Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >NCBI__GCF_900177295.1:WP_085124759.1 Length = 518 Score = 343 bits (880), Expect = 9e-99 Identities = 191/496 (38%), Positives = 293/496 (59%), Gaps = 12/496 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L+ +G+ +RFPGV+A+D VDF++ E+ L GENGAGKST+I ++ G L+P GE Sbjct: 23 LLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRF 82 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 GE VE +S A GIS + QE +L MTV EN+FL E+ R +D + Sbjct: 83 RGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTR------LGLLDRRAL 136 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 + R+ +L +G P V +LT A++QMVEI KA E ++ +DEPT+SLT ET Sbjct: 137 HDRADAILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETA 196 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 +LF++IE +K++G+ V++++HRL E+ RI DRI V+RDG+ + + ++++M Sbjct: 197 QLFKLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMT 256 Query: 254 GREV-EFFPHGIETRPGEIALEVRNLKW-KDKVKNVSFEVRKGEVLGFAGLVGAGRTETM 311 GR E FP + +PG L V L V S V GE++G AGLVG+G++E Sbjct: 257 GRVYDELFPK-VRFKPGRELLSVERLTTASGSVVEASLSVCAGEIVGLAGLVGSGKSEVA 315 Query: 312 LLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPS 371 FG+ + G + + G +V + P+ +K G +P DR+ +GL++ V++N+ LPS Sbjct: 316 RACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPS 375 Query: 372 LKKISRW-GLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNA 430 L G +LD R E + ++L+++ P I + E SGGNQQKV+LAK Sbjct: 376 LTLAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPV 435 Query: 431 DILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEIT 490 + FDEPT G+DVG + I+ IR+L G +++ISS+LPE+LNLS+R V + G + Sbjct: 436 QVFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQ 495 Query: 491 AVLDNREKRVTQEEIM 506 A L E +T+E+++ Sbjct: 496 AELAGDE--ITEEKVL 509 Score = 65.5 bits (158), Expect = 5e-15 Identities = 64/260 (24%), Positives = 106/260 (40%), Gaps = 10/260 (3%) Query: 1 MFPLLAFRGDRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKIL 60 +FP + F+ R E+L + + VV V EIV L G G+GKS + + Sbjct: 263 LFPKVRFKPGR-ELLSVERLTTASGSVV---EASLSVCAGEIVGLAGLVGSGKSEVARAC 318 Query: 61 TGVLKPDAGEILVNGERVEFHSPVDAFKKGISVI---HQELNLCDNMTVAENIFL-AYEA 116 G+ K G + + GE V P K+G + ++ L V EN+ L + Sbjct: 319 FGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPSLTL 378 Query: 117 VRGQKRTLSSRVDENYMYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPR 176 L R E R E L+L + + V + +Q V + K+ + + Sbjct: 379 APFGNGALLDRRGETDRVRRLAEQLNLQPPRI--ERAVEAFSGGNQQKVLLAKSRTRPVQ 436 Query: 177 IIFMDEPTSSLTVEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIG 236 + DEPT + V ++E I L G ++ +S L EV+ +S+R V G+ Sbjct: 437 VFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQA 496 Query: 237 ELKKGEFDVDTIIKMMVGRE 256 EL E + ++ R+ Sbjct: 497 ELAGDEITEEKVLSHFFERD 516 Lambda K H 0.319 0.138 0.381 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: 674 Number of extensions: 34 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 (21.7 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