Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate AO353_20820 AO353_20820 sugar ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__pseudo3_N2E3:AO353_20820 Length = 517 Score = 328 bits (840), Expect = 4e-94 Identities = 194/511 (37%), Positives = 310/511 (60%), Gaps = 22/511 (4%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L GI K + V + +D + E+++L GENGAGKSTL KI+ G++ P G++ Sbjct: 9 VLSVSGIGKTYAQPV-LTGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQF 67 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 G S A + GI ++ QELNL ++VAEN+FL G + ++ + + Sbjct: 68 QGRDYRPGSRTQAEELGIRMVMQELNLLPTLSVAENLFLDNLPSNGGWIS-RKQLRKAAI 126 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 ++ LD I PD LV L +QMVEI + L+ + ++ +DEPT+ LT E E Sbjct: 127 AAMAQVGLDAI----DPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVE 182 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 LFE I L++RG++++++SHRL+E+ R++ RI V+RDG + ++ + ++ +MV Sbjct: 183 MLFEQITRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVNLMV 242 Query: 254 GRE----VEFFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTE 309 GRE ++ P I G AL V+ L DKV++VSFEVR GE+ G +GL+GAGRTE Sbjct: 243 GRELGEHIDLGPRHI----GAPALTVKGLSRSDKVRDVSFEVRSGEIFGISGLIGAGRTE 298 Query: 310 TMLLVFGVNQKESGDIYVNG--RKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNI 367 + L+FG + +SG + + + V I++P DA+ GI LI EDRK +GL+L ++ NI Sbjct: 299 LLRLIFGADAADSGTVALGSPAQVVSIRSPADAVGHGIALITEDRKGEGLLLTQSISANI 358 Query: 368 VLPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLA 427 L ++ IS G+V + E +++ + + I++ S Q+ LSGGNQQKVV+ +WL Sbjct: 359 ALGNMPVISSGGIV-NSGDEMALAQRQIDAMRIRSSSPAQLVSELSGGNQQKVVIGRWLE 417 Query: 428 TNADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEG 487 +L+FDEPTRGIDVGAK +I+ ++ EL QGKA++++SS+L E++ + DRI V+ G Sbjct: 418 RECSVLLFDEPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAG 477 Query: 488 EITAVLDNREK-RVTQEEIMYYA-SGQKKQN 516 + +D E+ TQ++++ A +G +K++ Sbjct: 478 RL---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: 641 Number of extensions: 37 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 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