Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate H281DRAFT_04737 H281DRAFT_04737 glutaryl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >FitnessBrowser__Burk376:H281DRAFT_04737 Length = 396 Score = 728 bits (1880), Expect = 0.0 Identities = 360/393 (91%), Positives = 373/393 (94%) Query: 3 AATFHWDDPLLLDQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIG 62 AA FHW+DPLLLDQQL +DERMVRDAA AYAQ KL PRV EAFRHE TD IFREMGE+G Sbjct: 4 AAQFHWEDPLLLDQQLTEDERMVRDAAAAYAQDKLQPRVLEAFRHEKTDIEIFREMGELG 63 Query: 63 LLGPTIPEQYGGPGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEK 122 LLGPTIPEQYGGPGL+YV+YGLIAREVERVDSGYRSMMSVQSSLVMVPI+EFGS+AQK+K Sbjct: 64 LLGPTIPEQYGGPGLNYVAYGLIAREVERVDSGYRSMMSVQSSLVMVPIYEFGSEAQKQK 123 Query: 123 YLPKLATGEWIGCFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVW 182 YLPKLATGEWIGCFGLTEPNHGSDPGSMVTRA+KV GGYSLSGSKMWITNSPIADVFVVW Sbjct: 124 YLPKLATGEWIGCFGLTEPNHGSDPGSMVTRAKKVDGGYSLSGSKMWITNSPIADVFVVW 183 Query: 183 AKLDEDGRDEIRGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENILPHVKG 242 AKL+E+G+D IRGFILEKG KGLSAP IH KVGLRASITGEIVLDE FVPEEN P V G Sbjct: 184 AKLEENGKDAIRGFILEKGWKGLSAPTIHSKVGLRASITGEIVLDEVFVPEENRFPEVSG 243 Query: 243 LRGPFTCLNSARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTE 302 LRGPFTCLNSARYGIAWGALGAAESCWH ARQYVLDRKQFGRPLAANQLIQKKLADMQTE Sbjct: 244 LRGPFTCLNSARYGIAWGALGAAESCWHTARQYVLDRKQFGRPLAANQLIQKKLADMQTE 303 Query: 303 ITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVAR 362 ITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFG+AR Sbjct: 304 ITLGLQGVLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGIAR 363 Query: 363 HLVNLEVVNTYEGTHDIHALILGRAQTGIQAFF 395 HLVNLEVVNTYEGTHDIHALILGRAQTGIQAFF Sbjct: 364 HLVNLEVVNTYEGTHDIHALILGRAQTGIQAFF 396 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: 616 Number of extensions: 15 Number of successful extensions: 1 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: 396 Length adjustment: 31 Effective length of query: 364 Effective length of database: 365 Effective search space: 132860 Effective search space used: 132860 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 Apr 09 2024. 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