Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_036834050.1 N784_RS08285 butyryl-CoA dehydrogenase
Query= BRENDA::Q96329 (436 letters) >NCBI__GCF_000775615.1:WP_036834050.1 Length = 400 Score = 174 bits (440), Expect = 6e-48 Identities = 119/377 (31%), Positives = 186/377 (49%), Gaps = 5/377 (1%) Query: 58 EEQAIRKKVRECMEKEVAPIMTEYWEKAEFPFHITPKLGAMGVAGGSIKG-YGCPGLSIT 116 E+Q +RK VRE ++KE+ P M E+ E+ F I KL +G+ G I YG G+ Sbjct: 8 EQQMLRKTVREFVDKEIIPYMKEWDERGTFDPAIMHKLADLGLMGVCIPTKYGGSGMDYN 67 Query: 117 ANAIATAEIARVDASCSTFILVHSSLGMLTIALCGSEAQKEKYLPSLAQLNTVACWALTE 176 A AI E+ R D + T + VH+ L L++ G+E QKEKYL A+ + + LTE Sbjct: 68 ALAIVCEELERGDTAFRTAVSVHTGLNSLSLLQFGTEEQKEKYLIPQAKGEKIGAFGLTE 127 Query: 177 PDNGSDASGLGTTATKVEGGWKINGQKRWIGNSTFADLLIIFA---RNTTTNQINGFIVK 233 P GSD + + TTAT+ + +NGQK WI AD ++FA + I+ FIV+ Sbjct: 128 PGAGSDVASIQTTATRKGDYYTLNGQKSWISLCDSADHFLVFAYTDKEKKHQGISAFIVE 187 Query: 234 KDAPGLKATKIPNKIGLRMVQNGDILLQNVFVPDEDRL-PGVNSFQDTSKVLAVSRVMVA 292 + G + K+G+R G++ L++V VP ++RL + F+ L R VA Sbjct: 188 RTMEGFSSKATKGKLGIRAGNTGELFLEDVPVPVDNRLGEEGDGFKIAMASLDNGRFTVA 247 Query: 293 WQPIGISMGIYDMCHRYLKERKQFGAPLAAFQLNQQKLVQMLGNVQAMFLMGWRLCKLYE 352 G+ M + RY ER+ FG + QL QQ + M +Q L+ +R +L Sbjct: 248 AGACGLMMACLEASVRYCHERETFGKEIGKHQLVQQMIANMEAGLQMSRLLVYRAGELKN 307 Query: 353 TGQMTPGQASLGKAWISSKARETASLGRELLGGNGILADFLVAKAFCDLEPIYTYEGTYD 412 +G+ + SL K A + A ++ G G ++ V + + + YEGT + Sbjct: 308 SGKRNTRETSLAKWQACDFANKAADDAVQIHGAYGYSNEYAVERYLRNSKAPVIYEGTRE 367 Query: 413 INTLVTGREVTGIASFK 429 I+T++ V G + K Sbjct: 368 IHTIMQAEYVLGYRTDK 384 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: 349 Number of extensions: 17 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: 400 Length adjustment: 32 Effective length of query: 404 Effective length of database: 368 Effective search space: 148672 Effective search space used: 148672 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 24 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