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 AO356_28585 AO356_28585 ABC transporter
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28585 Length = 379 Score = 310 bits (793), Expect = 6e-89 Identities = 177/369 (47%), Positives = 236/369 (63%), Gaps = 24/369 (6%) Query: 4 LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63 LKLDN+ K+ A+ + + +L+I EF+VFVGPSGCGKST LR+IAGL+ I G+L Sbjct: 4 LKLDNVNKQLGGAR--ILRDVSLEISAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLL 61 Query: 64 IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123 ID + +ND P++R + MVFQ+YALYPHMSVY+N++FGLKL K +K + +RV + A+IL Sbjct: 62 IDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKTSLRERVLKTAQIL 121 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183 L + L+RKP +LSGGQRQRVAMGRA+ R+ + L DEPLSNLDA LRV MR EIA++H Sbjct: 122 QLDKLLQRKPRELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHG 181 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243 R+G+T IYVTHDQ EAMTLAD+IV+++ GRIEQ+G+P+ELY PA++FVA Sbjct: 182 RLGSTMIYVTHDQVEAMTLADKIVVLNG----------GRIEQVGSPRELYERPASRFVA 231 Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDISSD 303 GF+GSP MNF + +Q SL L +++LGIRPE Sbjct: 232 GFLGSPRMNFLAAFLHTPGETSQVE-SLVLGMTSLPFDSSGLAANTQLSLGIRPE----- 285 Query: 304 QIVHETFPNASVTADILVS--ELLGSESMLYVKFGSTE-FTARVNARDSHSPGEKVQLTF 360 H A TA I VS E LGSE+ +++ G + R G++V+L Sbjct: 286 ---HIALKAAQGTAGIAVSGVEYLGSETYVHLDTGQDDPMVCRCEVNAGWRVGDRVELQL 342 Query: 361 NIAKGHFFD 369 +I H FD Sbjct: 343 DIDNLHVFD 351 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: 356 Number of extensions: 18 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: 377 Length of database: 379 Length adjustment: 30 Effective length of query: 347 Effective length of database: 349 Effective search space: 121103 Effective search space used: 121103 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 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