GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kgtP in Pseudomonas fluorescens FW300-N1B4

Align alpha-ketoglutarate permease (MHS family) (characterized)
to candidate Pf1N1B4_180 L-Proline/Glycine betaine transporter ProP

Query= reanno::pseudo5_N2C3_1:AO356_17790
         (439 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_180
          Length = 459

 Score =  196 bits (499), Expect = 1e-54
 Identities = 132/436 (30%), Positives = 209/436 (47%), Gaps = 11/436 (2%)

Query: 4   SNALPIGSAAVPARERTTASRIKSIFSGSVGNMVEWYDWYVYA-AFSLYFAKVFFPKGDT 62
           S+  P+  +  P       S  K   +  +G  VEWYD +V+A A +L F KVFFP  D 
Sbjct: 2   SDLSPVEKSGAPPE--VAISMKKVAVASVIGTTVEWYDLFVFATASALVFNKVFFPDFDP 59

Query: 63  TAQLLNTAAIFAVGFLMRPIGGWLMGLYADRAGRKRALMASVYLMCFGSLIIALSPSYET 122
               L     FA  +L R +G  L G + DR GRK  L+ S+  M   +  I L P+Y  
Sbjct: 60  LIGTLLAFGTFASAYLARIVGAALFGHFGDRLGRKSMLLVSLLTMGAATFAIGLLPNYAA 119

Query: 123 IGVGAPILLVFARLLQGLSVGGEYGTSATYLSEMATKERRGFFSSFQYVTLISGQLIALG 182
           IG+ APILL+  R++QGL++GGE+G +     E A   +RG + S+  + + +G +IA  
Sbjct: 120 IGIWAPILLLLLRVIQGLALGGEWGGAVLMAVEHAPANKRGLYGSWVQIGVPAGTMIANL 179

Query: 183 VLIVLQQFLTTEQLYAWGWRIPFAIGALCAVVALYLRRGMEETESFTKKEKSKESAMRTL 242
             +V+  +L+ E L AWGWRIPF    L   V LY+R  + ET +F K ++++      L
Sbjct: 180 AFLVIAAWLSPEDLLAWGWRIPFLASVLLIAVGLYIRLNISETPAFNKVKEAEVQVKMPL 239

Query: 243 L----RHPKELMTVVGLTMGGTLAFYTYTTYMQKYLVNTVGMSISDSTTISAATLFLFMC 298
                ++ K+++     TM    +F     +   Y    +G S S    +   +    + 
Sbjct: 240 AEVFRKYWKQVVLGGIATMSTGASFNIIVAFGLTYGTQNLGFSRSVMLGVVLLSCAWCIV 299

Query: 299 LQPVIGGLSDKIGRRPILIAFGILGTLFTVPILTTLHTIQTWWGAFFLIMAALIIVSGYT 358
           + PV G LSD+ GR+PI++A  +   L   P+   + T +     F  ++      + Y 
Sbjct: 300 MLPVFGALSDRYGRKPIIVAGIVAEALVAFPMFWLMDTKELSLVIFGYLLLMTAFAANYG 359

Query: 359 SINAVVKAELFPTEIRALGVGLPYALTVSIFGGTAEYI--ALWFKSIGMETGYYWYVTAC 416
            I A   AELF T +R  G+ + Y L+  + G  A  I       + G  +   WY+   
Sbjct: 360 PI-ATFLAELFGTRVRYSGLSISYMLS-GLLGSAATPIVTTALLAATGKGSSVAWYMIGA 417

Query: 417 IAVSLLVYITMKDTRK 432
             +SL+  + + +T K
Sbjct: 418 AFISLVALLLLTETFK 433


Lambda     K      H
   0.326    0.138    0.416 

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: 570
Number of extensions: 30
Number of successful extensions: 4
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: 439
Length of database: 459
Length adjustment: 33
Effective length of query: 406
Effective length of database: 426
Effective search space:   172956
Effective search space used:   172956
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 (21.7 bits)
S2: 51 (24.3 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