GapMind for catabolism of small carbon sources

 

Aligments for a candidate for MFS-glucose in Pedobacter sp. GW460-11-11-14-LB5

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate CA265_RS23325 CA265_RS23325 MFS transporter

Query= TCDB::P15729
         (468 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS23325 CA265_RS23325 MFS
           transporter
          Length = 443

 Score =  278 bits (711), Expect = 3e-79
 Identities = 174/467 (37%), Positives = 262/467 (56%), Gaps = 38/467 (8%)

Query: 8   SQSTANVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHFQTDSLLTGLSVSLALLGS 67
           SQS  N  ++  IS +AA GG+LFGFD AVI+G++  L+K FQ      G +     LG+
Sbjct: 2   SQSKFNTAYITFISLLAAGGGYLFGFDFAVISGSLPFLEKQFQLTPYWEGFATGSLALGA 61

Query: 68  ALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLPFTIWDFIFWRVLGGIGVGAASVI 127
            +G   AG ++D +GR   +++AA +F  SS+   +      FI  R   GIGVG AS++
Sbjct: 62  MVGCLIAGYVSDAYGRKPGLMIAAFVFLASSLAMAMAPNRDFFIVSRFFSGIGVGMASML 121

Query: 128 APAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFIALMAGGSAQNPWLFGAAAWRW 187
           +P YIAE++P   RGRL ++ QL IV GI I  L N+ +              G  AWRW
Sbjct: 122 SPMYIAELAPPKFRGRLVAINQLTIVLGILITNLINYTLRNT-----------GEDAWRW 170

Query: 188 MFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAILWKVEG----GDVPSRIEE-IQ 242
           MF    IP+ ++ +   ++PESPR+LV +G+ EKA  +L K+       D    IE+ +Q
Sbjct: 171 MFGLGAIPSGIFLIGISILPESPRWLVQKGKNEKALKVLNKIGNHEFAADALKNIEQTLQ 230

Query: 243 ATVSLDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVIFYYSSVLWRSVGFTEEK 302
              +++H+  F+ +        P V IG+GL+  QQF GIN +F Y+  L+ S+G +++ 
Sbjct: 231 RKSNVEHESIFNKMY------FPAVMIGIGLAIFQQFCGINTVFNYAPKLFESIGTSQDD 284

Query: 303 SLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITLGILS-VVFGGATVVNGQ 361
            LL TV  G +N++ T+ A+  VDK GRKPL+L+G+ G+ +   ++S ++  G+T+V+  
Sbjct: 285 QLLQTVFIGAVNVIFTISAMFLVDKIGRKPLMLIGAGGLAVLYVLISQLLASGSTMVSW- 343

Query: 362 PTLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRAAALSVAAGVQWIANFI 421
             L  A G+ A+            S  P+ WVL+ E+F NK+R  A + A    W A F+
Sbjct: 344 -FLLSAIGVYAV------------SLAPVTWVLISEIFPNKVRVKATTWAILCLWGAYFV 390

Query: 422 ISTTFPPLLDTVGLGPAYGLYATSAAISIFFIWFFVKETKGKTLEQM 468
           +  TFP L D +     Y +YA    +    IW FVKETKGKTLE++
Sbjct: 391 LVFTFPILFDWLKESIFY-IYAAICTLGCIGIWKFVKETKGKTLEEI 436


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: 532
Number of extensions: 31
Number of successful extensions: 6
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: 443
Length adjustment: 33
Effective length of query: 435
Effective length of database: 410
Effective search space:   178350
Effective search space used:   178350
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