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 AZOBR_RS31550 AZOBR_RS31550 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__azobra:AZOBR_RS31550 Length = 392 Score = 289 bits (739), Expect = 1e-82 Identities = 153/364 (42%), Positives = 238/364 (65%), Gaps = 5/364 (1%) Query: 18 FAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSR 77 F + V+P+A +L+ ++ +P E VE+M + G+ G P+EYGG G Y +E +S Sbjct: 27 FLDRHVRPVALKLEHDDTYPDEIVERMKELGLFGATIPEEYGGLGLRPSTYAKMIERISS 86 Query: 78 VCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQ 137 V + I+++H + ++ + + G EEQK FL A+GE G LTEP+ GTD + Sbjct: 87 VWMSLSGIINSHLIM-AFIVTKTGTEEQKAAFLPRFATGELRGGLALTEPDCGTDLQAIR 145 Query: 138 TTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKG--NKGISAFIVEKGTPGFSFG 195 T A DGD+Y++NGSK +ITN I G + ++ TD + +KG++ F+ EKG PGF Sbjct: 146 TVAKRDGDDYVINGSKTWITNGIQGSCFALLVKTDPTAQPRHKGMTMFLAEKG-PGFKVS 204 Query: 196 VKEKKMGIRGSATSELIFEDCRIPKENLLGK-EGQGFKIAMSTLDGGRIGIAAQALGLAQ 254 K +K+G +G ++EL+FED R+P + L+G EG+G A+S L+ GR+ +A++ +G+AQ Sbjct: 205 RKLEKLGYKGIDSAELVFEDYRVPADRLIGGVEGRGMACAISGLELGRVNVASRGVGVAQ 264 Query: 255 GALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVE 314 ALDE+VKY ++R FG+P+ + Q +LADM +V AAR LV QAA D G+ E Sbjct: 265 AALDESVKYSQQRKTFGKPIHEHQAVAMKLADMATRVSAARLLVQQAAKALDRGERCDYE 324 Query: 315 AAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISG 374 A MAKLFA+E A+E + A+++HGGYGY++++ VER+ RDA + I EGT+E+QR++I+ Sbjct: 325 AGMAKLFASEAAVENSLDAMRIHGGYGYSKEFVVERLYRDAPLLCIGEGTNEIQRIIIAK 384 Query: 375 KLLK 378 +L++ Sbjct: 385 RLIE 388 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: 341 Number of extensions: 14 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: 392 Length adjustment: 30 Effective length of query: 348 Effective length of database: 362 Effective search space: 125976 Effective search space used: 125976 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: 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