GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuE in Synechococcus elongatus PCC 7942

Align ThuE aka RB0311 aka SMB20325, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate Synpcc7942_0950 Synpcc7942_0950 putative multiple sugar transport system substrate-binding protein

Query= TCDB::Q9R9Q7
         (423 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0950 Synpcc7942_0950 putative
           multiple sugar transport system substrate-binding
           protein
          Length = 438

 Score =  179 bits (454), Expect = 1e-49
 Identities = 133/431 (30%), Positives = 211/431 (48%), Gaps = 29/431 (6%)

Query: 1   MNVKPFVRTLISCAAIAGAIDLAAAAELSMAANSTGKNLSFL--------RDQIARFEKE 52
           + + P + TL    A+ G   L    + S AA+ST    + L        +  IARF  E
Sbjct: 14  LRLLPLLLTLFIVLALGG---LGTGTQRSAAADSTVVLRALLPAPFREAMQPAIARFTAE 70

Query: 53  TGH-KVNLVTMPASSSEQFSQYRLWLAAGNKDVDVYQTDVIWAPQL--AEQFVDLTEAT- 108
               ++ LV  P  +S     Y      GN   D+   DV W P+   A   +DL++   
Sbjct: 71  HPEIQLELVAGPNDTSLVSDLYTTAFLLGNAPYDLVFLDVTWLPKFVAAGWLLDLSDRVL 130

Query: 109 KDVVGEHFPSIIQSQTVNGKLVALPFYTDAPALYYRKDLLDKYGKTPPKTWDELAATAKE 168
            ++  E  P+ +       +L  LP       LYYR+DL+ +    PP+T+ EL   +++
Sbjct: 131 PEIQAEFLPAALNGSFYRDRLYRLPLNAAVGLLYYRQDLMPE----PPQTFTELVQRSQQ 186

Query: 169 VQDKERAAGSADIWGFVFQGNAYEGLTCNALEWIKSSGGGQIIEPDGTISVNNEKAAAAV 228
           +Q     A     WG+V+QG  YEGL CN LE +   GG  I    G + +++ +A AA 
Sbjct: 187 LQ-----AQGVVPWGYVWQGKQYEGLVCNFLEVLAGFGGYWIDPQTGEVGLDHPEAIAAA 241

Query: 229 EKVKEWI-GTIAPKGVLAYQEEESRGVWQTGNAVFMRNWPYAYALGNGDDSAVKGKFEVA 287
           + +   I   I+P GV  +QE E+  +++TG + FMRNWPYA  L    +SAV+GK  +A
Sbjct: 242 DWLHSTITDQISPAGVSTFQENEALKLFETGQSAFMRNWPYAEMLLERPESAVRGKVGIA 301

Query: 288 PLPAATDGDQPSSTLGGWNLAVSKYSDEQEAAIAFVKFLGSAETQKVRAIELSNLPTIAA 347
           P+  A  G   ++T G W + +++ ++  EAA+  +  L  AE+Q++ ++  + +PT +A
Sbjct: 302 PMVHA-PGQTSAATQGTWGVGIAQQTEHPEAALTALLALTDAESQRLISLGSNYIPTRSA 360

Query: 348 LYDDPEVAAAQPFMPHWKPIFQSAVPRPSAVAKVKYNEVSSKFWSAVHNTLSGNGTAAEN 407
           LY DPE+ A  PF     PI +S V R    A    +++  +  SA    +SG    A  
Sbjct: 361 LYQDPELLARYPFYATLPPILESTVLRSPLPAYDALSDILQRHLSA---AISGQTPVAIA 417

Query: 408 LELLEVELTEL 418
           L+    E  +L
Sbjct: 418 LQQAARESRQL 428


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: 428
Number of extensions: 23
Number of successful extensions: 5
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: 438
Length adjustment: 32
Effective length of query: 391
Effective length of database: 406
Effective search space:   158746
Effective search space used:   158746
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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