Query 028204
Match_columns 212
No_of_seqs 193 out of 608
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 07:53:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028204.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028204hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4018 Uncharacterized conser 100.0 1.9E-36 4.2E-41 257.0 10.2 147 10-159 45-194 (215)
2 smart00591 RWD domain in RING 99.6 1.4E-14 2.9E-19 109.0 8.7 68 11-78 39-106 (107)
3 PF05773 RWD: RWD domain; Int 99.5 2.3E-13 5E-18 102.9 7.5 70 7-76 43-113 (113)
4 KOG4445 Uncharacterized conser 99.2 2.5E-11 5.5E-16 108.6 7.8 69 11-79 43-111 (368)
5 KOG1763 Uncharacterized conser 98.6 1.8E-08 4E-13 90.1 3.7 64 102-167 224-287 (343)
6 KOG1035 eIF-2alpha kinase GCN2 97.7 9E-06 1.9E-10 84.1 1.0 72 12-83 49-120 (1351)
7 COG5252 Uncharacterized conser 96.2 0.0024 5.2E-08 56.3 1.7 61 102-164 209-270 (299)
8 KOG0309 Conserved WD40 repeat- 93.8 0.28 6.2E-06 49.7 8.4 55 6-60 459-514 (1081)
9 KOG1814 Predicted E3 ubiquitin 89.9 0.63 1.4E-05 44.1 5.4 66 7-79 68-134 (445)
10 KOG0419 Ubiquitin-protein liga 88.5 1.1 2.3E-05 36.6 5.1 25 13-37 51-75 (152)
11 PF00179 UQ_con: Ubiquitin-con 87.2 0.69 1.5E-05 36.5 3.4 25 13-37 45-69 (140)
12 cd00195 UBCc Ubiquitin-conjuga 85.4 0.91 2E-05 35.9 3.2 24 13-36 46-69 (141)
13 smart00212 UBCc Ubiquitin-conj 84.9 1.1 2.3E-05 35.7 3.4 25 13-37 46-70 (145)
14 PTZ00390 ubiquitin-conjugating 84.6 1.1 2.3E-05 36.7 3.3 24 13-36 49-72 (152)
15 PF08694 UFC1: Ubiquitin-fold 84.5 0.86 1.9E-05 37.5 2.6 27 13-39 75-101 (161)
16 PLN00172 ubiquitin conjugating 83.9 1.2 2.7E-05 36.0 3.4 24 13-36 48-71 (147)
17 COG5078 Ubiquitin-protein liga 83.3 1.3 2.8E-05 36.6 3.3 25 13-37 53-77 (153)
18 PRK02220 4-oxalocrotonate taut 78.1 4.7 0.0001 27.0 4.2 36 29-64 1-36 (61)
19 PRK02289 4-oxalocrotonate taut 76.6 5.3 0.00011 27.2 4.1 35 29-63 1-35 (60)
20 PRK00745 4-oxalocrotonate taut 74.2 7.1 0.00015 26.2 4.3 36 29-64 1-36 (62)
21 PF09026 CENP-B_dimeris: Centr 73.8 1 2.3E-05 34.6 0.0 6 192-197 55-60 (101)
22 PF12253 CAF1A: Chromatin asse 73.5 3 6.5E-05 30.7 2.3 37 141-177 23-60 (77)
23 KOG0425 Ubiquitin-protein liga 72.1 4.3 9.3E-05 34.0 3.2 25 13-37 53-77 (171)
24 KOG0418 Ubiquitin-protein liga 71.9 6.2 0.00013 33.9 4.2 44 13-56 53-99 (200)
25 TIGR00013 taut 4-oxalocrotonat 71.8 8.4 0.00018 25.9 4.2 35 30-64 1-36 (63)
26 KOG0421 Ubiquitin-protein liga 71.7 14 0.0003 30.6 6.0 25 13-37 76-100 (175)
27 PF05743 UEV: UEV domain; Int 71.6 7.5 0.00016 30.6 4.4 26 13-38 48-73 (121)
28 KOG0417 Ubiquitin-protein liga 70.4 5.1 0.00011 33.0 3.3 25 13-37 48-72 (148)
29 KOG0896 Ubiquitin-conjugating 70.1 3.9 8.5E-05 33.2 2.5 24 14-37 57-80 (138)
30 KOG0416 Ubiquitin-protein liga 69.7 13 0.00027 31.6 5.5 64 14-83 48-114 (189)
31 cd00491 4Oxalocrotonate_Tautom 69.5 11 0.00023 24.8 4.2 35 30-64 1-35 (58)
32 PF01361 Tautomerase: Tautomer 68.6 8 0.00017 25.9 3.5 35 30-64 1-35 (60)
33 PF14461 Prok-E2_B: Prokaryoti 68.3 8.3 0.00018 30.5 4.0 28 11-38 34-61 (133)
34 KOG0422 Ubiquitin-protein liga 65.3 7.3 0.00016 32.0 3.1 24 13-36 49-72 (153)
35 PRK01964 4-oxalocrotonate taut 64.3 14 0.0003 25.2 4.0 36 29-64 1-36 (64)
36 KOG3299 Uncharacterized conser 64.3 6.1 0.00013 34.2 2.7 58 24-83 2-59 (206)
37 PF14812 PBP1_TM: Transmembran 64.0 2.2 4.9E-05 31.7 0.0 14 176-189 35-48 (81)
38 KOG0420 Ubiquitin-protein liga 60.7 9.7 0.00021 32.3 3.2 23 14-36 77-99 (184)
39 PF05764 YL1: YL1 nuclear prot 57.0 8.6 0.00019 33.7 2.4 30 156-185 34-65 (240)
40 KOG1832 HIV-1 Vpr-binding prot 56.2 7.4 0.00016 40.8 2.1 21 147-167 1392-1412(1516)
41 KOG0427 Ubiquitin conjugating 55.3 16 0.00035 29.8 3.5 25 13-37 61-85 (161)
42 PF10446 DUF2457: Protein of u 52.8 6 0.00013 38.0 0.8 14 102-115 21-34 (458)
43 KOG3357 Uncharacterized conser 51.0 11 0.00024 30.7 2.0 27 13-39 78-104 (167)
44 PRK01271 4-oxalocrotonate taut 50.9 31 0.00067 25.1 4.1 35 29-63 1-36 (76)
45 KOG0894 Ubiquitin-protein liga 50.5 15 0.00032 32.3 2.8 22 18-39 57-78 (244)
46 KOG1832 HIV-1 Vpr-binding prot 50.3 7.7 0.00017 40.7 1.1 22 166-187 1406-1427(1516)
47 PF09606 Med15: ARC105 or Med1 40.8 9.1 0.0002 39.4 0.0 58 16-76 717-774 (799)
48 KOG0426 Ubiquitin-protein liga 40.7 22 0.00048 29.1 2.2 22 15-36 54-75 (165)
49 KOG0895 Ubiquitin-conjugating 39.8 27 0.00059 37.0 3.2 24 13-36 898-921 (1101)
50 KOG0428 Non-canonical ubiquiti 39.2 28 0.00061 31.3 2.8 21 18-38 62-82 (314)
51 PF04871 Uso1_p115_C: Uso1 / p 38.9 16 0.00036 29.3 1.2 10 162-171 111-120 (136)
52 KOG0424 Ubiquitin-protein liga 36.4 29 0.00064 28.7 2.3 24 14-37 57-80 (158)
53 PF14462 Prok-E2_E: Prokaryoti 36.1 32 0.0007 27.4 2.5 21 13-33 42-62 (122)
54 KOG0943 Predicted ubiquitin-pr 35.2 20 0.00044 39.1 1.4 20 146-165 1704-1723(3015)
55 PF05764 YL1: YL1 nuclear prot 34.5 24 0.00051 30.9 1.6 8 169-176 57-64 (240)
56 PF06524 NOA36: NOA36 protein; 31.5 32 0.0007 31.2 2.0 17 60-76 91-107 (314)
57 PF04889 Cwf_Cwc_15: Cwf15/Cwc 29.0 43 0.00093 29.6 2.3 14 183-196 142-155 (244)
58 COG1942 Uncharacterized protei 29.0 1.1E+02 0.0025 21.7 4.1 35 29-63 1-36 (69)
59 KOG3403 Translation initiation 27.3 37 0.0008 27.5 1.4 14 174-187 126-139 (145)
60 PF04931 DNA_pol_phi: DNA poly 24.9 39 0.00086 34.4 1.5 20 60-79 471-490 (784)
61 PRK04217 hypothetical protein; 24.6 3.2E+02 0.007 21.2 6.3 58 25-82 28-92 (110)
62 KOG2023 Nuclear transport rece 24.3 34 0.00073 35.0 0.8 35 23-57 124-161 (885)
63 PTZ00397 macrophage migration 22.8 1.2E+02 0.0025 23.0 3.5 34 30-63 2-35 (116)
64 KOG2662 Magnesium transporters 22.3 54 0.0012 31.3 1.7 16 185-200 246-261 (414)
65 KOG0898 40S ribosomal protein 21.9 61 0.0013 26.6 1.7 21 190-210 116-148 (152)
66 PF06524 NOA36: NOA36 protein; 20.6 60 0.0013 29.5 1.6 6 104-109 218-223 (314)
67 PF04281 Tom22: Mitochondrial 20.3 96 0.0021 25.2 2.6 24 177-200 38-61 (137)
68 PF11705 RNA_pol_3_Rpc31: DNA- 20.3 35 0.00076 29.5 0.1 13 115-127 116-128 (233)
69 KOG0897 Predicted ubiquitin-co 20.2 1E+02 0.0022 24.6 2.6 24 14-37 12-35 (122)
70 PF11705 RNA_pol_3_Rpc31: DNA- 20.1 59 0.0013 28.1 1.4 9 20-28 31-39 (233)
No 1
>KOG4018 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=100.00 E-value=1.9e-36 Score=257.04 Aligned_cols=147 Identities=43% Similarity=0.593 Sum_probs=129.1
Q ss_pred CCce-EEEEEEEeCCCCCCCCCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhhccccc--
Q 028204 10 LFAV-ELALIFSHTEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSERYSQDAGI-- 86 (212)
Q Consensus 10 ~~p~-~l~L~f~~p~~YP~e~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~MIFtLve~lqE~L~e~~~~~~~~-- 86 (212)
+.|. ++.|.|++|++||+++|+|.+..+.|+.+..+..|+..|+.+|++||||+|||+||+++|+||++++++....
