Query 031295
Match_columns 162
No_of_seqs 121 out of 322
Neff 3.2
Searched_HMMs 46136
Date Fri Mar 29 12:05:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031295.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031295hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00642 zf-CCCH: Zinc finger 98.7 2.5E-09 5.5E-14 63.0 0.8 26 100-125 2-27 (27)
2 KOG1677 CCCH-type Zn-finger pr 98.3 4.2E-07 9E-12 76.7 2.8 36 93-128 169-204 (332)
3 KOG1677 CCCH-type Zn-finger pr 98.3 5.8E-07 1.2E-11 75.8 3.0 63 93-159 124-187 (332)
4 smart00356 ZnF_C3H1 zinc finge 98.1 2.6E-06 5.6E-11 48.2 2.3 23 101-124 4-26 (27)
5 KOG2185 Predicted RNA-processi 97.1 0.00023 4.9E-09 66.0 1.4 40 89-129 128-167 (486)
6 PF14608 zf-CCCH_2: Zinc finge 96.6 0.0013 2.8E-08 36.4 1.5 19 103-124 1-19 (19)
7 COG5152 Uncharacterized conser 96.0 0.0022 4.8E-08 55.3 0.6 26 101-126 141-166 (259)
8 KOG2202 U2 snRNP splicing fact 95.4 0.0046 9.9E-08 54.0 0.1 39 95-133 9-47 (260)
9 KOG1039 Predicted E3 ubiquitin 94.7 0.012 2.6E-07 52.8 0.9 25 102-127 9-33 (344)
10 KOG1813 Predicted E3 ubiquitin 94.0 0.017 3.6E-07 51.8 0.3 26 101-126 186-211 (313)
11 KOG2494 C3H1-type Zn-finger pr 92.6 0.043 9.3E-07 49.5 0.7 26 101-127 37-63 (331)
12 KOG2333 Uncharacterized conser 90.4 0.11 2.3E-06 49.9 0.8 36 101-136 76-113 (614)
13 KOG1763 Uncharacterized conser 87.2 0.2 4.2E-06 45.4 0.2 32 97-129 88-119 (343)
14 KOG2202 U2 snRNP splicing fact 85.4 0.32 7E-06 42.7 0.6 28 98-126 149-176 (260)
15 KOG1040 Polyadenylation factor 81.4 0.6 1.3E-05 41.8 0.7 28 98-126 74-101 (325)
16 KOG1492 C3H1-type Zn-finger pr 73.0 1.6 3.4E-05 39.1 0.9 31 98-128 203-233 (377)
17 COG5063 CTH1 CCCH-type Zn-fing 72.5 1.9 4.1E-05 39.3 1.3 27 102-128 275-301 (351)
18 KOG1492 C3H1-type Zn-finger pr 69.4 2.3 5.1E-05 38.0 1.2 28 99-126 286-313 (377)
19 PF10283 zf-CCHH: Zinc-finger 69.2 1.5 3.2E-05 26.5 -0.1 10 112-121 2-11 (26)
20 KOG1595 CCCH-type Zn-finger pr 61.0 6.2 0.00014 37.9 2.3 24 102-126 237-260 (528)
21 KOG0153 Predicted RNA-binding 60.8 6 0.00013 36.6 2.1 31 95-126 155-185 (377)
22 KOG2333 Uncharacterized conser 57.8 4.6 0.0001 39.2 0.9 21 102-122 115-135 (614)
23 PF10650 zf-C3H1: Putative zin 49.4 11 0.00023 22.2 1.2 22 102-124 1-22 (23)
24 COG1482 ManA Phosphomannose is 48.4 20 0.00044 32.2 3.4 79 6-108 29-118 (312)
25 KOG4791 Uncharacterized conser 46.8 7.5 0.00016 37.8 0.4 24 102-126 4-27 (667)
26 COG5084 YTH1 Cleavage and poly 42.7 13 0.00029 33.0 1.3 54 73-126 103-159 (285)
27 KOG3702 Nuclear polyadenylated 41.0 32 0.00069 34.2 3.6 35 110-157 625-664 (681)
28 COG5252 Uncharacterized conser 40.6 8 0.00017 34.6 -0.4 28 98-126 82-109 (299)
29 COG5084 YTH1 Cleavage and poly 38.9 34 0.00075 30.4 3.3 29 100-128 162-192 (285)
30 KOG1039 Predicted E3 ubiquitin 36.0 20 0.00044 32.5 1.4 35 95-129 243-278 (344)
31 KOG1040 Polyadenylation factor 28.8 31 0.00068 31.1 1.4 28 99-126 103-130 (325)
32 PRK15131 mannose-6-phosphate i 24.1 59 0.0013 29.5 2.3 99 10-116 33-149 (389)
33 COG5063 CTH1 CCCH-type Zn-fing 23.3 43 0.00094 30.8 1.3 28 101-128 314-341 (351)
34 KOG3777 Uncharacterized conser 22.7 47 0.001 31.4 1.4 24 101-127 171-194 (443)
35 KOG2135 Proteins containing th 20.7 34 0.00074 33.0 0.1 34 96-129 207-240 (526)
No 1
>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=98.74 E-value=2.5e-09 Score=62.99 Aligned_cols=26 Identities=38% Similarity=1.000 Sum_probs=21.1
Q ss_pred CCCCCccchhccCCCCCCCCccCCCC
Q 031295 100 GVHDCSYYLRTGRCRFGMSCKFNHPV 125 (162)
Q Consensus 100 g~~~C~fYmKTG~CRFG~~CKFnHP~ 125 (162)
..++|.+|+++|.|+||++|+|.|+.
