Query 000151
Match_columns 2029
No_of_seqs 350 out of 613
Neff 6.3
Searched_HMMs 46136
Date Thu Mar 28 20:50:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/000151.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/000151hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1140 N-end rule pathway, re 100.0 2E-126 4E-131 1253.9 65.0 1280 279-2021 368-1726(1738)
2 KOG1139 Predicted ubiquitin-pr 100.0 1.5E-30 3.3E-35 319.3 6.4 581 1415-2026 169-782 (784)
3 KOG1140 N-end rule pathway, re 99.8 1.1E-21 2.5E-26 262.9 -0.5 928 18-1000 532-1502(1738)
4 smart00396 ZnF_UBR1 Putative z 99.8 1.5E-19 3.2E-24 170.9 5.8 70 116-185 1-71 (71)
5 PF02207 zf-UBR: Putative zinc 99.7 1.8E-18 3.8E-23 164.2 4.1 70 116-185 1-71 (71)
6 KOG1139 Predicted ubiquitin-pr 99.0 2.8E-09 6E-14 133.9 16.2 185 754-938 207-477 (784)
7 PF10390 ELL: RNA polymerase I 97.0 0.00044 9.5E-09 83.5 3.7 81 869-954 198-281 (284)
8 KOG1777 Putative Zn-finger pro 94.9 0.011 2.3E-07 72.0 1.3 62 112-174 540-606 (625)
9 PF13639 zf-RING_2: Ring finge 91.2 0.066 1.4E-06 46.4 0.2 20 1426-1445 16-35 (44)
10 cd00162 RING RING-finger (Real 91.1 0.16 3.4E-06 43.1 2.5 19 1428-1446 15-33 (45)
11 KOG4445 Uncharacterized conser 90.3 0.09 2E-06 61.7 0.3 48 1428-1477 133-183 (368)
12 KOG0943 Predicted ubiquitin-pr 89.9 0.094 2E-06 69.6 -0.0 63 116-184 1241-1309(3015)
13 PF13764 E3_UbLigase_R4: E3 ub 89.7 1.4 3E-05 60.4 10.6 70 1146-1229 422-497 (802)
14 cd02335 ZZ_ADA2 Zinc finger, Z 85.4 0.64 1.4E-05 41.6 2.5 39 117-159 5-48 (49)
15 KOG4796 RNA polymerase II elon 85.1 0.86 1.9E-05 57.8 4.3 77 869-951 211-290 (604)
16 cd02340 ZZ_NBR1_like Zinc fing 85.0 0.69 1.5E-05 40.3 2.4 37 117-158 5-41 (43)
17 cd02249 ZZ Zinc finger, ZZ typ 83.7 0.78 1.7E-05 40.4 2.2 38 117-159 5-45 (46)
18 PF00097 zf-C3HC4: Zinc finger 82.7 0.76 1.6E-05 39.1 1.7 20 1427-1446 13-32 (41)
19 smart00184 RING Ring finger. E 80.8 1.3 2.7E-05 36.1 2.4 18 1428-1445 13-30 (39)
20 cd02338 ZZ_PCMF_like Zinc fing 80.8 1.2 2.7E-05 39.8 2.4 38 117-159 5-48 (49)
21 KOG2905 Transcription initiati 80.1 1.1 2.5E-05 51.9 2.5 62 869-931 182-245 (254)
22 cd02344 ZZ_HERC2 Zinc finger, 80.0 1.4 3.1E-05 38.8 2.4 39 117-159 5-44 (45)
23 PF14634 zf-RING_5: zinc-RING 79.5 1.6 3.4E-05 38.0 2.7 31 1425-1477 14-44 (44)
24 PF12861 zf-Apc11: Anaphase-pr 78.4 1.5 3.3E-05 43.5 2.4 22 1425-1446 46-67 (85)
25 KOG2752 Uncharacterized conser 75.5 3.1 6.8E-05 50.0 4.4 61 112-173 37-101 (345)
26 PF11793 FANCL_C: FANCL C-term 75.3 0.83 1.8E-05 44.0 -0.3 39 1428-1477 25-63 (70)
27 PF00643 zf-B_box: B-box zinc 75.1 1.6 3.4E-05 37.4 1.4 28 126-158 13-40 (42)
28 PF09538 FYDLN_acid: Protein o 72.5 1.7 3.7E-05 45.4 1.2 27 1901-1927 8-38 (108)
29 PHA02926 zinc finger-like prot 72.3 2.8 6E-05 48.5 2.8 46 1423-1485 190-235 (242)
30 COG5243 HRD1 HRD ubiquitin lig 71.5 1.8 3.9E-05 52.6 1.2 16 1430-1445 317-332 (491)
31 cd02339 ZZ_Mind_bomb Zinc fing 69.0 3.3 7.1E-05 36.6 1.9 30 126-158 13-43 (45)
32 PLN03208 E3 ubiquitin-protein 65.3 5 0.00011 45.9 3.0 53 1428-1486 33-87 (193)
33 TIGR02300 FYDLN_acid conserved 63.8 3.5 7.6E-05 43.8 1.3 27 1901-1927 8-38 (129)
34 cd02341 ZZ_ZZZ3 Zinc finger, Z 60.5 5.8 0.00013 35.5 1.9 39 117-158 5-46 (48)
35 PF12678 zf-rbx1: RING-H2 zinc 59.0 2.3 5E-05 41.3 -0.9 17 1428-1444 47-63 (73)
36 KOG1940 Zn-finger protein [Gen 58.9 5.3 0.00011 48.2 1.8 35 1426-1482 175-209 (276)
37 cd02343 ZZ_EF Zinc finger, ZZ 58.9 5.4 0.00012 35.7 1.4 35 117-156 5-40 (48)
38 cd02336 ZZ_RSC8 Zinc finger, Z 55.4 4.1 9E-05 35.9 0.2 31 117-152 5-35 (45)
39 cd02337 ZZ_CBP Zinc finger, ZZ 54.8 6.8 0.00015 33.9 1.3 32 116-153 4-35 (41)
40 cd00021 BBOX B-Box-type zinc f 53.9 9.7 0.00021 31.8 2.2 28 126-158 10-37 (39)
41 PF13923 zf-C3HC4_2: Zinc fing 53.2 6 0.00013 33.5 0.8 20 1427-1446 13-32 (39)
42 KOG0828 Predicted E3 ubiquitin 50.2 9.6 0.00021 48.3 2.1 29 1428-1477 603-631 (636)
43 KOG0827 Predicted E3 ubiquitin 49.6 11 0.00024 46.6 2.5 30 1416-1446 12-41 (465)
44 PF13240 zinc_ribbon_2: zinc-r 49.5 8.4 0.00018 29.2 1.0 20 1904-1923 1-21 (23)
45 smart00291 ZnF_ZZ Zinc-binding 48.5 12 0.00025 32.8 1.8 33 116-153 8-40 (44)
46 smart00336 BBOX B-Box-type zin 48.2 14 0.00031 31.2 2.4 29 125-158 12-40 (42)
47 PF02270 TFIIF_beta: Transcrip 48.2 6.7 0.00014 47.8 0.4 31 899-930 244-274 (275)
48 PF10571 UPF0547: Uncharacteri 47.4 8.9 0.00019 30.0 0.8 22 1903-1924 1-23 (26)
49 PLN00209 ribosomal protein S27 46.7 7.1 0.00015 38.8 0.3 37 1885-1927 25-67 (86)
50 PF13248 zf-ribbon_3: zinc-rib 45.8 9.6 0.00021 29.6 0.8 22 1902-1923 2-24 (26)
51 cd02334 ZZ_dystrophin Zinc fin 45.1 14 0.00031 33.3 1.8 32 117-152 5-36 (49)
52 PTZ00083 40S ribosomal protein 45.1 7.4 0.00016 38.6 0.1 37 1885-1927 24-66 (85)
53 COG2051 RPS27A Ribosomal prote 45.1 8.5 0.00018 36.5 0.5 28 1900-1927 17-50 (67)
54 PHA02929 N1R/p28-like protein; 44.4 14 0.00031 43.9 2.3 37 1425-1484 195-231 (238)
55 PF13920 zf-C3HC4_3: Zinc fing 41.4 16 0.00035 32.6 1.7 18 1428-1445 17-35 (50)
56 cd02345 ZZ_dah Zinc finger, ZZ 39.1 21 0.00045 32.2 2.0 31 116-151 4-35 (49)
57 PF14446 Prok-RING_1: Prokaryo 39.0 12 0.00026 34.4 0.4 46 1900-1950 3-52 (54)
58 KOG4172 Predicted E3 ubiquitin 37.2 19 0.00041 32.8 1.4 15 1428-1442 22-37 (62)
59 KOG2114 Vacuolar assembly/sort 36.5 17 0.00036 49.3 1.3 23 1430-1477 858-880 (933)
60 PF01667 Ribosomal_S27e: Ribos 36.2 13 0.00027 34.4 0.2 28 1900-1927 5-38 (55)
61 PF00569 ZZ: Zinc finger, ZZ t 35.6 9.4 0.0002 33.8 -0.7 36 117-156 9-45 (46)
62 PRK00415 rps27e 30S ribosomal 35.1 16 0.00035 34.1 0.6 28 1900-1927 9-42 (59)
63 PF07800 DUF1644: Protein of u 32.7 31 0.00067 38.3 2.4 43 1435-1477 37-88 (162)
64 COG5194 APC11 Component of SCF 32.7 43 0.00093 33.0 3.0 25 1422-1446 45-69 (88)
65 KOG0457 Histone acetyltransfer 32.3 33 0.00072 43.5 2.9 43 117-163 19-66 (438)
66 PF08271 TF_Zn_Ribbon: TFIIB z 27.9 36 0.00077 29.6 1.6 25 1903-1927 1-31 (43)
67 COG4031 Predicted metal-bindin 26.4 30 0.00065 39.0 1.0 20 1904-1924 2-21 (227)
68 KOG1941 Acetylcholine receptor 24.8 39 0.00084 42.0 1.6 17 1428-1444 384-400 (518)
69 COG5114 Histone acetyltransfer 24.3 51 0.0011 39.9 2.5 33 126-162 18-56 (432)
70 PF02148 zf-UBP: Zn-finger in 21.8 74 0.0016 30.0 2.6 50 1905-1960 1-50 (63)
71 KOG0309 Conserved WD40 repeat- 21.7 44 0.00095 44.7 1.4 18 1428-1445 1045-1062(1081)
72 KOG0802 E3 ubiquitin ligase [P 20.4 56 0.0012 43.9 2.0 19 1428-1446 311-329 (543)
73 COG4530 Uncharacterized protei 20.1 48 0.001 34.4 1.0 24 1901-1924 8-35 (129)
74 KOG2930 SCF ubiquitin ligase, 20.0 68 0.0015 33.1 2.0 18 1428-1445 78-95 (114)
75 PRK02935 hypothetical protein; 20.0 46 0.00099 34.5 0.8 28 1900-1927 68-98 (110)
No 1
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2e-126 Score=1253.90 Aligned_cols=1280 Identities=22% Similarity=0.338 Sum_probs=813.6
Q ss_pred HHhccCCCCHHHHHHHHHHHH-HhhCChhhHHHHHHHHHhhhHHHHHHHHHhccCcccccCCccceeeeeccccCCcHHH
Q 000151 279 LVRAEMFSSDVVVRKLHELLL-KLLGEPIFKYEFAKVFLSYYPVFVKDAIREHSDDTIKKYPLLSTFSVQIFTVPTLTPR 357 (2029)
Q Consensus 279 ll~~d~~L~k~~r~~lh~Lll-sLL~d~efK~~fA~~Fv~~Y~~i~~~fl~~d~d~~~~~~s~v~~LSVQLFTvPSLA~~ 357 (2029)
++..|..+||..|..++.++. .+-++.++|+.||.+|+.+|..+..+|+.+|++.. .+.| .++||+||+|++|..
T Consensus 368 il~~d~~~~kr~r~~l~k~~~~~~~~~~~~k~~~~~~~~~~y~~~~~~~~~~d~e~~---~~vi-~~~vqf~t~~~~a~~ 443 (1738)
T KOG1140|consen 368 ILLFDNRYWKRLRKDLQKVIIPTFASSNLYKPIFAQQFVEHYNSITRDFAYMDREPD---LSVI-ELSVQFFTCPSLAKN 443 (1738)
T ss_pred HHHHHHHHHHHHHHHHhhcceeehhcchHHHHHHHHHHHHHHHHHHHHHHhhcCCcc---hhhH-hheeeeecCcHHHHH
Confidence 444566678999999999999 67789999999999999999999999999988743 3545 999999999999999
Q ss_pred HHHhhcHHHHHHHHHHHHhhhhcCCCCcceec---------cccccccchhhhhhhhhHhhcchhhhHHHhhhchHHHHH
Q 000151 358 LVKEMNLLEMLLGCLREIFDSCAGDDSCLQVA---------KWANLYETTNRVIGDIRFVMSHAAVSKYATHEQLNISKA 428 (2029)
Q Consensus 358 LV~e~nLL~iLl~tl~~~~~~~~~~~~~l~~~---------~~~~~~~~~~~I~~DLrylLsh~~v~~~l~~~~~~l~~~ 428 (2029)
+++...++..+..++..++..+...++..... +.....++.+..+.|+ +.+.++.+ -.++..+..
T Consensus 444 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~r~l~~~~~l-~~~~~~~~-----~~~~~~~~~ 517 (1738)
T KOG1140|consen 444 IVENQSFLDIVWSIIDIFKEFNKVEGGVLIDIRVQKSNLLKRYSISFRRTLYTFEDL-SKVHDPNI-----PLRPKEFIS 517 (1738)
T ss_pred hhhhccchHHHHHHHHHHHHhcccccceecceeeeechhhhHHHHHHHHHHHHHHHh-hccCCccc-----cccHHHHHH
Confidence 99999988877777766664444322221111 1122357777788888 77777762 357899999
Q ss_pred HHHHHHHhcCCCcccccccCcceeeCCceeehhhhhhHHHhhHHhhhhhccccccccccccccccccccCCCCCcccccc
Q 000151 429 WMKLLTFVQGMNPQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEETRYDFSMYKQDIGDGDSLRHAK 508 (2029)
Q Consensus 429 ~l~lLs~~QGMnp~kRq~~~HVEyE~e~w~~aF~L~~~la~i~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 508 (2029)
++.++..||||.|++|+.++||++|++ |+.+|.+-.++..++++++.||..++.
T Consensus 518 ~l~~~~v~qg~~~lkr~~~ehv~~e~~-~~~~~~~v~~~t~~~s~i~~~~~~~ep------------------------- 571 (1738)
T KOG1140|consen 518 LLLLLKVFQGVDPLKREELEHVEVEKE-WENFFSLVEYLTAIYSMIQSLVKTSEP------------------------- 571 (1738)
T ss_pred HHHHHHHhCCccHHHHHHhhhhcccch-HHHHHHHHHHHHHHHHHHHHHHHhccc-------------------------
Confidence 999999999999999999999999997 999999999999999999998866530
Q ss_pred ccccccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhhhcCCCCcccccccCCCCcccccC
Q 000151 509 VGRLSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENWLGVDDRSVSVNDILSPNASRISG 588 (2029)
Q Consensus 509 v~r~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~cl~~l~~~l~~~~~~~~~~~~~s~~~~~~~~ 588 (2029)
+- ..+++.|+.++.... ..