T Consensus 45 d~~~~~~~l~~s~tEnYPDe~Pli~~~~~~~~~~~~i~~i~~~l~~~aeenLGmaMiftLvss~ke~l~e~~~q~~~~e~ 124 (215)
T KOG4018|consen 45 DEPKGSFILVFSLTENYPDEAPLIEAFENENLEDAEIEGILEKLQQEAEENLGMAMIFTLVSSAKEELNEIVEQQKAAEQ 124 (215)
T ss_pred CCccccEEEEEEccCCCCCCCcceeccccccccHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555 8999999999999999999999999999999999999999999999999999999999999999999987665
Q ss_pred CCccchhhhhhcccCCCCCcccHHHHHHHHHHHHHHHHHHHHhcCccccccCCCCCCcchhHHhhcCcccccc
Q 028204 87 DNTGEEELEKDEVIVPHGEPVTVETFLAWRERFEAELALERAKLMPESALTAPKEKKLTGRQWFESGRATAVS 159 (212)
Q Consensus 87 ~e~~~~e~e~ee~~~~~GTpVT~EsF~~Wk~kf~~E~~~~k~k~~~e~~~~~~~~~kLTGRqlFe~~~~l~~~ 159 (212)
.+.+.++++++++++|||||||+++|.+||.+|+++++..+++.++. .+...+++||||+|++|+.+..+
T Consensus 125 ~e~~~~~~ee~e~~kfhgt~VT~esfl~Wk~~fe~el~~~~~k~~~~---~~~~~~k~tgRQ~f~~d~~~~~~ 194 (215)
T KOG4018|consen 125 REQEAREAEEEERKKFHGTPVTLESFLEWKLKFEEELLQIKAKVKKR---LQALAKKLTGRQLFETDHKGDRS 194 (215)
T ss_pred HHHHHHHHHHHhhccccCCceehhhhHHHHHhhhhhhhhhhhhhhhH---HHHHhhhHHHHHHHHhcccCChh
Confidence 22346677778899999999999999999999999996666665432 45667899999999999998544
No 2
>smart00591 RWD domain in RING finger and WD repeat containing proteins and DEXDc-like helicases subfamily related to the UBCc domain.
Probab=99.56 E-value=1.4e-14 Score=109.02 Aligned_cols=68 Identities=41% Similarity=0.589 Sum_probs=64.4
Q ss_pred CceEEEEEEEeCCCCCCCCCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHH
Q 028204 11 FAVELALIFSHTEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSE 78 (212)
Q Consensus 11 ~p~~l~L~f~~p~~YP~e~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~MIFtLve~lqE~L~e 78 (212)
..+++.|+|.+|++||..+|.|.+.+..+|+...+..|.+.|...+++++|++|||++++++|+||.+
T Consensus 39 ~~~~~~l~~~~p~~YP~~~P~i~~~~~~~l~~~~~~~l~~~l~~~~~e~~g~~~if~~v~~~~e~l~~ 106 (107)
T smart00591 39 QYVSLTLQVKLPENYPDEAPPISLLNSEGLSDEQLAELLKKLEEIAEENLGEVMIFELVEKLQEFLSE 106 (107)
T ss_pred cceEEEEEEECCCCCCCCCCCeEEECCCCCCHHHHHHHHHHHHHHHHHhCCCEEhhHHHHHHHHHHhc
Confidence 45679999999999999999999998889999999999999999999999999999999999999975
No 3
>PF05773 RWD: RWD domain; InterPro: IPR006575 The RWD eukaryotic domain is found in RING finger (IPR001841 from INTERPRO) and WD repeat (IPR001680 from INTERPRO) containing proteins and DEXDc-like helicase (IPR001410 from INTERPRO) subfamily related to the ubiquitin-conjugating enzymes domain (IPR000608 from INTERPRO). ; GO: 0005515 protein binding; PDB: 2EBM_A 2EBK_A 2DAX_A 2DAW_A 2DAY_A 2DMF_A 1UKX_A 2YZ0_A.
Probab=99.45 E-value=2.3e-13 Score=102.90 Aligned_cols=70 Identities=26% Similarity=0.413 Sum_probs=60.5
Q ss_pred cccCCceEEEEEEEeCCCCCCCCCceEEecCCCCCHHhHHHHHHHHHHHHHHhc-CChHHHHHHHHHHHHH
Q 028204 7 LKLLFAVELALIFSHTEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENL-GMAMIYTLVTSAKEWL 76 (212)
Q Consensus 7 ~~~~~p~~l~L~f~~p~~YP~e~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenl-Gm~MIFtLve~lqE~L 76 (212)
......+.+.|+|++|++||..+|.|.|....++....+..|.+.|...++++. |++|||+|++|+|++|
T Consensus 43 ~~~~~~~~~~l~~~~p~~YP~~~P~i~l~~~~~~~~~~~~~l~~~l~~~~~~~~~G~~~i~~ii~~~qe~~ 113 (113)
T PF05773_consen 43 FESSSFPSVTLHFTLPPGYPESPPKISLESPKNSRNEQIEKLNKELEQIAEENRQGEPCIFQIIEWLQENL 113 (113)
T ss_dssp CTTTTSEEEEEEEEE-SSTTSS--EEEEEEESSSHCHHHHHHHHHHHHHHHHSTTTS-CHHHHHHHHHHHH
T ss_pred cccccceeEEEEEeCCCcCCCcCCEEEEEcCCCCCHHHHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhhC
Confidence 345667899999999999999999999998887777899999999999999999 9999999999999986
No 4
>KOG4445 consensus Uncharacterized conserved protein, contains RWD domain [Function unknown]
Probab=99.22 E-value=2.5e-11 Score=108.59 Aligned_cols=69 Identities=25% Similarity=0.494 Sum_probs=66.4
Q ss_pred CceEEEEEEEeCCCCCCCCCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHH
Q 028204 11 FAVELALIFSHTEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSER 79 (212)
Q Consensus 11 ~p~~l~L~f~~p~~YP~e~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~MIFtLve~lqE~L~e~ 79 (212)
..++|+|.++.|+.||.+.|.|+|.+++||.+..+..|+..+++.+++|+||||||.|++.++|+|.+.
T Consensus 43 qyvcvtl~m~vs~gYP~esPtvtl~nPRGl~d~~~~~i~~~~~~iikq~~g~pii~~lie~~~e~LT~n 111 (368)
T KOG4445|consen 43 QYVCVTLEMTVSEGYPAESPTVTLSNPRGLGDPEFREIQRQIQEIIKQNSGMPIICQLIEHCSEFLTEN 111 (368)
T ss_pred eeEEEEEEEecCCCCCCcCCceEecCCCCCCcHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHcccC
Confidence 348999999999999999999999999999999999999999999999999999999999999999876
No 5
>KOG1763 consensus Uncharacterized conserved protein, contains CCCH-type Zn-finger [General function prediction only]
Probab=98.65 E-value=1.8e-08 Score=90.09 Aligned_cols=64 Identities=28% Similarity=0.328 Sum_probs=46.2
Q ss_pred CCCCcccHHHHHHHHHHHHHHHHHHHHhcCccccccCCCCCCcchhHHhhcCcccccccCCCcccc
Q 028204 102 PHGEPVTVETFLAWRERFEAELALERAKLMPESALTAPKEKKLTGRQWFESGRATAVSQKGAVTVN 167 (212)
Q Consensus 102 ~~GTpVT~EsF~~Wk~kf~~E~~~~k~k~~~e~~~~~~~~~kLTGRqlFe~~~~l~~~~~~~~~~~ 167 (212)
++-||||.++|.+|+.+..+|.....++.... ++..++.. ||||+||++++.||.++++.+..-
T Consensus 224 ~nlT~~T~e~F~~WKk~k~~er~~k~~~~~~~-~k~~gk~~-~sGRElF~~~~dl~~dd~~e~~d~ 287 (343)
T KOG1763|consen 224 PNLTPLTEETFKAWKKRKIRERKEKLAAEKAE-RKKVGKSN-MSGRELFESNADLVNDDDEEAGDL 287 (343)
T ss_pred CCCccccHHHHHHHHHhhHHHHHHHHHHHHHH-hhhhccCC-CchHHHHhhchhhccCchhhccch
Confidence 46899999999999999877776654443322 12223333 999999999999999885554433
No 6
>KOG1035 consensus eIF-2alpha kinase GCN2 [Translation, ribosomal structure and biogenesis]
Probab=97.74 E-value=9e-06 Score=84.13 Aligned_cols=72 Identities=24% Similarity=0.379 Sum_probs=67.3
Q ss_pred ceEEEEEEEeCCCCCCCCCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhhcc
Q 028204 12 AVELALIFSHTEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSERYSQD 83 (212)
Q Consensus 12 p~~l~L~f~~p~~YP~e~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~MIFtLve~lqE~L~e~~~~~ 83 (212)
.+++.|+|++++.||...|.+.+...+|+.+.++..|...|...++...|+.|||.|...+|++|.+....+
T Consensus 49 ~~~~~lh~~~~~~yp~~kp~i~lk~~~~~~d~~i~~L~~~l~~~~~~~~G~~~i~eLa~~vqefl~~~~~~~ 120 (1351)
T KOG1035|consen 49 KLSGRLHVKCKRKYPYSKPEIKLKDHQGVSDEDIELLSNELTALAKTLRGEVMIAELASIVQEFLKDHQDRP 120 (1351)
T ss_pred HHhhHhhhhhccccCCCCccccccccccchHHHHHHHHHHHHHhhccccccEEeeeHhhhhHHHHhccCCCC
Confidence 457889999999999999999999999999999999999999999999999999999999999998876544
No 7
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=96.18 E-value=0.0024 Score=56.30 Aligned_cols=61 Identities=21% Similarity=0.242 Sum_probs=37.5
Q ss_pred CCCCcccHHHHHHHHHHHHHHHHHHHHhcCccccccCCCCCCcchh-HHhhcCcccccccCCCc
Q 028204 102 PHGEPVTVETFLAWRERFEAELALERAKLMPESALTAPKEKKLTGR-QWFESGRATAVSQKGAV 164 (212)
Q Consensus 102 ~~GTpVT~EsF~~Wk~kf~~E~~~~k~k~~~e~~~~~~~~~kLTGR-qlFe~~~~l~~~~~~~~ 164 (212)
+.-||||.++|..|+.-.+-.+..++.+ ..+.++..+...+||+ ++||.+..+|-++-++.
