GapMind for catabolism of small carbon sources

 

Aligments for a candidate for MFS-glucose in Bacteroides thetaiotaomicron VPI-5482

Align The glucose uptake porter, GluP (characterized)
to candidate 353923 BT4397 xylose/H+ symporter (NCBI ptt file)

Query= TCDB::Q0SE66
         (483 letters)



>lcl|FitnessBrowser__Btheta:353923 BT4397 xylose/H+ symporter (NCBI
           ptt file)
          Length = 460

 Score =  278 bits (710), Expect = 4e-79
 Identities = 169/467 (36%), Positives = 263/467 (56%), Gaps = 29/467 (6%)

Query: 26  IAVVAALGGLLFGYDSAVINGAVSAIEGKFQVDSA--LLGFAIASALLGAAAGAMLAGRI 83
           I +V+A+GGLLFGYD  VI GA    E  F +  +  + G A++ ALLG   GAM+AG +
Sbjct: 12  ICLVSAMGGLLFGYDWVVIGGAKPFYELYFGIADSPTMQGLAMSVALLGCLIGAMVAGMM 71

Query: 84  ADRYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGLASVIAPAYIAEISP 143
           ADRYGR   +  +A +FL SA  TG  +     +  R +GGIG+G+AS ++P YIAE++P
Sbjct: 72  ADRYGRKPLLLISAFIFLSSAYATGAFSVFSWFLAARFLGGIGIGIASGLSPMYIAEVAP 131

Query: 144 ARVRGRLGSLQQLAIVTGIFVSLLVDYALA--AIAGGSQEEL---WFGLEAWRWMFLAMC 198
             +RG+L SL QL IV GI  + + ++ +A    A  +  ++   W G   WRWMF    
Sbjct: 132 TSIRGKLVSLNQLTIVLGILGAQIANWLIAEPIPADFTPADICASWNGQMGWRWMFWGAA 191

Query: 199 VPALAYGLLSLTIPESPRYLIAQGRLGEARGILAVLLGEKGLDLKIESIRSTLARETQPS 258
            PA  + LL+  IPESPR+L  +G+  +A  +L+ + G +  + +++ +  T A +++  
Sbjct: 192 FPAAVFLLLACFIPESPRWLAMKGKREKAWSVLSRIGGNRYAEQELQMVEQTSASKSEGG 251

Query: 259 IRDLKGSAFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSSLQITVITSV 318
           ++ L    F    ++ +G+ ++VFQQ+ G NVIF Y+  ++Q+ G+  G  L   V+T V
Sbjct: 252 LKLLFSRPF--RKVLVLGVIVAVFQQWCGTNVIFNYAQEIFQSAGYSLGDVLFNIVVTGV 309

Query: 319 VNIATTLIAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTGLQ 378
            N+  T +AI  ++R+GRR L+++G+ G    LA +  + GT     V G          
Sbjct: 310 ANVIFTFVAIYTVERLGRRALMLLGAGG----LAGIYLVLGTCYFFQVSGF--------- 356

Query: 379 GPIALVAANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAANWLITVTFPS 438
               +V   L +  + MS GP+ WVLL E FPNR+R  A++    A W  ++ +T TFP 
Sbjct: 357 --FMVVLVVLAIACYAMSLGPITWVLLAEIFPNRVRGVAMATCTFALWVGSFTLTYTFP- 413

Query: 439 MKDFSLGISYG---FYAVCAVLSLVFVLRWVKETKGVELEAMHSDSV 482
           + + +LG SYG    Y+   V   +F LR + ETKG  LE +  D +
Sbjct: 414 LLNTALG-SYGTFWIYSAICVFGFLFFLRALPETKGKSLETLEKDLI 459


Lambda     K      H
   0.324    0.138    0.405 

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: 592
Number of extensions: 32
Number of successful extensions: 7
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: 483
Length of database: 460
Length adjustment: 33
Effective length of query: 450
Effective length of database: 427
Effective search space:   192150
Effective search space used:   192150
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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