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 5207560 Shew_0094 ABC transporter-related protein (RefSeq)
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__PV4:5207560 Length = 369 Score = 149 bits (375), Expect = 2e-40 Identities = 93/257 (36%), Positives = 145/257 (56%), Gaps = 11/257 (4%) Query: 3 MAQVVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGK 62 M+Q V + K+++ + +A+ +A V + E + ++GPSG GK+T +RMIAGL + G+ Sbjct: 1 MSQDVADLSCKIFQQEGIAL-DAEFVCKAGEVLAVVGPSGGGKSTLMRMIAGLTKPESGE 59 Query: 63 IYIDGKVVNDVE------PKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRR 116 I V E P+ R + V Q++ L+P+MT N+ L PK E R Sbjct: 60 IRYGDSVWFSSESGRYLTPQQRHLGYVPQHFGLFPNMTALANVVAALD--HIPKAERVAR 117 Query: 117 VREAAKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMR 176 ++ + + + L DR P LSGGQRQRVA+ RA+ R P+V L DEP S +D + R ++ Sbjct: 118 AKDWLERVNLHGLPDRLPANLSGGQRQRVALARALAREPRVLLLDEPFSAVDRETRERLY 177 Query: 177 SELKKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGF 236 EL +L +L +I VTHD EA+ +AD+++++ G + Q G+P E+ + P N VA Sbjct: 178 LELARLKEQLAIPVIMVTHDLNEALLLADRMILISQGTLLQQGSPREVLSRPRNEAVAKQ 237 Query: 237 IGSPPMNFVNARVVRGE 253 +G N +A VV E Sbjct: 238 MGL--RNLFDAHVVAQE 252 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: 247 Number of extensions: 9 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: 369 Length adjustment: 30 Effective length of query: 339 Effective length of database: 339 Effective search space: 114921 Effective search space used: 114921 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