Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS03640 HSERO_RS03640 D-ribose transporter ATP-binding protein
Query= uniprot:D8J111 (520 letters) >FitnessBrowser__HerbieS:HSERO_RS03640 Length = 502 Score = 434 bits (1117), Expect = e-126 Identities = 236/499 (47%), Positives = 330/499 (66%), Gaps = 6/499 (1%) Query: 18 SSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSG 77 + P++ +R + K F LAL + + GE+HALMGENGAGKSTLMK+LSGV+ D G Sbjct: 6 TQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQG 65 Query: 78 DILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDEL 137 +ILLDG+PV + +P ++A GI +I+QEL + ++S A N+F+G E R +GL ID + Sbjct: 66 EILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGL-IDHAAM 124 Query: 138 NRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIA 197 + A+ ++ S G L++A QQ VEIA+AL SR++IMDEPTAAL+ E Sbjct: 125 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 184 Query: 198 ELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMV 257 +LF ++R L+ +G+ I+YISH+M E+ +ADRV+V+RDG ++ + E + I+ MMV Sbjct: 185 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 244 Query: 258 GRALDG---EQRIPP-DTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRT 313 GR+L QRI P D ++ V++VR L G+ IR SF +R GE+LGFAGL+GAGRT Sbjct: 245 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGK-IRPASFDVRAGEVLGFAGLVGAGRT 303 Query: 314 EVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIA 373 E+AR +FGADP G+I++ G I P A+ GI Y+ EDRK GL + M V AN Sbjct: 304 ELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANAT 363 Query: 374 LSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRD 433 ++ R TR+G + R++ A+ +++L +K E LSGGNQQK+++A+WL Sbjct: 364 MNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIA 423 Query: 434 CDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRI 493 +L DEPTRG+D+ AKSEIY+L+ LA QG A+V+ISSELPEV+ + RVLVM EG I Sbjct: 424 PKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMI 483 Query: 494 TGELARADATQEKIMQLAT 512 TGELA A TQE IM+LAT Sbjct: 484 TGELAGAAITQENIMRLAT 502 Score = 112 bits (281), Expect = 2e-29 Identities = 74/252 (29%), Positives = 131/252 (51%), Gaps = 10/252 (3%) Query: 267 IPPDTSRNDVVLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGA 322 IP D ++ + L++RG+ + A+ D+ T+R GEI G GAG++ + + + G Sbjct: 1 IPVDMTQTPL-LQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGV 59 Query: 323 DPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTR 382 + GEI++ G ++ P + A GI + ++ +A + V AN+ + S R TR Sbjct: 60 HAPDQGEILLDGRPVALRDPGASRAAGINLIYQE---LAVAPNISVAANVFMGSELR-TR 115 Query: 383 VGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEP 442 +G +D A+R +RQL + + RL S QQ++ IA+ L+ I+ DEP Sbjct: 116 LGLIDHAAMRSRTDAVLRQLGAGFGASDLAGRL-SIAEQQQVEIARALVHRSRIVIMDEP 174 Query: 443 TRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADA 502 T + +++ ++ L ++G AI+ IS + EV ++ RV V+ +G GEL R + Sbjct: 175 TAALSERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEI 234 Query: 503 TQEKIMQLATQR 514 E+I+Q+ R Sbjct: 235 DSERIVQMMVGR 246 Lambda K H 0.320 0.135 0.372 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: 698 Number of extensions: 35 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 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 (21.8 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