Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_066919048.1 ACG33_RS04455 acetyl-CoA acetyltransferase
Query= reanno::Marino:GFF2751 (415 letters) >NCBI__GCF_001579945.1:WP_066919048.1 Length = 402 Score = 254 bits (649), Expect = 3e-72 Identities = 173/431 (40%), Positives = 234/431 (54%), Gaps = 54/431 (12%) Query: 6 ILKDAYIVDAIRTPIGR--YGGALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCA 63 ++ AYI DAIRTP GR G+L V+ LGA ++ L R+ DLD +++DDV+ GC Sbjct: 1 MVNTAYIYDAIRTPRGRGKADGSLHEVKPVVLGAGLLRELQRRH-DLDTARVDDVVMGCV 59 Query: 64 NQAGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGV 123 GE D+ + + A + VPG I+R C S ++AV AA + +G +L++AGGV Sbjct: 60 TPVGEQGGDITKTVVQYADWDISVPGVQIDRFCASALEAVNLAAMKVASGWEELVVAGGV 119 Query: 124 ESMSRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPET--AENVAADFG 181 ESMSR MG A ++ I +K++ S+P+ A+ +A G Sbjct: 120 ESMSRVR--MGAAGGSWLNDPGI------------AIKER----SIPQGVGADTIATLDG 161 Query: 182 ISREDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPR-ETSLEKL 240 R D DAFAL SQQR AQ G + PV R ++++ DE + T++E L Sbjct: 162 WKRRDVDAFALLSQQRAHHAQANGFFDRSVVPV---RDVLGSMILEKDEFIKPNTTMEGL 218 Query: 241 ASLPTPFRENGTV--------------------TAGNASGVNDGACALLLAGADALKQYN 280 A L F G + T GN+SG+ DGA A L+ A K Sbjct: 219 AKLKPSFAAMGAMGFDEMMIGKYPQLGCIDHVHTPGNSSGIVDGASAALIGSEQAGKDLG 278 Query: 281 LKPRARVVAMATAGVEPRIMGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTR 340 L PR R+VA A +P IM GP PA +K LA AGLE+AD+D+ E+NEAFA+ AL + Sbjct: 279 LTPRGRIVATAVISTDPTIMLAGPGPAAKKCLAKAGLEVADIDLFEINEAFASVALRFMQ 338 Query: 341 DLGLPDDAEHVNPNGGAIALGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGV 400 DLG+ D E N NGGAIA+GHPLG +G L+ T L+ELERR K R L +C+G Sbjct: 339 DLGI--DREITNVNGGAIAMGHPLGATGCMLIGTLLDELERR-----KLRRGLVALCVGG 391 Query: 401 GQGIALIIERM 411 GQGIA IIER+ Sbjct: 392 GQGIATIIERV 402 Lambda K H 0.318 0.133 0.382 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: 435 Number of extensions: 25 Number of successful extensions: 6 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: 415 Length of database: 402 Length adjustment: 31 Effective length of query: 384 Effective length of database: 371 Effective search space: 142464 Effective search space used: 142464 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 (21.7 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