Query psy3468
Match_columns 68
No_of_seqs 112 out of 1069
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 17:27:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3468.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3468hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0178|consensus 99.9 8.6E-23 1.9E-27 132.3 6.8 64 1-66 72-135 (249)
2 KOG0181|consensus 99.9 1.2E-22 2.5E-27 130.6 4.7 64 1-66 72-135 (233)
3 KOG0183|consensus 99.9 8.5E-23 1.9E-27 132.5 3.2 64 1-66 70-133 (249)
4 KOG0182|consensus 99.8 1.7E-20 3.7E-25 121.7 5.7 64 1-66 76-139 (246)
5 KOG0863|consensus 99.8 2.1E-19 4.5E-24 117.7 5.6 63 1-65 70-132 (264)
6 cd03754 proteasome_alpha_type_ 99.8 9.3E-19 2E-23 112.9 7.6 64 1-66 69-132 (215)
7 KOG0184|consensus 99.8 5.7E-19 1.2E-23 115.2 5.2 64 1-66 74-137 (254)
8 cd03749 proteasome_alpha_type_ 99.8 2.2E-18 4.9E-23 110.8 7.6 64 1-66 65-128 (211)
9 COG0638 PRE1 20S proteasome, a 99.8 1.7E-18 3.7E-23 113.4 7.2 62 1-66 71-132 (236)
10 cd03752 proteasome_alpha_type_ 99.8 2.9E-18 6.2E-23 110.2 7.7 64 1-66 70-133 (213)
11 cd03755 proteasome_alpha_type_ 99.8 3E-18 6.6E-23 109.7 7.6 64 1-66 67-130 (207)
12 cd03751 proteasome_alpha_type_ 99.7 4.7E-18 1E-22 109.6 7.5 64 1-66 70-133 (212)
13 KOG0176|consensus 99.7 2E-18 4.3E-23 111.4 4.3 64 1-66 74-142 (241)
14 cd03750 proteasome_alpha_type_ 99.7 1.4E-17 2.9E-22 108.1 7.3 64 1-66 67-130 (227)
15 PTZ00246 proteasome subunit al 99.7 9.9E-17 2.1E-21 105.5 7.4 64 1-66 72-135 (253)
16 cd03758 proteasome_beta_type_2 99.7 1.4E-16 3E-21 101.2 7.9 62 1-66 42-103 (193)
17 PRK03996 proteasome subunit al 99.7 1.4E-16 3.1E-21 103.9 7.3 64 1-66 76-139 (241)
18 cd03765 proteasome_beta_bacter 99.7 2E-16 4.4E-21 104.0 7.4 66 1-66 44-114 (236)
19 cd03756 proteasome_alpha_arche 99.7 2.5E-16 5.4E-21 101.0 7.3 64 1-66 68-131 (211)
20 TIGR03690 20S_bact_beta protea 99.6 9.3E-16 2E-20 99.2 7.5 63 1-66 43-105 (219)
21 TIGR03633 arc_protsome_A prote 99.6 1E-15 2.2E-20 99.0 7.4 64 1-66 69-132 (224)
22 cd03753 proteasome_alpha_type_ 99.6 1.9E-15 4.1E-20 97.1 7.7 64 1-66 67-135 (213)
23 cd01911 proteasome_alpha prote 99.6 3.8E-15 8.3E-20 95.3 7.4 64 1-66 67-130 (209)
24 cd03761 proteasome_beta_type_5 99.6 4.7E-15 1E-19 93.8 7.6 60 1-66 41-100 (188)
25 cd03760 proteasome_beta_type_4 99.6 4.9E-15 1.1E-19 94.2 7.3 62 1-66 43-105 (197)
26 cd03759 proteasome_beta_type_3 99.6 1.7E-14 3.6E-19 91.7 7.5 60 1-66 44-103 (195)
27 cd01906 proteasome_protease_Hs 99.6 1.9E-14 4.1E-19 89.4 7.2 62 1-66 41-102 (182)
28 PF00227 Proteasome: Proteasom 99.5 3.5E-14 7.7E-19 88.7 7.5 64 1-66 46-109 (190)
29 cd03757 proteasome_beta_type_1 99.5 2.8E-14 6E-19 91.9 6.8 60 1-66 49-108 (212)
30 TIGR03634 arc_protsome_B prote 99.5 4.5E-14 9.7E-19 88.7 7.5 60 1-66 42-101 (185)
31 cd03764 proteasome_beta_archea 99.5 1.3E-13 2.8E-18 86.9 7.5 60 1-66 41-100 (188)
32 cd01912 proteasome_beta protea 99.5 1.1E-13 2.3E-18 86.9 7.1 60 1-66 41-100 (189)
33 cd03762 proteasome_beta_type_6 99.5 1E-13 2.3E-18 87.3 6.9 59 1-66 41-99 (188)
34 TIGR03691 20S_bact_alpha prote 99.5 8.8E-14 1.9E-18 90.9 6.5 63 1-66 60-123 (228)
35 PTZ00488 Proteasome subunit be 99.4 7.2E-13 1.6E-17 87.5 7.1 56 1-64 80-135 (247)
36 cd03763 proteasome_beta_type_7 99.4 1.1E-12 2.3E-17 82.9 6.9 59 1-66 41-99 (189)
37 cd01901 Ntn_hydrolase The Ntn 99.3 1.4E-11 3E-16 73.7 7.4 61 1-66 41-101 (164)
38 KOG0179|consensus 99.2 7.2E-11 1.6E-15 76.8 5.7 60 1-66 70-129 (235)
39 KOG0180|consensus 98.2 4.8E-06 1E-10 53.3 5.0 54 2-61 50-103 (204)
40 cd01913 protease_HslV Protease 97.7 6.9E-05 1.5E-09 47.6 3.9 32 1-32 42-73 (171)
41 KOG0175|consensus 97.6 0.00016 3.4E-09 48.7 5.1 47 4-50 115-161 (285)
42 PRK05456 ATP-dependent proteas 97.5 0.00038 8.3E-09 44.0 5.4 27 1-27 43-69 (172)
43 KOG0174|consensus 97.5 0.00048 1E-08 44.9 5.7 52 1-52 60-111 (224)
44 TIGR03692 ATP_dep_HslV ATP-dep 97.1 0.0013 2.8E-08 41.8 4.6 40 1-45 42-81 (171)
45 KOG0177|consensus 95.0 0.083 1.8E-06 34.4 5.1 61 2-66 43-103 (200)
46 KOG0173|consensus 80.2 4.6 9.9E-05 27.5 4.4 50 1-50 78-127 (271)
47 PF15412 Nse4-Nse3_bdg: Bindin 76.1 7.7 0.00017 20.1 3.7 36 11-47 1-39 (56)
48 PF04539 Sigma70_r3: Sigma-70 73.7 8.8 0.00019 20.3 3.7 30 16-45 3-32 (78)
49 COG5405 HslV ATP-dependent pro 73.2 4.2 9E-05 26.1 2.6 26 2-27 47-72 (178)
50 KOG0185|consensus 72.6 8.8 0.00019 26.0 4.1 46 2-47 83-129 (256)
51 PF01726 LexA_DNA_bind: LexA D 62.2 13 0.00028 19.8 2.8 24 22-45 14-37 (65)
52 PF01242 PTPS: 6-pyruvoyl tetr 61.9 18 0.00039 21.1 3.6 50 6-56 43-103 (123)
53 PF09069 EF-hand_3: EF-hand; 61.5 28 0.00062 19.9 4.7 45 16-63 2-46 (90)
54 PF15286 Bcl-2_3: Apoptosis re 56.4 33 0.00071 20.6 4.0 32 4-35 23-54 (126)
55 PF10668 Phage_terminase: Phag 54.6 25 0.00055 18.7 3.1 26 20-45 9-34 (60)
56 PF08208 RNA_polI_A34: DNA-dir 54.2 4.2 9.1E-05 25.9 0.0 10 56-65 115-124 (198)
57 TIGR03342 dsrC_tusE_dsvC sulfu 51.0 50 0.0011 19.5 4.8 35 8-46 38-72 (108)
58 COG4537 ComGC Competence prote 49.0 48 0.001 19.6 3.9 29 12-40 49-78 (107)
59 PF13120 DUF3974: Domain of un 47.3 6.7 0.00015 23.2 0.1 19 35-53 46-64 (126)
60 KOG4119|consensus 47.1 49 0.0011 18.2 4.6 37 9-51 9-45 (71)
61 PRK11508 sulfur transfer prote 46.9 60 0.0013 19.2 4.7 35 8-46 39-73 (109)
62 PF06018 CodY: CodY GAF-like d 44.4 73 0.0016 20.4 4.5 36 15-50 2-37 (177)
63 PF01972 SDH_sah: Serine dehyd 40.7 36 0.00078 23.5 2.8 33 25-57 222-265 (285)
64 COG0282 ackA Acetate kinase [E 40.4 12 0.00027 26.9 0.6 42 3-47 273-314 (396)
65 PF15606 Toxin_55: Putative to 37.0 50 0.0011 18.5 2.6 12 3-14 9-20 (77)
66 PF15054 DUF4535: Domain of un 36.7 59 0.0013 16.4 2.6 24 9-32 22-45 (46)
67 PF10113 Fibrillarin_2: Fibril 36.5 27 0.00058 25.8 1.8 41 26-66 19-61 (505)
68 TIGR00039 6PTHBS 6-pyruvoyl te 36.0 30 0.00066 20.4 1.7 45 6-50 45-97 (124)
69 PRK14752 delta-hemolysin; Prov 35.6 47 0.001 16.3 2.1 19 35-53 26-44 (44)
70 PRK09651 RNA polymerase sigma 35.1 77 0.0017 19.1 3.5 22 10-31 150-171 (172)
71 COG4114 FhuF Uncharacterized F 34.7 1.1E+02 0.0025 20.7 4.4 47 7-54 13-66 (251)
72 cd04742 NPD_FabD 2-Nitropropan 34.6 54 0.0012 23.7 3.1 30 33-67 47-76 (418)
73 PF08958 DUF1871: Domain of un 34.4 87 0.0019 17.4 4.7 31 18-49 40-70 (79)
74 PF06057 VirJ: Bacterial virul 34.3 71 0.0015 20.8 3.3 25 33-57 44-68 (192)
75 PRK04158 transcriptional repre 34.0 1.2E+02 0.0026 20.7 4.5 38 14-51 3-40 (256)
76 PF00392 GntR: Bacterial regul 33.8 45 0.00097 17.0 2.0 31 13-43 3-34 (64)
77 cd04795 SIS SIS domain. SIS (S 33.1 45 0.00099 17.3 2.0 21 1-21 52-72 (87)
78 PF02186 TFIIE_beta: TFIIE bet 31.1 65 0.0014 17.2 2.4 20 25-44 12-31 (65)
79 PF08279 HTH_11: HTH domain; 31.1 54 0.0012 16.0 2.0 20 25-44 7-26 (55)
80 PRK12427 flagellar biosynthesi 30.6 1.5E+02 0.0033 19.1 4.5 32 14-45 98-129 (231)
81 smart00345 HTH_GNTR helix_turn 30.2 33 0.00071 16.5 1.1 27 17-43 3-30 (60)
82 PF08388 GIIM: Group II intron 28.9 96 0.0021 16.2 4.5 35 20-54 5-39 (80)
83 PHA02131 hypothetical protein 28.8 93 0.002 16.6 2.7 27 3-29 43-69 (70)
84 PHA02745 hypothetical protein; 27.2 94 0.002 21.2 3.1 21 11-31 242-262 (265)
85 PF00165 HTH_AraC: Bacterial r 27.0 45 0.00098 15.5 1.2 16 29-44 4-19 (42)
86 PRK11414 colanic acid/biofilm 26.9 70 0.0015 20.2 2.4 32 13-44 14-45 (221)
87 PF05769 DUF837: Protein of un 26.7 43 0.00093 21.4 1.4 20 2-21 2-21 (181)
88 PRK07122 RNA polymerase sigma 26.7 1.9E+02 0.0042 19.0 4.8 32 14-45 124-155 (264)
89 cd05008 SIS_GlmS_GlmD_1 SIS (S 26.2 66 0.0014 18.1 2.1 21 1-21 51-71 (126)
90 PF14605 Nup35_RRM_2: Nup53/35 26.2 95 0.0021 15.5 2.4 15 2-16 3-17 (53)
91 PF10851 DUF2652: Protein of u 25.6 81 0.0018 19.0 2.3 25 28-53 28-52 (116)
92 cd07377 WHTH_GntR Winged helix 25.4 88 0.0019 15.2 2.3 29 15-43 6-35 (66)
93 PF04358 DsrC: DsrC like prote 25.4 1.5E+02 0.0033 17.4 4.7 35 8-46 39-73 (109)
94 PRK12397 propionate kinase; Re 25.2 63 0.0014 23.4 2.1 43 3-47 274-316 (404)
95 COG4018 Uncharacterized protei 25.1 87 0.0019 22.7 2.8 41 26-66 19-61 (505)
96 PRK12379 propionate/acetate ki 24.8 65 0.0014 23.2 2.1 43 3-47 270-312 (396)
97 TIGR00016 ackA acetate kinase. 24.1 2.3E+02 0.005 20.5 4.7 40 3-47 279-321 (404)
98 TIGR00636 PduO_Nterm ATP:cob(I 23.6 2E+02 0.0044 18.2 4.6 43 11-53 116-158 (171)
99 PRK07408 RNA polymerase sigma 23.4 2E+02 0.0044 18.8 4.2 31 15-45 111-141 (256)
100 PF12840 HTH_20: Helix-turn-he 23.4 1.2E+02 0.0025 15.3 3.2 31 13-44 5-35 (61)
101 PRK11534 DNA-binding transcrip 23.3 84 0.0018 19.8 2.3 30 14-43 11-40 (224)
102 COG0781 NusB Transcription ter 23.3 1.9E+02 0.0042 17.8 4.0 44 14-57 89-132 (151)
103 cd05014 SIS_Kpsf KpsF-like pro 23.2 81 0.0018 17.8 2.0 21 1-21 52-72 (128)
104 PF11950 DUF3467: Protein of u 23.2 1.5E+02 0.0033 16.6 3.2 22 11-32 68-89 (92)
105 PF12767 SAGA-Tad1: Transcript 23.1 97 0.0021 20.4 2.6 44 3-50 196-239 (252)
106 cd05017 SIS_PGI_PMI_1 The memb 23.1 83 0.0018 17.9 2.1 22 1-22 48-69 (119)
107 TIGR03367 queuosine_QueD queuo 23.0 80 0.0017 17.6 1.9 42 6-47 43-90 (92)
108 PRK12440 acetate kinase; Revie 23.0 70 0.0015 23.1 2.0 43 3-47 273-315 (397)
109 COG5174 TFA2 Transcription ini 22.3 1.1E+02 0.0023 21.0 2.6 26 22-47 87-112 (285)
110 cd05710 SIS_1 A subgroup of th 22.3 88 0.0019 17.9 2.1 22 1-22 52-73 (120)
111 PF01923 Cob_adeno_trans: Coba 21.8 2.1E+02 0.0045 17.6 4.6 40 11-50 119-158 (163)
112 KOG2227|consensus 21.8 2E+02 0.0044 21.7 4.2 43 5-47 358-416 (529)
113 PRK11511 DNA-binding transcrip 21.7 1.8E+02 0.0039 16.9 3.5 16 29-44 21-36 (127)
114 PF08720 Hema_stalk: Influenza 21.6 46 0.001 20.5 0.8 22 18-39 144-165 (175)
115 cd03063 TRX_Fd_FDH_beta TRX-li 21.5 76 0.0016 18.1 1.6 26 1-26 5-30 (92)
116 cd05005 SIS_PHI Hexulose-6-pho 21.4 85 0.0018 19.2 2.0 21 1-21 80-100 (179)
117 PRK07157 acetate kinase; Provi 21.3 3E+02 0.0065 20.0 4.9 43 3-47 272-314 (400)
118 COG4728 Uncharacterized protei 21.3 71 0.0015 19.1 1.5 31 1-31 17-50 (124)
119 smart00224 GGL G protein gamma 21.1 1.4E+02 0.0031 15.5 3.6 33 11-49 3-35 (63)
120 PRK11376 hlyE hemolysin E; Pro 21.1 2.7E+02 0.0058 19.0 4.3 52 6-57 2-61 (303)
121 COG3557 Uncharacterized domain 21.0 2.4E+02 0.0053 18.1 4.2 38 22-62 123-160 (177)
122 cd05564 PTS_IIB_chitobiose_lic 20.9 1.1E+02 0.0024 17.1 2.2 25 2-28 4-28 (96)
123 PF06711 DUF1198: Protein of u 20.8 97 0.0021 19.4 2.1 42 6-53 18-60 (148)
124 cd00068 GGL G protein gamma su 20.6 1.4E+02 0.0031 15.2 3.8 34 11-50 3-36 (57)
125 TIGR02393 RpoD_Cterm RNA polym 20.3 2.5E+02 0.0054 18.0 4.9 30 15-44 85-114 (238)
126 cd07977 TFIIE_beta_winged_heli 20.3 1.7E+02 0.0036 15.9 2.9 22 23-44 14-36 (75)
127 PF08289 Flu_M1_C: Influenza M 20.3 1.9E+02 0.0041 16.6 5.3 48 8-55 41-88 (95)
128 PF00382 TFIIB: Transcription 20.0 1E+02 0.0022 16.0 1.9 30 32-63 10-39 (71)
No 1
>KOG0178|consensus
Probab=99.88 E-value=8.6e-23 Score=132.31 Aligned_cols=64 Identities=64% Similarity=1.062 Sum_probs=62.2
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|.|+++|+++|+..|++.+|..|++|.+.|+++||++.|++.|+++.|.|||++|.| |||||..
