GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Pseudomonas simiae WCS417

Align KguT (characterized, see rationale)
to candidate GFF2741 PS417_13980 MFS transporter permease

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__WCS417:GFF2741
          Length = 436

 Score =  206 bits (523), Expect = 1e-57
 Identities = 133/409 (32%), Positives = 205/409 (50%), Gaps = 19/409 (4%)

Query: 14  IMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAIYA 73
           ++P +FI Y   YLDR N GFA    M D L  +  +  L   +FF+GY    VP  +  
Sbjct: 26  LIPFIFICYLFNYLDRVNVGFAKLQ-MLDALKFSETVYGLGAGIFFIGYVLCGVPSNLAL 84

Query: 74  EKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWFTR 133
            K   ++ I + +I+WG L+T    V + +    +R   G  EA   P +++YL  WF  
Sbjct: 85  TKFGPRRWIALMMIVWGTLSTCLLFVTTPTHFYTLRLFTGAAEAGFFPGVVLYLSQWFPT 144

Query: 134 AERSRANTFLILGNPVTILWMSVVSGYLVKHF--------DWRWMFIIEGLPAVLWAFIW 185
             R R     +   PV+ L  S  SG+++ HF         W+WMF+++G+P V+   + 
Sbjct: 145 FRRGRIMALFMSAIPVSGLLGSPFSGWILNHFAAGQGGLAGWQWMFLLQGIPTVVLGALA 204

Query: 186 WRLVDDRPEQASWLKAQEKTALREALAAEQQGIKP---VKNYREAFRSPKVIILSLQYFC 242
           + L+ D    A WLK  E+  L EA  A     KP     +  E F++P +    L YFC
Sbjct: 205 YFLLSDSFANAKWLKPHERAVL-EADQATDLANKPKTTTDSLAEVFKNPAIWAFGLIYFC 263

Query: 243 WSIGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVW 302
              GVY    WLPSI+K     D +  GWLSA+PYL A + ML V  ++D  ++R+  + 
Sbjct: 264 IQSGVYAINFWLPSIIKNLGFSDNLVIGWLSAIPYLLAAVFMLLVGRSADLRKERRWHLV 323

Query: 303 PPLLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYG-PFFAIVP-ELLPSNVAGGA 360
            P+L+ A+    +    T     +  +L +  A M A  G P F  VP  +L +  A G 
Sbjct: 324 VPMLMGAIGLVIAVNFATTP---AIAILGLTIATMGALTGLPMFWPVPTAMLSAGAAAGG 380

Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGALLVAVALTAV 409
           +ALINSMG +  F   ++VG++   TG    + L++  A++VA ++ A+
Sbjct: 381 LALINSMGQMAGFLSPYIVGFVKDATGSTDMA-LYLLAAVIVAGSVLAL 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: 596
Number of extensions: 38
Number of successful extensions: 6
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: 436
Length adjustment: 32
Effective length of query: 393
Effective length of database: 404
Effective search space:   158772
Effective search space used:   158772
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