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 PfGW456L13_1799 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1799 Length = 351 Score = 224 bits (572), Expect = 2e-63 Identities = 137/306 (44%), Positives = 185/306 (60%), Gaps = 25/306 (8%) Query: 1 MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60 M L L ++ K Y S +V+D +L + + + F+GPSGCGK+T LRM+AGLE ++ G Sbjct: 1 MSGLILENVEKHY--GSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGG 58 Query: 61 ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120 E+++DGE + R+ MVFQ+ AL+PHM+V +N+A+ LKLR SK RV E Sbjct: 59 EIRLDGEDIGHTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELL 118 Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180 +++ L + R A LSGGQRQRVA+ RAI K+ L+DEPLS LDAKLR SM+ EI + Sbjct: 119 ELIQLQAMINRPVAKLSGGQRQRVAIARAIANHPKILLLDEPLSALDAKLRESMQVEIRQ 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANK 240 + +R+ TTI VTHDQ EAMT+AD +V++ K V+QVGTP E+Y PAN+ Sbjct: 179 LQQRLNITTIMVTHDQREAMTMADIVVVLGEHK----------VQQVGTPIEIYRHPANE 228 Query: 241 FVAGFIGSPAMNFFDVTIKDGHLVS---KDGLTIAVTEGQLKMLESKGFKNKNLIFGIRP 297 FVA FIGS N F T+ VS D L + + + G K K L IRP Sbjct: 229 FVADFIGSG--NIFPATVLGNGKVSLPGGDALQVPICSSIV-----VGEKVKML---IRP 278 Query: 298 EDISSS 303 ED+ S Sbjct: 279 EDLQLS 284 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: 11 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: 351 Length adjustment: 29 Effective length of query: 348 Effective length of database: 322 Effective search space: 112056 Effective search space used: 112056 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: 49 (23.5 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