Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.42) (characterized)
to candidate WP_052669620.1 NITAL_RS11635 branched-chain amino acid transaminase
Query= metacyc::MONOMER-11914 (306 letters) >NCBI__GCF_000969705.1:WP_052669620.1 Length = 299 Score = 294 bits (753), Expect = 2e-84 Identities = 147/297 (49%), Positives = 204/297 (68%), Gaps = 5/297 (1%) Query: 11 LNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKRLFDSAKIYRM 70 ++GE+V W++ATVHVL+ +HYG VFEGIR Y +GSA+F+LR H+ RL SA+IY Sbjct: 1 MDGEVVAWDDATVHVLTPTLHYGYGVFEGIRAYPTDEGSAVFQLRTHLARLLRSARIYPP 60 Query: 71 --DIPYTQEQICDAIVETVRENGLEE-CYIRPVVFRGYGEMGVHPVNCPVDVAVAAWEWG 127 ++P++ + +CDA ++ + NG E+ CY+RP ++ GYGE+G++P+ VA+A WEWG Sbjct: 61 LDEVPFSVDDLCDATLDLIVRNGHEQGCYVRPTIYLGYGEIGLNPLPSEPKVAIATWEWG 120 Query: 128 AYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYDEAIMLDY 187 AYLG +A GV +S++RR+ NT+P KA G YLNS LAK+EA+R GYDEAIML Sbjct: 121 AYLGEQAQLDGVRVMISSYRRIGKNTIPPAGKANGQYLNSSLAKVEAIRAGYDEAIMLSE 180 Query: 188 HGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEPITREMLY 247 G+I+EG+GEN+F+V +G I TPP+ + L GITR +V+ IA G V E P+ R L+ Sbjct: 181 DGFIAEGTGENLFVVHDGVISTPPLWNGPLDGITRQAVMTIAEDLGHPVVERPLVRTDLF 240 Query: 248 IADEAFFTGTAAEITPIRSVDGIEIGAGRRGPVTKLLQDEFFRIIRAETEDSFGWLT 304 +ADE TGTAAEITP+R V+G IG RGP+T+ +Q F +R E WLT Sbjct: 241 LADEILLTGTAAEITPVREVEGRTIGP--RGPITEAIQSTFNDAVRGRVERYRDWLT 295 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: 325 Number of extensions: 11 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: 306 Length of database: 299 Length adjustment: 27 Effective length of query: 279 Effective length of database: 272 Effective search space: 75888 Effective search space used: 75888 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_052669620.1 NITAL_RS11635 (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.31049.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-117 378.3 0.0 1.4e-117 378.2 0.0 1.0 1 lcl|NCBI__GCF_000969705.1:WP_052669620.1 NITAL_RS11635 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000969705.1:WP_052669620.1 NITAL_RS11635 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.2 0.0 1.4e-117 1.4e-117 2 298 .] 1 297 [. 1 297 [. 0.98 Alignments for each domain: == domain 1 score: 378.2 bits; conditional E-value: 1.4e-117 TIGR01122 2 ldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilr.l.eipyske 68 +dGe+v ++da+vhvlt +lhYG gvfeGiRaY td+g+a+f+l+ h+ Rl+ sa+i+ l e+p+s + lcl|NCBI__GCF_000969705.1:WP_052669620.1 1 MDGEVVAWDDATVHVLTPTLHYGYGVFEGIRAYPTDEGSAVFQLRTHLARLLRSARIYPpLdEVPFSVD 69 8********************************************************953348****** PP TIGR01122 69 elvevtkevlrknnlks.aYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvs 136 +l+++t +++ +n+ ++ +Y+Rp +y+G++++gl+p +++v+ia+wewgaylge+a +G++v++s lcl|NCBI__GCF_000969705.1:WP_052669620.1 70 DLCDATLDLIVRNGHEQgCYVRPTIYLGYGEIGLNP-LPSEPKVAIATWEWGAYLGEQAQLDGVRVMIS 137 **********99999999******************.999***************************** PP TIGR01122 137 sfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvs 205 s+rr +n+ip++ ka+g+Ylns lak+ea+raGydeai+L+e+G++aeG+Gen+f+v+dgv+ tPp+ lcl|NCBI__GCF_000969705.1:WP_052669620.1 138 SYRRIGKNTIPPAGKANGQYLNSSLAKVEAIRAGYDEAIMLSEDGFIAEGTGENLFVVHDGVISTPPLW 206 ********************************************************************* PP TIGR01122 206 esiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtk 274 + L+gitr+av+++a++lg v+e+++ r++l++aDe+ ltGtaae+tP+rev+gr+ig rGp+t+ lcl|NCBI__GCF_000969705.1:WP_052669620.1 207 NGPLDGITRQAVMTIAEDLGHPVVERPLVRTDLFLADEILLTGTAAEITPVREVEGRTIGP--RGPITE 273 ***********************************************************85..8***** PP TIGR01122 275 klqeaffdlvegktekkeewltyv 298 +q++f d v+g++e++ +wlt+v lcl|NCBI__GCF_000969705.1:WP_052669620.1 274 AIQSTFNDAVRGRVERYRDWLTPV 297 *********************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (299 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: 00:00:00.00 # Mc/sec: 10.27 // [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