Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_017223337.1 A923_RS0119275 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000276805.1:WP_017223337.1 Length = 403 Score = 210 bits (535), Expect = 5e-59 Identities = 138/409 (33%), Positives = 216/409 (52%), Gaps = 35/409 (8%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M + IV+ RT +G ++ G+L + ATL AI+ A+ A ++P+ V++V++G + Sbjct: 1 MNKVFIVAAKRTALG-SFGGSLAGVDAATLGATAIKGALAAAKVNPEHVDEVIVGNVISA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G R+A ++AG+P + T++ C SG++ I A + +I V G ES+ Sbjct: 60 GQ-GMGPGRQAAMQAGIPASVPAYTLNMICGSGMKTIMDGAAHIKAGDADIVVAAGMESM 118 Query: 121 SLVQ---------NDKMNTFHAVDPALEAIKGDVY----MAMLDTAETVAKRYGISRERQ 167 S + KM VD + DV+ M M TAE + ++G++RE+Q Sbjct: 119 SNIPYLMPAKTRFGSKMGNMTMVDAMINDGLTDVFNNYHMGM--TAENIVDQFGLTREQQ 176 Query: 168 DEYSLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTA 227 D +++ SQ + AA +F DEI P+ K V + + + DE P+ T+ Sbjct: 177 DTFAVGSQHKAVAAIAAERFVDEIVPVEIK----------VRRQTQSFATDEYPKDNTSV 226 Query: 228 EGLAGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEP 287 EGLA L+ ++TA NAS ++DGASA ++ S GL+P+ G +P Sbjct: 227 EGLAKLRPAFKTDGSVTAANASGINDGASAIILASAAAVEKYGLEPMAELIAYGQGGVDP 286 Query: 288 DEMGIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKL----GID----PEKL 339 MG+GPV A+ + LKR +S++ + L ELNEAFA Q L L +D +K Sbjct: 287 QVMGLGPVPAIEQALKRADMSLEQMELLELNEAFAAQALGVMTNLTQEHNVDMDWFADKT 346 Query: 340 NVNGGAISVGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 NVNGGAI++GHP G SG R+ L E ++R Y + ++C+GGGMG+A Sbjct: 347 NVNGGAIALGHPLGASGGRITVTLLHEMQKRGVDYGLASLCIGGGMGTA 395 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: 427 Number of extensions: 32 Number of successful extensions: 6 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: 403 Length adjustment: 31 Effective length of query: 364 Effective length of database: 372 Effective search space: 135408 Effective search space used: 135408 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 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