T Consensus 2 k~~~C~~f~~~g~C~~G~~C~f~H~~ 27 (27)
T PF00642_consen 2 KTKLCRFFMRTGTCPFGDKCRFAHGE 27 (27)
T ss_dssp TSSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred ccccChhhccCCccCCCCCcCccCCC
Confidence 57899999999999999999999973
No 2
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.29 E-value=4.2e-07 Score=76.66 Aligned_cols=36 Identities=28% Similarity=0.706 Sum_probs=32.8
Q ss_pred cCCCCCCCCCCCccchhccCCCCCCCCccCCCCCcc
Q 031295 93 FCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQ 128 (162)
Q Consensus 93 ~~~P~RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~ 128 (162)
..++.+.+.++|.+|++||.|+||.+|+|+|+.+..
T Consensus 169 ~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~~ 204 (332)
T KOG1677|consen 169 VGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPED 204 (332)
T ss_pred hcCCCCCCCcCCCccccCCCCCCCCcCeecCCCccc
Confidence 467889999999999999999999999999998843
No 3
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.26 E-value=5.8e-07 Score=75.82 Aligned_cols=63 Identities=21% Similarity=0.364 Sum_probs=53.5
Q ss_pred cCCCCCCCCCCCccchhccCCCC-CCCCccCCCCCcccccccccccCcceeeccCCCCCccchhcccC
Q 031295 93 FCYPQRPGVHDCSYYLRTGRCRF-GMSCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSANSNRMSTG 159 (162)
Q Consensus 93 ~~~P~RPg~~~C~fYmKTG~CRF-G~~CKFnHP~~~~s~~~~~~vn~~~V~lp~rP~n~~~~~~~~~g 159 (162)
...|++-+.+.|.+|+++|.|+| |.+|||+|+........ ....++.+.++....|.+|.++|
T Consensus 124 ~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~----~~~~~~~~~~~kt~lC~~f~~tG 187 (332)
T KOG1677|consen 124 ERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPS----SENQVGNPPKYKTKLCPKFQKTG 187 (332)
T ss_pred ccCcccccCCcceeeecCccccccCchhhhcCCcccccccc----cchhhcCCCCCCCcCCCccccCC
Confidence 56788899999999999999999 99999999998643111 22468899999999999999987
No 4
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.08 E-value=2.6e-06 Score=48.18 Aligned_cols=23 Identities=39% Similarity=1.152 Sum_probs=21.2
Q ss_pred CCCCccchhccCCCCCCCCccCCC
Q 031295 101 VHDCSYYLRTGRCRFGMSCKFNHP 124 (162)
Q Consensus 101 ~~~C~fYmKTG~CRFG~~CKFnHP 124 (162)
..+|++| ++|.|++|++|+|.|.
T Consensus 4 ~~~C~~~-~~g~C~~g~~C~~~H~ 26 (27)
T smart00356 4 TELCKFF-KRGYCPYGDRCKFAHP 26 (27)
T ss_pred CCcCcCc-cCCCCCCCCCcCCCCc
Confidence 4589999 8899999999999996
No 5
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=97.06 E-value=0.00023 Score=66.01 Aligned_cols=40 Identities=35% Similarity=0.901 Sum_probs=32.6
Q ss_pred cccCcCCCCCCCCCCCccchhccCCCCCCCCccCCCCCccc
Q 031295 89 TRRKFCYPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI 129 (162)
Q Consensus 89 ~~~~~~~P~RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~s 129 (162)
++-..-+|.-..-.+|.|||. |.||||.+|||.|-.....
