GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsC in Collimonas pratensis Ter91

Align Ribose import permease protein RbsC (characterized)
to candidate WP_061940318.1 CPter91_RS11535 ABC transporter permease

Query= SwissProt::P0AGI1
         (321 letters)



>NCBI__GCF_001584185.1:WP_061940318.1
          Length = 334

 Score =  202 bits (515), Expect = 7e-57
 Identities = 114/301 (37%), Positives = 177/301 (58%), Gaps = 10/301 (3%)

Query: 23  LIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSVGSLLAL 82
           ++ L+ L    + L+ +F T++NL N+L +T+   I+AVGMT VI++ GIDLSVGS+ AL
Sbjct: 27  VLGLIGLCIAGTLLNGDFATVDNLMNVLTRTAFIGIIAVGMTFVIISGGIDLSVGSMAAL 86

Query: 83  TGA---------VAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVM 133
                       ++A  +G     L+ +A AL LG A G + G+++ KG+++AFI TL  
Sbjct: 87  IAGSMIYFMNMLMSAGTLGPLTILLIGIAMALLLGLAFGCLHGLLITKGKIEAFIVTLGT 146

Query: 134 MLLLRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHT 193
           + + R V     +G  +     + +DL+        LG+P P+W+   V L    +L+ T
Sbjct: 147 LGIFRSVLTYLADGGALTLD-NQLSDLYSPVYYTSLLGIPIPIWVFLAVALGGALILNRT 205

Query: 194 RLGRYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGY 253
             GR++ A+G NE   R + I V+ +K   Y L G+   +A ++ V RL SA PT G  +
Sbjct: 206 AFGRHVQAIGSNEQVARYAAIRVDFVKTCTYMLLGVCVGIATVLYVPRLGSASPTTGLLW 265

Query: 254 ELDAIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLA 313
           EL+AIAAVV+GGT+L GG GRIVGT++GA++L  ++N LNL  + S Y       V+++A
Sbjct: 266 ELEAIAAVVVGGTALKGGSGRIVGTVVGAILLSVISNILNLTSIISVYLNAAVQGVVIIA 325

Query: 314 V 314
           V
Sbjct: 326 V 326


Lambda     K      H
   0.324    0.139    0.393 

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: 261
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: 321
Length of database: 334
Length adjustment: 28
Effective length of query: 293
Effective length of database: 306
Effective search space:    89658
Effective search space used:    89658
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 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