Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 611 bits (1576), Expect = e-179 Identities = 325/504 (64%), Positives = 383/504 (75%), Gaps = 6/504 (1%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 PLL ++ I KTF G+R L+ V L Y GE+HALMGENGAGKSTLMKILSGAY ADPGGE Sbjct: 5 PLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEI 64 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 I GQ + P +A+ LG+AVIYQELSL PNLSVAENIYLGR L+R + R M C Sbjct: 65 RIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWTIDRKGMEAGC 124 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 L RLGA+F+PA V+SLSIA+RQLVEIARA+H A+ILVMDEPTTPLS+ ETDRLFA Sbjct: 125 IEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFA 184 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 LI+QLR +G+AI+YISHRMAEI L+DRV+VLRDG ++G L R LS ALVKMMVGRDL Sbjct: 185 LIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVGRDL 244 Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311 SGFY K H V++ VRD+ADG+RV+ CSFDL AGEVLG+AGLVGAGRTELARL+F Sbjct: 245 SGFYKKEHAAYNPGNVVMRVRDMADGKRVRHCSFDLHAGEVLGIAGLVGAGRTELARLIF 304 Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371 AD RT G + + G P P AI AG+ YLTEDRK QGLFLD SV +NIN Sbjct: 305 AADPRTSGTLEVV------GKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNIN 358 Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431 + DA G L+R A +R+ +AI +L IRVA +VN GALSGGNQQKV+L+RLLE+ Sbjct: 359 VCACVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEV 418 Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491 +P VLILDEPTRGVDIG+KSEIYR+IN LAQ+G+ I++ISSELPE++G CDRVL+MREG Sbjct: 419 KPHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQ 478 Query: 492 LAGEVRPAGSAAETQERIIALATG 515 L EV A A +QERII LATG Sbjct: 479 LVAEVGGASGQAISQERIIDLATG 502 Lambda K H 0.320 0.136 0.382 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: 762 Number of extensions: 30 Number of successful extensions: 5 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: 540 Length of database: 510 Length adjustment: 35 Effective length of query: 505 Effective length of database: 475 Effective search space: 239875 Effective search space used: 239875 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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