Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate WP_013705230.1 DESAC_RS01095 branched-chain amino acid transaminase
Query= reanno::BFirm:BPHYT_RS16285 (307 letters) >NCBI__GCF_000195295.1:WP_013705230.1 Length = 305 Score = 367 bits (941), Expect = e-106 Identities = 173/305 (56%), Positives = 224/305 (73%) Query: 3 MADRDGKIWMDGKLIDWRDAKIHVLTHTLHYGMGVFEGVRAYKTADGGTAIFRLQEHTKR 62 M D+ IW+DGK I W A++H+LTHTLHYG+GVFEGVRAY+ A+G TAIFRL EHT+R Sbjct: 1 MVDKAKFIWLDGKFIPWDQAQVHILTHTLHYGLGVFEGVRAYQCANGRTAIFRLPEHTRR 60 Query: 63 LLNSAKIFQMDVPFDHETLAAAQCEVVRENKLESCYLRPIIWVGSEKLGVSAKGNTIHVA 122 L +SA I QM++PF + + A E +R+N + YLRP+I++G +G+ + N I VA Sbjct: 61 LFDSAHILQMEIPFSEDDINQACIEALRQNDQKEAYLRPLIFIGDGAMGLHPQNNPIRVA 120 Query: 123 IAAWPWGAYLGEDGIAKGIRVKTSSFTRHHVNVSMVRAKASGWYVNSILANQEAIADGYD 182 + W WGAYLG++G+ GIR+KTSSFTRHHVNV M AK G YVNSILA +E GYD Sbjct: 121 VITWVWGAYLGDEGLLSGIRLKTSSFTRHHVNVMMTSAKGVGNYVNSILAKREVTKAGYD 180 Query: 183 EALLLDVDGYVSEGSGENFFLVNNGKLYTPDLSSCLDGITRDTVITLARDAGIQVIEKRI 242 EALLLD GYV+E SGEN F+V NG + TP +S L GITRD VI +A+D GI + E R Sbjct: 181 EALLLDTAGYVAEASGENIFMVKNGIIKTPPSTSILPGITRDCVIVIAKDLGIPIQEARF 240 Query: 243 TRDEVYTCDEAFFTGTAAEVTPIRELDNRTIGSGARGPITEKLQSGFFDIVNGKSDKYAN 302 +RD++Y DEAF +GTAAE+TP+RELD+R IG+G GPIT+K+Q +FD V+GK +Y + Sbjct: 241 SRDDLYIADEAFLSGTAAEITPVRELDDRRIGTGKPGPITKKIQETYFDAVHGKKPRYDS 300 Query: 303 WLTKI 307 WLT + Sbjct: 301 WLTYV 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: 333 Number of extensions: 9 Number of successful extensions: 1 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 WP_013705230.1 DESAC_RS01095 (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.11411.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-134 434.0 0.0 1.5e-134 433.8 0.0 1.0 1 lcl|NCBI__GCF_000195295.1:WP_013705230.1 DESAC_RS01095 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195295.1:WP_013705230.1 DESAC_RS01095 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 433.8 0.0 1.5e-134 1.5e-134 1 298 [] 9 305 .] 9 305 .] 0.99 Alignments for each domain: == domain 1 score: 433.8 bits; conditional E-value: 1.5e-134 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkg.laifrlkehveRlydsakilrleipyske 68 wldG+++++++a+vh+lth+lhYG gvfeG+RaY+ +g +aifrl eh+ Rl+dsa+il++eip+s++ lcl|NCBI__GCF_000195295.1:WP_013705230.1 9 WLDGKFIPWDQAQVHILTHTLHYGLGVFEGVRAYQCANGrTAIFRLPEHTRRLFDSAHILQMEIPFSED 77 9**********************************9995379*************************** PP TIGR01122 69 elvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvss 137 +++++++e+lr+n+ k+aY+Rpl+++G++ +gl+p + +++v++++w wgaylg+e+l +Gi+ k+ss lcl|NCBI__GCF_000195295.1:WP_013705230.1 78 DINQACIEALRQNDQKEAYLRPLIFIGDGAMGLHP-QNNPIRVAVITWVWGAYLGDEGLLSGIRLKTSS 145 ***********************************.666****************************** PP TIGR01122 138 frraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvse 206 f+r++vn+++t+ak +gnY+ns+lak e ++aGydea+lLd+ Gyvae sGenif+vk+g ++tPp + lcl|NCBI__GCF_000195295.1:WP_013705230.1 146 FTRHHVNVMMTSAKGVGNYVNSILAKREVTKAGYDEALLLDTAGYVAEASGENIFMVKNGIIKTPPS-T 213 ******************************************************************9.7 PP TIGR01122 207 siLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkk 275 siL gitrd vi +ak+lgi ++e+r+sr++ly+aDe+fl+Gtaae+tP+re+D+r+ig gk Gp+tkk lcl|NCBI__GCF_000195295.1:WP_013705230.1 214 SILPGITRDCVIVIAKDLGIPIQEARFSRDDLYIADEAFLSGTAAEITPVRELDDRRIGTGKPGPITKK 282 8******************************************************************** PP TIGR01122 276 lqeaffdlvegktekkeewltyv 298 +qe++fd v+gk++++++wltyv lcl|NCBI__GCF_000195295.1:WP_013705230.1 283 IQETYFDAVHGKKPRYDSWLTYV 305 *********************98 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: 9.63 // [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