Query 009239
Match_columns 539
No_of_seqs 171 out of 724
Neff 4.4
Searched_HMMs 46136
Date Thu Mar 28 22:07:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009239.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009239hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4791 Uncharacterized conser 99.9 1.3E-25 2.7E-30 236.4 11.8 463 2-536 25-545 (667)
2 KOG1040 Polyadenylation factor 99.3 3E-12 6.4E-17 132.8 4.0 104 6-113 74-183 (325)
3 KOG4791 Uncharacterized conser 99.2 4.6E-12 1E-16 134.9 3.9 81 8-111 2-83 (667)
4 KOG1492 C3H1-type Zn-finger pr 99.1 9.9E-11 2.2E-15 115.9 6.6 106 8-117 205-317 (377)
5 KOG1492 C3H1-type Zn-finger pr 98.8 3.8E-09 8.3E-14 104.8 4.9 104 7-114 231-336 (377)
6 KOG1040 Polyadenylation factor 98.8 9.6E-09 2.1E-13 106.9 7.0 105 9-113 45-158 (325)
7 COG5084 YTH1 Cleavage and poly 98.7 7.8E-08 1.7E-12 98.6 9.7 83 7-114 102-191 (285)
8 KOG1677 CCCH-type Zn-finger pr 98.1 3.5E-06 7.7E-11 86.6 6.0 96 10-113 87-202 (332)
9 KOG2494 C3H1-type Zn-finger pr 98.0 1.7E-06 3.7E-11 89.8 1.1 56 8-65 36-96 (331)
10 KOG1677 CCCH-type Zn-finger pr 97.7 2.1E-05 4.5E-10 81.0 3.3 60 4-64 127-203 (332)
11 COG5084 YTH1 Cleavage and poly 97.5 0.00025 5.4E-09 73.2 7.4 84 8-112 73-158 (285)
12 KOG1763 Uncharacterized conser 97.4 2.5E-05 5.4E-10 80.3 -1.0 56 7-64 90-192 (343)
13 KOG2494 C3H1-type Zn-finger pr 97.3 7.8E-05 1.7E-09 77.7 1.5 55 41-113 38-94 (331)
14 PF00642 zf-CCCH: Zinc finger 97.3 5.9E-05 1.3E-09 51.7 0.1 26 8-34 2-27 (27)
15 smart00356 ZnF_C3H1 zinc finge 97.2 0.00033 7.1E-09 46.7 2.6 25 88-112 3-27 (27)
16 smart00356 ZnF_C3H1 zinc finge 97.0 0.00049 1.1E-08 45.9 2.2 24 8-33 3-26 (27)
17 PF00642 zf-CCCH: Zinc finger 96.9 0.00017 3.6E-09 49.5 -0.5 25 88-112 2-27 (27)
18 KOG1595 CCCH-type Zn-finger pr 96.9 0.0006 1.3E-08 75.0 3.1 76 21-114 208-293 (528)
19 KOG3702 Nuclear polyadenylated 96.6 0.0042 9E-08 70.0 6.8 96 9-123 544-654 (681)
20 COG5252 Uncharacterized conser 96.1 0.00087 1.9E-08 67.6 -1.5 55 8-64 84-177 (299)
21 COG5063 CTH1 CCCH-type Zn-fing 95.8 0.013 2.7E-07 61.3 5.1 95 10-116 231-342 (351)
22 KOG1595 CCCH-type Zn-finger pr 95.5 0.021 4.5E-07 63.3 5.6 62 50-123 208-281 (528)
23 PF14608 zf-CCCH_2: Zinc finge 94.7 0.022 4.8E-07 36.4 1.8 19 91-111 1-19 (19)
24 COG5063 CTH1 CCCH-type Zn-fing 94.3 0.055 1.2E-06 56.7 4.6 25 88-112 273-298 (351)
25 PF14608 zf-CCCH_2: Zinc finge 94.1 0.032 6.9E-07 35.6 1.6 17 12-32 2-18 (19)
26 KOG3702 Nuclear polyadenylated 92.0 0.19 4E-06 57.2 4.7 20 92-113 647-666 (681)
27 KOG2185 Predicted RNA-processi 91.4 0.088 1.9E-06 57.0 1.4 32 83-114 134-165 (486)
28 KOG1763 Uncharacterized conser 91.1 0.059 1.3E-06 56.2 -0.2 28 86-113 89-116 (343)
29 PF10650 zf-C3H1: Putative zin 90.8 0.15 3.3E-06 34.4 1.5 20 42-61 2-22 (23)
30 KOG2185 Predicted RNA-processi 87.2 0.25 5.4E-06 53.6 1.0 22 42-63 142-164 (486)
31 KOG2333 Uncharacterized conser 84.9 0.41 8.9E-06 53.2 1.2 55 41-110 77-136 (614)
32 PF10650 zf-C3H1: Putative zin 83.4 0.69 1.5E-05 31.3 1.4 21 90-111 1-22 (23)
33 KOG2333 Uncharacterized conser 76.4 1.4 3E-05 49.3 1.6 60 5-64 72-140 (614)
34 COG5152 Uncharacterized conser 74.8 1.2 2.7E-05 44.6 0.7 28 88-115 140-168 (259)
35 KOG1039 Predicted E3 ubiquitin 73.2 1.3 2.9E-05 47.4 0.6 24 10-35 9-32 (344)
36 KOG0153 Predicted RNA-binding 71.3 2 4.3E-05 46.1 1.3 27 7-35 159-185 (377)
37 KOG1813 Predicted E3 ubiquitin 67.4 1.8 3.8E-05 45.6 -0.0 29 88-116 185-214 (313)
38 KOG1039 Predicted E3 ubiquitin 65.9 2.5 5.4E-05 45.3 0.8 32 32-64 1-33 (344)
39 COG5252 Uncharacterized conser 65.1 1.7 3.6E-05 44.6 -0.7 28 86-113 82-109 (299)
40 COG5152 Uncharacterized conser 61.4 3.5 7.5E-05 41.5 0.8 27 39-65 140-168 (259)
41 KOG0153 Predicted RNA-binding 60.3 4 8.8E-05 43.8 1.1 25 89-113 161-185 (377)
42 KOG2202 U2 snRNP splicing fact 39.6 13 0.00028 38.6 0.8 26 8-35 151-176 (260)
43 KOG1813 Predicted E3 ubiquitin 36.2 12 0.00026 39.6 0.1 27 8-35 185-211 (313)
44 PF03194 LUC7: LUC7 N_terminus 27.9 16 0.00035 37.6 -0.7 22 88-112 29-50 (254)
45 KOG2202 U2 snRNP splicing fact 21.0 46 0.00099 34.7 1.1 26 87-112 150-175 (260)
No 1
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.92 E-value=1.3e-25 Score=236.42 Aligned_cols=463 Identities=16% Similarity=0.117 Sum_probs=227.2
Q ss_pred hhhhccCCccccccccCccCCCCCCCCCCCCcccccC-CCccCcccccCc-cCCCCCCCCC--CCCCccc---CCCCCCC
Q 009239 2 EEELQKRNTDCVYFLASPLTCKKGLDCEYRHNEIARL-NPRDCWYWLAGN-CINPRCGFRH--PPLDAHV---TEAPSES 74 (539)
Q Consensus 2 e~~~~kk~~~CryFl~gpG~CkKGd~C~F~Hd~~~~~-~p~vCkyFL~G~-Ctn~~CpFsH--~~~d~~~---~ec~~~p 74 (539)
+|++++..++|+||+.+ ..|++ .|+|+|...+++ ++.+|+||++|+ |++++|-|+| +++.... ++.+...