T Consensus 572 ~~-----------------------------------------~~~~~~l~~~~~r~~------~s-------------- 590 (1738)
T KOG1140|consen 572 VK-----------------------------------------DSVYKKLLEAAIRIH------PS-------------- 590 (1738)
T ss_pred hh-----------------------------------------hhHHHHHHHHHhhcc------cc--------------
Confidence 00 001112222222110 00
Q ss_pred chhhhhHhhhhhccccccccccccCCccccccccccCCCccccccCccccccccCCcccccccccCcCCccccccchhcc
Q 000151 589 SNFVALKKTLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKITISGERDTASWRSAGFNDSEMEGECATEL 668 (2029)
Q Consensus 589 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 668 (2029)
++++ +. + -..+++++.
T Consensus 591 ----------------------~~~~---------------------~~---l---------------~~~i~~~S~--- 606 (1738)
T KOG1140|consen 591 ----------------------LTGS---------------------ES---L---------------TYTICGESH--- 606 (1738)
T ss_pred ----------------------cCcc---------------------ce---e---------------eehhhhhhH---
Confidence 0000 00 0 001223322
Q ss_pred ccccccccCccCceeeeccCCceeeehHHHHHHHHHHHHHHhhhccccccccccccCCCCCccccchhhhhcccCCCCCC
Q 000151 669 DNLHVLSLCYWPDITYDVSSQDVSVHIPLHRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPY 748 (2029)
Q Consensus 669 ~~~~~~~~~~~~~v~fdVs~~~VSfH~PLhr~Ls~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~ 748 (2029)
.++.|+|+.++||||+|+.|+|+++++....... ...+.+ ..+.+++.
T Consensus 607 -----------e~i~f~v~~~~~sv~~p~~~~l~~l~~~~~s~v~-------------------~~~d~~-~~~~~~~n- 654 (1738)
T KOG1140|consen 607 -----------ETINFSVSQERVSVSNPVSRLLAFLIELSCSSVV-------------------SLKDAY-ERLEDCSN- 654 (1738)
T ss_pred -----------hHhhhccccccceeeccHHHHhhhhhhcccchhh-------------------hcchhh-hhHhhhcc-
Confidence 5789999999999999999999999853211001 111111 11122222
Q ss_pred CcchhhccccHHHHHHHHHHhcCcccccchHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhcccc
Q 000151 749 GFSAFVMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSN 828 (2029)
Q Consensus 749 ~~~~~l~e~pLR~~Vl~aQI~aGmWvRNG~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~ 828 (2029)
..+|.|||||++|++|||.+|||||||+++.+|+.||++.+||+++|++||+++|.++++.||+.|+.++++||+|.+
T Consensus 655 --~~~i~e~~lr~~Vl~aqid~~~w~rNG~si~~q~~~y~~~~~r~~~y~~DI~~~Q~~la~~d~~~~l~~~l~r~~L~~ 732 (1738)
T KOG1140|consen 655 --FLAISEHSLRVLVLCAQIDVGFWVRNGFSILHQAAYYKNNPCRNESYDRDILMLQTGLAMEDPNRFLFTILSRFELLD 732 (1738)
T ss_pred --chhhcccchhheeeeeecceeeEeecCcchhhhhHhhcCccccccchhHHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Confidence 257899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCCCCC-ch---hHHHHHHHHHHHHhhcccccCCC---ChHHHHHHHHHHHHhcCCCChHHHHhhCCCCCCCcch
Q 000151 829 YLSLNLERPSE-YE---PILVQEMLTLIIQILQERRFCGL---TTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQ 901 (2029)
Q Consensus 829 w~~~~~~~~~~-y~---~~mvEe~L~lLI~llteR~~~g~---s~~e~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~~~~ 901 (2029)
|++|....... ++ ..|+|+|+.+||.|++||...|+ +..+.+|+||||+||++|++||+|.+++|++++++..
T Consensus 733 w~~g~~~~~~~d~~~~i~~~~ee~l~lii~ll~Er~~~~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~ 812 (1738)
T KOG1140|consen 733 WFTGEVDYQSNDTEDTISFMIEEFLALIILLLTERSYFGSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLS 812 (1738)
T ss_pred HhcCCCccccccHHHHHHHHHHHHHHHHHHHHHheeecccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhccc
Confidence 99998654332 22 37999999999999999997554 5778999999999999999999999999999999999
Q ss_pred HHHHHHHHccccCCCCC-CcceEEeehhhcccccccccccCchhHHHHHHHHHH--hhc---cccccCCC-CCCcccCC-
Q 000151 902 LQEILDAVAMYSHPSGF-NQGMYSLRWSYWKELDIYHPRWSSRDLQVAEERYLR--FCS---VSALTAQL-PRWTKIYY- 973 (2029)
Q Consensus 902 fe~iL~eVA~f~~P~g~-~~G~Y~LK~e~~~e~Dpy~~~y~~~~~q~aeer~~r--~~k---~~a~~~~~-P~~~~~~~- 973 (2029)
||.++++||+|++|.|+ +.|+|+||++||+++||||+||+++++.+++..+++ .++ ..|..+++ |++.+.+.
T Consensus 813 ~d~~~e~Va~~~~p~~~~~~gvf~lK~~~~~~~dpy~~~~s~s~q~~se~~~~k~~~~~~k~~~A~~~~i~~~~~~ll~~ 892 (1738)
T KOG1140|consen 813 FDEALEEVAVFKKPKGLADNGVFVLKESYYDEVDPYYKHLSKSEQSESEATIRKSRLAKKKDVIALVPPILPKFIKLLKK 892 (1738)
T ss_pred chHHHHHHHhhccCCccccceEEEechhhhhhcCchhhhhhHhHHhhhhHHHHHHHHHHhhccccccCCCcHHHHHHHHH
Confidence 99999999999999999 789999999999999999999999999888775543 211 12444332 33333221
Q ss_pred CccccccccccHHHHHHHHHHHHHHhccCCCCCCCCchhHHHHHHHHH-HHHHhhhhhcccCCCCCcccCCCcccccchh
Q 000151 974 PLESIAGIATCKVVLQVIRAVLFYAVFTDNPTDSRAPYGVLLTALHLL-ALALDVCFQKKKSGDQSCDIGGSTPILDFAS 1052 (2029)
Q Consensus 974 pf~~i~~il~s~~~~~il~~vL~~al~~~~~~~~~~~E~~L~~~LHLi-~laL~~~~~e~~~~~~~~~~~~~~p~~~~~~ 1052 (2029)
.+.++.+.+...+|-.||+.++.++.+.. .+.++..++|++ ++|++.+..--. |.+.- ++
T Consensus 893 ~~~~L~~~t~~~~~~~ii~r~~~~~~~~~-------s~~~l~~~~~~ihG~~~~~~l~~~~-----------~~~~~-~~ 953 (1738)
T KOG1140|consen 893 GADILGAAVRLTVFGLIIYRTLEHCLFME-------SSTLLSKVLHLIHGIALNEELINMK-----------FAFTQ-KT 953 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHhcc-----------ccccc-cc
Confidence 23556666667778888888888877654 488999999555 999986443111 10000 00
Q ss_pred hHHhhccCCCCCcccHHHHHHHHHhhhcccCCccccccccCCchhHHHHHHHHHHhhhHHHHHHHhhhchhhhhcccCCC
Q 000151 1053 EEIAEGLNNGAGKQSLLSLLVFLMGMYKKDGADNFLEAGNCNLSSVIESLLKKFAEIDSRCMTKLQQLAPEIVSHLSQSL 1132 (2029)
Q Consensus 1053 ~~~~~~~~~~~~~~Sll~LL~~L~~~~~~~~~~~~~~~~~~~i~~~I~~lL~~f~~~~~~c~~~l~~~~p~~~~~~~~~~ 1132 (2029)
+ ....++.+.+++.+..++....+ +.++.|+++.|..+.. .+...|++.. ....
T Consensus 954 e--------~~~~e~gl~~~e~lv~~~~~~~~-----------~~~~~v~~~l~~~~~~-----~~~n~~ea~~-~~~~- 1007 (1738)
T KOG1140|consen 954 E--------SIAREKGLSLYESLVRKPDSLVH-----------GKIIEVIVELFESLIK-----SRANDPEVAN-DEKD- 1007 (1738)
T ss_pred c--------ccccccchhhHHHhhhcchhhcC-----------CcceeeeHHHHhhhhh-----hhcCCccccc-cccc-
Confidence 1 11345577778877777554332 4567888888776544 2344443321 1100
Q ss_pred CCCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCccCCCCCCCccCCCCcccccccccCCCcccccCC
Q 000151 1133 PRDDTSGSFSASDSEKRKAKARERQAAILEKMKAEQFKFLSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDP 1212 (2029)
Q Consensus 1133 ~~~~~~~~~~~~e~ekkK~~AkeRQakIMaqf~~qQ~~Fl~~n~~~~~~~d~~~~e~~~s~~~~~~~e~~~~~CilCqe~ 1212 (2029)
.....+.+.++.+.++||++|++||+|+||||+.||.+||++|.+++|++++. .+++...+.. .....|.+|+..
T Consensus 1008 ~~~~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e~d~~~~~---~~~~~~~~~~--~~d~~~~~~~~~ 1082 (1738)
T KOG1140|consen 1008 KKEKQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDEFDEQENQ---TPSSGSKTYE--EEDFTCALCQDN 1082 (1738)
T ss_pred cccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccccCccccc---Cccccccchh--hhhccchhhhcc
Confidence 01112234444556788889999999999999999999999997665544321 1111101111 114567777643
Q ss_pred CC-CCCeEEEEeeecccccccccCCCCCCcccccccccccccccccccccCCCCCCCCCCCcchhhhHHHHHHHHHhhhc
Q 000151 1213 NS-RTPVSYLILLQKSRLLSFVDRGSPSWDQDQWLGKECGTISANNMVNQFGTNTPSSGLGVISSCQLAQVAEEAVNQFA 1291 (2029)
Q Consensus 1213 ~~-~~pfG~la~iq~S~~l~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~a~~~~~ 1291 (2029)
+. +.++ |++..+...
T Consensus 1083 s~~~~~~------~~~~~~~~~---------------------------------------------------------- 1098 (1738)
T KOG1140|consen 1083 SCTDFQV------KPASHLVKP---------------------------------------------------------- 1098 (1738)
T ss_pred chhcccc------ccchhhhcc----------------------------------------------------------
Confidence 22 1122 222221100
Q ss_pred cCCCchhhhhHHHHhhhcCCCCcCCCCCcCcCCCCcCCcchhhhhhhhhhhHHHHhhhccCCCCCCccccchhhhccCCc
Q 000151 1292 YNGKPEEVNSVLEFVKAQFPSLRNIPIPFTFSNGRKCTASSMEMFEQDLYLSICREMRKNMTYPDLMKEDEECSVAEGGL 1371 (2029)
Q Consensus 1292 ~~~r~~~~~~~~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~s~~~~~e~~~~~~~~~~~ 1371 (2029)
..-+||.| ++++.+..
T Consensus 1099 -----------------------------------------------~~~~~~i~------------~e~e~~~~----- 1114 (1738)
T KOG1140|consen 1099 -----------------------------------------------IFRECIIC------------DENEDVPN----- 1114 (1738)
T ss_pred -----------------------------------------------cccccccC------------ChhccCCC-----
Confidence 01123444 23333321
Q ss_pred cCCCCCccchhhhhhhhhhHHhhhcccccccccccccccccccCCCCCC-CcCCCccccccChHhhHHHHHHHHHHHHHh
Q 000151 1372 KNRGNSDSFLLGKYVASISKEMRENASASEVSRGDRIAAESLVYDGFGP-IDCDGIHLSSCGHAVHQGCLDRYVSSLKER 1450 (2029)
Q Consensus 1372 ~~~~~~~~~~l~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~gF~~-~~~~gvh~ssCGH~MH~~C~~~Y~~Sl~~r 1450 (2029)
..++.++..+|+++ ++. +..+++.| ....|+++|+|||.||+.||++|+.+.+.|
T Consensus 1115 ---~~~~~~v~~~f~~~-s~~--------------------~sd~l~~p~~~~~~~~~s~c~h~mh~~c~~~~~~a~r~~ 1170 (1738)
T KOG1140|consen 1115 ---WDGRYSVSSAFAQK-SDD--------------------VSDALTEPGSLSCGTVLSSCGHHMHYGCFKRYVQAKRFR 1170 (1738)
T ss_pred ---ccccchhhhHhhhh-ccc--------------------ccccccCCCCCcccceeeccCCcchHHHHHHHHHHHHHH
Confidence 11233466777776 221 12334434 556899999999999999999999999999
Q ss_pred hhccccccCCcccCCCCcccccccccccccceecCCCCCcccCCCCCcccCCCCCCCCCCccccccchhhHHHHHH----
Q 000151 1451 YNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRINEQPTVSGVGLSLDSSSSFTTREENTSFQLQQA---- 1526 (2029)
Q Consensus 1451 ~~~r~~~er~h~~d~e~gEFLCPLCksL~Ns~LPilp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---- 1526 (2029)
.+++..+.+.|.- ++|+|+||+||+|+|+++|..++.....++ .+. ........|++..
