Query 030599
Match_columns 174
No_of_seqs 136 out of 270
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 16:10:57 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030599.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030599hhsearch_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 4.3E-31 9.2E-36 193.3 0.0 62 65-126 1-78 (79)
2 PF13248 zf-ribbon_3: zinc-rib 59.3 2.6 5.6E-05 24.7 -0.3 12 103-114 15-26 (26)
3 PF13240 zinc_ribbon_2: zinc-r 59.2 2.5 5.4E-05 24.5 -0.4 12 103-114 12-23 (23)
4 TIGR03831 YgiT_finger YgiT-typ 54.2 5.3 0.00011 24.5 0.5 20 93-112 21-40 (46)
5 PF14803 Nudix_N_2: Nudix N-te 53.1 2.9 6.2E-05 26.5 -0.9 11 105-115 1-11 (34)
6 PF12108 SF3a60_bindingd: Spli 37.3 7.9 0.00017 24.0 -0.7 11 75-85 16-26 (28)
7 PF11706 zf-CGNR: CGNR zinc fi 30.9 29 0.00062 23.1 1.2 38 84-121 1-44 (44)
8 PF14776 UNC-79: Cation-channe 30.3 26 0.00056 34.2 1.2 37 85-123 262-307 (525)
9 PRK00241 nudC NADH pyrophospha 25.5 19 0.00041 30.9 -0.5 33 78-111 92-124 (256)
10 PRK14559 putative protein seri 24.8 29 0.00064 34.1 0.5 38 62-114 14-51 (645)
11 PF10161 DDDD: Putative mitoch 22.1 43 0.00094 25.2 0.9 10 22-31 70-79 (79)
12 PRK12496 hypothetical protein; 21.8 22 0.00048 28.8 -0.8 21 104-124 143-163 (164)
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=99.96 E-value=4.3e-31 Score=193.28 Aligned_cols=62 Identities=68% Similarity=1.167 Sum_probs=47.8
Q ss_pred ceecCCCccccccChhhhhhccchhhhhccceEEECCccccccHHHH----------------HHHhhhhhhhccccc
Q 030599 65 SCQVDKCGADLSDAKQYHRRHKVCEVHAKAQVVLMGGIRQRFCQQCS----------------RRLAGHNERRRKNAA 126 (174)
Q Consensus 65 ~CQVeGC~aDLs~~K~YhrRhRVCE~H~KAp~V~v~G~~qRFCQQCs----------------rrLa~HN~RRRK~~~ 126 (174)
+||||||++||+.+|.||+||+|||.|++||+|+++|.++||||||| ++|++||+|||+.++
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 59999999999999999999999999999999999999999999999 789999999999875
No 2
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=59.30 E-value=2.6 Score=24.69 Aligned_cols=12 Identities=33% Similarity=1.088 Sum_probs=9.3
Q ss_pred cccccHHHHHHH
Q 030599 103 RQRFCQQCSRRL 114 (174)
Q Consensus 103 ~qRFCQQCsrrL 114 (174)
..+||..||..|
T Consensus 15 ~~~fC~~CG~~L 26 (26)
T PF13248_consen 15 DAKFCPNCGAKL 26 (26)
T ss_pred ccccChhhCCCC
Confidence 478999998654
No 3
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=59.21 E-value=2.5 Score=24.54 Aligned_cols=12 Identities=33% Similarity=0.999 Sum_probs=8.6
Q ss_pred cccccHHHHHHH
Q 030599 103 RQRFCQQCSRRL 114 (174)
Q Consensus 103 ~qRFCQQCsrrL 114 (174)
..+||.+||..|
T Consensus 12 ~~~fC~~CG~~l 23 (23)
T PF13240_consen 12 DAKFCPNCGTPL 23 (23)
T ss_pred cCcchhhhCCcC
Confidence 467899998543
No 4
>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=54.19 E-value=5.3 Score=24.53 Aligned_cols=20 Identities=15% Similarity=0.602 Sum_probs=17.5
Q ss_pred ccceEEECCccccccHHHHH
Q 030599 93 KAQVVLMGGIRQRFCQQCSR 112 (174)
Q Consensus 93 KAp~V~v~G~~qRFCQQCsr 112 (174)
+.-.+++.+.+..+|++||.
