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 WP_012173167.1 AZC_RS23810 acyl-CoA dehydrogenase family protein
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_000010525.1:WP_012173167.1 Length = 564 Score = 226 bits (575), Expect = 2e-63 Identities = 140/373 (37%), Positives = 211/373 (56%), Gaps = 14/373 (3%) Query: 18 FAENEVKPLATELDEEERF-PYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELS 76 F E EV P A E + + P E + ++A+ G+ G+ P+EYGG G + EELS Sbjct: 190 FVEAEVVPHAHEWHLKNAYIPLEVIGRLAELGVFGLTIPEEYGGLGLPKEAMCVVTEELS 249 Query: 77 RVCGTTGV-ILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASG 135 R G GV L + + + I G +EQK +L LASGE L TEPN G+D + Sbjct: 250 R--GYIGVGSLGTRSEIAAELIIGGGTDEQKAHYLPKLASGEILPTAVFTEPNTGSDLAS 307 Query: 136 QQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSK-GNKGISAFIVEK--GTPGF 192 +T AV +GD Y ++G+K +IT+ + D+ ++ T+ ++ G KG+S + EK GT Sbjct: 308 LRTRAVKEGDVYKVSGNKTWITHPVRADLMTLLVRTNPAEPGYKGLSMLLAEKPRGTDED 367 Query: 193 SFGVKE------KKMGIRGSATSELIFEDCRIPKENLLGK-EGQGFKIAMSTLDGGRIGI 245 F K + +G RG E+ F+ +P LLG EGQGFK M+T + RI Sbjct: 368 PFPAKGMTGGEIEVLGYRGMKEFEIGFDGFEVPAGQLLGGVEGQGFKQLMNTFEAARIQT 427 Query: 246 AAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINK 305 AA+A+G+AQ A++ ++Y +ER+QFG+PL F ++ M V++ AR + Y AA K Sbjct: 428 AARAVGVAQAAMETGLRYAEERIQFGKPLIAFPRVADKIVMMAVEIAIARQITYFAARAK 487 Query: 306 DLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTS 365 D G+ +EA M+KL A A A+Q+HGG G+ +Y V R++ DA+I I+EG + Sbjct: 488 DEGRRTDLEAGMSKLLGARVAWAAADNALQIHGGNGFALEYQVSRLLCDARILNIFEGAA 547 Query: 366 EVQRMVISGKLLK 378 E+Q VI+ +LL+ Sbjct: 548 EIQAQVIARRLLE 560 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: 458 Number of extensions: 18 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: 378 Length of database: 564 Length adjustment: 33 Effective length of query: 345 Effective length of database: 531 Effective search space: 183195 Effective search space used: 183195 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 Apr 09 2024. 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