T Consensus 1171 ~n~~~~~l~~~~s--e~~l~lCp~c~slsn~~lp~~~~~~~~~n~-~t~--------------~~~~n~~~~i~~rs~~~ 1233 (1738)
T KOG1140|consen 1171 ENARTAPLCQHYS--ENGLFLCPLCKSLSNVSLPMFLPPELLLNP-LTL--------------ENQRNLNSWIEKRSRAS 1233 (1738)
T ss_pred HHhhhcCcccccc--cCCcccCCchHhhhhccCCcCCchhhhcCh-hhh--------------hchHHHHHHHHHhchhh
Confidence 9987765555543 899999999999999999987543332221 000 0011222333310
Q ss_pred --Hhhhhh---ccc-cccc---ccccccCCcchhhHHHHHHHHHHHHHHHHhhccc------cccccCCCCCChhHHHHH
Q 000151 1527 --VSLLQS---ASN-VVGK---ADVIESFPLMKNEIMASNVEAVSRRMCKMYFQNK------LDKFFGSARVNPSLIMWD 1591 (2029)
Q Consensus 1527 --~~~l~s---~~~-~~~~---~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~~------~~~~~~~~~~~~~~~l~~ 1591 (2029)
+..+.+ ... ...+ .++.+..-.++.+.....++.+.+.+....+..+ .....+.++. .....|-
T Consensus 1234 ~s~~~vs~~~s~~~~~~~ss~i~e~kp~~~~~l~~~~~~~ie~~~k~v~s~~~k~~~~i~~~~le~~~~~~~-~~~~~~~ 1312 (1738)
T KOG1140|consen 1234 FSLQDVSSILSDPWAAFTSSRIPELKPILIMDLPDSVVEQIELFQKIVGSAMFKPSSLLSTNTLELTLFSRE-FLIVCWQ 1312 (1738)
T ss_pred cchhhhhhhhcccchhhccccccccccchHhhhhhHHHHHHHHHHHHHhhheeecccceeecccccCcccch-hhhhhhh
Confidence 000000 000 0000 0010000001222222222323333222222111 1122234443 4567788
Q ss_pred HHhHhHHHHHHHhhccCCCCCCcchhhhHHHHhhcchhhHHHHHHHHHhhhcccchhHHHHHhh---hhhhhhhhhcCCC
Q 000151 1592 ALKYSLMSMEIAARSEKTSTTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVLQRFR---GIQLFAESICSGT 1668 (2029)
Q Consensus 1592 tl~YTi~s~Eia~Rg~~~~~~~~~~l~~L~~~l~s~~~~il~~l~~~~~~~r~~~~l~~l~r~~---~~~Ll~~si~~~~ 1668 (2029)
.+++..+++++.+=+.+.+ ++..+.+...+.++...++.... +...++..+ .+++|...+.+
T Consensus 1313 ~~s~a~~~~~~~l~~~~~~---------~~l~l~~~~~~~~~~~~~l~~~~----~~~~l~~~~~~~llk~~s~~~~~-- 1377 (1738)
T KOG1140|consen 1313 SLSDAEQSTKLLLSASKKP---------SFLKLNEDMTFCLVTISRLRALH----WEQILYELVYTFLLKSFSPTIPR-- 1377 (1738)
T ss_pred ccchHHHHHHHHHhccCCc---------ccccCchhhHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHhhcCCc--
Confidence 8888888877665443332 11111122222222222222211 122222211 11222211100
Q ss_pred CCCCCCCCcCCCCccccccccccccCCcchhhhhcccCCCccccCchhhHHHHHhhccccccccccchhhHHHH-HHHHH
Q 000151 1669 SIDNPGGRCKRGGNMLSILKHADVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFILCKESLLSLVHV-FYAVT 1747 (2029)
Q Consensus 1669 s~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~plL~~D~F~~Lv~~~~~lp~p~~s~~~~~~~iv~l-~y~a~ 1747 (2029)
|.. +. . + +..+...--.+..|.+..+- ....++ ...-....++++ ..+++
T Consensus 1378 -----------------i~~-~~-t---p--d~~~~~ll~~l~~~~~~~~~-l~~~~~----~~~~~~~~~~~~~i~~~~ 1428 (1738)
T KOG1140|consen 1378 -----------------ISV-LI-T---P--DQPENELLVILPHDFPKSLE-LELTLD----FVNKNPKKIFELKILMAS 1428 (1738)
T ss_pred -----------------chh-cc-C---C--CCCcchhhhccchhhhhhcc-HHHHHH----HhhhhHHHHHhHHHHHHH
Confidence 000 00 0 0 00000000011111111110 000001 111233344444 55666
Q ss_pred HHHH-HHHhhcccccc--cccccc-hhhHHHHHHHHhcccccccccccccCCCChhhHHHHHHHhhhhhhcc-----ccc
Q 000151 1748 LSQA-VLSCCGKLQSK--VNELGF-SDSLISDISKLLGEFGSAQEYFVSNYIDPSCDIKDMIRRLSFPYLRS-----DMM 1818 (2029)
Q Consensus 1748 ivQ~-ll~~~~~~~~~--~~~~~~-~d~l~~~i~~~~~~~~~~~~~~~s~~~~~~~~i~~~v~k~~lPFLRr-----h~~ 1818 (2029)
++|. +++.......+ .++... .+... .+...+-.....++......+-....++..+++.++||||| |++
T Consensus 1429 i~s~elits~s~l~~d~~~~~~q~s~~e~~-~~~t~l~~~~s~~~i~~~~~~~~~~~L~~~~~~~i~sfL~~~al~~h~l 1507 (1738)
T KOG1140|consen 1429 IISIELITSHSYLENDLEMAEEQKSIDEFK-SLLTYLLQLESSRTIPKLADIRLRLSLCLSCEAGILSFLRRAALFKHLL 1507 (1738)
T ss_pred hhhhhhheeccccCCccchhhhhhhHHhHh-HHHHHHHhccchhhCccccchhhhhHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 6666 34332221111 011110 11111 01110111111000000000111236888899999999999 666
Q ss_pred CCCCCcc-----C-ChhHHHHHHHhcCCCChHHHhhh---HHHHHHHHHHhhcccccchhhccccccccCCCCcccccCC
Q 000151 1819 DSSDDAL-----S-DLKEIQEVEKMFKIPSLDVILKD---EVLRSLVLKWFHHFSKEFEVHRFQHVLYSTPAVPFKLMCL 1889 (2029)
Q Consensus 1819 ~~~~~~~-----~-e~~E~d~L~~~L~LPsl~~ll~~---~~~~~li~~W~~h~~~~~~~~~~~~~~~~~~~~~~~Li~L 1889 (2029)
.++..+. + ..++...|++|+++|++...+.+ +.++.++.+||.-.........+.......|..+..|+.|
T Consensus 1508 n~v~~p~~~f~~~~~~s~~e~L~ty~slp~l~~~~~q~~~delr~~~~~~~~~~~~lk~~~~~~~~~~i~~r~~~~l~~l 1587 (1738)
T KOG1140|consen 1508 NNVFPPFGAFLDPSSNSELEHLCTYLSLPNLQACLLQSSGDELRQAIERWCGGTENLKREEHYLNTLSINPRIPNSLVEL 1587 (1738)
T ss_pred hcCCCchhhccCcccchhhhhhcccccCccHHHHHHhhhHHHHHHHHHHhhccchHHHHHHhhcceeeecCCCCCccccC
Confidence 6654332 1 13589999999999988876533 6788999999764221111111111122335557799999
Q ss_pred chhHHHHHHHHhhcccCCCCCCC-CCceeeecccccccCCCCcccCC-------CcchHhhhhcCCCeeEEEEecccEEE
Q 000151 1890 PHLYQDLLQRYIKQCCSDCKSVL-DEPALCLLCGRLCSPSWKPCCRE-------SSCQSHAVACGAGTGVFLLIRRTTIL 1961 (2029)
Q Consensus 1890 P~~~~~l~~~~~~~~C~~c~~~~-~~paiCL~CG~~~~~~~~~cc~~-------g~c~~H~~~Cg~g~GiFl~v~~~~il 1961 (2029)
|+.|+.+++++....|++|+..+ ..|++||+||..+|.+ +.||++ |+|++||..||+++||||.+++|.++
T Consensus 1588 pd~~s~lI~s~~~~~c~~~~~~~s~~p~lCl~cg~~~~~q-~~~~~~~~~~~~~g~~~~ha~~c~~~vgifl~v~~c~~~ 1666 (1738)
T KOG1140|consen 1588 PDEYSCLINSASFFFCPKSGKDDSIIPALCLLCGSEECGQ-SGFDQEGSNGESVGACTAHAAECTGAVGIFLRVRECSIL 1666 (1738)
T ss_pred CchhhhhHHhhhcccCcccCCccccCchHHhhcchHHhhh-hhhhhccccccchHHHHHhHHhhcceeceEEeeechhhh
Confidence 99999999999999999999986 8999999999987775 578843 89999999999999999999999999
Q ss_pred EEcc--CCCccCCCCcccCCCCCCCCCCCCCCcccCHHHHHHHHHHHHhCCccccccccccc
Q 000151 1962 LQRC--ARQAPWPSPYLDAFGEEDIEMHRGKPLYLNEERYAALTYMVASHGLDRSSKVLSQT 2021 (2029)
Q Consensus 1962 ~~~~--~rg~~~~~pYlD~~GE~D~~lrrg~pl~L~~~Ry~~L~~~w~~h~i~~~~~~~~~~ 2021 (2029)
++.+ ++|||+++||+|+|||+|+|+|||.|+|||++||+++..+|++|+|++ ++.+.+
T Consensus 1667 ll~~m~~~g~~~~~pylD~~gEtd~gl~rg~P~~L~~~ry~k~~~~w~~~~I~e--qv~~~~ 1726 (1738)
T KOG1140|consen 1667 LLEGMRNRGCFYPAPYLDEYGETDPGLRRGNPLHLNRERYRKLKELWLQQNITE--QVGRAT 1726 (1738)
T ss_pred hhhcCCcCCCcCCCCccccccCCChhhhcCCcccccHhhhhhhHHHHhhcchHH--HHhhhc
Confidence 9988 999999999999999999999999999999999999999999999977 444443
No 2
>KOG1139 consensus Predicted ubiquitin-protein ligase of the N-recognin family [Posttranslational modification, protein turnover, chaperones]
Probab=99.96 E-value=1.5e-30 Score=319.35 Aligned_cols=581 Identities=11% Similarity=-0.045 Sum_probs=403.2
Q ss_pred CCCCCCCcCCCccccccChHhhHHHHHHHHHHHHHhhhccccccCCcccCCCCcccccccccccccceecCCCCCcccCC
Q 000151 1415 YDGFGPIDCDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPWDLQRIN 1494 (2029)
Q Consensus 1415 ~~gF~~~~~~gvh~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCksL~Ns~LPilp~~~~~~~ 1494 (2029)
+++|.+..+.+.|.++|+|..|.+|..+|+.....+-..+-.+.+.|..+..+.++.||.|++++|+|.|..++++....
T Consensus 169 yD~fv~h~q~~~asTsi~hf~~dsv~~r~l~eell~wg~~ylf~~~ev~rll~~g~~~~~c~alAKvveq~y~~~~~s~~ 248 (784)
T KOG1139|consen 169 YDRFVDHIQSQHASTSITHFTEDSVRSRLLNEELLIWGLLYLFLRIEVARLLINGNMWVRCGALAKVVEQIYSQWNVSSA 248 (784)
T ss_pred CCcceecccccccchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHHhcCCCccccHHHHHHHHHhcccchhccc
Confidence 35666667889999999999999999999999988888888888999999999999999999999999999976655322
Q ss_pred CCCcccCCCCCCCCCCccccccchhhHHHHHHHhhhhhcccccccccccccCCcchhhHHH--HHHHHHHHHHHHHhhcc
Q 000151 1495 EQPTVSGVGLSLDSSSSFTTREENTSFQLQQAVSLLQSASNVVGKADVIESFPLMKNEIMA--SNVEAVSRRMCKMYFQN 1572 (2029)
Q Consensus 1495 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~s~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~~~~l~~~~~~~ 1572 (2029)
+. ...+...+..+ ..-..++|+.+.+..+..++......+.....+++...-.. ....++.++.+..+++.
T Consensus 249 kk-rhePdt~~~r~------~hi~~slfl~e~la~~~~~ec~~~di~r~v~~~p~~s~L~~~~~~~~~~~k~~~~~Hsr~ 321 (784)
T KOG1139|consen 249 KK-RHEPDTIRFRA------AHIDKSLFLKELLASFNITECIKIDIGRFVEKSPESSILFQETEVTIDFTKQSPIDHSRD 321 (784)
T ss_pred cc-CCCCchhcccc------ccccHHHHHHHHHHHhhhhhhhhhhccceeEeccccccchhhhhhhccccccCchhcccC
Confidence 21 11110000111 01235667777665544333221000000001111111111 11222333333333222
Q ss_pred cccccc-CCCCCChhHHHHHHHhHhHHHHHHHhhccCCCCCCcchhhhHHHHhhcchhhHHHHHHHHHhhhcccchhHHH
Q 000151 1573 KLDKFF-GSARVNPSLIMWDALKYSLMSMEIAARSEKTSTTPIYDVNALDKELKSSSGFVLSLLLKVVQSMRSKNSLHVL 1651 (2029)
Q Consensus 1573 ~~~~~~-~~~~~~~~~~l~~tl~YTi~s~Eia~Rg~~~~~~~~~~l~~L~~~l~s~~~~il~~l~~~~~~~r~~~~l~~l 1651 (2029)
....+- +--+......+|++++|...+.|+--|-.+-+..++.|...+...+++..+++++++.+++...+..+..++-
T Consensus 322 p~~~~l~~f~~p~lEaa~~d~l~~v~~~~e~~~R~~~~s~vlr~~~~~~~e~~~~~~~~~f~l~~~~v~~s~~~~ai~~~ 401 (784)
T KOG1139|consen 322 PRIPILGEFIRPHLEAAGVDALIDVEMEREFDPRLFDDSEVLRTIVIREPEWIDPMFWGMFKLVAELVVVSVNSGAIPEE 401 (784)
T ss_pred cchhHHHHhhccccccccCchHHHHhhhccccccccchhhhhHHhhhccccccchhhcchHHHHHHHhhhhcccccchHH
Confidence 111000 0000112346799999999999999998777777778888888899999999999999999988899989999
Q ss_pred HHhhhhhhhhhhhcCCCCCCCCCCCcCCCCccccccccccccCCcchhhhhcccCCCccccCchhhHHHHHhhccccccc
Q 000151 1652 QRFRGIQLFAESICSGTSIDNPGGRCKRGGNMLSILKHADVEVSYPDIQFWNRASDPVLARDPFSSLMWVLFCLPCQFIL 1731 (2029)
Q Consensus 1652 ~r~~~~~Ll~~si~~~~s~~~~~~~~~~~~~~~~il~~l~~~~~~~~~~~~~~~~~plL~~D~F~~Lv~~~~~lp~p~~s 1731 (2029)
+++.++.-++..++.+.++..++ .....+.....++.+. -.|.+.+.|++.+|||..++|.++++|.++..
