Query 006998
Match_columns 622
No_of_seqs 58 out of 60
Neff 2.6
Searched_HMMs 46136
Date Thu Mar 28 17:29:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/006998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/006998hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13236 CLU: Clustered mitoch 43.3 37 0.0008 34.0 4.6 41 104-144 4-50 (221)
2 KOG4025 Putative apoptosis rel 41.6 77 0.0017 32.1 6.4 84 52-135 50-135 (207)
3 COG4453 Uncharacterized protei 38.5 37 0.0008 31.0 3.4 29 110-144 15-56 (95)
4 PF06440 DNA_pol3_theta: DNA p 36.4 27 0.00058 30.9 2.1 23 108-134 4-26 (75)
5 COG4575 ElaB Uncharacterized c 31.7 1.8E+02 0.0038 27.3 6.6 71 65-144 11-83 (104)
6 PRK10969 DNA polymerase III su 29.6 49 0.0011 29.3 2.7 22 109-134 5-26 (75)
7 PF02984 Cyclin_C: Cyclin, C-t 20.7 82 0.0018 26.2 2.3 15 128-142 45-59 (118)
8 PF08988 DUF1895: Protein of u 16.3 1.8E+02 0.0039 25.0 3.4 22 121-142 41-62 (68)
9 COG2841 Uncharacterized protei 11.7 3.1E+02 0.0068 24.3 3.6 26 112-137 43-70 (72)
10 PLN03121 nucleic acid binding 11.3 3.8E+02 0.0083 28.2 4.8 53 94-146 132-208 (243)
No 1
>PF13236 CLU: Clustered mitochondria
Probab=43.30 E-value=37 Score=33.98 Aligned_cols=41 Identities=32% Similarity=0.504 Sum_probs=31.8
Q ss_pred HHHHHhhcCChH-HHhhhhHHHHHHH-----HHHHHHHHHHHHhhcC
Q 006998 104 EEFSKILDVSKE-ERDRIQRLQVIDR-----AAAAIAAARAILEEKN 144 (622)
Q Consensus 104 ~~f~~~l~v~~e-erdrvqr~qvidr-----aaaaiaaara~l~~~~ 144 (622)
++||.++++|.+ ..+|+.|-+.|-+ ..||+..|++|+.+.-
T Consensus 4 eefQ~~~elp~~t~~er~~r~r~l~~l~~dFv~aA~~~a~~Ii~~~~ 50 (221)
T PF13236_consen 4 EEFQSLRELPRETLEERIERDRKLSKLHSDFVEAATRGAMAIIDENI 50 (221)
T ss_pred HHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcc
Confidence 689999999863 4467777766644 5789999999999764
No 2
>KOG4025 consensus Putative apoptosis related protein [Function unknown]
Probab=41.58 E-value=77 Score=32.14 Aligned_cols=84 Identities=20% Similarity=0.236 Sum_probs=59.2
Q ss_pred Cch-HHHHHHHHhhhhhhHHHHHHhhcccccCCCCCCCCCCCCCchHHHHHhHHHHHHhh-cCChHHHhhhhHHHHHHHH
Q 006998 52 GSY-LDMWQKAVDRDRKEIEFQKIAGSLAESGDVDGNEGGGGRDLTEQLEKKSEEFSKIL-DVSKEERDRIQRLQVIDRA 129 (622)
Q Consensus 52 ~sy-ldmwk~av~rer~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~f~~~l-~v~~eerdrvqr~qvidra 129 (622)
+++ -|.=++.+|+-.-+++|+..--++...+++.+---.+-..+-.+|.+|.-....|| +||.|--||+.=+|-|--.
T Consensus 50 Pgf~yD~~~~il~~~~l~VNl~Es~LRm~~~~d~ney~v~r~E~~fqeLn~ka~aLk~iLSriPdEinDR~~FLeTIK~I 129 (207)
T KOG4025|consen 50 PGFLYDFTKVILDDSELSVNLQESYLRMHDTSDTNEYIVSRYEQDFQELNKKAIALKRILSRIPDEINDRHAFLETIKLI 129 (207)
T ss_pred CcHHHHHHHHHHhhhccccchHHHHHHhhcccchhhHhhcCCCccHHHHHHHHHHHHHHHHhCcHhhhhHHHHHHHHHHH
Confidence 444 48888999999999999964444443233222211122223457899999988888 6899999999999999999
Q ss_pred HHHHHH
Q 006998 130 AAAIAA 135 (622)
Q Consensus 130 aaaiaa 135 (622)
|.||--
T Consensus 130 ASaIKk 135 (207)
T KOG4025|consen 130 ASAIKK 135 (207)
T ss_pred HHHHHH
Confidence 988854
No 3
>COG4453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.51 E-value=37 Score=30.99 Aligned_cols=29 Identities=45% Similarity=0.767 Sum_probs=21.9
Q ss_pred hcCChHHHhhhhHHHHHHHHH-------------HHHHHHHHHHhhcC
Q 006998 110 LDVSKEERDRIQRLQVIDRAA-------------AAIAAARAILEEKN 144 (622)
Q Consensus 110 l~v~~eerdrvqr~qvidraa-------------aaiaaara~l~~~~ 144 (622)
|+|+.++|| +||||| ||+.+|..||.+..
