Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_084274637.1 B8779_RS00495 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_900176045.1:WP_084274637.1 Length = 304 Score = 335 bits (860), Expect = 6e-97 Identities = 169/299 (56%), Positives = 223/299 (74%), Gaps = 2/299 (0%) Query: 10 IWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLNSAKI 69 IWM+G+ + W DAK+HVLTHTLHYG GVFEG RAYKTA G AIFRL++HTKRLLNSAKI Sbjct: 7 IWMNGEFVPWDDAKVHVLTHTLHYGNGVFEGTRAYKTAKG-LAIFRLRDHTKRLLNSAKI 65 Query: 70 FQMDVPFDHETLAAAQCEVVRENKLE-SCYLRPIIWVGSEKLGVSAKGNTIHVAIAAWPW 128 + VP+ E L AQ E++R+N + + Y+RP+I++G +G+ + VAIAAW W Sbjct: 66 TAIKVPYTLEELENAQIELLRQNSFDGNVYIRPLIYLGYGVMGLYHVNAPVEVAIAAWKW 125 Query: 129 GAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALLLD 188 GAYLG++G+ KGIRVK SSF R+ V +M +AKA Y+NS +A EAI GY+EALLLD Sbjct: 126 GAYLGDEGLEKGIRVKVSSFARNSVKSTMGKAKAVANYLNSQMAKYEAIIAGYEEALLLD 185 Query: 189 VDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRDEVY 248 +G+V+EGSGE F+V +G L +P + L+ IT+DT++ +A + GI V +R+TRDEVY Sbjct: 186 EEGFVAEGSGECLFIVRDGVLISPPNDNSLESITQDTILKIAHEKGIPVERRRVTRDEVY 245 Query: 249 TCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYANWLTKI 307 DEAFFTGTAAEVTPIRE+D R IGSG+RG +T++LQ+ +FDIV G++ Y + LT I Sbjct: 246 IADEAFFTGTAAEVTPIREVDGRIIGSGSRGEMTKELQTAYFDIVYGRNPAYEHMLTYI 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: 340 Number of extensions: 10 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_084274637.1 B8779_RS00495 (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.8302.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-139 448.7 0.3 4.9e-139 448.6 0.3 1.0 1 lcl|NCBI__GCF_900176045.1:WP_084274637.1 B8779_RS00495 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900176045.1:WP_084274637.1 B8779_RS00495 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.6 0.3 4.9e-139 4.9e-139 1 298 [] 8 304 .] 8 304 .] 0.99 Alignments for each domain: == domain 1 score: 448.6 bits; conditional E-value: 4.9e-139 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w++Ge+v+++dakvhvlth+lhYG+gvfeG+RaY+t kglaifrl++h++Rl++saki+ +++py+ ee lcl|NCBI__GCF_900176045.1:WP_084274637.1 8 WMNGEFVPWDDAKVHVLTHTLHYGNGVFEGTRAYKTAKGLAIFRLRDHTKRLLNSAKITAIKVPYTLEE 76 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlks.aYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvss 137 l ++++e+lr+n ++ +YiRpl+y+G++ +gl++ v+++vev+iaaw+wgaylg+e+lekGi+vkvss lcl|NCBI__GCF_900176045.1:WP_084274637.1 77 LENAQIELLRQNSFDGnVYIRPLIYLGYGVMGLYH-VNAPVEVAIAAWKWGAYLGDEGLEKGIRVKVSS 144 **************977******************.********************************* PP TIGR01122 138 frraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvse 206 f+r++v+s + kaka++nYlns++ak ea+ aGy+ea+lLdeeG+vaeGsGe++fiv+dgvl+ Pp+ + lcl|NCBI__GCF_900176045.1:WP_084274637.1 145 FARNSVKSTMGKAKAVANYLNSQMAKYEAIIAGYEEALLLDEEGFVAEGSGECLFIVRDGVLISPPN-D 212 ******************************************************************9.8 PP TIGR01122 207 siLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkk 275 ++L++it+d+++k+a+e+gi v+++r++r+e+y+aDe+f+tGtaaevtPirevDgr ig+g+rG++tk+ lcl|NCBI__GCF_900176045.1:WP_084274637.1 213 NSLESITQDTILKIAHEKGIPVERRRVTRDEVYIADEAFFTGTAAEVTPIREVDGRIIGSGSRGEMTKE 281 89******************************************************************* PP TIGR01122 276 lqeaffdlvegktekkeewltyv 298 lq+a+fd+v+g+++++e++lty+ lcl|NCBI__GCF_900176045.1:WP_084274637.1 282 LQTAYFDIVYGRNPAYEHMLTYI 304 *********************97 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.83 // [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