T Consensus 209 ~~LTP~TeenFk~Wkd~~~~r~lkq~ee--~~s~Rk~~gr~~~~k~~e~FEt~~d~~~ddv~~g 270 (299)
T COG5252 209 EKLTPLTEENFKEWKDGRRLRILKQKEE--KESARKVKGRATGTKGVELFETRRDLFKDDVEAG 270 (299)
T ss_pred CcCCcccHHHHHHhccchHHHHHHHHHH--HHhcccchhhhhhccchhhhhccccccccccccc
Confidence 3679999999999996544332222111 1122222333456666 99999999988774443
No 8
>KOG0309 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=93.81 E-value=0.28 Score=49.68 Aligned_cols=55 Identities=15% Similarity=0.175 Sum_probs=49.5
Q ss_pred ccccCCceEEEEEEEeCCCCCCCC-CceEEecCCCCCHHhHHHHHHHHHHHHHHhc
Q 028204 6 WLKLLFAVELALIFSHTEKYPDEP-PLLNVKSLRGIQAGDLKILKEKLEQEASENL 60 (212)
Q Consensus 6 ~~~~~~p~~l~L~f~~p~~YP~e~-P~i~i~~~~gL~~~~l~~L~~~L~~~aeenl 60 (212)
|++.+..+.+.++|.+|..||..+ |.+.+....+|.......|.+.|...+...+
T Consensus 459 ~~~~d~y~flrm~V~FP~nYPn~a~P~Fq~e~~s~~t~~~~~~~l~~L~~i~~q~v 514 (1081)
T KOG0309|consen 459 NHRVDDYIFLRMLVKFPANYPNNAAPSFQFENPSTITSTMKAKLLKILKDIALQKV 514 (1081)
T ss_pred CCccccceeEEEEEeccccCCCCCCCceEEecCccccHHHHHHHHHHHHHHHHHHh
Confidence 778888899999999999999975 9999999999999999999999988887665
No 9
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=89.89 E-value=0.63 Score=44.12 Aligned_cols=66 Identities=23% Similarity=0.220 Sum_probs=49.9
Q ss_pred cccCCceEEEEEEEeCCCCCCC-CCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHH
Q 028204 7 LKLLFAVELALIFSHTEKYPDE-PPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSER 79 (212)
Q Consensus 7 ~~~~~p~~l~L~f~~p~~YP~e-~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~MIFtLve~lqE~L~e~ 79 (212)
++++.-.-+.|.|-+|+.||.. ||.+.|.+ .+++..++..|... +..|....|.+.+++++--..+
T Consensus 68 ~~~~~lPpivlkf~LP~~YPs~spP~f~l~s-~Wmn~~q~~~lc~~------el~~i~~~~q~m~~l~~~~~s~ 134 (445)
T KOG1814|consen 68 LPLDHLPPIVLKFHLPNDYPSVSPPKFELKS-YWMNPDQKSALCSK------ELRLIEELNQMMDFLKESTISI 134 (445)
T ss_pred cccccCCCeeeeeecCCccccCCCCceeeeh-cccCHHHhhhccch------hhccceeHHHHHHHHHHHHHHH
Confidence 4445545689999999999985 68888875 78888887777665 6678888888888888744333
No 10
>KOG0419 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=88.51 E-value=1.1 Score=36.58 Aligned_cols=25 Identities=32% Similarity=0.591 Sum_probs=21.5
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
..+.|.+.+|++||+.||.+.+.+.
T Consensus 51 gtFkLtl~FteeYpnkPP~VrFvs~ 75 (152)
T KOG0419|consen 51 GTFKLTLEFTEEYPNKPPTVRFVSK 75 (152)
T ss_pred ceEEEEEEcccccCCCCCeeEeeee
Confidence 4677888889999999999998864
No 11
>PF00179 UQ_con: Ubiquitin-conjugating enzyme; InterPro: IPR000608 The post-translational attachment of ubiquitin (IPR000626 from INTERPRO) to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [, , ]. Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade []. The E1 enzyme mediates an ATP-dependent transfer of a thioester-linked ubiquitin molecule to a cysteine residue on the E2 enzyme. The E2 enzyme (6.3.2.19 from EC) then either transfers the ubiquitin moiety directly to a substrate, or to an E3 ligase, which can also ubiquitinylate a substrate. There are several different E2 enzymes (over 30 in humans), which are broadly grouped into four classes, all of which have a core catalytic domain (containing the active site cysteine), and some of which have short N- and C-terminal amino acid extensions: class I enzymes consist of just the catalytic core domain (UBC), class II possess a UBC and a C-terminal extension, class III possess a UBC and an N-terminal extension, and class IV possess a UBC and both N- and C-terminal extensions. These extensions appear to be important for some subfamily function, including E2 localisation and protein-protein interactions []. In addition, there are proteins with an E2-like fold that are devoid of catalytic activity, but which appear to assist in poly-ubiquitin chain formation.; GO: 0016881 acid-amino acid ligase activity; PDB: 2AAK_A 3SY2_C 1FBV_C 3SQV_C 1C4Z_D 1JAT_B 2GMI_B 2H2Y_D 2R0J_A 3E95_B ....
Probab=87.20 E-value=0.69 Score=36.51 Aligned_cols=25 Identities=20% Similarity=0.293 Sum_probs=20.1
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
..+.+.|.+|++||..||.+.+...
T Consensus 45 g~f~~~i~~p~~YP~~pP~v~f~t~ 69 (140)
T PF00179_consen 45 GIFKFRISFPPDYPFSPPKVRFLTP 69 (140)
T ss_dssp SEEEEEEEETTTTTTS--EEEESSS
T ss_pred ccccccccccccccccccccccccc
Confidence 3688999999999999999999863
No 12
>cd00195 UBCc Ubiquitin-conjugating enzyme E2, catalytic (UBCc) domain. This is part of the ubiquitin-mediated protein degradation pathway in which a thiol-ester linkage forms between a conserved cysteine and the C-terminus of ubiquitin and complexes with ubiquitin protein ligase enzymes, E3. This pathway regulates many fundamental cellular processes. There are also other E2s which form thiol-ester linkages without the use of E3s as well as several UBC homologs (TSG101, Mms2, Croc-1 and similar proteins) which lack the active site cysteine essential for ubiquitination and appear to function in DNA repair pathways which were omitted from the scope of this CD.
Probab=85.41 E-value=0.91 Score=35.93 Aligned_cols=24 Identities=25% Similarity=0.394 Sum_probs=21.2
Q ss_pred eEEEEEEEeCCCCCCCCCceEEec
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKS 36 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~ 36 (212)
..+.+.|.+|++||.++|.+.+..
T Consensus 46 ~~~~~~~~~p~~yP~~pP~v~f~~ 69 (141)
T cd00195 46 GIFKLDIEFPEDYPFKPPKVRFVT 69 (141)
T ss_pred CEEEEEEECCCccCCCCCeEEEeC
Confidence 368889999999999999999964
No 13
>smart00212 UBCc Ubiquitin-conjugating enzyme E2, catalytic domain homologues. Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. This pathway functions in regulating many fundamental processes required for cell viability.TSG101 is one of several UBC homologues that lacks this active site cysteine.
Probab=84.90 E-value=1.1 Score=35.72 Aligned_cols=25 Identities=20% Similarity=0.340 Sum_probs=22.0
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
..+.++|.+|++||..+|.+.+...
T Consensus 46 ~~f~~~l~~p~~yP~~pP~v~f~~~ 70 (145)
T smart00212 46 GIFKLTIEFPPDYPFKPPKVKFITK 70 (145)
T ss_pred cEEEEEEECCcccCCCCCEEEEeCC
Confidence 4688899999999999999998764
No 14
>PTZ00390 ubiquitin-conjugating enzyme; Provisional
Probab=84.65 E-value=1.1 Score=36.66 Aligned_cols=24 Identities=29% Similarity=0.391 Sum_probs=21.4
Q ss_pred eEEEEEEEeCCCCCCCCCceEEec
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKS 36 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~ 36 (212)
..+.|.|.+|++||..||.+.+..
