Query 037148
Match_columns 463
No_of_seqs 248 out of 601
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 09:08:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037148.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037148hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1946 RNA polymerase I trans 100.0 4.4E-31 9.4E-36 257.4 8.1 169 75-243 7-181 (240)
2 smart00719 Plus3 Short conserv 99.9 3.4E-28 7.5E-33 211.4 7.9 100 301-402 1-109 (109)
3 KOG2570 SWI/SNF transcription 99.9 1.8E-26 3.9E-31 236.7 5.3 150 157-335 208-373 (420)
4 PF03126 Plus-3: Plus-3 domain 99.9 6E-26 1.3E-30 196.5 5.9 98 305-403 1-107 (108)
5 KOG2402 Paf1/RNA polymerase II 99.9 3.6E-25 7.7E-30 233.6 8.8 151 303-462 217-378 (525)
6 smart00151 SWIB SWI complex, B 99.8 1.1E-20 2.4E-25 155.0 6.3 71 162-238 7-77 (77)
7 PF02201 SWIB: SWIB/MDM2 domai 99.8 3E-21 6.6E-26 158.0 1.9 70 162-237 7-76 (76)
8 COG5296 Transcription factor i 99.8 1.7E-18 3.8E-23 176.8 12.0 136 297-437 205-349 (521)
9 COG5531 SWIB-domain-containing 99.7 3.9E-17 8.4E-22 159.1 7.5 82 155-242 118-202 (237)
10 PRK14724 DNA topoisomerase III 99.6 2.2E-16 4.7E-21 180.2 6.6 71 161-237 917-987 (987)
11 PRK06319 DNA topoisomerase I/S 99.1 6.4E-11 1.4E-15 134.3 4.3 71 162-238 790-860 (860)
12 PF00569 ZZ: Zinc finger, ZZ t 86.9 0.3 6.4E-06 36.5 1.0 30 4-33 4-38 (46)
13 cd02339 ZZ_Mind_bomb Zinc fing 84.5 0.49 1.1E-05 35.6 1.1 27 6-32 2-33 (45)
14 smart00291 ZnF_ZZ Zinc-binding 84.4 0.5 1.1E-05 34.9 1.2 28 6-33 6-37 (44)
15 smart00064 FYVE Protein presen 84.1 0.71 1.5E-05 36.4 2.0 48 5-52 11-66 (68)
16 cd02249 ZZ Zinc finger, ZZ typ 80.4 0.91 2E-05 33.8 1.2 28 6-33 2-33 (46)
17 cd02345 ZZ_dah Zinc finger, ZZ 78.2 0.9 2E-05 34.6 0.6 28 6-33 2-34 (49)
18 cd02340 ZZ_NBR1_like Zinc fing 78.1 1.3 2.9E-05 32.8 1.5 27 6-32 2-32 (43)
19 KOG2522 Filamentous baseplate 78.0 2.6 5.6E-05 45.8 4.2 54 167-220 368-421 (560)
20 cd02338 ZZ_PCMF_like Zinc fing 75.1 1.8 3.8E-05 32.9 1.5 28 6-33 2-34 (49)
21 cd02334 ZZ_dystrophin Zinc fin 74.3 1.6 3.5E-05 33.4 1.1 28 6-33 2-34 (49)
22 cd02341 ZZ_ZZZ3 Zinc finger, Z 74.1 1.7 3.6E-05 33.2 1.1 28 6-33 2-36 (48)
23 cd02335 ZZ_ADA2 Zinc finger, Z 73.8 1.8 4E-05 32.7 1.3 28 6-33 2-34 (49)
24 PF00643 zf-B_box: B-box zinc 73.7 1.4 3.1E-05 31.5 0.7 28 5-32 4-32 (42)
25 cd02344 ZZ_HERC2 Zinc finger, 73.4 1.9 4.2E-05 32.5 1.3 27 6-32 2-33 (45)
26 PF02318 FYVE_2: FYVE-type zin 72.8 3.1 6.6E-05 36.9 2.7 48 3-54 53-106 (118)
27 PF04438 zf-HIT: HIT zinc fing 71.9 1.4 3E-05 30.5 0.2 23 5-27 3-25 (30)
28 KOG3795 Uncharacterized conser 67.8 3 6.4E-05 40.3 1.6 22 2-23 13-34 (230)
29 smart00290 ZnF_UBP Ubiquitin C 66.0 4 8.6E-05 30.2 1.7 24 6-29 1-25 (50)
30 PF07649 C1_3: C1-like domain; 65.2 2.3 4.9E-05 28.9 0.2 25 6-30 2-30 (30)
31 cd02336 ZZ_RSC8 Zinc finger, Z 62.4 3.7 8.1E-05 31.0 0.9 30 7-36 3-36 (45)
32 cd00065 FYVE FYVE domain; Zinc 62.2 4.1 8.8E-05 30.8 1.1 46 5-50 3-56 (57)
33 cd02343 ZZ_EF Zinc finger, ZZ 61.3 4.1 9E-05 31.3 1.0 28 6-33 2-33 (48)
34 PF10281 Ish1: Putative stress 60.7 16 0.00035 26.1 4.0 37 158-194 1-38 (38)
35 TIGR03759 conj_TIGR03759 integ 59.3 11 0.00024 36.9 3.8 67 388-454 13-87 (200)
36 KOG1081 Transcription factor N 56.2 4.5 9.7E-05 44.1 0.6 90 2-108 141-230 (463)
37 PHA02696 hypothetical protein; 55.6 8 0.00017 32.0 1.8 25 378-402 38-62 (79)
38 PF01363 FYVE: FYVE zinc finge 55.0 5.6 0.00012 31.4 0.8 49 5-53 10-68 (69)
39 cd02342 ZZ_UBA_plant Zinc fing 54.8 7.1 0.00015 29.5 1.3 27 6-32 2-33 (43)
40 smart00336 BBOX B-Box-type zin 54.0 7.9 0.00017 27.2 1.4 28 5-32 4-32 (42)
41 PF11405 Inhibitor_I67: Bromel 53.5 4 8.7E-05 29.5 -0.2 13 15-27 2-15 (41)
42 cd00021 BBOX B-Box-type zinc f 53.3 8.4 0.00018 26.6 1.4 27 6-32 2-29 (39)
43 KOG1862 GYF domain containing 52.6 11 0.00023 42.9 2.9 62 4-78 5-68 (673)
44 PF02148 zf-UBP: Zn-finger in 52.6 6.7 0.00015 30.9 0.9 43 7-49 1-56 (63)
45 KOG4582 Uncharacterized conser 51.9 7.1 0.00015 39.8 1.2 28 6-33 154-186 (278)
46 PF03107 C1_2: C1 domain; Int 50.3 13 0.00027 25.4 1.9 26 5-30 1-30 (30)
47 PF13842 Tnp_zf-ribbon_2: DDE_ 49.6 9.2 0.0002 26.8 1.1 22 7-28 3-29 (32)
48 PTZ00303 phosphatidylinositol 48.3 13 0.00029 43.1 2.7 48 5-52 461-529 (1374)
49 PF02207 zf-UBR: Putative zinc 45.3 15 0.00032 29.7 1.9 34 13-46 11-54 (71)
50 PRK05350 acyl carrier protein; 42.8 16 0.00035 29.9 1.8 58 181-241 2-59 (82)
51 PF04570 DUF581: Protein of un 41.5 22 0.00048 28.4 2.3 37 18-58 19-56 (58)
52 cd02337 ZZ_CBP Zinc finger, ZZ 39.3 16 0.00034 27.0 1.0 26 7-32 3-31 (41)
53 PF00518 E6: Early Protein (E6 36.4 19 0.00041 31.8 1.3 32 17-48 73-110 (110)
54 smart00249 PHD PHD zinc finger 36.1 20 0.00044 24.9 1.2 30 6-35 1-34 (47)
55 PRK05828 acyl carrier protein; 34.4 39 0.00086 28.4 2.9 58 181-241 1-58 (84)
56 PHA02779 E6 protein; Provision 34.3 17 0.00037 34.0 0.7 37 17-53 103-145 (150)
57 KOG1311 DHHC-type Zn-finger pr 33.4 19 0.0004 36.4 0.9 29 3-33 112-140 (299)
58 PF00130 C1_1: Phorbol esters/ 32.2 28 0.00061 25.9 1.5 29 5-33 12-46 (53)
59 PRK13702 replication protein; 31.2 24 0.00051 30.3 1.0 39 152-192 38-76 (85)
60 CHL00124 acpP acyl carrier pro 30.8 32 0.0007 27.8 1.7 58 181-241 1-58 (82)
61 PF02037 SAP: SAP domain; Int 29.8 1.1E+02 0.0023 21.5 4.0 32 161-194 4-35 (35)
62 PRK12449 acyl carrier protein; 29.3 56 0.0012 26.3 2.9 58 181-241 1-58 (80)
63 PF07754 DUF1610: Domain of un 27.9 33 0.00072 22.9 1.1 17 7-23 1-24 (24)
64 PF05093 CIAPIN1: Cytokine-ind 27.5 32 0.00068 30.4 1.2 19 5-23 68-86 (100)
65 smart00513 SAP Putative DNA-bi 24.6 1.3E+02 0.0029 20.8 3.7 32 161-194 4-35 (35)
66 KOG0957 PHD finger protein [Ge 24.4 36 0.00079 37.8 1.2 46 4-49 119-177 (707)
67 PF05458 Siva: Cd27 binding pr 23.8 35 0.00076 32.7 0.8 42 4-49 111-154 (175)
68 KOG0696 Serine/threonine prote 23.3 52 0.0011 36.3 2.1 49 6-54 58-133 (683)
69 PF13545 HTH_Crp_2: Crp-like h 22.8 1.1E+02 0.0023 23.9 3.4 44 163-216 31-75 (76)
70 cd00238 ERp29c ERp29 and ERp38 22.0 1E+02 0.0022 26.5 3.3 38 385-422 54-91 (93)
71 PLN02436 cellulose synthase A 21.6 41 0.0009 40.4 1.0 73 3-79 35-116 (1094)
72 PRK04023 DNA polymerase II lar 21.6 47 0.001 39.8 1.5 68 3-93 625-698 (1121)
73 PF11553 DUF3231: Protein of u 21.3 82 0.0018 29.1 2.8 75 387-462 92-166 (166)
74 PF00098 zf-CCHC: Zinc knuckle 21.1 53 0.0011 20.1 1.0 12 6-17 2-13 (18)
75 cd08305 Pyrin Pyrin: a protein 21.1 1.4E+02 0.003 24.5 3.7 46 387-433 6-51 (73)
76 PF06844 DUF1244: Protein of u 20.5 41 0.00088 27.7 0.5 18 42-59 10-27 (68)
No 1
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=99.97 E-value=4.4e-31 Score=257.38 Aligned_cols=169 Identities=30% Similarity=0.423 Sum_probs=113.9
Q ss_pred cchHHHHHHHhhhccCCChHHHHHhhhcccCCCCCCCCCCCcC-CCCCCCCCCCCCcchhhhh---hccccCCccccccc
Q 037148 75 NSYFYEYWQIIKDKERLTSEQVISAYNRLKSGELYSGASDSFE-SDEGKDDSDESEDDSQIRK---RKRSKGKVSVANSK 150 (463)
Q Consensus 75 e~lFk~Yw~~lK~k~~lt~~~l~~A~~~~~~~~~~~~~~~~~~-~~~~~dd~~~~~~~s~~k~---rk~~~~k~~~~~~k 150 (463)
+|+|++||+.+++.++||.++|.+|.++|.+....+.....-. .++..+...+....+..++ ++..+.........
