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 3607842 Dshi_1250 ABC transporter related (RefSeq)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Dino:3607842 Length = 351 Score = 298 bits (762), Expect = 2e-85 Identities = 181/380 (47%), Positives = 234/380 (61%), Gaps = 35/380 (9%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M+ + L KRY + V +L I D EF VFVGPSGCGKST LRMIAGLE+ +EG Sbjct: 1 MSGITLRGAVKRYGETQ--VVHGVDLSIADGEFCVFVGPSGCGKSTLLRMIAGLEETSEG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 +++I + + P +R +AMVFQ YALYPHM+V ENM FGLK+ K +I +V A+ Sbjct: 59 SIHIGARDVTRLDPSERGVAMVFQTYALYPHMTVAENMGFGLKMNGVPKAEIKAKVAAAS 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 EIL L ++L RKP LSGGQRQRVA+GRAIVR +VFL DEPLSNLDA+LRV MR EIA+ Sbjct: 119 EILKLDDYLARKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIAR 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+ IGAT IYVTHDQ EAMTLAD+IV++ A GR+EQ+G P ELY +P N Sbjct: 179 LHKEIGATMIYVTHDQVEAMTLADKIVVLRA----------GRVEQVGAPLELYRDPDNV 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLA-LPQGQEKILEEKGYLGKK--VTLGIRP 297 FVAGFIGSPAMNF + +E D + LA LP L G G+ VT+G+RP Sbjct: 229 FVAGFIGSPAMNFLDGRIE------NDAVHLAGLPP-----LPVPGAAGRSGPVTVGVRP 277 Query: 298 EDISSDQIVHETFPNASVTADILVSELLGSESMLYVK-FGSTEFTARVNARDSHSPGEKV 356 + I+ + P + ++E LG S LY++ + T D + G V Sbjct: 278 QHIALE-------PGGDGYL-VELTESLGGVSYLYLRGADGSRLTVEAGEEDPIAEGTPV 329 Query: 357 QLTFNIAKGHFFDLETEKRI 376 L+ + F+ ET +R+ Sbjct: 330 GLSLAPDRVMLFEAETGQRL 349 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: 342 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: 351 Length adjustment: 29 Effective length of query: 348 Effective length of database: 322 Effective search space: 112056 Effective search space used: 112056 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