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 HSERO_RS21310 HSERO_RS21310 ABC transporter
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__HerbieS:HSERO_RS21310 Length = 518 Score = 338 bits (867), Expect = 3e-97 Identities = 195/504 (38%), Positives = 298/504 (59%), Gaps = 19/504 (3%) Query: 6 IEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKIN 65 +E+ + K + +AND ++L + GEIHA+LGENGAGKSTLM ++ G ++P +G I+ N Sbjct: 8 LEISHVRKAYPGVLANDDVSLAVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGEIRWN 67 Query: 66 GSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKAL 125 G AV I +P + +LGI MV QHF L + TVTENI LG + DLK+ + I Sbjct: 68 GEAVQIANPQVARKLGIAMVFQHFSLFDTLTVTENIALGLDAKT----DLKELAERITRT 123 Query: 126 SEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMK 185 EKYGL ++P + +SVG +QRVEI++ L +LI DEPT+VLTP +++L ++ Sbjct: 124 GEKYGLELEPQRHVHTLSVGERQRVEIVRALLTEPQLLILDEPTSVLTPQAVEKLFVTLR 183 Query: 186 SLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRS-VSF 244 L EG SI+ I+HKLDEIR++ TV+R G+ + +S L+ MM+G V Sbjct: 184 RLADEGCSILYISHKLDEIRALCHSATVMRGGRVTGNCDPRNESSASLSRMMIGDELVRL 243 Query: 245 TIEKTPTKPKETILSIKDLVVNENRGIPA-------IKGLSLEVKAGEIIGIAGIDGNGQ 297 E+ P E++ + + L VN +P +K + EV+AGEI+GIAG+ GNGQ Sbjct: 244 QRERNP----ESMRNERKLHVNR-LSLPKAHLFATELKDIECEVRAGEIVGIAGVSGNGQ 298 Query: 298 SELVQAITGLRKIKSGHLTIKGQD-VTKLSTRKITELSVGHVPEDRHRDGLILELTMAEN 356 EL+ A++G + + H+ + G V LS +G VPE+R G + L++ N Sbjct: 299 QELLAALSGEDQRAAPHMIMLGSKAVGDLSPNPRRAAGLGLVPEERLGRGAVPTLSLTAN 358 Query: 357 LALQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIARE 416 + L ++ KAP G++++ +++ F V+ A PAK SGGN QK I+ RE Sbjct: 359 MLL-SHQKAPYVKRGMIDFGFTRRAAASIIERFKVKAAGPDAPAKSLSGGNLQKFIVGRE 417 Query: 417 VDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIH 476 ++R P + +V+QPT G+DVGA IH ++ + EG AVL++S ELDE+ L DR+ VI Sbjct: 418 MERKPAVFVVAQPTWGVDVGAAAQIHGEILKLKQEGCAVLVISEELDELFALCDRLHVIA 477 Query: 477 DGQIQGIVTPETTNKQELGILMAG 500 G++ + E ++++G+ M+G Sbjct: 478 KGRLSPSIPIEQATREQVGVWMSG 501 Score = 76.3 bits (186), Expect = 3e-18 Identities = 66/236 (27%), Positives = 104/236 (44%), Gaps = 12/236 (5%) Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329 G+ A +SL V GEI + G +G G+S L++ I G K +G + G+ V + + Sbjct: 19 GVLANDDVSLAVAPGEIHAVLGENGAGKSTLMKIIFGAVKPDAGEIRWNGEAVQIANPQV 78 Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEF 389 +L + V + L LT+ EN+AL K L ++G L + Sbjct: 79 ARKLGIAMVFQ---HFSLFDTLTVTENIALGLDAKTDLKELAERITRTGEKYGLELEPQR 135 Query: 390 DVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAER 449 V S G +Q+ I R + +P LLI+ +PT L A+E + L Sbjct: 136 HVHT---------LSVGERQRVEIVRALLTEPQLLILDEPTSVLTPQAVEKLFVTLRRLA 186 Query: 450 DEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSIER 505 DEG ++L +S +LDEI L V+ G++ G P + L +M G + R Sbjct: 187 DEGCSILYISHKLDEIRALCHSATVMRGGRVTGNCDPRNESSASLSRMMIGDELVR 242 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: 543 Number of extensions: 26 Number of successful extensions: 6 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 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