Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_026596276.1 H035_RS0104765 3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::Q83E11 (438 letters) >NCBI__GCF_000421465.1:WP_026596276.1 Length = 439 Score = 459 bits (1181), Expect = e-134 Identities = 240/434 (55%), Positives = 308/434 (70%), Gaps = 2/434 (0%) Query: 1 MDYQTIPSQGLSGEICVPGDKSISHRAVLLAAIAEGQTQVDGFLMGADNLAMVSALQQMG 60 +DY P L G VPGDKSISHR+V+L +IAEG T+V GFL D LA + A +QMG Sbjct: 5 IDYVAAPGGALRGRARVPGDKSISHRSVMLGSIAEGVTRVSGFLEAEDALATLGAFRQMG 64 Query: 61 ASIQVIEDENILVVEGVGMTGLQAPPEALDCGNSGTAIRLLSGLLAGQPFNTVLTGDSSL 120 +++ D + + G GM GL+AP E L+ GNSGT++RLL GLL+GQPF++VLTGD+SL Sbjct: 65 VTVEGPVDGR-MTIHGAGMHGLKAPSEPLNLGNSGTSMRLLCGLLSGQPFDSVLTGDASL 123 Query: 121 QRRPMKRIIDPLTLMGAKIDSTGN-VPPLKIYGNPRLTGIHYQLPMASAQVKSCLLLAGL 179 RRPM+R+ +PL MGA I++T P++I+G L GI Y+LP+ASAQVKS LLLAGL Sbjct: 124 SRRPMRRVTEPLRRMGATIETTAEGTAPIRIFGKQSLHGIDYRLPVASAQVKSALLLAGL 183 Query: 180 YARGKTCITEPAPSRDHTERLLKHFHYTLQKDKQSICVSGGGKLKANDISIPGDISSAAF 239 YA+G+T + EPAP+RDHTER+L F Y L+++ + + GGGKL A ++ +P DISSAAF Sbjct: 184 YAQGETSVEEPAPTRDHTERMLAGFGYPLRREGSRVTLQGGGKLTATELDVPTDISSAAF 243 Query: 240 FIVAATITPGSAIRLCRVGVNPTRLGVINLLKMMGADIEVTHYTEKNEEPTADITVRHAR 299 F+V A+I P S + L VG+NPTR GVI++L++MGA IEV EP AD+ V Sbjct: 244 FLVGASIAPDSELVLEHVGINPTRTGVIDILRLMGAKIEVLDSRMVGGEPVADLKVVSRP 303 Query: 300 LKGIDIPPDQVPLTIDEFPVLLIAAAVAQGKTVLRDAAELRVKETDRIAAMVDGLQKLGI 359 L+GI IP VPL IDEFPVL +AAA A+G+TVL AAELRVKE+DRI M DGL LGI Sbjct: 304 LRGIQIPEKLVPLAIDEFPVLFVAAACAEGETVLTGAAELRVKESDRIQVMADGLGALGI 363 Query: 360 AAESLPDGVIIQGGTLEGGEVNSYDDHRIAMAFAVAGTLAKGPVRIRNCDNVKTSFPNFV 419 A PDG+I++GG + G V S+ DHRIAMAFA+A A GP+ I +C NV TSFP F Sbjct: 364 DACPTPDGMIVRGGRIGSGRVASHGDHRIAMAFAIAALRASGPIEIDDCANVNTSFPGFT 423 Query: 420 ELANEVGMNVKGVR 433 ELA +G+NV+ VR Sbjct: 424 ELARRLGLNVEVVR 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: 626 Number of extensions: 29 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: 439 Length adjustment: 32 Effective length of query: 406 Effective length of database: 407 Effective search space: 165242 Effective search space used: 165242 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_026596276.1 H035_RS0104765 (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.31498.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4e-128 413.7 0.0 4.6e-128 413.5 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_026596276.1 H035_RS0104765 3-phosphoshikimat Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_026596276.1 H035_RS0104765 3-phosphoshikimate 1-carboxyvinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 413.5 0.0 4.6e-128 4.6e-128 1 413 [. 17 430 .. 17 432 .. 0.96 Alignments for each domain: == domain 1 score: 413.5 bits; conditional E-value: 4.6e-128 TIGR01356 1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakve.eekeelviegvgg..l 66 g+ ++pg+KSishR+++l+++aeg t+v ++L++eD latl a+r++G++ve +++++i+g g+ l lcl|NCBI__GCF_000421465.1:WP_026596276.1 17 GRARVPGDKSISHRSVMLGSIAEGVTRVSGFLEAEDALATLGAFRQMGVTVEgPVDGRMTIHGAGMhgL 85 6789************************************************666********99999* PP TIGR01356 67 kepeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPla 135 k p++ l+lgnsGt++Rll g+l+ +++++vltgd sl++RP++r++e+Lr++ga+ie + eg++P++ lcl|NCBI__GCF_000421465.1:WP_026596276.1 86 KAPSEPLNLGNSGTSMRLLCGLLSGQPFDSVLTGDASLSRRPMRRVTEPLRRMGATIETTA-EGTAPIR 153 **********************************************************988.69***** PP TIGR01356 136 isgplkg.givelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeed 203 i g++++ gi + + aS+Q+ksallla+ l a++++ v+e+ +r+++e++L+ ++ +++e lcl|NCBI__GCF_000421465.1:WP_026596276.1 154 IFGKQSLhGIDYRLPVASAQVKSALLLAG---LYAQGETSVEEPAPTRDHTERMLAGFGYP---LRREG 216 ****8888*********************...77889999999***********9988766...99998 PP TIGR01356 204 erkivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadve 271 + +++++gg+k + +e++v+ D+SsAaffl+ a i++ e+++e++g+n+t+++ +i++L+ mGa++e lcl|NCBI__GCF_000421465.1:WP_026596276.1 217 S-RVTLQGGGKLTATELDVPTDISSAAFFLVGASIAPDsELVLEHVGINPTRTG--VIDILRLMGAKIE 282 7.*********88888**************************************..788********** PP TIGR01356 272 veeqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdR 331 v ++r d++v ++ l+g+++ ++ v+ +iDe+p+l v+aa+Aeget++++++elRvkEsdR lcl|NCBI__GCF_000421465.1:WP_026596276.1 283 VLDSRmvggepvaDLKVV-SRPLRGIQIpEKLVPLAIDEFPVLFVAAACAEGETVLTGAAELRVKESDR 350 *************9*999.689******99*************************************** PP TIGR01356 332 iaaiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvak 400 i+++a+ L +lG+++ +++dg++++G+ ++ +++v +++DHRiama+a+++l+a+g++ei+d + v++ lcl|NCBI__GCF_000421465.1:WP_026596276.1 351 IQVMADGLGALGIDACPTPDGMIVRGG--RIGSGRVASHGDHRIAMAFAIAALRASGPIEIDDCANVNT 417 ***************************..7*************************************** PP TIGR01356 401 sfPeFfevleqlg 413 sfP F e++++lg lcl|NCBI__GCF_000421465.1:WP_026596276.1 418 SFPGFTELARRLG 430 ********99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (439 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: 11.69 // [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