Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_010935819.1 DET_RS00045 branched-chain amino acid transaminase
Query= BRENDA::F0QW25 (314 letters) >NCBI__GCF_000011905.1:WP_010935819.1 Length = 306 Score = 289 bits (739), Expect = 7e-83 Identities = 130/300 (43%), Positives = 202/300 (67%), Gaps = 1/300 (0%) Query: 16 YVWVNGKLIPEKEATIPILTHALHYGTSIFEGIRAYWNSDNNNLYVFRARDHYVRFHDSA 75 Y + ++IP ++A I ++THALHYGT +FEGIR WN++ +Y+FR ++HY R A Sbjct: 5 YAYFKKQIIPLEDAKIGVMTHALHYGTGVFEGIRGNWNNEKKQMYIFRLKEHYTRLLTGA 64 Query: 76 KIMSIKVGYSVDELIDATVELLRANDVHEDVYIRPITFVSASTVNLDIRNLDVTTAIITV 135 K++ + + Y+VDEL T++L++ ED+YIRP+ + S+ T + + NLD I+ + Sbjct: 65 KVLKMNLPYTVDELCKITIDLIKKCGFKEDIYIRPLAYKSSETFGVRLHNLDCDLLIVAI 124 Query: 136 PFGHYLEPKGIKAKVVSWLRVHNSMFPMKAKVSGIYVNSVIAIIDAKVSGFDEAILLNRD 195 P+G Y++ V +W R +++ P + K +GIY+N+ +A +GFDE I+L D Sbjct: 125 PWGRYIDKDTCHCCVSTWHRPDDNVMPPQLKSTGIYLNNAFTKTEAVENGFDEGIMLTPD 184 Query: 196 GYVAEGSGENIFIIKDGILYTPPVYDSILEGITRDTVITIA-RDLGLTVTEKRITREELY 254 G+V+EGSGEN+FI++ G L TPP+ DSIL+GITR++V+ +A ++LGL V E+ I R ELY Sbjct: 185 GHVSEGSGENLFIVRKGKLITPPICDSILDGITRNSVMELAEKELGLEVLERSIDRVELY 244 Query: 255 TADEVFFTGTAAEVTPVVNIDGRVIGNGEPGPIALKVRSYYMDVVHGRVSKYKNWLTPIY 314 A+E F TGTAA +TPV +D R +GNGE GP+ K++ Y + + G ++KY +W TP+Y Sbjct: 245 IAEECFLTGTAAHLTPVSEVDHRKVGNGEIGPVTAKLKDLYFEAIKGNIAKYSSWCTPVY 304 Lambda K H 0.321 0.139 0.409 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: 286 Number of extensions: 8 Number of successful extensions: 2 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: 314 Length of database: 306 Length adjustment: 27 Effective length of query: 287 Effective length of database: 279 Effective search space: 80073 Effective search space used: 80073 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_010935819.1 DET_RS00045 (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.8892.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.1e-110 352.6 0.0 9.1e-110 352.5 0.0 1.0 1 lcl|NCBI__GCF_000011905.1:WP_010935819.1 DET_RS00045 branched-chain amino Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000011905.1:WP_010935819.1 DET_RS00045 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 352.5 0.0 9.1e-110 9.1e-110 1 298 [] 7 303 .. 7 303 .. 0.97 Alignments for each domain: == domain 1 score: 352.5 bits; conditional E-value: 9.1e-110 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdk..glaifrlkehveRlydsakilrleipysk 67 +++ ++++ edak+ v+thalhYGtgvfeGiR ++++ +++ifrlkeh+ Rl++ ak+l++++py+ lcl|NCBI__GCF_000011905.1:WP_010935819.1 7 YFKKQIIPLEDAKIGVMTHALHYGTGVFEGIRGNWNNEkkQMYIFRLKEHYTRLLTGAKVLKMNLPYTV 75 78889***************************9776543599*************************** PP TIGR01122 68 eelvevtkevlrknnlks.aYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkv 135 +el+++t+++++k ++k+ YiRpl+y+ +e +g++ +l+ +++i+a++wg+y+++ + + v lcl|NCBI__GCF_000011905.1:WP_010935819.1 76 DELCKITIDLIKKCGFKEdIYIRPLAYKSSETFGVRL-HNLDCDLLIVAIPWGRYIDK----DTCHCCV 139 ****************998*****************9.8999***************7....578999* PP TIGR01122 136 ssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpv 204 s+++r ++n++p+++k++g Yln++++k+ea+++G+de+i+L +G+v+eGsGen+fiv++g+l+tPp+ lcl|NCBI__GCF_000011905.1:WP_010935819.1 140 STWHRPDDNVMPPQLKSTGIYLNNAFTKTEAVENGFDEGIMLTPDGHVSEGSGENLFIVRKGKLITPPI 208 ********************************************************************* PP TIGR01122 205 sesiLkgitrdaviklak.elgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpv 272 +siL+gitr++v++la+ elg+ev e++i r ely+a+e fltGtaa +tP+ evD+rk+g+g++Gpv lcl|NCBI__GCF_000011905.1:WP_010935819.1 209 CDSILDGITRNSVMELAEkELGLEVLERSIDRVELYIAEECFLTGTAAHLTPVSEVDHRKVGNGEIGPV 277 *****************8799************************************************ PP TIGR01122 273 tkklqeaffdlvegktekkeewltyv 298 t kl++ +f+ ++g++ k+++w t+v lcl|NCBI__GCF_000011905.1:WP_010935819.1 278 TAKLKDLYFEAIKGNIAKYSSWCTPV 303 **********************9986 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 11.35 // [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