Align branched-chain amino acid aminotransferase subunit (EC 2.6.1.6; EC 2.6.1.42) (characterized)
to candidate WP_011973904.1 MAEO_RS06065 branched-chain-amino-acid transaminase
Query= metacyc::MONOMER-11904 (286 letters) >NCBI__GCF_000017185.1:WP_011973904.1 Length = 286 Score = 561 bits (1445), Expect = e-165 Identities = 286/286 (100%), Positives = 286/286 (100%) Query: 1 MKIYLNGEFVEKEQAKISVYDHGLLYGDGVFEGIRVYDGVIFKLKEHIDRLFDSATSLQM 60 MKIYLNGEFVEKEQAKISVYDHGLLYGDGVFEGIRVYDGVIFKLKEHIDRLFDSATSLQM Sbjct: 1 MKIYLNGEFVEKEQAKISVYDHGLLYGDGVFEGIRVYDGVIFKLKEHIDRLFDSATSLQM 60 Query: 61 DIQTSKDEISKIVIDTIRINELNNAYIRLVITRGVGDLGLDPRKCPKPTIFCIAEPMNPL 120 DIQTSKDEISKIVIDTIRINELNNAYIRLVITRGVGDLGLDPRKCPKPTIFCIAEPMNPL Sbjct: 61 DIQTSKDEISKIVIDTIRINELNNAYIRLVITRGVGDLGLDPRKCPKPTIFCIAEPMNPL 120 Query: 121 LGEDGIKVITSSIRRLPVDVLNPAVKSLNYLNSILAKIQANYAGCDEAFLLDSEGYVAEG 180 LGEDGIKVITSSIRRLPVDVLNPAVKSLNYLNSILAKIQANYAGCDEAFLLDSEGYVAEG Sbjct: 121 LGEDGIKVITSSIRRLPVDVLNPAVKSLNYLNSILAKIQANYAGCDEAFLLDSEGYVAEG 180 Query: 181 TGDNIFVIKNGKIKTPPVSSSVLKGITRDAVVDLAKEQGYEIIEEKLTLHDLYVADELFI 240 TGDNIFVIKNGKIKTPPVSSSVLKGITRDAVVDLAKEQGYEIIEEKLTLHDLYVADELFI Sbjct: 181 TGDNIFVIKNGKIKTPPVSSSVLKGITRDAVVDLAKEQGYEIIEEKLTLHDLYVADELFI 240 Query: 241 TGTAAELAHVVEIDGRVINNREMGVITKKLSEEFKKIRKIMGTKVY 286 TGTAAELAHVVEIDGRVINNREMGVITKKLSEEFKKIRKIMGTKVY Sbjct: 241 TGTAAELAHVVEIDGRVINNREMGVITKKLSEEFKKIRKIMGTKVY 286 Lambda K H 0.319 0.140 0.390 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: 436 Number of extensions: 1 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: 286 Length of database: 286 Length adjustment: 26 Effective length of query: 260 Effective length of database: 260 Effective search space: 67600 Effective search space used: 67600 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate WP_011973904.1 MAEO_RS06065 (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.20513.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-116 372.5 0.5 7.9e-116 372.4 0.5 1.0 1 lcl|NCBI__GCF_000017185.1:WP_011973904.1 MAEO_RS06065 branched-chain-amin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000017185.1:WP_011973904.1 MAEO_RS06065 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 372.4 0.5 7.9e-116 7.9e-116 1 285 [. 4 279 .. 4 286 .] 0.98 Alignments for each domain: == domain 1 score: 372.4 bits; conditional E-value: 7.9e-116 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 +l+Ge+v+ e+ak++v +h+l+YG+gvfeGiR+Y++ +if+lkeh++Rl+dsa +l+++i+ sk+e lcl|NCBI__GCF_000017185.1:WP_011973904.1 4 YLNGEFVEKEQAKISVYDHGLLYGDGVFEGIRVYDG----VIFKLKEHIDRLFDSATSLQMDIQTSKDE 68 89**********************************....***************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 +++++++++r n+l++aYiR ++++G++dlgl+p+ k++++++a ++ +lge +Gikv++ss+ lcl|NCBI__GCF_000017185.1:WP_011973904.1 69 ISKIVIDTIRINELNNAYIRLVITRGVGDLGLDPRKCPKPTIFCIAEPMNPLLGE----DGIKVITSSI 133 **********************************95559***************5....7********* PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr v+++++++k+ + Ylns+lak++a++aG dea+lLd+eGyvaeG+G+nif++k+g+++tPpvs+s lcl|NCBI__GCF_000017185.1:WP_011973904.1 134 RRLPVDVLNPAVKSLN-YLNSILAKIQANYAGCDEAFLLDSEGYVAEGTGDNIFVIKNGKIKTPPVSSS 201 ***************9.**************************************************** PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +Lkgitrdav++lake+g+e+ ee++++++ly+aDe+f+tGtaae++ ++e+Dgr i++ ++G +tkkl lcl|NCBI__GCF_000017185.1:WP_011973904.1 202 VLKGITRDAVVDLAKEQGYEIIEEKLTLHDLYVADELFITGTAAELAHVVEIDGRVINNREMGVITKKL 270 ********************************************************************* PP TIGR01122 277 qeaffdlve 285 e+f+++ + lcl|NCBI__GCF_000017185.1:WP_011973904.1 271 SEEFKKIRK 279 *****9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (286 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: 10.74 // [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