Query psy2824
Match_columns 242
No_of_seqs 115 out of 251
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 17:51:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2824hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04939 RRS1: Ribosome biogen 100.0 1.1E-72 2.5E-77 479.3 15.2 163 29-192 1-164 (164)
2 KOG1765|consensus 100.0 9.3E-69 2E-73 453.7 14.8 176 21-196 1-180 (181)
3 COG5225 RRS1 Uncharacterized p 100.0 1.9E-52 4.1E-57 347.9 8.3 167 22-194 2-171 (172)
4 PF12579 DUF3755: Protein of u 41.9 35 0.00075 22.4 2.9 23 57-79 9-31 (35)
5 KOG4538|consensus 30.1 66 0.0014 26.8 3.4 31 166-196 68-98 (130)
6 PF15232 DUF4585: Domain of un 28.6 25 0.00054 27.0 0.6 14 125-138 29-42 (75)
7 PF05178 Kri1: KRI1-like famil 22.8 84 0.0018 25.0 2.7 17 178-194 8-24 (101)
8 PRK10729 nudF ADP-ribose pyrop 21.3 94 0.002 27.2 3.0 28 151-178 79-107 (202)
9 PF08696 Dna2: DNA replication 19.4 53 0.0011 29.0 1.0 21 127-147 182-202 (209)
10 PF05627 AvrRpt-cleavage: Clea 18.2 22 0.00048 24.1 -1.3 19 159-177 19-37 (39)
No 1
>PF04939 RRS1: Ribosome biogenesis regulatory protein (RRS1); InterPro: IPR007023 This is a family of eukaryotic ribosomal biogenesis regulatory proteins.; GO: 0042254 ribosome biogenesis, 0005634 nucleus
Probab=100.00 E-value=1.1e-72 Score=479.28 Aligned_cols=163 Identities=55% Similarity=0.904 Sum_probs=158.7
Q ss_pred ccccccccccccccCCCCCcccccCCchHHHHHHHHHHHHHHHHHhhcCCccccCCceeeecCCCCcCCCCCCCCCCC-C
Q psy2824 29 IELEIDPGTLLAFDKNDINLGELRQDKDKYLKDLTRDNTQLLINKIWELPTERRDEDIVATLPDPTYILPREKPLPKI-T 107 (242)
Q Consensus 29 ~~~~~DLGnLla~D~~p~~~~~~~~~~e~~L~~~ardn~Q~Lin~l~~Lp~e~~~~g~~a~LP~p~t~lPReKPlPk~-p 107 (242)
++|+||||||||||+||||. .+.++.|+||.++||||+|+|||+||+||++++++|+||+||+|+|.||||||||+| |
T Consensus 1 t~~~~Dlg~Lla~D~~p~d~-~~~~~~e~~L~~~ardn~Q~Lin~l~~Lp~~~~~~g~~~~LP~p~t~LPReKplPk~K~ 79 (164)
T PF04939_consen 1 TPLEFDLGNLLAFDPNPLDP-SSSSDREEYLKSLARDNTQLLINQLFELPTERTEDGVLAKLPEPTTRLPREKPLPKPKP 79 (164)
T ss_pred CCceeeccceeeecCCcccc-cccCCcHHHHHHHHHHHHHHHHHHHHhCCceecCCCeEEECCCCCccCcccCCCCCCCC
Confidence 58999999999999999988 566679999999999999999999999999999999999999999999999999999 9
Q ss_pred CCcHHHHHHHhCCccccccccccccccCceecccccccccccccCCceeeCCCCCCCCcCHHHHHHHHHHHHHHhhHHHH
Q psy2824 108 MTKWEEFALEKGIRKTKKVKKKWDDILKEWVPTYGFKRRLAEKKHQWMLPVPANADPMEDQFAKKSAAQKERVARNEYQR 187 (242)
Q Consensus 108 ~TkWE~FA~~KGI~kkKksk~v~DE~~~eW~prwGyk~~~kd~~~~wiiEv~~~~d~~eDpf~~~~~eKkerv~KNe~~~ 187 (242)
+||||+||+.|||+|+|||+|||||++|+|||||||+|+|++.+++|||||++++++++|||+++++||++||+||++||
T Consensus 80 ~TkWE~FA~~KGI~K~Kk~~lv~DE~~~eW~prwGyk~~nkd~~~~wiiEv~~~~~~~eDpf~~~~~eKkerv~Kne~~~ 159 (164)
T PF04939_consen 80 PTKWEKFAKKKGIKKRKKSKLVYDEETGEWVPRWGYKRANKDKEKDWIIEVKPNDDPGEDPFEKKREEKKERVAKNEKQR 159 (164)
T ss_pred CChHHHHHHHcCCccccCcCccccccccchhhcccccccccccccCceEEcCCCCCCCcCHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhh
Q psy2824 188 LRNIA 192 (242)
Q Consensus 188 ~rN~~ 192 (242)
++|++
T Consensus 160 lrN~k 164 (164)
T PF04939_consen 160 LRNIK 164 (164)
