Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate N515DRAFT_0492 N515DRAFT_0492 hypothetical protein
Query= BRENDA::Q96329 (436 letters) >FitnessBrowser__Dyella79:N515DRAFT_0492 Length = 386 Score = 179 bits (453), Expect = 2e-49 Identities = 119/380 (31%), Positives = 189/380 (49%), Gaps = 10/380 (2%) Query: 56 TPEEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKG-YGCPGLS 114 T ++ +I+ R+ +K + P+ E K EFP ++G +G+ G + YG G+ Sbjct: 6 TEDQLSIQSIARDFAQKRIVPVAAELDAKGEFPLENIREMGQLGLMGIEVPHEYGGAGMD 65 Query: 115 ITANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWAL 174 A +A EIA DA+ ST + V++SL I G+E QK+KY+ ++AQ + +AL Sbjct: 66 PIAYVLAMIEIAAADAATSTVMSVNNSLFCNGILKHGNEEQKQKYVRAIAQGEAIGAYAL 125 Query: 175 TEPDNGSDASGLGTTATK-VEGGWKINGQKRWIGNSTFADLLIIFARNTT---TNQINGF 230 TEP +GSDAS + T ATK +G W ING+K WI + A +++FA +T ++ F Sbjct: 126 TEPQSGSDASAMHTRATKNADGDWVINGKKSWITSGPVARYIVLFAISTPGIGARGVSAF 185 Query: 231 IVKKDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL-PGVNSFQDTSKVLAVSRV 289 I+ PG A K K+G+R +I + P E+ L F VL R+ Sbjct: 186 IIDTQLPGFAAGKTEPKLGIRASATCEIEFSDYVCPKENLLGEEGKGFSIAMGVLDAGRI 245 Query: 290 MVAWQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLM----GW 345 +A Q +GI+ Y+ ++ ++RK FG + +FQ+ Q K+ M + A L+ W Sbjct: 246 GIASQSVGIARAAYEATLQWSRDRKAFGQAIGSFQMTQAKIADMKCKLDAATLLTLRAAW 305 Query: 346 RLCKLYETGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIY 405 + + G +AS+ K S A A ++ GG G + + + F D + Sbjct: 306 TKGQAEKNGGRFGTEASVAKLVASEAAMWIAHQAVQIHGGMGYSKEMPLERYFRDAKITE 365 Query: 406 TYEGTYDINTLVTGREVTGI 425 YEGT +I LV R TG+ Sbjct: 366 IYEGTSEIQRLVIARAETGL 385 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: 377 Number of extensions: 20 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: 436 Length of database: 386 Length adjustment: 31 Effective length of query: 405 Effective length of database: 355 Effective search space: 143775 Effective search space used: 143775 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