Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate AZOBR_RS28180 AZOBR_RS28180 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__azobra:AZOBR_RS28180 Length = 397 Score = 202 bits (515), Expect = 1e-56 Identities = 137/397 (34%), Positives = 206/397 (51%), Gaps = 28/397 (7%) Query: 5 VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64 VIVS ARTP+G+ ++G L+A L HA+ A+ RAG+ P+ V++V++G + G G Sbjct: 9 VIVSAARTPLGR-FQGELSALPAHALGAHAVRAALSRAGLAPERVDEVLLGCVLPAGQ-G 66 Query: 65 GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS--- 121 AR+A AGLP T TT+++ C SG++A LA + ++ V GG ES+S Sbjct: 67 QAPARQAARGAGLPDATGATTVNKVCGSGMKATMLAHDLIRAGSADLVVAGGMESMSNAP 126 Query: 122 ----------LVQNDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYS 171 + +D++ +D +A +G M D E A YG +R QD Y+ Sbjct: 127 YLLAKARGGYRIGHDRILDHLMLDGLEDAYEGGRPMG--DFGEATADLYGFTRAEQDAYA 184 Query: 172 LESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLA 231 +E+ R AA G F EIAP+ T AV + T++ DE P + E + Sbjct: 185 VETLTRARAAIASGAFTAEIAPV----------TLAVKGGERTVADDENPL-KVAPEKIP 233 Query: 232 GLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMG 291 LK TITA ++S +DGA+A ++ A +GL L G ++ +P Sbjct: 234 ALKPAFRRDGTITAASSSANADGAAALLLTRRSLAEREGLPVLATILGHATHSQDPAWFT 293 Query: 292 IGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHP 351 P+ A+ +LL R G + D+ L+E+NEAFAV + + LGI + LNVNGGA ++GHP Sbjct: 294 TAPIPAIRKLLDRVGWGIGDVDLFEINEAFAVVAMAAQRDLGIPRDALNVNGGACALGHP 353 Query: 352 YGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 G +GARL L R + V ++C+GGG +A Sbjct: 354 IGATGARLIVTLLHALAARGLRRGVASLCIGGGEATA 390 Lambda K H 0.316 0.134 0.378 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: 449 Number of extensions: 27 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 395 Length of database: 397 Length adjustment: 31 Effective length of query: 364 Effective length of database: 366 Effective search space: 133224 Effective search space used: 133224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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