T Consensus 25 ~E~al~n~t~C~~w~~~-~~C~k--~C~YRHSe~~~kr~e~~CYwe~~p~gC~k~~CgfRH~~pPLkg~l~~~p~~pe~e 101 (667)
T KOG4791|consen 25 CEAALGNETVCTLWQEG-RCCRK--VCRYRHSEIDKKRSEIPCYWENQPTGCQKLNCGFRHNRPPLKGVLPTVPESPEEE 101 (667)
T ss_pred hHHHhcCcchhhhhhhc-Ccccc--cccchhhHHhhhcCcccceeecCCCccCCCccccccCCCchhhhccCCCCCcccc
Confidence 57788888888888888 77776 888888887776 778888888888 8888888888 4443221 1122211
Q ss_pred CCCCCCCCCC--CCCCCcccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCcccccccCCcCcCCCCC--------
Q 009239 75 VSLPCQSSIP--VNKTSIPCYFYFNGFCSRGDRCSFLHGPDGIAPNGKSSKSASAVTDSLLSENKTSAGDGT-------- 144 (539)
Q Consensus 75 ~g~~C~~s~p--~~k~~~pC~Ff~~G~C~KGd~CpF~H~~~~p~~~G~~~k~~s~~~~~~pl~n~~~~g~~~-------- 144 (539)
+..+--.+-+ ......||-|+++|+|..++-|-|.|.+..-........ +.++++ .-+..+-+.|++-
T Consensus 102 v~~~~~SAq~~sV~~~p~P~l~~~K~~e~~~D~~s~Lh~P~A~~~~~d~e~-~~~A~~-e~~d~K~~~~l~~~KK~~~~~ 179 (667)
T KOG4791|consen 102 VKASQLSAQQNSVQSNPSPQLRSVKKVESSEDVPSPLHPPVAINAADDDED-DDDAFS-EEGDEKKTPTLQPTKKVHNGL 179 (667)
T ss_pred cccccccCCCcccccCCchHHHHhhhhhhhccccccCCCCcccccccCccc-cccccc-ccccCCCCCCCCcccccCCcc
Confidence 1111000001 234567899999999999999999999943111001110 111111 1111121222110
Q ss_pred CCCCCCCCCCCCCCccccccccccCCCcccccCCCCcCCCCCCCCccccccccceeeecCCCcccc---cCccccccccc
Q 009239 145 GSPPTEIRPNPSEAPLKLAVDVRVQPKGHLLQSAPKRIPERRASPQISLSEGETVAVVKSDSMVAA---EGFMKTKSHLY 221 (539)
Q Consensus 145 ~~~~~~~~~~~~~~~~~~~~~~k~Q~~~~~q~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~g~~~~~s~~~ 221 (539)
-.-...-+.|....+... ++++- +.-.+.++..++ ..|+.. .||..---+-+
T Consensus 180 ~~K~V~~H~~i~~~~~~~------------s~gi~-------D~~~v~~k~~k~------~~Pv~~~~G~Gv~s~~l~~e 234 (667)
T KOG4791|consen 180 RVKSVRKHAVNIKQGECL------------SFGIK-------DLEEIKSKKMKE------KSPVQGEGGSGVSSLLLHPE 234 (667)
T ss_pred cceeeccccccccccccc------------ccccc-------cHHHhccccccc------cCCCcccCCCCCChhhcCCC
Confidence 000001111111111000 00000 111122333333 111111 11110000000
Q ss_pred ccC-CCcc-ccc-----CCCC-ccccccCCCCcceeecchhhhcccCCCCChhhhhhcccccccccccccccccCCCccC
Q 009239 222 TDW-SSDE-HAD-----DHVE-PEERLESSPGFDVLVDNENRAENLGFEDDSEYLLATNREHRELNGHFLGYDFEGPIEY 293 (539)
Q Consensus 222 ~~q-~s~~-~~d-----~h~e-~ee~~esSpGfDVLVdd~~~~~n~~y~~~~e~~~~~~~d~~~l~~~~~~y~~~~~~~y 293 (539)
..| .+.+ .-+ +.-. +.-+++|+|||||||+++ +-|++|++-....- .+-+.-|+ -.||- |+
T Consensus 235 ~~~L~~k~~~~~~~~f~ng~d~d~~l~~s~~~~~~~v~~~--~~~s~y~~~~~~~~--~~~~er~~---~~~dp----d~ 303 (667)
T KOG4791|consen 235 PVPLPEKENVRLKRKFSNGGDSDPPLKRSLAQLGKKVEAP--ETNSDYTPKKAQVS--KSLKERLG---MSADP----DN 303 (667)
T ss_pred CccchhhhhhhhhhccccCCCCCchhhhhhhcccceecCc--CCCccccchHhhhh--hHHHHhcC---CCCCC----Ch
Confidence 000 0000 001 1111 233789999999999999 88888887766552 12222255 33443 22
Q ss_pred CCCCC-CCCCCCCCccccccccccccccccccCCCccchhhhhhhccccccccCCCCCccccCcchhHHHHhhhhcccCC
Q 009239 294 DPMYP-ESEPHEGETYNVHYYLDNEHILDKVREYPGRARERILDSMLSRKRKLFPMKVSVDDCNADLRDYLRKRRVVDGH 372 (539)
Q Consensus 294 d~~~~-d~e~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~DlR~~l~krr~~n~~ 372 (539)
.-+.+ +-|++..+-|++|+-.-.+ -|.+.+...+ |+-. ++. |-+...+-.++.-.||||++|-+||..|+-
T Consensus 304 ~~~~d~~~e~~~~~~~~s~~~r~~~-~wg~r~~~~~--~ed~----~~~-~~~~~~~r~e~~~esd~r~~~a~~~k~~~~ 375 (667)
T KOG4791|consen 304 EDATDKVGEIHVKTLEESLLERASQ-KWGERQTKLK--TEDS----TSG-ARSSSTIRIEVLAESDHRQQEAERQKSKKD 375 (667)
T ss_pred hhhccchhHHHHHHHHHHHHHHhhh-ccchhccccc--cccc----ccc-cccchhhHHHHHHhHHHHHHHHHHhhccCC
Confidence 22334 6678777889999876555 4777777654 2222 222 223333334455689999999999998887
Q ss_pred Ccccccccccc-----c----ccCCccc-cccCC---cccCCceecccCcc-----cccccCCCCCCCCCCCCCCccccC
Q 009239 373 SIVHSTRRHES-----S----RLMGRIQ-GRHRG---LLLHGRLASEFGKN-----YIESHGHKGTLPNGANQHGWARHS 434 (539)
Q Consensus 373 ~~~~~~~r~~s-----~----~~~~~~~-~~~~g---~r~~gRi~~~~~~~-----~i~~~~e~e~l~~~~~~~~~~~~~ 434 (539)
+...- =|++ + +..+|++ ++.-| +++.|||++.-.+. .++-++ .+++.+.- -+
T Consensus 376 ~~~i~--~hd~~~~~s~~~~~~~~sr~~s~~~~~~s~s~~~~~ik~re~~~~e~~~~~~~~s------e~~~~~~e--~~ 445 (667)
T KOG4791|consen 376 TTCIK--LHDSEIKKTVVLPPIVASRGQSEEPAGKTKSMQEVHIKTREEIKLEKALRVQQSS------ESSPSQHE--AT 445 (667)
T ss_pred ceeec--ccccccccccccchhhhcccCCcCccccchhhhhhhhhhHhhhcchhhceecccc------ccCccccc--CC
Confidence 54311 1111 0 1111111 11123 69999999944433 222223 33332222 25
Q ss_pred cchhhhhhhhccchhccccccccccc----CCccccccCCCCccccCCcccHHHHHHHHhhhhhcCCCccccC-----CC
Q 009239 435 KSNILRQHHKGKRLLKRKSHLSAISR----KPFSSERRSSQTETAFTGPKSLAEIREEKKKAEESGGHFGKVG-----HL 505 (539)
Q Consensus 435 ~~~~~r~~~~~k~~~k~~~~~s~~~r----~~~~k~r~~~~~~~~F~GPKsLAeik~eK~~~~~s~~~~~k~~-----~~ 505 (539)
.+.+|+-++++|+--+ -++|.. -|..+-|.-+++. =+.|||- ++|-+.+- +++|.. |.
T Consensus 446 ~~~rl~~ri~~r~ee~----~~~n~~~g~~~~wa~rr~me~e~--~sa~~s~---r~es~~ep----s~~k~~~~e~~~~ 512 (667)
T KOG4791|consen 446 PGARLLLRITKRTEEK----EEKNLQEGNEVDWASRRRMEAEE--ASAETTK---RCESMREP----SMQKQQEREKSVL 512 (667)
T ss_pred ccchHHHHHhhhhhhc----cccchhcccCCchHHhhhhhhhh--ccccccc---hhhccCCc----hhhhhhhhhhhhc
Confidence 5666666655544222 222221 1112223333332 1234442 11111111 133331 11
Q ss_pred --CCCCCCCCCCCcHHHHHhhhcCCCccCCCCC
Q 009239 506 --SRTLTDFQGPKPLSEILKEKRRPGTVSDADT 536 (539)
Q Consensus 506 --~~~~~~FegPKpLseILK~Kr~~~~~~~~~~ 536 (539)
-..-+.|--|||.++|||+|--+.|+.+-.+
T Consensus 513 s~~rs~~s~~a~~p~~~~~~~k~~~~sg~s~~n 545 (667)
T KOG4791|consen 513 TPLRSCNTQVAEKPVLTAVPKKLPTKSGDSLLN 545 (667)
T ss_pred ccccccccccccchHHHhhhhcccccccccccc
Confidence 1223489999999999999998877766543
No 2
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=99.25 E-value=3e-12 Score=132.80 Aligned_cols=104 Identities=24% Similarity=0.526 Sum_probs=81.9
Q ss_pred ccCCccccccccCccCCCCCCCCCCCCcccccCCCccCcccc-cCccCC-CCCCCCCCCCCcccCCCCCCCCCCCCCC-C
Q 009239 6 QKRNTDCVYFLASPLTCKKGLDCEYRHNEIARLNPRDCWYWL-AGNCIN-PRCGFRHPPLDAHVTEAPSESVSLPCQS-S 82 (539)
Q Consensus 6 ~kk~~~CryFl~gpG~CkKGd~C~F~Hd~~~~~~p~vCkyFL-~G~Ctn-~~CpFsH~~~d~~~~ec~~~p~g~~C~~-s 82 (539)
.++.++|+||+.| .|++||.|.|+|......++ .|.||. .|.|++ .+|+|.|.........|.++..+ +|+. .
T Consensus 74 ~~~~~vcK~~l~g--lC~kgD~C~Flhe~~~~k~r-ec~ff~~~g~c~~~~~c~y~h~dpqt~~k~c~~~~~g-~c~~g~ 149 (325)
T KOG1040|consen 74 SRGKVVCKHWLRG--LCKKGDQCEFLHEYDLTKMR-ECKFFSLFGECTNGKDCPYLHGDPQTAIKKCKWYKEG-FCRGGP 149 (325)
T ss_pred cCCceeehhhhhh--hhhccCcCcchhhhhhcccc-cccccccccccccccCCcccCCChhhhhhccchhhhc-cCCCcc
Confidence 4578999999999 99999999999999544444 777777 999999 99999999854344478888766 5553 3
Q ss_pred CCCCC--CCcccccccCCCCCCCCC-CCCCCCCC
Q 009239 83 IPVNK--TSIPCYFYFNGFCSRGDR-CSFLHGPD 113 (539)
Q Consensus 83 ~p~~k--~~~pC~Ff~~G~C~KGd~-CpF~H~~~ 113 (539)
.|..+ ...+|++|..|+|++|.+ |.+.|...