T Consensus 72 iaC~vaGlt~DAnvL~n~aRi~AQ~yl~~y~e~iP~eqLv~~lcdiKQayTQygG~R--PFGVSfL 135 (249)
T KOG0178|consen 72 IACAVAGLTSDANVLKNYARIIAQRYLFRYGEEIPCEQLVTFLCDIKQAYTQYGGKR--PFGVSFL 135 (249)
T ss_pred eEEEEecccccHHHHHHHHHHHHHHHHHHhCCCCcHHHHHHHHHHHHHHHhhccCcC--CCceeee
Confidence 679999999999999999999999999999999999999999999999999999999 9999864
No 2
>KOG0181|consensus
Probab=99.87 E-value=1.2e-22 Score=130.56 Aligned_cols=64 Identities=39% Similarity=0.627 Sum_probs=62.7
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|||++|||.||.|.||++.|..|++|...|++|||+..|+++++..||+|||.+|.| |||+++.
T Consensus 72 IG~vYSGmgpD~RvlV~~~rkiAe~Yy~vY~e~~pt~qlv~~~asvmQEyTqsgGvr--PFGvsll 135 (233)
T KOG0181|consen 72 IGCVYSGMGPDYRVLVHKSRKIAEQYYRVYGEPIPTTQLVQEVASVMQEYTQSGGVR--PFGVSLL 135 (233)
T ss_pred cceEEecCCCceeehhhHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHhhcCCcc--ccceEEE
Confidence 799999999999999999999999999999999999999999999999999999999 9999975
No 3
>KOG0183|consensus
Probab=99.86 E-value=8.5e-23 Score=132.50 Aligned_cols=64 Identities=30% Similarity=0.511 Sum_probs=62.2
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+|+++|+.||+|+|++++|.||++|+.+++.|++|+.|++.|+.+.|.|||.+|+| |||+|+.
T Consensus 70 V~mafaGl~aDArilinrArvecqShrlt~edpvtveyitRyiA~~kQrYTqs~grR--PFGvs~L 133 (249)
T KOG0183|consen 70 VVMAFAGLTADARILINRARVECQSHRLTLEDPVTVEYITRYIAGLKQRYTQSNGRR--PFGVSTL 133 (249)
T ss_pred eeEEecCCCccceeehhhHhHhhhhhhcccCCCcHHHHHHHHHHHhhhhhhccCCcc--cccceEE
Confidence 579999999999999999999999999999999999999999999999999999999 9999974
No 4
>KOG0182|consensus
Probab=99.82 E-value=1.7e-20 Score=121.69 Aligned_cols=64 Identities=27% Similarity=0.456 Sum_probs=62.8
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|||+++|++||+|..++++|.+|.+++|+||.+||++.||++++|+.|.|||++.+| |.||+++
T Consensus 76 ig~v~tG~~aDar~~v~rar~eAa~~~yk~Gyemp~DiL~k~~Ad~~QvytQ~a~mR--plg~~~~ 139 (246)
T KOG0182|consen 76 IGCVITGMIADARSQVQRARYEAAEFRYKYGYEMPCDILAKRMADKSQVYTQNAAMR--PLGVAAT 139 (246)
T ss_pred ceEEEecCCcchHHHHHHHHHHHHhhhhhcCCCCCHHHHHHHHhhHHHHHhhhhhhc--ccceeEE
Confidence 699999999999999999999999999999999999999999999999999999999 9999986
No 5
>KOG0863|consensus
Probab=99.78 E-value=2.1e-19 Score=117.72 Aligned_cols=63 Identities=35% Similarity=0.433 Sum_probs=61.3
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceecc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNK 65 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~ 65 (68)
+|++++|+++|+|.|++++|.||.++++.|++++||..|+..|++.+|+.||++|+| ||||-+
T Consensus 70 ~g~siAGLt~Darvl~~Ylr~ec~~~~~~~~r~~pv~rl~~~l~~k~q~~Tq~ygrR--pYGVGl 132 (264)
T KOG0863|consen 70 IGISIAGLTADARVLSRYLRQECLNSRFIYGRPLPVLRLVEDLGDKAQENTQRYGRR--PYGVGL 132 (264)
T ss_pred cceEEeccCcchHHHHHHHHHHHhhhhhccCCcccHHHHHHHHHHHHhhhhhhhCCc--cccceE
Confidence 689999999999999999999999999999999999999999999999999999999 999954
No 6
>cd03754 proteasome_alpha_type_6 proteasome_alpha_type_6. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.78 E-value=9.3e-19 Score=112.93 Aligned_cols=64 Identities=23% Similarity=0.377 Sum_probs=62.1
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+|++||+.+|++.+++++|.+++.|+++|+++||++.||+.||+++|.|||+++.| ||||+.+
T Consensus 69 i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~q~yt~~~~~R--P~~v~~i 132 (215)
T cd03754 69 IGCVMTGMIADSRSQVQRARYEAAEFKYKYGYEMPVDVLAKRIADINQVYTQHAYMR--PLGVSMI 132 (215)
T ss_pred EEEEEEechhhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhCCCCCc--CCeeEEE
Confidence 589999999999999999999999999999999999999999999999999999999 9999875
No 7
>KOG0184|consensus
Probab=99.77 E-value=5.7e-19 Score=115.17 Aligned_cols=64 Identities=27% Similarity=0.474 Sum_probs=62.6
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|||+++|+.||.+.|++++|.||.+|+.+|+.|||++.++.+++++.|.||.++..| ||||+++
T Consensus 74 iG~avaGl~~Dg~~l~~~ar~ea~~~~~~y~~piP~~~la~rva~yvh~~Tly~~vR--pfG~~~~ 137 (254)
T KOG0184|consen 74 IGMAVAGLIPDGRHLVNRARDEAASWRKNYGDPIPGKHLADRVADYVHAFTLYSSVR--PFGASTI 137 (254)
T ss_pred ccEEEeccccchHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHhhhheeehhhccc--cccceEE
Confidence 799999999999999999999999999999999999999999999999999999999 9999975
No 8
>cd03749 proteasome_alpha_type_1 proteasome_alpha_type_1. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.76 E-value=2.2e-18 Score=110.79 Aligned_cols=64 Identities=31% Similarity=0.470 Sum_probs=62.0
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+|++||+.+|++.+++++|.+++.|+++|+++||++.+|+.+++++|+|||+++.| ||||+.+
T Consensus 65 i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~is~~~~~~t~~~~~r--P~~v~~i 128 (211)
T cd03749 65 IGIAIAGLTADARVLSRYMRQECLNYRFVYDSPIPVSRLVSKVAEKAQINTQRYGRR--PYGVGLL 128 (211)
T ss_pred EEEEEEeChHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCCC--CceEEEE
Confidence 589999999999999999999999999999999999999999999999999999999 9999864
No 9
>COG0638 PRE1 20S proteasome, alpha and beta subunits [Posttranslational modification, protein turnover, chaperones]
Probab=99.76 E-value=1.7e-18 Score=113.42 Aligned_cols=62 Identities=39% Similarity=0.543 Sum_probs=60.3
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+|++||+.||++.|++++|.+|+.|++.|+++|+++.+++.||+++|.|||+ .| ||||+++
T Consensus 71 i~~~~sG~~aDa~~lv~~~r~~a~~~~~~~~~~i~v~~la~~ls~~l~~~~~~--~r--P~gv~~i 132 (236)
T COG0638 71 IGMAIAGLAADAQVLVRYARAEAQLYRLRYGEPISVEALAKLLSNILQEYTQS--GR--PYGVSLL 132 (236)
T ss_pred EEEEeccCcHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhccC--cc--cceEEEE
Confidence 68999999999999999999999999999999999999999999999999999 99 9999875
No 10
>cd03752 proteasome_alpha_type_4 proteasome_alpha_type_4. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.76 E-value=2.9e-18 Score=110.25 Aligned_cols=64 Identities=66% Similarity=1.034 Sum_probs=62.2
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+|++||+.+|++.+++++|.+++.|++.|+++|+++.+++.||..+|+|||+++.| ||||+.+
T Consensus 70 i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~v~~la~~ls~~~~~~t~~~~~R--P~~v~~l 133 (213)
T cd03752 70 IACAVAGITSDANILINYARLIAQRYLYSYQEPIPVEQLVQRLCDIKQGYTQYGGLR--PFGVSFL 133 (213)
T ss_pred EEEEEecChHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcCCCcc--cceeEEE
Confidence 689999999999999999999999999999999999999999999999999999999 9999875
No 11
>cd03755 proteasome_alpha_type_7 proteasome_alpha_type_7. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.76 E-value=3e-18 Score=109.74 Aligned_cols=64 Identities=30% Similarity=0.485 Sum_probs=62.0
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|++++||+.+|++.+++++|.+++.|++.++++||++.+++.|++++|+|||+++.| ||||+.+
T Consensus 67 i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~ls~~~~~y~~~~~~r--P~~vs~i 130 (207)
T cd03755 67 VCLAFAGLTADARVLINRARLECQSHRLTVEDPVTVEYITRYIAGLQQRYTQSGGVR--PFGISTL 130 (207)
T ss_pred EEEEEecchhhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHhcccCcc--cceeEEE
Confidence 589999999999999999999999999999999999999999999999999999999 9999864
No 12
>cd03751 proteasome_alpha_type_3 proteasome_alpha_type_3. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.75 E-value=4.7e-18 Score=109.60 Aligned_cols=64 Identities=30% Similarity=0.441 Sum_probs=62.0
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+++++|+.+|++.+++++|.++++|++.++++||++.+++.|++++|.|||+++.| ||||+.+
T Consensus 70 i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~~~v~~la~~ls~~~~~~t~~~~~r--P~~vs~l 133 (212)
T cd03751 70 IGIAVAGLLADGRHLVSRAREEAENYRDNYGTPIPVKVLADRVAMYMHAYTLYSSVR--PFGCSVL 133 (212)
T ss_pred EEEEEEEChHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccCCCcC--CceEEEE
Confidence 589999999999999999999999999999999999999999999999999999999 9999875
No 13
>KOG0176|consensus
Probab=99.74 E-value=2e-18 Score=111.38 Aligned_cols=64 Identities=25% Similarity=0.455 Sum_probs=60.0
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCC-----CCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGG-----QSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~-----~R~~P~g~~~~ 66 (68)
|||++||+.+|+|.|++++|.+|++|++.|+++|+|+.+.+.+|++.-.|....+ .| ||||++.
T Consensus 74 Igca~SGl~aDarTlve~arv~~qnh~f~Y~e~i~VEs~tq~v~~LaLrFGe~~~~~~~msR--PFGVall 142 (241)
T KOG0176|consen 74 IGCAMSGLIADARTLVERARVETQNHWFTYGEPISVESLTQAVSDLALRFGEGDDEEAIMSR--PFGVALL 142 (241)
T ss_pred eeeeccccccchHHHHHHHHHHhhhceeecCCcccHHHHHHHHHHHHhHhCCCcchhhhhcC--CcceEEE
Confidence 7999999999999999999999999999999999999999999999999988744 37 9999975
No 14
>cd03750 proteasome_alpha_type_2 proteasome_alpha_type_2. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.73 E-value=1.4e-17 Score=108.06 Aligned_cols=64 Identities=39% Similarity=0.608 Sum_probs=61.9
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+|+++|+.+|++.+++++|.++++|++.|+++||++.+++.|++++|+|||+++.| ||||+.+
T Consensus 67 i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~la~~l~~~~~~~t~~~~~r--P~~v~~l 130 (227)
T cd03750 67 IGMVYSGMGPDFRVLVKKARKIAQQYYLVYGEPIPVSQLVREIASVMQEYTQSGGVR--PFGVSLL 130 (227)
T ss_pred EEEEEeEcHHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCCC--ChheEEE
Confidence 589999999999999999999999999999999999999999999999999999999 9999864
No 15
>PTZ00246 proteasome subunit alpha; Provisional
Probab=99.69 E-value=9.9e-17 Score=105.49 Aligned_cols=64 Identities=52% Similarity=0.895 Sum_probs=61.8
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+++++|+.+|++.|++++|.+++.|++.+++++|++.+++.+++.+|.|||+++.| ||||+.+
T Consensus 72 i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~v~~l~~~l~~~~q~~~~~~~~r--P~~v~~l 135 (253)
T PTZ00246 72 IFCAVAGLTADANILINQCRLYAQRYRYTYGEPQPVEQLVVQICDLKQSYTQFGGLR--PFGVSFL 135 (253)
T ss_pred EEEEEEEcHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhccccCcc--cCCEEEE
Confidence 589999999999999999999999999999999999999999999999999999999 9999875
No 16
>cd03758 proteasome_beta_type_2 proteasome beta type-2 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis.Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.69 E-value=1.4e-16 Score=101.22 Aligned_cols=62 Identities=10% Similarity=0.064 Sum_probs=58.8
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|++++||+.+|++.|++++|.+++.|++.++++|+++.+++.|++++|.|+|.. | ||||+.+
T Consensus 42 i~~~~sG~~aD~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~l~~~~~~~~~~~--r--P~~~~~l 103 (193)
T cd03758 42 KLMACSGEAGDRLQFAEYIQKNIQLYKMRNGYELSPKAAANFTRRELAESLRSR--T--PYQVNLL 103 (193)
T ss_pred eEEEEccchHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhhcC--C--CeEEEEE
Confidence 589999999999999999999999999999999999999999999999998874 8 9999874
No 17
>PRK03996 proteasome subunit alpha; Provisional
Probab=99.68 E-value=1.4e-16 Score=103.94 Aligned_cols=64 Identities=41% Similarity=0.567 Sum_probs=61.9
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|++++||+.+|++.+++++|.+++.|++.++++||++.+++.|++.+|.|||+++.| ||||+.+
T Consensus 76 i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~i~~~~la~~ls~~~~~~~~~~~~r--P~~~~~i 139 (241)
T PRK03996 76 IGAASAGLVADARVLIDRARVEAQINRLTYGEPIGVETLTKKICDHKQQYTQHGGVR--PFGVALL 139 (241)
T ss_pred EEEEEcccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhcCCCCcc--chheEEE
Confidence 589999999999999999999999999999999999999999999999999999999 9999874
No 18
>cd03765 proteasome_beta_bacterial Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.67 E-value=2e-16 Score=103.99 Aligned_cols=66 Identities=12% Similarity=-0.073 Sum_probs=58.1
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHH-HHhhhcCCC---CCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNE-PIPCEQLVACLCDIK-QGYTQYGGQ---SIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~-~i~v~~la~~ls~~~-q~~Tq~~~~---R~~P~g~~~~ 66 (68)
|+|+.||+.+|++.|++++|.+++.|+++|++ +|||+.+|+.+++++ |.+||+++. +.+||||+.+
T Consensus 44 I~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~~~~v~~la~~i~~~l~~~~~q~~~~~~~~~rp~gvslI 114 (236)
T cd03765 44 IVLLTAGNLATTQAVISLLQRDLEDPEETNLLNAPTMFDAARYVGETLREVQEQDREALKKAGIDFSASFI 114 (236)
T ss_pred EEEEcCCcHHHHHHHHHHHHHHHHhhHHhhCCCCCCHHHHHHHHHHHHHHHHhhcccccccCCcceEEEEE
Confidence 68999999999999999999999999999999 899999999999985 567777764 1229999875
No 19
>cd03756 proteasome_alpha_archeal proteasome_alpha_archeal. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.67 E-value=2.5e-16 Score=101.04 Aligned_cols=64 Identities=41% Similarity=0.597 Sum_probs=61.8
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
+++++||+.+|++.+++++|.+++.|+++++++++++.+++.||+.+|.|||+++.| ||||+.+
T Consensus 68 i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~la~~ls~~~~~~~~~~~~r--P~~v~~l 131 (211)
T cd03756 68 VGAATSGLVADARVLIDRARVEAQIHRLTYGEPIDVEVLVKKICDLKQQYTQHGGVR--PFGVALL 131 (211)
T ss_pred EEEEEecCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCee--chhEEEE
Confidence 589999999999999999999999999999999999999999999999999999999 9999865
No 20
>TIGR03690 20S_bact_beta proteasome, beta subunit, bacterial type. Members of this family are the beta subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In Streptomyces, maturation during proteasome assembly was shown to remove a 53-amino acid propeptide. Most of the length of the propeptide is not included in this model.
Probab=99.64 E-value=9.3e-16 Score=99.18 Aligned_cols=63 Identities=13% Similarity=0.084 Sum_probs=58.7
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
++|+++|+.+|++.|++++|.+++.|++.++++||++.+++.|++++|.+++ ++.| ||+|+.+
T Consensus 43 i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~~~~i~~~~la~~ls~~~~~~~~-~~~r--p~~v~~i 105 (219)
T TIGR03690 43 SAVGIAGTAGLAIELVRLFQVELEHYEKIEGVPLTLDGKANRLAAMVRGNLP-AAMQ--GLAVVPL 105 (219)
T ss_pred EEEEecccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhhhh-hccC--CceEEEE
Confidence 5899999999999999999999999999999999999999999999999985 4488 9998864
No 21
>TIGR03633 arc_protsome_A proteasome endopeptidase complex, archaeal, alpha subunit. This protein family describes the archaeal proteasome alpha subunit, homologous to both the beta subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.
