Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate 3606773 Dshi_0204 acyl-CoA dehydrogenase domain protein (RefSeq)
Query= SwissProt::P81140 (408 letters) >FitnessBrowser__Dino:3606773 Length = 564 Score = 129 bits (325), Expect = 2e-34 Identities = 115/388 (29%), Positives = 179/388 (46%), Gaps = 23/388 (5%) Query: 32 DEI-LIRDTFRTYCQEHLMPRIVLAN-RNEVFHREIISEMGELGVLGPTI-KGYGCAGVS 88 DE+ +IR+ FR + + + P + ++E+ EII E+ E+GV G TI + YG G+S Sbjct: 181 DELEMIREQFRRFSVDKVEPHAHEWHLKDELIPMEIIEELAEMGVFGLTIPEEYGGFGLS 240 Query: 89 SVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQQQQKYLPRLAKGELLGCFG 148 + +++ EL R G S + +S + I G+EEQ+Q K+LPRLA E L Sbjct: 241 KASMCVVSEELSRGYIGVGS-LGTRSEIAAELIICGGTEEQKQ-KWLPRLASAETLPTAV 298 Query: 149 LTEPNHGSDPGSMETRALHNPSNRSYTLNGAKTWITNSPVADLFVVWARCEDNCI--RG- 205 TEPN GSD G++ TRA+ + N + + G KTWIT++ + + AR + + RG Sbjct: 299 FTEPNTGSDLGALRTRAVQD-ENGDWKVTGNKTWITHAARTHVMTLLARTKPDTTDHRGL 357 Query: 206 --FLLEK---------GMRGLSAPKIEGKFSLRASATGMIIMDDVEVPEENVL--PKASS 252 FL EK G++ +IE R + D+ V EN+L + Sbjct: 358 SMFLAEKTPGTDEAPFPTEGMTGGEIE-VLGYRGMKEYELAFDNFHVKGENLLGGEEGKG 416 Query: 253 LAVPFGCLNNARYGISWGVLGAAEFCLHTARQYTLDRIQFGVPLAKNQLIQRKLADMLTE 312 +AR + +G A+ L + QY +DR QFG L + KLA M E Sbjct: 417 FKQLMETFESARIQTAARAIGVAQSALDVSMQYAIDRKQFGKSLINFPRVSGKLAMMAVE 476 Query: 313 ITLGLHACLQLGRLKDQDKVTPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIR 372 I + KD+ + + K A A + GGNG + EY + R Sbjct: 477 IMVARQLTYFSAFEKDEGRRCDVEAGMAKLLGARVAWAAADNGLQIHGGNGFALEYGISR 536 Query: 373 HAMNLEAVNTYEGTHDIHALILGRAITG 400 + +N +EG +I A ++ R + G Sbjct: 537 ILCDARILNIFEGAAEIQAQVIARRLLG 564 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: 513 Number of extensions: 32 Number of successful extensions: 4 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: 564 Length adjustment: 34 Effective length of query: 374 Effective length of database: 530 Effective search space: 198220 Effective search space used: 198220 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