Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate CCNA_03184 CCNA_03184 acyl-CoA dehydrogenase
Query= metacyc::G1G01-166-MONOMER (393 letters) >FitnessBrowser__Caulo:CCNA_03184 Length = 564 Score = 174 bits (441), Expect = 6e-48 Identities = 125/390 (32%), Positives = 191/390 (48%), Gaps = 19/390 (4%) Query: 12 PLLLDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPA-IFREMGEVGLLGATIP 70 P L L E M+RD + FA++K+ P E ++ P + +E+GE+G+ G TIP Sbjct: 170 PTLEQTGLDETFEMIRDQFHAFAEEKVTPFAHEWHLKDELIPLELVQELGELGVFGLTIP 229 Query: 71 EQYGGSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLAS 130 E++GGSG+ +++ E+ R G S+ + +S + I GT+AQK+ +LP++AS Sbjct: 230 EEFGGSGMGKTAMCVVSEELSRAWIGVGSL-ATRSEIAGELILTGGTDAQKEYWLPRIAS 288 Query: 131 GEWIGCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAG- 189 E + TEPN GSD G++ TRA Y +TG+K WIT++ ADV + + D Sbjct: 289 AEILPTAVFTEPNTGSDLGALRTRAELKGDSYVVTGNKTWITHAARADVMTLLVRTDPAT 348 Query: 190 -DIRGFVL-----EKGW-------QGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFP 236 D RG + +G +G+S I G +G R E+ D VP EN+ Sbjct: 349 TDYRGLSMLLAPKPRGTDEAPFPAEGMSGGEI-GVIGYRGMKEYELGFDGFTVPAENLLG 407 Query: 237 DV--RGLKGPFTCLNSARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKL 294 V +G K SAR + A+G A+A Y LDR+QFG+P+ + KL Sbjct: 408 GVTGQGFKQLMATFESARIQTAARAVGVAQAALEVGLSYALDRKQFGQPIFDFPRVHNKL 467 Query: 295 ADMQTEITLALQGCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISD 354 A M EI Q KDEG + K + A A A + GGNG + Sbjct: 468 AMMAAEIMGVRQLTYFAAHQKDEGKRCDLEAGMAKLIAARVAWAAADNALQIHGGNGFAM 527 Query: 355 EFGVARHLVNLEVVNTYEGTHDVHALILGR 384 E+ +R L + ++N +EG ++ A ++ R Sbjct: 528 EYAASRLLADARILNIFEGAGEIQAQVIAR 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: 536 Number of extensions: 32 Number of successful extensions: 4 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: 564 Length adjustment: 33 Effective length of query: 360 Effective length of database: 531 Effective search space: 191160 Effective search space used: 191160 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