Query 035627
Match_columns 434
No_of_seqs 296 out of 624
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 04:43:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035627.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035627hhsearch_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 3E-48 6.4E-53 386.0 15.0 226 117-346 50-299 (299)
2 KOG1105 Transcription elongati 100.0 8.8E-48 1.9E-52 379.1 14.6 226 117-346 53-296 (296)
3 KOG1886 BAH domain proteins [T 100.0 1.9E-42 4E-47 356.6 11.0 368 3-396 56-446 (464)
4 cd04713 BAH_plant_3 BAH, or Br 100.0 8.5E-29 1.8E-33 223.8 11.7 116 3-124 26-146 (146)
5 cd04714 BAH_BAHCC1 BAH, or Bro 99.9 6.4E-26 1.4E-30 198.9 10.1 99 3-104 9-112 (121)
6 cd04716 BAH_plantDCM_I BAH, or 99.9 7.8E-25 1.7E-29 192.8 11.1 102 3-108 9-114 (122)
7 smart00510 TFS2M Domain in the 99.9 1.2E-24 2.6E-29 186.1 9.2 97 190-286 1-99 (102)
8 cd04717 BAH_polybromo BAH, or 99.9 4E-24 8.7E-29 186.6 10.2 99 3-104 9-109 (121)
9 PF07500 TFIIS_M: Transcriptio 99.9 2.7E-24 5.9E-29 186.5 7.6 113 188-300 1-115 (115)
10 smart00439 BAH Bromo adjacent 99.9 3E-22 6.6E-27 171.1 11.2 99 3-104 7-109 (120)
11 cd04718 BAH_plant_2 BAH, or Br 99.9 1.8E-23 3.9E-28 188.7 1.4 88 12-104 50-137 (148)
12 cd04370 BAH BAH, or Bromo Adja 99.9 6E-22 1.3E-26 168.8 9.8 99 3-104 9-112 (123)
13 cd04721 BAH_plant_1 BAH, or Br 99.9 6.7E-22 1.4E-26 175.9 8.7 97 3-104 13-114 (130)
14 cd04715 BAH_Orc1p_like BAH, or 99.9 1.5E-21 3.2E-26 179.1 10.1 99 3-104 35-144 (159)
15 cd04710 BAH_fungalPHD BAH, or 99.8 2.9E-21 6.3E-26 172.9 9.6 97 3-104 17-126 (135)
16 PF01426 BAH: BAH domain; Int 99.8 3.3E-21 7.2E-26 164.8 7.2 97 3-104 8-108 (119)
17 cd04709 BAH_MTA BAH, or Bromo 99.8 1.7E-20 3.6E-25 173.0 9.6 101 3-104 9-129 (164)
18 cd04712 BAH_DCM_I BAH, or Brom 99.8 3.7E-19 8E-24 158.3 10.5 94 3-104 11-118 (130)
19 cd04760 BAH_Dnmt1_I BAH, or Br 99.8 2.7E-19 5.9E-24 157.9 9.3 79 3-86 9-87 (124)
20 cd04719 BAH_Orc1p_animal BAH, 99.7 8.7E-18 1.9E-22 149.3 8.1 86 3-91 9-103 (128)
21 cd04720 BAH_Orc1p_Yeast BAH, o 99.7 2.9E-17 6.3E-22 153.4 9.2 100 3-104 58-167 (179)
22 cd04711 BAH_Dnmt1_II BAH, or B 99.7 5.1E-17 1.1E-21 144.9 7.3 89 10-104 22-125 (137)
23 cd04708 BAH_plantDCM_II BAH, o 99.7 1E-16 2.2E-21 152.0 9.5 98 3-104 13-135 (202)
24 smart00440 ZnF_C2C2 C2C2 Zinc 99.4 3.4E-13 7.5E-18 97.2 3.0 39 303-344 1-39 (40)
25 PF01096 TFIIS_C: Transcriptio 99.3 1E-12 2.2E-17 94.2 2.9 39 303-344 1-39 (39)
26 KOG1827 Chromatin remodeling c 99.3 3.7E-12 8.1E-17 137.1 5.7 100 2-104 195-296 (629)
27 COG1594 RPB9 DNA-directed RNA 99.2 3.7E-12 8.1E-17 111.2 2.8 42 302-346 72-113 (113)
28 PHA02998 RNA polymerase subuni 99.2 6.1E-12 1.3E-16 116.5 3.2 41 301-344 142-182 (195)
29 KOG2906 RNA polymerase III sub 99.1 2.3E-11 4.9E-16 102.8 1.0 49 293-344 56-104 (105)
30 TIGR01384 TFS_arch transcripti 99.0 2.1E-10 4.6E-15 97.7 3.4 43 299-344 59-101 (104)
31 KOG1634 Predicted transcriptio 98.9 6E-10 1.3E-14 122.1 4.5 67 221-287 273-342 (778)
32 KOG2907 RNA polymerase I trans 98.1 1.3E-06 2.9E-11 75.9 1.6 39 302-343 74-112 (116)
33 KOG2691 RNA polymerase II subu 97.9 7.4E-06 1.6E-10 70.7 2.5 41 301-344 72-112 (113)
34 KOG3554 Histone deacetylase co 95.4 0.0014 3.1E-08 69.1 -3.5 102 2-104 10-153 (693)
35 PF09855 DUF2082: Nucleic-acid 90.9 0.21 4.6E-06 39.8 2.7 40 303-342 1-45 (64)
36 COG5076 Transcription factor i 81.1 0.23 4.9E-06 51.5 -2.4 82 3-87 282-363 (371)
37 PF09332 Mcm10: Mcm10 replicat 72.8 1.1 2.5E-05 46.5 -0.0 33 303-349 286-318 (344)
38 PF03604 DNA_RNApol_7kD: DNA d 68.0 3 6.5E-05 28.9 1.2 26 304-343 2-27 (32)
39 smart00659 RPOLCX RNA polymera 67.9 3 6.4E-05 30.8 1.3 27 303-343 3-29 (44)
40 PF05180 zf-DNL: DNL zinc fing 66.8 1.1 2.4E-05 36.1 -1.3 37 302-344 4-40 (66)
41 PF08271 TF_Zn_Ribbon: TFIIB z 66.0 4.2 9.2E-05 29.4 1.8 29 303-343 1-29 (43)
42 PRK00398 rpoP DNA-directed RNA 64.7 4.1 8.9E-05 29.8 1.5 31 300-343 1-31 (46)
43 KOG3277 Uncharacterized conser 62.4 4.1 8.8E-05 38.0 1.4 37 302-344 79-115 (165)
44 PF04606 Ogr_Delta: Ogr/Delta- 58.5 7.9 0.00017 28.6 2.1 37 304-345 1-39 (47)
45 TIGR00244 transcriptional regu 57.5 8.7 0.00019 35.5 2.6 53 304-359 2-55 (147)
46 COG2051 RPS27A Ribosomal prote 57.4 6 0.00013 31.9 1.4 27 303-341 20-46 (67)
47 PF10080 DUF2318: Predicted me 57.2 5.5 0.00012 34.6 1.2 30 304-347 37-66 (102)
48 smart00401 ZnF_GATA zinc finge 54.6 7.3 0.00016 29.6 1.4 34 302-344 3-36 (52)
49 PF09297 zf-NADH-PPase: NADH p 54.4 8.5 0.00018 26.1 1.5 26 304-342 5-30 (32)
50 PF13717 zinc_ribbon_4: zinc-r 54.1 5.8 0.00013 27.9 0.7 11 334-344 26-36 (36)
51 PF13719 zinc_ribbon_5: zinc-r 53.4 6.8 0.00015 27.7 0.9 13 333-345 25-37 (37)
52 COG3478 Predicted nucleic-acid 53.3 12 0.00027 30.1 2.5 46 303-348 5-55 (68)
53 PRK09678 DNA-binding transcrip 51.1 11 0.00024 30.8 2.0 37 303-344 2-40 (72)
54 PF07282 OrfB_Zn_ribbon: Putat 50.3 4.7 0.0001 31.5 -0.3 40 301-355 27-66 (69)
55 COG2816 NPY1 NTP pyrophosphohy 49.8 8.6 0.00019 39.0 1.4 42 303-357 112-154 (279)
56 cd00202 ZnF_GATA Zinc finger D 49.5 5.7 0.00012 30.5 0.1 32 304-344 1-32 (54)
57 smart00509 TFS2N Domain in the 49.1 9.1 0.0002 31.1 1.2 27 117-143 48-74 (75)
58 PF08274 PhnA_Zn_Ribbon: PhnA 48.0 7.2 0.00016 26.7 0.4 9 335-343 21-29 (30)
59 COG1933 Archaeal DNA polymeras 46.3 11 0.00023 37.6 1.5 25 303-342 168-192 (253)
60 KOG3507 DNA-directed RNA polym 45.8 9.4 0.0002 30.2 0.8 28 302-343 20-47 (62)
61 PHA02942 putative transposase; 44.5 4.9 0.00011 42.2 -1.3 50 302-369 325-374 (383)
62 PRK04023 DNA polymerase II lar 42.2 11 0.00024 44.3 0.9 27 302-343 1037-1063(1121)
63 TIGR00686 phnA alkylphosphonat 41.6 15 0.00032 32.4 1.4 27 304-344 4-30 (109)
64 cd00183 TFIIS_I N-terminal dom 40.8 17 0.00037 29.4 1.6 27 117-143 50-76 (76)
65 COG1996 RPC10 DNA-directed RNA 40.5 12 0.00025 28.6 0.5 30 301-343 5-34 (49)
66 PF09723 Zn-ribbon_8: Zinc rib 40.0 19 0.00041 26.0 1.6 30 302-341 5-34 (42)
67 PF00628 PHD: PHD-finger; Int 39.8 25 0.00055 25.6 2.3 16 325-346 11-26 (51)
68 PRK06266 transcription initiat 39.4 25 0.00054 33.2 2.7 90 241-344 51-147 (178)
69 PLN00209 ribosomal protein S27 38.7 21 0.00047 30.2 1.9 29 302-342 36-64 (86)
70 PRK00415 rps27e 30S ribosomal 36.6 21 0.00046 28.2 1.5 28 303-342 12-39 (59)
71 PF06353 DUF1062: Protein of u 36.5 14 0.0003 33.9 0.5 19 335-353 15-36 (142)
72 PTZ00083 40S ribosomal protein 35.6 27 0.00058 29.6 2.0 29 302-342 35-63 (85)
73 PF02172 KIX: KIX domain; Int 34.6 2E+02 0.0042 24.1 6.9 61 190-251 12-76 (81)
74 TIGR00373 conserved hypothetic 34.5 20 0.00043 33.2 1.2 28 303-342 110-137 (158)
75 TIGR00354 polC DNA polymerase, 31.0 25 0.00054 41.3 1.4 27 302-343 1012-1038(1095)
76 PF01667 Ribosomal_S27e: Ribos 30.9 21 0.00046 27.8 0.6 27 303-341 8-34 (55)
77 PF00320 GATA: GATA zinc finge 30.5 11 0.00025 26.3 -0.9 10 335-344 22-31 (36)
78 COG2023 RPR2 RNase P subunit R 30.3 32 0.0007 30.2 1.7 32 303-344 57-93 (105)
79 PF04032 Rpr2: RNAse P Rpr2/Rp 29.9 34 0.00074 27.5 1.7 34 303-341 47-85 (85)
80 COG4332 Uncharacterized protei 29.8 45 0.00097 32.1 2.7 20 335-354 51-73 (203)
81 COG1096 Predicted RNA-binding 29.5 28 0.00061 33.5 1.3 26 303-343 150-175 (188)
82 PRK10220 hypothetical protein; 29.2 40 0.00086 29.8 2.1 28 304-345 5-32 (111)
83 TIGR02098 MJ0042_CXXC MJ0042 f 28.4 26 0.00056 24.3 0.7 12 334-345 26-37 (38)
84 COG1326 Uncharacterized archae 28.3 25 0.00054 34.1 0.7 35 303-344 7-41 (201)
85 PF11781 RRN7: RNA polymerase 27.5 26 0.00057 24.8 0.6 13 336-348 11-23 (36)
86 TIGR02300 FYDLN_acid conserved 26.7 36 0.00078 30.9 1.4 31 301-345 8-38 (129)
87 COG1327 Predicted transcriptio 26.4 52 0.0011 30.8 2.4 54 304-360 2-56 (156)
88 PRK05978 hypothetical protein; 26.4 39 0.00083 31.3 1.6 32 303-348 34-67 (148)
89 COG1997 RPL43A Ribosomal prote 25.7 55 0.0012 27.9 2.2 39 293-344 26-64 (89)
90 COG3364 Zn-ribbon containing p 25.6 24 0.00051 31.0 0.1 28 304-344 4-31 (112)
91 PF08921 DUF1904: Domain of un 25.5 29 0.00064 30.3 0.6 18 29-46 54-71 (108)
92 TIGR02605 CxxC_CxxC_SSSS putat 24.8 57 0.0012 24.0 2.0 30 302-341 5-34 (52)
93 PRK03954 ribonuclease P protei 24.0 53 0.0012 29.4 2.0 35 303-344 65-104 (121)
94 PRK14714 DNA polymerase II lar 23.9 39 0.00084 40.9 1.4 27 302-343 1253-1279(1337)
95 PF08711 Med26: TFIIS helical 23.2 24 0.00053 26.2 -0.3 26 118-143 27-53 (53)
96 PF15135 UPF0515: Uncharacteri 22.6 49 0.0011 33.3 1.6 18 333-350 155-173 (278)
97 COG4888 Uncharacterized Zn rib 22.5 65 0.0014 28.2 2.1 40 301-347 21-60 (104)
98 PF14354 Lar_restr_allev: Rest 22.1 80 0.0017 23.9 2.4 33 304-341 5-37 (61)
99 PF04216 FdhE: Protein involve 22.1 32 0.00069 34.5 0.2 39 303-350 173-214 (290)
100 PF12760 Zn_Tnp_IS1595: Transp 21.9 67 0.0014 23.4 1.8 28 303-342 19-46 (46)
101 PF14311 DUF4379: Domain of un 21.8 39 0.00085 25.4 0.6 13 334-346 29-41 (55)
102 smart00531 TFIIE Transcription 21.6 60 0.0013 29.4 1.9 36 302-344 99-134 (147)
103 PF09538 FYDLN_acid: Protein o 21.3 54 0.0012 28.7 1.5 32 301-346 8-39 (108)
104 smart00834 CxxC_CXXC_SSSS Puta 21.3 64 0.0014 22.3 1.6 9 302-310 5-13 (41)
105 PF09082 DUF1922: Domain of un 21.3 44 0.00095 27.2 0.8 27 303-344 4-30 (68)
106 PF06061 Baculo_ME53: Baculovi 21.2 45 0.00097 34.7 1.1 31 304-348 262-294 (327)
