Query 033320
Match_columns 122
No_of_seqs 126 out of 1123
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 12:28:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033320.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033320hhsearch_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 99.5 1.2E-14 2.6E-19 117.1 5.3 82 4-87 124-206 (332)
2 PF00642 zf-CCCH: Zinc finger 98.8 5.4E-10 1.2E-14 60.5 -0.2 27 10-36 1-27 (27)
3 KOG1763 Uncharacterized conser 98.7 2.3E-09 5E-14 86.9 0.4 78 7-85 87-193 (343)
4 KOG1040 Polyadenylation factor 98.7 1.1E-08 2.4E-13 83.9 2.5 88 9-104 74-174 (325)
5 KOG2333 Uncharacterized conser 98.6 9.6E-09 2.1E-13 88.1 1.9 88 11-108 75-171 (614)
6 PF00642 zf-CCCH: Zinc finger 98.6 6E-09 1.3E-13 56.3 -0.1 26 57-82 2-27 (27)
7 KOG1677 CCCH-type Zn-finger pr 98.6 1.1E-07 2.4E-12 76.6 5.8 82 5-86 79-161 (332)
8 COG5063 CTH1 CCCH-type Zn-fing 98.5 1.3E-07 2.9E-12 77.0 5.3 65 13-85 231-301 (351)
9 KOG2494 C3H1-type Zn-finger pr 98.4 9.1E-08 2E-12 78.3 2.0 60 11-85 36-96 (331)
10 smart00356 ZnF_C3H1 zinc finge 98.4 3.1E-07 6.8E-12 48.5 2.4 26 10-36 2-27 (27)
11 KOG1040 Polyadenylation factor 98.2 6E-07 1.3E-11 73.8 2.5 81 4-87 98-187 (325)
12 COG5252 Uncharacterized conser 98.2 2.1E-07 4.5E-12 73.9 -0.3 78 7-85 80-178 (299)
13 smart00356 ZnF_C3H1 zinc finge 98.1 1.9E-06 4.2E-11 45.4 2.4 25 57-82 3-27 (27)
14 KOG1492 C3H1-type Zn-finger pr 98.0 5.4E-06 1.2E-10 66.1 3.2 74 7-84 201-285 (377)
15 COG5063 CTH1 CCCH-type Zn-fing 97.9 1.6E-05 3.4E-10 65.1 4.1 73 9-87 271-343 (351)
16 KOG1492 C3H1-type Zn-finger pr 97.8 7.9E-06 1.7E-10 65.1 1.8 71 12-84 233-314 (377)
17 COG5084 YTH1 Cleavage and poly 97.8 3.5E-05 7.6E-10 62.5 4.6 75 10-85 102-192 (285)
18 KOG2185 Predicted RNA-processi 97.5 4.5E-05 9.8E-10 64.5 2.3 60 25-85 97-166 (486)
19 KOG1595 CCCH-type Zn-finger pr 97.4 0.00017 3.7E-09 62.5 4.2 55 23-85 208-262 (528)
20 KOG2185 Predicted RNA-processi 97.4 7.4E-05 1.6E-09 63.3 1.4 31 6-37 134-164 (486)
21 KOG4791 Uncharacterized conser 97.3 8.5E-05 1.8E-09 64.2 1.7 71 12-85 3-87 (667)
22 KOG1595 CCCH-type Zn-finger pr 97.3 0.00022 4.8E-09 61.8 4.1 61 10-85 234-294 (528)
23 COG5084 YTH1 Cleavage and poly 97.3 0.00088 1.9E-08 54.4 7.0 67 10-78 132-215 (285)
24 PF14608 zf-CCCH_2: Zinc finge 97.2 0.00026 5.6E-09 35.3 1.7 19 14-35 1-19 (19)
25 PF14608 zf-CCCH_2: Zinc finge 97.0 0.00041 8.9E-09 34.5 1.7 19 60-81 1-19 (19)
26 COG5152 Uncharacterized conser 97.0 0.00021 4.5E-09 55.9 0.5 32 8-39 137-168 (259)
27 KOG2494 C3H1-type Zn-finger pr 96.3 0.0013 2.8E-08 54.2 0.6 43 57-104 36-79 (331)
28 KOG1039 Predicted E3 ubiquitin 95.6 0.0045 9.8E-08 51.5 0.7 25 59-84 9-33 (344)
29 KOG1039 Predicted E3 ubiquitin 95.5 0.0047 1E-07 51.4 0.6 24 13-37 9-32 (344)
30 COG5152 Uncharacterized conser 95.3 0.0057 1.2E-07 47.9 0.6 28 58-85 141-168 (259)
31 KOG1813 Predicted E3 ubiquitin 95.0 0.0068 1.5E-07 49.6 0.0 30 10-39 184-213 (313)
32 KOG1763 Uncharacterized conser 93.9 0.017 3.6E-07 47.5 0.1 30 55-85 89-118 (343)
33 KOG2202 U2 snRNP splicing fact 93.6 0.024 5.3E-07 45.5 0.5 33 6-38 9-41 (260)
34 KOG1813 Predicted E3 ubiquitin 93.0 0.028 6.1E-07 46.1 0.0 28 58-85 186-213 (313)
35 PF10650 zf-C3H1: Putative zin 92.8 0.073 1.6E-06 27.8 1.4 22 13-35 1-22 (23)
36 KOG0153 Predicted RNA-binding 91.8 0.11 2.4E-06 43.5 2.0 33 4-37 153-185 (377)
37 KOG4791 Uncharacterized conser 90.6 0.27 5.9E-06 43.1 3.4 72 11-85 60-144 (667)
38 KOG0153 Predicted RNA-binding 84.7 0.51 1.1E-05 39.6 1.4 27 58-85 161-187 (377)
39 KOG3702 Nuclear polyadenylated 82.1 2.1 4.6E-05 38.6 4.3 25 11-39 584-608 (681)
40 KOG2202 U2 snRNP splicing fact 80.6 0.7 1.5E-05 37.2 0.8 28 9-37 149-176 (260)
41 KOG3702 Nuclear polyadenylated 80.5 3.9 8.4E-05 37.0 5.4 58 24-85 575-648 (681)
42 COG5252 Uncharacterized conser 76.6 0.68 1.5E-05 37.3 -0.4 30 55-85 82-111 (299)
43 KOG2333 Uncharacterized conser 57.1 4.7 0.0001 35.7 0.8 22 13-34 115-136 (614)
44 COG5175 MOT2 Transcriptional r 40.8 10 0.00023 32.2 0.4 29 11-40 201-229 (480)
45 PF03194 LUC7: LUC7 N_terminus 31.8 15 0.00033 29.2 -0.1 16 57-73 29-44 (254)
46 PF10283 zf-CCHH: Zinc-finger 30.4 14 0.00031 19.7 -0.3 9 69-77 2-10 (26)
47 COG5200 LUC7 U1 snRNP componen 26.8 21 0.00046 28.4 -0.0 15 58-73 31-45 (258)
48 KOG2135 Proteins containing th 26.4 26 0.00056 30.9 0.4 29 10-38 210-238 (526)
49 KOG3777 Uncharacterized conser 25.0 43 0.00093 29.1 1.5 26 57-85 170-195 (443)
50 KOG3777 Uncharacterized conser 20.2 59 0.0013 28.3 1.4 24 11-37 170-193 (443)
51 PHA03099 epidermal growth fact 20.0 57 0.0012 24.0 1.1 28 9-38 39-66 (139)
No 1
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.52 E-value=1.2e-14 Score=117.05 Aligned_cols=82 Identities=27% Similarity=0.681 Sum_probs=67.1
Q ss_pred CCCCCCCCccccccccccccCCC-CCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCcccccccCcCcCCCCCCCccCCCC
Q 033320 4 DEFPERPGQPECSYFLRTGDCKY-KSNCKYHHPKNRIPKSPPCTLSDKGLPLRPGQNVCSYYSRYGICKFGPACKYDHPI 82 (122)
Q Consensus 4 ~~~~~rp~~~~Cr~f~k~G~C~~-G~~C~F~H~~~~~~~~~~~~~~~~g~p~~~~~~~C~~f~~~G~C~~G~~Crf~H~~ 82 (122)
+..+++.++++|++|.+.|.|+| |++|+|+|...+..... .+...+.+...++++|.+|+++|.|+||.+|+|.|..
