Query psy996
Match_columns 221
No_of_seqs 156 out of 889
Neff 5.7
Searched_HMMs 46136
Date Sat Aug 17 00:02:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy996.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/996hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01385 TFSII transcription 100.0 1.1E-44 2.4E-49 326.2 19.6 166 39-219 126-291 (299)
2 KOG1105|consensus 100.0 3.8E-42 8.3E-47 307.6 18.1 193 10-220 94-289 (296)
3 smart00510 TFS2M Domain in the 99.9 1E-24 2.2E-29 168.9 10.0 101 51-164 1-101 (102)
4 PF07500 TFIIS_M: Transcriptio 99.9 3.9E-25 8.4E-30 173.5 5.2 115 49-176 1-115 (115)
5 KOG2906|consensus 99.6 4E-16 8.7E-21 119.2 -0.2 73 97-219 26-98 (105)
6 smart00440 ZnF_C2C2 C2C2 Zinc 99.5 6.9E-15 1.5E-19 95.9 3.8 33 187-219 1-33 (40)
7 PF01096 TFIIS_C: Transcriptio 99.5 2.7E-14 5.9E-19 92.6 3.8 33 187-219 1-33 (39)
8 COG1594 RPB9 DNA-directed RNA 99.3 2.4E-12 5.3E-17 101.5 3.7 37 183-219 69-105 (113)
9 PHA02998 RNA polymerase subuni 99.2 5.4E-12 1.2E-16 106.0 4.1 35 185-219 142-176 (195)
10 TIGR01384 TFS_arch transcripti 99.2 6.7E-12 1.4E-16 96.6 4.2 36 184-219 60-95 (104)
11 KOG1634|consensus 99.1 8.4E-11 1.8E-15 116.6 5.5 84 76-172 267-351 (778)
12 KOG2907|consensus 98.6 1.3E-08 2.9E-13 79.9 1.1 36 184-219 72-107 (116)
13 KOG2691|consensus 98.6 3.4E-08 7.3E-13 77.0 3.1 38 182-219 69-106 (113)
14 KOG2906|consensus 97.3 6E-05 1.3E-09 58.2 -0.2 21 136-156 77-97 (105)
15 smart00440 ZnF_C2C2 C2C2 Zinc 96.1 0.0011 2.3E-08 43.1 -0.7 17 138-154 14-30 (40)
16 PHA02998 RNA polymerase subuni 96.0 0.0021 4.7E-08 54.6 0.5 17 136-152 155-171 (195)
17 COG1594 RPB9 DNA-directed RNA 95.3 0.0054 1.2E-07 48.5 0.4 17 136-152 84-100 (113)
18 PF01096 TFIIS_C: Transcriptio 95.0 0.0047 1E-07 39.8 -0.6 17 138-154 14-30 (39)
19 KOG2907|consensus 94.4 0.015 3.3E-07 46.0 0.7 16 137-152 87-102 (116)
20 KOG1105|consensus 93.4 0.018 4E-07 52.5 -0.6 34 121-156 254-287 (296)
21 TIGR01384 TFS_arch transcripti 92.9 0.025 5.3E-07 43.3 -0.5 16 137-152 75-90 (104)
22 TIGR01385 TFSII transcription 91.1 0.048 1E-06 49.9 -0.8 29 122-152 258-286 (299)
23 COG3478 Predicted nucleic-acid 71.8 2.5 5.5E-05 30.5 1.6 25 186-212 4-28 (68)
24 PF02172 KIX: KIX domain; Int 61.3 30 0.00064 25.9 5.6 63 49-112 10-76 (81)
25 PRK09678 DNA-binding transcrip 60.6 8 0.00017 28.3 2.4 31 186-219 1-32 (72)
26 PF03719 Ribosomal_S5_C: Ribos 57.5 6.5 0.00014 28.6 1.5 12 4-15 10-21 (74)
27 PF13408 Zn_ribbon_recom: Reco 56.2 9.7 0.00021 25.2 2.1 30 184-220 3-32 (58)
28 PF09855 DUF2082: Nucleic-acid 54.5 8.1 0.00018 27.6 1.5 18 187-204 1-18 (64)
29 PF01396 zf-C4_Topoisom: Topoi 50.0 18 0.0004 23.0 2.5 24 188-219 3-26 (39)
30 PF12760 Zn_Tnp_IS1595: Transp 49.4 11 0.00024 24.6 1.4 14 186-199 18-31 (46)
31 PF07754 DUF1610: Domain of un 45.0 9.5 0.00021 22.2 0.5 11 184-194 14-24 (24)
32 PRK14892 putative transcriptio 41.5 11 0.00025 29.1 0.7 30 185-214 20-66 (99)
33 KOG2391|consensus 41.1 1E+02 0.0023 29.1 6.9 62 77-139 250-311 (365)
34 PRK00550 rpsE 30S ribosomal pr 40.8 15 0.00033 30.9 1.4 13 4-16 96-108 (168)
35 KOG4274|consensus 40.2 36 0.00077 34.3 3.9 59 51-116 9-67 (742)
36 PF08271 TF_Zn_Ribbon: TFIIB z 38.2 28 0.0006 22.3 2.0 10 187-196 1-10 (43)
37 PF03604 DNA_RNApol_7kD: DNA d 35.1 23 0.00049 21.9 1.1 14 183-196 14-27 (32)
38 KOG2703|consensus 34.4 27 0.00058 33.6 2.0 31 185-218 67-97 (460)
39 smart00659 RPOLCX RNA polymera 33.3 20 0.00042 23.6 0.7 15 183-197 16-30 (44)
40 PRK12495 hypothetical protein; 32.2 49 0.0011 29.3 3.2 18 180-197 36-53 (226)
41 PF14353 CpXC: CpXC protein 31.4 19 0.00042 28.1 0.5 12 185-196 37-48 (128)
42 PF11792 Baculo_LEF5_C: Baculo 30.9 3.6 7.7E-05 27.3 -3.1 22 191-213 12-33 (43)
43 PF14949 ARF7EP_C: ARF7 effect 28.4 26 0.00056 27.4 0.7 13 186-198 74-86 (103)
44 PF13943 WPP: WPP domain 28.0 1.5E+02 0.0032 23.1 4.8 44 51-94 9-57 (99)
45 COG5179 TAF1 Transcription ini 27.9 36 0.00079 34.7 1.8 41 153-194 905-945 (968)
46 PF05180 zf-DNL: DNL zinc fing 27.5 20 0.00043 25.8 -0.0 30 186-218 4-33 (66)
47 PHA00616 hypothetical protein 27.2 21 0.00045 23.8 -0.0 11 186-196 1-11 (44)
48 TIGR01021 rpsE_bact ribosomal 26.9 36 0.00077 28.3 1.3 13 4-16 85-97 (154)
49 TIGR02159 PA_CoA_Oxy4 phenylac 26.5 69 0.0015 26.3 3.0 12 187-198 106-117 (146)
50 COG1998 RPS31 Ribosomal protei 26.3 40 0.00086 23.1 1.2 9 185-193 36-44 (51)
51 COG2051 RPS27A Ribosomal prote 26.1 30 0.00064 25.1 0.6 18 186-203 19-36 (67)
52 KOG3507|consensus 25.8 23 0.0005 25.1 0.0 14 182-195 33-46 (62)
53 PF04606 Ogr_Delta: Ogr/Delta- 24.5 69 0.0015 21.0 2.2 31 188-220 1-31 (47)
54 PRK04044 rps5p 30S ribosomal p 23.9 40 0.00087 29.5 1.2 13 4-16 143-155 (211)
55 smart00531 TFIIE Transcription 23.8 50 0.0011 26.7 1.6 14 182-195 95-108 (147)