107 smart00653 eIF2B_5 domain pres 21.1 75 0.0016 27.9 2.3 31 302-342 79-110 (110)
108 COG1281 Disulfide bond chapero 20.7 31 0.00067 35.2 -0.2 84 262-353 198-286 (286)
109 PF01873 eIF-5_eIF-2B: Domain 20.5 71 0.0015 28.7 2.1 31 302-342 92-123 (125)
110 COG4306 Uncharacterized protei 20.3 43 0.00094 30.5 0.6 9 335-343 70-78 (160)
111 PF09345 DUF1987: Domain of un 20.1 64 0.0014 27.8 1.6 16 30-45 76-91 (99)
112 PF07754 DUF1610: Domain of un 20.0 59 0.0013 21.3 1.1 7 335-341 18-24 (24)
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=3e-48 Score=386.00 Aligned_cols=226 Identities=15% Similarity=0.186 Sum_probs=179.4
Q ss_pred hhhccccchhHHHHhHHHHhHhCCCCCCCcccchhh----h-h------hhhH--HhhhhhccccCCCCCCCCcC-Cccc
Q 035627 117 KTMKIISSMRLISLDQKTRVRFGDLPDIEPQETAAQ----E-Q------EDQL--KAKRMLWKKNISPLDVSREE-GCMT 182 (434)
Q Consensus 117 ~~~~~~~~~EId~Lv~Kti~kw~d~vd~EK~~k~~~----~-~------~~~~--~~~~~~~k~~~~~~~~~R~~-~d~v 182 (434)
.-++.|.+.+|..|+..+|..|++.|+.++.++.+. . + +... +.......++..+.+.+|++ ++++
T Consensus 50 n~lrkh~~~~I~~lAk~li~~WK~~v~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 129 (299)
T TIGR01385 50 NKLRKHPNEDISKLAKKIIKSWKKVVDKNKSDHPGGNPEDKTTVGESVNSVKQEAKSQSDKIEQPKYVSSSPRNAKNDFV 129 (299)
T ss_pred HHHHcCCcHHHHHHHHHHHHHHHHHHhhhcccCcccccccccccCCCCCCCCccccCCcccccCCCCCCCcccccCCCCC
Confidence 345679999999999999999999999875543211 0 0 0000 00001111223344566766 7888
Q ss_pred ccccccChhHHHHHHHHHHhhhccCCCCCCChhhHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhcc--cChhhhhhh
Q 035627 183 RFKALTRETYRDKWLERLLQGLQHNGNSFLWPDTAIAAVTALEKASHDALSSDFQKRNQKLRQLLFNLK--STALLALRF 260 (434)
Q Consensus 183 ~~~~~Tgd~~RDkcielLy~aL~~~~~s~~~~~~v~~~A~~IE~a~~~~~~~~~~~Yk~K~Rsl~~NLK--~Np~Lr~rv 260 (434)
.+ .+|||++||+|+++||+||+.+.+......++..+|.+||.++|..++.+..+|++|||||+|||| +||+||++|
T Consensus 130 ~~-~~t~d~~Rdk~r~~L~~aL~~~~~~~~~~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~v 208 (299)
T TIGR01385 130 PT-AVTNDKVRDKCRELLYDALAKDSDHPPQSIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNPDLRHNV 208 (299)
T ss_pred CC-ccCCcHHHHHHHHHHHHHHhhcCCCCccccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCHHHHHHH
Confidence 88 589999999999999999998744322222566789999999999999888899999999999998 699999999
Q ss_pred ccCCCCccccccCChhhhcchhcHHHHhhhhhHHHhhccc--------CccccCCCCCccccceeeecccCCCCcceeee
Q 035627 261 LKGKLEPSKILDMSPNELNEGLTAEETAKEESDESEQMQM--------TDARCSRCNECKVGLRDIIQAGLGDRYQQLSK 332 (434)
Q Consensus 261 l~G~I~p~~lv~Ms~eELas~~~~ee~~k~e~~~i~~~q~--------~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~ 332 (434)
|+|+|+|++|+.|+++||||+++++++++...+.++..|+ +.|+|++|++++|+|+|+ |||||||||| +
T Consensus 209 l~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~ke~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~-QtrsaDEpmT--~ 285 (299)
T TIGR01385 209 LTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQL-QTRSADEPMT--T 285 (299)
T ss_pred HcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccCCCCCCccceEEEe-cccCCCCCCe--E
Confidence 9999999999999999999988877776666666665544 347999999999999995 9999999999 5
Q ss_pred eeeccccCcccccC
Q 035627 333 ALGVYCHGHSWYAS 346 (434)
Q Consensus 333 FvtC~~CGnrWk~s 346 (434)
|++|++|||+|+||
T Consensus 286 f~~C~~Cg~~w~fc 299 (299)
T TIGR01385 286 FVTCEECGNRWKFC 299 (299)
T ss_pred EEEcCCCCCeeeeC
Confidence 88999999999998
No 2
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=100.00 E-value=8.8e-48 Score=379.10 Aligned_cols=226 Identities=19% Similarity=0.248 Sum_probs=180.2
Q ss_pred hhhccccchhHHHHhHHHHhHhCCCCCCC-cccchhhhh---h--hhHHhhhhhccccCCCCCCCCcCCcccc--ccccc
Q 035627 117 KTMKIISSMRLISLDQKTRVRFGDLPDIE-PQETAAQEQ---E--DQLKAKRMLWKKNISPLDVSREEGCMTR--FKALT 188 (434)
Q Consensus 117 ~~~~~~~~~EId~Lv~Kti~kw~d~vd~E-K~~k~~~~~---~--~~~~~~~~~~k~~~~~~~~~R~~~d~v~--~~~~T 188 (434)
..++++.+.||..+++.+|..|+.+++.. ..++....+ | ...+..........+..+.+|....|+. + .++
T Consensus 53 ~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~~~~~~k~~~~~~~~p~~~~~~~~s~~~~~~ks~~~~~~~~~~~~~~~~-~~~ 131 (296)
T KOG1105|consen 53 EVLKKHKNEEVRSLAKKLIKSWKKLVDKSPGREKSGDNKSHDPGEASSKSPSGAKQPEKSRGDSKRDKHSGSKDPV-PIT 131 (296)
T ss_pred HHHHhCCCHHHHHHHHHHHHHHHHHhhcccccccCccccCCCCCcCCcCCccCCCCccccccccccccccCcCCCC-CCC
Confidence 46788999999999999999999999985 111111110 0 0000000000001112223333222222 3 578
Q ss_pred ChhHHHHHHHHHHhhhccCCCCCCChhhHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhcc--cChhhhhhhccCCCC
Q 035627 189 RETYRDKWLERLLQGLQHNGNSFLWPDTAIAAVTALEKASHDALSSDFQKRNQKLRQLLFNLK--STALLALRFLKGKLE 266 (434)
Q Consensus 189 gd~~RDkcielLy~aL~~~~~s~~~~~~v~~~A~~IE~a~~~~~~~~~~~Yk~K~Rsl~~NLK--~Np~Lr~rvl~G~I~ 266 (434)
+|++|++|++|||+||..+.++...+.++..+|.+||.+||..++.+..+|+++|||+++||+ +||+||++||.|+|+
T Consensus 132 ~d~~r~k~~e~l~~al~~~~~~~~~~~~~~~~a~~iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~~Np~LR~~vl~G~i~ 211 (296)
T KOG1105|consen 132 NDPVRDKCRELLYAALTTEDDSRVTGADPLELAVQIEEAIFEKLGNTDSKYKNRYRSRVSNLKDKNNPDLRRNVLTGEIS 211 (296)
T ss_pred CchHHHHHHHHHHHHhcccccccccCCCHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccCCCCCHHHHHHHhcCCCC
Confidence 999999999999999998777777788999999999999999999999999999999999996 599999999999999
Q ss_pred ccccccCChhhhcchhcHHHHhhhhhHHHhhcccC--------ccccCCCCCccccceeeecccCCCCcceeeeeeeccc
Q 035627 267 PSKILDMSPNELNEGLTAEETAKEESDESEQMQMT--------DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYC 338 (434)
Q Consensus 267 p~~lv~Ms~eELas~~~~ee~~k~e~~~i~~~q~~--------~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~ 338 (434)
|++|+.|+++||||+.+++++.+...+.|+.+||. .|+||+|++++|||+|+ ||||+|||||| ||+|++
T Consensus 212 pe~la~mt~eEMaS~~lk~~~~k~~keal~~~q~~~~~gt~td~fkcgkckk~~cty~q~-Qtrs~DePmtT--fv~C~e 288 (296)
T KOG1105|consen 212 PERLATMTSEEMASEELKEERQKLTKEALREHQMAKIQGTQTDLFKCGKCKKKNCTYTQL-QTRSADEPMTT--FVTCNE 288 (296)
T ss_pred HHHhccCChhhhccHHHHHHHHHHHHHHHHHHhhcccccccccceeeccccccceeEEee-ccCCCCCCcce--eeeecc
Confidence 99999999999999988888877788888887762 38999999999999995 99999999994 889999
Q ss_pred cCcccccC
Q 035627 339 HGHSWYAS 346 (434)
Q Consensus 339 CGnrWk~s 346 (434)
||||||||
T Consensus 289 cgnrWkfc 296 (296)
T KOG1105|consen 289 CGNRWKFC 296 (296)
T ss_pred cCCccccC
Confidence 99999998
No 3
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=100.00 E-value=1.9e-42 Score=356.59 Aligned_cols=368 Identities=28% Similarity=0.361 Sum_probs=308.7
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCC-CceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEEE
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRD-GSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVVH 81 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~-g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V~ 81 (434)
.|++.|++++.+||||+|++||.... +.++++|+|||||+|+...++|.|....++|||+|+|+|++++++|+|+|.|+
T Consensus 56 ~vllvped~~~pPyvaii~~i~a~~~g~~~k~ev~W~YrPee~~~~~~~~~~a~~~relF~SfH~De~~A~ti~~rC~V~ 135 (464)
T KOG1886|consen 56 SVLLVPEDPGKPPYVAIIEDIYAQERGGNVKVEVQWFYRPEESEGGGSGKWGAKQPRELFLSFHEDEAFAETILHRCKVH 135 (464)
T ss_pred ceeecCCCCCCCCeeEEEeeeeccccCCCcceecccccCCCccCCCCCCCcccCCCccccccccccchhhhhhcccceee
Confidence 58999999999999999999998765 58999999999999999777788888889999999999999999999999999
Q ss_pred ecCccccCCCCCCCCceEEccce-----eecccCCCccchhhhccccchhHHHHhHHHHhHhCCCCCCCcccchhhhhhh
Q 035627 82 FVPIHKHLPNHKQHPGLSFKRFM-----TLWTGNSGSLLIKTMKIISSMRLISLDQKTRVRFGDLPDIEPQETAAQEQED 156 (434)
Q Consensus 82 ~~~ey~~lp~~~e~~~Fic~~~Y-----~l~~~~~~~~td~~~~~~~~~EId~Lv~Kti~kw~d~vd~EK~~k~~~~~~~ 156 (434)
+++.|.+++++..+++|+|+++| ++|++ ++.||....+.+|+.++.+++.+.+++++.++.....
T Consensus 136 fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~~~-----~~~~~~~~~k~e~d~~~~kt~~~~~~~~~p~~~~t~~----- 205 (464)
T KOG1886|consen 136 FVPAYKQLPNRVGHESFICRRVYDAVTSKLRKL-----RDGDFGDGQKLEIDMLVPKTGPRRGTLPDPKKVQTLN----- 205 (464)
T ss_pred eccccccccccCCCCCcccccccccccccccCc-----cccchhcccccCCccchhhhcccCCCCCCcccccccc-----
Confidence 99999999999889999999999 88888 9999999999999999999999999999999987532
Q ss_pred hHHhhhhhccccCCCCCCCCcC--Ccc---cccccccChhHHHHHHHHHHhhhccC-----------CCCCCChhhHHHH
Q 035627 157 QLKAKRMLWKKNISPLDVSREE--GCM---TRFKALTRETYRDKWLERLLQGLQHN-----------GNSFLWPDTAIAA 220 (434)
Q Consensus 157 ~~~~~~~~~k~~~~~~~~~R~~--~d~---v~~~~~Tgd~~RDkcielLy~aL~~~-----------~~s~~~~~~v~~~ 220 (434)
...+++..++..+. ..+|.. .++ -.|..+|+++.|||+++-|++++-.+ +....|++.++..
T Consensus 206 ~~~~~~~~~~s~~~--~~~r~ss~~~~~~~e~~~~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~~~~~~~~~p~~~v~~ 283 (464)
T KOG1886|consen 206 AAASKRSQQKSEIS--SLSRASSSVDGEILESFDLLTGRSDRDKVLGKLLEVVWQNSCSTSEAKPAGDQGSLWPNPSVSP 283 (464)
T ss_pred ccccceeccccccc--cccccccccccccccCCCCCCCcccccccccccchhhccccccccccCCCcccccCCCCcccch
Confidence 22233444442332 233333 233 24557899999999999999999442 2223689999999
Q ss_pred HHHHHHHHHHhccCChHHHHHHHHHHHHhcccChhhhhhhccCC-CCccccccCChhhhcchhcHHHHhhhhhHHHhhcc
Q 035627 221 VTALEKASHDALSSDFQKRNQKLRQLLFNLKSTALLALRFLKGK-LEPSKILDMSPNELNEGLTAEETAKEESDESEQMQ 299 (434)
Q Consensus 221 A~~IE~a~~~~~~~~~~~Yk~K~Rsl~~NLK~Np~Lr~rvl~G~-I~p~~lv~Ms~eELas~~~~ee~~k~e~~~i~~~q 299 (434)
..+||.+.|+.+..+..+|..+++.|.++||+-..|+.+.++|. +.|+-.+.|.+=++.++.....-.+..+.....+.
