Align MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized)
to candidate SMc04393 SMc04393 ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Smeli:SMc04393 Length = 370 Score = 339 bits (870), Expect = 6e-98 Identities = 184/373 (49%), Positives = 256/373 (68%), Gaps = 11/373 (2%) Query: 3 MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62 M+ + + N+ K Y + +K+ NL +E+ F+VL+GPSGCGK+T L IAGLE IT G Sbjct: 1 MSFLKITNLRKSY-GALEILKDINLEIEEGGFLVLVGPSGCGKSTLLNTIAGLEPITSGD 59 Query: 63 IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122 I I+G+ V+ + P RDIAMVFQ+YALYP+MTV N+AFG+++R PK+E ++ +++ A Sbjct: 60 IAINGRSVSGLHPSKRDIAMVFQSYALYPNMTVAGNIAFGMEIRGVPKEEREKAIKQVAD 119 Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182 +L I +LLDRKP QLSGGQRQRVA+GRA+VRNP+VFLFDEPLSNLDAKLRV MR+E+K+L Sbjct: 120 MLQIGHLLDRKPSQLSGGQRQRVAMGRALVRNPQVFLFDEPLSNLDAKLRVDMRTEIKRL 179 Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242 HHR++ TI+YVTHDQ+EAMT+A KI V+KDG +QQ GTP EIYN+PAN+FVA F+GSP M Sbjct: 180 HHRMKTTIVYVTHDQIEAMTLATKIAVLKDGVLQQFGTPAEIYNNPANMFVADFMGSPAM 239 Query: 243 NFVNARVVRGEGGLWI-----QASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLF 297 N + A++ + + A ++ VP L+ Y KE++FGIRPE + D Sbjct: 240 NLLKAQIETAGSQVSVTLARPNAEPLRLAVP--HNGALSAYAGKEVVFGIRPEALTDPDG 297 Query: 298 ALAPSPENTITG--VVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMT 355 A + + G +++VVEP GS+T ++G IVA + + Q L ++ Sbjct: 298 A-DRNAQFVAEGECLIEVVEPAGSDTFAVTRLGGKEIVARLRADARIAPGQTSRLAFNLD 356 Query: 356 RMHAFDKETEKAI 368 + FD ++EK I Sbjct: 357 KAVFFDPQSEKRI 369 Lambda K H 0.319 0.138 0.387 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: 351 Number of extensions: 10 Number of successful extensions: 3 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: 369 Length of database: 370 Length adjustment: 30 Effective length of query: 339 Effective length of database: 340 Effective search space: 115260 Effective search space used: 115260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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