T Consensus 128 vRVlfl~PTh~sMkpC~ffLe-g~CRF~enCRfSHG~~V~l 167 (486)
T KOG2185|consen 128 VRVLFLTPTHESMKPCKFFLE-GRCRFGENCRFSHGLDVPL 167 (486)
T ss_pred eEEEeecCcchhhccchHhhc-cccccCcccccccCcccch
Confidence 344456787777899999987 9999999999999877543
No 6
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=96.57 E-value=0.0013 Score=36.35 Aligned_cols=19 Identities=37% Similarity=0.966 Sum_probs=16.5
Q ss_pred CCccchhccCCCCCCCCccCCC
Q 031295 103 DCSYYLRTGRCRFGMSCKFNHP 124 (162)
Q Consensus 103 ~C~fYmKTG~CRFG~~CKFnHP 124 (162)
.|+|+.. |++|++|.|.||
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 4898843 999999999998
No 7
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.99 E-value=0.0022 Score=55.34 Aligned_cols=26 Identities=42% Similarity=0.791 Sum_probs=24.3
Q ss_pred CCCCccchhccCCCCCCCCccCCCCC
Q 031295 101 VHDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 101 ~~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
..+|.=|-.||.|.||++|||-|.++
T Consensus 141 pdVCKdyk~TGYCGYGDsCKflH~R~ 166 (259)
T COG5152 141 PDVCKDYKETGYCGYGDSCKFLHDRS 166 (259)
T ss_pred cccccchhhcccccCCchhhhhhhhh
Confidence 36899999999999999999999987
No 8
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=95.36 E-value=0.0046 Score=54.04 Aligned_cols=39 Identities=28% Similarity=0.627 Sum_probs=33.1
Q ss_pred CCCCCCCCCCccchhccCCCCCCCCccCCCCCccccccc
Q 031295 95 YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQIQSLN 133 (162)
Q Consensus 95 ~P~RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~s~~~~ 133 (162)
|-...++..|.||.|+|.||+|+.|+-.|-++..++..+
T Consensus 9 fgtekdKv~c~fy~k~gacR~gdrcsR~h~kpt~s~t~l 47 (260)
T KOG2202|consen 9 FGTEKDKVNCSFYFKIGACRHGDRCSRLHEKPTFSQTVL 47 (260)
T ss_pred hcccccccccchHHhhcccccccHHHHhhcccccchHHH
Confidence 444577899999999999999999999999998775533
No 9
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.69 E-value=0.012 Score=52.78 Aligned_cols=25 Identities=40% Similarity=1.150 Sum_probs=23.1
Q ss_pred CCCccchhccCCCCCCCCccCCCCCc
Q 031295 102 HDCSYYLRTGRCRFGMSCKFNHPVPR 127 (162)
Q Consensus 102 ~~C~fYmKTG~CRFG~~CKFnHP~~~ 127 (162)
.+|.||.+ |.|+||+.|+|.|-.+.
T Consensus 9 tic~~~~~-g~c~~g~~cr~~h~~~~ 33 (344)
T KOG1039|consen 9 TICKYYQK-GNCKFGDLCRLSHSLPD 33 (344)
T ss_pred hhhhhccc-ccccccceeeeeccCch
Confidence 89999966 99999999999999884
No 10
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.03 E-value=0.017 Score=51.75 Aligned_cols=26 Identities=42% Similarity=0.779 Sum_probs=24.0
Q ss_pred CCCCccchhccCCCCCCCCccCCCCC
Q 031295 101 VHDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 101 ~~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
.-+|.=|--||.|.||++|||.|.+.
T Consensus 186 pDicKdykeTgycg~gdSckFlh~r~ 211 (313)
T KOG1813|consen 186 PDICKDYKETGYCGYGDSCKFLHDRS 211 (313)
T ss_pred chhhhhhHhhCcccccchhhhhhhhh
Confidence 35899999999999999999999986
No 11
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=92.64 E-value=0.043 Score=49.49 Aligned_cols=26 Identities=38% Similarity=0.850 Sum_probs=23.4
Q ss_pred CCCCccchhccCCCCCCC-CccCCCCCc
Q 031295 101 VHDCSYYLRTGRCRFGMS-CKFNHPVPR 127 (162)
Q Consensus 101 ~~~C~fYmKTG~CRFG~~-CKFnHP~~~ 127 (162)
-.+|+-|+| |.|.=|++ |||.||...
