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_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 220 bits (560), Expect = 5e-62 Identities = 141/326 (43%), Positives = 193/326 (59%), Gaps = 17/326 (5%) Query: 6 VVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYI 65 + L + K + + +A++ +L + E VVLLGPSGCGKTTTLR+IAGLE G + + Sbjct: 7 ITLRHCGKTFADGTLALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVM 66 Query: 66 DGKVVNDVEP---KDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122 G NDV P + R + MVFQ+YAL+P+MTV EN+A+GL++R+ RRV E Sbjct: 67 FGD--NDVTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLA 124 Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182 ++ + +R+ QLSGGQRQRVA+ RAI P+V L DEPL+ LDAKLR +R+++ +L Sbjct: 125 MMHLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQL 184 Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242 L T +YVTHDQ EAM + D+I+VM G I Q GTP +IY +PAN FVA FIG+ M Sbjct: 185 LRSLHITAVYVTHDQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT--M 242 Query: 243 NFVNARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPS 302 N + A + E W G + A E++F RPED+ ALA + Sbjct: 243 NRLPAVL---EADAWRVPGGLVPRHGTAASLAAAPSPRAELLF--RPEDV-----ALAQA 292 Query: 303 PENTITGVVDVVEPLGSETILHVKVG 328 + + G V LG+ T L V VG Sbjct: 293 EDAHLGGSVVTALFLGNYTRLLVDVG 318 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: 306 Number of extensions: 11 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: 357 Length adjustment: 29 Effective length of query: 340 Effective length of database: 328 Effective search space: 111520 Effective search space used: 111520 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