Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxygluconokinase; 3-deoxy-2-oxo-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate WP_011653019.1 RL_RS18270 sugar kinase
Query= SwissProt::P45416 (310 letters) >NCBI__GCF_000009265.1:WP_011653019.1 Length = 306 Score = 197 bits (502), Expect = 2e-55 Identities = 121/301 (40%), Positives = 168/301 (55%), Gaps = 8/301 (2%) Query: 9 IGECMIELSQKGADLNR-GFGGDTLNTAVYISRQVKPDALDVHYVTALGTDSFSSEMMAS 67 IGECM+ELSQ G L R GF GDT NTA Y+ + PD V Y TALG D+ S EM+A Sbjct: 8 IGECMVELSQAGDGLLRKGFAGDTFNTAWYVRACLGPD-WSVDYFTALGDDAMSDEMVAF 66 Query: 68 WQKEGVKTDLIQRLDNKLPGLYFIETDATGERTFYYWRNDAAARYWLESPDADTISQQLA 127 K G+ T LI+R+ + PGLY I GER+F YWR+ AAAR PD + + + Sbjct: 67 IDKAGIGTSLIRRIRGRTPGLYMINLK-DGERSFSYWRDSAAARSLAADPDR--LREAVE 123 Query: 128 QFDYIYLSGISLAILNQASRARLLTVLRACRANGGKVIFDNNYRPRLWQSKEETRQAYSD 187 + +Y SGI+LAIL LL +R +A G V+FD N RPRLW S + S+ Sbjct: 124 SAEVVYFSGITLAILPHEDAETLLAEVRRAKAAGKLVVFDPNIRPRLWSSYDIMHTTISE 183 Query: 188 MLACTDIAFLTLDDEDMLWGELPVDEVLKRTHGAGVMEVVIKRGADACLVSIQGEALLEV 247 + + + DDE +G+ ++ + R G + +V+K GA+ ++ GE V Sbjct: 184 GARSSMLVMPSFDDEAAHFGDDSIEATIHRYRALGAVHIVVKNGAEGVTLNFAGEQTF-V 242 Query: 248 PAIKLPKEKVVDTTAAGDSFSAGYLSVRLNGGSAQDAAKRGHLTASTVIQYRGAIIPLEA 307 PA K+ EKVVDTT+AGDSF+ +L+ L G A AA+ A+ V+ GA++ E Sbjct: 243 PAEKV--EKVVDTTSAGDSFNGAFLARYLEAGDAPAAARFAAKVAARVVSEHGALVVREK 300 Query: 308 M 308 + Sbjct: 301 L 301 Lambda K H 0.318 0.134 0.390 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: 268 Number of extensions: 15 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: 310 Length of database: 306 Length adjustment: 27 Effective length of query: 283 Effective length of database: 279 Effective search space: 78957 Effective search space used: 78957 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: 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