Query 020213
Match_columns 329
No_of_seqs 142 out of 1391
Neff 9.0
Searched_HMMs 46136
Date Fri Mar 29 07:56:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020213.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020213hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03196 MOC1-like protein; Pr 100.0 7.7E-60 1.7E-64 450.7 25.2 318 7-327 122-441 (487)
2 PF02536 mTERF: mTERF; InterP 100.0 6.8E-53 1.5E-57 392.1 8.3 306 14-323 2-345 (345)
3 PLN03196 MOC1-like protein; Pr 100.0 1.3E-47 2.9E-52 366.5 22.9 304 8-319 91-405 (487)
4 PF02536 mTERF: mTERF; InterP 100.0 5.7E-38 1.2E-42 291.9 9.2 257 6-270 30-320 (345)
5 KOG1267 Mitochondrial transcri 100.0 2.5E-30 5.5E-35 245.2 14.7 296 3-306 85-410 (413)
6 KOG1267 Mitochondrial transcri 99.9 1.8E-21 4E-26 184.7 11.5 270 19-305 69-340 (413)
7 smart00733 Mterf Mitochondrial 97.1 0.00036 7.8E-09 40.0 1.9 28 245-274 3-30 (31)
8 smart00733 Mterf Mitochondrial 97.0 0.00079 1.7E-08 38.5 2.7 27 101-128 4-30 (31)
9 PF11955 PORR: Plant organelle 95.4 0.037 8E-07 51.0 6.1 94 17-110 45-150 (335)
10 cd04790 HTH_Cfa-like_unk Helix 89.5 2 4.3E-05 35.8 7.7 23 82-104 49-71 (172)
11 cd04790 HTH_Cfa-like_unk Helix 84.4 5.9 0.00013 32.9 7.7 115 118-245 49-167 (172)
12 TIGR01448 recD_rel helicase, p 82.5 3.6 7.9E-05 42.3 6.9 99 5-112 73-186 (720)
13 TIGR00601 rad23 UV excision re 82.2 8.8 0.00019 36.2 8.7 40 10-57 157-196 (378)
14 PF11955 PORR: Plant organelle 74.6 6 0.00013 36.6 5.1 47 96-147 22-68 (335)
15 PRK14135 recX recombination re 74.2 52 0.0011 29.1 11.1 25 189-213 235-259 (263)
16 PF14490 HHH_4: Helix-hairpin- 72.8 22 0.00047 26.2 6.9 27 7-33 6-32 (94)
17 PF04695 Pex14_N: Peroxisomal 70.8 3.5 7.6E-05 32.9 2.4 29 225-253 23-51 (136)
18 PRK14605 ruvA Holliday junctio 70.6 34 0.00075 29.0 8.5 24 81-104 149-172 (194)
19 PF14490 HHH_4: Helix-hairpin- 70.3 12 0.00026 27.6 5.1 26 78-103 6-31 (94)
20 PF00627 UBA: UBA/TS-N domain; 67.7 7.3 0.00016 23.2 2.8 23 227-249 4-26 (37)
21 PRK00116 ruvA Holliday junctio 67.0 18 0.00039 30.6 6.1 25 80-104 149-173 (192)
22 PRK00117 recX recombination re 66.2 65 0.0014 26.0 9.1 136 12-177 17-153 (157)
23 PF04695 Pex14_N: Peroxisomal 65.9 9.8 0.00021 30.3 4.0 36 67-106 14-49 (136)
24 PRK00117 recX recombination re 65.3 48 0.001 26.8 8.1 109 10-140 29-153 (157)
25 smart00165 UBA Ubiquitin assoc 63.0 9.9 0.00022 22.4 2.8 23 227-249 3-25 (37)
26 PF11212 DUF2999: Protein of u 62.6 16 0.00035 25.3 3.9 55 81-143 2-59 (82)
27 PHA01351 putative minor struct 61.1 2E+02 0.0043 29.5 14.1 266 11-280 549-889 (1070)
28 cd00194 UBA Ubiquitin Associat 59.1 13 0.00027 22.0 2.7 23 227-249 3-25 (38)
29 TIGR01448 recD_rel helicase, p 58.9 61 0.0013 33.5 9.2 89 42-140 75-167 (720)
30 cd08316 Death_FAS_TNFRSF6 Deat 57.3 24 0.00053 26.3 4.5 24 11-34 22-45 (97)
31 COG4669 EscJ Type III secretor 55.2 28 0.00062 30.3 5.1 28 78-105 64-91 (246)
32 COG1125 OpuBA ABC-type proline 54.4 15 0.00033 32.7 3.5 86 187-288 71-159 (309)
33 COG1393 ArsC Arsenate reductas 53.9 30 0.00064 26.8 4.7 41 201-246 75-115 (117)
34 PF06896 DUF1268: Protein of u 53.1 19 0.00041 27.7 3.4 50 43-100 54-106 (114)
35 KOG0400 40S ribosomal protein 52.7 28 0.0006 27.3 4.2 36 104-140 22-57 (151)
36 cd08315 Death_TRAILR_DR4_DR5 D 50.6 49 0.0011 24.5 5.3 23 12-34 22-44 (96)
37 PF06089 Asparaginase_II: L-as 50.5 16 0.00034 33.6 3.1 55 3-61 40-99 (324)
38 TIGR00084 ruvA Holliday juncti 50.2 1.3E+02 0.0027 25.5 8.3 23 81-103 148-170 (191)
39 PF02631 RecX: RecX family; I 50.2 37 0.0008 26.1 4.8 24 79-102 44-67 (121)
40 PF07499 RuvA_C: RuvA, C-termi 50.1 21 0.00045 22.6 2.8 25 10-34 4-28 (47)
41 PRK14601 ruvA Holliday junctio 49.1 55 0.0012 27.5 5.9 57 48-104 107-166 (183)
42 COG2137 OraA Uncharacterized p 48.8 1.6E+02 0.0034 24.6 9.8 24 225-248 139-163 (174)
43 PRK09875 putative hydrolase; P 47.2 1.1E+02 0.0025 27.7 8.1 27 116-142 262-288 (292)
44 COG3747 Phage terminase, small 47.1 17 0.00036 29.2 2.3 101 97-206 33-135 (160)
45 PRK14606 ruvA Holliday junctio 46.1 80 0.0017 26.6 6.5 57 48-104 107-167 (188)
46 PF11212 DUF2999: Protein of u 45.1 1E+02 0.0023 21.4 7.0 20 12-31 4-23 (82)
47 PRK14135 recX recombination re 43.9 2.2E+02 0.0047 25.2 9.4 109 19-140 40-149 (263)
48 smart00657 RPOL4c DNA-directed 43.8 20 0.00044 27.7 2.4 59 38-102 51-109 (118)
49 TIGR01616 nitro_assoc nitrogen 43.2 49 0.0011 25.9 4.5 48 200-252 72-119 (126)
50 cd08306 Death_FADD Fas-associa 43.1 66 0.0014 23.2 4.9 41 10-53 14-54 (86)
51 KOG0400 40S ribosomal protein 42.8 17 0.00038 28.4 1.8 32 34-65 23-54 (151)
52 PHA01351 putative minor struct 42.3 2.9E+02 0.0063 28.3 10.3 47 8-56 690-736 (1070)
53 cd08319 Death_RAIDD Death doma 40.7 1E+02 0.0022 22.2 5.5 23 12-34 16-38 (83)
54 cd08784 Death_DRs Death Domain 39.2 92 0.002 22.0 5.0 40 11-54 13-52 (79)
55 PF08069 Ribosomal_S13_N: Ribo 38.8 8.5 0.00018 25.9 -0.4 29 37-65 26-54 (60)
56 PF02022 Integrase_Zn: Integra 38.2 45 0.00097 20.4 2.8 25 228-252 11-36 (40)
57 cd08313 Death_TNFR1 Death doma 36.3 1.3E+02 0.0027 21.6 5.3 25 10-34 12-36 (80)
58 cd08804 Death_ank2 Death domai 36.1 1.3E+02 0.0029 21.5 5.5 22 13-34 19-40 (84)
59 cd03032 ArsC_Spx Arsenate Redu 36.0 1E+02 0.0022 23.4 5.2 40 201-245 74-113 (115)
60 PF06972 DUF1296: Protein of u 35.2 44 0.00095 22.4 2.5 26 153-178 22-47 (60)
61 PRK14136 recX recombination re 35.0 1.6E+02 0.0034 27.0 6.8 27 116-142 278-304 (309)
62 COG1125 OpuBA ABC-type proline 34.1 44 0.00096 29.9 3.1 154 145-326 67-236 (309)
63 COG3620 Predicted transcriptio 34.1 90 0.002 25.7 4.7 49 115-165 49-97 (187)
64 PRK01655 spxA transcriptional 33.4 1.4E+02 0.0031 23.3 5.8 41 201-246 74-114 (131)
65 PF00356 LacI: Bacterial regul 33.2 80 0.0017 19.9 3.5 42 14-58 4-45 (46)
66 PHA02591 hypothetical protein; 33.1 46 0.00099 23.6 2.5 28 3-30 42-69 (83)
67 PF03960 ArsC: ArsC family; I 32.7 79 0.0017 23.8 4.1 23 235-257 69-91 (110)
68 PF03960 ArsC: ArsC family; I 32.2 40 0.00086 25.4 2.4 22 127-148 70-91 (110)
69 COG3620 Predicted transcriptio 31.7 64 0.0014 26.5 3.5 23 8-30 6-28 (187)
70 PF02787 CPSase_L_D3: Carbamoy 31.2 26 0.00056 27.4 1.2 63 19-103 22-84 (123)
71 PRK14136 recX recombination re 30.8 4.2E+02 0.0092 24.3 9.9 136 12-180 168-305 (309)
72 cd08805 Death_ank1 Death domai 30.5 1.8E+02 0.004 20.9 5.4 22 13-34 19-40 (84)
73 cd08803 Death_ank3 Death domai 30.3 1.9E+02 0.004 20.9 5.4 40 12-54 18-57 (84)
74 PRK14604 ruvA Holliday junctio 30.2 1.5E+02 0.0033 25.1 5.8 19 119-137 152-170 (195)
75 PF03874 RNA_pol_Rpb4: RNA pol 29.9 28 0.0006 26.6 1.1 31 40-70 55-85 (117)
76 COG2137 OraA Uncharacterized p 29.9 3.3E+02 0.0071 22.7 8.8 83 13-103 27-110 (174)
77 PRK13344 spxA transcriptional 29.5 1.6E+02 0.0034 23.2 5.4 41 201-246 74-114 (132)
78 TIGR01083 nth endonuclease III 29.1 1.5E+02 0.0031 24.9 5.5 10 49-58 71-80 (191)
79 PRK00116 ruvA Holliday junctio 28.8 1.6E+02 0.0034 24.9 5.6 41 152-194 149-189 (192)
80 KOG2561 Adaptor protein NUB1, 28.4 1.7E+02 0.0037 28.3 6.1 140 81-249 304-453 (568)
81 PF13720 Acetyltransf_11: Udp 28.4 75 0.0016 22.8 3.1 18 16-33 23-40 (83)
82 PF12244 DUF3606: Protein of u 27.9 73 0.0016 21.1 2.7 28 7-34 18-45 (57)
83 PRK08561 rps15p 30S ribosomal 27.9 1E+02 0.0022 25.0 3.9 35 68-103 22-56 (151)
84 COG0177 Nth Predicted EndoIII- 27.9 2.4E+02 0.0051 24.3 6.5 54 48-102 73-127 (211)
85 COG4669 EscJ Type III secretor 27.7 1.6E+02 0.0034 25.9 5.4 96 7-112 31-129 (246)
86 cd01392 HTH_LacI Helix-turn-he 27.5 1.3E+02 0.0029 18.7 4.0 42 17-61 5-46 (52)
87 cd00166 SAM Sterile alpha moti 27.4 1.5E+02 0.0033 19.0 4.4 24 8-33 3-26 (63)
88 PF09278 MerR-DNA-bind: MerR, 26.5 64 0.0014 21.5 2.4 18 229-246 7-24 (65)
89 PF05119 Terminase_4: Phage te 26.4 86 0.0019 22.9 3.3 56 43-100 35-90 (100)
90 TIGR01558 sm_term_P27 phage te 25.6 1E+02 0.0022 23.6 3.6 55 44-100 45-99 (116)
91 PF10952 DUF2753: Protein of u 25.5 62 0.0013 25.4 2.3 21 122-142 95-115 (140)
92 PRK14134 recX recombination re 25.4 3.8E+02 0.0082 24.2 7.8 93 11-103 80-205 (283)
93 PF08004 DUF1699: Protein of u 25.3 3.4E+02 0.0073 21.3 6.4 78 93-176 29-116 (131)
94 cd04788 HTH_NolA-AlbR Helix-Tu 25.2 1.4E+02 0.0031 21.8 4.3 23 228-250 49-71 (96)
95 PF08671 SinI: Anti-repressor 25.1 58 0.0013 18.6 1.6 9 126-134 15-23 (30)
96 cd08318 Death_NMPP84 Death dom 25.1 2.4E+02 0.0051 20.3 5.3 17 53-69 27-43 (86)
97 PF09288 UBA_3: Fungal ubiquit 25.0 83 0.0018 20.8 2.5 21 228-248 12-32 (55)
98 PF10366 Vps39_1: Vacuolar sor 24.6 2.8E+02 0.0062 20.9 5.9 26 8-33 13-39 (108)
99 PRK10026 arsenate reductase; P 24.6 2E+02 0.0043 23.0 5.2 42 200-246 75-116 (141)
100 cd08777 Death_RIP1 Death Domai 24.5 2.5E+02 0.0054 20.2 5.3 53 10-65 14-68 (86)
101 smart00354 HTH_LACI helix_turn 24.4 2.2E+02 0.0048 19.3 4.9 46 15-63 6-51 (70)
102 PF10440 WIYLD: Ubiquitin-bind 24.2 76 0.0016 21.8 2.3 27 6-32 8-34 (65)
103 COG5457 Uncharacterized conser 23.7 87 0.0019 21.3 2.5 19 14-32 41-59 (63)
104 PF13331 DUF4093: Domain of un 23.5 73 0.0016 23.2 2.3 25 6-30 62-86 (87)
105 PTZ00072 40S ribosomal protein 23.2 1.4E+02 0.003 24.0 3.9 34 68-102 19-52 (148)
106 cd08317 Death_ank Death domain 23.1 2.8E+02 0.0061 19.6 5.5 23 12-34 18-40 (84)
107 cd04768 HTH_BmrR-like Helix-Tu 22.9 1.5E+02 0.0032 21.7 4.0 22 228-249 49-70 (96)
108 PTZ00072 40S ribosomal protein 22.0 3E+02 0.0065 22.2 5.5 61 103-165 18-78 (148)
109 TIGR00601 rad23 UV excision re 21.8 1.2E+02 0.0026 28.7 3.9 31 217-249 331-361 (378)
110 PRK08561 rps15p 30S ribosomal 21.5 2.8E+02 0.0061 22.5 5.4 36 33-68 22-57 (151)
111 cd01670 Death Death Domain: a 20.6 2.9E+02 0.0063 18.8 5.2 25 11-35 12-36 (79)
112 PF06757 Ins_allergen_rp: Inse 20.2 5E+02 0.011 21.4 9.8 63 22-99 16-78 (179)
113 PRK10702 endonuclease III; Pro 20.1 2.3E+02 0.005 24.3 5.1 19 83-101 107-126 (211)
114 KOG0062 ATPase component of AB 20.0 4.5E+02 0.0098 26.1 7.4 106 89-198 114-239 (582)
No 1
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=7.7e-60 Score=450.67 Aligned_cols=318 Identities=23% Similarity=0.501 Sum_probs=297.8
Q ss_pred CCcchHHHHHHhCCCChhHHHHHHHhhhcccCCcch-hhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHH
Q 020213 7 QNGNSVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKD-RAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVE 85 (329)
Q Consensus 7 ~~~~~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~-~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~ 85 (329)
.|...+++||.++|++.+++.+++.++|.+|..+++ ++.++++||+++|++++++.+++.++|++|.+++++++.++++
T Consensus 122 ~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~ 201 (487)
T PLN03196 122 KNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVA 201 (487)
T ss_pred hhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHH
Confidence 466779999999999999999999999999988876 7999999999999999999999999999999999888999999
Q ss_pred HHHHCCCChhhHHHHHHhCCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhCCceeccCcchhHhHHHHHHhhcCCC
Q 020213 86 CLATLGTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLA 165 (329)
Q Consensus 86 ~L~~lG~~~~~~~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~~ 165 (329)
||+++|++.+++++++.++|.+|+++++++++|+++||.++|++.+++++++.++|+++++++++++++++++|.++|++
T Consensus 202 fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~ 281 (487)
T PLN03196 202 YLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLPRLAVARILEKRPYILGFDLEETVKPNVECLLEFGVR 281 (487)
T ss_pred HHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999887899999999999997
Q ss_pred chhhHHHHHHhcCcccccccccchhHHHHHHHH-hCCChhhHHHHHhhcCceeeeccccccchhHHHHHHhCCChhHHHH
Q 020213 166 REGMIGKVLVKHPFIMGYSVDNRLRPTSEFLKS-VGLKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAA 244 (329)
Q Consensus 166 ~~~~i~~ll~~~p~ll~~~~~~~l~~~~~~l~~-~g~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~~~G~s~~~v~~ 244 (329)
+ +++..++.++|.+++++.++.+.++++++.. +|++++++..++.++|.+++.|.++ +++|++||.++|++.+++..
T Consensus 282 ~-~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~lSe~k-l~~kvefL~~~Gls~edI~~ 359 (487)
T PLN03196 282 K-EALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVSLNRNV-ALKHVEFLRGRGFSAQDVAK 359 (487)
T ss_pred H-HHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhcccHHH-HHHHHHHHHHcCCCHHHHHH
Confidence 5 5899999999999999888889999999976 9999999999999999999998765 99999999999999999999
Q ss_pred HHHhCchhhcccccchhhhHHHHHHHHhCCChhhhhcCCceeecCcchhhHHHHHHHHHcCCCCChhhhhcccHHHHHHh
Q 020213 245 LVAAYPPILIKSIKNSLEPRIKFLVEVMGRQIDEVADYPDFFRHGLKKRLELRHRLLKQRNIYCSLSEMLDCNAKKFLIK 324 (329)
Q Consensus 245 l~~~~P~iL~~s~~~~i~~k~~fL~~~~g~~~~~i~~~P~~l~~sl~~~i~~R~~~l~~~gl~~~l~~~l~~s~~~F~~~ 324 (329)
|+.++|++|++|. ++|++|++||+++||++.++|+++|.+|+||+|+||+|||++|+++|+++++.+++++||++|+++
T Consensus 360 mv~k~P~lL~~S~-~~l~~k~dFlvneMg~~~~~Iv~fP~~LsySLEkRI~PR~~~L~~kGl~~sL~~~L~~sd~~F~~r 438 (487)
T PLN03196 360 MVVRCPQILALNL-EIMKPSLEFFKKEMKRPLKELVEFPAYFTYGLESRIKPRYERVAKKGIKCSLAWFLNCSDDKFEQR 438 (487)
T ss_pred HHHhCCceeeccH-HHHHHHHHHHHHHhCCCHHHHHhChHHhccChhhhhHHHHHHHHHcCCCCCHHHHhccCHHHHHHH
Confidence 9999999999994 899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcc
Q 020213 325 FGL 327 (329)
Q Consensus 325 ~~~ 327 (329)
|+.
