Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate CA265_RS14465 CA265_RS14465 acyl-CoA dehydrogenase
Query= BRENDA::Q92947 (438 letters) >FitnessBrowser__Pedo557:CA265_RS14465 Length = 453 Score = 247 bits (630), Expect = 6e-70 Identities = 141/379 (37%), Positives = 212/379 (55%), Gaps = 2/379 (0%) Query: 57 EEQLTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREIISEMGELGVLGPTIKGYGCA 116 +E L ++ ++ R + ++ + P + F EII ++ EL + G T KGYGC Sbjct: 75 DEALKDEDRELQLKVRAFLEKEVKPIVNHYWNKAEFPFEIIPKLAELNICGLTYKGYGCP 134 Query: 117 GVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQRQKYLPQLAKGELLGC 176 G S++ G+LA E+ R+D+ + VQS L M IY GSEEQ+Q++LP + + +++G Sbjct: 135 GKSNLMEGILAMEMARIDTSISTFFGVQSGLAMGSIYLCGSEEQKQQWLPLMQQFKIIGA 194 Query: 177 FGLTEPNSGSDPSSMETRAHYNSSNKSYTLNGTKTWITNSPMADLFVVWARCED-GCIRG 235 FGLTEP GS + T K + LNG K WI N+ AD+ ++WAR E+ G ++G Sbjct: 195 FGLTEPEVGSAAAGGLTTTCKKVDGK-WVLNGQKKWIGNATFADILIIWARDEESGEVKG 253 Query: 236 FLLEKGMRGLSAPRIQGKFSLRASATGMIIMDGVEVPEENVLPGASSLGGPFGCLNNARY 295 F+++K G + ++Q K +LR G+I + EV E + L A+S L R Sbjct: 254 FIVKKDNPGFAVEKMQDKMALRIVQNGIITLTNCEVEEADRLQNANSFKDTAKVLQMTRA 313 Query: 296 GIAWGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKLADMLTEITLGLHACLQLGR 355 G+AW +G + A Y R QFG P+A QLIQ L +ML+ +T C +L + Sbjct: 314 GVAWQAVGCARGAYENALDYTRTRKQFGKPIASFQLIQNHLVEMLSNLTAMQTLCFRLSQ 373 Query: 356 LKDQDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVNTYEG 415 L+DQ E SL K + D+ +AR+++GGNGI EY+V R + EA+ +YEG Sbjct: 374 LQDQGLLKDEHASLAKVFCSLRTRDVVSRAREVMGGNGILLEYNVARFVADAEAIYSYEG 433 Query: 416 THDIHALILGRAITGIQAF 434 T +I+ LI+GRAITG AF Sbjct: 434 TKEINTLIVGRAITGFSAF 452 Lambda K H 0.319 0.135 0.400 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: 423 Number of extensions: 11 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: 438 Length of database: 453 Length adjustment: 32 Effective length of query: 406 Effective length of database: 421 Effective search space: 170926 Effective search space used: 170926 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: 51 (24.3 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