Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate GFF109 PGA1_c01110 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__Phaeo:GFF109 Length = 561 Score = 166 bits (419), Expect = 2e-45 Identities = 126/384 (32%), Positives = 188/384 (48%), Gaps = 20/384 (5%) Query: 19 LTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPA-IFREMGEVGLLGATIPEQYGGSG 77 L EE M+RD ++A +K+ P + ++ P I E+ E+G+ G TIPE+YGG G Sbjct: 176 LDEELEMIRDQFRRYALEKVEPNAHDWHLKDELIPMEIIEELAEMGVFGLTIPEEYGGFG 235 Query: 78 LNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWIGCF 137 L+ +++ E+ R G S+ +S + I GTE QK +LPK+AS E + Sbjct: 236 LSKASMCVVSEELSRGYIGVGSL-GTRSEIAAELIIAGGTEEQKASWLPKIASAEILPTA 294 Query: 138 GLTEPNHGSDPGSMITRARKVDGG-YRLTGSKMWITNSPIADVFVVWAK--DDAGDIRG- 193 TEPN GSD GS+ TRA K D G Y++TG+K WIT++ V + A+ D D RG Sbjct: 295 VFTEPNTGSDLGSLRTRAVKDDNGDYQITGNKTWITHAARTHVMTLLARTDPDTTDHRGL 354 Query: 194 --FVLEK---------GWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIF--PDVRG 240 F+ EK +G++ I +G R E+ D V EN+ + +G Sbjct: 355 SMFLAEKTPGTDENPFPTEGMTGGEIE-VLGYRGMKEYELGFDGFHVKRENLLGGDEGKG 413 Query: 241 LKGPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTE 300 K SAR + A+G A++ A QY DR+QFG+PL A + KLA M E Sbjct: 414 FKQLMETFESARIQTAARAIGVAQSALDIAMQYAQDRKQFGKPLIAFPRVASKLAMMAVE 473 Query: 301 ITLALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVAR 360 I +A Q KD G + K A A + GGNG + E+ ++R Sbjct: 474 IMIARQLTYFSAWEKDNGHRCDLEAGMAKLLGARVAWAAADNGLQIHGGNGFALEYKISR 533 Query: 361 HLVNLEVVNTYEGTHDVHALILGR 384 L + ++N +EG ++ A ++ R Sbjct: 534 VLCDARILNIFEGAAEIQAQVIAR 557 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: 550 Number of extensions: 33 Number of successful extensions: 5 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: 561 Length adjustment: 33 Effective length of query: 360 Effective length of database: 528 Effective search space: 190080 Effective search space used: 190080 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: 51 (24.3 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