Align 2-ketogluconokinase (EC 2.7.1.13) (characterized)
to candidate WP_017549879.1 C792_RS0112925 sugar kinase
Query= metacyc::MONOMER-12748 (320 letters) >NCBI__GCF_000330705.1:WP_017549879.1 Length = 315 Score = 154 bits (388), Expect = 4e-42 Identities = 104/302 (34%), Positives = 152/302 (50%), Gaps = 9/302 (2%) Query: 4 IDILSFGETMAMFVAEHGGDLAQVQHFHKRIAGADSNVAIGLARLGFKVAWLSRVGNDSL 63 ++++ GE+M V E G + F +AGA+ N IGL+RLG +W+S +G D L Sbjct: 1 MEVIGIGESMVALVNEPKGYIRHADSFKPYVAGAEMNTLIGLSRLGHGTSWVSALGEDEL 60 Query: 64 GRFVLDTLRAEGLDCRFVRCDPIHPTGFQLKSREDGGDDPRVEYFRRGSAASHLAISDLD 123 G +L +RAE +D V F + DG D V Y+R SAAS++ I D+D Sbjct: 61 GELILHKVRAENVDASHVTHKDKRTGVFFKQILPDGSVD--VTYYREDSAASNMDIRDID 118 Query: 124 -PALLRARHLHATGIPPALSDSARELSGHLMHTQRSAGHSVS--FDPNLRPALWPSEALM 180 A+ RA+ L+ TGI +LS SA+E+ L R AG V+ FDPN+R +W ++ Sbjct: 119 MDAIRRAKVLYLTGITLSLSSSAKEM---LFEAVRIAGDDVTVVFDPNIRLKMWSAKEAR 175 Query: 181 IREINRLAALAHWVLPGLAEGRLLTGRDDPADIAAFYLDQGAEAVVIKLGAHGAYYRTQL 240 I ++ G E +L G P + + + G VV+KLG GA Y Sbjct: 176 -ETILEFLPHVDCLIAGRDEVDILMGAMRPEEALKSFRELGCSKVVLKLGKEGAVYDFDG 234 Query: 241 DAGFVEGVPVAQVVDTVGAGDGFAVGLISALLESRGILEAVQRANWIGSRAVQSRGDMEG 300 G V+ + +D VGAGD FA G+IS LL +V++A ++G Q GD +G Sbjct: 235 IGGSVKNPKQFEEIDPVGAGDAFAAGIISGLLNGEDPEASVEKACFLGGYITQFVGDYQG 294 Query: 301 LP 302 P Sbjct: 295 FP 296 Lambda K H 0.321 0.138 0.414 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: 279 Number of extensions: 18 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: 320 Length of database: 315 Length adjustment: 27 Effective length of query: 293 Effective length of database: 288 Effective search space: 84384 Effective search space used: 84384 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 (21.9 bits) S2: 48 (23.1 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