GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Pseudomonas fluorescens GW456-L13

Align KguT (characterized, see rationale)
to candidate PfGW456L13_2481 Major facilitator family transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2481
          Length = 441

 Score =  185 bits (469), Expect = 3e-51
 Identities = 124/415 (29%), Positives = 204/415 (49%), Gaps = 16/415 (3%)

Query: 13  YIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAIY 72
           +++P+  I + + Y+DR N GF   S M  DL I  A   L   LFF+GY  F+VP  I 
Sbjct: 19  HVLPLFVIMFIVNYIDRVNIGFVR-SHMEHDLGIGAAAYGLGAGLFFIGYALFEVPSNIL 77

Query: 73  AEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWFT 132
            +K   +  +   ++ WG +A     +Q+ +    +RFLLGV EA   P ++ Y   W  
Sbjct: 78  LQKVGARIWLTRIMLTWGLVAAGMAFIQNETHFYILRFLLGVAEAGFFPGVIYYFTRWLP 137

Query: 133 RAERSRANTFLILGNPVTILWMSVVSGYLVK-----HFDWRWMFIIEGLPAV-LWAFIWW 186
             ER +A    + G+ +  L    +SG L++        W+WM+ IEG+ +V L  F+W+
Sbjct: 138 GVERGKAIAIFLSGSALASLISGPLSGLLLQIEGLGLHGWQWMYFIEGMFSVGLCVFVWF 197

Query: 187 RLVDDRPEQASWLKAQEKTALREALAAEQ---QGIKPVK-NYREAFRSPKVIILSLQYFC 242
            L D RP  A WL  +E+ AL +A+  EQ   +   P+K +  +  +  ++I+  L YF 
Sbjct: 198 WL-DSRPHDAKWLSREEQDALVKAIDDEQLAREAATPIKPSLGKLLKDRQIILFCLIYFF 256

Query: 243 WSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVW 302
             + +Y    WLPSI+K+   L  V  G  +++P+L +++ M   +  S + + ++ +V 
Sbjct: 257 IQLTIYAATFWLPSIIKKMGDLSDVQVGLFNSIPWLLSIVGMYAFASLSAKWKHQQAWVA 316

Query: 303 PPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMA 362
             LLIAA   + S   G     +++  +  A     +    F+ I    L + +A G +A
Sbjct: 317 TALLIAAAGMFMSTTGGPV---FAFVAICFAALGFKSASSLFWPIPQAYLDARIAAGVIA 373

Query: 363 LINSMGALGSFSGSWLVGYLNGVTGG-PGASYLFMCGALLVAVALTAVLNPSQQA 416
           LINS+G LG F      G L   TG   G  Y     +++ A+ + A  N  + A
Sbjct: 374 LINSVGNLGGFVAPTTFGLLEERTGSIQGGLYGLAATSIIAAIIVFAARNTPKPA 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: 601
Number of extensions: 28
Number of successful extensions: 5
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: 441
Length adjustment: 32
Effective length of query: 393
Effective length of database: 409
Effective search space:   160737
Effective search space used:   160737
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