Query psy11249
Match_columns 105
No_of_seqs 105 out of 156
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 21:56:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11249.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11249hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00099 btg1 tob/btg1 famil 100.0 7.8E-57 1.7E-61 310.5 11.4 102 1-105 1-104 (108)
2 PF07742 BTG: BTG family; Int 100.0 6E-56 1.3E-60 310.1 8.8 104 1-105 1-106 (118)
3 KOG4006|consensus 100.0 1.2E-36 2.5E-41 239.5 5.4 98 1-105 1-100 (311)
4 KOG4006|consensus 99.9 3E-26 6.5E-31 180.7 0.8 104 1-105 66-169 (311)
5 cd01768 RA RA (Ras-associating 91.4 0.5 1.1E-05 30.0 4.4 36 48-84 5-40 (87)
6 cd00153 RalGDS_RA Ubiquitin do 88.5 0.86 1.9E-05 30.6 3.8 31 55-85 15-45 (87)
7 smart00314 RA Ras association 85.1 2.3 5E-05 27.1 4.4 32 54-85 13-44 (90)
8 PF00788 RA: Ras association ( 84.2 2 4.4E-05 26.9 3.8 43 50-96 10-52 (93)
9 COG3112 Uncharacterized protei 82.5 1.4 3.1E-05 31.0 2.7 38 67-105 37-75 (121)
10 PF14026 DUF4242: Protein of u 80.7 4.7 0.0001 25.9 4.5 59 23-87 12-74 (77)
11 PF15123 DUF4562: Domain of un 68.7 5.7 0.00012 28.0 2.7 24 27-50 81-104 (116)
12 KOG3254|consensus 66.0 7 0.00015 29.9 3.0 27 23-58 169-195 (211)
13 PF06062 UPF0231: Uncharacteri 64.0 6 0.00013 27.8 2.2 38 68-105 39-77 (121)
14 PRK05248 hypothetical protein; 60.3 6.9 0.00015 27.6 1.9 38 67-105 37-75 (121)
15 PF01221 Dynein_light: Dynein 58.1 15 0.00033 23.7 3.2 42 1-48 13-55 (89)
16 PF05534 HicB: HicB family; I 53.0 6.8 0.00015 23.3 0.8 36 48-87 11-46 (51)
17 COG0560 SerB Phosphoserine pho 49.5 79 0.0017 23.6 6.3 63 8-85 52-119 (212)
18 TIGR01490 HAD-SF-IB-hyp1 HAD-s 49.0 47 0.001 23.4 4.8 56 23-83 67-127 (202)
19 PTZ00059 dynein light chain; P 48.4 48 0.001 21.7 4.4 18 31-48 39-56 (90)
20 PF11888 DUF3408: Protein of u 47.5 40 0.00087 23.6 4.1 20 26-47 117-136 (136)
21 COG3453 Uncharacterized protei 46.6 16 0.00035 26.2 2.0 35 54-88 25-65 (130)
22 COG4840 Uncharacterized protei 46.4 62 0.0014 20.8 4.5 30 8-38 40-69 (71)
23 PF15658 Latrotoxin_C: Latroto 45.6 36 0.00078 24.3 3.6 32 9-40 89-122 (127)
24 PF04273 DUF442: Putative phos 44.1 15 0.00032 25.0 1.5 34 55-88 25-64 (110)
25 PF08236 SRI: SRI (Set2 Rpb1 i 43.2 83 0.0018 20.5 4.9 35 8-42 13-47 (88)
26 PF04986 Y2_Tnp: Putative tran 43.1 4.3 9.3E-05 29.8 -1.4 47 6-64 104-150 (183)
27 cd06937 NR_LBD_RAR The ligand 41.6 29 0.00064 26.2 2.9 33 21-54 156-188 (231)
28 cd06951 NR_LBD_Dax1_like The l 40.7 35 0.00075 25.6 3.2 31 23-54 153-183 (222)
29 PF09899 DUF2126: Putative ami 40.3 29 0.00063 31.7 3.0 35 29-63 82-125 (819)
30 PF07208 DUF1414: Protein of u 39.4 78 0.0017 18.6 3.8 31 8-41 12-42 (44)
31 PF03361 Herpes_IE2_3: Herpes 39.4 1.2E+02 0.0026 22.4 5.7 52 23-80 71-128 (162)
32 cd04447 DEP_BRCC3 DEP (Disheve 38.7 78 0.0017 21.3 4.3 43 6-48 33-79 (92)
33 PF10025 DUF2267: Uncharacteri 38.2 72 0.0016 21.7 4.2 33 21-53 34-66 (125)
34 PF14898 DUF4491: Domain of un 38.0 19 0.00041 24.5 1.2 14 41-54 80-93 (94)
35 PF05494 Tol_Tol_Ttg2: Toluene 37.3 1E+02 0.0022 21.7 5.0 36 11-46 42-78 (170)
36 cd06952 NR_LBD_TR2_like The li 37.0 39 0.00084 25.0 2.9 29 24-53 150-178 (222)
37 PF14437 MafB19-deam: MafB19-l 36.1 43 0.00093 24.4 2.9 14 89-103 98-111 (146)
38 COG0721 GatC Asp-tRNAAsn/Glu-t 36.0 1E+02 0.0022 20.5 4.6 31 7-40 6-36 (96)
39 smart00295 B41 Band 4.1 homolo 35.8 61 0.0013 22.8 3.7 43 58-100 15-63 (207)
40 PRK09510 tolA cell envelope in 35.3 1.3E+02 0.0027 25.2 5.8 65 34-99 304-386 (387)
41 PF06183 DinI: DinI-like famil 35.3 40 0.00087 21.0 2.3 25 23-47 1-25 (65)
42 PF11470 TUG-UBL1: GLUT4 regul 35.2 20 0.00042 22.5 0.9 29 60-88 10-38 (65)
43 cd04446 DEP_DEPDC4 DEP (Dishev 35.2 1E+02 0.0022 20.7 4.4 43 6-48 31-78 (95)
44 cd05399 NT_Rel-Spo_like Nucleo 34.7 70 0.0015 21.4 3.7 30 34-64 68-102 (129)
45 PF09682 Holin_LLH: Phage holi 34.6 1.4E+02 0.0031 19.9 5.3 35 6-40 71-105 (108)
46 PRK10597 DNA damage-inducible 34.3 67 0.0014 21.1 3.3 42 21-63 11-52 (81)
47 cd06932 NR_LBD_PPAR The ligand 34.1 51 0.0011 25.4 3.2 33 21-54 182-214 (259)
48 COG1539 FolB Dihydroneopterin 33.9 1E+02 0.0022 21.4 4.4 33 12-48 61-93 (121)
49 KOG0614|consensus 33.9 1.3E+02 0.0029 26.9 5.9 56 3-63 265-321 (732)
50 smart00510 TFS2M Domain in the 33.0 32 0.00069 23.1 1.7 77 8-88 7-84 (102)
51 cd07348 NR_LBD_NGFI-B The liga 32.7 45 0.00098 25.5 2.7 34 21-54 157-191 (238)
52 PF15508 NAAA-beta: beta subun 32.6 1.4E+02 0.0031 19.3 4.9 39 2-43 26-64 (95)
53 cd00392 Ribosomal_L13 Ribosoma 32.5 79 0.0017 21.8 3.7 37 26-65 9-45 (114)
54 TIGR03654 L6_bact ribosomal pr 31.9 63 0.0014 23.6 3.3 28 23-59 135-162 (175)
55 KOG0653|consensus 31.7 1.5E+02 0.0034 24.2 5.8 68 3-78 177-244 (391)
56 PF07085 DRTGG: DRTGG domain; 31.3 53 0.0012 21.3 2.6 26 58-83 62-87 (105)
57 CHL00140 rpl6 ribosomal protei 30.9 69 0.0015 23.5 3.3 28 23-59 136-163 (178)
58 PF06569 DUF1128: Protein of u 30.8 1.5E+02 0.0033 19.1 4.5 24 14-38 46-69 (71)
59 PF14024 DUF4240: Protein of u 30.8 1.7E+02 0.0038 20.1 5.2 37 7-47 23-60 (128)
60 PF02603 Hpr_kinase_N: HPr Ser 30.3 53 0.0012 22.5 2.5 25 60-84 84-108 (127)
61 TIGR00053 addiction module tox 29.9 63 0.0014 20.3 2.7 38 26-64 23-63 (89)
62 TIGR00673 cynS cyanate hydrata 29.9 1.9E+02 0.0041 21.1 5.4 64 3-78 25-94 (150)
63 PF02817 E3_binding: e3 bindin 29.8 60 0.0013 18.2 2.3 21 68-88 4-24 (39)
64 PF07531 TAFH: NHR1 homology t 29.7 75 0.0016 21.6 3.1 34 4-42 24-57 (96)
65 PRK00754 signal recognition pa 29.6 42 0.00091 22.6 1.8 53 49-103 15-71 (95)
66 PF04405 ScdA_N: Domain of Unk 28.5 9.7 0.00021 23.2 -1.3 27 62-88 23-49 (56)
67 KOG0595|consensus 28.3 1.1E+02 0.0023 26.1 4.4 34 12-46 96-129 (429)
68 cd06954 NR_LBD_LXR The ligand 27.8 68 0.0015 23.9 2.9 34 21-55 162-195 (236)
69 TIGR00135 gatC glutamyl-tRNA(G 27.6 1.7E+02 0.0037 18.7 4.6 30 8-40 5-34 (93)
70 PRK00034 gatC aspartyl/glutamy 27.4 1.7E+02 0.0037 18.7 4.6 31 7-40 6-36 (95)
71 cd07349 NR_LBD_SHP The ligand 27.4 55 0.0012 24.7 2.3 33 21-54 149-181 (222)
72 KOG0648|consensus 27.1 16 0.00034 29.5 -0.7 62 24-97 39-101 (295)
73 PF00572 Ribosomal_L13: Riboso 27.0 1.1E+02 0.0024 21.4 3.7 37 26-65 9-45 (128)
74 PRK09731 putative general secr 27.0 62 0.0014 24.1 2.5 35 66-100 99-134 (178)
75 COG4517 Uncharacterized protei 26.7 60 0.0013 22.3 2.2 44 57-101 7-54 (109)
76 PF13103 TonB_2: TonB C termin 26.6 1.6E+02 0.0034 18.0 4.7 35 31-69 4-40 (85)
77 PF03622 IBV_3B: IBV 3B protei 26.2 30 0.00065 21.8 0.6 8 97-104 34-41 (64)
78 cd01781 AF6_RA_repeat2 Ubiquit 26.0 1.3E+02 0.0029 20.5 3.8 39 48-86 7-45 (100)
79 PF09379 FERM_N: FERM N-termin 25.9 1.5E+02 0.0032 17.9 3.8 43 59-101 9-57 (80)
80 cd07069 NR_LBD_Lrh-1 The ligan 25.9 71 0.0015 24.3 2.7 33 21-54 163-195 (241)
81 TIGR01205 D_ala_D_alaTIGR D-al 25.8 67 0.0014 24.4 2.6 32 57-88 275-308 (315)
82 PRK05498 rplF 50S ribosomal pr 25.3 1E+02 0.0022 22.6 3.3 28 23-59 136-163 (178)
83 PF03789 ELK: ELK domain ; In 25.3 26 0.00057 17.7 0.2 12 35-46 2-13 (22)
84 COG0108 RibB 3,4-dihydroxy-2-b 25.1 1.3E+02 0.0029 23.0 4.0 40 54-102 51-94 (203)
85 KOG2781|consensus 25.0 58 0.0013 26.1 2.1 44 22-83 91-134 (290)
86 KOG3853|consensus 24.7 37 0.0008 27.6 1.0 13 90-102 154-166 (350)
87 KOG3021|consensus 24.6 43 0.00093 26.9 1.3 36 21-62 265-300 (313)
88 PRK13689 hypothetical protein; 24.5 2E+02 0.0044 18.7 4.3 32 8-42 37-68 (75)
89 PF07137 VDE: Violaxanthin de- 24.2 58 0.0013 24.9 1.9 18 71-88 165-182 (198)
90 COG5398 Heme oxygenase [Inorga 24.2 2.2E+02 0.0047 22.4 5.1 31 3-36 15-45 (238)
91 TIGR03481 HpnM hopanoid biosyn 24.0 1.7E+02 0.0038 21.6 4.5 35 12-46 69-104 (198)
92 cd02185 AroH Chorismate mutase 23.9 2.1E+02 0.0045 20.1 4.6 61 2-64 15-90 (117)
93 PF13286 HD_assoc: Phosphohydr 23.9 1.9E+02 0.0042 18.0 5.0 37 1-39 3-39 (92)
94 PRK13289 bifunctional nitric o 23.7 2E+02 0.0042 22.9 5.0 42 8-49 74-116 (399)
95 PF02337 Gag_p10: Retroviral G 23.7 1.5E+02 0.0032 19.8 3.7 39 8-52 10-48 (90)
96 PF06519 TolA: TolA C-terminal 23.4 1.8E+02 0.0038 19.3 4.0 52 25-80 10-70 (96)
97 COG4196 Uncharacterized protei 23.2 73 0.0016 28.3 2.5 17 72-88 149-165 (808)
98 cd06941 NR_LBD_DmE78_like The 23.0 1E+02 0.0022 22.3 3.0 31 23-54 122-152 (195)
99 cd06936 NR_LBD_Fxr The ligand 22.9 94 0.002 23.2 2.9 31 23-54 153-183 (221)
100 PF08153 NGP1NT: NGP1NT (NUC09 22.7 66 0.0014 23.0 1.9 22 22-43 43-64 (130)
101 cd06940 NR_LBD_REV_ERB The lig 22.6 86 0.0019 22.8 2.6 32 21-53 130-161 (189)
102 COG5502 Uncharacterized conser 22.3 2E+02 0.0043 20.8 4.3 33 21-53 41-73 (135)
