Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate Dsui_3369 Dsui_3369 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >FitnessBrowser__PS:Dsui_3369 Length = 394 Score = 198 bits (504), Expect = 2e-55 Identities = 120/374 (32%), Positives = 196/374 (52%), Gaps = 2/374 (0%) Query: 3 DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGG 62 D +LS ++R +RD AR +++ + P + D + ++GELGLLG + + +G Sbjct: 13 DDQLSAEERQVRDTARQYSQDRLLPRIVQAFRHEQTDPAIFRELGELGLLGATL-DGYGC 71 Query: 63 SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIG 122 + YV+Y L EI D +++S+ +S+ P+ +GS+A K+ L ++A+G IG Sbjct: 72 AGASYVSYGLLAREIERVDSGYRSMVSVQSSLAMYPIHAFGSEALKERLLPKMATGELIG 131 Query: 123 CFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGL 182 CF LTEP GS+ ++ +RAE V G W L G+K + +N+ + + +V+A + + Sbjct: 132 CFGLTEPNHGSDPGSMESRAEAVPGGWELTGAKMWITNSPIADVFVVWAKDGQDEDGGEI 191 Query: 183 SAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEG 242 F++ G + + KMG+RAS T + + +PE NLL + KGL + L Sbjct: 192 RGFVLEKGMKGLSAPVIQGKMGLRASVTGEIVMDKVFVPEENLL-PKVKGLKGPFACLNQ 250 Query: 243 GRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILH 302 R GI ALG A A + AA Y +R QFG+P+A +Q + LADMQT++ L Sbjct: 251 ARYGIAWGALGAAEACWHAARQYTLDRPQFGRPLAANQLVQKKLADMQTEIALGLQGCLR 310 Query: 303 AARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQI 362 RLK G S K + A ++ A +HGG G +++ V R+ + + Sbjct: 311 LGRLKDEGKDAPEMTSLLKRNSCGKALEIARTARDMHGGNGISDEFHVVRHMLNLEVVNT 370 Query: 363 YEGSSEIQRLLIAR 376 YEG+ +I L++ R Sbjct: 371 YEGTHDIHALILGR 384 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: 345 Number of extensions: 18 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: 394 Length adjustment: 30 Effective length of query: 353 Effective length of database: 364 Effective search space: 128492 Effective search space used: 128492 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 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