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 GFF1029 HP15_1008 acyl-CoA dehydrogenase domain protein
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Marino:GFF1029 Length = 383 Score = 266 bits (680), Expect = 7e-76 Identities = 150/378 (39%), Positives = 214/378 (56%), Gaps = 1/378 (0%) Query: 1 MDLNSKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGG 60 + ++ ++ M ++ + E EV P ++ P E + AGM+ + P+E+GG Sbjct: 3 VSVDKEELAMFRDSVIKVLEKEVTPHYEAWEKSGLVPRELWNTLGNAGMLCVDVPEEWGG 62 Query: 61 EGGDTVGYIMAVEELSRV-CGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKL 119 G ++ EEL+R+ G + H+ + + + GNEEQ+Q++L L SGE + Sbjct: 63 IGAPFQFSVVVGEELARMGFGALSTNVMVHSDIVAPYLSHMGNEEQRQQWLPKLVSGEAV 122 Query: 120 GAFGLTEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKG 179 GA +TEP AG+D +T+AV DGDEYILNGSK FITN D+ +V A TD G +G Sbjct: 123 GAIAMTEPGAGSDLQAIRTSAVKDGDEYILNGSKTFITNGQHADMVIVAAKTDPKAGARG 182 Query: 180 ISAFIVEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLD 239 IS F+V+ PGFS G K+G TSEL F D RIP LLG+EGQGF M L Sbjct: 183 ISLFLVDTSLPGFSKGRNLDKIGQHSGDTSELFFSDMRIPASALLGEEGQGFVYLMKELP 242 Query: 240 GGRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVY 299 R+ I A + A+G+LD T+ Y +ER FG+ L++ QNT+F++A ME + + V Sbjct: 243 RERLVIGALGVAAARGSLDLTIAYAQERELFGQKLAQLQNTRFEIARMETDYRVNKAFVD 302 Query: 300 QAAINKDLGKPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITE 359 Q DLG+ A+MAK A E V +QL GGYGYT +YP+ R DA++ Sbjct: 303 QCIDQYDLGELDAPTASMAKYSATEMQCRVADGCLQLFGGYGYTTEYPISRAFIDARVQR 362 Query: 360 IYEGTSEVQRMVISGKLL 377 IY GTSEV + +I+ +L Sbjct: 363 IYGGTSEVMKEIIARSVL 380 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: 359 Number of extensions: 16 Number of successful extensions: 2 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: 383 Length adjustment: 30 Effective length of query: 348 Effective length of database: 353 Effective search space: 122844 Effective search space used: 122844 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