GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupG in Dyella japonica UNC79MFTsu3.2

Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate N515DRAFT_1323 N515DRAFT_1323 nucleoside transporter

Query= SwissProt::P45562
         (418 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1323
          Length = 401

 Score =  239 bits (609), Expect = 1e-67
 Identities = 131/399 (32%), Positives = 225/399 (56%), Gaps = 16/399 (4%)

Query: 6   RLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGIIADKW 65
           RL++M   +Y IWG+W VT+G+++  TLHF+G  +G +  +  I A+I P  +G++AD+ 
Sbjct: 4   RLRLMMLFEYAIWGAWYVTVGTWLGKTLHFSGQEIGAIAGTTAIGAMISPLFVGLLADRL 63

Query: 66  LRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSCLAQAG 125
               R     H++ A +L +AA  +   +++  +L  ++ +MPT+AL+ S++   +    
Sbjct: 64  FDTRRVLAALHVLGAVLLMFAARQSSFPLLYGTLLAYSLCYMPTLALTTSLAMRHIR--- 120

Query: 126 LDPVTAFPPIRVFGTVGFIVAMWAVSLLHLELSSLQLYIASGASLLLSAYALTLPKIPVA 185
            DP   F  IRV GT+G+IV    V    +E ++  L +A+G S++ + Y LTLP  P  
Sbjct: 121 -DPQEEFGGIRVLGTIGWIVVGLIVGAWGVEATATPLQLAAGLSVVTALYCLTLPPTPPL 179

Query: 186 EKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFLHDFARNPEFA 245
            +     L   L L++  L ++  MA+F L + ++   LQ    F N FL++        
Sbjct: 180 ARNQRFELRHALPLESLHLLRDRSMAVFALASFLICIPLQFYYAFTNLFLNEVG------ 233

Query: 246 DSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRFGFFAYGDPST 305
               V   +  ++  QM+E+  +L IP+F +R G+K ++ + M+AW LR+  FA+G P  
Sbjct: 234 ----VVNAAGKMTGGQMSEILCMLLIPWFFRRLGVKYMLAVGMLAWVLRYVLFAFGAPGD 289

Query: 306 TGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNGVGAWVGSILS 365
             + +L L ++++G  FDFF + G +++++E  S++RA+ QGL   +  G+G +VGS LS
Sbjct: 290 LMW-MLWLGIVLHGICFDFFFVVGQIYIDREAPSALRAATQGLITFLTYGLGMFVGSWLS 348

Query: 366 GMAVD-YFSVDGVKDWQTIWLVFAGYALFLAVIFFFGFK 403
           G+ VD Y       DW++IWL+  G A  + V+F   FK
Sbjct: 349 GVVVDTYAGAQNAHDWRSIWLIAGGCAAAVLVLFVLAFK 387


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: 501
Number of extensions: 22
Number of successful extensions: 6
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: 401
Length adjustment: 31
Effective length of query: 387
Effective length of database: 370
Effective search space:   143190
Effective search space used:   143190
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