GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glc-kinase in Sinorhizobium meliloti 1021

Align Glucosamine kinase GspK; GlcN kinase; EC 2.7.1.8 (characterized)
to candidate SMc02875 SMc02875 hypothetical protein

Query= SwissProt::Q9KUA9
         (294 letters)



>FitnessBrowser__Smeli:SMc02875
          Length = 294

 Score =  187 bits (475), Expect = 2e-52
 Identities = 105/280 (37%), Positives = 162/280 (57%), Gaps = 1/280 (0%)

Query: 3   YYVGIDGGGTSCRARIRNQQGEWVGEAKSGSANIMLGVEVALRSVVDAITQAAEQGGLSP 62
           Y +GIDGGGTSCRA +    G  +G  K+G+ANI+   E AL+++ DA   A    GL P
Sbjct: 4   YLIGIDGGGTSCRAAVAALDGRILGRGKAGAANILTDPETALQNITDAARDAFGDAGLDP 63

Query: 63  DDFPSMHVGLALAGAEQKEAWHAFMQQAHPFASITLNTDAYGACLGAHLGEEGAIMIAGT 122
               +    + +AG    +A H ++++  PFA   + +D   A  GA    +GA+ I GT
Sbjct: 64  AGIGASRAIVGVAGHNVGDAVH-YVKRRLPFAQADIESDGLIALQGALGDGDGAVAILGT 122

Query: 123 GSCGILLKGGKQYVVGGREFPISDQGSGAVMGLRLIQQVLLAQDGIRPHTPLCDVVMNHF 182
           G+  I  +G +   VGG  F I D GSGA +G  L+Q+ LLA DGI   + + D V+  F
Sbjct: 123 GTIYIARRGDEVSYVGGWGFTIGDHGSGARIGHALLQESLLAYDGIHQGSGVTDAVLAEF 182

Query: 183 NHDIDSIVAWSKTALPRDYGQFSPQIFSHAYCGDPLAIELLKQTAADIEMFLIALHHKGA 242
           N D   IV +++ A P ++G+++P++F  A  GDP+AI LLK  AA ++  L  +  +G+
Sbjct: 183 NDDPRDIVDFARLAKPGEFGRYAPRVFEFAERGDPVAISLLKAAAATVDEALDVVVSRGS 242

Query: 243 ERICLMGSIAERIQDWLSPPVQQWIVKPQSDAIEGALMFA 282
           E++CL+G +A   + WL+   Q   V+ ++DA+ GA+  A
Sbjct: 243 EKLCLLGGLAPLYRRWLADRHQPRFVEARADALTGAVALA 282


Lambda     K      H
   0.320    0.137    0.421 

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: 266
Number of extensions: 16
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: 294
Length of database: 294
Length adjustment: 26
Effective length of query: 268
Effective length of database: 268
Effective search space:    71824
Effective search space used:    71824
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 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