Align Gluconokinase; EC 2.7.1.12; Gluconate kinase (uncharacterized)
to candidate WP_013403936.1 CALHY_RS10535 xylulokinase
Query= curated2:P46834 (513 letters) >NCBI__GCF_000166355.1:WP_013403936.1 Length = 502 Score = 270 bits (690), Expect = 9e-77 Identities = 157/490 (32%), Positives = 250/490 (51%), Gaps = 7/490 (1%) Query: 4 YMLGIDIGTTSTKAVLFSEKGDVIQKESIGYALYTPDISTAEQNPDEIFQAVIQSTAKIM 63 Y +GID+GT+ TK +L KG+++ + Y LY P I AEQNP++ + A ++ ++ Sbjct: 2 YFIGIDVGTSGTKTILTDSKGNILATATFEYPLYQPQIGWAEQNPEDWWDASVKGIKAVL 61 Query: 64 QQHP--DKQPSFISFSSAMHSVIAMDENDKPLTSCITWADNRSEGWAHKIKEEMNGHNVY 121 ++ K+ + + MH ++ +D+N + I W D R+ +I E++ + Sbjct: 62 EKSKVDPKEVKAVGLTGQMHGLVMLDKNYNVIRPSIIWCDQRTAKECDEITEKIGKERLI 121 Query: 122 KRTGTPIHPMAPLSKITWIVNEHPEIAVKAKKYIGIKEYIFKKLFDQYVVDYSLASAMGM 181 + T P SKI W+ N P+ K K + K+YI KL ++ D S AS M + Sbjct: 122 EITANPALTGFTASKILWVRNNEPQNYEKVYKILLPKDYIRFKLTGEFATDVSDASGMQL 181 Query: 182 MNLKTLAWDEEALAIAGITPDHLSKLVPTTAIFHHCNPELAAMMGIDPQTPFVIGASDGV 241 +++K W +E L I D L K+ + + + + + + G+ T V G D Sbjct: 182 LDIKNRCWSDEVLEKLEIDKDLLGKVYESPEVTGKVSRQASEITGLWEGTLVVAGGGDQA 241 Query: 242 LSNLGVNAIKKGEIAVTIGTSGAIRPIIDKPQTDEKGRI--FCYALTENHWVIGGPVNNG 299 +G +K G I+ TIG+SG + +D+ + D +GR+ FC+A+ W + G Sbjct: 242 AGAVGNGIVKTGVISSTIGSSGVVFAHLDEFKIDPQGRVHTFCHAV-PGKWHVMGVTQGA 300 Query: 300 GIVLRWIRDEFASSEIETAKRLGIDPYDVLTKIAERVRPGADGLLFHPYLAGERAPLWNP 359 G+ L+W RD FA E + + DPY ++ + AE PG+DGL+F PYL GER P+ +P Sbjct: 301 GLSLKWFRDNFAHIEKAAFEFIDKDPYILMDQEAELANPGSDGLVFLPYLMGERTPILDP 360 Query: 360 DVPGSFFGLTMSHKKEHMIRAALEGVIYNLYTVFLALTECMDGPVARIQATGGFARSDVW 419 G FFG+T H + IRA +EGV+++L L E M V ++ +GG A+S +W Sbjct: 361 YAKGIFFGITAKHTRREFIRAVMEGVVFSLKNCLDILHE-MGIEVKEVRVSGGGAKSKLW 419 Query: 420 RQMMADIFESEVVVPESYESSCLGACILGLYATGKIDSFDVVSD-MIGSTHRHAPKEESA 478 RQM ADIFE +V S E GA IL G + + D MI +P ++ Sbjct: 420 RQMQADIFEMDVWTLNSKEGPAFGAAILATVGAGVYNKVEEACDTMIQKVESCSPNKDLF 479 Query: 479 KEYRKLMPLF 488 + YRK L+ Sbjct: 480 EVYRKTYKLY 489 Lambda K H 0.318 0.134 0.401 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: 552 Number of extensions: 33 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: 513 Length of database: 502 Length adjustment: 34 Effective length of query: 479 Effective length of database: 468 Effective search space: 224172 Effective search space used: 224172 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: 52 (24.6 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