Query 042240
Match_columns 241
No_of_seqs 164 out of 634
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 04:17:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042240.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042240hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1677 CCCH-type Zn-finger pr 99.6 9.7E-16 2.1E-20 139.3 4.4 76 101-177 123-207 (332)
2 COG5063 CTH1 CCCH-type Zn-fing 99.0 2.4E-10 5.3E-15 106.4 3.3 64 103-166 267-331 (351)
3 COG5063 CTH1 CCCH-type Zn-fing 99.0 2.9E-10 6.3E-15 105.9 3.3 73 101-174 219-301 (351)
4 PF00642 zf-CCCH: Zinc finger 98.8 6.4E-10 1.4E-14 68.9 0.1 27 108-134 1-27 (27)
5 KOG1677 CCCH-type Zn-finger pr 98.6 2.9E-08 6.2E-13 90.5 2.7 42 102-143 169-210 (332)
6 KOG1595 CCCH-type Zn-finger pr 98.4 2.6E-07 5.6E-12 91.2 6.1 64 102-172 228-292 (528)
7 smart00356 ZnF_C3H1 zinc finge 98.2 5.3E-07 1.2E-11 54.2 1.8 27 107-134 1-27 (27)
8 KOG2333 Uncharacterized conser 98.0 3.2E-06 6.9E-11 83.5 2.0 61 109-172 75-139 (614)
9 KOG1040 Polyadenylation factor 96.9 0.00038 8.1E-09 65.8 1.8 63 106-171 73-155 (325)
10 COG5252 Uncharacterized conser 96.8 0.00028 6.1E-09 64.8 -0.0 68 105-173 80-177 (299)
11 KOG1763 Uncharacterized conser 96.8 0.00029 6.3E-09 66.2 0.0 36 105-141 87-122 (343)
12 PF00642 zf-CCCH: Zinc finger 96.7 0.0005 1.1E-08 42.5 0.4 24 147-170 1-26 (27)
13 KOG2494 C3H1-type Zn-finger pr 95.8 0.0049 1.1E-07 58.4 2.1 62 103-171 29-93 (331)
14 KOG1595 CCCH-type Zn-finger pr 95.5 0.021 4.6E-07 57.1 5.3 59 101-165 192-251 (528)
15 smart00356 ZnF_C3H1 zinc finge 94.9 0.023 5E-07 33.7 2.2 23 147-170 2-26 (27)
16 PF14608 zf-CCCH_2: Zinc finge 94.8 0.015 3.3E-07 33.5 1.2 19 112-133 1-19 (19)
17 KOG2185 Predicted RNA-processi 94.2 0.018 3.8E-07 56.5 1.0 33 109-142 139-175 (486)
18 COG5152 Uncharacterized conser 93.8 0.021 4.6E-07 51.6 0.6 33 106-138 137-169 (259)
19 COG5084 YTH1 Cleavage and poly 92.6 0.35 7.5E-06 45.4 6.6 35 104-139 98-132 (285)
20 KOG1492 C3H1-type Zn-finger pr 91.6 0.28 6E-06 45.5 4.6 25 206-230 340-364 (377)
21 COG5084 YTH1 Cleavage and poly 91.4 0.53 1.2E-05 44.1 6.3 70 110-189 134-213 (285)
22 KOG1813 Predicted E3 ubiquitin 89.7 0.12 2.6E-06 48.8 0.5 33 105-137 181-213 (313)
23 KOG1492 C3H1-type Zn-finger pr 85.6 0.57 1.2E-05 43.5 2.4 24 111-134 207-230 (377)
24 KOG1040 Polyadenylation factor 85.3 0.59 1.3E-05 44.5 2.4 65 106-171 101-180 (325)
25 KOG1039 Predicted E3 ubiquitin 84.0 0.43 9.2E-06 45.8 0.8 24 111-135 9-32 (344)
26 PF10650 zf-C3H1: Putative zin 69.6 2.6 5.7E-05 25.8 1.0 20 112-132 2-21 (23)
27 KOG4791 Uncharacterized conser 61.2 2.8 6E-05 42.6 0.0 47 113-170 35-83 (667)
28 KOG2202 U2 snRNP splicing fact 59.8 4.2 9.1E-05 37.9 1.0 32 102-134 144-175 (260)
29 KOG2185 Predicted RNA-processi 54.6 8.6 0.00019 38.3 2.2 26 146-172 137-164 (486)
30 KOG2494 C3H1-type Zn-finger pr 49.2 8.3 0.00018 37.1 1.1 37 102-140 63-99 (331)
31 KOG2333 Uncharacterized conser 49.0 7.4 0.00016 39.7 0.8 21 112-132 116-136 (614)
32 COG5152 Uncharacterized conser 42.9 11 0.00024 34.5 0.9 27 146-172 138-166 (259)
33 KOG3161 Predicted E3 ubiquitin 34.8 11 0.00023 39.7 -0.6 40 102-141 195-234 (861)
34 KOG2202 U2 snRNP splicing fact 28.1 18 0.00039 33.8 -0.2 27 112-138 17-43 (260)
35 KOG4791 Uncharacterized conser 25.8 37 0.00079 34.8 1.4 48 112-169 5-52 (667)
36 PF10283 zf-CCHH: Zinc-finger 25.3 22 0.00048 22.3 -0.1 9 121-129 2-10 (26)
37 KOG2209 Oxysterol-binding prot 24.5 32 0.00068 33.8 0.7 31 5-35 150-180 (445)
38 PF08679 DsrD: Dissimilatory s 21.6 30 0.00065 26.3 -0.1 9 27-35 50-58 (67)
No 1
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.58 E-value=9.7e-16 Score=139.25 Aligned_cols=76 Identities=28% Similarity=0.454 Sum_probs=66.1
Q ss_pred CCCCCCCcchhhccccccCCcCCC-CCCccccCCccccc------cCCCCCCCCccccccccccccCCCCCC--CCcCcc
Q 042240 101 SSSSSSSSKTELCRSREEVGMCRF-GTKCQFAHGKEELR------STLFPTTKNKSEVMTDSALVLTIQMED--HSMKAS 171 (241)
Q Consensus 101 ~~~~~~~yKT~LCr~f~~~G~C~y-GdkC~FAHG~~ELr------~~~~~p~~yKTklCk~F~~~G~CpyG~--rf~H~~ 171 (241)
.......|||.||+.|...|.|+| |++|+|||+.+|++ ....++ +|||++|.+|...|+|+||. +|+|..
