Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate Dsui_2302 Dsui_2302 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2996 (376 letters) >FitnessBrowser__PS:Dsui_2302 Length = 597 Score = 131 bits (329), Expect = 6e-35 Identities = 117/371 (31%), Positives = 165/371 (44%), Gaps = 43/371 (11%) Query: 37 KDAHQGLAALGAYGICVPEEFGGANLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAIL 96 K+A+ A G + EFGG L L V E + + S +T + A L Sbjct: 79 KEAYTQFAENGWTALACSPEFGGQGLPKLISTAVNEMWKSANMAFSLCPMLTTGAIEA-L 137 Query: 97 MRYGNAQQKRDWLTPLARGEMLGAFCLTEPHVGSDASALRTTAVKQGD-EYVINGVKQFI 155 M G+ K+ +L + GE G LTEP GSD +A+RT A QGD Y I G K FI Sbjct: 138 MTAGSDALKQKFLPKMVSGEWTGTMNLTEPSAGSDLAAVRTRAEPQGDGSYKIFGQKIFI 197 Query: 156 TSGKNGQ----VAIVIA-VTDKGAGKKGMSAFLVP-----------TNNPGYVVARLEDK 199 T G + V +V+A + + G KG+S F+VP N Y V+ +E K Sbjct: 198 TYGDHNMTENIVHLVLARLPNAPEGVKGISLFVVPKFMVKDDGSLGERNDAYCVS-IEHK 256 Query: 200 LGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIALGALEGGRIGIAAQSVGMARSAFDAA 259 LG H+S TA + F + L+G E G + + R + + V +A A+ A Sbjct: 257 LGIHASPTAVMAFGDHGGAVGYLVGEENRGLEYMFIMMNAARFAVGMEGVALAERAYQQA 316 Query: 260 LAYSKERESFGT----------AIFNHQAVGFRLADCATQIEAARQLIWHAAALRDAGKP 309 + Y+K+R GT +I H V L +Q EAAR L + AA DA K Sbjct: 317 VWYAKDRIQ-GTELGVRGGPKVSILKHPDVRRLLMSMRSQTEAARALAYVVAAAMDAAKH 375 Query: 310 CLKEAAMA-------------KLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDVRV 356 EA A K ++EM+ V S +Q GG G + + + RD R+ Sbjct: 376 HPDEAVRAANQAFADLMIPVVKGHSTEMSIEVASEGVQVHGGMGFIEETGAAQHLRDARI 435 Query: 357 CQIYEGTSDVQ 367 IYEGT+ +Q Sbjct: 436 TAIYEGTTAIQ 446 Lambda K H 0.319 0.134 0.396 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: 499 Number of extensions: 26 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: 376 Length of database: 597 Length adjustment: 33 Effective length of query: 343 Effective length of database: 564 Effective search space: 193452 Effective search space used: 193452 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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