GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Putida:PP_3391 PP_3391 putative Tartrate MFS
           transporter
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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