GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglB in Sinorhizobium meliloti 1021

Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate SM_b20902 SM_b20902 sugar uptake ABC transporter substrate-binding protein precursor

Query= reanno::Phaeo:GFF3639
         (341 letters)



>FitnessBrowser__Smeli:SM_b20902
          Length = 345

 Score =  437 bits (1123), Expect = e-127
 Identities = 225/342 (65%), Positives = 268/342 (78%), Gaps = 4/342 (1%)

Query: 1   MKFLSGVSALAFAATASMAFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSAD 60
           +K ++G + +A  +  S A A+D+ +GVSWSNFQEERWKTDEAAIKAALEA G  Y+SAD
Sbjct: 5   LKLMAGAAIIA--SMHSAAIAKDLVIGVSWSNFQEERWKTDEAAIKAALEASGDKYISAD 62

Query: 61  AQSSSAKQLSDIESLIAQGVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRAF 120
           AQSS+AKQL+DIESLIAQG +ALIVLAQD+ AIGPA++ AA EGIPVV YDRLIE+  AF
Sbjct: 63  AQSSAAKQLTDIESLIAQGANALIVLAQDSDAIGPAIEKAAAEGIPVVGYDRLIENPDAF 122

Query: 121 YLTFDNVEVGRMQARAVLEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKI 180
           Y+TFDN EVGR+QAR V + +P GN+V IKGS  DPNADFL  GQ E+++ AID+G IK 
Sbjct: 123 YITFDNKEVGRLQAREVFKQKPEGNFVFIKGSSADPNADFLFSGQLEVLKEAIDAGKIKN 182

Query: 181 VGEAYTDGWLPANAQRNMEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSG 239
           VGEAYTDGW P NAQ+NMEQ LTANDNKVDAVVASNDGTAGG +AAL AQG+ G + VSG
Sbjct: 183 VGEAYTDGWKPENAQKNMEQFLTANDNKVDAVVASNDGTAGGAIAALDAQGLAGSVPVSG 242

Query: 240 QDGDHAALNRVAKGTQTVSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWT-SPAGT 298
           QD D AALNRVA GTQTVSVWKD+R+LGK AA IAV +A G  M +V G   +   P G 
Sbjct: 243 QDADKAALNRVALGTQTVSVWKDSRELGKKAAEIAVALAGGKTMDEVEGVQTFNGGPKGV 302

Query: 299 ELTARFLEPIPVTADNLSVVVDAGWITKEALCQGVTNGPAPC 340
            + + FL P+ +T DNL+VV+DAGWI+KE  CQG  +  A C
Sbjct: 303 AMKSVFLAPLAITKDNLNVVIDAGWISKEEACQGAKSDVAAC 344


Lambda     K      H
   0.313    0.128    0.362 

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: 356
Number of extensions: 15
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: 341
Length of database: 345
Length adjustment: 29
Effective length of query: 312
Effective length of database: 316
Effective search space:    98592
Effective search space used:    98592
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 (21.9 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