Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_068169777.1 HTA01S_RS09175 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_001592305.1:WP_068169777.1 Length = 312 Score = 457 bits (1176), Expect = e-133 Identities = 216/307 (70%), Positives = 261/307 (85%), Gaps = 2/307 (0%) Query: 2 SMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTK 61 SM+DRDGKIWMDG+++DWRDAKIHVLTHTLHYG G FEGVRAY A GGTAIFRL+EHT+ Sbjct: 7 SMSDRDGKIWMDGQMVDWRDAKIHVLTHTLHYGCGAFEGVRAYNAA-GGTAIFRLEEHTE 65 Query: 62 RLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHV 121 RL NSAKI +M +PF E + AQ VVRENKLESCY+RP+ W+G +KLGVS KGNTIH+ Sbjct: 66 RLFNSAKILRMKLPFTKEEVNEAQKAVVRENKLESCYIRPLTWIGDKKLGVSPKGNTIHL 125 Query: 122 AIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGY 181 +AAW WGAYLGE+G+ +GIRVKTSS+TRHHVN++M +AKA Y NSILAN E +GY Sbjct: 126 MVAAWAWGAYLGEEGLKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEVTDEGY 185 Query: 182 DEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSS-CLDGITRDTVITLARDAGIQVIEK 240 DEALLLD G+VSEG+GEN F+V NG +YTPDLS+ L+GITR+TV +A+D G+++++K Sbjct: 186 DEALLLDSSGFVSEGAGENIFVVKNGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQK 245 Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300 RITRDEVY DEAFFTGTAAEVTPIRELD +G+G+RGPITEK+QS FFDIVNG++DKY Sbjct: 246 RITRDEVYIADEAFFTGTAAEVTPIRELDRIELGAGSRGPITEKIQSAFFDIVNGRNDKY 305 Query: 301 ANWLTKI 307 A+WLTK+ Sbjct: 306 AHWLTKV 312 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: 382 Number of extensions: 6 Number of successful extensions: 3 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: 312 Length adjustment: 27 Effective length of query: 280 Effective length of database: 285 Effective search space: 79800 Effective search space used: 79800 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_068169777.1 HTA01S_RS09175 (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.16633.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-140 452.0 0.3 4.8e-140 451.9 0.3 1.0 1 lcl|NCBI__GCF_001592305.1:WP_068169777.1 HTA01S_RS09175 branched-chain am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001592305.1:WP_068169777.1 HTA01S_RS09175 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 451.9 0.3 4.8e-140 4.8e-140 1 298 [] 16 312 .] 16 312 .] 0.99 Alignments for each domain: == domain 1 score: 451.9 bits; conditional E-value: 4.8e-140 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w+dG++vd++dak+hvlth+lhYG g feG+RaY++ g+aifrl+eh+eRl++sakilr+++p++kee lcl|NCBI__GCF_001592305.1:WP_068169777.1 16 WMDGQMVDWRDAKIHVLTHTLHYGCGAFEGVRAYNAAGGTAIFRLEEHTERLFNSAKILRMKLPFTKEE 84 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 ++e++k v+r+n+l+s+YiRpl ++G+++lg++pk + ++++++aaw+wgaylgee+l++Gi+vk+ss+ lcl|NCBI__GCF_001592305.1:WP_068169777.1 85 VNEAQKAVVRENKLESCYIRPLTWIGDKKLGVSPKGN-TIHLMVAAWAWGAYLGEEGLKRGIRVKTSSY 152 **********************************665.9****************************** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 +r++vn+ +t+aka++nY ns+la++e + +Gydea+lLd++G+v+eG+Genif+vk+gv++tP++s lcl|NCBI__GCF_001592305.1:WP_068169777.1 153 TRHHVNITMTQAKAVSNYTNSILANMEVTDEGYDEALLLDSSGFVSEGAGENIFVVKNGVIYTPDLSAG 221 ********************************************************************* PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+gitr++v ++ak+lg+e++++ri+r+e+y+aDe+f+tGtaaevtPire+D +++g+g+rGp+t+k+ lcl|NCBI__GCF_001592305.1:WP_068169777.1 222 ALNGITRNTVFHIAKDLGLEIVQKRITRDEVYIADEAFFTGTAAEVTPIRELDRIELGAGSRGPITEKI 290 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewltyv 298 q+affd+v+g+++k+++wlt+v lcl|NCBI__GCF_001592305.1:WP_068169777.1 291 QSAFFDIVNGRNDKYAHWLTKV 312 *******************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (312 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: 00:00:00.01 # Mc/sec: 6.78 // [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