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_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= TCDB::Q9X103 (369 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 219 bits (558), Expect = 9e-62 Identities = 133/344 (38%), Positives = 192/344 (55%), Gaps = 41/344 (11%) Query: 3 MAQVVLENVTKVYENKVV-AVKNANLVVEDKEFVVLLGPSGCGKTTTLRMIAGLEEITDG 61 M+ + +NVTK Y AV NL + + E + LLGPSGCGKTTTLRM+AG E+ T G Sbjct: 1 MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60 Query: 62 KIYIDGKVVND----VEPKDRDIAMVFQNYALYPHMTVYENMAFGLKLRKYPKDEIDRRV 117 KI I +VV D + P+ R I MVFQ+YAL+PH+T+ +N+ FGL ++ + +R Sbjct: 61 KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLN--RWKNRDKKKRA 118 Query: 118 REAAKILGIENLLDRKPRQLSGGQRQRVAVGRAIVRNPKVFLFDEPLSNLDAKLRVQMRS 177 +E +++G+ R P +LSGGQ+QRVA+ RA+ PKV L DEP SNLDA LR +MR Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178 Query: 178 ELKKLHHRLQATIIYVTHDQVEAMTMADKIVVMKDGEIQQIGTPHEIYNSPANVFVAGFI 237 ++ + + AT I VTHDQ +A ++D++VVM +G IQQI P E+Y PAN FVA F+ Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNEGIIQQIAAPKEMYRCPANCFVAQFV 238 Query: 238 GS---------PPMNFVNARVVRGEGGLWIQASGFKVKVPKEFEDKLANYIDKEIIFGIR 288 G P + V + R V +P+E + + N ++ IR Sbjct: 239 GKTNLISGTLCPDLKHVETHIGR-------------VCLPQETDKVIEN-----VMVSIR 280 Query: 289 PEDIYDKLFALAPSPENTITGVVDVVEPLGSETILHVKVGDDLI 332 PE + + G+V+ V G +HV++ D + Sbjct: 281 PE-------GCRLAEKGRYAGLVERVTYSGEYQEVHVRLQSDQV 317 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: 307 Number of extensions: 18 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: 351 Length adjustment: 29 Effective length of query: 340 Effective length of database: 322 Effective search space: 109480 Effective search space used: 109480 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