Probab=99.64 E-value=1e-15 Score=98.96 Aligned_cols=64 Identities=39% Similarity=0.592 Sum_probs=61.8
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
+++++||+.+|++.+++.+|.++..|++.++++++++.+++.|++++|.|||+++.| ||+|+.+
T Consensus 69 i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~la~~ls~~l~~~~~~~~~r--P~~v~~l 132 (224)
T TIGR03633 69 IGAATSGLVADARVLIDRARIEAQINRLTYGEPIDVETLAKKICDLKQQYTQHGGVR--PFGVALL 132 (224)
T ss_pred EEEEEeecHHhHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcCCCCcc--ccceEEE
Confidence 579999999999999999999999999999999999999999999999999999999 9999875
No 22
>cd03753 proteasome_alpha_type_5 proteasome_alpha_type_5. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.62 E-value=1.9e-15 Score=97.08 Aligned_cols=64 Identities=25% Similarity=0.452 Sum_probs=59.9
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCC-----CCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGG-----QSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~-----~R~~P~g~~~~ 66 (68)
|+|+++|+.+|++.+++++|.+++.|++.++++||++.+++.|++++|.|||..+ .| ||||+.+
T Consensus 67 i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~i~~~~~~~~ls~~~~~~~~~~~~~~~~~r--P~~v~~i 135 (213)
T cd03753 67 IGCAMSGLIADARTLIDHARVEAQNHRFTYNEPMTVESVTQAVSDLALQFGEGDDGKKAMSR--PFGVALL 135 (213)
T ss_pred EEEEEecCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhCcccccccccc--cceEEEE
Confidence 5899999999999999999999999999999999999999999999999999753 57 9999865
No 23
>cd01911 proteasome_alpha proteasome alpha subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 different alpha and 10 different beta proteasome subunit genes while archaea have one of each.
Probab=99.60 E-value=3.8e-15 Score=95.33 Aligned_cols=64 Identities=48% Similarity=0.766 Sum_probs=61.7
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
++++++|+.+|++.+++.+|.++.+|++.++++|+++.+|+.+++.+|+||++++.| ||+|+.+
T Consensus 67 i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~g~~~~~~~la~~ls~~~~~~~~~~~~r--P~~v~~i 130 (209)
T cd01911 67 IGCAVAGLTADARVLVNRARVEAQNYRYTYGEPIPVEVLVKRIADLAQVYTQYGGVR--PFGVSLL 130 (209)
T ss_pred eEEEeccCcHhHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHhcccCcc--ChhheEE
Confidence 579999999999999999999999999999999999999999999999999999999 9999865
No 24
>cd03761 proteasome_beta_type_5 proteasome beta type-5 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.60 E-value=4.7e-15 Score=93.79 Aligned_cols=60 Identities=15% Similarity=0.205 Sum_probs=55.4
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
++++++|+.+|++.|++++|.++++|++.|+++||++.+|+.|++++|.+|| +||+|+.+
T Consensus 41 i~~~~sG~~~D~~~l~~~~r~~~~~y~~~~~~~i~~~~la~~ls~~l~~~~~------~~~~v~~l 100 (188)
T cd03761 41 LLGTMAGGAADCQYWERVLGRECRLYELRNKERISVAAASKLLSNMLYQYKG------MGLSMGTM 100 (188)
T ss_pred EEEEeCccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhcCC------CCeEEEEE
Confidence 5899999999999999999999999999999999999999999999998854 38888764
No 25
>cd03760 proteasome_beta_type_4 proteasome beta type-4 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis.Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.59 E-value=4.9e-15 Score=94.20 Aligned_cols=62 Identities=11% Similarity=0.156 Sum_probs=57.5
Q ss_pred CEEeecchHHHHHHHHHHHHHHHH-HHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQ-RYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~-~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+++++|+.+|++.+++++|.+++ +|++.++++||++.+++.|+++ .|||+++.| ||||+.+
T Consensus 43 i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~~la~~i~~~--~y~~~~~~r--P~~v~~i 105 (197)
T cd03760 43 TLLGASGDYADFQYLKRLLDQLVIDDECLDDGHSLSPKEIHSYLTRV--LYNRRSKMN--PLWNTLV 105 (197)
T ss_pred EEEEeCcchHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH--HHHHhhcCC--CceEEEE
Confidence 589999999999999999999997 6788999999999999999997 599999999 9999875
No 26
>cd03759 proteasome_beta_type_3 proteasome beta type-3 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.56 E-value=1.7e-14 Score=91.75 Aligned_cols=60 Identities=17% Similarity=0.324 Sum_probs=54.7
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+|+++|+.+|++.+++++|.+++.|++.++++||++.+|+.|++.+ |+|+ .| ||||+.+
T Consensus 44 i~~~~sG~~~D~~~l~~~~r~~~~~~~~~~~~~~~~~~la~~l~~~l--y~~r--~~--P~~v~~i 103 (195)
T cd03759 44 LYIGLAGLATDVQTLAQKLRFRVNLYRLREEREIKPKTFSSLISSLL--YEKR--FG--PYFVEPV 103 (195)
T ss_pred EEEEccchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH--HHhc--CC--CceEEEE
Confidence 58999999999999999999999999999999999999999999987 5554 35 9999864
No 27
>cd01906 proteasome_protease_HslV proteasome_protease_HslV. This group contains the eukaryotic proteosome alpha and beta subunits and the prokaryotic protease hslV subunit. Proteasomes are large multimeric self-compartmentalizing proteases, involved in the clearance of misfolded proteins, the breakdown of regulatory proteins, and the processing of proteins such as the preparation of peptides for immune presentation. Two main proteasomal types are distinguished by their different tertiary structures: the eukaryotic/archeal 20S proteasome and the prokaryotic proteasome-like heat shock protein encoded by heat shock locus V, hslV. The proteasome core particle is a highly conserved cylindrical structure made up of non-identical subunits that have their active sites on the inner walls of a large central cavity. The proteasome subunits of bacteria, archaea, and eukaryotes all share a conserved Ntn (N terminal nucleophile) hydrolase fold and a catalytic mechanism involving an N-terminal nucleo
Probab=99.55 E-value=1.9e-14 Score=89.40 Aligned_cols=62 Identities=37% Similarity=0.598 Sum_probs=59.3
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+++++|+.+|++.|++.+|.++.+|++.++++++++.+++.|++++|++|++ .| |||++.+
T Consensus 41 i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~--~~--p~~~~~l 102 (182)
T cd01906 41 IGCAFAGLAADAQTLVERLRKEAQLYRLRYGEPIPVEALAKLLANLLYEYTQS--LR--PLGVSLL 102 (182)
T ss_pred EEEEEeeCHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhCCC--cc--ChheEEE
Confidence 58999999999999999999999999999999999999999999999999998 88 9999864
No 28
>PF00227 Proteasome: Proteasome subunit; InterPro: IPR001353 ATP-dependent protease complexes are present in all three kingdoms of life, where they rid the cell of misfolded or damaged proteins and control the level of certain regulatory proteins. They include the proteasome in Eukaryotes, Archaea, and Actinomycetales and the HslVU (ClpQY, clpXP) complex in other eubacteria. Genes homologous to eubacterial HslV (ClpQ) and HslU (ClpY, clpX) have also been demonstrated in to be present in the genome of trypanosomatid protozoa []. The proteasome (or macropain) (3.4.25.1 from EC) [, , , , ] is a eukaryotic and archaeal multicatalytic proteinase complex that seems to be involved in an ATP/ubiquitin-dependent nonlysosomal proteolytic pathway. In eukaryotes the proteasome is composed of about 28 distinct subunits which form a highly ordered ring-shaped structure (20S ring) of about 700 kDa. Most proteasome subunits can be classified, on the basis on sequence similarities into two groups, alpha (A) and beta (B). The prokaryotic ATP-dependent proteasome is coded for by the heat-shock locus VU (HslVU). It consists of HslV, the protease (MEROPS peptidase subfamily T1B), and HslU, IPR004491 from INTERPRO, the ATPase and chaperone belonging to the AAA/Clp/Hsp100 family. The crystal structure of Thermotoga maritima HslV has been determined to 2.1-A resolution. The structure of the dodecameric enzyme is well conserved compared to those from Escherichia coli and Haemophilus influenzae [, ]. This entry contains threonine peptidases and non-peptidase homologs belong to MEROPS peptidase family T1 (proteasome family, clan PB(T)). The family consists of the protease components of the archaeal and bacterial proteasomes and the alpha and beta subunits of the eukaryotic proteasome. ; GO: 0004298 threonine-type endopeptidase activity, 0051603 proteolysis involved in cellular protein catabolic process, 0005839 proteasome core complex; PDB: 3KRD_1 3H6F_M 2FHH_F 3HF9_F 2FHG_D 3HFA_B 3H6I_K 3MI0_A 3MFE_1 3MKA_F ....
Probab=99.54 E-value=3.5e-14 Score=88.70 Aligned_cols=64 Identities=30% Similarity=0.503 Sum_probs=61.4
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+++++|..+|++.+++++|.++++|++.++++++++.+++.+++++|.+|++.+.| |++|+.+
T Consensus 46 i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~--p~~~~~l 109 (190)
T PF00227_consen 46 IIIGFSGLTADFQYLIRRLREEAQEYRFSYGRPISPEYLAKAIASLIQNYTYRSGRR--PYGVSLL 109 (190)
T ss_dssp EEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHTTTS--TTSEEEE
T ss_pred ceeeccccccchHHHHhhhcccchhhhhccCccccchhhhhhhHHHHhhhccccccc--Cccccce
Confidence 578999999999999999999999999999999999999999999999999999999 9999864
No 29
>cd03757 proteasome_beta_type_1 proteasome beta type-1 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.53 E-value=2.8e-14 Score=91.86 Aligned_cols=60 Identities=22% Similarity=0.299 Sum_probs=54.3
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+++++|+.+|++.+++++|.+++.|++.++++|+++.+++.|++.++ + .|++||||+.+
T Consensus 49 i~~~~sG~~aD~~~l~~~~r~~~~~~~~~~g~~i~~~~la~~ls~~ly--~----~R~~P~~~~~i 108 (212)
T cd03757 49 CVLGSSGFQADILALTKRLKARIKMYKYSHNKEMSTEAIAQLLSTILY--S----RRFFPYYVFNI 108 (212)
T ss_pred EEEEccchHHHHHHHHHHHHHHHHHHhHHhCCCCCHHHHHHHHHHHHH--h----hcCCCeEEEEE
Confidence 589999999999999999999999999999999999999999999983 3 34559999864
No 30
>TIGR03634 arc_protsome_B proteasome endopeptidase complex, archaeal, beta subunit. This protein family describes the archaeal proteasome beta subunit, homologous to both the alpha subunit and to the alpha and beta subunits of eukaryotic proteasome subunits. This family is universal in the first 29 complete archaeal genomes but occasionally is duplicated.
Probab=99.53 E-value=4.5e-14 Score=88.69 Aligned_cols=60 Identities=25% Similarity=0.345 Sum_probs=55.9
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+++++|..+|++.|++++|.+++.|++.+++++|++.+++.|++++|.+ ..| ||+|+.+
T Consensus 42 i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~----~~r--P~~v~~i 101 (185)
T TIGR03634 42 IAMTIAGSVGDAQSLVRILKAEAKLYELRRGRPMSVKALATLLSNILNSN----RFF--PFIVQLL 101 (185)
T ss_pred EEEEcCchHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc----CCC--CeEEEEE
Confidence 58999999999999999999999999999999999999999999999876 466 9999874
No 31
>cd03764 proteasome_beta_archeal Archeal proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme for non-lysosomal protein degradation in both the cytosol and the nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are both members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.50 E-value=1.3e-13 Score=86.90 Aligned_cols=60 Identities=23% Similarity=0.330 Sum_probs=55.3
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+++++|+.+|++.|++++|.+++.|++.++++++++.+++.+++++|.+ ..| ||+|+.+
T Consensus 41 i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~~~~~~----~~~--P~~~~~l 100 (188)
T cd03764 41 IAMTIAGSVGDAQSLVRILKAEARLYELRRGRPMSIKALATLLSNILNSS----KYF--PYIVQLL 100 (188)
T ss_pred EEEEcCccHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc----CCC--CcEEEEE
Confidence 58999999999999999999999999999999999999999999999875 345 9999864
No 32
>cd01912 proteasome_beta proteasome beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.49 E-value=1.1e-13 Score=86.90 Aligned_cols=60 Identities=18% Similarity=0.282 Sum_probs=56.8
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
++++++|+.+|++.|++++|.++++|++.++++++++.+++.+++.+|.+++ | ||+|+.+
T Consensus 41 i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~----~--P~~~~~i 100 (189)
T cd01912 41 ILLGTAGSAADTQALTRLLKRNLRLYELRNGRELSVKAAANLLSNILYSYRG----F--PYYVSLI 100 (189)
T ss_pred EEEEccccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhcCC----C--CeEEEEE
Confidence 5789999999999999999999999999999999999999999999999888 7 9999864
No 33
>cd03762 proteasome_beta_type_6 proteasome beta type-6 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.49 E-value=1e-13 Score=87.30 Aligned_cols=59 Identities=14% Similarity=0.228 Sum_probs=55.2
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|+++++|+.+|++.|++++|.+++.|++.++++++++.+++.|++++|++| | ||+|+.+
T Consensus 41 i~~~~sG~~~D~~~l~~~l~~~~~~~~~~~~~~~~~~~~a~~l~~~~~~~~-----~--~~~~~~i 99 (188)
T cd03762 41 IYCCRSGSAADTQAIADYVRYYLDMHSIELGEPPLVKTAASLFKNLCYNYK-----E--MLSAGII 99 (188)
T ss_pred EEEEecccHHHHHHHHHHHHHHHHHhHHhhCCCCCHHHHHHHHHHHHHhcc-----c--cceeeEE
Confidence 589999999999999999999999999999999999999999999998775 7 9999764
No 34
>TIGR03691 20S_bact_alpha proteasome, alpha subunit, bacterial type. Members of this family are the alpha subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In most Actinobacteria (an exception is Propionibacterium acnes), the proteasome is accompanied by a system of tagging proteins for degradation with Pup.
Probab=99.49 E-value=8.8e-14 Score=90.93 Aligned_cols=63 Identities=11% Similarity=0.053 Sum_probs=51.6
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYN-EPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~-~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
|||+++|+.+|++.|++++|.+++.|++.|+ .+++++.+|+.++..+..++ +++.| ||||+.+
T Consensus 60 ig~~~sG~~~D~~~lv~~~r~~a~~~~~~~~~~~~~v~~la~~~tq~~~~~~-~~~~R--P~gvs~L 123 (228)
T TIGR03691 60 IGFAAVGKYNEFENLRRAGIRYADMRGYSYDRRDVTGRGLANAYAQTLGTIF-TEQQK--PYEVEIC 123 (228)
T ss_pred EEEEEcCCHHHHHHHHHHHHHHHHHHhhhcCCCCccHHHHHHHHHhhccccc-ccccC--cceEEEE
Confidence 6899999999999999999999999999998 68999887754444444444 33468 9999875
No 35
>PTZ00488 Proteasome subunit beta type-5; Provisional
Probab=99.42 E-value=7.2e-13 Score=87.49 Aligned_cols=56 Identities=20% Similarity=0.262 Sum_probs=51.7
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceec
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRN 64 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~ 64 (68)
++++++|+.+|++.|++++|.+++.|++.++++||++.+|+.|++++|.+ | |||++
T Consensus 80 i~~~~sG~~aD~~~l~~~lr~~~~~y~~~~g~~isv~~la~~ls~~l~~~------R--~~~~~ 135 (247)
T PTZ00488 80 LLGTMAGGAADCSFWERELAMQCRLYELRNGELISVAAASKILANIVWNY------K--GMGLS 135 (247)
T ss_pred EEEEeCcCHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHhc------C--CCCee
Confidence 58999999999999999999999999999999999999999999999755 8 66655
No 36
>cd03763 proteasome_beta_type_7 proteasome beta type-7 subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.40 E-value=1.1e-12 Score=82.91 Aligned_cols=59 Identities=12% Similarity=0.110 Sum_probs=54.2
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
++++++|+.+|++.|++++|.+++.|++.++++++++.+++.|++.+|.|+ . ||||+.+
T Consensus 41 i~~~~sG~~~D~~~l~~~~~~~~~~~~~~~~~~~~~~~~a~~l~~~l~~~~-----~--p~~v~~i 99 (189)
T cd03763 41 IYCCGAGTAADTEAVTNMISSNLELHRLNTGRKPRVVTALTMLKQHLFRYQ-----G--HIGAALV 99 (189)
T ss_pred EEEEcCccHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHcC-----C--ccceeEE
Confidence 589999999999999999999999999999999999999999999998763 3 8988764
No 37
>cd01901 Ntn_hydrolase The Ntn hydrolases (N-terminal nucleophile) are a diverse superfamily of of enzymes that are activated autocatalytically via an N-terminally lcated nucleophilic amino acid. N-terminal nucleophile (NTN-) hydrolase superfamily, which contains a four-layered alpha, beta, beta, alpha core structure. This family of hydrolases includes penicillin acylase, the 20S proteasome alpha and beta subunits, and glutamate synthase. The mechanism of activation of these proteins is conserved, although they differ in their substrate specificities. All known members catalyze the hydrolysis of amide bonds in either proteins or small molecules, and each one of them is synthesized as a preprotein. For each, an autocatalytic endoproteolytic process generates a new N-terminal residue. This mature N-terminal residue is central to catalysis and acts as both a polarizing base and a nucleophile during the reaction. The N-terminal amino group acts as the proton acceptor and activates either t
Probab=99.31 E-value=1.4e-11 Score=73.70 Aligned_cols=61 Identities=36% Similarity=0.538 Sum_probs=58.2
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
++++++|+.+|++.+.++++.+++.|++.+++++++..+++.+++.++.+|+ .| |++++.+
T Consensus 41 ~~~~~sG~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~--p~~~~~i 101 (164)
T cd01901 41 IAWGLAGLAADAQTLVRRLREALQLYRLRYGEPISVVALAKELAKLLQVYTQ---GR--PFGVNLI 101 (164)
T ss_pred eEEEEecChHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhcC---CC--CcceEEE
Confidence 5789999999999999999999999999999999999999999999999999 78 9999865
No 38
>KOG0179|consensus
Probab=99.17 E-value=7.2e-11 Score=76.84 Aligned_cols=60 Identities=15% Similarity=0.223 Sum_probs=55.9
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
+.++.+|+.+|...|++.++.+.+.|++.+++.|++..+|+.||..+ +++|||||=+..+
T Consensus 70 ~vl~~sGF~aD~l~L~k~i~~r~~~Y~~~h~k~ms~~s~A~lls~~L------Y~kRFFPYYv~~i 129 (235)
T KOG0179|consen 70 IVLGSSGFYADTLALVKVIKSRIKQYEHDHNKKMSIHSAAQLLSTIL------YSKRFFPYYVFNI 129 (235)
T ss_pred eEEecccchhhHHHHHHHHHHHHHHHhhcccccccHHHHHHHHHHHH------hhcccccceeeee
Confidence 46889999999999999999999999999999999999999999999 8999999966543
No 39
>KOG0180|consensus
Probab=98.16 E-value=4.8e-06 Score=53.30 Aligned_cols=54 Identities=17% Similarity=0.272 Sum_probs=49.7
Q ss_pred EEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCc
Q psy3468 2 VCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPF 61 (68)
Q Consensus 2 g~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~ 61 (68)
.+..+|+.+|.+.|.+++|..-+.|++.-++.|..+.+++.+|+++ +..||=||
T Consensus 50 y~GL~glatDvqtl~~~~~fr~nLy~lre~R~i~P~~~s~mvS~~l------YekRfgpY 103 (204)
T KOG0180|consen 50 YLGLTGLATDVQTLLERLRFRKNLYELREEREIKPETFSSMVSSLL------YEKRFGPY 103 (204)
T ss_pred EEeccccchhHHHHHHHHHHHHhHHHhhhhcccCcHHHHHHHHHHH------HHhhcCCc
Confidence 3678999999999999999999999999999999999999999999 66777666
No 40
>cd01913 protease_HslV Protease HslV and the ATPase/chaperone HslU are part of an ATP-dependent proteolytic system that is the prokaryotic homolog of the proteasome. HslV is a dimer of hexamers (a dodecamer) that forms a central proteolytic chamber with active sites on the interior walls of the cavity. HslV shares significant sequence and structural similarity with the proteasomal beta-subunit and both are members of the Ntn-family of hydrolases. HslV has a nucleophilic threonine residue at its N-terminus that is exposed after processing of the propeptide and is directly involved in active site catalysis.
