Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_059153518.1 V474_RS22780 acyl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >NCBI__GCF_001046635.1:WP_059153518.1 Length = 596 Score = 87.4 bits (215), Expect = 1e-21 Identities = 93/322 (28%), Positives = 146/322 (45%), Gaps = 57/322 (17%) Query: 114 FGSDAQKEKYLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVP---GGYSLSGSKMWI 170 + SD K YLPK+ +G+W G LTEP+ G+D G + T+A VP Y LSGSK++I Sbjct: 140 YASDELKAFYLPKMVSGDWSGTMCLTEPHCGTDLGMLRTKA--VPQDDDSYKLSGSKIFI 197 Query: 171 T--NSPIAD--VFVVWAKLDE--DGRDEIRGFILEK----------GCKGLSAPAIHGKV 214 + + + V +V A+L + +G I FI+ K G+S AI K+ Sbjct: 198 SAGEHDLTENIVHLVLARLPDAPEGVKGISLFIVPKYLPKDDGTPGPSNGVSVAAIEHKM 257 Query: 215 GLRASITGEIVLDEA---FVPEENILPHVKGLRGPFTCLNSARYGIAWGALGAAESCWHI 271 GL+AS T ++ D++ V + PH KG+ FT +N+ R + LG E+ + Sbjct: 258 GLKASATCQLNFDDSTGWLVGK----PH-KGMEAMFTMMNTERVSVGVQGLGVGEAAYQS 312 Query: 272 ARQYVLDRKQFGRPLAANQ---------LIQKKLADMQTEITLGLQGVLRLGRMKDEGTA 322 A Y DR Q GR L+ + ++ + M + +G LG Sbjct: 313 AVWYAKDRLQ-GRSLSGVKNPKGPADPIIVHPDVRRMLMTMRAYNEGCRALGGWVSRALD 371 Query: 323 AVE-----------------ITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLV 365 A +T ++K + A LA + GG+G E GV +++ Sbjct: 372 AERYSTDPEVKQRAADFIALMTPVVKALFTDLGYENANLAVQVYGGHGYIAETGVEQYVR 431 Query: 366 NLEVVNTYEGTHDIHAL-ILGR 386 + + YEGT+ I AL ++GR Sbjct: 432 DGRIAMIYEGTNGIQALDLVGR 453 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: 516 Number of extensions: 29 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 395 Length of database: 596 Length adjustment: 34 Effective length of query: 361 Effective length of database: 562 Effective search space: 202882 Effective search space used: 202882 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: 52 (24.6 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