T Consensus 123 ~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~~~~~~~~~~-~~kt~lC~~f~~tG~C~yG~rC~F~H~~ 201 (332)
T KOG1677|consen 123 GERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPSSENQVGNPP-KYKTKLCPKFQKTGLCKYGSRCRFIHGE 201 (332)
T ss_pred cccCcccccCCcceeeecCccccccCchhhhcCCcccccccccchhhcCCC-CCCCcCCCccccCCCCCCCCcCeecCCC
Confidence 456778999999999999999999 99999999999999 333445 99999999999999999996 488988
Q ss_pred ccCCCC
Q 042240 172 VCESPV 177 (241)
Q Consensus 172 ~s~~~~ 177 (241)
.+...+
T Consensus 202 ~~~~~~ 207 (332)
T KOG1677|consen 202 PEDRAS 207 (332)
T ss_pred cccccc
Confidence 765543
No 2
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.98 E-value=2.4e-10 Score=106.37 Aligned_cols=64 Identities=19% Similarity=0.264 Sum_probs=57.8
Q ss_pred CCCCCcchhhccccccCCcCCCCCCccccCCccccccCCCCC-CCCccccccccccccCCCCCCC
Q 042240 103 SSSSSSKTELCRSREEVGMCRFGTKCQFAHGKEELRSTLFPT-TKNKSEVMTDSALVLTIQMEDH 166 (241)
Q Consensus 103 ~~~~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~ELr~~~~~p-~~yKTklCk~F~~~G~CpyG~r 166 (241)
...++|||+.|.+|+..|+|+||.||.|+||.+++....+++ ..|+...|+.|..+|.||+|.+
T Consensus 267 ~k~~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~ie~~~~~~~~y~~~~crt~~~~g~~p~g~~ 331 (351)
T COG5063 267 KKKQNFRTEPCINWEKSGYCPYGLRCCFKHGDDSDIEMYEEASLGYLDGPCRTRAKGGAFPSGGA 331 (351)
T ss_pred ccccccccCCccchhhcccCccccccccccCChhhccccccccccccccccccccccCccCCCCc
Confidence 456899999999999999999999999999999988776554 4799999999999999999985
No 3
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.97 E-value=2.9e-10 Score=105.86 Aligned_cols=73 Identities=27% Similarity=0.354 Sum_probs=63.8
Q ss_pred CCCCCCCcch--hhccccccCCcCCC---CCCcccc---CCccccccCCCCCCCCccccccccccccCCCCCCC--CcCc
Q 042240 101 SSSSSSSSKT--ELCRSREEVGMCRF---GTKCQFA---HGKEELRSTLFPTTKNKSEVMTDSALVLTIQMEDH--SMKA 170 (241)
Q Consensus 101 ~~~~~~~yKT--~LCr~f~~~G~C~y---GdkC~FA---HG~~ELr~~~~~p~~yKTklCk~F~~~G~CpyG~r--f~H~ 170 (241)
..+....||| +||.-|...|.|+| |++|+|| ||..||....... .|||++|.+|..-|+|+||.| |.|.
T Consensus 219 ~e~n~~L~kt~~~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~~k~k~~-~frTePcinwe~sGyc~yg~Rc~F~hg 297 (351)
T COG5063 219 QEQNKPLYKTNPELCESFTRKGTCPYWISGVKCQFACRGHGLNELKSKKKKQ-NFRTEPCINWEKSGYCPYGLRCCFKHG 297 (351)
T ss_pred hhccchhhcCCHHHhhccCcCCCCcccccccccccccccccccccccccccc-ccccCCccchhhcccCccccccccccC
Confidence 3577889999 99999999999999 9999999 9999998766443 899999999999999999986 6676
Q ss_pred cccC
Q 042240 171 SVCE 174 (241)
Q Consensus 171 ~~s~ 174 (241)
..+.
T Consensus 298 d~~~ 301 (351)
T COG5063 298 DDSD 301 (351)
T ss_pred Chhh
Confidence 6544
No 4
>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=98.82 E-value=6.4e-10 Score=68.93 Aligned_cols=27 Identities=56% Similarity=1.075 Sum_probs=22.7
Q ss_pred cchhhccccccCCcCCCCCCccccCCc
Q 042240 108 SKTELCRSREEVGMCRFGTKCQFAHGK 134 (241)
Q Consensus 108 yKT~LCr~f~~~G~C~yGdkC~FAHG~ 134 (241)
|||++|++|...|.|+||++|.|+|++
T Consensus 1 ~k~~~C~~f~~~g~C~~G~~C~f~H~~ 27 (27)
T PF00642_consen 1 YKTKLCRFFMRTGTCPFGDKCRFAHGE 27 (27)
T ss_dssp TTSSB-HHHHHTS--TTGGGSSSBSSG
T ss_pred CccccChhhccCCccCCCCCcCccCCC
Confidence 799999999999999999999999984
No 5
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.57 E-value=2.9e-08 Score=90.54 Aligned_cols=42 Identities=31% Similarity=0.732 Sum_probs=37.9
Q ss_pred CCCCCCcchhhccccccCCcCCCCCCccccCCccccccCCCC
Q 042240 102 SSSSSSSKTELCRSREEVGMCRFGTKCQFAHGKEELRSTLFP 143 (241)
Q Consensus 102 ~~~~~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~ELr~~~~~ 143 (241)
.....+|||+||.+|...|.|+||.+|+|+|+..|++.....
