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 RR42_RS21730 RR42_RS21730 pyruvate dehydrogenase subunit beta
Query= SwissProt::Q5SLR3 (324 letters) >FitnessBrowser__Cup4G11:RR42_RS21730 Length = 338 Score = 273 bits (699), Expect = 3e-78 Identities = 149/331 (45%), Positives = 212/331 (64%), Gaps = 14/331 (4%) Query: 4 MTMVQALNRALDEEMAKDPRVVVLGEDV-------GKR---GGVFLVTEGLLQKYGPDRV 53 ++M A+N A+D+EM +DP V++LGED+ G++ GGV VT+GL K+G DR+ Sbjct: 5 LSMKLAINEAIDQEMTRDPSVIMLGEDIVGGAGADGEKDAWGGVLGVTKGLYAKHG-DRL 63 Query: 54 MDTPLSEAAIVGAALGMAAHGLRPVAEIQFADYIFPGFDQLVSQVAKLRYRSGGQFTAPL 113 +DTPLSE+A VGAA+G AA G+RP+AE+ F D++ FDQ+ +Q AK RY GG+ P+ Sbjct: 64 LDTPLSESAYVGAAIGAAACGMRPIAELMFIDFMGVCFDQIFNQAAKFRYMFGGKAETPV 123 Query: 114 VVRMPSGGGVRGGHHHSQSPEAHFVHTAGLKVVAVSTPYDAKGLLKAAIRDEDPVVFLEP 173 V+R G G R HSQ F H GLKVV STPYD KGLL AIRD DPV+F E Sbjct: 124 VIRAMVGAGFRAAAQHSQMLTPLFTHIPGLKVVCPSTPYDTKGLLIQAIRDNDPVIFCEH 183 Query: 174 KRLYRSVKEEVPEEDYTLPIGKAALRREGKDLTLIGYGTVMPEVLQAAAELAKAGVSAEV 233 K LY + EVPE Y +P G+A + R+GKD++++ YG ++ L+AAA LAK G+ AE+ Sbjct: 184 KNLY-GFEGEVPENSYAIPFGEANIVRDGKDVSIVTYGLMVHRALEAAATLAKEGIEAEI 242 Query: 234 LDLRTLMPWDYEAVMNSVAKTGRVVLVSDAPRHASFVSEVAATIAEDLLDMLLAPPIRVT 293 +DLRTL P D + V+ SV TGR+V+V +A + ++++A +A+ L A V Sbjct: 243 VDLRTLSPLDIDTVLESVEHTGRLVVVDEASPRCNIATDISAQVAQRAFGALKAGIEMVC 302 Query: 294 GFDTPYPY--AQDKLYLPTVTRILNAAKRAL 322 TP P+ A + LY+P+ I +AA++ + Sbjct: 303 PPHTPVPFSPALEDLYIPSAAHIADAARKTV 333 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: 274 Number of extensions: 11 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: 338 Length adjustment: 28 Effective length of query: 296 Effective length of database: 310 Effective search space: 91760 Effective search space used: 91760 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: 49 (23.5 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