T Consensus 150 ~c~~~h~~~~~c~~y~~gfC~~g~q~c~~~hp~~ 183 (325)
T KOG1040|consen 150 SCKKRHERKVLCPPYNAGFCPKGPQRCDMLHPEF 183 (325)
T ss_pred hhhhhhhcccCCCchhhhhccCCCCcccccCCCC
Confidence 44432 247899999999999998 99999874
No 3
>KOG4791 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.23 E-value=4.6e-12 Score=134.92 Aligned_cols=81 Identities=38% Similarity=0.869 Sum_probs=72.7
Q ss_pred CCccccccccCccCCCCCCCCCCCCcccccCCCccCcccccCccCCCCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCC
Q 009239 8 RNTDCVYFLASPLTCKKGLDCEYRHNEIARLNPRDCWYWLAGNCINPRCGFRHPPLDAHVTEAPSESVSLPCQSSIPVNK 87 (539)
Q Consensus 8 k~~~CryFl~gpG~CkKGd~C~F~Hd~~~~~~p~vCkyFL~G~Ctn~~CpFsH~~~d~~~~ec~~~p~g~~C~~s~p~~k 87 (539)
...+|+||++. +|++++.|.|+|...++++..+|.||+.+.|....|+|+|..++.+ .
T Consensus 2 ~~~dcyff~ys--~cKk~d~c~~rh~E~al~n~t~C~~w~~~~~C~k~C~YRHSe~~~k--------------------r 59 (667)
T KOG4791|consen 2 QGEDCYFFFYS--TCKKGDSCPFRHCEAALGNETVCTLWQEGRCCRKVCRYRHSEIDKK--------------------R 59 (667)
T ss_pred Ccccchhhhhh--hhhccCcCcchhhHHHhcCcchhhhhhhcCcccccccchhhHHhhh--------------------c
Confidence 35789999999 9999999999999999999999999999999889999999987532 2
Q ss_pred CCcccccccCCC-CCCCCCCCCCCC
Q 009239 88 TSIPCYFYFNGF-CSRGDRCSFLHG 111 (539)
Q Consensus 88 ~~~pC~Ff~~G~-C~KGd~CpF~H~ 111 (539)
..++|||+.+|. |.|- +|-|.|.
T Consensus 60 ~e~~CYwe~~p~gC~k~-~CgfRH~ 83 (667)
T KOG4791|consen 60 SEIPCYWENQPTGCQKL-NCGFRHN 83 (667)
T ss_pred CcccceeecCCCccCCC-ccccccC
Confidence 578999999987 9996 9999994
No 4
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=99.11 E-value=9.9e-11 Score=115.92 Aligned_cols=106 Identities=22% Similarity=0.419 Sum_probs=86.2
Q ss_pred CCccccccccCccCCCCCCCCCCCCcccccCCCccCcccccCccCC-CCCCCCCCCCCcccCCCCCCCCC----CCCCCC
Q 009239 8 RNTDCVYFLASPLTCKKGLDCEYRHNEIARLNPRDCWYWLAGNCIN-PRCGFRHPPLDAHVTEAPSESVS----LPCQSS 82 (539)
Q Consensus 8 k~~~CryFl~gpG~CkKGd~C~F~Hd~~~~~~p~vCkyFL~G~Ctn-~~CpFsH~~~d~~~~ec~~~p~g----~~C~~s 82 (539)
....|+||... |.|-+|..|+|.|.+. ...+|.-|++|.|.+ ..|-++|......++.|-+|..| +.|++.
T Consensus 205 savycryynan-gicgkgaacrfvhept---rkticpkflngrcnkaedcnlsheldprripacryfllgkcnnpncryv 280 (377)
T KOG1492|consen 205 SAVYCRYYNAN-GICGKGAACRFVHEPT---RKTICPKFLNGRCNKAEDCNLSHELDPRRIPACRYFLLGKCNNPNCRYV 280 (377)
T ss_pred ceeEEEEecCC-CcccCCceeeeecccc---ccccChHHhcCccCchhcCCcccccCccccchhhhhhhccCCCCCceEE
Confidence 34789999977 8999999999999997 345999999999999 99999999777677788888765 234442
Q ss_pred CC-CCCCCcccc-cccCCCCCCCCCCCCCCCCCCCCC
Q 009239 83 IP-VNKTSIPCY-FYFNGFCSRGDRCSFLHGPDGIAP 117 (539)
Q Consensus 83 ~p-~~k~~~pC~-Ff~~G~C~KGd~CpF~H~~~~p~~ 117 (539)
+- -...+..|. |...|||.-|..|+-.|...|.++
T Consensus 281 hihysenapicfefakygfcelgtscknqhilqctdy 317 (377)
T KOG1492|consen 281 HIHYSENAPICFEFAKYGFCELGTSCKNQHILQCTDY 317 (377)
T ss_pred EEeecCCCceeeeehhcceeccccccccceeeeecch
Confidence 21 134577897 667899999999999999999776
No 5
>KOG1492 consensus C3H1-type Zn-finger protein [General function prediction only]
Probab=98.81 E-value=3.8e-09 Score=104.80 Aligned_cols=104 Identities=29% Similarity=0.570 Sum_probs=88.4
Q ss_pred cCCccccccccCccCCCCCCCCCCCCcccccCCCccCcccccCccCCCCCCCCCCCCCcccCCCCCCCCCCCCC-CCCCC
Q 009239 7 KRNTDCVYFLASPLTCKKGLDCEYRHNEIARLNPRDCWYWLAGNCINPRCGFRHPPLDAHVTEAPSESVSLPCQ-SSIPV 85 (539)
Q Consensus 7 kk~~~CryFl~gpG~CkKGd~C~F~Hd~~~~~~p~vCkyFL~G~Ctn~~CpFsH~~~d~~~~ec~~~p~g~~C~-~s~p~ 85 (539)
.+.++|.-|+.| .|.+...|...|...++..| .|+||+-|+|.+++|+|.|..+....+.|-.|.+-.+|. ...|+
T Consensus 231 trkticpkflng--rcnkaedcnlsheldprrip-acryfllgkcnnpncryvhihysenapicfefakygfcelgtsck 307 (377)
T KOG1492|consen 231 TRKTICPKFLNG--RCNKAEDCNLSHELDPRRIP-ACRYFLLGKCNNPNCRYVHIHYSENAPICFEFAKYGFCELGTSCK 307 (377)
T ss_pred cccccChHHhcC--ccCchhcCCcccccCccccc-hhhhhhhccCCCCCceEEEEeecCCCceeeeehhcceeccccccc
Confidence 467899999999 99999999999999998877 899999999999999999999887777776666544665 35577
Q ss_pred CCCCcccc-cccCCCCCCCCCCCCCCCCCC
Q 009239 86 NKTSIPCY-FYFNGFCSRGDRCSFLHGPDG 114 (539)
Q Consensus 86 ~k~~~pC~-Ff~~G~C~KGd~CpF~H~~~~ 114 (539)
+.+...|- |..-|.|.+. .|.+-|+...
T Consensus 308 nqhilqctdyamfgscnnp-qcslyhgavs 336 (377)
T KOG1492|consen 308 NQHILQCTDYAMFGSCNNP-QCSLYHGAVS 336 (377)
T ss_pred cceeeeecchhhhcCCCCC-cceeecceec
Confidence 88888997 4467999996 9999998754
No 6
>KOG1040 consensus Polyadenylation factor I complex, subunit, Yth1 (CPSF subunit) [RNA processing and modification]
Probab=98.78 E-value=9.6e-09 Score=106.95 Aligned_cols=105 Identities=24% Similarity=0.462 Sum_probs=80.2
Q ss_pred CccccccccCccCCCCCCCCCCCCcccc-cCCCccCcccccCccCC-CCCCCCCCCCCcccCCCCCCCCCCCCCC-CCC-
Q 009239 9 NTDCVYFLASPLTCKKGLDCEYRHNEIA-RLNPRDCWYWLAGNCIN-PRCGFRHPPLDAHVTEAPSESVSLPCQS-SIP- 84 (539)
Q Consensus 9 ~~~CryFl~gpG~CkKGd~C~F~Hd~~~-~~~p~vCkyFL~G~Ctn-~~CpFsH~~~d~~~~ec~~~p~g~~C~~-s~p- 84 (539)
...|.++....-.|.+|..|...|.... ....++|+|||.|.|++ +.|.|+|...-...++|..|-....|.. ..|
T Consensus 45 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vcK~~l~glC~kgD~C~Flhe~~~~k~rec~ff~~~g~c~~~~~c~ 124 (325)
T KOG1040|consen 45 RATCEFNESREKPCERGPICPKSHNDVSDSRGKVVCKHWLRGLCKKGDQCEFLHEYDLTKMRECKFFSLFGECTNGKDCP 124 (325)
T ss_pred cchhcccccCCCCccCCCCCccccCCccccCCceeehhhhhhhhhccCcCcchhhhhhcccccccccccccccccccCCc
Confidence 4688888851127999999999999953 34567999999999998 9999999863233347877765545543 222
Q ss_pred -----CCCCCcccccccCCCCCCCCCCCCCCCCC
Q 009239 85 -----VNKTSIPCYFYFNGFCSRGDRCSFLHGPD 113 (539)
Q Consensus 85 -----~~k~~~pC~Ff~~G~C~KGd~CpF~H~~~ 113 (539)
.......|.||..|||..|+.|++.|...
