Query 000460
Match_columns 1482
No_of_seqs 316 out of 560
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 09:32:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000460.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000460hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1140 N-end rule pathway, re 100.0 4.3E-87 9.3E-92 858.1 43.0 785 280-1330 369-1211(1738)
2 KOG1140 N-end rule pathway, re 99.9 4.2E-23 9E-28 269.0 1.6 936 18-1000 532-1502(1738)
3 smart00396 ZnF_UBR1 Putative z 99.8 4.4E-20 9.6E-25 169.8 5.8 70 116-185 1-71 (71)
4 PF02207 zf-UBR: Putative zinc 99.7 5.6E-19 1.2E-23 162.9 4.0 70 116-185 1-71 (71)
5 KOG1139 Predicted ubiquitin-pr 98.8 3.1E-08 6.7E-13 121.7 15.1 185 754-938 207-477 (784)
6 PF10390 ELL: RNA polymerase I 97.2 0.00018 4E-09 83.8 3.0 80 869-953 198-280 (284)
7 KOG1777 Putative Zn-finger pro 95.9 0.0032 6.8E-08 74.7 1.3 63 111-174 539-606 (625)
8 KOG0943 Predicted ubiquitin-pr 91.9 0.054 1.2E-06 70.2 0.5 64 115-184 1240-1309(3015)
9 KOG1139 Predicted ubiquitin-pr 91.5 0.13 2.8E-06 65.2 3.1 67 1343-1422 144-210 (784)
10 PF13764 E3_UbLigase_R4: E3 ub 90.2 1.6 3.4E-05 58.0 11.3 74 1145-1229 421-497 (802)
11 cd02335 ZZ_ADA2 Zinc finger, Z 86.9 0.51 1.1E-05 41.0 2.6 39 117-159 5-48 (49)
12 cd02340 ZZ_NBR1_like Zinc fing 86.7 0.59 1.3E-05 39.6 2.7 37 117-158 5-41 (43)
13 cd02249 ZZ Zinc finger, ZZ typ 85.5 0.64 1.4E-05 39.8 2.5 37 117-158 5-44 (46)
14 KOG4796 RNA polymerase II elon 85.4 0.96 2.1E-05 56.0 4.7 78 869-952 211-291 (604)
15 cd02338 ZZ_PCMF_like Zinc fing 83.3 0.97 2.1E-05 39.4 2.6 38 117-159 5-48 (49)
16 KOG2752 Uncharacterized conser 81.7 1.7 3.7E-05 50.8 4.6 61 112-173 37-101 (345)
17 cd02344 ZZ_HERC2 Zinc finger, 81.6 1.2 2.6E-05 38.2 2.5 39 117-159 5-44 (45)
18 PF00643 zf-B_box: B-box zinc 79.0 1.1 2.4E-05 37.2 1.5 37 116-158 4-40 (42)
19 KOG2905 Transcription initiati 75.0 2.1 4.5E-05 48.6 2.6 61 870-931 183-245 (254)
20 cd00162 RING RING-finger (Real 73.7 2.3 5E-05 34.5 2.0 23 1390-1412 11-33 (45)
21 cd02339 ZZ_Mind_bomb Zinc fing 72.7 2.4 5.3E-05 36.4 1.9 30 126-158 13-43 (45)
22 cd02341 ZZ_ZZZ3 Zinc finger, Z 64.2 4.7 0.0001 35.1 2.0 32 126-158 13-46 (48)
23 PF13639 zf-RING_2: Ring finge 62.0 4.7 0.0001 33.8 1.6 24 1389-1412 13-36 (44)
24 cd00021 BBOX B-Box-type zinc f 60.9 6.5 0.00014 31.7 2.2 28 126-158 10-37 (39)
25 cd02343 ZZ_EF Zinc finger, ZZ 60.5 4.9 0.00011 35.1 1.4 35 117-156 5-40 (48)
26 cd02336 ZZ_RSC8 Zinc finger, Z 59.5 3.2 6.9E-05 35.7 0.1 31 117-152 5-35 (45)
27 cd02337 ZZ_CBP Zinc finger, ZZ 57.5 5.8 0.00013 33.4 1.4 32 116-153 4-35 (41)
28 smart00184 RING Ring finger. E 55.6 8.6 0.00019 29.9 2.0 21 1391-1411 10-30 (39)
29 smart00336 BBOX B-Box-type zin 55.6 9.7 0.00021 31.2 2.4 29 125-158 12-40 (42)
30 PF02270 TFIIF_beta: Transcrip 51.6 7.9 0.00017 45.5 1.7 31 899-930 244-274 (275)
31 smart00291 ZnF_ZZ Zinc-binding 49.5 12 0.00026 31.8 2.0 33 116-153 8-40 (44)
32 PF13923 zf-C3HC4_2: Zinc fing 41.3 12 0.00026 30.7 0.7 22 1391-1412 11-32 (39)
33 PF00569 ZZ: Zinc finger, ZZ t 40.8 7.7 0.00017 33.3 -0.5 36 117-156 9-45 (46)
34 PF10367 Vps39_2: Vacuolar sor 40.5 8.5 0.00019 38.0 -0.3 17 1392-1408 93-109 (109)
35 cd02345 ZZ_dah Zinc finger, ZZ 39.2 21 0.00045 31.2 2.0 31 116-151 4-35 (49)
36 cd02334 ZZ_dystrophin Zinc fin 38.8 20 0.00043 31.5 1.8 33 117-153 5-37 (49)
37 KOG0457 Histone acetyltransfer 36.1 29 0.00062 42.9 3.1 36 125-163 26-66 (438)
38 PF00097 zf-C3HC4: Zinc finger 35.7 22 0.00047 29.1 1.5 22 1391-1412 11-32 (41)
39 PF14634 zf-RING_5: zinc-RING 32.0 32 0.0007 29.0 2.0 23 1388-1410 11-33 (44)
40 PHA02450 hypothetical protein 28.1 36 0.00077 29.3 1.5 25 163-187 13-44 (53)
41 PF12678 zf-rbx1: RING-H2 zinc 26.7 27 0.00058 33.0 0.6 21 1391-1411 44-64 (73)
42 PF12043 DUF3527: Domain of un 24.4 34 0.00073 41.5 1.0 18 162-184 258-275 (346)
43 KOG4445 Uncharacterized conser 22.8 62 0.0013 38.3 2.7 34 1385-1418 124-157 (368)
44 smart00744 RINGv The RING-vari 22.3 91 0.002 27.3 3.0 22 1391-1412 13-39 (49)
No 1
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=4.3e-87 Score=858.12 Aligned_cols=785 Identities=22% Similarity=0.310 Sum_probs=554.1
Q ss_pred HhcccCCCHHHHHHHHHHHH-HhhCChhHHHHHHHHHHhhhHHHHHHHHHhccccccccCCcccceeeecccCCCchHHH
Q 000460 280 VRAEMFSSDVVVRKLHELLL-KLLGEPIFKYEFAKVFLSYYPVFVKDAIREHSDDTIKKYPLLSTFSVQIFTVPTLTPRL 358 (1482)
Q Consensus 280 l~~~~~l~K~~r~~Lh~L~l-sLL~d~efK~~FA~~Fv~~Y~~i~~~fl~dd~d~~~~~~s~v~sLSVQLFTVPSLA~~L 358 (1482)
+..+..+||..|..++.++. .+-++.+||+.||.+|+.+|..+..+|+..|++. ..+.| .++||+||+|++|..+
T Consensus 369 l~~d~~~~kr~r~~l~k~~~~~~~~~~~~k~~~~~~~~~~y~~~~~~~~~~d~e~---~~~vi-~~~vqf~t~~~~a~~~ 444 (1738)
T KOG1140|consen 369 LLFDNRYWKRLRKDLQKVIIPTFASSNLYKPIFAQQFVEHYNSITRDFAYMDREP---DLSVI-ELSVQFFTCPSLAKNI 444 (1738)
T ss_pred HHHHHHHHHHHHHHHhhcceeehhcchHHHHHHHHHHHHHHHHHHHHHHhhcCCc---chhhH-hheeeeecCcHHHHHh
Confidence 33444567889999999999 6778999999999999999999999999998874 33545 9999999999999999
Q ss_pred HHhhcHHHHHHHHHHHHhhhhcCCCCccee---c-------ccccccchhhhHHhhhhhhhcchhHhHHHhhhchhHHHH
Q 000460 359 VKEMNLLEMLLGCLREIFDSCAGDDSCLQV---A-------KWANLYETTNRVIGDIRFVMSHAAVSKYATHEQLNISKA 428 (1482)
Q Consensus 359 V~E~nLL~iLl~tl~~~~~~~~~~~~~l~~---~-------~~~~~~~~~~~I~~DLrYvLsh~~Va~~l~~~~~~l~~~ 428 (1482)
+....++..+..++..++..+. .++...+ - +.....+|.+..+.|+ +.+.+|. +..++..+..
T Consensus 445 ~~~~~~~~l~~~~~~~~~~~~~-~~~~~~~~~~~~~s~~~~~~~~~~~r~l~~~~~l-~~~~~~~-----~~~~~~~~~~ 517 (1738)
T KOG1140|consen 445 VENQSFLDIVWSIIDIFKEFNK-VEGGVLIDIRVQKSNLLKRYSISFRRTLYTFEDL-SKVHDPN-----IPLRPKEFIS 517 (1738)
T ss_pred hhhccchHHHHHHHHHHHHhcc-cccceecceeeeechhhhHHHHHHHHHHHHHHHh-hccCCcc-----ccccHHHHHH
Confidence 9999877776666655543333 3332211 1 1122357777788888 7777766 2358899999
Q ss_pred HHHHHHHhcCCCcccccccCceeeeCCceehhhhhhhhHHhhhhhhhhcccccccccccccccccccccCCCCCcccccc
Q 000460 429 WMKLLTFVQGMNPQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEETRYDFSMYKQDIGDGDSLRHAK 508 (1482)
Q Consensus 429 ~l~lL~~mQGMnp~kRq~~~HVEyE~e~w~~AF~Le~~la~i~~l~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 508 (1482)
++.++..||||.|++|+.++||++|++ |+.+|.+-.++..++++++.||.....
