Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate GFF2770 PGA1_c28130 ABC transporter, ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__Phaeo:GFF2770 Length = 505 Score = 283 bits (724), Expect = 1e-80 Identities = 175/481 (36%), Positives = 264/481 (54%), Gaps = 14/481 (2%) Query: 2 EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61 + LL L+G+ KA+PGV A + ++ G V AL+GENGAGKST++K++ G+ D+G + Sbjct: 3 QPLLSLQGLTKAYPGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKM 62 Query: 62 LWLGKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121 L G+ T P+ ++ GI ++ Q +L L +AENI LG E + + + Sbjct: 63 LLHGEPYTPGEPRQARADGIAMVFQHFSLFDALNVAENIALGMETPPAL-----RDLATQ 117 Query: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181 K+ L + VGDLS G++Q VEI + L + K++IMDEPT LT E E LF Sbjct: 118 IRKVSETYGLPLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILF 177 Query: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241 + +++L+S+G I+YISH+++EI +CD T+ R G+ + E + + + EMMVG Sbjct: 178 QTLQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARDMAEMMVGTA 237 Query: 242 LEDQYPHLDKAPGDIRLKVDNLC-------GPGVNDVSFTLRKGEILGVSGLMGAGRTEL 294 L+ +A GD+ L + L G + +V T+RKGEILGV G+ G G+ EL Sbjct: 238 LQTP-ERSGRALGDVALDISGLSVPAPSAFGTALKNVHMTVRKGEILGVGGVAGNGQDEL 296 Query: 295 MKVLYGALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLT 354 + VL G + VTLDG + P GI+ E+R MS+ EN LT Sbjct: 297 LGVLSGETTTAADAVTLDGAPIGNLGPVARRRLGILAAPEERLGHAAAPDMSLTENAMLT 356 Query: 355 -ALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTR 413 A R + G LK Q+ I+ F+V+TP E A LSGGN QK I R ++ R Sbjct: 357 AATREGLASRGFLKWGLAQEFAEKVIKSFDVRTPGPENAARSLSGGNLQKFVIGREVLQR 416 Query: 414 PKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHL 473 P VL++++PT GVD A I Q + A G ++I +S ++ E++ ++D ++EG L Sbjct: 417 PDVLVVNQPTWGVDAAAAAAIRQSLLDLAAGGTAVICISQDLDELMEIADSFAALNEGRL 476 Query: 474 S 474 S Sbjct: 477 S 477 Score = 83.2 bits (204), Expect = 2e-20 Identities = 67/236 (28%), Positives = 115/236 (48%), Gaps = 24/236 (10%) Query: 266 PGV--ND-VSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRTSGYVTLDGHEVVTRSPQ 322 PGV ND VSF + GE+ + G GAG++ L+K++YG + SG + L G P+ Sbjct: 16 PGVVANDTVSFDIGAGEVHALLGENGAGKSTLVKMIYGLVKPDSGKMLLHGEPYTPGEPR 75 Query: 323 DGLANGIVYISEDRKRDGLVLGMSVKENMSL-----TALRYFSRAGGSLKHADEQQAVSD 377 A+GI + + L ++V EN++L ALR A + + VS+ Sbjct: 76 QARADGIAMVFQ---HFSLFDALNVAENIALGMETPPALRDL---------ATQIRKVSE 123 Query: 378 FIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQL 437 L + +G LS G +Q+V I R L+ PK+LI+DEPT + + ++Q Sbjct: 124 TYGL----PLDPYRTVGDLSAGERQRVEIIRCLLQDPKLLIMDEPTSVLTPQEVEILFQT 179 Query: 438 INQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVG 493 + + +++G SI+ +S ++ E+ + D ++ G GE + + + VG Sbjct: 180 LQKLRSEGTSILYISHKLEEIRTLCDHATILRLGKNVGECVPSETSARDMAEMMVG 235 Lambda K H 0.318 0.137 0.380 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: 596 Number of extensions: 34 Number of successful extensions: 7 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: 501 Length of database: 505 Length adjustment: 34 Effective length of query: 467 Effective length of database: 471 Effective search space: 219957 Effective search space used: 219957 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: 41 (21.7 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