Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_048065968.1 MA_RS22735 branched-chain-amino-acid transaminase
Query= BRENDA::A0A1B1L2T7 (298 letters) >NCBI__GCF_000007345.1:WP_048065968.1 Length = 292 Score = 319 bits (817), Expect = 5e-92 Identities = 156/293 (53%), Positives = 214/293 (73%), Gaps = 1/293 (0%) Query: 1 MNEQWIFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKS 60 M++ I+LNG+FVPKDEAKVSVYDHG+LYGDGVFEGIR Y+G VF+L+EH+ RLY+SAK+ Sbjct: 1 MSDLLIYLNGKFVPKDEAKVSVYDHGFLYGDGVFEGIRAYNGRVFKLKEHVDRLYDSAKA 60 Query: 61 ILLEIPYSLDEVTNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCKKPNVVVIAEQL 120 I ++IP + +E+T I++E +R+N L + YIR +VSRG G+LGLDP C KP+V+VIA+ Sbjct: 61 IAMDIPVTREEMTEIILEALRKNNLKDAYIRPIVSRGIGDLGLDPRKCGKPSVIVIAQGW 120 Query: 121 SLFPQEYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQ 180 + YE G+ V+V RRN PD LSP +KSLNYLNNIL +IEA G EA+ L+ Sbjct: 121 GAMYGDLYEVGLTGVSVCVRRNAPDALSPNIKSLNYLNNILAKIEANEKGGDEAIFLDHN 180 Query: 181 GYVAEGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYV 240 G+V EGSGDN+F+VK ++++T P + L+GITR +E+ +++GY V E D+Y Sbjct: 181 GFVCEGSGDNIFVVKDDRVLT-PFTISNLKGITRATAIELLDEMGYKVIESNLGLFDLYT 239 Query: 241 ADEVFLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLVVEDGEKIYE 293 ADE+F+TGTAAE VT +DGR IG G+ GP T +++E F K+ G +IY+ Sbjct: 240 ADEIFVTGTAAESAPVTRLDGRVIGTGKPGPLTMKMVEAFAKITQSTGTQIYK 292 Lambda K H 0.317 0.138 0.389 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: 293 Number of extensions: 14 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: 298 Length of database: 292 Length adjustment: 26 Effective length of query: 272 Effective length of database: 266 Effective search space: 72352 Effective search space used: 72352 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: 48 (23.1 bits)
Align candidate WP_048065968.1 MA_RS22735 (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.16866.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-112 361.6 0.0 1.7e-112 361.4 0.0 1.0 1 lcl|NCBI__GCF_000007345.1:WP_048065968.1 MA_RS22735 branched-chain-amino- Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000007345.1:WP_048065968.1 MA_RS22735 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 361.4 0.0 1.7e-112 1.7e-112 1 287 [. 7 286 .. 7 292 .] 0.97 Alignments for each domain: == domain 1 score: 361.4 bits; conditional E-value: 1.7e-112 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 +l+G++v+ ++akv+v +h+++YG+gvfeGiRaY++ ++f+lkehv+Rlydsak++ ++ip+++ee lcl|NCBI__GCF_000007345.1:WP_048065968.1 7 YLNGKFVPKDEAKVSVYDHGFLYGDGVFEGIRAYNG----RVFKLKEHVDRLYDSAKAIAMDIPVTREE 71 89**********************************....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpk.vdlkveviiaawewgaylgeealekGikvkvss 137 ++e++ e+lrknnlk+aYiRp+v +G++dlgl+p+ ++ k++vi++a wga++g+ +e G++ + lcl|NCBI__GCF_000007345.1:WP_048065968.1 72 MTEIILEALRKNNLKDAYIRPIVSRGIGDLGLDPRkCG-KPSVIVIAQGWGAMYGD-LYEVGLTGVSVC 138 **********************************9566.****************8.5*********** PP TIGR01122 138 frraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvse 206 +rr+a++++ +++k+ + Yln++lak+ea+++G deai+Ld++G+v eGsG+nif+vkd+ +ltP + lcl|NCBI__GCF_000007345.1:WP_048065968.1 139 VRRNAPDALSPNIKSLN-YLNNILAKIEANEKGGDEAIFLDHNGFVCEGSGDNIFVVKDDRVLTPFT-I 205 ****************9.***********************************************99.5 PP TIGR01122 207 siLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkk 275 s+Lkgitr + i+l+ e+g++v e+++++ +lytaDe+f+tGtaae +P++++Dgr ig gk Gp+t k lcl|NCBI__GCF_000007345.1:WP_048065968.1 206 SNLKGITRATAIELLDEMGYKVIESNLGLFDLYTADEIFVTGTAAESAPVTRLDGRVIGTGKPGPLTMK 274 69******************************************************************* PP TIGR01122 276 lqeaffdlvegk 287 + eaf ++++++ lcl|NCBI__GCF_000007345.1:WP_048065968.1 275 MVEAFAKITQST 286 ********9984 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (292 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: 7.01 // [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