Align branched-chain amino acid aminotransferase subunit (EC 2.6.1.6; EC 2.6.1.42) (characterized)
to candidate WP_011869290.1 MMARC5_RS07850 branched-chain-amino-acid transaminase
Query= metacyc::MONOMER-11904 (286 letters) >NCBI__GCF_000016125.1:WP_011869290.1 Length = 287 Score = 457 bits (1175), Expect = e-133 Identities = 228/284 (80%), Positives = 255/284 (89%) Query: 1 MKIYLNGEFVEKEQAKISVYDHGLLYGDGVFEGIRVYDGVIFKLKEHIDRLFDSATSLQM 60 MKIYL+G+FVEKE AK+SVYDHGLLYGDGVFEGIR Y+GV+FKL+EHI+RL+DSA SL M Sbjct: 1 MKIYLDGKFVEKEDAKVSVYDHGLLYGDGVFEGIRAYEGVVFKLEEHIERLYDSADSLAM 60 Query: 61 DIQTSKDEISKIVIDTIRINELNNAYIRLVITRGVGDLGLDPRKCPKPTIFCIAEPMNPL 120 I SK EI +IVI+T++ N+L +AYIRLV+TRG+GDLGLDPRKCP PT+FCIAE M PL Sbjct: 61 KIPVSKVEIGEIVIETLKTNDLKDAYIRLVVTRGIGDLGLDPRKCPVPTVFCIAEAMKPL 120 Query: 121 LGEDGIKVITSSIRRLPVDVLNPAVKSLNYLNSILAKIQANYAGCDEAFLLDSEGYVAEG 180 LGEDGIKVITSSIRRLPVDVLNPAVKSLNYLNSILAKIQANYAG +EAFLLDSEGYVAEG Sbjct: 121 LGEDGIKVITSSIRRLPVDVLNPAVKSLNYLNSILAKIQANYAGVEEAFLLDSEGYVAEG 180 Query: 181 TGDNIFVIKNGKIKTPPVSSSVLKGITRDAVVDLAKEQGYEIIEEKLTLHDLYVADELFI 240 TGDNIFVIKNGKIKTPP+SSSVLKGITRD VVDLA E GY IIEEK+TLHDL+VADE+FI Sbjct: 181 TGDNIFVIKNGKIKTPPLSSSVLKGITRDTVVDLANEAGYTIIEEKMTLHDLFVADEIFI 240 Query: 241 TGTAAELAHVVEIDGRVINNREMGVITKKLSEEFKKIRKIMGTK 284 TGTAAEL HVVEIDGR I N ++G ITK LS+ FK+IR +G K Sbjct: 241 TGTAAELIHVVEIDGRKIYNGKLGPITKDLSDRFKEIRSKIGKK 284 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: 386 Number of extensions: 5 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: 287 Length adjustment: 26 Effective length of query: 260 Effective length of database: 261 Effective search space: 67860 Effective search space used: 67860 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_011869290.1 MMARC5_RS07850 (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.23929.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-115 369.5 0.4 6.5e-115 369.3 0.4 1.0 1 lcl|NCBI__GCF_000016125.1:WP_011869290.1 MMARC5_RS07850 branched-chain-am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000016125.1:WP_011869290.1 MMARC5_RS07850 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 369.3 0.4 6.5e-115 6.5e-115 1 290 [. 4 284 .. 4 287 .] 0.97 Alignments for each domain: == domain 1 score: 369.3 bits; conditional E-value: 6.5e-115 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 +ldG++v+ edakv+v +h+l+YG+gvfeGiRaYe+ ++f+l+eh+eRlydsa +l ++ip+sk e lcl|NCBI__GCF_000016125.1:WP_011869290.1 4 YLDGKFVEKEDAKVSVYDHGLLYGDGVFEGIRAYEG----VVFKLEEHIERLYDSADSLAMKIPVSKVE 68 89**********************************....***************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpk.vdlkveviiaawewgaylgeealekGikvkvss 137 + e+++e+l++n+lk+aYiR +v++G++dlgl+p+ + ++v+++a ++ +lge +Gikv++ss lcl|NCBI__GCF_000016125.1:WP_011869290.1 69 IGEIVIETLKTNDLKDAYIRLVVTRGIGDLGLDPRkCP-VPTVFCIAEAMKPLLGE----DGIKVITSS 132 **********************************9555.789*************5....7******** PP TIGR01122 138 frraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvse 206 +rr v+++++++k+ + Ylns+lak++a++aG++ea+lLd+eGyvaeG+G+nif++k+g+++tPp+s+ lcl|NCBI__GCF_000016125.1:WP_011869290.1 133 IRRLPVDVLNPAVKSLN-YLNSILAKIQANYAGVEEAFLLDSEGYVAEGTGDNIFVIKNGKIKTPPLSS 200 ****************9.*************************************************** PP TIGR01122 207 siLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkk 275 s+Lkgitrd+v++la+e g+++ ee++++++l++aDe+f+tGtaae++ ++e+Dgrki +gk Gp+tk lcl|NCBI__GCF_000016125.1:WP_011869290.1 201 SVLKGITRDTVVDLANEAGYTIIEEKMTLHDLFVADEIFITGTAAELIHVVEIDGRKIYNGKLGPITKD 269 ********************************************************************* PP TIGR01122 276 lqeaffdlvegktek 290 l ++f+++ ++ +k lcl|NCBI__GCF_000016125.1:WP_011869290.1 270 LSDRFKEIRSKIGKK 284 *******99875555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (287 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: 9.68 // [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