Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate GFF3988 HP15_3928 acyl-CoA dehydrogenase domain protein
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Marino:GFF3988 Length = 378 Score = 352 bits (902), Expect = e-101 Identities = 183/375 (48%), Positives = 239/375 (63%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 MDF L+EEQ++L+++V L++G Y F+ R +Y++ G+S W + E GL +PF EE Sbjct: 1 MDFRLNEEQQMLQDTVARLVRGEYSFEKRLEYSESGLGFSADFWKQLGELGLTAVPFPEE 60 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120 GGFG VE VM LG L +EPYL +VV+GGG + +AG++AQ+ L GI G Sbjct: 61 LGGFGGTGVEVQSVMTELGRGLCVEPYLQSVVLGGGLISQAGNSAQQEQWLGGIASGEIR 120 Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180 A E S ++L DV T A+KS DG+V++G K VV+ G AD L+V+ART G RD Sbjct: 121 AAVGLQEPQSFYNLNDVDTRAEKSDDGYVLNGRKAVVIGGHCADVLVVSARTSGDSRDAE 180 Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240 G+ +FL+PADA+G+ R+ YPT DG D+ VQ+G DA +GD A E+IE A Sbjct: 181 GISLFLIPADAEGVERRTYPTIDGSKGCDLFLNNVQLGTDALLGDEGKAAEVIEYQSGRA 240 Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300 +ALC EAVG M+ + T+EY+K RKQFGVPIG FQVLQHR DM EQARSMA+ A Sbjct: 241 ISALCGEAVGAMEVACDLTLEYLKQRKQFGVPIGKFQVLQHRMVDMMSELEQARSMAILA 300 Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360 A+ + ER +AAAK IG+SG+F+ +Q IQ HGGIGMT E HY KRL MI Sbjct: 301 ASVADEPQSDERRRILAAAKNVIGRSGQFISEQGIQSHGGIGMTWEYNFAHYAKRLVMIN 360 Query: 361 QTFGDTDHHLARVSA 375 GD D HL R +A Sbjct: 361 HQLGDDDFHLERYAA 375 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: 400 Number of extensions: 18 Number of successful extensions: 1 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: 378 Length adjustment: 30 Effective length of query: 350 Effective length of database: 348 Effective search space: 121800 Effective search space used: 121800 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