T Consensus 439 ~v~ 441 (487)
T PLN03196 439 MSG 441 (487)
T ss_pred Hhh
Confidence 974
No 2
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=6.8e-53 Score=392.13 Aligned_cols=306 Identities=34% Similarity=0.653 Sum_probs=259.0
Q ss_pred HHHHhCCCChhHHHHHHHhhhcccCCcch-hhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHHHHHHCCC
Q 020213 14 WFLKDRGFNDRTIHDMFKRCKRLQGVEKD-RAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVECLATLGT 92 (329)
Q Consensus 14 ~~L~~~G~s~~~i~~i~~~~p~ll~~~~~-~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~lG~ 92 (329)
++|+++||++++|.++++++|.++..+++ .+.++++||.+.|++..++.+++.++|++|..+.++++.|.++||+++|+
T Consensus 2 ~~~~~~gf~~~~i~~~i~~~P~~l~~~~~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~ 81 (345)
T PF02536_consen 2 DLLKNHGFSDSQISKLIRRYPRLLLCDPEKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGL 81 (345)
T ss_dssp HHHHHHHHHTS-HHHHHH-H-HHHHT-SS-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS
T ss_pred hHHHHcCCCHHHHHHHHHhCCceEEecCccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcC
Confidence 68999999999999999999999888766 79999999999999999999999999999999988999999999999999
Q ss_pred ChhhHHHHHHhCCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhCCceeccCcchhHhHHHHHHhhcCCCchhhHHH
Q 020213 93 KPYEVASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLAREGMIGK 172 (329)
Q Consensus 93 ~~~~~~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~~~~~~i~~ 172 (329)
+++++.+++.++|.+++.+.++++.+++++|+++|++++.+.+++...|.++... +++.+.++++.++|+++ +++.+
T Consensus 82 s~~d~~~~l~r~p~~l~~~~~~~l~~~v~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~-~~~~~ 158 (345)
T PF02536_consen 82 SDEDIVKVLKRYPRILSFSVEENLSPNVAFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDP-EKIGR 158 (345)
T ss_dssp -HHHHHHHHHH-SHHHHS---HHHHHHHHHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSH-HHHCC
T ss_pred CHHHHHHHHHhcchhhccchHhhhhhhhhHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCc-hhhcc
Confidence 9999999999999999988877899999999999999988889999999876665 57999999999999985 69999
Q ss_pred HHHhcCcccccccccchhHHHHHHHHhCCChhhHHHHHhhcCceeeecccc-----------------------------
Q 020213 173 VLVKHPFIMGYSVDNRLRPTSEFLKSVGLKELDLQVVAVKFPEVLCRDVNK----------------------------- 223 (329)
Q Consensus 173 ll~~~p~ll~~~~~~~l~~~~~~l~~~g~~~~~i~~~i~~~P~il~~s~~~----------------------------- 223 (329)
++..+|.++....++.+++++++|+++|++.+++.+++.++|.++..+.++
T Consensus 159 vi~~~P~~l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~ 238 (345)
T PF02536_consen 159 VIAKNPRLLLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSL 238 (345)
T ss_dssp CHHHHHHHHCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------TH
T ss_pred cccccchhhccccHHHHHHHHHHHHhhcccchhhhHHhhcccceeccccccccccccccccccccccccccccccccccc
Confidence 999999877777678999999999999999999999999999999998875
Q ss_pred ---ccchhHHHHHHhCCChhHHHHHHHhCchhhcccccchhhhHHHHHHHHhCCChhhhhcCCceeecCcchhhHHH---
Q 020213 224 ---ILSPNFTFLKRCGFADGQIAALVAAYPPILIKSIKNSLEPRIKFLVEVMGRQIDEVADYPDFFRHGLKKRLELR--- 297 (329)
Q Consensus 224 ---~l~~k~~~L~~~G~s~~~v~~l~~~~P~iL~~s~~~~i~~k~~fL~~~~g~~~~~i~~~P~~l~~sl~~~i~~R--- 297 (329)
.+.++++||+++|++.+++.+|+.++|++|++|. +++++|++||.++||++.++|+++|.+|+||+|+||+||
T Consensus 239 ~~~~l~~~i~~L~~lG~s~~ei~~mv~~~P~iL~~s~-e~l~~k~~fl~~~m~~~~~~i~~~P~~l~~sLe~ri~PR~~~ 317 (345)
T PF02536_consen 239 SEEKLKPKIEFLQSLGFSEEEIAKMVRRFPQILSYSI-EKLKPKFEFLVKEMGLPLEEIVEFPQYLSYSLEKRIKPRYEV 317 (345)
T ss_dssp HHHHHHHHHHHHHTTT--HHHHHHHHHHSGGGGGS-H-HHHHHHHHHHHHCCT--HHHHHHSCHHHCS-HHHHHHHHHHH
T ss_pred chHhHHHHHHHHHHhcCcHHHHHHHHHhCcchhhcch-hhhhHHHHHHHHHhCcCHHHHhhCCceeEechhhhhhhHHHH
Confidence 4788999999999999999999999999999995 679999999999999999999999999999999999999
Q ss_pred HHHHHHcC--CCCChhhhhcccHHHHHH
Q 020213 298 HRLLKQRN--IYCSLSEMLDCNAKKFLI 323 (329)
Q Consensus 298 ~~~l~~~g--l~~~l~~~l~~s~~~F~~ 323 (329)
+++|+++| .++++.+++++||++|++
T Consensus 318 ~~~l~~~g~~~~~sl~~~l~~s~~~F~~ 345 (345)
T PF02536_consen 318 LKVLKSKGLIINPSLSSMLSCSDEEFLK 345 (345)
T ss_dssp HHTT--TTTGGGGGS-HHHHHHHHHHT-
T ss_pred HHHHHHCcCCCCCCHHHHhhccHHHhcC
Confidence 56777899 689999999999999975
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=100.00 E-value=1.3e-47 Score=366.52 Aligned_cols=304 Identities=20% Similarity=0.426 Sum_probs=282.4
Q ss_pred CcchHHHHHHhCCCChhHHHHHHHhhhcccCCcch-hhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHHH
Q 020213 8 NGNSVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKD-RAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVEC 86 (329)
Q Consensus 8 ~~~~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~-~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~ 86 (329)
+-...++||+++|++.++|. ++|.++..+++ ++.++++||.++|+++.++.+++.++|.+|..++++++.|+++|
T Consensus 91 ~~~~~l~~L~s~G~~~~~i~----~~P~iL~~~v~~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~f 166 (487)
T PLN03196 91 VMRERVEFLHKLGLTIEDIN----EYPLVLGCSVKKNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKY 166 (487)
T ss_pred HHHHHHHHHHHcCCChHHhc----cCcHHhhcCHhhhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHH
Confidence 34567899999999999996 69999999875 79999999999999999999999999999999999999999999
Q ss_pred HHHCCCChhhHHHHHHhCCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhCCceeccCcchhHhHHHHHHhhcCCCc
Q 020213 87 LATLGTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLAR 166 (329)
Q Consensus 87 L~~lG~~~~~~~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~~~ 166 (329)
|+++|++++++.+++.++|.+|++++++++.++++||.++|++++++++++.++|.++.+++++++.++++||.++|++
T Consensus 167 L~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~lGv~- 245 (487)
T PLN03196 167 LQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVAYLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLESLGLP- 245 (487)
T ss_pred HHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHHcCCC-
Confidence 9999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred hhhHHHHHHhcCcccccccccchhHHHHHHHHhCCChhhHHHHHhhcCceeeeccccccchhHHHHH-HhCCChhHHHHH
Q 020213 167 EGMIGKVLVKHPFIMGYSVDNRLRPTSEFLKSVGLKELDLQVVAVKFPEVLCRDVNKILSPNFTFLK-RCGFADGQIAAL 245 (329)
Q Consensus 167 ~~~i~~ll~~~p~ll~~~~~~~l~~~~~~l~~~g~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~-~~G~s~~~v~~l 245 (329)
.+++++++.++|++|+++++++++++++++.++|++++++..++.++|.+++.+.++.+.++++||. ++|++.+++..+
T Consensus 246 ~~~I~~il~~~P~iL~~sle~~lkp~v~~L~elGv~~~~i~~lI~~~P~iL~~s~e~kl~~~~~fL~~~lG~s~e~i~~~ 325 (487)
T PLN03196 246 RLAVARILEKRPYILGFDLEETVKPNVECLLEFGVRKEALPSVIAQYPDILGLDLKAKLAEQQYWLTSKLKIDPEDFGRV 325 (487)
T ss_pred HHHHHHHHHhCCceeEcCHHHhHHHHHHHHHHcCCCHHHHHHHHHhCCceeEecHHHhhhHHHHHHHHhhCCCHHHHHHH
Confidence 4699999999999999999889999999999999999999999999999999998888999999997 999999999999
Q ss_pred HHhCchhhcccccchhhhHHHHHHHHhCCChhhh----hcCCceeecCcchhhHHHHHHHH-HcCCC----CChhhhhcc
Q 020213 246 VAAYPPILIKSIKNSLEPRIKFLVEVMGRQIDEV----ADYPDFFRHGLKKRLELRHRLLK-QRNIY----CSLSEMLDC 316 (329)
Q Consensus 246 ~~~~P~iL~~s~~~~i~~k~~fL~~~~g~~~~~i----~~~P~~l~~sl~~~i~~R~~~l~-~~gl~----~~l~~~l~~ 316 (329)
+.++|++++.| ++++++|++||.+ +|++.++| .++|.+|++|. ++++++++||. ++|.. .....++.+
T Consensus 326 v~k~P~il~lS-e~kl~~kvefL~~-~Gls~edI~~mv~k~P~lL~~S~-~~l~~k~dFlvneMg~~~~~Iv~fP~~Lsy 402 (487)
T PLN03196 326 IEKLPQIVSLN-RNVALKHVEFLRG-RGFSAQDVAKMVVRCPQILALNL-EIMKPSLEFFKKEMKRPLKELVEFPAYFTY 402 (487)
T ss_pred HHhcchhhccc-HHHHHHHHHHHHH-cCCCHHHHHHHHHhCCceeeccH-HHHHHHHHHHHHHhCCCHHHHHhChHHhcc
Confidence 99999999999 7899999999996 99999997 68999999998 58999999998 46752 233445666
Q ss_pred cHH
Q 020213 317 NAK 319 (329)
Q Consensus 317 s~~ 319 (329)
|-|
T Consensus 403 SLE 405 (487)
T PLN03196 403 GLE 405 (487)
T ss_pred Chh
Confidence 643
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=100.00 E-value=5.7e-38 Score=291.91 Aligned_cols=257 Identities=31% Similarity=0.584 Sum_probs=217.5
Q ss_pred cCCcchHHHHHHhCCCChhHHHHHHHhhhcccCCc-chhhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHH
Q 020213 6 SQNGNSVIWFLKDRGFNDRTIHDMFKRCKRLQGVE-KDRAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMV 84 (329)
Q Consensus 6 ~~~~~~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~-~~~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l 84 (329)
..+....++||.+.|++.+++.+++.++|.++..+ .+++.+.+++|+++|.+++++.+++.++|++|..+.+.++.+.+
T Consensus 30 ~~~l~pk~~fl~s~G~s~~~i~~il~~~P~il~~s~~~~i~p~~~~L~~~~~s~~d~~~~l~r~p~~l~~~~~~~l~~~v 109 (345)
T PF02536_consen 30 EKTLLPKLEFLRSLGFSSSDIAKILSKNPQILSRSLEKNIIPVFDFLKSIGLSDEDIVKVLKRYPRILSFSVEENLSPNV 109 (345)
T ss_dssp S-HHHHHHHHHHHTT--HHHHHHHHHH-GGGGGS--HHHHHHHHHHHTTTSS-HHHHHHHHHH-SHHHHS---HHHHHHH
T ss_pred ccchhHHHHHHHHCCCCHHHHHHHHHhChHHHhccchhhHHHHHHHHHHHcCCHHHHHHHHHhcchhhccchHhhhhhhh
Confidence 44556789999999999999999999999999999 67899999999999999999999999999999988777899999
Q ss_pred HHHHHCCCChhhHHHHHHhCCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhCCceeccCcchhHhHHHHHHhhcCC
Q 020213 85 ECLATLGTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGL 164 (329)
Q Consensus 85 ~~L~~lG~~~~~~~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~ 164 (329)
++|+++|++.+.+.+.+...|.++... +.+++.++++.++|++++++++++..+|.++..+.+++++++++||+++|+
T Consensus 110 ~~L~~lGv~~~~~~~~l~~~~~~~~~~--~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~v~~L~~~G~ 187 (345)
T PF02536_consen 110 AFLRSLGVPPSQIISLLISRPPLFLSS--EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPKVEFLRSLGF 187 (345)
T ss_dssp HHHHHTT--HHHHHHHHHH-CHHHHS---HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHHHHHHHHCTT
T ss_pred hHHhhcCCcHHHHHHHHHhcCccccch--hHHHHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHHHHHHHhhcc
Confidence 999999999998889898888866655 479999999999999999999999999987777777899999999999999
Q ss_pred CchhhHHHHHHhcCccccccccc--------------------------------chhHHHHHHHHhCCChhhHHHHHhh
Q 020213 165 AREGMIGKVLVKHPFIMGYSVDN--------------------------------RLRPTSEFLKSVGLKELDLQVVAVK 212 (329)
Q Consensus 165 ~~~~~i~~ll~~~p~ll~~~~~~--------------------------------~l~~~~~~l~~~g~~~~~i~~~i~~ 212 (329)
+ ++++.+++.++|.++.++.++ .+.+++++|.++|++.+++.+|+.+
T Consensus 188 ~-~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~ 266 (345)
T PF02536_consen 188 S-KEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSLGFSEEEIAKMVRR 266 (345)
T ss_dssp --GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTTT--HHHHHHHHHH
T ss_pred c-chhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHhcCcHHHHHHHHHh
Confidence 8 579999999999999998764 5889999999999999999999999
Q ss_pred cCceeeeccccccchhHHHHH-HhCCChhHHHHHHHhCchhhcccccchhhhHHHHHHH
Q 020213 213 FPEVLCRDVNKILSPNFTFLK-RCGFADGQIAALVAAYPPILIKSIKNSLEPRIKFLVE 270 (329)
Q Consensus 213 ~P~il~~s~~~~l~~k~~~L~-~~G~s~~~v~~l~~~~P~iL~~s~~~~i~~k~~fL~~ 270 (329)
+|.+|+++.++ +++|++||. ++|++.+++. ++|++|++|+|++|+||++++..
T Consensus 267 ~P~iL~~s~e~-l~~k~~fl~~~m~~~~~~i~----~~P~~l~~sLe~ri~PR~~~~~~ 320 (345)
T PF02536_consen 267 FPQILSYSIEK-LKPKFEFLVKEMGLPLEEIV----EFPQYLSYSLEKRIKPRYEVLKV 320 (345)
T ss_dssp SGGGGGS-HHH-HHHHHHHHHHCCT--HHHHH----HSCHHHCS-HHHHHHHHHHHHHT
T ss_pred Ccchhhcchhh-hhHHHHHHHHHhCcCHHHHh----hCCceeEechhhhhhhHHHHHHH
Confidence 99999999997 999999998 8999999976 99999999999999999665554
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.97 E-value=2.5e-30 Score=245.22 Aligned_cols=296 Identities=28% Similarity=0.459 Sum_probs=261.8
Q ss_pred ccccCCcchHHHHHHhCCCChhHHHHHHHhhhcccCCcch-hhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchH
Q 020213 3 ISTSQNGNSVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKD-RAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLV 81 (329)
Q Consensus 3 ~~~~~~~~~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~-~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~ 81 (329)
.....||+++.++|+++|++..++.+++..+|.++..+.+ .+.++..+|.+.|++.+.+.+++...|.+|......++.
T Consensus 85 ~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~~i~s~~~~il~~~~~~~~~ 164 (413)
T KOG1267|consen 85 SEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELSSIVSVVPKILLKSKGESLS 164 (413)
T ss_pred hhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccchhhhccHHHHHhhcCCchh
Confidence 3567899999999999999999999999999999888766 577777788999999999999999999999887778999
Q ss_pred HHHHHHHHCC--CChhhHHHHHHhCCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhCCceeccCcchhHhHHHHHH
Q 020213 82 PMVECLATLG--TKPYEVASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVDFL 159 (329)
Q Consensus 82 ~~l~~L~~lG--~~~~~~~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l 159 (329)
+.++|+++++ .....+.+.....|..... +..+. ++++++++|..++++..++..+|....... .+...+.++
T Consensus 165 ~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~--~~~v~-~~~~~~~lg~~~~~L~~~l~~~~~~~~~~~--~l~~~~~~i 239 (413)
T KOG1267|consen 165 TFIEFLKSIPPELLSSVVERLLTPVPSFLLN--ENSVE-RLDIRRELGVKPRLLKSLLESQPRPVLLYL--KLKARLPFL 239 (413)
T ss_pred hHHHHhhccchhhhhhHHHHhcccccccccc--ccccc-cchhhHHhCCCHHHHHHHHhcCccceeeeh--hhhhhhhhH
Confidence 9999999985 7777777777666643222 22344 789999999999999999999999877653 688899999
Q ss_pred hhcCCCchhhHHHHHHhcCcccccccccchhHHHHHHHHhCCChhhHHHHHhhcCceeeecccc----------------
Q 020213 160 TSLGLAREGMIGKVLVKHPFIMGYSVDNRLRPTSEFLKSVGLKELDLQVVAVKFPEVLCRDVNK---------------- 223 (329)
Q Consensus 160 ~~~G~~~~~~i~~ll~~~p~ll~~~~~~~l~~~~~~l~~~g~~~~~i~~~i~~~P~il~~s~~~---------------- 223 (329)
.++|++|. . +++...|.++.++.++++++++++|+++|++.++++.|+.++|.+|+++.++
T Consensus 240 ~~~g~~p~-~--~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~~~~~~ 316 (413)
T KOG1267|consen 240 LTLGFDPK-T--REFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKNPKHIL 316 (413)
T ss_pred HHhccCCc-h--hHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhcchhhh
Confidence 99999874 3 7788889999988889999999999999999999999999999999999874
Q ss_pred -----------ccchhHHHHHHhCCChhHHHHHHHhCchhhcccccchhhhHHHHHHHHhCCChhhhhcCCceeecCcch
Q 020213 224 -----------ILSPNFTFLKRCGFADGQIAALVAAYPPILIKSIKNSLEPRIKFLVEVMGRQIDEVADYPDFFRHGLKK 292 (329)
Q Consensus 224 -----------~l~~k~~~L~~~G~s~~~v~~l~~~~P~iL~~s~~~~i~~k~~fL~~~~g~~~~~i~~~P~~l~~sl~~ 292 (329)
.+.++++|+..+|++..++..+++++|+++.+|+++.++.+.+|+.+.|+++.+.++.+|.++.|++++
T Consensus 317 k~p~~l~~s~~~l~~~ie~l~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p~~~~~~~p~~~~y~le~ 396 (413)
T KOG1267|consen 317 KFPQLLRSSEDKLKPRIEFLLSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRPLSALVSFPAFFGYSLEK 396 (413)
T ss_pred hhhhhhhccchhhhhhHHHHHHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCchHHHHhccchhhccchhh
Confidence 288999999999999999999999999999999755999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHcCC
Q 020213 293 RLELRHRLLKQRNI 306 (329)
Q Consensus 293 ~i~~R~~~l~~~gl 306 (329)
|+.||++..+.+|.
T Consensus 397 ri~pr~~~~~~~~~ 410 (413)
T KOG1267|consen 397 RIRPRFNVIKKLGV 410 (413)
T ss_pred cchhHHHHHHHHhc
Confidence 99999999887764
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.86 E-value=1.8e-21 Score=184.72 Aligned_cols=270 Identities=21% Similarity=0.359 Sum_probs=211.5
Q ss_pred CCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHHHHHHCCCChhhHH
Q 020213 19 RGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVECLATLGTKPYEVA 98 (329)
Q Consensus 19 ~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~lG~~~~~~~ 98 (329)
.|.+...+..+.. .+...+..+....+++|+++|+++.++..++..+|.++..+.++.+.+...+|++.|++..++.
