Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Synpcc7942_0427 Synpcc7942_0427 ATPase
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__SynE:Synpcc7942_0427 Length = 282 Score = 96.3 bits (238), Expect = 6e-25 Identities = 65/215 (30%), Positives = 110/215 (51%), Gaps = 24/215 (11%) Query: 14 KRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFR 73 K++G +++ F L PGE ++G NGAGKS+ I+ I+ P +G+I + G +Q Sbjct: 11 KQFGDRKVVNQLSFALAPGESFGLLGPNGAGKSTTIRMITTLTRPSQGQITIAGYDVQRD 70 Query: 74 SPMEARQAGIETVYQNLALSPALSIADNM-FLGREIRKPGIMGKWFRSLDRAAMEKQAR- 131 Q G+ V Q +++ ++ +N+ + GR P DR E+ R Sbjct: 71 RDRVRSQLGV--VLQQVSVKNDFTVWENLEYHGRLHHIP----------DRERQERINRW 118 Query: 132 ---AKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESR 188 +LS+ N V+TLSGG ++ + +ARA ++++DEPT L + R Sbjct: 119 LDYVELSD-------RRNDRVQTLSGGMKRRLQIARALLHEPSILLLDEPTVGLDPQTRR 171 Query: 189 RVLELILDVRRRGLPIVLISHNMPHVFEVADRIHI 223 R+ E+I D+ R+G+ ++L +H M V + DRI I Sbjct: 172 RIWEIIRDLNRQGMTVLLTTHYMEEVESLCDRIGI 206 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: 145 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: 260 Length of database: 282 Length adjustment: 25 Effective length of query: 235 Effective length of database: 257 Effective search space: 60395 Effective search space used: 60395 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: 47 (22.7 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