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_069331237.1 C8J29_RS14155 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= TCDB::Q9X103 (369 letters) >NCBI__GCF_003046325.1:WP_069331237.1 Length = 349 Score = 333 bits (855), Expect = 3e-96 Identities = 186/368 (50%), Positives = 246/368 (66%), Gaps = 21/368 (5%) Query: 3 MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62 MA++ L +V K Y V + +L + D EFVV++GPSGCGK+T LRM+AGLEEIT G+ Sbjct: 1 MAEISLRDVRKSYSGLEV-IHGVDLEIADGEFVVIVGPSGCGKSTLLRMVAGLEEITAGE 59 Query: 63 IYIDGKVVNDVEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAK 122 I I G+VVN +EP++RDIAMVFQNYALYPHMTV ENMA+GL++ K K EI+ RV +AK Sbjct: 60 IAIGGRVVNRLEPRERDIAMVFQNYALYPHMTVRENMAYGLRIAKLSKAEIEERVARSAK 119 Query: 123 ILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKL 182 +L + LLDRKPRQLSGGQRQRVA+GRA+VRNP FL DEPLSNLDAKLRVQMR ++K+L Sbjct: 120 MLELGQLLDRKPRQLSGGQRQRVAMGRALVRNPAAFLLDEPLSNLDAKLRVQMRLQIKEL 179 Query: 183 HHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPM 242 ++ T IYVTHDQVEAMT+AD++VVM G +QI TP EIY+ PA FVAGFIGSP M Sbjct: 180 QRTVRTTSIYVTHDQVEAMTLADRLVVMNAGVAEQIATPAEIYDRPATTFVAGFIGSPAM 239 Query: 243 NFVNARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPS 302 N + AR + G ++ +G ++ VP +++I GIRPE ++ A Sbjct: 240 NMLPARGL----GDALEVAGQRLAVPAP--------AGRDLILGIRPEHLHP-----AGP 282 Query: 303 PENTITGVVDVVEPLGSETILHVKVGD--DLIVASVNPRTQAKEEQKIDLVLDMTRMHAF 360 E V VE LG++ H + D DL++ + + +E ++ + D +H F Sbjct: 283 EEPGFELHVQAVEWLGADAFAHGSLADGTDLVLRTPG-KAPVRERDRLKVAPDAAALHLF 341 Query: 361 DKETEKAI 368 D T + + Sbjct: 342 DAGTGRRL 349 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: 14 Number of successful extensions: 1 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: 349 Length adjustment: 29 Effective length of query: 340 Effective length of database: 320 Effective search space: 108800 Effective search space used: 108800 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