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 AO353_25130 AO353_25130 ABC transporter
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25130 Length = 381 Score = 311 bits (798), Expect = 1e-89 Identities = 173/378 (45%), Positives = 243/378 (64%), Gaps = 32/378 (8%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M LKLDN+ K+ + + + +L+I EF+VFVGPSGCGKST LR+IAGL+ I G Sbjct: 1 MIKLKLDNVNKQLGGVR--ILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICAG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 +L ID++ +ND P++R + MVFQ+YALYPHMSVY+N++FGLKL K +K + +RV A Sbjct: 59 DLLIDERRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTEKSSLRERVLRTA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 +IL L + L+RKP +LSGGQRQRVAMGRA+ R+ + L DEPLSNLDA LRV MR EIA+ Sbjct: 119 QILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIAR 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H R+G+T IYVTHDQ EAMTLAD+IV+++ GR+EQ+G+P+ELY PA++ Sbjct: 179 LHARLGSTMIYVTHDQVEAMTLADKIVVLNG----------GRVEQVGSPRELYERPASR 228 Query: 241 FVAGFIGSPAMNFFEVTVE---KERLVNQDGLSL-ALPQGQEKILEEKGYLGKKVTLGIR 296 FVAGF+GSP MNF + + LV+ L + +LP + + ++LG+R Sbjct: 229 FVAGFLGSPRMNFLAARLHAPGETSLVDTPVLGMTSLPFDSSNLAAD-----TPLSLGVR 283 Query: 297 PEDISSDQIVHETFPNASVTADILVS--ELLGSESMLYVKFGSTE-FTARVNARDSHSPG 353 PE H + A T ++V+ E LGSE+ +++ G + R G Sbjct: 284 PE--------HVSLKAADGTVGVIVTGVEYLGSETYVHLDTGQDDPLICRCEVNAGWQVG 335 Query: 354 EKVQLTFNIAKGHFFDLE 371 ++V+L +I H FD + Sbjct: 336 DRVELQLDIGNLHLFDAD 353 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: 357 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: 381 Length adjustment: 30 Effective length of query: 347 Effective length of database: 351 Effective search space: 121797 Effective search space used: 121797 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