T Consensus 124 ~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~--~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~ 201 (332)
T KOG1677|consen 124 ERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPS--SENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGE 201 (332)
T ss_pred ccCcccccCCcceeeecCccccccCchhhhcCCcccccccc--cchhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCC
Confidence 56688999999999999999999 99999999987643110 1123445667789999999999999999999999999
Q ss_pred CCCCC
Q 033320 83 HPDAS 87 (122)
Q Consensus 83 ~~~~~ 87 (122)
.+...
T Consensus 202 ~~~~~ 206 (332)
T KOG1677|consen 202 PEDRA 206 (332)
T ss_pred ccccc
Confidence 87643
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=98.83 E-value=5.4e-10 Score=60.46 Aligned_cols=27 Identities=30% Similarity=0.897 Sum_probs=21.5
Q ss_pred CCccccccccccccCCCCCCCCCCCCC
Q 033320 10 PGQPECSYFLRTGDCKYKSNCKYHHPK 36 (122)
Q Consensus 10 p~~~~Cr~f~k~G~C~~G~~C~F~H~~ 36 (122)
+++++|++|++.|.|++|++|+|+|+.
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 467899999988999999999999973
No 3
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=98.73 E-value=2.3e-09 Score=86.87 Aligned_cols=78 Identities=27% Similarity=0.583 Sum_probs=56.4
Q ss_pred CCCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCccCC-------------------CCCCCCCCCcccccccC-
Q 033320 7 PERPGQPECSYFLRTGDCKYKSNCKYHHPKNRIPKSPPCTLSD-------------------KGLPLRPGQNVCSYYSR- 66 (122)
Q Consensus 7 ~~rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~~~~~~~-------------------~g~p~~~~~~~C~~f~~- 66 (122)
.+.|+..+|-||. .|.|..|+.|+|+|+.....+.+--.++. .+-|......+|+||+.
T Consensus 87 gvDPKSvvCafFk-~g~C~KG~kCKFsHdl~~~~k~eK~dly~d~rdemWD~~kl~~vv~~K~~k~k~~tdiVCKfFLeA 165 (343)
T KOG1763|consen 87 GVDPKSVVCAFFK-QGTCTKGDKCKFSHDLAVERKKEKIDLYPDTRDEMWDEEKLEEVVLKKHGKPKPTTDIVCKFFLEA 165 (343)
T ss_pred CCCchHHHHHHHh-ccCCCCCCcccccchHHHhhhccchhccccchhhhhhHHHHHHHHHhhccCCCCchhHHHHHHHHH
Confidence 4679999999997 79999999999999986544332222221 11233334569999984
Q ss_pred -----cC---cCCCCC-CCccCCCCCCC
Q 033320 67 -----YG---ICKFGP-ACKYDHPIHPD 85 (122)
Q Consensus 67 -----~G---~C~~G~-~Crf~H~~~~~ 85 (122)
+| .||+|- .|.|+|..++.
T Consensus 166 vE~~kYGWfW~CPnGg~~C~YrHaLP~G 193 (343)
T KOG1763|consen 166 VENGKYGWFWECPNGGDKCIYRHALPEG 193 (343)
T ss_pred HhcCCccceeECCCCCCeeeeeecCCcc
Confidence 45 399985 89999998876
No 4
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=98.66 E-value=1.1e-08 Score=83.92 Aligned_cols=88 Identities=25% Similarity=0.506 Sum_probs=62.6
Q ss_pred CCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCccCC-CCC------------CCCCCCcccccccCcCcCCCCCC
Q 033320 9 RPGQPECSYFLRTGDCKYKSNCKYHHPKNRIPKSPPCTLSD-KGL------------PLRPGQNVCSYYSRYGICKFGPA 75 (122)
Q Consensus 9 rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~~~~~~~-~g~------------p~~~~~~~C~~f~~~G~C~~G~~ 75 (122)
..+..+|+||++ |.|..|+.|.|+|.. .+.+.+.|.++. .|. ........|.+|.. |+|+.|..
T Consensus 74 ~~~~~vcK~~l~-glC~kgD~C~Flhe~-~~~k~rec~ff~~~g~c~~~~~c~y~h~dpqt~~k~c~~~~~-g~c~~g~~ 150 (325)
T KOG1040|consen 74 SRGKVVCKHWLR-GLCKKGDQCEFLHEY-DLTKMRECKFFSLFGECTNGKDCPYLHGDPQTAIKKCKWYKE-GFCRGGPS 150 (325)
T ss_pred cCCceeehhhhh-hhhhccCcCcchhhh-hhcccccccccccccccccccCCcccCCChhhhhhccchhhh-ccCCCcch
Confidence 457889999995 999999999999987 455555444322 111 10124578999999 99999999
Q ss_pred CccCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 033320 76 CKYDHPIHPDASAEYGLDPPPSFGDSTTR 104 (122)
Q Consensus 76 Crf~H~~~~~~~~~~~~~~~~~~~n~~~~ 104 (122)
|+++|..... .......||+....
T Consensus 151 c~~~h~~~~~-----c~~y~~gfC~~g~q 174 (325)
T KOG1040|consen 151 CKKRHERKVL-----CPPYNAGFCPKGPQ 174 (325)
T ss_pred hhhhhhcccC-----CCchhhhhccCCCC
Confidence 9999998854 33334556666544
No 5
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=98.65 E-value=9.6e-09 Score=88.14 Aligned_cols=88 Identities=15% Similarity=0.421 Sum_probs=61.8
Q ss_pred Ccccccccccc--ccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCcccccccCcCcCCCCCCCccC--CCCCCCC
Q 033320 11 GQPECSYFLRT--GDCKYKSNCKYHHPKNRIPKSPPCTLSDKGLPLRPGQNVCSYYSRYGICKFGPACKYD--HPIHPDA 86 (122)
Q Consensus 11 ~~~~Cr~f~k~--G~C~~G~~C~F~H~~~~~~~~~~~~~~~~g~p~~~~~~~C~~f~~~G~C~~G~~Crf~--H~~~~~~ 86 (122)
...+|...... -.|.||++|+|.||.+.+...+..++. +.|++|...|+|++|-+|||. |...+..
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~Dig----------~~Cp~f~s~G~Cp~G~~CRFl~aHld~~g~ 144 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAPDIG----------PSCPVFESLGFCPYGFKCRFLGAHLDIEGN 144 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHHHHHhccCcccC----------CccceeeccccCCccceeehhhcccCcccc
Confidence 46799999853 269999999999998876544433332 789999999999999999998 7766553
Q ss_pred CC-----CCCCCCCCCCCCCCcccccc
Q 033320 87 SA-----EYGLDPPPSFGDSTTRQETG 108 (122)
Q Consensus 87 ~~-----~~~~~~~~~~~n~~~~~~~~ 108 (122)
.- -.-...+.+.+|.-+.++|.
