Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 147 bits (370), Expect = 6e-40 Identities = 81/223 (36%), Positives = 138/223 (61%), Gaps = 9/223 (4%) Query: 6 ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65 IL + + K Y V AL+ L+ GE+ A++G+NGAGKS+++K ++GA + D G+I Sbjct: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 Query: 66 EGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAA 125 G+P F +PM+A++AGI TVYQ + L P L++A N+FLG E R+ G+ + Sbjct: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGL-------IHFKK 116 Query: 126 MEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVK 185 M ARA L++ L +++ + S +Q +A+AR A +KV+++DEPTA+L K Sbjct: 117 MYADARAVLTQFKLDI--DVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAK 174 Query: 186 ESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGR 228 E + + ++ ++ +G+ IV I+H + V++++DRI + R G+ Sbjct: 175 EVQVLFGILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQ 217 Score = 73.2 bits (178), Expect = 1e-17 Identities = 49/197 (24%), Positives = 101/197 (51%), Gaps = 9/197 (4%) Query: 32 GEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETVYQNLA 91 G+ + + G G+G+S + A+ G D G I L G+ + P++A AGI ++ Sbjct: 284 GQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRK 343 Query: 92 LSPA---LSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQNINQA 148 + LSI +N+ L + R +G W+R L ++ A+ + +L + T + ++ Sbjct: 344 IDGIIGPLSIRENIILALQAR----IG-WWRYLSNTRQQEIAQFFIDKLQIAT-PDADKP 397 Query: 149 VETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGLPIVLIS 208 +E LSGG +Q V +AR A ++++DEPT + + +++LI + G+ +++ S Sbjct: 398 IEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVAS 457 Query: 209 HNMPHVFEVADRIHIHR 225 + + ++++ + R Sbjct: 458 SELDELVAFSNKVVVLR 474 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: 252 Number of extensions: 11 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: 499 Length adjustment: 29 Effective length of query: 231 Effective length of database: 470 Effective search space: 108570 Effective search space used: 108570 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