Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_078430189.1 BK574_RS22720 branched-chain-amino-acid transaminase
Query= BRENDA::A0A1B1L2T7 (298 letters) >NCBI__GCF_002019605.1:WP_078430189.1 Length = 301 Score = 454 bits (1168), Expect = e-132 Identities = 223/295 (75%), Positives = 258/295 (87%) Query: 1 MNEQWIFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKS 60 M+EQWI+LNGEFV K AKVSVYDHG+LYGDGVFEGIRVY GN+F+L+EHL RLY SAKS Sbjct: 1 MSEQWIYLNGEFVEKHNAKVSVYDHGFLYGDGVFEGIRVYDGNIFQLKEHLERLYNSAKS 60 Query: 61 ILLEIPYSLDEVTNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCKKPNVVVIAEQL 120 ILL IP+SL+E+T I+VETI+ N+L + YIRLVVSRG GNLGLDP SC PNV+VIAEQL Sbjct: 61 ILLTIPHSLEELTQIIVETIKINELQDAYIRLVVSRGVGNLGLDPASCPTPNVIVIAEQL 120 Query: 121 SLFPQEYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQ 180 S+FP+E Y+KG+ +VTVATRRNRPDVLSP+VKSLNYLNNILV+IEA LAGV EALMLN++ Sbjct: 121 SIFPKELYDKGLEIVTVATRRNRPDVLSPKVKSLNYLNNILVKIEASLAGVSEALMLNNE 180 Query: 181 GYVAEGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYV 240 GYVAEGS DNVFIVKGNK++TPP GALEGITRNAI++I + LGY+V+EE FTRHDVYV Sbjct: 181 GYVAEGSADNVFIVKGNKILTPPGYIGALEGITRNAIIDIAKDLGYEVKEEPFTRHDVYV 240 Query: 241 ADEVFLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLVVEDGEKIYEEN 295 ADEVFLTGTAAEVIAV VDGR IG G+ G TN+LL+ FR+ VVEDGEK+Y N Sbjct: 241 ADEVFLTGTAAEVIAVVKVDGRVIGDGKPGKETNKLLQAFRQKVVEDGEKVYSAN 295 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: 374 Number of extensions: 11 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: 301 Length adjustment: 27 Effective length of query: 271 Effective length of database: 274 Effective search space: 74254 Effective search space used: 74254 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_078430189.1 BK574_RS22720 (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.26304.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.2e-107 342.6 0.6 1.1e-106 342.4 0.6 1.0 1 lcl|NCBI__GCF_002019605.1:WP_078430189.1 BK574_RS22720 branched-chain-ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_078430189.1 BK574_RS22720 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 342.4 0.6 1.1e-106 1.1e-106 1 289 [. 7 290 .. 7 298 .. 0.95 Alignments for each domain: == domain 1 score: 342.4 bits; conditional E-value: 1.1e-106 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 +l+Ge+v+ ++akv+v +h+++YG+gvfeGiR+Y++ if+lkeh+eRly+sak++ l ip s ee lcl|NCBI__GCF_002019605.1:WP_078430189.1 7 YLNGEFVEKHNAKVSVYDHGFLYGDGVFEGIRVYDG----NIFQLKEHLERLYNSAKSILLTIPHSLEE 71 89**********************************....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l+++++e+++ n+l++aYiR +v +G+++lgl+p + +++vi++a ++ + e ++kG+++ +++ lcl|NCBI__GCF_002019605.1:WP_078430189.1 72 LTQIIVETIKINELQDAYIRLVVSRGVGNLGLDPASCPTPNVIVIAEQLSIFPK-ELYDKGLEIVTVAT 139 **********************************74447889999988887766.67************ PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr++++++ +k+k+ + Yln++l+k+ea aG+ ea++L++eGyvaeGs +n+fivk +++ltPp + lcl|NCBI__GCF_002019605.1:WP_078430189.1 140 RRNRPDVLSPKVKSLN-YLNNILVKIEASLAGVSEALMLNNEGYVAEGSADNVFIVKGNKILTPPGYIG 207 ***************9.**************************************************** PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+gitr+a+i++ak+lg+evkee+++r+++y+aDevfltGtaaev+ +++vDgr ig+gk G+ t+kl lcl|NCBI__GCF_002019605.1:WP_078430189.1 208 ALEGITRNAIIDIAKDLGYEVKEEPFTRHDVYVADEVFLTGTAAEVIAVVKVDGRVIGDGKPGKETNKL 276 ********************************************************************* PP TIGR01122 277 qeaffd.lvegkte 289 +af + +ve +++ lcl|NCBI__GCF_002019605.1:WP_078430189.1 277 LQAFRQkVVEDGEK 290 **997614554544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (301 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: 6.54 // [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