Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate WP_089322472.1 CHB58_RS02185 branched-chain amino acid transaminase
Query= BRENDA::F0QW25 (314 letters) >NCBI__GCF_900188395.1:WP_089322472.1 Length = 305 Score = 292 bits (748), Expect = 6e-84 Identities = 150/302 (49%), Positives = 201/302 (66%), Gaps = 2/302 (0%) Query: 15 KYVWVNGKLIPEKEATIPILTHALHYGTSIFEGIRAYWNSDNNNLYVFRARDHYVRFHDS 74 +Y + GK +P EA I I T++ HYGT+IFEGIRAYWN + N L+ + HY R + Sbjct: 4 RYAYFEGKFVPIDEANINIQTNSFHYGTAIFEGIRAYWNEEKNQLFGLFFKKHYERMVAN 63 Query: 75 AKIMSIKVGYSVDELIDATVELLRANDVHEDVYIRPITFVSASTVNLDIRNLDVTTAIIT 134 KI+++K+ +VDEL + TVELLR + E+VYIRPI + ++ + D AI T Sbjct: 64 CKILNMKLDKTVDELTEITVELLRRCEHKENVYIRPIAYFPNLQISPKLIGYDTELAIYT 123 Query: 135 VPFGHYLE-PKGIKAKVVSWLRVHNSMFPMKAKVSGIYVNSVIAIIDAKVSGFDEAILLN 193 VP G YL+ KG+K S+ R+++SM P + KV+G YVNS A +A ++G DEAI+LN Sbjct: 124 VPLGDYLDTKKGLKVITSSFRRINDSMIPARCKVAGAYVNSAFAKTEAILAGADEAIMLN 183 Query: 194 RDGYVAEGSGENIFIIKDGILYTPPVYDSILEGITRDTVITIAR-DLGLTVTEKRITREE 252 DG VAEGS EN+FII++G+ T P Y +ILEGITR+ VI + + +LG+ V E+ I R E Sbjct: 184 TDGTVAEGSAENLFIIRNGVAITTPSYSNILEGITRNAVIELLKEELGVEVVERPILRSE 243 Query: 253 LYTADEVFFTGTAAEVTPVVNIDGRVIGNGEPGPIALKVRSYYMDVVHGRVSKYKNWLTP 312 LY ADE FFTGT A+V P+ IDGRVIG GE G I K++ Y D+V G V KY +WL P Sbjct: 244 LYIADEAFFTGTGAQVAPIAEIDGRVIGTGEIGKITSKLQELYFDIVKGNVDKYSHWLIP 303 Query: 313 IY 314 IY Sbjct: 304 IY 305 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: 305 Number of extensions: 16 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: 314 Length of database: 305 Length adjustment: 27 Effective length of query: 287 Effective length of database: 278 Effective search space: 79786 Effective search space used: 79786 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_089322472.1 CHB58_RS02185 (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.12859.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-109 349.3 0.5 9.5e-109 349.1 0.5 1.0 1 lcl|NCBI__GCF_900188395.1:WP_089322472.1 CHB58_RS02185 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900188395.1:WP_089322472.1 CHB58_RS02185 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 349.1 0.5 9.5e-109 9.5e-109 1 297 [. 7 303 .. 7 304 .. 0.97 Alignments for each domain: == domain 1 score: 349.1 bits; conditional E-value: 9.5e-109 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaif..rlkehveRlydsakilrleipysk 67 +++G++v++++a++++ t+++hYGt++feGiRaY+++++ ++f ++k+h+eR+ + kil+++++ + lcl|NCBI__GCF_900188395.1:WP_089322472.1 7 YFEGKFVPIDEANINIQTNSFHYGTAIFEGIRAYWNEEKNQLFglFFKKHYERMVANCKILNMKLDKTV 75 89**********************************99888874478********************** PP TIGR01122 68 eelvevtkevlrknnlks.aYiRplvyvGaedlglkpk.vdlkveviiaawewgaylgeealekGikvk 134 +el+e+t+e+lr+ + k+ +YiRp++y + +l+++pk +++++e++i+++++g yl++ +kG+kv+ lcl|NCBI__GCF_900188395.1:WP_089322472.1 76 DELTEITVELLRRCEHKEnVYIRPIAY--FPNLQISPKlIGYDTELAIYTVPLGDYLDT---KKGLKVI 139 *************999888********..899******9*******************8...7****** PP TIGR01122 135 vssfrraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPp 203 +ssfrr ++++ip++ k+ag+Y+ns++ak+ea+ aG+deai+L+++G vaeGs en+fi+++gv +t p lcl|NCBI__GCF_900188395.1:WP_089322472.1 140 TSSFRRINDSMIPARCKVAGAYVNSAFAKTEAILAGADEAIMLNTDGTVAEGSAENLFIIRNGVAITTP 208 ****************************************************************99999 PP TIGR01122 204 vsesiLkgitrdaviklak.elgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGp 271 +++iL+gitr+avi+l+k elg+ev+e++i r+ely+aDe+f+tGt a v+Pi e+Dgr ig g++G+ lcl|NCBI__GCF_900188395.1:WP_089322472.1 209 SYSNILEGITRNAVIELLKeELGVEVVERPILRSELYIADEAFFTGTGAQVAPIAEIDGRVIGTGEIGK 277 99***************99789*********************************************** PP TIGR01122 272 vtkklqeaffdlvegktekkeewlty 297 +t klqe +fd+v+g+++k+++wl + lcl|NCBI__GCF_900188395.1:WP_089322472.1 278 ITSKLQELYFDIVKGNVDKYSHWLIP 303 ***********************976 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.06 // [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