Query 041598
Match_columns 315
No_of_seqs 144 out of 269
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 08:49:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041598.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041598hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07496 zf-CW: CW-type Zinc F 99.7 7.9E-18 1.7E-22 121.8 1.2 44 21-65 1-49 (50)
2 smart00249 PHD PHD zinc finger 88.1 0.56 1.2E-05 30.8 2.8 30 19-48 10-45 (47)
3 PF00628 PHD: PHD-finger; Int 60.3 6.2 0.00013 27.5 1.7 32 17-48 8-46 (51)
4 PF13043 DUF3903: Domain of un 29.3 26 0.00056 25.3 0.8 14 162-175 16-30 (40)
5 PF06407 BDV_P40: Borna diseas 21.7 51 0.0011 33.0 1.5 25 157-182 156-180 (370)
6 COG5132 BUD31 Cell cycle contr 21.2 30 0.00065 30.8 -0.2 21 137-159 101-121 (146)
7 CHL00174 accD acetyl-CoA carbo 19.9 81 0.0018 31.1 2.5 15 17-31 32-46 (296)
8 PRK02113 putative hydrolase; P 19.8 46 0.001 29.9 0.7 22 134-156 17-38 (252)
9 KOG2894 Uncharacterized conser 19.6 2E+02 0.0044 28.9 5.0 11 163-173 80-90 (331)
10 smart00399 ZnF_C4 c4 zinc fing 19.1 63 0.0014 24.5 1.2 28 137-166 1-28 (70)
No 1
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=99.68 E-value=7.9e-18 Score=121.85 Aligned_cols=44 Identities=48% Similarity=1.036 Sum_probs=30.2
Q ss_pred CCeEecccCccccCCCCCC-----CCCCCceeecCCcCCCCCCCCccccc
Q 041598 21 EQWAPCDDCSKWRKLPTDA-----LLPPKWTCSDNVWDSIRCSCSAAEEM 65 (315)
Q Consensus 21 ~~WVQCD~C~KWRrLP~~~-----~lPd~W~C~mN~WD~~~~sCsaPEE~ 65 (315)
+.|||||.|+|||+||.++ .+|+.|||+||+ |+.+++|++|||.
T Consensus 1 ~~WVQCd~C~KWR~lp~~~~~~~~~~~d~W~C~~n~-~~~~~sC~~pee~ 49 (50)
T PF07496_consen 1 DYWVQCDSCLKWRRLPEEVDPIREELPDPWYCSMNP-DPPFNSCDAPEEI 49 (50)
T ss_dssp -EEEE-TTT--EEEE-CCHHCTSCCSSTT--GGGSS--CCC-STTS--SS
T ss_pred CeEEECCCCCceeeCChhhCcccccCCCeEEcCCCC-CCCCCCCCCcccC
Confidence 4799999999999999986 468899999999 8899999999985
No 2
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF00628 PHD: PHD-finger; InterPro: IPR019787 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. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=60.29 E-value=6.2 Score=27.50 Aligned_cols=32 Identities=19% Similarity=0.602 Sum_probs=22.2
Q ss_pred CCCCCCeEecccCccccCCCCC---C----CCCCCceee
Q 041598 17 LWEQEQWAPCDDCSKWRKLPTD---A----LLPPKWTCS 48 (315)
Q Consensus 17 ~~e~~~WVQCD~C~KWRrLP~~---~----~lPd~W~C~ 48 (315)
..+...||+||.|..|--+.=- . .....|+|.
T Consensus 8 ~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~ 46 (51)
T PF00628_consen 8 SDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCP 46 (51)
T ss_dssp SCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSH
T ss_pred cCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECc
Confidence 5668899999999999654322 1 223488885
No 4
>PF13043 DUF3903: Domain of unknown function (DUF3903)
Probab=29.35 E-value=26 Score=25.27 Aligned_cols=14 Identities=57% Similarity=0.923 Sum_probs=10.0
Q ss_pred HHHHHH-HHHHHHHH
Q 041598 162 TVKRRF-KTLMLRKK 175 (315)
Q Consensus 162 tvkrrf-ktlm~rkk 175 (315)
.-|||| |||++.-+
T Consensus 16 eckrrfgktlllqte 30 (40)
T PF13043_consen 16 ECKRRFGKTLLLQTE 30 (40)
T ss_pred HHHHHhchhhhhhhH
Confidence 348999 88887543
No 5
>PF06407 BDV_P40: Borna disease virus P40 protein; InterPro: IPR009441 This entry represents P40 nucleoproteins from several Borna disease virus (BDV) strains. BDV is an RNA virus that is a member of the Mononegavirales family, which includes such members as Measles virus and Ebola virus sp.. BDV causes an infection of the central nervous system in a wide range of vertebrates, which can progress to an often fatal immune-mediated disease. Viral nucleoproteins are central to transcription, replication, and packaging of the RNA genome. P40 nucleoprotein from BDV is multi-helical in structure and can be divided into two subdomains, each of which has an alpha-bundle topology []. The nucleoprotein assembles into a planar homotetramer, with the RNA genome either wrapping around the outside of the tetramer or possibly fitting within the charged central channel of the tetramer [].; PDB: 1N93_X 1PP1_X.
