Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate WP_007664454.1 BN137_RS17460 ribose ABC transporter ATP-binding protein RbsA
Query= TCDB::G4FGN3 (494 letters) >NCBI__GCF_000319285.1:WP_007664454.1 Length = 501 Score = 441 bits (1133), Expect = e-128 Identities = 230/494 (46%), Positives = 334/494 (67%), Gaps = 3/494 (0%) Query: 1 MKPILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGE 60 M+P+L++K I K FPGV AL G ++ Y G V A+VGENGAGKSTLMK++ G+Y D G Sbjct: 1 MEPLLQLKGIDKSFPGVKALSGATLNVYAGRVMALVGENGAGKSTLMKVLTGIYTRDAGS 60 Query: 61 IIYEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDE-EKRGIFIDYKKMYR 119 +++ G+ ++ P + AGI + QEL+++ LS+AENIF+G E R ID+KKMY Sbjct: 61 LVWLGQETAFSGPKASQEAGIGIIHQELNLIPQLSIAENIFLGREFVSRFGKIDWKKMYA 120 Query: 120 EAEKFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEK 179 EA+K + + + + +G SI QQMVEIA+ + +++V+I+DEPT +LT ET+ Sbjct: 121 EADKLLAK-LNLRFNSRRLVGDLSIGDQQMVEIAKVLSFESRVIIMDEPTDALTDTETDS 179 Query: 180 LFEVVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVG 239 LF ++ LK +G I++ISHR++EIFEICD V+V+RDG++I + +LT+E ++EMMVG Sbjct: 180 LFRAIRELKAQGCGIVYISHRMKEIFEICDDVTVMRDGQFIAEREVSSLTEETLIEMMVG 239 Query: 240 RKLEKFYIKEAHEPGEVVLEVKNLSGERFENVSFSLRRGEILGFAGLVGAGRTELMETIF 299 RKLE Y GEV L+V NLSG + VSF+LR+GEILG +GL+GAGRTELM+ ++ Sbjct: 240 RKLEDQYPHLDKASGEVRLKVDNLSGPGVDGVSFTLRQGEILGVSGLMGAGRTELMKVLY 299 Query: 300 GFRPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRI 359 G P+ GG + ++ + V P D + GI + EDRK+ GL+L MS+ N+SL +L Sbjct: 300 GALPRSGGSVTLDNRDVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYF 359 Query: 360 KK-GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILIL 418 + G + E++ I+ F+++ D+ + LSGGNQQKV +A+ L +PK+LIL Sbjct: 360 SRAGGSLKHHDEQQAVGDFIRLFNVKTPSMDQAIGLLSGGNQQKVAIARGLMTRPKVLIL 419 Query: 419 DEPTRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDA 478 DEPTRG+DVGAK EIY++++Q EG+ +I++SSE+PEVL MSDRI VM G L G Sbjct: 420 DEPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFTR 479 Query: 479 KEASQEKVMKLAAG 492 ++A+QE +M A G Sbjct: 480 EQATQELLMAAAVG 493 Score = 90.9 bits (224), Expect = 9e-23 Identities = 62/236 (26%), Positives = 117/236 (49%), Gaps = 17/236 (7%) Query: 15 PGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEIIYEGRGVRWNHPS 74 PGV GVS GE+ + G GAG++ LMK++ G G + + R V P Sbjct: 266 PGVD---GVSFTLRQGEILGVSGLMGAGRTELMKVLYGALPRSGGSVTLDNRDVVTRSPQ 322 Query: 75 EAINAGIVTVFQE---------LSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAEKFM 125 + + GIV + ++ +SV +N+S+ + + G + + + F+ Sbjct: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS---RAGGSLKHHDEQQAVGDFI 379 Query: 126 KEEFGIEIDP-EEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFEVV 184 + F ++ ++ +G S QQ V IAR + + KVLILDEPT + +++++++ Sbjct: 380 RL-FNVKTPSMDQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLI 438 Query: 185 KSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGR 240 K +G++II +S + E+ + D++ V+ +G G + E T+E ++ VG+ Sbjct: 439 NQFKAEGLSIILVSSEMPEVLGMSDRIMVMHEGHLGGEFTREQATQELLMAAAVGK 494 Lambda K H 0.318 0.138 0.385 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: 678 Number of extensions: 29 Number of successful extensions: 7 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: 494 Length of database: 501 Length adjustment: 34 Effective length of query: 460 Effective length of database: 467 Effective search space: 214820 Effective search space used: 214820 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 24 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