Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate CCNA_03024 CCNA_03024 branched-chain amino acid aminotransferase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >FitnessBrowser__Caulo:CCNA_03024 Length = 296 Score = 243 bits (621), Expect = 3e-69 Identities = 123/264 (46%), Positives = 167/264 (63%), Gaps = 5/264 (1%) Query: 5 DRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLL 64 DRDG IW+DG+ + WR+AK+HVLTH LHY VFEG R Y G IF+L EHT+RL Sbjct: 8 DRDGWIWLDGQFVPWREAKVHVLTHGLHYASSVFEGERMY-----GGEIFKLTEHTERLF 62 Query: 65 NSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVAIA 124 SA+I ++P+ + A +N L+ CY+RPI W GSE +GVSA+ + IHVAIA Sbjct: 63 KSAEILDFEIPYTVAEIDEACKATAAKNGLKDCYVRPIAWRGSEMIGVSAQQSKIHVAIA 122 Query: 125 AWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEA 184 W W +Y AKGIR+ + + R + + AKA+G Y+ ++ A DGY +A Sbjct: 123 VWEWPSYFDPATKAKGIRLTWAKYQRPDPKTAPIAAKAAGLYMICTISKHAAEKDGYADA 182 Query: 185 LLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITR 244 ++LD GYV+E +G N F V +G L+TP LDGITR TVI LA+ GI+V+E+ I + Sbjct: 183 MMLDYRGYVAEATGANVFFVKDGVLHTPKPDCFLDGITRRTVIDLAKAKGIEVVERHIQK 242 Query: 245 DEVYTCDEAFFTGTAAEVTPIREL 268 +E+ T E F GTAAEVTP+ E+ Sbjct: 243 EELATFTECFIVGTAAEVTPVSEV 266 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: 304 Number of extensions: 11 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: 307 Length of database: 296 Length adjustment: 27 Effective length of query: 280 Effective length of database: 269 Effective search space: 75320 Effective search space used: 75320 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 CCNA_03024 CCNA_03024 (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.229628.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-92 295.1 0.0 2.9e-92 295.0 0.0 1.0 1 FitnessBrowser__Caulo:CCNA_03024 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Caulo:CCNA_03024 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 295.0 0.0 2.9e-92 2.9e-92 1 287 [. 14 291 .. 14 296 .] 0.96 Alignments for each domain: == domain 1 score: 295.0 bits; conditional E-value: 2.9e-92 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtkev 77 wldG++v++++akvhvlth+lhY ++vfeG R+Y + if+l+eh+eRl++sa+il++eipy+ e+ e++k + FitnessBrowser__Caulo:CCNA_03024 14 WLDGQFVPWREAKVHVLTHGLHYASSVFEGERMYGG----EIFKLTEHTERLFKSAEILDFEIPYTVAEIDEACKAT 86 9*********************************99....9************************************ PP TIGR01122 78 lrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaag 154 kn+lk++Y+Rp++++G+e +g+++ + k++v+ia+wew+ y++ + kGi+ + + ++r ++++ p +akaag FitnessBrowser__Caulo:CCNA_03024 87 AAKNGLKDCYVRPIAWRGSEMIGVSA-QQSKIHVAIAVWEWPSYFDPATKAKGIRLTWAKYQRPDPKTAPIAAKAAG 162 **************************.778*********************************************** PP TIGR01122 155 nYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkee 231 Y+ ++ k+ a + Gy +a++Ld Gyvae +G n+f vkdgvl tP+ + L+gitr +vi+lak +giev+e+ FitnessBrowser__Caulo:CCNA_03024 163 LYMICTISKHAAEKDGYADAMMLDYRGYVAEATGANVFFVKDGVLHTPKP-DCFLDGITRRTVIDLAKAKGIEVVER 238 *************************************************9.99************************ PP TIGR01122 232 risreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegk 287 +i +eel t e f+ GtaaevtP+ ev + k k + l++++ lv+g+ FitnessBrowser__Caulo:CCNA_03024 239 HIQKEELATFTECFIVGTAAEVTPVSEVGEFKFTPAK---LSLDLMDTYAALVRGE 291 ****************************999987654...5667777777777776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (296 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 20.10 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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