Align 2-dehydro-3-deoxygluconokinase (EC 2.7.1.45) (characterized)
to candidate SM_b21374 SM_b21374 sugar kinase
Query= reanno::Cup4G11:RR42_RS28860 (311 letters) >FitnessBrowser__Smeli:SM_b21374 Length = 313 Score = 107 bits (267), Expect = 4e-28 Identities = 89/291 (30%), Positives = 128/291 (43%), Gaps = 8/291 (2%) Query: 5 ILAFGEALVEF--NQQPDDPSRYLQGFG----GDTSNFCIAAARQGARAGYISAVGEDTF 58 IL GE LVE ++ D + G G + F A + G IS VG D F Sbjct: 4 ILTIGEILVEIIATEKGDGFRKATPLIGPFPSGAPAIFIDQAGKLGQPCAIISRVGGDDF 63 Query: 59 GERLLALWTQERVDTRHVRIDAGAPTGVYFVTHDAHGHR-FDYLRSGSAASHYSHENLPH 117 G L ++ VD + +D A TG FV + G R F + SA + + Sbjct: 64 GTVNLERLKRDGVDISGIEVDPLATTGSAFVRYRPDGSRAFVFNIRDSACGKITLDERMT 123 Query: 118 HAIAEARYLHVSGISLAISTSACDAGLAAMEHARKAGCQVTLDTNLRLRLWTLARARGIM 177 + E ++HV G SL + S ++ LAA+ + G V+ D NLR + R + Sbjct: 124 RLVGECSHVHVMGSSL-YAPSVVESILAAIGIVKAGGGTVSFDPNLRPEILKSPGMREAL 182 Query: 178 REAFALTDVCLPSWDDITVLTGLDDRDAIVDYLLGCGIGLVALKLGEEGAYVATPEARTL 237 A TD+ LPS D++ + T V LL GI V +K G GA A Sbjct: 183 LTVLAETDLFLPSGDELFLFTEAKTESQAVAELLASGIKAVVVKRGAAGASYFDAGAALS 242 Query: 238 VPPYTVRPVDATGAGDCFGGSFVARLAAGDDPFDAARYANVAAALSTTGYG 288 +P + V +D TGAGDCFG +FV+ G P +A +A + A + +G Sbjct: 243 LPGFPVEEIDPTGAGDCFGATFVSFWLNGASPREALEFAAASGARAVMHFG 293 Lambda K H 0.321 0.136 0.409 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: 247 Number of extensions: 16 Number of successful extensions: 1 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: 311 Length of database: 313 Length adjustment: 27 Effective length of query: 284 Effective length of database: 286 Effective search space: 81224 Effective search space used: 81224 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 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