GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcP in Dyella japonica UNC79MFTsu3.2

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family

Query= TCDB::P15729
         (468 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0382
          Length = 472

 Score =  486 bits (1250), Expect = e-142
 Identities = 254/456 (55%), Positives = 332/456 (72%), Gaps = 6/456 (1%)

Query: 17  VLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGSALGAFGAGP 76
           V+LI+  AALGGFLFGFDTAVINGAV A++  F   +   G +VS ALLGSALGA+ AGP
Sbjct: 17  VVLIAAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAVSCALLGSALGAWYAGP 76

Query: 77  IADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVIAPAYIAEVS 136
           +ADR GR++TM +AAVL  +S++GSGL   +WD + WR++GGIGVG ASVIAP YIAEVS
Sbjct: 77  LADRWGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASVIAPTYIAEVS 136

Query: 137 PAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRWMFWTELIPA 196
           PA +RGRLGSLQQLAIV GIF ALLS+ ++A  AGG++Q  WL G  AWRWMF   ++PA
Sbjct: 137 PARVRGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWL-GLEAWRWMFLVAVVPA 195

Query: 197 LLYGVCAFLIPESPRYLVAQGQGEKAAAILWKV----EGGDVPSRIEEIQATVSLDHKPR 252
           L+YG     +PESPR+LVA+G+ ++A  +L +V    +   +  ++ +I  ++  +++P 
Sbjct: 196 LIYGSLVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHKLGDIAQSLRSEYRPG 255

Query: 253 FSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEKSLLITVITGF 312
             DL     GLLP+VW+G+ LS  QQFVGINVIFYYSS LW SVGF+E  +  I+V+T  
Sbjct: 256 LRDLRGSMAGLLPVVWVGILLSVFQQFVGINVIFYYSSTLWHSVGFSESDAFSISVVTSV 315

Query: 313 INILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILSVVFGGATVVNGQPTLTGAAGIIA 372
           +N+L TLVAIA VD+ GRKPLL +GS GMT+TLG+++  F  A       +L    G++A
Sbjct: 316 VNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAAGSGAALSLPAPWGMVA 375

Query: 373 LVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFIISTTFPPLLDT 432
           LV AN YV  FG SWGP+VWVLLGEMF N+IRA AL+VAA  QW+ANFII+++FP L + 
Sbjct: 376 LVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANFIITSSFPALSE- 434

Query: 433 VGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468
           +GL  AYG+YA  A +S+ F+   V+ETKG  LE+M
Sbjct: 435 LGLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470


Lambda     K      H
   0.325    0.140    0.430 

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: 679
Number of extensions: 31
Number of successful extensions: 4
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: 468
Length of database: 472
Length adjustment: 33
Effective length of query: 435
Effective length of database: 439
Effective search space:   190965
Effective search space used:   190965
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