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 CA265_RS17575 CA265_RS17575 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Pedo557:CA265_RS17575 Length = 597 Score = 251 bits (642), Expect = 3e-71 Identities = 146/396 (36%), Positives = 228/396 (57%), Gaps = 27/396 (6%) Query: 6 KKYQMLKELYVSFAENEVKPLATELDEEE--RFPYETVEKMAKAGMMGIPYPKEYGGEGG 63 ++ QM+ + F EV P ++D++E + K + G++G+ P+EYGG G Sbjct: 32 EEQQMIAQTCRDFLAAEVYPNLDKIDKQEDPELMPTLLTKAGELGILGVSVPEEYGGFGK 91 Query: 64 DTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFG 123 + M V ++ + V LSAHT +G+ PI YGNE QK K++ L SGE A+ Sbjct: 92 N-FNTSMLVADVVGAGHSFAVALSAHTGIGTLPILYYGNEAQKAKYIPKLGSGEWKAAYC 150 Query: 124 LTEPNAGTDASGQQTTAVL--DGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGIS 181 LTEPN+G+DA+ +T A L DG YI+ G K++ITN DI++V A D +K ++ Sbjct: 151 LTEPNSGSDANSGKTKATLSEDGKHYIITGQKMWITNGGFADIFIVFAKIDD---DKNLT 207 Query: 182 AFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGG 241 AFIVEK G + +E KMGI+GS+T ++ F DC +P EN+L GFKIA++ L+ G Sbjct: 208 AFIVEKDFGGITMNPEEHKMGIKGSSTRQVFFNDCPVPVENMLSDRENGFKIAVNILNIG 267 Query: 242 RIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQA 301 RI ++A A+G ++ L+ + Y ER+QFGRP+SK+ +F++A++ K+ A Y+A Sbjct: 268 RIKLSAAAIGASKATLNTAINYSNERIQFGRPISKYGAIRFKIAEIASKLYAVDAANYRA 327 Query: 302 AINKD------------LGK-------PYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGY 342 N D GK + VE A+ K++ +E + VQ++GG G+ Sbjct: 328 GQNIDDTYDQLVAGGMESGKARLKSVEQFAVECAILKVWGSEALDYTVDEGVQIYGGMGF 387 Query: 343 TRDYPVERMMRDAKITEIYEGTSEVQRMVISGKLLK 378 + D P++R RDA+I I+EGT+E+ R++ +LK Sbjct: 388 SADAPMDRAYRDARINRIFEGTNEINRLLTVDMMLK 423 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: 525 Number of extensions: 25 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: 378 Length of database: 597 Length adjustment: 33 Effective length of query: 345 Effective length of database: 564 Effective search space: 194580 Effective search space used: 194580 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: 51 (24.3 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