56 PHA02611 51 baseplate hub asse 23.1 1.4E+02 0.003 26.9 4.4 18 185-202 81-98 (249)
57 PF14354 Lar_restr_allev: Rest 22.4 1.1E+02 0.0023 20.6 2.9 32 185-218 2-33 (61)
58 PRK00398 rpoP DNA-directed RNA 22.3 43 0.00094 21.6 0.8 12 186-197 21-32 (46)
59 TIGR01020 rpsE_arch ribosomal 21.8 51 0.0011 28.9 1.4 14 4-17 143-156 (212)
60 PF00096 zf-C2H2: Zinc finger, 21.1 35 0.00075 18.3 0.2 9 187-195 1-9 (23)
61 PTZ00070 40S ribosomal protein 20.7 53 0.0011 29.7 1.3 20 4-23 171-190 (257)
62 PF13717 zinc_ribbon_4: zinc-r 20.5 38 0.00083 21.1 0.3 11 185-195 24-34 (36)
No 1
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=100.00 E-value=1.1e-44 Score=326.21 Aligned_cols=166 Identities=43% Similarity=0.618 Sum_probs=155.8
Q ss_pred ccCCCCCCCCCCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCChh
Q psy996 39 TQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPM 118 (221)
Q Consensus 39 ~~~pp~~~~~~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~ 118 (221)
+.+.| .+.++|++|++|+++|++||..+.++.+...++..+|.+||.++|+.++.++..|+.++|+|+|||||++||+
T Consensus 126 ~~~~~--~~~t~d~~Rdk~r~~L~~aL~~~~~~~~~~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~ 203 (299)
T TIGR01385 126 NDFVP--TAVTNDKVRDKCRELLYDALAKDSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPD 203 (299)
T ss_pred CCCCC--CccCCcHHHHHHHHHHHHHHhhcCCCCccccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHH
Confidence 34444 4579999999999999999998777666666788999999999999999888899999999999999999999
Q ss_pred hhhccccCcCChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHHHHHhHHHHHhhhhcCcccccccccccCCCcee
Q psy996 119 LSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKKRNCT 198 (221)
Q Consensus 119 L~~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~~~e~l~~~q~~~~~~~~T~~~~C~kC~~~~~~ 198 (221)
||.+|++|+|+|++|+.|+++ ||||+|++++++++.+++|+++|++..+++.|++|+|++||+++|+
T Consensus 204 Lr~~vl~G~i~p~~lv~Ms~e-------------Emas~e~k~~~e~~~ke~l~~~~~~~~~~~~t~~~~C~~C~~~~~~ 270 (299)
T TIGR01385 204 LRHNVLTGEITPEKLATMTAE-------------EMASAELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCT 270 (299)
T ss_pred HHHHHHcCCCCHHHHhcCCHH-------------HcCCHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccCCCCCCccce
Confidence 999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred EEEEeccCCCCCceEEEEeec
Q psy996 199 YNQVQTRSADEPMTTLHHFYI 219 (221)
Q Consensus 199 y~q~QtRsaDEpmT~f~~C~~ 219 (221)
|+|+|||+||||||+||+|++
T Consensus 271 ~~q~QtrsaDEpmT~f~~C~~ 291 (299)
T TIGR01385 271 YYQLQTRSADEPMTTFVTCEE 291 (299)
T ss_pred EEEecccCCCCCCeEEEEcCC
Confidence 999999999999999999985
No 2
>KOG1105|consensus
Probab=100.00 E-value=3.8e-42 Score=307.58 Aligned_cols=193 Identities=49% Similarity=0.721 Sum_probs=167.9
Q ss_pred CCCCCCCCCCCchh---hhccccccCCCCCCCccCCCCCCCCCCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHH
Q psy996 10 PPGISNNKDSSSKK---KEAKEEKKEDKKPSVTQYPPQKSHNLTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELE 86 (221)
Q Consensus 10 ~~~~~~~~~~s~~~---~~~~~~~~~~~~~~~~~~pp~~~~~~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE 86 (221)
.||+-..+..|.-+ +..-+.++++.+++ . +| .+..+|.+|++|+++|+.||...++....+.++..+|.+||
T Consensus 94 ~p~~~~~~~~s~~~~~~ks~~~~~~~~~~~~--~-~~--~~~~~d~~r~k~~e~l~~al~~~~~~~~~~~~~~~~a~~iE 168 (296)
T KOG1105|consen 94 DPGEASSKSPSGAKQPEKSRGDSKRDKHSGS--K-DP--VPITNDPVRDKCRELLYAALTTEDDSRVTGADPLELAVQIE 168 (296)
T ss_pred CCCcCCcCCccCCCCccccccccccccccCc--C-CC--CCCCCchHHHHHHHHHHHHhcccccccccCCCHHHHHHHHH
Confidence 34555555544433 22334444433342 2 33 55679999999999999999977766666788999999999
Q ss_pred HHHHHHhcCCChhhhhHHHHHHHhcCCCCChhhhhccccCcCChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHH
Q psy996 87 EAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKF 166 (221)
Q Consensus 87 ~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~ 166 (221)
++||..++.++.+|+.++|++++||+|++||+||++||+|+|+|++|+.|+++ ||+|++++++++++
T Consensus 169 ~~~~~~~g~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~e-------------EMaS~~lk~~~~k~ 235 (296)
T KOG1105|consen 169 EAIFEKLGNTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSE-------------EMASEELKEERQKL 235 (296)
T ss_pred HHHHHHhCCCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChh-------------hhccHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999 99999999999999
Q ss_pred HHHhHHHHHhhhhcCcccccccccccCCCceeEEEEeccCCCCCceEEEEeecc
Q psy996 167 IKESIDDAQLATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYIT 220 (221)
Q Consensus 167 ~~e~l~~~q~~~~~~~~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~~ 220 (221)
.+++|++||++..++++|+.|.|++|++++|+|+|+||||+||||||||+|...
