Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate Dsui_3339 Dsui_3339 branched-chain amino acid aminotransferase, group I
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >FitnessBrowser__PS:Dsui_3339 Length = 306 Score = 446 bits (1147), Expect = e-130 Identities = 215/304 (70%), Positives = 254/304 (83%), Gaps = 1/304 (0%) Query: 1 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60 MSM+DRDG IW DGKL+ WR+A H LTH+LHYGM VFEGVRAY+T D GTAIFRLQ+HT Sbjct: 1 MSMSDRDGFIWQDGKLVPWREATTHALTHSLHYGMAVFEGVRAYQT-DKGTAIFRLQDHT 59 Query: 61 KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120 +RL SA IFQM +P+ E L AQ EV+R N LES Y+RP+ + GSEK+GVS KG +H Sbjct: 60 QRLARSAHIFQMALPYSQEELNEAQKEVIRANNLESGYIRPLAFYGSEKMGVSPKGAKVH 119 Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180 V IAAWPWGAYLGE+G+ +GIR+KTSSFTRHHVN++MVRAKASG Y+NSILAN EA+ DG Sbjct: 120 VIIAAWPWGAYLGEEGMQRGIRIKTSSFTRHHVNITMVRAKASGNYMNSILANNEALTDG 179 Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEK 240 YDEA+LLD +GYV EG+GEN F+V NGKLYTPDL+SCL+GITR TVI LA + GI+V+EK Sbjct: 180 YDEAMLLDPEGYVCEGAGENIFIVKNGKLYTPDLTSCLEGITRATVIQLAGEMGIEVVEK 239 Query: 241 RITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKY 300 RITRDEVY DEAFFTGTAAEVTPIRELDNR IG G RGP+T+ LQ +FD+VNG+S + Sbjct: 240 RITRDEVYCADEAFFTGTAAEVTPIRELDNRQIGVGHRGPVTKALQEKYFDVVNGRSAAH 299 Query: 301 ANWL 304 A+WL Sbjct: 300 ADWL 303 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: 364 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 Dsui_3339 Dsui_3339 (branched-chain amino acid aminotransferase, group I)
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.3692975.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-143 463.2 0.1 1.9e-143 463.0 0.1 1.0 1 FitnessBrowser__PS:Dsui_3339 Domain annotation for each sequence (and alignments): >> FitnessBrowser__PS:Dsui_3339 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 463.0 0.1 1.9e-143 1.9e-143 1 298 [] 11 306 .] 11 306 .] 0.99 Alignments for each domain: == domain 1 score: 463.0 bits; conditional E-value: 1.9e-143 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvevtkevlrkn 81 w dG+lv++++a++h lth+lhYG++vfeG+RaY+tdkg+aifrl++h++Rl sa+i+++ +pys+eel+e++kev+r+n FitnessBrowser__PS:Dsui_3339 11 WQDGKLVPWREATTHALTHSLHYGMAVFEGVRAYQTDKGTAIFRLQDHTQRLARSAHIFQMALPYSQEELNEAQKEVIRAN 91 99******************************************************************************* PP TIGR01122 82 nlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsiptkakaagnYlnslla 162 nl+s YiRpl+++G+e++g++p ++kv+viiaaw+wgaylgee++++Gi++k+ssf+r++vn+ + +aka+gnY+ns+la FitnessBrowser__PS:Dsui_3339 92 NLESGYIRPLAFYGSEKMGVSP-KGAKVHVIIAAWPWGAYLGEEGMQRGIRIKTSSFTRHHVNITMVRAKASGNYMNSILA 171 **********************.6779****************************************************** PP TIGR01122 163 ksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkeerisreelytaDe 243 + eal+ Gydea+lLd eGyv eG+Genifivk+g+l+tP++ +s+L+gitr +vi+la e+giev+e+ri+r+e+y aDe FitnessBrowser__PS:Dsui_3339 172 NNEALTDGYDEAMLLDPEGYVCEGAGENIFIVKNGKLYTPDL-TSCLEGITRATVIQLAGEMGIEVVEKRITRDEVYCADE 251 ******************************************.78************************************ PP TIGR01122 244 vfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewltyv 298 +f+tGtaaevtPire+D+r+ig g+rGpvtk lqe++fd+v+g+ ++++wl v FitnessBrowser__PS:Dsui_3339 252 AFFTGTAAEVTPIRELDNRQIGVGHRGPVTKALQEKYFDVVNGRSAAHADWLAFV 306 ***************************************************9875 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 16.56 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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