Query 000140
Match_columns 2060
No_of_seqs 351 out of 628
Neff 6.5
Searched_HMMs 46136
Date Thu Mar 28 20:18:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000140.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000140hhsearch_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 6E-127 1E-131 1260.6 68.6 1282 282-2044 371-1720(1738)
2 KOG1139 Predicted ubiquitin-pr 100.0 2.1E-32 4.4E-37 336.0 5.7 610 1416-2057 170-782 (784)
3 KOG1140 N-end rule pathway, re 99.8 1.4E-21 3.1E-26 262.4 -2.1 927 18-1000 532-1502(1738)
4 smart00396 ZnF_UBR1 Putative z 99.8 1.4E-19 2.9E-24 171.1 5.8 70 116-185 1-71 (71)
5 PF02207 zf-UBR: Putative zinc 99.7 2E-18 4.3E-23 164.0 4.1 70 116-185 1-71 (71)
6 KOG1139 Predicted ubiquitin-pr 98.9 9E-09 1.9E-13 129.5 16.1 185 754-938 207-477 (784)
7 PF10390 ELL: RNA polymerase I 97.0 0.00045 9.8E-09 83.5 3.7 80 869-953 198-280 (284)
8 KOG1777 Putative Zn-finger pro 94.9 0.014 3E-07 71.1 2.2 62 112-174 540-606 (625)
9 PF13639 zf-RING_2: Ring finge 91.4 0.06 1.3E-06 46.7 0.2 20 1427-1446 17-36 (44)
10 cd00162 RING RING-finger (Real 91.3 0.16 3.5E-06 43.1 2.7 19 1428-1446 15-33 (45)
11 KOG0943 Predicted ubiquitin-pr 89.1 0.12 2.5E-06 68.8 -0.0 63 116-184 1241-1309(3015)
12 PF13764 E3_UbLigase_R4: E3 ub 88.3 1.8 4E-05 59.3 10.3 70 1146-1229 422-497 (802)
13 KOG4445 Uncharacterized conser 88.2 0.15 3.4E-06 59.9 0.2 48 1428-1477 133-183 (368)
14 KOG4796 RNA polymerase II elon 84.8 0.92 2E-05 57.6 4.3 77 869-951 211-290 (604)
15 cd02335 ZZ_ADA2 Zinc finger, Z 84.5 0.75 1.6E-05 41.1 2.5 39 117-159 5-48 (49)
16 cd02340 ZZ_NBR1_like Zinc fing 83.9 0.83 1.8E-05 39.7 2.4 37 117-158 5-41 (43)
17 PF00097 zf-C3HC4: Zinc finger 83.4 0.69 1.5E-05 39.3 1.8 20 1427-1446 13-32 (41)
18 cd02249 ZZ Zinc finger, ZZ typ 82.8 0.89 1.9E-05 40.1 2.3 37 117-158 5-44 (46)
19 PF12861 zf-Apc11: Anaphase-pr 82.4 0.82 1.8E-05 45.3 2.1 25 1422-1446 43-67 (85)
20 smart00184 RING Ring finger. E 81.2 1.3 2.7E-05 36.1 2.5 18 1428-1445 13-30 (39)
21 PF14634 zf-RING_5: zinc-RING 81.0 1.4 3E-05 38.4 2.7 31 1425-1477 14-44 (44)
22 cd02338 ZZ_PCMF_like Zinc fing 80.1 1.3 2.9E-05 39.6 2.4 38 117-159 5-48 (49)
23 KOG2905 Transcription initiati 78.8 1.3 2.9E-05 51.3 2.5 62 869-931 182-245 (254)
24 cd02344 ZZ_HERC2 Zinc finger, 77.5 1.9 4E-05 38.0 2.4 39 117-159 5-44 (45)
25 KOG2752 Uncharacterized conser 77.5 2.7 5.9E-05 50.5 4.6 61 112-173 37-101 (345)
26 COG5243 HRD1 HRD ubiquitin lig 74.6 1.4 3E-05 53.5 1.3 16 1430-1445 317-332 (491)
27 PF00643 zf-B_box: B-box zinc 74.5 1.7 3.7E-05 37.3 1.4 28 126-158 13-40 (42)
28 PF11793 FANCL_C: FANCL C-term 74.1 0.95 2.1E-05 43.6 -0.2 38 1429-1477 26-63 (70)
29 PHA02926 zinc finger-like prot 73.5 2.6 5.6E-05 48.7 3.0 46 1423-1485 190-235 (242)
30 PF09538 FYDLN_acid: Protein o 72.6 1.7 3.7E-05 45.4 1.2 27 1932-1958 8-38 (108)
31 PLN03208 E3 ubiquitin-protein 69.1 3.7 8.1E-05 46.9 3.0 53 1428-1486 33-87 (193)
32 cd02339 ZZ_Mind_bomb Zinc fing 68.0 3.5 7.6E-05 36.3 1.9 30 126-158 13-43 (45)
33 TIGR02300 FYDLN_acid conserved 63.9 3.4 7.3E-05 43.9 1.2 27 1932-1958 8-38 (129)
34 KOG1940 Zn-finger protein [Gen 61.6 4.1 8.8E-05 49.2 1.5 35 1426-1482 175-209 (276)
35 PF12678 zf-rbx1: RING-H2 zinc 58.3 2.4 5.2E-05 41.2 -0.9 18 1427-1444 46-63 (73)
36 cd02343 ZZ_EF Zinc finger, ZZ 58.2 5.6 0.00012 35.5 1.4 35 117-156 5-40 (48)
37 cd02341 ZZ_ZZZ3 Zinc finger, Z 55.9 7.8 0.00017 34.7 1.9 32 126-158 13-46 (48)
38 cd02336 ZZ_RSC8 Zinc finger, Z 55.8 4 8.8E-05 36.0 0.2 31 117-152 5-35 (45)
39 PHA02929 N1R/p28-like protein; 53.6 6.4 0.00014 46.8 1.4 35 1428-1484 197-231 (238)
40 COG2051 RPS27A Ribosomal prote 53.5 4.9 0.00011 37.9 0.3 28 1931-1958 17-50 (67)
41 cd00021 BBOX B-Box-type zinc f 53.4 10 0.00022 31.7 2.1 28 126-158 10-37 (39)
42 PF13923 zf-C3HC4_2: Zinc fing 53.2 5.8 0.00013 33.5 0.7 20 1427-1446 13-32 (39)
43 cd02337 ZZ_CBP Zinc finger, ZZ 51.0 8.5 0.00018 33.3 1.3 32 116-153 4-35 (41)
44 PF10571 UPF0547: Uncharacteri 49.4 7.7 0.00017 30.3 0.8 22 1934-1955 1-23 (26)
45 PF02270 TFIIF_beta: Transcrip 48.7 6.5 0.00014 48.0 0.4 31 899-930 244-274 (275)
46 KOG0828 Predicted E3 ubiquitin 48.4 11 0.00024 47.8 2.2 29 1428-1477 603-631 (636)
47 KOG0827 Predicted E3 ubiquitin 47.9 12 0.00027 46.2 2.5 30 1416-1446 12-41 (465)
48 smart00336 BBOX B-Box-type zin 47.7 15 0.00032 31.2 2.4 29 125-158 12-40 (42)
49 PF13240 zinc_ribbon_2: zinc-r 46.9 9.9 0.00022 28.8 1.0 20 1935-1954 1-21 (23)
50 smart00291 ZnF_ZZ Zinc-binding 46.6 13 0.00028 32.5 1.8 33 116-153 8-40 (44)
51 PLN00209 ribosomal protein S27 44.9 7.7 0.00017 38.6 0.2 38 1916-1959 25-68 (86)
52 PF13920 zf-C3HC4_3: Zinc fing 43.9 14 0.00031 32.9 1.7 18 1428-1445 17-35 (50)
53 PTZ00083 40S ribosomal protein 43.6 8.4 0.00018 38.2 0.2 38 1916-1959 24-67 (85)
54 cd02334 ZZ_dystrophin Zinc fin 43.6 15 0.00033 33.0 1.8 32 117-152 5-36 (49)
55 PF13248 zf-ribbon_3: zinc-rib 43.3 11 0.00025 29.2 0.9 22 1933-1954 2-24 (26)
56 PF14446 Prok-RING_1: Prokaryo 40.8 9.1 0.0002 35.0 -0.0 45 1931-1980 3-51 (54)
57 KOG4172 Predicted E3 ubiquitin 40.5 13 0.00029 33.7 0.9 15 1428-1442 22-37 (62)
58 PRK00415 rps27e 30S ribosomal 38.9 12 0.00027 34.8 0.5 28 1931-1958 9-42 (59)
59 PF01667 Ribosomal_S27e: Ribos 38.6 11 0.00023 34.8 0.1 28 1931-1958 5-38 (55)
60 KOG2114 Vacuolar assembly/sort 38.4 15 0.00033 49.7 1.4 23 1430-1477 858-880 (933)
61 cd02345 ZZ_dah Zinc finger, ZZ 37.9 22 0.00048 32.0 2.0 31 116-151 4-35 (49)
62 COG5194 APC11 Component of SCF 36.7 36 0.00078 33.5 3.2 26 1421-1446 44-69 (88)
63 PF00569 ZZ: Zinc finger, ZZ t 33.2 11 0.00024 33.4 -0.7 36 117-156 9-45 (46)
64 KOG0457 Histone acetyltransfer 32.5 33 0.00071 43.6 2.9 43 117-163 19-66 (438)
65 PF07800 DUF1644: Protein of u 32.1 33 0.00072 38.1 2.5 44 1435-1478 37-89 (162)
66 PF02148 zf-UBP: Zn-finger in 25.0 58 0.0012 30.7 2.5 51 1936-1992 1-51 (63)
67 COG4031 Predicted metal-bindin 24.6 34 0.00074 38.6 1.0 20 1935-1955 2-21 (227)
68 PF08271 TF_Zn_Ribbon: TFIIB z 24.0 44 0.00096 29.1 1.4 25 1934-1958 1-31 (43)
69 KOG1941 Acetylcholine receptor 23.5 43 0.00094 41.6 1.7 17 1428-1444 384-400 (518)
70 COG5114 Histone acetyltransfer 23.2 56 0.0012 39.6 2.5 33 126-162 18-56 (432)
71 KOG0309 Conserved WD40 repeat- 20.5 48 0.001 44.3 1.4 18 1428-1445 1045-1062(1081)
72 KOG0802 E3 ubiquitin ligase [P 20.3 58 0.0013 43.8 2.1 19 1428-1446 311-329 (543)
No 1
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.2e-127 Score=1260.55 Aligned_cols=1282 Identities=22% Similarity=0.334 Sum_probs=811.0
Q ss_pred hccCCCHHHHHHHHHHHH-HhhCChhhHHHHHHHHHhhhHHHHHHHHHhccCcccccCCccceeeeeccccCCcHHHHHH
Q 000140 282 AEMFSSDVVVRKLHELLL-KLLGEPIFKYEFAKVFLSYYPVFVKDAIREHSDDTIKKYPLLSTFSVQIFTVPTLTPRLVK 360 (2060)
Q Consensus 282 ~~~~l~k~~r~~lh~L~l-sLL~d~efK~~fa~~Fv~~Y~~i~~~fl~~d~d~~~~~~s~v~~LSVQLFTvPsLA~~LV~ 360 (2060)
.+..+||..|..++.++. .+-++.+||+.|+.+|+.+|..+..+++.+|++.. .+.| .++||+||+|++|..+++
T Consensus 371 ~d~~~~kr~r~~l~k~~~~~~~~~~~~k~~~~~~~~~~y~~~~~~~~~~d~e~~---~~vi-~~~vqf~t~~~~a~~~~~ 446 (1738)
T KOG1140|consen 371 FDNRYWKRLRKDLQKVIIPTFASSNLYKPIFAQQFVEHYNSITRDFAYMDREPD---LSVI-ELSVQFFTCPSLAKNIVE 446 (1738)
T ss_pred HHHHHHHHHHHHHhhcceeehhcchHHHHHHHHHHHHHHHHHHHHHHhhcCCcc---hhhH-hheeeeecCcHHHHHhhh
Confidence 334457889999999999 67789999999999999999999999999998744 3545 999999999999999999
Q ss_pred hhcHHHHHHHHHHHHhhhhcCCCCcceec----------cccccccchhhhhhhhhHhhcchhhhHHHhhhchHHHHHHH
Q 000140 361 EMNLLEMLLGCLREIFDSCAGDDSCLQVA----------KWANLYETTNRVIGDIRFVMSHAAVSKYATHEQLNISKAWM 430 (2060)
Q Consensus 361 e~nLL~iLl~tl~~~~~~~~~~~~~l~~~----------~~~~~~~~y~~I~~DLrylLsh~~v~~~l~~~~~~l~~~~l 430 (2060)
...++.++..++..++..+.. ++...++ +.....++.+..+.|+ +.+.++. +-.++..+..++
T Consensus 447 ~~~~~~l~~~~~~~~~~~~~~-~~~~~~~~~~~~s~~~~~~~~~~~r~l~~~~~l-~~~~~~~-----~~~~~~~~~~~l 519 (1738)
T KOG1140|consen 447 NQSFLDIVWSIIDIFKEFNKV-EGGVLIDIRVQKSNLLKRYSISFRRTLYTFEDL-SKVHDPN-----IPLRPKEFISLL 519 (1738)
T ss_pred hccchHHHHHHHHHHHHhccc-ccceecceeeeechhhhHHHHHHHHHHHHHHHh-hccCCcc-----ccccHHHHHHHH
Confidence 999888877777766654443 3222111 1222356677788888 7766666 235789999999
Q ss_pred HHHHHhcCCCcccccccCcceeeCCceeehhhhhhHHHHhHhhhhhccccccccchhccccccccccCCCCCcccccccc
Q 000140 431 KLLTFVQGMNPQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEETRYDFSMYKQDIGDGDSLRHAKVG 510 (2060)
Q Consensus 431 ~lL~~~QGMn~~kRq~~~HVEyE~~~w~~aF~L~~~la~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~ 510 (2060)
.++..||||.|++|+.++||++|++ |+.+|.+-.++..++++++.||...+ . +-
T Consensus 520 ~~~~v~qg~~~lkr~~~ehv~~e~~-~~~~~~~v~~~t~~~s~i~~~~~~~e--------p-----------------~~ 573 (1738)
T KOG1140|consen 520 LLLKVFQGVDPLKREELEHVEVEKE-WENFFSLVEYLTAIYSMIQSLVKTSE--------P-----------------VK 573 (1738)
T ss_pred HHHHHhCCccHHHHHHhhhhcccch-HHHHHHHHHHHHHHHHHHHHHHHhcc--------c-----------------hh
Confidence 9999999999999999999999997 99999999999999999998887644 0 00
Q ss_pred ccccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhhhcCCCCcccccccCCCCcccccCch
Q 000140 511 RLSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENWLGVDDRSVSVNDILSPNASRISGSN 590 (2060)
Q Consensus 511 r~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~cl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 590 (2060)
..++..|+.++..... .. +++.