T Consensus 169 ~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~~~~~~~~ 210 (332)
T KOG1677|consen 169 VGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPEDRASNRH 210 (332)
T ss_pred hcCCCCCCCcCCCccccCCCCCCCCcCeecCCCccccccccC
Confidence 456789999999999999999999999999999999987643
No 6
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.45 E-value=2.6e-07 Score=91.16 Aligned_cols=64 Identities=14% Similarity=0.149 Sum_probs=53.8
Q ss_pred CCCCCCcchhhccccccCCcCCCCCCccccCCccccccCCCCCCCCccccccccccccCCCCCCCC-cCccc
Q 042240 102 SSSSSSSKTELCRSREEVGMCRFGTKCQFAHGKEELRSTLFPTTKNKSEVMTDSALVLTIQMEDHS-MKASV 172 (241)
Q Consensus 102 ~~~~~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~ELr~~~~~p~~yKTklCk~F~~~G~CpyG~rf-~H~~~ 172 (241)
..++-.|--..|..|. +|.|..||.|+||||.-|-+. ||..|||++|+ .+|+|+.--+| .|...
T Consensus 228 DPRkyhYs~tpCPefr-kG~C~rGD~CEyaHgvfEcwL---HPa~YRT~~Ck---Dg~~C~RrvCfFAH~~e 292 (528)
T KOG1595|consen 228 DPRKYHYSSTPCPEFR-KGSCERGDSCEYAHGVFECWL---HPARYRTRKCK---DGGYCPRRVCFFAHSPE 292 (528)
T ss_pred CcccccccCccCcccc-cCCCCCCCccccccceehhhc---CHHHhcccccc---CCCCCccceEeeecChH
Confidence 4667788889999999 599999999999999999885 45799999999 67999996554 45443
No 7
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.24 E-value=5.3e-07 Score=54.18 Aligned_cols=27 Identities=44% Similarity=0.925 Sum_probs=24.2
Q ss_pred CcchhhccccccCCcCCCCCCccccCCc
Q 042240 107 SSKTELCRSREEVGMCRFGTKCQFAHGK 134 (241)
Q Consensus 107 ~yKT~LCr~f~~~G~C~yGdkC~FAHG~ 134 (241)
.+|+.+|+.| ..|.|++|++|+|+|+.
T Consensus 1 ~~k~~~C~~~-~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 1 KYKTELCKFF-KRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCCcCcCc-cCCCCCCCCCcCCCCcC
Confidence 3789999999 58999999999999973
No 8
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=97.96 E-value=3.2e-06 Score=83.54 Aligned_cols=61 Identities=21% Similarity=0.293 Sum_probs=51.4
Q ss_pred chhhccccccC--CcCCCCCCccccCCccccccCCCCCCCCccccccccccccCCCCC--CCCcCccc
Q 042240 109 KTELCRSREEV--GMCRFGTKCQFAHGKEELRSTLFPTTKNKSEVMTDSALVLTIQME--DHSMKASV 172 (241)
Q Consensus 109 KT~LCr~f~~~--G~C~yGdkC~FAHG~~ELr~~~~~p~~yKTklCk~F~~~G~CpyG--~rf~H~~~ 172 (241)
+..||...... ..|.||++|+|-|+.+.+..+..+ ....-|+.|...|+|||| +||+.++.
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~---Dig~~Cp~f~s~G~Cp~G~~CRFl~aHl 139 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAP---DIGPSCPVFESLGFCPYGFKCRFLGAHL 139 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHHHHHhccCc---ccCCccceeeccccCCccceeehhhccc
Confidence 57899999876 589999999999999999998753 356789999999999999 57875443
No 9
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=96.94 E-value=0.00038 Score=65.76 Aligned_cols=63 Identities=16% Similarity=0.188 Sum_probs=43.1
Q ss_pred CCcchhhccccccCCcCCCCCCccccCCccccccCCCC---------------C-----CCCccccccccccccCCCCCC
Q 042240 106 SSSKTELCRSREEVGMCRFGTKCQFAHGKEELRSTLFP---------------T-----TKNKSEVMTDSALVLTIQMED 165 (241)
Q Consensus 106 ~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~ELr~~~~~---------------p-----~~yKTklCk~F~~~G~CpyG~ 165 (241)
...++.+|++|. .|.|..||.|.|+|.. +|.....- + -.-+-+.|+ |...|+|+-|.
T Consensus 73 ~~~~~~vcK~~l-~glC~kgD~C~Flhe~-~~~k~rec~ff~~~g~c~~~~~c~y~h~dpqt~~k~c~-~~~~g~c~~g~ 149 (325)
T KOG1040|consen 73 DSRGKVVCKHWL-RGLCKKGDQCEFLHEY-DLTKMRECKFFSLFGECTNGKDCPYLHGDPQTAIKKCK-WYKEGFCRGGP 149 (325)
T ss_pred ccCCceeehhhh-hhhhhccCcCcchhhh-hhcccccccccccccccccccCCcccCCChhhhhhccc-hhhhccCCCcc
Confidence 489999999999 6999999999999987 55433210 0 012334566 44677888776
Q ss_pred CCcCcc
Q 042240 166 HSMKAS 171 (241)
Q Consensus 166 rf~H~~ 171 (241)
.+.|..