T Consensus 7 ~~~~~~~~l~~~~~~~lt~~~vr~~~~~~~~v~~~~~k~~~~~~~~~~~~~~~~~~~k~~~~k~~~~~~~~~~~~~~~~~ 86 (240)
T KOG1946|consen 7 EYLFKDYILSLKDQETLTPDDVRRAMAPRSGVDGTAQKSLLAKAIDESSDEDSALPVKGSKKKKRGSKTRSRKPKSLESS 86 (240)
T ss_pred hhhhhHHHhcccccccCCHHHHHHHhccccCCCCcchhhhhhhhhhcccccccccccccccccccccccccccCcccccc
Confidence 9999999999999999999999999999998777555532211 1111111111111111111 00111111111111
Q ss_pred c-cccccccccCCCHHHHHHHHhcCCCC-CcccCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccch
Q 037148 151 V-KSSRKEFVGWGSRPLLEFLASIGKDT-TRELSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSI 228 (463)
Q Consensus 151 ~-~~k~~~~~gw~S~eLa~fL~~~G~~t-~~~~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei 228 (463)
. +..+..-++|++..|..|+.+|+..+ ++++||++|++.||+|||+||||||.||+.|+||++|+.|||.++|+||+|
T Consensus 87 ~~~~~~~~~~~~g~~kl~~ls~~L~~~~G~~~lsR~~vvk~iw~YIke~nLqDP~nkr~IlCDekL~~iF~~k~v~~fem 166 (240)
T KOG1946|consen 87 GEKNKKKKKASWGSTKLIPLSPSLARFVGTSELSRTDVVKKIWAYIKEHNLQDPKNKREILCDEKLKSIFGKKRVGMFEM 166 (240)
T ss_pred cccchhccccCcCcccccccCHHHHhhcccccccHHHHHHHHHHHHHHhccCCccccCeeeeHHHHHHHhccCccceeeH
Confidence 1 11111226686444433333333333 588999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcccCCccccc
Q 037148 229 PKLLTIHLAENLELL 243 (463)
Q Consensus 229 ~klL~~Hl~~~~~~s 243 (463)
++||.+||.++.+.+
T Consensus 167 ~KLL~~H~~~~~d~~ 181 (240)
T KOG1946|consen 167 LKLLTKHFLKNQDMV 181 (240)
T ss_pred HHHHHHhccCccccc
Confidence 999999999988753
No 2
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=99.95 E-value=3.4e-28 Score=211.43 Aligned_cols=100 Identities=47% Similarity=0.664 Sum_probs=92.4
Q ss_pred eecccccchhhhchHHHHHHhhChhHHHhHhheeEEEEEeCCCCccCccceeEEEEeeEEeec-------ccchhhhhhC
Q 037148 301 SVVPKNIKLVYLRKSLVEELSKQLETFEAKVMGSFVRVRSDPNDYLQKNSHQLVQVSGIHKTS-------VNAEILLELS 373 (463)
Q Consensus 301 aI~~~nIn~irL~Rs~~~~l~~dP~~F~~kvvGsFVRI~ig~~~~~~k~~YRL~qV~Gi~k~~-------~~t~~~L~~~ 373 (463)
|++.+||++|||+|+.+++|++.| +|+++|+||||||+||++++++ ++||||||+||.++. ++|++.|.+.
T Consensus 1 ~~~l~~l~~i~L~R~~l~~~~~~p-~Fe~~v~GcFVRv~ig~~~~~~-~~Yrl~qI~gv~~~~k~Y~~~~~~t~~~L~v~ 78 (109)
T smart00719 1 AIVFDNLNLLRLRRSLVEELLKPP-TFESKVVGCFVRVKIGPNDQKQ-PIYRLVQVTGVKEADKPYELGGKTTNVLLEVL 78 (109)
T ss_pred CCChHHhheEEEEHHHHHHHhcCC-chhHhceEeEEEEEECCCCCCC-CeEEEEEEeeEEecCcceecCCceeeEEEEEe
Confidence 468899999999999999999999 6999999999999999999998 999999999999963 7888888884
Q ss_pred --CCceeEeeeeccCCCCCHHHHHHHHHHHH
Q 037148 374 --DRVKWVPICNLSNDDFSEEECEDLRQRVK 402 (463)
Q Consensus 374 --~~~k~~~i~~iSn~~FTE~E~~rlrq~~~ 402 (463)
+..++|+|++|||++|||+||++|++.|+
T Consensus 79 ~g~~~~~~~i~~iSn~~fte~E~~~w~~~~~ 109 (109)
T smart00719 79 NGDSEKVVQINFISNQDFTEEEFQRWKQAIK 109 (109)
T ss_pred cCCceEEEEEEEecCCCCCHHHHHHHHHHhC
Confidence 44799999999999999999999999984
No 3
>KOG2570 consensus SWI/SNF transcription activation complex subunit [Chromatin structure and dynamics; Transcription]
Probab=99.92 E-value=1.8e-26 Score=236.66 Aligned_cols=150 Identities=27% Similarity=0.320 Sum_probs=135.5
Q ss_pred ccccCCCHHHHHHHHhcCCCCCcccCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccchHHHHhccc
Q 037148 157 EFVGWGSRPLLEFLASIGKDTTRELSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSIPKLLTIHL 236 (463)
Q Consensus 157 ~~~gw~S~eLa~fL~~~G~~t~~~~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei~klL~~Hl 236 (463)
.|. +||.|+.+| |..| .||++||.+||+|||.|+||||+++.+|+||..|+++||++++.|.+|+.+|++||
T Consensus 208 ~fk--lsp~La~lL---Gi~t---~Trp~iI~alWqYIk~n~Lqd~~e~~~incD~~l~qif~~~rl~F~elp~~l~~lL 279 (420)
T KOG2570|consen 208 EFK--LSPRLANLL---GIHT---GTRPDIVTALWQYIKTNKLQDPEDSDFINCDKALEQIFGVDRLKFPELPQLLNPLL 279 (420)
T ss_pred ccc--cCHHHHHHh---hhcc---CcchHHHHHHHHHHHHhccCCcccchhhcchHHHHHhhcccccccccchhhhhhcc
Confidence 455 899999999 9866 99999999999999999999999999999999999999999999999999999999
Q ss_pred CCccccc-------cccc---CcccchhhhhhHHHHhhhccccccccccccccccccCccchhhhcccccccceeecc--
Q 037148 237 AENLELL-------EEEF---GSCSEIEVEEDLEACKRQSNSVKRSYTKEVVGDAQKNSHTKEVVMNVQESCFASVVP-- 304 (463)
Q Consensus 237 ~~~~~~s-------~~~d---~~~~~~dved~~~~~k~qk~~~~r~m~~~~~~~~~~~~~~~~~~s~~~~~~~aaI~~-- 304 (463)
.|++||. ..++ .+||||||| ++++.+.| |+ .++.++.++++++|+|.
T Consensus 280 ~P~dPIvi~h~I~v~~~~~~~tacyDIdV~-v~~p~~~q-------~~-------------nfl~~~~~~~eI~alD~kI 338 (420)
T KOG2570|consen 280 SPPDPIVIDHTISVDGNDTKVTACYDIDVE-VEDPRKSQ-------MS-------------NFLASTESQKEIAALDRKI 338 (420)
T ss_pred CCCCCeeecceeccCCCcccceeEEeeeec-cCCccchh-------hh-------------hhhcchhhhHHHHHHHHHH
Confidence 9999973 2222 279999994 88888777 54 38888899999999995
Q ss_pred ----cccchhhhchHHHHHHhhChhHHHhHhheeE
Q 037148 305 ----KNIKLVYLRKSLVEELSKQLETFEAKVMGSF 335 (463)
Q Consensus 305 ----~nIn~irL~Rs~~~~l~~dP~~F~~kvvGsF 335 (463)
++||..+.+|.||.+|+.+|..|+..|+-|-
T Consensus 339 ~~li~~ine~~~rr~Ff~~Fs~dPvefin~wi~Sq 373 (420)
T KOG2570|consen 339 TELIQQINESKERRDFFLEFSKDPVEFINEWIESQ 373 (420)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhCHHHHHHHHHHhc
Confidence 9999999999999999999999999999874
No 4
>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1. The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.
Probab=99.92 E-value=6e-26 Score=196.46 Aligned_cols=98 Identities=34% Similarity=0.472 Sum_probs=82.2
Q ss_pred cccchhhhchHHHHHHhhChhHHHhHhheeEEEEEeCCCCccCccceeEEEEeeEEeec-------ccchhhhhhC-CC-
Q 037148 305 KNIKLVYLRKSLVEELSKQLETFEAKVMGSFVRVRSDPNDYLQKNSHQLVQVSGIHKTS-------VNAEILLELS-DR- 375 (463)
Q Consensus 305 ~nIn~irL~Rs~~~~l~~dP~~F~~kvvGsFVRI~ig~~~~~~k~~YRL~qV~Gi~k~~-------~~t~~~L~~~-~~- 375 (463)
+||++|||+|+++++|++.| +|+++|+||||||+||++++++.++||||||+||.+++ +.|+..|.+. |.
T Consensus 1 e~i~~i~l~Rs~l~~~~~~P-~Fe~~v~G~fVRv~ig~~~~~~~~~Yrl~qI~~v~~~~k~Y~~~~~~t~~~L~l~~g~~ 79 (108)
T PF03126_consen 1 EDIKRIRLSRSQLEKWLFKP-FFEDAVVGCFVRVNIGPNDYTQNPVYRLCQIVGVKEGKKPYKLGSKKTNKYLVLRHGNS 79 (108)
T ss_dssp HHHHHTBE-HHHHHHHTTST-THHHHHTT-EEEEEEETTSSS-E--EEEEEEEEEEEEEEEEEETTEEEEEEEEEEETTE
T ss_pred CchHeEEEEHHHHHHHHcCC-ChhHheeEEEEEEEecCCCCCCceeEEEEEEEEEecccccEecCCeEEEEEEEEEECCc
Confidence 57999999999999999999 79999999999999999999886689999999999985 7888888885 44
Q ss_pred ceeEeeeeccCCCCCHHHHHHHHHHHHc
Q 037148 376 VKWVPICNLSNDDFSEEECEDLRQRVKN 403 (463)
Q Consensus 376 ~k~~~i~~iSn~~FTE~E~~rlrq~~~~ 403 (463)
.+.|+|++|||++|||+||++|++.|+.
T Consensus 80 ~r~~~i~~vSn~~~te~E~~~w~~~~~~ 107 (108)
T PF03126_consen 80 ERDFPIDMVSNSPFTEEEFERWKQSCEK 107 (108)
T ss_dssp EEEEEGGGBBSS---HHHHHHHHHHH--
T ss_pred eeEEEeEeeECCCCCHHHHHHHHHHhcc
Confidence 6999999999999999999999999975
No 5
>KOG2402 consensus Paf1/RNA polymerase II complex, RTF1 component (involved in regulation of TATA box-binding protein) [Transcription]
Probab=99.91 E-value=3.6e-25 Score=233.61 Aligned_cols=151 Identities=23% Similarity=0.284 Sum_probs=134.9
Q ss_pred cccccchhhhchHHHHHHhhChhHHHhHhheeEEEEEeCCCCccCccceeEEEEeeEEeec-------ccchhhhhhC-C
Q 037148 303 VPKNIKLVYLRKSLVEELSKQLETFEAKVMGSFVRVRSDPNDYLQKNSHQLVQVSGIHKTS-------VNAEILLELS-D 374 (463)
Q Consensus 303 ~~~nIn~irL~Rs~~~~l~~dP~~F~~kvvGsFVRI~ig~~~~~~k~~YRL~qV~Gi~k~~-------~~t~~~L~~~-~ 374 (463)
+..++|+++|+|++++.|++.| +|+..|+||||||+||+.+. +++||||+|+||.++. +.||..|.+. |
T Consensus 217 ~~~dln~~rlsR~~vak~~~~P-~Fe~~V~gCfvRv~ig~~~~--~p~YRv~~I~gV~es~k~Y~l~~~~Tnk~l~~~~G 293 (525)
T KOG2402|consen 217 SISDLNALRLSRHKVAKWLFSP-FFESTVTGCFVRVGIGGEGS--KPVYRVAEIVGVLESDKPYKLEGVKTNKYLRVRHG 293 (525)
T ss_pred CHHHHHHHHhhHHHHHHHHhhh-HHHHHhhhheEEeeecCcCC--CCceeEEEEeeecccCccccccceeecceeeeecC
Confidence 5788999999999999999999 79999999999999999955 5899999999999876 8899999984 6
Q ss_pred C-ceeEeeeeccCCCCCHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhcccccc
Q 037148 375 R-VKWVPICNLSNDDFSEEECEDLRQRVKNGLASRPTVVELRQKAVCLHEDITKHWIARELDILRKCVDRANEKGWRRQY 453 (463)
Q Consensus 375 ~-~k~~~i~~iSn~~FTE~E~~rlrq~~~~~~~k~pTv~~l~~Ka~~i~~~i~~~w~e~E~~~L~~l~d~A~EkG~~~e~ 453 (463)
- .++|.|.+|||++|||+||++|+..|.+..+.+||+..|.+|-.+|.+.+++.+.++|+..+ +.+|-..+--
T Consensus 294 ~s~r~f~m~~iSn~~f~e~Efq~w~~~~~~s~~~~PT~~~i~~K~~~i~~a~~~~~sd~~v~~~------v~~k~~~~~~ 367 (525)
T KOG2402|consen 294 RSERVFRMNFISNGEFTEEEFQDWLRACKNSHGIMPTVDLISRKKLDIVKALNYRLSDKEVDQM------VAEKFEASPR 367 (525)
T ss_pred cchhhcchhhhcCCcccHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHHHHhcCccCcccHHHH------HHhhhhcCcC
Confidence 5 69999999999999999999999999999999999999999999999999999999997777 5565444444
Q ss_pred c--cccccCCC
Q 037148 454 P--SFSGHTKL 462 (463)
Q Consensus 454 p--~~~~k~~l 462 (463)
| ++|+|++|
T Consensus 368 p~N~ameK~~l 378 (525)
T KOG2402|consen 368 PRNVAMEKTGL 378 (525)
T ss_pred cchHHHHHHhH
Confidence 4 66666654
No 6
>smart00151 SWIB SWI complex, BAF60b domains.
