GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Methylocystis bryophila S285

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_085771876.1 B1812_RS12430 adenosine kinase

Query= SwissProt::Q53W83
         (309 letters)



>NCBI__GCF_002117405.1:WP_085771876.1
          Length = 333

 Score = 93.2 bits (230), Expect = 8e-24
 Identities = 96/284 (33%), Positives = 127/284 (44%), Gaps = 29/284 (10%)

Query: 33  GGAEVNVAVALARLGVKVGFVGRVGEDELGAMVEERLRAEGVDL-THFRRAPGFTGLYLR 91
           GG+  N    LA LG +VGFVG+V EDE G      +R  GV   T F      T   L 
Sbjct: 59  GGSAANTMAGLASLGCRVGFVGKVKEDEAGREFAHDIRKAGVAFETPFATDGAATARCLI 118

Query: 92  EYLPLGQGRVFYYRKGSAGSALAPGAFDPDYLEGVRFLHLSGITPALSPEARAFSLWAME 151
              P GQ  +  +    A  AL P   D       + L+L G      P A+   L A +
Sbjct: 119 FVTPDGQRTMNTFL--GACQALGPADIDEAQAADAKVLYLEGYLWD-PPAAKEAFLKAAK 175

Query: 152 EAKRRGVRVSLDVN-------YRQTLWSPEEARGFLERALPGVDLLFLSEEEAELLFGRV 204
            ++ +G +V+L ++       YR      +E  G +   L  VD++F +E E   L+   
Sbjct: 176 LSRAKGRKVALSLSDAFCVDRYR------DEFLGLIRDQL--VDIVFANESELHSLYQTA 227

Query: 205 E-----EALRALSAPEVVLKRGAKGAWAFVDGRRVEGSAFAVEA-VDPVGAGDAFAAGYL 258
           +      ALRA      V+ R A+GA        V   AFAVE  VD  GAGD FAAG+L
Sbjct: 228 DFDTALVALRAEKGLLGVVTRSAQGALVADAAGVVSVPAFAVEEIVDTTGAGDLFAAGFL 287

Query: 259 AGAVWGLPVEERLRLANLLGASVAASRGDHEGAPYREDLEVLLK 302
           AG   GLP +   R    LGA  AA    H GA  ++DL  L +
Sbjct: 288 AGFTQGLPHDRSAR----LGALAAAEIISHFGARPQKDLAQLAR 327


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: 245
Number of extensions: 9
Number of successful extensions: 2
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: 333
Length adjustment: 28
Effective length of query: 281
Effective length of database: 305
Effective search space:    85705
Effective search space used:    85705
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: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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