Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate WP_085124759.1 B9O00_RS21320 sugar ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >NCBI__GCF_900177295.1:WP_085124759.1 Length = 518 Score = 306 bits (785), Expect = 9e-88 Identities = 167/493 (33%), Positives = 277/493 (56%), Gaps = 4/493 (0%) Query: 2 AQHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGS 61 A ++E+R ++++F +A D ++ LR GE+H L GENGAGKST+++M+AG L P+ G Sbjct: 20 AAPLLELRGVSRRFPGVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGE 79 Query: 62 IKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQE 121 + G V ++S + LGI V Q F LV TV EN+ LG E + G+LD + Sbjct: 80 FRFRGEPVELNSVHHARGLGISAVFQEFSLVPQMTVEENLFLGAESTRLGLLDRRALHDR 139 Query: 122 IKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELM 181 A+ ++ G + P ++ ++ QQ VEI K +LI DEPTA LT E +L Sbjct: 140 ADAILKRLGFPLRPRDRVLHLTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLF 199 Query: 182 TIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRS 241 +++ + +G +I ITH+L EIR + DR+TV+R G+ + TV+ T +L +M GR Sbjct: 200 KLIEQVKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTGRV 259 Query: 242 VSFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELV 301 K KP +LS++ L + A SL V AGEI+G+AG+ G+G+SE+ Sbjct: 260 YDELFPKVRFKPGRELLSVERLTTASGSVVEA----SLSVCAGEIVGLAGLVGSGKSEVA 315 Query: 302 QAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQT 361 +A GL KI GH+ +KG++VT +++ + +VP DR +GL++ + EN++L + Sbjct: 316 RACFGLEKIAEGHVRLKGEEVTGQGPKRMLKRGFFYVPPDRRDEGLMMMRPVRENVSLPS 375 Query: 362 YYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDP 421 AP + +L+ + R L ++ +++ + FSGGNQQK ++A+ R Sbjct: 376 LTLAPFGNGALLDRRGETDRVRRLAEQLNLQPPRIERAVEAFSGGNQQKVLLAKSRTRPV 435 Query: 422 DLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQ 481 + +PT G+DVG I++ + + G +LL+S +L E+LNLS+R V + G++Q Sbjct: 436 QVFAFDEPTVGVDVGTRVAIYEFIRDLCEAGAGILLISSDLPEVLNLSNRAYVFYRGRVQ 495 Query: 482 GIVTPETTNKQEL 494 + + ++++ Sbjct: 496 AELAGDEITEEKV 508 Score = 72.0 bits (175), Expect = 5e-17 Identities = 56/233 (24%), Positives = 109/233 (46%), Gaps = 12/233 (5%) Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329 G+ A+ + +++ GE+ + G +G G+S ++ I G + G +G+ V S Sbjct: 35 GVLALDKVDFQLRPGEVHVLFGENGAGKSTMISMIAGALRPSEGEFRFRGEPVELNSVHH 94 Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQE- 388 L + V ++ L+ ++T+ ENL L A + G+L+ +++ +++ Sbjct: 95 ARGLGISAVFQEF---SLVPQMTVEENLFLG----AESTRLGLLDRRALHDRADAILKRL 147 Query: 389 -FDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIA 447 F +R + ++ + QQ IA+ + +LI+ +PT L + K + Sbjct: 148 GFPLRPRDRVLH---LTRAEQQMVEIAKAFRSELSVLILDEPTASLTERETAQLFKLIEQ 204 Query: 448 ERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAG 500 + +G V+ ++ L EI + DRI V+ DG+ V +TT + EL LM G Sbjct: 205 VKAQGVGVIYITHRLSEIRRIGDRITVLRDGRYVATVDAQTTPEGELVRLMTG 257 Lambda K H 0.315 0.135 0.363 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: 545 Number of extensions: 29 Number of successful extensions: 5 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: 510 Length of database: 518 Length adjustment: 35 Effective length of query: 475 Effective length of database: 483 Effective search space: 229425 Effective search space used: 229425 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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