Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_012784175.1 AFER_RS00420 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_000023265.1:WP_012784175.1 Length = 391 Score = 254 bits (650), Expect = 2e-72 Identities = 162/397 (40%), Positives = 222/397 (55%), Gaps = 14/397 (3%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M +AVIV RTP+G+ GAL+ L +E V R GIDP VEDV+MG Q Sbjct: 1 MRDAVIVDVVRTPVGRR-NGALSGWHAVDLASTVLEALVARTGIDPALVEDVIMGCVSQV 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 G G N+AR A+L AG P + GTT+DRQC S QA+A AA+ VL ++ + G ES+ Sbjct: 60 GEQGINVARNAVLAAGFPESVPGTTVDRQCGSSQQAVAFAAQGVLAGAYDVVIAAGVESM 119 Query: 121 SLVQ--NDKMNTFHAVDPALE---AIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQ 175 S V ++ + P +E A +G + + +AE + +R+G++R+ D ++L S Sbjct: 120 SRVPMGSNGVGPGSPFGPRVEARYAARGGLVPQGI-SAELIVERWGLTRQELDAFALRSH 178 Query: 176 RRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKA 235 R A G+F EI PI + +A GA + L DEG RP+T+ E L LK Sbjct: 179 ERAWTATTEGRFKSEILPIEGR-----RADGAAA--PTVLEADEGIRPDTSLEALGSLKP 231 Query: 236 VRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPV 295 T+TAGNASQ+SDGA+A +IM + A GL P +P M P+ Sbjct: 232 AFVPTGTVTAGNASQISDGAAAALIMDAERARRLGLVPRARVVAFSLAADDPIMMLTAPI 291 Query: 296 FAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMS 355 A R+L+R LS+DDI L E+NEAFA VL +L D +++NVNGGAI++GHP G S Sbjct: 292 PATRRVLERAHLSLDDIDLVEINEAFASVVLAWGAELHPDWDRVNVNGGAIALGHPLGAS 351 Query: 356 GARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 GARL + E RR +Y + TMC GGGM +A + E Sbjct: 352 GARLLATLVNELERRGGRYGLQTMCEGGGMANALVIE 388 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: 388 Number of extensions: 18 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: 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 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