GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Pseudomonas stutzeri RCH2

Align glucose transporter, ATPase component (characterized)
to candidate GFF1276 Psest_1309 ABC-type branched-chain amino acid transport systems, ATPase component

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



>FitnessBrowser__psRCH2:GFF1276
          Length = 255

 Score =  110 bits (274), Expect = 4e-29
 Identities = 69/227 (30%), Positives = 118/227 (51%), Gaps = 11/227 (4%)

Query: 14  PLVEMKDISISFGGIKAVDHVSVDLYPGEVVGLLGHNGAGKSTLIKVLSGAYQMDAGEIR 73
           P++E++ + + FGG+ AV+ V + ++  +VV ++G NGAGK+T+   L+G YQ  AGEI 
Sbjct: 4   PILEVRGLMMRFGGLLAVNEVGLTVHDKQVVSMIGPNGAGKTTVFNCLTGFYQPTAGEIL 63

Query: 74  VNGDKVEITNPRDARSHNIETIYQTLALADNLDAASNLFLG--RELVTPF--GLVDDSAM 129
           ++G  +            +   +Q + L  ++ A  NL +   R L T F  GL+     
Sbjct: 64  LDGTPIHGLPGHKIARQGVVRTFQNVRLFKDMTAVENLLVAQHRHLNTNFLAGLLKTPGF 123

Query: 130 EAECRKIMNRLNPNFQKF------SEPVSALSGGQRQSVAIARAVYFNAKILIMDEPTAA 183
               R  M+      ++       + P   L+ GQ++ + IAR +    +IL++DEP A 
Sbjct: 124 RKSERAAMDFAAHWLEQVNLTDVANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAG 183

Query: 184 LGPHETQMVAELIQQLKAQ-GIGIFLIDHDVNAVMELCDRASVMKNG 229
           L P ET+ +  LI  L+ + G+ + LI+HD+  VM + D   V+  G
Sbjct: 184 LNPKETEDLKALIAMLRDEHGVTVLLIEHDMKLVMSISDHIYVINQG 230


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: 137
Number of extensions: 6
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: 260
Length of database: 255
Length adjustment: 24
Effective length of query: 236
Effective length of database: 231
Effective search space:    54516
Effective search space used:    54516
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 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