Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate WP_101588067.1 BJEO58_RS04410 acyl-CoA dehydrogenase
Query= SwissProt::P81140 (408 letters) >NCBI__GCF_900169175.1:WP_101588067.1 Length = 405 Score = 325 bits (834), Expect = 1e-93 Identities = 177/351 (50%), Positives = 233/351 (66%), Gaps = 12/351 (3%) Query: 63 REIISEMGELGVLGPTIKGYGCAGVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIY 122 RE+ +GELGVLG ++GY CAG ++ YGL RELE VDSG RS +SVQ SL M I+ Sbjct: 56 RELAEGLGELGVLGMHLEGYECAGSTATQYGLACRELEAVDSGLRSLVSVQGSLAMFSIH 115 Query: 123 AYGSEEQQQQKYLPRLAKGELLGCFGLTEPNHGSDPGSMETRALHNPSNRSYTLNGAKTW 182 +GSEEQ+Q+ +LP++A G +GCFGLTEP+ GSDP M+TRA + S+ + LNGAK W Sbjct: 116 HWGSEEQKQE-WLPQMAAGRAIGCFGLTEPDVGSDPAGMKTRATKDGSD--WILNGAKMW 172 Query: 183 ITNSPVADLFVVWARCED--------NCIRGFLLEKGMRGLSAPKIEGKFSLRASATGMI 234 ITNSPV+D+ VVWA+ ++ +RGF++ G+ P+++ K SLRAS TG I Sbjct: 173 ITNSPVSDVMVVWAKTDEVDEKTGEKGVVRGFVVPTDTPGVETPEVQRKLSLRASITGEI 232 Query: 235 IMDDVEVPEENVLPKASSLAVPFGCLNNARYGISWGVLGAAEFCLHTARQYTLDRIQFGV 294 ++D+V +PE +LPKAS L P L+ ARYGI +GV GAA L A +YT RIQF Sbjct: 233 VLDNVRLPESAMLPKASGLKGPLSALSEARYGIVFGVTGAARDSLEEALRYTDTRIQFDR 292 Query: 295 PLAKNQLIQRKLADMLTEITLGLHACLQLGRLKDQDK-VTPEMVSLLKRNNCGKALDIAR 353 PL+ Q+ Q+KLA E + +GRLKD V PE +SL K N A++IAR Sbjct: 293 PLSSFQISQQKLAKAFGEYSAITLTAAHIGRLKDSAAGVRPEQISLGKMVNVDTAMNIAR 352 Query: 354 QARDMLGGNGISDEYHVIRHAMNLEAVNTYEGTHDIHALILGRAITGIQAF 404 R + GG+GI+ EY +RHA+NLE V TYEGTH++H L LGRA+TGI AF Sbjct: 353 DLRALFGGSGITSEYSPLRHAINLETVLTYEGTHEVHQLTLGRAMTGINAF 403 Lambda K H 0.319 0.136 0.404 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: 435 Number of extensions: 17 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: 408 Length of database: 405 Length adjustment: 31 Effective length of query: 377 Effective length of database: 374 Effective search space: 140998 Effective search space used: 140998 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