GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpS in Synechococcus elongatus PCC 7942

Align GlpS, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase

Query= TCDB::G3LHY8
         (358 letters)



>FitnessBrowser__SynE:Synpcc7942_0960
          Length = 417

 Score =  170 bits (431), Expect = 5e-47
 Identities = 106/314 (33%), Positives = 160/314 (50%), Gaps = 35/314 (11%)

Query: 21  DLVLERGTLNVLLGPTLAGKTSLMRLMAGLDRPTGGSIHFDGTDVTGMPVQKRNVAMVYQ 80
           +L +  G   V++GP+  GK++L+RL+AGL+ P+ G I      V  +P + R++AMV+Q
Sbjct: 54  NLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAKARDIAMVFQ 113

Query: 81  QFINYPALTVYNNIASPMRISG------------------------KDAATIDREVRKAA 116
            +  YP L+VY+N+A  +R  G                        +  A I R VR+ A
Sbjct: 114 SYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEARIKRRVREVA 173

Query: 117 ELLKLTPYLDRTPLNLSGGQQQRTALARALVKNASLVLMDEPLANLDYKLREELREELPK 176
            +L+L   LDR P  LSGGQ+QR AL RA+ +N  + LMDEPL+NLD KLR E R ++  
Sbjct: 174 TMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLRAETRAQIVS 233

Query: 177 IFAQSGAIFVYATTEPSEALLLGGNTATLNQGRVTQFGPTIEVYRRPVNLATAGIFADPP 236
           +  Q G   +Y T + +EA+ +G   A LN+G + Q    +E+Y RP N   A     PP
Sbjct: 234 LQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRFVAQFIGSPP 293

Query: 237 LNTLDVTKSGNVFTRPSGVTIPVPSH----LAVVPDGPVTIAFHPHHLGLAPQTGDAARL 292
           +N + VT    +          +P      L +     V +   P HL    + G AA  
Sbjct: 294 MNLIPVTVRAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHL----EVGAAA-- 347

Query: 293 QARTLVSEITGSES 306
            ++ L+  +TG E+
Sbjct: 348 -SKNLLITVTGVEA 360


Lambda     K      H
   0.319    0.136    0.392 

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: 14
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: 358
Length of database: 417
Length adjustment: 30
Effective length of query: 328
Effective length of database: 387
Effective search space:   126936
Effective search space used:   126936
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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