T Consensus 145 ~~~~kek~~d~~~~~~t~N~~s~elq~ 171 (614)
T KOG2333|consen 145 NLIQKEKDPDGQFPPTTKNGVSKELQV 171 (614)
T ss_pred chhhhhhCcccCCCCccccccCHHHHH
Confidence 20 01112345555666565554
No 6
>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=98.62 E-value=6e-09 Score=56.31 Aligned_cols=26 Identities=31% Similarity=0.954 Sum_probs=20.8
Q ss_pred CCcccccccCcCcCCCCCCCccCCCC
Q 033320 57 GQNVCSYYSRYGICKFGPACKYDHPI 82 (122)
Q Consensus 57 ~~~~C~~f~~~G~C~~G~~Crf~H~~ 82 (122)
++.+|++|+++|.|++|++|+|+|+.
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 46899999999999999999999973
No 7
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.57 E-value=1.1e-07 Score=76.62 Aligned_cols=82 Identities=34% Similarity=0.796 Sum_probs=63.0
Q ss_pred CCCCCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCcccccccCcCcCCC-CCCCccCCCCC
Q 033320 5 EFPERPGQPECSYFLRTGDCKYKSNCKYHHPKNRIPKSPPCTLSDKGLPLRPGQNVCSYYSRYGICKF-GPACKYDHPIH 83 (122)
Q Consensus 5 ~~~~rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~~~~~~~~g~p~~~~~~~C~~f~~~G~C~~-G~~Crf~H~~~ 83 (122)
.+++++....|.+|.+.+.|.+++.|+|.|..................+.+.++++|.+|.+.|.|+| |++|+|.|...
T Consensus 79 ~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~p~~~~~~~~~~~~~~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~ 158 (332)
T KOG1677|consen 79 PYPERSGEGDCSAYLRTGVCGYGSSCRYNHPDLRLRPRPVRRSRGERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLE 158 (332)
T ss_pred cCCCCCCccccccccccCCCCCCCCCCccCcccccccCCccccccccCcccccCCcceeeecCccccccCchhhhcCCcc
Confidence 46777766899999999999999999999996332221110001122355678899999999999999 99999999998
Q ss_pred CCC
Q 033320 84 PDA 86 (122)
Q Consensus 84 ~~~ 86 (122)
++-
T Consensus 159 e~r 161 (332)
T KOG1677|consen 159 ELR 161 (332)
T ss_pred ccc
Confidence 885
No 8
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.53 E-value=1.3e-07 Score=77.02 Aligned_cols=65 Identities=25% Similarity=0.593 Sum_probs=54.3
Q ss_pred cccccccccccCCC---CCCCCCC---CCCCCCCCCCCCccCCCCCCCCCCCcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 13 PECSYFLRTGDCKY---KSNCKYH---HPKNRIPKSPPCTLSDKGLPLRPGQNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 13 ~~Cr~f~k~G~C~~---G~~C~F~---H~~~~~~~~~~~~~~~~g~p~~~~~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
.+|.-|.+.|.|.+ |+.|.|+ |...+....... ...++.+|..|.+.|.|+||.+|.|+|....+
T Consensus 231 ~lc~~ft~kg~~p~~~sG~~~q~a~~~HGlN~l~~k~k~--------~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~ 301 (351)
T COG5063 231 ELCESFTRKGTCPYWISGVKCQFACRGHGLNELKSKKKK--------QNFRTEPCINWEKSGYCPYGLRCCFKHGDDSD 301 (351)
T ss_pred HHhhccCcCCCCccccccccccccccccccccccccccc--------cccccCCccchhhcccCccccccccccCChhh
Confidence 78999988999999 9999999 997764322211 23568999999999999999999999998777
No 9
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=98.43 E-value=9.1e-08 Score=78.31 Aligned_cols=60 Identities=30% Similarity=0.571 Sum_probs=47.2
Q ss_pred CccccccccccccCCCCCC-CCCCCCCCCCCCCCCCccCCCCCCCCCCCcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 11 GQPECSYFLRTGDCKYKSN-CKYHHPKNRIPKSPPCTLSDKGLPLRPGQNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 11 ~~~~Cr~f~k~G~C~~G~~-C~F~H~~~~~~~~~~~~~~~~g~p~~~~~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
.-.+||.|+| |.|.+|++ |+|+|...... ++ .-+-..|.-|++ |.|.. ++|||.|+...+
T Consensus 36 ~~eVCReF~r-n~C~R~d~~CkfaHP~~~~~------V~------~g~v~aC~Ds~k-grCsR-~nCkylHpp~hl 96 (331)
T KOG2494|consen 36 TLEVCREFLR-NTCSRGDRECKFAHPPKNCQ------VS------NGRVIACFDSQK-GRCSR-ENCKYLHPPQHL 96 (331)
T ss_pred HHHHHHHHHh-ccccCCCccccccCCCCCCC------cc------CCeEEEEecccc-CccCc-ccceecCCChhh
Confidence 3469999997 99999999 99999975321 11 123467999999 99986 559999998776
No 10
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.36 E-value=3.1e-07 Score=48.50 Aligned_cols=26 Identities=35% Similarity=0.853 Sum_probs=22.5
Q ss_pred CCccccccccccccCCCCCCCCCCCCC
Q 033320 10 PGQPECSYFLRTGDCKYKSNCKYHHPK 36 (122)
Q Consensus 10 p~~~~Cr~f~k~G~C~~G~~C~F~H~~ 36 (122)
.++.+|++|. .|.|.+|++|+|+|+.
T Consensus 2 ~k~~~C~~~~-~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 2 YKTELCKFFK-RGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCcCcCcc-CCCCCCCCCcCCCCcC
Confidence 3567999995 7999999999999973
No 11
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=98.23 E-value=6e-07 Score=73.78 Aligned_cols=81 Identities=25% Similarity=0.607 Sum_probs=61.2
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCC--------CCCCcccccccCcCcCCCCCC
Q 033320 4 DEFPERPGQPECSYFLRTGDCKYKSNCKYHHPKNRIPKSPPCTLSDKGLPL--------RPGQNVCSYYSRYGICKFGPA 75 (122)
Q Consensus 4 ~~~~~rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~~~~~~~~g~p~--------~~~~~~C~~f~~~G~C~~G~~ 75 (122)
++| .-.++..|.||...|.|..|..|.|.|.... .....|.++..|+.. .....+|..|.. |+|+-|.+
T Consensus 98 he~-~~~k~rec~ff~~~g~c~~~~~c~y~h~dpq-t~~k~c~~~~~g~c~~g~~c~~~h~~~~~c~~y~~-gfC~~g~q 174 (325)
T KOG1040|consen 98 HEY-DLTKMRECKFFSLFGECTNGKDCPYLHGDPQ-TAIKKCKWYKEGFCRGGPSCKKRHERKVLCPPYNA-GFCPKGPQ 174 (325)
T ss_pred hhh-hhcccccccccccccccccccCCcccCCChh-hhhhccchhhhccCCCcchhhhhhhcccCCCchhh-hhccCCCC
Confidence 345 4467789999998999999999999998632 223345555555311 123489999998 99999999
Q ss_pred -CccCCCCCCCCC
Q 033320 76 -CKYDHPIHPDAS 87 (122)
Q Consensus 76 -Crf~H~~~~~~~ 87 (122)
|.+.|....+..
T Consensus 175 ~c~~~hp~~~~~~ 187 (325)
T KOG1040|consen 175 RCDMLHPEFQQPP 187 (325)
T ss_pred cccccCCCCCCCh
Confidence 999999988865
No 12
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=98.23 E-value=2.1e-07 Score=73.87 Aligned_cols=78 Identities=27% Similarity=0.584 Sum_probs=56.7
Q ss_pred CCCCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCccCCC------CC-----CCCCCCcccccccC------cC-
Q 033320 7 PERPGQPECSYFLRTGDCKYKSNCKYHHPKNRIPKSPPCTLSDK------GL-----PLRPGQNVCSYYSR------YG- 68 (122)
Q Consensus 7 ~~rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~~~~~~~~------g~-----p~~~~~~~C~~f~~------~G- 68 (122)
.+.|++.+|..|. .+.|..|+.|+|+|+....+.....+|+.. .+ |.-....+|+||.. +|
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 4679999999998 799999999999999765444333333321 11 22234679999984 34
Q ss_pred --cCCCC-CCCccCCCCCCC
Q 033320 69 --ICKFG-PACKYDHPIHPD 85 (122)
Q Consensus 69 --~C~~G-~~Crf~H~~~~~ 85 (122)
.|++| .+|.|.|..+..
