Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_005816049.1 DHAF_RS14315 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_000021925.1:WP_005816049.1 Length = 389 Score = 380 bits (977), Expect = e-110 Identities = 190/372 (51%), Positives = 261/372 (70%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 T++Q + R F +E + P AA D H FP + +M ELG G+ +PE++GG + Sbjct: 6 TEDQKMMRKMVRDFVEEEVIPQAAHTDETHEFPLALVHKMRELGLLGIPIPEEYGGAGSD 65 Query: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 + +Y +ALEEIA G + + IM+VH ++G PI FGN++QK+++L LA G MLGAFAL Sbjct: 66 FTSYTLALEEIARGCASTAVIMAVHTTLGTFPIYYFGNEEQKQKYLPKLAKGEMLGAFAL 125 Query: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TEP +GSDASSL T A+ GDHYV+NG K+FI++ AG+ V A TD + G RGI+AF+ Sbjct: 126 TEPNSGSDASSLVTTAKRRGDHYVINGSKRFISNTGYAGIYTVLASTDRTKGSRGITAFL 185 Query: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243 V D+PG + + E K+G H S T +++FED+ VPV NRLGEEG+G+KIA+A L+ GR+G Sbjct: 186 VDADTPGLIIGKKEKKMGLHGSSTRELIFEDMVVPVENRLGEEGQGFKIAMALLDDGRIG 245 Query: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 I +Q+VG+A+AAFEAA YA+ER F + I+ Q + F LADMA Q+ AR +V+ AA Sbjct: 246 IGAQAVGIAQAAFEAALAYAQERVQFKQEIMNFQGIQFMLADMAAQLEAARLLVYQAAVR 305 Query: 304 RDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 R G P EASMAKLFASEMA KV + A+Q GGYGY ++P+ER RD ++ QIYEGT Sbjct: 306 RVEGVPYSKEASMAKLFASEMAVKVTNDAMQIFGGYGYTREYPIERYLRDAKITQIYEGT 365 Query: 364 SDIQRMVISRNL 375 + IQR+VI+++L Sbjct: 366 NQIQRIVIAKHL 377 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: 352 Number of extensions: 13 Number of successful extensions: 1 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: 389 Length adjustment: 30 Effective length of query: 345 Effective length of database: 359 Effective search space: 123855 Effective search space used: 123855 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