Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 266 bits (681), Expect = 1e-75 Identities = 162/496 (32%), Positives = 275/496 (55%), Gaps = 15/496 (3%) Query: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63 L+ +KG+ K F V A +LN+YPGRV AL+GENGAGKST+M +L G Y DAGT+ Sbjct: 24 LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83 Query: 64 LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGRE---FVNRFGKIDWKTMYA 120 GK F+ + + EAGIG+++Q L+ +T+AEN+ LG+E F+N K M Sbjct: 84 DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEGSFFLNP------KEMRN 137 Query: 121 EADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180 +L + L V DLS+G++Q VEI K+L +S+V+I DEPT LT ET L Sbjct: 138 RVQELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHL 197 Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDS-LIEMMVG 239 F + ++ QG+ IV+ISH+++E+ + D++ + R G+ E + +T + L MVG Sbjct: 198 FEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVG 257 Query: 240 RKLEDQYPHLDKAPGDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLY 299 +++ + GD L+V NL G G+ D++F L +GE++ V G+ G G+ L++ + Sbjct: 258 KEVLLEVDREAMPHGDAVLQVRNLTGIGLEDITFDLHQGEVVAVVGVAGNGQKALVEAIC 317 Query: 300 GALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYF 359 G + + G + N + YI EDR +++ +N+ LT + F Sbjct: 318 GLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTTRQGF 377 Query: 360 SRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLIL 419 +R G L + ++ I+ F+++ + LSGGN QK +AR L P++++ Sbjct: 378 AR-GPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVA 436 Query: 420 DEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFT- 478 ++PT+G+D+ A ++++ + + + I+LV+ ++ E L ++DR+ V++ G F+ Sbjct: 437 EQPTQGLDIAATEQVWNHLLAAR-EMAGILLVTGDLNEALQLADRVAVIYRGRFMDVFSV 495 Query: 479 --REQATQEVLMAAAV 492 +++ + LM A V Sbjct: 496 SDKQKVNRIGLMMAGV 511 Score = 57.8 bits (138), Expect = 9e-13 Identities = 56/248 (22%), Positives = 115/248 (46%), Gaps = 11/248 (4%) Query: 2 EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61 +A+LQ++ + G+ L +++ G V+A+VG G G+ +++ + G+ T+ Sbjct: 273 DAVLQVRNLT----GI-GLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTM 327 Query: 62 LWLGKETTFTGPKSSQEAGIGIIHQE---LNLIPQLTIAENIFLG-REFVNRFGKIDWKT 117 +GK K S + + I ++ L L + +N+ L R+ R +D K Sbjct: 328 FIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFARGPWLDKKK 387 Query: 118 MYAEADKLLAKLNLR-FKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTE 176 + +L+ K ++R + L LS G+ Q +A+ L ++I+ ++PT L Sbjct: 388 AARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAA 447 Query: 177 TESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEM 236 TE ++ + + GI+ ++ + E ++ D V V G+F+ V+ + + I + Sbjct: 448 TEQVWNHLLAAREMA-GILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGL 506 Query: 237 MVGRKLED 244 M+ ED Sbjct: 507 MMAGVEED 514 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: 576 Number of extensions: 40 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: 2 Length of query: 501 Length of database: 514 Length adjustment: 34 Effective length of query: 467 Effective length of database: 480 Effective search space: 224160 Effective search space used: 224160 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 Apr 09 2024. 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