Query 000144
Match_columns 2057
No_of_seqs 346 out of 614
Neff 6.5
Searched_HMMs 46136
Date Thu Mar 28 20:30:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000144.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000144hhsearch_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 1E-127 3E-132 1266.9 69.5 1280 282-2041 371-1720(1738)
2 KOG1139 Predicted ubiquitin-pr 100.0 6.6E-32 1.4E-36 331.5 4.8 608 1416-2054 170-782 (784)
3 KOG1140 N-end rule pathway, re 99.8 5.7E-22 1.2E-26 266.1 -2.7 927 18-1000 532-1502(1738)
4 smart00396 ZnF_UBR1 Putative z 99.8 1.5E-19 3.3E-24 170.8 5.8 70 116-185 1-71 (71)
5 PF02207 zf-UBR: Putative zinc 99.7 2E-18 4.3E-23 163.9 4.1 70 116-185 1-71 (71)
6 KOG1139 Predicted ubiquitin-pr 99.0 2.8E-09 6.2E-14 133.9 16.2 185 754-938 207-477 (784)
7 PF10390 ELL: RNA polymerase I 97.0 0.00051 1.1E-08 83.0 3.6 80 869-953 198-280 (284)
8 KOG1777 Putative Zn-finger pro 95.0 0.012 2.7E-07 71.5 2.3 62 112-174 540-606 (625)
9 PF13639 zf-RING_2: Ring finge 91.3 0.064 1.4E-06 46.5 0.2 20 1427-1446 17-36 (44)
10 cd00162 RING RING-finger (Real 91.3 0.17 3.6E-06 43.0 2.7 19 1428-1446 15-33 (45)
11 PF13764 E3_UbLigase_R4: E3 ub 90.8 0.92 2E-05 62.1 10.3 70 1146-1229 422-497 (802)
12 KOG0943 Predicted ubiquitin-pr 88.8 0.13 2.7E-06 68.6 -0.0 63 116-184 1241-1309(3015)
13 KOG4445 Uncharacterized conser 88.5 0.15 3.1E-06 60.1 0.2 48 1428-1477 133-183 (368)
14 cd02335 ZZ_ADA2 Zinc finger, Z 85.3 0.65 1.4E-05 41.5 2.5 39 117-159 5-48 (49)
15 cd02340 ZZ_NBR1_like Zinc fing 84.4 0.75 1.6E-05 40.0 2.4 37 117-158 5-41 (43)
16 KOG4796 RNA polymerase II elon 83.9 1 2.2E-05 57.3 4.1 77 869-951 211-290 (604)
17 PF12861 zf-Apc11: Anaphase-pr 83.4 0.72 1.6E-05 45.7 2.1 24 1423-1446 44-67 (85)
18 PF00097 zf-C3HC4: Zinc finger 83.2 0.71 1.5E-05 39.3 1.8 20 1427-1446 13-32 (41)
19 cd02249 ZZ Zinc finger, ZZ typ 83.0 0.86 1.9E-05 40.2 2.2 37 117-158 5-44 (46)
20 PF14634 zf-RING_5: zinc-RING 81.1 1.3 2.9E-05 38.5 2.7 31 1425-1477 14-44 (44)
21 smart00184 RING Ring finger. E 81.0 1.3 2.8E-05 36.1 2.5 18 1428-1445 13-30 (39)
22 cd02338 ZZ_PCMF_like Zinc fing 80.7 1.3 2.7E-05 39.8 2.4 38 117-159 5-48 (49)
23 KOG2905 Transcription initiati 79.5 1.2 2.5E-05 51.8 2.3 62 869-931 182-245 (254)
24 cd02344 ZZ_HERC2 Zinc finger, 78.5 1.7 3.6E-05 38.3 2.4 39 117-159 5-44 (45)
25 KOG2752 Uncharacterized conser 77.4 2.6 5.6E-05 50.7 4.3 61 112-173 37-101 (345)
26 PF00643 zf-B_box: B-box zinc 77.2 1.3 2.9E-05 37.9 1.5 37 116-158 4-40 (42)
27 PF11793 FANCL_C: FANCL C-term 75.1 0.95 2E-05 43.6 0.0 39 1428-1477 25-63 (70)
28 PHA02926 zinc finger-like prot 74.2 2.4 5.3E-05 48.9 3.0 46 1423-1485 190-235 (242)
29 PF09538 FYDLN_acid: Protein o 73.9 1.5 3.3E-05 45.8 1.1 27 1932-1958 8-38 (108)
30 COG5243 HRD1 HRD ubiquitin lig 72.7 1.7 3.7E-05 52.8 1.3 16 1430-1445 317-332 (491)
31 PLN03208 E3 ubiquitin-protein 69.0 3.8 8.2E-05 46.9 3.0 53 1428-1486 33-87 (193)
32 cd02339 ZZ_Mind_bomb Zinc fing 68.0 3.5 7.5E-05 36.4 1.9 30 126-158 13-43 (45)
33 TIGR02300 FYDLN_acid conserved 65.6 3 6.4E-05 44.3 1.2 26 1932-1957 8-37 (129)
34 cd00021 BBOX B-Box-type zinc f 62.3 5.8 0.00013 33.1 2.2 28 126-158 10-37 (39)
35 KOG1940 Zn-finger protein [Gen 60.7 4.3 9.4E-05 48.9 1.5 35 1426-1482 175-209 (276)
36 cd02343 ZZ_EF Zinc finger, ZZ 59.7 5.1 0.00011 35.8 1.4 35 117-156 5-40 (48)
37 PF12678 zf-rbx1: RING-H2 zinc 58.4 2.4 5.2E-05 41.2 -0.9 18 1427-1444 46-63 (73)
38 PHA02929 N1R/p28-like protein; 56.6 4.9 0.00011 47.7 1.1 37 1425-1484 195-231 (238)
39 cd02341 ZZ_ZZZ3 Zinc finger, Z 56.6 7.3 0.00016 34.9 1.9 32 126-158 13-46 (48)
40 PF13923 zf-C3HC4_2: Zinc fing 54.2 5.6 0.00012 33.6 0.7 20 1427-1446 13-32 (39)
41 smart00291 ZnF_ZZ Zinc-binding 53.9 8.7 0.00019 33.6 1.9 35 116-155 8-43 (44)
42 cd02336 ZZ_RSC8 Zinc finger, Z 52.8 4.8 0.0001 35.5 0.1 31 117-152 5-35 (45)
43 cd02337 ZZ_CBP Zinc finger, ZZ 52.6 7.6 0.00017 33.6 1.3 32 116-153 4-35 (41)
44 smart00336 BBOX B-Box-type zin 50.4 13 0.00028 31.6 2.4 29 125-158 12-40 (42)
45 KOG0827 Predicted E3 ubiquitin 49.9 11 0.00024 46.6 2.5 30 1416-1446 12-41 (465)
46 KOG0828 Predicted E3 ubiquitin 48.9 11 0.00023 47.9 2.2 29 1428-1477 603-631 (636)
47 PF10571 UPF0547: Uncharacteri 48.8 8.1 0.00017 30.2 0.8 22 1934-1955 1-23 (26)
48 PF13240 zinc_ribbon_2: zinc-r 48.1 9.3 0.0002 28.9 1.0 20 1935-1954 1-21 (23)
49 PF02270 TFIIF_beta: Transcrip 47.6 7.1 0.00015 47.7 0.5 31 899-930 244-274 (275)
50 cd02334 ZZ_dystrophin Zinc fin 45.3 14 0.0003 33.3 1.8 32 117-152 5-36 (49)
51 COG2051 RPS27A Ribosomal prote 44.5 8.1 0.00018 36.5 0.3 28 1931-1958 17-50 (67)
52 PF13248 zf-ribbon_3: zinc-rib 44.1 11 0.00023 29.3 0.8 22 1933-1954 2-24 (26)
53 PF13920 zf-C3HC4_3: Zinc fing 43.0 15 0.00033 32.8 1.7 18 1428-1445 17-35 (50)
54 cd02345 ZZ_dah Zinc finger, ZZ 39.8 20 0.00043 32.3 1.9 31 116-151 4-35 (49)
55 COG5194 APC11 Component of SCF 39.5 31 0.00066 33.9 3.2 27 1420-1446 43-69 (88)
56 PLN00209 ribosomal protein S27 39.2 10 0.00023 37.7 0.1 37 1916-1958 25-67 (86)
57 PTZ00083 40S ribosomal protein 37.8 11 0.00025 37.3 0.2 37 1916-1958 24-66 (85)
58 KOG4172 Predicted E3 ubiquitin 37.8 15 0.00034 33.3 0.9 15 1428-1442 22-37 (62)
59 KOG2114 Vacuolar assembly/sort 37.7 16 0.00034 49.5 1.4 23 1430-1477 858-880 (933)
60 PF00569 ZZ: Zinc finger, ZZ t 34.5 10 0.00022 33.5 -0.6 36 117-156 9-45 (46)
61 PF07800 DUF1644: Protein of u 32.7 32 0.0007 38.2 2.5 44 1435-1478 37-89 (162)
62 KOG0457 Histone acetyltransfer 31.2 36 0.00077 43.3 2.9 42 118-163 20-66 (438)
63 PRK00415 rps27e 30S ribosomal 30.8 20 0.00043 33.5 0.5 28 1931-1958 9-42 (59)
64 PF01667 Ribosomal_S27e: Ribos 29.7 18 0.00039 33.4 0.0 28 1931-1958 5-38 (55)
65 PF02148 zf-UBP: Zn-finger in 25.5 60 0.0013 30.6 2.8 51 1936-1989 1-51 (63)
66 COG4031 Predicted metal-bindin 24.7 34 0.00073 38.6 1.1 20 1935-1955 2-21 (227)
67 KOG1941 Acetylcholine receptor 24.0 41 0.0009 41.8 1.7 17 1428-1444 384-400 (518)
68 KOG1493 Anaphase-promoting com 23.4 28 0.0006 33.9 0.1 25 1422-1446 42-66 (84)
69 PF08271 TF_Zn_Ribbon: TFIIB z 23.3 46 0.001 28.9 1.4 25 1934-1958 1-31 (43)
70 COG5114 Histone acetyltransfer 21.9 62 0.0013 39.3 2.5 33 126-162 18-56 (432)
71 KOG0309 Conserved WD40 repeat- 21.9 44 0.00095 44.7 1.4 18 1428-1445 1045-1062(1081)
72 COG4530 Uncharacterized protei 21.1 44 0.00094 34.7 0.9 24 1932-1955 8-35 (129)
73 TIGR00570 cdk7 CDK-activating 20.0 68 0.0015 39.7 2.4 17 1428-1444 23-39 (309)
No 1
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.3e-127 Score=1266.95 Aligned_cols=1280 Identities=23% Similarity=0.337 Sum_probs=812.9
Q ss_pred hccCCCHHHHHHHHHHHH-HhhCChhhHHHHHHHHHhhhHHHHHHHHHhccccccccCCccceeeeeccccCCcHHHHHH
Q 000144 282 AEMFSSDVVVRKLHELLL-KLLGEPIFKYEFAKVFLSYYPVFVKDAIREHSDDTIKKYPLLSTFSVQIFTVPTLTPRLVK 360 (2057)
Q Consensus 282 ~~~~l~k~~r~~lh~Lll-sLL~d~efK~~fa~~Fv~~Y~~i~~~fl~~d~d~~~~~~s~v~~LSVQLFTvPsLA~~LV~ 360 (2057)
.+..+||..|..++.++. .+-++.+||+.||.+|+.+|..+..+++.+|++.. .+.| .++||+||+|++|..+++
T Consensus 371 ~d~~~~kr~r~~l~k~~~~~~~~~~~~k~~~~~~~~~~y~~~~~~~~~~d~e~~---~~vi-~~~vqf~t~~~~a~~~~~ 446 (1738)
T KOG1140|consen 371 FDNRYWKRLRKDLQKVIIPTFASSNLYKPIFAQQFVEHYNSITRDFAYMDREPD---LSVI-ELSVQFFTCPSLAKNIVE 446 (1738)
T ss_pred HHHHHHHHHHHHHhhcceeehhcchHHHHHHHHHHHHHHHHHHHHHHhhcCCcc---hhhH-hheeeeecCcHHHHHhhh
Confidence 334457889999999999 67789999999999999999999999999998744 3545 999999999999999999
Q ss_pred hhcHHHHHHHHHHHHhhhhcCCCCcceec---------cccccccchhhhhhhhhHhhcchhhhHHHhhhchHHHHHHHH
Q 000144 361 EMNLLEMLLGCLREIFDSCAGDDSCLQVA---------KWANLYETTNRVIGDIRFVMSHAAVSKYATHEQLNISKAWMK 431 (2057)
Q Consensus 361 e~nLL~iLl~tl~~~~~~~~~~~~~l~~~---------~~~~~~~~y~~I~~DLrylLsh~~v~~~l~~~~~~l~~~~l~ 431 (2057)
...++..+..++..++..+...++...+. +.....++.+..+.|+ +.+.++.+ -.++..+..++.