T Consensus 284 ~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k~~~~l~~~~ln~~~~~~e~~~~l~~p~~p~~~~~~~~~~~~~d~~~~l~ 363 (464)
T KOG1886|consen 284 CGALEQPSHASLAKDLESYLGLRETLVLLLKGQALLKPEPLNPGETKPEPKQELHPPSFPDGQSSPSSMKLNDDDYDGLC 363 (464)
T ss_pred hhhhhhhhhhhHhhhhhhhhhhhhHHHhhhcchhhhccccCCCcccCchhhhhccCCCCCCCccCccccccCchhHHHHH
Confidence 99999999999999999999999999999999999999999995 99999999998877775442222234444445556
Q ss_pred cCccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccccCcccccceeecCCCCCCCcccccchhhhhhHhhh
Q 035627 300 MTDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWYASRNEASSLTIDGRGSAAKSIGIASLAAAKFDSLE 379 (434)
Q Consensus 300 ~~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~sr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 379 (434)
++-..|..|=+.-|+-.++|+.++.+.||.. |+.|+-+|...|++++.+++-.+.+++ ++.| ..-|
T Consensus 364 ~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~-----~v~~~~~a~~~~~~~~~~~~~~~~~~~---~q~~------~~~~ 429 (464)
T KOG1886|consen 364 VGLELTAGSLYLYCGQEGLICAGHLPCPMLP-----EVKLSPVAAVHREGLLLAPSSVPKGTP---FQHP------PWPE 429 (464)
T ss_pred HhhhhhccchhhhcccccceeccccCCCCCC-----CcCcccccccchhhhcccceeccCCCC---ccCC------CChh
Confidence 6666889999999999999999999999995 999999999999999999987776633 4432 3579
Q ss_pred hhhCCCccccchhhHhh
Q 035627 380 KNLSSPREFEKSANDLL 396 (434)
Q Consensus 380 ~~~~~~~~~~~~~~~~~ 396 (434)
|+|.||||++++++.++
T Consensus 430 k~~~~~ret~~~~ea~~ 446 (464)
T KOG1886|consen 430 KRLCSPRETGVNGEAIC 446 (464)
T ss_pred hcccCccccCCchhccc
Confidence 99999999999877753
No 4
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.96 E-value=8.5e-29 Score=223.77 Aligned_cols=116 Identities=47% Similarity=0.854 Sum_probs=106.1
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEEEe
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVVHF 82 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V~~ 82 (434)
+|||.+++ +.+||||+|.+||+..+|.++|+|+|||||+||..+.++.+..++++|||+|+|.|+||++||+|||+|++
T Consensus 26 ~Vlv~~~~-~~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~~~ElF~S~~~d~~~~~~I~gkc~V~~ 104 (146)
T cd04713 26 CVLLVPED-DQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAEDPRELFYSFHRDEVPAESVLHPCKVAF 104 (146)
T ss_pred EEEEeCCC-CCCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCCCCeEEEeCCCCcCCHHHCcceeEEEE
Confidence 79999987 49999999999999888999999999999999986555666677899999999999999999999999999
Q ss_pred cCccccCCCCCCCCceEEccce-----eecccCCCccchhhhccccc
Q 035627 83 VPIHKHLPNHKQHPGLSFKRFM-----TLWTGNSGSLLIKTMKIISS 124 (434)
Q Consensus 83 ~~ey~~lp~~~e~~~Fic~~~Y-----~l~~~~~~~~td~~~~~~~~ 124 (434)
+++|.++|....+++|+|++.| ++|+| ||+||..++|
T Consensus 105 ~~~~~~~~~~~~~~~F~cr~~yD~~~~~~~~~-----~~~~~~~~~~ 146 (146)
T cd04713 105 VPKGKQIPLRKGHSGFIVRRVYDNVNKKLWKL-----TDQDYEDERQ 146 (146)
T ss_pred CCccccCCccCCCCeEEEEEEEcCCCCcEeec-----cccccccccC
Confidence 9999999988677899999999 99999 9999998764
No 5
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.93 E-value=6.4e-26 Score=198.86 Aligned_cols=99 Identities=28% Similarity=0.445 Sum_probs=90.4
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEEEe
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVVHF 82 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V~~ 82 (434)
||||.+++.+.+||||+|.+||++.+|.++|+|+|||||+||. .|+...++++|||+|+|.|+||++||+|||.|++
T Consensus 9 ~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~---~~~~~~~~~~EvF~S~~~d~~~~~~I~gkc~V~~ 85 (121)
T cd04714 9 CVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETK---GGRKPNHGEKELFASDHQDENSVQTIEHKCYVLT 85 (121)
T ss_pred EEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHcc---CcccccCCCCceEecCCcccccHHHhCcccEEEe
Confidence 7999998867899999999999998899999999999999997 3666778999999999999999999999999999
Q ss_pred cCccccCCCC-----CCCCceEEccce
Q 035627 83 VPIHKHLPNH-----KQHPGLSFKRFM 104 (434)
Q Consensus 83 ~~ey~~lp~~-----~e~~~Fic~~~Y 104 (434)
+++|.++.+. ...+.|+|+..|
T Consensus 86 ~~ey~~~~~~~~~~~~~~d~~~Ce~~y 112 (121)
T cd04714 86 FAEYERLARVKKKPQDGVDFYYCAGTY 112 (121)
T ss_pred hhHheecccccCCCCcCCCEEEEeccC
Confidence 9999998753 256889999988
No 6
>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.92 E-value=7.8e-25 Score=192.79 Aligned_cols=102 Identities=17% Similarity=0.315 Sum_probs=89.7
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCC-CCCCCCCceeecCCcccccccceeceeEEE
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGN-WLSGDTRELFYSFHRDEIPVESVMHKCVVH 81 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~-~~~~~~rELF~S~h~D~~pv~sI~gKC~V~ 81 (434)
+|||.+++ +.+||||||++||++.+|..+|+|+|||||+||.. |+ ..+++++|||+|+|.|+||++||+|||+|+
T Consensus 9 ~V~v~~~~-~~~~yi~rI~~i~e~~~g~~~~~v~WyyRpeet~~---~r~~~~~~~rEvFlS~~~D~~pl~~I~~Kc~V~ 84 (122)
T cd04716 9 DAYVQGGE-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVI---ERQATNHDKKRVFYSEIKNDNPLDCLISKVKIL 84 (122)
T ss_pred EEEEECCC-CCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhcc---ccccccCCCceEEEecccCccchhheeeeeEEE
Confidence 69999986 59999999999999999999999999999999983 54 578899999999999999999999999999
Q ss_pred ecCccccCCC---CCCCCceEEccceeecc
Q 035627 82 FVPIHKHLPN---HKQHPGLSFKRFMTLWT 108 (434)
Q Consensus 82 ~~~ey~~lp~---~~e~~~Fic~~~Y~l~~ 108 (434)
+++++..++. .....+|.|+..|++-+
T Consensus 85 ~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~ 114 (122)
T cd04716 85 QVPPNVGTKRKKPNSEKCDYYYDMEYCVPY 114 (122)
T ss_pred EeCCCCCcccccccCCCceEEEeeEeccch
Confidence 9999998833 22367899999994443
No 7
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.91 E-value=1.2e-24 Score=186.11 Aligned_cols=97 Identities=26% Similarity=0.330 Sum_probs=84.9
Q ss_pred hhHHHHHHHHHHhhhccCCCCCCChhhHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhcc--cChhhhhhhccCCCCc
Q 035627 190 ETYRDKWLERLLQGLQHNGNSFLWPDTAIAAVTALEKASHDALSSDFQKRNQKLRQLLFNLK--STALLALRFLKGKLEP 267 (434)
Q Consensus 190 d~~RDkcielLy~aL~~~~~s~~~~~~v~~~A~~IE~a~~~~~~~~~~~Yk~K~Rsl~~NLK--~Np~Lr~rvl~G~I~p 267 (434)
|++||+|+++||+||+.+.........+..+|.+||.++|..++.+..+|++|+|||+|||| +||+||++|++|+|+|
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 68999999999999999854322223567789999999999998888899999999999999 6999999999999999
Q ss_pred cccccCChhhhcchhcHHH
Q 035627 268 SKILDMSPNELNEGLTAEE 286 (434)
Q Consensus 268 ~~lv~Ms~eELas~~~~ee 286 (434)
++|+.||++||||++++++
T Consensus 81 ~~lv~Ms~~ElAs~elk~~ 99 (102)
T smart00510 81 EKLATMTAEELASAELKEK 99 (102)
T ss_pred HHHhcCCHHHcCCHHHHHH
Confidence 9999999999999655443
No 8
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.91 E-value=4e-24 Score=186.63 Aligned_cols=99 Identities=22% Similarity=0.260 Sum_probs=89.0
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEEEe
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVVHF 82 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V~~ 82 (434)
||||.+++.+.+||||+|.+||++.+|.++|+|+|||||+||. + +....+.+||||+|.+.|+||+++|+|||.|++
T Consensus 9 ~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~-~--~~~~~~~~~Evfls~~~d~~~~~~I~~kc~Vl~ 85 (121)
T cd04717 9 CVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETF-H--EPTRKFYKNEVFKSPLYETVPVEEIVGKCAVMD 85 (121)
T ss_pred EEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHcc-C--CCccccccCceEEcCccccccHHHhcCeeEEEe
Confidence 7999998866999999999999998899999999999999997 2 233456799999999999999999999999999
Q ss_pred cCccccCCCCC--CCCceEEccce
Q 035627 83 VPIHKHLPNHK--QHPGLSFKRFM 104 (434)
Q Consensus 83 ~~ey~~lp~~~--e~~~Fic~~~Y 104 (434)
+++|.+..+.. +.+.|+|++.|
T Consensus 86 ~~~y~~~~p~~~~~~dvy~ce~~y 109 (121)
T cd04717 86 VKDYIKGRPTEISEEDVYVCESRY 109 (121)
T ss_pred hHHHhcCCCCCCCCCCEEEEeEEE
Confidence 99999988654 56889999998
No 9
>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=99.90 E-value=2.7e-24 Score=186.45 Aligned_cols=113 Identities=34% Similarity=0.436 Sum_probs=101.2
Q ss_pred cChhHHHHHHHHHHhhhccCCCCCCChhhHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhcc--cChhhhhhhccCCC
Q 035627 188 TRETYRDKWLERLLQGLQHNGNSFLWPDTAIAAVTALEKASHDALSSDFQKRNQKLRQLLFNLK--STALLALRFLKGKL 265 (434)
Q Consensus 188 Tgd~~RDkcielLy~aL~~~~~s~~~~~~v~~~A~~IE~a~~~~~~~~~~~Yk~K~Rsl~~NLK--~Np~Lr~rvl~G~I 265 (434)
|++++|++|+++|+++|....+....+..+..+|.+||.++|..|+++..+|++|+|+|+|||| +||.|+.+|++|+|
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 7899999999999999999854423678899999999999999998788899999999999999 79999999999999
Q ss_pred CccccccCChhhhcchhcHHHHhhhhhHHHhhccc
Q 035627 266 EPSKILDMSPNELNEGLTAEETAKEESDESEQMQM 300 (434)
Q Consensus 266 ~p~~lv~Ms~eELas~~~~ee~~k~e~~~i~~~q~ 300 (434)
+|.+||.||++|||++++++++++...+.++.+||
T Consensus 81 ~p~~lv~ms~~Elas~e~k~~~e~~~~~~l~~~~~ 115 (115)
T PF07500_consen 81 SPEELVTMSPEELASEELKEEREKIRKESLKQSQM 115 (115)
T ss_dssp TTCHHHHCTTTTTTTSCCCCCHCCHHHHHHHHTB-
T ss_pred CHHHHhcCCHHHhCCHHHHHHHHHHHHHHHHHhhC
Confidence 99999999999999998888887777788887776
No 10
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.88 E-value=3e-22 Score=171.13 Aligned_cols=99 Identities=25% Similarity=0.385 Sum_probs=89.0
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCCc-eEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEEE
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDGS-MMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVVH 81 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g~-~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V~ 81 (434)
+||+.+++..+++|||+|.+||++.+|. ++++|+|||||+||.. +....+++||||+|+|.|++|+++|.|||.|+
T Consensus 7 ~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~---~~~~~~~~~Elf~s~~~~~i~~~~I~~kc~V~ 83 (120)
T smart00439 7 FVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVL---EKAALFDKNEVFLSDEYDTVPLSDIIGKCNVL 83 (120)
T ss_pred EEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhccc---cccccCCCcceEEEccCccCChHHeeeEEEEE
Confidence 7999998877899999999999998888 8999999999999983 44445689999999999999999999999999
Q ss_pred ecCccccCCCCC---CCCceEEccce
Q 035627 82 FVPIHKHLPNHK---QHPGLSFKRFM 104 (434)
Q Consensus 82 ~~~ey~~lp~~~---e~~~Fic~~~Y 104 (434)
+.++|...++.. +.+.|+|++.|
T Consensus 84 ~~~~~~~~~~~~~~~~~~~f~cr~~y 109 (120)
T smart00439 84 SKSDYPGLRPEGKIGEPDVFFCESLY 109 (120)
T ss_pred EcchhcccccccCCCCCCeEEEEEEE
Confidence 999999887755 46899999988
No 11
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.87 E-value=1.8e-23 Score=188.72 Aligned_cols=88 Identities=19% Similarity=0.319 Sum_probs=82.6
Q ss_pred CCCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEEEecCccccCCC
Q 035627 12 NQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVVHFVPIHKHLPN 91 (434)
Q Consensus 12 ~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V~~~~ey~~lp~ 91 (434)
.+.+|||||++||++. |..+|+|+||||||||. +|++.+++.+|||+|+|.|++|+++|+|||.|+++.+|.++.+
T Consensus 50 ~~~~~vArIekiW~~~-G~~~~~grWy~rPEET~---~gr~~~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~ 125 (148)
T cd04718 50 SGDLWLARIEKLWEEN-GTYWYAARWYTLPEETH---MGRQPHNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASN 125 (148)
T ss_pred cCchHHHHHHHHHhcc-CceEEEEEEEeCchhcc---CccccccccceeeeccccccccHHHHhcccEEcCHHHcccccC
Confidence 4689999999999986 99999999999999998 6889999999999999999999999999999999999999887
Q ss_pred CCCCCceEEccce
Q 035627 92 HKQHPGLSFKRFM 104 (434)
Q Consensus 92 ~~e~~~Fic~~~Y 104 (434)
.+ .++|+|++.|
T Consensus 126 ~g-~Dvy~Ce~~Y 137 (148)
T cd04718 126 DG-DDVFLCEYEY 137 (148)
T ss_pred CC-CceEEEEEEE
Confidence 65 6789999999
No 12
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=99.87 E-value=6e-22 Score=168.83 Aligned_cols=99 Identities=37% Similarity=0.574 Sum_probs=88.0
Q ss_pred EEEEecCCC--CCCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEE
Q 035627 3 LFSFTPEDT--NQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVV 80 (434)
Q Consensus 3 ~Vll~p~~~--~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V 80 (434)
+||+.+++. .++||||+|.+||++.+|.++++|+|||||+||.. +....+++||||+|+|.|++|+++|.|||.|
T Consensus 9 ~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~---~~~~~~~~~Elf~s~~~~~i~v~~I~gkc~V 85 (123)
T cd04370 9 SVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPK---GLSPFALRRELFLSDHLDEIPVESIIGKCKV 85 (123)
T ss_pred EEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhcc---ccccccccceeEEecCccccCHHHhccccEE
Confidence 799999874 48999999999999989999999999999999983 4444678999999999999999999999999
Q ss_pred EecCccccCC---CCCCCCceEEccce
Q 035627 81 HFVPIHKHLP---NHKQHPGLSFKRFM 104 (434)
Q Consensus 81 ~~~~ey~~lp---~~~e~~~Fic~~~Y 104 (434)
++..+|.+.. .....+.|+|++.|
T Consensus 86 ~~~~~~~~~~~~~~~~~~~~f~~r~~y 112 (123)
T cd04370 86 LFVSEFEGLKQRPNKIDTDDFFCRLAY 112 (123)
T ss_pred EechHhhccccccccCCCCeEEEEEEE
Confidence 9999999874 34456789999988
No 13
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.86 E-value=6.7e-22 Score=175.88 Aligned_cols=97 Identities=23% Similarity=0.281 Sum_probs=86.0
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCCCCC-CCCCceeecCCcccccccceeceeEEE
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGNWLS-GDTRELFYSFHRDEIPVESVMHKCVVH 81 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~~~~-~~~rELF~S~h~D~~pv~sI~gKC~V~ 81 (434)
|||+.+++ +++|||+|++||++.+|.++|+|+|||||+|+.. |.... +.++|||+|+|.|+||++||+|||+|+
T Consensus 13 ~V~v~~~~--~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~---~~~~~~~~~~EvFlS~~~d~i~~~~I~gk~~Vl 87 (130)
T cd04721 13 FVYVLSEE--EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGA---ALSPDSVNPREIFLSPNLQVISVECIDGLATVL 87 (130)
T ss_pred EEEEeCCC--CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhcc---ccCCCCCCCCeEEEcCCccccchHHeeeeeEEC
Confidence 79999876 7889999999999988999999999999999973 33333 789999999999999999999999999
Q ss_pred ecCccccCCCC----CCCCceEEccce
Q 035627 82 FVPIHKHLPNH----KQHPGLSFKRFM 104 (434)
Q Consensus 82 ~~~ey~~lp~~----~e~~~Fic~~~Y 104 (434)
+.++|.++... .+...|+|++.|
T Consensus 88 s~~~y~k~~~~~~~~~~~~~f~C~~~~ 114 (130)
T cd04721 88 TREHYEKFQSVPKNSSELQAYFCYRQI 114 (130)
T ss_pred CHHHHhhhhccccCccccccEEEEEEe
Confidence 99999997753 245689999988
No 14
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.86 E-value=1.5e-21 Score=179.13 Aligned_cols=99 Identities=22% Similarity=0.322 Sum_probs=83.3
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCC--CceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCc-----cccccccee
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRD--GSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHR-----DEIPVESVM 75 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~--g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~-----D~~pv~sI~ 75 (434)
+|||++++ .+||||+|.+||+..+ |.++|+|+|||||+||.....+. ..+++||||+|.|. |+||++||+
T Consensus 35 ~Vlv~s~~--~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~~~~~~~~-~~~~~nEvFlS~~~d~~~~~~n~l~sI~ 111 (159)
T cd04715 35 DVYVHNGD--SEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEIRMELKGE-PKRHINEVFLACGRGEGLANINLLESII 111 (159)
T ss_pred EEEEeCCC--CCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHhccccccC-cccCCCcEEEecCcCccccccCcHHHcc
Confidence 79999854 8999999999999765 89999999999999998533343 56789999999996 668999999
Q ss_pred ceeEEEecCccccCCCCC----CCCceEEccce
Q 035627 76 HKCVVHFVPIHKHLPNHK----QHPGLSFKRFM 104 (434)
Q Consensus 76 gKC~V~~~~ey~~lp~~~----e~~~Fic~~~Y 104 (434)