T Consensus 49 g~f~~~i~~p~~YP~~pP~v~F~t 72 (152)
T PTZ00390 49 GYYKLELFLPEQYPMEPPKVRFLT 72 (152)
T ss_pred cEEEEEEECccccCCCCCEEEEec
Confidence 468889999999999999999875
No 15
>PF08694 UFC1: Ubiquitin-fold modifier-conjugating enzyme 1; InterPro: IPR014806 Ubiquitin-like (UBL) post-translational modifiers are covalently linked to most, if not all, target protein(s) through an enzymatic cascade analogous to ubiquitylation, consisting of E1 (activating), E2 (conjugating), and E3 (ligating) enzymes. Ubiquitin-fold modifier 1 (Ufm1) a ubiquitin-like protein is activated by a novel E1-like enzyme, Uba5, by forming a high-energy thioester bond. Activated Ufm1 is then transferred to its cognate E2-like enzyme, Ufc1, in a similar thioester linkage. This family represents the E2-like enzyme [].; PDB: 2Z6P_A 2K07_A 2Z6O_A 3EVX_D 3KPA_A.
Probab=84.48 E-value=0.86 Score=37.53 Aligned_cols=27 Identities=30% Similarity=0.540 Sum_probs=16.9
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecCCC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSLRG 39 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~~g 39 (212)
..+.|.|..|.+||.++|.|.|-...|
T Consensus 75 YEF~~eFdIP~tYP~t~pEi~lPeLdG 101 (161)
T PF08694_consen 75 YEFDLEFDIPVTYPTTAPEIALPELDG 101 (161)
T ss_dssp EEEEEEEE--TTTTTS----B-GGGTT
T ss_pred EEEeeecCCCccCCCCCcceeccccCC
Confidence 478899999999999999999977655
No 16
>PLN00172 ubiquitin conjugating enzyme; Provisional
Probab=83.92 E-value=1.2 Score=36.02 Aligned_cols=24 Identities=21% Similarity=0.348 Sum_probs=21.4
Q ss_pred eEEEEEEEeCCCCCCCCCceEEec
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKS 36 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~ 36 (212)
..+.+.|.+|++||..||.+.+..
T Consensus 48 g~f~~~i~fp~~YP~~pP~v~f~t 71 (147)
T PLN00172 48 GVFFLSILFPPDYPFKPPKVQFTT 71 (147)
T ss_pred CEEEEEEECCcccCCCCCEEEEec
Confidence 368899999999999999999875
No 17
>COG5078 Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=83.33 E-value=1.3 Score=36.64 Aligned_cols=25 Identities=24% Similarity=0.430 Sum_probs=22.3
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
..+.|++.+|++||..||.|.+.+.
T Consensus 53 g~f~~~l~fP~~YP~~PPkv~F~t~ 77 (153)
T COG5078 53 GIFKLTLEFPEDYPFKPPKVRFTTK 77 (153)
T ss_pred CEEEEEEECCCCCCCCCCeeeeccC
Confidence 4688899999999999999998865
No 18
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=78.11 E-value=4.7 Score=27.05 Aligned_cols=36 Identities=25% Similarity=0.402 Sum_probs=32.4
Q ss_pred CCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChH
Q 028204 29 PPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAM 64 (212)
Q Consensus 29 ~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~M 64 (212)
.|.|.|...+|.+..++..|.+.|.....+.+|.|.
T Consensus 1 MP~i~i~~~~Grs~eqk~~l~~~it~~l~~~~~~p~ 36 (61)
T PRK02220 1 MPYVHIKLIEGRTEEQLKALVKDVTAAVSKNTGAPA 36 (61)
T ss_pred CCEEEEEEcCCCCHHHHHHHHHHHHHHHHHHhCcCh
Confidence 388999888899999999999999999999999873
No 19
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=76.64 E-value=5.3 Score=27.17 Aligned_cols=35 Identities=11% Similarity=0.186 Sum_probs=32.0
Q ss_pred CCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCCh
Q 028204 29 PPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMA 63 (212)
Q Consensus 29 ~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~ 63 (212)
.|.+.|.-.+|.+.+++..|.+.|.+.+.+.+|.|
T Consensus 1 MP~i~i~~~~Grs~EqK~~L~~~it~a~~~~~~~p 35 (60)
T PRK02289 1 MPFVRIDLFEGRSQEQKNALAREVTEVVSRIAKAP 35 (60)
T ss_pred CCEEEEEECCCCCHHHHHHHHHHHHHHHHHHhCcC
Confidence 38899998899999999999999999999999987
No 20
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=74.20 E-value=7.1 Score=26.22 Aligned_cols=36 Identities=19% Similarity=0.328 Sum_probs=32.4
Q ss_pred CCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChH
Q 028204 29 PPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAM 64 (212)
Q Consensus 29 ~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~M 64 (212)
.|.|.|....|.+.+++..|.+.|.....+.+|.|.
T Consensus 1 MP~i~I~~~~grs~eqk~~l~~~it~~l~~~~~~p~ 36 (62)
T PRK00745 1 MPTFHIELFEGRTVEQKRKLVEEITRVTVETLGCPP 36 (62)
T ss_pred CCEEEEEEcCCCCHHHHHHHHHHHHHHHHHHcCCCh
Confidence 388999988898999999999999999999999884
No 21
>PF09026 CENP-B_dimeris: Centromere protein B dimerisation domain; InterPro: IPR015115 Centromere protein B (CENP-B) interacts with centromeric heterochromatin in chromosomes and binds to a specific subset of alphoid satellite DNA, called the CENP-B box. CENP-B may organise arrays of centromere satellite DNA into a higher order structure, which then directs centromere formation and kinetochore assembly in mammalian chromosomes. The CENP-B dimerisation domain is composed of two alpha-helices, which are folded into an antiparallel configuration. Dimerisation of CENP-B is mediated by this domain, in which monomers dimerise to form a symmetrical, antiparallel, four-helix bundle structure with a large hydrophobic patch in which 23 residues of one monomer form van der Waals contacts with the other monomer. This CENP-B dimer configuration may be suitable for capturing two distant CENP-B boxes during centromeric heterochromatin formation []. ; GO: 0003677 DNA binding, 0003682 chromatin binding, 0006355 regulation of transcription, DNA-dependent, 0000775 chromosome, centromeric region, 0005634 nucleus; PDB: 1UFI_A.
Probab=73.85 E-value=1 Score=34.61 Aligned_cols=6 Identities=50% Similarity=1.093 Sum_probs=2.5
Q ss_pred HHHHHH
Q 028204 192 MLEHYL 197 (212)
Q Consensus 192 ~~~~~~ 197 (212)
|..+||
T Consensus 55 ~v~rYl 60 (101)
T PF09026_consen 55 MVKRYL 60 (101)
T ss_dssp HHHHHH
T ss_pred hHhhhh
Confidence 334444
No 22
>PF12253 CAF1A: Chromatin assembly factor 1 subunit A; InterPro: IPR022043 The CAF-1 or chromatin assembly factor-1 consists of three subunits, and this is the first, or A []. The A domain is uniquely required for the progression of S phase in mouse cells [], independent of its ability to promote histone deposition [] but dependent on its ability to interact with HP1 - heterochromatin protein 1-rich heterochromatin domains next to centromeres that are crucial for chromosome segregation during mitosis. This HP1-CAF-1 interaction module functions as a built-in replication control for heterochromatin, which, like a control barrier, has an impact on S-phase progression in addition to DNA-based checkpoints [].
Probab=73.48 E-value=3 Score=30.69 Aligned_cols=37 Identities=19% Similarity=0.134 Sum_probs=25.5
Q ss_pred CCCcchhHHhhcC-cccccccCCCcccccCCCCccCCC
Q 028204 141 EKKLTGRQWFESG-RATAVSQKGAVTVNEVSDDEDDED 177 (212)
Q Consensus 141 ~~kLTGRqlFe~~-~~l~~~~~~~~~~~~e~~~~~~~d 177 (212)
...++||.-|-++ +.+.-+-+....+.++..+++.++
T Consensus 23 s~~v~~r~P~~~d~~~lDYdyDSd~EWeE~e~GEdl~~ 60 (77)
T PF12253_consen 23 SKIVTPRNPFAKDLPNLDYDYDSDDEWEEEEEGEDLDS 60 (77)
T ss_pred ccccccCCcccccccccceecCCccccccCCCCccccc
Confidence 4678999999998 777666666677755555555443
No 23
>KOG0425 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.10 E-value=4.3 Score=33.95 Aligned_cols=25 Identities=20% Similarity=0.308 Sum_probs=21.4
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
-.+.-+.++|.+||..||.+.+.+.
T Consensus 53 G~FkA~m~FP~dYP~sPP~~rF~s~ 77 (171)
T KOG0425|consen 53 GFFKAHMKFPQDYPLSPPTFRFTSK 77 (171)
T ss_pred ceeEEEEeCcccCCCCCCceeeehh
Confidence 4577788999999999999998863
No 24
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.88 E-value=6.2 Score=33.87 Aligned_cols=44 Identities=18% Similarity=0.221 Sum_probs=32.1
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecC---CCCCHHhHHHHHHHHHHHH
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSL---RGIQAGDLKILKEKLEQEA 56 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~---~gL~~~~l~~L~~~L~~~a 56 (212)
-.+.|.++.|.+||-.||.+.+... +|++......-...|+.+-
T Consensus 53 G~FeldI~iPe~YPF~pPkv~F~TkIwHPnVSs~tGaICLDilkd~W 99 (200)
T KOG0418|consen 53 GVFELDIKIPENYPFKPPKVKFITKIWHPNVSSQTGAICLDILKDQW 99 (200)
T ss_pred ceEEEEEecCCCCCCCCCceeeeeeeecCCCCcccccchhhhhhccc
Confidence 3688999999999999999987653 5676665555555555543
No 25
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=71.80 E-value=8.4 Score=25.88 Aligned_cols=35 Identities=26% Similarity=0.441 Sum_probs=31.0
Q ss_pred CceEEecC-CCCCHHhHHHHHHHHHHHHHHhcCChH
Q 028204 30 PLLNVKSL-RGIQAGDLKILKEKLEQEASENLGMAM 64 (212)
Q Consensus 30 P~i~i~~~-~gL~~~~l~~L~~~L~~~aeenlGm~M 64 (212)
|.+.|.-. +|.+..++..|.+.|.+...+.+|.|.
