Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate H281DRAFT_00426 H281DRAFT_00426 monosaccharide ABC transporter ATP-binding protein, CUT2 family
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Burk376:H281DRAFT_00426 Length = 503 Score = 421 bits (1083), Expect = e-122 Identities = 236/508 (46%), Positives = 327/508 (64%), Gaps = 11/508 (2%) Query: 4 TPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEI 63 TPL+ ++ + KSF AL D+ + GE+HALMGENGAGKSTLMK+L+GV+ D GEI Sbjct: 2 TPLISVKKLSKSFPGVRALHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGEI 61 Query: 64 LLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGL-IDHAAMRS 122 LL G+PV L+ P ++AAGI +I+QEL + +++VA N+F+G E R RLGL +D + + Sbjct: 62 LLGGQPVELQSPRDAQAAGIGIIHQELQLMNHLTVAQNIFIGREPRGRLGLFLDEDKLNA 121 Query: 123 RTDAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQL 182 + +L ++ + G L++A QQ VEIA+AL SR++IMDEPT+AL++ E +L Sbjct: 122 KAREILSRMHVNIDPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAEL 181 Query: 183 FNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGR 242 F ++R L+ G+ ++YISH+M E+ +ADRVTVLRDG +V + + E I+ MMVGR Sbjct: 182 FRIIRELKQRGVGVVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIGMMVGR 241 Query: 243 SLSEFYQHQRIAPAD--AAQLPTVMQVRAL-AGGKIRPASFDVRAGEVLGFAGLVGAGRT 299 +LS+ +APA A+Q ++VR L AG +R SF +R GE+LGFAGL+GAGRT Sbjct: 242 TLSD------VAPAGRAASQGEIALEVRNLHAGPLVRDVSFTLRKGEILGFAGLMGAGRT 295 Query: 300 ELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANAT 359 E+AR +FGADP G+I ++G I P A+ GI Y+ EDRK GL M V +N Sbjct: 296 EVARAVFGADPVESGEIFVKGAKASIRTPSDAVAHGIGYLSEDRKRFGLATGMDVESNIV 355 Query: 360 MNVASRHTRLGL-VRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEI 418 M+ L +R + A I L ++ V LSGGNQQK+++A+WLE Sbjct: 356 MSNLRNFLSLNFFLRRARMRRRASHFINLLAIRTPSAAQQVRLLSGGNQQKIVIAKWLER 415 Query: 419 APKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGM 478 VL DEPTRG+D+ AKSEIY+L+ LA +G A+V+ISSELPE++ + DRV+VM EG Sbjct: 416 DCDVLFFDEPTRGIDVGAKSEIYKLLRSLADEGKAIVMISSELPEILRMSDRVVVMCEGR 475 Query: 479 ITGELAGAAITQENIMRLATDTNVPRTA 506 ITGEL TQE IM LAT + A Sbjct: 476 ITGELPAEQATQERIMHLATQRQTLKAA 503 Score = 119 bits (297), Expect = 3e-31 Identities = 79/239 (33%), Positives = 125/239 (52%), Gaps = 6/239 (2%) Query: 275 IRPASFDVRAGEVLGFAGLVGAGRTELARLLFGADPRSGGDILLEGRPVHIDQPRAAMRA 334 + FD+ GEV G GAG++ L ++L G R G+ILL G+PV + PR A A Sbjct: 20 LHDVQFDLVEGEVHALMGENGAGKSTLMKILAGVYTRDSGEILLGGQPVELQSPRDAQAA 79 Query: 335 GIAYVPEDRKGQGLFLQMAVAANATMNVASRHTRLGLVRSRS-LGGVARAAIQRLNVKVA 393 GI + ++ + L + VA N + R RLGL L AR + R++V + Sbjct: 80 GIGIIHQELQ---LMNHLTVAQNIFIGREPRG-RLGLFLDEDKLNAKAREILSRMHVNI- 134 Query: 394 HPETPVGKLSGGNQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVA 453 P VG L+ +QQ V +A+ L +VLI+DEPT ++ +E+++++ L +GV Sbjct: 135 DPRAMVGNLTVASQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAELFRIIRELKQRGVG 194 Query: 454 VVVISSELPEVIGICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRTAPASHSS 512 VV IS ++ E+ I DRV V+R+G +A A + E I+ + + APA ++ Sbjct: 195 VVYISHKMDELKQIADRVTVLRDGEYVATVAAADTSVEAIIGMMVGRTLSDVAPAGRAA 253 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: 694 Number of extensions: 29 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: 503 Length adjustment: 35 Effective length of query: 486 Effective length of database: 468 Effective search space: 227448 Effective search space used: 227448 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