Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_084932744.1 HA51_RS05190 ribose ABC transporter ATP-binding protein RbsA
Query= CharProtDB::CH_003578 (501 letters) >NCBI__GCF_002095475.1:WP_084932744.1 Length = 502 Score = 840 bits (2171), Expect = 0.0 Identities = 428/494 (86%), Positives = 464/494 (93%) Query: 1 MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60 M+ LLQLKGI+K+FPGVKAL+GA+L VYPGRVMALVGENGAGKSTMMKVLTGIY+ DAG+ Sbjct: 1 MQPLLQLKGIEKSFPGVKALNGASLAVYPGRVMALVGENGAGKSTMMKVLTGIYSMDAGS 60 Query: 61 LLWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYA 120 L WLGK+ F+GPK+SQEAGIGIIHQELNLIPQLT+AENIFLGREFVNRFG+I+W MYA Sbjct: 61 LQWLGKDVAFSGPKASQEAGIGIIHQELNLIPQLTVAENIFLGREFVNRFGRIEWNRMYA 120 Query: 121 EADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180 EAD LL +LNLRF S KLVGDLSIGDQQMVEIAKVLSFES+VIIMDEPTDALTDTET SL Sbjct: 121 EADALLHRLNLRFNSHKLVGDLSIGDQQMVEIAKVLSFESQVIIMDEPTDALTDTETLSL 180 Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240 FRVI ELK+QG GIVYISHRMKEIFEICDDVTVFRDGQFIAER V+ L+E+SLIEMMVGR Sbjct: 181 FRVINELKAQGCGIVYISHRMKEIFEICDDVTVFRDGQFIAERAVSDLSEESLIEMMVGR 240 Query: 241 KLEDQYPHLDKAPGDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYG 300 KLEDQYPH+D+APGDIRL V++L GPGV++VSF LRKGEILG+SGLMGAGRTELMKVLYG Sbjct: 241 KLEDQYPHIDQAPGDIRLTVEHLSGPGVDNVSFNLRKGEILGISGLMGAGRTELMKVLYG 300 Query: 301 ALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360 ALPR+ G VTL+G E++TRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS Sbjct: 301 ALPRSKGTVTLNGREIMTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFS 360 Query: 361 RAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILD 420 A G+LKH++EQ AV DFIRLFNVKTPSMEQ IGLLSGGNQQKVAIARGLMTRP VLILD Sbjct: 361 HATGNLKHSEEQLAVGDFIRLFNVKTPSMEQPIGLLSGGNQQKVAIARGLMTRPNVLILD 420 Query: 421 EPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTRE 480 EPTRGVDVGAKKEIYQLINQFKA+GLSIILVSSEMPEVLGMSDRI+VMHEGHLSGEF+RE Sbjct: 421 EPTRGVDVGAKKEIYQLINQFKAEGLSIILVSSEMPEVLGMSDRILVMHEGHLSGEFSRE 480 Query: 481 QATQEVLMAAAVGK 494 QATQE LMAAAVGK Sbjct: 481 QATQESLMAAAVGK 494 Score = 94.7 bits (234), Expect = 7e-24 Identities = 65/237 (27%), Positives = 117/237 (49%), Gaps = 9/237 (3%) Query: 15 PGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFTGPK 74 PGV +S N+ G ++ + G GAG++ +MKVL G R GT+ G+E P+ Sbjct: 266 PGVDNVS---FNLRKGEILGISGLMGAGRTELMKVLYGALPRSKGTVTLNGREIMTRSPQ 322 Query: 75 SSQEAGIGIIHQELN---LIPQLTIAENIFLG--REFVNRFGKIDWKTMYAEADKLLAKL 129 GI I ++ L+ +++ EN+ L R F + G + + Sbjct: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSHATGNLKHSEEQLAVGDFIRLF 382 Query: 130 NLRFKS-DKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIRELK 188 N++ S ++ +G LS G+QQ V IA+ L V+I+DEPT + + ++++I + K Sbjct: 383 NVKTPSMEQPIGLLSGGNQQKVAIARGLMTRPNVLILDEPTRGVDVGAKKEIYQLINQFK 442 Query: 189 SQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLEDQ 245 ++G I+ +S M E+ + D + V +G E T++SL+ VG++ ++ Sbjct: 443 AEGLSIILVSSEMPEVLGMSDRILVMHEGHLSGEFSREQATQESLMAAAVGKQHSEE 499 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: 905 Number of extensions: 26 Number of successful extensions: 5 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: 502 Length adjustment: 34 Effective length of query: 467 Effective length of database: 468 Effective search space: 218556 Effective search space used: 218556 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