GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Slc28a3 in Shewanella oneidensis MR-1

Align Broadly selective nucleoside:Na+ cotransporter, hfCNT (transports uridine, thymidine, inosine, 3'-azido-3'deoxythymidine, 2'3'dideoxycytidine, and 2'3'dideoxyinosine) (Na+/uridine = 2) (characterized)
to candidate 202800 SO3706 NupC family protein (NCBI ptt file)

Query= TCDB::Q9UA35
         (683 letters)



>lcl|FitnessBrowser__MR1:202800 SO3706 NupC family protein (NCBI ptt
           file)
          Length = 422

 Score =  264 bits (675), Expect = 6e-75
 Identities = 144/421 (34%), Positives = 237/421 (56%), Gaps = 17/421 (4%)

Query: 196 VIPFFGLILYILLVFIFSKHPTKVRWRIVIWGLLLQFIFGLIILRTKPGLDAFNWLGIQV 255
           ++   G+I  + + ++ S++   + +R V    LLQ   G  ++ +  G      +   V
Sbjct: 4   LVSLLGIITLLAVAYLASENRRAINYRTVGLAFLLQLALGAFVMYSALGQSMIFSMAAAV 63

Query: 256 QTFLKYTDAGSRFLFGDDFQDHFF----------AFAVLPIVIFFSTVMSMMYYLGLMQW 305
              + Y++ G  F+FG    D  +          AF VLPI++FFS + +++YYLG+MQ 
Sbjct: 64  SNVISYSNDGMSFMFGGLVSDKMYELFGAGGFVIAFKVLPIIVFFSALSAVLYYLGIMQL 123

Query: 306 LILKVGWLMQITMGTSPMESMVSAGNIFVGQTESPLLIRPYLADLTISEMHSVMSSGFAT 365
           ++  VG  +Q  + TS  ESM ++ NIF+G TE+PLLI+PY+  +T SE+ +VM  G A+
Sbjct: 124 VVKAVGGALQKLLNTSKAESMSASANIFLGVTEAPLLIKPYMPRMTRSELFAVMCGGLAS 183

Query: 366 IAGSVLGAYISLGIPAAHLLTASVMSAPAALAISKTFWPETKKSKNSTQTSIKLEKGQEN 425
           IAG++L  Y  LGI   +LL AS M+AP  L  +K   P+T ++ N     +  E+ Q  
Sbjct: 184 IAGTMLAGYAQLGIKMEYLLAASFMAAPGGLLFAKLLIPQT-ETINDAHLQL-TEENQPR 241

Query: 426 NLVEAASQGASAAVPLVANIAANLIAFLAVLAFINATLSWLGSMFNYPQFSFEIICSYVL 485
           NL++AA+ G  + + L   + A L +F++++A  N  L  +G+ F     + + I  Y+ 
Sbjct: 242 NLLDAATTGTMSGLSLALAVGAMLFSFISLVALFNGMLGGIGAWFGLEGLTLQQILGYLF 301

Query: 486 MPFAFMMGVNYDDSFLVAELLGMKTFFNEFVAYQRLSEYIHNRESGGPLFVDGVRQYMSV 545
            P A++MG++++++ L    +G K   NEF AY  L+ Y+      G   V    Q MS 
Sbjct: 302 APLAWLMGISWNEAMLAGSFIGQKIVINEFFAYINLAPYL-----SGDALVATTGQPMSE 356

Query: 546 RSEAIATYALCGFANFGSLGIMIGGLSSLAPHRKSDIASCGIRALIAGTIACFSTACIAG 605
           R++ I ++ALCGFAN G++ I I G+  L P R+++IAS G++AL AG ++    A IAG
Sbjct: 357 RTQVILSFALCGFANIGTVAIAIAGIGGLVPERRAEIASLGLKALAAGILSNLMAATIAG 416

Query: 606 V 606
           +
Sbjct: 417 L 417


Lambda     K      H
   0.325    0.139    0.424 

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: 563
Number of extensions: 22
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: 683
Length of database: 422
Length adjustment: 35
Effective length of query: 648
Effective length of database: 387
Effective search space:   250776
Effective search space used:   250776
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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, the preprint on GapMind for carbon sources, 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