Align branched-chain-amino-acid aminotransferase; EC 2.6.1.42 (characterized)
to candidate BWI76_RS00970 BWI76_RS00970 branched chain amino acid aminotransferase
Query= CharProtDB::CH_024500 (309 letters) >FitnessBrowser__Koxy:BWI76_RS00970 Length = 309 Score = 610 bits (1574), Expect = e-179 Identities = 296/309 (95%), Positives = 306/309 (99%) Query: 1 MTTKKADYIWFNGEMVRWEDAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQR 60 MTTKKADYIWFNGEMV W +AKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQR Sbjct: 1 MTTKKADYIWFNGEMVPWGEAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQR 60 Query: 61 LHDSAKIYRFPVSQSIDELMEACRDVIRKNNLTSAYIRPLIFVGDVGMGVNPPAGYSTDV 120 LHDSAKIYRFPVSQS+DELMEACR+VIRKN+LTSAYIRPL+FVGDVGMGVNPP GY+TDV Sbjct: 61 LHDSAKIYRFPVSQSVDELMEACREVIRKNSLTSAYIRPLVFVGDVGMGVNPPPGYNTDV 120 Query: 121 IIAAFPWGAYLGAEALEQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY 180 IIAAFPWGAYLGAEAL+QGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY Sbjct: 121 IIAAFPWGAYLGAEALDQGIDAMVSSWNRAAPNTIPTAAKAGGNYLSSLLVGSEARRHGY 180 Query: 181 QEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKELGIEVREQ 240 QEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAK+LG+EVREQ Sbjct: 181 QEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGITRDAIIKLAKDLGLEVREQ 240 Query: 241 VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPVTKRIQQAFFGLFTGETEDK 300 VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGP+TKRIQQAFFGLFTGETEDK Sbjct: 241 VLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPITKRIQQAFFGLFTGETEDK 300 Query: 301 WGWLDQVNQ 309 WGWLDQVNQ Sbjct: 301 WGWLDQVNQ 309 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: 496 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: 309 Length of database: 309 Length adjustment: 27 Effective length of query: 282 Effective length of database: 282 Effective search space: 79524 Effective search space used: 79524 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 BWI76_RS00970 BWI76_RS00970 (branched chain amino acid aminotransferase)
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.9567.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-149 481.1 0.0 6.5e-149 481.0 0.0 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS00970 BWI76_RS00970 branched chain ami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS00970 BWI76_RS00970 branched chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 481.0 0.0 6.5e-149 6.5e-149 1 298 [] 10 307 .. 10 307 .. 1.00 Alignments for each domain: == domain 1 score: 481.0 bits; conditional E-value: 6.5e-149 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelv 71 w++Ge+v++ +akvhv++halhYGt+vfeGiR+Y+++kg+++fr++eh++Rl+dsaki+r+++++s +el+ lcl|FitnessBrowser__Koxy:BWI76_RS00970 10 WFNGEMVPWGEAKVHVMSHALHYGTSVFEGIRCYDSHKGPVVFRHREHMQRLHDSAKIYRFPVSQSVDELM 80 9********************************************************************** PP TIGR01122 72 evtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraa 142 e+++ev+rkn l+saYiRplv+vG+ ++g++p+ +++++viiaa++wgaylg+eal++Gi+++vss++raa lcl|FitnessBrowser__Koxy:BWI76_RS00970 81 EACREVIRKNSLTSAYIRPLVFVGDVGMGVNPPPGYNTDVIIAAFPWGAYLGAEALDQGIDAMVSSWNRAA 151 *********************************************************************** PP TIGR01122 143 vnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgit 213 +n+ipt+aka+gnYl+sll++sea+r+Gy+e+i+Ld +Gy++eG+Gen+f vkdgvl+tPp+++s+L git lcl|FitnessBrowser__Koxy:BWI76_RS00970 152 PNTIPTAAKAGGNYLSSLLVGSEARRHGYQEGIALDVNGYISEGAGENLFEVKDGVLFTPPFTSSALPGIT 222 *********************************************************************** PP TIGR01122 214 rdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlv 284 rda+iklak+lg+ev+e+++sre+ly+aDevf++Gtaae+tP+r+vDg+++geg++Gp+tk++q+aff l+ lcl|FitnessBrowser__Koxy:BWI76_RS00970 223 RDAIIKLAKDLGLEVREQVLSRESLYLADEVFMSGTAAEITPVRSVDGIQVGEGRCGPITKRIQQAFFGLF 293 *********************************************************************** PP TIGR01122 285 egktekkeewltyv 298 +g+te+k++wl++v lcl|FitnessBrowser__Koxy:BWI76_RS00970 294 TGETEDKWGWLDQV 307 ***********987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (309 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: 00:00:00.00 # Mc/sec: 10.01 // [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