Query 041051
Match_columns 168
No_of_seqs 170 out of 1337
Neff 8.2
Searched_HMMs 46136
Date Fri Mar 29 03:18:43 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041051.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041051hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01657 Stress-antifung: Salt 99.9 7.7E-28 1.7E-32 167.2 9.4 95 68-165 10-106 (106)
2 PF01657 Stress-antifung: Salt 99.7 4.5E-18 9.7E-23 118.0 4.5 52 1-52 55-106 (106)
3 PHA00008 J DNA packaging prote 24.7 50 0.0011 16.5 1.1 11 32-42 11-21 (26)
4 PF14570 zf-RING_4: RING/Ubox 22.0 69 0.0015 18.8 1.5 20 126-145 23-42 (48)
5 PF04726 Microvir_J: Microviru 19.2 37 0.00081 16.6 0.0 11 32-42 10-20 (24)
6 PF13923 zf-C3HC4_2: Zinc fing 15.4 69 0.0015 17.2 0.5 19 13-32 20-38 (39)
7 PF09065 Haemadin: Haemadin; 13.8 56 0.0012 16.1 -0.1 10 4-13 17-26 (27)
8 KOG0174 20S proteasome, regula 13.0 3.1E+02 0.0067 21.2 3.5 44 108-152 149-194 (224)
9 PF14787 zf-CCHC_5: GAG-polypr 12.6 39 0.00084 18.6 -1.0 22 28-49 3-24 (36)
10 PF06689 zf-C4_ClpX: ClpX C4-t 12.3 2E+02 0.0043 15.9 1.8 18 11-28 23-40 (41)
No 1
>PF01657 Stress-antifung: Salt stress response/antifungal; InterPro: IPR002902 This domain is found in plants and has no known function. The structure of this domain is known and it is thought to be involved in antifungal responses in plants []. Two copies of this domain are also found together in cysteine-rich protein kinases and cysteine-rich repeat secretory proteins. The domain contains four conserved cysteines.; PDB: 3A2E_D.
Probab=99.95 E-value=7.7e-28 Score=167.18 Aligned_cols=95 Identities=43% Similarity=0.839 Sum_probs=75.7
Q ss_pred ccC-cchhhhhHHHHHHHHHHHHHhccC-CCceeeeeeecccCCcceEEEEEecCCCCChhchHHHHHHHHhhccccCCC
Q 041051 68 NNV-SNRVTFNQKSKELLSRLANEASGN-PKLYAAGELELNEESKKKIYGLAQCTRDLSYNDCKMCLDRIIGDLPSCCDG 145 (168)
Q Consensus 68 ~~~-~~~~~f~~~~~~ll~~l~~~a~~s-~~~fa~~~~~~~~~~~~~vYglaQC~~Dls~~~C~~CL~~a~~~~~~~c~~ 145 (168)
+++ +++..|.+++..||.+|+..++.+ +.+|++++.+. ++++||||+||++||++++|..||+.++.+|+++|++
T Consensus 10 ~~~~~~~~~f~~~l~~ll~~l~~~a~~~~~~~f~~~~~~~---~~~~vYgl~qC~~Dls~~dC~~Cl~~a~~~~~~~C~~ 86 (106)
T PF01657_consen 10 NNYTTDNSTFEQNLNSLLSSLVSNAASSSSKGFATGSAGS---GPDTVYGLAQCRGDLSPSDCRACLADAVANISSCCPG 86 (106)
T ss_dssp B----TT-THHHHHHHHHHHHHHHGGGTT-TEEEEEE--S---T---EEEEEEE-TTS-HHHHHHHHHHHHCCHHHHTTS
T ss_pred CCcCCCCchHHHHHHHHHHHHHHHHhhccccCcEEeecCC---CCCeEEEEEEcCCCCChhhhHHHHHHHHHHHHHhCCC
Confidence 344 456669999999999999998753 47899998643 7789999999999999999999999999999999999
Q ss_pred CcceEEEcCceeEEEecCCC
Q 041051 146 KQGGRVITASCIINYEIYPF 165 (168)
Q Consensus 146 ~~g~~v~~~~C~lRy~~~~F 165 (168)
++||+|++++|+||||+++|
T Consensus 87 ~~g~~v~~~~C~lRY~~~~F 106 (106)
T PF01657_consen 87 SRGGRVWYDSCFLRYENYPF 106 (106)
T ss_dssp BSSEEEEESSEEEEEESS--
T ss_pred CceEEEECCCEEEEEECCCC
Confidence 99999999999999999998
No 2
>PF01657 Stress-antifung: Salt stress response/antifungal; InterPro: IPR002902 This domain is found in plants and has no known function. The structure of this domain is known and it is thought to be involved in antifungal responses in plants []. Two copies of this domain are also found together in cysteine-rich protein kinases and cysteine-rich repeat secretory proteins. The domain contains four conserved cysteines.; PDB: 3A2E_D.
