Query psy17828
Match_columns 1061
No_of_seqs 534 out of 1224
Neff 4.4
Searched_HMMs 46136
Date Sat Aug 17 00:01:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17828.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17828hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2098|consensus 100.0 7E-111 2E-115 923.6 17.6 476 1-497 1-552 (591)
2 KOG1556|consensus 100.0 4.1E-59 8.9E-64 485.4 19.9 238 632-1014 5-243 (309)
3 cd08062 MPN_RPN7_8 Mpr1p, Pad1 100.0 1.7E-48 3.6E-53 423.6 24.6 226 636-1004 1-227 (280)
4 PLN03246 26S proteasome regula 100.0 1.6E-48 3.5E-53 427.3 24.0 229 633-1004 3-233 (303)
5 cd08063 MPN_CSN6 Mpr1p, Pad1p 100.0 1.1E-44 2.3E-49 395.0 22.6 222 637-1004 2-231 (288)
6 cd08064 MPN_eIF3f Mpr1p, Pad1p 100.0 7.3E-44 1.6E-48 384.3 22.9 218 638-1003 1-222 (265)
7 KOG2975|consensus 100.0 3.9E-44 8.4E-49 377.4 16.5 228 628-1003 13-242 (288)
8 KOG2097|consensus 100.0 2.5E-39 5.3E-44 345.1 8.0 205 329-556 134-380 (397)
9 KOG3050|consensus 100.0 3.5E-36 7.6E-41 314.0 17.3 227 630-1002 3-234 (299)
10 COG4725 IME4 Transcriptional a 100.0 4E-33 8.6E-38 277.6 8.1 156 337-497 1-179 (198)
11 PF05063 MT-A70: MT-A70 ; Int 100.0 3.7E-32 8.1E-37 276.8 10.6 139 355-496 1-176 (176)
12 cd08057 MPN_euk_non_mb Mpr1p, 100.0 4.2E-30 9.2E-35 257.4 16.0 130 638-773 1-137 (157)
13 cd08065 MPN_eIF3h Mpr1p, Pad1p 99.9 1.4E-26 3E-31 250.7 18.5 132 637-773 2-137 (266)
14 PF01398 JAB: JAB1/Mov34/MPN/P 99.9 8.1E-23 1.7E-27 193.5 9.9 109 634-748 2-114 (114)
15 cd08069 MPN_RPN11_CSN5 Mov34/M 99.9 1.3E-21 2.8E-26 212.6 17.3 135 633-775 7-149 (268)
16 KOG1560|consensus 99.8 8.1E-21 1.8E-25 202.5 7.8 156 633-792 10-174 (339)
17 smart00232 JAB_MPN JAB/MPN dom 99.8 3.7E-19 7.9E-24 170.7 15.3 129 637-772 1-134 (135)
18 cd08064 MPN_eIF3f Mpr1p, Pad1p 99.7 1.1E-17 2.3E-22 181.6 5.8 182 806-1018 28-221 (265)
19 KOG1554|consensus 99.7 2.3E-16 5E-21 169.3 11.6 140 635-779 52-197 (347)
20 cd08063 MPN_CSN6 Mpr1p, Pad1p 99.6 1E-15 2.2E-20 168.1 7.0 183 806-1019 34-230 (288)
21 cd08057 MPN_euk_non_mb Mpr1p, 99.6 7.6E-16 1.7E-20 154.8 5.0 120 806-942 28-157 (157)
22 cd07767 MPN Mpr1p, Pad1p N-ter 99.5 3.9E-14 8.5E-19 133.1 12.1 111 646-768 2-116 (116)
23 cd08067 MPN_2A_DUB Mov34/MPN/P 99.5 2.6E-13 5.7E-18 141.2 17.3 132 635-776 4-150 (187)
24 cd08058 MPN_euk_mb Mpr1p, Pad1 99.5 2.3E-13 5.1E-18 131.0 11.7 110 644-771 2-119 (119)
25 KOG2356|consensus 99.5 5.4E-14 1.2E-18 152.5 6.1 164 332-498 157-354 (366)
26 PLN03246 26S proteasome regula 99.4 1.2E-13 2.6E-18 153.0 6.6 181 806-1018 36-231 (303)
27 KOG2098|consensus 99.4 6.7E-14 1.5E-18 157.4 2.4 327 88-453 45-459 (591)
28 cd08062 MPN_RPN7_8 Mpr1p, Pad1 99.4 2.6E-13 5.6E-18 149.0 6.7 181 806-1018 31-225 (280)
29 KOG1555|consensus 99.3 1.1E-11 2.4E-16 136.7 9.7 153 632-788 27-189 (316)
30 cd08068 MPN_BRCC36 Mov34/MPN/P 99.1 1.5E-09 3.3E-14 117.4 15.0 132 636-773 2-152 (244)
31 KOG1556|consensus 99.0 9.8E-11 2.1E-15 124.5 1.9 50 495-544 243-292 (309)
32 KOG2975|consensus 98.8 3.8E-09 8.2E-14 113.8 6.5 59 715-773 94-152 (288)
33 cd08065 MPN_eIF3h Mpr1p, Pad1p 98.7 7.5E-09 1.6E-13 113.2 3.0 178 806-989 28-229 (266)
34 cd08069 MPN_RPN11_CSN5 Mov34/M 98.7 1.5E-08 3.3E-13 111.1 4.8 135 806-949 37-202 (268)
35 cd08066 MPN_AMSH_like Mov34/MP 98.5 1.5E-06 3.3E-11 90.0 14.5 119 638-771 4-127 (173)
36 PF13012 MitMem_reg: Maintenan 98.5 1.7E-08 3.8E-13 96.5 -1.5 68 936-1003 1-69 (115)
37 PF01398 JAB: JAB1/Mov34/MPN/P 98.2 2.7E-07 5.9E-12 87.8 -0.5 76 806-888 31-113 (114)
38 cd08070 MPN_like Mpr1p, Pad1p 98.1 3E-05 6.6E-10 75.9 12.1 113 644-771 3-119 (128)
39 smart00232 JAB_MPN JAB/MPN dom 98.1 2.4E-06 5.1E-11 82.3 3.9 99 806-912 27-133 (135)
40 cd08060 MPN_UPF0172 Mov34/MPN/ 97.9 0.0002 4.3E-09 75.2 13.3 107 642-760 3-116 (182)
41 COG1310 Predicted metal-depend 97.8 5E-05 1.1E-09 75.0 7.4 100 639-756 3-106 (134)
42 KOG3050|consensus 97.7 2E-05 4.3E-10 84.8 2.9 53 846-898 76-128 (299)
43 cd07767 MPN Mpr1p, Pad1p N-ter 97.7 2.6E-05 5.6E-10 73.6 3.1 61 849-909 52-116 (116)
44 PF03665 UPF0172: Uncharacteri 97.2 0.0043 9.4E-08 66.0 13.3 114 637-760 3-122 (196)
45 TIGR02256 ICE_VC0181 integrati 95.7 0.11 2.3E-06 52.6 11.2 83 644-730 1-84 (131)
46 cd08072 MPN_archaeal Mov34/MPN 94.8 0.34 7.3E-06 47.6 11.2 99 645-771 6-108 (117)
47 KOG3289|consensus 94.2 0.77 1.7E-05 48.6 12.7 121 637-769 3-134 (199)
48 PF14464 Prok-JAB: Prokaryotic 93.6 0.17 3.7E-06 47.2 6.4 88 644-755 4-95 (104)
49 cd08056 MPN_PRP8 Mpr1p, Pad1p 91.3 0.91 2E-05 50.6 9.1 99 662-773 56-167 (252)
50 PF13012 MitMem_reg: Maintenan 88.7 0.13 2.8E-06 49.5 0.0 45 488-532 71-115 (115)
51 PRK13699 putative methylase; P 87.6 1.9 4.1E-05 46.9 8.1 117 353-474 19-161 (227)
52 cd08073 MPN_NLPC_P60 Mpr1p, Pa 85.9 1.9 4.1E-05 42.0 6.2 74 645-737 3-81 (108)
53 cd08058 MPN_euk_mb Mpr1p, Pad1 85.5 0.73 1.6E-05 44.9 3.2 60 849-910 54-117 (119)
54 PF13659 Methyltransf_26: Meth 83.5 0.18 4E-06 47.2 -1.9 63 336-399 51-116 (117)
55 PF01555 N6_N4_Mtase: DNA meth 83.0 0.71 1.5E-05 47.6 2.0 82 356-438 2-107 (231)
56 PF07106 TBPIP: Tat binding pr 82.1 5 0.00011 41.5 7.8 53 90-144 1-53 (169)
57 PRK11524 putative methyltransf 77.2 4.2 9.1E-05 45.4 5.8 84 338-425 10-105 (284)
58 PF10237 N6-adenineMlase: Prob 74.6 2.3 4.9E-05 44.5 2.7 51 353-416 85-138 (162)
59 cd08059 MPN_prok_mb Mpr1p, Pad 72.5 14 0.0003 34.8 7.1 72 647-739 5-80 (101)
60 TIGR03534 RF_mod_PrmC protein- 70.1 5.4 0.00012 42.5 4.3 78 337-418 139-237 (251)
61 TIGR01177 conserved hypothetic 69.9 4.7 0.0001 45.8 4.0 75 338-415 233-309 (329)
62 PF03665 UPF0172: Uncharacteri 69.8 3.1 6.8E-05 44.7 2.5 81 806-898 29-119 (196)
63 cd08068 MPN_BRCC36 Mov34/MPN/P 69.1 12 0.00025 41.8 6.7 80 853-936 82-170 (244)
64 KOG2880|consensus 68.0 4 8.7E-05 47.4 2.9 112 649-773 261-379 (424)
65 cd08061 MPN_NPL4 Mov34/MPN/PAD 64.4 52 0.0011 37.4 10.7 109 660-773 32-160 (274)
66 KOG1560|consensus 64.0 7.1 0.00015 44.2 3.8 140 848-989 86-257 (339)
67 PRK09328 N5-glutamine S-adenos 63.8 13 0.00028 40.4 5.8 78 337-416 160-256 (275)
68 TIGR03704 PrmC_rel_meth putati 60.8 9.8 0.00021 41.9 4.2 81 338-418 136-236 (251)
69 TIGR03697 NtcA_cyano global ni 60.0 22 0.00047 36.2 6.3 65 90-163 114-190 (193)
70 PRK11161 fumarate/nitrate redu 57.9 23 0.0005 37.6 6.3 67 90-165 155-233 (235)
71 cd08060 MPN_UPF0172 Mov34/MPN/ 57.3 15 0.00032 39.2 4.6 40 859-898 69-113 (182)
72 COG2263 Predicted RNA methylas 56.7 7 0.00015 42.3 2.1 26 338-367 96-121 (198)
73 cd08066 MPN_AMSH_like Mov34/MP 55.8 17 0.00037 38.4 4.7 50 859-912 74-127 (173)
74 COG1310 Predicted metal-depend 55.6 14 0.0003 36.8 3.9 35 860-896 69-105 (134)
75 PRK13918 CRP/FNR family transc 55.0 31 0.00067 35.6 6.5 69 90-167 120-200 (202)
76 PF01861 DUF43: Protein of unk 53.2 8.7 0.00019 42.8 2.2 35 332-366 89-124 (243)
77 TIGR00138 gidB 16S rRNA methyl 53.2 16 0.00036 38.3 4.2 66 338-416 95-163 (181)
78 PF06442 DHFR_2: R67 dihydrofo 53.1 6.5 0.00014 35.7 1.0 11 859-869 39-49 (78)
79 PF00325 Crp: Bacterial regula 52.8 16 0.00035 28.9 3.0 32 106-139 1-32 (32)
80 KOG1554|consensus 52.5 13 0.00027 42.4 3.3 61 851-911 122-188 (347)
81 PF09445 Methyltransf_15: RNA 52.4 5.5 0.00012 41.8 0.5 28 338-365 51-80 (163)
82 TIGR02085 meth_trns_rumB 23S r 51.8 15 0.00033 42.8 4.0 68 337-416 283-350 (374)
83 PF05175 MTS: Methyltransferas 49.4 3.2 6.9E-05 42.7 -1.8 73 337-414 83-155 (170)
84 PRK09391 fixK transcriptional 49.0 39 0.00084 36.3 6.3 68 89-164 153-228 (230)
85 PRK10402 DNA-binding transcrip 47.5 63 0.0014 34.5 7.5 70 90-168 150-221 (226)
86 PRK03522 rumB 23S rRNA methylu 47.3 19 0.00042 40.8 3.9 68 337-416 223-290 (315)
87 PF13545 HTH_Crp_2: Crp-like h 47.3 38 0.00082 29.9 4.9 38 103-142 24-61 (76)
88 TIGR00537 hemK_rel_arch HemK-r 46.9 39 0.00085 34.7 5.7 79 337-418 68-161 (179)
89 TIGR03533 L3_gln_methyl protei 44.1 34 0.00074 38.5 5.1 76 338-416 175-268 (284)
90 PF14608 zf-CCCH_2: Zinc finge 42.7 17 0.00036 25.5 1.5 19 289-307 1-19 (19)
91 PF01170 UPF0020: Putative RNA 40.9 15 0.00032 38.6 1.5 66 338-410 91-162 (179)
92 cd08067 MPN_2A_DUB Mov34/MPN/P 40.3 49 0.0011 35.5 5.3 62 849-912 70-145 (187)
93 PRK11783 rlmL 23S rRNA m(2)G24 38.2 19 0.00042 45.4 2.3 81 338-418 592-676 (702)
94 PF03602 Cons_hypoth95: Conser 38.1 16 0.00035 38.6 1.4 29 338-366 95-126 (183)
95 PF13412 HTH_24: Winged helix- 38.0 77 0.0017 25.9 5.1 46 90-140 3-48 (48)
96 PF02295 z-alpha: Adenosine de 37.6 70 0.0015 29.0 5.1 51 89-142 3-53 (66)
97 smart00419 HTH_CRP helix_turn_ 37.4 45 0.00098 26.5 3.5 39 102-142 3-41 (48)
98 TIGR03735 PRTRC_A PRTRC system 36.7 1.1E+02 0.0023 33.4 7.1 75 643-737 78-156 (192)
99 cd02440 AdoMet_MTases S-adenos 36.3 25 0.00055 30.2 2.1 56 336-397 48-103 (107)
100 PF05021 NPL4: NPL4 family; I 36.2 3.3E+02 0.0072 31.6 11.4 104 665-773 2-143 (306)
101 PHA03411 putative methyltransf 35.5 23 0.00049 40.4 2.0 78 337-417 111-209 (279)
102 PRK10909 rsmD 16S rRNA m(2)G96 35.2 16 0.00034 39.3 0.8 54 338-398 105-159 (199)
103 PRK00811 spermidine synthase; 33.7 24 0.00051 39.7 1.8 61 338-403 134-196 (283)
104 COG4123 Predicted O-methyltran 33.6 47 0.001 37.3 4.1 81 338-418 98-190 (248)
105 KOG1555|consensus 32.1 29 0.00062 40.2 2.2 58 852-911 108-171 (316)
106 KOG3350|consensus 31.7 17 0.00037 39.2 0.3 14 352-365 133-146 (217)
107 PF01978 TrmB: Sugar-specific 31.4 82 0.0018 27.6 4.5 49 90-143 8-56 (68)
108 smart00550 Zalpha Z-DNA-bindin 31.2 1.1E+02 0.0023 27.5 5.2 52 88-142 4-55 (68)
109 PF02082 Rrf2: Transcriptional 30.7 86 0.0019 28.8 4.7 50 93-144 11-60 (83)
110 TIGR01610 phage_O_Nterm phage 30.3 60 0.0013 30.9 3.7 38 104-143 44-81 (95)
111 TIGR00479 rumA 23S rRNA (uraci 30.1 74 0.0016 37.6 5.2 69 338-416 343-414 (431)
112 PRK13168 rumA 23S rRNA m(5)U19 29.0 46 0.001 39.6 3.3 69 337-416 347-418 (443)
113 PRK11753 DNA-binding transcrip 28.4 78 0.0017 32.8 4.5 38 104-143 165-202 (211)
114 PHA03412 putative methyltransf 28.4 39 0.00086 37.8 2.4 28 337-366 99-126 (241)
115 PRK14967 putative methyltransf 27.6 1.3E+02 0.0029 32.2 6.1 79 338-418 87-180 (223)
116 cd08768 Cdc6_C Winged-helix do 27.1 1.9E+02 0.0042 26.2 6.3 59 90-148 2-71 (87)
117 PRK15128 23S rRNA m(5)C1962 me 27.0 19 0.0004 42.7 -0.4 66 338-403 274-344 (396)
118 COG3355 Predicted transcriptio 26.8 2.8E+02 0.006 28.5 7.8 73 92-168 29-103 (126)
119 PF10672 Methyltrans_SAM: S-ad 26.8 30 0.00066 39.4 1.2 64 338-403 177-243 (286)
120 KOG2671|consensus 26.4 45 0.00098 39.4 2.4 33 333-367 260-297 (421)
121 KOG3289|consensus 25.2 67 0.0015 34.7 3.3 89 810-910 34-134 (199)
122 PRK15043 transcriptional regul 24.8 80 0.0017 35.5 3.9 45 353-414 188-232 (243)
123 PRK11805 N5-glutamine S-adenos 24.0 1.1E+02 0.0024 34.9 5.0 26 338-365 187-212 (307)
124 PRK06266 transcription initiat 23.7 3.4E+02 0.0073 29.1 8.2 85 92-181 24-114 (178)
125 PRK14968 putative methyltransf 23.6 1.7E+02 0.0036 29.6 5.8 78 337-416 75-167 (188)
126 COG1092 Predicted SAM-dependen 23.6 39 0.00084 40.2 1.3 59 338-396 271-334 (393)
127 COG0742 N6-adenine-specific me 22.5 46 0.001 35.9 1.5 28 338-365 96-125 (187)
128 PRK03612 spermidine synthase; 22.4 61 0.0013 39.7 2.7 77 338-416 357-438 (521)
129 PF08781 DP: Transcription fac 21.9 1E+02 0.0022 32.1 3.7 27 6-32 1-27 (142)
130 COG1695 Predicted transcriptio 21.3 1.9E+02 0.0041 28.8 5.5 74 90-167 9-92 (138)
131 TIGR02719 repress_PhaQ poly-be 20.6 2.2E+02 0.0047 29.5 5.7 76 89-168 23-106 (138)
132 PRK14966 unknown domain/N5-glu 20.2 67 0.0014 38.7 2.3 28 338-365 303-330 (423)
No 1
>KOG2098|consensus
Probab=100.00 E-value=7.2e-111 Score=923.60 Aligned_cols=476 Identities=42% Similarity=0.695 Sum_probs=419.3
Q ss_pred CchhHHHHHHHHHhhHHHHHHHHHhhhhhhh-hhccCCC--CCCCCCcCCccccccCcccchhccCCchHHHHHhhhccC
Q psy17828 1 MSDAWEEIQAIKSKRNSLREKLQKRKQERKD-ILERDGS--LSPARNEEDSVDTSYQTEEDAIKLNPDLELELLEKLCDV 77 (1061)
Q Consensus 1 msd~w~~iqa~k~~~~~lre~l~~r~~~~~~-~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 77 (1061)
||||| ++||||+++++||||||||||+... ++++++. +.|+ -++++.++ ++++++. ++.|+
T Consensus 1 m~d~~-d~~a~~t~~~~lr~rle~r~k~~d~hldl~~~~~~lv~~---------~~~s~d~v----l~a~sS~--~~lp~ 64 (591)
T KOG2098|consen 1 MSDTW-DSQAHKTQLDSLRERLERRRKQDDGHLDLRNPEAALVPT---------LFRSDDPV----LTAPSSG--GPLPS 64 (591)
T ss_pred CCcch-hhhhHHHHHHHHHHHHHHhhcccccchhhcCchhhhchh---------hhhccchh----hhccccC--CCCCc
Confidence 99999 6699999999999999999999444 6666644 4333 47888876 6676664 67778
Q ss_pred CcchhhhccCChhHHHH-HHHHhhccccccccchHHHHhhhhh---hhhHHHHHHHHHHhhccCcEeeecccC-CCC-ce
Q psy17828 78 SLTEEDAIKLNPDLELE-LLEKLCDVSLVLPITSQSLMGTLNQ---EYTHLCLINLLHKFATQKLITINESKD-DDN-QV 151 (1061)
Q Consensus 78 ~~~~~~~~~~d~~~e~~-ll~~L~d~~l~lP~~s~~l~~~~~~---~~~~~~v~~lL~k~a~q~lI~i~~~~~-~~~-~~ 151 (1061)
.++..+++..|+|+|+. +|++|+|..+.+|++-..++..+.. |.++..|..+|+++++|.+++.+.... ++. +.
T Consensus 65 vas~v~e~~~~~elekl~~~~~~a~q~~~~~~dl~~~cl~~sv~~~p~~~~~vl~~lndqn~~~ae~a~r~~~~dd~~pi 144 (591)
T KOG2098|consen 65 VASAVPELATDPELEKLRLLHHLADQALTLPTDLVSICLAISVPDAPATQDGVLSLLNDQNAQEAEEAKRGLLQDDAHPI 144 (591)
T ss_pred hhhcCcccccChHHHHHhhhhhhhhhhccCcHHhhhhheEecCCCCccchhHHHHHhhhhhhhhhhhhhhhhhcccccch
Confidence 88899999999999998 9999999999999999998888866 667899999999999999999998888 444 99
Q ss_pred EEEEeehHhHHhHHHHhhh--h----------hccccCCCCC-----------------CCcchhhhhhccCC-CC--hh
Q psy17828 152 EIVSVEHVKLLGMVNEVSK--G----------IKRKADTDTS-----------------DYEDDEDLKKFKDN-GD--ET 199 (1061)
Q Consensus 152 ~i~~~~~~kl~~m~~~~~~--~----------~kr~~~~~~s-----------------~~~~~e~~~k~~~~-~~--~~ 199 (1061)
.++..+++++.+++++++. | .+|++++++. ..+..+..+|++++ .+ ..
T Consensus 145 l~~~~~~~~~a~k~~s~~~~~g~~~vm~l~t~p~~~~eqds~qv~e~~l~lln~~~~sa~~p~~d~~~~~r~h~~~~v~~ 224 (591)
T KOG2098|consen 145 LVTYADHSKLAAKMGSVAEKKGPGEVMGLVTGPKRRAEQDSTQVAEFALSLLNGLNSSASEPAKDPAKKFRKHAASDVML 224 (591)
T ss_pred hhhHHHHHHHHHhccchhhccCCcceeeeecCchhhhhHHHHHHHHHHHHHHhccCccccCCCCCchhccCCcchhHHHH
Confidence 9999999999999999872 2 4555555422 23446667778876 32 78
Q ss_pred hhHhhhCCcchHHHHHHHHhHHHHHhcCCccHHHHHHHHHHHhhcCcccccccCccCHHHHhhcCCCccccccccccccc
Q psy17828 200 DVMSLLSKPSIREKQVKQIGEEILDLLTKPTAKERSLAERFRSQSGNQVQEYCSHGTRAECLRMKDTPNICTKLHFRKII 279 (1061)
Q Consensus 200 ~~e~Ll~~~s~~e~~~~~~~~e~~~ll~~~ta~e~~~~~~f~~~~~~~~~e~c~~~t~~~c~~~~~~~~~c~k~hf~~~i 279 (1061)
++|.||+++|++|++++++++|+++|+..+||+|.+..++|+++|++||+++|.++|+++|+.++++..+|+|+||+|||
T Consensus 225 ~ve~L~~qqst~e~~~~k~~~e~lelip~~ta~e~at~~~~k~~~~aqvi~~c~~~tke~c~~~s~~~~~c~KlHFrriI 304 (591)
T KOG2098|consen 225 EVESLLNQQSTKEQQSKKVSQEILELIPTTTAKEQATVEKFKSRGRAQVIEFCDYGTKEECMKASDADRPCRKLHFRRII 304 (591)
T ss_pred HHHHHHcCccHHHHHHHhhhhHHHHhcCCCchhhhhhhhhhhhhhhhhhhhhhccccHhhhhccccccchhhhhHHHhhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCCCcCCCCCCCCccceeeeeecCccCC-C--CCCCcc----ccccc---ccccccCCCCceecccCccCc
Q psy17828 280 QCHTDESLGDCSFLNTCFHMDSCKYVHYEVDGAKIKG-I--SDISDE----GNKSL---LEKTKLYPPQWIQCDLRYLDM 349 (1061)
Q Consensus 280 ~~htd~~lgdcs~L~tc~~~~tC~y~hy~~~~~~~~~-~--~~~~~~----~~~~~---~~~~~~~Ppq~i~cDlr~~d~ 349 (1061)
++|||+||||||||||||||+|||||||++|.+.... . .+.+.+ ...++ .+...++|||||+||||+|||
T Consensus 305 ~~hTD~SLGDCSfLnTC~hm~TCkYVHYe~d~~~~~~a~~~~~t~~k~~l~~~rsv~~~ss~~~l~p~QWI~CDiR~~dm 384 (591)
T KOG2098|consen 305 NKHTDESLGDCSFLNTCFHMDTCKYVHYEIDACMDSEAPGSKDTTPKQELALTRSVGGDSSADRLFPPQWICCDIRYLDM 384 (591)
T ss_pred ccccccccccchhHhhhhhhcccceeeeecccchhhhcCCCCCCChhhhhcccccccccccccccCCcceEEeeceeeee
Confidence 9999999999999999999999999999999998763 2 222211 12222 245569999999999999999
Q ss_pred ccCCCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEEecCccchHHHHHHhhcccee--ccceeEEEc--
Q psy17828 350 TVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAMELGRECLKLFMLQ--DEGLLFLWV-- 425 (1061)
Q Consensus 350 ~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~Le~g~elL~~WGf~--~et~~ivWV-- 425 (1061)
++||||.||||||||++||++||+||+++||+.|||+.||++|++||||||++||+|||||..|||+ ++ ++||
T Consensus 385 ~iLGkFaVVmADPpWdIHMeLPYGTm~DdEmr~L~vp~LQddGlIFLWVTGRAmELGrecLnlWGY~rVdE---iiWVKT 461 (591)
T KOG2098|consen 385 SILGKFAVVMADPPWDIHMELPYGTMTDDEMRRLNVPVLQDDGLIFLWVTGRAMELGRECLNLWGYERVDE---IIWVKT 461 (591)
T ss_pred eeeceeEEEeeCCCccceeecCccccchHHhhcCCCcccccCcEEEEEEcchHHHHHHHHHHhhchhhhhe---eEEEee
Confidence 9999999999999999999999999999999999999999999999999999999999999999999 77 9999
Q ss_pred -----------CCcccccCeE-EEe------cccccCCCccEEEecCCCCCccCCcccchhhhhhhccchhhh---cccc
Q psy17828 426 -----------TGRAMELGRE-CLK------LSLNCQLSQDVEFTWPYLGWMSKFSLHHFFQVVYLAAMIRSI---IALH 484 (1061)
Q Consensus 426 -----------tG~~l~~~kE-CLv------~~i~~nid~DVIvsep~~g~s~Kp~l~~~~~iE~f~~~~Rrl---gr~~ 484 (1061)
||+||+|+|| ||| .|+|+++||||||++.+.. |+||. |+|-+||.+.++.|+| ||+|
T Consensus 462 NQLqRiIrTGRTGHWLNH~KEHcLVG~KGNP~~~Nr~iD~DvIVaevReT-S~KPD-EiYgmiERlsp~tRKiElFgR~H 539 (591)
T KOG2098|consen 462 NQLQRIIRTGRTGHWLNHGKEHCLVGVKGNPQGFNRGLDCDVIVAEVRET-SHKPD-EIYGMIERLSPGTRKIELFGRPH 539 (591)
T ss_pred chhhhheecCccccccccCcceeEeeeccChhhhccCCCcceeehhhhhh-cCCcH-HHHHHHHHhCCCcceeeeecCcc
Confidence 5669999999 999 5799999999999996666 78886 7788999999999997 9999
Q ss_pred ccCCCccccCCcc
Q psy17828 485 NLINNKITNRDAE 497 (1061)
Q Consensus 485 nlr~gWvT~g~~~ 497 (1061)
|++|||+|+|++.
T Consensus 540 N~~p~WiTlGNQL 552 (591)
T KOG2098|consen 540 NVQPNWITLGNQL 552 (591)
T ss_pred CCCCCeEEecccc
Confidence 9999999999885
No 2
>KOG1556|consensus
Probab=100.00 E-value=4.1e-59 Score=485.38 Aligned_cols=238 Identities=67% Similarity=1.077 Sum_probs=220.2
Q ss_pred CcccceEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHH
Q psy17828 632 EVVTSKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGM 711 (1061)
Q Consensus 632 ~~~~~~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~Mlem 711 (1061)
+.+..+|.|||||||+++|||+|.++. +++||+|+|||..+++ +|+|+||||+||+||+++.++||+||+|+++|++|
T Consensus 5 ~~~~~kViVhPLVLLS~VDhynR~~k~-~~KRvvGvLLG~~~~~-~i~vtnSfAvpFeEDdk~~svWFlDh~Y~esM~~m 82 (309)
T KOG1556|consen 5 ELTVEKVIVHPLVLLSAVDHYNRVGKD-TNKRVVGVLLGSWNGD-VIDVTNSFAVPFEEDDKDKSVWFLDHNYIESMFGM 82 (309)
T ss_pred ccccceeeeehhHHHHHHHHHhhhccC-cCceEEEEEEecCCCC-eEEeecceeccccccCCCCceEEeccHHHHHHHHH
Confidence 456789999999999999999999874 4599999999999874 89999999999999999999999999999999999
Q ss_pred HHhhcCCCceEEEEecCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEecccccCCCCCCCCCCCCcccc
Q psy17828 712 FKKVNAREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEDKIRPEREPNPRPSANKA 791 (1061)
Q Consensus 712 fKkVnp~E~VVGWYsTGp~ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv~e~~~~~g~e~~~~~~~~~a 791 (1061)
|+|||++|++||||||||+++++|+.|+++|.+|++||+++++|..
T Consensus 83 fkKvNakekivGWYhTGPkl~~nDl~In~l~k~y~pnpvLvIIdvk---------------------------------- 128 (309)
T KOG1556|consen 83 FKKVNAKEKVVGWYHTGPKLRENDLDINELLKRYVPNPVLVIIDVK---------------------------------- 128 (309)
T ss_pred HHHhcchhheeeeeccCCccccchhhHHHHHhhcCCCceEEEEecc----------------------------------
Confidence 9999999999999999999999999999999999998888877653
Q ss_pred cccccccCCCCCccccccccCCCCccccccccccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCC
Q psy17828 792 AIGKWKTNTTPNKAFLCGRSSRGGKVGRIRCRSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPK 871 (1061)
Q Consensus 792 ~~~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGse 871 (1061)
T Consensus 129 -------------------------------------------------------------------------------- 128 (309)
T KOG1556|consen 129 -------------------------------------------------------------------------------- 128 (309)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCchHHHHHHHHhhcCCceEEEEcCCCCCCCCCceeEEEeeeccCCCCcceeeEEeecccccccccccccccccccccc
Q psy17828 872 LHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEEAEEVGVEHLLRDIK 951 (1061)
Q Consensus 872 lt~~s~lIHefys~~~~~PIhL~VDt~~~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeEAErIgVEhLlr~i~ 951 (1061)
+++-+||+.||++++++++||+++.++|+|+|++|+++|||+||||||+|+++
T Consensus 129 ---------------------------pk~~gLPT~AY~aVeev~dDgt~t~ktF~Hvps~I~AeEAEEvGVEHLlRDik 181 (309)
T KOG1556|consen 129 ---------------------------PKELGLPTEAYIAVEEVKDDGTPTSKTFVHVPSEIEAEEAEEVGVEHLLRDIK 181 (309)
T ss_pred ---------------------------cccCCCCchheeeeeeeecCCCCccceeEecCcccchhHHHHhhHHHHHHHHH
Confidence 33456888999999999999999999999999999999999999999999999
Q ss_pred ccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhc-CCCCHHHHHHHHhhccccccCCCcc
Q psy17828 952 DTTVGSLSQRVTNQLMGLKGLNQQIKEIEKYVGQVSRY-WPPFYVVVINLIDKRSVTHLSGPGR 1014 (1061)
Q Consensus 952 dat~s~L~s~l~~~~~aLk~L~~rL~~I~~YLd~V~~g-vpp~~~ilr~l~~~~~~~~~~~~gr 1014 (1061)
|+++|+|++++++++.+|++|..+|.+|.+||++|.+| +|.||.||+.+|+.++ .+|.++|
T Consensus 182 d~t~gtla~rit~ql~sLkgl~~~L~eI~~YL~~Vi~g~lpiNh~Il~~lQdvfN--llP~l~~ 243 (309)
T KOG1556|consen 182 DTTVGTLATRITNQLMSLKGLQSRLREIRSYLDKVIDGKLPINHEILYQLQDVFN--LLPNLTR 243 (309)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHh--hCccccc
Confidence 99999999999999999999999999999999999999 9999999999999643 3456666
No 3
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=100.00 E-value=1.7e-48 Score=423.61 Aligned_cols=226 Identities=72% Similarity=1.152 Sum_probs=200.1
Q ss_pred ceEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhh
Q psy17828 636 SKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKV 715 (1061)
Q Consensus 636 ~~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkV 715 (1061)
.+|+|||||||+|+|||+|+.. +.+.+|+|+|||.+.+ ++|+|+|||++|+++++++.++|++|++|+++|++|||+|
T Consensus 1 ~~V~ihplVLl~I~dh~~R~~~-~~~~~ViG~LLG~~~~-~~veItnsF~~p~~~~~~~~~~~~~d~~y~~~m~~~~kkv 78 (280)
T cd08062 1 KKVVVHPLVLLSVVDHYNRVAK-GTSKRVVGVLLGSWKK-GVLDVTNSFAVPFEEDEKDPSVWFLDHNYLENMYGMFKKV 78 (280)
T ss_pred CeEEEehHHHHHHHHHHhhhcC-CCCceEEEEEEEEEeC-CEEEEEEeeecCccCCCCCcchhhhhHHHHHHHHHHHHHh
Confidence 3799999999999999999765 5578999999999986 5899999999999988877778999999999999999999
Q ss_pred cCCCceEEEEecCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEecccccCCCCCCCCCCCCcccccccc
Q psy17828 716 NAREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEDKIRPEREPNPRPSANKAAIGK 795 (1061)
Q Consensus 716 np~E~VVGWYsTGp~ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv~e~~~~~g~e~~~~~~~~~a~~~~ 795 (1061)
||+|.+||||+|||+++++|+.||++|++++++||+|++||....++||++||+++
T Consensus 79 ~~~e~vVGWY~tg~~~~~~d~~ih~~~~~~~~~pv~l~vd~~~~~~~lpi~aY~s~------------------------ 134 (280)
T cd08062 79 NAKEKIVGWYSTGPKLRPNDLDINELFRRYCPNPVLVIIDVRPKDLGLPTEAYIAV------------------------ 134 (280)
T ss_pred CCCCCeEEEecCCCCCCcchHHHHHHHHHhCCCCEEEEEecCCCCCCCceEEEEEe------------------------
Confidence 99999999999999999999999999999998888888888665545555555554
Q ss_pred cccCCCCCccccccccCCCCccccccccccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCCCCCc
Q psy17828 796 WKTNTTPNKAFLCGRSSRGGKVGRIRCRSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPKLHQN 875 (1061)
Q Consensus 796 ~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGselt~~ 875 (1061)
T Consensus 135 -------------------------------------------------------------------------------- 134 (280)
T cd08062 135 -------------------------------------------------------------------------------- 134 (280)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hHHHHHHHHhhcCCceEEEEcCCCCCCCCCceeEEEeeeccCCCCcceeeEEeecccccccccccccccccccccccccc
Q psy17828 876 DIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEEAEEVGVEHLLRDIKDTTV 955 (1061)
Q Consensus 876 s~lIHefys~~~~~PIhL~VDt~~~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeEAErIgVEhLlr~i~dat~ 955 (1061)
.+...+|......|+++|++|+++|||||||||++|++.+.+.
