Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 209 bits (533), Expect = 7e-59 Identities = 108/242 (44%), Positives = 155/242 (64%), Gaps = 3/242 (1%) Query: 3 GLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFI 62 G+ + + K +G+ + +DL ++ G V +GPSG GKSTLLR+IAGLE+ G +F+ Sbjct: 2 GIQVSQVSKQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFL 61 Query: 63 DGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQ 122 G + R I VFQ YAL+ H+TV N+AFG+ + + +KE++ RV +++Q Sbjct: 62 TGRDATNESVRDRQIGFVFQHYALFKHLTVRKNIAFGLELRKHTKEKVRARVEELLELVQ 121 Query: 123 LTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSER 182 LT DR P LSGGQRQRVA+ RA+ P+V L DEP LDA +R R + KL + Sbjct: 122 LTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLRSWLRKLHDE 181 Query: 183 MSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNV 242 + TT ++VTHDQ EAM +AD+IVV++ G +EQ+G+P E+Y+ PA FV FIG +NV Sbjct: 182 VHVTT-VFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIG--PVNV 238 Query: 243 IP 244 +P Sbjct: 239 LP 240 Lambda K H 0.320 0.137 0.387 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: 314 Number of extensions: 8 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: 362 Length of database: 338 Length adjustment: 29 Effective length of query: 333 Effective length of database: 309 Effective search space: 102897 Effective search space used: 102897 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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