103 PF05184 SapB_1: Saposin-like 22.1 1.3E+02 0.0028 15.8 2.6 27 6-35 8-34 (39)
104 PF12767 SAGA-Tad1: Transcript 22.1 1.4E+02 0.0029 22.8 3.6 31 1-34 14-53 (252)
105 PF14941 OAF: Transcriptional 22.1 37 0.00081 26.6 0.5 15 47-61 195-216 (240)
106 PRK07179 hypothetical protein; 22.0 2.2E+02 0.0047 22.6 4.9 48 32-79 26-79 (407)
107 PF09371 Tex_N: Tex-like prote 22.0 1.6E+02 0.0034 22.1 3.9 32 7-38 23-54 (193)
108 cd06945 NR_LBD_Nurr1_like The 22.0 2.2E+02 0.0047 21.5 4.7 33 21-54 158-192 (239)
109 cd06950 NR_LBD_Tlx_PNR_like Th 21.6 1E+02 0.0023 22.6 2.8 29 24-53 147-175 (206)
110 PRK09216 rplM 50S ribosomal pr 21.5 1.8E+02 0.0038 21.0 3.9 37 26-65 23-59 (144)
111 PF09492 Pec_lyase: Pectic aci 21.5 1.9E+02 0.0041 23.2 4.5 55 7-64 43-98 (289)
112 PF08279 HTH_11: HTH domain; 21.5 62 0.0014 18.3 1.3 29 23-59 27-55 (55)
113 TIGR01066 rplM_bact ribosomal 21.5 1.7E+02 0.0036 21.0 3.8 37 26-65 21-57 (140)
114 PF08671 SinI: Anti-repressor 21.4 30 0.00065 18.7 -0.1 17 72-88 7-23 (30)
115 PF13558 SbcCD_C: Putative exo 21.3 2.3E+02 0.005 18.0 5.9 49 26-79 37-86 (90)
116 PF07500 TFIIS_M: Transcriptio 21.2 28 0.0006 23.4 -0.3 77 8-88 9-86 (115)
117 cd03123 alpha_CA_VI_IX_XII_XIV 21.2 1.3E+02 0.0028 23.0 3.4 39 22-63 208-246 (248)
118 cd01783 DAGK_delta_RA Ubiquiti 21.1 1.5E+02 0.0032 20.1 3.3 40 48-87 8-47 (97)
119 PF14769 CLAMP: Flagellar C1a 21.1 2.5E+02 0.0055 18.3 5.3 38 6-43 39-84 (101)
120 cd07070 NR_LBD_SF-1 The ligand 21.1 1.1E+02 0.0023 23.2 2.9 30 23-53 163-192 (237)
121 COG1908 FrhD Coenzyme F420-red 21.0 1.4E+02 0.0031 21.4 3.3 27 58-84 30-56 (132)
122 COG5086 Uncharacterized conser 20.8 63 0.0014 24.8 1.5 30 1-35 79-108 (218)
123 TIGR02116 toxin_Txe_YoeB toxin 20.7 2.2E+02 0.0048 17.6 4.5 39 25-64 17-57 (80)
124 cd07071 NR_LBD_Nurr1 The ligan 20.6 1.2E+02 0.0025 23.2 3.0 34 21-54 157-191 (238)
125 COG0394 Wzb Protein-tyrosine-p 20.6 1.4E+02 0.003 20.9 3.2 24 65-88 42-65 (139)
126 KOG4231|consensus 20.4 2.5E+02 0.0054 25.2 5.2 49 13-66 376-425 (763)
127 COG4226 HicB Predicted nucleas 20.3 2.2E+02 0.0048 19.9 4.0 57 27-87 43-99 (111)
128 PF08765 Mor: Mor transcriptio 20.2 1.4E+02 0.0031 19.8 3.1 37 9-46 11-47 (108)
129 COG0809 QueA S-adenosylmethion 20.2 1E+02 0.0022 25.6 2.7 41 54-100 246-286 (348)
No 1
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=100.00 E-value=7.8e-57 Score=310.47 Aligned_cols=102 Identities=45% Similarity=0.898 Sum_probs=99.8
Q ss_pred CHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHHHh
Q psy11249 1 MQDQISAAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAKAV 80 (105)
Q Consensus 1 M~~EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~s 80 (105)
|++||++|||||+++|+++ +++|+++++.|+++|++.|.+||+|||||++|+||||||||+|| +++||+|.+||.+|
T Consensus 1 M~~EI~~av~Fl~~~l~~~-~~l~~~~v~~F~~~L~~~L~~~y~~HWyP~~P~kGqayRCIrIn--~~~Dp~l~~Aa~~s 77 (108)
T smart00099 1 MKLEIAAAVNFITSLLRKH-NKLSKRRVEIFAEKLTRLLKEKYKNHWYPEKPYKGSGFRCIRIN--QKVDPVIEQACKES 77 (108)
T ss_pred ChHHHHHHHHHHHHHHHHc-CCCCHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCCcceEEEEEC--CcCCHHHHHHHHHh
Confidence 9999999999999999775 78999999999999999999999999999999999999999995 99999999999999
Q ss_pred CCCCcccC--CCCccEEEEcCCceeeC
Q psy11249 81 GMSYEDMR--LPVELTLWVDPHEVCCR 105 (105)
Q Consensus 81 gl~~~~l~--lP~e~tlWvDPgeVs~R 105 (105)
||+++||. ||+|+||||||||||||
T Consensus 78 Gl~~~~l~~~LP~eltiwvDP~eVs~R 104 (108)
T smart00099 78 GLDIDDLGGNLPKELTLWVDPFEVSYR 104 (108)
T ss_pred CCCHHHHHHhCCcccEEEECCCEEEEe
Confidence 99999999 99999999999999998
No 2
>PF07742 BTG: BTG family; InterPro: IPR002087 Anti-proliferative proteins have been shown to include mammalian and avian protein BTG1 (which appears to be involved in negative regulation of cell proliferation) and rat/mouse NGF-inducible protein PC3/TIS21 (BTG2) [, , ]. These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain. The sequence of the N-terminal half of these proteins is well conserved.; PDB: 3DJU_B 3E9V_A 2Z15_D 2D5R_B 3DJN_B.
Probab=100.00 E-value=6e-56 Score=310.06 Aligned_cols=104 Identities=50% Similarity=0.915 Sum_probs=91.6
Q ss_pred CHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHHHh
Q psy11249 1 MQDQISAAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAKAV 80 (105)
Q Consensus 1 M~~EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~s 80 (105)
|++||++||+||+++|+++ +++|+++++.|+++|++.|.+||++||||++|+||||||||+||+++++||+|.+||.++
T Consensus 1 M~~EI~~av~Fl~~~l~~~-~~l~~~~~~~F~~~L~~~L~~ry~~HW~P~~P~kGsayRcIrin~~~~~Dp~l~~Aa~~s 79 (118)
T PF07742_consen 1 MKTEIAAAVNFLTRLLYNK-GRLPRRQVDRFAEELENLLCERYKGHWYPENPSKGSAYRCIRINPGHKMDPVLEQAAKES 79 (118)
T ss_dssp CHHHHHHHHHHHHHHHHHH-C-B-HHHHHHHHHHHHHHHHHHHTTS--TTSTTTTHHHH-EEES--SSB-HHHHHHHHHT
T ss_pred CHHHHHHHHHHHHHHHHhc-CCCCHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCceEEEEEcCCCCCCHHHHHHHHHh
Confidence 9999999999999999986 579999999999999999999999999999999999999999998899999999999999
Q ss_pred CCCCcccC--CCCccEEEEcCCceeeC
Q psy11249 81 GMSYEDMR--LPVELTLWVDPHEVCCR 105 (105)
Q Consensus 81 gl~~~~l~--lP~e~tlWvDPgeVs~R 105 (105)
||++++|. ||+||||||||||||||
T Consensus 80 gl~~~~l~~~LP~eltlWvDPgeVs~R 106 (118)
T PF07742_consen 80 GLSYEDLRSLLPRELTLWVDPGEVSYR 106 (118)
T ss_dssp T--HHHHHHHS-TTEEEEEETTEEEEE
T ss_pred CCCHHHHHHhcchhcEEEECCCEEEEE
Confidence 99999999 99999999999999998
No 3
>KOG4006|consensus
Probab=100.00 E-value=1.2e-36 Score=239.47 Aligned_cols=98 Identities=33% Similarity=0.705 Sum_probs=96.0
Q ss_pred CHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHHHh
Q psy11249 1 MQDQISAAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAKAV 80 (105)
Q Consensus 1 M~~EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~s 80 (105)
|+.||++|+||+++||+ +|||||++++|+++|+++|.+||++||||++|.||||||||. +..||+++.|++++
T Consensus 1 m~~ei~valnfvisyly---nklprrrv~ifgeele~~l~~k~~~hwypekp~kgs~~rcih----~~~d~vme~eiaea 73 (311)
T KOG4006|consen 1 MQLEIQVALNFVISYLY---NKLPRRRVNIFGEELERLLKKKFEGHWYPEKPKKGSGFRCIH----ETVDPVMESEIAEA 73 (311)
T ss_pred CcchHHHHHHHHHHHHh---ccCCccccchhHHHHHHHHHHhhcCccCCCCCCCccccchhc----ccccHHHHHHHHHh
Confidence 99999999999999999 799999999999999999999999999999999999999998 68999999999999
Q ss_pred CCCCcccC--CCCccEEEEcCCceeeC
Q psy11249 81 GMSYEDMR--LPVELTLWVDPHEVCCR 105 (105)
Q Consensus 81 gl~~~~l~--lP~e~tlWvDPgeVs~R 105 (105)
|+..+|+. +|.++.+||||++|++|
T Consensus 74 g~fisdvlrnlp~~lsv~idpFevslq 100 (311)
T KOG4006|consen 74 GVFISDVLRNLPKLLSVWIDPFEVSLQ 100 (311)
T ss_pred cCCHHHHHHhCcchhheeecchhhHHh
Confidence 99999998 99999999999999986
No 4
>KOG4006|consensus
Probab=99.91 E-value=3e-26 Score=180.66 Aligned_cols=104 Identities=35% Similarity=0.648 Sum_probs=99.8
Q ss_pred CHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHHHh
Q psy11249 1 MQDQISAAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAKAV 80 (105)
Q Consensus 1 M~~EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~s 80 (105)
|..||++|+.|+.++|+++ .+.....|+.|...|+..|.++|+.||+||+|++||+||||+||..--.|+.+.+++.++
T Consensus 66 me~eiaeag~fisdvlrnl-p~~lsv~idpFevslqi~ekg~yK~hw~~d~p~kG~~~rcirIn~~~npdaq~~~~i~~~ 144 (311)
T KOG4006|consen 66 MESEIAEAGVFISDVLRNL-PKLLSVWIDPFEVSLQIGEKGAYKVHWFPDKPSKGQAYRCIRINKSFNPDAQVFRPIGAS 144 (311)
T ss_pred HHHHHHHhcCCHHHHHHhC-cchhheeecchhhHHhhhhccceeeeecCCCCCCCchhhhHHHhhccCCchhhhhccccc
Confidence 7899999999999999997 568889999999999999999999999999999999999999998888899999999999
Q ss_pred CCCCcccCCCCccEEEEcCCceeeC
Q psy11249 81 GMSYEDMRLPVELTLWVDPHEVCCR 105 (105)
Q Consensus 81 gl~~~~l~lP~e~tlWvDPgeVs~R 105 (105)
+.+.+.+.+|.|+|+|+||.+||||
T Consensus 145 ~ss~s~~~lPtelt~wvdP~evs~r 169 (311)
T KOG4006|consen 145 NSSVSNLGLPTELTLWVDPIEVSTR 169 (311)
T ss_pred ccchhccCCCcccccccCceEEEee
Confidence 9999999999999999999999997
No 5
>cd01768 RA RA (Ras-associating) ubiquitin domain. The RA (Ras-associating) domain is structurally similar to ubiquitin and is present in one or two copies in a number of signalling molecules that bind and regulate a small GTPase called Ras or the Ras-related GTPases, Ral and Rap. RA-containing proteins include RalGDS, AF6, RIN1, RASSF1, SNX27, CYR1, STE50, and phospholipase C epsilon.
Probab=91.40 E-value=0.5 Score=30.05 Aligned_cols=36 Identities=25% Similarity=0.648 Sum_probs=31.2
Q ss_pred CCCCCCCccceeEEEecCCCCCCHHHHHHHHHhCCCC
Q psy11249 48 FPEAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMSY 84 (105)
Q Consensus 48 ~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~ 84 (105)
|+.++ .|+.|++|+++.+....-++..|+.+.|++.
