Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_011384980.1 AMB_RS13080 acyl-CoA dehydrogenase
Query= reanno::SB2B:6937192 (389 letters) >NCBI__GCF_000009985.1:WP_011384980.1 Length = 383 Score = 273 bits (697), Expect = 8e-78 Identities = 147/376 (39%), Positives = 227/376 (60%), Gaps = 2/376 (0%) Query: 14 EDVDMLRDAVYEFAKGEIAPLAEKVDRDNAFPNELWAKFGDMGLLGVTVAEEYGGVNMGY 73 E ++ L D + F + + P E++ D+A P E+ A+ D+GL G+++ EEYGG+ + Sbjct: 6 EILNQLLDTLSRFVRERLVPNEERIAEDDALPAEIIAEMKDLGLFGLSIPEEYGGLGLTM 65 Query: 74 LAHVVAMEEISRASASIGLSYGAHSNLCVNQIYRNGNEAQRAKYLPKLISGEHIGALAMS 133 V+ EI + S + +G ++ + I +G E Q+ KYLP+L +GE I + A++ Sbjct: 66 EEEVLCAFEIGQTSPAFRSIFGTNNGIGSQGIIIDGTEEQKQKYLPRLATGELIASFALT 125 Query: 134 EPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDAHTYVIYAKTD-LDKGPHGITAFI 192 EPNAGSD S++ ARK+GD YI+NG K +ITN P+A + + A+TD +KG GI+AFI Sbjct: 126 EPNAGSDAASLRTTARKDGDHYIVNGTKRFITNAPEASIFTLMARTDPNNKGAGGISAFI 185 Query: 193 VERGFKGFSQAQKLDKLGMRGSNTCELVFEDCEVPEENILGGL-NNGVKVLMSGLDYERV 251 VE G S + K+G +G++TC+++FED VP NI+GG+ G K M LD R+ Sbjct: 186 VEADSPGLSLGKIDKKMGQKGAHTCDVIFEDVRVPAANIIGGIEGQGFKTAMKVLDRGRL 245 Query: 252 VLSGGPLGIMTACMDIVVPYVHERVQFGKSIGEFQLVQGKLADMYTGMNAAKSYVYNVAR 311 +S +G+ + V Y ERVQFGK IGEFQLVQ LAD T AA+ V + AR Sbjct: 246 HISATCVGVSERLIRDSVKYAAERVQFGKPIGEFQLVQAMLADSRTEAYAARCMVLDAAR 305 Query: 312 ACDRGETTRKDAAGVILYAAELATKMALDAIQLLGGNGYVNEYATGRLLRDAKLYEIGAG 371 D+G +AA ++A+E ++A A+Q+ GG GY+++Y R RD +L+ I G Sbjct: 306 KKDQGINVSTEAACCKMFASEAVGRIADRAVQVHGGAGYISDYGIERFYRDVRLFRIYEG 365 Query: 372 TSEIRRMLIGRELFNE 387 T++I++++I R + + Sbjct: 366 TTQIQQLVIARNMLKD 381 Lambda K H 0.318 0.137 0.396 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: 396 Number of extensions: 16 Number of successful extensions: 3 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: 383 Length adjustment: 30 Effective length of query: 359 Effective length of database: 353 Effective search space: 126727 Effective search space used: 126727 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 (21.7 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