Probab=99.72 E-value=4.5e-18 Score=118.02 Aligned_cols=52 Identities=50% Similarity=1.093 Sum_probs=47.4
Q ss_pred CEeEEecCCCChhchHHHHHHHHHHHHhhCCCCceEEEEccccEEEEecCcc
Q 041051 1 NGLALCRGDVSASDCKRCVADAVSTIRKSCPYSKSAKIFYDNCMFKYSNDNF 52 (168)
Q Consensus 1 ygl~~CrgD~~~~~C~~Cv~~A~~~~~~~Cp~~~~a~i~~d~C~lrys~~~f 52 (168)
|||+||++|+++++|..||+.|+..|.+.||+.++|+||++.|+|||++++|
T Consensus 55 Ygl~qC~~Dls~~dC~~Cl~~a~~~~~~~C~~~~g~~v~~~~C~lRY~~~~F 106 (106)
T PF01657_consen 55 YGLAQCRGDLSPSDCRACLADAVANISSCCPGSRGGRVWYDSCFLRYENYPF 106 (106)
T ss_dssp EEEEEE-TTS-HHHHHHHHHHHHCCHHHHTTSBSSEEEEESSEEEEEESS--
T ss_pred EEEEEcCCCCChhhhHHHHHHHHHHHHHhCCCCceEEEECCCEEEEEECCCC
Confidence 8999999999999999999999999999999999999999999999999987
No 3
>PHA00008 J DNA packaging protein
Probab=24.73 E-value=50 Score=16.48 Aligned_cols=11 Identities=27% Similarity=0.558 Sum_probs=8.7
Q ss_pred CCceEEEEccc
Q 041051 32 YSKSAKIFYDN 42 (168)
Q Consensus 32 ~~~~a~i~~d~ 42 (168)
.+|+|+.||-+
T Consensus 11 r~KGARLWYVG 21 (26)
T PHA00008 11 RRKGARLWYVG 21 (26)
T ss_pred ccCceEEEEec
Confidence 46999999853
No 4
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=22.01 E-value=69 Score=18.76 Aligned_cols=20 Identities=25% Similarity=0.728 Sum_probs=13.4
Q ss_pred hchHHHHHHHHhhccccCCC
Q 041051 126 NDCKMCLDRIIGDLPSCCDG 145 (168)
Q Consensus 126 ~~C~~CL~~a~~~~~~~c~~ 145 (168)
..|+.|+..+..+....||+
T Consensus 23 ~IC~~C~~~i~~~~~g~CPg 42 (48)
T PF14570_consen 23 QICRFCYHDILENEGGRCPG 42 (48)
T ss_dssp ---HHHHHHHTTSS-SB-TT
T ss_pred cHHHHHHHHHHhccCCCCCC
Confidence 56999999999888888886
No 5
>PF04726 Microvir_J: Microvirus J protein; InterPro: IPR006815 This small protein is involved in DNA packaging, interacting with DNA via its hydrophobic C terminus. In bacteriophage phi-X174, J is present in 60 copies, and forms an S-shaped polypeptide chain without any secondary structure. It is thought to interact with DNA through simple charge interactions [].; GO: 0003677 DNA binding, 0019073 viral DNA genome packaging, 0019028 viral capsid; PDB: 1M06_J 1GFF_3 1RB8_J 2BPA_3.
Probab=19.16 E-value=37 Score=16.56 Aligned_cols=11 Identities=27% Similarity=0.549 Sum_probs=4.9
Q ss_pred CCceEEEEccc
Q 041051 32 YSKSAKIFYDN 42 (168)
Q Consensus 32 ~~~~a~i~~d~ 42 (168)
.+|+|+.||-+
T Consensus 10 ~~kgarlwyvg 20 (24)
T PF04726_consen 10 KRKGARLWYVG 20 (24)
T ss_dssp SSSSS----SS
T ss_pred ccCceEEEEec
Confidence 46999999853
No 6
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=15.44 E-value=69 Score=17.18 Aligned_cols=19 Identities=32% Similarity=0.800 Sum_probs=14.1
Q ss_pred hchHHHHHHHHHHHHhhCCC
Q 041051 13 SDCKRCVADAVSTIRKSCPY 32 (168)
Q Consensus 13 ~~C~~Cv~~A~~~~~~~Cp~ 32 (168)
..|..|+..-.+. ...||.