T Consensus 236 ~keal~~~q~~~~~gt~td~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ec 289 (296)
T KOG1105|consen 236 TKEALREHQMAKIQGTQTDLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNEC 289 (296)
T ss_pred HHHHHHHHhhcccccccccceeeccccccceeEEeeccCCCCCCcceeeeeccc
Confidence 999999999999999999999999999999999999999999999999999753
No 3
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.92 E-value=1e-24 Score=168.93 Aligned_cols=101 Identities=46% Similarity=0.603 Sum_probs=94.4
Q ss_pred cHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCChhhhhccccCcCCh
Q psy996 51 DSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISA 130 (221)
Q Consensus 51 d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~isp 130 (221)
|++|++|+++|+++|..+.+..+...++..+|.+||.++|+.++..+..|++++|+|+|||||++||+|+.+|++|+|+|
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~vl~G~i~p 80 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITP 80 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCcccccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHHHHcCCCCH
Confidence 57999999999999998876655555788999999999999998878899999999999999999999999999999999
Q ss_pred hhhhcCChhhhhccCCCCchhHhhccHHHHHHHH
Q psy996 131 SKLATMTAEVQTRSADEPMTTFEMANDEMKTLRN 164 (221)
Q Consensus 131 ~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~ 164 (221)
++|+.|+++ ||||+|+|++++
T Consensus 81 ~~lv~Ms~~-------------ElAs~elk~~~e 101 (102)
T smart00510 81 EKLATMTAE-------------ELASAELKEKRE 101 (102)
T ss_pred HHHhcCCHH-------------HcCCHHHHHHHh
Confidence 999999999 999999999986
No 4
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=99.91 E-value=3.9e-25 Score=173.47 Aligned_cols=115 Identities=42% Similarity=0.635 Sum_probs=106.2
Q ss_pred CCcHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCChhhhhccccCcC
Q psy996 49 LTDSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAI 128 (221)
Q Consensus 49 ~~d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~i 128 (221)
+++++|++++++|+++|....+..+....+..+|.+||.+||..++.++..|++++|+|+|||||++|+.|+.+|++|.|
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~~~il~g~i 80 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDEQDDPEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLRRRILSGEI 80 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCCCCCTCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHHHHHHHSSS
T ss_pred CCcHHHHHHHHHHHHHHHhcCccccchhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHHHHHHcCCC
Confidence 57899999999999999998665334568899999999999999988889999999999999999999999999999999
Q ss_pred ChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHHHHHhHHHHHh
Q psy996 129 SASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQL 176 (221)
Q Consensus 129 sp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~~~e~l~~~q~ 176 (221)
+|.+||.|+++ ||+|+++|++++++.+++++++|+
T Consensus 81 ~p~~lv~ms~~-------------Elas~e~k~~~e~~~~~~l~~~~~ 115 (115)
T PF07500_consen 81 SPEELVTMSPE-------------ELASEELKEEREKIRKESLKQSQM 115 (115)
T ss_dssp TTCHHHHCTTT-------------TTTTSCCCCCHCCHHHHHHHHTB-
T ss_pred CHHHHhcCCHH-------------HhCCHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999 999999999999999999988764
No 5
>KOG2906|consensus
Probab=99.56 E-value=4e-16 Score=119.21 Aligned_cols=73 Identities=29% Similarity=0.394 Sum_probs=60.2
Q ss_pred ChhhhhHHHHHHHhcCCCCChhhhhccccCcCChhhhhcCChhhhhccCCCCchhHhhccHHHHHHHHHHHHHhHHHHHh
Q psy996 97 DNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEMANDEMKTLRNKFIKESIDDAQL 176 (221)
Q Consensus 97 ~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fElas~e~k~~r~k~~~e~l~~~q~ 176 (221)
.++|...|...|.+.+.++-+++ ++|+.|.-++++.
T Consensus 26 tCpY~~~I~~ei~~r~~~~~Kev-d~vlgg~~a~~nv------------------------------------------- 61 (105)
T KOG2906|consen 26 TCPYVFPISREISSRKYPKLKEV-DDVLGGDEAWENV------------------------------------------- 61 (105)
T ss_pred CCCceeeEeeeeeccccCchhhh-hhhcCCcccccch-------------------------------------------
Confidence 47888888877777777776776 4888887766554
Q ss_pred hhhcCcccccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996 177 ATVQGTKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219 (221)
Q Consensus 177 ~~~~~~~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~ 219 (221)
++|+. +|++||+.+++|.|+||||||||||+||.|.+
T Consensus 62 -----~~t~~-~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~ 98 (105)
T KOG2906|consen 62 -----DQTEA-TCPTCGHERAYFMQLQTRSADEPMTTFYKCCK 98 (105)
T ss_pred -----hhccC-cCCCCCCCceEEEEeeeccCCCcHhHhhhhhc
Confidence 45555 99999999999999999999999999999975
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.53 E-value=6.9e-15 Score=95.93 Aligned_cols=33 Identities=48% Similarity=0.685 Sum_probs=31.5
Q ss_pred ccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996 187 LKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219 (221)
Q Consensus 187 ~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~ 219 (221)
+.|++||+++++|+|+|+||||||||+||.|++
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~ 33 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTK 33 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCC
Confidence 579999999999999999999999999999975
No 7
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=99.48 E-value=2.7e-14 Score=92.61 Aligned_cols=33 Identities=45% Similarity=0.699 Sum_probs=28.7
Q ss_pred ccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996 187 LKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219 (221)
Q Consensus 187 ~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~ 219 (221)
++|++||++++.|+|+|+||||||||+||.|.+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~ 33 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCN 33 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESS
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCC
Confidence 589999999999999999999999999999974
No 8
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=99.28 E-value=2.4e-12 Score=101.52 Aligned_cols=37 Identities=43% Similarity=0.551 Sum_probs=33.5
Q ss_pred ccccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996 183 KTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219 (221)
Q Consensus 183 ~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~ 219 (221)
.+..+.||+||+++++|+|+||||||||||+||+|..
T Consensus 69 ~~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~ 105 (113)
T COG1594 69 PTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTR 105 (113)
T ss_pred ccccccCCCCCCceeEEEeeehhccCCCceEEEEecc
Confidence 3346899999999999999999999999999999963
No 9
>PHA02998 RNA polymerase subunit; Provisional
Probab=99.24 E-value=5.4e-12 Score=106.04 Aligned_cols=35 Identities=37% Similarity=0.432 Sum_probs=32.9
Q ss_pred ccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996 185 DLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219 (221)
Q Consensus 185 ~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~ 219 (221)
...+|++||+++++|+|+||||||||||+||.|..
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~ 176 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRD 176 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCC
Confidence 45799999999999999999999999999999975
No 10
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=99.24 E-value=6.7e-12 Score=96.60 Aligned_cols=36 Identities=36% Similarity=0.537 Sum_probs=33.2
Q ss_pred cccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996 184 TDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219 (221)
Q Consensus 184 T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~ 219 (221)
+....|++||+++++|+|+|+||||||||+||+|++
T Consensus 60 ~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~ 95 (104)
T TIGR01384 60 TTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTK 95 (104)
T ss_pred cccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCC
Confidence 345799999999999999999999999999999974
No 11
>KOG1634|consensus
Probab=99.10 E-value=8.4e-11 Score=116.63 Aligned_cols=84 Identities=32% Similarity=0.497 Sum_probs=77.4
Q ss_pred hcHHHHHHHHHHHHHHHhc-CCChhhhhHHHHHHHhcCCCCChhhhhccccCcCChhhhhcCChhhhhccCCCCchhHhh
Q psy996 76 ASLEELATELEEAIYNEFK-NTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAEVQTRSADEPMTTFEM 154 (221)
Q Consensus 76 ~~~~~lA~~IE~~i~~~~~-~~~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fEl 154 (221)
.+...++..||.++|..|+ ..+..|+.++|+|+|||||.+|+.|+.+|..|+|++++|+.|+.+ ||
T Consensus 267 ~d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msae-------------el 333 (778)
T KOG1634|consen 267 QDPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAE-------------EL 333 (778)
T ss_pred cchhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCch-------------hh
Confidence 3556777899999999999 788999999999999999999999999999999999999999999 99
Q ss_pred ccHHHHHHHHHHHHHhHH
Q psy996 155 ANDEMKTLRNKFIKESID 172 (221)
Q Consensus 155 as~e~k~~r~k~~~e~l~ 172 (221)
|+.++.+||++..++...