T Consensus 5 ~~~~~-~~~~~kti~V~~~~t~~~Vi~~~l~k~~l~~ 40 (87)
T cd01768 5 YPEDP-SGGTYKTLRVSKDTTAQDVIQQLLKKFGLDD 40 (87)
T ss_pred eCCcC-CCccEEEEEECCCCCHHHHHHHHHHHhCCcC
Confidence 34455 7999999999999999999999999999984
No 6
>cd00153 RalGDS_RA Ubiquitin domain of RalGDS-like factor (RLF) and related proteins. This CD represents the C-terminal Ras-associating (RA) domain of three closely related guanine-nucleotide exchange factors (GEF's), Ral guanine nucleotide dissociation stimulator (RalGDS), RalGDS-like (RGL), and RalGDS-like factor (RLF). The RalGDS proteins are downstream effectors of the Ras-related protein Ral, providing a mechanism for Ral activation by extracellular signals. The RA domain is structurally similar to ubiquitin and exists in a number of other signalling proteins including AF6, rasfadin, SNX27, CYR1, and STE50.
Probab=88.48 E-value=0.86 Score=30.58 Aligned_cols=31 Identities=23% Similarity=0.345 Sum_probs=29.0
Q ss_pred ccceeEEEecCCCCCCHHHHHHHHHhCCCCc
Q psy11249 55 GQGYRCIRLNKNVKKDTILENAAKAVGMSYE 85 (105)
Q Consensus 55 GsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~ 85 (105)
|.-|+||-+..+.+++.+|.+|-.+-|++.+
T Consensus 15 gn~YKSIlltsqDktP~VI~ral~Khnl~~~ 45 (87)
T cd00153 15 GNLYKSILLTSQDKAPQVIRRAMEKHNLESE 45 (87)
T ss_pred cceEEEEEEecCCcCHHHHHHHHHHhCCCcC
Confidence 9999999999999999999999999999765
No 7
>smart00314 RA Ras association (RalGDS/AF-6) domain. RasGTP effectors (in cases of AF6, canoe and RalGDS); putative RasGTP effectors in other cases. Kalhammer et al. have shown that not all RA domains bind RasGTP. Predicted structure similar to that determined, and that of the RasGTP-binding domain of Raf kinase. Predicted RA domains in PLC210 and nore1 found to bind RasGTP. Included outliers (Grb7, Grb14, adenylyl cyclases etc.)
Probab=85.08 E-value=2.3 Score=27.11 Aligned_cols=32 Identities=9% Similarity=0.347 Sum_probs=28.8
Q ss_pred CccceeEEEecCCCCCCHHHHHHHHHhCCCCc
Q psy11249 54 RGQGYRCIRLNKNVKKDTILENAAKAVGMSYE 85 (105)
Q Consensus 54 rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~ 85 (105)
.++.|++|.++.+....-+|..|++..|++.+
T Consensus 13 ~~~~~kti~v~~~tTa~~Vi~~~l~k~~l~~~ 44 (90)
T smart00314 13 PGGTYKTLRVSSRTTARDVIQQLLEKFHLTDD 44 (90)
T ss_pred CCCcEEEEEECCCCCHHHHHHHHHHHhCCCCC
Confidence 47889999999999999999999999999854
No 8
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=84.23 E-value=2 Score=26.92 Aligned_cols=43 Identities=19% Similarity=0.369 Sum_probs=34.1
Q ss_pred CCCCCccceeEEEecCCCCCCHHHHHHHHHhCCCCcccCCCCccEEE
Q psy11249 50 EAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMSYEDMRLPVELTLW 96 (105)
Q Consensus 50 ~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l~lP~e~tlW 96 (105)
....-|..|++|.|+.+....-+|..|++..|+ -.-|.++.||
T Consensus 10 ~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l----~~~~~~y~L~ 52 (93)
T PF00788_consen 10 GDGSPGSTYKTIKVSSSTTAREVIEMALEKFGL----AEDPSDYCLV 52 (93)
T ss_dssp TTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTT----SSSGGGEEEE
T ss_pred CCCCCCccEEEEEECCCCCHHHHHHHHHHHhCC----CCCCCCEEEE
Confidence 344456689999999999999999999999999 2246677776
No 9
>COG3112 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.54 E-value=1.4 Score=31.01 Aligned_cols=38 Identities=34% Similarity=0.426 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHHHhCCCCcccC-CCCccEEEEcCCceeeC
Q psy11249 67 VKKDTILENAAKAVGMSYEDMR-LPVELTLWVDPHEVCCR 105 (105)
Q Consensus 67 ~~~Dp~l~~Aa~~sgl~~~~l~-lP~e~tlWvDPgeVs~R 105 (105)
.++|.+ .+||...-=+..++. -..|.|||+|-.||.+|
T Consensus 37 akl~~v-l~~a~~~~~s~~~~~~~G~Eytl~~~geEVmVr 75 (121)
T COG3112 37 AKLDEV-LQAADTLKGSEREWQLAGHEYTLWMDGEEVMVR 75 (121)
T ss_pred HHHHHH-HHHHHHhhcChhhheecCcEEEEEEcCceeeee
Confidence 345554 445555444444666 68999999999999887
No 10
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=80.69 E-value=4.7 Score=25.86 Aligned_cols=59 Identities=14% Similarity=0.343 Sum_probs=45.7
Q ss_pred CCHHHHHHHHHHHHHHHHhh----cCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHHHhCCCCccc
Q psy11249 23 CDADQLEAFKTKLAELLNDR----FANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMSYEDM 87 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~r----y~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l 87 (105)
++.+++.....+..+.+.+- |...|.- |.+|.-| ||..- +--..|.++++++|++.+.+
T Consensus 12 it~e~l~~~~~~~~~~~~~~~~V~w~~s~v~--~d~~k~~-Cly~A---p~~eaV~~~~~~aG~p~d~I 74 (77)
T PF14026_consen 12 ITAEDLAAAHAKSCAVQAEMPGVQWLRSYVS--EDDGKIF-CLYEA---PDEEAVREHARRAGLPADRI 74 (77)
T ss_pred CCHHHHHHHHHHhHHHHhhcCCeEEEEEEEe--cCCCeEE-EEEEC---CCHHHHHHHHHHcCCCcceE
Confidence 88899999999999999888 8888873 4466666 88872 23356888888899988754
No 11
>PF15123 DUF4562: Domain of unknown function (DUF4562)
Probab=68.71 E-value=5.7 Score=27.99 Aligned_cols=24 Identities=21% Similarity=0.605 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCCC
Q psy11249 27 QLEAFKTKLAELLNDRFANHWFPE 50 (105)
Q Consensus 27 ~i~~F~~~L~~~L~~ry~~HW~P~ 50 (105)
+...|.+..++.++.||++=|+|.
T Consensus 81 k~gefr~aaed~~tHRyQnPW~p~ 104 (116)
T PF15123_consen 81 KRGEFRQAAEDRITHRYQNPWQPK 104 (116)
T ss_pred eHHHHHHHHHHHHhhccCCCCCCC
Confidence 347899999999999999999984
No 12
>KOG3254|consensus
Probab=66.01 E-value=7 Score=29.89 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccce
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGY 58 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsay 58 (105)
++++++-.|++++. .|.|.+|.||-|-
T Consensus 169 ~dKq~V~qFAAkvR---------sfkpPEPYKGKGI 195 (211)
T KOG3254|consen 169 IDKQKVTQFAAKVR---------SFKPPEPYKGKGI 195 (211)
T ss_pred ccHHHHHHHHHHHh---------ccCCCCCcCCCce
Confidence 89999999999986 5999999999883
No 13
>PF06062 UPF0231: Uncharacterised protein family (UPF0231); InterPro: IPR008249 The proteins in this entry are functionally uncharacterised.
Probab=63.98 E-value=6 Score=27.77 Aligned_cols=38 Identities=21% Similarity=0.236 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHhCCCCcccC-CCCccEEEEcCCceeeC
Q psy11249 68 KKDTILENAAKAVGMSYEDMR-LPVELTLWVDPHEVCCR 105 (105)
Q Consensus 68 ~~Dp~l~~Aa~~sgl~~~~l~-lP~e~tlWvDPgeVs~R 105 (105)
+.+.++..+.+.-+-...++. ..+|+||++|..||.+|
T Consensus 39 ~i~~vl~~i~~~~~~~~~e~~l~G~E~sL~l~~dEV~V~ 77 (121)
T PF06062_consen 39 KIDQVLAAIEQLKNSQRQEWQLEGKEYSLSLDQDEVMVQ 77 (121)
T ss_pred HHHHHHHHHHHHhcCCCccEEEeCceEEEEEccceeEee
Confidence 455655555555444444677 79999999999999875
No 14
>PRK05248 hypothetical protein; Provisional
Probab=60.30 E-value=6.9 Score=27.60 Aligned_cols=38 Identities=39% Similarity=0.533 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHHHhCCCCcccC-CCCccEEEEcCCceeeC
Q psy11249 67 VKKDTILENAAKAVGMSYEDMR-LPVELTLWVDPHEVCCR 105 (105)
Q Consensus 67 ~~~Dp~l~~Aa~~sgl~~~~l~-lP~e~tlWvDPgeVs~R 105 (105)
.+++.++..+....| +..++. ...|+|||+|-.||.+|
T Consensus 37 ~~i~~il~~~~~~~~-~~~e~~l~G~E~sL~l~~eEv~V~ 75 (121)
T PRK05248 37 AKLDEVLAAAAAVKG-SEREWQLAGHEYTLWLDGEEVMVR 75 (121)
T ss_pred HHHHHHHHHHHHHhC-CcccEEEeccEEEEEEcCCeEEEE
Confidence 345666665555666 666777 79999999999999875
No 15
>PF01221 Dynein_light: Dynein light chain type 1 ; InterPro: IPR001372 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits (see IPR004273 from INTERPRO), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, ]. Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer alpha-beta core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].; GO: 0007017 microtubule-based process, 0005875 microtubule associated complex; PDB: 1F95_A 1F96_A 1F3C_A 3P8M_B 2XQQ_C 1RE6_A 1CMI_A 1PWK_A 1PWJ_A 4DS1_C ....
Probab=58.10 E-value=15 Score=23.70 Aligned_cols=42 Identities=10% Similarity=0.409 Sum_probs=26.0
Q ss_pred CHHHHHH-HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCCCC
Q psy11249 1 MQDQISA-AVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFANHWF 48 (105)
Q Consensus 1 M~~EI~~-av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~HW~ 48 (105)
|-.|++. +++.....+.+ .+.. ...++.|.+.|-++|.+.|+
T Consensus 13 M~~~~~~~~~~~~~~a~~~----~~~~--~eiA~~iK~~lD~~yG~~Wh 55 (89)
T PF01221_consen 13 MPEEMQEEAIELAKEALKK----YQDE--KEIAEFIKQELDKKYGPTWH 55 (89)
T ss_dssp S-HHHHHHHHHHHHHHHHH----CSSH--HHHHHHHHHHHHHHHSS-EE
T ss_pred CCHHHHHHHHHHHHHHHHH----CCcH--HHHHHHHHHHHhcccCCceE
Confidence 3344443 44555555553 2222 55889999999999999998
No 16
>PF05534 HicB: HicB family; InterPro: IPR008651 This family consists of several bacterial HicB related proteins. The function of HicB is unknown although it is thought to be involved in pilus formation. It has been speculated that HicB performs a function antagonistic to that of pili and yet is necessary for invasion of certain niches [].
Probab=52.95 E-value=6.8 Score=23.30 Aligned_cols=36 Identities=31% Similarity=0.400 Sum_probs=25.9
Q ss_pred CCCCCCCccceeEEEecCCCCCCHHHHHHHHHhCCCCccc
Q psy11249 48 FPEAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMSYEDM 87 (105)
Q Consensus 48 ~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l 87 (105)
.|++|.+|+ -.||+ ...+..-+..+|.+.|++..++
T Consensus 11 ~p~k~~sg~--~~lRi--~~~Lh~~l~~~A~~~gvSlN~~ 46 (51)
T PF05534_consen 11 EPEKPYSGK--FNLRI--PPELHRALAEAAAAEGVSLNQW 46 (51)
T ss_pred CCCCCCCCc--eeeeC--CHHHHHHHHHHHHHhCCCHHHH
Confidence 477777754 46777 5566677788888999987654
No 17
>COG0560 SerB Phosphoserine phosphatase [Amino acid transport and metabolism]
Probab=49.48 E-value=79 Score=23.55 Aligned_cols=63 Identities=16% Similarity=0.282 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCC-----CCccceeEEEecCCCCCCHHHHHHHHHhCC
Q psy11249 8 AVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFANHWFPEAP-----NRGQGYRCIRLNKNVKKDTILENAAKAVGM 82 (105)
Q Consensus 8 av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P-----~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl 82 (105)
...+-+.+|. -++.+.++.+.++. ..++|.-. .|-.|++|+.| +++.+-.+...|+..|+
T Consensus 52 ~~~~~v~~l~----g~~~~~v~~~~~~~---------~~l~~ga~elv~~lk~~G~~v~ii--Sgg~~~lv~~ia~~lg~ 116 (212)
T COG0560 52 SLRLRVALLK----GLPVEVLEEVREEF---------LRLTPGAEELVAALKAAGAKVVII--SGGFTFLVEPIAERLGI 116 (212)
T ss_pred HHHHHHHHhC----CCCHHHHHHHHHhc---------CcCCccHHHHHHHHHHCCCEEEEE--cCChHHHHHHHHHHhCC
Confidence 3444455555 37888888888772 11222111 16788999999 78899999999999999
Q ss_pred CCc
Q psy11249 83 SYE 85 (105)
Q Consensus 83 ~~~ 85 (105)
++.
T Consensus 117 d~~ 119 (212)
T COG0560 117 DYV 119 (212)
T ss_pred chh
Confidence 863
No 18
>TIGR01490 HAD-SF-IB-hyp1 HAD-superfamily subfamily IB hydrolase, TIGR01490. A subset of these sequences, including the Caulobacter crescentus CicA protein, cluster together and may represent a separate equivalog.
