Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate Ga0059261_0840 Ga0059261_0840 Acyl-CoA dehydrogenases
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Korea:Ga0059261_0840 Length = 375 Score = 226 bits (576), Expect = 8e-64 Identities = 136/380 (35%), Positives = 205/380 (53%), Gaps = 8/380 (2%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRK--KYAKEKGGWSRAVWGKFAEQGLLGLPFS 58 M L+EEQ +L+++ + + + + + A + G+SR +W +FAE G G+ Sbjct: 1 MPLYLNEEQTMLRDAAQQFVGEAAPVSHMRGLRDANDPTGFSRDLWKQFAEMGFTGILIP 60 Query: 59 EEDGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGS 118 + GG G G VE +V+E +G +L P+L T V L+ +AQ+ PGI+ G Sbjct: 61 DSHGGLGLGHVEAGVVLEEIGRNLSPSPFLTTAVAAVEALK---GSAQRERWFPGILAGE 117 Query: 119 KTFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRD 178 A A EK + V+ A++SG+G+ + G K V +G AD LIV ART G D Sbjct: 118 TVAALAIDEKGKHGNA--VAMKAERSGNGFRLSGAKQFVTHGHVADLLIVAARTAGSPDD 175 Query: 179 RTGVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVD 238 GV +F V DA G+T D A+ +TF V+V ADA IG+ + ++ A++ Sbjct: 176 DAGVTLFAVAKDAAGLTADPQRLADSSLASRLTFENVEVDADAVIGEVDGGRSILNALLA 235 Query: 239 DARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAM 298 RT AE++G+ ++ TV+Y+K RKQFG IGSFQ LQHRAA ++ E AR+ + Sbjct: 236 AGRTGAAAESLGVGGGAMDLTVQYLKERKQFGTLIGSFQALQHRAAHLYTELEVARAAVL 295 Query: 299 FATMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTM 358 A + DAK A++ AK G + Q+ +Q+HGGIGMT E IG Y KR + Sbjct: 296 KAQQLLDAGDAK-AGEAVSVAKAMAGLASTLAVQEGVQMHGGIGMTDEFDIGFYMKRGRV 354 Query: 359 IEQTFGDTDHHLARVSAGGG 378 + + FGD + H +++ G Sbjct: 355 LAEMFGDANFHADQLARASG 374 Lambda K H 0.318 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: 361 Number of extensions: 21 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: 380 Length of database: 375 Length adjustment: 30 Effective length of query: 350 Effective length of database: 345 Effective search space: 120750 Effective search space used: 120750 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