Query 000264
Match_columns 1764
No_of_seqs 363 out of 573
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 01:53:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000264.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000264hhsearch_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 6.6E-91 1.4E-95 904.7 44.9 688 282-1214 371-1084(1738)
2 KOG1139 Predicted ubiquitin-pr 100.0 1.5E-30 3.2E-35 316.3 6.9 486 1221-1759 5-500 (784)
3 KOG1140 N-end rule pathway, re 99.9 7.2E-23 1.6E-27 270.4 0.6 929 18-1000 532-1502(1738)
4 smart00396 ZnF_UBR1 Putative z 99.8 1.5E-19 3.2E-24 169.5 5.8 70 116-185 1-71 (71)
5 PF02207 zf-UBR: Putative zinc 99.7 1.7E-18 3.6E-23 162.7 4.1 70 116-185 1-71 (71)
6 KOG1139 Predicted ubiquitin-pr 98.4 2.9E-06 6.4E-11 106.4 15.9 185 754-938 207-477 (784)
7 PF10390 ELL: RNA polymerase I 97.1 0.00029 6.3E-09 83.7 3.3 81 869-954 198-281 (284)
8 KOG1777 Putative Zn-finger pro 95.3 0.0067 1.5E-07 73.2 1.3 65 111-176 539-608 (625)
9 PF13639 zf-RING_2: Ring finge 94.2 0.017 3.7E-07 49.6 0.8 23 1423-1445 13-35 (44)
10 cd00162 RING RING-finger (Real 93.4 0.06 1.3E-06 44.9 2.6 22 1425-1446 12-33 (45)
11 PF13764 E3_UbLigase_R4: E3 ub 92.9 0.46 1E-05 63.8 11.0 69 1146-1228 422-496 (802)
12 KOG4445 Uncharacterized conser 92.3 0.051 1.1E-06 63.4 0.8 52 1424-1477 129-183 (368)
13 KOG0943 Predicted ubiquitin-pr 92.0 0.051 1.1E-06 71.4 0.5 64 115-184 1240-1309(3015)
14 smart00184 RING Ring finger. E 87.6 0.46 1E-05 38.1 2.6 22 1424-1445 9-30 (39)
15 COG5243 HRD1 HRD ubiquitin lig 87.5 0.25 5.4E-06 59.2 1.4 16 1430-1445 317-332 (491)
16 PF12861 zf-Apc11: Anaphase-pr 87.1 0.36 7.7E-06 47.7 1.9 28 1419-1446 40-67 (85)
17 PF14634 zf-RING_5: zinc-RING 86.8 0.55 1.2E-05 40.6 2.7 33 1423-1477 12-44 (44)
18 PF00097 zf-C3HC4: Zinc finger 86.8 0.43 9.4E-06 40.2 2.0 20 1427-1446 13-32 (41)
19 KOG4796 RNA polymerase II elon 84.6 1.1 2.4E-05 56.4 4.8 78 869-952 211-291 (604)
20 cd02335 ZZ_ADA2 Zinc finger, Z 83.8 0.91 2E-05 40.4 2.7 39 117-159 5-48 (49)
21 cd02340 ZZ_NBR1_like Zinc fing 82.5 1.1 2.4E-05 38.8 2.7 37 117-158 5-41 (43)
22 cd02249 ZZ Zinc finger, ZZ typ 82.1 1.1 2.3E-05 39.3 2.5 37 117-158 5-44 (46)
23 KOG2752 Uncharacterized conser 80.9 1.9 4E-05 51.5 4.6 61 112-173 37-101 (345)
24 PLN03208 E3 ubiquitin-protein 80.7 1.5 3.2E-05 49.7 3.5 57 1426-1488 31-89 (193)
25 cd02338 ZZ_PCMF_like Zinc fing 79.4 1.6 3.4E-05 38.9 2.6 38 117-159 5-48 (49)
26 PF13923 zf-C3HC4_2: Zinc fing 78.2 0.83 1.8E-05 38.4 0.5 22 1425-1446 11-32 (39)
27 PF11793 FANCL_C: FANCL C-term 78.0 0.75 1.6E-05 43.9 0.2 38 1429-1477 26-63 (70)
28 cd02344 ZZ_HERC2 Zinc finger, 77.1 2 4.3E-05 37.8 2.5 39 117-159 5-44 (45)
29 KOG2905 Transcription initiati 75.6 2 4.3E-05 49.7 2.7 61 870-931 183-245 (254)
30 PF12678 zf-rbx1: RING-H2 zinc 73.8 1.9 4E-05 41.6 1.7 21 1424-1444 43-63 (73)
31 PF00643 zf-B_box: B-box zinc 73.3 1.8 4E-05 36.7 1.3 37 116-158 4-40 (42)
32 KOG1940 Zn-finger protein [Gen 73.2 1.5 3.3E-05 52.1 1.1 33 1426-1480 175-207 (276)
33 KOG2114 Vacuolar assembly/sort 69.3 2.1 4.5E-05 56.7 1.2 24 1429-1477 857-880 (933)
34 cd02339 ZZ_Mind_bomb Zinc fing 64.9 4 8.7E-05 35.9 1.7 30 126-158 13-43 (45)
35 PHA02926 zinc finger-like prot 62.8 5 0.00011 46.2 2.4 42 1427-1484 193-234 (242)
36 PHA02929 N1R/p28-like protein; 60.2 4.4 9.6E-05 47.5 1.5 34 1428-1483 197-230 (238)
37 COG5194 APC11 Component of SCF 59.9 9.5 0.00021 37.3 3.3 28 1419-1446 42-69 (88)
38 KOG0827 Predicted E3 ubiquitin 57.8 7.4 0.00016 47.7 2.8 28 1417-1444 12-39 (465)
39 PF13920 zf-C3HC4_3: Zinc fing 56.6 7.1 0.00015 34.5 1.8 20 1426-1445 15-35 (50)
40 cd02343 ZZ_EF Zinc finger, ZZ 55.3 6.7 0.00014 35.1 1.4 35 117-156 5-40 (48)
41 cd00021 BBOX B-Box-type zinc f 53.9 9.8 0.00021 31.4 2.2 28 126-158 10-37 (39)
42 cd02336 ZZ_RSC8 Zinc finger, Z 53.2 4.7 0.0001 35.6 0.1 31 117-152 5-35 (45)
43 KOG4172 Predicted E3 ubiquitin 52.4 7.1 0.00015 35.5 1.1 16 1426-1441 20-36 (62)
44 cd02341 ZZ_ZZZ3 Zinc finger, Z 51.8 10 0.00022 34.0 1.9 39 117-158 5-46 (48)
45 smart00336 BBOX B-Box-type zin 49.6 14 0.00029 31.1 2.4 29 125-158 12-40 (42)
46 PF02270 TFIIF_beta: Transcrip 48.0 9.6 0.00021 45.7 1.7 31 899-930 244-274 (275)
47 cd02337 ZZ_CBP Zinc finger, ZZ 46.4 11 0.00024 32.6 1.3 32 116-153 4-35 (41)
48 cd02334 ZZ_dystrophin Zinc fin 41.5 17 0.00038 32.6 1.8 32 117-152 5-36 (49)
49 KOG0828 Predicted E3 ubiquitin 41.1 15 0.00033 46.3 1.9 31 1427-1478 602-632 (636)
50 smart00291 ZnF_ZZ Zinc-binding 40.9 19 0.00042 31.3 2.0 33 116-153 8-40 (44)
51 cd02345 ZZ_dah Zinc finger, ZZ 39.9 20 0.00043 32.1 2.0 31 116-151 4-35 (49)
52 KOG4628 Predicted E3 ubiquitin 35.3 16 0.00035 45.1 0.9 34 1423-1477 242-275 (348)
53 KOG1941 Acetylcholine receptor 32.7 26 0.00057 43.1 2.1 21 1424-1444 380-400 (518)
54 PF00569 ZZ: Zinc finger, ZZ t 32.4 12 0.00026 32.9 -0.6 36 117-156 9-45 (46)
55 PF07800 DUF1644: Protein of u 31.7 32 0.00069 38.0 2.3 54 1434-1487 36-98 (162)
56 KOG0802 E3 ubiquitin ligase [P 30.3 28 0.00061 45.8 2.0 26 1430-1477 313-338 (543)
57 KOG2930 SCF ubiquitin ligase, 29.5 36 0.00079 35.0 2.1 23 1423-1445 73-95 (114)
58 PF10367 Vps39_2: Vacuolar sor 27.5 14 0.0003 37.3 -1.2 16 1426-1441 93-108 (109)
59 COG5432 RAD18 RING-finger-cont 25.5 46 0.001 39.7 2.3 19 1426-1444 38-56 (391)
60 KOG0457 Histone acetyltransfer 25.2 56 0.0012 41.3 3.1 36 125-163 26-66 (438)
61 smart00744 RINGv The RING-vari 24.7 56 0.0012 29.3 2.2 23 1424-1446 12-39 (49)
62 COG5114 Histone acetyltransfer 24.6 44 0.00095 40.3 2.0 33 126-162 18-56 (432)
63 TIGR00599 rad18 DNA repair pro 24.4 38 0.00082 42.8 1.5 19 1427-1445 40-58 (397)
64 TIGR00570 cdk7 CDK-activating 23.3 47 0.001 40.5 2.0 18 1427-1444 22-39 (309)
65 KOG1493 Anaphase-promoting com 22.4 48 0.001 32.4 1.4 24 1422-1445 42-65 (84)
66 KOG0823 Predicted E3 ubiquitin 21.9 39 0.00083 39.5 0.8 49 1423-1490 57-107 (230)
67 PF15227 zf-C3HC4_4: zinc fing 20.6 55 0.0012 28.3 1.3 20 1425-1444 10-29 (42)
No 1
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.6e-91 Score=904.70 Aligned_cols=688 Identities=24% Similarity=0.381 Sum_probs=494.0
Q ss_pred ccCCCCHHHHHHHHHHHH-HhhCChhhHHHHHHHHHhhhHHHHHHHHHhccccccccCCcccceeeecccCCCchHHHHH
Q 000264 282 AEMFSSDVVVRKLHELLL-KLLGEPIFKYEFAKVFLSYYPVFVKDAIREHSDDTIKKYPLLSTFSVQIFTVPTLTPRLVK 360 (1764)
Q Consensus 282 ~~~~L~K~ar~~Lh~Lll-sLL~d~eFK~~FA~~Fvk~Y~~i~~~fL~dd~d~~~~~~siV~sLSVQLFTvPSLA~~LV~ 360 (1764)
.+..+||..|..++.+++ .+-++.+||+.||.+|+.+|..+..+|+..|++. ..+.| .++||+||+|++|..+++
T Consensus 371 ~d~~~~kr~r~~l~k~~~~~~~~~~~~k~~~~~~~~~~y~~~~~~~~~~d~e~---~~~vi-~~~vqf~t~~~~a~~~~~ 446 (1738)
T KOG1140|consen 371 FDNRYWKRLRKDLQKVIIPTFASSNLYKPIFAQQFVEHYNSITRDFAYMDREP---DLSVI-ELSVQFFTCPSLAKNIVE 446 (1738)
T ss_pred HHHHHHHHHHHHHhhcceeehhcchHHHHHHHHHHHHHHHHHHHHHHhhcCCc---chhhH-hheeeeecCcHHHHHhhh
Confidence 345567889999999999 6778999999999999999999999999998874 34545 999999999999999999
Q ss_pred hhcHHHHHHHHHHHHhhhhcCCCCcceee---------cccccccchhhhhhhhhhhccchhhhHHHhhhchHHHHHHHH
Q 000264 361 EMNLLEMLLGCLREIFDSCAGDDSCLQVA---------KWANLYETTNRVIGDIRFVMSHAAVSKYATHEQLNISKAWMK 431 (1764)
Q Consensus 361 e~nLL~iLl~tl~~~~~~~~~~d~~l~~~---------~~~~~~~ry~~I~~DLrYlLsh~~Va~~l~~~~~~l~~~~l~ 431 (1764)
...++..+..++..++..+...++...+. +.....+|.+..+.|+ +.+.++.+ -.++..+..++.