T Consensus 518 ~l~~~~v~qg~~~lkr~~~ehv~~e~~-~~~~~~~v~~~t~~~s~i~~~~~~~ep------------------------- 571 (1738)
T KOG1140|consen 518 LLLLLKVFQGVDPLKREELEHVEVEKE-WENFFSLVEYLTAIYSMIQSLVKTSEP------------------------- 571 (1738)
T ss_pred HHHHHHHhCCccHHHHHHhhhhcccch-HHHHHHHHHHHHHHHHHHHHHHHhccc-------------------------
Confidence 999999999999999999999999997 999999999999999999888766531
Q ss_pred ccccccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhhhcCCCCcccccccCCCCcccccC
Q 000460 509 VGRLSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENWLGVDDRSVSVNDILSPNASRISG 588 (1482)
Q Consensus 509 v~r~~~e~s~~~~~~~~~~~~~~~v~e~~~~~~~~~~~l~~~l~~l~~~cl~~l~~~l~~~~~~~~~~~~~~~~~~~~~~ 588 (1482)
+. ..++..|..++..... . + .+
T Consensus 572 ------------------------~~-----------------~~~~~~l~~~~~r~~~-----s-----~-------~~ 593 (1738)
T KOG1140|consen 572 ------------------------VK-----------------DSVYKKLLEAAIRIHP-----S-----L-------TG 593 (1738)
T ss_pred ------------------------hh-----------------hhHHHHHHHHHhhccc-----c-----c-------Cc
Confidence 00 0112223333322110 0 0 00
Q ss_pred cchhhhHhhhhhhcccccccccccCCccccccccccCCCccccccCccccccccCccccccccccCCCCccccccccccc
Q 000460 589 SNFVALKKTLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKITISGERDTASWRSAGFNDSEMEGECATEL 668 (1482)
Q Consensus 589 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 668 (1482)
... +..+ .| ++
T Consensus 594 ~~~--l~~~------------------------------------------------i~--------------~~----- 604 (1738)
T KOG1140|consen 594 SES--LTYT------------------------------------------------IC--------------GE----- 604 (1738)
T ss_pred cce--eeeh------------------------------------------------hh--------------hh-----
Confidence 000 0000 11 11
Q ss_pred ccccccccCccCceeeeccCCcceeechHHHHHHHHHHHHHhhhhcccccccccccCCCCCccccchhhhhhccCCCCCC
Q 000460 669 DNLHVLSLCYWPDITYDVSSQDVSVHIPLHRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPY 748 (1482)
Q Consensus 669 ~~~~~~~~~~~~~i~fdVs~~~VSfH~PLhr~Ls~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~ 748 (1482)
...++.|+|+.++||||+|+.|+|+.+++..... ++...+.+ ..+.+++.
T Consensus 605 ---------S~e~i~f~v~~~~~sv~~p~~~~l~~l~~~~~s~-------------------v~~~~d~~-~~~~~~~n- 654 (1738)
T KOG1140|consen 605 ---------SHETINFSVSQERVSVSNPVSRLLAFLIELSCSS-------------------VVSLKDAY-ERLEDCSN- 654 (1738)
T ss_pred ---------hHhHhhhccccccceeeccHHHHhhhhhhcccch-------------------hhhcchhh-hhHhhhcc-
Confidence 1146899999999999999999999998532110 00111111 11122221
Q ss_pred ccchhhhcccHHHHHHHHHHHhCccccccHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhcccc
Q 000460 749 GFSAFVMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSN 828 (1482)
Q Consensus 749 ~~~~~l~e~PLR~~Vl~AQI~AGmWVRNG~sl~~Q~~~Y~~~~~re~~~d~DlfLLQ~~asl~dp~~fl~~il~RF~L~~ 828 (1482)
...|.|||||++|++|||.+|||||||.++.+|+.+|++.+||+++|++||+++|.++++.||++|+.++++||+|.+
T Consensus 655 --~~~i~e~~lr~~Vl~aqid~~~w~rNG~si~~q~~~y~~~~~r~~~y~~DI~~~Q~~la~~d~~~~l~~~l~r~~L~~ 732 (1738)
T KOG1140|consen 655 --FLAISEHSLRVLVLCAQIDVGFWVRNGFSILHQAAYYKNNPCRNESYDRDILMLQTGLAMEDPNRFLFTILSRFELLD 732 (1738)
T ss_pred --chhhcccchhheeeeeecceeeEeecCcchhhhhHhhcCccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Confidence 256899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCCc-h---hHHHHHHHHHHHHHhhcccccCC---ChHHHHHHHHHHHHhcCCCChHHHHHhCCCCCCCcch
Q 000460 829 YLSLNLERPSEY-E---PILVQEMLTLIIQILQERRFCGL---TTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQ 901 (1482)
Q Consensus 829 w~~~~~~~~~~y-~---~~lvEE~L~lLI~LltER~~~g~---t~~e~lrrEIIh~Lc~~p~t~SeL~~~lpe~~~~~~~ 901 (1482)
|++|.......+ + ..|+|+|+.+||.|++||...|+ +..+.+|+||||+||++|++||+|++.+|++++++..
T Consensus 733 w~~g~~~~~~~d~~~~i~~~~ee~l~lii~ll~Er~~~~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~ 812 (1738)
T KOG1140|consen 733 WFTGEVDYQSNDTEDTISFMIEEFLALIILLLTERSYFGSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLS 812 (1738)
T ss_pred HhcCCCccccccHHHHHHHHHHHHHHHHHHHHHheeecccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhccc
Confidence 999986443322 2 37999999999999999997554 5778999999999999999999999999999999999
Q ss_pred HHHHHHHHhcccCCCCC-CcceeEehhhhhccccccccccCchhHHHHHHHHHH--hhcccccccCCCCCccCCCc----
Q 000460 902 LQEILDAVAMYSHPSGF-NQGMYSLRWSYWKELDIYHPRWSSRDLQVAEERYLR--FCSVSALTAQLPRWTKIYYP---- 974 (1482)
Q Consensus 902 fe~iL~eVA~fk~P~g~-~~G~Y~LK~e~~~e~DPy~~~y~~~d~q~Aeer~~r--~~k~~~~~~~~P~~~~~~~p---- 974 (1482)
||.++++||+|++|.++ +.|+|+||++||+++||||+||+++++.+++...++ ..+.......+|+..|.+-+
T Consensus 813 ~d~~~e~Va~~~~p~~~~~~gvf~lK~~~~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~ 892 (1738)
T KOG1140|consen 813 FDEALEEVAVFKKPKGLADNGVFVLKESYYDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKK 892 (1738)
T ss_pred chHHHHHHHhhccCCccccceEEEechhhhhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHH
Confidence 99999999999999999 789999999999999999999999999888765543 22211111222322233222
Q ss_pred -cchhhhccccHHHHHHHHHHHHHHhhcCCCCCCCCchhHHHHHHHH-HHHHHhhhhhhcccCCCCCCCCCCCcccchhh
Q 000460 975 -LESIAGIATCKVVLQVIRAVLFYAVFTDNPTDSRAPYGVLLTALHL-LALALDVCFQKKKSGDQSCDIGGSTPILDFAS 1052 (1482)
Q Consensus 975 -f~~i~~il~s~~~~~ii~~vL~~al~~~~~s~s~~~E~lL~~aLHL-l~laL~~~~~e~~~~~~s~~~~~~~p~~~~~~ 1052 (1482)
+.++.+.....+|-.||+.++.++.+. .++.++..++|+ ++.|++++..-- .+++..
T Consensus 893 ~~~~L~~~t~~~~~~~ii~r~~~~~~~~-------~s~~~l~~~~~~ihG~~~~~~l~~~--------------~~~~~~ 951 (1738)
T KOG1140|consen 893 GADILGAAVRLTVFGLIIYRTLEHCLFM-------ESSTLLSKVLHLIHGIALNEELINM--------------KFAFTQ 951 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHhc--------------cccccc
Confidence 244555555666677777777777654 347899999955 499998653211 011100
Q ss_pred HHHHhhccCCCCcccHHHHHHHHHhhhhccCCccccccccCcchhHHHHHHHHHHHhhHHHHHHHhhhchhhhccccCCC
Q 000460 1053 EEIAEGLNNGAGKQSLLSLLVFLMGMYKKDGADNFLEAGNCNLSSVIESLLKKFAEIDSRCMTKLQQLAPEIVSHLSQSL 1132 (1482)
Q Consensus 1053 ~~~~~~~~~~~~~~SllsLL~~L~~~~~~~~~d~~~e~~~~~i~~iI~~LL~kf~~v~~~c~~~l~~~~p~~~~~l~e~~ 1132 (1482)
. .. .....+.+.+++.+..++....+ +.++.++++.|..+.. .+...|++. +....
T Consensus 952 ~-----~e-~~~~e~gl~~~e~lv~~~~~~~~-----------~~~~~v~~~l~~~~~~-----~~~n~~ea~-~~~~~- 1007 (1738)
T KOG1140|consen 952 K-----TE-SIAREKGLSLYESLVRKPDSLVH-----------GKIIEVIVELFESLIK-----SRANDPEVA-NDEKD- 1007 (1738)
T ss_pred c-----cc-ccccccchhhHHHhhhcchhhcC-----------CcceeeeHHHHhhhhh-----hhcCCcccc-ccccc-
Confidence 0 00 12344567778888877654432 4678888888866543 333444332 11100
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCccCCCCcccc--------------c
Q 000460 1133 PRDDTSGSFSASDSEKRKAKARERQAAILEKMKAEQFKFLSSISSNIEDAPKSAPEVTNYDAEHV--------------S 1198 (1482)
Q Consensus 1133 ~~~~~~~~~~~sE~EkKKk~AkeRQaKIMAQmkaQQksFL~nn~~~~de~d~~~~e~~~~d~~~~--------------~ 1198 (1482)
.....+.+..+.+.+|||++|++||+|+||||+.||.+||++|.++.|+++...++......... .
T Consensus 1008 ~~~~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e~d~~~~~~~~~~~~~~~~~d~~~~~~~~~s~~~~ 1087 (1738)
T KOG1140|consen 1008 KKEKQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDEFDEQENQTPSSGSKTYEEEDFTCALCQDNSCTDF 1087 (1738)
T ss_pred cccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccccCcccccCccccccchhhhhccchhhhccchhcc
Confidence 01122344555667899999999999999999999999999997665554332111110000000 0
Q ss_pred ccc--------cCCceeecCCCCC-----CCCEEEEEEeecccccccccCCCCCccccccCCcccccccccccccCCCCC
Q 000460 1199 EES--------VQDVCALCHDPNS-----RTPVSYLILLQKSRLLSFVDRGSPSWDQDQWLGKECGTISANNMVNQFGTN 1265 (1482)
Q Consensus 1199 ~e~--------~~~tCILCqE~~s-----~~pfG~lalVQ~SsvL~~~~~~~ps~~~~~~~~~~~~~~~~~~~~~~~~~~ 1265 (1482)
.+. ...+|++|++..+ .++....+|+|+|+..+ .+.-..+ ..+.|+.
