GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Escherichia coli BW25113

Align Glucose/galactose transporter (characterized, see rationale)
to candidate 16885 b2801 L-fucose transporter (NCBI)

Query= uniprot:A0KXM0
         (423 letters)



>FitnessBrowser__Keio:16885
          Length = 438

 Score =  246 bits (627), Expect = 1e-69
 Identities = 147/426 (34%), Positives = 228/426 (53%), Gaps = 13/426 (3%)

Query: 3   SSINTSSHTSSVSEAGNG-NYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQA 61
           +SI T S+ +   +AG   +Y      L SLFF+W     LNDIL+P  +  F+L   QA
Sbjct: 4   TSIQTQSYRAVDKDAGQSRSYIIPFALLCSLFFLWAVANNLNDILLPQFQQAFTLTNFQA 63

Query: 62  MLIQFCFFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGA 121
            LIQ  F+  YF++ IPAG L+K+L Y+ GI+TGL + ++G  LF+PAA    Y LFL  
Sbjct: 64  GLIQSAFYFGYFIIPIPAGILMKKLSYKAGIITGLFLYALGAALFWPAAEIMNYTLFLVG 123

Query: 122 LFVLASGITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILS---- 177
           LF++A+G+  L+ AANP+V  LG   +   RLNL Q FN+ G  +A  FG  LILS    
Sbjct: 124 LFIIAAGLGCLETAANPFVTVLGPESSGHFRLNLAQTFNSFGAIIAVVFGQSLILSNVPH 183

Query: 178 ----VAASVSSELAQANAEAEV--VKLPYLLLAAALAVLAIIFAKLDLPVIREHSQAAAE 231
               V   +S E   A   + V  V+ PY+++ A + ++A++      P ++  + + A+
Sbjct: 184 QSQDVLDKMSPEQLSAYKHSLVLSVQTPYMIIVAIVLLVALLIMLTKFPALQSDNHSDAK 243

Query: 232 EVQTHLGKTSALQSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIA 291
           +       +   +  H     +  F YVGA+ +  S+L+ +  E  I GM    AA+Y+ 
Sbjct: 244 QGSFSASLSRLARIRHWRWAVLAQFCYVGAQTACWSYLIRYAVE-EIPGMTAGFAANYLT 302

Query: 292 YYWGGAMVGRFIGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNS 351
                  +GRF G+ ++ +     VLA  A +A  L L++    G V + A+     F S
Sbjct: 303 GTMVCFFIGRFTGTWLISRFAPHKVLAAYALIAMALCLISAFAGGHVGLIALTLCSAFMS 362

Query: 352 IMFPTIFSLALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNLG-IQLAFILPVVCY 410
           I +PTIFSL +++LG  T  GS  + + I+GG IV  + G ++D  G I  A ++P +C+
Sbjct: 363 IQYPTIFSLGIKNLGQDTKYGSSFIVMTIIGGGIVTPVMGFVSDAAGNIPTAELIPALCF 422

Query: 411 GFILFY 416
             I  +
Sbjct: 423 AVIFIF 428


Lambda     K      H
   0.326    0.138    0.402 

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: 489
Number of extensions: 33
Number of successful extensions: 5
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: 423
Length of database: 438
Length adjustment: 32
Effective length of query: 391
Effective length of database: 406
Effective search space:   158746
Effective search space used:   158746
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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