T Consensus 69 ~~~~~~~~~~~~~---~~~~~~~~~p~s~~~~l~s~g~~~~~i~s~i~~~p~ll~~~~~~~l~~~~~~l~~~g~~~s~l~ 145 (413)
T KOG1267|consen 69 LGLSIKLARKLSR---EVSSEDSVNPSSVLSSLRSLGFTDSQISSIILSSPKLLYLSSENILKPKLRLLDSLGLPSSELS 145 (413)
T ss_pred cccchhhHHHHHH---HHHhhhccCcHHHHHHHHhcCCchhhcccccccCchhhhccchhhhhhhhhhhhccCccccccc
Confidence 5555555554443 2234445677888999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhCCCcccccchhhHhHHHHHHHHCC--CCchhhhhhHhhCCceeccCcchhHhHHHHHHhhcCCCchhhHHHHHHh
Q 020213 99 SAITRFPPILSHSVEEKLCPLLAFFQALG--VPEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLAREGMIGKVLVK 176 (329)
Q Consensus 99 ~~l~~~P~ll~~~~e~~l~~~v~~L~~lG--~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~~~~~~i~~ll~~ 176 (329)
+++...|.+++.+...++.+.++|++.++ .....+.+++...|...... ..+. .++++.++|.. ...+..++.+
T Consensus 146 ~i~s~~~~il~~~~~~~~~~~~~~l~~~~~~~~~s~~~~~~~~~~~~~~~~--~~v~-~~~~~~~lg~~-~~~L~~~l~~ 221 (413)
T KOG1267|consen 146 SIVSVVPKILLKSKGESLSTFIEFLKSIPPELLSSVVERLLTPVPSFLLNE--NSVE-RLDIRRELGVK-PRLLKSLLES 221 (413)
T ss_pred hhhhccHHHHHhhcCCchhhHHHHhhccchhhhhhHHHHhccccccccccc--cccc-cchhhHHhCCC-HHHHHHHHhc
Confidence 99999999988777778999999999985 77777787777777443221 2344 89999999996 5688999999
Q ss_pred cCcccccccccchhHHHHHHHHhCCChhhHHHHHhhcCceeeeccccccchhHHHHHHhCCChhHHHHHHHhCchhhccc
Q 020213 177 HPFIMGYSVDNRLRPTSEFLKSVGLKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAALVAAYPPILIKS 256 (329)
Q Consensus 177 ~p~ll~~~~~~~l~~~~~~l~~~g~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~~~G~s~~~v~~l~~~~P~iL~~s 256 (329)
+|..+.... .+...+.++..+|+++.. .++.+.|.+++++.++.+++|+++|+++||+.+|+++|+.++|++|++|
T Consensus 222 ~~~~~~~~~--~l~~~~~~i~~~g~~p~~--~~~v~~~~~~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s 297 (413)
T KOG1267|consen 222 QPRPVLLYL--KLKARLPFLLTLGFDPKT--REFVKAPILLSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYS 297 (413)
T ss_pred Cccceeeeh--hhhhhhhhHHHhccCCch--hHHHhhhhhhcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEee
Confidence 999888652 688889999999988888 7778889999999999999999999999999999999999999999999
Q ss_pred ccchhhhHHHHHHHHhCCChhhhhcCCceeecCcchhhHHHHHHHHHcC
Q 020213 257 IKNSLEPRIKFLVEVMGRQIDEVADYPDFFRHGLKKRLELRHRLLKQRN 305 (329)
Q Consensus 257 ~~~~i~~k~~fL~~~~g~~~~~i~~~P~~l~~sl~~~i~~R~~~l~~~g 305 (329)
++++..+++|+.+. .+++.++|.++.++ +..+.+|++++...|
T Consensus 298 -~~~~~~~~~~~~~~----~~~~~k~p~~l~~s-~~~l~~~ie~l~~~g 340 (413)
T KOG1267|consen 298 -VKKNLKTTEYLLKN----PKHILKFPQLLRSS-EDKLKPRIEFLLSLG 340 (413)
T ss_pred -hhhhhHHHHHHHhc----chhhhhhhhhhhcc-chhhhhhHHHHHHcC
Confidence 46654444444443 12244444444444 224444444444444
No 7
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=97.07 E-value=0.00036 Score=40.02 Aligned_cols=28 Identities=32% Similarity=0.660 Sum_probs=18.3
Q ss_pred HHHhCchhhcccccchhhhHHHHHHHHhCC
Q 020213 245 LVAAYPPILIKSIKNSLEPRIKFLVEVMGR 274 (329)
Q Consensus 245 l~~~~P~iL~~s~~~~i~~k~~fL~~~~g~ 274 (329)
++.++|.+++.| +++++++++||. .+|+
T Consensus 3 ~~~~~P~il~~~-~~~l~~~~~~l~-~~g~ 30 (31)
T smart00733 3 ILKKFPQILGYS-EKKLKPKVEFLK-ELGF 30 (31)
T ss_pred hhhhCcCccccc-HHHhhHHHHHHH-HcCC
Confidence 456667777666 566667776666 4664
No 8
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=96.96 E-value=0.00079 Score=38.52 Aligned_cols=27 Identities=44% Similarity=0.816 Sum_probs=11.2
Q ss_pred HHhCCCcccccchhhHhHHHHHHHHCCC
Q 020213 101 ITRFPPILSHSVEEKLCPLLAFFQALGV 128 (329)
Q Consensus 101 l~~~P~ll~~~~e~~l~~~v~~L~~lG~ 128 (329)
+.++|.+++.+ +++++++++||+++|+
T Consensus 4 ~~~~P~il~~~-~~~l~~~~~~l~~~g~ 30 (31)
T smart00733 4 LKKFPQILGYS-EKKLKPKVEFLKELGF 30 (31)
T ss_pred hhhCcCccccc-HHHhhHHHHHHHHcCC
Confidence 33444444444 2334444444444443
No 9
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=95.39 E-value=0.037 Score=51.04 Aligned_cols=94 Identities=16% Similarity=0.265 Sum_probs=56.2
Q ss_pred HhCCCChhHHHHHHHhhhcccCCcc---h-----hhHHHHHHHHh--CCCCCCChhHHHhhCCCccccccccc-hHHHHH
Q 020213 17 KDRGFNDRTIHDMFKRCKRLQGVEK---D-----RAADNWAYLKS--IGILERKLPNVVSKCPKILTLGLNEK-LVPMVE 85 (329)
Q Consensus 17 ~~~G~s~~~i~~i~~~~p~ll~~~~---~-----~l~~~~~~L~~--~G~~~~~i~~i~~~~P~lL~~~~~~~-l~~~l~ 85 (329)
..+|+....+...+.++|.++..-. . .+.+...-|.. ..+-.+.-..++.+=-.+|.++.+.. .-.+++
T Consensus 45 ~~L~l~~~~~~~flrkyP~iF~~~~~~~~~~~~~~LT~~a~~L~~eE~~~~~~~e~~~v~rL~KLLMMS~~~rlpL~ki~ 124 (335)
T PF11955_consen 45 RQLGLKPRKVSRFLRKYPSIFEVFQHPSRSVPWFRLTPEAEDLLREERRVREEMEPDLVERLRKLLMMSKDRRLPLSKIA 124 (335)
T ss_pred HhcCCCcccHHHHHHhCCceEEEeccCCCCCceEEeCHHHHHHHHHHHHHHHhChHHHHHHHHHHhccCCCCcccHHHHH
Confidence 3489977888899999998865421 1 23333333321 11111111223333334676666533 356677
Q ss_pred HHH-HCCCChhhHHHHHHhCCCcccc
Q 020213 86 CLA-TLGTKPYEVASAITRFPPILSH 110 (329)
Q Consensus 86 ~L~-~lG~~~~~~~~~l~~~P~ll~~ 110 (329)
.++ ++|++.+=...++.+||..+..
T Consensus 125 ~l~~dLGLP~Df~~~lv~~yP~~Frv 150 (335)
T PF11955_consen 125 HLRRDLGLPDDFRDSLVPKYPDYFRV 150 (335)
T ss_pred HHHHHcCCChhhccchhhhCCCCcEE
Confidence 776 7999988888889999987664
No 10
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=89.52 E-value=2 Score=35.76 Aligned_cols=23 Identities=9% Similarity=0.106 Sum_probs=16.3
Q ss_pred HHHHHHHHCCCChhhHHHHHHhC
Q 020213 82 PMVECLATLGTKPYEVASAITRF 104 (329)
Q Consensus 82 ~~l~~L~~lG~~~~~~~~~l~~~ 104 (329)
..+..++++|++-+++..++...
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~ 71 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQP 71 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcC
Confidence 45556678888888888777644
No 11
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=84.39 E-value=5.9 Score=32.94 Aligned_cols=115 Identities=15% Similarity=0.228 Sum_probs=62.5
Q ss_pred HHHHHHHHCCCCchhhhhhHhhCCceeccCcchhHhHHHHHHhh----cCCCchhhHHHHHHhcCcccccccccchhHHH
Q 020213 118 PLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVDFLTS----LGLAREGMIGKVLVKHPFIMGYSVDNRLRPTS 193 (329)
Q Consensus 118 ~~v~~L~~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~----~G~~~~~~i~~ll~~~p~ll~~~~~~~l~~~~ 193 (329)
..+..++++|++-++|..++..... .....+...+..+.+ +.-. ...+..++...+.. .....-+...-+
T Consensus 49 ~~I~~lr~~G~sL~eI~~ll~~~~~----~~~~~L~~~~~~l~~ei~~L~~~-~~~l~~ll~~~~~~-~~~~~V~~~~w~ 122 (172)
T cd04790 49 EQICAYRSAGVSLEDIRSLLQQPGD----DATDVLRRRLAELNREIQRLRQQ-QRAIATLLKQPTLL-KEQRLVTKEKWV 122 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHHhcCCh----hHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHhhc-cccccCCHHHHH
Confidence 4567788999999999998865542 111223333333321 1100 12334444333222 211111234455
Q ss_pred HHHHHhCCChhhHHHHHhhcCceeeeccccccchhHHHHHHhCCChhHHHHH
Q 020213 194 EFLKSVGLKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAAL 245 (329)
Q Consensus 194 ~~l~~~g~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~~~G~s~~~v~~l 245 (329)
+.++..|++++++..+=..+- ...| ....+||..+|++.+++..+
T Consensus 123 ~l~~~~g~~~~~m~~wh~~fe---~~~p----~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 123 AILKAAGMDEADMRRWHIEFE---KMEP----EAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred HHHHHcCCChHHHHHHHHHHH---HhCc----HHHHHHHHHcCCCHHHHHHH
Confidence 666679999988765432211 1122 33568999999999998644
No 12
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=82.50 E-value=3.6 Score=42.31 Aligned_cols=99 Identities=17% Similarity=0.246 Sum_probs=70.0
Q ss_pred ccCCcchHHHHHHh---CCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhC-CCCCCChhHHHhhCCCccccccccch
Q 020213 5 TSQNGNSVIWFLKD---RGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSI-GILERKLPNVVSKCPKILTLGLNEKL 80 (329)
Q Consensus 5 ~~~~~~~v~~~L~~---~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~-G~~~~~i~~i~~~~P~lL~~~~~~~l 80 (329)
-+...++++.||.+ .|+-+..+.+|+...+. ...+.+...-+-|... |++++.+..+...+. . ....
T Consensus 73 ~p~~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~---~~~~~i~~~~~~L~~v~gi~~~~~~~i~~~~~---~---~~~~ 143 (720)
T TIGR01448 73 APTSKEGIVAYLSSRSIKGVGKKLAQRIVKTFGE---AAFDVLDDDPEKLLEVPGISKANLEKFVSQWS---Q---QGDE 143 (720)
T ss_pred CCCCHHHHHHHHhcCCCCCcCHHHHHHHHHHhCH---hHHHHHHhCHHHHhcCCCCCHHHHHHHHHHHH---H---hHHH
Confidence 34567889999987 58999999999987652 1123344445556665 999888888887652 1 2347
Q ss_pred HHHHHHHHHCCCChhhHHH-----------HHHhCCCcccccc
Q 020213 81 VPMVECLATLGTKPYEVAS-----------AITRFPPILSHSV 112 (329)
Q Consensus 81 ~~~l~~L~~lG~~~~~~~~-----------~l~~~P~ll~~~~ 112 (329)
...+.+|..+|++.....+ ++..+|..|..++
T Consensus 144 ~~~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i 186 (720)
T TIGR01448 144 RRLLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDV 186 (720)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhc
Confidence 8889999999999876665 4567887666543
No 13
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=82.24 E-value=8.8 Score=36.21 Aligned_cols=40 Identities=15% Similarity=0.300 Sum_probs=32.9
Q ss_pred chHHHHHHhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCC
Q 020213 10 NSVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGIL 57 (329)
Q Consensus 10 ~~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~ 57 (329)
...++-+-++||+++++.+.++.. -.+.+..++||.+ |+.
T Consensus 157 e~~I~~i~eMGf~R~qV~~ALRAa-------fNNPdRAVEYL~t-GIP 196 (378)
T TIGR00601 157 ETTIEEIMEMGYEREEVERALRAA-------FNNPDRAVEYLLT-GIP 196 (378)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHH-------hCCHHHHHHHHHh-CCC
Confidence 457888899999999999988754 3566889999988 887
No 14
>PF11955 PORR: Plant organelle RNA recognition domain; InterPro: IPR021099 The plant organelle RNA recognition (PORR) domain, previously known as DUF860, is a component of group II intron ribonucleoprotein particles in maize chloroplasts. It is required for the splicing of the introns with which it associates, and promotes splicing in the context of a heterodimer with the RNase III-domain protein RNC1. Proteins containing this domain are predicted to localise to mitochondria or chloroplasts []. It seems likely that most PORR proteins function in organellar RNA metabolism [].
Probab=74.60 E-value=6 Score=36.63 Aligned_cols=47 Identities=17% Similarity=0.282 Sum_probs=28.7
Q ss_pred hHHHHHHhCCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhCCceeccC
Q 020213 96 EVASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLNPRLISYS 147 (329)
Q Consensus 96 ~~~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~P~il~~~ 147 (329)
.+..+|.+.|. -+.++. ..-..-+.+|+++..+..++.+||.+|...
T Consensus 22 ~l~~~i~~~p~-~~~pl~----~l~k~~~~L~l~~~~~~~flrkyP~iF~~~ 68 (335)
T PF11955_consen 22 RLKDLILSQPS-HSLPLR----DLSKLRRQLGLKPRKVSRFLRKYPSIFEVF 68 (335)
T ss_pred HHHHHHHcCCC-CcccHH----HHHHHHHhcCCCcccHHHHHHhCCceEEEe
Confidence 45566777776 222221 112233468886677888888888887653
No 15
>PRK14135 recX recombination regulator RecX; Provisional
Probab=74.23 E-value=52 Score=29.15 Aligned_cols=25 Identities=12% Similarity=0.130 Sum_probs=19.5
Q ss_pred hhHHHHHHHHhCCChhhHHHHHhhc
Q 020213 189 LRPTSEFLKSVGLKELDLQVVAVKF 213 (329)
Q Consensus 189 l~~~~~~l~~~g~~~~~i~~~i~~~ 213 (329)
-.....||.+-||+.+.|..++...
T Consensus 235 k~K~~~~L~rrGF~~~~I~~~l~~~ 259 (263)
T PRK14135 235 KQKLKQALYRKGFSYDDIDSFLREY 259 (263)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHh
Confidence 3556688889999999998887643
No 16
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=72.80 E-value=22 Score=26.19 Aligned_cols=27 Identities=15% Similarity=0.421 Sum_probs=15.2
Q ss_pred CCcchHHHHHHhCCCChhHHHHHHHhh
Q 020213 7 QNGNSVIWFLKDRGFNDRTIHDMFKRC 33 (329)
Q Consensus 7 ~~~~~v~~~L~~~G~s~~~i~~i~~~~ 33 (329)
.....+..+|.++|++...+.++.+.+
T Consensus 6 ~~~~~~~~~L~~~gl~~~~a~kl~~~y 32 (94)
T PF14490_consen 6 RGLRELMAFLQEYGLSPKLAMKLYKKY 32 (94)
T ss_dssp ---HHHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 344566777777777777777666654
No 17
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=70.80 E-value=3.5 Score=32.86 Aligned_cols=29 Identities=17% Similarity=0.276 Sum_probs=19.5
Q ss_pred cchhHHHHHHhCCChhHHHHHHHhCchhh
Q 020213 225 LSPNFTFLKRCGFADGQIAALVAAYPPIL 253 (329)
Q Consensus 225 l~~k~~~L~~~G~s~~~v~~l~~~~P~iL 253 (329)
+..|++||++-|++.+||.+++.+.+.--
T Consensus 23 ~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 23 LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 46688888888888888888887766544
No 18
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.59 E-value=34 Score=28.99 Aligned_cols=24 Identities=29% Similarity=0.425 Sum_probs=12.1
Q ss_pred HHHHHHHHHCCCChhhHHHHHHhC
Q 020213 81 VPMVECLATLGTKPYEVASAITRF 104 (329)
Q Consensus 81 ~~~l~~L~~lG~~~~~~~~~l~~~ 104 (329)
.+.+..|.++|++..++.+++.+.
T Consensus 149 ~e~~~aL~~LGy~~~~a~~ai~~~ 172 (194)
T PRK14605 149 SDILATLTALGYSSSEAAKAISSL 172 (194)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 344455555555555555554443
No 19
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=70.33 E-value=12 Score=27.57 Aligned_cols=26 Identities=15% Similarity=0.215 Sum_probs=14.3
Q ss_pred cchHHHHHHHHHCCCChhhHHHHHHh
Q 020213 78 EKLVPMVECLATLGTKPYEVASAITR 103 (329)
Q Consensus 78 ~~l~~~l~~L~~lG~~~~~~~~~l~~ 103 (329)
..+...+.+|..+|++.....++...
T Consensus 6 ~~~~~~~~~L~~~gl~~~~a~kl~~~ 31 (94)
T PF14490_consen 6 RGLRELMAFLQEYGLSPKLAMKLYKK 31 (94)
T ss_dssp ---HHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 34566777777777777666665544
No 20
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=67.69 E-value=7.3 Score=23.17 Aligned_cols=23 Identities=22% Similarity=0.244 Sum_probs=16.5
Q ss_pred hhHHHHHHhCCChhHHHHHHHhC
Q 020213 227 PNFTFLKRCGFADGQIAALVAAY 249 (329)
Q Consensus 227 ~k~~~L~~~G~s~~~v~~l~~~~ 249 (329)
+.++-|.++||+.+++.+.+.++
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~~~ 26 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALRAC 26 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHT
T ss_pred HHHHHHHHcCCCHHHHHHHHHHc
Confidence 46777888888888887776655
No 21
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=66.98 E-value=18 Score=30.59 Aligned_cols=25 Identities=36% Similarity=0.558 Sum_probs=12.3
Q ss_pred hHHHHHHHHHCCCChhhHHHHHHhC
Q 020213 80 LVPMVECLATLGTKPYEVASAITRF 104 (329)
Q Consensus 80 l~~~l~~L~~lG~~~~~~~~~l~~~ 104 (329)
..+.+.+|.++|++..++.+++.++
T Consensus 149 ~~ev~~aL~~LG~~~~~a~~~~~~~ 173 (192)
T PRK00116 149 LEEAVSALVALGYKPKEASKAVAKI 173 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 3444555555555555555544443
No 22
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=66.23 E-value=65 Score=26.01 Aligned_cols=136 Identities=13% Similarity=0.144 Sum_probs=78.3
Q ss_pred HHHHHHhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCC-CCChhHHHhhCCCccccccccchHHHHHHHHHC
Q 020213 12 VIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGIL-ERKLPNVVSKCPKILTLGLNEKLVPMVECLATL 90 (329)
Q Consensus 12 v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~-~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~l 90 (329)
.+++|..-.-|..++..-+.+. ..+++.+...++.|...|.- +...+....+.= ... ..........|..-
T Consensus 17 al~~L~~r~~s~~el~~kL~~k----g~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~---~~~-~~g~~~I~~~L~~k 88 (157)
T PRK00117 17 ALRLLARREHSRAELRRKLAAK----GFSEEVIEAVLDRLKEEGLLDDERFAESFVRSR---ARK-GYGPRRIRQELRQK 88 (157)
T ss_pred HHHHHccchhHHHHHHHHHHhc----CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH---HhC-CchHHHHHHHHHHc
Confidence 4555555666666666666554 45667778888888877653 334444433321 111 23456677888999
Q ss_pred CCChhhHHHHHHhCCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhCCceeccCcchhHhHHHHHHhhcCCCchhhH
Q 020213 91 GTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLAREGMI 170 (329)
Q Consensus 91 G~~~~~~~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~~~~~~i 170 (329)
|++.+.+..++...+ .+ ........+. +. +...-..+. ..-.....+|..-||+. +.|
T Consensus 89 Gi~~~~I~~~l~~~~----~d---~~e~a~~~~~----------k~---~~~~~~~~~-~~k~Ki~~~L~rkGF~~-~~I 146 (157)
T PRK00117 89 GVDREIIEEALAELD----ID---WEELARELAR----------KK---FRRPLPDDA-KEKAKLVRFLARRGFSM-DVI 146 (157)
T ss_pred CCCHHHHHHHHHHcC----cc---HHHHHHHHHH----------HH---cCCCCCCCH-HHHHHHHHHHHHCCCCH-HHH
Confidence 999999999888764 11 1111111111 11 111111222 34566778888999985 477
Q ss_pred HHHHHhc
Q 020213 171 GKVLVKH 177 (329)
Q Consensus 171 ~~ll~~~ 177 (329)
.+++...
T Consensus 147 ~~~l~~~ 153 (157)
T PRK00117 147 QRVLRNA 153 (157)
T ss_pred HHHHHhh
Confidence 7777654
No 23
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=65.94 E-value=9.8 Score=30.29 Aligned_cols=36 Identities=22% Similarity=0.279 Sum_probs=22.8
Q ss_pred hCCCccccccccchHHHHHHHHHCCCChhhHHHHHHhCCC
Q 020213 67 KCPKILTLGLNEKLVPMVECLATLGTKPYEVASAITRFPP 106 (329)
Q Consensus 67 ~~P~lL~~~~~~~l~~~l~~L~~lG~~~~~~~~~l~~~P~ 106 (329)
.+|.+-. ..+..+++||++-|++.++|..++.+.+.
