Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_043765518.1 U743_RS03380 acyl-CoA dehydrogenase
Query= BRENDA::P12007 (424 letters) >NCBI__GCF_000733765.1:WP_043765518.1 Length = 381 Score = 185 bits (470), Expect = 2e-51 Identities = 120/378 (31%), Positives = 202/378 (53%), Gaps = 11/378 (2%) Query: 43 LNEEQKQLRHTISKFVQENLAPKAQEIDQSNDFKNLREFWKQLGSLGVLGITAPVQYGGS 102 LN E + +R +++FV+ + P +++ + R K GVL I P GG Sbjct: 8 LNAEHEAIRDQVARFVEREITPNIDAWEEAGELP--RALHKAAAEAGVLQIGYPEALGGI 65 Query: 103 GL-GYLEHVLVMEEISRASAAVGLSYGAHSN-LCINQIVRNGNEAQKEKYLPKLISGEFI 160 + + ++++EE+ RA + GL G S+ + + IV G + QKE+ + +++G+ I Sbjct: 66 DVPDHFYELVIVEELCRAGSG-GLIAGLMSHGIGLPPIVAAGTQEQKERLVAPVLAGDKI 124 Query: 161 GALAMSEPNAGSDVVSMRLKAEKKGDHYVLNGNKFWITNGPDADVLVVYAKTDLTAVPAS 220 AL ++EP+ GSDV ++R A ++G+HY++ G+K +IT+G ADV+ +T + Sbjct: 125 AALGITEPSGGSDVAAIRTAARREGNHYIVKGSKTFITSGMRADVITTAVRTGGEGI--- 181 Query: 221 RGITAFIVEKDMPGFSTSKKLDKLGMRGSNTCELVFEDCKVPAANILSQESKGVYVLMSG 280 GI+ VE D PG S + LDK+G R S+T L F++ +VP AN++ E+ G +M Sbjct: 182 GGISLLAVEADTPGLSRT-PLDKMGWRCSDTATLYFDEARVPVANLIGPENAGFMAIMQN 240 Query: 281 LDLERLVLAGGPLGIMQAVLDHTIPYLHVREAFGQKIGQFQLMQGKMADMYTRLMACRQY 340 + ERL LA G+ + + + + RE FG+ + Q+++ K+ DM + A Sbjct: 241 FNSERLGLAAQAWGLAKTCYEEALTWARERETFGKPLIARQVIRHKLVDMKMAIDAVGAQ 300 Query: 341 VYNVA-RACDEGHITAKDCAGVILYTAECATQVALDGIQCLGGNGYINDFPMGRFLRDAK 399 +Y +A R + + A+ C L T+ QVA + +Q LGG GY+ R R+ K Sbjct: 301 LYQLAWRVSQKQYPVAELCMLKNLATS-TLEQVAGEAVQILGGAGYLRGAKSERIFRETK 359 Query: 400 LYEIGGGTSEVRRLVIGR 417 + IGGG SEV + + R Sbjct: 360 VLSIGGGASEVMKDLAAR 377 Lambda K H 0.320 0.137 0.402 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: 353 Number of extensions: 19 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: 424 Length of database: 381 Length adjustment: 31 Effective length of query: 393 Effective length of database: 350 Effective search space: 137550 Effective search space used: 137550 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