T Consensus 21 ~~~~~~i~~vp~~~C~~CGE 40 (46)
T TIGR03831 21 GGELIVIENVPALVCPQCGE 40 (46)
T ss_pred CCEEEEEeCCCccccccCCC
Confidence 56788899999999999983
No 5
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=53.10 E-value=2.9 Score=26.53 Aligned_cols=11 Identities=45% Similarity=1.141 Sum_probs=4.8
Q ss_pred cccHHHHHHHh
Q 030599 105 RFCQQCSRRLA 115 (174)
Q Consensus 105 RFCQQCsrrLa 115 (174)
+||.|||..|+
T Consensus 1 kfC~~CG~~l~ 11 (34)
T PF14803_consen 1 KFCPQCGGPLE 11 (34)
T ss_dssp -B-TTT--B-E
T ss_pred CccccccChhh
Confidence 69999995553
No 6
>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=37.34 E-value=7.9 Score=23.96 Aligned_cols=11 Identities=55% Similarity=0.966 Sum_probs=6.8
Q ss_pred cccChhhhhhc
Q 030599 75 LSDAKQYHRRH 85 (174)
Q Consensus 75 Ls~~K~YhrRh 85 (174)
|..+|+||+||
T Consensus 16 lk~Ike~Hrr~ 26 (28)
T PF12108_consen 16 LKEIKEYHRRY 26 (28)
T ss_dssp HHHHHHHHHS-
T ss_pred HHHHHHHHHhC
Confidence 45567777776
No 7
>PF11706 zf-CGNR: CGNR zinc finger; InterPro: IPR021005 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 C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family. ; PDB: 3H0N_A.
Probab=30.86 E-value=29 Score=23.09 Aligned_cols=38 Identities=29% Similarity=0.547 Sum_probs=16.3
Q ss_pred hccchhhhhccceEEE--CCccccccH--HHH--HHHhhhhhhh
Q 030599 84 RHKVCEVHAKAQVVLM--GGIRQRFCQ--QCS--RRLAGHNERR 121 (174)
Q Consensus 84 RhRVCE~H~KAp~V~v--~G~~qRFCQ--QCs--rrLa~HN~RR 121 (174)
|-++|+.+-=.-.++. .+...|||- -|| .+.+.|-+|+
T Consensus 1 Rlr~C~~~~C~~~F~D~sr~~~RrwCsm~~Cgnr~k~~~~r~R~ 44 (44)
T PF11706_consen 1 RLRRCANPDCRWVFLDTSRNGRRRWCSMERCGNRAKVRRHRARR 44 (44)
T ss_dssp GEEE--STT---EEE--SSS-----SS-HHHHHHHHHHTTTT--
T ss_pred CccccCCCCCceEEEeCCCCCCceecCcccccCHHHHHHHHhcC
Confidence 4567755544444442 478899998 899 5667776553
No 8
>PF14776 UNC-79: Cation-channel complex subunit UNC-79
Probab=30.28 E-value=26 Score=34.18 Aligned_cols=37 Identities=41% Similarity=0.654 Sum_probs=25.3
Q ss_pred ccchhhhhccceEE---------ECCccccccHHHHHHHhhhhhhhcc
Q 030599 85 HKVCEVHAKAQVVL---------MGGIRQRFCQQCSRRLAGHNERRRK 123 (174)
Q Consensus 85 hRVCE~H~KAp~V~---------v~G~~qRFCQQCsrrLa~HN~RRRK 123 (174)
+|-|.-+.|..+|+ -++++.|+||||- -.+||.+|-.
