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 GFF1915 PGA1_c19470 ABC transporter, ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__Phaeo:GFF1915 Length = 363 Score = 310 bits (793), Expect = 5e-89 Identities = 184/374 (49%), Positives = 242/374 (64%), Gaps = 27/374 (7%) Query: 3 MAQVVLENVTK--------VYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAG 54 M QV +E +T V V +K+ NL ++ EF+VLLG SGCGK+T L IAG Sbjct: 1 MKQVKIETMTSHVSARDLSVRFGAVEVLKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAG 60 Query: 55 LEEITDGKIYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEID 114 L+E T+G+I+I+ + V EPKDR +AMVFQ+YALYP MTV N+AFGL++ K PK E D Sbjct: 61 LQEATEGQIWINDENVTWREPKDRGLAMVFQSYALYPKMTVRGNLAFGLRMNKVPKAEAD 120 Query: 115 RRVREAAKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQ 174 + V EAA++L +E LLDR+P +LSGGQRQRVA+GRA+VR VFLFDEPLSNLDAKLR + Sbjct: 121 KLVDEAARVLQLEELLDRRPGELSGGQRQRVAIGRALVRKVDVFLFDEPLSNLDAKLRAE 180 Query: 175 MRSELKKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVA 234 +R ELK+LH L AT+IYVTHDQVEA+T+AD+I VMKDG +QQ+ +P EIY PAN +VA Sbjct: 181 LRVELKRLHQELGATMIYVTHDQVEALTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVA 240 Query: 235 GFIGSPPMNFVNARVVRGEGGLWIQASGFKVKVPKEFEDKLAN--YIDKEIIFGIRPEDI 292 F+G P MNFVN VV G IQ F++ + + LA+ E+ GIRPE + Sbjct: 241 QFVGLPSMNFVNG-VVTESGA--IQTEDFELALD---QCNLASTPAPGTEVEIGIRPEHV 294 Query: 293 YDKLFALAPSPENTITGVVDV--VEPLGSETILHVKVGDDLIVASVNPRTQAKEEQKIDL 350 + P N ++DV VE LGSE ++ KVG+ IV +P T + ++ + Sbjct: 295 H---------PANAGGFMLDVGMVELLGSERLIWGKVGNTSIVMRDDPDTTIRSGDQVRI 345 Query: 351 VLDMTRMHAFDKET 364 L F +T Sbjct: 346 NLKPGAFSVFSAKT 359 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: 318 Number of extensions: 14 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: 363 Length adjustment: 30 Effective length of query: 339 Effective length of database: 333 Effective search space: 112887 Effective search space used: 112887 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