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 GFF2770 PGA1_c28130 ABC transporter, ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__Phaeo:GFF2770 Length = 505 Score = 325 bits (833), Expect = 2e-93 Identities = 182/501 (36%), Positives = 288/501 (57%), Gaps = 6/501 (1%) Query: 1 MAQHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSG 60 M Q ++ ++ +TK + VAND ++ D+ GE+HALLGENGAGKSTL+ M+ GL++P SG Sbjct: 1 MTQPLLSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSG 60 Query: 61 SIKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQ 120 + ++G T P ++ GI MV QHF L +A V ENI LG E L+ Sbjct: 61 KMLLHGEPYTPGEPRQARADGIAMVFQHFSLFDALNVAENIALGMETPPA----LRDLAT 116 Query: 121 EIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQEL 180 +I+ +SE YGL +DP + D+S G +QRVEI++ L + +LI DEPT+VLTP E++ L Sbjct: 117 QIRKVSETYGLPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEIL 176 Query: 181 MTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGR 240 ++ L EG SI+ I+HKL+EIR++ D T++R GK++ S T+++D+AEMMVG Sbjct: 177 FQTLQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARDMAEMMVGT 236 Query: 241 SVSFTIEKTPTKPKETILSIKDLVVNENRGI-PAIKGLSLEVKAGEIIGIAGIDGNGQSE 299 ++ T E++ + L I L V A+K + + V+ GEI+G+ G+ GNGQ E Sbjct: 237 ALQ-TPERSGRALGDVALDISGLSVPAPSAFGTALKNVHMTVRKGEILGVGGVAGNGQDE 295 Query: 300 LVQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLAL 359 L+ ++G + +T+ G + L L + PE+R ++++ EN L Sbjct: 296 LLGVLSGETTTAADAVTLDGAPIGNLGPVARRRLGILAAPEERLGHAAAPDMSLTENAML 355 Query: 360 QTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDR 419 + L+ G L + E +++ FDVR A+ SGGN QK +I REV + Sbjct: 356 TAATREGLASRGFLKWGLAQEFAEKVIKSFDVRTPGPENAARSLSGGNLQKFVIGREVLQ 415 Query: 420 DPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQ 479 PD+L+V+QPT G+D A I + L+ G AV+ +S +LDE++ ++D A +++G+ Sbjct: 416 RPDVLVVNQPTWGVDAAAAAAIRQSLLDLAAGGTAVICISQDLDELMEIADSFAALNEGR 475 Query: 480 IQGIVTPETTNKQELGILMAG 500 + + E+G++M G Sbjct: 476 LSAPRPTAGLSVDEIGLMMGG 496 Score = 82.4 bits (202), Expect = 3e-20 Identities = 65/238 (27%), Positives = 112/238 (47%), Gaps = 12/238 (5%) Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329 G+ A +S ++ AGE+ + G +G G+S LV+ I GL K SG + + G+ T R+ Sbjct: 17 GVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKMLLHGEPYTPGEPRQ 76 Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEF 389 + V + L L +AEN+AL P + K++E + + Sbjct: 77 ARADGIAMVFQ---HFSLFDALNVAENIALGME-TPPALRDLATQIRKVSETYGLPLDPY 132 Query: 390 DVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAER 449 G S G +Q+ I R + +DP LLI+ +PT L +E + + L R Sbjct: 133 RTVG--------DLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFQTLQKLR 184 Query: 450 DEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSIEREE 507 EG ++L +S +L+EI L D ++ G+ G P T+ +++ +M G +++ E Sbjct: 185 SEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARDMAEMMVGTALQTPE 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: 564 Number of extensions: 19 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: 505 Length adjustment: 34 Effective length of query: 476 Effective length of database: 471 Effective search space: 224196 Effective search space used: 224196 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