Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_036834050.1 N784_RS08285 butyryl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_000775615.1:WP_036834050.1 Length = 400 Score = 230 bits (587), Expect = 5e-65 Identities = 129/372 (34%), Positives = 211/372 (56%), Gaps = 5/372 (1%) Query: 15 LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74 +D +EE++M+R + +F ++ P + E DPAI ++ ++GL+G IP +YG Sbjct: 1 MDFTFSEEQQMLRKTVREFVDKEIIPYMKEWDERGTFDPAIMHKLADLGLMGVCIPTKYG 60 Query: 75 GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134 GSG++Y ++ E+ER D+ +R+ +SV + L + + +FGTE QK+KYL A GE I Sbjct: 61 GSGMDYNALAIVCEELERGDTAFRTAVSVHTGLNSLSLLQFGTEEQKEKYLIPQAKGEKI 120 Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDA----GD 190 G FGLTEP GSD S+ T A + Y L G K WI+ AD F+V+A D Sbjct: 121 GAFGLTEPGAGSDVASIQTTATRKGDYYTLNGQKSWISLCDSADHFLVFAYTDKEKKHQG 180 Query: 191 IRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEEN-IFPDVRGLKGPFTCLN 249 I F++E+ +G S+ A GK+G+RA TGE+ +++V VP +N + + G K L+ Sbjct: 181 ISAFIVERTMEGFSSKATKGKLGIRAGNTGELFLEDVPVPVDNRLGEEGDGFKIAMASLD 240 Query: 250 SARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCL 309 + R+ ++ GA G AC + +Y +R+ FG+ + +QL+Q+ +A+M+ + ++ Sbjct: 241 NGRFTVAAGACGLMMACLEASVRYCHERETFGKEIGKHQLVQQMIANMEAGLQMSRLLVY 300 Query: 310 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVN 369 R G +K+ G TS+ K +C A A A + G G S+E+ V R+L N + Sbjct: 301 RAGELKNSGKRNTRETSLAKWQACDFANKAADDAVQIHGAYGYSNEYAVERYLRNSKAPV 360 Query: 370 TYEGTHDVHALI 381 YEGT ++H ++ Sbjct: 361 IYEGTREIHTIM 372 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: 343 Number of extensions: 13 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: 393 Length of database: 400 Length adjustment: 31 Effective length of query: 362 Effective length of database: 369 Effective search space: 133578 Effective search space used: 133578 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