T Consensus 1 P~i~i~i~~~grt~eqK~~l~~~it~~l~~~lg~~~ 36 (63)
T TIGR00013 1 PFVNIYILKEGRTDEQKRQLIEGVTEAMAETLGANL 36 (63)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHHHHHHhCCCc
Confidence 77888877 788999999999999999999999884
No 26
>KOG0421 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=71.74 E-value=14 Score=30.61 Aligned_cols=25 Identities=24% Similarity=0.510 Sum_probs=20.9
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
....|...+|.+||-.||.|.+..+
T Consensus 76 l~yklSl~Fp~~YPy~pP~vkFltp 100 (175)
T KOG0421|consen 76 LKYKLSLSFPNNYPYKPPTVKFLTP 100 (175)
T ss_pred cEEEEEEecCCCCCCCCCeeEeecc
Confidence 4566777889999999999998865
No 27
>PF05743 UEV: UEV domain; InterPro: IPR008883 The N-terminal ubiquitin E2 variant (UEV) domain is ~145 amino acid residues in length and shows significant sequence similarity to E2 ubiquitin ligases but is unable to catalyze ubiquitin transfer as it lacks the active site cysteine that forms the transient thioester bond with the C terminus of ubiquitin (Ub). Nevertheless, at least some UEVs have retained the ability to bind Ub, and appear to act either as cofactors in ubiquitylation reactions, or as ubiquitin sensors. UEV domains also frequently contain other protein recognition motifs, and may generally serve to couple protein and Ub binding functions to facilitate the formation of multiprotein complexes [, , , ]. The UEV domain consists of a twisted four-stranded antiparallel beta-sheet having a meander topology, with four alpha-helices packed against one face of the sheet. The UEV fold is generally similar to canonical E2 ligases in the hydrophobic core and 'active site' regions, but differs significantly at both its N- and C-termini [, ]. The UEV domain is found in the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other Homo sapiens malignancies. However, the involvement of this gene in neoplastic transformation and tumourigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but this gene is not a tumour suppressor for sporadic forms of breast cancer [].; GO: 0006464 protein modification process, 0015031 protein transport; PDB: 3R3Q_A 3R42_A 1UZX_A 3OBX_A 3OBS_A 3P9H_A 2F0R_A 3P9G_A 3OBQ_A 3OBU_A ....
Probab=71.65 E-value=7.5 Score=30.56 Aligned_cols=26 Identities=23% Similarity=0.519 Sum_probs=20.7
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecCC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSLR 38 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~~ 38 (212)
..+-+.+.+|.+||..+|.+.+....
T Consensus 48 y~iPi~Iwlp~~yP~~pP~v~v~pt~ 73 (121)
T PF05743_consen 48 YNIPICIWLPENYPYSPPIVYVRPTP 73 (121)
T ss_dssp EEEEEEEEE-TTTTTSSSEEEE-GCC
T ss_pred cceeEEEEEcccCCCCCCEEEEeCCC
Confidence 46788999999999999999998543
No 28
>KOG0417 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=70.40 E-value=5.1 Score=33.03 Aligned_cols=25 Identities=24% Similarity=0.340 Sum_probs=22.0
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
-.+.|.|.+|+.||-.||.|.+...
T Consensus 48 G~F~l~I~~p~~YP~~PPkV~F~Tk 72 (148)
T KOG0417|consen 48 GVFFLEIHFPEDYPFKPPKVRFLTK 72 (148)
T ss_pred CEEEEEEECCCCCCCCCCceEeecc
Confidence 3688999999999999999998864
No 29
>KOG0896 consensus Ubiquitin-conjugating enzyme E2 [Posttranslational modification, protein turnover, chaperones]
Probab=70.07 E-value=3.9 Score=33.24 Aligned_cols=24 Identities=25% Similarity=0.438 Sum_probs=20.2
Q ss_pred EEEEEEEeCCCCCCCCCceEEecC
Q 028204 14 ELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 14 ~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
.-.|+|.+-++||+.||.+.+...
T Consensus 57 iysLKI~Cgp~YPe~PP~vrf~tk 80 (138)
T KOG0896|consen 57 IYSLKIECGPKYPELPPTVRFGTK 80 (138)
T ss_pred eeeEEEecCCCCCCCCceeEEEEE
Confidence 457889999999999999996653
No 30
>KOG0416 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.69 E-value=13 Score=31.63 Aligned_cols=64 Identities=14% Similarity=0.211 Sum_probs=44.9
Q ss_pred EEEEEEEeCCCCCCCCCceEEecC---CCCCHHhHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhhcc
Q 028204 14 ELALIFSHTEKYPDEPPLLNVKSL---RGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSERYSQD 83 (212)
Q Consensus 14 ~l~L~f~~p~~YP~e~P~i~i~~~---~gL~~~~l~~L~~~L~~~aeenlGm~MIFtLve~lqE~L~e~~~~~ 83 (212)
.-+++|.+|..||-..|.|-+... +|+...--.--...|++.. .-+|.|+.-..-+|.+.+--+
T Consensus 48 vWkv~V~lPd~YP~KSPSIGFvnKIfHPNIDe~SGsVCLDViNQtW------Sp~yDL~NIfetfLPQLL~YP 114 (189)
T KOG0416|consen 48 VWKVRVELPDNYPFKSPSIGFVNKIFHPNIDEASGSVCLDVINQTW------SPLYDLVNIFETFLPQLLRYP 114 (189)
T ss_pred eEEEEEECCCCCCCCCCcccceeeccCCCchhccCccHHHHHhhhh------hHHHHHHHHHHHHhHHHhcCC
Confidence 457889999999999999987653 3443333333344455543 457999999999999887544
No 31
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=69.45 E-value=11 Score=24.81 Aligned_cols=35 Identities=26% Similarity=0.387 Sum_probs=30.7
Q ss_pred CceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChH
Q 028204 30 PLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAM 64 (212)
Q Consensus 30 P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~M 64 (212)
|.+.|.-.+|.+.+++..|.+.|.+.+.+.+|.|.
T Consensus 1 P~i~i~~~~grt~eqk~~l~~~i~~~l~~~~g~~~ 35 (58)
T cd00491 1 PFVQIYILEGRTDEQKRELIERVTEAVSEILGAPE 35 (58)
T ss_pred CEEEEEEcCCCCHHHHHHHHHHHHHHHHHHhCcCc
Confidence 78888877888889999999999999999998873
No 32
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=68.59 E-value=8 Score=25.90 Aligned_cols=35 Identities=26% Similarity=0.401 Sum_probs=28.4
Q ss_pred CceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChH
Q 028204 30 PLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAM 64 (212)
Q Consensus 30 P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~M 64 (212)
|.|.|...+|.+..++..|.+.|...+.+.+|.|.
T Consensus 1 P~I~i~~~~g~~~e~K~~l~~~it~~~~~~lg~~~ 35 (60)
T PF01361_consen 1 PFITIKIPEGRTAEQKRELAEAITDAVVEVLGIPP 35 (60)
T ss_dssp -EEEEEEESTS-HHHHHHHHHHHHHHHHHHHTS-G
T ss_pred CEEEEEECCCCCHHHHHHHHHHHHHHHHHHhCcCC
Confidence 78888888888889999999999999999998873
No 33
>PF14461 Prok-E2_B: Prokaryotic E2 family B
Probab=68.34 E-value=8.3 Score=30.47 Aligned_cols=28 Identities=14% Similarity=0.287 Sum_probs=24.0
Q ss_pred CceEEEEEEEeCCCCCCCCCceEEecCC
Q 028204 11 FAVELALIFSHTEKYPDEPPLLNVKSLR 38 (212)
Q Consensus 11 ~p~~l~L~f~~p~~YP~e~P~i~i~~~~ 38 (212)
....+.|.+.+|+.||..||.+.+....
T Consensus 34 ~~~~~~l~l~~p~~FP~~pp~v~l~d~~ 61 (133)
T PF14461_consen 34 GGGPFPLRLVFPDDFPYLPPRVYLEDPK 61 (133)
T ss_pred CCeEEEEEEEECCcccCcCCEEEecCcc
Confidence 4567889999999999999999998654
No 34
>KOG0422 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.31 E-value=7.3 Score=32.04 Aligned_cols=24 Identities=25% Similarity=0.470 Sum_probs=21.8
Q ss_pred eEEEEEEEeCCCCCCCCCceEEec
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKS 36 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~ 36 (212)
..++|.+.+|..||--||-|.+..
T Consensus 49 gaF~l~I~fp~eYPFKPP~i~f~t 72 (153)
T KOG0422|consen 49 GAFRLEIDFPVEYPFKPPKIKFKT 72 (153)
T ss_pred cceEEEeeCCCCCCCCCCeeeeee
Confidence 478999999999999999999875
No 35
>PRK01964 4-oxalocrotonate tautomerase; Provisional
Probab=64.29 E-value=14 Score=25.16 Aligned_cols=36 Identities=19% Similarity=0.350 Sum_probs=31.7
Q ss_pred CCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChH
Q 028204 29 PPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAM 64 (212)
Q Consensus 29 ~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~M 64 (212)
.|.|.|.-.+|.+..++..|.+.|.+...+.+|.|.
