GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rhaP in Azospirillum brasilense Sp245

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 AZOBR_RS27940 AZOBR_RS27940 ABC transporter permease

Query= TCDB::Q7BSH3
         (333 letters)



>FitnessBrowser__azobra:AZOBR_RS27940
          Length = 329

 Score =  144 bits (363), Expect = 3e-39
 Identities = 102/303 (33%), Positives = 164/303 (54%), Gaps = 14/303 (4%)

Query: 13  FLIIVVMIVVFSTRAADFATPGNLAGIFNDTSILIILALAQMTVILTKSIDLSVAANLAF 72
           FL +  +IV+ +     F +PGN+  +   T+ + I+A+    VI    IDLSV +  AF
Sbjct: 20  FLALAALIVLGTIVNPVFLSPGNIGNVLTRTAFIGIIAVGATFVITAGGIDLSVGSLAAF 79

Query: 73  -TGMAIAMMNA----AHPDLPLVVL-ILMAVVIGACLGAINGFLVWALEIPPIVVTLGTL 126
            +G+ I +MNA        LP++++ +L+A+ +G   G +NG LV    +   +VTLGT+
Sbjct: 80  ASGVMIVVMNALVGSMGAGLPVILIGVLVALGLGLVAGLVNGLLVTKGRMEAFIVTLGTM 139

Query: 127 TIYRGM-AFVLSGGAWVNAHQMTPIFLSVPRTPVLGL--PVLSWVGIIIVILMYVLLRY- 182
            I+R +  ++  GG      ++  I+  V    V G+  P+L++    +V L+  L+ Y 
Sbjct: 140 GIFRSLVTYIADGGTLSLNSEIRTIYRPVYYGGVFGISYPILAFA---VVALIGALIMYR 196

Query: 183 TQFGRSAYATGGNPTAAVYAGIDTGWTKFLAFVLSGALAGLASYLWVSRYAVAYVDIANG 242
           T+FGR   A G +   A Y+ I+    K LAFVL G    +A  ++V R   A       
Sbjct: 197 TRFGRYCAAIGSSEDVARYSAINVDRVKLLAFVLQGICVAIAVVIYVPRLGSASATTGLL 256

Query: 243 FELDSVAACVIGGISIAGGVGSVAGTVLGALFLGVIKNALPVIG-ISPFTQMAISGTVII 301
           +EL+++AA +IGG  + GG G + GTV+GA+ L +I N L + G IS +    I G +II
Sbjct: 257 WELEAIAAVIIGGTMLKGGYGRIWGTVVGAVMLTLIDNILNLTGAISVYLNGTIQGVIII 316

Query: 302 LAV 304
           +AV
Sbjct: 317 VAV 319


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: 283
Number of extensions: 17
Number of successful extensions: 2
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: 329
Length adjustment: 28
Effective length of query: 305
Effective length of database: 301
Effective search space:    91805
Effective search space used:    91805
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