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_0947 Synpcc7942_0947 ATPase
Query= TCDB::P96483 (377 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 286 bits (733), Expect = 5e-82 Identities = 156/355 (43%), Positives = 216/355 (60%), Gaps = 21/355 (5%) Query: 21 VDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIA 80 V L + ++ GEFL L+GPSGCGKST+LR++AGL+ G+I +GDR++T LPP DRD+A Sbjct: 22 VANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIWLGDREITTLPPGDRDMA 81 Query: 81 MVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQ 140 MVFQ+YALYPH+ V N+ L+I AEI Q++++ A L+L LDR+P LSGGQ Sbjct: 82 MVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNLELDHLLDRRPAQLSGGQ 141 Query: 141 RQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAM 200 RQRVA+GRA+VR+P VFL+DEPLSNLDA LR R Q+ +L + VYVTHDQ EA+ Sbjct: 142 RQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFSQQASPVVYVTHDQTEAL 201 Query: 201 TMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSVV 260 ++ R+A+L G LQQ+DSP +Y PAN FVAGFIGSP MNL+ +PI G G+ + Sbjct: 202 SLSHRIAILNGGHLQQLDSPDRIYQAPANAFVAGFIGSPRMNLLPLPIHSGQAWLGSRAL 261 Query: 261 PVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEEL 320 P+ + + V G+RPEH L + + + V +++ E L Sbjct: 262 PIPSHLAARSQ-----VLWGLRPEH-------------LKLATPEVERAIPVQLHLTENL 303 Query: 321 GADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFSTSTGERL 375 G + EV+ ++ + + +P + L V P H F STG+RL Sbjct: 304 GMQRLLTVAIAANPEVRLRLLMPSDQPIP---TDLQVTFEPESQHWFCPSTGDRL 355 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: 365 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: 377 Length of database: 355 Length adjustment: 30 Effective length of query: 347 Effective length of database: 325 Effective search space: 112775 Effective search space used: 112775 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: 49 (23.5 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