Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate AZOBR_RS20220 AZOBR_RS20220 acetyl-CoA acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__azobra:AZOBR_RS20220 Length = 382 Score = 267 bits (682), Expect = 4e-76 Identities = 159/390 (40%), Positives = 220/390 (56%), Gaps = 16/390 (4%) Query: 5 VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64 VI AR+P A +G L LL H + V+R G++P+++EDVV+G A +G G Sbjct: 9 VIAGYARSPFAFANKGELAKVRPDDLLAHVVAALVERTGVNPQDIEDVVVGCAFPEGEQG 68 Query: 65 GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESISLVQ 124 NIAR A LP+T TTI+R C S +QAI AA ++ E+ + GG ES+S V Sbjct: 69 MNIARTVSFLAKLPLTAGATTINRYCGSSMQAIHQAAGAIQMGAGEVFLCGGIESMSRVP 128 Query: 125 NDKMNTFHAVDPALEAIKGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAAAQQG 184 N P L+ + Y +M TAE VA+RY ISR Q+ + ES + AAAQQ Sbjct: 129 MMGYNPLP--HPGLKDHYPEAYCSMGVTAENVARRYEISRADQEAMAAESHAKAAAAQQA 186 Query: 185 GKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKAVRGEGFTIT 244 G+ +EI I T G+V++ D RP T+ E L+GLK ++T Sbjct: 187 GRLAEEIVAIQTAAGLVER--------------DGCIRPGTSGETLSGLKPAFLADGSVT 232 Query: 245 AGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIGPVFAVPRLLKR 304 AG +S L+DGASA ++ ++ A A GL L R + GC P+ MG+GPV A + L R Sbjct: 233 AGTSSPLTDGASAVLVTTEAYAKANGLPILARIRSVAVAGCAPEVMGLGPVPAAQKALAR 292 Query: 305 HGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYGMSGARLAGHAL 364 GLS+ DI + ELNEAFA Q + C L IDP K+N++GGAI++GHP G +GAR+ G A Sbjct: 293 AGLSIRDIDVIELNEAFAAQAIACMRDLDIDPAKVNLDGGAIALGHPLGATGARITGKAA 352 Query: 365 IEGRRRKAKYAVVTMCVGGGMGSAGLFEIV 394 +R ++A+ T C+GGG G A + E V Sbjct: 353 ALLKREGKQFALATQCIGGGQGIATVLEAV 382 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: 376 Number of extensions: 16 Number of successful extensions: 3 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: 382 Length adjustment: 30 Effective length of query: 365 Effective length of database: 352 Effective search space: 128480 Effective search space used: 128480 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