Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate 202575 SO3472 ABC transporter, ATP-binding protein (NCBI ptt file)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__MR1:202575 Length = 555 Score = 78.6 bits (192), Expect = 3e-19 Identities = 63/225 (28%), Positives = 106/225 (47%), Gaps = 33/225 (14%) Query: 4 EPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEI 63 + ++ L K YG +D F + G I+ +IG NGAGKS++ + +SG+ PD G I Sbjct: 321 DKVIEVNNLTKSYGDRVLIDNLSFSVPKGAIVGIIGANGAGKSTLFRMLSGSEQPDSGSI 380 Query: 64 RLEGKPIQFRSPMEARQA--GIETVYQNLALSPALSIADNMFLGREIRKPGIMGKW-FRS 120 L G+ +Q S + R + T++Q ++ + +NM EI +G++ FR Sbjct: 381 EL-GETVQLASVEQFRDSMNDKNTIWQEISGGQDIMRINNM----EIPSRAYVGRFNFRG 435 Query: 121 LDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180 D+ + + TLSGG+R V +A+ G V+++DEPT Sbjct: 436 GDQ----------------------QKIIGTLSGGERNRVHLAKLLQAGGNVLLLDEPTN 473 Query: 181 ALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHR 225 L V+ R + E IL+ + +ISH+ + +A I +R Sbjct: 474 DLDVETLRALEEAILEFPGCAM---VISHDRWFLDRIATHILDYR 515 Score = 50.4 bits (119), Expect = 8e-11 Identities = 47/165 (28%), Positives = 80/165 (48%), Gaps = 19/165 (11%) Query: 30 YPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR-LEGKPIQFRSPMEARQAGIETVYQ 88 +PG + V+G NG+GKS++++ ++G T EGE R + G I + P E + +TV + Sbjct: 30 FPGAKIGVLGLNGSGKSTLLRIMAGIDTEIEGEARPMPGLKIGY-LPQEPKLDPNQTVRE 88 Query: 89 NLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEK-QARAKLSELGLMTIQNI-- 145 A+ A+S A N L R + D A E+ + A + + NI Sbjct: 89 --AIEEAVSEAKNA-LKRLDEVYAAYAEPDADFDALAKEQGELEAIIQAQDAHNLDNILE 145 Query: 146 -----------NQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPT 179 ++ +E LSGG+R+ VA+ R +++++DEPT Sbjct: 146 RAANALRLPDWDEKIEVLSGGERRRVAICRLLLEKPEMLLLDEPT 190 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: 305 Number of extensions: 16 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: 555 Length adjustment: 30 Effective length of query: 230 Effective length of database: 525 Effective search space: 120750 Effective search space used: 120750 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: 50 (23.9 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