Query 000158
Match_columns 2014
No_of_seqs 334 out of 583
Neff 6.4
Searched_HMMs 46136
Date Thu Mar 28 21:10:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000158.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000158hhsearch_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 2E-118 4E-123 1177.6 67.6 1243 282-2007 371-1683(1738)
2 KOG1139 Predicted ubiquitin-pr 99.9 1.1E-28 2.4E-33 302.9 6.6 560 1415-2007 169-732 (784)
3 KOG1140 N-end rule pathway, re 99.8 1E-21 2.3E-26 263.1 -1.1 929 18-1000 532-1502(1738)
4 smart00396 ZnF_UBR1 Putative z 99.8 1.3E-19 2.7E-24 171.2 5.8 70 116-185 1-71 (71)
5 PF02207 zf-UBR: Putative zinc 99.7 1.7E-18 3.6E-23 164.2 4.1 70 116-185 1-71 (71)
6 KOG1139 Predicted ubiquitin-pr 99.0 1.3E-08 2.9E-13 127.8 18.4 185 754-938 207-477 (784)
7 PF10390 ELL: RNA polymerase I 96.9 0.00057 1.2E-08 82.5 3.9 80 869-953 198-280 (284)
8 KOG1777 Putative Zn-finger pro 94.8 0.015 3.2E-07 70.8 2.2 63 111-174 539-606 (625)
9 KOG4445 Uncharacterized conser 92.8 0.036 7.7E-07 64.9 0.4 49 1427-1477 132-183 (368)
10 PF13764 E3_UbLigase_R4: E3 ub 92.6 0.5 1.1E-05 64.4 10.8 70 1146-1229 422-497 (802)
11 PF13639 zf-RING_2: Ring finge 92.6 0.033 7.2E-07 48.2 -0.1 20 1426-1445 16-35 (44)
12 cd00162 RING RING-finger (Real 92.5 0.088 1.9E-06 44.7 2.4 19 1428-1446 15-33 (45)
13 KOG0943 Predicted ubiquitin-pr 89.3 0.11 2.5E-06 68.8 0.2 63 116-184 1241-1309(3015)
14 PF00097 zf-C3HC4: Zinc finger 85.7 0.45 9.8E-06 40.4 1.7 20 1427-1446 13-32 (41)
15 smart00184 RING Ring finger. E 84.4 0.75 1.6E-05 37.4 2.4 19 1427-1445 12-30 (39)
16 cd02340 ZZ_NBR1_like Zinc fing 84.0 0.81 1.8E-05 39.8 2.4 37 117-158 5-41 (43)
17 cd02335 ZZ_ADA2 Zinc finger, Z 83.4 0.88 1.9E-05 40.7 2.5 39 117-159 5-48 (49)
18 KOG4796 RNA polymerase II elon 83.3 1.2 2.7E-05 56.5 4.5 77 869-951 211-290 (604)
19 KOG2905 Transcription initiati 83.3 0.78 1.7E-05 53.1 2.6 62 869-931 182-245 (254)
20 PF14634 zf-RING_5: zinc-RING 82.5 1 2.2E-05 39.1 2.5 31 1425-1477 14-44 (44)
21 cd02249 ZZ Zinc finger, ZZ typ 81.9 1 2.2E-05 39.7 2.3 37 117-158 5-44 (46)
22 PF12861 zf-Apc11: Anaphase-pr 79.9 1.1 2.4E-05 44.5 1.9 22 1425-1446 46-67 (85)
23 cd02338 ZZ_PCMF_like Zinc fing 78.1 1.7 3.6E-05 38.9 2.4 38 117-159 5-48 (49)
24 cd02344 ZZ_HERC2 Zinc finger, 77.2 1.9 4.2E-05 37.9 2.4 39 117-159 5-44 (45)
25 PF00643 zf-B_box: B-box zinc 75.1 1.6 3.5E-05 37.4 1.4 37 116-158 4-40 (42)
26 PLN03208 E3 ubiquitin-protein 74.0 2.9 6.3E-05 47.7 3.5 54 1427-1486 32-87 (193)
27 KOG2752 Uncharacterized conser 73.9 3.9 8.4E-05 49.2 4.6 61 112-173 37-101 (345)
28 PF09538 FYDLN_acid: Protein o 72.3 1.7 3.8E-05 45.3 1.2 24 1932-1955 8-35 (108)
29 COG5243 HRD1 HRD ubiquitin lig 71.1 1.8 4E-05 52.5 1.2 16 1430-1445 317-332 (491)
30 KOG1940 Zn-finger protein [Gen 69.3 2.3 5E-05 51.1 1.5 35 1426-1482 175-209 (276)
31 PF11793 FANCL_C: FANCL C-term 68.9 1.8 3.9E-05 41.7 0.4 39 1428-1477 25-63 (70)
32 cd02339 ZZ_Mind_bomb Zinc fing 66.9 3.5 7.7E-05 36.3 1.7 30 126-158 13-43 (45)
33 TIGR02300 FYDLN_acid conserved 65.9 3 6.5E-05 44.2 1.3 24 1932-1955 8-35 (129)
34 PHA02926 zinc finger-like prot 60.7 6.8 0.00015 45.4 3.0 43 1427-1485 193-235 (242)
35 PF12678 zf-rbx1: RING-H2 zinc 60.5 2 4.4E-05 41.7 -1.0 17 1428-1444 47-63 (73)
36 PF13923 zf-C3HC4_2: Zinc fing 59.9 3.8 8.3E-05 34.6 0.7 20 1427-1446 13-32 (39)
37 cd02341 ZZ_ZZZ3 Zinc finger, Z 56.4 7.6 0.00016 34.8 1.9 32 126-158 13-46 (48)
38 cd02336 ZZ_RSC8 Zinc finger, Z 55.1 4.2 9.1E-05 35.9 0.2 31 117-152 5-35 (45)
39 COG2051 RPS27A Ribosomal prote 55.0 4.7 0.0001 38.1 0.4 27 1932-1958 18-51 (67)
40 cd00021 BBOX B-Box-type zinc f 54.8 9.2 0.0002 31.9 2.1 28 126-158 10-37 (39)
41 cd02343 ZZ_EF Zinc finger, ZZ 54.4 7.1 0.00015 34.9 1.4 35 117-156 5-40 (48)
42 PF13240 zinc_ribbon_2: zinc-r 54.2 7.3 0.00016 29.5 1.2 20 1935-1954 1-21 (23)
43 PF02270 TFIIF_beta: Transcrip 53.3 4.9 0.00011 48.9 0.4 44 883-930 231-274 (275)
44 KOG2114 Vacuolar assembly/sort 51.4 6.9 0.00015 52.6 1.3 23 1430-1477 858-880 (933)
45 PF10571 UPF0547: Uncharacteri 50.1 7.6 0.00016 30.3 0.8 21 1934-1954 1-22 (26)
46 cd02337 ZZ_CBP Zinc finger, ZZ 49.3 9.4 0.0002 33.0 1.3 32 116-153 4-35 (41)
47 PF13248 zf-ribbon_3: zinc-rib 49.1 8.2 0.00018 30.0 0.9 22 1933-1954 2-24 (26)
48 smart00336 BBOX B-Box-type zin 49.0 14 0.0003 31.3 2.4 29 125-158 12-40 (42)
49 PF13920 zf-C3HC4_3: Zinc fing 45.6 13 0.00028 33.2 1.7 19 1427-1445 16-35 (50)
50 smart00291 ZnF_ZZ Zinc-binding 45.6 14 0.0003 32.4 1.8 33 116-153 8-40 (44)
51 PRK00415 rps27e 30S ribosomal 45.3 6.5 0.00014 36.5 -0.2 28 1931-1958 9-42 (59)
52 KOG4172 Predicted E3 ubiquitin 45.1 9.7 0.00021 34.6 0.8 15 1428-1442 22-37 (62)
53 PF01667 Ribosomal_S27e: Ribos 44.6 5.6 0.00012 36.5 -0.7 27 1932-1958 6-38 (55)
54 cd02334 ZZ_dystrophin Zinc fin 41.9 17 0.00037 32.7 1.9 33 117-153 5-37 (49)
55 PHA02929 N1R/p28-like protein; 40.2 18 0.00038 43.1 2.2 35 1428-1484 197-231 (238)
56 PLN00209 ribosomal protein S27 39.4 7.5 0.00016 38.6 -0.8 37 1916-1958 25-67 (86)
57 PTZ00083 40S ribosomal protein 37.8 8.3 0.00018 38.2 -0.8 37 1916-1958 24-66 (85)
58 KOG0828 Predicted E3 ubiquitin 37.7 20 0.00042 45.7 2.1 29 1428-1477 603-631 (636)
59 COG5194 APC11 Component of SCF 35.3 35 0.00076 33.6 2.9 26 1421-1446 44-69 (88)
60 COG4031 Predicted metal-bindin 34.9 18 0.00039 40.6 1.1 19 1935-1954 2-20 (227)
61 cd02345 ZZ_dah Zinc finger, ZZ 33.7 28 0.00062 31.3 2.0 31 116-151 4-35 (49)
62 PF05191 ADK_lid: Adenylate ki 33.6 16 0.00035 30.8 0.4 22 1933-1954 1-29 (36)
63 PF00569 ZZ: Zinc finger, ZZ t 32.8 11 0.00024 33.3 -0.7 36 117-156 9-45 (46)
64 KOG0457 Histone acetyltransfer 29.0 41 0.00088 42.8 2.9 42 118-163 20-66 (438)
65 PF15353 HECA: Headcase protei 27.7 44 0.00095 34.7 2.3 20 1431-1450 40-59 (107)
66 PF07800 DUF1644: Protein of u 27.5 42 0.0009 37.3 2.3 43 1435-1477 37-88 (162)
67 KOG0827 Predicted E3 ubiquitin 24.6 48 0.001 41.4 2.3 19 1428-1446 23-41 (465)
68 PF10367 Vps39_2: Vacuolar sor 24.2 15 0.00032 37.8 -1.7 15 1428-1442 95-109 (109)
69 COG5114 Histone acetyltransfer 23.0 57 0.0012 39.5 2.5 33 126-162 18-56 (432)
70 PF08271 TF_Zn_Ribbon: TFIIB z 22.8 31 0.00067 30.0 0.2 25 1934-1958 1-31 (43)
71 PF09237 GAGA: GAGA factor; I 22.3 21 0.00046 32.3 -0.8 23 1937-1959 15-37 (54)
72 PF02148 zf-UBP: Zn-finger in 22.0 72 0.0016 30.0 2.6 47 1936-1989 1-48 (63)
73 KOG0309 Conserved WD40 repeat- 21.7 44 0.00095 44.7 1.3 18 1428-1445 1045-1062(1081)
74 TIGR00570 cdk7 CDK-activating 21.6 57 0.0012 40.2 2.2 17 1428-1444 23-39 (309)
75 PRK02935 hypothetical protein; 21.0 34 0.00074 35.3 0.2 22 1933-1954 70-94 (110)
No 1
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2e-118 Score=1177.60 Aligned_cols=1243 Identities=22% Similarity=0.322 Sum_probs=789.9
Q ss_pred hccCCCHHHHHHHHHHHH-HhhCChhhHHHHHHHHHhhhHHHHHHHHHhccCcccccCCcccceeeeccccCCcHHHHHH
Q 000158 282 AEMFSSDVVVRKLHELLL-KLLGEPIFKYEFAKVFLSYYPVFVKDAIREHSDDTIKKYPLLSTFSVQIFTVPTLTPRLVK 360 (2014)
Q Consensus 282 ~~~~l~k~~r~~Lh~Lll-sLL~d~efK~~FA~~Fv~~Y~~i~~~fl~~d~d~~~~~~s~v~~lSVQLFTvPslA~~LV~ 360 (2014)
.+..+||..|.+++.++. .+-++.+||+.|+.+|+.+|..+..+++.+|++.. .+.| .++||+||+|++|..+++
T Consensus 371 ~d~~~~kr~r~~l~k~~~~~~~~~~~~k~~~~~~~~~~y~~~~~~~~~~d~e~~---~~vi-~~~vqf~t~~~~a~~~~~ 446 (1738)
T KOG1140|consen 371 FDNRYWKRLRKDLQKVIIPTFASSNLYKPIFAQQFVEHYNSITRDFAYMDREPD---LSVI-ELSVQFFTCPSLAKNIVE 446 (1738)
T ss_pred HHHHHHHHHHHHHhhcceeehhcchHHHHHHHHHHHHHHHHHHHHHHhhcCCcc---hhhH-hheeeeecCcHHHHHhhh
Confidence 334457889999999999 67789999999999999999999999999988743 3545 999999999999999999
Q ss_pred hhcHHHHHHHHHHHHhhhhcCCCCcceec---------cccccccchhhhhhhhhHhhcchhhhHHHhhhchHHHHHHHH
Q 000158 361 EMNLLEMLLGCLREIFDSCAGDDSCLQVA---------KWANLYETTNRVIGDIRFVMSHAAVSKYATHEQLNISKAWMK 431 (2014)
Q Consensus 361 e~nLL~ill~tl~~~~~~~~~~~~~l~~~---------~~~~~~~~~~~i~~DLryvLsh~~v~~~l~~~~~~l~~~~l~ 431 (2014)
...++..+..++..++..+...++...+. +.....++.+..+.|+ +.+.++.+ -.++..+..++.
