Query 015090
Match_columns 413
No_of_seqs 190 out of 614
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 02:59:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015090.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015090hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10343 RNA-binding protein Y 99.9 2E-27 4.4E-32 199.7 13.1 89 137-226 1-89 (97)
2 TIGR00253 RNA_bind_YhbY putati 99.9 3.1E-27 6.8E-32 197.6 12.9 87 139-226 1-87 (95)
3 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 8.7E-27 1.9E-31 188.8 11.0 84 139-223 1-84 (84)
4 KOG1990 Poly(A)-specific exori 99.9 1.7E-27 3.6E-32 247.8 7.9 208 72-281 307-527 (564)
5 COG1534 Predicted RNA-binding 99.9 1.5E-25 3.2E-30 188.9 12.4 91 138-230 1-91 (97)
6 KOG1990 Poly(A)-specific exori 97.8 1.3E-05 2.9E-10 85.0 3.0 152 78-230 114-268 (564)
7 COG1623 Predicted nucleic-acid 44.9 97 0.0021 32.4 7.9 72 192-275 104-176 (349)
8 PRK13482 DNA integrity scannin 42.2 62 0.0013 33.9 6.2 70 192-273 98-168 (352)
9 PF04472 DUF552: Protein of un 36.9 1.7E+02 0.0036 23.2 6.6 56 170-227 12-70 (73)
10 PF03641 Lysine_decarbox: Poss 35.6 41 0.0009 29.4 3.3 37 144-180 73-110 (133)
11 PF13604 AAA_30: AAA domain; P 34.7 2E+02 0.0044 26.5 7.7 69 138-211 1-71 (196)
12 PF07412 Geminin: Geminin; In 34.2 29 0.00063 33.7 2.2 34 242-277 115-148 (200)
13 KOG1763 Uncharacterized conser 27.7 1.4E+02 0.0029 31.3 5.8 29 94-122 226-254 (343)
14 COG4809 Archaeal ADP-dependent 25.9 1.4E+02 0.0031 32.3 5.8 108 163-280 296-404 (466)
15 PF02609 Exonuc_VII_S: Exonucl 24.9 83 0.0018 23.8 2.9 38 368-410 1-38 (53)
16 TIGR01223 Pmev_kin_anim phosph 23.3 45 0.00098 32.0 1.5 28 349-376 146-175 (182)
17 TIGR00730 conserved hypothetic 20.2 2.7E+02 0.0059 25.9 5.9 37 143-179 115-151 (178)
No 1
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.95 E-value=2e-27 Score=199.73 Aligned_cols=89 Identities=21% Similarity=0.340 Sum_probs=86.2
Q ss_pred CCCCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeC
Q 015090 137 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 216 (413)
Q Consensus 137 E~LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG 216 (413)
++||++||+|||++||+|+|+|+||++|||++|+++|+.+|++||||||++.+++.+++++++++|++.|||++||+ ||
T Consensus 1 m~Lt~kqr~~LR~~ah~l~Pvv~IGk~Glt~~vi~ei~~aL~~hELIKvkv~~~~~~~~~e~~~~i~~~~~ae~Vq~-IG 79 (97)
T PRK10343 1 MNLSTKQKQHLKGLAHPLKPVVLLGSNGLTEGVLAEIEQALEHHELIKVKIATEDRETKTLIVEAIVRETGACNVQV-IG 79 (97)
T ss_pred CCCCHHHHHHHHHhcCCCCCeEEECCCCCCHHHHHHHHHHHHHCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEee-eC
Confidence 46999999999999999999999999999999999999999999999999999999999999999999999999997 69
Q ss_pred cEEEEEeCCC
Q 015090 217 NTIIMYRGKN 226 (413)
Q Consensus 217 ~tIILYRGKN 226 (413)
+++||||++.