Probab=97.67 E-value=6.9e-05 Score=47.56 Aligned_cols=32 Identities=25% Similarity=0.280 Sum_probs=30.0
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCC
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNE 32 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~ 32 (68)
|+|+.||..+|++.|.+++|.+++.|+.+.++
T Consensus 42 i~~~~aG~~aD~~~l~~~~~~~~~~y~~~~~~ 73 (171)
T cd01913 42 VIAGFAGSTADAFTLFERFEAKLEQYPGNLLR 73 (171)
T ss_pred EEEEecccHHHHHHHHHHHHHHHHHhhchHHH
Confidence 57999999999999999999999999999885
No 41
>KOG0175|consensus
Probab=97.61 E-value=0.00016 Score=48.73 Aligned_cols=47 Identities=17% Similarity=0.189 Sum_probs=44.6
Q ss_pred eecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHh
Q psy3468 4 SVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGY 50 (68)
Q Consensus 4 ~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~ 50 (68)
+++|=.||+++--+.+-.||..|++.+++.|+|...++.||+++.+|
T Consensus 115 TmAGgAADCqfWer~L~kecRL~eLRnkeriSVsaASKllsN~~y~Y 161 (285)
T KOG0175|consen 115 TMAGGAADCQFWERVLAKECRLHELRNKERISVSAASKLLSNMVYQY 161 (285)
T ss_pred cccCcchhhHHHHHHHHHHHHHHHHhcCcceehHHHHHHHHHHHhhc
Confidence 68999999999999999999999999999999999999999999655
No 42
>PRK05456 ATP-dependent protease subunit HslV; Provisional
Probab=97.48 E-value=0.00038 Score=44.03 Aligned_cols=27 Identities=26% Similarity=0.266 Sum_probs=25.7
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHH
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYL 27 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~ 27 (68)
++|+.||..+|++.|.+.++.+++.|+
T Consensus 43 i~~~~aG~~aD~q~l~~~l~~~~~~y~ 69 (172)
T PRK05456 43 VLAGFAGSTADAFTLFERFEAKLEEHQ 69 (172)
T ss_pred EEEEEeccHHHHHHHHHHHHHHHHHcc
Confidence 478999999999999999999999998
No 43
>KOG0174|consensus
Probab=97.46 E-value=0.00048 Score=44.94 Aligned_cols=52 Identities=21% Similarity=0.355 Sum_probs=48.2
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhh
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQ 52 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq 52 (68)
|.|+-||..+|.+.+.+.+|.....|...+++|+.|...|+...++..+|-.
T Consensus 60 i~cCRSGSAADtQaiaD~~~Y~L~~~~~q~~~~p~v~~aA~l~r~~~Y~~re 111 (224)
T KOG0174|consen 60 IYCCRSGSAADTQAIADIVRYHLELYTIQENKPPLVHTAASLFREICYNYRE 111 (224)
T ss_pred EEEecCCchhhHHHHHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHHHhCHH
Confidence 5789999999999999999999999999999999999999999999876654
No 44
>TIGR03692 ATP_dep_HslV ATP-dependent protease HslVU, peptidase subunit. The ATP-dependent protease HslVU, a complex of hexameric HslU active as a protein-unfolding ATPase and dodecameric HslV, the catalytic threonine protease.
Probab=97.08 E-value=0.0013 Score=41.80 Aligned_cols=40 Identities=25% Similarity=0.241 Sum_probs=32.1
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCD 45 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~ 45 (68)
|+|+.||..+|++.|.+++|.+++.|+... .+.+++.+.+
T Consensus 42 i~~~~aG~~aD~q~l~~~~~~~~~~y~~~~-----~~~~a~l~~~ 81 (171)
T TIGR03692 42 VLAGFAGSTADAFTLFERFEAKLEEYQGNL-----TRAAVELAKD 81 (171)
T ss_pred EEEEecchHHHHHHHHHHHHHHHHHccCch-----HHHHHHHHHH
Confidence 579999999999999999999999998743 3555554444
No 45
>KOG0177|consensus
Probab=95.05 E-value=0.083 Score=34.36 Aligned_cols=61 Identities=13% Similarity=0.114 Sum_probs=51.1
Q ss_pred EEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCceeccc
Q psy3468 2 VCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKT 66 (68)
Q Consensus 2 g~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~ 66 (68)
.|+++|=.+|.-...++.....+.|+..+|.+++++..|+-+-..+.++-. +++ ||-|+..
T Consensus 43 lm~~~Ge~GDt~qF~eyi~~Ni~LYkirnGyeLSp~~aahFtR~~La~~LR--sr~--~yqV~~L 103 (200)
T KOG0177|consen 43 LMATVGEAGDTVQFTEYIQKNIQLYKIRNGYELSPSAAAHFTRRELAESLR--SRT--PYQVNIL 103 (200)
T ss_pred eeeeecCCCceehHHHHHHhhhhHHhhhcCCcCCHHHHHHHHHHHHHHHHh--cCC--CceEEEE
Confidence 578999999999999999999999999999999999999866655554433 477 8888753
No 46
>KOG0173|consensus
Probab=80.21 E-value=4.6 Score=27.52 Aligned_cols=50 Identities=14% Similarity=0.149 Sum_probs=41.0
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHh
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGY 50 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~ 50 (68)
|.|+-+|-.+|...+.+..-.+...|+++.++.++|-..-+.+-..+..|
T Consensus 78 IyccGAGtAADte~vt~m~ss~l~Lh~l~t~R~~rVv~A~~mlkQ~LFrY 127 (271)
T KOG0173|consen 78 IYCCGAGTAADTEMVTRMISSNLELHRLNTGRKPRVVTALRMLKQHLFRY 127 (271)
T ss_pred eEEccCCchhhHHHHHHHHHHHHHHHHhccCCCCceeeHHHHHHHHHHHh
Confidence 57888999999998888888888999999999999976666666665554
No 47
>PF15412 Nse4-Nse3_bdg: Binding domain of Nse4/EID3 to Nse3-MAGE
Probab=76.06 E-value=7.7 Score=20.08 Aligned_cols=36 Identities=14% Similarity=0.150 Sum_probs=29.4
Q ss_pred HHHHHH---HHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy3468 11 DANVLT---SELRAIAQRYLIQYNEPIPCEQLVACLCDIK 47 (68)
Q Consensus 11 D~r~lv---~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~ 47 (68)
|++.|+ +.+...+++.++. +.-+.++..+.++-.+|
T Consensus 1 DS~~Lv~aSdla~~ka~~lk~~-~~~fd~deFv~~l~~fm 39 (56)
T PF15412_consen 1 DSRLLVLASDLAAEKARNLKFG-GSGFDVDEFVSKLKTFM 39 (56)
T ss_pred CcHHHHHHHHHHHHHHHHhccC-CCccCHHHHHHHHHHHh
Confidence 566666 6677778888877 88899999999999988
No 48
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=73.71 E-value=8.8 Score=20.34 Aligned_cols=30 Identities=7% Similarity=-0.022 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy3468 16 TSELRAIAQRYLIQYNEPIPCEQLVACLCD 45 (68)
Q Consensus 16 v~~~r~~a~~y~~~~~~~i~v~~la~~ls~ 45 (68)
+++.+..........|++++.+.+|+.+.-
T Consensus 3 l~~i~~a~~~L~~~lgr~Pt~eEiA~~lgi 32 (78)
T PF04539_consen 3 LRKIERARRELEQELGREPTDEEIAEELGI 32 (78)
T ss_dssp HHHHHHHHHHHHHHHSS--BHHHHHHHHTS
T ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHHcc
Confidence 455666667888899999999999987653
No 49
>COG5405 HslV ATP-dependent protease HslVU (ClpYQ), peptidase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=73.18 E-value=4.2 Score=26.10 Aligned_cols=26 Identities=31% Similarity=0.397 Sum_probs=22.9
Q ss_pred EEeecchHHHHHHHHHHHHHHHHHHH
Q psy3468 2 VCSVAGITSDANVLTSELRAIAQRYL 27 (68)
Q Consensus 2 g~~~sGl~aD~r~lv~~~r~~a~~y~ 27 (68)
-..++|-++|+..|.++.-.+++.|.
T Consensus 47 laGFAGstADaftLfe~fe~kle~~~ 72 (178)
T COG5405 47 LAGFAGSTADAFTLFERFEAKLEQYQ 72 (178)
T ss_pred EEEecccchhHHHHHHHHHHHHHHcc
Confidence 46789999999999999988888886
No 50
>KOG0185|consensus
Probab=72.58 E-value=8.8 Score=25.96 Aligned_cols=46 Identities=11% Similarity=0.125 Sum_probs=37.6
Q ss_pred EEeecchHHHHHHHHHHHHHHHHHHH-HHhCCCCCHHHHHHHHHHHH
Q psy3468 2 VCSVAGITSDANVLTSELRAIAQRYL-IQYNEPIPCEQLVACLCDIK 47 (68)
Q Consensus 2 g~~~sGl~aD~r~lv~~~r~~a~~y~-~~~~~~i~v~~la~~ls~~~ 47 (68)
.++++|=.+|.+.|.+.+-+...+.. +.=++.+..+.+.+.|...|
T Consensus 83 llG~sGdisD~Q~i~r~L~~l~iedn~~~Dg~~l~Pk~ih~yltrvl 129 (256)
T KOG0185|consen 83 LLGASGDISDFQYIQRVLEQLVIEDNRLDDGQSLGPKAIHSYLTRVL 129 (256)
T ss_pred EEecCccHHHHHHHHHHHHHHHhcccccccccccChHHHHHHHHHHH
Confidence 46789999999999988877666632 33458899999999999998
No 51
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=62.22 E-value=13 Score=19.78 Aligned_cols=24 Identities=13% Similarity=0.232 Sum_probs=16.1
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHH
Q psy3468 22 IAQRYLIQYNEPIPCEQLVACLCD 45 (68)
Q Consensus 22 ~a~~y~~~~~~~i~v~~la~~ls~ 45 (68)
...+|...+|.|+++..+++.++-
T Consensus 14 ~I~~~~~~~G~~Pt~rEIa~~~g~ 37 (65)
T PF01726_consen 14 FIREYIEENGYPPTVREIAEALGL 37 (65)
T ss_dssp HHHHHHHHHSS---HHHHHHHHTS
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCC
Confidence 346777889999999999887653
No 52
>PF01242 PTPS: 6-pyruvoyl tetrahydropterin synthase; InterPro: IPR007115 The complex organic chemistry involved in the transformation of GTP to tetrahydrobiopterin is catalysed by only three enzymes: GTP cyclohydrolase I, 6-pyruvoyltetrahydropterin synthase and sepiapterin reductase. Tetrahydrobiopterin is the cofactor for several aromatic amino acid monooxygenases and the nitric oxide synthases. 6-Pyruvoyl tetrahydropterin synthase (PTPS) [] is a Zn-dependent metalloprotein, transforms dihydroneopterin triphosphate into 6-pyruvoyltetrahydropterin in the presence of Mg(II) and for which the crystal structure is known. The enzyme is a homohexameric, composed of a dimer of trimers. A transition metal binding site formed by the three histidine residues 23, 48 and 50 is present in each subunit, and bound Zn(II) is responsible for the enzymatic activity. Site-directed mutagenesis of each of these three histidine residues results in a complete loss of metal binding and enzymatic activity [, ]. The function of the bacterial branch of the sequence lineage appears not to have been established.; GO: 0003874 6-pyruvoyltetrahydropterin synthase activity, 0046872 metal ion binding, 0006729 tetrahydrobiopterin biosynthetic process; PDB: 3QNA_E 3QN9_A 3QN0_B 1Y13_C 3D7J_A 3I2B_J 2OBA_D 3M0N_A 2A0S_A 3LZE_A ....
Probab=61.86 E-value=18 Score=21.06 Aligned_cols=50 Identities=14% Similarity=0.137 Sum_probs=33.9
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHhCCC-----------CCHHHHHHHHHHHHHHhhhcCCC
Q psy3468 6 AGITSDANVLTSELRAIAQRYLIQYNEP-----------IPCEQLVACLCDIKQGYTQYGGQ 56 (68)
Q Consensus 6 sGl~aD~r~lv~~~r~~a~~y~~~~~~~-----------i~v~~la~~ls~~~q~~Tq~~~~ 56 (68)
.|++-|...|-+..+..+..+-+.+- + ++++.||..|.+.+...-...+.
T Consensus 43 ~g~v~DF~~lk~~~~~i~~~lDh~~L-n~~~~~~~~~~~pT~E~lA~~i~~~l~~~l~~~~~ 103 (123)
T PF01242_consen 43 DGMVVDFGDLKKIIKEIDDQLDHKFL-NEDDPEFDDINNPTAENLARWIFERLKEKLSPPGV 103 (123)
T ss_dssp TSSSS-HHHHHHHHHHHHHHHTTEEG-GHHSGCGCSSTS--HHHHHHHHHHHHHHHHHHTTT
T ss_pred CCEEEEHHHHHHHHHHHHHHhCcccc-cCCChhhhccCCCCHHHHHHHHHHHHHHHhccccc
Confidence 58888888888888876665544443 3 78999999999988776633333
No 53
>PF09069 EF-hand_3: EF-hand; InterPro: IPR015154 Like other EF hand domains, this domain forms a helix-loop-helix motif, though since it does not contain the canonical pattern of calcium binding residues found in many EF hand domains, it does not bind calcium ions. The main function of this domain is the provision of specificity in beta-dystroglycan recognition, though in dystrophin it serves an additional role: stabilisation of the WW domain (IPR001202 from INTERPRO), enhancing dystroglycan binding []. ; PDB: 1EG3_A 1EG4_A.
Probab=61.54 E-value=28 Score=19.86 Aligned_cols=45 Identities=18% Similarity=0.076 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCcee
Q psy3468 16 TSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFRR 63 (68)
Q Consensus 16 v~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~ 63 (68)
.++.|..-+.+ ..-+.-|+-+.|...|-+.+|..++-+... .||-
T Consensus 2 ~dKyRylFsli-sd~~g~~~~~~l~~lL~d~lqip~~vgE~~--aFg~ 46 (90)
T PF09069_consen 2 EDKYRYLFSLI-SDSNGCMDQRKLGLLLHDVLQIPRAVGEGP--AFGY 46 (90)
T ss_dssp HHHHHHHHHHH-S-TTS-B-HHHHHHHHHHHHHHHHHTT-GG--GGT-
T ss_pred hHHHHHHHHHH-cCCCCCCcHHHHHHHHHHHHHHHHHhCccc--cccC
Confidence 44555433333 223456888999999999999999999988 8874
No 54
>PF15286 Bcl-2_3: Apoptosis regulator M11, B cell 2 leukaemia/lymphoma like; PDB: 3BL2_B 3DVU_B 2ABO_A.
