Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate AZOBR_RS31550 AZOBR_RS31550 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__azobra:AZOBR_RS31550 Length = 392 Score = 270 bits (690), Expect = 5e-77 Identities = 154/376 (40%), Positives = 235/376 (62%), Gaps = 8/376 (2%) Query: 5 DEQLQ-ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 DEQ + I D+ +F ++P A + + + +P E + M ELG FG +PE++GG Sbjct: 14 DEQDRLILDSVDRFLDRHVRPVALKLEHDDTYPDEIVERMKELGLFGATIPEEYGGLGLR 73 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 YA +E I++ + S I++ H + + + K G ++QK FL A+G + G AL Sbjct: 74 PSTYAKMIERISSVWMSLSGIINSHLIMAFI-VTKTGTEEQKAAFLPRFATGELRGGLAL 132 Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKR--GISA 181 TEP G+D +++T A+ +GD YV+NG K +IT+G + TDP+A R G++ Sbjct: 133 TEPDCGTDLQAIRTVAKRDGDDYVINGSKTWITNGIQGSCFALLVKTDPTAQPRHKGMTM 192 Query: 182 FIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRL--GEEGEGYKIALANLEG 239 F+ PG+KV+R +KLG D+ +++FED +VP A+RL G EG G A++ LE Sbjct: 193 FLAEK-GPGFKVSRKLEKLGYKGIDSAELVFEDYRVP-ADRLIGGVEGRGMACAISGLEL 250 Query: 240 GRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHY 299 GRV +AS+ VG+A+AA + + Y+++R++FGKPI EHQAVA +LADMAT+++ AR +V Sbjct: 251 GRVNVASRGVGVAQAALDESVKYSQQRKTFGKPIHEHQAVAMKLADMATRVSAARLLVQQ 310 Query: 300 AAALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQI 359 AA D G+ EA MAKLFASE A + A++ GGYGY +F +ER+YRD + I Sbjct: 311 AAKALDRGERCDYEAGMAKLFASEAAVENSLDAMRIHGGYGYSKEFVVERLYRDAPLLCI 370 Query: 360 YEGTSDIQRMVISRNL 375 EGT++IQR++I++ L Sbjct: 371 GEGTNEIQRIIIAKRL 386 Lambda K H 0.319 0.134 0.389 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: 320 Number of extensions: 10 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: 375 Length of database: 392 Length adjustment: 30 Effective length of query: 345 Effective length of database: 362 Effective search space: 124890 Effective search space used: 124890 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 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