T Consensus 125 y~h~dpqt~~k~c~~~~~g~c~~g~~c~~~h~~~ 158 (325)
T KOG1040|consen 125 YLHGDPQTAIKKCKWYKEGFCRGGPSCKKRHERK 158 (325)
T ss_pred ccCCChhhhhhccchhhhccCCCcchhhhhhhcc
Confidence 23446689999999999999999999974
No 7
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=98.68 E-value=7.8e-08 Score=98.57 Aligned_cols=83 Identities=35% Similarity=0.781 Sum_probs=69.3
Q ss_pred cCCccccccccCccCCCCCCCCCCCCcccccC--CCccCccc-ccCccCC-CCCCCCCCCCCcccCCCCCCCCCCCCCCC
Q 009239 7 KRNTDCVYFLASPLTCKKGLDCEYRHNEIARL--NPRDCWYW-LAGNCIN-PRCGFRHPPLDAHVTEAPSESVSLPCQSS 82 (539)
Q Consensus 7 kk~~~CryFl~gpG~CkKGd~C~F~Hd~~~~~--~p~vCkyF-L~G~Ctn-~~CpFsH~~~d~~~~ec~~~p~g~~C~~s 82 (539)
...++|++|+.| .|++|..|.|+|....+. .+ .|++| +.|.|.. ..|.|.|...+.
T Consensus 102 ~s~V~c~~~~~g--~c~s~~~c~~lh~~d~~~s~~~-~c~~Fs~~G~cs~g~~c~~~h~dp~~----------------- 161 (285)
T COG5084 102 SSSVVCKFFLRG--LCKSGFSCEFLHEYDLRSSQGP-PCRSFSLKGSCSSGPSCGYSHIDPDS----------------- 161 (285)
T ss_pred cCCcccchhccc--cCcCCCccccccCCCcccccCC-CcccccccceeccCCCCCccccCccc-----------------
Confidence 457899999999 999999999999998665 44 89999 5999999 999999996432
Q ss_pred CCCCCCCccccccc---CCCCCCCCCCCCCCCCCC
Q 009239 83 IPVNKTSIPCYFYF---NGFCSRGDRCSFLHGPDG 114 (539)
Q Consensus 83 ~p~~k~~~pC~Ff~---~G~C~KGd~CpF~H~~~~ 114 (539)
....|.||. .|+|+.|..|+|.|+...
T Consensus 162 -----~~~~~~~~~~~~~~f~p~g~~c~~~H~~~~ 191 (285)
T COG5084 162 -----FAGNCDQYSGATYGFCPLGASCKFSHTLKR 191 (285)
T ss_pred -----ccccccccCcccccccCCCCcccccccccc
Confidence 245577776 799999999999999863
No 8
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=98.12 E-value=3.5e-06 Score=86.64 Aligned_cols=96 Identities=28% Similarity=0.606 Sum_probs=71.4
Q ss_pred ccccccccCccCCCCCCCCCCCCcc-cc---------------cCCCccCcccc-cCccCC--CCCCCCCCCCCcccCCC
Q 009239 10 TDCVYFLASPLTCKKGLDCEYRHNE-IA---------------RLNPRDCWYWL-AGNCIN--PRCGFRHPPLDAHVTEA 70 (539)
Q Consensus 10 ~~CryFl~gpG~CkKGd~C~F~Hd~-~~---------------~~~p~vCkyFL-~G~Ctn--~~CpFsH~~~d~~~~ec 70 (539)
..|.++... +.|..|..|+|.|.. .. .....+|.+|. .|.|.. ++|+|.|.......+.
T Consensus 87 ~~~~~~~~~-~~~~~~s~~~~~~p~~~~~~~~~~~~~~~~~p~~~kt~lc~~~~~~g~c~y~ge~crfah~~~e~r~~~- 164 (332)
T KOG1677|consen 87 GDCSAYLRT-GVCGYGSSCRYNHPDLRLRPRPVRRSRGERKPERYKTPLCRSFRKSGTCKYRGEQCRFAHGLEELRLPS- 164 (332)
T ss_pred ccccccccc-CCCCCCCCCCccCcccccccCCccccccccCcccccCCcceeeecCccccccCchhhhcCCcccccccc-
Confidence 699999987 799999999999996 11 11456899999 899985 9999999875432100
Q ss_pred CCCCCCCCCCCCCCCCCCCccccccc-CCCCCCCCCCCCCCCCC
Q 009239 71 PSESVSLPCQSSIPVNKTSIPCYFYF-NGFCSRGDRCSFLHGPD 113 (539)
Q Consensus 71 ~~~p~g~~C~~s~p~~k~~~pC~Ff~-~G~C~KGd~CpF~H~~~ 113 (539)
. .+....+...++++|.+|. .|.|++|..|.|.|...
T Consensus 165 ---~---~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~ 202 (332)
T KOG1677|consen 165 ---S---ENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEP 202 (332)
T ss_pred ---c---chhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCc
Confidence 0 0111223356799998775 59999999999999985
No 9
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=98.01 E-value=1.7e-06 Score=89.76 Aligned_cols=56 Identities=27% Similarity=0.585 Sum_probs=47.6
Q ss_pred CCccccccccCccCCCCCCC-CCCCCcccccC----CCccCcccccCccCCCCCCCCCCCCCc
Q 009239 8 RNTDCVYFLASPLTCKKGLD-CEYRHNEIARL----NPRDCWYWLAGNCINPRCGFRHPPLDA 65 (539)
Q Consensus 8 k~~~CryFl~gpG~CkKGd~-C~F~Hd~~~~~----~p~vCkyFL~G~Ctn~~CpFsH~~~d~ 65 (539)
..++||-|+++ +|++|+. |+|.|...... ....|..|++|.|++++|+|.|.+...
T Consensus 36 ~~eVCReF~rn--~C~R~d~~CkfaHP~~~~~V~~g~v~aC~Ds~kgrCsR~nCkylHpp~hl 96 (331)
T KOG2494|consen 36 TLEVCREFLRN--TCSRGDRECKFAHPPKNCQVSNGRVIACFDSQKGRCSRENCKYLHPPQHL 96 (331)
T ss_pred HHHHHHHHHhc--cccCCCccccccCCCCCCCccCCeEEEEeccccCccCcccceecCCChhh
Confidence 35799999999 9999998 99999997421 234699999999999999999998653
No 10
>KOG1677 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=97.72 E-value=2.1e-05 Score=81.04 Aligned_cols=60 Identities=27% Similarity=0.449 Sum_probs=51.3
Q ss_pred hhccCCccccccccCccCCCC-CCCCCCCCcccccC--------------CCccCcccc-cCccCC-CCCCCCCCCCC
Q 009239 4 ELQKRNTDCVYFLASPLTCKK-GLDCEYRHNEIARL--------------NPRDCWYWL-AGNCIN-PRCGFRHPPLD 64 (539)
Q Consensus 4 ~~~kk~~~CryFl~gpG~CkK-Gd~C~F~Hd~~~~~--------------~p~vCkyFL-~G~Ctn-~~CpFsH~~~d 64 (539)
..+.++..|++|... |+|+. |+.|+|.|...... ++++|.+|+ .|.|.. ..|.|.|....
T Consensus 127 p~~~kt~lc~~~~~~-g~c~y~ge~crfah~~~e~r~~~~~~~~~~~~~~kt~lC~~f~~tG~C~yG~rC~F~H~~~~ 203 (332)
T KOG1677|consen 127 PERYKTPLCRSFRKS-GTCKYRGEQCRFAHGLEELRLPSSENQVGNPPKYKTKLCPKFQKTGLCKYGSRCRFIHGEPE 203 (332)
T ss_pred cccccCCcceeeecC-ccccccCchhhhcCCcccccccccchhhcCCCCCCCcCCCccccCCCCCCCCcCeecCCCcc
Confidence 345688999999988 99999 99999999886543 357899999 699999 99999999754
No 11
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=97.49 E-value=0.00025 Score=73.25 Aligned_cols=84 Identities=21% Similarity=0.377 Sum_probs=66.9
Q ss_pred CCccccccccCccCCCCCCCCCCCCcccccCCCccCcccccCccCC-CCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCC
Q 009239 8 RNTDCVYFLASPLTCKKGLDCEYRHNEIARLNPRDCWYWLAGNCIN-PRCGFRHPPLDAHVTEAPSESVSLPCQSSIPVN 86 (539)
Q Consensus 8 k~~~CryFl~gpG~CkKGd~C~F~Hd~~~~~~p~vCkyFL~G~Ctn-~~CpFsH~~~d~~~~ec~~~p~g~~C~~s~p~~ 86 (539)
....|.+++.. +.+.....|++.|...-...-++|++|+.|.|.. ..|.|+|...-. .
T Consensus 73 n~~~~~~~~~~-~~~~~~~s~~~~~~~~~~~s~V~c~~~~~g~c~s~~~c~~lh~~d~~--------------------~ 131 (285)
T COG5084 73 NTVACISRNFN-SIRGSRLSTPNNHVNPVLSSSVVCKFFLRGLCKSGFSCEFLHEYDLR--------------------S 131 (285)
T ss_pred ccccccccccc-CCccccccCCccccCccccCCcccchhccccCcCCCccccccCCCcc--------------------c
Confidence 34568888865 4566666899999885545667999999999998 999999996321 1
Q ss_pred CCCcccccc-cCCCCCCCCCCCCCCCC
Q 009239 87 KTSIPCYFY-FNGFCSRGDRCSFLHGP 112 (539)
Q Consensus 87 k~~~pC~Ff-~~G~C~KGd~CpF~H~~ 112 (539)
....+|.+| ..|.|..|..|.|.|..