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 99988888777776665444333221111 1222357778888888 77777762 357899999999
Q ss_pred HHHHhcCCCcccccccCcceeeCCceeehhhhhHHHHHHHHhhhhhccccccccccccccccccccCCCCCccccccccc
Q 000264 432 LLTFVQGMNPQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEETRYDFSMYKQDIGDGDSLRHAKVGR 511 (1764)
Q Consensus 432 lLsl~QGMnp~kRq~~~HVEyE~e~W~~AF~Le~~la~I~~l~~~~~~s~~~~~e~~~~~~~~~~~~~~~~~~r~~kv~r 511 (1764)
++..||||.|++|+.++||++|++ |+.+|.+-.++..+++.++.||.... ++-
T Consensus 521 ~~~v~qg~~~lkr~~~ehv~~e~~-~~~~~~~v~~~t~~~s~i~~~~~~~e-------------------------p~~- 573 (1738)
T KOG1140|consen 521 LLKVFQGVDPLKREELEHVEVEKE-WENFFSLVEYLTAIYSMIQSLVKTSE-------------------------PVK- 573 (1738)
T ss_pred HHHHhCCccHHHHHHhhhhcccch-HHHHHHHHHHHHHHHHHHHHHHHhcc-------------------------chh-
Confidence 999999999999999999999996 99999999999999999998886653 000
Q ss_pred cccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhhhcCCCCcccccccCCCCcccccCcch
Q 000264 512 LSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENWLGVDDRSVSVNDILSPNASRISGSNF 591 (1764)
Q Consensus 512 ~~~e~sv~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~l~~l~~~cl~~l~~~l~~~~~~~~~~~~~s~~~~~~~~~~~ 591 (1764)
..++..|.-++..... .
T Consensus 574 ----------------------------------------~~~~~~l~~~~~r~~~-----s------------------ 590 (1738)
T KOG1140|consen 574 ----------------------------------------DSVYKKLLEAAIRIHP-----S------------------ 590 (1738)
T ss_pred ----------------------------------------hhHHHHHHHHHhhccc-----c------------------
Confidence 0011122212211100 0
Q ss_pred hhhhhhhhhccccccccccccCCccccccccccCCCccccccCccccccccCCcccccccccCcCCccccccchhccccc
Q 000264 592 VALKKTLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKITISGERDTASWRSAGFNDSEMEGECATELDNL 671 (1764)
Q Consensus 592 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 671 (1764)
++++ +. + ...++++
T Consensus 591 -------------------~~~~---------------------~~---l---------------~~~i~~~-------- 604 (1738)
T KOG1140|consen 591 -------------------LTGS---------------------ES---L---------------TYTICGE-------- 604 (1738)
T ss_pred -------------------cCcc---------------------ce---e---------------eehhhhh--------
Confidence 0000 00 0 0011222
Q ss_pred cccccCccCceeeeccCCceeeehHHHHHHHHHHHHHHhhhccccccccccccCCCCCccccchhhhhcccCCCCCCccc
Q 000264 672 HVLSLCYWPDITYDVSSQDVSVHIPLHRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFS 751 (1764)
Q Consensus 672 ~~~~~~~~~~v~fdVs~~~VSfH~PLHr~Ls~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~df~~~vl~~~~~~~~~ 751 (1764)
...++.|+|+.++||||+|+.|+|+++++..... ++...+.+ ..+.+.+. .
T Consensus 605 ------S~e~i~f~v~~~~~sv~~p~~~~l~~l~~~~~s~-------------------v~~~~d~~-~~~~~~~n---~ 655 (1738)
T KOG1140|consen 605 ------SHETINFSVSQERVSVSNPVSRLLAFLIELSCSS-------------------VVSLKDAY-ERLEDCSN---F 655 (1738)
T ss_pred ------hHhHhhhccccccceeeccHHHHhhhhhhcccch-------------------hhhcchhh-hhHhhhcc---c
Confidence 1256899999999999999999999998532110 11111111 11122222 2
Q ss_pred hhhhchhHHHHHHHHHHhhCceeechHHHhHHHHHhccccccccccchhHHHHHHHHhhCChHHHHHHHHHHhccccccc
Q 000264 752 AFVMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLS 831 (1764)
Q Consensus 752 ~~l~E~PLR~~Vl~AQI~AGmWVRNG~si~~Q~~~Y~~~~~re~~~d~DIfLLQ~~asl~dP~~Fl~~iL~RF~L~~w~~ 831 (1764)
.+|.|||||++|++|||.+|||||||.++.+|+++|++.+||+++|++||+++|.++++.||++|+.++++||+|.+|++
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 000264 832 LNLERPSE-YE---PILVQEMLTLIIQILQERRFCGL---TTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQE 904 (1764)
Q Consensus 832 ~~~~~~~~-ye---~~mvEE~L~lLI~LltER~~~g~---s~~e~lRrEIIh~Lc~~p~t~SeL~~~lpe~~~~~~~fe~ 904 (1764)
|....... ++ ..|+|+|+.+||.|++||...|+ +..+.+|+||||+||++|++||+|++.+|++++++..||.
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 5778999999999999999999999999999999999999
Q ss_pred HHHHHhcccCCCCC-CcceeEehhhhhccccccccccCchhHHHHHHHHHHh--hc---cccccCC-CCCCccCCC-ccc
Q 000264 905 ILDAVAMYSHPSGF-NQGMYSLRWSYWKELDIYHPRWSSRDLQVAEERYLRF--CS---VSALTAQ-LPRWTKIYY-PLE 976 (1764)
Q Consensus 905 iL~eVA~fk~Psgl-~~G~Y~LK~e~~~e~DPy~~~y~~~d~q~Aeer~~r~--~k---~~a~~~~-~P~~~~~~~-pf~ 976 (1764)
++++||+|++|.|+ +.|+|+||++||+++||||+||+++++.+++..+++. .+ ..|..++ .|++.+.+. .+.
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 7899999999999999999999999998887655432 11 1133322 223322221 134
Q ss_pred hhhhccccHHHHHHHHHHHHHHhccCCCCCCCCchhHHHHHHHHH-HHHHhhhhhhccCCCCCcccCCCcccccchhhHH
Q 000264 977 SIAGIATCKVVLQVIRAVLFYAVFTDNPTDSRAPYGVLLTALHLL-ALALDVCFQKKKSGDQSCDIGGSTPILDFASEEI 1055 (1764)
Q Consensus 977 ~I~~il~s~~f~~il~~vL~~al~~~~~s~s~~~E~lL~~aLHLi-~lAL~~~~~e~~~~~~s~~~~~~~p~~~~~~~~~ 1055 (1764)
++.+.....+|-.||+.++.++.+.. .+.++..++|++ ++|++++..-- . |. +..+++
T Consensus 896 ~L~~~t~~~~~~~ii~r~~~~~~~~~-------s~~~l~~~~~~ihG~~~~~~l~~~----~-------~~-~~~~~e-- 954 (1738)
T KOG1140|consen 896 ILGAAVRLTVFGLIIYRTLEHCLFME-------SSTLLSKVLHLIHGIALNEELINM----K-------FA-FTQKTE-- 954 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhc----c-------cc-cccccc--
Confidence 55666666777788888887777543 488999999554 99998653211 0 00 000011
Q ss_pred hhccCCCCCcccHHHHHHHHHhhhhccCCccccccccCcchhHHHHHHHHHHhhhHHHHHHHhhhchhhhhcccCCCCCC
Q 000264 1056 AEGLNNGAGKQSLLSLLVFLMGMYKKDGADNFLEAGNCNLSSVIESLLKKFAEIDSRCMTKLQQLAPEIVSHLSQSLPRD 1135 (1764)
Q Consensus 1056 ~~~~s~~~~~~SLlsLL~~L~~~~~~~~~~~~~e~~~~~i~~iI~~lL~~f~~~~~~c~~~l~~~~p~~~~~~~~~~~~~ 1135 (1764)
.-.+.+.+.+++.+..++....+ +.+++++++.|..+.. .+...|++.. .... ...
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 11244567777777777544322 3567888888765543 2333343321 1100 011
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCCCCCCCcccCCCccccccccCCCCceeccCCCC
Q 000264 1136 DTSGSFSASDSEKRKAKARERQAAILEKMKAEQFKFLSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS 1214 (1764)
Q Consensus 1136 ~~~~~~~~se~EkKKalAkeRQAKIMAQMkaQQkkFLenn~d~~dedd~~~~d~~~sd~~~~~~es~~~tCILCqE~~s 1214 (1764)
..+.+..+.+.++||++|++||+|+||||+.||.+||++|.++.|+++. ..+++...+..++ ..+|.+|+....
T Consensus 1011 ~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e~d~~~~---~~~~~~~~~~~~~--d~~~~~~~~~s~ 1084 (1738)
T KOG1140|consen 1011 KQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDEFDEQEN---QTPSSGSKTYEEE--DFTCALCQDNSC 1084 (1738)
T ss_pred ccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccccCcccc---cCccccccchhhh--hccchhhhccch
Confidence 1122334445677888999999999999999999999999766554432 2222221122122 567888887654
No 2
>KOG1139 consensus Predicted ubiquitin-protein ligase of the N-recognin family [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=1.5e-30 Score=316.30 Aligned_cols=486 Identities=11% Similarity=-0.043 Sum_probs=356.0
Q ss_pred EEeeecccccccccCCCCCccccccccccccccccccccccCCCCCCCCCCCCcchhhHHHHHHHHhhccccCCCChhhh
Q 000264 1221 LILLQKSRLLSFVDRGSPSWDQDQWLGKECGTISANNMVNQFGTNTPSSGLGVISSCQLAQVAEEAVNQFAYNGKPEEVN 1300 (1764)
Q Consensus 1221 la~vQ~SrILr~t~~~~p~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1300 (1764)
+.+.|+|-.....+.++|.|+..+.+-+.= -.+.+..-+.+...| .+..- ..-++.....++|-+.-
T Consensus 5 ~~~sqkSlckel~e~glpfl~if~~sR~~i---ggd~apsc~~~~e~S---------~fl~~-s~~l~sql~~~~Pk~Sa 71 (784)
T KOG1139|consen 5 QMLSQKSLCKELNENGLPFLTIFDVSRFLI---GGDSAPSCISLKEVS---------IFLES-SRFLNSQLTNGRPKWSA 71 (784)
T ss_pred hhhChHHHHHHHHhcCCchhhhhhHHHHHh---ccCCCchhHHHHHHH---------HHHHh-cccccccccCCChhHHh
Confidence 467889999999999999999988876542 222222211111110 00000 00112222445566666
Q ss_pred hHHHHHHhhCCCCcccCCCccccCCCcCCCcchhhHHhhh------HHHHHHHhhcCCCCCccccccchhhhhcCCccCC
Q 000264 1301 SVLEFVKAQFPSLRNIPIPFTFSNGRKCTASSMEMFEQDL------YLSICREMRKNMTYPDLMKEDEECSVAEGGLKNR 1374 (1764)
Q Consensus 1301 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 1374 (1764)
..++++.++| +.+.++=.+.+.+.+......|.++.++ |..+..||. ++. ..-......--.|..
