Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_025764976.1 X939_RS0119550 acyl-CoA dehydrogenase
Query= reanno::ANA3:7024494 (389 letters) >NCBI__GCF_000566685.1:WP_025764976.1 Length = 387 Score = 291 bits (745), Expect = 2e-83 Identities = 153/371 (41%), Positives = 220/371 (59%) Query: 14 EEVDMLRDAVQDFAKHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPEEYGGANMGY 73 E ++++ V+DFA I P + D FP E++ LG +GL+G+ VPE+YGGA +GY Sbjct: 15 ENCRLIQETVRDFALKNIQPHIMEWDESQHFPTEVFHSLGELGLMGMLVPEQYGGAGLGY 74 Query: 74 LAHVVAMEEISRASASIGLSYGAHSNLCVNQINRNGNAEQKAKYLPKLVSGEHIGALAMS 133 ++ A+ +S+ SIGLS AH++LC N I GN +QK KYLPKL SGE IGA ++ Sbjct: 75 QEYITAIIALSKVDPSIGLSMAAHNSLCTNHILMFGNEDQKNKYLPKLASGEWIGAWGLT 134 Query: 134 EPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKGAHGITAFIV 193 EPN GSD +MK A ++G+ +ILNG K +ITNG V+ +T HG TAFIV Sbjct: 135 EPNTGSDAGNMKTTAVRDGEDWILNGAKNFITNGQSGRVAVVITRTGEPGDKHGATAFIV 194 Query: 194 ERGFKGFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMSGLDYERVVL 253 E G GF+ +K +KLGMR S T EL+FED + + LG + G + LD R+ + Sbjct: 195 EHGTHGFTSGRKENKLGMRASETVELLFEDCRISDSQRLGQIGEGFIQSLKILDGGRISI 254 Query: 254 SGGPLGIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKAYVYSVAKSC 313 + +G + + Y ER QFGK+I FQ + KLADMYT + A+ + K Sbjct: 255 AALGVGTALGAYEAALAYSKERHQFGKAISSFQGIAFKLADMYTDIQASTLLTFQAGKEK 314 Query: 314 DRGETTRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAGTS 373 D G+ A A +S+E A ++A +A+Q+ GG G+ +Y + RD+KL IG GTS Sbjct: 315 DLGQKVSLSGAVAKYHSSETAVRVATEAVQIYGGYGFTKDYPAEKFYRDSKLCTIGEGTS 374 Query: 374 EIRRMLIGREL 384 EI++M+I +E+ Sbjct: 375 EIQKMVISKEI 385 Lambda K H 0.316 0.135 0.388 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: 370 Number of extensions: 15 Number of successful extensions: 1 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: 389 Length of database: 387 Length adjustment: 30 Effective length of query: 359 Effective length of database: 357 Effective search space: 128163 Effective search space used: 128163 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 (21.6 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