Query 013098
Match_columns 449
No_of_seqs 153 out of 220
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 00:23:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013098.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013098hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2560 RNA splicing factor - 100.0 6E-145 1E-149 1106.3 17.9 421 1-443 63-488 (529)
2 PF11708 Slu7: Pre-mRNA splici 100.0 5.1E-90 1.1E-94 666.4 18.5 238 88-359 1-239 (239)
3 PF00098 zf-CCHC: Zinc knuckle 92.6 0.067 1.4E-06 33.0 1.3 17 48-64 2-18 (18)
4 PF14392 zf-CCHC_4: Zinc knuck 79.1 0.71 1.5E-05 34.8 0.4 18 46-63 31-48 (49)
5 PF15288 zf-CCHC_6: Zinc knuck 71.8 1.7 3.7E-05 32.3 0.7 17 48-64 3-21 (40)
6 COG5082 AIR1 Arginine methyltr 71.8 1.9 4E-05 41.8 1.1 24 47-72 98-121 (190)
7 PF13917 zf-CCHC_3: Zinc knuck 68.5 2.2 4.8E-05 32.0 0.7 19 46-64 4-22 (42)
8 PTZ00368 universal minicircle 60.4 4.2 9.2E-05 36.7 1.1 19 47-65 130-148 (148)
9 smart00343 ZnF_C2HC zinc finge 58.3 4.8 0.0001 26.3 0.8 18 48-65 1-18 (26)
10 KOG0119 Splicing factor 1/bran 56.5 5 0.00011 44.0 1.0 19 47-65 262-280 (554)
11 COG5082 AIR1 Arginine methyltr 52.8 5.8 0.00013 38.5 0.7 22 42-63 56-77 (190)
12 PTZ00368 universal minicircle 50.1 9.3 0.0002 34.5 1.5 23 46-68 77-99 (148)
13 COG2947 Uncharacterized conser 45.7 10 0.00022 35.7 1.1 12 205-216 77-88 (156)
14 PF14787 zf-CCHC_5: GAG-polypr 41.8 16 0.00035 26.8 1.4 28 45-72 1-28 (36)
15 PF10429 Mtr2: Nuclear pore RN 35.6 14 0.0003 35.3 0.3 12 350-361 116-127 (166)
16 PF07535 zf-DBF: DBF zinc fing 35.3 14 0.00031 28.5 0.3 10 45-54 4-13 (49)
17 PF00779 BTK: BTK motif; Inte 34.7 20 0.00044 25.4 0.9 17 360-378 7-23 (32)
18 smart00107 BTK Bruton's tyrosi 34.6 20 0.00042 26.1 0.9 21 352-378 8-28 (36)
19 KOG4400 E3 ubiquitin ligase in 31.4 23 0.00049 35.1 1.1 19 47-65 144-162 (261)
20 PF09524 Phg_2220_C: Conserved 26.4 23 0.00051 29.5 0.2 18 95-112 25-43 (74)
21 smart00586 ZnF_DBF Zinc finger 25.9 25 0.00053 27.3 0.2 10 45-54 4-13 (49)
22 TIGR02220 phg_TIGR02220 phage 25.7 24 0.00053 29.6 0.2 17 95-111 28-45 (77)
23 KOG3490 Transcription elongati 25.0 24 0.00052 31.6 -0.0 17 42-59 21-37 (111)
24 TIGR03826 YvyF flagellar opero 21.9 40 0.00088 31.1 0.8 38 27-64 62-99 (137)
25 PF10593 Z1: Z1 domain; Inter 21.4 95 0.0021 30.8 3.4 35 90-124 165-209 (239)
No 1
>KOG2560 consensus RNA splicing factor - Slu7p [RNA processing and modification]
Probab=100.00 E-value=6.5e-145 Score=1106.25 Aligned_cols=421 Identities=59% Similarity=0.992 Sum_probs=378.3
Q ss_pred CCCCCcccCCCCCccccccccCCCCC---CccchhccCccc-ccccccccccccccccCCCCccccccccccccccccCC
Q 013098 1 MSSAPWYLNSEKPSLKHQRKWKSDPN---YTKSWYDRGAKV-FHAEKYRKGACANCGAMTHDAKSCMERPRKMGAKWTNI 76 (449)
Q Consensus 1 Is~aPWY~~~~~p~LkHQR~~~~~~~---~~~~wy~RG~k~-~~atKyRKGACeNCGAmtHk~KDClERPRK~GAk~t~~ 76 (449)
|+++|||+.+.+|+|+|||+++.++. ..+.||.||.+. +++||||||||+|||||||+.|||||||||+||+|||.