T Consensus 14 ~~p~V~~----sp~~~k~~FL~sKGLt~~EI~~al~~a~~ 49 (136)
T PF04695_consen 14 QDPKVRN----SPLEKKIAFLESKGLTEEEIDEALGRAGS 49 (136)
T ss_dssp CTTTCCC----S-HHHHHHHHHHCT--HHHHHHHHHHHT-
T ss_pred CCccccc----CCHHHHHHHHHcCCCCHHHHHHHHHhcCC
Confidence 3555544 24677888888888888888888877554
No 24
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=65.31 E-value=48 Score=26.80 Aligned_cols=109 Identities=14% Similarity=0.188 Sum_probs=59.7
Q ss_pred chHHHHHHhCCCChhHHHHHHHhhhcccCCcchh---------------hHHHHHHHHhCCCCCCChhHHHhhCCCcccc
Q 020213 10 NSVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDR---------------AADNWAYLKSIGILERKLPNVVSKCPKILTL 74 (329)
Q Consensus 10 ~~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~---------------l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~ 74 (329)
..+.+.|...|++++.|..++.+....-..+... ......-|...|++.+.|..++...+
T Consensus 29 ~el~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~g~~~I~~~L~~kGi~~~~I~~~l~~~~----- 103 (157)
T PRK00117 29 AELRRKLAAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRSRARKGYGPRRIRQELRQKGVDREIIEEALAELD----- 103 (157)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCchHHHHHHHHHHcCCCHHHHHHHHHHcC-----
Confidence 4577888889999999999888775432223221 11222344445555555554444321
Q ss_pred ccccchHHHHHHHHHCCCChhhHHHHHH-hCCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhC
Q 020213 75 GLNEKLVPMVECLATLGTKPYEVASAIT-RFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLN 140 (329)
Q Consensus 75 ~~~~~l~~~l~~L~~lG~~~~~~~~~l~-~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~ 140 (329)
++.. +.+.+++. +++..-..+. ..-+....+|..=|++.+.|.+++...
T Consensus 104 --~d~~--------------e~a~~~~~k~~~~~~~~~~-~~k~Ki~~~L~rkGF~~~~I~~~l~~~ 153 (157)
T PRK00117 104 --IDWE--------------ELARELARKKFRRPLPDDA-KEKAKLVRFLARRGFSMDVIQRVLRNA 153 (157)
T ss_pred --ccHH--------------HHHHHHHHHHcCCCCCCCH-HHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 0001 11222332 2333322222 233457789999999998888877654
No 25
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=63.02 E-value=9.9 Score=22.38 Aligned_cols=23 Identities=17% Similarity=0.193 Sum_probs=16.8
Q ss_pred hhHHHHHHhCCChhHHHHHHHhC
Q 020213 227 PNFTFLKRCGFADGQIAALVAAY 249 (329)
Q Consensus 227 ~k~~~L~~~G~s~~~v~~l~~~~ 249 (329)
++++-|.++||+.+++.+.+.++
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46677788888888877666554
No 26
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=62.58 E-value=16 Score=25.30 Aligned_cols=55 Identities=20% Similarity=0.437 Sum_probs=33.2
Q ss_pred HHHHHHHHHCCCChhhHHHHHHhCCCcccccchhhHhHHHHHHHHCCCCchhhhhh---HhhCCce
Q 020213 81 VPMVECLATLGTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRM---ILLNPRL 143 (329)
Q Consensus 81 ~~~l~~L~~lG~~~~~~~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~---l~~~P~i 143 (329)
.|.+..|++..+|++.+..+.... +. +--..+..+..+|++++.+..+ +..+|.+
T Consensus 2 NPIia~LKehnvsd~qi~elFq~l----T~----NPl~AMa~i~qLGip~eKLQ~lm~~VMqnP~L 59 (82)
T PF11212_consen 2 NPIIAILKEHNVSDEQINELFQAL----TQ----NPLAAMATIQQLGIPQEKLQQLMAQVMQNPAL 59 (82)
T ss_pred chHHHHHHHcCCCHHHHHHHHHHH----hh----CHHHHHHHHHHcCCCHHHHHHHHHHHhcChHH
Confidence 577788888888888777665431 21 1122455667788887665443 4455544
No 27
>PHA01351 putative minor structural protein
Probab=61.13 E-value=2e+02 Score=29.45 Aligned_cols=266 Identities=15% Similarity=0.119 Sum_probs=147.5
Q ss_pred hHHHHHHhCCCChhHHHHHHHhhhcc--cCCc---ch--------hhHHHHHHHHhCCCCCCChhHHHhhCCCcccccc-
Q 020213 11 SVIWFLKDRGFNDRTIHDMFKRCKRL--QGVE---KD--------RAADNWAYLKSIGILERKLPNVVSKCPKILTLGL- 76 (329)
Q Consensus 11 ~v~~~L~~~G~s~~~i~~i~~~~p~l--l~~~---~~--------~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~- 76 (329)
..-.=|.++|++++-|..++..+=.. +..- .+ +.++.-.-|+.+|..++-+.++..-+-++.....
T Consensus 549 D~EkELKkLg~s~alIqaiI~EyftepL~KlQLnvyEsLakKGY~d~qq~ksElk~LGidKe~i~klin~Y~ql~qt~~e 628 (1070)
T PHA01351 549 DLEKDLKHLGFDSAIISALIYENQVEQLIKFQLNNIESLAKKGYLSLDEIKKQFKAIGIIKEYEDAFINFYNQELQISAF 628 (1070)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhhccchhHHHHHHHHHHHHHHHHHH
Confidence 34455778899999888888765221 1100 11 2334445566677777766666655554433221
Q ss_pred -----------ccchHHHHHHHHHCCCChhhHHHHHHhC---CCccc-cc--------chhhHhHHHHHHHHCCCCchhh
Q 020213 77 -----------NEKLVPMVECLATLGTKPYEVASAITRF---PPILS-HS--------VEEKLCPLLAFFQALGVPEKQL 133 (329)
Q Consensus 77 -----------~~~l~~~l~~L~~lG~~~~~~~~~l~~~---P~ll~-~~--------~e~~l~~~v~~L~~lG~~~~~l 133 (329)
.-+-++.+.-|+.+|++++-+..++..+ |.+-. .+ +.-+......-|+++|+++..+
T Consensus 629 IkYIqe~LK~f~IspkeAitELKKL~ISdaLAn~IV~eYf~iP~l~~q~TViEnIikgvpint~~~~~ELKKL~IpdSqI 708 (1070)
T PHA01351 629 LTILKSQLRQFQIDPKEAETELKKLNINEYLANQIIQEEYNINIAKLQLSVLETIAKTLYYDQQQLSGELKKIHKDKTAL 708 (1070)
T ss_pred HHHHHHHHHHcccCHHHHHHHHHHcCchHHHHHHHHHHHhcchHHHHHHHHHHHHHhcCCcchHHHHHHHHHcCCCHHHH
Confidence 1123456677888888887666666665 43211 00 1111234567889999999988
Q ss_pred hhhHhhCCceeccCcchhHhHHHHHHhhcCCCch-hhHHHHHHhc---Ccccccccc---cch-----------hHHHHH
Q 020213 134 GRMILLNPRLISYSIESKLTETVDFLTSLGLARE-GMIGKVLVKH---PFIMGYSVD---NRL-----------RPTSEF 195 (329)
Q Consensus 134 ~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~~~~-~~i~~ll~~~---p~ll~~~~~---~~l-----------~~~~~~ 195 (329)
..+++.+-..-. .+ .+..-..-+.+.|.-.+ +.+.+.+..+ |.+..+-.. +.+ +...+-
T Consensus 709 nil~t~yy~~~~--~~-kls~~~~sl~~~g~l~~~s~i~e~~~~y~~~~a~~~y~~~~ei~yi~~~lkdl~i~~k~a~~e 785 (1070)
T PHA01351 709 ELYITKFYYEYI--YP-KISNYHLQLARHGILSDISKLPKEVNDYEYKPAVLTYQTTLEIEYIKESLKDLEIKPKTAINE 785 (1070)
T ss_pred HHHHHHHHHHHH--HH-HHHHHHHHHHhcCchhhHHHhhHHHHhccchhHHHhhhHHHHHHHHHHHHhhcccCchhHHHH
Confidence 888777643211 11 23333334445555310 1222222222 122221100 011 234567
Q ss_pred HHHhCCChhhHHHHHhhcCceeeeccccc------------------cchhHHHHHHhCCChhHHHHHHHhCchhhcccc
Q 020213 196 LKSVGLKELDLQVVAVKFPEVLCRDVNKI------------------LSPNFTFLKRCGFADGQIAALVAAYPPILIKSI 257 (329)
Q Consensus 196 l~~~g~~~~~i~~~i~~~P~il~~s~~~~------------------l~~k~~~L~~~G~s~~~v~~l~~~~P~iL~~s~ 257 (329)
|+++|++.+-...++..+...+ +|+... +..-..-|+.+|.+..++..++..+..-+++++
T Consensus 786 l~kl~~s~~i~~~iv~~~~p~~-~s~~t~~q~iieg~ly~i~kvpv~~~~~~~elkkl~ipdsqin~lidq~~s~~~l~i 864 (1070)
T PHA01351 786 LEKLGMQKDIAQLIVNTYIPTF-YSPHTIIQNIIEGQLYKIGKVPINLGNAESELRKLGIPDSQIKALLDQYESTFGLDI 864 (1070)
T ss_pred HHHcCchHHHHHHHHhhcCCcc-ccHHHHHHHHhhhhheeccccccchhhhHHHHHHcCCCHHHHHHHHHHHHHHHHHHH
Confidence 8889998877666665543333 233221 223345788999999999999999999898888
Q ss_pred cchhhhHHHHHHHH--hCCChhhhh
Q 020213 258 KNSLEPRIKFLVEV--MGRQIDEVA 280 (329)
Q Consensus 258 ~~~i~~k~~fL~~~--~g~~~~~i~ 280 (329)
|++--|.+.-..+. .|++.+.++
T Consensus 865 w~k~lpsls~i~nai~y~y~~~klv 889 (1070)
T PHA01351 865 WRKHLPSLSIIENAIKYNYLDQKLI 889 (1070)
T ss_pred HHHhCCcHHHHHHHHhcCCcHHHHH
Confidence 87776666655543 344444443
No 28
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=59.05 E-value=13 Score=22.04 Aligned_cols=23 Identities=17% Similarity=0.219 Sum_probs=16.3
Q ss_pred hhHHHHHHhCCChhHHHHHHHhC
Q 020213 227 PNFTFLKRCGFADGQIAALVAAY 249 (329)
Q Consensus 227 ~k~~~L~~~G~s~~~v~~l~~~~ 249 (329)
.+++-|.++||+.+++...+..+
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 46677778888887777665544
No 29
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=58.85 E-value=61 Score=33.54 Aligned_cols=89 Identities=20% Similarity=0.187 Sum_probs=57.6
Q ss_pred hhhHHHHHHHHhC---CCCCCChhHHHhhCCCccccccccchHHHHHHHHHC-CCChhhHHHHHHhCCCcccccchhhHh
Q 020213 42 DRAADNWAYLKSI---GILERKLPNVVSKCPKILTLGLNEKLVPMVECLATL-GTKPYEVASAITRFPPILSHSVEEKLC 117 (329)
Q Consensus 42 ~~l~~~~~~L~~~---G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~l-G~~~~~~~~~l~~~P~ll~~~~e~~l~ 117 (329)
...+..+.||.+- |+.+....+|+..++.=.. +.+..--+-|..+ |++++.+.++...... . ....
T Consensus 75 ~~~~~i~~yL~s~~~~GIG~~~A~~iv~~fg~~~~----~~i~~~~~~L~~v~gi~~~~~~~i~~~~~~----~--~~~~ 144 (720)
T TIGR01448 75 TSKEGIVAYLSSRSIKGVGKKLAQRIVKTFGEAAF----DVLDDDPEKLLEVPGISKANLEKFVSQWSQ----Q--GDER 144 (720)
T ss_pred CCHHHHHHHHhcCCCCCcCHHHHHHHHHHhCHhHH----HHHHhCHHHHhcCCCCCHHHHHHHHHHHHH----h--HHHH
Confidence 3456677888762 8888888888877654333 2334444556554 8888888777776521 1 1245
Q ss_pred HHHHHHHHCCCCchhhhhhHhhC
Q 020213 118 PLLAFFQALGVPEKQLGRMILLN 140 (329)
Q Consensus 118 ~~v~~L~~lG~~~~~l~~~l~~~ 140 (329)
..+.||.++|++.+...++...|
T Consensus 145 ~~~~~L~~~gi~~~~a~ki~~~y 167 (720)
T TIGR01448 145 RLLAGLQGLGIGIKLAQRIYKFY 167 (720)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHH
Confidence 67889999999986665554433
No 30
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=57.29 E-value=24 Score=26.26 Aligned_cols=24 Identities=17% Similarity=0.321 Sum_probs=14.4
Q ss_pred hHHHHHHhCCCChhHHHHHHHhhh
Q 020213 11 SVIWFLKDRGFNDRTIHDMFKRCK 34 (329)
Q Consensus 11 ~v~~~L~~~G~s~~~i~~i~~~~p 34 (329)
.+.+|-+.+|+|+.+|..|-..+|
T Consensus 22 ~wK~faR~lglse~~Id~I~~~~~ 45 (97)
T cd08316 22 DVKKFVRKSGLSEPKIDEIKLDNP 45 (97)
T ss_pred HHHHHHHHcCCCHHHHHHHHHcCC
Confidence 455555666666666666665555
No 31
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=55.21 E-value=28 Score=30.34 Aligned_cols=28 Identities=21% Similarity=0.237 Sum_probs=13.5
Q ss_pred cchHHHHHHHHHCCCChhhHHHHHHhCC
Q 020213 78 EKLVPMVECLATLGTKPYEVASAITRFP 105 (329)
Q Consensus 78 ~~l~~~l~~L~~lG~~~~~~~~~l~~~P 105 (329)
.++...++.|+.-|+++.....+-.-+|
T Consensus 64 ~~fa~Av~iL~~~GlPr~~f~~l~d~Fp 91 (246)
T COG4669 64 SDFAEAVEILNQNGLPRKKFTTLGDIFP 91 (246)
T ss_pred HHHHHHHHHHHhcCCCCCCCCcHHHhCC
Confidence 3455555555555555444444433344
No 32
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=54.42 E-value=15 Score=32.68 Aligned_cols=86 Identities=17% Similarity=0.266 Sum_probs=57.4
Q ss_pred cchhHHHHHHHH-hC-CChhhHHHHHhhcCceeeeccccccchhHHHHH-HhCCChhHHHHHHHhCchhhcccccchhhh
Q 020213 187 NRLRPTSEFLKS-VG-LKELDLQVVAVKFPEVLCRDVNKILSPNFTFLK-RCGFADGQIAALVAAYPPILIKSIKNSLEP 263 (329)
Q Consensus 187 ~~l~~~~~~l~~-~g-~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~-~~G~s~~~v~~l~~~~P~iL~~s~~~~i~~ 263 (329)
-.+++++.|.-+ .| |++-.+.+-|...|.++..+.++ ++.|++-|. -+|++..+. ..+||.=|+-- .
T Consensus 71 ~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k~~-i~~r~~ELl~lvgL~p~~~---~~RyP~eLSGG-Q----- 140 (309)
T COG1125 71 VELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDKER-IKKRADELLDLVGLDPSEY---ADRYPHELSGG-Q----- 140 (309)
T ss_pred HHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCHHH-HHHHHHHHHHHhCCCHHHH---hhcCchhcCcc-h-----
Confidence 356777777766 66 56677888888888888888775 788876554 778877653 36888777655 3
Q ss_pred HHHHHHHHhCCChhhhhcCCceeec
Q 020213 264 RIKFLVEVMGRQIDEVADYPDFFRH 288 (329)
Q Consensus 264 k~~fL~~~~g~~~~~i~~~P~~l~~ 288 (329)
.+..|+ ...++..|.++-.
T Consensus 141 -----QQRVGv-~RALAadP~ilLM 159 (309)
T COG1125 141 -----QQRVGV-ARALAADPPILLM 159 (309)
T ss_pred -----hhHHHH-HHHHhcCCCeEee
Confidence 224554 2345666666643
No 33
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=53.93 E-value=30 Score=26.77 Aligned_cols=41 Identities=22% Similarity=0.393 Sum_probs=24.8
Q ss_pred CChhhHHHHHhhcCceeeeccccccchhHHHHHHhCCChhHHHHHH
Q 020213 201 LKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAALV 246 (329)
Q Consensus 201 ~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~~~G~s~~~v~~l~ 246 (329)
.+.+++...+..+|.++-..+- +..+- ...|++.+++.+++
T Consensus 75 ~~~~~~~~~i~~~~~LikRPiv--v~~~~---~~iG~~~e~~~~~l 115 (117)
T COG1393 75 LSDEELIEALLENPSLIKRPIV--VDNKK---LRVGFNEEEIRAFL 115 (117)
T ss_pred cChHHHHHHHHhChhhccCCeE--EeCCc---eEecCCHHHHHHHh
Confidence 4456667777788855555432 22222 45788888877654
No 34
>PF06896 DUF1268: Protein of unknown function (DUF1268); InterPro: IPR009681 This entry is represented by Bacteriophage bIL286, Orf51. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial and phage proteins of around 115 residues in length. The function of this family is unknown.
Probab=53.09 E-value=19 Score=27.73 Aligned_cols=50 Identities=14% Similarity=0.293 Sum_probs=30.2
Q ss_pred hhHHHHHHHHhC-CCCCCChhHHHhhCCCccccccccchHHHHHHHHH--CCCChhhHHHH
Q 020213 43 RAADNWAYLKSI-GILERKLPNVVSKCPKILTLGLNEKLVPMVECLAT--LGTKPYEVASA 100 (329)
Q Consensus 43 ~l~~~~~~L~~~-G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~--lG~~~~~~~~~ 100 (329)
.+...++|++.. |++++++.++- . + +. .++.+.+.|+.. .|++++++...
T Consensus 54 ~~~~~~~Fi~~iL~L~dkq~ekl~-~----i--D~-~~~~e~~~yl~~rl~G~sD~~i~~~ 106 (114)
T PF06896_consen 54 ILKEMLKFIQDILKLNDKQVEKLE-D----I--DF-EDLQEIVSYLVMRLQGMSDEQIELA 106 (114)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHh-c----C--CH-HHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 356666777665 77777776662 1 1 32 356666666642 57777766654
No 35
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=52.70 E-value=28 Score=27.27 Aligned_cols=36 Identities=14% Similarity=0.230 Sum_probs=16.6
Q ss_pred CCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhC
Q 020213 104 FPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLN 140 (329)
Q Consensus 104 ~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~ 140 (329)
.|..+..+.+ .++..+--|..-|+++.+|+-++...
T Consensus 22 ~PtWlK~~~d-dvkeqI~K~akKGltpsqIGviLRDs 57 (151)
T KOG0400|consen 22 VPTWLKLTAD-DVKEQIYKLAKKGLTPSQIGVILRDS 57 (151)
T ss_pred CcHHHhcCHH-HHHHHHHHHHHcCCChhHceeeeecc
Confidence 4444444443 24444444445555555555444333
No 36
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=50.59 E-value=49 Score=24.53 Aligned_cols=23 Identities=9% Similarity=0.128 Sum_probs=11.5
Q ss_pred HHHHHHhCCCChhHHHHHHHhhh
Q 020213 12 VIWFLKDRGFNDRTIHDMFKRCK 34 (329)
Q Consensus 12 v~~~L~~~G~s~~~i~~i~~~~p 34 (329)
+..+.+.+|+|+.+|..|-..+|
T Consensus 22 Wk~laR~LGLse~~I~~i~~~~~ 44 (96)
T cd08315 22 WNRLMRQLGLSENEIDVAKANER 44 (96)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCC
Confidence 44444555555555555555444
No 37
>PF06089 Asparaginase_II: L-asparaginase II; InterPro: IPR010349 This family consists of several bacterial L-asparaginase II proteins. L-asparaginase (3.5.1.1 from EC) catalyses the hydrolysis of L-asparagine to L-aspartate and ammonium. Rhizobium etli possesses two asparaginases: asparaginase I, which is thermostable and constitutive, and asparaginase II, which is thermolabile, induced by asparagine and repressed by the carbon source [].
