Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate H281DRAFT_04737 H281DRAFT_04737 glutaryl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Burk376:H281DRAFT_04737 Length = 396 Score = 244 bits (624), Expect = 3e-69 Identities = 141/377 (37%), Positives = 215/377 (57%), Gaps = 3/377 (0%) Query: 55 LTPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSI-KGYGCPGL 113 LT +E+ +R + ++ P + E + + I ++G +G+ G +I + YG PGL Sbjct: 19 LTEDERMVRDAAAAYAQDKLQPRVLEAFRHEKTDIEIFREMGELGLLGPTIPEQYGGPGL 78 Query: 114 SITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWA 173 + A + E+ RVD+ + + V SSL M+ I GSEAQK+KYLP LA + C+ Sbjct: 79 NYVAYGLIAREVERVDSGYRSMMSVQSSLVMVPIYEFGSEAQKQKYLPKLATGEWIGCFG 138 Query: 174 LTEPDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFAR--NTTTNQINGFI 231 LTEP++GSD + T A KV+GG+ ++G K WI NS AD+ +++A+ + I GFI Sbjct: 139 LTEPNHGSDPGSMVTRAKKVDGGYSLSGSKMWITNSPIADVFVVWAKLEENGKDAIRGFI 198 Query: 232 VKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRLPGVNSFQDTSKVLAVSRVMV 291 ++K GL A I +K+GLR G+I+L VFVP+E+R P V+ + L +R + Sbjct: 199 LEKGWKGLSAPTIHSKVGLRASITGEIVLDEVFVPEENRFPEVSGLRGPFTCLNSARYGI 258 Query: 292 AWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLY 351 AW +G + + +Y+ +RKQFG PLAA QL Q+KL M + RL ++ Sbjct: 259 AWGALGAAESCWHTARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGRMK 318 Query: 352 ETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTY 411 + G S+ K KA + A L R++LGGNGI +F +A+ +LE + TYEGT+ Sbjct: 319 DEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGIARHLVNLEVVNTYEGTH 378 Query: 412 DINTLVTGREVTGIASF 428 DI+ L+ GR TGI +F Sbjct: 379 DIHALILGRAQTGIQAF 395 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: 384 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: 396 Length adjustment: 31 Effective length of query: 405 Effective length of database: 365 Effective search space: 147825 Effective search space used: 147825 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 Apr 09 2024. 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