Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate Ac3H11_3369 Branched-chain amino acid aminotransferase (EC 2.6.1.42)
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3369 Length = 305 Score = 458 bits (1178), Expect = e-134 Identities = 217/306 (70%), Positives = 260/306 (84%), Gaps = 2/306 (0%) Query: 3 MADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKR 62 MADRDGKIWMDG+++DWRDAKIHVLTHTLHYG G FEGVRAY TA+G TAIFRL+EHT R Sbjct: 1 MADRDGKIWMDGQMVDWRDAKIHVLTHTLHYGCGAFEGVRAYNTANG-TAIFRLEEHTDR 59 Query: 63 LLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVA 122 L NSAKI +M +PF E + AQ VVRENKLESCYLRP+ W+GS+KLGVS KGN IH+ Sbjct: 60 LFNSAKILRMKIPFTKEEVNEAQKAVVRENKLESCYLRPLTWIGSQKLGVSPKGNQIHLM 119 Query: 123 IAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYD 182 +AAW WGAYLGE+G+ +GIRVKTSS+TRHHVN++M +AKA Y NSILAN EA+ DGYD Sbjct: 120 VAAWAWGAYLGEEGLKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEALDDGYD 179 Query: 183 EALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSS-CLDGITRDTVITLARDAGIQVIEKR 241 EALLLD G+VSEG+GEN F++ NG +YTPDLS+ L+GITR+TV +A+D G+++++KR Sbjct: 180 EALLLDSSGFVSEGAGENIFVIKNGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQKR 239 Query: 242 ITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYA 301 ITRDEVY DEAFFTGTAAEVTPIRELD +GSG+RGPITEK+QS FFDIVNG++ YA Sbjct: 240 ITRDEVYIADEAFFTGTAAEVTPIRELDRIELGSGSRGPITEKIQSAFFDIVNGRNSNYA 299 Query: 302 NWLTKI 307 +WLTK+ Sbjct: 300 HWLTKV 305 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: 384 Number of extensions: 4 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: 305 Length adjustment: 27 Effective length of query: 280 Effective length of database: 278 Effective search space: 77840 Effective search space used: 77840 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 Ac3H11_3369 (Branched-chain amino acid aminotransferase (EC 2.6.1.42))
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.28128.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-141 455.2 0.2 5.1e-141 455.1 0.2 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369 Branched-chain amino acid aminot Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369 Branched-chain amino acid aminotransferase (EC 2.6.1.42) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 455.1 0.2 5.1e-141 5.1e-141 1 298 [] 9 305 .] 9 305 .] 0.99 Alignments for each domain: == domain 1 score: 455.1 bits; conditional E-value: 5.1e-141 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrle 62 w+dG++vd++dak+hvlth+lhYG g feG+RaY+t +g+aifrl+eh++Rl++sakilr++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369 9 WMDGQMVDWRDAKIHVLTHTLHYGCGAFEGVRAYNTANGTAIFRLEEHTDRLFNSAKILRMK 70 9************************************************************* PP TIGR01122 63 ipyskeelvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylge 124 ip++kee++e++k v+r+n+l+s+Y+Rpl ++G+++lg++pk + ++++++aaw+wgaylge lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369 71 IPFTKEEVNEAQKAVVRENKLESCYLRPLTWIGSQKLGVSPKGN-QIHLMVAAWAWGAYLGE 131 *****************************************655.9**************** PP TIGR01122 125 ealekGikvkvssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeG 186 e+l++Gi+vk+ss++r++vn+ +t+aka++nY ns+la++eal Gydea+lLd++G+v+eG lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369 132 EGLKRGIRVKTSSYTRHHVNITMTQAKAVSNYTNSILANMEALDDGYDEALLLDSSGFVSEG 193 ************************************************************** PP TIGR01122 187 sGenifivkdgvlltPpvsesiLkgitrdaviklakelgievkeerisreelytaDevfltG 248 +Genif++k+gv++tP++s +L+gitr++v ++ak+lg+e++++ri+r+e+y+aDe+f+tG lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369 194 AGENIFVIKNGVIYTPDLSAGALNGITRNTVFHIAKDLGLEIVQKRITRDEVYIADEAFFTG 255 ************************************************************** PP TIGR01122 249 taaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekkeewltyv 298 taaevtPire+D +++g+g+rGp+t+k+q+affd+v+g++ ++++wlt+v lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_3369 256 TAAEVTPIRELDRIELGSGSRGPITEKIQSAFFDIVNGRNSNYAHWLTKV 305 ***********************************************987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (305 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: 9.34 // [ok]
This GapMind analysis is from Apr 09 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