GapMind for catabolism of small carbon sources

 

Aligments for a candidate for hutX in Sinorhizobium meliloti 1021

Align HutX aka HISX, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate SMc00672 SMc00672 histidine-binding periplasmic signal peptide protein

Query= TCDB::Q9KKE3
         (346 letters)



>lcl|FitnessBrowser__Smeli:SMc00672 SMc00672 histidine-binding
           periplasmic signal peptide protein
          Length = 344

 Score =  692 bits (1787), Expect = 0.0
 Identities = 343/344 (99%), Positives = 343/344 (99%)

Query: 3   MSISTMRLTFAAAGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGY 62
           MSISTMRLTFAAAGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGY
Sbjct: 1   MSISTMRLTFAAAGLMLAASASGANASYCGDGKTVTFAGIDWESGAFITEVMKTILSKGY 60

Query: 63  DCQVDSIPGNSVTLEQATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFVGASEGW 122
           DCQVDSIPGNSVTLEQATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFVGASEGW
Sbjct: 61  DCQVDSIPGNSVTLEQATANNDVQIFAEEWLGRSDVWNKAVEEKKVIAVGKTFVGASEGW 120

Query: 123 FVPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGV 182
           FVPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGV
Sbjct: 121 FVPDYVVHGDPARNIEAKAPDLKSVSQLTDPKIAEIFADPEEPSKGRFLNCPSGWTCEGV 180

Query: 183 STAKLEAYKLGETYVNFRPGTGTALDAAITSAYLQGEPIFFYYWSPTAILGKFKLIQLEE 242
           STAKLEAYKLGETYVNFRPGTGTALDAAITSAYLQGEPI FYYWSPTAILGKFKLIQLEE
Sbjct: 181 STAKLEAYKLGETYVNFRPGTGTALDAAITSAYLQGEPILFYYWSPTAILGKFKLIQLEE 240

Query: 243 PAYNEACWKELSSANGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNA 302
           PAYNEACWKELSSANGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNA
Sbjct: 241 PAYNEACWKELSSANGKRDEGCAFPSVDVAYGVNSTFASEAPEIVEILEKATFPLDEVNA 300

Query: 303 SLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGLK 346
           SLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGLK
Sbjct: 301 SLAYMADNKVDATAAAAEFLKTKGDIWSKWVSDEARGKIEAGLK 344


Lambda     K      H
   0.314    0.130    0.391 

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: 561
Number of extensions: 7
Number of successful extensions: 1
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: 346
Length of database: 344
Length adjustment: 29
Effective length of query: 317
Effective length of database: 315
Effective search space:    99855
Effective search space used:    99855
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: 42 (22.0 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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