Query 020302
Match_columns 328
No_of_seqs 162 out of 300
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 08:39:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020302.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020302hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03110 SBP: SBP domain; Int 100.0 2E-40 4.4E-45 260.9 -2.9 78 181-258 1-78 (79)
2 PF09297 zf-NADH-PPase: NADH p 48.8 6.9 0.00015 25.8 0.4 30 199-229 1-30 (32)
3 PF14901 Jiv90: Cleavage induc 46.0 9.5 0.00021 32.0 0.9 18 219-236 26-43 (94)
4 PRK07217 replication factor A; 33.5 24 0.00052 35.0 1.6 75 141-223 145-232 (311)
5 PRK00241 nudC NADH pyrophospha 31.8 15 0.00033 34.3 -0.1 37 194-231 92-128 (256)
6 PRK06424 transcription factor; 30.6 29 0.00063 30.4 1.5 21 211-231 14-34 (144)
7 TIGR03831 YgiT_finger YgiT-typ 27.7 30 0.00065 23.1 0.9 20 209-228 21-40 (46)
8 KOG3993 Transcription factor ( 27.2 31 0.00068 36.1 1.3 50 240-292 305-355 (500)
9 COG2816 NPY1 NTP pyrophosphohy 22.3 26 0.00057 34.2 -0.3 35 195-230 105-139 (279)
10 PF02150 RNA_POL_M_15KD: RNA p 22.1 33 0.00072 23.5 0.2 34 202-235 2-35 (35)
11 PF12108 SF3a60_bindingd: Spli 22.0 31 0.00067 23.4 0.1 12 190-201 15-26 (28)
12 PF05896 NQRA: Na(+)-transloca 21.7 53 0.0012 31.7 1.6 21 306-326 130-152 (257)
No 1
>PF03110 SBP: SBP domain; InterPro: IPR004333 The SBP plant protein domain is a sequence specific DNA-binding domain []. Proteins with this domain probably function as transcription factors involved in the control of early flower development. The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands.; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 1UL4_A 1WJ0_A 1UL5_A.
Probab=100.00 E-value=2e-40 Score=260.92 Aligned_cols=78 Identities=68% Similarity=1.193 Sum_probs=63.2
Q ss_pred ccccCCCchhhhcchhhhhhccchhhhcCCcEEeEcCchhhhhhhhhccccccccccccchHHHHHHHHHHHhhccCC
Q 020302 181 RCQAEGCSADLTHAKHYHRRHKVCEFHSKASTVIAAGLTQRFCQQCSRFHLLSEFDNGKRSCRKRLADHNRRRRKSQQ 258 (328)
Q Consensus 181 ~CQVdGC~aDLs~aK~YhRRhRVCE~HsKAp~Vvv~G~~qRFCQQCsRFH~LsEFDg~KRSCRrrLarHN~RRRK~~~ 258 (328)
+||||||++||+.+|+||+||||||.|+||++|+++|+.+||||||+|||+|+||||+|||||++|++||+||||.++
T Consensus 1 ~CqV~gC~~dL~~~k~Y~rR~rICe~H~ka~~V~~~G~~~RFCQQC~rfh~l~eFdg~kRSCr~~L~~h~~RRr~~~~ 78 (79)
T PF03110_consen 1 RCQVDGCGADLSGAKEYHRRYRICEEHAKAPVVVVDGVEQRFCQQCGRFHPLSEFDGGKRSCRARLARHNERRRKRQQ 78 (79)
T ss_dssp C-SSTTEE-EETS--SSCCCTT--HHHHTHSEEEETTEEEEE-TTTSSEEETTCB-SSTTSBSTTTT-SSS---S-S-
T ss_pred CCcCCCCCcchhhhHHHhhccCcchhhcCCCeEEECChhHHHHHHHHcCCCHHHHcchhhhHHHHHHHHHHHhccccC
Confidence 599999999999999999999999999999999999999999999999999999999999999999999999999875
No 2
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=48.76 E-value=6.9 Score=25.82 Aligned_cols=30 Identities=33% Similarity=0.475 Sum_probs=17.0
Q ss_pred hhccchhhhcCCcEEeEcCchhhhhhhhhcc
Q 020302 199 RRHKVCEFHSKASTVIAAGLTQRFCQQCSRF 229 (328)
Q Consensus 199 RRhRVCE~HsKAp~Vvv~G~~qRFCQQCsRF 229 (328)
++||-|... -++++.+.+...|-|+.|+..