T Consensus 1088 ~~~~~~~~~~~~~~~~~i~~e~e~~~~~~~~~~v~~~f~~~s~~~s----------d~l~~p~----------~~~~~~~ 1147 (1738)
T KOG1140|consen 1088 QVKPASHLVKPIFRECIICDENEDVPNWDGRYSVSSAFAQKSDDVS----------DALTEPG----------SLSCGTV 1147 (1738)
T ss_pred ccccchhhhcccccccccCChhccCCCccccchhhhHhhhhccccc----------ccccCCC----------CCcccce
Confidence 000 0467888887532 46777778888887776 1111111 2378899
Q ss_pred CCCCCCCccchhHHHHHHHHHHHhh-hhcCCCcchhhHHHHhhccCCcccccCCC---CCCCccccchh
Q 000460 1266 TPSSGLGVISSCQLAQVAEEAVNQF-AYNGKPEEVNSVLEFVKAQFPSEMRKNMT---YPDLMKEDEEC 1330 (1482)
Q Consensus 1266 ~~~~~~~~~~~~~~~~~~~~a~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~ 1330 (1482)
.++|+| .||.+||+.+-+|.+-. ..+..+..-..- .++.+||++|++.+ .|.....++..
T Consensus 1148 ~s~c~h--~mh~~c~~~~~~a~r~~~n~~~~~l~~~~s---e~~l~lCp~c~slsn~~lp~~~~~~~~~ 1211 (1738)
T KOG1140|consen 1148 LSSCGH--HMHYGCFKRYVQAKRFRENARTAPLCQHYS---ENGLFLCPLCKSLSNVSLPMFLPPELLL 1211 (1738)
T ss_pred eeccCC--cchHHHHHHHHHHHHHHHHhhhcCcccccc---cCCcccCCchHhhhhccCCcCCchhhhc
Confidence 999998 69999999999999554 333333443333 78889999999988 34355555554
No 2
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.86 E-value=4.2e-23 Score=269.00 Aligned_cols=936 Identities=16% Similarity=0.036 Sum_probs=578.6
Q ss_pred HHHHHHhcCCchhhhchhhHHHHhhhCCCCchHHHhccCCCCHHHHHHHHHHHhhcccCCCCCCh-h-hhHHHHHHHHHH
Q 000460 18 IVRRLMNIGVPEEFLDYSGIVNFAKNDKSRIPELVSTILPPDEEVAEVIQDAKAKNKKVSVGPNM-K-GRFRESMLWLQW 95 (1482)
Q Consensus 18 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~l~~l~~ 95 (1482)
..+++--.++++++-...+++.|+...+..|...+.+..|..+.+...+..+..+..++-+..++ + ..|.+....+.|
T Consensus 532 kr~~~ehv~~e~~~~~~~~~v~~~t~~~s~i~~~~~~~ep~~~~~~~~l~~~~~r~~~s~~~~~~l~~~i~~~S~e~i~f 611 (1738)
T KOG1140|consen 532 KREELEHVEVEKEWENFFSLVEYLTAIYSMIQSLVKTSEPVKDSVYKKLLEAAIRIHPSLTGSESLTYTICGESHETINF 611 (1738)
T ss_pred HHHHhhhhcccchHHHHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHhhcccccCccceeeehhhhhhHhHhhh
Confidence 34667778888888777899999999999999999999999999998888877777776555445 3 458888888888
Q ss_pred HhcCCCHHHHHHHHHc--cCCCCcccccccCCCeeEEeccCCCCCCccccccccCCCCCCCceeEEEeCCCccccCCCcc
Q 000460 96 LMFEREPEKVLRKLSK--IGQRGVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDVT 173 (1482)
Q Consensus 96 ~~~~~dp~~~l~~l~~--~~~~~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~~~~~~gG~CDCGD~~ 173 (1482)
.++.+.+.-...-... -.-..+|+.+|......++|++|.- .+.+|..|++...|-.|.+.-+-..+|+|+|+ ..
T Consensus 612 ~v~~~~~sv~~p~~~~l~~l~~~~~s~v~~~~d~~~~~~~~~n--~~~i~e~~lr~~Vl~aqid~~~w~rNG~si~~-q~ 688 (1738)
T KOG1140|consen 612 SVSQERVSVSNPVSRLLAFLIELSCSSVVSLKDAYERLEDCSN--FLAISEHSLRVLVLCAQIDVGFWVRNGFSILH-QA 688 (1738)
T ss_pred ccccccceeeccHHHHhhhhhhcccchhhhcchhhhhHhhhcc--chhhcccchhheeeeeecceeeEeecCcchhh-hh
Confidence 8887654422221111 1225889999999999999999986 99999999999999999988877889999999 99
Q ss_pred cccccCCCCCCCCCCCCCCCcHHHHHhHHHHHHHHHHHHHHHhhhhhccCCCCCCCCChHHHHHHHHHHHHHHHHHHHHH
Q 000460 174 AWKREGFCSRHKGAEQIQPLPEKYANSAAPVLDALFIYWENKLSLAESVGQENPRASDHVAERRKLANELTFAVVEMLLE 253 (1482)
Q Consensus 174 awk~~~fC~~H~~~~~~~~lp~~l~~~~~~~~~~ll~~~~~~l~~~e~~~~~~~~~~d~~~~~~k~a~~l~~~i~~~Lle 253 (1482)
+|...++|..|....++-++-..++.. +..+.++.+|-............+....|...+..++.+++...|+.++.|
T Consensus 689 ~~y~~~~~r~~~y~~DI~~~Q~~la~~--d~~~~l~~~l~r~~L~~w~~g~~~~~~~d~~~~i~~~~ee~l~lii~ll~E 766 (1738)
T KOG1140|consen 689 AYYKNNPCRNESYDRDILMLQTGLAME--DPNRFLFTILSRFELLDWFTGEVDYQSNDTEDTISFMIEEFLALIILLLTE 766 (1738)
T ss_pred HhhcCccccccchhHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHhcCCCccccccHHHHHHHHHHHHHHHHHHHHHh
Confidence 999999999998765443333333222 333344333322111111111123344566667777888888778887777
Q ss_pred HHhchHHHHHHHHHHhhcccchHHHHHhcccCCCHHHHHHHHHHHHHhhCChhHHHHHHHHHHhhhHHHHHHHHHhcccc
Q 000460 254 FCKNSESLLSFVSKRVISVIGLLDILVRAEMFSSDVVVRKLHELLLKLLGEPIFKYEFAKVFLSYYPVFVKDAIREHSDD 333 (1482)
Q Consensus 254 ~~~~~~~lls~l~~~i~~~~~ll~~Ll~~~~~l~K~~r~~Lh~L~lsLL~d~efK~~FA~~Fv~~Y~~i~~~fl~dd~d~ 333 (1482)
+... .+..+........+++.+|........+.+++..|.+...+..|..++..++..+...|+...-..++..-++
T Consensus 767 r~~~---~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~~d~~~e~Va~~~~p~~~~~~gvf~lK~~~~~ 843 (1738)
T KOG1140|consen 767 RSYF---GSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLSFDEALEEVAVFKKPKGLADNGVFVLKESYYD 843 (1738)
T ss_pred eeec---ccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhcccchHHHHHHHhhccCCccccceEEEechhhhh
Confidence 6544 1122222222234566666666666667788899999988999999999999888888855433333333333
Q ss_pred ccccCCcccceeeecccCCCchHHHHHhhcHHHHHHHHHHHHhhhhc--CCCCcceecccccccchhhhHHhhhhhhhcc
Q 000460 334 TIKKYPLLSTFSVQIFTVPTLTPRLVKEMNLLEMLLGCLREIFDSCA--GDDSCLQVAKWANLYETTNRVIGDIRFVMSH 411 (1482)
Q Consensus 334 ~~~~~s~v~sLSVQLFTVPSLA~~LV~E~nLL~iLl~tl~~~~~~~~--~~~~~l~~~~~~~~~~~~~~I~~DLrYvLsh 411 (1482)
....|-...++|+|.-+++++++...++.+.+...+..+...|..++ ..++-+.............+.+.++++.+++
T Consensus 844 ~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~~~~~L~~~t~~~~~~~ii~r~~~~~~~~~s~ 923 (1738)
T KOG1140|consen 844 EVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKKGADILGAAVRLTVFGLIIYRTLEHCLFMESS 923 (1738)
T ss_pred hcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455556688999999999999888877766555555554444444 1222222222122223345677888888888
Q ss_pred hhHhHHHhhhchhHHHHHHHHHHHhcCCC--cccccccCceeeeCCceehhhhhhhhHHhhhhhhhhcccccccccccc-
Q 000460 412 AAVSKYATHEQLNISKAWMKLLTFVQGMN--PQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEETR- 488 (1482)
Q Consensus 412 ~~Va~~l~~~~~~l~~~~l~lL~~mQGMn--p~kRq~~~HVEyE~e~w~~AF~Le~~la~i~~l~~~~~~s~~~~~~~~- 488 (1482)
.-+++.+..-.-.+.+.++..+..+++|. |..|++|.-.-++...-...+.....+..++.++..+.++..++.|..
T Consensus 924 ~~l~~~~~~ihG~~~~~~l~~~~~~~~~~~e~~~~e~gl~~~e~lv~~~~~~~~~~~~~v~~~l~~~~~~~~~n~~ea~~ 1003 (1738)
T KOG1140|consen 924 TLLSKVLHLIHGIALNEELINMKFAFTQKTESIAREKGLSLYESLVRKPDSLVHGKIIEVIVELFESLIKSRANDPEVAN 1003 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccccccccccccccccchhhHHHhhhcchhhcCCcceeeeHHHHhhhhhhhcCCccccc
Confidence 66666554444578899999999999999 999999987755554223333444778888888888888888776554
Q ss_pred cccccccccCCCCCccccccccccccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhhhcC
Q 000460 489 YDFSMYKQDIGDGDSLRHAKVGRLSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENWLGV 568 (1482)
Q Consensus 489 ~~~~~~~~~~~~~~~~~~~~v~r~~~e~s~~~~~~~~~~~~~~~v~e~~~~~~~~~~~l~~~l~~l~~~cl~~l~~~l~~ 568 (1482)
+...|......+++..+.++.+|+..|..++...--+..+..=+....+. .|..+-+.|.+....+.+|......++..
