Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 1/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (subunit 1/2) (EC 1.3.8.1) (characterized)
to candidate CA265_RS09630 CA265_RS09630 acyl-CoA dehydrogenase
Query= BRENDA::D2RL84 (383 letters) >FitnessBrowser__Pedo557:CA265_RS09630 Length = 396 Score = 236 bits (603), Expect = 6e-67 Identities = 136/373 (36%), Positives = 215/373 (57%), Gaps = 5/373 (1%) Query: 1 MDFNLTEDQQMIKDMAAEFAEKFLAPTVEERDKAHIWDRKLIDKMGEAGFCGICFPEEYG 60 +D LT++ ++I+ A ++ +K ++P +E+ + + + LI + + G G P EYG Sbjct: 18 LDELLTDEHKLIRATARDWVKKEVSPIIEDYAQKAEFPKHLIKGLADIGAFGPTIPVEYG 77 Query: 61 GMGLDVLSYILAVEELSKVDDGTGITLSANVSLCATPIYMFGTEEQKQKYLAPIAEGTHV 120 G GLD +Y + ++E+ + D G T S SL PIY +G+EEQ++KYL +A G + Sbjct: 78 GAGLDYTAYGILMQEIERGDSGIRSTASVQGSLVMYPIYAYGSEEQRKKYLPKLASGEMM 137 Query: 121 GAFGLTEPSAGTDASAQQTTAVLKGDKYILNGSKIFITNGKEADTYVVFAMTDKSQGVHG 180 G FGLTEP G++ T G YILNG+K++I+N AD VV+A D+S + G Sbjct: 138 GCFGLTEPDHGSNPGGMVTNIKDAGSHYILNGAKMWISNAPFADIAVVWA-KDESGKIRG 196 Query: 181 ISAFILEKGMPGFRFGKIEDKMGGHTSITAELIFEDCEVPKENLLGKEGEGFKIAMETLD 240 + I+E+GM GF + K S T EL+F++ +VPKEN+ E G K + L+ Sbjct: 197 L---IVERGMEGFSTPETHHKWSLRASATGELVFDNVKVPKENIF-PEISGLKGPLGCLN 252 Query: 241 GGRIGVAAQALGIAEGALAAAVKYSKEREQFGRSISKFQALQFMMADMATKIEAARYLVY 300 R G+A ALG A A++YSKER QFG+ I FQ Q +A+M T+I + LV+ Sbjct: 253 QARYGIAWGALGAAMDCYDTALRYSKERVQFGKPIGGFQLQQKKLAEMVTEITKGQLLVW 312 Query: 301 HAAMLKNEGKPYSEAAAMAKCFASDVAMEVTTDAVQIFGGYGYTVDYPAERYMRNAKITQ 360 +LK+E + +E +MAK + ++A+++ +A Q+ GG G T +Y R+M N + Sbjct: 313 RLGVLKSENRASAEQISMAKRNSVEIALDIARNARQMLGGMGITGEYSIMRHMMNLESVV 372 Query: 361 IYEGTNQVMRIVT 373 YEGT+ + ++T Sbjct: 373 TYEGTHDIHLLIT 385 Lambda K H 0.318 0.134 0.379 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: 372 Number of extensions: 14 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: 383 Length of database: 396 Length adjustment: 30 Effective length of query: 353 Effective length of database: 366 Effective search space: 129198 Effective search space used: 129198 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