Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_029134232.1 A3GO_RS0115815 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >NCBI__GCF_000428045.1:WP_029134232.1 Length = 397 Score = 196 bits (498), Expect = 1e-54 Identities = 118/374 (31%), Positives = 198/374 (52%), Gaps = 6/374 (1%) Query: 3 DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGG 62 D +L+E++RM+RD A+ + + ++ P + D ++ +MGELGLLG+ + + + Sbjct: 20 DQQLTEEERMVRDTAQKYCQEQLMPRVLEANRHEHFDREIMNEMGELGLLGVTI-DGYDC 78 Query: 63 SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIG 122 + ++YV+Y L E+ D + MS+ +S+ P+ YG++ Q++++L +LA+G +G Sbjct: 79 AGLNYVSYGLIAREVERVDSGYRSAMSVQSSLVMHPIYAYGTEEQREKYLPKLATGELVG 138 Query: 123 CFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGL 182 CF LTEP GS+ ++TRA VDG + L+GSK + +N+ + + IV+A D + + Sbjct: 139 CFGLTEPDHGSDPAGMKTRARTVDGGYSLSGSKMWITNSPIADVFIVWAKDDEGV----I 194 Query: 183 SAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEG 242 F++ G + + E K +RAS T + + + +P NLL KGLA L Sbjct: 195 RGFILEKGMKGLSAPKIEGKFSLRASITGEIVMDEVFVPAENLL-PNVKGLAGPFGCLNR 253 Query: 243 GRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILH 302 R GI LG A + AL Y +R QFG+P+A +Q I LA+MQT++ L Sbjct: 254 ARYGIAWGVLGAAEDCWHRALTYTLDRKQFGRPLAANQLIQLKLANMQTEITLGLQGCLQ 313 Query: 303 AARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQI 362 RL AG S K + A + A +HGG G +++ V R+ + Sbjct: 314 LGRLFDAGQAAPEAISLMKRNNAGKALDIARIARDMHGGNGISDEFHVIRHAMNLEAVNT 373 Query: 363 YEGSSEIQRLLIAR 376 YEG+ ++ L++ R Sbjct: 374 YEGTHDVHALILGR 387 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: 347 Number of extensions: 21 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: 383 Length of database: 397 Length adjustment: 30 Effective length of query: 353 Effective length of database: 367 Effective search space: 129551 Effective search space used: 129551 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 Apr 09 2024. 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