Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 391 bits (1005), Expect = e-113 Identities = 225/507 (44%), Positives = 320/507 (63%), Gaps = 15/507 (2%) Query: 13 LLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGECH 72 LL + NI K FPGV AL V+L G V ALMGENGAGKSTLMKI++G Y D GE Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPD-AGEIR 81 Query: 73 IDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRA-LQRRGLVARGDMVRAC 131 + G+ + + P +A+ G+A+I+QEL+L P++S+AENI++GR L +V +M R Sbjct: 82 LRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCT 141 Query: 132 APTLARLGADFSPAANVASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETDRLFA 191 A LARL + P V +LSIA+RQ+VEIA+AV +++ IL+MDEPT+ ++ E LF+ Sbjct: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201 Query: 192 LIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMVGRDL 251 +I L+ +G I+YI+H+M E+ +AD V V RDG ++G ++ +L+ MMVGR+L Sbjct: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261 Query: 252 SGFYTKTHGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRTELARLVF 311 S + + +++L+VRD+ K SFDL AGE+LG+AGL+G+GRT +A +F Sbjct: 262 SQLFPLR--ETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319 Query: 312 GADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQSVHENIN 371 G + G++ + A + P AI+ G A LTEDRKL GLF SV EN+ Sbjct: 320 GITPSSSGQITLDGKA-------VRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENME 372 Query: 372 LIVAARDALGLGRLNRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQKVMLSRLLEI 431 + V G G + + A R + L ++ + + LSGGNQQK +L+R L Sbjct: 373 MAVLPHYT-GNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMT 431 Query: 432 QPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCDRVLVMREGT 491 PR+LILDEPTRG+D+GAK+EIYRLI LA G+A++MISSELPEV+G+ DRV+VM EG Sbjct: 432 NPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGE 491 Query: 492 LAGEVRPAGSAAETQERIIALATGAAA 518 L G + + TQE+++ LA+G A Sbjct: 492 LMGTL---DRSEATQEKVMQLASGMTA 515 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: 596 Number of extensions: 25 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: 540 Length of database: 517 Length adjustment: 35 Effective length of query: 505 Effective length of database: 482 Effective search space: 243410 Effective search space used: 243410 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 Apr 09 2024. 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