Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_011373491.1 SUDEN_RS09745 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000012965.1:WP_011373491.1 Length = 306 Score = 310 bits (794), Expect = 3e-89 Identities = 158/300 (52%), Positives = 210/300 (70%), Gaps = 3/300 (1%) Query: 10 IWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKRLLNSAKI 69 IWM+GK + W DAK+HVL+HTLHYG GV EG +AYKT G AIFRL +HTKRL SAK+ Sbjct: 7 IWMNGKFVSWDDAKVHVLSHTLHYGNGVIEGTKAYKTQKG-YAIFRLNDHTKRLKESAKM 65 Query: 70 FQMDVPFDHETLAAAQCEVVRENKL--ESCYLRPIIWVGSEKLGVSAKGNTIHVAIAAWP 127 M++P+ E L AQ E+V +N+ ++ YLRP ++G +GV K + +AAW Sbjct: 66 TIMEIPYSVEELNKAQIELVAKNEFKGDNVYLRPFAFLGYGVMGVYHKHAPVETVVAAWE 125 Query: 128 WGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYDEALLL 187 WGAYLGE+G+ KGI++K S +R +M +AKA Y+NS +A EAI GY+EALLL Sbjct: 126 WGAYLGEEGMKKGIKLKIVSMSRPANTSNMGKAKAVANYLNSQMAKYEAIDCGYEEALLL 185 Query: 188 DVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRITRDEV 247 D GYV+E SG +FF+V NG L TP + L+ IT+ TVI LA D GI+V +R++R++V Sbjct: 186 DDQGYVAEASGASFFMVKNGVLITPPNDNSLESITQKTVIELATDMGIKVERRRLSREDV 245 Query: 248 YTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYANWLTKI 307 Y DEAF TGTAAE+TP+R +D R IG GARG +TEKLQS +FD+V G+ KY ++LT + Sbjct: 246 YVADEAFLTGTAAEITPVRHVDGRDIGCGARGEMTEKLQSKYFDVVFGRDKKYEHYLTYV 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: 292 Number of extensions: 12 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: 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 WP_011373491.1 SUDEN_RS09745 (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.2851.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.4e-126 405.3 0.9 8.3e-126 405.1 0.9 1.0 1 lcl|NCBI__GCF_000012965.1:WP_011373491.1 SUDEN_RS09745 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000012965.1:WP_011373491.1 SUDEN_RS09745 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.1 0.9 8.3e-126 8.3e-126 1 298 [] 8 305 .. 8 305 .. 0.99 Alignments for each domain: == domain 1 score: 405.1 bits; conditional E-value: 8.3e-126 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w++G++v+++dakvhvl+h+lhYG+gv eG++aY+t+kg aifrl++h++Rl +sak++ +eipys ee lcl|NCBI__GCF_000012965.1:WP_011373491.1 8 WMNGKFVSWDDAKVHVLSHTLHYGNGVIEGTKAYKTQKGYAIFRLNDHTKRLKESAKMTIMEIPYSVEE 76 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlks..aYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvs 136 l+++++e++ kn++k +Y+Rp +++G++ +g+++ +++ve ++aawewgaylgee+++kGik k++ lcl|NCBI__GCF_000012965.1:WP_011373491.1 77 LNKAQIELVAKNEFKGdnVYLRPFAFLGYGVMGVYH-KHAPVETVVAAWEWGAYLGEEGMKKGIKLKIV 144 **************8556******************.5669**************************** PP TIGR01122 137 sfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvs 205 s+ r a+ s + kaka++nYlns++ak ea+ +Gy+ea+lLd++Gyvae sG ++f+vk+gvl+tPp+ lcl|NCBI__GCF_000012965.1:WP_011373491.1 145 SMSRPANTSNMGKAKAVANYLNSQMAKYEAIDCGYEEALLLDDQGYVAEASGASFFMVKNGVLITPPN- 212 *******************************************************************9. PP TIGR01122 206 esiLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtk 274 +++L++it+ +vi+la+++gi+v+++r+sre++y+aDe+fltGtaae+tP+r+vDgr ig g rG++t+ lcl|NCBI__GCF_000012965.1:WP_011373491.1 213 DNSLESITQKTVIELATDMGIKVERRRLSREDVYVADEAFLTGTAAEITPVRHVDGRDIGCGARGEMTE 281 889****************************************************************** PP TIGR01122 275 klqeaffdlvegktekkeewltyv 298 klq+++fd+v g+++k+e++ltyv lcl|NCBI__GCF_000012965.1:WP_011373491.1 282 KLQSKYFDVVFGRDKKYEHYLTYV 305 **********************98 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 11.24 // [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