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_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein
Query= TCDB::Q9X103 (369 letters) >NCBI__GCF_000007345.1:WP_011020381.1 Length = 353 Score = 192 bits (487), Expect = 2e-53 Identities = 109/318 (34%), Positives = 176/318 (55%), Gaps = 10/318 (3%) Query: 22 VKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDGKIYIDGKVVNDVEPKDRDIA 81 +K +L E ++V L+GPSG GK+ L I G G ++++G+ + P R I+ Sbjct: 18 LKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQGSVFLEGRDITFFSPDKRQIS 77 Query: 82 MVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRVREAAKILGIENLLDRKPRQLSGGQ 141 +V+Q+ L+PHM ++EN+A+ L+ + K +I+ V + A +LGI LL RKP LSGG+ Sbjct: 78 IVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIAGVLGIRELLHRKPDTLSGGE 137 Query: 142 RQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRSELKKLHHRLQATIIYVTHDQVEAM 201 +QR ++ R++V PK+ L DEP S LDA+ R ++R LKK T+++VTHD + Sbjct: 138 KQRASLARSLVARPKLLLLDEPFSALDARTREKLREMLKKAIADYSTTVLHVTHDFEDVW 197 Query: 202 TMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFIGSPPMNFVNARVVRGEGGLW-IQA 260 +A+++VV++ GE+ Q+G P ++ P+ FVA F+G+ N + V EG L I A Sbjct: 198 ALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGT---NVLKGTVKALEGKLTVIDA 254 Query: 261 SGFKVKVPKEFEDKLANYIDKEIIFGIRPEDIYDKLFALAPSPENTITGVVDVVEPLGSE 320 G ++ E + + IRPE+I + S NT+ G V + Sbjct: 255 EGMEIYSADPAEP------GENVTVSIRPEEIILAGGTVESSARNTLKGRVSGIFKKEHL 308 Query: 321 TILHVKVGDDLIVASVNP 338 ++ VK+G+ I A V P Sbjct: 309 VVVEVKMGNSEIKAVVTP 326 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: 299 Number of extensions: 15 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