Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 153 bits (386), Expect = 8e-42 Identities = 92/250 (36%), Positives = 141/250 (56%), Gaps = 10/250 (4%) Query: 1 MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 M+ EP+L +G+ K + + L +YPGEI A++G+NGAGKS+++K +SGA D Sbjct: 1 MSLEPLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADP 60 Query: 61 G-EIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFR 119 G EIR+ G+ I P A+ GI +YQ L+L P LS+A+N++LGRE+R+ W Sbjct: 61 GGEIRIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRG-----W-- 113 Query: 120 SLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPT 179 ++DR ME L LG V +LS +RQ V +ARA +K+++MDEPT Sbjct: 114 TIDRKGMEAGCIEVLQRLGAEFTPATR--VSSLSIAERQLVEIARALHAHAKILVMDEPT 171 Query: 180 AALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYT 239 L +E+ R+ LI +R +GL I+ ISH M ++ ++DR+ + R G + + + Sbjct: 172 TPLSSRETDRLFALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALS 231 Query: 240 MSDAVAFMTG 249 V M G Sbjct: 232 AEALVKMMVG 241 Score = 76.3 bits (186), Expect = 1e-18 Identities = 57/206 (27%), Positives = 100/206 (48%), Gaps = 9/206 (4%) Query: 27 FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQ-FRSPMEARQAGIET 85 FDL+ GE+L + G GAG++ + + I A G + + GK + R+P +A +AG+ Sbjct: 278 FDLHAGEVLGIAGLVGAGRTELARLIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVY 337 Query: 86 VYQNL---ALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGLMTI 142 + ++ L +S+ADN+ + + G LDR +++ + L + Sbjct: 338 LTEDRKAQGLFLDMSVADNINVCACVPDAHAGGV----LDRDHALQRSNDAIKSLSIRVA 393 Query: 143 QNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRRRGL 202 A LSGG +Q V +AR V+I+DEPT + + + +I + + G+ Sbjct: 394 SGKVNA-GALSGGNQQKVLLARLLEVKPHVLILDEPTRGVDIGSKSEIYRIINQLAQAGI 452 Query: 203 PIVLISHNMPHVFEVADRIHIHRLGR 228 IV+IS +P + DR+ I R G+ Sbjct: 453 GIVVISSELPEIIGTCDRVLIMREGQ 478 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: 18 Number of successful extensions: 5 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