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_004121794.1 RHSP_RS20075 5-dehydro-2-deoxygluconokinase

Query= SwissProt::Q53W83
         (309 letters)



>NCBI__GCF_000359745.1:WP_004121794.1
          Length = 644

 Score =  116 bits (291), Expect = 1e-30
 Identities = 94/305 (30%), Positives = 140/305 (45%), Gaps = 29/305 (9%)

Query: 2   LEVVTAGEPLVALVPQEPGH-LRGKRLLEVYVGGAEVNVAVALARLGVKVGFVGRVGEDE 60
           L+V+T G   V L  Q+ G  L         VGG   N+A+  ARLG+K G + RVG+++
Sbjct: 14  LDVITIGRSSVDLYGQQIGSKLEDIASFAKSVGGCPANIAIGTARLGLKSGLITRVGDEQ 73

Query: 61  LGAMVEERLRAEGVDLTHFRR-APGFTGLYLREYLPLGQGRVFYYRKGSAGSALAPGAFD 119
           +G  + E+   EGV +          T L L      G   + +YR   A  AL     D
Sbjct: 74  MGRFIREQAAREGVAVDGIATDKERLTALVLLAVEAEGVSPMIFYRSDCADMALNEDDID 133

Query: 120 PDYLEGVRFLHLSGITPALSPEARAFSLWAMEEAKRRGVRVSLDVNYRQTLWS-PEEARG 178
             +++    + +SG T    P   A    A+  AK  G +V  D++YR  LW     A G
Sbjct: 134 ESFIKSSNAVLVSG-THFSKPNTEAAQRKAIRIAKANGRKVIFDIDYRPNLWGLAGHAEG 192

Query: 179 F------------LERALPGVDLLFLSEEE------AELLFGRVEEALRALSAPEVVLKR 220
           F            ++  LP  DL+  +EEE      A+ + G ++E +R LS+  +VLKR
Sbjct: 193 FERYVKSDRVSSKMKETLPDCDLIVGTEEEIMIASGADDVLGALKE-IRRLSSAVIVLKR 251

Query: 221 GAKGAWAFVD------GRRVEGSAFAVEAVDPVGAGDAFAAGYLAGAVWGLPVEERLRLA 274
           GA G   +           + G  F +E  + +GAGDAF +G+L G + G P++     A
Sbjct: 252 GAMGCIVYEGPISDDLEAGIVGEGFPIEVFNVLGAGDAFMSGFLRGYLRGEPLKTSATWA 311

Query: 275 NLLGA 279
           N  GA
Sbjct: 312 NACGA 316


Lambda     K      H
   0.320    0.139    0.407 

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: 455
Number of extensions: 26
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: 309
Length of database: 644
Length adjustment: 32
Effective length of query: 277
Effective length of database: 612
Effective search space:   169524
Effective search space used:   169524
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 (21.8 bits)
S2: 51 (24.3 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