T Consensus 334 As~eL~~~rEek~ee~~~ 351 (778)
T KOG1634|consen 334 ASPELAEWREEKAEEMNE 351 (778)
T ss_pred cCchHHHHHHHHHHHHHh
Confidence 999999999988777653
No 12
>KOG2907|consensus
Probab=98.59 E-value=1.3e-08 Score=79.86 Aligned_cols=36 Identities=33% Similarity=0.414 Sum_probs=33.0
Q ss_pred cccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996 184 TDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219 (221)
Q Consensus 184 T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~ 219 (221)
+-...||+||+.+..|..+|+|||||.-|+||+|.+
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~k 107 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPK 107 (116)
T ss_pred chhccCcccCCchhhhhhhhcccccCCceEEEEcCc
Confidence 335699999999999999999999999999999964
No 13
>KOG2691|consensus
Probab=98.59 E-value=3.4e-08 Score=77.02 Aligned_cols=38 Identities=34% Similarity=0.470 Sum_probs=35.0
Q ss_pred cccccccccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996 182 TKTDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219 (221)
Q Consensus 182 ~~T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~ 219 (221)
..|....||+||++++.|+|.|+|.+|+.|+.||.|++
T Consensus 69 Prts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~ 106 (113)
T KOG2691|consen 69 PRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCS 106 (113)
T ss_pred CccccccCCccCCcceEEEecccccccceEEEEEEecc
Confidence 35577899999999999999999999999999999985
No 14
>KOG2906|consensus
Probab=97.26 E-value=6e-05 Score=58.15 Aligned_cols=21 Identities=57% Similarity=0.662 Sum_probs=17.8
Q ss_pred CChhhhhccCCCCchhHhhcc
Q psy996 136 MTAEVQTRSADEPMTTFEMAN 156 (221)
Q Consensus 136 m~~q~Q~rsadep~t~fElas 156 (221)
++.|||+||||||||+|+-+-
T Consensus 77 yF~qlQtRSADEPmT~FYkC~ 97 (105)
T KOG2906|consen 77 YFMQLQTRSADEPMTTFYKCC 97 (105)
T ss_pred EEEEeeeccCCCcHhHhhhhh
Confidence 667899999999999987543
No 15
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=96.09 E-value=0.0011 Score=43.11 Aligned_cols=17 Identities=65% Similarity=0.868 Sum_probs=14.2
Q ss_pred hhhhhccCCCCchhHhh
Q psy996 138 AEVQTRSADEPMTTFEM 154 (221)
Q Consensus 138 ~q~Q~rsadep~t~fEl 154 (221)
.++|+||||||||.|..
T Consensus 14 ~q~Q~RsaDE~mT~fy~ 30 (40)
T smart00440 14 FQLQTRSADEPMTVFYV 30 (40)
T ss_pred EEEcccCCCCCCeEEEE
Confidence 46899999999999643
No 16
>PHA02998 RNA polymerase subunit; Provisional
Probab=96.01 E-value=0.0021 Score=54.61 Aligned_cols=17 Identities=41% Similarity=0.438 Sum_probs=14.4
Q ss_pred CChhhhhccCCCCchhH
Q psy996 136 MTAEVQTRSADEPMTTF 152 (221)
Q Consensus 136 m~~q~Q~rsadep~t~f 152 (221)
...++|+||||||||+|
T Consensus 155 ~f~qlQTRSADEPmT~F 171 (195)
T PHA02998 155 TPMMIQTRAADEPPLVR 171 (195)
T ss_pred EEEEEeeccCCCCceEE
Confidence 44569999999999995
No 17
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=95.31 E-value=0.0054 Score=48.46 Aligned_cols=17 Identities=59% Similarity=0.696 Sum_probs=15.0
Q ss_pred CChhhhhccCCCCchhH
Q psy996 136 MTAEVQTRSADEPMTTF 152 (221)
Q Consensus 136 m~~q~Q~rsadep~t~f 152 (221)
+..++|+||||||||+|
T Consensus 84 ~y~~~QtRsaDEp~T~F 100 (113)
T COG1594 84 YYWQLQTRSADEPETRF 100 (113)
T ss_pred EEEeeehhccCCCceEE
Confidence 56679999999999995
No 18
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=95.02 E-value=0.0047 Score=39.84 Aligned_cols=17 Identities=65% Similarity=0.868 Sum_probs=14.2
Q ss_pred hhhhhccCCCCchhHhh
Q psy996 138 AEVQTRSADEPMTTFEM 154 (221)
Q Consensus 138 ~q~Q~rsadep~t~fEl 154 (221)
.++|+||||||||.|..
T Consensus 14 ~~~Q~rsaDE~~T~fy~ 30 (39)
T PF01096_consen 14 FQIQTRSADEPMTLFYV 30 (39)
T ss_dssp EEESSSSSSSSSEEEEE
T ss_pred EEeeccCCCCCCeEEEE
Confidence 36899999999999643
No 19
>KOG2907|consensus
Probab=94.36 E-value=0.015 Score=46.00 Aligned_cols=16 Identities=50% Similarity=0.520 Sum_probs=13.2
Q ss_pred ChhhhhccCCCCchhH
Q psy996 137 TAEVQTRSADEPMTTF 152 (221)
Q Consensus 137 ~~q~Q~rsadep~t~f 152 (221)
..-+|+|||||.+|.|
T Consensus 87 Y~T~QlRSADEGQTVF 102 (116)
T KOG2907|consen 87 YHTLQLRSADEGQTVF 102 (116)
T ss_pred hhhhhcccccCCceEE
Confidence 3449999999999984
No 20
>KOG1105|consensus
Probab=93.40 E-value=0.018 Score=52.52 Aligned_cols=34 Identities=41% Similarity=0.522 Sum_probs=27.4
Q ss_pred hccccCcCChhhhhcCChhhhhccCCCCchhHhhcc
Q psy996 121 RNYIFGAISASKLATMTAEVQTRSADEPMTTFEMAN 156 (221)
Q Consensus 121 ~~Il~G~isp~~l~~m~~q~Q~rsadep~t~fElas 156 (221)
..+.+|.+.-.++ -..|+|+||+|||||+|..|.
T Consensus 254 d~fkcgkckk~~c--ty~q~Qtrs~DePmtTfv~C~ 287 (296)
T KOG1105|consen 254 DLFKCGKCKKKNC--TYTQLQTRSADEPMTTFVTCN 287 (296)
T ss_pred cceeeccccccce--eEEeeccCCCCCCcceeeeec
Confidence 3678888888777 447899999999999986554
No 21
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=92.88 E-value=0.025 Score=43.27 Aligned_cols=16 Identities=56% Similarity=0.601 Sum_probs=13.7
Q ss_pred ChhhhhccCCCCchhH
Q psy996 137 TAEVQTRSADEPMTTF 152 (221)
Q Consensus 137 ~~q~Q~rsadep~t~f 152 (221)
+.++|+||||||||.|
T Consensus 75 f~~~Q~RsadE~~T~f 90 (104)
T TIGR01384 75 YWLLQTRRADEPETRF 90 (104)
T ss_pred EEEeccCCCCCCcEEE
Confidence 4458999999999995
No 22
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=91.10 E-value=0.048 Score=49.87 Aligned_cols=29 Identities=48% Similarity=0.610 Sum_probs=21.4
Q ss_pred ccccCcCChhhhhcCChhhhhccCCCCchhH
Q psy996 122 NYIFGAISASKLATMTAEVQTRSADEPMTTF 152 (221)
Q Consensus 122 ~Il~G~isp~~l~~m~~q~Q~rsadep~t~f 152 (221)
.+.|+.+.-.++ .+.|+|+||||||||+|
T Consensus 258 ~~~C~~C~~~~~--~~~q~QtrsaDEpmT~f 286 (299)
T TIGR01385 258 LFTCGKCKQKKC--TYYQLQTRSADEPMTTF 286 (299)
T ss_pred cccCCCCCCccc--eEEEecccCCCCCCeEE
Confidence 455666655454 44679999999999995
No 23
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=71.78 E-value=2.5 Score=30.46 Aligned_cols=25 Identities=24% Similarity=0.598 Sum_probs=17.4
Q ss_pred cccccccCCCceeEEEEeccCCCCCce
Q psy996 186 LLKCGKCKKRNCTYNQVQTRSADEPMT 212 (221)
Q Consensus 186 ~~~C~kC~~~~~~y~q~QtRsaDEpmT 212 (221)
+++|++||.+. |.+.+.+...+-..
