Align ABC transporter related; Flags: Precursor (characterized, see rationale)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= uniprot:B2T9V9 (510 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 267 bits (682), Expect = 8e-76 Identities = 170/483 (35%), Positives = 262/483 (54%), Gaps = 12/483 (2%) Query: 13 PVVEALEVTKRFGSTAALNDVSIRVMPGESHALVGRNGAGKSTLVSILTGLRKPDTG-EV 71 P++E ++K F L V ++V PGE HAL+G NGAGKSTL+ IL+G + D G E+ Sbjct: 5 PLLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEI 64 Query: 72 RFSGAAAPSIADRDAWRERVACVYQHSTIIRDLSVAENLFINRQPLRGGVIDWQAMRRDA 131 R +G P+ A +A +YQ ++ +LSVAEN+++ R+ RG ID + M Sbjct: 65 RIAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWTIDRKGMEAGC 124 Query: 132 RALLDHWKIDVREDARAGDLSVEARQLVEIARALSYGARFIILDEPTAQLDGDEIKRLFR 191 +L + R LS+ RQLVEIARAL A+ +++DEPT L E RLF Sbjct: 125 IEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRETDRLFA 184 Query: 192 RISELQREGVTFLFISHHLQEVYEICQAVTVLRDARHIVSAPVSALPREQLIEAMTG-ER 250 I +L+ +G+ ++ISH + E+Y + V+VLRD +I AL E L++ M G + Sbjct: 185 LIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMMVGRDL 244 Query: 251 GGLAVADAAARGALPADTAVALELKELT-GADYEGVSFTVKRGEVVGLTGATSSGRTSVA 309 G + AA P + V + ++++ G SF + GEV+G+ G +GRT +A Sbjct: 245 SGFYKKEHAAYN--PGN--VVMRVRDMADGKRVRHCSFDLHAGEVLGIAGLVGAGRTELA 300 Query: 310 EAIAGLRAAKRGTISVDGAILPPGDVPA-SLAHGIGCVPKDRHHEGLVLTQSVAENASMT 368 I GT+ V G + P PA ++ G+ + +DR +GL L SVA+N ++ Sbjct: 301 RLIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNINV- 359 Query: 369 IARVLGKFGIAAPAKKNAF--GQKMIDALGIVAQGPEHVVSGLSGGNQQKVVMARALATN 426 A V + +A I +L I + LSGGNQQKV++AR L Sbjct: 360 CACVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEVK 419 Query: 427 PNVLVLIDPTAGVDVKSKEALLSVVDRVREEGKAVLVVSGELDD-LRTCDRVLVMFRGRV 485 P+VL+L +PT GVD+ SK + +++++ + G ++V+S EL + + TCDRVL+M G++ Sbjct: 420 PHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQL 479 Query: 486 AAE 488 AE Sbjct: 480 VAE 482 Lambda K H 0.318 0.134 0.377 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: 618 Number of extensions: 31 Number of successful extensions: 8 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: 510 Length of database: 510 Length adjustment: 34 Effective length of query: 476 Effective length of database: 476 Effective search space: 226576 Effective search space used: 226576 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