GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glcP in Escherichia coli BW25113

Align Glucose/fructose:H+ symporter, GlcP (characterized)
to candidate 18059 b4031 D-xylose transporter (NCBI)

Query= TCDB::P15729
         (468 letters)



>lcl|FitnessBrowser__Keio:18059 b4031 D-xylose transporter (NCBI)
          Length = 491

 Score =  325 bits (834), Expect = 2e-93
 Identities = 194/489 (39%), Positives = 289/489 (59%), Gaps = 53/489 (10%)

Query: 13  NVKFVLLISGVAALGGFLFGFDTAVINGAVAALQKHF--------QTDSLLTGLSVSLAL 64
           N  ++  I+ VA LGG LFG+DTAVI+G V +L   F           + L G  V+ AL
Sbjct: 6   NSSYIFSITLVATLGGLLFGYDTAVISGTVESLNTVFVAPQNLSESAANSLLGFCVASAL 65

Query: 65  LGSALGAFGAGPIADRHGRIKTMILAAVLFTLSSIGSGLP---FT--------------- 106
           +G  +G    G  ++R GR  ++ +AAVLF +S +GS  P   FT               
Sbjct: 66  IGCIIGGALGGYCSNRFGRRDSLKIAAVLFFISGVGSAWPELGFTSINPDNTVPVYLAGY 125

Query: 107 IWDFIFWRVLGGIGVGAASVIAPAYIAEVSPAHLRGRLGSLQQLAIVSGIFIALLSNWFI 166
           + +F+ +R++GGIGVG AS+++P YIAE++PAH+RG+L S  Q AI+ G  +    N+FI
Sbjct: 126 VPEFVIYRIIGGIGVGLASMLSPMYIAELAPAHIRGKLVSFNQFAIIFGQLLVYCVNYFI 185

Query: 167 ALMAGGSAQNPWLFGAAAWRWMFWTELIPALLYGVCAFLIPESPRYLVAQGQGEKAAAIL 226
           A     S    WL     WR+MF +E IPALL+ +  + +PESPR+L+++G+ E+A  IL
Sbjct: 186 ARSGDAS----WL-NTDGWRYMFASECIPALLFLMLLYTVPESPRWLMSRGKQEQAEGIL 240

Query: 227 WKVEGGDVPSR-IEEIQATVSLDHKPRFSDLLSRRGGLLPIVWIGMGLSALQQFVGINVI 285
            K+ G  + ++ ++EI+   SLDH  +    L   G  + ++ IG+ LS  QQFVGINV+
Sbjct: 241 RKIMGNTLATQAVQEIKH--SLDHGRKTGGRLLMFG--VGVIVIGVMLSIFQQFVGINVV 296

Query: 286 FYYSSVLWRSVGFTEEKSLLITVITGFINILTTLVAIAFVDKFGRKPLLLMGSIGMTITL 345
            YY+  +++++G + + +LL T+I G IN+  T++AI  VDKFGRKPL ++G++GM I +
Sbjct: 297 LYYAPEVFKTLGASTDIALLQTIIVGVINLTFTVLAIMTVDKFGRKPLQIIGALGMAIGM 356

Query: 346 GILSVVFGGATVVNGQPTLTGAAGIIALVTANLYVFSFGFSWGPIVWVLLGEMFNNKIRA 405
             L   F            T A GI+AL++   YV +F  SWGP+ WVLL E+F N IR 
Sbjct: 357 FSLGTAF-----------YTQAPGIVALLSMLFYVAAFAMSWGPVCWVLLSEIFPNAIRG 405

Query: 406 AALSVAAGVQWIANFIISTTFPPLLDTVGL------GPAYGLYATSAAISIFFIWFFVKE 459
            AL++A   QW+AN+ +S TFP +     L      G +Y +Y     ++  F+W FV E
Sbjct: 406 KALAIAVAAQWLANYFVSWTFPMMDKNSWLVAHFHNGFSYWIYGCMGVLAALFMWKFVPE 465

Query: 460 TKGKTLEQM 468
           TKGKTLE++
Sbjct: 466 TKGKTLEEL 474


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: 623
Number of extensions: 33
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: 468
Length of database: 491
Length adjustment: 34
Effective length of query: 434
Effective length of database: 457
Effective search space:   198338
Effective search space used:   198338
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 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