Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_022529220.1 L248_RS05900 ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >NCBI__GCF_000469325.1:WP_022529220.1 Length = 516 Score = 312 bits (799), Expect = 2e-89 Identities = 180/502 (35%), Positives = 292/502 (58%), Gaps = 17/502 (3%) Query: 17 SSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS 76 S S I +R + KRF +A D+ ++ +GEVH L+GENGAGK+T+M +LSG+ Q S Sbjct: 2 SQSDIAIEVRGLTKRFGDFVANDHISMQIRSGEVHGLLGENGAGKTTMMNMLSGILQPTS 61 Query: 77 GDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDE 136 G+IL+ G+PV + + A LGIG++HQ L+ + + +NI +G E K +G+ Sbjct: 62 GEILVHGQPVHLASAKDATRLGIGMVHQHFMLVENFTVLENIMLGVEETKGLGV------ 115 Query: 137 LNRQAA-----AIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAAL 191 LNR+AA A+ + L +DP VG+++V QQ EI K L ++ +LI DEPTA L Sbjct: 116 LNRRAARDKVMALSKQYGLAVDPDAKVGDISVGMQQRAEILKVLYRNADILIFDEPTAVL 175 Query: 192 NNAEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDT 251 EI EL I + L +G ++ ISHK++EL+ +A +++R GK I TV + TS + Sbjct: 176 TPQEIKELLAIFQRLAQEGKAVILISHKLNELQAVAKVTTIIRRGKVIDTVDTKATSTEK 235 Query: 252 IISMMVGRALDGEQRIPPDTSRNDVV----LEVRGLNRGRAIRDVSFTLRKGEILGFAGL 307 + +MVGR + ++ P + +++ L+V + + D T+ GEI+G AG+ Sbjct: 236 LAELMVGRHVTFQRDRVPMPAGPEILKISHLQVVDNQKVTRVHDFDLTIHGGEIVGLAGI 295 Query: 308 MGAGRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMD 367 G G++E+ RAI G P G++ I G +P G+G++ EDR+ +GL + M Sbjct: 296 DGNGQSELVRAITGLMPTAGGQVTIAGQDRTGATPRQITRSGVGHIPEDRQRYGLILPMS 355 Query: 368 VQANIALS--SMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIV 425 + N++L ++ ++ G ++Q+A+ + + Q ++ S+ + A LSGGNQQK++ Sbjct: 356 LVDNMSLQVYTVAPYSHHGVLNQKAMVTTTEQLLDQYDVRHSSIMEPAGALSGGNQQKLI 415 Query: 426 IAKWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRV 485 IA+ L R+ +L PTRG+DVGA I+ L A G AI++IS EL E+ ++S RV Sbjct: 416 IARELSREPQLLIAVNPTRGLDVGAIEFIHSQLLAARAAGHAILLISYELDEIRQLSDRV 475 Query: 486 LVMCEGRITGELARADATQEKI 507 V+ +G I G+ +D ++ +I Sbjct: 476 AVIHQGTIVGQAKTSDLSESEI 497 Score = 107 bits (268), Expect = 8e-28 Identities = 75/249 (30%), Positives = 129/249 (51%), Gaps = 13/249 (5%) Query: 272 SRNDVVLEVRGLNR--GRAIRD--VSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEA 327 S++D+ +EVRGL + G + + +S +R GE+ G G GAG+T + + G + Sbjct: 2 SQSDIAIEVRGLTKRFGDFVANDHISMQIRSGEVHGLLGENGAGKTTMMNMLSGILQPTS 61 Query: 328 GEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMD 387 GEI++HG + S DA GIG + + HF L V NI L + +G ++ Sbjct: 62 GEILVHGQPVHLASAKDATRLGIGMVHQ---HFMLVENFTVLENIMLG-VEETKGLGVLN 117 Query: 388 QRAIREAAQMYVRQLAIKTPSVEQQARL--LSGGNQQKIVIAKWLLRDCDILFFDEPTRG 445 +RA R+ +Q + +V+ A++ +S G QQ+ I K L R+ DIL FDEPT Sbjct: 118 RRAARDKVMALSKQYGL---AVDPDAKVGDISVGMQQRAEILKVLYRNADILIFDEPTAV 174 Query: 446 IDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQE 505 + E+ + LA++GKA+++IS +L E+ ++ ++ G++ + + E Sbjct: 175 LTPQEIKELLAIFQRLAQEGKAVILISHKLNELQAVAKVTTIIRRGKVIDTVDTKATSTE 234 Query: 506 KIMQLATQR 514 K+ +L R Sbjct: 235 KLAELMVGR 243 Score = 80.5 bits (197), Expect = 1e-19 Identities = 60/229 (26%), Positives = 106/229 (46%), Gaps = 12/229 (5%) Query: 48 GEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII---HQ 104 GE+ L G +G G+S L++ ++G+ G + + G+ PRQ G+G I Q Sbjct: 287 GEIVGLAGIDGNGQSELVRAITGLMPTAGGQVTIAGQDRTGATPRQITRSGVGHIPEDRQ 346 Query: 105 ELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDM------DPSTPV 158 L+ +S N+ + + + LN++A LD P Sbjct: 347 RYGLILPMSLVDNMSL---QVYTVAPYSHHGVLNQKAMVTTTEQLLDQYDVRHSSIMEPA 403 Query: 159 GELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYISH 218 G L+ QQ + IA+ LS + ++LI PT L+ I + + +A G I+ IS+ Sbjct: 404 GALSGGNQQKLIIARELSREPQLLIAVNPTRGLDVGAIEFIHSQLLAARAAGHAILLISY 463 Query: 219 KMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRALDGEQRI 267 ++DE+RQ++DRV+V+ G + + S I +M G + G++ + Sbjct: 464 ELDEIRQLSDRVAVIHQGTIVGQAKTSDLSESEIGLLMAGETVPGKEEM 512 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: 619 Number of extensions: 35 Number of successful extensions: 10 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: 516 Length adjustment: 35 Effective length of query: 485 Effective length of database: 481 Effective search space: 233285 Effective search space used: 233285 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