Align short-chain acyl-CoA dehydrogenase monomer (EC 1.3.8.1) (characterized)
to candidate Ac3H11_2991 Isovaleryl-CoA dehydrogenase (EC 1.3.8.4)
Query= metacyc::MONOMER-17424 (375 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2991 Length = 396 Score = 251 bits (641), Expect = 2e-71 Identities = 132/378 (34%), Positives = 223/378 (58%), Gaps = 5/378 (1%) Query: 3 VNDEQQQIADAVRAFAQERLKPFAEQWDKDHRFPKEAIDEMAELGLFGMLVPEQWGGSDT 62 + ++ + DAVR FAQ + P A DK +FP + +M +LG+ G+ VPEQ+GG+ Sbjct: 14 LGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYGGAAM 73 Query: 63 GYVAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKEQFLTPLATGAMLGAFA 122 GY+A+ +A+EEI+ + H+++ I R GNE QK ++L+ L +G +GA A Sbjct: 74 GYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHVGALA 133 Query: 123 LTEPQAGSDASSLKTRARLEGDHYVLNGSKQFITSGQNAGVVIVFAVTDPEAGKRGISAF 182 ++EP AGSD S+K +A +G +Y+LNGSK +IT+G +A ++V+A T+PE G RG++AF Sbjct: 134 MSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVTAF 193 Query: 183 IVPTDSPGYQVARVEDKLGQHASDTCQIVFDNVQVPVANRLGAEGEGYKIALANLEGGRI 242 ++ G+ +A+ DKLG S T ++VF +V+VP N LG +G K+ ++ L+ R Sbjct: 194 LIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYERA 253 Query: 243 GIASQAVGMARAAFEVARDYANERQSFGKPLIEHQAVAFRLADMATKISVARQMVLHAAA 302 + +G+ ++ + Y ++R+ FG+ + E Q + ++ADM T + R A Sbjct: 254 VLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTVAK 313 Query: 303 L-----RDAGRPALVEASMAKLFASEMAEKVCSDALQTLGGYGYLSDFPLERIYRDVRVC 357 D R + + L+ +E A + + +Q GG GY++++PL R++RD ++ Sbjct: 314 NLDMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDAKLY 373 Query: 358 QIYEGTSDIQRMVIARNL 375 +I GTS+I+RM+I R L Sbjct: 374 EIGAGTSEIRRMLIGREL 391 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: 337 Number of extensions: 11 Number of successful extensions: 2 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: 396 Length adjustment: 30 Effective length of query: 345 Effective length of database: 366 Effective search space: 126270 Effective search space used: 126270 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