Probab=56.41 E-value=33 Score=20.64 Aligned_cols=32 Identities=13% Similarity=0.207 Sum_probs=27.9
Q ss_pred eecchHHHHHHHHHHHHHHHHHHHHHhCCCCC
Q psy3468 4 SVAGITSDANVLTSELRAIAQRYLIQYNEPIP 35 (68)
Q Consensus 4 ~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~ 35 (68)
.-||+.+|...|++........|...|+...+
T Consensus 23 v~s~vL~DV~~i~~LTqeF~~~YdSVy~~d~~ 54 (126)
T PF15286_consen 23 VDSGVLADVSKIITLTQEFRTHYDSVYGKDYG 54 (126)
T ss_dssp TCCCHHHHHHHHHHHHHHHHHHHHHHHSSTSG
T ss_pred cchhHHHhHHHHHHHHHHHHHHHHHHhcccCC
Confidence 45899999999999999999999999987544
No 55
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=54.58 E-value=25 Score=18.65 Aligned_cols=26 Identities=19% Similarity=0.068 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy3468 20 RAIAQRYLIQYNEPIPCEQLVACLCD 45 (68)
Q Consensus 20 r~~a~~y~~~~~~~i~v~~la~~ls~ 45 (68)
|.+|.+.....+..|+...+|..|+-
T Consensus 9 rdkA~e~y~~~~g~i~lkdIA~~Lgv 34 (60)
T PF10668_consen 9 RDKAFEIYKESNGKIKLKDIAEKLGV 34 (60)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHHCC
Confidence 56777777888999999999988763
No 56
>PF08208 RNA_polI_A34: DNA-directed RNA polymerase I subunit RPA34.5; InterPro: IPR013240 This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription [].; PDB: 3NFG_N.
Probab=54.21 E-value=4.2 Score=25.85 Aligned_cols=10 Identities=20% Similarity=0.438 Sum_probs=0.0
Q ss_pred CCCCCceecc
Q psy3468 56 QSIIPFRRNK 65 (68)
Q Consensus 56 ~R~~P~g~~~ 65 (68)
+||+|||.+.
T Consensus 115 ~Rf~P~G~~~ 124 (198)
T PF08208_consen 115 MRFFPFGYGS 124 (198)
T ss_dssp ----------
T ss_pred eeeecCCCCc
Confidence 6999999864
No 57
>TIGR03342 dsrC_tusE_dsvC sulfur relay protein, TusE/DsrC/DsvC family. Members of this protein family may be described as TusE, a partner to TusBCD in a sulfur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Other members are DsrC, a functionally similar protein in species where the sulfur relay system exists primarily for sulfur metabolism rather than tRNA base modification. Some members of this family are known explicitly as the gamma subunit of sulfite reductases.
Probab=51.05 E-value=50 Score=19.48 Aligned_cols=35 Identities=20% Similarity=0.236 Sum_probs=26.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Q psy3468 8 ITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDI 46 (68)
Q Consensus 8 l~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~ 46 (68)
|+.|---+|+.+|. |..+|+..+++..|++.+...
T Consensus 38 LT~~Hw~vI~~lR~----~y~e~~~~P~~R~l~K~~~~~ 72 (108)
T TIGR03342 38 LTEAHWEVINFLRD----FYAEYNISPAVRMLVKAMGKK 72 (108)
T ss_pred CCHHHHHHHHHHHH----HHHHHCCCCcHHHHHHHHHHH
Confidence 55666678888874 667788999999999877653
No 58
>COG4537 ComGC Competence protein ComGC [Intracellular trafficking and secretion]
Probab=49.04 E-value=48 Score=19.64 Aligned_cols=29 Identities=17% Similarity=0.281 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHhCC-CCCHHHHH
Q psy3468 12 ANVLTSELRAIAQRYLIQYNE-PIPCEQLV 40 (68)
Q Consensus 12 ~r~lv~~~r~~a~~y~~~~~~-~i~v~~la 40 (68)
+..+++....++..|+..+++ |++++.|-
T Consensus 49 c~A~vkmV~sQ~~~YeLdh~~~~pSl~~L~ 78 (107)
T COG4537 49 CEAVVKMVESQAEAYELDHNRLPPSLSDLK 78 (107)
T ss_pred HHHHHHHHHHHHHHHHhccCCCCCCHHHHH
Confidence 346788889999999999988 77766553
No 59
>PF13120 DUF3974: Domain of unknown function (DUF3974)
Probab=47.26 E-value=6.7 Score=23.23 Aligned_cols=19 Identities=26% Similarity=0.176 Sum_probs=14.9
Q ss_pred CHHHHHHHHHHHHHHhhhc
Q psy3468 35 PCEQLVACLCDIKQGYTQY 53 (68)
Q Consensus 35 ~v~~la~~ls~~~q~~Tq~ 53 (68)
+++.|.++--.++|+|||+
T Consensus 46 sieklsnkstpflqeftqh 64 (126)
T PF13120_consen 46 SIEKLSNKSTPFLQEFTQH 64 (126)
T ss_pred HHHHhcccCCHHHHHHhcC
Confidence 5666777667789999997
No 60
>KOG4119|consensus
Probab=47.07 E-value=49 Score=18.22 Aligned_cols=37 Identities=14% Similarity=0.017 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhh
Q psy3468 9 TSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYT 51 (68)
Q Consensus 9 ~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~T 51 (68)
.++.+..|+.+|.|+..-| ++|+.++..|.++.-..-
T Consensus 9 ~~q~k~~VeqLk~e~~~~R------~~vS~a~~el~~y~E~~~ 45 (71)
T KOG4119|consen 9 KPQMKKEVEQLKLEANIER------IKVSKAAAELLEYCETHA 45 (71)
T ss_pred hHHHHHHHHHHHHHHHhhH------hhHHHHHHHHHHHHHhcC
Confidence 4688899999998887654 778889988888875443
No 61
>PRK11508 sulfur transfer protein TusE; Provisional
Probab=46.94 E-value=60 Score=19.20 Aligned_cols=35 Identities=11% Similarity=0.294 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Q psy3468 8 ITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDI 46 (68)
Q Consensus 8 l~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~ 46 (68)
|+.|---+|+.+|. |..+|+..+++..|++.+...
T Consensus 39 LT~~HW~VI~~lR~----~y~e~~~~P~~R~l~K~~~~~ 73 (109)
T PRK11508 39 LSPEHWEVVRFVRD----FYLEFNTSPAIRMLVKAMANK 73 (109)
T ss_pred CCHHHHHHHHHHHH----HHHHHCCCCcHHHHHHHHHHH
Confidence 45566667888874 667789999999999977653
No 62
>PF06018 CodY: CodY GAF-like domain; InterPro: IPR010312 This family consists of several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; GO: 0003677 DNA binding, 0005525 GTP binding; PDB: 2HGV_A 2GX5_D 2B0L_C 2B18_A.
Probab=44.41 E-value=73 Score=20.40 Aligned_cols=36 Identities=19% Similarity=0.306 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHh
Q psy3468 15 LTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGY 50 (68)
Q Consensus 15 lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~ 50 (68)
|.++.|..-+--+..-+.+++-+.+|+.||+++..+
T Consensus 2 LLeKtRkIN~lLQ~~~~~~v~F~~ia~vL~dvl~aN 37 (177)
T PF06018_consen 2 LLEKTRKINRLLQKSAGEPVDFNDIAEVLSDVLEAN 37 (177)
T ss_dssp HHHHHHHHHHHHHSHTTSS--HHHHHHHHHHHHTSE
T ss_pred hHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhhcCc
Confidence 567777666666666889999999999999999644
No 63
>PF01972 SDH_sah: Serine dehydrogenase proteinase; InterPro: IPR002825 This family of archaebacterial proteins, formerly known as DUF114, has been found to be a serine dehydrogenase proteinase distantly related to ClpP proteinases that belong to the serine proteinase superfamily. The family belong to MEROPS peptidase family S49; they are mostly unassigned peptidases but include the archaean signal peptide peptidase 1 []. The family has a catalytic triad of Ser, Asp, His residues, which shows an altered residue ordering compared with the ClpP proteinases but similar to that of the carboxypeptidase clan []. ; GO: 0016021 integral to membrane
Probab=40.68 E-value=36 Score=23.55 Aligned_cols=33 Identities=15% Similarity=0.080 Sum_probs=25.4
Q ss_pred HHHHHhCCCCCHHHHHH-----------HHHHHHHHhhhcCCCC
Q psy3468 25 RYLIQYNEPIPCEQLVA-----------CLCDIKQGYTQYGGQS 57 (68)
Q Consensus 25 ~y~~~~~~~i~v~~la~-----------~ls~~~q~~Tq~~~~R 57 (68)
+-+++++.||+++.+-+ ++-.+|..|.|..+.|
T Consensus 222 ~g~~tHdypi~~eea~~lGL~V~t~~p~ei~~lm~lypq~~~~~ 265 (285)
T PF01972_consen 222 SGKWTHDYPITVEEAKELGLPVSTDMPEEIYELMDLYPQPVQRR 265 (285)
T ss_pred CCCCCCCCCCCHHHHHHcCCCcCCCCcHHHHHHHHhCccccCCC
Confidence 34567888888887653 7788889999988877
No 64
>COG0282 ackA Acetate kinase [Energy production and conversion]
Probab=40.42 E-value=12 Score=26.86 Aligned_cols=42 Identities=10% Similarity=0.068 Sum_probs=25.2
Q ss_pred EeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy3468 3 CSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIK 47 (68)
Q Consensus 3 ~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~ 47 (68)
+.+||+..|.|.|.+..-.- +. -..-..|-+.+++++++.++
T Consensus 273 lGlSg~ssD~R~l~~~~~~g--~~-A~lA~~~f~~Ri~kyIg~y~ 314 (396)
T COG0282 273 LGLSGLSSDMRDLEEAAAEG--NE-AKLALDMFVYRIAKYIGSYA 314 (396)
T ss_pred cccccccchHHHHHHHhccC--ch-HHHHHHHHHHHHHHHHHHHH
Confidence 46789999999997554333 10 11112344566777777665
No 65
>PF15606 Toxin_55: Putative toxin 55
Probab=36.95 E-value=50 Score=18.46 Aligned_cols=12 Identities=17% Similarity=0.398 Sum_probs=6.6
Q ss_pred EeecchHHHHHH
Q psy3468 3 CSVAGITSDANV 14 (68)
Q Consensus 3 ~~~sGl~aD~r~ 14 (68)
|+.-|..+|.-+
T Consensus 9 MAa~GNqaDTgI 20 (77)
T PF15606_consen 9 MAAPGNQADTGI 20 (77)
T ss_pred hccCCCchhHHH
Confidence 455566666543
No 66
>PF15054 DUF4535: Domain of unknown function (DUF4535)
Probab=36.74 E-value=59 Score=16.37 Aligned_cols=24 Identities=21% Similarity=0.216 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhCC
Q psy3468 9 TSDANVLTSELRAIAQRYLIQYNE 32 (68)
Q Consensus 9 ~aD~r~lv~~~r~~a~~y~~~~~~ 32 (68)
+|+.+-|++.+-..++++.-.|..
T Consensus 22 VPnv~kl~~~~~~~ak~~e~~yrK 45 (46)
T PF15054_consen 22 VPNVKKLAETGLDKAKDYEEQYRK 45 (46)
T ss_pred CCchHHHHHHHHHHHHHHHHHhCC
Confidence 355566666666666666665544
No 67
>PF10113 Fibrillarin_2: Fibrillarin-like archaeal protein; InterPro: IPR016760 Members of this protein family are HmdC, whose gene regularly occurs in the context of genes for HmdA (5,10-methenyltetrahydromethanopterin hydrogenase) and the radical SAM protein HmdB involved in biosynthesis of the HmdA cofactor. Bioinformatics suggests this protein, a homologue of eukaryotic fibrillarin, may be involved in biosynthesis of the guanylyl pyridinol cofactor in HmdA.
Probab=36.50 E-value=27 Score=25.76 Aligned_cols=41 Identities=12% Similarity=0.092 Sum_probs=30.9
Q ss_pred HHHHhCCCCCHHHHHHHHHHHHHHhhhcCCC--CCCCceeccc
Q psy3468 26 YLIQYNEPIPCEQLVACLCDIKQGYTQYGGQ--SIIPFRRNKT 66 (68)
Q Consensus 26 y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~--R~~P~g~~~~ 66 (68)
.+..++..-.+..++.-++++.-+=+|.=|. |=||+||-++
T Consensus 19 ~k~~~~~~~~i~evVdav~~Ls~ee~~kLG~nfk~FPlGCDL~ 61 (505)
T PF10113_consen 19 RKMIIEKEKDIIEVVDAVSDLSREEIIKLGSNFKRFPLGCDLT 61 (505)
T ss_pred HHhhccccccHHHHHHHHhhcCHHHHHHHhhhhccCCcCCchh
Confidence 3444556777888999999998888887665 4489999765
No 68
>TIGR00039 6PTHBS 6-pyruvoyl tetrahydropterin synthase/QueD family protein. This model has been downgraded from hypothetical_equivalog to subfamily. The animal enzymes are known to be 6-pyruvoyl tetrahydropterin synthase. The function of the bacterial branch of the sequence lineage had been thought to be the same, but many are now taken to be QueD, and enzyme of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of some tRNAs in most species. A new model is built to be the QueD equivalog model.
Probab=35.96 E-value=30 Score=20.38 Aligned_cols=45 Identities=16% Similarity=0.203 Sum_probs=31.4
Q ss_pred cchHHHHHHHHHHHHHHHHH---HHHHh-----CCCCCHHHHHHHHHHHHHHh
Q psy3468 6 AGITSDANVLTSELRAIAQR---YLIQY-----NEPIPCEQLVACLCDIKQGY 50 (68)
Q Consensus 6 sGl~aD~r~lv~~~r~~a~~---y~~~~-----~~~i~v~~la~~ls~~~q~~ 50 (68)
.|++-|...|-+..+..... |++-. ..+++.+.+|..+-+.++..
T Consensus 45 ~G~viDf~~lk~~~~~~~~~~lDH~~Ln~~~~~~~~pT~Enia~~i~~~l~~~ 97 (124)
T TIGR00039 45 TGMVMDFSDLKKIVKEVIDEPLDHKLLNDDVNYLENPTSENVAVYIFDNLKEY 97 (124)
T ss_pred ceEEEEHHHHHHHHHHHhccCCCCceeccCCCCCCCCCHHHHHHHHHHHHHHh
Confidence 46777888887777766643 44432 34578999999998887644
No 69
>PRK14752 delta-hemolysin; Provisional
Probab=35.64 E-value=47 Score=16.30 Aligned_cols=19 Identities=21% Similarity=0.279 Sum_probs=14.3
Q ss_pred CHHHHHHHHHHHHHHhhhc
Q psy3468 35 PCEQLVACLCDIKQGYTQY 53 (68)
Q Consensus 35 ~v~~la~~ls~~~q~~Tq~ 53 (68)
++..+++.+-+-.|+|||.
T Consensus 26 tig~~vk~ii~tv~kft~k 44 (44)
T PRK14752 26 TIGDLVKWIIDTVNKFTKK 44 (44)
T ss_pred HHHHHHHHHHHHHHHHccC
Confidence 3456778888888999873
No 70
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=35.10 E-value=77 Score=19.10 Aligned_cols=22 Identities=9% Similarity=0.197 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhC
Q psy3468 10 SDANVLTSELRAIAQRYLIQYN 31 (68)
Q Consensus 10 aD~r~lv~~~r~~a~~y~~~~~ 31 (68)
+..+..+.+++..|++++..||
T Consensus 150 ~tV~~~l~Ra~~~~~~~~~~~~ 171 (172)
T PRK09651 150 SSVKKYVAKATEHCLLFRLEYG 171 (172)
T ss_pred HHHHHHHHHHHHHHHHHHHHcC
Confidence 4567888999999999999987
No 71
>COG4114 FhuF Uncharacterized Fe-S protein [General function prediction only]
Probab=34.71 E-value=1.1e+02 Score=20.66 Aligned_cols=47 Identities=19% Similarity=0.362 Sum_probs=34.9
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHH-------HHHHHHHHHHhhhcC
Q psy3468 7 GITSDANVLTSELRAIAQRYLIQYNEPIPCEQL-------VACLCDIKQGYTQYG 54 (68)
Q Consensus 7 Gl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~l-------a~~ls~~~q~~Tq~~ 54 (68)
|+.+|.+-.+.+.|..-..+. +.++++|.+.. -.-+++++|+|..++
T Consensus 13 ~Lsaa~~e~~ak~r~hf~~~l-~ldd~~p~eam~la~ws~~~~l~~l~~~y~dh~ 66 (251)
T COG4114 13 GLSAAVRETIAKTREHFLEFL-RLDDPIPLEAMTLAQWSSPNTLSSLLAVYSDHY 66 (251)
T ss_pred hHHHHHHHHHHHHHHHHHHHH-hcCCCCChhhhhhhhccCccchHHHHHhhhhhh
Confidence 889999999999997777665 34588888776 235677777777653
No 72
>cd04742 NPD_FabD 2-Nitropropane dioxygenase (NPD)-like domain, associated with the (acyl-carrier-protein) S-malonyltransferase FabD. NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDPs are members of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN.
Probab=34.56 E-value=54 Score=23.73 Aligned_cols=30 Identities=13% Similarity=0.306 Sum_probs=20.0
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCCCCCCCceecccC
Q psy3468 33 PIPCEQLVACLCDIKQGYTQYGGQSIIPFRRNKTK 67 (68)
Q Consensus 33 ~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~~~~~ 67 (68)
.++.+.+-..|..+.+.-|- .+ |||||++-
T Consensus 47 ~l~~e~l~~~I~~ir~~lt~---~~--PfGVNL~~ 76 (418)
T cd04742 47 GLPLDEVEQAIERIQAALGN---GE--PYGVNLIH 76 (418)
T ss_pred CCCHHHHHHHHHHHHHhccC---CC--CeEEeeec
Confidence 35677777777777543332 47 99999874
No 73
>PF08958 DUF1871: Domain of unknown function (DUF1871); InterPro: IPR015053 This set of hypothetical proteins is produced by prokaryotes pertaining to the Bacillus genus. ; PDB: 1U84_A.