T Consensus 135 -------------------------------------~~~~~~g~~~~~~F~~vp~~i~~~eaE~igve~l~r~~~~~~~ 177 (280)
T cd08062 135 -------------------------------------EEVHDDGTPTSKTFVHVPSEIGAEEAEEVGVEHLLRDIKDVTV 177 (280)
T ss_pred -------------------------------------eeccCCCCcceeEEEEcceEeeccchHHHHHHHHHhhccCccc
Confidence 3333344435678999999999999999999999998887778
Q ss_pred ccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhc-CCCCHHHHHHHHhhc
Q psy17828 956 GSLSQRVTNQLMGLKGLNQQIKEIEKYVGQVSRY-WPPFYVVVINLIDKR 1004 (1061)
Q Consensus 956 s~L~s~l~~~~~aLk~L~~rL~~I~~YLd~V~~g-vpp~~~ilr~l~~~~ 1004 (1061)
+.+.+++.++.+|+++|+.||+.|.+||++|.+| +|+||.|+|.|++.+
T Consensus 178 ~~l~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~IlR~l~~~~ 227 (280)
T cd08062 178 STLSTRVTNKLNSLKGLQSKLKEIKDYLQLVVEGKLPINHQIIYNLQDIF 227 (280)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Confidence 8888899999999999999999999999999999 999999999999954
No 4
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=100.00 E-value=1.6e-48 Score=427.35 Aligned_cols=229 Identities=59% Similarity=0.968 Sum_probs=196.8
Q ss_pred cccceEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHH
Q psy17828 633 VVTSKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMF 712 (1061)
Q Consensus 633 ~~~~~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~Mlemf 712 (1061)
.+..+|+|||||||+|+|||+|+.+ +.+.||+|+|||.+.+ ++|||+|||++|+++++++.++|++|++|+++|+++|
T Consensus 3 ~~~~~V~vhPlVll~I~dh~~R~~~-~~~~rviG~LLG~~~~-~~ieItnsF~~p~~e~~~~~~~~~~D~~y~~~m~~~~ 80 (303)
T PLN03246 3 RGIEKVVVHPLVLLSIVDHYNRVAK-DTRKRVVGVLLGSSFR-GRVDVTNSFAVPFEEDDKDPSIWFLDHNYLESMFGMF 80 (303)
T ss_pred CCCcEEEECcHHHHHHHHHHHhccC-CCCCeeEEEEEeeecC-CEEEEEeccccCcccCCCCccceeecHHHHHHHHHHH
Confidence 3567899999999999999999764 4568999999999976 5899999999999888776677999999999999999
Q ss_pred HhhcCCCceEEEEecCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEecccccCCCCCCCCCCCCccccc
Q psy17828 713 KKVNAREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEDKIRPEREPNPRPSANKAA 792 (1061)
Q Consensus 713 KkVnp~E~VVGWYsTGp~ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv~e~~~~~g~e~~~~~~~~~a~ 792 (1061)
|+|||++.+||||+||++++++|+.||++|++++++||+|++|+....++||++||+++
T Consensus 81 k~V~~~~~vVGWY~tg~~i~~~d~~IH~~~~~~~~~Pv~L~vD~~~~~~~lpi~aY~s~--------------------- 139 (303)
T PLN03246 81 KRINAKEHVVGWYSTGPKLRENDLDIHELFNDYVPNPVLVIIDVQPKELGIPTKAYYAV--------------------- 139 (303)
T ss_pred HHhCCCCcEEeeecCCCCCCcchHHHHHHHHhhCCCCeEEEEecCCCCCCCceEEEEEE---------------------
Confidence 99999999999999999988888888888888877777777776554444555555554
Q ss_pred ccccccCCCCCccccccccCCCCccccccccccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCCC
Q psy17828 793 IGKWKTNTTPNKAFLCGRSSRGGKVGRIRCRSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPKL 872 (1061)
Q Consensus 793 ~~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGsel 872 (1061)
T Consensus 140 -------------------------------------------------------------------------------- 139 (303)
T PLN03246 140 -------------------------------------------------------------------------------- 139 (303)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCchHHHHHHHHhhcCCceEEEEcCCCCCCCCCceeEEEeeeccCCCC-cceeeEEeecccccccccccccccccccccc
Q psy17828 873 HQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHDDGS-PTTKTFDHVPSEIGAEEAEEVGVEHLLRDIK 951 (1061)
Q Consensus 873 t~~s~lIHefys~~~~~PIhL~VDt~~~~~~LPi~AYvsv~ev~~dGs-~~~k~Fv~VP~~I~aeEAErIgVEhLlr~i~ 951 (1061)
.++..+|. .....|+++|++|+++|||||||+|++|++.
T Consensus 140 ----------------------------------------~~~~~~~~~~~~~~F~~vp~~i~~~EaE~Igve~l~r~~~ 179 (303)
T PLN03246 140 ----------------------------------------EEVKENATQKSQKVFVHVPSEIGAHEAEEIGVEHLLRDVK 179 (303)
T ss_pred ----------------------------------------EeccCCCCcccccEEEECCeeeeecCHHHHHHHHHHhccc
Confidence 33322222 2345799999999999999999999999988
Q ss_pred ccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhc-CCCCHHHHHHHHhhc
Q psy17828 952 DTTVGSLSQRVTNQLMGLKGLNQQIKEIEKYVGQVSRY-WPPFYVVVINLIDKR 1004 (1061)
Q Consensus 952 dat~s~L~s~l~~~~~aLk~L~~rL~~I~~YLd~V~~g-vpp~~~ilr~l~~~~ 1004 (1061)
+.+.+.+.+++.++.+|+++|..||+.|.+||++|.+| +|+||.|+|.|++.+
T Consensus 180 ~~~~s~l~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~IlR~l~~l~ 233 (303)
T PLN03246 180 DTTVSTLATEVTGKLTALKGLDARLREIRSYLDLVVEGKLPLNHEILYHLQDVF 233 (303)
T ss_pred CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHH
Confidence 87888889999999999999999999999999999999 999999999999954
No 5
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=100.00 E-value=1.1e-44 Score=395.03 Aligned_cols=222 Identities=31% Similarity=0.507 Sum_probs=194.5
Q ss_pred eEEEeehhHhhHHHHHhhccccCC--ceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHh
Q psy17828 637 KVVVHPLVLLSVVDHFNRMSKIGN--QKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKK 714 (1061)
Q Consensus 637 ~V~VHPLVLLsIsDH~tR~~~~~~--~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKk 714 (1061)
+|+|||||||+|+|||+|+..... +.+|+|+|||.+.+ ++|+|+|||++|++++++ +.|++|++|+++|++|||+
T Consensus 2 ~V~lHPlVll~I~dH~~R~~~~~~~~~~~v~G~LLG~~~~-~~veItnsF~~p~~~~~~--~~~~id~~y~~~m~~~~kk 78 (288)
T cd08063 2 SVKLHPLVILNISDHITRHRAQSQSEPPRVVGALLGQQDG-REIEIENSFELKYDTNED--GEIVLDKEFLETRLEQFKQ 78 (288)
T ss_pred eEEEecceeeeHHhhHhHHhccCCCCCCcEEEEEEEEEcC-CEEEEEEEEecccccCCC--CceeeCHHHHHHHHHHHHH
Confidence 799999999999999999875433 68999999999876 579999999999988762 3589999999999999999
Q ss_pred hcCCCceEEEEecCCC-CCcccHHHHHHHHhhCCCcEEEEEcCCCC--CCCcceEEEEecccccCCCCCCCCCCCCcccc
Q psy17828 715 VNAREKVVGWYHTGPK-LHQNDIQINELIRRYCTNSVLVIIDAKPK--ELGLPTEAYRVVDEDKIRPEREPNPRPSANKA 791 (1061)
Q Consensus 715 Vnp~E~VVGWYsTGp~-ls~~Dl~Ihe~f~~~~~nPI~LivDPs~s--s~gLplKAYrlv~e~~~~~g~e~~~~~~~~~a 791 (1061)
|||++.+||||+||+. ++.+|+.||++|.+++++||+|++||... .++||++||+++.+
T Consensus 79 V~~~~~vVGWY~tg~~~~~~~~~~Ih~~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s~~~------------------ 140 (288)
T cd08063 79 VFKDLDFVGWYTTGPGGPTESDLPIHKQILEINESPVLLLLDPEANASGKDLPVTIYESVLE------------------ 140 (288)
T ss_pred hccCCceEEEEecCCCCCCHHHHHHHHHHHhhCCCcEEEEEccccccCCCCCceeEEEEEEe------------------
Confidence 9999999999999999 99999999999999999999999999773 44577777776643
Q ss_pred cccccccCCCCCccccccccCCCCccccccccccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCC
Q psy17828 792 AIGKWKTNTTPNKAFLCGRSSRGGKVGRIRCRSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPK 871 (1061)
Q Consensus 792 ~~~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGse 871 (1061)
T Consensus 141 -------------------------------------------------------------------------------- 140 (288)
T cd08063 141 -------------------------------------------------------------------------------- 140 (288)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred CCCchHHHHHHHHhhcCCceEEEEcCCCCCCCCCceeEEEeeeccCCCCcceeeEEeeccccccccccccccccccccc-
Q psy17828 872 LHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEEAEEVGVEHLLRDI- 950 (1061)
Q Consensus 872 lt~~s~lIHefys~~~~~PIhL~VDt~~~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeEAErIgVEhLlr~i- 950 (1061)
. .+| .....|+++|++|+++|||||||+|++|+.
T Consensus 141 -------------------------------------------~-~~~-~~~~~F~~i~~~i~~~eaErIgv~~l~~~~~ 175 (288)
T cd08063 141 -------------------------------------------L-VDG-EATLRFRELPYTIETGEAERIGVDHVARGGA 175 (288)
T ss_pred -------------------------------------------c-cCC-ccccEEEeeeeEEEeccCceeeHHHHHhcCC
Confidence 1 111 223569999999999999999999999987
Q ss_pred -cccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhc-CCCCHHHHHHHHhhc
Q psy17828 951 -KDTTVGSLSQRVTNQLMGLKGLNQQIKEIEKYVGQVSRY-WPPFYVVVINLIDKR 1004 (1061)
Q Consensus 951 -~dat~s~L~s~l~~~~~aLk~L~~rL~~I~~YLd~V~~g-vpp~~~ilr~l~~~~ 1004 (1061)
.+.+.+.+.+++..+.+|+++|..||+.|.+||++|.+| +|+|+.|+|.|++.+
T Consensus 176 ~~~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl~~V~~g~~~~d~~ilR~l~~~~ 231 (288)
T cd08063 176 SGSSEKSTVAAHLQAQHNAIKMLNSRVELILEYLKAVPVGEVPPDHSILRSISALC 231 (288)
T ss_pred CCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHH
Confidence 445566678999999999999999999999999999999 999999999999953
No 6
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=100.00 E-value=7.3e-44 Score=384.31 Aligned_cols=218 Identities=28% Similarity=0.494 Sum_probs=194.0
Q ss_pred EEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcC
Q psy17828 638 VVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNA 717 (1061)
Q Consensus 638 V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp 717 (1061)
|+|||||||+|+|||+|++ ..+.+|+|+|||.+.+ ++|+|||||++|++++++ .|++|++|+++|+++||+|||
T Consensus 1 v~ihPlVll~I~dH~~R~~--~~~~~V~G~LLG~~~~-~~veItnsF~~p~~~~~~---~~~~d~~y~~~m~~~~kkv~~ 74 (265)
T cd08064 1 VRVHPVVLFSILDSYERRN--EGQERVIGTLLGTRSE-GEVEITNCFAVPHNESED---QVAVDMEYHRTMYELHQKVNP 74 (265)
T ss_pred CEEccHHHHhHHHHHhhhc--CCCcEEEEEEEEEEeC-CEEEEEeCeecceeCCCC---eEEEcHHHHHHHHHHHHHhCC
Confidence 6899999999999999975 3568999999999986 689999999999988765 389999999999999999999
Q ss_pred CCceEEEEecCCCCCcccHHHHHHHHhhCC--CcEEEEEcCCCCCCCcceEEEEecccccCCCCCCCCCCCCcccccccc
Q psy17828 718 REKVVGWYHTGPKLHQNDIQINELIRRYCT--NSVLVIIDAKPKELGLPTEAYRVVDEDKIRPEREPNPRPSANKAAIGK 795 (1061)
Q Consensus 718 ~E~VVGWYsTGp~ls~~Dl~Ihe~f~~~~~--nPI~LivDPs~ss~gLplKAYrlv~e~~~~~g~e~~~~~~~~~a~~~~ 795 (1061)
++.+||||+||+.++++|..||++|+++++ +||+|++||..+++++|++||++++...
T Consensus 75 ~~~vVGWY~tg~~~~~~~~~Ih~~~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~~~~-------------------- 134 (265)
T cd08064 75 KEVIVGWYATGSEITEHSALIHDYYSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSPLGV-------------------- 134 (265)
T ss_pred CCcEEeeeeCCCCCCccHHHHHHHHHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEeccc--------------------
Confidence 999999999999999999999999999998 9999999998887789999998875410
Q ss_pred cccCCCCCccccccccCCCCccccccccccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCCCCCc
Q psy17828 796 WKTNTTPNKAFLCGRSSRGGKVGRIRCRSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPKLHQN 875 (1061)
Q Consensus 796 ~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGselt~~ 875 (1061)
T Consensus 135 -------------------------------------------------------------------------------- 134 (265)
T cd08064 135 -------------------------------------------------------------------------------- 134 (265)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred hHHHHHHHHhhcCCceEEEEcCCCCCCCCCceeEEEeeeccCCCCcceeeEEeecccccccccccccccccccccccccc
Q psy17828 876 DIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEEAEEVGVEHLLRDIKDTTV 955 (1061)
Q Consensus 876 s~lIHefys~~~~~PIhL~VDt~~~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeEAErIgVEhLlr~i~dat~ 955 (1061)
.+......|+++|++|.++|||||||+|++++..+.+.
T Consensus 135 ------------------------------------------~~~~~~~~F~~ip~~i~~~eaE~i~v~~l~~~~~~~~~ 172 (265)
T cd08064 135 ------------------------------------------PGKTLGSMFVPIPLELLYSEAERVALDLLAKTLASPSR 172 (265)
T ss_pred ------------------------------------------CCCCcceEEEEcceeeecCcHHHHHHHHHHhhccCCcc
Confidence 00012346999999999999999999999998876544
Q ss_pred c-cchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhc-CCCCHHHHHHHHhh
Q psy17828 956 G-SLSQRVTNQLMGLKGLNQQIKEIEKYVGQVSRY-WPPFYVVVINLIDK 1003 (1061)
Q Consensus 956 s-~L~s~l~~~~~aLk~L~~rL~~I~~YLd~V~~g-vpp~~~ilr~l~~~ 1003 (1061)
+ .+.+++..+.+++++|..+|+.|.+||++|.+| .|+|+.|+|.|++.
T Consensus 173 ~~~~~~~l~~~~~al~~L~~~l~~i~~Yl~~V~~g~~~~d~~i~r~l~~~ 222 (265)
T cd08064 173 SAPLTSDLEQLEASLEKLQEMLDRVLRYVEDVLAGKVKADNAIGRYLMDA 222 (265)
T ss_pred cccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 3 467899999999999999999999999999998 99999999999994
No 7
>KOG2975|consensus
Probab=100.00 E-value=3.9e-44 Score=377.39 Aligned_cols=228 Identities=28% Similarity=0.407 Sum_probs=200.3
Q ss_pred ccCCCcccceEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHH
Q psy17828 628 MVGQEVVTSKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLEN 707 (1061)
Q Consensus 628 ~~~~~~~~~~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~ 707 (1061)
++.+.....+|.|||+|+++|+|||.|+. .++.||||+|||+.. +|.|||||||++||.|.+++ ..+|.+|..+
T Consensus 13 ~~~~~ss~ltv~ihP~Vlf~ivD~~~RR~--~~~~rviGTLLG~~~-~g~ieitNCFaVPhnEssdq---vevdm~y~~~ 86 (288)
T KOG2975|consen 13 LPSPFSSNLTVRLHPVVLFSIVDAYERRN--KGAERVIGTLLGTVD-KGSVEVTNCFAVPHNESSDQ---VEVDMEYAKN 86 (288)
T ss_pred CCCCCCCCceEEEcceEEeEeehhhhcCC--ccchhhhhheeeccc-CCeEEEEEeeeccCcccccc---ceeeHHHHHH
Confidence 44455667899999999999999999976 467899999999986 57899999999999998765 5788888877
Q ss_pred HHHHHHhhcCCCceEEEEecCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEecccccCCCCCCCCCCCC
Q psy17828 708 MYGMFKKVNAREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEDKIRPEREPNPRPS 787 (1061)
Q Consensus 708 MlemfKkVnp~E~VVGWYsTGp~ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv~e~~~~~g~e~~~~~~ 787 (1061)
|+++
T Consensus 87 M~~l---------------------------------------------------------------------------- 90 (288)
T KOG2975|consen 87 MYEL---------------------------------------------------------------------------- 90 (288)
T ss_pred HHHH----------------------------------------------------------------------------
Confidence 7754
Q ss_pred cccccccccccCCCCCccccccccCCCCccccccccccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeec
Q psy17828 788 ANKAAIGKWKTNTTPNKAFLCGRSSRGGKVGRIRCRSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYH 867 (1061)
Q Consensus 788 ~~~a~~~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYs 867 (1061)
|+|+||+|.|||||+
T Consensus 91 -----------------------------------------------------------------~~k~npnE~vvGWya 105 (288)
T KOG2975|consen 91 -----------------------------------------------------------------HKKVNPNELVVGWYA 105 (288)
T ss_pred -----------------------------------------------------------------hcccCCCceeEEEEe
Confidence 456666677777788
Q ss_pred cCCCCCCchHHHHHHHHhhcCCceEEEEcCCCCCCCCCceeEEEeeeccCCCCcceeeEEeecccccccccccccccccc
Q psy17828 868 TGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEEAEEVGVEHLL 947 (1061)
Q Consensus 868 TGselt~~s~lIHefys~~~~~PIhL~VDt~~~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeEAErIgVEhLl 947 (1061)
||+.++.++++|||||.++|++||||+|||.++++.++++||+++. ++..|.....+|.++|+++...+||++|++.+.
T Consensus 106 Tg~dvt~~sslihdyYare~~~pvhLtVDT~~~n~rm~ikaYvss~-~Gvpg~~~~~mF~plpvel~~~~~ervgl~li~ 184 (288)
T KOG2975|consen 106 TGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQNGRMSIKAYVSSL-MGVPGRTMGVMFTPLPVELAYYDAERVGLDLIE 184 (288)
T ss_pred cCCCcccchhHHHHHhhccCCCCeEEEEeccccCCccceeEEEEec-cCCCCcccceeeeeeeeEEeecchhhhHHHHHH
Confidence 8888888999999999999999999999999999999999999877 777777777799999999999999999999999
Q ss_pred cccccc-ccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhc-CCCCHHHHHHHHhh
Q psy17828 948 RDIKDT-TVGSLSQRVTNQLMGLKGLNQQIKEIEKYVGQVSRY-WPPFYVVVINLIDK 1003 (1061)
Q Consensus 948 r~i~da-t~s~L~s~l~~~~~aLk~L~~rL~~I~~YLd~V~~g-vpp~~~ilr~l~~~ 1003 (1061)
+...++ ...+|.+++++...|...|+.+|+.++.|+++|++| ++||+.|-|.|++.
T Consensus 185 kt~~sp~r~~~l~~dLqQv~~at~~l~~~L~~Vl~YVedVl~gk~~pdn~VGR~Lmd~ 242 (288)
T KOG2975|consen 185 KTSFSPSRVAGLSSDLQQVEGATARLQSLLERVLKYVEDVLAGKVKPDNAVGRFLMDL 242 (288)
T ss_pred HhccChhhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCcchHHHHHHHH
Confidence 887543 345688899999999999999999999999999998 99999999999983
No 8
>KOG2097|consensus
Probab=100.00 E-value=2.5e-39 Score=345.09 Aligned_cols=205 Identities=22% Similarity=0.371 Sum_probs=177.5
Q ss_pred ccccccCCCCceecccCccCcccCC-CccEEEECCCccccc------cCCCCCCChHHHhcCCccccCC-CcEEEEecC-
Q psy17828 329 LEKTKLYPPQWIQCDLRYLDMTVLG-KFAVIMADPPWDIHM------ELPYGTMSDDEMRQLGIPQLQD-EGLLFLWVT- 399 (1061)
Q Consensus 329 ~~~~~~~Ppq~i~cDlr~~d~~~lg-kFdvIlaDPPW~~~~------~~~Y~tms~deI~~LPV~~La~-~g~LFLWvT- 399 (1061)
++...+++|+|+++||..+|.+.+| |||||+.+|||+++. ...-..|+|++|.+|||+.|++ +|||||||+
T Consensus 134 ~I~~sataPmylk~di~si~~~~l~~kfdvil~~pp~eeyv~~~g~~t~n~~fw~~~di~nL~id~iaa~psFlFlW~gs 213 (397)
T KOG2097|consen 134 LINQSATAPMYLKADIDSIDPTLLGNKFDVILNEPPLEEYVRMAGCLTENMQFWTWDDIQNLPIDEIAAKPSFLFLWCGS 213 (397)
T ss_pred HHhhccCCCceeecccceeehhhcccceeeeecCCcHHHHHHhccccccCceEecHHHhhcCchhhhccCCceEEEEecC
Confidence 4788999999999999999999887 999999999999652 2345789999999999999975 999999999
Q ss_pred ccchHHHHHHhhcccee--ccceeEEEc------CCc--------ccccCeE-EEe------------cccccCCCccEE
Q psy17828 400 GRAMELGRECLKLFMLQ--DEGLLFLWV------TGR--------AMELGRE-CLK------------LSLNCQLSQDVE 450 (1061)
Q Consensus 400 ~~~Le~g~elL~~WGf~--~et~~ivWV------tG~--------~l~~~kE-CLv------------~~i~~nid~DVI 450 (1061)
+..+++++.||++|||| ++ |||| .|. .|+.++| ||| +++|||||+|||
T Consensus 214 ~egl~lgrnclkkwgfRRcEd---icwvktnk~np~ptl~~d~ktvfqrtkeHClMgIkGTVrRSTDGh~IHaNVDtDli 290 (397)
T KOG2097|consen 214 GEGLDLGRNCLKKWGFRRCED---ICWVKTNKNNPGPTLDLDPKTVFQRTKEHCLMGIKGTVRRSTDGHFIHANVDTDLI 290 (397)
T ss_pred chhHHHHHHHHHHhcccchhc---eEEEeccCCCCCCccCCChHHHHHHHHHhhhhcccceEEeccCCceEEeecccceE
Confidence 77999999999999999 88 9999 221 8899999 999 789999999999
Q ss_pred Eec-CCCCCccCCcccchhhhhhhccchhhh---ccccccCCCccccCCccccccccccccchhHHHHHHHHHHHHHHHh
Q psy17828 451 FTW-PYLGWMSKFSLHHFFQVVYLAAMIRSI---IALHNLINNKITNRDAEVNIEFNFSLQHFSQVVYLAAMIRSIIALH 526 (1061)
Q Consensus 451 vse-p~~g~s~Kp~l~~~~~iE~f~~~~Rrl---gr~~nlr~gWvT~g~~~Vniefnv~~Nd~~~~vYla~~~~~~~alh 526 (1061)
|+| |..|+.+||+ ++|++|||||+|+||| ||++++||||||+||+..+ -++|-...+-|+|.
T Consensus 291 I~ee~~~gn~~kP~-~iyrIiEhF~lgrRRLhlfg~ds~iRpGWltVgp~lt~----sNf~pe~Y~~~fa~--------- 356 (397)
T KOG2097|consen 291 IEEEPETGNGEKPS-EIYRIIEHFCLGRRRLHLFGRDSKIRPGWLTVGPDLTN----SNFNPERYKEYFAN--------- 356 (397)
T ss_pred eeccCCcCCCcChH-HHHHHHHHHhcceeeeeeccCcCcccCceEEeCccccc----cCCCHHHHHHHhcc---------
Confidence 998 8899999997 8899999999999998 9999999999999999854 34555566666664
Q ss_pred hhhcccccchhHHHHHhhhcccCCCCCCCC
Q psy17828 527 NLINNKITNRDAEKKEITKSKVEDKPQEDK 556 (1061)
Q Consensus 527 ~li~nk~~~~~~~~~~~~~~~~~~~~~~~~ 556 (1061)
..+.-.++.|.|..+++.++++.|
T Consensus 357 ------~p~~~~~t~eIElLRPkSP~~ksq 380 (397)
T KOG2097|consen 357 ------APSLTGCTNEIELLRPKSPPPKSQ 380 (397)
T ss_pred ------CcccccCchhhhhcCCCCCCcccc
Confidence 223346788888889988888776
No 9
>KOG3050|consensus
Probab=100.00 E-value=3.5e-36 Score=314.02 Aligned_cols=227 Identities=25% Similarity=0.412 Sum_probs=190.5
Q ss_pred CCCcccceEEEeehhHhhHHHHHhhccccCCc--eeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHH
Q psy17828 630 GQEVVTSKVVVHPLVLLSVVDHFNRMSKIGNQ--KRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLEN 707 (1061)
Q Consensus 630 ~~~~~~~~V~VHPLVLLsIsDH~tR~~~~~~~--~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~ 707 (1061)
+.+..+.+|.+||||++||+|||+|.+.+.++ ++|+|+|+|.|.|+ +|||.|||++.++..++. ..+|.+|+++
T Consensus 3 ps~S~s~tv~LHPLVImniSdH~tR~k~Q~gpp~~~VyGaliG~Q~GR-~vEi~NSFeL~~d~~~~~---~~~dke~l~k 78 (299)
T KOG3050|consen 3 PSSSGSVTVKLHPLVIMNISDHYTRVKTQLGPPVKQVYGALIGKQRGR-NVEIMNSFELKMDTEEDT---ETIDKEYLEK 78 (299)
T ss_pred CCCCCceeEEeccEEEEehhHHHHHHHhhcCCcHHHhhhhheecccCc-eEEEeeeeEEEecchhhh---hhccHHHHHH
Confidence 33455679999999999999999998764443 48999999999987 599999999998766543 3699999999
Q ss_pred HHHHHHhhcCCCceEEEEecCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEecccccCCCCCCCCCCCC
Q psy17828 708 MYGMFKKVNAREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEDKIRPEREPNPRPS 787 (1061)
Q Consensus 708 MlemfKkVnp~E~VVGWYsTGp~ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv~e~~~~~g~e~~~~~~ 787 (1061)
..++||+|||+..++|||+||...++.|+.||.+....+++|++|.++|...
T Consensus 79 k~eqykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~t~---------------------------- 130 (299)
T KOG3050|consen 79 KEEQYKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPATN---------------------------- 130 (299)
T ss_pred HHHHHHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecchhc----------------------------
Confidence 9999999999999999999999999999999999999999999998777322
Q ss_pred cccccccccccCCCCCccccccccCCCCccccccccccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeec
Q psy17828 788 ANKAAIGKWKTNTTPNKAFLCGRSSRGGKVGRIRCRSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYH 867 (1061)
Q Consensus 788 ~~~a~~~~~~~~~~~~~~~~~g~~~~~g~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYs 867 (1061)
||
T Consensus 131 --------------------------------------------------------~t---------------------- 132 (299)
T KOG3050|consen 131 --------------------------------------------------------HT---------------------- 132 (299)
T ss_pred --------------------------------------------------------cc----------------------
Confidence 10
Q ss_pred cCCCCCCchHHHHHHHHhhcCCceEEEEcCCCCCCCCCceeEEEeeeccCCCCcceeeEEeecccccccccccccccccc
Q psy17828 868 TGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEEAEEVGVEHLL 947 (1061)
Q Consensus 868 TGselt~~s~lIHefys~~~~~PIhL~VDt~~~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeEAErIgVEhLl 947 (1061)
...|+.+|++...+ .||. .+..|+|+.|+++++|||||||+|++
T Consensus 133 ----------------------------------~~~pv~lfese~dv-idg~-~q~~f~~~tytl~teEaERIgVdHVA 176 (299)
T KOG3050|consen 133 ----------------------------------DKDPVTLFESEIDV-IDGE-AQMLFVPLTYTLATEEAERIGVDHVA 176 (299)
T ss_pred ----------------------------------cCCCceeeeeehee-ecCc-ceeeeeeeEEEEeehhhhhccchhhe
Confidence 11256666665444 3554 35579999999999999999999999
Q ss_pred ccccc--cccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhc-CCCCHHHHHHHHh
Q psy17828 948 RDIKD--TTVGSLSQRVTNQLMGLKGLNQQIKEIEKYVGQVSRY-WPPFYVVVINLID 1002 (1061)
Q Consensus 948 r~i~d--at~s~L~s~l~~~~~aLk~L~~rL~~I~~YLd~V~~g-vpp~~~ilr~l~~ 1002 (1061)
+-... ...+++..++.++-.|++||+.|++.|.+||++|.+| ++||++|||.+..
T Consensus 177 ~lt~~~gge~s~VaeHl~AQdsA~~ml~~Rvklil~Y~k~~e~G~l~~N~eILrea~~ 234 (299)
T KOG3050|consen 177 RLTPSDGGEGSSVAEHLEAQDSAIKMLDNRVKLILAYLKKVEAGTLQPNFEILREAYA 234 (299)
T ss_pred eeccCCCCCcchHHHHHhhHHHHHHHHhhHHHHHHHHHhhhhcCCcCccHHHHHHHHH
Confidence 95432 2234568899999999999999999999999999999 9999999999877
No 10
>COG4725 IME4 Transcriptional activator, adenine-specific DNA methyltransferase [Signal transduction mechanisms / Transcription]
Probab=99.98 E-value=4e-33 Score=277.61 Aligned_cols=156 Identities=26% Similarity=0.372 Sum_probs=141.7
Q ss_pred CCceecccCccCcccCCCccEEEECCCccccccCCCCCCChHHHhcCCccccCC-CcEEEEecCccchHHHHHHhhccce
Q psy17828 337 PQWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQD-EGLLFLWVTGRAMELGRECLKLFML 415 (1061)
Q Consensus 337 pq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~-~g~LFLWvT~~~Le~g~elL~~WGf 415 (1061)
.|||.||+|+|||.++|||.|+++||.|..++++||++|+.+||++|||++||| +|++|||+|+++|+.+.|||++|||
T Consensus 1 ~q~~~~~~r~~~~~v~~~~~~~i~~~~~~~~~~~pY~~m~~~EilaLPv~~L~d~g~~i~lw~T~~hl~~~~ecL~~WGf 80 (198)
T COG4725 1 AQWIRCDVRKFDFRVLGKFSVVIADMRALRKASAPYDVMSAEEILALPVGQLADMGCLIYLWATAPHLAFTVECLKAWGF 80 (198)
T ss_pred CceEEecceEEEEEEcCceEEEEcChhHhhhccCCCCccccHHHhcCchhHhhhCCcEEEEEecChHHHHHHHHHHHhCc
Confidence 489999999999999999999999999999999999999999999999999998 7799999999999999999999999
Q ss_pred eccceeEEEc------------CCcccccCeE-EEe------cccccCCCccEEEecCCCCCccCCcccchhhhhhhccc
Q psy17828 416 QDEGLLFLWV------------TGRAMELGRE-CLK------LSLNCQLSQDVEFTWPYLGWMSKFSLHHFFQVVYLAAM 476 (1061)
Q Consensus 416 ~~et~~ivWV------------tG~~l~~~kE-CLv------~~i~~nid~DVIvsep~~g~s~Kp~l~~~~~iE~f~~~ 476 (1061)
.+.+. +.|. ||+|+|+++| |++ .++|..+++++|+| |++.+|+||. |.|-++|.+|+-
T Consensus 81 ~~ks~-~~W~Ktt~~G~kv~~GtGhwlr~S~Eh~~vg~~GNpK~~~~~~~i~li~S-~~RE~SRKP~-E~y~i~ErL~~~ 157 (198)
T COG4725 81 EYKSF-MAWRKTTAAGRKVRMGTGHWLRTSGEHVFVGTLGNPKQSHVPPTISLIVS-MTRETSRKPD-ELYGIAERLAGT 157 (198)
T ss_pred ceeEE-EEEeeecccCceEEeecceeecCCCcEEEEEecCCchhhcCCCceEEEEc-cchhhccCCH-HHHHHHHHhCCc
Confidence 97766 8998 7889999999 999 56899999999999 4666688885 666677999966
Q ss_pred hhhh---ccccccCCCccccCCcc
Q psy17828 477 IRSI---IALHNLINNKITNRDAE 497 (1061)
Q Consensus 477 ~Rrl---gr~~nlr~gWvT~g~~~ 497 (1061)
--+| ||+| ||||-|+|++.
T Consensus 158 ~aKLEIF~Rd~--R~GW~~~GnQ~ 179 (198)
T COG4725 158 HAKLEIFGRDH--RPGWFTIGNQL 179 (198)
T ss_pred cceeeeecccC--CCCceeecccc
Confidence 6566 7777 99999999985
No 11
>PF05063 MT-A70: MT-A70 ; InterPro: IPR007757 N6-methyladenosine (m6A) is present at internal sites in eukaryotic mRNA. It is present only within a defined sequence context that has been shown to be conserved across species from plants to man. Despite its ubiquity and conserved sequence specificity, the functional significance of this modification remains a mystery [], []. MT-A70 is the S-adenosylmethionine-binding subunit of human mRNA N6-adenosine-methyltransferase (MTase), an enzyme that sequence-specifically methylates adenines in pre-mRNAs. Proteins with sequence similarity to MT-A70 have been identified in eukaryotes and prokaryotes. The resulting family is defined by sequence similarity in the carboxyl-proximal regions of the respective proteins. The amino-proximal regions of the eukaryotic proteins are highly diverse, often Pro-rich, and are conserved only within individual subfamilies []. Corresponding regions are not present in prokaryotic members of the family. MT-A70-like proteins contain examples of some of the consensus methyltransferase motifs that have been derived from mutational and structural studies of bacterial DNA methyltransferases, including the universally conserved motif IV catalytic residues and a proposed motif I (AdoMet binding) element []. The MT-A70-like family comprises four subfamilies with varying degrees of interrelatedness. One subfamily is a small group of bacterial DNA: m6A MTases. The other three are paralogous eukaryotic lineages, two of which have not been associated with MTase activity but include proteins that regulate mRNA levels via unknown mechanisms apparently not involving methylation []. Some proteins known to belong to the MT-A70-like family are listed below: Human N6-adenosine-methyltransferase 70 kDa subunit (MT-A70) (2.1.1.62 from EC). Yeast N6-adenosine-methyltransferase IME4 (2.1.1.62 from EC), which is important for induction of sporulation. Yeast karyogamy protein KAR4, a phosphoprotein required for expression of karyogamy-specific genes during mating and that it also acts during mitosis and meiosis. It has been suggested that KAR4 is inactive for methyltransfer and may not even bind AdoMet. ; GO: 0008168 methyltransferase activity, 0006139 nucleobase-containing compound metabolic process
Probab=99.97 E-value=3.7e-32 Score=276.81 Aligned_cols=139 Identities=29% Similarity=0.401 Sum_probs=123.1
Q ss_pred ccEEEECCCccccc-------cCCCCCCChHHHhcCCccccCC-CcEEEEecCccchHHH-HHHhhccceeccceeEEEc
Q psy17828 355 FAVIMADPPWDIHM-------ELPYGTMSDDEMRQLGIPQLQD-EGLLFLWVTGRAMELG-RECLKLFMLQDEGLLFLWV 425 (1061)
Q Consensus 355 FdvIlaDPPW~~~~-------~~~Y~tms~deI~~LPV~~La~-~g~LFLWvT~~~Le~g-~elL~~WGf~~et~~ivWV 425 (1061)
||||||||||++.+ ..+|+||+.++|++|||++|++ +|+|||||||+.+.++ .++|++|||++.+. |+|+
T Consensus 1 fdvI~~DPPW~~~~~~~~~~~~~~Y~tm~~~~i~~Lpv~~l~~~~~~lflWvTn~~~~~~~~~l~~~WGf~~~~~-~~Wv 79 (176)
T PF05063_consen 1 FDVIYADPPWPNKSASRKGGAEAHYPTMSLDEIKSLPVPQLAAPGALLFLWVTNSQLPEAKLELFPAWGFEYVTE-WVWV 79 (176)
T ss_pred CCEEEEeCCCCCcCcccccccccCCCccCHHHHHhCCHHHhCCCCcEEEEEeccchhhHHHHHHHHhCCCEEEEE-EEEE
Confidence 89999999999875 3699999999999999999975 8899999999999999 99999999996655 9999
Q ss_pred --------------CCcccccCeE-EEe------------cccccCCCccEEEecCCCCCccCCcccchhhhhhhccchh
Q psy17828 426 --------------TGRAMELGRE-CLK------------LSLNCQLSQDVEFTWPYLGWMSKFSLHHFFQVVYLAAMIR 478 (1061)
Q Consensus 426 --------------tG~~l~~~kE-CLv------------~~i~~nid~DVIvsep~~g~s~Kp~l~~~~~iE~f~~~~R 478 (1061)
+|++++++.| ||+ ..+++++++|||++ |...||+||+ +.|.+||+||++.+
T Consensus 80 K~~~~g~~~~~~~~~g~~~r~~~E~lLig~rg~~~~~~~~~~~~~~~~~~vi~~-~~~~HS~KP~-~~~~~ie~~~~~~~ 157 (176)
T PF05063_consen 80 KITKNGEPVFPDLGLGYYFRKPYEHLLIGRRGKPRRSSDKDIIHCNVDTDVIIS-PPREHSRKPP-ELYELIERLCPDAP 157 (176)
T ss_pred EecCCCCccccccCCcccccCCcCeEEeeecCCCCccccccccccCCCCcEEEe-cCCCCCCCCh-HHHHHHHHhcCCCc
Confidence 2458999999 888 13467889999999 5666699996 56778999999999
Q ss_pred hh-ccccccCCCccccCCc
Q psy17828 479 SI-IALHNLINNKITNRDA 496 (1061)
Q Consensus 479 rl-gr~~nlr~gWvT~g~~ 496 (1061)
+| .|+|++|+||+++|+|
T Consensus 158 ~LElFaR~~rpGW~~wGnE 176 (176)
T PF05063_consen 158 RLELFARNLRPGWDSWGNE 176 (176)
T ss_pred EEEEEeCCCCCCceEeCCC
Confidence 99 9999999999999986
No 12
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=99.97 E-value=4.2e-30 Score=257.39 Aligned_cols=130 Identities=37% Similarity=0.712 Sum_probs=117.8
Q ss_pred EEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcC
Q psy17828 638 VVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNA 717 (1061)
Q Consensus 638 V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp 717 (1061)
|+|||||||+|+|||+|... ++.+|+|+|||.+.+ ++|+|+|||++|++++++. +++|.+|+++|+++|++|||
T Consensus 1 V~ihplvll~I~dh~~R~~~--~~~~v~G~LlG~~~~-~~veV~nsF~lp~~~~~~~---~~~d~~y~~~m~~~~~~v~~ 74 (157)
T cd08057 1 VQLHPLVLLNISDHYTRRKY--GIKRVIGVLLGYVDG-DKIEVTNSFELPFDEEEES---IFIDTEYLEKRYNLHKKVYP 74 (157)
T ss_pred CEEccHHHhhHHHHHHhccC--CCCeEEEEEEeEEeC-CEEEEEEeEEccccCCCcc---hhhhHHHHHHHHHHHHHhCC
Confidence 68999999999999999653 468999999999985 5799999999999877543 78999999999999999999
Q ss_pred CCceEEEEecCCC----CCcccHHHHHHHHhh-CCCcEEEEEcCCC--CCCCcceEEEEeccc
Q psy17828 718 REKVVGWYHTGPK----LHQNDIQINELIRRY-CTNSVLVIIDAKP--KELGLPTEAYRVVDE 773 (1061)
Q Consensus 718 ~E~VVGWYsTGp~----ls~~Dl~Ihe~f~~~-~~nPI~LivDPs~--ss~gLplKAYrlv~e 773 (1061)
++.+||||++|+. ++..|..||++|..+ +++||+|++||.. +.+++|++|||++.+
T Consensus 75 ~~~vVGWY~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~ 137 (157)
T cd08057 75 QEKIVGWYSIGSNNSNEISKSDNSLHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQR 137 (157)
T ss_pred CCCEEEEEeecCCCCCCCChhHHHHHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecC
Confidence 9999999999998 899999999999988 8999999999988 346699999999864
No 13
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=99.94 E-value=1.4e-26 Score=250.74 Aligned_cols=132 Identities=28% Similarity=0.448 Sum_probs=111.6
Q ss_pred eEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhc
Q psy17828 637 KVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVN 716 (1061)
Q Consensus 637 ~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVn 716 (1061)
+|+|||+|+|+|+|||.| +.+.+|+|+|||...+ ++++|||||++|+.+++++...+..|.+|+.+|+++++++|
T Consensus 2 ~V~I~~~vllkIv~H~~~----~~p~~v~G~LLG~~~~-~~leVtn~Fp~P~~~~~~~~~~~~~~~~yq~~m~~~~r~v~ 76 (266)
T cd08065 2 SVQIDGLVVLKIIKHCKE----ELPELVQGQLLGLDVG-GTLEVTNCFPFPKSEEDDSDRADEDIADYQLEMMRLLREVN 76 (266)
T ss_pred EEEEeHHHHHHHHHHHhc----CCCcEEEEEEeeeEcC-CEEEEEeccCCCCCCCCCcchhhhhHHHHHHHHHHHHHHhC
Confidence 699999999999999998 4589999999999975 68999999999998876544456778899999999999999
Q ss_pred CCCceEEEEecCC-C--CCcccHHHHHHHHhhCCCcEEEEEcCCCCCCC-cceEEEEeccc
Q psy17828 717 AREKVVGWYHTGP-K--LHQNDIQINELIRRYCTNSVLVIIDAKPKELG-LPTEAYRVVDE 773 (1061)
Q Consensus 717 p~E~VVGWYsTGp-~--ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~g-LplKAYrlv~e 773 (1061)
+++.+||||||+| + .+..+++.+..|+..++++|+|++||..+.+| ++++|||+++.