T Consensus 447 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~r~l~~~~~l-~~~~~~~~-----~~~~~~~~~~l~ 520 (1738)
T KOG1140|consen 447 NQSFLDIVWSIIDIFKEFNKVEGGVLIDIRVQKSNLLKRYSISFRRTLYTFEDL-SKVHDPNI-----PLRPKEFISLLL 520 (1738)
T ss_pred hccchHHHHHHHHHHHHhcccccceecceeeeechhhhHHHHHHHHHHHHHHHh-hccCCccc-----cccHHHHHHHHH
Confidence 99988877777766664444322211111 1122356677778888 77666662 357899999999
Q ss_pred HHHHhcCCCcccccccCcceeeCCceeehhhhhhHHHHhHHhhhhhccccccccccccccccccccCCCCCccccccccc
Q 000144 432 LLTFVQGMNPQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEETRYDFSMYKQDIGDGDSLRHAKVGR 511 (2057)
Q Consensus 432 lL~~~QGMn~~kRq~~~HVEyE~e~w~~aF~L~~~la~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~r 511 (2057)
++..||||.|++|+.++||++|++ |+.+|.+-.++..++++++.||..++. +
T Consensus 521 ~~~v~qg~~~lkr~~~ehv~~e~~-~~~~~~~v~~~t~~~s~i~~~~~~~ep-------------------------~-- 572 (1738)
T KOG1140|consen 521 LLKVFQGVDPLKREELEHVEVEKE-WENFFSLVEYLTAIYSMIQSLVKTSEP-------------------------V-- 572 (1738)
T ss_pred HHHHhCCccHHHHHHhhhhcccch-HHHHHHHHHHHHHHHHHHHHHHHhccc-------------------------h--
Confidence 999999999999999999999997 999999999999999999998866530 0
Q ss_pred cccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhhhcCCCCcccccccCCCCcccccCchh
Q 000144 512 LSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENWLGVDDRSVSVNDILSPNASRISGSNF 591 (2057)
Q Consensus 512 ~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~cl~~l~~~~~~~~~~~~~~~~~s~~~~~~~~~~~ 591 (2057)
-..++..|..++..... |-+
T Consensus 573 ---------------------------------------~~~~~~~l~~~~~r~~~------------s~~--------- 592 (1738)
T KOG1140|consen 573 ---------------------------------------KDSVYKKLLEAAIRIHP------------SLT--------- 592 (1738)
T ss_pred ---------------------------------------hhhHHHHHHHHHhhccc------------ccC---------
Confidence 00011122222221100 000
Q ss_pred hhhHhhhhhccccccccccccCCccccccccccCCCccccccCccccccccCCcccccccccCcCCccccccchhccccc
Q 000144 592 VALKKTLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKITISGERDTASWRSAGFNDSEMEGECATELDNL 671 (2057)
Q Consensus 592 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 671 (2057)
++ +. + ..++++++.
T Consensus 593 ---------------------~~---------------------~~---l---------------~~~i~~~S~------ 606 (1738)
T KOG1140|consen 593 ---------------------GS---------------------ES---L---------------TYTICGESH------ 606 (1738)
T ss_pred ---------------------cc---------------------ce---e---------------eehhhhhhH------
Confidence 00 00 0 012234433
Q ss_pred cccccCccCceeeeccCCceeeehHHHHHHHHHHHHHHhhhccccccccccccCCCCCccccchhhhhcccCCCCCcccc
Q 000144 672 HVLSLCYWPDITYDVSSQDVSVHIPLHRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFS 751 (2057)
Q Consensus 672 ~~~~~~~~~~v~fdVs~~~VSfH~PLhr~Ls~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 751 (2057)
.++.|+|+.++||||+|+.|+|+++++.......+ ..+.+ ..+.+++. .
T Consensus 607 --------e~i~f~v~~~~~sv~~p~~~~l~~l~~~~~s~v~~-------------------~~d~~-~~~~~~~n---~ 655 (1738)
T KOG1140|consen 607 --------ETINFSVSQERVSVSNPVSRLLAFLIELSCSSVVS-------------------LKDAY-ERLEDCSN---F 655 (1738)
T ss_pred --------hHhhhccccccceeeccHHHHhhhhhhcccchhhh-------------------cchhh-hhHhhhcc---c
Confidence 57899999999999999999999998532110011 11111 11222222 2
Q ss_pred hhhccccHHHHHHHHhHhcCceeeccHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccc
Q 000144 752 AFVMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLS 831 (2057)
Q Consensus 752 ~~l~e~pLR~~Vl~aQI~aGmWvRNG~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~ 831 (2057)
.+|.|||||++|++|||.+|||||||+++.+|+.||++.+||+++|++||+++|.++++.||+.|+.++++||+|.+|++
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 000144 832 LNLERPSE-YE---PILVQEMLTLIIQILQERRFCGL---TTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQE 904 (2057)
Q Consensus 832 ~~~~~~~~-y~---~~mvEe~L~lLI~llteR~~~g~---t~~e~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~~~~fe~ 904 (2057)
|....... ++ ..|+|+|+.+||.|++||...|+ +..+.+|+||||+||++|++||+|.+++|++++++..||.
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-CcceEEEeccccccccccccccCchhHHHHHHHHHH--hhc---cccccCCC-CCCccccC-Ccc
Q 000144 905 ILDAVAMYSHPSGF-NQGMYSLRWSYWKELDIYHPRWSSRDLQVAEERYLR--FCS---VSALTAQL-PRWTKIYY-PLE 976 (2057)
Q Consensus 905 iL~eVA~f~~P~g~-~~G~Y~LK~e~~~e~dpy~~~y~~~~~q~aeer~~r--~~k---~~a~~~~~-P~~~~~~~-p~~ 976 (2057)
++++||+|++|.++ +.|+|+||++||+++||||+||++.++.+++..+++ ..+ ..|..+++ |++...+. .+.
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 789999999999999999999999999888766543 211 12444332 33333221 234
Q ss_pred ccccccccHHHHHHHHHHHHHHhccCCCCCCCCChhHHHHHHHHH-HHHHhhhhhcccCCCCCcccCCCcccccchhhHH
Q 000144 977 SIAGIATCKVVLQVIRAVLFYAVFTDNPTDSRAPYGVLLTALHLL-ALALDVCFQKKKSGDQSCDIGGSTPILDFASEEI 1055 (2057)
Q Consensus 977 ~l~~il~s~~~~~il~~vL~~al~~~~~~~~~~~E~~L~~~LHLi-~laL~~~~~e~~~~~~~~~~~~~~~~~~~~~~~i 1055 (2057)
++.+.+...+|-.||+.++.++.+.. .+.++..++|++ +.|++.+..--. |. +..+++
T Consensus 896 ~L~~~t~~~~~~~ii~r~~~~~~~~~-------s~~~l~~~~~~ihG~~~~~~l~~~~-----------~~-~~~~~e-- 954 (1738)
T KOG1140|consen 896 ILGAAVRLTVFGLIIYRTLEHCLFME-------SSTLLSKVLHLIHGIALNEELINMK-----------FA-FTQKTE-- 954 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhcc-----------cc-cccccc--
Confidence 55566666677777777777777643 488999999554 999986543211 10 000011
Q ss_pred hhccCCCCCcccHHHHHHHHHhhhcccCCccccccccCCchhHHHHHHHHHHhhhHHHHHHHhhhchhhhhcccCCCCCC
Q 000144 1056 AEGLNNGAGKQSLLSLLVFLMGMYKKDGADNFLEAGNCNLSSVIESLLKKFAEIDSRCMTKLQQLAPEIVSHLSQSLPRD 1135 (2057)
Q Consensus 1056 ~~~~~~~~~~~Sll~LL~~L~~~~~~~~~~~~~e~~~~~i~~~I~~lL~~f~~~~~~c~~~l~~~~p~~~~~~~~~~~~~ 1135 (2057)
.-.+++.+.+++.+..++....+ +.++.|+++.|..+.. .+...|++.. .+.. ...
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 11345577788877777554332 4568888888876544 2344443321 1100 011
Q ss_pred CCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccccCCCCCCCccCCCCcccccccccCCccccccCCCC-
Q 000144 1136 DTSGSFSASDSEKRKAKARERQAAILEKMKAEQFKFLSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS- 1214 (2057)
Q Consensus 1136 ~~~~~~~~~e~ekkK~~AkeRQakIMaqm~~qQ~~Fl~~n~~~~~~~~~~~~~~~~s~~~~~~~e~~~~~CilCqe~~~- 1214 (2057)
..+.+.++.+.++||++|++||+|+||||+.||.+||++|.++.|++++. ..++...+.. .....|.+|+..+.
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---TPSSGSKTYE--EEDFTCALCQDNSCT 1085 (1738)
T ss_pred ccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccccCccccc---Cccccccchh--hhhccchhhhccchh
Confidence 11223444556778889999999999999999999999997665544331 1111101111 11456777764332
Q ss_pred CCCeEEEeeeecccccccccCCCCCCcccccccccccccccccccccCCCCCCCCCCCcchhhhHHHHHHHHHhhhccCC
Q 000144 1215 RTPVSYLILLQKSRLLSFVDRGSPSWDQDQWLGKECGTISANNMVNQFGTNTPSSGLGVISSCQLAQVAEEAVNQFAYNG 1294 (2057)
Q Consensus 1215 ~~pfg~la~iq~S~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 1294 (2057)
+.++ |+++.+...
T Consensus 1086 ~~~~------~~~~~~~~~------------------------------------------------------------- 1098 (1738)
T KOG1140|consen 1086 DFQV------KPASHLVKP------------------------------------------------------------- 1098 (1738)
T ss_pred cccc------ccchhhhcc-------------------------------------------------------------
Confidence 1222 222221110
Q ss_pred CchhhhhHHHHhhhcCCCCcCCCCCCCcCCCCcCCccchhhhhhhhhhHHHHhhhccCCCCCCccccchhhhccCCccCC
Q 000144 1295 KPEEVNSVLEFVKAQFPSLRNIPIPFTFSNGRKCTASSMEMFEQDLYLSICREMRKNMTYPDLMKEDEECSVAEGGLKNR 1374 (2057)
Q Consensus 1295 r~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~s~~~~~e~~~~~~~~~~~~~~ 1374 (2057)
...+||+| |+++.+...
T Consensus 1099 --------------------------------------------~~~~~~i~------------~e~e~~~~~------- 1115 (1738)
T KOG1140|consen 1099 --------------------------------------------IFRECIIC------------DENEDVPNW------- 1115 (1738)
T ss_pred --------------------------------------------cccccccC------------ChhccCCCc-------
Confidence 00123333 222222211
Q ss_pred CCCccchhhhhhhhhhHHhhhcccccccccccccccccccCCCCCC-CcCCCccccccChHhhHHHHHHHHHHHHHhhhc
Q 000144 1375 GNSDSFLLGKYVASISKEMRENASASEVSRGDRIAAESLVYDGFGP-IDCDGIHLSSCGHAVHQGCLDRYVSSLKERYNR 1453 (2057)
Q Consensus 1375 ~~~~~~~l~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~F~~-~~~~gvh~SsCGH~MH~~C~~~Y~~Sl~~r~~~ 1453 (2057)
.++.++..+|+++ ++. ...+++.| ....|+++|+|||.||+.||++|+.+.+.|.++
T Consensus 1116 -~~~~~v~~~f~~~-s~~--------------------~sd~l~~p~~~~~~~~~s~c~h~mh~~c~~~~~~a~r~~~n~ 1173 (1738)
T KOG1140|consen 1116 -DGRYSVSSAFAQK-SDD--------------------VSDALTEPGSLSCGTVLSSCGHHMHYGCFKRYVQAKRFRENA 1173 (1738)
T ss_pred -cccchhhhHhhhh-ccc--------------------ccccccCCCCCcccceeeccCCcchHHHHHHHHHHHHHHHHh
Confidence 1123355666665 211 12334433 567899999999999999999999999999988
Q ss_pred ccccCCCcccCCCCcccccccccccccceecCCCCCcccCCCCCcccCCCCCCCCCCccccccchhhHHHHHH------H
Q 000144 1454 RIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRINEQPTVSGVGLSLDSSSSFTTREENTSFQLQQA------V 1527 (2057)
Q Consensus 1454 r~~~er~h~~d~e~gEFLCPLCKsLsNsvLPilp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~------~ 1527 (2057)
+..+-+.|.. ++|+|+||+||+|+|+++|..++.....+.. +.. ..+....|++.. +
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 8999999999999999999875433322210 000 001122233210 0
Q ss_pred HHhhh---ccc-cccc---ccccccCCcchhhHHHHHHHHHHHHHHHHhhccc------cccccCCCCCChhHHHHHHHh
Q 000144 1528 SLLQS---ASN-VVGK---ADVIESFPLMKNEIMASNVEAVSRRMCKMYFQNK------LDKFFGSARVNPSLIMWDALK 1594 (2057)
Q Consensus 1528 ~~l~s---~~~-~~~~---~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~------~~~~~~~~~~~~~~~l~~tl~ 1594 (2057)
..+.+ ... .... .++.+..-.++.+.....++.+.+.+....+... .....+.++. .....|-.++
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 00000 000 0000 0000000001112211222223222222222111 1122234443 4567888888
Q ss_pred HhHHHHHHHhcccCCCCCCcchhhhHHHhhccchhHHHHHHHHHHhhhccchhHHHHHHhhc---cchhhhhccCCCCCC
Q 000144 1595 YSLMSMEIAARSEKTSTTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVLQRFRG---IQLFAESICSGTSID 1671 (2057)
Q Consensus 1595 yTi~s~Eia~Rg~~~~~~~~~~l~~L~~~l~~~~~~~l~ll~~~~~~~r~~~~~~~l~r~~~---~~Ll~~si~~~~s~~ 1671 (2057)
+..+++++.+-+.+.. ++..+.+...+.+....++.... +...++...- +.++...+.+ .