T Consensus 20 ~fC~~C~~~~~~~-~~~CP~ 38 (39)
T PF13923_consen 20 SFCKECIEKYLEK-NPKCPV 38 (39)
T ss_dssp EEEHHHHHHHHHC-TSB-TT
T ss_pred chhHHHHHHHHHC-cCCCcC
Confidence 3689999998877 677873
No 7
>PF09065 Haemadin: Haemadin; InterPro: IPR015150 Members of this family adopt a secondary structure consisting of five short beta-strands (beta1-beta5), which are arranged in two antiparallel distorted sheets formed by strands beta1-beta4-beta5 and beta2-beta3 facing each other. This beta-sandwich is stabilised by six enclosed cysteines arranged in a [1-2, 3-5, 4-6] disulphide pairing resulting in a disulphide-rich hydrophobic core that is largely inaccessible to bulk solvent. The close proximity of disulphide bonds [3-5] and [4-6] organises haemadin into four distinct loops. The N-terminal segment of this domain binds to the active site of thrombin, inhibiting it []. ; PDB: 1E0F_K.
Probab=13.77 E-value=56 Score=16.15 Aligned_cols=10 Identities=40% Similarity=0.743 Sum_probs=3.6
Q ss_pred EEecCCCChh
Q 041051 4 ALCRGDVSAS 13 (168)
Q Consensus 4 ~~CrgD~~~~ 13 (168)
+||.||..++
T Consensus 17 gqcsgdpkps 26 (27)
T PF09065_consen 17 GQCSGDPKPS 26 (27)
T ss_dssp S-EES----S
T ss_pred CcccCCCCCC
Confidence 5888887654
No 8
>KOG0174 consensus 20S proteasome, regulatory subunit beta type PSMB6/PSMB9/PRE3 [Posttranslational modification, protein turnover, chaperones]
Probab=13.00 E-value=3.1e+02 Score=21.24 Aligned_cols=44 Identities=18% Similarity=0.406 Sum_probs=32.7
Q ss_pred CCcceEEEEE--ecCCCCChhchHHHHHHHHhhccccCCCCcceEEE
Q 041051 108 ESKKKIYGLA--QCTRDLSYNDCKMCLDRIIGDLPSCCDGKQGGRVI 152 (168)
Q Consensus 108 ~~~~~vYgla--QC~~Dls~~~C~~CL~~a~~~~~~~c~~~~g~~v~ 152 (168)
++..-|||.. +=++.++.++|..=+..|+...... .|+.||.|.
T Consensus 149 SGStfIYGf~D~~~r~nMt~EE~~~fvk~Av~lAi~r-DGsSGGviR 194 (224)
T KOG0174|consen 149 SGSTFIYGFCDANWRPNMTLEECVRFVKNAVSLAIER-DGSSGGVIR 194 (224)
T ss_pred CCceeeeeeehhhcCCCCCHHHHHHHHHHHHHHHHhc-cCCCCCEEE
Confidence 4667788874 5679999999999999999865444 355666554
No 9
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=12.64 E-value=39 Score=18.59 Aligned_cols=22 Identities=18% Similarity=0.268 Sum_probs=13.1
Q ss_pred hhCCCCceEEEEccccEEEEec
Q 041051 28 KSCPYSKSAKIFYDNCMFKYSN 49 (168)
Q Consensus 28 ~~Cp~~~~a~i~~d~C~lrys~ 49 (168)
.+||.=+.+..|..+|..++..
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~d~ 24 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKTDV 24 (36)
T ss_dssp -C-TTTSSSCS-TTT---TCCC
T ss_pred ccCcccCCCcchhhhhhhhhcc
Confidence 4799889999999999776553
No 10
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=12.26 E-value=2e+02 Score=15.92 Aligned_cols=18 Identities=28% Similarity=0.610 Sum_probs=14.6
Q ss_pred ChhchHHHHHHHHHHHHh
Q 041051 11 SASDCKRCVADAVSTIRK 28 (168)
Q Consensus 11 ~~~~C~~Cv~~A~~~~~~ 28 (168)
++--|..||..+...|.+
T Consensus 23 ~~~IC~~Cv~~~~~il~~ 40 (41)
T PF06689_consen 23 GAYICDECVEQAYEILKE 40 (41)
T ss_dssp SEEEEHHHHHHHHHHHHT
T ss_pred CcEECHHHHHHHHHHHhc
Confidence 467899999999887753
Done!