Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate PP_4402 PP_4402 branched-chain alpha-keto acid dehydrogenase complex, beta subunit
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Putida:PP_4402 Length = 339 Score = 273 bits (699), Expect = 3e-78 Identities = 155/328 (47%), Positives = 196/328 (59%), Gaps = 21/328 (6%) Query: 4 ITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAESAI 63 +TM +AL +A+ L D +++G+D+G GGVFR T+GL ++G R FD P++ES I Sbjct: 6 MTMIQALRSAMDVMLERDDNVVVYGQDVGYFGGVFRCTEGLQNKYGKSRVFDAPISESGI 65 Query: 64 LGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYGGGI 123 +GTAVGM YG RPVVE+QF + YPA +Q+VS +A+LR R+ G PLT+R+P GGGI Sbjct: 66 VGTAVGMGAYGLRPVVEIQFADYFYPASDQIVSELARLRYRSAGEFIAPLTLRMPCGGGI 125 Query: 124 GGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY------ 177 G + HS S E + GL V P+ DA LL SI DPV+FLEPKRLY Sbjct: 126 YGGQTHSQSPEAMFTQVCGLRTVMPSNPYDAKGLLIASIECDDPVIFLEPKRLYNGPFDG 185 Query: 178 --------WRKEALGLPVD---TGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAAAEH 226 W K D T PL A I R G T++ YG TT A AA E Sbjct: 186 HHDRPVTPWSKHPHSAVPDGYYTVPLDKAAITRPGNDVTVLTYG---TTVYVAQVAAEES 242 Query: 227 GWDLEVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYHLEA 286 G D EVIDLR+L PLD T+ SV++TGR VVVHEA G GAE+ + + E CF+HLEA Sbjct: 243 GVDAEVIDLRSLWPLDLDTIVESVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHLEA 302 Query: 287 PVRRVTGFDVPYPPPLLERHYLPGVDRI 314 P+ RVTG+D PY P E Y PG R+ Sbjct: 303 PIERVTGWDTPY-PHAQEWAYFPGPSRV 329 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: 348 Number of extensions: 14 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: 339 Length adjustment: 28 Effective length of query: 300 Effective length of database: 311 Effective search space: 93300 Effective search space used: 93300 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