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 WP_090274680.1 BLU11_RS14815 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >NCBI__GCF_900105005.1:WP_090274680.1 Length = 378 Score = 224 bits (570), Expect = 4e-63 Identities = 135/337 (40%), Positives = 196/337 (58%), Gaps = 22/337 (6%) Query: 6 VVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYI 65 V +E V+K +++ +AV + L + E LLG SG GK+T LR++AG E ++G++ + Sbjct: 21 VKIERVSKQFDD-ALAVDDVTLTINRGEIFALLGGSGSGKSTLLRILAGFETPSEGRVLL 79 Query: 66 DGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILG 125 DG+ + + P R I M+FQ+YAL+PHMTV +N+AFGLK K EI RV E K++ Sbjct: 80 DGQNITALPPHKRPINMMFQSYALFPHMTVEQNIAFGLKQDKLSNTEISERVAEMLKLVH 139 Query: 126 IENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHR 185 + RKP QLSGGQRQRVA+ R++ + PK+ L DEP+ LD KLR QM+ EL ++ R Sbjct: 140 MAKYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIER 199 Query: 186 LQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFV 245 + T I VTHDQ EAMTMA +I +M G I Q+GTP +IY SP N VA F+GS +N Sbjct: 200 VGVTCIMVTHDQEEAMTMAQRIAIMDQGWIVQVGTPMDIYESPVNRHVAEFVGS--VNIF 257 Query: 246 NARVVRGEGGLWIQASGFKVKVPK-EFEDKLANYI-----DKEIIFGIRPEDIYDKLFAL 299 +V I ++ P+ + + L + + DK I+ +RPE K+F Sbjct: 258 EGEIVADMDDHVI------IECPQLDRQIYLGHGVTTRAEDKSAIYALRPE----KVFVT 307 Query: 300 APSPE---NTITGVVDVVEPLGSETILHVKVGDDLIV 333 PE N G V + LG ++ ++K+ +V Sbjct: 308 TEQPEQPYNWAHGEVHDIAYLGGHSVYYIKLDSGKMV 344 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: 345 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: 378 Length adjustment: 30 Effective length of query: 339 Effective length of database: 348 Effective search space: 117972 Effective search space used: 117972 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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