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 RR42_RS18590 RR42_RS18590 hypothetical protein
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Cup4G11:RR42_RS18590 Length = 359 Score = 349 bits (895), Expect = e-101 Identities = 187/367 (50%), Positives = 252/367 (68%), Gaps = 9/367 (2%) Query: 3 MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62 MA V + + K + + V ++ ++ + D +F VL+GPSGCGK+T LRMIAGLEEIT G+ Sbjct: 1 MASVQIRGIQKYFGSTQV-IRGVDIDIADGQFTVLVGPSGCGKSTLLRMIAGLEEITTGE 59 Query: 63 IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122 I I +VVN + PK+RDIAMVFQNYALYPHMTVY+NMAF LKL K K+EI R+V +A+ Sbjct: 60 IAIGNRVVNRLPPKERDIAMVFQNYALYPHMTVYDNMAFSLKLAKGDKEEIKRKVAKASA 119 Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182 ILG+++LL+R PRQLSGGQRQRVA+GRAIVR+P+VFLFDEPLSNLDAKLRVQMR+E+K+L Sbjct: 120 ILGLDSLLERYPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRAEIKEL 179 Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242 H RL+ T +YVTHDQ+EAMTMAD+IVVM+DG ++Q G P +Y+ P N+FVAGFIGSP M Sbjct: 180 HQRLRTTSVYVTHDQIEAMTMADQIVVMRDGRVEQRGKPLALYDHPDNLFVAGFIGSPAM 239 Query: 243 NFVNARVVRGEGGLWIQ-ASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAP 301 NFV + R G ++ G ++ P F D A + +I+G+RPE + Sbjct: 240 NFVPGVLRRSGGDAAVEFPDGTRLPAPARF-DATAGTDGQRVIYGVRPEHL------TLG 292 Query: 302 SPENTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMHAFD 361 P + V VVEP G+ T ++ + + ++ R ++LV D H FD Sbjct: 293 MPGQGLQTRVSVVEPTGANTEIYSRFCEAEFISIFRERHDFAAGDILNLVPDHQHTHLFD 352 Query: 362 KETEKAI 368 ++ + + Sbjct: 353 ADSGQTL 359 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: 368 Number of extensions: 10 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: 359 Length adjustment: 29 Effective length of query: 340 Effective length of database: 330 Effective search space: 112200 Effective search space used: 112200 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