T Consensus 77 ~~e~iVGWY~S~p~~~~~~~s~id~~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~~~ 137 (266)
T cd08065 77 VDHNHVGWYQSTYLGSFFTRDLIETQYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLSEK 137 (266)
T ss_pred CCCcEEEeEeecCCCCcCCHHHHHHHHHHhccCCCCEEEEECCCcccccceeeEEEEEcHH
Confidence 9999999999999 3 23444455555555568899999999986554 99999999865
No 14
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=99.88 E-value=8.1e-23 Score=193.53 Aligned_cols=109 Identities=38% Similarity=0.704 Sum_probs=93.7
Q ss_pred ccceEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHH
Q psy17828 634 VTSKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFK 713 (1061)
Q Consensus 634 ~~~~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfK 713 (1061)
+..+|+|||+|+|+|+||+.|... .+|+|+|||.+.++++++|+|||++|+.+++.+. ...+.++..+|+++++
T Consensus 2 s~~~V~i~p~vll~i~~h~~r~~~----~~v~G~LlG~~~~~~~v~I~~~f~~p~~~~~~~~--~~~~~~~~~~~~~~~~ 75 (114)
T PF01398_consen 2 SVQTVQIHPLVLLKIIDHATRSSP----NEVIGLLLGTQDGDNTVEITNSFPVPHSESEDDC--DMDDEDFQKKMIELLK 75 (114)
T ss_dssp SCEEEEEEHHHHHHHHHHHHHHHC----TEEEEEEEEEEETT-EEEEEEEEEESEEEESSEE--EEECCHHHHHHHHHHH
T ss_pred CcEEEEECHHHHHHHHHHHhcCCC----CEEEEEEEEEecCceEEEEEEEEEeeEecCcccc--ccchhhHHHHHHhhhc
Confidence 467999999999999999999643 4999999999987548999999999998776542 3455566699999999
Q ss_pred hhcCCCceEEEEecCCCC----CcccHHHHHHHHhhCCC
Q psy17828 714 KVNAREKVVGWYHTGPKL----HQNDIQINELIRRYCTN 748 (1061)
Q Consensus 714 kVnp~E~VVGWYsTGp~l----s~~Dl~Ihe~f~~~~~n 748 (1061)
+++|++.+||||||+|.. +..|+.+|..|++++++
T Consensus 76 ~~~~~~~iVGWY~s~p~~~~~~S~~di~~q~~~q~~~~~ 114 (114)
T PF01398_consen 76 KVNPNLEIVGWYHSHPNISCFPSPTDIETQKQYQRMNPN 114 (114)
T ss_dssp HCSTTSEEEEEEEEESSS-SS--HHHHHHHHHHHHHTTT
T ss_pred cccccceEEEEEEccCCccccCCHHHHHHHHHHHHhCCC
Confidence 999999999999999986 99999999999999874
No 15
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=99.87 E-value=1.3e-21 Score=212.61 Aligned_cols=135 Identities=26% Similarity=0.411 Sum_probs=119.8
Q ss_pred cccceEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHH--
Q psy17828 633 VVTSKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYG-- 710 (1061)
Q Consensus 633 ~~~~~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~Mle-- 710 (1061)
....+|.|+|+|+++|++|+.| +.+.+|+|+|||...+ ++++|++||++|..+.+.. ...+.+|++.|++
T Consensus 7 ~~~~~V~Is~~allkil~Ha~~----~~p~Ev~GlLlG~~~~-~~v~Vt~~fp~p~~~t~~~---v~~~~e~~~~m~~~~ 78 (268)
T cd08069 7 DYFEKVYISSLALLKMLKHARA----GGPIEVMGLMLGKVDD-YTIIVVDVFALPVEGTETR---VNAQDEFQEYMVQYE 78 (268)
T ss_pred CcccEEEECHHHHHHHHHHHhc----cCCceEEEEEEeeecC-CeEEEEEEEECCcCCCCCc---eeccHHHHHHHHHHH
Confidence 3467899999999999999988 5678999999999754 5799999999998776543 3456699999999
Q ss_pred HHHhhcCCCceEEEEecCCC----CCcccHHHHHHHHhhCCCcEEEEEcCCCC-CC-CcceEEEEeccccc
Q psy17828 711 MFKKVNAREKVVGWYHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPK-EL-GLPTEAYRVVDEDK 775 (1061)
Q Consensus 711 mfKkVnp~E~VVGWYsTGp~----ls~~Dl~Ihe~f~~~~~nPI~LivDPs~s-s~-gLplKAYrlv~e~~ 775 (1061)
+++++++++.+||||||+|. ++..|+.+|..|+++++++|+|++||..+ .+ ++.++|||++++..
T Consensus 79 ~~~~~~~~~~vVGWYHSHP~~g~~~S~~Dv~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~~~ 149 (268)
T cd08069 79 MLKQTGRPENVVGWYHSHPGYGCWLSGIDVNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGY 149 (268)
T ss_pred HHHHhCCCceeEeeeccCCCcCCcCCHHHHHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECccc
Confidence 99999999999999999997 99999999999999999999999999887 44 49999999998854
No 16
>KOG1560|consensus
Probab=99.82 E-value=8.1e-21 Score=202.54 Aligned_cols=156 Identities=27% Similarity=0.395 Sum_probs=131.0
Q ss_pred cccceEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccC-CCCC-CccccccH---HHHHH
Q psy17828 633 VVTSKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDE-DDKD-NSVWFLDH---DYLEN 707 (1061)
Q Consensus 633 ~~~~~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eE-de~d-~~v~~lD~---~Y~e~ 707 (1061)
.+..+|.+..||+++|++||.... .+..-+.|+|||.+.+ ++++|||||+.|..+ .+++ .+.-..|. .|+..
T Consensus 10 p~vk~v~ldsLvVMkiiKHc~ee~--~n~d~~~GvL~Glvvd-~~LeITncFp~p~~~~~edda~~~~~~de~rq~~~l~ 86 (339)
T KOG1560|consen 10 PPVKRVELDSLVVMKIIKHCREEF--PNGDGTQGVLLGLVVD-GRLEITNCFPFPSVLENEDDAVNKSVSDEARQAYQLA 86 (339)
T ss_pred CccceeeehhHHHHHHHHHHHhhc--CCcchhhheeeeeeec-ceeEeecccCCCccCCCccchhhhhhhHHHHHHHHHH
Confidence 567899999999999999998754 2346789999999985 689999999999743 2222 11112332 69999
Q ss_pred HHHHHHhhcCCCceEEEEec---CCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCC-cceEEEEecccccCCCCCCCC
Q psy17828 708 MYGMFKKVNAREKVVGWYHT---GPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELG-LPTEAYRVVDEDKIRPEREPN 783 (1061)
Q Consensus 708 MlemfKkVnp~E~VVGWYsT---Gp~ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~g-LplKAYrlv~e~~~~~g~e~~ 783 (1061)
|++.++.||.+...||||.+ |+.++..-++.+..|+.-++..|.|+|||..+++| |.++|||++++ ++....+.+
T Consensus 87 mlrrlr~vnid~~hVGwYqs~~vgs~lS~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp~-am~~~kekd 165 (339)
T KOG1560|consen 87 MLRRLRYVNIDHLHVGWYQSAYVGSFLSPALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTPE-AMAAHKEKD 165 (339)
T ss_pred HHHHhhhcCccceeeeeeeeehhccccCHHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCHH-HHHHHhcCC
Confidence 99999999999999999988 56788888888999999999999999999999887 99999999987 556788999
Q ss_pred CCCCccccc
Q psy17828 784 PRPSANKAA 792 (1061)
Q Consensus 784 ~~~~~~~a~ 792 (1061)
|||++.++|
T Consensus 166 wtpealk~~ 174 (339)
T KOG1560|consen 166 WTPEALKSA 174 (339)
T ss_pred CCHHHHHhc
Confidence 999999998
No 17
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=99.81 E-value=3.7e-19 Score=170.66 Aligned_cols=129 Identities=35% Similarity=0.480 Sum_probs=113.7
Q ss_pred eEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhc
Q psy17828 637 KVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVN 716 (1061)
Q Consensus 637 ~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVn 716 (1061)
.|.|||+|+++|++|+.| ..+.+++|+|+|...+ ++++|+++|++|...+.+. ....+.+|++.|.+++++++
T Consensus 1 ~v~i~~~v~~~i~~h~~~----~~p~e~~G~L~G~~~~-~~~~i~~~~~~p~~~~~~~--~~~~~~~~~~~~~~~~~~~~ 73 (135)
T smart00232 1 EVKVHPLVPLNILKHAIR----DGPEEVCGVLLGKSNK-DRPEVKEVFAVPNEPQDDS--VQEYDEDYSHLMDEELKKVN 73 (135)
T ss_pred CEEEcHHHHHHHHHHHhc----CCCcEEEEEEEEEEcC-CEEEEEEEEecCcCCCCcc--hhhhhhhHHHHHHHHHHhhC
Confidence 478999999999999988 3578999999999875 4799999999998764432 34678899999999999999
Q ss_pred CCCceEEEEecCC----CCCcccHHHHHHHHhhCCCcEEEEEcCCCCC-CCcceEEEEecc
Q psy17828 717 AREKVVGWYHTGP----KLHQNDIQINELIRRYCTNSVLVIIDAKPKE-LGLPTEAYRVVD 772 (1061)
Q Consensus 717 p~E~VVGWYsTGp----~ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss-~gLplKAYrlv~ 772 (1061)
+++.+||||||+| .++..|+.+|..++.+...++++++|+..+. ++++++||++++
T Consensus 74 ~~~~~vGwyhshp~~~~~pS~~D~~~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~~ 134 (135)
T smart00232 74 KDLEIVGWYHSHPDESPFPSEVDVATHESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLTP 134 (135)
T ss_pred CCceEEEEEEcCCCCCCCcCHHHHHHHHHHHhcCCceEEEEECCCccccCcEEEEEEEecC
Confidence 9999999999988 4788899999999999999999999999987 559999999974
No 18
>cd08064 MPN_eIF3f Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF3f. Eukaryotic translation initiation factor 3 (eIF3) subunit F (eIF3F; EIF3S5; eIF3-p47; eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa; Mov34/MPN/PAD-1 family protein) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity. It has been shown that eIF3f mRNA expression is significantly decreased in many human tumors including pancreatic cancer and melanoma. EIF3f is a potent inhibitor of HIV-1 replication; it mediates restriction of HIV-1 expression through several factors including the serine/arginine-rich (SR) protein 9G8, and cyclin-dependent kinase 11 (CDK11). EIF3f phosphorylation by CDK11 is important in regulating its function in translation and ap
Probab=99.70 E-value=1.1e-17 Score=181.57 Aligned_cols=182 Identities=21% Similarity=0.356 Sum_probs=131.3
Q ss_pred ccccccCCCCccccccc---cccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCCCCCchHHHHHH
Q psy17828 806 FLCGRSSRGGKVGRIRC---RSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPKLHQNDIQINEL 882 (1061)
Q Consensus 806 ~~~g~~~~~g~~~~~~~---~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGselt~~s~lIHef 882 (1061)
.|+|+.. ||.+.+++| .+..+.+ .+- +|.--+++|+++|+||||+|.+||||+||+.+++++.+||+|
T Consensus 28 ~LLG~~~-~~~veItnsF~~p~~~~~~---~~~-----~d~~y~~~m~~~~kkv~~~~~vVGWY~tg~~~~~~~~~Ih~~ 98 (265)
T cd08064 28 TLLGTRS-EGEVEITNCFAVPHNESED---QVA-----VDMEYHRTMYELHQKVNPKEVIVGWYATGSEITEHSALIHDY 98 (265)
T ss_pred EEEEEEe-CCEEEEEeCeecceeCCCC---eEE-----EcHHHHHHHHHHHHHhCCCCcEEeeeeCCCCCCccHHHHHHH
Confidence 5899997 589999999 3444433 111 354446899999999999999999999999999999999999
Q ss_pred HHhhcC--CceEEEEcCCCCCCCCCceeEEEeeeccCCCCcceeeEEeeccccccccccccccccccccccccccccchh
Q psy17828 883 IRRYCT--NSVLVIIDAKPKELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEEAEEVGVEHLLRDIKDTTVGSLSQ 960 (1061)
Q Consensus 883 ys~~~~--~PIhL~VDt~~~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeEAErIgVEhLlr~i~dat~s~L~s 960 (1061)
|+++++ +||||++|+...++++|++||+++. .| ++-+-.....++|.++-...+....++..+..
T Consensus 99 ~~~~~~~~~pI~L~~D~~~~~~~l~i~ay~~~~----~~---------~~~~~~~~~F~~ip~~i~~~eaE~i~v~~l~~ 165 (265)
T cd08064 99 YSRECTSYNPIHLTVDTSLDDGKMSIKAYVSSP----LG---------VPGKTLGSMFVPIPLELLYSEAERVALDLLAK 165 (265)
T ss_pred HHhhCCCCCCEEEEEeCCCCCCCcceEEEEEEe----cc---------cCCCCcceEEEEcceeeecCcHHHHHHHHHHh
Confidence 999998 9999999999888899999998553 22 11111111244555443332222222222221
Q ss_pred ------hhhhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHh-hccccccCCCcccccc
Q psy17828 961 ------RVTNQLMGLKGLNQQIKEIEKYVGQVSRYWPPFYVVVINLID-KRSVTHLSGPGRWLLP 1018 (1061)
Q Consensus 961 ------~l~~~~~aLk~L~~rL~~I~~YLd~V~~gvpp~~~ilr~l~~-~~~~~~~~~~gr~l~~ 1018 (1061)
.-......+..+...++.+..-|+.+.+|+ +++.+ +...++ .+||+|..
T Consensus 166 ~~~~~~~~~~~~~~l~~~~~al~~L~~~l~~i~~Yl-------~~V~~g~~~~d~--~i~r~l~~ 221 (265)
T cd08064 166 TLASPSRSAPLTSDLEQLEASLEKLQEMLDRVLRYV-------EDVLAGKVKADN--AIGRYLMD 221 (265)
T ss_pred hccCCcccccchhhHHHHHHHHHHHHHHHHHHHHHH-------HHHHcCCCCCCH--HHHHHHHH
Confidence 111223568889999999999999999998 77777 677666 99999864
No 19
>KOG1554|consensus
Probab=99.67 E-value=2.3e-16 Score=169.25 Aligned_cols=140 Identities=26% Similarity=0.408 Sum_probs=124.8
Q ss_pred cceEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHh
Q psy17828 635 TSKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKK 714 (1061)
Q Consensus 635 ~~~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKk 714 (1061)
...|+|..|+||+|+-|..| |++-.|||.|+|...++ ++.|.+||++|.+..+...+......+|+....++.+.
T Consensus 52 fk~vkISalAllKm~~hA~~----GgnlEiMGlm~Gkv~g~-t~IvmD~FaLPVeGTETRVNAq~~AyEYmv~Y~e~~k~ 126 (347)
T KOG1554|consen 52 FKHVKISALALLKMVMHARS----GGNLEIMGLMQGKVDGD-TIIVMDSFALPVEGTETRVNAQAEAYEYMVQYIEEAKN 126 (347)
T ss_pred hhhhhhHHHHHHHHHHHHhc----CCCeEEEeeecccccCC-eEEEEeccccccccccceechHHHHHHHHHHHHHHHHH
Confidence 45899999999999999877 78899999999998764 79999999999999887766666678999999999999
Q ss_pred hcCCCceEEEEecCCC----CCcccHHHHHHHHhhCCCcEEEEEcCCCC--CCCcceEEEEecccccCCCC
Q psy17828 715 VNAREKVVGWYHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPK--ELGLPTEAYRVVDEDKIRPE 779 (1061)
Q Consensus 715 Vnp~E~VVGWYsTGp~----ls~~Dl~Ihe~f~~~~~nPI~LivDPs~s--s~gLplKAYrlv~e~~~~~g 779 (1061)
+++.|++|||||++|+ ++..|+..|.+-++|.+.-|++++||.++ ++++.+.|||..+++.-.+.
T Consensus 127 ~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRTyp~gyk~~d 197 (347)
T KOG1554|consen 127 VGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRTYPKGYKPPD 197 (347)
T ss_pred hhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeecccCCCCCCC
Confidence 9999999999999997 89999999999999998889999999986 46699999999998654333
No 20
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=99.59 E-value=1e-15 Score=168.10 Aligned_cols=183 Identities=16% Similarity=0.185 Sum_probs=127.2
Q ss_pred ccccccCCCCccccccc---cccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCC-CCCchHHHHH
Q psy17828 806 FLCGRSSRGGKVGRIRC---RSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPK-LHQNDIQINE 881 (1061)
Q Consensus 806 ~~~g~~~~~g~~~~~~~---~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGse-lt~~s~lIHe 881 (1061)
.|+|+.. ||.+.++.| .+..+.+|... +|.--+++|+++++||||+|.|||||+||+. ++++|..||+
T Consensus 34 ~LLG~~~-~~~veItnsF~~p~~~~~~~~~~-------id~~y~~~m~~~~kkV~~~~~vVGWY~tg~~~~~~~~~~Ih~ 105 (288)
T cd08063 34 ALLGQQD-GREIEIENSFELKYDTNEDGEIV-------LDKEFLETRLEQFKQVFKDLDFVGWYTTGPGGPTESDLPIHK 105 (288)
T ss_pred EEEEEEc-CCEEEEEEEEecccccCCCCcee-------eCHHHHHHHHHHHHHhccCCceEEEEecCCCCCCHHHHHHHH
Confidence 4889874 788999999 34433324332 3555679999999999999999999999999 9999999999
Q ss_pred HHHhhcCCceEEEEcCCC--CCCCCCceeEEEeeeccCCCCcceeeEEeeccccccccccccccccccccccccccccch
Q psy17828 882 LIRRYCTNSVLVIIDAKP--KELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEEAEEVGVEHLLRDIKDTTVGSLS 959 (1061)
Q Consensus 882 fys~~~~~PIhL~VDt~~--~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeEAErIgVEhLlr~i~dat~s~L~ 959 (1061)
+|++++++||||++|+.. ..+++|++||++ .. .-.+- -......++..+-...+....++..+.
T Consensus 106 ~~~~~~~~pv~L~~D~~~~~~~~~lpi~ay~s----~~---------~~~~~-~~~~~F~~i~~~i~~~eaErIgv~~l~ 171 (288)
T cd08063 106 QILEINESPVLLLLDPEANASGKDLPVTIYES----VL---------ELVDG-EATLRFRELPYTIETGEAERIGVDHVA 171 (288)
T ss_pred HHHhhCCCcEEEEEccccccCCCCCceeEEEE----EE---------eccCC-ccccEEEeeeeEEEeccCceeeHHHHH
Confidence 999999999999999998 577899998871 01 00010 000112222222222222211222221
Q ss_pred -------hhhhhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHh-hccccccCCCccccccc
Q psy17828 960 -------QRVTNQLMGLKGLNQQIKEIEKYVGQVSRYWPPFYVVVINLID-KRSVTHLSGPGRWLLPW 1019 (1061)
Q Consensus 960 -------s~l~~~~~aLk~L~~rL~~I~~YLd~V~~gvpp~~~ilr~l~~-~~~~~~~~~~gr~l~~~ 1019 (1061)
.........+..+...+..+..-|+.+++|+ +++.+ +...++ .+||.|..-
T Consensus 172 ~~~~~~~~~~~~~~~~l~~~~~al~~L~~rl~~i~~Yl-------~~V~~g~~~~d~--~ilR~l~~~ 230 (288)
T cd08063 172 RGGASGSSEKSTVAAHLQAQHNAIKMLNSRVELILEYL-------KAVPVGEVPPDH--SILRSISAL 230 (288)
T ss_pred hcCCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHhcCCCCCCCH--HHHHHHHHH
Confidence 1222335678889999999999999999998 78777 566666 999998754
No 21
>cd08057 MPN_euk_non_mb Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity (non metal-binding); eukaryotic. This family contains MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains variants lacking key residues in the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Rpn7/PSMD7, Rpn8/PSMD8, CSN6, Prp8p, and the translation initiation factor 3 subunits f and h do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function. Rpn7 is known to be critical for the integrity of the 26S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. CSN6 is a highly conserved protein complex with diverse functions, including several import
Probab=99.59 E-value=7.6e-16 Score=154.83 Aligned_cols=120 Identities=20% Similarity=0.292 Sum_probs=100.3
Q ss_pred ccccccCCCCccccccc---cccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCC----CCCchHH
Q psy17828 806 FLCGRSSRGGKVGRIRC---RSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPK----LHQNDIQ 878 (1061)
Q Consensus 806 ~~~g~~~~~g~~~~~~~---~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGse----lt~~s~l 878 (1061)
.|+|+.. |+.+.+.+| .+..+.+.. .+|.--+++|+++++||||+|.|||||+||+. ++..+.+
T Consensus 28 ~LlG~~~-~~~veV~nsF~lp~~~~~~~~--------~~d~~y~~~m~~~~~~v~~~~~vVGWY~~~~~~~~~~~~~~~~ 98 (157)
T cd08057 28 VLLGYVD-GDKIEVTNSFELPFDEEEESI--------FIDTEYLEKRYNLHKKVYPQEKIVGWYSIGSNNSNEISKSDNS 98 (157)
T ss_pred EEEeEEe-CCEEEEEEeEEccccCCCcch--------hhhHHHHHHHHHHHHHhCCCCCEEEEEeecCCCCCCCChhHHH
Confidence 5899998 889999999 444333321 23555678999999999999999999999998 9999999
Q ss_pred HHHHHHhh-cCCceEEEEcCCC--CCCCCCceeEEEeeeccCCCCcceeeEEeeccccccccccccc
Q psy17828 879 INELIRRY-CTNSVLVIIDAKP--KELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEEAEEVG 942 (1061)
Q Consensus 879 IHefys~~-~~~PIhL~VDt~~--~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeEAErIg 942 (1061)
||++|+.. +++||+|++|+.. ..+++|++||.+.... . .+.++|+++.++|+||||
T Consensus 99 i~~~~~~~~~~~~v~L~~D~~~~~~~~~l~i~ay~~~~~~----~----~~~~~~~~i~~~e~E~I~ 157 (157)
T cd08057 99 LHSQFSLISEENPLILILDPSLQSDSEKLEISTFTSAQRE----E----NGAEITYEIGTEETERIA 157 (157)
T ss_pred HHHHHHhccCCCCEEEEEcCCcccCCCcccEEEEEEecCC----C----CCceeeeEEecccccccC
Confidence 99999998 8899999999976 5688999999977521 1 233999999999999996
No 22
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=99.55 E-value=3.9e-14 Score=133.11 Aligned_cols=111 Identities=45% Similarity=0.726 Sum_probs=91.1
Q ss_pred hhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcCCCceEEEE
Q psy17828 646 LSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNAREKVVGWY 725 (1061)
Q Consensus 646 LsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp~E~VVGWY 725 (1061)
.+|++|+.+ ..+.+|+|+|+|...+ ++++|+++|++|..+.+.. .+... -|..+.+.+..++.+||||
T Consensus 2 k~il~~a~~----~~~~ev~G~L~G~~~~-~~~~i~~~~~~~~~~~~~~-----~~~~~--~~~~~~~~~~~~~~iVGwy 69 (116)
T cd07767 2 KMFLDAAKS----INGKEVIGLLYGSKTK-KVLDVDEVIAVPFDEGDKD-----DNVWF--LMYLDFKKLNAGLRIVGWY 69 (116)
T ss_pred HhHHHHHhc----CCCcEEEEEeEEEEcC-CEEEEEEEEecccCCCCCc-----cHHHH--HHHHHHHHhcCCCeEEEEE
Confidence 468888866 3478999999999876 4799999999998765432 12111 2777788889999999999
Q ss_pred ecCCC----CCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEE
Q psy17828 726 HTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAY 768 (1061)
Q Consensus 726 sTGp~----ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAY 768 (1061)
||+|. ++..|+.+|..|++..+++++|++|+.....+++++||
T Consensus 70 hshp~~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~~~~~~~~~ 116 (116)
T cd07767 70 HTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVKPKDLGNSWKCY 116 (116)
T ss_pred EcCCCCCCccCHHHHHHHHHHHHhCCCCEEEEEECCCccCCCCcccC
Confidence 99886 78999999999998888999999999987667888887
No 23
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=99.52 E-value=2.6e-13 Score=141.20 Aligned_cols=132 Identities=20% Similarity=0.222 Sum_probs=108.8
Q ss_pred cceEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEec-CcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHH
Q psy17828 635 TSKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKG-KGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFK 713 (1061)
Q Consensus 635 ~~~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g-~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfK 713 (1061)
+.+|.|+++|||+|+.|+.. +. ..|+|.|+|...+ .+.++|+++|++|-.....+ ..+|+.++.+|++..+
T Consensus 4 pf~V~Is~~all~m~~Ha~~----~~-~EvcGlL~G~~d~~~~~l~Vt~~~p~~~~~~~~~---~e~dp~~q~e~~~~l~ 75 (187)
T cd08067 4 PFKVTVSSNALLLMDFHCHL----TT-SEVIGYLGGTWDPNTQNLTILQAFPCRSRLTGLD---CEMDPVSETEIRESLE 75 (187)
T ss_pred CEEEEECHHHHHHHHHHhcC----CC-cEEEEEEEeEEcCCCCeEEEEEEEecCCCCCCcc---cccCHHHHHHHHHHHH
Confidence 56899999999999999965 33 7899999999754 45799999999997554322 4579999999999999
Q ss_pred hhcCCCceEEEEecCCC----CCcccHHHHHHHHhhCC-------CcEEEEEcCCCCC---CCcceEEEEecccccC
Q psy17828 714 KVNAREKVVGWYHTGPK----LHQNDIQINELIRRYCT-------NSVLVIIDAKPKE---LGLPTEAYRVVDEDKI 776 (1061)
Q Consensus 714 kVnp~E~VVGWYsTGp~----ls~~Dl~Ihe~f~~~~~-------nPI~LivDPs~ss---~gLplKAYrlv~e~~~ 776 (1061)
+.+ +.+||||||+|. ++..|++.|..||...+ ..|.||+||..+. ....+++|.+.++...
T Consensus 76 ~~g--l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~~~~~~ 150 (187)
T cd08067 76 SRG--LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVMPPPEN 150 (187)
T ss_pred HcC--CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEECCCCC
Confidence 877 599999999984 78899999999988754 4699999998753 3378999999987543
No 24
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=99.48 E-value=2.3e-13 Score=130.99 Aligned_cols=110 Identities=21% Similarity=0.274 Sum_probs=91.0
Q ss_pred hHhhHHHHHhhccccCCceeEEEEEeeEEec----CcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcCCC
Q psy17828 644 VLLSVVDHFNRMSKIGNQKRVVGVLLGCWKG----KGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNARE 719 (1061)
Q Consensus 644 VLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g----~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp~E 719 (1061)
|+++|++|+.+ +.+..++|+|+|...+ ..+++|+++|+.|+..+. .+.|..+.+..+.++
T Consensus 2 ~~~~i~~ha~~----~~p~E~cGlL~G~~~~~~~~~~~~~v~~~~p~~~~~~~------------~~~~~~~~~~~~~g~ 65 (119)
T cd08058 2 ALLKMLQHAES----NTGIEVMGLLCGELTHNEFTDKHVIVPKQSAGPDSCTG------------ENVEELFNVQTGRPL 65 (119)
T ss_pred HHHHHHHHhcC----CCCeEEEEEeeeEEecCccceeEEEEeecCCCCCCchh------------HHHHHHHHHHhCCCC
Confidence 78999999977 4578999999998753 345899999999874321 225566667789999
Q ss_pred ceEEEEecCC----CCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEec
Q psy17828 720 KVVGWYHTGP----KLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVV 771 (1061)
Q Consensus 720 ~VVGWYsTGp----~ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv 771 (1061)
.+||||||+| .++..|++.|..|+...+..++||+||..+ .+.++|||++
T Consensus 66 ~~vG~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~--~~~~~a~rl~ 119 (119)
T cd08058 66 LVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR--NKDTGIFRLT 119 (119)
T ss_pred eEEEEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC--CcccceEEeC
Confidence 9999999998 388999999999998889999999999773 7889999984
No 25
>KOG2356|consensus
Probab=99.46 E-value=5.4e-14 Score=152.45 Aligned_cols=164 Identities=16% Similarity=0.237 Sum_probs=120.4
Q ss_pred cccCCCC--ceecccCccCcccCC---CccEEEECCCcccc---ccCCCCCCChH-HHhcCCccccCC-CcEEEEecCcc
Q psy17828 332 TKLYPPQ--WIQCDLRYLDMTVLG---KFAVIMADPPWDIH---MELPYGTMSDD-EMRQLGIPQLQD-EGLLFLWVTGR 401 (1061)
Q Consensus 332 ~~~~Ppq--~i~cDlr~~d~~~lg---kFdvIlaDPPW~~~---~~~~Y~tms~d-eI~~LPV~~La~-~g~LFLWvT~~ 401 (1061)
++.+||+ |+..||..++--..+ .+|+|++||||... ++..|...+.. ++.++||..+++ .|++..||||+
T Consensus 157 kYyIPpkSsF~~gDv~~~~qll~~H~llpdlIIiDPPW~NKSVkRs~~Ysmlsnl~ql~~IPI~kl~~p~~lvA~WcTNr 236 (366)
T KOG2356|consen 157 KYYIPPKSSFHVGDVKDIEQLLRAHDLLPDLIIIDPPWFNKSVKRSRTYSMLSNLLQLLDIPIIKLHDPLCLVAFWCTNR 236 (366)
T ss_pred eEEeCCccceecccHHHHHHHhHHHhhcCCeEEeCCCCCCcccccccceecccchhhhhcCCchhhcCCCceEEEEEcCc
Confidence 6778885 999999987754443 67999999999865 47889999998 999999999965 99999999999
Q ss_pred chHH---HHHHhhccceeccceeEEEc----CCc------ccccCe--E-EEe-----cccccC-CCccEEEecCCCCCc
Q psy17828 402 AMEL---GRECLKLFMLQDEGLLFLWV----TGR------AMELGR--E-CLK-----LSLNCQ-LSQDVEFTWPYLGWM 459 (1061)
Q Consensus 402 ~Le~---g~elL~~WGf~~et~~ivWV----tG~------~l~~~k--E-CLv-----~~i~~n-id~DVIvsep~~g~s 459 (1061)
.... -.+++.+||.+-... |.|. .|. +..|.+ | .++ ..+... ..+-||++.|-.-++
T Consensus 237 qkhi~f~k~eLf~kWnl~lv~t-w~wlKitt~gepv~d~~~~~~k~P~E~L~~a~~s~s~y~~~ip~tf~i~svP~~vHS 315 (366)
T KOG2356|consen 237 QKHIEFEKIELFDKWNLELVAT-WKWLKITTQGEPVYDFDNQKHKVPFESLMLAKKSDSMYKFEIPETFVIASVPMSVHS 315 (366)
T ss_pred HHHHHHHHHHHHHhhccceEEE-EEEEEeccCCCcccCchhhhccCcHHHHhhhhcccccccccCCCceEEEecchhhhc
Confidence 5544 358999999993322 8888 343 333333 6 333 111111 245689999955558
Q ss_pred cCCcccchhhhhhhcc-chhhh-ccccccCCCccccCCccc
Q psy17828 460 SKFSLHHFFQVVYLAA-MIRSI-IALHNLINNKITNRDAEV 498 (1061)
Q Consensus 460 ~Kp~l~~~~~iE~f~~-~~Rrl-gr~~nlr~gWvT~g~~~V 498 (1061)
.||++-. .++||-. -...| .|+|.|-|+|.|+|-|.+
T Consensus 316 hKPpLl~--~lrhf~~~~~~~LElFaRsL~P~~~s~G~Epl 354 (366)
T KOG2356|consen 316 HKPPLLD--LLRHFGIEFTEPLELFARSLLPSTHSVGYEPL 354 (366)
T ss_pred CCCchHH--HHHHhCCCCCcHHHHHHhhcCcccccccchhH
Confidence 8888532 3488852 24455 889999999999999864
No 26
>PLN03246 26S proteasome regulatory subunit; Provisional
Probab=99.43 E-value=1.2e-13 Score=152.99 Aligned_cols=181 Identities=29% Similarity=0.391 Sum_probs=126.1
Q ss_pred ccccccCCCCccccccc---cccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCCCCCchHHHHHH
Q psy17828 806 FLCGRSSRGGKVGRIRC---RSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPKLHQNDIQINEL 882 (1061)
Q Consensus 806 ~~~g~~~~~g~~~~~~~---~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGselt~~s~lIHef 882 (1061)
.|+|... ||.+.++.| .+. .+++-.++.. +|+--+++|+++++||||+|.+||||+||++++++|++||+|
T Consensus 36 ~LLG~~~-~~~ieItnsF~~p~~-e~~~~~~~~~----~D~~y~~~m~~~~k~V~~~~~vVGWY~tg~~i~~~d~~IH~~ 109 (303)
T PLN03246 36 VLLGSSF-RGRVDVTNSFAVPFE-EDDKDPSIWF----LDHNYLESMFGMFKRINAKEHVVGWYSTGPKLRENDLDIHEL 109 (303)
T ss_pred EEEeeec-CCEEEEEeccccCcc-cCCCCcccee----ecHHHHHHHHHHHHHhCCCCcEEeeecCCCCCCcchHHHHHH
Confidence 4999986 578999998 222 1222111111 344446899999999999999999999999999999999999
Q ss_pred HHhhcCCceEEEEcCCCCCCCCCceeEEEeeeccCCCCcceeeEEeecccccccc-cccccccccccccc--cc---ccc
Q psy17828 883 IRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEE-AEEVGVEHLLRDIK--DT---TVG 956 (1061)
Q Consensus 883 ys~~~~~PIhL~VDt~~~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeE-AErIgVEhLlr~i~--da---t~s 956 (1061)
|++++++||||+|||.+.++++|++|| +.++..+.... ....-+-++.-.+. ++ ++.
T Consensus 110 ~~~~~~~Pv~L~vD~~~~~~~lpi~aY-----------------~s~~~~~~~~~~~~~~~F~~vp~~i~~~EaE~Igve 172 (303)
T PLN03246 110 FNDYVPNPVLVIIDVQPKELGIPTKAY-----------------YAVEEVKENATQKSQKVFVHVPSEIGAHEAEEIGVE 172 (303)
T ss_pred HHhhCCCCeEEEEecCCCCCCCceEEE-----------------EEEEeccCCCCcccccEEEECCeeeeecCHHHHHHH
Confidence 999999999999999988888888765 33332222111 11222233332222 11 111
Q ss_pred cch-----hhhhhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHh-hccccccCCCcccccc
Q psy17828 957 SLS-----QRVTNQLMGLKGLNQQIKEIEKYVGQVSRYWPPFYVVVINLID-KRSVTHLSGPGRWLLP 1018 (1061)
Q Consensus 957 ~L~-----s~l~~~~~aLk~L~~rL~~I~~YLd~V~~gvpp~~~ilr~l~~-~~~~~~~~~~gr~l~~ 1018 (1061)
.+. .........|..+...|+.+.+.|+.|++|+ +++.+ +...++ .+||+|..