T Consensus 1004 ~~~~~~~~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e-~d~~~~~~~~~~~~~~~~~d~~~~~~~~~ 1082 (1738)
T KOG1140|consen 1004 DEKDKKEKQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDE-FDEQENQTPSSGSKTYEEEDFTCALCQDN 1082 (1738)
T ss_pred cccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccc-cCcccccCccccccchhhhhccchhhhcc
Confidence 56666666555777778888888888887664332222222111111122 23455566777777777777766554432
Q ss_pred CCCcccccccCCCCcccccCcchhhhHhhhhhhcccccccccccCCccccccccccCC-----Cccc---c-ccCccccc
Q 000460 569 DDRSVSVNDILSPNASRISGSNFVALKKTLSKIKKGKSIFSRLAGSSEVTAGIQESGD-----LDNA---T-SMGKESKI 639 (1482)
Q Consensus 569 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~---~-~~~~~~~~ 639 (1482)
....... ...++ ..+-++ +..++.++.+ .-++.+ |..|.... -+++ + ...+...+
T Consensus 1083 s~~~~~~-~~~~~----~~~~~~--------~~~~i~~e~e--~~~~~~-~~~~v~~~f~~~s~~~sd~l~~p~~~~~~~ 1146 (1738)
T KOG1140|consen 1083 SCTDFQV-KPASH----LVKPIF--------RECIICDENE--DVPNWD-GRYSVSSAFAQKSDDVSDALTEPGSLSCGT 1146 (1738)
T ss_pred chhcccc-ccchh----hhcccc--------cccccCChhc--cCCCcc-ccchhhhHhhhhcccccccccCCCCCcccc
Confidence 2211000 00000 000000 0111111111 000000 00000000 0000 0 00111111
Q ss_pred cccCccccccccccCC-------C-------CcccccccccccccccccccCccCceeeeccCCcceeechHHHHHHHHH
Q 000460 640 TISGERDTASWRSAGF-------N-------DSEMEGECATELDNLHVLSLCYWPDITYDVSSQDVSVHIPLHRLLSLII 705 (1482)
Q Consensus 640 ~~~~~~~~~~~~~~~~-------~-------~~~~~~~~~~~~~~~~~~~~~~~~~i~fdVs~~~VSfH~PLhr~Ls~Ll 705 (1482)
.+. .||+-.-+.- . ...+.-|. + ...+...-|.-..++|+-..+.-|.++++.++...
T Consensus 1147 ~~s---~c~h~mh~~c~~~~~~a~r~~~n~~~~~l~~~~-s----e~~l~lCp~c~slsn~~lp~~~~~~~~~n~~t~~~ 1218 (1738)
T KOG1140|consen 1147 VLS---SCGHHMHYGCFKRYVQAKRFRENARTAPLCQHY-S----ENGLFLCPLCKSLSNVSLPMFLPPELLLNPLTLEN 1218 (1738)
T ss_pred eee---ccCCcchHHHHHHHHHHHHHHHHhhhcCccccc-c----cCCcccCCchHhhhhccCCcCCchhhhcChhhhhc
Confidence 111 1221000000 0 00000000 0 00111222233457788888999999999888887
Q ss_pred HHHHhhhhcccccccccccCCCCCccccchhhhhhccCCCCCCccchhhhcccHHHHHHHHHHHhCccccccHHHhHHHH
Q 000460 706 QKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFSAFVMEHPLRIRVFCAQVHAGMWRRNGDAALSSCE 785 (1482)
Q Consensus 706 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~l~e~PLR~~Vl~AQI~AGmWVRNG~sl~~Q~~ 785 (1482)
+..+..+++...-.+..--+.......+...|.......+.|-++..+-..+...+.+++.+++++||-- |. .
T Consensus 1219 ~~n~~~~i~~rs~~~~s~~~vs~~~s~~~~~~~ss~i~e~kp~~~~~l~~~~~~~ie~~~k~v~s~~~k~-~~------~ 1291 (1738)
T KOG1140|consen 1219 QRNLNSWIEKRSRASFSLQDVSSILSDPWAAFTSSRIPELKPILIMDLPDSVVEQIELFQKIVGSAMFKP-SS------L 1291 (1738)
T ss_pred hHHHHHHHHHhchhhcchhhhhhhhcccchhhccccccccccchHhhhhhHHHHHHHHHHHHHhhheeec-cc------c
Confidence 7766555441100000000000000111222221122223332222233455677999999999999977 21 1
Q ss_pred HhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccccCCCCCCCchh-HHHHHHHHHHHHHhhcccccCC
Q 000460 786 WYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLNLERPSEYEP-ILVQEMLTLIIQILQERRFCGL 864 (1482)
Q Consensus 786 ~Y~~~~~re~~~d~DlfLLQ~~asl~dp~~fl~~il~RF~L~~w~~~~~~~~~~y~~-~lvEE~L~lLI~LltER~~~g~ 864 (1482)
. ...+-+..-+.+.+++|++.++.+.......++.+++...++.++......+.. ..+.. ...++++.++...++
T Consensus 1292 i--~~~~le~~~~~~~~~~~~~~~~s~a~~~~~~~l~~~~~~~~l~l~~~~~~~~~~~~~l~~--~~~~~~l~~~~~~~l 1367 (1738)
T KOG1140|consen 1292 L--STNTLELTLFSREFLIVCWQSLSDAEQSTKLLLSASKKPSFLKLNEDMTFCLVTISRLRA--LHWEQILYELVYTFL 1367 (1738)
T ss_pred e--eecccccCcccchhhhhhhhccchHHHHHHHHHhccCCcccccCchhhHHHHHHHHHHHH--HHHHHHHHHHHHHHH
Confidence 2 235667888899999999999999999999999999988888776543333322 22222 445677777776666
Q ss_pred ChHHHHHHHHHHHHhcCCCChHHHHHhCCCCCCCcchHHHHHHHHhcccCCCCCCcceeEehhhhhccccccccccCchh
Q 000460 865 TTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRD 944 (1482)
Q Consensus 865 t~~e~lrrEIIh~Lc~~p~t~SeL~~~lpe~~~~~~~fe~iL~eVA~fk~P~g~~~G~Y~LK~e~~~e~DPy~~~y~~~d 944 (1482)
-.....+.++|-.+..++.+++.+...+|.+..+...++.++..|- ..|.+.-.+.+.++.-.|.+.+-++..+.. |
T Consensus 1368 lk~~s~~~~~i~~~~tpd~~~~~ll~~l~~~~~~~~~l~~~~~~~~--~~~~~~~~~~i~~~~i~s~elits~s~l~~-d 1444 (1738)
T KOG1140|consen 1368 LKSFSPTIPRISVLITPDQPENELLVILPHDFPKSLELELTLDFVN--KNPKKIFELKILMASIISIELITSHSYLEN-D 1444 (1738)
T ss_pred HHHHhhcCCcchhccCCCCCcchhhhccchhhhhhccHHHHHHHhh--hhHHHHHhHHHHHHHhhhhhhheeccccCC-c
Confidence 6666677778888888899999999999999999999999999998 677777889999999999999999888877 8
Q ss_pred HHHHHHHHHHhhcccccc--cCCCCCccCCCccchhhhccccHHHHHHHHHHHHHHhh
Q 000460 945 LQVAEERYLRFCSVSALT--AQLPRWTKIYYPLESIAGIATCKVVLQVIRAVLFYAVF 1000 (1482)
Q Consensus 945 ~q~Aeer~~r~~k~~~~~--~~~P~~~~~~~pf~~i~~il~s~~~~~ii~~vL~~al~ 1000 (1482)
.+.|+++..+..-.++.. ...+.+....++-.++.++--+....+.+...|.++..
T Consensus 1445 ~~~~~~q~s~~e~~~~~t~l~~~~s~~~i~~~~~~~~~~~L~~~~~~~i~sfL~~~al 1502 (1738)
T KOG1140|consen 1445 LEMAEEQKSIDEFKSLLTYLLQLESSRTIPKLADIRLRLSLCLSCEAGILSFLRRAAL 1502 (1738)
T ss_pred cchhhhhhhHHhHhHHHHHHHhccchhhCccccchhhhhHHHHHHHHHHHHHHHHHHH
Confidence 877777654322222222 23344444433334555666677788888888877653
No 3
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=99.80 E-value=4.4e-20 Score=169.83 Aligned_cols=70 Identities=44% Similarity=1.070 Sum_probs=66.3
Q ss_pred CcccccccCCCeeEEeccCCCCCCccccccccCCCCCCCceeEEEeC-CCccccCCCcccccccCCCCCCC
Q 000460 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYT-GGGCCDCGDVTAWKREGFCSRHK 185 (1482)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~~~~~-~gG~CDCGD~~awk~~~fC~~H~ 185 (1482)
.+|+++|+.|+++|+|+||+.++++++|.+||+++.|+||+|.+.+. +||+|||||++|||+++||++|.
