GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araU in Sinorhizobium meliloti 1021

Align AraU, component of Arabinose, fructose, xylose porter (characterized)
to candidate SM_b20632 SM_b20632 sugar uptake ABC transporter permease

Query= TCDB::Q97UF3
         (295 letters)



>FitnessBrowser__Smeli:SM_b20632
          Length = 287

 Score =  122 bits (305), Expect = 1e-32
 Identities = 85/263 (32%), Positives = 129/263 (49%), Gaps = 15/263 (5%)

Query: 31  WLVPLYAMILGGLKSNLEAASTPILLPP---SKPSLDAY-AFAWFGYATIPGLEPTLLRY 86
           +L P     L   + N E+   P  LPP   S  S DAY A   FG     G+   +   
Sbjct: 30  FLAPFAVSFLASFRPNSESGRPP--LPPWPISGLSFDAYRALDSFG----AGIWQHMFNS 83

Query: 87  LLVAIPSVLLSVVIGTMTAYFFFVLSEKHGIISNGLFSIMALATFLPIETVTFPLIELET 146
           L+V+I +V+L+V +  +  Y F   S       N LF ++     +P +++  PL  +  
Sbjct: 84  LIVSIGTVVLTVAVSVLAGYGF---SRYRFPFKNALFVLIIATLMIPFQSILTPLFIILA 140

Query: 147 SLNVYNTYIGLIFAMLIFYVPTSALLMSIFLPVVPKYLIESARMDGAGDWTILWRVVFPL 206
              + N+ +GL+   +   +P S  +M      VPK + E+AR+DGA D  +L RV+ PL
Sbjct: 141 RFGLNNSLVGLMLVYVTLQLPFSVFMMRNAFDAVPKEIEEAARIDGARDLKLLVRVLLPL 200

Query: 207 IFPGFLSTLIFVFLQIWNEFFIPLILTNTPNMLMLPVAARFYTAAYALIYN-RSFAAGVI 265
           + PG  +  IF FL  WNEFF  L+L ++ +   LPV      A      N  +  AGV 
Sbjct: 201 VMPGIATVSIFAFLNAWNEFFAALVLLSSNDNYTLPVLMTAVRAGRLGAINWGAVQAGVA 260

Query: 266 SSLIP-LIIFIFLGRYFIRGLAA 287
             ++P L +F+ L RY++RGL A
Sbjct: 261 VMVVPCLFVFLLLQRYYMRGLMA 283


Lambda     K      H
   0.330    0.145    0.436 

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: 200
Number of extensions: 11
Number of successful extensions: 1
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: 295
Length of database: 287
Length adjustment: 26
Effective length of query: 269
Effective length of database: 261
Effective search space:    70209
Effective search space used:    70209
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: 48 (23.1 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