T Consensus 132 s~~~~c~~Fs~~G~cs~g~~c~~~h~d 158 (285)
T COG5084 132 SQGPPCRSFSLKGSCSSGPSCGYSHID 158 (285)
T ss_pred ccCCCcccccccceeccCCCCCccccC
Confidence 136789988 89999999999999996
No 12
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=97.41 E-value=2.5e-05 Score=80.34 Aligned_cols=56 Identities=29% Similarity=0.720 Sum_probs=44.0
Q ss_pred cCCccccccccCccCCCCCCCCCCCCcccccC-----------------------------------CCccCcccc----
Q 009239 7 KRNTDCVYFLASPLTCKKGLDCEYRHNEIARL-----------------------------------NPRDCWYWL---- 47 (539)
Q Consensus 7 kk~~~CryFl~gpG~CkKGd~C~F~Hd~~~~~-----------------------------------~p~vCkyFL---- 47 (539)
.+..+|.||.+| +|.+|+.|.|+|+..... .-+||+|||
T Consensus 90 PKSvvCafFk~g--~C~KG~kCKFsHdl~~~~k~eK~dly~d~rdemWD~~kl~~vv~~K~~k~k~~tdiVCKfFLeAvE 167 (343)
T KOG1763|consen 90 PKSVVCAFFKQG--TCTKGDKCKFSHDLAVERKKEKIDLYPDTRDEMWDEEKLEEVVLKKHGKPKPTTDIVCKFFLEAVE 167 (343)
T ss_pred chHHHHHHHhcc--CCCCCCcccccchHHHhhhccchhccccchhhhhhHHHHHHHHHhhccCCCCchhHHHHHHHHHHh
Confidence 367899999999 999999999999986321 113899999
Q ss_pred cCc------cCC--CCCCCCCCCCC
Q 009239 48 AGN------CIN--PRCGFRHPPLD 64 (539)
Q Consensus 48 ~G~------Ctn--~~CpFsH~~~d 64 (539)
+|. |-| ..|-|+|..++
T Consensus 168 ~~kYGWfW~CPnGg~~C~YrHaLP~ 192 (343)
T KOG1763|consen 168 NGKYGWFWECPNGGDKCIYRHALPE 192 (343)
T ss_pred cCCccceeECCCCCCeeeeeecCCc
Confidence 332 888 67999998754
No 13
>KOG2494 consensus C3H1-type Zn-finger protein [Transcription]
Probab=97.33 E-value=7.8e-05 Score=77.68 Aligned_cols=55 Identities=40% Similarity=0.855 Sum_probs=43.9
Q ss_pred ccCcccccCccCC-CC-CCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCcccccccCCCCCCCCCCCCCCCCC
Q 009239 41 RDCWYWLAGNCIN-PR-CGFRHPPLDAHVTEAPSESVSLPCQSSIPVNKTSIPCYFYFNGFCSRGDRCSFLHGPD 113 (539)
Q Consensus 41 ~vCkyFL~G~Ctn-~~-CpFsH~~~d~~~~ec~~~p~g~~C~~s~p~~k~~~pC~Ff~~G~C~KGd~CpF~H~~~ 113 (539)
.||+-||+|.|.+ +. |+|.|++....+ . +-..+.|+-|++|.|.+- +|+|.|.+.
T Consensus 38 eVCReF~rn~C~R~d~~CkfaHP~~~~~V------~-----------~g~v~aC~Ds~kgrCsR~-nCkylHpp~ 94 (331)
T KOG2494|consen 38 EVCREFLRNTCSRGDRECKFAHPPKNCQV------S-----------NGRVIACFDSQKGRCSRE-NCKYLHPPQ 94 (331)
T ss_pred HHHHHHHhccccCCCccccccCCCCCCCc------c-----------CCeEEEEeccccCccCcc-cceecCCCh
Confidence 4899999999998 66 999999753211 1 124677999999999995 899999983
No 14
>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=97.30 E-value=5.9e-05 Score=51.71 Aligned_cols=26 Identities=31% Similarity=0.766 Sum_probs=19.6
Q ss_pred CCccccccccCccCCCCCCCCCCCCcc
Q 009239 8 RNTDCVYFLASPLTCKKGLDCEYRHNE 34 (539)
Q Consensus 8 k~~~CryFl~gpG~CkKGd~C~F~Hd~ 34 (539)
++.+|++|+.. |.|+.|+.|.|.|+.
T Consensus 2 k~~~C~~f~~~-g~C~~G~~C~f~H~~ 27 (27)
T PF00642_consen 2 KTKLCRFFMRT-GTCPFGDKCRFAHGE 27 (27)
T ss_dssp TSSB-HHHHHT-S--TTGGGSSSBSSG
T ss_pred ccccChhhccC-CccCCCCCcCccCCC
Confidence 57899999985 599999999999974
No 15
>smart00356 ZnF_C3H1 zinc finger.
Probab=97.16 E-value=0.00033 Score=46.75 Aligned_cols=25 Identities=40% Similarity=0.964 Sum_probs=21.9
Q ss_pred CCcccccccCCCCCCCCCCCCCCCC
Q 009239 88 TSIPCYFYFNGFCSRGDRCSFLHGP 112 (539)
Q Consensus 88 ~~~pC~Ff~~G~C~KGd~CpF~H~~ 112 (539)
...+|.+|.+|.|.+|++|+|.|..
T Consensus 3 k~~~C~~~~~g~C~~g~~C~~~H~~ 27 (27)
T smart00356 3 KTELCKFFKRGYCPYGDRCKFAHPL 27 (27)
T ss_pred CCCcCcCccCCCCCCCCCcCCCCcC
Confidence 3568998899999999999999974
No 16
>smart00356 ZnF_C3H1 zinc finger.
Probab=96.98 E-value=0.00049 Score=45.90 Aligned_cols=24 Identities=25% Similarity=0.697 Sum_probs=18.9
Q ss_pred CCccccccccCccCCCCCCCCCCCCc
Q 009239 8 RNTDCVYFLASPLTCKKGLDCEYRHN 33 (539)
Q Consensus 8 k~~~CryFl~gpG~CkKGd~C~F~Hd 33 (539)
+..+|++|..| .|.+|+.|.|+|.
T Consensus 3 k~~~C~~~~~g--~C~~g~~C~~~H~ 26 (27)
T smart00356 3 KTELCKFFKRG--YCPYGDRCKFAHP 26 (27)
T ss_pred CCCcCcCccCC--CCCCCCCcCCCCc
Confidence 45678888666 8888888888886
No 17
>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=96.92 E-value=0.00017 Score=49.49 Aligned_cols=25 Identities=40% Similarity=1.031 Sum_probs=18.3
Q ss_pred CCccccccc-CCCCCCCCCCCCCCCC
Q 009239 88 TSIPCYFYF-NGFCSRGDRCSFLHGP 112 (539)
Q Consensus 88 ~~~pC~Ff~-~G~C~KGd~CpF~H~~ 112 (539)
...+|.+|. .|.|+.|++|+|.|++
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 467899775 5999999999999974
No 18
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=96.89 E-value=0.0006 Score=74.99 Aligned_cols=76 Identities=25% Similarity=0.522 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCC-cccccC--------CCccCcccccCccCC-CCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCc
Q 009239 21 TCKKGLDCEYRH-NEIARL--------NPRDCWYWLAGNCIN-PRCGFRHPPLDAHVTEAPSESVSLPCQSSIPVNKTSI 90 (539)
Q Consensus 21 ~CkKGd~C~F~H-d~~~~~--------~p~vCkyFL~G~Ctn-~~CpFsH~~~d~~~~ec~~~p~g~~C~~s~p~~k~~~ 90 (539)
.|.-+-.|+|.| ...+++ .-.+|.-|-+|.|.. +.|-|.|... +|+-.| ....+.
T Consensus 208 ~shDwteCPf~HpgEkARRRDPRkyhYs~tpCPefrkG~C~rGD~CEyaHgvf-----EcwLHP----------a~YRT~ 272 (528)
T KOG1595|consen 208 RSHDWTECPFAHPGEKARRRDPRKYHYSSTPCPEFRKGSCERGDSCEYAHGVF-----ECWLHP----------ARYRTR 272 (528)
T ss_pred cCCCcccCCccCCCcccccCCcccccccCccCcccccCCCCCCCcccccccee-----hhhcCH----------HHhccc
Confidence 677789999999 555554 235899999999998 9999999974 565433 345678
Q ss_pred ccccccCCCCCCCCCCCCCCCCCC
Q 009239 91 PCYFYFNGFCSRGDRCSFLHGPDG 114 (539)
Q Consensus 91 pC~Ff~~G~C~KGd~CpF~H~~~~ 114 (539)
.|+-. |+|++ .-|-|.|.+..
