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_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 294 bits (753), Expect = 2e-84 Identities = 172/375 (45%), Positives = 227/375 (60%), Gaps = 48/375 (12%) Query: 1 MVELNLNHIYKKYPNS--SHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDIT 58 M L+L +I K+Y + ++ + + ++K+ EF+V VGPSGCGKST LRMVAGLE+I+ Sbjct: 1 MASLSLRNITKRYGHGPKANQVIHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEIS 60 Query: 59 KGELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKE 118 GEL+I VVND P RDIAMVFQNYALYPHM+ ++NMA+GLK+ K+ I RV + Sbjct: 61 GGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVDK 120 Query: 119 AAQILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEI 178 AA+IL L LERKP +LSGGQRQRVAMGRAIVR +VFL DEPLSNLDAKLR R EI Sbjct: 121 AAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLEI 180 Query: 179 AKIHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPA 238 K+HR +G T+++VTHDQ EAMTLA R+++M++ G +EQ GTP+E+Y+ PA Sbjct: 181 QKLHRELGITSLFVTHDQVEAMTLAQRMIVMNA----------GNMEQFGTPEEVYHTPA 230 Query: 239 NKFVAGFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIRPE 298 FVA FIGSP MN +L++ I GIRPE Sbjct: 231 TTFVASFIGSPPMN---------------------------LLKNAPGAQPGTILGIRPE 263 Query: 299 DISSSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTEFAARV-DARDFHEPGEKVS 357 + V+ TV+ ELLG+E ++Y ++ + RV + EP + Sbjct: 264 HLD----VRSEGWAVTVE----TVELLGAERLIYGRINGEQVIVRVEEGTHSPEPDSVIH 315 Query: 358 LTFNVAKGHFFDAET 372 + + H FDA T Sbjct: 316 VQPRADRLHAFDAAT 330 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: 359 Number of extensions: 15 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 377 Length of database: 334 Length adjustment: 29 Effective length of query: 348 Effective length of database: 305 Effective search space: 106140 Effective search space used: 106140 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