|||.|+++++|.+.++.. +.+.|++.+.|
T Consensus 112 gKC~Vl~~~ey~~~~~~s~~~~~~~~~~f~~~f 144 (159)
T cd04715 112 GKCNVVCISEDFRNPQPSDGIPTSADFLFPCNF 144 (159)
T ss_pred ceeEEEEehHhhhCCCCcCCccccCcceeeeEE
Confidence 999999999999987762 45666666666
No 15
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.85 E-value=2.9e-21 Score=172.88 Aligned_cols=97 Identities=24% Similarity=0.434 Sum_probs=83.2
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCC------------CceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCccccc
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRD------------GSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIP 70 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~------------g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~p 70 (434)
+|||.|+++++|+|||||++|+...+ +..+|+|+|||||+||.. + ..++++|||+|+|.|++|
T Consensus 17 ~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~---~--~~~d~relf~S~h~d~~p 91 (135)
T cd04710 17 HIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISR---R--VVADSRLLYASMHSDICP 91 (135)
T ss_pred EEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCC---c--ccCCceEEEEEeeEeeec
Confidence 79999998899999999999998542 346899999999999862 2 267999999999999999
Q ss_pred ccceeceeEEEecCccccCCCCC-CCCceEEccce
Q 035627 71 VESVMHKCVVHFVPIHKHLPNHK-QHPGLSFKRFM 104 (434)
Q Consensus 71 v~sI~gKC~V~~~~ey~~lp~~~-e~~~Fic~~~Y 104 (434)
+++|.|||+|.+..++..+..-. ....|.|.++|
T Consensus 92 ~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~ly 126 (135)
T cd04710 92 IGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLF 126 (135)
T ss_pred hHHEEeEEEEEEecccchhhhhccCCCEEEEEeee
Confidence 99999999999999987766533 34679999988
No 16
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=99.84 E-value=3.3e-21 Score=164.76 Aligned_cols=97 Identities=34% Similarity=0.544 Sum_probs=86.4
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCCc--eEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEE
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDGS--MMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVV 80 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g~--~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V 80 (434)
|||+.+++++.++|||+|++||++.++. ++++|+|||||+||. .+ ....+||||+|+|+|++|+++|.|||.|
T Consensus 8 ~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~---~~--~~~~~~Elf~s~~~~~~~~~~I~gkc~V 82 (119)
T PF01426_consen 8 FVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTS---LG--KTFSPRELFLSDHCDDIPVESIRGKCNV 82 (119)
T ss_dssp EEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGST---TG--GHSCTTEEEEEEEEEEEEGGGEEEEEEE
T ss_pred EEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECccccc---cc--ccCCCCEEEEECcEeEEehhhEEeeeEE
Confidence 7999999888999999999999988776 999999999999993 12 2334699999999999999999999999
Q ss_pred EecCccccCCCCC--CCCceEEccce
Q 035627 81 HFVPIHKHLPNHK--QHPGLSFKRFM 104 (434)
Q Consensus 81 ~~~~ey~~lp~~~--e~~~Fic~~~Y 104 (434)
++.++|.+..... ..+.|+|++.|
T Consensus 83 ~~~~~~~~~~~~~~~~~~~F~cr~~y 108 (119)
T PF01426_consen 83 LHLEDYEQARPYGKEEPDTFFCRYAY 108 (119)
T ss_dssp EEHHHHTTGCCHCHHTTTEEEEEEEE
T ss_pred EECCccccccccccCCCCEEEEEEEE
Confidence 9999999887665 57899999998
No 17
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.83 E-value=1.7e-20 Score=172.98 Aligned_cols=101 Identities=14% Similarity=0.218 Sum_probs=85.7
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCCceEEEEEEEeChhccCcc-----CCCC--------------CCCCCCCceeec
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRK-----GGGN--------------WLSGDTRELFYS 63 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~-----~~G~--------------~~~~~~rELF~S 63 (434)
||||.++ ++.|+|||||++||+..+|.++|+|+|||||+||... ..++ ....+.+|||+|
T Consensus 9 ~Vy~~~~-~~~Py~I~rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~~~rELF~S 87 (164)
T cd04709 9 YVYFESS-PNNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQLRHRELFLS 87 (164)
T ss_pred EEEEECC-CCCCCEEEEEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhccCcceeEEe
Confidence 7999988 4678889999999999999999999999999998531 0111 123479999999
Q ss_pred CCcccccccceeceeEEEecCccccCCCCC-CCCceEEccce
Q 035627 64 FHRDEIPVESVMHKCVVHFVPIHKHLPNHK-QHPGLSFKRFM 104 (434)
Q Consensus 64 ~h~D~~pv~sI~gKC~V~~~~ey~~lp~~~-e~~~Fic~~~Y 104 (434)
.|.|.+||.+|.|||.|+++.+|..+..-. ..+.|.|+.+|
T Consensus 88 ~~~d~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~Y 129 (164)
T cd04709 88 RQVETLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVY 129 (164)
T ss_pred cccccccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEE
Confidence 999999999999999999999999987543 46789999988
No 18
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.79 E-value=3.7e-19 Score=158.33 Aligned_cols=94 Identities=19% Similarity=0.302 Sum_probs=80.8
Q ss_pred EEEEecCCCC----------CCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCccccccc
Q 035627 3 LFSFTPEDTN----------QKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVE 72 (434)
Q Consensus 3 ~Vll~p~~~~----------~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~ 72 (434)
+|++.+++++ .+|||++|+.||++.+|.++|+++|||||+||.. |+ .+++||||+|+|+|.+|++
T Consensus 11 ~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~---g~--~~~~~ElFLSd~c~~~~~~ 85 (130)
T cd04712 11 VVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVL---GN--YANERELFLTNECTCLELD 85 (130)
T ss_pred EEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccc---cc--cCCCceEEEeccccccccc
Confidence 6899998866 4999999999999999999999999999999993 54 7889999999999999999
Q ss_pred ----ceeceeEEEecCccccCCCCCCCCceEEccce
Q 035627 73 ----SVMHKCVVHFVPIHKHLPNHKQHPGLSFKRFM 104 (434)
Q Consensus 73 ----sI~gKC~V~~~~ey~~lp~~~e~~~Fic~~~Y 104 (434)
.|+|||.|++...+.. ......|+|+.+|
T Consensus 86 ~~~~~I~~k~~V~~~~~~~~---~~~~~~F~r~syy 118 (130)
T cd04712 86 LLSTEIKGVHKVDWSGTPWG---KGLPEFFVRQSYY 118 (130)
T ss_pred cccceeEEEEEEEEecCcCC---cCCCCEEEEEEEE
Confidence 9999999998887754 1223457777766
No 19
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.79 E-value=2.7e-19 Score=157.92 Aligned_cols=79 Identities=22% Similarity=0.364 Sum_probs=73.2
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEEEe
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVVHF 82 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V~~ 82 (434)
||++.+++++.+||||+|+.||++.+|.++|+|+|||||+||.+ |+ .++++|||+|+|+|++++.+|.+||+|+.
T Consensus 9 ~V~v~~~~~~~p~~I~rV~~mfe~~~g~k~~h~rWf~Rg~dTVl---G~--~~~~kEvFlsd~c~d~~l~~I~~Kv~V~~ 83 (124)
T cd04760 9 CVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVL---GE--TSDPLELFLVDECEDMALSSIHGKVNVIY 83 (124)
T ss_pred EEEEecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCcccc---cc--cCCCcEEEeecccCCcchHHheeeeEEEE
Confidence 79999988899999999999999999999999999999999983 54 37899999999999999999999999998
Q ss_pred cCcc
Q 035627 83 VPIH 86 (434)
Q Consensus 83 ~~ey 86 (434)
.+.-
T Consensus 84 ~~p~ 87 (124)
T cd04760 84 KAPS 87 (124)
T ss_pred eCCC
Confidence 7754
No 20
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.72 E-value=8.7e-18 Score=149.30 Aligned_cols=86 Identities=23% Similarity=0.366 Sum_probs=74.4
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCC---ceEEEEEEEeChhccCc---cCCCCCCCCCCCceeecCCc---ccccccc
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDG---SMMVTGRWFYHPEEADR---KGGGNWLSGDTRELFYSFHR---DEIPVES 73 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g---~~~v~v~WFYRPeEt~~---~~~G~~~~~~~rELF~S~h~---D~~pv~s 73 (434)
||||.+++. .+||||+|++||++.+| ...++|||||||+|+.. +..|++ .+++|||+++|. |+++++|
T Consensus 9 ~VlI~~~d~-~~~yVAkI~~i~e~~~~~~~~~~~~VqWy~R~~Ev~~~~~~~~~~~--~~~~EvF~~~~~~~~~~i~~et 85 (128)
T cd04719 9 FVLIEGEDA-DGPDVARILHLYEDGNEDDDPKRAIVQWFSRPSEVPKNKRKLLGRE--PHSQEVFFYSRSSCDNDIDAET 85 (128)
T ss_pred EEEEECCCC-CCCcEeeehhhhccccCCcccceEEEEcccChHHccccchhhccCC--CCCcEEEEecCccccCcEeHHH
Confidence 899999885 88999999999998765 56999999999999953 124444 369999999997 4999999
Q ss_pred eeceeEEEecCccccCCC
Q 035627 74 VMHKCVVHFVPIHKHLPN 91 (434)
Q Consensus 74 I~gKC~V~~~~ey~~lp~ 91 (434)
|.|||.|+.+++|..++.
T Consensus 86 I~gkc~V~~~~~y~~l~~ 103 (128)
T cd04719 86 IIGKVRVEPVEPKTDLPE 103 (128)
T ss_pred cccEEEEEEcCCccchhh
Confidence 999999999999999994
No 21
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.71 E-value=2.9e-17 Score=153.43 Aligned_cols=100 Identities=13% Similarity=0.096 Sum_probs=83.4
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCC-CceEEEEEEEeChhccCccCCCCCCCC-------CCCceeecCCcccccccce
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRD-GSMMVTGRWFYHPEEADRKGGGNWLSG-------DTRELFYSFHRDEIPVESV 74 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~-g~~~v~v~WFYRPeEt~~~~~G~~~~~-------~~rELF~S~h~D~~pv~sI 74 (434)
+|||++++ ..+||||+|.+|+.+.. +.+.+.|+|||||.|+.. ..+...++ .+||||+|.|.|++++.+|
T Consensus 58 ~Vlik~~~-~~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~-~~~~~~~~~~~~~~~~~nElflT~~~d~i~l~~I 135 (179)
T cd04720 58 TILVKDDV-ANSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINP-ARYYKQFDPEFRSESNKNELYLTAELSEIKLKDI 135 (179)
T ss_pred EEEEeCCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHccc-ccccccccchhcccCCCceEEEecccceEEhhhe
Confidence 79999987 48999999999998755 567999999999999962 11212333 3899999999999999999
Q ss_pred eceeEEEecCccccCCCCC--CCCceEEccce
Q 035627 75 MHKCVVHFVPIHKHLPNHK--QHPGLSFKRFM 104 (434)
Q Consensus 75 ~gKC~V~~~~ey~~lp~~~--e~~~Fic~~~Y 104 (434)
+|||+|++..+|.++.... .+..|+|++.|
T Consensus 136 i~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~ 167 (179)
T cd04720 136 IDKANVLSESEFNDLSTDDKNGERTFFCRYAC 167 (179)
T ss_pred eeeEEEecHHHhhhhcccccCCCceEEEEEEE
Confidence 9999999999999876552 35789999988
No 22
>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.68 E-value=5.1e-17 Score=144.90 Aligned_cols=89 Identities=19% Similarity=0.240 Sum_probs=70.2
Q ss_pred CCCCCCeEEEEeEeeecCCC-------ceEEEEEEEeChhccCccCCCCCCCC-CCCceeecCCcccccccceeceeEEE
Q 035627 10 DTNQKPYAASIKDITQSRDG-------SMMVTGRWFYHPEEADRKGGGNWLSG-DTRELFYSFHRDEIPVESVMHKCVVH 81 (434)
Q Consensus 10 ~~~~~pYIarI~~iwe~~~g-------~~~v~v~WFYRPeEt~~~~~G~~~~~-~~rELF~S~h~D~~pv~sI~gKC~V~ 81 (434)
+.+.|+|||||++|...+++ ..+|+|+||||||||.. +..+.+| +-||||+|+|.|++|+.+|.|||+|+
T Consensus 22 d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~--g~~~ayhsDirevy~Sd~~~~~~~~~I~GKC~V~ 99 (137)
T cd04711 22 DAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHK--GFKATYHADINMLYWSDEEATVDFSAVQGRCTVE 99 (137)
T ss_pred CCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEeccccccc--ccccccccceeeEEeecceeecChhhccceEEEE
Confidence 56799999999999875432 46899999999999982 2223244 56999999999999999999999999
Q ss_pred -------ecCccccCCCCCCCCceEEccce
Q 035627 82 -------FVPIHKHLPNHKQHPGLSFKRFM 104 (434)
Q Consensus 82 -------~~~ey~~lp~~~e~~~Fic~~~Y 104 (434)
++.+|. .. -.+.|.|+..|
T Consensus 100 ~~~di~~s~~~y~---~~-gpd~Fyf~~~Y 125 (137)
T cd04711 100 YGEDLPESVQEYS---GG-GPDRFYFLEAY 125 (137)
T ss_pred eccccchhHHHHh---cC-CCcceEEhhhh
Confidence 555661 12 23679999988
No 23
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=99.68 E-value=1e-16 Score=151.97 Aligned_cols=98 Identities=21% Similarity=0.287 Sum_probs=81.6
Q ss_pred EEEEecC------------------CCCCCCeEEEEeEeeecCCC------ceEEEEEEEeChhccCccCCCCCCCCCCC
Q 035627 3 LFSFTPE------------------DTNQKPYAASIKDITQSRDG------SMMVTGRWFYHPEEADRKGGGNWLSGDTR 58 (434)
Q Consensus 3 ~Vll~p~------------------~~~~~pYIarI~~iwe~~~g------~~~v~v~WFYRPeEt~~~~~G~~~~~~~r 58 (434)
+||+.|+ + ..+.+||+|.+|+..+++ ..+|+|+||||||||.. .....++.+
T Consensus 13 ~VYv~p~~f~~~~~~~~~~~~G~N~~-~~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt~~---~~~y~sd~r 88 (202)
T cd04708 13 FLYVSPDAFAEEERERATFKAGRNVG-LKAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDVSP---EKAYASDIR 88 (202)
T ss_pred eEEECcccccccccccccccccccCC-CCCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhcCc---ccceecCce
Confidence 6889888 3 369999999999986554 67999999999999862 223445999
Q ss_pred ceeecCCcccccccceeceeEEEecCccccCCCC-CCCCceEEccce
Q 035627 59 ELFYSFHRDEIPVESVMHKCVVHFVPIHKHLPNH-KQHPGLSFKRFM 104 (434)
Q Consensus 59 ELF~S~h~D~~pv~sI~gKC~V~~~~ey~~lp~~-~e~~~Fic~~~Y 104 (434)
|||+|+|.|++|+++|.|||+|+...++..+... ...+.|.|+..|
T Consensus 89 ely~Sde~~~~~~~~I~GKC~V~~~~d~~~~~~~~~~~~~Ffc~~~Y 135 (202)
T cd04708 89 EVYYSEDTLTVPVEAVEGKCEVRKKSDLPDSDAPVIFEHVFFCELLY 135 (202)
T ss_pred eEEEeccceeechhHcceEEEEEecCcchhhhccccCCCceEEEEEE
Confidence 9999999999999999999999999998876541 235789999988
No 24
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.36 E-value=3.4e-13 Score=97.15 Aligned_cols=39 Identities=21% Similarity=0.365 Sum_probs=36.2
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
++|.+|+.+++.|.|+ |+|||||||| +|..|.+|||+|+
T Consensus 1 ~~Cp~C~~~~a~~~q~-Q~RsaDE~mT--~fy~C~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREATFFQL-QTRSADEPMT--VFYVCTKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEEEEEE-cccCCCCCCe--EEEEeCCCCCEeC
Confidence 4799999999999995 9999999999 5889999999997
No 25
>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=99.31 E-value=1e-12 Score=94.23 Aligned_cols=39 Identities=21% Similarity=0.376 Sum_probs=33.1
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
++|.+||.+++.|.|+ |+|||||||| +|..|.+|||+|+
T Consensus 1 ~~Cp~Cg~~~a~~~~~-Q~rsaDE~~T--~fy~C~~C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQI-QTRSADEPMT--LFYVCCNCGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEE-SSSSSSSSSE--EEEEESSSTEEEE
T ss_pred CCCcCCCCCeEEEEEe-eccCCCCCCe--EEEEeCCCCCeeC
Confidence 4799999999999995 9999999999 5788999999995
No 26
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.27 E-value=3.7e-12 Score=137.11 Aligned_cols=100 Identities=19% Similarity=0.199 Sum_probs=90.7
Q ss_pred cEEEEecCCCCCCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEEE
Q 035627 2 ILFSFTPEDTNQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVVH 81 (434)
Q Consensus 2 ~~Vll~p~~~~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V~ 81 (434)
.+||+.++..+..|.|++|..+|+..+|..++.++|||||++|. |..++.+ ..+|+|.+..+++.+++-|+|+|.|+
T Consensus 195 d~vlv~~~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~-H~a~r~F--~k~Evfkt~~~~~~~~q~l~g~c~v~ 271 (629)
T KOG1827|consen 195 DYVLVQNPADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETV-HRADRKF--YKQEVFKTSLYRDDLVQRLLGKCYVM 271 (629)
T ss_pred ceeeecCcccccCCceeeecccccCcccccccceeEeeCCccCc-cccccch--hcccceecccccccHHHHhhcceEEe
Confidence 58999988877999999999999999999999999999999998 5566543 48999999999999999999999999
Q ss_pred ecCccccCCCCC--CCCceEEccce
Q 035627 82 FVPIHKHLPNHK--QHPGLSFKRFM 104 (434)
Q Consensus 82 ~~~ey~~lp~~~--e~~~Fic~~~Y 104 (434)
++.+|....+.. +.+.|+|+++|
T Consensus 272 ~~~~yi~~~p~~ls~~dv~lcesRy 296 (629)
T KOG1827|consen 272 KPTEYISGDPENLSEEDVFLCESRY 296 (629)
T ss_pred ehhHhhhcCcccccccceeeEEeee
Confidence 999999877654 77899999999
No 27
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=99.23 E-value=3.7e-12 Score=111.15 Aligned_cols=42 Identities=14% Similarity=0.321 Sum_probs=38.9
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccccC
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWYAS 346 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~s 346 (434)
++.|++||.+++.|.|+ |||||||||| +|.+|..|||+|++.
