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_073037934.1 BUB04_RS06025 ABC transporter ATP-binding protein
Query= TCDB::Q00752 (377 letters) >NCBI__GCF_900129305.1:WP_073037934.1 Length = 365 Score = 259 bits (661), Expect = 1e-73 Identities = 152/375 (40%), Positives = 214/375 (57%), Gaps = 30/375 (8%) Query: 2 VELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGE 61 +++ + + K Y +V ++ + +V +GPSGCGK+T LR++AGLE +T G Sbjct: 1 MQIEIRDVRKDYGRVQ--AVRGVSFSVEEGQLLVILGPSGCGKTTLLRLIAGLEPVTSGT 58 Query: 62 LKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQ 121 + I G V P R+I+MVFQ+YAL+PH++V +N+ FGLK+R + I++R+K Sbjct: 59 IHIAGTDVTHLPPVKRNISMVFQSYALFPHLNVRENIIFGLKVRKVPADEIERRLKRVVD 118 Query: 122 ILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKI 181 +LGL+ L+ KP +LSGG +QRVA+GRAI+ + V LMDEPLSNLDAKLR SMR EI + Sbjct: 119 LLGLSGRLDSKPGELSGGMQQRVALGRAIIAEKPVTLMDEPLSNLDAKLRNSMRREICSL 178 Query: 182 HRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKF 241 RR+G T IYVTHDQ EAMT+ADRIV+M G++ Q +P+ Y RPAN F Sbjct: 179 QRRLGITMIYVTHDQVEAMTMADRIVLMRD----------GQIVQDDSPENFYERPANTF 228 Query: 242 VAGFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRPEDIS 301 VA FIG+P MN + G + G G+L G +FGIRPE++ Sbjct: 229 VARFIGTPPMNIVPLCPTQGGAALEPG-------GRLLF---PGMDPDRYLFGIRPENLR 278 Query: 302 SSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTEFAARVDARDFHEPGEKVSLTFN 361 L + P A V E LGS+T + ++ E R R G V LT++ Sbjct: 279 ---LAESGQP-----AMVTGREYLGSDTFVSCEIHGQEVIVRTRGRRNIREGTVVHLTWD 330 Query: 362 VAKGHFFDAETEAAI 376 + FDA T+ + Sbjct: 331 PGDVNLFDARTQERV 345 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: 340 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: 365 Length adjustment: 30 Effective length of query: 347 Effective length of database: 335 Effective search space: 116245 Effective search space used: 116245 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 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