T Consensus 447 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~r~l~~~~~l-~~~~~~~~-----~~~~~~~~~~l~ 520 (1738)
T KOG1140|consen 447 NQSFLDIVWSIIDIFKEFNKVEGGVLIDIRVQKSNLLKRYSISFRRTLYTFEDL-SKVHDPNI-----PLRPKEFISLLL 520 (1738)
T ss_pred hccchHHHHHHHHHHHHhcccccceecceeeeechhhhHHHHHHHHHHHHHHHh-hccCCccc-----cccHHHHHHHHH
Confidence 99988888877776665444322221111 1222357777788888 77666662 357899999999
Q ss_pred HHHHhcCCCcccccccCcceeeCCceeehhhhhhHHHHhHHhhhhhccccccccccccccccccccCCCCCccccccccc
Q 000158 432 LLTFVQGMNPQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEETRYDFSMYKQDIGDGDSLRHAKVGR 511 (2014)
Q Consensus 432 lL~~~QGMn~~kRq~~~HVEyE~e~w~~aF~L~~~la~i~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~r 511 (2014)
++..||||.|++|+.++||++|++ |+.+|.+-.++..+++.++.||..... +-
T Consensus 521 ~~~v~qg~~~lkr~~~ehv~~e~~-~~~~~~~v~~~t~~~s~i~~~~~~~ep-------------------------~~- 573 (1738)
T KOG1140|consen 521 LLKVFQGVDPLKREELEHVEVEKE-WENFFSLVEYLTAIYSMIQSLVKTSEP-------------------------VK- 573 (1738)
T ss_pred HHHHhCCccHHHHHHhhhhcccch-HHHHHHHHHHHHHHHHHHHHHHHhccc-------------------------hh-
Confidence 999999999999999999999997 999999999999999999998866530 00
Q ss_pred cccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhhhcCCCCcccccccCCCCcccccCchh
Q 000158 512 LSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENWLGVDDRSVSVNDILSPNASRISGSNF 591 (2014)
Q Consensus 512 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~cl~~l~~~l~~~~~~~~~~~~~s~~~~~~~~~~~ 591 (2014)
..++..|+-++.... .. -
T Consensus 574 ----------------------------------------~~~~~~l~~~~~r~~------~s------~---------- 591 (1738)
T KOG1140|consen 574 ----------------------------------------DSVYKKLLEAAIRIH------PS------L---------- 591 (1738)
T ss_pred ----------------------------------------hhHHHHHHHHHhhcc------cc------c----------
Confidence 001111221121110 00 0
Q ss_pred hhhHhhhhhccccccccccccCCccccccccccCCCccccccCccccccccCCcccccccccCcCCccccccchhccccc
Q 000158 592 VALKKTLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKITISGERDTASWRSAGFNDSEMEGECATELDNL 671 (2014)
Q Consensus 592 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 671 (2014)
+++ +. + ...+++++.
T Consensus 592 --------------------~~~---------------------~~---l---------------~~~i~~~S~------ 606 (1738)
T KOG1140|consen 592 --------------------TGS---------------------ES---L---------------TYTICGESH------ 606 (1738)
T ss_pred --------------------Ccc---------------------ce---e---------------eehhhhhhH------
Confidence 000 00 0 011223322
Q ss_pred cccccCccCceeeeccCCceeeehHHHHHHHHHHHHHHhhhcccCccccccccCCCCCccccchhhhhcccCCCCCcccc
Q 000158 672 HVLSLCYWPDITYDVSSQDVSVHIPLHRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFS 751 (2014)
Q Consensus 672 ~~~~~~~~~~v~fdVs~~~VSfH~PLhr~Ls~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 751 (2014)
.++.|+|+..+||||.|+.|+|+.+++..... ++...+.+. .+.+.+. .
T Consensus 607 --------e~i~f~v~~~~~sv~~p~~~~l~~l~~~~~s~-------------------v~~~~d~~~-~~~~~~n---~ 655 (1738)
T KOG1140|consen 607 --------ETINFSVSQERVSVSNPVSRLLAFLIELSCSS-------------------VVSLKDAYE-RLEDCSN---F 655 (1738)
T ss_pred --------hHhhhccccccceeeccHHHHhhhhhhcccch-------------------hhhcchhhh-hHhhhcc---c
Confidence 57899999999999999999999998532110 011111111 1122221 2
Q ss_pred hhhhcccHHHHHHHHHHhhCcccccchhHhHHHHHhccccccccccchhHHHHHHHHhhCChHHHHHHHHHHhccccccc
Q 000158 752 AFVMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLS 831 (2014)
Q Consensus 752 ~~l~e~pLR~~Vl~aQI~aGmWvRNG~sl~~Q~~~Y~~~~~r~~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~ 831 (2014)
.+|.|||||++|++|||.+|||||||.++.+|+.+|++.++|+++|++||+++|.++++.||++|+.++++||+|.+|++
T Consensus 656 ~~i~e~~lr~~Vl~aqid~~~w~rNG~si~~q~~~y~~~~~r~~~y~~DI~~~Q~~la~~d~~~~l~~~l~r~~L~~w~~ 735 (1738)
T KOG1140|consen 656 LAISEHSLRVLVLCAQIDVGFWVRNGFSILHQAAYYKNNPCRNESYDRDILMLQTGLAMEDPNRFLFTILSRFELLDWFT 735 (1738)
T ss_pred hhhcccchhheeeeeecceeeEeecCcchhhhhHhhcCccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhc
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCC-ch---hHHHHHHHHHHHHHhhcccccCC---ChHHHHHHHHHHHHhcCCCChHHHHHhCCCCCCCcchHHH
Q 000158 832 LNLERPSE-YE---PILVQEMLTLIIQILQERRFCGL---TTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQE 904 (2014)
Q Consensus 832 ~~~~~~~~-y~---~~~vEe~L~lLI~llteR~~~g~---s~~e~lr~eIIh~Lc~~p~t~S~L~~~lpe~~~~~~~fe~ 904 (2014)
+....... ++ ..|+|+|+.+||.|++||...|+ +..+.+|+||||+||++|++||+|.+++|+++.++..||.
T Consensus 736 g~~~~~~~d~~~~i~~~~ee~l~lii~ll~Er~~~~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~~d~ 815 (1738)
T KOG1140|consen 736 GEVDYQSNDTEDTISFMIEEFLALIILLLTERSYFGSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLSFDE 815 (1738)
T ss_pred CCCccccccHHHHHHHHHHHHHHHHHHHHHheeecccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhcccchH
Confidence 98654332 22 37999999999999999996554 5678999999999999999999999999999999999999
Q ss_pred HHHHHccccCCCCC-CcceEEeehhhhccccccccccCchhHHHHHHHHHHh--hc---cccccCC-CCCCccccC-Ccc
Q 000158 905 ILDAVAMYSHPSGF-NQGMYSLRWSYWKELDIYHPRWSSRDLQVAEERYLRF--CS---VSALTAQ-LPRWTKIYY-PLE 976 (2014)
Q Consensus 905 iL~eVA~f~~P~g~-~~G~Y~LK~e~~~e~dpy~~~y~~~~~q~aeer~~~~--~~---~~a~~~~-~P~~~~~~~-~f~ 976 (2014)
++++||+|++|.++ +.|+|+||++||+++||||+||++.++.+++..+++. ++ ..|..+. .|++...+. .+.
T Consensus 816 ~~e~Va~~~~p~~~~~~gvf~lK~~~~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~~~~ 895 (1738)
T KOG1140|consen 816 ALEEVAVFKKPKGLADNGVFVLKESYYDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKKGAD 895 (1738)
T ss_pred HHHHHHhhccCCccccceEEEechhhhhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHHHHH
Confidence 99999999999999 6799999999999999999999999998887655432 11 1133322 233333221 234
Q ss_pred chhhccccHHHHHHHHHHHHHHhccCCCCCCCCchhHHHHHHHH-HHHHHhhhhhhccCCCCCcccCCCcccccchhhHH
Q 000158 977 SIAGIATCKVVLQVIRAVLFYAVFTDNPTDSRAPYGVLLTALHL-LALALDVCFQKKKSGDQSCDIGGSTPILDFASEEI 1055 (2014)
Q Consensus 977 ~i~~il~s~~~~~il~~vL~~al~~~~~~~~~~~E~~L~~~LHL-i~lal~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~ 1055 (2014)
++.+.....+|-.||+.++.++.+.. .+.++..++|+ ++.|++++..--. |.+... ++
T Consensus 896 ~L~~~t~~~~~~~ii~r~~~~~~~~~-------s~~~l~~~~~~ihG~~~~~~l~~~~-----------~~~~~~-~e-- 954 (1738)
T KOG1140|consen 896 ILGAAVRLTVFGLIIYRTLEHCLFME-------SSTLLSKVLHLIHGIALNEELINMK-----------FAFTQK-TE-- 954 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhcc-----------cccccc-cc--
Confidence 55566666677777777777777543 48999999955 5999986442110 100000 00
Q ss_pred hhccCCCCCcccHHHHHHHHHhhhcccCCccccccccCCchhHHHHHHHHHHhhhHHHHHHHhhhchhhhhcccCCCCCC
Q 000158 1056 AEGLNNGAGKQSLLSLLVFLMGMYKKDGADNFLEAGNCNLSSVIESLLKKFAEIDSRCMTKLQQLAPEIVSHLSQSLPRD 1135 (2014)
Q Consensus 1056 ~~~~~~~~~~~SllsLL~~L~~~~~~~~~d~~~e~~~~~i~~~I~~lL~~f~~~~~~c~~~i~~~~~~~~~~~~~~~~~~ 1135 (2014)
.....+.+.+++.+..++....+ +.++.|+++.|..+.. .+...|++.. .+.. ...
T Consensus 955 ------~~~~e~gl~~~e~lv~~~~~~~~-----------~~~~~v~~~l~~~~~~-----~~~n~~ea~~-~~~~-~~~ 1010 (1738)
T KOG1140|consen 955 ------SIAREKGLSLYESLVRKPDSLVH-----------GKIIEVIVELFESLIK-----SRANDPEVAN-DEKD-KKE 1010 (1738)
T ss_pred ------ccccccchhhHHHhhhcchhhcC-----------CcceeeeHHHHhhhhh-----hhcCCccccc-cccc-ccc
Confidence 11345577778877777554332 4578888888876544 2344443321 1100 011
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCccCCCCccccccccCCCCcccccCCCC-
Q 000158 1136 DTSGSFSASDSEKRKAKARERQAAILEKMKAEQFKFLSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS- 1214 (2014)
Q Consensus 1136 ~~~~~~~~~e~ekKK~~AkeRQakIMAQm~~QQk~Fl~~n~~~~de~d~~~~e~~~~d~~~~~~e~~~~~CiLCqe~~s- 1214 (2014)
..+.+.++.+.++||++|++||+|+||||+.||.+||++|.+++|++++..++ +...+..+ ...+|.+|+....
T Consensus 1011 ~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e~d~~~~~~~~---~~~~~~~~--~d~~~~~~~~~s~~ 1085 (1738)
T KOG1140|consen 1011 KQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDEFDEQENQTPS---SGSKTYEE--EDFTCALCQDNSCT 1085 (1738)
T ss_pred ccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccccCcccccCcc---ccccchhh--hhccchhhhccchh
Confidence 12234444556788889999999999999999999999997666554332111 11011111 1356777764322
Q ss_pred CCCeEEEEeeecccccccccCCCCCccccccccccccccccccccccCCCCCCCCCCCccchhhHHHHHHHHHhhhccCC
Q 000158 1215 RTPVSYLILLQKSRLLSFVDRGSPSWDQDQWLGKECGTISANNMVNQFGTNTPSSGLGVISSCQLAQVAEEAVNQFAYNG 1294 (2014)
Q Consensus 1215 ~~p~G~la~iq~S~il~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~a~~~~~~~~ 1294 (2014)
+.+. +++..+..
T Consensus 1086 ~~~~------~~~~~~~~-------------------------------------------------------------- 1097 (1738)
T KOG1140|consen 1086 DFQV------KPASHLVK-------------------------------------------------------------- 1097 (1738)
T ss_pred cccc------ccchhhhc--------------------------------------------------------------
Confidence 1111 11111100
Q ss_pred CchhhhhHHHHhhhcCCCCcccCCCcCcCCCCcCCcchhhhhhhhhhhHHHHhhhccCCCCCCccccchhhcccCCcccC
Q 000158 1295 KPEEVNSVLEFVKAQFPSLRNIPIPFTFSNGRKCTASSMEMFEQDLYLSICREMRKNMTYPDLMKEDEECSVAEGGLKNR 1374 (2014)
Q Consensus 1295 r~~e~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~s~~~~~e~~~~~~~~~~~~~~ 1374 (2014)
....+||.| ||++.+..
T Consensus 1098 -------------------------------------------~~~~~~~i~------------~e~e~~~~-------- 1114 (1738)
T KOG1140|consen 1098 -------------------------------------------PIFRECIIC------------DENEDVPN-------- 1114 (1738)
T ss_pred -------------------------------------------ccccccccC------------ChhccCCC--------
Confidence 001234445 23333321
Q ss_pred CCCcchhhhhhhhhhhHHhhhcccccccccccchhccccccCCCCC-CCCCCccccccchHhhHHHHHHHHHHHHHhhhh
Q 000158 1375 GNSDSFLLGKYVASISKEMRENASASEVSRGDRIAAESLVYDGFGP-IDCDGIHLSSCGHAVHQGCLDRYVSSLKERYNR 1453 (2014)
Q Consensus 1375 ~~~~~~~l~~f~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~F~p-~~~~G~H~SsCGH~MH~~C~~~Y~~Sl~~R~~~ 1453 (2014)
..++.++..+|.++ ++. +..+++.| ....|+++|+|||.||+.||++|+.+.+.|.+.
T Consensus 1115 ~~~~~~v~~~f~~~-s~~--------------------~sd~l~~p~~~~~~~~~s~c~h~mh~~c~~~~~~a~r~~~n~ 1173 (1738)
T KOG1140|consen 1115 WDGRYSVSSAFAQK-SDD--------------------VSDALTEPGSLSCGTVLSSCGHHMHYGCFKRYVQAKRFRENA 1173 (1738)
T ss_pred ccccchhhhHhhhh-ccc--------------------ccccccCCCCCcccceeeccCCcchHHHHHHHHHHHHHHHHh
Confidence 12234466777776 221 12445544 567999999999999999999999999999998
Q ss_pred ccccCCCCccCCCCCccccccccccccceeccCCCCcccCCCCCcccCCCCCCCCCCccccccchhhHHHHHH-------
Q 000158 1454 RIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRINEQPTVSGVGLSLDSSSSFTTREENTSFQLQQA------- 1526 (2014)
Q Consensus 1454 R~~~er~h~~d~e~gEFLCPLCK~L~N~vLPi~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------- 1526 (2014)
+....+.|.- ++|+|+||+||+|+|+++|..++.....++. +. ........|++..
