GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Btheta:353923 BT4397 xylose/H+ symporter (NCBI
           ptt file)
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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