Probab=48.97 E-value=47 Score=23.38 Aligned_cols=56 Identities=13% Similarity=0.321 Sum_probs=37.3
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCCCC-----CCccceeEEEecCCCCCCHHHHHHHHHhCCC
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPEAP-----NRGQGYRCIRLNKNVKKDTILENAAKAVGMS 83 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P-----~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~ 83 (105)
++.+.++.|.+++... .+...++|.-. .+.+|++++.+ +...++.+..-++..|++
T Consensus 67 ~~~~~l~~~~~~~~~~---~~~~~~~~~~~~~l~~l~~~g~~v~iv--S~s~~~~v~~~~~~lg~~ 127 (202)
T TIGR01490 67 LLEEDVRAIVEEFVNQ---KIESILYPEARDLIRWHKAEGHTIVLV--SASLTILVKPLARILGID 127 (202)
T ss_pred CCHHHHHHHHHHHHHH---HHHHhccHHHHHHHHHHHHCCCEEEEE--eCCcHHHHHHHHHHcCCc
Confidence 7888887777665432 11223333222 15678999999 567889999999888885
No 19
>PTZ00059 dynein light chain; Provisional
Probab=48.44 E-value=48 Score=21.67 Aligned_cols=18 Identities=6% Similarity=0.464 Sum_probs=15.8
Q ss_pred HHHHHHHHHHhhcCCCCC
Q psy11249 31 FKTKLAELLNDRFANHWF 48 (105)
Q Consensus 31 F~~~L~~~L~~ry~~HW~ 48 (105)
-++.+.+.|-++|.+.|.
T Consensus 39 iA~~IK~~fD~~yg~~Wh 56 (90)
T PTZ00059 39 IAAYIKKEFDKKYNPTWH 56 (90)
T ss_pred HHHHHHHHHHhhcCCCCE
Confidence 377888899999999998
No 20
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=47.46 E-value=40 Score=23.56 Aligned_cols=20 Identities=25% Similarity=0.853 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHhhcCCCC
Q psy11249 26 DQLEAFKTKLAELLNDRFANHW 47 (105)
Q Consensus 26 ~~i~~F~~~L~~~L~~ry~~HW 47 (105)
+-++.|++.+..++.++|+ |
T Consensus 117 ~Hle~~~eeI~~l~~~~~~--~ 136 (136)
T PF11888_consen 117 HHLEEYREEINELYEKKYK--W 136 (136)
T ss_pred HHHHHHHHHHHHHHHHhhc--C
Confidence 5678999999999999998 8
No 21
>COG3453 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.58 E-value=16 Score=26.16 Aligned_cols=35 Identities=23% Similarity=0.415 Sum_probs=26.6
Q ss_pred CccceeEEEecC------CCCCCHHHHHHHHHhCCCCcccC
Q psy11249 54 RGQGYRCIRLNK------NVKKDTILENAAKAVGMSYEDMR 88 (105)
Q Consensus 54 rGsayRcIrin~------~~~~Dp~l~~Aa~~sgl~~~~l~ 88 (105)
+..||+.|..|+ +++---.+.+||.++|+.+..+-
T Consensus 25 aa~GFksiI~nRPDgEe~~QP~~~~i~~aa~~aGl~y~~iP 65 (130)
T COG3453 25 AALGFKSIICNRPDGEEPGQPGFAAIAAAAEAAGLTYTHIP 65 (130)
T ss_pred HHhccceecccCCCCCCCCCCChHHHHHHHHhcCCceEEee
Confidence 467899998885 44444678999999999986554
No 22
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.44 E-value=62 Score=20.84 Aligned_cols=30 Identities=10% Similarity=0.305 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHH
Q psy11249 8 AVLFLAKLIERSNTSCDADQLEAFKTKLAEL 38 (105)
Q Consensus 8 av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~ 38 (105)
+...|-+++.++ .+++++..+.|+++|..+
T Consensus 40 dLtdiy~mvkkk-enfSpsEmqaiA~eL~rl 69 (71)
T COG4840 40 DLTDIYDMVKKK-ENFSPSEMQAIADELGRL 69 (71)
T ss_pred HHHHHHHHHHHh-ccCCHHHHHHHHHHHHHh
Confidence 445677788776 579999999999999864
No 23
>PF15658 Latrotoxin_C: Latrotoxin C-terminal domain
Probab=45.60 E-value=36 Score=24.32 Aligned_cols=32 Identities=16% Similarity=0.315 Sum_probs=25.8
Q ss_pred HHHHHHHHHh--hcCCCCHHHHHHHHHHHHHHHH
Q psy11249 9 VLFLAKLIER--SNTSCDADQLEAFKTKLAELLN 40 (105)
Q Consensus 9 v~Fl~~~l~~--~~~~l~~~~i~~F~~~L~~~L~ 40 (105)
..+|++++.+ ++++|+..+++.|..++...|-
T Consensus 89 s~~L~Sy~e~a~p~~~Ls~kq~~kfl~~f~~~~~ 122 (127)
T PF15658_consen 89 SKILCSYAEKACPGSKLSPKQFDKFLAEFNSHLD 122 (127)
T ss_pred HHHHHHHHHHhCcccCCCHHHHHHHHHHHHhccc
Confidence 4589999987 3478999999999998877653
No 24
>PF04273 DUF442: Putative phosphatase (DUF442); InterPro: IPR005939 Although this domain is uncharacterised it seems likely that it performs a phosphatase function.; GO: 0016787 hydrolase activity; PDB: 2F46_A 3GXH_B 3GXG_B.
Probab=44.13 E-value=15 Score=25.04 Aligned_cols=34 Identities=21% Similarity=0.322 Sum_probs=18.8
Q ss_pred ccceeEEEecCCCC------CCHHHHHHHHHhCCCCcccC
Q psy11249 55 GQGYRCIRLNKNVK------KDTILENAAKAVGMSYEDMR 88 (105)
Q Consensus 55 GsayRcIrin~~~~------~Dp~l~~Aa~~sgl~~~~l~ 88 (105)
-+||+.|..|+... ....+.++|++.||.|-.+-
T Consensus 25 ~~GfktVInlRpd~E~~~qp~~~~~~~~a~~~Gl~y~~iP 64 (110)
T PF04273_consen 25 AQGFKTVINLRPDGEEPGQPSSAEEAAAAEALGLQYVHIP 64 (110)
T ss_dssp HCT--EEEE-S-TTSTTT-T-HHCHHHHHHHCT-EEEE--
T ss_pred HCCCcEEEECCCCCCCCCCCCHHHHHHHHHHcCCeEEEee
Confidence 36899888875221 22347789999999987665
No 25
>PF08236 SRI: SRI (Set2 Rpb1 interacting) domain; InterPro: IPR013257 The SRI (Set2 Rpb1 interacting) domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation []. This domain is conserved from yeast to humans. Members of this family form a compact, closed three-helix bundle, with an up-down-up topology. The first and second helices are antiparallel to each other and are of similar length; the third helix, which is packed across helices alpha1 and alpha2 is slightly shorter, consisting of only 15 amino acids. Most conserved hydrophobic residues are largely buried in the interior of the structure and form an extensive and contiguous hydrophobic core that stabilises the packing of the three-helix bundle. This domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation []. ; GO: 0018024 histone-lysine N-methyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0034968 histone lysine methylation, 0005694 chromosome; PDB: 2A7O_A 2C5Z_A.
Probab=43.21 E-value=83 Score=20.45 Aligned_cols=35 Identities=14% Similarity=0.284 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhh
Q psy11249 8 AVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDR 42 (105)
Q Consensus 8 av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~r 42 (105)
...|+..+|.+....++.+.+-.++.+|+..|.++
T Consensus 13 l~~~V~~~l~~y~~~~~~ddfK~~ar~lt~~l~~K 47 (88)
T PF08236_consen 13 LAKHVVNLLNKYRKKLSKDDFKHLARKLTHKLVEK 47 (88)
T ss_dssp HHHHHHHHHCTTTTT--HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccccCCHHHHHHHHHHHHHHHHHH
Confidence 34567777777556799999999999999999874
No 26
>PF04986 Y2_Tnp: Putative transposase; InterPro: IPR007069 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases IS1294 and IS801 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=43.05 E-value=4.3 Score=29.80 Aligned_cols=47 Identities=11% Similarity=0.340 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEec
Q psy11249 6 SAAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLN 64 (105)
Q Consensus 6 ~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin 64 (105)
+.++.||.||+.+ ..++..+|..+. .....-+|++|+ +.+...+.++
T Consensus 104 ~~~~~YL~RY~~R--~~is~~Ri~~~~---~~~V~f~y~d~~-------~~~~~~~~l~ 150 (183)
T PF04986_consen 104 EQVLEYLGRYLHR--PAISNSRIVSYD---DGTVTFRYKDHR-------TKKTKTLTLS 150 (183)
T ss_pred hHHHHHHHHHHhh--ccccccceEEec---cceeEEEEEcCC-------CCcEEEEEec
Confidence 5789999999997 679999988776 667778999986 4555556654
No 27
>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily. The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to
Probab=41.58 E-value=29 Score=26.15 Aligned_cols=33 Identities=21% Similarity=0.290 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFPEAPNR 54 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~r 54 (105)
+--..++|+..++.+.++|.+..+.+ ||+.|.|
T Consensus 156 gL~~~~~Ve~lQe~~~~aL~~yi~~~-~p~~p~r 188 (231)
T cd06937 156 DLEEPDRVEKLQEPLLEALKIYARKR-RPDKPHM 188 (231)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHhh-CCCcccH
Confidence 34578899999999999999877766 8888875
No 28
>cd06951 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.
Probab=40.72 E-value=35 Score=25.64 Aligned_cols=31 Identities=19% Similarity=0.172 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPEAPNR 54 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~r 54 (105)
+++++|+.+++.+.++|.++...+ ||+.|.|
T Consensus 153 l~~~~Ve~lQe~~~~aL~~yi~~~-~p~~~~R 183 (222)
T cd06951 153 LCPHYIEALQKEAQQALNEHTMMT-RPLEQLR 183 (222)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHhh-CCCcccH
Confidence 488999999999999999977765 7777764
No 29
>PF09899 DUF2126: Putative amidoligase enzyme (DUF2126); InterPro: IPR018667 This domain is found in bacterial transglutaminase and transglutaminase-like proteins. Their exact function is, as yet, unknown.
Probab=40.28 E-value=29 Score=31.65 Aligned_cols=35 Identities=20% Similarity=0.377 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHhhc---------CCCCCCCCCCCccceeEEEe
Q psy11249 29 EAFKTKLAELLNDRF---------ANHWFPEAPNRGQGYRCIRL 63 (105)
Q Consensus 29 ~~F~~~L~~~L~~ry---------~~HW~P~~P~rGsayRcIri 63 (105)
-.++..|...|.++| +|.|||.+|.=-=++.|.--
T Consensus 82 r~~A~~L~~rLr~r~apggllh~gQGKWYPGE~LPRWal~lyWR 125 (819)
T PF09899_consen 82 RRLADDLIRRLRARFAPGGLLHYGQGKWYPGEPLPRWALGLYWR 125 (819)
T ss_pred HHHHHHHHHHHHHhhcCCceeeeccCCCCCCCCcchhhheeeec
Confidence 356777777788777 68999999998777777743
No 30
>PF07208 DUF1414: Protein of unknown function (DUF1414); InterPro: IPR009857 This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown.; PDB: 2JPQ_A 2JUZ_B 2JUW_B 2QTI_A 2OTA_A 2JR2_A 2JRX_A.
Probab=39.45 E-value=78 Score=18.63 Aligned_cols=31 Identities=23% Similarity=0.284 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHh
Q psy11249 8 AVLFLAKLIERSNTSCDADQLEAFKTKLAELLND 41 (105)
Q Consensus 8 av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ 41 (105)
.=|-++.++. .+++..|....++++.++|..
T Consensus 12 LGN~vTniln---~~V~~~qR~~iAe~Fa~AL~~ 42 (44)
T PF07208_consen 12 LGNMVTNILN---TSVPPAQRQAIAEKFAQALKS 42 (44)
T ss_dssp HHHHHHHHHH---HCS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHh---hcCCHHHHHHHHHHHHHHHHh
Confidence 3366777777 468999988888888877754
No 31
>PF03361 Herpes_IE2_3: Herpes virus intermediate/early protein 2/3; InterPro: IPR005028 This domain of unknown function is found in the intermediate/early proteins of the Herpes virus. Many of these proteins play a role in transcriptional regulation.; GO: 0006355 regulation of transcription, DNA-dependent
Probab=39.37 E-value=1.2e+02 Score=22.43 Aligned_cols=52 Identities=17% Similarity=0.236 Sum_probs=36.5
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCC------CCCCccceeEEEecCCCCCCHHHHHHHHHh
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPE------APNRGQGYRCIRLNKNVKKDTILENAAKAV 80 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~------~P~rGsayRcIrin~~~~~Dp~l~~Aa~~s 80 (105)
-+++.+.+|.+.+.+-+. ..|.-. .=-|-||||.+.| ..-..+.+..|++-+
T Consensus 71 h~p~t~~~~~~a~~~g~~----~~wd~~e~~~h~~~~r~Sd~rtm~I--~AATp~Dfl~A~~lC 128 (162)
T PF03361_consen 71 HDPETVRRFSEACRQGVK----AVWDLKENHTHSLCPRSSDYRTMII--SAATPKDFLGAAKLC 128 (162)
T ss_pred CCHHHHHHHHHHHHhCch----hHhhcccccccccCcCCCCceEEEE--eCCCcHHHHHHHHHH
Confidence 356778888887765433 334432 3348899999999 566778888888754
No 32
>cd04447 DEP_BRCC3 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.