Probab=99.82 E-value=1.1e-20 Score=155.00 Aligned_cols=71 Identities=35% Similarity=0.597 Sum_probs=68.3
Q ss_pred CCHHHHHHHHhcCCCCCcccCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccchHHHHhcccCC
Q 037148 162 GSRPLLEFLASIGKDTTRELSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSIPKLLTIHLAE 238 (463)
Q Consensus 162 ~S~eLa~fL~~~G~~t~~~~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei~klL~~Hl~~ 238 (463)
+||+|++|+ |. +++||++|+++||+|||.||||||++|+.|+||+.|+++||+++|.+++|+++|++||.+
T Consensus 7 ls~~L~~~l---g~---~~~tr~ev~~~lw~YIk~n~L~d~~~k~~i~~D~~L~~l~~~~~v~~~~~~~ll~~Hl~~ 77 (77)
T smart00151 7 LSPELAKVL---GA---PEMTRTEIIKRLWEYIKEHNLQDPQNKREILCDSKLEQIFGKDRMDMFEMNKLLTPHLIK 77 (77)
T ss_pred CCHHHHHHh---CC---CcCcHHHHHHHHHHHHHHhcccCCccCCEEecCHHHHHHHCcCeecHHHHHHHHHHHcCC
Confidence 699999999 86 579999999999999999999999999999999999999999999999999999999974
No 7
>PF02201 SWIB: SWIB/MDM2 domain; InterPro: IPR003121 The SWI/SNF family of complexes, which are conserved from yeast to humans, are ATP-dependent chromatin-remodelling proteins that facilitate transcription activation []. The mammalian complexes are made up of 9-12 proteins called BAFs (BRG1-associated factors). The BAF60 family have at least three members: BAF60a, which is ubiquitous, BAF60b and BAF60c, which are expressed in muscle and pancreatic tissues, respectively. BAF60b is present in alternative forms of the SWI/SNF complex, including complex B (SWIB), which lacks BAF60a. The SWIB domain is a conserved region found within the BAF60b proteins [], and can be found fused to the C terminus of DNA topoisomerase in Chlamydia. MDM2 is an oncoprotein that acts as a cellular inhibitor of the p53 tumour suppressor by binding to the transactivation domain of p53 and suppressing its ability to activate transcription []. p53 acts in response to DNA damage, inducing cell cycle arrest and apoptosis. Inactivation of p53 is a common occurrence in neoplastic transformations. The core of MDM2 folds into an open bundle of four helices, which is capped by two small 3-stranded beta-sheets. It consists of a duplication of two structural repeats. MDM2 has a deep hydrophobic cleft on which the p53 alpha-helix binds; p53 residues involved in transactivation are buried deep within the cleft of MDM2, thereby concealing the p53 transactivation domain. The SWIB and MDM2 domains are homologous and share a common fold.; GO: 0005515 protein binding; PDB: 1V31_A 3FE7_A 3JZQ_B 3EQY_B 2VYR_A 3JZO_A 3DAB_E 3LBJ_E 3FEA_A 3FDO_A ....
Probab=99.82 E-value=3e-21 Score=157.95 Aligned_cols=70 Identities=53% Similarity=0.748 Sum_probs=65.1
Q ss_pred CCHHHHHHHHhcCCCCCcccCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccchHHHHhcccC
Q 037148 162 GSRPLLEFLASIGKDTTRELSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSIPKLLTIHLA 237 (463)
Q Consensus 162 ~S~eLa~fL~~~G~~t~~~~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei~klL~~Hl~ 237 (463)
+||+|++|+ |.+ ++||++|++.||+|||+||||||++++.|+||++|+.|||.++|++++|+++|.+||.
T Consensus 7 ls~~L~~~l---g~~---~~sr~~v~~~lw~YIk~~~L~dp~~k~~I~cD~~L~~lf~~~~v~~~~i~~~l~~hl~ 76 (76)
T PF02201_consen 7 LSPELAEFL---GED---ELSRSEVVKRLWQYIKENNLQDPKDKRIIICDEKLKKLFGKDSVNFFEIPKLLKPHLI 76 (76)
T ss_dssp HHHHHHHHT---T-S---CEEHHHHHHHHHHHHHHTTSBESSSTTEEE-TTSHHHHHHTSECSEEETTHHHHHHHE
T ss_pred CCHHHHHHh---CCC---CCCHHHHHHHHHHHHHHhcCCCcccCceEecCHHHHHHhCCCeecHhhHHHHHHHhcC
Confidence 589999999 975 4999999999999999999999999999999999999999999999999999999973
No 8
>COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
Probab=99.77 E-value=1.7e-18 Score=176.83 Aligned_cols=136 Identities=24% Similarity=0.306 Sum_probs=120.0
Q ss_pred ccceeecccccchhhhchHHHHHHhhChhHHHhHhheeEEEEEeCCCCccCccceeEEEEeeEEeec-------ccchhh
Q 037148 297 SCFASVVPKNIKLVYLRKSLVEELSKQLETFEAKVMGSFVRVRSDPNDYLQKNSHQLVQVSGIHKTS-------VNAEIL 369 (463)
Q Consensus 297 ~~~aaI~~~nIn~irL~Rs~~~~l~~dP~~F~~kvvGsFVRI~ig~~~~~~k~~YRL~qV~Gi~k~~-------~~t~~~ 369 (463)
++||- +-++|+++++|++++.+++.| .|+..|+|||+||+||-.++ +-+||||+|.|+.... +-|+.-
T Consensus 205 d~~a~--l~Dfn~~rvgR~~VA~~~f~P-~Fed~v~Gcf~Rv~Ig~R~g--~~vyRiv~V~~~~~~~kpy~~~~v~Tn~y 279 (521)
T COG5296 205 DDFAE--LYDFNQCRVGRDMVARNVFKP-IFEDEVIGCFTRVRIGERGG--YLVYRIVGVGKGSTYSKPYGRKEVKTNRY 279 (521)
T ss_pred chhhh--hhhhhhhhhhHHHHHHHhccc-chhhhhcceeeEEEecccCC--eeEEEEEEeccceeccccccccceeeeee
Confidence 45554 567999999999999999999 59999999999999995555 4799999999998854 556666
Q ss_pred hhh-CCCc-eeEeeeeccCCCCCHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHhccchHHHHHHH
Q 037148 370 LEL-SDRV-KWVPICNLSNDDFSEEECEDLRQRVKNGLASRPTVVELRQKAVCLHEDITKHWIARELDIL 437 (463)
Q Consensus 370 L~~-~~~~-k~~~i~~iSn~~FTE~E~~rlrq~~~~~~~k~pTv~~l~~Ka~~i~~~i~~~w~e~E~~~L 437 (463)
|.+ +|.. |+|.|..+||++|.++||+||...+++|.+.+|++.-|.+|...|-..+.+-.+++|+..+
T Consensus 280 l~v~~Gr~~kvF~in~~Sn~pf~~~eyQr~~r~~~~~kl~~PS~~~v~~k~~~l~d~~~~~LSdkeis~~ 349 (521)
T COG5296 280 LDVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVDTMGRRLSDKEISKM 349 (521)
T ss_pred EeeecCcceeeeEeecccCCcccHHHHHHHHHHHhccccccchHHHHHHHHHHHHHHhCCcCchhHHHHH
Confidence 666 5874 8999999999999999999999999999999999999999999999999999999995443
No 9
>COG5531 SWIB-domain-containing proteins implicated in chromatin remodeling [Chromatin structure and dynamics]
Probab=99.68 E-value=3.9e-17 Score=159.07 Aligned_cols=82 Identities=24% Similarity=0.376 Sum_probs=73.3
Q ss_pred ccccccC--CCHHHHHHHHhcCCCCCcccCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccchHHHH
Q 037148 155 RKEFVGW--GSRPLLEFLASIGKDTTRELSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSIPKLL 232 (463)
Q Consensus 155 ~~~~~gw--~S~eLa~fL~~~G~~t~~~~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei~klL 232 (463)
...+++. +||.||.|| |.+ ++||++||+.||+|||.||||||.||+.|+||++|+.|||.+.+.||+|+++|
T Consensus 118 ~~~~~~~~~lS~~La~il---G~~---~~tr~~~v~~lw~YIk~h~lq~~~nkr~I~~D~~L~~v~g~~p~~mf~~~k~l 191 (237)
T COG5531 118 NSPSGEKVKLSPKLAAIL---GLE---PGTRPEAVKKLWKYIKKHNLQDPNNKRLILCDSKLKKVLGSDPIDMFELTKPL 191 (237)
T ss_pred ccCCCCceecCHHHHHHh---CCC---CCCccHHHHHHHHHHHHhcCCCccccceecccHHHHHHhCCCchhhhhhhccc
Confidence 3344443 699999999 974 59999999999999999999999999999999999999999999999999999
Q ss_pred hcccCC-cccc
Q 037148 233 TIHLAE-NLEL 242 (463)
Q Consensus 233 ~~Hl~~-~~~~ 242 (463)
.+|+.+ +..+
T Consensus 192 ~~hl~~~~~~v 202 (237)
T COG5531 192 SPHLIKYTIDV 202 (237)
T ss_pred ccceecCcccc
Confidence 999998 4433
No 10
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.63 E-value=2.2e-16 Score=180.15 Aligned_cols=71 Identities=27% Similarity=0.438 Sum_probs=68.0
Q ss_pred CCCHHHHHHHHhcCCCCCcccCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccchHHHHhcccC
Q 037148 161 WGSRPLLEFLASIGKDTTRELSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSIPKLLTIHLA 237 (463)
Q Consensus 161 w~S~eLa~fL~~~G~~t~~~~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei~klL~~Hl~ 237 (463)
-+||+|++|| |. .++||++|++.||+|||+||||||.||+.|+||++|+.|||+++|.||+|+++|++||.
T Consensus 917 ~ls~~La~~l---g~---~~~~r~~v~~~lW~YIK~~~Lqdp~~k~~i~cD~~L~~vfg~~~~~~~~~~~~l~~hl~ 987 (987)
T PRK14724 917 KPSAALAAVI---GA---EPVARPEVIKKLWDYIKANNLQDPADKRAINADAKLRPVFGKDQVTMFELAGIVGKHLS 987 (987)
T ss_pred CCCHHHHHHh---CC---CcCCHHHHHHHHHHHHHHccCCCcccCCeeccchHHHHHhCCCcccHHHHHHHHHHhcC
Confidence 3799999999 87 46999999999999999999999999999999999999999999999999999999984
No 11
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.08 E-value=6.4e-11 Score=134.31 Aligned_cols=71 Identities=28% Similarity=0.438 Sum_probs=67.6
Q ss_pred CCHHHHHHHHhcCCCCCcccCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccchHHHHhcccCC
Q 037148 162 GSRPLLEFLASIGKDTTRELSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSIPKLLTIHLAE 238 (463)
Q Consensus 162 ~S~eLa~fL~~~G~~t~~~~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei~klL~~Hl~~ 238 (463)
+|++|+.++ |. .+++|.++++.||+|||.|+||||.+|+.|+||++|+.+||++++.||+|+++|++||.+
T Consensus 790 ~S~~La~~~---g~---~~~sr~~~~~~lw~yIk~~~lqdp~~Kr~i~~d~kl~kvf~~~~~~~~~~~k~l~~hl~~ 860 (860)
T PRK06319 790 PSPALAAMI---GA---EPVGRGEATKKVWDYIKEHGLQSPENKKLIIPDSKLQGVIGPDPIDMFQLSKKLSQHLIK 860 (860)
T ss_pred ccccccccc---Cc---CccCchHHHHHHHHHHHHhcccCccccccCCCchhhhhhhCcCccchhhhHHHHHhhhcC
Confidence 699999999 75 579999999999999999999999999999999999999999999999999999999863
No 12
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=86.92 E-value=0.3 Score=36.54 Aligned_cols=30 Identities=27% Similarity=0.807 Sum_probs=22.3
Q ss_pred ccccccCCC----CCceeeecCC-cccccccccCC
Q 037148 4 LHACYECGK----APKFYCLCSP-KAICGHCICDA 33 (463)
Q Consensus 4 wH~C~~C~k----~~~~~C~~C~-~s~C~~C~~~~ 33 (463)
...|..|+. ...|.|..|| |.||..|+...
T Consensus 4 ~~~C~~C~~~~i~g~Ry~C~~C~d~dLC~~C~~~g 38 (46)
T PF00569_consen 4 GYTCDGCGTDPIIGVRYHCLVCPDYDLCEDCFSKG 38 (46)
T ss_dssp SCE-SSS-SSSEESSEEEESSSSS-EEEHHHHHH-
T ss_pred CeECcCCCCCcCcCCeEECCCCCCCchhhHHHhCc
Confidence 357999998 6789999999 99999998653
No 13
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=84.51 E-value=0.49 Score=35.61 Aligned_cols=27 Identities=26% Similarity=0.725 Sum_probs=23.4
Q ss_pred ccccCCC----CCceeeecCC-cccccccccC
Q 037148 6 ACYECGK----APKFYCLCSP-KAICGHCICD 32 (463)
Q Consensus 6 ~C~~C~k----~~~~~C~~C~-~s~C~~C~~~ 32 (463)
+|..|++ ...|.|..|+ |.||..|...