T Consensus 159 ~W~CPng~~~C~y~H~Lp~G 178 (299)
T COG5252 159 GWTCPNGNMRCSYIHKLPDG 178 (299)
T ss_pred eeeCCCCCceeeeeeccCcc
Confidence 49998 789999998874
No 13
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.14 E-value=1.9e-06 Score=45.37 Aligned_cols=25 Identities=36% Similarity=1.216 Sum_probs=21.5
Q ss_pred CCcccccccCcCcCCCCCCCccCCCC
Q 033320 57 GQNVCSYYSRYGICKFGPACKYDHPI 82 (122)
Q Consensus 57 ~~~~C~~f~~~G~C~~G~~Crf~H~~ 82 (122)
+..+|++|.. |.|++|++|+|.|..
T Consensus 3 k~~~C~~~~~-g~C~~g~~C~~~H~~ 27 (27)
T smart00356 3 KTELCKFFKR-GYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCcCcCccC-CCCCCCCCcCCCCcC
Confidence 3568999965 999999999999974
No 14
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=97.97 E-value=5.4e-06 Score=66.09 Aligned_cols=74 Identities=28% Similarity=0.639 Sum_probs=54.5
Q ss_pred CCCCCccccccccccccCCCCCCCCCCCCCCCCCCCC-----------CCccCCCCCCCCCCCcccccccCcCcCCCCCC
Q 033320 7 PERPGQPECSYFLRTGDCKYKSNCKYHHPKNRIPKSP-----------PCTLSDKGLPLRPGQNVCSYYSRYGICKFGPA 75 (122)
Q Consensus 7 ~~rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~-----------~~~~~~~g~p~~~~~~~C~~f~~~G~C~~G~~ 75 (122)
.-.|..+.||||.-.|.|-.|..|+|.|.+.+....| .|.++..-.| ++.+.|++|+- |.|. ..+
T Consensus 201 gnspsavycryynangicgkgaacrfvheptrkticpkflngrcnkaedcnlsheldp--rripacryfll-gkcn-npn 276 (377)
T KOG1492|consen 201 GNSPSAVYCRYYNANGICGKGAACRFVHEPTRKTICPKFLNGRCNKAEDCNLSHELDP--RRIPACRYFLL-GKCN-NPN 276 (377)
T ss_pred CCCCceeEEEEecCCCcccCCceeeeeccccccccChHHhcCccCchhcCCcccccCc--cccchhhhhhh-ccCC-CCC
Confidence 3457888999998789999999999999987654432 2333221112 35688999998 9996 789
Q ss_pred CccCCCCCC
Q 033320 76 CKYDHPIHP 84 (122)
Q Consensus 76 Crf~H~~~~ 84 (122)
|||.|..-.
T Consensus 277 cryvhihys 285 (377)
T KOG1492|consen 277 CRYVHIHYS 285 (377)
T ss_pred ceEEEEeec
Confidence 999986543
No 15
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=97.87 E-value=1.6e-05 Score=65.11 Aligned_cols=73 Identities=15% Similarity=0.159 Sum_probs=55.7
Q ss_pred CCCccccccccccccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCcccccccCcCcCCCCCCCccCCCCCCCCC
Q 033320 9 RPGQPECSYFLRTGDCKYKSNCKYHHPKNRIPKSPPCTLSDKGLPLRPGQNVCSYYSRYGICKFGPACKYDHPIHPDAS 87 (122)
Q Consensus 9 rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~~~~~~~~g~p~~~~~~~C~~f~~~G~C~~G~~Crf~H~~~~~~~ 87 (122)
..++.+|..|.+.|.|+||.+|.|.|..+....... . ........+|+-++.+|.|++|..|.+.|....+..
T Consensus 271 ~frTePcinwe~sGyc~yg~Rc~F~hgd~~~ie~~~-~-----~~~~y~~~~crt~~~~g~~p~g~~~c~~~dkkn~~~ 343 (351)
T COG5063 271 NFRTEPCINWEKSGYCPYGLRCCFKHGDDSDIEMYE-E-----ASLGYLDGPCRTRAKGGAFPSGGAVCKSFDKKNLDF 343 (351)
T ss_pred ccccCCccchhhcccCccccccccccCChhhccccc-c-----ccccccccccccccccCccCCCCchhhccccchhhh
Confidence 356789999999999999999999998764221110 0 000134578999999999999999999999988754
No 16
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=97.83 E-value=7.9e-06 Score=65.15 Aligned_cols=71 Identities=27% Similarity=0.685 Sum_probs=47.8
Q ss_pred ccccccccccccCCCCCCCCCCCCCCCCCCCCCCccCCCCC---C--------CCCCCcccccccCcCcCCCCCCCccCC
Q 033320 12 QPECSYFLRTGDCKYKSNCKYHHPKNRIPKSPPCTLSDKGL---P--------LRPGQNVCSYYSRYGICKFGPACKYDH 80 (122)
Q Consensus 12 ~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~~~~~~~~g~---p--------~~~~~~~C~~f~~~G~C~~G~~Crf~H 80 (122)
..+|.-|+ .|.|...+.|..+|..++.+ .|.|...-.|. | -....++|.-|+++|+|-.|..|+-.|
T Consensus 233 kticpkfl-ngrcnkaedcnlsheldprr-ipacryfllgkcnnpncryvhihysenapicfefakygfcelgtscknqh 310 (377)
T KOG1492|consen 233 KTICPKFL-NGRCNKAEDCNLSHELDPRR-IPACRYFLLGKCNNPNCRYVHIHYSENAPICFEFAKYGFCELGTSCKNQH 310 (377)
T ss_pred cccChHHh-cCccCchhcCCcccccCccc-cchhhhhhhccCCCCCceEEEEeecCCCceeeeehhcceeccccccccce
Confidence 45777777 57788777788888766532 22222211110 1 123578999999999999999999999
Q ss_pred CCCC
Q 033320 81 PIHP 84 (122)
Q Consensus 81 ~~~~ 84 (122)
...-
T Consensus 311 ilqc 314 (377)
T KOG1492|consen 311 ILQC 314 (377)
T ss_pred eeee
Confidence 7653
No 17
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=97.77 E-value=3.5e-05 Score=62.46 Aligned_cols=75 Identities=31% Similarity=0.689 Sum_probs=52.9
Q ss_pred CCccccccccccccCCCCCCCCCCCCCCCCCC-CCCCccC-CCC---------CC---CCCCCcccccccC--cCcCCCC
Q 033320 10 PGQPECSYFLRTGDCKYKSNCKYHHPKNRIPK-SPPCTLS-DKG---------LP---LRPGQNVCSYYSR--YGICKFG 73 (122)
Q Consensus 10 p~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~-~~~~~~~-~~g---------~p---~~~~~~~C~~f~~--~G~C~~G 73 (122)
...++|++|+ .|.|+.|..|.|+|..+.... .++|... ..| .. .......|.+|.. +++|+.|
T Consensus 102 ~s~V~c~~~~-~g~c~s~~~c~~lh~~d~~~s~~~~c~~Fs~~G~cs~g~~c~~~h~dp~~~~~~~~~~~~~~~~f~p~g 180 (285)
T COG5084 102 SSSVVCKFFL-RGLCKSGFSCEFLHEYDLRSSQGPPCRSFSLKGSCSSGPSCGYSHIDPDSFAGNCDQYSGATYGFCPLG 180 (285)
T ss_pred cCCcccchhc-cccCcCCCccccccCCCcccccCCCcccccccceeccCCCCCccccCcccccccccccCcccccccCCC
Confidence 5678999998 599999999999999875442 2233211 111 10 1123567999984 5999999
Q ss_pred CCCccCCCCCCC
Q 033320 74 PACKYDHPIHPD 85 (122)
Q Consensus 74 ~~Crf~H~~~~~ 85 (122)
..|++.|.....
