Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_108402105.1 B9Z44_RS07660 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_003063475.1:WP_108402105.1 Length = 313 Score = 446 bits (1148), Expect = e-130 Identities = 210/307 (68%), Positives = 258/307 (84%), Gaps = 2/307 (0%) Query: 2 SMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTK 61 SM+DRDGKIWMDG+++DWRDAKIHVL+HTLHYG G FEGVRAYKT + GTAIFRLQEHT Sbjct: 8 SMSDRDGKIWMDGQMVDWRDAKIHVLSHTLHYGCGAFEGVRAYKT-EQGTAIFRLQEHTD 66 Query: 62 RLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHV 121 RL NSAKI +M++PF E + AQC VVREN LES Y+RP+ W+G +KLGVS +GN IHV Sbjct: 67 RLFNSAKILRMNMPFTKEQINNAQCAVVRENNLESGYIRPLTWIGDKKLGVSPRGNDIHV 126 Query: 122 AIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGY 181 +AAW WGAYLGE+G+ +GIRVKTSS+TRHHVN++M +AKA Y NSILAN E +GY Sbjct: 127 MVAAWTWGAYLGEEGMKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEVTDEGY 186 Query: 182 DEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSS-CLDGITRDTVITLARDAGIQVIEK 240 DEALLLD G+VSEG+GEN F+V +G +YTPDLS+ L+GITR+TV +A+D G+++++K Sbjct: 187 DEALLLDTSGFVSEGAGENIFVVKDGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQK 246 Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300 RITRDE+Y DEAFFTGTAAEVTPIRELD +G G+RGPITEK+Q+ FFDIVNG++ KY Sbjct: 247 RITRDEIYIADEAFFTGTAAEVTPIRELDRIQLGEGSRGPITEKIQTAFFDIVNGRNPKY 306 Query: 301 ANWLTKI 307 A+WLTK+ Sbjct: 307 AHWLTKV 313 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: 378 Number of extensions: 8 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: 313 Length adjustment: 27 Effective length of query: 280 Effective length of database: 286 Effective search space: 80080 Effective search space used: 80080 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_108402105.1 B9Z44_RS07660 (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.carbon/TIGR01122.hmm # target sequence database: /tmp/gapView.3993170.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-141 456.0 0.3 3e-141 455.8 0.3 1.0 1 NCBI__GCF_003063475.1:WP_108402105.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003063475.1:WP_108402105.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.8 0.3 3e-141 3e-141 1 298 [] 17 313 .] 17 313 .] 0.99 Alignments for each domain: == domain 1 score: 455.8 bits; conditional E-value: 3e-141 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 w+dG++vd++dak+hvl+h+lhYG g feG+RaY+t++g+aifrl+eh++Rl++sakilr+++p++ke+++++ NCBI__GCF_003063475.1:WP_108402105.1 17 WMDGQMVDWRDAKIHVLSHTLHYGCGAFEGVRAYKTEQGTAIFRLQEHTDRLFNSAKILRMNMPFTKEQINNA 89 9************************************************************************ PP TIGR01122 74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146 + v+r+nnl+s YiRpl ++G+++lg++p+ + +++v++aaw+wgaylgee++++Gi+vk+ss++r++vn+ NCBI__GCF_003063475.1:WP_108402105.1 90 QCAVVRENNLESGYIRPLTWIGDKKLGVSPRGN-DIHVMVAAWTWGAYLGEEGMKRGIRVKTSSYTRHHVNIT 161 ******************************765.9************************************** PP TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219 +t+aka++nY ns+la++e + +Gydea+lLd++G+v+eG+Genif+vkdgv++tP++s +L+gitr++v + NCBI__GCF_003063475.1:WP_108402105.1 162 MTQAKAVSNYTNSILANMEVTDEGYDEALLLDTSGFVSEGAGENIFVVKDGVIYTPDLSAGALNGITRNTVFH 234 ************************************************************************* PP TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekke 292 +ak+lg+e++++ri+r+e+y+aDe+f+tGtaaevtPire+D +++geg+rGp+t+k+q+affd+v+g+++k++ NCBI__GCF_003063475.1:WP_108402105.1 235 IAKDLGLEIVQKRITRDEIYIADEAFFTGTAAEVTPIRELDRIQLGEGSRGPITEKIQTAFFDIVNGRNPKYA 307 ************************************************************************* PP TIGR01122 293 ewltyv 298 +wlt+v NCBI__GCF_003063475.1:WP_108402105.1 308 HWLTKV 313 ***987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (313 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 20.30 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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