Query 042538
Match_columns 167
No_of_seqs 111 out of 356
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 07:09:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042538.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042538hhsearch_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 99.3 5.2E-13 1.1E-17 112.9 2.7 51 1-51 153-207 (332)
2 PF00642 zf-CCCH: Zinc finger 98.8 1E-09 2.2E-14 65.0 -0.5 26 20-45 1-27 (27)
3 COG5063 CTH1 CCCH-type Zn-fing 98.7 3.4E-09 7.3E-14 94.6 2.2 45 3-50 258-303 (351)
4 smart00356 ZnF_C3H1 zinc finge 98.4 1.9E-07 4.1E-12 53.2 1.9 26 20-45 2-27 (27)
5 KOG1677 CCCH-type Zn-finger pr 97.3 0.00011 2.4E-09 62.5 2.4 33 17-49 127-161 (332)
6 COG5063 CTH1 CCCH-type Zn-fing 96.6 0.0011 2.3E-08 60.0 2.1 46 1-50 135-182 (351)
7 COG5152 Uncharacterized conser 96.4 0.0013 2.8E-08 57.0 1.3 37 22-58 141-179 (259)
8 KOG1595 CCCH-type Zn-finger pr 95.9 0.0056 1.2E-07 58.1 2.7 50 1-53 217-267 (528)
9 PF14608 zf-CCCH_2: Zinc finge 94.9 0.016 3.5E-07 32.1 1.4 19 24-44 1-19 (19)
10 KOG1595 CCCH-type Zn-finger pr 94.2 0.054 1.2E-06 51.6 4.2 40 1-48 255-294 (528)
11 KOG1813 Predicted E3 ubiquitin 91.8 0.05 1.1E-06 49.0 0.0 58 20-77 184-243 (313)
12 KOG2185 Predicted RNA-processi 90.2 0.12 2.6E-06 48.7 1.0 39 21-60 139-179 (486)
13 COG5252 Uncharacterized conser 87.5 0.17 3.8E-06 44.9 0.0 53 1-53 104-183 (299)
14 KOG2494 C3H1-type Zn-finger pr 87.2 0.19 4E-06 45.7 0.1 26 22-47 37-63 (331)
15 KOG1039 Predicted E3 ubiquitin 84.7 0.41 8.8E-06 43.4 0.9 25 23-47 9-33 (344)
16 KOG2202 U2 snRNP splicing fact 81.8 0.57 1.2E-05 41.4 0.6 28 20-47 150-177 (260)
17 KOG2333 Uncharacterized conser 79.6 0.78 1.7E-05 44.4 0.8 26 21-46 75-103 (614)
18 KOG1763 Uncharacterized conser 79.0 0.57 1.2E-05 42.6 -0.2 27 20-46 90-116 (343)
19 KOG1040 Polyadenylation factor 71.6 1.6 3.4E-05 39.4 0.5 27 19-45 74-100 (325)
20 KOG2333 Uncharacterized conser 68.4 2.1 4.5E-05 41.6 0.6 22 23-44 115-137 (614)
21 KOG1763 Uncharacterized conser 66.1 2.3 5E-05 38.9 0.5 30 23-52 157-197 (343)
22 COG5252 Uncharacterized conser 56.8 3 6.5E-05 37.3 -0.5 27 20-46 83-109 (299)
23 PF10283 zf-CCHH: Zinc-finger 52.8 3.9 8.4E-05 24.7 -0.3 9 32-40 2-10 (26)
24 KOG1492 C3H1-type Zn-finger pr 45.7 10 0.00022 34.2 1.0 27 22-48 206-233 (377)
25 KOG3777 Uncharacterized conser 43.9 12 0.00026 35.4 1.3 18 31-48 178-195 (443)
26 COG5084 YTH1 Cleavage and poly 37.0 21 0.00045 31.9 1.7 29 20-48 102-130 (285)
27 COG5084 YTH1 Cleavage and poly 34.3 29 0.00062 31.1 2.1 23 23-45 135-158 (285)
28 PF08157 NUC129: NUC129 domain 30.3 16 0.00035 26.3 -0.1 16 136-151 17-32 (63)
29 KOG1039 Predicted E3 ubiquitin 29.7 29 0.00062 31.7 1.3 30 21-50 248-279 (344)
30 KOG2494 C3H1-type Zn-finger pr 28.4 43 0.00094 30.8 2.2 27 20-47 69-95 (331)
31 KOG2202 U2 snRNP splicing fact 23.3 29 0.00063 30.9 0.2 28 23-50 16-44 (260)
32 COG1908 FrhD Coenzyme F420-red 21.0 45 0.00097 27.1 0.8 15 32-47 61-75 (132)