T Consensus 1174 ~~~~l~~~~s--e~~l~lCp~c~slsn~~lp~~~~~~~~~n~~---t~------------~~~~n~~~~i~~rs~~~~s~ 1236 (1738)
T KOG1140|consen 1174 RTAPLCQHYS--ENGLFLCPLCKSLSNVSLPMFLPPELLLNPL---TL------------ENQRNLNSWIEKRSRASFSL 1236 (1738)
T ss_pred hhcCcccccc--cCCcccCCchHhhhhccCCcCCchhhhcChh---hh------------hchHHHHHHHHHhchhhcch
Confidence 8776666654 8999999999999999999764433322210 00 0011222233310
Q ss_pred --HHHhhhcccc-cC---cccccccCC-cchhhHHHHhHHHHHHHHHHHhhcc------ccccccCCCCCchhHHHHHHH
Q 000158 1527 --VSLLQSASNV-VG---KADVIESFP-LMKNEIMASNVEAVSRRMCKMYFQN------KLDKFFGSARVNPSLIMWDAL 1593 (2014)
Q Consensus 1527 --~~~~~~~~~~-~~---~~~~~~~~~-~~~~~~~~~~l~~~~~~l~~~~~~~------~~~~~~~~~~v~~~~~lw~t~ 1593 (2014)
++..-+.... .. ..++ ++.. .++.+.....++.+.+.+...++.. ......++++. .....|..+
T Consensus 1237 ~~vs~~~s~~~~~~~ss~i~e~-kp~~~~~l~~~~~~~ie~~~k~v~s~~~k~~~~i~~~~le~~~~~~~-~~~~~~~~~ 1314 (1738)
T KOG1140|consen 1237 QDVSSILSDPWAAFTSSRIPEL-KPILIMDLPDSVVEQIELFQKIVGSAMFKPSSLLSTNTLELTLFSRE-FLIVCWQSL 1314 (1738)
T ss_pred hhhhhhhcccchhhcccccccc-ccchHhhhhhHHHHHHHHHHHHHhhheeecccceeecccccCcccch-hhhhhhhcc
Confidence 0000000000 00 0000 0000 0111111111222222222222111 11223334553 567789999
Q ss_pred hHhHHHHHHHhhccCCCCCCccchhhHHHhhccchhHHHHHHHHHHHhhccchhHHHHHHHhhhhhhhhhccCCCCCCCC
Q 000158 1594 KYSLMSMEIAARSEKTSTTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVLQRFRGIQLFAESICSGTSIDNP 1673 (2014)
Q Consensus 1594 aYTI~s~Eia~Rg~~~~~~~~~~~~~L~~~l~~~~~~~l~~l~~~~~~~r~~~~l~~l~r~~~~qL~~~s~~~~~s~~~~ 1673 (2014)
++..+++++.+-+.+.+ ++..+.+...+.++...++..+.+..-.++..+-+ .+++|...+.+ ..
T Consensus 1315 s~a~~~~~~~l~~~~~~---------~~l~l~~~~~~~~~~~~~l~~~~~~~~l~~~~~~~-llk~~s~~~~~----i~- 1379 (1738)
T KOG1140|consen 1315 SDAEQSTKLLLSASKKP---------SFLKLNEDMTFCLVTISRLRALHWEQILYELVYTF-LLKSFSPTIPR----IS- 1379 (1738)
T ss_pred chHHHHHHHHHhccCCc---------ccccCchhhHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHhhcCCc----ch-
Confidence 99999999876655442 23334444444544444444433333222222222 12333211111 00
Q ss_pred CCCcCCCCCcccccccccccCCccccccccccCCCccccchhHHHHHHHhhccccccccchhhhhHHHH-HHHHHHHHH-
Q 000158 1674 GGRCKRGGNMLSILKHADVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFILCKESLLSLVHV-FYAVTLSQA- 1751 (2014)
Q Consensus 1674 ~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~plL~~D~F~~Lv~~~~~lP~p~~~~~~~~~~lv~L-~y~a~ivQ~- 1751 (2014)
.+.++ | ..+.. ++..-|+.++-+..+-+-.+ ...-....++++ .-+++++|.
T Consensus 1380 ------~~~tp-------------d--~~~~~---ll~~l~~~~~~~~~l~~~~~--~~~~~~~~~~~~~i~~~~i~s~e 1433 (1738)
T KOG1140|consen 1380 ------VLITP-------------D--QPENE---LLVILPHDFPKSLELELTLD--FVNKNPKKIFELKILMASIISIE 1433 (1738)
T ss_pred ------hccCC-------------C--CCcch---hhhccchhhhhhccHHHHHH--HhhhhHHHHHhHHHHHHHhhhhh
Confidence 00000 0 00000 11111111111110000000 011233344444 444566666
Q ss_pred HHHhcccccccc--ccccc-hhh---HHHHHHHHhcccCcccccccccCCCChhhHHHHHHHhhhhHHHHHHHHHHhhhC
Q 000158 1752 VLSCCGKLQSKV--NELGF-SDS---LISDISKLLGEFGSAQEYFVSNYIDPSCDIKDMIRRLSFPYLRRCALLWKLLNS 1825 (2014)
Q Consensus 1752 ll~~~~~~~~~~--~~~~~-~d~---l~~~i~~~~~~~~~~~~~~~s~~~d~~~~l~~~v~k~~LPFLRraALL~~~l~g 1825 (2014)
+++.......+- ++... .+. +.+.+.+..+. ++.......-....++..++++++|||||+|++.|++++
T Consensus 1434 lits~s~l~~d~~~~~~q~s~~e~~~~~t~l~~~~s~----~~i~~~~~~~~~~~L~~~~~~~i~sfL~~~al~~h~ln~ 1509 (1738)
T KOG1140|consen 1434 LITSHSYLENDLEMAEEQKSIDEFKSLLTYLLQLESS----RTIPKLADIRLRLSLCLSCEAGILSFLRRAALFKHLLNN 1509 (1738)
T ss_pred hheeccccCCccchhhhhhhHHhHhHHHHHHHhccch----hhCccccchhhhhHHHHHHHHHHHHHHHHHHHhhhhhhc
Confidence 344332221110 01010 011 11111111111 110000001113468899999999999999999999999
Q ss_pred CCCCCCCCccccccccccCccCcCCCccccccchHHHHHHHHhcCCCChhhhh-hh--HHHHHHHHHhhhccccchhhhh
Q 000158 1826 TVPPPFSDRDHVLARSSHGISDMMDSSDDALSDLKEIQEVEKMFKIPSLDVIL-KD--EVLRSLVLKWFHHFSKEFEVHR 1902 (2014)
Q Consensus 1826 v~~p~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~E~~rLc~~L~LPsl~~ll-~~--~~~~~Lv~~Wc~h~~~~~~~~~ 1902 (2014)
+.+|... | .+. ...+|+..||+|+++|++...+ +. +.++.++.+||.-.........
T Consensus 1510 v~~p~~~-----f-------~~~--------~~~s~~e~L~ty~slp~l~~~~~q~~~delr~~~~~~~~~~~~lk~~~~ 1569 (1738)
T KOG1140|consen 1510 VFPPFGA-----F-------LDP--------SSNSELEHLCTYLSLPNLQACLLQSSGDELRQAIERWCGGTENLKREEH 1569 (1738)
T ss_pred CCCchhh-----c-------cCc--------ccchhhhhhcccccCccHHHHHHhhhHHHHHHHHHHhhccchHHHHHHh
Confidence 9988311 1 000 1125889999999999877644 33 7899999999887443222111
Q ss_pred cccccccCCCCcccccCCchHHHHHHHHHHhcccCCCCCCC-CCCcchhccccc-cCCCCCcCCCc-------chHHHHH
Q 000158 1903 FQHVLYSTPAVPFKLMCLPHLYQDLLQRYIKQCCSDCKSVL-DEPALCLLCGRL-CSPSWKPCCRE-------SSCQSHA 1973 (2014)
Q Consensus 1903 ~~~~~~~~p~~~~~Li~LP~~yd~L~~~~~~~~Cp~c~~~p-~dPalCL~CG~l-c~qs~~~CC~~-------GeC~~Ha 1973 (2014)
+.......|..++.|++||++|+.++++++.+.|++|++.+ .-|++||+||.. |+| ++||++ |+|++||
T Consensus 1570 ~~~~~~i~~r~~~~l~~lpd~~s~lI~s~~~~~c~~~~~~~s~~p~lCl~cg~~~~~q--~~~~~~~~~~~~~g~~~~ha 1647 (1738)
T KOG1140|consen 1570 YLNTLSINPRIPNSLVELPDEYSCLINSASFFFCPKSGKDDSIIPALCLLCGSEECGQ--SGFDQEGSNGESVGACTAHA 1647 (1738)
T ss_pred hcceeeecCCCCCccccCCchhhhhHHhhhcccCcccCCccccCchHHhhcchHHhhh--hhhhhccccccchHHHHHhH
Confidence 11122334556789999999999999999999999999986 999999999995 777 589953 8999999
Q ss_pred hhcCCCeEEEEEeccceEeEeeC--Ccceeeecccc
Q 000158 1974 VACGAGTGVFLLIRVFSAPSFNR--KLNIIVLCVYC 2007 (2014)
Q Consensus 1974 ~~CGagvGIFL~IR~~~v~~~~~--~~~~~~~~~~~ 2007 (2014)
..||+++||||.+|+|+++++.. .+|||-+.+|+
T Consensus 1648 ~~c~~~vgifl~v~~c~~~ll~~m~~~g~~~~~pyl 1683 (1738)
T KOG1140|consen 1648 AECTGAVGIFLRVRECSILLLEGMRNRGCFYPAPYL 1683 (1738)
T ss_pred HhhcceeceEEeeechhhhhhhcCCcCCCcCCCCcc
Confidence 99999999999999999999966 99999999996
No 2
>KOG1139 consensus Predicted ubiquitin-protein ligase of the N-recognin family [Posttranslational modification, protein turnover, chaperones]
Probab=99.95 E-value=1.1e-28 Score=302.95 Aligned_cols=560 Identities=10% Similarity=-0.078 Sum_probs=392.5
Q ss_pred cCCCCCCCCCCccccccchHhhHHHHHHHHHHHHHhhhhccccCCCCccCCCCCccccccccccccceeccCCCCcccCC
Q 000158 1415 YDGFGPIDCDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRIN 1494 (2014)
Q Consensus 1415 ~~~F~p~~~~G~H~SsCGH~MH~~C~~~Y~~Sl~~R~~~R~~~er~h~~d~e~gEFLCPLCK~L~N~vLPi~P~~~~~~~ 1494 (2014)
+++|.+..+.+.|.++|+|+.|.+|..+|+.....+-..+-.|++.|..|..++++.||.|++++|+|.|.+|++.....
T Consensus 169 yD~fv~h~q~~~asTsi~hf~~dsv~~r~l~eell~wg~~ylf~~~ev~rll~~g~~~~~c~alAKvveq~y~~~~~s~~ 248 (784)
T KOG1139|consen 169 YDRFVDHIQSQHASTSITHFTEDSVRSRLLNEELLIWGLLYLFLRIEVARLLINGNMWVRCGALAKVVEQIYSQWNVSSA 248 (784)
T ss_pred CCcceecccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHhcCCCccccHHHHHHHHHhcccchhccc
Confidence 46677777889999999999999999999999999988888899999999999999999999999999999977654222
Q ss_pred CCCcccCCCCCCCCCCccccccchhhHHHHHHHHHhhhcccccCcccccccCCcchhhHHH--HhHHHHHHHHHHHhhcc
Q 000158 1495 EQPTVSGVGLSLDSSSSFTTREENTSFQLQQAVSLLQSASNVVGKADVIESFPLMKNEIMA--SNVEAVSRRMCKMYFQN 1572 (2014)
Q Consensus 1495 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~~~l~~~~~~~ 1572 (2014)
. .+..+...+..+ .....++|+.+.+..+..++......+..+..+++...-.. ....++.++.+..+++.
T Consensus 249 k-krhePdt~~~r~------~hi~~slfl~e~la~~~~~ec~~~di~r~v~~~p~~s~L~~~~~~~~~~~k~~~~~Hsr~ 321 (784)
T KOG1139|consen 249 K-KRHEPDTIRFRA------AHIDKSLFLKELLASFNITECIKIDIGRFVEKSPESSILFQETEVTIDFTKQSPIDHSRD 321 (784)
T ss_pred c-cCCCCchhcccc------ccccHHHHHHHHHHHhhhhhhhhhhccceeEeccccccchhhhhhhccccccCchhcccC
Confidence 1 111110000010 01246778887776655554432211111111222111111 22233444444333332
Q ss_pred cccccc-CCCCCchhHHHHHHHhHhHHHHHHHhhccCCCCCCccchhhHHHhhccchhHHHHHHHHHHHhhccchhHHHH
Q 000158 1573 KLDKFF-GSARVNPSLIMWDALKYSLMSMEIAARSEKTSTTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVL 1651 (2014)
Q Consensus 1573 ~~~~~~-~~~~v~~~~~lw~t~aYTI~s~Eia~Rg~~~~~~~~~~~~~L~~~l~~~~~~~l~~l~~~~~~~r~~~~l~~l 1651 (2014)
....+- +--+......+|++++|...+.|+--|--+-+.-+..|...+...+++..+.+++++.+++...+..+..++-
T Consensus 322 p~~~~l~~f~~p~lEaa~~d~l~~v~~~~e~~~R~~~~s~vlr~~~~~~~e~~~~~~~~~f~l~~~~v~~s~~~~ai~~~ 401 (784)
T KOG1139|consen 322 PRIPILGEFIRPHLEAAGVDALIDVEMEREFDPRLFDDSEVLRTIVIREPEWIDPMFWGMFKLVAELVVVSVNSGAIPEE 401 (784)
T ss_pred cchhHHHHhhccccccccCchHHHHhhhccccccccchhhhhHHhhhccccccchhhcchHHHHHHHhhhhcccccchHH
Confidence 111100 0011123456799999999999999998877777788889999999999999999999999999999999999
Q ss_pred HHHhhhhhhhhhccCCCCCCCCCCCcCCCCCcccccccccccCCccccccccccCCCccccchhHHHHHHHhhccccccc
Q 000158 1652 QRFRGIQLFAESICSGTSIDNPGGRCKRGGNMLSILKHADVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFIL 1731 (2014)
Q Consensus 1652 ~r~~~~qL~~~s~~~~~s~~~~~~~~~~~~~~~~il~~~~~~~~~~~~~~~~~~~~plL~~D~F~~Lv~~~~~lP~p~~~ 1731 (2014)
+++.++.-+|++++.+.+...++... ..+.....++.+ .-.|+....|++.+|||..++|.++++|.++..
