Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate N515DRAFT_0941 N515DRAFT_0941 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >FitnessBrowser__Dyella79:N515DRAFT_0941 Length = 385 Score = 255 bits (651), Expect = 2e-72 Identities = 135/373 (36%), Positives = 218/373 (58%), Gaps = 2/373 (0%) Query: 5 EEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTGY 64 EE +R+ FAE+ + P A + D ++ FP + + E+G GM +PE +GG GY Sbjct: 8 EELDLLRESVHAFAEKEIAPRATQIDHDNVFPADLWRKFGEMGLLGMTIPEAYGGTGLGY 67 Query: 65 LAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFALT 124 LA+ + +EEI+ G+ H+++ + GN+EQ+ K++ L SG +GA A++ Sbjct: 68 LAHMVAMEEISRASGSVGLSYGAHSNLCVQNLFHNGNEEQRRKYIPRLCSGEYVGALAMS 127 Query: 125 EPQAGSDA-SSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPS-AGKRGISAF 182 EP AGSD S+ +A L GD +V NG K +IT+G +A V++V+ T P AG R ++AF Sbjct: 128 EPGAGSDVVGSMSCKAELRGDVWVANGTKMWITNGPDADVLLVYMRTAPRPAGSRCMTAF 187 Query: 183 IVPTDSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRV 242 I+ G+S A+ DKLG S+TC+++FED ++P N +GE EG ++ ++ L+ R+ Sbjct: 188 IIEKGMKGFSTAQKLDKLGMRGSNTCELVFEDCEIPAANIVGEVNEGVRVLMSGLDTERL 247 Query: 243 GIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAA 302 ++ +G+ +AA + Y RER F PI + ++ADM T + +R + A Sbjct: 248 VLSGGPLGLMQAAMDLVLPYVRERKQFNAPIGTFGMMQAKVADMYTALQSSRGFAYMVAR 307 Query: 303 LRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEG 362 D G + ++ + L AS+ A KV A+Q LGG GY+N+FP R+ RD ++ +I G Sbjct: 308 EFDQGSKSRIDPAACLLNASQNAVKVALEAIQALGGNGYINEFPAGRLLRDAKLYEIGAG 367 Query: 363 TSDIQRMVISRNL 375 T++I+RM+I R L Sbjct: 368 TNEIRRMLIGREL 380 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: 317 Number of extensions: 17 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 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