GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc28a3 in Sphingomonas koreensis DSMZ 15582

Align Broadly selective nucleoside:Na+ cotransporter, hfCNT (transports uridine, thymidine, inosine, 3'-azido-3'deoxythymidine, 2'3'dideoxycytidine, and 2'3'dideoxyinosine) (Na+/uridine = 2) (characterized)
to candidate Ga0059261_2532 Ga0059261_2532 Nucleoside permease

Query= TCDB::Q9UA35
         (683 letters)



>FitnessBrowser__Korea:Ga0059261_2532
          Length = 423

 Score =  253 bits (646), Expect = 1e-71
 Identities = 151/435 (34%), Positives = 235/435 (54%), Gaps = 37/435 (8%)

Query: 194 NQVIPFFGLILYILLVFIFSKHPTKVRWRIVIWGLLLQFIFGLIILRTKPGLDAFNWLGI 253
           N  I   G++  + + F  S +   +R R+V     LQ    +++L    G      +  
Sbjct: 3   NLPIGILGIVAILAIAFALSSNRRAIRLRVVGAAFALQAGIAILVLYVPAGRAVIEGMSR 62

Query: 254 QVQTFLKYTDAGSRFLFGD----DFQDHFFAFAVLPIVIFFSTVMSMMYYLGLMQWLILK 309
            V   L Y  AG+ F+FG     +   H FA A LP++IFF++++S++YYL +M  +I  
Sbjct: 63  GVSALLGYAQAGTDFIFGPLAKPEMGGHSFAIAALPVIIFFASLVSILYYLRIMPLVIRW 122

Query: 310 VGWLMQITMGTSPMESMVSAGNIFVGQTESPLLIRPYLADLTISEMHSVMSSGFATIAGS 369
           +G  ++   G S +ES+ SA NIFVGQ+ESPL+IRPYLA LT ++M +VMS G A +AG+
Sbjct: 123 IGGAIEKVTGVSKVESLCSAANIFVGQSESPLVIRPYLAGLTPAQMFAVMSVGMAGVAGT 182

Query: 370 VLGAYISLGIPAAHLLTASVMSAPAALAISKTFWPETKKSK------------NSTQTSI 417
           +L AY ++GI   +LL AS M+AP  L ++K   P+    +            +    +I
Sbjct: 183 ILAAYAAMGINIQYLLAASFMAAPGGLLMAKIMMPDEPVKQPELPLDGEGAPLDPEDAAI 242

Query: 418 K-----LEKGQENNLVEAASQGASAAVPLVANIAANLIAFLAVLAFINATLSWLGSMFNY 472
           +     L++ +  N++ AA+ GA   V +   + A ++AF+A++A  N  L  +G  F Y
Sbjct: 243 RAVEKDLDEERPANIIMAAAMGAQIGVKIAVAVGAMVLAFVALVALANGLLGVVGGWFGY 302

Query: 473 PQFSFEIICSYVLMPFAFMMGVNYDDSFLVAELLGMKTFFNEFVAYQRLSEYIHNRESGG 532
              +F+ +   V  P  F++G+ + +S     L G K   NEFVA+  L           
Sbjct: 303 GDLTFQGVIGTVFAPVMFLIGIPWAESGAAGSLFGTKMVLNEFVAFLNL----------- 351

Query: 533 PLFVDGVRQYMSVRSEAIATYALCGFANFGSLGIMIGGLSSLAPHRKSDIASCGIRALIA 592
                G    +S RS AI T+ALCGFANF S+ I +    SLAP+++  IA  GI+ALIA
Sbjct: 352 -----GSTAGLSPRSVAIITFALCGFANFSSIAIQMAAAGSLAPNQRPVIARLGIKALIA 406

Query: 593 GTIACFSTACIAGVL 607
           G++A   +A +AG+L
Sbjct: 407 GSLANLMSAALAGLL 421


Lambda     K      H
   0.325    0.139    0.424 

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: 585
Number of extensions: 20
Number of successful extensions: 4
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: 683
Length of database: 423
Length adjustment: 35
Effective length of query: 648
Effective length of database: 388
Effective search space:   251424
Effective search space used:   251424
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: 52 (24.6 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