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_093396481.1 BM091_RS13320 thiolase family protein
Query= SwissProt::P0C7L2 (401 letters) >NCBI__GCF_900114975.1:WP_093396481.1 Length = 397 Score = 287 bits (734), Expect = 4e-82 Identities = 180/415 (43%), Positives = 234/415 (56%), Gaps = 38/415 (9%) Query: 1 MREAFICDGIRTPIGRYG--GALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCAN 58 + E + D IRTP GR G G RA+DLA + LL RNP LD IDD I G N Sbjct: 5 LEEVVVVDSIRTPFGRAGEKGIFWKTRAEDLAVAVFKALLERNPSLDLSTIDDSIWGVTN 64 Query: 59 QAGEDNRNVARMATLLA------GLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLL 112 Q E + RM +LA G+P G +I+R+C S L A+GF A I +G + + Sbjct: 65 QVREQGGTLGRMVPILAYGEKGWGIP----GCSIDRMCASSLTAVGFGAAMIASGMAECI 120 Query: 113 IAGGVESMSRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDS---MPETAEN 169 IAGGVE M P F R ++P A+ G ++ M +TAEN Sbjct: 121 IAGGVEHMGHLPM-------GFMRD------------LHPRAAEALGDETALVMGQTAEN 161 Query: 170 VAELL-KISREDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRP 228 + + + +RE D +A SQQ+ AKA +G + + +VPV ++ G I+ D+ RP Sbjct: 162 IHDRFPEFTREMADMYAFMSQQKAAKAIRAGKMRDMMVPVEVELPDGTKALIREDQTPRP 221 Query: 229 ETTLEQLRGLKAPFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATA 288 +TTLE+L LK FR NG +TAGNA + DGAAA++I SE A GLTP+ R V A A Sbjct: 222 DTTLEKLASLKPAFRENGRVTAGNACPLTDGAAAVLIMSESRARKLGLTPKMRFVTCAVA 281 Query: 289 GVEPRLMGLGPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNP 348 GV+PR+MG PVPAT++ L +AGL + D+DVIE+NEAFA Q L L LGL D P VN Sbjct: 282 GVDPRIMGTAPVPATQKALAKAGLKMDDIDVIEINEAFAVQVLYCLDRLGLTADDPRVNM 341 Query: 349 NGGAIALGHPLGMSGARLA--LAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401 GGAIA GHPL SGARL L E H RY + T+C+G GQG +I E + Sbjct: 342 WGGAIAYGHPLAASGARLIAFLQRIFEEHPEY-RYGITTLCVGRGQGYTVIWENL 395 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: 437 Number of extensions: 34 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: 397 Length adjustment: 31 Effective length of query: 370 Effective length of database: 366 Effective search space: 135420 Effective search space used: 135420 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