Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_011885913.1 branched chain amino acid aminotransferase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000016205.1:WP_011885913.1 Length = 307 Score = 590 bits (1520), Expect = e-173 Identities = 288/307 (93%), Positives = 299/307 (97%) Query: 1 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADG TAIFRL+EHT Sbjct: 1 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGSTAIFRLREHT 60 Query: 61 KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120 KRLLNSAKIFQMDVPFD ETL AAQ EVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH Sbjct: 61 KRLLNSAKIFQMDVPFDRETLEAAQLEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120 Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180 VAIAAWPWGAYLGEDG+AKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEA ADG Sbjct: 121 VAIAAWPWGAYLGEDGLAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEATADG 180 Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDT+ITLA+DAGI+VIEK Sbjct: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTIITLAKDAGIEVIEK 240 Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300 RITRDEVYT DEAFFTGTAAEVTPIRELDNRTIGSGARGP+TEKLQS FFDIV+GK+ KY Sbjct: 241 RITRDEVYTADEAFFTGTAAEVTPIRELDNRTIGSGARGPVTEKLQSAFFDIVSGKNAKY 300 Query: 301 ANWLTKI 307 A+WL+K+ Sbjct: 301 AHWLSKV 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: 524 Number of extensions: 4 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_011885913.1 (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.13735.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-141 456.0 0.0 2.9e-141 455.9 0.0 1.0 1 lcl|NCBI__GCF_000016205.1:WP_011885913.1 branched chain amino acid aminot Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016205.1:WP_011885913.1 branched chain amino acid aminotransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.9 0.0 2.9e-141 2.9e-141 1 298 [] 11 307 .] 11 307 .] 0.98 Alignments for each domain: == domain 1 score: 455.9 bits; conditional E-value: 2.9e-141 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyske 68 w+dG+l+d++dak+hvlth+lhYG+gvfeG+RaY+t + +aifrl+eh++Rl++saki+++++p+ +e lcl|NCBI__GCF_000016205.1:WP_011885913.1 11 WMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADgSTAIFRLREHTKRLLNSAKIFQMDVPFDRE 79 9**********************************9983579*************************** PP TIGR01122 69 elvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvss 137 +l ++ ev+r+n+l+s+Y+Rp+++vG+e+lg+++k + +++v+iaaw+wgaylge++l kGi+vk+ss lcl|NCBI__GCF_000016205.1:WP_011885913.1 80 TLEAAQLEVVRENKLESCYLRPIIWVGSEKLGVSAKGN-TIHVAIAAWPWGAYLGEDGLAKGIRVKTSS 147 ***********************************655.9***************************** PP TIGR01122 138 frraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvse 206 f+r++vn+ + +aka+g Y+ns+la++ea++ Gydea+lLd +Gyv+eGsGen+f+v++g+l+tP++ + lcl|NCBI__GCF_000016205.1:WP_011885913.1 148 FTRHHVNVSMVRAKASGWYVNSILANQEATADGYDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDL-S 215 *******************************************************************.8 PP TIGR01122 207 siLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkk 275 s+L+gitrd++i+lak+ giev e+ri+r+e+ytaDe+f+tGtaaevtPire+D+r+ig+g rGpvt+k lcl|NCBI__GCF_000016205.1:WP_011885913.1 216 SCLDGITRDTIITLAKDAGIEVIEKRITRDEVYTADEAFFTGTAAEVTPIRELDNRTIGSGARGPVTEK 284 8******************************************************************** PP TIGR01122 276 lqeaffdlvegktekkeewltyv 298 lq+affd+v+gk+ k+++wl++v lcl|NCBI__GCF_000016205.1:WP_011885913.1 285 LQSAFFDIVSGKNAKYAHWLSKV 307 *******************9876 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: 11.31 // [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