T Consensus 37 ~eVCReF~r-n~C~R~d~~CkfaHP~~~ 63 (331)
T KOG2494|consen 37 LEVCREFLR-NTCSRGDRECKFAHPPKN 63 (331)
T ss_pred HHHHHHHHh-ccccCCCccccccCCCCC
Confidence 379999977 99999999 999999874
No 12
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=90.43 E-value=0.11 Score=49.87 Aligned_cols=36 Identities=22% Similarity=0.594 Sum_probs=27.4
Q ss_pred CCCCccchhc--cCCCCCCCCccCCCCCcccccccccc
Q 031295 101 VHDCSYYLRT--GRCRFGMSCKFNHPVPRQIQSLNQSI 136 (162)
Q Consensus 101 ~~~C~fYmKT--G~CRFG~~CKFnHP~~~~s~~~~~~v 136 (162)
-..|.--.+. -.|.||++|||.|..+.-...-...|
T Consensus 76 n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~Di 113 (614)
T KOG2333|consen 76 NRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAPDI 113 (614)
T ss_pred hccChHhhcCCCccCcccccccccccHHHHHhccCccc
Confidence 4679999887 68999999999999986443333334
No 13
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=87.23 E-value=0.2 Score=45.40 Aligned_cols=32 Identities=28% Similarity=0.726 Sum_probs=27.0
Q ss_pred CCCCCCCCccchhccCCCCCCCCccCCCCCccc
Q 031295 97 QRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI 129 (162)
Q Consensus 97 ~RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~s 129 (162)
+-|-.-+|.|| +.|.|.=|+.|||.|.-....
T Consensus 88 vDPKSvvCafF-k~g~C~KG~kCKFsHdl~~~~ 119 (343)
T KOG1763|consen 88 VDPKSVVCAFF-KQGTCTKGDKCKFSHDLAVER 119 (343)
T ss_pred CCchHHHHHHH-hccCCCCCCcccccchHHHhh
Confidence 34667899999 889999999999999876543
No 14
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=85.38 E-value=0.32 Score=42.73 Aligned_cols=28 Identities=29% Similarity=0.471 Sum_probs=25.7
Q ss_pred CCCCCCCccchhccCCCCCCCCccCCCCC
Q 031295 98 RPGVHDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 98 RPg~~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
++.+..|.+|.++ .|..|..|-|.|...
T Consensus 149 ~~rea~C~~~e~~-~C~rG~~CnFmH~k~ 176 (260)
T KOG2202|consen 149 DFREAICGQFERT-ECSRGGACNFMHVKR 176 (260)
T ss_pred chhhhhhcccccc-cCCCCCcCcchhhhh
Confidence 7788999999886 999999999999984
No 15
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=81.39 E-value=0.6 Score=41.81 Aligned_cols=28 Identities=36% Similarity=0.721 Sum_probs=24.8
Q ss_pred CCCCCCCccchhccCCCCCCCCccCCCCC
Q 031295 98 RPGVHDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 98 RPg~~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
--++.+|.||++ |.|+-|+.|-|.|-.+
T Consensus 74 ~~~~~vcK~~l~-glC~kgD~C~Flhe~~ 101 (325)
T KOG1040|consen 74 SRGKVVCKHWLR-GLCKKGDQCEFLHEYD 101 (325)
T ss_pred cCCceeehhhhh-hhhhccCcCcchhhhh
Confidence 457899999977 9999999999999774
No 16
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=72.98 E-value=1.6 Score=39.05 Aligned_cols=31 Identities=35% Similarity=0.799 Sum_probs=27.3
Q ss_pred CCCCCCCccchhccCCCCCCCCccCCCCCcc
Q 031295 98 RPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQ 128 (162)
Q Consensus 98 RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~ 128 (162)
.|..--|+||--.|.|.-|..|||.|..-+.
T Consensus 203 spsavycryynangicgkgaacrfvheptrk 233 (377)
T KOG1492|consen 203 SPSAVYCRYYNANGICGKGAACRFVHEPTRK 233 (377)
T ss_pred CCceeEEEEecCCCcccCCceeeeecccccc
Confidence 4677789999999999999999999987665
No 17
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=72.46 E-value=1.9 Score=39.35 Aligned_cols=27 Identities=26% Similarity=0.755 Sum_probs=22.9
Q ss_pred CCCccchhccCCCCCCCCccCCCCCcc
Q 031295 102 HDCSYYLRTGRCRFGMSCKFNHPVPRQ 128 (162)
Q Consensus 102 ~~C~fYmKTG~CRFG~~CKFnHP~~~~ 128 (162)
+.|....+-|.|+||.+|-|.|-.+..
T Consensus 275 ePcinwe~sGyc~yg~Rc~F~hgd~~~ 301 (351)
T COG5063 275 EPCINWEKSGYCPYGLRCCFKHGDDSD 301 (351)
T ss_pred CCccchhhcccCccccccccccCChhh
Confidence 557777888999999999999988754
No 18
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=69.44 E-value=2.3 Score=37.99 Aligned_cols=28 Identities=29% Similarity=0.579 Sum_probs=24.6
Q ss_pred CCCCCCccchhccCCCCCCCCccCCCCC
Q 031295 99 PGVHDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 99 Pg~~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
...++|.-|.|.|.|..|.+||..|--.