T Consensus 4 ~~kCpKCgn~~--~~ekei~~tg~~ls 28 (68)
T COG3478 4 AFKCPKCGNTN--YEEKEIAATGGGLS 28 (68)
T ss_pred cccCCCcCCcc--hhhceeeccCCCcc
Confidence 57899999875 56666666655444
No 24
>PF02172 KIX: KIX domain; InterPro: IPR003101 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner []. This provides a model for activator:coactivator interactions. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.; GO: 0003712 transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2KWF_A 1KDX_A 2LQH_A 2LQI_A 1SB0_A 2AGH_B.
Probab=61.33 E-value=30 Score=25.85 Aligned_cols=63 Identities=16% Similarity=0.223 Sum_probs=44.3
Q ss_pred CCcHHHHHHHHHHHHHhhcCCCCCC--c--hhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcC
Q psy996 49 LTDSVRLKCREMLQNSIQVGDLDMD--G--LASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLK 112 (221)
Q Consensus 49 ~~d~vR~k~~~lL~~aL~~~~d~~~--~--~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk 112 (221)
-+..+|+..+.-|..++-...+... + -.++...|..||..+|....+ ...|-..+-.+++.++
T Consensus 10 vt~~lR~hlV~KLv~aI~P~pdp~a~~d~rm~~l~~yarkvE~~~fe~A~s-reeYY~llA~kiy~iq 76 (81)
T PF02172_consen 10 VTPDLRNHLVHKLVQAIFPTPDPNAMNDPRMKNLIEYARKVEKDMFETAQS-REEYYHLLAEKIYKIQ 76 (81)
T ss_dssp T-HHHHHHHHHHHHHHHS-SSSCCCCCSHHHHHHHHHHHHHHHHHHHC-SS-HHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHhcc-HHHHHHHHHHHHHHHH
Confidence 4468999999888888876433221 1 246789999999999988644 4678788877777764
No 25
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=60.65 E-value=8 Score=28.29 Aligned_cols=31 Identities=16% Similarity=0.336 Sum_probs=18.3
Q ss_pred cccccccCCCceeEEEEeccCC-CCCceEEEEeec
Q psy996 186 LLKCGKCKKRNCTYNQVQTRSA-DEPMTTLHHFYI 219 (221)
Q Consensus 186 ~~~C~kC~~~~~~y~q~QtRsa-DEpmT~f~~C~~ 219 (221)
|+.|+.||..-- ..- +|.. |+-.-.|+.|.|
T Consensus 1 mm~CP~Cg~~a~-irt--Sr~~s~~~~~~Y~qC~N 32 (72)
T PRK09678 1 MFHCPLCQHAAH-ART--SRYITDTTKERYHQCQN 32 (72)
T ss_pred CccCCCCCCccE-EEE--ChhcChhhheeeeecCC
Confidence 468999998762 211 2222 333448888875
No 26
>PF03719 Ribosomal_S5_C: Ribosomal protein S5, C-terminal domain; InterPro: IPR005324 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This is a family of proteins related to the 30S ribosomal protein S5P from Sulfolobus acidocaldarius (O05641 from SWISSPROT). Ribosomal protein S5 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in S5 have been shown to increase translational error frequencies.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_E 2XZM_E 2WDK_E 3KNJ_E 3HUY_E 2B9M_E 2Y18_E 1XMQ_E 1IBM_E 3TVF_H ....
Probab=57.54 E-value=6.5 Score=28.63 Aligned_cols=12 Identities=58% Similarity=1.093 Sum_probs=9.9
Q ss_pred eeeecCCCCCCC
Q psy996 4 IFLFPAPPGISN 15 (221)
Q Consensus 4 ~~~~~~~~~~~~ 15 (221)
|+|.|||+|.|.
T Consensus 10 V~l~Pap~G~Gl 21 (74)
T PF03719_consen 10 VFLKPAPPGTGL 21 (74)
T ss_dssp EEEEESCTTSCE
T ss_pred EEEEeCCCCcce
Confidence 688899998875
No 27
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=56.19 E-value=9.7 Score=25.19 Aligned_cols=30 Identities=20% Similarity=0.393 Sum_probs=19.6
Q ss_pred cccccccccCCCceeEEEEeccCCCCCceEEEEeecc
Q psy996 184 TDLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFYIT 220 (221)
Q Consensus 184 T~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~~ 220 (221)
++.+.|+.||+.-.. +++. --..+|.|.+.
T Consensus 3 ~g~l~C~~CG~~m~~----~~~~---~~~~yy~C~~~ 32 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTR----RKRK---GKYRYYRCSNR 32 (58)
T ss_pred CCcEEcccCCcEeEE----EECC---CCceEEEcCCC
Confidence 567899999987554 2222 22288888753
No 28
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=54.45 E-value=8.1 Score=27.60 Aligned_cols=18 Identities=28% Similarity=0.628 Sum_probs=14.1
Q ss_pred ccccccCCCceeEEEEec
Q psy996 187 LKCGKCKKRNCTYNQVQT 204 (221)
Q Consensus 187 ~~C~kC~~~~~~y~q~Qt 204 (221)
+.|+|||++....-+++.
T Consensus 1 y~C~KCg~~~~e~~~v~~ 18 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRA 18 (64)
T ss_pred CCCCCCCCcceecceEEc
Confidence 479999998877766654
No 29
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=50.03 E-value=18 Score=23.00 Aligned_cols=24 Identities=17% Similarity=0.236 Sum_probs=16.1
Q ss_pred cccccCCCceeEEEEeccCCCCCceEEEEeec
Q psy996 188 KCGKCKKRNCTYNQVQTRSADEPMTTLHHFYI 219 (221)
Q Consensus 188 ~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~ 219 (221)
.|++||+ ...+.+.|.. .|+-|.+
T Consensus 3 ~CP~Cg~---~lv~r~~k~g-----~F~~Cs~ 26 (39)
T PF01396_consen 3 KCPKCGG---PLVLRRGKKG-----KFLGCSN 26 (39)
T ss_pred CCCCCCc---eeEEEECCCC-----CEEECCC
Confidence 7999993 2344455544 8888876
No 30
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=49.39 E-value=11 Score=24.64 Aligned_cols=14 Identities=14% Similarity=0.299 Sum_probs=10.7
Q ss_pred cccccccCCCceeE
Q psy996 186 LLKCGKCKKRNCTY 199 (221)
Q Consensus 186 ~~~C~kC~~~~~~y 199 (221)
.|.||+||+.+.+.
