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 HSERO_RS16715 HSERO_RS16715 sugar ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__HerbieS:HSERO_RS16715 Length = 361 Score = 361 bits (927), Expect = e-104 Identities = 196/367 (53%), Positives = 259/367 (70%), Gaps = 10/367 (2%) Query: 3 MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62 MA V + V K + + + ++ ++ + D EF VL+GPSGCGK+T LRM+AGLEEIT G+ Sbjct: 1 MASVQIRAVKKQFGSTQI-IRGVDIDIADGEFTVLVGPSGCGKSTLLRMLAGLEEITGGE 59 Query: 63 IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122 I I G VVN+V+PKDRDIAMVFQNYALYPHMTV +NMAF L L K K +D RV++AA Sbjct: 60 ILIGGTVVNNVQPKDRDIAMVFQNYALYPHMTVRDNMAFSLTLAKKDKAFVDERVKKAAD 119 Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182 ILG+ LLDR PRQLSGGQRQRVA+GRAIVR+P+VFLFDEPLSNLDAKLRVQMR+E+K+L Sbjct: 120 ILGLNQLLDRYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRTEIKEL 179 Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242 H RL+ T IYVTHDQ+EAMTMAD+IVVM+DG ++Q G P ++Y+ PAN+FVAGFIGSP M Sbjct: 180 HQRLKTTSIYVTHDQIEAMTMADQIVVMRDGLVEQRGRPLDLYDYPANLFVAGFIGSPAM 239 Query: 243 NFVNARVVRGEGGLWIQ-ASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAP 301 NF+ A + R G ++ A G +VP + L +++ +G+RPE + ++ Sbjct: 240 NFIPATLRRNATGAEVEFADG--TRVPAPYGAALQGNDGQKVTYGVRPEHL-----SIGA 292 Query: 302 SPENTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMHAFD 361 + + T V+ VVEP G++T + + GD + + R I LV D +R H FD Sbjct: 293 AGQGIATKVI-VVEPTGADTEVFSRFGDTSLTSIFRERHDFGAGDVIHLVPDHSRTHLFD 351 Query: 362 KETEKAI 368 E+ K++ Sbjct: 352 AESGKSL 358 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: 398 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: 369 Length of database: 361 Length adjustment: 30 Effective length of query: 339 Effective length of database: 331 Effective search space: 112209 Effective search space used: 112209 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