Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_078429421.1 BK574_RS17060 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_002019605.1:WP_078429421.1 Length = 351 Score = 224 bits (572), Expect = 2e-63 Identities = 128/302 (42%), Positives = 183/302 (60%), Gaps = 24/302 (7%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M+ ++ DN+ K Y A +V+ NL+I + E I +GPSGCGK+TTLRM+AG E T G Sbjct: 1 MSFIQFDNVTKYYNRAATPAVDQLNLEILEGEIITLLGPSGCGKTTTLRMLAGFEQPTTG 60 Query: 61 NLYIDDKLMND----ASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRV 116 + I D+++ D P+ R I MVFQ+YAL+PH+++ +N+ FGL ++K D KR Sbjct: 61 KIRIGDEVVYDDRRALPPEKRGIGMVFQDYALFPHLTIEKNVTFGLN--RWKNRDKKKRA 118 Query: 117 HEAAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRA 176 E E++GL EF R P++LSGGQ+QRVA+ RA+ KV LMDEP SNLDA LR MR Sbjct: 119 QEVLELVGLGEFGHRLPSELSGGQQQRVALARALAPRPKVILMDEPFSNLDAGLREKMRY 178 Query: 177 EIAKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNE 236 ++ I R+ AT I VTHDQ +A ++DR+V+M+ G I+QI P+E+Y Sbjct: 179 DVTNILRKANATAIIVTHDQKDAFAVSDRVVVMNE----------GIIQQIAAPKEMYRC 228 Query: 237 PANKFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIR 296 PAN FVA F+G + + + + + G + LPQ +K++E V + IR Sbjct: 229 PANCFVAQFVGKTNLISGTLCPDLKHVETHIG-RVCLPQETDKVIE-------NVMVSIR 280 Query: 297 PE 298 PE Sbjct: 281 PE 282 Lambda K H 0.318 0.135 0.379 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: 12 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: 377 Length of database: 351 Length adjustment: 29 Effective length of query: 348 Effective length of database: 322 Effective search space: 112056 Effective search space used: 112056 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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