T Consensus 72 ~~~CpkCg~~ea~y~~~-QtRsaDEp~T--~Fy~C~~Cg~~wre~ 113 (113)
T COG1594 72 KEKCPKCGNKEAYYWQL-QTRSADEPET--RFYKCTRCGYRWREY 113 (113)
T ss_pred cccCCCCCCceeEEEee-ehhccCCCce--EEEEecccCCEeecC
Confidence 67999999999999996 9999999999 588999999999863
No 28
>PHA02998 RNA polymerase subunit; Provisional
Probab=99.21 E-value=6.1e-12 Score=116.48 Aligned_cols=41 Identities=12% Similarity=0.093 Sum_probs=38.1
Q ss_pred CccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 301 TDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 301 ~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
++.+|.+|+.+++.|.|+ |||||||||| +|+.|.+|||+|+
T Consensus 142 t~v~CPkCg~~~A~f~ql-QTRSADEPmT--~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMI-QTRAADEPPL--VRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEE-eeccCCCCce--EEEEcCCCCCccC
Confidence 567999999999999995 9999999999 5889999999997
No 29
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=99.09 E-value=2.3e-11 Score=102.78 Aligned_cols=49 Identities=18% Similarity=0.314 Sum_probs=43.4
Q ss_pred HHHhhcccCccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 293 DESEQMQMTDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 293 ~~i~~~q~~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
+++...+.++.+|.+|+..+..+-|| ||||||||||+ |--|.+|+|||+
T Consensus 56 ~a~~nv~~t~~~Cp~Cgh~rayF~ql-QtRSADEPmT~--FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 56 EAWENVDQTEATCPTCGHERAYFMQL-QTRSADEPMTT--FYKCCKCKHRWR 104 (105)
T ss_pred ccccchhhccCcCCCCCCCceEEEEe-eeccCCCcHhH--hhhhhccccccc
Confidence 45556677889999999999999996 99999999995 778999999997
No 30
>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=99.00 E-value=2.1e-10 Score=97.74 Aligned_cols=43 Identities=16% Similarity=0.264 Sum_probs=39.0
Q ss_pred ccCccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 299 QMTDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 299 q~~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
+.++.+|.+||..+..|.|+ |+|||||||| +|.+|.+|||+|+
T Consensus 59 ~~~~~~Cp~Cg~~~a~f~~~-Q~RsadE~~T--~fy~C~~C~~~w~ 101 (104)
T TIGR01384 59 PTTRVECPKCGHKEAYYWLL-QTRRADEPET--RFYKCTKCGYVWR 101 (104)
T ss_pred CcccCCCCCCCCCeeEEEEe-ccCCCCCCcE--EEEEeCCCCCeeE
Confidence 44578999999999999995 9999999999 5788999999997
No 31
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=98.93 E-value=6e-10 Score=122.12 Aligned_cols=67 Identities=30% Similarity=0.393 Sum_probs=60.5
Q ss_pred HHHHHHHHHHhcc-CChHHHHHHHHHHHHhcc--cChhhhhhhccCCCCccccccCChhhhcchhcHHHH
Q 035627 221 VTALEKASHDALS-SDFQKRNQKLRQLLFNLK--STALLALRFLKGKLEPSKILDMSPNELNEGLTAEET 287 (434)
Q Consensus 221 A~~IE~a~~~~~~-~~~~~Yk~K~Rsl~~NLK--~Np~Lr~rvl~G~I~p~~lv~Ms~eELas~~~~ee~ 287 (434)
+..||..+|..|+ +-+.+|+.|+|+|+|||| +||.||.+|+.|+|+|++|+.|+++|||+.++++.+
T Consensus 273 ~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL~~~r 342 (778)
T KOG1634|consen 273 LEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPELAEWR 342 (778)
T ss_pred hhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchHHHHH
Confidence 4499999999998 667899999999999996 499999999999999999999999999997665544
No 32
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=98.07 E-value=1.3e-06 Score=75.88 Aligned_cols=39 Identities=13% Similarity=0.204 Sum_probs=35.8
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
+-+|-|||..+-+|.-+ |+|||||-|| ||-||.+||++-
T Consensus 74 ~~kCpkCghe~m~Y~T~-QlRSADEGQT--VFYTC~kC~~k~ 112 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTL-QLRSADEGQT--VFYTCPKCKYKF 112 (116)
T ss_pred hccCcccCCchhhhhhh-hcccccCCce--EEEEcCccceee
Confidence 46999999999999996 9999999998 788999999875
No 33
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=97.87 E-value=7.4e-06 Score=70.75 Aligned_cols=41 Identities=22% Similarity=0.435 Sum_probs=35.7
Q ss_pred CccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 301 TDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 301 ~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
.+-.|+||++++--|+|. |+|-+|+-|+- |-.|.+|||||-
T Consensus 72 s~~~C~~C~~~eavffQ~-~~~r~d~~m~l--~yvC~~C~h~wt 112 (113)
T KOG2691|consen 72 SDKHCPKCGHREAVFFQA-QTRRADEAMRL--FYVCCSCGHRWT 112 (113)
T ss_pred ccccCCccCCcceEEEec-ccccccceEEE--EEEecccccccc
Confidence 356899999999999996 99999999985 455888999994
No 34
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=95.37 E-value=0.0014 Score=69.13 Aligned_cols=102 Identities=13% Similarity=0.213 Sum_probs=75.2
Q ss_pred cEEEEecCCCCCCCeEEEEeEeeecCCCceEEEEEEEeChhccCcc-------CCC-----------------CC----C
Q 035627 2 ILFSFTPEDTNQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRK-------GGG-----------------NW----L 53 (434)
Q Consensus 2 ~~Vll~p~~~~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~-------~~G-----------------~~----~ 53 (434)
-||||.... ..|+.|-||+++-...+|.+-.+|--|||-.||..+ +.. .. +
T Consensus 10 d~vYf~~ss-s~PYliRrIEELnKTa~GnVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e~EEe~e 88 (693)
T KOG3554|consen 10 DYVYFENSS-SNPYLIRRIEELNKTANGNVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAEIEEESE 88 (693)
T ss_pred ceEEEecCC-CChHHHHHHHHHhccccCCcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhhhhhhcc
Confidence 479999876 347778999999988899999999999999988641 000 00 0
Q ss_pred C-------------CCCCceeecCCcccccccceeceeEEEecCccccCCCCCC-CCceEEccce
Q 035627 54 S-------------GDTRELFYSFHRDEIPVESVMHKCVVHFVPIHKHLPNHKQ-HPGLSFKRFM 104 (434)
Q Consensus 54 ~-------------~~~rELF~S~h~D~~pv~sI~gKC~V~~~~ey~~lp~~~e-~~~Fic~~~Y 104 (434)
. .--+|||+|.....-|+..|.|||.|..+.+-..+.+--+ .+.|.---+|
T Consensus 89 ~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVy 153 (693)
T KOG3554|consen 89 CPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVY 153 (693)
T ss_pred CCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeee
Confidence 0 0138999999999999999999999999888776554332 2455555555
No 35
>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=90.85 E-value=0.21 Score=39.83 Aligned_cols=40 Identities=15% Similarity=0.300 Sum_probs=28.3
Q ss_pred cccCCCCCccccceeeecccCC-----CCcceeeeeeeccccCcc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLG-----DRYQQLSKALGVYCHGHS 342 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsa-----De~mtt~~FvtC~~CGnr 342 (434)
+.|-||+.+...--++.=|+.. |-..-+|++++|.+||..
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 3699999988776664334443 334446788999999986
No 36
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=81.07 E-value=0.23 Score=51.53 Aligned_cols=82 Identities=10% Similarity=-0.102 Sum_probs=66.2
Q ss_pred EEEEecCCCCCCCeEEEEeEeeecCCCceEEEEEEEeChhccCccCCCCCCCCCCCceeecCCcccccccceeceeEEEe
Q 035627 3 LFSFTPEDTNQKPYAASIKDITQSRDGSMMVTGRWFYHPEEADRKGGGNWLSGDTRELFYSFHRDEIPVESVMHKCVVHF 82 (434)
Q Consensus 3 ~Vll~p~~~~~~pYIarI~~iwe~~~g~~~v~v~WFYRPeEt~~~~~G~~~~~~~rELF~S~h~D~~pv~sI~gKC~V~~ 82 (434)
.+++.+.+....|.++.+...|.+.++..+.-++|||||+++. +.. -..+..+++++....+.+++....+.|.|..
T Consensus 282 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 358 (371)
T COG5076 282 WPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETF-VRD--AKLFFDNCVMYNGEVTDYYKNANVLEDFVIK 358 (371)
T ss_pred ccccccCCcccccchhhhhhcccccccchhhhhcccCCCcccc-ccc--cchhhhcccccchhhhhhhhhccchhhhHhh
Confidence 4567777778999999999999988877777999999999765 222 2344579999999999999999999999976
Q ss_pred cCccc
Q 035627 83 VPIHK 87 (434)
Q Consensus 83 ~~ey~ 87 (434)
.-++.
T Consensus 359 ~~~~~ 363 (371)
T COG5076 359 KTRLI 363 (371)
T ss_pred hhhhh
Confidence 55544
No 37
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=72.83 E-value=1.1 Score=46.45 Aligned_cols=33 Identities=18% Similarity=0.343 Sum_probs=13.5
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccccCccc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWYASRNE 349 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~sr~~ 349 (434)
|+|..|+.|.+||..+ |.. .|.+||.. +|-|+.
T Consensus 286 FkC~~C~~Rt~sl~r~--------P~~-----~C~~Cg~~-~wer~~ 318 (344)
T PF09332_consen 286 FKCKDCGNRTISLERL--------PKK-----HCSNCGSS-KWERTG 318 (344)
T ss_dssp EE-T-TS-EEEESSSS----------S-------TTT-S----EEE-
T ss_pred EECCCCCCeeeecccC--------CCC-----CCCcCCcC-ceeehh
Confidence 5788888888877332 433 48888754 344443
No 38
>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=68.00 E-value=3 Score=28.90 Aligned_cols=26 Identities=19% Similarity=0.309 Sum_probs=14.9
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
.||+||...- . ++.. -+.|.+||+|=
T Consensus 2 ~C~~Cg~~~~-~----------~~~~---~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVE-L----------KPGD---PIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE--B----------STSS---TSSBSSSS-SE
T ss_pred CCCcCCCeeE-c----------CCCC---cEECCcCCCeE
Confidence 5999987544 1 1111 12599999983
No 39
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=67.92 E-value=3 Score=30.84 Aligned_cols=27 Identities=11% Similarity=0.178 Sum_probs=17.1
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
+.||+||.. ++- . +... +-|.+||+|=
T Consensus 3 Y~C~~Cg~~-~~~----~----~~~~-----irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRE-NEI----K----SKDV-----VRCRECGYRI 29 (44)
T ss_pred EECCCCCCE-eec----C----CCCc-----eECCCCCceE
Confidence 689999984 221 1 1122 2599999985
No 40
>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=66.78 E-value=1.1 Score=36.08 Aligned_cols=37 Identities=8% Similarity=0.111 Sum_probs=20.6
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
.|+|.+|+.|..-. =|..-|..-+|++.|-+|.|+=.
T Consensus 4 ~FTC~~C~~Rs~~~------~sk~aY~~GvViv~C~gC~~~Hl 40 (66)
T PF05180_consen 4 TFTCNKCGTRSAKM------FSKQAYHKGVVIVQCPGCKNRHL 40 (66)
T ss_dssp EEEETTTTEEEEEE------EEHHHHHTSEEEEE-TTS--EEE
T ss_pred EEEcCCCCCcccee------eCHHHHhCCeEEEECCCCcceee
Confidence 37999998765421 11111333348999999998743
No 41
>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=66.02 E-value=4.2 Score=29.36 Aligned_cols=29 Identities=17% Similarity=0.194 Sum_probs=18.3
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
++|..|+.+. .+.+ +++- ...|.+||.=.
T Consensus 1 m~Cp~Cg~~~-~~~D---------~~~g--~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFD---------PERG--ELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSE-EEEE---------TTTT--EEEETTT-BBE
T ss_pred CCCcCCcCCc-eEEc---------CCCC--eEECCCCCCEe
Confidence 4799999988 4444 3321 23599999644
No 42
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=64.73 E-value=4.1 Score=29.79 Aligned_cols=31 Identities=26% Similarity=0.531 Sum_probs=19.5
Q ss_pred cCccccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 300 MTDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 300 ~~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
|..++|++||.. ..+.+ .++ -.+|..||++=
T Consensus 1 ~~~y~C~~CG~~-~~~~~---------~~~---~~~Cp~CG~~~ 31 (46)
T PRK00398 1 MAEYKCARCGRE-VELDE---------YGT---GVRCPYCGYRI 31 (46)
T ss_pred CCEEECCCCCCE-EEECC---------CCC---ceECCCCCCeE
Confidence 446899999874 44322 111 12599999875
No 43
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=62.43 E-value=4.1 Score=38.00 Aligned_cols=37 Identities=11% Similarity=0.104 Sum_probs=26.4
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
.|+|..|+.|.. +|=|.--|.--+|||+|..|.|+-.
T Consensus 79 ~yTCkvCntRs~------ktisk~AY~~GvVivqC~gC~~~Hl 115 (165)
T KOG3277|consen 79 AYTCKVCNTRST------KTISKQAYEKGVVIVQCPGCKNHHL 115 (165)
T ss_pred EEEeeccCCccc------cccChhhhhCceEEEECCCCcccee
Confidence 479999999875 2333333555559999999998754
No 44
>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=58.53 E-value=7.9 Score=28.65 Aligned_cols=37 Identities=16% Similarity=0.139 Sum_probs=21.9
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccc--cCccccc
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYC--HGHSWYA 345 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~--CGnrWk~ 345 (434)
+|..||.+-.. ++...--+.+.-.++.|.| ||++|..
T Consensus 1 ~CP~Cg~~a~i-----r~S~~~s~~~~~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 1 RCPHCGSKARI-----RTSRQLSPLTRELYCQCTNPECGHTFVA 39 (47)
T ss_pred CcCCCCCeeEE-----EEchhhCcceEEEEEEECCCcCCCEEEE
Confidence 48888886543 2222222222225677998 9999973
No 45
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=57.47 E-value=8.7 Score=35.54 Aligned_cols=53 Identities=13% Similarity=0.184 Sum_probs=36.6
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc-cCcccccceeecCCC
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY-ASRNEASSLTIDGRG 359 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk-~sr~~~~~~~~~~~~ 359 (434)
+|..|+...... +-+|.+++-..-=-=-.|.+||.|+- +-|-+...|.|--.+
T Consensus 2 ~CP~C~~~dtkV---iDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l~ViKkd 55 (147)
T TIGR00244 2 HCPFCQHHNTRV---LDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQD 55 (147)
T ss_pred CCCCCCCCCCEe---eeccccCCCCeeeecccCCccCCccceeeeccccccEEEcCC
Confidence 688998877665 56788887665221235999999994 777777776654333
No 46
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=57.44 E-value=6 Score=31.94 Aligned_cols=27 Identities=15% Similarity=0.380 Sum_probs=21.6
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGH 341 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGn 341 (434)
.+|..|+-..|-|.- ++| -|+|..||.
