Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate RR42_RS15400 RR42_RS15400 acyl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Cup4G11:RR42_RS15400 Length = 397 Score = 236 bits (601), Expect = 1e-66 Identities = 137/381 (35%), Positives = 215/381 (56%), Gaps = 4/381 (1%) Query: 52 NDLLTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGC 110 +D L+ +E+ +R + ++AP + + + + I ++G +G+ G +I + YG Sbjct: 16 DDQLSADERMVRDAALAYCQDKLAPRVLQSFRNEKTDIEIFREMGELGLLGPTIPEEYGG 75 Query: 111 PGLSITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVA 170 PGL+ A + E+ RVD+ + + V SSL M+ I GSEAQK+KYLP LA + Sbjct: 76 PGLNYVAYGLIAREVERVDSGYRSMMSVQSSLVMVPIHEFGSEAQKQKYLPKLATGEWIG 135 Query: 171 CWALTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR---NTTTNQI 227 C+ LTEP++GSD + T A KV GG++++G K WI NS AD+ +++ + + I Sbjct: 136 CFGLTEPNHGSDPGSMITRAKKVAGGYELSGAKMWITNSPIADVFVVWGKLVGDDGKEAI 195 Query: 228 NGFIVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVS 287 GFI++K GL A I K+GLR G+I++ VFVP+E+ +PGV+ + L + Sbjct: 196 RGFILEKGWKGLSAPAIHGKVGLRTSITGEIVMDQVFVPEENLMPGVSGLKGPFTCLNSA 255 Query: 288 RVMVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRL 347 R +AW +G + + +Y +RKQFG PLAA QL Q+KL M + RL Sbjct: 256 RYGIAWGALGAAEFCWHTARQYTLDRKQFGRPLAANQLVQKKLADMQTEITLGLQGCLRL 315 Query: 348 CKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTY 407 ++ + G S+ K K+ + A + R++LGGNGI +F V + +LE + TY Sbjct: 316 GRMKDEGTAAVEITSIMKRNSCGKSLDIARVARDMLGGNGISDEFGVIRHVVNLEVVNTY 375 Query: 408 EGTYDINTLVTGREVTGIASF 428 EGT+DI+ L+ GR TGI +F Sbjct: 376 EGTHDIHALILGRAQTGIQAF 396 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: 393 Number of extensions: 16 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: 436 Length of database: 397 Length adjustment: 31 Effective length of query: 405 Effective length of database: 366 Effective search space: 148230 Effective search space used: 148230 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