Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate 201539 SO2395 acyl-CoA dehydrogenase family protein (NCBI ptt file)
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__MR1:201539 Length = 585 Score = 144 bits (364), Expect = 5e-39 Identities = 118/386 (30%), Positives = 181/386 (46%), Gaps = 73/386 (18%) Query: 42 EKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYG 101 ++ ++ G +G+ E+GG G + ++ V+E++ + + T+ + I +G Sbjct: 85 DQYSQGGWVGLCGEPEFGGMGMPKMLGVL-VDEMAYSACNAFTLYGSLTAGAALCINAHG 143 Query: 102 NEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQTTAVLDGD-EYILNGSKIFITNA- 159 +E KQ +L L SGE GA +TEP AG+D +T AV D Y ++GSKIFIT Sbjct: 144 SEVLKQAYLPKLYSGEWAGAMDMTEPQAGSDLRNIRTRAVPQEDGSYAISGSKIFITGGD 203 Query: 160 ---IAGDIYVVMAMTDKSKGNKGISAFIVEK----------GTPGFSFGVKEKKMGIRGS 206 I++V+A +SKG IS F+V K GT G S G E KMG++GS Sbjct: 204 HDLTENVIHLVLAKLPESKG---ISLFLVPKITVNKDGCLGGTNGVSVGSIEHKMGLKGS 260 Query: 207 ATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQALGLAQGALDETVKYVKE 266 AT + F++ K L+G+ +G + ++ R+ I Q LG AQ A Y KE Sbjct: 261 ATCVMNFDEA---KGYLIGEPNRGLVCMFTMMNYERLAIGIQGLGSAQAAYQMATDYAKE 317 Query: 267 RVQ----------------------------------FGRPLSKFQNTQFQLADM---EV 289 R Q GR LS F Q LA +V Sbjct: 318 RSQGVAAGGSPTGSDSDPIIVHGDVRRMLLTIRAMTEAGRALSVFTGKQLDLAKYAQDDV 377 Query: 290 KVQAARHLVYQAAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVE 349 K +AAR++ G+ +AK F + ++ T A Q+ GG+GY R+ VE Sbjct: 378 KAKAARYV--------------GLLTPVAKAFLTDRGLDATIMAQQVFGGHGYIRETGVE 423 Query: 350 RMMRDAKITEIYEGTSEVQRMVISGK 375 +++RD +I +IYEGT+ +Q + G+ Sbjct: 424 QLVRDTRIAQIYEGTNGIQAIDFLGR 449 Lambda K H 0.315 0.133 0.373 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: 491 Number of extensions: 35 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: 378 Length of database: 585 Length adjustment: 33 Effective length of query: 345 Effective length of database: 552 Effective search space: 190440 Effective search space used: 190440 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: 42 (22.0 bits) S2: 51 (24.3 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