Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_024981451.1 BXU11_RS04315 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_002017945.1:WP_024981451.1 Length = 379 Score = 216 bits (551), Expect = 7e-61 Identities = 133/378 (35%), Positives = 199/378 (52%), Gaps = 5/378 (1%) Query: 15 LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74 +D LTEE M++ +A FAQ +L V+E H + + MG +G LG + +YG Sbjct: 1 MDFNLTEEHLMIQQAARDFAQTELQAGVIERDEHSKFPTEQVKMMGNLGFLGMMVDPKYG 60 Query: 75 GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134 G+GL+ + Y L E+ ++D+ +MSV +SLV + ++ +E QK KYL LA GE I Sbjct: 61 GAGLDSISYVLAMTEIAKVDASAAVIMSVNNSLVCAGLEKYCSEEQKMKYLVPLAKGEVI 120 Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDA----GD 190 G F L+EP GSD S T A + Y L G+K WITN A ++V A+ D Sbjct: 121 GAFCLSEPEAGSDATSQKTTAIDMGDHYLLNGTKNWITNGGTASTYLVIAQTDIEKGHKG 180 Query: 191 IRGFVLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEEN-IFPDVRGLKGPFTCLN 249 I F++EKGW G K+G+R S T ++ +V VP+EN I D G LN Sbjct: 181 INAFIVEKGWAGFEIGPKEKKMGIRGSDTHSLMFTDVKVPKENRIGADGFGFAFAMNVLN 240 Query: 250 SARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCL 309 R GI+ ALG A + A +Y+ +R+ FG+ + +Q I KLADM +IT A + Sbjct: 241 GGRIGIASQALGIATGAYELALKYSKERKAFGKEIFNHQAIAFKLADMYVKITAAKLLIM 300 Query: 310 RLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVN 369 + KD G ++ K + AL++A A + GGNG E+ V R + + ++ Sbjct: 301 KAACEKDAGQDIAHSGAMAKLYASEIALEVANEAVQIHGGNGYVAEYHVERMMRDSKITQ 360 Query: 370 TYEGTHDVHALILGRAQT 387 YEGT ++ +++ R T Sbjct: 361 IYEGTSEIQRIVISRGLT 378 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: 318 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: 393 Length of database: 379 Length adjustment: 30 Effective length of query: 363 Effective length of database: 349 Effective search space: 126687 Effective search space used: 126687 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