T Consensus 402 ~~~~em~n~~a~~~~~~s~~~aS-~~~~~~~~~~~f~~i~--------~~~~~~~~P~~~~~p~~~~s~~l~~~~~~~~~ 472 (784)
T KOG1139|consen 402 HYRSEMVNCMAMGNVPYSRLRAS-ISEKGSMIDKHFETIL--------NEIGDFIEPIETTTPLMQGSYQLKTSIWDSEV 472 (784)
T ss_pred HHHHHHHhHHHhcCCCccccccc-ccCCCccccccccccc--------ccccccccchhhcCccccchhhccccCCcccc
Confidence 99999888888888777766653 2222221212223222 45788999999999999999999999888888
Q ss_pred cccchhhHHHHHHHHHHHHHHHHhhcccccccccccchhhHHHHHHHHhcccccccccccccCCCChhhHHHHHHHhhhh
Q 000151 1732 CKESLLSLVHVFYAVTLSQAVLSCCGKLQSKVNELGFSDSLISDISKLLGEFGSAQEYFVSNYIDPSCDIKDMIRRLSFP 1811 (2029)
Q Consensus 1732 ~~~~~~~iv~l~y~a~ivQ~ll~~~~~~~~~~~~~~~~d~l~~~i~~~~~~~~~~~~~~~s~~~~~~~~i~~~v~k~~lP 1811 (2029)
+..++...++.+--+..+|+++++...........++..... ++...+...+.+ ++|.+...+..+++.+.++++-+|
T Consensus 473 c~~~~~~~~~s~~~~~~v~~~~~~~a~k~s~d~~l~~~~~~e-d~s~~lr~~g~s-~l~~~l~~~~~~d~~dt~~~~~~~ 550 (784)
T KOG1139|consen 473 CPVFFMMRSTSIKQAREVFAKMEIRAQKNSLDKDLEVAKIEE-DFSDQLRHRGIS-NLYNVLLTERFLDHCDTVLASEAD 550 (784)
T ss_pred ccchheeeeeeccchhHHHHHHHHhhccchhhhhccccchhH-HHHHHHHHhhhH-HHhhhhhhhhhhcccchhhccccc
Confidence 888888888888889999999987643211000111111111 222222222221 233333333456788889999999
Q ss_pred hhcc-cc--------------------cCCC---------CCccCChhHHHHHHHhcCCCChHHHhhhHHHHHHHHHHhh
Q 000151 1812 YLRS-DM--------------------MDSS---------DDALSDLKEIQEVEKMFKIPSLDVILKDEVLRSLVLKWFH 1861 (2029)
Q Consensus 1812 FLRr-h~--------------------~~~~---------~~~~~e~~E~d~L~~~L~LPsl~~ll~~~~~~~li~~W~~ 1861 (2029)
|+|+ |. .... ..++.+..-.+.+..+..||.+.+... .-.+.|.+
T Consensus 551 ~~~~c~~~~~~la~~~~tl~~e~~~s~~~~~~i~~~m~~I~~~pf~l~~kq~~~~~~~i~~i~e~~~-----k~~e~~~~ 625 (784)
T KOG1139|consen 551 ETAKCHDGTYQLAVYLLTLGVEYAQSYVGDEKIKKQMIDIFHTPFQLILKQTRKNGALIVVIKEGKL-----KREELRIS 625 (784)
T ss_pred hhhhHHHHHHHHHHHHHHHhhhhhhhhcCCcchhhhhhhccCCchhhhHHHHHhcccCCchhHHHhH-----HHHHHHHH
Confidence 9999 11 0000 011122233456777888888875442 33567888
Q ss_pred cccccchhhccccccccCCCCcccccCCchhHHHHHHHHhhcccCCCCCCCCCceeeecccccccCCCCcccCCCcchHh
Q 000151 1862 HFSKEFEVHRFQHVLYSTPAVPFKLMCLPHLYQDLLQRYIKQCCSDCKSVLDEPALCLLCGRLCSPSWKPCCRESSCQSH 1941 (2029)
Q Consensus 1862 h~~~~~~~~~~~~~~~~~~~~~~~Li~LP~~~~~l~~~~~~~~C~~c~~~~~~paiCL~CG~~~~~~~~~cc~~g~c~~H 1941 (2029)
|....++..+........++++|.+.++|.-|+++..+..+. +..+++.|+.||..|..-+.|||.+.+ .+|
T Consensus 626 ~~~r~~e~~k~~r~~~~k~~~~fa~~~~~~~~q~~a~~s~~~-------~g~ed~~~~~~~~~q~~~k~y~C~icg-~n~ 697 (784)
T KOG1139|consen 626 KHSRNQEKMKAPRDPVKKAAKEFAKRRMEAIMQNSAKKSAQT-------EGMEDAEVNKVDPSQQNRKVYECPICG-QNA 697 (784)
T ss_pred HHHHHHHHhhcccchHHHHhHHHHHHHHHHHHHHHHHhhhcc-------cCCChHHHhhhCcccCCccCCcCCcCC-CCC
Confidence 877666655444444445677889999999999877654332 678999999999999887789998866 569
Q ss_pred hhhcCCCeeEEEEecccEEEEEccCCCccCCCCcccCCCCCCCCCCCCCCcccCHHHHHHHHHHHHhCCccccccccccc
Q 000151 1942 AVACGAGTGVFLLIRRTTILLQRCARQAPWPSPYLDAFGEEDIEMHRGKPLYLNEERYAALTYMVASHGLDRSSKVLSQT 2021 (2029)
Q Consensus 1942 ~~~Cg~g~GiFl~v~~~~il~~~~~rg~~~~~pYlD~~GE~D~~lrrg~pl~L~~~Ry~~L~~~w~~h~i~~~~~~~~~~ 2021 (2029)
..+||+++|+|++|+++.|+.-+-.+..-||.||||..|++|.+.-||+.+|++..||.+|....=+|++++.++.+.+|
T Consensus 698 p~T~~np~G~~~l~~~~~I~~~r~~~~~~~p~p~l~~de~e~~~~~Rl~~e~~rr~~~~~l~~~~es~~l~~~~~~l~gt 777 (784)
T KOG1139|consen 698 PNTVENPFGMLALLSTNFICEERIDASINTPDPLLKFDEYEHVSANRLQSETRRRFFSKRLQATFESQDLVKVNPPLVGT 777 (784)
T ss_pred CcccCCCceEEEEEeecchHHHHHhhccCCCChhhhcchhhhhHHHHHHHHHHHHHHHHHhhhcccccchhhccccccCc
Confidence 99999999999999999999988899999999999999999999999999999999999999999999999999999999
Q ss_pred ccccc
Q 000151 2022 TIGGF 2026 (2029)
Q Consensus 2022 ~~~~~ 2026 (2029)
+|++.
T Consensus 778 ~~~~c 782 (784)
T KOG1139|consen 778 DLKTC 782 (784)
T ss_pred chhcc
Confidence 99853
No 3
>KOG1140 consensus N-end rule pathway, recognition component UBR1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.82 E-value=1.1e-21 Score=262.94 Aligned_cols=928 Identities=17% Similarity=0.043 Sum_probs=569.7
Q ss_pred HHHHHHhcCCchhhhchhhHHHHhhhCCCChhHHHhccCCCCHHHHHHHHHHHhhccccCCCCCh-h-hhHHHHHHHHHH
Q 000151 18 IVRRLMNIGVPEEFLDYSGIVNFAKNDKSRIPELVSTILPPDEEVAEVIQDAKAKNKKVSVGPNM-K-GRFRESMLWLQW 95 (2029)
Q Consensus 18 ~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~l~~ 95 (2029)
..+++--.++++++-...+++.|+...+..|...+....|....+...+..+..+..++.+..++ + ..+.+....+.|
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 34667778888888777899999999999999999999999999998888888887777655445 3 448888888888
Q ss_pred HhcCCCHHHHH---HHHHccCCCccccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecCCccccCCCc
Q 000151 96 LMFEREPEKVL---RKLSKIGQRGVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDV 172 (2029)
Q Consensus 96 ~~~~~~~~~~l---~~l~~~~~~~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~~gG~CDCGd~ 172 (2029)
.++.+.+.-.. ..+. -.-..+|+-+|...+.+++|++|.. .+.+|..|++...|-.|.+..+-..+|+|+|+ .
T Consensus 612 ~v~~~~~sv~~p~~~~l~-~l~~~~~s~v~~~~d~~~~~~~~~n--~~~i~e~~lr~~Vl~aqid~~~w~rNG~si~~-q 687 (1738)
T KOG1140|consen 612 SVSQERVSVSNPVSRLLA-FLIELSCSSVVSLKDAYERLEDCSN--FLAISEHSLRVLVLCAQIDVGFWVRNGFSILH-Q 687 (1738)
T ss_pred ccccccceeeccHHHHhh-hhhhcccchhhhcchhhhhHhhhcc--chhhcccchhheeeeeecceeeEeecCcchhh-h
Confidence 77775443211 1111 1125889999999999999999997 99999999999999999998888889999999 8
Q ss_pred ccccccCCCCcCCCCCCCCCCcHHHHHhhHHHHHHHHHHHHHHh--hhhcccCCCCCCCCChHHHHHHHHHHHHHHHHHH
Q 000151 173 TAWKREGFCSRHKGAEQIQPLPEKYANSAAPVLDALFIYWENKL--SLAESVGQENPRASDHVAERRKLANELTFAVVEM 250 (2029)
Q Consensus 173 ~awk~~~fC~~H~~~~~~~~lp~~l~~~~~~~~~~ll~~~~~~l--~~~e~~~~~~~~~~~~~~~~~k~a~~l~~~i~~~ 250 (2029)
.+|...++|..|....++-++-..++.. +..+.++.+|-... .|... ..+....|...+..++.+++...|+.+
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--DPNRFLFTILSRFELLDWFTG--EVDYQSNDTEDTISFMIEEFLALIILL 763 (1738)
T ss_pred hHhhcCccccccchhHHHHHHHHHHhcC--CHHHHHHHHHHHHHHHHHhcC--CCccccccHHHHHHHHHHHHHHHHHHH
Confidence 9999999999998775544433333322 22333333322211 12211 123334566677778888888777777
Q ss_pred HHHHHhchHHHHHHHHHHhhccchhHHHHHhccCCCCHHHHHHHHHHHHHhhCChhhHHHHHHHHHhhhHHHHHHHHHhc
Q 000151 251 LLEFCKNSESLLSFVSKRVISVIGLLDILVRAEMFSSDVVVRKLHELLLKLLGEPIFKYEFAKVFLSYYPVFVKDAIREH 330 (2029)
Q Consensus 251 L~e~~~~~~~ll~~l~~~l~~~~~ll~~ll~~d~~L~k~~r~~lh~LllsLL~d~efK~~fA~~Fv~~Y~~i~~~fl~~d 330 (2029)
+.|+... .+.......+...+++..|........+.+++..|.+...+..|..++..++..+...|+...--.++..
T Consensus 764 l~Er~~~---~~~kv~~~d~~k~~iIh~L~~~~lays~lv~s~~~dl~~~l~~d~~~e~Va~~~~p~~~~~~gvf~lK~~ 840 (1738)
T KOG1140|consen 764 LTERSYF---GSSKVRRMDIIKSEIIHILCFKPLSYSQLVRKIPHDLTKTLSFDEALEEVAVFKKPKGLADNGVFVLKES 840 (1738)
T ss_pred HHheeec---ccccccHHHHHHHHHHHHHHhcchhHHHHHHhchhhhhhcccchHHHHHHHhhccCCccccceEEEechh
Confidence 7765543 1111222222234555556655555667788899999988999999999999988888855433334444
Q ss_pred cCcccccCCccceeeeeccccCCcHHHHHHhhcHHHHHHHHHHHHhhhhcC--CCCcceeccccccccchhhhhhhhhHh
Q 000151 331 SDDTIKKYPLLSTFSVQIFTVPTLTPRLVKEMNLLEMLLGCLREIFDSCAG--DDSCLQVAKWANLYETTNRVIGDIRFV 408 (2029)
Q Consensus 331 ~d~~~~~~s~v~~LSVQLFTvPSLA~~LV~e~nLL~iLl~tl~~~~~~~~~--~~~~l~~~~~~~~~~~~~~I~~DLryl 408 (2029)
-++.+..|-...++|+|.-+++++++...++.+.+...+..+...+..++. .++-+........-..-.+.+.++++.
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 444444555567899999999999998888776664444444444444331 122222111111122334566778888
Q ss_pred hcchhhhHHHhhhchHHHHHHHHHHHHhcCCC--cccccccCcceeeCCceeehhhhhhHHHhhHHhhhhhccccccccc
Q 000151 409 MSHAAVSKYATHEQLNISKAWMKLLTFVQGMN--PQKRETGIHIREENEYMHLPLVLDHSIANIQPLLVDGAFSSAVSEE 486 (2029)
Q Consensus 409 Lsh~~v~~~l~~~~~~l~~~~l~lLs~~QGMn--p~kRq~~~HVEyE~e~w~~aF~L~~~la~i~~~~~~~~~s~~~~~~ 486 (2029)
+++--+.+.+..-.-...+.|...+.+++++. +..|++|--.-++...=...+...+.+..++.++..+.++..++.|
T Consensus 921 ~s~~~l~~~~~~ihG~~~~~~l~~~~~~~~~~~e~~~~e~gl~~~e~lv~~~~~~~~~~~~~v~~~l~~~~~~~~~n~~e 1000 (1738)
T KOG1140|consen 921 ESSTLLSKVLHLIHGIALNEELINMKFAFTQKTESIAREKGLSLYESLVRKPDSLVHGKIIEVIVELFESLIKSRANDPE 1000 (1738)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccchhhHHHhhhcchhhcCCcceeeeHHHHhhhhhhhcCCcc
Confidence 88765555543334478899999999999999 9999999877555542233334447788889998888888887754
Q ss_pred cc-cccccccccCCCCCccccccccccccccccccccCCCcccccccccccccccccccccchhhHHHHHHHHHHHHHhh
Q 000151 487 TR-YDFSMYKQDIGDGDSLRHAKVGRLSQESSVCGAMGRSSLSASTLKADDVIFDAVSDVLLPHSVTWVAHECLRAMENW 565 (2029)
Q Consensus 487 ~~-~~~~~~~~~~~~~~~~~~~~v~r~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~cl~~l~~~ 565 (2029)
.. ...-|.+..+.+++..+.++.+|+..|..++...--+.-+..=+.+..++ .+..+-+.|.+....+.++.......