T Consensus 80 ~~~vlYR~~~ 89 (97)
T PRK10343 80 KTLVLYRPTK 89 (97)
T ss_pred cEEEEEecCC
Confidence 9999999964
No 2
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=99.95 E-value=3.1e-27 Score=197.64 Aligned_cols=87 Identities=28% Similarity=0.369 Sum_probs=84.7
Q ss_pred CCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 015090 139 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT 218 (413)
Q Consensus 139 LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG~t 218 (413)
||++||++||++||+|+|+|+||++|||++||++|+++|++||||||++.+++.++++++|++|++.|||++||+ +|++
T Consensus 1 Lt~kqr~~Lr~~ah~l~p~v~IGK~Glt~~vi~ei~~aL~~hELIKVkvl~~~~~~~~e~a~~i~~~~~a~~Vq~-iG~~ 79 (95)
T TIGR00253 1 LTGKQKRHLRGKAHHLKPVVLVGKNGLTEGVIKEIEQALEHRELIKVKVATEDREDKTLIAEALVKETGACNVQV-IGKT 79 (95)
T ss_pred CCHHHHHHHHHHhCCCCCeEEECCCCCCHHHHHHHHHHHHhCCcEEEEecCCChhHHHHHHHHHHHHHCCEEEEE-EccE
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999997 6999
Q ss_pred EEEEeCCC
Q 015090 219 IIMYRGKN 226 (413)
Q Consensus 219 IILYRGKN 226 (413)
+||||++.
T Consensus 80 ~vlYR~~~ 87 (95)
T TIGR00253 80 IVLYRPTK 87 (95)
T ss_pred EEEEecCC
Confidence 99999864
No 3
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=99.94 E-value=8.7e-27 Score=188.84 Aligned_cols=84 Identities=36% Similarity=0.522 Sum_probs=74.9
Q ss_pred CCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 015090 139 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT 218 (413)
Q Consensus 139 LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG~t 218 (413)
||++|+++||++||+|+|+|+||++|||++|+++|+.+|++||||||+|.+++.++++++|+.|++.|||++|++ +|++
T Consensus 1 Lt~ke~~~Lr~~a~~l~p~v~IGk~Glt~~vi~~i~~~l~~~eLvKVk~~~~~~~~~~~~~~~l~~~t~~~~V~~-iG~~ 79 (84)
T PF01985_consen 1 LTSKERKFLRKLAHHLKPVVQIGKNGLTDGVIEEIDDALEKHELVKVKVLGNCREDRKEIAEQLAEKTGAEVVQV-IGRT 79 (84)
T ss_dssp --HHHHHHHHHHHTTC--SEEE-TTSS-HHHHHHHHHHHHHHSEEEEEETT--HHHHHHHHHHHHHHHTEEEEEE-ETTE
T ss_pred CCHHHHHHHHHHhcCCCCeEEECCCCCCHHHHHHHHHHHHhCCeeEEEEccCCHHHHHHHHHHHHHHhCCEEEEE-ECCE
Confidence 799999999999999999999999999999999999999999999999999999999999999999999999986 6999
Q ss_pred EEEEe
Q 015090 219 IIMYR 223 (413)
Q Consensus 219 IILYR 223 (413)
+||||
T Consensus 80 ~vlyR 84 (84)
T PF01985_consen 80 IVLYR 84 (84)
T ss_dssp EEEEE
T ss_pred EEEEC
Confidence 99998
No 4
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=99.94 E-value=1.7e-27 Score=247.83 Aligned_cols=208 Identities=41% Similarity=0.596 Sum_probs=188.2
Q ss_pred hhhhhhhhhhhhhhhhhhh-----hHHhhhcChH---HHHHHHHHHHHHHHHHHHHhhcccCCC-CCCCCCCCCCCCCHH
Q 015090 72 KLKGKRAVVRWLKHFRYKK-----KKEYERMTAE---EKILYKLRKARKKEERIVEGLKKIEPK-ESSEMTHDPEILTPE 142 (413)
Q Consensus 72 k~~~k~a~~~~~~~~r~~~-----kke~~~~~~e---~ri~~KL~~A~~K~e~~~e~L~K~E~~-~paE~~~DpE~LT~e 142 (413)
-..-..++++|.+.+.+.. +.+.+.+..+ +.+.+++..+++|++++...|++++.+ .|++..+|++.+|.+
T Consensus 307 ~~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~e 386 (564)
T KOG1990|consen 307 LLELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEE 386 (564)
T ss_pred HHHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChH
Confidence 3344566677777666654 6677777655 788999999999999999999999986 899999999999999
Q ss_pred HHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCH-HHHHHHHHHHHHHhCCEEEEEe---eCcE
Q 015090 143 EHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA-EEVKEIAAELARLTGGIVLEIH---EENT 218 (413)
Q Consensus 143 ERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~-ed~keiAeeLee~TGGeLVQvi---iG~t 218 (413)
++.+++++|.+|++++.+|++|+++|+|.++|.||++||++||+|+.... .+++..|..++..+|+++|++. .|..
