Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate WP_035235479.1 Q366_RS00870 acetyl-CoA C-acyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000745975.1:WP_035235479.1 Length = 392 Score = 264 bits (675), Expect = 3e-75 Identities = 161/409 (39%), Positives = 223/409 (54%), Gaps = 25/409 (6%) Query: 1 MREAFICDGIRTP-IGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQ 59 MR+A+I +RTP + G + R ++L + ++E + R L E IDDV+LGCA Sbjct: 1 MRDAYIVQSVRTPGCKQKKGLFNQTRPEELISFIMKEAVERTVNLKPEDIDDVMLGCAFP 60 Query: 60 AGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVES 119 E N+ R+A +AG P VSG T+NR C SGL+A+ A+ + AG D+ + G ES Sbjct: 61 EAEQGLNLGRIAAKMAGFPDEVSGATVNRFCASGLEAIALASVRVSAGWSDICVGAGCES 120 Query: 120 MSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRE 179 M+ P R + T +V SM TAENVA K+SRE Sbjct: 121 MTFVPM-----GGNVPRPHPEYSKTYPEMYV-----------SMGITAENVASRYKVSRE 164 Query: 180 DQDSFALRSQQRTAKAQSSGILAEEIVPVVLK-------NKKGVVTEIQHDEHLRPETTL 232 DQD FA SQ + A+ +G E I K K ++HD+ +R T Sbjct: 165 DQDIFAAASQAKATAARDNGKFTEIIPTPAYKYVVQPDGTYKKETFIVEHDDGIRLSTP- 223 Query: 233 EQLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEP 292 E L L A F+ NG +TAGN+S DGAAA IIAS++ GLTP AR+V T G + Sbjct: 224 EGLAKLGAVFKVNGSVTAGNSSQTTDGAAASIIASKEKCKELGLTPIARLVGYTTVGCKA 283 Query: 293 RLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGA 352 MG+GP A +VL++ G++I D+D+ E+NEAFA+QAL +RELG+ +N +GGA Sbjct: 284 DEMGVGPKYAIPKVLKQVGMTIDDIDIYEINEAFASQALHCIRELGIEKYMDKINIHGGA 343 Query: 353 IALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 IALGHPLG +GA+L L G+Y + +MCIG G G A + E++ Sbjct: 344 IALGHPLGCTGAKLTATCIANLREVGGKYGVVSMCIGGGMGAAAVFEKL 392 Lambda K H 0.319 0.135 0.384 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: 428 Number of extensions: 19 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: 401 Length of database: 392 Length adjustment: 31 Effective length of query: 370 Effective length of database: 361 Effective search space: 133570 Effective search space used: 133570 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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