T Consensus 15 lR~~~d~~~------Li~~AAai~g~s~tdFvl~aA~~~A~~vi~~~~ 56 (95)
T COG4453 15 LRLTPDQRD------LIDRAAAIEGKSLTDFVLSAALEAAEDVIEDQR 56 (95)
T ss_pred eecCHHHHH------HHHHHHHHHCCcHHHHHHHHHHHHHHHHHHhhH
Confidence 677777775 667777 47888998888765
No 4
>PF06440 DNA_pol3_theta: DNA polymerase III, theta subunit; InterPro: IPR009052 This entry represents the theta subunit of DNA polymerase III from bacteria, whose core structure consists of an irregular array of three helices []. DNA polymerase III (Pol III) is the primary enzyme responsible for replication of Escherichia coli chromosomal DNA. The holoenzyme consists of 17 proteins and contains two core polymerases. The Pol III catalytic core has three tightly associated subunits: alpha, epsilon and theta. The alpha subunit is responsible for the DNA polymerase activity, while the epsilon subunit is the 3'-5' proofreading exonuclease. The epsilon subunit binds to both the alpha and theta subunits in the linear order alpha-epsilon-theta. The theta subunit is the smallest, and may act to enhance the proofreading activity of epsilon, especially under extreme conditions []. This entry also includes a homologue of polymerase III theta called HOT (homologue of theta) from Bacteriophage P1. HOT contains three alpha-helices, as reported for theta, but the folding topology of the two is different, which could account for the suggested greater heat stability of HOT as compared to theta [].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1SE7_A 2IDO_D 2AE9_A 1DU2_A 2XY8_B 2AXD_S.
Probab=36.44 E-value=27 Score=30.92 Aligned_cols=23 Identities=39% Similarity=0.674 Sum_probs=19.1
Q ss_pred HhhcCChHHHhhhhHHHHHHHHHHHHH
Q 006998 108 KILDVSKEERDRIQRLQVIDRAAAAIA 134 (622)
Q Consensus 108 ~~l~v~~eerdrvqr~qvidraaaaia 134 (622)
.|-.+|+||||+|- ||-||.++|
T Consensus 4 Nla~lskee~dKvn----vDLaAsgVa 26 (75)
T PF06440_consen 4 NLAELSKEEMDKVN----VDLAASGVA 26 (75)
T ss_dssp -CHHSTCHHHHHHH----HHHHHHHHH
T ss_pred cHhhcCHHHHHHHH----HHHHHHHHH
Confidence 35678999999995 899998887
No 5
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=31.71 E-value=1.8e+02 Score=27.28 Aligned_cols=71 Identities=27% Similarity=0.334 Sum_probs=45.2
Q ss_pred hhhhHHHHHHhhcccccCCCCCCCCCCCCCchHHHHHhHHHHHHhhcCChHHHhhhhHH--HHHHHHHHHHHHHHHHHhh
Q 006998 65 DRKEIEFQKIAGSLAESGDVDGNEGGGGRDLTEQLEKKSEEFSKILDVSKEERDRIQRL--QVIDRAAAAIAAARAILEE 142 (622)
Q Consensus 65 er~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~f~~~l~v~~eerdrvqr~--qvidraaaaiaaara~l~~ 142 (622)
++--.||+.|..++-+.-...+.. ..+..++--+.-+.+| ++-|+|++.. -|+-|+-+|+.+|--.+.+
T Consensus 11 ~~l~~el~~L~d~lEevL~ssg~~------a~~e~~~lR~r~~~~L---k~~r~rl~~~~d~v~~~sk~a~~~tD~yV~e 81 (104)
T COG4575 11 DQLLAELQELLDTLEEVLKSSGSL------AGDEAEELRSKAESAL---KEARDRLGDTGDAVVQRSKAAADATDDYVRE 81 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHhcccc------hhhHHHHHHHHHHHHH---HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHc
Confidence 445567776665543322222222 2333444444445555 6889999987 5889999999999999988
Q ss_pred cC
Q 006998 143 KN 144 (622)
Q Consensus 143 ~~ 144 (622)
+|
T Consensus 82 ~P 83 (104)
T COG4575 82 NP 83 (104)
T ss_pred CC
Confidence 88
No 6
>PRK10969 DNA polymerase III subunit theta; Reviewed
Probab=29.60 E-value=49 Score=29.30 Aligned_cols=22 Identities=36% Similarity=0.634 Sum_probs=18.7
Q ss_pred hhcCChHHHhhhhHHHHHHHHHHHHH
Q 006998 109 ILDVSKEERDRIQRLQVIDRAAAAIA 134 (622)
Q Consensus 109 ~l~v~~eerdrvqr~qvidraaaaia 134 (622)
|-..|+||||+|+ +|-||+++|
T Consensus 5 lA~l~qee~dKvn----vDLaASgVa 26 (75)
T PRK10969 5 LAKLSQEEMDKVN----VDLAASGVA 26 (75)
T ss_pred hhhcCHHHHHHHH----HHHHHHHHH
Confidence 4568999999997 798888887
No 7
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=20.65 E-value=82 Score=26.23 Aligned_cols=15 Identities=60% Similarity=0.532 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHhh
Q 006998 128 RAAAAIAAARAILEE 142 (622)
Q Consensus 128 raaaaiaaara~l~~ 142 (622)
-|||||..||.+|..
