Align Putative acyl-CoA dehydrogenase AidB; EC 1.3.99.- (characterized)
to candidate H281DRAFT_05560 H281DRAFT_05560 putative acyl-CoA dehydrogenase
Query= SwissProt::P33224 (541 letters) >FitnessBrowser__Burk376:H281DRAFT_05560 Length = 572 Score = 337 bits (864), Expect = 7e-97 Identities = 204/529 (38%), Positives = 285/529 (53%), Gaps = 15/529 (2%) Query: 3 WQTHTVFNQPIPLNNSNLYLSDGALCEAVTREGAGWDSDFLASIGQQLGTAESLELGRLA 62 + TH V NQ + N + D L AV RE A W + +++G+ G EL RLA Sbjct: 19 YSTHVVKNQAASASGFNAFDGDVILKSAVERE-APWAASRCSALGKLAGDEAVQELARLA 77 Query: 63 NVNPPELLRYDAQGRRLDDVRFHPAWHLLMQALCTNRVHNLAWEEDARSGAFVARAARFM 122 N N PEL +D G R+D V FHP+WH LM + V +LAW + F ARA Sbjct: 78 NRNLPELKTHDRYGNRIDWVEFHPSWHELMSLAWRHEVPSLAWTAKEQQPHF-ARAVLSY 136 Query: 123 LHAQVEAGSLCPITMTFAATPLLLQMLPAPFQDWTTPLLSDRYDSHLLPGGQKRGLLIGM 182 L QVE G+ CP M +A+ M + W Y+ K ++IG Sbjct: 137 LWNQVEQGTGCPTGMAYASHAGF--MAEPALKIWAEKACGTVYEFSRREVSLKPSVVIGY 194 Query: 183 GMTEKQGGSDVMSNTTRAERLEDGSYR--------LVGHKWFFSVPQSDAHLVLAQTAGG 234 MTEKQGGSD+ T A Y L GHKWF SVPQSD LA+ AG Sbjct: 195 AMTEKQGGSDLRETQTTAVYSHSAGYHGETAHWYELTGHKWFCSVPQSDGFFTLAKVAGE 254 Query: 235 LSCFFVPRFLPDGQRNAIRLERLKDKLGNRSNASCEVEFQDAIGWLLGLEGEGIRLILKM 294 ++CFF+PR LPDG N ++RLKDK GN+SNAS EVE+ + +G EG GIR IL Sbjct: 255 VTCFFLPRTLPDGSYNRFFVQRLKDKCGNKSNASSEVEYSGTMAIRVGEEGRGIREILSH 314 Query: 295 GGMTRFDCALGSHAMMRRAFSLAIYHAHQRHVFGNPLIQQPLMRHVLSRMALQLEGQTAL 354 +TR D A+GS +MR+A LA+ HA R+ FG+ L +P+M +VL+ MA+++E T L Sbjct: 315 AHLTRLDFAVGSAGLMRQALGLALNHASTRNGFGSSLADRPMMTNVLADMAVEVEAATLL 374 Query: 355 LFRLARAWDR-RADAKEALWARLFTPAAKFVICKRGMPFVAEAMEVLGGIGYCEESELPR 413 R+A+A D D ++ +AR+ TP AKF C R EA++ GG G+ EE+ + R Sbjct: 375 ALRIAKATDHIDTDEQQKAFARVATPMAKFFNCSRAPAVAYEALQCHGGNGFIEENPMAR 434 Query: 414 LYREMPVNSIWEGSGNIMCLDVLRVLNKQAGVYDLLSEAFVEVKGQDRYFDRAVRRLQQQ 473 LYRE P+NS+WEG+ N+MC+DV R + KQA + L +V+GQ FD + + Sbjct: 435 LYREAPLNSVWEGTANMMCMDVRRAMLKQASCREALIAELQDVRGQHAGFDSFIDSMGPL 494 Query: 474 LRKPAEE--LGREITHQLFLLGCGAQMLKYASPPMAQAWCQVMLDTRGG 520 L + ++ L R T + GA++L++++ + A+ + L G Sbjct: 495 LDRVVKDEFLARPATEAIARAVQGAELLRHSTSEVVDAFMKTRLTGPSG 543 Lambda K H 0.324 0.138 0.428 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: 660 Number of extensions: 33 Number of successful extensions: 5 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: 541 Length of database: 572 Length adjustment: 36 Effective length of query: 505 Effective length of database: 536 Effective search space: 270680 Effective search space used: 270680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 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