T Consensus 18 g~~CP~Cg~~~~~~ 31 (46)
T PF12760_consen 18 GFVCPHCGSTKHYR 31 (46)
T ss_pred CCCCCCCCCeeeEE
Confidence 38999999995433
No 31
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=44.97 E-value=9.5 Score=22.22 Aligned_cols=11 Identities=18% Similarity=0.443 Sum_probs=8.8
Q ss_pred cccccccccCC
Q psy996 184 TDLLKCGKCKK 194 (221)
Q Consensus 184 T~~~~C~kC~~ 194 (221)
...|.||+||.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 45699999984
No 32
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=41.47 E-value=11 Score=29.08 Aligned_cols=30 Identities=17% Similarity=0.483 Sum_probs=20.7
Q ss_pred ccccccccCCCce-----------------eEEEEeccCCCCCceEE
Q psy996 185 DLLKCGKCKKRNC-----------------TYNQVQTRSADEPMTTL 214 (221)
Q Consensus 185 ~~~~C~kC~~~~~-----------------~y~q~QtRsaDEpmT~f 214 (221)
..|.|+.||.... +|+..|..+-|||.-+|
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~V~~l~epIDVY 66 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEFEVPSVYDEVDVY 66 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCccCEECCccccchhhH
Confidence 5788999985443 35666777888876544
No 33
>KOG2391|consensus
Probab=41.09 E-value=1e+02 Score=29.06 Aligned_cols=62 Identities=16% Similarity=0.128 Sum_probs=43.1
Q ss_pred cHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCChhhhhccccCcCChhhhhcCChh
Q psy996 77 SLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKNPMLSRNYIFGAISASKLATMTAE 139 (221)
Q Consensus 77 ~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN~~L~~~Il~G~isp~~l~~m~~q 139 (221)
.....-..||..+...-.+. ..|+.+++.-+..+++.++..+...|.++.--.++.+.+.+.
T Consensus 250 kL~~~~etLEqq~~~L~~ni-DIL~~k~~eal~~~~n~~~~~~D~~~~~~~~l~kq~l~~~A~ 311 (365)
T KOG2391|consen 250 KLVAMKETLEQQLQSLQKNI-DILKSKVREALEKAENLEALDIDEAIECTAPLYKQILECYAL 311 (365)
T ss_pred HHHHHHHHHHHHHHHHHhhh-HHHHHHHHHHHhhhccCcCCCchhhhhccchHHHHHHHhhhh
Confidence 34455566777766554443 678899998655556566677777777777777888888888
No 34
>PRK00550 rpsE 30S ribosomal protein S5; Validated
Probab=40.78 E-value=15 Score=30.91 Aligned_cols=13 Identities=31% Similarity=0.439 Sum_probs=11.1
Q ss_pred eeeecCCCCCCCC
Q psy996 4 IFLFPAPPGISNN 16 (221)
Q Consensus 4 ~~~~~~~~~~~~~ 16 (221)
++|.|||||.|--
T Consensus 96 V~l~Pap~G~Gl~ 108 (168)
T PRK00550 96 VLLKPASEGTGVI 108 (168)
T ss_pred EEEEeCCCCCceE
Confidence 7899999998863
No 35
>KOG4274|consensus
Probab=40.17 E-value=36 Score=34.31 Aligned_cols=59 Identities=15% Similarity=0.275 Sum_probs=46.0
Q ss_pred cHHHHHHHHHHHHHhhcCCCCCCchhcHHHHHHHHHHHHHHHhcCCChhhhhHHHHHHHhcCCCCC
Q psy996 51 DSVRLKCREMLQNSIQVGDLDMDGLASLEELATELEEAIYNEFKNTDNRYKNRVRSRIANLKDPKN 116 (221)
Q Consensus 51 d~vR~k~~~lL~~aL~~~~d~~~~~~~~~~lA~~IE~~i~~~~~~~~~~Yk~k~Rsl~~nLk~~kN 116 (221)
-+.|.+++.-|.++|....- +..+-|..+|+.||.+... ..+|-..+-.+|-.+++..|
T Consensus 9 ~kFRq~vIsried~l~~n~q------~~~k~a~~mE~hVF~K~~t-kDEYl~lvAkli~h~~d~s~ 67 (742)
T KOG4274|consen 9 PKFRQHVISRIEDELRKNGQ------AHSKSAKDMESHVFLKAKT-KDEYLSLVAKLIIHFRDISN 67 (742)
T ss_pred HHHHHHHHHHhhhhhhhhhh------ccCcchHHHHHHHHHhhhh-HHHHHHHHHHHHHHHHhhhh
Confidence 67899999999999987542 2236688999999999765 46898888888888877543
No 36
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=38.16 E-value=28 Score=22.29 Aligned_cols=10 Identities=30% Similarity=1.026 Sum_probs=7.2
Q ss_pred ccccccCCCc
Q psy996 187 LKCGKCKKRN 196 (221)
Q Consensus 187 ~~C~kC~~~~ 196 (221)
+.||.||++.
T Consensus 1 m~Cp~Cg~~~ 10 (43)
T PF08271_consen 1 MKCPNCGSKE 10 (43)
T ss_dssp ESBTTTSSSE
T ss_pred CCCcCCcCCc
Confidence 3678888766
No 37
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=35.13 E-value=23 Score=21.89 Aligned_cols=14 Identities=29% Similarity=0.719 Sum_probs=10.2
Q ss_pred ccccccccccCCCc
Q psy996 183 KTDLLKCGKCKKRN 196 (221)
Q Consensus 183 ~T~~~~C~kC~~~~ 196 (221)
..+.+.|+.||++=
T Consensus 14 ~~~~irC~~CG~RI 27 (32)
T PF03604_consen 14 PGDPIRCPECGHRI 27 (32)
T ss_dssp TSSTSSBSSSS-SE
T ss_pred CCCcEECCcCCCeE
Confidence 45678999999874
No 38
>KOG2703|consensus
Probab=34.38 E-value=27 Score=33.62 Aligned_cols=31 Identities=13% Similarity=0.237 Sum_probs=23.1
Q ss_pred ccccccccCCCceeEEEEeccCCCCCceEEEEee
Q psy996 185 DLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFY 218 (221)
Q Consensus 185 ~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~ 218 (221)
..|.|++||.+++ ++|-.+.+.+--+-|+|.
T Consensus 67 mSF~CpHCG~kN~---eiQ~a~~iQ~~Gvri~l~ 97 (460)
T KOG2703|consen 67 MSFECPHCGHKNN---EIQSAEEIQEGGVRIELR 97 (460)
T ss_pred EEeecCccCCccc---cccchhccccCceEEEEE
Confidence 4599999999987 566666777766666664
No 39
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=33.27 E-value=20 Score=23.63 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=11.8
Q ss_pred ccccccccccCCCce
Q psy996 183 KTDLLKCGKCKKRNC 197 (221)
Q Consensus 183 ~T~~~~C~kC~~~~~ 197 (221)
..+.+.|+.||++=.
T Consensus 16 ~~~~irC~~CG~rIl 30 (44)
T smart00659 16 SKDVVRCRECGYRIL 30 (44)
T ss_pred CCCceECCCCCceEE
Confidence 456789999999754
No 40
>PRK12495 hypothetical protein; Provisional
Probab=32.22 E-value=49 Score=29.31 Aligned_cols=18 Identities=22% Similarity=0.464 Sum_probs=12.7
Q ss_pred cCcccccccccccCCCce
Q psy996 180 QGTKTDLLKCGKCKKRNC 197 (221)
Q Consensus 180 ~~~~T~~~~C~kC~~~~~ 197 (221)
.+.....+.|+.||..=.
T Consensus 36 ~gatmsa~hC~~CG~PIp 53 (226)
T PRK12495 36 QGATMTNAHCDECGDPIF 53 (226)
T ss_pred hhcccchhhcccccCccc
Confidence 345566789999997543
No 41
>PF14353 CpXC: CpXC protein
Probab=31.43 E-value=19 Score=28.14 Aligned_cols=12 Identities=17% Similarity=0.448 Sum_probs=9.5
Q ss_pred ccccccccCCCc
Q psy996 185 DLLKCGKCKKRN 196 (221)
Q Consensus 185 ~~~~C~kC~~~~ 196 (221)
-.++||.||+.-
T Consensus 37 ~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 37 FSFTCPSCGHKF 48 (128)
T ss_pred CEEECCCCCCce
Confidence 368999999753
No 42
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain.
