Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Synpcc7942_1680 Synpcc7942_1680 Sulphate transport system permease protein 1
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__SynE:Synpcc7942_1680 Length = 338 Score = 92.8 bits (229), Expect = 8e-24 Identities = 69/237 (29%), Positives = 122/237 (51%), Gaps = 20/237 (8%) Query: 14 KRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFR 73 K++G A+ D + G ++A++G +G+GKS++++ I+G PD G I L G+ Sbjct: 10 KQFGSFQAVKDVDLTVETGSLVALLGPSGSGKSTLLRLIAGLEQPDSGRIFLTGRDATNE 69 Query: 74 SPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAK 133 S + RQ G V+Q+ AL L++ N+ G E+RK +++ RA+ Sbjct: 70 S-VRDRQIGF--VFQHYALFKHLTVRKNIAFGLELRK--------------HTKEKVRAR 112 Query: 134 LSE-LGLMTIQNINQAVET-LSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVL 191 + E L L+ + + + LSGGQRQ VA+ARA A +V+++DEP AL K + + Sbjct: 113 VEELLELVQLTGLGDRYPSQLSGGQRQRVALARALAVQPQVLLLDEPFGALDAKVRKDLR 172 Query: 192 ELILDVRRR-GLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFM 247 + + + V ++H+ EVAD+I + G+ + +P + + A F+ Sbjct: 173 SWLRKLHDEVHVTTVFVTHDQEEAMEVADQIVVMNHGKVEQIGSPAEIYDNPATPFV 229 Lambda K H 0.321 0.136 0.383 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: 166 Number of extensions: 14 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: 260 Length of database: 338 Length adjustment: 26 Effective length of query: 234 Effective length of database: 312 Effective search space: 73008 Effective search space used: 73008 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: 48 (23.1 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