Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate RR42_RS26090 RR42_RS26090 acetyl-CoA acetyltransferase
Query= SwissProt::P14611 (393 letters) >FitnessBrowser__Cup4G11:RR42_RS26090 Length = 391 Score = 600 bits (1547), Expect = e-176 Identities = 304/392 (77%), Positives = 340/392 (86%), Gaps = 1/392 (0%) Query: 1 MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60 M DVVIV+AARTAVGKFGGSLAK+PAPELGA VIKA LER+G+KPE V EV++GQVLTAG Sbjct: 1 MEDVVIVAAARTAVGKFGGSLAKVPAPELGATVIKALLERSGLKPEMVDEVLLGQVLTAG 60 Query: 61 SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120 GQNPARQAAIKAGLP VPAMTI KVCGSGLKAV LAA AI GDA+IV+AGGQENMSA Sbjct: 61 GGQNPARQAAIKAGLPNTVPAMTIGKVCGSGLKAVHLAAQAIKCGDADIVIAGGQENMSA 120 Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180 +PHVL GSRDG RMGD KL DTMIVDGLWD +NQYHMG TAENVAK Y I+RE QD FA Sbjct: 121 SPHVLAGSRDGQRMGDWKLTDTMIVDGLWDAFNQYHMGTTAENVAKAYHISREQQDAFAA 180 Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240 SQ KAE AQK G+F +EIVPV I +KG V F TDEF++ G T D+++GL+PAFDKAG Sbjct: 181 ASQQKAELAQKTGRFKDEIVPVSIVSKKG-TVVFDTDEFIKHGTTADALAGLRPAFDKAG 239 Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300 +VTA NASGLNDGAAAV++MSA+KA+ELGLTPLA I SYA+AG+DP +MGMGPVPAS+R Sbjct: 240 SVTAGNASGLNDGAAAVLMMSASKARELGLTPLARIASYASAGLDPAIMGMGPVPASQRC 299 Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360 L +A W+ DLDLMEINEAFAAQA AV+Q+M WD SK+NVNGGAIAIGHPIGASGCRILV Sbjct: 300 LHKAGWSINDLDLMEINEAFAAQACAVNQEMDWDASKINVNGGAIAIGHPIGASGCRILV 359 Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392 TLLHEM RRDA++GLASLCIGGGMGVALAVER Sbjct: 360 TLLHEMARRDARRGLASLCIGGGMGVALAVER 391 Lambda K H 0.315 0.131 0.369 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: 552 Number of extensions: 18 Number of successful extensions: 2 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: 393 Length of database: 391 Length adjustment: 31 Effective length of query: 362 Effective length of database: 360 Effective search space: 130320 Effective search space used: 130320 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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