GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupG in Pedobacter sp. GW460-11-11-14-LB5

Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate CA265_RS15375 CA265_RS15375 MFS transporter

Query= SwissProt::P45562
         (418 letters)



>FitnessBrowser__Pedo557:CA265_RS15375
          Length = 405

 Score =  253 bits (645), Expect = 1e-71
 Identities = 138/406 (33%), Positives = 234/406 (57%), Gaps = 18/406 (4%)

Query: 6   RLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGIIADKW 65
           +L  M FL++FIWG+W VT+G+Y+   L      +G  YS++ + AII P I+G+IADK+
Sbjct: 8   KLSAMMFLEFFIWGAWFVTMGTYLGKNLLANDVQIGSAYSTQSLGAIIAPFIIGLIADKF 67

Query: 66  LRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSCLAQAG 125
             A++   + HLV   +L+ A +  + D  F  +L   +A+MPT+AL NS+S+  +    
Sbjct: 68  FSAQKVLGVLHLVGGALLWVAGTSLNFDSFFPFILGYMIAYMPTLALVNSISFKQMK--- 124

Query: 126 LDPVTAFPPIRVFGTVGFIVAMWAVSLLHLELSSLQLY---IASGASLLLSAYALTLPKI 182
            DP   FP IRVFGT+G+I+A   +  L+ E S   ++   +AS AS++L   +  LP  
Sbjct: 125 -DPGKEFPSIRVFGTIGWIIAGLVIGWLNWEQSGNLVFTFKMASVASIILGLLSFFLPNT 183

Query: 183 PVAEKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFLHDFARNP 242
           P  +K   T+    +GLDA  L KN    +FFL ++ +   L     F NPFL++     
Sbjct: 184 PPVKKGEKTTFGEIIGLDAIGLLKNKSYLLFFLASVAICIPLAFYYNFTNPFLNEVG--- 240

Query: 243 EFADSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRFGFFAYGD 302
                  +K  + + S+ Q++E  F+L +P F  R G+K ++ + M+AW +R+ FFA+G+
Sbjct: 241 -------MKGAAGVQSLGQVSETLFMLLMPLFFARLGVKKMLAIGMIAWVVRYLFFAFGN 293

Query: 303 PSTTGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNGVGAWVGS 362
            + + + +L+  ++++G  +DFF ++G ++ ++      +++AQG       GVG  +GS
Sbjct: 294 -ADSNYWMLIGGIVLHGICYDFFFVTGQIYTDRLAGEKFKSAAQGFITLATYGVGMLIGS 352

Query: 363 ILSGMAVDYFSVDGVKDWQTIWLVFAGYALFLAVIFFFGFKYNHDP 408
           I+SGM V+ + V+G   WQ+IW++ AG A  +A++F   F   + P
Sbjct: 353 IISGMVVNKYVVEGGHIWQSIWIIPAGIAGLVALLFLLFFSDKNKP 398


Lambda     K      H
   0.330    0.141    0.435 

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: 526
Number of extensions: 26
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: 418
Length of database: 405
Length adjustment: 31
Effective length of query: 387
Effective length of database: 374
Effective search space:   144738
Effective search space used:   144738
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 (21.9 bits)
S2: 50 (23.9 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