Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_057509233.1 ABB28_RS14140 acetyl-CoA C-acyltransferase
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_001431535.1:WP_057509233.1 Length = 426 Score = 177 bits (448), Expect = 7e-49 Identities = 128/405 (31%), Positives = 199/405 (49%), Gaps = 71/405 (17%) Query: 39 VKRAGIDPKEVEDVVMGAAMQQGATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIA 98 V+R G+ +++ +V MGA ++ ++ N+ R+A L +GL T G T+ R C + L I Sbjct: 41 VERFGLHGQQLGEVAMGAVIKH-SSDWNLGREAALSSGLSPLTPGITMQRACGTSLDTII 99 Query: 99 LAARSVLFDGVEIAVGGGGESIS--------------LVQNDKMNTFHAVDPALEAIKGD 144 A + +E +GGG ++ S L N +T + K Sbjct: 100 AVANKIALGQIESGIGGGSDTTSDVPIVYGKKLRARLLAANRAKSTGDKIRALTRGFKFS 159 Query: 145 VYM-------------AMLDTAETVAKRYGISRERQDEYSLESQRRTAAAQQGGKFNDEI 191 + +M D E +AK + ISR+ QDE+++ S R+ AAA + G FND I Sbjct: 160 EFKPEFPGVAEPRTGKSMGDHCEDMAKEWNISRDSQDEWAVSSHRKLAAAYERGFFNDLI 219 Query: 192 APISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGLKA----VRGEGFTITAGN 247 AP F+ + +D R +T+ E LA LK V G G T+TA N Sbjct: 220 AP----------------FRGV--ERDNILRADTSLEKLATLKPAFDKVSGRG-TLTAAN 260 Query: 248 ASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCE---PDEMGIGPVFAVPRLLKR 304 ++ L+DGASA ++ S++ A A G PL R + + + + P AVP +LKR Sbjct: 261 STPLTDGASAVLLASEEWARAHGHAPLAYLRDSQVAAVDFVHGEGLLMAPTVAVPEMLKR 320 Query: 305 HGLSVDDIGLWELNEAFAVQVL----------YCRDKLG-------IDPEKLNVNGGAIS 347 +GL++ D ++E++EAFA QVL YCR++LG IDPEK+N G +++ Sbjct: 321 NGLTLQDFDIYEIHEAFAAQVLCTLRAWESEDYCRNRLGLDAPLGRIDPEKINPLGSSLA 380 Query: 348 VGHPYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 GHP+ +GAR+ A + R A+V++C GGMG + E Sbjct: 381 TGHPFAATGARVIATAAKQLAERGGGRALVSICTAGGMGVVAIVE 425 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: 389 Number of extensions: 18 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: 426 Length adjustment: 31 Effective length of query: 364 Effective length of database: 395 Effective search space: 143780 Effective search space used: 143780 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