Align branched-chain amino acid aminotransferase 2; EC 2.6.1.42 (characterized)
to candidate WP_022949156.1 H035_RS0111660 branched-chain-amino-acid transaminase
Query= CharProtDB::CH_012531 (298 letters) >NCBI__GCF_000421465.1:WP_022949156.1 Length = 292 Score = 246 bits (628), Expect = 4e-70 Identities = 133/281 (47%), Positives = 174/281 (61%), Gaps = 1/281 (0%) Query: 7 FLNGEFVPKDEAKVSVYDHGYLYGDGVFEGIRVYSGNVFRLREHLVRLYESAKSIMLEIP 66 ++NG +P + A V V DHG LYGDGVFEGIR Y FRL HL RL +S +I L +P Sbjct: 8 WINGRLLPGNAATVPVTDHGLLYGDGVFEGIRFYRRRAFRLAAHLQRLADSCAAIRLTLP 67 Query: 67 YSLDEITNIVVETIRQNKLSNGYIRLVVSRGAGNLGLDPDSCTKPNVVVIAEQLSLFPQE 126 + +T V E I +GY+RL+V+RG+G +GL+P+ CT+PNV++IA +L L + Sbjct: 68 CPRERLTRAVEEVIAAFAEDDGYLRLIVTRGSGPMGLNPEDCTRPNVILIATRLQLVSER 127 Query: 127 YYEKGIPVVTVATRRNRPDVLSPQVKSLNYLNNILVRIEAKLAGVQEALMLNDQGYVAEG 186 +G+ V+ ATRR D L P++KSLNYLN IL R+EA AG EA+MLN G +AEG Sbjct: 128 KRREGVRVIIAATRRLPADGLDPRIKSLNYLNPILARMEAHQAGADEAVMLNRAGRIAEG 187 Query: 187 SGDNVFIVKGNKLITPPSSAGALEGITRNAILEIGEKLGYDVREELFTRHDVYVADEVFL 246 + DNVF+V+ +L TPP GAL GITR I+ + G V E +D+Y A E FL Sbjct: 188 TADNVFVVRQGELATPPPVEGALAGITRELIMGLARDAGISVAEIPLAPYDLYTAGECFL 247 Query: 247 TGTAAEVIAVTTVDGRTIGLGQTGPHTNRLLEEFRKLVIED 287 TGT AE+I V VDGR +G GP L F LV E+ Sbjct: 248 TGTGAELIPVAEVDGRPMG-DCPGPVFLELRRRFHALVQEE 287 Lambda K H 0.317 0.138 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: 253 Number of extensions: 7 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: 298 Length of database: 292 Length adjustment: 26 Effective length of query: 272 Effective length of database: 266 Effective search space: 72352 Effective search space used: 72352 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
Align candidate WP_022949156.1 H035_RS0111660 (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.7770.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.4e-80 255.9 0.0 2.6e-80 255.7 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_022949156.1 H035_RS0111660 branched-chain-am Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_022949156.1 H035_RS0111660 branched-chain-amino-acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 255.7 0.0 2.6e-80 2.6e-80 1 288 [. 8 288 .. 8 292 .] 0.96 Alignments for each domain: == domain 1 score: 255.7 bits; conditional E-value: 2.6e-80 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w++G+l++ + a+v v +h+l+YG+gvfeGiR Y+ + frl h++Rl ds ++rl +p +e+ lcl|NCBI__GCF_000421465.1:WP_022949156.1 8 WINGRLLPGNAATVPVTDHGLLYGDGVFEGIRFYRR----RAFRLAAHLQRLADSCAAIRLTLPCPRER 72 9**********************************9....89*************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l+ ++ ev+ + ++ Y+R +v++G++ +gl+p+ ++++vi++a ++ +++ e +G++v++++ lcl|NCBI__GCF_000421465.1:WP_022949156.1 73 LTRAVEEVIAAFAEDDGYLRLIVTRGSGPMGLNPEDCTRPNVILIATRL-QLVSERKRREGVRVIIAAT 140 **********************************855589999999988.56777889*********** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr + + +++k+ + Yln +la++ea +aG+dea++L++ G +aeG+ +n+f+v++g+l tPp e lcl|NCBI__GCF_000421465.1:WP_022949156.1 141 RRLPADGLDPRIKSLN-YLNPILARMEAHQAGADEAVMLNRAGRIAEGTADNVFVVRQGELATPPPVEG 208 ***************9.**************************************************** PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L gitr+ ++ la++ gi+v e +++ ++lyta e fltGt ae++P+ evDgr +g+ Gpv +l lcl|NCBI__GCF_000421465.1:WP_022949156.1 209 ALAGITRELIMGLARDAGISVAEIPLAPYDLYTAGECFLTGTGAELIPVAEVDGRPMGDC-PGPVFLEL 276 **********************************************************86.8******* PP TIGR01122 277 qeaffdlvegkt 288 + +f lv+++ lcl|NCBI__GCF_000421465.1:WP_022949156.1 277 RRRFHALVQEEC 288 *******99865 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (292 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: 9.25 // [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