Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_037575735.1 BS73_RS23895 acyl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_000744815.1:WP_037575735.1 Length = 385 Score = 305 bits (780), Expect = 2e-87 Identities = 162/373 (43%), Positives = 236/373 (63%), Gaps = 2/373 (0%) Query: 4 TEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63 +EE +RD R AE ++ PFAAE D + RFPREA+D + + VPE++GG Sbjct: 13 SEEHEMLRDTVRSLAEAKIAPFAAEVDEQARFPREALDALVANDLHAVHVPEEYGGAGAD 72 Query: 64 YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123 LA + +EE++ + S I +V N +G +P++ G +E KAK+L PLA G + ++ L Sbjct: 73 ALATVLVIEEVSRVCVSSSLIPAV-NKLGSLPVILSGGEELKAKYLAPLARGEAMFSYCL 131 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 +EP AGSDA+ +KTRA +GD +VLNG K++IT+ + V AVTDP +GISAF+ Sbjct: 132 SEPDAGSDAAGMKTRAVRDGDAWVLNGVKRWITNAGESEYYTVMAVTDPEKRSKGISAFV 191 Query: 184 VPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRVG 243 V G S E KLG S T ++ F+++++P +GEEG G+ A+ L+ R+ Sbjct: 192 VEKSDEGVSFGAPEKKLGIKGSPTREVYFDNVRIPADRMIGEEGTGFATAMKTLDHTRIT 251 Query: 244 IAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 IAAQA+G+A+ A + A+ Y +ER FGKPI + Q V F LADMA +I ARQ+ + AAA Sbjct: 252 IAAQALGVAQGALDYAKGYVQERKQFGKPIGDFQGVQFMLADMAMKIEAARQLTYAAAAK 311 Query: 304 RDSGQPALV-EASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEG 362 + L + AK +AS++A V + A+Q LGGYGY D+PLER+ RD ++ QIYEG Sbjct: 312 SERVDSDLTFFGAAAKCYASDVAMAVTTDAVQLLGGYGYTRDYPLERMMRDAKITQIYEG 371 Query: 363 TSDIQRMVISRNL 375 T+ +QR+V++RNL Sbjct: 372 TNQVQRIVMARNL 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: 341 Number of extensions: 20 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: 385 Length adjustment: 30 Effective length of query: 345 Effective length of database: 355 Effective search space: 122475 Effective search space used: 122475 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