T Consensus 1316 ~a~~~~~~~l~~~~~~---------~~l~l~~~~~~~~~~~~~l~~~~----~~~~l~~~~~~~llk~~s~~~~~----i 1378 (1738)
T KOG1140|consen 1316 DAEQSTKLLLSASKKP---------SFLKLNEDMTFCLVTISRLRALH----WEQILYELVYTFLLKSFSPTIPR----I 1378 (1738)
T ss_pred hHHHHHHHHHhccCCc---------ccccCchhhHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhhcCCc----c
Confidence 8888877754443332 11222222223333332222211 1222222111 1122111100 0
Q ss_pred CCCCCcCCCCccchhccccccccCcchhhhhhhcCCCccccChhhHHHHHHhhcccccccccchhhhHHHH-HHHHHHHH
Q 000144 1672 NPGGRCKRGGNMLSILKHADVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFILCKESLLSLVHV-FYAVTLSQ 1750 (2057)
Q Consensus 1672 ~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~plL~~D~F~~Lv~~~~~lp~p~~~~~~~~~~iv~l-~y~a~ivQ 1750 (2057)
. ...++. .+.......+..++...|-+-.+ ++ . .......++++ ..+++++|
T Consensus 1379 ~-------~~~tpd----------~~~~~ll~~l~~~~~~~~~l~~~------~~--~--~~~~~~~~~~~~i~~~~i~s 1431 (1738)
T KOG1140|consen 1379 S-------VLITPD----------QPENELLVILPHDFPKSLELELT------LD--F--VNKNPKKIFELKILMASIIS 1431 (1738)
T ss_pred h-------hccCCC----------CCcchhhhccchhhhhhccHHHH------HH--H--hhhhHHHHHhHHHHHHHhhh
Confidence 0 000000 00000000000111111111110 01 0 01233334444 45567777
Q ss_pred H-Hhhhhcccccc--cccccchhhhHHHHHHHhcccccccccccccCCCChhhHHHHHHHhhhhHHHHHHHHHHhhcCCC
Q 000144 1751 A-VLSCCGKLQSK--VNELGFSDSLISDISKLLGEFGSAQEYFVSNYIDPSCDIKDMIRRLSFPYLRRCALLWKLLNSTV 1827 (2057)
Q Consensus 1751 ~-ll~~~~~~~~~--~~~~~~~d~~~~~i~~~~~~~~~~~~~~~s~~~d~~~~l~~~v~k~~lPFLRraaLL~~~l~~~~ 1827 (2057)
. +++.......+ .++....-.....++..+-.....+.......+-....++..+++.++|||||+++++|++.++.
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 11111110001111110000000000000000111235888899999999999999999999998
Q ss_pred CCCCCCccccccccccCccCCCCCCcccccchHHHHHHHHhcCCCChhhhh-hh--HHHHHHHHHHhhcccccchhhccc
Q 000144 1828 PPPFSDRDHVLARSSHGISDMMDSSDDALSDLKEIQEVEKMFKIPSLDVIL-KD--EVLRSLVLKWFHHFSKEFEVHRFQ 1904 (2057)
Q Consensus 1828 ~p~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~E~~~L~~~L~LPsl~~ll-~~--~~~~~li~~W~~h~~~~~~~~~~~ 1904 (2057)
+|... + .++ ....|+..||+|+++|++...+ +. +.++.++.+||.-.........+.
T Consensus 1512 ~p~~~-----f-------~~~--------~~~s~~e~L~ty~slp~l~~~~~q~~~delr~~~~~~~~~~~~lk~~~~~~ 1571 (1738)
T KOG1140|consen 1512 PPFGA-----F-------LDP--------SSNSELEHLCTYLSLPNLQACLLQSSGDELRQAIERWCGGTENLKREEHYL 1571 (1738)
T ss_pred Cchhh-----c-------cCc--------ccchhhhhhcccccCccHHHHHHhhhHHHHHHHHHHhhccchHHHHHHhhc
Confidence 76210 1 110 0124888999999999887654 32 678899999986422111111111
Q ss_pred cccccCCCCcccccCCchhHHHHHHHHhhcccCCCCCCC-CCceeeeccCccccCCCCcccc----------hhHHHhhc
Q 000144 1905 HVLYSTPAVPFKLMCLPHLYQDLLQRYIKQCCSDCKSVL-DEPALCLLCGRLCSPSWKPCCS----------CQSHAVAC 1973 (2057)
Q Consensus 1905 ~~~~~~~~~~~~Li~LP~~y~~l~~~~~~~~C~~c~~~~-~~paiCL~CG~~~~~~~~~cc~----------c~~H~~~C 1973 (2057)
......|..+..|++||+.|+.+++++....|++|++.+ ..|++||+||..+|.+ .+||+ |++|+..|
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 8999999999988774 79996 99999999
Q ss_pred CCCeeEEEEecccEEEEEcc--CCcccCCCCccCCCCCCCCCCcCCCCcccCHHHHHHHHHHHHcCCcCc
Q 000144 1974 GAGTGVFLLIRRTTILLQRC--ARQAPWPSPYLDAFGEEDIEMHRGKPLYLNEERYAALTYMVASHGLDR 2041 (2057)
Q Consensus 1974 g~~~Gifl~v~~~~ill~~~--~rg~~~~spYLD~~GE~D~~lrrg~pl~L~~~Ry~~l~~~w~~h~i~~ 2041 (2057)
||++||||.+++|.++++.+ ++|||+|+||+|+|||+|+|+|||.|+|||++||+++..+|++|+|++
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=6.6e-32 Score=331.52 Aligned_cols=608 Identities=11% Similarity=-0.044 Sum_probs=421.6
Q ss_pred CCCCCCcCCCccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccccccceecCCCCCcccCCC
Q 000144 1416 DGFGPIDCDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRINE 1495 (2057)
Q Consensus 1416 ~~F~~~~~~gvh~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCKsLsNsvLPilp~~~~~~~~ 1495 (2057)
++|.+..+.+.|.++|+|+.|.+|..+|+.....+-..+-.+.++|..+..+.++.||.|++++|+|.|..++++....+
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 56666667889999999999999999999999888777777888889999999999999999999999999765553222
Q ss_pred CCcccCCCCCCCCCCccccccchhhHHHHHHHHHhhhcccccccccccccCCcchhhHHH--HHHHHHHHHHHHHhhccc
Q 000144 1496 QPTVSGVGLSLDSSSSFTTREENTSFQLQQAVSLLQSASNVVGKADVIESFPLMKNEIMA--SNVEAVSRRMCKMYFQNK 1573 (2057)
Q Consensus 1496 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~s~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~~~l~~~~~~~~ 1573 (2057)
+. ..+...+..+ ..-..++|+.+.+..+..+.......+......|+.+.-.. ....++.++.+..+++..
T Consensus 250 kr-hePdt~~~r~------~hi~~slfl~e~la~~~~~ec~~~di~r~v~~~p~~s~L~~~~~~~~~~~k~~~~~Hsr~p 322 (784)
T KOG1139|consen 250 KR-HEPDTIRFRA------AHIDKSLFLKELLASFNITECIKIDIGRFVEKSPESSILFQETEVTIDFTKQSPIDHSRDP 322 (784)
T ss_pred cC-CCCchhcccc------ccccHHHHHHHHHHHhhhhhhhhhhccceeEeccccccchhhhhhhccccccCchhcccCc
Confidence 10 0000000000 01134556666554443332221100000111121111111 111223333332222211
Q ss_pred ccccc-CCCCCChhHHHHHHHhHhHHHHHHHhcccCCCCCCcchhhhHHHhhccchhHHHHHHHHHHhhhccchhHHHHH
Q 000144 1574 LDKFF-GSARVNPSLIMWDALKYSLMSMEIAARSEKTSTTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVLQ 1652 (2057)
Q Consensus 1574 ~~~~~-~~~~~~~~~~l~~tl~yTi~s~Eia~Rg~~~~~~~~~~l~~L~~~l~~~~~~~l~ll~~~~~~~r~~~~~~~l~ 1652 (2057)
..++- +--+...-..+|++++|...+.|+--|--+-+..++.|...+...+++..+.+++++...+...+..+.++.-+
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 00001123457999999999999999987777777888888889999999999999999999999999999889
Q ss_pred HhhccchhhhhccCCCCCCCCCCCcCCCCccchhccccccccCcchhhhhhhcCCCccccChhhHHHHHHhhcccccccc
Q 000144 1653 RFRGIQLFAESICSGTSIDNPGGRCKRGGNMLSILKHADVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFILC 1732 (2057)
Q Consensus 1653 r~~~~~Ll~~si~~~~s~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~plL~~D~F~~Lv~~~~~lp~p~~~~ 1732 (2057)
++.++.=++.+++.+.++...+ .....+.....++ +..-.|+++..|++.+|||..+.+..+++|+++..+
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 9888877777777766665553 2222221111222 223468889999999999999999999999888888
Q ss_pred cchhhhHHHHHHHHHHHHHHhhhhcccccccccccchhhhHHHHHHHhcccccccccccccCCCChhhHHHHHHHhhhhH
Q 000144 1733 KESLLSLVHVFYAVTLSQAVLSCCGKLQSKVNELGFSDSLISDISKLLGEFGSAQEYFVSNYIDPSCDIKDMIRRLSFPY 1812 (2057)
Q Consensus 1733 ~~~~~~iv~l~y~a~ivQ~ll~~~~~~~~~~~~~~~~d~~~~~i~~~~~~~~~~~~~~~s~~~d~~~~l~~~v~k~~lPF 1812 (2057)
..++...++.+--+..+|+++++...........++..... |+...+...+.+ ++|.+.+.+...++.+.+.++-+||
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 2233333334457788899999999
Q ss_pred HHHHHHHHHhhcCCCCCCCCCccccccccccCccCCCCCCcccccchHHHHHHHHhcCCCChhhhhhhHHHHHHHHHHhh
Q 000144 1813 LRRCALLWKLLNSTVPPPFSDRDHVLARSSHGISDMMDSSDDALSDLKEIQEVEKMFKIPSLDVILKDEVLRSLVLKWFH 1892 (2057)
Q Consensus 1813 LRraaLL~~~l~~~~~p~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~E~~~L~~~L~LPsl~~ll~~~~~~~li~~W~~ 1892 (2057)
+|+|+.+++.+-..+.. .....+++..+.+-++++|+......+.++--+.+-..+.||.+++.. .+-.+.|++
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 99999999988653321 112223344445556777777766665555567778888999887543 234677999
Q ss_pred cccccchhhccccccccCCCCcccccCCchhHHHHHHHHhhcccCCCCCCCCCceeeeccCccccCCCCcccc-hh-HHH
Q 000144 1893 HFSKEFEVHRFQHVLYSTPAVPFKLMCLPHLYQDLLQRYIKQCCSDCKSVLDEPALCLLCGRLCSPSWKPCCS-CQ-SHA 1970 (2057)
Q Consensus 1893 h~~~~~~~~~~~~~~~~~~~~~~~Li~LP~~y~~l~~~~~~~~C~~c~~~~~~paiCL~CG~~~~~~~~~cc~-c~-~H~ 1970 (2057)
|+...++.++........++++|.+.++|.-|+.+..+..+. ...+++.|+.||..|.--+.|||. |. +|.
