Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_011782036.1 MVAN_RS24580 acetyl-CoA C-acyltransferase
Query= SwissProt::P14611 (393 letters) >NCBI__GCF_000015305.1:WP_011782036.1 Length = 392 Score = 363 bits (933), Expect = e-105 Identities = 205/386 (53%), Positives = 254/386 (65%), Gaps = 3/386 (0%) Query: 5 VIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAGSGQN 64 V+V+ ART +GKF GSLA + ELG V I AAL +AG+ QV VIMGQVLTAG+GQ Sbjct: 8 VLVAGARTPIGKFMGSLAGLTGAELGGVAIAAALAKAGISGSQVQYVIMGQVLTAGAGQI 67 Query: 65 PARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSAAPHV 124 PARQAA+ G+P VPA+T+NKVC SGL A+ LA I AG ++VVAGGQE+MS APH+ Sbjct: 68 PARQAAVAGGIPMTVPALTVNKVCLSGLDAIALADQLIRAGAFDVVVAGGQESMSQAPHL 127 Query: 125 LPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAVGSQN 184 L R G + GDA L D + VDGL DV+ MG ++V ++R QDEFA S Sbjct: 128 LENLRAGTKFGDAALRDHVAVDGLRDVFTDQAMGSLTDSVN---ALSRADQDEFAAASHR 184 Query: 185 KAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAGTVTA 244 +A AA+K G FD E+VPV+IPQRKGDPV DE +R T S++ L+PAF GTVTA Sbjct: 185 RAAAARKNGVFDGEVVPVVIPQRKGDPVQVTVDEGIRADTTTASLARLRPAFVADGTVTA 244 Query: 245 ANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRALSRA 304 NAS +NDGAAAVVVMS AKA E+GLT +A I ++ + M P A A + Sbjct: 245 GNASTMNDGAAAVVVMSKAKATEVGLTWIAEIGAHGVVAGPDSTLQMQPANAIAAACAIE 304 Query: 305 EWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILVTLLH 364 P LDL+EINEAFAA + + +G D +VNVNGGAIAIGHP+G SG RI++ L Sbjct: 305 GIDPAALDLVEINEAFAAVGIESTRALGLDPERVNVNGGAIAIGHPLGMSGARIVLHLAL 364 Query: 365 EMKRRDAKKGLASLCIGGGMGVALAV 390 E++RR G A+LC GGG G AL V Sbjct: 365 ELQRRGGGTGAAALCGGGGQGSALIV 390 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: 449 Number of extensions: 23 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: 392 Length adjustment: 31 Effective length of query: 362 Effective length of database: 361 Effective search space: 130682 Effective search space used: 130682 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 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