Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate N515DRAFT_0941 N515DRAFT_0941 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >FitnessBrowser__Dyella79:N515DRAFT_0941 Length = 385 Score = 210 bits (534), Expect = 6e-59 Identities = 123/373 (32%), Positives = 205/373 (54%), Gaps = 4/373 (1%) Query: 18 LADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGL 77 L ++ ++R++ HA+A+ ++APR T+ A ++R+ GE+GLLG TIPE YGG GL Sbjct: 6 LGEELDLLRESVHAFAEKEIAPRATQIDHDNVFPADLWRKFGEMGLLGMTIPEAYGGTGL 65 Query: 78 DYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFG 137 Y+++ + E+ R S+L + +F G++ Q+ KY+P+L +GE++G Sbjct: 66 GYLAHMVAMEEISRASGSVGLSYGAHSNLCVQNLFHNGNEEQRRKYIPRLCSGEYVGALA 125 Query: 138 LTEPNHGSD-PGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKL--DEDGRDEIR 194 ++EP GSD GSM +A + +G+KMWITN P ADV +V+ + G + Sbjct: 126 MSEPGAGSDVVGSMSCKAELRGDVWVANGTKMWITNGPDADVLLVYMRTAPRPAGSRCMT 185 Query: 195 GFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHV-KGLRGPFTCLNSA 253 FI+EKG KG S K+G+R S T E+V ++ +P NI+ V +G+R + L++ Sbjct: 186 AFIIEKGMKGFSTAQKLDKLGMRGSNTCELVFEDCEIPAANIVGEVNEGVRVLMSGLDTE 245 Query: 254 RYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRL 313 R ++ G LG ++ + YV +RKQF P+ ++Q K+ADM T + + Sbjct: 246 RLVLSGGPLGLMQAAMDLVLPYVRERKQFNAPIGTFGMMQAKVADMYTALQSSRGFAYMV 305 Query: 314 GRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTY 373 R D+G+ + + N+ A+ +A A LGGNG +EF R L + ++ Sbjct: 306 AREFDQGSKSRIDPAACLLNASQNAVKVALEAIQALGGNGYINEFPAGRLLRDAKLYEIG 365 Query: 374 EGTHDIHALILGR 386 GT++I +++GR Sbjct: 366 AGTNEIRRMLIGR 378 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: 384 Number of extensions: 25 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: 395 Length of database: 385 Length adjustment: 31 Effective length of query: 364 Effective length of database: 354 Effective search space: 128856 Effective search space used: 128856 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