GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Pantoea rwandensis LMG 26275

Align Myo-Inositol uptake porter, IolT1 (Km=0.2mM) (characterized)
to candidate WP_084931443.1 HA51_RS01415 sugar porter family MFS transporter

Query= TCDB::Q8NTX0
         (491 letters)



>NCBI__GCF_002095475.1:WP_084931443.1
          Length = 477

 Score =  334 bits (856), Expect = 5e-96
 Identities = 189/465 (40%), Positives = 283/465 (60%), Gaps = 19/465 (4%)

Query: 20  LTEGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFGA 79
           +   P  KR   + LV+T GGL FGYDTGVI+GAL  MT++LGL+  +EG++TSSLLFGA
Sbjct: 15  IAASPNMKR---ITLVSTIGGLCFGYDTGVISGALLFMTKDLGLSPTSEGIITSSLLFGA 71

Query: 80  AAGAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGASTV 139
           A G++F G +SD  GRRK ++ +A+ F  G +    A     M+  R +LGLAVG AS  
Sbjct: 72  AFGSLFGGLLSDRQGRRKNLLWVAIIFIFGALATAVAWDITSMLAARFILGLAVGCASVT 131

Query: 140 VPVYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAIP 199
           VPVY+AELAP   R  L   NELMIV GQ  A+ +NA I N +      WR MLAI AIP
Sbjct: 132 VPVYIAELAPANQRERLVTVNELMIVTGQFLAYSVNAGIVNAYPELSHNWRIMLAIPAIP 191

Query: 200 AIALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSEK 259
            + L+FGM+ +PESPR+ ++RG+  EAR VL  +R       E+ D+ ++     A+   
Sbjct: 192 GVLLWFGMMMMPESPRFFLQRGKEKEARHVLSGVREPGEIDKEIEDIRNII----ALDAS 247

Query: 260 SMGLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVAP 319
              LR+ LS KW+++++L+G+ + +A ++TG+N+IMYY   VL   G  + AA+ A VA 
Sbjct: 248 QPSLRQELSKKWVIQLILIGLMIVLATRVTGVNTIMYYAPTVLKSTGLGDAAAVTAAVAN 307

Query: 320 GVIAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAF---PVGDPL------ 370
           G+I+++   + + ++ +  RR   ++G    T+  V+IG+A   F    + D +      
Sbjct: 308 GLISILATILGMALIGKFPRRKMFLSGQIGVTVVLVMIGLAFKMFFHTEIRDGVSVLQGN 367

Query: 371 ---RPYVILTLVVVFVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGL 427
                Y+IL L+ +F+  MQ ++    W+MLSE++PL +RG  +GI+VF L+  +  +  
Sbjct: 368 FEGASYIILGLMSLFLVFMQGWIAPVFWLMLSEIYPLRIRGLGMGIAVFGLFAFDFVIQS 427

Query: 428 FFPTIMEAVGLTGTFFMFAGIGVVALIFIYTQVPETRGRTLEEID 472
            FP ++ A G   TF +FAG  +V L  ++  +PETRG +LEEI+
Sbjct: 428 LFPIMLNAWGGGATFGIFAGCNLVMLALLFKFLPETRGLSLEEIE 472


Lambda     K      H
   0.327    0.142    0.420 

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: 556
Number of extensions: 21
Number of successful extensions: 4
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: 491
Length of database: 477
Length adjustment: 34
Effective length of query: 457
Effective length of database: 443
Effective search space:   202451
Effective search space used:   202451
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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