Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__azobra:AZOBR_RS30610 Length = 391 Score = 255 bits (652), Expect = 1e-72 Identities = 161/397 (40%), Positives = 228/397 (57%), Gaps = 21/397 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 MTE VI S ARTPIG ++ GAL++ L AI A+ RA D EV +V++G + Sbjct: 1 MTEVVIASAARTPIG-SFNGALSSVPAHYLGEIAIREALSRAKTDAAEVTEVILGQILTA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G N AR+A + AG+P + I++ C SGL+++AL +++ E+ V GG ES+ Sbjct: 60 GQ-GQNPARQAAVNAGIPASATAFGINQLCGSGLRSVALGYQAIRNGDAEVMVVGGQESM 118 Query: 121 S-------LVQNDKMNTFHAVDPALEAIKGDVYMA--MLDTAETVAKRYGISRERQDEYS 171 S L KM +D L+ D + M TAE VA+++ ++RE QD ++ Sbjct: 119 SQAPHVMHLRNGVKMGAAEMLDTMLKDGLMDAFKGYHMGTTAENVAQKWQLTREEQDVFA 178 Query: 172 LESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLA 231 SQ++ AAQ+ G+F DEI P++ K G DI ++ DE P+ TTAE LA Sbjct: 179 AASQQKAEAAQKSGRFKDEIIPVTIK--------GRKG--DIIVADDEYPKHGTTAESLA 228 Query: 232 GLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMG 291 L+ + T+TAGNAS ++DGA+A V+M+ + AA +GL PL + G +P MG Sbjct: 229 KLRPAFSKEGTVTAGNASGINDGAAALVLMTAENAARRGLTPLARIVSWATAGVDPAIMG 288 Query: 292 IGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHP 351 GP+ A L++ G DD+ L E NEAFA Q L LG D K+NVNGGAI++GHP Sbjct: 289 TGPIPASRLALEKAGWKHDDLDLIEANEAFAAQALAVNKDLGWDTSKVNVNGGAIALGHP 348 Query: 352 YGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 G SGAR+ L E ++R AK + T+C+GGGMG A Sbjct: 349 VGASGARVLTTLLYEMQKRDAKKGLATLCIGGGMGIA 385 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: 371 Number of extensions: 19 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: 395 Length of database: 391 Length adjustment: 31 Effective length of query: 364 Effective length of database: 360 Effective search space: 131040 Effective search space used: 131040 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