T Consensus 2 ~Cd~C~~~~i~G~RykC~~C~dyDLC~~C~~~ 33 (45)
T cd02339 2 ICDTCRKQGIIGIRWKCAECPNYDLCTTCYHG 33 (45)
T ss_pred CCCCCCCCCcccCeEECCCCCCccchHHHhCC
Confidence 6899994 6789999998 9999999874
No 14
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=84.42 E-value=0.5 Score=34.95 Aligned_cols=28 Identities=32% Similarity=0.990 Sum_probs=23.4
Q ss_pred ccccCCC---CCceeeecCC-cccccccccCC
Q 037148 6 ACYECGK---APKFYCLCSP-KAICGHCICDA 33 (463)
Q Consensus 6 ~C~~C~k---~~~~~C~~C~-~s~C~~C~~~~ 33 (463)
.|..|++ ...|+|..|+ |.||..|+...
T Consensus 6 ~C~~C~~~i~g~ry~C~~C~d~dlC~~Cf~~~ 37 (44)
T smart00291 6 SCDTCGKPIVGVRYHCLVCPDYDLCQSCFAKG 37 (44)
T ss_pred CCCCCCCCCcCCEEECCCCCCccchHHHHhCc
Confidence 5888885 3689999998 99999999765
No 15
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=80.36 E-value=0.91 Score=33.77 Aligned_cols=28 Identities=25% Similarity=0.734 Sum_probs=23.4
Q ss_pred ccccCCCC---CceeeecCC-cccccccccCC
Q 037148 6 ACYECGKA---PKFYCLCSP-KAICGHCICDA 33 (463)
Q Consensus 6 ~C~~C~k~---~~~~C~~C~-~s~C~~C~~~~ 33 (463)
.|..|++. ..|+|..|+ |.+|..|+...
T Consensus 2 ~C~~C~~~i~g~r~~C~~C~d~dLC~~Cf~~~ 33 (46)
T cd02249 2 SCDGCLKPIVGVRYHCLVCEDFDLCSSCYAKG 33 (46)
T ss_pred CCcCCCCCCcCCEEECCCCCCCcCHHHHHCcC
Confidence 47777764 688999999 99999999865
No 17
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=78.15 E-value=0.9 Score=34.56 Aligned_cols=28 Identities=25% Similarity=0.676 Sum_probs=23.6
Q ss_pred ccccCCC----CCceeeecCC-cccccccccCC
Q 037148 6 ACYECGK----APKFYCLCSP-KAICGHCICDA 33 (463)
Q Consensus 6 ~C~~C~k----~~~~~C~~C~-~s~C~~C~~~~ 33 (463)
.|+.|++ ...|.|.-|+ |.||-.|+...
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~dydLC~~Cf~~~ 34 (49)
T cd02345 2 SCSACRKQDISGIRFPCQVCRDYSLCLGCYTKG 34 (49)
T ss_pred cCCCCCCCCceEeeEECCCCCCcCchHHHHhCC
Confidence 5889998 4568999999 99999998743
No 18
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=78.06 E-value=1.3 Score=32.82 Aligned_cols=27 Identities=26% Similarity=0.797 Sum_probs=22.4
Q ss_pred ccccCCCC---CceeeecCC-cccccccccC
Q 037148 6 ACYECGKA---PKFYCLCSP-KAICGHCICD 32 (463)
Q Consensus 6 ~C~~C~k~---~~~~C~~C~-~s~C~~C~~~ 32 (463)
.|..|+.. ..|.|..|+ |-+|..|...
T Consensus 2 ~Cd~C~~~i~G~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 2 ICDGCQGPIVGVRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCCcCcCCeEECCCCCCccchHHhhCc
Confidence 57888863 689999997 9999999875
No 19
>KOG2522 consensus Filamentous baseplate protein Ligatin, contains PUA domain [Translation, ribosomal structure and biogenesis]
Probab=78.02 E-value=2.6 Score=45.80 Aligned_cols=54 Identities=19% Similarity=0.303 Sum_probs=45.8
Q ss_pred HHHHHhcCCCCCcccCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCC
Q 037148 167 LEFLASIGKDTTRELSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGR 220 (463)
Q Consensus 167 a~fL~~~G~~t~~~~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~ 220 (463)
..++...|.+.....+-.+|..++..||+.|||-||.||..|+.|+-|-....+
T Consensus 368 ~~Lf~evg~~kg~lyt~seir~~V~kYi~knnLad~~nKg~VrLDpILfd~~~k 421 (560)
T KOG2522|consen 368 KDLFKEVGLAKGTLYTSSEIRSAVSKYISKNNLADTKNKGKVRLDPILFDMVNK 421 (560)
T ss_pred HHHHHhcCccccceeeHHHHHHHHHHHhhhhhccccccCCcEEeccHHHHHHHh
Confidence 445556677666789999999999999999999999999999999888776554
No 20
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=75.08 E-value=1.8 Score=32.93 Aligned_cols=28 Identities=29% Similarity=0.821 Sum_probs=23.2
Q ss_pred ccccCCCC----CceeeecCC-cccccccccCC
Q 037148 6 ACYECGKA----PKFYCLCSP-KAICGHCICDA 33 (463)
Q Consensus 6 ~C~~C~k~----~~~~C~~C~-~s~C~~C~~~~ 33 (463)
.|..|++. ..|.|..|+ |.+|..|+...
T Consensus 2 ~C~~C~~~~i~g~R~~C~~C~d~dlC~~Cf~~~ 34 (49)
T cd02338 2 SCDGCGKSNFTGRRYKCLICYDYDLCADCYDSG 34 (49)
T ss_pred CCCCCcCCCcEEeeEEeCCCCCCccchhHHhCC
Confidence 58889843 569999999 99999998754
No 21
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=74.26 E-value=1.6 Score=33.42 Aligned_cols=28 Identities=21% Similarity=0.606 Sum_probs=23.6
Q ss_pred ccccCCCC----CceeeecCC-cccccccccCC
Q 037148 6 ACYECGKA----PKFYCLCSP-KAICGHCICDA 33 (463)
Q Consensus 6 ~C~~C~k~----~~~~C~~C~-~s~C~~C~~~~ 33 (463)
.|..|++. ..|.|..|+ |-||..|+...
T Consensus 2 ~Cd~C~~~pi~g~RykC~~C~d~DLC~~Cf~~g 34 (49)
T cd02334 2 KCNICKEFPITGFRYRCLKCFNYDLCQSCFFSG 34 (49)
T ss_pred CCCCCCCCCceeeeEECCCCCCcCchHHHHhCC
Confidence 58899864 478999999 99999999754
No 22
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=74.09 E-value=1.7 Score=33.23 Aligned_cols=28 Identities=21% Similarity=0.740 Sum_probs=23.3
Q ss_pred ccccCCC----CCceeeecCC---cccccccccCC
Q 037148 6 ACYECGK----APKFYCLCSP---KAICGHCICDA 33 (463)
Q Consensus 6 ~C~~C~k----~~~~~C~~C~---~s~C~~C~~~~ 33 (463)
.|.+|+. ...|+|..|+ |.+|..|+...
T Consensus 2 ~Cd~C~~~pI~G~R~~C~~C~~~d~DlC~~C~~~~ 36 (48)
T cd02341 2 KCDSCGIEPIPGTRYHCSECDDGDFDLCQDCVVKG 36 (48)
T ss_pred CCCCCCCCccccceEECCCCCCCCCccCHHHHhCc
Confidence 4888887 4569999999 99999998754
No 23
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=73.83 E-value=1.8 Score=32.71 Aligned_cols=28 Identities=25% Similarity=0.637 Sum_probs=22.9
Q ss_pred ccccCCCC----CceeeecCC-cccccccccCC
Q 037148 6 ACYECGKA----PKFYCLCSP-KAICGHCICDA 33 (463)
Q Consensus 6 ~C~~C~k~----~~~~C~~C~-~s~C~~C~~~~ 33 (463)
.|..|.+. ..|.|..|+ |.||..|+...
T Consensus 2 ~Cd~C~~~~~~g~r~~C~~C~d~dLC~~Cf~~g 34 (49)
T cd02335 2 HCDYCSKDITGTIRIKCAECPDFDLCLECFSAG 34 (49)
T ss_pred CCCCcCCCCCCCcEEECCCCCCcchhHHhhhCc
Confidence 48888874 448899997 99999999864
No 24
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=73.65 E-value=1.4 Score=31.49 Aligned_cols=28 Identities=18% Similarity=0.553 Sum_probs=24.3
Q ss_pred cccccCCCC-CceeeecCCcccccccccC
Q 037148 5 HACYECGKA-PKFYCLCSPKAICGHCICD 32 (463)
Q Consensus 5 H~C~~C~k~-~~~~C~~C~~s~C~~C~~~ 32 (463)
..|..|++. ..|.|.+|-..+|..|...
T Consensus 4 ~~C~~H~~~~~~~~C~~C~~~~C~~C~~~ 32 (42)
T PF00643_consen 4 PKCPEHPEEPLSLFCEDCNEPLCSECTVS 32 (42)
T ss_dssp SB-SSTTTSBEEEEETTTTEEEEHHHHHT
T ss_pred ccCccCCccceEEEecCCCCccCccCCCC
Confidence 479999998 9999999999999999764
No 25
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=73.42 E-value=1.9 Score=32.53 Aligned_cols=27 Identities=26% Similarity=0.696 Sum_probs=23.1
Q ss_pred ccccCCCC----CceeeecCC-cccccccccC
Q 037148 6 ACYECGKA----PKFYCLCSP-KAICGHCICD 32 (463)
Q Consensus 6 ~C~~C~k~----~~~~C~~C~-~s~C~~C~~~ 32 (463)
.|..|+.. ..|.|..|+ |.||..|+..
T Consensus 2 ~Cd~C~~~pI~G~RykC~~C~dyDLC~~Cf~~ 33 (45)
T cd02344 2 TCDGCQMFPINGPRFKCRNCDDFDFCENCFKT 33 (45)
T ss_pred CCCCCCCCCCccCeEECCCCCCccchHHhhCC
Confidence 58888863 689999999 9999999876
No 26
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=72.77 E-value=3.1 Score=36.87 Aligned_cols=48 Identities=25% Similarity=0.434 Sum_probs=34.3
Q ss_pred CccccccCCC------CCceeeecCCcccccccccCCeEEEEeCCcccchhhhHHHHH
Q 037148 3 DLHACYECGK------APKFYCLCSPKAICGHCICDAEFAIVKGNKGLCSGCLELVLL 54 (463)
Q Consensus 3 gwH~C~~C~k------~~~~~C~~C~~s~C~~C~~~~~f~~vrgnkGfC~~C~~~~~l 54 (463)
|-+.|..|++ ++.-.|.-|.+.||..|-.. .-+.+.-+|..|.+..-+
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~----~~~~~~WlC~vC~k~rel 106 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY----SKKEPIWLCKVCQKQREL 106 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE----TSSSCCEEEHHHHHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc----CCCCCCEEChhhHHHHHH
Confidence 5688999987 45677999999999999765 112234489999886544
No 27
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=71.92 E-value=1.4 Score=30.54 Aligned_cols=23 Identities=26% Similarity=0.707 Sum_probs=17.9
Q ss_pred cccccCCCCCceeeecCCccccc
Q 037148 5 HACYECGKAPKFYCLCSPKAICG 27 (463)
Q Consensus 5 H~C~~C~k~~~~~C~~C~~s~C~ 27 (463)
++|+.|+..+.|.|..|...+|-
T Consensus 3 ~~C~vC~~~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGNPAKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSSEESEE-TTT--EESS
T ss_pred CCCccCcCCCEEECCCcCCceeC
Confidence 68999999999999999888774
No 28
>KOG3795 consensus Uncharacterized conserved protein [Function unknown]
Probab=67.82 E-value=3 Score=40.33 Aligned_cols=22 Identities=23% Similarity=0.570 Sum_probs=19.6
Q ss_pred CCccccccCCCCCceeeecCCc
Q 037148 2 TDLHACYECGKAPKFYCLCSPK 23 (463)
Q Consensus 2 ~gwH~C~~C~k~~~~~C~~C~~ 23 (463)
-|.|.|-.|+..-+|.||+|-.
