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 GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__psRCH2:GFF4209 Length = 383 Score = 217 bits (552), Expect = 5e-61 Identities = 130/340 (38%), Positives = 198/340 (58%), Gaps = 23/340 (6%) Query: 4 LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63 LK+D + K++ +V++ +L IH E +G SG GKST LRM+AG E TEG ++ Sbjct: 23 LKIDRVTKKFDET--VAVDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIF 80 Query: 64 IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123 +D + + D P +R I M+FQ+YAL+PHM+V +N+AFGLK K +I +RV E ++ Sbjct: 81 LDGQDITDMPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDGLPKAEIEERVKEMLGLV 140 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183 +T++ +RKP LSGGQRQRVA+ R++ + K+ L+DEP+ LD KLR M+ E+ +I Sbjct: 141 QMTQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVQIIE 200 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243 R+G T + VTHDQ EAMT+A+RI IM +G I Q+G+P ++Y PA++ V Sbjct: 201 RVGVTCVMVTHDQEEAMTMAERIAIM----------HLGWIAQVGSPMDIYETPASRLVC 250 Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYL----GKKVTLGIRPED 299 FIG+ +N F+ + ++ D +A P + I G K++T IRPE Sbjct: 251 EFIGN--VNLFDGELIEDM---GDHAVIASPGLENPIYVGHGISTRAEDKQITYAIRPEK 305 Query: 300 ISSDQIVHETFPNASVTADILVSEL--LGSESMLYVKFGS 337 + + E A +V ++ LG S+ Y+K S Sbjct: 306 LLIGTELPELERPGYNWAKGVVHDIAYLGGHSVYYIKLPS 345 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: 338 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: 383 Length adjustment: 30 Effective length of query: 347 Effective length of database: 353 Effective search space: 122491 Effective search space used: 122491 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