Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_035242511.1 Q366_RS19385 acyl-CoA dehydrogenase
Query= reanno::pseudo5_N2C3_1:AO356_26355 (375 letters) >NCBI__GCF_000745975.1:WP_035242511.1 Length = 604 Score = 139 bits (351), Expect = 2e-37 Identities = 110/356 (30%), Positives = 162/356 (45%), Gaps = 44/356 (12%) Query: 56 QWGGCDTGYLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASG 115 QWGG + A T E + S+ G + I +FG EQK +L + +G Sbjct: 99 QWGGQGMPFTVAAATAEYFNGANYPFMMYCSLTQGAGHL-IEQFGTQEQKNTYLKNMYTG 157 Query: 116 AMLGAFALTEPQAGSDASSLKTRARLEGDH-YVLNGCKQFITSGQNAGVV-----IVFAV 169 G LTEP AGSD +L T+A GD Y + G K FI+ G++ V ++ + Sbjct: 158 KWTGTMLLTEPDAGSDVGALTTKATPNGDGTYNIVGEKIFISGGEHDLVENIIHPVLARI 217 Query: 170 TDPSAGKRGISAFIVPT----------DSPGYSVARVEDKLGQHASDTCQILFEEVKVPV 219 AG +GIS F+VP + +E K+G H + TC + V Sbjct: 218 EGAPAGTKGISLFLVPKFRVNEDGSLGEFNDVVCTGIEHKMGIHGNSTCSLSLGAKGNCV 277 Query: 220 GNRLGEEGEGYKIALANLEGGRVGIAAQAVGMARAAFEAARDYARERSSFGKPIIE---- 275 G LGEE +G K + R+ + Q A AA+ A DYA+ R G+ ++E Sbjct: 278 GTLLGEENKGMKAMFLMMNAARLLVGVQGFACATAAYMYALDYAKNRIQ-GRNLMEIMNP 336 Query: 276 -HQAVA-FRLADMATQIAVARQMVHYAAALR-------DSGQPALVEASMAKL------- 319 QAVA FR D+ Q+ V + V AL D + A + AK Sbjct: 337 EAQAVAIFRHPDVRRQLMVMKSNVEAMRALLYFVHYCIDMSRYAATDEEKAKYQGFIEVL 396 Query: 320 ------FASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEGTSDIQRM 369 + ++ A +VCS +Q GGYG++ ++P+ ++ RDVR+ IYEGT+ IQ M Sbjct: 397 TPIAKGYVTDRAFEVCSQGMQVYGGYGFIEEYPMAQLLRDVRITLIYEGTNGIQAM 452 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: 498 Number of extensions: 24 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: 604 Length adjustment: 33 Effective length of query: 342 Effective length of database: 571 Effective search space: 195282 Effective search space used: 195282 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: 51 (24.3 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