Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate BPHYT_RS16285 BPHYT_RS16285 branched-chain amino acid aminotransferase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >FitnessBrowser__BFirm:BPHYT_RS16285 Length = 307 Score = 624 bits (1609), Expect = 0.0 Identities = 307/307 (100%), Positives = 307/307 (100%) Query: 1 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT Sbjct: 1 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60 Query: 61 KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120 KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH Sbjct: 61 KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120 Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG Sbjct: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180 Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK Sbjct: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240 Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY Sbjct: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300 Query: 301 ANWLTKI 307 ANWLTKI Sbjct: 301 ANWLTKI 307 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: 553 Number of extensions: 5 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 BPHYT_RS16285 BPHYT_RS16285 (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.21896.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-140 452.2 0.0 4.4e-140 452.0 0.0 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS16285 BPHYT_RS16285 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS16285 BPHYT_RS16285 branched-chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 452.0 0.0 4.4e-140 4.4e-140 1 298 [] 11 307 .] 11 307 .] 0.99 Alignments for each domain: == domain 1 score: 452.0 bits; conditional E-value: 4.4e-140 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyskee 69 w+dG+l+d++dak+hvlth+lhYG+gvfeG+RaY+t + g+aifrl+eh++Rl++saki+++++p+ +e+ lcl|FitnessBrowser__BFirm:BPHYT_RS16285 11 WMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADgGTAIFRLQEHTKRLLNSAKIFQMDVPFDHET 80 9**********************************987689***************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfr 139 l ++ ev+r+n+l+s+Y+Rp+++vG+e+lg+++k + +++v+iaaw+wgaylge+++ kGi+vk+ssf+ lcl|FitnessBrowser__BFirm:BPHYT_RS16285 81 LAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGN-TIHVAIAAWPWGAYLGEDGIAKGIRVKTSSFT 149 **********************************655.9******************************* PP TIGR01122 140 raavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiL 209 r++vn+ + +aka+g Y+ns+la++ea++ Gydea+lLd +Gyv+eGsGen+f+v++g+l+tP++ +s+L lcl|FitnessBrowser__BFirm:BPHYT_RS16285 150 RHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDL-SSCL 218 *****************************************************************.88** PP TIGR01122 210 kgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqea 279 +gitrd+vi+la++ gi+v e+ri+r+e+yt De+f+tGtaaevtPire+D+r+ig+g rGp+t+klq+ lcl|FitnessBrowser__BFirm:BPHYT_RS16285 219 DGITRDTVITLARDAGIQVIEKRITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSG 288 ********************************************************************** PP TIGR01122 280 ffdlvegktekkeewltyv 298 ffd+v+gk +k+++wlt++ lcl|FitnessBrowser__BFirm:BPHYT_RS16285 289 FFDIVNGKSDKYANWLTKI 307 ****************986 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 9.40 // [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