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_2414 N515DRAFT_2414 simple sugar transport system permease protein

Query= TCDB::Q7BSH3
         (333 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2414
          Length = 358

 Score =  119 bits (297), Expect = 1e-31
 Identities = 95/295 (32%), Positives = 139/295 (47%), Gaps = 8/295 (2%)

Query: 34  GNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLAFTGMAIAMMNAAHPD----LPL 89
           GNL  I +  + L +++L    VI  + +D+SV A LA     +A     H      LPL
Sbjct: 63  GNLIDIAHRAAPLALVSLGMTLVIALRGLDISVGAVLAIAA-TVAAWTIGHVSNDGLLPL 121

Query: 90  VVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRGMAFVLSGGAWVNAHQMTP 149
            + I  A+  GA  G  NG+LV    + PIV TL  +   RG+A  +SGG  +  +    
Sbjct: 122 WLAIAAALAAGALCGLWNGWLVVGAGMQPIVATLILMVAGRGIAQSISGGQILTLYYAPY 181

Query: 150 IFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYATGGNPTAAVYAGIDTGWT 209
            FL      VLGLP   +V   +  L+ + LR T  G    A G NP AA  AG+     
Sbjct: 182 SFLG--NGFVLGLPFSLFVVAAVFALLQLALRKTALGLFVRAIGHNPQAAHVAGVRARAI 239

Query: 210 KFLAFVLSGALAGLASYLWVSRYAVAYVDIAN-GFELDSVAACVIGGISIAGGVGSVAGT 268
              A+V  G  A LA  L  S    A  + A    ELD++ A  +GG  + GG  S+AG+
Sbjct: 240 TLGAYVFCGIAAALAGLLVSSNVNSADANNAGLLLELDAILAVALGGSLLGGGRFSLAGS 299

Query: 269 VLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFNARRERNRGRIILRDRA 323
           +LGAL +  +   +  IG+ P   +A+   ++   +   +   R + R +LR RA
Sbjct: 300 LLGALIIQALTTTIYAIGVPPQVNLAVKAVLVFAVMLLQSPLCRGQLRALLRLRA 354


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: 276
Number of extensions: 13
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: 358
Length adjustment: 29
Effective length of query: 304
Effective length of database: 329
Effective search space:   100016
Effective search space used:   100016
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