T ss_pred HhcCC
Confidence 99984
No 2
>KOG1765|consensus
Probab=100.00 E-value=9.3e-69 Score=453.68 Aligned_cols=176 Identities=47% Similarity=0.813 Sum_probs=169.6
Q ss_pred CCccccccccccccccccccccCCCCCcccccCC---chHHHHHHHHHHHHHHHHHhhcCCccccCCceeeecCCCCcCC
Q psy2824 21 KPTTVNKLIELEIDPGTLLAFDKNDINLGELRQD---KDKYLKDLTRDNTQLLINKIWELPTERRDEDIVATLPDPTYIL 97 (242)
Q Consensus 21 ~~~~V~k~~~~~~DLGnLla~D~~p~~~~~~~~~---~e~~L~~~ardn~Q~Lin~l~~Lp~e~~~~g~~a~LP~p~t~l 97 (242)
.+++|++++++.||||||+|||.||++...+.++ .+..|.+++|||||+|||+||+||++++++|+|++||+|||.|
T Consensus 1 ~~~~vek~i~~~~DlGNllafd~n~l~~~~~~ss~a~~~~~l~~~~rdnvQ~lvN~l~~lp~~rt~e~vv~qLPe~Tt~L 80 (181)
T KOG1765|consen 1 MSTEVEKEIPLQFDLGNLLAFDRNPLDLLTLVSSGAEREKELNSLTRDNVQLLVNKLWSLPSKRTEEGVVVQLPEPTTRL 80 (181)
T ss_pred CCccccccccceeecchhhhccCCcCccccccCCchhhhHHHHHHHHHHHHHHHHHHHhCcccccccceeEeCCCccccC
Confidence 3789999999999999999999999998877665 8999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCC-CCCcHHHHHHHhCCccccccccccccccCceecccccccccccccCCceeeCCCCCCCCcCHHHHHHHHH
Q psy2824 98 PREKPLPKI-TMTKWEEFALEKGIRKTKKVKKKWDDILKEWVPTYGFKRRLAEKKHQWMLPVPANADPMEDQFAKKSAAQ 176 (242)
Q Consensus 98 PReKPlPk~-p~TkWE~FA~~KGI~kkKksk~v~DE~~~eW~prwGyk~~~kd~~~~wiiEv~~~~d~~eDpf~~~~~eK 176 (242)
|||||||+| |+||||+||+.|||.||||+++||||++|+|+|||||+|+|++...+||||+++++.+.+|||++.+++|
T Consensus 81 PReK~lPr~k~~TkWe~FAr~KGI~krKk~~lV~DEasgew~pr~GY~~~ndd~~~~wLvEi~dk~~~~~D~fa~~r~~k 160 (181)
T KOG1765|consen 81 PREKPLPRPKPETKWERFARKKGIEKRKKEKLVYDEASGEWKPRWGYKRKNDDLDKQWLVEIPDKEKTLVDPFALRRRQK 160 (181)
T ss_pred ccccCCCCCCCccHHHHHHHHcCcchhhccCcceeccccccccccCccccccchhhhhhhccCCcccccccHHHHHHHHH
Confidence 999999999 9999999999999999999999999999999999999999966666999999999999999999999999
Q ss_pred HHHHHhhHHHHHHHhhhhcC
Q psy2824 177 KERVARNEYQRLRNIARSNK 196 (242)
Q Consensus 177 kerv~KNe~~~~rN~~~a~~ 196 (242)
|+||+|||+|||+|++||.|
T Consensus 161 K~rv~Kne~nRl~Nl~ra~k 180 (181)
T KOG1765|consen 161 KNRVKKNEKNRLRNLKRARK 180 (181)
T ss_pred HHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999976
No 3
>COG5225 RRS1 Uncharacterized protein involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-52 Score=347.89 Aligned_cols=167 Identities=35% Similarity=0.569 Sum_probs=156.7
Q ss_pred CccccccccccccccccccccCCCCCcccccCC-chHHHHHHHHHHHHHHHHHhhcCCccccCCceeeecCCCCcCCCCC
Q psy2824 22 PTTVNKLIELEIDPGTLLAFDKNDINLGELRQD-KDKYLKDLTRDNTQLLINKIWELPTERRDEDIVATLPDPTYILPRE 100 (242)
Q Consensus 22 ~~~V~k~~~~~~DLGnLla~D~~p~~~~~~~~~-~e~~L~~~ardn~Q~Lin~l~~Lp~e~~~~g~~a~LP~p~t~lPRe 100 (242)
|++++..+++.|||||+.|||.|++|...++++ .|+.|.++.|||+|.|+|+|+.||..++.++++.+||+++|.|||+
T Consensus 2 ~~~~e~~ip~v~dlGn~aafD~n~ld~~~l~~s~~es~i~sL~rdnVQ~l~nql~slp~~rtsd~VllqLPe~tt~lPR~ 81 (172)
T COG5225 2 PVMNELKIPTVVDLGNVAAFDLNVLDKNDLDSSQEESNIKSLKRDNVQELKNQLCSLPARRTSDLVLLQLPESTTALPRE 81 (172)
T ss_pred CcccccCcceEeeccchhhcccccccccccchhhhhHHHHhhhHHHHHHHHHHHhcCchhcccceeEEeCCCccccCccc
Confidence 789999999999999999999999999988875 7788999999999999999999999999999999999999999999
