Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate AZOBR_RS22365 AZOBR_RS22365 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__azobra:AZOBR_RS22365 Length = 379 Score = 320 bits (820), Expect = 4e-92 Identities = 165/373 (44%), Positives = 239/373 (64%), Gaps = 3/373 (0%) Query: 5 SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGD 64 S++ Q ++ FA+ E+ P A DE FP +T+ + A G GI +E+GG G Sbjct: 6 SEEQQAFRDTARDFAQQEMAPNAAHWDENSVFPVDTLRQAAALGFAGIYVGEEFGGSGLG 65 Query: 65 TVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGL 124 + + EELS C +T +S H ++ SW I ++GN EQ+++FL L + E ++ L Sbjct: 66 RLDAALIFEELSAACPSTAAYISIH-NMASWMIDRFGNAEQRERFLPKLTTMEHFASYCL 124 Query: 125 TEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFI 184 TEP AG+DA+ +T A GD Y+LNGSK FI+ D+YV M T + G KGIS Sbjct: 125 TEPGAGSDAASLRTRAERVGDHYVLNGSKAFISGGGTSDVYVCMVRTGEP-GPKGISCIA 183 Query: 185 VEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIG 244 VEKGTPG SFG +E K+G + TS +IFE+CR+P N +G+EG+GF+IAM LDGGR+ Sbjct: 184 VEKGTPGLSFGKQEHKLGWKSQPTSAVIFENCRVPVANRIGEEGEGFRIAMKGLDGGRLN 243 Query: 245 IAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAIN 304 IAA ++G A+ L++ V Y ER QFG+PL+ FQ QF+LADM ++ AAR ++++AA + Sbjct: 244 IAACSVGGARFCLEQAVAYTTERKQFGKPLNAFQALQFKLADMATELDAARLMLHRAAAS 303 Query: 305 KDLGKPYG-VEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEG 363 D G P AMAK FA + +V +A+QLHGGYGY ++YP+ER+ RD ++ +I EG Sbjct: 304 LDAGSPEATAHCAMAKRFATDAGFQVVNEALQLHGGYGYIKEYPIERIFRDLRVHQILEG 363 Query: 364 TSEVQRMVISGKL 376 T+E+ R++I+ L Sbjct: 364 TNEIMRVIIARHL 376 Lambda K H 0.315 0.133 0.373 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: 368 Number of extensions: 12 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: 378 Length of database: 379 Length adjustment: 30 Effective length of query: 348 Effective length of database: 349 Effective search space: 121452 Effective search space used: 121452 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 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