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_012784175.1 AFER_RS00420 acetyl-CoA C-acyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000023265.1:WP_012784175.1 Length = 391 Score = 309 bits (791), Expect = 1e-88 Identities = 186/403 (46%), Positives = 244/403 (60%), Gaps = 15/403 (3%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 MR+A I D +RTP+GR GALS A DLA+ L E LV +D ++DVI+GC +Q Sbjct: 1 MRDAVIVDVVRTPVGRRNGALSGWHAVDLASTVL-EALVARTGIDPALVEDVIMGCVSQV 59 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 GE NVAR A L AG P+SV GTT++R CGS A+ FAA+ + AG D++IA GVESM Sbjct: 60 GEQGINVARNAVLAAGFPESVPGTTVDRQCGSSQQAVAFAAQGVLAGAYDVVIAAGVESM 119 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180 SR P MG F + R+ A + G +AE + E ++R++ Sbjct: 120 SRVP--MGSNGVG---PGSPFGPRVEARY-----AARGGLVPQGISAELIVERWGLTRQE 169 Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVV--TEIQHDEHLRPETTLEQLRGL 238 D+FALRS +R A + G EI+P+ + G T ++ DE +RP+T+LE L L Sbjct: 170 LDAFALRSHERAWTATTEGRFKSEILPIEGRRADGAAAPTVLEADEGIRPDTSLEALGSL 229 Query: 239 KAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLG 298 K F G +TAGNAS ++DGAAA +I + A GL PRAR+VA + A +P +M Sbjct: 230 KPAFVPTGTVTAGNASQISDGAAAALIMDAERARRLGLVPRARVVAFSLAADDPIMMLTA 289 Query: 299 PVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHP 358 P+PATRRVLERA LS+ D+D++E+NEAFA+ L E L D VN NGGAIALGHP Sbjct: 290 PIPATRRVLERAHLSLDDIDLVEINEAFASVVLAWGAE--LHPDWDRVNVNGGAIALGHP 347 Query: 359 LGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 LG SGARL +EL RR GRY L TMC G G A+++ER+ Sbjct: 348 LGASGARLLATLVNELERRGGRYGLQTMCEGGGMANALVIERL 390 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: 473 Number of extensions: 21 Number of successful extensions: 5 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: 391 Length adjustment: 31 Effective length of query: 370 Effective length of database: 360 Effective search space: 133200 Effective search space used: 133200 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