Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 261 bits (666), Expect = 6e-74 Identities = 157/485 (32%), Positives = 264/485 (54%), Gaps = 12/485 (2%) Query: 20 VPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDI 79 +P+++++ + KRF V+A D+ + G V AL+GENGAGKSTLM +L+G YQ D+G I Sbjct: 22 IPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTI 81 Query: 80 LLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNR 139 LDGKPV + R A GIG+++Q L+ ++ A+N+ +G+E F++ E+ Sbjct: 82 ALDGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEG----SFFLNPKEMRN 137 Query: 140 QAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAEL 199 + + R LD+DP+ V +L++ +Q VEI K L DSRVLI DEPTA L E L Sbjct: 138 RVQELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHL 197 Query: 200 FRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQE-TSMDTIISMMVG 258 F + + QG IV+ISHK++E+ +AD ++++R G+ E TS + MVG Sbjct: 198 FEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVG 257 Query: 259 R--ALDGEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVA 316 + L+ ++ P D VL+VR L G + D++F L +GE++ G+ G G+ + Sbjct: 258 KEVLLEVDREAMP---HGDAVLQVRNLT-GIGLEDITFDLHQGEVVAVVGVAGNGQKALV 313 Query: 317 RAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSS 376 AI G + I G + + + + Y+ EDR +++ N+ L++ Sbjct: 314 EAICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTT 373 Query: 377 MGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDI 436 F R ++D++ +++ I+ + A LSGGN QK V+A+ L R + Sbjct: 374 RQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRL 433 Query: 437 LFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGE 496 + ++PT+G+D+ A +++ L A E I++++ +L E L+++ RV V+ GR Sbjct: 434 IVAEQPTQGLDIAATEQVWNHLLAAREMA-GILLVTGDLNEALQLADRVAVIYRGRFMDV 492 Query: 497 LARAD 501 + +D Sbjct: 493 FSVSD 497 Score = 105 bits (261), Expect = 5e-27 Identities = 75/249 (30%), Positives = 128/249 (51%), Gaps = 24/249 (9%) Query: 270 DTSRNDV------VLEVRGLNR--GRAIR--DVSFTLRKGEILGFAGLMGAGRTEVARAI 319 D S+ DV ++ ++GL + G+ + D+S + G + G GAG++ + + Sbjct: 11 DRSKRDVPPQGIPLVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSML 70 Query: 320 FGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGR 379 G +AG I + G S DA+ GIG + + HF L M V N+ L G Sbjct: 71 AGRYQPDAGTIALDGKPVRFSSARDAIEAGIGMVYQ---HFMLVESMTVAENVLLGQEGS 127 Query: 380 FTRVGFMDQRAIREAAQMYVRQLAIKTP-SVEQQARL--LSGGNQQKIVIAKWLLRDCDI 436 F F++ + +R Q +L+++ ++ AR+ LS G +Q++ I K L RD + Sbjct: 128 F----FLNPKEMRNRVQ----ELSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRV 179 Query: 437 LFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGE 496 L FDEPT + +++ L +AEQGK+IV IS +L EVL ++ + ++ +GRI GE Sbjct: 180 LIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGE 239 Query: 497 LARADATQE 505 + ++ T + Sbjct: 240 FSESEVTSK 248 Score = 52.0 bits (123), Expect = 5e-11 Identities = 45/228 (19%), Positives = 105/228 (46%), Gaps = 9/228 (3%) Query: 36 LALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQ 95 + L++ F+L GEV A++G G G+ L++ + G+ + + + GK + + Sbjct: 284 IGLEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSW 343 Query: 96 ALGIGIIHQE---LNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDM 152 + I ++ L +L+ N+ + A G ++D+ + R + + D+ Sbjct: 344 KNSLAYIPEDRLGLATCRNLNLVDNLLLTTRQGFARGPWLDKKKAARDTTELIKKF--DI 401 Query: 153 DPSTPVG---ELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQ 209 P +L+ Q +A+ L R+++ ++PT L+ A +++ + + Sbjct: 402 RPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHLLAAREM 461 Query: 210 GVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMV 257 GI+ ++ ++E Q+ADRV+V+ G+++ + + I +M+ Sbjct: 462 A-GILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMM 508 Lambda K H 0.320 0.135 0.372 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: 556 Number of extensions: 24 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 520 Length of database: 514 Length adjustment: 35 Effective length of query: 485 Effective length of database: 479 Effective search space: 232315 Effective search space used: 232315 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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