T Consensus 181 ~~c~~~H~~~~~ 192 (285)
T COG5084 181 ASCKFSHTLKRV 192 (285)
T ss_pred Cccccccccccc
Confidence 999999999855
No 18
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=97.54 E-value=4.5e-05 Score=64.53 Aligned_cols=60 Identities=20% Similarity=0.485 Sum_probs=40.1
Q ss_pred CCCCCCCCCCCCCCCC---CCCCCccCC-CC------CCCCCCCcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 25 KYKSNCKYHHPKNRIP---KSPPCTLSD-KG------LPLRPGQNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 25 ~~G~~C~F~H~~~~~~---~~~~~~~~~-~g------~p~~~~~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
.-|++|.+-|..+.-. +.-.+.+.+ .+ .|......+|+||+. |.|+||.+|||+|...-.
T Consensus 97 L~GsKcsaph~ss~gl~yHna~I~g~E~sarvRVlfl~PTh~sMkpC~ffLe-g~CRF~enCRfSHG~~V~ 166 (486)
T KOG2185|consen 97 LDGSKCSAPHTSSRGLYYHNARIIGFEGSARVRVLFLTPTHESMKPCKFFLE-GRCRFGENCRFSHGLDVP 166 (486)
T ss_pred ccCCcccccccCCccceecceeEEeeccccceEEEeecCcchhhccchHhhc-cccccCcccccccCcccc
Confidence 3489999999866421 100000000 11 255556789999999 999999999999987544
No 19
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=97.41 E-value=0.00017 Score=62.49 Aligned_cols=55 Identities=20% Similarity=0.559 Sum_probs=38.4
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 23 DCKYKSNCKYHHPKNRIPKSPPCTLSDKGLPLRPGQNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 23 ~C~~G~~C~F~H~~~~~~~~~~~~~~~~g~p~~~~~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
.|.-+..|.|+|..+..+...+..+ .....+|+.|.+ |.|..|+.|.|.|..-+.
T Consensus 208 ~shDwteCPf~HpgEkARRRDPRky-------hYs~tpCPefrk-G~C~rGD~CEyaHgvfEc 262 (528)
T KOG1595|consen 208 RSHDWTECPFAHPGEKARRRDPRKY-------HYSSTPCPEFRK-GSCERGDSCEYAHGVFEC 262 (528)
T ss_pred cCCCcccCCccCCCcccccCCcccc-------cccCccCccccc-CCCCCCCccccccceehh
Confidence 4566788999997543222111111 145688999998 999999999999977665
No 20
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=97.36 E-value=7.4e-05 Score=63.26 Aligned_cols=31 Identities=29% Similarity=0.896 Sum_probs=27.0
Q ss_pred CCCCCCccccccccccccCCCCCCCCCCCCCC
Q 033320 6 FPERPGQPECSYFLRTGDCKYKSNCKYHHPKN 37 (122)
Q Consensus 6 ~~~rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~ 37 (122)
+|.-..+.+|.||+ .|.|+||.+|||+|...
T Consensus 134 ~PTh~sMkpC~ffL-eg~CRF~enCRfSHG~~ 164 (486)
T KOG2185|consen 134 TPTHESMKPCKFFL-EGRCRFGENCRFSHGLD 164 (486)
T ss_pred cCcchhhccchHhh-ccccccCcccccccCcc
Confidence 46566788999999 69999999999999864
No 21
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=97.35 E-value=8.5e-05 Score=64.18 Aligned_cols=71 Identities=21% Similarity=0.533 Sum_probs=52.8
Q ss_pred ccccccccccccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCC-------------CCCCcccccccCcCc-CCCCCCCc
Q 033320 12 QPECSYFLRTGDCKYKSNCKYHHPKNRIPKSPPCTLSDKGLPL-------------RPGQNVCSYYSRYGI-CKFGPACK 77 (122)
Q Consensus 12 ~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~~~~~~~~g~p~-------------~~~~~~C~~f~~~G~-C~~G~~Cr 77 (122)
.+.|+||+ .-.|++++.|.|.|..+.......|.+...+++- .++..+|.++.+ +. |. -++|-
T Consensus 3 ~~dcyff~-ys~cKk~d~c~~rh~E~al~n~t~C~~w~~~~~C~k~C~YRHSe~~~kr~e~~CYwe~~-p~gC~-k~~Cg 79 (667)
T KOG4791|consen 3 GEDCYFFF-YSTCKKGDSCPFRHCEAALGNETVCTLWQEGRCCRKVCRYRHSEIDKKRSEIPCYWENQ-PTGCQ-KLNCG 79 (667)
T ss_pred cccchhhh-hhhhhccCcCcchhhHHHhcCcchhhhhhhcCcccccccchhhHHhhhcCcccceeecC-CCccC-CCccc
Confidence 46899998 6899999999999997665554455444333211 135678999998 77 86 68999
Q ss_pred cCCCCCCC
Q 033320 78 YDHPIHPD 85 (122)
Q Consensus 78 f~H~~~~~ 85 (122)
|+|..+++
T Consensus 80 fRH~~pPL 87 (667)
T KOG4791|consen 80 FRHNRPPL 87 (667)
T ss_pred cccCCCch
Confidence 99987666
No 22
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=97.34 E-value=0.00022 Score=61.79 Aligned_cols=61 Identities=26% Similarity=0.537 Sum_probs=49.5
Q ss_pred CCccccccccccccCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCCCCcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 10 PGQPECSYFLRTGDCKYKSNCKYHHPKNRIPKSPPCTLSDKGLPLRPGQNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 10 p~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~~~~~~~~g~p~~~~~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
..-.+|.-|.+ |.|..||.|.|+|..-+ |.| .|++.++..|+-- |.|+. .=|-|+|...++
T Consensus 234 Ys~tpCPefrk-G~C~rGD~CEyaHgvfE------cwL----HPa~YRT~~CkDg---~~C~R-rvCfFAH~~eqL 294 (528)
T KOG1595|consen 234 YSSTPCPEFRK-GSCERGDSCEYAHGVFE------CWL----HPARYRTRKCKDG---GYCPR-RVCFFAHSPEQL 294 (528)
T ss_pred ccCccCccccc-CCCCCCCccccccceeh------hhc----CHHHhccccccCC---CCCcc-ceEeeecChHHh
Confidence 45679999985 99999999999999754 222 2556788999874 88998 789999998877
No 23
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=97.31 E-value=0.00088 Score=54.41 Aligned_cols=67 Identities=21% Similarity=0.438 Sum_probs=42.1
Q ss_pred CCccccccccccccCCCCCCCCCCCCCCCCCCCCCCccCC---CCC--------------CCCCCCcccccccCcCcCCC
Q 033320 10 PGQPECSYFLRTGDCKYKSNCKYHHPKNRIPKSPPCTLSD---KGL--------------PLRPGQNVCSYYSRYGICKF 72 (122)
Q Consensus 10 p~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~~~~~~~~~~---~g~--------------p~~~~~~~C~~f~~~G~C~~ 72 (122)
+-...|++|...|.|..|..|.+.|..... ....++.+. .++ .......+|.+|+- ++|+.
