GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Pseudomonas putida KT2440

Align KguT (characterized, see rationale)
to candidate PP_3391 PP_3391 putative Tartrate MFS transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__Putida:PP_3391
          Length = 438

 Score =  179 bits (453), Expect = 2e-49
 Identities = 126/413 (30%), Positives = 199/413 (48%), Gaps = 16/413 (3%)

Query: 12  WYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAI 71
           W IMP+  I +  +Y DR N  FA    M  +L ++ A   L  ++FF+GY  F+VP ++
Sbjct: 28  WRIMPLAIICFLFSYFDRINISFAKTQ-MQQELGLSDAAYGLAASMFFVGYVLFEVPSSL 86

Query: 72  YAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWF 131
             ++      I   ++ WG          +   L  +RFL+GV+EA   PA+L YL  WF
Sbjct: 87  GLKRYGAPAWICRIMVSWGLATAALVFAYTQYTLYFLRFLIGVMEAGFGPAILFYLACWF 146

Query: 132 TRAERSRANTFLILGNPVTILWMSVVSGYLVKHFD-------WRWMFIIEGLPAVLWAF- 183
            R   ++ N    L  P+        +G+L+   D       W W+F++ GLP VL    
Sbjct: 147 PRKHLAKMNGLWFLAVPLAGAVGGPAAGFLLGTMDGVLGLAGWHWLFLMSGLPCVLLGLL 206

Query: 184 IWWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVK-NYREAFRSPKVIILSLQYFC 242
           + W+L D   E A WL  +EK  L E LA +++  KP+  +      + +V I++  Y+ 
Sbjct: 207 VLWKL-DRDIEAAKWLSREEKDLLAENLAQDKRTAKPILGSIWRVLLTREVAIMAFIYYV 265

Query: 243 WSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVW 302
                YG   W+P ++K +   D++  G LSA+PY  A + M+ ++  SDR  +RKR++ 
Sbjct: 266 VKTASYGLNFWMPHLIKSSGVQDMLWVGVLSALPYAVACIGMVLLTRHSDRTGERKRYLV 325

Query: 303 PPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVA-GGAM 361
             LL AA+ +  + +     F    T LV+A A  +    P F  +P+   S +A     
Sbjct: 326 YCLLAAAVGYLLACLFSDSPF-AMMTALVLATAGTFIAI-PIFWTIPQSTFSGLAIATGT 383

Query: 362 ALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVA--VALTAVLNP 412
           A INS+G L       +VG +N +T       L +   +LVA  V +  V NP
Sbjct: 384 AAINSVGQLSGIVAPVMVGKINDLTDSTYMGMLSIAPLILVACLVVMRYVRNP 436


Lambda     K      H
   0.328    0.140    0.457 

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: 603
Number of extensions: 49
Number of successful extensions: 7
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: 425
Length of database: 438
Length adjustment: 32
Effective length of query: 393
Effective length of database: 406
Effective search space:   159558
Effective search space used:   159558
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 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