T Consensus 45 iAaAai~lA~~~~~~ 59 (118)
T PF02984_consen 45 IAAAAILLARKILGK 59 (118)
T ss_dssp HHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHhCc
Confidence 499999999999984
No 8
>PF08988 DUF1895: Protein of unknown function (DUF1895); InterPro: IPR015081 The YscE protein, produced by the pathogen Yersinia, assumes a secondary structure composed of two anti-parallel alpha-helices separated by a flexible loop. The function of this protein is, as yet, unknown. ; PDB: 1ZW0_B 2P58_A 2UWJ_E 2Q1K_D 3PH0_B.
Probab=16.32 E-value=1.8e+02 Score=25.00 Aligned_cols=22 Identities=36% Similarity=0.416 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhh
Q 006998 121 QRLQVIDRAAAAIAAARAILEE 142 (622)
Q Consensus 121 qr~qvidraaaaiaaara~l~~ 142 (622)
|..|+.-..+-||.||++||.-
T Consensus 41 ~eyQq~q~~~~AieAA~~Vie~ 62 (68)
T PF08988_consen 41 QEYQQLQQQYDAIEAAIAVIET 62 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4578888889999999999864
No 9
>COG2841 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=11.69 E-value=3.1e+02 Score=24.35 Aligned_cols=26 Identities=31% Similarity=0.363 Sum_probs=19.6
Q ss_pred CChHHHh--hhhHHHHHHHHHHHHHHHH
Q 006998 112 VSKEERD--RIQRLQVIDRAAAAIAAAR 137 (622)
Q Consensus 112 v~~eerd--rvqr~qvidraaaaiaaar 137 (622)
++.+|-+ +-||+|+=|--+.+|+.|+
T Consensus 43 ~s~~ev~~LKKqkL~LKDEi~~~L~~a~ 70 (72)
T COG2841 43 GSDAEVSNLKKQKLQLKDEIASILQKAK 70 (72)
T ss_pred CcHHHHHHHHHHHHHhHHHHHHHHHHHh
Confidence 4444433 4589999999999999885
No 10
>PLN03121 nucleic acid binding protein; Provisional
Probab=11.28 E-value=3.8e+02 Score=28.18 Aligned_cols=53 Identities=19% Similarity=0.163 Sum_probs=33.5
Q ss_pred CchHHHHHhHHHHHHhhcCCh-------HH-----------------HhhhhHHHHHHHHHHHHHHHHHHHhhcCCC
Q 006998 94 DLTEQLEKKSEEFSKILDVSK-------EE-----------------RDRIQRLQVIDRAAAAIAAARAILEEKNGS 146 (622)
Q Consensus 94 ~~~~~~~~k~~~f~~~l~v~~-------ee-----------------rdrvqr~qvidraaaaiaaara~l~~~~~~ 146 (622)
.+..|.-.|-+.|.+=-+|+. +- |.-=||.||-|+.-+|++||-.-+...-++
T Consensus 132 vLgkda~~KAkafDE~h~lss~a~a~v~~~d~~iglt~k~~~g~~~vk~vDeky~vs~~tksA~~aa~~~~~~a~sa 208 (243)
T PLN03121 132 VLGKDALSKAKAFDESHQVSATAAAKVAELSKRIGLTDKIFAGMEAVRSVDEKYHVSEFTKSAATATGRTAAAAANA 208 (243)
T ss_pred hhhHHHHHHHHHHHHhcCccHhhhhhhhhhhhhccchhhhhhhHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHhhhh
Confidence 344455556666766666653 21 222389999999999999986555433333
Done!