T Consensus 173 ~l~r~~~~~~~s~l~~~l~~~~~al~~L~~rl~~i~~Yl-------~~V~~g~~~~d~--~IlR~l~~ 231 (303)
T PLN03246 173 HLLRDVKDTTVSTLATEVTGKLTALKGLDARLREIRSYL-------DLVVEGKLPLNH--EILYHLQD 231 (303)
T ss_pred HHHhcccCCccchhHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHhcCCCCCCH--HHHHHHHH
Confidence 221 1223344478888999999999999999998 88887 677776 99999864
No 27
>KOG2098|consensus
Probab=99.40 E-value=6.7e-14 Score=157.40 Aligned_cols=327 Identities=26% Similarity=0.322 Sum_probs=204.8
Q ss_pred ChhHHHHHHHHhhccccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeecccCCCCceEEEEeeh-----HhHH
Q psy17828 88 NPDLELELLEKLCDVSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINESKDDDNQVEIVSVEH-----VKLL 162 (1061)
Q Consensus 88 d~~~e~~ll~~L~d~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~~~~~~~~~~i~~~~~-----~kl~ 162 (1061)
+-+....+|+.++. ...+|..++.+-+.... +..+-..+|.++|.|.++...++.. .+.++++.- +-+.
T Consensus 45 ~~~s~d~vl~a~sS-~~~lp~vas~v~e~~~~--~elekl~~~~~~a~q~~~~~~dl~~---~cl~~sv~~~p~~~~~vl 118 (591)
T KOG2098|consen 45 LFRSDDPVLTAPSS-GGPLPSVASAVPELATD--PELEKLRLLHHLADQALTLPTDLVS---ICLAISVPDAPATQDGVL 118 (591)
T ss_pred hhhccchhhhcccc-CCCCCchhhcCcccccC--hHHHHHhhhhhhhhhhccCcHHhhh---hheEecCCCCccchhHHH
Confidence 34445667888777 88999998877663322 3344444899999999998886655 667777662 3333
Q ss_pred hHHHHhh----hhhccccCCCCCCCcc--hhhhhh-ccCCCC------hhhhHhhhCCcchHHHH-HHHHhHHHHHhcC-
Q psy17828 163 GMVNEVS----KGIKRKADTDTSDYED--DEDLKK-FKDNGD------ETDVMSLLSKPSIREKQ-VKQIGEEILDLLT- 227 (1061)
Q Consensus 163 ~m~~~~~----~~~kr~~~~~~s~~~~--~e~~~k-~~~~~~------~~~~e~Ll~~~s~~e~~-~~~~~~e~~~ll~- 227 (1061)
..+++++ ++.||+...+.-+..+ .-..++ ..|.+| ..+|+.|+.+|+.+++| ++++.+++++||+
T Consensus 119 ~~lndqn~~~ae~a~r~~~~dd~~pil~~~~~~~~~a~k~~s~~~~~g~~~vm~l~t~p~~~~eqds~qv~e~~l~lln~ 198 (591)
T KOG2098|consen 119 SLLNDQNAQEAEEAKRGLLQDDAHPILVTYADHSKLAAKMGSVAEKKGPGEVMGLVTGPKRRAEQDSTQVAEFALSLLNG 198 (591)
T ss_pred HHhhhhhhhhhhhhhhhhhcccccchhhhHHHHHHHHHhccchhhccCCcceeeeecCchhhhhHHHHHHHHHHHHHHhc
Confidence 3334443 4477776555543211 000111 222211 45899999999999998 8999999999999
Q ss_pred -CccHHH--HHHHHHHHhhcCcccccccCccCHHHHhhcCCC--------------------------------------
Q psy17828 228 -KPTAKE--RSLAERFRSQSGNQVQEYCSHGTRAECLRMKDT-------------------------------------- 266 (1061)
Q Consensus 228 -~~ta~e--~~~~~~f~~~~~~~~~e~c~~~t~~~c~~~~~~-------------------------------------- 266 (1061)
.+||+| +..+.+||+.++.+++ +..+|+..+.+
T Consensus 199 ~~~sa~~p~~d~~~~~r~h~~~~v~------~~ve~L~~qqst~e~~~~k~~~e~lelip~~ta~e~at~~~~k~~~~aq 272 (591)
T KOG2098|consen 199 LNSSASEPAKDPAKKFRKHAASDVM------LEVESLLNQQSTKEQQSKKVSQEILELIPTTTAKEQATVEKFKSRGRAQ 272 (591)
T ss_pred cCccccCCCCCchhccCCcchhHHH------HHHHHHHcCccHHHHHHHhhhhHHHHhcCCCchhhhhhhhhhhhhhhhh
Confidence 999999 8888888887777666 33445443221
Q ss_pred ---------cccccc--ccccccccCCCCC---CCCCCCCcCCCCCCCCccceeeeeecCccCC-CCCCCcccccccccc
Q psy17828 267 ---------PNICTK--LHFRKIIQCHTDE---SLGDCSFLNTCFHMDSCKYVHYEVDGAKIKG-ISDISDEGNKSLLEK 331 (1061)
Q Consensus 267 ---------~~~c~k--~hf~~~i~~htd~---~lgdcs~L~tc~~~~tC~y~hy~~~~~~~~~-~~~~~~~~~~~~~~~ 331 (1061)
...|.+ .-=+++-+-|+-. +.+|.| |++|.+++|| |++++|.|+. ..+..... .-...
T Consensus 273 vi~~c~~~tke~c~~~s~~~~~c~KlHFrriI~~hTD~S-LGDCSfLnTC----~hm~TCkYVHYe~d~~~~~--~a~~~ 345 (591)
T KOG2098|consen 273 VIEFCDYGTKEECMKASDADRPCRKLHFRRIINKHTDES-LGDCSFLNTC----FHMDTCKYVHYEIDACMDS--EAPGS 345 (591)
T ss_pred hhhhhccccHhhhhccccccchhhhhHHHhhcccccccc-cccchhHhhh----hhhcccceeeeecccchhh--hcCCC
Confidence 114433 1123456668877 459999 9999999999 9999999995 22211000 00011
Q ss_pred cccCCCCceecccCccCcccCCCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEE---ecCccchHHH--
Q psy17828 332 TKLYPPQWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFL---WVTGRAMELG-- 406 (1061)
Q Consensus 332 ~~~~Ppq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFL---WvT~~~Le~g-- 406 (1061)
+...|.+=|.. .|...+...+ +. +=||-++. .||+.|.+.-|.+.|++.. |-. +|++.
T Consensus 346 ~~t~~k~~l~~-~rsv~~~ss~--~~--l~p~QWI~----------CDiR~~dm~iLGkFaVVmADPpWdI--HMeLPYG 408 (591)
T KOG2098|consen 346 KDTTPKQELAL-TRSVGGDSSA--DR--LFPPQWIC----------CDIRYLDMSILGKFAVVMADPPWDI--HMELPYG 408 (591)
T ss_pred CCCChhhhhcc-cccccccccc--cc--cCCcceEE----------eeceeeeeeeeceeEEEeeCCCccc--eeecCcc
Confidence 22223331111 1111111111 00 23444454 4566677777777777764 664 44442
Q ss_pred ---HHHhhcccee---ccceeEEEcCCcccccCeEEEe-cccccCCCccEEEec
Q psy17828 407 ---RECLKLFMLQ---DEGLLFLWVTGRAMELGRECLK-LSLNCQLSQDVEFTW 453 (1061)
Q Consensus 407 ---~elL~~WGf~---~et~~ivWVtG~~l~~~kECLv-~~i~~nid~DVIvse 453 (1061)
-+=|+.-+.- +++++|.|||||.+..++|||- +++++ .|-|+|.
T Consensus 409 Tm~DdEmr~L~vp~LQddGlIFLWVTGRAmELGrecLnlWGY~r---VdEiiWV 459 (591)
T KOG2098|consen 409 TMTDDEMRRLNVPVLQDDGLIFLWVTGRAMELGRECLNLWGYER---VDEIIWV 459 (591)
T ss_pred ccchHHhhcCCCcccccCcEEEEEEcchHHHHHHHHHHhhchhh---hheeEEE
Confidence 2445555544 8899999999999999999999 66887 5678886
No 28
>cd08062 MPN_RPN7_8 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in 19S proteasomal subunits Rpn7 and Rpn8. This family includes lid subunits of the 26 S proteasome regulatory particles, Rpn7 (PSMD7; proteasome 26S non-ATPase subunit 7; p44), and Rpn8 (PSMD8; proteasome 26S non-ATPase subunit 8; p40; Mov34). Rpn7 is known to be critical for the integrity of the 26 S proteasome complex by establishing a correct lid structure. It is necessary for the incorporation/anchoring of Rpn3 and Rpn12 to the lid and essential for viability and normal mitosis. Rpn7 and Rpn8 are ATP-independent components of the 19S regulator subunit, and contain the MPN structural motif on its N-terminal region. However, while they show a typical MPN metalloprotease fold, they lack the canonical JAMM motif, and therefore do not show catalytic isopeptidase activity. It is suggested that Rpn7 function is primarily structural.
Probab=99.40 E-value=2.6e-13 Score=148.99 Aligned_cols=181 Identities=28% Similarity=0.388 Sum_probs=128.0
Q ss_pred ccccccCCCCccccccc---cccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCCCCCchHHHHHH
Q psy17828 806 FLCGRSSRGGKVGRIRC---RSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPKLHQNDIQINEL 882 (1061)
Q Consensus 806 ~~~g~~~~~g~~~~~~~---~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGselt~~s~lIHef 882 (1061)
.|+|+.. ||.+.+.+| -+.-+.++.- +. -+|.--+++|+++++||||+|.|||||+||++++++|++||++
T Consensus 31 ~LLG~~~-~~~veItnsF~~p~~~~~~~~~-~~----~~d~~y~~~m~~~~kkv~~~e~vVGWY~tg~~~~~~d~~ih~~ 104 (280)
T cd08062 31 VLLGSWK-KGVLDVTNSFAVPFEEDEKDPS-VW----FLDHNYLENMYGMFKKVNAKEKIVGWYSTGPKLRPNDLDINEL 104 (280)
T ss_pred EEEEEEe-CCEEEEEEeeecCccCCCCCcc-hh----hhhHHHHHHHHHHHHHhCCCCCeEEEecCCCCCCcchHHHHHH
Confidence 5899996 589999999 2322222210 00 1355556899999999999999999999999999999999999
Q ss_pred HHhhcCCceEEEEcCCCCCCCCCceeEEEeeeccCCCCcceeeEEeeccccccccccccccccccccccc--ccc---cc
Q psy17828 883 IRRYCTNSVLVIIDAKPKELGLPTEAYRVVDEVHDDGSPTTKTFDHVPSEIGAEEAEEVGVEHLLRDIKD--TTV---GS 957 (1061)
Q Consensus 883 ys~~~~~PIhL~VDt~~~~~~LPi~AYvsv~ev~~dGs~~~k~Fv~VP~~I~aeEAErIgVEhLlr~i~d--at~---s~ 957 (1061)
|++++++||||+|||...+.++|++| |+.++..+..+.+...-+-++.-.+.. ++. ..
T Consensus 105 ~~~~~~~pv~l~vd~~~~~~~lpi~a-----------------Y~s~~~~~~~g~~~~~~F~~vp~~i~~~eaE~igve~ 167 (280)
T cd08062 105 FRRYCPNPVLVIIDVRPKDLGLPTEA-----------------YIAVEEVHDDGTPTSKTFVHVPSEIGAEEAEEVGVEH 167 (280)
T ss_pred HHHhCCCCEEEEEecCCCCCCCceEE-----------------EEEeeeccCCCCcceeEEEEcceEeeccchHHHHHHH
Confidence 99999999999999998777777765 444443332222233333334333331 111 11
Q ss_pred ch-----hhhhhHHHHHHHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHh-hccccccCCCcccccc
Q psy17828 958 LS-----QRVTNQLMGLKGLNQQIKEIEKYVGQVSRYWPPFYVVVINLID-KRSVTHLSGPGRWLLP 1018 (1061)
Q Consensus 958 L~-----s~l~~~~~aLk~L~~rL~~I~~YLd~V~~gvpp~~~ilr~l~~-~~~~~~~~~~gr~l~~ 1018 (1061)
+. .....+...+..+...|+.+.+-|+.|.+|+ +++.+ +...++ .+||+|..
T Consensus 168 l~r~~~~~~~~~l~~~l~~~~~al~~L~~~l~~i~~Yl-------~~V~~g~~~~d~--~IlR~l~~ 225 (280)
T cd08062 168 LLRDIKDVTVSTLSTRVTNKLNSLKGLQSKLKEIKDYL-------QLVVEGKLPINH--QIIYNLQD 225 (280)
T ss_pred HHhhccCcccchhHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHCCCCCCCH--HHHHHHHH
Confidence 11 1222344478888999999999999999998 88887 677777 99999864
No 29
>KOG1555|consensus
Probab=99.27 E-value=1.1e-11 Score=136.67 Aligned_cols=153 Identities=25% Similarity=0.420 Sum_probs=128.6
Q ss_pred CcccceEEEeehhHhhHHHHHhhccccCCcee-EEEEE-ee---EEecCcEEEEEEEeeccccCCCCCCccccccHHHHH
Q psy17828 632 EVVTSKVVVHPLVLLSVVDHFNRMSKIGNQKR-VVGVL-LG---CWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLE 706 (1061)
Q Consensus 632 ~~~~~~V~VHPLVLLsIsDH~tR~~~~~~~~r-VvGvL-LG---~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e 706 (1061)
.....+|.++.++++.+++|-.- +.+.. |+|.+ || ......++.|...|+.|+....-..-+-++|+-|+.
T Consensus 27 ~~~~e~v~i~slall~m~rh~r~----~~p~e~v~Glm~lg~~~~fv~~~Tv~vv~v~am~~sg~~is~~~e~~d~V~q~ 102 (316)
T KOG1555|consen 27 SDEKETVYISSLALLKMLRHDRA----GSPEETVMGLMSLGRLPEFVDDYTVRVVDVFAMPQSGTGISKFVEAVDPVFQT 102 (316)
T ss_pred ccCcceeeeehhhhhhccccccc----CCchhhccceeecccccceeeecceeeeeeeccccccceecccchhccHHHHH
Confidence 34567999999999999998632 44555 99999 99 555556899999999998765422124578999999
Q ss_pred HHHHHHHhhcCCCceEEEEecCCC----CCcccHHHHHHHHhhCCCcEEEEEcCCCCCCC-cceEEEEecccccCCCCCC
Q psy17828 707 NMYGMFKKVNAREKVVGWYHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPKELG-LPTEAYRVVDEDKIRPERE 781 (1061)
Q Consensus 707 ~MlemfKkVnp~E~VVGWYsTGp~----ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~g-LplKAYrlv~e~~~~~g~e 781 (1061)
+|+++.+.....+.||||||++|+ ++..|+..|..|+.+.++.+..++||..+..| ....||+++....+.+++|
T Consensus 103 q~~~~l~~tGrp~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d~f~~In~~~~~~~~e 182 (316)
T KOG1555|consen 103 QMMDLLKQTGRPELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPDAFSSINPQWISPGGE 182 (316)
T ss_pred HHHHHHHhcCCcceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCChhhhcCcccccCCCC
Confidence 999999999988999999999996 78899999999999999999999999998754 6677999999999999999
Q ss_pred CCCCCCc
Q psy17828 782 PNPRPSA 788 (1061)
Q Consensus 782 ~~~~~~~ 788 (1061)
++++.+.
T Consensus 183 prqtts~ 189 (316)
T KOG1555|consen 183 PRQTTSN 189 (316)
T ss_pred Ccccccc
Confidence 8776654
No 30
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=99.08 E-value=1.5e-09 Score=117.38 Aligned_cols=132 Identities=18% Similarity=0.267 Sum_probs=100.0
Q ss_pred ceEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEec------CcEEEEEEEeeccccCCCCCCccccccHHH----H
Q psy17828 636 SKVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKG------KGILDVSNSFAVPFDEDDKDNSVWFLDHDY----L 705 (1061)
Q Consensus 636 ~~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g------~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y----~ 705 (1061)
.+|.|.+.+++.|+.|..+ +.+..|+|.|+|...+ ...+.|+.-++.+..+ ....-+.+|++- .
T Consensus 2 ~~V~Is~~~l~~il~HA~~----~~P~EvCGLL~G~~~~~~~~~~~~~v~i~~~~~~~~~~--~s~~r~eidPee~~~a~ 75 (244)
T cd08068 2 SKVHLSADVYLVCLTHALS----TEKEEVMGLLIGEIEVSKKGEEVAIVHISAVIILRRSD--KRKDRVEISPEQLSAAS 75 (244)
T ss_pred cEEEECHHHHHHHHHHHHh----CCCcceeEEEEeecccccccccceeEEEeeeccccccC--CCCceEEeCHHHHHHHH
Confidence 4789999999999999977 5688999999998742 2345555544443322 223346778753 3
Q ss_pred HHHHHHHHhhcCCCceEEEEecCCC----CCcccHHHHHHHHhhCCCcEEEEEcCCC----CC-CCcceEEEEeccc
Q psy17828 706 ENMYGMFKKVNAREKVVGWYHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKP----KE-LGLPTEAYRVVDE 773 (1061)
Q Consensus 706 e~MlemfKkVnp~E~VVGWYsTGp~----ls~~Dl~Ihe~f~~~~~nPI~LivDPs~----ss-~gLplKAYrlv~e 773 (1061)
..+.+|.+.+..++.+||||||+|. ++..|+..|..|+...+..++||+++.. +. +...++||++.+.
T Consensus 76 ~ea~~~~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~g 152 (244)
T cd08068 76 TEAERLTEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQG 152 (244)
T ss_pred HHHHHHHhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecCC
Confidence 5667778889999999999999985 7899999988998888888999997543 22 3488999999754
No 31
>KOG1556|consensus
Probab=99.01 E-value=9.8e-11 Score=124.52 Aligned_cols=50 Identities=42% Similarity=0.675 Sum_probs=45.5
Q ss_pred CccccccccccccchhHHHHHHHHHHHHHHHhhhhcccccchhHHHHHhh
Q psy17828 495 DAEVNIEFNFSLQHFSQVVYLAAMIRSIIALHNLINNKITNRDAEKKEIT 544 (1061)
Q Consensus 495 ~~~Vniefnv~~Nd~~~~vYla~~~~~~~alh~li~nk~~~~~~~~~~~~ 544 (1061)
...+..+|+|++||.++++|+++|+|||+||||||+||++|+++|+++.+
T Consensus 243 ~~~~~~a~~vktndql~~iY~sslvrsViAlhdLi~Nkl~nk~~e~~d~K 292 (309)
T KOG1556|consen 243 RNELVKAFNVKTNDQLMVIYLSSLVRSVIALHDLINNKLANKKAEKEDSK 292 (309)
T ss_pred chhhhhhhccccCceeeeeeHHHHHHHHHHHHHHHHhHhhhhhhhhhhcc
Confidence 35677899999999999999999999999999999999999999986654
No 32
>KOG2975|consensus
Probab=98.84 E-value=3.8e-09 Score=113.76 Aligned_cols=59 Identities=29% Similarity=0.437 Sum_probs=56.5
Q ss_pred hcCCCceEEEEecCCCCCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEeccc
Q psy17828 715 VNAREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDE 773 (1061)
Q Consensus 715 Vnp~E~VVGWYsTGp~ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv~e 773 (1061)
+||+|.+||||.||+.++.....||++|.+.+++||+|.+|++.+++.+++|||.++.-
T Consensus 94 ~npnE~vvGWyaTg~dvt~~sslihdyYare~~~pvhLtVDT~~~n~rm~ikaYvss~~ 152 (288)
T KOG2975|consen 94 VNPNELVVGWYATGHDVTEHSSLIHDYYAREAPNPVHLTVDTSLQNGRMSIKAYVSSLM 152 (288)
T ss_pred cCCCceeEEEEecCCCcccchhHHHHHhhccCCCCeEEEEeccccCCccceeEEEEecc
Confidence 89999999999999999999999999999999999999999999988899999998853
No 33
>cd08065 MPN_eIF3h Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in eIF2h. Eukaryotic translation initiation factor 3 (eIF3) subunit h (eIF3h; eIF3 subunit 3; eIF3S3; eIF3-gamma; eIF3-p40) is an evolutionarily non-conserved subunit of the functional core that comprises eIF3a, eIF3b, eIF3c, eIF3e, eIF3f, and eIF3h, and contains the MPN domain. However, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.Together with eIF3e and eIF3f, eIF3h stabilizes the eIF3 complex. Results suggest that eIF3h regulates cell growth and viability, and that over-expression of the gene may provide growth advantage to prostate, breast, and liver cancer cells. For example, EIF3h gene amplification is common in late-stage prostate cancer suggesting that it may be functionally involved in the progression of the disease. It has been shown that coamplification of MYC, a well characterized oncogene involved in cell growth, different
Probab=98.69 E-value=7.5e-09 Score=113.21 Aligned_cols=178 Identities=16% Similarity=0.189 Sum_probs=120.5
Q ss_pred ccccccCCCCccccccc---cccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCC-CCCCchHHHHH
Q psy17828 806 FLCGRSSRGGKVGRIRC---RSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGP-KLHQNDIQINE 881 (1061)
Q Consensus 806 ~~~g~~~~~g~~~~~~~---~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGs-elt~~s~lIHe 881 (1061)
.|+|... ||.+.+++| -+.-+.+.. + |.-.+..-..+|+++++|+|++|.|||||+|++ +-.-+..+||.
T Consensus 28 ~LLG~~~-~~~leVtn~Fp~P~~~~~~~~---~--~~~~~~~yq~~m~~~~r~v~~~e~iVGWY~S~p~~~~~~~s~id~ 101 (266)
T cd08065 28 QLLGLDV-GGTLEVTNCFPFPKSEEDDSD---R--ADEDIADYQLEMMRLLREVNVDHNHVGWYQSTYLGSFFTRDLIET 101 (266)
T ss_pred EEeeeEc-CCEEEEEeccCCCCCCCCCcc---h--hhhhHHHHHHHHHHHHHHhCCCCcEEEeEeecCCCCcCCHHHHHH
Confidence 5889986 688899999 232222221 1 111233345789999999999999999999999 44445999999
Q ss_pred HHHhhc--CCceEEEEcCCC-CCCCCCceeEEEeeeccC--------------CCCcceeeEEeeccccccccccccccc
Q psy17828 882 LIRRYC--TNSVLVIIDAKP-KELGLPTEAYRVVDEVHD--------------DGSPTTKTFDHVPSEIGAEEAEEVGVE 944 (1061)
Q Consensus 882 fys~~~--~~PIhL~VDt~~-~~~~LPi~AYvsv~ev~~--------------dGs~~~k~Fv~VP~~I~aeEAErIgVE 944 (1061)
+|+..+ ++||||++|+.. .++.++++||........ .+......|.+||++|...+.+.+-+.
T Consensus 102 ~~~~q~~~~~~v~Li~D~~~s~~g~l~lkAyrl~~~~~~~~~~~~~~~~~l~~~~~~~~~if~eiPv~i~n~~l~~~~L~ 181 (266)
T cd08065 102 QYNYQEAIEESVVLVYDPSKTSQGSLSLKAYRLSEKFMELYKEGKFSTESLREANLTFSNIFEEIPVVIRNSHLVNALLS 181 (266)
T ss_pred HHHHhccCCCCEEEEECCCcccccceeeEEEEEcHHHHHHhhcCCcCHHHHHHhcCchhcEEEEEEEEEEchHHHHHHHH
Confidence 999976 789999999986 467799999998664221 023456789999999999998888887
Q ss_pred ccccccccc--ccccc-hhhhhhHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy17828 945 HLLRDIKDT--TVGSL-SQRVTNQLMGLKGLNQQIKEIEKYVGQVSRY 989 (1061)
Q Consensus 945 hLlr~i~da--t~s~L-~s~l~~~~~aLk~L~~rL~~I~~YLd~V~~g 989 (1061)
.+......+ ..+.| .+....+...|+.|.+.|+.+..+..+...|
T Consensus 182 ~l~~~~~~~~~~~~~l~l~~~~~le~~l~~l~~~id~l~~e~~~~~~y 229 (266)
T cd08065 182 ELEEDSPSSQSDFDRLDLSTNSFLEKNLELLMESVDELSQEQGKFNYY 229 (266)
T ss_pred hcccCCCcccCCcccccccCchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 775543321 11111 1222333444555555555555555555443
No 34
>cd08069 MPN_RPN11_CSN5 Mov34/MPN/PAD-1 family: proteasomal regulatory protein Rpn11 and signalosome complex subunit CSN5. This family contains proteasomal regulatory protein Rpn11 (26S proteasome regulatory subunit rpn11; PAD1; POH1; RPN11; PSMD14; Rpn11 subunit of the 19S-proteasome; regulatory particle number 11) and signalosomal CSN5 (COP9 signalosome complex subunit 5; COP9 complex homolog subunit 5; c-Jun activation domain-binding protein-1; CSN5/JAB1; JAB1). COP9 signalosome (CSN) and the proteasome lid are paralogous complexes and their respective subunits CSN5 and Rpn11 are most closely related between the two complexes, both containing the conserved JAMM (JAB1/MPN/Mov34 metalloenzyme) motif involved in zinc ion coordination and providing the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology; mutations i
Probab=98.67 E-value=1.5e-08 Score=111.07 Aligned_cols=135 Identities=17% Similarity=0.177 Sum_probs=103.9
Q ss_pred ccccccCCCCccccccc---cccccccccceeeeecCCCCCcceecccC--cCCCCCCccceeeeeccCCC----CCCch
Q psy17828 806 FLCGRSSRGGKVGRIRC---RSHFSTTGVLSIRRIFNPIGTWTFIRIPT--TTWPSRAREKVVGWYHTGPK----LHQND 876 (1061)
Q Consensus 806 ~~~g~~~~~g~~~~~~~---~~~~~~~g~~~~~~~~~~~~~~~~~~m~~--L~qKVNPkE~IVGWYsTGse----lt~~s 876 (1061)
+|+|+. .++.+.+++| .+.-+.+ + ++-.+ -.++.|.+ +++++++.|.|||||+|++. +...|
T Consensus 37 lLlG~~-~~~~v~Vt~~fp~p~~~t~~---~----v~~~~-e~~~~m~~~~~~~~~~~~~~vVGWYHSHP~~g~~~S~~D 107 (268)
T cd08069 37 LMLGKV-DDYTIIVVDVFALPVEGTET---R----VNAQD-EFQEYMVQYEMLKQTGRPENVVGWYHSHPGYGCWLSGID 107 (268)
T ss_pred EEEeee-cCCeEEEEEEEECCcCCCCC---c----eeccH-HHHHHHHHHHHHHHhCCCceeEeeeccCCCcCCcCCHHH
Confidence 688886 3567778888 3322222 1 12222 23578999 99999999999999999997 99999
Q ss_pred HHHHHHHHhhcCCceEEEEcCCC--CCCCCCceeEEEeeeccCC---CC-----------------cceeeEEeeccccc
Q psy17828 877 IQINELIRRYCTNSVLVIIDAKP--KELGLPTEAYRVVDEVHDD---GS-----------------PTTKTFDHVPSEIG 934 (1061)
Q Consensus 877 ~lIHefys~~~~~PIhL~VDt~~--~~~~LPi~AYvsv~ev~~d---Gs-----------------~~~k~Fv~VP~~I~ 934 (1061)
..+|.+|.+.++++|+|+||+.. ..+.+.+.||..+...... +. .....|.+||+++.
T Consensus 108 v~tq~~yq~~~~~~V~lViDP~~t~~~g~~~i~Afr~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~y~~l~i~~~ 187 (268)
T cd08069 108 VNTQQLNQQLQDPFVAVVVDPIRSLVKGKVVIGAFRTIPPGYKPLEPRQTTSNIGHLPKPKIEDFGGHNKQYYSLPIEYF 187 (268)
T ss_pred HHHHHHHHhcCCCcEEEEEeCCccccCCcceeeEEEEECccccccCcccCccccCccCcHHHHHhCchhcEEEEeeeEEe
Confidence 99999999999999999999754 4677899999987743221 11 14578999999999
Q ss_pred ccccccccccccccc
Q psy17828 935 AEEAEEVGVEHLLRD 949 (1061)
Q Consensus 935 aeEAErIgVEhLlr~ 949 (1061)
..+.|+..++.|.+.
T Consensus 188 ~s~l~~~~L~~l~~~ 202 (268)
T cd08069 188 KSSLDRKLLLNLWNK 202 (268)
T ss_pred cCHHHHHHHHHHHHH
Confidence 999999999877764
No 35
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=98.53 E-value=1.5e-06 Score=90.03 Aligned_cols=119 Identities=13% Similarity=0.191 Sum_probs=87.3
Q ss_pred EEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhh-c
Q psy17828 638 VVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKV-N 716 (1061)
Q Consensus 638 V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkV-n 716 (1061)
+.|-.-.+-+|+.|..+.. ..+..+.|.|+|...+ ++.+|++.|-.|....... +...|.. ++++.. -
T Consensus 4 l~Ipk~il~~~l~~A~~~~--~~p~E~cGlL~G~~~~-~~~~I~~i~~~~q~~~~~~--~~~~~~~------e~~~~~~~ 72 (173)
T cd08066 4 VVVPADLMDKFLQLAEPNT--SRNLETCGILCGKLSN-NAFFITHLIIPKQSGTSDS--CQTTNEE------ELFDFQDQ 72 (173)
T ss_pred EEECHHHHHHHHHHHHhCC--CCCCeEEEEEEeEcCC-CeEEEEEEEeccccCCCce--ecCCCHH------HHHHHHHh
Confidence 4555567788888887631 1246899999998654 5789999877776654432 2223421 123322 3
Q ss_pred CCCceEEEEecCCC----CCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEec
Q psy17828 717 AREKVVGWYHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVV 771 (1061)
Q Consensus 717 p~E~VVGWYsTGp~----ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv 771 (1061)
.++.+||||||+|. +++.|+..|..|+...+..++|+++|. ...++||++.
T Consensus 73 ~gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~----~~~l~afrl~ 127 (173)
T cd08066 73 HDLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK----YNEFGIFRLT 127 (173)
T ss_pred CCCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC----CcEEeEEEee
Confidence 57899999999884 899999999999888899999999973 5789999998
No 36
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=98.47 E-value=1.7e-08 Score=96.50 Aligned_cols=68 Identities=35% Similarity=0.466 Sum_probs=14.0
Q ss_pred ccccccccccccccccccccccchhhhhhHHHHHHHHHHHHHHHHHHHHHHhhc-CCCCHHHHHHHHhh
Q psy17828 936 EEAEEVGVEHLLRDIKDTTVGSLSQRVTNQLMGLKGLNQQIKEIEKYVGQVSRY-WPPFYVVVINLIDK 1003 (1061)
Q Consensus 936 eEAErIgVEhLlr~i~dat~s~L~s~l~~~~~aLk~L~~rL~~I~~YLd~V~~g-vpp~~~ilr~l~~~ 1003 (1061)
+|||||||+|++++..+...+++.+++..+..++.+|+.+|..+..||++|.+| +|+|+.|+|.|++.
T Consensus 1 eEaErigv~~l~~~~~~~~~s~~~~~l~~~~~al~~L~~~l~~i~~Yl~~v~~g~~~~d~~i~r~l~~l 69 (115)
T PF13012_consen 1 EEAERIGVDHLARGLGDHYYSSLSSQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQDL 69 (115)
T ss_dssp SHHHHHHHHHHHHH--S----------------------------------------------------
T ss_pred CchHHHHHHHHHccCCCccccHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHHHH
Confidence 589999999999988877777889999999999999999999999999999999 99999999999884
No 37
>PF01398 JAB: JAB1/Mov34/MPN/PAD-1 ubiquitin protease; InterPro: IPR000555 Members of this family are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This family is also known as the MPN domain [] and PAD-1-like domain []. It has been shown that this domain occurs in prokaryotes []. Mov34 proteins act as the regulatory subunit of the 26 proteasome, which is involved in the ATP-dependent degradation of ubiquitinated proteins. The function of this domain is unclear, but it is found in the N terminus of the proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. A number of the proteins associated with this family belong to MEROPS peptidase family M67 (clan M-). This includes the Poh1 peptidase of Saccharomyces cerevisiae (Baker's yeast) which is a component of the 19S proteasome regulatory particle.; GO: 0005515 protein binding; PDB: 2ZNV_D 2ZNR_A 4E0Q_A 2P87_A 2P8R_A 2O96_B 2O95_A 3RZU_F 3RZV_A.
Probab=98.18 E-value=2.7e-07 Score=87.83 Aligned_cols=76 Identities=17% Similarity=0.232 Sum_probs=57.5
Q ss_pred ccccccCCCCccccccc---cccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCCC----CCchHH
Q psy17828 806 FLCGRSSRGGKVGRIRC---RSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPKL----HQNDIQ 878 (1061)
Q Consensus 806 ~~~g~~~~~g~~~~~~~---~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGsel----t~~s~l 878 (1061)
+|+|+...++.+.+++| .+.-+.++...+-. +.. ..|+++++|++|++.+||||+|++.+ +..|..
T Consensus 31 ~LlG~~~~~~~v~I~~~f~~p~~~~~~~~~~~~~-----~~~--~~~~~~~~~~~~~~~iVGWY~s~p~~~~~~S~~di~ 103 (114)
T PF01398_consen 31 LLLGTQDGDNTVEITNSFPVPHSESEDDCDMDDE-----DFQ--KKMIELLKKVNPNLEIVGWYHSHPNISCFPSPTDIE 103 (114)
T ss_dssp EEEEEEETT-EEEEEEEEEESEEEESSEEEEECC-----HHH--HHHHHHHHHCSTTSEEEEEEEEESSS-SS--HHHHH
T ss_pred EEEEEecCceEEEEEEEEEeeEecCccccccchh-----hHH--HHHHhhhccccccceEEEEEEccCCccccCCHHHHH
Confidence 69999987778889998 34434443322111 111 48999999999999999999999988 999999
Q ss_pred HHHHHHhhcC
Q psy17828 879 INELIRRYCT 888 (1061)
Q Consensus 879 IHefys~~~~ 888 (1061)
+|..|.+.++
T Consensus 104 ~q~~~q~~~~ 113 (114)
T PF01398_consen 104 TQKQYQRMNP 113 (114)
T ss_dssp HHHHHHHHTT
T ss_pred HHHHHHHhCC
Confidence 9999999864
No 38
>cd08070 MPN_like Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding). This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=98.11 E-value=3e-05 Score=75.87 Aligned_cols=113 Identities=18% Similarity=0.213 Sum_probs=81.3
Q ss_pred hHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcCCCceEE
Q psy17828 644 VLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNAREKVVG 723 (1061)
Q Consensus 644 VLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp~E~VVG 723 (1061)
++-+|+.|+.+ ..+..+.|.|+|...+.. ..|+..|++|....+.. ..+.+|+..+..+.+..++. .+.+||
T Consensus 3 ~~~~il~ha~~----~~P~E~cGlL~G~~~~~~-~~i~~~~p~~n~~~~~~-~~f~~d~~~~~~~~~~~~~~--g~~~vG 74 (128)
T cd08070 3 LLEAILAHAEA----EYPEECCGLLLGKGGGVT-AIVTEVYPVRNVAESPR-RRFEIDPAEQLAAQREARER--GLEVVG 74 (128)
T ss_pred HHHHHHHHHHh----CCCCceEEEEEeecCCCC-ceEEEEEEccCCCCCCC-ceEEECHHHHHHHHHHHHHC--CCeEEE
Confidence 45678888876 467899999999986543 46788999987554321 34678998887777777765 589999
Q ss_pred EEecCCC----CCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEec
Q psy17828 724 WYHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVV 771 (1061)
Q Consensus 724 WYsTGp~----ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv 771 (1061)
||||+|. ++..|+.... ....++||+..... ...++||+..
T Consensus 75 ~~HSHP~~~~~PS~~D~~~~~-----~~~~~~lIv~~~~~--~~~~~~~~~~ 119 (128)
T cd08070 75 IYHSHPDGPARPSETDLRLAW-----PPGVSYLIVSLAGG--APELRAWRLE 119 (128)
T ss_pred EEeCCCCCCCCCCHHHHHhcc-----CCCCeEEEEECCCC--CcEEEEEEEc
Confidence 9999985 4555554432 12468888886443 4568899875
No 39
>smart00232 JAB_MPN JAB/MPN domain. Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.
Probab=98.09 E-value=2.4e-06 Score=82.34 Aligned_cols=99 Identities=19% Similarity=0.210 Sum_probs=73.4
Q ss_pred ccccccCCCCccccccc---cccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCC----CCCCchHH
Q psy17828 806 FLCGRSSRGGKVGRIRC---RSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGP----KLHQNDIQ 878 (1061)
Q Consensus 806 ~~~g~~~~~g~~~~~~~---~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGs----elt~~s~l 878 (1061)
+|+|... ++.+.+.+| ......+.. +-++.-+++.|.++++++++.+.+||||+|++ .++..|..
T Consensus 27 ~L~G~~~-~~~~~i~~~~~~p~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~vGwyhshp~~~~~pS~~D~~ 98 (135)
T smart00232 27 VLLGKSN-KDRPEVKEVFAVPNEPQDDSV-------QEYDEDYSHLMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVA 98 (135)
T ss_pred EEEEEEc-CCEEEEEEEEecCcCCCCcch-------hhhhhhHHHHHHHHHHhhCCCceEEEEEEcCCCCCCCcCHHHHH
Confidence 6777765 345555555 222111111 01244556899999999999999999999987 67888999
Q ss_pred HHHHHHhhcCCceEEEEcCCCCC-CCCCceeEEEe
Q psy17828 879 INELIRRYCTNSVLVIIDAKPKE-LGLPTEAYRVV 912 (1061)
Q Consensus 879 IHefys~~~~~PIhL~VDt~~~~-~~LPi~AYvsv 912 (1061)
+|..|..+...++++++|+.... +.++++||+.+
T Consensus 99 ~~~~~~~~~~~~~~~~v~~~~s~~g~~~~~af~~~ 133 (135)
T smart00232 99 THESYQAPWPISVVLIVDPIKSFQGRLSLRAFRLT 133 (135)
T ss_pred HHHHHHhcCCceEEEEECCCccccCcEEEEEEEec
Confidence 99999999999999999988755 66889998854
No 40
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=97.86 E-value=0.0002 Score=75.18 Aligned_cols=107 Identities=18% Similarity=0.267 Sum_probs=75.1
Q ss_pred ehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHH--HHHHHHHHHhhcCCC
Q psy17828 642 PLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDY--LENMYGMFKKVNARE 719 (1061)
Q Consensus 642 PLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y--~e~MlemfKkVnp~E 719 (1061)
+.+..+|+.|..+ ..+..|.|+|+|....++++.|++++|+.+.. ..+++.. ...+.+.+-+- ...
