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_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 222 bits (566), Expect = 1e-62 Identities = 120/224 (53%), Positives = 157/224 (70%), Gaps = 6/224 (2%) Query: 22 VKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDGKVVND------VEP 75 +K +L V E V LLGPSG GKTT LR IAGLE + G I I ++V + V Sbjct: 21 LKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIRIGEQMVFESAKKIEVSV 80 Query: 76 KDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIENLLDRKPR 135 + R + VFQ+YAL+PH TVYEN+A+GLKLRK P EI +RV+E LG+ +L +R P Sbjct: 81 EKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQEVLANLGLGDLSERHPH 140 Query: 136 QLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQATIIYVTH 195 QLSGGQ+QRVA+ R++V NP+V L DEPLSNLDAKLR + R L++L L + + VTH Sbjct: 141 QLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIWLRQLIIDLNLSAVCVTH 200 Query: 196 DQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGS 239 DQ EAM MADK+V++KDG I+Q GTP E+Y +P ++FVA F+G+ Sbjct: 201 DQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMGA 244 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: 312 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: 353 Length adjustment: 29 Effective length of query: 340 Effective length of database: 324 Effective search space: 110160 Effective search space used: 110160 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 Apr 09 2024. 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