T Consensus 63 is~aPwY~~s~~ptLkHQr~~~~epk~m~~~~ewy~rG~kk~~~atkyRKGACeNCGAmtHk~KDCmERPRK~gAk~t~~ 142 (529)
T KOG2560|consen 63 ISKAPWYVHSEGPTLKHQRPWKEEPKIMGIKDEWYDRGKKKGSVATKYRKGACENCGAMTHKVKDCMERPRKVGAKYTDL 142 (529)
T ss_pred ccCCCceecccCccccccCCCccCCccccccchhhhcccccchHHHHHhhhhhhhhhhhhcchHHHhhcchhhcccCCCc
Confidence 89999999999999999999977544 689999999965 99999999999999999999999999999999999999
Q ss_pred cCCCCcceec-cccccccccCccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCCCCcch
Q 013098 77 NIAPDEKIET-FELDYDGKRDRWNGYDTSSYARVVERYEARDDARRKFNKEQQLKKLEEKNNNNDSGGGGDSDGEDEDDD 155 (449)
Q Consensus 77 dI~~De~iq~-~~ldyDaKRDRWnGYdp~ey~~vve~~e~~e~~rk~~~~e~~~~~~~~~~~~~~~~~~~~~d~dd~d~e 155 (449)
||++||+||+ +.+|||+||||||||||++|.+||++|++++++|.+-..+++++ .+ +. -.+.+++.
T Consensus 143 Nia~De~iq~~~~~dyD~KRDRWnGYdps~y~~vIe~yEk~eeak~K~l~~~q~~--------~d---~~--~~d~eE~~ 209 (529)
T KOG2560|consen 143 NIAPDEKIQSVLELDYDGKRDRWNGYDPSEYKEVIERYEKLEEAKIKGLKEQQKN--------GD---EA--LWDTEEGI 209 (529)
T ss_pred ccCcccccccccccccccccccccCCChHHHHHHHHHHHHHHHHHHHHHHHhhcc--------Cc---cc--cccccccc
Confidence 9999999998 89999999999999999999999999999999996543333311 11 11 11111222
Q ss_pred hhhhhhhhhhhhccchhhhhhhhcccCCCCCCcccccccccchHHHhccCCCCCCcccCCCcccccCCCCCCCCCCCccC
Q 013098 156 LRIDEAKVDESKQMDFAKVEKRVRTTGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYG 235 (449)
Q Consensus 156 ~~~de~ky~d~~d~~~~k~d~~~r~~~~~~~~tvrnLRIREDtAKYL~NLd~nSa~YDPKSRsMRe~p~~~~d~~~~~f~ 235 (449)
++.+++.|+|.++|.+. +|.+++++++|||||||||||||||+|||+|||||||||||||++|+|+.++...+|.
T Consensus 210 ~~~dee~y~D~a~~~k~-----v~~~d~~s~iTvrnLRiRED~AkYL~nld~Nsa~YDPKSRsMReep~~~~~~~e~~~~ 284 (529)
T KOG2560|consen 210 EDLDEELYADFADMLKT-----VRDTDDGSRITVRNLRIREDTAKYLRNLDVNSAYYDPKSRSMREEPLPGKDPNEDEYS 284 (529)
T ss_pred chhhHHhhhhhhccccc-----ccccCCCceeeeecceechhHHHHHHhcCCcccccCccccccccCCCCCCChhhhhhc
Confidence 23478899998888654 4556677778999999999999999999999999999999999999999999999999
Q ss_pred CCCceecccchHHHHHHHHHHHHHhhCCCCcccccCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHhcCccccccchhhhh
Q 013098 236 VNNQYRNSGQALEFKELNIHAWEAFDKGQDIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKYGNAAAEEELPRELL 315 (449)
Q Consensus 236 GdNFvR~SGea~e~~~lQ~FAWea~~kG~DvHl~AnPT~~Ell~Ke~~~kke~~k~~~k~~ileKYGg~e~l~~~p~el~ 315 (449)
|+||||+||++.+|.+||+|||+|+++|++|||||+||++|||++.|+.+++.|+.+++++||+||||.+|++.+|++||
T Consensus 285 gdnfvr~SGe~~~~~qlq~FAweA~~kG~~~H~~A~Ptk~Ell~k~~k~kke~lK~q~kq~il~kYG~~~~~d~~p~ell 364 (529)
T KOG2560|consen 285 GDNFVRNSGEALEFNQLQMFAWEAFDKGVDVHMQADPTKLELLYKENKVKKETLKKQTKQEILDKYGGGEHKDLPPKELL 364 (529)
T ss_pred ccceeeccchhhhHHHHHHHHHHHhcccceeeeecCcHHHHHHHHHhHHHHHHHHHHHHHHHHhhcCCccccccChHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccchhhhhcccccccccCccccccCccchhhhccCCCcccccccccCCccccccccccccccccCchhhHHHHHHHHHH