T Consensus 273 ~CkDg--~~C~R-rvCfFAH~~eq 293 (528)
T KOG1595|consen 273 KCKDG--GYCPR-RVCFFAHSPEQ 293 (528)
T ss_pred cccCC--CCCcc-ceEeeecChHH
Confidence 89865 99999 79999999854
No 19
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=96.58 E-value=0.0042 Score=69.97 Aligned_cols=96 Identities=20% Similarity=0.419 Sum_probs=62.6
Q ss_pred CccccccccCccCCCCCCCCCCCCcccccC---------------CCccCcccccCccCCCCCCCCCCCCCcccCCCCCC
Q 009239 9 NTDCVYFLASPLTCKKGLDCEYRHNEIARL---------------NPRDCWYWLAGNCINPRCGFRHPPLDAHVTEAPSE 73 (539)
Q Consensus 9 ~~~CryFl~gpG~CkKGd~C~F~Hd~~~~~---------------~p~vCkyFL~G~Ctn~~CpFsH~~~d~~~~ec~~~ 73 (539)
.+.|.||. .|. +..|.|.|...+.+ ....|+| .-.|++..|.|.|...... ..
T Consensus 544 l~~Cky~~----~Ct-~a~Ce~~HPtaa~~~~s~p~k~fa~~~~ks~p~Ck~--~~kCtasDC~~sH~~~~~p--vq--- 611 (681)
T KOG3702|consen 544 LTRCKYGP----ACT-SAECEFAHPTAAENAKSLPNKKFASKCLKSHPGCKF--GKKCTASDCNYSHAGRRIP--VQ--- 611 (681)
T ss_pred eccccCCC----cCC-chhhhhcCCcchhhhhccccccccccceeccccccc--ccccccccCcccccCCCCC--Cc---
Confidence 47899997 688 89999999987621 1113554 3459999999999865321 11
Q ss_pred CCCCCCCCCCCCCCCCcccccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 009239 74 SVSLPCQSSIPVNKTSIPCYFYFNGFCSRGDRCSFLHGPDGIAPNGKSSK 123 (539)
Q Consensus 74 p~g~~C~~s~p~~k~~~pC~Ff~~G~C~KGd~CpF~H~~~~p~~~G~~~k 123 (539)
+...+|-. +......+|+|+ |.|.+- .|+|.|.+.|- .++.|.
T Consensus 612 ~t~ip~~~--~~~ti~~~CrY~--pnCrnm-~C~F~HPk~cR--f~~~c~ 654 (681)
T KOG3702|consen 612 PTRIPPPF--PGGTIRGLCRYR--PNCRNM-QCKFYHPKTCR--FNTNCP 654 (681)
T ss_pred cccCCCCC--CCCCccccceec--cCcCCc-cccccCCcccc--ccccCC
Confidence 11111111 112357789986 779997 99999999764 455555
No 20
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=96.12 E-value=0.00087 Score=67.59 Aligned_cols=55 Identities=33% Similarity=0.762 Sum_probs=43.7
Q ss_pred CCccccccccCccCCCCCCCCCCCCcccccC---------------------------CCccCcccc----cCc------
Q 009239 8 RNTDCVYFLASPLTCKKGLDCEYRHNEIARL---------------------------NPRDCWYWL----AGN------ 50 (539)
Q Consensus 8 k~~~CryFl~gpG~CkKGd~C~F~Hd~~~~~---------------------------~p~vCkyFL----~G~------ 50 (539)
+..+|..|+.+ +|.+|+.|.|+|.....+ .-+||+||+ +|.
T Consensus 84 K~~vcalF~~~--~c~kg~~ckF~h~~ee~r~~eK~DLYsDvRd~~ed~pl~krP~intd~VCkffieA~e~GkYgw~W~ 161 (299)
T COG5252 84 KTVVCALFLNK--TCAKGDACKFAHGKEEARKTEKPDLYSDVRDKEEDVPLGKRPWINTDRVCKFFIEAMESGKYGWGWT 161 (299)
T ss_pred hhHHHHHhccC--ccccCchhhhhcchHHHhhhcccchhhhhhhhhccCCcccCCCCChhHHHHHHHHHHhcCCccceee
Confidence 56899999999 999999999999954211 125799998 343
Q ss_pred cCC--CCCCCCCCCCC
Q 009239 51 CIN--PRCGFRHPPLD 64 (539)
Q Consensus 51 Ctn--~~CpFsH~~~d 64 (539)
|-| ..|-|.|..++
T Consensus 162 CPng~~~C~y~H~Lp~ 177 (299)
T COG5252 162 CPNGNMRCSYIHKLPD 177 (299)
T ss_pred CCCCCceeeeeeccCc
Confidence 887 69999999765
No 21
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=95.80 E-value=0.013 Score=61.26 Aligned_cols=95 Identities=21% Similarity=0.356 Sum_probs=70.4
Q ss_pred ccccccccCccCCCC---CCCCCCC---CcccccC--------CCccCcccc-cCccCC-CCCCCCCCCCCcccCCCCCC
Q 009239 10 TDCVYFLASPLTCKK---GLDCEYR---HNEIARL--------NPRDCWYWL-AGNCIN-PRCGFRHPPLDAHVTEAPSE 73 (539)
Q Consensus 10 ~~CryFl~gpG~CkK---Gd~C~F~---Hd~~~~~--------~p~vCkyFL-~G~Ctn-~~CpFsH~~~d~~~~ec~~~ 73 (539)
.+|.-|... |+|.- |+.|.|. |-..... .+.+|..|. .|.|-. ..|.|.|......- -...
T Consensus 231 ~lc~~ft~k-g~~p~~~sG~~~q~a~~~HGlN~l~~k~k~~~frTePcinwe~sGyc~yg~Rc~F~hgd~~~ie--~~~~ 307 (351)
T COG5063 231 ELCESFTRK-GTCPYWISGVKCQFACRGHGLNELKSKKKKQNFRTEPCINWEKSGYCPYGLRCCFKHGDDSDIE--MYEE 307 (351)
T ss_pred HHhhccCcC-CCCccccccccccccccccccccccccccccccccCCccchhhcccCccccccccccCChhhcc--cccc
Confidence 789999877 79999 9999999 8876532 457899999 899988 99999998754221 1100
Q ss_pred CCCCCCCCCCCCCCCCcccc-cccCCCCCCCCCCCCCCCCCCCC
Q 009239 74 SVSLPCQSSIPVNKTSIPCY-FYFNGFCSRGDRCSFLHGPDGIA 116 (539)
Q Consensus 74 p~g~~C~~s~p~~k~~~pC~-Ff~~G~C~KGd~CpF~H~~~~p~ 116 (539)
+. .....-+|. |...|.|+-|-.|-|.|.+...+
T Consensus 308 ~~---------~~y~~~~crt~~~~g~~p~g~~~c~~~dkkn~~ 342 (351)
T COG5063 308 AS---------LGYLDGPCRTRAKGGAFPSGGAVCKSFDKKNLD 342 (351)
T ss_pred cc---------ccccccccccccccCccCCCCchhhccccchhh
Confidence 00 022456787 66789999999999999885533
No 22
>KOG1595 consensus CCCH-type Zn-finger protein [General function prediction only]
Probab=95.47 E-value=0.021 Score=63.28 Aligned_cols=62 Identities=29% Similarity=0.592 Sum_probs=41.5
Q ss_pred ccCC-CCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCcccccccCCCCCCCCCCCCCCCC-----------CCCCC
Q 009239 50 NCIN-PRCGFRHPPLDAHVTEAPSESVSLPCQSSIPVNKTSIPCYFYFNGFCSRGDRCSFLHGP-----------DGIAP 117 (539)
Q Consensus 50 ~Ctn-~~CpFsH~~~d~~~~ec~~~p~g~~C~~s~p~~k~~~pC~Ff~~G~C~KGd~CpF~H~~-----------~~p~~ 117 (539)
.|-. -.|||.|+-...+. -.| + .| .....+|+-|.+|.|.+||.|.|.|+. ...|.
T Consensus 208 ~shDwteCPf~HpgEkARR-RDP---R----ky----hYs~tpCPefrkG~C~rGD~CEyaHgvfEcwLHPa~YRT~~Ck 275 (528)
T KOG1595|consen 208 RSHDWTECPFAHPGEKARR-RDP---R----KY----HYSSTPCPEFRKGSCERGDSCEYAHGVFECWLHPARYRTRKCK 275 (528)
T ss_pred cCCCcccCCccCCCccccc-CCc---c----cc----cccCccCcccccCCCCCCCccccccceehhhcCHHHhcccccc
Confidence 4544 58999996432222 011 0 01 224789999999999999999999995 45566
Q ss_pred CCCCCC
Q 009239 118 NGKSSK 123 (539)
Q Consensus 118 ~G~~~k 123 (539)
.|..|+
T Consensus 276 Dg~~C~ 281 (528)
T KOG1595|consen 276 DGGYCP 281 (528)
T ss_pred CCCCCc
Confidence 666664
No 23
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=94.69 E-value=0.022 Score=36.36 Aligned_cols=19 Identities=53% Similarity=1.158 Sum_probs=16.4
Q ss_pred ccccccCCCCCCCCCCCCCCC
Q 009239 91 PCYFYFNGFCSRGDRCSFLHG 111 (539)
Q Consensus 91 pC~Ff~~G~C~KGd~CpF~H~ 111 (539)
+|+|+.. |.+|++|+|.|.
T Consensus 1 ~Ck~~~~--C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPN--CTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCC--CCCCCcCccCCc
Confidence 5888755 999999999995
No 24
>COG5063 CTH1 CCCH-type Zn-finger protein [General function prediction only]
Probab=94.27 E-value=0.055 Score=56.67 Aligned_cols=25 Identities=40% Similarity=0.974 Sum_probs=21.7
Q ss_pred CCcccccc-cCCCCCCCCCCCCCCCC
Q 009239 88 TSIPCYFY-FNGFCSRGDRCSFLHGP 112 (539)
Q Consensus 88 ~~~pC~Ff-~~G~C~KGd~CpF~H~~ 112 (539)
...||..| .-|+|+.|.+|.|.|+.
