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 200844 SO1679 acyl-CoA dehydrogenase family protein (NCBI ptt file)
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__MR1:200844 Length = 385 Score = 301 bits (771), Expect = 2e-86 Identities = 162/379 (42%), Positives = 234/379 (61%), Gaps = 4/379 (1%) Query: 1 MDLNSKKYQ-MLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYG 59 MD N + Q EL FA +E+ P A + DEE FP + ++K + G + P+ G Sbjct: 1 MDFNFNEDQRQFAELARQFATDELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60 Query: 60 GEGGDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKL 119 G G + + EELS+ C T +L+ H ++ +W + +G E +Q + PL +G+ L Sbjct: 61 GMGLSRLDASIIFEELSKGCTATTAMLTIH-NMATWMVTTWGTETLRQAWSEPLTTGQML 119 Query: 120 GAFGLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKG 179 ++ LTEP AG+DA+ QT AV DGDEY+++GSK+FI+ A + ++ VVM T ++ G KG Sbjct: 120 ASYCLTEPGAGSDAASLQTKAVPDGDEYVVSGSKMFISGAGSTELLVVMCRTGQA-GPKG 178 Query: 180 ISAFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLD 239 ISA + + G +G E KMG T + F++ R+P NLLG+EGQGF AM LD Sbjct: 179 ISAIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLD 238 Query: 240 GGRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVY 299 GGRI IA ++G AQ AL+ +Y+ ER QFG+PL+ FQ QF+LADM ++ AAR +V Sbjct: 239 GGRINIATCSVGTAQAALERASQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVR 298 Query: 300 QAAINKDLGKPYGVE-AAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKIT 358 AA D G P G AMAK FA + +V A+Q+HGGYGY R+YP+ER RD ++ Sbjct: 299 LAAFKLDSGDPEGTAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVH 358 Query: 359 EIYEGTSEVQRMVISGKLL 377 +I EGT+E+ R++I+ +LL Sbjct: 359 QILEGTNEIMRLIIARRLL 377 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: 350 Number of extensions: 20 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: 378 Length of database: 385 Length adjustment: 30 Effective length of query: 348 Effective length of database: 355 Effective search space: 123540 Effective search space used: 123540 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