Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate AZOBR_RS31550 AZOBR_RS31550 acyl-CoA dehydrogenase
Query= reanno::Smeli:SM_b21121 (387 letters) >FitnessBrowser__azobra:AZOBR_RS31550 Length = 392 Score = 252 bits (644), Expect = 1e-71 Identities = 145/369 (39%), Positives = 213/369 (57%), Gaps = 5/369 (1%) Query: 20 SVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEAHGGAGLGYLAHCVAME 79 SV RF + P+A + + +P + M ELGL G T E +GG GL + +E Sbjct: 23 SVDRFLDRHVRPVALKLEHDDTYPDEIVERMKELGLFGATIPEEYGGLGLRPSTYAKMIE 82 Query: 80 EISRASASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISGEHVGALAMSEPGAGSDV 139 IS S+ +H + + + G QK+ +LP+ +GE G LA++EP G+D+ Sbjct: 83 RISSVWMSLSGIINSHLIMAFI-VTKTGTEEQKAAFLPRFATGELRGGLALTEPDCGTDL 141 Query: 140 VSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAGPR--GITAFLVEKAFPG 197 +++ A + GD YV+NGSK WITNG + KTDP A PR G+T FL EK PG Sbjct: 142 QAIRTVAKRDGDDYVINGSKTWITNGIQGSCFALLVKTDPTAQPRHKGMTMFLAEKG-PG 200 Query: 198 FSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGV-GEGVKVLMSGLDYERVVLSAGPL 256 F +KL+KLG +G +++EL+F D VP + ++GGV G G+ +SGL+ RV +++ + Sbjct: 201 FKVSRKLEKLGYKGIDSAELVFEDYRVPADRLIGGVEGRGMACAISGLELGRVNVASRGV 260 Query: 257 GIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARAYVYAVAAACDRGET 316 G+ A LD V Y +RK FG+PI E Q + KLADM ++AAR V A A DRGE Sbjct: 261 GVAQAALDESVKYSQQRKTFGKPIHEHQAVAMKLADMATRVSAARLLVQQAAKALDRGER 320 Query: 317 ARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAKLYEIGAGTSEIRRM 376 +A L+A+E A +L+A++ GG GY+ ++ RL RDA L IG GT+EI+R+ Sbjct: 321 CDYEAGMAKLFASEAAVENSLDAMRIHGGYGYSKEFVVERLYRDAPLLCIGEGTNEIQRI 380 Query: 377 LIGRELFAE 385 +I + L + Sbjct: 381 IIAKRLIEQ 389 Lambda K H 0.318 0.135 0.391 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: 323 Number of extensions: 12 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: 387 Length of database: 392 Length adjustment: 30 Effective length of query: 357 Effective length of database: 362 Effective search space: 129234 Effective search space used: 129234 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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