Probab=38.73 E-value=78 Score=21.35 Aligned_cols=43 Identities=19% Similarity=0.277 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHhh---cCCCCHHHHHHHHHHHHH-HHHhhcCCCCC
Q psy11249 6 SAAVLFLAKLIERS---NTSCDADQLEAFKTKLAE-LLNDRFANHWF 48 (105)
Q Consensus 6 ~~av~Fl~~~l~~~---~~~l~~~~i~~F~~~L~~-~L~~ry~~HW~ 48 (105)
++||+||..+|... ...+++.++-.+.++|-. ...+.-.|.|.
T Consensus 33 sEAVDwL~~~l~~n~~fg~~vtR~~av~l~qkll~~hVie~V~g~~~ 79 (92)
T cd04447 33 SEAVDWLHELLRSNSNFGPEVTRQQTVQLLKKFLKNHVIEDIKGRWG 79 (92)
T ss_pred HHHHHHHHHHHHhccccCCCCCHHHHHHHHHHHHHcCCchhhccccc
Confidence 57999999999641 125788877666444432 22333344444
No 33
>PF10025 DUF2267: Uncharacterized conserved protein (DUF2267); InterPro: IPR018727 This entry contains proteins that have no known function. ; PDB: 2YSK_A.
Probab=38.24 E-value=72 Score=21.67 Aligned_cols=33 Identities=12% Similarity=0.219 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCC
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFPEAPN 53 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~ 53 (105)
.+|+......|++.|-..|..-|..-|.|..+.
T Consensus 34 ~rL~~~ea~~La~qLP~~l~~~l~~gw~~~~~~ 66 (125)
T PF10025_consen 34 ERLPPEEAADLAAQLPMELRGILYEGWRPSEGP 66 (125)
T ss_dssp TTS-HHHHHHHHTTS-HHHHHHHHTT--TTS--
T ss_pred HHCCHHHHHHHHHhCCHHHHHHHHhcccCCCCC
Confidence 689999999999999999999999999976554
No 34
>PF14898 DUF4491: Domain of unknown function (DUF4491)
Probab=38.05 E-value=19 Score=24.49 Aligned_cols=14 Identities=43% Similarity=1.130 Sum_probs=12.2
Q ss_pred hhcCCCCCCCCCCC
Q psy11249 41 DRFANHWFPEAPNR 54 (105)
Q Consensus 41 ~ry~~HW~P~~P~r 54 (105)
+|-+.-|||.||.|
T Consensus 80 kRV~kGWFP~NPkr 93 (94)
T PF14898_consen 80 KRVEKGWFPKNPKR 93 (94)
T ss_pred HHHHcCCCCCCCCC
Confidence 67788899999986
No 35
>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation []. Many proteins are involved in these processes. This family is a transporter which shows similarity to ABC transporters [].; PDB: 2QGU_A.
Probab=37.27 E-value=1e+02 Score=21.73 Aligned_cols=36 Identities=19% Similarity=0.268 Sum_probs=27.0
Q ss_pred HHHHHH-HhhcCCCCHHHHHHHHHHHHHHHHhhcCCC
Q psy11249 11 FLAKLI-ERSNTSCDADQLEAFKTKLAELLNDRFANH 46 (105)
Q Consensus 11 Fl~~~l-~~~~~~l~~~~i~~F~~~L~~~L~~ry~~H 46 (105)
.++++. -++..++++.+.+.|.+.+.+.|...|...
T Consensus 42 ~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~ 78 (170)
T PF05494_consen 42 RMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKR 78 (170)
T ss_dssp HHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 344443 346789999999999999999999887654
No 36
>cd06952 NR_LBD_TR2_like The ligand binding domain of the orphan nuclear receptors TR4 and TR2. The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D
Probab=37.05 E-value=39 Score=24.95 Aligned_cols=29 Identities=24% Similarity=0.310 Sum_probs=24.3
Q ss_pred CHHHHHHHHHHHHHHHHhhcCCCCCCCCCC
Q psy11249 24 DADQLEAFKTKLAELLNDRFANHWFPEAPN 53 (105)
Q Consensus 24 ~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~ 53 (105)
..+.++.+++++.+.|.+++..+ +|+.|.
T Consensus 150 ~~~~v~~lq~~i~~aL~~y~~~~-~p~~~~ 178 (222)
T cd06952 150 LRQQIEKLQEKALMELRDYVGKT-YPEDEY 178 (222)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHh-CCCccc
Confidence 56889999999999999988777 776654
No 37
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=36.07 E-value=43 Score=24.40 Aligned_cols=14 Identities=36% Similarity=0.878 Sum_probs=11.8
Q ss_pred CCCccEEEEcCCcee
Q psy11249 89 LPVELTLWVDPHEVC 103 (105)
Q Consensus 89 lP~e~tlWvDPgeVs 103 (105)
.|.++||||| ..||
T Consensus 98 ~g~~~tm~Vd-r~vC 111 (146)
T PF14437_consen 98 VGRSMTMYVD-RDVC 111 (146)
T ss_pred cCCeEEEEEC-cccc
Confidence 3999999999 7776
No 38
>COG0721 GatC Asp-tRNAAsn/Glu-tRNAGln amidotransferase C subunit [Translation, ribosomal structure and biogenesis]
Probab=36.03 E-value=1e+02 Score=20.52 Aligned_cols=31 Identities=35% Similarity=0.521 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q psy11249 7 AAVLFLAKLIERSNTSCDADQLEAFKTKLAELLN 40 (105)
Q Consensus 7 ~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~ 40 (105)
+-|..|+++-+ =.++...++.|+.+|..+|.
T Consensus 6 e~v~~la~Lar---L~lseee~e~~~~~l~~Il~ 36 (96)
T COG0721 6 EEVKHLAKLAR---LELSEEELEKFATQLEDILG 36 (96)
T ss_pred HHHHHHHHHhh---cccCHHHHHHHHHHHHHHHH
Confidence 34567777777 36899999999999999875
No 39
>smart00295 B41 Band 4.1 homologues. Also known as ezrin/radixin/moesin (ERM) protein domains. Present in myosins, ezrin, radixin, moesin, protein tyrosine phosphatases. Plasma membrane-binding domain. These proteins play structural and regulatory roles in the assembly and stabilization of specialized plasmamembrane domains. Some PDZ domain containing proteins bind one or more of this family. Now includes JAKs.
Probab=35.83 E-value=61 Score=22.77 Aligned_cols=43 Identities=16% Similarity=0.403 Sum_probs=31.5
Q ss_pred eeEEEecCCCCCCHHHHHHHHHhCCCCcccC------CCCccEEEEcCC
Q psy11249 58 YRCIRLNKNVKKDTILENAAKAVGMSYEDMR------LPVELTLWVDPH 100 (105)
Q Consensus 58 yRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l~------lP~e~tlWvDPg 100 (105)
..-+.++......-++...|...||...+.. -..+.+.|.||.
T Consensus 15 ~~~~~~~~~~t~~ev~~~v~~~~~l~~~~~F~L~~~~~~~~~~~~l~~~ 63 (207)
T smart00295 15 TLEFEVDSSTTAEELLETVCRKLGIRESEYFGLQFEDPDEDLSHWLDPA 63 (207)
T ss_pred EEEEEECCCCCHHHHHHHHHHHhCCCccceeEEEEEcCCCCcCeeCCCc
Confidence 5567888788888999999999999664443 123455788764
No 40
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=35.30 E-value=1.3e+02 Score=25.23 Aligned_cols=65 Identities=17% Similarity=0.182 Sum_probs=35.8
Q ss_pred HHHHHHHhhcCCCCCCCCCCCcccee-EEEecCCC--------CCCHHHHHHHHHhCCCCcccC---------CCCccEE
Q psy11249 34 KLAELLNDRFANHWFPEAPNRGQGYR-CIRLNKNV--------KKDTILENAAKAVGMSYEDMR---------LPVELTL 95 (105)
Q Consensus 34 ~L~~~L~~ry~~HW~P~~P~rGsayR-cIrin~~~--------~~Dp~l~~Aa~~sgl~~~~l~---------lP~e~tl 95 (105)
.....+...++..|+.+...+|--.+ -|++++++ .=||.+.+|+..+ ....-+. -..+++|
T Consensus 304 ~Y~a~Ira~Iqr~~~~~~~~~gktc~VrI~LapDG~V~sV~~sSGd~aldrAA~~A-ar~a~lP~pP~~~vye~~k~i~l 382 (387)
T PRK09510 304 QYAGQIKSAIQSKFYDASSYAGKTCTLRIKLAPDGTLLDIKKEGGDPALCQAALAA-AKTAKIPKPPSQEVYEKFKNAPL 382 (387)
T ss_pred hHHHHHHHHHHHhccCCccccCceEEEEEEEcCCCcEEeeeeCCCCHHHHHHHHHH-HHcCCCCCCCchHHHHhhcccee
Confidence 44455566777788887666654333 13333322 2278888887776 4333333 1234666
Q ss_pred EEcC
Q psy11249 96 WVDP 99 (105)
Q Consensus 96 WvDP 99 (105)
=+||
T Consensus 383 tF~P 386 (387)
T PRK09510 383 DFKP 386 (387)
T ss_pred eeCC
Confidence 6666
No 41
>PF06183 DinI: DinI-like family; InterPro: IPR010391 This family of short proteins includes DNA-damage-inducible protein I (DinI) and related proteins. The SOS response, a set of cellular phenomena exhibited by eubacteria, is initiated by various causes that include DNA damage-induced replication arrest, and is positively regulated by the co- protease activity of RecA. Escherichia coli DinI, a LexA-regulated SOS gene product, shuts off the initiation of the SOS response when overexpressed in vivo. Biochemical and genetic studies indicated that DinI physically interacts with RecA to inhibit its co-protease activity []. The structure of DinI is known [].; PDB: 1GHH_A.
Probab=35.28 E-value=40 Score=21.03 Aligned_cols=25 Identities=24% Similarity=0.381 Sum_probs=18.5
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCC
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHW 47 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW 47 (105)
+|...++.+.++|.+-|..+|.+..
T Consensus 1 lp~ga~~AL~~EL~kRl~~~yPd~~ 25 (65)
T PF06183_consen 1 LPAGALEALESELTKRLHRQYPDAE 25 (65)
T ss_dssp --TTHHHHHHHHHHHHHHHH-SS-E
T ss_pred CCccHHHHHHHHHHHHHHHHCCCce
Confidence 4667789999999999999998753
No 42
>PF11470 TUG-UBL1: GLUT4 regulating protein TUG; InterPro: IPR021569 TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane []. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions []. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site []. ; PDB: 2AL3_A.
Probab=35.21 E-value=20 Score=22.47 Aligned_cols=29 Identities=21% Similarity=0.382 Sum_probs=19.5
Q ss_pred EEEecCCCCCCHHHHHHHHHhCCCCcccC
Q psy11249 60 CIRLNKNVKKDTILENAAKAVGMSYEDMR 88 (105)
Q Consensus 60 cIrin~~~~~Dp~l~~Aa~~sgl~~~~l~ 88 (105)
-|.++++..+--++.+||+.-|++.++..
T Consensus 10 ~vkvtp~~~l~~VL~eac~k~~l~~~~~~ 38 (65)
T PF11470_consen 10 KVKVTPNTTLNQVLEEACKKFGLDPSSYD 38 (65)
T ss_dssp EE---TTSBHHHHHHHHHHHTT--GGG-E
T ss_pred EEEECCCCCHHHHHHHHHHHcCCCccceE
Confidence 45667788889999999999999987543
No 43
>cd04446 DEP_DEPDC4 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.
Probab=35.16 E-value=1e+02 Score=20.75 Aligned_cols=43 Identities=12% Similarity=0.116 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhh----cCCCCHHHHHHHHHHHHHH-HHhhcCCCCC
Q psy11249 6 SAAVLFLAKLIERS----NTSCDADQLEAFKTKLAEL-LNDRFANHWF 48 (105)
Q Consensus 6 ~~av~Fl~~~l~~~----~~~l~~~~i~~F~~~L~~~-L~~ry~~HW~ 48 (105)
.+||++|..+|... +..++|.+.-.+++.|-+. +.++-.++|+
T Consensus 31 sEaVDwL~~~l~~n~~f~~~~~tR~~Av~l~q~Ll~~gvi~~V~~~~~ 78 (95)
T cd04446 31 SEAVDVVLAHLMQNKYFGDVDVPRAKAVRLCQALMDCRVFEAVGTKVF 78 (95)
T ss_pred HHHHHHHHHHHhhccccCcccCCHHHHHHHHHHHHHcCCeeeccchhc
Confidence 47999999999641 1256888888777776542 3344455566
No 44
>cd05399 NT_Rel-Spo_like Nucleotidyltransferase (NT) domain of RelA- and SpoT-like ppGpp synthetases and hydrolases. This family includes the catalytic domains of Escherichia coli ppGpp synthetase (RelA), ppGpp synthetase/hydrolase (SpoT), and related proteins. RelA synthesizes (p)ppGpp in response to amino-acid starvation and in association with ribosomes. (p)ppGpp triggers the bacterial stringent response. SpoT catalyzes (p)ppGpp synthesis under carbon limitation in a ribosome-independent manner. It also catalyzes (p)ppGpp degradation. Gram-negative bacteria have two enzymes involved in (p)ppGpp metabolism while most Gram-positive organisms have a single Rel-Spo enzyme (Rel), which both synthesizes and degrades (p)ppGpp. The Arabidopsis thaliana Rel-Spo proteins, At-RSH1,-2, and-3 appear to regulate a rapid (p)ppGpp-mediated response to pathogens and other stresses. This catalytic domain is found in association with an N-terminal HD domain and a C-terminal metal dependent phosphohydro
Probab=34.73 E-value=70 Score=21.38 Aligned_cols=30 Identities=23% Similarity=0.494 Sum_probs=17.6
Q ss_pred HHHHHHHhhcCCC-----CCCCCCCCccceeEEEec
Q psy11249 34 KLAELLNDRFANH-----WFPEAPNRGQGYRCIRLN 64 (105)
Q Consensus 34 ~L~~~L~~ry~~H-----W~P~~P~rGsayRcIrin 64 (105)
.....|...|... .|-.+| +.+|||++.+.