Probab=30.93 E-value=3.6 Score=27.32 Aligned_cols=22 Identities=27% Similarity=0.439 Sum_probs=16.1
Q ss_pred ccCCCceeEEEEeccCCCCCceE
Q psy996 191 KCKKRNCTYNQVQTRSADEPMTT 213 (221)
Q Consensus 191 kC~~~~~~y~q~QtRsaDEpmT~ 213 (221)
.|.+.-. ..+.|+|++||..+-
T Consensus 12 ~C~H~f~-~~E~Q~RAGDE~VSf 33 (43)
T PF11792_consen 12 QCKHKFV-TIEKQLRAGDEAVSF 33 (43)
T ss_pred cceeeee-ehhhhhcccchHHHH
Confidence 3777654 456899999997653
No 43
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=28.38 E-value=26 Score=27.40 Aligned_cols=13 Identities=38% Similarity=0.948 Sum_probs=10.7
Q ss_pred cccccccCCCcee
Q psy996 186 LLKCGKCKKRNCT 198 (221)
Q Consensus 186 ~~~C~kC~~~~~~ 198 (221)
-|.|++||+++|-
T Consensus 74 ~~PC~~C~S~KCG 86 (103)
T PF14949_consen 74 HYPCPKCGSRKCG 86 (103)
T ss_pred cccCCCCCCCccC
Confidence 4789999998873
No 44
>PF13943 WPP: WPP domain
Probab=28.05 E-value=1.5e+02 Score=23.07 Aligned_cols=44 Identities=16% Similarity=0.142 Sum_probs=27.9
Q ss_pred cHHHHHHHHHHHHHhhcCCC----C-CCchhcHHHHHHHHHHHHHHHhc
Q psy996 51 DSVRLKCREMLQNSIQVGDL----D-MDGLASLEELATELEEAIYNEFK 94 (221)
Q Consensus 51 d~vR~k~~~lL~~aL~~~~d----~-~~~~~~~~~lA~~IE~~i~~~~~ 94 (221)
..+|+-+++-|.+-|....- + .-....+...|..||+.-|..-+
T Consensus 9 q~tR~~vv~Rm~~nLss~s~~s~ryg~l~~eeA~~~Ak~IEe~AF~~A~ 57 (99)
T PF13943_consen 9 QRTRDAVVERMTENLSSPSILSKRYGTLPKEEAEEAAKRIEEEAFAAAN 57 (99)
T ss_pred chHHHHHHHHHHHhhhhhHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 55666666666666654321 1 11234678999999999997653
No 45
>COG5179 TAF1 Transcription initiation factor TFIID, subunit TAF1 [Transcription]
Probab=27.94 E-value=36 Score=34.73 Aligned_cols=41 Identities=29% Similarity=0.405 Sum_probs=22.4
Q ss_pred hhccHHHHHHHHHHHHHhHHHHHhhhhcCcccccccccccCC
Q psy996 153 EMANDEMKTLRNKFIKESIDDAQLATVQGTKTDLLKCGKCKK 194 (221)
Q Consensus 153 Elas~e~k~~r~k~~~e~l~~~q~~~~~~~~T~~~~C~kC~~ 194 (221)
|||+-|....|.+.++.+-+...++..+...|.. +|+.||+
T Consensus 905 ELAn~eKs~qRR~AR~~sk~G~dL~G~GRK~Ttr-~C~nCGQ 945 (968)
T COG5179 905 ELANLEKSQQRRAARQNSKNGSDLAGKGRKNTTR-TCGNCGQ 945 (968)
T ss_pred HHHhhhhhHHHHHHHhhhcccccccCCCCCCcce-ecccccc
Confidence 5555555555554444443333444433344554 9999996
No 46
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=27.45 E-value=20 Score=25.84 Aligned_cols=30 Identities=17% Similarity=0.246 Sum_probs=19.4
Q ss_pred cccccccCCCceeEEEEeccCCCCCceEEEEee
Q psy996 186 LLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFY 218 (221)
Q Consensus 186 ~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~ 218 (221)
.|+|..|+.|...-+-. .|=+--+++++|-
T Consensus 4 ~FTC~~C~~Rs~~~~sk---~aY~~GvViv~C~ 33 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSK---QAYHKGVVIVQCP 33 (66)
T ss_dssp EEEETTTTEEEEEEEEH---HHHHTSEEEEE-T
T ss_pred EEEcCCCCCccceeeCH---HHHhCCeEEEECC
Confidence 48899998887655533 3445566777774
No 47
>PHA00616 hypothetical protein
Probab=27.16 E-value=21 Score=23.76 Aligned_cols=11 Identities=18% Similarity=0.543 Sum_probs=8.6
Q ss_pred cccccccCCCc
Q psy996 186 LLKCGKCKKRN 196 (221)
Q Consensus 186 ~~~C~kC~~~~ 196 (221)
+++|++||..=
T Consensus 1 pYqC~~CG~~F 11 (44)
T PHA00616 1 MYQCLRCGGIF 11 (44)
T ss_pred CCccchhhHHH
Confidence 47899999743
No 48
>TIGR01021 rpsE_bact ribosomal protein S5, bacterial/organelle type. This model finds chloroplast ribosomal protein S5 as well as bacterial ribosomal protein S5. A candidate mitochondrial form (Saccharomyces cerevisiae YBR251W and its homolog) differs substantially and is not included in this model.
Probab=26.88 E-value=36 Score=28.29 Aligned_cols=13 Identities=38% Similarity=0.646 Sum_probs=10.9
Q ss_pred eeeecCCCCCCCC
Q psy996 4 IFLFPAPPGISNN 16 (221)
Q Consensus 4 ~~~~~~~~~~~~~ 16 (221)
++|.|||+|.|--
T Consensus 85 V~l~Pap~G~Gi~ 97 (154)
T TIGR01021 85 VLLKPASPGTGVI 97 (154)
T ss_pred EEEEECCCCCceE
Confidence 6899999998864
No 49
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=26.46 E-value=69 Score=26.26 Aligned_cols=12 Identities=25% Similarity=0.833 Sum_probs=10.5
Q ss_pred ccccccCCCcee
Q psy996 187 LKCGKCKKRNCT 198 (221)
Q Consensus 187 ~~C~kC~~~~~~ 198 (221)
..||+||+.++.
