Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_041929725.1 MPE_RS16000 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_000015725.1:WP_041929725.1 Length = 391 Score = 687 bits (1774), Expect = 0.0 Identities = 333/388 (85%), Positives = 362/388 (93%) Query: 5 ASFNWIDPLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGL 64 ASF+W DPLLLD QL+E+ER VRD+A + +D+LAPRVLEAFRHE+TDPAIFREMGE+GL Sbjct: 3 ASFHWDDPLLLDSQLSEDERAVRDAAQAYCRDRLAPRVLEAFRHEKTDPAIFREMGELGL 62 Query: 65 LGATIPEQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKY 124 LGAT+PE YGG+GLN+VCYGL+AREVER+DSGYRSMMSVQSSLVMVPI+ FGTEAQKQKY Sbjct: 63 LGATLPEAYGGAGLNHVCYGLVAREVERVDSGYRSMMSVQSSLVMVPIHAFGTEAQKQKY 122 Query: 125 LPKLASGEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWA 184 LPKLA GEWIGCFGLTEPNHGSDPGS+ TRAR V GGY L+G+KMWITNSPIADVFVVWA Sbjct: 123 LPKLARGEWIGCFGLTEPNHGSDPGSLATRARAVQGGYVLSGAKMWITNSPIADVFVVWA 182 Query: 185 KDDAGDIRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGLKGP 244 KDD G IRGF+L+KG +GL APA+HGKVGLRAS+TGEIVMD VF PEEN FP+VRGLKGP Sbjct: 183 KDDGGQIRGFILDKGMKGLEAPAVHGKVGLRASLTGEIVMDEVFCPEENAFPEVRGLKGP 242 Query: 245 FTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLA 304 FTCLNSARYGI+WGALGAAE C+H ARQY LDR QFGRPLAANQLIQKKLADMQTEITL Sbjct: 243 FTCLNSARYGIAWGALGAAEDCFHRARQYVLDRPQFGRPLAANQLIQKKLADMQTEITLG 302 Query: 305 LQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVN 364 LQGCLRLGRMKDEGTAAVEITSIMKRNSCGK+L+IARMARDM+GGNGISDEFGVARHLVN Sbjct: 303 LQGCLRLGRMKDEGTAAVEITSIMKRNSCGKSLEIARMARDMMGGNGISDEFGVARHLVN 362 Query: 365 LEVVNTYEGTHDVHALILGRAQTGIQAF 392 LEVVNTYEGTHDVHALILGRA TGIQAF Sbjct: 363 LEVVNTYEGTHDVHALILGRAITGIQAF 390 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: 616 Number of extensions: 16 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: 393 Length of database: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 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