T Consensus 286 enapicfefakygfcelgtscknqhilq 313 (377)
T KOG1492|consen 286 ENAPICFEFAKYGFCELGTSCKNQHILQ 313 (377)
T ss_pred CCCceeeeehhcceeccccccccceeee
Confidence 4579999999999999999999998643
No 19
>PF10283 zf-CCHH: Zinc-finger (CX5CX6HX5H) motif; InterPro: IPR019406 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 []. This entry represents a C2H2-type Znf motif that in humans is part of the APLF (aprataxin- and PNK-like) forkead association domain-containing protein []. The Znf is highly conserved both in primary sequence and in the spacing between the putative zinc coordinating residues, and is configured CX5CX6HX5H. Many of the proteins containing this Znf are involved in DNA strand break repair and/or contain domains implicated in DNA metabolism. This Znf motif appears to be specialised for the non-covalent binding of poly ADP-ribose; Aprataxin also appears to covalently bind poly ADP-ribose, but not through its Znf motif [].; PDB: 2KQC_A 2KUO_A 2KQE_A 2KQD_A 2KQB_A.
Probab=69.24 E-value=1.5 Score=26.46 Aligned_cols=10 Identities=30% Similarity=1.019 Sum_probs=5.9
Q ss_pred CCCCCCCCcc
Q 031295 112 RCRFGMSCKF 121 (162)
Q Consensus 112 ~CRFG~~CKF 121 (162)
.|+||.+|-.
T Consensus 2 ~C~YG~~CYR 11 (26)
T PF10283_consen 2 PCKYGAKCYR 11 (26)
T ss_dssp E-TTGGG-S-
T ss_pred CCCcchhhhc
Confidence 4999999953
No 20
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=60.97 E-value=6.2 Score=37.90 Aligned_cols=24 Identities=38% Similarity=0.840 Sum_probs=20.7
Q ss_pred CCCccchhccCCCCCCCCccCCCCC
Q 031295 102 HDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 102 ~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
..|+-| |+|.|+=|++|-|.|-+-
T Consensus 237 tpCPef-rkG~C~rGD~CEyaHgvf 260 (528)
T KOG1595|consen 237 TPCPEF-RKGSCERGDSCEYAHGVF 260 (528)
T ss_pred ccCccc-ccCCCCCCCcccccccee
Confidence 568888 779999999999998753
No 21
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=60.79 E-value=6 Score=36.60 Aligned_cols=31 Identities=35% Similarity=0.963 Sum_probs=26.8
Q ss_pred CCCCCCCCCCccchhccCCCCCCCCccCCCCC
Q 031295 95 YPQRPGVHDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 95 ~P~RPg~~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
|=.|.-..+|.||.+ |.|+=|..|-|+|.++
T Consensus 155 ~ykrn~p~Icsf~v~-geckRG~ec~yrhEkp 185 (377)
T KOG0153|consen 155 YYKRNRPHICSFFVK-GECKRGAECPYRHEKP 185 (377)
T ss_pred cccCCCCccccceee-ccccccccccccccCC
Confidence 335666789999987 7999999999999998
No 22
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=57.85 E-value=4.6 Score=39.15 Aligned_cols=21 Identities=29% Similarity=0.898 Sum_probs=19.9
Q ss_pred CCCccchhccCCCCCCCCccC
Q 031295 102 HDCSYYLRTGRCRFGMSCKFN 122 (162)
Q Consensus 102 ~~C~fYmKTG~CRFG~~CKFn 122 (162)
+.|.+|-..|.|-||-+|||.