T Consensus 574 -----------------------------------------~~~~~~l~~~~~r~~~-----s~------------~~~~ 595 (1738)
T KOG1140|consen 574 -----------------------------------------DSVYKKLLEAAIRIHP-----SL------------TGSE 595 (1738)
T ss_pred -----------------------------------------hhHHHHHHHHHhhccc-----cc------------Cccc
Confidence 0011122222221100 00 0000
Q ss_pred hhHhHhhhhhhcccccccccccCCccccccccccCCCccccccCccccccccCCcccccccccCcCCccccccccccccc
Q 000140 591 FVALKKTLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKITISGERDTASWRSAGFNDSEMEGECATELDN 670 (2060)
Q Consensus 591 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 670 (2060)
. ++ ..+++++
T Consensus 596 ~--l~--------------------------------------------------------------~~i~~~S------ 605 (1738)
T KOG1140|consen 596 S--LT--------------------------------------------------------------YTICGES------ 605 (1738)
T ss_pred e--ee--------------------------------------------------------------ehhhhhh------
Confidence 0 00 1223332
Q ss_pred ccccccCccCceeeeccCCceeeehhHHHHHHHHHHHHHhhhccccccccccccCCCCCccccchhhhhcccCCCCCccc
Q 000140 671 LHVLSLCYWPDITYDVSSQDVSVHIPLHRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGF 750 (2060)
Q Consensus 671 l~~~~~~~~~~v~fdVs~~~VSfH~PLhr~Ls~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 750 (2060)
..++.|+|+.++||||.|+.|+|+++++..... ++...+.+ ..+.+++.
T Consensus 606 --------~e~i~f~v~~~~~sv~~p~~~~l~~l~~~~~s~-------------------v~~~~d~~-~~~~~~~n--- 654 (1738)
T KOG1140|consen 606 --------HETINFSVSQERVSVSNPVSRLLAFLIELSCSS-------------------VVSLKDAY-ERLEDCSN--- 654 (1738)
T ss_pred --------HhHhhhccccccceeeccHHHHhhhhhhcccch-------------------hhhcchhh-hhHhhhcc---
Confidence 347899999999999999999999998432110 00111111 11222222
Q ss_pred chhhccccHHHHHHHHhHhcCceeeccHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhcccccc
Q 000140 751 SAFVMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYL 830 (2060)
Q Consensus 751 ~~~l~e~pLR~~Vl~aQI~aGmWvRNG~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~ 830 (2060)
..+|.|||||++|++|||.+|||||||+++.+|+.+|++.+||+++||+||+++|.++++.||++|+.++++||+|.+|+
T Consensus 655 ~~~i~e~~lr~~Vl~aqid~~~w~rNG~si~~q~~~y~~~~~r~~~y~~DI~~~Q~~la~~d~~~~l~~~l~r~~L~~w~ 734 (1738)
T KOG1140|consen 655 FLAISEHSLRVLVLCAQIDVGFWVRNGFSILHQAAYYKNNPCRNESYDRDILMLQTGLAMEDPNRFLFTILSRFELLDWF 734 (1738)
T ss_pred chhhcccchhheeeeeecceeeEeecCcchhhhhHhhcCccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHh
Confidence 25789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCCCCC-ch---hHHHHHHHHHHHHhhcccccCCC---ChHHHHHHHHHHHHhcCCCChHHHHhhCCCCCCCcchHH
Q 000140 831 SLNLERPSE-YE---PILVQEMLTLIIQILQERRFCGL---TTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQ 903 (2060)
Q Consensus 831 ~~~~~~~~~-y~---~~mvEe~L~lLI~lltER~~~g~---s~~e~lr~EIIh~Lc~~p~t~S~L~~~lpe~~~~~~~fe 903 (2060)
+|....... ++ ..|+|+|+.+||.|++||...|+ +..+.+|+||||+||++|++||+|.+++|++++++..||
T Consensus 735 ~g~~~~~~~d~~~~i~~~~ee~l~lii~ll~Er~~~~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~~d 814 (1738)
T KOG1140|consen 735 TGEVDYQSNDTEDTISFMIEEFLALIILLLTERSYFGSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLSFD 814 (1738)
T ss_pred cCCCccccccHHHHHHHHHHHHHHHHHHHHHheeecccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhcccch
Confidence 998654332 22 37999999999999999996554 577899999999999999999999999999999999999
Q ss_pred HHHHHHccccCCCCC-CcceEEeehhhhccccccccccCchhHHHHHHHHHH--hhc---cccccCCC-CCCcccCC-Cc
Q 000140 904 EILDAVAMYSHPSGF-NQGMYSLRWSYWKELDIYHPRWSSRDLQVAEERYLR--FCS---VSALTAQL-PRWTKIYY-PL 975 (2060)
Q Consensus 904 ~iL~eVA~f~~P~g~-~~G~Y~LK~e~~~e~dpy~~~y~~~~~q~aeer~~r--~~~---~~a~~~~~-P~~~~~~~-p~ 975 (2060)
.++++||+|++|.++ +.|+|+||++||+++||||+||+++++.+++..+++ .++ ..|..+++ |++.+.+. .+
T Consensus 815 ~~~e~Va~~~~p~~~~~~gvf~lK~~~~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~~~ 894 (1738)
T KOG1140|consen 815 EALEEVAVFKKPKGLADNGVFVLKESYYDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKKGA 894 (1738)
T ss_pred HHHHHHHhhccCCccccceEEEechhhhhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHHHH
Confidence 999999999999999 789999999999999999999999999888765533 211 12444332 33333221 12
Q ss_pred cccccccCcHHHHHHHHHHHHHHhccCCCCCCCCchhHHHHHHHHH-HHHHhhhhhcccCCCCCcccCCCCccccchhhH
Q 000140 976 ESIAGIATCKVVLQVIRAVLFYAVFTDNPTDSRAPYGVLLTALHLL-ALALDVCFQKKKSGDQSCDIGGSTPILDFASEE 1054 (2060)
Q Consensus 976 ~~i~~il~s~~~~~il~~vL~~al~~~~~~~~~~~E~~L~~~LHLi-~laL~~~~~e~~~~~~~~~~~~~~p~~~~~~~~ 1054 (2060)
.++.+.....+|-.||+.++.++.+.. .+.++..++|++ +.|++++..--. |.+.-. ++
T Consensus 895 ~~L~~~t~~~~~~~ii~r~~~~~~~~~-------s~~~l~~~~~~ihG~~~~~~l~~~~-----------~~~~~~-~e- 954 (1738)
T KOG1140|consen 895 DILGAAVRLTVFGLIIYRTLEHCLFME-------SSTLLSKVLHLIHGIALNEELINMK-----------FAFTQK-TE- 954 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhcc-----------cccccc-cc-
Confidence 455555566667777777777776543 488999999554 899986543211 110010 11
Q ss_pred HhhccCCCCCcccHHHHHHHHHhhhccCCCccccccccCCchhHHHHHHHHHHhhhHHHHHHHhhhchhhhhcccCCCCC
Q 000140 1055 IAEGLNNGAGKQSLLSLLVFLMGMYKKDGADNFLEAGNCNLSSVIESLLKKFAEIDSRCMTKLQQLAPEIVSHLSQSLPR 1134 (2060)
Q Consensus 1055 i~~~~~~~~~~~SllsLL~~L~~~~~~~~~~~~~~~~~~~i~~~I~~lL~~f~~~~~~c~~~l~~~~p~~~~~~~~~~~~ 1134 (2060)
....+..+.+++.+..++....+ +.+++|+++.|..+.. .+...|++.. .... ..
T Consensus 955 -------~~~~e~gl~~~e~lv~~~~~~~~-----------~~~~~v~~~l~~~~~~-----~~~n~~ea~~-~~~~-~~ 1009 (1738)
T KOG1140|consen 955 -------SIAREKGLSLYESLVRKPDSLVH-----------GKIIEVIVELFESLIK-----SRANDPEVAN-DEKD-KK 1009 (1738)
T ss_pred -------ccccccchhhHHHhhhcchhhcC-----------CcceeeeHHHHhhhhh-----hhcCCccccc-cccc-cc
Confidence 11345577788877777554332 4568888888876544 2444443321 1100 01
Q ss_pred CCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCccCCCCcccccccccCCccccccCCCC
Q 000140 1135 DDTSGSFSASDSEKRKAKARERQAAILEKMKAEQFKFLSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS 1214 (2060)
Q Consensus 1135 ~~~~~~~~~~e~ekkK~~AkeRQakIMaqf~~qQ~~Fl~~n~~~~d~~~~~~~~~~~s~~~~~~~e~~~~~CilCqe~~~ 1214 (2060)
...+.+.++.+.++||++|++||+|+||||+.||.+||++|.++.|++++. .+++...+.. .....|.+|+..+.
T Consensus 1010 ~~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e~d~~~~~---~~~~~~~~~~--~~d~~~~~~~~~s~ 1084 (1738)
T KOG1140|consen 1010 EKQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDEFDEQENQ---TPSSGSKTYE--EEDFTCALCQDNSC 1084 (1738)
T ss_pred cccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccccCccccc---Cccccccchh--hhhccchhhhccch
Confidence 112234445556788889999999999999999999999997666554331 1111101111 11456777764322
Q ss_pred -CCCeEEEeeeecccccccccCCCCCCcccccccccccccccccccccCCCCCCCCCCCcchhhhhHHHHHHHHhhhccC
Q 000140 1215 -RTPVSYLILLQKSRLLSFVDRGSPSWDQDQWLGKECGTISANNMVNQFGTNTPSSGLGVISSCQLAQVAEEAVNQFAYN 1293 (2060)
Q Consensus 1215 -~~pfg~la~iq~S~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~ 1293 (2060)
+.++ |+++.+...
T Consensus 1085 ~~~~~------~~~~~~~~~------------------------------------------------------------ 1098 (1738)
T KOG1140|consen 1085 TDFQV------KPASHLVKP------------------------------------------------------------ 1098 (1738)
T ss_pred hcccc------ccchhhhcc------------------------------------------------------------
Confidence 1222 222221110
Q ss_pred CCchhhhhHHHHhhhcCCCCcCCCCCcccCCCCcCCccchhhhhhhhhhHHHHhhhccCCCCCCccccchhhhccCCccc
Q 000140 1294 GKPEEVNSVLEFVKAQFPSLRNIPIPFTFSNGRKCTASSMEMFEQDLYLSICREMRKNMTYPDLMKEDEECSVAEGGLKN 1373 (2060)
Q Consensus 1294 ~r~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~s~~~~~e~~~~~~~~~~~~~ 1373 (2060)
...+||+| |+++.+...
T Consensus 1099 ---------------------------------------------~~~~~~i~------------~e~e~~~~~------ 1115 (1738)
T KOG1140|consen 1099 ---------------------------------------------IFRECIIC------------DENEDVPNW------ 1115 (1738)
T ss_pred ---------------------------------------------cccccccC------------ChhccCCCc------
Confidence 00123333 222222111
Q ss_pred CCCCccchhhhhhhhhhHHhhhcccccccccccccccccccCCCCCC-CcCCCccccccChHhhHHHHHHHHHHHHHhhh
Q 000140 1374 RGNSDSFLLGKYVASISKEMRENASASEVSRGDRIAAESLVYDGFGP-IDCDGIHLSSCGHAVHQGCLDRYVSSLKERYN 1452 (2060)
Q Consensus 1374 ~~~~~~~~l~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~F~~-~~~~gvh~SsCGH~MH~~C~~~Y~~Sl~~r~~ 1452 (2060)
.++.++..+|+++. +. ...+++.| ....|+++|+|||.||+.||++|+++.+.|.+
T Consensus 1116 --~~~~~v~~~f~~~s-~~--------------------~sd~l~~p~~~~~~~~~s~c~h~mh~~c~~~~~~a~r~~~n 1172 (1738)
T KOG1140|consen 1116 --DGRYSVSSAFAQKS-DD--------------------VSDALTEPGSLSCGTVLSSCGHHMHYGCFKRYVQAKRFREN 1172 (1738)
T ss_pred --cccchhhhHhhhhc-cc--------------------ccccccCCCCCcccceeeccCCcchHHHHHHHHHHHHHHHH
Confidence 01223555666552 11 11334434 56789999999999999999999999999998
Q ss_pred cccccCCCcccCCCCcccccccccccccceecCCCCCcccCCCCCcccCCCCCCCCCCccccccchhhHHHHHH------
Q 000140 1453 RRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRINEQPTVSGVGLSLDSSSSFTTREENTSFQLQQA------ 1526 (2060)
Q Consensus 1453 ~r~~~~r~h~~d~e~gEFLCPLCKsLsNs~LPilp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------ 1526 (2060)
++..+-+.|.. ++|+|+||+||+|+|++||..++.....+.. +.. ..+....|++..
