Align pimeloyl-CoA dehydrogenase small subunit (EC 1.3.1.62) (characterized)
to candidate Ac3H11_1712 Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)
Query= metacyc::MONOMER-20677 (380 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1712 Length = 371 Score = 266 bits (681), Expect = 5e-76 Identities = 158/375 (42%), Positives = 214/375 (57%), Gaps = 14/375 (3%) Query: 1 MDFDLSEEQRLLKESVEGLLKGSYDFDSRKKYAKEKGGWSRAVWGKFAEQGLLGLPFSEE 60 MDFD S++Q L+++V + Y F+ R++ GG+ RA WG+ AE GL L E Sbjct: 1 MDFDFSDDQEQLRDAVRKWVDKGYTFE-RRRATVAAGGFDRAAWGELAELGLTALTVPEA 59 Query: 61 DGGFGAGAVETMIVMEALGHSLVLEPYLPTVVIGGGFLRRAGSAAQKAAHLPGIIDGSKT 120 G G GA++ M+V E LG +VLEP + I L A ++A LP + G Sbjct: 60 HDGMGQGAIDAMVVAEELGRGMVLEP-IAQAFIASSVLSHCAPADVQSAWLPRVASGEAL 118 Query: 121 FAFAQLEKNSRWDLGDVSTTAKKSGDGWVIDGEKFVVLNGEAADTLIVTARTKGGQRDRT 180 A E+ +R+ L A + G+ + K +V G+ AD IV A+ G Sbjct: 119 VVLAYQERKARYRLDVCEAKAASAPAGYAVTATKSIVAAGDQADAFIVPAQLDGK----- 173 Query: 181 GVGVFLVPADAKGITRKGYPTQDGLHAADITFTGVQVGADAAIGDPENALELIEAVVDDA 240 + +FLV A G+T +GY TQDG AA+ VQ+ A + L +E VD Sbjct: 174 -IALFLVERSAAGVTTRGYVTQDGSRAAE-----VQLANAPATLITTDGLAALELAVDTG 227 Query: 241 RTALCAEAVGLMDESLTTTVEYIKTRKQFGVPIGSFQVLQHRAADMFVATEQARSMAMFA 300 A CAEAVG+MD+++ TVEY+ RKQFGV I SFQ L+HR ADM + E ARSM+ +A Sbjct: 228 IAATCAEAVGVMDKTVALTVEYMNQRKQFGVFIASFQALRHRVADMKMQLELARSMSYYA 287 Query: 301 TMAAEFDDAKERAGAIAAAKVQIGKSGKFVGQQSIQLHGGIGMTMEAKIGHYFKRLTMIE 360 ++ A+ RA A+A AKVQ+G+S +FVGQQS+QLHGGIG+T E HYFK+LT +E Sbjct: 288 SLKLGAPAAERRA-AMARAKVQLGQSMRFVGQQSVQLHGGIGVTDEYIGSHYFKKLTQLE 346 Query: 361 QTFGDTDHHLARVSA 375 TFGDT HHL VSA Sbjct: 347 MTFGDTLHHLGEVSA 361 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: 337 Number of extensions: 17 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: 371 Length adjustment: 30 Effective length of query: 350 Effective length of database: 341 Effective search space: 119350 Effective search space used: 119350 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