T Consensus 13 eGRs~C~~C~~SRkFfCY~C~V 34 (230)
T KOG3795|consen 13 EGRSTCPGCKSSRKFFCYDCRV 34 (230)
T ss_pred cccccCCCCCCcceEEEEeecc
Confidence 4889999999999999999943
No 29
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=65.95 E-value=4 Score=30.23 Aligned_cols=24 Identities=29% Similarity=0.754 Sum_probs=19.3
Q ss_pred ccccCCCCC-ceeeecCCccccccc
Q 037148 6 ACYECGKAP-KFYCLCSPKAICGHC 29 (463)
Q Consensus 6 ~C~~C~k~~-~~~C~~C~~s~C~~C 29 (463)
.|..|+... -|.|+.|++..|+.-
T Consensus 1 ~C~~C~~~~~l~~CL~C~~~~c~~~ 25 (50)
T smart00290 1 RCSVCGTIENLWLCLTCGQVGCGRY 25 (50)
T ss_pred CcccCCCcCCeEEecCCCCcccCCC
Confidence 488898766 567999999999754
No 30
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=65.17 E-value=2.3 Score=28.88 Aligned_cols=25 Identities=24% Similarity=0.549 Sum_probs=11.6
Q ss_pred ccccCCCCC----ceeeecCCcccccccc
Q 037148 6 ACYECGKAP----KFYCLCSPKAICGHCI 30 (463)
Q Consensus 6 ~C~~C~k~~----~~~C~~C~~s~C~~C~ 30 (463)
.|..|+++. .|.|..|-|.++..|+
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 478888775 5889999999999884
No 31
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=62.37 E-value=3.7 Score=30.97 Aligned_cols=30 Identities=23% Similarity=0.754 Sum_probs=23.7
Q ss_pred cccCCC---CCceeeecCC-cccccccccCCeEE
Q 037148 7 CYECGK---APKFYCLCSP-KAICGHCICDAEFA 36 (463)
Q Consensus 7 C~~C~k---~~~~~C~~C~-~s~C~~C~~~~~f~ 36 (463)
|..|+. ...|+|..++ +.||..|+.++.|.
T Consensus 3 C~~Cg~D~t~vryh~~~~~~~dLC~~CF~~G~f~ 36 (45)
T cd02336 3 CFTCGNDCTRVRYHNLKAKKYDLCPSCYQEGRFP 36 (45)
T ss_pred ccCCCCccCceEEEecCCCccccChHHHhCcCCC
Confidence 444443 4789999999 99999999998763
No 32
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=62.16 E-value=4.1 Score=30.83 Aligned_cols=46 Identities=22% Similarity=0.553 Sum_probs=33.7
Q ss_pred cccccCCC-----CCceeeecCCcccccccccCCeEEEEe---CCcccchhhhH
Q 037148 5 HACYECGK-----APKFYCLCSPKAICGHCICDAEFAIVK---GNKGLCSGCLE 50 (463)
Q Consensus 5 H~C~~C~k-----~~~~~C~~C~~s~C~~C~~~~~f~~vr---gnkGfC~~C~~ 50 (463)
..|+.|++ ...++|.-|...+|..|.....++... ...-.|..|..
T Consensus 3 ~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~~~~~~~rvC~~C~~ 56 (57)
T cd00065 3 SSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCYE 56 (57)
T ss_pred CcCcccCccccCCccccccCcCcCCcChHHcCCeeecCcccCCCccEeChHHhC
Confidence 45788877 457889999999999999987655431 23467777753
No 33
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=61.34 E-value=4.1 Score=31.29 Aligned_cols=28 Identities=21% Similarity=0.738 Sum_probs=22.4
Q ss_pred ccccCCCC---CceeeecCC-cccccccccCC
Q 037148 6 ACYECGKA---PKFYCLCSP-KAICGHCICDA 33 (463)
Q Consensus 6 ~C~~C~k~---~~~~C~~C~-~s~C~~C~~~~ 33 (463)
.|..|++. ..|.|+.|+ |-+|..|+..+
T Consensus 2 ~CdgC~~~~~~~RykCl~C~d~DlC~~Cf~~g 33 (48)
T cd02343 2 SCDGCDEIAPWHRYRCLQCTDMDLCKTCFLGG 33 (48)
T ss_pred CCCCCCCcCCCceEECCCCCCchhHHHHHhCC
Confidence 37777754 468899999 99999998765
No 34
>PF10281 Ish1: Putative stress-responsive nuclear envelope protein; InterPro: IPR018803 This group of proteins, found primarily in fungi, consists of putative stress-responsive nuclear envelope protein Ish1 and homologues [].
Probab=60.72 E-value=16 Score=26.05 Aligned_cols=37 Identities=19% Similarity=0.350 Sum_probs=31.4
Q ss_pred cccCCCHHHHHHHHhcCCCCCccc-CHHHHHHHHHHHh
Q 037148 158 FVGWGSRPLLEFLASIGKDTTREL-SDDAITTIISGYC 194 (463)
Q Consensus 158 ~~gw~S~eLa~fL~~~G~~t~~~~-sR~~Vv~~lW~YI 194 (463)
|-.|-..+|.++|.+-|+...+.. +|.+++..+-+|+
T Consensus 1 fdtWs~~~L~~wL~~~gi~~~~~~~~rd~Ll~~~k~~y 38 (38)
T PF10281_consen 1 FDTWSDSDLKSWLKSHGIPVPKSAKTRDELLKLAKKNY 38 (38)
T ss_pred CCCCCHHHHHHHHHHcCCCCCCCCCCHHHHHHHHHHhC
Confidence 567999999999999998776666 9999999887764
No 35
>TIGR03759 conj_TIGR03759 integrating conjugative element protein, PFL_4693 family. Members of this protein family, such as model protein PFL_4693 from Pseudomonas fluorescens Pf-5, belong to extended genomic regions that appear to be spread by conjugative transfer. Most members have a predicted N-terminal signal sequence. The function is unknown.
Probab=59.26 E-value=11 Score=36.90 Aligned_cols=67 Identities=19% Similarity=0.390 Sum_probs=50.8
Q ss_pred CCCHHHHHHHHHHHHc------CCCCCCcHHHHHHHHHHHHHHHhccchHHHHHHHHHHH--HHHhhhccccccc
Q 037148 388 DFSEEECEDLRQRVKN------GLASRPTVVELRQKAVCLHEDITKHWIARELDILRKCV--DRANEKGWRRQYP 454 (463)
Q Consensus 388 ~FTE~E~~rlrq~~~~------~~~k~pTv~~l~~Ka~~i~~~i~~~w~e~E~~~L~~l~--d~A~EkG~~~e~p 454 (463)
-+||+|+.||++.|.. -++.+.|.--|+.+-..=.+-..--|-..|-.|.++.+ .+|=.+-|.+-||
T Consensus 13 GLt~~Ew~RY~~LmqG~rG~~SPgLdPLtaLGIeArsd~ERrryAEl~vk~E~~rvekeLA~qrayd~A~~RL~p 87 (200)
T TIGR03759 13 GLTEDEWQRYQQLMQGPRGVYSPGLDPLTALGIEARSDEERRRYAELWVKQEAQRVEKELAFQRAYDAAWQRLYP 87 (200)
T ss_pred CCCHHHHHHHHHHhcCCccCcCCCCChhhhhccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 3799999999999983 24677787777766555555556667788888888885 5666678999998
No 36
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=56.15 E-value=4.5 Score=44.09 Aligned_cols=90 Identities=7% Similarity=-0.242 Sum_probs=63.6
Q ss_pred CCccccccCCCCCceeeecCCcccccccccCCeEEEEeCCcccchhhhHHHHHHhcccccCCCCccccCCCCCcchHHHH
Q 037148 2 TDLHACYECGKAPKFYCLCSPKAICGHCICDAEFAIVKGNKGLCSGCLELVLLIEENKDVDSHGCKIDFSDPENSYFYEY 81 (463)
Q Consensus 2 ~gwH~C~~C~k~~~~~C~~C~~s~C~~C~~~~~f~~vrgnkGfC~~C~~~~~lIE~~~~~~~~~~~vDf~d~~e~lFk~Y 81 (463)
|.||.|..|+..+-++|..|.+. .+++.. ..++.-| ...+.+.....+ ..+|.+.-.++|+.|
T Consensus 141 ~vw~~vg~~~~~~c~vc~~~~~~-------~~~~~~----~~~f~~~-~~~~~~~~~~~~-----~g~~~~~l~~~~~~~ 203 (463)
T KOG1081|consen 141 LVWSKVGEYPWWPCMVCHDPLLP-------KGMKHD----HVNFFGC-YAWTHEKRVFPY-----EGQSSKLIPHSKKPA 203 (463)
T ss_pred EEeEEcCcccccccceecCcccc-------hhhccc----cceeccc-hhhHHHhhhhhc-----cchHHHhhhhccccc
Confidence 68999999999996666665544 233332 2333334 666666666664 455555558999999
Q ss_pred HHHhhhccCCChHHHHHhhhcccCCCC
Q 037148 82 WQIIKDKERLTSEQVISAYNRLKSGEL 108 (463)
Q Consensus 82 w~~lK~k~~lt~~~l~~A~~~~~~~~~ 108 (463)
|..-+....++..--..|-.+|++...
T Consensus 204 s~~~~~~~~~~~r~~~~~~q~~~~~~~ 230 (463)
T KOG1081|consen 204 STMSEKIKEAKARFGKLKAQWEAGIKQ 230 (463)
T ss_pred hhhhhhhhcccchhhhcccchhhccch
Confidence 999999998888888888777777665
No 37
>PHA02696 hypothetical protein; Provisional
Probab=55.63 E-value=8 Score=31.99 Aligned_cols=25 Identities=36% Similarity=0.371 Sum_probs=20.8
Q ss_pred eEeeeeccCCCCCHHHHHHHHHHHH
Q 037148 378 WVPICNLSNDDFSEEECEDLRQRVK 402 (463)
Q Consensus 378 ~~~i~~iSn~~FTE~E~~rlrq~~~ 402 (463)
+--|..|.|.-|||+||.+=+|.+.
T Consensus 38 VsViQtCdDDYFTEeEFdDgkQvVa 62 (79)
T PHA02696 38 VSVIQTCDDDYFTEEEFDDGKQVVA 62 (79)
T ss_pred EEeeeecccccccHhhcccHHHHHH
Confidence 4456789999999999999988764
No 38
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=55.03 E-value=5.6 Score=31.39 Aligned_cols=49 Identities=18% Similarity=0.480 Sum_probs=27.8
Q ss_pred cccccCCCC-----CceeeecCCcccccccccCCeEEEE-----eCCcccchhhhHHHH
Q 037148 5 HACYECGKA-----PKFYCLCSPKAICGHCICDAEFAIV-----KGNKGLCSGCLELVL 53 (463)
Q Consensus 5 H~C~~C~k~-----~~~~C~~C~~s~C~~C~~~~~f~~v-----rgnkGfC~~C~~~~~ 53 (463)
..|..|++. ..++|..|...+|..|......+.. ....-.|..|+..+.
T Consensus 10 ~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~~~~~ 68 (69)
T PF01363_consen 10 SNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCYSKLQ 68 (69)
T ss_dssp SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHHHHHH
T ss_pred CcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHHHHhc
Confidence 568888875 5678999999999999976554430 112357888887664
No 39
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=54.78 E-value=7.1 Score=29.46 Aligned_cols=27 Identities=22% Similarity=0.675 Sum_probs=22.6
Q ss_pred ccccCCCC----CceeeecCC-cccccccccC
Q 037148 6 ACYECGKA----PKFYCLCSP-KAICGHCICD 32 (463)
Q Consensus 6 ~C~~C~k~----~~~~C~~C~-~s~C~~C~~~ 32 (463)
.|..|+.. ..|.|..|+ |-||..|...
T Consensus 2 ~CDgCg~~PI~G~RykC~~C~dyDLC~~C~~~ 33 (43)
T cd02342 2 QCDGCGVLPITGPRYKSKVKEDYDLCTICFSR 33 (43)
T ss_pred CCCCCCCCcccccceEeCCCCCCccHHHHhhh
Confidence 47888874 579999999 9999999875
No 40
>smart00336 BBOX B-Box-type zinc finger.
Probab=54.04 E-value=7.9 Score=27.16 Aligned_cols=28 Identities=21% Similarity=0.570 Sum_probs=24.1
Q ss_pred cccccCC-CCCceeeecCCcccccccccC
Q 037148 5 HACYECG-KAPKFYCLCSPKAICGHCICD 32 (463)
Q Consensus 5 H~C~~C~-k~~~~~C~~C~~s~C~~C~~~ 32 (463)
-.|..|+ ....|.|-+|.-.+|..|...
T Consensus 4 ~~C~~h~~~~~~~~C~~c~~~iC~~C~~~ 32 (42)
T smart00336 4 PKCDSHGDEPAEFFCEECGALLCRTCDEA 32 (42)
T ss_pred CcCCCCCCCceEEECCCCCcccccccChh
Confidence 4688898 888999999999999999854
No 41
>PF11405 Inhibitor_I67: Bromelain inhibitor VI; InterPro: IPR022713 Bromelain inhibitor VI is a double-chain inhibitor consisting of an 11-residue and a 41-residue chain. This protein is the 41-residue heavy chain which is joined to the 11-residue chain by disulphide bonds. The inhibitor acts to inhibit the cysteine proteinase bromelain. ; PDB: 2BI6_H 1BI6_H.
Probab=53.50 E-value=4 Score=29.54 Aligned_cols=13 Identities=23% Similarity=0.848 Sum_probs=4.7
Q ss_pred ceeeecCC-ccccc
Q 037148 15 KFYCLCSP-KAICG 27 (463)
Q Consensus 15 ~~~C~~C~-~s~C~ 27 (463)
.|.|||=. ||-|+
T Consensus 2 eykcyctdtysdcp 15 (41)
T PF11405_consen 2 EYKCYCTDTYSDCP 15 (41)
T ss_dssp -SS-EE----SS--
T ss_pred cceEEeecccccCc
Confidence 47788654 88887
No 42
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=53.31 E-value=8.4 Score=26.62 Aligned_cols=27 Identities=22% Similarity=0.582 Sum_probs=23.3
Q ss_pred ccccCCC-CCceeeecCCcccccccccC
Q 037148 6 ACYECGK-APKFYCLCSPKAICGHCICD 32 (463)
Q Consensus 6 ~C~~C~k-~~~~~C~~C~~s~C~~C~~~ 32 (463)
+|..++. +..|.|.+|.-.+|..|.-.