T Consensus 72 mm~e~n~arF--i~~lq~ykr~ssn~e~h~sqgeallIdeek~~~P~~~~L~elt-rmd------fQ~r~~~tcs~~Nsv 142 (784)
T KOG1139|consen 72 MMMENNAARF--IHGLQFYKRDSSNVETHTSQGEALLIDEEKFGGPYMKMLCELT-RMD------FQWRIISTCSQENSV 142 (784)
T ss_pred hhhhhhHHHH--hhcceEEeccCCCCccccccchhhhHHHHHhcCcHHHHHHHHh-ccC------ccceecccchhccCC
Confidence 6677777665 6666666666665555444556666666 677777877 333 111111111111222
Q ss_pred CCCcccccchhhhhhhhhhhccccccccccccchhhhccccCCCCCCCCCCceEcccchHhhHHHHHHHHHHHHHhhhcc
Q 000264 1375 GNSDSFLLGKYVASISKEMRENASASEVSRGDRIAAESLVYDGFGPIDCDGIHLSSCGHAVHQGCLDRYVSSLKERYNRR 1454 (1764)
Q Consensus 1375 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~g~~~~~CgH~~H~~C~~~y~~sl~~r~~~~ 1454 (1764)
+.+.. +-+..+.-..+...... .+.+|++|.+..+++.|.++|+|+.|.+|..+|+.....+-...
T Consensus 143 ~k~pt-len~cp~frl~k~L~a~-------------qqssyD~fv~h~q~~~asTsi~hf~~dsv~~r~l~eell~wg~~ 208 (784)
T KOG1139|consen 143 QKAPT-LENECPAFRLFKILAAI-------------QQSSYDRFVDHIQSQHASTSITHFTEDSVRSRLLNEELLIWGLL 208 (784)
T ss_pred CCCCc-ccccccceechhhcccc-------------cccCCCcceecccccccchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22211 33455544444433221 12236999999999999999999999999999999999988888
Q ss_pred cccCCCcccCCCCccccccchhhccccccccCCCCcccCCC-CccccccccccCCCCCcccccccchhhHHHHHHHHHHh
Q 000264 1455 IIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRINE-QPTVSGVGLSLDSSSSFTTREENTSFQLQQAVSLLQSA 1533 (1764)
Q Consensus 1455 ~~~~~~~~~~~~~~Ef~CPlCr~l~N~~lP~~p~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~l~l~~~~ 1533 (1764)
..|.+.+..+....++.|+.|+++||+|.|..|+..-+... +.-|-+...|.+ --..++++.++|..+..+
T Consensus 209 ylf~~~ev~rll~~g~~~~~c~alAKvveq~y~~~~~s~~kkrhePdt~~~r~~--------hi~~slfl~e~la~~~~~ 280 (784)
T KOG1139|consen 209 YLFLRIEVARLLINGNMWVRCGALAKVVEQIYSQWNVSSAKKRHEPDTIRFRAA--------HIDKSLFLKELLASFNIT 280 (784)
T ss_pred hhhhhhhHHHHHhcCCCccccHHHHHHHHHhcccchhcccccCCCCchhccccc--------cccHHHHHHHHHHHhhhh
Confidence 88999999999999999999999999999999776653333 222222222221 124688999999999999
Q ss_pred hhhhccCccccccCCchhhHHh--hhHHHHHHHhhhhhcccccccccCCCC-CCCchhhHHHHhhhhhhhhhhhccCCCC
Q 000264 1534 SNVVGKADVIESFPLMKNEIMA--SNVEAVSRRMCKMYFQNKLDKFFGSAR-VNPSLIMWDALKYSLMSMEIAARSEKTS 1610 (1764)
Q Consensus 1534 ~~~v~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~y~p~~~~~~~~~~~-~~~~l~lw~~~~ysl~s~Ei~~R~~~~~ 1610 (1764)
+.+....+......++...-.. .+..++.++.|..|+|...+.+-..-+ .+...-+||++.|..++.|+..|--+-+
T Consensus 281 ec~~~di~r~v~~~p~~s~L~~~~~~~~~~~k~~~~~Hsr~p~~~~l~~f~~p~lEaa~~d~l~~v~~~~e~~~R~~~~s 360 (784)
T KOG1139|consen 281 ECIKIDIGRFVEKSPESSILFQETEVTIDFTKQSPIDHSRDPRIPILGEFIRPHLEAAGVDALIDVEMEREFDPRLFDDS 360 (784)
T ss_pred hhhhhhccceeEeccccccchhhhhhhccccccCchhcccCcchhHHHHhhccccccccCchHHHHhhhccccccccchh
Confidence 8776666666677766555333 677778999999999888777653333 4577789999999999999999999999
Q ss_pred CCCCcchHHHHHHhhhccchHHHHHHHHHHHhhccchHHHHHHhhhhhHhhhhhcccccCCCCCCCcCCCCCcchhhccc
Q 000264 1611 TTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVLQRFRGIQLFAESICSGTSIDNPGGRCKRGGNMLSILKHA 1690 (1764)
Q Consensus 1611 ~~~~~~~~~l~~~~~s~~g~~l~~l~~~~~~~~~~~~~~vl~r~~g~ql~~~s~~~~~s~~~~~~~~~~~~~~~~~~~~~ 1690 (1764)
..+++|..+++++++.+-|++++|++.+++..|++|.+|+-+||-||.-+|+++|.|+|+-.++...+.+|.- -++++|
T Consensus 361 ~vlr~~~~~~~e~~~~~~~~~f~l~~~~v~~s~~~~ai~~~~~~~em~n~~a~~~~~~s~~~aS~~~~~~~~~-~~f~~i 439 (784)
T KOG1139|consen 361 EVLRTIVIREPEWIDPMFWGMFKLVAELVVVSVNSGAIPEEHYRSEMVNCMAMGNVPYSRLRASISEKGSMID-KHFETI 439 (784)
T ss_pred hhhHHhhhccccccchhhcchHHHHHHHhhhhcccccchHHHHHHHHHhHHHhcCCCcccccccccCCCcccc-cccccc
Confidence 9999999999999999999999999999999999999999999999999999999999999997555544422 224444
Q ss_pred cccCCCccchhccccCCCccccCcchhHHHHHHHhccccccccCcchHHHHHHHHHHHHHHHHHhccCC
Q 000264 1691 DVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFILCKESLLSLVHVFYAVTLSQYYHVVGNFN 1759 (1764)
Q Consensus 1691 ~~~~~~~~~~~w~~~~~pvl~~d~~s~~~~~l~~l~~~~~~~~~~~~~~v~~~~~~~~~q~~~~~~~~~ 1759 (1764)
. --|+++.|||++||||+++||.|||+|.||..|.++|+.++|.|..+..+|++++.+-=-
T Consensus 440 ~--------~~~~~~~~P~~~~~p~~~~s~~l~~~~~~~~~c~~~~~~~~~s~~~~~~v~~~~~~~a~k 500 (784)
T KOG1139|consen 440 L--------NEIGDFIEPIETTTPLMQGSYQLKTSIWDSEVCPVFFMMRSTSIKQAREVFAKMEIRAQK 500 (784)
T ss_pred c--------ccccccccchhhcCccccchhhccccCCccccccchheeeeeeccchhHHHHHHHHhhcc
Confidence 3 569999999999999999999999999999999999999999999999999999876433
No 3
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.85 E-value=7.2e-23 Score=270.39 Aligned_cols=929 Identities=17% Similarity=0.051 Sum_probs=576.3
Q ss_pred HHHHHHhcCCchhhhchhhHHHHhhhCCCChhHHHhccCCCCHHHHHHHHHHHhhcccCCCCCCh-h-hhHHHHHHHHHH
Q 000264 18 IVRRLMNIGVPEEFLDYSGIVNFAKNDKSRIPELVSTILPPDEEVAEVIQDAKAKNKKVSVGPNM-K-GRFRESMLWLQW 95 (1764)
Q Consensus 18 ~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~l~~l~~ 95 (1764)
..+++--.++++++-...+++.|+...+..|-..+.+..|..+.+...+..+..+..++-+..++ + ..|.+....+.|
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 34667778888888777899999999999999999999999999998888877777776555444 3 447888888888
Q ss_pred HhcCCCHHHHHHHHHc--cCCCCcccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecCCccccCCCcc
Q 000264 96 LMFEREPEKVLRKLSK--IGQRGVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDVT 173 (1764)
Q Consensus 96 ~~~~~~~~~~l~~l~~--~~~~~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~~~~~~gG~CDCGD~~ 173 (1764)
.++.+.+.-...-... -.-...|+.+|...+.+++|++|.- .+.+|..|++...|-.|.+..+-..+|+|+|+ ..
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 7776544321111111 1226889999999999999999986 89999999999999999988887889999999 99
Q ss_pred cccccCCCCCCCCCCCCCCCcHHHHHhHHHHHHHHHHHHHHH--hhhccccCCCCCCCCchHHHHHHHHHHHHHHHHHHH
Q 000264 174 AWKREGFCSRHKGAEQIQPLPEKYANSAAPVLDALFIYWENK--LSLAESVGQENPRASDHVAERRKLANELTFAVVEML 251 (1764)
Q Consensus 174 awk~~~fC~~H~~~~~~~~lp~~l~~~~~~~~~~ll~~~~~~--L~~~e~~~~~~~~~~d~~~~~~kva~~l~~~ii~~L 251 (1764)
+|...++|..|....++-++-..+... +..+.++.+|-.. ..|...+ .+....|...+..++.+++...|+.++
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--DPNRFLFTILSRFELLDWFTGE--VDYQSNDTEDTISFMIEEFLALIILLL 764 (1738)
T ss_pred HhhcCccccccchhHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHhcCC--CccccccHHHHHHHHHHHHHHHHHHHH
Confidence 999999999998876554444443332 3333333332221 1222211 223345666677777888877777777
Q ss_pred HHHHhchHHHHHHHHHHhhcccchHHHHHhccCCCCHHHHHHHHHHHHHhhCChhhHHHHHHHHHhhhHHHHHHHHHhcc
Q 000264 252 LEFCKNSESLLSFVSKRVISVIGLLDILVRAEMFSSDVVVRKLHELLLKLLGEPIFKYEFAKVFLSYYPVFVKDAIREHS 331 (1764)
Q Consensus 252 ~e~~~~s~~Llswl~~~l~~~~~Ll~~Ll~~~~~L~K~ar~~Lh~LllsLL~d~eFK~~FA~~Fvk~Y~~i~~~fL~dd~ 331 (1764)
.++... .+...........+++-+|......+.+.+++..|.+...+..|..++..++..+...|+...--.+++.-
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 11112122222335555666555556677888999999889999999999998888888554333334433
Q ss_pred ccccccCCcccceeeecccCCCchHHHHHhhcHHHHHHHHHHHHhhhhc--CCCCcceeecccccccchhhhhhhhhhhc
Q 000264 332 DDTIKKYPLLSTFSVQIFTVPTLTPRLVKEMNLLEMLLGCLREIFDSCA--GDDSCLQVAKWANLYETTNRVIGDIRFVM 409 (1764)
Q Consensus 332 d~~~~~~siV~sLSVQLFTvPSLA~~LV~e~nLL~iLl~tl~~~~~~~~--~~d~~l~~~~~~~~~~ry~~I~~DLrYlL 409 (1764)
++....|-...++|+|.-+++++++...+..+.+...+-.+...+..++ +.++-+........-....+.+.++++.+
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 3334455556688999999999999888887766555555444444443 12222222221111223345667788888
Q ss_pred cchhhhHHHhhhchHHHHHHHHHHHHhcCCC--cccccccCcceeeCCceeehhhhhHHHHHHHHhhhhhcccccccccc
Q 000264 410 SHAAVSKYATHEQLNISKAWMKLLTFVQGMN--PQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEET 487 (1764)
Q Consensus 410 sh~~Va~~l~~~~~~l~~~~l~lLsl~QGMn--p~kRq~~~HVEyE~e~W~~AF~Le~~la~I~~l~~~~~~s~~~~~e~ 487 (1764)
++--..+.+..-.-...+.++..+.+++++. +..|++|--.-++...=...+...+.+..++.++....++..++.|.