T Consensus 387 e~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~a 466 (564)
T KOG1990|consen 387 ERLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYA 466 (564)
T ss_pred HHHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhh
Confidence 99999999999999999999999999999999999999999999998665 9999999999999999999975 4666
Q ss_pred EEEEeCCCCCCCCCccCCCCcccchHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHhhhc
Q 015090 219 IIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRS 281 (413)
Q Consensus 219 IILYRGKNY~rP~~~~~~P~~lLtKrkAL~rS~~~Qr~eslk~~i~~le~~ie~l~~~~~~~~ 281 (413)
|++|||+||.+|.+ |+|.++|+||+|+.+++++|+.+|+++||..+++++++++.++....
T Consensus 467 i~~yr~k~y~~p~~--l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~ 527 (564)
T KOG1990|consen 467 IIAYRGKNYDRPTS--LRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMP 527 (564)
T ss_pred HHHhhhhhccCCcc--cCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhccc
Confidence 99999999999975 99999999999999999999999999999999999999999876543
No 5
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=1.5e-25 Score=188.95 Aligned_cols=91 Identities=26% Similarity=0.421 Sum_probs=86.5
Q ss_pred CCCHHHHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 015090 138 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN 217 (413)
Q Consensus 138 ~LT~eERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQviiG~ 217 (413)
+||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++.+++|+.|++.+||.+||+ +|+
T Consensus 1 ~Lt~kq~~~Lrs~Ah~l~piv~IGk~Glte~vi~Ei~~aL~~reLIKVkvl~~~~edr~eia~~l~~~~~a~lVqv-iG~ 79 (97)
T COG1534 1 MLTGKQKRFLRSKAHHLKPIVQIGKNGLTEGVIKEIDRALEARELIKVKVLQNAREDKKEIAEALAEETGAELVQV-IGK 79 (97)
T ss_pred CCcHHHHHHHHHhhccCCceEEecCCccCHHHHHHHHHHHHhCCcEEEEeeccchhhHHHHHHHHHHHhCCEEeee-eee
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999999997 699
Q ss_pred EEEEEeCCCCCCC
Q 015090 218 TIIMYRGKNYAQP 230 (413)
Q Consensus 218 tIILYRGKNY~rP 230 (413)
++||||. +..++
T Consensus 80 ~~vlyr~-~~e~~ 91 (97)
T COG1534 80 TLVLYRE-SKEKR 91 (97)
T ss_pred EEEEEec-Ccccc
Confidence 9999994 44444
No 6
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=97.77 E-value=1.3e-05 Score=84.96 Aligned_cols=152 Identities=22% Similarity=0.306 Sum_probs=125.4
Q ss_pred hhhhhhhhhhhhhhHHhhhcChHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCCCHHHHHHHHhhcccCCCe
Q 015090 78 AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNY 157 (413)