T Consensus 3 ~~ay~ki~~HA~k----~p~~evcGlLlG~~~~~~~~~V~d~vPl~h~~-------~~l~P~~Eval~~ve~~~~~-~gl 70 (182)
T cd08060 3 TLAYVKMLLHAAK----YPHCAVNGLLLGKKSSGGSVEITDAVPLFHSC-------LALAPMLEVALALVDAYCKS-SGL 70 (182)
T ss_pred HHHHHHHHHHHHH----cCCchheEEEEeeecCCCCEEEEEEEEcCCCc-------cccCHHHHHHHHHHHHHHHH-CCC
Confidence 4677899999987 23568999999998623468999999998732 3466653 11122222222 368
Q ss_pred ceEEEEecCCCCC-----cccHHHHHHHHhhCCCcEEEEEcCCCCC
Q psy17828 720 KVVGWYHTGPKLH-----QNDIQINELIRRYCTNSVLVIIDAKPKE 760 (1061)
Q Consensus 720 ~VVGWYsTGp~ls-----~~Dl~Ihe~f~~~~~nPI~LivDPs~ss 760 (1061)
.|||+||++|.+. ..-..|-+-+.++++++++|++|-....
T Consensus 71 ~IvG~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~~l~ 116 (182)
T cd08060 71 VIVGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNEKLT 116 (182)
T ss_pred EEEEEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCcccc
Confidence 9999999999654 3334555666778889999999987653
No 41
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=97.80 E-value=5e-05 Score=75.02 Aligned_cols=100 Identities=22% Similarity=0.348 Sum_probs=63.7
Q ss_pred EEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcC-
Q psy17828 639 VVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNA- 717 (1061)
Q Consensus 639 ~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp- 717 (1061)
.+-..++-.|+.|..| ..+.+++|.|+|...+ ...|+++.... +..+..++..|..++...+.
T Consensus 3 ~i~~~~l~~il~~a~~----~~p~E~~g~l~~~~~~------~~~~~~~n~~~------~~~~~~~~~~~~~~~~~~~~~ 66 (134)
T COG1310 3 VIPKEVLGAILEHARR----EHPREVCGLLAGTREG------ERYFPLKNVSV------EPVEYFEIDPEYSLFYLAAED 66 (134)
T ss_pred eecHHHHHHHHHHHHh----cCChheEEEEEeeccc------ceeeccccccC------CcceeEeeCHHHHHHHHHHhh
Confidence 4566788899999988 4568999999999754 33444443222 12333333334333333332
Q ss_pred -CCceEEEEecCCC--CCcccHHHHHHHHhhCCCcEEEEEcC
Q psy17828 718 -REKVVGWYHTGPK--LHQNDIQINELIRRYCTNSVLVIIDA 756 (1061)
Q Consensus 718 -~E~VVGWYsTGp~--ls~~Dl~Ihe~f~~~~~nPI~LivDP 756 (1061)
.+.+||||||+|. ..+++..++ ++++.+.|.+++..+
T Consensus 67 ~g~~vvg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~~ 106 (134)
T COG1310 67 AGEVVVGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSVP 106 (134)
T ss_pred CCCEEEEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEcC
Confidence 3999999999995 445555555 777777776666553
No 42
>KOG3050|consensus
Probab=97.69 E-value=2e-05 Score=84.81 Aligned_cols=53 Identities=17% Similarity=0.308 Sum_probs=48.3
Q ss_pred eecccCcCCCCCCccceeeeeccCCCCCCchHHHHHHHHhhcCCceEEEEcCC
Q psy17828 846 FIRIPTTTWPSRAREKVVGWYHTGPKLHQNDIQINELIRRYCTNSVLVIIDAK 898 (1061)
Q Consensus 846 ~~~m~~L~qKVNPkE~IVGWYsTGselt~~s~lIHefys~~~~~PIhL~VDt~ 898 (1061)
+++=-+++++|.|...|+||||||+..++.|..||.....-++.|++|.+++.
T Consensus 76 l~kk~eqykqVFpdl~vlGwYttG~d~t~sd~~i~k~l~~i~esplflkLNp~ 128 (299)
T KOG3050|consen 76 LEKKEEQYKQVFPDLYVLGWYTTGSDPTPSDIHIHKQLMDINESPLFLKLNPA 128 (299)
T ss_pred HHHHHHHHHHhcccceEEEEeecCCCCChhhhHHHHHHHhhhcCceEEEecch
Confidence 44455789999999999999999999999999999999999999999999754
No 43
>cd07767 MPN Mpr1p, Pad1p N-terminal (MPN) domains. MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. J
Probab=97.68 E-value=2.6e-05 Score=73.57 Aligned_cols=61 Identities=41% Similarity=0.734 Sum_probs=52.4
Q ss_pred ccCcCCCCCCccceeeeeccCCC----CCCchHHHHHHHHhhcCCceEEEEcCCCCCCCCCceeE
Q psy17828 849 IPTTTWPSRAREKVVGWYHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAY 909 (1061)
Q Consensus 849 m~~L~qKVNPkE~IVGWYsTGse----lt~~s~lIHefys~~~~~PIhL~VDt~~~~~~LPi~AY 909 (1061)
|......++..+.+||||+|.+. ++..|...|..|.+..+++++|++|+.+.+.++|++||
T Consensus 52 ~~~~~~~~~~~~~iVGwyhshp~~~~~~s~~dv~~~~~~q~~~~~~v~li~~~~~~~~~~~~~~~ 116 (116)
T cd07767 52 MYLDFKKLNAGLRIVGWYHTHPKPSCFLSPNDLATHELFQRYFPEKVMIIVDVKPKDLGNSWKCY 116 (116)
T ss_pred HHHHHHHhcCCCeEEEEEEcCCCCCCccCHHHHHHHHHHHHhCCCCEEEEEECCCccCCCCcccC
Confidence 44556677899999999999875 89999999999998888999999999987777888876
No 44
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=97.23 E-value=0.0043 Score=65.99 Aligned_cols=114 Identities=16% Similarity=0.203 Sum_probs=80.6
Q ss_pred eEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecCcE-EEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhh
Q psy17828 637 KVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGI-LDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKV 715 (1061)
Q Consensus 637 ~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gt-VEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkV 715 (1061)
+|.+.+.+..+|+=|..+.. ...|.|+|||...+++. |.|++|.|+=+..-.=.| . .+-.-.+.+.|-+.
T Consensus 3 ~v~is~~AY~K~~LHaaKyP----~~aVnGvLlg~~~~~~~~v~i~DaVPLfH~~~~L~P---m--lEvAL~qvd~~~~~ 73 (196)
T PF03665_consen 3 SVEISSRAYAKMILHAAKYP----HCAVNGVLLGKSSKSSSEVEIVDAVPLFHHWLSLSP---M--LEVALAQVDAYAKS 73 (196)
T ss_pred eEEEcHHHHHHHHHHhccCC----CCceeeEEEeccCCCCceEEEeeceeccccccCcch---H--HHHHHHHHHHHHhh
Confidence 68899999999999997742 46899999999865543 999999999774321111 0 12223334444433
Q ss_pred cCCCceEEEEecCCC-----CCcccHHHHHHHHhhCCCcEEEEEcCCCCC
Q psy17828 716 NAREKVVGWYHTGPK-----LHQNDIQINELIRRYCTNSVLVIIDAKPKE 760 (1061)
Q Consensus 716 np~E~VVGWYsTGp~-----ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss 760 (1061)
.+..|||+|+.... +++.-..|-+.+.++++++++|++|-..-.
T Consensus 74 -~gl~IvGyY~Ane~~~d~~~~~~a~kiad~I~~~~~~a~ll~idn~kl~ 122 (196)
T PF03665_consen 74 -NGLVIVGYYQANERLDDNSPSPVAEKIADKIAENFSDACLLMIDNKKLS 122 (196)
T ss_pred -CCCEEEEEEEeccccccCCCCHHHHHHHHHHHhhCCCcEEEEEECcccc
Confidence 45999999999764 444445666677778899999999987643
No 45
>TIGR02256 ICE_VC0181 integrative and conjugative element protein, VC0181 family. This uncharacterized protein is found in several Proteobacteria, among them Rhizobium sp. NGR234, Vibrio cholerae, Myxococcus xanthus, and E. coli strain ECOR31. In the latter, it is part of an integrative and conjugative element that is readily induced to excise and circularize.
Probab=95.72 E-value=0.11 Score=52.57 Aligned_cols=83 Identities=17% Similarity=0.276 Sum_probs=54.5
Q ss_pred hHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHH-HHHHhhcCCCceE
Q psy17828 644 VLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMY-GMFKKVNAREKVV 722 (1061)
Q Consensus 644 VLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~Ml-emfKkVnp~E~VV 722 (1061)
+++.++..|.... ..+...-|+|+|.+.++ .+.|+.. ..|..++-....-+..+...++..+ +.|++.+-....|
T Consensus 1 ~v~~~~~~~~Q~~--~~~~EtGGiLiG~~~~~-~~ii~~~-t~P~p~d~~tr~~F~r~~~~~q~~i~~~~~~s~g~~~yl 76 (131)
T TIGR02256 1 VVVAMLKSYRQWH--DLSTETGGVLIGERRGA-HAVITKI-SEPGSGDIRTRKRFSRDGEHHQSEVDEHFEVSGGVDTYL 76 (131)
T ss_pred CHHHHHHHHHhCc--CCCCccceEEEEEEcCC-cEEEEEE-EcCCCCcccCceEEEeCcHHHHHHHHHHHHHhCCceEEE
Confidence 4667777775532 45678999999999865 5777663 3454444333333344556665554 4556666669999
Q ss_pred EEEecCCC
Q psy17828 723 GWYHTGPK 730 (1061)
Q Consensus 723 GWYsTGp~ 730 (1061)
|=+||+|.
T Consensus 77 GeWHtHP~ 84 (131)
T TIGR02256 77 GEWHTHPE 84 (131)
T ss_pred EecCcCCC
Confidence 99999986
No 46
>cd08072 MPN_archaeal Mov34/MPN/PAD-1 family: archaeal JAB1/MPN/Mov34 metalloenzyme. This family contains only archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=94.77 E-value=0.34 Score=47.59 Aligned_cols=99 Identities=18% Similarity=0.147 Sum_probs=61.4
Q ss_pred HhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcCCCceEEE
Q psy17828 645 LLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNAREKVVGW 724 (1061)
Q Consensus 645 LLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp~E~VVGW 724 (1061)
+-.|++|..+ ..+..+.|.|+|... .|++.+.+|....... . ...+. .|. -....+||-
T Consensus 6 ~~~i~~ha~~----~~P~E~CGlL~G~~~-----~v~~~~~~~n~~~~~~-~-~~f~~----~~~------~~g~~ivgi 64 (117)
T cd08072 6 LDSILEAAKS----SHPNEFAALLRGKDG-----VITELLILPGTESGEV-S-AVFPL----LML------PLDMSIVGS 64 (117)
T ss_pred HHHHHHHHhh----cCCceEEEEEEeecc-----EEEEEEECCCCCCCCc-c-eeech----HHh------cCCCeEEEE
Confidence 4467888866 567899999999752 4888999985443211 1 11222 122 247899999
Q ss_pred EecCCC----CCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEec
Q psy17828 725 YHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVV 771 (1061)
Q Consensus 725 YsTGp~----ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv 771 (1061)
|||+|. ++..|+... . .+..++||+.+... .=.++||...
T Consensus 65 ~HSHP~~~~~PS~~D~~~~----~-~~~~~~lIvs~~~~--~~~~~a~~~~ 108 (117)
T cd08072 65 VHSHPSGSPRPSDADLSFF----S-KTGLVHIIVGYPYD--EDDWRAYDSD 108 (117)
T ss_pred EEcCCCCCCCCCHHHHHhh----h-cCCCEEEEEECcCC--CCCEEEEecC
Confidence 999985 667775422 1 23456777764221 1347888764
No 47
>KOG3289|consensus
Probab=94.19 E-value=0.77 Score=48.65 Aligned_cols=121 Identities=17% Similarity=0.325 Sum_probs=81.5
Q ss_pred eEEEeehhHhhHHHHHhhccccCCceeEEEEEeeEEecC-cEEEEEEEeeccccCCCCCCccccccH--HHHHHHHHHHH
Q psy17828 637 KVVVHPLVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGK-GILDVSNSFAVPFDEDDKDNSVWFLDH--DYLENMYGMFK 713 (1061)
Q Consensus 637 ~V~VHPLVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~-gtVEVTNSFaVP~eEde~d~~v~~lD~--~Y~e~MlemfK 713 (1061)
+|.+.-++-.+|+=|+.|.. ..-|-|+|+|...++ +.++|++|.|+=++--. +-+ +-.-.|.+-+-
T Consensus 3 ~veis~~aY~kmiLH~akyp----h~aVnGLLla~~~~kg~~v~itdcVPLfH~~la-------LaPmlEvAl~lId~~~ 71 (199)
T KOG3289|consen 3 EVEISALAYVKMILHAAKYP----HAAVNGLLLAPATGKGECVEITDCVPLFHSHLA-------LAPMLEVALNLIDVWG 71 (199)
T ss_pred ceeehhhHHHHHHHHhccCc----ccceeeEEEeccCCCCCeEEEEecchhhccccc-------cccHHHHHHHHHHHHH
Confidence 57788899999999998843 467999999965543 47999999998554321 111 12222222222
Q ss_pred hhcCCCceEEEEecCCCCC-----cccHHHHHHHHhhCCCcEEEEEcCCCCC-CC--cceEEEE
Q psy17828 714 KVNAREKVVGWYHTGPKLH-----QNDIQINELIRRYCTNSVLVIIDAKPKE-LG--LPTEAYR 769 (1061)
Q Consensus 714 kVnp~E~VVGWYsTGp~ls-----~~Dl~Ihe~f~~~~~nPI~LivDPs~ss-~g--LplKAYr 769 (1061)
+-....|+|.|+....++ ..-..|-.-++++.++..+|++|...-+ +. -|+-+|+
T Consensus 72 -~~~GlviaGyy~Ane~~~D~s~~~~A~kiadrIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e 134 (199)
T KOG3289|consen 72 -AQAGLVIAGYYHANERVNDQSLNPVALKIADRISEFFPDAAILVLDNKKLVPQCERPPVIVLE 134 (199)
T ss_pred -HhcCeEEEEEeecCCCccccCccHHHHHHHHHHHhhCCCCeEEEEeccccccccCCCCEEEee
Confidence 235688999999976543 3335666778888888777777776533 22 6788887
No 48
>PF14464 Prok-JAB: Prokaryotic homologs of the JAB domain; PDB: 1OI0_A 1R5X_B 2KKS_A 2KCQ_A.
Probab=93.65 E-value=0.17 Score=47.23 Aligned_cols=88 Identities=20% Similarity=0.316 Sum_probs=47.9
Q ss_pred hHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcCCCceEE
Q psy17828 644 VLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNAREKVVG 723 (1061)
Q Consensus 644 VLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp~E~VVG 723 (1061)
++-.|+.|..+ ..+....|+|+|...+. .+.|+.... .+..+ ++.... ++.......+||
T Consensus 4 ~~~~i~~~~~~----~~p~E~~G~L~g~~~~~-~~~~~~~~~----~~p~~---------~~~~~~--~~~~~~~~~~vg 63 (104)
T PF14464_consen 4 VLEQIIAHARA----AYPNEACGLLLGRRDDQ-RFIVVPNVN----PDPRD---------SFRRER--FEARERGLEIVG 63 (104)
T ss_dssp HHHHHHHHHHH----HTTS-EEEEEEEEEECC-EEEEEEEEE------HHC---------HHHHHH---HHHHHT-EEEE
T ss_pred HHHHHHHHHhh----CCCCeEEEEEEEEecCC-EEEEEeCCC----CCcHH---------HHHHHh--hhhhcccceeeE
Confidence 34567777766 35689999999998543 455655554 11111 111111 145667899999
Q ss_pred EEecCCC----CCcccHHHHHHHHhhCCCcEEEEEc
Q psy17828 724 WYHTGPK----LHQNDIQINELIRRYCTNSVLVIID 755 (1061)
Q Consensus 724 WYsTGp~----ls~~Dl~Ihe~f~~~~~nPI~LivD 755 (1061)
.|||+|. ++..|...... ...+++||+-
T Consensus 64 ~~HSHP~~~a~pS~~D~~~~~~----~~~~~~iI~~ 95 (104)
T PF14464_consen 64 IWHSHPSGPAFPSSTDIRSMRD----LAPPSYIIVG 95 (104)
T ss_dssp EEEEESSSSSS--HHHHHTHCC----S-SCEEEEEE
T ss_pred EEEcCCCCCCCCCHHHHHhhhc----cCCeEEEEEe
Confidence 9999885 55566443211 1155666653
No 49
>cd08056 MPN_PRP8 Mpr1p, Pad1p N-terminal (MPN) domains without isopeptidase activity found in splicing factor Prp8. Members of this family are found in pre-mRNA-processing factor 8 (Prp8) which is a critical splicing factor, interacting with several other spliceosomal proteins, snRNAs, and the pre-mRNA, thus organizing and stabilizing the spliceosome catalytic core. Prp8 is one of the largest and most highly conserved of nuclear proteins, occupying a central position in the catalytic core of the spliceosome. Its C-terminal domain exhibits a JAB1/MPN-like core similar to deubiquitinating enzymes, but does not show catalytic isopeptidase activity, possibly because the putative isopeptidase center is covered by insertions and terminal appendices that are grafted onto this core, thus impairing the metal binding site. It is proposed that this domain is a protein interaction domain instead of a Zn(2+)-dependent metalloenzyme as proposed for some MPN proteins. The DEAD-box protein Brr2 and t
Probab=91.30 E-value=0.91 Score=50.55 Aligned_cols=99 Identities=20% Similarity=0.319 Sum_probs=67.4
Q ss_pred eeEEEEEeeEEecC--cEEEEEEEeeccccCCCCCCc--cccccHHHHHHHHHHHHhhcCCCceEEEEecCCC----CCc
Q psy17828 662 KRVVGVLLGCWKGK--GILDVSNSFAVPFDEDDKDNS--VWFLDHDYLENMYGMFKKVNAREKVVGWYHTGPK----LHQ 733 (1061)
Q Consensus 662 ~rVvGvLLG~~~g~--gtVEVTNSFaVP~eEde~d~~--v~~lD~~Y~e~MlemfKkVnp~E~VVGWYsTGp~----ls~ 733 (1061)
..+.|.|.|....+ ++-||+--..+|...+.+... .+..+++|+ -++..+||=||.+. +++
T Consensus 56 tQ~~GyLyG~~~~d~~~vkeI~cIvipPQ~gt~~sv~l~~~~~~~~~l-----------~~Le~LGWIHTqp~e~~~Lss 124 (252)
T cd08056 56 TQIAGYLYGKSPPDNPQVKEIRCIVLVPQLGTHQTVTLPQQLPQHEYL-----------EDLEPLGWIHTQPNELPQLSP 124 (252)
T ss_pred ceEEEEEeccCCCCCCCeEEEEEEEECCEeCCcCcEECCccCccchhh-----------CCCEeeEEEEcCCCCccccCH
Confidence 47999999996432 566887777777665443211 011122332 24789999999763 789
Q ss_pred ccHHHHHHHHhhCC-----CcEEEEEcCCCCCCCcceEEEEeccc
Q psy17828 734 NDIQINELIRRYCT-----NSVLVIIDAKPKELGLPTEAYRVVDE 773 (1061)
Q Consensus 734 ~Dl~Ihe~f~~~~~-----nPI~LivDPs~ss~gLplKAYrlv~e 773 (1061)
.|+..|.-|+.-++ +.|.++ .+.+.|...+.||+++++
T Consensus 125 ~Dv~tha~~~~~~~~w~~~~~V~it--~SftpGs~sl~ay~LT~~ 167 (252)
T cd08056 125 QDVTTHAKILADNPSWDGEKTVILT--CSFTPGSCSLTAYKLTPE 167 (252)
T ss_pred HHHHHHHHHHHhccccCCCcEEEEE--EcCCCCceEEEEEecCHH
Confidence 99999998877765 344444 455556699999999965
No 50
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=88.67 E-value=0.13 Score=49.51 Aligned_cols=45 Identities=29% Similarity=0.373 Sum_probs=0.0
Q ss_pred CCccccCCccccccccccccchhHHHHHHHHHHHHHHHhhhhccc
Q psy17828 488 NNKITNRDAEVNIEFNFSLQHFSQVVYLAAMIRSIIALHNLINNK 532 (1061)
Q Consensus 488 ~gWvT~g~~~Vniefnv~~Nd~~~~vYla~~~~~~~alh~li~nk 532 (1061)
.-.-..+++.+..+|+.+.||..++.|||+++|+..+++.+|+||
T Consensus 71 ~~lp~~~~~~~~~~~~~~~~D~l~v~yL~~l~k~~~~l~e~l~~~ 115 (115)
T PF13012_consen 71 SSLPKYDPEEFEEEFNSEINDVLMVSYLAKLTKKQHALNELLNNN 115 (115)
T ss_dssp ---------------------------------------------
T ss_pred HhcccccHHHHHHHHHhhchHHHHHHHHHHHhHHHHHHHHHHhcC
Confidence 333345788889999999999999999999999999999999986
No 51
>PRK13699 putative methylase; Provisional
Probab=87.64 E-value=1.9 Score=46.91 Aligned_cols=117 Identities=13% Similarity=0.055 Sum_probs=64.1
Q ss_pred CCccEEEECCCccccccCC-CCCCChH---HHh-c-C-Cc-cccCCCcEEEEecCccchHHHHHHhhcccee--ccceeE
Q psy17828 353 GKFAVIMADPPWDIHMELP-YGTMSDD---EMR-Q-L-GI-PQLQDEGLLFLWVTGRAMELGRECLKLFMLQ--DEGLLF 422 (1061)
Q Consensus 353 gkFdvIlaDPPW~~~~~~~-Y~tms~d---eI~-~-L-PV-~~La~~g~LFLWvT~~~Le~g~elL~~WGf~--~et~~i 422 (1061)
+.+|+|+.|||+.+..... ...+..+ +.. . + -+ ..|.++|.++.|++...+..-...+++=||. .. |
T Consensus 19 ~SVDLIiTDPPY~i~~~~~~~~~~~~~~~~ew~~~~l~E~~RVLKpgg~l~if~~~~~~~~~~~al~~~GF~l~~~---I 95 (227)
T PRK13699 19 NAVDFILTDPPYLVGFRDRQGRTIAGDKTDEWLQPACNEMYRVLKKDALMVSFYGWNRVDRFMAAWKNAGFSVVGH---L 95 (227)
T ss_pred cccceEEeCCCcccccccCCCcccccccHHHHHHHHHHHHHHHcCCCCEEEEEeccccHHHHHHHHHHCCCEEeeE---E
Confidence 4799999999997521100 0111111 110 0 0 01 2345688888888765555445667777888 55 9
Q ss_pred EEc-----CCcccccCeE-EEe--cc----cccCCCccEEEec---CCCCCccCCcccchh-hhhhhc
Q psy17828 423 LWV-----TGRAMELGRE-CLK--LS----LNCQLSQDVEFTW---PYLGWMSKFSLHHFF-QVVYLA 474 (1061)
Q Consensus 423 vWV-----tG~~l~~~kE-CLv--~~----i~~nid~DVIvse---p~~g~s~Kp~l~~~~-~iE~f~ 474 (1061)
+|. .|++....+| +++ .. .+.+. .||..+. ...|..+||. +.+. +|+.++
T Consensus 96 iW~K~~~~~~~~~~~~~E~i~~~~k~k~~~~~~~~-~~v~~~~~~~~~~hp~~kP~-~l~~~~i~~~s 161 (227)
T PRK13699 96 VFTKNYTSKAAYVGYRHECAYILAKGRPALPQNPL-PDVLGWKYSGNRHHPTEKPV-TSLQPLIESFT 161 (227)
T ss_pred EEECCCCCCCCCCccceeEEEEEECCCCCcccccC-CCcccccCCCCCCCCCCCcH-HHHHHHHHHhC
Confidence 999 3446667788 444 11 11122 4555443 2346788985 4333 345555
No 52
>cd08073 MPN_NLPC_P60 Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains. This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=85.88 E-value=1.9 Score=41.96 Aligned_cols=74 Identities=11% Similarity=0.118 Sum_probs=44.2
Q ss_pred HhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHH-HHHHHHHHHHhhcCCCceEE
Q psy17828 645 LLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHD-YLENMYGMFKKVNAREKVVG 723 (1061)
Q Consensus 645 LLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~-Y~e~MlemfKkVnp~E~VVG 723 (1061)
+-.|++|..+ ..+....|.|+|.. + ++..|++.-...+. ...+.+|+. |+.-+ ....+||
T Consensus 3 ~~~i~~ha~~----~~P~E~CGll~g~~---~---~~~~~p~~N~~~~p-~~~F~idp~e~~~a~--------~~~~ivg 63 (108)
T cd08073 3 EDAILAHAKA----EYPREACGLVVRKG---R---KLRYIPCRNIAADP-EEHFEISPEDYAAAE--------DEGEIVA 63 (108)
T ss_pred HHHHHHHHhH----CCCCcceEEEEecC---C---ceEEEECccCCCCc-cceEEeCHHHHHHHh--------cCCCEEE
Confidence 3467788766 56788999999975 1 23345554222111 124667764 33322 1238999
Q ss_pred EEecCCC----CCcccHH
Q psy17828 724 WYHTGPK----LHQNDIQ 737 (1061)
Q Consensus 724 WYsTGp~----ls~~Dl~ 737 (1061)
-|||+|. ++..|+.
T Consensus 64 i~HSHP~~~a~PS~~D~~ 81 (108)
T cd08073 64 VVHSHPDGSPAPSEADRA 81 (108)
T ss_pred EEEcCCCCCCCCCHHHHH
Confidence 9999984 5666653
No 53
>cd08058 MPN_euk_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); eukaryotic. This family contains eukaryotic MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains found in proteins with a variety of functions, including AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM), H2A-DUB (histone H2A deubiquitinase), BRCC36 (BRCA1/BRCA2-containing complex subunit 36), as well as Rpn11 (regulatory particle number 11) and CSN5 (COP9 signalosome complex subunit 5). These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity. Rpn11 is responsible for substrate deubiquitination during proteasomal degradation. It is essential for maintaining a correct cell cycle and normal mitochondrial morphology and physiology. CSN5 is critical for nuclear export and the degradation of several tumor suppressor prot
Probab=85.54 E-value=0.73 Score=44.86 Aligned_cols=60 Identities=22% Similarity=0.360 Sum_probs=41.4
Q ss_pred ccCcCCCCCCccceeeeeccCC----CCCCchHHHHHHHHhhcCCceEEEEcCCCCCCCCCceeEE
Q psy17828 849 IPTTTWPSRAREKVVGWYHTGP----KLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYR 910 (1061)
Q Consensus 849 m~~L~qKVNPkE~IVGWYsTGs----elt~~s~lIHefys~~~~~PIhL~VDt~~~~~~LPi~AYv 910 (1061)
|-.+....+-.+.+||||++-+ -+...|..-|-.|....++.++|++|+... ...+++|.
T Consensus 54 ~~~~~~~~~~g~~~vG~YHSHP~~~~~pS~~Di~~~~~~q~~~p~~~~lI~s~~~~--~~~~~a~r 117 (119)
T cd08058 54 EELFNVQTGRPLLVVGWYHSHPTFTAWLSSVDIHTQASYQLMLPEAIAIVVSPKHR--NKDTGIFR 117 (119)
T ss_pred HHHHHHHhCCCCeEEEEEecCCCCCCccCHHHHHHHHHHhccCCCeEEEEECcCCC--CcccceEE
Confidence 3344455677899999998866 466667666665665667889999998642 45566654
No 54
>PF13659 Methyltransf_26: Methyltransferase domain; PDB: 3GJY_A 3LPM_B 2NP6_D 1AQI_B 2ADM_B 2IH2_A 2JG3_A 2IBS_D 2NP7_A 2IBT_A ....
Probab=83.55 E-value=0.18 Score=47.24 Aligned_cols=63 Identities=21% Similarity=0.244 Sum_probs=33.5
Q ss_pred CCCceecccCccC-cccCCCccEEEECCCcccccc--CCCCCCChHHHhcCCccccCCCcEEEEecC
Q psy17828 336 PPQWIQCDLRYLD-MTVLGKFAVIMADPPWDIHME--LPYGTMSDDEMRQLGIPQLQDEGLLFLWVT 399 (1061)
Q Consensus 336 Ppq~i~cDlr~~d-~~~lgkFdvIlaDPPW~~~~~--~~Y~tms~deI~~LPV~~La~~g~LFLWvT 399 (1061)
+.++++.|++.+. ....++||+|+.||||-.... ..+.. ...++..-=...|.++|.+++|+.
T Consensus 51 ~~~~~~~D~~~~~~~~~~~~~D~Iv~npP~~~~~~~~~~~~~-~~~~~~~~~~~~L~~gG~~~~~~~ 116 (117)
T PF13659_consen 51 RVEVIVGDARDLPEPLPDGKFDLIVTNPPYGPRSGDKAALRR-LYSRFLEAAARLLKPGGVLVFITP 116 (117)
T ss_dssp TEEEEESHHHHHHHTCTTT-EEEEEE--STTSBTT----GGC-HHHHHHHHHHHHEEEEEEEEEEEE
T ss_pred eEEEEECchhhchhhccCceeEEEEECCCCccccccchhhHH-HHHHHHHHHHHHcCCCeEEEEEeC
Confidence 3579999998876 223479999999999964321 11111 112222222233456777776653
No 55
>PF01555 N6_N4_Mtase: DNA methylase; InterPro: IPR002941 This domain is found in DNA methylases. In prokaryotes, the major role of DNA methylation is to protect host DNA against degradation by restriction enzymes. This family contains both N-4 cytosine-specific DNA methylases and N-6 Adenine-specific DNA methylases. N-4 cytosine-specific DNA methylases (2.1.1.113 from EC) [] are enzymes that specifically methylate the amino group at the C-4 position of cytosines in DNA. Such enzymes are found as components of type II restriction-modification systems in prokaryotes. Such enzymes recognise a specific sequence in DNA and methylate a cytosine in that sequence. By this action they protect DNA from cleavage by type II restriction enzymes that recognise the same sequence. N-6 adenine-specific DNA methylases (2.1.1.72 from EC) (A-Mtase) are enzymes that specifically methylate the amino group at the C-6 position of adenines in DNA. Such enzymes are found in the three existing types of bacterial restriction-modification systems (in type I system the A-Mtase is the product of the hsdM gene, and in type III it is the product of the mod gene). All of these enzymes recognise a specific sequence in DNA and methylate an adenine in that sequence.; GO: 0003677 DNA binding, 0008170 N-methyltransferase activity, 0006306 DNA methylation; PDB: 2ZIF_A 2ZIE_A 2ZIG_A 1NW6_A 1NW8_A 1NW7_A 1NW5_A 1EG2_A 1BOO_A 1G60_B ....
Probab=82.96 E-value=0.71 Score=47.64 Aligned_cols=82 Identities=20% Similarity=0.352 Sum_probs=43.8
Q ss_pred cEEEECCCcccccc-----CCCCCCChHHHhcC-------CccccCCCcEEEEecCccchH--HHHHHhhccc-eeccce
Q psy17828 356 AVIMADPPWDIHME-----LPYGTMSDDEMRQL-------GIPQLQDEGLLFLWVTGRAME--LGRECLKLFM-LQDEGL 420 (1061)
Q Consensus 356 dvIlaDPPW~~~~~-----~~Y~tms~deI~~L-------PV~~La~~g~LFLWvT~~~Le--~g~elL~~WG-f~~et~ 420 (1061)
|+|+.|||...... .-...++.++-.+. -..-|.++|.+|+++....+. ....+++..| |.....
T Consensus 2 dliitDPPY~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~rvLk~~g~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~ 81 (231)
T PF01555_consen 2 DLIITDPPYNIGKDYNNYFDYGDNKNHEEYLEWMEEWLKECYRVLKPGGSIFIFIDDREIAGFLFELALEIFGGFFLRNE 81 (231)
T ss_dssp EEEEE---TSSSCS-----CSCHCCHHHHHHHHHHHHHHHHHHHEEEEEEEEEEE-CCEECTHHHHHHHHHHTT-EEEEE
T ss_pred CEEEECCCCCCCCCcchhhhccCCCCHHHHHHHHHHHHHHHHhhcCCCeeEEEEecchhhhHHHHHHHHHHhhhhheecc
Confidence 79999999975432 12223443333332 122345799999999977765 4555566556 772222
Q ss_pred eEEEc-C-------CcccccCeE-EEe
Q psy17828 421 LFLWV-T-------GRAMELGRE-CLK 438 (1061)
Q Consensus 421 ~ivWV-t-------G~~l~~~kE-CLv 438 (1061)
++|. . +..++...| +|+
T Consensus 82 -iiW~K~~~~~~~~~~~~~~~~E~il~ 107 (231)
T PF01555_consen 82 -IIWNKPNGMPKSNKKRFSNSHEYILV 107 (231)
T ss_dssp -EEEE-SSSTTSSTCCS-B--EEEEEE
T ss_pred -ceeEecCccccccccccccchhhhhc
Confidence 9998 2 126777889 766
No 56
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=82.06 E-value=5 Score=41.54 Aligned_cols=53 Identities=17% Similarity=0.233 Sum_probs=46.9
Q ss_pred hHHHHHHHHhhccccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeecc
Q psy17828 90 DLELELLEKLCDVSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINES 144 (1061)
Q Consensus 90 ~~e~~ll~~L~d~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~~ 144 (1061)
|.|..+|+||-. =.=|-+...|++++...++...|...|-.|+.+|.|..|..
T Consensus 1 eAe~~Il~y~~~--qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~ 53 (169)
T PF07106_consen 1 EAEDAILEYMKE--QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEY 53 (169)
T ss_pred ChHHHHHHHHHH--cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeee
Confidence 457888999876 46799999999999888999999999999999999999954
No 57
>PRK11524 putative methyltransferase; Provisional
Probab=77.18 E-value=4.2 Score=45.40 Aligned_cols=84 Identities=15% Similarity=0.212 Sum_probs=46.9
Q ss_pred CceecccCccCccc-CCCccEEEECCCcccccc--CCCCCCCh-------HHHhcCCccccCCCcEEEEecCccchHHHH
Q psy17828 338 QWIQCDLRYLDMTV-LGKFAVIMADPPWDIHME--LPYGTMSD-------DEMRQLGIPQLQDEGLLFLWVTGRAMELGR 407 (1061)
Q Consensus 338 q~i~cDlr~~d~~~-lgkFdvIlaDPPW~~~~~--~~Y~tms~-------deI~~LPV~~La~~g~LFLWvT~~~Le~g~ 407 (1061)
+.++.|...+--.. -+.||+|++|||...... ...+.+.. ++....-...|.++|.+|+++....+.. .
T Consensus 10 ~i~~gD~~~~l~~l~~~siDlIitDPPY~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~rvLK~~G~i~i~~~~~~~~~-~ 88 (284)
T PRK11524 10 TIIHGDALTELKKIPSESVDLIFADPPYNIGKNFDGLIEAWKEDLFIDWLYEWIDECHRVLKKQGTMYIMNSTENMPF-I 88 (284)
T ss_pred EEEeccHHHHHHhcccCcccEEEECCCcccccccccccccccHHHHHHHHHHHHHHHHHHhCCCcEEEEEcCchhhhH-H
Confidence 46777777632111 258999999999964211 11111211 2233322344567999999887655543 2
Q ss_pred HHhhcccee--ccceeEEEc
Q psy17828 408 ECLKLFMLQ--DEGLLFLWV 425 (1061)
Q Consensus 408 elL~~WGf~--~et~~ivWV 425 (1061)
.++..-||. .. |+|.
T Consensus 89 ~~~~~~~f~~~~~---iiW~ 105 (284)
T PRK11524 89 DLYCRKLFTIKSR---IVWS 105 (284)
T ss_pred HHHHhcCcceEEE---EEEE
Confidence 333334554 55 8897
No 58
>PF10237 N6-adenineMlase: Probable N6-adenine methyltransferase; InterPro: IPR019369 This family of proteins, which are of approximately 200 residues in length, contain a highly conserved Glu-Phe-Trp (QFW) motif close to the N terminus and an Asp/Asn-Pro-Pro-Tyr/Phe motif in the centre. This latter motif is characteristic of N-6 adenine-specific DNA methylases and could be involved in substrate binding or in the catalytic activity (, ).
Probab=74.59 E-value=2.3 Score=44.49 Aligned_cols=51 Identities=35% Similarity=0.516 Sum_probs=32.7
Q ss_pred CCccEEEECCCccccccCCCCCCChHHH--hcCCccccCCCcEEEEecCccch-HHHHHHhhcccee
Q psy17828 353 GKFAVIMADPPWDIHMELPYGTMSDDEM--RQLGIPQLQDEGLLFLWVTGRAM-ELGRECLKLFMLQ 416 (1061)
Q Consensus 353 gkFdvIlaDPPW~~~~~~~Y~tms~deI--~~LPV~~La~~g~LFLWvT~~~L-e~g~elL~~WGf~ 416 (1061)
++||+|++|||+- +.+=+ -+.=|..|++++.=.+|+|+..| +...++| |++
T Consensus 85 ~~~d~vv~DPPFl----------~~ec~~k~a~ti~~L~k~~~kii~~Tg~~~~~~~~~ll---~~~ 138 (162)
T PF10237_consen 85 GKFDVVVIDPPFL----------SEECLTKTAETIRLLLKPGGKIILCTGEEMEELIKKLL---GLR 138 (162)
T ss_pred CCceEEEECCCCC----------CHHHHHHHHHHHHHHhCccceEEEecHHHHHHHHHHHh---Cee
Confidence 6999999999992 11111 12233445555555679998877 4566777 666
No 59
>cd08059 MPN_prok_mb Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic. This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.
