Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_011428126.1 RHE_RS25445 acyl-CoA dehydrogenase
Query= BRENDA::Q9SWG0 (409 letters) >NCBI__GCF_000092045.1:WP_011428126.1 Length = 395 Score = 202 bits (515), Expect = 1e-56 Identities = 126/367 (34%), Positives = 190/367 (51%), Gaps = 7/367 (1%) Query: 39 KESVSKFAQDNIAPHAERIDKTNSFPKDVNLWKLMGEFNLHGITAPEEYGGLGLGYLYHC 98 +++ +AQ +AP +D + D +++ MGE L G T EYGG GLGY + Sbjct: 28 QDTAHAYAQQKLAPRV--LDAFRNEKTDPAIFREMGELGLLGPTISPEYGGAGLGYTAYG 85 Query: 99 IAMEEISRASGSVALSYGAHSNLCINQLVRNGTAAQKEKYLPKLISGEHVGALAMSEPNA 158 + E+ R S+L + + G+AAQK+KYLPKL +GE +G ++EP+ Sbjct: 86 LIAREVERVDSGYRSMMSVQSSLVMVPIETFGSAAQKQKYLPKLATGEWIGCFGLTEPDH 145 Query: 159 GSDVVGMKCKAEKVDGGYILNGNKMWCTNGPSAETLVVYAKTDTKAGSKGITAFIIEKGM 218 GSD M +A+KVDGGY L G+K W +N P A+ VV+AKT+ I FI+EKG Sbjct: 146 GSDPGSMATRAKKVDGGYSLTGSKTWISNAPIADVFVVWAKTEDGL----IRGFILEKGW 201 Query: 219 TGFSTAQKLDKLGMRGSDTCELVFENCFVPEENILDKEGKGVYVLMSGLDLERLVLAAGP 278 G S K+G+R S T E+V + FVPEEN+L G+ + L+ R +A G Sbjct: 202 KGLSAPAIHGKVGLRASITGEVVMDGVFVPEENLLPGV-TGLKGPFTCLNSARFGIAWGA 260 Query: 279 LGIMQACLDNVLPYIRQREQFGRPVGEFQFIQGKVADMYTALQSSRSYVYSVARDCDNGK 338 LG + C Y+ +R+QFGRP+ Q IQ K+ADM + + R + G Sbjct: 261 LGAAEDCYARARQYVLERKQFGRPLAANQLIQKKLADMAAEIALGLQGCLRLGRMKEEGH 320 Query: 339 VDPKDCAGTILCAAERATQVALQAIQCLGGNGYINEYATGRLLRDAKLYEIGAGTSEIRR 398 + + + +A ++A A LGGNG +E+ R L + ++ GT +I Sbjct: 321 PPVELTSILKRNSCGKALEMARAARDMLGGNGISDEFGIARHLVNLEVVNTYEGTHDIHA 380 Query: 399 IVIGREL 405 ++IGR + Sbjct: 381 LIIGRSI 387 Lambda K H 0.318 0.135 0.395 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: 360 Number of extensions: 19 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: 409 Length of database: 395 Length adjustment: 31 Effective length of query: 378 Effective length of database: 364 Effective search space: 137592 Effective search space used: 137592 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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