33 PHA03099 epidermal growth fact 20.8 45 0.00099 27.3 0.8 25 22-47 42-66 (139)
34 PF12363 DUF3647: Phage protei 20.5 26 0.00056 26.6 -0.6 23 121-144 57-79 (113)
No 1
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=99.33 E-value=5.2e-13 Score=112.91 Aligned_cols=51 Identities=47% Similarity=0.772 Sum_probs=41.2
Q ss_pred CCCCcccccCC---CCCCCCCcccccccccc-cccccCCCCCCeecCCCCChhHH
Q 042538 1 FAHGKEELRST---LFPTTKNKSEAQICKSF-TTGSCIYGSKCRFIHQVMTDSAL 51 (167)
Q Consensus 1 FAHG~eELR~~---~~P~~knKYKTklCk~F-~tG~CPYG~RC~FiH~~~~~aa~ 51 (167)
||||.+|||.. ......++|||++|.+| .+|.|+||.||+|||+.++..+.
T Consensus 153 fah~~~e~r~~~~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~~~~~ 207 (332)
T KOG1677|consen 153 FAHGLEELRLPSSENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPEDRAS 207 (332)
T ss_pred hcCCcccccccccchhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCcccccc
Confidence 89999999933 11222356999999999 88999999999999999866543
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=98.76 E-value=1e-09 Score=64.96 Aligned_cols=26 Identities=42% Similarity=1.060 Sum_probs=21.3
Q ss_pred ccccccccc-cccccCCCCCCeecCCC
Q 042538 20 SEAQICKSF-TTGSCIYGSKCRFIHQV 45 (167)
Q Consensus 20 YKTklCk~F-~tG~CPYG~RC~FiH~~ 45 (167)
||+++|+.| .+|.|+||++|.|+|+.
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 689999999 88999999999999973
No 3
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=98.75 E-value=3.4e-09 Score=94.59 Aligned_cols=45 Identities=33% Similarity=0.636 Sum_probs=39.5
Q ss_pred CCcccccCCCCCCCCCcccccccccc-cccccCCCCCCeecCCCCChhH
Q 042538 3 HGKEELRSTLFPTTKNKSEAQICKSF-TTGSCIYGSKCRFIHQVMTDSA 50 (167)
Q Consensus 3 HG~eELR~~~~P~~knKYKTklCk~F-~tG~CPYG~RC~FiH~~~~~aa 50 (167)
||..||.... .++.|||++|.+| ..|+|+||.||+|.|+.+.+..
T Consensus 258 HGlN~l~~k~---k~~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~ie 303 (351)
T COG5063 258 HGLNELKSKK---KKQNFRTEPCINWEKSGYCPYGLRCCFKHGDDSDIE 303 (351)
T ss_pred cccccccccc---cccccccCCccchhhcccCccccccccccCChhhcc
Confidence 9999999863 2567999999999 9999999999999999987643
No 4
>smart00356 ZnF_C3H1 zinc finger.
Probab=98.37 E-value=1.9e-07 Score=53.16 Aligned_cols=26 Identities=38% Similarity=1.055 Sum_probs=24.2
Q ss_pred ccccccccccccccCCCCCCeecCCC
Q 042538 20 SEAQICKSFTTGSCIYGSKCRFIHQV 45 (167)
Q Consensus 20 YKTklCk~F~tG~CPYG~RC~FiH~~ 45 (167)
+|+.+|+.|.+|.|++|.+|+|+|..
T Consensus 2 ~k~~~C~~~~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 2 YKTELCKFFKRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCcCcCccCCCCCCCCCcCCCCcC
Confidence 78999999999999999999999973
No 5
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=97.35 E-value=0.00011 Score=62.47 Aligned_cols=33 Identities=33% Similarity=0.878 Sum_probs=30.0
Q ss_pred CCcccccccccc-cccccCC-CCCCeecCCCCChh
Q 042538 17 KNKSEAQICKSF-TTGSCIY-GSKCRFIHQVMTDS 49 (167)
Q Consensus 17 knKYKTklCk~F-~tG~CPY-G~RC~FiH~~~~~a 49 (167)
...|||.+|..| .+|.|.| |.+|+|.|+.....
