Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate WP_011735260.1 PPRO_RS06685 3-phosphoshikimate 1-carboxyvinyltransferase
Query= BRENDA::A6TL04 (425 letters) >NCBI__GCF_000015045.1:WP_011735260.1 Length = 431 Score = 435 bits (1119), Expect = e-126 Identities = 217/408 (53%), Positives = 293/408 (71%), Gaps = 1/408 (0%) Query: 10 LEGKMTVPGDKSISHRAIMLSSISKGTSRVKGFLRGEDCLSTISCFRDLGIDIEDRGTEI 69 L+G++ VPGDKSISHR+IML +I+ G + V+GFLRGED ++T++ FR +G+ I+D G + Sbjct: 12 LKGELVVPGDKSISHRSIMLGAIANGVTTVRGFLRGEDNMATMAAFRAMGVRIDDDGHLL 71 Query: 70 IIQGKGLHGLSEPLNVLDAGNSGTTIRLISGILAGQKFLTIVTGDASLRKRPMERIATPL 129 I G+GLHGL EP +VLD GNSGT++RL++G+LAGQ F ++++GD LRKRPM+R+ PL Sbjct: 72 SIHGRGLHGLEEPGDVLDCGNSGTSMRLLTGLLAGQNFFSVLSGDQYLRKRPMKRVVEPL 131 Query: 130 RKMGAFIEGRDYGNLAPLVIRGGNLKGMDYASPVSSAQVKSAILLAGLYGEGDTIVREKI 189 +MGA I GR GNLAPL I GG L + Y SPVSSAQ+KSAI+LAGLY +GDT VRE Sbjct: 132 SRMGARILGRAGGNLAPLAISGGTLNAIGYESPVSSAQIKSAIMLAGLYADGDTSVREPS 191 Query: 190 TSRDHTEKMLKGLGANIST-DQGVTRLGKSELYGQSIEVPGDISSAAFFMAGAAALPGSF 248 SRDH+E+M GA++ T GVT G EL+ Q I VPGDISSAAFF+ A P S Sbjct: 192 LSRDHSERMFALFGASLETFHNGVTVKGGIELHAQEIHVPGDISSAAFFIVAALITPDSE 251 Query: 249 LITEGVGLNPTRTGIIDVLRDMGGDIEIHNLRQSGGEEIGDIMIRGKKLYGTEIGKEIIP 308 L+ VG+NPTRTGIIDVLR MGG IE+ + R+ E + DI++R +L G I + +P Sbjct: 252 LLIRNVGVNPTRTGIIDVLRSMGGSIELVDEREVSAEPVADILVRSSRLKGVRIEGQTVP 311 Query: 309 RLIDEIPVLAIIAATAEGKTIITGAEELKVKESNRITAMVTEMQKVGIKVTELPDGMEIE 368 R IDE P + + AA AEG T I A EL+VKE++RI+AM ++ +G+ V E +GM+I Sbjct: 312 RAIDEFPAICVAAACAEGTTSIRDARELRVKETDRISAMAVNLRTLGVTVDECDEGMDIT 371 Query: 369 GGQVITGGRVESYGDHRIAMAMAICGLFAQEPIKINDSQCIDISFPNF 416 G + + GG ES+GDHRIAM++++ GL + + +++ND C+ SFPNF Sbjct: 372 GVERLGGGVAESFGDHRIAMSLSVAGLVSADAVRVNDIDCVSTSFPNF 419 Lambda K H 0.317 0.138 0.383 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: 545 Number of extensions: 20 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: 425 Length of database: 431 Length adjustment: 32 Effective length of query: 393 Effective length of database: 399 Effective search space: 156807 Effective search space used: 156807 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_011735260.1 PPRO_RS06685 (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.18926.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.1e-132 427.8 0.0 2.3e-132 427.6 0.0 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011735260.1 PPRO_RS06685 3-phosphoshikimate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011735260.1 PPRO_RS06685 3-phosphoshikimate 1-carboxyvinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.6 0.0 2.3e-132 2.3e-132 1 412 [. 