T Consensus 1 MP~v~i~l~~grt~eqk~~l~~~it~~l~~~lg~p~ 36 (64)
T PRK01964 1 MPIVQIQLLEGRPEEKIKNLIREVTEAISATLDVPK 36 (64)
T ss_pred CCEEEEEEeCCCCHHHHHHHHHHHHHHHHHHhCcCh
Confidence 388888877888899999999999999999999883
No 36
>KOG3299 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.27 E-value=6.1 Score=34.21 Aligned_cols=58 Identities=19% Similarity=0.267 Sum_probs=38.3
Q ss_pred CCCCCCCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHHHHHhhcc
Q 028204 24 KYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWLSERYSQD 83 (212)
Q Consensus 24 ~YP~e~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~MIFtLve~lqE~L~e~~~~~ 83 (212)
.||.++|.|.-.....+.-....-|-..+ ..-.+.|.+|+|..++.++..+++...+.
T Consensus 2 ~yps~ap~i~e~~~v~~~~~~~~~l~~a~--~~~s~~~~~l~~~~~~~~~~~~~~~~~~l 59 (206)
T KOG3299|consen 2 DYPSSAPTIKELVGVEKELAKRKLLSNAL--VYISEIGDSLFLLWVEDPRDVLNKRASKL 59 (206)
T ss_pred CCCCCCCcHhHhhhHHHHHHHHHhhhhhh--HHHHhhhhhhhhhhhccHHHHHHHhHhhc
Confidence 69998776653322222222222233333 56678899999999999999999887664
No 37
>PF14812 PBP1_TM: Transmembrane domain of transglycosylase PBP1 at N-terminal; PDB: 3FWL_A 3VMA_A.
Probab=64.04 E-value=2.2 Score=31.73 Aligned_cols=14 Identities=57% Similarity=0.857 Sum_probs=0.0
Q ss_pred CCCCCCCCCCCCCH
Q 028204 176 EDIDFDDDDFEDDE 189 (212)
Q Consensus 176 ~d~~~~d~~~~~~~ 189 (212)
+|.|+.|||++|||
T Consensus 35 ~ddd~~DDD~dDde 48 (81)
T PF14812_consen 35 YDDDYEDDDDDDDE 48 (81)
T ss_dssp --------------
T ss_pred cccccccccccchh
Confidence 33344444444433
No 38
>KOG0420 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=60.73 E-value=9.7 Score=32.29 Aligned_cols=23 Identities=26% Similarity=0.619 Sum_probs=19.9
Q ss_pred EEEEEEEeCCCCCCCCCceEEec
Q 028204 14 ELALIFSHTEKYPDEPPLLNVKS 36 (212)
Q Consensus 14 ~l~L~f~~p~~YP~e~P~i~i~~ 36 (212)
.+.+.|+.|+.||.+||.+....
T Consensus 77 kf~F~~~v~~~Yp~~PPKVkClt 99 (184)
T KOG0420|consen 77 KFRFKFKVPNAYPHEPPKVKCLT 99 (184)
T ss_pred eEEEEEECCCCCCCCCCeeeeee
Confidence 47788899999999999998765
No 39
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=57.05 E-value=8.6 Score=33.66 Aligned_cols=30 Identities=27% Similarity=0.424 Sum_probs=13.8
Q ss_pred cccccCCCcccccCCCCccCC--CCCCCCCCC
Q 028204 156 TAVSQKGAVTVNEVSDDEDDE--DIDFDDDDF 185 (212)
Q Consensus 156 l~~~~~~~~~~~~e~~~~~~~--d~~~~d~~~ 185 (212)
||-++.+...-..++..+++. |.||++++.
T Consensus 34 ~f~Eee~D~ef~~~~~eed~~~~Dsdf~~se~ 65 (240)
T PF05764_consen 34 LFQEEEDDEEFESEEEEEDEEEDDSDFDDSED 65 (240)
T ss_pred cccccCCCccccCCCccccccccccccCcccc
Confidence 566555544433333323332 666655443
No 40
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=56.18 E-value=7.4 Score=40.85 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=9.7
Q ss_pred hHHhhcCcccccccCCCcccc
Q 028204 147 RQWFESGRATAVSQKGAVTVN 167 (212)
Q Consensus 147 RqlFe~~~~l~~~~~~~~~~~ 167 (212)
=.|+|-++.-..+|++...+.
T Consensus 1392 ~r~yEIGR~r~~~dd~DeeeD 1412 (1516)
T KOG1832|consen 1392 ARMYEIGRRRPTDDDSDEEED 1412 (1516)
T ss_pred hhhhhhcccCCCccccCcccc
Confidence 345555555444444444333
No 41
>KOG0427 consensus Ubiquitin conjugating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=55.29 E-value=16 Score=29.80 Aligned_cols=25 Identities=24% Similarity=0.307 Sum_probs=21.4
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
-...|+|.+|+.||-+.|.+-+...
T Consensus 61 e~~qLq~~F~~~YP~esPqVmF~~~ 85 (161)
T KOG0427|consen 61 ETYQLQVEFPEHYPMESPQVMFVGP 85 (161)
T ss_pred cEEEEEEecCCCCCCCCCeEEEecC
Confidence 3678999999999999999887754
No 42
>PF10446 DUF2457: Protein of unknown function (DUF2457); InterPro: IPR018853 This entry represents a family of uncharacterised proteins.
Probab=52.82 E-value=6 Score=37.96 Aligned_cols=14 Identities=14% Similarity=0.050 Sum_probs=8.7
Q ss_pred CCCCcccHHHHHHH
Q 028204 102 PHGEPVTVETFLAW 115 (212)
Q Consensus 102 ~~GTpVT~EsF~~W 115 (212)
.+++.+|+.-.+.=
T Consensus 21 ~~~~KlTi~DtlkK 34 (458)
T PF10446_consen 21 DYKRKLTINDTLKK 34 (458)
T ss_pred cccccccHHHHHHH
Confidence 35677777666543
No 43
>KOG3357 consensus Uncharacterized conserved protein [Function unknown]
Probab=51.01 E-value=11 Score=30.69 Aligned_cols=27 Identities=26% Similarity=0.503 Sum_probs=22.6
Q ss_pred eEEEEEEEeCCCCCCCCCceEEecCCC
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKSLRG 39 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~~~g 39 (212)
..+.+.|..|-+||.++|.|.+-...|
T Consensus 78 yefdvefdipityp~tapeialpeldg 104 (167)
T KOG3357|consen 78 YEFDVEFDIPITYPTTAPEIALPELDG 104 (167)
T ss_pred heeeeeeccccccCCCCccccccccCc
Confidence 467889999999999999999866544
No 44
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=50.92 E-value=31 Score=25.10 Aligned_cols=35 Identities=11% Similarity=0.218 Sum_probs=31.0
Q ss_pred CCceEEecCCC-CCHHhHHHHHHHHHHHHHHhcCCh
Q 028204 29 PPLLNVKSLRG-IQAGDLKILKEKLEQEASENLGMA 63 (212)
Q Consensus 29 ~P~i~i~~~~g-L~~~~l~~L~~~L~~~aeenlGm~ 63 (212)
.|.|.|.-..| .+.++...|-+.|...+.+.+|.+
T Consensus 1 MP~I~I~~~~g~~s~EqK~~La~~iT~a~~~~lg~~ 36 (76)
T PRK01271 1 MPHIDIKCFPRELDEEQKAALAADITDVIIRHLNSK 36 (76)
T ss_pred CCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHhCcC
Confidence 38899988886 899999999999999999999887
No 45
>KOG0894 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.53 E-value=15 Score=32.32 Aligned_cols=22 Identities=23% Similarity=0.513 Sum_probs=18.6
Q ss_pred EEEeCCCCCCCCCceEEecCCC
Q 028204 18 IFSHTEKYPDEPPLLNVKSLRG 39 (212)
Q Consensus 18 ~f~~p~~YP~e~P~i~i~~~~g 39 (212)
++.+|++||-.||-|.+..+.|
T Consensus 57 kl~FP~eyP~KPPaI~MiTPNG 78 (244)
T KOG0894|consen 57 KLIFPPEYPFKPPAITMITPNG 78 (244)
T ss_pred EEeCCCCCCCCCCeeEEECCCC
Confidence 4578999999999999987654
No 46
>KOG1832 consensus HIV-1 Vpr-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=50.28 E-value=7.7 Score=40.71 Aligned_cols=22 Identities=36% Similarity=0.584 Sum_probs=8.6
Q ss_pred cccCCCCccCCCCCCCCCCCCC
Q 028204 166 VNEVSDDEDDEDIDFDDDDFED 187 (212)
Q Consensus 166 ~~~e~~~~~~~d~~~~d~~~~~ 187 (212)
++||.+.++.+|-|.|||++||
T Consensus 1406 d~DeeeD~e~Ed~dEddd~edd 1427 (1516)
T KOG1832|consen 1406 DSDEEEDDETEDEDEDDDEEDD 1427 (1516)
T ss_pred ccCccccchhhccccccccccc
Confidence 3333333333444444433333
No 47
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=40.80 E-value=9.1 Score=39.38 Aligned_cols=58 Identities=14% Similarity=0.150 Sum_probs=0.0
Q ss_pred EEEEEeCCCCCCCCCceEEecCCCCCHHhHHHHHHHHHHHHHHhcCChHHHHHHHHHHHHH
Q 028204 16 ALIFSHTEKYPDEPPLLNVKSLRGIQAGDLKILKEKLEQEASENLGMAMIYTLVTSAKEWL 76 (212)
Q Consensus 16 ~L~f~~p~~YP~e~P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~MIFtLve~lqE~L 76 (212)
-|.++.|++||..+|.+.+.....=....+..|...|.. .++=+|=.|+|...|--|-
T Consensus 717 Pl~l~vP~~YP~~sp~~~~~~~~y~~~~Fl~~v~~~~~~---Rl~~lP~~~svt~lL~tWe 774 (799)
T PF09606_consen 717 PLRLTVPADYPRQSPQCSVDRDEYDATPFLQDVQNALTS---RLAKLPDKHSVTQLLNTWE 774 (799)
T ss_dssp -------------------------------------------------------------
T ss_pred CeeEeCCCCCCccCCcCcccHHHhccChHHHHHHHHHHH---HHHhCCCceeHHHHHHHHH
Confidence 345567999999999998754321011122223333322 2334566777777776664
No 48
>KOG0426 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.69 E-value=22 Score=29.06 Aligned_cols=22 Identities=23% Similarity=0.436 Sum_probs=17.5
Q ss_pred EEEEEEeCCCCCCCCCceEEec
Q 028204 15 LALIFSHTEKYPDEPPLLNVKS 36 (212)
Q Consensus 15 l~L~f~~p~~YP~e~P~i~i~~ 36 (212)
+.-++++|.+||-+||.+.+..
