GapMind for catabolism of small carbon sources

 

Aligments for a candidate for msiK in Synechococcus elongatus PCC 7942

Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase

Query= TCDB::P96483
         (377 letters)



>lcl|FitnessBrowser__SynE:Synpcc7942_0960 Synpcc7942_0960 ATPase
          Length = 417

 Score =  317 bits (811), Expect = 5e-91
 Identities = 189/414 (45%), Positives = 249/414 (60%), Gaps = 61/414 (14%)

Query: 1   MATVTFDKATRIYPGSDKP-------AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAG 53
           +A V F++  + +P   +         ++ +++ I DGEF+V+VGPSGCGKST LR+LAG
Sbjct: 23  VAGVVFEEIEKRFPEQARSPQKGEVVVLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAG 82

Query: 54  LEDVNGGAIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAG------- 106
           LE  + G I++GDR V  LP K RDIAMVFQ+YALYPH++V DN+ F L+  G       
Sbjct: 83  LETPSRGLIKVGDRRVDRLPAKARDIAMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQ 142

Query: 107 --------VPK---------AEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQRVAMGRA 149
                   +PK         A I+++V E A +L L   LDR+PK LSGGQ+QRVA+GRA
Sbjct: 143 QLALATRSLPKSLQYEPEQEARIKRRVREVATMLQLDTLLDRQPKQLSGGQKQRVALGRA 202

Query: 150 IVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMGDRVAVL 209
           I R PQVFLMDEPLSNLDAKLR  TR QI SLQR+LG+TT+YVTHDQ EAMTMGDR+AVL
Sbjct: 203 IARNPQVFLMDEPLSNLDAKLRAETRAQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVL 262

Query: 210 KDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEV----PITDGGVKFGNSVVPVNRE 265
             G LQQV SP  +YD+PAN FVA FIGSP MNL+ V    P+      F  ++      
Sbjct: 263 NRGHLQQVASPLEIYDRPANRFVAQFIGSPPMNLIPVTVRAPLQLTTENFRCTLPEAWEP 322

Query: 266 ALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEELGADGY 325
            L   D   +TV +G+RPEH +V               A A   L ++V  VE LG+D +
Sbjct: 323 VLRLYD--GQTVELGIRPEHLEV--------------GAAASKNLLITVTGVEALGSDTF 366

Query: 326 VYGTAEVGGEVKDLVVRVNGRQVPEK----GSTLHVVPRPGETHVFSTSTGERL 375
                 + GE+K+  + V  R  P++    G  L +  +P + H+F   TG+ +
Sbjct: 367 ------IAGELKESGIAVQARLAPQQCWQMGDRLWLTFKPDQIHLFDLETGKAI 414


Lambda     K      H
   0.317    0.135    0.379 

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: 432
Number of extensions: 14
Number of successful extensions: 4
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: 377
Length of database: 417
Length adjustment: 31
Effective length of query: 346
Effective length of database: 386
Effective search space:   133556
Effective search space used:   133556
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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