T Consensus 150 ~c~~~h 155 (325)
T KOG1040|consen 150 SCKKRH 155 (325)
T ss_pred hhhhhh
Confidence 655433
No 10
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=96.83 E-value=0.00028 Score=64.76 Aligned_cols=68 Identities=28% Similarity=0.256 Sum_probs=49.9
Q ss_pred CCCcchhhccccccCCcCCCCCCccccCCccccccCCCC------------------CCCCcccccccccc------cc-
Q 042240 105 SSSSKTELCRSREEVGMCRFGTKCQFAHGKEELRSTLFP------------------TTKNKSEVMTDSAL------VL- 159 (241)
Q Consensus 105 ~~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~ELr~~~~~------------------p~~yKTklCk~F~~------~G- 159 (241)
...-||..|..|. .+.|.-|+.|.|+|+.+|-|.+..+ |-..-.++|++|.. +|
T Consensus 80 gvdpK~~vcalF~-~~~c~kg~~ckF~h~~ee~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkYgw 158 (299)
T COG5252 80 GVDPKTVVCALFL-NKTCAKGDACKFAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKYGW 158 (299)
T ss_pred ccCchhHHHHHhc-cCccccCchhhhhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCccc
Confidence 4567999999999 7999999999999999988876532 11112368998764 23
Q ss_pred --CCCCCC-C--CcCcccc
Q 042240 160 --TIQMED-H--SMKASVC 173 (241)
Q Consensus 160 --~CpyG~-r--f~H~~~s 173 (241)
.||.|. + .+|.+..
T Consensus 159 ~W~CPng~~~C~y~H~Lp~ 177 (299)
T COG5252 159 GWTCPNGNMRCSYIHKLPD 177 (299)
T ss_pred eeeCCCCCceeeeeeccCc
Confidence 799994 3 4576654
No 11
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=96.82 E-value=0.00029 Score=66.17 Aligned_cols=36 Identities=28% Similarity=0.517 Sum_probs=30.4
Q ss_pred CCCcchhhccccccCCcCCCCCCccccCCccccccCC
Q 042240 105 SSSSKTELCRSREEVGMCRFGTKCQFAHGKEELRSTL 141 (241)
Q Consensus 105 ~~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~ELr~~~ 141 (241)
...-|+.+|.+|. .|.|.-|++|.|+|+...-|...
T Consensus 87 gvDPKSvvCafFk-~g~C~KG~kCKFsHdl~~~~k~e 122 (343)
T KOG1763|consen 87 GVDPKSVVCAFFK-QGTCTKGDKCKFSHDLAVERKKE 122 (343)
T ss_pred CCCchHHHHHHHh-ccCCCCCCcccccchHHHhhhcc
Confidence 3567999999998 69999999999999988666544
No 12
>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=96.69 E-value=0.0005 Score=42.45 Aligned_cols=24 Identities=13% Similarity=-0.060 Sum_probs=17.9
Q ss_pred CccccccccccccCCCCCC--CCcCc
Q 042240 147 NKSEVMTDSALVLTIQMED--HSMKA 170 (241)
Q Consensus 147 yKTklCk~F~~~G~CpyG~--rf~H~ 170 (241)
||+.+|+.|...|.|+||. +|+|.
T Consensus 1 ~k~~~C~~f~~~g~C~~G~~C~f~H~ 26 (27)
T PF00642_consen 1 YKTKLCRFFMRTGTCPFGDKCRFAHG 26 (27)
T ss_dssp TTSSB-HHHHHTS--TTGGGSSSBSS
T ss_pred CccccChhhccCCccCCCCCcCccCC
Confidence 6899999999999999996 47774
No 13
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=95.82 E-value=0.0049 Score=58.43 Aligned_cols=62 Identities=21% Similarity=0.326 Sum_probs=44.4
Q ss_pred CCCCCcch-hhccccccCCcCCCCCC-ccccCCccccccCCCCCCCCccccccccccccCCCCCC-CCcCcc
Q 042240 103 SSSSSSKT-ELCRSREEVGMCRFGTK-CQFAHGKEELRSTLFPTTKNKSEVMTDSALVLTIQMED-HSMKAS 171 (241)
Q Consensus 103 ~~~~~yKT-~LCr~f~~~G~C~yGdk-C~FAHG~~ELr~~~~~p~~yKTklCk~F~~~G~CpyG~-rf~H~~ 171 (241)
++..++-| ++||.|+ .|.|..|++ |+|||-.+-+... +-+-.-|..| ..|.|.... +|+|..
T Consensus 29 ~kd~~wl~~eVCReF~-rn~C~R~d~~CkfaHP~~~~~V~-----~g~v~aC~Ds-~kgrCsR~nCkylHpp 93 (331)
T KOG2494|consen 29 VKDTKWLTLEVCREFL-RNTCSRGDRECKFAHPPKNCQVS-----NGRVIACFDS-QKGRCSRENCKYLHPP 93 (331)
T ss_pred ccccchhHHHHHHHHH-hccccCCCccccccCCCCCCCcc-----CCeEEEEecc-ccCccCcccceecCCC
Confidence 33334433 8999999 699999999 9999987744433 3455668766 578888774 588843
No 14
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=95.51 E-value=0.021 Score=57.12 Aligned_cols=59 Identities=20% Similarity=0.131 Sum_probs=46.8
Q ss_pred CCCCCCCcchhhccccccCCcCCCCCCccccC-CccccccCCCCCCCCccccccccccccCCCCCC
Q 042240 101 SSSSSSSSKTELCRSREEVGMCRFGTKCQFAH-GKEELRSTLFPTTKNKSEVMTDSALVLTIQMED 165 (241)
Q Consensus 101 ~~~~~~~yKT~LCr~f~~~G~C~yGdkC~FAH-G~~ELr~~~~~p~~yKTklCk~F~~~G~CpyG~ 165 (241)
+.-..-.|||+-|. .+.|.=+-.|-||| |++.-|...+-- .|....|+.|. .|.|..|+
T Consensus 192 DeFrMy~fKir~C~----R~~shDwteCPf~HpgEkARRRDPRky-hYs~tpCPefr-kG~C~rGD 251 (528)
T KOG1595|consen 192 DEFRMYSFKIRRCS----RPRSHDWTECPFAHPGEKARRRDPRKY-HYSSTPCPEFR-KGSCERGD 251 (528)
T ss_pred cceEEEeeeecccC----CccCCCcccCCccCCCcccccCCcccc-cccCccCcccc-cCCCCCCC
Confidence 34556789999998 56999999999999 988777544322 57789999995 59999996
No 15
>smart00356 ZnF_C3H1 zinc finger.
