Align Ribose import ATP-binding protein RbsA 1; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein
Query= uniprot:Q9WXX0 (520 letters) >NCBI__GCF_003046325.1:WP_069332735.1 Length = 499 Score = 337 bits (864), Expect = 6e-97 Identities = 200/499 (40%), Positives = 298/499 (59%), Gaps = 13/499 (2%) Query: 14 ILKAKGIVKRFPGVVAVDNVDFEVYENEIVSLIGENGAGKSTLIKILTGVLKPDAGEILV 73 +L + + + F V + +VDF++ E+ +LIGENGAGKST +KIL G L P AGE+L+ Sbjct: 5 VLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSAGEVLL 64 Query: 74 NGERVEFHSPVDAFKKGISVIHQELNLCDNMTVAENIFLAYEAVRGQKRTLSSRVDENYM 133 +G V F S +A G+ +IHQE NL +TV ENIFL E RG +D M Sbjct: 65 DGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPF------LDHRAM 118 Query: 134 YTRSKELLDLIGAKFSPDALVRNLTTAQRQMVEICKALVKEPRIIFMDEPTSSLTVEETE 193 S+ LL+ + P A V L+ RQMVEI KAL + R++ MDEPT+ LT ET+ Sbjct: 119 QAESRRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETD 178 Query: 194 RLFEIIEMLKSRGISVVFVSHRLDEVMRISDRIVVMRDGKRIGELKKGEFDVDTIIKMMV 253 L E ++ L++ G ++++ SH+LDEV RI+DR+ V+RDG+R+ D + + MV Sbjct: 179 TLLEQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPAKGLSEDRMAETMV 238 Query: 254 GREVE-FFPHGIETRPGEIALEVRNLKWKDKVKNVSFEVRKGEVLGFAGLVGAGRTETML 312 GRE+ FP P E LEV L V++ SF +R+GEVLGFAGLVG+GRTE M Sbjct: 239 GRELSGLFPPKSSPAP-EPVLEVAGLTVPGFVRDASFTLRRGEVLGFAGLVGSGRTELME 297 Query: 313 LVFGVNQKESGDIYVNGRKVEIKNPEDAIKMGIGLIPEDRKLQGLVLRMTVKDNIVLPSL 372 + G+ + +G++ + G + + A G+ + EDRK +GL+L + +N+ L +L Sbjct: 298 GIVGL-RPATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKPLGENLTLLAL 356 Query: 373 KKISRWGLVLDERKEEEISEDYVKRLSIKTPSIYQITENLSGGNQQKVVLAKWLATNADI 432 + R +++D+ EE + I+ +LSGGNQQK++LAK + + Sbjct: 357 DRFGR--VLIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLAKTMLAEPRV 414 Query: 433 LIFDEPTRGIDVGAKAEIHRMIRELAAQGKAVIMISSELPEILNLSDRIVVMWEGEITAV 492 +I DEPTRGIDVG K +I+ I LAA+G++VI++SSELPE++ L++R+VVM G I Sbjct: 415 VIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVVMSAGRIAGE 474 Query: 493 LDNREKRVTQEEIMYYASG 511 ++ + +T+E I+ A G Sbjct: 475 VEG--EAITEENIVRLAMG 491 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: 673 Number of extensions: 32 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: 499 Length adjustment: 34 Effective length of query: 486 Effective length of database: 465 Effective search space: 225990 Effective search space used: 225990 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 24 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