Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_027178111.1 G496_RS0103795 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000429985.1:WP_027178111.1 Length = 307 Score = 362 bits (930), Expect = e-105 Identities = 172/302 (56%), Positives = 220/302 (72%) Query: 3 MADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKR 62 M + KIW DG+ + W +A++HVLTHTLHYG+GVFEG+RAY TADG +A+FRL+EH R Sbjct: 1 MVQKAEKIWFDGEFVPWDEAQVHVLTHTLHYGVGVFEGIRAYNTADGRSAVFRLREHVVR 60 Query: 63 LLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVA 122 L +SAKI + +PF E + A E +R N + Y+RP++++G +GV I V Sbjct: 61 LFDSAKILGIKIPFSVEEIETAIIETLRINGHKEAYIRPLVFIGEGSMGVHPGTCPIRVC 120 Query: 123 IAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYD 182 IA W WGAYLGED + KGIR+KTSSFTRHHVN M +AKA G YVNS+LA EA+ DGYD Sbjct: 121 IATWYWGAYLGEDALEKGIRIKTSSFTRHHVNAMMTKAKACGNYVNSVLAKMEAVTDGYD 180 Query: 183 EALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRI 242 EAL+LD G+VSE +GEN F+V +G + T L+S L GITRD+++ L + G +V E+ Sbjct: 181 EALMLDPQGFVSEATGENIFIVKDGVIKTTPLTSVLRGITRDSLMKLMKSLGYEVQEQLF 240 Query: 243 TRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYAN 302 TRDE+YT DEAFF+GTAAEVTPIRE+DNR IG+G RGP+ EKLQ FFDIV G + Y+ Sbjct: 241 TRDELYTADEAFFSGTAAEVTPIREVDNRIIGAGRRGPVAEKLQKEFFDIVKGANSDYSE 300 Query: 303 WL 304 WL Sbjct: 301 WL 302 Lambda K H 0.319 0.136 0.411 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: 345 Number of extensions: 7 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: 307 Length of database: 307 Length adjustment: 27 Effective length of query: 280 Effective length of database: 280 Effective search space: 78400 Effective search space used: 78400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_027178111.1 G496_RS0103795 (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.11307.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.7e-139 448.3 0.1 6.5e-139 448.1 0.1 1.0 1 lcl|NCBI__GCF_000429985.1:WP_027178111.1 G496_RS0103795 branched-chain am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000429985.1:WP_027178111.1 G496_RS0103795 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.1 0.1 6.5e-139 6.5e-139 1 297 [. 9 304 .. 9 305 .. 0.99 Alignments for each domain: == domain 1 score: 448.1 bits; conditional E-value: 6.5e-139 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyske 68 w+dGe+v++++a+vhvlth+lhYG gvfeGiRaY+t + +a+frl+ehv Rl+dsakil ++ip+s e lcl|NCBI__GCF_000429985.1:WP_027178111.1 9 WFDGEFVPWDEAQVHVLTHTLHYGVGVFEGIRAYNTADgRSAVFRLREHVVRLFDSAKILGIKIPFSVE 77 9**********************************9983579*************************** PP TIGR01122 69 elvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvss 137 e+ +++e+lr n+ k+aYiRplv++G +++g++p ++++v+ia+w wgaylge+alekGi++k+ss lcl|NCBI__GCF_000429985.1:WP_027178111.1 78 EIETAIIETLRINGHKEAYIRPLVFIGEGSMGVHP-GTCPIRVCIATWYWGAYLGEDALEKGIRIKTSS 145 ***********************************.999****************************** PP TIGR01122 138 frraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvse 206 f+r++vn+++tkaka gnY+ns+lak+ea++ Gydea++Ld +G+v+e +Genifivkdgv++t p+ + lcl|NCBI__GCF_000429985.1:WP_027178111.1 146 FTRHHVNAMMTKAKACGNYVNSVLAKMEAVTDGYDEALMLDPQGFVSEATGENIFIVKDGVIKTTPL-T 213 ******************************************************************9.7 PP TIGR01122 207 siLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkk 275 s+L+gitrd+++kl+k lg+ev+e+ ++r+elytaDe+f++GtaaevtPirevD+r ig+g+rGpv +k lcl|NCBI__GCF_000429985.1:WP_027178111.1 214 SVLRGITRDSLMKLMKSLGYEVQEQLFTRDELYTADEAFFSGTAAEVTPIREVDNRIIGAGRRGPVAEK 282 8******************************************************************** PP TIGR01122 276 lqeaffdlvegktekkeewlty 297 lq++ffd+v+g + +++ewl+y lcl|NCBI__GCF_000429985.1:WP_027178111.1 283 LQKEFFDIVKGANSDYSEWLDY 304 ********************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (307 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: 10.03 // [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