Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate BPHYT_RS25400 BPHYT_RS25400 butyryl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__BFirm:BPHYT_RS25400 Length = 381 Score = 399 bits (1025), Expect = e-116 Identities = 205/372 (55%), Positives = 263/372 (70%), Gaps = 1/372 (0%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 T++Q I D AR+ A E + P AAE D + +P+ + +AELGF GML+PEQ+GG G Sbjct: 10 TEQQTLIRDTARRVANEIIAPTAAERDLQSAWPRSELKALAELGFLGMLIPEQYGGSGAG 69 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 L + +A E AA D +TIM VHN + I++ G + QK+R+L +A G +GAF L Sbjct: 70 ILDFCIAQHEFAAVDAGLATIMHVHNFTA-LTIVEHGTETQKQRYLPAMACGESIGAFLL 128 Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEP AGSD +SL+ AR GDHYVLNG KQFI++G AGV I FA+TD +AGKRG S FI Sbjct: 129 TEPHAGSDTASLRASARREGDHYVLNGTKQFISNGSEAGVGIAFAITDKAAGKRGASTFI 188 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243 + ++PGY V R+E KLGQH + T QI E +VP N LG EG+GY+ +A + GR+G Sbjct: 189 IDPNAPGYSVTRIESKLGQHTAHTAQIALEGYRVPAENLLGLEGDGYRTVMAGVSDGRIG 248 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IA S G+AR A +AA YARERE++G P+ + QAVAF LADMA Q+ VA Q +AA L Sbjct: 249 IAFISAGVARGALDAAVKYAREREAYGGPLTKLQAVAFDLADMAAQVDVAWQYCLHAARL 308 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 RD+G + EAS+AKLFASE+AEKVCS ALQ GGYGYL+DFP+ER RDVR+C+IYEGT Sbjct: 309 RDAGFDCIKEASIAKLFASEIAEKVCSDALQIHGGYGYLTDFPVERYLRDVRICKIYEGT 368 Query: 364 SDIQRMVISRNL 375 S IQ+++ISRNL Sbjct: 369 SHIQKLIISRNL 380 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: 395 Number of extensions: 15 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: 375 Length of database: 381 Length adjustment: 30 Effective length of query: 345 Effective length of database: 351 Effective search space: 121095 Effective search space used: 121095 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