Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate AO353_26640 AO353_26640 2-oxoisovalerate dehydrogenase
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__pseudo3_N2E3:AO353_26640 Length = 352 Score = 272 bits (696), Expect = 8e-78 Identities = 152/328 (46%), Positives = 195/328 (59%), Gaps = 21/328 (6%) Query: 4 ITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAI 63 +TM +AL +A+ L D ++FG+D+G GGVFR T+GL +++G R FD P++ES I Sbjct: 19 MTMIQALRSAMDVMLERDDNVVVFGQDVGYFGGVFRCTEGLQSKYGTSRVFDAPISESGI 78 Query: 64 LGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGI 123 +G AVGM YG RPV E+QF + YPA +Q++S A+LR R+ G P+T+R+P GGGI Sbjct: 79 VGVAVGMGAYGLRPVAEIQFADYVYPASDQIISEAARLRYRSAGEFTAPMTLRMPCGGGI 138 Query: 124 GGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY------ 177 G + HS S E + GL V P+ DA LL SI + DPV+FLEPKRLY Sbjct: 139 YGGQTHSQSIEAMFTQVCGLRTVMPSNPYDAKGLLIASIENDDPVIFLEPKRLYNGPFDG 198 Query: 178 --------WRKEALGLPVD---TGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEH 226 W K D T PL A I R G T++ YG TT + AA E Sbjct: 199 HHDRPVTPWSKHPAAQVPDGYYTVPLDLAAITRPGKDVTILTYG---TTVYVSQVAAEET 255 Query: 227 GWDLEVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEA 286 G D EVIDLR+L PLD T+ SV++TGR VVVHEA G GAE+ A + E CF+HLEA Sbjct: 256 GIDAEVIDLRSLWPLDLETIVKSVKKTGRCVVVHEATRTCGFGAELVALVQEHCFHHLEA 315 Query: 287 PVRRVTGFDVPYPPPLLERHYLPGVDRI 314 P+ RVTG+D PY P E Y PG R+ Sbjct: 316 PIERVTGWDTPY-PHAQEWAYFPGPSRV 342 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: 349 Number of extensions: 17 Number of successful extensions: 2 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: 352 Length adjustment: 28 Effective length of query: 300 Effective length of database: 324 Effective search space: 97200 Effective search space used: 97200 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 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