T Consensus 54 fpA~l~FP~DYPLsPPkm~Ftc 75 (165)
T KOG0426|consen 54 FPARLSFPLDYPLSPPKMRFTC 75 (165)
T ss_pred cceeeecCCCCCCCCCceeeec
Confidence 3445678999999999998775
No 49
>KOG0895 consensus Ubiquitin-conjugating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=39.76 E-value=27 Score=37.03 Aligned_cols=24 Identities=29% Similarity=0.573 Sum_probs=21.2
Q ss_pred eEEEEEEEeCCCCCCCCCceEEec
Q 028204 13 VELALIFSHTEKYPDEPPLLNVKS 36 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~i~~ 36 (212)
..+.+.|.+|.+||.+||.+...+
T Consensus 898 ~~f~fd~~~~~~yp~~pp~~~~~s 921 (1101)
T KOG0895|consen 898 GLFFFDFQFPQDYPSSPPLVHYHS 921 (1101)
T ss_pred ceEEEEeecCCCCCCCCCceEeec
Confidence 357889999999999999999875
No 50
>KOG0428 consensus Non-canonical ubiquitin conjugating enzyme 1 [Posttranslational modification, protein turnover, chaperones]
Probab=39.18 E-value=28 Score=31.27 Aligned_cols=21 Identities=19% Similarity=0.354 Sum_probs=17.9
Q ss_pred EEEeCCCCCCCCCceEEecCC
Q 028204 18 IFSHTEKYPDEPPLLNVKSLR 38 (212)
Q Consensus 18 ~f~~p~~YP~e~P~i~i~~~~ 38 (212)
.|.+|++||-.||.|-+..+.
T Consensus 62 RI~lPadYPmKPPs~iLLTpN 82 (314)
T KOG0428|consen 62 RIVLPADYPMKPPSIILLTPN 82 (314)
T ss_pred eEecCCCCCCCCCeEEEEcCC
Confidence 567899999999999888654
No 51
>PF04871 Uso1_p115_C: Uso1 / p115 like vesicle tethering protein, C terminal region; InterPro: IPR006955 This domain identifies a group of proteins, which are described as: General vesicular transport factor, Transcytosis associate protein (TAP) and Vesicle docking protein. This myosin-shaped molecule consists of an N-terminal globular head region, a coiled-coil tail which mediates dimerisation, and a short C-terminal acidic region []. p115 tethers COP1 vesicles to the Golgi by binding the coiled coil proteins giantin (on the vesicles) and GM130 (on the Golgi), via its C-terminal acidic region. It is required for intercisternal transport in the Golgi stack. This domain is found in the acidic C-terminal region, which binds to the golgins giantin and GM130. p115 is thought to juxtapose two membranes by binding giantin with one acidic region, and GM130 with another [].; GO: 0008565 protein transporter activity, 0006886 intracellular protein transport, 0005737 cytoplasm, 0016020 membrane
Probab=38.88 E-value=16 Score=29.31 Aligned_cols=10 Identities=10% Similarity=0.258 Sum_probs=5.0
Q ss_pred CCcccccCCC
Q 028204 162 GAVTVNEVSD 171 (212)
Q Consensus 162 ~~~~~~~e~~ 171 (212)
|-.|..++.+
T Consensus 111 G~eVSddE~~ 120 (136)
T PF04871_consen 111 GEEVSDDEDS 120 (136)
T ss_pred CCCccCCccc
Confidence 5555445533
No 52
>KOG0424 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=36.44 E-value=29 Score=28.68 Aligned_cols=24 Identities=25% Similarity=0.477 Sum_probs=19.7
Q ss_pred EEEEEEEeCCCCCCCCCceEEecC
Q 028204 14 ELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 14 ~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
...|.+.||.+||..||...+...
T Consensus 57 ~y~l~v~F~~dyP~~PPkckF~~p 80 (158)
T KOG0424|consen 57 LYKLTVNFPDDYPSSPPKCKFKPP 80 (158)
T ss_pred eEEEEEeCCccCCCCCCccccCCC
Confidence 356778889999999999988753
No 53
>PF14462 Prok-E2_E: Prokaryotic E2 family E
Probab=36.11 E-value=32 Score=27.41 Aligned_cols=21 Identities=24% Similarity=0.395 Sum_probs=17.0
Q ss_pred eEEEEEEEeCCCCCCCCCceE
Q 028204 13 VELALIFSHTEKYPDEPPLLN 33 (212)
Q Consensus 13 ~~l~L~f~~p~~YP~e~P~i~ 33 (212)
-++.+-|..|+.||.++|..-
T Consensus 42 ~~~dili~iP~gYP~~~~Dmf 62 (122)
T PF14462_consen 42 NEVDILILIPPGYPDAPLDMF 62 (122)
T ss_pred cceEEEEECCCCCCCCCCCcE
Confidence 468888999999999986543
No 54
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=35.16 E-value=20 Score=39.14 Aligned_cols=20 Identities=5% Similarity=0.129 Sum_probs=11.1
Q ss_pred hhHHhhcCcccccccCCCcc
Q 028204 146 GRQWFESGRATAVSQKGAVT 165 (212)
Q Consensus 146 GRqlFe~~~~l~~~~~~~~~ 165 (212)
-|.|..-+.+-.++.++...
T Consensus 1704 rrrllsgnttndtnaDnEEr 1723 (3015)
T KOG0943|consen 1704 RRRLLSGNTTNDTNADNEER 1723 (3015)
T ss_pred hhhhccCCccCccccchhhh
Confidence 45566666666666554433
No 55
>PF05764 YL1: YL1 nuclear protein; InterPro: IPR008895 The proteins in this family are designated YL1 []. They have been shown to be DNA-binding and may be transcription factors [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=34.51 E-value=24 Score=30.90 Aligned_cols=8 Identities=50% Similarity=0.459 Sum_probs=3.4
Q ss_pred CCCCccCC
Q 028204 169 VSDDEDDE 176 (212)
Q Consensus 169 e~~~~~~~ 176 (212)
.|+|++.+
T Consensus 57 Dsdf~~se 64 (240)
T PF05764_consen 57 DSDFDDSE 64 (240)
T ss_pred ccccCccc
Confidence 34444443
No 56
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=31.53 E-value=32 Score=31.18 Aligned_cols=17 Identities=18% Similarity=0.595 Sum_probs=14.6
Q ss_pred cCChHHHHHHHHHHHHH
Q 028204 60 LGMAMIYTLVTSAKEWL 76 (212)
Q Consensus 60 lGm~MIFtLve~lqE~L 76 (212)
.|+.||=.|.....-|+
T Consensus 91 tGl~mvGaiCDfCEawv 107 (314)
T PF06524_consen 91 TGLGMVGAICDFCEAWV 107 (314)
T ss_pred cccchhhhhhccchhhe
Confidence 48899999999888886
No 57
>PF04889 Cwf_Cwc_15: Cwf15/Cwc15 cell cycle control protein; InterPro: IPR006973 This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing [].; GO: 0000398 nuclear mRNA splicing, via spliceosome, 0005681 spliceosomal complex
Probab=29.05 E-value=43 Score=29.61 Aligned_cols=14 Identities=43% Similarity=0.601 Sum_probs=7.0
Q ss_pred CCCCCCHHHHHHHH
Q 028204 183 DDFEDDEVDMLEHY 196 (212)
Q Consensus 183 ~~~~~~~~~~~~~~ 196 (212)
+|.|||++.||..+
T Consensus 142 ~ddeDd~~~Ll~EL 155 (244)
T PF04889_consen 142 DDDEDDTAALLREL 155 (244)
T ss_pred cccchHHHHHHHHH
Confidence 34444455665544
No 58
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=28.96 E-value=1.1e+02 Score=21.75 Aligned_cols=35 Identities=23% Similarity=0.415 Sum_probs=28.1
Q ss_pred CCceEEecCCC-CCHHhHHHHHHHHHHHHHHhcCCh
Q 028204 29 PPLLNVKSLRG-IQAGDLKILKEKLEQEASENLGMA 63 (212)
Q Consensus 29 ~P~i~i~~~~g-L~~~~l~~L~~~L~~~aeenlGm~ 63 (212)
.|.+.|...+| ++..+...|-..|-+...+.+|.+
T Consensus 1 MP~v~Ik~~~g~~~~~~K~~la~~vT~~~~~~lg~~ 36 (69)
T COG1942 1 MPFVNIKLFEGRLDEEQKAELAAEVTEVTVETLGKD 36 (69)
T ss_pred CCEEEEEecCCCCCHHHHHHHHHHHHHHHHHHhCCC
Confidence 38888888765 666778889999988888888876
No 59
>KOG3403 consensus Translation initiation factor 1A (eIF-1A) [Translation, ribosomal structure and biogenesis]
Probab=27.28 E-value=37 Score=27.46 Aligned_cols=14 Identities=64% Similarity=1.040 Sum_probs=8.1
Q ss_pred cCCCCCCCCCCCCC
Q 028204 174 DDEDIDFDDDDFED 187 (212)
Q Consensus 174 ~~~d~~~~d~~~~~ 187 (212)
.++|++|++..+++
T Consensus 126 ~d~~~~~~~~~~~~ 139 (145)
T KOG3403|consen 126 DDDDIDFDDIEDDD 139 (145)
T ss_pred Cccccccccccccc
Confidence 55677776654433
No 60
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=24.93 E-value=39 Score=34.38 Aligned_cols=20 Identities=45% Similarity=0.509 Sum_probs=16.1
Q ss_pred cCChHHHHHHHHHHHHHHHH
Q 028204 60 LGMAMIYTLVTSAKEWLSER 79 (212)
Q Consensus 60 lGm~MIFtLve~lqE~L~e~ 79 (212)
.|++.+++|+..+...|...
