Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate AO356_01580 AO356_01580 isovaleryl-CoA dehydrogenase
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01580 Length = 387 Score = 273 bits (698), Expect = 6e-78 Identities = 140/366 (38%), Positives = 227/366 (62%) Query: 10 IADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDTGYVAYAM 69 + D V+AF + L P A Q D D+ FP + + ++GL G+ VPE++GG+ GY+A+ + Sbjct: 17 LRDQVQAFVKAELAPRAAQIDIDNLFPADMWRKFGDMGLLGITVPEEYGGAGLGYLAHVV 76 Query: 70 ALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFALTEPQAG 129 A+EEI+ G + + H+++ I R GN +QK ++L L +G +GA A++EP AG Sbjct: 77 AMEEISRGSASVALSYGAHSNLCVNQINRNGNHEQKTKYLPKLISGEHIGALAMSEPNAG 136 Query: 130 SDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAFIVPTDSP 189 SD S+K RA GDHYVLNGSK +IT+G +A +++A TD E G GI+AFIV D Sbjct: 137 SDVVSMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLEKGPHGITAFIVERDWK 196 Query: 190 GYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRIGIASQAV 249 G+ + DKLG S+TC++ FD+V+VP N LGA G K+ ++ L+ R+ ++ Sbjct: 197 GFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGALNGGVKVLMSGLDYERVVLSGGPT 256 Query: 250 GMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAALRDAGRP 309 G+ +A ++ Y ++R+ FG+ + E Q + ++ADM T+++ +R + A + G Sbjct: 257 GIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNASRAYLYAVAQACERGET 316 Query: 310 ALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRM 369 +A+ L+++E A ++ DA+Q LGG GY+++FP R+ RD ++ +I GTS+I+RM Sbjct: 317 TRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPAGRLLRDAKLYEIGAGTSEIRRM 376 Query: 370 VIARNL 375 +I R L Sbjct: 377 LIGREL 382 Lambda K H 0.319 0.134 0.382 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: 302 Number of extensions: 11 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: 387 Length adjustment: 30 Effective length of query: 345 Effective length of database: 357 Effective search space: 123165 Effective search space used: 123165 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 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