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 Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 287 bits (735), Expect = 3e-82 Identities = 160/349 (45%), Positives = 214/349 (61%), Gaps = 26/349 (7%) Query: 25 DLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVVNDKAPKDRDIAMVFQ 84 D+ + EF++ VGPSGCGKST L ++AGL++ T+GE++I G+ V P+DRDIAMVFQ Sbjct: 28 DIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTEGEIRIGGKNVVGMPPRDRDIAMVFQ 87 Query: 85 NYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQILGLTEFLERKPADLSGGQRQRV 144 +YALYP +SV DN+ F L++R K KR+ E A +L ++ L+R+P+ LSGGQRQRV Sbjct: 88 SYALYPTLSVADNIGFALEMRKMPKPERQKRIDEVAAMLQISHLLDRRPSQLSGGQRQRV 147 Query: 145 AMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRIGATTIYVTHDQTEAMTLAD 204 AMGRA+ R ++FL DEPLSNLDAKLRV MRAEI ++H+ G T++YVTHDQ EAMTL Sbjct: 148 AMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIKRLHQASGITSVYVTHDQVEAMTLGS 207 Query: 205 RIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGFIGSPAMNFFDVTIKDGHLV 264 RI +M G V+Q+GTP E+YNRPAN +VA FIGSP MN + G Sbjct: 208 RIAVMKG----------GVVQQLGTPDEIYNRPANTYVATFIGSPTMNLLRGAVTGGQF- 256 Query: 265 SKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRPEDISSSLLVQETYPDATVDAEVVVSEL 324 G+ +G L ++ G+RPE L++QET P V V E Sbjct: 257 ---GI-----QGAALNLAPPPSSANEVLLGVRPE----HLVMQETAP---WRGRVSVVEP 301 Query: 325 LGSETMLYLKLGQTEFAARVDARDFHEPGEKVSLTFNVAKGHFFDAETE 373 G +T + + R DA+ +PGE V L A H+FDA++E Sbjct: 302 TGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSE 350 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: 334 Number of extensions: 11 Number of successful extensions: 3 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: 355 Length adjustment: 30 Effective length of query: 347 Effective length of database: 325 Effective search space: 112775 Effective search space used: 112775 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