Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_047093915.1 AAV99_RS08480 alpha-ketoacid dehydrogenase subunit beta
Query= uniprot:G1UHX5 (328 letters) >NCBI__GCF_001013305.1:WP_047093915.1 Length = 355 Score = 261 bits (668), Expect = 1e-74 Identities = 154/332 (46%), Positives = 193/332 (58%), Gaps = 21/332 (6%) Query: 4 ITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAI 63 + M +A+N+AL L D L GEDIG GGVFR T GL + G R FDTP++E I Sbjct: 22 MNMIEAINSALDVMLTRDSDVTLLGEDIGYFGGVFRCTAGLQEKHGKTRVFDTPISECGI 81 Query: 64 LGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGI 123 +G AVGM YG RPV E+QF + YP +QL+S A+LR R+ P+T+R P+GGGI Sbjct: 82 IGVAVGMGAYGLRPVPEIQFADYIYPGLDQLISEAARLRYRSAAEFIAPMTVRSPFGGGI 141 Query: 124 GGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY------ 177 G + HS S E + GL V PAT DA LL I DPV+F EPKR+Y Sbjct: 142 FGGQTHSQSPESIFTHVCGLKTVIPATPYDAKGLLISCIEDNDPVIFFEPKRIYNGPFDG 201 Query: 178 --------WR-KEALGLP--VDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEH 226 W+ +E +P PLG A G T++AYG V A E Sbjct: 202 YYDRPAKNWKGREDAQVPDGYYKIPLGKARTVTEGDAMTILAYGTMVHV---AESVCREK 258 Query: 227 GWDLEVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEA 286 G E++DLRTL+PLD + ASV+RTGR ++VHEA +G GAE++A +TERCFYHLEA Sbjct: 259 GVAAEILDLRTLVPLDIEAIEASVKRTGRCLIVHEATRTSGFGAELSALVTERCFYHLEA 318 Query: 287 PVRRVTGFDVPYPPPLLERHYLPGVDRILDAV 318 PV RVTGFD PYP LE Y PG RI +A+ Sbjct: 319 PVERVTGFDTPYPHS-LEWAYFPGPVRIGEAI 349 Lambda K H 0.322 0.138 0.418 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: 377 Number of extensions: 19 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: 328 Length of database: 355 Length adjustment: 29 Effective length of query: 299 Effective length of database: 326 Effective search space: 97474 Effective search space used: 97474 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 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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