Query 015654
Match_columns 403
No_of_seqs 90 out of 92
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 08:19:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015654.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015654hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10453 NUFIP1: Nuclear fragi 99.1 7.9E-11 1.7E-15 90.8 4.4 31 133-163 16-46 (56)
2 PF00642 zf-CCCH: Zinc finger 60.9 3 6.5E-05 27.6 0.2 24 221-246 2-26 (27)
3 smart00356 ZnF_C3H1 zinc finge 42.3 21 0.00045 22.4 1.9 23 222-246 4-26 (27)
4 KOG2185 Predicted RNA-processi 30.7 21 0.00046 38.2 0.8 28 221-250 139-166 (486)
5 KOG4031 Vesicle coat protein c 25.1 2.4E+02 0.0051 28.0 6.6 21 130-150 98-118 (216)
6 PF12728 HTH_17: Helix-turn-he 23.2 42 0.00091 24.0 1.0 16 133-148 36-51 (51)
7 KOG1677 CCCH-type Zn-finger pr 22.2 54 0.0012 31.9 1.8 29 218-248 173-202 (332)
8 COG3311 AlpA Predicted transcr 20.6 82 0.0018 25.9 2.2 18 133-150 50-67 (70)
9 KOG1492 C3H1-type Zn-finger pr 20.1 44 0.00096 33.6 0.8 26 221-249 205-232 (377)
10 PF10471 APC_CDC26: Anaphase-p 17.3 29 0.00063 28.0 -1.0 23 127-149 3-25 (79)
No 1
>PF10453 NUFIP1: Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1); InterPro: IPR019496 Nuclear fragile X mental retardation-interacting protein 1 (Nufip1) has been implicated in the assembly of the large subunit of the ribosome [] and in telomere maintenance []. It is known to bind RNA [] and is phosphorylated upon DNA damage []. This entry represents a conserved domain found within Nufip1. Some proteins containing this region also contain a CCCH zinc finger.
Probab=99.10 E-value=7.9e-11 Score=90.84 Aligned_cols=31 Identities=61% Similarity=0.901 Sum_probs=28.3
Q ss_pred cccCHHHHHHHHHHHHhcCCChHHHHHHHHh
Q 015654 133 LTYTEQEVKQWCEERRKNYPTKANINKKLTE 163 (403)
Q Consensus 133 l~~t~~eI~~WreeRkKn~PT~anVe~K~~e 163 (403)
.++||+||++||+||||||||++||++|+++
T Consensus 16 ~L~t~eeI~~W~eERrk~~PT~~~i~~k~~~ 46 (56)
T PF10453_consen 16 KLQTPEEIAKWIEERRKNYPTKANIEKKKAE 46 (56)
T ss_pred ecCCHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 4479999999999999999999999988875
No 2
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 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 C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=60.89 E-value=3 Score=27.61 Aligned_cols=24 Identities=21% Similarity=0.141 Sum_probs=15.9
Q ss_pred CCCCcceecc-CCCccccCCCCccchh
Q 015654 221 LNKRGRFQNN-YDKRGRYKRKDQFSKE 246 (403)
Q Consensus 221 ~sk~CKF~nr-g~~RGRcgrKcRF~Kr 246 (403)
.+..|+||.+ |.|+ +|..|+|+|.
T Consensus 2 k~~~C~~f~~~g~C~--~G~~C~f~H~ 26 (27)
T PF00642_consen 2 KTKLCRFFMRTGTCP--FGDKCRFAHG 26 (27)
T ss_dssp TSSB-HHHHHTS--T--TGGGSSSBSS
T ss_pred ccccChhhccCCccC--CCCCcCccCC
Confidence 3678998887 6654 7788988875
No 3
>smart00356 ZnF_C3H1 zinc finger.
Probab=42.27 E-value=21 Score=22.36 Aligned_cols=23 Identities=13% Similarity=0.159 Sum_probs=15.7
Q ss_pred CCCcceeccCCCccccCCCCccchh
Q 015654 222 NKRGRFQNNYDKRGRYKRKDQFSKE 246 (403)
Q Consensus 222 sk~CKF~nrg~~RGRcgrKcRF~Kr 246 (403)
+..|++|.+|.|. .|..|+|.|.
T Consensus 4 ~~~C~~~~~g~C~--~g~~C~~~H~ 26 (27)
T smart00356 4 TELCKFFKRGYCP--YGDRCKFAHP 26 (27)
T ss_pred CCcCcCccCCCCC--CCCCcCCCCc
Confidence 4579999777754 5666777654
No 4
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=30.69 E-value=21 Score=38.15 Aligned_cols=28 Identities=18% Similarity=0.146 Sum_probs=23.6
Q ss_pred CCCCcceeccCCCccccCCCCccchhhhhc
Q 015654 221 LNKRGRFQNNYDKRGRYKRKDQFSKEQKLA 250 (403)
Q Consensus 221 ~sk~CKF~nrg~~RGRcgrKcRF~Kr~~~~ 250 (403)
.-++|+||.-|-|| ++-.|||+|-.-++
T Consensus 139 sMkpC~ffLeg~CR--F~enCRfSHG~~V~ 166 (486)
T KOG2185|consen 139 SMKPCKFFLEGRCR--FGENCRFSHGLDVP 166 (486)
T ss_pred hhccchHhhccccc--cCcccccccCcccc
Confidence 45799999999886 99999999876665
No 5
>KOG4031 consensus Vesicle coat protein clathrin, light chain [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.08 E-value=2.4e+02 Score=27.96 Aligned_cols=21 Identities=24% Similarity=0.477 Sum_probs=17.4
Q ss_pred ccccccCHHHHHHHHHHHHhc
Q 015654 130 SLALTYTEQEVKQWCEERRKN 150 (403)
Q Consensus 130 ~~~l~~t~~eI~~WreeRkKn 150 (403)
++++...|+=|++|++++++.
