Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate CCNA_01412 CCNA_01412 acyl-CoA dehydrogenase, short-chain specific
Query= BRENDA::Q3JP94 (395 letters) >FitnessBrowser__Caulo:CCNA_01412 Length = 381 Score = 180 bits (456), Expect = 7e-50 Identities = 119/375 (31%), Positives = 191/375 (50%), Gaps = 3/375 (0%) Query: 14 LDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYG 73 +D L +D+ ++DAA A+A+G+LAP + ++ + R+ E+G G + E G Sbjct: 3 MDFALNEDQVAIQDAARAFAEGQLAPHSADWDENKHFPVDVLRQAAELGFAGIYVNEDVG 62 Query: 74 GPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWI 133 G GL + +I + D + +++ + + I FGSD +++YLP+L T E I Sbjct: 63 GSGLSRLDASIIFEALSYGDVPVAAYLTIHNMASWM-IDRFGSDDLRQRYLPRLTTMELI 121 Query: 134 GCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDEDGRDEI 193 + LTEP GSD +M T A+ Y L+G K +I+ ++D++VV A+ +G + Sbjct: 122 ASYCLTEPGSGSDAAAMRTTAKLDGDHYVLNGGKAFISGGGVSDIYVVMARTGGEGAKGV 181 Query: 194 RGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEEN-ILPHVKGLRGPFTCLNS 252 F++EKG +GLS A K+G A T ++ D VP N I +G R L+ Sbjct: 182 SAFVVEKGMEGLSFGANERKMGWNAQPTAQVNFDNCRVPVANRIGQEGEGFRFAMMGLDG 241 Query: 253 ARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLR 312 R IA +LG A+ A+ Y+ R QFGRPL Q +Q KLADM TE+ V R Sbjct: 242 GRLNIASCSLGGAQFALDTAKAYLETRNQFGRPLKDFQALQFKLADMATELEAARLMVRR 301 Query: 313 LGRMKD-EGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVN 371 D + A ++ ++ KR + +A A + GG G ++ + R + +L V Sbjct: 302 AAHALDSKHPEATKLCAMAKRFATDAGFQVANDALQLHGGYGYLQDYPLERLVRDLRVHQ 361 Query: 372 TYEGTHDIHALILGR 386 EGT++I +I+ R Sbjct: 362 ILEGTNEIMRVIIAR 376 Lambda K H 0.320 0.138 0.414 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: 355 Number of extensions: 18 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: 395 Length of database: 381 Length adjustment: 30 Effective length of query: 365 Effective length of database: 351 Effective search space: 128115 Effective search space used: 128115 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