Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate GFF1043 Psest_1076 acetyl-CoA acetyltransferases
Query= metacyc::MONOMER-20679 (395 letters) >FitnessBrowser__psRCH2:GFF1043 Length = 393 Score = 249 bits (636), Expect = 1e-70 Identities = 152/398 (38%), Positives = 226/398 (56%), Gaps = 21/398 (5%) Query: 1 MTEAVIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQ 60 M + VIV+ RT IG +++G+L L I +++ GI+P +V++V++G + Sbjct: 1 MQDVVIVAATRTAIG-SFQGSLANVPAVELGATVIRALLEKTGIEPAQVDEVILGHVLTA 59 Query: 61 GATGGNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESI 120 GA G N AR+A ++AGLP T+++ C SGL+A+ LA +++ ++ + GG E++ Sbjct: 60 GA-GQNTARQASIKAGLPHAVPSMTLNKVCGSGLKAVHLAVQAIRCGDADVIIAGGMENM 118 Query: 121 SLVQ--------NDKMNTFHAVDPALEAIKGDVY--MAMLDTAETVAKRYGISRERQDEY 170 SL +M VD + D + M TAE +A++YGI R +QD + Sbjct: 119 SLAPYVLPGARTGLRMGHAQIVDTMITDGLWDAFNDYHMGITAENLAEKYGIDRAQQDAF 178 Query: 171 SLESQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGL 230 + +SQ+R AAA + G+F+ EI P+ D + ++DE PR TTAE L Sbjct: 179 AAQSQQRAAAAIESGRFDAEITPVMIPQRKGDP---------LAFARDEQPRAGTTAESL 229 Query: 231 AGLKAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEM 290 GL+A + +TAGNAS L+DGA+A V+MS A A GL L G + G +P M Sbjct: 230 GGLRAAFKKDGCVTAGNASTLNDGAAAVVLMSASKAEALGLPVLAKIAGYANAGVDPAIM 289 Query: 291 GIGPVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGH 350 GIGPV A R L + G ++ ++ L E NEAFAVQ L +LG D +K+NVNGGAI++GH Sbjct: 290 GIGPVTATRRCLDKAGWTLAELDLIEANEAFAVQALSVGKELGWDADKVNVNGGAIALGH 349 Query: 351 PYGMSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSA 388 P G SG R+ L E +RR + + T+C+GGG G A Sbjct: 350 PIGASGCRILVTLLHEMQRRDVRKGLATLCIGGGQGVA 387 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: 431 Number of extensions: 27 Number of successful extensions: 4 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: 393 Length adjustment: 31 Effective length of query: 364 Effective length of database: 362 Effective search space: 131768 Effective search space used: 131768 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 Apr 09 2024. 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