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 5210419 Shew_2860 acyl-CoA dehydrogenase domain-containing protein (RefSeq)
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__PV4:5210419 Length = 432 Score = 177 bits (449), Expect = 5e-49 Identities = 126/395 (31%), Positives = 206/395 (52%), Gaps = 21/395 (5%) Query: 5 SKKYQMLKELYVSFAENEVKPLAT----ELDEEERF--PYETVEKMAKA---GMMGIPYP 55 S K Q L+E ++F + + P + +++E +R+ P E AKA G+ + P Sbjct: 18 SPKVQALRERLLAFMDEHIYPNESLWEQQVEEGDRWESPAILAELKAKAKDAGLWNLFLP 77 Query: 56 KEYG--GEGGDTVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIY-QYGNEEQKQKFLRP 112 + YG G + Y E + RV + V + G+ + +YGN+EQ++++L+P Sbjct: 78 QVYGEFSPGLTNLEYAPLAEIMGRVYWASEVFNCSAPDTGNMEVLARYGNKEQQERWLQP 137 Query: 113 LASGEKLGAFGLTEPN-AGTDASGQQTTAVLDGDEYILNGSKIFITNAIAG--DIYVVMA 169 L +GE AF +TEP+ A +DA+ +T+ V DGDEY++NG K +I+ A I++VM Sbjct: 138 LLNGEIRSAFSMTEPDVASSDATNVETSIVRDGDEYVINGRKWYISGACNNHTQIHIVMG 197 Query: 170 MTDKSKGNKGI--SAFIVEKGTPGFSFGVKEKKMGIRGSAT--SELIFEDCRIPKENLLG 225 TD NK I S +V TPG K G + +E+I+++ R+P N+L Sbjct: 198 KTDPDNSNKYIQQSMILVPANTPGVKVVRPMKVFGYDDAPEGHAEVIYDNVRVPVSNMLL 257 Query: 226 KEGQGFKIAMSTLDGGRIGIAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLA 285 EG+GF+IA L GRI + +GLAQ AL++ + + R+ FG+PLSK Q+ + +A Sbjct: 258 GEGRGFEIAQGRLGPGRIHHCMRTVGLAQRALEQMCERAETRIAFGKPLSKQQSVREAIA 317 Query: 286 DMEVKVQAARHLVYQAAINKDLGKPYGVE--AAMAKLFAAETAMEVTTKAVQLHGGYGYT 343 +V+ AR L +AA D G + AM K+ A V +A+QLHGG G + Sbjct: 318 KSACEVEQARLLTLKAAAKMDQGGNKAAKDLIAMIKIVAPNMGCAVIDRAIQLHGGGGLS 377 Query: 344 RDYPVERMMRDAKITEIYEGTSEVQRMVISGKLLK 378 +D+ + + + + +G +V M + L + Sbjct: 378 QDFFLAKAYTITRSIRLADGPDQVHMMQLGRNLAR 412 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: 334 Number of extensions: 18 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: 432 Length adjustment: 31 Effective length of query: 347 Effective length of database: 401 Effective search space: 139147 Effective search space used: 139147 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