Probab=50.51 E-value=16 Score=33.64 Aligned_cols=55 Identities=15% Similarity=0.160 Sum_probs=46.3
Q ss_pred ccccCCcchHHHHHHh-----CCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCCCCCh
Q 020213 3 ISTSQNGNSVIWFLKD-----RGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGILERKL 61 (329)
Q Consensus 3 ~~~~~~~~~v~~~L~~-----~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~~~~i 61 (329)
.||+.+|-+.+.++++ ||+++++++=+-..| .-.+.+++..-..|.+.|++.+++
T Consensus 40 ~RSa~KP~QAlp~l~sGa~e~~~l~~~elAl~cASH----~Ge~~H~~~v~~~L~k~gL~e~~L 99 (324)
T PF06089_consen 40 PRSAAKPFQALPLLESGAAEAFGLTDEELALACASH----SGEPEHVEAVRSMLAKAGLSEEDL 99 (324)
T ss_pred hhhhccHHHHHHHHHcCchhhcCCCHHHHHHHhhcc----cChHHHHHHHHHHHHHcCCCHHHc
Confidence 6899999999999977 899999998776655 345678998999999999998863
No 38
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=50.17 E-value=1.3e+02 Score=25.49 Aligned_cols=23 Identities=35% Similarity=0.605 Sum_probs=11.4
Q ss_pred HHHHHHHHHCCCChhhHHHHHHh
Q 020213 81 VPMVECLATLGTKPYEVASAITR 103 (329)
Q Consensus 81 ~~~l~~L~~lG~~~~~~~~~l~~ 103 (329)
.+.++.|.++|+++.++.+++.+
T Consensus 148 ~e~~~aL~~LGy~~~e~~~ai~~ 170 (191)
T TIGR00084 148 DELFEALVSLGYKPQEIQQALKK 170 (191)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 34444555555555555554443
No 39
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=50.16 E-value=37 Score=26.11 Aligned_cols=24 Identities=13% Similarity=0.047 Sum_probs=13.7
Q ss_pred chHHHHHHHHHCCCChhhHHHHHH
Q 020213 79 KLVPMVECLATLGTKPYEVASAIT 102 (329)
Q Consensus 79 ~l~~~l~~L~~lG~~~~~~~~~l~ 102 (329)
.......-|+.-|++.+.+..++.
T Consensus 44 G~~~I~~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 44 GPRRIRQKLKQKGIDREIIEEALE 67 (121)
T ss_dssp -HHHHHHHHHHTT--HHHHHHHHT
T ss_pred cHHHHHHHHHHHCCChHHHHHHHH
Confidence 345555666777777777776665
No 40
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=50.06 E-value=21 Score=22.55 Aligned_cols=25 Identities=8% Similarity=0.133 Sum_probs=19.6
Q ss_pred chHHHHHHhCCCChhHHHHHHHhhh
Q 020213 10 NSVIWFLKDRGFNDRTIHDMFKRCK 34 (329)
Q Consensus 10 ~~v~~~L~~~G~s~~~i~~i~~~~p 34 (329)
+.++.-|.++|++..++.+++.+..
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 4677888899999999999888763
No 41
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=49.10 E-value=55 Score=27.48 Aligned_cols=57 Identities=16% Similarity=0.235 Sum_probs=26.3
Q ss_pred HHHHHhC-CCCCCChhHHHhhCCCcc-c-cccccchHHHHHHHHHCCCChhhHHHHHHhC
Q 020213 48 WAYLKSI-GILERKLPNVVSKCPKIL-T-LGLNEKLVPMVECLATLGTKPYEVASAITRF 104 (329)
Q Consensus 48 ~~~L~~~-G~~~~~i~~i~~~~P~lL-~-~~~~~~l~~~l~~L~~lG~~~~~~~~~l~~~ 104 (329)
...|.+. |+.++...+|+..=-.=+ . ....+...+.++-|.++|+++.++.+++.+-
T Consensus 107 ~~~L~~vpGIGkKtAeRIilELkdK~~~~~~~~~~~~ea~~AL~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 107 ESVLKKVPGIGPKSAKRIIAELSDAKTKLENVSDDKSEALAALLTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHHHhhccCCCCccHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 3455554 666665555552210000 0 0001123455556666666666666665554
No 42
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=48.84 E-value=1.6e+02 Score=24.56 Aligned_cols=24 Identities=25% Similarity=0.336 Sum_probs=14.9
Q ss_pred cchhH-HHHHHhCCChhHHHHHHHh
Q 020213 225 LSPNF-TFLKRCGFADGQIAALVAA 248 (329)
Q Consensus 225 l~~k~-~~L~~~G~s~~~v~~l~~~ 248 (329)
.+.|+ .+|..-||+.+.+..++..
T Consensus 139 ~k~Ki~r~L~~rGFs~~~i~~~l~~ 163 (174)
T COG2137 139 EKAKIQRFLLRRGFSYEVIKEALNE 163 (174)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 44444 4666778887777765543
No 43
>PRK09875 putative hydrolase; Provisional
Probab=47.18 E-value=1.1e+02 Score=27.66 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=23.1
Q ss_pred HhHHHHHHHHCCCCchhhhhhHhhCCc
Q 020213 116 LCPLLAFFQALGVPEKQLGRMILLNPR 142 (329)
Q Consensus 116 l~~~v~~L~~lG~~~~~l~~~l~~~P~ 142 (329)
+...+-.|++.|+++++|.+|+..+|.
T Consensus 262 ~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 262 LTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 455677888999999999999999995
No 44
>COG3747 Phage terminase, small subunit [DNA replication, recombination, and repair]
Probab=47.08 E-value=17 Score=29.20 Aligned_cols=101 Identities=16% Similarity=0.170 Sum_probs=49.9
Q ss_pred HHHHHHhCCCcccccchhhHhHHHHHHHHCCCC-chhhhhhHhhCCceeccCcchhHhHHHHHHhhcCCCchhhHHHHHH
Q 020213 97 VASAITRFPPILSHSVEEKLCPLLAFFQALGVP-EKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLAREGMIGKVLV 175 (329)
Q Consensus 97 ~~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~-~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~~~~~~i~~ll~ 175 (329)
+.+..-++|.-|...-.+.++..+-+|.+++.- +.|+.- +..| |..+ +.....+.-++..|+.-..+-..-++
T Consensus 33 ~~r~~pkaPdwLd~~A~~~Wrrvvp~L~e~~ll~~~D~~~-Le~Y----C~~y-siY~~av~~lkk~G~ii~~~~~g~~k 106 (160)
T COG3747 33 FGRLAPKAPDWLDPTAKKEWRRVVPFLEELKLLKPADLTL-LELY----CVAY-SIYRNAVAHLKKHGFIITNQFSGRVK 106 (160)
T ss_pred ccccCCCCccccCHHHHHHHHHHHHHHHHhccCCHHHHHH-HHHH----HHHH-HHHHHHHHHHHHcceeeeccccceec
Confidence 334444556555544444566667777766543 333322 2222 2333 24555666666666643222233356
Q ss_pred hcCcccccccccchhHHHHHHHH-hCCChhhH
Q 020213 176 KHPFIMGYSVDNRLRPTSEFLKS-VGLKELDL 206 (329)
Q Consensus 176 ~~p~ll~~~~~~~l~~~~~~l~~-~g~~~~~i 206 (329)
+||.+-.++ .....+--+.+ +|+++..=
T Consensus 107 rNPav~~~s---dA~~~l~klaSeLGltP~ar 135 (160)
T COG3747 107 RNPAVQAAS---DAIRNLLKLASELGLTPSAR 135 (160)
T ss_pred CChHHHHHH---HHHHHHHHHHHHhCCChHHH
Confidence 677655554 23334444444 77776553
No 45
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=46.15 E-value=80 Score=26.63 Aligned_cols=57 Identities=16% Similarity=0.177 Sum_probs=28.9
Q ss_pred HHHHHhC-CCCCCChhHHHhhCCCccc---cccccchHHHHHHHHHCCCChhhHHHHHHhC
Q 020213 48 WAYLKSI-GILERKLPNVVSKCPKILT---LGLNEKLVPMVECLATLGTKPYEVASAITRF 104 (329)
Q Consensus 48 ~~~L~~~-G~~~~~i~~i~~~~P~lL~---~~~~~~l~~~l~~L~~lG~~~~~~~~~l~~~ 104 (329)
+..|.+. |+.++...+|+..=-.=+. ........+.++-|.++|+++.++.+++.+-
T Consensus 107 ~~~L~~vpGIGkKtAerIilELkdK~~~~~~~~~~~~~e~~~AL~~LGy~~~ea~~av~~~ 167 (188)
T PRK14606 107 VEGLSKLPGISKKTAERIVMELKDEFESAGIKDMRIYHESLEALVSLGYPEKQAREAVKHV 167 (188)
T ss_pred HHHHhhCCCCCHHHHHHHHHHHHHhhccccCCCcccHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 4555555 6766666665522111000 0001134556666667777777776666554
No 46
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=45.07 E-value=1e+02 Score=21.42 Aligned_cols=20 Identities=30% Similarity=0.679 Sum_probs=10.8
Q ss_pred HHHHHHhCCCChhHHHHHHH
Q 020213 12 VIWFLKDRGFNDRTIHDMFK 31 (329)
Q Consensus 12 v~~~L~~~G~s~~~i~~i~~ 31 (329)
+++.|.+..+|+++|..++.
T Consensus 4 Iia~LKehnvsd~qi~elFq 23 (82)
T PF11212_consen 4 IIAILKEHNVSDEQINELFQ 23 (82)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 44555555555555555554
No 47
>PRK14135 recX recombination regulator RecX; Provisional
Probab=43.94 E-value=2.2e+02 Score=25.16 Aligned_cols=109 Identities=9% Similarity=0.081 Sum_probs=52.7
Q ss_pred CCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHHHHHHCCC-ChhhH
Q 020213 19 RGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVECLATLGT-KPYEV 97 (329)
Q Consensus 19 ~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~lG~-~~~~~ 97 (329)
.-++.+++..+...... ..-....+.+|....-+..++.+-+.+. ..+ +..+..+++.|...|. ++...
T Consensus 40 ~~l~~~~~~~i~~~~~~-----~~a~~~Al~~L~~r~~s~~el~~kL~~k----g~~-~~~Ie~vl~~l~~~~~ldD~~~ 109 (263)
T PRK14135 40 KELDEEDLEEIQYADQV-----SKGKNLALYYLSYQMRTEKEVRDYLKKH----EIS-EEIISEVIDKLKEEKYIDDKEY 109 (263)
T ss_pred CcCCHHHHHHHHHHHHH-----HHHHHHHHHHhhhccccHHHHHHHHHHC----CCC-HHHHHHHHHHHHHcCCCCHHHH
Confidence 34556666666543210 1123333555555455555555544443 222 2467777788877764 44344
Q ss_pred HHHHHhCCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhC
Q 020213 98 ASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLN 140 (329)
Q Consensus 98 ~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~ 140 (329)
+....+. .+.... ..-.....-|..-|++.+.+..++...
T Consensus 110 a~~~~~~--~~~~~~-~g~~~I~~kL~~kGi~~~~Ie~~l~~l 149 (263)
T PRK14135 110 AESYVRT--NINTGD-KGPRVIKQKLLQKGIEDEIIEEALSEY 149 (263)
T ss_pred HHHHHHH--HHhccc-cchHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 4333221 111110 011223455667788877777666543
No 48
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=43.78 E-value=20 Score=27.66 Aligned_cols=59 Identities=12% Similarity=0.093 Sum_probs=42.4
Q ss_pred CCcchhhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHHHHHHCCCChhhHHHHHH
Q 020213 38 GVEKDRAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVECLATLGTKPYEVASAIT 102 (329)
Q Consensus 38 ~~~~~~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~lG~~~~~~~~~l~ 102 (329)
..+++.+....+.|...|+.+.++..++.-.|.=. ..+...+.-+.+- ++.+++.+++.
T Consensus 51 ~~~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~s~-----~E~~~lI~sl~~r-~~ee~l~~iL~ 109 (118)
T smart00657 51 FKNREIVRAVRTLLKSKKLHKFEIAQLGNLRPETA-----EEAQLLIPSLEER-IDEEELEELLD 109 (118)
T ss_pred CCCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCCCH-----HHHHHHhhhhhcc-CCHHHHHHHHH
Confidence 45677888888889889999999999998877542 2455555555433 67777776654
No 49
>TIGR01616 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in Pfam model pfam03960.
Probab=43.19 E-value=49 Score=25.90 Aligned_cols=48 Identities=15% Similarity=0.200 Sum_probs=33.7
Q ss_pred CCChhhHHHHHhhcCceeeeccccccchhHHHHHHhCCChhHHHHHHHhCchh
Q 020213 200 GLKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAALVAAYPPI 252 (329)
Q Consensus 200 g~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~~~G~s~~~v~~l~~~~P~i 252 (329)
.++.+++..++..+|.++-+.+-. -..+ ...||+.+++.+++...|..
T Consensus 72 ~ls~~e~i~lm~~~P~LIKRPIi~-~~~~----~~iGf~~e~~~~~l~~~~~~ 119 (126)
T TIGR01616 72 SIDEASALALMVSDPLLIRRPLMD-LGGI----RCAGFDREPVLSWIGLQTQE 119 (126)
T ss_pred cCCHHHHHHHHHhCcCeEeCCEEE-ECCE----EEEcCCHHHHHHHhCCCCCC
Confidence 356688889999999999886532 1222 24699999988877666543
No 50
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=43.15 E-value=66 Score=23.22 Aligned_cols=41 Identities=10% Similarity=0.123 Sum_probs=23.1
Q ss_pred chHHHHHHhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHh
Q 020213 10 NSVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKS 53 (329)
Q Consensus 10 ~~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~ 53 (329)
.....+-+.+|+|+.+|..+-..+|. --.+...+.+..++.
T Consensus 14 ~~Wk~laR~LGlse~~Id~i~~~~~~---~~~eq~~~mL~~W~~ 54 (86)
T cd08306 14 RDWRKLARKLGLSETKIESIEEAHPR---NLREQVRQSLREWKK 54 (86)
T ss_pred hhHHHHHHHcCCCHHHHHHHHHHCCC---CHHHHHHHHHHHHHH
Confidence 34555666677777777777776662 112344445544443
No 51
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=42.79 E-value=17 Score=28.38 Aligned_cols=32 Identities=9% Similarity=0.136 Sum_probs=14.5
Q ss_pred hcccCCcchhhHHHHHHHHhCCCCCCChhHHH
Q 020213 34 KRLQGVEKDRAADNWAYLKSIGILERKLPNVV 65 (329)
Q Consensus 34 p~ll~~~~~~l~~~~~~L~~~G~~~~~i~~i~ 65 (329)
|.-+..+++++.+-+--|.+.|++++||+-++
T Consensus 23 PtWlK~~~ddvkeqI~K~akKGltpsqIGviL 54 (151)
T KOG0400|consen 23 PTWLKLTADDVKEQIYKLAKKGLTPSQIGVIL 54 (151)
T ss_pred cHHHhcCHHHHHHHHHHHHHcCCChhHceeee
Confidence 33344444444444444444455555444433
No 52
>PHA01351 putative minor structural protein
Probab=42.31 E-value=2.9e+02 Score=28.33 Aligned_cols=47 Identities=11% Similarity=0.006 Sum_probs=29.9
Q ss_pred CcchHHHHHHhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCC
Q 020213 8 NGNSVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGI 56 (329)
Q Consensus 8 ~~~~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~ 56 (329)
|-+.+..-|++.|.+++++.-+...+=. .+-...+..-.-.+.++|.
T Consensus 690 nt~~~~~ELKKL~IpdSqInil~t~yy~--~~~~~kls~~~~sl~~~g~ 736 (1070)
T PHA01351 690 DQQQLSGELKKIHKDKTALELYITKFYY--EYIYPKISNYHLQLARHGI 736 (1070)
T ss_pred chHHHHHHHHHcCCCHHHHHHHHHHHHH--HHHHHHHHHHHHHHHhcCc
Confidence 3455677788999999999887765421 1112345555555666776
No 53
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=40.73 E-value=1e+02 Score=22.19 Aligned_cols=23 Identities=17% Similarity=0.054 Sum_probs=14.3
Q ss_pred HHHHHHhCCCChhHHHHHHHhhh
Q 020213 12 VIWFLKDRGFNDRTIHDMFKRCK 34 (329)
Q Consensus 12 v~~~L~~~G~s~~~i~~i~~~~p 34 (329)
.-.+.+.+|+|..+|..|-..+|
T Consensus 16 W~~Lar~Lgls~~~I~~i~~~~p 38 (83)
T cd08319 16 WEQVLLDLGLSQTDIYRCKENHP 38 (83)
T ss_pred HHHHHHHcCCCHHHHHHHHHhCC
Confidence 33455666666666666666665
No 54
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=39.20 E-value=92 Score=22.03 Aligned_cols=40 Identities=15% Similarity=0.182 Sum_probs=24.2
Q ss_pred hHHHHHHhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhC
Q 020213 11 SVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSI 54 (329)
Q Consensus 11 ~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~ 54 (329)
..-.+.+.+|+++.+|..|-..+|. ..+...+.+.-++..
T Consensus 13 ~Wk~laR~LGls~~~I~~ie~~~~~----~~eq~~~mL~~W~~k 52 (79)
T cd08784 13 QHKRFFRKLGLSDNEIKVAELDNPQ----HRDRVYELLRIWRNK 52 (79)
T ss_pred HHHHHHHHcCCCHHHHHHHHHcCCc----hHHHHHHHHHHHHhc
Confidence 3556667777777777777777764 124445555555443
No 55
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=38.84 E-value=8.5 Score=25.90 Aligned_cols=29 Identities=7% Similarity=0.109 Sum_probs=13.0
Q ss_pred cCCcchhhHHHHHHHHhCCCCCCChhHHH
Q 020213 37 QGVEKDRAADNWAYLKSIGILERKLPNVV 65 (329)
Q Consensus 37 l~~~~~~l~~~~~~L~~~G~~~~~i~~i~ 65 (329)
+..+++++++.+--|...|+++++|+-++
T Consensus 26 ~~~~~~eVe~~I~klakkG~tpSqIG~iL 54 (60)
T PF08069_consen 26 LKYSPEEVEELIVKLAKKGLTPSQIGVIL 54 (60)
T ss_dssp --S-HHHHHHHHHHHCCTTHCHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHHcCCCHHHhhhhh
Confidence 34444455555544444455555554444
No 56
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=38.16 E-value=45 Score=20.42 Aligned_cols=25 Identities=20% Similarity=0.259 Sum_probs=13.8
Q ss_pred hHHHHH-HhCCChhHHHHHHHhCchh
Q 020213 228 NFTFLK-RCGFADGQIAALVAAYPPI 252 (329)
Q Consensus 228 k~~~L~-~~G~s~~~v~~l~~~~P~i 252 (329)
+...|. ++|++.....+++..||..
T Consensus 11 n~~~L~~~f~ip~~vAk~IV~~C~~C 36 (40)
T PF02022_consen 11 NAKALRHKFGIPRLVAKQIVNQCPKC 36 (40)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHSCCH
T ss_pred CHHHHHHHHccCHHHHHHHHHHCHHH
Confidence 445555 6666666666666666654
No 57
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=36.33 E-value=1.3e+02 Score=21.58 Aligned_cols=25 Identities=16% Similarity=0.206 Sum_probs=16.0
Q ss_pred chHHHHHHhCCCChhHHHHHHHhhh
Q 020213 10 NSVIWFLKDRGFNDRTIHDMFKRCK 34 (329)
Q Consensus 10 ~~v~~~L~~~G~s~~~i~~i~~~~p 34 (329)
..+.+|.+.+|+|+.+|..|-..+|
T Consensus 12 ~~wk~~~R~LGlse~~Id~ie~~~~ 36 (80)
T cd08313 12 RRWKEFVRRLGLSDNEIERVELDHR 36 (80)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhCC
Confidence 3455666667777777766666554
No 58
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=36.10 E-value=1.3e+02 Score=21.53 Aligned_cols=22 Identities=14% Similarity=0.243 Sum_probs=11.6
Q ss_pred HHHHHhCCCChhHHHHHHHhhh
Q 020213 13 IWFLKDRGFNDRTIHDMFKRCK 34 (329)
Q Consensus 13 ~~~L~~~G~s~~~i~~i~~~~p 34 (329)
..+-+.+||+..+|..+-..+|
T Consensus 19 k~LAr~Lg~se~dI~~i~~~~~ 40 (84)
T cd08804 19 TELARELDFTEEQIHQIRIENP 40 (84)
T ss_pred HHHHHHcCCCHHHHHHHHHHCc
Confidence 3444555555555555555544
No 59
>cd03032 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif.