Q Consensus 78 a~~~~~~~~r~~~kke~~~~~~e~ri~~KL~~A~~K~e~~~e~L~K~E~~~paE~~~DpE~LT~eERk~LRKlAhkLKPV 157 (413)
+...|+..++..++.-...|.++..--|-..........+.+.+..+..|...-+...+..||..+.-++|.+|-...|+
T Consensus 114 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dl~~~~i~~~~~p~r~l~~~~~~~l~~~~~~~~r~~~~~~p~~ 193 (564)
T KOG1990|consen 114 QAGKWPSELEKEKNELLDSLGPELSDWGGSDRLSVDADLLPEKIPDYMRPFRTLPVGSPPLLTSIESTLLRRLGYKLPPH 193 (564)
T ss_pred hhhhhHHHHHHHHHHHhhccCcccccCCCCCCccchhhhchhhhhcccChhccCCCCChhhhhhHHHHHHHHhccccccc
Confidence 45557777777778888888888544444444555666778888888888777778888899999999999999999999
Q ss_pred eeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCC-CHHHHHHHHHHH--HHHhCCEEEEEeeCcEEEEEeCCCCCCC
Q 015090 158 VPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTF-SAEEVKEIAAEL--ARLTGGIVLEIHEENTIIMYRGKNYAQP 230 (413)
Q Consensus 158 V~IGKrGVTdgVIeeIh~AwK~HELVKVKvk~~-s~ed~keiAeeL--ee~TGGeLVQviiG~tIILYRGKNY~rP 230 (413)
+.+|.++.-.++.-.|..+|..|+..|+-+... .......+|..+ -..+|+.||. +-|..+|+||++|+-.|
T Consensus 194 ~~~~~~~~~~~~~~~~~~~~~k~~~~k~~~~rg~~~~~~~~~a~~l~~~~~tg~~lv~-hN~~~dv~y~~~~Fl~~ 268 (564)
T KOG1990|consen 194 FALGRSRKLQGLAVAMVSFWEKHEFAKILIKRGVLETRKERMADELQELLLTGKVLVL-HNKLLDVMYRYKNFLSP 268 (564)
T ss_pred ceehhccccccchhHHHHHHHHHHHHHHHHHhcchhhhccchHHHHHHHHhcCCeEEe-eccceeeeeehhhcccc
Confidence 999999999999999999999999999877654 344556778888 8899999996 46889999999999775
No 7
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=44.88 E-value=97 Score=32.36 Aligned_cols=72 Identities=26% Similarity=0.402 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHHhCCEEEEEe-eCcEEEEEeCCCCCCCCCccCCCCcccchHHHHHHHHHHhhhHHHHhhHHHHHHHH
Q 015090 192 AEEVKEIAAELARLTGGIVLEIH-EENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQEL 270 (413)
Q Consensus 192 ~ed~keiAeeLee~TGGeLVQvi-iG~tIILYRGKNY~rP~~~~~~P~~lLtKrkAL~rS~~~Qr~eslk~~i~~le~~i 270 (413)
...+...|+-.|..||..||+|. .-++|.||.+ |+..- +-.+-.+|+| .-|-++.|..|-..|.+.+
T Consensus 104 tGtRHRTAER~AkqTG~~VIaiS~rrNvITlY~~-~~ky~---L~d~~~il~r--------anQAi~TLEkYk~~Ld~~~ 171 (349)
T COG1623 104 TGTRHRTAERVAKQTGNPVIAISERRNVITLYVG-NLKYV---LKDSAFILSR--------ANQAIQTLEKYKTVLDRVL 171 (349)
T ss_pred CccccchHHHHHHHhCCeEEEEecccceEEEEec-Ceeee---ecChHHHHHH--------HHHHHHHHHHHHHHHHHHh
Confidence 45788999999999999999874 3579999997 55442 1223334544 4566667777777777766
Q ss_pred HHHHH
Q 015090 271 ELLRA 275 (413)
Q Consensus 271 e~l~~ 275 (413)
..|..
