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_085545256.1 B9Y55_RS10130 ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >NCBI__GCF_900177735.1:WP_085545256.1 Length = 503 Score = 435 bits (1118), Expect = e-126 Identities = 222/499 (44%), Positives = 336/499 (67%), Gaps = 2/499 (0%) Query: 8 MREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKINGS 67 M+ ITK F AND I+L L+KGE+ ALLGENGAGKSTLMN+L+G+ P G+I I G+ Sbjct: 1 MKGITKSFQGIKANDQIDLTLKKGEVLALLGENGAGKSTLMNVLSGIYLPDGGTIDIGGT 60 Query: 68 AVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKALSE 127 ++ SP+ + GIGMVHQHFMLV + TV EN++LG + IL K EI A+S+ Sbjct: 61 RLSFRSPNDAISAGIGMVHQHFMLVPSQTVWENMVLGLPDLPQ-ILPKGKIISEITAISK 119 Query: 128 KYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSL 187 +YGL VDP A I +S+G QQRVEILKTLYR A +LI DEPTAVLTP E + L +K + Sbjct: 120 QYGLEVDPEAIIWQLSIGEQQRVEILKTLYRNAQVLILDEPTAVLTPQEARSLFNTIKRM 179 Query: 188 VKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVSFTIE 247 +EG+ II I+HKLDE+ ++DRVTV+R+GK I TV+ + + +AEMMVG+ ++ ++ Sbjct: 180 TEEGRGIIFISHKLDEVMEISDRVTVLRKGKLIGTVDRENASKEKIAEMMVGKRINLDLD 239 Query: 248 KTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGL 307 K P E + S+ +RG+ A+ +SLE++ G+I+G+AG+ GNGQ+EL Q + GL Sbjct: 240 KKDITPGEVVYSLSQANAISDRGLKALDQVSLELREGQILGLAGVAGNGQTELCQVMAGL 299 Query: 308 RKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPL 367 RK+ SG L +KG++VT S R++ + + ++P DR G++ + + EN L+ Y++ P+ Sbjct: 300 RKMTSGKLILKGKEVTDSSPRELIDGGIRYIPADRKGTGMVSNMDVRENSTLKRYWRRPV 359 Query: 368 SHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVS 427 + ++++ + +H +++ F+V + P + SGGN QK ++ RE+ P +LI Sbjct: 360 ARGVLIDWKAVLKHALGIVKNFNVDTPSVETPVRNLSGGNIQKLMLGRELSDIPKVLIAM 419 Query: 428 QPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIV-TP 486 PT GLDV A ++ ++L+ ER++G A+ L+S +LDE+++LSDRIAV++ G+I G+V P Sbjct: 420 NPTWGLDVAATRFVREQLLEEREKGAAIFLISEDLDELMSLSDRIAVMYRGKIMGLVEDP 479 Query: 487 ETTNKQELGILMAGGSIER 505 T + +G++MAG IE+ Sbjct: 480 NTFGIERIGMMMAGTRIEQ 498 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: 649 Number of extensions: 32 Number of successful extensions: 7 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: 510 Length of database: 503 Length adjustment: 34 Effective length of query: 476 Effective length of database: 469 Effective search space: 223244 Effective search space used: 223244 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 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