Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate N515DRAFT_3009 N515DRAFT_3009 acetyl-CoA C-acetyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__Dyella79:N515DRAFT_3009 Length = 427 Score = 169 bits (428), Expect = 1e-46 Identities = 125/405 (30%), Positives = 195/405 (48%), Gaps = 71/405 (17%) Query: 39 VKRAGIDPKEVEDVVMGAAMQQGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIA 98 V+R + +E+ +V MGA ++ + N+AR+A+L +GL TT G T R C + L Sbjct: 42 VERFRLHGEELGEVAMGAVIKHSSEW-NLAREAVLSSGLAPTTPGITTARACGTSLDNAI 100 Query: 99 LAARSVLFDGVEIAVGGGGESISLVQ--------------------NDKMNTF------H 132 + A + +E + GG ++ S V DKM F Sbjct: 101 IIANKIAAGQIEAGIAGGSDTTSDVPIVLGERFRKRLLAINRAKGWQDKMAAFTRGFSLK 160 Query: 133 AVDPALEAI-KGDVYMAMLDTAETVAKRYGISRERQDEYSLESQRRTAAAQQGGKFNDEI 191 + P+ + + M+M D E +AK + I RE QD +LES ++ AAA + G F D + Sbjct: 161 ELKPSFPGVAEPRTGMSMGDHCERMAKEWHIGREAQDRLALESHQKLAAAYEAGFFEDLV 220 Query: 192 APISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKA----VRGEGFTITAGN 247 P L +D R +++ E L LK + G G T+TAGN Sbjct: 221 VPFRG------------------LKRDGFLRADSSMEKLGTLKPAFDKISGHG-TLTAGN 261 Query: 248 ASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCE---PDEMGIGPVFAVPRLLKR 304 ++ LSDGA+A ++ SD+ AA +GLK F + + + + P AVPR+L R Sbjct: 262 STGLSDGAAAVLLGSDEWAARRGLKVQAYFLDAEVAAVDFVHGEGLLMAPTVAVPRMLAR 321 Query: 305 HGLSVDDIGLWELNEAFAVQVL----------YCRDKLG-------IDPEKLNVNGGAIS 347 HGL++ D +E++EAFA QVL YCR++LG IDP KLNV+G +++ Sbjct: 322 HGLTLQDFDFYEIHEAFAAQVLCTLRAWESETYCRNRLGLEQPLGSIDPAKLNVHGSSLA 381 Query: 348 VGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 GHP+ +GAR+ + + ++++C GGMG + E Sbjct: 382 AGHPFAATGARIVATLAKMLEEKGSGRGLISICTAGGMGVTAILE 426 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: 405 Number of extensions: 21 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: 427 Length adjustment: 31 Effective length of query: 364 Effective length of database: 396 Effective search space: 144144 Effective search space used: 144144 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