Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate Pf1N1B4_5115 Maltose/maltodextrin transport ATP-binding protein MalK (EC 3.6.3.19)
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5115 Length = 381 Score = 322 bits (824), Expect = 1e-92 Identities = 183/379 (48%), Positives = 240/379 (63%), Gaps = 22/379 (5%) Query: 1 MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60 +++L L+++ K+ + D L+I EF+VFVGPSGCGKST LR++AGL+ I G Sbjct: 1 VIKLKLDNVNKQLGGMR--ILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGG 58 Query: 61 ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120 +L IDG VND P++R + MVFQ+YALYPHMSVYDN++FGLKL K ++ +RV + A Sbjct: 59 DLLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTA 118 Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180 QIL L + L+RKP +LSGGQRQRVAMGRA+ R+ + L DEPLSNLDA LRV MR EIA+ Sbjct: 119 QILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIAR 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANK 240 +H R+G+T IYVTHDQ EAMTLAD+IV+++ GRVEQVG+P+ELY RPA++ Sbjct: 179 LHDRLGSTMIYVTHDQVEAMTLADKIVVLNG----------GRVEQVGSPRELYERPASR 228 Query: 241 FVAGFIGSPAMNFFDVTIK-DGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRPED 299 FVAGF+GSP MNF ++ G D L +T L S L GIRPE Sbjct: 229 FVAGFLGSPRMNFLSARLQTPGETSLVDTLVWGIT--SLPFDSSNLAAGTPLSLGIRPEH 286 Query: 300 ISSSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTE-FAARVDARDFHEPGEKVSL 358 +S D T V E LGSET ++L+ GQ E R + + G++V L Sbjct: 287 VSLKA------ADGTAGVVVTAVEYLGSETYVHLETGQDEPLICRCEVSAGWQAGDRVEL 340 Query: 359 TFNVAKGHFFDAETEAAIR 377 ++ H FDA+ A R Sbjct: 341 LLDLDNLHLFDADGVALSR 359 Lambda K H 0.318 0.135 0.375 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: 13 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: 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 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