GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Dyella japonica UNC79MFTsu3.2

Align KguT (characterized, see rationale)
to candidate N515DRAFT_2085 N515DRAFT_2085 Sugar phosphate permease

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2085
          Length = 434

 Score =  200 bits (508), Expect = 8e-56
 Identities = 125/411 (30%), Positives = 208/411 (50%), Gaps = 13/411 (3%)

Query: 14  IMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAIYA 73
           ++P +FI Y  AYLDR N GFA    M  DLH + A+  L   +FF+GYF F+VP  +  
Sbjct: 23  LLPFLFICYVAAYLDRVNIGFAKLQ-MLSDLHFSEAVYGLGAGVFFIGYFLFEVPSNMLL 81

Query: 74  EKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWFTR 133
            +   +  I   ++ W  ++  T +V + +    +RFLLGV EA   P +++YL +W+  
Sbjct: 82  HRLGARLWISRIMVSWALVSAATMLVTTPTAFYVLRFLLGVAEAGFFPGIVLYLTYWYPS 141

Query: 134 AERSRANTFLILGNPVTILWMSVVSGYLVKHF-------DWRWMFIIEGLPAVLWAFIWW 186
           A R R N   + G P+  +    +SG+++  F       +W+W+F++E LP++       
Sbjct: 142 ARRGRMNALFMTGIPIAGVLGGPLSGWIMHAFGGVHGLANWQWLFLLEALPSLALGIATP 201

Query: 187 RLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWSIG 246
            ++ +    ASWL A+EK  L + LA + Q      + R      +V  L+  YFC  +G
Sbjct: 202 FVLPNGIRSASWLDAREKQLLEDRLAGDPQAGSEA-SLRSVMADVRVWRLAAIYFCCMMG 260

Query: 247 VYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPPLL 306
           +YG   +LP+++  A   D +  G L+A+PY  AV++M+ ++ +SDR  +R+  +    +
Sbjct: 261 LYGVSFYLPTLIAAAGVDDALDVGLLTAIPYAVAVVSMILLARSSDRHNERRWHLAAASI 320

Query: 307 IAALAFYGSYILGTEHFWWSYTL-LVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALIN 365
             A   Y S + G+E       L L  AG     P   F+     +L    A   +A+IN
Sbjct: 321 AGAAGLYASTLCGSELVLGLIALSLGTAGVLSTMPV--FWTWPSSVLAGTAAAAGIAMIN 378

Query: 366 SMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAVLNPSQQA 416
           S+G L  F    ++G++  +T    A    +  ALL+  AL A+L  + +A
Sbjct: 379 SIGNLAGFVSPSIIGWMKDLTHSTNAGLWVVAVALLLGAAL-ALLGSAAKA 428


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: 612
Number of extensions: 37
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 425
Length of database: 434
Length adjustment: 32
Effective length of query: 393
Effective length of database: 402
Effective search space:   157986
Effective search space used:   157986
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