Probab=94.86 E-value=0.023 Score=33.70 Aligned_cols=23 Identities=13% Similarity=-0.133 Sum_probs=19.4
Q ss_pred CccccccccccccCCCCCCC--CcCc
Q 042240 147 NKSEVMTDSALVLTIQMEDH--SMKA 170 (241)
Q Consensus 147 yKTklCk~F~~~G~CpyG~r--f~H~ 170 (241)
+|+.+|+.| ..|.|++|.. |+|.
T Consensus 2 ~k~~~C~~~-~~g~C~~g~~C~~~H~ 26 (27)
T smart00356 2 YKTELCKFF-KRGYCPYGDRCKFAHP 26 (27)
T ss_pred CCCCcCcCc-cCCCCCCCCCcCCCCc
Confidence 688999988 8999999964 6674
No 16
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=94.80 E-value=0.015 Score=33.45 Aligned_cols=19 Identities=32% Similarity=0.786 Sum_probs=15.8
Q ss_pred hccccccCCcCCCCCCccccCC
Q 042240 112 LCRSREEVGMCRFGTKCQFAHG 133 (241)
Q Consensus 112 LCr~f~~~G~C~yGdkC~FAHG 133 (241)
+|++|. .|+++++|.|+|.
T Consensus 1 ~Ck~~~---~C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGP---NCTNGDNCPFSHP 19 (19)
T ss_pred CCcCcC---CCCCCCcCccCCc
Confidence 488765 4999999999994
No 17
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=94.25 E-value=0.018 Score=56.47 Aligned_cols=33 Identities=36% Similarity=0.761 Sum_probs=26.6
Q ss_pred chhhccccccCCcCCCCCCccccCCcc----ccccCCC
Q 042240 109 KTELCRSREEVGMCRFGTKCQFAHGKE----ELRSTLF 142 (241)
Q Consensus 109 KT~LCr~f~~~G~C~yGdkC~FAHG~~----ELr~~~~ 142 (241)
-.+.|.+|. .|.|+||++|+|.||.. +||.-..
T Consensus 139 sMkpC~ffL-eg~CRF~enCRfSHG~~V~lsslr~yq~ 175 (486)
T KOG2185|consen 139 SMKPCKFFL-EGRCRFGENCRFSHGLDVPLSSLRNYQQ 175 (486)
T ss_pred hhccchHhh-ccccccCcccccccCcccchhhcccCCC
Confidence 347899999 69999999999999964 5665543
No 18
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=93.83 E-value=0.021 Score=51.63 Aligned_cols=33 Identities=24% Similarity=0.887 Sum_probs=28.3
Q ss_pred CCcchhhccccccCCcCCCCCCccccCCccccc
Q 042240 106 SSSKTELCRSREEVGMCRFGTKCQFAHGKEELR 138 (241)
Q Consensus 106 ~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~ELr 138 (241)
..|-...|+.|...|+|-|||.|.|.|..+++.
T Consensus 137 iD~qpdVCKdyk~TGYCGYGDsCKflH~R~D~K 169 (259)
T COG5152 137 IDTQPDVCKDYKETGYCGYGDSCKFLHDRSDFK 169 (259)
T ss_pred eecCcccccchhhcccccCCchhhhhhhhhhhh
Confidence 346667899999999999999999999887554
No 19
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=92.63 E-value=0.35 Score=45.36 Aligned_cols=35 Identities=26% Similarity=0.500 Sum_probs=28.8
Q ss_pred CCCCcchhhccccccCCcCCCCCCccccCCcccccc
Q 042240 104 SSSSSKTELCRSREEVGMCRFGTKCQFAHGKEELRS 139 (241)
Q Consensus 104 ~~~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~ELr~ 139 (241)
....+-...|++|. .|.|+-+..|.|+|+.+-++.
T Consensus 98 ~~~~~s~V~c~~~~-~g~c~s~~~c~~lh~~d~~~s 132 (285)
T COG5084 98 NPVLSSSVVCKFFL-RGLCKSGFSCEFLHEYDLRSS 132 (285)
T ss_pred CccccCCcccchhc-cccCcCCCccccccCCCcccc
Confidence 33368888999998 699999999999999876663
No 20
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=91.56 E-value=0.28 Score=45.51 Aligned_cols=25 Identities=24% Similarity=0.404 Sum_probs=17.2
Q ss_pred ccccccCccccCCCCCCCCCCeEEE
Q 042240 206 DVQSRATSTSSRDNWSPQDDGIEVT 230 (241)
Q Consensus 206 ~~~~~~~~t~s~~~~~~~d~~ie~~ 230 (241)
+-|..++.+.+...--|.|.|-||-
T Consensus 340 peqteapisktagsinpedsgseig 364 (377)
T KOG1492|consen 340 PEQTEAPISKTAGSINPEDSGSEIG 364 (377)
T ss_pred cccccCCchhccCCCCccccccccc
Confidence 3455566666666677889998874
No 21
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=91.37 E-value=0.53 Score=44.13 Aligned_cols=70 Identities=16% Similarity=0.114 Sum_probs=47.5
Q ss_pred hhhccccccCCcCCCCCCccccCCccccccCCCCCCCCcccccccccc--ccCCCCCCC--CcCccccC------CCCCC
Q 042240 110 TELCRSREEVGMCRFGTKCQFAHGKEELRSTLFPTTKNKSEVMTDSAL--VLTIQMEDH--SMKASVCE------SPVTP 179 (241)
Q Consensus 110 T~LCr~f~~~G~C~yGdkC~FAHG~~ELr~~~~~p~~yKTklCk~F~~--~G~CpyG~r--f~H~~~s~------~~~~p 179 (241)
+--|+.|...|.|..|..|.++|.+. .-.-..|..|.. .+.||+|.. +-|.+... +....