T Consensus 20 VkCpdC~N~q~vFsh---------ast---~V~C~~CG~ 46 (67)
T COG2051 20 VKCPDCGNEQVVFSH---------AST---VVTCLICGT 46 (67)
T ss_pred EECCCCCCEEEEecc---------Cce---EEEeccccc
Confidence 399999999998844 554 468999995
No 47
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=57.20 E-value=5.5 Score=34.58 Aligned_cols=30 Identities=17% Similarity=0.203 Sum_probs=21.7
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccccCc
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWYASR 347 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~sr 347 (434)
-|--| ...+|+|- +.. +.|.+||.||...+
T Consensus 37 aCeiC--~~~GY~q~------g~~------lvC~~C~~~~~~~~ 66 (102)
T PF10080_consen 37 ACEIC--GPKGYYQE------GDQ------LVCKNCGVRFNLPT 66 (102)
T ss_pred ecccc--CCCceEEE------CCE------EEEecCCCEEehhh
Confidence 79999 67789773 222 24999999997543
No 48
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=54.63 E-value=7.3 Score=29.56 Aligned_cols=34 Identities=18% Similarity=0.297 Sum_probs=21.8
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
...|..|+-...+. | +.+ .+.+.+ +|+.||-+|+
T Consensus 3 ~~~C~~C~~~~T~~--W-R~g-~~g~~~-----LCnaCgl~~~ 36 (52)
T smart00401 3 GRSCSNCGTTETPL--W-RRG-PSGNKT-----LCNACGLYYK 36 (52)
T ss_pred CCCcCCCCCCCCCc--c-ccC-CCCCCc-----EeecccHHHH
Confidence 35799999777753 3 222 222222 4999999995
No 49
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=54.44 E-value=8.5 Score=26.10 Aligned_cols=26 Identities=19% Similarity=0.347 Sum_probs=14.0
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccCcc
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHS 342 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnr 342 (434)
-|++||..-... .++.+.+ |..||+.
T Consensus 5 fC~~CG~~t~~~--------~~g~~r~-----C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPA--------PGGWARR-----CPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE---------SSSS-EE-----ESSSS-E
T ss_pred ccCcCCccccCC--------CCcCEeE-----CCCCcCE
Confidence 599999876542 3356663 9999985
No 50
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=54.13 E-value=5.8 Score=27.93 Aligned_cols=11 Identities=18% Similarity=0.459 Sum_probs=9.5
Q ss_pred eeccccCcccc
Q 035627 334 LGVYCHGHSWY 344 (434)
Q Consensus 334 vtC~~CGnrWk 344 (434)
|.|.+|||.|+
T Consensus 26 v~C~~C~~~f~ 36 (36)
T PF13717_consen 26 VRCSKCGHVFF 36 (36)
T ss_pred EECCCCCCEeC
Confidence 46999999995
No 51
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=53.39 E-value=6.8 Score=27.66 Aligned_cols=13 Identities=15% Similarity=0.174 Sum_probs=10.3
Q ss_pred eeeccccCccccc
Q 035627 333 ALGVYCHGHSWYA 345 (434)
Q Consensus 333 FvtC~~CGnrWk~ 345 (434)
-|.|..||+.|.+
T Consensus 25 ~vrC~~C~~~f~v 37 (37)
T PF13719_consen 25 KVRCPKCGHVFRV 37 (37)
T ss_pred EEECCCCCcEeeC
Confidence 3579999999964
No 52
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=53.31 E-value=12 Score=30.12 Aligned_cols=46 Identities=17% Similarity=0.292 Sum_probs=26.8
Q ss_pred cccCCCCCccccceeeecccCC-----CCcceeeeeeeccccCcccccCcc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLG-----DRYQQLSKALGVYCHGHSWYASRN 348 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsa-----De~mtt~~FvtC~~CGnrWk~sr~ 348 (434)
++|-||+-++----+|+-|+-. |=.--+|.-+||.+||..=..+.+
T Consensus 5 ~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY~a~ 55 (68)
T COG3478 5 FKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFYSAK 55 (68)
T ss_pred ccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhheecc
Confidence 5799999877554444222111 111123456799999987654443
No 53
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=51.08 E-value=11 Score=30.83 Aligned_cols=37 Identities=5% Similarity=0.054 Sum_probs=24.0
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeecc--ccCcccc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVY--CHGHSWY 344 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~--~CGnrWk 344 (434)
++|-.||.+-.. ..+|-.++-... ..+.|. +||++|.
T Consensus 2 m~CP~Cg~~a~i----rtSr~~s~~~~~-~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 2 FHCPLCQHAAHA----RTSRYITDTTKE-RYHQCQNVNCSATFI 40 (72)
T ss_pred ccCCCCCCccEE----EEChhcChhhhe-eeeecCCCCCCCEEE
Confidence 689999997732 123333333222 567798 9999997
No 54
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=50.34 E-value=4.7 Score=31.55 Aligned_cols=40 Identities=18% Similarity=0.282 Sum_probs=25.9
Q ss_pred CccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccccCcccccceee
Q 035627 301 TDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWYASRNEASSLTI 355 (434)
Q Consensus 301 ~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~sr~~~~~~~~ 355 (434)
|--.|..||...-.- . ..-. .+|.+||.. +.||..+++.|
T Consensus 27 TSq~C~~CG~~~~~~-------~---~~r~---~~C~~Cg~~--~~rD~naA~NI 66 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKR-------R---SGRV---FTCPNCGFE--MDRDVNAARNI 66 (69)
T ss_pred CccCccCcccccccc-------c---ccce---EEcCCCCCE--ECcHHHHHHHH
Confidence 335799999876651 1 1111 149999987 67887776655
No 55
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=49.85 E-value=8.6 Score=39.01 Aligned_cols=42 Identities=17% Similarity=0.226 Sum_probs=25.7
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc-cCcccccceeecC
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY-ASRNEASSLTIDG 357 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk-~sr~~~~~~~~~~ 357 (434)
.-||+||.+.-.+. ++.-. .|.+|||+=+ ---..|-+|++++
T Consensus 112 RFCg~CG~~~~~~~--------~g~~~-----~C~~cg~~~fPR~dP~vIv~v~~~ 154 (279)
T COG2816 112 RFCGRCGTKTYPRE--------GGWAR-----VCPKCGHEHFPRIDPCVIVAVIRG 154 (279)
T ss_pred cCCCCCCCcCcccc--------Cceee-----eCCCCCCccCCCCCCeEEEEEecC
Confidence 46999999876531 23333 3999999976 2223344555544
No 56
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=49.53 E-value=5.7 Score=30.49 Aligned_cols=32 Identities=19% Similarity=0.279 Sum_probs=20.6
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
.|..|+-.+.. +| +... +...+ +|+.||-+|+
T Consensus 1 ~C~~C~~~~Tp--~W-R~g~-~~~~~-----LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTP--LW-RRGP-SGGST-----LCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCc--cc-ccCC-CCcch-----HHHHHHHHHH
Confidence 38888887775 33 2222 23333 4999999996
No 57
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=49.14 E-value=9.1 Score=31.08 Aligned_cols=27 Identities=11% Similarity=0.076 Sum_probs=23.6
Q ss_pred hhhccccchhHHHHhHHHHhHhCCCCC
Q 035627 117 KTMKIISSMRLISLDQKTRVRFGDLPD 143 (434)
Q Consensus 117 ~~~~~~~~~EId~Lv~Kti~kw~d~vd 143 (434)
..++.|.+++|..++..++..|+..++
T Consensus 48 ~~Lrkh~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 48 NGLRKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred HHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence 346778999999999999999998875
No 58
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=47.95 E-value=7.2 Score=26.73 Aligned_cols=9 Identities=33% Similarity=0.604 Sum_probs=8.2
Q ss_pred eccccCccc
Q 035627 335 GVYCHGHSW 343 (434)
Q Consensus 335 tC~~CGnrW 343 (434)
.|..||+.|
T Consensus 21 vCp~C~~ew 29 (30)
T PF08274_consen 21 VCPECGHEW 29 (30)
T ss_dssp EETTTTEEE
T ss_pred eCCcccccC
Confidence 399999999
No 59
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=46.30 E-value=11 Score=37.59 Aligned_cols=25 Identities=24% Similarity=0.299 Sum_probs=18.7
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCcc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHS 342 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnr 342 (434)
|+|++|+.+ |+-+ ||. ++|..|||.
T Consensus 168 ~rc~~c~~k---~rr~--------pl~----g~c~kcg~~ 192 (253)
T COG1933 168 FRCVKCNTK---FRRP--------PLD----GKCPICGGK 192 (253)
T ss_pred eehHhhhhh---hcCC--------Ccc----ccccccCCe
Confidence 689999775 4444 886 379999983
No 60
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=45.83 E-value=9.4 Score=30.21 Aligned_cols=28 Identities=18% Similarity=0.247 Sum_probs=18.8
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
.+-||.|++++.= +. .| -+.|-+||+|-
T Consensus 20 iYiCgdC~~en~l-----k~--~D-------~irCReCG~RI 47 (62)
T KOG3507|consen 20 IYICGDCGQENTL-----KR--GD-------VIRCRECGYRI 47 (62)
T ss_pred EEEeccccccccc-----cC--CC-------cEehhhcchHH
Confidence 3589999998753 11 11 12499999985
No 61
>PHA02942 putative transposase; Provisional
Probab=44.48 E-value=4.9 Score=42.25 Aligned_cols=50 Identities=20% Similarity=0.419 Sum_probs=32.0
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccccCcccccceeecCCCCCCCcccccc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWYASRNEASSLTIDGRGSAAKSIGIAS 369 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~sr~~~~~~~~~~~~~~~~~~~~~~ 369 (434)
--.|..||...-.. .++ .| .|.+||..+ -||-+.++.|-... --.+||||
T Consensus 325 Sq~Cs~CG~~~~~l--------~~r---~f---~C~~CG~~~--drD~nAA~NI~~rg--~~~~~~~~ 374 (383)
T PHA02942 325 SVSCPKCGHKMVEI--------AHR---YF---HCPSCGYEN--DRDVIAIMNLNGRG--SLTLSTAP 374 (383)
T ss_pred CccCCCCCCccCcC--------CCC---EE---ECCCCCCEe--CcHHHHHHHHHHHH--HHHhccCc
Confidence 34799999854321 111 23 499999864 78988888885432 24456666
No 62
>PRK04023 DNA polymerase II large subunit; Validated
Probab=42.15 E-value=11 Score=44.27 Aligned_cols=27 Identities=19% Similarity=0.247 Sum_probs=20.7
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
.|||.||+.+ |+-+ |.+. .|..||.+=
T Consensus 1037 ~fRC~kC~~k---YRR~--------PL~G----~C~kCGg~l 1063 (1121)
T PRK04023 1037 EFRCTKCGAK---YRRP--------PLSG----KCPKCGGNL 1063 (1121)
T ss_pred ceeecccCcc---cccC--------CCCC----cCccCCCeE
Confidence 4789999764 7666 7775 599999874
No 63
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=41.56 E-value=15 Score=32.44 Aligned_cols=27 Identities=22% Similarity=0.363 Sum_probs=17.5
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
.|-+|.. .-||-+ ..+. .|..|||-|-
T Consensus 4 ~CP~C~s-eytY~d--------g~~~-----iCpeC~~EW~ 30 (109)
T TIGR00686 4 PCPKCNS-EYTYHD--------GTQL-----ICPSCLYEWN 30 (109)
T ss_pred cCCcCCC-cceEec--------CCee-----ECcccccccc
Confidence 5788854 345633 2332 3999999995
No 64
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=40.76 E-value=17 Score=29.38 Aligned_cols=27 Identities=15% Similarity=0.210 Sum_probs=23.2
Q ss_pred hhhccccchhHHHHhHHHHhHhCCCCC
Q 035627 117 KTMKIISSMRLISLDQKTRVRFGDLPD 143 (434)
Q Consensus 117 ~~~~~~~~~EId~Lv~Kti~kw~d~vd 143 (434)
..++.|.+++|..++..++.+|+..++
T Consensus 50 ~~Lrkh~~~~i~~~A~~Lv~~Wk~~v~ 76 (76)
T cd00183 50 NSLRKHSNEKIRKLAKALIKSWKKLVD 76 (76)
T ss_pred HHHHcCCcHHHHHHHHHHHHHHHHhcC
Confidence 346778899999999999999998774
No 65
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.47 E-value=12 Score=28.59 Aligned_cols=30 Identities=20% Similarity=0.396 Sum_probs=19.3
Q ss_pred CccccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 301 TDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 301 ~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
...+|.+||..- .- .|.+ .-+-|..||+|=
T Consensus 5 ~~Y~C~~Cg~~~-~~-----------~~~~-~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREV-EL-----------DQET-RGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCee-eh-----------hhcc-CceeCCCCCcEE
Confidence 346999998754 21 2221 234699999985
No 66
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=40.05 E-value=19 Score=26.01 Aligned_cols=30 Identities=20% Similarity=0.163 Sum_probs=18.5
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGH 341 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGn 341 (434)
+|+|..||..--- +|..+.+.+. .|-.||.
T Consensus 5 ey~C~~Cg~~fe~----~~~~~~~~~~------~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEV----LQSISEDDPV------PCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEE----EEEcCCCCCC------cCCCCCC
Confidence 5799999854322 3444442332 4999997
No 67
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=39.83 E-value=25 Score=25.55 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=11.6
Q ss_pred CCcceeeeeeeccccCcccccC
Q 035627 325 DRYQQLSKALGVYCHGHSWYAS 346 (434)
Q Consensus 325 De~mtt~~FvtC~~CGnrWk~s 346 (434)
++.|++ |..|+ +|++-
T Consensus 11 ~~~~i~-----C~~C~-~~~H~ 26 (51)
T PF00628_consen 11 DGDMIQ-----CDSCN-RWYHQ 26 (51)
T ss_dssp TSSEEE-----BSTTS-CEEET
T ss_pred CCCeEE-----cCCCC-hhhCc
Confidence 456664 99999 88854
No 68
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=39.38 E-value=25 Score=33.20 Aligned_cols=90 Identities=14% Similarity=0.109 Sum_probs=44.8
Q ss_pred HHHHHHHHhcccChhhh-hhhcc-CCCCccccccCChhhhcchhcHHHHhhhhhHHH----hhcccCc-cccCCCCCccc
Q 035627 241 QKLRQLLFNLKSTALLA-LRFLK-GKLEPSKILDMSPNELNEGLTAEETAKEESDES----EQMQMTD-ARCSRCNECKV 313 (434)
Q Consensus 241 ~K~Rsl~~NLK~Np~Lr-~rvl~-G~I~p~~lv~Ms~eELas~~~~ee~~k~e~~~i----~~~q~~~-~~CgkCk~~k~ 313 (434)
+-+|.++.-|....-+. +++-. |.=-|-.+-.++.+++....... . +...+.+ +...... +.|.+|+ ++.
T Consensus 51 ~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~-~-~~~~~klk~~l~~e~~~~~Y~Cp~C~-~ry 127 (178)
T PRK06266 51 NTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKK-K-MEELKKLKEQLEEEENNMFFFCPNCH-IRF 127 (178)
T ss_pred HHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHH-H-HHHHHHHHHHhhhccCCCEEECCCCC-cEE
Confidence 34677777775422211 11222 22245566668888877633211 1 1111222 2112223 5999998 555
Q ss_pred cceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 314 GLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 314 ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
|+-++ ....| +|..||..=.
