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_013723230.1 ALIDE2_RS22605 putative 2-aminoethylphosphonate ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000204645.1:WP_013723230.1 Length = 377 Score = 207 bits (528), Expect = 3e-58 Identities = 116/296 (39%), Positives = 183/296 (61%), Gaps = 19/296 (6%) Query: 4 LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63 L++ I+K + N ++ + +L + E + F+GPSGCGK+T LR+IAGLE T G++ Sbjct: 20 LEIKGIHKNFENFS--ALRDIDLTVRQGEMLCFLGPSGCGKTTLLRIIAGLETQTSGSIV 77 Query: 64 IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123 + ++ +RD +VFQ+YAL+P++++ EN+A+GL K +K +I RV E + Sbjct: 78 QSGRDISWLPASERDYGIVFQSYALFPNLTIAENVAYGLVNGKMRKAEIQARVAELLAMA 137 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183 GL + P+ LSGGQ+QRVA+ RA+ + + L+DEPLS LDA +RV +RAEI ++ + Sbjct: 138 GLPTAGGKYPSQLSGGQQQRVALARALATNPGLLLLDEPLSALDATVRVRLRAEIRRLQK 197 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243 ++G TTI VTHDQ EA++++DRIV+M+ G IEQ+GTP E+Y PA+ FVA Sbjct: 198 QVGITTIMVTHDQEEALSMSDRIVVMNH----------GVIEQVGTPMEIYERPASPFVA 247 Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPED 299 F+G +V V + + + + + + + E LG+ V+L +RPED Sbjct: 248 NFVG-------KVNVLRGQALGGKRFRVGKMEIECEASEGSFRLGEDVSLYLRPED 296 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: 337 Number of extensions: 17 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: 377 Length of database: 377 Length adjustment: 30 Effective length of query: 347 Effective length of database: 347 Effective search space: 120409 Effective search space used: 120409 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: 50 (23.9 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