T Consensus 626 ~~~r~~e~~k~~r~~~~k~~~~fa~~~~~~~~q~~a~~s~~~-------~g~ed~~~~~~~~~q~~~k~y~C~icg~n~p 698 (784)
T KOG1139|consen 626 KHSRNQEKMKAPRDPVKKAAKEFAKRRMEAIMQNSAKKSAQT-------EGMEDAEVNKVDPSQQNRKVYECPICGQNAP 698 (784)
T ss_pred HHHHHHHHhhcccchHHHHhHHHHHHHHHHHHHHHHHhhhcc-------cCCChHHHhhhCcccCCccCCcCCcCCCCCC
Confidence 987777765555445556777899999999888877643222 578999999999998876789998 53 588
Q ss_pred hhcCCCeeEEEEecccEEEEEccCCcccCCCCccCCCCCCCCCCcCCCCcccCHHHHHHHHHHHHcCCcCcccccccccc
Q 000144 1971 VACGAGTGVFLLIRRTTILLQRCARQAPWPSPYLDAFGEEDIEMHRGKPLYLNEERYAALTYMVASHGLDRSSKVLSQTT 2050 (2057)
Q Consensus 1971 ~~Cg~~~Gifl~v~~~~ill~~~~rg~~~~spYLD~~GE~D~~lrrg~pl~L~~~Ry~~l~~~w~~h~i~~~~~~~~~~~ 2050 (2057)
.+||+++|+|++|+++.|+.-+-.+..-||.||||..|++|.+.-||+-+|+++.||..|....=+|++++.++++.+|+
T Consensus 699 ~T~~np~G~~~l~~~~~I~~~r~~~~~~~p~p~l~~de~e~~~~~Rl~~e~~rr~~~~~l~~~~es~~l~~~~~~l~gt~ 778 (784)
T KOG1139|consen 699 NTVENPFGMLALLSTNFICEERIDASINTPDPLLKFDEYEHVSANRLQSETRRRFFSKRLQATFESQDLVKVNPPLVGTD 778 (784)
T ss_pred cccCCCceEEEEEeecchHHHHHhhccCCCChhhhcchhhhhHHHHHHHHHHHHHHHHHhhhcccccchhhccccccCcc
Confidence 88999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccc
Q 000144 2051 IGGF 2054 (2057)
Q Consensus 2051 ~~~~ 2054 (2057)
|+..
T Consensus 779 ~~~c 782 (784)
T KOG1139|consen 779 LKTC 782 (784)
T ss_pred hhcc
Confidence 9864
No 3
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.82 E-value=5.7e-22 Score=266.12 Aligned_cols=927 Identities=17% Similarity=0.046 Sum_probs=571.7
Q ss_pred HHHHHHhcCCchhhhchhhHHHHhhhCCCChhHHHhccCCCCHHHHHHHHHHHhhccccCCCCCh-h-hhHHHHHHHHHH
Q 000144 18 IVRRLMNIGVPEEFLDYSGIVNFAKNDKSRIPELVSTILPPDEEVAEVIQDAKAKNKKVSVGPNM-K-GRFRESMLWLQW 95 (2057)
Q Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~l~~ 95 (2057)
..+++--.++++++-...+++.|+...+..|...+.+..|....+...+..+..+..++.+..++ + ..+.+....+.|
T Consensus 532 kr~~~ehv~~e~~~~~~~~~v~~~t~~~s~i~~~~~~~ep~~~~~~~~l~~~~~r~~~s~~~~~~l~~~i~~~S~e~i~f 611 (1738)
T KOG1140|consen 532 KREELEHVEVEKEWENFFSLVEYLTAIYSMIQSLVKTSEPVKDSVYKKLLEAAIRIHPSLTGSESLTYTICGESHETINF 611 (1738)
T ss_pred HHHHhhhhcccchHHHHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHhhcccccCccceeeehhhhhhHhHhhh
Confidence 34667778888888777899999999999999999999999999998888888887777665555 3 448888888888
Q ss_pred HhcCCCHHHHHH---HHHccCCCccccccccCCceeEEecccCCCCCccccccccCCCCCCCceeEEEecCCccccCCCc
Q 000144 96 LMFEREPEKVLR---KLSKIGQRGVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDV 172 (2057)
Q Consensus 96 ~~~~~~~~~~l~---~l~~~~~~~~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~~~~~~gG~CDCGd~ 172 (2057)
.++.+.+.-... .+. -.-...|+-+|...+.+++|++|.. .+.+|..|++...|-.|.+..+-..+|+|+|+ .
T Consensus 612 ~v~~~~~sv~~p~~~~l~-~l~~~~~s~v~~~~d~~~~~~~~~n--~~~i~e~~lr~~Vl~aqid~~~w~rNG~si~~-q 687 (1738)
T KOG1140|consen 612 SVSQERVSVSNPVSRLLA-FLIELSCSSVVSLKDAYERLEDCSN--FLAISEHSLRVLVLCAQIDVGFWVRNGFSILH-Q 687 (1738)
T ss_pred ccccccceeeccHHHHhh-hhhhcccchhhhcchhhhhHhhhcc--chhhcccchhheeeeeecceeeEeecCcchhh-h
Confidence 777754432211 111 1125889999999999999999997 89999999999999999988887889999999 8
Q ss_pred ccccccCCCCcCCCCCCCCCCcHHHHhhhHHHHHHHHHHHHHHh--hhccccCCCCCCCCChHHHHHHHHHHHHHHHHHH
Q 000144 173 TAWKREGFCSRHKGAEQIQPLPEKYANSAAPVLDALFIYWENKL--SLAESVGQENPRASDHVAERRKLANELTFAVVEM 250 (2057)
Q Consensus 173 ~awk~~~fC~~H~~~~~~~~lp~~l~~~~~~~~~~ll~~~~~~l--~~~e~~~~~~~~~~~~~~~~~k~a~~l~~~i~~~ 250 (2057)
.+|...++|..|....++-++-..++.. +..+.++.+|-... .|.. ...+....|...+..++++++...|+.+
T Consensus 688 ~~~y~~~~~r~~~y~~DI~~~Q~~la~~--d~~~~l~~~l~r~~L~~w~~--g~~~~~~~d~~~~i~~~~ee~l~lii~l 763 (1738)
T KOG1140|consen 688 AAYYKNNPCRNESYDRDILMLQTGLAME--DPNRFLFTILSRFELLDWFT--GEVDYQSNDTEDTISFMIEEFLALIILL 763 (1738)
T ss_pred hHhhcCccccccchhHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHhc--CCCccccccHHHHHHHHHHHHHHHHHHH
Confidence 9999999999998775544443333322 22333333322211 1211 1123334566667778888887777777
Q ss_pred HHHHHhchHHHHHHHHHHhhccchhHHHHHhhccCCCHHHHHHHHHHHHHhhCChhhHHHHHHHHHhhhHHHHHHHHHhc
Q 000144 251 LLEFCKNSESLLSFVSKRVISVIGLLDILVRAEMFSSDVVVRKLHELLLKLLGEPIFKYEFAKVFLSYYPVFVKDAIREH 330 (2057)
Q Consensus 251 l~e~~~~~~~ll~~l~~~l~~~~~ll~~l~~~~~~l~k~~r~~lh~LllsLL~d~efK~~fa~~Fv~~Y~~i~~~fl~~d 330 (2057)
+.|+... .+..+........+++.+|......+.+.+++..|.+...+..|..++..++..+...|+...--.++..
T Consensus 764 l~Er~~~---~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~~d~~~e~Va~~~~p~~~~~~gvf~lK~~ 840 (1738)
T KOG1140|consen 764 LTERSYF---GSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLSFDEALEEVAVFKKPKGLADNGVFVLKES 840 (1738)
T ss_pred HHheeec---ccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhcccchHHHHHHHhhccCCccccceEEEechh
Confidence 7665543 1111111122233455556655555667788899999988999999999999888888855433333433
Q ss_pred cccccccCCccceeeeeccccCCcHHHHHHhhcHHHHHHHHHHHHhhhhc--CCCCcceeccccccccchhhhhhhhhHh
Q 000144 331 SDDTIKKYPLLSTFSVQIFTVPTLTPRLVKEMNLLEMLLGCLREIFDSCA--GDDSCLQVAKWANLYETTNRVIGDIRFV 408 (2057)
Q Consensus 331 ~d~~~~~~s~v~~LSVQLFTvPsLA~~LV~e~nLL~iLl~tl~~~~~~~~--~~~~~l~~~~~~~~~~~y~~I~~DLryl 408 (2057)
-++.+..|-...++|+|.-+++++++...++.+.+...+..+...+..++ ..++-+.............+.+.++++.
T Consensus 841 ~~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~~~~~L~~~t~~~~~~~ii~r~~~~~~~~ 920 (1738)
T KOG1140|consen 841 YYDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKKGADILGAAVRLTVFGLIIYRTLEHCLFM 920 (1738)
T ss_pred hhhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33334455556688999999999999888877665444444444443333 1222222211111122334566778888
Q ss_pred hcchhhhHHHhhhchHHHHHHHHHHHHhcCCC--cccccccCcceeeCCceeehh-hhhhHHHHhHHhhhhhcccccccc
Q 000144 409 MSHAAVSKYATHEQLNISKAWMKLLTFVQGMN--PQKRETGIHIREENEYMHLPL-VLDHSIANIQPLLVDGAFSSAVSE 485 (2057)
Q Consensus 409 Lsh~~v~~~l~~~~~~l~~~~l~lL~~~QGMn--~~kRq~~~HVEyE~e~w~~aF-~L~~~la~i~~~~~~~~~~~~~~~ 485 (2057)
+++--..+.+..-.-...+.++..+..+++|. +..|++|--.-++.. ...++ ...+.+..++.++..+.++..++.
T Consensus 921 ~s~~~l~~~~~~ihG~~~~~~l~~~~~~~~~~~e~~~~e~gl~~~e~lv-~~~~~~~~~~~~~v~~~l~~~~~~~~~n~~ 999 (1738)
T KOG1140|consen 921 ESSTLLSKVLHLIHGIALNEELINMKFAFTQKTESIAREKGLSLYESLV-RKPDSLVHGKIIEVIVELFESLIKSRANDP 999 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccchhhHHHhh-hcchhhcCCcceeeeHHHHhhhhhhhcCCc
Confidence 88765555543334578899999999999999 999999977755554 43333 344778888999888888888775
Q ss_pred ccc-cccccccccCCCCCccccccccccccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHh
Q 000144 486 ETR-YDFSMYKQDIGDGDSLRHAKVGRLSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMEN 564 (2057)
Q Consensus 486 ~~~-~~~~~~~~~~~~~~~~~~~~v~r~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~cl~~l~~ 564 (2057)
|.. ...-|.+..+.+++..+.++.+|+..|..++...--+.-+..=+.+..+. .+..+-+.|.+....+.++......
