GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsC in Pseudovibrio axinellae Ad2

Align Ribose import permease protein RbsC (characterized)
to candidate WP_068006265.1 PsAD2_RS12365 ABC transporter permease

Query= SwissProt::P0AGI1
         (321 letters)



>NCBI__GCF_001623255.1:WP_068006265.1
          Length = 368

 Score =  148 bits (373), Expect = 2e-40
 Identities = 103/338 (30%), Positives = 165/338 (48%), Gaps = 37/338 (10%)

Query: 17  LMEQKSLIAL----LVLIAIVSTLSPNFFTINNLFNILQQTSVNAIMAVGMTLVILTSGI 72
           LM++  L AL    LV I    T  P  F++    N +   S   I+A+G  L+++    
Sbjct: 22  LMKRPELGALAGLALVTIFFAFTADPKMFSLAGFLNFMTPASQLGILAIGAALLMIGGEF 81

Query: 73  DLSVGSLLALTGAV-AASIVGIEVNALVAVAAALALGAAIGAVTGVIVAKGRVQAFIATL 131
           DLSVGS++A TG +  A++V  E+    A+     + AA+GAV G IV +  + +FI TL
Sbjct: 82  DLSVGSMVAFTGLIFGAAMVTFELPLYAAIIVTFMVAAAMGAVNGQIVIRTGLPSFIVTL 141

Query: 132 VMMLLLRGVTMV----YTNGSPVNTGFTENAD---------------LFGW--------- 163
             + +LRG+++V     T GS    G  E  +               LF W         
Sbjct: 142 AFLFILRGLSLVGLKAATGGSTQLRGVREKVEGSWIADFFSGEAFTPLFYWLAENGLVDT 201

Query: 164 FGIGRPL--GVPTPV-WIMGIVFLAAWYMLHHTRLGRYIYALGGNEAATRLSGINVNKIK 220
           F  G+P   G+P  + W   +  +A W +L  +R G +I+A GG+ +A   SG+ V ++K
Sbjct: 202 FKSGKPKVDGIPVEIIWFTLLAGVATWILLR-SRFGSWIFASGGDSSAASNSGVPVRRVK 260

Query: 221 IIVYSLCGLLASLAGIIEVARLSSAQPTAGTGYELDAIAAVVLGGTSLAGGKGRIVGTLI 280
           + ++      A+L  I+ V    S     G   E +AI A V+GG+ L GG G  +G   
Sbjct: 261 MYLFMFTACCAALVAILTVMDAGSTDARRGFQKEFEAIIAAVIGGSLLTGGYGSAIGAFF 320

Query: 281 GALILGFLNNGLNLLGVSSYYQMIVKAVVILLAVLVDN 318
           G++I G +  GL+   +   + ++    ++LLAVL +N
Sbjct: 321 GSIIFGMVLIGLSYTNIDQDWYLVFLGSMLLLAVLFNN 358


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: 250
Number of extensions: 17
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: 368
Length adjustment: 29
Effective length of query: 292
Effective length of database: 339
Effective search space:    98988
Effective search space used:    98988
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: 49 (23.5 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