Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 402 bits (1034), Expect = e-116 Identities = 221/501 (44%), Positives = 326/501 (65%), Gaps = 9/501 (1%) Query: 1 MEALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGT 60 +E LL+++GI K F G++ L L VYPG + AL+GENGAGKST+MK+L+G Y D G Sbjct: 3 LEPLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGG 62 Query: 61 LLWLGKETTFT-GPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMY 119 + + + T P +++ GI +I+QEL+L P L++AENI+LGRE + R ID K M Sbjct: 63 EIRIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRE-LRRGWTIDRKGME 121 Query: 120 AEADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETES 179 A ++L +L F V LSI ++Q+VEIA+ L +K+++MDEPT L+ ET+ Sbjct: 122 AGCIEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDR 181 Query: 180 LFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVG 239 LF +I++L+SQG I+YISHRM EI+ + D V+V RDG +I E +L+ ++L++MMVG Sbjct: 182 LFALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVG 241 Query: 240 RKLEDQYP--HLDKAPGDIRLKVDNLC-GPGVNDVSFTLRKGEILGVSGLMGAGRTELMK 296 R L Y H PG++ ++V ++ G V SF L GE+LG++GL+GAGRTEL + Sbjct: 242 RDLSGFYKKEHAAYNPGNVVMRVRDMADGKRVRHCSFDLHAGEVLGIAGLVGAGRTELAR 301 Query: 297 VLYGALPRTSGYVTLDGHEVVT-RSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTA 355 +++ A PRTSG + + G V R+P D + G+VY++EDRK GL L MSV +N+++ A Sbjct: 302 LIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNINVCA 361 Query: 356 LRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPK 415 + AGG L Q +D I+ +++ S + G LSGGNQQKV +AR L +P Sbjct: 362 CVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEVKPH 421 Query: 416 VLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSG 475 VLILDEPTRGVD+G+K EIY++INQ G+ I+++SSE+PE++G DR+++M EG L Sbjct: 422 VLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQLVA 481 Query: 476 EF---TREQATQEVLMAAAVG 493 E + + +QE ++ A G Sbjct: 482 EVGGASGQAISQERIIDLATG 502 Score = 100 bits (249), Expect = 1e-25 Identities = 73/225 (32%), Positives = 109/225 (48%), Gaps = 8/225 (3%) Query: 271 VSFTLRKGEILGVSGLMGAGRTELMKVLYGALPRT-SGYVTLDGHEVVTRSPQDGLANGI 329 V + GEI + G GAG++ LMK+L GA G + + G + T P A GI Sbjct: 25 VGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEIRIAGQLIPTFDPATAKALGI 84 Query: 330 VYISEDRKRDGLVLGMSVKENMSLTALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSM 389 I ++ L +SV EN+ L R R + E + RL TP+ Sbjct: 85 AVIYQELS---LCPNLSVAENIYLG--RELRRGWTIDRKGMEAGCIEVLQRLGAEFTPAT 139 Query: 390 EQAIGLLSGGNQQKVAIARGLMTRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSII 449 + LS +Q V IAR L K+L++DEPT + ++ LI Q ++ GL+II Sbjct: 140 R--VSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFALIKQLRSQGLAII 197 Query: 450 LVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQATQEVLMAAAVGK 494 +S M E+ +SDR+ V+ +GH GE TR+ + E L+ VG+ Sbjct: 198 YISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVGR 242 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: 661 Number of extensions: 27 Number of successful extensions: 9 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: 510 Length adjustment: 34 Effective length of query: 467 Effective length of database: 476 Effective search space: 222292 Effective search space used: 222292 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