Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate WP_099018480.1 CCS90_RS05525 pyruvate dehydrogenase
Query= uniprot:G1UHX5 (328 letters) >NCBI__GCF_002591915.1:WP_099018480.1 Length = 701 Score = 181 bits (460), Expect = 4e-50 Identities = 115/325 (35%), Positives = 176/325 (54%), Gaps = 12/325 (3%) Query: 4 ITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAI 63 I M A+ L L + + ++FGED+GA GGV +T GL + G+ + FDT L+E I Sbjct: 381 INMVTAIRKTLDYELSHNNKMLVFGEDVGAKGGVHAVTLGLQEKHGEAQVFDTSLSEEGI 440 Query: 64 LGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGI 123 +G ++G+A+ G PV E+QF +A PA EQL + +R RT P+ +R+ GG Sbjct: 441 IGRSIGLALAGLLPVPEIQFRKYADPAEEQL-NETGSMRWRTNNRFAAPMVVRMA-GGYF 498 Query: 124 G-GVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY---WR 179 G G HS +E+ ++ G V P+ A DA LLR ++ + +P +F E +++ W Sbjct: 499 GCGDPWHSQCAEVKWVHAIGWQVAMPSNAEDAVGLLRYALRNNNPTIFFEHRKMLDHAWS 558 Query: 180 KEALGLPVDTGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEHGWDLEVIDLRTLM 239 + P G G T++++G V A E + G ++IDLRTL Sbjct: 559 RRPYPGDQYIIPFGQGNKILSGDRVTVVSWGGMVHMCQTAIE---QTGIQADLIDLRTLR 615 Query: 240 PLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEAPVRRVTGFDV--P 297 P D A V SV++TGR ++VHE + AG GAEIAA + + F++L+AP+ R+ D+ P Sbjct: 616 PWDKAMVLQSVKKTGRCLIVHEDNMSAGFGAEIAAILAKEAFFYLDAPIERLATADIGNP 675 Query: 298 YPPPLLERHYLPGVDRILDAVASLE 322 + P L+E H LP D I + L+ Sbjct: 676 HDPKLME-HALPNPDSIAQRLMELD 699 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: 544 Number of extensions: 27 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: 701 Length adjustment: 33 Effective length of query: 295 Effective length of database: 668 Effective search space: 197060 Effective search space used: 197060 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: 51 (24.3 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