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 GFF3591 Psest_3658 spermidine/putrescine ABC transporter ATP-binding subunit
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__psRCH2:GFF3591 Length = 369 Score = 222 bits (566), Expect = 1e-62 Identities = 123/296 (41%), Positives = 177/296 (59%), Gaps = 22/296 (7%) Query: 9 IYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEV 68 I K Y S V D +LDI+ EF+ +GPSG GK+T+L M+AG E T GE+ +DG Sbjct: 16 IQKSYDGES-LIVRDLNLDIRRGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEILLDGRA 74 Query: 69 VNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEF 128 +N+ P RD+ MVFQNYAL+PHM+V +N+AF L +R +K I +RVK A ++ L F Sbjct: 75 INNVPPHKRDMGMVFQNYALFPHMTVSENLAFPLSVRGMAKPDIKERVKRALAMVQLEGF 134 Query: 129 LERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGAT 188 R PA LSGGQ+QRVA+ RA+V + ++ LMDEPL LD +LR M+ EI +H R+G T Sbjct: 135 RNRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREQMQMEIKHLHERLGVT 194 Query: 189 TIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGFIGS 248 +YVTHDQ EA+T++DR+ + G+++Q+ P+ LY +P N FVA F+G Sbjct: 195 VVYVTHDQGEALTMSDRVAVFHQ----------GQIQQIEDPRTLYEKPVNTFVANFLG- 243 Query: 249 PAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLE----SKGFKNKNLIFGIRPEDI 300 + HL+ + G + V G+ + +E + G + IRPE + Sbjct: 244 ------ENNRLPAHLLDRRGDSCTVKLGRGETVEALAVNVGAAGTPVSLSIRPERV 293 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: 300 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: 369 Length adjustment: 30 Effective length of query: 347 Effective length of database: 339 Effective search space: 117633 Effective search space used: 117633 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