T Consensus 402 ~~~~em~n~~a~~~~~~s~~~aS~~~-~~~~~~~~f~~i--------~~~~~~~~~P~~~~~p~~~~s~~l~~~~~~~~~ 472 (784)
T KOG1139|consen 402 HYRSEMVNCMAMGNVPYSRLRASISE-KGSMIDKHFETI--------LNEIGDFIEPIETTTPLMQGSYQLKTSIWDSEV 472 (784)
T ss_pred HHHHHHHhHHHhcCCCcccccccccC-CCcccccccccc--------cccccccccchhhcCccccchhhccccCCcccc
Confidence 99999988899888877776653222 222222222222 235788999999999999999999999999999
Q ss_pred cchhhhhHHHHHHHHHHHHHHHHhccc-cccccccccchhhHHHHHHHHhcccCcccccccccCCCChhhHHHHHHHhhh
Q 000158 1732 CKESLLSLVHVFYAVTLSQAVLSCCGK-LQSKVNELGFSDSLISDISKLLGEFGSAQEYFVSNYIDPSCDIKDMIRRLSF 1810 (2014)
Q Consensus 1732 ~~~~~~~lv~L~y~a~ivQ~ll~~~~~-~~~~~~~~~~~d~l~~~i~~~~~~~~~~~~~~~s~~~d~~~~l~~~v~k~~L 1810 (2014)
+..++...++.+.-+-.+|+...++.. ...+. .-++..... |+...+...|.+ ++|.+...+...+....++++-+
T Consensus 473 c~~~~~~~~~s~~~~~~v~~~~~~~a~k~s~d~-~l~~~~~~e-d~s~~lr~~g~s-~l~~~l~~~~~~d~~dt~~~~~~ 549 (784)
T KOG1139|consen 473 CPVFFMMRSTSIKQAREVFAKMEIRAQKNSLDK-DLEVAKIEE-DFSDQLRHRGIS-NLYNVLLTERFLDHCDTVLASEA 549 (784)
T ss_pred ccchheeeeeeccchhHHHHHHHHhhccchhhh-hccccchhH-HHHHHHHHhhhH-HHhhhhhhhhhhcccchhhcccc
Confidence 999999999999999999999987542 11111 011111111 222222222221 22333333334567888999999
Q ss_pred hHHHHHHHHHHhhhCCCCCCCCCccccccccccCccCcCCCccccccchHHHHHHHHhcCCCChhhhhhhHHHHHHHHHh
Q 000158 1811 PYLRRCALLWKLLNSTVPPPFSDRDHVLARSSHGISDMMDSSDDALSDLKEIQEVEKMFKIPSLDVILKDEVLRSLVLKW 1890 (2014)
Q Consensus 1811 PFLRraALL~~~l~gv~~p~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~E~~rLc~~L~LPsl~~ll~~~~~~~Lv~~W 1890 (2014)
||+|+|+..++.+...+... ....+++......++++|+......+++.--+.+..+..||.+++.. .+-.+-|
T Consensus 550 ~~~~~c~~~~~~la~~~~tl-~~e~~~s~~~~~~i~~~m~~I~~~pf~l~~kq~~~~~~~i~~i~e~~-----~k~~e~~ 623 (784)
T KOG1139|consen 550 DETAKCHDGTYQLAVYLLTL-GVEYAQSYVGDEKIKKQMIDIFHTPFQLILKQTRKNGALIVVIKEGK-----LKREELR 623 (784)
T ss_pred chhhhHHHHHHHHHHHHHHH-hhhhhhhhcCCcchhhhhhhccCCchhhhHHHHHhcccCCchhHHHh-----HHHHHHH
Confidence 99999999999887644331 22335555556677888888887777777788889999999988643 3345679
Q ss_pred hhccccchhhhhcccccccCCCCcccccCCchHHHHHHHHHHhcccCCCCCCCCCCcchhccccccCCCCCcCCCcchHH
Q 000158 1891 FHHFSKEFEVHRFQHVLYSTPAVPFKLMCLPHLYQDLLQRYIKQCCSDCKSVLDEPALCLLCGRLCSPSWKPCCRESSCQ 1970 (2014)
Q Consensus 1891 c~h~~~~~~~~~~~~~~~~~p~~~~~Li~LP~~yd~L~~~~~~~~Cp~c~~~p~dPalCL~CG~lc~qs~~~CC~~GeC~ 1970 (2014)
.+|....++.++.+......++++|.+.++|.-|+++.++..+. +..+|+.|+.||..|.--|.|||...+ .
T Consensus 624 ~~~~~r~~e~~k~~r~~~~k~~~~fa~~~~~~~~q~~a~~s~~~-------~g~ed~~~~~~~~~q~~~k~y~C~icg-~ 695 (784)
T KOG1139|consen 624 ISKHSRNQEKMKAPRDPVKKAAKEFAKRRMEAIMQNSAKKSAQT-------EGMEDAEVNKVDPSQQNRKVYECPICG-Q 695 (784)
T ss_pred HHHHHHHHHHhhcccchHHHHhHHHHHHHHHHHHHHHHHhhhcc-------cCCChHHHhhhCcccCCccCCcCCcCC-C
Confidence 99987776665555555556777899999999999998864322 789999999999999888999998755 5
Q ss_pred HHHhhcCCCeEEEEEeccceEeEeeCCcceeeecccc
Q 000158 1971 SHAVACGAGTGVFLLIRVFSAPSFNRKLNIIVLCVYC 2007 (2014)
Q Consensus 1971 ~Ha~~CGagvGIFL~IR~~~v~~~~~~~~~~~~~~~~ 2007 (2014)
.|..+||+++|+|++|+...|+.=..++.+=|-.+|+
T Consensus 696 n~p~T~~np~G~~~l~~~~~I~~~r~~~~~~~p~p~l 732 (784)
T KOG1139|consen 696 NAPNTVENPFGMLALLSTNFICEERIDASINTPDPLL 732 (784)
T ss_pred CCCcccCCCceEEEEEeecchHHHHHhhccCCCChhh
Confidence 6899999999999999999887666555555555554
No 3
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.82 E-value=1e-21 Score=263.11 Aligned_cols=929 Identities=17% Similarity=0.045 Sum_probs=570.9
Q ss_pred HHHHHHhcCCchhhhchhhHHHHhhhCCCChhHHHhccCCCCHHHHHHHHHHHhhcccCCCCCCh-h-hhHHHHHHHHHH
Q 000158 18 IVRRLMNIGVPEEFLDYSGIVNFAKNDKSRIPELVSTILPPDEEVAEVIQDAKAKNKKVSVGPNM-K-GRFRESMLWLQW 95 (2014)
Q Consensus 18 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~l~~l~~ 95 (2014)
..+++--.++++++-...+++.|+...+..|...+.+..|..+.+...+..+..+..++-+..++ + ..+.+....+.|
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 34667778888888778899999999999999999999999999998888877777776555444 3 447888888888
Q ss_pred HhcCCCHHHHHHHHHc--cCCCCcccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecCCccccCCCcc
Q 000158 96 LMFEREPEKVLRKLSK--IGQRGVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDVT 173 (2014)
Q Consensus 96 ~~~~~~~~~~l~~l~~--~~~~~~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~~~~~~gG~CDCGd~~ 173 (2014)
.++.+.+.-...-... -.-...|+-+|......++|++|.- .+.+|..|++...|-.|.+..+-..+|+|+|+ ..
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 7777654322111111 1225889999999999999999997 99999999999999999988877889999999 99
Q ss_pred cccccCCCCcCCCCCCCCCCcHHHHHhhHHHHHHHHHHHHHHh--hhhcccCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Q 000158 174 AWKREGFCSRHKGAEQIQPLPEKYANSAAPVLDALFIYWENKL--SLAESVGQENPRASDHVAERRKLANELTFAVVEML 251 (2014)
Q Consensus 174 awk~~~fC~~H~~~~~~~~lp~~l~~~~~~~~~~ll~~~~~~l--~~~e~~~~~~~~~~~~~~~~~k~a~~l~~~i~~~L 251 (2014)
+|...++|..|....++-++-..++.. +..+.++.+|-... .|.. ...+....|...+..++++++...|+.++
T Consensus 689 ~~y~~~~~r~~~y~~DI~~~Q~~la~~--d~~~~l~~~l~r~~L~~w~~--g~~~~~~~d~~~~i~~~~ee~l~lii~ll 764 (1738)
T KOG1140|consen 689 AYYKNNPCRNESYDRDILMLQTGLAME--DPNRFLFTILSRFELLDWFT--GEVDYQSNDTEDTISFMIEEFLALIILLL 764 (1738)
T ss_pred HhhcCccccccchhHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHhc--CCCccccccHHHHHHHHHHHHHHHHHHHH
Confidence 999999999998775544443333322 23333333332211 1221 11233345666777788888887777777
Q ss_pred HHHHhchHHHHHHHHHHhhcchhhHHHHHhhccCCCHHHHHHHHHHHHHhhCChhhHHHHHHHHHhhhHHHHHHHHHhcc
Q 000158 252 LEFCKNSESLLSFVSKRVISVIGLLDILVRAEMFSSDVVVRKLHELLLKLLGEPIFKYEFAKVFLSYYPVFVKDAIREHS 331 (2014)
Q Consensus 252 ~e~~~~~~~ll~~l~~~l~~~~~ll~~l~~~~~~l~k~~r~~Lh~LllsLL~d~efK~~FA~~Fv~~Y~~i~~~fl~~d~ 331 (2014)
.|+... .+.......+...+++.+|......+.+.+++..|.+...+..|..++..++..+...|+...--.++..-
T Consensus 765 ~Er~~~---~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~~d~~~e~Va~~~~p~~~~~~gvf~lK~~~ 841 (1738)
T KOG1140|consen 765 TERSYF---GSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLSFDEALEEVAVFKKPKGLADNGVFVLKESY 841 (1738)
T ss_pred Hheeec---ccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhcccchHHHHHHHhhccCCccccceEEEechhh
Confidence 765543 11112222222345555666665556677888999999899999999999999988888655433444444
Q ss_pred CcccccCCcccceeeeccccCCcHHHHHHhhcHHHHHHHHHHHHhhhhcC--CCCcceeccccccccchhhhhhhhhHhh
Q 000158 332 DDTIKKYPLLSTFSVQIFTVPTLTPRLVKEMNLLEMLLGCLREIFDSCAG--DDSCLQVAKWANLYETTNRVIGDIRFVM 409 (2014)
Q Consensus 332 d~~~~~~s~v~~lSVQLFTvPslA~~LV~e~nLL~ill~tl~~~~~~~~~--~~~~l~~~~~~~~~~~~~~i~~DLryvL 409 (2014)
++....|-...++|+|.-+++++++...++.+.+...+..+...+..++. .++-+........-....+.+.++++.+
T Consensus 842 ~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~~~~~L~~~t~~~~~~~ii~r~~~~~~~~~ 921 (1738)
T KOG1140|consen 842 YDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKKGADILGAAVRLTVFGLIIYRTLEHCLFME 921 (1738)
T ss_pred hhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444555567899999999999998888776654444444444444331 2222222111111122345667788888
Q ss_pred cchhhhHHHhhhchHHHHHHHHHHHHhcCCC--cccccccCcceeeCCceeehhhhhhHHHHhHHhhhhhcccccccccc
Q 000158 410 SHAAVSKYATHEQLNISKAWMKLLTFVQGMN--PQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEET 487 (2014)
Q Consensus 410 sh~~v~~~l~~~~~~l~~~~l~lL~~~QGMn--~~kRq~~~HVEyE~e~w~~aF~L~~~la~i~~~~~~~~~s~~~~~~~ 487 (2014)
++--+.+.+..-.-...+.|...+..++++. +..|++|--.-++...=...+...+.+..++.++..+.++..++.|.
T Consensus 922 s~~~l~~~~~~ihG~~~~~~l~~~~~~~~~~~e~~~~e~gl~~~e~lv~~~~~~~~~~~~~v~~~l~~~~~~~~~n~~ea 1001 (1738)
T KOG1140|consen 922 SSTLLSKVLHLIHGIALNEELINMKFAFTQKTESIAREKGLSLYESLVRKPDSLVHGKIIEVIVELFESLIKSRANDPEV 1001 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccchhhHHHhhhcchhhcCCcceeeeHHHHhhhhhhhcCCccc
Confidence 7765555443334478889999999999999 99999998775555422333344477888899988888888877543
Q ss_pred c-cccccccccCCCCCccccccccccccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhhh
Q 000158 488 R-YDFSMYKQDIGDGDSLRHAKVGRLSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENWL 566 (2014)
Q Consensus 488 ~-~~~~~~~~~~~~~~~~~~~~v~r~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~cl~~l~~~l 566 (2014)
. ++.-|.+..+.+++..+.++.+|+..|..++...--+.-+..=+.+..+. .+..+-+.|.+....+.++.......+
T Consensus 1002 ~~~~~~~~~~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e-~d~~~~~~~~~~~~~~~~~d~~~~~~~ 1080 (1738)
T KOG1140|consen 1002 ANDEKDKKEKQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDE-FDEQENQTPSSGSKTYEEEDFTCALCQ 1080 (1738)
T ss_pred cccccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccc-cCcccccCccccccchhhhhccchhhh
Confidence 3 56656666556777777788888888887775332222222111111111 123334556566666666665554443
Q ss_pred cCCCCcccccccCCCCcccccCchhhhhHh-----hhhhccccccccccccCCccccccccccCCCccccccCccccccc
Q 000158 567 GVDDRSVSVNDILSPNASRISGSNFVALKK-----TLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKITI 641 (2014)
Q Consensus 567 ~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 641 (2014)
+........ ...++. .+-++...+- -+..+.......+.|++...+.+ ..-+-
T Consensus 1081 ~~s~~~~~~-~~~~~~----~~~~~~~~~i~~e~e~~~~~~~~~~v~~~f~~~s~~~s-----------------d~l~~ 1138 (1738)
T KOG1140|consen 1081 DNSCTDFQV-KPASHL----VKPIFRECIICDENEDVPNWDGRYSVSSAFAQKSDDVS-----------------DALTE 1138 (1738)
T ss_pred ccchhcccc-ccchhh----hcccccccccCChhccCCCccccchhhhHhhhhccccc-----------------ccccC
Confidence 221110000 000111 0000000000 00000111111111111111110 00000
Q ss_pred cCCcccccccccCcCCccccccch-----------------hccccc------cccccCccCceeeeccCCceeeehHHH
Q 000158 642 SGERDTASWRSAGFNDSEMEGECA-----------------TELDNL------HVLSLCYWPDITYDVSSQDVSVHIPLH 698 (2014)
Q Consensus 642 ~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~------~~~~~~~~~~v~fdVs~~~VSfH~PLh 698 (2014)
++...|+.. ...+||.- .+.-+| ..+....|.-..++|+-..+.-|-+++
T Consensus 1139 p~~~~~~~~-------~s~c~h~mh~~c~~~~~~a~r~~~n~~~~~l~~~~se~~l~lCp~c~slsn~~lp~~~~~~~~~ 1211 (1738)
T KOG1140|consen 1139 PGSLSCGTV-------LSSCGHHMHYGCFKRYVQAKRFRENARTAPLCQHYSENGLFLCPLCKSLSNVSLPMFLPPELLL 1211 (1738)
T ss_pred CCCCcccce-------eeccCCcchHHHHHHHHHHHHHHHHhhhcCcccccccCCcccCCchHhhhhccCCcCCchhhhc
Confidence 111111100 00011100 000000 011112223344778888899999999
Q ss_pred HHHHHHHHHHHhhhcccCccccccccCCCCCccccchhhhhcccCCCCCcccchhhhcccHHHHHHHHHHhhCcccccch
Q 000158 699 RLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFSAFVMEHPLRIRVFCAQVHAGMWRRNGD 778 (2014)
Q Consensus 699 r~Ls~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~pLR~~Vl~aQI~aGmWvRNG~ 778 (2014)
+.++...+..+..+++.-...+...-+.......+...|.+.....+.|-++...-..+...+.+++.+++++||-- |.
