GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagK in Desulfovibrio vulgaris Hildenborough

Align Glucose kinase (characterized, see rationale)
to candidate 206469 DVU1035 glucokinase, putative

Query= uniprot:Q8P6M4
         (344 letters)



>MicrobesOnline__882:206469
          Length = 354

 Score = 78.2 bits (191), Expect = 3e-19
 Identities = 83/272 (30%), Positives = 109/272 (40%), Gaps = 21/272 (7%)

Query: 71  DSRAVDAVVIASAGVALDDGRFISNNLPWTIAPRQLRDTLGVR-AVHLVNDFEAVAYAAP 129
           D+        A AG   +  R +  N+ W I    L  T G+  A  L+NDFEA  +A  
Sbjct: 93  DASVTAFAAFAVAGPVEEGARCLPPNIGWHI---DLATTRGLPCAASLLNDFEAQGWACL 149

Query: 130 QMEQRAVVQLSGPTPRHAQPGGPILVVGPGTGLGAAVWINGPRQPTVLATEAGQVALASN 189
               +  +QL    P       P+ VVG GTGLG  + + G     VL +E G    A  
Sbjct: 150 LPGAQQCLQL---LPGKPDATAPVAVVGAGTGLGKCLLLPGTPH-RVLPSEGGHATFAFE 205

Query: 190 DPDTAQVLRILAR--DASYLPIEHVLSGPGLRNLYLALCELHAATPIHPLPADITHAALH 247
               A+     A       L  + VLSGPGL  LY      H  T    LP     A L 
Sbjct: 206 GRAEAEYAAFAADRLGVGRLIGDDVLSGPGLSLLY---AYHHGET----LPPHEVAARLT 258

Query: 248 SDDALARRCLQLFCALLGSAVGDMALAYGASGGVYLAGGILPSIGQFLAASDFRERFLAK 307
             D +    ++ F    G    D AL   A GGV +AGG+  +    +    F E F   
Sbjct: 259 GSDVV----VEWFARFYGRTCRDWALHTLARGGVRIAGGVAAANPMLVQHGAFAEAFFDC 314

Query: 308 GRMRPVLERIPVKLVEHGQLGVLGAASWYLQH 339
                +L  IPV LV +   G+ GAA + L H
Sbjct: 315 PTHTHLLRTIPVSLVTNADAGLWGAAIFALLH 346


Lambda     K      H
   0.321    0.136    0.410 

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: 408
Number of extensions: 24
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 344
Length of database: 354
Length adjustment: 29
Effective length of query: 315
Effective length of database: 325
Effective search space:   102375
Effective search space used:   102375
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 (21.9 bits)
S2: 49 (23.5 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