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 8765555443334578889999999999999 99999997775555522333344577888999998888888877754
Q ss_pred c-cccccccccCCCCCccccccccccccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhhh
Q 000264 488 R-YDFSMYKQDIGDGDSLRHAKVGRLSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENWL 566 (1764)
Q Consensus 488 ~-~~~~~~~~~~~~~~~~r~~kv~r~~~e~sv~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~l~~l~~~cl~~l~~~l 566 (1764)
. +..-|.+....+++..+.++.+|+..|..+|...--+.-+..=+.+..+.+ +..+-+.|.+..+.+.+|........
T Consensus 1002 ~~~~~~~~~~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e~-d~~~~~~~~~~~~~~~~~d~~~~~~~ 1080 (1738)
T KOG1140|consen 1002 ANDEKDKKEKQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDEF-DEQENQTPSSGSKTYEEEDFTCALCQ 1080 (1738)
T ss_pred cccccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhccccc-CcccccCccccccchhhhhccchhhh
Confidence 3 555566665567777788888888888877764333322222111111121 23334566666666767766554443
Q ss_pred cCCCCcccccccCCCCcccccCcchhhhhh-----hhhhccccccccccccCCccccccccccCCCccccccCccccccc
Q 000264 567 GVDDRSVSVNDILSPNASRISGSNFVALKK-----TLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKITI 641 (1764)
Q Consensus 567 ~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 641 (1764)
+....... ....++. .+-++...+. -+..+.+..++.+.|++...+. + ..-+-
T Consensus 1081 ~~s~~~~~-~~~~~~~----~~~~~~~~~i~~e~e~~~~~~~~~~v~~~f~~~s~~~-----------s------d~l~~ 1138 (1738)
T KOG1140|consen 1081 DNSCTDFQ-VKPASHL----VKPIFRECIICDENEDVPNWDGRYSVSSAFAQKSDDV-----------S------DALTE 1138 (1738)
T ss_pred ccchhccc-cccchhh----hcccccccccCChhccCCCccccchhhhHhhhhcccc-----------c------ccccC
Confidence 21111000 0000110 0001100000 0000011111111111111111 0 00111
Q ss_pred cCCcccccccccCcCCccccccch-----------------hccccc------cccccCccCceeeeccCCceeeehHHH
Q 000264 642 SGERDTASWRSAGFNDSEMEGECA-----------------TELDNL------HVLSLCYWPDITYDVSSQDVSVHIPLH 698 (1764)
Q Consensus 642 ~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~l------~~~~~~~~~~v~fdVs~~~VSfH~PLH 698 (1764)
++...|+ .. ...+||.. ...-.| ..+...-|.-..++|+-..+.-|-+++
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 PGSLSCG---TV----LSSCGHHMHYGCFKRYVQAKRFRENARTAPLCQHYSENGLFLCPLCKSLSNVSLPMFLPPELLL 1211 (1738)
T ss_pred CCCCccc---ce----eeccCCcchHHHHHHHHHHHHHHHHhhhcCcccccccCCcccCCchHhhhhccCCcCCchhhhc
Confidence 1222222 00 01111110 000000 011122233344778888899999999
Q ss_pred HHHHHHHHHHHhhhccccccccccccCCCCCccccchhhhhcccCCCCCCccchhhhchhHHHHHHHHHHhhCceeechH
Q 000264 699 RLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFSAFVMEHPLRIRVFCAQVHAGMWRRNGD 778 (1764)
Q Consensus 699 r~Ls~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~df~~~vl~~~~~~~~~~~l~E~PLR~~Vl~AQI~AGmWVRNG~ 778 (1764)
+.++...+..+..+++........--........+...|.......+.|-++...-..+...+.+++.+++++||-- |.
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 98888887766555441000000000000001122333332222223333222333456677999999999999987 22
Q ss_pred HHhHHHHHhccccccccccchhHHHHHHHHhhCChHHHHHHHHHHhccccccccCCCCCCCchh-HHHHHHHHHHHHHhh
Q 000264 779 AALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLNLERPSEYEP-ILVQEMLTLIIQILQ 857 (1764)
Q Consensus 779 si~~Q~~~Y~~~~~re~~~d~DIfLLQ~~asl~dP~~Fl~~iL~RF~L~~w~~~~~~~~~~ye~-~mvEE~L~lLI~Llt 857 (1764)
- . ...+-+..-+.+.+++|++..+.+.......++.+++...++.++......+.. ..+.. ...++++.
T Consensus 1291 ~------i--~~~~le~~~~~~~~~~~~~~~~s~a~~~~~~~l~~~~~~~~l~l~~~~~~~~~~~~~l~~--~~~~~~l~ 1360 (1738)
T KOG1140|consen 1291 L------L--STNTLELTLFSREFLIVCWQSLSDAEQSTKLLLSASKKPSFLKLNEDMTFCLVTISRLRA--LHWEQILY 1360 (1738)
T ss_pred c------e--eecccccCcccchhhhhhhhccchHHHHHHHHHhccCCcccccCchhhHHHHHHHHHHHH--HHHHHHHH
Confidence 1 2 234667888899999999999999999999999999988887765433333322 22222 44577778
Q ss_pred ccccCCCChHHHHHHHHHHHHhcCCCChHHHHhhCCcCCCCcchHHHHHHHHhcccCCCCCCcceeEehhhhhccccccc
Q 000264 858 ERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYH 937 (1764)
Q Consensus 858 ER~~~g~s~~e~lRrEIIh~Lc~~p~t~SeL~~~lpe~~~~~~~fe~iL~eVA~fk~Psgl~~G~Y~LK~e~~~e~DPy~ 937 (1764)
++...++-.....+.++|-.+..++.+++++...+|.+..+...++.++..|- ..|.+.-.+.+.++.-.|.|.+-++
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 87766666666777788888888899999999999999999999999999997 6677778899999999999999998
Q ss_pred cccCchhHHHHHHHHHHhhcccccc--CCCCCCccCCCccchhhhccccHHHHHHHHHHHHHHhc
Q 000264 938 PRWSSRDLQVAEERYLRFCSVSALT--AQLPRWTKIYYPLESIAGIATCKVVLQVIRAVLFYAVF 1000 (1764)
Q Consensus 938 ~~y~~~d~q~Aeer~~r~~k~~a~~--~~~P~~~~~~~pf~~I~~il~s~~f~~il~~vL~~al~ 1000 (1764)
..+.. |.+.|+++..+..-..+.. ...+.+....++-.++.++--+....+.+...|.++..
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 8777776544322222222 23344444443345556666677778888888877653
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=1.5e-19 Score=169.46 Aligned_cols=70 Identities=44% Similarity=1.070 Sum_probs=66.3
Q ss_pred CcccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEec-CCccccCCCcccccccCCCCCCC
Q 000264 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYT-GGGCCDCGDVTAWKREGFCSRHK 185 (1764)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~~~~~-~gG~CDCGD~~awk~~~fC~~H~ 185 (1764)
.+|+++|+.++++|+|+||+.++++++|.+||+++.|+||+|.+.+. +||+|||||++|||+++||++|.
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=162.74 Aligned_cols=70 Identities=49% Similarity=1.112 Sum_probs=54.0
Q ss_pred CcccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecC-CccccCCCcccccccCCCCCCC
Q 000264 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTG-GGCCDCGDVTAWKREGFCSRHK 185 (1764)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~~~~~~-gG~CDCGD~~awk~~~fC~~H~ 185 (1764)
+.|+++|++++++|+|+||+.+++.+||.+||.++.|+||+|.+..+. +|+|||||+++||+++||++|+
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=98.42 E-value=2.9e-06 Score=106.41 Aligned_cols=185 Identities=21% Similarity=0.309 Sum_probs=139.7
Q ss_pred hhchhHHHHHHHHHHhhCceeechHHHhHHHHHhccccccccccchhHHHHHHHHhhCChHHHHHHHHHHhccccccccC
Q 000264 754 VMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLN 833 (1764)
Q Consensus 754 l~E~PLR~~Vl~AQI~AGmWVRNG~si~~Q~~~Y~~~~~re~~~d~DIfLLQ~~asl~dP~~Fl~~iL~RF~L~~w~~~~ 833 (1764)
+.-+++++.|--.-++..||+|+|.-..--...|-+..+....---+--.+=.|+..+++..|+...+.+|.+.+.-..+
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 45567899999999999999999998877777775544433333334445556888999999999999999876522111
Q ss_pred C---------C----------------------CC---------------------------------------------
Q 000264 834 L---------E----------------------RP--------------------------------------------- 837 (1764)
Q Consensus 834 ~---------~----------------------~~--------------------------------------------- 837 (1764)
- + ..
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 00
Q ss_pred --CCch--hHHHHHHHHHHHHHhhccccCCCChHHHHHHHHHHHHhcCCCChHHHHhhCCcCC-CCcchHHHHHHHHhcc
Q 000264 838 --SEYE--PILVQEMLTLIIQILQERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDL-SKFDQLQEILDAVAMY 912 (1764)
Q Consensus 838 --~~ye--~~mvEE~L~lLI~LltER~~~g~s~~e~lRrEIIh~Lc~~p~t~SeL~~~lpe~~-~~~~~fe~iL~eVA~f 912 (1764)
.+|+ +.|...++.++..+|.++.+.|..+++..+-|+.|.-+++...||-+..++.+.. ...+.|+.|+.+..+|
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 0000 2456677888888999999888899999999999999999999999998776654 4467899999999999
Q ss_pred cCCCC----CCcceeEehhhhhc-ccccccc
Q 000264 913 SHPSG----FNQGMYSLRWSYWK-ELDIYHP 938 (1764)
Q Consensus 913 k~Psg----l~~G~Y~LK~e~~~-e~DPy~~ 938 (1764)
-.|-- .-+|.|.||...|+ +.-|-+.
T Consensus 447 ~~P~~~~~p~~~~s~~l~~~~~~~~~c~~~~ 477 (784)
T KOG1139|consen 447 IEPIETTTPLMQGSYQLKTSIWDSEVCPVFF 477 (784)
T ss_pred ccchhhcCccccchhhccccCCccccccchh
Confidence 99943 24799999999998 4556444
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=97.11 E-value=0.00029 Score=83.67 Aligned_cols=81 Identities=27% Similarity=0.433 Sum_probs=61.0
Q ss_pred HHHHHHHHHHhcCCCChHHHHhhCCcCCCC---cchHHHHHHHHhcccCCCCCCcceeEehhhhhccccccccccCchhH
Q 000264 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSK---FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (1764)
Q Consensus 869 ~lRrEIIh~Lc~~p~t~SeL~~~lpe~~~~---~~~fe~iL~eVA~fk~Psgl~~G~Y~LK~e~~~e~DPy~~~y~~~d~ 945 (1764)
-+|.-|||.|+.+|....||..+|..+... -..++.||.+||... .++.|.||+.+|+++|.=++.|+-.|+
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 599999999999999999999888664433 356999999999965 378999999999999987889999999
Q ss_pred HHHHHHHHH
Q 000264 946 QVAEERYLR 954 (1764)
Q Consensus 946 q~Aeer~~r 954 (1764)
|..+-+..+
T Consensus 273 q~l~r~l~~ 281 (284)
T PF10390_consen 273 QLLKRRLSR 281 (284)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHh
Confidence 887665443
No 8
>KOG1777 consensus Putative Zn-finger protein [General function prediction only]
Probab=95.30 E-value=0.0067 Score=73.20 Aligned_cols=65 Identities=34% Similarity=0.556 Sum_probs=52.5
Q ss_pred ccCCCCccccccc-----CCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecCCccccCCCccccc
Q 000264 111 KIGQRGVCGAVWG-----NNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDVTAWK 176 (1764)
Q Consensus 111 ~~~~~~~Cg~v~~-----~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~~~~~~gG~CDCGD~~awk 176 (1764)
+.-+.++|-.... .=.-+|||-||...+..+||..|-++ -|+||++-+.+....+||||-..+=.