T Consensus 68 ~v~~~l~~~f~~~~~~~~D~~~~p-~~~GYrslH~~ 102 (129)
T cd05399 68 RVLDLLHSLFKVIPGRVKDYIAEP-KENGYQSLHLV 102 (129)
T ss_pred HHHHHHHhCCcccCccccCCcCCC-CCCCceEEEEE
Confidence 3344455555443 222335 56799999886
No 45
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=34.64 E-value=1.4e+02 Score=19.94 Aligned_cols=35 Identities=14% Similarity=0.273 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q psy11249 6 SAAVLFLAKLIERSNTSCDADQLEAFKTKLAELLN 40 (105)
Q Consensus 6 ~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~ 40 (105)
+.|++|+...|...+=+++.++++.|-|.--..|.
T Consensus 71 ~~A~~~v~~~L~~~gi~~t~~~i~~~IEaAV~~m~ 105 (108)
T PF09682_consen 71 AEAVQYVKERLKKKGIKVTDEQIEGAIEAAVKEMN 105 (108)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHh
Confidence 57889999999875557899999999887665543
No 46
>PRK10597 DNA damage-inducible protein I; Provisional
Probab=34.29 E-value=67 Score=21.10 Aligned_cols=42 Identities=10% Similarity=0.105 Sum_probs=31.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEe
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRL 63 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIri 63 (105)
+++|...++.+..+|.+-|..+|.+-+..=.=.+||+- -|.+
T Consensus 11 ~~lp~ga~~AL~~EL~kRl~~~fPd~~~~v~Vr~~s~n-~lsv 52 (81)
T PRK10597 11 SPLPAGAIDALAGELSRRIQYAFPDNEGHVSVRYAAAN-NLSV 52 (81)
T ss_pred CCCChhHHHHHHHHHHHHHHhhCCCCCccEEEeecCCC-ceEe
Confidence 58999999999999999999999886633333445553 4444
No 47
>cd06932 NR_LBD_PPAR The ligand binding domain of peroxisome proliferator-activated receptors. The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, P
Probab=34.11 E-value=51 Score=25.42 Aligned_cols=33 Identities=12% Similarity=0.304 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFPEAPNR 54 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~r 54 (105)
|-.++++|+.+++.+.++|.+....+ ||+.|.+
T Consensus 182 gL~~~~~Ve~lQe~~~~aL~~~i~~~-~p~~~~r 214 (259)
T cd06932 182 GLINRKPVERIQEHVLQALELQLKKN-HPDSPQL 214 (259)
T ss_pred cCcCHHHHHHHHHHHHHHHHHHHhhh-CCCcccH
Confidence 44678999999999999999888765 7887765
No 48
>COG1539 FolB Dihydroneopterin aldolase [Coenzyme metabolism]
Probab=33.90 E-value=1e+02 Score=21.41 Aligned_cols=33 Identities=21% Similarity=0.384 Sum_probs=26.4
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCCCC
Q psy11249 12 LAKLIERSNTSCDADQLEAFKTKLAELLNDRFANHWF 48 (105)
Q Consensus 12 l~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~HW~ 48 (105)
+..++. ++ +..-++++++++.+.|.++|...|.
T Consensus 61 i~~~v~---~~-~~~LiE~lA~~ia~~l~~~~~~v~~ 93 (121)
T COG1539 61 IKEIVE---GK-RFALIETLAEEIADLLLARFPRVEL 93 (121)
T ss_pred HHHHHh---CC-ccchHHHHHHHHHHHHHhhCCccEE
Confidence 455555 33 7788999999999999999977775
No 49
>KOG0614|consensus
Probab=33.86 E-value=1.3e+02 Score=26.89 Aligned_cols=56 Identities=14% Similarity=0.192 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhc-CCCCCCCCCCCccceeEEEe
Q psy11249 3 DQISAAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRF-ANHWFPEAPNRGQGYRCIRL 63 (105)
Q Consensus 3 ~EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry-~~HW~P~~P~rGsayRcIri 63 (105)
.+..+-.|||.+.-.- +.+|.+.+-..++-|+. ++| .++.-..++.+|+.|-.|+-
T Consensus 265 ~r~~~~~~fLrsv~~~--q~l~Ee~L~KiaD~le~---~~Yd~g~yIirqge~G~~ffii~~ 321 (732)
T KOG0614|consen 265 ERHEQYMNFLRSVPLF--QNLPEELLLKIADVLEE---EYYDAGEYIIRQGEKGDTFFIISK 321 (732)
T ss_pred HHHHHHHHHHHhhhhh--ccCCHHHHHHHHHHHHH---HhhcCCceEEeecCCCCeEEEEec
Confidence 4567788999876553 57999988877777776 666 77888899999999988764
No 50
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=32.99 E-value=32 Score=23.11 Aligned_cols=77 Identities=13% Similarity=0.154 Sum_probs=50.6
Q ss_pred HHHHHHHHHHhhcCCCCH-HHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHHHhCCCCcc
Q psy11249 8 AVLFLAKLIERSNTSCDA-DQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMSYED 86 (105)
Q Consensus 8 av~Fl~~~l~~~~~~l~~-~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~ 86 (105)
++..|...|.......+. .....++.+++..|...|.+ ....--+.+|+|.+|=..+-.|.|..-...--|++++
T Consensus 7 ~~~~L~~al~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~----~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~vl~G~i~p~~ 82 (102)
T smart00510 7 CQEMLYKALQKISDPEEIELDPTELAVQIEAEMFSEFGT----TDKKYKNKYRSLYFNLKDKKNPDLRRKVLNGEITPEK 82 (102)
T ss_pred HHHHHHHHHHhcCCCCcccccHHHHHHHHHHHHHHHcCC----CcHHHHHHHHHHHHHhcCCCCHHHHHHHHcCCCCHHH
Confidence 455666666642111111 24677999999999988754 2334556788999975555788888777766677666
Q ss_pred cC
Q psy11249 87 MR 88 (105)
Q Consensus 87 l~ 88 (105)
|.
T Consensus 83 lv 84 (102)
T smart00510 83 LA 84 (102)
T ss_pred Hh
Confidence 65
No 51
>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LB
Probab=32.67 E-value=45 Score=25.48 Aligned_cols=34 Identities=18% Similarity=0.324 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCC-CCCCCCC
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHW-FPEAPNR 54 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW-~P~~P~r 54 (105)
|--.+++|+.+++.+.++|.++...+. +|+.|.+
T Consensus 157 gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~r 191 (238)
T cd07348 157 GLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNC 191 (238)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccH
Confidence 445788999999999999999886643 5777664
No 52
>PF15508 NAAA-beta: beta subunit of N-acylethanolamine-hydrolyzing acid amidase
Probab=32.58 E-value=1.4e+02 Score=19.34 Aligned_cols=39 Identities=21% Similarity=0.267 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhc
Q psy11249 2 QDQISAAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRF 43 (105)
Q Consensus 2 ~~EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry 43 (105)
+.+|+..++++..++.. .++...+-.|.+.+...|...|
T Consensus 26 k~~i~~l~~~~~~~~~~---~~~~~~~~~~v~~~~~~l~~~~ 64 (95)
T PF15508_consen 26 KDEIRELIEVLKDLLQS---FVPSGKVLDFVDKLLPHLLRYL 64 (95)
T ss_pred HHHHHHHHHHHHHHHHH---hCCchHHHHHHHHHHHHHHHhC
Confidence 57899999999999884 4566566677777666666555
No 53
>cd00392 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
Probab=32.47 E-value=79 Score=21.75 Aligned_cols=37 Identities=22% Similarity=0.312 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecC
Q psy11249 26 DQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNK 65 (105)
Q Consensus 26 ~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~ 65 (105)
+.+.+.++..+..|..+.+..+. |..-.|-.+|.||+
T Consensus 9 ~~lGRlAs~iA~~L~gKhKp~y~---p~~d~Gd~VvViNa 45 (114)
T cd00392 9 QVLGRLASKVAKLLLGKHKPTYT---PHVDCGDYVVVVNA 45 (114)
T ss_pred CchHHHHHHHHHHHcCCCCCCcC---CCccCCCEEEEEec
Confidence 45688999999999999999985 55677999999984
No 54
>TIGR03654 L6_bact ribosomal protein L6, bacterial type.
Probab=31.86 E-value=63 Score=23.62 Aligned_cols=28 Identities=18% Similarity=0.405 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCcccee
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYR 59 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayR 59 (105)
.+.+.+..|++.+.. +.|-+|.||-|-|
T Consensus 135 ~dke~Vgq~AA~Ir~---------~r~pepYKgkGi~ 162 (175)
T TIGR03654 135 IDKQLVGQVAAEIRA---------FRKPEPYKGKGIR 162 (175)
T ss_pred CCHHHHHHHHHHHhc---------cCCCCCcCCCcEe
Confidence 688999999999876 7899999999976
No 55
>KOG0653|consensus
Probab=31.68 E-value=1.5e+02 Score=24.16 Aligned_cols=68 Identities=9% Similarity=0.110 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHH
Q psy11249 3 DQISAAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAK 78 (105)
Q Consensus 3 ~EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~ 78 (105)
+-+--|||.+-|||.+ .++++.+++..+-.=--.+..||+..|-|. .+.+-.|.= +...=+.|.++-+
T Consensus 177 ETL~LaVnliDRfL~~--~~v~~~~lqLvgvsalf~IA~K~EE~~~P~----v~dlv~isd--~~~s~~~il~mE~ 244 (391)
T KOG0653|consen 177 ETLYLAVNLIDRFLSK--VKVPLKKLQLVGVSALLSIACKYEEISLPS----VEDLVLITD--GAYSREEILRMEK 244 (391)
T ss_pred HHHHHHHHHHHHHHHH--hcccHHHhhHHhHHHHHHHHHhhhhccCCc----cceeEeeeC--CccchHHHHHHHH
Confidence 4466799999999997 469999999887655223889999999887 444533332 3333344444433
No 56
>PF07085 DRTGG: DRTGG domain; InterPro: IPR010766 This presumed domain is about 120 amino acids in length. It is found associated with CBS domains IPR000644 from INTERPRO, as well as the CbiA domain IPR002586 from INTERPRO. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea. ; PDB: 3L31_B 3L2B_A 2IOJ_A.
Probab=31.26 E-value=53 Score=21.30 Aligned_cols=26 Identities=23% Similarity=0.402 Sum_probs=18.8
Q ss_pred eeEEEecCCCCCCHHHHHHHHHhCCC
Q psy11249 58 YRCIRLNKNVKKDTILENAAKAVGMS 83 (105)
Q Consensus 58 yRcIrin~~~~~Dp~l~~Aa~~sgl~ 83 (105)
-+||.+..+..+++.+.+.|++.|++
T Consensus 62 i~~iIltg~~~~~~~v~~la~~~~i~ 87 (105)
T PF07085_consen 62 IACIILTGGLEPSEEVLELAKELGIP 87 (105)
T ss_dssp ECEEEEETT----HHHHHHHHHHT-E
T ss_pred CCEEEEeCCCCCCHHHHHHHHHCCCE
Confidence 67999988999999999999999965
No 57
>CHL00140 rpl6 ribosomal protein L6; Validated
Probab=30.92 E-value=69 Score=23.54 Aligned_cols=28 Identities=29% Similarity=0.558 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCcccee
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYR 59 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayR 59 (105)
.+.+.+..||+.+.. +.|-+|.||-|-|
T Consensus 136 ~dke~Vgq~AA~Ir~---------~r~pepYKGKGI~ 163 (178)
T CHL00140 136 IDKELVGQFAAKIRS---------VRPPEPYKGKGIR 163 (178)
T ss_pred CCHHHHHHHHHHHhc---------cCCCCCcCCccEe
Confidence 788999999999976 7889999999977
No 58
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=30.83 E-value=1.5e+02 Score=19.08 Aligned_cols=24 Identities=17% Similarity=0.393 Sum_probs=18.2
Q ss_pred HHHHhhcCCCCHHHHHHHHHHHHHH
Q psy11249 14 KLIERSNTSCDADQLEAFKTKLAEL 38 (105)
Q Consensus 14 ~~l~~~~~~l~~~~i~~F~~~L~~~ 38 (105)
.++.++ ..++...++.|+++|.++
T Consensus 46 ~~V~~K-~~fS~sEm~aI~~ELG~L 69 (71)
T PF06569_consen 46 EMVMSK-DSFSPSEMQAIAEELGQL 69 (71)
T ss_pred HHHHhc-cCCCHHHHHHHHHHHHhh
Confidence 334443 679999999999999874
No 59
>PF14024 DUF4240: Protein of unknown function (DUF4240)
Probab=30.82 E-value=1.7e+02 Score=20.08 Aligned_cols=37 Identities=22% Similarity=0.459 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhc-CCCC
Q psy11249 7 AAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRF-ANHW 47 (105)
Q Consensus 7 ~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry-~~HW 47 (105)
+....|+..|. ++|.+.|-.|...|...|.+-| ...|
T Consensus 23 ~~~~~L~~~L~----~l~~~ei~~F~~~~~~~~~~~~~~~lw 60 (128)
T PF14024_consen 23 EVAEPLVELLA----KLPPEEIVAFDKILDQLLDEAYTWDLW 60 (128)
T ss_pred HHHHHHHHHHH----cCCHHHHHHHHHHHHHHHHHhccHHHH
Confidence 45567777777 5999999999999999999988 4457
No 60
>PF02603 Hpr_kinase_N: HPr Serine kinase N terminus; InterPro: IPR011126 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria []. This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes []. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains []. ; GO: 0000155 two-component sensor activity, 0004672 protein kinase activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006109 regulation of carbohydrate metabolic process; PDB: 1KNX_B 1KO7_A.