T Consensus 1173 ~~~~~l~~~~s--e~~l~lCp~c~slsn~~lp~~~~~~~~~n~~-t~~--------------~~~n~~~~i~~rs~~~~s 1235 (1738)
T KOG1140|consen 1173 ARTAPLCQHYS--ENGLFLCPLCKSLSNVSLPMFLPPELLLNPL-TLE--------------NQRNLNSWIEKRSRASFS 1235 (1738)
T ss_pred hhhcCcccccc--cCCcccCCchHhhhhccCCcCCchhhhcChh-hhh--------------chHHHHHHHHHhchhhcc
Confidence 77665554443 8999999999999999999875433322210 000 001222233310
Q ss_pred HHHhhhc---c-ccccc---ccccccCCcchhhHHHHHHHHHHHHHHHHhhccc------cccccCCCCCChhHHHHHHH
Q 000140 1527 VSLLQSA---S-NVVGK---ADVIESFPLMKNEIMASNVEAVSRRMCKMYFQNK------LDKFFGSARVNPSLIMWDAL 1593 (2060)
Q Consensus 1527 ~~~l~s~---~-~~~~~---~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~------~~~~~~~~~~~~~~~l~~tl 1593 (2060)
+..+.+. . ..... .++.+..-.++.+.....++.+.+.+....+... .....+.++. .....|-.+
T Consensus 1236 ~~~vs~~~s~~~~~~~ss~i~e~kp~~~~~l~~~~~~~ie~~~k~v~s~~~k~~~~i~~~~le~~~~~~~-~~~~~~~~~ 1314 (1738)
T KOG1140|consen 1236 LQDVSSILSDPWAAFTSSRIPELKPILIMDLPDSVVEQIELFQKIVGSAMFKPSSLLSTNTLELTLFSRE-FLIVCWQSL 1314 (1738)
T ss_pred hhhhhhhhcccchhhccccccccccchHhhhhhHHHHHHHHHHHHHhhheeecccceeecccccCcccch-hhhhhhhcc
Confidence 0000000 0 00000 0000000001222222223333333332222111 1122234443 456778888
Q ss_pred hHhHHHHHHHhhccCCCCCCccchhhHHHhhhhchhHHHHHHHHHHhhhcccchHHHHHHhhc---cchhhhhccCCCCC
Q 000140 1594 KYSLMSMEIAARSEKTSTTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVLQRFRG---IQLFAESICSGTSI 1670 (2060)
Q Consensus 1594 ~yTi~s~Eia~Rg~~~~~~~~~~l~~L~~~l~~~~~~~l~ll~~~~~~~r~~~~~~~l~r~~~---~~Ll~~si~~~~s~ 1670 (2060)
++..+++++.+-+.+... +..+.+...+.+....++.... +...++...- +.++...+.+
T Consensus 1315 s~a~~~~~~~l~~~~~~~---------~l~l~~~~~~~~~~~~~l~~~~----~~~~l~~~~~~~llk~~s~~~~~---- 1377 (1738)
T KOG1140|consen 1315 SDAEQSTKLLLSASKKPS---------FLKLNEDMTFCLVTISRLRALH----WEQILYELVYTFLLKSFSPTIPR---- 1377 (1738)
T ss_pred chHHHHHHHHHhccCCcc---------cccCchhhHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhhcCCc----
Confidence 888888777544433321 1111111112222221111111 1112222111 1111110000
Q ss_pred CCCCCccCCCCcccccccccccccCcchhhhhhhcCCCccccChhhHHHHHHhhcccccccccchhhhHHHH-HHHHHHH
Q 000140 1671 DNPGGRCKRGGNMLSILKHADVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFILCKESLLSLVHV-FYAVTLS 1749 (2060)
Q Consensus 1671 ~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~plL~~D~F~~Lv~~~~~lp~~~~~~~~~~~~iv~l-~y~~~iv 1749 (2060)
.. .+... +.+.......+..++...|-+-. .++ ........++++ ..+++++
T Consensus 1378 i~----------------~~~tp-d~~~~~ll~~l~~~~~~~~~l~~------~~~----~~~~~~~~~~~~~i~~~~i~ 1430 (1738)
T KOG1140|consen 1378 IS----------------VLITP-DQPENELLVILPHDFPKSLELEL------TLD----FVNKNPKKIFELKILMASII 1430 (1738)
T ss_pred ch----------------hccCC-CCCcchhhhccchhhhhhccHHH------HHH----HhhhhHHHHHhHHHHHHHhh
Confidence 00 00000 00000000000011111111111 001 011233344444 4556777
Q ss_pred HH-Hhhhhcccccc--cccccchhhhHHHHHHHhcccccccccccccCCCChhhHHHHHHHhhhhHHHHHHHHHHhhcCC
Q 000140 1750 QA-VLSCCGKLQSK--VNELGFSDSLISDISKLLGEFGSAQEYFVSNYIDPSCDIKDMIRRLSFPYLRRCALLWKLLNST 1826 (2060)
Q Consensus 1750 Q~-li~~~~~~~~~--~~~~~~~~~~~~~i~~~~~~~~~~~~~~~s~~~d~~~~l~~~v~k~~lPFLRraaLL~~~l~~~ 1826 (2060)
|. +++.......+ .++....-.....+...+-.....+.......+-....++..+++.++|||||+++++|++.++
T Consensus 1431 s~elits~s~l~~d~~~~~~q~s~~e~~~~~t~l~~~~s~~~i~~~~~~~~~~~L~~~~~~~i~sfL~~~al~~h~ln~v 1510 (1738)
T KOG1140|consen 1431 SIELITSHSYLENDLEMAEEQKSIDEFKSLLTYLLQLESSRTIPKLADIRLRLSLCLSCEAGILSFLRRAALFKHLLNNV 1510 (1738)
T ss_pred hhhhheeccccCCccchhhhhhhHHhHhHHHHHHHhccchhhCccccchhhhhHHHHHHHHHHHHHHHHHHHhhhhhhcC
Confidence 76 44432221111 0011100000111111000000000000000001123578889999999999999999999999
Q ss_pred CCCCCCCccccccccccCccCCCCCCcccccchHHHHHHHHhcCCCChhhhh-hh--HHHHHHHHHHhhccccchhhhcc
Q 000140 1827 VPPPFSDRDHVLARSSHGISDMMDSSDDALSDLKEIQEVEKMFKIPSLDVIL-KD--EVLRSLVLKWFHHFSKEFEVHRF 1903 (2060)
Q Consensus 1827 ~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~L~~~L~LPsl~~il-~~--~~~~~li~~W~~h~~~~~~~~~~ 1903 (2060)
.+|... +.++ ....|+..||+|+++|++...+ +. +.++.++.+||.-.........+
T Consensus 1511 ~~p~~~------------f~~~--------~~~s~~e~L~ty~slp~l~~~~~q~~~delr~~~~~~~~~~~~lk~~~~~ 1570 (1738)
T KOG1140|consen 1511 FPPFGA------------FLDP--------SSNSELEHLCTYLSLPNLQACLLQSSGDELRQAIERWCGGTENLKREEHY 1570 (1738)
T ss_pred CCchhh------------ccCc--------ccchhhhhhcccccCccHHHHHHhhhHHHHHHHHHHhhccchHHHHHHhh
Confidence 876210 1110 0124788899999999877644 33 67889999998643211111111
Q ss_pred ccccccCCCCCccccCCchhHHHHHHHHhhcccCCCCCCC-CCceEeeccCccccCCCCcccC-------CCchhHhhhh
Q 000140 1904 QHVLYSTPAVPFKLMCLPHLYQDLLQRYIKQCCSDCKSVL-DEPALCLLCGRLCSPSWKPCCR-------ESSCQSHAVA 1975 (2060)
Q Consensus 1904 ~~~~~~~~~~~~~Li~LP~~y~~l~~~~~~~~C~~c~~~~-~~paiCL~CG~~~~~~~~~cc~-------~gec~~H~~~ 1975 (2060)
.......|..+..|++||+.|+.+++++....|++|+..+ ..|++||+||..+|.+ ..||+ .|+|++|+..
T Consensus 1571 ~~~~~i~~r~~~~l~~lpd~~s~lI~s~~~~~c~~~~~~~s~~p~lCl~cg~~~~~q-~~~~~~~~~~~~~g~~~~ha~~ 1649 (1738)
T KOG1140|consen 1571 LNTLSINPRIPNSLVELPDEYSCLINSASFFFCPKSGKDDSIIPALCLLCGSEECGQ-SGFDQEGSNGESVGACTAHAAE 1649 (1738)
T ss_pred cceeeecCCCCCccccCCchhhhhHHhhhcccCcccCCccccCchHHhhcchHHhhh-hhhhhccccccchHHHHHhHHh
Confidence 1223344566789999999999999999999999999986 8999999999988876 57884 3899999999
Q ss_pred cCCCeEEEEEecccEEEEEec--CCcccCCCCcccccCCCCcCcccCCCcccCHHHHHHHHHHHHcCCcCc
Q 000140 1976 CGAGTGVFLLIRRTTILLQRC--ARQAPWPSPYLDAFGEEDIEMHRGKPLYLNEERYAALTYMVASHGLDR 2044 (2060)
Q Consensus 1976 Cg~~~GiFl~v~~~~ill~~~--~rg~~~~spYLD~~GE~D~~lrrg~pl~L~~~Ry~~L~~~w~~h~i~~ 2044 (2060)
||+++||||.+++|.++++.+ ++|||+|+||+|+|||+|+|+|||.|+|||++||+++..+|++|+|++
T Consensus 1650 c~~~vgifl~v~~c~~~ll~~m~~~g~~~~~pylD~~gEtd~gl~rg~P~~L~~~ry~k~~~~w~~~~I~e 1720 (1738)
T KOG1140|consen 1650 CTGAVGIFLRVRECSILLLEGMRNRGCFYPAPYLDEYGETDPGLRRGNPLHLNRERYRKLKELWLQQNITE 1720 (1738)
T ss_pred hcceeceEEeeechhhhhhhcCCcCCCcCCCCccccccCCChhhhcCCcccccHhhhhhhHHHHhhcchHH
Confidence 999999999999999999988 999999999999999999999999999999999999999999999987
No 2
>KOG1139 consensus Predicted ubiquitin-protein ligase of the N-recognin family [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=2.1e-32 Score=335.99 Aligned_cols=610 Identities=11% Similarity=-0.050 Sum_probs=422.9
Q ss_pred CCCCCCcCCCccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccccccceecCCCCCcccCCC
Q 000140 1416 DGFGPIDCDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRINE 1495 (2060)
Q Consensus 1416 ~~F~~~~~~gvh~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKsLsNs~LPilp~~~~~~~~ 1495 (2060)
++|.+..+.+.|.++|+|..|.+|..+|+.....+-..+-.+.+.|..+..+.++.||.|++++|+|.|..++++.....
T Consensus 170 D~fv~h~q~~~asTsi~hf~~dsv~~r~l~eell~wg~~ylf~~~ev~rll~~g~~~~~c~alAKvveq~y~~~~~s~~k 249 (784)
T KOG1139|consen 170 DRFVDHIQSQHASTSITHFTEDSVRSRLLNEELLIWGLLYLFLRIEVARLLINGNMWVRCGALAKVVEQIYSQWNVSSAK 249 (784)
T ss_pred CcceecccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHhcCCCccccHHHHHHHHHhcccchhcccc
Confidence 55666667888999999999999999999999888777777888899999999999999999999999999765543222
Q ss_pred CCcccCCCCCCCCCCccccccchhhHHHHHHHHHhhhcccccccccccccCCcchhhHHH--HHHHHHHHHHHHHhhccc
Q 000140 1496 QPTVSGVGLSLDSSSSFTTREENTSFQLQQAVSLLQSASNVVGKADVIESFPLMKNEIMA--SNVEAVSRRMCKMYFQNK 1573 (2060)
Q Consensus 1496 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~s~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~~~l~~~~~~~~ 1573 (2060)
. ...+...+..+ ..-..++|+.+.+.....+.......+.....+++...-.. ....++.++.+..+++..
T Consensus 250 k-rhePdt~~~r~------~hi~~slfl~e~la~~~~~ec~~~di~r~v~~~p~~s~L~~~~~~~~~~~k~~~~~Hsr~p 322 (784)
T KOG1139|consen 250 K-RHEPDTIRFRA------AHIDKSLFLKELLASFNITECIKIDIGRFVEKSPESSILFQETEVTIDFTKQSPIDHSRDP 322 (784)
T ss_pred c-CCCCchhcccc------ccccHHHHHHHHHHHhhhhhhhhhhccceeEeccccccchhhhhhhccccccCchhcccCc
Confidence 1 00000000011 01134566666554433322211000000111111111111 111222222222222211
Q ss_pred ccccc-CCCCCChhHHHHHHHhHhHHHHHHHhhccCCCCCCccchhhHHHhhhhchhHHHHHHHHHHhhhcccchHHHHH
Q 000140 1574 LDKFF-GSARVNPSLIMWDALKYSLMSMEIAARSEKTSTTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVLQ 1652 (2060)
Q Consensus 1574 ~~~~~-~~~~~~~~~~l~~tl~yTi~s~Eia~Rg~~~~~~~~~~l~~L~~~l~~~~~~~l~ll~~~~~~~r~~~~~~~l~ 1652 (2060)
...+- +--+...-..+|++++|...+.|+--|--+-+..++.|...+...+++..+.+++++...+...+..+.++.-+
T Consensus 323 ~~~~l~~f~~p~lEaa~~d~l~~v~~~~e~~~R~~~~s~vlr~~~~~~~e~~~~~~~~~f~l~~~~v~~s~~~~ai~~~~ 402 (784)
T KOG1139|consen 323 RIPILGEFIRPHLEAAGVDALIDVEMEREFDPRLFDDSEVLRTIVIREPEWIDPMFWGMFKLVAELVVVSVNSGAIPEEH 402 (784)
T ss_pred chhHHHHhhccccccccCchHHHHhhhccccccccchhhhhHHhhhccccccchhhcchHHHHHHHhhhhcccccchHHH
Confidence 11000 00001122457999999999999999987777778888888889999999999999999999999999999999
Q ss_pred HhhccchhhhhccCCCCCCCCCCccCCCCcccccccccccccCcchhhhhhhcCCCccccChhhHHHHHHhhcccccccc
Q 000140 1653 RFRGIQLFAESICSGTSIDNPGGRCKRGGNMLSILKHADVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFILC 1732 (2060)
Q Consensus 1653 r~~~~~Ll~~si~~~~s~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~plL~~D~F~~Lv~~~~~lp~~~~~~ 1732 (2060)
