GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Rhizobium freirei PRF 81

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_037151409.1 RHSP_RS11620 sugar kinase

Query= SwissProt::P45416
         (310 letters)



>NCBI__GCF_000359745.1:WP_037151409.1
          Length = 304

 Score =  184 bits (467), Expect = 2e-51
 Identities = 118/296 (39%), Positives = 158/296 (53%), Gaps = 8/296 (2%)

Query: 9   IGECMIELSQKG-ADLNRGFGGDTLNTAVYISRQVKPDALDVHYVTALGTDSFSSEMMAS 67
           IGECM+ELSQ     L +GF GDT NTA Y +R   P+   V Y TALG D+ S EM   
Sbjct: 8   IGECMVELSQADDGHLRKGFAGDTFNTAWY-ARACLPEDWSVDYFTALGDDAMSDEMATF 66

Query: 68  WQKEGVKTDLIQRLDNKLPGLYFIETDATGERTFYYWRNDAAARYWLESPDADTISQQLA 127
               G+ T  I+RL  K PGLY I     GER+F YWR+ +AAR    + D D +   + 
Sbjct: 67  MGSAGIGTASIRRLRGKTPGLYMINLK-DGERSFSYWRDSSAARQL--AADGDALRAAIE 123

Query: 128 QFDYIYLSGISLAILNQASRARLLTVLRACRANGGKVIFDNNYRPRLWQSKEETRQAYSD 187
             D +Y SGI+LAIL +     LL  LR  +A G  V FD N RPRLW S +      +D
Sbjct: 124 ASDVLYFSGITLAILPREDAYTLLAELRRAKAVGKLVAFDPNLRPRLWSSLDAMHTLIAD 183

Query: 188 MLACTDIAFLTLDDEDMLWGELPVDEVLKRTHGAGVMEVVIKRGADACLVSIQGEALLEV 247
               + +   + DDE   +G+  +   ++R    G   VV+K G +   +    +  L V
Sbjct: 184 GARASTLVMPSFDDEAAHFGDDSISSTIRRYRQYGANMVVVKNGPEGATIGSGADETL-V 242

Query: 248 PAIKLPKEKVVDTTAAGDSFSAGYLSVRLNGGSAQDAAKRGHLTASTVIQYRGAII 303
           PA+K+   KVVDTT+AGDSF+ G+L+  L  G    AA      A+ VIQ  GA++
Sbjct: 243 PAVKV--NKVVDTTSAGDSFNGGFLAHYLQHGDPLAAAAFAAEIAAKVIQEHGALV 296


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: 269
Number of extensions: 16
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: 304
Length adjustment: 27
Effective length of query: 283
Effective length of database: 277
Effective search space:    78391
Effective search space used:    78391
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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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