Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate N515DRAFT_0484 N515DRAFT_0484 glutaryl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Dyella79:N515DRAFT_0484 Length = 389 Score = 228 bits (580), Expect = 3e-64 Identities = 134/384 (34%), Positives = 205/384 (53%), Gaps = 5/384 (1%) Query: 47 DYYHFNDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI- 105 D Y LLT EE+ ++ V +++ V PI+ + +++ FP + P++ +G+ G ++ Sbjct: 9 DLYDVRSLLTDEERMVQDTVGRFVDERVLPIIGDAFDQGRFPKELIPEIAGLGLLGATLP 68 Query: 106 KGYGCPGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQ 165 + YGC G++ + + E+ R D+ +F V SSL M I G+E QK YLP +A Sbjct: 69 EQYGCAGMNGVSYGLICQELERGDSGLRSFASVQSSLCMYPIYAYGTEEQKLHYLPKMAA 128 Query: 166 LNTVACWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFARNTTTN 225 + C+ LTEP GSD + + T A K G W ING K WI N A + I++A+ T + Sbjct: 129 GEIIGCFGLTEPHGGSDPANMKTNARKDGGDWIINGAKMWITNGNLAHIAIVWAQ--TED 186 Query: 226 QINGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLA 285 I GFIV D+ G A ++ K+ LR + +V VP+ +RLP V + L Sbjct: 187 GIQGFIVPTDSQGFTAQEVHKKMSLRASVTSALFFDSVRVPEANRLPNVKGLKGPLGCLT 246 Query: 286 VSRVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGW 345 +R + W PIG + Y +ER FG PLA+ Q Q KL +M + L+ Sbjct: 247 QARYGITWGPIGAAQACLKEVLDYTQERVLFGRPLASNQAIQLKLAEMARRITMAQLLSL 306 Query: 346 RLCKLYETGQMTPGQASLGKAWISSK-ARETASLGRELLGGNGILADFLVAKAFCDLEPI 404 +L +L + G M P Q SL K W + + A + A R++LGG GI + + + +LE + Sbjct: 307 QLGRLKDAGNMQPTQVSLAK-WNNCRIAIDIARECRDILGGAGITTEHVAIRHALNLESV 365 Query: 405 YTYEGTYDINTLVTGREVTGIASF 428 TYEGT ++ LV GRE+TGI +F Sbjct: 366 ITYEGTETVHQLVVGRELTGINAF 389 Lambda K H 0.319 0.133 0.399 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: 326 Number of extensions: 20 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: 436 Length of database: 389 Length adjustment: 31 Effective length of query: 405 Effective length of database: 358 Effective search space: 144990 Effective search space used: 144990 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 (21.7 bits) S2: 50 (23.9 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