T Consensus 172 ~~L~~ 176 (349)
T COG1623 172 NQLNL 176 (349)
T ss_pred hhhhh
Confidence 66554
No 8
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=42.19 E-value=62 Score=33.86 Aligned_cols=70 Identities=26% Similarity=0.386 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHHhCCEEEEEe-eCcEEEEEeCCCCCCCCCccCCCCcccchHHHHHHHHHHhhhHHHHhhHHHHHHHH
Q 015090 192 AEEVKEIAAELARLTGGIVLEIH-EENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQEL 270 (413)
Q Consensus 192 ~ed~keiAeeLee~TGGeLVQvi-iG~tIILYRGKNY~rP~~~~~~P~~lLtKrkAL~rS~~~Qr~eslk~~i~~le~~i 270 (413)
...++.+|.-+++.||+.+|.|. .-++|-+|.+. .... +..|..+++|- -|-+..|.+|-..|.+.+
T Consensus 98 ~GtRHRaA~gise~Tda~vIvVSee~g~Isl~~~g-~~~~---~~d~~~l~~~a--------nQal~TlekY~~~ld~~~ 165 (352)
T PRK13482 98 TGTRHRTAERVAKQTGVPVIAVSQRRNIITLYVGG-LRYV---LEDIGVILSRA--------NQALQTLEKYKARLDEVL 165 (352)
T ss_pred CcHHHHHhhHHHHhcCCEEEEEecccCeEEEEECC-EEEe---cCCHHHHHHHH--------HHHHHHHHHHHHHHHHHH
Confidence 45789999999999999999764 23477777752 2222 23455566543 444444444444444444
Q ss_pred HHH
Q 015090 271 ELL 273 (413)
Q Consensus 271 e~l 273 (413)
..|
T Consensus 166 ~~L 168 (352)
T PRK13482 166 TNL 168 (352)
T ss_pred hhc
Confidence 433
No 9
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=36.94 E-value=1.7e+02 Score=23.23 Aligned_cols=56 Identities=13% Similarity=0.141 Sum_probs=39.0
Q ss_pred HHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHH---HhCCEEEEEeeCcEEEEEeCCCC
Q 015090 170 ILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELAR---LTGGIVLEIHEENTIIMYRGKNY 227 (413)
Q Consensus 170 IeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee---~TGGeLVQviiG~tIILYRGKNY 227 (413)
+.+|-++++....|=|.+.....++.+.+.+.|.. ..+|.+.. +|..+++|=|++.
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~--i~~~~~l~~P~~V 70 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQK--ISEKVFLLTPKGV 70 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEE--EETTEEEEE----
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEE--EcCCEEEEECCCc
Confidence 35588999999999999999888889999888876 67999996 3777888877653
No 10
>PF03641 Lysine_decarbox: Possible lysine decarboxylase; InterPro: IPR005269 This entry represents a cytokinin-activating enzyme working in the direct activation pathway. It is a phosphoribohydrolase that converts inactive cytokinin nucleotides to the biologically active free-base forms [, ]. The proteins in this entry belong to the LOG family of proteins.; PDB: 1YDH_B 2Q4D_A 1RCU_C 1WEH_B 3SBX_F 3BQ9_B 2PMB_D 3GH1_D 1WEK_C 3QUA_A ....
Probab=35.55 E-value=41 Score=29.38 Aligned_cols=37 Identities=11% Similarity=0.263 Sum_probs=30.1
Q ss_pred HHHHHhhcccCC-CeeeeCCCCCcHHHHHHHHHHHHhC
Q 015090 144 HFYFLKMGRKCK-NYVPVGRRGIYQGVILNMHLHWKKH 180 (413)
Q Consensus 144 Rk~LRKlAhkLK-PVV~IGKrGVTdgVIeeIh~AwK~H 180 (413)
--.+.+++.+-+ |++.++.+|.++.+++.++..+...
T Consensus 73 ~~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~g 110 (133)
T PF03641_consen 73 ALTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEEG 110 (133)
T ss_dssp HHHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHTT
T ss_pred HHHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHCC
Confidence 345677888888 9999999999999999997655543
No 11
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=34.70 E-value=2e+02 Score=26.46 Aligned_cols=69 Identities=16% Similarity=0.053 Sum_probs=46.9
Q ss_pred CCCHHHHHHHHhhcccCCCeeee-CCCCCcHH-HHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEE
Q 015090 138 ILTPEEHFYFLKMGRKCKNYVPV-GRRGIYQG-VILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVL 211 (413)
Q Consensus 138 ~LT~eERk~LRKlAhkLKPVV~I-GKrGVTdg-VIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLV 211 (413)
.||++|+..++.+...-..++.| |..|.--+ ++..+..+|..+. .+|.+...+. .++..|...+|....
