GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaP in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_4287 Inositol transport system permease protein

Query= TCDB::Q7BSH3
         (333 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4287
          Length = 340

 Score =  158 bits (400), Expect = 2e-43
 Identities = 101/322 (31%), Positives = 169/322 (52%), Gaps = 23/322 (7%)

Query: 9   ETLLFLIIVVMIVVFS-----TRAADFATPGN-LAGIFNDTSILIILALAQMTVILTKSI 62
           E  +FL+++ + +VF       R   F      L  +    SI+ +LA+    VI+T  I
Sbjct: 23  ELSIFLVLIGIGLVFEMFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGI 82

Query: 63  DLSVAANLAFTGMAIAMM-------NAAHP---DLPLVVLILMAVVIGACLGAINGFLVW 112
           DLS  + LA + M  A +        A  P   DLP+ + +++ + +G   GAING ++ 
Sbjct: 83  DLSSGSVLALSAMIAASLAQTSDFARAVFPSLTDLPVWIPVIVGLGVGLLAGAINGSIIA 142

Query: 113 ALEIPPIVVTLGTLTIYRGMAFVLSGGAWVNAHQMTPIFLSVPRTPVLGLPVLSWVGIII 172
              IPP + TLG +   RG+A   + G  V+    +   +     PV+       + +++
Sbjct: 143 ITGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAMPVI-------IFLVV 195

Query: 173 VILMYVLLRYTQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRY 232
            ++ ++ LRYT++G+  YA GGN  AA  +GI+      + + ++G LAGLA  +  +R 
Sbjct: 196 AVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLVIVYSIAGLLAGLAGVVASARA 255

Query: 233 AVAYVDIANGFELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIGISPFTQ 292
           A     +   +ELD++AA VIGG S+AGGVG + GTV+GAL LGV+ +    +G+  + Q
Sbjct: 256 ATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQ 315

Query: 293 MAISGTVIILAVAFNARRERNR 314
             I G +I++AV  +  R + +
Sbjct: 316 DIIKGLIIVVAVVIDQYRNKRK 337


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: 293
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: 340
Length adjustment: 28
Effective length of query: 305
Effective length of database: 312
Effective search space:    95160
Effective search space used:    95160
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