Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_041458939.1 ADEG_RS01120 branched-chain-amino-acid transaminase
Query= BRENDA::A0A1B1L2T7 (298 letters) >NCBI__GCF_000024605.1:WP_041458939.1 Length = 292 Score = 346 bits (888), Expect = e-100 Identities = 165/287 (57%), Positives = 218/287 (75%) Query: 6 IFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSILLEI 65 ++L+G FVP++EA VSV+DHG LYGDGVFEGIR Y G VF+L+EH+ RLY+SAK+I L I Sbjct: 5 VYLDGRFVPEEEAVVSVFDHGLLYGDGVFEGIRAYHGRVFKLKEHIDRLYDSAKAIALTI 64 Query: 66 PYSLDEVTNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCKKPNVVVIAEQLSLFPQ 125 P S +E+T +V+ET R+N++ +GYIRLVV+RG G+LGLDP C P + IA + L+P Sbjct: 65 PLSREEMTEVVLETCRRNEIKDGYIRLVVTRGKGDLGLDPRKCPNPTIFCIAASIQLYPP 124 Query: 126 EYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVAE 185 E Y+KG+ V+TV TRRN P+ L+P++KSLNYLNNIL +IEA LAGV EA+ML +GYVAE Sbjct: 125 ELYQKGMKVITVPTRRNVPEALNPRIKSLNYLNNILAKIEANLAGVPEAIMLTQEGYVAE 184 Query: 186 GSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVADEVF 245 +GDNVFIV+ L+TPP G LEGITRN ++++ +G +VRE +FTR+D++ A+E F Sbjct: 185 ATGDNVFIVRNGVLMTPPPHLGILEGITRNTVMDLARDMGVEVREAVFTRYDLFTAEECF 244 Query: 246 LTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLVVEDGEKIY 292 LTGTAAE++ V VDGR IG G G T L+ FR+L +GE IY Sbjct: 245 LTGTAAEIVPVIEVDGRPIGEGCPGELTLELIRAFRELTKVEGEPIY 291 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: 279 Number of extensions: 8 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: 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_041458939.1 ADEG_RS01120 (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.11755.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-108 347.2 0.0 4.4e-108 346.9 0.0 1.0 1 lcl|NCBI__GCF_000024605.1:WP_041458939.1 ADEG_RS01120 branched-chain-amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024605.1:WP_041458939.1 ADEG_RS01120 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 346.9 0.0 4.4e-108 4.4e-108 1 287 [. 6 286 .. 6 291 .. 0.97 Alignments for each domain: == domain 1 score: 346.9 bits; conditional E-value: 4.4e-108 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 +ldG++v++e+a v+v++h+l+YG+gvfeGiRaY++ ++f+lkeh++Rlydsak++ l ip+s+ee lcl|NCBI__GCF_000024605.1:WP_041458939.1 6 YLDGRFVPEEEAVVSVFDHGLLYGDGVFEGIRAYHG----RVFKLKEHIDRLYDSAKAIALTIPLSREE 70 89**********************************....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 ++ev+ e+ r+n++k+ YiR +v++G++dlgl+p+ +++++++a ++ y e ++kG+kv+++ lcl|NCBI__GCF_000024605.1:WP_041458939.1 71 MTEVVLETCRRNEIKDGYIRLVVTRGKGDLGLDPRKCPNPTIFCIAASIQLYPPE-LYQKGMKVITVPT 138 **********************************955599********9988885.7************ PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr+ ++++++++k+ + Yln++lak+ea+ aG+ eai+L +eGyvae +G+n+fiv++gvl+tPp + lcl|NCBI__GCF_000024605.1:WP_041458939.1 139 RRNVPEALNPRIKSLN-YLNNILAKIEANLAGVPEAIMLTQEGYVAEATGDNVFIVRNGVLMTPPPHLG 206 ***************9.**************************************************** PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 iL+gitr++v++la+++g+ev+e++++r++l+ta+e fltGtaae++P+ evDgr igeg G++t +l lcl|NCBI__GCF_000024605.1:WP_041458939.1 207 ILEGITRNTVMDLARDMGVEVREAVFTRYDLFTAEECFLTGTAAEIVPVIEVDGRPIGEGCPGELTLEL 275 ********************************************************************* PP TIGR01122 277 qeaffdlvegk 287 af +l++ + lcl|NCBI__GCF_000024605.1:WP_041458939.1 276 IRAFRELTKVE 286 *****998764 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: 6.55 // [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