T Consensus 1 ~L~~~Q~~a~~~~l~~~~~~~~l~G~aGtGKT~~l~~~~~~~~~~g-~~v~~~apT~----~Aa~~L~~~~~~~a~ 71 (196)
T PF13604_consen 1 TLNEEQREAVRAILTSGDRVSVLQGPAGTGKTTLLKALAEALEAAG-KRVIGLAPTN----KAAKELREKTGIEAQ 71 (196)
T ss_dssp -S-HHHHHHHHHHHHCTCSEEEEEESTTSTHHHHHHHHHHHHHHTT---EEEEESSH----HHHHHHHHHHTS-EE
T ss_pred CCCHHHHHHHHHHHhcCCeEEEEEECCCCCHHHHHHHHHHHHHhCC-CeEEEECCcH----HHHHHHHHhhCcchh
Confidence 48999999999997666655555 99886544 4667899999987 7777766653 355557777775544
No 12
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=34.21 E-value=29 Score=33.73 Aligned_cols=34 Identities=24% Similarity=0.391 Sum_probs=22.6
Q ss_pred chHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHH
Q 015090 242 SRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQA 277 (413)
Q Consensus 242 tKrkAL~rS~~~Qr~eslk~~i~~le~~ie~l~~~~ 277 (413)
.||+||.-++++-.. |..-|..++.+|..|+.+.
T Consensus 115 ~RR~AL~eaL~ENe~--Lh~~ie~~~eEi~~lk~en 148 (200)
T PF07412_consen 115 ERRKALEEALEENEK--LHKEIEQKDEEIAKLKEEN 148 (200)
T ss_dssp HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH
Confidence 477888888876533 5555666667777676544
No 13
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=27.74 E-value=1.4e+02 Score=31.27 Aligned_cols=29 Identities=24% Similarity=0.337 Sum_probs=19.7
Q ss_pred hhhcChHHHHHHHHHHHHHHHHHHHHhhc
Q 015090 94 YERMTAEEKILYKLRKARKKEERIVEGLK 122 (413)
Q Consensus 94 ~~~~~~e~ri~~KL~~A~~K~e~~~e~L~ 122 (413)
.-.+|++-=+.||..+.+.+++.+....+
T Consensus 226 lT~~T~e~F~~WKk~k~~er~~k~~~~~~ 254 (343)
T KOG1763|consen 226 LTPLTEETFKAWKKRKIRERKEKLAAEKA 254 (343)
T ss_pred CccccHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 34567777778999887777766555443
No 14
>COG4809 Archaeal ADP-dependent phosphofructokinase/glucokinase [Carbohydrate transport and metabolism]
Probab=25.89 E-value=1.4e+02 Score=32.27 Aligned_cols=108 Identities=18% Similarity=0.074 Sum_probs=79.1
Q ss_pred CCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEe-eCcEEEEEeCCCCCCCCCccCCCCccc
Q 015090 163 RGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIH-EENTIIMYRGKNYAQPPTEIMSPRITL 241 (413)
Q Consensus 163 rGVTdgVIeeIh~AwK~HELVKVKvk~~s~ed~keiAeeLee~TGGeLVQvi-iG~tIILYRGKNY~rP~~~~~~P~~lL 241 (413)
=|+.+.=++++-..+-++||.+=++..+...++-+-+-.|...+|-+.|+++ .|..+-+.|+- +| ...-
T Consensus 296 vGldE~ElA~vl~vlG~~eLa~~I~~~~~~~avieg~~~L~~e~~~e~i~vHT~~y~l~i~~~~---np-------l~~E 365 (466)
T COG4809 296 VGLDEVELANVLNVLGYRELADRIISKDDIEAVIEGAMILLDELGLERIHVHTYGYYLAITKRG---NP-------LSGE 365 (466)
T ss_pred cCCCHHHHHHHHHhhChHHHHHhhhccccHHHHHHHHHHHHHhcCccEEEEEEeeEEEEEecCC---Cc-------ccHH
Confidence 4788888999999999999999888777889999999999999999999874 67766666652 33 1233
Q ss_pred chHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHhhh
Q 015090 242 SRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETR 280 (413)
Q Consensus 242 tKrkAL~rS~~~Qr~eslk~~i~~le~~ie~l~~~~~~~ 280 (413)
-.|+||.=|.-.-.-.|+.-.|.++...=+-|+.+....