T Consensus 1001 a~~~~~~~~~~~~~s~~~~e~~rk~rlA~~r~~k~m~k~s~qq~kfm~~~e~e-~d~~~~~~~~~~~~~~~~~d~~~~~~ 1079 (1738)
T KOG1140|consen 1001 VANDEKDKKEKQSVSLDEEEKERKKRLARERQKKLMAKFSNQQTKFMAENEDE-FDEQENQTPSSGSKTYEEEDFTCALC 1079 (1738)
T ss_pred ccccccccccccccccccccccchhhhHHHHHHHHHHHHHHHHHHHHHhcccc-cCcccccCccccccchhhhhccchhh
Confidence 33 55555555556777777888888888887775332222221111111111 12333445556666666666554433
Q ss_pred hcCCCCcccccccCCCCcccccCchhhhhHh-----hhhhccccccccccccCCccccccccccCCCccccccCcccccc
Q 000151 566 LGVDDRSVSVNDILSPNASRISGSNFVALKK-----TLSKIKKGKSIFSRLAGSSEVTAGIQESGDLDNATSMGKESKIT 640 (2029)
Q Consensus 566 l~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 640 (2029)
++....... ....++. .+-++...+- .+..........+.|++...+.+ .+.+
T Consensus 1080 ~~~s~~~~~-~~~~~~~----~~~~~~~~~i~~e~e~~~~~~~~~~v~~~f~~~s~~~s-------------d~l~---- 1137 (1738)
T KOG1140|consen 1080 QDNSCTDFQ-VKPASHL----VKPIFRECIICDENEDVPNWDGRYSVSSAFAQKSDDVS-------------DALT---- 1137 (1738)
T ss_pred hccchhccc-cccchhh----hcccccccccCChhccCCCccccchhhhHhhhhccccc-------------cccc----
Confidence 321111000 0000111 0000000000 00000001111111111111100 0000
Q ss_pred ccCCcccccccccCcCCccccccch-----------------hcccccc------ccccCccCceeeeccCCceeeehHH
Q 000151 641 ISGERDTASWRSAGFNDSEMEGECA-----------------TELDNLH------VLSLCYWPDITYDVSSQDVSVHIPL 697 (2029)
Q Consensus 641 ~~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~------~~~~~~~~~v~fdVs~~~VSfH~PL 697 (2029)
-++...|+ .. ...+||.- ....+|. .+...-|.-..++|+-..+.-|-++
T Consensus 1138 ~p~~~~~~---~~----~s~c~h~mh~~c~~~~~~a~r~~~n~~~~~l~~~~se~~l~lCp~c~slsn~~lp~~~~~~~~ 1210 (1738)
T KOG1140|consen 1138 EPGSLSCG---TV----LSSCGHHMHYGCFKRYVQAKRFRENARTAPLCQHYSENGLFLCPLCKSLSNVSLPMFLPPELL 1210 (1738)
T ss_pred CCCCCccc---ce----eeccCCcchHHHHHHHHHHHHHHHHhhhcCcccccccCCcccCCchHhhhhccCCcCCchhhh
Confidence 00111111 00 01111100 0000010 1111222333467888889999999
Q ss_pred HHHHHHHHHHHHhhhccccccccccccCCCCCccccchhhhhcccCCCCCCCcchhhccccHHHHHHHHHHhcCcccccc
Q 000151 698 HRLLSLIIQKALRRCYGESAASESADTGAENPLSAVSLDFFGHILGGCHPYGFSAFVMEHPLRIRVFCAQVHAGMWRRNG 777 (2029)
Q Consensus 698 hr~Ls~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~l~e~pLR~~Vl~aQI~aGmWvRNG 777 (2029)
++.++...+..+..+++.-...+...-........++..|.......+.|-++...-..+...+.+++.+++++||-- |
T Consensus 1211 ~n~~t~~~~~n~~~~i~~rs~~~~s~~~vs~~~s~~~~~~~ss~i~e~kp~~~~~l~~~~~~~ie~~~k~v~s~~~k~-~ 1289 (1738)
T KOG1140|consen 1211 LNPLTLENQRNLNSWIEKRSRASFSLQDVSSILSDPWAAFTSSRIPELKPILIMDLPDSVVEQIELFQKIVGSAMFKP-S 1289 (1738)
T ss_pred cChhhhhchHHHHHHHHHhchhhcchhhhhhhhcccchhhccccccccccchHhhhhhHHHHHHHHHHHHHhhheeec-c
Confidence 998888777766555441000000000000001122222322111222232211223455677999999999999986 2
Q ss_pred hHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccccCCCCCCCchh-HHHHHHHHHHHHhh
Q 000151 778 DAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLNLERPSEYEP-ILVQEMLTLIIQIL 856 (2029)
Q Consensus 778 ~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~~~~~~~~~y~~-~mvEe~L~lLI~ll 856 (2029)
. .. ...+-+..-+.+.|++|++.++.+.......++.+++...++.++......+.. ..+.. ...++++
T Consensus 1290 ~------~i--~~~~le~~~~~~~~~~~~~~~~s~a~~~~~~~l~~~~~~~~l~l~~~~~~~~~~~~~l~~--~~~~~~l 1359 (1738)
T KOG1140|consen 1290 S------LL--STNTLELTLFSREFLIVCWQSLSDAEQSTKLLLSASKKPSFLKLNEDMTFCLVTISRLRA--LHWEQIL 1359 (1738)
T ss_pred c------ce--eecccccCcccchhhhhhhhccchHHHHHHHHHhccCCcccccCchhhHHHHHHHHHHHH--HHHHHHH
Confidence 1 12 234667888899999999999999999999999999998887776543332322 22222 4567777
Q ss_pred cccccCCCChHHHHHHHHHHHHhcCCCChHHHHhhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEeehhhccccccc
Q 000151 857 QERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIY 936 (2029)
Q Consensus 857 teR~~~g~s~~e~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~Dpy 936 (2029)
.++...++-.....+.++|-.+..++.+++++...+|.+..+...++.++..|- +.|.+.-.+.+.++.-.|.|.+-+
T Consensus 1360 ~~~~~~~llk~~s~~~~~i~~~~tpd~~~~~ll~~l~~~~~~~~~l~~~~~~~~--~~~~~~~~~~i~~~~i~s~elits 1437 (1738)
T KOG1140|consen 1360 YELVYTFLLKSFSPTIPRISVLITPDQPENELLVILPHDFPKSLELELTLDFVN--KNPKKIFELKILMASIISIELITS 1437 (1738)
T ss_pred HHHHHHHHHHHHhhcCCcchhccCCCCCcchhhhccchhhhhhccHHHHHHHhh--hhHHHHHhHHHHHHHhhhhhhhee
Confidence 887777776777778888888888899999999999999999999999999988 668777889999999999999988
Q ss_pred ccccCchhHHHHHHHHHHhhcccccc--CCCCCCcccCCCccccccccccHHHHHHHHHHHHHHhc
Q 000151 937 HPRWSSRDLQVAEERYLRFCSVSALT--AQLPRWTKIYYPLESIAGIATCKVVLQVIRAVLFYAVF 1000 (2029)
Q Consensus 937 ~~~y~~~~~q~aeer~~r~~k~~a~~--~~~P~~~~~~~pf~~i~~il~s~~~~~il~~vL~~al~ 1000 (2029)
+..+.. |.+.|+++..+..-..+.. ...+.++....+-.++.++--+....+.+...|.++..
T Consensus 1438 ~s~l~~-d~~~~~~q~s~~e~~~~~t~l~~~~s~~~i~~~~~~~~~~~L~~~~~~~i~sfL~~~al 1502 (1738)
T KOG1140|consen 1438 HSYLEN-DLEMAEEQKSIDEFKSLLTYLLQLESSRTIPKLADIRLRLSLCLSCEAGILSFLRRAAL 1502 (1738)
T ss_pred ccccCC-ccchhhhhhhHHhHhHHHHHHHhccchhhCccccchhhhhHHHHHHHHHHHHHHHHHHH
Confidence 888877 8777776544322222222 23334443333334555666677777888888877654
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=170.87 Aligned_cols=70 Identities=44% Similarity=1.070 Sum_probs=66.3
Q ss_pred ccccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEec-CCccccCCCcccccccCCCCcCC
Q 000151 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYT-GGGCCDCGDVTAWKREGFCSRHK 185 (2029)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~-~gG~CDCGd~~awk~~~fC~~H~ 185 (2029)
.+||++|++++++|+|+||+.++++++|.+||+++.|+||+|.+++. +||.|||||++|||+++||++|.
T Consensus 1 ~~C~~~~~~~~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~~~~~~~~~~~~CDCG~~~~~~~~~~C~~h~ 71 (71)
T smart00396 1 DVCTYKFTGGEVIYRCKTCGLDPTCVLCSDCFRSNCHKGHDYSLKTSRGSGICDCGDKEAWNEDLKCKAHE 71 (71)
T ss_pred CCCCCccCCCCEEEECcCCCCCCCEeEChHHCCCCCCCCCCEEEEEecCCEEECCCChhccCCCccccccC
Confidence 47999999999999999999999999999999999999999999885 45999999999999999999994
No 5
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=99.73 E-value=1.8e-18 Score=164.21 Aligned_cols=70 Identities=49% Similarity=1.112 Sum_probs=54.0
Q ss_pred ccccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecC-CccccCCCcccccccCCCCcCC
Q 000151 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTG-GGCCDCGDVTAWKREGFCSRHK 185 (2029)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~~-gG~CDCGd~~awk~~~fC~~H~ 185 (2029)
+.|+++|++++++|+|+||+.+++.+||.+||.++.|+||++.+..+. +|.|||||+++||+++||++|+
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=0.330 Sum_probs=142.2
Q ss_pred hccccHHHHHHHHHHhcCcccccchHHhHHHHHhccccccccccchhhHHHHHHHhccChHHHHHHHHHHhccccccccC
Q 000151 754 VMEHPLRIRVFCAQVHAGMWRRNGDAALSSCEWYRAVRWSEQGLELDLFLLQCCAALAPADLYVNRIIERFGLSNYLSLN 833 (2029)
Q Consensus 754 l~e~pLR~~Vl~aQI~aGmWvRNG~si~~Q~~~Y~~~~~re~~~d~DifLLQ~~a~~~dp~~fl~~il~RF~L~~w~~~~ 833 (2029)
+.-+++++.|--.-++..||+|+|.-...-...|-+-.+-...---+--.+-.++..+++..|+..++-+|.+.+.-..+
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 45667899999999999999999998877777775544433333333445556888999999999999999876542211
Q ss_pred C--------C-----C-------------------C--------------------------------------------
Q 000151 834 L--------E-----R-------------------P-------------------------------------------- 837 (2029)
Q Consensus 834 ~--------~-----~-------------------~-------------------------------------------- 837 (2029)
. . . +
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--hHHHHHHHHHHHHhhcccccCCCChHHHHHHHHHHHHhcCCCChHHHHhhCCCCCC-CcchHHHHHHHHccc
Q 000151 838 --SEYE--PILVQEMLTLIIQILQERRFCGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDLS-KFDQLQEILDAVAMY 912 (2029)
Q Consensus 838 --~~y~--~~mvEe~L~lLI~llteR~~~g~s~~e~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~-~~~~fe~iL~eVA~f 912 (2029)
..|+ +.|...++.++..+|.++.+.|..+++..+-|+.|.-+++...||-+..++.+... .++.|+.|+.+..+|
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 25677888999999999999999999999999999999999999999988777654 578899999999999
Q ss_pred cCCCC----CCcceEEeehhhcc-ccccccc
Q 000151 913 SHPSG----FNQGMYSLRWSYWK-ELDIYHP 938 (2029)
Q Consensus 913 ~~P~g----~~~G~Y~LK~e~~~-e~Dpy~~ 938 (2029)
-.|-- .-+|.|.||.-.|+ +.-|-++
T Consensus 447 ~~P~~~~~p~~~~s~~l~~~~~~~~~c~~~~ 477 (784)
T KOG1139|consen 447 IEPIETTTPLMQGSYQLKTSIWDSEVCPVFF 477 (784)
T ss_pred ccchhhcCccccchhhccccCCccccccchh
Confidence 99943 34799999999997 4556444
No 7
>PF10390 ELL: RNA polymerase II elongation factor ELL ; InterPro: IPR019464 ELL is a family of RNA polymerase II elongation factors. It is bound stably to elongation-associated factors 1 and 2, EAFs, and together these act as a strong regulator of transcription activity. by direct interaction with Pol II. ELL binds to pol II on its own but the affinity is greatly increased by the cooperation of EAF []. Some members carry an occludin domain (IPR010844 from INTERPRO) just downstream. There is no Saccharomyces cerevisiae (Baker's yeast) member. ; GO: 0006368 transcription elongation from RNA polymerase II promoter, 0008023 transcription elongation factor complex; PDB: 2E5N_A 2DOA_A.
Probab=97.01 E-value=0.00044 Score=83.48 Aligned_cols=81 Identities=27% Similarity=0.433 Sum_probs=61.2
Q ss_pred HHHHHHHHHHhcCCCChHHHHhhCCCCCCC---cchHHHHHHHHccccCCCCCCcceEEeehhhcccccccccccCchhH
Q 000151 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSK---FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (2029)
Q Consensus 869 ~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~---~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~Dpy~~~y~~~~~ 945 (2029)
.+|.-|||.||.+|....||...|..+... -..++.||.+||... .++.|.||+.+|+|+|.=++.|+-.|+
T Consensus 198 plReRvIHLLALkpykK~ELl~rL~~dg~~~~dk~~l~~iL~~Va~l~-----~~~~y~Lk~~~ykevq~dWP~yse~er 272 (284)
T PF10390_consen 198 PLRERVIHLLALKPYKKPELLLRLQKDGLSPKDKDELDSILQEVANLN-----KDNSYTLKDHFYKEVQKDWPGYSEEER 272 (284)
T ss_dssp -HHHHHHHHHHHS-EEHHHHHHHHHHH---HHHHHHHHHHHHHCCEEE-----TTTEEEE-STHHHHS-TT-TT--TCHH
T ss_pred cccccchhhhhcCccccHHHHHHHHhcCCChHHHHHHHHHHHHHhccC-----cCCeEEehHHHHhhhccCCCCCCHHHH
Confidence 599999999999999999999988765543 246999999999974 378999999999999977888998888
Q ss_pred HHHHHHHHH
Q 000151 946 QVAEERYLR 954 (2029)
Q Consensus 946 q~aeer~~r 954 (2029)
|..+-+..+
T Consensus 273 q~l~r~l~~ 281 (284)
T PF10390_consen 273 QLLKRRLSR 281 (284)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHh
Confidence 888665443
No 8
>KOG1777 consensus Putative Zn-finger protein [General function prediction only]
Probab=94.87 E-value=0.011 Score=72.03 Aligned_cols=62 Identities=34% Similarity=0.562 Sum_probs=50.4
Q ss_pred cCCCcccc-----ccccCCceeEEeccCCCCCCccccccccCCCCCCCceeEEEecCCccccCCCccc
Q 000151 112 IGQRGVCG-----AVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTGGGCCDCGDVTA 174 (2029)
Q Consensus 112 ~~~~~~Cg-----~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~~~gG~CDCGd~~a 174 (2029)
.-+.+.|- +.+-+=.-+|||-||...+.-+||..|.++ -|+||++-..+...-.||||-..+
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 44456674 334444568999999999999999999988 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=91.22 E-value=0.066 Score=46.41 Aligned_cols=20 Identities=25% Similarity=0.845 Sum_probs=16.6
Q ss_pred ccccccChHhhHHHHHHHHH
Q 000151 1426 IHLSSCGHAVHQGCLDRYVS 1445 (2029)
Q Consensus 1426 vh~ssCGH~MH~~C~~~Y~~ 1445 (2029)
+..-.|||..|.+|++.|++
T Consensus 16 ~~~l~C~H~fh~~Ci~~~~~ 35 (44)
T PF13639_consen 16 VVKLPCGHVFHRSCIKEWLK 35 (44)
T ss_dssp EEEETTSEEEEHHHHHHHHH
T ss_pred EEEccCCCeeCHHHHHHHHH
Confidence 33556999999999999983
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=91.15 E-value=0.16 Score=43.10 Aligned_cols=19 Identities=37% Similarity=1.001 Sum_probs=16.3
Q ss_pred ccccChHhhHHHHHHHHHH
Q 000151 1428 LSSCGHAVHQGCLDRYVSS 1446 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~~S 1446 (2029)
+..|||..|..|+.+|++.
