Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate BWI76_RS14860 BWI76_RS14860 ABC transporter
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Koxy:BWI76_RS14860 Length = 510 Score = 159 bits (401), Expect = 1e-43 Identities = 91/250 (36%), Positives = 152/250 (60%), Gaps = 10/250 (4%) Query: 1 MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 ++ P+L G+ KRYG AL+ FDL+ GE+ A++G+NGAGKS+++K +SG D Sbjct: 4 ISSPPLLRLEGISKRYGATLALNNVRFDLFAGEVHALMGENGAGKSTLMKILSGNEQRDS 63 Query: 61 GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRK-PGIMGKWFR 119 G I ++G+ I R+P +AR+ GI ++Q L P +++A+N+FLG+E GI Sbjct: 64 GVIFIDGQAIDIRTPRDARKYGIAIIHQELNTVPDMTVAENLFLGQEPTSFAGI------ 117 Query: 120 SLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPT 179 LDR M ++A+ KL+ + + + +LS G++Q V +ARA + +KV+++DEPT Sbjct: 118 -LDRKRMHREAKEKLNRINADI--DPQAPLGSLSIGRQQMVEIARAVSENAKVLVLDEPT 174 Query: 180 AALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYT 239 AAL E+ ++ LI +R+ G+ +V ISH M V+++A+R+ + R G + N + + Sbjct: 175 AALSRAETLQLYRLIAQMRQDGVGMVYISHRMEEVWQLANRVTVFRDGTWIGTENLGNVS 234 Query: 240 MSDAVAFMTG 249 +D V M G Sbjct: 235 TTDIVRMMVG 244 Score = 84.0 bits (206), Expect = 6e-21 Identities = 64/241 (26%), Positives = 114/241 (47%), Gaps = 25/241 (10%) Query: 20 TALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEAR 79 +A F++ GE++++ G G+G++ + + + GA +G +RL G+ Q P A Sbjct: 271 SATGPVSFEVSAGEVVSMSGLVGSGRTEVARLLFGADPRSQGSVRLAGRESQPSDPTAAI 330 Query: 80 QAGIETVY-----QNLALSPA------LSIADNMFLGREIRKPGIMGKWFRSLDRAAMEK 128 GI V Q L L + +S DN G +++ +++ A +E+ Sbjct: 331 ADGIGMVTEDRKTQGLFLGHSVEHNIDISSLDNFVAGGVVKR--------KTIRAAVLEQ 382 Query: 129 QARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESR 188 R +L E + V LSGG +Q A+AR S+++I+DEPT + + R Sbjct: 383 MRRLRLRE------NAVELPVSALSGGNQQKAALARWLLRDSRLLILDEPTRGVDIGAKR 436 Query: 189 RVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMT 248 + ELI + R G I++IS ++P ++DR+ + R GR + + T + + T Sbjct: 437 EIYELIDRLARAGKAILVISSDLPEAIGISDRVLVMRGGRIVHQLPSCSATEEEVMLHAT 496 Query: 249 G 249 G Sbjct: 497 G 497 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: 279 Number of extensions: 15 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: 510 Length adjustment: 29 Effective length of query: 231 Effective length of database: 481 Effective search space: 111111 Effective search space used: 111111 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