Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate RR42_RS03360 RR42_RS03360 sugar ABC transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__Cup4G11:RR42_RS03360 Length = 537 Score = 382 bits (982), Expect = e-110 Identities = 218/504 (43%), Positives = 311/504 (61%), Gaps = 15/504 (2%) Query: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63 LL L+ I K FPGV+AL L Y G V AL+GENGAGKST+MK+L+G YT D G Sbjct: 10 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 69 Query: 64 L-GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEA 122 + G+ GP+S+++ G+ +I+QEL+L P L++AENI+LGR R G + M Sbjct: 70 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRR-GLVARGDMVRAC 128 Query: 123 DKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182 LA+L F V LSI +Q+VEIA+ + FE+++++MDEPT L+ ET+ LF Sbjct: 129 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 188 Query: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKL 242 +IR+L+ +G I+YISHRM EI E+ D VTV RDG F+ + A L++ +L++MMVGR L Sbjct: 189 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 248 Query: 243 EDQYP--HLDKAPGDIRLKVDNLC-GPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLY 299 Y H ++ L V ++ G V SF LR GE+LG++GL+GAGRTEL ++++ Sbjct: 249 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 308 Query: 300 GALPRTSGYVTLDGHE-------VVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMS 352 GA RT G V + + P+ + GI Y++EDRK GL L SV EN++ Sbjct: 309 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 368 Query: 353 LTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMT 412 L + G L ++ ++ I ++ + +G LSGGNQQKV ++R L Sbjct: 369 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 428 Query: 413 RPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGH 472 +P+VLILDEPTRGVD+GAK EIY+LIN G++I+++SSE+PEV+G+ DR++VM EG Sbjct: 429 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 488 Query: 473 LSGEFT---REQATQEVLMAAAVG 493 L+GE TQE ++A A G Sbjct: 489 LAGEVRPAGSAAETQERIIALATG 512 Score = 88.6 bits (218), Expect = 5e-22 Identities = 70/243 (28%), Positives = 112/243 (46%), Gaps = 13/243 (5%) Query: 258 LKVDNLCG--PGVN---DVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRT-SGYVTL 311 L + N+C PGV V T GE+ + G GAG++ LMK+L GA G + Sbjct: 11 LALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECHI 70 Query: 312 DGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADE 371 DG V PQ G+ I ++ L +SV EN+ L R R G + Sbjct: 71 DGQRVQIDGPQSARDLGVAVIYQELS---LAPNLSVAENIYLG--RALQRRGLVARGDMV 125 Query: 372 QQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAK 431 + RL +P+ + LS +Q V IAR + ++L++DEPT + Sbjct: 126 RACAPTLARLGADFSPAAN--VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHET 183 Query: 432 KEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAA 491 ++ LI Q + +G++I+ +S M E+ ++DR+ V+ +G G R +Q L+ Sbjct: 184 DRLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMM 243 Query: 492 VGK 494 VG+ Sbjct: 244 VGR 246 Lambda K H 0.318 0.137 0.380 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: 671 Number of extensions: 40 Number of successful extensions: 8 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: 501 Length of database: 537 Length adjustment: 35 Effective length of query: 466 Effective length of database: 502 Effective search space: 233932 Effective search space used: 233932 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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