T Consensus 1 ~~C~~~~~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~~~~~~~~~~~CDCG~~~~~~~~~~C~~h~ 71 (71)
T smart00396 1 DVCTYKFTGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDYSLKTSRGSGICDCGDKEAWNEDLKCKAHE 71 (71)
T ss_pred CCCCCccCCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCEEEEEecCCEEECCCChhccCCCccccccC
Confidence 47999999999999999999999999999999999999999999885 45999999999999999999994
No 4
>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=99.75 E-value=5.6e-19 Score=162.89 Aligned_cols=70 Identities=49% Similarity=1.112 Sum_probs=54.0
Q ss_pred CcccccccCCCeeEEeccCCCCCCccccccccCCCCCCCceeEEEeCC-CccccCCCcccccccCCCCCCC
Q 000460 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTG-GGCCDCGDVTAWKREGFCSRHK 185 (1482)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~~~~~~-gG~CDCGD~~awk~~~fC~~H~ 185 (1482)
+.|+++|.+++++|+|+||+.+++.+||.+||.++.|+||++.+..+. +|+|||||+++||+++||++|+
T Consensus 1 ~~C~~~~~~~q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~~~~~CDCG~~~~~k~~~~C~~H~ 71 (71)
T PF02207_consen 1 KKCTYVWTSGQIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSSSGGCCDCGDPEAWKKEGFCKKHK 71 (71)
T ss_dssp -SS--B--TT-EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--SCEBB-TT-GGGBSS--S-TTT-
T ss_pred CcCCCCCcCCCEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeCCCeEEeCCCCccccCCCCCCCCC
Confidence 479999999999999999999999999999999999999999998865 9999999999999999999995
No 5
>KOG1139 consensus Predicted ubiquitin-protein ligase of the N-recognin family [Posttranslational modification, protein turnover, chaperones]
Probab=98.84 E-value=3.1e-08 Score=121.67 Aligned_cols=185 Identities=21% Similarity=0.316 Sum_probs=143.5
Q ss_pred hhcccHHHHHHHHHHHhCccccccHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccccC
Q 000460 754 VMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLN 833 (1482)
Q Consensus 754 l~e~PLR~~Vl~AQI~AGmWVRNG~sl~~Q~~~Y~~~~~re~~~d~DlfLLQ~~asl~dp~~fl~~il~RF~L~~w~~~~ 833 (1482)
+.-+++++.|--.-++..||+|+|.-...-...|-+..+....---+--.+-.|+..+++..|+..++.+|.+.+.-..+
T Consensus 207 ~~ylf~~~ev~rll~~g~~~~~c~alAKvveq~y~~~~~s~~kkrhePdt~~~r~~hi~~slfl~e~la~~~~~ec~~~d 286 (784)
T KOG1139|consen 207 LLYLFLRIEVARLLINGNMWVRCGALAKVVEQIYSQWNVSSAKKRHEPDTIRFRAAHIDKSLFLKELLASFNITECIKID 286 (784)
T ss_pred HHhhhhhhhHHHHHhcCCCccccHHHHHHHHHhcccchhcccccCCCCchhccccccccHHHHHHHHHHHhhhhhhhhhh
Confidence 45667899999999999999999998887778886655544444444455566889999999999999999877632211
Q ss_pred CC-------------C-------------------C--------------------------------------------
Q 000460 834 LE-------------R-------------------P-------------------------------------------- 837 (1482)
Q Consensus 834 ~~-------------~-------------------~-------------------------------------------- 837 (1482)
.. . +
T Consensus 287 i~r~v~~~p~~s~L~~~~~~~~~~~k~~~~~Hsr~p~~~~l~~f~~p~lEaa~~d~l~~v~~~~e~~~R~~~~s~vlr~~ 366 (784)
T KOG1139|consen 287 IGRFVEKSPESSILFQETEVTIDFTKQSPIDHSRDPRIPILGEFIRPHLEAAGVDALIDVEMEREFDPRLFDDSEVLRTI 366 (784)
T ss_pred ccceeEeccccccchhhhhhhccccccCchhcccCcchhHHHHhhccccccccCchHHHHhhhccccccccchhhhhHHh
Confidence 00 0 0
Q ss_pred --CCch--hHHHHHHHHHHHHHhhcccccCCChHHHHHHHHHHHHhcCCCChHHHHHhCCCCC-CCcchHHHHHHHHhcc
Q 000460 838 --SEYE--PILVQEMLTLIIQILQERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDL-SKFDQLQEILDAVAMY 912 (1482)
Q Consensus 838 --~~y~--~~lvEE~L~lLI~LltER~~~g~t~~e~lrrEIIh~Lc~~p~t~SeL~~~lpe~~-~~~~~fe~iL~eVA~f 912 (1482)
.+|+ +.+...++.++..+|.++.+.|..+++..+-|+.|.-+++..+||-+.+++.+.. ...+.|+.|+.+..+|
T Consensus 367 ~~~~~e~~~~~~~~~f~l~~~~v~~s~~~~ai~~~~~~~em~n~~a~~~~~~s~~~aS~~~~~~~~~~~f~~i~~~~~~~ 446 (784)
T KOG1139|consen 367 VIREPEWIDPMFWGMFKLVAELVVVSVNSGAIPEEHYRSEMVNCMAMGNVPYSRLRASISEKGSMIDKHFETILNEIGDF 446 (784)
T ss_pred hhccccccchhhcchHHHHHHHhhhhcccccchHHHHHHHHHhHHHhcCCCcccccccccCCCccccccccccccccccc
Confidence 0001 2456778899999999999999999999999999999999999999998776655 4567899999999999
Q ss_pred cCCCC----CCcceeEehhhhhc-ccccccc
Q 000460 913 SHPSG----FNQGMYSLRWSYWK-ELDIYHP 938 (1482)
Q Consensus 913 k~P~g----~~~G~Y~LK~e~~~-e~DPy~~ 938 (1482)
-.|-- ..+|.|.||...|+ +.-|-+.
T Consensus 447 ~~P~~~~~p~~~~s~~l~~~~~~~~~c~~~~ 477 (784)
T KOG1139|consen 447 IEPIETTTPLMQGSYQLKTSIWDSEVCPVFF 477 (784)
T ss_pred ccchhhcCccccchhhccccCCccccccchh
Confidence 99943 34799999999998 4666544
No 6
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=97.21 E-value=0.00018 Score=83.84 Aligned_cols=80 Identities=26% Similarity=0.419 Sum_probs=60.5
Q ss_pred HHHHHHHHHHhcCCCChHHHHHhCCCCCCC---cchHHHHHHHHhcccCCCCCCcceeEehhhhhccccccccccCchhH
Q 000460 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSK---FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (1482)
Q Consensus 869 ~lrrEIIh~Lc~~p~t~SeL~~~lpe~~~~---~~~fe~iL~eVA~fk~P~g~~~G~Y~LK~e~~~e~DPy~~~y~~~d~ 945 (1482)
.+|.-|||.|+++|....||..+|..+... -..++.||++||... .++.|.||+.+|+++|.=++.|+-.|+
T Consensus 198 plReRvIHLLALkpykK~ELl~rL~~dg~~~~dk~~l~~iL~~Va~l~-----~~~~y~Lk~~~ykevq~dWP~yse~er 272 (284)
T PF10390_consen 198 PLRERVIHLLALKPYKKPELLLRLQKDGLSPKDKDELDSILQEVANLN-----KDNSYTLKDHFYKEVQKDWPGYSEEER 272 (284)
T ss_dssp -HHHHHHHHHHHS-EEHHHHHHHHHHH---HHHHHHHHHHHHHCCEEE-----TTTEEEE-STHHHHS-TT-TT--TCHH
T ss_pred cccccchhhhhcCccccHHHHHHHHhcCCChHHHHHHHHHHHHHhccC-----cCCeEEehHHHHhhhccCCCCCCHHHH
Confidence 599999999999999999999988765433 346999999999965 378999999999999988889999998
Q ss_pred HHHHHHHH
Q 000460 946 QVAEERYL 953 (1482)
Q Consensus 946 q~Aeer~~ 953 (1482)
|..+-+..
T Consensus 273 q~l~r~l~ 280 (284)
T PF10390_consen 273 QLLKRRLS 280 (284)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 88765543
No 7
>KOG1777 consensus Putative Zn-finger protein [General function prediction only]
Probab=95.86 E-value=0.0032 Score=74.70 Aligned_cols=63 Identities=35% Similarity=0.564 Sum_probs=51.5
Q ss_pred ccCCCCcccccc-----cCCCeeEEeccCCCCCCccccccccCCCCCCCceeEEEeCCCccccCCCccc
Q 000460 111 KIGQRGVCGAVW-----GNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDVTA 174 (1482)
Q Consensus 111 ~~~~~~~Cg~v~-----~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~~~~~~gG~CDCGD~~a 174 (1482)
+.-+.++|-... -+=.-+|||-||...+..+||..|.++ -|+||++-+.+...-+||||-..+
T Consensus 539 kAik~GqCLfkvSs~~syPMHnFYRC~TCNttdRNAIC~nCI~~-CH~GH~Vefir~Drffcdcgagtl 606 (625)
T KOG1777|consen 539 KAIKKGQCLFKVSSYTSYPMHNFYRCITCNTTDRNAICVNCIKR-CHEGHDVEFIRHDRFFCDCGAGTL 606 (625)
T ss_pred HHhhcCceEEEecCCCcccccceeEeeecCCccccHHHHHHHHH-hcCCCceEEEeeceEEEecCCcee
Confidence 345557774433 333468999999999999999999988 799999999998899999998654
No 8
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=91.89 E-value=0.054 Score=70.19 Aligned_cols=64 Identities=27% Similarity=0.686 Sum_probs=51.7
Q ss_pred CCcccccccCCC----eeEEeccCCCCCCccccccccCCCCCCCceeEEEe-CCCccccCCCcccccc-cCCCCCC
Q 000460 115 RGVCGAVWGNND----IAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVTAWKR-EGFCSRH 184 (1482)
Q Consensus 115 ~~~Cg~v~~~ge----~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~~~~-~~gG~CDCGD~~awk~-~~fC~~H 184 (1482)
...|...|...+ -.|.|+||+.-.+-|-|.+|-.. .|+||++++-+ +.-.+||| |-+ ++.|+.-
T Consensus 1240 NDtCSFTWTGadHINQDIfECkTCGL~~SLCCCsECAlt-CHk~HDCkLKRTSPTAYCDC-----WEKssCkCKaL 1309 (3015)
T KOG0943|consen 1240 NDTCSFTWTGADHINQDIFECKTCGLLESLCCCSECALT-CHKGHDCKLKRTSPTAYCDC-----WEKSSCKCKAL 1309 (3015)
T ss_pred cCccceeecchhhccchhhhhcccccchhhhhhHHHHHH-hccCCccceeccCCcceeeh-----hhcccccchhh
Confidence 357899998644 57999999999999999999875 79999999987 46899999 643 4557654
No 9
>KOG1139 consensus Predicted ubiquitin-protein ligase of the N-recognin family [Posttranslational modification, protein turnover, chaperones]
Probab=91.48 E-value=0.13 Score=65.25 Aligned_cols=67 Identities=13% Similarity=-0.069 Sum_probs=50.4