T Consensus 127 p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r 161 (332)
T KOG1677|consen 127 PERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELR 161 (332)
T ss_pred cccccCCcceeeecCccccccCchhhhcCCccccc
Confidence 357999999999 9999999 99999999998765
No 6
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=96.63 E-value=0.0011 Score=59.99 Aligned_cols=46 Identities=30% Similarity=0.475 Sum_probs=40.3
Q ss_pred CCCCcccccCCC-CCCCCCcccccccccc-cccccCCCCCCeecCCCCChhH
Q 042538 1 FAHGKEELRSTL-FPTTKNKSEAQICKSF-TTGSCIYGSKCRFIHQVMTDSA 50 (167)
Q Consensus 1 FAHG~eELR~~~-~P~~knKYKTklCk~F-~tG~CPYG~RC~FiH~~~~~aa 50 (167)
|||...+++-.. |+ ||||+-|..| ..|+|||+.||.|+|-.-++.+
T Consensus 135 fahs~~issl~~~~~----K~kt~slev~in~~~vp~s~~~~~~slP~t~~~ 182 (351)
T COG5063 135 FAHSKAISSLAQTHP----KYKTESLEVFINPGYVPYSKRCCFISLPLTDIN 182 (351)
T ss_pred CCCccccccccccCc----cccccceeEEecCCccccccccccccccccccC
Confidence 899999998876 44 5999999999 9999999999999999887643
No 7
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=96.41 E-value=0.0013 Score=56.99 Aligned_cols=37 Identities=30% Similarity=0.680 Sum_probs=28.7
Q ss_pred ccccccc-cccccCCCCCCeecCCCCChhHH-Hhhcccc
Q 042538 22 AQICKSF-TTGSCIYGSKCRFIHQVMTDSAL-VLTIQME 58 (167)
Q Consensus 22 TklCk~F-~tG~CPYG~RC~FiH~~~~~aa~-~~~~q~e 58 (167)
-.+|+.| .+|+|-||+.|.|+|.-..-.+. .+.+-|.
T Consensus 141 pdVCKdyk~TGYCGYGDsCKflH~R~D~KtGWkLn~EWn 179 (259)
T COG5152 141 PDVCKDYKETGYCGYGDSCKFLHDRSDFKTGWKLNQEWN 179 (259)
T ss_pred cccccchhhcccccCCchhhhhhhhhhhhcccccchhhc
Confidence 3589999 99999999999999987643322 5556664
No 8
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=95.87 E-value=0.0056 Score=58.08 Aligned_cols=50 Identities=32% Similarity=0.586 Sum_probs=40.2
Q ss_pred CCC-CcccccCCCCCCCCCcccccccccccccccCCCCCCeecCCCCChhHHHh
Q 042538 1 FAH-GKEELRSTLFPTTKNKSEAQICKSFTTGSCIYGSKCRFIHQVMTDSALVL 53 (167)
Q Consensus 1 FAH-G~eELR~~~~P~~knKYKTklCk~F~tG~CPYG~RC~FiH~~~~~aa~~~ 53 (167)
||| |+..-|.. |+ |.+|....|=.|..|.|.=|+-|+|.|+.-+.-++-+
T Consensus 217 f~HpgEkARRRD--PR-kyhYs~tpCPefrkG~C~rGD~CEyaHgvfEcwLHPa 267 (528)
T KOG1595|consen 217 FAHPGEKARRRD--PR-KYHYSSTPCPEFRKGSCERGDSCEYAHGVFECWLHPA 267 (528)
T ss_pred ccCCCcccccCC--cc-cccccCccCcccccCCCCCCCccccccceehhhcCHH
Confidence 889 88877765 55 7889999999997799999999999999877554433
No 9
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=94.91 E-value=0.016 Score=32.07 Aligned_cols=19 Identities=37% Similarity=0.767 Sum_probs=15.4
Q ss_pred ccccccccccCCCCCCeecCC
Q 042538 24 ICKSFTTGSCIYGSKCRFIHQ 44 (167)
Q Consensus 24 lCk~F~tG~CPYG~RC~FiH~ 44 (167)
+|+.|.. |++|+.|.|+|+
T Consensus 1 ~Ck~~~~--C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN--CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC--CCCCCcCccCCc
