Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 202 bits (513), Expect = 2e-56 Identities = 121/314 (38%), Positives = 172/314 (54%), Gaps = 25/314 (7%) Query: 23 LDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNVAMVF 82 +DL + G V LLGPSG GKST+LR+IAGLE G + + G + R+R + VF Sbjct: 21 VDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLTGRDATNESVRDRQIGFVF 80 Query: 83 QNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKPRAMSGGQQQR 142 Q+YAL+ H++V NIAFGL K ++ RV E+ L+ L L +R P +SGGQ+QR Sbjct: 81 QHYALFKHLTVRKNIAFGLELRKHTKEKVRARVEELLELVQLTGLGDRYPSQLSGGQRQR 140 Query: 143 AAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVTHDQLEAMTLA 202 A+ARA+ P V L DEP LDAK+R LR +++LH + TTV+VTHDQ EAM +A Sbjct: 141 VALARALAVQPQVLLLDEPFGALDAKVRKDLRSWLRKLHDEVHVTTVFVTHDQEEAMEVA 200 Query: 203 DRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDGQLFIETAHQR 262 D++++M G++ Q GSPAE+Y P F FIG + S + + G ++T H Sbjct: 201 DQIVVMNHGKVEQIGSPAEIYDNPATPFVMSFIGPVNVLPNSSHIFQAGG---LDTPHP- 256 Query: 263 WALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASLTCPVSVELVEILGADALLTTRC 322 ++ +RP + IA + P T P ++ + LG + R Sbjct: 257 -----------------EVFLRPHDIEIAIDPIPE---TVPARIDRIVHLGWEVQAEVRL 296 Query: 323 GD-QTLTALVPADR 335 D Q L A +P DR Sbjct: 297 EDGQVLVAHLPRDR 310 Lambda K H 0.321 0.137 0.403 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: 338 Number of extensions: 7 Number of successful extensions: 1 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: 406 Length of database: 338 Length adjustment: 30 Effective length of query: 376 Effective length of database: 308 Effective search space: 115808 Effective search space used: 115808 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