Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate AZOBR_RS30610 AZOBR_RS30610 acetyl-CoA acetyltransferase
Query= SwissProt::P0C7L2 (401 letters) >FitnessBrowser__azobra:AZOBR_RS30610 Length = 391 Score = 330 bits (847), Expect = 3e-95 Identities = 189/400 (47%), Positives = 254/400 (63%), Gaps = 10/400 (2%) Query: 1 MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60 M E I RTPIG + GALSSV A L I +RE L R + DA + +VILG A Sbjct: 1 MTEVVIASAARTPIGSFNGALSSVPAHYLGEIAIREALSR-AKTDAAEVTEVILGQILTA 59 Query: 61 GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120 G+ +N AR A + AG+P S + IN+LCGSGL ++ +AI+ GD ++++ GG ESM Sbjct: 60 GQ-GQNPARQAAVNAGIPASATAFGINQLCGSGLRSVALGYQAIRNGDAEVMVVGGQESM 118 Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180 S+AP VM AEM DT + ++ GT TAENVA+ +++RE+ Sbjct: 119 SQAPHVMHLRNGVKMGAAEMLDTMLKDGLMDAFKGYHMGT-----TAENVAQKWQLTREE 173 Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240 QD FA SQQ+ AQ SG +EI+PV +K +KG + + DE+ + TT E L L+ Sbjct: 174 QDVFAAASQQKAEAAQKSGRFKDEIIPVTIKGRKGDII-VADDEYPKHGTTAESLAKLRP 232 Query: 241 PFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPV 300 F G +TAGNASG+NDGAAAL++ + + AA +GLTP ARIV+ ATAGV+P +MG GP+ Sbjct: 233 AFSKEGTVTAGNASGINDGAAALVLMTAENAARRGLTPLARIVSWATAGVDPAIMGTGPI 292 Query: 301 PATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLG 360 PA+R LE+AG D+D+IE NEAFAAQAL V ++LG D VN NGGAIALGHP+G Sbjct: 293 PASRLALEKAGWKHDDLDLIEANEAFAAQALAVNKDLGW--DTSKVNVNGGAIALGHPVG 350 Query: 361 MSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILER 400 SGAR+ +E+ +R+ + L T+CIG G GIA+ +ER Sbjct: 351 ASGARVLTTLLYEMQKRDAKKGLATLCIGGGMGIALTVER 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: 429 Number of extensions: 15 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 17 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