Q ss_pred CCCCCC-CCCcHHHHHHHhCCcccccc-ccccccccCceecccccccccccccCCceeeCCCCCCCCcCHHHHHHHHHHH
Q psy2824 101 KPLPKI-TMTKWEEFALEKGIRKTKKV-KKKWDDILKEWVPTYGFKRRLAEKKHQWMLPVPANADPMEDQFAKKSAAQKE 178 (242)
Q Consensus 101 KPlPk~-p~TkWE~FA~~KGI~kkKks-k~v~DE~~~eW~prwGyk~~~kd~~~~wiiEv~~~~d~~eDpf~~~~~eKke 178 (242)
||+|++ +.||||+||+.|||.+|||+ +|||||.+|||||+|||+++|+...++||+|+... --+..++++|.
T Consensus 82 kplpk~k~eTkWerFAr~KGI~pkkr~g~lvyDEasGEwvPkwGykgknk~l~~qwlve~~~k------~k~l~r~qrkn 155 (172)
T COG5225 82 KPLPKEKIETKWERFARTKGIEPKKRSGPLVYDEASGEWVPKWGYKGKNKRLLKQWLVEGEVK------LKTLLRRQRKN 155 (172)
T ss_pred ccccccchHHHHHHHHHhcCCCccccCCCceeeccccccccccCccccchHHHHHHHHhhhHH------HHHHHHHHHHH
Confidence 999999 99999999999999999997 89999999999999999999999999999986543 12467889999
Q ss_pred HHHhhHHHHHHHhhhh
Q psy2824 179 RVARNEYQRLRNIARS 194 (242)
Q Consensus 179 rv~KNe~~~~rN~~~a 194 (242)
.+.|||.+|++||.++
T Consensus 156 ~ikKne~~rr~n~~~~ 171 (172)
T COG5225 156 NIKKNEANRRGNISRR 171 (172)
T ss_pred HHHHHHHHHhcchhhc
Confidence 9999999999999875
No 4
>PF12579 DUF3755: Protein of unknown function (DUF3755); InterPro: IPR022228 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue N that may be functionally important.
Probab=41.93 E-value=35 Score=22.44 Aligned_cols=23 Identities=30% Similarity=0.351 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCc
Q psy2824 57 KYLKDLTRDNTQLLINKIWELPT 79 (242)
Q Consensus 57 ~~L~~~ardn~Q~Lin~l~~Lp~ 79 (242)
-.|.-.+|||+..++|.+-+.|-
T Consensus 9 idLf~~~R~NI~~il~~m~~mpg 31 (35)
T PF12579_consen 9 IDLFCQTRDNILAILNDMNDMPG 31 (35)
T ss_pred HHHHHHHHHHHHHHHHHHHcchh
Confidence 46889999999999999988773
No 5
>KOG4538|consensus
Probab=30.08 E-value=66 Score=26.79 Aligned_cols=31 Identities=23% Similarity=0.361 Sum_probs=25.6
Q ss_pred cCHHHHHHHHHHHHHHhhHHHHHHHhhhhcC
Q psy2824 166 EDQFAKKSAAQKERVARNEYQRLRNIARSNK 196 (242)
Q Consensus 166 eDpf~~~~~eKkerv~KNe~~~~rN~~~a~~ 196 (242)
+|--...+++|++|...|+.+||.|-.+|.-
T Consensus 68 ~ek~~~~rqeKkqRrvEn~kRRLeNERkaEv 98 (130)
T KOG4538|consen 68 REKQVQERQEKKQRRVENEKRRLENERKAEV 98 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHH
Confidence 3455667889999999999999999998853
No 6
>PF15232 DUF4585: Domain of unknown function (DUF4585)
Probab=28.56 E-value=25 Score=27.01 Aligned_cols=14 Identities=29% Similarity=0.385 Sum_probs=12.1
Q ss_pred ccccccccccCcee
Q psy2824 125 KVKKKWDDILKEWV 138 (242)
Q Consensus 125 ksk~v~DE~~~eW~ 138 (242)
|.|+.||.+||.||
T Consensus 29 ~~k~lfDPETGqYV 42 (75)
T PF15232_consen 29 KTKTLFDPETGQYV 42 (75)
T ss_pred ceeeeecCCCCcEE
Confidence 56789999999995
No 7
>PF05178 Kri1: KRI1-like family; InterPro: IPR018034 The Kri1 protein is also known as KRR1-interacting protein 1. The Saccharomyces cerevisiae member of this family is found to be required for the assembly of preribosomal 40S subunits in the nucleolus []. KRR1 is highly expressed in dividing cells and its expression ceases almost completely when cells enter the stationary phase.