T Consensus 128 tf~eA--------~~~~F---~Cp~Cg~~L~ 147 (178)
T PRK06266 128 TFDEA--------MEYGF---RCPQCGEMLE 147 (178)
T ss_pred eHHHH--------hhcCC---cCCCCCCCCe
Confidence 55443 12233 5999998654
No 69
>PLN00209 ribosomal protein S27; Provisional
Probab=38.71 E-value=21 Score=30.19 Aligned_cols=29 Identities=14% Similarity=0.201 Sum_probs=22.2
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHS 342 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnr 342 (434)
+.+|..|+.-.+-|.. .++ -|.|..||.-
T Consensus 36 ~VkCp~C~n~q~VFSh---------A~t---~V~C~~Cg~~ 64 (86)
T PLN00209 36 DVKCQGCFNITTVFSH---------SQT---VVVCGSCQTV 64 (86)
T ss_pred EEECCCCCCeeEEEec---------Cce---EEEccccCCE
Confidence 3499999999888855 343 4789999963
No 70
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=36.61 E-value=21 Score=28.18 Aligned_cols=28 Identities=14% Similarity=0.409 Sum_probs=21.2
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCcc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHS 342 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnr 342 (434)
.+|..|+.-.+-|.- .++ -|.|..||+-
T Consensus 12 VkCp~C~n~q~vFsh---------a~t---~V~C~~Cg~~ 39 (59)
T PRK00415 12 VKCPDCGNEQVVFSH---------AST---VVRCLVCGKT 39 (59)
T ss_pred EECCCCCCeEEEEec---------CCc---EEECcccCCC
Confidence 489999998887743 343 4689999974
No 71
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=36.53 E-value=14 Score=33.90 Aligned_cols=19 Identities=16% Similarity=0.188 Sum_probs=15.7
Q ss_pred eccccCcccc---cCcccccce
Q 035627 335 GVYCHGHSWY---ASRNEASSL 353 (434)
Q Consensus 335 tC~~CGnrWk---~sr~~~~~~ 353 (434)
-|..||+.|+ |+|-.++++
T Consensus 15 rC~~C~~TwN~ti~eR~~~~~I 36 (142)
T PF06353_consen 15 RCEKCDYTWNMTIFERVNVRSI 36 (142)
T ss_pred EcccCcCccccceEeecCcccc
Confidence 4999999998 788777665
No 72
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=35.57 E-value=27 Score=29.56 Aligned_cols=29 Identities=14% Similarity=0.249 Sum_probs=22.2
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHS 342 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnr 342 (434)
+.+|..|..-.+-|.. .++ -|.|..||.-
T Consensus 35 ~VkCp~C~n~q~VFSh---------A~t---~V~C~~Cg~~ 63 (85)
T PTZ00083 35 DVKCPGCSQITTVFSH---------AQT---VVLCGGCSSQ 63 (85)
T ss_pred EEECCCCCCeeEEEec---------Cce---EEEccccCCE
Confidence 3499999998888855 343 4789999963
No 73
>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=34.60 E-value=2e+02 Score=24.11 Aligned_cols=61 Identities=11% Similarity=0.195 Sum_probs=43.4
Q ss_pred hhHHHHHHHHHHhhhccCCCCCCC----hhhHHHHHHHHHHHHHHhccCChHHHHHHHHHHHHhcc
Q 035627 190 ETYRDKWLERLLQGLQHNGNSFLW----PDTAIAAVTALEKASHDALSSDFQKRNQKLRQLLFNLK 251 (434)
Q Consensus 190 d~~RDkcielLy~aL~~~~~s~~~----~~~v~~~A~~IE~a~~~~~~~~~~~Yk~K~Rsl~~NLK 251 (434)
...|+-.++.|+.|+-...+..+. -..++.-|..||..+|+.- .+-..|=+.+--.+.+++
T Consensus 12 ~~lR~hlV~KLv~aI~P~pdp~a~~d~rm~~l~~yarkvE~~~fe~A-~sreeYY~llA~kiy~iq 76 (81)
T PF02172_consen 12 PDLRNHLVHKLVQAIFPTPDPNAMNDPRMKNLIEYARKVEKDMFETA-QSREEYYHLLAEKIYKIQ 76 (81)
T ss_dssp HHHHHHHHHHHHHHHS-SSSCCCCCSHHHHHHHHHHHHHHHHHHHC--SSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhCCCCChhhhhhHHHHHHHHHHHHHHHHHHHHh-ccHHHHHHHHHHHHHHHH
Confidence 578999999999999775332221 2467899999999999765 345578777776666663
No 74
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=34.53 E-value=20 Score=33.17 Aligned_cols=28 Identities=7% Similarity=0.052 Sum_probs=19.2
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCcc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHS 342 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnr 342 (434)
+.|.+|+ .+.|+-+++ ...| +|..||..
T Consensus 110 Y~Cp~c~-~r~tf~eA~--------~~~F---~Cp~Cg~~ 137 (158)
T TIGR00373 110 FICPNMC-VRFTFNEAM--------ELNF---TCPRCGAM 137 (158)
T ss_pred EECCCCC-cEeeHHHHH--------HcCC---cCCCCCCE
Confidence 4999998 566665542 2234 59999986
No 75
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=31.01 E-value=25 Score=41.35 Aligned_cols=27 Identities=26% Similarity=0.448 Sum_probs=20.6
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
.|||.||+.+ |+-+ |.+. .|..||.+=
T Consensus 1012 ~fRC~kC~~k---YRR~--------PL~G----~C~kCGg~l 1038 (1095)
T TIGR00354 1012 EVRCTKCNTK---YRRI--------PLVG----KCLKCGNNL 1038 (1095)
T ss_pred ceeecccCCc---cccC--------CCCC----cccccCCeE
Confidence 4789999764 7666 7775 599999864
No 76
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=30.92 E-value=21 Score=27.77 Aligned_cols=27 Identities=15% Similarity=0.362 Sum_probs=17.0
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGH 341 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGn 341 (434)
.+|..|....+-|.. .++ -|.|..||.
T Consensus 8 VkCp~C~~~q~vFSh---------a~t---~V~C~~Cg~ 34 (55)
T PF01667_consen 8 VKCPGCYNIQTVFSH---------AQT---VVKCVVCGT 34 (55)
T ss_dssp EE-TTT-SEEEEETT----------SS----EE-SSSTS
T ss_pred EECCCCCCeeEEEec---------CCe---EEEcccCCC
Confidence 489999998887744 343 468999996
No 77
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=30.52 E-value=11 Score=26.34 Aligned_cols=10 Identities=10% Similarity=-0.057 Sum_probs=8.9
Q ss_pred eccccCcccc
Q 035627 335 GVYCHGHSWY 344 (434)
Q Consensus 335 tC~~CGnrWk 344 (434)
+|+.||-+|+
T Consensus 22 LCn~Cg~~~k 31 (36)
T PF00320_consen 22 LCNACGLYYK 31 (36)
T ss_dssp EEHHHHHHHH
T ss_pred HHHHHHHHHH
Confidence 5999999996
No 78
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=30.34 E-value=32 Score=30.17 Aligned_cols=32 Identities=13% Similarity=0.219 Sum_probs=19.9
Q ss_pred cccCCCCC-----ccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 303 ARCSRCNE-----CKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 303 ~~CgkCk~-----~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
.-|.+|.. +++.+ ..+++- +-+||.+||.-=.
T Consensus 57 ~~CkkC~t~Lvpg~n~rv----R~~~~~------v~vtC~~CG~~~R 93 (105)
T COG2023 57 TICKKCYTPLVPGKNARV----RLRKGR------VVVTCLECGTIRR 93 (105)
T ss_pred HhccccCcccccCcceEE----EEcCCe------EEEEecCCCcEEE
Confidence 37999987 45553 222222 2358999997543
No 79
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=29.93 E-value=34 Score=27.52 Aligned_cols=34 Identities=15% Similarity=0.305 Sum_probs=15.9
Q ss_pred cccCCCCC-----ccccceeeecccCCCCcceeeeeeeccccCc
Q 035627 303 ARCSRCNE-----CKVGLRDIIQAGLGDRYQQLSKALGVYCHGH 341 (434)
Q Consensus 303 ~~CgkCk~-----~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGn 341 (434)
.-|.+|+. .+|+.+- ........- +.++|..|||
T Consensus 47 ~~Ck~C~~~liPG~~~~vri--~~~~~~~~~---l~~~C~~C~~ 85 (85)
T PF04032_consen 47 TICKKCGSLLIPGVNCSVRI--RKKKKKKNF---LVYTCLNCGH 85 (85)
T ss_dssp TB-TTT--B--CTTTEEEEE--E---SSS-E---EEEEETTTTE
T ss_pred ccccCCCCEEeCCCccEEEE--EecCCCCCE---EEEEccccCC
Confidence 47999998 4455322 211222222 3457999996
No 80
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.78 E-value=45 Score=32.11 Aligned_cols=20 Identities=15% Similarity=0.212 Sum_probs=16.4
Q ss_pred eccccCcccc---cCccccccee
Q 035627 335 GVYCHGHSWY---ASRNEASSLT 354 (434)
Q Consensus 335 tC~~CGnrWk---~sr~~~~~~~ 354 (434)
-|++|.+.|. |+|--++++.
T Consensus 51 kC~~Cd~tWN~~IfeR~~~~~Ie 73 (203)
T COG4332 51 KCTHCDYTWNISIFERLNVSDIE 73 (203)
T ss_pred EeeccCCccchhhhhccCcccCC
Confidence 5999999997 7887777653
No 81
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=29.45 E-value=28 Score=33.48 Aligned_cols=26 Identities=31% Similarity=0.355 Sum_probs=19.2
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
++|.||++--+- ++.|+ .|.+|||.=
T Consensus 150 A~CsrC~~~L~~----------~~~~l-----~Cp~Cg~tE 175 (188)
T COG1096 150 ARCSRCRAPLVK----------KGNML-----KCPNCGNTE 175 (188)
T ss_pred EEccCCCcceEE----------cCcEE-----ECCCCCCEE
Confidence 599999985443 24666 499999975
No 82
>PRK10220 hypothetical protein; Provisional
Probab=29.16 E-value=40 Score=29.84 Aligned_cols=28 Identities=21% Similarity=0.426 Sum_probs=17.9
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccCccccc
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWYA 345 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~ 345 (434)
.|-+|.. .-||-+ ..+. .|..|||-|-.
T Consensus 5 ~CP~C~s-eytY~d--------~~~~-----vCpeC~hEW~~ 32 (111)
T PRK10220 5 HCPKCNS-EYTYED--------NGMY-----ICPECAHEWND 32 (111)
T ss_pred cCCCCCC-cceEcC--------CCeE-----ECCcccCcCCc
Confidence 5777854 345633 2332 39999999963
No 83
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=28.43 E-value=26 Score=24.27 Aligned_cols=12 Identities=42% Similarity=0.797 Sum_probs=10.0
Q ss_pred eeccccCccccc
Q 035627 334 LGVYCHGHSWYA 345 (434)
Q Consensus 334 vtC~~CGnrWk~ 345 (434)
+.|-+||+.|++
T Consensus 26 v~C~~C~~~~~~ 37 (38)
T TIGR02098 26 VRCGKCGHVWYA 37 (38)
T ss_pred EECCCCCCEEEe
Confidence 469999999974
No 84
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=28.31 E-value=25 Score=34.07 Aligned_cols=35 Identities=17% Similarity=0.244 Sum_probs=23.9
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
..|--|++-.++.. .+.+| +++|+. .|++||.=|.
T Consensus 7 ~~Cp~Cg~eev~hE-Vik~~-g~~~lv-----rC~eCG~V~~ 41 (201)
T COG1326 7 IECPSCGSEEVSHE-VIKER-GREPLV-----RCEECGTVHP 41 (201)
T ss_pred EECCCCCcchhhHH-HHHhc-CCceEE-----EccCCCcEee
Confidence 48999998777532 22332 344665 5999999993
No 85
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=27.53 E-value=26 Score=24.76 Aligned_cols=13 Identities=23% Similarity=0.590 Sum_probs=10.6
Q ss_pred ccccCcccccCcc
Q 035627 336 VYCHGHSWYASRN 348 (434)
Q Consensus 336 C~~CGnrWk~sr~ 348 (434)
|..||.+|..+.|
T Consensus 11 C~~C~~~~~~~~d 23 (36)
T PF11781_consen 11 CPVCGSRWFYSDD 23 (36)
T ss_pred CCCCCCeEeEccC
Confidence 9999999876654
No 86
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=26.70 E-value=36 Score=30.90 Aligned_cols=31 Identities=16% Similarity=0.186 Sum_probs=21.6
Q ss_pred CccccCCCCCccccceeeecccCCCCcceeeeeeeccccCccccc
Q 035627 301 TDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWYA 345 (434)
Q Consensus 301 ~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~ 345 (434)
+++.|-.||.| ||+|-+ .|. +|..||..|-.
T Consensus 8 tKr~Cp~cg~k---FYDLnk-----~p~------vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICPNTGSK---FYDLNR-----RPA------VSPYTGEQFPP 38 (129)
T ss_pred ccccCCCcCcc---ccccCC-----CCc------cCCCcCCccCc
Confidence 46789999876 556411 244 49999999953
No 87
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=26.44 E-value=52 Score=30.77 Aligned_cols=54 Identities=13% Similarity=0.256 Sum_probs=37.0
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc-cCcccccceeecCCCC
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY-ASRNEASSLTIDGRGS 360 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk-~sr~~~~~~~~~~~~~ 360 (434)
+|..|+...... +-.|.+++-++---=-.|.+||.|.- |-|-+...|.|-..+.
T Consensus 2 ~CPfC~~~~tkV---iDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~~~VvKkdg 56 (156)
T COG1327 2 KCPFCGHEDTKV---IDSRPAEEGNAIRRRRECLECGERFTTFERAELRPLIVVKKDG 56 (156)
T ss_pred CCCCCCCCCCee---eecccccccchhhhhhcccccccccchhheeeeccceEECcCC
Confidence 688888766654 45677777654221224999999994 8888888777654444
No 88
>PRK05978 hypothetical protein; Provisional
Probab=26.43 E-value=39 Score=31.33 Aligned_cols=32 Identities=22% Similarity=0.392 Sum_probs=22.9
Q ss_pred cccCCCCCccc--cceeeecccCCCCcceeeeeeeccccCcccccCcc
Q 035627 303 ARCSRCNECKV--GLRDIIQAGLGDRYQQLSKALGVYCHGHSWYASRN 348 (434)
Q Consensus 303 ~~CgkCk~~k~--ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~sr~ 348 (434)
-+|-+|++-+. +|..+ --.|..||..+.+-|.
T Consensus 34 grCP~CG~G~LF~g~Lkv--------------~~~C~~CG~~~~~~~a 67 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKP--------------VDHCAACGEDFTHHRA 67 (148)
T ss_pred CcCCCCCCCccccccccc--------------CCCccccCCccccCCc
Confidence 38999999886 44221 2259999999986653
No 89
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=25.67 E-value=55 Score=27.92 Aligned_cols=39 Identities=18% Similarity=0.183 Sum_probs=25.5
Q ss_pred HHHhhcccCccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 293 DESEQMQMTDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 293 ~~i~~~q~~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
.+|+..|-+...|..|+.+.|.-.- +-.-.|..||+.|.
T Consensus 26 ~~ie~~~~~~~~Cp~C~~~~VkR~a-------------~GIW~C~kCg~~fA 64 (89)
T COG1997 26 KEIEAQQRAKHVCPFCGRTTVKRIA-------------TGIWKCRKCGAKFA 64 (89)
T ss_pred HHHHHHHhcCCcCCCCCCcceeeec-------------cCeEEcCCCCCeec
Confidence 3555555667899999998664211 01224999998874
No 90
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=25.64 E-value=24 Score=30.99 Aligned_cols=28 Identities=25% Similarity=0.418 Sum_probs=20.0
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
+|-|||..=-+ +|+-|+. -|.+||++-+
T Consensus 4 ~CtrCG~vf~~---------g~~~il~----GCp~CG~nkF 31 (112)
T COG3364 4 QCTRCGEVFDD---------GSEEILS----GCPKCGCNKF 31 (112)
T ss_pred eeccccccccc---------ccHHHHc----cCccccchhe
Confidence 79999874322 3566765 5999998874
No 91
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=25.50 E-value=29 Score=30.33 Aligned_cols=18 Identities=28% Similarity=0.466 Sum_probs=10.9
Q ss_pred CceEEEEEEEeChhccCc
Q 035627 29 GSMMVTGRWFYHPEEADR 46 (434)
Q Consensus 29 g~~~v~v~WFYRPeEt~~ 46 (434)
+..+|.|.||-|+.|++.
T Consensus 54 ~~pfVEV~WF~R~qe~qd 71 (108)
T PF08921_consen 54 GYPFVEVLWFDRGQEVQD 71 (108)
T ss_dssp ---EEEEEES---HHHHH
T ss_pred cceeEEEEEecCCHHHHH
Confidence 456899999999999973
No 92
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=24.79 E-value=57 Score=24.00 Aligned_cols=30 Identities=20% Similarity=0.225 Sum_probs=17.0
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGH 341 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGn 341 (434)
+|+|.+|+..= .. .+.- +|...+ .|-.||.