Probab=21.68 E-value=51 Score=33.03 Aligned_cols=25 Identities=36% Similarity=0.660 Sum_probs=15.6
Q ss_pred cchhHHHHHHHHHHHHHHHhhhhHHH
Q 041598 157 CNVCMTVKRRFKTLMLRKKRRQSERE 182 (315)
Q Consensus 157 cnvc~tvkrrfktlm~rkkkrqse~e 182 (315)
|.--..|+||||++|- -+.|-+-.|
T Consensus 156 ~a~s~qI~RRfkAMmA-sinrPshge 180 (370)
T PF06407_consen 156 CAGSLQIQRRFKAMMA-SINRPSHGE 180 (370)
T ss_dssp HS--HHHHHHHHHHHH-HTT-TTHHH
T ss_pred cccHHHHHHHHHHHHH-hcCCCCcch
Confidence 5556789999999765 455655544
No 6
>COG5132 BUD31 Cell cycle control protein, G10 family [Transcription / Cell division and chromosome partitioning]
Probab=21.18 E-value=30 Score=30.76 Aligned_cols=21 Identities=52% Similarity=1.153 Sum_probs=17.3
Q ss_pred ceeeeecCCCCCCCCCCccccch
Q 041598 137 TCIVCIQPPSGKGKHKPTCTCNV 159 (315)
Q Consensus 137 sCIvCiqppsGkgkhk~tCtcnv 159 (315)
-|.-||||-.- ||-.||.|-|
T Consensus 101 CCLRCIQ~~es--k~GstCICRV 121 (146)
T COG5132 101 CCLRCIQPIES--KHGSTCICRV 121 (146)
T ss_pred hhHhhcCcccc--cCCCEEEEeC
Confidence 48999998643 6999999976
No 7
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=19.89 E-value=81 Score=31.10 Aligned_cols=15 Identities=20% Similarity=0.700 Sum_probs=11.3
Q ss_pred CCCCCCeEecccCcc
Q 041598 17 LWEQEQWAPCDDCSK 31 (315)
Q Consensus 17 ~~e~~~WVQCD~C~K 31 (315)
......|++|+.|.+
T Consensus 32 ~~p~~lw~kc~~C~~ 46 (296)
T CHL00174 32 QKYKHLWVQCENCYG 46 (296)
T ss_pred CCCCCCeeECCCccc
Confidence 344557999999975
No 8
>PRK02113 putative hydrolase; Provisional
Probab=19.82 E-value=46 Score=29.88 Aligned_cols=22 Identities=32% Similarity=0.668 Sum_probs=15.7
Q ss_pred CCcceeeeecCCCCCCCCCCccc
Q 041598 134 PGCTCIVCIQPPSGKGKHKPTCT 156 (315)
Q Consensus 134 pGCsCIvCiqppsGkgkhk~tCt 156 (315)
+||.|-+|-.. .++.+..++|.
T Consensus 17 ~~c~c~~C~~~-~~~~~R~~~s~ 38 (252)
T PRK02113 17 IGCTCPVCTSK-DPRDNRLRTSA 38 (252)
T ss_pred CCCCCccCCCC-CCCCcceeeEE
Confidence 89999999884 45545555554
No 9
>KOG2894 consensus Uncharacterized conserved protein XAP-5 [Function unknown]
Probab=19.58 E-value=2e+02 Score=28.88 Aligned_cols=11 Identities=36% Similarity=0.437 Sum_probs=9.3
Q ss_pred HHHHHHHHHHH
Q 041598 163 VKRRFKTLMLR 173 (315)
Q Consensus 163 vkrrfktlm~r 173 (315)
|+.|||.|-.+
T Consensus 80 VreRekqlak~ 90 (331)
T KOG2894|consen 80 VREREKQLAKK 90 (331)
T ss_pred HHHHHHHHHHh
Confidence 89999998873
No 10
>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors.
Probab=19.09 E-value=63 Score=24.50 Aligned_cols=28 Identities=36% Similarity=0.787 Sum_probs=22.5
Q ss_pred ceeeeecCCCCCCCCCCccccchhHHHHHH
Q 041598 137 TCIVCIQPPSGKGKHKPTCTCNVCMTVKRR 166 (315)
Q Consensus 137 sCIvCiqppsGkgkhk~tCtcnvc~tvkrr 166 (315)
.|.||-++ +-|.|-..-+|+.|-..-||
T Consensus 1 ~C~vC~~~--~~~~hygv~~C~aC~~FFRR 28 (70)
T smart00399 1 LCCVCGDH--ASGFHFGVCSCRACKAFFRR 28 (70)
T ss_pred CCeEeCCc--CcccEeCCcEechhhhhhhh
Confidence 38899765 45568889999999988777
Done!