GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuE in Azospirillum brasilense Sp245

Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate AZOBR_RS25580 AZOBR_RS25580 ABC transporter substrate-binding protein

Query= TCDB::Q9R9Q7
         (423 letters)



>FitnessBrowser__azobra:AZOBR_RS25580
          Length = 427

 Score =  356 bits (914), Expect = e-103
 Identities = 186/403 (46%), Positives = 257/403 (63%), Gaps = 2/403 (0%)

Query: 23  AAAAELSMAANSTGKNLSFLRDQIARFEKETGHKVNLVTMPASSSEQFSQYRLWLAAGNK 82
           AA A +++A +  G +    RD    + + +G++V  V+ P  +SEQ + Y+  LAAG+ 
Sbjct: 25  AAGATVTLACSGLGISFDLCRDGAQEWARRSGNEVRFVSPPKGASEQLALYQQLLAAGSP 84

Query: 83  DVDVYQTDVIWAPQLAEQFVDLTE-ATKDVVGEHFPSIIQSQTVNGKLVALPFYTDAPAL 141
           D+DV+Q DV+W   L   F+DL + A  D VG H P++I++ TV G+LVA+P++ DA  L
Sbjct: 85  DIDVFQIDVVWPGILGNYFIDLKDRAGPDTVGRHLPAMIEAATVKGRLVAMPWFADAGVL 144

Query: 142 YYRKDLLDKYGKTPPKTWDELAATAKEVQDKERAAGSADIWGFVFQGNAYEGLTCNALEW 201
           Y RKDLL+ +G+  P+TW+EL  TA  +Q  ERAAG   +WG+V+QG AYEGLT NALEW
Sbjct: 145 YARKDLLEAHGRPVPQTWEELQDTAALIQRAERAAGRDRMWGYVWQGRAYEGLTVNALEW 204

Query: 202 IKSSGGGQIIEPDGTISVNNEKAAAAVEKVKEWIGTIAPKGVLAYQEEESRGVWQTGNAV 261
           I S  GG I+ PDG I+++N +AA A+   + W+G+I+P GVL Y EEE+RGV+Q+GNAV
Sbjct: 205 IASRNGGTIVAPDGAITIDNPQAAEALAMARGWVGSISPPGVLNYMEEEARGVFQSGNAV 264

Query: 262 FMRNWPYAYALGNGDDSAVKGKFEVAPLPAATDGDQPSSTLGGWNLAVSKYSDEQEAAIA 321
           FMRNWPYA+ L N  DSAV GK  V PLP      + +STLGG  LAVSK+S   + A  
Sbjct: 265 FMRNWPYAWTLVNAADSAVGGKVAVVPLPKGGPEGRHTSTLGGQLLAVSKFSAHADEAAD 324

Query: 322 FVKFLGSAETQKVRAIELSNLPTIAALYDDPEVAAAQPFMPHWKPIFQSAVPRPSAVAKV 381
              +L     QK RAI  ++ PTI ALY+D EV AA PF         +AV RP+    +
Sbjct: 325 LALYLTGLAEQKRRAIHGASNPTIPALYEDAEVVAANPFFAALAESIANAVNRPAQATGM 384

Query: 382 KYNEVSSKFWSAVHNTLSGNGTAAENLELLEVELTEL-KGDAW 423
           +YN+VS++F++ VH  LSG   A   L  L+  L  + +G  W
Sbjct: 385 RYNQVSAEFYANVHEVLSGRQDAKAMLSDLKEALVRISRGGRW 427


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: 418
Number of extensions: 12
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: 423
Length of database: 427
Length adjustment: 32
Effective length of query: 391
Effective length of database: 395
Effective search space:   154445
Effective search space used:   154445
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: 51 (24.3 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