T Consensus 1212 n~~t~~~~~n~~~~i~~rs~~~~s~~~vs~~~s~~~~~~~ss~i~e~kp~~~~~l~~~~~~~ie~~~k~v~s~~~k~-~~ 1290 (1738)
T KOG1140|consen 1212 NPLTLENQRNLNSWIEKRSRASFSLQDVSSILSDPWAAFTSSRIPELKPILIMDLPDSVVEQIELFQKIVGSAMFKP-SS 1290 (1738)
T ss_pred ChhhhhchHHHHHHHHHhchhhcchhhhhhhhcccchhhccccccccccchHhhhhhHHHHHHHHHHHHHhhheeec-cc
Confidence 98888777766555441000000000000001112222322222223332222233455677999999999999986 21
Q ss_pred hHhHHHHHhccccccccccchhHHHHHHHHhhCChHHHHHHHHHHhccccccccCCCCCCCchh-HHHHHHHHHHHHHhh
Q 000158 779 AALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLNLERPSEYEP-ILVQEMLTLIIQILQ 857 (2014)
Q Consensus 779 sl~~Q~~~Y~~~~~r~~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~~~~~~~~~y~~-~~vEe~L~lLI~llt 857 (2014)
.. ...+-+...+.+.|++|++.++.+.......++.+++...++.++......+.. ..+.. ...++++.
T Consensus 1291 ------~i--~~~~le~~~~~~~~~~~~~~~~s~a~~~~~~~l~~~~~~~~l~l~~~~~~~~~~~~~l~~--~~~~~~l~ 1360 (1738)
T KOG1140|consen 1291 ------LL--STNTLELTLFSREFLIVCWQSLSDAEQSTKLLLSASKKPSFLKLNEDMTFCLVTISRLRA--LHWEQILY 1360 (1738)
T ss_pred ------ce--eecccccCcccchhhhhhhhccchHHHHHHHHHhccCCcccccCchhhHHHHHHHHHHHH--HHHHHHHH
Confidence 11 235667788899999999999999999999999999998888776533322322 22222 44577777
Q ss_pred cccccCCChHHHHHHHHHHHHhcCCCChHHHHHhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEeehhhhccccccc
Q 000158 858 ERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYH 937 (2014)
Q Consensus 858 eR~~~g~s~~e~lr~eIIh~Lc~~p~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dpy~ 937 (2014)
++...++-.....+.++|-.+..++.+++++...+|.+..+...++.++..|- ..|.+.-.+.+.++.-.|.|.+-++
T Consensus 1361 ~~~~~~llk~~s~~~~~i~~~~tpd~~~~~ll~~l~~~~~~~~~l~~~~~~~~--~~~~~~~~~~i~~~~i~s~elits~ 1438 (1738)
T KOG1140|consen 1361 ELVYTFLLKSFSPTIPRISVLITPDQPENELLVILPHDFPKSLELELTLDFVN--KNPKKIFELKILMASIISIELITSH 1438 (1738)
T ss_pred HHHHHHHHHHHhhcCCcchhccCCCCCcchhhhccchhhhhhccHHHHHHHhh--hhHHHHHhHHHHHHHhhhhhhheec
Confidence 87766666667777788888888899999999999999999999999999997 6677778899999999999999888
Q ss_pred cccCchhHHHHHHHHHHhhcccccc--CCCCCCccccCCccchhhccccHHHHHHHHHHHHHHhc
Q 000158 938 PRWSSRDLQVAEERYLRFCSVSALT--AQLPRWTKIYYPLESIAGIATCKVVLQVIRAVLFYAVF 1000 (2014)
Q Consensus 938 ~~y~~~~~q~aeer~~~~~~~~a~~--~~~P~~~~~~~~f~~i~~il~s~~~~~il~~vL~~al~ 1000 (2014)
..+.. |.+.|+++..+..-..+.. ...+.++...++-.++.++--+....+.+...|.++..
T Consensus 1439 s~l~~-d~~~~~~q~s~~e~~~~~t~l~~~~s~~~i~~~~~~~~~~~L~~~~~~~i~sfL~~~al 1502 (1738)
T KOG1140|consen 1439 SYLEN-DLEMAEEQKSIDEFKSLLTYLLQLESSRTIPKLADIRLRLSLCLSCEAGILSFLRRAAL 1502 (1738)
T ss_pred cccCC-ccchhhhhhhHHhHhHHHHHHHhccchhhCccccchhhhhHHHHHHHHHHHHHHHHHHH
Confidence 88877 7777776544322222222 23344444333334555666677777788777776653
No 4
>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=99.78 E-value=1.3e-19 Score=171.20 Aligned_cols=70 Identities=44% Similarity=1.070 Sum_probs=66.3
Q ss_pred CcccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEec-CCccccCCCcccccccCCCCcCC
Q 000158 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYT-GGGCCDCGDVTAWKREGFCSRHK 185 (2014)
Q Consensus 116 ~~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~~~~~-~gG~CDCGd~~awk~~~fC~~H~ 185 (2014)
.+||++|++|+++|+|+||+.+++++||.+||+++.|+||+|.+.++ +||+|||||++|||+++||++|.
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 5
>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=99.73 E-value=1.7e-18 Score=164.23 Aligned_cols=70 Identities=49% Similarity=1.112 Sum_probs=54.0
Q ss_pred CcccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecC-CccccCCCcccccccCCCCcCC
Q 000158 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTG-GGCCDCGDVTAWKREGFCSRHK 185 (2014)
Q Consensus 116 ~~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~~~~~~-gG~CDCGd~~awk~~~fC~~H~ 185 (2014)
+.|+++|.+++++|+|+||+.+++.+||.+||.++.|+||++.+..++ +|+|||||+++||+++||++|+
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 6
>KOG1139 consensus Predicted ubiquitin-protein ligase of the N-recognin family [Posttranslational modification, protein turnover, chaperones]
Probab=98.96 E-value=1.3e-08 Score=127.79 Aligned_cols=185 Identities=21% Similarity=0.309 Sum_probs=139.4
Q ss_pred hhcccHHHHHHHHHHhhCcccccchhHhHHHHHhccccccccccchhHHHHHHHHhhCChHHHHHHHHHHhccccccccC
Q 000158 754 VMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLN 833 (2014)
Q Consensus 754 l~e~pLR~~Vl~aQI~aGmWvRNG~sl~~Q~~~Y~~~~~r~~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~~~ 833 (2014)
+.-+++++.|--.-++..||+|+|.-...-...|-+..+....---+--.+-.++..+++..|+..++.+|.+.+.-..+
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 45567899999999999999999998877777775443332222233334556888999999999999999876542211
Q ss_pred C--------C-----C------------------C---------------------------------------------
Q 000158 834 L--------E-----R------------------P--------------------------------------------- 837 (2014)
Q Consensus 834 ~--------~-----~------------------~--------------------------------------------- 837 (2014)
. . . .
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 0 0 0 0
Q ss_pred --CCch--hHHHHHHHHHHHHHhhcccccCCChHHHHHHHHHHHHhcCCCChHHHHHhCCCCC-CCcchHHHHHHHHccc
Q 000158 838 --SEYE--PILVQEMLTLIIQILQERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDL-SKFDQLQEILDAVAMY 912 (2014)
Q Consensus 838 --~~y~--~~~vEe~L~lLI~llteR~~~g~s~~e~lr~eIIh~Lc~~p~t~S~L~~~lpe~~-~~~~~fe~iL~eVA~f 912 (2014)
..|+ +.|...++.++..+|.++.+.|..+++..+-|++|.-+++...||-+..++.+.. ...+.|+.|+.+..+|
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 2466778888989999999889999999999999999999999999988776654 4578899999999999
Q ss_pred cCCCC----CCcceEEeehhhhc-ccccccc
Q 000158 913 SHPSG----FNQGMYSLRWSYWK-ELDIYHP 938 (2014)
Q Consensus 913 ~~P~g----~~~G~Y~LK~e~~~-e~dpy~~ 938 (2014)
-.|-- .-+|.|.||.-.|+ +.-|-+.
T Consensus 447 ~~P~~~~~p~~~~s~~l~~~~~~~~~c~~~~ 477 (784)
T KOG1139|consen 447 IEPIETTTPLMQGSYQLKTSIWDSEVCPVFF 477 (784)
T ss_pred ccchhhcCccccchhhccccCCccccccchh
Confidence 99943 24799999999998 4555444
No 7
>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=96.95 E-value=0.00057 Score=82.48 Aligned_cols=80 Identities=26% Similarity=0.419 Sum_probs=60.6
Q ss_pred HHHHHHHHHHhcCCCChHHHHHhCCCCCCC---cchHHHHHHHHccccCCCCCCcceEEeehhhhccccccccccCchhH
Q 000158 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSK---FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (2014)
Q Consensus 869 ~lr~eIIh~Lc~~p~t~S~L~~~lpe~~~~---~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dpy~~~y~~~~~ 945 (2014)
.+|.-|||+||.+|....||..+|..+... -..++.||.+||... .++.|.||+.+|+++|.=++.|+-.|+
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 599999999999999999999888765443 246999999999975 378999999999999977888998998
Q ss_pred HHHHHHHH
Q 000158 946 QVAEERYL 953 (2014)
Q Consensus 946 q~aeer~~ 953 (2014)
|..+-+..
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 8
>KOG1777 consensus Putative Zn-finger protein [General function prediction only]
Probab=94.81 E-value=0.015 Score=70.81 Aligned_cols=63 Identities=35% Similarity=0.560 Sum_probs=50.9
Q ss_pred ccCCCCccccc-----ccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecCCccccCCCccc
Q 000158 111 KIGQRGVCGAV-----WGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDVTA 174 (2014)
Q Consensus 111 ~~~~~~~Cg~v-----~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~~~~~~gG~CDCGd~~a 174 (2014)
+.-+.+.|-.. +-+=.-+|||-||...+.-+||..|.++ -|+||++-+.+...-.||||-..+
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 34455777443 3344568999999999999999999988 699999999998889999997543
No 9
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=92.75 E-value=0.036 Score=64.88 Aligned_cols=49 Identities=35% Similarity=0.732 Sum_probs=36.9
Q ss_pred cccccchHhhHHHHHHHHHHHHHhhhhcc---ccCCCCccCCCCCccccccccc
Q 000158 1427 HLSSCGHAVHQGCLDRYVSSLKERYNRRI---IFEGGHIVDPDQGEFLCPVCRQ 1477 (2014)
Q Consensus 1427 H~SsCGH~MH~~C~~~Y~~Sl~~R~~~R~---~~er~h~~d~e~gEFLCPLCK~ 1477 (2014)
-.+.|-|.||+.|+.||+...++..++.. .-+|.|. .+.-|=+||+||-
T Consensus 132 t~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~--~~~~eavcpVcre 183 (368)
T KOG4445|consen 132 TVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHM--KEQVEAVCPVCRE 183 (368)
T ss_pred eeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--hhhHhhhhhHhhh
Confidence 37889999999999999999987655332 2344454 4577888999984
No 10
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=92.59 E-value=0.5 Score=64.41 Aligned_cols=70 Identities=14% Similarity=0.181 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-H--HhhccccccCCCCCCCccCCCCccccccccCCCCcccccCCCC---CCCeE
Q 000158 1146 SEKRKAKARERQAAILEKMKAEQFK-F--LSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS---RTPVS 1219 (2014)
Q Consensus 1146 ~ekKK~~AkeRQakIMAQm~~QQk~-F--l~~n~~~~de~d~~~~e~~~~d~~~~~~e~~~~~CiLCqe~~s---~~p~G 1219 (2014)
+.+||++|.++|+|.+.+|.-++.+ - ..+..-. .+ .+ +.++ | ...+|++|+|..+ ++++|
T Consensus 422 r~ekk~~Am~~Rek~L~~lgm~~~~~G~v~~~~~~l-~~----------~~-~l~e-e-~gl~C~ICrEGy~~~p~~~lG 487 (802)
T PF13764_consen 422 RQEKKRLAMAMREKQLKKLGMRVNEKGQVVVSSSIL-QN----------ME-DLEE-E-DGLTCCICREGYKFRPDEVLG 487 (802)
T ss_pred HHHHHHHHHHHHHHHHHHccCccccccceecCchhh-cC----------cc-cccc-c-CCCeEEEcCCccccCCcccee
Confidence 5677889999999999998433200 0 0001000 00 00 0111 1 1467999999853 46899
Q ss_pred EEEeeecccc
Q 000158 1220 YLILLQKSRL 1229 (2014)
Q Consensus 1220 ~la~iq~S~i 1229 (2014)
+-+|.-+-.+
T Consensus 488 iY~f~kr~~l 497 (802)
T PF13764_consen 488 IYAFSKRVNL 497 (802)
T ss_pred eEEEeecccc
Confidence 9999866665
No 11
>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=92.57 E-value=0.033 Score=48.22 Aligned_cols=20 Identities=25% Similarity=0.845 Sum_probs=16.7
Q ss_pred ccccccchHhhHHHHHHHHH
Q 000158 1426 IHLSSCGHAVHQGCLDRYVS 1445 (2014)
Q Consensus 1426 ~H~SsCGH~MH~~C~~~Y~~ 1445 (2014)
+....|||+.|.+|+++|+.
T Consensus 16 ~~~l~C~H~fh~~Ci~~~~~ 35 (44)
T PF13639_consen 16 VVKLPCGHVFHRSCIKEWLK 35 (44)
T ss_dssp EEEETTSEEEEHHHHHHHHH
T ss_pred EEEccCCCeeCHHHHHHHHH
Confidence 34556999999999999983
No 12
>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=92.49 E-value=0.088 Score=44.66 Aligned_cols=19 Identities=37% Similarity=1.001 Sum_probs=16.2
Q ss_pred ccccchHhhHHHHHHHHHH
Q 000158 1428 LSSCGHAVHQGCLDRYVSS 1446 (2014)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~S 1446 (2014)
+..|||.+|..|+++|+..