Probab=30.30 E-value=53 Score=22.53 Aligned_cols=25 Identities=16% Similarity=0.321 Sum_probs=17.2
Q ss_pred EEEecCCCCCCHHHHHHHHHhCCCC
Q psy11249 60 CIRLNKNVKKDTILENAAKAVGMSY 84 (105)
Q Consensus 60 cIrin~~~~~Dp~l~~Aa~~sgl~~ 84 (105)
||.+..+...++.+.++|.+.|++.
T Consensus 84 ~iIvt~~~~~p~~l~e~a~~~~ipl 108 (127)
T PF02603_consen 84 CIIVTRGLEPPPELIELAEKYNIPL 108 (127)
T ss_dssp -EEEETTT---HHHHHHHHHCT--E
T ss_pred EEEEECcCCCCHHHHHHHHHhCCcE
Confidence 8888888899999999999999864
No 61
>TIGR00053 addiction module toxin component, YafQ family. This model represents a cluster of eubacterial proteins and a cluster of archaeal proteins, all of which are uncharacterized, from 85 to 102 residues in length, and similar in sequence. These include YafQ, a ribosome-associated endoribonuclease that serves as part of a toxin-antitoxin system, for which DinJ is the antidote component.
Probab=29.90 E-value=63 Score=20.34 Aligned_cols=38 Identities=29% Similarity=0.665 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHh-hcCCCCCCCCCCCc--cceeEEEec
Q psy11249 26 DQLEAFKTKLAELLND-RFANHWFPEAPNRG--QGYRCIRLN 64 (105)
Q Consensus 26 ~~i~~F~~~L~~~L~~-ry~~HW~P~~P~rG--sayRcIrin 64 (105)
.....|.+.|..++.. ...++ +-.+|.+| +||+-+|++
T Consensus 23 ~~~~~i~~~i~~l~~~~~~p~~-~~~~~L~G~~~g~~r~rv~ 63 (89)
T TIGR00053 23 KDLKKLLKKMEELINTLPLPEH-YKDHPLRGPWKGFRRCHIK 63 (89)
T ss_pred ccHHHHHHHHHHHHcCCCCCcc-cCCccCcCCcCCCEEEeeC
Confidence 3446677777765542 22222 23447888 468888883
No 62
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=29.87 E-value=1.9e+02 Score=21.10 Aligned_cols=64 Identities=19% Similarity=0.139 Sum_probs=40.7
Q ss_pred HHHHHHHH----HHHHHHHhhcCCCCHHHHHHHHHHHHH--HHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHH
Q psy11249 3 DQISAAVL----FLAKLIERSNTSCDADQLEAFKTKLAE--LLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENA 76 (105)
Q Consensus 3 ~EI~~av~----Fl~~~l~~~~~~l~~~~i~~F~~~L~~--~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~A 76 (105)
.+|++++. |++..++.. .+++.++....++.|.- ......+ .-|.|||. .+.-..||+|++-
T Consensus 25 e~IAe~iG~sevwvaaa~lGQ-~~ls~e~A~kla~lLgL~~e~~~~l~-----~~P~rg~~------~~~~ptdP~iYR~ 92 (150)
T TIGR00673 25 ADIADGLGLAEVFVAAALYGQ-AAAPADEARLVGAKLDLDEDSILELQ-----MAPLRGCI------DPVIPTDPTMYRF 92 (150)
T ss_pred HHHHHHHCCCHHHHHHHHhCC-CCCCHHHHHHHHHHhCcCHHHHHHHh-----cCCCCCCC------CCCCCCCchHHHH
Confidence 35555553 777777764 67999999888887732 1222223 34778752 4466789998875
Q ss_pred HH
Q psy11249 77 AK 78 (105)
Q Consensus 77 a~ 78 (105)
=.
T Consensus 93 yE 94 (150)
T TIGR00673 93 YE 94 (150)
T ss_pred HH
Confidence 43
No 63
>PF02817 E3_binding: e3 binding domain; InterPro: IPR004167 A small domain of the E2 subunit of 2-oxo-acid dehydrogenases that is responsible for the binding of the E3 subunit. Proteins containing this domain include the branched-chain alpha-keto acid dehydrogenase complex of bacteria, which catalyses the overall conversion of alpha-keto acids to acyl-CoA and carbon dioxide; and the E-3 binding protein of eukaryotic pyruvate dehydrogenase.; GO: 0016746 transferase activity, transferring acyl groups, 0008152 metabolic process; PDB: 1BBL_A 1W4H_A 1BAL_A 2WXC_A 2BTH_A 2BTG_A 2CYU_A 2EQ7_C 2EQ8_C 3RNM_E ....
Probab=29.83 E-value=60 Score=18.20 Aligned_cols=21 Identities=14% Similarity=0.322 Sum_probs=16.6
Q ss_pred CCCHHHHHHHHHhCCCCcccC
Q psy11249 68 KKDTILENAAKAVGMSYEDMR 88 (105)
Q Consensus 68 ~~Dp~l~~Aa~~sgl~~~~l~ 88 (105)
...|...+.|++.||+.+++.
T Consensus 4 ~asP~ar~la~e~gidl~~v~ 24 (39)
T PF02817_consen 4 KASPAARKLAAELGIDLSQVK 24 (39)
T ss_dssp CCSHHHHHHHHHTT--GGGSS
T ss_pred ccCHHHHHHHHHcCCCccccc
Confidence 467999999999999999876
No 64
>PF07531 TAFH: NHR1 homology to TAF; InterPro: IPR003894 The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO [, ]. The human eight twenty-one (ETO or MTG8) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain []. The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2P6V_A 2KNH_A 2PP4_A 2H7B_A.
Probab=29.67 E-value=75 Score=21.57 Aligned_cols=34 Identities=29% Similarity=0.384 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhh
Q psy11249 4 QISAAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDR 42 (105)
Q Consensus 4 EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~r 42 (105)
|+.+.|.-|+.-|. +++++. +.|.++|...|..-
T Consensus 24 ev~~~Vr~LV~~L~--~~~i~~---EeF~~~Lq~~lns~ 57 (96)
T PF07531_consen 24 EVGENVRELVQNLV--DGKIEA---EEFTSKLQEELNSS 57 (96)
T ss_dssp CHHHHHHHHHHHHH--TTSS-H---HHHHHHHHHHCTSS
T ss_pred HHHHHHHHHHHHHH--cCCCCH---HHHHHHHHHHhcCC
Confidence 67788888888777 477876 45999999887643
No 65
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=29.58 E-value=42 Score=22.56 Aligned_cols=53 Identities=19% Similarity=0.186 Sum_probs=35.3
Q ss_pred CCCCCCccceeEEEecC-CCCCCHHHHHHHHHhCCCCccc---CCCCccEEEEcCCcee
Q psy11249 49 PEAPNRGQGYRCIRLNK-NVKKDTILENAAKAVGMSYEDM---RLPVELTLWVDPHEVC 103 (105)
Q Consensus 49 P~~P~rGsayRcIrin~-~~~~Dp~l~~Aa~~sgl~~~~l---~lP~e~tlWvDPgeVs 103 (105)
..+-++.+|.|.=.-.+ ..+.-..|.+||.+.|+++.-- .-|.+| |-.+|-|-
T Consensus 15 d~~~tr~eGRrv~k~~aV~~P~~~EI~~a~~~lgl~~~~e~~K~yPr~~--~e~~GRv~ 71 (95)
T PRK00754 15 DSTRSRSEGRIISRKLAVKEPRLEEIIEAAEKLGLNPEVEPDKAYPRSW--WEVSGRVL 71 (95)
T ss_pred cCCCChhhcCccCHHHhccCCCHHHHHHHHHHcCCCeEEeeCCCCCchH--hcCCCEEE
Confidence 34567778854322211 4556678999999999998543 279886 65777664
No 66
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=28.47 E-value=9.7 Score=23.15 Aligned_cols=27 Identities=19% Similarity=0.252 Sum_probs=20.1
Q ss_pred EecCCCCCCHHHHHHHHHhCCCCcccC
Q psy11249 62 RLNKNVKKDTILENAAKAVGMSYEDMR 88 (105)
Q Consensus 62 rin~~~~~Dp~l~~Aa~~sgl~~~~l~ 88 (105)
.|+--.+=+..|..||++.||+.+++.
T Consensus 23 gIDfCCgG~~~L~eA~~~~~ld~~~vl 49 (56)
T PF04405_consen 23 GIDFCCGGNRSLEEACEEKGLDPEEVL 49 (56)
T ss_pred CCcccCCCCchHHHHHHHcCCCHHHHH
Confidence 455445556779999999999987653
No 67
>KOG0595|consensus
Probab=28.33 E-value=1.1e+02 Score=26.10 Aligned_cols=34 Identities=24% Similarity=0.242 Sum_probs=30.1
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCC
Q psy11249 12 LAKLIERSNTSCDADQLEAFKTKLAELLNDRFANH 46 (105)
Q Consensus 12 l~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~H 46 (105)
|..|++++ +++++..+..|...|+..|..=+++|
T Consensus 96 Ls~yi~~~-~~l~e~t~r~Fm~QLA~alq~L~~~~ 129 (429)
T KOG0595|consen 96 LSDYIRRR-GRLPEATARHFMQQLASALQFLHENN 129 (429)
T ss_pred HHHHHHHc-CCCCHHHHHHHHHHHHHHHHHHHHCC
Confidence 56788886 68999999999999999999888876
No 68
>cd06954 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors. The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, splee
Probab=27.82 E-value=68 Score=23.93 Aligned_cols=34 Identities=15% Similarity=0.095 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCc
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFPEAPNRG 55 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rG 55 (105)
+--+..+|+.+++.+.++|.+....+ ||+.|.++
T Consensus 162 gL~~~~~V~~lQ~~~~~aL~~y~~~~-~p~~~~rf 195 (236)
T cd06954 162 NVQDHHRVERLQETYVEALHSYIKIK-RPSDRLMF 195 (236)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHhc-CCCcccHH
Confidence 33467899999999999999877654 88888775
No 69
>TIGR00135 gatC glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, C subunit. This model has been revised to remove the candidate sequence from Methanococcus jannaschii, now part of a related model.
Probab=27.60 E-value=1.7e+02 Score=18.73 Aligned_cols=30 Identities=30% Similarity=0.427 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q psy11249 8 AVLFLAKLIERSNTSCDADQLEAFKTKLAELLN 40 (105)
Q Consensus 8 av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~ 40 (105)
-|..|+++.+ =.++.+.++.|...|.++|.
T Consensus 5 ~v~~lA~La~---L~l~eee~~~~~~~l~~il~ 34 (93)
T TIGR00135 5 EVKHLAKLAR---LELSEEEAESFAGDLDKILG 34 (93)
T ss_pred HHHHHHHHhC---CCCCHHHHHHHHHHHHHHHH
Confidence 4557777777 36999999999999999886
No 70
>PRK00034 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed
Probab=27.43 E-value=1.7e+02 Score=18.67 Aligned_cols=31 Identities=32% Similarity=0.483 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHH
Q psy11249 7 AAVLFLAKLIERSNTSCDADQLEAFKTKLAELLN 40 (105)
Q Consensus 7 ~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~ 40 (105)
.-|..|+++.+ =.++.+.++.|...|.++|.
T Consensus 6 e~i~~la~La~---l~l~~ee~~~~~~~l~~il~ 36 (95)
T PRK00034 6 EEVKHLAKLAR---LELSEEELEKFAGQLNKILD 36 (95)
T ss_pred HHHHHHHHHhC---CCCCHHHHHHHHHHHHHHHH
Confidence 45677888888 36999999999999999885
No 71
>cd07349 NR_LBD_SHP The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain. The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.
