Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate 5207770 Shew_0291 branched-chain amino acid aminotransferase (RefSeq)
Query= CharProtDB::CH_024500 (309 letters) >FitnessBrowser__PV4:5207770 Length = 307 Score = 429 bits (1102), Expect = e-125 Identities = 202/305 (66%), Positives = 246/305 (80%) Query: 1 MTTKKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQR 60 M K A+ IWFNGE++ W DAKVHVMSHALHYGTSVFEGIR YD+ +GP FR +H+QR Sbjct: 1 MAAKTAELIWFNGEIMPWGDAKVHVMSHALHYGTSVFEGIRVYDTPQGPAGFRLTDHVQR 60 Query: 61 LHDSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120 L+DSAKIYR PV S DE M+ACRD+++ N L +AYIRPL+F GDVGMG+ PP D+ Sbjct: 61 LYDSAKIYRMPVPYSFDETMQACRDIVKSNKLDAAYIRPLVFFGDVGMGITPPKDAKCDL 120 Query: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY 180 ++AAFPWGAYLG ++E+G+D V+SWNR APNTIPT AKAGGNYLSSL + +EA+R+G+ Sbjct: 121 MVAAFPWGAYLGEGSMERGVDVAVTSWNRLAPNTIPTGAKAGGNYLSSLQISTEAKRNGF 180 Query: 181 QEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQ 240 EGIALDVNG +SEGAG NLF VK L+TPP T++ L GITRD II LA++LG EV E+ Sbjct: 181 DEGIALDVNGLVSEGAGANLFVVKKNKLYTPPATAAILLGITRDTIITLARDLGYEVVEE 240 Query: 241 VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDK 300 +SRE LYLADE+FM+GTAAEI PVRSVD I+VG G GPVT+ +Q +FFGLF GET+DK Sbjct: 241 PMSREFLYLADEIFMTGTAAEIVPVRSVDRIEVGAGGRGPVTQALQASFFGLFNGETQDK 300 Query: 301 WGWLD 305 WGWL+ Sbjct: 301 WGWLE 305 Lambda K H 0.319 0.136 0.413 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: 366 Number of extensions: 9 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: 309 Length of database: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 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 5207770 Shew_0291 (branched-chain amino acid aminotransferase (RefSeq))
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.31029.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-132 427.8 0.0 1.1e-132 427.7 0.0 1.0 1 lcl|FitnessBrowser__PV4:5207770 Shew_0291 branched-chain amino a Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PV4:5207770 Shew_0291 branched-chain amino acid aminotransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.7 0.0 1.1e-132 1.1e-132 1 296 [. 10 305 .. 10 307 .] 1.00 Alignments for each domain: == domain 1 score: 427.7 bits; conditional E-value: 1.1e-132 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtkevl 78 w++Ge++++ dakvhv++halhYGt+vfeGiR+Y+t++g+a frl++hv+Rlydsaki+r+++pys +e ++++++++ lcl|FitnessBrowser__PV4:5207770 10 WFNGEIMPWGDAKVHVMSHALHYGTSVFEGIRVYDTPQGPAGFRLTDHVQRLYDSAKIYRMPVPYSFDETMQACRDIV 87 9***************************************************************************** PP TIGR01122 79 rknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaagnY 156 ++n+l+ aYiRplv+ G+ ++g++p+ d+k ++++aa++wgaylge ++e+G++v v+s++r a+n+ipt aka+gnY lcl|FitnessBrowser__PV4:5207770 88 KSNKLDAAYIRPLVFFGDVGMGITPPKDAKCDLMVAAFPWGAYLGEGSMERGVDVAVTSWNRLAPNTIPTGAKAGGNY 165 ****************************************************************************** PP TIGR01122 157 lnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkeeris 234 l+sl + +ea+r+G+de+i+Ld +G v+eG+G n+f+vk+++l+tPp + +iL gitrd++i+la++lg+ev+ee++s lcl|FitnessBrowser__PV4:5207770 166 LSSLQISTEAKRNGFDEGIALDVNGLVSEGAGANLFVVKKNKLYTPPATAAILLGITRDTIITLARDLGYEVVEEPMS 243 ****************************************************************************** PP TIGR01122 235 reelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewlt 296 re ly+aDe+f+tGtaae++P+r+vD +++g+g rGpvt+ lq +ff l++g+t++k++wl+ lcl|FitnessBrowser__PV4:5207770 244 REFLYLADEIFMTGTAAEIVPVRSVDRIEVGAGGRGPVTQALQASFFGLFNGETQDKWGWLE 305 ************************************************************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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.88 // [ok]
This GapMind analysis is from Apr 09 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