Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286 Length = 526 Score = 148 bits (374), Expect = 2e-40 Identities = 86/236 (36%), Positives = 134/236 (56%), Gaps = 8/236 (3%) Query: 14 KRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFR 73 K + V AL + PG +LA++G+NGAGKS+++K I+G PD GE+RL GKP+ F Sbjct: 40 KGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRLRGKPVVFE 99 Query: 74 SPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAK 133 +P+ A QAGI ++Q L L P +SIA+N+++GRE +D M + AK Sbjct: 100 TPLAALQAGIAMIHQELNLMPHMSIAENIWIGRE------QLNGLHMIDHREMHR-CTAK 152 Query: 134 LSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLEL 193 L E L + + V LS +RQ V +A+A ++ S ++IMDEPT+A+ KE + + Sbjct: 153 LLE-RLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 211 Query: 194 ILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTG 249 I D++R+G I+ I+H M VF +AD + + R G + + ++ M G Sbjct: 212 IADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVG 267 Score = 101 bits (251), Expect = 4e-26 Identities = 63/226 (27%), Positives = 116/226 (51%), Gaps = 9/226 (3%) Query: 27 FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETV 86 FDL+ GEIL + G G+G++++ +AI G D GEIRL+G+ ++ P A + G + Sbjct: 302 FDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGFALL 361 Query: 87 YQNLALS---PALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQ 143 ++ LS P LS+ +NM + P +G F + + A+ +L + T Sbjct: 362 TEDRKLSGLFPCLSVLENMEMAV---LPHYVGNGF--IQQKALRALCEDMCKKLRVKT-P 415 Query: 144 NINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGLP 203 ++ Q ++TLSGG +Q +AR +++I+DEPT + V + LI + G+ Sbjct: 416 SLEQCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMA 475 Query: 204 IVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTG 249 +++IS +P V ++DR+ + G + ++ + T + +G Sbjct: 476 VIMISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 521 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: 291 Number of extensions: 12 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: 526 Length adjustment: 30 Effective length of query: 230 Effective length of database: 496 Effective search space: 114080 Effective search space used: 114080 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