GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuE in Sinorhizobium meliloti 1021

Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate SM_b20325 SM_b20325 trehalosemaltose-binding protein

Query= TCDB::Q9R9Q7
         (423 letters)



>FitnessBrowser__Smeli:SM_b20325
          Length = 423

 Score =  848 bits (2191), Expect = 0.0
 Identities = 423/423 (100%), Positives = 423/423 (100%)

Query: 1   MNVKPFVRTLISCAAIAGAIDLAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLV 60
           MNVKPFVRTLISCAAIAGAIDLAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLV
Sbjct: 1   MNVKPFVRTLISCAAIAGAIDLAAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLV 60

Query: 61  TMPASSSEQFSQYRLWLAAGNKDVDVYQTDVIWAPQLAEQFVDLTEATKDVVGEHFPSII 120
           TMPASSSEQFSQYRLWLAAGNKDVDVYQTDVIWAPQLAEQFVDLTEATKDVVGEHFPSII
Sbjct: 61  TMPASSSEQFSQYRLWLAAGNKDVDVYQTDVIWAPQLAEQFVDLTEATKDVVGEHFPSII 120

Query: 121 QSQTVNGKLVALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSAD 180
           QSQTVNGKLVALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSAD
Sbjct: 121 QSQTVNGKLVALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSAD 180

Query: 181 IWGFVFQGNAYEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAP 240
           IWGFVFQGNAYEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAP
Sbjct: 181 IWGFVFQGNAYEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAP 240

Query: 241 KGVLAYQEEESRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSS 300
           KGVLAYQEEESRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSS
Sbjct: 241 KGVLAYQEEESRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSS 300

Query: 301 TLGGWNLAVSKYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPF 360
           TLGGWNLAVSKYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPF
Sbjct: 301 TLGGWNLAVSKYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPF 360

Query: 361 MPHWKPIFQSAVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKG 420
           MPHWKPIFQSAVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKG
Sbjct: 361 MPHWKPIFQSAVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTELKG 420

Query: 421 DAW 423
           DAW
Sbjct: 421 DAW 423


Lambda     K      H
   0.313    0.129    0.383 

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: 771
Number of extensions: 23
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: 423
Length of database: 423
Length adjustment: 32
Effective length of query: 391
Effective length of database: 391
Effective search space:   152881
Effective search space used:   152881
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: 50 (23.9 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