GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nupC in Sphingomonas koreensis DSMZ 15582

Align Nucleoside permease; Flags: Precursor (characterized, see rationale)
to candidate Ga0059261_2532 Ga0059261_2532 Nucleoside permease

Query= uniprot:A0KU05
         (419 letters)



>lcl|FitnessBrowser__Korea:Ga0059261_2532 Ga0059261_2532 Nucleoside
           permease
          Length = 423

 Score =  411 bits (1057), Expect = e-119
 Identities = 213/435 (48%), Positives = 305/435 (70%), Gaps = 34/435 (7%)

Query: 2   NILMSLVGVVVLLAIGFLLSNNKKAINLRTVGGALAIQAAFGGFVLYVPVGKDILKSVSD 61
           N+ + ++G+V +LAI F LS+N++AI LR VG A A+QA     VLYVP G+ +++ +S 
Sbjct: 3   NLPIGILGIVAILAIAFALSSNRRAIRLRVVGAAFALQAGIAILVLYVPAGRAVIEGMSR 62

Query: 62  AVSSVIGYAQNGIGFLFGDLANFKLG-FIFAVNVLPVIVFFSSLIAVLYYLGIMQWIIRI 120
            VS+++GYAQ G  F+FG LA  ++G   FA+  LPVI+FF+SL+++LYYL IM  +IR 
Sbjct: 63  GVSALLGYAQAGTDFIFGPLAKPEMGGHSFAIAALPVIIFFASLVSILYYLRIMPLVIRW 122

Query: 121 IGGGLQKALGTSRTESMSATANIFVGQTEAPLVVRPFIPTMTQSELFAIMVGGLASIAGS 180
           IGG ++K  G S+ ES+ + ANIFVGQ+E+PLV+RP++  +T +++FA+M  G+A +AG+
Sbjct: 123 IGGAIEKVTGVSKVESLCSAANIFVGQSESPLVIRPYLAGLTPAQMFAVMSVGMAGVAGT 182

Query: 181 VLAGYAQMGVPIEYLVAASFMAAPGGLLMAKLMHPETEVAKNDM----DELPEDP----- 231
           +LA YA MG+ I+YL+AASFMAAPGGLLMAK+M P+  V + ++    +  P DP     
Sbjct: 183 ILAAYAAMGINIQYLLAASFMAAPGGLLMAKIMMPDEPVKQPELPLDGEGAPLDPEDAAI 242

Query: 232 ---------DKPANVLDAAAAGASSGMHLALNVGAMLLAFVGLIAMINGIIGGVGGWFGV 282
                    ++PAN++ AAA GA  G+ +A+ VGAM+LAFV L+A+ NG++G VGGWFG 
Sbjct: 243 RAVEKDLDEERPANIIMAAAMGAQIGVKIAVAVGAMVLAFVALVALANGLLGVVGGWFGY 302

Query: 283 EGLTLELILGYIFMPLAFLIGVPWNEALVAGSFIGQKIVVNEFVAYLNFAPYLKDIADGG 342
             LT + ++G +F P+ FLIG+PW E+  AGS  G K+V+NEFVA+LN            
Sbjct: 303 GDLTFQGVIGTVFAPVMFLIGIPWAESGAAGSLFGTKMVLNEFVAFLNLG---------- 352

Query: 343 MIVADTGLAMTDRTKAIISFALCGFANLSSIAILLGGLGAMAPNRRHDLAKLGIRAVIAG 402
                +   ++ R+ AII+FALCGFAN SSIAI +   G++APN+R  +A+LGI+A+IAG
Sbjct: 353 -----STAGLSPRSVAIITFALCGFANFSSIAIQMAAAGSLAPNQRPVIARLGIKALIAG 407

Query: 403 SLANLMSATIAGLFL 417
           SLANLMSA +AGL L
Sbjct: 408 SLANLMSAALAGLLL 422


Lambda     K      H
   0.325    0.142    0.407 

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: 597
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: 419
Length of database: 423
Length adjustment: 32
Effective length of query: 387
Effective length of database: 391
Effective search space:   151317
Effective search space used:   151317
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: 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