GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupG in Pseudomonas fluorescens FW300-N2E2

Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate Pf6N2E2_326 Putative nucleoside transporter YegT

Query= SwissProt::P45562
         (418 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_326
          Length = 410

 Score =  259 bits (661), Expect = 1e-73
 Identities = 147/408 (36%), Positives = 233/408 (57%), Gaps = 25/408 (6%)

Query: 6   RLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGIIADKW 65
           RL VM FLQ+FIWG W VTLG+++ +TL  +G  +GM +S++   AII P ++G+IAD++
Sbjct: 7   RLSVMMFLQFFIWGGWFVTLGTFLSSTLGASGGQIGMAFSTQSWGAIIAPFVIGLIADRF 66

Query: 66  LRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSCLAQAG 125
             AER   + HL+ A +L+   S  D  + +  +LV  + +MPT+AL NSV++  +    
Sbjct: 67  FNAERILAVLHLLGAVLLYQLYSAADFSVFYPYVLVYMVVYMPTLALVNSVAFRQMR--- 123

Query: 126 LDPVTAFPPIRVFGTVGFIVAMWAVSLLH-------LELSSLQ--LYIASGASLLLSAYA 176
            DP   F  IRV+GT+G+IVA   +S +        +    L+    +A+ ASL+L  Y+
Sbjct: 124 -DPALEFSRIRVWGTIGWIVAGVVISFVFAWDSREAISAGGLRNTFLMAAVASLVLGLYS 182

Query: 177 LTLP-KIPVAEKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFL 235
            TLP   P+ E+     +   LGLDA  L K+    +FF+ ++++   L       NPFL
Sbjct: 183 FTLPATAPLKEQARAGGVRQLLGLDALGLLKDRSYLVFFIASILICIPLAFYYQNANPFL 242

Query: 236 HDFARNPEFADSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRF 295
            +            +  P+  +++ Q++EV F+L +P F++RFGIK  +L+ M+AW LR+
Sbjct: 243 AETG----------MTNPTAKMAIGQVSEVLFMLLLPLFIQRFGIKLALLVGMLAWALRY 292

Query: 296 GFFAYGDPSTTGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNG 355
             FAYG+     F +L   + ++G  +DFF +SG ++ + +     R+SAQGL      G
Sbjct: 293 LLFAYGNNGDLAF-MLFTGIALHGICYDFFFVSGQIYTDAKAPERFRSSAQGLITLATYG 351

Query: 356 VGAWVGSILSGMAVDYFSVDGVKDWQTIWLVFAGYALFLAVIFFFGFK 403
           VG  +G  ++G   D+F V G  DWQ+IWL  AG+AL + + F F F+
Sbjct: 352 VGMLIGFWVAGQVTDHFVVAGGHDWQSIWLFPAGFALLVLLCFLFTFR 399


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: 496
Number of extensions: 25
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: 410
Length adjustment: 31
Effective length of query: 387
Effective length of database: 379
Effective search space:   146673
Effective search space used:   146673
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