Q 013098 316 LGQSEREIEYDRAGRIIKGQETALPRSKYEEDVYINNHTCVWGSWWKDHQWGYKCCKQVIRNSYCTGAAGIEAAEAASDL 395 (449)
Q Consensus 316 l~qtE~yvEY~~~G~vikg~~~~~~kSkY~EDv~~~nHTsVwGSy~~~~~WGy~CC~s~~k~s~Ctg~~g~~a~~~~~~~ 395 (449)
|+|||.|+||++.|.||||+++.+++|+|+||||+|||||||||||..|+|||+|||||++||||||.+||+|+ +.++
T Consensus 365 l~qte~~iey~rkg~v~KG~e~~~~~S~yeedV~~~nht~vwgs~w~~~rwgykcc~~f~~~syctg~~g~e~~--~~~~ 442 (529)
T KOG2560|consen 365 LAQTEEYIEYSRKGKVIKGQEKIVPKSKYEEDVYINNHTSVWGSFWKEGRWGYKCCHQFIKNSYCTGSAGIEAV--AEEL 442 (529)
T ss_pred ccccHHHHHHhhccceecccccccccccchhheeccccchhhhhhhhccchhHHHHHHHHhhhcccCccchhHH--hHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999994 3345
Q ss_pred HHHhhhhhhhhhccCCccccccccccCCCCCCcccCCHHHHHHHHHHh
Q 013098 396 MKANIARKEASEETQTPVEGKRLATWGTDLPDDLVLDEDLLAEALKKV 443 (449)
Q Consensus 396 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~l~~a~~~~ 443 (449)
|.. ..+++..+.++..++....+||...+.+++++...|..+++++
T Consensus 443 ~~~--~~~~~~~~~~~~~e~k~~~~~~~~~~~~~~~~~~~~~ss~~~~ 488 (529)
T KOG2560|consen 443 SKA--SRKEASKEPPKKVEEKEMERWGERKPEDLDSNEESLPSSLSKE 488 (529)
T ss_pred hhh--hhhhccCCChhhhHHhhhhcccccchhhhccccccccccccch
Confidence 544 5566677767777788999999999999999998888877664
No 2
>PF11708 Slu7: Pre-mRNA splicing Prp18-interacting factor; InterPro: IPR021715 The spliceosome, an assembly of snRNAs (U1, U2, U4/U6, and U5) and proteins, catalyses the excision of introns from pre-mRNAs in two successive trans-esterification reactions. Step 2 depends upon integral spliceosome constituents such as U5 snRNA and Prp8 and non-spliceosomal proteins Prp16, Slu7, Prp18, and Prp22. ATP hydrolysis by the DEAH-box enzyme Prp16 promotes a conformational change in the spliceosome that leads to protection of the 3'ss from targeted RNase H cleavage. This change, which probably reflects binding of the 3'ss PyAG in the catalytic centre of the spliceosome, requires the ordered recruitment of Slu7, Prp18, and Prp22 to the spliceosome. There is a close functional relationship between Prp8, Prp18, and Slu7, and Prp18 interacts with Slu7, so that together they recruit Prp22 to the spliceosome. Most members of the family carry a zinc-finger of the CCHC-type upstream of this domain.
Probab=100.00 E-value=5.1e-90 Score=666.40 Aligned_cols=238 Identities=55% Similarity=0.877 Sum_probs=214.9
Q ss_pred ccccccccCccCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCCCCCCCCCCCcchhhhhhhhhhhhh
Q 013098 88 ELDYDGKRDRWNGYDTSSYARVVERYEARDDARRKFNKEQQLKKLEEKNNNNDSGGGGDSDGEDEDDDLRIDEAKVDESK 167 (449)
Q Consensus 88 ~ldyDaKRDRWnGYdp~ey~~vve~~e~~e~~rk~~~~e~~~~~~~~~~~~~~~~~~~~~d~dd~d~e~~~de~ky~d~~ 167 (449)
+|+|||||||||||||++|++||++|++++++|++++.+++ ..+++++|+ +..++++|.+..