T Consensus 15 ~~~C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 15 LLPCGHVFCRSCIDKWLKS 33 (45)
T ss_pred ecCCCChhcHHHHHHHHHh
Confidence 5569999999999998654
No 13
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=89.32 E-value=0.11 Score=68.81 Aligned_cols=63 Identities=25% Similarity=0.675 Sum_probs=50.9
Q ss_pred CcccccccCC----ceeEEeccCCCCCCccccccccCCCCCCCceeEEEe-cCCccccCCCcccccc-cCCCCcC
Q 000158 116 GVCGAVWGNN----DIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVTAWKR-EGFCSRH 184 (2014)
Q Consensus 116 ~~Cg~v~~~g----~~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~~~~-~~gG~CDCGd~~awk~-~~fC~~H 184 (2014)
..|...|+.. .-+|.|+|||.-.+-+-|.+|-.- .|+||+.++-+ +.-.+||| |-+ +..|+.-
T Consensus 1241 DtCSFTWTGadHINQDIfECkTCGL~~SLCCCsECAlt-CHk~HDCkLKRTSPTAYCDC-----WEKssCkCKaL 1309 (3015)
T KOG0943|consen 1241 DTCSFTWTGADHINQDIFECKTCGLLESLCCCSECALT-CHKGHDCKLKRTSPTAYCDC-----WEKSSCKCKAL 1309 (3015)
T ss_pred CccceeecchhhccchhhhhcccccchhhhhhHHHHHH-hccCCccceeccCCcceeeh-----hhcccccchhh
Confidence 5789999853 457999999999888889999764 79999999987 56899999 754 4556554
No 14
>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=85.69 E-value=0.45 Score=40.38 Aligned_cols=20 Identities=30% Similarity=0.843 Sum_probs=18.3
Q ss_pred cccccchHhhHHHHHHHHHH
Q 000158 1427 HLSSCGHAVHQGCLDRYVSS 1446 (2014)
Q Consensus 1427 H~SsCGH~MH~~C~~~Y~~S 1446 (2014)
.+..|||.++..|+.+|+++
T Consensus 13 ~~~~C~H~fC~~C~~~~~~~ 32 (41)
T PF00097_consen 13 ILLPCGHSFCRDCLRKWLEN 32 (41)
T ss_dssp EETTTSEEEEHHHHHHHHHH
T ss_pred EEecCCCcchHHHHHHHHHh
Confidence 37899999999999999887
No 15
>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=84.42 E-value=0.75 Score=37.43 Aligned_cols=19 Identities=21% Similarity=0.810 Sum_probs=16.7
Q ss_pred cccccchHhhHHHHHHHHH
Q 000158 1427 HLSSCGHAVHQGCLDRYVS 1445 (2014)
Q Consensus 1427 H~SsCGH~MH~~C~~~Y~~ 1445 (2014)
....|||.+|..|+++|+.
T Consensus 12 ~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 12 VVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred EEecCCChHHHHHHHHHHH
Confidence 3567999999999999977
No 16
>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=83.99 E-value=0.81 Score=39.81 Aligned_cols=37 Identities=27% Similarity=0.654 Sum_probs=29.5
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000158 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2014)
Q Consensus 117 ~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~ 158 (2014)
.|+..+ .| .-|+|.+|. ..-+|.+||.++.|.+|.+.
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 46799999999999888874
No 17
>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=83.44 E-value=0.88 Score=40.67 Aligned_cols=39 Identities=28% Similarity=0.869 Sum_probs=29.5
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCC----CC-CceeEE
Q 000158 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN----HK-EHDYSI 159 (2014)
Q Consensus 117 ~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~----H~-~H~~~~ 159 (2014)
.|++.... ..-|+|..|. ..-+|.+||..+. |+ .|.|.+
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 57777664 4899999996 3669999999984 53 577765
No 18
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=83.31 E-value=1.2 Score=56.49 Aligned_cols=77 Identities=27% Similarity=0.379 Sum_probs=63.0
Q ss_pred HHHHHHHHHHhcCCCChHHHHHhCCCCCCCc---chHHHHHHHHccccCCCCCCcceEEeehhhhccccccccccCchhH
Q 000158 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSKF---DQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (2014)
Q Consensus 869 ~lr~eIIh~Lc~~p~t~S~L~~~lpe~~~~~---~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dpy~~~y~~~~~ 945 (2014)
-+|..|||+|+.++..--||.++|-.+...+ ..+..||.+. +.+.+|+|.|++.+|+|+|-=++.|+-.|.
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 4999999999999999999999887776543 3577888882 124689999999999999988888988887
Q ss_pred HHHHHH
Q 000158 946 QVAEER 951 (2014)
Q Consensus 946 q~aeer 951 (2014)
|..+-+
T Consensus 285 ~~lkr~ 290 (604)
T KOG4796|consen 285 QHLKRV 290 (604)
T ss_pred HHHHHH
Confidence 766444
No 19
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=83.25 E-value=0.78 Score=53.11 Aligned_cols=62 Identities=23% Similarity=0.212 Sum_probs=45.2
Q ss_pred HHHHHHHHHH--hcCCCChHHHHHhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEeehhhhc
Q 000158 869 SLKRELVHRL--AIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWK 931 (2014)
Q Consensus 869 ~lr~eIIh~L--c~~p~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~ 931 (2014)
.=|+||+-.| ||....|=-|...+-..-+...-+.+||++|++|.+ .|..+|+|+|||||-+
T Consensus 182 ~dk~evld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~icv~Nk-Kg~~k~tyeLKPEYK~ 245 (254)
T KOG2905|consen 182 RDKNEVLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDICVLNK-KGPYKNTYELKPEYKK 245 (254)
T ss_pred ccHHHHHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHHHHhc-cCcccCceecCHHHhh
Confidence 4577777777 777666655554443333445568999999999986 3678999999999864
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=82.50 E-value=1 Score=39.14 Aligned_cols=31 Identities=35% Similarity=0.864 Sum_probs=25.4
Q ss_pred CccccccchHhhHHHHHHHHHHHHHhhhhccccCCCCccCCCCCccccccccc
Q 000158 1425 GIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2014)
Q Consensus 1425 G~H~SsCGH~MH~~C~~~Y~~Sl~~R~~~R~~~er~h~~d~e~gEFLCPLCK~ 1477 (2014)
...+.+|||++...|.++-. .+...||+||+
T Consensus 14 ~~~l~~CgH~~C~~C~~~~~----------------------~~~~~CP~C~k 44 (44)
T PF14634_consen 14 RPRLTSCGHIFCEKCLKKLK----------------------GKSVKCPICRK 44 (44)
T ss_pred CeEEcccCCHHHHHHHHhhc----------------------CCCCCCcCCCC
Confidence 46699999999999998754 35678999984
No 21
>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=81.90 E-value=1 Score=39.68 Aligned_cols=37 Identities=27% Similarity=0.812 Sum_probs=29.2
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCC--CCC-CceeE
Q 000158 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG--NHK-EHDYS 158 (2014)
Q Consensus 117 ~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~--~H~-~H~~~ 158 (2014)
.|++.+. | .-|+|.+|. ..-+|.+||..+ .|. +|.+.
T Consensus 5 ~C~~~i~-g-~r~~C~~C~---d~dLC~~Cf~~~~~~H~~~H~~~ 44 (46)
T cd02249 5 GCLKPIV-G-VRYHCLVCE---DFDLCSSCYAKGKKGHPPDHSFT 44 (46)
T ss_pred CCCCCCc-C-CEEECCCCC---CCcCHHHHHCcCcCCCCCCCCEe
Confidence 5778444 5 899999997 577999999998 676 67764
No 22
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=79.87 E-value=1.1 Score=44.51 Aligned_cols=22 Identities=23% Similarity=0.650 Sum_probs=18.3
Q ss_pred CccccccchHhhHHHHHHHHHH
Q 000158 1425 GIHLSSCGHAVHQGCLDRYVSS 1446 (2014)
Q Consensus 1425 G~H~SsCGH~MH~~C~~~Y~~S 1446 (2014)
.+=...|||.-|..|..+.+++
T Consensus 46 plv~g~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 46 PLVWGKCSHNFHMHCILKWLST 67 (85)
T ss_pred ceeeccCccHHHHHHHHHHHcc
Confidence 3346779999999999999875
No 23
>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=78.11 E-value=1.7 Score=38.95 Aligned_cols=38 Identities=26% Similarity=0.792 Sum_probs=28.8
Q ss_pred ccc-ccccCCceeEEeccCCCCCCccccccccCCC----CCC-CceeEE
Q 000158 117 VCG-AVWGNNDIAYRCRTCEHDPTCAICVPCFQNG----NHK-EHDYSI 159 (2014)
Q Consensus 117 ~Cg-~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~----~H~-~H~~~~ 159 (2014)
.|+ ..+. ..-|+|..|. ..-+|.+||..+ .|+ .|.+.+
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 3454 4889999995 577999999988 676 777754
No 24
>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=77.25 E-value=1.9 Score=37.92 Aligned_cols=39 Identities=26% Similarity=0.695 Sum_probs=29.7
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC-CCceeEE
Q 000158 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYSI 159 (2014)
Q Consensus 117 ~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H-~~H~~~~ 159 (2014)
.|+..--.| .-|+|.+|. ..-+|..||....| .+|.|..
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 789999999 46699999999999 5898753
No 25
>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=75.11 E-value=1.6 Score=37.38 Aligned_cols=37 Identities=24% Similarity=0.595 Sum_probs=28.0
Q ss_pred CcccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000158 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2014)
Q Consensus 116 ~~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~ 158 (2014)
..|..--+ ....|.|.+|.. .+|.+|+..+ |++|++.
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 45543332 348999999986 7999999998 9999975
No 26
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=73.98 E-value=2.9 Score=47.70 Aligned_cols=54 Identities=20% Similarity=0.472 Sum_probs=35.8
Q ss_pred cccccchHhhHHHHHHHHHHHHHhhhhccccCCCCccCCCCCccccccccccc--cceeccC
Q 000158 1427 HLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLA--NSVLPAL 1486 (2014)
Q Consensus 1427 H~SsCGH~MH~~C~~~Y~~Sl~~R~~~R~~~er~h~~d~e~gEFLCPLCK~L~--N~vLPi~ 1486 (2014)
.++.|||.-...|..+|+.+-. ..++. ..-.+-.++...||+||+-- +.++|++
T Consensus 32 VvT~CGH~FC~~CI~~wl~~s~--~s~~~----~~~~~~~k~~~~CPvCR~~Is~~~LvPiy 87 (193)
T PLN03208 32 VVTLCGHLFCWPCIHKWTYASN--NSRQR----VDQYDHKREPPKCPVCKSDVSEATLVPIY 87 (193)
T ss_pred EEcCCCchhHHHHHHHHHHhcc--ccccc----cccccccCCCCcCCCCCCcCChhcEEEee
Confidence 3678999999999999865321 11111 11112246789999999864 4588887
No 27
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=73.89 E-value=3.9 Score=49.20 Aligned_cols=61 Identities=25% Similarity=0.597 Sum_probs=47.0
Q ss_pred cCCCCcccccc--cCCceeEEeccCCCCC-CccccccccCCCCCCCceeEEEe-cCCccccCCCcc
Q 000158 112 IGQRGVCGAVW--GNNDIAYRCRTCEHDP-TCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVT 173 (2014)
Q Consensus 112 ~~~~~~Cg~v~--~~g~~~y~C~~C~~d~-t~~~C~~CF~~~~H~~H~~~~~~-~~gG~CDCGd~~ 173 (2014)
...+..|++.- .+-.+.|.|.||...| ...+|.-|=.. -|.||.-..-. .+.--||||..-
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 35566786553 3336889999999998 88899999765 79999987655 467889999843
No 28
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=72.34 E-value=1.7 Score=45.29 Aligned_cols=24 Identities=29% Similarity=0.789 Sum_probs=21.4
Q ss_pred HhcccCCCCCC----CCCCcchhccccc
Q 000158 1932 IKQCCSDCKSV----LDEPALCLLCGRL 1955 (2014)
Q Consensus 1932 ~~~~Cp~c~~~----p~dPalCL~CG~l 1955 (2014)
.+|.||+||+. -++|++|-.||+.
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCc
Confidence 46999999987 5999999999995
No 29
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=71.07 E-value=1.8 Score=52.47 Aligned_cols=16 Identities=38% Similarity=1.059 Sum_probs=14.4
Q ss_pred ccchHhhHHHHHHHHH
Q 000158 1430 SCGHAVHQGCLDRYVS 1445 (2014)
Q Consensus 1430 sCGH~MH~~C~~~Y~~ 1445 (2014)
.|||+.|++|.++.++
T Consensus 317 pCGHilHl~CLknW~E 332 (491)
T COG5243 317 PCGHILHLHCLKNWLE 332 (491)
T ss_pred cccceeeHHHHHHHHH
Confidence 5999999999999864
No 30
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=69.28 E-value=2.3 Score=51.07 Aligned_cols=35 Identities=26% Similarity=0.835 Sum_probs=27.8
Q ss_pred ccccccchHhhHHHHHHHHHHHHHhhhhccccCCCCccCCCCCccccccccccccce
Q 000158 1426 IHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSV 1482 (2014)
Q Consensus 1426 ~H~SsCGH~MH~~C~~~Y~~Sl~~R~~~R~~~er~h~~d~e~gEFLCPLCK~L~N~v 1482 (2014)
++.-.|||.||+.||+.|. -.+ |-||+|..++|+.
T Consensus 175 ~~~~~CgH~~h~~cf~e~~---------------------~~~-y~CP~C~~~~d~~ 209 (276)
T KOG1940|consen 175 AGVLKCGHYMHSRCFEEMI---------------------CEG-YTCPICSKPGDMS 209 (276)
T ss_pred CCccCcccchHHHHHHHHh---------------------ccC-CCCCcccchHHHH
Confidence 3478999999999999872 135 9999999966654
No 31
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=68.88 E-value=1.8 Score=41.65 Aligned_cols=39 Identities=38% Similarity=0.710 Sum_probs=20.8
Q ss_pred ccccchHhhHHHHHHHHHHHHHhhhhccccCCCCccCCCCCccccccccc
Q 000158 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2014)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~R~~~R~~~er~h~~d~e~gEFLCPLCK~ 1477 (2014)
-..||+..|..|+.+||.+.... |. .+++-.|+ ||.|+.