Probab=36.03 E-value=1e+02 Score=23.43 Aligned_cols=40 Identities=18% Similarity=0.268 Sum_probs=26.5
Q ss_pred CChhhHHHHHhhcCceeeeccccccchhHHHHHHhCCChhHHHHH
Q 020213 201 LKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAAL 245 (329)
Q Consensus 201 ~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~~~G~s~~~v~~l 245 (329)
++.+++..++..+|.++-+.+-. -..+ ...|++.+++..+
T Consensus 74 ls~~e~i~~l~~~p~LikRPii~-~~~~----~~vG~~~e~~~~~ 113 (115)
T cd03032 74 LSLSELIRLISEHPSLLRRPIII-DEKR----LQIGYNEDEIRQF 113 (115)
T ss_pred CCHHHHHHHHHhChhheeCCEEE-eCCE----EEeCCCHHHHHHh
Confidence 56677888899999988776532 1111 2468887776644
No 60
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=35.21 E-value=44 Score=22.37 Aligned_cols=26 Identities=15% Similarity=0.340 Sum_probs=18.9
Q ss_pred hHHHHHHhhcCCCchhhHHHHHHhcC
Q 020213 153 TETVDFLTSLGLAREGMIGKVLVKHP 178 (329)
Q Consensus 153 ~~~~~~l~~~G~~~~~~i~~ll~~~p 178 (329)
.+.+..|++++++|++.+.+++...|
T Consensus 22 ~eIya~L~ecnMDpnea~qrLL~qD~ 47 (60)
T PF06972_consen 22 EEIYAMLKECNMDPNEAVQRLLSQDP 47 (60)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHhcCc
Confidence 45667777888888777777777655
No 61
>PRK14136 recX recombination regulator RecX; Provisional
Probab=34.99 E-value=1.6e+02 Score=27.00 Aligned_cols=27 Identities=11% Similarity=0.213 Sum_probs=21.7
Q ss_pred HhHHHHHHHHCCCCchhhhhhHhhCCc
Q 020213 116 LCPLLAFFQALGVPEKQLGRMILLNPR 142 (329)
Q Consensus 116 l~~~v~~L~~lG~~~~~l~~~l~~~P~ 142 (329)
....+.||..-|++.+.|.++|..+-.
T Consensus 278 k~K~iRfL~rRGFS~D~I~~vLk~~~d 304 (309)
T PRK14136 278 RAKQARFLAARGFSSATIVKLLKVGDD 304 (309)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHhchh
Confidence 345689999999999999998876543
No 62
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=34.08 E-value=44 Score=29.89 Aligned_cols=154 Identities=21% Similarity=0.377 Sum_probs=94.5
Q ss_pred ccCcchhHhHHHHHHh-hcCCCchhhHHHHHHhcCcccccccccchhHHHHHHHH-hCCChhhHHHHHhhcCceeeeccc
Q 020213 145 SYSIESKLTETVDFLT-SLGLAREGMIGKVLVKHPFIMGYSVDNRLRPTSEFLKS-VGLKELDLQVVAVKFPEVLCRDVN 222 (329)
Q Consensus 145 ~~~~~~~l~~~~~~l~-~~G~~~~~~i~~ll~~~p~ll~~~~~~~l~~~~~~l~~-~g~~~~~i~~~i~~~P~il~~s~~ 222 (329)
..+. -.+..++.|.- +.|+=|.-.+..=|.--|.++.-+- ..++.+++-|.. +|+++++.. .++|.=|+-.
T Consensus 67 ~~d~-~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~k-~~i~~r~~ELl~lvgL~p~~~~---~RyP~eLSGG-- 139 (309)
T COG1125 67 DLDP-VELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWDK-ERIKKRADELLDLVGLDPSEYA---DRYPHELSGG-- 139 (309)
T ss_pred cCCH-HHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCCH-HHHHHHHHHHHHHhCCCHHHHh---hcCchhcCcc--
Confidence 4443 36888999884 7887776667777888899999885 588999888887 999988754 5889877553
Q ss_pred cccchhHHHHHHhCCChhHHHHHHHhCchhhccc-----c----cchhhhHHHHHHHHhCCChhhhhcCCceeecCcchh
Q 020213 223 KILSPNFTFLKRCGFADGQIAALVAAYPPILIKS-----I----KNSLEPRIKFLVEVMGRQIDEVADYPDFFRHGLKKR 293 (329)
Q Consensus 223 ~~l~~k~~~L~~~G~s~~~v~~l~~~~P~iL~~s-----~----~~~i~~k~~fL~~~~g~~~~~i~~~P~~l~~sl~~~ 293 (329)
-++|+...+ .+...|.++..+ + .++++.-+.-+.+++| +.--+.++.++.-
T Consensus 140 --QQQRVGv~R-----------ALAadP~ilLMDEPFgALDpI~R~~lQ~e~~~lq~~l~-------kTivfVTHDidEA 199 (309)
T COG1125 140 --QQQRVGVAR-----------ALAADPPILLMDEPFGALDPITRKQLQEEIKELQKELG-------KTIVFVTHDIDEA 199 (309)
T ss_pred --hhhHHHHHH-----------HHhcCCCeEeecCCccccChhhHHHHHHHHHHHHHHhC-------CEEEEEecCHHHH
Confidence 255555444 344667777533 1 1333333334444444 2334555665432
Q ss_pred h--HHHHHHHHHcCC---CCChhhhhcccHHHHHHhhc
Q 020213 294 L--ELRHRLLKQRNI---YCSLSEMLDCNAKKFLIKFG 326 (329)
Q Consensus 294 i--~~R~~~l~~~gl---~~~l~~~l~~s~~~F~~~~~ 326 (329)
+ ..|.-.+. .|- ...-..++.-+..+|++.|+
T Consensus 200 ~kLadri~vm~-~G~i~Q~~~P~~il~~Pan~FV~~f~ 236 (309)
T COG1125 200 LKLADRIAVMD-AGEIVQYDTPDEILANPANDFVEDFF 236 (309)
T ss_pred HhhhceEEEec-CCeEEEeCCHHHHHhCccHHHHHHHh
Confidence 2 22332333 232 34555677777777777764
No 63
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=34.06 E-value=90 Score=25.68 Aligned_cols=49 Identities=10% Similarity=0.295 Sum_probs=33.9
Q ss_pred hHhHHHHHHHHCCCCchhhhhhHhhCCceeccCcchhHhHHHHHHhhcCCC
Q 020213 115 KLCPLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLA 165 (329)
Q Consensus 115 ~l~~~v~~L~~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~~ 165 (329)
+++..+++|.+..-. .-.++-+...|-+.+.+ ++.+...++.+++.|+|
T Consensus 49 t~k~Il~aL~e~e~~-~ita~~iM~spvv~v~p-dDsi~~vv~lM~~~g~S 97 (187)
T COG3620 49 TVKRILEALEEAEKT-RITAKTIMHSPVVSVSP-DDSISDVVNLMRDKGIS 97 (187)
T ss_pred HHHHHHHHHHHhhcc-eEeHhhhccCCeeEECc-hhhHHHHHHHHHHcCCc
Confidence 456667777654332 22456677888887665 56799999999999886
No 64
>PRK01655 spxA transcriptional regulator Spx; Reviewed
Probab=33.44 E-value=1.4e+02 Score=23.32 Aligned_cols=41 Identities=22% Similarity=0.291 Sum_probs=28.7
Q ss_pred CChhhHHHHHhhcCceeeeccccccchhHHHHHHhCCChhHHHHHH
Q 020213 201 LKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAALV 246 (329)
Q Consensus 201 ~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~~~G~s~~~v~~l~ 246 (329)
++.+++..++..+|.++-..+-. -..+ ...|++.+++..++
T Consensus 74 ls~~e~i~ll~~~p~LikRPIi~-~~~~----~~vG~~~e~~~~~l 114 (131)
T PRK01655 74 LSLQDLIKLISDNPGLLRRPIII-DEKR----LQVGYNEDEIRAFL 114 (131)
T ss_pred CCHHHHHHHHHhCcceEeCCEEE-ECCE----EEecCCHHHHHHHh
Confidence 45678889999999998876532 1211 24799988887655
No 65
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 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. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=33.23 E-value=80 Score=19.86 Aligned_cols=42 Identities=10% Similarity=0.145 Sum_probs=28.2
Q ss_pred HHHHhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCCC
Q 020213 14 WFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGILE 58 (329)
Q Consensus 14 ~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~~ 58 (329)
+.-+..|+|.+.+.+++...| ..+++.-+...+..+.+|+.+
T Consensus 4 dIA~~agvS~~TVSr~ln~~~---~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 4 DIAREAGVSKSTVSRVLNGPP---RVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp HHHHHHTSSHHHHHHHHTTCS---SSTHHHHHHHHHHHHHHTB-S
T ss_pred HHHHHHCcCHHHHHHHHhCCC---CCCHHHHHHHHHHHHHHCCCC
Confidence 445667889888888888765 345555566666667777643
No 66
>PHA02591 hypothetical protein; Provisional
Probab=33.10 E-value=46 Score=23.64 Aligned_cols=28 Identities=21% Similarity=0.328 Sum_probs=22.0
Q ss_pred ccccCCcchHHHHHHhCCCChhHHHHHH
Q 020213 3 ISTSQNGNSVIWFLKDRGFNDRTIHDMF 30 (329)
Q Consensus 3 ~~~~~~~~~v~~~L~~~G~s~~~i~~i~ 30 (329)
+-|.++..++..-|.+.|++.++|++.+
T Consensus 42 i~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 42 VESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred EeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 3466777778888888999999998765
No 67
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=32.68 E-value=79 Score=23.77 Aligned_cols=23 Identities=17% Similarity=0.413 Sum_probs=18.4
Q ss_pred hCCChhHHHHHHHhCchhhcccc
Q 020213 235 CGFADGQIAALVAAYPPILIKSI 257 (329)
Q Consensus 235 ~G~s~~~v~~l~~~~P~iL~~s~ 257 (329)
-.++.+++.+++.++|.++...+
T Consensus 69 ~~~s~~e~i~~l~~~p~LikRPI 91 (110)
T PF03960_consen 69 DDLSDEELIELLLENPKLIKRPI 91 (110)
T ss_dssp TTSBHHHHHHHHHHSGGGB-SSE
T ss_pred hhhhhHHHHHHHHhChhheeCCE
Confidence 34789999999999999987654
No 68
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=32.15 E-value=40 Score=25.43 Aligned_cols=22 Identities=32% Similarity=0.597 Sum_probs=12.6
Q ss_pred CCCchhhhhhHhhCCceeccCc
Q 020213 127 GVPEKQLGRMILLNPRLISYSI 148 (329)
Q Consensus 127 G~~~~~l~~~l~~~P~il~~~~ 148 (329)
.++.+++..++..+|.++..++
T Consensus 70 ~~s~~e~i~~l~~~p~LikRPI 91 (110)
T PF03960_consen 70 DLSDEELIELLLENPKLIKRPI 91 (110)
T ss_dssp TSBHHHHHHHHHHSGGGB-SSE
T ss_pred hhhhHHHHHHHHhChhheeCCE
Confidence 3555666666666666665554
No 69
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=31.71 E-value=64 Score=26.52 Aligned_cols=23 Identities=9% Similarity=0.059 Sum_probs=14.1
Q ss_pred CcchHHHHHHhCCCChhHHHHHH
Q 020213 8 NGNSVIWFLKDRGFNDRTIHDMF 30 (329)
Q Consensus 8 ~~~~v~~~L~~~G~s~~~i~~i~ 30 (329)
+|+.+..-=.++|++.+++++..
T Consensus 6 ~pedlrk~Rk~LGitQ~dLA~~a 28 (187)
T COG3620 6 TPEDLRKRRKELGITQKDLARRA 28 (187)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHc
Confidence 35555555556777777776543
No 70
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=31.17 E-value=26 Score=27.36 Aligned_cols=63 Identities=22% Similarity=0.169 Sum_probs=29.0
Q ss_pred CCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHHHHHHCCCChhhHH
Q 020213 19 RGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVECLATLGTKPYEVA 98 (329)
Q Consensus 19 ~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~lG~~~~~~~ 98 (329)
-|+|-++|..+-.-+|++|.. .+++-..-..|.+. ....-.+.+.-.+.+|+|+..|+
T Consensus 22 rG~sveeI~e~T~ID~wFL~~-i~~Iv~~e~~L~~~---------------------~~~~~~~~L~~aK~~GFsD~~IA 79 (123)
T PF02787_consen 22 RGYSVEEIHELTKIDPWFLEQ-IKNIVDMEKELKEY---------------------LNELDPELLRKAKRLGFSDRQIA 79 (123)
T ss_dssp TTB-HHHHHHHH---HHHHHH-HHHHHHHHHHHHHH---------------------GGG--HHHHHHHHHTT--HHHHH
T ss_pred cCCCHHHHHHHHCccHHHHHH-HHHHHHHHHHHHHh---------------------hccchHHHHHHHHHcCCCHHHHH
Confidence 488888888877777776432 11222111222211 01112335555677888888888
Q ss_pred HHHHh
Q 020213 99 SAITR 103 (329)
Q Consensus 99 ~~l~~ 103 (329)
.+...
T Consensus 80 ~l~~~ 84 (123)
T PF02787_consen 80 RLWGV 84 (123)
T ss_dssp HHHTS
T ss_pred hccCC
Confidence 87655
No 71
>PRK14136 recX recombination regulator RecX; Provisional
Probab=30.80 E-value=4.2e+02 Score=24.26 Aligned_cols=136 Identities=15% Similarity=0.178 Sum_probs=81.2
Q ss_pred HHHHHHhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCC-CCChhHHHhhCCCccccccccchHHHHHHHHHC
Q 020213 12 VIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGIL-ERKLPNVVSKCPKILTLGLNEKLVPMVECLATL 90 (329)
Q Consensus 12 v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~-~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~l 90 (329)
.+++|..---+..++.+-+.+. ..+++.+...++.|...|+- +....+.+.+. .. . ..-..-+..-|+.-
T Consensus 168 AL~lLSrReRSe~ELr~KL~kk----G~~ee~IE~VIerLke~gYLDDeRFAesyVr~-R~---~-kkGp~rIrqELrQK 238 (309)
T PRK14136 168 ALGYLSRREYSRAELARKLAPY----ADESDSVEPLLDALEREGWLSDARFAESLVHR-RA---S-RVGSARIVSELKRH 238 (309)
T ss_pred HHHHhhcccccHHHHHHHHHHc----CCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHH-Hh---h-chhHHHHHHHHHHc
Confidence 4556655566777777666654 45667888899999888664 45555555532 11 1 12344556778899
Q ss_pred CCChhhHHHHHHhCCCcccccchhhHhHHHHHHH-HCCCCchhhhhhHhhCCceeccCcchhHhHHHHHHhhcCCCchhh
Q 020213 91 GTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQ-ALGVPEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLAREGM 169 (329)
Q Consensus 91 G~~~~~~~~~l~~~P~ll~~~~e~~l~~~v~~L~-~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~~~~~~ 169 (329)
|++.+.|..++... . ++.+......++ .++ ..|. .. ......+.||..-||+. +.
T Consensus 239 GId~eLIEqALeei------e-EDE~E~A~~L~eKK~~-----------~~~~----d~-kek~K~iRfL~rRGFS~-D~ 294 (309)
T PRK14136 239 AVGDALVESVGAQL------R-ETEFERAQAVWRKKFG-----------ALPQ----TP-AERAKQARFLAARGFSS-AT 294 (309)
T ss_pred CCCHHHHHHHHHhc------c-HhHHHHHHHHHHHHhc-----------ccCc----CH-HHHHHHHHHHHHCCCCH-HH
Confidence 99999888887743 1 122322223332 121 1111 11 22445589999999985 57
Q ss_pred HHHHHHhcCcc
Q 020213 170 IGKVLVKHPFI 180 (329)
Q Consensus 170 i~~ll~~~p~l 180 (329)
|..+|..+-..
T Consensus 295 I~~vLk~~~de 305 (309)
T PRK14136 295 IVKLLKVGDDE 305 (309)
T ss_pred HHHHHHhchhc
Confidence 88888765543
No 72
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=30.53 E-value=1.8e+02 Score=20.94 Aligned_cols=22 Identities=9% Similarity=0.060 Sum_probs=11.8
Q ss_pred HHHHHhCCCChhHHHHHHHhhh
Q 020213 13 IWFLKDRGFNDRTIHDMFKRCK 34 (329)
Q Consensus 13 ~~~L~~~G~s~~~i~~i~~~~p 34 (329)
-.+.+.+|++.++|..|-..+|
T Consensus 19 ~~Lar~L~vs~~dI~~I~~e~p 40 (84)
T cd08805 19 AELARELQFSVEDINRIRVENP 40 (84)
T ss_pred HHHHHHcCCCHHHHHHHHHhCC
Confidence 3344555555555555555555
No 73
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=30.25 E-value=1.9e+02 Score=20.85 Aligned_cols=40 Identities=5% Similarity=-0.121 Sum_probs=20.9
Q ss_pred HHHHHHhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhC
Q 020213 12 VIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSI 54 (329)
Q Consensus 12 v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~ 54 (329)
...+.+.+||+..+|..+-..+|. ...+.....+..+++.
T Consensus 18 W~~LA~eLg~s~~dI~~i~~e~p~---~~~~q~~~lL~~W~~r 57 (84)
T cd08803 18 WTELARELNFSVDEINQIRVENPN---SLIAQSFMLLKKWVTR 57 (84)
T ss_pred HHHHHHHcCCCHHHHHHHHHhCCC---CHHHHHHHHHHHHHHh
Confidence 344556677777777666555552 1123344444445444
No 74
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.20 E-value=1.5e+02 Score=25.09 Aligned_cols=19 Identities=21% Similarity=0.305 Sum_probs=9.0
Q ss_pred HHHHHHHCCCCchhhhhhH
Q 020213 119 LLAFFQALGVPEKQLGRMI 137 (329)
Q Consensus 119 ~v~~L~~lG~~~~~l~~~l 137 (329)
.++.|..+|++++++.+.+
T Consensus 152 ~~~aL~~LGy~~~ea~~ai 170 (195)
T PRK14604 152 LSEILISLGYSAAEAAAAI 170 (195)
T ss_pred HHHHHHHcCCCHHHHHHHH
Confidence 3444445555554444444
No 75
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=29.91 E-value=28 Score=26.64 Aligned_cols=31 Identities=16% Similarity=0.289 Sum_probs=20.6
Q ss_pred cchhhHHHHHHHHhCCCCCCChhHHHhhCCC
Q 020213 40 EKDRAADNWAYLKSIGILERKLPNVVSKCPK 70 (329)
Q Consensus 40 ~~~~l~~~~~~L~~~G~~~~~i~~i~~~~P~ 70 (329)
+++.+...++.|..+|+++.++.+|+.-.|.
T Consensus 55 ~~e~~~~l~~~L~~~~L~~~E~~qi~Nl~P~ 85 (117)
T PF03874_consen 55 NPESIKELREELKKFGLTEFEILQIINLRPT 85 (117)
T ss_dssp SHHHHHHHHHHHTTSTS-HHHHHHHHHH--S
T ss_pred CHHHHHHHHHHHhcccCCHHHHHHHhcCCCC
Confidence 3566777777777778887788888877774
No 76
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=29.88 E-value=3.3e+02 Score=22.68 Aligned_cols=83 Identities=8% Similarity=0.101 Sum_probs=50.6
Q ss_pred HHHHHhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCC-CCCChhHHHhhCCCccccccccchHHHHHHHHHCC
Q 020213 13 IWFLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGI-LERKLPNVVSKCPKILTLGLNEKLVPMVECLATLG 91 (329)
Q Consensus 13 ~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~-~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~lG 91 (329)
+.+|.----|..++..-+..+ ..+++.+++++++|...|. ++...+....+.-.--. ........-|...|
T Consensus 27 l~~Ls~R~rse~ELr~kL~k~----~~~~~~Ie~Vi~~l~~~~~ldD~~fAe~~i~~r~~~g----~G~~rl~qeL~qkG 98 (174)
T COG2137 27 LRLLSRRDRSEKELRRKLAKK----EFSEEIIEEVIDRLAEEGYLDDTRFAEAYIRSRSRKG----KGPARLKQELKQKG 98 (174)
T ss_pred HHHHHHHHHHHHHHHHHHHhc----cCCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhcc----cChHHHHHHHHHcC
Confidence 344444444666666666555 2445568888888888865 44455554433311111 23455667788899
Q ss_pred CChhhHHHHHHh
Q 020213 92 TKPYEVASAITR 103 (329)
Q Consensus 92 ~~~~~~~~~l~~ 103 (329)
++++.+..++..
