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 GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 318 bits (815), Expect = 2e-91 Identities = 173/374 (46%), Positives = 231/374 (61%), Gaps = 15/374 (4%) Query: 1 MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60 M L L ++ K Y NS +++D L I EF++ VGPSGCGKST + +AGLE+IT G Sbjct: 1 MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60 Query: 61 ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120 E+ +DGE ++ +PKDRDIAMVFQ+YALYP MSV DN+AFGLK+R I++ V A Sbjct: 61 EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120 Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180 ++L + LERKP+ LSGGQ+QRVAMGRA+ R K++L DEPLSNLDAKLRV MR EI Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANK 240 +H+R+ TT+YVTHDQ EAMTL D++ +M G ++Q GTP E+YN PAN Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKD----------GVIQQFGTPHEIYNNPANL 230 Query: 241 FVAGFIGSPAMNFFDVTI--KDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRPE 298 FVA FIGSP MNF + I +DG V E L + G +++ LI GIRPE Sbjct: 231 FVASFIGSPPMNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPE 290 Query: 299 DISSSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTEFAARVDARDFHEPGEKVSL 358 I L D ++ ++ V E G +T++ L Q + R+ GE ++L Sbjct: 291 QIG---LAPAGSADFSLAVDIEVVEPTGPDTLVVFTLNQVKACCRLAPDQAPRVGETLNL 347 Query: 359 TFNVAKGHFFDAET 372 F+ + FDA+T Sbjct: 348 QFDPRRALLFDAQT 361 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: 377 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: 390 Length adjustment: 30 Effective length of query: 347 Effective length of database: 360 Effective search space: 124920 Effective search space used: 124920 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