Probab=72.46 E-value=14 Score=34.85 Aligned_cols=72 Identities=18% Similarity=0.297 Sum_probs=45.0
Q ss_pred hHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcCCCceEEEEe
Q psy17828 647 SVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNAREKVVGWYH 726 (1061)
Q Consensus 647 sIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp~E~VVGWYs 726 (1061)
.|.+|+.. ..+..+.|+|+|... + .|.+...+|....+ .+..+ ......-+..+||-||
T Consensus 5 ~i~~~~~~----~~p~E~~gll~~~~~--~--~~~~~~~~~~~~~~-------~~~~~------~~~a~~~~~~~v~i~H 63 (101)
T cd08059 5 TILVHAKD----AHPDEFCGFLSGSKD--N--VMDELIFLPFVSGS-------VSAVI------DLAALEIGMKVVGLVH 63 (101)
T ss_pred HHHHHHHh----cCChhhheeeecCCC--C--eEEEEEeCCCcCCc-------cChHH------HHHHhhCCCcEEEEEe
Confidence 35555544 236789999999853 2 47788888754321 23333 2223344678999999
Q ss_pred cCCC----CCcccHHHH
Q psy17828 727 TGPK----LHQNDIQIN 739 (1061)
Q Consensus 727 TGp~----ls~~Dl~Ih 739 (1061)
++|. ++..|+...
T Consensus 64 sHP~g~~~PS~~D~~~~ 80 (101)
T cd08059 64 SHPSGSCRPSEADLSLF 80 (101)
T ss_pred cCcCCCCCCCHHHHHHH
Confidence 9984 667776543
No 60
>TIGR03534 RF_mod_PrmC protein-(glutamine-N5) methyltransferase, release factor-specific. Members of this protein family are HemK (PrmC), a protein once thought to be involved in heme biosynthesis but now recognized to be a protein-glutamine methyltransferase that modifies the peptide chain release factors. All members of the seed alignment are encoded next to the release factor 1 gene (prfA) and confirmed by phylogenetic analysis. SIMBAL analysis (manuscript in prep.) shows the motif [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers specificity for the release factors rather than for ribosomal protein L3.
Probab=70.06 E-value=5.4 Score=42.46 Aligned_cols=78 Identities=19% Similarity=0.205 Sum_probs=48.8
Q ss_pred CCceecccCccCcccCCCccEEEECCCccccccCCCCCCCh---------------------HHHhcCCccccCCCcEEE
Q psy17828 337 PQWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSD---------------------DEMRQLGIPQLQDEGLLF 395 (1061)
Q Consensus 337 pq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~---------------------deI~~LPV~~La~~g~LF 395 (1061)
-.++++|+.. ....++||+|+++||+-.....+ .+.. ..+..--..-|.++|.++
T Consensus 139 ~~~~~~d~~~--~~~~~~fD~Vi~npPy~~~~~~~--~~~~~~~~~e~~~~~~~~~~~~~~~~~~i~~~~~~L~~gG~~~ 214 (251)
T TIGR03534 139 VTFLQSDWFE--PLPGGKFDLIVSNPPYIPEADIH--LLDPEVRFHEPRLALFGGEDGLDFYRRIIAQAPRLLKPGGWLL 214 (251)
T ss_pred EEEEECchhc--cCcCCceeEEEECCCCCchhhhh--hcChhhhhcCCHHHHcCCCcHHHHHHHHHHHHHHhcccCCEEE
Confidence 3578888765 12246899999999986322111 0110 111121223456789999
Q ss_pred EecCccchHHHHHHhhccceecc
Q psy17828 396 LWVTGRAMELGRECLKLFMLQDE 418 (1061)
Q Consensus 396 LWvT~~~Le~g~elL~~WGf~~e 418 (1061)
+.......+.-.+.|++=||++.
T Consensus 215 ~~~~~~~~~~~~~~l~~~gf~~v 237 (251)
T TIGR03534 215 LEIGYDQGEAVRALFEAAGFADV 237 (251)
T ss_pred EEECccHHHHHHHHHHhCCCCce
Confidence 98876667777888999999843
No 61
>TIGR01177 conserved hypothetical protein TIGR01177. This family is found exclusively in the Archaea.
Probab=69.90 E-value=4.7 Score=45.85 Aligned_cols=75 Identities=16% Similarity=0.060 Sum_probs=44.8
Q ss_pred CceecccCccCcccCCCccEEEECCCccccccCCCCCC-C-hHHHhcCCccccCCCcEEEEecCccchHHHHHHhhccce
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTM-S-DDEMRQLGIPQLQDEGLLFLWVTGRAMELGRECLKLFML 415 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tm-s-~deI~~LPV~~La~~g~LFLWvT~~~Le~g~elL~~WGf 415 (1061)
.++++|.+.+++. .++||+|++|||+-.......... . ..++.+-=...|.++|.+.+|.+... ...++++.=||
T Consensus 233 ~~~~~D~~~l~~~-~~~~D~Iv~dPPyg~~~~~~~~~~~~l~~~~l~~~~r~Lk~gG~lv~~~~~~~--~~~~~~~~~g~ 309 (329)
T TIGR01177 233 FVKRGDATKLPLS-SESVDAIATDPPYGRSTTAAGDGLESLYERSLEEFHEVLKSEGWIVYAVPTRI--DLESLAEDAFR 309 (329)
T ss_pred eEEecchhcCCcc-cCCCCEEEECCCCcCcccccCCchHHHHHHHHHHHHHHccCCcEEEEEEcCCC--CHHHHHhhcCc
Confidence 6788999887654 468999999999865432211100 0 12222221233567899988987542 22356777677
No 62
>PF03665 UPF0172: Uncharacterised protein family (UPF0172); InterPro: IPR005366 This is a small family of proteins of unknown function.
Probab=69.84 E-value=3.1 Score=44.68 Aligned_cols=81 Identities=20% Similarity=0.333 Sum_probs=54.8
Q ss_pred ccccccCCCCc-cccccc---cc-cccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCC-----CCCCc
Q psy17828 806 FLCGRSSRGGK-VGRIRC---RS-HFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGP-----KLHQN 875 (1061)
Q Consensus 806 ~~~g~~~~~g~-~~~~~~---~~-~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGs-----elt~~ 875 (1061)
+|+|+.+.++. +.+.|| -| +.+..=|+.|- +.-+++| -+ ....+|||+|.... .+++.
T Consensus 29 vLlg~~~~~~~~v~i~DaVPLfH~~~~L~PmlEvA--L~qvd~~---------~~-~~gl~IvGyY~Ane~~~d~~~~~~ 96 (196)
T PF03665_consen 29 VLLGKSSKSSSEVEIVDAVPLFHHWLSLSPMLEVA--LAQVDAY---------AK-SNGLVIVGYYQANERLDDNSPSPV 96 (196)
T ss_pred EEEeccCCCCceEEEeeceeccccccCcchHHHHH--HHHHHHH---------Hh-hCCCEEEEEEEeccccccCCCCHH
Confidence 78888887776 888998 35 33333344332 1223444 22 24599999998876 45556
Q ss_pred hHHHHHHHHhhcCCceEEEEcCC
Q psy17828 876 DIQINELIRRYCTNSVLVIIDAK 898 (1061)
Q Consensus 876 s~lIHefys~~~~~PIhL~VDt~ 898 (1061)
-.-|=+-..+..+.+++|+||-.
T Consensus 97 a~kiad~I~~~~~~a~ll~idn~ 119 (196)
T PF03665_consen 97 AEKIADKIAENFSDACLLMIDNK 119 (196)
T ss_pred HHHHHHHHHhhCCCcEEEEEECc
Confidence 66677777888889999999966
No 63
>cd08068 MPN_BRCC36 Mov34/MPN/PAD-1 family: BRCC36, a subunit of BRCA1-A complex. BRCC36 (BRCA1-A complex subunit BRCC36; BRCA1/BRCA2-containing complex subunit 36; BRCA1/BRCA2-containing complex subunit 3; BRCC3; BRISC complex subunit BRCC36; BRCC36 isopeptidase complex; Lys-63-specific deubiquitinase BRCC36) and BRCC36-like domains are members of JAMM/MPN+ deubiquitinases (DUBs), possibly with Zn2+-dependent ubiquitin isopeptidase activity. BRCC36 is part of the BRCA1/BRCA2/BARD1-containing nuclear complex that displays an E3 ubiquitin ligase activity. It is targeted to DNA damage foci after irradiation; RAP80 recruits the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA double strand breaks (DSBs) for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs. A new protein, MERIT40 (mediator of RAP80 interactions and targeting 40 kDa), also named NBA1 (new component of the BRCA1 A complex), exists in the same BRCA1-contai
Probab=69.12 E-value=12 Score=41.84 Aligned_cols=80 Identities=20% Similarity=0.269 Sum_probs=48.8
Q ss_pred CCCCCCccceeeeeccCC----CCCCchHHHHHHHHhhcCCceEEEEcCCCCC-----CCCCceeEEEeeeccCCCCcce
Q psy17828 853 TWPSRAREKVVGWYHTGP----KLHQNDIQINELIRRYCTNSVLVIIDAKPKE-----LGLPTEAYRVVDEVHDDGSPTT 923 (1061)
Q Consensus 853 ~qKVNPkE~IVGWYsTGs----elt~~s~lIHefys~~~~~PIhL~VDt~~~~-----~~LPi~AYvsv~ev~~dGs~~~ 923 (1061)
....+-.+.|||||+|=+ -+...|..-|.-|-...+.-+.|+|++...+ +..-+.+|...+ +.....
T Consensus 82 ~~~~~rgl~vVGwYHSHP~~~a~PS~~Dv~tq~~~q~~~p~~v~lIvS~~~~~~~~~~~~~~i~aFr~~~----g~~~~~ 157 (244)
T cd08068 82 TEETGRPMRVVGWYHSHPHITVWPSHVDVRTQAMYQMMDSGFVGLIFSCFNEDKSTKMGEVQVTCFQSVQ----GNKAGQ 157 (244)
T ss_pred HhhccCCceEEEEEecCCCCCCCCCHhHHHHHHHHHhhCCCcEEEEEEecCCccccccCCEEEEEEEecC----CCCCCc
Confidence 344567789999998754 4556666654444334467899999875432 334567777543 112234
Q ss_pred eeEEeeccccccc
Q psy17828 924 KTFDHVPSEIGAE 936 (1061)
Q Consensus 924 k~Fv~VP~~I~ae 936 (1061)
...+++|+.|...
T Consensus 158 ~~~~e~pl~i~~~ 170 (244)
T cd08068 158 YERIEVPLEIVPT 170 (244)
T ss_pred ceEEEeeeEEecC
Confidence 5567777777653
No 64
>KOG2880|consensus
Probab=67.96 E-value=4 Score=47.37 Aligned_cols=112 Identities=18% Similarity=0.343 Sum_probs=70.9
Q ss_pred HHHHhhccccCC--ceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhh-cCCCceEEEE
Q psy17828 649 VDHFNRMSKIGN--QKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKV-NAREKVVGWY 725 (1061)
Q Consensus 649 sDH~tR~~~~~~--~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkV-np~E~VVGWY 725 (1061)
.+-|.+.++..+ .-.-.|+|-|.-. ++.+-||+-. +|-.+...| .-+..-- -++|.-- -.++-.+||-
T Consensus 261 ~~~Fl~la~~NT~knlETCGiL~g~L~-~n~f~IThli-iPkQeatsd----~C~t~ne---eelF~vQdq~~L~tlGWI 331 (424)
T KOG2880|consen 261 MEVFLQLAKSNTKKNLETCGILAGKLE-RNEFYITHLI-IPKQEATSD----SCNTMNE---EELFEVQDQHELLTLGWI 331 (424)
T ss_pred HHHHHHHHhhcccccchHHHHhhhHhh-cCcEEEEEEE-eecccCCCc----cccccCH---HHHheecccccceeeeee
Confidence 344555544222 2356799999864 4568888765 454433221 0111111 1122211 1346679999
Q ss_pred ecCCC----CCcccHHHHHHHHhhCCCcEEEEEcCCCCCCCcceEEEEeccc
Q psy17828 726 HTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVVDE 773 (1061)
Q Consensus 726 sTGp~----ls~~Dl~Ihe~f~~~~~nPI~LivDPs~ss~gLplKAYrlv~e 773 (1061)
||+|. +++.|+..|-.|+-..+.+|+++.-|...+.| +||+.+.
T Consensus 332 HTHPTQt~FmSSVDlHTHcSYQiMlPEAiAIV~aPk~~~tG----iFrLt~~ 379 (424)
T KOG2880|consen 332 HTHPTQTCFMSSVDLHTHCSYQIMLPEAIAIVCAPKSKTTG----IFRLTDP 379 (424)
T ss_pred ecCCccchhheeccccccceeeeecchheeEEeccccCCcc----eEEecCC
Confidence 99984 88999999999988899999999998765544 7888854
No 65
>cd08061 MPN_NPL4 Mov34/MPN/PAD-1 family: nuclear protein localization-4 (Npl4) domain. Npl4p (nuclear protein localization-4) is identical to Hmg-CoA reductase degradation 4 (HRD4) protein and contains a domain that is part of the pfam clan MPN/Mov34-like. Npl4 plays an intermediate role between endoplasmic reticulum-associated degradation (ERAD) substrate ubiquitylation and proteasomal degradation. Npl4p associates with Cdc48p (Cdc48 in yeast and p97 or valosin-containing protein (VCP) in higher eukaryotes), the highly conserved ATPase of the AAA family, via ubiquitin fusion degradation-1 protein (Ufd1p) to form a Cdc48p-Ufd1p-Npl4p complex which then functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=64.40 E-value=52 Score=37.44 Aligned_cols=109 Identities=17% Similarity=0.269 Sum_probs=69.9
Q ss_pred CceeEEEEEeeEEecC------cEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcCCCceEEEEecCCC---
Q psy17828 660 NQKRVVGVLLGCWKGK------GILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNAREKVVGWYHTGPK--- 730 (1061)
Q Consensus 660 ~~~rVvGvLLG~~~g~------gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp~E~VVGWYsTGp~--- 730 (1061)
....-+|.|.|+.... ..+.|..-|+=|...+.++ +..++....+.--+.-. .-.+..|||=-|...
T Consensus 32 ~~~QR~G~LyG~y~~~~~~plgika~VeaIYEPPQ~~~~d~--~~~l~d~~~~~vd~iA~--~lGL~~VG~IfT~l~~~~ 107 (274)
T cd08061 32 TGQQRIGFLYGRYDEDEDVPLGIKAVVEAIYEPPQEGTPDG--FELLEDPNADTVDAIAA--ALGLERVGWIFTDLPRED 107 (274)
T ss_pred hcceeEEEEEEEeecccCCCCceEEEEEEEECCCccCCCCC--eEEccchhhhHHHHHHH--HcCCeEEEEEEecCCCCC
Confidence 3466789999998754 3688888888887665543 23333333333222222 235899999777552
Q ss_pred -----CCcccHHHHHHHHh------hCCCcEEEEEcCCCCCCCcceEEEEeccc
Q psy17828 731 -----LHQNDIQINELIRR------YCTNSVLVIIDAKPKELGLPTEAYRVVDE 773 (1061)
Q Consensus 731 -----ls~~Dl~Ihe~f~~------~~~nPI~LivDPs~ss~gLplKAYrlv~e 773 (1061)
+++..+.....+|. +.++-|-+++.+... +...+.||.+++.
T Consensus 108 ~d~~~LSs~Evi~aA~~Q~~~~~g~~gskFvT~vvs~~~~-g~i~~~ayQvSdq 160 (274)
T cd08061 108 KDGYFLSAEEVILAAKFQLKHPTGKFGSKFVTVVVTGDKD-GQIHFEAYQVSDQ 160 (274)
T ss_pred CCceeECHHHHHHHHHHhhhcccCCcCCeEEEEEEecCCC-CceeeeeeeecHH
Confidence 55555655566662 445567788877654 4589999999976
No 66
>KOG1560|consensus
Probab=64.00 E-value=7.1 Score=44.17 Aligned_cols=140 Identities=22% Similarity=0.328 Sum_probs=81.6
Q ss_pred cccCcCCCCCCccceeeeecc---CCCCCCchHHHHHHHH--hhcCCceEEEEcCCCC-CCCCCceeEEEeee---ccCC
Q psy17828 848 RIPTTTWPSRAREKVVGWYHT---GPKLHQNDIQINELIR--RYCTNSVLVIIDAKPK-ELGLPTEAYRVVDE---VHDD 918 (1061)
Q Consensus 848 ~m~~L~qKVNPkE~IVGWYsT---Gselt~~s~lIHefys--~~~~~PIhL~VDt~~~-~~~LPi~AYvsv~e---v~~d 918 (1061)
+|+.=.+.+|-.--.||||-+ |+-+. -+++-.+|. .-.+..|.|+.|+.-. ++.|..+||....+ +..+
T Consensus 86 ~mlrrlr~vnid~~hVGwYqs~~vgs~lS--~~lveSqy~YQ~a~pesVvliYD~~kssqG~L~lrAyrLTp~am~~~ke 163 (339)
T KOG1560|consen 86 AMLRRLRYVNIDHLHVGWYQSAYVGSFLS--PALVESQYAYQKAIPESVVLIYDPIKSSQGTLSLRAYRLTPEAMAAHKE 163 (339)
T ss_pred HHHHHhhhcCccceeeeeeeeehhccccC--HHHHHHHHHHHhcCCccEEEEeccccccCceEEeehhhcCHHHHHHHhc
Confidence 455566788888889999965 55666 344444443 3447899999999854 57788999986443 2222
Q ss_pred C--C---------cceeeEEeeccccccc-----------ccccccccccccccccc-ccccchhhhhhHHHHHHHHHHH
Q psy17828 919 G--S---------PTTKTFDHVPSEIGAE-----------EAEEVGVEHLLRDIKDT-TVGSLSQRVTNQLMGLKGLNQQ 975 (1061)
Q Consensus 919 G--s---------~~~k~Fv~VP~~I~ae-----------EAErIgVEhLlr~i~da-t~s~L~s~l~~~~~aLk~L~~r 975 (1061)
+ + .-...|.++|.-|... |+|.+..+.-+-.--+- +...|...+..++..++.|+..
T Consensus 164 kdwtpealk~~nltyenmfeElPIVIknS~L~nvlmseLs~~e~c~sdk~~~~~fdlgs~t~leknir~lme~vDEl~qe 243 (339)
T KOG1560|consen 164 KDWTPEALKSANLTYENMFEELPIVIKNSHLANVLMSELSEPEDCESDKPLHSNFDLGSGTRLEKNIRLLMERVDELHQE 243 (339)
T ss_pred CCCCHHHHHhcCCCHHHHHhhcCeeeeccHHHHHHHHhccccccccccccccccccccchhhHHHHHHHHHHHHHHHHHH
Confidence 2 1 1245688888877654 33333322110000010 1112445555666666666666
Q ss_pred HHHHHHHHHHHhhc
Q psy17828 976 IKEIEKYVGQVSRY 989 (1061)
Q Consensus 976 L~~I~~YLd~V~~g 989 (1061)
+..+-.|-.++...
T Consensus 244 ~~~l~kyqr~~~rq 257 (339)
T KOG1560|consen 244 IVNLNKYQRQLARQ 257 (339)
T ss_pred HHHHHHHHHHHHHH
Confidence 66666676666543
No 67
>PRK09328 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=63.81 E-value=13 Score=40.37 Aligned_cols=78 Identities=18% Similarity=0.168 Sum_probs=44.8
Q ss_pred CCceecccCccCcccCCCccEEEECCCccccccCC--------CCCC-C----------hHHHhcCCccccCCCcEEEEe
Q psy17828 337 PQWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELP--------YGTM-S----------DDEMRQLGIPQLQDEGLLFLW 397 (1061)
Q Consensus 337 pq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~--------Y~tm-s----------~deI~~LPV~~La~~g~LFLW 397 (1061)
-.++.+|+.. ....++||+|+++||+--....+ |... . ...+..--..-|.++|.+++-
T Consensus 160 i~~~~~d~~~--~~~~~~fD~Iv~npPy~~~~~~~~~~~~v~~~ep~~al~~g~~g~~~~~~~~~~~~~~Lk~gG~l~~e 237 (275)
T PRK09328 160 VEFLQGDWFE--PLPGGRFDLIVSNPPYIPEADIHLLQPEVRDHEPHLALFGGEDGLDFYRRIIEQAPRYLKPGGWLLLE 237 (275)
T ss_pred EEEEEccccC--cCCCCceeEEEECCCcCCcchhhhCCchhhhcCCchhhcCCCCHHHHHHHHHHHHHHhcccCCEEEEE
Confidence 3567777732 11236999999999985321100 1000 0 011111111234678999887
Q ss_pred cCccchHHHHHHhhcccee
Q psy17828 398 VTGRAMELGRECLKLFMLQ 416 (1061)
Q Consensus 398 vT~~~Le~g~elL~~WGf~ 416 (1061)
++...-+.-+++|+++||.
T Consensus 238 ~g~~~~~~~~~~l~~~gf~ 256 (275)
T PRK09328 238 IGYDQGEAVRALLAAAGFA 256 (275)
T ss_pred ECchHHHHHHHHHHhCCCc
Confidence 7655666677899999997
No 68
>TIGR03704 PrmC_rel_meth putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific. This protein family is closely related to two different families of protein-(glutamine-N5) methyltransferase. The first is PrmB, which modifies ribosomal protein L3 in some bacteria. The second is PrmC (HemK), which modifies peptide chain release factors 1 and 2 in most bacteria and also in eukaryotes. The glutamine side chain-binding motif NPPY shared by PrmB and PrmC is N[VAT]PY in this family. The protein substrate is unknown.
Probab=60.78 E-value=9.8 Score=41.92 Aligned_cols=81 Identities=16% Similarity=0.089 Sum_probs=46.0
Q ss_pred CceecccCccCcc-cCCCccEEEECCCccccccC--------CCC-CCCh----------HHHhcCCccccCCCcEEEEe
Q psy17828 338 QWIQCDLRYLDMT-VLGKFAVIMADPPWDIHMEL--------PYG-TMSD----------DEMRQLGIPQLQDEGLLFLW 397 (1061)
Q Consensus 338 q~i~cDlr~~d~~-~lgkFdvIlaDPPW~~~~~~--------~Y~-tms~----------deI~~LPV~~La~~g~LFLW 397 (1061)
.++++|+...-.. ..++||+|++||||--.... .|. .+.+ .+|..-=-.-|.++|.+++=
T Consensus 136 ~~~~~D~~~~l~~~~~~~fDlVv~NPPy~~~~~~~~~~~e~~~~ep~~al~gg~dgl~~~~~i~~~a~~~L~~gG~l~l~ 215 (251)
T TIGR03704 136 TVHEGDLYDALPTALRGRVDILAANAPYVPTDAIALMPPEARDHEPRVALDGGADGLDVLRRVAAGAPDWLAPGGHLLVE 215 (251)
T ss_pred EEEEeechhhcchhcCCCEeEEEECCCCCCchhhhcCCHHHHhCCCHHHhcCCCcHHHHHHHHHHHHHHhcCCCCEEEEE
Confidence 5788887653211 13689999999999522110 111 1111 12221111234568887765
Q ss_pred cCccchHHHHHHhhccceecc
Q psy17828 398 VTGRAMELGRECLKLFMLQDE 418 (1061)
Q Consensus 398 vT~~~Le~g~elL~~WGf~~e 418 (1061)
......+...++|++-||+.+
T Consensus 216 ~~~~~~~~v~~~l~~~g~~~~ 236 (251)
T TIGR03704 216 TSERQAPLAVEAFARAGLIAR 236 (251)
T ss_pred ECcchHHHHHHHHHHCCCCce
Confidence 555566777888998888843
No 69
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=59.95 E-value=22 Score=36.25 Aligned_cols=65 Identities=22% Similarity=0.350 Sum_probs=47.5
Q ss_pred hHHHHHHHHhhcc------------ccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeecccCCCCceEEEEee
Q psy17828 90 DLELELLEKLCDV------------SLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINESKDDDNQVEIVSVE 157 (1061)
Q Consensus 90 ~~e~~ll~~L~d~------------~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~~~~~~~~~~i~~~~ 157 (1061)
.++.+|..+|... .+.+|.+-.+|.+.+.. +++.|.-+|.+|..+|+|.+.. . .|+=.|
T Consensus 114 ~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~--tretvsR~l~~l~~~g~I~~~~-----~--~i~I~d 184 (193)
T TIGR03697 114 DMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGS--TRVTITRLLGDLRKKKLISIHK-----K--KITVHD 184 (193)
T ss_pred CHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCC--cHHHHHHHHHHHHHCCCEEecC-----C--EEEEeC
Confidence 4566666665321 35689999999999976 8999999999999999999872 2 233345
Q ss_pred hHhHHh
Q psy17828 158 HVKLLG 163 (1061)
Q Consensus 158 ~~kl~~ 163 (1061)
..+|.+
T Consensus 185 ~~~L~~ 190 (193)
T TIGR03697 185 PIALGQ 190 (193)
T ss_pred HHHHHH
Confidence 556653
No 70
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=57.93 E-value=23 Score=37.55 Aligned_cols=67 Identities=15% Similarity=0.212 Sum_probs=47.7
Q ss_pred hHHHHHHHHhhcc------------ccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeecccCCCCceEEEEee
Q psy17828 90 DLELELLEKLCDV------------SLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINESKDDDNQVEIVSVE 157 (1061)
Q Consensus 90 ~~e~~ll~~L~d~------------~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~~~~~~~~~~i~~~~ 157 (1061)
.++.++..+|.+. .+.+|.+-.+|.+.++. +++.|..+|++|..+|+|.++. ... .=.|
T Consensus 155 ~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~--sr~tvsR~l~~l~~~g~I~~~~-----~~i--~i~d 225 (235)
T PRK11161 155 NAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGL--TVETISRLLGRFQKSGMLAVKG-----KYI--TIEN 225 (235)
T ss_pred CHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCC--cHHHHHHHHHHHHHCCCEEecC-----CEE--EEcC
Confidence 4466666665432 34578888888888876 8899999999999999999883 233 3336
Q ss_pred hHhHHhHH
Q psy17828 158 HVKLLGMV 165 (1061)
Q Consensus 158 ~~kl~~m~ 165 (1061)
.++|.++.
T Consensus 226 ~~~L~~~~ 233 (235)
T PRK11161 226 NDALAQLA 233 (235)
T ss_pred HHHHHHHh
Confidence 66666543
No 71
>cd08060 MPN_UPF0172 Mov34/MPN/PAD-1 family: UPF0172 family of unknown function includes neighbor of COX4 (Noc4p). This family includes Noc4p (neighbor of COX4; neighbor of Cytochrome c Oxidase 4; nucleolar complex associated 4 homolog) which belongs to the family of unknown function, UPF0172, with MPN/JAMM-like domains. Proteins in this family are homologs of the NOC4 gene which is conserved in eukaryotic members including human, dog, mouse, rat, chicken, zebrafish, fruit fly, mosquito, S.pombe, K.lactis, E.gossypii, M.grisea, N.crassa, A.thaliana, and rice. NOC4 highly expressed in the pancreas and moderately in liver, heart, lung, kidney, brain, skeletal muscle, and placenta. This nucleolar protein forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits. This family of eukaryotic MPN-like domains lacks the key residues that coordinate a metal ion and therefore does not show catalytic isopeptidase activity.
Probab=57.28 E-value=15 Score=39.22 Aligned_cols=40 Identities=20% Similarity=0.375 Sum_probs=32.1
Q ss_pred ccceeeeeccCC-----CCCCchHHHHHHHHhhcCCceEEEEcCC
Q psy17828 859 REKVVGWYHTGP-----KLHQNDIQINELIRRYCTNSVLVIIDAK 898 (1061)
Q Consensus 859 kE~IVGWYsTGs-----elt~~s~lIHefys~~~~~PIhL~VDt~ 898 (1061)
...|||+|++-+ .+.+....|=+-..+.++++++|+||-.
T Consensus 69 gl~IvG~Yhsh~~~~d~~~~~~a~kIadki~~~~~~a~ll~vdn~ 113 (182)
T cd08060 69 GLVIVGYYQANERLDDSSPSPVAKKIADKIAENFSNACLLMVDNE 113 (182)
T ss_pred CCEEEEEEecCCcccCCCCcHHHHHHHHHHHHhCCCCEEEEEeCc
Confidence 469999999887 4555666777778888889999999866
No 72
>COG2263 Predicted RNA methylase [Translation, ribosomal structure and biogenesis]
Probab=56.69 E-value=7 Score=42.28 Aligned_cols=26 Identities=23% Similarity=0.699 Sum_probs=22.9
Q ss_pred CceecccCccCcccCCCccEEEECCCcccc
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWDIH 367 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~~~ 367 (1061)
.|+.||++.|+ ++||+++++|||-..
T Consensus 96 ~f~~~dv~~~~----~~~dtvimNPPFG~~ 121 (198)
T COG2263 96 EFVVADVSDFR----GKFDTVIMNPPFGSQ 121 (198)
T ss_pred EEEEcchhhcC----CccceEEECCCCccc
Confidence 58999999877 899999999999754
No 73
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=55.80 E-value=17 Score=38.39 Aligned_cols=50 Identities=18% Similarity=0.292 Sum_probs=38.5
Q ss_pred ccceeeeeccCC----CCCCchHHHHHHHHhhcCCceEEEEcCCCCCCCCCceeEEEe
Q psy17828 859 REKVVGWYHTGP----KLHQNDIQINELIRRYCTNSVLVIIDAKPKELGLPTEAYRVV 912 (1061)
Q Consensus 859 kE~IVGWYsTGs----elt~~s~lIHefys~~~~~PIhL~VDt~~~~~~LPi~AYvsv 912 (1061)
.+.+||||+|=+ -+.+.|..-|--|....+..++|+|++. ...+.+|...
T Consensus 74 gle~vGwyHSHP~~~~~pS~~Dv~t~~~~~~~~p~~~~lIvSp~----~~~l~afrl~ 127 (173)
T cd08066 74 DLITLGWIHTHPTQTCFLSSVDLHTHCSYQLMLPEAIAIVCAPK----YNEFGIFRLT 127 (173)
T ss_pred CCeeEEEEeccCCCCCccCHHHHHHHHHHHhcCCCeEEEEECCC----CcEEeEEEee
Confidence 578999998844 5788888888777766788999999964 3457777754
No 74
>COG1310 Predicted metal-dependent protease of the PAD1/JAB1 superfamily [General function prediction only]
Probab=55.62 E-value=14 Score=36.81 Aligned_cols=35 Identities=26% Similarity=0.487 Sum_probs=26.8
Q ss_pred cceeeeeccCC--CCCCchHHHHHHHHhhcCCceEEEEc
Q psy17828 860 EKVVGWYHTGP--KLHQNDIQINELIRRYCTNSVLVIID 896 (1061)
Q Consensus 860 E~IVGWYsTGs--elt~~s~lIHefys~~~~~PIhL~VD 896 (1061)
|.|||||+|.+ ...+.++-++ +++..+.|-++++.
T Consensus 69 ~~vvg~yHSHP~~~~~pS~~D~~--~~~~~~~~~~iv~~ 105 (134)
T COG1310 69 EVVVGWYHSHPGGPPYPSEADRR--LSKLGPLPWLIVSV 105 (134)
T ss_pred CEEEEEEcCCCCCCCCcCHHHHh--hccccCCCEEEEEc
Confidence 99999999998 6777888887 66666666565554
No 75
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=54.99 E-value=31 Score=35.59 Aligned_cols=69 Identities=12% Similarity=0.148 Sum_probs=52.1
Q ss_pred hHHHHHHHHhh---c---------cccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeecccCCCCceEEEEee
Q psy17828 90 DLELELLEKLC---D---------VSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINESKDDDNQVEIVSVE 157 (1061)
Q Consensus 90 ~~e~~ll~~L~---d---------~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~~~~~~~~~~i~~~~ 157 (1061)
.++.+|.++|. + ..+.+|.+-.+|.+.+.. +++.|..+|.+|..+|+|.+. ... |+=.|
T Consensus 120 ~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~--tretvsR~l~~l~~~g~I~~~-----~~~--i~I~d 190 (202)
T PRK13918 120 RLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGS--VRETVTKVIGELSREGYIRSG-----YGK--IQLLD 190 (202)
T ss_pred chHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCc--cHHHHHHHHHHHHHCCCEEcC-----CCE--EEEEC
Confidence 35677777653 2 245789999999999977 899999999999999999865 222 33367
Q ss_pred hHhHHhHHHH
Q psy17828 158 HVKLLGMVNE 167 (1061)
Q Consensus 158 ~~kl~~m~~~ 167 (1061)
.++|.++.++
T Consensus 191 ~~~L~~~~~~ 200 (202)
T PRK13918 191 LKGLEELAES 200 (202)
T ss_pred HHHHHHHHhc
Confidence 7888877655
No 76
>PF01861 DUF43: Protein of unknown function DUF43; InterPro: IPR002723 This family of prokaryotic proteins have not been characterised. All the members are 350-400 amino acids long.; PDB: 2QM3_A.
Probab=53.24 E-value=8.7 Score=42.83 Aligned_cols=35 Identities=34% Similarity=0.567 Sum_probs=17.0
Q ss_pred cccCCCCceecccCc-cCcccCCCccEEEECCCccc
Q psy17828 332 TKLYPPQWIQCDLRY-LDMTVLGKFAVIMADPPWDI 366 (1061)
Q Consensus 332 ~~~~Ppq~i~cDlr~-~d~~~lgkFdvIlaDPPW~~ 366 (1061)
+.-+|=.-+..|+|. |+-...|+||+++.||||..
T Consensus 89 ~~gl~i~~~~~DlR~~LP~~~~~~fD~f~TDPPyT~ 124 (243)
T PF01861_consen 89 EEGLPIEAVHYDLRDPLPEELRGKFDVFFTDPPYTP 124 (243)
T ss_dssp HHT--EEEE---TTS---TTTSS-BSEEEE---SSH
T ss_pred HcCCceEEEEecccccCCHHHhcCCCEEEeCCCCCH
Confidence 334454457778885 34455789999999999974
No 77
>TIGR00138 gidB 16S rRNA methyltransferase GidB. GidB (glucose-inhibited division protein B) appears to be present and in a single copy in nearly all complete eubacterial genomes. It is missing only from some obligate intracellular species of various lineages (Chlamydiae, Ehrlichia, Wolbachia, Anaplasma, Buchnera, etc.). GidB shows a methytransferase fold in its the crystal structure, and acts as a 7-methylguanosine (m(7)G) methyltransferase, apparently specific to 16S rRNA.
Probab=53.23 E-value=16 Score=38.26 Aligned_cols=66 Identities=11% Similarity=0.136 Sum_probs=45.0
Q ss_pred CceecccCccCcccCCCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEEecCccchHHHHHHhhc---cc
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAMELGRECLKL---FM 414 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~Le~g~elL~~---WG 414 (1061)
.++++|+..+ ...++||+|+++. +. + .+++.+.=-..|.++|.+++|..........++.+. ||
T Consensus 95 ~~i~~d~~~~--~~~~~fD~I~s~~-~~-----~-----~~~~~~~~~~~LkpgG~lvi~~~~~~~~~~~~~~e~~~~~~ 161 (181)
T TIGR00138 95 EIVNGRAEDF--QHEEQFDVITSRA-LA-----S-----LNVLLELTLNLLKVGGYFLAYKGKKYLDEIEEAKRKCQVLG 161 (181)
T ss_pred EEEecchhhc--cccCCccEEEehh-hh-----C-----HHHHHHHHHHhcCCCCEEEEEcCCCcHHHHHHHHHhhhhcC
Confidence 5788998875 3357999999985 21 1 112221112336789999999987777777666666 99
Q ss_pred ee
Q psy17828 415 LQ 416 (1061)
Q Consensus 415 f~ 416 (1061)
|+
T Consensus 162 ~~ 163 (181)
T TIGR00138 162 VE 163 (181)
T ss_pred ce
Confidence 99
No 78
>PF06442 DHFR_2: R67 dihydrofolate reductase; InterPro: IPR009159 Dihydrofolate reductase (DHFR) (1.5.1.3 from EC) catalyses the NADPH-dependent reduction of dihydrofolate to tetrahydrofolate, an essential step in de novo synthesis both of glycine and of purines and deoxythymidine phosphate (the precursors of DNA synthesis) [], and important also in the conversion of deoxyuridine monophosphate to deoxythymidine monophosphate. Although DHFR is found ubiquitously in prokaryotes and eukaryotes, and is found in all dividing cells, maintaining levels of fully reduced folate coenzymes, the catabolic steps are still not well understood []. Bacterial species possesses distinct DHFR enzymes (based on their pattern of binding diaminoheterocyclic molecules), but mammalian DHFRs are highly similar []. The active site is situated in the N-terminal half of the sequence, which includes a conserved Pro-Trp dipeptide; the tryptophan has been shown [] to be involved in the binding of substrate by the enzyme. Its central role in DNA precursor synthesis, coupled with its inhibition by antagonists such as trimethoprim and methotrexate, which are used as anti-bacterial or anti-cancer agents, has made DHFR a target of anticancer chemotherapy. However, resistance has developed against some drugs, as a result of changes in DHFR itself []. This entry represents a plasmid-encoded DHFR which shows a high level of resistance to the antibiotic trimethoprim. It is a homotetramer with an unusual pore, which contains the active site, passing through the middle of the molecule []. Its structure is unrelated to that of chromosomal DHFRs.; GO: 0004146 dihydrofolate reductase activity, 0042493 response to drug, 0055114 oxidation-reduction process; PDB: 1VIF_A 3SFM_A 2P4T_A 2GQV_A 2RK2_A 2RH2_A 2RK1_A 1VIE_A.
