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_084931685.1 HA51_RS02405 sugar porter family MFS transporter

Query= TCDB::Q8NTX0
         (491 letters)



>NCBI__GCF_002095475.1:WP_084931685.1
          Length = 469

 Score =  331 bits (849), Expect = 3e-95
 Identities = 187/464 (40%), Positives = 278/464 (59%), Gaps = 18/464 (3%)

Query: 22  EGPYRKRLFYVALVATFGGLLFGYDTGVINGALNPMTRELGLTAFTEGVVTSSLLFGAAA 81
           + P R RL  + +V+T GGL FGYDTGVI+GAL  M  +L LT   EG +TS LLFGAA 
Sbjct: 8   QNPQRMRL--ITIVSTIGGLCFGYDTGVISGALIFMKYDLNLTPTQEGFITSFLLFGAAL 65

Query: 82  GAMFFGRISDNWGRRKTIISLAVAFFVGTMICVFAPSFAVMVVGRVLLGLAVGGASTVVP 141
           G++F G +SD  GRRK ++ +A  F  G +   FA     M+V R +LGLAVG AS  VP
Sbjct: 66  GSLFGGYLSDKQGRRKNLLWVAAIFMFGALGTAFAWDVPSMIVARFILGLAVGCASVTVP 125

Query: 142 VYLAELAPFEIRGSLAGRNELMIVVGQLAAFVINAIIGNVFGHHDGVWRYMLAIAAIPAI 201
           +Y++ELA  + R  L   NELMIV GQ  A+ +NA I N++      WR MLAI A+P  
Sbjct: 126 IYISELARADQRERLVTVNELMIVTGQFLAYSVNAAIVNLYPEMQHNWRIMLAIPALPGA 185

Query: 202 ALFFGMLRVPESPRWLVERGRIDEARAVLETIRPLERAHAEVADVEHLAREEHAVSEKSM 261
            L+FGML +PESPR+ + RG  ++A  VL+T+R  E    EV +++ + + +    E   
Sbjct: 186 LLWFGMLMMPESPRFFIRRGETEKAVKVLKTLRLPEEVDREVKEIQQIVKAD----EVKF 241

Query: 262 GLREILSSKWLVRILLVGIGLGVAQQLTGINSIMYYGQVVLIEAGFSENAALIANVAPGV 321
            L   L ++W+++++L+G+ + +A ++TG+N+IMYY   VL   G  + AA+   VA G+
Sbjct: 242 NLFAELKNRWVIQLVLIGLMIVLATRVTGVNTIMYYAPTVLKATGLGDAAAVTGAVANGI 301

Query: 322 IAVVGAFIALWMMDRINRRTTLITGYSLTTISHVLIGIASVAFPVGDPLR---------- 371
           I+V+   + + ++ + +RR    TG +  T+S VLIG+A   F   + +           
Sbjct: 302 ISVLATLLGMALIGKHSRRKMFFTGQAGVTVSLVLIGLAFKLFFHTETINGVDTLHANFA 361

Query: 372 --PYVILTLVVVFVGSMQTFLNVATWVMLSELFPLAMRGFAIGISVFFLWIANAFLGLFF 429
             PYVIL L++VF+  MQ ++    W+ML+E++PL MRG  +G +VF LWI +  +   F
Sbjct: 362 NAPYVILGLMLVFLVFMQGWIAPVFWLMLAEIYPLRMRGVGMGFAVFGLWIFDFMIQSIF 421

Query: 430 PTIMEAVGLTGTFFMFAGIGVVALIFIYTQVPETRGRTLEEIDE 473
           P ++   G   TF  F    V+ LI +   +PETRG TLE+I++
Sbjct: 422 PYLLGHYGGGMTFGFFGATNVIMLILLVKYLPETRGLTLEQIEK 465


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: 572
Number of extensions: 26
Number of successful extensions: 3
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: 469
Length adjustment: 34
Effective length of query: 457
Effective length of database: 435
Effective search space:   198795
Effective search space used:   198795
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: 51 (24.3 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