Confidence 4785533 999999999996
No 10
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=94.25 E-value=0.054 Score=51.61 Aligned_cols=40 Identities=30% Similarity=0.459 Sum_probs=33.4
Q ss_pred CCCCcccccCCCCCCCCCcccccccccccccccCCCCCCeecCCCCCh
Q 042538 1 FAHGKEELRSTLFPTTKNKSEAQICKSFTTGSCIYGSKCRFIHQVMTD 48 (167)
Q Consensus 1 FAHG~eELR~~~~P~~knKYKTklCk~F~tG~CPYG~RC~FiH~~~~~ 48 (167)
||||.=|-.- ||- .|||++||.= |+|+- .=|-|+|..+.-
T Consensus 255 yaHgvfEcwL--HPa---~YRT~~CkDg--~~C~R-rvCfFAH~~eqL 294 (528)
T KOG1595|consen 255 YAHGVFECWL--HPA---RYRTRKCKDG--GYCPR-RVCFFAHSPEQL 294 (528)
T ss_pred cccceehhhc--CHH---HhccccccCC--CCCcc-ceEeeecChHHh
Confidence 8999988553 564 4999999986 99999 999999998753
No 11
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=91.75 E-value=0.05 Score=48.96 Aligned_cols=58 Identities=28% Similarity=0.547 Sum_probs=36.0
Q ss_pred ccccccccc-cccccCCCCCCeecCCCCChhH-HHhhccccccccCCccccCCCcccccC
Q 042538 20 SEAQICKSF-TTGSCIYGSKCRFIHQVMTDSA-LVLTIQMEDHSMKACVCESPVTPVTFK 77 (167)
Q Consensus 20 YKTklCk~F-~tG~CPYG~RC~FiH~~~~~aa-~~~~~q~e~s~~p~~~~~sp~~~~~~~ 77 (167)
|--.+|+.| +||+|-||.-|-|+|.-..=-+ -.+..+|+.+.=.++......-.|.|+
T Consensus 184 ~qpDicKdykeTgycg~gdSckFlh~r~DyK~GWqi~~e~d~~ke~~~~~~~D~~~~Pf~ 243 (313)
T KOG1813|consen 184 YQPDICKDYKETGYCGYGDSCKFLHDRSDYKAGWQIEFEWDSAKEKKRVKIEDIELLPFK 243 (313)
T ss_pred cCchhhhhhHhhCcccccchhhhhhhhhhccccceeehhhhccccccceecCCcccCCcc
Confidence 455699999 9999999999999998753211 133456665543333333333333333
No 12
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=90.23 E-value=0.12 Score=48.66 Aligned_cols=39 Identities=31% Similarity=0.541 Sum_probs=29.4
Q ss_pred cccccccccccccCCCCCCeecCCCCChhHHHh--hcccccc
Q 042538 21 EAQICKSFTTGSCIYGSKCRFIHQVMTDSALVL--TIQMEDH 60 (167)
Q Consensus 21 KTklCk~F~tG~CPYG~RC~FiH~~~~~aa~~~--~~q~e~s 60 (167)
-.++|+.|..|.|.+|..|+|.|+..- .+..+ -|+.++|
T Consensus 139 sMkpC~ffLeg~CRF~enCRfSHG~~V-~lsslr~yq~pD~s 179 (486)
T KOG2185|consen 139 SMKPCKFFLEGRCRFGENCRFSHGLDV-PLSSLRNYQQPDWS 179 (486)
T ss_pred hhccchHhhccccccCcccccccCccc-chhhcccCCCccHH
Confidence 457999999999999999999999863 22222 2556666
No 13
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=87.48 E-value=0.17 Score=44.95 Aligned_cols=53 Identities=40% Similarity=0.702 Sum_probs=36.9
Q ss_pred CCCCcccccCCCCC--------------CCCCcc--cccccccc----ccc------ccCCC-CCCeecCCCCChhHHHh
Q 042538 1 FAHGKEELRSTLFP--------------TTKNKS--EAQICKSF----TTG------SCIYG-SKCRFIHQVMTDSALVL 53 (167)
Q Consensus 1 FAHG~eELR~~~~P--------------~~knKY--KTklCk~F----~tG------~CPYG-~RC~FiH~~~~~aa~~~ 53 (167)
||||.+|-|...-| ..+..+ --++|+-| .+| .||.| .||.++|......+++.
