GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_512 5-keto-2-deoxygluconokinase (EC 2.7.1.92) / uncharacterized domain

Query= SwissProt::Q704D0
         (325 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_512
          Length = 645

 Score =  117 bits (294), Expect = 6e-31
 Identities = 106/352 (30%), Positives = 157/352 (44%), Gaps = 42/352 (11%)

Query: 1   MAEGRCSQGKEPAEAMISLVALGEPLIQLNAVTPGP-LRYVAYFEKHVAGSEANFCIAAT 59
           M + R + G++     + ++ LG   + L A   G  L  VA F K++ GS AN      
Sbjct: 1   MGQTRFASGRQ-----LDVICLGRLGVDLYAQQVGARLEDVASFAKYLGGSSANIAFGTA 55

Query: 60  MAGARCSLIARVGDDEFGRNIVEYLRGRGVDVSHVKVDPGAPTGIYFV----QRHFPVPG 115
             G R ++++RVGDD  GR +VE L   G DVS +KVDP   T +  +    +  FP   
Sbjct: 56  RLGLRSAMLSRVGDDHMGRFLVESLAREGCDVSGIKVDPERLTAMVLLGIKDRETFP--- 112

Query: 116 RSRLIYYRKGSAGSRVGPDDVDSSLISSADAVHSTGITLALSDSANRAVHKAFGEAKRR- 174
              L++YR+  A   +  +D+D + I+S+ A+  TG T   +D   +A  +A   A++  
Sbjct: 113 ---LVFYRENCADMALRVEDIDETFIASSKALLITG-THFSTDGVYKASTQALDYAEKHN 168

Query: 175 ---TFDTNIRPALWPDLAAARRAILDVLNYGV-----------DVLVTDPDDTQILLGVR 220
                D + RP LW     A      V +  V           D++V   ++  I  G  
Sbjct: 169 VKCVLDIDYRPVLWGLAGKADGETRFVADQKVSQHVQGILPRFDLIVGTEEEFLIAGGSE 228

Query: 221 DPEEAYRKYRELGVQTLVYKLGAEGAYVFW--------NGGSYFRDALKVAVEDPTGAGD 272
           D   A R  R L   TLV KLGA+G  V          +G  Y    ++V V +  GAGD
Sbjct: 229 DLLSALRTVRSLTAATLVVKLGAQGCTVIHGAIPARLEDGALY--PGVRVEVLNVLGAGD 286

Query: 273 AVAGYFVALYLSGVDPRRALDLAVAASALVVGVRGDNEALPSPREAEELLKA 324
           A    F+A +L      R   LA A   LVV       A+P+  E + L K+
Sbjct: 287 AFMSGFLAGWLEDASDERCCQLANACGGLVVSRHACAPAMPTRAELDYLFKS 338


Lambda     K      H
   0.319    0.137    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: 467
Number of extensions: 25
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: 325
Length of database: 645
Length adjustment: 33
Effective length of query: 292
Effective length of database: 612
Effective search space:   178704
Effective search space used:   178704
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 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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