T Consensus 132 s~~~~c~~Fs~~G~cs~g~~c~~~h~dp~~-~~~~~~~~~~~~~~f~p~g~~c~~~H~~~~~~~~~~p~~~y~~-~fsP~ 209 (285)
T COG5084 132 SQGPPCRSFSLKGSCSSGPSCGYSHIDPDS-FAGNCDQYSGATYGFCPLGASCKFSHTLKRVSYGSSPCGNYTP-PFSPP 209 (285)
T ss_pred ccCCCcccccccceeccCCCCCccccCccc-ccccccccCcccccccCCCCccccccccccccccccccccCcC-CcCCC
Confidence 357899999547999999999999985221 112222221 111 01111227999998 99998
Q ss_pred CCCCcc
Q 033320 73 GPACKY 78 (122)
Q Consensus 73 G~~Crf 78 (122)
|..=-+
T Consensus 210 g~~~~~ 215 (285)
T COG5084 210 GTPSES 215 (285)
T ss_pred CCCccc
Confidence 875433
No 24
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=97.18 E-value=0.00026 Score=35.26 Aligned_cols=19 Identities=32% Similarity=0.908 Sum_probs=16.6
Q ss_pred ccccccccccCCCCCCCCCCCC
Q 033320 14 ECSYFLRTGDCKYKSNCKYHHP 35 (122)
Q Consensus 14 ~Cr~f~k~G~C~~G~~C~F~H~ 35 (122)
+|+||.. |++|++|.|+|.
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 5998872 999999999995
No 25
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=97.05 E-value=0.00041 Score=34.51 Aligned_cols=19 Identities=32% Similarity=0.978 Sum_probs=16.7
Q ss_pred ccccccCcCcCCCCCCCccCCC
Q 033320 60 VCSYYSRYGICKFGPACKYDHP 81 (122)
Q Consensus 60 ~C~~f~~~G~C~~G~~Crf~H~ 81 (122)
+|+||.. |++|++|.|.|+
T Consensus 1 ~Ck~~~~---C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN---CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC---CCCCCcCccCCc
Confidence 5888875 999999999995
No 26
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=97.00 E-value=0.00021 Score=55.87 Aligned_cols=32 Identities=25% Similarity=0.603 Sum_probs=27.2
Q ss_pred CCCCccccccccccccCCCCCCCCCCCCCCCC
Q 033320 8 ERPGQPECSYFLRTGDCKYKSNCKYHHPKNRI 39 (122)
Q Consensus 8 ~rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~ 39 (122)
......+|+.|..+|.|-||+.|+|+|+.+..
T Consensus 137 iD~qpdVCKdyk~TGYCGYGDsCKflH~R~D~ 168 (259)
T COG5152 137 IDTQPDVCKDYKETGYCGYGDSCKFLHDRSDF 168 (259)
T ss_pred eecCcccccchhhcccccCCchhhhhhhhhhh
Confidence 34456799999889999999999999998754
No 27
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=96.30 E-value=0.0013 Score=54.23 Aligned_cols=43 Identities=21% Similarity=0.349 Sum_probs=33.0
Q ss_pred CCcccccccCcCcCCCCCC-CccCCCCCCCCCCCCCCCCCCCCCCCCcc
Q 033320 57 GQNVCSYYSRYGICKFGPA-CKYDHPIHPDASAEYGLDPPPSFGDSTTR 104 (122)
Q Consensus 57 ~~~~C~~f~~~G~C~~G~~-Crf~H~~~~~~~~~~~~~~~~~~~n~~~~ 104 (122)
...+||-|++ |.|..|++ |+|.|+..... ++.-.-.+|-|+.+
T Consensus 36 ~~eVCReF~r-n~C~R~d~~CkfaHP~~~~~----V~~g~v~aC~Ds~k 79 (331)
T KOG2494|consen 36 TLEVCREFLR-NTCSRGDRECKFAHPPKNCQ----VSNGRVIACFDSQK 79 (331)
T ss_pred HHHHHHHHHh-ccccCCCccccccCCCCCCC----ccCCeEEEEecccc
Confidence 4579999999 99999999 99999998663 33334556666544
No 28
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.56 E-value=0.0045 Score=51.48 Aligned_cols=25 Identities=40% Similarity=1.145 Sum_probs=24.0
Q ss_pred cccccccCcCcCCCCCCCccCCCCCC
Q 033320 59 NVCSYYSRYGICKFGPACKYDHPIHP 84 (122)
Q Consensus 59 ~~C~~f~~~G~C~~G~~Crf~H~~~~ 84 (122)
.+|++|++ |.|+||+.|||.|+.+.
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 89999999 99999999999999984
No 29
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=95.49 E-value=0.0047 Score=51.37 Aligned_cols=24 Identities=29% Similarity=0.908 Sum_probs=22.6
Q ss_pred cccccccccccCCCCCCCCCCCCCC
Q 033320 13 PECSYFLRTGDCKYKSNCKYHHPKN 37 (122)
Q Consensus 13 ~~Cr~f~k~G~C~~G~~C~F~H~~~ 37 (122)
.+|+||++ |.|++|+.|+|+|+..
T Consensus 9 tic~~~~~-g~c~~g~~cr~~h~~~ 32 (344)
T KOG1039|consen 9 TICKYYQK-GNCKFGDLCRLSHSLP 32 (344)
T ss_pred hhhhhccc-ccccccceeeeeccCc
Confidence 79999996 9999999999999976
No 30
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=95.33 E-value=0.0057 Score=47.92 Aligned_cols=28 Identities=32% Similarity=0.742 Sum_probs=24.8
Q ss_pred CcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 58 QNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 58 ~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
..+|+-|..+|+|-||+.|+|.|.+...
T Consensus 141 pdVCKdyk~TGYCGYGDsCKflH~R~D~ 168 (259)
T COG5152 141 PDVCKDYKETGYCGYGDSCKFLHDRSDF 168 (259)
T ss_pred cccccchhhcccccCCchhhhhhhhhhh
Confidence 3579999999999999999999988743
No 31
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.96 E-value=0.0068 Score=49.57 Aligned_cols=30 Identities=27% Similarity=0.613 Sum_probs=26.5
Q ss_pred CCccccccccccccCCCCCCCCCCCCCCCC
Q 033320 10 PGQPECSYFLRTGDCKYKSNCKYHHPKNRI 39 (122)
Q Consensus 10 p~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~ 39 (122)
....+|+.|..+|.|-||+.|+|+|+...+
T Consensus 184 ~qpDicKdykeTgycg~gdSckFlh~r~Dy 213 (313)
T KOG1813|consen 184 YQPDICKDYKETGYCGYGDSCKFLHDRSDY 213 (313)
T ss_pred cCchhhhhhHhhCcccccchhhhhhhhhhc
Confidence 455799999889999999999999998765
No 32
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=93.94 E-value=0.017 Score=47.51 Aligned_cols=30 Identities=30% Similarity=0.892 Sum_probs=26.2
Q ss_pred CCCCcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 55 RPGQNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 55 ~~~~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
.+.+.+|.||.. |.|..|+.|+|+|.....
T Consensus 89 DPKSvvCafFk~-g~C~KG~kCKFsHdl~~~ 118 (343)
T KOG1763|consen 89 DPKSVVCAFFKQ-GTCTKGDKCKFSHDLAVE 118 (343)
T ss_pred CchHHHHHHHhc-cCCCCCCcccccchHHHh
Confidence 356789999998 999999999999987554
No 33
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=93.58 E-value=0.024 Score=45.47 Aligned_cols=33 Identities=24% Similarity=0.680 Sum_probs=26.8
Q ss_pred CCCCCCccccccccccccCCCCCCCCCCCCCCC
Q 033320 6 FPERPGQPECSYFLRTGDCKYKSNCKYHHPKNR 38 (122)
Q Consensus 6 ~~~rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~~ 38 (122)
|......+-|.||.++|.|++|+.|-=.|....