T Consensus 104 F~h~~ee~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkYgw~W~CPng~~~C~y~H~Lp~GyVLsr 183 (299)
T COG5252 104 FAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKYGWGWTCPNGNMRCSYIHKLPDGYVLSR 183 (299)
T ss_pred hhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCccceeeCCCCCceeeeeeccCccceecc
Confidence 89999998876422 211111 12589988 344 79998 69999999988766554
No 14
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=87.24 E-value=0.19 Score=45.69 Aligned_cols=26 Identities=27% Similarity=0.853 Sum_probs=24.0
Q ss_pred ccccccccccccCCCCC-CeecCCCCC
Q 042538 22 AQICKSFTTGSCIYGSK-CRFIHQVMT 47 (167)
Q Consensus 22 TklCk~F~tG~CPYG~R-C~FiH~~~~ 47 (167)
-++|+.|..|.|.-|+| |.|.|+.+.
T Consensus 37 ~eVCReF~rn~C~R~d~~CkfaHP~~~ 63 (331)
T KOG2494|consen 37 LEVCREFLRNTCSRGDRECKFAHPPKN 63 (331)
T ss_pred HHHHHHHHhccccCCCccccccCCCCC
Confidence 36999999999999999 999999984
No 15
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=84.67 E-value=0.41 Score=43.41 Aligned_cols=25 Identities=36% Similarity=0.946 Sum_probs=23.5
Q ss_pred cccccccccccCCCCCCeecCCCCC
Q 042538 23 QICKSFTTGSCIYGSKCRFIHQVMT 47 (167)
Q Consensus 23 klCk~F~tG~CPYG~RC~FiH~~~~ 47 (167)
.+|+.|..|.|.||.+|+|.|....
T Consensus 9 tic~~~~~g~c~~g~~cr~~h~~~~ 33 (344)
T KOG1039|consen 9 TICKYYQKGNCKFGDLCRLSHSLPD 33 (344)
T ss_pred hhhhhcccccccccceeeeeccCch
Confidence 6999999999999999999999874
No 16
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=81.76 E-value=0.57 Score=41.42 Aligned_cols=28 Identities=29% Similarity=0.636 Sum_probs=24.6
Q ss_pred ccccccccccccccCCCCCCeecCCCCC
Q 042538 20 SEAQICKSFTTGSCIYGSKCRFIHQVMT 47 (167)
Q Consensus 20 YKTklCk~F~tG~CPYG~RC~FiH~~~~ 47 (167)
++.-.|..|..+.|++|..|.|+|.-+-
T Consensus 150 ~rea~C~~~e~~~C~rG~~CnFmH~k~~ 177 (260)
T KOG2202|consen 150 FREAICGQFERTECSRGGACNFMHVKRL 177 (260)
T ss_pred hhhhhhcccccccCCCCCcCcchhhhhh
Confidence 6778999996669999999999998853
No 17
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=79.62 E-value=0.78 Score=44.39 Aligned_cols=26 Identities=31% Similarity=0.989 Sum_probs=21.7
Q ss_pred cccccccc-cc--cccCCCCCCeecCCCC
Q 042538 21 EAQICKSF-TT--GSCIYGSKCRFIHQVM 46 (167)
Q Consensus 21 KTklCk~F-~t--G~CPYG~RC~FiH~~~ 46 (167)
+..||-+. .. ..|+||++|+|.|+..
T Consensus 75 ~n~LCPsli~g~~~~C~f~d~Crf~HDi~ 103 (614)
T KOG2333|consen 75 QNRLCPSLIQGDISKCSFGDNCRFVHDIE 103 (614)
T ss_pred hhccChHhhcCCCccCcccccccccccHH
Confidence 45799999 55 5899999999999886
No 18
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=78.98 E-value=0.57 Score=42.65 Aligned_cols=27 Identities=33% Similarity=0.917 Sum_probs=24.9
Q ss_pred ccccccccccccccCCCCCCeecCCCC
Q 042538 20 SEAQICKSFTTGSCIYGSKCRFIHQVM 46 (167)
Q Consensus 20 YKTklCk~F~tG~CPYG~RC~FiH~~~ 46 (167)
-|+.+|-.|..|.|.=|.+|.|.|+..