T Consensus 1 ~l~yDaKRDRWnGYd~~ey~~vve~~e~~e~~r~~~~~~~~-----------------~~~~~d~d~-~~e~~~~~~~~~ 62 (239)
T PF11708_consen 1 ELDYDAKRDRWNGYDPEEYKEVVEEYEKIEEARKKLKAEKL-----------------EDDSDDEDE-EDEDEELYLDEA 62 (239)
T ss_pred CCCccccccccCCCCHHHHHHHHHHHHHHHHHHHHHHhhhc-----------------ccccccchh-hhhhhhcccchh
Confidence 47999999999999999999999999999999998754322 012222322 344566788888
Q ss_pred ccchhhhhhhhcccCCCCCCcccccccccchHHHhccCCCCCCcccCCCcccccCCCCCCCCCCCccCCCCceecccchH
Q 013098 168 QMDFAKVEKRVRTTGGGSTGTVRNLRIREDTAKYLLNLDVNSAHYDPKTRSMREDPLPDADPNDKFYGVNNQYRNSGQAL 247 (449)
Q Consensus 168 d~~~~k~d~~~r~~~~~~~~tvrnLRIREDtAKYL~NLd~nSa~YDPKSRsMRe~p~~~~d~~~~~f~GdNFvR~SGea~ 247 (449)
+|+ +.+. ++++|+|||||||||||||+|||+|||||||||||||++|+ .++...+|+|+||||+|||+.
T Consensus 63 d~~--~~~~-------k~~~t~rnLRiREDtAkYL~NLd~nsa~YDPKSRsmrd~p~--~~~~~~~~~gdnFvR~sGea~ 131 (239)
T PF11708_consen 63 DMG--KKDS-------KTRITVRNLRIREDTAKYLLNLDSNSAYYDPKSRSMRDNPA--KDPGDVLFAGDNFVRLSGEAQ 131 (239)
T ss_pred hcc--cccc-------ccccccccccccccHHHHHHhCCCCCccCCCCccccccCCC--CChhhccccccCceeccccHH
Confidence 886 3443 44559999999999999999999999999999999999997 788899999999999999999
Q ss_pred HHHHHHHHHHHHhhCCC-CcccccCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHhcCccccccchhhhhhccchhhhhcc
Q 013098 248 EFKELNIHAWEAFDKGQ-DIHMQAAPSQAELLYKNYIVIKDKLKSRTKETIMEKYGNAAAEEELPRELLLGQSEREIEYD 326 (449)
Q Consensus 248 e~~~lQ~FAWea~~kG~-DvHl~AnPT~~Ell~Ke~~~kke~~k~~~k~~ileKYGg~e~l~~~p~el~l~qtE~yvEY~ 326 (449)
+|++||+|||+++++|. +||||||||++|||+|+|+++|++++.+.+++||+||||++|+..+|++++++|||.||||+
T Consensus 132 e~~~lq~FAWea~~kg~~~~hl~AnPT~~E~l~k~~~~kk~~~~~~~k~~ll~kYGg~e~~~~~~~e~~~~qtE~yvey~ 211 (239)
T PF11708_consen 132 EFEKLQRFAWEAAKKGGLDVHLQANPTKAELLRKEFKEKKEELKEEKKQSLLEKYGGEEHLDKPPKELLLAQTERYVEYD 211 (239)
T ss_pred HHHHHHHHHHHHHhccCCceeeeeCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccCcchhhhccccccccccc
Confidence 99999999999999999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccCccccccCccchhhhccCCCcccccc
Q 013098 327 RAGRIIKGQETALPRSKYEEDVYINNHTCVWGS 359 (449)
Q Consensus 327 ~~G~vikg~~~~~~kSkY~EDv~~~nHTsVwGS 359 (449)
++ |.++.+++|||+||||+|||||||||
T Consensus 212 ~~-----g~~~~~~kSkY~EDv~~~NHtsVWGS 239 (239)
T PF11708_consen 212 RS-----GAEKAKAKSKYEEDVYINNHTSVWGS 239 (239)
T ss_pred cc-----ccccccccccchhhhccCCCCeecCC
Confidence 99 78999999999999999999999998
No 3
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 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 the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. 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: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=92.60 E-value=0.067 Score=33.04 Aligned_cols=17 Identities=41% Similarity=0.888 Sum_probs=15.3
Q ss_pred cccccccCCCCcccccc
Q 013098 48 ACANCGAMTHDAKSCME 64 (449)
Q Consensus 48 ACeNCGAmtHk~KDClE 64 (449)
.|-|||.++|..+||.+
T Consensus 2 ~C~~C~~~GH~~~~Cp~ 18 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCPK 18 (18)
T ss_dssp BCTTTSCSSSCGCTSSS
T ss_pred cCcCCCCcCcccccCcc
Confidence 59999999999999963
No 4
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=79.15 E-value=0.71 Score=34.84 Aligned_cols=18 Identities=33% Similarity=0.816 Sum_probs=16.3
Q ss_pred cccccccccCCCCccccc
Q 013098 46 KGACANCGAMTHDAKSCM 63 (449)
Q Consensus 46 KGACeNCGAmtHk~KDCl 63 (449)
...|.+||.++|..++|.
