Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 386 bits (992), Expect = e-112 Identities = 217/507 (42%), Positives = 327/507 (64%), Gaps = 11/507 (2%) Query: 21 PVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRD-SGDI 79 P++ ++ + K F G+ L ++ GE+HALMGENGAGKSTLMKILSG YQ D G+I Sbjct: 5 PLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEI 64 Query: 80 LLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNR 139 + G+ + +P A+ALGI +I+QEL+L +LS A+NI++GRE R+ G ID + Sbjct: 65 RIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRR--GWTIDRKGMEA 122 Query: 140 QAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAEL 199 + R+ + P+T V L++A +Q+VEIA+AL +++L+MDEPT L++ E L Sbjct: 123 GCIEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRL 182 Query: 200 FRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGR 259 F +I+ L++QG+ I+YISH+M E+ ++DRVSV+RDG YI + S + ++ MMVGR Sbjct: 183 FALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVGR 242 Query: 260 ALDG-EQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARA 318 L G ++ + +VV+ VR + G+ +R SF L GE+LG AGL+GAGRTE+AR Sbjct: 243 DLSGFYKKEHAAYNPGNVVMRVRDMADGKRVRHCSFDLHAGEVLGIAGLVGAGRTELARL 302 Query: 319 IFGADPLEAGEIIIHGGKAV--IKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSS 376 IF ADP +G + + GKAV +++PADA+ G+ YL+EDRK GL + M V NI + + Sbjct: 303 IFAADPRTSGTLEV-VGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNINVCA 361 Query: 377 MGRFTRV-GFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCD 435 G +D+ + + ++ L+I+ S + A LSGGNQQK+++A+ L Sbjct: 362 CVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEVKPH 421 Query: 436 ILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITG 495 +L DEPTRG+D+G+KSEIY++++ LA+ G IV+ISSELPE++ RVL+M EG++ Sbjct: 422 VLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQLVA 481 Query: 496 ELARADA---TQEKIMQLATQRESAVA 519 E+ A +QE+I+ LAT + VA Sbjct: 482 EVGGASGQAISQERIIDLATGGDQVVA 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: 665 Number of extensions: 36 Number of successful extensions: 11 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 520 Length of database: 510 Length adjustment: 35 Effective length of query: 485 Effective length of database: 475 Effective search space: 230375 Effective search space used: 230375 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 17 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