Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate Synpcc7942_0947 Synpcc7942_0947 ATPase
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__SynE:Synpcc7942_0947 Length = 355 Score = 240 bits (613), Expect = 4e-68 Identities = 144/375 (38%), Positives = 214/375 (57%), Gaps = 27/375 (7%) Query: 4 LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63 L+L + K Y + V N +L + EF+ +GPSGCGKSTTLR+IAGL+ T G+++ Sbjct: 6 LELRQLRKAY-SPSVVPVANLSLQLQPGEFLTLLGPSGCGKSTTLRLIAGLDQPTSGSIW 64 Query: 64 IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123 + D+ + P DRD+AMVFQ+YALYPH++V +N+ GL++R+ +I +R+ + A L Sbjct: 65 LGDREITTLPPGDRDMAMVFQSYALYPHLNVRQNLTLGLQIRRTSAAEIEQRLQQVAHNL 124 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183 L L+R+PA LSGGQRQRVA+GRA+VR VFL+DEPLSNLDA LR +RA++ + Sbjct: 125 ELDHLLDRRPAQLSGGQRQRVALGRALVRQPSVFLLDEPLSNLDALLREQVRAQMKALFS 184 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243 + + +YVTHDQTEA++L+ RI I++ G ++Q+ +P +Y PAN FVA Sbjct: 185 QQASPVVYVTHDQTEALSLSHRIAILNG----------GHLQQLDSPDRIYQAPANAFVA 234 Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGL-SLALPQGQEKILEEKGYLGKKVTLGIRPEDISS 302 GFIGSP MN + + Q L S ALP + +V G+RPE + Sbjct: 235 GFIGSPRMNLLPLPIHS----GQAWLGSRALP------IPSHLAARSQVLWGLRPEHLK- 283 Query: 303 DQIVHETFPNASVTADILVSELLGSESMLYVKFGST-EFTARVNARDSHSPGEKVQLTFN 361 + ++ + ++E LG + +L V + E R+ +Q+TF Sbjct: 284 ---LATPEVERAIPVQLHLTENLGMQRLLTVAIAANPEVRLRLLMPSDQPIPTDLQVTFE 340 Query: 362 IAKGHFFDLETEKRI 376 H+F T R+ Sbjct: 341 PESQHWFCPSTGDRL 355 Lambda K H 0.318 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: 316 Number of extensions: 17 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 (21.7 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