Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_034275109.1 AMYHA_RS25070 acyl-CoA dehydrogenase family protein
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_000504245.1:WP_034275109.1 Length = 386 Score = 269 bits (687), Expect = 1e-76 Identities = 155/374 (41%), Positives = 229/374 (61%), Gaps = 5/374 (1%) Query: 5 EEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGY 64 EE ++R R AE+ + P A E D R+P EA++ + + GF + +P+++GG Sbjct: 13 EEHEELRAAVRALAEKEIAPHAEEVDETERYPVEALEALNKAGFSAVHIPDEYGGQGADA 72 Query: 65 LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALT 124 +A + +EE+A + S I +V N +G + ++ G++E K K L +A GA ++AL+ Sbjct: 73 IATDIVIEEVARVCASSSLIPAV-NKLGTMNVILGGSEELKHKVLGDVAGGAT-ASYALS 130 Query: 125 EPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGK--RGISAF 182 E +AGSD +S++T+A +GD++VLNG K +IT+ + V AVTDP A GISAF Sbjct: 131 EREAGSDPASMRTKAIRDGDNWVLNGTKCWITNAGESSWYTVMAVTDPDAKNPAAGISAF 190 Query: 183 IVPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRV 242 V + PG+ V E KLG S T +I FE+ +P +GE G+G K+A + L+ R Sbjct: 191 AVHAEDPGFVVGPKERKLGIKGSPTREIYFENCTIPGDRIIGEPGQGLKLAFSTLDHTRH 250 Query: 243 GIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAA 302 I AQA+G+A+ A +A DY +ER FGK I E Q V F LADMA ++ AR +V+ AAA Sbjct: 251 SIGAQALGIAQGALDATIDYVKERQQFGKAIAEFQGVQFMLADMAMKVEAARHLVYSAAA 310 Query: 303 LRDSGQ-PALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYE 361 + G +S AK FAS++A +V + A+Q GG GY DFP+ER+ RD ++ QIYE Sbjct: 311 KVERGDADKSFASSAAKTFASDVAMEVTTDAVQLFGGAGYTRDFPVERMMRDAKITQIYE 370 Query: 362 GTSDIQRMVISRNL 375 GT+ IQRMV++R L Sbjct: 371 GTNQIQRMVMARQL 384 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: 351 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: 375 Length of database: 386 Length adjustment: 30 Effective length of query: 345 Effective length of database: 356 Effective search space: 122820 Effective search space used: 122820 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