T Consensus 471 ~~~~~~~~l~~~~~~~l~~~ 490 (784)
T PF04931_consen 471 SGMKWLYTLVQIASELLFSI 490 (784)
T ss_pred cccchHHHHHHHHHHHHhcc
Confidence 47888999999988877653
No 61
>PRK04217 hypothetical protein; Provisional
Probab=24.57 E-value=3.2e+02 Score=21.18 Aligned_cols=58 Identities=21% Similarity=0.342 Sum_probs=35.9
Q ss_pred CCCCCCceEEecCCCCCHHhHHHHHHHH-----HHHHHHhcCChH--HHHHHHHHHHHHHHHhhc
Q 028204 25 YPDEPPLLNVKSLRGIQAGDLKILKEKL-----EQEASENLGMAM--IYTLVTSAKEWLSERYSQ 82 (212)
Q Consensus 25 YP~e~P~i~i~~~~gL~~~~l~~L~~~L-----~~~aeenlGm~M--IFtLve~lqE~L~e~~~~ 82 (212)
||.-+|...=..+..|+..+...+...- ..++-+.+|+.- |+.++..++..|.+.+..
T Consensus 28 ~~~~~~~~~~~p~~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~ 92 (110)
T PRK04217 28 YPAIPPVGPPKPPIFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVE 92 (110)
T ss_pred eCCCCCccCCCCcccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 7776665554445668877765444332 223444555554 888888888888777653
No 62
>KOG2023 consensus Nuclear transport receptor Karyopherin-beta2/Transportin (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=24.29 E-value=34 Score=35.02 Aligned_cols=35 Identities=23% Similarity=0.319 Sum_probs=19.0
Q ss_pred CCCCCCCCceE-Ee-cCC-CCCHHhHHHHHHHHHHHHH
Q 028204 23 EKYPDEPPLLN-VK-SLR-GIQAGDLKILKEKLEQEAS 57 (212)
Q Consensus 23 ~~YP~e~P~i~-i~-~~~-gL~~~~l~~L~~~L~~~ae 57 (212)
.+.|+-.|.+. +. +.. +.....+..|++..+..|+
T Consensus 124 ~~wpelLp~L~~~L~s~d~n~~EgA~~AL~KIcEDsa~ 161 (885)
T KOG2023|consen 124 QHWPELLPQLCELLDSPDYNTCEGAFGALQKICEDSAQ 161 (885)
T ss_pred ccchhHHHHHHHHhcCCcccccchhHHHHHHHHhhhHH
Confidence 36677766554 22 222 4445566666666655554
No 63
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=22.79 E-value=1.2e+02 Score=23.02 Aligned_cols=34 Identities=15% Similarity=0.187 Sum_probs=29.5
Q ss_pred CceEEecCCCCCHHhHHHHHHHHHHHHHHhcCCh
Q 028204 30 PLLNVKSLRGIQAGDLKILKEKLEQEASENLGMA 63 (212)
Q Consensus 30 P~i~i~~~~gL~~~~l~~L~~~L~~~aeenlGm~ 63 (212)
|.|.|....+++......|.+.+.+.+.+.+|-|
T Consensus 2 P~~~i~tn~~~~~~~~~~~~~~~~~~l~~~lgkP 35 (116)
T PTZ00397 2 PCCQVSTNVNATDDQADAALSDIENAIADVLGKP 35 (116)
T ss_pred CeEEEEecCCCccccHHHHHHHHHHHHHHHhCCC
Confidence 7888887777777788999999999999999998
No 64
>KOG2662 consensus Magnesium transporters: CorA family [Inorganic ion transport and metabolism]
Probab=22.26 E-value=54 Score=31.32 Aligned_cols=16 Identities=50% Similarity=0.719 Sum_probs=12.7
Q ss_pred CCCCHHHHHHHHHhcc
Q 028204 185 FEDDEVDMLEHYLAEK 200 (212)
Q Consensus 185 ~~~~~~~~~~~~~~~~ 200 (212)
.=||++||.+-||.+|
T Consensus 246 LLddd~Dma~mYLT~K 261 (414)
T KOG2662|consen 246 LLDDDDDMAEMYLTRK 261 (414)
T ss_pred HhcChHHHHHHHHhHH
Confidence 3445678999999999
No 65
>KOG0898 consensus 40S ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=21.93 E-value=61 Score=26.64 Aligned_cols=21 Identities=48% Similarity=0.618 Sum_probs=15.1
Q ss_pred HHHHHHHHhcc------------CCCCCCCCCC
Q 028204 190 VDMLEHYLAEK------------SDSSTHSSRQ 210 (212)
Q Consensus 190 ~~~~~~~~~~~------------~~~~~~~~~~ 210 (212)
..|+-|||++= .-.+|||||-
T Consensus 116 PEMIGhYL~eFsiTykpvkHgrpgigat~Ssrf 148 (152)
T KOG0898|consen 116 PEMIGHYLGEFSITYKPVKHGRPGIGATHSSRF 148 (152)
T ss_pred HHHHhhhhhhccccccccccCCCCCCccccccc
Confidence 58999999953 2235788874
No 66
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=20.60 E-value=60 Score=29.53 Aligned_cols=6 Identities=17% Similarity=-0.119 Sum_probs=2.3
Q ss_pred CCcccH
Q 028204 104 GEPVTV 109 (212)
Q Consensus 104 GTpVT~ 109 (212)
.|..|.
T Consensus 218 et~eTk 223 (314)
T PF06524_consen 218 ETQETK 223 (314)
T ss_pred cccccc
Confidence 343333
No 67
>PF04281 Tom22: Mitochondrial import receptor subunit Tom22 ; InterPro: IPR005683 The mitochondrial protein translocase family, which is responsible for movement of nuclear encoded pre-proteins into mitochondria, is very complex with at least 19 components. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family represents the Tom22 proteins []. The N-terminal region of Tom22 has been shown to have chaperone-like activity, and the C-terminal region faces the intermembrane face []. ; GO: 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane
Probab=20.33 E-value=96 Score=25.21 Aligned_cols=24 Identities=33% Similarity=0.508 Sum_probs=12.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHhcc
Q 028204 177 DIDFDDDDFEDDEVDMLEHYLAEK 200 (212)
Q Consensus 177 d~~~~d~~~~~~~~~~~~~~~~~~ 200 (212)
|.|++||++++.+|-++|.+.|=+
T Consensus 38 ~sd~~dd~d~e~dETl~ERl~aLk 61 (137)
T PF04281_consen 38 DSDISDDSDDEEDETLLERLWALK 61 (137)
T ss_pred cccccccccCCccccHHHHHHHHh
Confidence 444444222225567777766543
No 68
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=20.32 E-value=35 Score=29.49 Aligned_cols=13 Identities=31% Similarity=-0.020 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHH
Q 028204 115 WRERFEAELALER 127 (212)
Q Consensus 115 Wk~kf~~E~~~~k 127 (212)
.+..|-+|+....
T Consensus 116 ~~~~fP~EL~~~~ 128 (233)
T PF11705_consen 116 DWEFFPKELWPTL 128 (233)
T ss_pred cHhhChHHHHhhc
Confidence 3445666665543
No 69
>KOG0897 consensus Predicted ubiquitin-conjugating enzyme [Posttranslational modification, protein turnover, chaperones]
Probab=20.25 E-value=1e+02 Score=24.63 Aligned_cols=24 Identities=21% Similarity=0.380 Sum_probs=20.9
Q ss_pred EEEEEEEeCCCCCCCCCceEEecC
Q 028204 14 ELALIFSHTEKYPDEPPLLNVKSL 37 (212)
Q Consensus 14 ~l~L~f~~p~~YP~e~P~i~i~~~ 37 (212)
.+.|.+.++.+||..||...+..+
T Consensus 12 ~ill~~~f~~~fp~~ppf~rvv~p 35 (122)
T KOG0897|consen 12 NILLLDIFDDNFPFMPPFPRVVKP 35 (122)
T ss_pred eeEeeeecccCCCCCCCcceeeee
Confidence 577889999999999999998764
No 70
>PF11705 RNA_pol_3_Rpc31: DNA-directed RNA polymerase III subunit Rpc31; InterPro: IPR024661 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase III contains seventeen subunits in yeasts and in human cells. Twelve of these are akin to RNA polymerase I or II and the other five are RNA polymerase III-specific, and form the functionally distinct groups: (i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31, Rpc34 and Rpc82 form a cluster of enzyme-specific subunits that contribute to transcription initiation in Saccharomyces cerevisiae and Homo sapiens. There is evidence that these subunits are anchored at or near the N-terminal Zn-fold of Rpc1, itself prolonged by a highly conserved but RNA polymerase III-specific domain []. This entry represents the Rpc31 subunit.
Probab=20.08 E-value=59 Score=28.06 Aligned_cols=9 Identities=11% Similarity=0.217 Sum_probs=5.3
Q ss_pred EeCCCCCCC
Q 028204 20 SHTEKYPDE 28 (212)
Q Consensus 20 ~~p~~YP~e 28 (212)
.-|+.||..
T Consensus 31 ~P~~lfP~~ 39 (233)
T PF11705_consen 31 QPPPLFPPL 39 (233)
T ss_pred CCCCCCCCC
Confidence 444667774
Done!