T Consensus 366 e~~daL~Fs~~lAa~~A~~GnIe~~~d~~~glkvp~~~~ 404 (466)
T COG4809 366 ELRDALLFSTLLAAAKAMLGNIERLDDLKEGLKVPISEQ 404 (466)
T ss_pred HHHHHHHHHHHHHHHHHhcCCccchhhHHhhccCCchhh
Confidence 467888888877777777777765544433343333333
No 15
>PF02609 Exonuc_VII_S: Exonuclease VII small subunit; InterPro: IPR003761 Exonuclease VII is composed of two non-identical subunits; one large subunit and 4 small ones []. This enzyme catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield nucleoside 5'-phosphates.; GO: 0008855 exodeoxyribonuclease VII activity, 0006308 DNA catabolic process, 0009318 exodeoxyribonuclease VII complex; PDB: 1VP7_F.
Probab=24.90 E-value=83 Score=23.77 Aligned_cols=38 Identities=29% Similarity=0.406 Sum_probs=28.8
Q ss_pred HHHHHHhhhhcccccccCCCCCCCCCchhHHHHHHHHHHhhhh
Q 015090 368 FEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKK 410 (413)
Q Consensus 368 ~~~~~~~~~~~~~~~~~~~~~~~~~~~de~d~~fl~a~s~lkk 410 (413)
||+.+.++-.-..+.++ .++| +|+.=++|-+|..|+++
T Consensus 1 fEe~~~~Le~Iv~~Le~----~~~s-Ldes~~lyeeg~~l~~~ 38 (53)
T PF02609_consen 1 FEEAMERLEEIVEKLES----GELS-LDESLKLYEEGMELIKK 38 (53)
T ss_dssp HHHHHHHHHHHHHHHHT----T-S--HHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHc----CCCC-HHHHHHHHHHHHHHHHH
Confidence 77887777777677664 3444 99999999999999885
No 16
>TIGR01223 Pmev_kin_anim phosphomevalonate kinase, animal type. This enzyme is part of the mevalonate pathway, one of two alternative pathways for the biosynthesis of IPP. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found. One is this type, found in animals. The other is the ERG8 type, found in plants and fungi (TIGR01219) and in Gram-positive bacteria (TIGR01220).
Probab=23.32 E-value=45 Score=32.00 Aligned_cols=28 Identities=29% Similarity=0.506 Sum_probs=24.4
Q ss_pred cchhhhcCCC--CCCCCCcchHHHHHHhhh
Q 015090 349 LYLDQFDKFP--VQNDEEHEDFEEHLRQIS 376 (413)
Q Consensus 349 ~~~~~~~~~~--~~~~~~~~~~~~~~~~~~ 376 (413)
.+||.|..|- ++||+..+.+++||.+|-
T Consensus 146 c~lDd~~~~D~vi~Nd~~~~~l~~~l~~l~ 175 (182)
T TIGR01223 146 CGLDNFGDFDWVIENHGVEQRLEEQLENLI 175 (182)
T ss_pred cCCCcccceeEEEecCCChHHHHHHHHHHH
Confidence 6899997777 999999999999998874
No 17
>TIGR00730 conserved hypothetical protein, DprA/Smf-related, family 2. This model represents one branch of a subfamily of proteins of unknown function. Both PSI-BLAST and weak hits by this model show a low level of similarity to and suggest an evolutionary relationship of the subfamily to the DprA/Smf family of DNA-processing proteins involved in chromosomal transformation with foreign DNA. Both Aquifex aeolicus and Mycobacterium leprae have one member in each of two branches of this subfamily, suggesting that the branches may have distinct functions.
Probab=20.16 E-value=2.7e+02 Score=25.92 Aligned_cols=37 Identities=14% Similarity=0.286 Sum_probs=29.9
Q ss_pred HHHHHHhhcccCCCeeeeCCCCCcHHHHHHHHHHHHh
Q 015090 143 EHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKK 179 (413)
Q Consensus 143 ERk~LRKlAhkLKPVV~IGKrGVTdgVIeeIh~AwK~ 179 (413)
+--.+.++|.+-||++.++-+|.++.+++-++.....
T Consensus 115 e~~~~~qlg~~~kPiil~n~~g~~~~l~~~l~~~~~~ 151 (178)
T TIGR00730 115 EVLTWAQLGIHQKPIILFNVNGHFDGLVEWLKYSIQE 151 (178)
T ss_pred HHHHHHHcCCCCCCEEEECCcchHHHHHHHHHHHHHC
Confidence 3345677888999999999999999999988855443
Done!