GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_326 Putative nucleoside
           transporter YegT
          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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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