GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dgoK in Cronobacter condimenti 1330

Align 2-dehydro-3-deoxyglucono/galactono-kinase (EC 2.7.1.178) (characterized)
to candidate WP_007680610.1 BN137_RS02010 sugar kinase

Query= BRENDA::Q97U29
         (313 letters)



>NCBI__GCF_000319285.1:WP_007680610.1
          Length = 312

 Score =  138 bits (348), Expect = 1e-37
 Identities = 98/305 (32%), Positives = 150/305 (49%), Gaps = 9/305 (2%)

Query: 2   VDVIALGEPLIQFNSFNPGPLRFVNYFEKHVAGSELNFCIAVVRNHLSCSLIARVGNDEF 61
           +DVI +GE +  F +  PG L  V +F K VAG+ELN    + R  L+ S ++RVGND F
Sbjct: 5   LDVITIGEAMAMFVATEPGDLAQVEHFFKRVAGAELNVATGLARLGLNVSWVSRVGNDSF 64

Query: 62  GKNIIEYSRAQGIDTSHIKVDNESFTGIYFIQRGYPIPMKSELVYYRKGSAGSRLSPEDI 121
           G+ ++     +GI T  + +D+   TG + ++          + Y+RKGSA S LS ED 
Sbjct: 65  GRFVLSQLEKEGISTRGVTIDDRFPTG-FQLKSKVTDGTDPSVEYFRKGSAASHLSGEDF 123

Query: 122 NENYVRNSRLVHSTGITLAISDNAKEAVIKAFELAKSR----SLDTNIRPKLWSSLEKAK 177
           N     ++R +H +G+  A+S ++ E +  A    K++    S D N+RP LW S  +  
Sbjct: 124 NAPLFYSARHLHLSGVAAALSGSSYELLDHAARAMKTQGKTISFDPNLRPVLWKSEAEMV 183

Query: 178 ETILSILKKYDIEVLITDPDDTKILLDVTDPDEAYRKYKELGVKVLLYKLGSKGA-IAYK 236
           E +  +    D   ++    +  IL     P+     Y   GVK ++ K G+ GA     
Sbjct: 184 EKLNHLATLAD--WVLPGLKEGHILTGQQHPEGIADFYLSRGVKAVVIKTGADGAWYQTA 241

Query: 237 DNVKAFKDAYKVP-VEDPTGAGDAMAGTFVSLYLQGKDIEYSLAHGIAASTLVITVRGDN 295
              +   +A KV  V D  GAGD  A   +S  L+GK +  +   G     L I V+GD+
Sbjct: 242 SGEQGTVEAVKVDNVVDTVGAGDGFAVGVISALLEGKTLHQAATRGNKIGALAIQVQGDS 301

Query: 296 ELTPT 300
           E  PT
Sbjct: 302 EGLPT 306


Lambda     K      H
   0.317    0.136    0.383 

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: 237
Number of extensions: 10
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: 313
Length of database: 312
Length adjustment: 27
Effective length of query: 286
Effective length of database: 285
Effective search space:    81510
Effective search space used:    81510
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 (21.6 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