Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_011384980.1 AMB_RS13080 acyl-CoA dehydrogenase
Query= BRENDA::Q92947 (438 letters) >NCBI__GCF_000009985.1:WP_011384980.1 Length = 383 Score = 181 bits (459), Expect = 4e-50 Identities = 124/380 (32%), Positives = 190/380 (50%), Gaps = 12/380 (3%) Query: 55 VLEEQLTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREIISEMGELGVLGPTI-KGY 113 ++ +Q +++L DT + +ERL+P ++ EII+EM +LG+ G +I + Y Sbjct: 1 MIRDQEILNQLL--DTLSRFVRERLVPNEERIAEDDALPAEIIAEMKDLGLFGLSIPEEY 58 Query: 114 GCAGVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQRQKYLPQLAKGEL 173 G G++ L A E+ + +RS + + I G+EEQ+QKYLP+LA GEL Sbjct: 59 GGLGLTMEEEVLCAFEIGQTSPAFRSIFGTNNGIGSQGIIIDGTEEQKQKYLPRLATGEL 118 Query: 174 LGCFGLTEPNSGSDPSSMETRAHYNSSNKSYTLNGTKTWITNSPMADLFVVWARCED--- 230 + F LTEPN+GSD +S+ T A + + Y +NGTK +ITN+P A +F + AR + Sbjct: 119 IASFALTEPNAGSDAASLRTTARKDGDH--YIVNGTKRFITNAPEASIFTLMARTDPNNK 176 Query: 231 --GCIRGFLLEKGMRGLSAPRIQGKFSLRASATGMIIMDGVEVPEENVLPGASSLG--GP 286 G I F++E GLS +I K + + T +I + V VP N++ G G Sbjct: 177 GAGGISAFIVEADSPGLSLGKIDKKMGQKGAHTCDVIFEDVRVPAANIIGGIEGQGFKTA 236 Query: 287 FGCLNNARYGIAWGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKLADMLTEITLG 346 L+ R I+ +G SE + + +YA +R+QFG P+ QL+Q LAD TE Sbjct: 237 MKVLDRGRLHISATCVGVSERLIRDSVKYAAERVQFGKPIGEFQLVQAMLADSRTEAYAA 296 Query: 347 LHACLQLGRLKDQDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMN 406 L R KDQ + K IA +A + GG G +Y + R + Sbjct: 297 RCMVLDAARKKDQGINVSTEAACCKMFASEAVGRIADRAVQVHGGAGYISDYGIERFYRD 356 Query: 407 LEAVNTYEGTHDIHALILGR 426 + YEGT I L++ R Sbjct: 357 VRLFRIYEGTTQIQQLVIAR 376 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: 376 Number of extensions: 26 Number of successful extensions: 5 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: 383 Length adjustment: 31 Effective length of query: 407 Effective length of database: 352 Effective search space: 143264 Effective search space used: 143264 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