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~~~ 29 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCDLS 29 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcChh
Confidence 5888888 88999999999999999743
No 43
>KOG1862 consensus GYF domain containing proteins [General function prediction only]
Probab=52.65 E-value=11 Score=42.91 Aligned_cols=62 Identities=3% Similarity=-0.206 Sum_probs=52.6
Q ss_pred ccccccCCCCCceeeecCCcccccccccCCeEEEEeCCcccchhhhHHHHHHhcccccCCCCccccCCCCC--cchH
Q 037148 4 LHACYECGKAPKFYCLCSPKAICGHCICDAEFAIVKGNKGLCSGCLELVLLIEENKDVDSHGCKIDFSDPE--NSYF 78 (463)
Q Consensus 4 wH~C~~C~k~~~~~C~~C~~s~C~~C~~~~~f~~vrgnkGfC~~C~~~~~lIE~~~~~~~~~~~vDf~d~~--e~lF 78 (463)
|+ |+.|..+..|+|+.|+..+|.+|.....|...||++..|+ .........++++.+. .|++
T Consensus 5 ~~-s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~~~a~~~~~~~~~~~p~~~~~~ 68 (673)
T KOG1862|consen 5 SF-SFPEVSTLLYQVPFPALNRGRGEGSTGIESQGRGRMSNGN------------VGSASSKGESGKEERPNLRKVR 68 (673)
T ss_pred cc-CcccCCcccccCCCcccccCCCCCCccccccccccccCCC------------cccccccccCCcccCccccccC
Confidence 88 9999999999999999999999999999999999999999 2233455667777666 6666
No 44
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 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 UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=52.64 E-value=6.7 Score=30.89 Aligned_cols=43 Identities=21% Similarity=0.442 Sum_probs=26.3
Q ss_pred cccCCCC--CceeeecCCcccccc----cccC-------CeEEEEeCCcccchhhh
Q 037148 7 CYECGKA--PKFYCLCSPKAICGH----CICD-------AEFAIVKGNKGLCSGCL 49 (463)
Q Consensus 7 C~~C~k~--~~~~C~~C~~s~C~~----C~~~-------~~f~~vrgnkGfC~~C~ 49 (463)
|+.|... .-|+|++|++..|+. .... .-++.++...-+|-.|-
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~~~Ha~~H~~~~~H~l~v~~~~~~i~C~~C~ 56 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYSNGHALKHYKETGHPLAVSLSTGSIWCYACD 56 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTSTSHHHHHHHHHT--EEEETTTTCEEETTTT
T ss_pred CCCCCCcCCceEEeCCCCcccccCCcCcHHHHhhcccCCeEEEECCCCeEEEcCCC
Confidence 5666644 778899999999994 3221 24555555566666663
No 45
>KOG4582 consensus Uncharacterized conserved protein, contains ZZ-type Zn-finger [General function prediction only]
Probab=51.87 E-value=7.1 Score=39.78 Aligned_cols=28 Identities=29% Similarity=0.909 Sum_probs=25.2
Q ss_pred ccccCCC----CCceeeecCC-cccccccccCC
Q 037148 6 ACYECGK----APKFYCLCSP-KAICGHCICDA 33 (463)
Q Consensus 6 ~C~~C~k----~~~~~C~~C~-~s~C~~C~~~~ 33 (463)
.|.+|++ ...|.|.-|+ |-+|..|-...
T Consensus 154 ~CD~C~~~~IvG~RyKC~~C~dYDLCe~Ce~~~ 186 (278)
T KOG4582|consen 154 PCDNCGKPGIVGARYKCTVCPDYDLCERCEAGN 186 (278)
T ss_pred cCCCccCCccccceeeecCCCccchhHHhhcCC
Confidence 6999999 6789999999 99999998764
No 46
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=50.26 E-value=13 Score=25.38 Aligned_cols=26 Identities=15% Similarity=0.297 Sum_probs=20.2
Q ss_pred cccccCCCCC----ceeeecCCcccccccc
Q 037148 5 HACYECGKAP----KFYCLCSPKAICGHCI 30 (463)
Q Consensus 5 H~C~~C~k~~----~~~C~~C~~s~C~~C~ 30 (463)
+.|..|++.. -|.|-.|.+.++..|.
T Consensus 1 ~~C~~C~~~~~~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCCcCCCEeEEeCCCCCeEcCccC
Confidence 4688888765 5778888899988884
No 47
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=49.64 E-value=9.2 Score=26.76 Aligned_cols=22 Identities=23% Similarity=0.696 Sum_probs=17.4
Q ss_pred cccCCCC-----CceeeecCCcccccc
Q 037148 7 CYECGKA-----PKFYCLCSPKAICGH 28 (463)
Q Consensus 7 C~~C~k~-----~~~~C~~C~~s~C~~ 28 (463)
|..|-+. +.|+|-.|...+|..
T Consensus 3 C~vC~~~k~rk~T~~~C~~C~v~lC~~ 29 (32)
T PF13842_consen 3 CKVCSKKKRRKDTRYMCSKCDVPLCVE 29 (32)
T ss_pred CeECCcCCccceeEEEccCCCCcccCC
Confidence 5555555 889999999999875
No 48
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=48.33 E-value=13 Score=43.06 Aligned_cols=48 Identities=29% Similarity=0.660 Sum_probs=34.9
Q ss_pred cccccCCCCC----------ceeeecCCcccccccccCC---eEEEE-e-CCc------ccchhhhHHH
Q 037148 5 HACYECGKAP----------KFYCLCSPKAICGHCICDA---EFAIV-K-GNK------GLCSGCLELV 52 (463)
Q Consensus 5 H~C~~C~k~~----------~~~C~~C~~s~C~~C~~~~---~f~~v-r-gnk------GfC~~C~~~~ 52 (463)
+.|..|++.= +++|.+|...+|..|-..- .|.-| + |.. --|..|++-.
T Consensus 461 dtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs~yp~aKLpKPgsseE~ppRRVCD~CYdq~ 529 (1374)
T PTZ00303 461 DSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRAHYSFAKLAKPGSSDEAEERLVCDTCYKEY 529 (1374)
T ss_pred CcccCcCCcccccccccccccccccCCccccCccccCCcccCcccccCCCCCcccccccchhHHHHHHH
Confidence 6799999986 5679999999999998642 34433 1 221 2799999554
No 49
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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 N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=45.32 E-value=15 Score=29.68 Aligned_cols=34 Identities=21% Similarity=0.604 Sum_probs=22.9
Q ss_pred CCceeeecCC----cccccccccC-----CeEEEEeCC-cccch
Q 037148 13 APKFYCLCSP----KAICGHCICD-----AEFAIVKGN-KGLCS 46 (463)
Q Consensus 13 ~~~~~C~~C~----~s~C~~C~~~-----~~f~~vrgn-kGfC~ 46 (463)
...|.|+||. .++|..|+.. .+++.++.+ -|+|.
T Consensus 11 q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~~~~~CD 54 (71)
T PF02207_consen 11 QIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSSSGGCCD 54 (71)
T ss_dssp -EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--SCEBB-
T ss_pred CEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeCCCeEEe
Confidence 5678999997 5899999544 588888877 56653
No 50
>PRK05350 acyl carrier protein; Provisional
Probab=42.78 E-value=16 Score=29.90 Aligned_cols=58 Identities=12% Similarity=0.084 Sum_probs=48.7
Q ss_pred cCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccchHHHHhcccCCccc
Q 037148 181 LSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSIPKLLTIHLAENLE 241 (463)
Q Consensus 181 ~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei~klL~~Hl~~~~~ 241 (463)
|+|.+|...|.++|.+. +.-|. ..|..|..|..-+|-+++.+.+|--.|+.+|--.-|
T Consensus 2 m~~~~i~~~v~~ii~~~-~~~~~--~~i~~d~~l~~dlg~DSld~veli~~lE~~fgI~i~ 59 (82)
T PRK05350 2 MTREEILERLRAILVEL-FEIDP--EDITPEANLYEDLDLDSIDAVDLVVHLQKLTGKKIK 59 (82)
T ss_pred CCHHHHHHHHHHHHHHH-hCCCH--HHCCCCccchhhcCCCHHHHHHHHHHHHHHHCCccC
Confidence 78999999999999987 53222 469999999888999999999999999999965433
No 51
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=41.54 E-value=22 Score=28.35 Aligned_cols=37 Identities=24% Similarity=0.594 Sum_probs=27.3
Q ss_pred eecCCcccccccccCCeEEEEeCCcccch-hhhHHHHHHhcc
Q 037148 18 CLCSPKAICGHCICDAEFAIVKGNKGLCS-GCLELVLLIEEN 58 (463)
Q Consensus 18 C~~C~~s~C~~C~~~~~f~~vrgnkGfC~-~C~~~~~lIE~~ 58 (463)
|+.|-+.|.. +.+...-||.++||+ .|-.--|+++..
T Consensus 19 C~~C~k~L~~----~~DiymYrGd~aFCS~ECR~~qi~~de~ 56 (58)
T PF04570_consen 19 CYLCKKKLDP----GKDIYMYRGDKAFCSEECRSQQILMDEE 56 (58)
T ss_pred HHccCCCCCC----CCCeeeeccccccccHHHHHHHHHHHHh
Confidence 6666666654 456777899999997 588888877654
No 52
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=39.30 E-value=16 Score=26.97 Aligned_cols=26 Identities=23% Similarity=0.703 Sum_probs=20.6
Q ss_pred cccCCC--CCceeeecCC-cccccccccC
Q 037148 7 CYECGK--APKFYCLCSP-KAICGHCICD 32 (463)
Q Consensus 7 C~~C~k--~~~~~C~~C~-~s~C~~C~~~ 32 (463)
|..|.+ ...|.|..|| |-+|-.|++.
T Consensus 3 C~~C~~~~~~r~~C~~C~dfDLC~~C~~~ 31 (41)
T cd02337 3 CNECKHHVETRWHCTVCEDYDLCITCYNT 31 (41)
T ss_pred CCCCCCcCCCceECCCCcchhhHHHHhCC
Confidence 555554 3678899999 9999999875
No 53
>PF00518 E6: Early Protein (E6); InterPro: IPR001334 The papillomavirus E6 oncoproteins are small zinc-binding proteins that share a conserved zinc-binding CXXC motif and do not have identified intrinsic enzymatic activity. E6 proteins are thought to act as adapter proteins, thereby altering the function of E6-associated cellular proteins. This model for E6 function is best supported by observations of human papillomavirus type 16 (HPV-16) E6 (16E6), which can alter the metabolism of the p53 tumor suppressor through association with a cellular E3 ubiquitin ligase called E6AP. HPV-16 E6 interacts with an 18-amino-acid sequence in E6AP, and in an as yet ill-defined fashion the E6AP-16E6 complex binds to p53, inducing the ubiquitin-dependent degradation of the trimolecular complex. 16E6 apparently functions as an adapter protein in the complex with p53, since E6AP does not interact with p53 in the absence of E6 and since the degradation of p53 requires both E6 and E6AP. Despite the similarity in structure of the E6 oncoproteins, studies have indicated surprising biochemical diversity among E6 oncoproteins of different papillomavirus types. E6 from the cancer-associated human papillomaviruses (HPVs) complex with a cellular protein termed E6-AP and together with E6-AP bind to the p53 tumor suppressor protein thereby degrading p53 through ubiquitin-mediated proteolysis. E6 from the non-cancer-associated HPV types do not bind E6-AP or degrade p53. Bovine papilloma virus E6 (BE6) binds E6-AP but fails either to complex with p53 or to degrade associated proteins, implying that BE6 might transform cells through a mechanism different from that of the HPVs. In addition to targeting p53, E6 of both cancer-associated HPVs and BPV-1 have been shown to associate with a cellular-calcium-binding protein localized to the endoplasmic reticulum [, ].; GO: 0003677 DNA binding, 0042025 host cell nucleus; PDB: 2LJY_B 2LJX_A 2LJZ_A 2FK4_A 3PY7_A.
