Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_013430883.1 CALKRO_RS09925 branched-chain-amino-acid transaminase
Query= BRENDA::A0A1B1L2T7 (298 letters) >NCBI__GCF_000166775.1:WP_013430883.1 Length = 293 Score = 352 bits (902), Expect = e-102 Identities = 169/293 (57%), Positives = 221/293 (75%) Query: 1 MNEQWIFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKS 60 M E+ I+++G+F K EAK+SV+DHG+LYGDGVFEGIRVY+G +F+ +EH+ RLY++AK+ Sbjct: 1 MEEKLIYIDGKFYKKSEAKISVFDHGFLYGDGVFEGIRVYNGKIFKCKEHVDRLYQAAKA 60 Query: 61 ILLEIPYSLDEVTNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCKKPNVVVIAEQL 120 I +EIP S +E+ + +T R N + GYIRLVVSRG G+LGL P C KP +V+IA+ + Sbjct: 61 IYMEIPISKEEMIEALKKTCRVNNIREGYIRLVVSRGVGDLGLSPTKCPKPTIVIIADSI 120 Query: 121 SLFPQEYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQ 180 L+PQE YEKG+ V+T +TRRN P + PQ+KSLNYLNNIL +IEA AGV EA+ML Sbjct: 121 VLYPQEMYEKGMKVITASTRRNSPQCVDPQIKSLNYLNNILAKIEANRAGVPEAIMLTQD 180 Query: 181 GYVAEGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYV 240 GYV E +GDN+FIVK +LITPP GAL+GITR ++ + + LG V E++FT +++Y Sbjct: 181 GYVTECTGDNIFIVKDGELITPPVYLGALDGITRRTVMALAKDLGIPVYEKVFTLYNLYN 240 Query: 241 ADEVFLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLVVEDGEKIYE 293 ADE F TGTAAEVIAVT VDGR IG G+ GP T +L+EEF+KL DG IYE Sbjct: 241 ADECFFTGTAAEVIAVTEVDGRKIGNGEVGPITKKLMEEFKKLTQIDGVDIYE 293 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: 311 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: 293 Length adjustment: 26 Effective length of query: 272 Effective length of database: 267 Effective search space: 72624 Effective search space used: 72624 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_013430883.1 CALKRO_RS09925 (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.242078.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-109 352.2 0.3 1.4e-109 351.9 0.3 1.0 1 NCBI__GCF_000166775.1:WP_013430883.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_013430883.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 351.9 0.3 1.4e-109 1.4e-109 1 285 [. 7 285 .. 7 292 .. 0.96 Alignments for each domain: == domain 1 score: 351.9 bits; conditional E-value: 1.4e-109 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 ++dG++ + +ak++v++h+++YG+gvfeGiR+Y++ if+ kehv+Rly++ak++ +eip+skee++e+ NCBI__GCF_000166775.1:WP_013430883.1 7 YIDGKFYKKSEAKISVFDHGFLYGDGVFEGIRVYNG----KIFKCKEHVDRLYQAAKAIYMEIPISKEEMIEA 75 89**********************************....9******************************** PP TIGR01122 74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146 k++ r+nn+++ YiR +v +G++dlgl+p k++++i+a ++ y e +ekG+kv+++s rr++++ + NCBI__GCF_000166775.1:WP_013430883.1 76 LKKTCRVNNIREGYIRLVVSRGVGDLGLSPTKCPKPTIVIIADSIVLYPQ-EMYEKGMKVITASTRRNSPQCV 147 ******************************63337777788877776665.68******************** PP TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219 +++k+ + Yln++lak+ea+raG+ eai+L ++Gyv+e +G+nifivkdg+l+tPpv+ +L+gitr +v+ NCBI__GCF_000166775.1:WP_013430883.1 148 DPQIKSLN-YLNNILAKIEANRAGVPEAIMLTQDGYVTECTGDNIFIVKDGELITPPVYLGALDGITRRTVMA 219 *******9.**************************************************************** PP TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlve 285 lak+lgi v e+++++++ly aDe f+tGtaaev+ ++evDgrkig+g++Gp+tkkl+e+f++l++ NCBI__GCF_000166775.1:WP_013430883.1 220 LAKDLGIPVYEKVFTLYNLYNADECFFTGTAAEVIAVTEVDGRKIGNGEVGPITKKLMEEFKKLTQ 285 **************************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (293 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: 25.24 // [ok]
This GapMind analysis is from Jul 26 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