Align branched-chain-amino-acid aminotransferase subunit (EC 2.6.1.42) (characterized)
to candidate WP_053767056.1 BVI061214_RS01840 branched-chain amino acid transaminase
Query= metacyc::MONOMER-11914 (306 letters) >NCBI__GCF_001280255.1:WP_053767056.1 Length = 318 Score = 318 bits (815), Expect = 1e-91 Identities = 162/302 (53%), Positives = 204/302 (67%), Gaps = 2/302 (0%) Query: 6 SGKIWLNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKRLFDSA 65 +G IW NG++V EEA VLSH +HYG+SVFEGIR Y KG AIFRL+EHVKRL++SA Sbjct: 15 AGLIWFNGKLVPQEEAKTSVLSHALHYGTSVFEGIRAYETPKGPAIFRLKEHVKRLYNSA 74 Query: 66 KIYRMDIPYTQEQICDAIVETVRENGLEECYIRPVVFRGYGEMGVHPV-NCPVDVAVAAW 124 K+ RM+IPYT E++ +AI E VR NG + CYIRP+ + G +GV+P+ N P +V VAAW Sbjct: 75 KVLRMEIPYTPEEMEEAIKEVVRRNGYKSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAW 134 Query: 125 EWGAYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYDEAIM 184 EWGAYLG EA+ G S+W R N MP AK GGNY+NS LAKMEA+ G DEA++ Sbjct: 135 EWGAYLGEEAVRKGARLITSSWARFPANVMPGKAKVGGNYVNSALAKMEALAAGADEALL 194 Query: 185 LDYHGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEPITRE 244 LD GY++EGSGEN+F V +G IY S + L GITRDSVI+IAR G V TR+ Sbjct: 195 LDEEGYVAEGSGENLFFVRDGVIYALEHSVN-LEGITRDSVIRIARDLGYQVQVVRATRD 253 Query: 245 MLYIADEAFFTGTAAEITPIRSVDGIEIGAGRRGPVTKLLQDEFFRIIRAETEDSFGWLT 304 LY+ADE F TGTAAE+TP+ +D IG G GPV L++ + + WLT Sbjct: 254 QLYMADEVFMTGTAAEVTPVSMIDWRPIGEGTAGPVALRLREVYLEAATGRRPEYEHWLT 313 Query: 305 YI 306 Y+ Sbjct: 314 YV 315 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: 354 Number of extensions: 18 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: 306 Length of database: 318 Length adjustment: 27 Effective length of query: 279 Effective length of database: 291 Effective search space: 81189 Effective search space used: 81189 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_053767056.1 BVI061214_RS01840 (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.1843479.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-130 419.4 0.0 4.3e-130 419.2 0.0 1.0 1 NCBI__GCF_001280255.1:WP_053767056.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001280255.1:WP_053767056.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 419.2 0.0 4.3e-130 4.3e-130 1 298 [] 19 315 .. 19 315 .. 0.99 Alignments for each domain: == domain 1 score: 419.2 bits; conditional E-value: 4.3e-130 TIGR01122 1 wldGelvdvedakvhvlthalhYGtgvfeGiRaYetdkglaifrlkehveRlydsakilrleipyskeelvev 73 w++G+lv+ e+ak++vl+halhYGt+vfeGiRaYet+kg+aifrlkehv+Rly+sak+lr+eipy+ ee+ e+ NCBI__GCF_001280255.1:WP_053767056.1 19 WFNGKLVPQEEAKTSVLSHALHYGTSVFEGIRAYETPKGPAIFRLKEHVKRLYNSAKVLRMEIPYTPEEMEEA 91 9************************************************************************ PP TIGR01122 74 tkevlrknnlksaYiRplvyvGaedlglkpkvdlkveviiaawewgaylgeealekGikvkvssfrraavnsi 146 +kev+r+n+ ks+YiRpl+++Ga+ lg++p + + ev++aawewgaylgeea+ kG + ++ss++r n++ NCBI__GCF_001280255.1:WP_053767056.1 92 IKEVVRRNGYKSCYIRPLAWMGAKALGVNPLPNNPAEVMVAAWEWGAYLGEEAVRKGARLITSSWARFPANVM 164 ******************************9999*************************************** PP TIGR01122 147 ptkakaagnYlnsllaksealraGydeailLdeeGyvaeGsGenifivkdgvlltPpvsesiLkgitrdavik 219 p kak++gnY+ns+lak+eal+aG+dea+lLdeeGyvaeGsGen+f v+dgv++ + + +L+gitrd+vi+ NCBI__GCF_001280255.1:WP_053767056.1 165 PGKAKVGGNYVNSALAKMEALAAGADEALLLDEEGYVAEGSGENLFFVRDGVIYALEH-SVNLEGITRDSVIR 236 *******************************************************999.89************ PP TIGR01122 220 lakelgievkeerisreelytaDevfltGtaaevtPirevDgrkigegkrGpvtkklqeaffdlvegktekke 292 +a++lg++v+ r +r++ly+aDevf+tGtaaevtP+ +D r igeg++Gpv +l+e + + +g+ +++e NCBI__GCF_001280255.1:WP_053767056.1 237 IARDLGYQVQVVRATRDQLYMADEVFMTGTAAEVTPVSMIDWRPIGEGTAGPVALRLREVYLEAATGRRPEYE 309 ************************************************************************* PP TIGR01122 293 ewltyv 298 +wltyv NCBI__GCF_001280255.1:WP_053767056.1 310 HWLTYV 315 ****98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (298 nodes) Target sequences: 1 (318 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: 14.44 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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