Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate RR42_RS36390 RR42_RS36390 acyl-CoA dehydrogenase
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Cup4G11:RR42_RS36390 Length = 381 Score = 320 bits (820), Expect = 4e-92 Identities = 175/373 (46%), Positives = 228/373 (61%), Gaps = 3/373 (0%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQ-GLLGLPFSE 59 MDF SEEQ +L++++ L Y F++R+ + GW + W A++ GLLG F E Sbjct: 1 MDFQFSEEQSMLRDTLARYLADHYSFEARQAAIRSPAGWRASCWQALAQELGLLGAAFPE 60 Query: 60 EDGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSK 119 GG G AVE IVME G LV+EPYL TVV+GGG L GS A+ LP II G Sbjct: 61 RFGGLGGNAVEHTIVMEQFGRHLVVEPYLSTVVLGGGALLH-GSETLAASWLPAIIGGEA 119 Query: 120 TFAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDR 179 T A+A E SR+ L DV +A ++ GW +DG K VV+ A L+V+ART G +RDR Sbjct: 120 TVAWAHAEPRSRYCLHDVQASAARAQGGWRLDGHKAVVVAAPWATHLVVSARTGGSRRDR 179 Query: 180 TGVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDD 239 G+ +F + DA G+T + YPT DG AADI V V +G AL LIE + D+ Sbjct: 180 DGISLFWIARDAPGVTLQEYPTVDGSRAADIRLDNVFVPDGGLLGAEGEALTLIERLSDE 239 Query: 240 ARTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMF 299 A ALCAEA G M L TV+Y + RKQFGVPI +FQVLQHR ADM+V EQ ++ Sbjct: 240 AAVALCAEAGGAMSRMLGDTVDYARQRKQFGVPIATFQVLQHRMADMYVQLEQTVALTQV 299 Query: 300 ATMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMI 359 A M +RA A +AAK Q G++G+FVGQ ++Q+HGG+G+T E +GHYFKR+T I Sbjct: 300 AAMQVGAQPT-QRALAASAAKAQAGQAGRFVGQAAVQIHGGMGVTEELAVGHYFKRVTAI 358 Query: 360 EQTFGDTDHHLAR 372 + FG +HHL R Sbjct: 359 DLQFGSAEHHLRR 371 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: 416 Number of extensions: 24 Number of successful extensions: 4 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: 381 Length adjustment: 30 Effective length of query: 350 Effective length of database: 351 Effective search space: 122850 Effective search space used: 122850 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