T Consensus 99 i~~~~Ie~aL~~ 110 (174)
T COG2137 99 IDDEIIEEALEL 110 (174)
T ss_pred CCHHHHHHHHhc
Confidence 999888887764
No 77
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=29.46 E-value=1.6e+02 Score=23.19 Aligned_cols=41 Identities=15% Similarity=0.263 Sum_probs=27.6
Q ss_pred CChhhHHHHHhhcCceeeeccccccchhHHHHHHhCCChhHHHHHH
Q 020213 201 LKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAALV 246 (329)
Q Consensus 201 ~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~~~G~s~~~v~~l~ 246 (329)
++.+++..++..+|.++-..+- +..+- ...|++.+++..++
T Consensus 74 ls~~e~i~ll~~~P~LikRPIv--~~~~~---~~iG~~~e~~~~~l 114 (132)
T PRK13344 74 LSVNEVIDLIQENPRILKSPIL--IDDKR---LQVGYKEDDIRAFL 114 (132)
T ss_pred CCHHHHHHHHHhCccceeCcEE--EeCCE---EEeCCCHHHHHHHc
Confidence 4557788888999998877643 12110 24788888877665
No 78
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=29.15 E-value=1.5e+02 Score=24.94 Aligned_cols=10 Identities=50% Similarity=0.992 Sum_probs=5.9
Q ss_pred HHHHhCCCCC
Q 020213 49 AYLKSIGILE 58 (329)
Q Consensus 49 ~~L~~~G~~~ 58 (329)
+.++..|+..
T Consensus 71 ~~ir~~G~~~ 80 (191)
T TIGR01083 71 EYIKSIGLYR 80 (191)
T ss_pred HHHHhcCChH
Confidence 4456667754
No 79
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=28.80 E-value=1.6e+02 Score=24.88 Aligned_cols=41 Identities=27% Similarity=0.250 Sum_probs=23.6
Q ss_pred HhHHHHHHhhcCCCchhhHHHHHHhcCcccccccccchhHHHH
Q 020213 152 LTETVDFLTSLGLAREGMIGKVLVKHPFIMGYSVDNRLRPTSE 194 (329)
Q Consensus 152 l~~~~~~l~~~G~~~~~~i~~ll~~~p~ll~~~~~~~l~~~~~ 194 (329)
..+.+.+|.++|+++ .++.+++.....- ..+.++-++..+.
T Consensus 149 ~~ev~~aL~~LG~~~-~~a~~~~~~~~~~-~~~~~~~i~~aL~ 189 (192)
T PRK00116 149 LEEAVSALVALGYKP-KEASKAVAKILKE-AASVEELIREALK 189 (192)
T ss_pred HHHHHHHHHHcCCCH-HHHHHHHHHHhcc-CCCHHHHHHHHHH
Confidence 566777777777774 4677766665321 1333445555444
No 80
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=28.42 E-value=1.7e+02 Score=28.26 Aligned_cols=140 Identities=14% Similarity=0.213 Sum_probs=0.0
Q ss_pred HHHHHHHHHCCCChhhHHHHHHhCCCcccccchhhHhHHHHHHHHCCCCchhhh-hhHhhCCceeccCcchh-------H
Q 020213 81 VPMVECLATLGTKPYEVASAITRFPPILSHSVEEKLCPLLAFFQALGVPEKQLG-RMILLNPRLISYSIESK-------L 152 (329)
Q Consensus 81 ~~~l~~L~~lG~~~~~~~~~l~~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~-~~l~~~P~il~~~~~~~-------l 152 (329)
...+..+.++|+.+++.+-.++.| .+++...+.|+.+---.-++.+ +-....-.++....-.+ .
T Consensus 304 d~~lsllv~mGfeesdaRlaLRsc--------~g~Vd~AvqfI~erre~laq~R~k~~a~Ere~~~r~k~~n~~~~~wvn 375 (568)
T KOG2561|consen 304 DETLSLLVGMGFEESDARLALRSC--------NGDVDSAVQFIIERREKLAQKREKDLAREREILERKKYGNTPMKKWVN 375 (568)
T ss_pred chHHHHHHHcCCCchHHHHHHHhc--------cccHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCcccccC
Q ss_pred hHHHHHHhhcCCCchhhHHHHHHhcCcccccccccchhHHHHHHHH--hCCChhhHHHHHhhcCceeeeccccccchhHH
Q 020213 153 TETVDFLTSLGLAREGMIGKVLVKHPFIMGYSVDNRLRPTSEFLKS--VGLKELDLQVVAVKFPEVLCRDVNKILSPNFT 230 (329)
Q Consensus 153 ~~~~~~l~~~G~~~~~~i~~ll~~~p~ll~~~~~~~l~~~~~~l~~--~g~~~~~i~~~i~~~P~il~~s~~~~l~~k~~ 230 (329)
...+.+|.++|+++. -...+++++ ++.+...++.+.. -.+..+. |. .|+..-..++.
T Consensus 376 ~rs~~rL~~mGyer~-la~eaL~r~--------~Ndi~~aldllq~esdel~~n~--------~~----~p~~vd~~~la 434 (568)
T KOG2561|consen 376 PRSLERLVSMGYERE-LAAEALRRN--------ENDIQKALDLLQDESDELESNK--------PK----RPEQVDGISLA 434 (568)
T ss_pred HHHHHHHHhcchHhH-HHHHHHHhc--------cCcHHHHHHhcCCcchhhhccC--------CC----CCcccchhhHH
Q ss_pred HHHHhCCChhHHHHHHHhC
Q 020213 231 FLKRCGFADGQIAALVAAY 249 (329)
Q Consensus 231 ~L~~~G~s~~~v~~l~~~~ 249 (329)
-|..+||+.-.....+...
T Consensus 435 ~Lv~mGF~e~~A~~ALe~~ 453 (568)
T KOG2561|consen 435 ELVSMGFEEGKARSALEAG 453 (568)
T ss_pred HHHHhccccchHHHHHHhc
No 81
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=28.41 E-value=75 Score=22.83 Aligned_cols=18 Identities=28% Similarity=0.576 Sum_probs=8.7
Q ss_pred HHhCCCChhHHHHHHHhh
Q 020213 16 LKDRGFNDRTIHDMFKRC 33 (329)
Q Consensus 16 L~~~G~s~~~i~~i~~~~ 33 (329)
|+-.|++.+++..+-..+
T Consensus 23 LrR~Gfs~~~i~~l~~ay 40 (83)
T PF13720_consen 23 LRRRGFSKEEISALRRAY 40 (83)
T ss_dssp HHHTTS-HHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHHHHH
Confidence 344555655555554444
No 82
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=27.94 E-value=73 Score=21.10 Aligned_cols=28 Identities=11% Similarity=0.267 Sum_probs=22.8
Q ss_pred CCcchHHHHHHhCCCChhHHHHHHHhhh
Q 020213 7 QNGNSVIWFLKDRGFNDRTIHDMFKRCK 34 (329)
Q Consensus 7 ~~~~~v~~~L~~~G~s~~~i~~i~~~~p 34 (329)
.++.+|-.|-+.+|+|.+++..++....
T Consensus 18 ~e~~ev~ywa~~~gvt~~~L~~AV~~vG 45 (57)
T PF12244_consen 18 SEPYEVRYWAKRFGVTEEQLREAVRAVG 45 (57)
T ss_pred CCHHHHHHHHHHHCcCHHHHHHHHHHHC
Confidence 4566677777889999999999998773
No 83
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=27.94 E-value=1e+02 Score=25.01 Aligned_cols=35 Identities=17% Similarity=0.233 Sum_probs=18.1
Q ss_pred CCCccccccccchHHHHHHHHHCCCChhhHHHHHHh
Q 020213 68 CPKILTLGLNEKLVPMVECLATLGTKPYEVASAITR 103 (329)
Q Consensus 68 ~P~lL~~~~~~~l~~~l~~L~~lG~~~~~~~~~l~~ 103 (329)
.|..+..+.+ .+.+.+--|..-|.++++|+-+++.
T Consensus 22 ~P~W~~~~~e-eve~~I~~lakkG~~pSqIG~~LRD 56 (151)
T PRK08561 22 PPEWVDYSPE-EIEELVVELAKQGYSPSMIGIILRD 56 (151)
T ss_pred CCccccCCHH-HHHHHHHHHHHCCCCHHHhhhhHhh
Confidence 3444555543 4555555555555555555555543
No 84
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=27.90 E-value=2.4e+02 Score=24.33 Aligned_cols=54 Identities=20% Similarity=0.247 Sum_probs=25.7
Q ss_pred HHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHHHHHHC-CCChhhHHHHHH
Q 020213 48 WAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVECLATL-GTKPYEVASAIT 102 (329)
Q Consensus 48 ~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~l-G~~~~~~~~~l~ 102 (329)
-++.++.|+-......|..-.-.++. +....+-...+-|.++ |+.++...-++.
T Consensus 73 ~~~I~~iGlyr~KAk~I~~~~~~l~e-~~~g~vP~~~~eL~~LPGVGrKTAnvVL~ 127 (211)
T COG0177 73 EELIKSIGLYRNKAKNIKELARILLE-KFGGEVPDTREELLSLPGVGRKTANVVLS 127 (211)
T ss_pred HHHHHhcCCcHHHHHHHHHHHHHHHH-HcCCCCCchHHHHHhCCCcchHHHHHHHH
Confidence 35556777766665555544433332 2222333444444443 555554443333
No 85
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=27.75 E-value=1.6e+02 Score=25.91 Aligned_cols=96 Identities=15% Similarity=0.210 Sum_probs=47.6
Q ss_pred CCcchHHHHHHhCCCChhHHHHHHHhhhcc-cCCcchhhHHHHHHHHhCCCCCCChhHHHhhCCC--ccccccccchHHH
Q 020213 7 QNGNSVIWFLKDRGFNDRTIHDMFKRCKRL-QGVEKDRAADNWAYLKSIGILERKLPNVVSKCPK--ILTLGLNEKLVPM 83 (329)
Q Consensus 7 ~~~~~v~~~L~~~G~s~~~i~~i~~~~p~l-l~~~~~~l~~~~~~L~~~G~~~~~i~~i~~~~P~--lL~~~~~~~l~~~ 83 (329)
+.++.++.+|.+.|++.+.. ....... +..+..++...+++|...|+++.....+-.-+|. +.+...+ =+.+
T Consensus 31 ~eANemlAlL~~~gI~A~K~---~~~~g~~~l~Ve~~~fa~Av~iL~~~GlPr~~f~~l~d~Fp~dgLVsSP~e--EkaR 105 (246)
T COG4669 31 KEANEMLALLMSHGINAEKK---ADKDGGTSLLVEESDFAEAVEILNQNGLPRKKFTTLGDIFPKDGLVSSPTE--EKAR 105 (246)
T ss_pred hHHHHHHHHHHHcCCcceee---ccCCCceEEEEcHHHHHHHHHHHHhcCCCCCCCCcHHHhCCcccccCCcHH--HHHH
Confidence 44556666666666664443 2222222 3444556666666666666666555555444442 2222211 1333
Q ss_pred HHHHHHCCCChhhHHHHHHhCCCcccccc
Q 020213 84 VECLATLGTKPYEVASAITRFPPILSHSV 112 (329)
Q Consensus 84 l~~L~~lG~~~~~~~~~l~~~P~ll~~~~ 112 (329)
+.|..+ +++...+++-..++.+++
T Consensus 106 ~~~~~e-----Q~le~tLs~mDGVi~ArV 129 (246)
T COG4669 106 LNYAKE-----QQLEQTLSKMDGVISARV 129 (246)
T ss_pred HHHHHH-----HHHHHHHHhcCceEEEEE
Confidence 333332 345555666666555554
No 86
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=27.52 E-value=1.3e+02 Score=18.67 Aligned_cols=42 Identities=12% Similarity=0.150 Sum_probs=25.5
Q ss_pred HhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCCCCCh
Q 020213 17 KDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGILERKL 61 (329)
Q Consensus 17 ~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~~~~i 61 (329)
...|++.+.+.+++...+ ..+++......+....+|+.+...
T Consensus 5 ~~~gvs~~tvs~~l~g~~---~vs~~~~~~i~~~~~~l~~~~~~~ 46 (52)
T cd01392 5 RAAGVSVATVSRVLNGKP---RVSEETRERVLAAAEELGYRPNAA 46 (52)
T ss_pred HHHCcCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHhCCCCCHH
Confidence 446777777777776554 234455555566666667665543
No 87
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=27.38 E-value=1.5e+02 Score=18.98 Aligned_cols=24 Identities=21% Similarity=0.321 Sum_probs=16.5
Q ss_pred CcchHHHHHHhCCCChhHHHHHHHhh
Q 020213 8 NGNSVIWFLKDRGFNDRTIHDMFKRC 33 (329)
Q Consensus 8 ~~~~v~~~L~~~G~s~~~i~~i~~~~ 33 (329)
+++.|.+||.++|+ .+....+.++
T Consensus 3 ~~~~V~~wL~~~~~--~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGL--GQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcCh--HHHHHHHHHc
Confidence 46778888888887 4555555544
No 88
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=26.45 E-value=64 Score=21.49 Aligned_cols=18 Identities=28% Similarity=0.445 Sum_probs=12.8
Q ss_pred HHHHHHhCCChhHHHHHH
Q 020213 229 FTFLKRCGFADGQIAALV 246 (329)
Q Consensus 229 ~~~L~~~G~s~~~v~~l~ 246 (329)
+..++.+|||.+++..++
T Consensus 7 I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 7 IRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHTT--HHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHH
Confidence 345568999999999988
No 89
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=26.40 E-value=86 Score=22.91 Aligned_cols=56 Identities=21% Similarity=0.200 Sum_probs=30.4
Q ss_pred hhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHHHHHHCCCChhhHHHH
Q 020213 43 RAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVECLATLGTKPYEVASA 100 (329)
Q Consensus 43 ~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~lG~~~~~~~~~ 100 (329)
........+...|+.-..-......+|.+-... +.......+...+|+++..=.++
T Consensus 35 ~~~~~~~~l~~~G~~~~~~~G~~~~nP~~~~~~--~~~~~~~~l~~~lGLtP~sR~kl 90 (100)
T PF05119_consen 35 RYREAEKELKKEGFVVETKNGNPKKNPAVSILN--KAMKQMRSLASELGLTPASRAKL 90 (100)
T ss_pred HHHHHHHHHHHcCceeeCCCCCcccCHHHHHHH--HHHHHHHHHHHHcCCCHHHHhhc
Confidence 444555555556664222112456666665443 44566666667777777654443
No 90
>TIGR01558 sm_term_P27 phage terminase, small subunit, putative, P27 family. Members tend to be adjacent to the phage terminase large subunit gene.
Probab=25.56 E-value=1e+02 Score=23.58 Aligned_cols=55 Identities=13% Similarity=0.126 Sum_probs=24.9
Q ss_pred hHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHHHHHHCCCChhhHHHH
Q 020213 44 AADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVECLATLGTKPYEVASA 100 (329)
Q Consensus 44 l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~lG~~~~~~~~~ 100 (329)
.....+.+...|.....-......+|.+-..+ +.......+...+|+++..=.++
T Consensus 45 ~~~a~~~i~~~G~~~~~~~g~~k~nPa~~i~~--~a~~~~~~l~~elGLtP~sR~kl 99 (116)
T TIGR01558 45 YREATDDLEATGITATVEDGSPKANPALTVVE--DAFKQLRSIGSALGLTPSSRSRL 99 (116)
T ss_pred HHHHHHHHHHcCeeEEeCCCCeecChHHHHHH--HHHHHHHHHHHHcCCCHHHHHHh
Confidence 34444444445553221111133455543332 33455555555666666554444
No 91
>PF10952 DUF2753: Protein of unknown function (DUF2753); InterPro: IPR020206 This entry represents a group of uncharacterised proteins.
Probab=25.52 E-value=62 Score=25.39 Aligned_cols=21 Identities=29% Similarity=0.475 Sum_probs=12.8
Q ss_pred HHHHCCCCchhhhhhHhhCCc
Q 020213 122 FFQALGVPEKQLGRMILLNPR 142 (329)
Q Consensus 122 ~L~~lG~~~~~l~~~l~~~P~ 142 (329)
|+..+|.-.+.+...+.++|.
T Consensus 95 fi~sLGCCk~ALl~F~KRHPN 115 (140)
T PF10952_consen 95 FIDSLGCCKKALLDFMKRHPN 115 (140)
T ss_pred HHHhhhccHHHHHHHHHhCCC
Confidence 455566666666666666663
No 92
>PRK14134 recX recombination regulator RecX; Provisional
Probab=25.41 E-value=3.8e+02 Score=24.17 Aligned_cols=93 Identities=10% Similarity=0.044 Sum_probs=0.0
Q ss_pred hHHHHHHhCCCChhHHHHHHHhhhcccCCcchh--------------hHHHHHHHHhCCCCCCChhHHHhhCCCc-----
Q 020213 11 SVIWFLKDRGFNDRTIHDMFKRCKRLQGVEKDR--------------AADNWAYLKSIGILERKLPNVVSKCPKI----- 71 (329)
Q Consensus 11 ~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~~~~--------------l~~~~~~L~~~G~~~~~i~~i~~~~P~l----- 71 (329)
.+.+.|...|+++..|..++.+--..--.|.+. -...-.-|...|++++.|...+...+.-
T Consensus 80 Elr~KL~~k~~~~~~Ie~vI~~L~e~~yldD~ryA~~yv~~~~~~~G~~~I~~eL~qKGI~~~iIe~al~~~~~e~e~e~ 159 (283)
T PRK14134 80 QIKEKLYLKEYDEDAVNRVIRFLKEYNFIDDDKYCDMYIREKINSYGRNKIKYTLLNKGIKENIIIEKINNIDEEKEKKV 159 (283)
T ss_pred HHHHHHHhCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhhHHHHHHHHHHCCCCHHHHHHHHHhCChhhHHHH
Q ss_pred --------------cccccccchHHHHHHHHHCCCChhhHHHHHHh
Q 020213 72 --------------LTLGLNEKLVPMVECLATLGTKPYEVASAITR 103 (329)
Q Consensus 72 --------------L~~~~~~~l~~~l~~L~~lG~~~~~~~~~l~~ 103 (329)
-..+....-+....||..-|++.+.+..++..
T Consensus 160 a~~l~~Kk~~~~~~~~~~~~k~k~Kl~~~L~rrGFs~~~I~~vl~~ 205 (283)
T PRK14134 160 AYKLAEKKYKILILSEKNKFKIYKKLGPYLISRGYSSNIAEWILNE 205 (283)
T ss_pred HHHHHHHhhcccccccccHHHHHHHHHHHHHHCCCCHHHHHHHHHH
No 93
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=25.30 E-value=3.4e+02 Score=21.31 Aligned_cols=78 Identities=19% Similarity=0.288 Sum_probs=42.6
Q ss_pred ChhhHHHHHHhCCCcccccc----hhhHhHHHH-HHHHCCCC--chhhh---hhHhhCCceeccCcchhHhHHHHHHhhc
Q 020213 93 KPYEVASAITRFPPILSHSV----EEKLCPLLA-FFQALGVP--EKQLG---RMILLNPRLISYSIESKLTETVDFLTSL 162 (329)
Q Consensus 93 ~~~~~~~~l~~~P~ll~~~~----e~~l~~~v~-~L~~lG~~--~~~l~---~~l~~~P~il~~~~~~~l~~~~~~l~~~ 162 (329)
|+.++-.++.+||.+-...+ -.++...+. ||.--|+. +.|+. +=+..| +.+...+..++.-|.+-
T Consensus 29 SN~Dif~Lv~~CP~lk~iqiP~SY~~t~Sksi~mfL~mqgI~LleGDVwGHRKDinEY-----y~i~~~vi~~I~el~~e 103 (131)
T PF08004_consen 29 SNKDIFSLVERCPNLKAIQIPPSYYKTLSKSIKMFLEMQGIELLEGDVWGHRKDINEY-----YEIPESVIERIKELKSE 103 (131)
T ss_pred cchHHHHHHHhCCCCeEEeCChHHHHHHhHHHHHHHHhcCceeeccccccccCCCccc-----ccCCHHHHHHHHHHHHc
Confidence 56677788888887643322 223333333 55434442 22222 112222 33345688888888888
Q ss_pred CCCchhhHHHHHHh
Q 020213 163 GLAREGMIGKVLVK 176 (329)
Q Consensus 163 G~~~~~~i~~ll~~ 176 (329)
|.+. +++..-+.+
T Consensus 104 G~s~-eei~~ki~~ 116 (131)
T PF08004_consen 104 GKSE-EEIAEKISR 116 (131)
T ss_pred CCCH-HHHHHHHHH
Confidence 9874 577654444
No 94
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.18 E-value=1.4e+02 Score=21.80 Aligned_cols=23 Identities=22% Similarity=0.306 Sum_probs=15.4
Q ss_pred hHHHHHHhCCChhHHHHHHHhCc
Q 020213 228 NFTFLKRCGFADGQIAALVAAYP 250 (329)
Q Consensus 228 k~~~L~~~G~s~~~v~~l~~~~P 250 (329)
.+..|+.+|++.+++..++....
