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 GFF2209 HP15_2163 sugar ABC transporter, ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Marino:GFF2209 Length = 366 Score = 215 bits (547), Expect = 2e-60 Identities = 132/357 (36%), Positives = 203/357 (56%), Gaps = 20/357 (5%) Query: 3 MAQVVLENVTKVYENKVV-----AVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEE 57 MA++ L+++ Y + A++ + V LLGPSGCGK+T L +I+GL + Sbjct: 1 MAEIQLKSLAHSYSDMPTGPDDYAIRQLDHVWHKGGAYALLGPSGCGKSTMLNIISGLVQ 60 Query: 58 ITDGKIYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRV 117 ++G + DGK VN++ P+DR+IA VFQ +Y MTVY+N+AF LK K P +I RV Sbjct: 61 PSEGDVLFDGKRVNELSPRDRNIAQVFQFPVIYDSMTVYDNLAFPLKNNKVPASKIKARV 120 Query: 118 REAAKILGIENLLDRKPRQLSGGQRQRVAVGRAIVR-NPKVFLFDEPLSNLDAKLRVQMR 176 E A++L IE+ L +K + L+ ++Q+V++GR +VR + LFDEPL+ +D +L+ ++R Sbjct: 121 HEIAEVLEIEDKLYKKAKNLTADEKQKVSMGRGLVREDVSAILFDEPLTVIDPQLKWKLR 180 Query: 177 SELKKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGF 236 +LK++H + T++YVTHDQ+EA T ADKI VM G+I Q GTP E++ P + FV F Sbjct: 181 RKLKQIHEQFDITMVYVTHDQLEASTFADKIAVMYGGQIVQFGTPTELFEQPNHTFVGFF 240 Query: 237 IGSPPMNFVNA-RVVRGE--GGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIY 293 IGSP MN + R RG G + ++V D L I GIRPE + Sbjct: 241 IGSPGMNLIEVQRCPRGVCFGSTVVSLESWQV-------DVLQRTRSTNIKIGIRPEFVE 293 Query: 294 DKLFALAPSPENTITGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDL 350 + + ++T V VE LG+ I+ V++ + + + A K+ L Sbjct: 294 ----VSSVASDDTFEAEVLDVEDLGTYKIVTVQLDHEKMKVRQSEEFAASIGSKVHL 346 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: 310 Number of extensions: 16 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: 366 Length adjustment: 30 Effective length of query: 339 Effective length of database: 336 Effective search space: 113904 Effective search space used: 113904 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