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 206675 DVU1236 amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >MicrobesOnline__882:206675 Length = 247 Score = 156 bits (395), Expect = 5e-43 Identities = 88/237 (37%), Positives = 143/237 (60%), Gaps = 7/237 (2%) Query: 6 VVLENVTKVYENKVVAVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYI 65 + + NV K + ++ A+ + +L V+ E VV++GPSG GK+T LR I LE + G I + Sbjct: 9 ISIRNVWKFF-GELTALHDVSLDVQAGEKVVIIGPSGSGKSTLLRSINRLENVDKGSIIV 67 Query: 66 DGKVV----NDVEPKDRDIAMVFQNYALYPHMTVYENMAFG-LKLRKYPKDEIDRRVREA 120 DGK + +D+ +D+ MVFQ++ L+PH TV +N+ ++LRK P+DE + R + Sbjct: 68 DGKDIRAEDSDINVIRQDLGMVFQSFNLFPHKTVLQNLTMAPMRLRKVPRDEAESRALDL 127 Query: 121 AKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELK 180 K +GI + + P LSGGQ+QRVA+ RA+ NPK+ LFDEP S LD ++ ++ + Sbjct: 128 LKKVGISDKANVYPAMLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMIGEVLDVMV 187 Query: 181 KLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFI 237 L + T++ VTH+ A +AD+I+ M G+I + GTP + +P + + F+ Sbjct: 188 TL-AKEGMTMVCVTHEMGFAREVADRIIFMDHGQILEQGTPQHFFEAPEHPRLQKFL 243 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: 220 Number of extensions: 10 Number of successful extensions: 4 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: 247 Length adjustment: 27 Effective length of query: 342 Effective length of database: 220 Effective search space: 75240 Effective search space used: 75240 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: 48 (23.1 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