T Consensus 31 p~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 31 PRFCFHCGRIGHSDKECP 48 (49)
T ss_pred ChhhcCCCCcCcCHhHcC
Confidence 478999999999999994
No 5
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=71.79 E-value=1.7 Score=32.33 Aligned_cols=17 Identities=47% Similarity=0.940 Sum_probs=14.1
Q ss_pred cccccccCCCCc--ccccc
Q 013098 48 ACANCGAMTHDA--KSCME 64 (449)
Q Consensus 48 ACeNCGAmtHk~--KDClE 64 (449)
-|.|||+.+|.+ +.|.-
T Consensus 3 kC~~CG~~GH~~t~k~CP~ 21 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKRCPM 21 (40)
T ss_pred cccccccccccccCccCCC
Confidence 599999999988 66753
No 6
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=71.79 E-value=1.9 Score=41.85 Aligned_cols=24 Identities=38% Similarity=0.739 Sum_probs=17.7
Q ss_pred ccccccccCCCCcccccccccccccc
Q 013098 47 GACANCGAMTHDAKSCMERPRKMGAK 72 (449)
Q Consensus 47 GACeNCGAmtHk~KDClERPRK~GAk 72 (449)
--|-|||..+|-..||. |++.+-+
T Consensus 98 ~~C~~Cg~~GH~~~dC~--P~~~~~~ 121 (190)
T COG5082 98 KKCYNCGETGHLSRDCN--PSKDQQK 121 (190)
T ss_pred cccccccccCccccccC--cccccCc
Confidence 35888888888888888 6555543
No 7
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=68.52 E-value=2.2 Score=31.96 Aligned_cols=19 Identities=26% Similarity=0.629 Sum_probs=17.1
Q ss_pred cccccccccCCCCcccccc
Q 013098 46 KGACANCGAMTHDAKSCME 64 (449)
Q Consensus 46 KGACeNCGAmtHk~KDClE 64 (449)
.+.|.|||..+|-+-+|--
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4689999999999999974
No 8
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=60.44 E-value=4.2 Score=36.72 Aligned_cols=19 Identities=32% Similarity=0.870 Sum_probs=14.9
Q ss_pred ccccccccCCCCccccccc
Q 013098 47 GACANCGAMTHDAKSCMER 65 (449)
Q Consensus 47 GACeNCGAmtHk~KDClER 65 (449)
.+|-|||+++|-.+||.++
T Consensus 130 ~~C~~Cg~~gH~~~dCp~~ 148 (148)
T PTZ00368 130 KTCYNCGQTGHLSRDCPDK 148 (148)
T ss_pred CccccCCCcCcccccCCCC
Confidence 5788888888888888764
No 9
>smart00343 ZnF_C2HC zinc finger.
Probab=58.33 E-value=4.8 Score=26.28 Aligned_cols=18 Identities=39% Similarity=0.835 Sum_probs=15.5
Q ss_pred cccccccCCCCccccccc
Q 013098 48 ACANCGAMTHDAKSCMER 65 (449)
Q Consensus 48 ACeNCGAmtHk~KDClER 65 (449)
.|-+||...|..++|.+.
T Consensus 1 ~C~~CG~~GH~~~~C~~~ 18 (26)
T smart00343 1 KCYNCGKEGHIARDCPKX 18 (26)
T ss_pred CCccCCCCCcchhhCCcc
Confidence 389999999999999643
No 10
>KOG0119 consensus Splicing factor 1/branch point binding protein (RRM superfamily) [RNA processing and modification]
Probab=56.54 E-value=5 Score=44.02 Aligned_cols=19 Identities=42% Similarity=0.899 Sum_probs=18.2
Q ss_pred ccccccccCCCCccccccc
Q 013098 47 GACANCGAMTHDAKSCMER 65 (449)
Q Consensus 47 GACeNCGAmtHk~KDClER 65 (449)
-+|.|||...|+.-||-+|
T Consensus 262 ~~c~~cg~~~H~q~~cp~r 280 (554)
T KOG0119|consen 262 RACRNCGSTGHKQYDCPGR 280 (554)
T ss_pred ccccccCCCccccccCCcc
Confidence 5899999999999999998
No 11
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=52.76 E-value=5.8 Score=38.53 Aligned_cols=22 Identities=27% Similarity=0.581 Sum_probs=18.8
Q ss_pred cccccccccccccCCCCccccc
Q 013098 42 EKYRKGACANCGAMTHDAKSCM 63 (449)
Q Consensus 42 tKyRKGACeNCGAmtHk~KDCl 63 (449)
.+-+--+|-|||-.+|.++||-
T Consensus 56 ~~~~~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 56 IREENPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccccccchhcccCcccccCC
Confidence 3344689999999999999998
No 12
>PTZ00368 universal minicircle sequence binding protein (UMSBP); Provisional
Probab=50.13 E-value=9.3 Score=34.51 Aligned_cols=23 Identities=30% Similarity=0.748 Sum_probs=17.0
Q ss_pred cccccccccCCCCcccccccccc
Q 013098 46 KGACANCGAMTHDAKSCMERPRK 68 (449)
Q Consensus 46 KGACeNCGAmtHk~KDClERPRK 68 (449)
.+.|-+||.+.|..+||.++++.
