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_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q9X103 (369 letters) >NCBI__GCF_002115805.1:WP_085637757.1 Length = 365 Score = 333 bits (855), Expect = 3e-96 Identities = 181/357 (50%), Positives = 247/357 (69%), Gaps = 3/357 (0%) Query: 8 LENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDG 67 ++N+ K Y + +K+ N+ +E +F+VL+GPSGCGK+T L IAGLE IT G I I G Sbjct: 7 IKNLYKSYGTTEI-LKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSINIGG 65 Query: 68 KVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIE 127 K + V PKDRDIAMVFQ+YALYP MTV +N+ FG+K+R + DR++ + A+ L IE Sbjct: 66 KDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQLQIE 125 Query: 128 NLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQ 187 LL+R+P QLSGGQRQRVA+GRA+VR+PK+FLFDEPLSNLDAKLRV+MR+E+K LHH L Sbjct: 126 PLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHHNLG 185 Query: 188 ATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNA 247 A+++YVTHDQ+EAMT+A KIVVMK G IQQIG+P EIYN PAN+FVA F+GSP MN + A Sbjct: 186 ASMVYVTHDQIEAMTLATKIVVMKGGVIQQIGSPAEIYNRPANLFVADFMGSPAMNLIPA 245 Query: 248 RVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPENTI 307 + R + G I+ + K P D + +++I G+RPEDI D A + + Sbjct: 246 KAHRADEGTRIEITR-KSGEPIVLTDTKNRDLPEDVILGVRPEDIADPDLRGAEAAQ-AA 303 Query: 308 TGVVDVVEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDLVLDMTRMHAFDKET 364 ++D+VEP G++T +++G + A ++ T AK Q L D+ ++ F ET Sbjct: 304 ECLIDMVEPAGADTFAVMQLGGKHVTARLHAETTAKPGQPKRLSFDLGKVSYFAPET 360 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: 354 Number of extensions: 21 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: 365 Length adjustment: 30 Effective length of query: 339 Effective length of database: 335 Effective search space: 113565 Effective search space used: 113565 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 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