T Consensus 1000 ea~~~~~~~~~~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e-~d~~~~~~~~~~~~~~~~~d~~~~~ 1078 (1738)
T KOG1140|consen 1000 EVANDEKDKKEKQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDE-FDEQENQTPSSGSKTYEEEDFTCAL 1078 (1738)
T ss_pred cccccccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccc-cCcccccCccccccchhhhhccchh
Confidence 443 44455555556777777888888888887775433332222211111111 2334445666666677776665544
Q ss_pred hhcCCCCcccccccCCCCcccccCchhhhh-----HhhhhhccccccccccccCCccccccccccCCCccccccCccccc
Q 000144 565 WLGVDDRSVSVNDILSPNASRISGSNFVAL-----KKTLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKI 639 (2057)
Q Consensus 565 ~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 639 (2057)
.++....... ....++. .+-++... ...+..........+.|++...+.+ .+.+
T Consensus 1079 ~~~~s~~~~~-~~~~~~~----~~~~~~~~~i~~e~e~~~~~~~~~~v~~~f~~~s~~~s-------------d~l~--- 1137 (1738)
T KOG1140|consen 1079 CQDNSCTDFQ-VKPASHL----VKPIFRECIICDENEDVPNWDGRYSVSSAFAQKSDDVS-------------DALT--- 1137 (1738)
T ss_pred hhccchhccc-cccchhh----hcccccccccCChhccCCCccccchhhhHhhhhccccc-------------cccc---
Confidence 4321111000 0001111 00000000 0000011111122222222111110 0000
Q ss_pred cccCCcccccccccCcCCccccccch-----------------hcccccc------ccccCccCceeeeccCCceeeehH
Q 000144 640 TISGERDTASWRSAGFNDSEMEGECA-----------------TELDNLH------VLSLCYWPDITYDVSSQDVSVHIP 696 (2057)
Q Consensus 640 ~~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~------~~~~~~~~~v~fdVs~~~VSfH~P 696 (2057)
-++...|+ .....+||.- -+.-+|. .+...-|.-..++|+-..+.-|-+
T Consensus 1138 -~p~~~~~~-------~~~s~c~h~mh~~c~~~~~~a~r~~~n~~~~~l~~~~se~~l~lCp~c~slsn~~lp~~~~~~~ 1209 (1738)
T KOG1140|consen 1138 -EPGSLSCG-------TVLSSCGHHMHYGCFKRYVQAKRFRENARTAPLCQHYSENGLFLCPLCKSLSNVSLPMFLPPEL 1209 (1738)
T ss_pred -CCCCCccc-------ceeeccCCcchHHHHHHHHHHHHHHHHhhhcCcccccccCCcccCCchHhhhhccCCcCCchhh
Confidence 00111111 0001122110 0000000 111112223346778788899999
Q ss_pred HHHHHHHHHHHHHhhhccccccccccccCCCCCccccchhhhhcccCCCCCcccchhhccccHHHHHHHHhHhcCceeec
Q 000144 697 LHRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFSAFVMEHPLRIRVFCAQVHAGMWRRN 776 (2057)
Q Consensus 697 Lhr~Ls~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~e~pLR~~Vl~aQI~aGmWvRN 776 (2057)
+++.++...+..+..+++.-...+...-..+.....++..|.......+.+-++..+-..+...+.+++.+++++||--
T Consensus 1210 ~~n~~t~~~~~n~~~~i~~rs~~~~s~~~vs~~~s~~~~~~~ss~i~e~kp~~~~~l~~~~~~~ie~~~k~v~s~~~k~- 1288 (1738)
T KOG1140|consen 1210 LLNPLTLENQRNLNSWIEKRSRASFSLQDVSSILSDPWAAFTSSRIPELKPILIMDLPDSVVEQIELFQKIVGSAMFKP- 1288 (1738)
T ss_pred hcChhhhhchHHHHHHHHHhchhhcchhhhhhhhcccchhhccccccccccchHhhhhhHHHHHHHHHHHHHhhheeec-
Confidence 9998888777766555441000000000000001122222322112222232211223456677999999999999977
Q ss_pred cHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccccCCCCCCCchh-HHHHHHHHHHHHh
Q 000144 777 GDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLNLERPSEYEP-ILVQEMLTLIIQI 855 (2057)
Q Consensus 777 G~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~~~~~~~~~y~~-~mvEe~L~lLI~l 855 (2057)
|. .. ...+-+..-+.+.|++|++.++.+.......++.+++...++.++......+.. ..+.. ...+++
T Consensus 1289 ~~------~i--~~~~le~~~~~~~~~~~~~~~~s~a~~~~~~~l~~~~~~~~l~l~~~~~~~~~~~~~l~~--~~~~~~ 1358 (1738)
T KOG1140|consen 1289 SS------LL--STNTLELTLFSREFLIVCWQSLSDAEQSTKLLLSASKKPSFLKLNEDMTFCLVTISRLRA--LHWEQI 1358 (1738)
T ss_pred cc------ce--eecccccCcccchhhhhhhhccchHHHHHHHHHhccCCcccccCchhhHHHHHHHHHHHH--HHHHHH
Confidence 21 12 234667888899999999999999999999999999988887776543333322 22222 456777
Q ss_pred hcccccCCCChHHHHHHHHHHHHhcCCCChHHHHhhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEEeccccccccc
Q 000144 856 LQERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDI 935 (2057)
Q Consensus 856 lteR~~~g~t~~e~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dp 935 (2057)
+.++...++-.....+.++|-.+..++.+++.+...+|.+..+...++.++..|- +.|.+.-.+.+.++.-.|.|.+-
T Consensus 1359 l~~~~~~~llk~~s~~~~~i~~~~tpd~~~~~ll~~l~~~~~~~~~l~~~~~~~~--~~~~~~~~~~i~~~~i~s~elit 1436 (1738)
T KOG1140|consen 1359 LYELVYTFLLKSFSPTIPRISVLITPDQPENELLVILPHDFPKSLELELTLDFVN--KNPKKIFELKILMASIISIELIT 1436 (1738)
T ss_pred HHHHHHHHHHHHHhhcCCcchhccCCCCCcchhhhccchhhhhhccHHHHHHHhh--hhHHHHHhHHHHHHHhhhhhhhe
Confidence 8888777776677778888888888899999999999999999999999999988 56777788999999999999998
Q ss_pred cccccCchhHHHHHHHHHHhhcccccc--CCCCCCccccCCccccccccccHHHHHHHHHHHHHHhc
Q 000144 936 YHPRWSSRDLQVAEERYLRFCSVSALT--AQLPRWTKIYYPLESIAGIATCKVVLQVIRAVLFYAVF 1000 (2057)
Q Consensus 936 y~~~y~~~~~q~aeer~~r~~k~~a~~--~~~P~~~~~~~p~~~l~~il~s~~~~~il~~vL~~al~ 1000 (2057)
++..+.. |.+.|+++..+..-..+.. ...+.++....+-.++.++--+....+.+...|.++..
T Consensus 1437 s~s~l~~-d~~~~~~q~s~~e~~~~~t~l~~~~s~~~i~~~~~~~~~~~L~~~~~~~i~sfL~~~al 1502 (1738)
T KOG1140|consen 1437 SHSYLEN-DLEMAEEQKSIDEFKSLLTYLLQLESSRTIPKLADIRLRLSLCLSCEAGILSFLRRAAL 1502 (1738)
T ss_pred eccccCC-ccchhhhhhhHHhHhHHHHHHHhccchhhCccccchhhhhHHHHHHHHHHHHHHHHHHH
Confidence 8888877 8777776644322222222 22334443333334555666677777888887877643
No 4
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=99.78 E-value=1.5e-19 Score=170.78 Aligned_cols=70 Identities=44% Similarity=1.070 Sum_probs=66.3
Q ss_pred ccccccccCCceeEEecccCCCCCccccccccCCCCCCCceeEEEec-CCccccCCCcccccccCCCCcCC
Q 000144 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYT-GGGCCDCGDVTAWKREGFCSRHK 185 (2057)
Q Consensus 116 ~~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~~~~~-~gG~CDCGd~~awk~~~fC~~H~ 185 (2057)
.+||++|++++++|+|+||+.++++++|.+||+++.|+||+|.++++ +||.|||||++|||++|||++|.
T Consensus 1 ~~C~~~~~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~~~~~~~~~~~CDCG~~~~~~~~~~C~~h~ 71 (71)
T smart00396 1 DVCTYKFTGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDYSLKTSRGSGICDCGDKEAWNEDLKCKAHE 71 (71)
T ss_pred CCCCCccCCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCEEEEEecCCEEECCCChhccCCCccccccC
Confidence 47999999999999999999999999999999999999999999885 45999999999999999999994
No 5
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=99.72 E-value=2e-18 Score=163.93 Aligned_cols=70 Identities=49% Similarity=1.112 Sum_probs=54.0
Q ss_pred ccccccccCCceeEEecccCCCCCccccccccCCCCCCCceeEEEecC-CccccCCCcccccccCCCCcCC
Q 000144 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTG-GGCCDCGDVTAWKREGFCSRHK 185 (2057)
Q Consensus 116 ~~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~~~~~~-gG~CDCGd~~awk~~~fC~~H~ 185 (2057)
+.|+++|++++++|+|+||+.+++.+||.+||.++.|+||++.+..+. +|.|||||+++||+++||++|+
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=99.03 E-value=2.8e-09 Score=133.85 Aligned_cols=185 Identities=22% Similarity=0.324 Sum_probs=142.2
Q ss_pred hccccHHHHHHHHhHhcCceeeccHHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccccC
Q 000144 754 VMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLN 833 (2057)
Q Consensus 754 l~e~pLR~~Vl~aQI~aGmWvRNG~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~~~ 833 (2057)
+.-++++..|--.-++..||+|+|.-...-...|-+-.+-...---+--.+-.++..+++..|+...+-+|.+.+.-..+
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 45667899999999999999999998877777775544433333333445556888999999999999999877542211
Q ss_pred C--------C-----C-------------------C--------------------------------------------
Q 000144 834 L--------E-----R-------------------P-------------------------------------------- 837 (2057)
Q Consensus 834 ~--------~-----~-------------------~-------------------------------------------- 837 (2057)
- . . +
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 000144 838 --SEYE--PILVQEMLTLIIQILQERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDL-SKFDQLQEILDAVAMY 912 (2057)
Q Consensus 838 --~~y~--~~mvEe~L~lLI~llteR~~~g~t~~e~lrrEIIh~Lc~~p~t~S~L~~~lpe~~-~~~~~fe~iL~eVA~f 912 (2057)
..|+ +.|...++.++..+|.++.+.|...++..+-|+.|.-+++..+||-+..++.+.. ...+.|+.|+.+..+|
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----CCcceEEEeccccc-ccccccc
Q 000144 913 SHPSG----FNQGMYSLRWSYWK-ELDIYHP 938 (2057)
Q Consensus 913 ~~P~g----~~~G~Y~LK~e~~~-e~dpy~~ 938 (2057)
-.|-- .-+|.|.||.-.|+ +.-|-++
T Consensus 447 ~~P~~~~~p~~~~s~~l~~~~~~~~~c~~~~ 477 (784)
T KOG1139|consen 447 IEPIETTTPLMQGSYQLKTSIWDSEVCPVFF 477 (784)
T ss_pred ccchhhcCccccchhhccccCCccccccchh
Confidence 99942 24799999999997 4556444
No 7
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=96.96 E-value=0.00051 Score=83.04 Aligned_cols=80 Identities=26% Similarity=0.419 Sum_probs=60.7
Q ss_pred HHHHHHHHHHhcCCCChHHHHhhCCCCCCC---cchHHHHHHHHccccCCCCCCcceEEEeccccccccccccccCchhH
Q 000144 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSK---FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (2057)
Q Consensus 869 ~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~---~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dpy~~~y~~~~~ 945 (2057)
.+|.-|||.||.+|....||...|..+... -..++.||.+||... .++.|.||+.+|+|+|.=++.|+-.|+
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 246999999999975 378999999999999977888998888
Q ss_pred HHHHHHHH
Q 000144 946 QVAEERYL 953 (2057)
Q Consensus 946 q~aeer~~ 953 (2057)
|..+-+..
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=94.99 E-value=0.012 Score=71.45 Aligned_cols=62 Identities=34% Similarity=0.561 Sum_probs=50.6
Q ss_pred cCCCccccc-----cccCCceeEEecccCCCCCccccccccCCCCCCCceeEEEecCCccccCCCccc
Q 000144 112 IGQRGVCGA-----VWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDVTA 174 (2057)
Q Consensus 112 ~~~~~~C~~-----v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~~~~~~gG~CDCGd~~a 174 (2057)
.-+.++|-. .+-+=.-+|||-||...+.-+||..|.++ -|+||++-..+...-.||||-..+
T Consensus 540 Aik~GqCLfkvSs~~syPMHnFYRC~TCNttdRNAIC~nCI~~-CH~GH~Vefir~Drffcdcgagtl 606 (625)
T KOG1777|consen 540 AIKKGQCLFKVSSYTSYPMHNFYRCITCNTTDRNAICVNCIKR-CHEGHDVEFIRHDRFFCDCGAGTL 606 (625)
T ss_pred HhhcCceEEEecCCCcccccceeEeeecCCccccHHHHHHHHH-hcCCCceEEEeeceEEEecCCcee
Confidence 445567743 34444568999999999999999999988 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=91.31 E-value=0.064 Score=46.51 Aligned_cols=20 Identities=25% Similarity=0.790 Sum_probs=16.5
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000144 1427 HLSSCGHAVHQGCLDRYVSS 1446 (2057)
Q Consensus 1427 h~SsCGH~MH~~C~~~Y~~S 1446 (2057)
..-.|||..|.+|+++|++.
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=91.26 E-value=0.17 Score=43.04 Aligned_cols=19 Identities=37% Similarity=1.001 Sum_probs=16.3
Q ss_pred ccccChHhhHHHHHHHHHH
Q 000144 1428 LSSCGHAVHQGCLDRYVSS 1446 (2057)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~S 1446 (2057)
+..|||..|..|+++|++.
T Consensus 15 ~~~C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 15 LLPCGHVFCRSCIDKWLKS 33 (45)
T ss_pred ecCCCChhcHHHHHHHHHh
Confidence 5669999999999998664
No 11
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=90.78 E-value=0.92 Score=62.10 Aligned_cols=70 Identities=16% Similarity=0.197 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH-H--HhhccccccCCCCCCCccCCCCcccccccccCCccccccCCCC---CCCeE
Q 000144 1146 SEKRKAKARERQAAILEKMKAEQFK-F--LSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS---RTPVS 1219 (2057)
Q Consensus 1146 ~ekkK~~AkeRQakIMaqm~~qQ~~-F--l~~n~~~~~~~~~~~~~~~~s~~~~~~~e~~~~~CilCqe~~~---~~pfg 1219 (2057)
+.+||++|.++|+|.+.+|.-++.+ - +.+..... + .+ +.+ +|. -..|.+|+|.-+ ++++|
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-N----------ME-DLE-EED-GLTCCICREGYKFRPDEVLG 487 (802)
T ss_pred HHHHHHHHHHHHHHHHHHccCccccccceecCchhhc-C----------cc-ccc-ccC-CCeEEEcCCccccCCcccee
Confidence 5677889999999999998433200 0 00111000 0 00 011 122 367999999853 46899
Q ss_pred EEeeeecccc
Q 000144 1220 YLILLQKSRL 1229 (2057)
Q Consensus 1220 ~la~iq~S~l 1229 (2057)
+-+|.-+-.+
T Consensus 488 iY~f~kr~~l 497 (802)
T PF13764_consen 488 IYAFSKRVNL 497 (802)
T ss_pred eEEEeecccc
Confidence 9887755444
No 12
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=88.80 E-value=0.13 Score=68.56 Aligned_cols=63 Identities=27% Similarity=0.695 Sum_probs=50.5
Q ss_pred ccccccccCCc----eeEEecccCCCCCccccccccCCCCCCCceeEEEe-cCCccccCCCcccccc-cCCCCcC
Q 000144 116 GVCGAVWGNND----IAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVTAWKR-EGFCSRH 184 (2057)
Q Consensus 116 ~~C~~v~~~~e----~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~~~~-~~gG~CDCGd~~awk~-~~fC~~H 184 (2057)
..|.-.|+..+ -+|.|+||+.-.+-|-|.+|-.- .|+||+.++-+ +.-.+||| |-+ +..|+.-
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 57999999999888899999765 69999999987 56899999 655 3446544
No 13
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=88.46 E-value=0.15 Score=60.08 Aligned_cols=48 Identities=35% Similarity=0.749 Sum_probs=34.3
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhccc---ccCCCcccCCCCcccccccccc
Q 000144 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRI---IFEGGHIVDPDQGEFLCPVCRQ 1477 (2057)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~---~~er~h~~d~e~gEFLCPLCKs 1477 (2057)
...|-|.||+.|+.+|+...+...++.. .-++.|. .+.-|=+||+||-
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 6889999999999999999876554221 1223332 3456778999984
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=85.27 E-value=0.65 Score=41.52 Aligned_cols=39 Identities=28% Similarity=0.878 Sum_probs=29.7
Q ss_pred cccccccCCceeEEecccCCCCCccccccccCCC----CCC-CceeEE
Q 000144 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG----NHK-EHDYSI 159 (2057)
Q Consensus 117 ~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~----~H~-~H~~~~ 159 (2057)
.|++.... ..-|+|..|. ..-+|.+||..+ .|+ +|.|.+
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 4899999996 367999999998 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=84.41 E-value=0.75 Score=40.01 Aligned_cols=37 Identities=27% Similarity=0.654 Sum_probs=29.6
Q ss_pred cccccccCCceeEEecccCCCCCccccccccCCCCCCCceeE
Q 000144 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2057)
Q Consensus 117 ~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~ 158 (2057)
.|+..+ .| .-|+|.+|. ..-+|.+||.++.|.+|.+.
