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 Pf6N2E2_1649 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1649 Length = 384 Score = 316 bits (809), Expect = 8e-91 Identities = 176/357 (49%), Positives = 238/357 (66%), Gaps = 7/357 (1%) Query: 8 LENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDG 67 L+NV K + +++ +L + EFVV +GPSGCGK+T LR+IAGL+ I DG + IDG Sbjct: 6 LDNVNKQLGGARI-LRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICDGDLLIDG 64 Query: 68 KVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIE 127 + VND+EP++R + MVFQ+YALYPHM+VY+N++FGLKL K K + RV + A+IL ++ Sbjct: 65 RRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKASLRERVLKTAQILQLD 124 Query: 128 NLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQ 187 LL RKPR+LSGGQRQRVA+GRA+ R P + LFDEPLSNLDA LRVQMR+E+ +LH RL Sbjct: 125 KLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHGRLG 184 Query: 188 ATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNA 247 +T+IYVTHDQVEAMT+ADKIVV+ G I+Q+G+P E+Y PA+ FVAGF+GSP MNF+ A Sbjct: 185 STMIYVTHDQVEAMTLADKIVVLNGGRIEQVGSPRELYEHPASRFVAGFLGSPKMNFLPA 244 Query: 248 RVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPENTI 307 R + G S P F D + + GIRPE + L A S + Sbjct: 245 R-LHSPGETSQIDSPLLGMTPLPF-DSAHLAVGSPLTLGIRPEHM--SLKAAQGSAGVGV 300 Query: 308 TGVVDVVEPLGSETILHVKVG-DDLIVASVNPRTQAKEEQKIDLVLDMTRMHAFDKE 363 GVV VE LGSET +H++ G D+ ++ + +++L L +H FD + Sbjct: 301 VGVVG-VEYLGSETYVHLESGEDEPLICRCEVNAGWRVGDRVELQLAFGSVHLFDAD 356 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: 374 Number of extensions: 15 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: 384 Length adjustment: 30 Effective length of query: 339 Effective length of database: 354 Effective search space: 120006 Effective search space used: 120006 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 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