Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate CCNA_00436 CCNA_00436 acyl-CoA dehydrogenase, short-chain specific
Query= SwissProt::P81140 (408 letters) >FitnessBrowser__Caulo:CCNA_00436 Length = 382 Score = 148 bits (373), Expect = 3e-40 Identities = 115/369 (31%), Positives = 172/369 (46%), Gaps = 16/369 (4%) Query: 38 DTFRTYCQEHLMPRIVLANRNEVFHREIISEMGELGVLGPTI-KGYGCAGVSSVAYGLLA 96 DT + E L P N+ ++I EM LG+ G TI + +G G++ L+A Sbjct: 13 DTVARFVAERLRPIEAQVAENDAVPDDVIEEMKGLGLFGLTIPEEFGGLGLTMEEEALVA 72 Query: 97 RELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQQQQKYLPRLAKGELLGCFGLTEPNHGS 156 EL R +RS + + +G++EQ+ K+LP +A G ++ F LTEP GS Sbjct: 73 IELGRASPAFRSVFGTNVGIGSQGLVMFGNDEQKA-KWLPGIASGAVITSFALTEPEAGS 131 Query: 157 DPGSMETRALHNPSNRSYTLNGAKTWITNSPVADLFVVWARCEDNC-----IRGFLLEKG 211 D +++TRA + + Y LNG+K +ITN+ A LF V AR + + FL+ + Sbjct: 132 DSAAVQTRATRDGDD--YILNGSKRYITNAGKASLFTVMARTNPDAKGGAGVSAFLVPRD 189 Query: 212 MRGLSAPKIEGKFSLRASATGMIIMDDVEVPEENVL-PKASSLAVPFGCLNNARYGISWG 270 + GL+ K E K + + + D+V VP N L + V L+ R I+ Sbjct: 190 LPGLTVGKPEKKMGQQGAHIHDVTFDNVRVPAWNRLGAEGEGFKVAMQVLDRGRLHIAAV 249 Query: 271 VLGAAEFCLHTARQYTLDRIQFGVPLAKNQLIQRKLADMLTEITLGLHACLQLGRLKDQD 330 +G AE + Y +R QFG P+A QLIQ +AD TE L+ R +D Sbjct: 250 CVGVAERLIADCVAYASERKQFGQPIASFQLIQAMIADSKTEALAAKALVLETARKRDAG 309 Query: 331 -KVTPEMVS--LLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVNTYEGTH 387 VT E S L G+ D A Q + GG G +Y + R ++ YEGT Sbjct: 310 VNVTLEAASSKLFASEMVGRVADRAVQ---VFGGAGYVADYGIERLYRDVRIFRIYEGTS 366 Query: 388 DIHALILGR 396 + LI+ R Sbjct: 367 QVQQLIIAR 375 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: 315 Number of extensions: 23 Number of successful extensions: 6 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: 382 Length adjustment: 31 Effective length of query: 377 Effective length of database: 351 Effective search space: 132327 Effective search space used: 132327 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