Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_041097288.1 SUTH_RS04050 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000828635.1:WP_041097288.1 Length = 306 Score = 442 bits (1138), Expect = e-129 Identities = 214/307 (69%), Positives = 255/307 (83%), Gaps = 1/307 (0%) Query: 1 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60 MSMADRDG IW DGKL+ WRDA HVLTH+LHYG+ VFEGVRAYKT G TAIFRL+EHT Sbjct: 1 MSMADRDGFIWYDGKLVPWRDATTHVLTHSLHYGLAVFEGVRAYKTVSG-TAIFRLKEHT 59 Query: 61 KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120 RL NSA I++M +P+D TL A EVVR NKLESCYLRPI + GSEK+GVS +G H Sbjct: 60 DRLFNSAHIYRMPMPYDKATLIEAHKEVVRSNKLESCYLRPIAFYGSEKMGVSPRGAATH 119 Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180 V+IAAWPWGAYLGE+G+ KGIRVKTSS++RHHVNV+M RAK +G Y NSILAN EA DG Sbjct: 120 VSIAAWPWGAYLGEEGMEKGIRVKTSSYSRHHVNVNMARAKFAGTYANSILANMEATEDG 179 Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240 YDEALLLDVDG+V+EG+GEN F++ +G +Y P+++S L GITR+TVITLA + G QVI K Sbjct: 180 YDEALLLDVDGFVAEGAGENLFVIKDGVIYEPEIASALMGITRNTVITLAAELGYQVIAK 239 Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300 R+TRD++Y DEAFFTGTAAEVTPIRELDNRTIG+G+RGPIT+K+QS FFD+VNGK + Sbjct: 240 RLTRDDIYIADEAFFTGTAAEVTPIRELDNRTIGAGSRGPITQKIQSLFFDVVNGKVPAH 299 Query: 301 ANWLTKI 307 +WL+ I Sbjct: 300 KDWLSYI 306 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: 386 Number of extensions: 6 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: 306 Length adjustment: 27 Effective length of query: 280 Effective length of database: 279 Effective search space: 78120 Effective search space used: 78120 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_041097288.1 SUTH_RS04050 (branched-chain amino acid transaminase)
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.25390.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-138 446.3 0.1 2.7e-138 446.1 0.1 1.0 1 lcl|NCBI__GCF_000828635.1:WP_041097288.1 SUTH_RS04050 branched-chain amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000828635.1:WP_041097288.1 SUTH_RS04050 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.1 0.1 2.7e-138 2.7e-138 1 298 [] 11 306 .] 11 306 .] 0.99 Alignments for each domain: == domain 1 score: 446.1 bits; conditional E-value: 2.7e-138 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w+dG+lv+++da++hvlth+lhYG +vfeG+RaY+t g+aifrlkeh++Rl++sa+i+r+++py k + lcl|NCBI__GCF_000828635.1:WP_041097288.1 11 WYDGKLVPWRDATTHVLTHSLHYGLAVFEGVRAYKTVSGTAIFRLKEHTDRLFNSAHIYRMPMPYDKAT 79 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l+e+ kev+r+n+l+s+Y+Rp++++G+e++g++p ++ ++v iaaw+wgaylgee++ekGi+vk+ss+ lcl|NCBI__GCF_000828635.1:WP_041097288.1 80 LIEAHKEVVRSNKLESCYLRPIAFYGSEKMGVSP-RGAATHVSIAAWPWGAYLGEEGMEKGIRVKTSSY 147 **********************************.6669****************************** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 r++vn+ +++ak ag+Y ns+la++ea++ Gydea+lLd +G+vaeG+Gen+f++kdgv++ P++ s lcl|NCBI__GCF_000828635.1:WP_041097288.1 148 SRHHVNVNMARAKFAGTYANSILANMEATEDGYDEALLLDVDGFVAEGAGENLFVIKDGVIYEPEI-AS 215 *****************************************************************9.78 PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L gitr++vi+la+elg++v +r++r+++y+aDe+f+tGtaaevtPire+D+r+ig+g+rGp+t+k+ lcl|NCBI__GCF_000828635.1:WP_041097288.1 216 ALMGITRNTVITLAAELGYQVIAKRLTRDDIYIADEAFFTGTAAEVTPIRELDNRTIGAGSRGPITQKI 284 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewltyv 298 q+ ffd+v+gk++++++wl+y+ lcl|NCBI__GCF_000828635.1:WP_041097288.1 285 QSLFFDVVNGKVPAHKDWLSYI 306 *******************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (306 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: 11.37 // [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