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 789999997 46799999999999888874
No 16
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=83.87 E-value=1 Score=57.30 Aligned_cols=77 Identities=26% Similarity=0.375 Sum_probs=63.1
Q ss_pred HHHHHHHHHHhcCCCChHHHHhhCCCCCCCc---chHHHHHHHHccccCCCCCCcceEEEeccccccccccccccCchhH
Q 000144 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSKF---DQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (2057)
Q Consensus 869 ~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~~---~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~dpy~~~y~~~~~ 945 (2057)
-||.-|||+|+.++..--||.++|-.+...+ ..+..||.+.. ...+|+|.|++.+|+|+|-=++.|+-.|.
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 24789999999999999988888888887
Q ss_pred HHHHHH
Q 000144 946 QVAEER 951 (2057)
Q Consensus 946 q~aeer 951 (2057)
|..+-+
T Consensus 285 ~~lkr~ 290 (604)
T KOG4796|consen 285 QHLKRV 290 (604)
T ss_pred HHHHHH
Confidence 766444
No 17
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=83.35 E-value=0.72 Score=45.74 Aligned_cols=24 Identities=21% Similarity=0.508 Sum_probs=19.7
Q ss_pred CCCccccccChHhhHHHHHHHHHH
Q 000144 1423 CDGIHLSSCGHAVHQGCLDRYVSS 1446 (2057)
Q Consensus 1423 ~~gvh~SsCGH~MH~~C~~~Y~~S 1446 (2057)
..++=...|||.-|..|..+.+++
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 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=83.23 E-value=0.71 Score=39.25 Aligned_cols=20 Identities=30% Similarity=0.843 Sum_probs=18.4
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000144 1427 HLSSCGHAVHQGCLDRYVSS 1446 (2057)
Q Consensus 1427 h~SsCGH~MH~~C~~~Y~~S 1446 (2057)
.+..|||..+..|+.+|+++
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
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=82.97 E-value=0.86 Score=40.16 Aligned_cols=37 Identities=27% Similarity=0.812 Sum_probs=29.4
Q ss_pred cccccccCCceeEEecccCCCCCccccccccCCC--CCC-CceeE
Q 000144 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG--NHK-EHDYS 158 (2057)
Q Consensus 117 ~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~--~H~-~H~~~ 158 (2057)
.|++.+. | .-|+|.+|. ..-+|.+||..+ .|. +|.+.
T Consensus 5 ~C~~~i~-g-~r~~C~~C~---d~dLC~~Cf~~~~~~H~~~H~~~ 44 (46)
T cd02249 5 GCLKPIV-G-VRYHCLVCE---DFDLCSSCYAKGKKGHPPDHSFT 44 (46)
T ss_pred CCCCCCc-C-CEEECCCCC---CCcCHHHHHCcCcCCCCCCCCEe
Confidence 5788544 5 899999997 477999999998 776 77764
No 20
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=81.13 E-value=1.3 Score=38.46 Aligned_cols=31 Identities=35% Similarity=0.864 Sum_probs=25.1
Q ss_pred CccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccc
Q 000144 1425 GIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2057)
Q Consensus 1425 gvh~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCKs 1477 (2057)
...+.+|||.+..+|.++-. .+...||+|++
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 24567999984
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=81.05 E-value=1.3 Score=36.09 Aligned_cols=18 Identities=22% Similarity=0.892 Sum_probs=16.3
Q ss_pred ccccChHhhHHHHHHHHH
Q 000144 1428 LSSCGHAVHQGCLDRYVS 1445 (2057)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~ 1445 (2057)
...|||..|..|+++|++
T Consensus 13 ~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 13 VLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred EecCCChHHHHHHHHHHH
Confidence 567999999999999977
No 22
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=80.65 E-value=1.3 Score=39.76 Aligned_cols=38 Identities=26% Similarity=0.792 Sum_probs=29.0
Q ss_pred ccc-ccccCCceeEEecccCCCCCccccccccCCC----CCC-CceeEE
Q 000144 117 VCG-AVWGNNDIAYRCRTCEHDPTCAICVPCFQNG----NHK-EHDYSI 159 (2057)
Q Consensus 117 ~C~-~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~----~H~-~H~~~~ 159 (2057)
.|+ ..+. ..-|+|..|. ..-+|.+||..+ .|+ .|.+.+
T Consensus 5 ~C~~~~i~--g~R~~C~~C~---d~dlC~~Cf~~~~~~~~H~~~H~~~~ 48 (49)
T cd02338 5 GCGKSNFT--GRRYKCLICY---DYDLCADCYDSGVTTERHLFDHPMQC 48 (49)
T ss_pred CCcCCCcE--EeeEEeCCCC---CCccchhHHhCCCcCCCCCCCCCEEE
Confidence 477 4455 4889999995 577999999988 676 777754
No 23
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=79.55 E-value=1.2 Score=51.80 Aligned_cols=62 Identities=23% Similarity=0.212 Sum_probs=46.6
Q ss_pred HHHHHHHHHH--hcCCCChHHHHhhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEEeccccc
Q 000144 869 SLKRELVHRL--AIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWK 931 (2057)
Q Consensus 869 ~lrrEIIh~L--c~~p~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~ 931 (2057)
.=|+||+-.| ||.-..|=-|...+-..-....-+.+||++||+|.+ .|..+|+|+|||||-+
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 788777766655444444445678999999999976 3667899999999864
No 24
>cd02344 ZZ_HERC2 Zinc finger, ZZ type. Zinc finger present in HERC2 and related proteins. HERC2 is a potential E3 ubiquitin protein ligase and/or guanine nucleotide exchange factor. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=78.50 E-value=1.7 Score=38.31 Aligned_cols=39 Identities=26% Similarity=0.695 Sum_probs=29.8
Q ss_pred cccccccCCceeEEecccCCCCCccccccccCCCCC-CCceeEE
Q 000144 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYSI 159 (2057)
Q Consensus 117 ~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H-~~H~~~~ 159 (2057)
.|+..--.| .-|+|.+|. ..-+|..||....| .+|.|..
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 355443334 789999998 45699999999999 5898853
No 25
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=77.39 E-value=2.6 Score=50.66 Aligned_cols=61 Identities=25% Similarity=0.638 Sum_probs=47.6
Q ss_pred cCCCcccccc--ccCCceeEEecccCCCC-CccccccccCCCCCCCceeEEEe-cCCccccCCCcc
Q 000144 112 IGQRGVCGAV--WGNNDIAYRCRTCEHDP-TCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVT 173 (2057)
Q Consensus 112 ~~~~~~C~~v--~~~~e~~y~C~~C~~d~-t~~~C~~CF~~~~H~~H~~~~~~-~~gG~CDCGd~~ 173 (2057)
...+..|++. ..+-...|.|.||..+| ...+|..|=.+ -|.||.-..-. .+..-||||+.-
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 3556778654 33446889999999998 88899999775 69999987655 567889999853
No 26
>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=77.18 E-value=1.3 Score=37.89 Aligned_cols=37 Identities=24% Similarity=0.610 Sum_probs=28.2
Q ss_pred ccccccccCCceeEEecccCCCCCccccccccCCCCCCCceeE
Q 000144 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2057)
Q Consensus 116 ~~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~ 158 (2057)
..|..-- +....|.|.+|.. .+|..|+..+ |++|++.
T Consensus 4 ~~C~~H~-~~~~~~~C~~C~~----~~C~~C~~~~-H~~H~~~ 40 (42)
T PF00643_consen 4 PKCPEHP-EEPLSLFCEDCNE----PLCSECTVSG-HKGHKIV 40 (42)
T ss_dssp SB-SSTT-TSBEEEEETTTTE----EEEHHHHHTS-TTTSEEE
T ss_pred ccCccCC-ccceEEEecCCCC----ccCccCCCCC-CCCCEEe
Confidence 4453332 2348999999997 8999999998 9999975
No 27
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=75.07 E-value=0.95 Score=43.62 Aligned_cols=39 Identities=38% Similarity=0.710 Sum_probs=21.0
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccc
Q 000144 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2057)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCKs 1477 (2057)
-..||+..|..|+.+||.+.... |. .+++-.|+ ||.|+.
T Consensus 25 n~~C~~~fH~~CL~~wf~~~~~~---~~------~~~~~~G~--CP~C~~ 63 (70)
T PF11793_consen 25 NPSCGKKFHLLCLSEWFLSLEKS---RQ------SFIPIFGE--CPYCSS 63 (70)
T ss_dssp -TT----B-SGGGHHHHHHHHSS---S-------TTT--EEE---TTT-S
T ss_pred CcccCCHHHHHHHHHHHHHcccC---Ce------eecccccC--CcCCCC
Confidence 35899999999999999887642 11 23455666 999986
No 28
>PHA02926 zinc finger-like protein; Provisional
Probab=74.23 E-value=2.4 Score=48.87 Aligned_cols=46 Identities=24% Similarity=0.532 Sum_probs=35.3
Q ss_pred CCCccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccccccceecC
Q 000144 1423 CDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPA 1485 (2057)
Q Consensus 1423 ~~gvh~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCKsLsNsvLPi 1485 (2057)
.+|+ ++.|||.-.+.|..+..++-+ + ..++-.||+||.-...|.|-
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 4677 999999999999999765311 0 12566899999998887764
No 29
>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=73.89 E-value=1.5 Score=45.79 Aligned_cols=27 Identities=30% Similarity=0.790 Sum_probs=22.5
Q ss_pred hhcccCCCCCC----CCCceeeeccCccccC
Q 000144 1932 IKQCCSDCKSV----LDEPALCLLCGRLCSP 1958 (2057)
Q Consensus 1932 ~~~~C~~c~~~----~~~paiCL~CG~~~~~ 1958 (2057)
.+|.||+||+. .++|++|-.||+..-.
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCc
Confidence 47899999986 6899999999996443
No 30
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=72.72 E-value=1.7 Score=52.82 Aligned_cols=16 Identities=38% Similarity=1.059 Sum_probs=14.8
Q ss_pred ccChHhhHHHHHHHHH
Q 000144 1430 SCGHAVHQGCLDRYVS 1445 (2057)
Q Consensus 1430 sCGH~MH~~C~~~Y~~ 1445 (2057)
.|||..|++|+++.++
T Consensus 317 pCGHilHl~CLknW~E 332 (491)
T COG5243 317 PCGHILHLHCLKNWLE 332 (491)
T ss_pred cccceeeHHHHHHHHH
Confidence 6999999999999875
No 31
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=69.01 E-value=3.8 Score=46.88 Aligned_cols=53 Identities=21% Similarity=0.517 Sum_probs=35.2
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccccc--cceecCC
Q 000144 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLA--NSVLPAL 1486 (2057)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCKsLs--NsvLPil 1486 (2057)
+..|||.-...|..+|+..-.. .++ +....+-.++...||+||+-- +.++|+.
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=36.37 Aligned_cols=30 Identities=27% Similarity=0.907 Sum_probs=24.8
Q ss_pred ceeEEecccCCCCCccccccccCCCCC-CCceeE
Q 000144 126 DIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYS 158 (2057)
Q Consensus 126 e~~y~C~~C~~d~t~~~C~~CF~~~~H-~~H~~~ 158 (2057)
..-|+|.+|. ..-+|.+||..+.| .+|.|.
