Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate AO356_00965 AO356_00965 sugar ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_00965 Length = 517 Score = 333 bits (853), Expect = 1e-95 Identities = 196/516 (37%), Positives = 311/516 (60%), Gaps = 24/516 (4%) Query: 10 DRMEILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAG 69 D +L GI K + V D ++ + E+++L GENGAGKSTL KI+ G++ P G Sbjct: 5 DPNAVLCVSGIGKTYAQPVLTD-INLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTG 63 Query: 70 EILVNGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVD 129 ++ G+ S A + G+ ++ QELNL ++VAEN+FL G + Sbjct: 64 QMQFQGQDYRPGSRTQAEELGVRMVMQELNLLPTLSVAENLFLDNLPSHG------GWIS 117 Query: 130 ENYMYTRSKELLDLIGAK-FSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLT 188 + + E + +G PD LV L +QMVEI + L+ + ++ +DEPT+ LT Sbjct: 118 RKQLRKAAIEAMAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLT 177 Query: 189 VEETERLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTI 248 E E LFE I L++RG++++++SHRL+E+ R++ RI V+RDG + +D + + Sbjct: 178 AREVEMLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYDSEQL 237 Query: 249 IKMMVGRE----VEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVG 304 + +MVGRE ++ P I G AL V+ L DKV++VSFEVR GE+ G +GL+G Sbjct: 238 VTLMVGRELGEHIDLGPRQI----GAPALTVKGLTRSDKVRDVSFEVRSGEIFGISGLIG 293 Query: 305 AGRTETMLLVFGVNQKESGDIYVN--GRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMT 362 AGRTE + L+FG + +SG + + R V I++P DA+ GI LI EDRK +GL+L + Sbjct: 294 AGRTELLRLIFGADPADSGTVALGSPARVVSIRSPSDAVAHGIALITEDRKGEGLLLTQS 353 Query: 363 VKDNIVLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVL 422 + NI L ++ +IS GLV + E +++ V + I++ S Q+ LSGGNQQKVV+ Sbjct: 354 IAANIALGNMPEISSAGLV-NGSAELALAQRQVDAMRIRSSSPTQLVSELSGGNQQKVVI 412 Query: 423 AKWLATNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIV 482 +WL + +++FDEPTRGIDVGAK +I+ ++ EL QGKA++++SS+L E++ + DRI Sbjct: 413 GRWLERDCAVMLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIG 472 Query: 483 VMWEGEITAVLDNREK-RVTQEEIMYYA-SGQKKQN 516 V+ G + +D E+ TQ++++ A +G +K++ Sbjct: 473 VLSAGRL---IDTFERDSWTQDDLLAAAFAGYQKRD 505 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: 650 Number of extensions: 35 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: 520 Length of database: 517 Length adjustment: 35 Effective length of query: 485 Effective length of database: 482 Effective search space: 233770 Effective search space used: 233770 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