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 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 218 bits (554), Expect = 3e-61 Identities = 123/301 (40%), Positives = 185/301 (61%), Gaps = 25/301 (8%) Query: 4 LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63 LK++ + K + + + +V++ +L I+ E +G SG GKST LRM+AG E TEG +Y Sbjct: 21 LKIERVSKLFDDVR--AVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIY 78 Query: 64 IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123 +D + + D P +R I M+FQ+YAL+PHM+V +N+AFGLK K K DI++RV E +++ Sbjct: 79 LDGQDITDLPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLV 138 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183 + ++ +RKP LSGGQRQRVA+ R++ + K+ L+DEP+ LD KLR M+ E+ +I Sbjct: 139 HMEQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILE 198 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243 R+G T + VTHDQ EAMT+A RI IMS G I Q+G+P ++Y P ++ +A Sbjct: 199 RVGVTCVMVTHDQEEAMTMAGRIAIMSD----------GWIAQVGSPMDIYESPNSRMIA 248 Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQ------GQEKILEEKGYLGKKVTLGIRP 297 FIG+ +N F+ + ++ + S LPQ G LE+ K V L +RP Sbjct: 249 EFIGT--VNLFDCEIIEDEADHAILKSPTLPQPFLIGHGVTTSLED-----KHVWLAVRP 301 Query: 298 E 298 E Sbjct: 302 E 302 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: 341 Number of extensions: 13 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: 378 Length adjustment: 30 Effective length of query: 347 Effective length of database: 348 Effective search space: 120756 Effective search space used: 120756 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: 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