T Consensus 9 fgtekdKv~c~fy~k~gacR~gdrcsR~h~kpt 41 (260)
T KOG2202|consen 9 FGTEKDKVNCSFYFKIGACRHGDRCSRLHEKPT 41 (260)
T ss_pred hcccccccccchHHhhcccccccHHHHhhcccc
Confidence 334456788999999999999999988887644
No 34
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.01 E-value=0.028 Score=46.06 Aligned_cols=28 Identities=29% Similarity=0.758 Sum_probs=24.8
Q ss_pred CcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 58 QNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 58 ~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
..+|+-|..||+|-||++|+|.|.+...
T Consensus 186 pDicKdykeTgycg~gdSckFlh~r~Dy 213 (313)
T KOG1813|consen 186 PDICKDYKETGYCGYGDSCKFLHDRSDY 213 (313)
T ss_pred chhhhhhHhhCcccccchhhhhhhhhhc
Confidence 3579999999999999999999988644
No 35
>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=92.76 E-value=0.073 Score=27.79 Aligned_cols=22 Identities=36% Similarity=0.913 Sum_probs=18.1
Q ss_pred cccccccccccCCCCCCCCCCCC
Q 033320 13 PECSYFLRTGDCKYKSNCKYHHP 35 (122)
Q Consensus 13 ~~Cr~f~k~G~C~~G~~C~F~H~ 35 (122)
++|.|-+..|.|.. +.|.|.|-
T Consensus 1 ~lC~yEl~Gg~Cnd-~~C~~QHf 22 (23)
T PF10650_consen 1 PLCPYELTGGVCND-PDCEFQHF 22 (23)
T ss_pred CCCccccCCCeeCC-CCCCcccc
Confidence 48999996559986 77999995
No 36
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=91.76 E-value=0.11 Score=43.50 Aligned_cols=33 Identities=33% Similarity=0.828 Sum_probs=28.5
Q ss_pred CCCCCCCCccccccccccccCCCCCCCCCCCCCC
Q 033320 4 DEFPERPGQPECSYFLRTGDCKYKSNCKYHHPKN 37 (122)
Q Consensus 4 ~~~~~rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~ 37 (122)
..|..+....+|.||++ |.|++|+.|.|.|...
T Consensus 153 ~p~ykrn~p~Icsf~v~-geckRG~ec~yrhEkp 185 (377)
T KOG0153|consen 153 TPYYKRNRPHICSFFVK-GECKRGAECPYRHEKP 185 (377)
T ss_pred CccccCCCCccccceee-ccccccccccccccCC
Confidence 45567778889999995 8999999999999865
No 37
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=90.57 E-value=0.27 Score=43.05 Aligned_cols=72 Identities=14% Similarity=0.165 Sum_probs=46.4
Q ss_pred Ccccccccccccc-CCCCCCCCCCCCCCCCC----CCC-CCccCCCC--C--C---CCCCCcccccccCcCcCCCCCCCc
Q 033320 11 GQPECSYFLRTGD-CKYKSNCKYHHPKNRIP----KSP-PCTLSDKG--L--P---LRPGQNVCSYYSRYGICKFGPACK 77 (122)
Q Consensus 11 ~~~~Cr~f~k~G~-C~~G~~C~F~H~~~~~~----~~~-~~~~~~~g--~--p---~~~~~~~C~~f~~~G~C~~G~~Cr 77 (122)
....|+|+.+ +. |.. .+|-|.|...++. ..+ +......+ + + ....-.+|-+|++ |.|-.++-|-
T Consensus 60 ~e~~CYwe~~-p~gC~k-~~CgfRH~~pPLkg~l~~~p~~pe~ev~~~~~SAq~~sV~~~p~P~l~~~K-~~e~~~D~~s 136 (667)
T KOG4791|consen 60 SEIPCYWENQ-PTGCQK-LNCGFRHNRPPLKGVLPTVPESPEEEVKASQLSAQQNSVQSNPSPQLRSVK-KVESSEDVPS 136 (667)
T ss_pred CcccceeecC-CCccCC-CccccccCCCchhhhccCCCCCcccccccccccCCCcccccCCchHHHHhh-hhhhhccccc
Confidence 5678999985 66 996 8999999543321 111 00011111 0 0 1112357999999 9999999999
Q ss_pred cCCCCCCC
Q 033320 78 YDHPIHPD 85 (122)
Q Consensus 78 f~H~~~~~ 85 (122)
|.|+....
T Consensus 137 ~Lh~P~A~ 144 (667)
T KOG4791|consen 137 PLHPPVAI 144 (667)
T ss_pred cCCCCccc
Confidence 99988554
No 38
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=84.67 E-value=0.51 Score=39.65 Aligned_cols=27 Identities=41% Similarity=1.048 Sum_probs=24.3
Q ss_pred CcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 58 QNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 58 ~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
..+|.||.. |.|+.|+.|.|.|..++.
T Consensus 161 p~Icsf~v~-geckRG~ec~yrhEkp~d 187 (377)
T KOG0153|consen 161 PHICSFFVK-GECKRGAECPYRHEKPPD 187 (377)
T ss_pred Cccccceee-ccccccccccccccCCCC
Confidence 458999999 999999999999999954
No 39
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=82.07 E-value=2.1 Score=38.61 Aligned_cols=25 Identities=36% Similarity=0.911 Sum_probs=18.4
Q ss_pred CccccccccccccCCCCCCCCCCCCCCCC
Q 033320 11 GQPECSYFLRTGDCKYKSNCKYHHPKNRI 39 (122)
Q Consensus 11 ~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~ 39 (122)
..+-|.|=.+ |.. ..|.|+|.....
T Consensus 584 s~p~Ck~~~k---Cta-sDC~~sH~~~~~ 608 (681)
T KOG3702|consen 584 SHPGCKFGKK---CTA-SDCNYSHAGRRI 608 (681)
T ss_pred cccccccccc---ccc-ccCcccccCCCC
Confidence 4557888864 888 569999987654
No 40
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=80.61 E-value=0.7 Score=37.21 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=24.3
Q ss_pred CCCccccccccccccCCCCCCCCCCCCCC
Q 033320 9 RPGQPECSYFLRTGDCKYKSNCKYHHPKN 37 (122)
Q Consensus 9 rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~ 37 (122)
++....|..|.+ +.|.+|..|.|.|...
T Consensus 149 ~~rea~C~~~e~-~~C~rG~~CnFmH~k~ 176 (260)
T KOG2202|consen 149 DFREAICGQFER-TECSRGGACNFMHVKR 176 (260)
T ss_pred chhhhhhccccc-ccCCCCCcCcchhhhh
Confidence 466779999995 7999999999999963
No 41
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=80.53 E-value=3.9 Score=36.99 Aligned_cols=58 Identities=29% Similarity=0.661 Sum_probs=31.2
Q ss_pred CCCCCCCCCCCCCCCCCC---CCCCccCCCC--CCC-----------CCCCcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 24 CKYKSNCKYHHPKNRIPK---SPPCTLSDKG--LPL-----------RPGQNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 24 C~~G~~C~F~H~~~~~~~---~~~~~~~~~g--~p~-----------~~~~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
|.+++.|.++|..-...+ ...|.+...+ .|. .....+|+|+- .|+ -..|+|.|+..--
T Consensus 575 k~fa~~~~ks~p~Ck~~~kCtasDC~~sH~~~~~pvq~t~ip~~~~~~ti~~~CrY~p---nCr-nm~C~F~HPk~cR 648 (681)
T KOG3702|consen 575 KKFASKCLKSHPGCKFGKKCTASDCNYSHAGRRIPVQPTRIPPPFPGGTIRGLCRYRP---NCR-NMQCKFYHPKTCR 648 (681)
T ss_pred ccccccceecccccccccccccccCcccccCCCCCCccccCCCCCCCCCccccceecc---CcC-CccccccCCcccc
Confidence 788999999998643221 2334332211 111 11234566643 354 3567888877655
No 42
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=76.59 E-value=0.68 Score=37.31 Aligned_cols=30 Identities=30% Similarity=0.657 Sum_probs=25.7
Q ss_pred CCCCcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 55 RPGQNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 55 ~~~~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
.+.+.+|..|+. +.|..|+.|.|+|...+.
