Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate BPHYT_RS28215 BPHYT_RS28215 D-ribose transporter ATP binding protein
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__BFirm:BPHYT_RS28215 Length = 509 Score = 455 bits (1170), Expect = e-132 Identities = 243/509 (47%), Positives = 338/509 (66%), Gaps = 9/509 (1%) Query: 5 PLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQGEIL 64 P L++R KSFG ALSD L + PGE+HAL+GENGAGKST++K+L+GVH PD GE++ Sbjct: 9 PRLELRHASKSFGRVRALSDGDLALWPGEVHALLGENGAGKSTVVKILAGVHQPDTGELV 68 Query: 65 LDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMRSRT 124 +DG P +R AG+ +IYQE + ++S+A N+FMG + R+G I + AMR Sbjct: 69 VDGEARRFATPAEARDAGLAVIYQEPTLFFDLSIAENIFMGRQPVDRIGRIQYDAMRREV 128 Query: 125 DAVLRQLGAGFGASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAALSERETEQLFN 184 D +L LG A L LSIA+QQ +EIA+AL + ++IMDEPTAALS E E+LF Sbjct: 129 DGLLASLGVDLRADQLVRGLSIADQQVIEIAKALSLNANVLIMDEPTAALSLPEVERLFT 188 Query: 185 VVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSERIVQMMVGRSL 244 +VR+LR+ +AI++I+HR+ EV+AL RVT++RDG+ V + + ++++E IV MVGR L Sbjct: 189 IVRKLRERDVAILFITHRLDEVFALTQRVTIMRDGAKVFDGLTTDLNTEAIVAKMVGRDL 248 Query: 245 SEFYQHQRIAPADAAQLPTVMQVRALAG-GKIRPASFDVRAGEVLGFAGLVGAGRTELAR 303 FY P + + VR L G + SFDVRAGE++ AGLVGAGR+E+AR Sbjct: 249 ETFYPKAERPPGEVR-----LSVRGLTRVGVFKDISFDVRAGEIVALAGLVGAGRSEVAR 303 Query: 304 LLFGADPRSGGDILLEGRPVHIDQPRAAMRAGIAYVPEDRKGQGLFLQMAVAANATMNVA 363 +FG DP G+I + G+ + +P AA+RAG+A VPEDR+ QGL L++++A NA+M V Sbjct: 304 AIFGIDPLDSGEIWIAGKRLTAGRPAAAVRAGLALVPEDRRQQGLALELSIARNASMTVL 363 Query: 364 SRHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGGNQQKVLLARWLEIAPKVL 423 R + GL+ +RS +A RL +K P PVG LSGGNQQKV+L +WL PKVL Sbjct: 364 GRLVKHGLISARSETQLANQWGTRLRLKAGDPNAPVGTLSGGNQQKVVLGKWLATGPKVL 423 Query: 424 ILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVIGICDRVLVMREGMITGEL 483 I+DEPTRG+D+ AK+E+Y + L G+AV++ISSELPEV+G+ DRVLVM EG I+ ++ Sbjct: 424 IIDEPTRGIDVGAKAEVYSALAELVRDGMAVLMISSELPEVLGMADRVLVMHEGRISADI 483 Query: 484 AGAAITQENIMRLATDTNVPRTAPASHSS 512 A A +E IM A +P P H++ Sbjct: 484 ARADADEERIMGAALGQPMP---PLGHAA 509 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: 793 Number of extensions: 44 Number of successful extensions: 6 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: 509 Length adjustment: 35 Effective length of query: 486 Effective length of database: 474 Effective search space: 230364 Effective search space used: 230364 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