T Consensus 539 kAik~GqCLfkvSs~~syPMHnFYRC~TCNttdRNAIC~nCI~~-CH~GH~Vefir~Drffcdcgagtl~~ 608 (625)
T KOG1777|consen 539 KAIKKGQCLFKVSSYTSYPMHNFYRCITCNTTDRNAICVNCIKR-CHEGHDVEFIRHDRFFCDCGAGTLSN 608 (625)
T ss_pred HHhhcCceEEEecCCCcccccceeEeeecCCccccHHHHHHHHH-hcCCCceEEEeeceEEEecCCceecc
Confidence 3455677754433 33458999999999999999999988 79999999999989999999876533
No 9
>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=94.23 E-value=0.017 Score=49.57 Aligned_cols=23 Identities=22% Similarity=0.729 Sum_probs=19.5
Q ss_pred CCCceEcccchHhhHHHHHHHHH
Q 000264 1423 CDGIHLSSCGHAVHQGCLDRYVS 1445 (1764)
Q Consensus 1423 ~~g~~~~~CgH~~H~~C~~~y~~ 1445 (1764)
...+....|||..|.+|...|++
T Consensus 13 ~~~~~~l~C~H~fh~~Ci~~~~~ 35 (44)
T PF13639_consen 13 GEKVVKLPCGHVFHRSCIKEWLK 35 (44)
T ss_dssp TSCEEEETTSEEEEHHHHHHHHH
T ss_pred CCeEEEccCCCeeCHHHHHHHHH
Confidence 35667778999999999999973
No 10
>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=93.35 E-value=0.06 Score=44.95 Aligned_cols=22 Identities=32% Similarity=0.857 Sum_probs=17.6
Q ss_pred CceEcccchHhhHHHHHHHHHH
Q 000264 1425 GIHLSSCGHAVHQGCLDRYVSS 1446 (1764)
Q Consensus 1425 g~~~~~CgH~~H~~C~~~y~~s 1446 (1764)
-+.+..|||.+|..|++.|++.
T Consensus 12 ~~~~~~C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 12 PVVLLPCGHVFCRSCIDKWLKS 33 (45)
T ss_pred ceEecCCCChhcHHHHHHHHHh
Confidence 3455669999999999998654
No 11
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=92.94 E-value=0.46 Score=63.82 Aligned_cols=69 Identities=14% Similarity=0.180 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-H--HhhcCCCCcCCCCCCCcccCCCccccccccCCCCceeccCCCC---CCCeE
Q 000264 1146 SEKRKAKARERQAAILEKMKAEQFK-F--LSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS---RTPVS 1219 (1764)
Q Consensus 1146 ~EkKKalAkeRQAKIMAQMkaQQkk-F--Lenn~d~~dedd~~~~d~~~sd~~~~~~es~~~tCILCqE~~s---~~pfG 1219 (1764)
..+||++|.++|+|.+.+|.-++.+ - ..+.... .. . . ..+ +|. ..+|++|+|.-+ ++++|
T Consensus 422 r~ekk~~Am~~Rek~L~~lgm~~~~~G~v~~~~~~l-~~-------~--~--~l~-ee~-gl~C~ICrEGy~~~p~~~lG 487 (802)
T PF13764_consen 422 RQEKKRLAMAMREKQLKKLGMRVNEKGQVVVSSSIL-QN-------M--E--DLE-EED-GLTCCICREGYKFRPDEVLG 487 (802)
T ss_pred HHHHHHHHHHHHHHHHHHccCccccccceecCchhh-cC-------c--c--ccc-ccC-CCeEEEcCCccccCCcccee
Confidence 5677889999999999998433200 0 0000000 00 0 0 011 122 468999999853 46899
Q ss_pred EEEeeeccc
Q 000264 1220 YLILLQKSR 1228 (1764)
Q Consensus 1220 ~la~vQ~Sr 1228 (1764)
+-+|.-+-.
T Consensus 488 iY~f~kr~~ 496 (802)
T PF13764_consen 488 IYAFSKRVN 496 (802)
T ss_pred eEEEeeccc
Confidence 999874433
No 12
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=92.28 E-value=0.051 Score=63.39 Aligned_cols=52 Identities=33% Similarity=0.660 Sum_probs=36.4
Q ss_pred CCceEcccchHhhHHHHHHHHHHHHHhhhcccc---cCCCcccCCCCccccccchhh
Q 000264 1424 DGIHLSSCGHAVHQGCLDRYVSSLKERYNRRII---FEGGHIVDPDQGEFLCPVCRQ 1477 (1764)
Q Consensus 1424 ~g~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~---~~~~~~~~~~~~Ef~CPlCr~ 1477 (1764)
..+-++.|-|+||..|+.+|+..+++-..+.+. -++.| --+.-|=+||+||-
T Consensus 129 ~~ft~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh--~~~~~eavcpVcre 183 (368)
T KOG4445|consen 129 PAFTVTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQH--MKEQVEAVCPVCRE 183 (368)
T ss_pred CceeeehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hhhhHhhhhhHhhh
Confidence 456789999999999999999998775443321 11112 22356778999995
No 13
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=92.05 E-value=0.051 Score=71.43 Aligned_cols=64 Identities=27% Similarity=0.673 Sum_probs=51.6
Q ss_pred CCcccccccC----CceeEEeccCCCCCCccccccccCCCCCCCceeEEEe-cCCccccCCCccccc-ccCCCCCC
Q 000264 115 RGVCGAVWGN----NDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVTAWK-REGFCSRH 184 (1764)
Q Consensus 115 ~~~Cg~v~~~----ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~~~~-~~gG~CDCGD~~awk-~~~fC~~H 184 (1764)
...|...|+. ++-.|.|+||+.-.+-|-|.+|-.. .|+||++++-+ +.-.+||| |- .++-|+.-
T Consensus 1240 NDtCSFTWTGadHINQDIfECkTCGL~~SLCCCsECAlt-CHk~HDCkLKRTSPTAYCDC-----WEKssCkCKaL 1309 (3015)
T KOG0943|consen 1240 NDTCSFTWTGADHINQDIFECKTCGLLESLCCCSECALT-CHKGHDCKLKRTSPTAYCDC-----WEKSSCKCKAL 1309 (3015)
T ss_pred cCccceeecchhhccchhhhhcccccchhhhhhHHHHHH-hccCCccceeccCCcceeeh-----hhcccccchhh
Confidence 3578999985 4567999999999998899999865 79999999987 57899999 63 34556554
No 14
>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=87.65 E-value=0.46 Score=38.09 Aligned_cols=22 Identities=18% Similarity=0.670 Sum_probs=18.7
Q ss_pred CCceEcccchHhhHHHHHHHHH
Q 000264 1424 DGIHLSSCGHAVHQGCLDRYVS 1445 (1764)
Q Consensus 1424 ~g~~~~~CgH~~H~~C~~~y~~ 1445 (1764)
..+.+..|||.+|+.|.+.|++
T Consensus 9 ~~~~~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 9 KDPVVLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred CCcEEecCCChHHHHHHHHHHH
Confidence 3456678999999999999976
No 15
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=87.55 E-value=0.25 Score=59.25 Aligned_cols=16 Identities=38% Similarity=1.059 Sum_probs=14.2
Q ss_pred ccchHhhHHHHHHHHH
Q 000264 1430 SCGHAVHQGCLDRYVS 1445 (1764)
Q Consensus 1430 ~CgH~~H~~C~~~y~~ 1445 (1764)
.|||+.|.+|.+.+++
T Consensus 317 pCGHilHl~CLknW~E 332 (491)
T COG5243 317 PCGHILHLHCLKNWLE 332 (491)
T ss_pred cccceeeHHHHHHHHH
Confidence 5999999999998864
No 16
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=87.13 E-value=0.36 Score=47.67 Aligned_cols=28 Identities=25% Similarity=0.466 Sum_probs=22.6
Q ss_pred CCCCCCCceEcccchHhhHHHHHHHHHH
Q 000264 1419 GPIDCDGIHLSSCGHAVHQGCLDRYVSS 1446 (1764)
Q Consensus 1419 ~~~~~~g~~~~~CgH~~H~~C~~~y~~s 1446 (1764)
-|.|...+-.-.|||..|..|..+.+++
T Consensus 40 ~Pgd~Cplv~g~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 40 FPGDDCPLVWGKCSHNFHMHCILKWLST 67 (85)
T ss_pred CCCCCCceeeccCccHHHHHHHHHHHcc
Confidence 3456666777789999999999999775
No 17
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=86.80 E-value=0.55 Score=40.57 Aligned_cols=33 Identities=33% Similarity=0.779 Sum_probs=27.5
Q ss_pred CCCceEcccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhh
Q 000264 1423 CDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (1764)
Q Consensus 1423 ~~g~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~ 1477 (1764)
...+.+.+|||++...|.++-. .....||+||+
T Consensus 12 ~~~~~l~~CgH~~C~~C~~~~~----------------------~~~~~CP~C~k 44 (44)
T PF14634_consen 12 ERRPRLTSCGHIFCEKCLKKLK----------------------GKSVKCPICRK 44 (44)
T ss_pred CCCeEEcccCCHHHHHHHHhhc----------------------CCCCCCcCCCC
Confidence 4568999999999999998775 25678999985
No 18
>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=86.79 E-value=0.43 Score=40.16 Aligned_cols=20 Identities=30% Similarity=0.843 Sum_probs=18.7
Q ss_pred eEcccchHhhHHHHHHHHHH
Q 000264 1427 HLSSCGHAVHQGCLDRYVSS 1446 (1764)
Q Consensus 1427 ~~~~CgH~~H~~C~~~y~~s 1446 (1764)
.+..|||.++..|+.+|++.
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 68999999999999999887
No 19
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=84.56 E-value=1.1 Score=56.43 Aligned_cols=78 Identities=26% Similarity=0.370 Sum_probs=63.4
Q ss_pred HHHHHHHHHHhcCCCChHHHHhhCCcCCCCc---chHHHHHHHHhcccCCCCCCcceeEehhhhhccccccccccCchhH
Q 000264 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSKF---DQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (1764)
Q Consensus 869 ~lRrEIIh~Lc~~p~t~SeL~~~lpe~~~~~---~~fe~iL~eVA~fk~Psgl~~G~Y~LK~e~~~e~DPy~~~y~~~d~ 945 (1764)
-||..|||+|+.++..--||.++|-.+.... ..+..||.+.. ...+|+|.|++.+|+|+|-=++.|+-.|.
T Consensus 211 ~ir~RviHLlalk~ykk~El~~rLk~dGl~~~e~~~i~~il~~~~------~~~~~t~~Lrd~~~~evdq~Wp~yse~d~ 284 (604)
T KOG4796|consen 211 PIRDRVIHLLALKAYKKPELLARLKKDGLPQEEKNKIRSILQQNS------RSKDGTYTLRDSMLKEVDQNWPGYSEGDK 284 (604)
T ss_pred chHHHHHHHHHhhhcccHHHHHHHhhcCCcHHHHHHHHHHHHhhc------ccccccchHHHHhhhHHHhcCCCcchHHH
Confidence 4999999999999999999998877665443 45788888821 24689999999999999988888998887
Q ss_pred HHHHHHH
Q 000264 946 QVAEERY 952 (1764)
Q Consensus 946 q~Aeer~ 952 (1764)
|..+-+.
