Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate H281DRAFT_02091 H281DRAFT_02091 hypothetical protein
Query= BRENDA::Q92947 (438 letters) >FitnessBrowser__Burk376:H281DRAFT_02091 Length = 378 Score = 177 bits (449), Expect = 5e-49 Identities = 113/376 (30%), Positives = 183/376 (48%), Gaps = 8/376 (2%) Query: 60 LTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREIISEMGELGVLGPTI-KGYGCAGV 118 L D +++RD RT+ +E + P +R F +++ ++ ELG G + + YG AG+ Sbjct: 3 LDQDHLMVRDALRTFVREAVTPYAATWDRERTFPKDVHRQLAELGAYGVLVPETYGGAGM 62 Query: 119 SSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQRQKYLPQLAKGELLGCFG 178 ++A L+ E+ D G +A+SV + V + YG++ Q++++L LA+GE+LG F Sbjct: 63 DALALALILEEIAAGDGGTSTAISVNNCPVCSILLTYGNDAQKREWLTPLARGEMLGAFC 122 Query: 179 LTEPNSGSDPSSMETRAHYNSSNKSYTLNGTKTWITNSPMADLFVVWARCEDGC----IR 234 LTEP +GSD S++ T A + +Y LNG K +IT+ D+ +V A + I Sbjct: 123 LTEPQAGSDASALRTTATRDKDGDAYVLNGVKQFITSGKNGDVAIVMAVTDKAAGKRGIS 182 Query: 235 GFLLEKGMRGLSAPRIQGKFSLRASATGMIIMDGVEVPEENVLPGASSLGGPFGC--LNN 292 F++ +G R++ K +S T II + VP N++ GA G L Sbjct: 183 AFIVPTDSKGYVVARVEDKLGQHSSDTAQIIFEDCRVPAANLI-GAEGEGYRIALSGLEG 241 Query: 293 ARYGIAWGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKLADMLTEITLGLHACLQ 352 R GIA +G + A YA +R FG PL +Q +Q +LADM T++ Sbjct: 242 GRIGIAAQSVGMARAAYEAALTYAKERESFGQPLFSHQAVQFRLADMATQLEAARQLIWH 301 Query: 353 LGRLKDQDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVNT 412 LKD + ++ K A I A + GG G ++ V R ++ Sbjct: 302 AASLKDAGQPCLTEAAMAKLFASEAAERICSAALQIHGGYGYLSDFPVERIYRDVRVCQI 361 Query: 413 YEGTHDIHALILGRAI 428 YEGT DI +++ R + Sbjct: 362 YEGTSDIQKILIARGL 377 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: 349 Number of extensions: 15 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: 378 Length adjustment: 31 Effective length of query: 407 Effective length of database: 347 Effective search space: 141229 Effective search space used: 141229 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 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