Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate WP_011513566.1 PCRYO_RS06325 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >NCBI__GCF_000013905.1:WP_011513566.1 Length = 384 Score = 204 bits (519), Expect = 3e-57 Identities = 128/366 (34%), Positives = 193/366 (52%), Gaps = 7/366 (1%) Query: 26 VRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYGGSGLNYVCYGL 85 + D+ QF ++L P +++ I +M E+GL G TIPE+YGG G+ Sbjct: 11 ITDTIRQFVNNQLIPMEHWVAENDRLPDDIINQMRELGLFGLTIPEEYGGLGVTMEEEVT 70 Query: 86 IAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCFGLTEPNHG 145 +A E+ R +RS++ + + + GTEAQKQKYLP+LASGE IG F LTEP+ G Sbjct: 71 LAFELGRTSPAFRSLIGTNNGIGSSGLVIDGTEAQKQKYLPRLASGEIIGSFCLTEPDSG 130 Query: 146 SDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDD-----AGDIRGFVLEKGW 200 SD S+ T A K Y + G+K +ITN+P A VF V A+ D +G I F++E Sbjct: 131 SDAASLKTTAIKDGDTYIINGTKRYITNAPEAGVFTVMARTDPQNKRSGGISAFIVESDT 190 Query: 201 QGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDVRGL--KGPFTCLNSARYGISWG 258 G++ I K+G + + T +++ DN VP + + V G+ K L+ R I+ Sbjct: 191 PGITLGKIDKKMGQKGAHTCDVIFDNCIVPADALIGGVEGVGFKTAMKVLDKGRLHIAAA 250 Query: 259 ALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQGCLRLGRMKDEG 318 + GAA A Y ++R+QFG+P+A QLIQ LAD + EI A L R++DEG Sbjct: 251 STGAATRMLDDALHYAVERKQFGQPIANFQLIQAMLADSKAEIYAAKSMVLDASRLRDEG 310 Query: 319 TAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLEVVNTYEGTHDVH 378 V +S K + +A A + GG G ++G+ R ++ + YEGT + Sbjct: 311 KDVVTESSCAKMFATEMCGRVADRAVQIHGGAGYIADYGIERFYRDVRLYRLYEGTTQIQ 370 Query: 379 ALILGR 384 +I+ R Sbjct: 371 QIIIAR 376 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: 369 Number of extensions: 14 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: 384 Length adjustment: 30 Effective length of query: 363 Effective length of database: 354 Effective search space: 128502 Effective search space used: 128502 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