GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruE in Sinorhizobium meliloti 1021

Align Fructose import binding protein FruE (characterized)
to candidate SM_b21345 SM_b21345 sugar uptake ABC transporter substrate-binding protein precursor

Query= SwissProt::Q8G848
         (327 letters)



>FitnessBrowser__Smeli:SM_b21345
          Length = 327

 Score =  138 bits (348), Expect = 2e-37
 Identities = 96/323 (29%), Positives = 164/323 (50%), Gaps = 8/323 (2%)

Query: 5   KKAIALVASAAALVSVAACGS-SNAGGSSDSGKKTVGFVAVGPEGGFRTANEKDIQKAFE 63
           ++A  L A+AA  +++A   + +     +      VGF        +R A    ++   E
Sbjct: 6   RRAFMLAATAAGAIAIAGTVAFAELPKLAQKETYKVGFAQTESNNPWRIAQTNSMKAEAE 65

Query: 64  DAGFDLTYSPTQNNDQQKQIQAFNKFVNDEVDAIILSSTEDSGWDDSLKKAAEAEIPVFT 123
             G  L Y+    +   KQ+   N  +   VD I L+  E+     ++  A +A IPV  
Sbjct: 66  KLGHQLVYTDAAGS-AAKQVADVNSMIAQGVDLIFLAPREEKPLIPAVMAAKKAGIPVIL 124

Query: 124 VDRNVDVKDAEAKKAIVAHIGPSNVWCGEQAAEFVNKNFPDGANGFILEGPAGLSVVKDR 183
           +DR+VD   A+A +  V  IG   +  G++ AE++ KN    +    LEG  G S   DR
Sbjct: 125 LDRSVDPSLAKAGEDYVTFIGSDFIEEGKRIAEWLVKNANGKSKIIELEGTTGSSPANDR 184

Query: 184 GTGWGN--KVASNVKVLESQSANWSTDEAKTVTAGLLDKYKSDNPQFIFAQNDEMGLGAA 241
             G+    K A   +++ SQS +++ D+ + V   LL  +   +   ++A NDEM +GA 
Sbjct: 185 KKGFDETIKAAGGFEIVASQSGDFARDKGRQVAEALLQAH--PDADIVYAHNDEMAIGAI 242

Query: 242 QAVDAAG-LKGK-VKIITIDGTKNALQALVDGDLSYVIEYNPIFGKETAQAVKDYLDGKT 299
            A++AAG + GK V +++IDG K A+QA++DG ++ V+E NP FG +  + +  Y  G+ 
Sbjct: 243 AAIEAAGKVPGKDVLVLSIDGGKEAVQAVIDGKIAAVVECNPRFGPKAFETMLRYAKGEK 302

Query: 300 VEKDIEIESKTFDAASAKEALDN 322
           ++  +  E K +D+++A   L N
Sbjct: 303 IDPMVINEDKFYDSSNAAAELAN 325


Lambda     K      H
   0.310    0.128    0.360 

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: 231
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: 327
Length of database: 327
Length adjustment: 28
Effective length of query: 299
Effective length of database: 299
Effective search space:    89401
Effective search space used:    89401
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (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