T Consensus 90 PKSvvCafFk~g~C~KG~kCKFsHdl~ 116 (343)
T KOG1763|consen 90 PKSVVCAFFKQGTCTKGDKCKFSHDLA 116 (343)
T ss_pred chHHHHHHHhccCCCCCCcccccchHH
Confidence 488999999999999999999999865
No 19
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=71.58 E-value=1.6 Score=39.43 Aligned_cols=27 Identities=30% Similarity=0.810 Sum_probs=24.6
Q ss_pred cccccccccccccccCCCCCCeecCCC
Q 042538 19 KSEAQICKSFTTGSCIYGSKCRFIHQV 45 (167)
Q Consensus 19 KYKTklCk~F~tG~CPYG~RC~FiH~~ 45 (167)
+.++.+|+.|..|.|.-|+.|-|+|..
T Consensus 74 ~~~~~vcK~~l~glC~kgD~C~Flhe~ 100 (325)
T KOG1040|consen 74 SRGKVVCKHWLRGLCKKGDQCEFLHEY 100 (325)
T ss_pred cCCceeehhhhhhhhhccCcCcchhhh
Confidence 578899999999999999999999965
No 20
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=68.40 E-value=2.1 Score=41.62 Aligned_cols=22 Identities=45% Similarity=1.014 Sum_probs=19.1
Q ss_pred cccccc-cccccCCCCCCeecCC
Q 042538 23 QICKSF-TTGSCIYGSKCRFIHQ 44 (167)
Q Consensus 23 klCk~F-~tG~CPYG~RC~FiH~ 44 (167)
--|--| ..|.||||-+|+|+-.
T Consensus 115 ~~Cp~f~s~G~Cp~G~~CRFl~a 137 (614)
T KOG2333|consen 115 PSCPVFESLGFCPYGFKCRFLGA 137 (614)
T ss_pred CccceeeccccCCccceeehhhc
Confidence 369999 8999999999999743
No 21
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=66.10 E-value=2.3 Score=38.85 Aligned_cols=30 Identities=33% Similarity=0.695 Sum_probs=24.3
Q ss_pred cccccc----ccc------ccCCCC-CCeecCCCCChhHHH
Q 042538 23 QICKSF----TTG------SCIYGS-KCRFIHQVMTDSALV 52 (167)
Q Consensus 23 klCk~F----~tG------~CPYG~-RC~FiH~~~~~aa~~ 52 (167)
.+|+.| .+| .||.|. .|+|+|...+..++.
T Consensus 157 iVCKfFLeAvE~~kYGWfW~CPnGg~~C~YrHaLP~GyVLk 197 (343)
T KOG1763|consen 157 IVCKFFLEAVENGKYGWFWECPNGGDKCIYRHALPEGYVLK 197 (343)
T ss_pred HHHHHHHHHHhcCCccceeECCCCCCeeeeeecCCcchhhh
Confidence 489999 333 899997 999999998877654
No 22
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=56.76 E-value=3 Score=37.34 Aligned_cols=27 Identities=26% Similarity=0.696 Sum_probs=24.7
Q ss_pred ccccccccccccccCCCCCCeecCCCC
Q 042538 20 SEAQICKSFTTGSCIYGSKCRFIHQVM 46 (167)
Q Consensus 20 YKTklCk~F~tG~CPYG~RC~FiH~~~ 46 (167)
-|+..|-.|..+.|--|..|.|+|+-.
T Consensus 83 pK~~vcalF~~~~c~kg~~ckF~h~~e 109 (299)
T COG5252 83 PKTVVCALFLNKTCAKGDACKFAHGKE 109 (299)
T ss_pred chhHHHHHhccCccccCchhhhhcchH
Confidence 489999999999999999999999943
No 23
>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=52.79 E-value=3.9 Score=24.75 Aligned_cols=9 Identities=56% Similarity=1.412 Sum_probs=5.9
Q ss_pred ccCCCCCCe
Q 042538 32 SCIYGSKCR 40 (167)
Q Consensus 32 ~CPYG~RC~ 40 (167)
.|+||.+|.
