GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:18059
          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:

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