GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsC in Phaeobacter inhibens BS107

Align Ribose import permease protein RbsC (characterized)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC

Query= SwissProt::P0AGI1
         (321 letters)



>FitnessBrowser__Phaeo:GFF2276
          Length = 324

 Score =  190 bits (482), Expect = 5e-53
 Identities = 105/301 (34%), Positives = 174/301 (57%), Gaps = 2/301 (0%)

Query: 17  LMEQKSLIALLVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGIDLSV 76
           L +Q  LIA  + I   +  +P F T++N  N+++ +++  +MA+G+T V+++  +DLSV
Sbjct: 13  LAKQGILIAFALFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSV 72

Query: 77  GSLLALTGAVAASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATLVMMLL 136
           GS+++ +  V   +   ++   +A+ A  A+   +GA+ G +V   ++ + I TL M+  
Sbjct: 73  GSMMSFSTIVVLDLHD-KLGPTLAIPAMFAMTLCLGALIGFLVGYLKLNSLIVTLGMLSA 131

Query: 137 LRGVTMVYTNGSPVNTGFTENADLFGWFGIGRPLGVPTPVWIMGIVFLAAWYMLHHTRLG 196
           + G+T+ Y+ G  ++    E    F  FG G  LG+ TP+ I   +      +L  T  G
Sbjct: 132 IHGLTLTYSGGKNMDIADKEGT-WFAIFGQGNILGIQTPILIFIALAALLGIILAKTPFG 190

Query: 197 RYIYALGGNEAATRLSGINVNKIKIIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELD 256
           R +YA+GGN  A   SGI   ++  + Y +  L  + AG+I+ +R   +Q T G G EL+
Sbjct: 191 RKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNTVGQGLELE 250

Query: 257 AIAAVVLGGTSLAGGKGRIVGTLIGALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLV 316
            +AAV+LGG SL GG G I  T+IG LILGF+ NGL L+G+    Q +V  ++I+LAV +
Sbjct: 251 VLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIIIILAVWL 310

Query: 317 D 317
           D
Sbjct: 311 D 311


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: 235
Number of extensions: 7
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: 321
Length of database: 324
Length adjustment: 28
Effective length of query: 293
Effective length of database: 296
Effective search space:    86728
Effective search space used:    86728
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 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