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_011022097.1 MA_RS10955 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >NCBI__GCF_000007345.1:WP_011022097.1 Length = 267 Score = 122 bits (307), Expect = 1e-32 Identities = 94/272 (34%), Positives = 136/272 (50%), Gaps = 28/272 (10%) Query: 3 QHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSI 62 Q+++ ++ +TKKFDD A I+ D+ G I A LG NGAGKST + ML +L PTSG I Sbjct: 2 QNILSVKSLTKKFDDLTAVKGISFDVETGSIFAFLGPNGAGKSTTIKMLTTVLRPTSGEI 61 Query: 63 KINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQE- 121 ING A+ G+V Q + L T EN+ + + K + KA +E Sbjct: 62 LINGYNAL--KEQDKARSSFGIVFQDYSLDSELTAYENMEYHSVIYK-----VPKAEREE 114 Query: 122 -IKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQEL 180 IK E GL N + S G ++R+EI + L +L DEPT L P + Sbjct: 115 RIKTALEIVGLWNRRNDLVKKYSGGMKRRLEIARALVHYPKVLFLDEPTVGLDPQTRMSI 174 Query: 181 MTIMKSLVKEGK-SIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVG 239 +K L +E K +I L TH +DE ++AD++ +I GK IE SGT LAE+M Sbjct: 175 WNHIKRLNEERKMTIFLTTHYMDEAEAMADKIAIIDHGKIIE----SGT----LAEIM-- 224 Query: 240 RSVSFTIEKTPTKP-KETILSIKDLVVNENRG 270 E+T T+ +E+ L + + + G Sbjct: 225 -------ERTETESLEESFLKLTGRDIRDENG 249 Score = 74.7 bits (182), Expect = 4e-18 Identities = 72/268 (26%), Positives = 123/268 (45%), Gaps = 32/268 (11%) Query: 255 ETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGH 314 + ILS+K L + + A+KG+S +V+ G I G +G G+S ++ +T + + SG Sbjct: 2 QNILSVKSLTKKFD-DLTAVKGISFDVETGSIFAFLGPNGAGKSTTIKMLTTVLRPTSGE 60 Query: 315 LTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQT-YYKAPLSHNGVL 373 + I G + K + S G V +D D ELT EN+ + YK P + Sbjct: 61 ILINGYNALKEQDK--ARSSFGIVFQDYSLDS---ELTAYENMEYHSVIYKVPKA----- 110 Query: 374 NYSKINEHGRHLMQEFDVRG----ANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQP 429 E + ++ G N+L+ K +SGG +++ IAR + P +L + +P Sbjct: 111 ------EREERIKTALEIVGLWNRRNDLV--KKYSGGMKRRLEIARALVHYPKVLFLDEP 162 Query: 430 TRGLDVGAIEYIHKRLIAERDEGK-AVLLVSFELDEILNLSDRIAVIHDGQI-------Q 481 T GLD I + +E K + L + +DE ++D+IA+I G+I + Sbjct: 163 TVGLDPQTRMSIWNHIKRLNEERKMTIFLTTHYMDEAEAMADKIAIIDHGKIIESGTLAE 222 Query: 482 GIVTPETTNKQELGILMAGGSIEREEIN 509 + ET + +E + + G I E N Sbjct: 223 IMERTETESLEESFLKLTGRDIRDENGN 250 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: 307 Number of extensions: 22 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: 267 Length adjustment: 30 Effective length of query: 480 Effective length of database: 237 Effective search space: 113760 Effective search space used: 113760 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: 49 (23.5 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