Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Synpcc7942_0960 Synpcc7942_0960 ATPase
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__SynE:Synpcc7942_0960 Length = 417 Score = 287 bits (735), Expect = 4e-82 Identities = 165/369 (44%), Positives = 224/369 (60%), Gaps = 31/369 (8%) Query: 19 VLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLPARERNV 78 VL+ ++L I DGEF+V++GPSGCGKST+LR++AGLE S G +++G V+ LPA+ R++ Sbjct: 49 VLNGINLEIADGEFMVVVGPSGCGKSTLLRLLAGLETPSRGLIKVGDRRVDRLPAKARDI 108 Query: 79 AMVFQNYALYPHMSVYDNIAFGLRRL-KRP-----------------------AAEIDRR 114 AMVFQ+YALYPH+SVYDN+AFGLRR RP A I RR Sbjct: 109 AMVFQSYALYPHLSVYDNLAFGLRRQGDRPWWQQQLALATRSLPKSLQYEPEQEARIKRR 168 Query: 115 VREVAALLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLR 174 VREVA +L L+ LL+R+P+ +SGGQ+QR A+ RAI + P VFL DEPLSNLDAKLRA+ R Sbjct: 169 VREVATMLQLDTLLDRQPKQLSGGQKQRVALGRAIARNPQVFLMDEPLSNLDAKLRAETR 228 Query: 175 GDIKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGF 234 I L ++L TT+YVTHDQ EAMT+ DR+ ++ G + Q SP E+Y P N F A F Sbjct: 229 AQIVSLQRQLGVTTLYVTHDQTEAMTMGDRIAVLNRGHLQQVASPLEIYDRPANRFVAQF 288 Query: 235 IGTPAMNFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGER 294 IG+P MN + TV R QL E E RL V+L +RP+H+ + Sbjct: 289 IGSPPMNLIPVTV-RAPLQLTTENFRCTLPEAWEPVLRLYDGQTVELGIRPEHLEVGA-- 345 Query: 295 EPAASLTCPVSVELVEILGADALLTTRCGDQ--TLTALVPADRLPQPGATLTLALDQHEL 352 AAS ++V VE LG+D + + + A + + Q G L L ++ Sbjct: 346 --AASKNLLITVTGVEALGSDTFIAGELKESGIAVQARLAPQQCWQMGDRLWLTFKPDQI 403 Query: 353 HVFDVESGE 361 H+FD+E+G+ Sbjct: 404 HLFDLETGK 412 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: 406 Number of extensions: 16 Number of successful extensions: 4 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: 417 Length adjustment: 31 Effective length of query: 375 Effective length of database: 386 Effective search space: 144750 Effective search space used: 144750 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: 50 (23.9 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