T Consensus 15 ~~~C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 15 LLPCGHVFCRSCIDKWLKS 33 (45)
T ss_pred ecCCCChhcHHHHHHHHHh
Confidence 5669999999999998664
No 11
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=90.35 E-value=0.09 Score=61.72 Aligned_cols=48 Identities=35% Similarity=0.711 Sum_probs=34.9
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhccc---cccCCcccCCCCcccccccccc
Q 000151 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRI---IFEGGHIVDPDQGEFLCPVCRQ 1477 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~---~~er~h~~d~e~gEFLCPLCks 1477 (2029)
.+.|-|.||+.||.+|+...+...++.. .-+|.| ..+.-|=+||+|+-
T Consensus 133 ~T~C~Hy~H~~ClaRyl~~~~~~lrqe~q~~~~~~qh--~~~~~eavcpVcre 183 (368)
T KOG4445|consen 133 VTACDHYMHFACLARYLTECLTGLRQEIQDAQKERQH--MKEQVEAVCPVCRE 183 (368)
T ss_pred eehhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--hhhhHhhhhhHhhh
Confidence 6889999999999999999886654321 122333 23466778999984
No 12
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=89.89 E-value=0.094 Score=69.62 Aligned_cols=63 Identities=27% Similarity=0.695 Sum_probs=50.7
Q ss_pred ccccccccCCc----eeEEeccCCCCCCccccccccCCCCCCCceeEEEe-cCCccccCCCcccccc-cCCCCcC
Q 000151 116 GVCGAVWGNND----IAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVTAWKR-EGFCSRH 184 (2029)
Q Consensus 116 ~~Cg~v~~~ge----~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~~~~-~~gG~CDCGd~~awk~-~~fC~~H 184 (2029)
..|.-.|+..+ -+|.|+|||.-.+-+-|.+|-.- .|+||+.++-+ +.-.+||| |-+ +..|+.-
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 57889998543 57999999999888889999765 69999999987 57899999 655 4446544
No 13
>PF13764 E3_UbLigase_R4: E3 ubiquitin-protein ligase UBR4
Probab=89.72 E-value=1.4 Score=60.40 Aligned_cols=70 Identities=14% Similarity=0.200 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH---HHhhcccCccCCCCCCCccCCCCcccccccccCCCcccccCCCC---CCCeE
Q 000151 1146 SEKRKAKARERQAAILEKMKAEQFK---FLSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNS---RTPVS 1219 (2029)
Q Consensus 1146 ~ekkK~~AkeRQakIMaqf~~qQ~~---Fl~~n~~~~~~~d~~~~e~~~s~~~~~~~e~~~~~CilCqe~~~---~~pfG 1219 (2029)
+.+||++|.++|+|.+.+|.-++.+ =+.+.....+ .+ +.++ |. --.|.+|+|..+ ++++|
T Consensus 422 r~ekk~~Am~~Rek~L~~lgm~~~~~G~v~~~~~~l~~-----------~~-~l~e-e~-gl~C~ICrEGy~~~p~~~lG 487 (802)
T PF13764_consen 422 RQEKKRLAMAMREKQLKKLGMRVNEKGQVVVSSSILQN-----------ME-DLEE-ED-GLTCCICREGYKFRPDEVLG 487 (802)
T ss_pred HHHHHHHHHHHHHHHHHHccCccccccceecCchhhcC-----------cc-cccc-cC-CCeEEEcCCccccCCcccee
Confidence 5677889999999999998433200 0001100000 00 0111 22 367999999753 56899
Q ss_pred EEEeeecccc
Q 000151 1220 YLILLQKSRL 1229 (2029)
Q Consensus 1220 ~la~iq~S~~ 1229 (2029)
+-+|.-+-.+
T Consensus 488 iY~f~kr~~l 497 (802)
T PF13764_consen 488 IYAFSKRVNL 497 (802)
T ss_pred eEEEeecccc
Confidence 9997755444
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=85.41 E-value=0.64 Score=41.58 Aligned_cols=39 Identities=28% Similarity=0.869 Sum_probs=29.6
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCC----CC-CceeEE
Q 000151 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN----HK-EHDYSI 159 (2029)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~----H~-~H~~~~ 159 (2029)
.|++.... ..-|+|..|. ..-+|.+||..+. |+ .|.|.+
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 3669999999984 53 677765
No 15
>KOG4796 consensus RNA polymerase II elongation factor [Transcription]
Probab=85.11 E-value=0.86 Score=57.82 Aligned_cols=77 Identities=26% Similarity=0.375 Sum_probs=63.4
Q ss_pred HHHHHHHHHHhcCCCChHHHHhhCCCCCCCc---chHHHHHHHHccccCCCCCCcceEEeehhhcccccccccccCchhH
Q 000151 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSKF---DQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (2029)
Q Consensus 869 ~lrrEIIh~Lc~~p~t~S~L~~~lpe~~~~~---~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~e~Dpy~~~y~~~~~ 945 (2029)
-||.-|||+|+.++..--||.++|-.+...+ ..+..||.+.. ...+|+|.|++.+|+|+|-=++.|+-.|.
T Consensus 211 ~ir~RviHLlalk~ykk~El~~rLk~dGl~~~e~~~i~~il~~~~------~~~~~t~~Lrd~~~~evdq~Wp~yse~d~ 284 (604)
T KOG4796|consen 211 PIRDRVIHLLALKAYKKPELLARLKKDGLPQEEKNKIRSILQQNS------RSKDGTYTLRDSMLKEVDQNWPGYSEGDK 284 (604)
T ss_pred chHHHHHHHHHhhhcccHHHHHHHhhcCCcHHHHHHHHHHHHhhc------ccccccchHHHHhhhHHHhcCCCcchHHH
Confidence 4999999999999999999999987776543 35778888821 24789999999999999988888988887
Q ss_pred HHHHHH
Q 000151 946 QVAEER 951 (2029)
Q Consensus 946 q~aeer 951 (2029)
|..+-+
T Consensus 285 ~~lkr~ 290 (604)
T KOG4796|consen 285 QHLKRV 290 (604)
T ss_pred HHHHHH
Confidence 776544
No 16
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=85.02 E-value=0.69 Score=40.27 Aligned_cols=37 Identities=27% Similarity=0.654 Sum_probs=29.6
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000151 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2029)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 158 (2029)
.|+..+ .| .-|+|.+|. ..-+|.+||.++.|.+|.+.
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 477733 34 789999997 46699999999999888875
No 17
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=83.67 E-value=0.78 Score=40.41 Aligned_cols=38 Identities=26% Similarity=0.767 Sum_probs=29.7
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCC--CCC-CceeEE
Q 000151 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNG--NHK-EHDYSI 159 (2029)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~--~H~-~H~~~~ 159 (2029)
.|++.+. | .-|+|.+|. ..-+|.+||..+ .|. +|.+..
T Consensus 5 ~C~~~i~-g-~r~~C~~C~---d~dLC~~Cf~~~~~~H~~~H~~~~ 45 (46)
T cd02249 5 GCLKPIV-G-VRYHCLVCE---DFDLCSSCYAKGKKGHPPDHSFTE 45 (46)
T ss_pred CCCCCCc-C-CEEECCCCC---CCcCHHHHHCcCcCCCCCCCCEeE
Confidence 5788544 5 899999997 577999999998 676 777643
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=82.69 E-value=0.76 Score=39.06 Aligned_cols=20 Identities=30% Similarity=0.843 Sum_probs=18.4
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000151 1427 HLSSCGHAVHQGCLDRYVSS 1446 (2029)
Q Consensus 1427 h~ssCGH~MH~~C~~~Y~~S 1446 (2029)
.+..|||..+..|+.+|+++
T Consensus 13 ~~~~C~H~fC~~C~~~~~~~ 32 (41)
T PF00097_consen 13 ILLPCGHSFCRDCLRKWLEN 32 (41)
T ss_dssp EETTTSEEEEHHHHHHHHHH
T ss_pred EEecCCCcchHHHHHHHHHh
Confidence 37899999999999999887
No 19
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=80.82 E-value=1.3 Score=36.07 Aligned_cols=18 Identities=22% Similarity=0.892 Sum_probs=16.3
Q ss_pred ccccChHhhHHHHHHHHH
Q 000151 1428 LSSCGHAVHQGCLDRYVS 1445 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~~ 1445 (2029)
...|||..|..|+++|++
T Consensus 13 ~~~C~H~~c~~C~~~~~~ 30 (39)
T smart00184 13 VLPCGHTFCRSCIRKWLK 30 (39)
T ss_pred EecCCChHHHHHHHHHHH
Confidence 667999999999999977
No 20
>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=80.78 E-value=1.2 Score=39.83 Aligned_cols=38 Identities=26% Similarity=0.792 Sum_probs=29.0
Q ss_pred ccc-ccccCCceeEEeccCCCCCCccccccccCCC----CCC-CceeEE
Q 000151 117 VCG-AVWGNNDIAYRCRTCEHDPTCAICVPCFQNG----NHK-EHDYSI 159 (2029)
Q Consensus 117 ~Cg-~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~----~H~-~H~~~~ 159 (2029)
.|+ ..+. ..-|+|..|. ..-+|.+||..+ .|+ .|.+.+
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 21
>KOG2905 consensus Transcription initiation factor IIF, small subunit (RAP30) [Transcription]
Probab=80.12 E-value=1.1 Score=51.86 Aligned_cols=62 Identities=23% Similarity=0.212 Sum_probs=45.1
Q ss_pred HHHHHHHHHH--hcCCCChHHHHhhCCCCCCCcchHHHHHHHHccccCCCCCCcceEEeehhhcc
Q 000151 869 SLKRELVHRL--AIGDATHSQLVKSLPRDLSKFDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWK 931 (2029)
Q Consensus 869 ~lrrEIIh~L--c~~p~t~S~L~~~lpe~~~~~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~~ 931 (2029)
.=|+||+-.| ||.-..|=-|...+-..-+...-+.+||++||+|-+ .|..+|+|+|||||-+
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 3567777777 777766666655443333445568999999999975 3667899999999864
No 22
>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=79.98 E-value=1.4 Score=38.76 Aligned_cols=39 Identities=26% Similarity=0.695 Sum_probs=29.8
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC-CCceeEE
Q 000151 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYSI 159 (2029)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H-~~H~~~~ 159 (2029)
.|+..--.| .-|+|.+|. ..-+|..||....| .+|.|..
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 789999999 45699999999999 5898754
No 23
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=79.48 E-value=1.6 Score=38.01 Aligned_cols=31 Identities=35% Similarity=0.864 Sum_probs=24.9
Q ss_pred CccccccChHhhHHHHHHHHHHHHHhhhccccccCCcccCCCCcccccccccc
Q 000151 1425 GIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2029)
Q Consensus 1425 gvh~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCks 1477 (2029)
...+.+|||.+..+|.++-. .+...||+|++
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 24
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=78.36 E-value=1.5 Score=43.54 Aligned_cols=22 Identities=23% Similarity=0.650 Sum_probs=18.3
Q ss_pred CccccccChHhhHHHHHHHHHH
Q 000151 1425 GIHLSSCGHAVHQGCLDRYVSS 1446 (2029)
Q Consensus 1425 gvh~ssCGH~MH~~C~~~Y~~S 1446 (2029)
.+=...|||.-|..|..+.+++
T Consensus 46 plv~g~C~H~FH~hCI~kWl~~ 67 (85)
T PF12861_consen 46 PLVWGKCSHNFHMHCILKWLST 67 (85)
T ss_pred ceeeccCccHHHHHHHHHHHcc
Confidence 3337789999999999999875
No 25
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=75.53 E-value=3.1 Score=49.97 Aligned_cols=61 Identities=25% Similarity=0.638 Sum_probs=47.5
Q ss_pred cCCCcccccc--ccCCceeEEeccCCCCC-CccccccccCCCCCCCceeEEEe-cCCccccCCCcc
Q 000151 112 IGQRGVCGAV--WGNNDIAYRCRTCEHDP-TCAICVPCFQNGNHKEHDYSIIY-TGGGCCDCGDVT 173 (2029)
Q Consensus 112 ~~~~~~Cg~v--~~~ge~~y~C~~C~~d~-t~~lC~~CF~~~~H~~H~~~~~~-~~gG~CDCGd~~ 173 (2029)
...+..|++. .++-...|.|.||..+| ...+|.-|=.. -|.||.-..-. .+..-||||+.-
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 88899999765 69999987755 577889999853
No 26
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=75.29 E-value=0.83 Score=43.98 Aligned_cols=39 Identities=38% Similarity=0.710 Sum_probs=20.9
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhccccccCCcccCCCCcccccccccc
Q 000151 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCks 1477 (2029)
-..||+..|..|+.+||.+.... |. .+++-.|+ ||.|++
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 35899999999999999888642 11 13445566 999986
No 27
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=75.07 E-value=1.6 Score=37.42 Aligned_cols=28 Identities=29% Similarity=0.789 Sum_probs=25.1
Q ss_pred ceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000151 126 DIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2029)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 158 (2029)
...|.|.+|.. .+|.+|+..+ |++|++.
T Consensus 13 ~~~~~C~~C~~----~~C~~C~~~~-H~~H~~~ 40 (42)
T PF00643_consen 13 PLSLFCEDCNE----PLCSECTVSG-HKGHKIV 40 (42)
T ss_dssp BEEEEETTTTE----EEEHHHHHTS-TTTSEEE
T ss_pred ceEEEecCCCC----ccCccCCCCC-CCCCEEe
Confidence 48999999986 7999999998 9999975
No 28
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=72.52 E-value=1.7 Score=45.36 Aligned_cols=27 Identities=30% Similarity=0.790 Sum_probs=22.5
Q ss_pred hhcccCCCCCC----CCCceeeecccccccC
Q 000151 1901 IKQCCSDCKSV----LDEPALCLLCGRLCSP 1927 (2029)
Q Consensus 1901 ~~~~C~~c~~~----~~~paiCL~CG~~~~~ 1927 (2029)
.+|.||+||+. .++|++|-.||+..-.
T Consensus 8 tKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDPIVCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhccCCCCCccCCCCCCccCc
Confidence 46899999986 5799999999996443
No 29
>PHA02926 zinc finger-like protein; Provisional
Probab=72.32 E-value=2.8 Score=48.45 Aligned_cols=46 Identities=24% Similarity=0.532 Sum_probs=35.0
Q ss_pred CCCccccccChHhhHHHHHHHHHHHHHhhhccccccCCcccCCCCcccccccccccccceecC
Q 000151 1423 CDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPA 1485 (2029)
Q Consensus 1423 ~~gvh~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCksL~Ns~LPi 1485 (2029)
.+|+ ++.|||.-.+.|..+..++-+ + ..++-.||+||.-...|.|-
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 999999999999998765311 0 13566899999988877764
No 30
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=71.53 E-value=1.8 Score=52.58 Aligned_cols=16 Identities=38% Similarity=1.059 Sum_probs=14.7
Q ss_pred ccChHhhHHHHHHHHH
Q 000151 1430 SCGHAVHQGCLDRYVS 1445 (2029)
Q Consensus 1430 sCGH~MH~~C~~~Y~~ 1445 (2029)
.|||..|++|+++.++
T Consensus 317 pCGHilHl~CLknW~E 332 (491)
T COG5243 317 PCGHILHLHCLKNWLE 332 (491)
T ss_pred cccceeeHHHHHHHHH
Confidence 6999999999999875
No 31
>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=69.04 E-value=3.3 Score=36.56 Aligned_cols=30 Identities=27% Similarity=0.907 Sum_probs=24.8
Q ss_pred ceeEEeccCCCCCCccccccccCCCCC-CCceeE
Q 000151 126 DIAYRCRTCEHDPTCAICVPCFQNGNH-KEHDYS 158 (2029)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~~H-~~H~~~ 158 (2029)
..-|+|.+|. ..-||.+||..+.| .+|.|.
T Consensus 13 G~RykC~~C~---dyDLC~~C~~~~~H~~~H~f~ 43 (45)
T cd02339 13 GIRWKCAECP---NYDLCTTCYHGDKHDLEHRFY 43 (45)
T ss_pred cCeEECCCCC---CccchHHHhCCCCCCCCCCEE
Confidence 5679999996 36699999999998 588874
No 32
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=65.31 E-value=5 Score=45.93 Aligned_cols=53 Identities=21% Similarity=0.517 Sum_probs=35.2
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhccccccCCcccCCCCcccccccccccc--cceecCC
Q 000151 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLA--NSVLPAL 1486 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCksL~--Ns~LPil 1486 (2029)
++.|||.-...|..+|+.+-.. .++ +....+-.++...||+||+-- +.++|+.
