Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_068000812.1 PsAD2_RS00245 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >NCBI__GCF_001623255.1:WP_068000812.1 Length = 514 Score = 300 bits (767), Expect = 1e-85 Identities = 185/505 (36%), Positives = 282/505 (55%), Gaps = 20/505 (3%) Query: 5 LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64 ++L G++K+F V A L V G + ++GENGAGKST+M +L G Y D+GT+ Sbjct: 9 IELIGVNKSFGPVHANKDIDLVVGKGSIHGIIGENGAGKSTLMSILYGFYHADSGTIKID 68 Query: 65 GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124 GK TT KS+ GIG++HQ L+ T+ EN+ LG E G K A A + Sbjct: 69 GKATTIPDSKSAISQGIGMVHQHFMLVDPFTVLENVVLGAE-----GGALLKDGVANARR 123 Query: 125 LLAKL----NLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESL 180 L +L ++ D +VG+L +G QQ VEI K L + ++I+DEPT LT +E + L Sbjct: 124 ELKRLADEYDMTIDPDAVVGELPVGLQQRVEILKALYRGADILILDEPTGVLTPSEADHL 183 Query: 181 FRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGR 240 FR++R L+ QG+ ++ I+H+++EI ++ D V+V R G+ +A R+ A + + L E+MVGR Sbjct: 184 FRILRVLRDQGKTVLLITHKLREIMDVTDTVSVMRRGEMVASRKTAQTSMEELAELMVGR 243 Query: 241 KLEDQYPHLDKAPGDIRLKVDNLCGPG------VNDVSFTLRKGEILGVSGLMGAGRTEL 294 + + D G LKV+ L V DVSF +R GE+LG++G+ G G++EL Sbjct: 244 SVLLEVSKPDVEVGKPLLKVEGLNVKDERGVRRVKDVSFEVRAGEVLGIAGVSGNGQSEL 303 Query: 295 MKVLYGALPRTSGYVTLDGHEVVTRSPQDGLA---NGIVYISEDRKRDGLVLGMSVKENM 351 M L G SG + L G ++ D G+ ++ EDR R GLV S EN Sbjct: 304 MAALAGITRAESGSMELAGQKLDLSEVHDAAQMRDRGMSHVPEDRHRMGLVNKFSEAENS 363 Query: 352 SLTALRYFSRAGGSLKHADE-QQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGL 410 L R + G D ++ + I ++++ P E SGGNQQK+ +AR + Sbjct: 364 ILGYHRESKYSKGMFLDKDAIRKEAKERIEKYDIRPPLTEMTAAKFSGGNQQKIVLAREI 423 Query: 411 MTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHE 470 P VL++ +PTRGVD+GA + I+ I +A G +++LVS E+ E+ +SDRIIVM + Sbjct: 424 ECNPDVLLIGQPTRGVDIGAIEYIHNRIMDMRAQGKAVLLVSVELDEIRSLSDRIIVMFD 483 Query: 471 GHLSGEFTREQATQEV-LMAAAVGK 494 G++ GE E Q++ L+ A V + Sbjct: 484 GNVVGERGPEATEQDLGLLMAGVNQ 508 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: 594 Number of extensions: 32 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 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 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