Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate 3609459 Dshi_2843 ABC transporter related (RefSeq)
Query= uniprot:D8IZC7 (521 letters) >FitnessBrowser__Dino:3609459 Length = 548 Score = 279 bits (714), Expect = 2e-79 Identities = 174/520 (33%), Positives = 279/520 (53%), Gaps = 27/520 (5%) Query: 2 TQTPLLQMRGIRKSFGATLALSDMHLTIRPGEIHALMGENGAGKSTLMKVLSGVHAPDQG 61 TQ P +++RGI K+FG A D+ + + PG IH ++GENGAGKSTLM +L G + D G Sbjct: 21 TQAPAIELRGISKAFGPVQANKDISIRVMPGTIHGIIGENGAGKSTLMSILYGFYKADAG 80 Query: 62 EILLDGRPVALRDPGASRAAGINLIYQELAVAPNISVAANVFMGSELRTRLGLIDHAAMR 121 EI + G+ + D A+ AGI +++Q + N +V NV +G+E + A +R Sbjct: 81 EIFIKGQKTEIPDSQAAIRAGIGMVFQHFKLVENFTVLENVVLGAE--------EGALLR 132 Query: 122 ---SRTDAVLRQLGAGF----GASDLAGRLSIAEQQQVEIARALVHRSRIVIMDEPTAAL 174 ++ +LR+L + L LS+ QQ+VEI +AL ++ I+I+DEPT L Sbjct: 133 PSLAKARKLLRELSEEYELNVAPDALIEDLSVGHQQRVEILKALYRKADILILDEPTGVL 192 Query: 175 SERETEQLFNVVRRLRDEGLAIIYISHRMAEVYALADRVTVLRDGSFVGELVRDEIDSER 234 + E + LF ++ L+ EG II I+H++ E+ D V+V+R G + + E+ Sbjct: 193 TPAEADHLFRILEGLKAEGKTIILITHKLREIMETTDTVSVMRRGEMTATVKTADTSPEQ 252 Query: 235 IVQMMVGRSLSEFYQHQRIAPADAAQLPTVMQVRAL---AGGKIRPASFDVRAGEVLGFA 291 + ++MVGR + + + A + TV +R + +++ S VRAGEVLG A Sbjct: 253 LAELMVGRKV--LLRVDKTPAQPGAPILTVDDLRVVDDQGVERVKGISLQVRAGEVLGIA 310 Query: 292 GLVGAGRTELARLLFGADPRSGGDILLEGRPVHI----DQPRAAMRAGIAYVPEDRKGQG 347 G+ G G++EL +L G P + G + + G+ + + + GIA+VPEDR+ +G Sbjct: 311 GVAGNGQSELLEVLGGMRPAT-GRVTVSGQQIDLTGKHSNGKTRRAQGIAHVPEDRQAEG 369 Query: 348 LFLQMAVAANATMNVAS--RHTRLGLVRSRSLGGVARAAIQRLNVKVAHPETPVGKLSGG 405 L + N + R L+ +R++ A I R +V+ A SGG Sbjct: 370 LIMDYHAWENVAFGYHDDPAYNRGLLMDNRAVRADAEGKIARFDVRPADCWLAAKNFSGG 429 Query: 406 NQQKVLLARWLEIAPKVLILDEPTRGVDIYAKSEIYQLVHRLASQGVAVVVISSELPEVI 465 NQQK++LAR +E P++L++ +PTRGVDI A I+Q + L G A++++S EL E++ Sbjct: 430 NQQKIVLAREIERNPELLLVGQPTRGVDIGAIEFIHQQIIALRDAGKAILLVSVELEEIL 489 Query: 466 GICDRVLVMREGMITGELAGAAITQENIMRLATDTNVPRT 505 + DRV VM +G I GE A ++ + L P T Sbjct: 490 SLSDRVAVMFDGRIMGERPAAETNEKELGLLMAGITEPPT 529 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: 724 Number of extensions: 44 Number of successful extensions: 9 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: 548 Length adjustment: 35 Effective length of query: 486 Effective length of database: 513 Effective search space: 249318 Effective search space used: 249318 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