Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 434 bits (1117), Expect = e-126 Identities = 236/499 (47%), Positives = 330/499 (66%), Gaps = 6/499 (1%) Query: 2 TQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQG 61 + P++ +R + K F LAL + + GE+HALMGENGAGKSTLMK+LSGV+ D G Sbjct: 18 SSVPVIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSG 77 Query: 62 EILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGL-IDHAAM 120 +ILLDG+PV + +P ++A GI +I+QEL + ++S A N+F+G E R +GL ID + Sbjct: 78 DILLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDEL 137 Query: 121 RSRTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180 + A+ ++ S G L++A QQ VEIA+AL SR++IMDEPTAAL+ E Sbjct: 138 NRQAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIA 197 Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240 +LF ++R L+ +G+ I+YISH+M E+ +ADRV+V+RDG ++ + E + I+ MMV Sbjct: 198 ELFRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMV 257 Query: 241 GRSLSEFYQHQRIAPADAAQLPTVMQVRALAGGK-IRPASFDVRAGEVLGFAGLVGAGRT 299 GR+L QRI P D ++ V++VR L G+ IR SF +R GE+LGFAGL+GAGRT Sbjct: 258 GRALDG---EQRIPP-DTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRT 313 Query: 300 ELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANAT 359 E+AR +FGADP G+I++ G I P A+ GI Y+ EDRK GL + M V AN Sbjct: 314 EVARAIFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIA 373 Query: 360 MNVASRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIA 419 ++ R TR+G + R++ A+ +++L +K E LSGGNQQK+++A+WL Sbjct: 374 LSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRD 433 Query: 420 PKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMI 479 +L DEPTRG+D+ AKSEIY+L+ LA QG A+V+ISSELPEV+ + RVLVM EG I Sbjct: 434 CDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRI 493 Query: 480 TGELAGAAITQENIMRLAT 498 TGELA A TQE IM+LAT Sbjct: 494 TGELARADATQEKIMQLAT 512 Score = 111 bits (278), Expect = 6e-29 Identities = 71/242 (29%), Positives = 126/242 (52%), Gaps = 9/242 (3%) Query: 6 LLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEILL 65 +L++RG+ + A+ D+ T+R GEI G GAG++ + + + G + GEI++ Sbjct: 277 VLEVRGLNRG----RAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGADPLEAGEIII 332 Query: 66 DGRPVALRDPGASRAAGINLIYQE---LAVAPNISVAANVFMGSELR-TRLGLIDHAAMR 121 G ++ P + A GI + ++ +A + V AN+ + S R TR+G +D A+R Sbjct: 333 HGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTRVGFMDQRAIR 392 Query: 122 SRTDAVLRQLGAGFGASDLAGRL-SIAEQQQVEIARALVHRSRIVIMDEPTAALSERETE 180 +RQL + + RL S QQ++ IA+ L+ I+ DEPT + Sbjct: 393 EAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEPTRGIDVGAKS 452 Query: 181 QLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMV 240 +++ ++ L ++G AI+ IS + EV ++ RV V+ +G GEL R + E+I+Q+ Sbjct: 453 EIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADATQEKIMQLAT 512 Query: 241 GR 242 R Sbjct: 513 QR 514 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: 725 Number of extensions: 33 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: 521 Length of database: 520 Length adjustment: 35 Effective length of query: 486 Effective length of database: 485 Effective search space: 235710 Effective search space used: 235710 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