Probab=36.37 E-value=19 Score=31.79 Aligned_cols=32 Identities=28% Similarity=0.658 Sum_probs=23.0
Q ss_pred eeecCCccccc-----ccccCCeEEEEeCC-cccchhh
Q 037148 17 YCLCSPKAICG-----HCICDAEFAIVKGN-KGLCSGC 48 (463)
Q Consensus 17 ~C~~C~~s~C~-----~C~~~~~f~~vrgn-kGfC~~C 48 (463)
+|+.|..-|.. .+..+..|..|||. +|.|.+|
T Consensus 73 RC~~C~k~L~~~EK~~~~~~~~~f~~VRg~WRg~C~~C 110 (110)
T PF00518_consen 73 RCYYCLKPLTPSEKLDHIERGEPFHLVRGRWRGRCRNC 110 (110)
T ss_dssp EETTT--B--HHHHHHHHCCTSEEEEECCEEECHHHHH
T ss_pred EhHHcCCcCCHHHHHHHHHCCCCEEEECCeEEEECCCC
Confidence 58888777765 36667899999988 9999998
No 54
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PRK05828 acyl carrier protein; Validated
Probab=34.43 E-value=39 Score=28.38 Aligned_cols=58 Identities=12% Similarity=0.062 Sum_probs=47.1
Q ss_pred cCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccchHHHHhcccCCccc
Q 037148 181 LSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSIPKLLTIHLAENLE 241 (463)
Q Consensus 181 ~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei~klL~~Hl~~~~~ 241 (463)
|||.+|...|-+-|.+.++.= +-..|..|..|.. +|-+++.+.+|--.|+..|--.-|
T Consensus 1 m~~~eI~~~i~~ii~e~~~~~--~~d~i~~~~~~~d-Lg~DSLd~velv~~lE~~f~I~i~ 58 (84)
T PRK05828 1 MQEMEILLKIKEIAKKKNFAV--TLDESNINKPYRE-LKIDSLDMFSIIVSLESEFNIEFS 58 (84)
T ss_pred CCHHHHHHHHHHHHHHhccCC--CcccccCCCCHHh-cCCCHHHHHHHHHHHHHHHCCCcC
Confidence 789999999999998865532 2244678889977 999999999999999999975544
No 56
>PHA02779 E6 protein; Provisional
Probab=34.29 E-value=17 Score=33.98 Aligned_cols=37 Identities=27% Similarity=0.579 Sum_probs=28.7
Q ss_pred eeecCCccccc-----ccccCCeEEEEeCC-cccchhhhHHHH
Q 037148 17 YCLCSPKAICG-----HCICDAEFAIVKGN-KGLCSGCLELVL 53 (463)
Q Consensus 17 ~C~~C~~s~C~-----~C~~~~~f~~vrgn-kGfC~~C~~~~~ 53 (463)
+|+.|-.-|+. .|....-|..|||+ +|.|.+|.+..+
T Consensus 103 RC~~C~k~L~~~EK~~~~~~~~~F~~Vrg~WrG~C~~C~~~~~ 145 (150)
T PHA02779 103 RCYLCHKPLCPVEKVNHILKKARFIKLNCSWKGRCLHCWTKCM 145 (150)
T ss_pred EHhHcCCcCCHHHHHHHHHcCCCEEEECCeEEEEcccccChhh
Confidence 47888777775 35566779999988 999999987443
No 57
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=33.39 E-value=19 Score=36.40 Aligned_cols=29 Identities=14% Similarity=0.377 Sum_probs=23.6
Q ss_pred CccccccCCCCCceeeecCCcccccccccCC
Q 037148 3 DLHACYECGKAPKFYCLCSPKAICGHCICDA 33 (463)
Q Consensus 3 gwH~C~~C~k~~~~~C~~C~~s~C~~C~~~~ 33 (463)
.|++|..|+.-.-=++.-| |+|+.|+..=
T Consensus 112 ~~~~C~~C~~~rPpRs~HC--svC~~CV~rf 140 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRSSHC--SVCNNCVLRF 140 (299)
T ss_pred ceEEcCcCcccCCCCcccc--hhhccccccc
Confidence 5899999998777667766 6899999874
No 58
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=32.20 E-value=28 Score=25.87 Aligned_cols=29 Identities=21% Similarity=0.459 Sum_probs=22.9
Q ss_pred cccccCCCCC------ceeeecCCcccccccccCC
Q 037148 5 HACYECGKAP------KFYCLCSPKAICGHCICDA 33 (463)
Q Consensus 5 H~C~~C~k~~------~~~C~~C~~s~C~~C~~~~ 33 (463)
-.|..|++.- -|+|-.|.+.+.+.|+..+
T Consensus 12 ~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~ 46 (53)
T PF00130_consen 12 TYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKV 46 (53)
T ss_dssp EB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTS
T ss_pred CCCcccCcccCCCCCCeEEECCCCChHhhhhhhhc
Confidence 4688888765 8999999999999999875
No 59
>PRK13702 replication protein; Provisional
Probab=31.16 E-value=24 Score=30.33 Aligned_cols=39 Identities=15% Similarity=0.264 Sum_probs=33.6
Q ss_pred cccccccccCCCHHHHHHHHhcCCCCCcccCHHHHHHHHHH
Q 037148 152 KSSRKEFVGWGSRPLLEFLASIGKDTTRELSDDAITTIISG 192 (463)
Q Consensus 152 ~~k~~~~~gw~S~eLa~fL~~~G~~t~~~~sR~~Vv~~lW~ 192 (463)
+...++..-|++++|.+-|.-|+.. +.+||.+++..|.+
T Consensus 38 r~THkei~vfi~n~lK~~L~elc~~--~glTQAe~IE~LIe 76 (85)
T PRK13702 38 RATHKEIKVFIQNPLKDKLMELCEE--EGLTQAEMIERLIE 76 (85)
T ss_pred HHhhhhhheeecHHHHHHHHHHHHH--cCCcHHHHHHHHHH
Confidence 5567799999999999999988874 57999999998874
No 60
>CHL00124 acpP acyl carrier protein; Validated
Probab=30.82 E-value=32 Score=27.84 Aligned_cols=58 Identities=10% Similarity=0.157 Sum_probs=47.9
Q ss_pred cCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccchHHHHhcccCCccc
Q 037148 181 LSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSIPKLLTIHLAENLE 241 (463)
Q Consensus 181 ~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei~klL~~Hl~~~~~ 241 (463)
|+|.+|...|-++|.+.-=.+|. .|..|..|..-+|-+++.+.+|.-.|+..|--.-|
T Consensus 1 M~~~~i~~~l~~ii~~~~~~~~~---~i~~d~~l~~dlg~DSl~~~eli~~le~~f~i~i~ 58 (82)
T CHL00124 1 MTKNDIFEKVQSIVAEQLGIEKS---EVTLDANFTRDLGADSLDVVELVMAIEEKFDIEIP 58 (82)
T ss_pred CCHHHHHHHHHHHHHHHHCCCHH---HCCCCcchhhhcCCcHHHHHHHHHHHHHHHCCccC
Confidence 67889999999999887433343 49999999999999999999999999998875443
No 61
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=29.78 E-value=1.1e+02 Score=21.53 Aligned_cols=32 Identities=13% Similarity=-0.017 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHhcCCCCCcccCHHHHHHHHHHHh
Q 037148 161 WGSRPLLEFLASIGKDTTRELSDDAITTIISGYC 194 (463)
Q Consensus 161 w~S~eLa~fL~~~G~~t~~~~sR~~Vv~~lW~YI 194 (463)
|--++|.++|...|.. ...++.+++..|-+||
T Consensus 4 l~v~eLk~~l~~~gL~--~~G~K~~Li~Rl~~~l 35 (35)
T PF02037_consen 4 LTVAELKEELKERGLS--TSGKKAELIERLKEHL 35 (35)
T ss_dssp SHHHHHHHHHHHTTS---STSSHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHCCCC--CCCCHHHHHHHHHHhC
Confidence 3347899999999985 4688999999999986
No 62
>PRK12449 acyl carrier protein; Provisional
Probab=29.28 E-value=56 Score=26.29 Aligned_cols=58 Identities=9% Similarity=0.071 Sum_probs=46.7
Q ss_pred cCHHHHHHHHHHHhhhcCCCCCCCCCccccchhHhhhhCCCcccccchHHHHhcccCCccc
Q 037148 181 LSDDAITTIISGYCKENKLFHPERKRKIICDARLKALFGRKSVNKNSIPKLLTIHLAENLE 241 (463)
Q Consensus 181 ~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD~kL~~LFg~~rv~~~ei~klL~~Hl~~~~~ 241 (463)
|+|.+|...|-+.+.+.-=-+| ..|..|..|..-+|-+++.+.+|.-.|+..|--.-|
T Consensus 1 m~~~~i~~~l~~il~~~~~~~~---~~i~~~~~l~~dlg~DSl~~~~li~~lE~~f~i~i~ 58 (80)
T PRK12449 1 MTREEIFERLINLIQKQRSYLS---LAITEQTHLKDDLAVDSIELVEFIINVEDEFHIAIP 58 (80)
T ss_pred CCHHHHHHHHHHHHHHHhCCCc---cccCCCCcHHHHcCCcHHHHHHHHHHHHHHhCCCCC
Confidence 5788899999998886543333 259999999999999999999999999988865433
No 63
>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=27.92 E-value=33 Score=22.85 Aligned_cols=17 Identities=29% Similarity=0.550 Sum_probs=13.3
Q ss_pred cccC------CC-CCceeeecCCc
Q 037148 7 CYEC------GK-APKFYCLCSPK 23 (463)
Q Consensus 7 C~~C------~k-~~~~~C~~C~~ 23 (463)
|++| .+ +..|.|..|.+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 7788 44 88999988864
No 64
>PF05093 CIAPIN1: Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis; InterPro: IPR007785 Anamorsin, subsequently named CIAPIN1 for cytokine-induced anti-apoptosis inhibitor 1, in humans is the homologue of yeast Dre2, a conserved soluble eukaryotic Fe-S cluster protein, that functions in cytosolic Fe-S protein biogenesis. It is found in both the cytoplasm and in the mitochondrial intermembrane space (IMS) []. CIAPIN1 is found to be up-regulated in hepatocellular cancer, is considered to be a downstream effector of the receptor tyrosine kinase-Ras signalling pathway, and is essential in mouse definitive haematopoiesis []. In addition, it has also anti-apoptotic effects in the cell. It is involved in negative control of cell death upon cytokine withdrawal and promotes development of hematopoietic cells [].
Probab=27.52 E-value=32 Score=30.39 Aligned_cols=19 Identities=26% Similarity=0.571 Sum_probs=17.6
Q ss_pred cccccCCCCCceeeecCCc
Q 037148 5 HACYECGKAPKFYCLCSPK 23 (463)
Q Consensus 5 H~C~~C~k~~~~~C~~C~~ 23 (463)
-.|.+|--.--|+|-+|||
T Consensus 68 ssCGsC~LGDAFRCa~CPY 86 (100)
T PF05093_consen 68 SSCGSCYLGDAFRCAGCPY 86 (100)
T ss_pred CccccccccccceecCCCc
Confidence 4699999999999999998
No 65
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=24.64 E-value=1.3e+02 Score=20.82 Aligned_cols=32 Identities=13% Similarity=0.004 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHhcCCCCCcccCHHHHHHHHHHHh
Q 037148 161 WGSRPLLEFLASIGKDTTRELSDDAITTIISGYC 194 (463)
Q Consensus 161 w~S~eLa~fL~~~G~~t~~~~sR~~Vv~~lW~YI 194 (463)
+--.+|.++|...|.++ ..++.+++..|-+|+
T Consensus 4 l~~~~Lk~~l~~~gl~~--~G~K~~Lv~Rl~~~~ 35 (35)
T smart00513 4 LKVSELKDELKKRGLST--SGTKAELVDRLLEAL 35 (35)
T ss_pred CcHHHHHHHHHHcCCCC--CCCHHHHHHHHHHhC
Confidence 44578999999999864 678999999998884
No 66
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=24.42 E-value=36 Score=37.82 Aligned_cols=46 Identities=20% Similarity=0.434 Sum_probs=0.0
Q ss_pred ccccccC-----CCCCcee-eecCCcccccccccCCeEEEEe-CCcc------cchhhh
Q 037148 4 LHACYEC-----GKAPKFY-CLCSPKAICGHCICDAEFAIVK-GNKG------LCSGCL 49 (463)
Q Consensus 4 wH~C~~C-----~k~~~~~-C~~C~~s~C~~C~~~~~f~~vr-gnkG------fC~~C~ 49 (463)
|.||..| ..+..+. |-.|..+|..||.+-.+=+.+- |+-- ||+.|+
T Consensus 119 ~~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~ 177 (707)
T KOG0957|consen 119 AVICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACL 177 (707)
T ss_pred ceEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHh
No 67
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=23.83 E-value=35 Score=32.69 Aligned_cols=42 Identities=29% Similarity=0.581 Sum_probs=31.7
Q ss_pred ccccccCCCC--CceeeecCCcccccccccCCeEEEEeCCcccchhhh
Q 037148 4 LHACYECGKA--PKFYCLCSPKAICGHCICDAEFAIVKGNKGLCSGCL 49 (463)
Q Consensus 4 wH~C~~C~k~--~~~~C~~C~~s~C~~C~~~~~f~~vrgnkGfC~~C~ 49 (463)
.+.|+.|.++ .+.-|.-|...+|..|+.. |.-=..-||..|.