T Consensus 273 rTePcinwe~sGyc~yg~Rc~F~hgd 298 (351)
T COG5063 273 RTEPCINWEKSGYCPYGLRCCFKHGD 298 (351)
T ss_pred ccCCccchhhcccCccccccccccCC
Confidence 46799955 67999999999999996
No 25
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=94.08 E-value=0.032 Score=35.65 Aligned_cols=17 Identities=29% Similarity=0.921 Sum_probs=10.2
Q ss_pred ccccccCccCCCCCCCCCCCC
Q 009239 12 CVYFLASPLTCKKGLDCEYRH 32 (539)
Q Consensus 12 CryFl~gpG~CkKGd~C~F~H 32 (539)
|+||. .|++|++|.|+|
T Consensus 2 Ck~~~----~C~~~~~C~f~H 18 (19)
T PF14608_consen 2 CKFGP----NCTNGDNCPFSH 18 (19)
T ss_pred CcCcC----CCCCCCcCccCC
Confidence 56553 366666666666
No 26
>KOG3702 consensus Nuclear polyadenylated RNA binding protein [RNA processing and modification]
Probab=91.97 E-value=0.19 Score=57.24 Aligned_cols=20 Identities=30% Similarity=0.773 Sum_probs=13.0
Q ss_pred cccccCCCCCCCCCCCCCCCCC
Q 009239 92 CYFYFNGFCSRGDRCSFLHGPD 113 (539)
Q Consensus 92 C~Ff~~G~C~KGd~CpF~H~~~ 113 (539)
|.|- -.|.+-..|-|.|...
T Consensus 647 cRf~--~~c~~~~sc~fYh~r~ 666 (681)
T KOG3702|consen 647 CRFN--TNCPNNPSCTFYHERP 666 (681)
T ss_pred cccc--ccCCCCcccccccCCc
Confidence 5542 3477667888888863
No 27
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=91.39 E-value=0.088 Score=56.98 Aligned_cols=32 Identities=38% Similarity=0.920 Sum_probs=27.9
Q ss_pred CCCCCCCcccccccCCCCCCCCCCCCCCCCCC
Q 009239 83 IPVNKTSIPCYFYFNGFCSRGDRCSFLHGPDG 114 (539)
Q Consensus 83 ~p~~k~~~pC~Ff~~G~C~KGd~CpF~H~~~~ 114 (539)
.|......||+||+.|.|..+.+|+|.|+..-
T Consensus 134 ~PTh~sMkpC~ffLeg~CRF~enCRfSHG~~V 165 (486)
T KOG2185|consen 134 TPTHESMKPCKFFLEGRCRFGENCRFSHGLDV 165 (486)
T ss_pred cCcchhhccchHhhccccccCcccccccCccc
Confidence 45566789999999999999999999999854
No 28
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=91.13 E-value=0.059 Score=56.18 Aligned_cols=28 Identities=36% Similarity=0.929 Sum_probs=25.5
Q ss_pred CCCCcccccccCCCCCCCCCCCCCCCCC
Q 009239 86 NKTSIPCYFYFNGFCSRGDRCSFLHGPD 113 (539)
Q Consensus 86 ~k~~~pC~Ff~~G~C~KGd~CpF~H~~~ 113 (539)
.+.+++|.||.+|.|.+|+.|.|.|..+
T Consensus 89 DPKSvvCafFk~g~C~KG~kCKFsHdl~ 116 (343)
T KOG1763|consen 89 DPKSVVCAFFKQGTCTKGDKCKFSHDLA 116 (343)
T ss_pred CchHHHHHHHhccCCCCCCcccccchHH
Confidence 4578899999999999999999999974
No 29
>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=90.78 E-value=0.15 Score=34.41 Aligned_cols=20 Identities=45% Similarity=0.909 Sum_probs=17.7
Q ss_pred cCcccccC-ccCCCCCCCCCC
Q 009239 42 DCWYWLAG-NCINPRCGFRHP 61 (539)
Q Consensus 42 vCkyFL~G-~Ctn~~CpFsH~ 61 (539)
+|.|-+.| .|.++.|.|.|-
T Consensus 2 lC~yEl~Gg~Cnd~~C~~QHf 22 (23)
T PF10650_consen 2 LCPYELTGGVCNDPDCEFQHF 22 (23)
T ss_pred CCccccCCCeeCCCCCCcccc
Confidence 79999966 999999999995
No 30
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=87.17 E-value=0.25 Score=53.63 Aligned_cols=22 Identities=32% Similarity=0.729 Sum_probs=16.2
Q ss_pred cCcccccCccCC-CCCCCCCCCC
Q 009239 42 DCWYWLAGNCIN-PRCGFRHPPL 63 (539)
Q Consensus 42 vCkyFL~G~Ctn-~~CpFsH~~~ 63 (539)
+|+||+.|.|.- .+|+|+|...
T Consensus 142 pC~ffLeg~CRF~enCRfSHG~~ 164 (486)
T KOG2185|consen 142 PCKFFLEGRCRFGENCRFSHGLD 164 (486)
T ss_pred cchHhhccccccCcccccccCcc
Confidence 677888788865 7788888753
No 31
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=84.86 E-value=0.41 Score=53.24 Aligned_cols=55 Identities=31% Similarity=0.561 Sum_probs=35.8
Q ss_pred ccCcccccC---ccCC-CCCCCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCcccccc-cCCCCCCCCCCCCCC
Q 009239 41 RDCWYWLAG---NCIN-PRCGFRHPPLDAHVTEAPSESVSLPCQSSIPVNKTSIPCYFY-FNGFCSRGDRCSFLH 110 (539)
Q Consensus 41 ~vCkyFL~G---~Ctn-~~CpFsH~~~d~~~~ec~~~p~g~~C~~s~p~~k~~~pC~Ff-~~G~C~KGd~CpF~H 110 (539)
..|.-...| .|.. ++|+|.|+...=..+.. ..-..-|++| ..|+|+.|-.|+|.-
T Consensus 77 ~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~---------------~Dig~~Cp~f~s~G~Cp~G~~CRFl~ 136 (614)
T KOG2333|consen 77 RLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKA---------------PDIGPSCPVFESLGFCPYGFKCRFLG 136 (614)
T ss_pred ccChHhhcCCCccCcccccccccccHHHHHhccC---------------cccCCccceeeccccCCccceeehhh
Confidence 467777754 5877 88888888532111000 1124569966 589999999999953
No 32
>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=83.39 E-value=0.69 Score=31.30 Aligned_cols=21 Identities=29% Similarity=0.686 Sum_probs=18.0
Q ss_pred cccccccCC-CCCCCCCCCCCCC
Q 009239 90 IPCYFYFNG-FCSRGDRCSFLHG 111 (539)
Q Consensus 90 ~pC~Ff~~G-~C~KGd~CpF~H~ 111 (539)
..|+|...| .|... .|.|.|-
T Consensus 1 ~lC~yEl~Gg~Cnd~-~C~~QHf 22 (23)
T PF10650_consen 1 PLCPYELTGGVCNDP-DCEFQHF 22 (23)
T ss_pred CCCccccCCCeeCCC-CCCcccc
Confidence 369999887 99986 9999995
No 33
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=76.41 E-value=1.4 Score=49.31 Aligned_cols=60 Identities=28% Similarity=0.501 Sum_probs=44.9
Q ss_pred hccCCccccccccCc-cCCCCCCCCCCCCcccccC---CC---ccCcccc-cCccCC-CCCCCCCCCCC
Q 009239 5 LQKRNTDCVYFLASP-LTCKKGLDCEYRHNEIARL---NP---RDCWYWL-AGNCIN-PRCGFRHPPLD 64 (539)
Q Consensus 5 ~~kk~~~CryFl~gp-G~CkKGd~C~F~Hd~~~~~---~p---~vCkyFL-~G~Ctn-~~CpFsH~~~d 64 (539)
++-++..|.-...+. -.|..|++|+|.|+..+-. .+ .-|.+|- .|.|-. -.|+|.-..++
T Consensus 72 ~q~~n~LCPsli~g~~~~C~f~d~Crf~HDi~ayLatK~~Dig~~Cp~f~s~G~Cp~G~~CRFl~aHld 140 (614)
T KOG2333|consen 72 AQVQNRLCPSLIQGDISKCSFGDNCRFVHDIEAYLATKAPDIGPSCPVFESLGFCPYGFKCRFLGAHLD 140 (614)
T ss_pred hhhhhccChHhhcCCCccCcccccccccccHHHHHhccCcccCCccceeeccccCCccceeehhhcccC
Confidence 344577888777652 3799999999999997532 11 2599999 899998 99999765544
No 34
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=74.80 E-value=1.2 Score=44.56 Aligned_cols=28 Identities=36% Similarity=0.790 Sum_probs=23.6
Q ss_pred CCcccccc-cCCCCCCCCCCCCCCCCCCC
Q 009239 88 TSIPCYFY-FNGFCSRGDRCSFLHGPDGI 115 (539)
Q Consensus 88 ~~~pC~Ff-~~G~C~KGd~CpF~H~~~~p 115 (539)
+..+|+-| +.|+|-.|+.|+|+|...-+
T Consensus 140 qpdVCKdyk~TGYCGYGDsCKflH~R~D~ 168 (259)
T COG5152 140 QPDVCKDYKETGYCGYGDSCKFLHDRSDF 168 (259)
T ss_pred CcccccchhhcccccCCchhhhhhhhhhh
Confidence 46689855 79999999999999998653
No 35
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=73.22 E-value=1.3 Score=47.38 Aligned_cols=24 Identities=33% Similarity=0.605 Sum_probs=22.2
Q ss_pred ccccccccCccCCCCCCCCCCCCccc
Q 009239 10 TDCVYFLASPLTCKKGLDCEYRHNEI 35 (539)
Q Consensus 10 ~~CryFl~gpG~CkKGd~C~F~Hd~~ 35 (539)
++|+||..| .|+.|+.|+|.|...
