Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 407 bits (1046), Expect = e-118 Identities = 232/517 (44%), Positives = 332/517 (64%), Gaps = 15/517 (2%) Query: 14 ASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQ 73 + +S+ P++ALRN+CK FPGV AL + AGEVHALMGENGAGKSTLMKILSG Y Sbjct: 2 SDTSTKAPLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYT 61 Query: 74 RD-SGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFI 132 D G+ +DG+ V+I P+ A+ LG+ +I+QEL+L +LS A+NI++GR ++ GL + Sbjct: 62 ADPGGECHIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GL-V 119 Query: 133 DEDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALN 192 ++ R A AR+ D P+ V L++A++Q+VEIA+A+ F++R+L+MDEPT L+ Sbjct: 120 ARGDMVRACAPTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLS 179 Query: 193 NAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTI 252 E LF +IR L+ +G+ I+YISH+M E+ ++ADRV+V+RDG ++ T+ S + Sbjct: 180 THETDRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAAL 239 Query: 253 ISMMVGRALDG-EQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAG 311 + MMVGR L G + +V+L VR + GR ++ SF LR GE+LG AGL+GAG Sbjct: 240 VKMMVGRDLSGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAG 299 Query: 312 RTEVARAIFGADPLEAGEIII-----HGGKAVIKS--PADAVAHGIGYLSEDRKHFGLAV 364 RTE+AR +FGAD GE+ I GG + + P A+ GI YL+EDRK GL + Sbjct: 300 RTELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFL 359 Query: 365 GMDVQANIALSSMGR-FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQK 423 V NI L R +G +++ A R + L I+ + LSGGNQQK Sbjct: 360 DQSVHENINLIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQK 419 Query: 424 IVIAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSH 483 +++++ L +L DEPTRG+D+GAKSEIY+L++ALA+ G AI+MISSELPEV+ + Sbjct: 420 VMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCD 479 Query: 484 RVLVMCEGRITGELARADA---TQEKIMQLATQRESA 517 RVLVM EG + GE+ A + TQE+I+ LAT +A Sbjct: 480 RVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAA 516 Lambda K H 0.320 0.135 0.372 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: 677 Number of extensions: 35 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 520 Length of database: 537 Length adjustment: 35 Effective length of query: 485 Effective length of database: 502 Effective search space: 243470 Effective search space used: 243470 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: 52 (24.6 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