T Consensus 111 ~~aCs~C~r~~~~~~~C~~Cdr~lC~~C~~~----C~~C~~~~Cs~Cs 154 (175)
T PF05458_consen 111 SRACSVCQRTQRIKSVCSQCDRALCESCIRS----CSSCSEVFCSLCS 154 (175)
T ss_pred CccCcCCcCCCCCCccccccCcHHHHHHHhh----hhchhhhhhcCcc
Confidence 4679999876 6777999999999999887 3444455666665
No 68
>KOG0696 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=23.31 E-value=52 Score=36.27 Aligned_cols=49 Identities=20% Similarity=0.404 Sum_probs=36.0
Q ss_pred ccccCCC------CCceeeecCCcccccccccCCeEEEEeCCc---------------------ccchhhhHHHHH
Q 037148 6 ACYECGK------APKFYCLCSPKAICGHCICDAEFAIVKGNK---------------------GLCSGCLELVLL 54 (463)
Q Consensus 6 ~C~~C~k------~~~~~C~~C~~s~C~~C~~~~~f~~vrgnk---------------------GfC~~C~~~~~l 54 (463)
+||.|.. .-.|.|-.|.|-|.+.|-.=..|.|--..| -||.||-.|..-
T Consensus 58 fCsHCkDFiwGfgKQGfQCqvC~fvvHkrChefVtF~CPGadkg~dtDdpr~kHkf~~~tYssPTFCDhCGsLLyG 133 (683)
T KOG0696|consen 58 FCSHCKDFIWGFGKQGFQCQVCCFVVHKRCHEFVTFSCPGADKGPDTDDPRSKHKFKIHTYSSPTFCDHCGSLLYG 133 (683)
T ss_pred hhhhhhhheeccccCceeeeEEeehhhhhhcceEEEECCCCCCCCCCCCcccccceeeeecCCCchhhhHHHHHHH
Confidence 6888863 567999999999999997655555543333 589999876543
No 69
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=22.77 E-value=1.1e+02 Score=23.94 Aligned_cols=44 Identities=25% Similarity=0.508 Sum_probs=30.4
Q ss_pred CHHHHHHHHhcCCCCCcccCHHHHHHHHHHHhhhcCCCCCCCCCccccc-hhHhh
Q 037148 163 SRPLLEFLASIGKDTTRELSDDAITTIISGYCKENKLFHPERKRKIICD-ARLKA 216 (463)
Q Consensus 163 S~eLa~fL~~~G~~t~~~~sR~~Vv~~lW~YIK~nnLQDP~~Kr~I~CD-~kL~~ 216 (463)
-.+||+++ | +||..|...|-. .++.++-+-..+..++.| ++|+.
T Consensus 31 ~~~iA~~~---g------~sr~tv~r~l~~-l~~~g~I~~~~~~i~I~d~~~L~~ 75 (76)
T PF13545_consen 31 QEEIADML---G------VSRETVSRILKR-LKDEGIIEVKRGKIIILDPERLEE 75 (76)
T ss_dssp HHHHHHHH---T------SCHHHHHHHHHH-HHHTTSEEEETTEEEESSHHHHHH
T ss_pred HHHHHHHH---C------CCHHHHHHHHHH-HHHCCCEEEcCCEEEECCHHHHhc
Confidence 45899999 7 788886665555 455556667777888888 45543
No 70
>cd00238 ERp29c ERp29 and ERp38, C-terminal domain; composed of the protein disulfide isomerase (PDI)-like proteins ERp29 and ERp38. ERp29 (also called ERp28) is a ubiquitous endoplasmic reticulum (ER)-resident protein expressed in high levels in secretory cells. It contains a redox inactive TRX-like domain at the N-terminus. The expression profile of ERp29 suggests a role in secretory protein production, distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex and is essential in regulating the secretion of thyroglobulin. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase. ERp38 is a P5-like protein, first isolated from alfalfa (the cDNA clone was named G1), which contains two redox active TRX domains at the N-terminus, like human P5.
Probab=22.04 E-value=1e+02 Score=26.48 Aligned_cols=38 Identities=18% Similarity=0.248 Sum_probs=34.0
Q ss_pred cCCCCCHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHHH
Q 037148 385 SNDDFSEEECEDLRQRVKNGLASRPTVVELRQKAVCLH 422 (463)
Q Consensus 385 Sn~~FTE~E~~rlrq~~~~~~~k~pTv~~l~~Ka~~i~ 422 (463)
-+.+|-+.|..||...+..+.+..-+.++|..|...|.
T Consensus 54 kg~~yv~~E~~RL~~iL~~~~ls~~K~del~~R~NIL~ 91 (93)
T cd00238 54 KGEDYVEKELARLERLLEKKGLAPEKADELTRRLNILR 91 (93)
T ss_pred cchhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHh
Confidence 47899999999999999888889999999999988775
No 71
>PLN02436 cellulose synthase A
Probab=21.59 E-value=41 Score=40.42 Aligned_cols=73 Identities=23% Similarity=0.423 Sum_probs=48.0
Q ss_pred CccccccCCCCC-------cee-eecCCcccccccccCCeEEEEeCCcccchhhhHHHHHHhcccccCCCCccccCCCCC
Q 037148 3 DLHACYECGKAP-------KFY-CLCSPKAICGHCICDAEFAIVKGNKGLCSGCLELVLLIEENKDVDSHGCKIDFSDPE 74 (463)
Q Consensus 3 gwH~C~~C~k~~-------~~~-C~~C~~s~C~~C~~~~~f~~vrgnkGfC~~C~~~~~lIE~~~~~~~~~~~vDf~d~~ 74 (463)
+-++|-.|+... -|- |--|.|.||.-|. ||-.=-|| --|.+|-....-.-....+.-|.+..|+||-+
T Consensus 35 ~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cy---eyer~eg~-~~Cpqckt~Y~r~kgs~~~~~d~ee~~~dd~e 110 (1094)
T PLN02436 35 SGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCY---EYERREGN-QACPQCKTRYKRIKGSPRVEGDEEEDDIDDLE 110 (1094)
T ss_pred CCccccccccccCcCCCCCEEEeeccCCCccccchh---hhhhhcCC-ccCcccCCchhhccCCCCcCCccccccchhhh
Confidence 457999999875 344 9999999999998 33322233 45777766655433333332233467788887
Q ss_pred -cchHH
Q 037148 75 -NSYFY 79 (463)
Q Consensus 75 -e~lFk 79 (463)
||-|.
T Consensus 111 ~ef~~~ 116 (1094)
T PLN02436 111 NEFDYG 116 (1094)
T ss_pred hhhcCc
Confidence 77776
No 72
>PRK04023 DNA polymerase II large subunit; Validated
Probab=21.56 E-value=47 Score=39.76 Aligned_cols=68 Identities=15% Similarity=0.211 Sum_probs=39.0
Q ss_pred CccccccCCCCC-ceeeecCC-----cccccccccCCeEEEEeCCcccchhhhHHHHHHhcccccCCCCccccCCCCCcc
Q 037148 3 DLHACYECGKAP-KFYCLCSP-----KAICGHCICDAEFAIVKGNKGLCSGCLELVLLIEENKDVDSHGCKIDFSDPENS 76 (463)
Q Consensus 3 gwH~C~~C~k~~-~~~C~~C~-----~s~C~~C~~~~~f~~vrgnkGfC~~C~~~~~lIE~~~~~~~~~~~vDf~d~~e~ 76 (463)
|-.+|.+|+... .+.|..|. .-.|+.|-..+ +...|..|-.-+ .. .... ..
T Consensus 625 g~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~CG~~~-------~~y~CPKCG~El-------~~-~s~~--------~i 681 (1121)
T PRK04023 625 GRRKCPSCGKETFYRRCPFCGTHTEPVYRCPRCGIEV-------EEDECEKCGREP-------TP-YSKR--------KI 681 (1121)
T ss_pred cCccCCCCCCcCCcccCCCCCCCCCcceeCccccCcC-------CCCcCCCCCCCC-------Cc-cceE--------Ee
Confidence 456899999874 34477674 44677774332 224466663211 00 1112 34
Q ss_pred hHHHHHHHhhhccCCCh
Q 037148 77 YFYEYWQIIKDKERLTS 93 (463)
Q Consensus 77 lFk~Yw~~lK~k~~lt~ 93 (463)
-+++||..--+++++.-
T Consensus 682 ~l~~~~~~A~~~lg~~~ 698 (1121)
T PRK04023 682 DLKELYDRALENLGERK 698 (1121)
T ss_pred cHHHHHHHHHHHhCCcC
Confidence 46888888888777754
No 73
>PF11553 DUF3231: Protein of unknown function (DUF3231); InterPro: IPR021617 This bacterial family of proteins has no known function. ; PDB: 2RBD_B.
Probab=21.32 E-value=82 Score=29.05 Aligned_cols=75 Identities=17% Similarity=0.138 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHhhhccccccccccccCCC
Q 037148 387 DDFSEEECEDLRQRVKNGLASRPTVVELRQKAVCLHEDITKHWIARELDILRKCVDRANEKGWRRQYPSFSGHTKL 462 (463)
Q Consensus 387 ~~FTE~E~~rlrq~~~~~~~k~pTv~~l~~Ka~~i~~~i~~~w~e~E~~~L~~l~d~A~EkG~~~e~p~~~~k~~l 462 (463)
..||+..+-.+-..+...++..-+.+--.-=-.|| +..-..++.++++..+...+-..+|||-.+-|++-.+.+|
T Consensus 92 ~lfsD~~~l~~~~~~~~~~~~~~~~al~~s~R~Dl-~~~f~~~~~~~~~~~~~~~~l~~~KGwl~~pP~~~~~~~l 166 (166)
T PF11553_consen 92 PLFSDKFMLFYISFMSQAGITNYGRALSSSVRNDL-RAFFMKFLMEALELYDKIVKLMKEKGWLERPPYIPDPKKL 166 (166)
T ss_dssp -G--HHHHHHHHHHHHHHHHHHHHHHHHH--SHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT------B-------
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCCcCCCCCCCCCCCC
Confidence 35999999888887776555444433333222333 3344557788899999999999999999999988776654
No 74
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=21.10 E-value=53 Score=20.11 Aligned_cols=12 Identities=25% Similarity=0.958 Sum_probs=10.4
Q ss_pred ccccCCCCCcee
Q 037148 6 ACYECGKAPKFY 17 (463)
Q Consensus 6 ~C~~C~k~~~~~ 17 (463)
.|++|++..|+.
T Consensus 2 ~C~~C~~~GH~~ 13 (18)
T PF00098_consen 2 KCFNCGEPGHIA 13 (18)
T ss_dssp BCTTTSCSSSCG
T ss_pred cCcCCCCcCccc
Confidence 599999999875
No 75
>cd08305 Pyrin Pyrin: a protein-protein interaction domain. The Pyrin domain (or PYD), also called DAPIN or PAAD, is a subfamily of the Death Domain (DD) superfamily and it functions in several signaling pathways. The Pyrin domain is found at the N-terminus of a variety of proteins and serves as a linker that recruits other domains into signaling complexes. Pyrin-containing proteins include NALPs, ASC (Apoptosis-associated speck-like protein containing a CARD), and the interferon-inducible p200 (IFI-200) family of proteins which includes the human IFI-16, myeloid cell nuclear differentiation antigen (MNDA) and absent in melanoma (AIM) 2. NALPs are members of the NBS-LRR family of proteins possessing a tripartite domain structure including a C-terminal LRR (leucine-rich repeats), a central nucleotide-binding site (NBS) domain or NACHT (for neuronal apoptosis inhibitor protein, CIITA, HET-E and TP1), and an N-terminal protein-protein interaction domain, which is a Pyrin domain in the case
Probab=21.09 E-value=1.4e+02 Score=24.52 Aligned_cols=46 Identities=13% Similarity=0.208 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHhccchHHH
Q 037148 387 DDFSEEECEDLRQRVKNGLASRPTVVELRQKAVCLHEDITKHWIARE 433 (463)
Q Consensus 387 ~~FTE~E~~rlrq~~~~~~~k~pTv~~l~~Ka~~i~~~i~~~w~e~E 433 (463)
++.+++||++.+.....+ .+.|+-..++.-..+|-..+..++.++-
T Consensus 6 e~L~~~efk~FK~~L~~~-~~~~~~~~~~~a~~~la~lL~~~y~~~~ 51 (73)
T cd08305 6 ENITDEELKRFKSLLAND-LFLETKAQLEYTRIQIADLMEQKFGAVS 51 (73)
T ss_pred HHcCHHHHHHHHHHHHhc-CCCCCcccccccHHHHHHHHHHHcChhH
Confidence 357899999999999987 5666666666667888899999988875
No 76
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=20.46 E-value=41 Score=27.74 Aligned_cols=18 Identities=22% Similarity=0.521 Sum_probs=10.9
Q ss_pred cccchhhhHHHHHHhccc
Q 037148 42 KGLCSGCLELVLLIEENK 59 (463)
Q Consensus 42 kGfC~~C~~~~~lIE~~~ 59 (463)
-|||.+|+.--..-+-.+
T Consensus 10 AgFCRNCLskWy~~aA~~ 27 (68)
T PF06844_consen 10 AGFCRNCLSKWYREAAEE 27 (68)
T ss_dssp HS--HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHh
Confidence 499999998766554433
Done!