T Consensus 82 dpK~~vcalF~~-~~c~kg~~ckF~h~~ee~ 111 (299)
T COG5252 82 DPKTVVCALFLN-KTCAKGDACKFAHGKEEA 111 (299)
T ss_pred CchhHHHHHhcc-CccccCchhhhhcchHHH
Confidence 356789999998 999999999999986544
No 43
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=57.11 E-value=4.7 Score=35.68 Aligned_cols=22 Identities=32% Similarity=0.833 Sum_probs=20.0
Q ss_pred cccccccccccCCCCCCCCCCC
Q 033320 13 PECSYFLRTGDCKYKSNCKYHH 34 (122)
Q Consensus 13 ~~Cr~f~k~G~C~~G~~C~F~H 34 (122)
+-|.+|...|.|.+|-+|||+-
T Consensus 115 ~~Cp~f~s~G~Cp~G~~CRFl~ 136 (614)
T KOG2333|consen 115 PSCPVFESLGFCPYGFKCRFLG 136 (614)
T ss_pred CccceeeccccCCccceeehhh
Confidence 6799998889999999999974
No 44
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=40.84 E-value=10 Score=32.21 Aligned_cols=29 Identities=24% Similarity=0.519 Sum_probs=23.6
Q ss_pred CccccccccccccCCCCCCCCCCCCCCCCC
Q 033320 11 GQPECSYFLRTGDCKYKSNCKYHHPKNRIP 40 (122)
Q Consensus 11 ~~~~Cr~f~k~G~C~~G~~C~F~H~~~~~~ 40 (122)
.++.|.+|+|.-.|.+++ |-|+|...+..
T Consensus 201 TTKYCtsYLRn~~CpNp~-CMyLHEpg~e~ 229 (480)
T COG5175 201 TTKYCTSYLRNAVCPNPD-CMYLHEPGPEK 229 (480)
T ss_pred chHHHHHHHcCCCCCCCC-eeeecCCCccc
Confidence 357899999988899865 99999986643
No 45
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=31.83 E-value=15 Score=29.22 Aligned_cols=16 Identities=31% Similarity=0.924 Sum_probs=13.7
Q ss_pred CCcccccccCcCcCCCC
Q 033320 57 GQNVCSYYSRYGICKFG 73 (122)
Q Consensus 57 ~~~~C~~f~~~G~C~~G 73 (122)
...+|++|+- |+||+.
T Consensus 29 D~~VCk~~L~-g~CPhd 44 (254)
T PF03194_consen 29 DPDVCKYFLV-GFCPHD 44 (254)
T ss_pred CcccCHHHHh-CCCcHH
Confidence 3579999998 999975
No 46
>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=30.36 E-value=14 Score=19.67 Aligned_cols=9 Identities=44% Similarity=1.224 Sum_probs=5.4
Q ss_pred cCCCCCCCc
Q 033320 69 ICKFGPACK 77 (122)
Q Consensus 69 ~C~~G~~Cr 77 (122)
.|+||.+|-
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 488999884
No 47
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=26.79 E-value=21 Score=28.44 Aligned_cols=15 Identities=33% Similarity=0.773 Sum_probs=13.1
Q ss_pred CcccccccCcCcCCCC
Q 033320 58 QNVCSYYSRYGICKFG 73 (122)
Q Consensus 58 ~~~C~~f~~~G~C~~G 73 (122)
..+|+.|+- |+|||.
T Consensus 31 ~kvC~s~Lv-g~CP~d 45 (258)
T COG5200 31 KKVCISMLV-GFCPFD 45 (258)
T ss_pred hHHHHHHHH-ccCcHH
Confidence 489999998 999974
No 48
>KOG2135 consensus Proteins containing the RNA recognition motif [General function prediction only]
Probab=26.45 E-value=26 Score=30.87 Aligned_cols=29 Identities=17% Similarity=0.201 Sum_probs=25.3
Q ss_pred CCccccccccccccCCCCCCCCCCCCCCC
Q 033320 10 PGQPECSYFLRTGDCKYKSNCKYHHPKNR 38 (122)
Q Consensus 10 p~~~~Cr~f~k~G~C~~G~~C~F~H~~~~ 38 (122)
.....|++|.++|.|..|+.|++.|....
T Consensus 210 ~s~~r~k~fee~g~~~r~el~p~~hg~~~ 238 (526)
T KOG2135|consen 210 NSENRRKFFEEFGVLERGELCPTHHGCVP 238 (526)
T ss_pred ccHHhhhhhHhhceeeeccccccccccce
Confidence 44568999999999999999999998764
No 49
>KOG3777 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.01 E-value=43 Score=29.11 Aligned_cols=26 Identities=31% Similarity=0.850 Sum_probs=20.6
Q ss_pred CCcccccccCcCcCCCCCCCccCCCCCCC
Q 033320 57 GQNVCSYYSRYGICKFGPACKYDHPIHPD 85 (122)
Q Consensus 57 ~~~~C~~f~~~G~C~~G~~Crf~H~~~~~ 85 (122)
+..+|.+-.+ |+||.+|+|.|+....
T Consensus 170 ~~q~Cpygkk---ctyg~kck~~h~~~~~ 195 (443)
T KOG3777|consen 170 NKQPCPYGKK---CTYGGKCKFYHPEIAR 195 (443)
T ss_pred cccCCCcccc---cCCCCceeeccccccc
Confidence 4567987554 9999999999987555
No 50
>KOG3777 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.19 E-value=59 Score=28.25 Aligned_cols=24 Identities=33% Similarity=0.877 Sum_probs=18.8
Q ss_pred CccccccccccccCCCCCCCCCCCCCC
Q 033320 11 GQPECSYFLRTGDCKYKSNCKYHHPKN 37 (122)
Q Consensus 11 ~~~~Cr~f~k~G~C~~G~~C~F~H~~~ 37 (122)
...+|.+=. +|.||.+|+|.|...
T Consensus 170 ~~q~Cpygk---kctyg~kck~~h~~~ 193 (443)
T KOG3777|consen 170 NKQPCPYGK---KCTYGGKCKFYHPEI 193 (443)
T ss_pred cccCCCccc---ccCCCCceeeccccc
Confidence 346787765 499999999999864
No 51
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=20.04 E-value=57 Score=23.96 Aligned_cols=28 Identities=18% Similarity=0.217 Sum_probs=22.0
Q ss_pred CCCccccccccccccCCCCCCCCCCCCCCC
Q 033320 9 RPGQPECSYFLRTGDCKYKSNCKYHHPKNR 38 (122)
Q Consensus 9 rp~~~~Cr~f~k~G~C~~G~~C~F~H~~~~ 38 (122)
-|.-..|.-=. .+.|-+| .|.|.++.+.
T Consensus 39 ~~~i~~Cp~ey-~~YClHG-~C~yI~dl~~ 66 (139)
T PHA03099 39 IPAIRLCGPEG-DGYCLHG-DCIHARDIDG 66 (139)
T ss_pred CcccccCChhh-CCEeECC-EEEeeccCCC
Confidence 35567888777 4899999 7999999763
Done!