GapMind for catabolism of small carbon sources

 

Alignments for a candidate for MFS-glucose in Flavobacterium glycines Gm-149

Align Glucose/galactose transporter (characterized, see rationale)
to candidate WP_083189367.1 BLR17_RS03160 L-fucose:H+ symporter permease

Query= uniprot:A0KXM0
         (423 letters)



>NCBI__GCF_900100165.1:WP_083189367.1
          Length = 433

 Score =  290 bits (741), Expect = 8e-83
 Identities = 172/422 (40%), Positives = 245/422 (58%), Gaps = 20/422 (4%)

Query: 15  SEAGNG-NYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFCFFGAYF 73
           +E G G NY    + +TSLFF+WG    L+ ILIPHLK    LN  Q+ LI    F AYF
Sbjct: 15  TEKGQGPNYVLPFILITSLFFLWGMAHNLDSILIPHLKKACQLNNRQSTLIDTSVFLAYF 74

Query: 74  LVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLASGITILQ 133
           L++IPAG ++K++GY+  I+ GL++ + G  LF PAA+   Y LFL ALF++  G+TIL+
Sbjct: 75  LMAIPAGMIIKKVGYKNSIIIGLLVFATGAFLFVPAANTQAYELFLVALFIIGCGLTILE 134

Query: 134 VAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILS---------VAASVSS 184
            +ANPY   LG  E++S RLNL  +FN L   VAP  GS+ ILS          A   + 
Sbjct: 135 TSANPYAAILGPPESSSKRLNLAASFNGLAAMVAPIVGSMFILSGKSFTPEQMAAMPEAE 194

Query: 185 ELAQANAEAEVVKLPYLLLAAALAVLAIIFAKLDLPVIR-EHSQAAAEEVQTHLGKTSAL 243
            L     EA  VKLPY++L   L ++A++F  + LP ++ EH+     EV+   G  S L
Sbjct: 195 RLTYLAGEAAAVKLPYIILGTILVLVAVLFYFMHLPSMKPEHT-----EVEVKPGFFSVL 249

Query: 244 QSMHLVLGAVGIFVYVGAEVSIGSFLVNFLGEAHIVGMPEEQAAHYIAYYWGGAMVGRFI 303
           +  HL    V  F YVGA+V + SF +    +     M E  AA+Y+  Y    M GRFI
Sbjct: 250 KHRHLSWAVVAQFFYVGAQVCVTSFFIRMAEQG--ANMDEITAAYYLGLYGVLFMAGRFI 307

Query: 304 GSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGVGLFNSIMFPTIFSLALR 363
           G+  ++ +    +L+  A ++A+L  VA+  SG   ++A+  +G F SIMFPTIFSL L 
Sbjct: 308 GTFFLKYVKDYVLLSIYAVLSAILCAVAIYGSGIYVIYALGAIGFFMSIMFPTIFSLGLV 367

Query: 364 DLGPHTSQGSGILCLAIVGGAIVPLLQGVLAD--NLGIQLAFILPVVCYGFILFYGAKGS 421
            L  +T  GS  L ++IVGGAI+P   G L D  +  IQ  +++P+VC+  IL++G  G 
Sbjct: 368 GLKSNTETGSSWLVMSIVGGAILPYGMGTLIDMNHDDIQSGYLIPLVCFLIILYFGVFGH 427

Query: 422 KM 423
           K+
Sbjct: 428 KV 429


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: 536
Number of extensions: 34
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: 433
Length adjustment: 32
Effective length of query: 391
Effective length of database: 401
Effective search space:   156791
Effective search space used:   156791
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 24 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