Align 2-oxoisovalerate dehydrogenase subunit beta; Branched-chain alpha-keto acid dehydrogenase E1 component beta chain; BCKDH E1-beta; EC 1.2.4.4 (characterized)
to candidate 6938692 Sama_2795 transketolase, central region (RefSeq)
Query= SwissProt::Q5SLR3 (324 letters) >FitnessBrowser__SB2B:6938692 Length = 761 Score = 172 bits (437), Expect = 2e-47 Identities = 123/332 (37%), Positives = 172/332 (51%), Gaps = 20/332 (6%) Query: 6 MVQALNRALDEEMAKDPRVVVLGEDVGKRGGVFLVTEGLLQKYGPDRVMDTPLSEAAIVG 65 M + +N L E MA VVV GEDVGK+GGV+ VT L++++GP RV++T L E +I+G Sbjct: 404 MGKLINLTLTELMASHDNVVVCGEDVGKKGGVYHVTSRLVERFGPSRVINTLLDETSILG 463 Query: 66 AALGMAAHGLRPVAEIQFADYIFPGFDQLVSQVAKLRYRSGGQFTAPLVVRMPSGGGVR- 124 A GMA +GL P+ EIQF Y+ DQ+ + A L + S GQ+T P+V+R+ + Sbjct: 464 LATGMAHNGLLPIPEIQFLAYVHNAEDQIRGEAATLPFFSNGQYTNPMVIRIAGLAYQKG 523 Query: 125 -GGHHHSQSPEAHFVHTAGLKVVAVSTPYDAKGLLKAAIR----DEDPVVFLEPKRLYRS 179 GGH H+ + F GL + S DA+G+L+ +R ++ V+FLEP LY + Sbjct: 524 FGGHFHNDNSFTVFRDIPGLILACPSNGADAQGMLRECVRLAREEQRLVIFLEPIALYMT 583 Query: 180 -----------VKEEVPEEDYT-LPIGKAALRREGKDLTLIGYGTVMPEVLQAAAELAKA 227 + VPE + T LP G+ EGKDL +I YG QA LA+A Sbjct: 584 RDLHEPGDSLWAAQYVPEREATPLPFGEPGRFGEGKDLCIISYGNGYYLSRQAEKALAEA 643 Query: 228 GVSAEVLDLRTLMPWDYEAVMNSVAKTGRVVLVSDAPRHASFVSEVAATIAEDLLDMLLA 287 G+ ++DLR L P + EA + +A R VLV D R + VSE T + L Sbjct: 644 GIDCTLVDLRYLAPLN-EAAICDIAANCRHVLVVDECRRSGSVSEAIVTALHERLGSACP 702 Query: 288 PPIRVTGFDTPYPYAQ-DKLYLPTVTRILNAA 318 R+ D P A L LP I+ AA Sbjct: 703 KLARLNAEDCFIPLADAATLPLPGKDSIVAAA 734 Lambda K H 0.319 0.136 0.389 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: 452 Number of extensions: 19 Number of successful extensions: 4 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: 324 Length of database: 761 Length adjustment: 34 Effective length of query: 290 Effective length of database: 727 Effective search space: 210830 Effective search space used: 210830 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: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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