Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 149 bits (375), Expect = 2e-40 Identities = 84/226 (37%), Positives = 135/226 (59%), Gaps = 15/226 (6%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P+++ +GL KR+G+V A D ++YPG + A++G+NGAGKS+++ ++G PD G I Sbjct: 23 PLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIA 82 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124 L+GKP++F S +A +AGI VYQ+ L ++++A+N+ LG+E G +F + Sbjct: 83 LDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE-------GSFFLN---- 131 Query: 125 AMEKQARAKLSELGLMTIQNINQA--VETLSGGQRQGVAVARAAAFGSKVVIMDEPTAAL 182 K+ R ++ EL + +I+ A V LS G++Q V + + S+V+I DEPTA L Sbjct: 132 --PKEMRNRVQELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVL 189 Query: 183 GVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGR 228 +E+ + E + + +G IV ISH + V VAD I I R GR Sbjct: 190 TPRETFHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGR 235 Score = 60.8 bits (146), Expect = 5e-14 Identities = 55/234 (23%), Positives = 102/234 (43%), Gaps = 10/234 (4%) Query: 22 LDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGK---PIQFRSPMEA 78 L+ FDL+ GE++AV+G G G+ ++++AI G P + + GK + + Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345 Query: 79 RQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELG 138 A I LA L++ DN+ L R+ G W LD+ + + + Sbjct: 346 SLAYIPEDRLGLATCRNLNLVDNLLL--TTRQGFARGPW---LDKKKAARDTTELIKKFD 400 Query: 139 LMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVR 198 + I LSGG Q +AR ++++ ++PT L + + +V +L R Sbjct: 401 IRP-GRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAR 459 Query: 199 RRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTGAKE 252 I+L++ ++ ++ADR+ + GR + V + D + + M E Sbjct: 460 EMA-GILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMMAGVE 512 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: 284 Number of extensions: 12 Number of successful extensions: 3 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: 514 Length adjustment: 29 Effective length of query: 231 Effective length of database: 485 Effective search space: 112035 Effective search space used: 112035 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 Apr 09 2024. 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