Query 013147
Match_columns 449
No_of_seqs 194 out of 615
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 00:53:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013147.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013147hhsearch_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 1.3E-27 2.7E-32 202.6 12.7 89 173-262 1-89 (97)
2 TIGR00253 RNA_bind_YhbY putati 99.9 2.1E-27 4.5E-32 200.3 12.6 87 175-262 1-87 (95)
3 PF01985 CRS1_YhbY: CRS1 / Yhb 99.9 8.9E-27 1.9E-31 190.1 11.0 84 175-259 1-84 (84)
4 KOG1990 Poly(A)-specific exori 99.9 3.6E-27 7.8E-32 246.9 8.2 209 109-319 308-529 (564)
5 COG1534 Predicted RNA-binding 99.9 6.8E-26 1.5E-30 192.5 12.4 91 174-266 1-91 (97)
6 KOG1990 Poly(A)-specific exori 97.7 1.8E-05 3.9E-10 84.6 2.7 152 114-266 114-268 (564)
7 COG1623 Predicted nucleic-acid 49.5 74 0.0016 33.5 7.9 71 228-310 104-175 (349)
8 PF04472 DUF552: Protein of un 48.5 87 0.0019 25.1 6.7 56 206-263 12-70 (73)
9 PRK13482 DNA integrity scannin 40.0 70 0.0015 33.8 6.2 50 227-280 97-147 (352)
10 PF07412 Geminin: Geminin; In 36.2 26 0.00056 34.4 2.3 33 279-313 116-148 (200)
11 PF13604 AAA_30: AAA domain; P 33.1 2.4E+02 0.0051 26.3 8.0 69 174-247 1-71 (196)
12 PF03641 Lysine_decarbox: Poss 31.9 51 0.0011 29.1 3.3 35 181-215 74-109 (133)
13 PF12207 DUF3600: Domain of un 27.7 6.9 0.00015 37.1 -3.0 97 137-233 27-138 (162)
14 COG4809 Archaeal ADP-dependent 26.0 1.4E+02 0.0029 32.8 5.6 109 199-317 296-405 (466)
15 PF02609 Exonuc_VII_S: Exonucl 22.8 91 0.002 23.8 2.8 38 404-446 1-38 (53)
16 TIGR01223 Pmev_kin_anim phosph 22.5 48 0.001 32.2 1.5 28 385-412 146-175 (182)
No 1
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=99.95 E-value=1.3e-27 Score=202.58 Aligned_cols=89 Identities=21% Similarity=0.340 Sum_probs=86.2
Q ss_pred CCCCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeC
Q 013147 173 EILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEE 252 (449)
Q Consensus 173 E~LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG 252 (449)
++||++||+|||++||+|+|+|+||++|||++|+++|+.+|++||||||++.+++++++++++++|++.|||++||+ ||
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 013147 253 NTIIMYRGKN 262 (449)
Q Consensus 253 ~tIILYRGKN 262 (449)
+++||||++.
T Consensus 80 ~~~vlYR~~~ 89 (97)
T PRK10343 80 KTLVLYRPTK 89 (97)
T ss_pred cEEEEEecCC
Confidence 9999999864
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=2.1e-27 Score=200.26 Aligned_cols=87 Identities=28% Similarity=0.369 Sum_probs=84.7
Q ss_pred CCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 013147 175 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT 254 (449)
Q Consensus 175 LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG~t 254 (449)
||++||++||++||+|+|+|+||++|||++||++|+++|++||||||++.++++++++++|++|++.|||++||+ ||++
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 013147 255 IIMYRGKN 262 (449)
Q Consensus 255 IILYRGKN 262 (449)
+||||++.
