Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate WP_012042345.1 BBTA_RS09915 sugar ABC transporter ATP-binding protein
Query= uniprot:D8IZC7 (521 letters) >NCBI__GCF_000015165.1:WP_012042345.1 Length = 516 Score = 374 bits (961), Expect = e-108 Identities = 208/491 (42%), Positives = 304/491 (61%), Gaps = 5/491 (1%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 LL++RG+ KSFGA AL D+ T+ GEIHAL+GENGAGKSTL+KV++GV A D G + L Sbjct: 14 LLEIRGLTKSFGALKALQDVDFTLGEGEIHALLGENGAGKSTLIKVVTGVFARDAGTVRL 73 Query: 66 DGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRTD 125 G +A R + AGI +YQE+ + PN+SVA N+++G + TR G++ A MR R Sbjct: 74 AGDEIAPRSAKDAVEAGIATVYQEVNLLPNLSVAQNLYLGRQ-PTRFGVVRQAEMRRRAH 132 Query: 126 AVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFNV 185 A+L G S+A Q IARA+ +R++I+DEPTA+L E E LF V Sbjct: 133 ALLLDYGLDIDVGAPLASYSVAVQHITAIARAVDLSARVLILDEPTASLDRHEVEILFRV 192 Query: 186 VRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERI--VQMMVGRS 243 +R+L +G+ I+++SH + +VY + DRVTVLR+G +G RD D R+ ++MM+GR Sbjct: 193 MRKLAADGIGIVFVSHFLDQVYEICDRVTVLRNGRLIG--TRDITDLPRLDLIRMMLGRE 250 Query: 244 LSEFYQHQRIAPADAAQLPTVMQVRALAGGKIRPASFDVRAGEVLGFAGLVGAGRTELAR 303 L+E + + D A+ V G + P ++R GEV+G AGL+G+GRTE AR Sbjct: 251 LAETTHERAASQPDTAREVCVSFKGFGKQGYVAPFDLELRRGEVVGLAGLLGSGRTETAR 310 Query: 304 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA 363 L+FGA+ G+ + G+ V ++ PR A G Y PE+RK +G+ + V N + + Sbjct: 311 LVFGAERADSGEASVAGKAVRLNSPRDAAGLGFGYCPEERKTEGIVADLTVRENIVLALQ 370 Query: 364 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423 +R + R +A I+ L+++ PE P+G LSGGNQQK LLARWL +PK+L Sbjct: 371 ARRGLHRPLSRREQDEIAMRYIRMLDIRPPDPERPIGLLSGGNQQKALLARWLATSPKLL 430 Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483 +LDEPTRG+D+ A +EI +LV L QG+A++VISSEL E++ +RV+V+R+ EL Sbjct: 431 VLDEPTRGIDVGAHAEIIRLVRDLCEQGLALLVISSELDEIVTYSNRVVVLRDRAHVEEL 490 Query: 484 AGAAITQENIM 494 G A+ +I+ Sbjct: 491 KGDAVEVSSIL 501 Lambda K H 0.320 0.135 0.378 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: 723 Number of extensions: 38 Number of successful extensions: 7 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: 521 Length of database: 516 Length adjustment: 35 Effective length of query: 486 Effective length of database: 481 Effective search space: 233766 Effective search space used: 233766 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 (21.8 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