T Consensus 98 ~~~~~~epE~IRkWkeeQ~~r 118 (216)
T KOG4031|consen 98 GPRLRDEPEKIRKWKEEQMKR 118 (216)
T ss_pred CCCcccChHHHHHHHHHHHHH
Confidence 344778899999999999874
No 6
>PF12728 HTH_17: Helix-turn-helix domain
Probab=23.20 E-value=42 Score=24.03 Aligned_cols=16 Identities=25% Similarity=0.677 Sum_probs=14.4
Q ss_pred cccCHHHHHHHHHHHH
Q 015654 133 LTYTEQEVKQWCEERR 148 (403)
Q Consensus 133 l~~t~~eI~~WreeRk 148 (403)
+.++.+||.+|+++|+
T Consensus 36 ~~~~~~~l~~~~~~~~ 51 (51)
T PF12728_consen 36 WRIPKSDLDRWLERRR 51 (51)
T ss_pred EEEeHHHHHHHHHhCc
Confidence 7899999999999875
No 7
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=22.17 E-value=54 Score=31.94 Aligned_cols=29 Identities=10% Similarity=-0.075 Sum_probs=22.9
Q ss_pred CCCCCCCcceecc-CCCccccCCCCccchhhh
Q 015654 218 TMPLNKRGRFQNN-YDKRGRYKRKDQFSKEQK 248 (403)
Q Consensus 218 kk~~sk~CKF~nr-g~~RGRcgrKcRF~Kr~~ 248 (403)
.+-.++-|.+|.+ |.|. ||..|+|.|-..
T Consensus 173 ~~~kt~lC~~f~~tG~C~--yG~rC~F~H~~~ 202 (332)
T KOG1677|consen 173 PKYKTKLCPKFQKTGLCK--YGSRCRFIHGEP 202 (332)
T ss_pred CCCCCcCCCccccCCCCC--CCCcCeecCCCc
Confidence 3558899999887 7775 899999987655
No 8
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=20.58 E-value=82 Score=25.93 Aligned_cols=18 Identities=22% Similarity=0.728 Sum_probs=15.1
Q ss_pred cccCHHHHHHHHHHHHhc
Q 015654 133 LTYTEQEVKQWCEERRKN 150 (403)
Q Consensus 133 l~~t~~eI~~WreeRkKn 150 (403)
+.-...||.+|++.|+.+
T Consensus 50 v~W~~SEI~~Wi~~~~~~ 67 (70)
T COG3311 50 VAWPESEIDEWIASRKAA 67 (70)
T ss_pred ccccHHHHHHHHHHHHhc
Confidence 566789999999999764
No 9
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=20.14 E-value=44 Score=33.63 Aligned_cols=26 Identities=15% Similarity=0.082 Sum_probs=19.5
Q ss_pred CCCCcceeccCCCccccCCC--Cccchhhhh
Q 015654 221 LNKRGRFQNNYDKRGRYKRK--DQFSKEQKL 249 (403)
Q Consensus 221 ~sk~CKF~nrg~~RGRcgrK--cRF~Kr~~~ 249 (403)
..--||||+.+| -||++ |||+|.|..
T Consensus 205 savycryynang---icgkgaacrfvheptr 232 (377)
T KOG1492|consen 205 SAVYCRYYNANG---ICGKGAACRFVHEPTR 232 (377)
T ss_pred ceeEEEEecCCC---cccCCceeeeeccccc
Confidence 344699998776 68888 999887654
No 10
>PF10471 APC_CDC26: Anaphase-promoting complex APC subunit 1; InterPro: IPR018860 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents subunit CDC26, whose exact function is not known [].; GO: 0030071 regulation of mitotic metaphase/anaphase transition, 0031145 anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process, 0005680 anaphase-promoting complex; PDB: 2XPI_E 3HYM_A.
Probab=17.34 E-value=29 Score=28.00 Aligned_cols=23 Identities=17% Similarity=0.498 Sum_probs=11.2
Q ss_pred cccccccccCHHHHHHHHHHHHh
Q 015654 127 KRKSLALTYTEQEVKQWCEERRK 149 (403)
Q Consensus 127 ~rk~~~l~~t~~eI~~WreeRkK 149 (403)
+|+|-.|..|++||+.|.+.|+.
T Consensus 3 RR~pT~I~Lt~eDi~eye~~~~~ 25 (79)
T PF10471_consen 3 RRKPTTIELTLEDIAEYEDRRKE 25 (79)
T ss_dssp ----------CHHHHHHCCCHHH
T ss_pred CCCCcEEEecHHHHHHHHHHHHH
Confidence 57788899999999999887764
Done!