Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2673 PS417_13635 D-ribose transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__WCS417:GFF2673 Length = 510 Score = 385 bits (990), Expect = e-111 Identities = 215/503 (42%), Positives = 322/503 (64%), Gaps = 11/503 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPD-AGEIL 72 +L+ +GI K F G+ + V +VY EI +L+GENGAGKSTL+KIL+G + D GEI Sbjct: 6 LLEMQGISKTFNGLRVLKTVGLKVYPGEIHALMGENGAGKSTLMKILSGAYQADPGGEIR 65 Query: 73 VNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENY 132 + G+ + P A GI+VI+QEL+LC N++VAENI+L E RG +D Sbjct: 66 IAGQLIPTFDPATAKALGIAVIYQELSLCPNLSVAENIYLGRELRRGWT------IDRKG 119 Query: 133 MYTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEET 192 M E+L +GA+F+P V +L+ A+RQ+VEI +AL +I+ MDEPT+ L+ ET Sbjct: 120 MEAGCIEVLQRLGAEFTPATRVSSLSIAERQLVEIARALHAHAKILVMDEPTTPLSSRET 179 Query: 193 ERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMM 252 +RLF +I+ L+S+G++++++SHR+ E+ +SDR+ V+RDG IGEL + + ++KMM Sbjct: 180 DRLFALIKQLRSQGLAIIYISHRMAEIYALSDRVSVLRDGHYIGELTRDALSAEALVKMM 239 Query: 253 VGREVEFF--PHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTET 310 VGR++ F PG + + VR++ +V++ SF++ GEVLG AGLVGAGRTE Sbjct: 240 VGRDLSGFYKKEHAAYNPGNVVMRVRDMADGKRVRHCSFDLHAGEVLGIAGLVGAGRTEL 299 Query: 311 MLLVFGVNQKESGDIYVNGRKVE-IKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVL 369 L+F + + SG + V G+ V ++ P DAI+ G+ + EDRK QGL L M+V DNI + Sbjct: 300 ARLIFAADPRTSGTLEVVGKAVTPLRTPADAIRAGVVYLTEDRKAQGLFLDMSVADNINV 359 Query: 370 PSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATN 429 + + G VLD + S D +K LSI+ S LSGGNQQKV+LA+ L Sbjct: 360 CACVPDAHAGGVLDRDHALQRSNDAIKSLSIRVASGKVNAGALSGGNQQKVLLARLLEVK 419 Query: 430 ADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEI 489 +LI DEPTRG+D+G+K+EI+R+I +LA G +++ISSELPEI+ DR+++M EG++ Sbjct: 420 PHVLILDEPTRGVDIGSKSEIYRIINQLAQAGIGIVVISSELPEIIGTCDRVLIMREGQL 479 Query: 490 TAVLDNRE-KRVTQEEIMYYASG 511 A + + ++QE I+ A+G Sbjct: 480 VAEVGGASGQAISQERIIDLATG 502 Lambda K H 0.319 0.138 0.381 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: 632 Number of extensions: 37 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: 520 Length of database: 510 Length adjustment: 35 Effective length of query: 485 Effective length of database: 475 Effective search space: 230375 Effective search space used: 230375 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 (21.7 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