Align 3-oxopimeloyl-CoA:CoA acetyltransferase (characterized)
to candidate WP_110206636.1 DNK54_RS08955 thiolase family protein
Query= metacyc::MONOMER-20679 (395 letters) >NCBI__GCF_003194585.1:WP_110206636.1 Length = 392 Score = 242 bits (617), Expect = 2e-68 Identities = 156/399 (39%), Positives = 218/399 (54%), Gaps = 26/399 (6%) Query: 5 VIVSTARTPIGKAYRGALNATEGATLLGHAIEHAVKRAGIDPKEVEDVVMGAAMQQGATG 64 VIV ARTPIG ++ G L L A+ A+ RAG+ +++ +VVMG Q G Sbjct: 7 VIVDGARTPIG-SFGGVLKDVPAHELGAVAVTEALSRAGVRGEQIREVVMGQIGQVGPDA 65 Query: 65 GNIARKALLRAGLPVTTAGTTIDRQCASGLQAIALAARSVLFDGVEIAVGGGGESIS--- 121 N AR+ L AGLP + T++R C SGLQAI AA + ++ ++ A+GGG ES+S Sbjct: 66 YN-ARRVALAAGLPQSVPAYTVNRLCGSGLQAIWSAAMEMRWNNLDFAIGGGDESMSRMP 124 Query: 122 LVQNDKMNTFHAVDPALEAIKGDVYMA--------MLDTAETVAKRYGISRERQDEYSLE 173 + N + D AL + G V M M TAE VA +YG+ R +QDE+++E Sbjct: 125 FLDFGARNGYKLGDRAL--VDGTVGMLTDPFSNKHMGVTAENVAAKYGVDRVQQDEFAVE 182 Query: 174 SQRRTAAAQQGGKFNDEIAPISTKMGVVDKATGAVSFKDITLSQDEGPRPETTAEGLAGL 233 SQRR A + F +EI P+ K T+ DE P+P TT E L L Sbjct: 183 SQRRAATDEAKAAFAEEIVPVEV-----------AGRKPYTVEVDEHPKPGTTMETLGKL 231 Query: 234 KAVRGEGFTITAGNASQLSDGASATVIMSDKTAAAKGLKPLGIFRGMVSYGCEPDEMGIG 293 +A + ++TAGNAS ++DGA A V+ ++ AA GL PL + + EP+ MG Sbjct: 232 RAAFVKDGSVTAGNASGINDGAGAVVLATEAAAAEHGLSPLVSIEAVSTGAMEPELMGYA 291 Query: 294 PVFAVPRLLKRHGLSVDDIGLWELNEAFAVQVLYCRDKLGIDPEKLNVNGGAISVGHPYG 353 PV A+ L +R GL+ DIG ELNEAFA Q + G+DP ++N GGAI++GHP G Sbjct: 292 PVLALKDLFERTGLTPKDIGTIELNEAFASQAVAVSRDAGLDPAQVNPYGGAIALGHPVG 351 Query: 354 MSGARLAGHALIEGRRRKAKYAVVTMCVGGGMGSAGLFE 392 +GA L+ A R ++ +VTMC+GGG A LF+ Sbjct: 352 ATGAILSVRAAKTMVRNDLEFGIVTMCIGGGQALAALFK 390 Lambda K H 0.316 0.134 0.378 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: 446 Number of extensions: 29 Number of successful extensions: 4 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: 395 Length of database: 392 Length adjustment: 31 Effective length of query: 364 Effective length of database: 361 Effective search space: 131404 Effective search space used: 131404 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