T Consensus 285 ~~lkr~~ 291 (604)
T KOG4796|consen 285 QHLKRVL 291 (604)
T ss_pred HHHHHHh
Confidence 7664443
No 20
>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=83.80 E-value=0.91 Score=40.36 Aligned_cols=39 Identities=28% Similarity=0.869 Sum_probs=29.3
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCC----CC-CceeEE
Q 000264 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN----HK-EHDYSI 159 (1764)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~----H~-gH~~~~ 159 (1764)
.|++.... ..-|+|..|. .--+|.+||..+. |+ .|.|.+
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 57777764 4899999995 3569999999984 43 577765
No 21
>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=82.55 E-value=1.1 Score=38.84 Aligned_cols=37 Identities=27% Similarity=0.652 Sum_probs=29.3
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000264 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (1764)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~ 158 (1764)
.|+..+ . ..-|+|.+|. .--+|.+||.++.|.+|.+.
T Consensus 5 ~C~~~i-~-G~ry~C~~C~---d~dLC~~C~~~~~H~~H~f~ 41 (43)
T cd02340 5 GCQGPI-V-GVRYKCLVCP---DYDLCESCEAKGVHPEHAML 41 (43)
T ss_pred CCCCcC-c-CCeEECCCCC---CccchHHhhCcCCCCCCCEE
Confidence 477733 3 3789999997 46699999999999888874
No 22
>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=82.07 E-value=1.1 Score=39.31 Aligned_cols=37 Identities=27% Similarity=0.812 Sum_probs=29.0
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCC--CCC-CceeE
Q 000264 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG--NHK-EHDYS 158 (1764)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~--~H~-gH~~~ 158 (1764)
.|++.+. | .-|+|.+|. .--+|.+||..+ .|. +|.+.
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 5788544 5 899999996 467999999998 676 67664
No 23
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=80.90 E-value=1.9 Score=51.46 Aligned_cols=61 Identities=25% Similarity=0.638 Sum_probs=47.4
Q ss_pred cCCCCccccc--ccCCceeEEeccCCCCC-CccccccccCCCCCCCceeEEEe-cCCccccCCCcc
Q 000264 112 IGQRGVCGAV--WGNNDIAYRCRTCEHDP-TCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVT 173 (1764)
Q Consensus 112 ~~~~~~Cg~v--~~~ge~~y~C~~C~~d~-t~~lC~~CF~~~~H~gH~~~~~~-~~gG~CDCGD~~ 173 (1764)
......|++. ..+-++.|.|.||...+ ...+|..|=.. -|.||.-..-. .+..-||||+.-
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 3555678654 33447899999999999 77899999775 79999977655 567889999953
No 24
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=80.74 E-value=1.5 Score=49.67 Aligned_cols=57 Identities=19% Similarity=0.436 Sum_probs=36.6
Q ss_pred ceEcccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhhcc--ccccccCCC
Q 000264 1426 IHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLA--NSVLPALPW 1488 (1764)
Q Consensus 1426 ~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l~--N~~lP~~p~ 1488 (1764)
+.++.|||.....|...|+.+-.. .++ ..+..+-.++...||+||+-- +.++|+...
T Consensus 31 PVvT~CGH~FC~~CI~~wl~~s~~--s~~----~~~~~~~~k~~~~CPvCR~~Is~~~LvPiygr 89 (193)
T PLN03208 31 PVVTLCGHLFCWPCIHKWTYASNN--SRQ----RVDQYDHKREPPKCPVCKSDVSEATLVPIYGR 89 (193)
T ss_pred cEEcCCCchhHHHHHHHHHHhccc--ccc----ccccccccCCCCcCCCCCCcCChhcEEEeecc
Confidence 466889999999999998653211 110 000012245778999999865 447788754
No 25
>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=79.42 E-value=1.6 Score=38.95 Aligned_cols=38 Identities=26% Similarity=0.792 Sum_probs=28.7
Q ss_pred ccc-ccccCCceeEEeccCCCCCCccccccccCCC----CCC-CceeEE
Q 000264 117 VCG-AVWGNNDIAYRCRTCEHDPTCAICVPCFQNG----NHK-EHDYSI 159 (1764)
Q Consensus 117 ~Cg-~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~----~H~-gH~~~~ 159 (1764)
.|+ ..+. ..-|+|..|. .--+|.+||..+ .|+ .|.+.+
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 4455 4889999994 467999999988 676 777654
No 26
>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=78.21 E-value=0.83 Score=38.36 Aligned_cols=22 Identities=23% Similarity=0.871 Sum_probs=18.9
Q ss_pred CceEcccchHhhHHHHHHHHHH
Q 000264 1425 GIHLSSCGHAVHQGCLDRYVSS 1446 (1764)
Q Consensus 1425 g~~~~~CgH~~H~~C~~~y~~s 1446 (1764)
-+.+..|||.+..+|+++|++.
T Consensus 11 ~~~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 11 PVVVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp EEEECTTSEEEEHHHHHHHHHC
T ss_pred cCEECCCCCchhHHHHHHHHHC
Confidence 3468999999999999999664
No 27
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=78.00 E-value=0.75 Score=43.94 Aligned_cols=38 Identities=37% Similarity=0.721 Sum_probs=20.8
Q ss_pred cccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhh
Q 000264 1429 SSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (1764)
Q Consensus 1429 ~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~ 1477 (1764)
..||+..|..|+..|+.++..... .+++..|+ ||.|+.
T Consensus 26 ~~C~~~fH~~CL~~wf~~~~~~~~---------~~~~~~G~--CP~C~~ 63 (70)
T PF11793_consen 26 PSCGKKFHLLCLSEWFLSLEKSRQ---------SFIPIFGE--CPYCSS 63 (70)
T ss_dssp TT----B-SGGGHHHHHHHHSSS----------TTT--EEE---TTT-S
T ss_pred cccCCHHHHHHHHHHHHHcccCCe---------eecccccC--CcCCCC
Confidence 489999999999999988875222 14455555 999986
No 28
>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=77.08 E-value=2 Score=37.80 Aligned_cols=39 Identities=26% Similarity=0.695 Sum_probs=29.5
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC-CCceeEE
Q 000264 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYSI 159 (1764)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H-~gH~~~~ 159 (1764)
.|+..--.| .-|+|.+|. .--+|..||....| .+|.|..
T Consensus 5 ~C~~~pI~G-~RykC~~C~---dyDLC~~Cf~~~~H~~~H~F~r 44 (45)
T cd02344 5 GCQMFPING-PRFKCRNCD---DFDFCENCFKTRKHNTRHTFGR 44 (45)
T ss_pred CCCCCCCcc-CeEECCCCC---CccchHHhhCCCCcCCCCceee
Confidence 355443344 789999998 45699999999999 5898753
No 29
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=75.63 E-value=2 Score=49.69 Aligned_cols=61 Identities=23% Similarity=0.217 Sum_probs=42.6
Q ss_pred HHHHHHHHH--hcCCCChHHHHhhCCcCCCCcchHHHHHHHHhcccCCCCCCcceeEehhhhhc
Q 000264 870 LKRELVHRL--AIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWK 931 (1764)
Q Consensus 870 lRrEIIh~L--c~~p~t~SeL~~~lpe~~~~~~~fe~iL~eVA~fk~Psgl~~G~Y~LK~e~~~ 931 (1764)
=|+||+-.| ||.-..|=-|...+-..-+-..-+.+||++||+|.. .|..+|+|+|||||-+
T Consensus 183 dk~evld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~icv~Nk-Kg~~k~tyeLKPEYK~ 245 (254)
T KOG2905|consen 183 DKNEVLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDICVLNK-KGPYKNTYELKPEYKK 245 (254)
T ss_pred cHHHHHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHHHHhc-cCcccCceecCHHHhh
Confidence 466777666 466555555544433333334568999999999986 3668999999999874
No 30
>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=73.80 E-value=1.9 Score=41.55 Aligned_cols=21 Identities=29% Similarity=0.713 Sum_probs=16.5
Q ss_pred CCceEcccchHhhHHHHHHHH
Q 000264 1424 DGIHLSSCGHAVHQGCLDRYV 1444 (1764)
Q Consensus 1424 ~g~~~~~CgH~~H~~C~~~y~ 1444 (1764)
.-+-...|||+-|..|..+.+
T Consensus 43 ~~i~~~~C~H~FH~~Ci~~Wl 63 (73)
T PF12678_consen 43 CPIVWGPCGHIFHFHCISQWL 63 (73)
T ss_dssp S-EEEETTSEEEEHHHHHHHH
T ss_pred cceEecccCCCEEHHHHHHHH
Confidence 445566799999999998875
No 31
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=73.27 E-value=1.8 Score=36.72 Aligned_cols=37 Identities=24% Similarity=0.595 Sum_probs=28.0
Q ss_pred CcccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000264 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (1764)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~ 158 (1764)
..|..--+ ....|.|.+|.. .+|..|+..+ |++|++.
T Consensus 4 ~~C~~H~~-~~~~~~C~~C~~----~~C~~C~~~~-H~~H~~~ 40 (42)
T PF00643_consen 4 PKCPEHPE-EPLSLFCEDCNE----PLCSECTVSG-HKGHKIV 40 (42)
T ss_dssp SB-SSTTT-SBEEEEETTTTE----EEEHHHHHTS-TTTSEEE
T ss_pred ccCccCCc-cceEEEecCCCC----ccCccCCCCC-CCCCEEe
Confidence 45544332 348999999985 7999999998 9999975
No 32
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=73.21 E-value=1.5 Score=52.09 Aligned_cols=33 Identities=27% Similarity=0.943 Sum_probs=25.9
Q ss_pred ceEcccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhhccc
Q 000264 1426 IHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLAN 1480 (1764)
Q Consensus 1426 ~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l~N 1480 (1764)
+++-.|||.||+.||+.|.. .+ |.||+|..++|
T Consensus 175 ~~~~~CgH~~h~~cf~e~~~---------------------~~-y~CP~C~~~~d 207 (276)
T KOG1940|consen 175 AGVLKCGHYMHSRCFEEMIC---------------------EG-YTCPICSKPGD 207 (276)
T ss_pred CCccCcccchHHHHHHHHhc---------------------cC-CCCCcccchHH
Confidence 55678999999999998831 15 99999998443
No 33
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=69.33 E-value=2.1 Score=56.71 Aligned_cols=24 Identities=46% Similarity=0.944 Sum_probs=21.4
Q ss_pred cccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhh
Q 000264 1429 SSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (1764)
Q Consensus 1429 ~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~ 1477 (1764)
--|||..|++|++ ++|+.||-|+.
T Consensus 857 F~CgHsyHqhC~e-------------------------~~~~~CP~C~~ 880 (933)
T KOG2114|consen 857 FLCGHSYHQHCLE-------------------------DKEDKCPKCLP 880 (933)
T ss_pred eecccHHHHHhhc-------------------------cCcccCCccch
Confidence 4699999999998 28999999987
No 34
>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=64.94 E-value=4 Score=35.91 Aligned_cols=30 Identities=27% Similarity=0.907 Sum_probs=24.5
Q ss_pred ceeEEeccCCCCCCccccccccCCCCC-CCceeE
Q 000264 126 DIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYS 158 (1764)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~~H-~gH~~~ 158 (1764)
..-|+|..|. .--+|.+||..+.| .+|.|.
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 35699999999998 588764
No 35
>PHA02926 zinc finger-like protein; Provisional
Probab=62.80 E-value=5 Score=46.21 Aligned_cols=42 Identities=21% Similarity=0.503 Sum_probs=31.8
Q ss_pred eEcccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhhccccccc
Q 000264 1427 HLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLP 1484 (1764)
Q Consensus 1427 ~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l~N~~lP 1484 (1764)
....|||....+|.....++-+ . ...+-.||+||.-...+.|
T Consensus 193 IL~~CnHsFCl~CIr~Wr~~r~---~-------------~~~~rsCPiCR~~f~~I~p 234 (242)
T PHA02926 193 LLDSCNHIFCITCINIWHRTRR---E-------------TGASDNCPICRTRFRNITM 234 (242)
T ss_pred ccCCCCchHHHHHHHHHHHhcc---c-------------cCcCCcCCCCcceeeeecc
Confidence 6789999999999998865211 1 1256789999998887765
No 36
>PHA02929 N1R/p28-like protein; Provisional
Probab=60.21 E-value=4.4 Score=47.53 Aligned_cols=34 Identities=38% Similarity=0.723 Sum_probs=24.8
Q ss_pred EcccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhhcccccc
Q 000264 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVL 1483 (1764)
Q Consensus 1428 ~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l~N~~l 1483 (1764)
+..|||..|..|...+++. + -.||+||+---.+.