Probab=34.45 E-value=87 Score=17.42 Aligned_cols=31 Identities=13% Similarity=0.178 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHH
Q psy3468 18 ELRAIAQRYLIQYNEPIPCEQLVACLCDIKQG 49 (68)
Q Consensus 18 ~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~ 49 (68)
.|+..-.-|.+.|++.+|.+.+- .+|..+-.
T Consensus 40 LA~~Iq~If~~SF~e~~~~e~C~-~iA~klL~ 70 (79)
T PF08958_consen 40 LAKKIQSIFEFSFGEWLPIEECE-EIAEKLLA 70 (79)
T ss_dssp HHHHHHHHHHHHHSS---HHHHH-HHHHHHHH
T ss_pred HHHHHHHHHHHHHcccCCHHHHH-HHHHHHHh
Confidence 34444578999999999998875 67766543
No 74
>PF06057 VirJ: Bacterial virulence protein (VirJ); InterPro: IPR010333 This entry contains several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localised to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium [].
Probab=34.26 E-value=71 Score=20.77 Aligned_cols=25 Identities=28% Similarity=0.194 Sum_probs=21.4
Q ss_pred CCCHHHHHHHHHHHHHHhhhcCCCC
Q psy3468 33 PIPCEQLVACLCDIKQGYTQYGGQS 57 (68)
Q Consensus 33 ~i~v~~la~~ls~~~q~~Tq~~~~R 57 (68)
.=+.++.|..|+.+++.|.+.|+.+
T Consensus 44 ~rtP~~~a~Dl~~~i~~y~~~w~~~ 68 (192)
T PF06057_consen 44 ERTPEQTAADLARIIRHYRARWGRK 68 (192)
T ss_pred hCCHHHHHHHHHHHHHHHHHHhCCc
Confidence 3455899999999999999998875
No 75
>PRK04158 transcriptional repressor CodY; Validated
Probab=34.03 E-value=1.2e+02 Score=20.68 Aligned_cols=38 Identities=18% Similarity=0.260 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhh
Q psy3468 14 VLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYT 51 (68)
Q Consensus 14 ~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~T 51 (68)
.|.++.|..-.--+...+.|++-+.+|..||+.+..+.
T Consensus 3 ~LL~ktR~in~~lq~~~~~~v~f~~~a~~L~~~l~~nv 40 (256)
T PRK04158 3 SLLEKTRKINRLLQKSAGEPVDFNEMAEVLSDVIDCNV 40 (256)
T ss_pred hHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHhhCCCE
Confidence 47788887777777777999999999999999986443
No 76
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=33.82 E-value=45 Score=17.00 Aligned_cols=31 Identities=10% Similarity=0.081 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHhCCCC-CHHHHHHHH
Q psy3468 13 NVLTSELRAIAQRYLIQYNEPI-PCEQLVACL 43 (68)
Q Consensus 13 r~lv~~~r~~a~~y~~~~~~~i-~v~~la~~l 43 (68)
..+.+.++.....-++..|+.+ +...|++.+
T Consensus 3 ~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~ 34 (64)
T PF00392_consen 3 EQIYDQLRQAILSGRLPPGDRLPSERELAERY 34 (64)
T ss_dssp HHHHHHHHHHHHTTSS-TTSBE--HHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHh
Confidence 4567778888888888888888 666666543
No 77
>cd04795 SIS SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=33.07 E-value=45 Score=17.32 Aligned_cols=21 Identities=14% Similarity=0.086 Sum_probs=16.5
Q ss_pred CEEeecchHHHHHHHHHHHHH
Q psy3468 1 MVCSVAGITSDANVLTSELRA 21 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~ 21 (68)
|+++.+|..+|...+++.+|.
T Consensus 52 i~iS~sg~t~~~~~~~~~a~~ 72 (87)
T cd04795 52 IALSYSGRTEELLAALEIAKE 72 (87)
T ss_pred EEEECCCCCHHHHHHHHHHHH
Confidence 467788998888888888765
No 78
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=31.09 E-value=65 Score=17.15 Aligned_cols=20 Identities=20% Similarity=0.557 Sum_probs=12.0
Q ss_pred HHHHHhCCCCCHHHHHHHHH
Q psy3468 25 RYLIQYNEPIPCEQLVACLC 44 (68)
Q Consensus 25 ~y~~~~~~~i~v~~la~~ls 44 (68)
+|-.+-+.|.+++.+..+++
T Consensus 12 eymK~r~~Plt~~eI~d~l~ 31 (65)
T PF02186_consen 12 EYMKKRDHPLTLEEILDYLS 31 (65)
T ss_dssp HHHHHH-S-B-HHHHHHHHT
T ss_pred HHHHhcCCCcCHHHHHHHHc
Confidence 34334499999999888776
No 79
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=31.06 E-value=54 Score=15.98 Aligned_cols=20 Identities=30% Similarity=0.532 Sum_probs=13.9
Q ss_pred HHHHHhCCCCCHHHHHHHHH
Q psy3468 25 RYLIQYNEPIPCEQLVACLC 44 (68)
Q Consensus 25 ~y~~~~~~~i~v~~la~~ls 44 (68)
......+.+++.+.||+.+.
T Consensus 7 ~~L~~~~~~it~~eLa~~l~ 26 (55)
T PF08279_consen 7 KLLLESKEPITAKELAEELG 26 (55)
T ss_dssp HHHHHTTTSBEHHHHHHHCT
T ss_pred HHHHHcCCCcCHHHHHHHhC
Confidence 34446777799988887653
No 80
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=30.59 E-value=1.5e+02 Score=19.09 Aligned_cols=32 Identities=13% Similarity=-0.028 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy3468 14 VLTSELRAIAQRYLIQYNEPIPCEQLVACLCD 45 (68)
Q Consensus 14 ~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~ 45 (68)
..+++++.....+.-..|..++++.+|..++-
T Consensus 98 ~~~~~i~~~~~~l~~~~g~~pt~~eiA~~lg~ 129 (231)
T PRK12427 98 QKTHKTNDAIREIAKRLGHEPNFEEISAELNL 129 (231)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHHHHHhCC
Confidence 34444444445555566777777777775543
No 81
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=30.21 E-value=33 Score=16.52 Aligned_cols=27 Identities=19% Similarity=0.129 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHHhCCCC-CHHHHHHHH
Q psy3468 17 SELRAIAQRYLIQYNEPI-PCEQLVACL 43 (68)
Q Consensus 17 ~~~r~~a~~y~~~~~~~i-~v~~la~~l 43 (68)
+.++.......+.-+..+ +...|++.+
T Consensus 3 ~~l~~~i~~~~~~~~~~l~s~~~la~~~ 30 (60)
T smart00345 3 ERLREDIVSGELRPGDKLPSERELAAQL 30 (60)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHH
Confidence 344444444444445556 576666654
No 82
>PF08388 GIIM: Group II intron, maturase-specific domain; InterPro: IPR013597 This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing [].
Probab=28.95 E-value=96 Score=16.23 Aligned_cols=35 Identities=23% Similarity=0.265 Sum_probs=20.8
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcC
Q psy3468 20 RAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYG 54 (68)
Q Consensus 20 r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~ 54 (68)
+....+-...-....|++.++..|..++.-...++
T Consensus 5 ~~kik~~~~~~~~~~~~~~~i~~LN~~lrGW~nYy 39 (80)
T PF08388_consen 5 RRKIKEITRRRNRGKSLEELIKKLNPILRGWANYY 39 (80)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHhh
Confidence 33333333233456777778888877776666554
No 83
>PHA02131 hypothetical protein
Probab=28.85 E-value=93 Score=16.59 Aligned_cols=27 Identities=15% Similarity=0.225 Sum_probs=19.8
Q ss_pred EeecchHHHHHHHHHHHHHHHHHHHHH
Q psy3468 3 CSVAGITSDANVLTSELRAIAQRYLIQ 29 (68)
Q Consensus 3 ~~~sGl~aD~r~lv~~~r~~a~~y~~~ 29 (68)
|++--=++..|.+-+.+|+.|.++.|.
T Consensus 43 ctfk~dtaqfr~mek~ar~vaaehqyt 69 (70)
T PHA02131 43 CTFKNDTAQFRSMEKAARQVAAEHQYT 69 (70)
T ss_pred eeecCcHHHHhhHHHHHHHHHHhhccc
Confidence 444455677888888999988888764
No 84
>PHA02745 hypothetical protein; Provisional
Probab=27.21 E-value=94 Score=21.21 Aligned_cols=21 Identities=14% Similarity=0.096 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhC
Q psy3468 11 DANVLTSELRAIAQRYLIQYN 31 (68)
Q Consensus 11 D~r~lv~~~r~~a~~y~~~~~ 31 (68)
|.+.|.+-+|...++.|.+|+
T Consensus 242 D~~~I~ntiR~KiqeiR~K~g 262 (265)
T PHA02745 242 DHQAIINVIRNKMQESRRKDR 262 (265)
T ss_pred chHHHHHHHHHHHHHHHHHhC
Confidence 444444444444444444443
No 85
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=27.00 E-value=45 Score=15.49 Aligned_cols=16 Identities=6% Similarity=0.121 Sum_probs=9.6
Q ss_pred HhCCCCCHHHHHHHHH
Q psy3468 29 QYNEPIPCEQLVACLC 44 (68)
Q Consensus 29 ~~~~~i~v~~la~~ls 44 (68)
.+.++++++.+|..++
T Consensus 4 ~~~~~~~l~~iA~~~g 19 (42)
T PF00165_consen 4 NLQQKLTLEDIAEQAG 19 (42)
T ss_dssp TT-SS--HHHHHHHHT
T ss_pred cccCCCCHHHHHHHHC
Confidence 4567889988888664
No 86
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=26.87 E-value=70 Score=20.16 Aligned_cols=32 Identities=9% Similarity=0.025 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q psy3468 13 NVLTSELRAIAQRYLIQYNEPIPCEQLVACLC 44 (68)
Q Consensus 13 r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls 44 (68)
..+.+.+|....+-++.-|+.+|.+.|++.++
T Consensus 14 e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lg 45 (221)
T PRK11414 14 LQVENDLKHQLSIGALKPGARLITKNLAEQLG 45 (221)
T ss_pred HHHHHHHHHHHHhCCCCCCCccCHHHHHHHHC
Confidence 45778889999999999999999887776553
No 87
>PF05769 DUF837: Protein of unknown function (DUF837); InterPro: IPR008555 This family consists of several eukaryotic proteins of unknown function. One of the family members (O02197 from SWISSPROT) is a circulating cathodic antigen (CCA) found in Schistosoma mansoni (Blood fluke) [].
Probab=26.75 E-value=43 Score=21.38 Aligned_cols=20 Identities=30% Similarity=0.581 Sum_probs=16.7
Q ss_pred EEeecchHHHHHHHHHHHHH
Q psy3468 2 VCSVAGITSDANVLTSELRA 21 (68)
Q Consensus 2 g~~~sGl~aD~r~lv~~~r~ 21 (68)
-|++-++.+|++.|+.+++.
T Consensus 2 ~~ti~~il~dak~L~~rL~~ 21 (181)
T PF05769_consen 2 SCTIEQILADAKRLVERLKD 21 (181)
T ss_pred cCcHHHHHHHHHHHHHHHHH
Confidence 46778899999999988875
No 88
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=26.73 E-value=1.9e+02 Score=19.04 Aligned_cols=32 Identities=16% Similarity=0.039 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy3468 14 VLTSELRAIAQRYLIQYNEPIPCEQLVACLCD 45 (68)
Q Consensus 14 ~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~ 45 (68)
.++++++.......-.+|++++.+.+|+.+.-
T Consensus 124 ~~~~~i~~~~~~l~~~lg~~pt~~eiA~~lg~ 155 (264)
T PRK07122 124 ELHLRLGRATAELSQRLGRAPTASELAAELGM 155 (264)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCC
Confidence 34455555566666778888888888887653
No 89
>cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=26.20 E-value=66 Score=18.10 Aligned_cols=21 Identities=19% Similarity=0.148 Sum_probs=17.3
Q ss_pred CEEeecchHHHHHHHHHHHHH
Q psy3468 1 MVCSVAGITSDANVLTSELRA 21 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~ 21 (68)
|+++.+|-..|....++.+|.
T Consensus 51 I~iS~sG~t~e~~~~~~~a~~ 71 (126)
T cd05008 51 IAISQSGETADTLAALRLAKE 71 (126)
T ss_pred EEEeCCcCCHHHHHHHHHHHH
Confidence 567889999998888888875
No 90
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=26.19 E-value=95 Score=15.54 Aligned_cols=15 Identities=27% Similarity=0.215 Sum_probs=11.5
Q ss_pred EEeecchHHHHHHHH
Q psy3468 2 VCSVAGITSDANVLT 16 (68)
Q Consensus 2 g~~~sGl~aD~r~lv 16 (68)
.++++|+.+|....+
T Consensus 3 wI~V~Gf~~~~~~~v 17 (53)
T PF14605_consen 3 WISVSGFPPDLAEEV 17 (53)
T ss_pred EEEEEeECchHHHHH
Confidence 478899998887544
No 91
>PF10851 DUF2652: Protein of unknown function (DUF2652) ; InterPro: IPR020503 This entry contains proteins with no known function.
Probab=25.61 E-value=81 Score=19.01 Aligned_cols=25 Identities=12% Similarity=0.266 Sum_probs=20.3
Q ss_pred HHhCCCCCHHHHHHHHHHHHHHhhhc
Q psy3468 28 IQYNEPIPCEQLVACLCDIKQGYTQY 53 (68)
Q Consensus 28 ~~~~~~i~v~~la~~ls~~~q~~Tq~ 53 (68)
|.++.+.+++ +++.+..+...|-++
T Consensus 28 y~~~~~~~~~-v~~q~~~M~~aF~~~ 52 (116)
T PF10851_consen 28 YKYGKDTSVE-VCRQCERMRRAFHQR 52 (116)
T ss_pred EcCCCCccHH-HHHHHHHHHHHHHHH
Confidence 5688888988 888888888877665
No 92
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=25.42 E-value=88 Score=15.22 Aligned_cols=29 Identities=17% Similarity=0.256 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHhCCCCC-HHHHHHHH
Q psy3468 15 LTSELRAIAQRYLIQYNEPIP-CEQLVACL 43 (68)
Q Consensus 15 lv~~~r~~a~~y~~~~~~~i~-v~~la~~l 43 (68)
+.+..+.......+.-+..++ ++.|++.+
T Consensus 6 ~~~~i~~~i~~~~~~~~~~~~~~~~la~~~ 35 (66)
T cd07377 6 IADQLREAILSGELKPGDRLPSERELAEEL 35 (66)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHH
Confidence 344444444444344444444 66665533
No 93
>PF04358 DsrC: DsrC like protein; InterPro: IPR007453 DsrC (P45573 from SWISSPROT) has been observed to co-purify with Desulphovibrio vulgaris dissimilatory sulphite reductase []. However, DsrC appears to be only loosely associated to the sulphite reductase, which suggests that it may not be an integral part of the dissimilatory sulphite reductase. Many proteins in this entry are found in organisms such as Escherichia coli and Haemophilus influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins []. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds []. Also included in this entry is TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Many proteins in this entry are annotated as the third (gamma) subunit of dissimilatory sulphite reductase ; PDB: 2V4J_F 2A5W_C 1SAU_A 1JI8_A 1YX3_A.
Probab=25.37 E-value=1.5e+02 Score=17.36 Aligned_cols=35 Identities=20% Similarity=0.250 Sum_probs=23.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Q psy3468 8 ITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDI 46 (68)
Q Consensus 8 l~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~ 46 (68)
|+.|---+|+.+| +|...|+..+++..|++.+..-
T Consensus 39 Ltd~HW~vI~flR----~~y~~~~~~P~~R~l~K~~~~~ 73 (109)
T PF04358_consen 39 LTDEHWEVIRFLR----DYYQEYGVSPAIRMLIKALGED 73 (109)
T ss_dssp --HHHHHHHHHHH----HHHHHHSS---HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH----HHHHHHCCCCcHHHHHHHHhhh
Confidence 5566667777776 5667788889999999988766
No 94
>PRK12397 propionate kinase; Reviewed
Probab=25.21 E-value=63 Score=23.35 Aligned_cols=43 Identities=14% Similarity=0.162 Sum_probs=24.8
Q ss_pred EeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy3468 3 CSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIK 47 (68)
Q Consensus 3 ~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~ 47 (68)
++++|++.|.|.|.+.+..--..-++-+ .+-+-++++.|+.+.
T Consensus 274 lg~sG~s~D~R~l~~~~~~gd~~A~lA~--d~f~yri~k~IGa~~ 316 (404)
T PRK12397 274 LGVSGVSSDYRDVEQAANTGNRQAKLAL--TLFAERIRATIGSYI 316 (404)
T ss_pred eEecCCCCCHHHHHHHHHCCCHHHHHHH--HHHHHHHHHHHHHHH
Confidence 4678999999999766531111112221 223455677777665
No 95
>COG4018 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.07 E-value=87 Score=22.73 Aligned_cols=41 Identities=12% Similarity=0.221 Sum_probs=32.1
Q ss_pred HHHHhCCCCCHHHHHHHHHHHHHHhhhcCC--CCCCCceeccc
Q psy3468 26 YLIQYNEPIPCEQLVACLCDIKQGYTQYGG--QSIIPFRRNKT 66 (68)
Q Consensus 26 y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~--~R~~P~g~~~~ 66 (68)
-++.|..+.+|..++.-++++.-+--|.-| .|-||.||-++
T Consensus 19 ~kl~~~~~~dv~EvVdav~dLs~ee~~kLG~nlrtFPmGCDL~ 61 (505)
T COG4018 19 KKLAYEGKLDVDEVVDAVGDLSDEELEKLGDNLRTFPMGCDLI 61 (505)
T ss_pred HHHHhcccccHHHHHHHhhhhcHHHHHHHhhhhccCCCCCcee
Confidence 356678899999999999998866666533 58899999776
No 96
>PRK12379 propionate/acetate kinase; Provisional
Probab=24.82 E-value=65 Score=23.21 Aligned_cols=43 Identities=14% Similarity=0.197 Sum_probs=25.2
Q ss_pred EeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy3468 3 CSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIK 47 (68)
Q Consensus 3 ~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~ 47 (68)
++++|++.|.|.|.+.+..--..-++-+ .+-+-++++.|+.+.
