GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Caulobacter crescentus NA1000

Align glucose transporter, ATPase component (characterized)
to candidate CCNA_02751 CCNA_02751 ABC transporter ATP-binding protein

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



>FitnessBrowser__Caulo:CCNA_02751
          Length = 332

 Score =  116 bits (291), Expect = 5e-31
 Identities = 77/233 (33%), Positives = 128/233 (54%), Gaps = 14/233 (6%)

Query: 15  LVEMKDISISF--GGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEI 72
           ++  +D+S ++  GG  A+  VS+ +  GEV G++G +GAGKSTLI++++G     AG++
Sbjct: 1   MITFQDVSKTYAQGGHPALSGVSLSVKAGEVFGVIGASGAGKSTLIRLINGLETPSAGQV 60

Query: 73  RVNGDKVEITNPRDARS--HNIETIYQTLALADNLDAASNLFLGRELVTPFGLVDDSAME 130
            V+GD V        R+    +  I+Q   L      A N      +  P  L    A E
Sbjct: 61  IVDGDDVAALGVAGLRALRRRVGMIFQHFNLLSGKTVAQN------VAFPLKLAGRPAAE 114

Query: 131 AECR--KIMNRLNPNFQKFSEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAALGPHE 188
            + R  +++ R+  +      P + LSGGQ+Q V IARA+  N K+L+ DE T+AL P  
Sbjct: 115 VKARTAELLERVGLSAHAGKYP-AQLSGGQKQRVGIARALATNPKVLLCDEATSALDPET 173

Query: 189 TQMVAELIQQLKAQ-GIGIFLIDHDVNAVMELCDRASVMKNGQLVGTVDIDDV 240
           T+ + +LI  L  + G+ I LI H+++ V  +CDR +V+  G++V    +++V
Sbjct: 174 TEQILDLIAGLNRELGLTIVLITHEMDVVRRVCDRVAVLDAGRVVEEGAVEEV 226


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: 197
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: 332
Length adjustment: 26
Effective length of query: 234
Effective length of database: 306
Effective search space:    71604
Effective search space used:    71604
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: 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