T Consensus 77 ~~~C~~Cg~~GH~~~~C~~~~~~ 99 (148)
T PTZ00368 77 PRSCYNCGQTGHISRECPNRAKG 99 (148)
T ss_pred CcccCcCCCCCcccccCCCcccc
Confidence 35688888888888888886653
No 13
>COG2947 Uncharacterized conserved protein [Function unknown]
Probab=45.68 E-value=10 Score=35.66 Aligned_cols=12 Identities=50% Similarity=0.800 Sum_probs=11.2
Q ss_pred CCCCCCcccCCC
Q 013098 205 LDVNSAHYDPKT 216 (449)
Q Consensus 205 Ld~nSa~YDPKS 216 (449)
.||+|-|||||+
T Consensus 77 ~d~~spYyDPka 88 (156)
T COG2947 77 FDPASPYYDPKA 88 (156)
T ss_pred cCCCCcccCccc
Confidence 799999999997
No 14
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=41.83 E-value=16 Score=26.76 Aligned_cols=28 Identities=29% Similarity=0.536 Sum_probs=16.6
Q ss_pred ccccccccccCCCCcccccccccccccc
Q 013098 45 RKGACANCGAMTHDAKSCMERPRKMGAK 72 (449)
Q Consensus 45 RKGACeNCGAmtHk~KDClERPRK~GAk 72 (449)
+++.|-.||.-.|-..||--+-...|--
T Consensus 1 ~~~~CprC~kg~Hwa~~C~sk~d~~G~p 28 (36)
T PF14787_consen 1 PPGLCPRCGKGFHWASECRSKTDVDGNP 28 (36)
T ss_dssp ---C-TTTSSSCS-TTT---TCCCCCEE
T ss_pred CCccCcccCCCcchhhhhhhhhcccCCC
Confidence 3689999999999999998776666543
No 15
>PF10429 Mtr2: Nuclear pore RNA shuttling protein Mtr2; InterPro: IPR019488 Mtr2 is a monomeric, dual-action, RNA-shuttle protein found in yeasts. Transport across the nuclear-cytoplasmic membrane is via the macro-molecular membrane-spanning nuclear pore complex, NPC. The pore is lined by a subset of NPC members called nucleoporins that present FG (Phe-Gly) receptors, characteristically GLFG and FXFG motifs, for shuttling RNAs and proteins. RNA cargo is bound to soluble transport proteins (nuclear export factors) such as Mex67 in yeasts, and TAP in metazoa, which pass along the pore by binding to successive FG receptors. Mtr2 when bound to Mex67 maximises this FG-binding. Mtr2 also acts independently of Mex67 in transporting the large ribosomal RNA subunit through the pore []. ; PDB: 1Q40_A 1Q42_A 1OF5_B.
Probab=35.56 E-value=14 Score=35.32 Aligned_cols=12 Identities=33% Similarity=0.872 Sum_probs=1.9
Q ss_pred cCCCcccccccc
Q 013098 350 INNHTCVWGSWW 361 (449)
Q Consensus 350 ~~nHTsVwGSy~ 361 (449)
..++-.+|||||
T Consensus 116 ~~~~Rp~wgs~f 127 (166)
T PF10429_consen 116 STNTRPLWGSYF 127 (166)
T ss_dssp -------B---E
T ss_pred CCCCCCCccccc
Confidence 356778999999
No 16
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=35.28 E-value=14 Score=28.45 Aligned_cols=10 Identities=40% Similarity=1.079 Sum_probs=8.4
Q ss_pred cccccccccc
Q 013098 45 RKGACANCGA 54 (449)
Q Consensus 45 RKGACeNCGA 54 (449)
++|-||||-.
