Sbjct: 73 SR-RVVHGVGIDGLQAPDGELDCGNAGTGMRLIAGVLAGQAFDSVLVGDESLSRRPMRRV 131 Query: 129 IDPLTLMGAKIDSTGN-VPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGLYARGKTCI 187 PL MGA+ID+ + PPL ++G L GI + P+ASAQVKS +LLAGLYA G+T + Sbjct: 132 TGPLAQMGARIDTQDDGTPPLHVHGGQALKGIDFASPVASAQVKSAVLLAGLYAEGETSV 191 Query: 188 TEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAFFIVAATIT 247 EP P+RD+TER+L F + + GG +L+A DI +P D SSAAFF+VAA+I Sbjct: 192 VEPHPTRDYTERMLAAFGVEITYSPGKARLRGGQRLRATDIVVPADFSSAAFFLVAASII 251 Query: 248 PGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHARLKGIDIPP 307 PGS +RL +VG+NP R G+++ L++MGADI + E+ EP AD+ VR+A LKG IP Sbjct: 252 PGSELRLQQVGLNPRRTGLLHALRLMGADITEENPAEQGGEPVADLVVRYAPLKGAQIPE 311 Query: 308 DQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGIAAESLPDG 367 VP IDEFP L +AAA A+G+TV+ AAELRVKE+DR+AAM GL+ LG+ + DG Sbjct: 312 ALVPDMIDEFPALFVAAAAAEGQTVVTGAAELRVKESDRLAAMATGLRTLGVQVDETEDG 371 Query: 368 VIIQGGTLEG-GEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFVELANEVG 426 I GG + G G + S+ DHRIAMAFA+AG L +G VRI + NV TSFP F LA G Sbjct: 372 ATIHGGAVLGSGTIESHGDHRIAMAFAIAGQLTEGEVRINDVANVATSFPGFDSLAGGAG 431 Query: 427 MNV 429 + Sbjct: 432 FGL 434 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: 620 Number of extensions: 26 Number of successful extensions: 4 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: 437 Length adjustment: 32 Effective length of query: 406 Effective length of database: 405 Effective search space: 164430 Effective search space used: 164430 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_057506776.1 ABB28_RS00670 (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.5175.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-126 408.7 0.0 1.6e-126 408.4 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057506776.1 ABB28_RS00670 3-phosphoshikimate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057506776.1 ABB28_RS00670 3-phosphoshikimate 1-carboxyvinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 408.4 0.0 1.6e-126 1.6e-126 1 407 [. 17 425 .. 17 431 .. 0.95 Alignments for each domain: == domain 1 score: 408.4 bits; conditional E-value: 1.6e-126 TIGR01356 1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveee.keelviegvgg..l 66 g++ ipg+KS+shRa+++aaLa+g+++++++L++eDt+at ++++++Ga++e + v++gvg l lcl|NCBI__GCF_001431535.1:WP_057506776.1 17 GSLVIPGDKSVSHRAVMFAALADGTSTIDGFLEGEDTRATARIFSQMGARMETPsPSRRVVHGVGIdgL 85 57889***********************************************5549999****99888* PP TIGR01356 67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135 + p+ eld+gn+Gt +Rl+ gvla +++++vl gdesl++RP++r++ +L ++ga+i+ ++ +g++Pl+ lcl|NCBI__GCF_001431535.1:WP_057506776.1 86 QAPDGELDCGNAGTGMRLIAGVLAGQAFDSVLVGDESLSRRPMRRVTGPLAQMGARIDTQD-DGTPPLH 153 **********************************************************887.69***** PP TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203 ++g++ + gi s+ aS+Q+ksa+lla+ l a++++ v e+ +r+y+e++L+ +fgve++ + lcl|NCBI__GCF_001431535.1:WP_057506776.1 154 VHGGQALkGIDFASPVASAQVKSAVLLAG---LYAEGETSVVEPHPTRDYTERMLA---AFGVEITYSP 216 ****8888*********************...56677888888**********986...56788***99 PP TIGR01356 204 erkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadve 271 + k +++ggq + +++ v++D+SsAaffl+aa i ++ e++++++g n+ +++ ++ L+ mGad++ lcl|NCBI__GCF_001431535.1:WP_057506776.1 217 G-KARLRGGQRLRATDIVVPADFSSAAFFLVAASIIPGsELRLQQVGLNPRRTG--LLHALRLMGADIT 282 8.*********99999******************99999***************..788*********9 PP TIGR01356 272 veeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdR 331 e+ d++v+ lkg ++ ++ v+++iDe+p+l v+aa Aeg+t++++++elRvkEsdR lcl|NCBI__GCF_001431535.1:WP_057506776.1 283 EENPAeqggepvaDLVVR-YAPLKGAQIpEALVPDMIDEFPALFVAAAAAEGQTVVTGAAELRVKESDR 350 99988899**********.568******99*************************************** PP TIGR01356 332 iaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvak 400 +aa+a+ L++lGv+v+e+edg +i+G+ + l ++++++++DHRiama+a++g egev+i+d + va+ lcl|NCBI__GCF_001431535.1:WP_057506776.1 351 LAAMATGLRTLGVQVDETEDGATIHGG-AVLGSGTIESHGDHRIAMAFAIAGQLTEGEVRINDVANVAT 418 ***************************.69999************************************ PP TIGR01356 401 sfPeFfe 407 sfP F lcl|NCBI__GCF_001431535.1:WP_057506776.1 419 SFPGFDS 425 ****965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (437 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.38 // [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