T Consensus 13 G~RykC~~C~---dyDLC~~C~~~~~H~~~H~f~ 43 (45)
T cd02339 13 GIRWKCAECP---NYDLCTTCYHGDKHDLEHRFY 43 (45)
T ss_pred cCeEECCCCC---CccchHHHhCCCCCCCCCCEE
Confidence 5679999996 36799999999998 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=65.63 E-value=3 Score=44.28 Aligned_cols=26 Identities=23% Similarity=0.350 Sum_probs=22.2
Q ss_pred hhcccCCCCCC----CCCceeeeccCcccc
Q 000144 1932 IKQCCSDCKSV----LDEPALCLLCGRLCS 1957 (2057)
Q Consensus 1932 ~~~~C~~c~~~----~~~paiCL~CG~~~~ 1957 (2057)
.+|.||+|+++ .++|++|-.||+..-
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFP 37 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccC
Confidence 46889999986 589999999999643
No 34
>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=62.32 E-value=5.8 Score=33.12 Aligned_cols=28 Identities=25% Similarity=0.451 Sum_probs=23.9
Q ss_pred ceeEEecccCCCCCccccccccCCCCCCCceeE
Q 000144 126 DIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2057)
Q Consensus 126 e~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~ 158 (2057)
...|-|.+|+. .+|..|-..+ |++|.+.
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 45788999886 8999999888 9999875
No 35
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=60.67 E-value=4.3 Score=48.94 Aligned_cols=35 Identities=26% Similarity=0.866 Sum_probs=27.2
Q ss_pred ccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccccccce
Q 000144 1426 IHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSV 1482 (2057)
Q Consensus 1426 vh~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCKsLsNsv 1482 (2057)
++.-.|||.||+.||+.|.. .+ |-||+|..++|+.
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 34778999999999998721 25 8999999866554
No 36
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=59.66 E-value=5.1 Score=35.78 Aligned_cols=35 Identities=29% Similarity=0.691 Sum_probs=27.1
Q ss_pred cccccccCCceeEEecccCCCCCccccccccCCCCCC-Cce
Q 000144 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK-EHD 156 (2057)
Q Consensus 117 ~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H~-~H~ 156 (2057)
.|++... ..-|+|..|. ..-+|.+||.++.+. +|+
T Consensus 5 gC~~~~~--~~RykCl~C~---d~DlC~~Cf~~g~~~~~H~ 40 (48)
T cd02343 5 GCDEIAP--WHRYRCLQCT---DMDLCKTCFLGGVKPEGHE 40 (48)
T ss_pred CCCCcCC--CceEECCCCC---CchhHHHHHhCCccCCCCC
Confidence 4777543 4799999997 477999999998874 454
No 37
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=58.43 E-value=2.4 Score=41.19 Aligned_cols=18 Identities=28% Similarity=0.846 Sum_probs=15.5
Q ss_pred cccccChHhhHHHHHHHH
Q 000144 1427 HLSSCGHAVHQGCLDRYV 1444 (2057)
Q Consensus 1427 h~SsCGH~MH~~C~~~Y~ 1444 (2057)
-...|||+-|..|..+.+
T Consensus 46 ~~~~C~H~FH~~Ci~~Wl 63 (73)
T PF12678_consen 46 VWGPCGHIFHFHCISQWL 63 (73)
T ss_dssp EEETTSEEEEHHHHHHHH
T ss_pred EecccCCCEEHHHHHHHH
Confidence 367799999999998776
No 38
>PHA02929 N1R/p28-like protein; Provisional
Probab=56.64 E-value=4.9 Score=47.74 Aligned_cols=37 Identities=41% Similarity=0.800 Sum_probs=27.2
Q ss_pred CccccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccccccceec
Q 000144 1425 GIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLP 1484 (2057)
Q Consensus 1425 gvh~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCKsLsNsvLP 1484 (2057)
|+ +..|||..|..|....++. + . .||+||.---.|+|
T Consensus 195 ~v-l~~C~H~FC~~CI~~Wl~~-------~-------~--------tCPlCR~~~~~v~~ 231 (238)
T PHA02929 195 GI-LSNCNHVFCIECIDIWKKE-------K-------N--------TCPVCRTPFISVIK 231 (238)
T ss_pred ee-cCCCCCcccHHHHHHHHhc-------C-------C--------CCCCCCCEeeEEee
Confidence 44 7789999999999986521 0 0 49999986655554
No 39
>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=56.61 E-value=7.3 Score=34.87 Aligned_cols=32 Identities=25% Similarity=0.736 Sum_probs=24.4
Q ss_pred ceeEEecccCCCCCccccccccCCC-CC-CCceeE
Q 000144 126 DIAYRCRTCEHDPTCAICVPCFQNG-NH-KEHDYS 158 (2057)
Q Consensus 126 e~~y~C~~C~~d~t~~~C~~CF~~~-~H-~~H~~~ 158 (2057)
.+-|+|.+|.- ...-+|.+||.++ .| .+|.+.
T Consensus 13 G~R~~C~~C~~-~d~DlC~~C~~~~~~H~~~H~~~ 46 (48)
T cd02341 13 GTRYHCSECDD-GDFDLCQDCVVKGESHQEDHWLV 46 (48)
T ss_pred cceEECCCCCC-CCCccCHHHHhCcCCCCCCCcee
Confidence 56699999973 3466999999999 67 467654
No 40
>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=54.19 E-value=5.6 Score=33.63 Aligned_cols=20 Identities=25% Similarity=0.933 Sum_probs=17.9
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000144 1427 HLSSCGHAVHQGCLDRYVSS 1446 (2057)
Q Consensus 1427 h~SsCGH~MH~~C~~~Y~~S 1446 (2057)
.+..|||....+|+++|++.
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 41
>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=53.90 E-value=8.7 Score=33.62 Aligned_cols=35 Identities=31% Similarity=0.846 Sum_probs=26.1
Q ss_pred ccccccccCCceeEEecccCCCCCccccccccCCCCCC-Cc
Q 000144 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK-EH 155 (2057)
Q Consensus 116 ~~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H~-~H 155 (2057)
..|++.+. ..-|+|..|. ..-||.+||..+.|. +|
T Consensus 8 ~~C~~~i~--g~ry~C~~C~---d~dlC~~Cf~~~~~~~~h 43 (44)
T smart00291 8 DTCGKPIV--GVRYHCLVCP---DYDLCQSCFAKGSAGGEH 43 (44)
T ss_pred CCCCCCCc--CCEEECCCCC---CccchHHHHhCcCcCCCC
Confidence 46888554 4578999994 577999999988664 44
No 42
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=52.76 E-value=4.8 Score=35.51 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=22.2
Q ss_pred cccccccCCceeEEecccCCCCCccccccccCCCCC
Q 000144 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 152 (2057)
Q Consensus 117 ~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H 152 (2057)
.||.-.+ .+-|+|..+. ...||.+||..|.-
T Consensus 5 ~Cg~D~t--~vryh~~~~~---~~dLC~~CF~~G~f 35 (45)
T cd02336 5 TCGNDCT--RVRYHNLKAK---KYDLCPSCYQEGRF 35 (45)
T ss_pred CCCCccC--ceEEEecCCC---ccccChHHHhCcCC
Confidence 4666665 4777777655 46799999988754
No 43
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=52.57 E-value=7.6 Score=33.59 Aligned_cols=32 Identities=25% Similarity=0.824 Sum_probs=25.0
Q ss_pred ccccccccCCceeEEecccCCCCCccccccccCCCCCC
Q 000144 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (2057)
Q Consensus 116 ~~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H~ 153 (2057)
..|+++ +++-|+|..|. -.-+|..||.+..|.
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 24999999997 366999999998883
No 44
>smart00336 BBOX B-Box-type zinc finger.
Probab=50.36 E-value=13 Score=31.56 Aligned_cols=29 Identities=21% Similarity=0.636 Sum_probs=24.0
Q ss_pred CceeEEecccCCCCCccccccccCCCCCCCceeE
Q 000144 125 NDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2057)
Q Consensus 125 ~e~~y~C~~C~~d~t~~~C~~CF~~~~H~~H~~~ 158 (2057)
....|-|.+|+. ++|..|... .|++|.+.
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 445777999885 899999988 99999875
No 45
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.85 E-value=11 Score=46.63 Aligned_cols=30 Identities=30% Similarity=0.601 Sum_probs=22.6
Q ss_pred CCCCCCcCCCccccccChHhhHHHHHHHHHH
Q 000144 1416 DGFGPIDCDGIHLSSCGHAVHQGCLDRYVSS 1446 (2057)
Q Consensus 1416 ~~F~~~~~~gvh~SsCGH~MH~~C~~~Y~~S 1446 (2057)
++|+.+...|. +++|||+.|..|+...|+-
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 34444444566 8999999999999988764
No 46
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.87 E-value=11 Score=47.94 Aligned_cols=29 Identities=41% Similarity=1.065 Sum_probs=25.1
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccc
Q 000144 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2057)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCKs 1477 (2057)
++-|-|++|-.|+++.|+.-+ ..||+||+
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 46999998
No 47
>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=48.75 E-value=8.1 Score=30.17 Aligned_cols=22 Identities=23% Similarity=0.717 Sum_probs=18.7
Q ss_pred cccCCCCCC-CCCceeeeccCcc
Q 000144 1934 QCCSDCKSV-LDEPALCLLCGRL 1955 (2057)
Q Consensus 1934 ~~C~~c~~~-~~~paiCL~CG~~ 1955 (2057)
++||.|+.. |..-..|-.||-.
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYD 23 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCC
Confidence 479999987 8888999999963
No 48
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=48.06 E-value=9.3 Score=28.93 Aligned_cols=20 Identities=30% Similarity=0.896 Sum_probs=17.4
Q ss_pred ccCCCCCC-CCCceeeeccCc
Q 000144 1935 CCSDCKSV-LDEPALCLLCGR 1954 (2057)
Q Consensus 1935 ~C~~c~~~-~~~paiCL~CG~ 1954 (2057)
.||+||.. +.+...|-.||+
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 59999988 778889999997
No 49
>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=47.57 E-value=7.1 Score=47.69 Aligned_cols=31 Identities=29% Similarity=0.463 Sum_probs=16.1
Q ss_pred cchHHHHHHHHccccCCCCCCcceEEEecccc
Q 000144 899 FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYW 930 (2057)
Q Consensus 899 ~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~ 930 (2057)
+.-+-+||++||+|.+ +|...|+|+|||||-
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 50
>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=45.30 E-value=14 Score=33.32 Aligned_cols=32 Identities=28% Similarity=0.742 Sum_probs=23.9
Q ss_pred cccccccCCceeEEecccCCCCCccccccccCCCCC
Q 000144 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 152 (2057)
Q Consensus 117 ~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~H 152 (2057)
.|++.=-.| .-|+|..|. ..-||.+||..+.|
T Consensus 5 ~C~~~pi~g-~RykC~~C~---d~DLC~~Cf~~g~~ 36 (49)
T cd02334 5 ICKEFPITG-FRYRCLKCF---NYDLCQSCFFSGRT 36 (49)
T ss_pred CCCCCCcee-eeEECCCCC---CcCchHHHHhCCCc
Confidence 466542233 789999997 46799999988865
No 51
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=44.50 E-value=8.1 Score=36.55 Aligned_cols=28 Identities=25% Similarity=0.744 Sum_probs=22.5
Q ss_pred HhhcccCCCCCC------CCCceeeeccCccccC
Q 000144 1931 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2057)
Q Consensus 1931 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1958 (2057)
+.+.+||.|++. +...+-|+.||+.++.
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 356789999874 6788999999996554
No 52
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=44.14 E-value=11 Score=29.34 Aligned_cols=22 Identities=23% Similarity=0.708 Sum_probs=18.8
Q ss_pred hcccCCCCCC-CCCceeeeccCc
Q 000144 1933 KQCCSDCKSV-LDEPALCLLCGR 1954 (2057)
Q Consensus 1933 ~~~C~~c~~~-~~~paiCL~CG~ 1954 (2057)
.+.||+|+.. +.+-..|-.||+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 4679999987 788889999997
No 53
>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=43.02 E-value=15 Score=32.79 Aligned_cols=18 Identities=33% Similarity=0.824 Sum_probs=16.6
Q ss_pred ccccChH-hhHHHHHHHHH
Q 000144 1428 LSSCGHA-VHQGCLDRYVS 1445 (2057)
Q Consensus 1428 ~SsCGH~-MH~~C~~~Y~~ 1445 (2057)
+.-|||. +-..|+.++++
T Consensus 17 ~~pCgH~~~C~~C~~~~~~ 35 (50)
T PF13920_consen 17 LLPCGHLCFCEECAERLLK 35 (50)
T ss_dssp EETTCEEEEEHHHHHHHHH
T ss_pred EeCCCChHHHHHHhHHhcc
Confidence 6789999 99999999987
No 54
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=39.77 E-value=20 Score=32.28 Aligned_cols=31 Identities=23% Similarity=0.842 Sum_probs=24.4
Q ss_pred ccccc-cccCCceeEEecccCCCCCccccccccCCCC
Q 000144 116 GVCGA-VWGNNDIAYRCRTCEHDPTCAICVPCFQNGN 151 (2057)
Q Consensus 116 ~~C~~-v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~ 151 (2057)
..|.+ -+. ++-|+|..|. .--+|.+||..+.
