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 H281DRAFT_00169 H281DRAFT_00169 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Burk376:H281DRAFT_00169 Length = 371 Score = 361 bits (926), Expect = e-104 Identities = 188/370 (50%), Positives = 256/370 (69%), Gaps = 4/370 (1%) Query: 3 MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62 MA + + +V K Y N V +K N+ +ED +F++L+G SGCGK+T L MIAGLE +T G+ Sbjct: 1 MASLSIRDVYKTYPNGVPVLKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKGE 60 Query: 63 IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122 I IDGK VN++ PKDRDIAMVFQ+YALYP MTV EN++FGL +RK PK E + V + Sbjct: 61 IQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKQEQAQIVDRVSN 120 Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182 L I +LLDRKP QLSGGQRQRVA+GRA+ R+P +FLFDEPLSNLDAKLR++MRSE+K L Sbjct: 121 TLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKLL 180 Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242 H RL TI+YVTHDQ+EAMT+ D+I VMKDG +QQ G P EIY+SP+N+FVAGFIG+PPM Sbjct: 181 HQRLGTTIVYVTHDQIEAMTLGDRIAVMKDGIVQQFGAPQEIYDSPSNLFVAGFIGAPPM 240 Query: 243 NFVNARVV-RGEG-GLWIQASGFKVKVPKEFED-KLANYIDKEIIFGIRPEDIYDKLFAL 299 NF+ ++V +G G G+ + + + F+ K+ +++ +E+I G+RPE I D A Sbjct: 241 NFIQGKLVEQGAGVGIELDTGVTRTALNLPFDSAKVKSHVGREVILGLRPERITDARGAH 300 Query: 300 APSPE-NTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMH 358 I VDV+EP G +T++ +V +V+ V+P + + L+ D ++ Sbjct: 301 GDHARLQQIEVKVDVIEPTGPDTLVFAQVNGKRVVSRVHPASNPQPLTNTTLLFDTSKAV 360 Query: 359 AFDKETEKAI 368 FD E+ I Sbjct: 361 LFDPSNEERI 370 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: 386 Number of extensions: 17 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: 371 Length adjustment: 30 Effective length of query: 339 Effective length of database: 341 Effective search space: 115599 Effective search space used: 115599 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