T Consensus 80 ~vlYR~~~ 87 (95)
T TIGR00253 80 IVLYRPTK 87 (95)
T ss_pred EEEEecCC
Confidence 99999863
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=8.9e-27 Score=190.15 Aligned_cols=84 Identities=36% Similarity=0.522 Sum_probs=74.9
Q ss_pred CCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCcE
Q 013147 175 LTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEENT 254 (449)
Q Consensus 175 LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG~t 254 (449)
||++|+++||++||+|+|+|+||++|||++|+++|+.+|++||||||+|.+++.++++++|+.|++.|||++||+ +|++
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 013147 255 IIMYR 259 (449)
Q Consensus 255 IILYR 259 (449)
+||||
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=3.6e-27 Score=246.94 Aligned_cols=209 Identities=41% Similarity=0.592 Sum_probs=188.4
Q ss_pred hhhhhhhhhhhhhhhhhh-----hHHhhccChH---HHHHHHHHHHHHHHHHHHHhhcccCCC-CCCCCCCCCCCCCHHH
Q 013147 109 LKGKRAVVRWLKHFRYKK-----KKEYERMTAE---EKILYKLRKARKKEERIVEGLKKIEPK-ESSEMTHDPEILTPEE 179 (449)
Q Consensus 109 ~~~k~a~~~~l~~~r~~~-----kk~~~~~~~e---~ri~~KL~~A~kK~e~~~e~L~K~E~~-~paEp~~DpE~LT~EQ 179 (449)
..-.+++++|.+.+.+.. +.+.+.+..+ +.+.+++..+++|++++...|++++.+ .|++..+|++.+|.++
T Consensus 308 ~e~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~e~~t~ee 387 (564)
T KOG1990|consen 308 LELARAKAKKEKEIERRSISSRLKLEFEKASSEKLTEAIFHKLEKAKKKLASANRILAKLEDPKIPAELRYDPESITEEE 387 (564)
T ss_pred HHHHHHhcccccCcccccccchhhhhhhccchhhHHHHHHHHHhhhhhhccchhhhhhcccccccccccccchhhcChHH
Confidence 344556667776666654 6666667655 788899999999999999999999986 8999999999999999
Q ss_pred HHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCH-HHHHHHHHHHHHHhCCEEEEEe---eCcEE
Q 013147 180 HFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSA-EEVKEIAAELARLTGGIVLEIH---EENTI 255 (449)
Q Consensus 180 Rk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~-ed~keiAeeLee~SGGeLVQVi---IG~tI 255 (449)
+.+++++|.+|++++.+|++|+++||+.++|.||++||++||+|+.... .+++..|..++..+|+++|++. .|..|
T Consensus 388 ~~~~~k~g~k~~~~~~~~rrg~f~g~i~n~~l~wk~~e~~k~i~~~~~~~~~~~~~a~~le~esg~~~v~~~~~~~~~ai 467 (564)
T KOG1990|consen 388 RLMLRKVGLKMKRRLLSGRRGVFDGVIENMHLHWKSRELVKVICKEKNLPSQVKQYASALERESGGILVSIDKNPKGYAI 467 (564)
T ss_pred HHHHHHHHHhhccccccCCcccccceeecchhhhhhcccceeeeccccccHHHHHHHHHHHHHhCCceeeeccCCchhhH
Confidence 9999999999999999999999999999999999999999999999765 9999999999999999999975 46669
Q ss_pred EEEeCCCCCCCCCccCCCCcccchHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHhhhccc
Q 013147 256 IMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRSEN 319 (449)
Q Consensus 256 ILYRGKNY~rP~~~il~P~nlLtKrkAL~rS~e~Qr~eslk~~i~~le~~ie~l~~~~~~~~~~ 319 (449)
+.|||+||.+|.+ |+|.++|+||+|+.+++++|+.+|+++||+.+++++++++.++...-.+
T Consensus 468 ~~yr~k~y~~p~~--l~P~~~l~~~k~~~~~~~~~~~~a~~~~i~~~~~~~e~~~~~~~~~~~~ 529 (564)
T KOG1990|consen 468 IAYRGKNYDRPTS--LRPRNLLSRRKALERSLEEQRKEALKSHISDLEQEIEQLQASVEAMPAI 529 (564)
T ss_pred HHhhhhhccCCcc--cCchhhhcccCCccccHHHHHHHHHhhhcchhhhhHHHhhcchhccccc
