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 17628 b3567 fused D-xylose transporter subunits of ABC superfamily: ATP-binding components (NCBI)
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__Keio:17628 Length = 513 Score = 293 bits (750), Expect = 1e-83 Identities = 179/514 (34%), Positives = 290/514 (56%), Gaps = 12/514 (2%) Query: 4 HVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTS--GS 61 +++EM+ ITK F A D++ L L GEI +L GENG+GKSTLM +L G+ S G Sbjct: 3 YLLEMKNITKTFGSVKAIDNVCLRLNAGEIVSLCGENGSGKSTLMKVLCGIYPHGSYEGE 62 Query: 62 IKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQE 121 I G + + + GI ++HQ LV+ TV ENI LGNE+ NGI+D Sbjct: 63 IIFAGEEIQASHIRDTERKGIAIIHQELALVKELTVLENIFLGNEITHNGIMDYDLMTLR 122 Query: 122 IKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELM 181 + L + L++ P+ ++ D+ +G QQ VEI K L + +LI DEPTA LT E L+ Sbjct: 123 CQKLLAQVSLSISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETSILL 182 Query: 182 TIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRS 241 I++ L + G + I I+HKL+E+++++D + VIR G+ I T + +G + D+ MMVGR Sbjct: 183 DIIRDLQQHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRDAAGMSEDDIITMMVGRE 242 Query: 242 VSFTIEKTPTKPKETILSIKDLVV--NENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSE 299 ++ P + IL I+ L NR I + +S +K GEI+GIAG+ G G++E Sbjct: 243 LTALYPNEPHTTGDEILRIEHLTAWHPVNRHIKRVNDVSFSLKRGEILGIAGLVGAGRTE 302 Query: 300 LVQAITGLRKIK-SGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLA 358 +Q + G+ + G + I G+ V + ++ + VPEDR RDG++ + + +N+ Sbjct: 303 TIQCLFGVWPGQWEGKIYIDGKQVDIRNCQQAIAQGIAMVPEDRKRDGIVPVMAVGKNIT 362 Query: 359 LQTYYKAPLSHNGVLNYSKINEHGRHL--MQEFDVRGANELIPAKGFSGGNQQKAIIARE 416 L K G+ E L +Q+ V+ ++ + SGGNQQKAI+AR Sbjct: 363 LAALNKFT---GGISQLDDAAEQKCILESIQQLKVKTSSPDLAIGRLSGGNQQKAILARC 419 Query: 417 VDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIH 476 + +P +LI+ +PTRG+D+GA I+K + +G AV+++S EL E+L LSDR+ V+H Sbjct: 420 LLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRVLVMH 479 Query: 477 DGQIQ-GIVTPETTNKQEL-GILMAGGSIEREEI 508 +G+++ ++ T +Q + L + +E++ + Sbjct: 480 EGKLKANLINHNLTQEQVMEAALRSEHHVEKQSV 513 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: 580 Number of extensions: 26 Number of successful extensions: 8 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: 513 Length adjustment: 35 Effective length of query: 475 Effective length of database: 478 Effective search space: 227050 Effective search space used: 227050 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 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