Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__Putida:PP_2455 Length = 524 Score = 119 bits (299), Expect = 1e-31 Identities = 84/249 (33%), Positives = 126/249 (50%), Gaps = 9/249 (3%) Query: 1 MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 +A E +L A GL K Y + L L GE+LA+ G+NGAGKS++ K ISG P Sbjct: 11 LANEVVLAASGLGKTYAQ-PVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTT 69 Query: 61 GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRS 120 G + G+ S EA + G+ V Q L L P L++A+N+FL + F Sbjct: 70 GHMTYRGQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDN-------LPSRFGW 122 Query: 121 LDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180 + + + A A ++ +GL I + + V L G +Q V +AR V+I+DEPTA Sbjct: 123 ISHKRLRQLATAAMARVGLDAI-DPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTA 181 Query: 181 ALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTM 240 L +E + I +R RG+ IV ISH + + VA RI + R G+ +C + Y+ Sbjct: 182 MLTAREVALLFTQIERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCDEPIQRYSS 241 Query: 241 SDAVAFMTG 249 ++ V M G Sbjct: 242 AELVNLMVG 250 Score = 76.3 bits (186), Expect = 1e-18 Identities = 65/241 (26%), Positives = 115/241 (47%), Gaps = 20/241 (8%) Query: 27 FDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKP--IQFRSPMEARQAGIE 84 F++ GEI + G GAG++ +++ I GA D G I L P + SP A +AGI Sbjct: 285 FEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRAGIA 344 Query: 85 TVYQNL---ALSPALSIADNMFLGR--EIRKPGIMGKWFRSLDRAAMEKQARAKLSELGL 139 + ++ L SI+ N+ LG + + G++ ++A E+Q +A Sbjct: 345 LITEDRKGEGLLLTQSISANIALGNLGAVSRAGVLDS---EAEKALAERQIQA------- 394 Query: 140 MTIQNIN--QAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDV 197 M I++ Q V LSGG +Q V + R +V++ DEPT + V + L+ ++ Sbjct: 395 MRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAEL 454 Query: 198 RRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAVAFMTGAKEPPREA 257 R+G +V++S ++ + + DRI + GR + +D+ D + A R+A Sbjct: 455 ARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTF-ARDHWSQDQLLAAAFAGYQKRDA 513 Query: 258 I 258 + Sbjct: 514 L 514 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: 289 Number of extensions: 11 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: 524 Length adjustment: 30 Effective length of query: 230 Effective length of database: 494 Effective search space: 113620 Effective search space used: 113620 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