Probab=53.09 E-value=6.5 Score=35.70 Aligned_cols=11 Identities=55% Similarity=1.141 Sum_probs=7.3
Q ss_pred ccceeeeeccC
Q psy17828 859 REKVVGWYHTG 869 (1061)
Q Consensus 859 kE~IVGWYsTG 869 (1061)
.-+|||||||-
T Consensus 39 qg~vvgwy~t~ 49 (78)
T PF06442_consen 39 QGQVVGWYCTK 49 (78)
T ss_dssp EEEEEEEE--S
T ss_pred cceEeEEEecc
Confidence 46899999964
No 79
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=52.82 E-value=16 Score=28.92 Aligned_cols=32 Identities=34% Similarity=0.468 Sum_probs=26.5
Q ss_pred cccchHHHHhhhhhhhhHHHHHHHHHHhhccCcE
Q psy17828 106 LPITSQSLMGTLNQEYTHLCLINLLHKFATQKLI 139 (1061)
Q Consensus 106 lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI 139 (1061)
||++-.+|.+.+.. +.+-|.-+|-||..+|+|
T Consensus 1 l~mtr~diA~~lG~--t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 1 LPMTRQDIADYLGL--TRETVSRILKKLERQGLI 32 (32)
T ss_dssp EE--HHHHHHHHTS---HHHHHHHHHHHHHTTSE
T ss_pred CCcCHHHHHHHhCC--cHHHHHHHHHHHHHcCCC
Confidence 68888999999976 889999999999999998
No 80
>KOG1554|consensus
Probab=52.51 E-value=13 Score=42.41 Aligned_cols=61 Identities=30% Similarity=0.434 Sum_probs=37.5
Q ss_pred CcCCCCCCccceeeeeccCCC----CCCchHHHHHHHHhhcCCceEEEEcCCC--CCCCCCceeEEE
Q psy17828 851 TTTWPSRAREKVVGWYHTGPK----LHQNDIQINELIRRYCTNSVLVIIDAKP--KELGLPTEAYRV 911 (1061)
Q Consensus 851 ~L~qKVNPkE~IVGWYsTGse----lt~~s~lIHefys~~~~~PIhL~VDt~~--~~~~LPi~AYvs 911 (1061)
+..+.+..+|.|||||++-++ +..-|..-|..=.++-+|=+-++||+.- ..+.+-+.||..
T Consensus 122 e~~k~~gr~envVGWyHSHPgYgCWLSgIDVsTQ~lNQ~fQePfvAvViDP~Rtlsagkv~iGAFRT 188 (347)
T KOG1554|consen 122 EEAKNVGRLENVVGWYHSHPGYGCWLSGIDVSTQMLNQRFQEPFVAVVIDPTRTLSAGKVNIGAFRT 188 (347)
T ss_pred HHHHHhhhhhceeeeeecCCCCCccccCcchhHHHHhhhhcCCeEEEEecCccccccCceeeceeec
Confidence 345677889999999998662 4444444444444444456778888873 344455555544
No 81
>PF09445 Methyltransf_15: RNA cap guanine-N2 methyltransferase; InterPro: IPR019012 RNA cap guanine-N2 methyltransferases such as Schizosaccharomyces pombe (Fission yeast) trimethylguanosine synthase (Tgs1) and Giardia lamblia (Giardia intestinalis) Tgs2, catalyse the methylation step(s) for the conversion of the 7-monomethylguanosine (m(7)G) caps of snRNAs and snoRNAs to a 2,2,7-trimethylguanosine (m(2,2,7)G) cap structure [, , ]. Trimethylguanosine synthase is specific for guanine, and N7 methylation must precede N2 methylation. This enzyme is required for pre-mRNA splicing, pre-rRNA processing and small ribosomal subunit synthesis. As such, this enzyme plays a role in transcriptional regulation. ; GO: 0008168 methyltransferase activity, 0001510 RNA methylation, 0009452 RNA capping; PDB: 3EGI_B 3GDH_A.
Probab=52.38 E-value=5.5 Score=41.79 Aligned_cols=28 Identities=29% Similarity=0.535 Sum_probs=14.5
Q ss_pred CceecccCccCcccC-C-CccEEEECCCcc
Q psy17828 338 QWIQCDLRYLDMTVL-G-KFAVIMADPPWD 365 (1061)
Q Consensus 338 q~i~cDlr~~d~~~l-g-kFdvIlaDPPW~ 365 (1061)
.|+++|...+--... + .||+|.+||||-
T Consensus 51 ~~i~gD~~~~~~~~~~~~~~D~vFlSPPWG 80 (163)
T PF09445_consen 51 DFICGDFFELLKRLKSNKIFDVVFLSPPWG 80 (163)
T ss_dssp EEEES-HHHHGGGB------SEEEE---BS
T ss_pred EEEeCCHHHHHhhccccccccEEEECCCCC
Confidence 688998876432221 1 289999999996
No 82
>TIGR02085 meth_trns_rumB 23S rRNA (uracil-5-)-methyltransferase RumB. This family consists of RNA methyltransferases designated RumB, formerly YbjF. Members act on 23S rRNA U747 and the equivalent position in other proteobacterial species. This family is homologous to the other 23S rRNA methyltransferase RumA and to the tRNA methyltransferase TrmA.
Probab=51.81 E-value=15 Score=42.80 Aligned_cols=68 Identities=13% Similarity=0.163 Sum_probs=42.2
Q ss_pred CCceecccCccCcccCCCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEEecCccchHHHHHHhhcccee
Q psy17828 337 PQWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAMELGRECLKLFMLQ 416 (1061)
Q Consensus 337 pq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~Le~g~elL~~WGf~ 416 (1061)
-.|+++|+..+.....++||+|++|||.. . +..+-+..| ..+++++++++=|-...+.+-...| =||+
T Consensus 283 ~~~~~~d~~~~~~~~~~~~D~vi~DPPr~---G-----~~~~~l~~l--~~~~p~~ivyvsc~p~TlaRDl~~L--~gy~ 350 (374)
T TIGR02085 283 LSFAALDSAKFATAQMSAPELVLVNPPRR---G-----IGKELCDYL--SQMAPKFILYSSCNAQTMAKDIAEL--SGYQ 350 (374)
T ss_pred EEEEECCHHHHHHhcCCCCCEEEECCCCC---C-----CcHHHHHHH--HhcCCCeEEEEEeCHHHHHHHHHHh--cCce
Confidence 35889999776533335799999999963 1 222222222 1356788999888644444444455 3787
No 83
>PF05175 MTS: Methyltransferase small domain; InterPro: IPR007848 This domain is found in ribosomal RNA small subunit methyltransferase C and in other methyltransferases.; GO: 0008168 methyltransferase activity; PDB: 1WY7_A 1DUS_A 2OZV_A 2PJD_A 1VQ1_A 1NV9_A 1SG9_C 1NV8_A 3Q87_B 3DMF_A ....
Probab=49.39 E-value=3.2 Score=42.65 Aligned_cols=73 Identities=26% Similarity=0.303 Sum_probs=36.1
Q ss_pred CCceecccCccCcccCCCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEEecCccchHHHHHHhhccc
Q psy17828 337 PQWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAMELGRECLKLFM 414 (1061)
Q Consensus 337 pq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~Le~g~elL~~WG 414 (1061)
-+++.+|+.. .-..++||+|+++||+..... .+....+++..---.-|.++|.+|+ +.++.+.....+-+.+|
T Consensus 83 v~~~~~d~~~--~~~~~~fD~Iv~NPP~~~~~~--~~~~~~~~~i~~a~~~Lk~~G~l~l-v~~~~~~~~~~l~~~f~ 155 (170)
T PF05175_consen 83 VEVVQSDLFE--ALPDGKFDLIVSNPPFHAGGD--DGLDLLRDFIEQARRYLKPGGRLFL-VINSHLGYERLLKELFG 155 (170)
T ss_dssp EEEEESSTTT--TCCTTCEEEEEE---SBTTSH--CHHHHHHHHHHHHHHHEEEEEEEEE-EEETTSCHHHHHHHHHS
T ss_pred cccccccccc--cccccceeEEEEccchhcccc--cchhhHHHHHHHHHHhccCCCEEEE-EeecCCChHHHHHHhcC
Confidence 4567777743 222579999999999653211 0111123333332334566888765 55555544433444444
No 84
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=48.99 E-value=39 Score=36.31 Aligned_cols=68 Identities=16% Similarity=0.238 Sum_probs=49.1
Q ss_pred hhHHHHHHHHhhcc--------ccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeecccCCCCceEEEEeehHh
Q psy17828 89 PDLELELLEKLCDV--------SLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINESKDDDNQVEIVSVEHVK 160 (1061)
Q Consensus 89 ~~~e~~ll~~L~d~--------~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~~~~~~~~~~i~~~~~~k 160 (1061)
..++.+|.+.|.+. .+.+|.+-.+|...+.. +++.|..+|.+|..+|+|.++. ...+.| .|.++
T Consensus 153 ~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGi--sretlsR~L~~L~~~GlI~~~~----~~~i~I--~D~~~ 224 (230)
T PRK09391 153 KTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGL--TIETVSRALSQLQDRGLIGLSG----ARQIEL--RNRQA 224 (230)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCC--CHHHHHHHHHHHHHCCcEEecC----CceEEE--cCHHH
Confidence 45677777776542 35688888888888876 8899999999999999998861 012333 46667
Q ss_pred HHhH
Q psy17828 161 LLGM 164 (1061)
Q Consensus 161 l~~m 164 (1061)
|.+|
T Consensus 225 L~~l 228 (230)
T PRK09391 225 LRNL 228 (230)
T ss_pred HHHh
Confidence 6654
No 85
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=47.45 E-value=63 Score=34.50 Aligned_cols=70 Identities=16% Similarity=0.109 Sum_probs=48.8
Q ss_pred hHHHHHHHHhhccc--cccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeecccCCCCceEEEEeehHhHHhHHHH
Q psy17828 90 DLELELLEKLCDVS--LVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINESKDDDNQVEIVSVEHVKLLGMVNE 167 (1061)
Q Consensus 90 ~~e~~ll~~L~d~~--l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~~~~~~~~~~i~~~~~~kl~~m~~~ 167 (1061)
.++.+|..+|.... -.+|.+-.+|...+.. +++.|...|.+|..+|+|.+. ...+.| .|..+|.++..+
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~--sretvsR~L~~L~~~G~I~~~-----~~~i~I--~d~~~L~~~~~~ 220 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGV--SYRHLLYVLAQFIQDGYLKKS-----KRGYLI--KNRKQLSGLALE 220 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCC--cHHHHHHHHHHHHHCCCEEee-----CCEEEE--eCHHHHHHHHHH
Confidence 34666666654321 1345566677777755 889999999999999999997 334444 578888888766
Q ss_pred h
Q psy17828 168 V 168 (1061)
Q Consensus 168 ~ 168 (1061)
.
T Consensus 221 ~ 221 (226)
T PRK10402 221 L 221 (226)
T ss_pred h
Confidence 4
No 86
>PRK03522 rumB 23S rRNA methyluridine methyltransferase; Reviewed
Probab=47.33 E-value=19 Score=40.78 Aligned_cols=68 Identities=13% Similarity=0.153 Sum_probs=43.6
Q ss_pred CCceecccCccCcccCCCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEEecCccchHHHHHHhhcccee
Q psy17828 337 PQWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAMELGRECLKLFMLQ 416 (1061)
Q Consensus 337 pq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~Le~g~elL~~WGf~ 416 (1061)
-+|++.|+..+.....++||+|++|||..- +. .++..+ +..+..+.++|+=|....+.+-.+.|. ||+
T Consensus 223 v~~~~~D~~~~~~~~~~~~D~Vv~dPPr~G--------~~-~~~~~~-l~~~~~~~ivyvsc~p~t~~rd~~~l~--~y~ 290 (315)
T PRK03522 223 VQFQALDSTQFATAQGEVPDLVLVNPPRRG--------IG-KELCDY-LSQMAPRFILYSSCNAQTMAKDLAHLP--GYR 290 (315)
T ss_pred eEEEEcCHHHHHHhcCCCCeEEEECCCCCC--------cc-HHHHHH-HHHcCCCeEEEEECCcccchhHHhhcc--CcE
Confidence 468899988765443468999999999531 11 112111 233455788888887666666666663 777
No 87
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=47.32 E-value=38 Score=29.85 Aligned_cols=38 Identities=16% Similarity=0.407 Sum_probs=34.1
Q ss_pred ccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeee
Q psy17828 103 SLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITIN 142 (1061)
Q Consensus 103 ~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~ 142 (1061)
.+.+|.+-.+|.+.+.. ++..|..+|.+|.++|+|.++
T Consensus 24 ~~~~~lt~~~iA~~~g~--sr~tv~r~l~~l~~~g~I~~~ 61 (76)
T PF13545_consen 24 RIPLPLTQEEIADMLGV--SRETVSRILKRLKDEGIIEVK 61 (76)
T ss_dssp EEEEESSHHHHHHHHTS--CHHHHHHHHHHHHHTTSEEEE
T ss_pred eEEecCCHHHHHHHHCC--CHHHHHHHHHHHHHCCCEEEc
Confidence 46788899999999876 888899999999999999987
No 88
>TIGR00537 hemK_rel_arch HemK-related putative methylase. The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase (Medline 95189105). Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. This model represents an archaeal and eukaryotic protein family that lacks an N-terminal domain found in HemK and its eubacterial homologs. It is found in a single copy in the first six completed archaeal and eukaryotic genomes.
Probab=46.87 E-value=39 Score=34.73 Aligned_cols=79 Identities=18% Similarity=0.056 Sum_probs=44.6
Q ss_pred CCceecccCccCcccCCCccEEEECCCcccccc----CCCCCCC----------hHHHhcCCccccCCCcEEE-EecCcc
Q psy17828 337 PQWIQCDLRYLDMTVLGKFAVIMADPPWDIHME----LPYGTMS----------DDEMRQLGIPQLQDEGLLF-LWVTGR 401 (1061)
Q Consensus 337 pq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~----~~Y~tms----------~deI~~LPV~~La~~g~LF-LWvT~~ 401 (1061)
..++++|+..+. .++||+|+++|||..... .++..+. .+++..-=-.-|.++|.++ ...+..
T Consensus 68 ~~~~~~d~~~~~---~~~fD~Vi~n~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~Lk~gG~~~~~~~~~~ 144 (179)
T TIGR00537 68 LDVVMTDLFKGV---RGKFDVILFNPPYLPLEDDLRRGDWLDVAIDGGKDGRKVIDRFLDELPEILKEGGRVQLIQSSLN 144 (179)
T ss_pred eEEEEccccccc---CCcccEEEECCCCCCCcchhcccchhhhhhhcCCchHHHHHHHHHhHHHhhCCCCEEEEEEeccC
Confidence 356788875532 469999999999952210 1111000 1112111112345677554 444455
Q ss_pred chHHHHHHhhccceecc
Q psy17828 402 AMELGRECLKLFMLQDE 418 (1061)
Q Consensus 402 ~Le~g~elL~~WGf~~e 418 (1061)
......++|++=||..+
T Consensus 145 ~~~~~~~~l~~~gf~~~ 161 (179)
T TIGR00537 145 GEPDTFDKLDERGFRYE 161 (179)
T ss_pred ChHHHHHHHHhCCCeEE
Confidence 57788999999999843
No 89
>TIGR03533 L3_gln_methyl protein-(glutamine-N5) methyltransferase, ribosomal protein L3-specific. Members of this protein family methylate ribosomal protein L3 on a glutamine side chain. This family is related to HemK, a protein-glutamine methyltranferase for peptide chain release factors.
Probab=44.13 E-value=34 Score=38.46 Aligned_cols=76 Identities=18% Similarity=0.217 Sum_probs=42.2
Q ss_pred CceecccCccCcccCCCccEEEECCCccccccC-------CC-CCCC----------hHHHhcCCccccCCCcEEEEecC
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWDIHMEL-------PY-GTMS----------DDEMRQLGIPQLQDEGLLFLWVT 399 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~-------~Y-~tms----------~deI~~LPV~~La~~g~LFLWvT 399 (1061)
.|+++|+... + ..++||+|++|||+--.... +| +.+. ...|.+--..-|.++|.+++-++
T Consensus 175 ~~~~~D~~~~-~-~~~~fD~Iv~NPPy~~~~~~~~l~~~~~~ep~~al~gg~dGl~~~~~il~~a~~~L~~gG~l~~e~g 252 (284)
T TIGR03533 175 TLIQSDLFAA-L-PGRKYDLIVSNPPYVDAEDMADLPAEYHHEPELALASGEDGLDLVRRILAEAADHLNENGVLVVEVG 252 (284)
T ss_pred EEEECchhhc-c-CCCCccEEEECCCCCCccchhhCCHhhhcCHHHHhcCCCcHHHHHHHHHHHHHHhcCCCCEEEEEEC
Confidence 4788887431 1 12489999999998532110 01 0000 01122211224467899998887
Q ss_pred ccchHHHHHHhhcccee
Q psy17828 400 GRAMELGRECLKLFMLQ 416 (1061)
Q Consensus 400 ~~~Le~g~elL~~WGf~ 416 (1061)
... +..++++..=||.
T Consensus 253 ~~~-~~v~~~~~~~~~~ 268 (284)
T TIGR03533 253 NSM-EALEEAYPDVPFT 268 (284)
T ss_pred cCH-HHHHHHHHhCCCc
Confidence 644 6777788765543
No 90
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=42.67 E-value=17 Score=25.45 Aligned_cols=19 Identities=32% Similarity=0.765 Sum_probs=16.6
Q ss_pred CCCCcCCCCCCCCccceee
Q psy17828 289 DCSFLNTCFHMDSCKYVHY 307 (1061)
Q Consensus 289 dcs~L~tc~~~~tC~y~hy 307 (1061)
.|.|.-.|...+.|.|.|.
T Consensus 1 ~Ck~~~~C~~~~~C~f~HP 19 (19)
T PF14608_consen 1 PCKFGPNCTNGDNCPFSHP 19 (19)
T ss_pred CCcCcCCCCCCCcCccCCc
Confidence 4888889999999999993
No 91
>PF01170 UPF0020: Putative RNA methylase family UPF0020; InterPro: IPR000241 This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains [].; PDB: 3LDU_A 3LDG_A 3K0B_A 3V8V_B 3V97_A 3TLJ_A 3TM5_B 3TM4_A 3TMA_A.
Probab=40.88 E-value=15 Score=38.57 Aligned_cols=66 Identities=23% Similarity=0.386 Sum_probs=34.4
Q ss_pred CceecccCccCcccCCCccEEEECCCccccccCCCCCCChHHHhcC------CccccCCCcEEEEecCccchHHHHHHh
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQL------GIPQLQDEGLLFLWVTGRAMELGRECL 410 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~L------PV~~La~~g~LFLWvT~~~Le~g~elL 410 (1061)
++.++|.+.+. ..-+.||+|+.||||-.... +..++..| -+.++-++..+|+-.....++...+..
T Consensus 91 ~~~~~D~~~l~-~~~~~~d~IvtnPPyG~r~~------~~~~~~~ly~~~~~~~~~~l~~~~v~l~~~~~~~~~~~~~~ 162 (179)
T PF01170_consen 91 DFIQWDARELP-LPDGSVDAIVTNPPYGRRLG------SKKDLEKLYRQFLRELKRVLKPRAVFLTTSNRELEKALGLK 162 (179)
T ss_dssp EEEE--GGGGG-GTTSBSCEEEEE--STTSHC------HHHHHHHHHHHHHHHHHCHSTTCEEEEEESCCCHHHHHTST
T ss_pred EEEecchhhcc-cccCCCCEEEECcchhhhcc------CHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHhcch
Confidence 46788888877 22358999999999976532 11222222 011212345666666666666554443
No 92
>cd08067 MPN_2A_DUB Mov34/MPN/PAD-1 family: Histone H2A deubiquitinase. This family includes histone H2A deubiquitinase (Histone H2A DUB;MYSM1; myb-like, SWIRM and MPN domains 1; 2ADUB; 2A-DUB; KIAA19152ADUB, or KIAA1915/MYSM1), a member of JAMM/MPN+ deubiquitinases (DUBs), with possible Zn2+-dependent ubiquitin isopeptidase activity. It contains the SWIRM (Swi3p, Rsc8p and Moira), and SANT (SWI-SNF, ADA N-CoR, TFIIIB)/Myb domains; the SANT, but not the SWIRM, domain can bind directly to DNA. 2A-DUB is specific for monoubiquitinated H2A (uH2A), regulating transcription by coordinating histone acetylation and deubiquitination, and destabilizing the association of linker histone H1 with nucleosomes. 2A-DUB interacts with p/CAF (p300/CBP-associated factor) in a co-regulatory protein complex, where the status of acetylation of nucleosomal histones modulates its deubiquitinase activity. 2A-DUB is a positive regulator of androgen receptor (AR) transactivation activity on a reporter gene; it p
Probab=40.34 E-value=49 Score=35.51 Aligned_cols=62 Identities=21% Similarity=0.259 Sum_probs=35.6
Q ss_pred ccCcCCCCCCccceeeeeccCC----CCCCchHHHHHHHHhhc-------CCceEEEEcCCCCCC---CCCceeEEEe
Q psy17828 849 IPTTTWPSRAREKVVGWYHTGP----KLHQNDIQINELIRRYC-------TNSVLVIIDAKPKEL---GLPTEAYRVV 912 (1061)
Q Consensus 849 m~~L~qKVNPkE~IVGWYsTGs----elt~~s~lIHefys~~~-------~~PIhL~VDt~~~~~---~LPi~AYvsv 912 (1061)
|++.-.+.+ +.+||||+|-+ .+...|..-|--|..-. .+-|-+++|+-..+. ...+.+|...
T Consensus 70 ~~~~l~~~g--l~vVGwYHSHP~~~~~pS~~Di~tQ~~yQ~~~~~~~~~~~p~v~~I~~P~~~~~~~~~s~i~~f~~~ 145 (187)
T cd08067 70 IRESLESRG--LSVVGWYHSHPTFPPNPSLRDIDTQLDYQIMFKGSDSGYEPCVGLICSPYDRRNSTPESQITCFWVM 145 (187)
T ss_pred HHHHHHHcC--CEEEEEEecCCCCCcCCCHHHHHHHHHHHhhccccccCCCCeEEEEEccccCCCCCCCCcEEEEEEE
Confidence 443334444 58999998865 34444455555555432 367888898765432 2235555543
No 93
>PRK11783 rlmL 23S rRNA m(2)G2445 methyltransferase; Provisional
Probab=38.17 E-value=19 Score=45.44 Aligned_cols=81 Identities=20% Similarity=0.177 Sum_probs=47.7
Q ss_pred CceecccCccCcccCCCccEEEECCCccccccCCCC----CCChHHHhcCCccccCCCcEEEEecCccchHHHHHHhhcc
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYG----TMSDDEMRQLGIPQLQDEGLLFLWVTGRAMELGRECLKLF 413 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~----tms~deI~~LPV~~La~~g~LFLWvT~~~Le~g~elL~~W 413 (1061)
.|+++|+..+--...++||+|++|||--........ .-...++...-...|.++|++++-+....+....+.+..=
T Consensus 592 ~~i~~D~~~~l~~~~~~fDlIilDPP~f~~~~~~~~~~~~~~~y~~l~~~a~~lL~~gG~l~~~~~~~~~~~~~~~~~~~ 671 (702)
T PRK11783 592 RLIQADCLAWLKEAREQFDLIFIDPPTFSNSKRMEDSFDVQRDHVALIKDAKRLLRPGGTLYFSNNKRGFKMDEEGLAKL 671 (702)
T ss_pred EEEEccHHHHHHHcCCCcCEEEECCCCCCCCCccchhhhHHHHHHHHHHHHHHHcCCCCEEEEEeCCccCChhHHHHHhC
Confidence 688999864310113589999999997432110000 0012233333344567789887766666666667777766
Q ss_pred ceecc
Q psy17828 414 MLQDE 418 (1061)
Q Consensus 414 Gf~~e 418 (1061)
||+..
T Consensus 672 g~~~~ 676 (702)
T PRK11783 672 GLKAE 676 (702)
T ss_pred CCeEE
Confidence 77744
No 94
>PF03602 Cons_hypoth95: Conserved hypothetical protein 95; InterPro: IPR004398 This entry contains Ribosomal RNA small subunit methyltransferase D as well as the putative rRNA methyltransferase YlbH. They methylate the guanosine in position 966 of 16S rRNA in the assembled 30S particle [].; GO: 0008168 methyltransferase activity, 0031167 rRNA methylation; PDB: 3P9N_A 2ESR_B 2IFT_A 1WS6_A 2FPO_B 2FHP_A.
Probab=38.10 E-value=16 Score=38.62 Aligned_cols=29 Identities=28% Similarity=0.387 Sum_probs=16.1
Q ss_pred CceecccCccCcc---cCCCccEEEECCCccc
Q psy17828 338 QWIQCDLRYLDMT---VLGKFAVIMADPPWDI 366 (1061)
Q Consensus 338 q~i~cDlr~~d~~---~lgkFdvIlaDPPW~~ 366 (1061)
+.+++|...+=.. ...+||+|++|||+..
T Consensus 95 ~v~~~d~~~~l~~~~~~~~~fDiIflDPPY~~ 126 (183)
T PF03602_consen 95 RVIKGDAFKFLLKLAKKGEKFDIIFLDPPYAK 126 (183)
T ss_dssp EEEESSHHHHHHHHHHCTS-EEEEEE--STTS
T ss_pred eeeccCHHHHHHhhcccCCCceEEEECCCccc
Confidence 4566774432111 2359999999999975
No 95
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=38.04 E-value=77 Score=25.92 Aligned_cols=46 Identities=22% Similarity=0.270 Sum_probs=36.1
Q ss_pred hHHHHHHHHhhccccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEe
Q psy17828 90 DLELELLEKLCDVSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLIT 140 (1061)
Q Consensus 90 ~~e~~ll~~L~d~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~ 140 (1061)
+.++++|.+|.+ .=+++-.+|...++- +..-|...|.+|.++|+|+
T Consensus 3 ~~~~~Il~~l~~---~~~~t~~ela~~~~i--s~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 3 ETQRKILNYLRE---NPRITQKELAEKLGI--SRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHH---CTTS-HHHHHHHHTS---HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHH---cCCCCHHHHHHHhCC--CHHHHHHHHHHHHHCcCcC
Confidence 457889999888 334777888888764 8899999999999999985
No 96
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=37.62 E-value=70 Score=28.95 Aligned_cols=51 Identities=18% Similarity=0.125 Sum_probs=39.5
Q ss_pred hhHHHHHHHHhhccccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeee
Q psy17828 89 PDLELELLEKLCDVSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITIN 142 (1061)
Q Consensus 89 ~~~e~~ll~~L~d~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~ 142 (1061)
.++|.++|++|.++. ..++...++.-.+.. ...+|...|=+|..||.|.-.
T Consensus 3 ~~~ee~Il~~L~~~g-~~~a~~ia~~~~L~~--~kk~VN~~LY~L~k~g~v~k~ 53 (66)
T PF02295_consen 3 QDLEEKILDFLKELG-GSTATAIAKALGLSV--PKKEVNRVLYRLEKQGKVCKE 53 (66)
T ss_dssp HHHHHHHHHHHHHHT-SSEEEHHHHHHHHTS---HHHHHHHHHHHHHTTSEEEE
T ss_pred hhHHHHHHHHHHhcC-CccHHHHHHHhCcch--hHHHHHHHHHHHHHCCCEeeC
Confidence 368999999999977 566655555555543 578999999999999999754
No 97
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=37.40 E-value=45 Score=26.53 Aligned_cols=39 Identities=23% Similarity=0.359 Sum_probs=34.2
Q ss_pred cccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeee
Q psy17828 102 VSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITIN 142 (1061)
Q Consensus 102 ~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~ 142 (1061)
..+.+|++-.+|.+.+.. +...+...|.+|.++|+|...
T Consensus 3 ~~~~~~~s~~~la~~l~~--s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 3 IRVRLPLTRQEIAELLGL--TRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred ceEEeccCHHHHHHHHCC--CHHHHHHHHHHHHHCCCEEEe
Confidence 467889999999999876 788899999999999999865
No 98
>TIGR03735 PRTRC_A PRTRC system protein A. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated protein A.
Probab=36.72 E-value=1.1e+02 Score=33.43 Aligned_cols=75 Identities=12% Similarity=-0.007 Sum_probs=47.8
Q ss_pred hhHhhHHHHHhhccccCCceeEEEEEeeEEecCcEEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcCCCceE
Q psy17828 643 LVLLSVVDHFNRMSKIGNQKRVVGVLLGCWKGKGILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNAREKVV 722 (1061)
Q Consensus 643 LVLLsIsDH~tR~~~~~~~~rVvGvLLG~~~g~gtVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp~E~VV 722 (1061)
-.+=.|+.|+.+ ..+..+.|.|.|... ++ +...+++.-.+. .+.....|.. |. ..+|.+|
T Consensus 78 ~l~~~ii~hAr~----~~P~EacG~Iag~~~-~~---~~r~~p~~N~~~--Sp~~~~~d~~----~~------~~ge~lV 137 (192)
T TIGR03735 78 SLLEEFAEAARA----ALPNEVAAWIVWNSE-TG---SLRLAALESIEA--SPGHIDYRRP----RL------DDGEHLV 137 (192)
T ss_pred HHHHHHHHHHHh----cCCcceEEEEEEcCC-CC---EEEEEecccccc--CCceEEEcch----HH------hCCCeEE
Confidence 345677888766 567899999999732 23 334566654332 2222333433 22 7889999
Q ss_pred EEEecCCC----CCcccHH
Q psy17828 723 GWYHTGPK----LHQNDIQ 737 (1061)
Q Consensus 723 GWYsTGp~----ls~~Dl~ 737 (1061)
+-|||++. +++.|..
T Consensus 138 ~iyHSH~~spA~PS~tD~~ 156 (192)
T TIGR03735 138 VDLHSHGTGSAFFSETDDA 156 (192)
T ss_pred EEEcCCCCCCCCCCcccch
Confidence 99999875 6666643
No 99
>cd02440 AdoMet_MTases S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).
Probab=36.26 E-value=25 Score=30.22 Aligned_cols=56 Identities=21% Similarity=0.209 Sum_probs=34.3
Q ss_pred CCCceecccCccCcccCCCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEEe
Q psy17828 336 PPQWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLW 397 (1061)
Q Consensus 336 Ppq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLW 397 (1061)
+.+|+.+|+..+.....++||+|+++++.... .-....+.+-=...+.++|.++++
T Consensus 48 ~~~~~~~~~~~~~~~~~~~~d~i~~~~~~~~~------~~~~~~~l~~~~~~l~~~g~~~~~ 103 (107)
T cd02440 48 NVEVLKGDAEELPPEADESFDVIISDPPLHHL------VEDLARFLEEARRLLKPGGVLVLT 103 (107)
T ss_pred ceEEEEcChhhhccccCCceEEEEEccceeeh------hhHHHHHHHHHHHHcCCCCEEEEE
Confidence 45788889887665456799999999998641 001112211112234568887776
No 100
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=36.21 E-value=3.3e+02 Score=31.64 Aligned_cols=104 Identities=18% Similarity=0.278 Sum_probs=61.0
Q ss_pred EEEEeeEEecCc------EEEEEEEeeccccCCCCCCccccccHHHHHHHHHHHHhhcCCCceEEEEecCCC--------
Q psy17828 665 VGVLLGCWKGKG------ILDVSNSFAVPFDEDDKDNSVWFLDHDYLENMYGMFKKVNAREKVVGWYHTGPK-------- 730 (1061)
Q Consensus 665 vGvLLG~~~g~g------tVEVTNSFaVP~eEde~d~~v~~lD~~Y~e~MlemfKkVnp~E~VVGWYsTGp~-------- 730 (1061)
+|.|.|+..... .+.|..-|+=|.+.+.++ +..++....+..-++-+.. .+..|||=-|...
T Consensus 2 ~G~LYG~Y~~~~~vplGika~VeaIYEPpQ~~~~d~--~~l~~d~~~~~vd~iA~~l--GL~rVG~IfTdl~~~~~~~g~ 77 (306)
T PF05021_consen 2 FGFLYGRYEEYDDVPLGIKAVVEAIYEPPQEGEPDG--FTLLPDENEERVDAIASAL--GLERVGWIFTDLTDDGSGDGT 77 (306)
T ss_pred eEEEEEEEeccCCCCCceEEEEEEEECCCcCCCCCC--EEEcCCccHHHHHHHHHHC--CCEEEEEEEecCcccccCCCc
Confidence 699999987544 578888888887655443 2334433333322222222 6899999655432
Q ss_pred -----------CCcccHHHHHHHHhhC-------------CCcEEEEEcCCCCCCCcceEEEEeccc
Q psy17828 731 -----------LHQNDIQINELIRRYC-------------TNSVLVIIDAKPKELGLPTEAYRVVDE 773 (1061)
Q Consensus 731 -----------ls~~Dl~Ihe~f~~~~-------------~nPI~LivDPs~ss~gLplKAYrlv~e 773 (1061)
+++..+..-..||... .+-|-+++.+. ..+.+.+.||.++..
T Consensus 78 v~~~r~~~~~~LSs~Eii~aA~~Q~~~p~~~~~s~~g~fgSkFVT~vvsg~-~~g~i~~~ayQvS~q 143 (306)
T PF05021_consen 78 VKCKRHKDSYFLSSLEIIFAAKLQNKHPNPCKYSETGYFGSKFVTCVVSGD-EEGEIHFEAYQVSNQ 143 (306)
T ss_pred eeeccccccccccHHHHHHHHHHHHhcCccccccCCCccCCeEEEEEEeCC-CCCceeeEEeeehHH
Confidence 3444443333343322 22366666664 345599999999976
No 101
>PHA03411 putative methyltransferase; Provisional
Probab=35.53 E-value=23 Score=40.38 Aligned_cols=78 Identities=17% Similarity=0.206 Sum_probs=44.3
Q ss_pred CCceecccCccCcccCCCccEEEECCCcccccc------CCC-------CCCChHHHhcCCcccc-CC-CcEEEEecCcc
Q psy17828 337 PQWIQCDLRYLDMTVLGKFAVIMADPPWDIHME------LPY-------GTMSDDEMRQLGIPQL-QD-EGLLFLWVTGR 401 (1061)
Q Consensus 337 pq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~------~~Y-------~tms~deI~~LPV~~L-a~-~g~LFLWvT~~ 401 (1061)
..|+++|++.+.. .++||+|+++|||-.... ..| ..++.++..+ +++.+ .+ ..+.|++-+.+
T Consensus 111 v~~v~~D~~e~~~--~~kFDlIIsNPPF~~l~~~d~~~~~~~~GG~~g~~~l~~~~~l~-~v~~~L~p~G~~~~~yss~~ 187 (279)
T PHA03411 111 AEWITSDVFEFES--NEKFDVVISNPPFGKINTTDTKDVFEYTGGEFEFKVMTLGQKFA-DVGYFIVPTGSAGFAYSGRP 187 (279)
T ss_pred CEEEECchhhhcc--cCCCcEEEEcCCccccCchhhhhhhhhccCccccccccHHHHHh-hhHheecCCceEEEEEeccc
Confidence 3589999987652 368999999999974221 122 2222222211 22322 23 33556655533
Q ss_pred chHH------HHHHhhccceec
Q psy17828 402 AMEL------GRECLKLFMLQD 417 (1061)
Q Consensus 402 ~Le~------g~elL~~WGf~~ 417 (1061)
..+. -+.+|+.=||..
T Consensus 188 ~y~~sl~~~~y~~~l~~~g~~~ 209 (279)
T PHA03411 188 YYDGTMKSNKYLKWSKQTGLVT 209 (279)
T ss_pred cccccCCHHHHHHHHHhcCcEe
Confidence 3332 358899999983
No 102
>PRK10909 rsmD 16S rRNA m(2)G966-methyltransferase; Provisional
Probab=35.23 E-value=16 Score=39.27 Aligned_cols=54 Identities=17% Similarity=0.244 Sum_probs=28.8
Q ss_pred CceecccCccCcccCCCccEEEECCCccccccCCCCCCChHHHhcCCc-cccCCCcEEEEec
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGI-PQLQDEGLLFLWV 398 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV-~~La~~g~LFLWv 398 (1061)
.++++|+..+-....++||+|++|||+... +..+-+..|-- +-|.+++++++=+
T Consensus 105 ~~~~~D~~~~l~~~~~~fDlV~~DPPy~~g-------~~~~~l~~l~~~~~l~~~~iv~ve~ 159 (199)
T PRK10909 105 RVVNTNALSFLAQPGTPHNVVFVDPPFRKG-------LLEETINLLEDNGWLADEALIYVES 159 (199)
T ss_pred EEEEchHHHHHhhcCCCceEEEECCCCCCC-------hHHHHHHHHHHCCCcCCCcEEEEEe
Confidence 466777654211112469999999997421 22222233322 2245677776543
No 103
>PRK00811 spermidine synthase; Provisional
Probab=33.67 E-value=24 Score=39.67 Aligned_cols=61 Identities=16% Similarity=0.161 Sum_probs=37.9
Q ss_pred CceecccCccCcccCCCccEEEEC--CCccccccCCCCCCChHHHhcCCccccCCCcEEEEecCccch
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMAD--PPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAM 403 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaD--PPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~L 403 (1061)
..+..|.+.+--..-++||+|++| +||... .. +-..++.+.--..|.++|++.+|+.++..
