GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Echvi_1880 in Dinoroseobacter shibae DFL-12

Align SSS sodium solute transporter (characterized, see rationale)
to candidate 3610525 Dshi_3906 SSS sodium solute transporter superfamily (RefSeq)

Query= uniprot:L0FZT5
         (624 letters)



>lcl|FitnessBrowser__Dino:3610525 Dshi_3906 SSS sodium solute
           transporter superfamily (RefSeq)
          Length = 533

 Score =  264 bits (675), Expect = 6e-75
 Identities = 163/474 (34%), Positives = 252/474 (53%), Gaps = 49/474 (10%)

Query: 8   LDYVIFIVYALAIVSVGLWVSRTKKGLEKTAQEYFLADKSLTWWAVGASLLAANISAEHF 67
           +DY I ++Y + +++ G++VSR     E+ A  YFLA +SL W+ +G SL A+N+S   F
Sbjct: 11  IDYAIVVIYFIGVIAHGVYVSRKN---EEGADGYFLAGRSLPWYLIGFSLFASNMSGSSF 67

Query: 68  IGTSGSGFAIGLGISAYEWIAAIALIIVAKYFLPIFLKHGVYTMPQFLSERFNKGVSTAF 127
           +G  G  +A G+ I  YEW AA+ LI+ A + LP FLK  + T+P+FL +R++     AF
Sbjct: 68  VGLMGGAYANGIVIFNYEWTAALVLILFAIFVLPSFLKAKISTVPEFLEQRYDVRSRRAF 127

Query: 128 AVFWLLVYVFVNLTSVSYLGALALDKIMG-IPLQYGIIGLLIFSGIYSIYGGLEAVAWTD 186
           ++F +L  +F++     Y G L +  + G + L   +  L + +GIY+I GGL AV  TD
Sbjct: 128 SIFTILAILFIDTAGALYAGGLVISNVTGYLNLWTAVAVLALVAGIYTILGGLSAVVVTD 187

Query: 187 VVQVIILVAGGLITTFLALDAVGMGDGIFAGMSNLYNDAKDHFVMIMPQGRVMVP-DGLG 245
            VQ I+L+ G  I  +L LD +G  + +F  +       + H  +I+P     +P  GL 
Sbjct: 188 TVQAILLIIGAAILFWLGLDEIGGWEQLFVDI------PEGHDQLILPADDDFLPWTGLW 241

Query: 246 GSRDAFQDLPGLAVILGGMWLTNLGYWGFNQYIIQKGLAAKSIEEAKKGLLFAGYLKLLM 305
           G            V+L G +     YW  NQ+++Q+ L AK+++E + G LFAG+LKL  
Sbjct: 242 G------------VVLLGFY-----YWTINQFVVQRTLGAKNLKEGQIGALFAGFLKLPN 284

Query: 306 PIIVVIPGIAAYVLINDYSPEQLAAILNMPVEHIGTIQKSDEAYPWLLRNFIPNGIRGLA 365
             +++IPG+ A  L     PE               ++  D A+P L    +P G+RGL 
Sbjct: 285 IFLMIIPGVIALKLY----PE---------------LETPDLAFPTLAFELMPIGVRGLI 325

Query: 366 FAALAAAIVSSLASMINSTSTIFTMDIYKVYFKPNANNHQLVRTGRIVAVVALAIAMIVA 425
            AAL AAI+SSL S +NS ST+   D  +  ++   +  + V  GR+V    +    I A
Sbjct: 326 MAALIAAIMSSLDSAMNSASTLVVKDFVEPIWE--VDEGKQVWIGRLVTGAVMVFGAIYA 383

Query: 426 PQLASLDQVFQYIQEYTGYIYPGVVVVFGMGLIWRQATASAALWTAIATIPAGI 479
           P +A  + +F Y Q    YI P +VVV+ +GL       + A WT I  +  GI
Sbjct: 384 PSIAGFESLFSYFQSSLSYIIPTIVVVYIVGLFVPWLNGNGAFWTIILGLVVGI 437


Lambda     K      H
   0.327    0.142    0.427 

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: 1094
Number of extensions: 76
Number of successful extensions: 6
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: 624
Length of database: 533
Length adjustment: 36
Effective length of query: 588
Effective length of database: 497
Effective search space:   292236
Effective search space used:   292236
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 (21.7 bits)
S2: 53 (25.0 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 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