Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate WP_084935209.1 HA51_RS14055 sugar ABC transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >NCBI__GCF_002095475.1:WP_084935209.1 Length = 494 Score = 471 bits (1213), Expect = e-137 Identities = 242/488 (49%), Positives = 338/488 (69%), Gaps = 2/488 (0%) Query: 5 LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64 L+ +GI K FPGVKAL +L + PG V AL+GENGAGKST+MK L G+Y D GT+ Sbjct: 6 LEAEGISKFFPGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIK 65 Query: 65 GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124 G+ F + +GI +IHQELNL+P +T+AENI+LGRE + ++G +D + + + Sbjct: 66 GEPVQFQDTMDALRSGISMIHQELNLVPYMTVAENIWLGREPM-KYGFVDHGKLNKQTQE 124 Query: 125 LLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVI 184 LL +LN+R K+D++VG+LSI QQMVEIAK +S+ S ++IMDEPT ALT+TE LF +I Sbjct: 125 LLNRLNIRLKADRMVGELSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAHLFTII 184 Query: 185 RELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLED 244 R+L+ QG+ I+YISH+M EIF I D++++FRDG ++ + T SLI MVGR+L Sbjct: 185 RDLREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMVGRELTQ 244 Query: 245 QYPHLDKAPGDIRLKVDNL-CGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALP 303 +P + G L V NL C D++FT+RKGEILGV+GL+GAGR+E+M+ L+G Sbjct: 245 LFPKFNGEIGADVLTVRNLTCKDRFTDINFTVRKGEILGVAGLVGAGRSEVMESLFGMES 304 Query: 304 RTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAG 363 SG V +DG V SP + G+ +++EDRK+ GL L +SV ENMS+ + + Sbjct: 305 FDSGEVLIDGVPVKIDSPSTAIEKGMAFLTEDRKKSGLFLVLSVMENMSIVNMPDYVSKA 364 Query: 364 GSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPT 423 G + H Q + IR N+KTP+M+Q I LSGGNQQKV IAR L+ +PK+LILDEPT Sbjct: 365 GFVSHMKMAQDCMEQIRKLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKILILDEPT 424 Query: 424 RGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQAT 483 RG+DVGAK EIY+LI++ G++II+VSSE+PE+LGMSDR++VMH G ++G +E+A Sbjct: 425 RGIDVGAKAEIYRLISELANRGVAIIMVSSELPEILGMSDRVMVMHGGRITGILDKEEAN 484 Query: 484 QEVLMAAA 491 QE +++ A Sbjct: 485 QETILSLA 492 Score = 88.2 bits (217), Expect = 6e-22 Identities = 62/234 (26%), Positives = 113/234 (48%), Gaps = 14/234 (5%) Query: 266 PGV---NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322 PGV ++VS ++ G + + G GAG++ LMK L G G + + G V + Sbjct: 16 PGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIKGEPVQFQDTM 75 Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSL--TALRYFSRAGGSLKHADEQQAVSDFIR 380 D L +GI I ++ LV M+V EN+ L ++Y G + H + + + Sbjct: 76 DALRSGISMIHQELN---LVPYMTVAENIWLGREPMKY-----GFVDHGKLNKQTQELLN 127 Query: 381 LFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQ 440 N++ + ++ +G LS QQ V IA+ + ++I+DEPT + ++ +I Sbjct: 128 RLNIRLKA-DRMVGELSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAHLFTIIRD 186 Query: 441 FKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494 + G +II +S +M E+ ++D I + +G G + T++ L+ VG+ Sbjct: 187 LREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMVGR 240 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: 685 Number of extensions: 36 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: 501 Length of database: 494 Length adjustment: 34 Effective length of query: 467 Effective length of database: 460 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