T Consensus 49 ~I~~lr~~G~~l~eI~~~l~~~~ 71 (96)
T cd04788 49 QIIALRRLGFSLREIGRALDGPD 71 (96)
T ss_pred HHHHHHHcCCCHHHHHHHHhCCC
Confidence 44566677888888877765443
No 95
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=25.09 E-value=58 Score=18.59 Aligned_cols=9 Identities=11% Similarity=0.468 Sum_probs=2.6
Q ss_pred CCCCchhhh
Q 020213 126 LGVPEKQLG 134 (329)
Q Consensus 126 lG~~~~~l~ 134 (329)
.|++.+++.
T Consensus 15 ~Gls~eeir 23 (30)
T PF08671_consen 15 SGLSKEEIR 23 (30)
T ss_dssp TT--HHHHH
T ss_pred cCCCHHHHH
Confidence 333333333
No 96
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=25.06 E-value=2.4e+02 Score=20.28 Aligned_cols=17 Identities=6% Similarity=0.274 Sum_probs=7.9
Q ss_pred hCCCCCCChhHHHhhCC
Q 020213 53 SIGILERKLPNVVSKCP 69 (329)
Q Consensus 53 ~~G~~~~~i~~i~~~~P 69 (329)
.+|++..+|..|-..+|
T Consensus 27 ~LGls~~dI~~i~~~~~ 43 (86)
T cd08318 27 HLEMKDKEIRAIESDSE 43 (86)
T ss_pred HcCCCHHHHHHHHhcCC
Confidence 34555555544444433
No 97
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=25.04 E-value=83 Score=20.77 Aligned_cols=21 Identities=10% Similarity=0.281 Sum_probs=11.8
Q ss_pred hHHHHHHhCCChhHHHHHHHh
Q 020213 228 NFTFLKRCGFADGQIAALVAA 248 (329)
Q Consensus 228 k~~~L~~~G~s~~~v~~l~~~ 248 (329)
-++-+..+||+.+.|...+++
T Consensus 12 lVd~F~~mGF~~dkVvevlrr 32 (55)
T PF09288_consen 12 LVDQFENMGFERDKVVEVLRR 32 (55)
T ss_dssp HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHcCCcHHHHHHHHHH
Confidence 345566777777776666554
No 98
>PF10366 Vps39_1: Vacuolar sorting protein 39 domain 1; InterPro: IPR019452 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised.
Probab=24.64 E-value=2.8e+02 Score=20.89 Aligned_cols=26 Identities=12% Similarity=0.055 Sum_probs=13.2
Q ss_pred CcchHHHHHHh-CCCChhHHHHHHHhh
Q 020213 8 NGNSVIWFLKD-RGFNDRTIHDMFKRC 33 (329)
Q Consensus 8 ~~~~v~~~L~~-~G~s~~~i~~i~~~~ 33 (329)
|++.+..|++. .-|+.+++.+.+..+
T Consensus 13 ~~~~l~~llr~~N~C~~~~~e~~L~~~ 39 (108)
T PF10366_consen 13 NPSLLGPLLRLPNYCDLEEVEEVLKEH 39 (108)
T ss_pred CHHHHHHHHccCCcCCHHHHHHHHHHc
Confidence 44555555544 455555555555443
No 99
>PRK10026 arsenate reductase; Provisional
Probab=24.58 E-value=2e+02 Score=23.03 Aligned_cols=42 Identities=10% Similarity=0.110 Sum_probs=26.3
Q ss_pred CCChhhHHHHHhhcCceeeeccccccchhHHHHHHhCCChhHHHHHH
Q 020213 200 GLKELDLQVVAVKFPEVLCRDVNKILSPNFTFLKRCGFADGQIAALV 246 (329)
Q Consensus 200 g~~~~~i~~~i~~~P~il~~s~~~~l~~k~~~L~~~G~s~~~v~~l~ 246 (329)
+++.+++..++..+|.++-..+-- -..+ ...|.+.+.|..++
T Consensus 75 ~ls~~e~l~ll~~~P~LIKRPIi~-~~~~----a~i~Rp~e~v~~~l 116 (141)
T PRK10026 75 KFTDDQLIDFMLQHPILINRPIVV-TPLG----TRLCRPSEVVLEIL 116 (141)
T ss_pred CCCHHHHHHHHHhCccceeCcEEE-cCCC----eEEECCHHHHHHHh
Confidence 356677888888888888776421 0111 24566777777666
No 100
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=24.52 E-value=2.5e+02 Score=20.24 Aligned_cols=53 Identities=13% Similarity=0.150 Sum_probs=29.4
Q ss_pred chHHHHHHhCCCChhHHHHHHHhhhcccCCc-chhhHHHHHHHHhC-CCCCCChhHHH
Q 020213 10 NSVIWFLKDRGFNDRTIHDMFKRCKRLQGVE-KDRAADNWAYLKSI-GILERKLPNVV 65 (329)
Q Consensus 10 ~~v~~~L~~~G~s~~~i~~i~~~~p~ll~~~-~~~l~~~~~~L~~~-G~~~~~i~~i~ 65 (329)
...-.+.+.+||++.+|..+-..++. .+ .+.....+..++.. |-..+.+..++
T Consensus 14 ~~Wk~lar~LG~s~~eI~~ie~~~~r---~~~~eq~~~mL~~W~~r~g~~~ATv~~L~ 68 (86)
T cd08777 14 KKWKRCARKLGFTESEIEEIDHDYER---DGLKEKVHQMLHKWKMKEGSKGATVGKLA 68 (86)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhccc---CCHHHHHHHHHHHHHHccCCCCcHHHHHH
Confidence 34556777788888888777544421 11 23455555555543 43445444433
No 101
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=24.45 E-value=2.2e+02 Score=19.31 Aligned_cols=46 Identities=13% Similarity=0.291 Sum_probs=31.0
Q ss_pred HHHhCCCChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCCCCChhH
Q 020213 15 FLKDRGFNDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGILERKLPN 63 (329)
Q Consensus 15 ~L~~~G~s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~~~~i~~ 63 (329)
+-+..|+|.+.+.+++...+. .+++......+....+|..+.....
T Consensus 6 iA~~~gvS~~TVSr~ln~~~~---v~~~t~~~i~~~~~~~gy~~~~~~~ 51 (70)
T smart00354 6 VARLAGVSKATVSRVLNGNGR---VSEETREKVLAAMEELGYIPNRVAR 51 (70)
T ss_pred HHHHHCCCHHHHHHHHCCCCC---CCHHHHHHHHHHHHHhCCCCCHHHH
Confidence 344578888888887776554 3456666677777888887665444
No 102
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=24.20 E-value=76 Score=21.75 Aligned_cols=27 Identities=11% Similarity=0.361 Sum_probs=20.9
Q ss_pred cCCcchHHHHHHhCCCChhHHHHHHHh
Q 020213 6 SQNGNSVIWFLKDRGFNDRTIHDMFKR 32 (329)
Q Consensus 6 ~~~~~~v~~~L~~~G~s~~~i~~i~~~ 32 (329)
....++.++..+.+||+..++..++.+
T Consensus 8 ~~R~daA~dam~~lG~~~~~v~~vl~~ 34 (65)
T PF10440_consen 8 NERIDAALDAMRQLGFSKKQVRPVLKN 34 (65)
T ss_pred cHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 345677788888899998888887764
No 103
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=23.71 E-value=87 Score=21.33 Aligned_cols=19 Identities=21% Similarity=0.305 Sum_probs=16.4
Q ss_pred HHHHhCCCChhHHHHHHHh
Q 020213 14 WFLKDRGFNDRTIHDMFKR 32 (329)
Q Consensus 14 ~~L~~~G~s~~~i~~i~~~ 32 (329)
..|.++|+|.+++...+.+
T Consensus 41 ~~L~DiGisR~d~~~e~~k 59 (63)
T COG5457 41 HLLSDIGISRADIEAEAAK 59 (63)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 5688899999999988876
No 104
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=23.50 E-value=73 Score=23.19 Aligned_cols=25 Identities=12% Similarity=0.167 Sum_probs=20.0
Q ss_pred cCCcchHHHHHHhCCCChhHHHHHH
Q 020213 6 SQNGNSVIWFLKDRGFNDRTIHDMF 30 (329)
Q Consensus 6 ~~~~~~v~~~L~~~G~s~~~i~~i~ 30 (329)
-.|+.+++.-|..+|+|.+++..++
T Consensus 62 y~N~KqllkrLN~f~it~~e~~~al 86 (87)
T PF13331_consen 62 YGNAKQLLKRLNMFGITREEFEEAL 86 (87)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHh
Confidence 4677888888888888888887765
No 105
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=23.19 E-value=1.4e+02 Score=23.99 Aligned_cols=34 Identities=21% Similarity=0.280 Sum_probs=16.5
Q ss_pred CCCccccccccchHHHHHHHHHCCCChhhHHHHHH
Q 020213 68 CPKILTLGLNEKLVPMVECLATLGTKPYEVASAIT 102 (329)
Q Consensus 68 ~P~lL~~~~~~~l~~~l~~L~~lG~~~~~~~~~l~ 102 (329)
.|..+..+.+ .+.+.+--|..-|.++++|+-+++
T Consensus 19 ~P~w~~~~~e-eVe~~I~klaKkG~~pSqIG~iLR 52 (148)
T PTZ00072 19 PPSWLKLSSS-EVEDQICKLAKKGLTPSQIGVILR 52 (148)
T ss_pred CCchhcCCHH-HHHHHHHHHHHCCCCHhHhhhhhh
Confidence 3444444432 455555555555555555555444
No 106
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=23.09 E-value=2.8e+02 Score=19.64 Aligned_cols=23 Identities=9% Similarity=0.052 Sum_probs=14.2
Q ss_pred HHHHHHhCCCChhHHHHHHHhhh
Q 020213 12 VIWFLKDRGFNDRTIHDMFKRCK 34 (329)
Q Consensus 12 v~~~L~~~G~s~~~i~~i~~~~p 34 (329)
...+-+.+|++..+|..|-..+|
T Consensus 18 W~~LAr~Lg~~~~dI~~i~~~~~ 40 (84)
T cd08317 18 WPQLARELGVSETDIDLIKAENP 40 (84)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCC
Confidence 34455566666666666666665
No 107
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.87 E-value=1.5e+02 Score=21.71 Aligned_cols=22 Identities=27% Similarity=0.442 Sum_probs=15.1
Q ss_pred hHHHHHHhCCChhHHHHHHHhC
Q 020213 228 NFTFLKRCGFADGQIAALVAAY 249 (329)
Q Consensus 228 k~~~L~~~G~s~~~v~~l~~~~ 249 (329)
.+.+|+.+|++.+++.+++...
T Consensus 49 ~I~~lr~~G~~l~~I~~~l~~~ 70 (96)
T cd04768 49 FILFLRELGFSLAEIKELLDTE 70 (96)
T ss_pred HHHHHHHcCCCHHHHHHHHhcC
Confidence 3456667788888887776554
No 108
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=21.98 E-value=3e+02 Score=22.17 Aligned_cols=61 Identities=16% Similarity=0.164 Sum_probs=39.3
Q ss_pred hCCCcccccchhhHhHHHHHHHHCCCCchhhhhhHhhCCceeccCcchhHhHHHHHHhhcCCC
Q 020213 103 RFPPILSHSVEEKLCPLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVDFLTSLGLA 165 (329)
Q Consensus 103 ~~P~ll~~~~e~~l~~~v~~L~~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~~l~~~G~~ 165 (329)
..|..+..+.+ .+...+--|.+-|.++.+|+-++...-.+=....- +=......|++-|+.
T Consensus 18 ~~P~w~~~~~e-eVe~~I~klaKkG~~pSqIG~iLRD~~gi~~vk~v-tG~kI~rILk~~Gla 78 (148)
T PTZ00072 18 KPPSWLKLSSS-EVEDQICKLAKKGLTPSQIGVILRDSMGIPQVKNV-TGSKILRILKKNGLA 78 (148)
T ss_pred CCCchhcCCHH-HHHHHHHHHHHCCCCHhHhhhhhhhccCccceeec-cchHHHHHHHhcCCC
Confidence 46676777776 58888888999999999999888765433211111 123345566666643
No 109
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.85 E-value=1.2e+02 Score=28.74 Aligned_cols=31 Identities=16% Similarity=0.133 Sum_probs=20.9
Q ss_pred eeeccccccchhHHHHHHhCCChhHHHHHHHhC
Q 020213 217 LCRDVNKILSPNFTFLKRCGFADGQIAALVAAY 249 (329)
Q Consensus 217 l~~s~~~~l~~k~~~L~~~G~s~~~v~~l~~~~ 249 (329)
+..+.+. +.-|+-|+.+||+...|.+.+..|
T Consensus 331 i~lT~eE--~~AIeRL~~LGF~r~~viqaY~AC 361 (378)
T TIGR00601 331 IQVTPEE--KEAIERLCALGFDRGLVIQAYFAC 361 (378)
T ss_pred cccCHHH--HHHHHHHHHcCCCHHHHHHHHHhc
Confidence 3444443 567788888888888877775554
No 110
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=21.49 E-value=2.8e+02 Score=22.48 Aligned_cols=36 Identities=6% Similarity=-0.047 Sum_probs=25.3
Q ss_pred hhcccCCcchhhHHHHHHHHhCCCCCCChhHHHhhC
Q 020213 33 CKRLQGVEKDRAADNWAYLKSIGILERKLPNVVSKC 68 (329)
Q Consensus 33 ~p~ll~~~~~~l~~~~~~L~~~G~~~~~i~~i~~~~ 68 (329)
.|.=+..+++++++.+.-|...|.++++|+-++...
T Consensus 22 ~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~ 57 (151)
T PRK08561 22 PPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQ 57 (151)
T ss_pred CCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhc
Confidence 344456677777777777777788888887776554
No 111
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=20.59 E-value=2.9e+02 Score=18.84 Aligned_cols=25 Identities=16% Similarity=0.193 Sum_probs=15.3
Q ss_pred hHHHHHHhCCCChhHHHHHHHhhhc
Q 020213 11 SVIWFLKDRGFNDRTIHDMFKRCKR 35 (329)
Q Consensus 11 ~v~~~L~~~G~s~~~i~~i~~~~p~ 35 (329)
....+-+.+|++..+|..+-..+|.
T Consensus 12 ~W~~la~~Lgl~~~~I~~i~~~~~~ 36 (79)
T cd01670 12 DWKKLARKLGLSDGEIDQIEEDNPR 36 (79)
T ss_pred HHHHHHHHhCCCHHHHHHHHHhCCC
Confidence 3444555666777777666666654
No 112
>PF06757 Ins_allergen_rp: Insect allergen related repeat, nitrile-specifier detoxification; InterPro: IPR010629 This entry represents several insect specific allergen repeats. These repeats are commonly found in various proteins from cockroaches, fruit flies and mosquitos. It has been suggested that the repeat sequences have evolved by duplication of an ancestral amino acid domain, which may have arisen from the mitochondrial energy transfer proteins []. This family exemplifies a case of novel gene evolution. The case in point is the arms-race between plants and their infective insective herbivores in the area of the glucosinolate-myrosinase system. Brassicas have developed the glucosinolate-myrosinase system as chemical defence mechanism against the insects, and consequently the insects have adapted to produce a detoxifying molecule, nitrile-specifier protein (NSP). NSP is present in the Pieris rapae (Cabbage white butterfly). NSP is structurally different from and has no amino acid homology to any known detoxifying enzymes, and it appears to have arisen by a process of domain and gene duplication of a sequence of unknown function that is widespread in insect species and referred to as insect-allergen-repeat protein. Thus this family is found either as a single domain or as a multiple repeat-domain [].
Probab=20.17 E-value=5e+02 Score=21.41 Aligned_cols=63 Identities=19% Similarity=0.280 Sum_probs=40.1
Q ss_pred ChhHHHHHHHhhhcccCCcchhhHHHHHHHHhCCCCCCChhHHHhhCCCccccccccchHHHHHHHHHCCCChhhHHH
Q 020213 22 NDRTIHDMFKRCKRLQGVEKDRAADNWAYLKSIGILERKLPNVVSKCPKILTLGLNEKLVPMVECLATLGTKPYEVAS 99 (329)
Q Consensus 22 s~~~i~~i~~~~p~ll~~~~~~l~~~~~~L~~~G~~~~~i~~i~~~~P~lL~~~~~~~l~~~l~~L~~lG~~~~~~~~ 99 (329)
+..++..++.+|- ......+..++|+.+.++ .++..- +.+. ......++||++-|+.-.....
T Consensus 16 p~~~i~~i~~~Y~----~~D~efq~~~~yl~s~~f--~~l~~~------l~~~---pE~~~l~~yL~~~gldv~~~i~ 78 (179)
T PF06757_consen 16 PMEEIQDIVQRYY----LEDAEFQAAVRYLNSSEF--KQLWQQ------LEAL---PEVKALLDYLESAGLDVYYYIN 78 (179)
T ss_pred CHHHHHHHHHHHH----HcCHHHHHHHHHHcChHH--HHHHHH------HHcC---HHHHHHHHHHHHCCCCHHHHHH
Confidence 4556777777662 234578889999987654 222222 2231 3478889999999998665433
No 113
>PRK10702 endonuclease III; Provisional
Probab=20.15 E-value=2.3e+02 Score=24.30 Aligned_cols=19 Identities=11% Similarity=0.036 Sum_probs=8.8
Q ss_pred HHHHHHH-CCCChhhHHHHH
Q 020213 83 MVECLAT-LGTKPYEVASAI 101 (329)
Q Consensus 83 ~l~~L~~-lG~~~~~~~~~l 101 (329)
..+.|.+ =|+.++...-++
T Consensus 107 ~~~~Ll~lpGVG~ktA~~il 126 (211)
T PRK10702 107 DRAALEALPGVGRKTANVVL 126 (211)
T ss_pred hHHHHhcCCcccHHHHHHHH
Confidence 3444443 366555444433
No 114
>KOG0062 consensus ATPase component of ABC transporters with duplicated ATPase domains/Translation elongation factor EF-3b [Amino acid transport and metabolism; Translation, ribosomal structure and biogenesis]
Probab=20.04 E-value=4.5e+02 Score=26.11 Aligned_cols=106 Identities=18% Similarity=0.192 Sum_probs=57.8
Q ss_pred HCCCChhhHHHHHHhCCCcccccchhhHh-HHHHHHHHCCCCchhhhhhHhhCCceeccCcchhHhHHHH-HHhhcCCCc
Q 020213 89 TLGTKPYEVASAITRFPPILSHSVEEKLC-PLLAFFQALGVPEKQLGRMILLNPRLISYSIESKLTETVD-FLTSLGLAR 166 (329)
Q Consensus 89 ~lG~~~~~~~~~l~~~P~ll~~~~e~~l~-~~v~~L~~lG~~~~~l~~~l~~~P~il~~~~~~~l~~~~~-~l~~~G~~~ 166 (329)
.-|+.++.+.+.+... ++=...+++.+. -.+.-+...--++.....++...+.+.... ++++... .|.++||++
T Consensus 114 rNG~GKsTLLRaia~~-~v~~f~veqE~~g~~t~~~~~~l~~D~~~~dfl~~e~~l~~~~---~l~ei~~~~L~glGFt~ 189 (582)
T KOG0062|consen 114 RNGIGKSTLLRAIANG-QVSGFHVEQEVRGDDTEALQSVLESDTERLDFLAEEKELLAGL---TLEEIYDKILAGLGFTP 189 (582)
T ss_pred CCCCcHHHHHHHHHhc-CcCccCchhheeccchHHHhhhhhccHHHHHHHHhhhhhhccc---hHHHHHHHHHHhCCCCH
Confidence 4567777788877762 222222332221 123333333334445666777777665431 3455555 778888875
Q ss_pred h----------------hhHHHHHHhcCcccccc-cccch-hHHHHHHHH
Q 020213 167 E----------------GMIGKVLVKHPFIMGYS-VDNRL-RPTSEFLKS 198 (329)
Q Consensus 167 ~----------------~~i~~ll~~~p~ll~~~-~~~~l-~~~~~~l~~ 198 (329)
+ -++++++-..|.+|.++ |.+.+ ..++.||..
T Consensus 190 emq~~pt~slSGGWrMrlaLARAlf~~pDlLLLDEPTNhLDv~av~WLe~ 239 (582)
T KOG0062|consen 190 EMQLQPTKSLSGGWRMRLALARALFAKPDLLLLDEPTNHLDVVAVAWLEN 239 (582)
T ss_pred HHHhccccccCcchhhHHHHHHHHhcCCCEEeecCCcccchhHHHHHHHH
Confidence 3 23667777788887775 33333 235555554
Done!