Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.42) (characterized)
to candidate WP_013643702.1 METBO_RS00490 branched-chain amino acid transaminase
Query= metacyc::MONOMER-11914 (306 letters) >NCBI__GCF_000191585.1:WP_013643702.1 Length = 306 Score = 435 bits (1119), Expect = e-127 Identities = 199/306 (65%), Positives = 248/306 (81%) Query: 1 MSCEASGKIWLNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKR 60 M+ + +GKIW NG V+W++A +HVLSHVVHYG+SVFEGIRCY G A+FRL++H+KR Sbjct: 1 MAFDENGKIWFNGNFVDWKDANLHVLSHVVHYGTSVFEGIRCYDTKNGPAVFRLQDHIKR 60 Query: 61 LFDSAKIYRMDIPYTQEQICDAIVETVRENGLEECYIRPVVFRGYGEMGVHPVNCPVDVA 120 L +S KIYRM+IPY+ E + A+++T++ N L+ECYIRPV FRGYGE+GV+P+NCPV+ Sbjct: 61 LINSGKIYRMEIPYSVEDLSQAVLDTIKINQLKECYIRPVAFRGYGELGVYPLNCPVETV 120 Query: 121 VAAWEWGAYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYD 180 VAAW WG YLG EA+E GV+ G S+WRRMAP TMPNMAKAG NY+NSQLAKME++ +GYD Sbjct: 121 VAAWAWGKYLGEEAIENGVNIGTSSWRRMAPGTMPNMAKAGSNYMNSQLAKMESIANGYD 180 Query: 181 EAIMLDYHGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEP 240 EAIMLDY G +SEGSGENIF+V +G IYTPP+SSSLL G+TRDSVIKIA+ + V EE Sbjct: 181 EAIMLDYQGMVSEGSGENIFVVLDGAIYTPPISSSLLSGLTRDSVIKIAQKLSLEVREEN 240 Query: 241 ITREMLYIADEAFFTGTAAEITPIRSVDGIEIGAGRRGPVTKLLQDEFFRIIRAETEDSF 300 I REMLYIADE F TGTAAE+TP+RS+D I IG G RG VTK +Q+ FF ++ E ED Sbjct: 241 IPREMLYIADEVFLTGTAAEVTPVRSIDKIIIGNGTRGAVTKKIQENFFSLVNGEEEDEH 300 Query: 301 GWLTYI 306 GWL+Y+ Sbjct: 301 GWLSYV 306 Lambda K H 0.320 0.136 0.414 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: 379 Number of extensions: 13 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: 306 Length of database: 306 Length adjustment: 27 Effective length of query: 279 Effective length of database: 279 Effective search space: 77841 Effective search space used: 77841 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_013643702.1 METBO_RS00490 (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.1132.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-140 452.5 0.0 3.5e-140 452.3 0.0 1.0 1 lcl|NCBI__GCF_000191585.1:WP_013643702.1 METBO_RS00490 branched-chain ami Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000191585.1:WP_013643702.1 METBO_RS00490 branched-chain amino acid transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 452.3 0.0 3.5e-140 3.5e-140 1 298 [] 10 306 .] 10 306 .] 1.00 Alignments for each domain: == domain 1 score: 452.3 bits; conditional E-value: 3.5e-140 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskee 69 w++G++vd++da++hvl+h++hYGt+vfeGiR+Y+t++g+a+frl++h++Rl +s ki+r+eipys e+ lcl|NCBI__GCF_000191585.1:WP_013643702.1 10 WFNGNFVDWKDANLHVLSHVVHYGTSVFEGIRCYDTKNGPAVFRLQDHIKRLINSGKIYRMEIPYSVED 78 9******************************************************************** PP TIGR01122 70 lvevtkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssf 138 l++++ ++++ n+lk++YiRp++++G+++lg++p +++ve ++aaw+wg+ylgeea+e+G+++ +ss+ lcl|NCBI__GCF_000191585.1:WP_013643702.1 79 LSQAVLDTIKINQLKECYIRPVAFRGYGELGVYP-LNCPVETVVAAWAWGKYLGEEAIENGVNIGTSSW 146 **********************************.********************************** PP TIGR01122 139 rraavnsiptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvses 207 rr+a+ ++p++aka++nY+ns+lak+e++++Gydeai+Ld +G v+eGsGenif+v dg+++tPp+s+s lcl|NCBI__GCF_000191585.1:WP_013643702.1 147 RRMAPGTMPNMAKAGSNYMNSQLAKMESIANGYDEAIMLDYQGMVSEGSGENIFVVLDGAIYTPPISSS 215 ********************************************************************* PP TIGR01122 208 iLkgitrdaviklakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkkl 276 +L+g+trd+vik+a++l++ev+ee+i re+ly+aDevfltGtaaevtP+r++D++ ig+g+rG vtkk+ lcl|NCBI__GCF_000191585.1:WP_013643702.1 216 LLSGLTRDSVIKIAQKLSLEVREENIPREMLYIADEVFLTGTAAEVTPVRSIDKIIIGNGTRGAVTKKI 284 ********************************************************************* PP TIGR01122 277 qeaffdlvegktekkeewltyv 298 qe+ff lv+g++e++++wl+yv lcl|NCBI__GCF_000191585.1:WP_013643702.1 285 QENFFSLVNGEEEDEHGWLSYV 306 *******************997 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.45 // [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