Align Fructose import ATP-binding protein FrcA; EC 7.5.2.- (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= SwissProt::Q9F9B0 (260 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 160 bits (406), Expect = 4e-44 Identities = 90/245 (36%), Positives = 148/245 (60%), Gaps = 7/245 (2%) Query: 5 PILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIR 64 P++ R + KR+ V ALD F+L GE+ A++G+NGAGKS+++K +SG D G+I Sbjct: 21 PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80 Query: 65 LEGKPIQFRSPMEARQAGIETVYQNLALSPALSIADNMFLGREIRKPGIMGKWFRSLDRA 124 L+GKP++ P +A+ GI ++Q L L LS A N+F+GRE RK MG + +D Sbjct: 81 LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRK--AMGLF---IDED 135 Query: 125 AMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTAALGV 184 + +QA A + + L + + V L+ ++Q V +A+A +F S+V+IMDEPTAAL Sbjct: 136 ELNRQAAAIFARMRL--DMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNN 193 Query: 185 KESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGRRLCVINPKDYTMSDAV 244 E + +I D++ +G+ IV ISH M + ++ADR+ + R G+ + + ++ +M + Sbjct: 194 AEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTII 253 Query: 245 AFMTG 249 + M G Sbjct: 254 SMMVG 258 Score = 82.4 bits (202), Expect = 2e-20 Identities = 63/228 (27%), Positives = 110/228 (48%), Gaps = 17/228 (7%) Query: 6 ILTARGLVKRYGRVTALDRADFDLYPGEILAVIGDNGAGKSSMIKAISGAVTPDEGEIRL 65 +L RGL R A+ F L GEIL G GAG++ + +AI GA + GEI + Sbjct: 277 VLEVRGL----NRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332 Query: 66 EGKPIQFRSPMEARQAGIETVYQN---LALSPALSIADNMFLGREIRKPGIMGKWFRS-- 120 G +SP +A GI + ++ L+ + + N+ L MG++ R Sbjct: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSS-------MGRFTRVGF 385 Query: 121 LDRAAMEKQARAKLSELGLMTIQNINQAVETLSGGQRQGVAVARAAAFGSKVVIMDEPTA 180 +D+ A+ + A+ + +L + T ++ Q LSGG +Q + +A+ ++ DEPT Sbjct: 386 MDQRAIREAAQMYVRQLAIKT-PSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTR 444 Query: 181 ALGVKESRRVLELILDVRRRGLPIVLISHNMPHVFEVADRIHIHRLGR 228 + V + +L+ + +G IV+IS +P V ++ R+ + GR Sbjct: 445 GIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGR 492 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: 296 Number of extensions: 17 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: 520 Length adjustment: 30 Effective length of query: 230 Effective length of database: 490 Effective search space: 112700 Effective search space used: 112700 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