T Consensus 134 ~~~c~~Fs~~G~cs~g~~c~~~h~dp----------~~~~~~~~~~~~~~~~f~p~g~~c~~~H~~~~~~~~~~p~~~y~ 203 (285)
T COG5084 134 GPPCRSFSLKGSCSSGPSCGYSHIDP----------DSFAGNCDQYSGATYGFCPLGASCKFSHTLKRVSYGSSPCGNYT 203 (285)
T ss_pred CCCcccccccceeccCCCCCccccCc----------ccccccccccCcccccccCCCCccccccccccccccccccccCc
Confidence 56699998899999999999999971 122345665543 899999975 44655422 33444
Q ss_pred CccCCCcccc
Q 042240 180 VTFKPRLTNT 189 (241)
Q Consensus 180 ~~~rPkl~~s 189 (241)
..+.|+.+.+
T Consensus 204 ~~fsP~g~~~ 213 (285)
T COG5084 204 PPFSPPGTPS 213 (285)
T ss_pred CCcCCCCCCc
Confidence 5556666553
No 22
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.66 E-value=0.12 Score=48.80 Aligned_cols=33 Identities=24% Similarity=0.814 Sum_probs=29.4
Q ss_pred CCCcchhhccccccCCcCCCCCCccccCCcccc
Q 042240 105 SSSSKTELCRSREEVGMCRFGTKCQFAHGKEEL 137 (241)
Q Consensus 105 ~~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~EL 137 (241)
...|-..+|+.|..+|+|-||+.|.|-|....+
T Consensus 181 ~~d~qpDicKdykeTgycg~gdSckFlh~r~Dy 213 (313)
T KOG1813|consen 181 RIDYQPDICKDYKETGYCGYGDSCKFLHDRSDY 213 (313)
T ss_pred eeecCchhhhhhHhhCcccccchhhhhhhhhhc
Confidence 456778899999999999999999999988866
No 23
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=85.61 E-value=0.57 Score=43.49 Aligned_cols=24 Identities=33% Similarity=0.793 Sum_probs=20.1
Q ss_pred hhccccccCCcCCCCCCccccCCc
Q 042240 111 ELCRSREEVGMCRFGTKCQFAHGK 134 (241)
Q Consensus 111 ~LCr~f~~~G~C~yGdkC~FAHG~ 134 (241)
..|++|..+|.|-.|..|+|.|..
T Consensus 207 vycryynangicgkgaacrfvhep 230 (377)
T KOG1492|consen 207 VYCRYYNANGICGKGAACRFVHEP 230 (377)
T ss_pred eEEEEecCCCcccCCceeeeeccc
Confidence 358988888999999999998863
No 24
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=85.29 E-value=0.59 Score=44.47 Aligned_cols=65 Identities=12% Similarity=0.216 Sum_probs=43.4
Q ss_pred CCcchhhccccccCCcCCCCCCccccCCcc--ccccCCC------C--C----CCCccccccccccccCCCCCCC-CcCc
Q 042240 106 SSSKTELCRSREEVGMCRFGTKCQFAHGKE--ELRSTLF------P--T----TKNKSEVMTDSALVLTIQMEDH-SMKA 170 (241)
Q Consensus 106 ~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~--ELr~~~~------~--p----~~yKTklCk~F~~~G~CpyG~r-f~H~ 170 (241)
..-|..-|.+|...|.|.-|.+|.|-|+.- .+..-+- . + ...+-.+|..| ..|.|+-|.. +.|.
T Consensus 101 ~~~k~rec~ff~~~g~c~~~~~c~y~h~dpqt~~k~c~~~~~g~c~~g~~c~~~h~~~~~c~~y-~~gfC~~g~q~c~~~ 179 (325)
T KOG1040|consen 101 DLTKMRECKFFSLFGECTNGKDCPYLHGDPQTAIKKCKWYKEGFCRGGPSCKKRHERKVLCPPY-NAGFCPKGPQRCDML 179 (325)
T ss_pred hhcccccccccccccccccccCCcccCCChhhhhhccchhhhccCCCcchhhhhhhcccCCCch-hhhhccCCCCccccc
Confidence 455666799999999999999999999982 2221110 0 0 12233678855 6899999964 5543
Q ss_pred c
Q 042240 171 S 171 (241)
Q Consensus 171 ~ 171 (241)
.