Confidence 9999999999976 9999999999999999999999999999999999999999987764443
No 5
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=99.93 E-value=6.8e-26 Score=192.53 Aligned_cols=91 Identities=26% Similarity=0.429 Sum_probs=86.8
Q ss_pred CCCHHHHHHHHhhhccCCCeeeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEeeCc
Q 013147 174 ILTPEEHFYFLKMGRKCKNYVPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIHEEN 253 (449)
Q Consensus 174 ~LT~EQRk~LRKlGhkLKPVV~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQViIG~ 253 (449)
+||++|+++||+.||+++|+|+||++|||++||.+|+.+|++||||||++.+++.++.+++|+.|++.+||.+||+ +|+
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 6999999999999999999999999999999999999999999999999999999999999999999999999998 599
Q ss_pred EEEEEeCCCCCCC
Q 013147 254 TIIMYRGKNYAQP 266 (449)
Q Consensus 254 tIILYRGKNY~rP 266 (449)
++|||| .+..++
T Consensus 80 ~~vlyr-~~~e~~ 91 (97)
T COG1534 80 TLVLYR-ESKEKR 91 (97)
T ss_pred EEEEEe-cCcccc
Confidence 999999 455554
No 6
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=97.70 E-value=1.8e-05 Score=84.57 Aligned_cols=152 Identities=22% Similarity=0.308 Sum_probs=125.5
Q ss_pred hhhhhhhhhhhhhhHHhhccChHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCCCCCCCHHHHHHHHhhhccCCCe
Q 013147 114 AVVRWLKHFRYKKKKEYERMTAEEKILYKLRKARKKEERIVEGLKKIEPKESSEMTHDPEILTPEEHFYFLKMGRKCKNY 193 (449)
Q Consensus 114 a~~~~l~~~r~~~kk~~~~~~~e~ri~~KL~~A~kK~e~~~e~L~K~E~~~paEp~~DpE~LT~EQRk~LRKlGhkLKPV 193 (449)
+...|+..++..++.-...|.++..--|-..........+.+.+..+..|...-+...+..||..+..++|.+|-...|+
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 44557777777778888888888555554445556666788888888888777788888899999999999999999999
Q ss_pred eeeCCCCCcHHHHHHHHHHHHhCCeeeEEecCCC-HHHHHHHHHHH--HHHhCCEEEEEeeCcEEEEEeCCCCCCC
Q 013147 194 VPVGRRGIYQGVILNMHLHWKKHQTLKVIVKTFS-AEEVKEIAAEL--ARLTGGIVLEIHEENTIIMYRGKNYAQP 266 (449)
Q Consensus 194 V~IGKrGVTdgVIeeIh~Awk~HELVKVKVkqns-~ed~keiAeeL--ee~SGGeLVQViIG~tIILYRGKNY~rP 266 (449)
+.+|.++.-.++...|..+|..|+..|+-+...- ......++..+ -..+|+.||. +-|..+++||++|+-.|
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 9999999999999999999999999998876643 44556777788 7889999996 46889999999999774
No 7
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=49.50 E-value=74 Score=33.51 Aligned_cols=71 Identities=27% Similarity=0.413 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHHHhCCEEEEEe-eCcEEEEEeCCCCCCCCCccCCCCcccchHHHHHHHHHHhhhHHHHhhHHHHHHHH
Q 013147 228 AEEVKEIAAELARLTGGIVLEIH-EENTIIMYRGKNYAQPPTEIMSPRITLSRKKALDKSKYRDGLRAVKKYIPKLEQEL 306 (449)
Q Consensus 228 ~ed~keiAeeLee~SGGeLVQVi-IG~tIILYRGKNY~rP~~~il~P~nlLtKrkAL~rS~e~Qr~eslk~~i~~le~~i 306 (449)
...+.+.|+-.|..||..||+|. --++|.||.+ |++.- +-.+-.+|+| ..|-+..|..|-..|.+.+
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 45688999999999999999874 3679999987 65442 1223334554 4555566666666666655
Q ss_pred HHHH
Q 013147 307 ELLR 310 (449)
Q Consensus 307 e~l~ 310 (449)
..|.