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 499999995
No 24
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=45.71 E-value=10 Score=34.20 Aligned_cols=27 Identities=33% Similarity=0.834 Sum_probs=23.9
Q ss_pred ccccccc-cccccCCCCCCeecCCCCCh
Q 042538 22 AQICKSF-TTGSCIYGSKCRFIHQVMTD 48 (167)
Q Consensus 22 TklCk~F-~tG~CPYG~RC~FiH~~~~~ 48 (167)
...|+-| ..|.|--|..|+|.|....+
T Consensus 206 avycryynangicgkgaacrfvheptrk 233 (377)
T KOG1492|consen 206 AVYCRYYNANGICGKGAACRFVHEPTRK 233 (377)
T ss_pred eeEEEEecCCCcccCCceeeeecccccc
Confidence 4579999 99999999999999998754
No 25
>KOG3777 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.93 E-value=12 Score=35.38 Aligned_cols=18 Identities=39% Similarity=1.019 Sum_probs=15.6
Q ss_pred cccCCCCCCeecCCCCCh
Q 042538 31 GSCIYGSKCRFIHQVMTD 48 (167)
Q Consensus 31 G~CPYG~RC~FiH~~~~~ 48 (167)
..|+||.+|.|.|+++..
T Consensus 178 kkctyg~kck~~h~~~~~ 195 (443)
T KOG3777|consen 178 KKCTYGGKCKFYHPEIAR 195 (443)
T ss_pred cccCCCCceeeccccccc
Confidence 379999999999999864
No 26
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=36.96 E-value=21 Score=31.92 Aligned_cols=29 Identities=34% Similarity=0.714 Sum_probs=24.8
Q ss_pred ccccccccccccccCCCCCCeecCCCCCh
Q 042538 20 SEAQICKSFTTGSCIYGSKCRFIHQVMTD 48 (167)
Q Consensus 20 YKTklCk~F~tG~CPYG~RC~FiH~~~~~ 48 (167)
+....|+.|..|.|+=|.+|.|+|+.+..
T Consensus 102 ~s~V~c~~~~~g~c~s~~~c~~lh~~d~~ 130 (285)
T COG5084 102 SSSVVCKFFLRGLCKSGFSCEFLHEYDLR 130 (285)
T ss_pred cCCcccchhccccCcCCCccccccCCCcc
Confidence 66788999999999999999999998843
No 27
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=34.29 E-value=29 Score=31.07 Aligned_cols=23 Identities=39% Similarity=0.842 Sum_probs=13.9
Q ss_pred cccccc-cccccCCCCCCeecCCC
Q 042538 23 QICKSF-TTGSCIYGSKCRFIHQV 45 (167)
Q Consensus 23 klCk~F-~tG~CPYG~RC~FiH~~ 45 (167)
-.|+.| ..|.|--|..|.++|..
T Consensus 135 ~~c~~Fs~~G~cs~g~~c~~~h~d 158 (285)
T COG5084 135 PPCRSFSLKGSCSSGPSCGYSHID 158 (285)
T ss_pred CCcccccccceeccCCCCCccccC
Confidence 356666 66666666666666654
No 28
>PF08157 NUC129: NUC129 domain; InterPro: IPR012579 This C-terminal domain is found in a novel family of hypothetical nucleolar proteins [].; GO: 0005634 nucleus
Probab=30.32 E-value=16 Score=26.33 Aligned_cols=16 Identities=19% Similarity=0.426 Sum_probs=13.4
Q ss_pred chhhhhcceeeeecCc
Q 042538 136 VKVDEYIDTVLCCPTT 151 (167)
Q Consensus 136 ~ev~~~i~~~l~~~~~ 151 (167)
+.-++||.+-||||.+
T Consensus 17 qaAk~Fi~~~LYGpgs 32 (63)
T PF08157_consen 17 QAAKDFIQSRLYGPGS 32 (63)
T ss_pred HHHHHHHHHhccCCCC
Confidence 3457899999999987
No 29
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=29.65 E-value=29 Score=31.71 Aligned_cols=30 Identities=40% Similarity=0.793 Sum_probs=25.0
Q ss_pred cccccccc--cccccCCCCCCeecCCCCChhH
Q 042538 21 EAQICKSF--TTGSCIYGSKCRFIHQVMTDSA 50 (167)
Q Consensus 21 KTklCk~F--~tG~CPYG~RC~FiH~~~~~aa 50 (167)
.-+.|+-| ..|.||||..|-+.|.....+.
