Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23205 Length = 517 Score = 144 bits (362), Expect = 5e-39 Identities = 82/244 (33%), Positives = 133/244 (54%), Gaps = 8/244 (3%) Query: 6 ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65 +L + K + V AL + PG +LA++G+NGAGKS+++K I+G PD GE+RL Sbjct: 26 LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 85 Query: 66 EGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAA 125 GKP+ F +P+ A QAGI ++Q L L P +SIA+N+++GRE +D Sbjct: 86 RGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE------QLNGLHMVDHGE 139 Query: 126 MEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVK 185 M + L L + + + V LS +RQ V +A+A ++ S ++IMDEPT+A+ Sbjct: 140 MHRCTARLLERLRIKL--DPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITET 197 Query: 186 ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVA 245 E + +I D++ +G I+ I+H M VF +AD + + R G + + ++ Sbjct: 198 EVAHLFSIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQRADSMDGDSLIS 257 Query: 246 FMTG 249 M G Sbjct: 258 MMVG 261 Score = 102 bits (254), Expect = 2e-26 Identities = 63/226 (27%), Positives = 116/226 (51%), Gaps = 9/226 (3%) Query: 27 FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETV 86 FDL+ GEIL + G G+G++++ +AI G GEIRL+G+P++ P A + G + Sbjct: 296 FDLHAGEILGIAGLMGSGRTNVAEAIFGVTPSTGGEIRLDGQPVRISDPHMAIEKGFALL 355 Query: 87 YQNLALS---PALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQ 143 ++ LS P LS+ +NM + P +G F + + A+ +L + T Sbjct: 356 TEDRKLSGLFPCLSVLENMEMAV---LPHYVGNGF--IQQKALRALCEDMCKKLRVKT-P 409 Query: 144 NINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGLP 203 ++ Q ++TLSGG +Q +AR +++I+DEPT + V + LI + G+ Sbjct: 410 SLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMA 469 Query: 204 IVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTG 249 +++IS +P V ++DR+ + G + ++ + T + +G Sbjct: 470 VIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 515 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: 292 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 517 Length adjustment: 30 Effective length of query: 230 Effective length of database: 487 Effective search space: 112010 Effective search space used: 112010 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