Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_086509764.1 BZY95_RS09860 acyl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >NCBI__GCF_002151265.1:WP_086509764.1 Length = 383 Score = 202 bits (513), Expect = 2e-56 Identities = 134/381 (35%), Positives = 189/381 (49%), Gaps = 12/381 (3%) Query: 10 DPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIP 69 DP LL Q + R VR+ +L P + A + EM E+GL G +IP Sbjct: 4 DPELLAQLIDTISRFVRE--------RLIPNEARLAEEDAVPAELLEEMKEMGLFGLSIP 55 Query: 70 EQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLAT 129 E+YGG GL L+A E+ + +RS+ + + I G+ QK KY+P+LAT Sbjct: 56 EEYGGLGLTMEEEALVAMEIGKTSPAFRSIFGTNNGIGAQGILIDGTPEQKAKYVPRLAT 115 Query: 130 GEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD--E 187 GE + F LTEP+ GSD S+ T A + Y L+G+K +ITN P ADVF V A+ D Sbjct: 116 GELLSSFCLTEPDAGSDAASLRTTAVRDGDHYVLNGTKRFITNGPEADVFTVMARTDPGN 175 Query: 188 DGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHV--KGLRG 245 G I FI+E GL K+G + + T +I+ ++ VP ENI+ V KG + Sbjct: 176 KGAGGITAFIVEGDTPGLKRGPADSKMGQKGAHTCDIIFEDCRVPAENIIGGVEGKGFKT 235 Query: 246 PFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITL 305 L+ R I+ +G AE + Y ++RKQFG PLA +QL+Q LAD +TE Sbjct: 236 AMKVLDRGRLHISAVCVGVAERLVEESLNYAIERKQFGVPLAEHQLVQAMLADSKTEAYA 295 Query: 306 GLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLV 365 G VL R KD G A + S K +A A + GG G E+ V R Sbjct: 296 GRTMVLDAARRKDAGENASTLASCCKLFCAEMVGRVADRAVQVHGGAGYMAEYAVERFYR 355 Query: 366 NLEVVNTYEGTHDIHALILGR 386 ++ + YEGT I +++ R Sbjct: 356 DVRLFRIYEGTTQIQQVVIAR 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: 360 Number of extensions: 12 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: 383 Length adjustment: 30 Effective length of query: 365 Effective length of database: 353 Effective search space: 128845 Effective search space used: 128845 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 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