++.++.=++.+++.+.++..++ .....+.....++ +..-.|+++..|++.+|||..+.+.++++|+++..+
T Consensus 403 ~~~em~n~~a~~~~~~s~~~aS-~~~~~~~~~~~f~--------~i~~~~~~~~~P~~~~~p~~~~s~~l~~~~~~~~~c 473 (784)
T KOG1139|consen 403 YRSEMVNCMAMGNVPYSRLRAS-ISEKGSMIDKHFE--------TILNEIGDFIEPIETTTPLMQGSYQLKTSIWDSEVC 473 (784)
T ss_pred HHHHHHhHHHhcCCCccccccc-ccCCCcccccccc--------cccccccccccchhhcCccccchhhccccCCccccc
Confidence 9888877777777666665553 2211221111222 223568889999999999999999999999888888
Q ss_pred cchhhhHHHHHHHHHHHHHHhhhhcccccccccccchhhhHHHHHHHhcccccccccccccCCCChhhHHHHHHHhhhhH
Q 000140 1733 KESLLSLVHVFYAVTLSQAVLSCCGKLQSKVNELGFSDSLISDISKLLGEFGSAQEYFVSNYIDPSCDIKDMIRRLSFPY 1812 (2060)
Q Consensus 1733 ~~~~~~iv~l~y~~~ivQ~li~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~s~~~d~~~~l~~~v~k~~lPF 1812 (2060)
..++...++.+--+..+|+++++...........++..... |+...+...+.+ .+|.+.+.+..+++.+.+.++-+||
T Consensus 474 ~~~~~~~~~s~~~~~~v~~~~~~~a~k~s~d~~l~~~~~~e-d~s~~lr~~g~s-~l~~~l~~~~~~d~~dt~~~~~~~~ 551 (784)
T KOG1139|consen 474 PVFFMMRSTSIKQAREVFAKMEIRAQKNSLDKDLEVAKIEE-DFSDQLRHRGIS-NLYNVLLTERFLDHCDTVLASEADE 551 (784)
T ss_pred cchheeeeeeccchhHHHHHHHHhhccchhhhhccccchhH-HHHHHHHHhhhH-HHhhhhhhhhhhcccchhhccccch
Confidence 88888888888888999999887532111000111111111 222222222221 2233333444567888999999999
Q ss_pred HHHHHHHHHhhcCCCCCCCCCccccccccccCccCCCCCCcccccchHHHHHHHHhcCCCChhhhhhhHHHHHHHHHHhh
Q 000140 1813 LRRCALLWKLLNSTVPPPFSDRDHVLARSSHGISDMMDSSDDALSDLKEIQEVEKMFKIPSLDVILKDEVLRSLVLKWFH 1892 (2060)
Q Consensus 1813 LRraaLL~~~l~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~L~~~L~LPsl~~il~~~~~~~li~~W~~ 1892 (2060)
+|+|+.+++.+-..... .....+++..+..-++++|+........++--+.+...+.||.+.+.. ..-.+.|++
T Consensus 552 ~~~c~~~~~~la~~~~t-l~~e~~~s~~~~~~i~~~m~~I~~~pf~l~~kq~~~~~~~i~~i~e~~-----~k~~e~~~~ 625 (784)
T KOG1139|consen 552 TAKCHDGTYQLAVYLLT-LGVEYAQSYVGDEKIKKQMIDIFHTPFQLILKQTRKNGALIVVIKEGK-----LKREELRIS 625 (784)
T ss_pred hhhHHHHHHHHHHHHHH-HhhhhhhhhcCCcchhhhhhhccCCchhhhHHHHHhcccCCchhHHHh-----HHHHHHHHH
Confidence 99999999987653321 112223334445556677777665555554466778888899887543 234577999
Q ss_pred ccccchhhhccccccccCCCCCccccCCchhHHHHHHHHhhcccCCCCCCCCCceEeeccCccccCCCCcccCCCchhHh
Q 000140 1893 HFSKEFEVHRFQHVLYSTPAVPFKLMCLPHLYQDLLQRYIKQCCSDCKSVLDEPALCLLCGRLCSPSWKPCCRESSCQSH 1972 (2060)
Q Consensus 1893 h~~~~~~~~~~~~~~~~~~~~~~~Li~LP~~y~~l~~~~~~~~C~~c~~~~~~paiCL~CG~~~~~~~~~cc~~gec~~H 1972 (2060)
|+...++.++........++++|.+.++|.-|+.+..+..+. +..+++.|+.||..|..-+.|||.+.+ .+|
T Consensus 626 ~~~r~~e~~k~~r~~~~k~~~~fa~~~~~~~~q~~a~~s~~~-------~g~ed~~~~~~~~~q~~~k~y~C~icg-~n~ 697 (784)
T KOG1139|consen 626 KHSRNQEKMKAPRDPVKKAAKEFAKRRMEAIMQNSAKKSAQT-------EGMEDAEVNKVDPSQQNRKVYECPICG-QNA 697 (784)
T ss_pred HHHHHHHHhhcccchHHHHhHHHHHHHHHHHHHHHHHhhhcc-------cCCChHHHhhhCcccCCccCCcCCcCC-CCC
Confidence 987777765555445556777889999999888876542222 578999999999999887789998866 569
Q ss_pred hhhcCCCeEEEEEecccEEEEEecCCcccCCCCcccccCCCCcCcccCCCcccCHHHHHHHHHHHHcCCcCccccccccc
Q 000140 1973 AVACGAGTGVFLLIRRTTILLQRCARQAPWPSPYLDAFGEEDIEMHRGKPLYLNEERYAALTYMVASHGLDRSSKVLSQT 2052 (2060)
Q Consensus 1973 ~~~Cg~~~GiFl~v~~~~ill~~~~rg~~~~spYLD~~GE~D~~lrrg~pl~L~~~Ry~~L~~~w~~h~i~~~~~~~~~~ 2052 (2060)
..+||+++|+|++|+++.|+.-+-.+..-||.||||..|++|.+.-||+.+|+++.||.+|....=+|++++.++++.+|
T Consensus 698 p~T~~np~G~~~l~~~~~I~~~r~~~~~~~p~p~l~~de~e~~~~~Rl~~e~~rr~~~~~l~~~~es~~l~~~~~~l~gt 777 (784)
T KOG1139|consen 698 PNTVENPFGMLALLSTNFICEERIDASINTPDPLLKFDEYEHVSANRLQSETRRRFFSKRLQATFESQDLVKVNPPLVGT 777 (784)
T ss_pred CcccCCCceEEEEEeecchHHHHHhhccCCCChhhhcchhhhhHHHHHHHHHHHHHHHHHhhhcccccchhhccccccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccce
Q 000140 2053 TIGGF 2057 (2060)
Q Consensus 2053 ~~~~~ 2057 (2060)
+|++.
T Consensus 778 ~~~~c 782 (784)
T KOG1139|consen 778 DLKTC 782 (784)
T ss_pred chhcc
Confidence 99864
No 3
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.81 E-value=1.4e-21 Score=262.37 Aligned_cols=927 Identities=17% Similarity=0.054 Sum_probs=568.5
Q ss_pred HHHHHHhcCCchhhhchhhHHHHhhhCCCChhHHHhccCCCCHHHHHHHHHHHhhccccCCCCCh-h-hhHHHHHHHHHH
Q 000140 18 IVRRLMNIGVPEEFLDYSGIVNFAKNDKSRIPELVSTILPPDEEVAEVIQDAKAKNKKVSVGPNM-K-GRFRESMLWLQW 95 (2060)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~l~~ 95 (2060)
..+++--.++++++-...+++.|+...+..|...+.+..|....+...+..+..+..++.+..++ + ..+.+....+.|
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 34667778888888778899999999999999999999999999998888888887777655445 3 447888888888
Q ss_pred HhcCCCHHHHH---HHHHccCCCccccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecCCccccCCCc
Q 000140 96 LMFEREPEKVL---RKLSKIGQRGVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDV 172 (2060)
Q Consensus 96 ~~~~~~~~~~l---~~l~~~~~~~~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~~gG~CDCGd~ 172 (2060)
.++.+.+.-.. ..+. -.-...|+.+|...+..++|++|.- .+.+|..|++...|-.|.+..+-..+|+|+|+ .
T Consensus 612 ~v~~~~~sv~~p~~~~l~-~l~~~~~s~v~~~~d~~~~~~~~~n--~~~i~e~~lr~~Vl~aqid~~~w~rNG~si~~-q 687 (1738)
T KOG1140|consen 612 SVSQERVSVSNPVSRLLA-FLIELSCSSVVSLKDAYERLEDCSN--FLAISEHSLRVLVLCAQIDVGFWVRNGFSILH-Q 687 (1738)
T ss_pred ccccccceeeccHHHHhh-hhhhcccchhhhcchhhhhHhhhcc--chhhcccchhheeeeeecceeeEeecCcchhh-h
Confidence 77775443211 1111 1115889999999999999999986 99999999999999999998887889999999 8
Q ss_pred ccccccCCCCcCCCCCCCCCCcHHHHhhhHHHHHHHHHHHHHHh--hhhcccCCCCCCCCChHHHHHHHHHHHHHHHHHH
Q 000140 173 TAWKREGFCSRHKGAEQIQPLPEKYANSAAPVLDALFIYWENKL--SLAESVGQENPRASDHVAERRKLANELTFAVVEM 250 (2060)
Q Consensus 173 ~awk~~~fC~~H~~~~~~~~lp~~l~~~~~~~~~~ll~~~~~~l--~~~e~~~~~~~~~~~~~~~~~k~a~~l~~~i~~~ 250 (2060)
.+|...++|..|....++-++-..++.. +..+.++.+|-... .|.. ...+....|...+..++++++...|+.+
T Consensus 688 ~~~y~~~~~r~~~y~~DI~~~Q~~la~~--d~~~~l~~~l~r~~L~~w~~--g~~~~~~~d~~~~i~~~~ee~l~lii~l 763 (1738)
T KOG1140|consen 688 AAYYKNNPCRNESYDRDILMLQTGLAME--DPNRFLFTILSRFELLDWFT--GEVDYQSNDTEDTISFMIEEFLALIILL 763 (1738)
T ss_pred hHhhcCccccccchhHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHhc--CCCccccccHHHHHHHHHHHHHHHHHHH
Confidence 9999999999998775544333333322 33334433332211 2221 1123344566677778888888777777
Q ss_pred HHHHHhchHHHHHHHHHHhhccchhHHHHHhhccCCCHHHHHHHHHHHHHhhCChhhHHHHHHHHHhhhHHHHHHHHHhc
Q 000140 251 LLEFCKNSESLLSFVSKRVISVIGLLDILVRAEMFSSDVVVRKLHELLLKLLGEPIFKYEFAKVFLSYYPVFVKDAIREH 330 (2060)
Q Consensus 251 l~e~~~~~~~ll~~l~~~l~~~~~ll~~l~~~~~~l~k~~r~~lh~L~lsLL~d~efK~~fa~~Fv~~Y~~i~~~fl~~d 330 (2060)
+.|+... .+...........+++.+|......+.+.+++..|.+...+..|..++..++..+...|+...--.++..
T Consensus 764 l~Er~~~---~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~~d~~~e~Va~~~~p~~~~~~gvf~lK~~ 840 (1738)
T KOG1140|consen 764 LTERSYF---GSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLSFDEALEEVAVFKKPKGLADNGVFVLKES 840 (1738)
T ss_pred HHheeec---ccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhcccchHHHHHHHhhccCCccccceEEEechh
Confidence 7765543 1111111222233555556655555667788899999989999999999999888888855433333333
Q ss_pred cCcccccCCccceeeeeccccCCcHHHHHHhhcHHHHHHHHHHHHhhhhcC--CCCcceeccccccccchhhhhhhhhHh
Q 000140 331 SDDTIKKYPLLSTFSVQIFTVPTLTPRLVKEMNLLEMLLGCLREIFDSCAG--DDSCLQVAKWANLYETTNRVIGDIRFV 408 (2060)
Q Consensus 331 ~d~~~~~~s~v~~LSVQLFTvPsLA~~LV~e~nLL~iLl~tl~~~~~~~~~--~~~~l~~~~~~~~~~~y~~I~~DLryl 408 (2060)
-++....|-...++|+|.=+++++++...++.+.+...+..+...+..++. .++-+.............+.+.++++.
T Consensus 841 ~~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~~~~~L~~~t~~~~~~~ii~r~~~~~~~~ 920 (1738)
T KOG1140|consen 841 YYDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKKGADILGAAVRLTVFGLIIYRTLEHCLFM 920 (1738)
T ss_pred hhhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344555566889999999999998888776654444444444433331 222222211111122334566778888
Q ss_pred hcchhhhHHHhhhchHHHHHHHHHHHHhcCCC--cccccccCcceeeCCceeehh-hhhhHHHHhHhhhhhccccccccc
Q 000140 409 MSHAAVSKYATHEQLNISKAWMKLLTFVQGMN--PQKRETGIHIREENEYMHLPL-VLDHSIANIQPLLVDGAFSSAVSE 485 (2060)
Q Consensus 409 Lsh~~v~~~l~~~~~~l~~~~l~lL~~~QGMn--~~kRq~~~HVEyE~~~w~~aF-~L~~~la~i~~~~~~~~~~~~~~~ 485 (2060)
+++--..+.+..-.-...+.++..+..++++. +..|++|--.-++.. ...++ ...+.+..++.++..+.++..++.
T Consensus 921 ~s~~~l~~~~~~ihG~~~~~~l~~~~~~~~~~~e~~~~e~gl~~~e~lv-~~~~~~~~~~~~~v~~~l~~~~~~~~~n~~ 999 (1738)
T KOG1140|consen 921 ESSTLLSKVLHLIHGIALNEELINMKFAFTQKTESIAREKGLSLYESLV-RKPDSLVHGKIIEVIVELFESLIKSRANDP 999 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccchhhHHHhh-hcchhhcCCcceeeeHHHHhhhhhhhcCCc
Confidence 88765555543334578899999999999999 999999977755544 43333 344778888888888888887776
Q ss_pred hhc-cccccccccCCCCCccccccccccccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHh
Q 000140 486 ETR-YDFSMYKQDIGDGDSLRHAKVGRLSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMEN 564 (2060)
Q Consensus 486 ~~~-~~~~~~~~~~~~~~~~~~~~v~r~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~cl~~l~~ 564 (2060)
|.. +..-|.+....+++..+.++.+|+..+..++...--+.-+..=|..+.+.+ +..+-+.|.+....+.++......