T Consensus 134 ~v~~~Da~~~l~~~~~~yDvIi~D~~dp~~~~----~~-l~t~ef~~~~~~~L~~gGvlv~~~~~~~~ 196 (283)
T PRK00811 134 ELVIGDGIKFVAETENSFDVIIVDSTDPVGPA----EG-LFTKEFYENCKRALKEDGIFVAQSGSPFY 196 (283)
T ss_pred EEEECchHHHHhhCCCcccEEEECCCCCCCch----hh-hhHHHHHHHHHHhcCCCcEEEEeCCCccc
Confidence 467788776433345699999999 566211 11 11234433333567889999999886543
No 104
>COG4123 Predicted O-methyltransferase [General function prediction only]
Probab=33.64 E-value=47 Score=37.31 Aligned_cols=81 Identities=19% Similarity=0.220 Sum_probs=53.6
Q ss_pred CceecccCccCcccC-CCccEEEECCCccccc-----------cCCCCCCChHHHhcCCccccCCCcEEEEecCccchHH
Q psy17828 338 QWIQCDLRYLDMTVL-GKFAVIMADPPWDIHM-----------ELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAMEL 405 (1061)
Q Consensus 338 q~i~cDlr~~d~~~l-gkFdvIlaDPPW~~~~-----------~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~Le~ 405 (1061)
+.++.|+..|-.... .+||+|++.||.--.. ..|-.+.+.+++.+--=.-|-++|.+++=--...+..
T Consensus 98 ~v~~~Di~~~~~~~~~~~fD~Ii~NPPyf~~~~~~~~~~~~~~Ar~e~~~~le~~i~~a~~~lk~~G~l~~V~r~erl~e 177 (248)
T COG4123 98 QVIEADIKEFLKALVFASFDLIICNPPYFKQGSRLNENPLRAIARHEITLDLEDLIRAAAKLLKPGGRLAFVHRPERLAE 177 (248)
T ss_pred eEehhhHHHhhhcccccccCEEEeCCCCCCCccccCcChhhhhhhhhhcCCHHHHHHHHHHHccCCCEEEEEecHHHHHH
Confidence 578999998765443 4799999999995321 1223466677776654444566887776554444555
Q ss_pred HHHHhhccceecc
Q psy17828 406 GRECLKLFMLQDE 418 (1061)
Q Consensus 406 g~elL~~WGf~~e 418 (1061)
-.++|++.+|...
T Consensus 178 i~~~l~~~~~~~k 190 (248)
T COG4123 178 IIELLKSYNLEPK 190 (248)
T ss_pred HHHHHHhcCCCce
Confidence 5788888777744
No 105
>KOG1555|consensus
Probab=32.10 E-value=29 Score=40.17 Aligned_cols=58 Identities=28% Similarity=0.442 Sum_probs=40.8
Q ss_pred cCCCCCCccceeeeeccCC----CCCCchHHHHHHHHhhcCCceEEEEcCCC--CCCCCCceeEEE
Q psy17828 852 TTWPSRAREKVVGWYHTGP----KLHQNDIQINELIRRYCTNSVLVIIDAKP--KELGLPTEAYRV 911 (1061)
Q Consensus 852 L~qKVNPkE~IVGWYsTGs----elt~~s~lIHefys~~~~~PIhL~VDt~~--~~~~LPi~AYvs 911 (1061)
|++--.| |-|||||++=+ .+...|+--|.=|...++..+-++||+-. .++..|. ||-.
T Consensus 108 l~~tGrp-~~VVGWYHSHP~f~~wpS~vDi~tQ~syq~~~~r~~a~~v~~i~S~~g~vv~d-~f~~ 171 (316)
T KOG1555|consen 108 LKQTGRP-ELVVGWYHSHPGFGCWPSLVDIDTQQSYQALSSRAVAVVVDPIQSPYGKVVPD-AFSS 171 (316)
T ss_pred HHhcCCc-ceEEeeccCCCCCCCCccccchhHHHHHhhhccCCcceeeecccCCCCCccCC-hhhh
Confidence 3444445 99999998844 67888888899898888877888888874 3333443 4444
No 106
>KOG3350|consensus
Probab=31.73 E-value=17 Score=39.19 Aligned_cols=14 Identities=43% Similarity=0.864 Sum_probs=12.2
Q ss_pred CCCccEEEECCCcc
Q psy17828 352 LGKFAVIMADPPWD 365 (1061)
Q Consensus 352 lgkFdvIlaDPPW~ 365 (1061)
.++||+|+||||.=
T Consensus 133 k~~fdiivaDPPfL 146 (217)
T KOG3350|consen 133 KAHFDIIVADPPFL 146 (217)
T ss_pred HhcccEEEeCCccc
Confidence 46899999999984
No 107
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=31.40 E-value=82 Score=27.64 Aligned_cols=49 Identities=16% Similarity=0.207 Sum_probs=40.2
Q ss_pred hHHHHHHHHhhccccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeec
Q psy17828 90 DLELELLEKLCDVSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINE 143 (1061)
Q Consensus 90 ~~e~~ll~~L~d~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~ 143 (1061)
+.|.+++.+|.+ .=|++..+|.+.+.- ++..|...|.+|..+|+|....
T Consensus 8 ~~E~~vy~~Ll~---~~~~t~~eIa~~l~i--~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 8 ENEAKVYLALLK---NGPATAEEIAEELGI--SRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHH---HCHEEHHHHHHHHTS--SHHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHH---cCCCCHHHHHHHHCc--CHHHHHHHHHHHHHCCCEEEEc
Confidence 458888888753 347888888888754 8899999999999999999886
No 108
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=31.20 E-value=1.1e+02 Score=27.55 Aligned_cols=52 Identities=17% Similarity=0.108 Sum_probs=41.1
Q ss_pred ChhHHHHHHHHhhccccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeee
Q psy17828 88 NPDLELELLEKLCDVSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITIN 142 (1061)
Q Consensus 88 d~~~e~~ll~~L~d~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~ 142 (1061)
..++|.++|.+|.+.-=. +++..+|...+.- +...|..+|.+|...|+|+-.
T Consensus 4 ~~~~~~~IL~~L~~~g~~-~~ta~eLa~~lgl--~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 4 QDSLEEKILEFLENSGDE-TSTALQLAKNLGL--PKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred chHHHHHHHHHHHHCCCC-CcCHHHHHHHHCC--CHHHHHHHHHHHHHCCCEEec
Confidence 346789999999984211 3778888888865 667999999999999999764
No 109
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=30.68 E-value=86 Score=28.76 Aligned_cols=50 Identities=22% Similarity=0.260 Sum_probs=38.2
Q ss_pred HHHHHHhhccccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeecc
Q psy17828 93 LELLEKLCDVSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINES 144 (1061)
Q Consensus 93 ~~ll~~L~d~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~~ 144 (1061)
-++|-+|....=.-|.++.+|.+.++. +..-|..+|++|...|+|+-..+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i--~~~~l~kil~~L~~~Gli~s~~G 60 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGI--SPSYLRKILQKLKKAGLIESSRG 60 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS---HHHHHHHHHHHHHTTSEEEETS
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCc--CHHHHHHHHHHHhhCCeeEecCC
Confidence 355666666555667999999998876 77889999999999999977653
No 110
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=30.35 E-value=60 Score=30.86 Aligned_cols=38 Identities=8% Similarity=0.083 Sum_probs=33.7
Q ss_pred cccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeec
Q psy17828 104 LVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINE 143 (1061)
Q Consensus 104 l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~ 143 (1061)
...|++-.+|.+.+.. +++-|...|.+|..+|+|..+.
T Consensus 44 ~~~~is~~eLa~~~g~--sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 44 KQDRVTATVIAELTGL--SRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred cCCccCHHHHHHHHCc--CHHHHHHHHHHHHHCCCeeeec
Confidence 6788889999998876 8889999999999999998764
No 111
>TIGR00479 rumA 23S rRNA (uracil-5-)-methyltransferase RumA. This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA.
Probab=30.12 E-value=74 Score=37.63 Aligned_cols=69 Identities=16% Similarity=0.168 Sum_probs=42.7
Q ss_pred CceecccCccC--ccc-CCCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEEecCccchHHHHHHhhccc
Q psy17828 338 QWIQCDLRYLD--MTV-LGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAMELGRECLKLFM 414 (1061)
Q Consensus 338 q~i~cDlr~~d--~~~-lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~Le~g~elL~~WG 414 (1061)
+|++.|+..+- +.. .++||+|++|||.. -+..+-+.. +.++.+++++|+=|....+.+-.+.|.+.|
T Consensus 343 ~~~~~d~~~~l~~~~~~~~~~D~vi~dPPr~--------G~~~~~l~~--l~~l~~~~ivyvsc~p~tlard~~~l~~~g 412 (431)
T TIGR00479 343 EFLAGTLETVLPKQPWAGQIPDVLLLDPPRK--------GCAAEVLRT--IIELKPERIVYVSCNPATLARDLEFLCKEG 412 (431)
T ss_pred EEEeCCHHHHHHHHHhcCCCCCEEEECcCCC--------CCCHHHHHH--HHhcCCCEEEEEcCCHHHHHHHHHHHHHCC
Confidence 46777775531 111 24699999999963 121222222 224566788887776556666677888889
Q ss_pred ee
Q psy17828 415 LQ 416 (1061)
Q Consensus 415 f~ 416 (1061)
|+
T Consensus 413 y~ 414 (431)
T TIGR00479 413 YG 414 (431)
T ss_pred ee
Confidence 98
No 112
>PRK13168 rumA 23S rRNA m(5)U1939 methyltransferase; Reviewed
Probab=28.97 E-value=46 Score=39.63 Aligned_cols=69 Identities=14% Similarity=0.204 Sum_probs=44.2
Q ss_pred CCceecccCccCcc--c-CCCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEEecCccchHHHHHHhhcc
Q psy17828 337 PQWIQCDLRYLDMT--V-LGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAMELGRECLKLF 413 (1061)
Q Consensus 337 pq~i~cDlr~~d~~--~-lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~Le~g~elL~~W 413 (1061)
-.|+++|+..+-.. . .++||+|++|||+.- + .+.+.. +..+..++++|+=|....+.+-...|..=
T Consensus 347 v~~~~~d~~~~l~~~~~~~~~fD~Vi~dPPr~g--------~-~~~~~~--l~~~~~~~ivyvSCnp~tlaRDl~~L~~~ 415 (443)
T PRK13168 347 VTFYHANLEEDFTDQPWALGGFDKVLLDPPRAG--------A-AEVMQA--LAKLGPKRIVYVSCNPATLARDAGVLVEA 415 (443)
T ss_pred eEEEEeChHHhhhhhhhhcCCCCEEEECcCCcC--------h-HHHHHH--HHhcCCCeEEEEEeChHHhhccHHHHhhC
Confidence 46888888653211 1 247999999999852 2 223322 23456788988888655555555667666
Q ss_pred cee
Q psy17828 414 MLQ 416 (1061)
Q Consensus 414 Gf~ 416 (1061)
||+
T Consensus 416 gY~ 418 (443)
T PRK13168 416 GYR 418 (443)
T ss_pred CcE
Confidence 898
No 113
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=28.41 E-value=78 Score=32.81 Aligned_cols=38 Identities=18% Similarity=0.211 Sum_probs=32.7
Q ss_pred cccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeec
Q psy17828 104 LVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINE 143 (1061)
Q Consensus 104 l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~ 143 (1061)
+.+|.+-.+|...++. +++.|..+|.+|..+|+|.+.+
T Consensus 165 ~~~~~t~~~lA~~lG~--tr~tvsR~l~~l~~~gii~~~~ 202 (211)
T PRK11753 165 MQIKITRQEIGRIVGC--SREMVGRVLKMLEDQGLISAHG 202 (211)
T ss_pred eecCCCHHHHHHHhCC--CHHHHHHHHHHHHHCCCEEecC
Confidence 4568888888888875 8899999999999999999874
No 114
>PHA03412 putative methyltransferase; Provisional
Probab=28.37 E-value=39 Score=37.78 Aligned_cols=28 Identities=21% Similarity=0.536 Sum_probs=23.0
Q ss_pred CCceecccCccCcccCCCccEEEECCCccc
Q psy17828 337 PQWIQCDLRYLDMTVLGKFAVIMADPPWDI 366 (1061)
Q Consensus 337 pq~i~cDlr~~d~~~lgkFdvIlaDPPW~~ 366 (1061)
..|+++|+..+++ .++||+|+..||.-.
T Consensus 99 ~~~~~~D~~~~~~--~~~FDlIIsNPPY~~ 126 (241)
T PHA03412 99 ATWINADALTTEF--DTLFDMAISNPPFGK 126 (241)
T ss_pred CEEEEcchhcccc--cCCccEEEECCCCCC
Confidence 4699999987654 469999999999964
No 115
>PRK14967 putative methyltransferase; Provisional
Probab=27.59 E-value=1.3e+02 Score=32.20 Aligned_cols=79 Identities=19% Similarity=0.130 Sum_probs=41.3
Q ss_pred CceecccCccCcccCCCccEEEECCCccccccC---CCC-----------CCChHHHhcCCccccCCCcEEEEe-cCccc
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWDIHMEL---PYG-----------TMSDDEMRQLGIPQLQDEGLLFLW-VTGRA 402 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~---~Y~-----------tms~deI~~LPV~~La~~g~LFLW-vT~~~ 402 (1061)
.+++.|+.. +...++||+|++|||+...... .+. ....+.+.+-=..-|.++|.+++= -+...
T Consensus 87 ~~~~~d~~~--~~~~~~fD~Vi~npPy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~Lk~gG~l~~~~~~~~~ 164 (223)
T PRK14967 87 DVRRGDWAR--AVEFRPFDVVVSNPPYVPAPPDAPPSRGPARAWDAGPDGRAVLDRLCDAAPALLAPGGSLLLVQSELSG 164 (223)
T ss_pred EEEECchhh--hccCCCeeEEEECCCCCCCCcccccccChhHhhhCCCcHHHHHHHHHHHHHHhcCCCcEEEEEEecccC
Confidence 466777654 2223689999999998533211 000 000111221112234567775542 22235
Q ss_pred hHHHHHHhhccceecc
Q psy17828 403 MELGRECLKLFMLQDE 418 (1061)
Q Consensus 403 Le~g~elL~~WGf~~e 418 (1061)
.....+.++.=||..+
T Consensus 165 ~~~~~~~l~~~g~~~~ 180 (223)
T PRK14967 165 VERTLTRLSEAGLDAE 180 (223)
T ss_pred HHHHHHHHHHCCCCeE
Confidence 6678888887788733
No 116
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=27.13 E-value=1.9e+02 Score=26.15 Aligned_cols=59 Identities=14% Similarity=0.041 Sum_probs=41.5
Q ss_pred hHHHHHHHHhhcccc---ccccchHHHHhhhhh--------hhhHHHHHHHHHHhhccCcEeeecccCCC
Q psy17828 90 DLELELLEKLCDVSL---VLPITSQSLMGTLNQ--------EYTHLCLINLLHKFATQKLITINESKDDD 148 (1061)
Q Consensus 90 ~~e~~ll~~L~d~~l---~lP~~s~~l~~~~~~--------~~~~~~v~~lL~k~a~q~lI~i~~~~~~~ 148 (1061)
.-||-+|..|.-..- .=+.+..++++.... |.+...+..+|.+|...|+|.++...-|.
T Consensus 2 ~~~Kl~L~Al~~~~~~~~~~~~~~~~vy~~Y~~~c~~~~~~~l~~~~~~~~l~~L~~~gli~~~~~~~g~ 71 (87)
T cd08768 2 LHQKLVLLALLLLFKRGGEEEATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELEMLGLLETEVSSKGR 71 (87)
T ss_pred chHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHcCCeEEEEecCCC
Confidence 346777776553221 234667777655433 66789999999999999999998876644
No 117
>PRK15128 23S rRNA m(5)C1962 methyltransferase; Provisional
Probab=26.95 E-value=19 Score=42.67 Aligned_cols=66 Identities=24% Similarity=0.320 Sum_probs=36.0
Q ss_pred CceecccCcc--Cccc-CCCccEEEECCCcccccc--CCCCCCChHHHhcCCccccCCCcEEEEecCccch
Q psy17828 338 QWIQCDLRYL--DMTV-LGKFAVIMADPPWDIHME--LPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAM 403 (1061)
Q Consensus 338 q~i~cDlr~~--d~~~-lgkFdvIlaDPPW~~~~~--~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~L 403 (1061)
.++++|+..+ ++.. .++||+|++|||--.... +....-...++..+-...|.++|+++.-..+.++
T Consensus 274 ~~i~~D~~~~l~~~~~~~~~fDlVilDPP~f~~~k~~l~~~~~~y~~l~~~a~~lLk~gG~lv~~scs~~~ 344 (396)
T PRK15128 274 EFVRDDVFKLLRTYRDRGEKFDVIVMDPPKFVENKSQLMGACRGYKDINMLAIQLLNPGGILLTFSCSGLM 344 (396)
T ss_pred EEEEccHHHHHHHHHhcCCCCCEEEECCCCCCCChHHHHHHHHHHHHHHHHHHHHcCCCeEEEEEeCCCcC
Confidence 5889998764 1221 348999999999632211 0000112233433444455678877755544444
No 118
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=26.80 E-value=2.8e+02 Score=28.51 Aligned_cols=73 Identities=12% Similarity=0.163 Sum_probs=52.4
Q ss_pred HHHHHHHhhccccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeecccC-CCCceEEE-EeehHhHHhHHHHh
Q psy17828 92 ELELLEKLCDVSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINESKD-DDNQVEIV-SVEHVKLLGMVNEV 168 (1061)
Q Consensus 92 e~~ll~~L~d~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~~~~-~~~~~~i~-~~~~~kl~~m~~~~ 168 (1061)
+..++..|-. -.=|.+-.+|.+.++. ++.-|..-||+|...|||.=...+. ++..+.|- -+|.+++..++...
T Consensus 29 Dv~v~~~LL~--~~~~~tvdelae~lnr--~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~ 103 (126)
T COG3355 29 DVEVYKALLE--ENGPLTVDELAEILNR--SRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKD 103 (126)
T ss_pred HHHHHHHHHh--hcCCcCHHHHHHHHCc--cHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHH
Confidence 4444444332 3458899999999987 8899999999999999998777776 33344443 57888877666554
No 119
>PF10672 Methyltrans_SAM: S-adenosylmethionine-dependent methyltransferase; InterPro: IPR019614 Members of this entry are S-adenosylmethionine-dependent methyltransferases from gamma-proteobacterial species. The diversity in the roles of methylation is matched by the almost bewildering number of methyltransferase enzymes that catalyse the methylation reaction. Although several classes of methyltransferase enzymes are known, the great majority of methylation reactions are catalysed by the S-adenosylmethionine-dependent methyltransferases. SAM (S-adenosylmethionine, also known as AdoMet) is well known as the methyl donor for the majority of methyltransferases that modify DNA, RNA, histones and other proteins, dictating replicational, transcriptional and translational fidelity, mismatch repair, chromatin modelling, epigenetic modifications and imprinting [].; GO: 0008168 methyltransferase activity; PDB: 2IGT_B 1WXX_A 1WXW_D 2CWW_B 2AS0_B 3V8V_B 3V97_A 3C0K_A 2B78_A 3LDF_A.
Probab=26.78 E-value=30 Score=39.40 Aligned_cols=64 Identities=20% Similarity=0.365 Sum_probs=29.1
Q ss_pred CceecccCcc-C-cccCCCccEEEECCCccccccCCCC-CCChHHHhcCCccccCCCcEEEEecCccch
Q psy17828 338 QWIQCDLRYL-D-MTVLGKFAVIMADPPWDIHMELPYG-TMSDDEMRQLGIPQLQDEGLLFLWVTGRAM 403 (1061)
Q Consensus 338 q~i~cDlr~~-d-~~~lgkFdvIlaDPPW~~~~~~~Y~-tms~deI~~LPV~~La~~g~LFLWvT~~~L 403 (1061)
.|++.|+-.+ . +...++||+|++|||= +.... .. .-...+|...-+.-|.++|+|+.=....++
T Consensus 177 ~~~~~Dvf~~l~~~~~~~~fD~IIlDPPs-F~k~~-~~~~~~y~~L~~~a~~ll~~gG~l~~~scs~~i 243 (286)
T PF10672_consen 177 RFIQGDVFKFLKRLKKGGRFDLIILDPPS-FAKSK-FDLERDYKKLLRRAMKLLKPGGLLLTCSCSHHI 243 (286)
T ss_dssp EEEES-HHHHHHHHHHTT-EEEEEE--SS-EESST-CEHHHHHHHHHHHHHHTEEEEEEEEEEE--TTS
T ss_pred EEEecCHHHHHHHHhcCCCCCEEEECCCC-CCCCH-HHHHHHHHHHHHHHHHhcCCCCEEEEEcCCccc
Confidence 5888888642 1 1234699999999993 32110 00 001123333333445678887654444444
No 120
>KOG2671|consensus
Probab=26.41 E-value=45 Score=39.36 Aligned_cols=33 Identities=27% Similarity=0.461 Sum_probs=21.9
Q ss_pred ccCCCCceecccCccCcccC-----CCccEEEECCCcccc
Q psy17828 333 KLYPPQWIQCDLRYLDMTVL-----GKFAVIMADPPWDIH 367 (1061)
Q Consensus 333 ~~~Ppq~i~cDlr~~d~~~l-----gkFdvIlaDPPW~~~ 367 (1061)
+-.-|||+ ||-..|++.. -+||.|++|||.-++
T Consensus 260 Yg~~~~fl--dvl~~D~sn~~~rsn~~fDaIvcDPPYGVR 297 (421)
T KOG2671|consen 260 YGSSSQFL--DVLTADFSNPPLRSNLKFDAIVCDPPYGVR 297 (421)
T ss_pred hCCcchhh--heeeecccCcchhhcceeeEEEeCCCcchh
Confidence 33356663 4444555543 389999999999764
No 121
>KOG3289|consensus
Probab=25.20 E-value=67 Score=34.69 Aligned_cols=89 Identities=20% Similarity=0.452 Sum_probs=54.9
Q ss_pred ccCCCCccccccc----cccccccccceeeeecCCCCCcceecccCcCCCCCCccceeeeeccCCCCCCc-----hHHHH
Q psy17828 810 RSSRGGKVGRIRC----RSHFSTTGVLSIRRIFNPIGTWTFIRIPTTTWPSRAREKVVGWYHTGPKLHQN-----DIQIN 880 (1061)
Q Consensus 810 ~~~~~g~~~~~~~----~~~~~~~g~~~~~~~~~~~~~~~~~~m~~L~qKVNPkE~IVGWYsTGselt~~-----s~lIH 880 (1061)
-.|.|+.+.++|| -++..-.-||-+-- |-||-| -+.-..+|+|.|.+...++.. -.-|=
T Consensus 34 ~~~kg~~v~itdcVPLfH~~laLaPmlEvAl--~lId~~----------~~~~GlviaGyy~Ane~~~D~s~~~~A~kia 101 (199)
T KOG3289|consen 34 ATGKGECVEITDCVPLFHSHLALAPMLEVAL--NLIDVW----------GAQAGLVIAGYYHANERVNDQSLNPVALKIA 101 (199)
T ss_pred cCCCCCeEEEEecchhhccccccccHHHHHH--HHHHHH----------HHhcCeEEEEEeecCCCccccCccHHHHHHH
Confidence 3678899999999 34444455553322 334665 234567899999988755443 34566
Q ss_pred HHHHhhcCCceEEEEcCC-C--CCCCCCceeEE
Q psy17828 881 ELIRRYCTNSVLVIIDAK-P--KELGLPTEAYR 910 (1061)
Q Consensus 881 efys~~~~~PIhL~VDt~-~--~~~~LPi~AYv 910 (1061)
+-.+++.+++.+|++|-. + +...-|+.+|+
T Consensus 102 drIse~f~~A~ilv~dn~~l~~~~e~~~v~v~e 134 (199)
T KOG3289|consen 102 DRISEFFPDAAILVLDNKKLVPQCERPPVIVLE 134 (199)
T ss_pred HHHHhhCCCCeEEEEeccccccccCCCCEEEee
Confidence 667776665555566544 2 22334677776
No 122
>PRK15043 transcriptional regulator MirA; Provisional
Probab=24.84 E-value=80 Score=35.45 Aligned_cols=45 Identities=11% Similarity=0.192 Sum_probs=38.9
Q ss_pred CCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEEecCccchHHHHHHhhccc
Q psy17828 353 GKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAMELGRECLKLFM 414 (1061)
Q Consensus 353 gkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~Le~g~elL~~WG 414 (1061)
..|.|.+++.|+. .|-++|-+...+|+|++...-..-.+.+.+|.
T Consensus 188 ~g~~v~vl~~~~~-----------------~~~pelf~~~~~~~~~~~~~t~~q~~~~~~w~ 232 (243)
T PRK15043 188 QGWRIDVLAHSLN-----------------QLRPELFEGRTLLVWCGENRTSAQQQQLTSWQ 232 (243)
T ss_pred CCceEEEeCCccc-----------------ccChhhcCCCeEEEEeCCCCCHHHHHHHHHHH
Confidence 3799999999987 47778888788999999988888889999995
No 123
>PRK11805 N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
Probab=24.00 E-value=1.1e+02 Score=34.91 Aligned_cols=26 Identities=23% Similarity=0.480 Sum_probs=18.6
Q ss_pred CceecccCccCcccCCCccEEEECCCcc
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWD 365 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~ 365 (1061)
.|+++|+... + ..++||+|++|||+-
T Consensus 187 ~~~~~D~~~~-l-~~~~fDlIvsNPPyi 212 (307)
T PRK11805 187 TLIESDLFAA-L-PGRRYDLIVSNPPYV 212 (307)
T ss_pred EEEECchhhh-C-CCCCccEEEECCCCC
Confidence 5788887431 1 124899999999984
No 124
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.74 E-value=3.4e+02 Score=29.07 Aligned_cols=85 Identities=18% Similarity=0.235 Sum_probs=58.3
Q ss_pred HHHHHHHhhccccccccchHHHHhhhhhhhhHHHHHHHHHHhhccCcEeeecccC-CCC-ceEEEEeehHhHHhHHHHhh
Q psy17828 92 ELELLEKLCDVSLVLPITSQSLMGTLNQEYTHLCLINLLHKFATQKLITINESKD-DDN-QVEIVSVEHVKLLGMVNEVS 169 (1061)
Q Consensus 92 e~~ll~~L~d~~l~lP~~s~~l~~~~~~~~~~~~v~~lL~k~a~q~lI~i~~~~~-~~~-~~~i~~~~~~kl~~m~~~~~ 169 (1061)
-..+|..|-.-. +.+..+|...+. .+...|-.+|.+|..++||.-+.... +.. ++.+-.++.+++-..+..-.
T Consensus 24 ~~~Vl~~L~~~g---~~tdeeLA~~Lg--i~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~ 98 (178)
T PRK06266 24 GFEVLKALIKKG---EVTDEEIAEQTG--IKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKKK 98 (178)
T ss_pred HhHHHHHHHHcC---CcCHHHHHHHHC--CCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHHH
Confidence 345555554422 456667766664 37799999999999999999877666 444 78888899988876665443
Q ss_pred ----hhhccccCCCCC
Q psy17828 170 ----KGIKRKADTDTS 181 (1061)
Q Consensus 170 ----~~~kr~~~~~~s 181 (1061)
+.+|.+.+.+.+
T Consensus 99 ~~~~~klk~~l~~e~~ 114 (178)
T PRK06266 99 MEELKKLKEQLEEEEN 114 (178)
T ss_pred HHHHHHHHHHhhhccC
Confidence 335666554444
No 125
>PRK14968 putative methyltransferase; Provisional
Probab=23.64 E-value=1.7e+02 Score=29.63 Aligned_cols=78 Identities=21% Similarity=0.179 Sum_probs=43.4
Q ss_pred CCceecccCccCcccCCCccEEEECCCccccc-----------cCCCCCCChHHHhcC---CccccCCCcEEEEecCcc-
Q psy17828 337 PQWIQCDLRYLDMTVLGKFAVIMADPPWDIHM-----------ELPYGTMSDDEMRQL---GIPQLQDEGLLFLWVTGR- 401 (1061)
Q Consensus 337 pq~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~-----------~~~Y~tms~deI~~L---PV~~La~~g~LFLWvT~~- 401 (1061)
..|+.+|+.. ....++||+|+++||+.... ..+.+....+.+..+ =..-|.++|.+++.+...
T Consensus 75 ~~~~~~d~~~--~~~~~~~d~vi~n~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~Lk~gG~~~~~~~~~~ 152 (188)
T PRK14968 75 VEVIRSDLFE--PFRGDKFDVILFNPPYLPTEEEEEWDDWLNYALSGGKDGREVIDRFLDEVGRYLKPGGRILLLQSSLT 152 (188)
T ss_pred eEEEeccccc--cccccCceEEEECCCcCCCCchhhhhhhhhhhhccCcChHHHHHHHHHHHHHhcCCCeEEEEEEcccC
Confidence 4577788754 22223899999999974311 001111111111111 112345688887776543
Q ss_pred chHHHHHHhhcccee
Q psy17828 402 AMELGRECLKLFMLQ 416 (1061)
Q Consensus 402 ~Le~g~elL~~WGf~ 416 (1061)
..+...+.|+.=||+
T Consensus 153 ~~~~l~~~~~~~g~~ 167 (188)
T PRK14968 153 GEDEVLEYLEKLGFE 167 (188)
T ss_pred CHHHHHHHHHHCCCe
Confidence 456677888888998
No 126
>COG1092 Predicted SAM-dependent methyltransferases [General function prediction only]
Probab=23.58 E-value=39 Score=40.25 Aligned_cols=59 Identities=22% Similarity=0.307 Sum_probs=31.6
Q ss_pred CceecccCccC--cccCC-CccEEEECCCccccccCC-CC-CCChHHHhcCCccccCCCcEEEE
Q psy17828 338 QWIQCDLRYLD--MTVLG-KFAVIMADPPWDIHMELP-YG-TMSDDEMRQLGIPQLQDEGLLFL 396 (1061)
Q Consensus 338 q~i~cDlr~~d--~~~lg-kFdvIlaDPPW~~~~~~~-Y~-tms~deI~~LPV~~La~~g~LFL 396 (1061)
.||+.|+-.+= ....| +||||++|||==...... ++ .-..-+|..+-+.-|+++|.++.
T Consensus 271 ~~i~~Dvf~~l~~~~~~g~~fDlIilDPPsF~r~k~~~~~~~rdy~~l~~~~~~iL~pgG~l~~ 334 (393)
T COG1092 271 RFIVGDVFKWLRKAERRGEKFDLIILDPPSFARSKKQEFSAQRDYKDLNDLALRLLAPGGTLVT 334 (393)
T ss_pred eeehhhHHHHHHHHHhcCCcccEEEECCcccccCcccchhHHHHHHHHHHHHHHHcCCCCEEEE
Confidence 59999875421 12235 899999999953322100 00 01112344444555677776654
No 127
>COG0742 N6-adenine-specific methylase [DNA replication, recombination, and repair]
Probab=22.48 E-value=46 Score=35.94 Aligned_cols=28 Identities=18% Similarity=0.411 Sum_probs=17.2
Q ss_pred CceecccCcc--CcccCCCccEEEECCCcc
Q psy17828 338 QWIQCDLRYL--DMTVLGKFAVIMADPPWD 365 (1061)
Q Consensus 338 q~i~cDlr~~--d~~~lgkFdvIlaDPPW~ 365 (1061)
+.+..|...+ .....+.||+|++|||..
T Consensus 96 ~~~~~da~~~L~~~~~~~~FDlVflDPPy~ 125 (187)
T COG0742 96 RVLRNDALRALKQLGTREPFDLVFLDPPYA 125 (187)
T ss_pred EEEeecHHHHHHhcCCCCcccEEEeCCCCc
Confidence 3456665522 111122499999999997
No 128
>PRK03612 spermidine synthase; Provisional
Probab=22.38 E-value=61 Score=39.67 Aligned_cols=77 Identities=22% Similarity=0.066 Sum_probs=46.1
Q ss_pred CceecccCccCcccCCCccEEEECCCccccccCCCCCCChHHHhcCCccccCCCcEEEEecCccch-----HHHHHHhhc
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWDIHMELPYGTMSDDEMRQLGIPQLQDEGLLFLWVTGRAM-----ELGRECLKL 412 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~~~~~~~Y~tms~deI~~LPV~~La~~g~LFLWvT~~~L-----e~g~elL~~ 412 (1061)
+++..|.+.+--...++||+|++|+|-.... ......+ .|+.+.--..|.++|++.++.+++.. ....+.|++
T Consensus 357 ~vi~~Da~~~l~~~~~~fDvIi~D~~~~~~~-~~~~L~t-~ef~~~~~~~L~pgG~lv~~~~~~~~~~~~~~~i~~~l~~ 434 (521)
T PRK03612 357 TVVNDDAFNWLRKLAEKFDVIIVDLPDPSNP-ALGKLYS-VEFYRLLKRRLAPDGLLVVQSTSPYFAPKAFWSIEATLEA 434 (521)
T ss_pred EEEEChHHHHHHhCCCCCCEEEEeCCCCCCc-chhccch-HHHHHHHHHhcCCCeEEEEecCCcccchHHHHHHHHHHHH
Confidence 4678888864223346999999998743211 0111222 33433333567889999998775433 234567777
Q ss_pred ccee
Q psy17828 413 FMLQ 416 (1061)
Q Consensus 413 WGf~ 416 (1061)
=||.
T Consensus 435 ~gf~ 438 (521)
T PRK03612 435 AGLA 438 (521)
T ss_pred cCCE
Confidence 7774
No 129
>PF08781 DP: Transcription factor DP; InterPro: IPR014889 DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer [] and negatively regulates the G1-S transition. ; PDB: 2AZE_A.
Probab=21.86 E-value=1e+02 Score=32.14 Aligned_cols=27 Identities=19% Similarity=0.555 Sum_probs=23.8
Q ss_pred HHHHHHHHhhHHHHHHHHHhhhhhhhh
Q psy17828 6 EEIQAIKSKRNSLREKLQKRKQERKDI 32 (1061)
Q Consensus 6 ~~iqa~k~~~~~lre~l~~r~~~~~~~ 32 (1061)
++|+.+|..+..+|||+++.+.+-|+|
T Consensus 1 q~~~~Le~ek~~~~~rI~~K~~~LqEL 27 (142)
T PF08781_consen 1 QECEELEEEKQRRRERIKKKKEQLQEL 27 (142)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999888874
No 130
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=21.27 E-value=1.9e+02 Score=28.76 Aligned_cols=74 Identities=19% Similarity=0.254 Sum_probs=58.1
Q ss_pred hHHHHHHHHhhccccccccchHHHHhhhhh------hhhHHHHHHHHHHhhccCcEeeecccCCC----CceEEEEeehH
Q psy17828 90 DLELELLEKLCDVSLVLPITSQSLMGTLNQ------EYTHLCLINLLHKFATQKLITINESKDDD----NQVEIVSVEHV 159 (1061)
Q Consensus 90 ~~e~~ll~~L~d~~l~lP~~s~~l~~~~~~------~~~~~~v~~lL~k~a~q~lI~i~~~~~~~----~~~~i~~~~~~ 159 (1061)
.++-.+|..|++ . |+++-+|...+.. ..+.-.|-++|.+|..+|+|+......++ .-|.+|..=..
T Consensus 9 ~l~~~iL~~L~~---~-~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~ 84 (138)
T COG1695 9 SLELLILSLLSE---K-PSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKE 84 (138)
T ss_pred hHHHHHHHHHhc---C-CchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHH
Confidence 567888888887 2 9999999988866 34568999999999999999998666643 37888877777
Q ss_pred hHHhHHHH
Q psy17828 160 KLLGMVNE 167 (1061)
Q Consensus 160 kl~~m~~~ 167 (1061)
.|....++
T Consensus 85 ~l~~~~~~ 92 (138)
T COG1695 85 ELAELREE 92 (138)
T ss_pred HHHHHHHH
Confidence 77765544
No 131
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=20.56 E-value=2.2e+02 Score=29.54 Aligned_cols=76 Identities=17% Similarity=0.057 Sum_probs=56.6
Q ss_pred hhHHHHHHHHhhccccccccchHHHHhhhhh----hhhHHHHHHHHHHhhccCcEeeecccCC-CC---ceEEEEeehHh
Q psy17828 89 PDLELELLEKLCDVSLVLPITSQSLMGTLNQ----EYTHLCLINLLHKFATQKLITINESKDD-DN---QVEIVSVEHVK 160 (1061)
Q Consensus 89 ~~~e~~ll~~L~d~~l~lP~~s~~l~~~~~~----~~~~~~v~~lL~k~a~q~lI~i~~~~~~-~~---~~~i~~~~~~k 160 (1061)
..++-.||..|.+- |+.+-+|...|.. .++.-.|-++|.+|..+|+|.-.....+ .. -|.||..=.+.
T Consensus 23 g~l~~~IL~~L~~~----p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~ 98 (138)
T TIGR02719 23 NFLVPFLLLCLKDW----NLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQY 98 (138)
T ss_pred HHHHHHHHHHHccC----CCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHH
Confidence 35688899999883 8999999888866 4566889999999999999987543332 22 56777777666
Q ss_pred HHhHHHHh
Q psy17828 161 LLGMVNEV 168 (1061)
Q Consensus 161 l~~m~~~~ 168 (1061)
|.++..+.
T Consensus 99 L~~~~~~w 106 (138)
T TIGR02719 99 LSMCANSF 106 (138)
T ss_pred HHHHHHHH
Confidence 66655554
No 132
>PRK14966 unknown domain/N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase fusion protein; Provisional
Probab=20.16 E-value=67 Score=38.73 Aligned_cols=28 Identities=25% Similarity=0.502 Sum_probs=21.4
Q ss_pred CceecccCccCcccCCCccEEEECCCcc
Q psy17828 338 QWIQCDLRYLDMTVLGKFAVIMADPPWD 365 (1061)
Q Consensus 338 q~i~cDlr~~d~~~lgkFdvIlaDPPW~ 365 (1061)
.++++|+...++...++||+|+++||+-
T Consensus 303 ~fi~gDl~e~~l~~~~~FDLIVSNPPYI 330 (423)
T PRK14966 303 EFAHGSWFDTDMPSEGKWDIIVSNPPYI 330 (423)
T ss_pred EEEEcchhccccccCCCccEEEECCCCC
Confidence 5788888665443346899999999973
Done!