14 426 .. 14 429 .. 0.96 Alignments for each domain: == domain 1 score: 427.6 bits; conditional E-value: 2.3e-132 TIGR01356 1 geikipgsKSishRalllaaLaegetvvtnlLkseDtlatlealrklGakveeekeelviegvgg..lk 67 ge+ +pg+KSishR+++l+a+a+g t+v+++L++eD at+ a+r++G+++ +++ l i+g g l+ lcl|NCBI__GCF_000015045.1:WP_011735260.1 14 GELVVPGDKSISHRSIMLGAIANGVTTVRGFLRGEDNMATMAAFRAMGVRIDDDGHLLSIHGRGLhgLE 82 7889************************************************99*******998788** PP TIGR01356 68 epeaeldlgnsGttaRlltgvlalasgevvltgdeslkkRPierlveaLrelgaeieskeeegslPlai 136 ep ++ld+gnsGt++Rlltg+la +++ +vl+gd+ l+kRP++r+ve+L+++ga+i + + + +Plai lcl|NCBI__GCF_000015045.1:WP_011735260.1 83 EPGDVLDCGNSGTSMRLLTGLLAGQNFFSVLSGDQYLRKRPMKRVVEPLSRMGARILGRAGGNLAPLAI 151 ********************************************************************* PP TIGR01356 137 sgplkggivelsgsaSsQyksalllaaplalqavtleivgeklisrpyieitLkllksfgveveeeder 205 sg+ +i + s+ S+Q ksa++la+ l a++ + v e+ +sr++ e++ +l+++ +e ++ lcl|NCBI__GCF_000015045.1:WP_011735260.1 152 SGGTLNAIGYESPVSSAQIKSAIMLAG---LYADGDTSVREPSLSRDHSERMFALFGAS---LETFHN- 213 **8777*********************...66778889999***********9999977...777665. PP TIGR01356 206 kivvkggqkykqkevevegDaSsAafflaaaaitge.evtvenlgenstqgdkaiiivLeemGadveve 273 ++vkgg + + +e++v+gD+SsAaff++aa+it+ e+ ++n+g n+t+++ ii+vL++mG+++e+ lcl|NCBI__GCF_000015045.1:WP_011735260.1 214 GVTVKGGIELHAQEIHVPGDISSAAFFIVAALITPDsELLIRNVGVNPTRTG--IIDVLRSMGGSIELV 280 9******9966666**************************************..888************ PP TIGR01356 274 eqr........dvevegasklkgvkv.didvdsliDelptlavlaafAegetriknieelRvkEsdRia 333 ++r d+ v+ +s lkgv++ + v+++iDe+p++ v+aa+Aeg+t i++++elRvkE+dRi+ lcl|NCBI__GCF_000015045.1:WP_011735260.1 281 DERevsaepvaDILVR-SSRLKGVRIeGQTVPRAIDEFPAICVAAACAEGTTSIRDARELRVKETDRIS 348 **99999999999999.789******88***************************************** PP TIGR01356 334 aiaeeLeklGveveeledgllieGkkkelkgavvdtydDHRiamalavlglaaegeveiedaecvaksf 402 a+a +L++lGv+v+e +g+ i+G ++l g+v+++++DHRiam+l+v+gl+ ++ v+++d cv++sf lcl|NCBI__GCF_000015045.1:WP_011735260.1 349 AMAVNLRTLGVTVDECDEGMDITGV-ERLGGGVAESFGDHRIAMSLSVAGLVSADAVRVNDIDCVSTSF 416 *************************.6****************************************** PP TIGR01356 403 PeFfevleql 412 P+Ff +le++ lcl|NCBI__GCF_000015045.1:WP_011735260.1 417 PNFFSLLERF 426 *******987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (415 nodes) Target sequences: 1 (431 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 0.00s 00:00:00.01 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