GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaP in Pseudomonas fluorescens GW456-L13

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 PfGW456L13_3910 Ribose ABC transport system, permease protein RbsC (TC 3.A.1.2.1)

Query= TCDB::Q7BSH3
         (333 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3910
          Length = 325

 Score =  138 bits (348), Expect = 2e-37
 Identities = 94/303 (31%), Positives = 150/303 (49%), Gaps = 8/303 (2%)

Query: 16  IVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLAFTG- 74
           ++ MIV+FS  ++ F +    + + N    L++LA+    V++   IDLSV + LA    
Sbjct: 27  LLAMIVLFSVLSSHFLSYDTFSTLANQIPDLMVLAVGMTFVLIIGGIDLSVGSVLALAAS 86

Query: 75  -MAIAMMNAAHPDLPLVVLILMAVVIGACLGAINGFLVWALEIPPIVVTLGTLTIYRGMA 133
            +++A++      LP     L+ + + A  G I G +  A  IP  +V+LG L + RG+A
Sbjct: 87  TVSVAILGWGWGVLPAA---LLGMAVAALAGTITGSITVAWRIPSFIVSLGVLEMARGVA 143

Query: 134 FVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIIIVILMYVLLRYTQFGRSAYATG 193
           + ++G        +   F  +      G+     + ++I+ +   +L  T FGR     G
Sbjct: 144 YQMTGS---RTAYIGDAFAWLSNPIAFGISPSFIIALLIIFVAQAVLTRTVFGRYLIGIG 200

Query: 194 GNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANGFELDSVAACVI 253
            N  A   AGI+    K L F L G LAG+A+   +SR   A  +  +G EL  +AA VI
Sbjct: 201 TNEEAVRLAGINPKPYKVLVFSLMGLLAGVAALFQISRLEAADPNAGSGLELQVIAAVVI 260

Query: 254 GGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQMAISGTVIILAVAFNARRERN 313
           GG S+ GG GSV  T  G L + V+   L  IG +  T+  I+G VI++AV  +  R + 
Sbjct: 261 GGTSLMGGRGSVISTFFGVLIISVLAAGLAQIGATEPTKRIITGAVIVVAVVLDTYRSQR 320

Query: 314 RGR 316
             R
Sbjct: 321 ASR 323


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: 258
Number of extensions: 16
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: 325
Length adjustment: 28
Effective length of query: 305
Effective length of database: 297
Effective search space:    90585
Effective search space used:    90585
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.

Links

Downloads

Related tools

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