Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate Pf6N2E2_993 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_993 Length = 501 Score = 146 bits (368), Expect = 1e-39 Identities = 90/260 (34%), Positives = 137/260 (52%), Gaps = 11/260 (4%) Query: 1 MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 M + I+ GL K YG +TAL DF+L GEI + G+NGAGKS+++K + G V P E Sbjct: 1 MQSQKIVQVTGLHKTYGGITALKSIDFELNAGEIHGLCGENGAGKSTLVKILGGLVQPTE 60 Query: 61 GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRS 120 G+I +G + R + I V+Q L++ PALS+ DN+ +G +G+ + Sbjct: 61 GQILFDGAVL--RPGRRTDPSCISIVHQELSIIPALSVLDNVLMGN-----AQVGRLYL- 112 Query: 121 LDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180 R + R +L +GL + ++Q+ LS +RQ V ++R G+KV+I+DEPTA Sbjct: 113 --RGRFKNDVRRQLDSIGLSHV-TLDQSASELSLAERQLVEISRCVLHGAKVLILDEPTA 169 Query: 181 ALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTM 240 L E RV + +R +G +V ISH + VF++ DRI I R G R+ + T Sbjct: 170 TLAESEIARVFTAVRWLRDQGTTVVFISHRLNEVFDLTDRITIFRSGERVLTAPTSEMTT 229 Query: 241 SDAVAFMTGAKEPPREAIAA 260 V M G + R + A Sbjct: 230 ESLVLAMVGHEVERRSTLDA 249 Score = 88.6 bits (218), Expect = 2e-22 Identities = 61/212 (28%), Positives = 103/212 (48%), Gaps = 14/212 (6%) Query: 15 RYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRS 74 R+G A D ++ GEIL V+G G+G +I+AI+G V G + ++G+ + +S Sbjct: 263 RFGVPNACQSLDLEVPAGEILGVVGQLGSGADRLIEAIAG-VRSHTGNLSIDGQQVDIQS 321 Query: 75 PMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFR-----SLDRAAMEKQ 129 P +A + Q +A P +FL I + F+ L+R + E+ Sbjct: 322 PRKA-------ISQGIAYVPEDRAGKGVFLEANIGQNSTASILFQFSRFGRLER-SQERD 373 Query: 130 ARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRR 189 A L + + I V +LSGG +Q VA+A+AAA K++I++EPT + V Sbjct: 374 AALDLMKRFTIDTTRIGSKVSSLSGGNQQKVAMAKAAAISPKILILNEPTRGVDVGARAE 433 Query: 190 VLELILDVRRRGLPIVLISHNMPHVFEVADRI 221 + + + GL ++ S + V E+ADR+ Sbjct: 434 IYAQLRSMAATGLTVIFFSTDFEEVLELADRV 465 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: 280 Number of extensions: 16 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: 501 Length adjustment: 29 Effective length of query: 231 Effective length of database: 472 Effective search space: 109032 Effective search space used: 109032 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