T Consensus 1 ~~~rfC~~C-G~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 1 RNHRFCGRC-GAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp HTTSB-TTT---BEEE-SSSS-EEESSSS-E
T ss_pred CCCcccCcC-CccccCCCCcCEeECCCCcCE
Confidence 356666655 567777777788888888764
No 3
>PF14901 Jiv90: Cleavage inducing molecular chaperone
Probab=46.01 E-value=9.5 Score=32.00 Aligned_cols=18 Identities=39% Similarity=0.685 Sum_probs=15.1
Q ss_pred hhhhhhhhhccccccccc
Q 020302 219 TQRFCQQCSRFHLLSEFD 236 (328)
Q Consensus 219 ~qRFCQQCsRFH~LsEFD 236 (328)
.-|+|++|+.+|+..+=|
T Consensus 26 ~AR~C~~C~~~H~Ak~gD 43 (94)
T PF14901_consen 26 AARYCQDCKIRHPAKEGD 43 (94)
T ss_pred hhHhHHHhhhhcccccCC
Confidence 469999999999877654
No 4
>PRK07217 replication factor A; Reviewed
Probab=33.51 E-value=24 Score=34.96 Aligned_cols=75 Identities=25% Similarity=0.337 Sum_probs=47.3
Q ss_pred cccceeecCCccccCCCchh-hhhccccCCC----CCCCCCCCCCccccCCCchhhhcchhhhhhccchhhhcCCc----
Q 020302 141 ASRIGLNLGGRTYFSSADDD-FVSRLYRRPR----PGEAGSANIPRCQAEGCSADLTHAKHYHRRHKVCEFHSKAS---- 211 (328)
Q Consensus 141 ~~~igLkLG~rtyf~~~e~~-~v~~~~kr~R----~~~pgs~~~p~CQVdGC~aDLs~aK~YhRRhRVCE~HsKAp---- 211 (328)
.|++.||||+.+..+..+++ .+....-..+ ...+|+.--.+|-.+||+.-|+. -.|+.|=+..
T Consensus 145 ~G~~~lnlg~~t~I~~~de~IeV~~~~vei~G~lVdi~~GsglI~rCP~~~C~Rvl~~--------g~C~~HG~ve~~~D 216 (311)
T PRK07217 145 QGRFSVKLNRTTSIEELDEDIEVGDDEVEVEGALVDIQSGSGLIKRCPEEDCTRVLQN--------GRCSEHGKVEGEFD 216 (311)
T ss_pred CCEEEEEeCCceEEEeCCCCccccCccccceeEEEEEeCCCCCeecCCccccCccccC--------CCCCCCCCcCCcee
Confidence 38899999998766653321 1111100011 24567778899999999999942 3799997654
Q ss_pred ----EEeEcCchhhhh
Q 020302 212 ----TVIAAGLTQRFC 223 (328)
Q Consensus 212 ----~Vvv~G~~qRFC 223 (328)
.|+-+|.....|
T Consensus 217 Lrik~vlDDGt~~~~~ 232 (311)
T PRK07217 217 LRIKGVLDDGEEVQEV 232 (311)
T ss_pred eEEEEEEECCCCeEEE
Confidence 445577665444
No 5
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=31.76 E-value=15 Score=34.27 Aligned_cols=37 Identities=14% Similarity=0.331 Sum_probs=28.8
Q ss_pred chhhhhhccchhhhcCCcEEeEcCchhhhhhhhhcccc
Q 020302 194 AKHYHRRHKVCEFHSKASTVIAAGLTQRFCQQCSRFHL 231 (328)
Q Consensus 194 aK~YhRRhRVCE~HsKAp~Vvv~G~~qRFCQQCsRFH~ 231 (328)
+-.+|++||-|..+-....+. .+...|.|..|+..|-
T Consensus 92 l~~w~~~~~fC~~CG~~~~~~-~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 92 LAEFYRSHRFCGYCGHPMHPS-KTEWAMLCPHCRERYY 128 (256)
T ss_pred HHHHhhcCccccccCCCCeec-CCceeEECCCCCCEEC
Confidence 357999999999998766554 5556689999997663
No 6
>PRK06424 transcription factor; Provisional
Probab=30.58 E-value=29 Score=30.44 Aligned_cols=21 Identities=24% Similarity=0.681 Sum_probs=18.5
Q ss_pred cEEeEcCchhhhhhhhhcccc
Q 020302 211 STVIAAGLTQRFCQQCSRFHL 231 (328)
Q Consensus 211 p~Vvv~G~~qRFCQQCsRFH~ 231 (328)
-.|+|+|.+.+-|..|.+|=.
T Consensus 14 ~~v~ieg~~l~vC~~Ca~~G~ 34 (144)
T PRK06424 14 TKVMIDGAILNVCDDCAKFGT 34 (144)
T ss_pred eEEEEcCeeeehhHHHHHcCC
Confidence 578999999999999998754
No 7
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=27.73 E-value=30 Score=23.11 Aligned_cols=20 Identities=15% Similarity=0.501 Sum_probs=17.5
Q ss_pred CCcEEeEcCchhhhhhhhhc
Q 020302 209 KASTVIAAGLTQRFCQQCSR 228 (328)
Q Consensus 209 KAp~Vvv~G~~qRFCQQCsR 228 (328)
+...+++.++...+|.+|+.
