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_110803830.1 C8J30_RS00780 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_003217355.1:WP_110803830.1 Length = 386 Score = 266 bits (679), Expect = 9e-76 Identities = 145/367 (39%), Positives = 218/367 (59%), Gaps = 2/367 (0%) Query: 10 ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAM 69 + D + +A++RL P AA DR++ FP E EM LG G+ VPE++GG GYLA+ + Sbjct: 17 LRDMVQAWARDRLAPIAARVDRDNLFPNELWPEMGALGLLGITVPEEYGGAGMGYLAHVV 76 Query: 70 ALEEIAAGDGACSTIMSVHNSVGCVPILKF-GNDDQKERFLKPLASGAMLGAFALTEPQA 128 A EEIA + S H+++ CV LK G+ +QK ++L L SGA +GA A++E A Sbjct: 77 ATEEIARVSASISLSYGAHSNL-CVNQLKLNGSPEQKRKYLPDLVSGAKIGALAMSETGA 135 Query: 129 GSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDS 188 GSD +K RA GD YVLNG K +IT+G +A ++V+A TDP AG +GI+AF++ Sbjct: 136 GSDVVGMKLRAEKRGDVYVLNGHKYWITNGCDADTLVVYAKTDPGAGSKGITAFLIEKGM 195 Query: 189 PGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQS 248 G+ + DKLG S+T Q+ F++ +VP N LG EG+G ++ ++ L+ RV ++ Sbjct: 196 KGFSTSPHFDKLGMRGSNTAQLFFDNCEVPAENVLGAEGKGVRVLMSGLDYERVVLSGIG 255 Query: 249 VGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGK 308 G+ A + YA+ RE FG+PI Q + ++ADM AR + A D G+ Sbjct: 256 TGILMACLDEVVPYAQTREQFGQPIGTFQLMQAKIADMYVAANTARAYTYEVAKACDRGE 315 Query: 309 PALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQR 368 +A+ L+ASE A A+Q LGG G+L+D + R++RD ++ +I GTS+I+R Sbjct: 316 VTRQDAAATVLYASEQAMVQAHQAVQALGGAGFLNDSTVSRLFRDAKLMEIGAGTSEIRR 375 Query: 369 MVISRNL 375 M+I R L Sbjct: 376 MLIGREL 382 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: 313 Number of extensions: 17 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: 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