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 WP_078717009.1 B5D49_RS06865 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= TCDB::Q00752 (377 letters) >NCBI__GCF_900167125.1:WP_078717009.1 Length = 370 Score = 230 bits (586), Expect = 5e-65 Identities = 134/311 (43%), Positives = 192/311 (61%), Gaps = 24/311 (7%) Query: 4 LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63 + L H+ K++ + + D LDI++ EF+ +GPSGCGK+T LR++AG E + GE+ Sbjct: 8 IRLEHVAKEFDGET--VLHDVCLDIRHGEFLTILGPSGCGKTTLLRLLAGFESPSSGEII 65 Query: 64 IDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQIL 123 +DG + D P R + VFQ+YAL+PHMSV+DN+AFGL++ K I +RV +A +++ Sbjct: 66 LDGRSMRDVPPDGRRVNTVFQSYALFPHMSVFDNVAFGLRMSGIPKVEIGERVAKALRMV 125 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHR 183 GL R+P LSGGQ+QRVA+ RA+V V L+DEPLS LD KLRV MR E+ ++ R Sbjct: 126 GLAGQAGRRPTSLSGGQQQRVAIARAVVNRPLVLLLDEPLSALDYKLRVQMRTELKQLRR 185 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVA 243 +G T I+VTHDQ EA +++DR+V+M+ G V QVGTP E+Y +P N FVA Sbjct: 186 EMGITFIFVTHDQEEAFSMSDRVVVMNE----------GCVAQVGTPVEVYEQPVNMFVA 235 Query: 244 GFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLES-KGFKNKNLI-FGIRPEDIS 301 F+G N F+ S G+ A+ EG+ L S +GF+ + I +RPED Sbjct: 236 RFVGE--TNVFEGVAGQ----SDGGILQALVEGRTCELSSHRGFQPGDRIRVLLRPED-- 287 Query: 302 SSLLVQETYPD 312 LLV+ P+ Sbjct: 288 --LLVEREEPE 296 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: 345 Number of extensions: 15 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: 370 Length adjustment: 30 Effective length of query: 347 Effective length of database: 340 Effective search space: 117980 Effective search space used: 117980 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