T Consensus 172 ~~L~ 175 (349)
T COG1623 172 NQLN 175 (349)
T ss_pred hhhh
Confidence 5543
No 8
>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=48.55 E-value=87 Score=25.11 Aligned_cols=56 Identities=14% Similarity=0.181 Sum_probs=39.4
Q ss_pred HHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHH---HhCCEEEEEeeCcEEEEEeCCCC
Q 013147 206 ILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELAR---LTGGIVLEIHEENTIIMYRGKNY 263 (449)
Q Consensus 206 IeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee---~SGGeLVQViIG~tIILYRGKNY 263 (449)
+.+|-++++....|=|.+..-..++.+++.+.|.. ..+|.+..+ |..++++=++|.
T Consensus 12 ~~~i~~~l~~g~~Vivnl~~l~~~~~~Ri~Dfl~G~~~al~G~i~~i--~~~~~l~~P~~V 70 (73)
T PF04472_consen 12 AREIVDALREGKIVIVNLENLDDEEAQRILDFLSGAVYALDGDIQKI--SEKVFLLTPKGV 70 (73)
T ss_dssp HHHHHHHHHTT--EEEE-TTS-HHHHHHHHHHHHHHHHHTT-EEEEE--ETTEEEEE----
T ss_pred HHHHHHHHHcCCEEEEECCCCCHHHHHHHHHHHhchheeeCCEEEEE--cCCEEEEECCCc
Confidence 34588999999999999999888899999998876 779999963 777887876654
No 9
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=40.05 E-value=70 Score=33.82 Aligned_cols=50 Identities=24% Similarity=0.323 Sum_probs=34.0
Q ss_pred CHHHHHHHHHHHHHHhCCEEEEEe-eCcEEEEEeCCCCCCCCCccCCCCcccchH
Q 013147 227 SAEEVKEIAAELARLTGGIVLEIH-EENTIIMYRGKNYAQPPTEIMSPRITLSRK 280 (449)
Q Consensus 227 s~ed~keiAeeLee~SGGeLVQVi-IG~tIILYRGKNY~rP~~~il~P~nlLtKr 280 (449)
....++.+|.-+++.||+.+|.|. ..++|-+|.+ +.... +..|..+++|-
T Consensus 97 e~GtRHRaA~gise~Tda~vIvVSee~g~Isl~~~-g~~~~---~~d~~~l~~~a 147 (352)
T PRK13482 97 ETGTRHRTAERVAKQTGVPVIAVSQRRNIITLYVG-GLRYV---LEDIGVILSRA 147 (352)
T ss_pred cCcHHHHHhhHHHHhcCCEEEEEecccCeEEEEEC-CEEEe---cCCHHHHHHHH
Confidence 345789999999999999999764 2357777775 32222 24455666654
No 10
>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=36.17 E-value=26 Score=34.40 Aligned_cols=33 Identities=24% Similarity=0.400 Sum_probs=21.3
Q ss_pred hHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHH
Q 013147 279 RKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQA 313 (449)
Q Consensus 279 KrkAL~rS~e~Qr~eslk~~i~~le~~ie~l~~~~ 313 (449)
||+||.-++++-.. |..-|..++.+|..|+.+.
T Consensus 116 RR~AL~eaL~ENe~--Lh~~ie~~~eEi~~lk~en 148 (200)
T PF07412_consen 116 RRKALEEALEENEK--LHKEIEQKDEEIAKLKEEN 148 (200)
T ss_dssp HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH
Confidence 67788887776533 5555666666666666543
No 11
>PF13604 AAA_30: AAA domain; PDB: 1W36_G 3K70_G 3UPU_B 3GPL_A 3E1S_A 3GP8_A.
Probab=33.12 E-value=2.4e+02 Score=26.26 Aligned_cols=69 Identities=16% Similarity=0.053 Sum_probs=47.3
Q ss_pred CCCHHHHHHHHhhhccCCCeeee-CCCCCcHH-HHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEE
Q 013147 174 ILTPEEHFYFLKMGRKCKNYVPV-GRRGIYQG-VILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVL 247 (449)
Q Consensus 174 ~LT~EQRk~LRKlGhkLKPVV~I-GKrGVTdg-VIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLV 247 (449)
.||++|+..++.+-..-+.++.| |..|---. ++..+..+|..+. .+|.+...+. .++..|...+|....