T Consensus 197 l~~C~H~FC~~CI~~Wl~~----~------------------~tCPlCR~~~~~v~ 230 (238)
T PHA02929 197 LSNCNHVFCIECIDIWKKE----K------------------NTCPVCRTPFISVI 230 (238)
T ss_pred cCCCCCcccHHHHHHHHhc----C------------------CCCCCCCCEeeEEe
Confidence 5689999999999987521 0 16999998544443
No 37
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=59.89 E-value=9.5 Score=37.29 Aligned_cols=28 Identities=29% Similarity=0.580 Sum_probs=24.2
Q ss_pred CCCCCCCceEcccchHhhHHHHHHHHHH
Q 000264 1419 GPIDCDGIHLSSCGHAVHQGCLDRYVSS 1446 (1764)
Q Consensus 1419 ~~~~~~g~~~~~CgH~~H~~C~~~y~~s 1446 (1764)
.|.+..-+.-..|-|+.|..|..+++++
T Consensus 42 ~~~~eC~v~wG~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 42 TPGDECPVVWGVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred CCCCcceEEEEecchHHHHHHHHHHHhh
Confidence 4567777888899999999999999887
No 38
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.84 E-value=7.4 Score=47.74 Aligned_cols=28 Identities=29% Similarity=0.584 Sum_probs=20.6
Q ss_pred CCCCCCCCCceEcccchHhhHHHHHHHH
Q 000264 1417 GFGPIDCDGIHLSSCGHAVHQGCLDRYV 1444 (1764)
Q Consensus 1417 ~f~~~~~~g~~~~~CgH~~H~~C~~~y~ 1444 (1764)
.|-|++++=--+.+|||+.|..|....+
T Consensus 12 d~~p~~~~l~~i~~cGhifh~~cl~qwf 39 (465)
T KOG0827|consen 12 DGRPNDHELGPIGTCGHIFHTTCLTQWF 39 (465)
T ss_pred cCCccccccccccchhhHHHHHHHHHHH
Confidence 3445555444567899999999998874
No 39
>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=56.61 E-value=7.1 Score=34.53 Aligned_cols=20 Identities=30% Similarity=0.760 Sum_probs=18.0
Q ss_pred ceEcccchH-hhHHHHHHHHH
Q 000264 1426 IHLSSCGHA-VHQGCLDRYVS 1445 (1764)
Q Consensus 1426 ~~~~~CgH~-~H~~C~~~y~~ 1445 (1764)
+.+.-|||. +-..|++++++
T Consensus 15 ~~~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 15 VVLLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp EEEETTCEEEEEHHHHHHHHH
T ss_pred eEEeCCCChHHHHHHhHHhcc
Confidence 677789999 99999999977
No 40
>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=55.31 E-value=6.7 Score=35.09 Aligned_cols=35 Identities=29% Similarity=0.691 Sum_probs=26.8
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCCC-Cce
Q 000264 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK-EHD 156 (1764)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~-gH~ 156 (1764)
.|++... ..-|+|..|. ..-+|..||..+.+. +|+
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 5777543 4799999996 467999999998874 454
No 41
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=53.91 E-value=9.8 Score=31.42 Aligned_cols=28 Identities=25% Similarity=0.466 Sum_probs=23.2
Q ss_pred ceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000264 126 DIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (1764)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~ 158 (1764)
...|-|.+|+ ..+|..|-..+ |++|.+.
T Consensus 10 ~~~~fC~~~~----~~iC~~C~~~~-H~~H~~~ 37 (39)
T cd00021 10 PLSLFCETDR----ALLCVDCDLSV-HSGHRRV 37 (39)
T ss_pred ceEEEeCccC----hhhhhhcChhh-cCCCCEe
Confidence 4578898887 47999999888 9999875
No 42
>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=53.24 E-value=4.7 Score=35.56 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=21.9
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC
Q 000264 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 152 (1764)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H 152 (1764)
.||.-.+ .+-|+|..+. ...||.+||..|.-
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 4666665 4777777654 46799999988753
No 43
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=52.36 E-value=7.1 Score=35.55 Aligned_cols=16 Identities=31% Similarity=0.530 Sum_probs=11.2
Q ss_pred ceEcccchH-hhHHHHH
Q 000264 1426 IHLSSCGHA-VHQGCLD 1441 (1764)
Q Consensus 1426 ~~~~~CgH~-~H~~C~~ 1441 (1764)
..+.+|||+ |-|+|--
T Consensus 20 sVlYtCGHMCmCy~Cg~ 36 (62)
T KOG4172|consen 20 SVLYTCGHMCMCYACGL 36 (62)
T ss_pred HHHHHcchHHhHHHHHH
Confidence 345799998 6677753
No 44
>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=51.76 E-value=10 Score=33.96 Aligned_cols=39 Identities=26% Similarity=0.699 Sum_probs=26.9
Q ss_pred cccc-cccCCceeEEeccCCCCCCccccccccCCC-CC-CCceeE
Q 000264 117 VCGA-VWGNNDIAYRCRTCEHDPTCAICVPCFQNG-NH-KEHDYS 158 (1764)
Q Consensus 117 ~Cg~-v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~-~H-~gH~~~ 158 (1764)
.|+. -+. ..-|+|.+|.- ...-+|.+||.++ .| .+|.+.
T Consensus 5 ~C~~~pI~--G~R~~C~~C~~-~d~DlC~~C~~~~~~H~~~H~~~ 46 (48)
T cd02341 5 SCGIEPIP--GTRYHCSECDD-GDFDLCQDCVVKGESHQEDHWLV 46 (48)
T ss_pred CCCCCccc--cceEECCCCCC-CCCccCHHHHhCcCCCCCCCcee
Confidence 4555 222 56799999963 3456999999999 66 366653
No 45
>smart00336 BBOX B-Box-type zinc finger.
Probab=49.55 E-value=14 Score=31.06 Aligned_cols=29 Identities=21% Similarity=0.636 Sum_probs=23.6
Q ss_pred CceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000264 125 NDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (1764)
Q Consensus 125 ge~~y~C~~C~~d~t~~lC~~CF~~~~H~gH~~~ 158 (1764)
....|.|.+|+. ++|..|... .|++|.+.
T Consensus 12 ~~~~~~C~~c~~----~iC~~C~~~-~H~~H~~~ 40 (42)
T smart00336 12 EPAEFFCEECGA----LLCRTCDEA-EHRGHTVV 40 (42)
T ss_pred CceEEECCCCCc----ccccccChh-hcCCCcee
Confidence 445777988874 799999988 99999875
No 46
>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=48.00 E-value=9.6 Score=45.74 Aligned_cols=31 Identities=29% Similarity=0.456 Sum_probs=16.1
Q ss_pred cchHHHHHHHHhcccCCCCCCcceeEehhhhh
Q 000264 899 FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYW 930 (1764)
Q Consensus 899 ~~~fe~iL~eVA~fk~Psgl~~G~Y~LK~e~~ 930 (1764)
+.-+-+||++||+|..- |...|+|+|||||-
T Consensus 244 ~~yLKeiL~eIa~~~k~-g~~~~~w~LKpeyk 274 (275)
T PF02270_consen 244 EAYLKEILEEIAVLNKR-GPHKNMWELKPEYK 274 (275)
T ss_dssp HHHHHHHHHHH--EE---TT---EE----SS-
T ss_pred HHHHHHHHHHHHHHhcc-CCcCCcEecchHHc
Confidence 34588999999999964 67789999999984
No 47
>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=46.38 E-value=11 Score=32.56 Aligned_cols=32 Identities=25% Similarity=0.824 Sum_probs=24.7
Q ss_pred CcccccccCCceeEEeccCCCCCCccccccccCCCCCC
Q 000264 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (1764)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~ 153 (1764)
..|+++ +++-|+|..|. .--+|..||....|.
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 357664 24999999996 355999999998883
No 48
>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=41.46 E-value=17 Score=32.62 Aligned_cols=32 Identities=28% Similarity=0.742 Sum_probs=23.7
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC
Q 000264 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 152 (1764)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H 152 (1764)
.|++.=-.| .-|+|..|. .--||..||..+.|
T Consensus 5 ~C~~~pi~g-~RykC~~C~---d~DLC~~Cf~~g~~ 36 (49)
T cd02334 5 ICKEFPITG-FRYRCLKCF---NYDLCQSCFFSGRT 36 (49)
T ss_pred CCCCCCcee-eeEECCCCC---CcCchHHHHhCCCc
Confidence 466542233 789999996 46699999988865
No 49
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.11 E-value=15 Score=46.28 Aligned_cols=31 Identities=39% Similarity=0.958 Sum_probs=25.2
Q ss_pred eEcccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhhc
Q 000264 1427 HLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQL 1478 (1764)
Q Consensus 1427 ~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l 1478 (1764)
-++-|-|++|..|+++.++.-+ -.||.||+.
T Consensus 602 m~tPC~HifH~~CL~~WMd~yk---------------------l~CPvCR~p 632 (636)
T KOG0828|consen 602 MLTPCHHIFHRQCLLQWMDTYK---------------------LICPVCRCP 632 (636)
T ss_pred cccchHHHHHHHHHHHHHhhhc---------------------ccCCccCCC
Confidence 3567999999999999987554 359999973
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=40.86 E-value=19 Score=31.32 Aligned_cols=33 Identities=27% Similarity=0.801 Sum_probs=24.9
Q ss_pred CcccccccCCceeEEeccCCCCCCccccccccCCCCCC
Q 000264 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (1764)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~ 153 (1764)
..|++.+. ..-|+|..|. .--+|.+||..+.|.
T Consensus 8 ~~C~~~i~--g~ry~C~~C~---d~dlC~~Cf~~~~~~ 40 (44)
T smart00291 8 DTCGKPIV--GVRYHCLVCP---DYDLCQSCFAKGSAG 40 (44)
T ss_pred CCCCCCCc--CCEEECCCCC---CccchHHHHhCcCcC
Confidence 46888543 4678999994 577999999987664
No 51
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=39.87 E-value=20 Score=32.13 Aligned_cols=31 Identities=23% Similarity=0.842 Sum_probs=24.2
Q ss_pred Ccccc-cccCCceeEEeccCCCCCCccccccccCCCC
Q 000264 116 GVCGA-VWGNNDIAYRCRTCEHDPTCAICVPCFQNGN 151 (1764)
Q Consensus 116 ~~Cg~-v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~ 151 (1764)
..|.+ -+. ++-|+|..|. .--+|.+||..+.