T Consensus 4 k~GYCE~C~~ 13 (49)
T PF07535_consen 4 KPGYCENCRV 13 (49)
T ss_pred CCccCccccc
Confidence 5799999975
No 17
>PF00779 BTK: BTK motif; InterPro: IPR001562 The Btk-type zinc finger or Btk motif (BM) is a conserved zinc-binding motif containing conserved cysteines and a histidine that is present in certain eukaryotic signalling proteins. The motif is named after Bruton's tyrosine kinase (Btk), an enzyme which is essential for B cell maturation in humans and mice [, ]. Btk is a member of the Tec family of protein tyrosine kinases (PTK). These kinases contain a conserved Tec homology (TH) domain between the N-terminal pleckstrin homology (PH) domain (IPR001849 from INTERPRO) and the Src homology 3 (SH3) domain (IPR001452 from INTERPRO). The N-terminal of the TH domain is highly conserved and known as the Btf motif, while the C-terminal region of the TH domain contains a proline-rich region (PRR). The Btk motif contains a conserved His and three Cys residues that form a zinc finger (although these differ from known zinc finger topologies), while PRRs are commonly involved in protein-protein interactions, including interactions with G proteins [, ]. The TH domain may be of functional importance in various signalling pathways in different species []. A complete TH domain, containing both the Btk and PRR regions, has not been found outside the Tec family; however, the Btk motif on its own does occur in other proteins, usually C-terminal to a PH domain (note that although a Btk motif always occurs C-terminal to a PH domain, not all PH domains are followed by a Btk motif). The crystal structures of Btk show that the Btk-type zinc finger has a globular core, formed by a long loop which is held together by a zinc ion, and that the Btk motif is packed against the PH domain []. The zinc-binding residues are a histidine and three cysteines, which are fully conserved in the Btk motif []. Proteins known to contain a Btk-type zinc finger include: Mammalian Bruton's tyrosine kinase (Btk), a protein tyrosine kinase involved in modulation of diverse cellular processes. Mutations affecting Btk are the cause of X-linked agammaglobulinemia (XLA) in humans and X-linked immunodeficiency in mice. Mammalian Tec, Bmx, and Itk proteins, which are tyrosine protein kinases of the Tec subfamily. Drosophila tyrosine-protein kinase Btk29A, which is required for the development of proper ring canals and of male genitalia and required for adult survival. Mammalian Ras GTPase-activating proteins (RasGAP), which regulate the activation of inactive GDP-bound Ras by converting GDP to GTP. ; GO: 0035556 intracellular signal transduction; PDB: 2E6I_A 2YS2_A 2Z0P_A 1B55_A 1BTK_B 1BWN_A.
Probab=34.69 E-value=20 Score=25.40 Aligned_cols=17 Identities=35% Similarity=1.085 Sum_probs=11.8
Q ss_pred cccCCcccccccccccccc
Q 013098 360 WWKDHQWGYKCCKQVIRNS 378 (449)
Q Consensus 360 y~~~~~WGy~CC~s~~k~s 378 (449)
.|.+|+| .||+++.+++
T Consensus 7 ~~~~g~W--~CC~q~~k~a 23 (32)
T PF00779_consen 7 AWRGGKW--LCCKQTDKSA 23 (32)
T ss_dssp -EETTCE--SSSS-SSTTS
T ss_pred cccCCcC--cCCCCcCcCC
Confidence 4467777 6999999875
No 18
>smart00107 BTK Bruton's tyrosine kinase Cys-rich motif. Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains (but not all PH domains are followed by BTK motifs). The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region.
Probab=34.62 E-value=20 Score=26.08 Aligned_cols=21 Identities=38% Similarity=1.037 Sum_probs=15.2
Q ss_pred CCcccccccccCCcccccccccccccc
Q 013098 352 NHTCVWGSWWKDHQWGYKCCKQVIRNS 378 (449)
Q Consensus 352 nHTsVwGSy~~~~~WGy~CC~s~~k~s 378 (449)
-|.++| .+|+| .||+++.++.
T Consensus 8 yHP~~~----~~G~W--~CC~q~~k~a 28 (36)
T smart00107 8 YHPSFW----VDGKW--LCCQQSEKNA 28 (36)
T ss_pred cCCCce----eCCeE--ccCCCcCcCC
Confidence 455544 67776 6999999875
No 19
>KOG4400 consensus E3 ubiquitin ligase interacting with arginine methyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=31.36 E-value=23 Score=35.07 Aligned_cols=19 Identities=32% Similarity=0.765 Sum_probs=18.1
Q ss_pred ccccccccCCCCccccccc
Q 013098 47 GACANCGAMTHDAKSCMER 65 (449)
Q Consensus 47 GACeNCGAmtHk~KDClER 65 (449)
.-|=|||.|+|-..+|.|+
T Consensus 144 ~~Cy~Cg~~GH~s~~C~~~ 162 (261)
T KOG4400|consen 144 AKCYSCGEQGHISDDCPEN 162 (261)
T ss_pred CccCCCCcCCcchhhCCCC
Confidence 6799999999999999998
No 20
>PF09524 Phg_2220_C: Conserved phage C-terminus (Phg_2220_C); InterPro: IPR011741 This entry is represented by the C-terminal domain of Bacteriophage r1t, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=26.35 E-value=23 Score=29.51 Aligned_cols=18 Identities=28% Similarity=0.757 Sum_probs=15.9
Q ss_pred cCccC-CCCchhHHHHHHH
Q 013098 95 RDRWN-GYDTSSYARVVER 112 (449)
Q Consensus 95 RDRWn-GYdp~ey~~vve~ 112 (449)
|.||+ ||..++.+.||+.
