Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate 201059 SO1897 isovaleryl-CoA dehydrogenase (NCBI ptt file)
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__MR1:201059 Length = 389 Score = 269 bits (688), Expect = 8e-77 Identities = 143/366 (39%), Positives = 218/366 (59%) Query: 10 ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAM 69 + DA FAQ + P AA+ D ++ FP E + +G G+ VPE++GG + GYLA+ + Sbjct: 19 LRDAVHDFAQHEIAPIAAKVDHDNAFPNEIWPVLGGMGLLGVTVPEEYGGANMGYLAHVV 78 Query: 70 ALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAG 129 A+EEI+ + H+++ I + GN QK ++L L SG +GA A++EP AG Sbjct: 79 AMEEISRASASIGLSYGAHSNLCVNQINRNGNAAQKAKYLPKLVSGEHIGALAMSEPNAG 138 Query: 130 SDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSP 189 SD S+K AR GD Y+LNG K +IT+G +A +++A TD + G GI+AFIV Sbjct: 139 SDVVSMKLHARKEGDRYILNGNKMWITNGPDANTYVIYAKTDLTKGAHGITAFIVERGFK 198 Query: 190 GYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSV 249 G+ A+ DKLG S+TC+++FEDV+VP N LG G K+ ++ L+ RV ++ + Sbjct: 199 GFSQAQKLDKLGMRGSNTCELVFEDVEVPEENILGGLNNGVKVLMSGLDYERVVLSGGPL 258 Query: 250 GMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKP 309 G+ A + Y ERE FGK I E Q V +LADM T + A+ V+ A D G+ Sbjct: 259 GIMNACMDIVVPYIHEREQFGKSIGEFQLVQGKLADMYTGMNAAKAYVYSVAKSCDRGET 318 Query: 310 ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRM 369 +A+ A L+++E+A K+ A+Q LGG GY++++ R+ RD ++ +I GTS+I+RM Sbjct: 319 TRKDAAGAILYSAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAGTSEIRRM 378 Query: 370 VISRNL 375 +I R L Sbjct: 379 LIGREL 384 Lambda K H 0.319 0.134 0.389 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: 319 Number of extensions: 12 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: 375 Length of database: 389 Length adjustment: 30 Effective length of query: 345 Effective length of database: 359 Effective search space: 123855 Effective search space used: 123855 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 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