GapMind for catabolism of small carbon sources

 

Aligments for a candidate for kguT in Pseudomonas fluorescens FW300-N2C3

Align KguT (characterized, see rationale)
to candidate AO356_22860 AO356_22860 MFS transporter permease

Query= uniprot:A0A167V864
         (425 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_22860 AO356_22860 MFS
           transporter permease
          Length = 436

 Score =  202 bits (515), Expect = 1e-56
 Identities = 133/414 (32%), Positives = 204/414 (49%), Gaps = 22/414 (5%)

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
            +   ++ I + +I WG L+T    V + +    +R   G  EA   P +++YL  WF  
Sbjct: 85  TRFGPRRWIALMMITWGTLSTCLLFVTTPTEFYTLRLFTGAAEAGFFPGVVLYLSQWFPT 144

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

Query: 186 WRLVDDRPEQASWLKAQEKTALREALAAEQQGIKP---VKNYREAFRSPKVIILSLQYFC 242
           + L+ D    A WL A+E+  L  A  AE    KP     +    F++P +    L YFC
Sbjct: 205 FFLLSDTFANAKWLTAEERAVLT-ADHAEDLANKPKSTTDSLLAVFKNPAIWAFGLVYFC 263

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

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

Query: 361 MALINSMGALGSFSGSWLVGYLNGVTGGPGASYLFMCGAL----LVAVALTAVL 410
           +ALINSMG +  F   +LVG++   TG   A+   + G +    L+A+ +T  L
Sbjct: 381 LALINSMGQMAGFLSPYLVGWVKDTTGSTDAALYLLAGVIVCGSLLALRMTRTL 434


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: 590
Number of extensions: 44
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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