T Consensus 270 lg~sG~s~D~R~v~~~~~~gd~~A~lA~--d~f~yri~k~IGa~~ 312 (396)
T PRK12379 270 LGISGLSSDLRVLEKAWHEGHERAQLAI--KTFVHRIARHIAGHA 312 (396)
T ss_pred eEecCCCCCHHHHHHHHHCCCHHHHHHH--HHHHHHHHHHHHHHH
Confidence 4678999999999776542111222222 223455667777665
No 97
>TIGR00016 ackA acetate kinase. Acetate kinase is involved in the activation of acetate to acetyl CoA and in the secretion of acetate. It catalyzes the reaction ATP + acetate = ADP + acetyl phosphate. Some members of this family have been shown to act on propionate as well as acetate. An example of a propionate/acetate kinase is TdcD of E. coli, an enzyme of an anaerobic pathway of threonine catabolism. It is not known how many members of this family act on additional substrates besides acetate.
Probab=24.09 E-value=2.3e+02 Score=20.54 Aligned_cols=40 Identities=13% Similarity=0.144 Sum_probs=24.3
Q ss_pred EeecchHHHHHHHHHHHH---HHHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy3468 3 CSVAGITSDANVLTSELR---AIAQRYLIQYNEPIPCEQLVACLCDIK 47 (68)
Q Consensus 3 ~~~sGl~aD~r~lv~~~r---~~a~~y~~~~~~~i~v~~la~~ls~~~ 47 (68)
++++|++.|.|.|...+. ..|+.- ..+-+-++++.|+.+.
T Consensus 279 lg~sG~s~D~Rel~~~~~~gd~~A~lA-----~~~f~yri~k~Iga~~ 321 (404)
T TIGR00016 279 LGISGLSSDLRDIEDAYAEGNEQAQLA-----IKMYVHRIAKYIGSYI 321 (404)
T ss_pred eEecCCCCCHHHHHHHHHCCCHHHHHH-----HHHHHHHHHHHHHHHH
Confidence 467899999999977654 122211 1222455666666665
No 98
>TIGR00636 PduO_Nterm ATP:cob(I)alamin adenosyltransferase. This model represents as ATP:cob(I)alamin adenosyltransferase family corresponding to the N-terminal half of Salmonella PduO, a 1,2-propanediol utilization protein that probably is bifunctional. PduO represents one of at least three families of ATP:corrinoid adenosyltransferase: others are CobA (which partially complements PduO) and EutT. It was not clear originally whether ATP:cob(I)alamin adenosyltransferase activity resides in the N-terminal region of PduO, modeled here, but this has now become clear from the characterization of MeaD from Methylobacterium extorquens.
Probab=23.64 E-value=2e+02 Score=18.17 Aligned_cols=43 Identities=9% Similarity=-0.076 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhc
Q psy3468 11 DANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQY 53 (68)
Q Consensus 11 D~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~ 53 (68)
-+|+++.++=..+-.-....+.+.++-.-.++|||++......
T Consensus 116 ~aRtv~RRAER~~v~l~~~~~v~~~~l~ylNRLSD~lFvlAR~ 158 (171)
T TIGR00636 116 VARTVARRAERRVVALLKEEEINEVVLVYLNRLSDLLFVLARV 158 (171)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3556666665444443223333455667889999999766543
No 99
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=23.38 E-value=2e+02 Score=18.76 Aligned_cols=31 Identities=10% Similarity=0.091 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy3468 15 LTSELRAIAQRYLIQYNEPIPCEQLVACLCD 45 (68)
Q Consensus 15 lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~ 45 (68)
.+++.+.....+.-..|++++.+.+|..++-
T Consensus 111 ~~~~~~~~~~~l~~~lgr~pt~~elA~~lgi 141 (256)
T PRK07408 111 LQRQAKKVRQELRQELGRQPTDQEIAQALDI 141 (256)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHcCC
Confidence 3344444555566667888888888876643
No 100
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=23.35 E-value=1.2e+02 Score=15.25 Aligned_cols=31 Identities=26% Similarity=0.309 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q psy3468 13 NVLTSELRAIAQRYLIQYNEPIPCEQLVACLC 44 (68)
Q Consensus 13 r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls 44 (68)
+.|.+-.|.....+- .-+.|+++..|++.+.
T Consensus 5 ~aL~~p~R~~Il~~L-~~~~~~t~~ela~~l~ 35 (61)
T PF12840_consen 5 KALSDPTRLRILRLL-ASNGPMTVSELAEELG 35 (61)
T ss_dssp HHHTSHHHHHHHHHH-HHCSTBEHHHHHHHHT
T ss_pred HHhCCHHHHHHHHHH-hcCCCCCHHHHHHHHC
Confidence 455566665555555 5679999999998774
No 101
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=23.33 E-value=84 Score=19.80 Aligned_cols=30 Identities=17% Similarity=-0.084 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHH
Q psy3468 14 VLTSELRAIAQRYLIQYNEPIPCEQLVACL 43 (68)
Q Consensus 14 ~lv~~~r~~a~~y~~~~~~~i~v~~la~~l 43 (68)
.+.+.+|....+-++.-|+.+|.+.|++.+
T Consensus 11 ~vy~~i~~~I~~g~l~pG~~L~e~eLae~l 40 (224)
T PRK11534 11 DGYRWLKNDIIRGNFQPDEKLRMSLLTSRY 40 (224)
T ss_pred HHHHHHHHHHHhCCCCCCCcCCHHHHHHHH
Confidence 467888888889999999999988877754
No 102
>COG0781 NusB Transcription termination factor [Transcription]
Probab=23.31 E-value=1.9e+02 Score=17.85 Aligned_cols=44 Identities=7% Similarity=0.183 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCC
Q psy3468 14 VLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQS 57 (68)
Q Consensus 14 ~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R 57 (68)
..++++-..+.-|++.|..++|...+..+-=++.-.|....+.+
T Consensus 89 ~~verAILRla~yEl~~~~dvP~~VvInEaielaK~f~~e~s~k 132 (151)
T COG0781 89 DLVERAILRLALYELLFRDDVPYKVVINEAIELAKKFSGEDSHK 132 (151)
T ss_pred hHHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHhCCCCchH
Confidence 45677777788899999887888888888877777776665544
No 103
>cd05014 SIS_Kpsf KpsF-like protein. KpsF is an arabinose-5-phosphate isomerase which contains SIS (Sugar ISomerase) domains. SIS domains are found in many phosphosugar isomerases and phosphosugar binding proteins. KpsF catalyzes the reversible reaction of ribulose 5-phosphate to arabinose 5-phosphate. This is the second step in the CMP-Kdo biosynthesis pathway.
Probab=23.18 E-value=81 Score=17.78 Aligned_cols=21 Identities=24% Similarity=0.246 Sum_probs=17.3
Q ss_pred CEEeecchHHHHHHHHHHHHH
Q psy3468 1 MVCSVAGITSDANVLTSELRA 21 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~ 21 (68)
|+++.+|-.+|....++.+|.
T Consensus 52 i~iS~sG~t~~~~~~~~~a~~ 72 (128)
T cd05014 52 IAISNSGETDELLNLLPHLKR 72 (128)
T ss_pred EEEeCCCCCHHHHHHHHHHHH
Confidence 467888999999888888875
No 104
>PF11950 DUF3467: Protein of unknown function (DUF3467); InterPro: IPR021857 This entry is represented by Bacteriophage 92, 0rf53. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins are functionally uncharacterised. This protein is found in bacteria, archaea and viruses. Proteins in this family are typically between 101 to 118 amino acids in length.
Probab=23.16 E-value=1.5e+02 Score=16.58 Aligned_cols=22 Identities=27% Similarity=0.377 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhCC
Q psy3468 11 DANVLTSELRAIAQRYLIQYNE 32 (68)
Q Consensus 11 D~r~lv~~~r~~a~~y~~~~~~ 32 (68)
=++.|.+.+......|+-.||+
T Consensus 68 ~AKrL~~aL~~~l~~YE~~fG~ 89 (92)
T PF11950_consen 68 HAKRLLKALQQNLQKYEQRFGE 89 (92)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC
Confidence 3567777777777888777764
No 105
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=23.12 E-value=97 Score=20.40 Aligned_cols=44 Identities=18% Similarity=0.134 Sum_probs=30.2
Q ss_pred EeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHh
Q psy3468 3 CSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGY 50 (68)
Q Consensus 3 ~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~ 50 (68)
|.-+|..||...|.+++...|.++=+ ..++.+ +|+.|..-++.|
T Consensus 196 c~es~~LPD~~~L~~Rm~~ia~e~GL---~gvs~~-~a~ll~~ale~~ 239 (252)
T PF12767_consen 196 CSESGELPDTQSLRKRMEQIAWEHGL---GGVSDD-CANLLNLALEVH 239 (252)
T ss_pred HHHhCcCCCHHHHHHHHHHHHHHcCC---CCCCHH-HHHHHHHHHHHH
Confidence 34568899999999999988865544 455543 566665555544
No 106
>cd05017 SIS_PGI_PMI_1 The members of this protein family contain the SIS (Sugar ISomerase) domain and have both the phosphoglucose isomerase (PGI) and the phosphomannose isomerase (PMI) functions. These functions catalyze the reversible reactions of glucose 6-phosphate to fructose 6-phosphate, and mannose 6-phosphate to fructose 6-phosphate, respectively at an equal rate. This protein contains two SIS domains. This alignment is based on the first SIS domain.
Probab=23.10 E-value=83 Score=17.90 Aligned_cols=22 Identities=14% Similarity=0.160 Sum_probs=18.2
Q ss_pred CEEeecchHHHHHHHHHHHHHH
Q psy3468 1 MVCSVAGITSDANVLTSELRAI 22 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~ 22 (68)
|+++.+|-..|....++.+|..
T Consensus 48 I~iS~SG~t~e~i~~~~~a~~~ 69 (119)
T cd05017 48 IAVSYSGNTEETLSAVEQAKER 69 (119)
T ss_pred EEEECCCCCHHHHHHHHHHHHC
Confidence 5688899999999998888753
No 107
>TIGR03367 queuosine_QueD queuosine biosynthesis protein QueD. Members of this protein family, closely related to eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase enzymes, are the QueD protein of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of tRNAs for Tyr, His, Asp, and Asn in many species. This modification, although widespread, appears not to be important for viability. The queuosine precursor made by this enzyme may be converted instead to archeaosine as in some Archaea.
Probab=23.02 E-value=80 Score=17.60 Aligned_cols=42 Identities=19% Similarity=0.252 Sum_probs=28.1
Q ss_pred cchHHHHHHHHHHHHHHHHHH--HHHhCC----CCCHHHHHHHHHHHH
Q psy3468 6 AGITSDANVLTSELRAIAQRY--LIQYNE----PIPCEQLVACLCDIK 47 (68)
Q Consensus 6 sGl~aD~r~lv~~~r~~a~~y--~~~~~~----~i~v~~la~~ls~~~ 47 (68)
.|++-|...|-+..+.....+ ++-... +++.+.+|+.+-+.+
T Consensus 43 ~g~v~Df~~lk~~~~~i~~~lDh~~Lne~~~~~~pT~E~ia~~i~~~l 90 (92)
T TIGR03367 43 AGMVMDFSDLKAIVKEVVDRLDHALLNDVPGLENPTAENLARWIYDRL 90 (92)
T ss_pred ccEEEEHHHHHHHHHHHHHhCCCcEeeCCCCCCCCCHHHHHHHHHHHH
Confidence 577788888887777655543 332221 468899998887765
No 108
>PRK12440 acetate kinase; Reviewed
Probab=22.97 E-value=70 Score=23.07 Aligned_cols=43 Identities=14% Similarity=0.197 Sum_probs=24.6
Q ss_pred EeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy3468 3 CSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIK 47 (68)
Q Consensus 3 ~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~ 47 (68)
++++|++.|.|.|.+.+..--..-++-+ .+-+.++++.|+.+.
T Consensus 273 lg~sG~s~D~R~l~~~~~~gd~~A~lA~--d~f~yri~k~Ig~~~ 315 (397)
T PRK12440 273 LGVSGLTSDARGILEAMEEGHEGATLAF--EVFTYRVAKYIASYL 315 (397)
T ss_pred eEecCCCCCHHHHHHHHHCCCHHHHHHH--HHHHHHHHHHHHHHH
Confidence 4678999999999766542111111111 223455667776665
No 109
>COG5174 TFA2 Transcription initiation factor IIE, beta subunit [Transcription]
Probab=22.35 E-value=1.1e+02 Score=20.98 Aligned_cols=26 Identities=27% Similarity=0.295 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy3468 22 IAQRYLIQYNEPIPCEQLVACLCDIK 47 (68)
Q Consensus 22 ~a~~y~~~~~~~i~v~~la~~ls~~~ 47 (68)
-|.+|.-..++|.++++++.++|--+
T Consensus 87 ~aieylk~~~~P~~~eEi~dyls~~l 112 (285)
T COG5174 87 AAIEYLKQHDRPLSFEEIKDYLSIDL 112 (285)
T ss_pred HHHHHHHHcCCcccHHHHHHHhcCcc
Confidence 35688889999999999999887544
No 110
>cd05710 SIS_1 A subgroup of the SIS domain. SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Probab=22.32 E-value=88 Score=17.89 Aligned_cols=22 Identities=14% Similarity=0.134 Sum_probs=18.3
Q ss_pred CEEeecchHHHHHHHHHHHHHH
Q psy3468 1 MVCSVAGITSDANVLTSELRAI 22 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~ 22 (68)
|+++.+|-+.|....++.+|..
T Consensus 52 I~iS~SG~t~~~~~~~~~a~~~ 73 (120)
T cd05710 52 ILASHSGNTKETVAAAKFAKEK 73 (120)
T ss_pred EEEeCCCCChHHHHHHHHHHHc
Confidence 4678899999999998888853
No 111
>PF01923 Cob_adeno_trans: Cobalamin adenosyltransferase; InterPro: IPR002779 ATP:cob(I)alamin (or ATP:corrinoid) adenosyltransferases (2.5.1.17 from EC), catalyse the conversion of cobalamin (vitamin B12) into its coenzyme form, adenosylcobalamin (coenzyme B12) []. Adenosylcobalamin (AdoCbl) is required for the ativity of certain enzymes. AdoCbl contains an adenosyl moiety liganded to the cobalt ion of cobalamin via a covalent Co-C bond, and its synthesis is unique to certain prokaryotes. ATP:cob(I)alamin adenosyltransferases are classed into three groups: CobA-type [], EutT-type [] and PduO-type []. Each of the three enzyme types appears to be specialised for particular AdoCbl-dependent enzymes or for the de novo synthesis AdoCbl. PduO and EutT are distantly related, sharing short conserved motifs, while CobA is evolutionarily unrelated and is an example of convergent evolution. This entry represents EutT- and PduO-type ATP:cob(I)alamin adenosyltransferases. PduO functions to convert cobalamin to AdoCbl for 1,2-propanediol degradation [], while EutT produces AdoCbl for ethanolamine utilisation []. ; GO: 0005524 ATP binding, 0008817 cob(I)yrinic acid a,c-diamide adenosyltransferase activity, 0009236 cobalamin biosynthetic process; PDB: 2ZHY_A 2ZHZ_B 3KE5_C 3KE4_B 2AH6_C 1NOG_A 2IDX_C 3GAH_A 3CI1_A 3CI3_A ....
Probab=21.80 E-value=2.1e+02 Score=17.60 Aligned_cols=40 Identities=13% Similarity=-0.051 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHh
Q psy3468 11 DANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGY 50 (68)
Q Consensus 11 D~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~ 50 (68)
-+|+++.++=..+..-.....-+..+-...++|||++...