T Consensus 4 ~~C~~~~i~--g~R~~C~~C~---dydLC~~Cf~~~~ 35 (49)
T cd02345 4 SACRKQDIS--GIRFPCQVCR---DYSLCLGCYTKGR 35 (49)
T ss_pred CCCCCCCce--EeeEECCCCC---CcCchHHHHhCCC
Confidence 35777 566 4889999994 5779999999874
No 55
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=39.46 E-value=31 Score=33.91 Aligned_cols=27 Identities=30% Similarity=0.615 Sum_probs=21.9
Q ss_pred CCcCCCccccccChHhhHHHHHHHHHH
Q 000144 1420 PIDCDGIHLSSCGHAVHQGCLDRYVSS 1446 (2057)
Q Consensus 1420 ~~~~~gvh~SsCGH~MH~~C~~~Y~~S 1446 (2057)
|.+.+.+--+.|-|+-|..|-.+.+++
T Consensus 43 ~~~eC~v~wG~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 43 PGDECPVVWGVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred CCCcceEEEEecchHHHHHHHHHHHhh
Confidence 334455558889999999999999987
No 56
>PLN00209 ribosomal protein S27; Provisional
Probab=39.18 E-value=10 Score=37.66 Aligned_cols=37 Identities=16% Similarity=0.520 Sum_probs=29.8
Q ss_pred cccCCchhHHHHHHHHhhcccCCCCCC------CCCceeeeccCccccC
Q 000144 1916 KLMCLPHLYQDLLQRYIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2057)
Q Consensus 1916 ~Li~LP~~y~~l~~~~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1958 (2057)
+||+=|+.| +.+.+||.|++. ...++.|..||++++.
T Consensus 25 ~Lv~~PnS~------Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 25 RLVQSPNSF------FMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred eeecCCCCE------EEEEECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 577777765 467899999875 5789999999998775
No 57
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=37.81 E-value=11 Score=37.30 Aligned_cols=37 Identities=22% Similarity=0.539 Sum_probs=29.9
Q ss_pred cccCCchhHHHHHHHHhhcccCCCCCC------CCCceeeeccCccccC
Q 000144 1916 KLMCLPHLYQDLLQRYIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2057)
Q Consensus 1916 ~Li~LP~~y~~l~~~~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1958 (2057)
+||+=|+.| +...+|+.|++. ...++.|..||++++.
T Consensus 24 ~Lv~~PnS~------Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 24 RLVQGPNSY------FMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred eEecCCCCe------EEEEECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 577777765 467899999875 5789999999998776
No 58
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.77 E-value=15 Score=33.30 Aligned_cols=15 Identities=40% Similarity=0.753 Sum_probs=10.8
Q ss_pred ccccChH-hhHHHHHH
Q 000144 1428 LSSCGHA-VHQGCLDR 1442 (2057)
Q Consensus 1428 ~SsCGH~-MH~~C~~~ 1442 (2057)
+-+|||+ |-+.|--+
T Consensus 22 lYtCGHMCmCy~Cg~r 37 (62)
T KOG4172|consen 22 LYTCGHMCMCYACGLR 37 (62)
T ss_pred HHHcchHHhHHHHHHH
Confidence 7799998 66666443
No 59
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.67 E-value=16 Score=49.54 Aligned_cols=23 Identities=48% Similarity=1.025 Sum_probs=20.7
Q ss_pred ccChHhhHHHHHHHHHHHHHhhhcccccCCCcccCCCCcccccccccc
Q 000144 1430 SCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2057)
Q Consensus 1430 sCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCKs 1477 (2057)
.|||..|+.|++ .+|+-||-|+.
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 60
>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=34.46 E-value=10 Score=33.50 Aligned_cols=36 Identities=28% Similarity=0.709 Sum_probs=22.4
Q ss_pred cccccccCCceeEEecccCCCCCccccccccCCCC-CCCce
Q 000144 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN-HKEHD 156 (2057)
Q Consensus 117 ~C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~-H~~H~ 156 (2057)
.|+..--. ..-|+|..|. ..-||.+||..+. +.+|+
T Consensus 9 ~C~~~~i~-g~Ry~C~~C~---d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 9 GCGTDPII-GVRYHCLVCP---DYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SS-SSSEE-SSEEEESSSS---S-EEEHHHHHH--H-SSSS
T ss_pred CCCCCcCc-CCeEECCCCC---CCchhhHHHhCcCCCCCcC
Confidence 46663222 3679999995 5779999999964 45664
No 61
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=32.66 E-value=32 Score=38.20 Aligned_cols=44 Identities=23% Similarity=0.479 Sum_probs=26.5
Q ss_pred hhHHHHHHHHHHHHHhhhcccc------cC---CCcccCCCCccccccccccc
Q 000144 1435 VHQGCLDRYVSSLKERYNRRII------FE---GGHIVDPDQGEFLCPVCRQL 1478 (2057)
Q Consensus 1435 MH~~C~~~Y~~Sl~~r~~~r~~------~e---r~h~~d~e~gEFLCPLCKsL 1478 (2057)
-|-+|+++|-++-......... .. ..+....+..+..|||||.=
T Consensus 37 rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~CPLCRG~ 89 (162)
T PF07800_consen 37 RHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPELACPLCRGE 89 (162)
T ss_pred chhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccccCccccCc
Confidence 4899999997775433211100 00 01234556789999999973
No 62
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=31.15 E-value=36 Score=43.29 Aligned_cols=42 Identities=33% Similarity=0.819 Sum_probs=30.2
Q ss_pred ccccccCCceeEEecccCCCCCccccccccCCCC----C-CCceeEEEecC
Q 000144 118 CGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN----H-KEHDYSIIYTG 163 (2057)
Q Consensus 118 C~~v~~~~e~~y~C~~C~~d~t~~~C~~CF~~~~----H-~~H~~~~~~~~ 163 (2057)
|..-.. |-+-.+|-.| |..-+|..||..|. | .+|.|.++.++
T Consensus 20 C~~dit-~~i~ikCaeC---p~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~ 66 (438)
T KOG0457|consen 20 CSLDIT-GLIRIKCAEC---PDFDLCLQCFSVGAETGKHQNDHPYRIMDTN 66 (438)
T ss_pred HhHHhc-cceEEEeecC---CCcchhHHHHhcccccCCCCCCCCceeecCC
Confidence 444443 4555889999 45569999997764 6 48999998764
No 63
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=30.84 E-value=20 Score=33.51 Aligned_cols=28 Identities=29% Similarity=0.762 Sum_probs=23.0
Q ss_pred HhhcccCCCCCC------CCCceeeeccCccccC
Q 000144 1931 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2057)
Q Consensus 1931 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1958 (2057)
+.+.+||.|++. +..+..|..||+.++.
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 456799999975 5789999999997664
No 64
>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=29.73 E-value=18 Score=33.39 Aligned_cols=28 Identities=18% Similarity=0.705 Sum_probs=18.5
Q ss_pred HhhcccCCCCCC------CCCceeeeccCccccC
Q 000144 1931 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1958 (2057)
Q Consensus 1931 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1958 (2057)
+...+||.|++. ...+..|..||++++.
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 345789999874 6789999999997765
No 65
>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=25.52 E-value=60 Score=30.60 Aligned_cols=51 Identities=24% Similarity=0.350 Sum_probs=30.7
Q ss_pred cCCCCCCCCCceeeeccCccccCCCCcccchhHHHhhcCCCeeEEEEecccEEE
Q 000144 1936 CSDCKSVLDEPALCLLCGRLCSPSWKPCCSCQSHAVACGAGTGVFLLIRRTTIL 1989 (2057)
Q Consensus 1936 C~~c~~~~~~paiCL~CG~~~~~~~~~cc~c~~H~~~Cg~~~Gifl~v~~~~il 1989 (2057)
|..|+....+.-+||.||.+.|.. ..-..-..|+.+=| =-+++.+++..|.
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~-~~~~Ha~~H~~~~~--H~l~v~~~~~~i~ 51 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGR-YSNGHALKHYKETG--HPLAVSLSTGSIW 51 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETT-TSTSHHHHHHHHHT----EEEETTTTCEE
T ss_pred CCCCCCcCCceEEeCCCCcccccC-CcCcHHHHhhcccC--CeEEEECCCCeEE
Confidence 667776578999999999986552 11112667777655 4456666665553
No 66
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=24.72 E-value=34 Score=38.61 Aligned_cols=20 Identities=50% Similarity=1.157 Sum_probs=17.9
Q ss_pred ccCCCCCCCCCceeeeccCcc
Q 000144 1935 CCSDCKSVLDEPALCLLCGRL 1955 (2057)
Q Consensus 1935 ~C~~c~~~~~~paiCL~CG~~ 1955 (2057)
.| +|+..-..|+.||.||+-
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 999999999999999983
No 67
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=24.02 E-value=41 Score=41.78 Aligned_cols=17 Identities=29% Similarity=0.698 Sum_probs=15.6
Q ss_pred ccccChHhhHHHHHHHH
Q 000144 1428 LSSCGHAVHQGCLDRYV 1444 (2057)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~ 1444 (2057)
+=-|.|+.|..|.+.|+
T Consensus 384 ALpCsHIfH~rCl~e~L 400 (518)
T KOG1941|consen 384 ALPCSHIFHLRCLQEIL 400 (518)
T ss_pred ccchhHHHHHHHHHHHH
Confidence 55799999999999998
No 68
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=23.44 E-value=28 Score=33.93 Aligned_cols=25 Identities=24% Similarity=0.489 Sum_probs=19.8
Q ss_pred cCCCccccccChHhhHHHHHHHHHH
Q 000144 1422 DCDGIHLSSCGHAVHQGCLDRYVSS 1446 (2057)
Q Consensus 1422 ~~~gvh~SsCGH~MH~~C~~~Y~~S 1446 (2057)
+...+-.+-|-|+-|..|-.+.+.+
T Consensus 42 DdCPLv~G~C~h~fh~hCI~~wl~~ 66 (84)
T KOG1493|consen 42 DDCPLVWGYCLHAFHAHCILKWLNT 66 (84)
T ss_pred CCCccHHHHHHHHHHHHHHHHHhcC
Confidence 3445558899999999999988654
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=23.31 E-value=46 Score=28.95 Aligned_cols=25 Identities=24% Similarity=0.527 Sum_probs=17.1
Q ss_pred cccCCCCCCC------CCceeeeccCccccC
Q 000144 1934 QCCSDCKSVL------DEPALCLLCGRLCSP 1958 (2057)
Q Consensus 1934 ~~C~~c~~~~------~~paiCL~CG~~~~~ 1958 (2057)
++||+|+... ..-.+|-.||.++..
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 344599999997654
No 70
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=21.95 E-value=62 Score=39.27 Aligned_cols=33 Identities=45% Similarity=0.944 Sum_probs=23.7
Q ss_pred ceeEEeccc-CCCCCccccccccCCCC----C-CCceeEEEec
Q 000144 126 DIAYRCRTC-EHDPTCAICVPCFQNGN----H-KEHDYSIIYT 162 (2057)
Q Consensus 126 e~~y~C~~C-~~d~t~~~C~~CF~~~~----H-~~H~~~~~~~ 162 (2057)
-+..+|-.| .+| +|..||-+|. | .-|.|+++.+
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 455677777 443 8999998765 3 4699999864
No 71
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=21.87 E-value=44 Score=44.70 Aligned_cols=18 Identities=28% Similarity=0.803 Sum_probs=15.7
Q ss_pred ccccChHhhHHHHHHHHH
Q 000144 1428 LSSCGHAVHQGCLDRYVS 1445 (2057)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~~ 1445 (2057)
-.+|||+||.+|....++
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
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.12 E-value=44 Score=34.65 Aligned_cols=24 Identities=13% Similarity=0.171 Sum_probs=20.6
Q ss_pred hhcccCCCCCC----CCCceeeeccCcc
Q 000144 1932 IKQCCSDCKSV----LDEPALCLLCGRL 1955 (2057)
Q Consensus 1932 ~~~~C~~c~~~----~~~paiCL~CG~~ 1955 (2057)
.++.||+|+++ .++|++|-.||+-
T Consensus 8 tKridPetg~KFYDLNrdPiVsPytG~s 35 (129)
T COG4530 8 TKRIDPETGKKFYDLNRDPIVSPYTGKS 35 (129)
T ss_pred ccccCccccchhhccCCCccccCccccc
Confidence 46789999986 6899999999983
No 73
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.01 E-value=68 Score=39.67 Aligned_cols=17 Identities=29% Similarity=0.880 Sum_probs=15.1
Q ss_pred ccccChHhhHHHHHHHH
Q 000144 1428 LSSCGHAVHQGCLDRYV 1444 (2057)
Q Consensus 1428 ~SsCGH~MH~~C~~~Y~ 1444 (2057)
++.|||.|=.+|.++.+
T Consensus 23 i~~CGH~~C~sCv~~l~ 39 (309)
T TIGR00570 23 VNVCGHTLCESCVDLLF 39 (309)
T ss_pred cCCCCCcccHHHHHHHh
Confidence 45899999999999986
Done!