Probab=22.76 E-value=84 Score=25.03 Aligned_cols=17 Identities=29% Similarity=0.573 Sum_probs=12.7
Q ss_pred HHHHhhHHHHHHHhhhh
Q psy2824 178 ERVARNEYQRLRNIARS 194 (242)
Q Consensus 178 erv~KNe~~~~rN~~~a 194 (242)
....+.+++||+|+++.
T Consensus 8 k~~k~eElkrlK~lK~~ 24 (101)
T PF05178_consen 8 KQEKEEELKRLKNLKRK 24 (101)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34456788999999875
No 8
>PRK10729 nudF ADP-ribose pyrophosphatase NudF; Provisional
Probab=21.31 E-value=94 Score=27.16 Aligned_cols=28 Identities=18% Similarity=0.223 Sum_probs=22.0
Q ss_pred cCCceeeCCCCC-CCCcCHHHHHHHHHHH
Q psy2824 151 KHQWMLPVPANA-DPMEDQFAKKSAAQKE 178 (242)
Q Consensus 151 ~~~wiiEv~~~~-d~~eDpf~~~~~eKke 178 (242)
...|++|+|.|. |++|||....++|-.|
T Consensus 79 ~~~~~lE~PAG~vd~gE~p~~aA~REL~E 107 (202)
T PRK10729 79 ETPWLLEMVAGMIEEGESVEDVARREAIE 107 (202)
T ss_pred CCCeEEEccceEcCCCCCHHHHHHHHHHH
Confidence 357999999875 7899998877766554
No 9
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=19.36 E-value=53 Score=28.95 Aligned_cols=21 Identities=29% Similarity=0.578 Sum_probs=18.7
Q ss_pred ccccccccCceeccccccccc
Q psy2824 127 KKKWDDILKEWVPTYGFKRRL 147 (242)
Q Consensus 127 k~v~DE~~~eW~prwGyk~~~ 147 (242)
..|.|-+-.=|.|+||-||+=
T Consensus 182 ~~vlDIEEnIWSp~~GLKGkI 202 (209)
T PF08696_consen 182 SKVLDIEENIWSPRFGLKGKI 202 (209)
T ss_pred eeehhccccccccccCcceeE
Confidence 468899999999999999975
No 10
>PF05627 AvrRpt-cleavage: Cleavage site for pathogenic type III effector avirulence factor Avr; InterPro: IPR008700 This domain is conserved in small families of otherwise unrelated proteins in both mono-cots and di-cots, suggesting that it has a conserved, plant-specific function. It is found both in the plant RIN4 (resistance R membrane-bound host-target protein) where it appears to contribute to the binding of the protein to both RCS (AvrRpt2 auto-cleavage site) and AvrB, the virulence factor from the infecting bacterium []. The cleavage site for the AvrRpt2 avirulence protein would appear to be the sequence motifs VPQFGDW and LPKFGEW, both of which are highly conserved within the domain []. ; PDB: 2NUD_C.
Probab=18.19 E-value=22 Score=24.06 Aligned_cols=19 Identities=32% Similarity=0.415 Sum_probs=5.8
Q ss_pred CCCCCCCcCHHHHHHHHHH
Q psy2824 159 PANADPMEDQFAKKSAAQK 177 (242)
Q Consensus 159 ~~~~d~~eDpf~~~~~eKk 177 (242)
+.+++.+.-.|.+.|++|+
T Consensus 19 ~~~~~~yT~iF~kar~~Kk 37 (39)
T PF05627_consen 19 PASAEGYTVIFEKAREEKK 37 (39)
T ss_dssp TT---SS-EEEE-------
T ss_pred CCCCCCeeehHHHHhhhcc
Confidence 4455667788888888875
Done!