Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__HerbieS:HSERO_RS03640 Length = 502 Score = 168 bits (426), Expect = 2e-46 Identities = 93/228 (40%), Positives = 140/228 (61%), Gaps = 10/228 (4%) Query: 1 MAQEPILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDE 60 M Q P+L RG+ K +G AL + PGEI A++G+NGAGKS+++K +SG PD+ Sbjct: 5 MTQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQ 64 Query: 61 GEIRLEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIR-KPGIMGKWFR 119 GEI L+G+P+ R P +R AGI +YQ LA++P +S+A N+F+G E+R + G+ Sbjct: 65 GEILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGL------ 118 Query: 120 SLDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPT 179 +D AAM + A L +LG + LS ++Q V +ARA S++VIMDEPT Sbjct: 119 -IDHAAMRSRTDAVLRQLGAGF--GASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPT 175 Query: 180 AALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLG 227 AAL +E+ ++ ++ +R GL I+ ISH M V+ +ADR+ + R G Sbjct: 176 AALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDG 223 Score = 89.7 bits (221), Expect = 1e-22 Identities = 64/208 (30%), Positives = 103/208 (49%), Gaps = 13/208 (6%) Query: 25 ADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRLEGKPIQFRSPMEARQAGIE 84 A FD+ GE+L G GAG++ + + + GA G+I LEG+P+ P A +AGI Sbjct: 282 ASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIA 341 Query: 85 TVY-----QNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRAAMEKQARAKLSELGL 139 V Q L L A++ M + + G++ RSL A RA + L + Sbjct: 342 YVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRS--RSLGGVA-----RAAIQRLNV 394 Query: 140 MTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGVKESRRVLELILDVRR 199 + + V LSGG +Q V +AR KV+I+DEPT + + + +L+ + Sbjct: 395 K-VAHPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLAS 453 Query: 200 RGLPIVLISHNMPHVFEVADRIHIHRLG 227 +G+ +V+IS +P V + DR+ + R G Sbjct: 454 QGVAVVVISSELPEVIGICDRVLVMREG 481 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: 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: 502 Length adjustment: 29 Effective length of query: 231 Effective length of database: 473 Effective search space: 109263 Effective search space used: 109263 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