T Consensus 21 ~~~~~~i~~vp~~~C~~CGE 40 (46)
T TIGR03831 21 GGELIVIENVPALVCPQCGE 40 (46)
T ss_pred CCEEEEEeCCCccccccCCC
Confidence 56678899999999999995
No 8
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=27.17 E-value=31 Score=36.09 Aligned_cols=50 Identities=30% Similarity=0.372 Sum_probs=34.8
Q ss_pred chHHHHHHHHHHHhh-ccCCCCCCCCCccCccccCccccccCCCCCCCCCcccc
Q 020302 240 RSCRKRLADHNRRRR-KSQQQPTTTPLQDNQKSQLEPEILAKSPPDSGAHSSSS 292 (328)
Q Consensus 240 RSCRrrLarHN~RRR-K~~~~a~~~~~~~~~~~~~~~~~~~~sp~dsga~~~ss 292 (328)
-||=+-|+-| ||| |++++|+.+.++.. |.+.+..+..++..-||+-+++-
T Consensus 305 FsCPANLASH--RRWHKPR~eaa~a~~~P~-k~~~~~rae~~ea~rsg~dss~g 355 (500)
T KOG3993|consen 305 FSCPANLASH--RRWHKPRPEAAKAGSPPP-KQAVETRAEVQEAERSGDDSSSG 355 (500)
T ss_pred ccCchhhhhh--hcccCCchhhhhcCCCCh-hhhhhhhhhhhhccccCCcccCc
Confidence 5899999988 555 77777764444333 33366667778888899987665
No 9
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=22.27 E-value=26 Score=34.20 Aligned_cols=35 Identities=26% Similarity=0.460 Sum_probs=29.1
Q ss_pred hhhhhhccchhhhcCCcEEeEcCchhhhhhhhhccc
Q 020302 195 KHYHRRHKVCEFHSKASTVIAAGLTQRFCQQCSRFH 230 (328)
Q Consensus 195 K~YhRRhRVCE~HsKAp~Vvv~G~~qRFCQQCsRFH 230 (328)
-+++++||.|..+ ..++...+|..-|-|++|+.-|
T Consensus 105 ~~w~~~~RFCg~C-G~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 105 LEWYRSHRFCGRC-GTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HHHHhhCcCCCCC-CCcCccccCceeeeCCCCCCcc
Confidence 4688999999876 6778888999999999998643
No 10
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=22.08 E-value=33 Score=23.53 Aligned_cols=34 Identities=15% Similarity=0.245 Sum_probs=20.6
Q ss_pred cchhhhcCCcEEeEcCchhhhhhhhhcccccccc
Q 020302 202 KVCEFHSKASTVIAAGLTQRFCQQCSRFHLLSEF 235 (328)
Q Consensus 202 RVCE~HsKAp~Vvv~G~~qRFCQQCsRFH~LsEF 235 (328)
+-|+.....+.+.-+....+.|..|+--++++.|
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~~~ 35 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGYEEPISQF 35 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-EEE-SS-
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCCccCCCCC
Confidence 3466666666666555554479999988888776
No 11
>PF12108 SF3a60_bindingd: Splicing factor SF3a60 binding domain; InterPro: IPR021966 This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription. ; PDB: 2DT7_A.
Probab=22.00 E-value=31 Score=23.40 Aligned_cols=12 Identities=50% Similarity=0.778 Sum_probs=7.8
Q ss_pred hhhcchhhhhhc
Q 020302 190 DLTHAKHYHRRH 201 (328)
Q Consensus 190 DLs~aK~YhRRh 201 (328)
.|..+|+||+||
T Consensus 15 rlk~Ike~Hrr~ 26 (28)
T PF12108_consen 15 RLKEIKEYHRRY 26 (28)
T ss_dssp HHHHHHHHHHS-
T ss_pred HHHHHHHHHHhC
Confidence 356677888876
No 12
>PF05896 NQRA: Na(+)-translocating NADH-quinone reductase subunit A (NQRA); InterPro: IPR008703 This family consists of several bacterial Na+-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na+-translocating NADH: ubiquinone oxidoreductase (Na+-NQR) generates an electrochemical Na+ potential driven by aerobic respiration [].; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0006814 sodium ion transport, 0055114 oxidation-reduction process
Probab=21.74 E-value=53 Score=31.71 Aligned_cols=21 Identities=29% Similarity=0.569 Sum_probs=16.5
Q ss_pred ccccCcCCcccc--Cccceeeec
Q 020302 306 CFRQKPSQATAS--TSAGSLFFS 326 (328)
Q Consensus 306 ~frqr~~q~~~~--~~~~s~f~~ 326 (328)
.||||||.-.|. ++..++|.+
T Consensus 130 ~irqRPy~~va~p~~~P~aIFVs 152 (257)
T PF05896_consen 130 AIRQRPYSKVANPDSTPKAIFVS 152 (257)
T ss_pred hhccCCCCCCCCCCCCCceEEEE
Confidence 499999998887 566677764
Done!