GapMind for catabolism of small carbon sources

 

Alignments for a candidate for HMIT in Bacteroides thetaiotaomicron VPI-5482

Align Proton myo-inositol cotransporter; H(+)-myo-inositol cotransporter; Hmit; H(+)-myo-inositol symporter; Solute carrier family 2 member 13 (characterized)
to candidate 353923 BT4397 xylose/H+ symporter (NCBI ptt file)

Query= SwissProt::Q96QE2
         (648 letters)



>FitnessBrowser__Btheta:353923
          Length = 460

 Score =  171 bits (432), Expect = 9e-47
 Identities = 120/360 (33%), Positives = 183/360 (50%), Gaps = 33/360 (9%)

Query: 80  FVYVVAVFSALGGFLFGYDTGVVSGAMLLLKRQLSL--DALWQELLVSSTVGAAAVSALA 137
           FVY + + SA+GG LFGYD  V+ GA    +    +      Q L +S  +    + A+ 
Sbjct: 8   FVYSICLVSAMGGLLFGYDWVVIGGAKPFYELYFGIADSPTMQGLAMSVALLGCLIGAMV 67

Query: 138 GGALNGVFGRRAAILLASALFTAGSAVLAAANNKETLLAGRLVVGLGIGIASMTVPVYIA 197
            G +   +GR+  +L+++ +F + +    A +     LA R + G+GIGIAS   P+YIA
Sbjct: 68  AGMMADRYGRKPLLLISAFIFLSSAYATGAFSVFSWFLAARFLGGIGIGIASGLSPMYIA 127

Query: 198 EVSPPNLRGRLVTINTLFITGGQFFASV---------------VDGAFSYLQKDGWRYML 242
           EV+P ++RG+LV++N L I  G   A +                D   S+  + GWR+M 
Sbjct: 128 EVAPTSIRGKLVSLNQLTIVLGILGAQIANWLIAEPIPADFTPADICASWNGQMGWRWMF 187

Query: 243 GLAAVPAVIQFFGFLFLPESPRWLIQKGQTQKARRILSQMRGNQTIDEEYDSIKNNIEEE 302
             AA PA +      F+PESPRWL  KG+ +KA  +LS++ GN+  ++E   +     E+
Sbjct: 188 WGAAFPAAVFLLLACFIPESPRWLAMKGKREKAWSVLSRIGGNRYAEQELQMV-----EQ 242

Query: 303 EKEVGSAGPVICRMLSYPPTRRALIVGCGLQMFQQLSGINTIMYYSATILQMSGVEDDRL 362
                S G +  ++L   P R+ L++G  + +FQQ  G N I  Y+  I Q +G     +
Sbjct: 243 TSASKSEGGL--KLLFSRPFRKVLVLGVIVAVFQQWCGTNVIFNYAQEIFQSAGYSLGDV 300

Query: 363 AIWLASVTAFTNFIFTLVGVWLVEKVGRRKLTF---GSLAGTTVALIILALGFVLSAQVS 419
            ++   VT   N IFT V ++ VE++GRR L     G LAG     I L LG     QVS
Sbjct: 301 -LFNIVVTGVANVIFTFVAIYTVERLGRRALMLLGAGGLAG-----IYLVLGTCYFFQVS 354



 Score = 63.2 bits (152), Expect = 3e-14
 Identities = 31/94 (32%), Positives = 49/94 (52%)

Query: 513 LILYLVFFAPGMGPMPWTVNSEIYPLWARSTGNACSSGINWIFNVLVSLTFLHTAEYLTY 572
           ++L +  +A  +GP+ W + +EI+P   R    A  +   W+ +  ++ TF      L  
Sbjct: 362 VVLAIACYAMSLGPITWVLLAEIFPNRVRGVAMATCTFALWVGSFTLTYTFPLLNTALGS 421

Query: 573 YGAFFLYAGFAAVGLLFIYGCLPETKGKKLEEIE 606
           YG F++Y+     G LF    LPETKGK LE +E
Sbjct: 422 YGTFWIYSAICVFGFLFFLRALPETKGKSLETLE 455


Lambda     K      H
   0.321    0.136    0.410 

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: 697
Number of extensions: 32
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: 2
Length of query: 648
Length of database: 460
Length adjustment: 35
Effective length of query: 613
Effective length of database: 425
Effective search space:   260525
Effective search space used:   260525
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 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