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 GFF4209 Psest_4282 spermidine/putrescine ABC transporter ATP-binding subunit
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__psRCH2:GFF4209 Length = 383 Score = 219 bits (558), Expect = 1e-61 Identities = 131/340 (38%), Positives = 199/340 (58%), Gaps = 23/340 (6%) Query: 2 VELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGE 61 V L ++ + KK+ + +V+D L I E +G SG GKST LRM+AG E T+G Sbjct: 21 VLLKIDRVTKKFDET--VAVDDVSLSIHQGEIFALLGGSGSGKSTLLRMLAGFERPTEGR 78 Query: 62 LKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQ 121 + +DG+ + D P +R I M+FQ+YAL+PHM+V N+AFGLK K I++RVKE Sbjct: 79 IFLDGQDITDMPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDGLPKAEIEERVKEMLG 138 Query: 122 ILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKI 181 ++ +T++ +RKP LSGGQRQRVA+ R++ + K+ L+DEP+ LD KLR M+ E+ +I Sbjct: 139 LVQMTQYAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVQI 198 Query: 182 HRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKF 241 R+G T + VTHDQ EAMT+A+RI IM +G + QVG+P ++Y PA++ Sbjct: 199 IERVGVTCVMVTHDQEEAMTMAERIAIMH----------LGWIAQVGSPMDIYETPASRL 248 Query: 242 VAGFIGSPAMNFFD----VTIKDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRP 297 V FIG+ +N FD + D +++ GL + G S ++K + + IRP Sbjct: 249 VCEFIGN--VNLFDGELIEDMGDHAVIASPGLENPIYVGH---GISTRAEDKQITYAIRP 303 Query: 298 EDISSSLLVQETYPDATVDAEVVVSEL--LGSETMLYLKL 335 E + + E A+ VV ++ LG ++ Y+KL Sbjct: 304 EKLLIGTELPELERPGYNWAKGVVHDIAYLGGHSVYYIKL 343 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: 332 Number of extensions: 13 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: 383 Length adjustment: 30 Effective length of query: 347 Effective length of database: 353 Effective search space: 122491 Effective search space used: 122491 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