T Consensus 1000 ea~~~~~~~~~~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e~-d~~~~~~~~~~~~~~~~~d~~~~~ 1078 (1738)
T KOG1140|consen 1000 EVANDEKDKKEKQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDEF-DEQENQTPSSGSKTYEEEDFTCAL 1078 (1738)
T ss_pred cccccccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhccccc-CcccccCccccccchhhhhccchh
Confidence 444 333333334446777777788888888877744432222222222222222 244456666666777777665544
Q ss_pred hhcCCCCcccccccCCCCcccccCchhhHhHh-----hhhhhcccccccccccCCccccccccccCCCccccccCccccc
Q 000140 565 WLGVDDRSVSVNDILSPNASRISGSNFVALKK-----TLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKI 639 (2060)
Q Consensus 565 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 639 (2060)
.++........ ...++. .+-++...+- .+..+.......+.|++... ++ .-.-
T Consensus 1079 ~~~~s~~~~~~-~~~~~~----~~~~~~~~~i~~e~e~~~~~~~~~~v~~~f~~~s~-----------~~------sd~l 1136 (1738)
T KOG1140|consen 1079 CQDNSCTDFQV-KPASHL----VKPIFRECIICDENEDVPNWDGRYSVSSAFAQKSD-----------DV------SDAL 1136 (1738)
T ss_pred hhccchhcccc-ccchhh----hcccccccccCChhccCCCccccchhhhHhhhhcc-----------cc------cccc
Confidence 43321110000 000000 0000000000 00000000000011111000 00 0011
Q ss_pred cccCCcccccccccCcCCcccccccc-----------------ccccccc------ccccCccCceeeeccCCceeeehh
Q 000140 640 TISGERDTASWRSAGFNDSEMEGECA-----------------TELDNLH------VLSLCYWPDITYDVSSQDVSVHIP 696 (2060)
Q Consensus 640 ~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~l~------~~~~~~~~~v~fdVs~~~VSfH~P 696 (2060)
+-|+...|| +....+||.- .+.-.|. .+...-|.-..++|+-..+.-|.+
T Consensus 1137 ~~p~~~~~~-------~~~s~c~h~mh~~c~~~~~~a~r~~~n~~~~~l~~~~se~~l~lCp~c~slsn~~lp~~~~~~~ 1209 (1738)
T KOG1140|consen 1137 TEPGSLSCG-------TVLSSCGHHMHYGCFKRYVQAKRFRENARTAPLCQHYSENGLFLCPLCKSLSNVSLPMFLPPEL 1209 (1738)
T ss_pred cCCCCCccc-------ceeeccCCcchHHHHHHHHHHHHHHHHhhhcCcccccccCCcccCCchHhhhhccCCcCCchhh
Confidence 111222221 0011122210 0000000 011111222346778788899999
Q ss_pred HHHHHHHHHHHHHhhhccccccccccccCCCCCccccchhhhhcccCCCCCcccchhhccccHHHHHHHHhHhcCceeec
Q 000140 697 LHRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFSAFVMEHPLRIRVFCAQVHAGMWRRN 776 (2060)
Q Consensus 697 Lhr~Ls~Ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~pLR~~Vl~aQI~aGmWvRN 776 (2060)
+++.++...+..+..+++.....+...-+.+.....++..|.+.....+.|-++..+-..+...+.+++.+++++||--
T Consensus 1210 ~~n~~t~~~~~n~~~~i~~rs~~~~s~~~vs~~~s~~~~~~~ss~i~e~kp~~~~~l~~~~~~~ie~~~k~v~s~~~k~- 1288 (1738)
T KOG1140|consen 1210 LLNPLTLENQRNLNSWIEKRSRASFSLQDVSSILSDPWAAFTSSRIPELKPILIMDLPDSVVEQIELFQKIVGSAMFKP- 1288 (1738)
T ss_pred hcChhhhhchHHHHHHHHHhchhhcchhhhhhhhcccchhhccccccccccchHhhhhhHHHHHHHHHHHHHhhheeec-
Confidence 9998888777766555441000000000000011122222322112222332211223456677999999999999987
Q ss_pred cHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccccCCCCCCCchh-HHHHHHHHHHHHh
Q 000140 777 GDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLNLERPSEYEP-ILVQEMLTLIIQI 855 (2060)
Q Consensus 777 G~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~~~~~~~~~y~~-~mvEe~L~lLI~l 855 (2060)
|. .. ...+-+..-+.+.|++|++.++.+.......++.+++...++.++......+.. ..+.. ...+++
T Consensus 1289 ~~------~i--~~~~le~~~~~~~~~~~~~~~~s~a~~~~~~~l~~~~~~~~l~l~~~~~~~~~~~~~l~~--~~~~~~ 1358 (1738)
T KOG1140|consen 1289 SS------LL--STNTLELTLFSREFLIVCWQSLSDAEQSTKLLLSASKKPSFLKLNEDMTFCLVTISRLRA--LHWEQI 1358 (1738)
T ss_pred cc------ce--eecccccCcccchhhhhhhhccchHHHHHHHHHhccCCcccccCchhhHHHHHHHHHHHH--HHHHHH
Confidence 21 12 234667888999999999999999999999999999988887776433322322 22222 456777
Q ss_pred hcccccCCCChHHHHHHHHHHHHhcCCCChHHHHhhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEeehhhhccccc
Q 000140 856 LQERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDI 935 (2060)
Q Consensus 856 ltER~~~g~s~~e~lr~EIIh~Lc~~p~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dp 935 (2060)
+.++...++-.....+.++|-.+..++.+++++...+|.+..+...++.++..|- +.|.+.-.+.+.++.-.|.|.+-
T Consensus 1359 l~~~~~~~llk~~s~~~~~i~~~~tpd~~~~~ll~~l~~~~~~~~~l~~~~~~~~--~~~~~~~~~~i~~~~i~s~elit 1436 (1738)
T KOG1140|consen 1359 LYELVYTFLLKSFSPTIPRISVLITPDQPENELLVILPHDFPKSLELELTLDFVN--KNPKKIFELKILMASIISIELIT 1436 (1738)
T ss_pred HHHHHHHHHHHHHhhcCCcchhccCCCCCcchhhhccchhhhhhccHHHHHHHhh--hhHHHHHhHHHHHHHhhhhhhhe
Confidence 8887776776677777888888888899999999999999999999999999988 66777788999999999999998
Q ss_pred cccccCchhHHHHHHHHHHhhcccccc--CCCCCCcccCCCccccccccCcHHHHHHHHHHHHHHhc
Q 000140 936 YHPRWSSRDLQVAEERYLRFCSVSALT--AQLPRWTKIYYPLESIAGIATCKVVLQVIRAVLFYAVF 1000 (2060)
Q Consensus 936 y~~~y~~~~~q~aeer~~r~~~~~a~~--~~~P~~~~~~~p~~~i~~il~s~~~~~il~~vL~~al~ 1000 (2060)
++..+.. |.+.|+++..+..-..+.. ...+.++....+-.++.++--+....+.+...|.++..
T Consensus 1437 s~s~l~~-d~~~~~~q~s~~e~~~~~t~l~~~~s~~~i~~~~~~~~~~~L~~~~~~~i~sfL~~~al 1502 (1738)
T KOG1140|consen 1437 SHSYLEN-DLEMAEEQKSIDEFKSLLTYLLQLESSRTIPKLADIRLRLSLCLSCEAGILSFLRRAAL 1502 (1738)
T ss_pred eccccCC-ccchhhhhhhHHhHhHHHHHHHhccchhhCccccchhhhhHHHHHHHHHHHHHHHHHHH
Confidence 8888877 8777777544322222222 23344444433334555566677777788777777653
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=1.4e-19 Score=171.14 Aligned_cols=70 Identities=44% Similarity=1.070 Sum_probs=66.3
Q ss_pred ccccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEec-CCccccCCCcccccccCCCCcCC
Q 000140 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYT-GGGCCDCGDVTAWKREGFCSRHK 185 (2060)
Q Consensus 116 ~~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~-~gG~CDCGd~~awk~~~fC~~H~ 185 (2060)
.+||++|++++++|+|+||+.++++++|.+||+++.|+||+|.+++. +||.|||||++|||+++||++|.
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=99.72 E-value=2e-18 Score=163.95 Aligned_cols=70 Identities=49% Similarity=1.112 Sum_probs=54.0
Q ss_pred ccccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecC-CccccCCCcccccccCCCCcCC
Q 000140 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTG-GGCCDCGDVTAWKREGFCSRHK 185 (2060)
Q Consensus 116 ~~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~~-gG~CDCGd~~awk~~~fC~~H~ 185 (2060)
+.|+++|++++++|+|+||+.+++.+||.+||.++.|+||+|.+..+. +|+|||||+++||+++||++|+
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=98.95 E-value=9e-09 Score=129.50 Aligned_cols=185 Identities=22% Similarity=0.324 Sum_probs=139.9
Q ss_pred hccccHHHHHHHHhHhcCceeeccHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccccC
Q 000140 754 VMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLN 833 (2060)
Q Consensus 754 l~e~pLR~~Vl~aQI~aGmWvRNG~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~~~ 833 (2060)
+.-++++..|--.-++..||+|+|.-...-...|-+..+-...---+--.+=.++..+++..|+...+-+|.+.+.-..+
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 45567899999999999999999998877777775444432222223334456888999999999999999876532211
Q ss_pred C--------C-----C-------------------C--------------------------------------------
Q 000140 834 L--------E-----R-------------------P-------------------------------------------- 837 (2060)
Q Consensus 834 ~--------~-----~-------------------~-------------------------------------------- 837 (2060)
. . . +
T Consensus 287 i~r~v~~~p~~s~L~~~~~~~~~~~k~~~~~Hsr~p~~~~l~~f~~p~lEaa~~d~l~~v~~~~e~~~R~~~~s~vlr~~ 366 (784)
T KOG1139|consen 287 IGRFVEKSPESSILFQETEVTIDFTKQSPIDHSRDPRIPILGEFIRPHLEAAGVDALIDVEMEREFDPRLFDDSEVLRTI 366 (784)
T ss_pred ccceeEeccccccchhhhhhhccccccCchhcccCcchhHHHHhhccccccccCchHHHHhhhccccccccchhhhhHHh
Confidence 0 0 0 0
Q ss_pred --CCch--hHHHHHHHHHHHHhhcccccCCCChHHHHHHHHHHHHhcCCCChHHHHhhCCCCC-CCcchHHHHHHHHccc
Q 000140 838 --SEYE--PILVQEMLTLIIQILQERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDL-SKFDQLQEILDAVAMY 912 (2060)
Q Consensus 838 --~~y~--~~mvEe~L~lLI~lltER~~~g~s~~e~lr~EIIh~Lc~~p~t~S~L~~~lpe~~-~~~~~fe~iL~eVA~f 912 (2060)
..|+ +.|..-++-++..+|.++.+.|...++..+-|+.|.-+++...||-+..++.+.. ...+.|+.|+.+..+|
T Consensus 367 ~~~~~e~~~~~~~~~f~l~~~~v~~s~~~~ai~~~~~~~em~n~~a~~~~~~s~~~aS~~~~~~~~~~~f~~i~~~~~~~ 446 (784)
T KOG1139|consen 367 VIREPEWIDPMFWGMFKLVAELVVVSVNSGAIPEEHYRSEMVNCMAMGNVPYSRLRASISEKGSMIDKHFETILNEIGDF 446 (784)
T ss_pred hhccccccchhhcchHHHHHHHhhhhcccccchHHHHHHHHHhHHHhcCCCcccccccccCCCccccccccccccccccc
Confidence 0001 2566778888989999999899899999999999999999999999998877664 4577899999999999
Q ss_pred cCCCC----CCcceEEeehhhhc-ccccccc
Q 000140 913 SHPSG----FNQGMYSLRWSYWK-ELDIYHP 938 (2060)
Q Consensus 913 ~~P~g----~~~G~Y~LK~e~~~-e~dpy~~ 938 (2060)
-.|-- .-+|.|.||.-.|+ +.-|-++
T Consensus 447 ~~P~~~~~p~~~~s~~l~~~~~~~~~c~~~~ 477 (784)
T KOG1139|consen 447 IEPIETTTPLMQGSYQLKTSIWDSEVCPVFF 477 (784)
T ss_pred ccchhhcCccccchhhccccCCccccccchh
Confidence 99943 24799999999997 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=97.00 E-value=0.00045 Score=83.47 Aligned_cols=80 Identities=26% Similarity=0.419 Sum_probs=60.8
Q ss_pred HHHHHHHHHHhcCCCChHHHHhhCCCCCCC---cchHHHHHHHHccccCCCCCCcceEEeehhhhccccccccccCchhH
Q 000140 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSK---FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (2060)
Q Consensus 869 ~lr~EIIh~Lc~~p~t~S~L~~~lpe~~~~---~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dpy~~~y~~~~~ 945 (2060)
.+|.-|||+||.+|....||...|..+... -..++.||.+||... .++.|.||+.+|+|+|.=++.|+-.|+
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 599999999999999999999988765543 246999999999974 378999999999999977888898888
Q ss_pred HHHHHHHH
Q 000140 946 QVAEERYL 953 (2060)
Q Consensus 946 q~aeer~~ 953 (2060)
|..+-+..
T Consensus 273 q~l~r~l~ 280 (284)
T PF10390_consen 273 QLLKRRLS 280 (284)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHH
Confidence 88866544
No 8
>KOG1777 consensus Putative Zn-finger protein [General function prediction only]
Probab=94.88 E-value=0.014 Score=71.09 Aligned_cols=62 Identities=34% Similarity=0.561 Sum_probs=50.5
Q ss_pred cCCCccccc-----cccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecCCccccCCCccc
Q 000140 112 IGQRGVCGA-----VWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDVTA 174 (2060)
Q Consensus 112 ~~~~~~Cg~-----v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~~gG~CDCGd~~a 174 (2060)
.-+.++|-. .+-+=.-+|||-||...+.-+||..|.++ -|+||++-..+...-.||||-..+
T Consensus 540 Aik~GqCLfkvSs~~syPMHnFYRC~TCNttdRNAIC~nCI~~-CH~GH~Vefir~Drffcdcgagtl 606 (625)
T KOG1777|consen 540 AIKKGQCLFKVSSYTSYPMHNFYRCITCNTTDRNAICVNCIKR-CHEGHDVEFIRHDRFFCDCGAGTL 606 (625)
T ss_pred HhhcCceEEEecCCCcccccceeEeeecCCccccHHHHHHHHH-hcCCCceEEEeeceEEEecCCcee
Confidence 445577743 33444568999999999999999999988 599999999998889999997544
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=91.44 E-value=0.06 Score=46.67 Aligned_cols=20 Identities=25% Similarity=0.790 Sum_probs=16.5
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000140 1427 HLSSCGHAVHQGCLDRYVSS 1446 (2060)
Q Consensus 1427 h~SsCGH~MH~~C~~~Y~~S 1446 (2060)
..-.|||..|.+|++.|++.
T Consensus 17 ~~l~C~H~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 17 VKLPCGHVFHRSCIKEWLKR 36 (44)
T ss_dssp EEETTSEEEEHHHHHHHHHH
T ss_pred EEccCCCeeCHHHHHHHHHh
Confidence 35559999999999999843
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=91.30 E-value=0.16 Score=43.10 Aligned_cols=19 Identities=37% Similarity=1.001 Sum_probs=16.3
Q ss_pred ccccChHhhHHHHHHHHHH
Q 000140 1428 LSSCGHAVHQGCLDRYVSS 1446 (2060)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~S 1446 (2060)
+..|||..|..|+++|++.
T Consensus 15 ~~~C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 15 LLPCGHVFCRSCIDKWLKS 33 (45)
T ss_pred ecCCCChhcHHHHHHHHHh
Confidence 5669999999999998664
No 11
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=89.08 E-value=0.12 Score=68.82 Aligned_cols=63 Identities=27% Similarity=0.695 Sum_probs=50.4
Q ss_pred ccccccccCCc----eeEEeccCCCCCCccccccccCCCCCCCceeEEEe-cCCccccCCCcccccc-cCCCCcC
Q 000140 116 GVCGAVWGNND----IAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVTAWKR-EGFCSRH 184 (2060)
Q Consensus 116 ~~Cg~v~~~~e----~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~-~~gG~CDCGd~~awk~-~~fC~~H 184 (2060)
..|.-.|+..+ -+|.|+||+.-.+-+-|.+|-.- .|+||+.++-+ +.-.+||| |-+ +..|+.-
T Consensus 1241 DtCSFTWTGadHINQDIfECkTCGL~~SLCCCsECAlt-CHk~HDCkLKRTSPTAYCDC-----WEKssCkCKaL 1309 (3015)
T KOG0943|consen 1241 DTCSFTWTGADHINQDIFECKTCGLLESLCCCSECALT-CHKGHDCKLKRTSPTAYCDC-----WEKSSCKCKAL 1309 (3015)
T ss_pred CccceeecchhhccchhhhhcccccchhhhhhHHHHHH-hccCCccceeccCCcceeeh-----hhcccccchhh
Confidence 57888998543 57999999999888889999765 69999999987 56899999 655 3446544
No 12
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=88.33 E-value=1.8 Score=59.31 Aligned_cols=70 Identities=19% Similarity=0.225 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-H--HhhccccccCCCCCCCccCCCCcccccccccCCccccccCCCC---CCCeE
Q 000140 1146 SEKRKAKARERQAAILEKMKAEQFK-F--LSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS---RTPVS 1219 (2060)
Q Consensus 1146 ~ekkK~~AkeRQakIMaqf~~qQ~~-F--l~~n~~~~d~~~~~~~~~~~s~~~~~~~e~~~~~CilCqe~~~---~~pfg 1219 (2060)
+.+||++|.++|+|.+.+|.-++.+ - +.+..... +. ++.++|. --.|.+|+|.-+ ++++|
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 RQEKKRLAMAMREKQLKKLGMRVNEKGQVVVSSSILQ-----------NM--EDLEEED-GLTCCICREGYKFRPDEVLG 487 (802)
T ss_pred HHHHHHHHHHHHHHHHHHccCccccccceecCchhhc-----------Cc--ccccccC-CCeEEEcCCccccCCcccee
Confidence 5677889999999999998433200 0 00000000 00 0111122 367999999743 46899
Q ss_pred EEeeeecccc
Q 000140 1220 YLILLQKSRL 1229 (2060)
Q Consensus 1220 ~la~iq~S~l 1229 (2060)
+-+|.-+-.+
T Consensus 488 iY~f~kr~~l 497 (802)
T PF13764_consen 488 IYAFSKRVNL 497 (802)
T ss_pred eEEEeecccc
Confidence 9887755544
No 13
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=88.23 E-value=0.15 Score=59.86 Aligned_cols=48 Identities=35% Similarity=0.749 Sum_probs=34.3
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhccc---ccCCCcccCCCCcccccccccc
Q 000140 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRI---IFEGGHIVDPDQGEFLCPVCRQ 1477 (2060)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~---~~~r~h~~d~e~gEFLCPLCKs 1477 (2060)
...|-|.||+.|+.+|+...+...++.. .-++.|. .+.-|=+||+||-
T Consensus 133 ~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh~--~~~~eavcpVcre 183 (368)
T KOG4445|consen 133 VTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQHM--KEQVEAVCPVCRE 183 (368)
T ss_pred eehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--hhhHhhhhhHhhh
Confidence 7889999999999999999876554221 1223332 3456778999984
No 14
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=84.81 E-value=0.92 Score=57.63 Aligned_cols=77 Identities=26% Similarity=0.375 Sum_probs=63.4
Q ss_pred HHHHHHHHHHhcCCCChHHHHhhCCCCCCCc---chHHHHHHHHccccCCCCCCcceEEeehhhhccccccccccCchhH
Q 000140 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSKF---DQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (2060)
Q Consensus 869 ~lr~EIIh~Lc~~p~t~S~L~~~lpe~~~~~---~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dpy~~~y~~~~~ 945 (2060)
-+|..|||+|+.++..--||.++|-.+...+ ..+..||.+.. .+.+|+|.|++.+|.|+|-=++.|+-.|.
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 4999999999999999999999987776543 35778888821 24789999999999999988888988887
Q ss_pred HHHHHH
Q 000140 946 QVAEER 951 (2060)
Q Consensus 946 q~aeer 951 (2060)
|..+-+
T Consensus 285 ~~lkr~ 290 (604)
T KOG4796|consen 285 QHLKRV 290 (604)
T ss_pred HHHHHH
Confidence 776544
No 15
>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=84.46 E-value=0.75 Score=41.14 Aligned_cols=39 Identities=28% Similarity=0.878 Sum_probs=29.5
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCC----CCC-CceeEE
Q 000140 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG----NHK-EHDYSI 159 (2060)
Q Consensus 117 ~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~----~H~-~H~~~~ 159 (2060)
.|++.... ..-|+|..|. ..-+|.+||..+ .|+ +|.|.+
T Consensus 5 ~C~~~~~~-g~r~~C~~C~---d~dLC~~Cf~~g~~~~~H~~~H~~~~ 48 (49)
T cd02335 5 YCSKDITG-TIRIKCAECP---DFDLCLECFSAGAEIGKHRNDHNYRV 48 (49)
T ss_pred CcCCCCCC-CcEEECCCCC---CcchhHHhhhCcCCCCCCCCCCCeEe
Confidence 57777664 4899999995 366999999998 453 677765
No 16
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=83.86 E-value=0.83 Score=39.74 Aligned_cols=37 Identities=27% Similarity=0.654 Sum_probs=29.5
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000140 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2060)
Q Consensus 117 ~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 158 (2060)
.|+..+ .| .-|+|.+|. ..-+|.+||.++.|.+|.+.
T Consensus 5 ~C~~~i-~G-~ry~C~~C~---d~dLC~~C~~~~~H~~H~f~ 41 (43)
T cd02340 5 GCQGPI-VG-VRYKCLVCP---DYDLCESCEAKGVHPEHAML 41 (43)
T ss_pred CCCCcC-cC-CeEECCCCC---CccchHHhhCcCCCCCCCEE
Confidence 477633 33 789999997 46799999999999888874
No 17
>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=83.37 E-value=0.69 Score=39.31 Aligned_cols=20 Identities=30% Similarity=0.843 Sum_probs=18.4
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000140 1427 HLSSCGHAVHQGCLDRYVSS 1446 (2060)
Q Consensus 1427 h~SsCGH~MH~~C~~~Y~~S 1446 (2060)
.+..|||..+..|+.+|+++
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 37899999999999999988
No 18
>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=82.80 E-value=0.89 Score=40.05 Aligned_cols=37 Identities=27% Similarity=0.812 Sum_probs=29.3
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCC--CCC-CceeE
Q 000140 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG--NHK-EHDYS 158 (2060)
Q Consensus 117 ~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~--~H~-~H~~~ 158 (2060)
.|++.+. | .-|+|.+|. ..-+|.+||..+ .|. +|.+.
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 577999999998 776 77764
No 19
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=82.38 E-value=0.82 Score=45.35 Aligned_cols=25 Identities=24% Similarity=0.550 Sum_probs=20.0
Q ss_pred cCCCccccccChHhhHHHHHHHHHH
Q 000140 1422 DCDGIHLSSCGHAVHQGCLDRYVSS 1446 (2060)
Q Consensus 1422 ~~~gvh~SsCGH~MH~~C~~~Y~~S 1446 (2060)
+..++=...|||.-|..|..+.+++
T Consensus 43 d~Cplv~g~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 43 DDCPLVWGKCSHNFHMHCILKWLST 67 (85)
T ss_pred CCCceeeccCccHHHHHHHHHHHcc
Confidence 3344447789999999999999876
No 20
>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=81.15 E-value=1.3 Score=36.13 Aligned_cols=18 Identities=22% Similarity=0.892 Sum_probs=16.3
Q ss_pred ccccChHhhHHHHHHHHH
Q 000140 1428 LSSCGHAVHQGCLDRYVS 1445 (2060)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~ 1445 (2060)
...|||..|..|+++|++
T Consensus 13 ~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 13 VLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred EecCCChHHHHHHHHHHH
Confidence 567999999999999977
No 21
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=80.99 E-value=1.4 Score=38.43 Aligned_cols=31 Identities=35% Similarity=0.864 Sum_probs=25.1
Q ss_pred CccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccc
Q 000140 1425 GIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2060)
Q Consensus 1425 gvh~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKs 1477 (2060)
...+.+|||.+..+|.++-. .+...||+||+
T Consensus 14 ~~~l~~CgH~~C~~C~~~~~----------------------~~~~~CP~C~k 44 (44)
T PF14634_consen 14 RPRLTSCGHIFCEKCLKKLK----------------------GKSVKCPICRK 44 (44)
T ss_pred CeEEcccCCHHHHHHHHhhc----------------------CCCCCCcCCCC
Confidence 35599999999999998865 24567999985
No 22
>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=80.09 E-value=1.3 Score=39.59 Aligned_cols=38 Identities=26% Similarity=0.792 Sum_probs=28.9
Q ss_pred ccc-ccccCCceeEEeccCCCCCCccccccccCCC----CCC-CceeEE
Q 000140 117 VCG-AVWGNNDIAYRCRTCEHDPTCAICVPCFQNG----NHK-EHDYSI 159 (2060)
Q Consensus 117 ~Cg-~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~----~H~-~H~~~~ 159 (2060)
.|+ ..+. ..-|+|..|. ..-+|.+||..+ .|+ .|.+.+
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 577999999988 676 777754
No 23
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=78.79 E-value=1.3 Score=51.34 Aligned_cols=62 Identities=23% Similarity=0.212 Sum_probs=46.5
Q ss_pred HHHHHHHHHH--hcCCCChHHHHhhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEeehhhhc
Q 000140 869 SLKRELVHRL--AIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWK 931 (2060)
Q Consensus 869 ~lr~EIIh~L--c~~p~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~ 931 (2060)
.=|+||+-.| ||.-..|=-|...+-..-+...-+.+||++||+|-+ .|..+|+|+|||||-+
T Consensus 182 ~dk~evld~lFk~FEk~~ywtlK~Lv~~t~QP~~fLKEiL~~icv~Nk-Kg~~k~tyeLKPEYK~ 245 (254)
T KOG2905|consen 182 RDKNEVLDMLFKAFEKYQYWTLKDLVEITKQPEAFLKEILKDICVLNK-KGPYKNTYELKPEYKK 245 (254)
T ss_pred ccHHHHHHHHHHHhhcCccccHHHHHHHhcCHHHHHHHHHHHHHHHhc-cCcccCceecCHHHhh
Confidence 4577888887 788777766655444444445568999999999975 3667899999999864
No 24
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=77.54 E-value=1.9 Score=38.00 Aligned_cols=39 Identities=26% Similarity=0.695 Sum_probs=29.6
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC-CCceeEE
Q 000140 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYSI 159 (2060)
Q Consensus 117 ~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H-~~H~~~~ 159 (2060)
.|+..--.| .-|+|.+|. ..-+|..||....| .+|.|..
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 355433334 789999998 45699999999999 5898753
No 25
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=77.51 E-value=2.7 Score=50.46 Aligned_cols=61 Identities=25% Similarity=0.638 Sum_probs=47.5
Q ss_pred cCCCcccccc--ccCCceeEEeccCCCCC-CccccccccCCCCCCCceeEEEe-cCCccccCCCcc
Q 000140 112 IGQRGVCGAV--WGNNDIAYRCRTCEHDP-TCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVT 173 (2060)
Q Consensus 112 ~~~~~~Cg~v--~~~~e~~y~C~~C~~d~-t~~lC~~CF~~~~H~~H~~~~~~-~~gG~CDCGd~~ 173 (2060)
...+..|++. ..+-.+.|.|.||..+| ...+|.-|=.. -|.||.-..-. .+..-||||+.-
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 3556778655 33446889999999998 78899999775 69999987755 567889999853
No 26
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=74.57 E-value=1.4 Score=53.48 Aligned_cols=16 Identities=38% Similarity=1.059 Sum_probs=14.7
Q ss_pred ccChHhhHHHHHHHHH
Q 000140 1430 SCGHAVHQGCLDRYVS 1445 (2060)
Q Consensus 1430 sCGH~MH~~C~~~Y~~ 1445 (2060)
.|||..|++|+++.++
T Consensus 317 pCGHilHl~CLknW~E 332 (491)
T COG5243 317 PCGHILHLHCLKNWLE 332 (491)
T ss_pred cccceeeHHHHHHHHH
Confidence 6999999999999875
No 27
>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=74.49 E-value=1.7 Score=37.27 Aligned_cols=28 Identities=29% Similarity=0.789 Sum_probs=24.9
Q ss_pred ceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000140 126 DIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2060)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 158 (2060)
...|.|.+|.. .+|.+|+..+ |++|++.
T Consensus 13 ~~~~~C~~C~~----~~C~~C~~~~-H~~H~~~ 40 (42)
T PF00643_consen 13 PLSLFCEDCNE----PLCSECTVSG-HKGHKIV 40 (42)
T ss_dssp BEEEEETTTTE----EEEHHHHHTS-TTTSEEE
T ss_pred ceEEEecCCCC----ccCccCCCCC-CCCCEEe
Confidence 48999999985 7999999998 9999975
No 28
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=74.15 E-value=0.95 Score=43.61 Aligned_cols=38 Identities=39% Similarity=0.755 Sum_probs=21.0
Q ss_pred cccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccc
Q 000140 1429 SSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2060)
Q Consensus 1429 SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKs 1477 (2060)
..||+..|..|+.+||.++... |. .+++-.|+ ||.|+.
T Consensus 26 ~~C~~~fH~~CL~~wf~~~~~~---~~------~~~~~~G~--CP~C~~ 63 (70)
T PF11793_consen 26 PSCGKKFHLLCLSEWFLSLEKS---RQ------SFIPIFGE--CPYCSS 63 (70)
T ss_dssp TT----B-SGGGHHHHHHHHSS---S-------TTT--EEE---TTT-S
T ss_pred cccCCHHHHHHHHHHHHHcccC---Ce------eecccccC--CcCCCC
Confidence 5899999999999999887642 11 23455666 999986
No 29
>PHA02926 zinc finger-like protein; Provisional
Probab=73.54 E-value=2.6 Score=48.66 Aligned_cols=46 Identities=24% Similarity=0.532 Sum_probs=35.2
Q ss_pred CCCccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccccccceecC
Q 000140 1423 CDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPA 1485 (2060)
Q Consensus 1423 ~~gvh~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKsLsNs~LPi 1485 (2060)
.+|+ ++.|||.-.+.|..+..++-+ + ..++-.||+||.-...|.|-
T Consensus 190 rFGI-L~~CnHsFCl~CIr~Wr~~r~---------~-------~~~~rsCPiCR~~f~~I~pS 235 (242)
T PHA02926 190 YFGL-LDSCNHIFCITCINIWHRTRR---------E-------TGASDNCPICRTRFRNITMS 235 (242)
T ss_pred cccc-cCCCCchHHHHHHHHHHHhcc---------c-------cCcCCcCCCCcceeeeeccc
Confidence 4676 999999999999999865311 0 12566899999998887764
No 30
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=72.61 E-value=1.7 Score=45.41 Aligned_cols=27 Identities=30% Similarity=0.790 Sum_probs=22.6
Q ss_pred hhcccCCCCCC----CCCceEeeccCccccC
Q 000140 1932 IKQCCSDCKSV----LDEPALCLLCGRLCSP 1958 (2060)
Q Consensus 1932 ~~~~C~~c~~~----~~~paiCL~CG~~~~~ 1958 (2060)
.+|.||+||+. .++|++|-.||+..-.
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCc
Confidence 46889999986 6899999999996443
No 31
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=69.13 E-value=3.7 Score=46.91 Aligned_cols=53 Identities=21% Similarity=0.517 Sum_probs=35.1
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccccc--cceecCC
Q 000140 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLA--NSVLPAL 1486 (2060)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKsLs--Ns~LPil 1486 (2060)
+..|||.-...|..+|+..-.. .++ +....+-.++...||+||+-- +.++|+.
T Consensus 33 vT~CGH~FC~~CI~~wl~~s~~--s~~----~~~~~~~~k~~~~CPvCR~~Is~~~LvPiy 87 (193)
T PLN03208 33 VTLCGHLFCWPCIHKWTYASNN--SRQ----RVDQYDHKREPPKCPVCKSDVSEATLVPIY 87 (193)
T ss_pred EcCCCchhHHHHHHHHHHhccc--ccc----ccccccccCCCCcCCCCCCcCChhcEEEee
Confidence 6789999999999998654211 111 111112246788999999865 4578887
No 32
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=68.01 E-value=3.5 Score=36.33 Aligned_cols=30 Identities=27% Similarity=0.907 Sum_probs=24.7
Q ss_pred ceeEEeccCCCCCCccccccccCCCCC-CCceeE
Q 000140 126 DIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYS 158 (2060)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~~H-~~H~~~ 158 (2060)
..-|+|.+|. ..-||.+||..+.| .+|.|.
T Consensus 13 G~RykC~~C~---dyDLC~~C~~~~~H~~~H~f~ 43 (45)
T cd02339 13 GIRWKCAECP---NYDLCTTCYHGDKHDLEHRFY 43 (45)
T ss_pred cCeEECCCCC---CccchHHHhCCCCCCCCCCEE
Confidence 5679999996 36699999999998 588874
No 33
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=63.94 E-value=3.4 Score=43.90 Aligned_cols=27 Identities=26% Similarity=0.431 Sum_probs=22.6
Q ss_pred hhcccCCCCCC----CCCceEeeccCccccC
Q 000140 1932 IKQCCSDCKSV----LDEPALCLLCGRLCSP 1958 (2060)
Q Consensus 1932 ~~~~C~~c~~~----~~~paiCL~CG~~~~~ 1958 (2060)
.+|.||+|++. .++|++|-.||+..-.
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccCc
Confidence 46889999986 6899999999997433
No 34
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=61.64 E-value=4.1 Score=49.16 Aligned_cols=35 Identities=26% Similarity=0.866 Sum_probs=27.2
Q ss_pred ccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccccccce
Q 000140 1426 IHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSV 1482 (2060)
Q Consensus 1426 vh~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKsLsNs~ 1482 (2060)
++.-.|||.||+.||+.|.. .+ |-||+|..++|+.
T Consensus 175 ~~~~~CgH~~h~~cf~e~~~---------------------~~-y~CP~C~~~~d~~ 209 (276)
T KOG1940|consen 175 AGVLKCGHYMHSRCFEEMIC---------------------EG-YTCPICSKPGDMS 209 (276)
T ss_pred CCccCcccchHHHHHHHHhc---------------------cC-CCCCcccchHHHH
Confidence 44778999999999998721 25 8999999866554
No 35
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=58.32 E-value=2.4 Score=41.17 Aligned_cols=18 Identities=28% Similarity=0.846 Sum_probs=15.4
Q ss_pred cccccChHhhHHHHHHHH
Q 000140 1427 HLSSCGHAVHQGCLDRYV 1444 (2060)
Q Consensus 1427 h~SsCGH~MH~~C~~~Y~ 1444 (2060)
-...|||+-|..|..+.+
T Consensus 46 ~~~~C~H~FH~~Ci~~Wl 63 (73)
T PF12678_consen 46 VWGPCGHIFHFHCISQWL 63 (73)
T ss_dssp EEETTSEEEEHHHHHHHH
T ss_pred EecccCCCEEHHHHHHHH
Confidence 367799999999998776
No 36
>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=58.17 E-value=5.6 Score=35.52 Aligned_cols=35 Identities=29% Similarity=0.691 Sum_probs=27.0
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCCC-Cce
Q 000140 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK-EHD 156 (2060)
Q Consensus 117 ~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H~-~H~ 156 (2060)
.|++... ..-|+|..|. ..-+|.+||..+.+. +|+
T Consensus 5 gC~~~~~--~~RykCl~C~---d~DlC~~Cf~~g~~~~~H~ 40 (48)
T cd02343 5 GCDEIAP--WHRYRCLQCT---DMDLCKTCFLGGVKPEGHE 40 (48)
T ss_pred CCCCcCC--CceEECCCCC---CchhHHHHHhCCccCCCCC
Confidence 4777543 4799999997 477999999998874 454
No 37
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=55.91 E-value=7.8 Score=34.72 Aligned_cols=32 Identities=25% Similarity=0.736 Sum_probs=24.3
Q ss_pred ceeEEeccCCCCCCccccccccCCC-CC-CCceeE
Q 000140 126 DIAYRCRTCEHDPTCAICVPCFQNG-NH-KEHDYS 158 (2060)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~-~H-~~H~~~ 158 (2060)
..-|+|.+|.- ...-+|.+||.++ .| .+|.+.
T Consensus 13 G~R~~C~~C~~-~d~DlC~~C~~~~~~H~~~H~~~ 46 (48)
T cd02341 13 GTRYHCSECDD-GDFDLCQDCVVKGESHQEDHWLV 46 (48)
T ss_pred cceEECCCCCC-CCCccCHHHHhCcCCCCCCCcee
Confidence 56699999963 3466999999999 67 467654
No 38
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=55.81 E-value=4 Score=35.97 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=21.6
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC
Q 000140 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 152 (2060)
Q Consensus 117 ~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H 152 (2060)
.||.-.+ .+-|+|..+. ...||.+||..|.-
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 4677776654 46699999988753
No 39
>PHA02929 N1R/p28-like protein; Provisional
Probab=53.57 E-value=6.4 Score=46.78 Aligned_cols=35 Identities=37% Similarity=0.745 Sum_probs=26.2
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccccccceec
Q 000140 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLP 1484 (2060)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKsLsNs~LP 1484 (2060)
+..|||..|..|....++. + . .||+||.---.|+|
T Consensus 197 l~~C~H~FC~~CI~~Wl~~-------~-------~--------tCPlCR~~~~~v~~ 231 (238)
T PHA02929 197 LSNCNHVFCIECIDIWKKE-------K-------N--------TCPVCRTPFISVIK 231 (238)
T ss_pred cCCCCCcccHHHHHHHHhc-------C-------C--------CCCCCCCEeeEEee
Confidence 7789999999999986531 0 0 49999986555554
No 40
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=53.55 E-value=4.9 Score=37.93 Aligned_cols=28 Identities=25% Similarity=0.744 Sum_probs=23.3
Q ss_pred HhhcccCCCCCC------CCCceEeeccCccccC
Q 000140 1931 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2060)
Q Consensus 1931 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1958 (2060)
+.+.+||.|++. +...+-|+.||+.++.
T Consensus 17 Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 17 FLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EEEEECCCCCCEEEEeccCceEEEecccccEEEe
Confidence 456799999874 7888999999997665
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=53.36 E-value=10 Score=31.70 Aligned_cols=28 Identities=25% Similarity=0.451 Sum_probs=23.1
Q ss_pred ceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000140 126 DIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2060)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 158 (2060)
...|-|.+|+. .+|..|-..+ |++|.+.
T Consensus 10 ~~~~fC~~~~~----~iC~~C~~~~-H~~H~~~ 37 (39)
T cd00021 10 PLSLFCETDRA----LLCVDCDLSV-HSGHRRV 37 (39)
T ss_pred ceEEEeCccCh----hhhhhcChhh-cCCCCEe
Confidence 45778988864 7999999888 9999874
No 42
>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=53.25 E-value=5.8 Score=33.53 Aligned_cols=20 Identities=25% Similarity=0.933 Sum_probs=17.9
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000140 1427 HLSSCGHAVHQGCLDRYVSS 1446 (2060)
Q Consensus 1427 h~SsCGH~MH~~C~~~Y~~S 1446 (2060)
.+..|||....+|+++|++.
T Consensus 13 ~~~~CGH~fC~~C~~~~~~~ 32 (39)
T PF13923_consen 13 VVTPCGHSFCKECIEKYLEK 32 (39)
T ss_dssp EECTTSEEEEHHHHHHHHHC
T ss_pred EECCCCCchhHHHHHHHHHC
Confidence 47899999999999999765
No 43
>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=50.98 E-value=8.5 Score=33.31 Aligned_cols=32 Identities=25% Similarity=0.824 Sum_probs=24.9
Q ss_pred ccccccccCCceeEEeccCCCCCCccccccccCCCCCC
Q 000140 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (2060)
Q Consensus 116 ~~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H~ 153 (2060)
..|+++ +++-|+|..|. -.-+|..||....|.
T Consensus 4 ~~C~~~---~~~r~~C~~C~---dfDLC~~C~~~~~H~ 35 (41)
T cd02337 4 NECKHH---VETRWHCTVCE---DYDLCITCYNTKNHP 35 (41)
T ss_pred CCCCCc---CCCceECCCCc---chhhHHHHhCCCCCC
Confidence 357663 24999999996 366999999998883
No 44
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=49.38 E-value=7.7 Score=30.26 Aligned_cols=22 Identities=23% Similarity=0.717 Sum_probs=18.9
Q ss_pred cccCCCCCC-CCCceEeeccCcc
Q 000140 1934 QCCSDCKSV-LDEPALCLLCGRL 1955 (2060)
Q Consensus 1934 ~~C~~c~~~-~~~paiCL~CG~~ 1955 (2060)
++||.|+.. |..-..|-.||-.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYD 23 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCC
Confidence 579999987 8899999999963
No 45
>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=48.66 E-value=6.5 Score=48.00 Aligned_cols=31 Identities=29% Similarity=0.463 Sum_probs=16.1
Q ss_pred cchHHHHHHHHccccCCCCCCcceEEeehhhh
Q 000140 899 FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYW 930 (2060)
Q Consensus 899 ~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~ 930 (2060)
+.-+-+||++||+|.+ +|...|+|+|||||-
T Consensus 244 ~~yLKeiL~eIa~~~k-~g~~~~~w~LKpeyk 274 (275)
T PF02270_consen 244 EAYLKEILEEIAVLNK-RGPHKNMWELKPEYK 274 (275)
T ss_dssp HHHHHHHHHHH--EE---TT---EE----SS-
T ss_pred HHHHHHHHHHHHHHhc-cCCcCCcEecchHHc
Confidence 4458899999999986 366789999999984
No 46
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.37 E-value=11 Score=47.84 Aligned_cols=29 Identities=41% Similarity=1.065 Sum_probs=25.2
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccc
Q 000140 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2060)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKs 1477 (2060)
++-|-|++|-.|+++.|+.-+ ..||+||+
T Consensus 603 ~tPC~HifH~~CL~~WMd~yk---------------------l~CPvCR~ 631 (636)
T KOG0828|consen 603 LTPCHHIFHRQCLLQWMDTYK---------------------LICPVCRC 631 (636)
T ss_pred ccchHHHHHHHHHHHHHhhhc---------------------ccCCccCC
Confidence 677999999999999998644 46999997
No 47
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.94 E-value=12 Score=46.24 Aligned_cols=30 Identities=30% Similarity=0.601 Sum_probs=22.5
Q ss_pred CCCCCCcCCCccccccChHhhHHHHHHHHHH
Q 000140 1416 DGFGPIDCDGIHLSSCGHAVHQGCLDRYVSS 1446 (2060)
Q Consensus 1416 ~~F~~~~~~gvh~SsCGH~MH~~C~~~Y~~S 1446 (2060)
++|+.+...|. +++|||+.|..|....|+-
T Consensus 12 d~~p~~~~l~~-i~~cGhifh~~cl~qwfe~ 41 (465)
T KOG0827|consen 12 DGRPNDHELGP-IGTCGHIFHTTCLTQWFEG 41 (465)
T ss_pred cCCcccccccc-ccchhhHHHHHHHHHHHcc
Confidence 34444444565 8999999999999988764
No 48
>smart00336 BBOX B-Box-type zinc finger.
Probab=47.72 E-value=15 Score=31.16 Aligned_cols=29 Identities=21% Similarity=0.636 Sum_probs=23.4
Q ss_pred CceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000140 125 NDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2060)
Q Consensus 125 ~e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 158 (2060)
....|-|.+|+. ++|..|... .|++|.+.
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 444777988874 799999988 99999875
No 49
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=46.93 E-value=9.9 Score=28.78 Aligned_cols=20 Identities=30% Similarity=0.896 Sum_probs=17.5
Q ss_pred ccCCCCCC-CCCceEeeccCc
Q 000140 1935 CCSDCKSV-LDEPALCLLCGR 1954 (2060)
Q Consensus 1935 ~C~~c~~~-~~~paiCL~CG~ 1954 (2060)
.||+||.. +.+...|--||+
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 59999988 778889999997
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=46.55 E-value=13 Score=32.54 Aligned_cols=33 Identities=27% Similarity=0.801 Sum_probs=25.1
Q ss_pred ccccccccCCceeEEeccCCCCCCccccccccCCCCCC
Q 000140 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (2060)
Q Consensus 116 ~~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H~ 153 (2060)
..|++.+. ..-|+|..|. ..-||.+||..+.|.
T Consensus 8 ~~C~~~i~--g~ry~C~~C~---d~dlC~~Cf~~~~~~ 40 (44)
T smart00291 8 DTCGKPIV--GVRYHCLVCP---DYDLCQSCFAKGSAG 40 (44)
T ss_pred CCCCCCCc--CCEEECCCCC---CccchHHHHhCcCcC
Confidence 46888554 4578999994 577999999988664
No 51
>PLN00209 ribosomal protein S27; Provisional
Probab=44.88 E-value=7.7 Score=38.56 Aligned_cols=38 Identities=16% Similarity=0.510 Sum_probs=30.5
Q ss_pred cccCCchhHHHHHHHHhhcccCCCCCC------CCCceEeeccCccccCC
Q 000140 1916 KLMCLPHLYQDLLQRYIKQCCSDCKSV------LDEPALCLLCGRLCSPS 1959 (2060)
Q Consensus 1916 ~Li~LP~~y~~l~~~~~~~~C~~c~~~------~~~paiCL~CG~~~~~~ 1959 (2060)
+||+=|+.| +...+||.|++. ...++.|..||++++.-
T Consensus 25 ~Lv~~PnS~------Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 68 (86)
T PLN00209 25 RLVQSPNSF------FMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQP 68 (86)
T ss_pred eeecCCCCE------EEEEECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 577777665 567899999975 57899999999988773
No 52
>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=43.91 E-value=14 Score=32.93 Aligned_cols=18 Identities=33% Similarity=0.824 Sum_probs=16.6
Q ss_pred ccccChH-hhHHHHHHHHH
Q 000140 1428 LSSCGHA-VHQGCLDRYVS 1445 (2060)
Q Consensus 1428 ~SsCGH~-MH~~C~~~Y~~ 1445 (2060)
+.-|||. +-..|+.++++
T Consensus 17 ~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 17 LLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp EETTCEEEEEHHHHHHHHH
T ss_pred EeCCCChHHHHHHhHHhcc
Confidence 6779999 99999999987
No 53
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=43.60 E-value=8.4 Score=38.20 Aligned_cols=38 Identities=21% Similarity=0.529 Sum_probs=30.6
Q ss_pred cccCCchhHHHHHHHHhhcccCCCCCC------CCCceEeeccCccccCC
Q 000140 1916 KLMCLPHLYQDLLQRYIKQCCSDCKSV------LDEPALCLLCGRLCSPS 1959 (2060)
Q Consensus 1916 ~Li~LP~~y~~l~~~~~~~~C~~c~~~------~~~paiCL~CG~~~~~~ 1959 (2060)
+||+=|+.| +...+|+.|++. ...++.|..||+++|.-
T Consensus 24 ~Lv~~PnS~------Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 67 (85)
T PTZ00083 24 RLVQGPNSY------FMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQP 67 (85)
T ss_pred eEecCCCCe------EEEEECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 577777765 567899999875 57899999999988873
No 54
>cd02334 ZZ_dystrophin Zinc finger, ZZ type. Zinc finger present in dystrophin and dystrobrevin. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dystrophin attaches actin filaments to an integral membrane glycoprotein complex in muscle cells. The ZZ domain in dystrophin has been shown to be essential for binding to the membrane protein beta-dystroglycan.
