Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_028310814.1 H566_RS0106550 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000482785.1:WP_028310814.1 Length = 308 Score = 459 bits (1182), Expect = e-134 Identities = 216/308 (70%), Positives = 263/308 (85%), Gaps = 1/308 (0%) Query: 1 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60 MSMADRDG IWMDGK++DWRDAKIHVLTHTLHYGMGVFEGVRAY+ ADG TA+FRL+EHT Sbjct: 1 MSMADRDGVIWMDGKMVDWRDAKIHVLTHTLHYGMGVFEGVRAYQQADGSTAVFRLKEHT 60 Query: 61 KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120 +RL NSA+IFQM++PF E ++ A VVRENKLESCY+RPI W+GS+KLG+ A+ NTIH Sbjct: 61 RRLFNSARIFQMNLPFTEEQISEATKAVVRENKLESCYIRPIAWIGSDKLGIGARTNTIH 120 Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180 VA+AAWPWGAYLG +G+ +GIRVKTSSFT HH NV+M +AKA G Y SIL+NQEA +G Sbjct: 121 VAVAAWPWGAYLGAEGMERGIRVKTSSFTHHHPNVTMCKAKAVGNYPVSILSNQEATNEG 180 Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLS-SCLDGITRDTVITLARDAGIQVIE 239 YDEA+L+D G+V +GSGEN FLV +G+L+TPDL+ LDGITR+++ TLA + GI+V+E Sbjct: 181 YDEAMLMDPQGFVCQGSGENVFLVKDGELHTPDLAGGALDGITRNSIFTLAAEHGIKVVE 240 Query: 240 KRITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDK 299 +RITRDE Y DEAFFTGTAAEVTPIRELD RTIG+G+RGP+T KLQ+ FFD+VNG++ K Sbjct: 241 RRITRDEFYIGDEAFFTGTAAEVTPIRELDGRTIGAGSRGPVTTKLQAAFFDVVNGRNPK 300 Query: 300 YANWLTKI 307 YA WL K+ Sbjct: 301 YAEWLAKV 308 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: 418 Number of extensions: 7 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: 308 Length adjustment: 27 Effective length of query: 280 Effective length of database: 281 Effective search space: 78680 Effective search space used: 78680 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_028310814.1 H566_RS0106550 (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.21153.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-135 435.9 0.0 3.9e-135 435.7 0.0 1.0 1 lcl|NCBI__GCF_000482785.1:WP_028310814.1 H566_RS0106550 branched-chain am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000482785.1:WP_028310814.1 H566_RS0106550 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 435.7 0.0 3.9e-135 3.9e-135 1 298 [] 11 308 .] 11 308 .] 0.99 Alignments for each domain: == domain 1 score: 435.7 bits; conditional E-value: 3.9e-135 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk.glaifrlkehveRlydsakilrleipyske 68 w+dG++vd++dak+hvlth+lhYG+gvfeG+RaY++ + +a+frlkeh+ Rl++sa+i+++++p+++e lcl|NCBI__GCF_000482785.1:WP_028310814.1 11 WMDGKMVDWRDAKIHVLTHTLHYGMGVFEGVRAYQQADgSTAVFRLKEHTRRLFNSARIFQMNLPFTEE 79 9*********************************99883579*************************** PP TIGR01122 69 elvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvss 137 +++e+tk v+r+n+l+s+YiRp++++G+++lg+ ++++ +++v++aaw+wgaylg+e++e+Gi+vk+ss lcl|NCBI__GCF_000482785.1:WP_028310814.1 80 QISEATKAVVRENKLESCYIRPIAWIGSDKLGIGARTN-TIHVAVAAWPWGAYLGAEGMERGIRVKTSS 147 ***********************************887.9***************************** PP TIGR01122 138 frraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvse 206 f+++++n+ + kaka+gnY s+l ++ea+++Gydea+l+d +G+v GsGen+f+vkdg+l tP+++ lcl|NCBI__GCF_000482785.1:WP_028310814.1 148 FTHHHPNVTMCKAKAVGNYPVSILSNQEATNEGYDEAMLMDPQGFVCQGSGENVFLVKDGELHTPDLAG 216 ********************************************************************* PP TIGR01122 207 siLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkk 275 +L+gitr+++ +la+e+gi+v+e+ri+r+e y+ De+f+tGtaaevtPire+Dgr+ig+g+rGpvt k lcl|NCBI__GCF_000482785.1:WP_028310814.1 217 GALDGITRNSIFTLAAEHGIKVVERRITRDEFYIGDEAFFTGTAAEVTPIRELDGRTIGAGSRGPVTTK 285 ********************************************************************* PP TIGR01122 276 lqeaffdlvegktekkeewltyv 298 lq affd+v+g+++k++ewl +v lcl|NCBI__GCF_000482785.1:WP_028310814.1 286 LQAAFFDVVNGRNPKYAEWLAKV 308 *******************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (308 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: 9.99 // [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