T Consensus 5 ey~C~~Cg~~f---e~-~~~~-~~~~~~-----~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRF---EV-LQKM-SDDPLA-----TCPECGG 34 (52)
T ss_pred EEEeCCCCCEe---EE-EEec-CCCCCC-----CCCCCCC
Confidence 57899988522 12 2322 232222 4999998
No 93
>PRK03954 ribonuclease P protein component 4; Validated
Probab=23.99 E-value=53 Score=29.44 Aligned_cols=35 Identities=14% Similarity=0.232 Sum_probs=21.3
Q ss_pred cccCCCCCc-----cccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 303 ARCSRCNEC-----KVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 303 ~~CgkCk~~-----k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
.-|.+|..- ++++ ..+..-.+- +.+||+.||+.=.
T Consensus 65 ~~CK~C~t~LiPG~n~~v----Ri~~~~~~~---vvitCl~CG~~kR 104 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARV----RLRQKRMPH---VVITCLECGHIMR 104 (121)
T ss_pred HHhhcCCCeeecCCceEE----EEecCCcce---EEEECccCCCEEe
Confidence 369999773 5664 333322222 4678999998543
No 94
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=23.89 E-value=39 Score=40.90 Aligned_cols=27 Identities=19% Similarity=0.270 Sum_probs=20.6
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCccc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSW 343 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrW 343 (434)
.|||.||+. .|+-+ |.+. .|..||.+=
T Consensus 1253 ~~RC~kC~~---kyRR~--------PL~G----~C~kCGg~i 1279 (1337)
T PRK14714 1253 EFRCLKCGT---KYRRM--------PLAG----KCRKCGGRI 1279 (1337)
T ss_pred ceeecccCc---ccccC--------CCCC----cccccCCeE
Confidence 478999976 47666 7775 599999864
No 95
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=23.16 E-value=24 Score=26.23 Aligned_cols=26 Identities=8% Similarity=0.162 Sum_probs=19.7
Q ss_pred hhccc-cchhHHHHhHHHHhHhCCCCC
Q 035627 118 TMKII-SSMRLISLDQKTRVRFGDLPD 143 (434)
Q Consensus 118 ~~~~~-~~~EId~Lv~Kti~kw~d~vd 143 (434)
.+..| .+.+|..++..++.+|+..+|
T Consensus 27 ~l~k~~~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 27 KLRKHSENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp HHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred HHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence 34456 899999999999999987654
No 96
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=22.60 E-value=49 Score=33.31 Aligned_cols=18 Identities=6% Similarity=-0.025 Sum_probs=12.6
Q ss_pred eeeccccCcccc-cCcccc
Q 035627 333 ALGVYCHGHSWY-ASRNEA 350 (434)
Q Consensus 333 FvtC~~CGnrWk-~sr~~~ 350 (434)
+..|.+|||.|+ +..-.+
T Consensus 155 ef~C~~C~h~F~G~~qm~v 173 (278)
T PF15135_consen 155 EFHCPKCRHNFRGFAQMGV 173 (278)
T ss_pred eeecccccccchhhhhcCC
Confidence 446999999998 444333
No 97
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=22.51 E-value=65 Score=28.21 Aligned_cols=40 Identities=18% Similarity=0.188 Sum_probs=25.3
Q ss_pred CccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccccCc
Q 035627 301 TDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWYASR 347 (434)
Q Consensus 301 ~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~sr 347 (434)
.-|.|-+|+.-+++-.-+ .. --+. -+..|-+||-+.-+--
T Consensus 21 k~FtCp~Cghe~vs~ctv-kk----~~~~--g~~~Cg~CGls~e~ev 60 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTV-KK----TVNI--GTAVCGNCGLSFECEV 60 (104)
T ss_pred ceEecCccCCeeeeEEEE-Ee----cCce--eEEEcccCcceEEEec
Confidence 348999999988762111 00 0111 3567999999987543
No 98
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=22.12 E-value=80 Score=23.92 Aligned_cols=33 Identities=18% Similarity=0.067 Sum_probs=20.3
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccCc
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGH 341 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGn 341 (434)
-|--||...+.+.+- ...+.-+. .+|.|.+||-
T Consensus 5 PCPFCG~~~~~~~~~---~~~~~~~~--~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQD---EGFDYGMY--YYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecc---cCCCCCCE--EEEEcCCCCC
Confidence 488898888876441 11111111 3678999998
No 99
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=22.05 E-value=32 Score=34.51 Aligned_cols=39 Identities=23% Similarity=0.520 Sum_probs=16.8
Q ss_pred cccCCCCCcc-ccceeeecccC--CCCcceeeeeeeccccCcccccCcccc
Q 035627 303 ARCSRCNECK-VGLRDIIQAGL--GDRYQQLSKALGVYCHGHSWYASRNEA 350 (434)
Q Consensus 303 ~~CgkCk~~k-~ty~q~~qtrs--aDe~mtt~~FvtC~~CGnrWk~sr~~~ 350 (434)
-.|-=||..- .++ + .... +-+|+ .|.-||..|.|-|-.=
T Consensus 173 g~CPvCGs~P~~s~--l-~~~~~~G~R~L------~Cs~C~t~W~~~R~~C 214 (290)
T PF04216_consen 173 GYCPVCGSPPVLSV--L-RGGEREGKRYL------HCSLCGTEWRFVRIKC 214 (290)
T ss_dssp SS-TTT---EEEEE--E-E------EEEE------EETTT--EEE--TTS-
T ss_pred CcCCCCCCcCceEE--E-ecCCCCccEEE------EcCCCCCeeeecCCCC
Confidence 4899999864 443 2 2221 33444 5999999998666443
No 100
>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=21.86 E-value=67 Score=23.44 Aligned_cols=28 Identities=11% Similarity=0.172 Sum_probs=18.1
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCcc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHS 342 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnr 342 (434)
+.|.+|+..++.. + .+ ++. -.|..|+++
T Consensus 19 ~~CP~Cg~~~~~~--~-~~-----~~~----~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYR--L-KT-----RGR----YRCKACRKQ 46 (46)
T ss_pred CCCCCCCCeeeEE--e-CC-----CCe----EECCCCCCc
Confidence 7899999985543 2 21 222 149999874
No 101
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=21.84 E-value=39 Score=25.44 Aligned_cols=13 Identities=38% Similarity=0.527 Sum_probs=10.4
Q ss_pred eeccccCcccccC
Q 035627 334 LGVYCHGHSWYAS 346 (434)
Q Consensus 334 vtC~~CGnrWk~s 346 (434)
=.|..|||.|+.+
T Consensus 29 W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 29 WKCPKCGHEWKAS 41 (55)
T ss_pred EECCCCCCeeEcc
Confidence 3599999999854
No 102
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.55 E-value=60 Score=29.40 Aligned_cols=36 Identities=17% Similarity=0.146 Sum_probs=20.1
Q ss_pred ccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 302 DARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 302 ~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
-+.|..|+ .+.++.++... .| +--.| +|.+||..=.
T Consensus 99 ~Y~Cp~C~-~~y~~~ea~~~--~d-~~~~f---~Cp~Cg~~l~ 134 (147)
T smart00531 99 YYKCPNCQ-SKYTFLEANQL--LD-MDGTF---TCPRCGEELE 134 (147)
T ss_pred EEECcCCC-CEeeHHHHHHh--cC-CCCcE---ECCCCCCEEE
Confidence 35999997 44444443221 22 11113 5999998654
No 103
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=21.30 E-value=54 Score=28.73 Aligned_cols=32 Identities=16% Similarity=0.238 Sum_probs=22.5
Q ss_pred CccccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccccC
Q 035627 301 TDARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWYAS 346 (434)
Q Consensus 301 ~~~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk~s 346 (434)
+++.|-.||.| ||+| .. .|. +|-.||+-|--+
T Consensus 8 tKR~Cp~CG~k---FYDL-nk----~Pi------vCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPSCGAK---FYDL-NK----DPI------VCPKCGTEFPPE 39 (108)
T ss_pred CcccCCCCcch---hccC-CC----CCc------cCCCCCCccCcc
Confidence 46789888875 6665 11 354 399999999754
No 104
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.29 E-value=64 Score=22.27 Aligned_cols=9 Identities=33% Similarity=1.069 Sum_probs=6.4
Q ss_pred ccccCCCCC
Q 035627 302 DARCSRCNE 310 (434)
Q Consensus 302 ~~~CgkCk~ 310 (434)
+|+|..||.
T Consensus 5 ~y~C~~Cg~ 13 (41)
T smart00834 5 EYRCEDCGH 13 (41)
T ss_pred EEEcCCCCC
Confidence 467777776
No 105
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=21.28 E-value=44 Score=27.19 Aligned_cols=27 Identities=15% Similarity=0.252 Sum_probs=15.7
Q ss_pred cccCCCCCccccceeeecccCCCCcceeeeeeeccccCcccc
Q 035627 303 ARCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHSWY 344 (434)
Q Consensus 303 ~~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnrWk 344 (434)
|+| +||- ..|. |+..-|. +| .||++=+
T Consensus 4 frC-~Cgr--~lya--------~e~~kTk---kC-~CG~~l~ 30 (68)
T PF09082_consen 4 FRC-DCGR--YLYA--------KEGAKTK---KC-VCGKTLK 30 (68)
T ss_dssp EEE-TTS----EEE--------ETT-SEE---EE-TTTEEEE
T ss_pred EEe-cCCC--EEEe--------cCCccee---Ee-cCCCeee
Confidence 688 6875 3442 3444443 59 8999876
No 106
>PF06061 Baculo_ME53: Baculoviridae ME53; InterPro: IPR010336 ME53 is one of the major early-transcribed genes. The ME53 protein is reported to contain a putative zinc finger motif [].; GO: 0003677 DNA binding, 0008270 zinc ion binding
Probab=21.23 E-value=45 Score=34.70 Aligned_cols=31 Identities=19% Similarity=0.249 Sum_probs=22.6
Q ss_pred ccCCCCCccccceeeecccCCCCcceeeeeeeccccC--cccccCcc
Q 035627 304 RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHG--HSWYASRN 348 (434)
Q Consensus 304 ~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CG--nrWk~sr~ 348 (434)
-|..|++.|.=+.- |-+ .|..|| |+|+|.++
T Consensus 262 ~C~~Ck~~K~yk~n---------PVL-----yCS~CGFTd~~yF~~~ 294 (327)
T PF06061_consen 262 ECKYCKKNKLYKNN---------PVL-----YCSKCGFTDPNYFKKN 294 (327)
T ss_pred hhhhccccceecCC---------ceE-----EEcccCCCChhhhccc
Confidence 49999966653322 666 499999 68899873
No 107
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=21.11 E-value=75 Score=27.90 Aligned_cols=31 Identities=16% Similarity=0.223 Sum_probs=21.2
Q ss_pred cc-ccCCCCCccccceeeecccCCCCcceeeeeeeccccCcc
Q 035627 302 DA-RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHS 342 (434)
Q Consensus 302 ~~-~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnr 342 (434)
.| .|.-|+...+.+. .. + -+ .|..|..||.+
T Consensus 79 ~yVlC~~C~spdT~l~---k~---~-r~---~~l~C~aCGa~ 110 (110)
T smart00653 79 EYVLCPECGSPDTELI---KE---N-RL---FFLKCEACGAR 110 (110)
T ss_pred hcEECCCCCCCCcEEE---Ee---C-Ce---EEEEccccCCC
Confidence 35 8999999987762 21 1 11 25579999975
No 108
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=20.71 E-value=31 Score=35.22 Aligned_cols=84 Identities=17% Similarity=0.171 Sum_probs=44.3
Q ss_pred cCCCCccccccCChhhhcchhcHHHHhhhhhHHHhhcccCccccCCCCCccccceeeecccCCCC--ccee---eeeeec
Q 035627 262 KGKLEPSKILDMSPNELNEGLTAEETAKEESDESEQMQMTDARCSRCNECKVGLRDIIQAGLGDR--YQQL---SKALGV 336 (434)
Q Consensus 262 ~G~I~p~~lv~Ms~eELas~~~~ee~~k~e~~~i~~~q~~~~~CgkCk~~k~ty~q~~qtrsaDe--~mtt---~~FvtC 336 (434)
-..|++..+..|++++|-..+.-++. =.+-..+.-.|+|+ |-.-++.- ++-+=+.+| .|.. -.-++|
T Consensus 198 ~~ti~~~~~~~~~~e~ll~rL~~e~~-----v~ile~~~v~f~C~-CSrEr~~~--aL~~lg~eEi~~m~eedg~iev~C 269 (286)
T COG1281 198 LPTITEEELFGLPAEELLYRLFHEEG-----VQLLEPQPVEFRCS-CSRERVAA--ALLSLGKEELEDMLEEDGGIEVTC 269 (286)
T ss_pred hccccHHHHcCCCHHHHHHHHhcccc-----ccccCCccceEEcC-CCHHHHHH--HHHhcCHHHHHHHHhcCCCeEEEe
Confidence 34577788888888888753332110 01111122458886 65555431 011111111 1110 023579
Q ss_pred cccCcccccCcccccce
Q 035627 337 YCHGHSWYASRNEASSL 353 (434)
Q Consensus 337 ~~CGnrWk~sr~~~~~~ 353 (434)
.=||+...|+..+|-.|
T Consensus 270 ~FC~~~Y~f~~~ei~~l 286 (286)
T COG1281 270 EFCGTKYLFDEEEIEEL 286 (286)
T ss_pred eccCCEEecCHHHHhcC
Confidence 99999999998877543
No 109
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=20.49 E-value=71 Score=28.65 Aligned_cols=31 Identities=19% Similarity=0.223 Sum_probs=21.6
Q ss_pred cc-ccCCCCCccccceeeecccCCCCcceeeeeeeccccCcc
Q 035627 302 DA-RCSRCNECKVGLRDIIQAGLGDRYQQLSKALGVYCHGHS 342 (434)
Q Consensus 302 ~~-~CgkCk~~k~ty~q~~qtrsaDe~mtt~~FvtC~~CGnr 342 (434)
.| .|..|+...+.+.- . ..+ .|..|..||.+
T Consensus 92 ~yVlC~~C~spdT~l~k---~----~r~---~~l~C~aCGa~ 123 (125)
T PF01873_consen 92 EYVLCPECGSPDTELIK---E----GRL---IFLKCKACGAS 123 (125)
T ss_dssp HHSSCTSTSSSSEEEEE---E----TTC---CEEEETTTSCE
T ss_pred HEEEcCCCCCCccEEEE---c----CCE---EEEEecccCCc
Confidence 35 89999999987632 1 122 25679999975
No 110
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.26 E-value=43 Score=30.51 Aligned_cols=9 Identities=11% Similarity=-0.023 Sum_probs=7.7
Q ss_pred eccccCccc
Q 035627 335 GVYCHGHSW 343 (434)
Q Consensus 335 tC~~CGnrW 343 (434)
.|.|||.|+
T Consensus 70 fchncgs~f 78 (160)
T COG4306 70 FCHNCGSRF 78 (160)
T ss_pred hhhcCCCCC
Confidence 499999985
No 111
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=20.06 E-value=64 Score=27.79 Aligned_cols=16 Identities=31% Similarity=0.740 Sum_probs=13.3
Q ss_pred ceEEEEEEEeChhccC
Q 035627 30 SMMVTGRWFYHPEEAD 45 (434)
Q Consensus 30 ~~~v~v~WFYRPeEt~ 45 (434)
...|+|+|||.++|..
T Consensus 76 g~~V~v~Wyyd~dD~~ 91 (99)
T PF09345_consen 76 GGKVTVNWYYDEDDED 91 (99)
T ss_pred CCcEEEEEEECCCCch
Confidence 4679999999988864
No 112
>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=20.03 E-value=59 Score=21.28 Aligned_cols=7 Identities=14% Similarity=-0.059 Sum_probs=4.8
Q ss_pred eccccCc
Q 035627 335 GVYCHGH 341 (434)
Q Consensus 335 tC~~CGn 341 (434)
.|-+||.
T Consensus 18 ~CPnCG~ 24 (24)
T PF07754_consen 18 PCPNCGF 24 (24)
T ss_pred eCCCCCC
Confidence 3888874
Done!