Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate GFF385 PGA1_c03960 ribose import ATP-binding protein RbsA
Query= CharProtDB::CH_003578 (501 letters) >FitnessBrowser__Phaeo:GFF385 Length = 509 Score = 286 bits (732), Expect = 1e-81 Identities = 174/506 (34%), Positives = 287/506 (56%), Gaps = 20/506 (3%) Query: 5 LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64 ++LKGI KAF V+A ++ V PG + ++GENGAGKST+M +L G Y D G + Sbjct: 6 IELKGISKAFGPVQANKDISIRVAPGTIHGIIGENGAGKSTLMSILYGFYKADKGEVWIH 65 Query: 65 GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124 GK T +++ AGIG++ Q L+ T+ ENI LG E K + D Sbjct: 66 GKRTEIPDSQAAISAGIGMVFQHFKLVENFTVLENIILGAEDGGLLKPSLSKARKSLKD- 124 Query: 125 LLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVI 184 L A+ L D + ++ +G QQ VEI K L ++ ++I+DEPT LT E + LFR++ Sbjct: 125 LAAEYELNVDPDARIDEIGVGMQQRVEILKALYRQADILILDEPTGVLTPAEADQLFRIL 184 Query: 185 RELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRKLED 244 L+++G+ I+ I+H+++EI E D V+V R G+ A + A + + L E+MVGRK+ Sbjct: 185 DRLRAEGKTIILITHKLREIMEYTDTVSVMRRGEMTATVKTAETSPEHLAELMVGRKVLL 244 Query: 245 QYPHLDKAPGDIRLKVDNLC------GPGVNDVSFTLRKGEILGVSGLMGAGRTELMKVL 298 + + PG L+++NL V ++ T+R GEILG++G+ G G++ELM+VL Sbjct: 245 RVDKVPATPGKPILEIENLSVVDEAGVARVKNIDLTVRAGEILGIAGVAGNGQSELMEVL 304 Query: 299 YGALPRTSGYVTLDGHEV-VTRSPQDGLAN---GIVYISEDRKRDGLVLGMSVKENMSL- 353 G + G + L+G + ++ + D A + ++ EDR+R+GL++ EN++ Sbjct: 305 -GGMREGQGSIRLNGAPLPLSGAGSDARARRAAHVAHVPEDRQREGLIMDFHAWENVAFG 363 Query: 354 --TALRYFSRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLM 411 A Y + G + +A + + F+V+ P A SGGNQQK+ +AR + Sbjct: 364 YHHAPEY--QRGLLMNNAALRADTEAKMAKFDVRPPDPWLAAKNFSGGNQQKIVVAREIE 421 Query: 412 TRPKVLILDEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEG 471 P++L++ +PTRGVD+GA + I++ I + + G +I+LVS E+ E+L ++DR+ VM +G Sbjct: 422 RNPELLLIGQPTRGVDIGAIEFIHKQIVELRDQGKAILLVSVELEEILSLADRVAVMFDG 481 Query: 472 HLSGEFTREQATQE---VLMAAAVGK 494 + GE +Q ++ +LMA G+ Sbjct: 482 MIMGERPADQTDEKELGLLMAGVAGE 507 Lambda K H 0.318 0.137 0.380 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: 632 Number of extensions: 33 Number of successful extensions: 8 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: 501 Length of database: 509 Length adjustment: 34 Effective length of query: 467 Effective length of database: 475 Effective search space: 221825 Effective search space used: 221825 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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