Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate RR42_RS32900 RR42_RS32900 sugar ABC transporter ATPase
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Cup4G11:RR42_RS32900 Length = 502 Score = 164 bits (415), Expect = 3e-45 Identities = 93/247 (37%), Positives = 140/247 (56%), Gaps = 7/247 (2%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P+ RG+ K + V ALD F +YPGE+ ++G+NGAGKSS++K + G D GE Sbjct: 9 PLFEMRGICKNFPGVKALDDVSFAIYPGEVHMLLGENGAGKSSLMKVLCGVYVADAGEFY 68 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124 +G P+ SP + GI ++Q +L P L IA N+FLGRE R G+ S+D A Sbjct: 69 HDGSPVAITSPADTMGLGIAVIFQEFSLVPYLDIAQNIFLGREPR-----GRIPGSVDAA 123 Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184 M +AR L LG+ + V L Q+Q V +A+A + ++++++DEPTAAL Sbjct: 124 RMHAEARRILDILGMEV--STRTPVHRLGVAQQQMVEIAKALSQNARILVLDEPTAALSD 181 Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244 +E+ ++ +I ++ G+ ++ ISH M VF + DRI I R GR++ P D T + V Sbjct: 182 RETEKLFAVIARLKADGVSMIYISHRMAEVFALGDRITILRDGRKVGACLPGDATPDELV 241 Query: 245 AFMTGAK 251 A M G K Sbjct: 242 ARMVGRK 248 Score = 82.4 bits (202), Expect = 2e-20 Identities = 59/200 (29%), Positives = 103/200 (51%), Gaps = 10/200 (5%) Query: 32 GEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIETVYQNL- 90 GEI+ + G G+G+S + +A+ GA +GEI + GK + P AR+ G + ++ Sbjct: 287 GEIVGLAGLVGSGRSEVARAVFGADPIRQGEIYIFGKRLT-GGPDRARELGAALIPESRK 345 Query: 91 --ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTIQNINQA 148 L+ ++ DN+ L R +W+R+ D+A E A +++ L + T NQ Sbjct: 346 SEGLALIRTVRDNLLLAGLRR--AFPARWYRA-DKA--EALAEREIARLRIATPDG-NQL 399 Query: 149 VETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGLPIVLIS 208 + LSGG +Q + + + +K+ I DEPT + V + LI + ++G ++LIS Sbjct: 400 AQFLSGGNQQKIVIGKWLVAEAKLFIFDEPTRGIDVGAKAEIFALIDSLVKQGAGVLLIS 459 Query: 209 HNMPHVFEVADRIHIHRLGR 228 +P + V DR ++ R GR Sbjct: 460 SELPEIINVCDRTYVMRGGR 479 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: 309 Number of extensions: 17 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: 502 Length adjustment: 29 Effective length of query: 231 Effective length of database: 473 Effective search space: 109263 Effective search space used: 109263 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