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 Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= TCDB::Q9X103 (369 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 241 bits (615), Expect = 2e-68 Identities = 140/326 (42%), Positives = 197/326 (60%), Gaps = 27/326 (8%) Query: 21 AVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDGKVVNDVEPKDRDI 80 AVK+ +L VE V LLGPSG GK+T LR+IAGLE+ G+I++ G+ + +DR I Sbjct: 17 AVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLTGRDATNESVRDRQI 76 Query: 81 AMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIENLLDRKPRQLSGG 140 VFQ+YAL+ H+TV +N+AFGL+LRK+ K+++ RV E +++ + L DR P QLSGG Sbjct: 77 GFVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARVEELLELVQLTGLGDRYPSQLSGG 136 Query: 141 QRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQATIIYVTHDQVEA 200 QRQRVA+ RA+ P+V L DEP LDAK+R +RS L+KLH + T ++VTHDQ EA Sbjct: 137 QRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWLRKLHDEVHVTTVFVTHDQEEA 196 Query: 201 MTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNARVVRGEGGLWIQA 260 M +AD+IVVM G+++QIG+P EIY++PA FV FIG P+N V QA Sbjct: 197 MEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIG--PVN------VLPNSSHIFQA 248 Query: 261 SGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPENTITGVVDVVEPLGSE 320 G P+ F +RP DI A+ P PE T+ +D + LG E Sbjct: 249 GGLDTPHPEVF---------------LRPHDIE---IAIDPIPE-TVPARIDRIVHLGWE 289 Query: 321 TILHVKVGDDLIVASVNPRTQAKEEQ 346 V++ D ++ + PR + ++ Q Sbjct: 290 VQAEVRLEDGQVLVAHLPRDRYRDLQ 315 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: 342 Number of extensions: 10 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: 338 Length adjustment: 29 Effective length of query: 340 Effective length of database: 309 Effective search space: 105060 Effective search space used: 105060 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