Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.42) (characterized)
to candidate WP_012505142.1 PAES_RS02730 branched-chain amino acid transaminase
Query= metacyc::MONOMER-11914 (306 letters) >NCBI__GCF_000020625.1:WP_012505142.1 Length = 303 Score = 376 bits (966), Expect = e-109 Identities = 177/301 (58%), Positives = 227/301 (75%), Gaps = 1/301 (0%) Query: 6 SGKIWLNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKRLFDSA 65 S KIW+NGE+V W +A +H+LSHV+HYGSS FEGIRCY KGSAI EH+KRL+ S+ Sbjct: 4 SEKIWMNGELVNWHDAKIHILSHVIHYGSSTFEGIRCYDTDKGSAILFFDEHIKRLYQSS 63 Query: 66 KIYRMDIPYTQEQICDAIVETVRENGLEECYIRPVVFRGYGEMGVHPVNCPVDVAVAAWE 125 KIYRM+IPY+++++ DAI+ T++ NG + CYIRP+V RG G +GV+P ++VA+A WE Sbjct: 64 KIYRMEIPYSEQELKDAIIATIKANGHKACYIRPLVKRGQGALGVNPALASIEVAIATWE 123 Query: 126 WGAYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYDEAIML 185 WG+YLG E LE GVD VS+W R+APNT+P AKAGGNYLNSQL KMEA+ Y E I L Sbjct: 124 WGSYLGEEVLENGVDVCVSSWARLAPNTLPTWAKAGGNYLNSQLIKMEALMDNYAEGIGL 183 Query: 186 DYHGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEPITREM 245 D HGY++EGSGENIF++ +G IYTP S+L GITR++VI IAR G V E I RE Sbjct: 184 DVHGYVAEGSGENIFVIRDGIIYTPMSGQSILPGITRNAVIHIARELGYEVQETLIPREA 243 Query: 246 LYIADEAFFTGTAAEITPIRSVDGIEIGAGRRGPVTKLLQDEFFRIIRAETEDSFGWLTY 305 LYIADE F TGTAAEITP+RS+D +G +RGP+T+LLQ ++ I++ T D + WLT+ Sbjct: 244 LYIADEVFLTGTAAEITPVRSIDKYAVGDEKRGPITELLQSKYLDIVKKGT-DPYNWLTF 302 Query: 306 I 306 I Sbjct: 303 I 303 Lambda K H 0.320 0.136 0.414 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: 326 Number of extensions: 6 Number of successful extensions: 1 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: 306 Length of database: 303 Length adjustment: 27 Effective length of query: 279 Effective length of database: 276 Effective search space: 77004 Effective search space used: 77004 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_012505142.1 PAES_RS02730 (branched-chain amino acid transaminase)
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))
# 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/TIGR01122.hmm # target sequence database: /tmp/gapView.25603.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01122 [M=298] Accession: TIGR01122 Description: ilvE_I: branched-chain amino acid aminotransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-132 425.0 0.0 7.9e-132 424.9 0.0 1.0 1 lcl|NCBI__GCF_000020625.1:WP_012505142.1 PAES_RS02730 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020625.1:WP_012505142.1 PAES_RS02730 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 424.9 0.0 7.9e-132 7.9e-132 1 297 [. 8 302 .. 8 303 .] 0.99 Alignments for each domain: == domain 1 score: 424.9 bits; conditional E-value: 7.9e-132 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w++Gelv+++dak+h+l+h++hYG++ feGiR+Y+tdkg+ai++++eh++Rly+s+ki+r+eipys++e lcl|NCBI__GCF_000020625.1:WP_012505142.1 8 WMNGELVNWHDAKIHILSHVIHYGSSTFEGIRCYDTDKGSAILFFDEHIKRLYQSSKIYRMEIPYSEQE 76 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l ++++ ++++n+ k +YiRplv +G++ lg++p + +++ev+ia+wewg ylgee le+G++v vss+ lcl|NCBI__GCF_000020625.1:WP_012505142.1 77 LKDAIIATIKANGHKACYIRPLVKRGQGALGVNP-ALASIEVAIATWEWGSYLGEEVLENGVDVCVSSW 144 **********************************.7779****************************** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r a+n++pt aka+gnYlns+l+k+eal+ y e+i Ld +GyvaeGsGenif+++dg ++tP +s lcl|NCBI__GCF_000020625.1:WP_012505142.1 145 ARLAPNTLPTWAKAGGNYLNSQLIKMEALMDNYAEGIGLDVHGYVAEGSGENIFVIRDGIIYTPMSGQS 213 ********************************************************************* PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 iL gitr+avi++a+elg+ev+e+ i re+ly+aDevfltGtaae+tP+r++D+ +g+ krGp+t+ l lcl|NCBI__GCF_000020625.1:WP_012505142.1 214 ILPGITRNAVIHIARELGYEVQETLIPREALYIADEVFLTGTAAEITPVRSIDKYAVGDEKRGPITELL 282 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewlty 297 q+++ d+v+++t+ ++ wlt lcl|NCBI__GCF_000020625.1:WP_012505142.1 283 QSKYLDIVKKGTDPYN-WLTF 302 **********988876.8886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (303 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 8.04 // [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