GapMind for catabolism of small carbon sources

 

Alignments for a candidate for braF in Photobacterium gaetbulicola Gung47

Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_044621547.1 H744_RS07090 urea ABC transporter ATP-binding protein UrtD

Query= TCDB::Q55164
         (267 letters)



>NCBI__GCF_000940995.1:WP_044621547.1
          Length = 283

 Score =  144 bits (362), Expect = 3e-39
 Identities = 87/250 (34%), Positives = 145/250 (58%), Gaps = 9/250 (3%)

Query: 18  LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77
           LL  +G++KSF G +A+D  ++ V+EG +  +IGPNGAGKTT+ ++++   +PD G+V  
Sbjct: 42  LLYVEGVNKSFDGFKAIDDLNLYVREGELRCIIGPNGAGKTTMMDIITGKTKPDSGQVWL 101

Query: 78  NGD-SIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRV 136
             + ++  +   QIA  G  R FQ   V+  L+V +N+ LA    +G + +      R  
Sbjct: 102 GANINLLTMNESQIANAGVGRKFQKPTVIECLSVWQNLELA---MSGVRTVWATYRARLT 158

Query: 137 QKEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAG 196
            ++    ++K  ++L  + L   A   AG LS GQ++ LE+   LM NPKL+L+DEP AG
Sbjct: 159 TEQ----KDKLESVLALINLADNAALLAGNLSHGQKQWLEIGMLLMQNPKLLLVDEPVAG 214

Query: 197 VNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSD 256
           +    + +  E ++N      + +V+EH+MD + ++   V VL +G  LA+GT +Q+Q+ 
Sbjct: 215 MTHQEMDKTAE-LLNSLAGKHSVVVVEHDMDFVRSIASEVTVLHQGHVLAEGTMDQVQNH 273

Query: 257 PRVLEAYLGD 266
           P V   YLG+
Sbjct: 274 PEVKRVYLGE 283


Lambda     K      H
   0.319    0.136    0.389 

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: 10
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: 267
Length of database: 283
Length adjustment: 25
Effective length of query: 242
Effective length of database: 258
Effective search space:    62436
Effective search space used:    62436
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 (21.7 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