GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaP in Dyella japonica UNC79MFTsu3.2

Align RhaP, 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 N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein

Query= TCDB::Q7BSH3
         (333 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2415
          Length = 337

 Score =  125 bits (314), Expect = 2e-33
 Identities = 95/304 (31%), Positives = 153/304 (50%), Gaps = 10/304 (3%)

Query: 6   RKRETLLFLIIVVMIVVFSTRAA----DFATPGNLAGIFNDTSILIILALAQMTVILTKS 61
           R+R  +  L+ +V+ V  +         F TP     +  D + L I+A+    VIL   
Sbjct: 20  RRRAQVPLLVTLVLFVAMAGAGGVLYHGFLTPQVFLNLLIDNAFLCIVAVGMTFVILAGG 79

Query: 62  IDLSVAANLAFTGMAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVV 121
           IDLSV A +AF+ + +A +   H   PL  + L+ + +G   GA  G L+    + P VV
Sbjct: 80  IDLSVGAVVAFSTVLLAELVQRHGWPPLAAIALV-LAVGTGFGAGMGVLIQRFRLQPFVV 138

Query: 122 TLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLS---WVGIIIVILMYV 178
           TL  + + RG+A ++S  + ++  Q     ++  R P+ G  +LS    V + +V    +
Sbjct: 139 TLAGMFLARGVATLISVDS-IDIDQPWLASVANLRLPLGGGSMLSVGALVALAVVAAGAL 197

Query: 179 LLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVD 238
           L   + FGR+ YA GG+ ++A   G+    T    + LSG  A LA  ++       Y  
Sbjct: 198 LAGASSFGRTVYAIGGSESSARLMGLPVDATVVRVYALSGFCAALAGVVYTLYMLSGYSQ 257

Query: 239 IANGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIG-ISPFTQMAISG 297
            A G ELD++AA VIGG  +AGG G V GT+LG L LG+I+  +   G +S +    + G
Sbjct: 258 HALGLELDAIAAVVIGGTVLAGGSGYVLGTLLGVLVLGLIQTLIVFDGELSSWWTRIVIG 317

Query: 298 TVII 301
            +++
Sbjct: 318 ALLL 321


Lambda     K      H
   0.328    0.141    0.413 

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: 297
Number of extensions: 17
Number of successful extensions: 3
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: 333
Length of database: 337
Length adjustment: 28
Effective length of query: 305
Effective length of database: 309
Effective search space:    94245
Effective search space used:    94245
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 (21.8 bits)
S2: 49 (23.5 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:

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