Aligments for a candidate for rhaT' in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Aligments for a candidate for rhaT' in Dinoroseobacter shibae DFL-12

Align RhaT, component of Rhamnose porter (Richardson et al., 2004) (Transport activity is dependent on rhamnokinase (RhaK; AAQ92412) activity (Richardson and Oresnik, 2007) This could be an example of group translocation!) (characterized)
to candidate 3609044 Dshi_2433 ABC transporter related (RefSeq)

Query= TCDB::Q7BSH4
         (512 letters)



>lcl|FitnessBrowser__Dino:3609044 Dshi_2433 ABC transporter related
           (RefSeq)
          Length = 510

 Score =  619 bits (1597), Expect = 0.0
 Identities = 318/505 (62%), Positives = 391/505 (77%), Gaps = 1/505 (0%)

Query: 6   QQPVTDSKTGDAPAILEMRGISQIFPGVKALDNVSIALHPGTVTALIGENGAGKSTLVKI 65
           Q+P+       + A L +  I++ FPGVKAL +VS++L+PG VTALIGENGAGKST+VKI
Sbjct: 6   QRPLPSEDPPVSQAALALAHITKTFPGVKALSDVSLSLYPGKVTALIGENGAGKSTVVKI 65

Query: 66  LTGIYRPNEGEILVDGRPTTFASAQAAIDAGVTAIHQETVLFDELTVAENIFLGHAPRTR 125
           LTGIY+P+ G ILVDG+P  F++ QAA D GVTAIHQETVLFDEL+VAENIFLGHAPR  
Sbjct: 66  LTGIYQPDGGRILVDGQPVPFSTPQAAADHGVTAIHQETVLFDELSVAENIFLGHAPRGA 125

Query: 126 FRTIDWQTMNSRSKALLTALESNIDPTIRLKDLSIAQRHLVAIARALSIEARIVIMDEPT 185
           F  IDW+     ++ALLT++ + +DP  +LKDL IA +HLVAIARALSIEAR+VIMDEPT
Sbjct: 126 FGLIDWKKTTENARALLTSIGAELDPDHKLKDLGIANKHLVAIARALSIEARVVIMDEPT 185

Query: 186 AALSRKEIDDLFRIVRGLKEQGKAILFISHKFDELYEIADDFVVFPRRSRRPVRGVSRKT 245
           AALS KEI++L+ +V  LK QGKAILFISHKFDE++ IAD++ VF R  +    G     
Sbjct: 186 AALSHKEIEELYELVESLKAQGKAILFISHKFDEIFRIADNYTVF-RDGQLIGDGAIADV 244

Query: 246 PQDEIVRMMVGRDVENVFPKIDVAIGGPVLEIRNYSHRTEFRDISFTLRKGEILGVYGLI 305
            + ++V+MMVGRDV  +FP+    +G  VL ++ Y+H TEF DISFTLR+GEILG YGL+
Sbjct: 245 TEADLVKMMVGRDVSQIFPQRAPNVGDTVLTVQGYAHPTEFDDISFTLREGEILGFYGLV 304

Query: 306 GAGRSELSQSLFGITKPLSGKMVLEGQEITIHSPQDAIRAGIVYVPEERGRHGLALPMPI 365
           GAGRSE  QSLFGIT+P +G + + G    I SP DA+  GIVYVPE+RG+ G  L +PI
Sbjct: 305 GAGRSEFMQSLFGITRPSAGSVEIGGARAEISSPADAVDHGIVYVPEDRGKQGAILDLPI 364

Query: 366 FQNMTLPSLARTSRRGFLRAANEFALARKYAERLDLRAAALSVPVGTLSGGNQQKVVIGK 425
           FQN+TLPSL R SR+GFLR A EFALAR+Y ERLDLRAA+L   VG LSGGNQQKVVI K
Sbjct: 365 FQNVTLPSLGRISRKGFLRLAEEFALAREYTERLDLRAASLDTHVGNLSGGNQQKVVIAK 424

Query: 426 WLATAPKVIILDEPTKGIDIGSKAAVHGFISELAAEGLSIIMVSSELPEIIGMSDRVLVM 485
           WLAT P+VIILDEPTKG+DIGSKAAVH F++ELAA+GL++IMVSSE+PE++GMSDRV+VM
Sbjct: 425 WLATRPRVIILDEPTKGVDIGSKAAVHDFMAELAAQGLAVIMVSSEIPEVLGMSDRVIVM 484

Query: 486 KEGLSAGIFERAELSPEALVRAATG 510
           +EG         +L PE LVR A G
Sbjct: 485 REGRIVAELAGDDLQPETLVRHAAG 509


Lambda     K      H
   0.320    0.137    0.382 

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: 777
Number of extensions: 27
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: 512
Length of database: 510
Length adjustment: 35
Effective length of query: 477
Effective length of database: 475
Effective search space:   226575
Effective search space used:   226575
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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