Q ss_pred CcccccchhhhhhhhhccccccccccccccchhhhhccccCCCCCCCCcceecCCchhhhhhhHHHHHHHHHhhhcccCC
Q 000460 1343 SDSFLLGKYVASISKEMRENASASEVSRGDRIAAESLVYDGFGPIDCDGIHLSSCGHAVHQGCLDRYVSSLKERQVLPTT 1422 (1482)
Q Consensus 1343 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~s~c~h~~h~~c~~~y~~~l~~r~~~~~~ 1422 (1482)
.+.++-+..++-..+....... +. +||+|-|.+++|.|.++|+|++|+.|+.||+.+.+.+..++.-
T Consensus 144 k~ptlen~cp~frl~k~L~a~q-----------qs--syD~fv~h~q~~~asTsi~hf~~dsv~~r~l~eell~wg~~yl 210 (784)
T KOG1139|consen 144 KAPTLENECPAFRLFKILAAIQ-----------QS--SYDRFVDHIQSQHASTSITHFTEDSVRSRLLNEELLIWGLLYL 210 (784)
T ss_pred CCCcccccccceechhhccccc-----------cc--CCCcceecccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3333556666655555442211 11 3799999999999999999999999999999999999877654
No 10
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=90.16 E-value=1.6 Score=57.97 Aligned_cols=74 Identities=14% Similarity=0.232 Sum_probs=42.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCCCCCCCccCCCCcccccccccCCceeecCCCCC---CCCEEEE
Q 000460 1145 DSEKRKAKARERQAAILEKMKAEQFKFLSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS---RTPVSYL 1221 (1482)
Q Consensus 1145 E~EkKKk~AkeRQaKIMAQmkaQQksFL~nn~~~~de~d~~~~e~~~~d~~~~~~e~~~~tCILCqE~~s---~~pfG~l 1221 (1482)
.+.+||++|.++|+|.+.+|.-++. .+..- . ..+..-... ++.++|. -.+|++|+|.-. .+++|+-
T Consensus 421 Tr~ekk~~Am~~Rek~L~~lgm~~~-----~~G~v--~--~~~~~l~~~-~~l~ee~-gl~C~ICrEGy~~~p~~~lGiY 489 (802)
T PF13764_consen 421 TRQEKKRLAMAMREKQLKKLGMRVN-----EKGQV--V--VSSSILQNM-EDLEEED-GLTCCICREGYKFRPDEVLGIY 489 (802)
T ss_pred HHHHHHHHHHHHHHHHHHHccCccc-----cccce--e--cCchhhcCc-ccccccC-CCeEEEcCCccccCCccceeeE
Confidence 4678888999999999999844330 00000 0 000000000 1111233 378999999853 6789999
Q ss_pred EEeecccc
Q 000460 1222 ILLQKSRL 1229 (1482)
Q Consensus 1222 alVQ~Ssv 1229 (1482)
+|.-+-.+
T Consensus 490 ~f~kr~~l 497 (802)
T PF13764_consen 490 AFSKRVNL 497 (802)
T ss_pred EEeecccc
Confidence 99855444
No 11
>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=86.91 E-value=0.51 Score=41.01 Aligned_cols=39 Identities=28% Similarity=0.869 Sum_probs=29.4
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCC----CC-CceeEE
Q 000460 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN----HK-EHDYSI 159 (1482)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~----H~-gH~~~~ 159 (1482)
.|++.... ..-|+|..|. ..-+|.+||..+. |+ .|.|.+
T Consensus 5 ~C~~~~~~-g~r~~C~~C~---d~dLC~~Cf~~g~~~~~H~~~H~~~~ 48 (49)
T cd02335 5 YCSKDITG-TIRIKCAECP---DFDLCLECFSAGAEIGKHRNDHNYRV 48 (49)
T ss_pred CcCCCCCC-CcEEECCCCC---CcchhHHhhhCcCCCCCCCCCCCeEe
Confidence 57776664 4899999995 4679999999984 53 577755
No 12
>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=86.67 E-value=0.59 Score=39.64 Aligned_cols=37 Identities=27% Similarity=0.654 Sum_probs=29.5
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000460 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (1482)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~ 158 (1482)
.|+..+ .| .-|+|.+|. ..-+|.+||.++.|.+|.+.
T Consensus 5 ~C~~~i-~G-~ry~C~~C~---d~dLC~~C~~~~~H~~H~f~ 41 (43)
T cd02340 5 GCQGPI-VG-VRYKCLVCP---DYDLCESCEAKGVHPEHAML 41 (43)
T ss_pred CCCCcC-cC-CeEECCCCC---CccchHHhhCcCCCCCCCEE
Confidence 477633 33 789999997 47799999999999888874
No 13
>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=85.55 E-value=0.64 Score=39.77 Aligned_cols=37 Identities=27% Similarity=0.822 Sum_probs=29.1
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCC--CCC-CceeE
Q 000460 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG--NHK-EHDYS 158 (1482)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~--~H~-gH~~~ 158 (1482)
.|++.+ .| .-|+|.+|. ..-+|.+||..+ .|. +|.+.
T Consensus 5 ~C~~~i-~g-~r~~C~~C~---d~dLC~~Cf~~~~~~H~~~H~~~ 44 (46)
T cd02249 5 GCLKPI-VG-VRYHCLVCE---DFDLCSSCYAKGKKGHPPDHSFT 44 (46)
T ss_pred CCCCCC-cC-CEEECCCCC---CCcCHHHHHCcCcCCCCCCCCEe
Confidence 578844 35 899999996 577999999998 676 67664
No 14
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=85.40 E-value=0.96 Score=56.02 Aligned_cols=78 Identities=27% Similarity=0.374 Sum_probs=63.6
Q ss_pred HHHHHHHHHHhcCCCChHHHHHhCCCCCCCc---chHHHHHHHHhcccCCCCCCcceeEehhhhhccccccccccCchhH
Q 000460 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSKF---DQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (1482)
Q Consensus 869 ~lrrEIIh~Lc~~p~t~SeL~~~lpe~~~~~---~~fe~iL~eVA~fk~P~g~~~G~Y~LK~e~~~e~DPy~~~y~~~d~ 945 (1482)
-||.-|||+|+.++..--||.++|-.+.... ..+..||.+. +...+|+|.|++.+|+|+|-=++.|+-.|.
T Consensus 211 ~ir~RviHLlalk~ykk~El~~rLk~dGl~~~e~~~i~~il~~~------~~~~~~t~~Lrd~~~~evdq~Wp~yse~d~ 284 (604)
T KOG4796|consen 211 PIRDRVIHLLALKAYKKPELLARLKKDGLPQEEKNKIRSILQQN------SRSKDGTYTLRDSMLKEVDQNWPGYSEGDK 284 (604)
T ss_pred chHHHHHHHHHhhhcccHHHHHHHhhcCCcHHHHHHHHHHHHhh------cccccccchHHHHhhhHHHhcCCCcchHHH
Confidence 4999999999999999999999887766543 4578888882 124689999999999999988889998888
Q ss_pred HHHHHHH
Q 000460 946 QVAEERY 952 (1482)
Q Consensus 946 q~Aeer~ 952 (1482)
|..+-+.
T Consensus 285 ~~lkr~~ 291 (604)
T KOG4796|consen 285 QHLKRVL 291 (604)
T ss_pred HHHHHHh
Confidence 7665443
No 15
>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=83.31 E-value=0.97 Score=39.37 Aligned_cols=38 Identities=26% Similarity=0.792 Sum_probs=28.9
Q ss_pred ccc-ccccCCCeeEEeccCCCCCCccccccccCCC----CCC-CceeEE
Q 000460 117 VCG-AVWGNNDIAYRCRTCEHDPTCAICVPCFQNG----NHK-EHDYSI 159 (1482)
Q Consensus 117 ~Cg-~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~----~H~-gH~~~~ 159 (1482)
.|+ ..+. ..-|+|..|. ..-+|.+||..+ .|+ .|.+.+
T Consensus 5 ~C~~~~i~--g~R~~C~~C~---d~dlC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02338 5 GCGKSNFT--GRRYKCLICY---DYDLCADCYDSGVTTERHLFDHPMQC 48 (49)
T ss_pred CCcCCCcE--EeeEEeCCCC---CCccchhHHhCCCcCCCCCCCCCEEE
Confidence 477 4454 4889999994 577999999988 776 777654
No 16
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=81.74 E-value=1.7 Score=50.77 Aligned_cols=61 Identities=25% Similarity=0.597 Sum_probs=47.3
Q ss_pred cCCCCcccccc--cCCCeeEEeccCCCCC-CccccccccCCCCCCCceeEEEe-CCCccccCCCcc
Q 000460 112 IGQRGVCGAVW--GNNDIAYRCRTCEHDP-TCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVT 173 (1482)
Q Consensus 112 ~~~~~~Cg~v~--~~ge~~y~C~~C~~d~-t~~lC~~CF~~~~H~gH~~~~~~-~~gG~CDCGD~~ 173 (1482)
...+..|++.- ++-.+.|.|.||...+ ...+|..|=.. -|.||.-..-. .+..-||||+.-
T Consensus 37 ~~~~~~CTy~~Gy~~rQ~l~sClTC~P~~~~agvC~~C~~~-CH~~H~lveL~tKR~FrCDCg~sk 101 (345)
T KOG2752|consen 37 TQNPDVCTYAKGYKKRQALFSCLTCTPAPEMAGVCYACSLS-CHDGHELVELYTKRNFRCDCGNSK 101 (345)
T ss_pred CCCCcccccccCcccccceeEeecccCChhhceeEEEeeee-ecCCceeeeccccCCccccccccc
Confidence 35566787653 3336889999999999 77899999775 79999987655 467889999964
No 17
>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=81.56 E-value=1.2 Score=38.21 Aligned_cols=39 Identities=26% Similarity=0.695 Sum_probs=29.7
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCCC-CCceeEE
Q 000460 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYSI 159 (1482)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H-~gH~~~~ 159 (1482)
.|+..--.| +-|+|.+|. ..-+|..||....| .+|.+..
T Consensus 5 ~C~~~pI~G-~RykC~~C~---dyDLC~~Cf~~~~H~~~H~F~r 44 (45)
T cd02344 5 GCQMFPING-PRFKCRNCD---DFDFCENCFKTRKHNTRHTFGR 44 (45)
T ss_pred CCCCCCCcc-CeEECCCCC---CccchHHhhCCCCcCCCCceee
Confidence 355443344 789999998 56799999999999 5898753
No 18
>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=78.96 E-value=1.1 Score=37.18 Aligned_cols=37 Identities=24% Similarity=0.595 Sum_probs=28.1
Q ss_pred CcccccccCCCeeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000460 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (1482)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~ 158 (1482)
..|..--+ ....|.|.+|.. .+|.+|+..+ |++|++.