T Consensus 115 ~~Cp~f~s~G~Cp~G~~CRFl 135 (614)
T KOG2333|consen 115 PSCPVFESLGFCPYGFKCRFL 135 (614)
T ss_pred CccceeeccccCCccceeehh
Confidence 789999999999999999995
No 23
>PF10650 zf-C3H1: Putative zinc-finger domain; InterPro: IPR019607 This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Probab=49.36 E-value=11 Score=22.22 Aligned_cols=22 Identities=36% Similarity=0.785 Sum_probs=17.6
Q ss_pred CCCccchhccCCCCCCCCccCCC
Q 031295 102 HDCSYYLRTGRCRFGMSCKFNHP 124 (162)
Q Consensus 102 ~~C~fYmKTG~CRFG~~CKFnHP 124 (162)
+.|.|-++-|.|. -.+|.|.|=
T Consensus 1 ~lC~yEl~Gg~Cn-d~~C~~QHf 22 (23)
T PF10650_consen 1 PLCPYELTGGVCN-DPDCEFQHF 22 (23)
T ss_pred CCCccccCCCeeC-CCCCCcccc
Confidence 4699998877996 468999984
No 24
>COG1482 ManA Phosphomannose isomerase [Carbohydrate transport and metabolism]
Probab=48.36 E-value=20 Score=32.16 Aligned_cols=79 Identities=28% Similarity=0.335 Sum_probs=48.7
Q ss_pred cccccCcceEEeecCCCcCccccccccccccCC-----CCCCCCCC-----ccccccCCCCCC-CCCcCCchHHHHhhhc
Q 031295 6 SESYIPSKWIFLMHPFDSNVNEENRYYTQLSLP-----PNSDLDPP-----PLDMQNLDIEDP-EDQVDSDTEEEVENVD 74 (162)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p-----~~~~l~pp-----~~~~~n~~~e~~-s~qv~s~~e~e~~~~a 74 (162)
+...+-.-|.+ +||-.+..-...+|+. .+|. ++.+|+.. +|+++=||.++. |-|||.|.+...+.
T Consensus 29 ~~~~~gE~W~~-AHp~~~S~v~~~~~~~-~~L~el~~~~~ellG~~~~~~FplL~KiLdA~~~LSiQVHP~d~~A~~~-- 104 (312)
T COG1482 29 PSEPIGELWAG-AHPNGPSTVANGPGQG-KSLSELIADPRELLGNKSFDRFPLLFKILDANDPLSIQVHPSDEYAEEG-- 104 (312)
T ss_pred CCCceEeEEEE-ecCCCCeeEEecCcCC-cCHHHHHhCcHhhcCCcchhhccceeeeeccCCcceEEECCCHHHHhhc--
Confidence 34445556999 9998886544444433 2222 12344432 388888887775 66999997655443
Q ss_pred ccccccccccCccccccCcCCCCCCCCCCCccch
Q 031295 75 KNNKQVDEVTGNQMTRRKFCYPQRPGVHDCSYYL 108 (162)
Q Consensus 75 ~l~khv~l~s~~~m~~~~~~~P~RPg~~~C~fYm 108 (162)
+. ...|+..||+|.
T Consensus 105 ----~~----------------g~~gkte~w~y~ 118 (312)
T COG1482 105 ----EE----------------GILGKTECWYYK 118 (312)
T ss_pred ----cc----------------CccCCCcceeec
Confidence 11 127789999993
No 25
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.82 E-value=7.5 Score=37.81 Aligned_cols=24 Identities=33% Similarity=0.780 Sum_probs=20.6
Q ss_pred CCCccchhccCCCCCCCCccCCCCC
Q 031295 102 HDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 102 ~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
++|.|| ....||||+.|-|-|--+
T Consensus 4 ~dcyff-~ys~cKk~d~c~~rh~E~ 27 (667)
T KOG4791|consen 4 EDCYFF-FYSTCKKGDSCPFRHCEA 27 (667)
T ss_pred ccchhh-hhhhhhccCcCcchhhHH
Confidence 689999 559999999999999754
No 26
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=42.70 E-value=13 Score=33.00 Aligned_cols=54 Identities=19% Similarity=0.173 Sum_probs=34.6
Q ss_pred hcccccccccccCcccccc--CcCCCC-CCCCCCCccchhccCCCCCCCCccCCCCC
Q 031295 73 VDKNNKQVDEVTGNQMTRR--KFCYPQ-RPGVHDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 73 ~a~l~khv~l~s~~~m~~~--~~~~P~-RPg~~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
-.+..++..++....-... .+++.. ++-...|++|-..|.|.+|..|.+.|--+
T Consensus 103 s~V~c~~~~~g~c~s~~~c~~lh~~d~~~s~~~~c~~Fs~~G~cs~g~~c~~~h~dp 159 (285)
T COG5084 103 SSVVCKFFLRGLCKSGFSCEFLHEYDLRSSQGPPCRSFSLKGSCSSGPSCGYSHIDP 159 (285)
T ss_pred CCcccchhccccCcCCCccccccCCCcccccCCCcccccccceeccCCCCCccccCc
Confidence 3455666666533221111 123443 33467899998889999999999999753
No 27
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=40.99 E-value=32 Score=34.22 Aligned_cols=35 Identities=31% Similarity=0.605 Sum_probs=22.8
Q ss_pred ccCCCCCC-----CCccCCCCCcccccccccccCcceeeccCCCCCccchhcc
Q 031295 110 TGRCRFGM-----SCKFNHPVPRQIQSLNQSINSNTVSIEMNPNNSANSNRMS 157 (162)
Q Consensus 110 TG~CRFG~-----~CKFnHP~~~~s~~~~~~vn~~~V~lp~rP~n~~~~~~~~ 157 (162)
++.|||+. -|+|-||....-.. ..+++.-|+||..