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 48999999999997666665555 98886554 4667899999987 7777776663 355567777775544
No 12
>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=31.94 E-value=51 Score=29.07 Aligned_cols=35 Identities=11% Similarity=0.299 Sum_probs=29.2
Q ss_pred HHHHhhhccCC-CeeeeCCCCCcHHHHHHHHHHHHh
Q 013147 181 FYFLKMGRKCK-NYVPVGRRGIYQGVILNMHLHWKK 215 (449)
Q Consensus 181 k~LRKlGhkLK-PVV~IGKrGVTdgVIeeIh~Awk~ 215 (449)
-.+.++|.+-+ |++.++.+|.++.+++.++.....
T Consensus 74 ~~~~~l~~~~~~Piil~~~~g~w~~l~~~l~~~~~~ 109 (133)
T PF03641_consen 74 LTLMQLGRHNKVPIILLNIDGFWDPLLEFLDRMIEE 109 (133)
T ss_dssp HHHHHTTSSTS-EEEEEECGGCCHHHHHHHHHHHHT
T ss_pred HHHHhhccccCCCEEEeCCcchHHHHHHHHHHHHHC
Confidence 45677888888 999999999999999999755554
No 13
>PF12207 DUF3600: Domain of unknown function (DUF3600); InterPro: IPR022019 This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C-terminal of the putative ecf-type sigma factor negative effector. ; PDB: 3FGG_A 3FH3_A.
Probab=27.69 E-value=6.9 Score=37.11 Aligned_cols=97 Identities=22% Similarity=0.162 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHHH-----HHHHHHhhcccCCC----CCCCCCCCCCCCCHHHHHHHHhhhccCCCeee------eCCCCC
Q 013147 137 EKILYKLRKARKK-----EERIVEGLKKIEPK----ESSEMTHDPEILTPEEHFYFLKMGRKCKNYVP------VGRRGI 201 (449)
Q Consensus 137 ~ri~~KL~~A~kK-----~e~~~e~L~K~E~~----~paEp~~DpE~LT~EQRk~LRKlGhkLKPVV~------IGKrGV 201 (449)
.++.-||..|+-. -+...+.|+++-.. .-+.-..|.+.|+..++..++++...|.|++- --|.=+
T Consensus 27 ~~~eaKLqqAK~~lgeeEfeef~~lLK~lt~~kLkygD~NGnidye~ls~~eqee~k~~~~eLqPYFdKLN~~~SsK~vl 106 (162)
T PF12207_consen 27 LRLEAKLQQAKGELGEEEFEEFKELLKKLTNAKLKYGDKNGNIDYEKLSKEEQEEYKKLTMELQPYFDKLNGHKSSKEVL 106 (162)
T ss_dssp HHHHHHHHHHHHCS-HHHHHHHHHHHHHHHHHHHHHB-TTS-B-GGGS-HHHHHHHHHHHHHHHHHHHHHTT---HHHHS
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhHHhhcccCCCcCHHhCCHHHHHHHHHHHHhcchHHHHhcCCcchhhhc
Confidence 4666777766532 23344455554321 34566788999999999999999999999873 223446
Q ss_pred cHHHHHHHHHHHHhCCeeeEEecCCCHHHHHH
Q 013147 202 YQGVILNMHLHWKKHQTLKVIVKTFSAEEVKE 233 (449)
Q Consensus 202 TdgVIeeIh~Awk~HELVKVKVkqns~ed~ke 233 (449)
|+.-.+.--.||-.+|.|+|+........+.+
T Consensus 107 t~~E~d~y~eALm~~e~v~vk~~~~~~~~ve~ 138 (162)
T PF12207_consen 107 TQEEYDQYIEALMTYETVRVKTKSSGGITVEE 138 (162)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHCT-SS---GGG
T ss_pred CHHHHHHHHHHHhhhheeeeeccCCCCCcHHh
Confidence 66667778889999999999987654444433
