Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_123809394.1 BTUS_RS04760 branched-chain-amino-acid transaminase
Query= BRENDA::A0A1B1L2T7 (298 letters) >NCBI__GCF_000092905.1:WP_123809394.1 Length = 295 Score = 377 bits (968), Expect = e-109 Identities = 185/289 (64%), Positives = 226/289 (78%) Query: 6 IFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSILLEI 65 ++LNGEFV A VSV+DHG+LYGDG+FEGIR Y GN+FRLR+H+VRLYESAKSILL+I Sbjct: 1 MYLNGEFVDPKRATVSVFDHGFLYGDGIFEGIRAYGGNIFRLRQHIVRLYESAKSILLQI 60 Query: 66 PYSLDEVTNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCKKPNVVVIAEQLSLFPQ 125 P + +E+ V ET+R+N L + YIRLVVSRG G+LGLDP +C NV++IA+Q+ L+PQ Sbjct: 61 PLTFEEMQQAVAETVRRNGLKDAYIRLVVSRGPGDLGLDPHNCSGANVIIIADQIKLYPQ 120 Query: 126 EYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVAE 185 E+Y++G+ VVTV TRRN PD L+P++KSLNYLNNIL +IEA AG EAL+LN GYV E Sbjct: 121 EFYDQGLRVVTVPTRRNNPDALNPKIKSLNYLNNILTKIEASRAGALEALILNQDGYVCE 180 Query: 186 GSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVADEVF 245 SGDNVFIVK ++ITPP+ GALEGITRNAI+EI ++ G V EE FTRHDV+VADE F Sbjct: 181 ASGDNVFIVKNGRVITPPTYLGALEGITRNAIIEICQREGIPVAEEPFTRHDVFVADECF 240 Query: 246 LTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLVVEDGEKIYEE 294 LTGTAAE+I V VDGR IG G G T RLLE FR L DG ++Y E Sbjct: 241 LTGTAAELIPVVEVDGREIGRGVPGEMTKRLLEHFRALTRVDGYQVYPE 289 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: 333 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: 295 Length adjustment: 26 Effective length of query: 272 Effective length of database: 269 Effective search space: 73168 Effective search space used: 73168 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_123809394.1 BTUS_RS04760 (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.1189.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.4e-105 337.4 0.0 4.1e-105 337.2 0.0 1.0 1 lcl|NCBI__GCF_000092905.1:WP_123809394.1 BTUS_RS04760 branched-chain-amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_123809394.1 BTUS_RS04760 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 337.2 0.0 4.1e-105 4.1e-105 1 286 [. 2 281 .. 2 291 .. 0.96 Alignments for each domain: == domain 1 score: 337.2 bits; conditional E-value: 4.1e-105 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 +l+Ge+vd + a+v+v++h+++YG+g+feGiRaY + ifrl++h+ Rly+sak++ l+ip++ ee lcl|NCBI__GCF_000092905.1:WP_123809394.1 2 YLNGEFVDPKRATVSVFDHGFLYGDGIFEGIRAYGG----NIFRLRQHIVRLYESAKSILLQIPLTFEE 66 89********************************99....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 +++++ e++r+n+lk+aYiR +v +G +dlgl+p+ +vii+a ++ y +e +++G++v ++ lcl|NCBI__GCF_000092905.1:WP_123809394.1 67 MQQAVAETVRRNGLKDAYIRLVVSRGPGDLGLDPHNCSGANVIIIADQIKLY-PQEFYDQGLRVVTVPT 134 **********************************644467777777777655.5579************ PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr++++++++k+k+ + Yln++l+k+ea raG+ ea++L+++Gyv e sG+n+fivk+g ++tPp++ lcl|NCBI__GCF_000092905.1:WP_123809394.1 135 RRNNPDALNPKIKSLN-YLNNILTKIEASRAGALEALILNQDGYVCEASGDNVFIVKNGRVITPPTYLG 202 ***************9.**************************************************** PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+gitr+a+i++ +++gi v ee+++r+++++aDe fltGtaae++P++evDgr+ig g G++tk+l lcl|NCBI__GCF_000092905.1:WP_123809394.1 203 ALEGITRNAIIEICQREGIPVAEEPFTRHDVFVADECFLTGTAAELIPVVEVDGREIGRGVPGEMTKRL 271 ********************************************************************* PP TIGR01122 277 qeaffdlveg 286 e+f l++ lcl|NCBI__GCF_000092905.1:WP_123809394.1 272 LEHFRALTRV 281 ****998865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (295 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.33 // [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