GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Salinicoccus carnicancri Crm

Align glucose transporter, ATPase component (characterized)
to candidate WP_083854810.1 C792_RS0100870 ATP-binding cassette domain-containing protein

Query= reanno::Phaeo:GFF3641
         (260 letters)



>NCBI__GCF_000330705.1:WP_083854810.1
          Length = 261

 Score =  115 bits (288), Expect = 9e-31
 Identities = 74/238 (31%), Positives = 133/238 (55%), Gaps = 21/238 (8%)

Query: 11  GATPLVEMKDISISFGG----IKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQ 66
           G   L+++K  + SF G     KAVD +++ +   E+ G++G +GAGKSTL++ ++    
Sbjct: 13  GGCGLIDIKAATKSFAGKNGDFKAVDSITLSIQNKEIFGIIGESGAGKSTLMRFINALET 72

Query: 67  MDAGEIRVNGDKVEITNPRDARSH--NIETIYQTLALADNLDAASNLFLGREL---VTPF 121
            D+G++ V+G  V     +D R H  +I  I+Q   L  N     N+ L   L    TP 
Sbjct: 73  PDSGQVIVDGTDVVTLGKKDLRKHQKDISMIFQHFNLLGNKTVEDNIRLPLTLHKYKTPL 132

Query: 122 GLVDDSAMEAECRKIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPT 181
             VD+         ++  +  + ++ S P + LSGGQ+Q V IARA+    KIL+ DEPT
Sbjct: 133 S-VDE---------VIEFVGLDDKRDSYP-AELSGGQKQRVGIARALVTRPKILLCDEPT 181

Query: 182 AALGPHETQMVAELIQQLKAQ-GIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDID 238
           +AL  + T  + +++ + + +  + + ++ H++  + +LC RA+VM+ G+L+ T+D++
Sbjct: 182 SALDENTTDEIVDVLGRAQEEFDMTVVIVTHELGVIKQLCRRAAVMERGRLIDTIDVN 239


Lambda     K      H
   0.317    0.135    0.373 

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: 176
Number of extensions: 13
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: 260
Length of database: 261
Length adjustment: 25
Effective length of query: 235
Effective length of database: 236
Effective search space:    55460
Effective search space used:    55460
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 (21.7 bits)
S2: 47 (22.7 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