No 14
>COG4809 Archaeal ADP-dependent phosphofructokinase/glucokinase [Carbohydrate transport and metabolism]
Probab=26.00 E-value=1.4e+02 Score=32.76 Aligned_cols=109 Identities=18% Similarity=0.084 Sum_probs=80.5
Q ss_pred CCCcHHHHHHHHHHHHhCCeeeEEecCCCHHHHHHHHHHHHHHhCCEEEEEe-eCcEEEEEeCCCCCCCCCccCCCCccc
Q 013147 199 RGIYQGVILNMHLHWKKHQTLKVIVKTFSAEEVKEIAAELARLTGGIVLEIH-EENTIIMYRGKNYAQPPTEIMSPRITL 277 (449)
Q Consensus 199 rGVTdgVIeeIh~Awk~HELVKVKVkqns~ed~keiAeeLee~SGGeLVQVi-IG~tIILYRGKNY~rP~~~il~P~nlL 277 (449)
=|+.+.=++++-..+-++||-+=++..+..+++-+-+-+|...+|-+.||++ .|..+-+.|+-| | ...=
T Consensus 296 vGldE~ElA~vl~vlG~~eLa~~I~~~~~~~avieg~~~L~~e~~~e~i~vHT~~y~l~i~~~~n---p-------l~~E 365 (466)
T COG4809 296 VGLDEVELANVLNVLGYRELADRIISKDDIEAVIEGAMILLDELGLERIHVHTYGYYLAITKRGN---P-------LSGE 365 (466)
T ss_pred cCCCHHHHHHHHHhhChHHHHHhhhccccHHHHHHHHHHHHHhcCccEEEEEEeeEEEEEecCCC---c-------ccHH
Confidence 4788888999999999999999888888889999999999999999999974 677777777533 2 1123
Q ss_pred chHHHHHHHHHHhhhHHHHhhHHHHHHHHHHHHHHHhhhc
Q 013147 278 SRKKALDKSKYRDGLRAVKKYIPKLEQELELLRAQAETRS 317 (449)
Q Consensus 278 tKrkAL~rS~e~Qr~eslk~~i~~le~~ie~l~~~~~~~~ 317 (449)
-.|+||.=|.-.-.-.|+.-.|.++...=+-|+.+....|
T Consensus 366 e~~daL~Fs~~lAa~~A~~GnIe~~~d~~~glkvp~~~~g 405 (466)
T COG4809 366 ELRDALLFSTLLAAAKAMLGNIERLDDLKEGLKVPISEQG 405 (466)
T ss_pred HHHHHHHHHHHHHHHHHhcCCccchhhHHhhccCCchhhh
Confidence 4578888887777777777777655444444444433333
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=22.77 E-value=91 Score=23.81 Aligned_cols=38 Identities=29% Similarity=0.406 Sum_probs=28.7
Q ss_pred HHHHHHhhhhcccccccCCCCCCCCCchhHHHHHHHHHHhhhh
Q 013147 404 FEEHLRQISIDSRNAKSLGKDEDSSHFDEVDKMFLRAASLLKK 446 (449)
Q Consensus 404 f~~~~~~~~~~~~~~~~~~~~~~~~~~de~d~~flra~s~lkk 446 (449)
||+.+.++-.-..+.++ .++| +|+.=++|-+|..|+++
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 77877777776676664 3444 99999999999999886
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=22.51 E-value=48 Score=32.17 Aligned_cols=28 Identities=29% Similarity=0.506 Sum_probs=24.3
Q ss_pred cchhhhcCCC--CCCCCCcchHHHHHHhhh
Q 013147 385 LYLDQFDKFP--VQNDEEHEDFEEHLRQIS 412 (449)
Q Consensus 385 l~l~~~~~f~--~~~~~~~~df~~~~~~~~ 412 (449)
..||.|..|- ++||+..+.+++||.+|-
T Consensus 146 c~lDd~~~~D~vi~Nd~~~~~l~~~l~~l~ 175 (182)
T TIGR01223 146 CGLDNFGDFDWVIENHGVEQRLEEQLENLI 175 (182)
T ss_pred cCCCcccceeEEEecCCChHHHHHHHHHHH
Confidence 5899997777 999999999999998874
Done!