T Consensus 625 ~~~CrY~pnCrnm~C~F~HPk~cRf~~-------------~c~~~~sc~fYh~ 664 (681)
T KOG3702|consen 625 RGLCRYRPNCRNMQCKFYHPKTCRFNT-------------NCPNNPSCTFYHE 664 (681)
T ss_pred cccceeccCcCCccccccCCccccccc-------------cCCCCcccccccC
Confidence 36677666 57799999753211 2344777888876
No 28
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=40.63 E-value=8 Score=34.56 Aligned_cols=28 Identities=29% Similarity=0.618 Sum_probs=24.4
Q ss_pred CCCCCCCccchhccCCCCCCCCccCCCCC
Q 031295 98 RPGVHDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 98 RPg~~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
-|-..+|..| +.|.|-=|+.|+|.|...
T Consensus 82 dpK~~vcalF-~~~~c~kg~~ckF~h~~e 109 (299)
T COG5252 82 DPKTVVCALF-LNKTCAKGDACKFAHGKE 109 (299)
T ss_pred CchhHHHHHh-ccCccccCchhhhhcchH
Confidence 3666799999 779999999999999965
No 29
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=38.91 E-value=34 Score=30.44 Aligned_cols=29 Identities=38% Similarity=0.758 Sum_probs=25.2
Q ss_pred CCCCCccchh--ccCCCCCCCCccCCCCCcc
Q 031295 100 GVHDCSYYLR--TGRCRFGMSCKFNHPVPRQ 128 (162)
Q Consensus 100 g~~~C~fYmK--TG~CRFG~~CKFnHP~~~~ 128 (162)
....|.+|.+ .|.|..|..|||-|-..+.
T Consensus 162 ~~~~~~~~~~~~~~f~p~g~~c~~~H~~~~~ 192 (285)
T COG5084 162 FAGNCDQYSGATYGFCPLGASCKFSHTLKRV 192 (285)
T ss_pred ccccccccCcccccccCCCCccccccccccc
Confidence 4688999976 8999999999999987754
No 30
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.99 E-value=20 Score=32.52 Aligned_cols=35 Identities=31% Similarity=0.840 Sum_probs=27.9
Q ss_pred CCCCCCCCCCccchhc-cCCCCCCCCccCCCCCccc
Q 031295 95 YPQRPGVHDCSYYLRT-GRCRFGMSCKFNHPVPRQI 129 (162)
Q Consensus 95 ~P~RPg~~~C~fYmKT-G~CRFG~~CKFnHP~~~~s 129 (162)
|-..-++++|.||.+- |.|-||+.|-|.|-.+...
T Consensus 243 ~~~~~s~~~c~yf~~~~g~cPf~s~~~y~h~~~~~~ 278 (344)
T KOG1039|consen 243 YEAEMSAKDCKYFSQGLGSCPFGSKCFYKHLLPSGA 278 (344)
T ss_pred HHHHhhccchhhhcCCCCCCCCCCcccccccccccc
Confidence 3335678999999764 8999999999999876544
No 31
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=28.82 E-value=31 Score=31.09 Aligned_cols=28 Identities=25% Similarity=0.740 Sum_probs=23.3
Q ss_pred CCCCCCccchhccCCCCCCCCccCCCCC
Q 031295 99 PGVHDCSYYLRTGRCRFGMSCKFNHPVP 126 (162)
Q Consensus 99 Pg~~~C~fYmKTG~CRFG~~CKFnHP~~ 126 (162)
.-.+.|.||-.+|.|.=|..|-|-|-.+
T Consensus 103 ~k~rec~ff~~~g~c~~~~~c~y~h~dp 130 (325)
T KOG1040|consen 103 TKMRECKFFSLFGECTNGKDCPYLHGDP 130 (325)
T ss_pred cccccccccccccccccccCCcccCCCh
Confidence 4456899999999999999999999774
No 32
>PRK15131 mannose-6-phosphate isomerase; Provisional
Probab=24.09 E-value=59 Score=29.54 Aligned_cols=99 Identities=15% Similarity=0.152 Sum_probs=62.0
Q ss_pred cCcceEEeecCCCcCcccccc-ccc-cc----------cCCCC--CCCCCCccccccCCCCCC-CCCcCCchHHHHhhhc
