Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 392 bits (1007), Expect = e-113 Identities = 221/492 (44%), Positives = 311/492 (63%), Gaps = 7/492 (1%) Query: 21 PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDIL 80 PV+A+R V + F V L + F+L GEVHAL+GENGAGKST MKIL+G +G++L Sbjct: 4 PVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVL 63 Query: 81 LDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQ 140 LDG+PV R+A+A G+ +IHQE NL L+ +NIF+GRE ++ G F+D + + Sbjct: 64 LDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKR--GPFLDHRAMQAE 121 Query: 141 AAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELF 200 + + R+ +DP V L+V +QMVEIAKAL +RVLIMDEPTA L + E L Sbjct: 122 SRRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETDTLL 181 Query: 201 RIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRA 260 + L+A G I+Y SHK+DE+ +IADRV+V+RDG+ + T P + S D + MVGR Sbjct: 182 EQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMVGRE 241 Query: 261 LDGEQRIPPDTS-RNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAI 319 L G PP +S + VLEV GL +RD SFTLR+GE+LGFAGL+G+GRTE+ I Sbjct: 242 LSG--LFPPKSSPAPEPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELMEGI 299 Query: 320 FGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGR 379 G P GE+ + G S + A A G+ YL+EDRK GL +G + N+ L ++ R Sbjct: 300 VGLRP-ATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLALDR 358 Query: 380 FTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFF 439 F RV +D+ A A + I+ A LSGGNQQK+++AK +L + ++ Sbjct: 359 FGRV-LIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRVVII 417 Query: 440 DEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELAR 499 DEPTRGIDVG K +IY + LA +G++++++SSELPEV+ +++RV+VM GRI GE+ Sbjct: 418 DEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGEVEG 477 Query: 500 ADATQEKIMQLA 511 T+E I++LA Sbjct: 478 EAITEENIVRLA 489 Score = 85.9 bits (211), Expect = 3e-21 Identities = 72/246 (29%), Positives = 123/246 (50%), Gaps = 16/246 (6%) Query: 277 VLEVRGLNR----GRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332 VL +R ++R + + DV F LR GE+ G GAG++ + + G AGE+++ Sbjct: 5 VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64 Query: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVG-FMDQRAI 391 G S +A A G+ + ++ F LA + V+ NI L GR + G F+D RA+ Sbjct: 65 DGRPVHFPSSREAEAAGVVMIHQE---FNLATPLTVEENIFL---GRELKRGPFLDHRAM 118 Query: 392 REAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVG 449 + ++ + +L +V+ +AR+ LS N+Q + IAK L +L DEPT + Sbjct: 119 QAESRRLLERLHC---AVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHR 175 Query: 450 AKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQ 509 + + +D L G AI+ S +L EV R++ RV V+ +GR +++++ + Sbjct: 176 ETDTLLEQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAE 235 Query: 510 LATQRE 515 RE Sbjct: 236 TMVGRE 241 Score = 72.0 bits (175), Expect = 5e-17 Identities = 65/270 (24%), Positives = 123/270 (45%), Gaps = 18/270 (6%) Query: 1 MQEDKETST------TGVAASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALM 54 + ED+ T +G+ SS P L PG + + F L GEV Sbjct: 228 LSEDRMAETMVGRELSGLFPPKSSPAPEPVLEVAGLTVPGFVR--DASFTLRRGEVLGFA 285 Query: 55 GENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII---HQELNLMNH 111 G G+G++ LM+ + G+ + +G++ ++G P+ A+A G+ + +E L+ Sbjct: 286 GLVGSGRTELMEGIVGL-RPATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLG 344 Query: 112 LSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDM---DPSTPVGELTVARQQM 168 +N+ + R L D+ + A A D+ D G L+ QQ Sbjct: 345 KPLGENLTLLALDRFGRVLI---DKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQK 401 Query: 169 VEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIAD 228 + +AK + + RV+I+DEPT ++ +++ I L A+G ++ +S ++ E+ +A+ Sbjct: 402 LLLAKTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLAN 461 Query: 229 RVSVMRDGKYIATVPMQETSMDTIISMMVG 258 RV VM G+ V + + + I+ + +G Sbjct: 462 RVVVMSAGRIAGEVEGEAITEENIVRLAMG 491 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: 652 Number of extensions: 33 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: 499 Length adjustment: 34 Effective length of query: 486 Effective length of database: 465 Effective search space: 225990 Effective search space used: 225990 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 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