T Consensus 262 nK~C~S~~k~AvvtCFS~eCt~~~gn~PiRlC~~Ch--~~~H~n~~~~ 307 (525)
T PF14776_consen 262 NKNCRSSDKSAVVTCFSTECTSYNGNRPIRLCQQCH--SNRHNNRRGS 307 (525)
T ss_pred CCCCcCCCCCeEEEEechhhccccCCCcchhHHHHh--hhhccccccc
Confidence 44555566666554 3789999999998 3457777644
No 9
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.48 E-value=19 Score=30.87 Aligned_cols=33 Identities=15% Similarity=0.377 Sum_probs=26.5
Q ss_pred ChhhhhhccchhhhhccceEEECCccccccHHHH
Q 030599 78 AKQYHRRHKVCEVHAKAQVVLMGGIRQRFCQQCS 111 (174)
Q Consensus 78 ~K~YhrRhRVCE~H~KAp~V~v~G~~qRFCQQCs 111 (174)
+-.+|++|+-|..+-....+ ..+...+.|..|+
T Consensus 92 l~~w~~~~~fC~~CG~~~~~-~~~~~~~~C~~c~ 124 (256)
T PRK00241 92 LAEFYRSHRFCGYCGHPMHP-SKTEWAMLCPHCR 124 (256)
T ss_pred HHHHhhcCccccccCCCCee-cCCceeEECCCCC
Confidence 45889999999998875544 4566778999999
No 10
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=24.78 E-value=29 Score=34.06 Aligned_cols=38 Identities=32% Similarity=0.692 Sum_probs=26.0
Q ss_pred CCcceecCCCccccccChhhhhhccchhhhhccceEEECCccccccHHHHHHH
Q 030599 62 GLRSCQVDKCGADLSDAKQYHRRHKVCEVHAKAQVVLMGGIRQRFCQQCSRRL 114 (174)
Q Consensus 62 g~~~CQVeGC~aDLs~~K~YhrRhRVCE~H~KAp~V~v~G~~qRFCQQCsrrL 114 (174)
+...|+ .|++.|. +++|..+-.. .-...+||.+||..|
T Consensus 14 ~akFC~--~CG~~l~--------~~~Cp~CG~~-----~~~~~~fC~~CG~~~ 51 (645)
T PRK14559 14 NNRFCQ--KCGTSLT--------HKPCPQCGTE-----VPVDEAHCPNCGAET 51 (645)
T ss_pred CCcccc--ccCCCCC--------CCcCCCCCCC-----CCcccccccccCCcc
Confidence 355687 6999885 2568777655 224578999999443
No 11
>PF10161 DDDD: Putative mitochondrial precursor protein; InterPro: IPR018782 This entry represents a family of small conserved proteins found from nematodes to humans. The C-terminal region is rich in asparagine. These proteins have been putatively designated as mitochondrial precursor proteins but this has not been confirmed.
Probab=22.13 E-value=43 Score=25.23 Aligned_cols=10 Identities=80% Similarity=1.268 Sum_probs=5.8
Q ss_pred ccccCCCCCC
Q 030599 22 FVDSDDDDDD 31 (174)
Q Consensus 22 ~~~~~~~~~~ 31 (174)
||-+|||||+
T Consensus 70 FvP~DDDDDd 79 (79)
T PF10161_consen 70 FVPEDDDDDD 79 (79)
T ss_pred cCCCcCCCCC
Confidence 5555666663
No 12
>PRK12496 hypothetical protein; Provisional
Probab=21.78 E-value=22 Score=28.75 Aligned_cols=21 Identities=19% Similarity=0.485 Sum_probs=16.9
Q ss_pred ccccHHHHHHHhhhhhhhccc
Q 030599 104 QRFCQQCSRRLAGHNERRRKN 124 (174)
Q Consensus 104 qRFCQQCsrrLa~HN~RRRK~ 124 (174)
.-||.-||..|.+.+.++|+.
T Consensus 143 ~~~C~~CG~~~~r~~~~~~~~ 163 (164)
T PRK12496 143 DDVCEICGSPVKRKMVKRRLK 163 (164)
T ss_pred CCcCCCCCChhhhcchhhhcc
Confidence 358999998898888887764
Done!