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 566 4889999994 4679999999874
No 52
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.28 E-value=16 Score=45.09 Aligned_cols=34 Identities=32% Similarity=0.940 Sum_probs=27.8
Q ss_pred CCCceEcccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhh
Q 000264 1423 CDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (1764)
Q Consensus 1423 ~~g~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~ 1477 (1764)
.+++.+-.|+|..|-.|-+..+... |+ .||+||+
T Consensus 242 GdklRiLPC~H~FH~~CIDpWL~~~--r~-------------------~CPvCK~ 275 (348)
T KOG4628|consen 242 GDKLRILPCSHKFHVNCIDPWLTQT--RT-------------------FCPVCKR 275 (348)
T ss_pred CCeeeEecCCCchhhccchhhHhhc--Cc-------------------cCCCCCC
Confidence 4678889999999999999886543 22 5999999
No 53
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=32.70 E-value=26 Score=43.15 Aligned_cols=21 Identities=24% Similarity=0.656 Sum_probs=17.0
Q ss_pred CCceEcccchHhhHHHHHHHH
Q 000264 1424 DGIHLSSCGHAVHQGCLDRYV 1444 (1764)
Q Consensus 1424 ~g~~~~~CgH~~H~~C~~~y~ 1444 (1764)
..+-.--|.|+.|..|...|+
T Consensus 380 e~LqALpCsHIfH~rCl~e~L 400 (518)
T KOG1941|consen 380 ERLQALPCSHIFHLRCLQEIL 400 (518)
T ss_pred ccccccchhHHHHHHHHHHHH
Confidence 334455699999999999998
No 54
>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=32.39 E-value=12 Score=32.91 Aligned_cols=36 Identities=28% Similarity=0.709 Sum_probs=22.3
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCC-CCCce
Q 000264 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN-HKEHD 156 (1764)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~-H~gH~ 156 (1764)
.|+..--. ..-|+|..|. .--||..||..+. +.+|+
T Consensus 9 ~C~~~~i~-g~Ry~C~~C~---d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 9 GCGTDPII-GVRYHCLVCP---DYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SS-SSSEE-SSEEEESSSS---S-EEEHHHHHH--H-SSSS
T ss_pred CCCCCcCc-CCeEECCCCC---CCchhhHHHhCcCCCCCcC
Confidence 46663222 3679999994 5679999999964 45664
No 55
>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=31.68 E-value=32 Score=38.03 Aligned_cols=54 Identities=20% Similarity=0.365 Sum_probs=31.2
Q ss_pred HhhHHHHHHHHHHHHHhhhcccc---------cCCCcccCCCCccccccchhhccccccccCC
Q 000264 1434 AVHQGCLDRYVSSLKERYNRRII---------FEGGHIVDPDQGEFLCPVCRQLANSVLPALP 1487 (1764)
Q Consensus 1434 ~~H~~C~~~y~~sl~~r~~~~~~---------~~~~~~~~~~~~Ef~CPlCr~l~N~~lP~~p 1487 (1764)
+-|-+|+++|-++-......... -...+.+.....+-.|||||-=-.--..+-|
T Consensus 36 ~rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~CPLCRG~V~GWtvve~ 98 (162)
T PF07800_consen 36 YRHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPELACPLCRGEVKGWTVVEP 98 (162)
T ss_pred cchhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccccCccccCceeceEEchH
Confidence 34899999997765443321100 0011234556789999999975444444443
No 56
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=30.33 E-value=28 Score=45.75 Aligned_cols=26 Identities=38% Similarity=1.068 Sum_probs=21.9
Q ss_pred ccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhh
Q 000264 1430 SCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (1764)
Q Consensus 1430 ~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~ 1477 (1764)
.|||+-|..|..+.++. +-.||.||.
T Consensus 313 ~C~Hifh~~CL~~W~er----------------------~qtCP~CR~ 338 (543)
T KOG0802|consen 313 PCGHIFHDSCLRSWFER----------------------QQTCPTCRT 338 (543)
T ss_pred ecccchHHHHHHHHHHH----------------------hCcCCcchh
Confidence 49999999999988764 126999999
No 57
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=29.51 E-value=36 Score=34.97 Aligned_cols=23 Identities=26% Similarity=0.603 Sum_probs=18.0
Q ss_pred CCCceEcccchHhhHHHHHHHHH
Q 000264 1423 CDGIHLSSCGHAVHQGCLDRYVS 1445 (1764)
Q Consensus 1423 ~~g~~~~~CgH~~H~~C~~~y~~ 1445 (1764)
..-+-=..|.|+.|+.|..++++
T Consensus 73 EC~VaWG~CNHaFH~hCisrWlk 95 (114)
T KOG2930|consen 73 ECTVAWGVCNHAFHFHCISRWLK 95 (114)
T ss_pred ceEEEeeecchHHHHHHHHHHHh
Confidence 44444567999999999999964
No 58
>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=27.55 E-value=14 Score=37.29 Aligned_cols=16 Identities=38% Similarity=0.947 Sum_probs=10.5
Q ss_pred ceEcccchHhhHHHHH
Q 000264 1426 IHLSSCGHAVHQGCLD 1441 (1764)
Q Consensus 1426 ~~~~~CgH~~H~~C~~ 1441 (1764)
+.+..|||++|+.|.+
T Consensus 93 f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 93 FVVFPCGHVVHYSCIK 108 (109)
T ss_pred EEEeCCCeEEeccccc
Confidence 4555677777777764
No 59
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=25.53 E-value=46 Score=39.70 Aligned_cols=19 Identities=26% Similarity=0.595 Sum_probs=16.0
Q ss_pred ceEcccchHhhHHHHHHHH
Q 000264 1426 IHLSSCGHAVHQGCLDRYV 1444 (1764)
Q Consensus 1426 ~~~~~CgH~~H~~C~~~y~ 1444 (1764)
+-.++|||..-+=|..+|+
T Consensus 38 p~~TtCgHtFCslCIR~hL 56 (391)
T COG5432 38 PCETTCGHTFCSLCIRRHL 56 (391)
T ss_pred ceecccccchhHHHHHHHh
Confidence 3468999999999998884
No 60
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=25.20 E-value=56 Score=41.28 Aligned_cols=36 Identities=33% Similarity=0.845 Sum_probs=25.7
Q ss_pred CceeEEeccCCCCCCccccccccCCC----CC-CCceeEEEecC
Q 000264 125 NDIAYRCRTCEHDPTCAICVPCFQNG----NH-KEHDYSIIYTG 163 (1764)
Q Consensus 125 ge~~y~C~~C~~d~t~~lC~~CF~~~----~H-~gH~~~~~~~~ 163 (1764)
|-+-.+|-.|. .--+|..||..| .| .+|.|.++.++
T Consensus 26 ~~i~ikCaeCp---~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~ 66 (438)
T KOG0457|consen 26 GLIRIKCAECP---DFDLCLQCFSVGAETGKHQNDHPYRIMDTN 66 (438)
T ss_pred cceEEEeecCC---CcchhHHHHhcccccCCCCCCCCceeecCC
Confidence 34457888883 334899999765 46 48999998764
No 61
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=24.71 E-value=56 Score=29.28 Aligned_cols=23 Identities=35% Similarity=0.746 Sum_probs=17.0
Q ss_pred CCceEcccc-----hHhhHHHHHHHHHH
Q 000264 1424 DGIHLSSCG-----HAVHQGCLDRYVSS 1446 (1764)
Q Consensus 1424 ~g~~~~~Cg-----H~~H~~C~~~y~~s 1446 (1764)
..+-+.-|. |++|.+|+++++..
T Consensus 12 ~~~l~~PC~C~G~~~~vH~~Cl~~W~~~ 39 (49)
T smart00744 12 GDPLVSPCRCKGSLKYVHQECLERWINE 39 (49)
T ss_pred CCeeEeccccCCchhHHHHHHHHHHHHH
Confidence 344456664 99999999999754
No 62
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=24.61 E-value=44 Score=40.27 Aligned_cols=33 Identities=45% Similarity=0.944 Sum_probs=22.9
Q ss_pred ceeEEeccC-CCCCCccccccccCCCC----C-CCceeEEEec
Q 000264 126 DIAYRCRTC-EHDPTCAICVPCFQNGN----H-KEHDYSIIYT 162 (1764)
Q Consensus 126 e~~y~C~~C-~~d~t~~lC~~CF~~~~----H-~gH~~~~~~~ 162 (1764)
-+..+|-.| .+| +|..||-+|. | .-|.|+++.+
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 345566666 333 8999998765 3 4689999864
No 63
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.39 E-value=38 Score=42.82 Aligned_cols=19 Identities=37% Similarity=0.719 Sum_probs=16.6
Q ss_pred eEcccchHhhHHHHHHHHH
Q 000264 1427 HLSSCGHAVHQGCLDRYVS 1445 (1764)
Q Consensus 1427 ~~~~CgH~~H~~C~~~y~~ 1445 (1764)
.+..|||.....|...|+.
T Consensus 40 vitpCgH~FCs~CI~~~l~ 58 (397)
T TIGR00599 40 VLTSCSHTFCSLCIRRCLS 58 (397)
T ss_pred cCCCCCCchhHHHHHHHHh
Confidence 4689999999999999864
No 64
>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=23.29 E-value=47 Score=40.54 Aligned_cols=18 Identities=28% Similarity=0.807 Sum_probs=15.3
Q ss_pred eEcccchHhhHHHHHHHH
Q 000264 1427 HLSSCGHAVHQGCLDRYV 1444 (1764)
Q Consensus 1427 ~~~~CgH~~H~~C~~~y~ 1444 (1764)
.++.|||-|=-+|.++.+
T Consensus 22 ~i~~CGH~~C~sCv~~l~ 39 (309)
T TIGR00570 22 MVNVCGHTLCESCVDLLF 39 (309)
T ss_pred ccCCCCCcccHHHHHHHh
Confidence 344899999999999986
No 65
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=22.40 E-value=48 Score=32.45 Aligned_cols=24 Identities=25% Similarity=0.488 Sum_probs=17.6
Q ss_pred CCCCceEcccchHhhHHHHHHHHH
Q 000264 1422 DCDGIHLSSCGHAVHQGCLDRYVS 1445 (1764)
Q Consensus 1422 ~~~g~~~~~CgH~~H~~C~~~y~~ 1445 (1764)
|-.-+..--|-|+.|..|..+.+.
T Consensus 42 DdCPLv~G~C~h~fh~hCI~~wl~ 65 (84)
T KOG1493|consen 42 DDCPLVWGYCLHAFHAHCILKWLN 65 (84)
T ss_pred CCCccHHHHHHHHHHHHHHHHHhc
Confidence 333344557999999999988853
No 66
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.85 E-value=39 Score=39.48 Aligned_cols=49 Identities=27% Similarity=0.538 Sum_probs=35.6
Q ss_pred CCCceEcccchHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCccccccchhhc--cccccccCCCCc
Q 000264 1423 CDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQL--ANSVLPALPWDL 1490 (1764)
Q Consensus 1423 ~~g~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l--~N~~lP~~p~~~ 1490 (1764)
.-++.++.|||.-=..|+.+.+.. +-.. =.||+||+- -..|+|+..-..
T Consensus 57 akdPVvTlCGHLFCWpClyqWl~~---~~~~----------------~~cPVCK~~Vs~~~vvPlYGrG~ 107 (230)
T KOG0823|consen 57 AKDPVVTLCGHLFCWPCLYQWLQT---RPNS----------------KECPVCKAEVSIDTVVPLYGRGS 107 (230)
T ss_pred cCCCEEeecccceehHHHHHHHhh---cCCC----------------eeCCccccccccceEEeeeccCC
Confidence 568899999999999998777432 2221 148999986 478999985433
No 67
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=20.64 E-value=55 Score=28.32 Aligned_cols=20 Identities=30% Similarity=0.632 Sum_probs=16.1
Q ss_pred CceEcccchHhhHHHHHHHH
Q 000264 1425 GIHLSSCGHAVHQGCLDRYV 1444 (1764)
Q Consensus 1425 g~~~~~CgH~~H~~C~~~y~ 1444 (1764)
-+.+-.|||..=.+|.++|.
T Consensus 10 ~Pv~l~CGH~FC~~Cl~~~~ 29 (42)
T PF15227_consen 10 DPVSLPCGHSFCRSCLERLW 29 (42)
T ss_dssp SEEE-SSSSEEEHHHHHHHH
T ss_pred CccccCCcCHHHHHHHHHHH
Confidence 35677899999999999883
Done!