GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Dyella japonica UNC79MFTsu3.2

Align The glucose uptake porter, GluP (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family

Query= TCDB::Q0SE66
         (483 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0382
          Length = 472

 Score =  524 bits (1350), Expect = e-153
 Identities = 271/461 (58%), Positives = 343/461 (74%), Gaps = 7/461 (1%)

Query: 20  TSVPVRIAVVAALGGLLFGYDSAVINGAVSAIEGKFQVDSALLGFAIASALLGAAAGAML 79
           T+  V IA  AALGG LFG+D+AVINGAV A+ G F + +  +GFA++ ALLG+A GA  
Sbjct: 14  TARVVLIAAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAVSCALLGSALGAWY 73

Query: 80  AGRIADRYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGLASVIAPAYIA 139
           AG +ADR+GR+ TM+ AAV+  +SA+G+G  A V  LV +R+VGGIGVG+ASVIAP YIA
Sbjct: 74  AGPLADRWGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASVIAPTYIA 133

Query: 140 EISPARVRGRLGSLQQLAIVTGIFVSLLVDYALAAIAGGSQEELWFGLEAWRWMFLAMCV 199
           E+SPARVRGRLGSLQQLAIV GIF +LL D  LA  AGG+ ++LW GLEAWRWMFL   V
Sbjct: 134 EVSPARVRGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLGLEAWRWMFLVAVV 193

Query: 200 PALAYGLLSLTIPESPRYLIAQGRLGEARGILAVLL---GEKGLDLKIESIRSTLARETQ 256
           PAL YG L L +PESPR+L+A+GR+ EA+ +L  +L    E  L  K+  I  +L  E +
Sbjct: 194 PALIYGSLVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHKLGDIAQSLRSEYR 253

Query: 257 PSIRDLKGSAFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSSLQITVIT 316
           P +RDL+GS  GL+P+VW+GI LSVFQQFVGINVIFYYSS LW +VGF E  +  I+V+T
Sbjct: 254 PGLRDLRGSMAGLLPVVWVGILLSVFQQFVGINVIFYYSSTLWHSVGFSESDAFSISVVT 313

Query: 317 SVVNIATTLIAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGVTTPQLTG 376
           SVVN+  TL+AIA +DR+GR+PLL IGSAGM VTL  MA+ F  A+           L  
Sbjct: 314 SVVNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAA----GSGAALSLPA 369

Query: 377 LQGPIALVAANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAANWLITVTF 436
             G +ALVAAN +VV FG+SWGP+VWVLLGE FPNRIRA AL++AA AQW AN++IT +F
Sbjct: 370 PWGMVALVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANFIITSSF 429

Query: 437 PSMKDFSLGISYGFYAVCAVLSLVFVLRWVKETKGVELEAM 477
           P++ +  L  +YG YA  A++SLVFV++ V+ETKG+ELE M
Sbjct: 430 PALSELGLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470


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: 738
Number of extensions: 32
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: 483
Length of database: 472
Length adjustment: 34
Effective length of query: 449
Effective length of database: 438
Effective search space:   196662
Effective search space used:   196662
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:

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