Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >FitnessBrowser__HerbieS:HSERO_RS03640 Length = 502 Score = 387 bits (993), Expect = e-112 Identities = 215/502 (42%), Positives = 316/502 (62%), Gaps = 14/502 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L+ +GI K F +A+ ++ + EI +L+GENGAGKSTL+K+L+GV PD GEIL+ Sbjct: 10 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 69 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 +G V P + GI++I+QEL + N++VA N+F+ E RT +D M Sbjct: 70 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSEL-----RTRLGLIDHAAM 124 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 +R+ +L +GA F L L+ A++Q VEI +ALV RI+ MDEPT++L+ ETE Sbjct: 125 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 184 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 +LF ++ L+ G++++++SHR+ EV ++DR+ V+RDG +GEL + E D + I++MMV Sbjct: 185 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 244 Query: 254 GREVEFFPHGIETRPGEIA-----LEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRT 308 GR + F P + A ++VR L K++ SF+VR GEVLGFAGLVGAGRT Sbjct: 245 GRSLSEFYQHQRIAPADAAQLPTVMQVRALA-GGKIRPASFDVRAGEVLGFAGLVGAGRT 303 Query: 309 ETMLLVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIV 368 E L+FG + + GDI + GR V I P A++ GI +PEDRK QGL L+M V N Sbjct: 304 ELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANAT 363 Query: 369 LPSLKKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLAT 428 + + +R GLV R ++ ++RL++K LSGGNQQKV+LA+WL Sbjct: 364 MNVASRHTRLGLV-RSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEI 422 Query: 429 NADILIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGE 488 +LI DEPTRG+D+ AK+EI++++ LA+QG AV++ISSELPE++ + DR++VM EG Sbjct: 423 APKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGM 482 Query: 489 ITAVLDNREKRVTQEEIMYYAS 510 IT L +TQE IM A+ Sbjct: 483 ITGELAG--AAITQENIMRLAT 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: 30 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: 502 Length adjustment: 35 Effective length of query: 485 Effective length of database: 467 Effective search space: 226495 Effective search space used: 226495 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