GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguT in Pseudomonas simiae WCS417

Align KguT (characterized, see rationale)
to candidate GFF2124 PS417_10835 major facilitator transporter

Query= uniprot:A0A167V864
         (425 letters)



>FitnessBrowser__WCS417:GFF2124
          Length = 438

 Score =  218 bits (554), Expect = 4e-61
 Identities = 126/403 (31%), Positives = 195/403 (48%), Gaps = 17/403 (4%)

Query: 12  WYIMPIVFITYSLAYLDRANYGFAAASGMADDLHITPALSSLLGALFFLGYFFFQVPGAI 71
           W ++P++FI Y  AYLDR N GFA    M  DL ++ A       +FF+GY  F++P  +
Sbjct: 22  WRLLPLLFIGYVFAYLDRINVGFAKLQ-MQSDLGLSDAAYGAGAGIFFVGYVLFELPSTL 80

Query: 72  YAEKRSVKKLIFVSLILWGGLATLTGMVQSVSLLIAIRFLLGVVEAAVMPAMLIYLCHWF 131
              +   +K     L+LWG  +     V+ V    A+RFLLGV EA   P M+ YL  W+
Sbjct: 81  MLPRIGARKTFSRILVLWGITSACMLFVRDVPTFYAMRFLLGVFEAGFAPGMIYYLSRWY 140

Query: 132 TRAERSRANTFLILGNPVTILWMSVVSGYLVKHF-------DWRWMFIIEGLPAVLWAFI 184
             +  +RA   + +  P+  +    +S +L+  F        W+WMF+IEGLP V    +
Sbjct: 141 GPSRMARAIAIVFIAGPMGGILGGPISAWLITTFAGVGGLAGWQWMFLIEGLPCVFLGVL 200

Query: 185 WWRLVDDRPEQASWLKAQEKTALREALAAEQQGIKPVKNYREAFRSPKVIILSLQYFCWS 244
            + ++ DRP  A WL A EK  L   L           ++R   R PK+ +L+  YFC  
Sbjct: 201 MYVVLCDRPADAPWLNAAEKQLLETELGTAS---ARSHSFRTVLRDPKLYVLASAYFCII 257

Query: 245 IGVYGFVLWLPSILKQAAALDIVTAGWLSAVPYLGAVLAMLGVSWASDRMQKRKRFVWPP 304
             +Y    WLP+++K     D    GW +A+PY+GA L M  +   SDR+ +R+     P
Sbjct: 258 FSIYAMSFWLPAVIKALGVNDTQQLGWYAALPYVGAALGMYWIGRRSDRLGERRLHCAIP 317

Query: 305 LLIAALAFYGSYILGTEHFWWSYTLLVIAGACMYAPYGPFFAIVPELLPSNVAGGAMALI 364
               A+     Y L   +   S  LL ++ + M+  Y   +A+  E +    A G +ALI
Sbjct: 318 AATGAVLLI-LYPLAGGNLLVSMALLTLSISMMFMAYTVLWAMPSEHIKGEAAAGGIALI 376

Query: 365 NSMGALGSFSGSWLVGYLNGVTGGPGASYL-----FMCGALLV 402
           N++G  G F G  ++G+    TG      +     F+C A ++
Sbjct: 377 NTIGLSGGFWGPAMIGWAKTATGSLDTGLIAVGCVFLCAAFVI 419


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: 624
Number of extensions: 35
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: 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:

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