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 SM_b20235 SM_b20235 sugar ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Smeli:SM_b20235 Length = 363 Score = 353 bits (905), Expect = e-102 Identities = 198/366 (54%), Positives = 244/366 (66%), Gaps = 27/366 (7%) Query: 3 MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62 MA V + NV K + + V + + D EFV L+GPSGCGK+T LRMIAGLEEI+DG Sbjct: 1 MASVEIRNVVKRF-GALEVVHGVSAEIADGEFVALVGPSGCGKSTLLRMIAGLEEISDGA 59 Query: 63 IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122 + I G +VN+V PKDR+I+MVFQNYALYPHMTV ENMAF L+L + PKDE R+V EAA Sbjct: 60 VVIGGDIVNEVAPKDRNISMVFQNYALYPHMTVAENMAFALRLARLPKDEQKRKVGEAAT 119 Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182 +LG+ LLDR P QLSGGQRQRVA+GRAIVR P+VFLFDEPLSNLDAKLRVQMR+E+K L Sbjct: 120 MLGLGGLLDRYPGQLSGGQRQRVAMGRAIVRRPEVFLFDEPLSNLDAKLRVQMRAEIKGL 179 Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242 H RL+ T IYVTHDQ+EAMTMAD+IVVM+DG ++QIGTP EI++ P N+FVA FIGSP M Sbjct: 180 HQRLRTTSIYVTHDQIEAMTMADRIVVMRDGNVEQIGTPLEIFDYPRNLFVASFIGSPSM 239 Query: 243 NFVNARVV----RGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFA 298 NF+ VV R GG+ I A K P + GIRP + ++ A Sbjct: 240 NFIEGEVVGGTFRAPGGIIIPAPDLAHKGP--------------TVAGIRPNKL--QIGA 283 Query: 299 LAPSPENTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMH 358 PS + V +VEP G ET L V++G + + RT +I L +H Sbjct: 284 TGPSAK------VLIVEPTGDETHLLVELGGAQLAMLLRERTSLAPGDEIGLAFASADVH 337 Query: 359 AFDKET 364 FD +T Sbjct: 338 FFDGQT 343 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: 374 Number of extensions: 9 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: 369 Length of database: 363 Length adjustment: 30 Effective length of query: 339 Effective length of database: 333 Effective search space: 112887 Effective search space used: 112887 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