Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_012965508.1 FERP_RS05015 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2397 (379 letters) >NCBI__GCF_000025505.1:WP_012965508.1 Length = 381 Score = 294 bits (753), Expect = 2e-84 Identities = 157/377 (41%), Positives = 236/377 (62%), Gaps = 4/377 (1%) Query: 4 NEDQNAIAEMARQFAQERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSDTG 63 +E+ + E R+FA++ +KP+ ++ + +YP E + A LG+ G VPE++ G+ Sbjct: 6 SEEHKMLQEAVREFAEKEIKPYGREYDEKKQYPMEIYKKAAKLGYIGASVPEEYDGAGMD 65 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKSDFLTPLARGEQIGAFAL 123 LA A+ E D + + + + ++G +LRFG+E+QK +F+ + RGE A A+ Sbjct: 66 CLAEAIISMEFCRADSSIGSAIDLA-TLGVPMVLRFGSEEQK-EFVAKVVRGEGPSAIAV 123 Query: 124 TEPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVT-DPDAGKGGISAF 182 TEP G+D +++RTRA ++GD +V+NG KQFIT+G +V A T D GISAF Sbjct: 124 TEPDCGTDVAAMRTRAVKEGDEWVINGTKQFITNGSVGIYTVVLAKTAQVDPPHRGISAF 183 Query: 183 IVPTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGGRI 242 +V D GY+ +E K+G H DTC++A +++RVP + +GEE G+ +A R+ Sbjct: 184 LVEQDREGYEARPIE-KMGMHCHDTCEVALKNVRVPADHLIGEENRGFYQLMAFFNESRV 242 Query: 243 GIAAQAVGMARAAFEAARDYARDRETFGKPIIEHQAVAFRLADMATQIAVARQMVHHAAA 302 IAA G+A A+E A +YA++R+ FGKP+IEHQA+ F+LA+M I A+ +V AA Sbjct: 243 KIAALHTGIAIGAYERALEYAKERKAFGKPLIEHQAIQFKLAEMFKDIEAAKLLVFKAAW 302 Query: 303 LREVGRPALVEASMAKLFASEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQIYEG 362 L + G+P +S AKLFASEMA KV A+Q GGYGY ++ VER YRD RV IYEG Sbjct: 303 LIDQGKPDPALSSAAKLFASEMAVKVTYEAVQIFGGYGYSKEYDVERYYRDARVGTIYEG 362 Query: 363 TSDIQRLVISRNLGGPV 379 TS+ Q++VI+R + G + Sbjct: 363 TSEAQKMVIARRIIGKI 379 Lambda K H 0.320 0.135 0.391 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: 369 Number of extensions: 21 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: 379 Length of database: 381 Length adjustment: 30 Effective length of query: 349 Effective length of database: 351 Effective search space: 122499 Effective search space used: 122499 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: 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