T Consensus 119 ~aRtv~RraER~~v~l~~~~~v~~~il~ylNRLSd~lfvl 158 (163)
T PF01923_consen 119 VARTVCRRAERRAVRLFREEEVRPDILRYLNRLSDYLFVL 158 (163)
T ss_dssp HHHHHHHHHHHHHHHHHHHSSS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHH
Confidence 4566666665555555445444556666778999988654
No 112
>KOG2227|consensus
Probab=21.79 E-value=2e+02 Score=21.66 Aligned_cols=43 Identities=14% Similarity=0.094 Sum_probs=27.3
Q ss_pred ecchHHHHHHHHHHHHHHHHHH--HHHhC--------------CCCCHHHHHHHHHHHH
Q psy3468 5 VAGITSDANVLTSELRAIAQRY--LIQYN--------------EPIPCEQLVACLCDIK 47 (68)
Q Consensus 5 ~sGl~aD~r~lv~~~r~~a~~y--~~~~~--------------~~i~v~~la~~ls~~~ 47 (68)
++|..+|.|-+.+.+|....-+ ..... .++-++.++.-+|..-
T Consensus 358 vaa~SGDlRkaLdv~R~aiEI~E~e~r~~~~~~l~~~~~p~~~~~v~~~~va~viSk~~ 416 (529)
T KOG2227|consen 358 VAAPSGDLRKALDVCRRAIEIAEIEKRKILDDPLSPGTSPEKKKKVGVEHVAAVISKVD 416 (529)
T ss_pred hccCchhHHHHHHHHHHHHHHHHHHHhhccccCCCCCCCcccccccchHHHHHHhhhhc
Confidence 5789999999999999444333 33333 2334666666666553
No 113
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=21.75 E-value=1.8e+02 Score=16.89 Aligned_cols=16 Identities=13% Similarity=0.225 Sum_probs=12.5
Q ss_pred HhCCCCCHHHHHHHHH
Q psy3468 29 QYNEPIPCEQLVACLC 44 (68)
Q Consensus 29 ~~~~~i~v~~la~~ls 44 (68)
.+.++++++.+|+.++
T Consensus 21 ~~~~~~sl~~lA~~~g 36 (127)
T PRK11511 21 NLESPLSLEKVSERSG 36 (127)
T ss_pred hcCCCCCHHHHHHHHC
Confidence 4668899999998653
No 114
>PF08720 Hema_stalk: Influenza C hemagglutinin stalk; InterPro: IPR014831 Haemagglutinin (HA) is one of two main surface fusion glycoproteins embedded in the envelope of influenza viruses, the other being neuraminidase (NA). There are sixteen known HA subtypes (H1-H16) and nine NA subtypes (N1-N9), which together are used to classify influenza viruses (e.g. H5N1). The antigenic variations in HA and NA enable the virus to evade host antibodies made to previous influenza strains, accounting for recurrent influenza epidemics []. The HA glycoprotein is present in the viral membrane as a single polypeptide (HA0), which must be cleaved by the host's trypsin-like proteases to produce two peptides (HA1 and HA2) in order for the virus to be infectious. Once HA0 is cleaved, the newly exposed N-terminal of the HA2 peptide then acts to fuse the viral envelope to the cellular membrane of the host cell, which allows the viral negative-stranded RNA to infect the host cell. The type of host protease can influence the infectivity and pathogenicity of the virus. The haemagglutinin glycoprotein is a trimer containing three structurally distinct regions: a globular head consisting of anti-parallel beta-sheets that form a beta-sandwich with a jelly-roll fold (contains the receptor binding site and the HA1/HA2 cleavage site); a triple-stranded, coiled-coil, alpha-helical stalk; and a globular foot composed of anti-parallel beta-sheets [, ]. Each monomer consists of an intact HA0 polypeptide with the HA1 and HA2 regions linked by disulphide bonds. The N terminus of HA1 provides the central strand in the 5-stranded globular foot, while the rest of the HA1 chain makes its way to the 8-stranded globular head. HA2 provides two alpha helices, which form part of the triple-stranded coiled-coil that stabilises the trimer, its C terminus providing the remaining strands of the 5-stranded globular foot. This entry represents the stalk segment of haemagglutinin in influenza C virus. It forms a coiled coil structure []. More information about haemagglutinin proteins can be found at Protein of the Month: Bird Flu, Haemagglutinin [].; GO: 0046789 host cell surface receptor binding, 0019064 viral envelope fusion with host membrane, 0019031 viral envelope; PDB: 1FLC_B.
Probab=21.57 E-value=46 Score=20.51 Aligned_cols=22 Identities=18% Similarity=0.442 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHhCCCCCHHHH
Q psy3468 18 ELRAIAQRYLIQYNEPIPCEQL 39 (68)
Q Consensus 18 ~~r~~a~~y~~~~~~~i~v~~l 39 (68)
.+-+.|++|-|+|++.-||..+
T Consensus 144 icdqscqnfifkfnetapvpti 165 (175)
T PF08720_consen 144 ICDQSCQNFIFKFNETAPVPTI 165 (175)
T ss_dssp TS-HHHHHHHTT---SSS-S--
T ss_pred hhhHHHHHHhhhccCcCCCCCC
Confidence 3457899999999998887654
No 115
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=21.46 E-value=76 Score=18.05 Aligned_cols=26 Identities=15% Similarity=0.137 Sum_probs=21.1
Q ss_pred CEEeecchHHHHHHHHHHHHHHHHHH
Q psy3468 1 MVCSVAGITSDANVLTSELRAIAQRY 26 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~a~~y 26 (68)
|+++..|+.+-++.+.+.++.++.+.
T Consensus 5 Vc~gT~ciAaGA~~V~~al~~ei~~~ 30 (92)
T cd03063 5 VPRDAAALALGADEVAEAIEAEAAAR 30 (92)
T ss_pred EeCChhhhhhCHHHHHHHHHHHHHHc
Confidence 35677888899999999998888764
No 116
>cd05005 SIS_PHI Hexulose-6-phosphate isomerase (PHI). PHI is a member of the SIS (Sugar ISomerase domain) superfamily. In the ribulose monophosphate pathway of formaldehyde fixation, hexulose-6-phosphate synthase catalyzes the condensation of ribulose-5-phosphate with formadelhyde to become hexulose-6-phosphate, which is then isomerized to fructose-6-phosphate by PHI.
Probab=21.40 E-value=85 Score=19.16 Aligned_cols=21 Identities=19% Similarity=0.132 Sum_probs=17.0
Q ss_pred CEEeecchHHHHHHHHHHHHH
Q psy3468 1 MVCSVAGITSDANVLTSELRA 21 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~ 21 (68)
|+++.+|-.+|...+++.+|.
T Consensus 80 I~iS~sG~t~~~i~~~~~ak~ 100 (179)
T cd05005 80 IAISGSGETSSVVNAAEKAKK 100 (179)
T ss_pred EEEcCCCCcHHHHHHHHHHHH
Confidence 467888999998888888874
No 117
>PRK07157 acetate kinase; Provisional
Probab=21.34 E-value=3e+02 Score=19.97 Aligned_cols=43 Identities=19% Similarity=0.235 Sum_probs=23.8
Q ss_pred EeecchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Q psy3468 3 CSVAGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIK 47 (68)
Q Consensus 3 ~~~sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~ 47 (68)
++++|++.|.|.|.+.+..--..-++-+ .+=+-++++.|+.+.
T Consensus 272 lg~sG~s~D~R~l~~~~~~gd~~A~lA~--d~f~yri~k~Ig~~~ 314 (400)
T PRK07157 272 LGVSGISSDLRDVIKAAESGNKRAKFAL--DLYAQKIVDYLANYI 314 (400)
T ss_pred eEecCCCCcHHHHHHHHHCCCHHHHHHH--HHHHHHHHHHHHHHH
Confidence 4678999999999766541111111111 122345666666654
No 118
>COG4728 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.33 E-value=71 Score=19.11 Aligned_cols=31 Identities=10% Similarity=0.116 Sum_probs=22.5
Q ss_pred CEEeecchHHHHHHHHHHHHHH---HHHHHHHhC
Q psy3468 1 MVCSVAGITSDANVLTSELRAI---AQRYLIQYN 31 (68)
Q Consensus 1 ig~~~sGl~aD~r~lv~~~r~~---a~~y~~~~~ 31 (68)
.|+.+-|.+||....++++|.. |..|++..|
T Consensus 17 ~gl~~v~~~~~~s~~~~k~~~~~~~A~~YRHYKG 50 (124)
T COG4728 17 LGLTFVSKSADMSIQVEKAERLIKKASYYRHYKG 50 (124)
T ss_pred cCcEEEEecchhHHHHHHHHHhhccchheEeecC
Confidence 3678889999999999888864 445554444
No 119
>smart00224 GGL G protein gamma subunit-like motifs.
Probab=21.15 E-value=1.4e+02 Score=15.55 Aligned_cols=33 Identities=18% Similarity=0.101 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHH
Q psy3468 11 DANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQG 49 (68)
Q Consensus 11 D~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~ 49 (68)
+.+..++.+|.++.. +-++|+..+..|=++..+
T Consensus 3 ~~~~~ve~Lr~el~~------~RikvS~a~~~li~y~e~ 35 (63)
T smart00224 3 QLRKEVEQLRKELSR------ERIKVSKAAEELLAYCEQ 35 (63)
T ss_pred HHHHHHHHHHHHHCC------ceehHHHHHHHHHHHHHc
Confidence 556677777777765 457777666665555543
No 120
>PRK11376 hlyE hemolysin E; Provisional
Probab=21.06 E-value=2.7e+02 Score=19.05 Aligned_cols=52 Identities=21% Similarity=0.255 Sum_probs=34.4
Q ss_pred cchHHHHHHH-----HHHHHHHHHHHHHHhCCCCCHHHH---HHHHHHHHHHhhhcCCCC
Q psy3468 6 AGITSDANVL-----TSELRAIAQRYLIQYNEPIPCEQL---VACLCDIKQGYTQYGGQS 57 (68)
Q Consensus 6 sGl~aD~r~l-----v~~~r~~a~~y~~~~~~~i~v~~l---a~~ls~~~q~~Tq~~~~R 57 (68)
+|+.+|--+= ++-+--...-|+-.++..++...| .+.|+..|+.|-+.+..+
T Consensus 2 t~i~a~~tve~vk~ai~tad~ald~Yr~ELDqkVkf~eLQeAIdeIDRaMlgYqG~AK~~ 61 (303)
T PRK11376 2 TEIVADKTVEVVKNAIETADGALDLYNKYLDQVIPWQTFDETIKELSRFKQEYSQAASVL 61 (303)
T ss_pred cchhhhhhHHHHHHHHHhhhhHHHHHHHHHhccCCHHHHHHHHHHHHHHhhhhhhHHHHh
Confidence 5666765432 233333345688889999987765 567888889888876543
No 121
>COG3557 Uncharacterized domain/protein associated with RNAses G and E [Translation, ribosomal structure and biogenesis]
Probab=21.04 E-value=2.4e+02 Score=18.14 Aligned_cols=38 Identities=13% Similarity=0.143 Sum_probs=28.4
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCCCCCCCce
Q psy3468 22 IAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGGQSIIPFR 62 (68)
Q Consensus 22 ~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g 62 (68)
|-+.++..++.|.++..+.++--+.+..+-.. ..+ ||.
T Consensus 123 Ey~~h~k~m~Yp~did~il~~~v~~L~~wi~~-~~g--pf~ 160 (177)
T COG3557 123 EYEEHRKKMHYPPDIDRILKENVDILVDWIEE-YKG--PFS 160 (177)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHh-ccC--CCC
Confidence 55677788888988888888877777766655 466 764
No 122
>cd05564 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins from chbA, chbB, and chbC of the chb operon (formerly the cel (cellulose) operon). In the lichenan system, these subunits are expressed from licA, licB, and licC of the lic operon. The lic operon of Bacillus subtilis is required for the transport and degradation of oligomeric beta-glucosides, which are produced by extracellular enzymes on substrates such as lichenan or barley glucan. The lic operon is transcribed from a gammaA-dependent promoter and is inducible by lichenan, lichenan hydrolysate, and cellobiose. The IIB d
Probab=20.94 E-value=1.1e+02 Score=17.10 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=18.5
Q ss_pred EEeecchHHHHHHHHHHHHHHHHHHHH
Q psy3468 2 VCSVAGITSDANVLTSELRAIAQRYLI 28 (68)
Q Consensus 2 g~~~sGl~aD~r~lv~~~r~~a~~y~~ 28 (68)
.++.+|+.+. .++++++..+.++..
T Consensus 4 ~~Cg~G~sTS--~~~~ki~~~~~~~~~ 28 (96)
T cd05564 4 LVCSAGMSTS--ILVKKMKKAAEKRGI 28 (96)
T ss_pred EEcCCCchHH--HHHHHHHHHHHHCCC
Confidence 4677888887 468888888876544
No 123
>PF06711 DUF1198: Protein of unknown function (DUF1198); InterPro: IPR009587 This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.
Probab=20.79 E-value=97 Score=19.43 Aligned_cols=42 Identities=19% Similarity=0.265 Sum_probs=27.5
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHH-HHhhhc
Q psy3468 6 AGITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIK-QGYTQY 53 (68)
Q Consensus 6 sGl~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~-q~~Tq~ 53 (68)
-=+++|.|..++.+-.. + .=+|++||++..+++.-. ++|+++
T Consensus 18 RvLtSdtR~A~~~Ls~r-----L-~I~Pv~iESMl~qMGk~~~~~Firy 60 (148)
T PF06711_consen 18 RVLTSDTRRAIRRLSER-----L-NIKPVYIESMLDQMGKRAGQEFIRY 60 (148)
T ss_pred EecccchHHHHHHHHHH-----h-CCCceeHHHHHHHHhHhHHHHHHHH
Confidence 33677888776665422 2 238999999998887653 455544
No 124
>cd00068 GGL G protein gamma subunit-like motifs, the alpha-helical G-gamma chain dimerizes with the G-beta propeller subunit as part of the heterotrimeric G-protein complex; involved in signal transduction via G-protein-coupled receptors
Probab=20.57 E-value=1.4e+02 Score=15.24 Aligned_cols=34 Identities=18% Similarity=0.109 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHh
Q psy3468 11 DANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGY 50 (68)
Q Consensus 11 D~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~ 50 (68)
+.+.+++.+|.++.. +-++|+..+..|=.+..++
T Consensus 3 ~~~~~veqLr~el~~------~RikvS~a~~~l~~y~e~~ 36 (57)
T cd00068 3 QLKKEVEQLRKELSR------ERLKVSKAAAELLKYCEQN 36 (57)
T ss_pred HHHHHHHHHHHHHCC------chhhHHHHHHHHHHHHHhc
Confidence 456677777777665 3577776666555555433
No 125
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=20.27 E-value=2.5e+02 Score=17.97 Aligned_cols=30 Identities=10% Similarity=0.055 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q psy3468 15 LTSELRAIAQRYLIQYNEPIPCEQLVACLC 44 (68)
Q Consensus 15 lv~~~r~~a~~y~~~~~~~i~v~~la~~ls 44 (68)
.++.++.....+....+++++++.+|+.+.
T Consensus 85 ~~~~~~~~~~~l~~~~g~~pt~~eia~~l~ 114 (238)
T TIGR02393 85 TINKLIKAERQLTQELGREPTDEELAERMG 114 (238)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhC
Confidence 445555555666777889999988887765
No 126
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=20.27 E-value=1.7e+02 Score=15.92 Aligned_cols=22 Identities=14% Similarity=0.433 Sum_probs=17.2
Q ss_pred HHHHHHHhC-CCCCHHHHHHHHH
Q psy3468 23 AQRYLIQYN-EPIPCEQLVACLC 44 (68)
Q Consensus 23 a~~y~~~~~-~~i~v~~la~~ls 44 (68)
+.+|--.-+ +|.+++.+..+++
T Consensus 14 aV~ymK~r~~~Plt~~EIl~~ls 36 (75)
T cd07977 14 IVDYMKKRHQHPLTLDEILDYLS 36 (75)
T ss_pred HHHHHHhcCCCCccHHHHHHHHh
Confidence 345555666 9999999999888
No 127
>PF08289 Flu_M1_C: Influenza Matrix protein (M1) C-terminal domain; InterPro: IPR013188 Matrix protein (M1) of Influenza virus is a bifunctional membrane/RNA-binding protein that mediates the encapsidation of RNA-nucleoprotein cores into the membrane envelope. It is therefore required that M1 binds both membrane and RNA simultaneously. M1 is comprised of two domains connected by a linker sequence. The C-terminal domain contains alpha-helical structure and appears to be involved in growth and virulence of the virus [, ].; GO: 0003723 RNA binding, 0005198 structural molecule activity
Probab=20.26 E-value=1.9e+02 Score=16.59 Aligned_cols=48 Identities=23% Similarity=0.205 Sum_probs=39.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHhhhcCC
Q psy3468 8 ITSDANVLTSELRAIAQRYLIQYNEPIPCEQLVACLCDIKQGYTQYGG 55 (68)
Q Consensus 8 l~aD~r~lv~~~r~~a~~y~~~~~~~i~v~~la~~ls~~~q~~Tq~~~ 55 (68)
-.+|+.-|.+.+|...+--+-.=-.|-+.+-|++.|-+.+|.|--+-|
T Consensus 41 q~~e~~eiAsq~r~~i~amRsiGt~~~~~~Gl~dDlle~Lq~yQk~MG 88 (95)
T PF08289_consen 41 QAAEAMEIASQARSMIQAMRSIGTHPKNSEGLADDLLENLQAYQKRMG 88 (95)
T ss_pred hHHHHHHHHHHHHHHHHHHHHhcCCCCCccchHHHHHHHHHHHHHHHh
Confidence 457899999999999888888877888888899999999987754433
No 128
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=20.04 E-value=1e+02 Score=15.96 Aligned_cols=30 Identities=17% Similarity=0.069 Sum_probs=14.7
Q ss_pred CCCCHHHHHHHHHHHHHHhhhcCCCCCCCcee
Q psy3468 32 EPIPCEQLVACLCDIKQGYTQYGGQSIIPFRR 63 (68)
Q Consensus 32 ~~i~v~~la~~ls~~~q~~Tq~~~~R~~P~g~ 63 (68)
-|.++...|..|....+......|++ |-++
T Consensus 10 L~~~v~~~A~~i~~~~~~~~~~~Gr~--~~~i 39 (71)
T PF00382_consen 10 LPEDVRERAKEIYKKAQERGLLKGRS--PESI 39 (71)
T ss_dssp --HHHHHHHHHHHHHHHHTTTSTTS---HHHH
T ss_pred CCHHHHHHHHHHHHHHHHcCCcccCC--HHHH
Confidence 34455555555655555555555555 5443
Done!