Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_043536562.1 SACCYDRAFT_RS16135 acyl-CoA dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_26355 (375 letters) >NCBI__GCF_000244975.1:WP_043536562.1 Length = 383 Score = 278 bits (711), Expect = 2e-79 Identities = 149/373 (39%), Positives = 220/373 (58%), Gaps = 2/373 (0%) Query: 4 TEEQTQIRDMARQFAQERLKPFAAEWDREHRFPREAIAEMAELGFFGMLVPEQWGGCDTG 63 TEE +RD+AR F + L P A W R+ RE + E+G + VPE +GG G Sbjct: 12 TEELDDVRDLARTFCRNELAPHQARWARQKHIDREVWTKAGEVGLLALSVPETYGG-GGG 70 Query: 64 YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123 A+ L E A G + ++VHN + +L + ++E+K ++L LASG +GA A+ Sbjct: 71 TFAHEAVLYEEQARSGDSAWGVTVHNGIVAHYLLAYASEEKKREWLPKLASGEYVGAIAM 130 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEP GSD ++ TRA +GDHYV+NG K FIT+G A +V+V TDP AG RG+S + Sbjct: 131 TEPGTGSDLQAISTRAVRDGDHYVVNGAKTFITNGGLADLVVVAVKTDPDAGARGVSLIV 190 Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEEVKVPVGNRLG-EEGEGYKIALANLEGGRV 242 V T +PG+ RV DK+G H DT ++ F++V+VP N LG EEG+G+ + L R+ Sbjct: 191 VETSTPGFRRGRVLDKVGMHGQDTAELFFDDVRVPAENLLGDEEGQGFVQLMQQLPQERL 250 Query: 243 GIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAA 302 IA AV +A E DY +ER++FG+P+ Q + LA+ AT+ AVAR + Sbjct: 251 IIAITAVAGMESAIEQTIDYTKERTAFGRPLFGFQNTKYTLAEAATEAAVARAFLDQCIE 310 Query: 303 LRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEG 362 G+ + A+M KL+++E KV +Q GGYGY+ ++P+ R + DVRV +I+ G Sbjct: 311 RHLRGELDVQGAAMVKLWSTERVNKVVDDCVQLFGGYGYMTEYPIARAWADVRVSRIFGG 370 Query: 363 TSDIQRMVISRNL 375 T++I + +ISR L Sbjct: 371 TNEIMKDIISRTL 383 Lambda K H 0.320 0.134 0.388 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: 335 Number of extensions: 13 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: 375 Length of database: 383 Length adjustment: 30 Effective length of query: 345 Effective length of database: 353 Effective search space: 121785 Effective search space used: 121785 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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