T Consensus 25 ~aRl~eG~t~edf~~VID~ 43 (74)
T PF09524_consen 25 KARLNEGYTLEDFKKVIDN 43 (74)
T ss_pred HHHHHCCCCHHHHHHHHHH
Confidence 67998 9999999999874
No 21
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=25.88 E-value=25 Score=27.30 Aligned_cols=10 Identities=40% Similarity=1.076 Sum_probs=7.9
Q ss_pred cccccccccc
Q 013098 45 RKGACANCGA 54 (449)
Q Consensus 45 RKGACeNCGA 54 (449)
.+|-||||-.
T Consensus 4 k~GYCE~Cr~ 13 (49)
T smart00586 4 KPGYCENCRE 13 (49)
T ss_pred CCcccccHhH
Confidence 4689999964
No 22
>TIGR02220 phg_TIGR02220 phage conserved hypothetical protein, C-terminal domain. This model represents the conserved C-terminal domain of a family of proteins found exclusively in bacteriophage and in bacterial prophage regions. The functions of this domain and the proteins containing it are unknown.
Probab=25.69 E-value=24 Score=29.59 Aligned_cols=17 Identities=35% Similarity=1.087 Sum_probs=15.7
Q ss_pred cCccC-CCCchhHHHHHH
Q 013098 95 RDRWN-GYDTSSYARVVE 111 (449)
Q Consensus 95 RDRWn-GYdp~ey~~vve 111 (449)
|+||+ ||..++++.||+
T Consensus 28 ~aR~~eg~~~~dfk~VId 45 (77)
T TIGR02220 28 KARWNEGYTLEDFKKVID 45 (77)
T ss_pred HHHHHcCCCHHHHHHHHH
Confidence 78999 999999999995
No 23
>KOG3490 consensus Transcription elongation factor SPT4 [Transcription]
Probab=24.96 E-value=24 Score=31.58 Aligned_cols=17 Identities=35% Similarity=0.772 Sum_probs=14.0
Q ss_pred cccccccccccccCCCCc
Q 013098 42 EKYRKGACANCGAMTHDA 59 (449)
Q Consensus 42 tKyRKGACeNCGAmtHk~ 59 (449)
.-|++--|+||+ |-|-+
T Consensus 21 ~~F~~dGC~Nc~-~l~mk 37 (111)
T KOG3490|consen 21 NGFRKDGCENCP-MLNMK 37 (111)
T ss_pred hhhhhcCCCCch-hhhhc
Confidence 458999999999 87754
No 24
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=21.86 E-value=40 Score=31.10 Aligned_cols=38 Identities=13% Similarity=0.294 Sum_probs=24.0
Q ss_pred CccchhccCcccccccccccccccccccCCCCcccccc
Q 013098 27 YTKSWYDRGAKVFHAEKYRKGACANCGAMTHDAKSCME 64 (449)
Q Consensus 27 ~~~~wy~RG~k~~~atKyRKGACeNCGAmtHk~KDClE 64 (449)
.|..|+.-|--....--.=---||+||++.+.-+-|-+
T Consensus 62 ~I~~~IreGRL~~~~~~nl~~~CE~CG~~I~~Gr~C~~ 99 (137)
T TIGR03826 62 LILKFIREGRLQLKHFPNLGYPCERCGTSIREGRLCDS 99 (137)
T ss_pred HHHHHHHcCCeeccCCCCCcCcccccCCcCCCCCccHH
Confidence 47778887753211100112469999999998888854
No 25
>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases. This domain is found associated with a helicase domain of superfamily type II [].
Probab=21.39 E-value=95 Score=30.77 Aligned_cols=35 Identities=20% Similarity=0.511 Sum_probs=23.6
Q ss_pred cccc--ccCccCCCCch--h------HHHHHHHHHHHHHHHHHHH
Q 013098 90 DYDG--KRDRWNGYDTS--S------YARVVERYEARDDARRKFN 124 (449)
Q Consensus 90 dyDa--KRDRWnGYdp~--e------y~~vve~~e~~e~~rk~~~ 124 (449)
.||. -+-|||||.|. + -.++++.|..+-+.-..++
T Consensus 165 ~~DTL~QmgRwFGYR~gY~dl~Ri~~~~~l~~~f~~i~~~~e~lr 209 (239)
T PF10593_consen 165 QYDTLMQMGRWFGYRPGYEDLCRIYMPEELYDWFRHIAEAEEELR 209 (239)
T ss_pred hHHHHHHHhhcccCCcccccceEEecCHHHHHHHHHHHHHHHHHH
Confidence 4553 47899999987 1 1577888877765555443
Done!