Aligments for a candidate for Slc28a3 in Echinicola vietnamensis KMM 6221, DSM 17526

GapMind for catabolism of small carbon sources

Aligments for a candidate for Slc28a3 in Echinicola vietnamensis KMM 6221, DSM 17526

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 Echvi_2954 Echvi_2954 Nucleoside permease

Query= TCDB::Q9UA35
         (683 letters)



>FitnessBrowser__Cola:Echvi_2954
          Length = 428

 Score =  290 bits (743), Expect = 7e-83
 Identities = 176/433 (40%), Positives = 255/433 (58%), Gaps = 39/433 (9%)

Query: 201 GLILYILLVFIFSKHPTKVRWRIVIWGLLLQFIFGLIILRTKPGLDAFNWLGIQVQTFLK 260
           G++  + + F+FS     V W++V  G++LQ +FG +I +       F  +       L 
Sbjct: 9   GIVALLGVAFLFSASRKSVDWKLVGIGVILQIVFGFLITKVAFVESVFASISGAFVKLLS 68

Query: 261 YTDAGSRFLFGDDFQDHF---FAFAVLPIVIFFSTVMSMMYYLGLMQWLILKVGWLMQIT 317
           +  AG+ FLFGD   D F   FAF VLP +IFFSTV + +YYLG++Q ++  + W+M  T
Sbjct: 69  FAQAGAIFLFGDLATDSFGTIFAFQVLPTIIFFSTVSAGLYYLGVLQKIVFGIAWVMART 128

Query: 318 MGTSPMESMVSAGNIFVGQTESPLLIRPYLADLTISEMHSVMSSGFATIAGSVLGAYIS- 376
           M  S  ES+ +AGNIF+GQTE+PLL+RP++  +T SE+  +M+ G ATIAG VL AY++ 
Sbjct: 129 MKLSGAESLSAAGNIFLGQTEAPLLVRPFIPTMTRSELMCLMTGGMATIAGGVLAAYVAF 188

Query: 377 LGIP--------AAHLLTASVMSAPAALAISKTFWPETKKSKNSTQTSIKLEKGQENNLV 428
           LG          A++LL AS+M+APAA+ +SK   PET K   + +  +  E G   NL+
Sbjct: 189 LGGDDPAEQSKFASYLLGASIMNAPAAIVMSKLIIPETNKEGLNDKLEVSSE-GMGVNLI 247

Query: 429 EAASQGASAAVPLVANIAANLIAFLAVLAFINATLSW-LGSMFNYPQ------------F 475
           +A S GA+  + L  N+   L+AF+AV+A +N  LS  LG +    Q            F
Sbjct: 248 DAMSIGAADGLKLALNVGGMLLAFIAVIAMLNYLLSGVLGDVTGLNQFVVDTTNGRFDGF 307

Query: 476 SFEIICSYVLMPFAFMMGVNYDDSFLVAELLGMKTFFNEFVAYQRLSEYIHNRESGGPLF 535
           S E I   V   FA++MGV + D+  V  LLG KT  NEFVAY  LS    + ++ G L 
Sbjct: 308 SLEYILGQVFRIFAWLMGVEWQDTLQVGSLLGQKTVINEFVAYSDLS----SMKAEGDL- 362

Query: 536 VDGVRQYMSVRSEAIATYALCGFANFGSLGIMIGGLSSLAPHRKSDIASCGIRALIAGTI 595
                   S +S  IATYALCGF+NF S+ I +GG+ S+AP ++ +++  G+ AL+A T+
Sbjct: 363 --------SPKSIIIATYALCGFSNFSSIAIQVGGIGSIAPGQQGNLSKLGMHALLAATL 414

Query: 596 ACFSTACIAGVLY 608
           AC  TA IAG+L+
Sbjct: 415 ACMMTATIAGMLF 427


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: 615
Number of extensions: 25
Number of successful extensions: 7
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: 428
Length adjustment: 35
Effective length of query: 648
Effective length of database: 393
Effective search space:   254664
Effective search space used:   254664
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.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources