Query 000142
Match_columns 2058
No_of_seqs 347 out of 628
Neff 6.4
Searched_HMMs 46136
Date Thu Mar 28 20:24:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000142.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000142hhsearch_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 1283 280-2042 371-1720(1738)
2 KOG1139 Predicted ubiquitin-pr 100.0 2.2E-32 4.7E-37 335.8 5.7 610 1414-2055 170-782 (784)
3 KOG1140 N-end rule pathway, re 99.8 2.3E-22 5E-27 269.9 -2.5 934 10-998 526-1502(1738)
4 smart00396 ZnF_UBR1 Putative z 99.8 1.6E-19 3.4E-24 170.7 5.9 70 114-183 1-71 (71)
5 PF02207 zf-UBR: Putative zinc 99.7 2.2E-18 4.7E-23 163.7 4.1 70 114-183 1-71 (71)
6 KOG1139 Predicted ubiquitin-pr 99.0 3.3E-09 7.2E-14 133.3 16.1 185 752-936 207-477 (784)
7 PF10390 ELL: RNA polymerase I 97.0 0.00048 1E-08 83.3 3.7 80 867-951 198-280 (284)
8 KOG1777 Putative Zn-finger pro 94.9 0.01 2.2E-07 72.1 1.3 63 109-172 539-606 (625)
9 PF13639 zf-RING_2: Ring finge 91.3 0.064 1.4E-06 46.5 0.2 20 1425-1444 17-36 (44)
10 cd00162 RING RING-finger (Real 91.1 0.17 3.7E-06 42.9 2.7 19 1426-1444 15-33 (45)
11 KOG0943 Predicted ubiquitin-pr 89.6 0.11 2.3E-06 69.2 0.1 63 114-182 1241-1309(3015)
12 KOG4445 Uncharacterized conser 88.0 0.16 3.5E-06 59.7 0.2 48 1426-1475 133-183 (368)
13 PF13764 E3_UbLigase_R4: E3 ub 87.7 2.1 4.6E-05 58.8 10.3 70 1144-1227 422-497 (802)
14 cd02335 ZZ_ADA2 Zinc finger, Z 85.1 0.7 1.5E-05 41.3 2.6 39 115-157 5-48 (49)
15 cd02340 ZZ_NBR1_like Zinc fing 85.0 0.71 1.5E-05 40.2 2.5 37 115-156 5-41 (43)
16 KOG4796 RNA polymerase II elon 84.1 1 2.2E-05 57.2 4.3 77 867-949 211-290 (604)
17 cd02249 ZZ Zinc finger, ZZ typ 83.9 0.78 1.7E-05 40.4 2.3 37 115-156 5-44 (46)
18 PF00097 zf-C3HC4: Zinc finger 83.1 0.72 1.6E-05 39.2 1.8 20 1425-1444 13-32 (41)
19 cd02344 ZZ_HERC2 Zinc finger, 82.1 1.1 2.4E-05 39.4 2.5 39 115-157 5-44 (45)
20 PF12861 zf-Apc11: Anaphase-pr 81.7 0.91 2E-05 45.1 2.1 24 1421-1444 44-67 (85)
21 smart00184 RING Ring finger. E 80.8 1.3 2.9E-05 36.0 2.5 18 1426-1443 13-30 (39)
22 PF14634 zf-RING_5: zinc-RING 80.4 1.5 3.2E-05 38.2 2.7 31 1423-1475 14-44 (44)
23 cd02338 ZZ_PCMF_like Zinc fing 80.2 1.3 2.9E-05 39.6 2.4 38 115-157 5-48 (49)
24 KOG2905 Transcription initiati 79.5 1.2 2.7E-05 51.6 2.5 62 867-929 182-245 (254)
25 KOG2752 Uncharacterized conser 75.6 3.4 7.4E-05 49.7 4.7 61 110-171 37-101 (345)
26 COG5243 HRD1 HRD ubiquitin lig 74.7 1.4 3E-05 53.5 1.3 16 1428-1443 317-332 (491)
27 PF00643 zf-B_box: B-box zinc 74.4 1.7 3.7E-05 37.2 1.5 37 114-156 4-40 (42)
28 PF11793 FANCL_C: FANCL C-term 73.5 0.99 2.1E-05 43.5 -0.3 38 1427-1475 26-63 (70)
29 PHA02926 zinc finger-like prot 73.0 2.7 5.9E-05 48.5 3.0 46 1421-1483 190-235 (242)
30 PF09538 FYDLN_acid: Protein o 72.5 1.7 3.7E-05 45.4 1.2 27 1930-1956 8-38 (108)
31 PLN03208 E3 ubiquitin-protein 68.6 3.9 8.5E-05 46.8 3.0 53 1426-1484 33-87 (193)
32 cd02339 ZZ_Mind_bomb Zinc fing 68.0 3.5 7.7E-05 36.3 2.0 30 124-156 13-43 (45)
33 TIGR02300 FYDLN_acid conserved 63.8 3.4 7.4E-05 43.9 1.2 27 1930-1956 8-38 (129)
34 KOG1940 Zn-finger protein [Gen 61.6 4.1 8.8E-05 49.1 1.5 35 1424-1480 175-209 (276)
35 cd02343 ZZ_EF Zinc finger, ZZ 58.7 5.7 0.00012 35.5 1.5 35 115-154 5-40 (48)
36 PF12678 zf-rbx1: RING-H2 zinc 57.7 2.5 5.5E-05 41.1 -0.9 17 1426-1442 47-63 (73)
37 cd02341 ZZ_ZZZ3 Zinc finger, Z 56.8 7.4 0.00016 34.9 1.9 40 115-156 5-46 (48)
38 cd02336 ZZ_RSC8 Zinc finger, Z 55.7 4.1 8.9E-05 35.9 0.2 31 115-150 5-35 (45)
39 cd02337 ZZ_CBP Zinc finger, ZZ 53.6 7.6 0.00016 33.6 1.4 32 114-151 4-35 (41)
40 COG2051 RPS27A Ribosomal prote 53.5 4.9 0.00011 37.9 0.3 28 1929-1956 17-50 (67)
41 cd00021 BBOX B-Box-type zinc f 53.1 10 0.00022 31.7 2.2 28 124-156 10-37 (39)
42 cd02334 ZZ_dystrophin Zinc fin 52.6 9.4 0.0002 34.4 1.9 32 115-150 5-36 (49)
43 PHA02929 N1R/p28-like protein; 52.6 6.8 0.00015 46.6 1.4 35 1426-1482 197-231 (238)
44 PF13923 zf-C3HC4_2: Zinc fing 52.5 6.1 0.00013 33.4 0.7 20 1425-1444 13-32 (39)
45 PF10571 UPF0547: Uncharacteri 49.4 7.8 0.00017 30.3 0.8 22 1932-1953 1-23 (26)
46 PF02270 TFIIF_beta: Transcrip 48.7 6.5 0.00014 48.0 0.4 31 897-928 244-274 (275)
47 smart00336 BBOX B-Box-type zin 47.9 15 0.00032 31.2 2.4 29 123-156 12-40 (42)
48 KOG0827 Predicted E3 ubiquitin 47.4 13 0.00027 46.1 2.5 30 1414-1444 12-41 (465)
49 PF13240 zinc_ribbon_2: zinc-r 46.9 10 0.00022 28.8 1.0 20 1933-1952 1-21 (23)
50 KOG0828 Predicted E3 ubiquitin 46.6 12 0.00026 47.5 2.2 29 1426-1475 603-631 (636)
51 PLN00209 ribosomal protein S27 45.0 7.6 0.00017 38.6 0.2 38 1914-1957 25-68 (86)
52 PTZ00083 40S ribosomal protein 43.7 8.4 0.00018 38.2 0.2 38 1914-1957 24-67 (85)
53 PF13248 zf-ribbon_3: zinc-rib 43.3 11 0.00025 29.2 0.9 22 1931-1952 2-24 (26)
54 PF13920 zf-C3HC4_3: Zinc fing 43.0 15 0.00033 32.8 1.7 18 1426-1443 17-35 (50)
55 PF14446 Prok-RING_1: Prokaryo 40.8 9.2 0.0002 35.0 0.0 45 1929-1978 3-51 (54)
56 smart00291 ZnF_ZZ Zinc-binding 40.3 21 0.00045 31.3 2.1 33 114-151 8-40 (44)
57 KOG4172 Predicted E3 ubiquitin 39.9 14 0.0003 33.6 0.9 15 1426-1440 22-37 (62)
58 PRK00415 rps27e 30S ribosomal 39.0 12 0.00027 34.8 0.5 28 1929-1956 9-42 (59)
59 PF01667 Ribosomal_S27e: Ribos 38.7 11 0.00023 34.8 0.1 28 1929-1956 5-38 (55)
60 cd02345 ZZ_dah Zinc finger, ZZ 38.4 22 0.00047 32.0 2.0 31 114-149 4-35 (49)
61 KOG2114 Vacuolar assembly/sort 37.5 16 0.00035 49.5 1.4 23 1428-1475 858-880 (933)
62 PF00569 ZZ: Zinc finger, ZZ t 35.7 10 0.00022 33.5 -0.4 36 115-154 9-45 (46)
63 COG5194 APC11 Component of SCF 34.9 40 0.00086 33.2 3.2 26 1419-1444 44-69 (88)
64 KOG0457 Histone acetyltransfer 32.3 33 0.00071 43.6 2.9 43 115-161 19-66 (438)
65 PF07800 DUF1644: Protein of u 31.1 36 0.00077 37.9 2.6 44 1433-1476 37-89 (162)
66 PF02148 zf-UBP: Zn-finger in 25.0 57 0.0012 30.8 2.5 51 1934-1990 1-51 (63)
67 COG4031 Predicted metal-bindin 24.5 34 0.00075 38.6 1.1 20 1933-1953 2-21 (227)
68 COG5114 Histone acetyltransfer 24.1 52 0.0011 39.8 2.5 33 124-160 18-56 (432)
69 PF08271 TF_Zn_Ribbon: TFIIB z 24.0 44 0.00096 29.1 1.4 25 1932-1956 1-31 (43)
70 KOG1941 Acetylcholine receptor 23.0 45 0.00097 41.5 1.7 17 1426-1442 384-400 (518)
71 KOG0309 Conserved WD40 repeat- 20.5 49 0.0011 44.3 1.4 18 1426-1443 1045-1062(1081)
72 KOG0802 E3 ubiquitin ligase [P 20.2 58 0.0013 43.8 2.1 19 1426-1444 311-329 (543)
No 1
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6e-127 Score=1260.57 Aligned_cols=1283 Identities=22% Similarity=0.330 Sum_probs=810.1
Q ss_pred hccCCCHHHHHHHHHHHH-HhhCChhhHHHHHHHHHhhhHHHHHHHHHhccCcccccCCccceeeeeccccCCcHHHHHH
Q 000142 280 AEMFSSDVVVRKLHELLL-KLLGEPIFKYEFAKVFLSYYPVFVKDAIREHSDDTIKKYPLLSTFSVQIFTVPTLTPRLVK 358 (2058)
Q Consensus 280 ~~~~l~k~~r~~lh~L~l-sLL~d~efK~~FA~~Fv~~Y~~i~~~fl~~d~d~~~~~~s~v~~LSVQLFTvPsLA~~LV~ 358 (2058)
.+..+||..|..++.++. .+-++.+||+.||.+|+.+|..+..+++.+|++.. .+.| .++||+||+|++|..+++
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 67789999999999999999999999999998743 3545 999999999999999999
Q ss_pred hhcHHHHHHHHHHHHhhhhcCCCCccee--c-------cccccccchhhhhhhhhHhhcchhhhHHHhhhchHHHHHHHH
Q 000142 359 EMNLLEMLLGCLREIFDSCAGDDSCLQV--A-------KWANLYETTNRVIGDIRFVMSHAAVSKYATHEQLNISKAWMK 429 (2058)
Q Consensus 359 e~nLL~iLl~tl~~~~~~~~~~~~~l~~--~-------~~~~~~~~y~~I~~DLrylLsh~~v~~~l~~~~~~~~~~~l~ 429 (2058)
...++.++..++..++..+...++...+ - +.....++.+..+.|+ +.+.++. +-.++..+..++.
T Consensus 447 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~r~l~~~~~l-~~~~~~~-----~~~~~~~~~~~l~ 520 (1738)
T KOG1140|consen 447 NQSFLDIVWSIIDIFKEFNKVEGGVLIDIRVQKSNLLKRYSISFRRTLYTFEDL-SKVHDPN-----IPLRPKEFISLLL 520 (1738)
T ss_pred hccchHHHHHHHHHHHHhcccccceecceeeeechhhhHHHHHHHHHHHHHHHh-hccCCcc-----ccccHHHHHHHHH
Confidence 9998888777776666544432221111 1 1122356677778888 7766666 2357899999999
Q ss_pred HHHHhcCCCcccccccCcceeeCCceeehhhhhhHHHHhHhhhhhcccccccccccccccccccccCCCCCccccccccc
Q 000142 430 LLTFVQGMNPQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEETRYDFSMYKQDIGDGDSLRHAKVGR 509 (2058)
Q Consensus 430 lL~~~QGMn~~kRq~~~HVEyE~e~w~~aF~L~~~la~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~r 509 (2058)
++..||||.|++|+.++||++|++ |+.+|.+-.++..++++++.||...+ . +-
T Consensus 521 ~~~v~qg~~~lkr~~~ehv~~e~~-~~~~~~~v~~~t~~~s~i~~~~~~~e--------p-----------------~~- 573 (1738)
T KOG1140|consen 521 LLKVFQGVDPLKREELEHVEVEKE-WENFFSLVEYLTAIYSMIQSLVKTSE--------P-----------------VK- 573 (1738)
T ss_pred HHHHhCCccHHHHHHhhhhcccch-HHHHHHHHHHHHHHHHHHHHHHHhcc--------c-----------------hh-
Confidence 999999999999999999999997 99999999999999999998887644 0 00
Q ss_pred cccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhhhcCCCCcccccccCCCCcccccCchh
Q 000142 510 LSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENWLGVDDRSVSVNDILSPNASRISGSNF 589 (2058)
Q Consensus 510 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~cl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 589 (2058)
..++..|+.++..... ..
T Consensus 574 ----------------------------------------~~~~~~l~~~~~r~~~-----s~----------------- 591 (1738)
T KOG1140|consen 574 ----------------------------------------DSVYKKLLEAAIRIHP-----SL----------------- 591 (1738)
T ss_pred ----------------------------------------hhHHHHHHHHHhhccc-----cc-----------------
Confidence 0011122222221100 00
Q ss_pred hHhHhhhhhhcccccccccccCCccccccccccCCCccccccCccccccccCCcccccccccCcCCcccccccccccccc
Q 000142 590 VALKKTLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKITISGERDTASWRSAGFNDSEMEGECATELDNL 669 (2058)
Q Consensus 590 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l 669 (2058)
+++ + .-...+++++
T Consensus 592 --------------------~~~-----------------------------~----------~l~~~i~~~S------- 605 (1738)
T KOG1140|consen 592 --------------------TGS-----------------------------E----------SLTYTICGES------- 605 (1738)
T ss_pred --------------------Ccc-----------------------------c----------eeeehhhhhh-------
Confidence 000 0 0001223332
Q ss_pred ccccCCccCceeeeccCCceeeehHHHHHHHHHHHHHHhhhccccccccccccCCCCCccccchhhhhcccCCCCCcccc
Q 000142 670 HVLSLCYWPDITYDVSSQDVSVHIPLHRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFS 749 (2058)
Q Consensus 670 ~~~~~~~~~~v~fdVs~~~VSfH~PLhr~Ls~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 749 (2058)
..++.|+|+.++||||.|+.|+|+++++....... ...+.+ ..+.+++. .
T Consensus 606 -------~e~i~f~v~~~~~sv~~p~~~~l~~l~~~~~s~v~-------------------~~~d~~-~~~~~~~n---~ 655 (1738)
T KOG1140|consen 606 -------HETINFSVSQERVSVSNPVSRLLAFLIELSCSSVV-------------------SLKDAY-ERLEDCSN---F 655 (1738)
T ss_pred -------HhHhhhccccccceeeccHHHHhhhhhhcccchhh-------------------hcchhh-hhHhhhcc---c
Confidence 34789999999999999999999998843211000 111111 11122222 2
Q ss_pred hhhccccHHHHHHHHhHhcCceeeccHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccc
Q 000142 750 AFVMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLS 829 (2058)
Q Consensus 750 ~~l~e~pLR~~Vl~aQI~aGmWvRNG~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~ 829 (2058)
.+|.|||||++|++|||.+|||||||+++.+|+.||++.+||+++|++||+++|.++++.||+.|+.++++||+|.+|++
T Consensus 656 ~~i~e~~lr~~Vl~aqid~~~w~rNG~si~~q~~~y~~~~~r~~~y~~DI~~~Q~~la~~d~~~~l~~~l~r~~L~~w~~ 735 (1738)
T KOG1140|consen 656 LAISEHSLRVLVLCAQIDVGFWVRNGFSILHQAAYYKNNPCRNESYDRDILMLQTGLAMEDPNRFLFTILSRFELLDWFT 735 (1738)
T ss_pred hhhcccchhheeeeeecceeeEeecCcchhhhhHhhcCccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHhc
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCC-ch---hHHHHHHHHHHHHhhcccccCCC---ChHHHHHHHHHHHHhcCCCChHHHHhhCCCCCCCcchHHH
Q 000142 830 LNLERPSE-YE---PILVQEMLTLIIQILQERRFCGL---TTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQE 902 (2058)
Q Consensus 830 ~~~~~~~~-y~---~~mvEe~L~lLI~llteR~~~g~---s~~e~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~~~~fe~ 902 (2058)
|....... ++ ..|+|+|+.+||.|++||...|+ +..+.+|+||||+||++|++||+|.+++|++++++..||.
T Consensus 736 g~~~~~~~d~~~~i~~~~ee~l~lii~ll~Er~~~~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~~d~ 815 (1738)
T KOG1140|consen 736 GEVDYQSNDTEDTISFMIEEFLALIILLLTERSYFGSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLSFDE 815 (1738)
T ss_pred CCCccccccHHHHHHHHHHHHHHHHHHHHHheeecccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhcccchH
Confidence 98654332 22 37999999999999999997554 5778999999999999999999999999999999999999
Q ss_pred HHHHHccccCCCCC-CcceEEeehhhhccccccccccCchhHHHHHHHHHH--hhc---cccccCCC-CCCcccCC-Ccc
Q 000142 903 ILDAVAMYSHPSGF-NQGMYSLRWSYWKELDIYHPRWSSRDLQVAEERYLR--FCS---VSALTAQL-PRWTKIYY-PLE 974 (2058)
Q Consensus 903 iL~eVA~f~~P~g~-~~G~Y~LK~e~~~e~dpy~~~y~~~~~q~aeer~~r--~~~---~~a~~~~~-P~~~~~~~-p~~ 974 (2058)
++++||+|++|.++ +.|+|+||++||+++||||+||++.++.+++..+++ .++ ..|..+++ |++.+.+. .+.
T Consensus 816 ~~e~Va~~~~p~~~~~~gvf~lK~~~~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~~~~ 895 (1738)
T KOG1140|consen 816 ALEEVAVFKKPKGLADNGVFVLKESYYDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKKGAD 895 (1738)
T ss_pred HHHHHHhhccCCccccceEEEechhhhhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHHHHH
Confidence 99999999999999 789999999999999999999999998888765533 211 12443332 33333221 124
Q ss_pred ccccccCcHHHHHHHHHHHHHHhccCCCCCCCCchhHHHHHHH-HHHHHHhhhhhcccCCCCCcccCCCCccccchhhHH
Q 000142 975 SIAGIATCKVVLQVIRAVLFYAVFTDNPTDSRAPYGVLLTALH-LLALALDVCFQKKKSGDQSCDIGGSTPILDFASEEI 1053 (2058)
Q Consensus 975 ~i~~il~s~~~~~il~~vL~~al~~~~~~~~~~~E~~L~~~LH-Li~laL~~~~~e~~~~~~~~~~~~~~~~~~~~~~~i 1053 (2058)
++.+.....+|-.||+.++.++.+.. .+.++..++| +++.|++.+..--. |.+.-. ++
T Consensus 896 ~L~~~t~~~~~~~ii~r~~~~~~~~~-------s~~~l~~~~~~ihG~~~~~~l~~~~-----------~~~~~~-~e-- 954 (1738)
T KOG1140|consen 896 ILGAAVRLTVFGLIIYRTLEHCLFME-------SSTLLSKVLHLIHGIALNEELINMK-----------FAFTQK-TE-- 954 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhcc-----------cccccc-cc--
Confidence 45555556667777777777776543 4889999995 45899986543211 110010 11
Q ss_pred hhccCCCCCcccHHHHHHHHHhhhccCCCccccccccCCchhHHHHHHHHHHhhhHHHHHHHhhhchhhhhcccCCCCCC
Q 000142 1054 AEGLNNGAGKQSLLSLLVFLMGMYKKDGADNFLEAGNCNLSSVIESLLKKFAEIDSRCMTKLQQLAPEIVSHLSQSLPRD 1133 (2058)
Q Consensus 1054 ~~~~~~~~~~~SllsLL~~L~~~~~~~~~~~~~~~~~~~i~~~I~~lL~~f~~~~~~c~~~l~~~~p~~~~~~~~~~~~~ 1133 (2058)
....+..+.+++.+..++....+ +.++.|+++.|..+.. .+...|++.. .... ...
T Consensus 955 ------~~~~e~gl~~~e~lv~~~~~~~~-----------~~~~~v~~~l~~~~~~-----~~~n~~ea~~-~~~~-~~~ 1010 (1738)
T KOG1140|consen 955 ------SIAREKGLSLYESLVRKPDSLVH-----------GKIIEVIVELFESLIK-----SRANDPEVAN-DEKD-KKE 1010 (1738)
T ss_pred ------ccccccchhhHHHhhhcchhhcC-----------CcceeeeHHHHhhhhh-----hhcCCccccc-cccc-ccc
Confidence 11345577788888777554332 4568888888876544 2444443321 1100 011
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCccCCCCcccccccccCCccccccCCCC-
Q 000142 1134 DTSGSFSASDSEKRKAKARERQAAILEKMKAEQFKFLSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS- 1212 (2058)
Q Consensus 1134 ~~~~~~~~~e~ekkK~~AkeRQakIMaqf~~qQ~~Fl~~n~~~~d~~~~~~~~~~~s~~~~~~~e~~~~~CilCqe~~~- 1212 (2058)
..+.+.++.+.++||++|++||+|+||||+.||.+||++|.++.|++++. .+++...+. ......|.+|+..+.
T Consensus 1011 ~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e~d~~~~~---~~~~~~~~~--~~~d~~~~~~~~~s~~ 1085 (1738)
T KOG1140|consen 1011 KQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDEFDEQENQ---TPSSGSKTY--EEEDFTCALCQDNSCT 1085 (1738)
T ss_pred ccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccccCccccc---Cccccccch--hhhhccchhhhccchh
Confidence 12234444556788889999999999999999999999997665544331 111110111 111456777764322
Q ss_pred CCCeEEEeeeecccccccccCCCCCCcccccccccccccccccccccCCCCCCCCCCCcchhhhhHHHHHHHHhhhccCC
Q 000142 1213 RTPVSYLILLQKSRLLSFVDRGSPSWDQDQWLGKECGTISANNMVNQFGTNTPSSGLGVISSCQLAQVAEEAVNQFAYNG 1292 (2058)
Q Consensus 1213 ~~p~g~la~iq~S~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 1292 (2058)
+.++ |+++.+...
T Consensus 1086 ~~~~------~~~~~~~~~------------------------------------------------------------- 1098 (1738)
T KOG1140|consen 1086 DFQV------KPASHLVKP------------------------------------------------------------- 1098 (1738)
T ss_pred cccc------ccchhhhcc-------------------------------------------------------------
Confidence 1222 222221100
Q ss_pred CchhhhhHHHHhhhcCCCCcCCCCCcccCCCCcCCccchhhhhhhhhhHHHHhhhccCCCCCCccccchhhhccCCccCC
Q 000142 1293 KPEEVNSVLEFVKAQFPSLRNIPIPFTFSNGRKCTASSMEMFEQDLYLSICREMRKNMTYPDLMKEDEECSVAEGGLKNR 1372 (2058)
Q Consensus 1293 r~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~s~~~~~e~~~~~~~~~~~~~~ 1372 (2058)
...+||+| |+++.+...
T Consensus 1099 --------------------------------------------~~~~~~i~------------~e~e~~~~~------- 1115 (1738)
T KOG1140|consen 1099 --------------------------------------------IFRECIIC------------DENEDVPNW------- 1115 (1738)
T ss_pred --------------------------------------------cccccccC------------ChhccCCCc-------
Confidence 00123333 233333211
Q ss_pred CCCccchhhhhhhhhhHHhhhcccccccccccccccccccCCCCCC-CcCCCccccccChHhhHHHHHHHHHHHHHhhhc
Q 000142 1373 GNSDSFLLGKYVASISKEMRENASASEVSRGDRIAAESLVYDGFGP-IDCDGIHLSSCGHAVHQGCLDRYVSSLKERYNR 1451 (2058)
Q Consensus 1373 ~~~~~~~l~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~F~~-~~~~gvh~ssCGH~MH~~C~~~Y~~Sl~~r~~~ 1451 (2058)
.++.++..+|+++. +. ...+++.| ....|+++|+|||.||+.||++|+++.+.|.++
T Consensus 1116 -~~~~~v~~~f~~~s-~~--------------------~sd~l~~p~~~~~~~~~s~c~h~mh~~c~~~~~~a~r~~~n~ 1173 (1738)
T KOG1140|consen 1116 -DGRYSVSSAFAQKS-DD--------------------VSDALTEPGSLSCGTVLSSCGHHMHYGCFKRYVQAKRFRENA 1173 (1738)
T ss_pred -cccchhhhHhhhhc-cc--------------------ccccccCCCCCcccceeeccCCcchHHHHHHHHHHHHHHHHh
Confidence 11223555666552 11 11334434 567899999999999999999999999999987
Q ss_pred ccccCCCcccCCCCCccccccccccccceecCCCCCcccCCCCCcccCCCCCCCCCCccccccchhhHHHHHH------H
Q 000142 1452 RIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRINEQPTVSGVGLSLDSSSSFTTREENTSFQLQQA------V 1525 (2058)
Q Consensus 1452 r~~~~r~h~~d~e~gEFLCPLCKsL~Ns~LPilp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~ 1525 (2058)
+..+-+.|.- ++|+|+||+||+|+|++||..++.....+.. +.. ..+....|++.. +
T Consensus 1174 ~~~~l~~~~s--e~~l~lCp~c~slsn~~lp~~~~~~~~~n~~-t~~--------------~~~n~~~~i~~rs~~~~s~ 1236 (1738)
T KOG1140|consen 1174 RTAPLCQHYS--ENGLFLCPLCKSLSNVSLPMFLPPELLLNPL-TLE--------------NQRNLNSWIEKRSRASFSL 1236 (1738)
T ss_pred hhcCcccccc--cCCcccCCchHhhhhccCCcCCchhhhcChh-hhh--------------chHHHHHHHHHhchhhcch
Confidence 7665554443 8999999999999999999775433322210 000 001122233310 0
Q ss_pred HHhhhc----cccccc---ccccccCCcchhhHHHHHHHHHHHHHHHHhhccc------cccccCCCCCChhHHHHHHHh
Q 000142 1526 SLLQSA----SNVVGK---ADVIESFPLMKNEIMASNVEAVSRRMCKMYFQNK------LDKFFGSARVNPSLIMWDALK 1592 (2058)
Q Consensus 1526 ~~l~s~----~~~~~~---~~~~~~~~~~~~~~~~~~l~~~~~~l~~l~~~~~------~~~~~~~~~~~~~~~l~~tl~ 1592 (2058)
..+.+. ...... .++.+..-.++.+.....++.+.+.+....+... .....+.++. .....|-.++
T Consensus 1237 ~~vs~~~s~~~~~~~ss~i~e~kp~~~~~l~~~~~~~ie~~~k~v~s~~~k~~~~i~~~~le~~~~~~~-~~~~~~~~~s 1315 (1738)
T KOG1140|consen 1237 QDVSSILSDPWAAFTSSRIPELKPILIMDLPDSVVEQIELFQKIVGSAMFKPSSLLSTNTLELTLFSRE-FLIVCWQSLS 1315 (1738)
T ss_pred hhhhhhhcccchhhccccccccccchHhhhhhHHHHHHHHHHHHHhhheeecccceeecccccCcccch-hhhhhhhccc
Confidence 000000 000000 0000000001222222223333333332222111 1122234443 4567788888
Q ss_pred HhHHHHHHHhhccCCCCCCccchhhHHHhhhhchhHHHHHHHHHHhhhcccchHHHHHHhhc---cchhhhhccCCCCCC
Q 000142 1593 YSLMSMEIAARSEKTSTTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVLQRFRG---IQLFAESICSGTSID 1669 (2058)
Q Consensus 1593 yTi~s~Eia~Rg~~~~~~~~~~l~~L~~~l~~~~~~~l~ll~~~~~~~r~~~~~~~l~r~~~---~~Ll~~si~~~~s~~ 1669 (2058)
+..+++++.+-+.+... +..+.+...+.+....++.... +...++...- +.++...+.+ .
T Consensus 1316 ~a~~~~~~~l~~~~~~~---------~l~l~~~~~~~~~~~~~l~~~~----~~~~l~~~~~~~llk~~s~~~~~----i 1378 (1738)
T KOG1140|consen 1316 DAEQSTKLLLSASKKPS---------FLKLNEDMTFCLVTISRLRALH----WEQILYELVYTFLLKSFSPTIPR----I 1378 (1738)
T ss_pred hHHHHHHHHHhccCCcc---------cccCchhhHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhhcCCc----c
Confidence 88888777544433321 1111111112222221111111 1112222111 1111110000 0
Q ss_pred CCCCccCCCCcccccccccccccCcchhhhhhhcCCCccccChhhHHHHHHhhcccccccccchhhhHHHH-HHHHHHHH
Q 000142 1670 NPGGRCKRGGNMLSILKHADVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFILCKESLLSLVHV-FYAVTLSQ 1748 (2058)
Q Consensus 1670 ~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~plL~~D~F~~Lv~~~~~lp~~~~~~~~~~~~iv~l-~y~~~ivQ 1748 (2058)
. .+... +.+.......+..++...|-+-. .++ ........++++ ..+++++|
T Consensus 1379 ~----------------~~~tp-d~~~~~ll~~l~~~~~~~~~l~~------~~~----~~~~~~~~~~~~~i~~~~i~s 1431 (1738)
T KOG1140|consen 1379 S----------------VLITP-DQPENELLVILPHDFPKSLELEL------TLD----FVNKNPKKIFELKILMASIIS 1431 (1738)
T ss_pred h----------------hccCC-CCCcchhhhccchhhhhhccHHH------HHH----HhhhhHHHHHhHHHHHHHhhh
Confidence 0 00000 00000000000011111111111 001 011233344444 45567777
Q ss_pred H-Hhhhhcccccc--cccccchhhhHHHHHHHhcccccccccccccCCCChhhHHHHHHHhhhhHHHHHHHHHHhhcCCC
Q 000142 1749 A-VLSCCGKLQSK--VNELGFSDSLISDISKLLGEFGSAQEYFVSNYIDPSCDIKDMIRRLSFPYLRRCALLWKLLNSTV 1825 (2058)
Q Consensus 1749 ~-li~~~~~~~~~--~~~~~~~~~~~~~i~~~~~~~~~~~~~~~s~~~d~~~~l~~~v~k~~lPFLRr~aLL~~~l~~~~ 1825 (2058)
. +++.......+ .++....-.....+...+-.....+.......+-....++..+++.++|||||+++++|++.++.
T Consensus 1432 ~elits~s~l~~d~~~~~~q~s~~e~~~~~t~l~~~~s~~~i~~~~~~~~~~~L~~~~~~~i~sfL~~~al~~h~ln~v~ 1511 (1738)
T KOG1140|consen 1432 IELITSHSYLENDLEMAEEQKSIDEFKSLLTYLLQLESSRTIPKLADIRLRLSLCLSCEAGILSFLRRAALFKHLLNNVF 1511 (1738)
T ss_pred hhhheeccccCCccchhhhhhhHHhHhHHHHHHHhccchhhCccccchhhhhHHHHHHHHHHHHHHHHHHHhhhhhhcCC
Confidence 6 44432221111 00111000001111110000000000000000111235788899999999999999999999998
Q ss_pred CCCCCCccccccccccCccCCCCCCcccccchHHHHHHHHhcCCCChhhhh-hh--HHHHHHHHHHhhccccchhhhccc
Q 000142 1826 PPPFSDRDHVLARSSHGISDMMDSSDDALSDLKEIQEVEKMFKIPSLDVIL-KD--EVLRSLVLKWFHHFSKEFEVHRFQ 1902 (2058)
Q Consensus 1826 ~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~L~~~L~LPsl~~il-~~--~~~~~li~~W~~h~~~~~~~~~~~ 1902 (2058)
+|... +.++ ....|+..||+|+++|++...+ +. +.++.++.+||.-.........+.
T Consensus 1512 ~p~~~------------f~~~--------~~~s~~e~L~ty~slp~l~~~~~q~~~delr~~~~~~~~~~~~lk~~~~~~ 1571 (1738)
T KOG1140|consen 1512 PPFGA------------FLDP--------SSNSELEHLCTYLSLPNLQACLLQSSGDELRQAIERWCGGTENLKREEHYL 1571 (1738)
T ss_pred Cchhh------------ccCc--------ccchhhhhhcccccCccHHHHHHhhhHHHHHHHHHHhhccchHHHHHHhhc
Confidence 76210 1110 0124788899999999877644 33 678899999986422111111111
Q ss_pred cccccCCCCCccccCCchhHHHHHHHHhhcccCCCCCCC-CCceEeeccCccccCCCCcccC-------CCchhHhhhhc
Q 000142 1903 HVLYSTPAVPFKLMCLPHLYQDLLQRYIKQCCSDCKSVL-DEPALCLLCGRLCSPSWKPCCR-------ESSCQSHAVAC 1974 (2058)
Q Consensus 1903 ~~~~~~~~~~~~Li~LP~~y~~l~~~~~~~~C~~c~~~~-~~paiCL~CG~~~~~~~~~cc~-------~gec~~H~~~C 1974 (2058)
......|..+..|++||+.|+.+++++....|++|+..+ ..|++||+||..+|.+ ..||+ .|+|++|+..|
T Consensus 1572 ~~~~i~~r~~~~l~~lpd~~s~lI~s~~~~~c~~~~~~~s~~p~lCl~cg~~~~~q-~~~~~~~~~~~~~g~~~~ha~~c 1650 (1738)
T KOG1140|consen 1572 NTLSINPRIPNSLVELPDEYSCLINSASFFFCPKSGKDDSIIPALCLLCGSEECGQ-SGFDQEGSNGESVGACTAHAAEC 1650 (1738)
T ss_pred ceeeecCCCCCccccCCchhhhhHHhhhcccCcccCCccccCchHHhhcchHHhhh-hhhhhccccccchHHHHHhHHhh
Confidence 223344566789999999999999999999999999986 8999999999988876 57884 38999999999
Q ss_pred CCCeEEEEEecccEEEEEec--CCcccCCCCccccCCCCCcCcccCCCcccCHHHHHHHHHHHHcCCcCc
Q 000142 1975 GAGTGVFLLIRRTTILLQRC--ARQAPWPSPYLDAFGEEDIEMHRGKPLYLNEERYAALTYMVASHGLDR 2042 (2058)
Q Consensus 1975 g~~~GiFl~v~~~~ill~~~--~rg~~~~spYLD~~GE~D~~lrrg~pl~L~~~Ry~~L~~~w~~h~i~~ 2042 (2058)
|+++||||.+++|.++++.+ ++|||+|+||+|+|||+|+|+|||.|+|||++||+++..+|++|+|++
T Consensus 1651 ~~~vgifl~v~~c~~~ll~~m~~~g~~~~~pylD~~gEtd~gl~rg~P~~L~~~ry~k~~~~w~~~~I~e 1720 (1738)
T KOG1140|consen 1651 TGAVGIFLRVRECSILLLEGMRNRGCFYPAPYLDEYGETDPGLRRGNPLHLNRERYRKLKELWLQQNITE 1720 (1738)
T ss_pred cceeceEEeeechhhhhhhcCCcCCCcCCCCccccccCCChhhhcCCcccccHhhhhhhHHHHhhcchHH
Confidence 99999999999999999988 999999999999999999999999999999999999999999999987
No 2
>KOG1139 consensus Predicted ubiquitin-protein ligase of the N-recognin family [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=2.2e-32 Score=335.79 Aligned_cols=610 Identities=11% Similarity=-0.050 Sum_probs=422.9
Q ss_pred CCCCCCcCCCccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCCccccccccccccceecCCCCCcccCCC
Q 000142 1414 DGFGPIDCDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRINE 1493 (2058)
Q Consensus 1414 ~~F~~~~~~gvh~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKsL~Ns~LPilp~~~~~~~~ 1493 (2058)
++|.+..+.+.|.++|+|..|.+|..+|+.....+-..+-.+.+.|..+..+.++.||.|++++|+|.|..++++.....
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 55666667889999999999999999999999888777777888899999999999999999999999999765543222
Q ss_pred CCcccCCCCCCCCCCccccccchhhHHHHHHHHHhhhcccccccccccccCCcchhhHHH--HHHHHHHHHHHHHhhccc
Q 000142 1494 QPTVSGVGLSLDSSSSFTTREENTSFQLQQAVSLLQSASNVVGKADVIESFPLMKNEIMA--SNVEAVSRRMCKMYFQNK 1571 (2058)
Q Consensus 1494 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~s~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~~~l~~l~~~~~ 1571 (2058)
. ...+...+..+ ..-..++|+.+.+.....+.......+.....+|+.+.-.. ....++.++.+..+++..
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 01134556666554433322211000000111111111111 111122222222222111
Q ss_pred ccccc-CCCCCChhHHHHHHHhHhHHHHHHHhhccCCCCCCccchhhHHHhhhhchhHHHHHHHHHHhhhcccchHHHHH
Q 000142 1572 LDKFF-GSARVNPSLIMWDALKYSLMSMEIAARSEKTSTTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVLQ 1650 (2058)
Q Consensus 1572 ~~~~~-~~~~~~~~~~l~~tl~yTi~s~Eia~Rg~~~~~~~~~~l~~L~~~l~~~~~~~l~ll~~~~~~~r~~~~~~~l~ 1650 (2058)
...+- +--+...-..+|++++|...+.|+--|--+-+..++.|...+...+++..+.+++++...+...+..+.++.-+
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 00001123457999999999999999987777778888888889999999999999999999999999999999
Q ss_pred HhhccchhhhhccCCCCCCCCCCccCCCCcccccccccccccCcchhhhhhhcCCCccccChhhHHHHHHhhcccccccc
Q 000142 1651 RFRGIQLFAESICSGTSIDNPGGRCKRGGNMLSILKHADVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFILC 1730 (2058)
Q Consensus 1651 r~~~~~Ll~~si~~~~s~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~plL~~D~F~~Lv~~~~~lp~~~~~~ 1730 (2058)
++.++.=++.+++.+.++..++ .....+.....++ +..-.|+++..|++.+|||..+.+.++++|+++..+
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 000142 1731 KESLLSLVHVFYAVTLSQAVLSCCGKLQSKVNELGFSDSLISDISKLLGEFGSAQEYFVSNYIDPSCDIKDMIRRLSFPY 1810 (2058)
Q Consensus 1731 ~~~~~~iv~l~y~~~ivQ~li~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~s~~~d~~~~l~~~v~k~~lPF 1810 (2058)
..++...++.+--+..+|+++++...........++..... |+...+...+.+ .+|.+.+.+..+++.+.+.++-+||
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 000142 1811 LRRCALLWKLLNSTVPPPFSDRDHVLARSSHGISDMMDSSDDALSDLKEIQEVEKMFKIPSLDVILKDEVLRSLVLKWFH 1890 (2058)
Q Consensus 1811 LRr~aLL~~~l~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~~L~~~L~LPsl~~il~~~~~~~li~~W~~ 1890 (2058)
+|+|+.+++.+-..... .....+++..+..-++++|+........++--+.+...+.||.+.+.. ..-.+.|++
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 112223334445556677777666555554466778888899887543 234677999
Q ss_pred ccccchhhhccccccccCCCCCccccCCchhHHHHHHHHhhcccCCCCCCCCCceEeeccCccccCCCCcccCCCchhHh
Q 000142 1891 HFSKEFEVHRFQHVLYSTPAVPFKLMCLPHLYQDLLQRYIKQCCSDCKSVLDEPALCLLCGRLCSPSWKPCCRESSCQSH 1970 (2058)
Q Consensus 1891 h~~~~~~~~~~~~~~~~~~~~~~~Li~LP~~y~~l~~~~~~~~C~~c~~~~~~paiCL~CG~~~~~~~~~cc~~gec~~H 1970 (2058)
|+...++.++........++++|.+.++|.-|+.+..+..+. +..+++.|+.||..|..-+.|||.+.+ .+|
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 000142 1971 AVACGAGTGVFLLIRRTTILLQRCARQAPWPSPYLDAFGEEDIEMHRGKPLYLNEERYAALTYMVASHGLDRSSKVLSQT 2050 (2058)
Q Consensus 1971 ~~~Cg~~~GiFl~v~~~~ill~~~~rg~~~~spYLD~~GE~D~~lrrg~pl~L~~~Ry~~L~~~w~~h~i~~~~~~~~~~ 2050 (2058)
..+||+++|+|++|+++.|+.-+-.+..-||.||||..|++|.+.-||+.+|+++.||.+|....=+|++++.++++.+|
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 000142 2051 TIGGF 2055 (2058)
Q Consensus 2051 ~~~~~ 2055 (2058)
+|++.
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=99.83 E-value=2.3e-22 Score=269.86 Aligned_cols=934 Identities=17% Similarity=0.048 Sum_probs=574.0
Q ss_pred CCCChhhhhhhhccCCchhhhcchhhHHHhhhccCchHHHHHccCCCChHHHHHHHHHHhhcccCCCCCCh-h-hhHHHH
Q 000142 10 SPPKPRDRIRLMNIGVPEEFLDYSGIVNFAKNDKSRIPELVSTILPPDEEVAEVIQDAKAKNKKVSVGPNM-K-GRFRES 87 (2058)
Q Consensus 10 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~ 87 (2058)
+.+.|..|-++--.+|++++-.-.+++.|++..++.|...+.+-.|..+.+...+..+..+..++.+..++ + ..+.+.
T Consensus 526 qg~~~lkr~~~ehv~~e~~~~~~~~~v~~~t~~~s~i~~~~~~~ep~~~~~~~~l~~~~~r~~~s~~~~~~l~~~i~~~S 605 (1738)
T KOG1140|consen 526 QGVDPLKREELEHVEVEKEWENFFSLVEYLTAIYSMIQSLVKTSEPVKDSVYKKLLEAAIRIHPSLTGSESLTYTICGES 605 (1738)
T ss_pred CCccHHHHHHhhhhcccchHHHHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHhhcccccCccceeeehhhhhh
Confidence 44556666688889999977777799999999999999999999999999999998888888877655545 3 448888
Q ss_pred HHHHHHHhcCCCHHHHHHHHH--ccCCCCcccccccCCCeeEEeccCCCCCCccccccccCCCCCCCceeEEEecCCccc
Q 000142 88 MLWLQWLMFEREPEKVLRKLS--KIGQRGVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCC 165 (2058)
Q Consensus 88 ~~~l~~~~~~~~~~~~l~~l~--~~~~~~~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~~gG~C 165 (2058)
...+.|.++.+.+.-...-.. .-.-...|+.+|...+.+++|++|.- .+.+|..|++...|-.|-+..+-..+|+|
T Consensus 606 ~e~i~f~v~~~~~sv~~p~~~~l~~l~~~~~s~v~~~~d~~~~~~~~~n--~~~i~e~~lr~~Vl~aqid~~~w~rNG~s 683 (1738)
T KOG1140|consen 606 HETINFSVSQERVSVSNPVSRLLAFLIELSCSSVVSLKDAYERLEDCSN--FLAISEHSLRVLVLCAQIDVGFWVRNGFS 683 (1738)
T ss_pred HhHhhhccccccceeeccHHHHhhhhhhcccchhhhcchhhhhHhhhcc--chhhcccchhheeeeeecceeeEeecCcc
Confidence 888888877754432111111 01125889999999999999999986 99999999999999999988887889999
Q ss_pred cCCCcccccccCCCCcCCCCCCCCCCcHHHHhhhHHHHHHHHHHHHHHh--hhccccCCCCCCCCChHHHHHHHHHHHHH
Q 000142 166 DCGDVTAWKREGFCSRHKGAEQIQPLPEKYANSAAPVLDALFIYWENKL--SLAESVGQENPRASDHVAERRKLANELTF 243 (2058)
Q Consensus 166 DCGd~~awk~~~fC~~H~~~~~~~~lp~~l~~~~~~~~~~ll~~~~~~l--~~~e~~~~~~~~~~~~~~~~~k~a~~l~~ 243 (2058)
+|+ ..+|...++|..|....++-++-..++.. +..+.++.+|-... .|.. ...+....|...+..++++++..
T Consensus 684 i~~-q~~~y~~~~~r~~~y~~DI~~~Q~~la~~--d~~~~l~~~l~r~~L~~w~~--g~~~~~~~d~~~~i~~~~ee~l~ 758 (1738)
T KOG1140|consen 684 ILH-QAAYYKNNPCRNESYDRDILMLQTGLAME--DPNRFLFTILSRFELLDWFT--GEVDYQSNDTEDTISFMIEEFLA 758 (1738)
T ss_pred hhh-hhHhhcCccccccchhHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHhc--CCCccccccHHHHHHHHHHHHHH
Confidence 999 89999999999998775544433333322 33334433332211 1221 11233445666777788888887
Q ss_pred HHHHHHHHHHhchHHHHHHHHHHhhccchhHHHHHhhccCCCHHHHHHHHHHHHHhhCChhhHHHHHHHHHhhhHHHHHH
Q 000142 244 AVVEMLLEFCKNSESLLSFVSKRVISVIGLLDILVRAEMFSSDVVVRKLHELLLKLLGEPIFKYEFAKVFLSYYPVFVKD 323 (2058)
Q Consensus 244 ~i~~~l~e~~~~~~~ll~~l~~~l~~~~~ll~~l~~~~~~l~k~~r~~lh~L~lsLL~d~efK~~FA~~Fv~~Y~~i~~~ 323 (2058)
.|+.++.|+... .+..+....+...+++.+|......+.+.+++..|.+...+..|..++..++..+...|+...--
T Consensus 759 lii~ll~Er~~~---~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~~d~~~e~Va~~~~p~~~~~~gvf 835 (1738)
T KOG1140|consen 759 LIILLLTERSYF---GSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLSFDEALEEVAVFKKPKGLADNGVF 835 (1738)
T ss_pred HHHHHHHheeec---ccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhcccchHHHHHHHhhccCCccccceEE
Confidence 777777765543 11112122222335555566555556677888999999899999999999998888888554333
Q ss_pred HHHhccCcccccCCccceeeeeccccCCcHHHHHHhhcHHHHHHHHHHHHhhhhc--CCCCcceeccccccccchhhhhh
Q 000142 324 AIREHSDDTIKKYPLLSTFSVQIFTVPTLTPRLVKEMNLLEMLLGCLREIFDSCA--GDDSCLQVAKWANLYETTNRVIG 401 (2058)
Q Consensus 324 fl~~d~d~~~~~~s~v~~LSVQLFTvPsLA~~LV~e~nLL~iLl~tl~~~~~~~~--~~~~~l~~~~~~~~~~~y~~I~~ 401 (2058)
.+++.-++....|-...++|+|.-+++++++...++.+.+...+..+...+..++ ..++-+.............+.+.
T Consensus 836 ~lK~~~~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~~~~~L~~~t~~~~~~~ii~r~~~ 915 (1738)
T KOG1140|consen 836 VLKESYYDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKKGADILGAAVRLTVFGLIIYRTLE 915 (1738)
T ss_pred EechhhhhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3343333334455556688999999999999888877665444444444443333 12222222111111223345667
Q ss_pred hhhHhhcchhhhHHHhhhchHHHHHHHHHHHHhcCCC--cccccccCcceeeCCceeehh-hhhhHHHHhHhhhhhcccc
Q 000142 402 DIRFVMSHAAVSKYATHEQLNISKAWMKLLTFVQGMN--PQKRETGIHIREENEYMHLPL-VLDHSIANIQPLLVDGAFS 478 (2058)
Q Consensus 402 DLrylLsh~~v~~~l~~~~~~~~~~~l~lL~~~QGMn--~~kRq~~~HVEyE~e~w~~aF-~L~~~la~i~~~~~~~~~~ 478 (2058)
++++.+++--..+.+..-.-...+.++..+..++++. +..|++|--.-++.. ...++ ...+.+..++.++..+.++
T Consensus 916 ~~~~~~s~~~l~~~~~~ihG~~~~~~l~~~~~~~~~~~e~~~~e~gl~~~e~lv-~~~~~~~~~~~~~v~~~l~~~~~~~ 994 (1738)
T KOG1140|consen 916 HCLFMESSTLLSKVLHLIHGIALNEELINMKFAFTQKTESIAREKGLSLYESLV-RKPDSLVHGKIIEVIVELFESLIKS 994 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccchhhHHHhh-hcchhhcCCcceeeeHHHHhhhhhh
Confidence 7888888765555543334578899999999999999 999999977755544 43333 3447788888888888888
Q ss_pred cccccccc-cccccccccCCCCCccccccccccccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHH
Q 000142 479 SAVSEETR-YDFSMYKQDIGDGDSLRHAKVGRLSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECL 557 (2058)
Q Consensus 479 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~v~r~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~cl 557 (2058)
..++.|.. +..-|.+....+++..+.++.+|+..+..++...--+.-+..=+..+.+.+ +..+-+.|.+....+.++.
T Consensus 995 ~~n~~ea~~~~~~~~~~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e~-d~~~~~~~~~~~~~~~~~d 1073 (1738)
T KOG1140|consen 995 RANDPEVANDEKDKKEKQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDEF-DEQENQTPSSGSKTYEEED 1073 (1738)
T ss_pred hcCCccccccccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhccccc-CcccccCccccccchhhhh
Confidence 77776444 333333334446777777788888888877744432222222222222222 2444566666666777766
Q ss_pred HHHHhhhcCCCCcccccccCCCCcccccCchhhHhHhhhhhhcccccccccccCCccccccccccCCCccc-----cccC
Q 000142 558 RAMENWLGVDDRSVSVNDILSPNASRISGSNFVALKKTLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNA-----TSMG 632 (2058)
Q Consensus 558 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~ 632 (2058)
......++........ ...++. .+-++ ++.+-... .++-.+..+...+. +.+.
T Consensus 1074 ~~~~~~~~~s~~~~~~-~~~~~~----~~~~~----------~~~~i~~e-------~e~~~~~~~~~~v~~~f~~~s~~ 1131 (1738)
T KOG1140|consen 1074 FTCALCQDNSCTDFQV-KPASHL----VKPIF----------RECIICDE-------NEDVPNWDGRYSVSSAFAQKSDD 1131 (1738)
T ss_pred ccchhhhccchhcccc-ccchhh----hcccc----------cccccCCh-------hccCCCccccchhhhHhhhhccc
Confidence 6554443321110000 000000 00000 00000000 00000001000000 0000
Q ss_pred ccccccccCCcccccccccCcCCcccccccc-----------------ccccccc------cccCCccCceeeeccCCce
Q 000142 633 KESKITISGERDTASWRSAGFNDSEMEGECA-----------------TELDNLH------VLSLCYWPDITYDVSSQDV 689 (2058)
Q Consensus 633 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~l~------~~~~~~~~~v~fdVs~~~V 689 (2058)
..-.-+-|+...|| +....+||.- .+.-.|. .+...-|.-..++|+-..+
T Consensus 1132 ~sd~l~~p~~~~~~-------~~~s~c~h~mh~~c~~~~~~a~r~~~n~~~~~l~~~~se~~l~lCp~c~slsn~~lp~~ 1204 (1738)
T KOG1140|consen 1132 VSDALTEPGSLSCG-------TVLSSCGHHMHYGCFKRYVQAKRFRENARTAPLCQHYSENGLFLCPLCKSLSNVSLPMF 1204 (1738)
T ss_pred ccccccCCCCCccc-------ceeeccCCcchHHHHHHHHHHHHHHHHhhhcCcccccccCCcccCCchHhhhhccCCcC
Confidence 00011112222221 0011122210 0000000 0111112223467887889
Q ss_pred eeehHHHHHHHHHHHHHHhhhccccccccccccCCCCCccccchhhhhcccCCCCCcccchhhccccHHHHHHHHhHhcC
Q 000142 690 SVHIPLHRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFSAFVMEHPLRIRVFCAQVHAG 769 (2058)
Q Consensus 690 SfH~PLhr~Ls~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~pLR~~Vl~aQI~aG 769 (2058)
.-|.++++.++...+..+..+++.-...+...-........+...|.+.....+.|-++..+-..+...+.+++.+++++
T Consensus 1205 ~~~~~~~n~~t~~~~~n~~~~i~~rs~~~~s~~~vs~~~s~~~~~~~ss~i~e~kp~~~~~l~~~~~~~ie~~~k~v~s~ 1284 (1738)
T KOG1140|consen 1205 LPPELLLNPLTLENQRNLNSWIEKRSRASFSLQDVSSILSDPWAAFTSSRIPELKPILIMDLPDSVVEQIELFQKIVGSA 1284 (1738)
T ss_pred CchhhhcChhhhhchHHHHHHHHHhchhhcchhhhhhhhcccchhhccccccccccchHhhhhhHHHHHHHHHHHHHhhh
Confidence 99999999888877776655544100000000000000112222222211122223221122345667799999999999
Q ss_pred ceeeccHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccccCCCCCCCchh-HHHHHHHH
Q 000142 770 MWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLNLERPSEYEP-ILVQEMLT 848 (2058)
Q Consensus 770 mWvRNG~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~~~~~~~~~y~~-~mvEe~L~ 848 (2058)
||-- |. .. ...+-+..-+.+.|++|++.++.+.......++.+++...++.++......+.. ..+.. .
T Consensus 1285 ~~k~-~~------~i--~~~~le~~~~~~~~~~~~~~~~s~a~~~~~~~l~~~~~~~~l~l~~~~~~~~~~~~~l~~--~ 1353 (1738)
T KOG1140|consen 1285 MFKP-SS------LL--STNTLELTLFSREFLIVCWQSLSDAEQSTKLLLSASKKPSFLKLNEDMTFCLVTISRLRA--L 1353 (1738)
T ss_pred eeec-cc------ce--eecccccCcccchhhhhhhhccchHHHHHHHHHhccCCcccccCchhhHHHHHHHHHHHH--H
Confidence 9977 21 12 234667888899999999999999999999999999988887776433322322 22222 4
Q ss_pred HHHHhhcccccCCCChHHHHHHHHHHHHhcCCCChHHHHhhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEeehhhh
Q 000142 849 LIIQILQERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYW 928 (2058)
Q Consensus 849 lLI~llteR~~~g~s~~e~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~ 928 (2058)
..++++.++...++-.....+.++|-.+..++.+|+++...+|.+..+...++.++..|- +.|.+.-.+.+.++.-.|
T Consensus 1354 ~~~~~l~~~~~~~llk~~s~~~~~i~~~~tpd~~~~~ll~~l~~~~~~~~~l~~~~~~~~--~~~~~~~~~~i~~~~i~s 1431 (1738)
T KOG1140|consen 1354 HWEQILYELVYTFLLKSFSPTIPRISVLITPDQPENELLVILPHDFPKSLELELTLDFVN--KNPKKIFELKILMASIIS 1431 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHhhcCCcchhccCCCCCcchhhhccchhhhhhccHHHHHHHhh--hhHHHHHhHHHHHHHhhh
Confidence 567778888777776677778888888888899999999999999999999999999988 667777889999999999
Q ss_pred ccccccccccCchhHHHHHHHHHHhhcccccc--CCCCCCcccCCCccccccccCcHHHHHHHHHHHHHHhc
Q 000142 929 KELDIYHPRWSSRDLQVAEERYLRFCSVSALT--AQLPRWTKIYYPLESIAGIATCKVVLQVIRAVLFYAVF 998 (2058)
Q Consensus 929 ~e~dpy~~~y~~~~~q~aeer~~r~~~~~a~~--~~~P~~~~~~~p~~~i~~il~s~~~~~il~~vL~~al~ 998 (2058)
.|.+-++..+.. |.+.|+++..+..-..+.. ...+.++....+-.++.++--+....+.+...|.++..
T Consensus 1432 ~elits~s~l~~-d~~~~~~q~s~~e~~~~~t~l~~~~s~~~i~~~~~~~~~~~L~~~~~~~i~sfL~~~al 1502 (1738)
T KOG1140|consen 1432 IELITSHSYLEN-DLEMAEEQKSIDEFKSLLTYLLQLESSRTIPKLADIRLRLSLCLSCEAGILSFLRRAAL 1502 (1738)
T ss_pred hhhheeccccCC-ccchhhhhhhHHhHhHHHHHHHhccchhhCccccchhhhhHHHHHHHHHHHHHHHHHHH
Confidence 999888888776 8777777544322222222 23344444433334555566677777788777777643
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=1.6e-19 Score=170.74 Aligned_cols=70 Identities=44% Similarity=1.070 Sum_probs=66.3
Q ss_pred CcccccccCCCeeEEeccCCCCCCccccccccCCCCCCCceeEEEec-CCccccCCCcccccccCCCCcCC
Q 000142 114 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYT-GGGCCDCGDVTAWKREGFCSRHK 183 (2058)
Q Consensus 114 ~~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~-~gG~CDCGd~~awk~~~fC~~H~ 183 (2058)
.+|+++|++++++|+|+||+.++++++|.+||+++.|+||+|.+++. +||.|||||++|||+++||++|.
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=2.2e-18 Score=163.68 Aligned_cols=70 Identities=49% Similarity=1.112 Sum_probs=54.0
Q ss_pred CcccccccCCCeeEEeccCCCCCCccccccccCCCCCCCceeEEEecC-CccccCCCcccccccCCCCcCC
Q 000142 114 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTG-GGCCDCGDVTAWKREGFCSRHK 183 (2058)
Q Consensus 114 ~~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~~-gG~CDCGd~~awk~~~fC~~H~ 183 (2058)
+.|+++|.+++++|+|+||+.+++.+||.+||.++.|+||+|.+..+. +|+|||||+++||+++||++|+
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=99.02 E-value=3.3e-09 Score=133.27 Aligned_cols=185 Identities=22% Similarity=0.324 Sum_probs=141.5
Q ss_pred hccccHHHHHHHHhHhcCceeeccHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccccC
Q 000142 752 VMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLN 831 (2058)
Q Consensus 752 l~e~pLR~~Vl~aQI~aGmWvRNG~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~~~ 831 (2058)
+.-+++++.|--.-++..||+|+|.-...-+..|-+-.+-...---+--.+-.|+..+++..|+..++-+|.+.+.-..+
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 45667899999999999999999998877777775544433333333334556888999999999999999886542211
Q ss_pred C--------C-----C-------------------C--------------------------------------------
Q 000142 832 L--------E-----R-------------------P-------------------------------------------- 835 (2058)
Q Consensus 832 ~--------~-----~-------------------~-------------------------------------------- 835 (2058)
. . . +
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 000142 836 --SEYE--PILVQEMLTLIIQILQERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDL-SKFDQLQEILDAVAMY 910 (2058)
Q Consensus 836 --~~y~--~~mvEe~L~lLI~llteR~~~g~s~~e~lrrEIIh~Lc~~p~t~S~L~~~lpe~~-~~~~~fe~iL~eVA~f 910 (2058)
.+|+ +.|...++.++..+|.++.+.|...++..+-|+.|.-+++..+||-+..++.+.. ...+.|+.|+.+..+|
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 2567788899999999999999999999999999999999999999998877665 4577899999999999
Q ss_pred cCCCC----CCcceEEeehhhhc-ccccccc
Q 000142 911 SHPSG----FNQGMYSLRWSYWK-ELDIYHP 936 (2058)
Q Consensus 911 ~~P~g----~~~G~Y~LK~e~~~-e~dpy~~ 936 (2058)
-.|-- .-+|.|.||.-.|+ +.-|-++
T Consensus 447 ~~P~~~~~p~~~~s~~l~~~~~~~~~c~~~~ 477 (784)
T KOG1139|consen 447 IEPIETTTPLMQGSYQLKTSIWDSEVCPVFF 477 (784)
T ss_pred ccchhhcCccccchhhccccCCccccccchh
Confidence 99942 34799999999997 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=96.99 E-value=0.00048 Score=83.29 Aligned_cols=80 Identities=26% Similarity=0.419 Sum_probs=60.8
Q ss_pred HHHHHHHHHHhcCCCChHHHHhhCCCCCCC---cchHHHHHHHHccccCCCCCCcceEEeehhhhccccccccccCchhH
Q 000142 867 SLKRELVHRLAIGDATHSQLVKSLPRDLSK---FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 943 (2058)
Q Consensus 867 ~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~---~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dpy~~~y~~~~~ 943 (2058)
.+|.-|||+||.+|....||...|..+... -..++.||.+||... .++.|.||+.+|+|+|.=++.|+-.|+
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 000142 944 QVAEERYL 951 (2058)
Q Consensus 944 q~aeer~~ 951 (2058)
|..+-+..
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 88866543
No 8
>KOG1777 consensus Putative Zn-finger protein [General function prediction only]
Probab=94.89 E-value=0.01 Score=72.13 Aligned_cols=63 Identities=35% Similarity=0.587 Sum_probs=51.1
Q ss_pred ccCCCCccccccc-----CCCeeEEeccCCCCCCccccccccCCCCCCCceeEEEecCCccccCCCccc
Q 000142 109 KIGQRGVCGAVWG-----NNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDVTA 172 (2058)
Q Consensus 109 ~~~~~~~C~~v~~-----~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~~gG~CDCGd~~a 172 (2058)
+.-+.++|-.... +=.-+|||-||...+.-+||..|.++ -|+||++-..+...-.||||-..+
T Consensus 539 kAik~GqCLfkvSs~~syPMHnFYRC~TCNttdRNAIC~nCI~~-CH~GH~Vefir~Drffcdcgagtl 606 (625)
T KOG1777|consen 539 KAIKKGQCLFKVSSYTSYPMHNFYRCITCNTTDRNAICVNCIKR-CHEGHDVEFIRHDRFFCDCGAGTL 606 (625)
T ss_pred HHhhcCceEEEecCCCcccccceeEeeecCCccccHHHHHHHHH-hcCCCceEEEeeceEEEecCCcee
Confidence 3455677754433 33468999999999999999999988 599999999998889999997554
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=91.26 E-value=0.064 Score=46.50 Aligned_cols=20 Identities=25% Similarity=0.790 Sum_probs=16.5
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000142 1425 HLSSCGHAVHQGCLDRYVSS 1444 (2058)
Q Consensus 1425 h~ssCGH~MH~~C~~~Y~~S 1444 (2058)
..-.|||..|.+|++.|++.
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=91.14 E-value=0.17 Score=42.93 Aligned_cols=19 Identities=37% Similarity=1.001 Sum_probs=16.3
Q ss_pred ccccChHhhHHHHHHHHHH
Q 000142 1426 LSSCGHAVHQGCLDRYVSS 1444 (2058)
Q Consensus 1426 ~ssCGH~MH~~C~~~Y~~S 1444 (2058)
+..|||..|..|+++|++.
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=89.60 E-value=0.11 Score=69.18 Aligned_cols=63 Identities=27% Similarity=0.695 Sum_probs=50.9
Q ss_pred CcccccccCCC----eeEEeccCCCCCCccccccccCCCCCCCceeEEEe-cCCccccCCCcccccc-cCCCCcC
Q 000142 114 GVCGAVWGNND----IAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVTAWKR-EGFCSRH 182 (2058)
Q Consensus 114 ~~C~~v~~~ge----~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~-~~gG~CDCGd~~awk~-~~fC~~H 182 (2058)
..|.-.|+..+ -+|.|+||+.-.+-+-|.+|-.- .|+||+.++-+ +.-++||| |-+ +..|+.-
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 57899999 655 4556554
No 12
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=88.02 E-value=0.16 Score=59.72 Aligned_cols=48 Identities=35% Similarity=0.749 Sum_probs=34.2
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhccc---ccCCCcccCCCCCccccccccc
Q 000142 1426 LSSCGHAVHQGCLDRYVSSLKERYNRRI---IFEGGHIVDPDQGEFLCPVCRQ 1475 (2058)
Q Consensus 1426 ~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~---~~~r~h~~d~e~gEFLCPLCKs 1475 (2058)
...|-|.||+.|+.+|+...+...++.. .-++.|. .+.-|=+||+||-
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 13
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=87.69 E-value=2.1 Score=58.75 Aligned_cols=70 Identities=19% Similarity=0.225 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-H--HhhccccccCCCCCCCccCCCCcccccccccCCccccccCCCC---CCCeE
Q 000142 1144 SEKRKAKARERQAAILEKMKAEQFK-F--LSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS---RTPVS 1217 (2058)
Q Consensus 1144 ~ekkK~~AkeRQakIMaqf~~qQ~~-F--l~~n~~~~d~~~~~~~~~~~s~~~~~~~e~~~~~CilCqe~~~---~~p~g 1217 (2058)
+.+||++|.++|+|.+.+|.-++.+ - +.+..... +. ++.++|. --.|.+|+|.-+ ++++|
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 56899
Q ss_pred EEeeeecccc
Q 000142 1218 YLILLQKSRL 1227 (2058)
Q Consensus 1218 ~la~iq~S~l 1227 (2058)
+-+|.-+-.+
T Consensus 488 iY~f~kr~~l 497 (802)
T PF13764_consen 488 IYAFSKRVNL 497 (802)
T ss_pred eEEEeecccc
Confidence 9887755544
No 14
>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=85.05 E-value=0.7 Score=41.34 Aligned_cols=39 Identities=28% Similarity=0.878 Sum_probs=29.6
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCC----CCC-CceeEE
Q 000142 115 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG----NHK-EHDYSI 157 (2058)
Q Consensus 115 ~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~----~H~-~H~~~~ 157 (2058)
.|++.... ..-|+|..|. ..-+|.+||..+ .|+ .|.|.+
T Consensus 5 ~C~~~~~~-g~r~~C~~C~---d~dLC~~Cf~~g~~~~~H~~~H~~~~ 48 (49)
T cd02335 5 YCSKDITG-TIRIKCAECP---DFDLCLECFSAGAEIGKHRNDHNYRV 48 (49)
T ss_pred CcCCCCCC-CcEEECCCCC---CcchhHHhhhCcCCCCCCCCCCCeEe
Confidence 57777764 4899999995 466999999998 453 677765
No 15
>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=85.01 E-value=0.71 Score=40.17 Aligned_cols=37 Identities=27% Similarity=0.654 Sum_probs=29.5
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000142 115 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 156 (2058)
Q Consensus 115 ~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 156 (2058)
.|+..+ .| .-|+|.+|. ..-+|.+||.++.|.+|.+.
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 34 789999996 46799999999999888874
No 16
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=84.15 E-value=1 Score=57.24 Aligned_cols=77 Identities=26% Similarity=0.375 Sum_probs=63.4
Q ss_pred HHHHHHHHHHhcCCCChHHHHhhCCCCCCCc---chHHHHHHHHccccCCCCCCcceEEeehhhhccccccccccCchhH
Q 000142 867 SLKRELVHRLAIGDATHSQLVKSLPRDLSKF---DQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 943 (2058)
Q Consensus 867 ~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~~---~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dpy~~~y~~~~~ 943 (2058)
-||..|||+|+.++..--||.++|-.+...+ ..+..||.+.. ...+|+|.|++.+|+|+|-=++.|+-.|.
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 000142 944 QVAEER 949 (2058)
Q Consensus 944 q~aeer 949 (2058)
|..+-+
T Consensus 285 ~~lkr~ 290 (604)
T KOG4796|consen 285 QHLKRV 290 (604)
T ss_pred HHHHHH
Confidence 776544
No 17
>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=83.89 E-value=0.78 Score=40.42 Aligned_cols=37 Identities=27% Similarity=0.812 Sum_probs=29.2
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCC--CCC-CceeE
Q 000142 115 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG--NHK-EHDYS 156 (2058)
Q Consensus 115 ~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~--~H~-~H~~~ 156 (2058)
.|++.+. | .-|+|.+|. ..-+|.+||..+ .|. +|.+.
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 5788443 5 899999996 577999999998 776 77764
No 18
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=83.10 E-value=0.72 Score=39.19 Aligned_cols=20 Identities=30% Similarity=0.843 Sum_probs=18.4
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000142 1425 HLSSCGHAVHQGCLDRYVSS 1444 (2058)
Q Consensus 1425 h~ssCGH~MH~~C~~~Y~~S 1444 (2058)
.+..|||..+..|+.+|+++
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 37899999999999999888
No 19
>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=82.09 E-value=1.1 Score=39.36 Aligned_cols=39 Identities=26% Similarity=0.695 Sum_probs=30.4
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCCC-CCceeEE
Q 000142 115 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYSI 157 (2058)
Q Consensus 115 ~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H-~~H~~~~ 157 (2058)
.|+..--.| .-|+|.+|. ..-+|..||....| .+|.|..
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 466544445 889999997 46699999999999 5898753
No 20
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=81.68 E-value=0.91 Score=45.08 Aligned_cols=24 Identities=21% Similarity=0.508 Sum_probs=19.6
Q ss_pred CCCccccccChHhhHHHHHHHHHH
Q 000142 1421 CDGIHLSSCGHAVHQGCLDRYVSS 1444 (2058)
Q Consensus 1421 ~~gvh~ssCGH~MH~~C~~~Y~~S 1444 (2058)
..++=...|||.-|..|..+.+++
T Consensus 44 ~Cplv~g~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 44 DCPLVWGKCSHNFHMHCILKWLST 67 (85)
T ss_pred CCceeeccCccHHHHHHHHHHHcc
Confidence 344447789999999999999876
No 21
>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=80.77 E-value=1.3 Score=35.99 Aligned_cols=18 Identities=22% Similarity=0.892 Sum_probs=16.3
Q ss_pred ccccChHhhHHHHHHHHH
Q 000142 1426 LSSCGHAVHQGCLDRYVS 1443 (2058)
Q Consensus 1426 ~ssCGH~MH~~C~~~Y~~ 1443 (2058)
...|||..|..|+++|++
T Consensus 13 ~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 13 VLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred EecCCChHHHHHHHHHHH
Confidence 567999999999999977
No 22
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=80.44 E-value=1.5 Score=38.25 Aligned_cols=31 Identities=35% Similarity=0.864 Sum_probs=25.0
Q ss_pred CccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCCccccccccc
Q 000142 1423 GIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1475 (2058)
Q Consensus 1423 gvh~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKs 1475 (2058)
...+.+|||.+..+|.++-. .+...||+|++
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 23
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=80.19 E-value=1.3 Score=39.64 Aligned_cols=38 Identities=26% Similarity=0.792 Sum_probs=28.8
Q ss_pred ccc-ccccCCCeeEEeccCCCCCCccccccccCCC----CCC-CceeEE
Q 000142 115 VCG-AVWGNNDIAYRCRTCEHDPTCAICVPCFQNG----NHK-EHDYSI 157 (2058)
Q Consensus 115 ~C~-~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~----~H~-~H~~~~ 157 (2058)
.|+ ..+. ..-|+|..|. ..-+|.+||..+ .|+ .|.+.+
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 3444 4889999994 577999999988 676 777754
No 24
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=79.53 E-value=1.2 Score=51.63 Aligned_cols=62 Identities=23% Similarity=0.212 Sum_probs=46.2
Q ss_pred HHHHHHHHHH--hcCCCChHHHHhhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEeehhhhc
Q 000142 867 SLKRELVHRL--AIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWK 929 (2058)
Q Consensus 867 ~lrrEIIh~L--c~~p~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~ 929 (2058)
.=|+||+-.| ||.-..|=-|...+-..-+...-+.+||++||+|-+ .|..+|+|+|||||-+
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 3577888887 787777666655443334445568999999999975 3667899999999864
No 25
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=75.61 E-value=3.4 Score=49.66 Aligned_cols=61 Identities=25% Similarity=0.597 Sum_probs=47.3
Q ss_pred cCCCCcccccc--cCCCeeEEeccCCCCC-CccccccccCCCCCCCceeEEEe-cCCccccCCCcc
Q 000142 110 IGQRGVCGAVW--GNNDIAYRCRTCEHDP-TCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVT 171 (2058)
Q Consensus 110 ~~~~~~C~~v~--~~ge~~y~C~~C~~d~-t~~lC~~CF~~~~H~~H~~~~~~-~~gG~CDCGd~~ 171 (2058)
...+..|++.- ++-...|.|.||..++ ...+|..|=.. -|.||.-..-. .+..-||||+.-
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 35567787543 3336889999999998 88899999775 69999987655 567889999853
No 26
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=74.70 E-value=1.4 Score=53.53 Aligned_cols=16 Identities=38% Similarity=1.059 Sum_probs=14.7
Q ss_pred ccChHhhHHHHHHHHH
Q 000142 1428 SCGHAVHQGCLDRYVS 1443 (2058)
Q Consensus 1428 sCGH~MH~~C~~~Y~~ 1443 (2058)
.|||..|++|+++.++
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=74.39 E-value=1.7 Score=37.22 Aligned_cols=37 Identities=24% Similarity=0.595 Sum_probs=27.8
Q ss_pred CcccccccCCCeeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000142 114 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 156 (2058)
Q Consensus 114 ~~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 156 (2058)
..|..--+ ....|.|.+|.. .+|.+|+..+ |++|++.
T Consensus 4 ~~C~~H~~-~~~~~~C~~C~~----~~C~~C~~~~-H~~H~~~ 40 (42)
T PF00643_consen 4 PKCPEHPE-EPLSLFCEDCNE----PLCSECTVSG-HKGHKIV 40 (42)
T ss_dssp SB-SSTTT-SBEEEEETTTTE----EEEHHHHHTS-TTTSEEE
T ss_pred ccCccCCc-cceEEEecCCCC----ccCccCCCCC-CCCCEEe
Confidence 45533322 348999999986 7999999998 9999975
No 28
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=73.48 E-value=0.99 Score=43.49 Aligned_cols=38 Identities=39% Similarity=0.755 Sum_probs=21.0
Q ss_pred cccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCCccccccccc
Q 000142 1427 SSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1475 (2058)
Q Consensus 1427 ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKs 1475 (2058)
..||+..|..|+.+||.++... |. .+++-.|+ ||.|+.
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 23455566 999986
No 29
>PHA02926 zinc finger-like protein; Provisional
Probab=73.00 E-value=2.7 Score=48.50 Aligned_cols=46 Identities=24% Similarity=0.532 Sum_probs=35.1
Q ss_pred CCCccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCCccccccccccccceecC
Q 000142 1421 CDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPA 1483 (2058)
Q Consensus 1421 ~~gvh~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKsL~Ns~LPi 1483 (2058)
.+|+ ++.|||.-.+.|..+..++-+ + ..++-.||+||.-...|.|-
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 999999999999999765311 0 12566899999998877764
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=72.49 E-value=1.7 Score=45.38 Aligned_cols=27 Identities=30% Similarity=0.790 Sum_probs=22.6
Q ss_pred hhcccCCCCCC----CCCceEeeccCccccC
Q 000142 1930 IKQCCSDCKSV----LDEPALCLLCGRLCSP 1956 (2058)
Q Consensus 1930 ~~~~C~~c~~~----~~~paiCL~CG~~~~~ 1956 (2058)
.+|.||+||+. .++|++|-.||+..-.
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=68.61 E-value=3.9 Score=46.77 Aligned_cols=53 Identities=21% Similarity=0.517 Sum_probs=35.1
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCCccccccccccc--cceecCC
Q 000142 1426 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLA--NSVLPAL 1484 (2058)
Q Consensus 1426 ~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKsL~--Ns~LPil 1484 (2058)
+..|||.-...|..+|+..-.. .++ +....+-.++...||+||+-- +.++|+.
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=68.03 E-value=3.5 Score=36.33 Aligned_cols=30 Identities=27% Similarity=0.907 Sum_probs=24.8
Q ss_pred CeeEEeccCCCCCCccccccccCCCCC-CCceeE
Q 000142 124 DIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYS 156 (2058)
Q Consensus 124 e~~y~C~~C~~d~t~~lC~~CF~~~~H-~~H~~~ 156 (2058)
..-|+|.+|. ..-||.+||..+.| .+|.|.
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 5679999995 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=63.81 E-value=3.4 Score=43.87 Aligned_cols=27 Identities=26% Similarity=0.431 Sum_probs=22.6
Q ss_pred hhcccCCCCCC----CCCceEeeccCccccC
Q 000142 1930 IKQCCSDCKSV----LDEPALCLLCGRLCSP 1956 (2058)
Q Consensus 1930 ~~~~C~~c~~~----~~~paiCL~CG~~~~~ 1956 (2058)
.+|.||+|++. .++|++|-.||+..-.
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=61.62 E-value=4.1 Score=49.15 Aligned_cols=35 Identities=26% Similarity=0.866 Sum_probs=27.2
Q ss_pred ccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCCccccccccccccce
Q 000142 1424 IHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSV 1480 (2058)
Q Consensus 1424 vh~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKsL~Ns~ 1480 (2058)
++.-.|||.||+.||+.|.. .+ |-||+|..++|+.
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
>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=58.65 E-value=5.7 Score=35.53 Aligned_cols=35 Identities=29% Similarity=0.691 Sum_probs=27.0
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCCCC-Cce
Q 000142 115 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK-EHD 154 (2058)
Q Consensus 115 ~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~-~H~ 154 (2058)
.|++... ..-|+|..|. ..-+|.+||..+.+. +|+
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 4799999996 477999999998874 454
No 36
>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=57.66 E-value=2.5 Score=41.05 Aligned_cols=17 Identities=29% Similarity=0.935 Sum_probs=15.1
Q ss_pred ccccChHhhHHHHHHHH
Q 000142 1426 LSSCGHAVHQGCLDRYV 1442 (2058)
Q Consensus 1426 ~ssCGH~MH~~C~~~Y~ 1442 (2058)
...|||+-|..|..+.+
T Consensus 47 ~~~C~H~FH~~Ci~~Wl 63 (73)
T PF12678_consen 47 WGPCGHIFHFHCISQWL 63 (73)
T ss_dssp EETTSEEEEHHHHHHHH
T ss_pred ecccCCCEEHHHHHHHH
Confidence 67799999999998776
No 37
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=56.80 E-value=7.4 Score=34.86 Aligned_cols=40 Identities=25% Similarity=0.622 Sum_probs=27.5
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCC-CC-CCceeE
Q 000142 115 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG-NH-KEHDYS 156 (2058)
Q Consensus 115 ~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~-~H-~~H~~~ 156 (2058)
.|+..--. ..-|+|.+|.- ...-+|.+||.++ .| .+|.+.
T Consensus 5 ~C~~~pI~-G~R~~C~~C~~-~d~DlC~~C~~~~~~H~~~H~~~ 46 (48)
T cd02341 5 SCGIEPIP-GTRYHCSECDD-GDFDLCQDCVVKGESHQEDHWLV 46 (48)
T ss_pred CCCCCccc-cceEECCCCCC-CCCccCHHHHhCcCCCCCCCcee
Confidence 46652222 56799999963 2466999999999 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=55.66 E-value=4.1 Score=35.95 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=21.3
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCCC
Q 000142 115 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 150 (2058)
Q Consensus 115 ~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H 150 (2058)
.||.-.. .+-|+|..+. ...||.+||..|.-
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 4666655 4677776654 46699999988753
No 39
>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=53.55 E-value=7.6 Score=33.62 Aligned_cols=32 Identities=25% Similarity=0.824 Sum_probs=25.0
Q ss_pred CcccccccCCCeeEEeccCCCCCCccccccccCCCCCC
Q 000142 114 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 151 (2058)
Q Consensus 114 ~~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~ 151 (2058)
..|+++ +++-|+|..|. -.-+|..||....|.
T Consensus 4 ~~C~~~---~~~r~~C~~C~---dfDLC~~C~~~~~H~ 35 (41)
T cd02337 4 NECKHH---VETRWHCTVCE---DYDLCITCYNTKNHP 35 (41)
T ss_pred CCCCCc---CCCceECCCCc---chhhHHHHhCCCCCC
Confidence 357663 34999999996 366999999998883
No 40
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=53.53 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 000142 1929 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1956 (2058)
Q Consensus 1929 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1956 (2058)
+.+.+||.|++. +...+-|+.||+.++.
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=53.14 E-value=10 Score=31.66 Aligned_cols=28 Identities=25% Similarity=0.451 Sum_probs=23.2
Q ss_pred CeeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000142 124 DIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 156 (2058)
Q Consensus 124 e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 156 (2058)
...|-|.+|+. .+|..|-..+ |++|.+.
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 45778998865 7999999888 9999975
No 42
>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=52.61 E-value=9.4 Score=34.36 Aligned_cols=32 Identities=28% Similarity=0.742 Sum_probs=24.4
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCCC
Q 000142 115 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 150 (2058)
Q Consensus 115 ~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H 150 (2058)
.|++.--.| .-|+|..|. ..-||.+||..+.|
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 577653334 789999996 46799999988865
No 43
>PHA02929 N1R/p28-like protein; Provisional
Probab=52.55 E-value=6.8 Score=46.57 Aligned_cols=35 Identities=37% Similarity=0.745 Sum_probs=26.2
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCCccccccccccccceec
Q 000142 1426 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLP 1482 (2058)
Q Consensus 1426 ~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKsL~Ns~LP 1482 (2058)
+..|||..|..|....++. + . .||+||.---.|+|
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 44
>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=52.52 E-value=6.1 Score=33.42 Aligned_cols=20 Identities=25% Similarity=0.933 Sum_probs=17.9
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000142 1425 HLSSCGHAVHQGCLDRYVSS 1444 (2058)
Q Consensus 1425 h~ssCGH~MH~~C~~~Y~~S 1444 (2058)
.+..|||....+|+++|++.
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 45
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=49.36 E-value=7.8 Score=30.26 Aligned_cols=22 Identities=23% Similarity=0.717 Sum_probs=18.9
Q ss_pred cccCCCCCC-CCCceEeeccCcc
Q 000142 1932 QCCSDCKSV-LDEPALCLLCGRL 1953 (2058)
Q Consensus 1932 ~~C~~c~~~-~~~paiCL~CG~~ 1953 (2058)
++||.|+.. |..-..|-.||-.
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 46
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=48.70 E-value=6.5 Score=48.01 Aligned_cols=31 Identities=29% Similarity=0.463 Sum_probs=16.1
Q ss_pred cchHHHHHHHHccccCCCCCCcceEEeehhhh
Q 000142 897 FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYW 928 (2058)
Q Consensus 897 ~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~ 928 (2058)
+.-+-+||++||+|.+ +|...|+|+|||||-
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 4568899999999986 366789999999984
No 47
>smart00336 BBOX B-Box-type zinc finger.
Probab=47.85 E-value=15 Score=31.18 Aligned_cols=29 Identities=21% Similarity=0.636 Sum_probs=23.5
Q ss_pred CCeeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000142 123 NDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 156 (2058)
Q Consensus 123 ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 156 (2058)
....|-|.+|+. ++|..|... .|++|.+.
