Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate PfGW456L13_2494 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2494 Length = 390 Score = 192 bits (488), Expect = 1e-53 Identities = 132/385 (34%), Positives = 187/385 (48%), Gaps = 12/385 (3%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLL-GLPFSE 59 M+F S+EQ +++ S EG L D + + + G+ A+W + ++ + E Sbjct: 1 MEFAFSDEQEMIRASAEGFLADVSDSAAVRAAMVSERGFDEALWQRLCQEMYWPAIHIPE 60 Query: 60 EDGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSK 119 GG G G VE I++E +G L+ P+ T + L A + QK LP I DGS Sbjct: 61 TYGGLGLGFVELTILLEQMGRRLLCSPFFATACMATPALLLAANDQQKQRWLPSIADGSV 120 Query: 120 TFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDR 179 T A N W DV T GDG+V+DG VL+G AD LI+ AR G ++ Sbjct: 121 TATLAFSSANG-WSADDVQATVVAEGDGYVLDGTLKHVLDGHGADLLIIAARQPGTTGEK 179 Query: 180 TGVGVFLVPADAKGITRKGYPTQDGLHA-ADITFTGVQVGADAAIGDPENALELIEAVVD 238 G+ +F + A+ GI R+ PT D A I G+ + AD +G+ N +E V+ Sbjct: 180 -GISLFAMSAERAGIERQMLPTMDQTRRQARIQLKGLYLEADCLLGEFGNGWSHLERVLQ 238 Query: 239 DARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAM 298 A L AE G + L +V Y++ R+QFG PI SFQ L+HRAADM + E ARS + Sbjct: 239 LACIGLAAEQTGGAQQVLDLSVAYMQERQQFGRPIASFQALKHRAADMMLQVECARSASY 298 Query: 299 FATMAAEF--------DDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIG 350 +A A+ A E A A AK Q ++ +SIQLHGG+G T E Sbjct: 299 YAACVAQEVLDPQGDPQVAAELPLAAALAKAQCSETYFSCASESIQLHGGVGFTWEYDPH 358 Query: 351 HYFKRLTMIEQTFGDTDHHLARVSA 375 YFKR E G H R+++ Sbjct: 359 LYFKRARASESFLGLPAWHRERIAS 383 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: 358 Number of extensions: 19 Number of successful extensions: 5 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: 390 Length adjustment: 30 Effective length of query: 350 Effective length of database: 360 Effective search space: 126000 Effective search space used: 126000 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