T Consensus 9 tic~~~~~g--~c~~g~~cr~~h~~~ 32 (344)
T KOG1039|consen 9 TICKYYQKG--NCKFGDLCRLSHSLP 32 (344)
T ss_pred hhhhhcccc--cccccceeeeeccCc
Confidence 899999988 999999999999987
No 36
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=71.28 E-value=2 Score=46.12 Aligned_cols=27 Identities=37% Similarity=0.978 Sum_probs=23.6
Q ss_pred cCCccccccccCccCCCCCCCCCCCCccc
Q 009239 7 KRNTDCVYFLASPLTCKKGLDCEYRHNEI 35 (539)
Q Consensus 7 kk~~~CryFl~gpG~CkKGd~C~F~Hd~~ 35 (539)
....+|-||..| .|++|+.|.|+|...
T Consensus 159 n~p~Icsf~v~g--eckRG~ec~yrhEkp 185 (377)
T KOG0153|consen 159 NRPHICSFFVKG--ECKRGAECPYRHEKP 185 (377)
T ss_pred CCCccccceeec--cccccccccccccCC
Confidence 456789999998 999999999999886
No 37
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.43 E-value=1.8 Score=45.60 Aligned_cols=29 Identities=31% Similarity=0.726 Sum_probs=24.3
Q ss_pred CCcccc-cccCCCCCCCCCCCCCCCCCCCC
Q 009239 88 TSIPCY-FYFNGFCSRGDRCSFLHGPDGIA 116 (539)
Q Consensus 88 ~~~pC~-Ff~~G~C~KGd~CpF~H~~~~p~ 116 (539)
...+|+ |-..|+|-+|+.|+|+|...+.-
T Consensus 185 qpDicKdykeTgycg~gdSckFlh~r~DyK 214 (313)
T KOG1813|consen 185 QPDICKDYKETGYCGYGDSCKFLHDRSDYK 214 (313)
T ss_pred CchhhhhhHhhCcccccchhhhhhhhhhcc
Confidence 356898 55799999999999999998753
No 38
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.95 E-value=2.5 Score=45.33 Aligned_cols=32 Identities=28% Similarity=0.501 Sum_probs=26.0
Q ss_pred CcccccCCCccCcccccCccCC-CCCCCCCCCCC
Q 009239 32 HNEIARLNPRDCWYWLAGNCIN-PRCGFRHPPLD 64 (539)
Q Consensus 32 Hd~~~~~~p~vCkyFL~G~Ctn-~~CpFsH~~~d 64 (539)
|+...... .+|+||+.|+|.. ..|+|.|+...
T Consensus 1 ~d~~~~~~-tic~~~~~g~c~~g~~cr~~h~~~~ 33 (344)
T KOG1039|consen 1 HDLSLSQE-TICKYYQKGNCKFGDLCRLSHSLPD 33 (344)
T ss_pred Cccccccc-hhhhhcccccccccceeeeeccCch
Confidence 44444434 6999999999998 99999999874
No 39
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=65.10 E-value=1.7 Score=44.64 Aligned_cols=28 Identities=32% Similarity=0.969 Sum_probs=25.0
Q ss_pred CCCCcccccccCCCCCCCCCCCCCCCCC
Q 009239 86 NKTSIPCYFYFNGFCSRGDRCSFLHGPD 113 (539)
Q Consensus 86 ~k~~~pC~Ff~~G~C~KGd~CpF~H~~~ 113 (539)
.+.+.+|..|..+.|.+|+.|.|.|..+
T Consensus 82 dpK~~vcalF~~~~c~kg~~ckF~h~~e 109 (299)
T COG5252 82 DPKTVVCALFLNKTCAKGDACKFAHGKE 109 (299)
T ss_pred CchhHHHHHhccCccccCchhhhhcchH
Confidence 3567899999999999999999999974
No 40
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=61.37 E-value=3.5 Score=41.48 Aligned_cols=27 Identities=30% Similarity=0.528 Sum_probs=22.3
Q ss_pred CCccCcccc-cCccCC-CCCCCCCCCCCc
Q 009239 39 NPRDCWYWL-AGNCIN-PRCGFRHPPLDA 65 (539)
Q Consensus 39 ~p~vCkyFL-~G~Ctn-~~CpFsH~~~d~ 65 (539)
.|.||+.|. +|.|-. +.|.|+|...+-
T Consensus 140 qpdVCKdyk~TGYCGYGDsCKflH~R~D~ 168 (259)
T COG5152 140 QPDVCKDYKETGYCGYGDSCKFLHDRSDF 168 (259)
T ss_pred CcccccchhhcccccCCchhhhhhhhhhh
Confidence 567899888 899987 999999987653
No 41
>KOG0153 consensus Predicted RNA-binding protein (RRM superfamily) [General function prediction only]
Probab=60.30 E-value=4 Score=43.85 Aligned_cols=25 Identities=32% Similarity=0.834 Sum_probs=22.9
Q ss_pred CcccccccCCCCCCCCCCCCCCCCC
Q 009239 89 SIPCYFYFNGFCSRGDRCSFLHGPD 113 (539)
Q Consensus 89 ~~pC~Ff~~G~C~KGd~CpF~H~~~ 113 (539)
..+|.||..|.|++|+.|+|.|...
T Consensus 161 p~Icsf~v~geckRG~ec~yrhEkp 185 (377)
T KOG0153|consen 161 PHICSFFVKGECKRGAECPYRHEKP 185 (377)
T ss_pred CccccceeeccccccccccccccCC
Confidence 4579999999999999999999986
No 42
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=39.57 E-value=13 Score=38.62 Aligned_cols=26 Identities=27% Similarity=0.622 Sum_probs=22.3
Q ss_pred CCccccccccCccCCCCCCCCCCCCccc
Q 009239 8 RNTDCVYFLASPLTCKKGLDCEYRHNEI 35 (539)
Q Consensus 8 k~~~CryFl~gpG~CkKGd~C~F~Hd~~ 35 (539)
+..+|..|..+ .|.+|..|-|.|...
T Consensus 151 rea~C~~~e~~--~C~rG~~CnFmH~k~ 176 (260)
T KOG2202|consen 151 REAICGQFERT--ECSRGGACNFMHVKR 176 (260)
T ss_pred hhhhhcccccc--cCCCCCcCcchhhhh
Confidence 34689999988 999999999999884
No 43
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.23 E-value=12 Score=39.56 Aligned_cols=27 Identities=19% Similarity=0.443 Sum_probs=20.4
Q ss_pred CCccccccccCccCCCCCCCCCCCCccc
Q 009239 8 RNTDCVYFLASPLTCKKGLDCEYRHNEI 35 (539)
Q Consensus 8 k~~~CryFl~gpG~CkKGd~C~F~Hd~~ 35 (539)
...+|+-|-.+ |-|.+|+.|.|+|+..
T Consensus 185 qpDicKdykeT-gycg~gdSckFlh~r~ 211 (313)
T KOG1813|consen 185 QPDICKDYKET-GYCGYGDSCKFLHDRS 211 (313)
T ss_pred CchhhhhhHhh-Ccccccchhhhhhhhh
Confidence 45678777765 6888888888888875
No 44
>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=27.87 E-value=16 Score=37.55 Aligned_cols=22 Identities=23% Similarity=0.706 Sum_probs=16.8
Q ss_pred CCcccccccCCCCCCCCCCCCCCCC
Q 009239 88 TSIPCYFYFNGFCSRGDRCSFLHGP 112 (539)
Q Consensus 88 ~~~pC~Ff~~G~C~KGd~CpF~H~~ 112 (539)
...+|++|+-|+|++- -|.++.
T Consensus 29 D~~VCk~~L~g~CPhd---LF~nTK 50 (254)
T PF03194_consen 29 DPDVCKYFLVGFCPHD---LFVNTK 50 (254)
T ss_pred CcccCHHHHhCCCcHH---HHhhcc
Confidence 4678999999999986 344444
No 45
>KOG2202 consensus U2 snRNP splicing factor, small subunit, and related proteins [RNA processing and modification]
Probab=20.98 E-value=46 Score=34.71 Aligned_cols=26 Identities=31% Similarity=0.558 Sum_probs=23.2
Q ss_pred CCCcccccccCCCCCCCCCCCCCCCC
Q 009239 87 KTSIPCYFYFNGFCSRGDRCSFLHGP 112 (539)
Q Consensus 87 k~~~pC~Ff~~G~C~KGd~CpF~H~~ 112 (539)
.....|.+|..+.|.+|-.|-|.|.+
T Consensus 150 ~rea~C~~~e~~~C~rG~~CnFmH~k 175 (260)
T KOG2202|consen 150 FREAICGQFERTECSRGGACNFMHVK 175 (260)
T ss_pred hhhhhhcccccccCCCCCcCcchhhh
Confidence 34668999988899999999999998
Done!