Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Putida:PP_2759 Length = 512 Score = 131 bits (330), Expect = 2e-35 Identities = 74/243 (30%), Positives = 130/243 (53%), Gaps = 8/243 (3%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P+L RG+VK +G ALD A + G + ++G+NGAGKS++IK ++G PD G + Sbjct: 4 PVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLL 63 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124 L+G+P SP + + GI ++Q L ++ + +F G E R + LDR Sbjct: 64 LDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPL-------LDRR 116 Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184 + +++A L + + + N + LS ++Q V + RA +V++ DEP+ AL Sbjct: 117 SQQREAARLLDDYFGLRLP-ANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQ 175 Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244 +E R+L ++ +R GL IV ISH + + + DR+ + R GR + ++P++ ++ Sbjct: 176 REVERLLRIVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQIT 235 Query: 245 AFM 247 M Sbjct: 236 RLM 238 Score = 100 bits (248), Expect = 8e-26 Identities = 73/257 (28%), Positives = 122/257 (47%), Gaps = 19/257 (7%) Query: 6 ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65 +L RGL GR A D + GEI+ + G G+G +++++ G PD GE+RL Sbjct: 258 LLDVRGL----GRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFGLAPPDSGEVRL 313 Query: 66 EGKPIQFRSPMEARQAGI-----ETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFR- 119 +G+P+ RSP EA G+ E Q +AL LS+ +N L + ++ R Sbjct: 314 DGQPLSLRSPREAVAQGVALMPEERRRQGVALD--LSVQENTTL-------AALSRFVRL 364 Query: 120 SLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPT 179 L A E+ +L E + + V LSGG +Q VA+A+ A S + ++DEP+ Sbjct: 365 GLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDEPS 424 Query: 180 AALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYT 239 + V + LI ++ + G ++++S ++P + + DRIH+ G + Sbjct: 425 VGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGEAN 484 Query: 240 MSDAVAFMTGAKEPPRE 256 +A TGA+ E Sbjct: 485 SDRLLAVATGAQRAQNE 501 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: 282 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: 512 Length adjustment: 29 Effective length of query: 231 Effective length of database: 483 Effective search space: 111573 Effective search space used: 111573 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