Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >NCBI__GCF_900177295.1:WP_085124759.1 Length = 518 Score = 362 bits (929), Expect = e-104 Identities = 196/509 (38%), Positives = 307/509 (60%), Gaps = 10/509 (1%) Query: 14 ASSSSSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQ 73 A+ + P++ LR V +RFPGVLALD F+L GEVH L GENGAGKST++ +++G + Sbjct: 15 AAPLPAAPLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALR 74 Query: 74 RDSGDILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFID 133 G+ G+PVE+ A+ LGI + QE +L+ ++ +N+F+G E + +GL +D Sbjct: 75 PSEGEFRFRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTR-LGL-LD 132 Query: 134 EDELNRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNN 193 L+ +A AI R+ + P V LT A QQMVEIAKA + VLI+DEPTA+L Sbjct: 133 RRALHDRADAILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTE 192 Query: 194 AEIAELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTII 253 E A+LF++I ++AQGVG++YI+H++ E+R+I DR++V+RDG+Y+ATV Q T ++ Sbjct: 193 RETAQLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELV 252 Query: 254 SMMVGRALD---GEQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGA 310 +M GR D + R P +++ R ++ + S ++ GEI+G AGL+G+ Sbjct: 253 RLMTGRVYDELFPKVRFKPG---RELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGS 309 Query: 311 GRTEVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQA 370 G++EVARA FG + + G + + G + + P + G Y+ DR+ GL + V+ Sbjct: 310 GKSEVARACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRE 369 Query: 371 NIALSS--MGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAK 428 N++L S + F +D+R + + QL ++ P +E+ SGGNQQK+++AK Sbjct: 370 NVSLPSLTLAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAK 429 Query: 429 WLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVM 488 R + FDEPT G+DVG + IY+ + L E G I++ISS+LPEVL +S+R V Sbjct: 430 SRTRPVQVFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVF 489 Query: 489 CEGRITGELARADATQEKIMQLATQRESA 517 GR+ ELA + T+EK++ +R++A Sbjct: 490 YRGRVQAELAGDEITEEKVLSHFFERDAA 518 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: 604 Number of extensions: 34 Number of successful extensions: 9 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: 518 Length adjustment: 35 Effective length of query: 485 Effective length of database: 483 Effective search space: 234255 Effective search space used: 234255 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