Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_007474688.1 CMTB2_RS05655 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000170735.1:WP_007474688.1 Length = 304 Score = 340 bits (871), Expect = 3e-98 Identities = 169/299 (56%), Positives = 223/299 (74%), Gaps = 2/299 (0%) Query: 10 IWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLNSAKI 69 IWMDG+ I W +AK+HVLTHTLHYG GVFEG RAY+T + G AIFRL++HTKRLLNSAKI Sbjct: 7 IWMDGEFIPWSEAKVHVLTHTLHYGNGVFEGTRAYQT-ENGLAIFRLEDHTKRLLNSAKI 65 Query: 70 FQMDVPFDHETLAAAQCEVVRENKLE-SCYLRPIIWVGSEKLGVSAKGNTIHVAIAAWPW 128 ++DVPF L AQ E++R+N + + Y+RP+I++G K+G+ G +HV+IAAW W Sbjct: 66 LKIDVPFSQNELEKAQIELLRKNDFKGNVYIRPLIFLGYGKMGLYHIGAPVHVSIAAWEW 125 Query: 129 GAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALLLD 188 GAYLGE+G+ KGIRVK SS R+ V + +AKA Y+NS +A EAI GY+EAL+LD Sbjct: 126 GAYLGEEGLEKGIRVKISSIVRNPVKSTFGKAKAVANYLNSQMAKYEAIECGYEEALMLD 185 Query: 189 VDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRDEVY 248 DG+V+EGSGE FF+V +G L TP + L+ IT+ T++ LA++ I + +RITRDEVY Sbjct: 186 DDGFVAEGSGECFFIVRDGVLITPPNDNSLESITQATILELAKERDIPIERRRITRDEVY 245 Query: 249 TCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYANWLTKI 307 DEAFFTGTAAEVTP+RE+D R IG+G RG IT++LQ +FD+V G+ Y ++LT I Sbjct: 246 ISDEAFFTGTAAEVTPVREVDGRVIGNGKRGEITKELQDAYFDVVYGRDKGYKHYLTYI 304 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: 348 Number of extensions: 15 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: 304 Length adjustment: 27 Effective length of query: 280 Effective length of database: 277 Effective search space: 77560 Effective search space used: 77560 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_007474688.1 CMTB2_RS05655 (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.22606.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-137 443.7 0.1 1.6e-137 443.6 0.1 1.0 1 lcl|NCBI__GCF_000170735.1:WP_007474688.1 CMTB2_RS05655 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000170735.1:WP_007474688.1 CMTB2_RS05655 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 443.6 0.1 1.6e-137 1.6e-137 1 298 [] 8 304 .] 8 304 .] 0.99 Alignments for each domain: == domain 1 score: 443.6 bits; conditional E-value: 1.6e-137 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w+dGe++++ +akvhvlth+lhYG+gvfeG+RaY+t++glaifrl++h++Rl++sakil++++p+s++e lcl|NCBI__GCF_000170735.1:WP_007474688.1 8 WMDGEFIPWSEAKVHVLTHTLHYGNGVFEGTRAYQTENGLAIFRLEDHTKRLLNSAKILKIDVPFSQNE 76 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlks.aYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvss 137 l ++++e+lrkn++k +YiRpl+++G++++gl++ ++++v+v iaawewgaylgee+lekGi+vk+ss lcl|NCBI__GCF_000170735.1:WP_007474688.1 77 LEKAQIELLRKNDFKGnVYIRPLIFLGYGKMGLYH-IGAPVHVSIAAWEWGAYLGEEGLEKGIRVKISS 144 **************977******************.********************************* PP TIGR01122 138 frraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvse 206 + r+ v+s kaka++nYlns++ak ea+++Gy+ea++Ld++G+vaeGsGe++fiv+dgvl+tPp+ + lcl|NCBI__GCF_000170735.1:WP_007474688.1 145 IVRNPVKSTFGKAKAVANYLNSQMAKYEAIECGYEEALMLDDDGFVAEGSGECFFIVRDGVLITPPN-D 212 ******************************************************************9.8 PP TIGR01122 207 siLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkk 275 ++L++it+ ++++lake+ i ++++ri+r+e+y++De+f+tGtaaevtP+revDgr ig+gkrG++tk+ lcl|NCBI__GCF_000170735.1:WP_007474688.1 213 NSLESITQATILELAKERDIPIERRRITRDEVYISDEAFFTGTAAEVTPVREVDGRVIGNGKRGEITKE 281 89******************************************************************* PP TIGR01122 276 lqeaffdlvegktekkeewltyv 298 lq+a+fd+v+g+++ ++++lty+ lcl|NCBI__GCF_000170735.1:WP_007474688.1 282 LQDAYFDVVYGRDKGYKHYLTYI 304 ********************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (304 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.84 // [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