T Consensus 180 h 180 (325)
T KOG1040|consen 180 H 180 (325)
T ss_pred C
Confidence 3
No 25
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.00 E-value=0.43 Score=45.77 Aligned_cols=24 Identities=29% Similarity=0.877 Sum_probs=22.2
Q ss_pred hhccccccCCcCCCCCCccccCCcc
Q 042240 111 ELCRSREEVGMCRFGTKCQFAHGKE 135 (241)
Q Consensus 111 ~LCr~f~~~G~C~yGdkC~FAHG~~ 135 (241)
.+|++|+ .|.|+||++|+|.|..-
T Consensus 9 tic~~~~-~g~c~~g~~cr~~h~~~ 32 (344)
T KOG1039|consen 9 TICKYYQ-KGNCKFGDLCRLSHSLP 32 (344)
T ss_pred hhhhhcc-cccccccceeeeeccCc
Confidence 7899999 79999999999999876
No 26
>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=69.57 E-value=2.6 Score=25.77 Aligned_cols=20 Identities=35% Similarity=0.893 Sum_probs=16.2
Q ss_pred hccccccCCcCCCCCCccccC
Q 042240 112 LCRSREEVGMCRFGTKCQFAH 132 (241)
Q Consensus 112 LCr~f~~~G~C~yGdkC~FAH 132 (241)
||.+-..+|.|. -+.|.|.|
T Consensus 2 lC~yEl~Gg~Cn-d~~C~~QH 21 (23)
T PF10650_consen 2 LCPYELTGGVCN-DPDCEFQH 21 (23)
T ss_pred CCccccCCCeeC-CCCCCccc
Confidence 788777666998 57799988
No 27
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=61.18 E-value=2.8 Score=42.55 Aligned_cols=47 Identities=17% Similarity=0.199 Sum_probs=24.4
Q ss_pred ccccccCCcCCCCCCccccCCccccccCCCCCCCCccccccccccccC-CCCCCC-CcCc
Q 042240 113 CRSREEVGMCRFGTKCQFAHGKEELRSTLFPTTKNKSEVMTDSALVLT-IQMEDH-SMKA 170 (241)
Q Consensus 113 Cr~f~~~G~C~yGdkC~FAHG~~ELr~~~~~p~~yKTklCk~F~~~G~-CpyG~r-f~H~ 170 (241)
|++|+..-.|+ +.|.|.|..-.+. ....+|- |+..+. |.--.+ |.|+
T Consensus 35 C~~w~~~~~C~--k~C~YRHSe~~~k--------r~e~~CY-we~~p~gC~k~~CgfRH~ 83 (667)
T KOG4791|consen 35 CTLWQEGRCCR--KVCRYRHSEIDKK--------RSEIPCY-WENQPTGCQKLNCGFRHN 83 (667)
T ss_pred hhhhhhcCccc--ccccchhhHHhhh--------cCcccce-eecCCCccCCCccccccC
Confidence 66666544444 2566666533332 1235666 445555 765543 6773
No 28
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=59.77 E-value=4.2 Score=37.88 Aligned_cols=32 Identities=28% Similarity=0.523 Sum_probs=27.5
Q ss_pred CCCCCCcchhhccccccCCcCCCCCCccccCCc
Q 042240 102 SSSSSSSKTELCRSREEVGMCRFGTKCQFAHGK 134 (241)
Q Consensus 102 ~~~~~~yKT~LCr~f~~~G~C~yGdkC~FAHG~ 134 (241)
-.....++-..|..|.. +.|.+|..|.|-|-.
T Consensus 144 ~~pvT~~rea~C~~~e~-~~C~rG~~CnFmH~k 175 (260)
T KOG2202|consen 144 LSPVTDFREAICGQFER-TECSRGGACNFMHVK 175 (260)
T ss_pred ecCcCchhhhhhccccc-ccCCCCCcCcchhhh
Confidence 45567899999999995 699999999999965
No 29
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=54.61 E-value=8.6 Score=38.31 Aligned_cols=26 Identities=4% Similarity=-0.259 Sum_probs=19.7
Q ss_pred CCccccccccccccCCCCC--CCCcCccc
Q 042240 146 KNKSEVMTDSALVLTIQME--DHSMKASV 172 (241)
Q Consensus 146 ~yKTklCk~F~~~G~CpyG--~rf~H~~~ 172 (241)
---.++|++| ..|.|.|+ |||-|..+
T Consensus 137 h~sMkpC~ff-Leg~CRF~enCRfSHG~~ 164 (486)
T KOG2185|consen 137 HESMKPCKFF-LEGRCRFGENCRFSHGLD 164 (486)
T ss_pred chhhccchHh-hccccccCcccccccCcc
Confidence 3445899955 89999999 46778664
No 30
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=49.17 E-value=8.3 Score=37.08 Aligned_cols=37 Identities=19% Similarity=0.494 Sum_probs=29.6
Q ss_pred CCCCCCcchhhccccccCCcCCCCCCccccCCccccccC
Q 042240 102 SSSSSSSKTELCRSREEVGMCRFGTKCQFAHGKEELRST 140 (241)
Q Consensus 102 ~~~~~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~ELr~~ 140 (241)
.....+-+-..|-.++ +|.|.. ++|+|+|...+|+..
T Consensus 63 ~~~V~~g~v~aC~Ds~-kgrCsR-~nCkylHpp~hlkdq 99 (331)
T KOG2494|consen 63 NCQVSNGRVIACFDSQ-KGRCSR-ENCKYLHPPQHLKDQ 99 (331)
T ss_pred CCCccCCeEEEEeccc-cCccCc-ccceecCCChhhhhh
Confidence 4445566778899999 799995 779999999988764
No 31
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=48.97 E-value=7.4 Score=39.69 Aligned_cols=21 Identities=38% Similarity=0.933 Sum_probs=19.1
Q ss_pred hccccccCCcCCCCCCccccC
Q 042240 112 LCRSREEVGMCRFGTKCQFAH 132 (241)
Q Consensus 112 LCr~f~~~G~C~yGdkC~FAH 132 (241)
-|.-|...|.|+||-+|+|+-
T Consensus 116 ~Cp~f~s~G~Cp~G~~CRFl~ 136 (614)
T KOG2333|consen 116 SCPVFESLGFCPYGFKCRFLG 136 (614)
T ss_pred ccceeeccccCCccceeehhh
Confidence 499999999999999999964
No 32
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=42.87 E-value=11 Score=34.47 Aligned_cols=27 Identities=11% Similarity=0.037 Sum_probs=21.6
Q ss_pred CCccccccccccccCCCCCC--CCcCccc
Q 042240 146 KNKSEVMTDSALVLTIQMED--HSMKASV 172 (241)
Q Consensus 146 ~yKTklCk~F~~~G~CpyG~--rf~H~~~ 172 (241)
.|-..+|+.|...|||-||+ .|+|...
