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 5208389 Shew_0901 transketolase, central region (RefSeq)
Query= SwissProt::Q5SLR3 (324 letters) >FitnessBrowser__PV4:5208389 Length = 763 Score = 184 bits (466), Expect = 8e-51 Identities = 121/332 (36%), Positives = 185/332 (55%), Gaps = 20/332 (6%) Query: 6 MVQALNRALDEEMAKDPRVVVLGEDVGKRGGVFLVTEGLLQKYGPDRVMDTPLSEAAIVG 65 M + +N L E MA+ +VV GEDVGK+GGV+ VT L++++GP+RV++T L E +I+G Sbjct: 401 MGKLINMTLTELMARQQNIVVCGEDVGKKGGVYHVTSRLVERFGPNRVINTLLDETSILG 460 Query: 66 AALGMAAHGLRPVAEIQFADYIFPGFDQLVSQVAKLRYRSGGQFTAPLVVRMPSGGGVR- 124 A+GMA +GL P+ EIQF Y+ DQ+ + A L + S GQF+ P+V+R+ G + Sbjct: 461 LAIGMAHNGLLPIPEIQFLAYVHNAEDQIRGEAATLPFFSNGQFSNPMVIRIAGLGYQKG 520 Query: 125 -GGHHHSQSPEAHFVHTAGLKVVAVSTPYDAKGLLKAAIR----DEDPVVFLEPKRLY-- 177 GGH H+ + A F GL + S DA G+L+ +R ++ V+FLEP LY Sbjct: 521 FGGHFHNDNSLAVFRDIPGLILACPSNGADAMGMLRECVRLAEQEQRLVIFLEPIALYMT 580 Query: 178 RSVKEE----------VPEEDYTLPIGKAALRREGKDLTLIGYGTVMPEVLQAAAELAKA 227 R + EE E+ LP G+ + +GK L ++ YG QA EL+K Sbjct: 581 RDLHEEGDGLWSHDYCPQEKAKALPYGELGVYGKGKTLAILSYGNGYYLSRQAERELSKL 640 Query: 228 GVSAEVLDLRTLMPWDYEAVMNSVAKTGRVVLVSDAPRHASFVSEVAATIAEDLLDMLLA 287 G+ V+DLR L+P + EA++ +V++ +++V + R S VSE T + L L Sbjct: 641 GIDCRVIDLRYLIPLNEEAIIAAVSECEHLLIVDECRRSGS-VSEAIVTCVHERLGDLAP 699 Query: 288 PPIRVTGFDTPYPYAQ-DKLYLPTVTRILNAA 318 R+T D P A+ L LP+ ++I+ AA Sbjct: 700 QMARLTAEDCFIPLAEAATLPLPSRSQIVEAA 731 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: 447 Number of extensions: 16 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: 324 Length of database: 763 Length adjustment: 34 Effective length of query: 290 Effective length of database: 729 Effective search space: 211410 Effective search space used: 211410 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