T Consensus 248 s~~~c~yf~~~~g~cPf~s~~~y~h~~~~~~~ 279 (344)
T KOG1039|consen 248 SAKDCKYFSQGLGSCPFGSKCFYKHLLPSGAS 279 (344)
T ss_pred hccchhhhcCCCCCCCCCCccccccccccccc
Confidence 34689999 6779999999999999886543
No 30
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=28.36 E-value=43 Score=30.80 Aligned_cols=27 Identities=19% Similarity=0.536 Sum_probs=23.5
Q ss_pred ccccccccccccccCCCCCCeecCCCCC
Q 042538 20 SEAQICKSFTTGSCIYGSKCRFIHQVMT 47 (167)
Q Consensus 20 YKTklCk~F~tG~CPYG~RC~FiH~~~~ 47 (167)
-+..-|-.|..|.|.--+ |+|+|+...
T Consensus 69 g~v~aC~Ds~kgrCsR~n-CkylHpp~h 95 (331)
T KOG2494|consen 69 GRVIACFDSQKGRCSREN-CKYLHPPQH 95 (331)
T ss_pred CeEEEEeccccCccCccc-ceecCCChh
Confidence 466799999999999877 999999875
No 31
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=23.28 E-value=29 Score=30.92 Aligned_cols=28 Identities=29% Similarity=0.572 Sum_probs=24.1
Q ss_pred cccccc-cccccCCCCCCeecCCCCChhH
Q 042538 23 QICKSF-TTGSCIYGSKCRFIHQVMTDSA 50 (167)
Q Consensus 23 klCk~F-~tG~CPYG~RC~FiH~~~~~aa 50 (167)
.-|.-| .+|.|.+|.+|.=+|...+-+.
T Consensus 16 v~c~fy~k~gacR~gdrcsR~h~kpt~s~ 44 (260)
T KOG2202|consen 16 VNCSFYFKIGACRHGDRCSRLHEKPTFSQ 44 (260)
T ss_pred cccchHHhhcccccccHHHHhhcccccch
Confidence 468888 9999999999999999887653
No 32
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=21.03 E-value=45 Score=27.13 Aligned_cols=15 Identities=27% Similarity=0.747 Sum_probs=13.5
Q ss_pred ccCCCCCCeecCCCCC
Q 042538 32 SCIYGSKCRFIHQVMT 47 (167)
Q Consensus 32 ~CPYG~RC~FiH~~~~ 47 (167)
.|+||. |+|+|+...
T Consensus 61 GC~~ge-CHy~~GN~k 75 (132)
T COG1908 61 GCKIGE-CHYISGNYK 75 (132)
T ss_pred cccccc-eeeeccchH
Confidence 899999 999999864
No 33
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=20.78 E-value=45 Score=27.31 Aligned_cols=25 Identities=20% Similarity=0.559 Sum_probs=21.9
Q ss_pred ccccccccccccCCCCCCeecCCCCC
Q 042538 22 AQICKSFTTGSCIYGSKCRFIHQVMT 47 (167)
Q Consensus 22 TklCk~F~tG~CPYG~RC~FiH~~~~ 47 (167)
-++|..=..++|-.| .|+|+++.++
T Consensus 42 i~~Cp~ey~~YClHG-~C~yI~dl~~ 66 (139)
T PHA03099 42 IRLCGPEGDGYCLHG-DCIHARDIDG 66 (139)
T ss_pred cccCChhhCCEeECC-EEEeeccCCC
Confidence 468999888999999 8999998874
No 34
>PF12363 DUF3647: Phage protein ; InterPro: IPR024410 Proteins in this entry are frequently annotated as phage proteins, however there is little accompanying literature to back this up or to describe the nature of these phage proteins.
Probab=20.49 E-value=26 Score=26.56 Aligned_cols=23 Identities=17% Similarity=0.433 Sum_probs=17.4
Q ss_pred ceeEcCCCCCCCCCcchhhhhcce
Q 042538 121 IEVTLPCHPSKTPPRVKVDEYIDT 144 (167)
Q Consensus 121 ~e~~l~~~~~~~~~~~ev~~~i~~ 144 (167)
|..++.+.+.++ |++|+++||+.
T Consensus 57 i~~a~~~~~~~~-s~~eIe~~ie~ 79 (113)
T PF12363_consen 57 IYAATAHEKKRP-SREEIEDYIED 79 (113)
T ss_pred HHHHhcccCCCC-CHHHHHHHHHH
Confidence 445556666655 99999999996
Done!