T Consensus 138 D~qpdVCKdyk~TGYCGYGDsCKflH~R~ 166 (259)
T COG5152 138 DTQPDVCKDYKETGYCGYGDSCKFLHDRS 166 (259)
T ss_pred ecCcccccchhhcccccCCchhhhhhhhh
Confidence 34557899999999999996 4788654
No 33
>KOG3161 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.83 E-value=11 Score=39.72 Aligned_cols=40 Identities=25% Similarity=0.199 Sum_probs=36.1
Q ss_pred CCCCCCcchhhccccccCCcCCCCCCccccCCccccccCC
Q 042240 102 SSSSSSSKTELCRSREEVGMCRFGTKCQFAHGKEELRSTL 141 (241)
Q Consensus 102 ~~~~~~yKT~LCr~f~~~G~C~yGdkC~FAHG~~ELr~~~ 141 (241)
.....+++|-||+..+.+|.|..+..|.|+|...|+....
T Consensus 195 Pamq~~vl~l~l~~Le~g~~~~Rk~lvmfvvq~le~~~pq 234 (861)
T KOG3161|consen 195 PAMQSKVLTLMLRDLEQGGGCPRKTLVMFVVQQLELEKPQ 234 (861)
T ss_pred cchHHHHHHHHHHHHHhcCCccccceEEEEeeeccccchh
Confidence 4667899999999999999999999999999999988654
No 34
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=28.06 E-value=18 Score=33.77 Aligned_cols=27 Identities=30% Similarity=0.646 Sum_probs=23.6
Q ss_pred hccccccCCcCCCCCCccccCCccccc
Q 042240 112 LCRSREEVGMCRFGTKCQFAHGKEELR 138 (241)
Q Consensus 112 LCr~f~~~G~C~yGdkC~FAHG~~ELr 138 (241)
-|..|.+.|.|++|++|.=.|...++.
T Consensus 17 ~c~fy~k~gacR~gdrcsR~h~kpt~s 43 (260)
T KOG2202|consen 17 NCSFYFKIGACRHGDRCSRLHEKPTFS 43 (260)
T ss_pred ccchHHhhcccccccHHHHhhcccccc
Confidence 499999999999999998888877654
No 35
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.83 E-value=37 Score=34.84 Aligned_cols=48 Identities=19% Similarity=0.133 Sum_probs=32.8
Q ss_pred hccccccCCcCCCCCCccccCCccccccCCCCCCCCccccccccccccCCCCCCCCcC
Q 042240 112 LCRSREEVGMCRFGTKCQFAHGKEELRSTLFPTTKNKSEVMTDSALVLTIQMEDHSMK 169 (241)
Q Consensus 112 LCr~f~~~G~C~yGdkC~FAHG~~ELr~~~~~p~~yKTklCk~F~~~G~CpyG~rf~H 169 (241)
-|-+|. .-.|++++.|.|.|.+.-|... ..|.+|...-.|.--+++.|
T Consensus 5 dcyff~-ys~cKk~d~c~~rh~E~al~n~---------t~C~~w~~~~~C~k~C~YRH 52 (667)
T KOG4791|consen 5 DCYFFF-YSTCKKGDSCPFRHCEAALGNE---------TVCTLWQEGRCCRKVCRYRH 52 (667)
T ss_pred cchhhh-hhhhhccCcCcchhhHHHhcCc---------chhhhhhhcCcccccccchh
Confidence 366666 5789999999999998866532 45777766555555444444
No 36
>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=25.30 E-value=22 Score=22.31 Aligned_cols=9 Identities=44% Similarity=1.372 Sum_probs=5.1
Q ss_pred cCCCCCCcc
Q 042240 121 MCRFGTKCQ 129 (241)
Q Consensus 121 ~C~yGdkC~ 129 (241)
.|+||.+|.
T Consensus 2 ~C~YG~~CY 10 (26)
T PF10283_consen 2 PCKYGAKCY 10 (26)
T ss_dssp E-TTGGG-S
T ss_pred CCCcchhhh
Confidence 488888884
No 37
>KOG2209 consensus Oxysterol-binding protein [Signal transduction mechanisms]
Probab=24.55 E-value=32 Score=33.76 Aligned_cols=31 Identities=16% Similarity=0.424 Sum_probs=25.6
Q ss_pred HHHHHhhccCCCCCCCCCCcccccccccCCC
Q 042240 5 VESVYKSKMGKQKSPNGNVSPLMKYWSSSST 35 (241)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 35 (241)
|..+|..-++..|-=.|-|.|+|+|||.|--
T Consensus 150 iSAfhaEgl~~dF~fhGsi~PklkFWgksve 180 (445)
T KOG2209|consen 150 ISAFHAEGLNNDFIFHGSIYPKLKFWGKSVE 180 (445)
T ss_pred hhHhhhcccCcceEEeeeecccceeccceee
Confidence 3456777788899999999999999998743
No 38
>PF08679 DsrD: Dissimilatory sulfite reductase D (DsrD); InterPro: IPR014793 The structure of the dissimilatory sulphite reductase D (DsrD) protein has shown it to contain a winged-helix motif similar to those found in DNA binding proteins []. The structure suggests a possible role for DsrD in transcription or translation of genes, which catalyse dissimilatory sulphite reduction. ; PDB: 1WQ2_B 1UCR_B.
Probab=21.55 E-value=30 Score=26.27 Aligned_cols=9 Identities=67% Similarity=1.313 Sum_probs=7.9
Q ss_pred ccccccCCC
Q 042240 27 MKYWSSSST 35 (241)
Q Consensus 27 ~~~~~~~~~ 35 (241)
|.||+|+||
T Consensus 50 l~yWSSGST 58 (67)
T PF08679_consen 50 LEYWSSGST 58 (67)
T ss_dssp EEEEEETTE
T ss_pred EEEEcCCCc
Confidence 899998886
Done!