Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate YP_004145059.1 Mesci_6002 acetyl-CoA acetyltransferase
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_000185905.1:YP_004145059.1 Length = 402 Score = 254 bits (649), Expect = 3e-72 Identities = 163/424 (38%), Positives = 228/424 (53%), Gaps = 45/424 (10%) Query: 1 MREAFICDGIRTPIGR--YGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCAN 58 M EA++ D +RTP G+ G+L V A LAA L L RN LD +DD+I GC + Sbjct: 1 MAEAYVYDAVRTPRGKGKKDGSLHEVPAVRLAAKTLEALRDRNG-LDTANVDDIIFGCVD 59 Query: 59 QAGEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVE 118 GE + R A AG G I+R C SGLDA+ F A I G +++IAGGVE Sbjct: 60 PVGEAGSVIPRAAAFEAGYDTKAPGMQISRFCASGLDAINFGAAKIAQGADEIVIAGGVE 119 Query: 119 SMSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISR 178 SMSR MG + A+ F++P + +A+ +A R Sbjct: 120 SMSRVG--MGASGGAW--------------FMDPSVGLPGWFVPQGISADLIATKYGFRR 163 Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238 +D D++A+ SQ+R AK+ + G + ++P+ K++ G+ T + HDEH+RP T ++ L L Sbjct: 164 DDVDAYAVESQKRAAKSWADGRFKKSVIPI--KDQNGL-TILDHDEHMRPSTDMQSLASL 220 Query: 239 KAPF---------------------RANGVITAGNASGVNDGAAALIIASEQMAAAQGLT 277 F N V AGN+SG+ DGAAA+++ S++ A GL Sbjct: 221 NPSFVMPGEMGGFDAVAVQKHPEVEEVNHVHHAGNSSGIVDGAAAVLLGSKKAGKAMGLK 280 Query: 278 PRARIVAMATAGVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLREL 337 PRARI A G EP LM GPV T ++L+RA + + D+D+ ELNEAFA+ L ++ Sbjct: 281 PRARIRTFANIGSEPVLMLTGPVDVTEKLLKRAKMKLSDIDLFELNEAFASVVLRYMQAF 340 Query: 338 GLPDDAPHVNPNGGAIALGHPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMI 397 +P D +N NGGAIA+GHPLG +GA + EL RR+ AL T+CIG G G A I Sbjct: 341 DIPHD--KINVNGGAIAMGHPLGATGAMIFGTVLDELERRDLNTALVTLCIGAGMGTATI 398 Query: 398 LERV 401 +ERV Sbjct: 399 IERV 402 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: 421 Number of extensions: 16 Number of successful extensions: 7 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: 402 Length adjustment: 31 Effective length of query: 370 Effective length of database: 371 Effective search space: 137270 Effective search space used: 137270 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