Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate 206505 DVU1070 branched chain amino acid ABC transporter, ATP-binding protein (TIGR)
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__DvH:206505 Length = 524 Score = 286 bits (731), Expect = 2e-81 Identities = 167/485 (34%), Positives = 272/485 (56%), Gaps = 13/485 (2%) Query: 4 LLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLW 63 +++L+GI K+F V+A L++ PGR+ AL+GENGAGKST+M +L+G +D G + Sbjct: 34 VVRLEGIGKSFGPVRANHDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHV 93 Query: 64 LGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123 G+ F PK + +AGIG+++Q L+ +T+AEN+ LG+ + + AE Sbjct: 94 DGEAVRFRSPKDALKAGIGMVYQHFMLVDSMTVAENVLLGQSGA-WLSPVHMSRVVAE-- 150 Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183 L A+ L V DLS+G++Q VEI K+L +S+V+I+DEPT LT ETE LF Sbjct: 151 -LAARYGLDIDPAARVCDLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEA 209 Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLT-EDSLIEMMVGRKL 242 + + G+ IV+ISH+M+E+ + D++ + R G+ + E + + E L MVGR++ Sbjct: 210 LHRMAENGKAIVFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELANRMVGREV 269 Query: 243 EDQYPHLDKAPGDIRLKVDNLCGPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVLYGAL 302 + PGD L VD L G G+ +SF +RKGE+ ++G+ G G+ EL++ + G Sbjct: 270 ILEVAAEPLEPGDRVLHVDGLAGDGLKGLSFEVRKGEVFAIAGVAGNGQRELVECVTGLR 329 Query: 303 PRTSGYVTLDG---HEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYF 359 G V L G + T++P+ G G+ YI EDR+ L + + +N LTA F Sbjct: 330 RPAEGEVELLGIPWRQFFTKAPRQG---GLAYIPEDRQGLATCLSLDLVDNFLLTARGCF 386 Query: 360 SRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLIL 419 +R G L A D + +NV+ E LSGGN QK+ + R +P +++ Sbjct: 387 TR-GPFLDRKSADAAARDILAEYNVQPGRAEAPARSLSGGNLQKLVVGREFYRKPSLIVA 445 Query: 420 DEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTR 479 + PT+G+D+ A +E++ + + ++ ++LVS ++ EVL ++DR+ VM+ G G R Sbjct: 446 ENPTQGLDIAATEEVWARLLEVRSHA-GVLLVSGDLNEVLALADRVAVMYRGCFIGLLDR 504 Query: 480 EQATQ 484 + Sbjct: 505 SDTNK 509 Score = 95.9 bits (237), Expect = 3e-24 Identities = 63/221 (28%), Positives = 113/221 (51%), Gaps = 10/221 (4%) Query: 269 NDVSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANG 328 +D++ + G I + G GAG++ LM +L G L + +G + +DG V RSP+D L G Sbjct: 51 HDITLDIVPGRIKALLGENGAGKSTLMSILSGRLAQDTGIIHVDGEAVRFRSPKDALKAG 110 Query: 329 IVYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPS 388 I + + LV M+V EN+ L ++G L + V++ + + Sbjct: 111 IGMVYQHFM---LVDSMTVAENVLL------GQSGAWLSPVHMSRVVAELAARYGLDIDP 161 Query: 389 MEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSI 448 + L S G +Q+V I + L +VLILDEPT + G +++++ +++ +G +I Sbjct: 162 AARVCDL-SMGERQRVEILKLLYRDSRVLILDEPTAVLTPGETEQLFEALHRMAENGKAI 220 Query: 449 ILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMA 489 + +S +M EVL ++D I ++ G + EF + E +A Sbjct: 221 VFISHKMQEVLALADEIAILRRGEVVDEFHESEVPGEAELA 261 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: 644 Number of extensions: 34 Number of successful extensions: 8 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: 524 Length adjustment: 35 Effective length of query: 466 Effective length of database: 489 Effective search space: 227874 Effective search space used: 227874 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