Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate CCNA_01884 CCNA_01884 acyl-CoA dehydrogenase, short-chain specific
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__Caulo:CCNA_01884 Length = 382 Score = 273 bits (697), Expect = 8e-78 Identities = 158/375 (42%), Positives = 214/375 (57%), Gaps = 2/375 (0%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 M+FDLSEEQ+LLK+S DF + + + + A W + A+ G L L E+ Sbjct: 1 MNFDLSEEQQLLKDSARRYGADHGDFTAWRARVERGEAYDAASWRRMADLGWLMLNVPED 60 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120 DGG GAG ETM+V EA+G L+L P++ T VI L A + A +A + G+ +G Sbjct: 61 DGGLGAGPTETMVVAEAVGRYLMLVPFVSTGVIAPTLLT-AATEALRAHLMAGLAEGKLV 119 Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180 + A E N R+DL ++T A+ G+ + G K L+G AAD IV ART + Sbjct: 120 ISLADAEPNGRFDLNRIATRAEAVEGGFRLTGAKSHALDGGAADWFIVPARTTAADDSQD 179 Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240 GV +FLVPA+ +G+T D H A + GV V A IG L+ VD Sbjct: 180 GVSLFLVPAEIEGLTVMRSRAMDNRHNASLKLDGVVVPAANLIGGLGEGFPLLRDAVDRG 239 Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300 A AEAVG MD T+EY+KTRKQFG +G+FQ LQHRA DM +A E+ARSM A Sbjct: 240 VVARLAEAVGAMDAVREMTMEYLKTRKQFGQTLGAFQALQHRAVDMAIACEEARSMMYLA 299 Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360 T+A ER IAAAK ++G++ +VG+Q++QLHGG+G T E + HY KRL MI+ Sbjct: 300 TLALS-GAPVERRKVIAAAKARVGQTSLYVGRQAVQLHGGVGFTEELAVAHYLKRLIMID 358 Query: 361 QTFGDTDHHLARVSA 375 FG+ DHH A ++A Sbjct: 359 MAFGNADHHRAELAA 373 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: 401 Number of extensions: 19 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: 382 Length adjustment: 30 Effective length of query: 350 Effective length of database: 352 Effective search space: 123200 Effective search space used: 123200 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