Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_029001507.1 H537_RS0134400 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000430725.1:WP_029001507.1 Length = 307 Score = 456 bits (1173), Expect = e-133 Identities = 219/308 (71%), Positives = 258/308 (83%), Gaps = 2/308 (0%) Query: 1 MSMADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHT 60 MSM DRDGKIWMDG+L+DWRDAKIHVLTHTLHYG G FEGVRAY T +G TAIFRL+EHT Sbjct: 1 MSMHDRDGKIWMDGELVDWRDAKIHVLTHTLHYGCGAFEGVRAYNTVNG-TAIFRLREHT 59 Query: 61 KRLLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIH 120 +RL NSAKI +M +PF E + AQ EVVR N LESCYLRP++W+GSEKLGVS KGNTIH Sbjct: 60 ERLFNSAKILRMKMPFSIEQIEEAQREVVRVNNLESCYLRPLVWIGSEKLGVSPKGNTIH 119 Query: 121 VAIAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADG 180 V +AAW WGAYLGE+G+ +GIRVKTSS+TRHHVN++M +AKA Y NSILAN EA DG Sbjct: 120 VMVAAWSWGAYLGEEGLKRGIRVKTSSYTRHHVNITMTQAKAVSNYSNSILANMEATEDG 179 Query: 181 YDEALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSS-CLDGITRDTVITLARDAGIQVIE 239 YDEALLLD G+VSEG+GEN F++ NG +YTPDLS+ L+GITR+T+ + +D G++++E Sbjct: 180 YDEALLLDAAGFVSEGAGENIFVIKNGVVYTPDLSAGALNGITRNTIFAICQDLGLKLVE 239 Query: 240 KRITRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDK 299 KRITRDEVY DEAFFTGTAAEVTPIRELD IG G RGPITEK+Q+ FFDIVNG++ K Sbjct: 240 KRITRDEVYIADEAFFTGTAAEVTPIRELDRVEIGRGYRGPITEKIQAAFFDIVNGRNAK 299 Query: 300 YANWLTKI 307 YA WLTK+ Sbjct: 300 YAEWLTKV 307 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: 387 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: 307 Length adjustment: 27 Effective length of query: 280 Effective length of database: 280 Effective search space: 78400 Effective search space used: 78400 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_029001507.1 H537_RS0134400 (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.3165193.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.8e-141 456.5 0.4 2e-141 456.4 0.4 1.0 1 NCBI__GCF_000430725.1:WP_029001507.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000430725.1:WP_029001507.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 456.4 0.4 2e-141 2e-141 1 298 [] 11 307 .] 11 307 .] 0.99 Alignments for each domain: == domain 1 score: 456.4 bits; conditional E-value: 2e-141 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 w+dGelvd++dak+hvlth+lhYG g feG+RaY+t +g+aifrl+eh+eRl++sakilr+++p+s e++ e+ NCBI__GCF_000430725.1:WP_029001507.1 11 WMDGELVDWRDAKIHVLTHTLHYGCGAFEGVRAYNTVNGTAIFRLREHTERLFNSAKILRMKMPFSIEQIEEA 83 9************************************************************************ PP TIGR01122 74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146 ++ev+r+nnl+s+Y+Rplv++G+e+lg++pk + +++v++aaw+wgaylgee+l++Gi+vk+ss++r++vn+ NCBI__GCF_000430725.1:WP_029001507.1 84 QREVVRVNNLESCYLRPLVWIGSEKLGVSPKGN-TIHVMVAAWSWGAYLGEEGLKRGIRVKTSSYTRHHVNIT 155 ******************************665.9************************************** PP TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219 +t+aka++nY ns+la++ea++ Gydea+lLd G+v+eG+Genif++k+gv++tP++s +L+gitr+++ NCBI__GCF_000430725.1:WP_029001507.1 156 MTQAKAVSNYSNSILANMEATEDGYDEALLLDAAGFVSEGAGENIFVIKNGVVYTPDLSAGALNGITRNTIFA 228 ************************************************************************* PP TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekke 292 + ++lg++++e+ri+r+e+y+aDe+f+tGtaaevtPire+D ++ig g rGp+t+k+q affd+v+g++ k++ NCBI__GCF_000430725.1:WP_029001507.1 229 ICQDLGLKLVEKRITRDEVYIADEAFFTGTAAEVTPIRELDRVEIGRGYRGPITEKIQAAFFDIVNGRNAKYA 301 ************************************************************************* PP TIGR01122 293 ewltyv 298 ewlt+v NCBI__GCF_000430725.1:WP_029001507.1 302 EWLTKV 307 ***987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (307 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: 15.25 // [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