T Consensus 25 n~~C~~~fH~~CL~~wf~~~~~~---~~------~~~~~~G~--CP~C~~ 63 (70)
T PF11793_consen 25 NPSCGKKFHLLCLSEWFLSLEKS---RQ------SFIPIFGE--CPYCSS 63 (70)
T ss_dssp -TT----B-SGGGHHHHHHHHSS---S-------TTT--EEE---TTT-S
T ss_pred CcccCCHHHHHHHHHHHHHcccC---Ce------eecccccC--CcCCCC
Confidence 45899999999999999888642 11 13455566 999986
No 32
>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=66.90 E-value=3.5 Score=36.31 Aligned_cols=30 Identities=27% Similarity=0.907 Sum_probs=24.7
Q ss_pred ceeEEeccCCCCCCccccccccCCCCC-CCceeE
Q 000158 126 DIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYS 158 (2014)
Q Consensus 126 ~~~y~C~~C~~d~t~~~C~~CF~~~~H-~~H~~~ 158 (2014)
..-|+|.+|. ..-+|.+||....| .+|.|.
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 36699999999998 588764
No 33
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=65.85 E-value=3 Score=44.25 Aligned_cols=24 Identities=25% Similarity=0.385 Sum_probs=21.5
Q ss_pred HhcccCCCCCC----CCCCcchhccccc
Q 000158 1932 IKQCCSDCKSV----LDEPALCLLCGRL 1955 (2014)
Q Consensus 1932 ~~~~Cp~c~~~----p~dPalCL~CG~l 1955 (2014)
.+|.||+||+. -++|++|-.||+.
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCc
Confidence 46899999987 4999999999996
No 34
>PHA02926 zinc finger-like protein; Provisional
Probab=60.67 E-value=6.8 Score=45.36 Aligned_cols=43 Identities=26% Similarity=0.536 Sum_probs=33.0
Q ss_pred cccccchHhhHHHHHHHHHHHHHhhhhccccCCCCccCCCCCccccccccccccceecc
Q 000158 1427 HLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPA 1485 (2014)
Q Consensus 1427 H~SsCGH~MH~~C~~~Y~~Sl~~R~~~R~~~er~h~~d~e~gEFLCPLCK~L~N~vLPi 1485 (2014)
..+.|||.....|..+..++- + + ..++-.||+||.-...|.|-
T Consensus 193 IL~~CnHsFCl~CIr~Wr~~r------~---~-------~~~~rsCPiCR~~f~~I~pS 235 (242)
T PHA02926 193 LLDSCNHIFCITCINIWHRTR------R---E-------TGASDNCPICRTRFRNITMS 235 (242)
T ss_pred ccCCCCchHHHHHHHHHHHhc------c---c-------cCcCCcCCCCcceeeeeccc
Confidence 588999999999999875521 1 1 13567899999998888774
No 35
>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=60.48 E-value=2 Score=41.67 Aligned_cols=17 Identities=29% Similarity=0.935 Sum_probs=15.0
Q ss_pred ccccchHhhHHHHHHHH
Q 000158 1428 LSSCGHAVHQGCLDRYV 1444 (2014)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~ 1444 (2014)
.+.|||+-|..|..+.+
T Consensus 47 ~~~C~H~FH~~Ci~~Wl 63 (73)
T PF12678_consen 47 WGPCGHIFHFHCISQWL 63 (73)
T ss_dssp EETTSEEEEHHHHHHHH
T ss_pred ecccCCCEEHHHHHHHH
Confidence 57799999999998876
No 36
>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=59.94 E-value=3.8 Score=34.58 Aligned_cols=20 Identities=25% Similarity=0.933 Sum_probs=17.8
Q ss_pred cccccchHhhHHHHHHHHHH
Q 000158 1427 HLSSCGHAVHQGCLDRYVSS 1446 (2014)
Q Consensus 1427 H~SsCGH~MH~~C~~~Y~~S 1446 (2014)
....|||.+..+|+++|++.
T Consensus 13 ~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 13 VVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp EECTTSEEEEHHHHHHHHHC
T ss_pred EECCCCCchhHHHHHHHHHC
Confidence 47899999999999999765
No 37
>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=56.37 E-value=7.6 Score=34.77 Aligned_cols=32 Identities=25% Similarity=0.736 Sum_probs=24.2
Q ss_pred ceeEEeccCCCCCCccccccccCCC-CC-CCceeE
Q 000158 126 DIAYRCRTCEHDPTCAICVPCFQNG-NH-KEHDYS 158 (2014)
Q Consensus 126 ~~~y~C~~C~~d~t~~~C~~CF~~~-~H-~~H~~~ 158 (2014)
..-|+|.+|.- ...-+|.+||.++ .| .+|.+.
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 56699999973 3466999999999 67 366653
No 38
>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=55.14 E-value=4.2 Score=35.86 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=20.9
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC
Q 000158 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 152 (2014)
Q Consensus 117 ~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H 152 (2014)
.||.-.+ .+-|+|..+. -..||.+||..|.-
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 4555554 3667766554 46699999988754
No 39
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=55.03 E-value=4.7 Score=38.06 Aligned_cols=27 Identities=30% Similarity=0.822 Sum_probs=21.7
Q ss_pred HhcccCCCCCC------CCCCcchhccccc-cCC
Q 000158 1932 IKQCCSDCKSV------LDEPALCLLCGRL-CSP 1958 (2014)
Q Consensus 1932 ~~~~Cp~c~~~------p~dPalCL~CG~l-c~q 1958 (2014)
.+.+||.|+.+ +....-|+.||+. |-.
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 45799999976 6888999999995 543
No 40
>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=54.77 E-value=9.2 Score=31.88 Aligned_cols=28 Identities=25% Similarity=0.451 Sum_probs=23.2
Q ss_pred ceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000158 126 DIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2014)
Q Consensus 126 ~~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~ 158 (2014)
...|-|.+|+. .+|..|-..+ |++|.+.
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 41
>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=54.42 E-value=7.1 Score=34.92 Aligned_cols=35 Identities=29% Similarity=0.691 Sum_probs=27.0
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCCC-Cce
Q 000158 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK-EHD 156 (2014)
Q Consensus 117 ~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H~-~H~ 156 (2014)
.|++... ..-|+|..|. ..-+|.+||..+.+. +|+
T Consensus 5 gC~~~~~--~~RykCl~C~---d~DlC~~Cf~~g~~~~~H~ 40 (48)
T cd02343 5 GCDEIAP--WHRYRCLQCT---DMDLCKTCFLGGVKPEGHE 40 (48)
T ss_pred CCCCcCC--CceEECCCCC---CchhHHHHHhCCccCCCCC
Confidence 4777543 4799999997 477999999998874 454
No 42
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=54.19 E-value=7.3 Score=29.49 Aligned_cols=20 Identities=30% Similarity=0.896 Sum_probs=17.4
Q ss_pred ccCCCCCC-CCCCcchhcccc
Q 000158 1935 CCSDCKSV-LDEPALCLLCGR 1954 (2014)
Q Consensus 1935 ~Cp~c~~~-p~dPalCL~CG~ 1954 (2014)
+||+||.+ +.+-..|-.||+
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 59999988 677888999997
No 43
>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=53.30 E-value=4.9 Score=48.93 Aligned_cols=44 Identities=23% Similarity=0.310 Sum_probs=20.7
Q ss_pred CChHHHHHhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEeehhhh
Q 000158 883 ATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYW 930 (2014)
Q Consensus 883 ~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~ 930 (2014)
.+..+|..... +-+.-+-+||++||+|.+- |...|+|+|||||-
T Consensus 231 wslK~L~~~t~---QP~~yLKeiL~eIa~~~k~-g~~~~~w~LKpeyk 274 (275)
T PF02270_consen 231 WSLKDLRQRTQ---QPEAYLKEILEEIAVLNKR-GPHKNMWELKPEYK 274 (275)
T ss_dssp B-HHHHHHH-----S-HHHHHHHHHHH--EE---TT---EE----SS-
T ss_pred CCHHHHHHHHC---CCHHHHHHHHHHHHHHhcc-CCcCCcEecchHHc
Confidence 34455555442 3345689999999999974 67789999999984
No 44
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=51.41 E-value=6.9 Score=52.63 Aligned_cols=23 Identities=48% Similarity=1.025 Sum_probs=21.0
Q ss_pred ccchHhhHHHHHHHHHHHHHhhhhccccCCCCccCCCCCccccccccc
Q 000158 1430 SCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2014)
Q Consensus 1430 sCGH~MH~~C~~~Y~~Sl~~R~~~R~~~er~h~~d~e~gEFLCPLCK~ 1477 (2014)
.|||..|++|++ .+|+-||-|+.
T Consensus 858 ~CgHsyHqhC~e-------------------------~~~~~CP~C~~ 880 (933)
T KOG2114|consen 858 LCGHSYHQHCLE-------------------------DKEDKCPKCLP 880 (933)
T ss_pred ecccHHHHHhhc-------------------------cCcccCCccch
Confidence 599999999998 48999999986
No 45
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=50.06 E-value=7.6 Score=30.32 Aligned_cols=21 Identities=24% Similarity=0.814 Sum_probs=18.1
Q ss_pred cccCCCCCC-CCCCcchhcccc
Q 000158 1934 QCCSDCKSV-LDEPALCLLCGR 1954 (2014)
Q Consensus 1934 ~~Cp~c~~~-p~dPalCL~CG~ 1954 (2014)
++||.|+++ |..-..|-.||-
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCC
Confidence 479999987 788899999985
No 46
>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=49.29 E-value=9.4 Score=33.05 Aligned_cols=32 Identities=25% Similarity=0.824 Sum_probs=25.0
Q ss_pred CcccccccCCceeEEeccCCCCCCccccccccCCCCCC
Q 000158 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (2014)
Q Consensus 116 ~~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H~ 153 (2014)
..|+++ +++-|+|..|. -.-+|..||....|.
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 34999999997 366999999998883
No 47
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.10 E-value=8.2 Score=29.98 Aligned_cols=22 Identities=23% Similarity=0.708 Sum_probs=19.2
Q ss_pred hcccCCCCCC-CCCCcchhcccc
Q 000158 1933 KQCCSDCKSV-LDEPALCLLCGR 1954 (2014)
Q Consensus 1933 ~~~Cp~c~~~-p~dPalCL~CG~ 1954 (2014)
...||+||.. +.+-..|-.||+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 4689999998 788899999997
No 48
>smart00336 BBOX B-Box-type zinc finger.
Probab=48.98 E-value=14 Score=31.31 Aligned_cols=29 Identities=21% Similarity=0.636 Sum_probs=23.6
Q ss_pred CceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000158 125 NDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2014)
Q Consensus 125 g~~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~ 158 (2014)
....|-|.+|+. ++|..|... .|++|.+.
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 445777988884 799999988 99999875
No 49
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=45.62 E-value=13 Score=33.20 Aligned_cols=19 Identities=32% Similarity=0.746 Sum_probs=16.8
Q ss_pred cccccchH-hhHHHHHHHHH
Q 000158 1427 HLSSCGHA-VHQGCLDRYVS 1445 (2014)
Q Consensus 1427 H~SsCGH~-MH~~C~~~Y~~ 1445 (2014)
...-|||. +-..|++++..
T Consensus 16 ~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 16 VLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp EEETTCEEEEEHHHHHHHHH
T ss_pred EEeCCCChHHHHHHhHHhcc
Confidence 36679999 99999999977
No 50
>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=45.57 E-value=14 Score=32.37 Aligned_cols=33 Identities=27% Similarity=0.801 Sum_probs=25.2
Q ss_pred CcccccccCCceeEEeccCCCCCCccccccccCCCCCC
Q 000158 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (2014)
Q Consensus 116 ~~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H~ 153 (2014)
..|++.+. ..-|+|..|. ..-+|.+||..+.|.
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 46888554 4688999994 577999999988664
No 51
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=45.29 E-value=6.5 Score=36.54 Aligned_cols=28 Identities=29% Similarity=0.762 Sum_probs=22.4
Q ss_pred HHhcccCCCCCC------CCCCcchhccccccCC
Q 000158 1931 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2014)
Q Consensus 1931 ~~~~~Cp~c~~~------p~dPalCL~CG~lc~q 1958 (2014)
+.+.+||.|+.+ +..+..|..||+..+.
T Consensus 9 F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 9 FLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EEEEECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 345799999987 5889999999995333
No 52
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.08 E-value=9.7 Score=34.55 Aligned_cols=15 Identities=40% Similarity=0.753 Sum_probs=11.2
Q ss_pred ccccchH-hhHHHHHH
Q 000158 1428 LSSCGHA-VHQGCLDR 1442 (2014)
Q Consensus 1428 ~SsCGH~-MH~~C~~~ 1442 (2014)
.-+|||+ |-++|-.+
T Consensus 22 lYtCGHMCmCy~Cg~r 37 (62)
T KOG4172|consen 22 LYTCGHMCMCYACGLR 37 (62)
T ss_pred HHHcchHHhHHHHHHH
Confidence 6789998 77777544
No 53
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=44.60 E-value=5.6 Score=36.54 Aligned_cols=27 Identities=19% Similarity=0.668 Sum_probs=17.5
Q ss_pred HhcccCCCCCC------CCCCcchhccccccCC
Q 000158 1932 IKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2014)
Q Consensus 1932 ~~~~Cp~c~~~------p~dPalCL~CG~lc~q 1958 (2014)
.+.+||.|+.+ ...+..|..||++.++
T Consensus 6 m~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred EEEECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 45799999986 5899999999995433
No 54
>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=41.86 E-value=17 Score=32.75 Aligned_cols=33 Identities=27% Similarity=0.720 Sum_probs=24.4
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCCC
Q 000158 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (2014)
Q Consensus 117 ~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~H~ 153 (2014)
.|++.=-.| .-|+|..|. ..-||.+||..+.|.