Probab=43.57 E-value=15 Score=33.03 Aligned_cols=32 Identities=28% Similarity=0.742 Sum_probs=23.8
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC
Q 000140 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 152 (2060)
Q Consensus 117 ~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~H 152 (2060)
.|++.=-.| .-|+|..|. ..-||.+||..+.|
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 466542223 789999996 46799999988865
No 55
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=43.32 E-value=11 Score=29.20 Aligned_cols=22 Identities=23% Similarity=0.708 Sum_probs=19.0
Q ss_pred hcccCCCCCC-CCCceEeeccCc
Q 000140 1933 KQCCSDCKSV-LDEPALCLLCGR 1954 (2060)
Q Consensus 1933 ~~~C~~c~~~-~~~paiCL~CG~ 1954 (2060)
.+.||+|+.. +.+-..|-.||+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 4679999998 788899999997
No 56
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=40.80 E-value=9.1 Score=35.03 Aligned_cols=45 Identities=27% Similarity=0.628 Sum_probs=34.3
Q ss_pred HhhcccCCCCCC---CCCceEeeccCccccCCCCccc-CCCchhHhhhhcCCCe
Q 000140 1931 YIKQCCSDCKSV---LDEPALCLLCGRLCSPSWKPCC-RESSCQSHAVACGAGT 1980 (2060)
Q Consensus 1931 ~~~~~C~~c~~~---~~~paiCL~CG~~~~~~~~~cc-~~gec~~H~~~Cg~~~ 1980 (2060)
+...+|+.|++. ..|.++|--||+.-.- .|. ..|+|..+. ||++.
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR---~C~~~~g~C~~~~--c~~~~ 51 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHR---DCWEKAGGCINYS--CGTGF 51 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccH---HHHhhCCceEecc--CCCCc
Confidence 345789999987 3688999999997554 355 469998877 88764
No 57
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.50 E-value=13 Score=33.72 Aligned_cols=15 Identities=40% Similarity=0.753 Sum_probs=10.9
Q ss_pred ccccChH-hhHHHHHH
Q 000140 1428 LSSCGHA-VHQGCLDR 1442 (2060)
Q Consensus 1428 ~SsCGH~-MH~~C~~~ 1442 (2060)
+-+|||+ |-++|=-+
T Consensus 22 lYtCGHMCmCy~Cg~r 37 (62)
T KOG4172|consen 22 LYTCGHMCMCYACGLR 37 (62)
T ss_pred HHHcchHHhHHHHHHH
Confidence 7799998 66777543
No 58
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=38.89 E-value=12 Score=34.79 Aligned_cols=28 Identities=29% Similarity=0.762 Sum_probs=23.6
Q ss_pred HhhcccCCCCCC------CCCceEeeccCccccC
Q 000140 1931 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2060)
Q Consensus 1931 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1958 (2060)
+.+.+||.|++. +..++.|..||+.++.
T Consensus 9 F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 9 FLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EEEEECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 466799999975 5789999999998776
No 59
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=38.58 E-value=11 Score=34.78 Aligned_cols=28 Identities=18% Similarity=0.705 Sum_probs=19.1
Q ss_pred HhhcccCCCCCC------CCCceEeeccCccccC
Q 000140 1931 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2060)
Q Consensus 1931 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1958 (2060)
+...+||.|++. ...++.|..||+++|.
T Consensus 5 Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 5 FMDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EEEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred EEEEECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 456799999874 6789999999998776
No 60
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=38.40 E-value=15 Score=49.70 Aligned_cols=23 Identities=48% Similarity=1.025 Sum_probs=20.7
Q ss_pred ccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccc
Q 000140 1430 SCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2060)
Q Consensus 1430 sCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKs 1477 (2060)
.|||..|+.|++ .+|+-||-|+.
T Consensus 858 ~CgHsyHqhC~e-------------------------~~~~~CP~C~~ 880 (933)
T KOG2114|consen 858 LCGHSYHQHCLE-------------------------DKEDKCPKCLP 880 (933)
T ss_pred ecccHHHHHhhc-------------------------cCcccCCccch
Confidence 699999999998 27899999986
No 61
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=37.86 E-value=22 Score=31.96 Aligned_cols=31 Identities=23% Similarity=0.842 Sum_probs=24.2
Q ss_pred ccccc-cccCCceeEEeccCCCCCCccccccccCCCC
Q 000140 116 GVCGA-VWGNNDIAYRCRTCEHDPTCAICVPCFQNGN 151 (2060)
Q Consensus 116 ~~Cg~-v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~ 151 (2060)
..|.+ -+. ++-|+|..|. .--+|.+||..+.
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 5779999999774
No 62
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=36.70 E-value=36 Score=33.47 Aligned_cols=26 Identities=27% Similarity=0.542 Sum_probs=21.4
Q ss_pred CcCCCccccccChHhhHHHHHHHHHH
Q 000140 1421 IDCDGIHLSSCGHAVHQGCLDRYVSS 1446 (2060)
Q Consensus 1421 ~~~~gvh~SsCGH~MH~~C~~~Y~~S 1446 (2060)
.+.+.+--+.|-|+-|..|-.+.+++
T Consensus 44 ~~eC~v~wG~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 44 GDECPVVWGVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred CCcceEEEEecchHHHHHHHHHHHhh
Confidence 34455558889999999999999987
No 63
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=33.22 E-value=11 Score=33.37 Aligned_cols=36 Identities=28% Similarity=0.709 Sum_probs=22.3
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCC-CCCce
Q 000140 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN-HKEHD 156 (2060)
Q Consensus 117 ~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~-H~~H~ 156 (2060)
.|+..--. ..-|+|..|. ..-||.+||..+. +.+|+
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 5779999999964 45664
No 64
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=32.53 E-value=33 Score=43.61 Aligned_cols=43 Identities=33% Similarity=0.791 Sum_probs=30.5
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCC----C-CCceeEEEecC
Q 000140 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN----H-KEHDYSIIYTG 163 (2060)
Q Consensus 117 ~Cg~v~~~~e~~y~C~~C~~d~t~~lC~~CF~~~~----H-~~H~~~~~~~~ 163 (2060)
.|..-.. |-+-.+|-.| |..-||..||..|. | .+|.|.++.++
T Consensus 19 ~C~~dit-~~i~ikCaeC---p~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~ 66 (438)
T KOG0457|consen 19 YCSLDIT-GLIRIKCAEC---PDFDLCLQCFSVGAETGKHQNDHPYRIMDTN 66 (438)
T ss_pred cHhHHhc-cceEEEeecC---CCcchhHHHHhcccccCCCCCCCCceeecCC
Confidence 3444443 4555889999 55569999997764 6 48999998764
No 65
>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=32.15 E-value=33 Score=38.08 Aligned_cols=44 Identities=23% Similarity=0.479 Sum_probs=26.7
Q ss_pred hhHHHHHHHHHHHHHhhhcccc-c-----C---CCcccCCCCccccccccccc
Q 000140 1435 VHQGCLDRYVSSLKERYNRRII-F-----E---GGHIVDPDQGEFLCPVCRQL 1478 (2060)
Q Consensus 1435 MH~~C~~~Y~~Sl~~r~~~r~~-~-----~---r~h~~d~e~gEFLCPLCKsL 1478 (2060)
-|-+|+++|-++-......... . . ..+....+..+..|||||.=
T Consensus 37 rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~CPLCRG~ 89 (162)
T PF07800_consen 37 RHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPELACPLCRGE 89 (162)
T ss_pred chhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccccCccccCc
Confidence 4899999997775433221100 0 0 01234556789999999973
No 66
>PF02148 zf-UBP: Zn-finger in ubiquitin-hydrolases and other protein; InterPro: IPR001607 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents UBP-type zinc finger domains, which display some similarity with the Zn-binding domain of the insulinase family. The UBP-type zinc finger domain is found only in a small subfamily of ubiquitin C-terminal hydrolases (deubiquitinases or UBP) [, ], All members of this subfamily are isopeptidase-T, which are known to cleave isopeptide bonds between ubiquitin moieties. Some of the proteins containing an UBP zinc finger include: Homo sapiens (Human) deubiquitinating enzyme 13 (UBPD) Human deubiquitinating enzyme 5 (UBP5) Dictyostelium discoideum (Slime mold) deubiquitinating enzyme A (UBPA) Saccharomyces cerevisiae (Baker's yeast) deubiquitinating enzyme 8 (UBP8) Yeast deubiquitinating enzyme 14 (UBP14) More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3GV4_A 3PHD_B 3C5K_A 2UZG_A 3IHP_B 2G43_B 2G45_D 2I50_A 3MHH_A 3MHS_A ....
Probab=24.98 E-value=58 Score=30.74 Aligned_cols=51 Identities=24% Similarity=0.420 Sum_probs=31.9
Q ss_pred cCCCCCCCCCceEeeccCccccCCCCcccCCCchhHhhhhcCCCeEEEEEecccEEE
Q 000140 1936 CSDCKSVLDEPALCLLCGRLCSPSWKPCCRESSCQSHAVACGAGTGVFLLIRRTTIL 1992 (2060)
Q Consensus 1936 C~~c~~~~~~paiCL~CG~~~~~~~~~cc~~gec~~H~~~Cg~~~GiFl~v~~~~il 1992 (2060)
|..|+....+.-+||.||.+.|... ..|--..|+.+=| =-+++.+++..|.
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~----~~~Ha~~H~~~~~--H~l~v~~~~~~i~ 51 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRY----SNGHALKHYKETG--HPLAVSLSTGSIW 51 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTT----STSHHHHHHHHHT----EEEETTTTCEE
T ss_pred CCCCCCcCCceEEeCCCCcccccCC----cCcHHHHhhcccC--CeEEEECCCCeEE
Confidence 6677765789999999999866631 1355577877555 4456666666553
No 67
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=24.63 E-value=34 Score=38.59 Aligned_cols=20 Identities=50% Similarity=1.157 Sum_probs=17.8
Q ss_pred ccCCCCCCCCCceEeeccCcc
Q 000140 1935 CCSDCKSVLDEPALCLLCGRL 1955 (2060)
Q Consensus 1935 ~C~~c~~~~~~paiCL~CG~~ 1955 (2060)
.| +||..-..|+.||.||+-
T Consensus 2 ~C-rCG~~l~~p~~Cl~Cg~~ 21 (227)
T COG4031 2 IC-RCGAELSSPAFCLNCGRR 21 (227)
T ss_pred cc-ccCCcccccchhcccCCc
Confidence 58 999999999999999973
No 68
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=24.00 E-value=44 Score=29.07 Aligned_cols=25 Identities=24% Similarity=0.527 Sum_probs=17.3
Q ss_pred cccCCCCCCC------CCceEeeccCccccC
Q 000140 1934 QCCSDCKSVL------DEPALCLLCGRLCSP 1958 (2060)
Q Consensus 1934 ~~C~~c~~~~------~~paiCL~CG~~~~~ 1958 (2060)
++||.|+... ..-.+|-.||.++..
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEE 31 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeec
Confidence 4799998752 344599999998764
No 69
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=23.49 E-value=43 Score=41.63 Aligned_cols=17 Identities=29% Similarity=0.698 Sum_probs=15.6
Q ss_pred ccccChHhhHHHHHHHH
Q 000140 1428 LSSCGHAVHQGCLDRYV 1444 (2060)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~ 1444 (2060)
+=-|.|+.|..|.+.|+
T Consensus 384 ALpCsHIfH~rCl~e~L 400 (518)
T KOG1941|consen 384 ALPCSHIFHLRCLQEIL 400 (518)
T ss_pred ccchhHHHHHHHHHHHH
Confidence 55799999999999998
No 70
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=23.23 E-value=56 Score=39.61 Aligned_cols=33 Identities=45% Similarity=0.944 Sum_probs=23.6
Q ss_pred ceeEEeccC-CCCCCccccccccCCCC----C-CCceeEEEec
Q 000140 126 DIAYRCRTC-EHDPTCAICVPCFQNGN----H-KEHDYSIIYT 162 (2060)
Q Consensus 126 e~~y~C~~C-~~d~t~~lC~~CF~~~~----H-~~H~~~~~~~ 162 (2060)
-+..+|-.| .+| +|..||-+|. | .-|.|+++.+
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 455667777 444 8999998765 3 4699999864
No 71
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=20.55 E-value=48 Score=44.33 Aligned_cols=18 Identities=28% Similarity=0.803 Sum_probs=15.7
Q ss_pred ccccChHhhHHHHHHHHH
Q 000140 1428 LSSCGHAVHQGCLDRYVS 1445 (2060)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~ 1445 (2060)
-.+|||+||.+|....++
T Consensus 1045 Cg~C~Hv~H~sc~~eWf~ 1062 (1081)
T KOG0309|consen 1045 CGTCGHVGHTSCMMEWFR 1062 (1081)
T ss_pred hccccccccHHHHHHHHh
Confidence 567999999999998874
No 72
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.26 E-value=58 Score=43.83 Aligned_cols=19 Identities=32% Similarity=0.807 Sum_probs=16.4
Q ss_pred ccccChHhhHHHHHHHHHH
Q 000140 1428 LSSCGHAVHQGCLDRYVSS 1446 (2060)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~S 1446 (2060)
.-.|||+-|..|+.+.++-
T Consensus 311 rL~C~Hifh~~CL~~W~er 329 (543)
T KOG0802|consen 311 RLPCGHIFHDSCLRSWFER 329 (543)
T ss_pred eeecccchHHHHHHHHHHH
Confidence 4569999999999998865
Done!