T Consensus 106 ~~cp~c~s~~t~ 117 (146)
T TIGR02159 106 VQCPRCGSADTT 117 (146)
T ss_pred CcCCCCCCCCcE
Confidence 699999999874
No 50
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=26.25 E-value=40 Score=23.15 Aligned_cols=9 Identities=56% Similarity=1.224 Sum_probs=4.5
Q ss_pred ccccccccC
Q psy996 185 DLLKCGKCK 193 (221)
Q Consensus 185 ~~~~C~kC~ 193 (221)
+...|++||
T Consensus 36 dR~~CGkCg 44 (51)
T COG1998 36 DRWACGKCG 44 (51)
T ss_pred ceeEecccc
Confidence 344555554
No 51
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=26.06 E-value=30 Score=25.09 Aligned_cols=18 Identities=17% Similarity=0.611 Sum_probs=14.6
Q ss_pred cccccccCCCceeEEEEe
Q psy996 186 LLKCGKCKKRNCTYNQVQ 203 (221)
Q Consensus 186 ~~~C~kC~~~~~~y~q~Q 203 (221)
..+|+.|++..+.|--.|
T Consensus 19 ~VkCpdC~N~q~vFshas 36 (67)
T COG2051 19 RVKCPDCGNEQVVFSHAS 36 (67)
T ss_pred EEECCCCCCEEEEeccCc
Confidence 458999999999886444
No 52
>KOG3507|consensus
Probab=25.81 E-value=23 Score=25.12 Aligned_cols=14 Identities=29% Similarity=0.914 Sum_probs=10.7
Q ss_pred cccccccccccCCC
Q psy996 182 TKTDLLKCGKCKKR 195 (221)
Q Consensus 182 ~~T~~~~C~kC~~~ 195 (221)
...|-++|+.||.|
T Consensus 33 k~~D~irCReCG~R 46 (62)
T KOG3507|consen 33 KRGDVIRCRECGYR 46 (62)
T ss_pred cCCCcEehhhcchH
Confidence 45678888888875
No 53
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=24.46 E-value=69 Score=20.96 Aligned_cols=31 Identities=10% Similarity=0.109 Sum_probs=16.8
Q ss_pred cccccCCCceeEEEEeccCCCCCceEEEEeecc
Q psy996 188 KCGKCKKRNCTYNQVQTRSADEPMTTLHHFYIT 220 (221)
Q Consensus 188 ~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~~~ 220 (221)
.||.||.+-....-.+ -++.=-..|+.|.|.
T Consensus 1 ~CP~Cg~~a~ir~S~~--~s~~~~~~Y~qC~N~ 31 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQ--LSPLTRELYCQCTNP 31 (47)
T ss_pred CcCCCCCeeEEEEchh--hCcceEEEEEEECCC
Confidence 4999998654222111 122223378888773
No 54
>PRK04044 rps5p 30S ribosomal protein S5P; Reviewed
Probab=23.92 E-value=40 Score=29.54 Aligned_cols=13 Identities=38% Similarity=0.588 Sum_probs=10.7
Q ss_pred eeeecCCCCCCCC
Q psy996 4 IFLFPAPPGISNN 16 (221)
Q Consensus 4 ~~~~~~~~~~~~~ 16 (221)
++|.|||+|.|.-
T Consensus 143 V~l~Pap~GtGii 155 (211)
T PRK04044 143 VTLKPAPRGLGLV 155 (211)
T ss_pred EEEEECCCCCeEE
Confidence 6889999998864
No 55
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=23.79 E-value=50 Score=26.71 Aligned_cols=14 Identities=29% Similarity=0.790 Sum_probs=9.8
Q ss_pred cccccccccccCCC
Q psy996 182 TKTDLLKCGKCKKR 195 (221)
Q Consensus 182 ~~T~~~~C~kC~~~ 195 (221)
.....|.||.||.+
T Consensus 95 ~~~~~Y~Cp~C~~~ 108 (147)
T smart00531 95 TNNAYYKCPNCQSK 108 (147)
T ss_pred cCCcEEECcCCCCE
Confidence 34457899999843
No 56
>PHA02611 51 baseplate hub assembly protein; Provisional
Probab=23.08 E-value=1.4e+02 Score=26.93 Aligned_cols=18 Identities=28% Similarity=0.538 Sum_probs=13.0
Q ss_pred ccccccccCCCceeEEEE
Q psy996 185 DLLKCGKCKKRNCTYNQV 202 (221)
Q Consensus 185 ~~~~C~kC~~~~~~y~q~ 202 (221)
-.++||+||+.+...+.+
T Consensus 81 ~~~tCp~Cg~e~~v~~~l 98 (249)
T PHA02611 81 VTFTCPKCKKEKTVLFNL 98 (249)
T ss_pred EEEECCCCCCceeEEEEe
Confidence 348999999996555443
No 57
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=22.38 E-value=1.1e+02 Score=20.60 Aligned_cols=32 Identities=19% Similarity=0.181 Sum_probs=17.6
Q ss_pred ccccccccCCCceeEEEEeccCCCCCceEEEEee
Q psy996 185 DLLKCGKCKKRNCTYNQVQTRSADEPMTTLHHFY 218 (221)
Q Consensus 185 ~~~~C~kC~~~~~~y~q~QtRsaDEpmT~f~~C~ 218 (221)
.+..||-||.......+.- ..+..+..+|.|.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~--~~~~~~~~~V~C~ 33 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDE--GFDYGMYYYVECT 33 (61)
T ss_pred CCcCCCCCCCcceEeeccc--CCCCCCEEEEEcC
Confidence 3568999977666554422 2222233666665
No 58
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=22.30 E-value=43 Score=21.65 Aligned_cols=12 Identities=25% Similarity=0.462 Sum_probs=10.1
Q ss_pred cccccccCCCce
Q psy996 186 LLKCGKCKKRNC 197 (221)
Q Consensus 186 ~~~C~kC~~~~~ 197 (221)
.+.|+.||++-.
T Consensus 21 ~~~Cp~CG~~~~ 32 (46)
T PRK00398 21 GVRCPYCGYRIL 32 (46)
T ss_pred ceECCCCCCeEE
Confidence 789999998765
No 59
>TIGR01020 rpsE_arch ribosomal protein S5(archaeal type)/S2(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S2 as well as archaeal ribosomal protein S5.
Probab=21.81 E-value=51 Score=28.93 Aligned_cols=14 Identities=36% Similarity=0.615 Sum_probs=11.1
Q ss_pred eeeecCCCCCCCCC
Q psy996 4 IFLFPAPPGISNNK 17 (221)
Q Consensus 4 ~~~~~~~~~~~~~~ 17 (221)
++|.|||+|.|---
T Consensus 143 V~L~PAP~GtGlia 156 (212)
T TIGR01020 143 VRLIPAPRGLGLVA 156 (212)
T ss_pred EEEEeCCCCCceec
Confidence 68899999988643
No 60
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=21.15 E-value=35 Score=18.29 Aligned_cols=9 Identities=44% Similarity=0.903 Sum_probs=7.0
Q ss_pred ccccccCCC
Q psy996 187 LKCGKCKKR 195 (221)
Q Consensus 187 ~~C~kC~~~ 195 (221)
|.|+.|+..
T Consensus 1 y~C~~C~~~ 9 (23)
T PF00096_consen 1 YKCPICGKS 9 (23)
T ss_dssp EEETTTTEE
T ss_pred CCCCCCCCc
Confidence 579999863
No 61
>PTZ00070 40S ribosomal protein S2; Provisional
Probab=20.70 E-value=53 Score=29.67 Aligned_cols=20 Identities=35% Similarity=0.502 Sum_probs=14.1
Q ss_pred eeeecCCCCCCCCCCCCchh
Q psy996 4 IFLFPAPPGISNNKDSSSKK 23 (221)
Q Consensus 4 ~~~~~~~~~~~~~~~~s~~~ 23 (221)
++|.|||+|.|.--...-++
T Consensus 171 V~L~PAP~GtGivAg~~vk~ 190 (257)
T PTZ00070 171 VRLVPAPRGTGIVAAPTPKK 190 (257)
T ss_pred EEEEeCCCCccEEeCcHHHH
Confidence 78999999998654444333
No 62
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=20.48 E-value=38 Score=21.13 Aligned_cols=11 Identities=27% Similarity=0.794 Sum_probs=8.8
Q ss_pred ccccccccCCC
Q psy996 185 DLLKCGKCKKR 195 (221)
Q Consensus 185 ~~~~C~kC~~~ 195 (221)
..++|++||+.
T Consensus 24 ~~v~C~~C~~~ 34 (36)
T PF13717_consen 24 RKVRCSKCGHV 34 (36)
T ss_pred cEEECCCCCCE
Confidence 46899999973
Done!