Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_058857486.1 AS188_RS02305 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >NCBI__GCF_001482365.1:WP_058857486.1 Length = 398 Score = 237 bits (605), Expect = 4e-67 Identities = 138/380 (36%), Positives = 202/380 (53%), Gaps = 2/380 (0%) Query: 3 DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGG 62 D +LS ++ RD R+F R I P W + +V +M +LGLLGM + +G Sbjct: 18 DADLSPEELATRDAVREFVDRRIRPEIARWYEDAHFPREIVPEMAQLGLLGMHL-HGYGC 76 Query: 63 SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIG 122 + V Y LA++E+ AGD +S+ S+ + +GS+ QK WL +A+G IG Sbjct: 77 AGRSAVEYGLAMQELEAGDSGLRTFVSVQGSLAMSAIAKHGSEEQKQRWLPGMAAGEIIG 136 Query: 123 CFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGL 182 CF LTEP AGS+ + T A G WVL G+K++ A + +A+++A D G + + Sbjct: 137 CFGLTEPTAGSDPSTMATTAVREGGEWVLTGAKRWIGLASIADVAVIWARADDGSGSERV 196 Query: 183 SAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEG 242 FLVPTDTPGF E K+ +RAS C + L+ R+P +L E GL S L Sbjct: 197 RGFLVPTDTPGFTATPIEPKLSMRASIQCDIELAGVRLPADAILPE-NPGLRGPFSCLNE 255 Query: 243 GRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILH 302 R GI ALG AR +FEAAL YA+ER+QF KP+A +Q L DM ++ +LL L Sbjct: 256 ARYGIVWGALGAARDSFEAALAYAQERIQFDKPLAAYQLTQRKLVDMALEIQKGQLLALR 315 Query: 303 AARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQI 362 RLK AG S KL +A ++C +A + GG G ++ R+ + + Sbjct: 316 LGRLKDAGRLENQMISVGKLNNCRIAIEICREARTVLGGNGVTLEHSPLRHANNLESVRT 375 Query: 363 YEGSSEIQRLLIARELANYA 382 YEG+ E+ L++ + L +A Sbjct: 376 YEGTDEVHTLILGQHLTGHA 395 Lambda K H 0.318 0.133 0.390 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: 352 Number of extensions: 14 Number of successful extensions: 3 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: 383 Length of database: 398 Length adjustment: 31 Effective length of query: 352 Effective length of database: 367 Effective search space: 129184 Effective search space used: 129184 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: 41 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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