GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kdgK in Sinorhizobium meliloti 1021

Align 2-dehydro-3-deoxygluconokinase; 2-keto-3-deoxy-D-gluconate kinase; KDG kinase; EC 2.7.1.45 (characterized)
to candidate SMc02875 SMc02875 hypothetical protein

Query= SwissProt::Q9HLV3
         (336 letters)



>FitnessBrowser__Smeli:SMc02875
          Length = 294

 Score = 94.7 bits (234), Expect = 2e-24
 Identities = 82/257 (31%), Positives = 124/257 (48%), Gaps = 16/257 (6%)

Query: 7   ILGVDGGSTKTLAIVFDERSERIMGVGISGPSNFTNAPRETAESNISDAVRKACSEAGTD 66
           ++G+DGG T   A V      RI+G G +G +N    P ETA  NI+DA R A  +AG D
Sbjct: 5   LIGIDGGGTSCRAAVA-ALDGRILGRGKAGAANILTDP-ETALQNITDAARDAFGDAGLD 62

Query: 67  LDGIGIR--VFGLAG--IGDSREATELGKDIVRSIVGHADVYSDGLGAYKFANLNDDGVV 122
             GIG    + G+AG  +GD+    +      R     AD+ SDGL A + A  + DG V
Sbjct: 63  PAGIGASRAIVGVAGHNVGDAVHYVKR-----RLPFAQADIESDGLIALQGALGDGDGAV 117

Query: 123 FAPGTGSVGFIKNGSDPERFGGWGWFIGDEASASWMAKQAILFAEREHDGIAE-TGFLDV 181
              GTG++   + G +    GGWG+ IGD  S + +    +  +   +DGI + +G  D 
Sbjct: 118 AILGTGTIYIARRGDEVSYVGGWGFTIGDHGSGARIGHALLQESLLAYDGIHQGSGVTDA 177

Query: 182 VRRYFGMDLYETVYAISKEKIAKRVVAALAPQVSAMARSGNRYAISIFEESSSYIADLLN 241
           V   F  D  + V      K  +      AP+V   A  G+  AIS+ + +++ + + L+
Sbjct: 178 VLAEFNDDPRDIVDFARLAKPGE--FGRYAPRVFEFAERGDPVAISLLKAAAATVDEALD 235

Query: 242 AKSRIFGRSGKYSVLGG 258
               +   S K  +LGG
Sbjct: 236 VV--VSRGSEKLCLLGG 250


Lambda     K      H
   0.317    0.136    0.386 

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: 295
Number of extensions: 17
Number of successful extensions: 3
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: 336
Length of database: 294
Length adjustment: 27
Effective length of query: 309
Effective length of database: 267
Effective search space:    82503
Effective search space used:    82503
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 17 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