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_RS07080 HSERO_RS07080 ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__HerbieS:HSERO_RS07080 Length = 522 Score = 313 bits (802), Expect = 1e-89 Identities = 197/516 (38%), Positives = 299/516 (57%), Gaps = 25/516 (4%) Query: 4 HVIEMREIT--KKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGS 61 H +E+ I K F F A D ++L +R G IHALLGENGAGKSTL+ L G GS Sbjct: 2 HALELEIINAGKSFGSFRALDEVSLKIRAGTIHALLGENGAGKSTLVKGLVGYSPLDQGS 61 Query: 62 IKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQE 121 I + V I S QLGIGMV+QHF L + TV EN++L G L + Sbjct: 62 ILADRREVDIRSARVPNQLGIGMVYQHFTLAPSLTVAENLLLA-----RGDLPWRIRWSS 116 Query: 122 IKALSE----KYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEI 177 +A+ E K + P ++ +S G +Q++EILK LY LI DEPT+VLTP E Sbjct: 117 ERAVLEEFMAKMPFKLSPERTVSSLSAGEKQKLEILKQLYLRRRFLILDEPTSVLTPQEA 176 Query: 178 QELMTIMKSLVKEGK-SIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEM 236 E++ +M +L ++ + ++++ITHK E+ + AD VTV+R+G+ + + V+ T+ LA Sbjct: 177 DEVLGLMHALTRQQELTVLMITHKFHEVSAYADDVTVLRKGRLVGSARVAETSPDMLAHW 236 Query: 237 MVGRSVSFTIE-KTPTKPKETI--LSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGID 293 M+G++ + + P P + L ++DL VN +RG+ A++ LSL+V+ GEI+G+AGI Sbjct: 237 MMGQARAEKAQVARPAVPVQASVGLEVRDLTVNNDRGVAAVRALSLQVRRGEIVGLAGIS 296 Query: 294 GNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTM 353 GNGQ ELV+A+ G R++ G + ++G + ++ L V +PE+ R+ I +++ Sbjct: 297 GNGQKELVEALLGQRRLLLGEIRVEGAPYA-ATREEMRRLRVFALPEEPLRNACIAGMSV 355 Query: 354 AENLALQTYYKAPLSHNG-VLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAI 412 AEN+AL+ + AP G ++ S + + L+ F+V+ P SGGN Q+A+ Sbjct: 356 AENMALRNFDVAPFKRGGWRIDRSAMKRQAQALISAFNVKPPVPERPIGTLSGGNVQRAV 415 Query: 413 IAREVDRD-----PDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILN 467 +ARE+ D ++LIV+ P GLD ++ IH RL+ R G AVLLVS +LDE+L Sbjct: 416 LARELGEDGQDGAANVLIVANPVFGLDFASVADIHARLLQARARGAAVLLVSEDLDELLE 475 Query: 468 LSDRIAVIHDGQIQGI---VTPETTNKQELGILMAG 500 LSDRI V+ +G+I + V E ++ LG MAG Sbjct: 476 LSDRILVMTEGRIVHVAQDVAKEGADRAALGRWMAG 511 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: 576 Number of extensions: 31 Number of successful extensions: 9 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: 522 Length adjustment: 35 Effective length of query: 475 Effective length of database: 487 Effective search space: 231325 Effective search space used: 231325 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