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) >FitnessBrowser__SynE:Synpcc7942_0960 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.
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:
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