Q 031295 10 IPSKWIFLMHPFDSNVNEENR-YYT-QL----------SLPPN--SDLDPPPLDMQNLDIEDP-EDQVDSDTEEEVENVD 74 (162)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~-~~~-~~----------~~p~~--~~l~pp~~~~~n~~~e~~-s~qv~s~~e~e~~~~a 74 (162)
+..-|+ -+||-.|..-. ++ ++. +| .|-+. ...+.-+|+++=||.+.. |-|||.|.+...+-.+
T Consensus 33 ~aE~W~-gaHp~~pS~v~-~~~~~~~~L~~~i~~~~~~~LG~~~~~~f~~lP~L~KiL~a~~~LSIQvHPd~~~A~~~f~ 110 (389)
T PRK15131 33 MAELWM-GAHPKSSSRVQ-DANGDIVSLRDVIESDKSALLGEAVAKRFGELPFLFKVLCAAQPLSIQVHPNKRAAEIGFA 110 (389)
T ss_pred eeEEEE-EECCCCCeEEe-CCCCCCCcHHHHHHhCHHHHcCcchhhhcCCCceEeeeeccCCCceeEeCCCHHHHHHHhh
Confidence 455687 99997766542 31 111 11 11111 111346788888888765 7799999766664333
Q ss_pred -ccccccccccCccccccCcCCCCCCCCCCCccchh--ccCCCCC
Q 031295 75 -KNNKQVDEVTGNQMTRRKFCYPQRPGVHDCSYYLR--TGRCRFG 116 (162)
Q Consensus 75 -~l~khv~l~s~~~m~~~~~~~P~RPg~~~C~fYmK--TG~CRFG 116 (162)
.....+.+.... ..|+-+.+|+.|++-+. .+.|.|.
T Consensus 111 ~e~~~gip~~~~~------r~Y~D~nhKpEm~~aLt~F~al~GfR 149 (389)
T PRK15131 111 KENAAGIPLDAAE------RNYKDPNHKPELVFALTPFLAMNAFR 149 (389)
T ss_pred hcccccCccccch------hccCCCCCCceEEEEcchhHHhcCCC
Confidence 234566665544 47999999999999876 3666665
No 33
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=23.34 E-value=43 Score=30.83 Aligned_cols=28 Identities=11% Similarity=-0.008 Sum_probs=24.7
Q ss_pred CCCCccchhccCCCCCCCCccCCCCCcc
Q 031295 101 VHDCSYYLRTGRCRFGMSCKFNHPVPRQ 128 (162)
Q Consensus 101 ~~~C~fYmKTG~CRFG~~CKFnHP~~~~ 128 (162)
...|+-+|++|.|.+|..|.|.|.....
T Consensus 314 ~~~crt~~~~g~~p~g~~~c~~~dkkn~ 341 (351)
T COG5063 314 DGPCRTRAKGGAFPSGGAVCKSFDKKNL 341 (351)
T ss_pred ccccccccccCccCCCCchhhccccchh
Confidence 4679999999999999999999987653
No 34
>KOG3777 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.68 E-value=47 Score=31.35 Aligned_cols=24 Identities=38% Similarity=0.895 Sum_probs=20.0
Q ss_pred CCCCccchhccCCCCCCCCccCCCCCc
Q 031295 101 VHDCSYYLRTGRCRFGMSCKFNHPVPR 127 (162)
Q Consensus 101 ~~~C~fYmKTG~CRFG~~CKFnHP~~~ 127 (162)
+..|.|= -.|.||..|||-||...
T Consensus 171 ~q~Cpyg---kkctyg~kck~~h~~~~ 194 (443)
T KOG3777|consen 171 KQPCPYG---KKCTYGGKCKFYHPEIA 194 (443)
T ss_pred ccCCCcc---cccCCCCceeecccccc
Confidence 5679865 57999999999999863
No 35
>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]
Probab=20.74 E-value=34 Score=33.00 Aligned_cols=34 Identities=15% Similarity=0.220 Sum_probs=29.7
Q ss_pred CCCCCCCCCccchhccCCCCCCCCccCCCCCccc
Q 031295 96 PQRPGVHDCSYYLRTGRCRFGMSCKFNHPVPRQI 129 (162)
Q Consensus 96 P~RPg~~~C~fYmKTG~CRFG~~CKFnHP~~~~s 129 (162)
-.|..+..|.+|.++|.|.=|..|+++|-.....
T Consensus 207 ks~~s~~r~k~fee~g~~~r~el~p~~hg~~~vv 240 (526)
T KOG2135|consen 207 KSRNSENRRKFFEEFGVLERGELCPTHHGCVPVV 240 (526)
T ss_pred cccccHHhhhhhHhhceeeeccccccccccceeE
Confidence 3477888999999999999999999999987544
Done!