Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_092483004.1 BM299_RS08275 branched-chain-amino-acid transaminase
Query= BRENDA::A0A1B1L2T7 (298 letters) >NCBI__GCF_900115975.1:WP_092483004.1 Length = 292 Score = 352 bits (904), Expect = e-102 Identities = 172/288 (59%), Positives = 221/288 (76%) Query: 6 IFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSILLEI 65 I+L+G+FVP++EA VSV+DHG LYGDGVFEGIR Y VF+L +HLVRLYESA++I LEI Sbjct: 5 IYLDGKFVPEEEAVVSVFDHGLLYGDGVFEGIRAYHNRVFKLHDHLVRLYESARTIGLEI 64 Query: 66 PYSLDEVTNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCKKPNVVVIAEQLSLFPQ 125 ++E+ +V+ET+R+N L + YIRLVV+RG G+LGLDP C KP V IA + L+P Sbjct: 65 SIGMEEMQEVVLETLRRNNLRDAYIRLVVTRGKGDLGLDPRKCPKPTVFCIAASIQLYPD 124 Query: 126 EYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVAE 185 E YE+G+ +VTVATRRN P+ +P+VKSLNYLNNI +IEA LAGV EA+MLN +GYVAE Sbjct: 125 ELYERGLEMVTVATRRNIPEACNPRVKSLNYLNNIYAKIEANLAGVPEAIMLNQEGYVAE 184 Query: 186 GSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVADEVF 245 +GDN+F+VK +KLITPP G LEGITRN ++++ G +V E++FTRHDVY+ADE F Sbjct: 185 ATGDNIFLVKNDKLITPPIHVGLLEGITRNTVMDLARAKGIEVVEKVFTRHDVYIADECF 244 Query: 246 LTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLVVEDGEKIYE 293 LTGTAAE+I VDGRTIG G+ G LL++FR+L DG I+E Sbjct: 245 LTGTAAELIPCVKVDGRTIGDGKPGEVFRGLLKDFRELTKIDGPVIFE 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: 313 Number of extensions: 12 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_092483004.1 BM299_RS08275 (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.1181536.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-107 344.3 0.0 3.4e-107 344.0 0.0 1.0 1 NCBI__GCF_900115975.1:WP_092483004.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900115975.1:WP_092483004.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 344.0 0.0 3.4e-107 3.4e-107 1 285 [. 6 284 .. 6 289 .. 0.98 Alignments for each domain: == domain 1 score: 344.0 bits; conditional E-value: 3.4e-107 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 +ldG++v++e+a v+v++h+l+YG+gvfeGiRaY++ ++f+l++h+ Rly+sa+++ lei++ ee++ev NCBI__GCF_900115975.1:WP_092483004.1 6 YLDGKFVPEEEAVVSVFDHGLLYGDGVFEGIRAYHN----RVFKLHDHLVRLYESARTIGLEISIGMEEMQEV 74 89**********************************....9******************************** PP TIGR01122 74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146 + e+lr+nnl++aYiR +v++G++dlgl+p+ k++v+++a ++ y +e +e+G+++ +++ rr+ ++++ NCBI__GCF_900115975.1:WP_092483004.1 75 VLETLRRNNLRDAYIRLVVTRGKGDLGLDPRKCPKPTVFCIAASIQLYPDE-LYERGLEMVTVATRRNIPEAC 146 ******************************95559**********999885.7******************** PP TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219 ++++k+ + Yln++ ak+ea+ aG+ eai+L++eGyvae +G+nif+vk+++l+tPp++ +L+gitr++v++ NCBI__GCF_900115975.1:WP_092483004.1 147 NPRVKSLN-YLNNIYAKIEANLAGVPEAIMLNQEGYVAEATGDNIFLVKNDKLITPPIHVGLLEGITRNTVMD 218 *******9.**************************************************************** PP TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlve 285 la+ +giev+e++++r+++y+aDe fltGtaae++P ++vDgr+ig+gk G+v + l + f +l++ NCBI__GCF_900115975.1:WP_092483004.1 219 LARAKGIEVVEKVFTRHDVYIADECFLTGTAAELIPCVKVDGRTIGDGKPGEVFRGLLKDFRELTK 284 *************************************************************99976 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 25.03 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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