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 466542234 789999997 477999999888653
No 55
>PHA02929 N1R/p28-like protein; Provisional
Probab=40.18 E-value=18 Score=43.13 Aligned_cols=35 Identities=37% Similarity=0.777 Sum_probs=25.7
Q ss_pred ccccchHhhHHHHHHHHHHHHHhhhhccccCCCCccCCCCCccccccccccccceec
Q 000158 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLP 1484 (2014)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~R~~~R~~~er~h~~d~e~gEFLCPLCK~L~N~vLP 1484 (2014)
++.|||..|.+|..+.+. + + . .||+||.---.|+|
T Consensus 197 l~~C~H~FC~~CI~~Wl~----~---~-------------~--tCPlCR~~~~~v~~ 231 (238)
T PHA02929 197 LSNCNHVFCIECIDIWKK----E---K-------------N--TCPVCRTPFISVIK 231 (238)
T ss_pred cCCCCCcccHHHHHHHHh----c---C-------------C--CCCCCCCEeeEEee
Confidence 578999999999998652 1 0 0 59999986555544
No 56
>PLN00209 ribosomal protein S27; Provisional
Probab=39.39 E-value=7.5 Score=38.62 Aligned_cols=37 Identities=16% Similarity=0.520 Sum_probs=29.6
Q ss_pred cccCCchHHHHHHHHHHhcccCCCCCC------CCCCcchhccccccCC
Q 000158 1916 KLMCLPHLYQDLLQRYIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2014)
Q Consensus 1916 ~Li~LP~~yd~L~~~~~~~~Cp~c~~~------p~dPalCL~CG~lc~q 1958 (2014)
+||+=|..| +.+.+||.|+.+ ...+..|..||++.++
T Consensus 25 ~Lv~~PnS~------Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 25 RLVQSPNSF------FMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred eeecCCCCE------EEEEECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 577777654 566899999987 5889999999996444
No 57
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=37.81 E-value=8.3 Score=38.23 Aligned_cols=37 Identities=22% Similarity=0.539 Sum_probs=29.6
Q ss_pred cccCCchHHHHHHHHHHhcccCCCCCC------CCCCcchhccccccCC
Q 000158 1916 KLMCLPHLYQDLLQRYIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2014)
Q Consensus 1916 ~Li~LP~~yd~L~~~~~~~~Cp~c~~~------p~dPalCL~CG~lc~q 1958 (2014)
+||+=|..| +...+||.|+.+ ...+..|..||++.++
T Consensus 24 ~Lv~~PnS~------Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 24 RLVQGPNSY------FMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred eEecCCCCe------EEEEECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 577777654 566899999987 4889999999996544
No 58
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.70 E-value=20 Score=45.66 Aligned_cols=29 Identities=41% Similarity=1.065 Sum_probs=24.8
Q ss_pred ccccchHhhHHHHHHHHHHHHHhhhhccccCCCCccCCCCCccccccccc
Q 000158 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2014)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~R~~~R~~~er~h~~d~e~gEFLCPLCK~ 1477 (2014)
.+-|-|++|-.|.++..+.-+ -.||+||+
T Consensus 603 ~tPC~HifH~~CL~~WMd~yk---------------------l~CPvCR~ 631 (636)
T KOG0828|consen 603 LTPCHHIFHRQCLLQWMDTYK---------------------LICPVCRC 631 (636)
T ss_pred ccchHHHHHHHHHHHHHhhhc---------------------ccCCccCC
Confidence 567999999999999987654 46999998
No 59
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=35.30 E-value=35 Score=33.55 Aligned_cols=26 Identities=27% Similarity=0.542 Sum_probs=21.0
Q ss_pred CCCCCccccccchHhhHHHHHHHHHH
Q 000158 1421 IDCDGIHLSSCGHAVHQGCLDRYVSS 1446 (2014)
Q Consensus 1421 ~~~~G~H~SsCGH~MH~~C~~~Y~~S 1446 (2014)
++-.-+--+.|-|+-|..|-.+.+++
T Consensus 44 ~~eC~v~wG~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 44 GDECPVVWGVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred CCcceEEEEecchHHHHHHHHHHHhh
Confidence 33344557889999999999999987
No 60
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=34.95 E-value=18 Score=40.63 Aligned_cols=19 Identities=53% Similarity=1.256 Sum_probs=18.0
Q ss_pred ccCCCCCCCCCCcchhcccc
Q 000158 1935 CCSDCKSVLDEPALCLLCGR 1954 (2014)
Q Consensus 1935 ~Cp~c~~~p~dPalCL~CG~ 1954 (2014)
.| +||....-|+-||.||+
T Consensus 2 ~C-rCG~~l~~p~~Cl~Cg~ 20 (227)
T COG4031 2 IC-RCGAELSSPAFCLNCGR 20 (227)
T ss_pred cc-ccCCcccccchhcccCC
Confidence 58 99999999999999998
No 61
>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=33.72 E-value=28 Score=31.26 Aligned_cols=31 Identities=23% Similarity=0.842 Sum_probs=24.2
Q ss_pred Ccccc-cccCCceeEEeccCCCCCCccccccccCCCC
Q 000158 116 GVCGA-VWGNNDIAYRCRTCEHDPTCAICVPCFQNGN 151 (2014)
Q Consensus 116 ~~Cg~-v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~ 151 (2014)
..|.+ -+. ++-|+|..|. ..-+|.+||..+.
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 62
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=33.56 E-value=16 Score=30.77 Aligned_cols=22 Identities=23% Similarity=0.735 Sum_probs=18.2
Q ss_pred hcccCCCCCC-------CCCCcchhcccc
Q 000158 1933 KQCCSDCKSV-------LDEPALCLLCGR 1954 (2014)
Q Consensus 1933 ~~~Cp~c~~~-------p~dPalCL~CG~ 1954 (2014)
++.|++||++ |+.+.+|-.||.
T Consensus 1 Rr~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 1 RRICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEEETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred CcCcCCCCCccccccCCCCCCCccCCCCC
Confidence 3679999975 789999999998
No 63
>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=32.82 E-value=11 Score=33.28 Aligned_cols=36 Identities=28% Similarity=0.709 Sum_probs=22.4
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCC-CCCce
Q 000158 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN-HKEHD 156 (2014)
Q Consensus 117 ~Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~-H~~H~ 156 (2014)
.|+..--. ..-|+|..|. ..-||.+||..+. +.+|+
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 3679999995 5779999999864 45664
No 64
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=29.03 E-value=41 Score=42.75 Aligned_cols=42 Identities=33% Similarity=0.819 Sum_probs=29.9
Q ss_pred ccccccCCceeEEeccCCCCCCccccccccCCCC----C-CCceeEEEecC
Q 000158 118 CGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN----H-KEHDYSIIYTG 163 (2014)
Q Consensus 118 Cg~v~~~g~~~y~C~~C~~d~t~~~C~~CF~~~~----H-~~H~~~~~~~~ 163 (2014)
|..-.. |-+-.+|-.| |..-+|..||..|. | .+|.|.++.++
T Consensus 20 C~~dit-~~i~ikCaeC---p~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~ 66 (438)
T KOG0457|consen 20 CSLDIT-GLIRIKCAEC---PDFDLCLQCFSVGAETGKHQNDHPYRIMDTN 66 (438)
T ss_pred HhHHhc-cceEEEeecC---CCcchhHHHHhcccccCCCCCCCCceeecCC
Confidence 444443 4555889999 55569999997764 6 48999998764
No 65
>PF15353 HECA: Headcase protein family homologue
Probab=27.68 E-value=44 Score=34.73 Aligned_cols=20 Identities=20% Similarity=0.617 Sum_probs=17.7
Q ss_pred cchHhhHHHHHHHHHHHHHh
Q 000158 1431 CGHAVHQGCLDRYVSSLKER 1450 (2014)
Q Consensus 1431 CGH~MH~~C~~~Y~~Sl~~R 1450 (2014)
.|+.||-+||+.+=+++..+
T Consensus 40 ~~~~MH~~CF~~wE~~iL~~ 59 (107)
T PF15353_consen 40 FGQYMHRECFEKWEDSILKY 59 (107)
T ss_pred CCCchHHHHHHHHHHHHHHH
Confidence 39999999999999998764
No 66
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=27.46 E-value=42 Score=37.33 Aligned_cols=43 Identities=23% Similarity=0.496 Sum_probs=26.5
Q ss_pred hhHHHHHHHHHHHHHhhhhccc----c-----CCCCccCCCCCccccccccc
Q 000158 1435 VHQGCLDRYVSSLKERYNRRII----F-----EGGHIVDPDQGEFLCPVCRQ 1477 (2014)
Q Consensus 1435 MH~~C~~~Y~~Sl~~R~~~R~~----~-----er~h~~d~e~gEFLCPLCK~ 1477 (2014)
=|-+|+++|-.+-......... . ...+....+..|-.|||||.
T Consensus 37 rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~CPLCRG 88 (162)
T PF07800_consen 37 RHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPELACPLCRG 88 (162)
T ss_pred chhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccccCccccC
Confidence 3899999997765433221100 0 01123566778999999996
No 67
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.59 E-value=48 Score=41.35 Aligned_cols=19 Identities=32% Similarity=0.961 Sum_probs=16.6
Q ss_pred ccccchHhhHHHHHHHHHH
Q 000158 1428 LSSCGHAVHQGCLDRYVSS 1446 (2014)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~S 1446 (2014)
+++|||+.|..|.+..|+-
T Consensus 23 i~~cGhifh~~cl~qwfe~ 41 (465)
T KOG0827|consen 23 IGTCGHIFHTTCLTQWFEG 41 (465)
T ss_pred ccchhhHHHHHHHHHHHcc
Confidence 7789999999999988753
No 68
>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=24.19 E-value=15 Score=37.76 Aligned_cols=15 Identities=47% Similarity=1.136 Sum_probs=9.7
Q ss_pred ccccchHhhHHHHHH
Q 000158 1428 LSSCGHAVHQGCLDR 1442 (2014)
Q Consensus 1428 ~SsCGH~MH~~C~~~ 1442 (2014)
+--|||++|++|.+|
T Consensus 95 ~~p~~~v~H~~C~~r 109 (109)
T PF10367_consen 95 VFPCGHVVHYSCIKR 109 (109)
T ss_pred EeCCCeEEecccccC
Confidence 335677777777653
No 69
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=23.00 E-value=57 Score=39.53 Aligned_cols=33 Identities=42% Similarity=0.887 Sum_probs=23.3
Q ss_pred ceeEEeccC-CCCCCccccccccCCCCC-----CCceeEEEec
Q 000158 126 DIAYRCRTC-EHDPTCAICVPCFQNGNH-----KEHDYSIIYT 162 (2014)
Q Consensus 126 ~~~y~C~~C-~~d~t~~~C~~CF~~~~H-----~~H~~~~~~~ 162 (2014)
-+..+|-.| .+| +|..||-++.- .-|.|+++.+
T Consensus 18 ~~~i~C~eC~~~D----LC~pCF~~g~~tg~H~pyH~YRiiet 56 (432)
T COG5114 18 LTFIKCNECPAVD----LCLPCFVNGIETGVHSPYHGYRIIET 56 (432)
T ss_pred ceeeeeecccccc----eehhhhhccccccccCCCCCeeEeec
Confidence 345567777 444 88999988753 4689999864
No 70
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=22.77 E-value=31 Score=29.98 Aligned_cols=25 Identities=24% Similarity=0.527 Sum_probs=16.6
Q ss_pred cccCCCCCCC------CCCcchhccccccCC
Q 000158 1934 QCCSDCKSVL------DEPALCLLCGRLCSP 1958 (2014)
Q Consensus 1934 ~~Cp~c~~~p------~dPalCL~CG~lc~q 1958 (2014)
++||+|+... +--.+|-.||.+...
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEE 31 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeec
Confidence 4799999852 333499999987543
No 71
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=22.28 E-value=21 Score=32.25 Aligned_cols=23 Identities=35% Similarity=0.694 Sum_probs=14.2
Q ss_pred CCCCCCCCCCcchhccccccCCC
Q 000158 1937 SDCKSVLDEPALCLLCGRLCSPS 1959 (2014)
Q Consensus 1937 p~c~~~p~dPalCL~CG~lc~qs 1959 (2014)
++.+.....|+.|-+||.+|.++
T Consensus 15 ~k~~~~S~~PatCP~C~a~~~~s 37 (54)
T PF09237_consen 15 PKSKSQSEQPATCPICGAVIRQS 37 (54)
T ss_dssp -CCCCTTS--EE-TTT--EESSH
T ss_pred HHHhhccCCCCCCCcchhhccch
Confidence 45566789999999999999985
No 72
>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=22.02 E-value=72 Score=30.04 Aligned_cols=47 Identities=26% Similarity=0.430 Sum_probs=29.0
Q ss_pred cCCCCCCCCCCcchhccccc-cCCCCCcCCCcchHHHHHhhcCCCeEEEEEeccc
Q 000158 1936 CSDCKSVLDEPALCLLCGRL-CSPSWKPCCRESSCQSHAVACGAGTGVFLLIRVF 1989 (2014)
Q Consensus 1936 Cp~c~~~p~dPalCL~CG~l-c~qs~~~CC~~GeC~~Ha~~CGagvGIFL~IR~~ 1989 (2014)
|..|+....+.-+||.||.+ |.... .|--..|+.+=|. -+++.++..
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~-----~~Ha~~H~~~~~H--~l~v~~~~~ 48 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYS-----NGHALKHYKETGH--PLAVSLSTG 48 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTS-----TSHHHHHHHHHT----EEEETTTT
T ss_pred CCCCCCcCCceEEeCCCCcccccCCc-----CcHHHHhhcccCC--eEEEECCCC
Confidence 66777557889999999996 66531 3667888886553 344444433
No 73
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=21.74 E-value=44 Score=44.66 Aligned_cols=18 Identities=28% Similarity=0.803 Sum_probs=15.9
Q ss_pred ccccchHhhHHHHHHHHH
Q 000158 1428 LSSCGHAVHQGCLDRYVS 1445 (2014)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~ 1445 (2014)
-..|||+||-+|....|+
T Consensus 1045 Cg~C~Hv~H~sc~~eWf~ 1062 (1081)
T KOG0309|consen 1045 CGTCGHVGHTSCMMEWFR 1062 (1081)
T ss_pred hccccccccHHHHHHHHh
Confidence 568999999999999874
No 74
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.59 E-value=57 Score=40.23 Aligned_cols=17 Identities=29% Similarity=0.880 Sum_probs=15.0
Q ss_pred ccccchHhhHHHHHHHH
Q 000158 1428 LSSCGHAVHQGCLDRYV 1444 (2014)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~ 1444 (2014)
++.|||.|=.+|.++.+
T Consensus 23 i~~CGH~~C~sCv~~l~ 39 (309)
T TIGR00570 23 VNVCGHTLCESCVDLLF 39 (309)
T ss_pred cCCCCCcccHHHHHHHh
Confidence 44899999999999986
No 75
>PRK02935 hypothetical protein; Provisional
Probab=21.02 E-value=34 Score=35.33 Aligned_cols=22 Identities=23% Similarity=0.747 Sum_probs=17.8
Q ss_pred hcccCCCCCC---CCCCcchhcccc
Q 000158 1933 KQCCSDCKSV---LDEPALCLLCGR 1954 (2014)
Q Consensus 1933 ~~~Cp~c~~~---p~dPalCL~CG~ 1954 (2014)
+..||+|+++ .-.--.|..|++
T Consensus 70 qV~CP~C~K~TKmLGrvD~CM~C~~ 94 (110)
T PRK02935 70 QVICPSCEKPTKMLGRVDACMHCNQ 94 (110)
T ss_pred eeECCCCCchhhhccceeecCcCCC
Confidence 4489999987 355669999999
Done!