Query 008770
Match_columns 554
No_of_seqs 176 out of 322
Neff 3.3
Searched_HMMs 46136
Date Thu Mar 28 16:21:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/008770.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/008770hhsearch_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 1.2E-37 2.5E-42 261.7 -0.7 78 171-248 1-78 (79)
2 PF14901 Jiv90: Cleavage induc 34.6 17 0.00037 32.8 0.7 18 209-226 26-43 (94)
3 PRK00241 nudC NADH pyrophospha 24.2 31 0.00066 35.1 0.6 36 184-220 92-127 (256)
4 PF09297 zf-NADH-PPase: NADH p 23.5 36 0.00077 24.2 0.6 31 189-220 1-31 (32)
5 COG2816 NPY1 NTP pyrophosphohy 17.2 50 0.0011 34.8 0.4 36 184-220 104-139 (279)
6 TIGR03831 YgiT_finger YgiT-typ 16.5 73 0.0016 23.2 1.0 20 199-218 21-40 (46)
7 TIGR01674 phage_lambda_G phage 14.7 80 0.0017 30.4 1.0 19 515-534 10-28 (138)
8 PRK06424 transcription factor; 14.4 92 0.002 29.7 1.3 21 201-221 14-34 (144)
9 PF14776 UNC-79: Cation-channe 14.0 1E+02 0.0022 35.2 1.8 28 191-218 262-298 (525)
10 PF05485 THAP: THAP domain; I 13.7 90 0.002 25.5 1.0 13 190-202 48-60 (84)
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=1.2e-37 Score=261.74 Aligned_cols=78 Identities=65% Similarity=1.149 Sum_probs=63.2
Q ss_pred CcccCCCchhccCChhhhccccchhhhcCCCeEEECCccchhhhhhhccccccccccccchHHHHHhhHHhhhcCCCC
Q 008770 171 YCQVYGCNKDLSSSKDYHKRHKVCEAHSKAAKVIVNEIEQRFCQQCSRFHFLDEFDDGKRSCRKRLAGHNERRRKPQV 248 (554)
Q Consensus 171 ~CQVdGC~~dLs~~k~Y~rRhrVCe~H~kA~~V~v~G~~qRFCQQCsrFH~L~eFDg~kRSCR~rL~~hn~RRRk~q~ 248 (554)
+||||||++||+.+|.||+||||||.|+|||+|+++|.++||||||+|||+|+||||.|||||++|++||+||||+++
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
>PF14901 Jiv90: Cleavage inducing molecular chaperone
Probab=34.55 E-value=17 Score=32.76 Aligned_cols=18 Identities=39% Similarity=0.654 Sum_probs=14.0
Q ss_pred cchhhhhhhccccccccc
Q 008770 209 EQRFCQQCSRFHFLDEFD 226 (554)
Q Consensus 209 ~qRFCQQCsrFH~L~eFD 226 (554)
.-|+||+|..+|+..+=|
T Consensus 26 ~AR~C~~C~~~H~Ak~gD 43 (94)
T PF14901_consen 26 AARYCQDCKIRHPAKEGD 43 (94)
T ss_pred hhHhHHHhhhhcccccCC
Confidence 459999999999865543
No 3
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=24.17 E-value=31 Score=35.11 Aligned_cols=36 Identities=11% Similarity=0.303 Sum_probs=27.5
Q ss_pred ChhhhccccchhhhcCCCeEEECCccchhhhhhhccc
Q 008770 184 SKDYHKRHKVCEAHSKAAKVIVNEIEQRFCQQCSRFH 220 (554)
Q Consensus 184 ~k~Y~rRhrVCe~H~kA~~V~v~G~~qRFCQQCsrFH 220 (554)
+..+|++||-|..+-....+ ..+...|.|..|++.|
T Consensus 92 l~~w~~~~~fC~~CG~~~~~-~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 92 LAEFYRSHRFCGYCGHPMHP-SKTEWAMLCPHCRERY 127 (256)
T ss_pred HHHHhhcCccccccCCCCee-cCCceeEECCCCCCEE
Confidence 34799999999988776554 4566678999998654
No 4
>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=23.47 E-value=36 Score=24.23 Aligned_cols=31 Identities=23% Similarity=0.378 Sum_probs=17.3
Q ss_pred ccccchhhhcCCCeEEECCccchhhhhhhccc
Q 008770 189 KRHKVCEAHSKAAKVIVNEIEQRFCQQCSRFH 220 (554)
Q Consensus 189 rRhrVCe~H~kA~~V~v~G~~qRFCQQCsrFH 220 (554)
++||-|... -+|++.+.+...|-|+.|+..|
T Consensus 1 ~~~rfC~~C-G~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 1 RNHRFCGRC-GAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp HTTSB-TTT---BEEE-SSSS-EEESSSS-EE
T ss_pred CCCcccCcC-CccccCCCCcCEeECCCCcCEe
Confidence 356666653 5677777777888888887643
No 5
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=17.18 E-value=50 Score=34.80 Aligned_cols=36 Identities=17% Similarity=0.360 Sum_probs=29.6
Q ss_pred ChhhhccccchhhhcCCCeEEECCccchhhhhhhccc
Q 008770 184 SKDYHKRHKVCEAHSKAAKVIVNEIEQRFCQQCSRFH 220 (554)
Q Consensus 184 ~k~Y~rRhrVCe~H~kA~~V~v~G~~qRFCQQCsrFH 220 (554)
+-.+|++||.|.. +-++....+|...|-|++|+.-|
T Consensus 104 l~~w~~~~RFCg~-CG~~~~~~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 104 LLEWYRSHRFCGR-CGTKTYPREGGWARVCPKCGHEH 139 (279)
T ss_pred HHHHHhhCcCCCC-CCCcCccccCceeeeCCCCCCcc
Confidence 3468999999985 56788888999999999998643
No 6
>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=16.52 E-value=73 Score=23.20 Aligned_cols=20 Identities=15% Similarity=0.584 Sum_probs=17.4
Q ss_pred CCCeEEECCccchhhhhhhc
Q 008770 199 KAAKVIVNEIEQRFCQQCSR 218 (554)
Q Consensus 199 kA~~V~v~G~~qRFCQQCsr 218 (554)
+...+++.+.+.++|.+|+.