T Consensus 4 ~~C~~H~~-~~~~~~C~~C~~----~~C~~C~~~~-H~~H~~~ 40 (42)
T PF00643_consen 4 PKCPEHPE-EPLSLFCEDCNE----PLCSECTVSG-HKGHKIV 40 (42)
T ss_dssp SB-SSTTT-SBEEEEETTTTE----EEEHHHHHTS-TTTSEEE
T ss_pred ccCccCCc-cceEEEecCCCC----ccCccCCCCC-CCCCEEe
Confidence 45544332 348999999985 7999999998 9999975
No 19
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=75.04 E-value=2.1 Score=48.61 Aligned_cols=61 Identities=23% Similarity=0.217 Sum_probs=41.3
Q ss_pred HHHHHHHHH--hcCCCChHHHHHhCCCCCCCcchHHHHHHHHhcccCCCCCCcceeEehhhhhc
Q 000460 870 LKRELVHRL--AIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWK 931 (1482)
Q Consensus 870 lrrEIIh~L--c~~p~t~SeL~~~lpe~~~~~~~fe~iL~eVA~fk~P~g~~~G~Y~LK~e~~~ 931 (1482)
=|+||+-.| ||.-..|=-|...+-..-+...-+.+||++||+|-+ .|..+|+|+|||||-+
T Consensus 183 dk~evld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~icv~Nk-Kg~~k~tyeLKPEYK~ 245 (254)
T KOG2905|consen 183 DKNEVLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDICVLNK-KGPYKNTYELKPEYKK 245 (254)
T ss_pred cHHHHHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHHHHhc-cCcccCceecCHHHhh
Confidence 456666665 455555544443333333344568999999999976 3668999999999864
No 20
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=73.70 E-value=2.3 Score=34.49 Aligned_cols=23 Identities=30% Similarity=0.859 Sum_probs=19.5
Q ss_pred CcceecCCchhhhhhhHHHHHHH
Q 000460 1390 DGIHLSSCGHAVHQGCLDRYVSS 1412 (1482)
Q Consensus 1390 ~g~~~s~c~h~~h~~c~~~y~~~ 1412 (1482)
+-+.+..|||..|.+|.++|+..
T Consensus 11 ~~~~~~~C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 11 EPVVLLPCGHVFCRSCIDKWLKS 33 (45)
T ss_pred CceEecCCCChhcHHHHHHHHHh
Confidence 45667789999999999999875
No 21
>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=72.67 E-value=2.4 Score=36.39 Aligned_cols=30 Identities=27% Similarity=0.907 Sum_probs=24.7
Q ss_pred CeeEEeccCCCCCCccccccccCCCCC-CCceeE
Q 000460 126 DIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYS 158 (1482)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~~H-~gH~~~ 158 (1482)
..-|+|..|. ..-+|.+||.++.| .+|.|.
T Consensus 13 G~RykC~~C~---dyDLC~~C~~~~~H~~~H~f~ 43 (45)
T cd02339 13 GIRWKCAECP---NYDLCTTCYHGDKHDLEHRFY 43 (45)
T ss_pred cCeEECCCCC---CccchHHHhCCCCCCCCCCEE
Confidence 5679999996 46799999999998 488764
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=64.16 E-value=4.7 Score=35.15 Aligned_cols=32 Identities=25% Similarity=0.739 Sum_probs=24.2
Q ss_pred CeeEEeccCCCCCCccccccccCCC-CCC-CceeE
Q 000460 126 DIAYRCRTCEHDPTCAICVPCFQNG-NHK-EHDYS 158 (1482)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~-~H~-gH~~~ 158 (1482)
..-|+|.+|.- ...-+|.+||.++ .|+ +|...
T Consensus 13 G~R~~C~~C~~-~d~DlC~~C~~~~~~H~~~H~~~ 46 (48)
T cd02341 13 GTRYHCSECDD-GDFDLCQDCVVKGESHQEDHWLV 46 (48)
T ss_pred cceEECCCCCC-CCCccCHHHHhCcCCCCCCCcee
Confidence 56799999963 3567999999999 674 66653
No 23
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=62.01 E-value=4.7 Score=33.81 Aligned_cols=24 Identities=21% Similarity=0.696 Sum_probs=19.7
Q ss_pred CCcceecCCchhhhhhhHHHHHHH
Q 000460 1389 CDGIHLSSCGHAVHQGCLDRYVSS 1412 (1482)
Q Consensus 1389 ~~g~~~s~c~h~~h~~c~~~y~~~ 1412 (1482)
.+.+..-.|||..|.+|..+|+.+
T Consensus 13 ~~~~~~l~C~H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 13 GEKVVKLPCGHVFHRSCIKEWLKR 36 (44)
T ss_dssp TSCEEEETTSEEEEHHHHHHHHHH
T ss_pred CCeEEEccCCCeeCHHHHHHHHHh
Confidence 455666669999999999999965
No 24
>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=60.85 E-value=6.5 Score=31.72 Aligned_cols=28 Identities=25% Similarity=0.451 Sum_probs=23.3
Q ss_pred CeeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000460 126 DIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (1482)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~ 158 (1482)
...|-|.+|+. .+|..|-..+ |++|.+.
T Consensus 10 ~~~~fC~~~~~----~iC~~C~~~~-H~~H~~~ 37 (39)
T cd00021 10 PLSLFCETDRA----LLCVDCDLSV-HSGHRRV 37 (39)
T ss_pred ceEEEeCccCh----hhhhhcChhh-cCCCCEe
Confidence 45788988874 7999999888 9999875
No 25
>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=60.46 E-value=4.9 Score=35.06 Aligned_cols=35 Identities=29% Similarity=0.697 Sum_probs=26.9
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCCCC-Cce
Q 000460 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK-EHD 156 (1482)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~-gH~ 156 (1482)
.|++.. . ..-|+|..|. ..-+|.+||..+.+. +|+
T Consensus 5 gC~~~~-~-~~RykCl~C~---d~DlC~~Cf~~g~~~~~H~ 40 (48)
T cd02343 5 GCDEIA-P-WHRYRCLQCT---DMDLCKTCFLGGVKPEGHE 40 (48)
T ss_pred CCCCcC-C-CceEECCCCC---CchhHHHHHhCCccCCCCC
Confidence 477754 2 4799999996 478999999998875 444
No 26
>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=59.53 E-value=3.2 Score=35.71 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=21.0
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCCC
Q 000460 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 152 (1482)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H 152 (1482)
.||.-.. .+-|+|..+. ...||.+||..|.-
T Consensus 5 ~Cg~D~t--~vryh~~~~~---~~dLC~~CF~~G~f 35 (45)
T cd02336 5 TCGNDCT--RVRYHNLKAK---KYDLCPSCYQEGRF 35 (45)
T ss_pred CCCCccC--ceEEEecCCC---ccccChHHHhCcCC
Confidence 4565554 3667766554 46799999988753
No 27
>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=57.54 E-value=5.8 Score=33.42 Aligned_cols=32 Identities=25% Similarity=0.824 Sum_probs=25.1
Q ss_pred CcccccccCCCeeEEeccCCCCCCccccccccCCCCCC
Q 000460 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (1482)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~ 153 (1482)
..|+++ +++-|+|..|. ..-+|..||....|.
T Consensus 4 ~~C~~~---~~~r~~C~~C~---dfDLC~~C~~~~~H~ 35 (41)
T cd02337 4 NECKHH---VETRWHCTVCE---DYDLCITCYNTKNHP 35 (41)
T ss_pred CCCCCc---CCCceECCCCc---chhhHHHHhCCCCCC
Confidence 357663 34999999996 467999999998883
No 28
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=55.62 E-value=8.6 Score=29.88 Aligned_cols=21 Identities=19% Similarity=0.694 Sum_probs=18.2
Q ss_pred cceecCCchhhhhhhHHHHHH
Q 000460 1391 GIHLSSCGHAVHQGCLDRYVS 1411 (1482)
Q Consensus 1391 g~~~s~c~h~~h~~c~~~y~~ 1411 (1482)
-..+..|||..|..|.++|+.
T Consensus 10 ~~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 10 DPVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CcEEecCCChHHHHHHHHHHH
Confidence 455678999999999999987
No 29
>smart00336 BBOX B-Box-type zinc finger.
Probab=55.58 E-value=9.7 Score=31.19 Aligned_cols=29 Identities=21% Similarity=0.636 Sum_probs=23.7
Q ss_pred CCeeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000460 125 NDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (1482)
Q Consensus 125 ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~ 158 (1482)
+...|.|.+|+. ++|..|... .|+||.+.
T Consensus 12 ~~~~~~C~~c~~----~iC~~C~~~-~H~~H~~~ 40 (42)
T smart00336 12 EPAEFFCEECGA----LLCRTCDEA-EHRGHTVV 40 (42)
T ss_pred CceEEECCCCCc----ccccccChh-hcCCCcee
Confidence 445777988874 799999988 99999875
No 30
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=51.61 E-value=7.9 Score=45.54 Aligned_cols=31 Identities=29% Similarity=0.456 Sum_probs=15.9
Q ss_pred cchHHHHHHHHhcccCCCCCCcceeEehhhhh
Q 000460 899 FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYW 930 (1482)
Q Consensus 899 ~~~fe~iL~eVA~fk~P~g~~~G~Y~LK~e~~ 930 (1482)
+.-+-+||++||+|.+- |...|+|+|||||-
T Consensus 244 ~~yLKeiL~eIa~~~k~-g~~~~~w~LKpeyk 274 (275)
T PF02270_consen 244 EAYLKEILEEIAVLNKR-GPHKNMWELKPEYK 274 (275)
T ss_dssp HHHHHHHHHHH--EE---TT---EE----SS-
T ss_pred HHHHHHHHHHHHHHhcc-CCcCCcEecchHHc
Confidence 34578999999999864 67789999999984
No 31
>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=49.54 E-value=12 Score=31.79 Aligned_cols=33 Identities=27% Similarity=0.801 Sum_probs=25.0
Q ss_pred CcccccccCCCeeEEeccCCCCCCccccccccCCCCCC
Q 000460 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (1482)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~ 153 (1482)
..|++.+. ..-|+|..|. ..-||.+||..+.|.
T Consensus 8 ~~C~~~i~--g~ry~C~~C~---d~dlC~~Cf~~~~~~ 40 (44)
T smart00291 8 DTCGKPIV--GVRYHCLVCP---DYDLCQSCFAKGSAG 40 (44)
T ss_pred CCCCCCCc--CCEEECCCCC---CccchHHHHhCcCcC
Confidence 46888543 4578999993 578999999987664
No 32
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=41.34 E-value=12 Score=30.71 Aligned_cols=22 Identities=23% Similarity=0.871 Sum_probs=19.6
Q ss_pred cceecCCchhhhhhhHHHHHHH
Q 000460 1391 GIHLSSCGHAVHQGCLDRYVSS 1412 (1482)
Q Consensus 1391 g~~~s~c~h~~h~~c~~~y~~~ 1412 (1482)
-+.+..|||...++|..+|+..
