Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_012964603.1 FERP_RS00315 branched-chain-amino-acid transaminase
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_000025505.1:WP_012964603.1 Length = 292 Score = 312 bits (800), Expect = 5e-90 Identities = 159/293 (54%), Positives = 207/293 (70%), Gaps = 1/293 (0%) Query: 1 MNEQWIFLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKS 60 M E I++NGEFVPK EAK+SV+DHG+LYGDGVFEGIR Y+G VFRL EHL RLY+ AK Sbjct: 1 MEELLIYINGEFVPKSEAKISVFDHGFLYGDGVFEGIRAYNGKVFRLYEHLDRLYDCAKV 60 Query: 61 IMLEIPYSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQL 120 I LEIP + +E ++ET+R NKL + YIR +V+RG G+LGLDP C +PNV++IA+ Sbjct: 61 IDLEIPLTKEEFAQAILETLRVNKLRDAYIRPIVTRGIGDLGLDPRKCGRPNVIIIAQPW 120 Query: 121 SLFPQEYYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQ 180 + YEKG+ VTVA RRN D L P +KSLNYLNNIL +IEA + G EA+ L+ Sbjct: 121 DRLYGDLYEKGLKAVTVAVRRNAIDSLPPNIKSLNYLNNILAKIEANVKGGDEAIFLDHN 180 Query: 181 GYVAEGSGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYV 240 GYV+EGSGDN+FIVK + TPP + L+GITR ++EI E+ +E + D+Y Sbjct: 181 GYVSEGSGDNIFIVKKKVVYTPP-TINNLKGITREVVIEILEEENIPFKETHLSLFDLYS 239 Query: 241 ADEVFLTGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLVIEDGEKIYE 293 ADEVF+TGTAAE+ VT +DGR IG G+ G T L+++FR+ ++G IYE Sbjct: 240 ADEVFVTGTAAEIAPVTVIDGRKIGDGKPGELTKFLMKKFREKTEKEGVPIYE 292 Lambda K H 0.317 0.138 0.390 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: 319 Number of extensions: 17 Number of successful extensions: 2 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_012964603.1 FERP_RS00315 (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.22493.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-116 373.0 0.0 6.2e-116 372.7 0.0 1.0 1 lcl|NCBI__GCF_000025505.1:WP_012964603.1 FERP_RS00315 branched-chain-amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000025505.1:WP_012964603.1 FERP_RS00315 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 372.7 0.0 6.2e-116 6.2e-116 1 286 [. 7 285 .. 7 291 .. 0.98 Alignments for each domain: == domain 1 score: 372.7 bits; conditional E-value: 6.2e-116 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 +++Ge+v+ +ak++v++h+++YG+gvfeGiRaY++ +frl eh++Rlyd ak+++leip++kee lcl|NCBI__GCF_000025505.1:WP_012964603.1 7 YINGEFVPKSEAKISVFDHGFLYGDGVFEGIRAYNG----KVFRLYEHLDRLYDCAKVIDLEIPLTKEE 71 89**********************************....9**************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpk.vdlkveviiaawewgaylgeealekGikvkvss 137 + +++ e+lr+n+l++aYiRp+v++G++dlgl+p+ ++ +++vii+a +w +++g+ +ekG+k+ +++ lcl|NCBI__GCF_000025505.1:WP_012964603.1 72 FAQAILETLRVNKLRDAYIRPIVTRGIGDLGLDPRkCG-RPNVIIIAQPWDRLYGD-LYEKGLKAVTVA 138 **********************************9566.9***************8.5*********** PP TIGR01122 138 frraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvse 206 +rr+a +s+p+++k+ + Yln++lak+ea+ +G deai+Ld++Gyv+eGsG+nifivk+ v++tPp+++ lcl|NCBI__GCF_000025505.1:WP_012964603.1 139 VRRNAIDSLPPNIKSLN-YLNNILAKIEANVKGGDEAIFLDHNGYVSEGSGDNIFIVKKKVVYTPPTIN 206 ****************9.*************************************************77 PP TIGR01122 207 siLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkk 275 +Lkgitr++vi++++e+ i +ke+++s+ +ly aDevf+tGtaae++P++ +Dgrkig+gk G++tk lcl|NCBI__GCF_000025505.1:WP_012964603.1 207 -NLKGITREVVIEILEEENIPFKETHLSLFDLYSADEVFVTGTAAEIAPVTVIDGRKIGDGKPGELTKF 274 .9******************************************************************* PP TIGR01122 276 lqeaffdlveg 286 l+++f + +e+ lcl|NCBI__GCF_000025505.1:WP_012964603.1 275 LMKKFREKTEK 285 *****987665 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.98 // [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