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 4588887
No 33
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=63.82 E-value=3.5 Score=43.79 Aligned_cols=27 Identities=26% Similarity=0.431 Sum_probs=22.5
Q ss_pred hhcccCCCCCC----CCCceeeecccccccC
Q 000151 1901 IKQCCSDCKSV----LDEPALCLLCGRLCSP 1927 (2029)
Q Consensus 1901 ~~~~C~~c~~~----~~~paiCL~CG~~~~~ 1927 (2029)
.+|.||+||++ .++|++|-.||+..-.
T Consensus 8 tKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRPAVSPYTGEQFPP 38 (129)
T ss_pred ccccCCCcCccccccCCCCccCCCcCCccCc
Confidence 46889999986 5899999999997433
No 34
>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=60.51 E-value=5.8 Score=35.51 Aligned_cols=39 Identities=26% Similarity=0.699 Sum_probs=27.3
Q ss_pred cccc-cccCCceeEEeccCCCCCCccccccccCCC-CC-CCceeE
Q 000151 117 VCGA-VWGNNDIAYRCRTCEHDPTCAICVPCFQNG-NH-KEHDYS 158 (2029)
Q Consensus 117 ~Cg~-v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~-~H-~~H~~~ 158 (2029)
.|+. -+. .+-|+|.+|.- ...-+|.+||.++ .| .+|.+.
T Consensus 5 ~C~~~pI~--G~R~~C~~C~~-~d~DlC~~C~~~~~~H~~~H~~~ 46 (48)
T cd02341 5 SCGIEPIP--GTRYHCSECDD-GDFDLCQDCVVKGESHQEDHWLV 46 (48)
T ss_pred CCCCCccc--cceEECCCCCC-CCCccCHHHHhCcCCCCCCCcee
Confidence 4555 232 56799999973 3466999999999 67 367654
No 35
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=58.97 E-value=2.3 Score=41.28 Aligned_cols=17 Identities=29% Similarity=0.935 Sum_probs=15.1
Q ss_pred ccccChHhhHHHHHHHH
Q 000151 1428 LSSCGHAVHQGCLDRYV 1444 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~ 1444 (2029)
...|||+-|..|..+.+
T Consensus 47 ~~~C~H~FH~~Ci~~Wl 63 (73)
T PF12678_consen 47 WGPCGHIFHFHCISQWL 63 (73)
T ss_dssp EETTSEEEEHHHHHHHH
T ss_pred ecccCCCEEHHHHHHHH
Confidence 67799999999998776
No 36
>KOG1940 consensus Zn-finger protein [General function prediction only]
Probab=58.94 E-value=5.3 Score=48.20 Aligned_cols=35 Identities=26% Similarity=0.866 Sum_probs=27.2
Q ss_pred ccccccChHhhHHHHHHHHHHHHHhhhccccccCCcccCCCCcccccccccccccce
Q 000151 1426 IHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSV 1482 (2029)
Q Consensus 1426 vh~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCksL~Ns~ 1482 (2029)
++.-.|||.||+.||+.|.. .+ |-||+|..++|+.
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 34678999999999998721 25 8999999866554
No 37
>cd02343 ZZ_EF Zinc finger, ZZ type. Zinc finger present in proteins with an EF_hand motif. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=58.87 E-value=5.4 Score=35.66 Aligned_cols=35 Identities=29% Similarity=0.691 Sum_probs=27.0
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCCC-Cce
Q 000151 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK-EHD 156 (2029)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~-~H~ 156 (2029)
.|++... ..-|+|..|. ..-+|.+||..+.+. +|+
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 4777643 4799999997 477999999998874 454
No 38
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=55.37 E-value=4.1 Score=35.93 Aligned_cols=31 Identities=23% Similarity=0.650 Sum_probs=21.7
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC
Q 000151 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 152 (2029)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H 152 (2029)
.||.-.. .+-|+|..+. ...||.+||..|.-
T Consensus 5 ~Cg~D~t--~vryh~~~~~---~~dLC~~CF~~G~f 35 (45)
T cd02336 5 TCGNDCT--RVRYHNLKAK---KYDLCPSCYQEGRF 35 (45)
T ss_pred CCCCccC--ceEEEecCCC---ccccChHHHhCcCC
Confidence 4666665 4777777654 46799999988753
No 39
>cd02337 ZZ_CBP Zinc finger, ZZ type. Zinc finger present in CBP/p300 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. CREB-binding protein (CBP) is a large multidomain protein that provides binding sites for transcriptional coactivators, the role of the ZZ domain in CBP/p300 is unclear.
Probab=54.82 E-value=6.8 Score=33.92 Aligned_cols=32 Identities=25% Similarity=0.824 Sum_probs=25.0
Q ss_pred ccccccccCCceeEEeccCCCCCCccccccccCCCCCC
Q 000151 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (2029)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~ 153 (2029)
..|+++ +++-|+|..|. -.-+|..||....|.
T Consensus 4 ~~C~~~---~~~r~~C~~C~---dfDLC~~C~~~~~H~ 35 (41)
T cd02337 4 NECKHH---VETRWHCTVCE---DYDLCITCYNTKNHP 35 (41)
T ss_pred CCCCCc---CCCceECCCCc---chhhHHHHhCCCCCC
Confidence 357664 24999999997 366999999998883
No 40
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=53.92 E-value=9.7 Score=31.77 Aligned_cols=28 Identities=25% Similarity=0.451 Sum_probs=23.2
Q ss_pred ceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000151 126 DIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2029)
Q Consensus 126 e~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 158 (2029)
...|-|.+|+. .+|..|-..+ |++|.+.
T Consensus 10 ~~~~fC~~~~~----~iC~~C~~~~-H~~H~~~ 37 (39)
T cd00021 10 PLSLFCETDRA----LLCVDCDLSV-HSGHRRV 37 (39)
T ss_pred ceEEEeCccCh----hhhhhcChhh-cCCCCEe
Confidence 45788988874 7999999888 9999975
No 41
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=53.22 E-value=6 Score=33.45 Aligned_cols=20 Identities=25% Similarity=0.933 Sum_probs=17.8
Q ss_pred cccccChHhhHHHHHHHHHH
Q 000151 1427 HLSSCGHAVHQGCLDRYVSS 1446 (2029)
Q Consensus 1427 h~ssCGH~MH~~C~~~Y~~S 1446 (2029)
.+..|||....+|+++|++.
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 42
>KOG0828 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.19 E-value=9.6 Score=48.28 Aligned_cols=29 Identities=41% Similarity=1.065 Sum_probs=25.2
Q ss_pred ccccChHhhHHHHHHHHHHHHHhhhccccccCCcccCCCCcccccccccc
Q 000151 1428 LSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCks 1477 (2029)
++-|-|++|-.|+++.|+.-+ ..||+||+
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 678999999999999998654 46999997
No 43
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=49.57 E-value=11 Score=46.60 Aligned_cols=30 Identities=30% Similarity=0.601 Sum_probs=22.3
Q ss_pred CCCCCCcCCCccccccChHhhHHHHHHHHHH
Q 000151 1416 DGFGPIDCDGIHLSSCGHAVHQGCLDRYVSS 1446 (2029)
Q Consensus 1416 ~gF~~~~~~gvh~ssCGH~MH~~C~~~Y~~S 1446 (2029)
++|+.+...|. +++|||+.|..|+...|+-
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 8999999999999988753
No 44
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=49.50 E-value=8.4 Score=29.19 Aligned_cols=20 Identities=30% Similarity=0.896 Sum_probs=17.6
Q ss_pred ccCCCCCC-CCCceeeecccc
Q 000151 1904 CCSDCKSV-LDEPALCLLCGR 1923 (2029)
Q Consensus 1904 ~C~~c~~~-~~~paiCL~CG~ 1923 (2029)
.||+||.. +.+...|-.||+
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGT 21 (23)
T ss_pred CCcccCCCCCCcCcchhhhCC
Confidence 59999988 788889999997
No 45
>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=48.45 E-value=12 Score=32.85 Aligned_cols=33 Identities=27% Similarity=0.801 Sum_probs=25.2
Q ss_pred ccccccccCCceeEEeccCCCCCCccccccccCCCCCC
Q 000151 116 GVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHK 153 (2029)
Q Consensus 116 ~~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H~ 153 (2029)
..|++.+. ..-|+|..|. ..-||.+||..+.|.
T Consensus 8 ~~C~~~i~--g~ry~C~~C~---d~dlC~~Cf~~~~~~ 40 (44)
T smart00291 8 DTCGKPIV--GVRYHCLVCP---DYDLCQSCFAKGSAG 40 (44)
T ss_pred CCCCCCCc--CCEEECCCCC---CccchHHHHhCcCcC
Confidence 46888554 4578999994 577999999988664
No 46
>smart00336 BBOX B-Box-type zinc finger.
Probab=48.22 E-value=14 Score=31.23 Aligned_cols=29 Identities=21% Similarity=0.636 Sum_probs=23.6
Q ss_pred CceeEEeccCCCCCCccccccccCCCCCCCceeE
Q 000151 125 NDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYS 158 (2029)
Q Consensus 125 ge~~y~C~~C~~d~t~~lC~~CF~~~~H~~H~~~ 158 (2029)
....|-|.+|+. ++|..|... .|++|.+.
T Consensus 12 ~~~~~~C~~c~~----~iC~~C~~~-~H~~H~~~ 40 (42)
T smart00336 12 EPAEFFCEECGA----LLCRTCDEA-EHRGHTVV 40 (42)
T ss_pred CceEEECCCCCc----ccccccChh-hcCCCcee
Confidence 445777988874 789999988 99999875
No 47
>PF02270 TFIIF_beta: Transcription initiation factor IIF, beta subunit; InterPro: IPR003196 Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter. ; GO: 0005524 ATP binding, 0006367 transcription initiation from RNA polymerase II promoter, 0005674 transcription factor TFIIF complex; PDB: 1F3U_C 2BBY_A 1BBY_A.
Probab=48.20 E-value=6.7 Score=47.83 Aligned_cols=31 Identities=29% Similarity=0.463 Sum_probs=16.1
Q ss_pred cchHHHHHHHHccccCCCCCCcceEEeehhhc
Q 000151 899 FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYW 930 (2029)
Q Consensus 899 ~~~fe~iL~eVA~f~~P~g~~~G~Y~LK~e~~ 930 (2029)
+.-+-+||++||+|.+ +|...|+|+|||||-
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 48
>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=47.45 E-value=8.9 Score=29.98 Aligned_cols=22 Identities=23% Similarity=0.717 Sum_probs=19.0
Q ss_pred cccCCCCCC-CCCceeeeccccc
Q 000151 1903 QCCSDCKSV-LDEPALCLLCGRL 1924 (2029)
Q Consensus 1903 ~~C~~c~~~-~~~paiCL~CG~~ 1924 (2029)
++||.|++. |..-..|-.||..
T Consensus 1 K~CP~C~~~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHCGYD 23 (26)
T ss_pred CcCCCCcCCchhhcCcCCCCCCC
Confidence 479999987 8899999999964
No 49
>PLN00209 ribosomal protein S27; Provisional
Probab=46.72 E-value=7.1 Score=38.81 Aligned_cols=37 Identities=16% Similarity=0.520 Sum_probs=30.8
Q ss_pred cccCCchhHHHHHHHHhhcccCCCCCC------CCCceeeecccccccC
Q 000151 1885 KLMCLPHLYQDLLQRYIKQCCSDCKSV------LDEPALCLLCGRLCSP 1927 (2029)
Q Consensus 1885 ~Li~LP~~~~~l~~~~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1927 (2029)
+||+=|+.| +.+.+||.|+.. ...++.|..||++++.
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 588888765 567899999975 5789999999998877
No 50
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=45.84 E-value=9.6 Score=29.63 Aligned_cols=22 Identities=23% Similarity=0.708 Sum_probs=19.1
Q ss_pred hcccCCCCCC-CCCceeeecccc
Q 000151 1902 KQCCSDCKSV-LDEPALCLLCGR 1923 (2029)
Q Consensus 1902 ~~~C~~c~~~-~~~paiCL~CG~ 1923 (2029)
.+.||+||.. +.+-..|-.||+
T Consensus 2 ~~~Cp~Cg~~~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAEIDPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCcCCcccccChhhCC
Confidence 4679999998 788899999997
No 51
>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=45.11 E-value=14 Score=33.29 Aligned_cols=32 Identities=28% Similarity=0.742 Sum_probs=23.9
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCCC
Q 000151 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNH 152 (2029)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~H 152 (2029)
.|++.=-.| .-|+|..|. ..-||.+||..+.|
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 566542234 789999997 46799999988865
No 52
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=45.06 E-value=7.4 Score=38.59 Aligned_cols=37 Identities=22% Similarity=0.539 Sum_probs=30.8
Q ss_pred cccCCchhHHHHHHHHhhcccCCCCCC------CCCceeeecccccccC
Q 000151 1885 KLMCLPHLYQDLLQRYIKQCCSDCKSV------LDEPALCLLCGRLCSP 1927 (2029)
Q Consensus 1885 ~Li~LP~~~~~l~~~~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1927 (2029)
+||+-|+.| +...+||.|+.. ...++.|..||+++|+
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 588888765 567899999975 4789999999998887
No 53
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=45.06 E-value=8.5 Score=36.45 Aligned_cols=28 Identities=25% Similarity=0.743 Sum_probs=23.1
Q ss_pred HhhcccCCCCC------CCCCceeeecccccccC
Q 000151 1900 YIKQCCSDCKS------VLDEPALCLLCGRLCSP 1927 (2029)
Q Consensus 1900 ~~~~~C~~c~~------~~~~paiCL~CG~~~~~ 1927 (2029)
+.+.+||.|+. .++..+-|+.||+.++.
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 45789999985 37889999999997665
No 54
>PHA02929 N1R/p28-like protein; Provisional
Probab=44.37 E-value=14 Score=43.89 Aligned_cols=37 Identities=41% Similarity=0.800 Sum_probs=27.1
Q ss_pred CccccccChHhhHHHHHHHHHHHHHhhhccccccCCcccCCCCcccccccccccccceec
Q 000151 1425 GIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLP 1484 (2029)
Q Consensus 1425 gvh~ssCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCksL~Ns~LP 1484 (2029)
|+ +..|||..|..|....++. + . .||+||.---.|+|
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 7799999999999986521 1 0 49999986555554
No 55
>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=41.39 E-value=16 Score=32.56 Aligned_cols=18 Identities=33% Similarity=0.824 Sum_probs=16.6
Q ss_pred ccccChH-hhHHHHHHHHH
Q 000151 1428 LSSCGHA-VHQGCLDRYVS 1445 (2029)
Q Consensus 1428 ~ssCGH~-MH~~C~~~Y~~ 1445 (2029)
+.-|||. +-..|+.++++
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 56
>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=39.07 E-value=21 Score=32.17 Aligned_cols=31 Identities=23% Similarity=0.842 Sum_probs=24.3
Q ss_pred ccccc-cccCCceeEEeccCCCCCCccccccccCCCC
Q 000151 116 GVCGA-VWGNNDIAYRCRTCEHDPTCAICVPCFQNGN 151 (2029)
Q Consensus 116 ~~Cg~-v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~ 151 (2029)
..|.+ -+. ++-|+|..|. .--+|.+||..+.