T Consensus 11 ~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 11 PVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp EEEECTTSEEEEHHHHHHHHHC
T ss_pred cCEECCCCCchhHHHHHHHHHC
Confidence 4578999999999999999876
No 33
>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=40.78 E-value=7.7 Score=33.33 Aligned_cols=36 Identities=28% Similarity=0.709 Sum_probs=22.3
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCC-CCCce
Q 000460 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN-HKEHD 156 (1482)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~-H~gH~ 156 (1482)
.|+..--. ..-|+|..|. ..-||.+||..+. +.+|+
T Consensus 9 ~C~~~~i~-g~Ry~C~~C~---d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 9 GCGTDPII-GVRYHCLVCP---DYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SS-SSSEE-SSEEEESSSS---S-EEEHHHHHH--H-SSSS
T ss_pred CCCCCcCc-CCeEECCCCC---CCchhhHHHhCcCCCCCcC
Confidence 46663222 3679999994 5789999999864 45664
No 34
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=40.46 E-value=8.5 Score=38.00 Aligned_cols=17 Identities=41% Similarity=0.983 Sum_probs=8.0
Q ss_pred ceecCCchhhhhhhHHH
Q 000460 1392 IHLSSCGHAVHQGCLDR 1408 (1482)
Q Consensus 1392 ~~~s~c~h~~h~~c~~~ 1408 (1482)
+.+-.|||.||..|.+|
T Consensus 93 f~~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 93 FVVFPCGHVVHYSCIKR 109 (109)
T ss_pred EEEeCCCeEEecccccC
Confidence 34444455555555443
No 35
>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=39.17 E-value=21 Score=31.22 Aligned_cols=31 Identities=23% Similarity=0.842 Sum_probs=24.2
Q ss_pred Ccccc-cccCCCeeEEeccCCCCCCccccccccCCCC
Q 000460 116 GVCGA-VWGNNDIAYRCRTCEHDPTCAICVPCFQNGN 151 (1482)
Q Consensus 116 ~~Cg~-v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~ 151 (1482)
..|.+ -+. ++-|+|..|. ..-+|.+||..+.
T Consensus 4 ~~C~~~~i~--g~R~~C~~C~---dydLC~~Cf~~~~ 35 (49)
T cd02345 4 SACRKQDIS--GIRFPCQVCR---DYSLCLGCYTKGR 35 (49)
T ss_pred CCCCCCCce--EeeEECCCCC---CcCchHHHHhCCC
Confidence 35777 555 4889999994 5779999999774
No 36
>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=38.84 E-value=20 Score=31.49 Aligned_cols=33 Identities=27% Similarity=0.720 Sum_probs=24.2
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCCCC
Q 000460 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (1482)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~ 153 (1482)
.|++.=-.| .-|+|..|. ..-||.+||..+.|.
T Consensus 5 ~C~~~pi~g-~RykC~~C~---d~DLC~~Cf~~g~~~ 37 (49)
T cd02334 5 ICKEFPITG-FRYRCLKCF---NYDLCQSCFFSGRTS 37 (49)
T ss_pred CCCCCCcee-eeEECCCCC---CcCchHHHHhCCCcC
Confidence 466542233 789999996 477999999888653
No 37
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=36.14 E-value=29 Score=42.88 Aligned_cols=36 Identities=36% Similarity=0.916 Sum_probs=26.7
Q ss_pred CCeeEEeccCCCCCCccccccccCCCC----CC-CceeEEEeCC
Q 000460 125 NDIAYRCRTCEHDPTCAICVPCFQNGN----HK-EHDYSIIYTG 163 (1482)
Q Consensus 125 ge~~y~C~~C~~d~t~~lC~~CF~~~~----H~-gH~~~~~~~~ 163 (1482)
|-+-.+|-.| |..-+|..||..|. |+ +|.|.++.++
T Consensus 26 ~~i~ikCaeC---p~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~ 66 (438)
T KOG0457|consen 26 GLIRIKCAEC---PDFDLCLQCFSVGAETGKHQNDHPYRIMDTN 66 (438)
T ss_pred cceEEEeecC---CCcchhHHHHhcccccCCCCCCCCceeecCC
Confidence 4455788888 45559999997764 64 8999998764
No 38
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=35.70 E-value=22 Score=29.15 Aligned_cols=22 Identities=27% Similarity=0.789 Sum_probs=19.8
Q ss_pred cceecCCchhhhhhhHHHHHHH
Q 000460 1391 GIHLSSCGHAVHQGCLDRYVSS 1412 (1482)
Q Consensus 1391 g~~~s~c~h~~h~~c~~~y~~~ 1412 (1482)
.+.+..|||....+|..+|+++
T Consensus 11 ~~~~~~C~H~fC~~C~~~~~~~ 32 (41)
T PF00097_consen 11 PVILLPCGHSFCRDCLRKWLEN 32 (41)
T ss_dssp EEEETTTSEEEEHHHHHHHHHH
T ss_pred CCEEecCCCcchHHHHHHHHHh
Confidence 3378999999999999999987
No 39
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=31.97 E-value=32 Score=29.00 Aligned_cols=23 Identities=30% Similarity=0.635 Sum_probs=19.9
Q ss_pred CCCcceecCCchhhhhhhHHHHH
Q 000460 1388 DCDGIHLSSCGHAVHQGCLDRYV 1410 (1482)
Q Consensus 1388 ~~~g~~~s~c~h~~h~~c~~~y~ 1410 (1482)
+.....|.+|||.+.+.|.++-.
T Consensus 11 ~~~~~~l~~CgH~~C~~C~~~~~ 33 (44)
T PF14634_consen 11 EERRPRLTSCGHIFCEKCLKKLK 33 (44)
T ss_pred CCCCeEEcccCCHHHHHHHHhhc
Confidence 55678999999999999998765
No 40
>PHA02450 hypothetical protein
Probab=28.13 E-value=36 Score=29.32 Aligned_cols=25 Identities=32% Similarity=0.858 Sum_probs=17.6
Q ss_pred CCccccCCCcccc-------cccCCCCCCCCC
Q 000460 163 GGGCCDCGDVTAW-------KREGFCSRHKGA 187 (1482)
Q Consensus 163 ~gG~CDCGD~~aw-------k~~~fC~~H~~~ 187 (1482)
-||-|.||-.-.+ .-.+||++|...
T Consensus 13 yggdc~cg~iyty~g~~epg~fdpfcpdhg~~ 44 (53)
T PHA02450 13 YGGDCTCGPIYTYGGHAEPGQFDPFCPDHGNP 44 (53)
T ss_pred eCCcccccceeeeCCcCCCCccCCCCCCCCCh
Confidence 4789999864333 236899999654
No 41
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=26.68 E-value=27 Score=32.95 Aligned_cols=21 Identities=29% Similarity=0.765 Sum_probs=17.0
Q ss_pred cceecCCchhhhhhhHHHHHH
Q 000460 1391 GIHLSSCGHAVHQGCLDRYVS 1411 (1482)
Q Consensus 1391 g~~~s~c~h~~h~~c~~~y~~ 1411 (1482)
-+=+..|||+-|..|..+++.
T Consensus 44 ~i~~~~C~H~FH~~Ci~~Wl~ 64 (73)
T PF12678_consen 44 PIVWGPCGHIFHFHCISQWLK 64 (73)
T ss_dssp -EEEETTSEEEEHHHHHHHHT
T ss_pred ceEecccCCCEEHHHHHHHHh
Confidence 345677999999999999873
No 42
>PF12043 DUF3527: Domain of unknown function (DUF3527); InterPro: IPR021916 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is about 120 amino acids in length. This domain has a conserved CDCGGWD sequence motif.
Probab=24.37 E-value=34 Score=41.50 Aligned_cols=18 Identities=44% Similarity=1.302 Sum_probs=13.6
Q ss_pred CCCccccCCCcccccccCCCCCC
Q 000460 162 TGGGCCDCGDVTAWKREGFCSRH 184 (1482)
Q Consensus 162 ~~gG~CDCGD~~awk~~~fC~~H 184 (1482)
-.||.||||. |.-. |+..
T Consensus 258 rSGG~CDCGG---WDmg--C~L~ 275 (346)
T PF12043_consen 258 RSGGSCDCGG---WDMG--CPLR 275 (346)
T ss_pred hhCCCcCCCC---cccC--CCeE
Confidence 3578999999 8865 6655
No 43
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=22.83 E-value=62 Score=38.25 Aligned_cols=34 Identities=24% Similarity=0.504 Sum_probs=27.1
Q ss_pred CCCCCCcceecCCchhhhhhhHHHHHHHHHhhhc
Q 000460 1385 GPIDCDGIHLSSCGHAVHQGCLDRYVSSLKERQV 1418 (1482)
Q Consensus 1385 ~~~~~~g~~~s~c~h~~h~~c~~~y~~~l~~r~~ 1418 (1482)
|=.|-+.+-..+|-|.+|-.|+.|||--+.+-|.
T Consensus 124 gfa~~~~ft~T~C~Hy~H~~ClaRyl~~~~~~lr 157 (368)
T KOG4445|consen 124 GFASSPAFTVTACDHYMHFACLARYLTECLTGLR 157 (368)
T ss_pred eecCCCceeeehhHHHHHHHHHHHHHHHHHHHHH
Confidence 4455566778899999999999999988766553
No 44
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=22.33 E-value=91 Score=27.28 Aligned_cols=22 Identities=36% Similarity=0.779 Sum_probs=16.6
Q ss_pred cceecCCc-----hhhhhhhHHHHHHH
Q 000460 1391 GIHLSSCG-----HAVHQGCLDRYVSS 1412 (1482)
Q Consensus 1391 g~~~s~c~-----h~~h~~c~~~y~~~ 1412 (1482)
..-++-|. |-||+.|++|++..
T Consensus 13 ~~l~~PC~C~G~~~~vH~~Cl~~W~~~ 39 (49)
T smart00744 13 DPLVSPCRCKGSLKYVHQECLERWINE 39 (49)
T ss_pred CeeEeccccCCchhHHHHHHHHHHHHH
Confidence 33455553 99999999999964
Done!