T Consensus 21 ~~~~~~i~~vp~~~C~~CGE 40 (46)
T TIGR03831 21 GGELIVIENVPALVCPQCGE 40 (46)
T ss_pred CCEEEEEeCCCccccccCCC
Confidence 55678899999999999986
No 7
>TIGR01674 phage_lambda_G phage minor tail protein G. This model describes a family of bacteriophage proteins including G of phage lambda. This protein has been described as undergoing a translational frameshift at a Gly-Lys dipeptide near the C-terminus of protein G from phage lambda, with about 4 % efficiency, to produce tail assembly protein G-T. The Lys of the Gly-Lys pair is the conserved second-to-last residue of seed alignment for this family.
Probab=14.71 E-value=80 Score=30.41 Aligned_cols=19 Identities=47% Similarity=0.856 Sum_probs=16.7
Q ss_pred CCCCcchhhhhhhhhHHHHH
Q 008770 515 EDGATIDLLKLSSQLQRVEH 534 (554)
Q Consensus 515 e~~~tidllqlss~l~rve~ 534 (554)
-+|.+|-|.+|| -|||+|+
T Consensus 10 ~nG~sVtLsELS-ALQRiey 28 (138)
T TIGR01674 10 CNGSSVTLFELS-ALQRIEH 28 (138)
T ss_pred eCCEEEEehhhh-HHHHHHH
Confidence 479999999996 5999997
No 8
>PRK06424 transcription factor; Provisional
Probab=14.36 E-value=92 Score=29.65 Aligned_cols=21 Identities=24% Similarity=0.659 Sum_probs=18.6
Q ss_pred CeEEECCccchhhhhhhcccc
Q 008770 201 AKVIVNEIEQRFCQQCSRFHF 221 (554)
Q Consensus 201 ~~V~v~G~~qRFCQQCsrFH~ 221 (554)
-.|+|+|.+.+-|..|.+|=.
T Consensus 14 ~~v~ieg~~l~vC~~Ca~~G~ 34 (144)
T PRK06424 14 TKVMIDGAILNVCDDCAKFGT 34 (144)
T ss_pred eEEEEcCeeeehhHHHHHcCC
Confidence 478999999999999999854
No 9
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=14.02 E-value=1e+02 Score=35.21 Aligned_cols=28 Identities=36% Similarity=0.649 Sum_probs=21.1
Q ss_pred ccchhhhcCCCeEEE---------CCccchhhhhhhc
Q 008770 191 HKVCEAHSKAAKVIV---------NEIEQRFCQQCSR 218 (554)
Q Consensus 191 hrVCe~H~kA~~V~v---------~G~~qRFCQQCsr 218 (554)
+|-|.-+.|..+|+- ++++.|+||||..
T Consensus 262 nK~C~S~~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch~ 298 (525)
T PF14776_consen 262 NKNCRSSDKSAVVTCFSTECTSYNGNRPIRLCQQCHS 298 (525)
T ss_pred CCCCcCCCCCeEEEEechhhccccCCCcchhHHHHhh
Confidence 456667777777763 7788999999964
No 10
>PF05485 THAP: THAP domain; InterPro: IPR006612 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. The THAP domain is an ~90-residue domain restricted to animals, which is shared between the THAP family of cellular DNA-binding proteins, and transposases from mobile genomic parasites. The defined THAP domain includes: a C2CH signature (consensus: C-x(2,4)-C-x(35,50)-C-x(2)-H); three additional key residues that are strictly conserved in all THAP domains that have been found to date (THAP1 amino acids P26, W36, F58); a C-terminal AVPTIF box; and several other conserved amino acid positions with distinct physicochemical properties (e.g. hydrophobic and polar). The THAP domain can be found in one or more copies and can be associated with other domains, such as the C2H2-type zinc finger. The THAP domain is supposed to be a DNA-binding domain (DBD) [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding; PDB: 3KDE_C 2D8R_A 2JM3_A 2KO0_A 2JTG_A 2L1G_A.
Probab=13.70 E-value=90 Score=25.47 Aligned_cols=13 Identities=15% Similarity=0.562 Sum_probs=6.8
Q ss_pred cccchhhhcCCCe
Q 008770 190 RHKVCEAHSKAAK 202 (554)
Q Consensus 190 RhrVCe~H~kA~~ 202 (554)
..+||..|.....
T Consensus 48 ~~~ICs~HF~~~~ 60 (84)
T PF05485_consen 48 NSRICSRHFEPDD 60 (84)
T ss_dssp TSEEEGGGSTGGG
T ss_pred CccchhhhCchhh
Confidence 3456666655443
Done!