T Consensus 4 ~~C~~~~i~--g~R~~C~~C~---dydLC~~Cf~~~~ 35 (49)
T cd02345 4 SACRKQDIS--GIRFPCQVCR---DYSLCLGCYTKGR 35 (49)
T ss_pred CCCCCCCce--EeeEECCCCC---CcCchHHHHhCCC
Confidence 35777 566 4889999994 5779999999774
No 57
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=39.00 E-value=12 Score=34.36 Aligned_cols=46 Identities=26% Similarity=0.655 Sum_probs=35.0
Q ss_pred HhhcccCCCCCCC---CCceeeecccccccCCCCccc-CCCcchHhhhhcCCCee
Q 000151 1900 YIKQCCSDCKSVL---DEPALCLLCGRLCSPSWKPCC-RESSCQSHAVACGAGTG 1950 (2029)
Q Consensus 1900 ~~~~~C~~c~~~~---~~paiCL~CG~~~~~~~~~cc-~~g~c~~H~~~Cg~g~G 1950 (2029)
+...+|+-|++.. .|.++|--||+.-.- .|. ..|+|..+. ||++..
T Consensus 3 ~~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR---~C~~~~g~C~~~~--c~~~~~ 52 (54)
T PF14446_consen 3 YEGCKCPVCGKKFKDGDDIVVCPECGAPYHR---DCWEKAGGCINYS--CGTGFE 52 (54)
T ss_pred ccCccChhhCCcccCCCCEEECCCCCCcccH---HHHhhCCceEecc--CCCCcc
Confidence 3457899999874 688999999997654 466 469998877 887653
No 58
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=37.24 E-value=19 Score=32.84 Aligned_cols=15 Identities=40% Similarity=0.753 Sum_probs=10.8
Q ss_pred ccccChH-hhHHHHHH
Q 000151 1428 LSSCGHA-VHQGCLDR 1442 (2029)
Q Consensus 1428 ~ssCGH~-MH~~C~~~ 1442 (2029)
+-+|||+ |-+.|-.+
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=36.48 E-value=17 Score=49.32 Aligned_cols=23 Identities=48% Similarity=1.025 Sum_probs=20.7
Q ss_pred ccChHhhHHHHHHHHHHHHHhhhccccccCCcccCCCCcccccccccc
Q 000151 1430 SCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQ 1477 (2029)
Q Consensus 1430 sCGH~MH~~C~~~Y~~Sl~~r~~~r~~~er~h~~d~e~gEFLCPLCks 1477 (2029)
.|||.-|+.|++ .+|+-||-|+.
T Consensus 858 ~CgHsyHqhC~e-------------------------~~~~~CP~C~~ 880 (933)
T KOG2114|consen 858 LCGHSYHQHCLE-------------------------DKEDKCPKCLP 880 (933)
T ss_pred ecccHHHHHhhc-------------------------cCcccCCccch
Confidence 599999999998 38899999986
No 60
>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=36.18 E-value=13 Score=34.37 Aligned_cols=28 Identities=18% Similarity=0.705 Sum_probs=19.1
Q ss_pred HhhcccCCCCCC------CCCceeeecccccccC
Q 000151 1900 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1927 (2029)
Q Consensus 1900 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1927 (2029)
+...+||.|+.. ...++.|..||+++|.
T Consensus 5 Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 5 FMDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EEEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred EEEEECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 456799999874 5889999999998776
No 61
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=35.55 E-value=9.4 Score=33.77 Aligned_cols=36 Identities=28% Similarity=0.709 Sum_probs=22.4
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCC-CCCce
Q 000151 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN-HKEHD 156 (2029)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~-H~~H~ 156 (2029)
.|+..--. ..-|+|..|. ..-||.+||..+. +.+|+
T Consensus 9 ~C~~~~i~-g~Ry~C~~C~---d~dLC~~C~~~g~~~~~H~ 45 (46)
T PF00569_consen 9 GCGTDPII-GVRYHCLVCP---DYDLCEDCFSKGRHSHNHK 45 (46)
T ss_dssp SS-SSSEE-SSEEEESSSS---S-EEEHHHHHH--H-SSSS
T ss_pred CCCCCcCc-CCeEECCCCC---CCchhhHHHhCcCCCCCcC
Confidence 46663222 3679999995 5779999999864 45664
No 62
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=35.06 E-value=16 Score=34.12 Aligned_cols=28 Identities=29% Similarity=0.762 Sum_probs=23.6
Q ss_pred HhhcccCCCCCC------CCCceeeecccccccC
Q 000151 1900 YIKQCCSDCKSV------LDEPALCLLCGRLCSP 1927 (2029)
Q Consensus 1900 ~~~~~C~~c~~~------~~~paiCL~CG~~~~~ 1927 (2029)
+.+.+||.|+.. +..++.|..||+.++.
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 457899999875 5889999999998766
No 63
>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=32.67 E-value=31 Score=38.34 Aligned_cols=43 Identities=23% Similarity=0.512 Sum_probs=26.7
Q ss_pred hhHHHHHHHHHHHHHhhhcccc------cc---CCcccCCCCcccccccccc
Q 000151 1435 VHQGCLDRYVSSLKERYNRRII------FE---GGHIVDPDQGEFLCPVCRQ 1477 (2029)
Q Consensus 1435 MH~~C~~~Y~~Sl~~r~~~r~~------~e---r~h~~d~e~gEFLCPLCks 1477 (2029)
-|-+|+++|-++-......... .+ ..+....+..+..|||||.
T Consensus 37 rhSNCLdqfkka~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~CPLCRG 88 (162)
T PF07800_consen 37 RHSNCLDQFKKAYGKSSSSSSQSSSSAPSDSSSSESSESQEQPELACPLCRG 88 (162)
T ss_pred chhHHHHHHHHHhcCCCCccccccccCcCCCcccccccccccccccCccccC
Confidence 4899999997766543321100 00 0123556678999999997
No 64
>COG5194 APC11 Component of SCF ubiquitin ligase and anaphase-promoting complex [Posttranslational modification, protein turnover, chaperones / Cell division and chromosome partitioning]
Probab=32.66 E-value=43 Score=32.99 Aligned_cols=25 Identities=28% Similarity=0.623 Sum_probs=20.5
Q ss_pred cCCCccccccChHhhHHHHHHHHHH
Q 000151 1422 DCDGIHLSSCGHAVHQGCLDRYVSS 1446 (2029)
Q Consensus 1422 ~~~gvh~ssCGH~MH~~C~~~Y~~S 1446 (2029)
+.+.+--+.|-|+-|..|-.+.+++
T Consensus 45 ~eC~v~wG~CnHaFH~HCI~rWL~T 69 (88)
T COG5194 45 DECPVVWGVCNHAFHDHCIYRWLDT 69 (88)
T ss_pred CcceEEEEecchHHHHHHHHHHHhh
Confidence 3344447889999999999999987
No 65
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=32.30 E-value=33 Score=43.52 Aligned_cols=43 Identities=33% Similarity=0.791 Sum_probs=30.5
Q ss_pred cccccccCCceeEEeccCCCCCCccccccccCCCC----C-CCceeEEEecC
Q 000151 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGN----H-KEHDYSIIYTG 163 (2029)
Q Consensus 117 ~Cg~v~~~ge~~y~C~~C~~d~t~~lC~~CF~~~~----H-~~H~~~~~~~~ 163 (2029)
.|..-.. |-+-.+|-.| |..-||..||..|. | .+|.|.++.++
T Consensus 19 ~C~~dit-~~i~ikCaeC---p~fdLCl~CFs~GaE~~~H~~~H~Yrim~~~ 66 (438)
T KOG0457|consen 19 YCSLDIT-GLIRIKCAEC---PDFDLCLQCFSVGAETGKHQNDHPYRIMDTN 66 (438)
T ss_pred cHhHHhc-cceEEEeecC---CCcchhHHHHhcccccCCCCCCCCceeecCC
Confidence 3444444 4555889999 55569999997764 6 48999998764
No 66
>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=27.93 E-value=36 Score=29.64 Aligned_cols=25 Identities=24% Similarity=0.527 Sum_probs=17.7
Q ss_pred cccCCCCCCC------CCceeeecccccccC
Q 000151 1903 QCCSDCKSVL------DEPALCLLCGRLCSP 1927 (2029)
Q Consensus 1903 ~~C~~c~~~~------~~paiCL~CG~~~~~ 1927 (2029)
++||.|+... +.-.+|-.||.++..
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 4799999853 455699999998754
No 67
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=26.43 E-value=30 Score=39.01 Aligned_cols=20 Identities=50% Similarity=1.157 Sum_probs=17.8
Q ss_pred ccCCCCCCCCCceeeeccccc
Q 000151 1904 CCSDCKSVLDEPALCLLCGRL 1924 (2029)
Q Consensus 1904 ~C~~c~~~~~~paiCL~CG~~ 1924 (2029)
.| +||..-..|+.||.||+-
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 999999999999999984
No 68
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=24.77 E-value=39 Score=42.01 Aligned_cols=17 Identities=29% Similarity=0.698 Sum_probs=15.6
Q ss_pred ccccChHhhHHHHHHHH
Q 000151 1428 LSSCGHAVHQGCLDRYV 1444 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~ 1444 (2029)
+--|.|+.|..|.+.|+
T Consensus 384 ALpCsHIfH~rCl~e~L 400 (518)
T KOG1941|consen 384 ALPCSHIFHLRCLQEIL 400 (518)
T ss_pred ccchhHHHHHHHHHHHH
Confidence 55799999999999998
No 69
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=24.32 E-value=51 Score=39.90 Aligned_cols=33 Identities=45% Similarity=0.944 Sum_probs=23.6
Q ss_pred ceeEEeccC-CCCCCccccccccCCCC----C-CCceeEEEec
Q 000151 126 DIAYRCRTC-EHDPTCAICVPCFQNGN----H-KEHDYSIIYT 162 (2029)
Q Consensus 126 e~~y~C~~C-~~d~t~~lC~~CF~~~~----H-~~H~~~~~~~ 162 (2029)
-+..+|-.| .+| +|..||-++. | .-|.|+++.+
T Consensus 18 ~~~i~C~eC~~~D----LC~pCF~~g~~tg~H~pyH~YRiiet 56 (432)
T COG5114 18 LTFIKCNECPAVD----LCLPCFVNGIETGVHSPYHGYRIIET 56 (432)
T ss_pred ceeeeeecccccc----eehhhhhccccccccCCCCCeeEeec
Confidence 455667777 444 8999998765 3 4699999864
No 70
>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=21.84 E-value=74 Score=29.99 Aligned_cols=50 Identities=24% Similarity=0.435 Sum_probs=31.4
Q ss_pred cCCCCCCCCCceeeecccccccCCCCcccCCCcchHhhhhcCCCeeEEEEecccEE
Q 000151 1905 CSDCKSVLDEPALCLLCGRLCSPSWKPCCRESSCQSHAVACGAGTGVFLLIRRTTI 1960 (2029)
Q Consensus 1905 C~~c~~~~~~paiCL~CG~~~~~~~~~cc~~g~c~~H~~~Cg~g~GiFl~v~~~~i 1960 (2029)
|..|+....+.-+||.||.+.|.... .|--..|+.+=| =-+++.++...|
T Consensus 1 C~~C~~~~~~lw~CL~Cg~~~C~~~~----~~Ha~~H~~~~~--H~l~v~~~~~~i 50 (63)
T PF02148_consen 1 CSVCGSTNSNLWLCLTCGYVGCGRYS----NGHALKHYKETG--HPLAVSLSTGSI 50 (63)
T ss_dssp -SSSHTCSSSEEEETTTS-EEETTTS----TSHHHHHHHHHT----EEEETTTTCE
T ss_pred CCCCCCcCCceEEeCCCCcccccCCc----CcHHHHhhcccC--CeEEEECCCCeE
Confidence 66777557899999999998555211 355677887655 445666666654
No 71
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=21.73 E-value=44 Score=44.67 Aligned_cols=18 Identities=28% Similarity=0.803 Sum_probs=15.6
Q ss_pred ccccChHhhHHHHHHHHH
Q 000151 1428 LSSCGHAVHQGCLDRYVS 1445 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~~ 1445 (2029)
-.+|||+||.+|....++
T Consensus 1045 Cg~C~Hv~H~sc~~eWf~ 1062 (1081)
T KOG0309|consen 1045 CGTCGHVGHTSCMMEWFR 1062 (1081)
T ss_pred hccccccccHHHHHHHHh
Confidence 567999999999998874
No 72
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.37 E-value=56 Score=43.86 Aligned_cols=19 Identities=32% Similarity=0.807 Sum_probs=16.3
Q ss_pred ccccChHhhHHHHHHHHHH
Q 000151 1428 LSSCGHAVHQGCLDRYVSS 1446 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~~S 1446 (2029)
.-.|||+-|..|+.+.++-
T Consensus 311 rL~C~Hifh~~CL~~W~er 329 (543)
T KOG0802|consen 311 RLPCGHIFHDSCLRSWFER 329 (543)
T ss_pred eeecccchHHHHHHHHHHH
Confidence 4469999999999999865
No 73
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.11 E-value=48 Score=34.41 Aligned_cols=24 Identities=13% Similarity=0.171 Sum_probs=20.7
Q ss_pred hhcccCCCCCC----CCCceeeeccccc
Q 000151 1901 IKQCCSDCKSV----LDEPALCLLCGRL 1924 (2029)
Q Consensus 1901 ~~~~C~~c~~~----~~~paiCL~CG~~ 1924 (2029)
.++.||.|+++ .++|++|-.||+-
T Consensus 8 tKridPetg~KFYDLNrdPiVsPytG~s 35 (129)
T COG4530 8 TKRIDPETGKKFYDLNRDPIVSPYTGKS 35 (129)
T ss_pred ccccCccccchhhccCCCccccCccccc
Confidence 36789999986 6899999999984
No 74
>KOG2930 consensus SCF ubiquitin ligase, Rbx1 component [Posttranslational modification, protein turnover, chaperones]
Probab=20.05 E-value=68 Score=33.13 Aligned_cols=18 Identities=33% Similarity=0.863 Sum_probs=15.5
Q ss_pred ccccChHhhHHHHHHHHH
Q 000151 1428 LSSCGHAVHQGCLDRYVS 1445 (2029)
Q Consensus 1428 ~ssCGH~MH~~C~~~Y~~ 1445 (2029)
=+.|-|+-|+.|..+.++
T Consensus 78 WG~CNHaFH~hCisrWlk 95 (114)
T KOG2930|consen 78 WGVCNHAFHFHCISRWLK 95 (114)
T ss_pred eeecchHHHHHHHHHHHh
Confidence 456999999999999875
No 75
>PRK02935 hypothetical protein; Provisional
Probab=20.01 E-value=46 Score=34.51 Aligned_cols=28 Identities=14% Similarity=0.481 Sum_probs=21.2
Q ss_pred HhhcccCCCCCCC---CCceeeecccccccC
Q 000151 1900 YIKQCCSDCKSVL---DEPALCLLCGRLCSP 1927 (2029)
Q Consensus 1900 ~~~~~C~~c~~~~---~~paiCL~CG~~~~~ 1927 (2029)
+.+..||+|++.. ...-.|.+||+.+-.
T Consensus 68 avqV~CP~C~K~TKmLGrvD~CM~C~~PLTL 98 (110)
T PRK02935 68 AVQVICPSCEKPTKMLGRVDACMHCNQPLTL 98 (110)
T ss_pred ceeeECCCCCchhhhccceeecCcCCCcCCc
Confidence 3455899999874 456699999996555
Done!