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 48
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.36 E-value=13 Score=46.13 Aligned_cols=30 Identities=30% Similarity=0.601 Sum_probs=22.5
Q ss_pred CCCCCCcCCCccccccChHhhHHHHHHHHHH
Q 000142 1414 DGFGPIDCDGIHLSSCGHAVHQGCLDRYVSS 1444 (2058)
Q Consensus 1414 ~~F~~~~~~gvh~ssCGH~MH~~C~~~Y~~S 1444 (2058)
++|+.+...|. +++|||+.|..|....|+-
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 49
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=46.94 E-value=10 Score=28.78 Aligned_cols=20 Identities=30% Similarity=0.896 Sum_probs=17.5
Q ss_pred ccCCCCCC-CCCceEeeccCc
Q 000142 1933 CCSDCKSV-LDEPALCLLCGR 1952 (2058)
Q Consensus 1933 ~C~~c~~~-~~~paiCL~CG~ 1952 (2058)
.||+||.. +.+...|--||+
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
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.65 E-value=12 Score=47.49 Aligned_cols=29 Identities=41% Similarity=1.065 Sum_probs=25.1
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCCccccccccc
Q 000142 1426 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1475 (2058)
Q Consensus 1426 ~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKs 1475 (2058)
++-|-|++|-.|+++.|+.-+ ..||+||+
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 51
>PLN00209 ribosomal protein S27; Provisional
Probab=44.97 E-value=7.6 Score=38.57 Aligned_cols=38 Identities=16% Similarity=0.510 Sum_probs=30.5
Q ss_pred cccCCchhHHHHHHHHhhcccCCCCCC------CCCceEeeccCccccCC
Q 000142 1914 KLMCLPHLYQDLLQRYIKQCCSDCKSV------LDEPALCLLCGRLCSPS 1957 (2058)
Q Consensus 1914 ~Li~LP~~y~~l~~~~~~~~C~~c~~~------~~~paiCL~CG~~~~~~ 1957 (2058)
+||+=|+.| +...+||.|++. ...++.|..||++++.-
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
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=43.69 E-value=8.4 Score=38.22 Aligned_cols=38 Identities=21% Similarity=0.529 Sum_probs=30.6
Q ss_pred cccCCchhHHHHHHHHhhcccCCCCCC------CCCceEeeccCccccCC
Q 000142 1914 KLMCLPHLYQDLLQRYIKQCCSDCKSV------LDEPALCLLCGRLCSPS 1957 (2058)
Q Consensus 1914 ~Li~LP~~y~~l~~~~~~~~C~~c~~~------~~~paiCL~CG~~~~~~ 1957 (2058)
+||+=|+.| +...+|+.|++. ...++.|..||+++|.-
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 53
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=43.34 E-value=11 Score=29.20 Aligned_cols=22 Identities=23% Similarity=0.708 Sum_probs=19.0
Q ss_pred hcccCCCCCC-CCCceEeeccCc
Q 000142 1931 KQCCSDCKSV-LDEPALCLLCGR 1952 (2058)
Q Consensus 1931 ~~~C~~c~~~-~~~paiCL~CG~ 1952 (2058)
.+.||+|+.. +.+-..|-.||+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 4679999998 788899999997
No 54
>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=43.01 E-value=15 Score=32.79 Aligned_cols=18 Identities=33% Similarity=0.824 Sum_probs=16.5
Q ss_pred ccccChH-hhHHHHHHHHH
Q 000142 1426 LSSCGHA-VHQGCLDRYVS 1443 (2058)
Q Consensus 1426 ~ssCGH~-MH~~C~~~Y~~ 1443 (2058)
+.-|||. +-..|+.++++
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 55
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=40.76 E-value=9.2 Score=35.01 Aligned_cols=45 Identities=27% Similarity=0.628 Sum_probs=34.3
Q ss_pred HhhcccCCCCCC---CCCceEeeccCccccCCCCccc-CCCchhHhhhhcCCCe
Q 000142 1929 YIKQCCSDCKSV---LDEPALCLLCGRLCSPSWKPCC-RESSCQSHAVACGAGT 1978 (2058)
Q Consensus 1929 ~~~~~C~~c~~~---~~~paiCL~CG~~~~~~~~~cc-~~gec~~H~~~Cg~~~ 1978 (2058)
+...+|+.|++. ..|.++|--||+.-.- .|. ..|+|..+. ||++.
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 56
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=40.33 E-value=21 Score=31.32 Aligned_cols=33 Identities=27% Similarity=0.801 Sum_probs=25.0
Q ss_pred CcccccccCCCeeEEeccCCCCCCccccccccCCCCCC
Q 000142 114 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 151 (2058)
Q Consensus 114 ~~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~ 151 (2058)
..|++.+. ..-|+|..|. ..-||.+||..+.|.
T Consensus 8 ~~C~~~i~--g~ry~C~~C~---d~dlC~~Cf~~~~~~ 40 (44)
T smart00291 8 DTCGKPIV--GVRYHCLVCP---DYDLCQSCFAKGSAG 40 (44)
T ss_pred CCCCCCCc--CCEEECCCCC---CccchHHHHhCcCcC
Confidence 46888543 4578999993 577999999988664
No 57
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=39.90 E-value=14 Score=33.64 Aligned_cols=15 Identities=40% Similarity=0.753 Sum_probs=10.9
Q ss_pred ccccChH-hhHHHHHH
Q 000142 1426 LSSCGHA-VHQGCLDR 1440 (2058)
Q Consensus 1426 ~ssCGH~-MH~~C~~~ 1440 (2058)
+-+|||+ |-++|--+
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=38.96 E-value=12 Score=34.81 Aligned_cols=28 Identities=29% Similarity=0.762 Sum_probs=23.6
Q ss_pred HhhcccCCCCCC------CCCceEeeccCccccC
Q 000142 1929 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1956 (2058)
Q Consensus 1929 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1956 (2058)
+.+.+||.|++. +..++.|..||+.++.
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 6789999999998776
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=38.73 E-value=11 Score=34.79 Aligned_cols=28 Identities=18% Similarity=0.705 Sum_probs=19.1
Q ss_pred HhhcccCCCCCC------CCCceEeeccCccccC
Q 000142 1929 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1956 (2058)
Q Consensus 1929 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1956 (2058)
+...+||.|++. ...++.|..||+++|.
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
>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=38.37 E-value=22 Score=32.04 Aligned_cols=31 Identities=23% Similarity=0.842 Sum_probs=24.1
Q ss_pred Ccccc-cccCCCeeEEeccCCCCCCccccccccCCCC
Q 000142 114 GVCGA-VWGNNDIAYRCRTCEHDPTCAICVPCFQNGN 149 (2058)
Q Consensus 114 ~~C~~-v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~ 149 (2058)
..|.+ -+. ++-|+|..|. .--+|.+||..+.
T Consensus 4 ~~C~~~~i~--g~R~~C~~C~---dydLC~~Cf~~~~ 35 (49)
T cd02345 4 SACRKQDIS--GIRFPCQVCR---DYSLCLGCYTKGR 35 (49)
T ss_pred CCCCCCCce--EeeEECCCCC---CcCchHHHHhCCC
Confidence 35777 555 4889999994 5779999999774
No 61
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.48 E-value=16 Score=49.49 Aligned_cols=23 Identities=48% Similarity=1.025 Sum_probs=20.7
Q ss_pred ccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCCccccccccc
Q 000142 1428 SCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1475 (2058)
Q Consensus 1428 sCGH~MH~~C~~~Y~~Sl~~r~~~r~~~~r~h~~d~e~gEFLCPLCKs 1475 (2058)
.|||..|+.|++ .+|+-||-|+.
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 62
>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=35.71 E-value=10 Score=33.50 Aligned_cols=36 Identities=28% Similarity=0.712 Sum_probs=22.5
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCC-CCCce
Q 000142 115 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN-HKEHD 154 (2058)
Q Consensus 115 ~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~-H~~H~ 154 (2058)
.|+..--.| .-|+|..|. ..-||.+||..+. +.+|+
T Consensus 9 ~C~~~~i~g-~Ry~C~~C~---d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 9 GCGTDPIIG-VRYHCLVCP---DYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SS-SSSEES-SEEEESSSS---S-EEEHHHHHH--H-SSSS
T ss_pred CCCCCcCcC-CeEECCCCC---CCchhhHHHhCcCCCCCcC
Confidence 466632223 679999994 5779999999964 45664
No 63
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=34.94 E-value=40 Score=33.19 Aligned_cols=26 Identities=27% Similarity=0.542 Sum_probs=21.3
Q ss_pred CcCCCccccccChHhhHHHHHHHHHH
Q 000142 1419 IDCDGIHLSSCGHAVHQGCLDRYVSS 1444 (2058)
Q Consensus 1419 ~~~~gvh~ssCGH~MH~~C~~~Y~~S 1444 (2058)
.+.+.+--+.|-|+-|..|-.+.+++
T Consensus 44 ~~eC~v~wG~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 44 GDECPVVWGVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred CCcceEEEEecchHHHHHHHHHHHhh
Confidence 34455557889999999999999987
No 64
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=32.29 E-value=33 Score=43.58 Aligned_cols=43 Identities=33% Similarity=0.791 Sum_probs=30.4
Q ss_pred cccccccCCCeeEEeccCCCCCCccccccccCCCC----C-CCceeEEEecC
Q 000142 115 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN----H-KEHDYSIIYTG 161 (2058)
Q Consensus 115 ~C~~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~----H-~~H~~~~~~~~ 161 (2058)
.|..-.. |-+-.+|-.| |..-||..||..|. | .+|.|.++.++
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 58999998764
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=31.10 E-value=36 Score=37.88 Aligned_cols=44 Identities=23% Similarity=0.479 Sum_probs=26.6
Q ss_pred hhHHHHHHHHHHHHHhhhcccc-c-----C---CCcccCCCCCcccccccccc
Q 000142 1433 VHQGCLDRYVSSLKERYNRRII-F-----E---GGHIVDPDQGEFLCPVCRQL 1476 (2058)
Q Consensus 1433 MH~~C~~~Y~~Sl~~r~~~r~~-~-----~---r~h~~d~e~gEFLCPLCKsL 1476 (2058)
-|-+|+++|-++-......... . . ..+....+..+..|||||.=
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=24.99 E-value=57 Score=30.76 Aligned_cols=51 Identities=24% Similarity=0.420 Sum_probs=31.9
Q ss_pred cCCCCCCCCCceEeeccCccccCCCCcccCCCchhHhhhhcCCCeEEEEEecccEEE
Q 000142 1934 CSDCKSVLDEPALCLLCGRLCSPSWKPCCRESSCQSHAVACGAGTGVFLLIRRTTIL 1990 (2058)
Q Consensus 1934 C~~c~~~~~~paiCL~CG~~~~~~~~~cc~~gec~~H~~~Cg~~~GiFl~v~~~~il 1990 (2058)
|..|+....+.-+||.||.+.|... ..|--..|+.+=| =-+++.+++..|.
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 1355577877655 4456666666553
No 67
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=24.53 E-value=34 Score=38.57 Aligned_cols=20 Identities=50% Similarity=1.157 Sum_probs=17.7
Q ss_pred ccCCCCCCCCCceEeeccCcc
Q 000142 1933 CCSDCKSVLDEPALCLLCGRL 1953 (2058)
Q Consensus 1933 ~C~~c~~~~~~paiCL~CG~~ 1953 (2058)
.| +||..-..|+.||.||+-
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
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=24.09 E-value=52 Score=39.84 Aligned_cols=33 Identities=45% Similarity=0.944 Sum_probs=23.5
Q ss_pred CeeEEeccC-CCCCCccccccccCCCC----C-CCceeEEEec
Q 000142 124 DIAYRCRTC-EHDPTCAICVPCFQNGN----H-KEHDYSIIYT 160 (2058)
Q Consensus 124 e~~y~C~~C-~~d~t~~lC~~CF~~~~----H-~~H~~~~~~~ 160 (2058)
-+..+|-.| .+| +|..||-+|. | .-|.|+++.+
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 343 8999998765 3 4689999864
No 69
>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=23.98 E-value=44 Score=29.07 Aligned_cols=25 Identities=24% Similarity=0.527 Sum_probs=17.3
Q ss_pred cccCCCCCCC------CCceEeeccCccccC
Q 000142 1932 QCCSDCKSVL------DEPALCLLCGRLCSP 1956 (2058)
Q Consensus 1932 ~~C~~c~~~~------~~paiCL~CG~~~~~ 1956 (2058)
++||.|+... ..-.+|-.||.++..
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 70
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=22.99 E-value=45 Score=41.51 Aligned_cols=17 Identities=29% Similarity=0.698 Sum_probs=15.6
Q ss_pred ccccChHhhHHHHHHHH
Q 000142 1426 LSSCGHAVHQGCLDRYV 1442 (2058)
Q Consensus 1426 ~ssCGH~MH~~C~~~Y~ 1442 (2058)
+=-|.|+.|..|.+.|+
T Consensus 384 ALpCsHIfH~rCl~e~L 400 (518)
T KOG1941|consen 384 ALPCSHIFHLRCLQEIL 400 (518)
T ss_pred ccchhHHHHHHHHHHHH
Confidence 55699999999999998
No 71
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=20.49 E-value=49 Score=44.31 Aligned_cols=18 Identities=28% Similarity=0.803 Sum_probs=15.7
Q ss_pred ccccChHhhHHHHHHHHH
Q 000142 1426 LSSCGHAVHQGCLDRYVS 1443 (2058)
Q Consensus 1426 ~ssCGH~MH~~C~~~Y~~ 1443 (2058)
-.+|||+||.+|....++
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=20.23 E-value=58 Score=43.81 Aligned_cols=19 Identities=32% Similarity=0.807 Sum_probs=16.4
Q ss_pred ccccChHhhHHHHHHHHHH
Q 000142 1426 LSSCGHAVHQGCLDRYVSS 1444 (2058)
Q Consensus 1426 ~ssCGH~MH~~C~~~Y~~S 1444 (2058)
.-.|||+-|..|+.+.++-
T Consensus 311 rL~C~Hifh~~CL~~W~er 329 (543)
T KOG0802|consen 311 RLPCGHIFHDSCLRSWFER 329 (543)
T ss_pred eeecccchHHHHHHHHHHH
Confidence 4569999999999999865
Done!