Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate Ac3H11_3533 Glutaryl-CoA dehydrogenase (EC 1.3.99.7)
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3533 Length = 398 Score = 671 bits (1730), Expect = 0.0 Identities = 329/393 (83%), Positives = 360/393 (91%), Gaps = 5/393 (1%) Query: 5 ASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGL 64 A+F W DP LL+QQLT++ER +RD+A + QDKLAPRVL+AFRHE+ D +IFREMGEVGL Sbjct: 4 AAFQWDDPFLLNQQLTDDERAIRDAAAAYCQDKLAPRVLDAFRHEKMDVSIFREMGEVGL 63 Query: 65 LGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKY 124 LG TIPEQYGG GL+YV YGLIAREVER+DSGYRSM SVQSSLVMVPINEFGTEAQKQKY Sbjct: 64 LGPTIPEQYGGPGLSYVAYGLIAREVERVDSGYRSMASVQSSLVMVPINEFGTEAQKQKY 123 Query: 125 LPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWA 184 LPKLA+GEWIGCFGLTEP+HGSDPGSM TRA KVDGGY+L GSKMWITNSP+ADVFVVWA Sbjct: 124 LPKLATGEWIGCFGLTEPDHGSDPGSMATRAYKVDGGYKLKGSKMWITNSPVADVFVVWA 183 Query: 185 KDDA-----GDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVR 239 K+ + G IRGFVLEKG +GL+APAIHGKVGLRASITGEIVMD+VFVPEEN FP+V+ Sbjct: 184 KEVSEGGAVGPIRGFVLEKGMKGLTAPAIHGKVGLRASITGEIVMDDVFVPEENAFPEVQ 243 Query: 240 GLKGPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQT 299 GLKGPFTCLNSARYGI+WGALGAAE CWHTARQYTLDR+QFGRPLAANQLIQKKLADMQT Sbjct: 244 GLKGPFTCLNSARYGIAWGALGAAEFCWHTARQYTLDRKQFGRPLAANQLIQKKLADMQT 303 Query: 300 EITLALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVA 359 EI + LQ CL+ GRMKD GTA+VE TSI+KRNSCGKALDIAR+ARDM+GGNGISDEFGVA Sbjct: 304 EIAIGLQACLQFGRMKDAGTASVEGTSIIKRNSCGKALDIARLARDMMGGNGISDEFGVA 363 Query: 360 RHLVNLEVVNTYEGTHDVHALILGRAQTGIQAF 392 RHLVNLEVVNTYEGTHDVHALILGRAQTGI AF Sbjct: 364 RHLVNLEVVNTYEGTHDVHALILGRAQTGIAAF 396 Lambda K H 0.320 0.137 0.413 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: 624 Number of extensions: 17 Number of successful extensions: 2 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: 393 Length of database: 398 Length adjustment: 31 Effective length of query: 362 Effective length of database: 367 Effective search space: 132854 Effective search space used: 132854 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