Probab=27.40 E-value=55 Score=24.68 Aligned_cols=33 Identities=9% Similarity=0.131 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFPEAPNR 54 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~r 54 (105)
+--+.++|+.+.++..++|.+....+ ||+.|.|
T Consensus 149 gl~~~~~V~~lqe~~~~aL~~~~~~~-~p~~~~r 181 (222)
T cd07349 149 GLTASSHVGHLQQEAQWALCEVLEPL-HPQDQGR 181 (222)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHH-CCCcccH
Confidence 33467899999999999999887655 6776653
No 72
>KOG0648|consensus
Probab=27.13 E-value=16 Score=29.54 Aligned_cols=62 Identities=24% Similarity=0.449 Sum_probs=40.0
Q ss_pred CHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHHHhCCCCcccC-CCCccEEEE
Q psy11249 24 DADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMSYEDMR-LPVELTLWV 97 (105)
Q Consensus 24 ~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l~-lP~e~tlWv 97 (105)
++.....|.++|...|. +||+ +|..-+=++| .......+..| ..-|.++-+.. ++..++-|+
T Consensus 39 ~~~d~~~f~~~l~~Sl~-----~W~~----~Gr~~iwl~l--~~~~~~lV~~a-~~~gf~~hHae~~~~~l~~Wl 101 (295)
T KOG0648|consen 39 EPMDEKLFIEELRASLQ-----KWYL----QGRKGIWLKL--PEELARLVEEA-AKYGFDYHHAESLYVMLTSWL 101 (295)
T ss_pred CCCCHHHHHHHHHHHHH-----HHHH----ccCcccceec--hHHHHhHHHHH-HhcCcEEecccccceeeeeee
Confidence 45566889999998886 7987 5555555666 33334434333 34456666655 788888886
No 73
>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....
Probab=26.98 E-value=1.1e+02 Score=21.39 Aligned_cols=37 Identities=22% Similarity=0.345 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecC
Q psy11249 26 DQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNK 65 (105)
Q Consensus 26 ~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~ 65 (105)
..+.++++..+..|.-+.+..+.|. .-.|.++|.||+
T Consensus 9 ~~lGRLAs~iAk~L~GKhk~~y~p~---~d~Gd~VvViNa 45 (128)
T PF00572_consen 9 QILGRLASKIAKLLLGKHKPTYTPN---VDCGDHVVVINA 45 (128)
T ss_dssp BBHHHHHHHHHHHHCTTSSTSSBTT---SSTTEEEEEECG
T ss_pred CchHHHHHHHHHHHhCCCCCccCcC---ccCCCEEEEEcC
Confidence 3468899999999999999999866 677889999984
No 74
>PRK09731 putative general secretion pathway protein YghD; Provisional
Probab=26.95 E-value=62 Score=24.13 Aligned_cols=35 Identities=11% Similarity=0.383 Sum_probs=30.0
Q ss_pred CCCCCHHHHHHHHHhCCCCcccC-CCCccEEEEcCC
Q psy11249 66 NVKKDTILENAAKAVGMSYEDMR-LPVELTLWVDPH 100 (105)
Q Consensus 66 ~~~~Dp~l~~Aa~~sgl~~~~l~-lP~e~tlWvDPg 100 (105)
+..+--.|-+.|.+-||....+. -.+.+.+|+||-
T Consensus 99 ~~sL~~~V~~SA~~~gL~i~R~QP~Ge~vQVwld~v 134 (178)
T PRK09731 99 PAQVSRVISDSASAHSVVIKRIAERGENIQVWIEPV 134 (178)
T ss_pred CccHHHHHHHHHHHCCCeEEEecCCCCEEEEEECCC
Confidence 56677899999999999998888 566799999985
No 75
>COG4517 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.74 E-value=60 Score=22.34 Aligned_cols=44 Identities=23% Similarity=0.259 Sum_probs=26.4
Q ss_pred ceeEEEecCCCCCCHHHHHHHHHhCC----CCcccCCCCccEEEEcCCc
Q psy11249 57 GYRCIRLNKNVKKDTILENAAKAVGM----SYEDMRLPVELTLWVDPHE 101 (105)
Q Consensus 57 ayRcIrin~~~~~Dp~l~~Aa~~sgl----~~~~l~lP~e~tlWvDPge 101 (105)
-||.|.+| .++.=.+-.+....|.| ..+|+-+-..-++-|||.|
T Consensus 7 lYkiiFvN-qGkvyelYar~i~sS~LwGF~EI~efVFd~~s~lvVDPse 54 (109)
T COG4517 7 LYKIIFVN-QGKVYELYARCIISSHLWGFNEISEFVFDVHSGLVVDPSE 54 (109)
T ss_pred eEEEEEee-CCeeeehhHhhHhhhhhhhhhhHHHHhcccccceEECccH
Confidence 48899998 45544443333333332 2334447777888888875
No 76
>PF13103 TonB_2: TonB C terminal; PDB: 1LR0_A.
Probab=26.59 E-value=1.6e+02 Score=17.96 Aligned_cols=35 Identities=9% Similarity=0.212 Sum_probs=15.3
Q ss_pred HHHHHHHHHHhhcCCCCC-CC-CCCCccceeEEEecCCCCC
Q psy11249 31 FKTKLAELLNDRFANHWF-PE-APNRGQGYRCIRLNKNVKK 69 (105)
Q Consensus 31 F~~~L~~~L~~ry~~HW~-P~-~P~rGsayRcIrin~~~~~ 69 (105)
+...+.+.+.. +|. |. .+..+++.=.|.|++++.+
T Consensus 4 Y~~~i~~~i~~----~w~~p~~~~~~~~~~V~i~i~~dG~v 40 (85)
T PF13103_consen 4 YFAQIQARIQQ----NWNPPPQDSGGLSVTVRITIDPDGRV 40 (85)
T ss_dssp ----HHHHHHH----H----TT--TT--EEEEEEE-TTSBE
T ss_pred hHHHHHHHHHH----HcCCCCCCCCCcEEEEEEEECCCCCE
Confidence 34455555555 473 23 3777888888888876665
No 77
>PF03622 IBV_3B: IBV 3B protein ; InterPro: IPR005295 These proteins are the product of ORF 3B from Infectious bronchitis virus). Currently, the function of this protein remains unknown [].
Probab=26.22 E-value=30 Score=21.84 Aligned_cols=8 Identities=63% Similarity=1.261 Sum_probs=5.8
Q ss_pred EcCCceee
Q psy11249 97 VDPHEVCC 104 (105)
Q Consensus 97 vDPgeVs~ 104 (105)
-||.||||
T Consensus 34 FDPFE~cy 41 (64)
T PF03622_consen 34 FDPFEVCY 41 (64)
T ss_pred cCCeeEEE
Confidence 37888876
No 78
>cd01781 AF6_RA_repeat2 Ubiquitin domain of AT-6, second repeat. The AF-6 protein (also known as afadin and canoe) is a multidomain cell junction protein that contains two N-terminal Ras-associating (RA) domains in addition to FHA (forkhead-associated), DIL (class V myosin homology region), and PDZ domains and a proline-rich region. AF6 acts downstream of the Egfr (Epidermal Growth Factor-receptor)/Ras signalling pathway and provides a link from Egfr to cytoskeletal elements.
Probab=26.01 E-value=1.3e+02 Score=20.48 Aligned_cols=39 Identities=23% Similarity=0.316 Sum_probs=32.7
Q ss_pred CCCCCCCccceeEEEecCCCCCCHHHHHHHHHhCCCCcc
Q psy11249 48 FPEAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMSYED 86 (105)
Q Consensus 48 ~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~ 86 (105)
||+.=.-|=.|..|.++.....+-+|.+|=..-|++.++
T Consensus 7 Yg~~L~~~~~YKSIlvt~~~~a~~vV~eALeKygL~~e~ 45 (100)
T cd01781 7 YGGSLVPTRPYKTILLSINDNADRIVGEALEKYGLEKSD 45 (100)
T ss_pred cCCcccCCCCeEEEEecCCccHHHHHHHHHHHhCCCccC
Confidence 455555677899999999999999999999999998774
No 79
>PF09379 FERM_N: FERM N-terminal domain ; InterPro: IPR018979 This domain is the N-terminal ubiquitin-like structural domain of the FERM domain. The FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane []. FERM domains are found in a number of cytoskeletal-associated proteins that associate with various proteins at the interface between the plasma membrane and the cytoskeleton. The FERM domain is located at the N terminus of the majority of FERM-containing proteins [, ], which includes: Band 4.1, which links the spectrin-actin cytoskeleton of erythrocytes to the plasma membrane. Ezrin, a component of the undercoat of the microvilli plasma membrane. Moesin, which is probably involved in binding major cytoskeletal structures to the plasma membrane. Radixin, which is involved in the binding of the barbed end of actin filaments to the plasma membrane in the undercoat of the cell- to-cell adherens junction. Talin, a cytoskeletal protein concentrated in regions of cell-substratum contact and, in lymphocytes, of cell-cell contacts. Filopodin, a slime mold protein that binds actin and which is involved in the control of cell motility and chemotaxis. Merlin (or schwannomin). Protein NBL4. Unconventional myosins X, VIIa and XV, which are mutated in congenital deafness. Focal-adhesion kinases (FAKs), cytoplasmic protein tyrosine kinases involved in signalling through integrins. Janus tyrosine kinases (JAKs), cytoplasmic tyrosine kinases that are non-covalently associated with the cytoplasmic tails of receptors for cytokines or polypeptidic hormones. Non-receptor tyrosine-protein kinase TYK2. Protein-tyrosine phosphatases PTPN3 and PTPN4, enzyme that appear to act at junctions between the membrane and the cytoskeleton. Protein-tyrosine phosphatases PTPN14 and PTP-D1, PTP-RL10 and PTP2E. Caenorhabditis elegans protein phosphatase ptp-1. Ezrin, moesin, and radixin are highly related proteins (ERM protein family), but the other proteins in which the FERM domain is found do not share any region of similarity outside of this domain. ERM proteins are made of three domains, the FERM domain, a central helical domain and a C-terminal tail domain, which binds F-actin. The amino-acid sequence of the FERM domain is highly conserved among ERM proteins and is responsible for membrane association by direct binding to the cytoplasmic domain or tail of integral membrane proteins. ERM proteins are regulated by an intramolecular association of the FERM and C-terminal tail domains that masks their binding sites for other molecules. For cytoskeleton-membrane cross-linking, the dormant molecules becomes activated and the FERM domain attaches to the membrane by binding specific membrane proteins, while the last 34 residues of the tail bind actin filaments. Aside from binding to membranes, the activated FERM domain of ERM proteins can also bind the guanine nucleotide dissociation inhibitor of Rho GTPase (RhoDGI), which suggests that in addition to functioning as a cross-linker, ERM proteins may influence Rho signalling pathways. The crystal structure of the FERM domain reveals that it is composed of three structural modules (F1, F2, and F3) that together form a compact clover-shaped structure []. The FERM domain has also been called the amino-terminal domain, the 30kDa domain, 4.1N30, the membrane-cytoskeletal-linking domain, the ERM-like domain, the ezrin-like domain of the band 4.1 superfamily, the conserved N-terminal region, and the membrane attachment domain [].; PDB: 1EF1_B 1SGH_A 1E5W_A 2KC2_A 2KMA_A 3IVF_A 1H4R_B 3U8Z_A 1ISN_A 3BIN_A ....
Probab=25.94 E-value=1.5e+02 Score=17.86 Aligned_cols=43 Identities=12% Similarity=0.275 Sum_probs=32.6
Q ss_pred eEEEecCCCCCCHHHHHHHHHhCCCCcccC------CCCccEEEEcCCc
Q psy11249 59 RCIRLNKNVKKDTILENAAKAVGMSYEDMR------LPVELTLWVDPHE 101 (105)
Q Consensus 59 RcIrin~~~~~Dp~l~~Aa~~sgl~~~~l~------lP~e~tlWvDPge 101 (105)
.-+.++++...-.++.+.|...||...+.. .+.+-..|+||..
T Consensus 9 ~~~~v~~~~t~~~l~~~v~~~l~l~e~~~FgL~~~~~~~~~~~wL~~~k 57 (80)
T PF09379_consen 9 KTFEVDPKTTGQDLLEQVCDKLGLKEKEYFGLQYQVDKDGEHHWLDLDK 57 (80)
T ss_dssp EEEEEETTSBHHHHHHHHHHHHTTSSGGGEEEEE-EBTTSSEEEE-SSS
T ss_pred EEEEEcCCCcHHHHHHHHHHHcCCCCccEEEEEEeecCCCcceeccCcc
Confidence 456677777777899999999999877665 3567789999864
No 80
>cd07069 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,. The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=25.90 E-value=71 Score=24.32 Aligned_cols=33 Identities=12% Similarity=0.182 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFPEAPNR 54 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~r 54 (105)
+--..++|+.+.++..++|.+... ..||+.|.|
T Consensus 163 gL~~~~~Ve~lQe~~~~aL~~yi~-~~~p~~~~R 195 (241)
T cd07069 163 NLENFQLVEGVQEQVNAALLDYTM-CNYPQQTEK 195 (241)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHH-hcCCCchhH
Confidence 334678899999999999998666 458887754
No 81
>TIGR01205 D_ala_D_alaTIGR D-alanine--D-alanine ligase. but a number of antibiotic resistance proteins score above the trusted cutoff of this model.
Probab=25.84 E-value=67 Score=24.45 Aligned_cols=32 Identities=16% Similarity=0.194 Sum_probs=25.3
Q ss_pred ceeEEEecCCCCC--CHHHHHHHHHhCCCCcccC
Q psy11249 57 GYRCIRLNKNVKK--DTILENAAKAVGMSYEDMR 88 (105)
Q Consensus 57 ayRcIrin~~~~~--Dp~l~~Aa~~sgl~~~~l~ 88 (105)
.+..|-+|+..++ +..+..+|+++|+++.++.
T Consensus 275 ~~~viEvN~~pg~~~~s~~~~~~~~~G~~~~~l~ 308 (315)
T TIGR01205 275 EIYLNEINTIPGMTAISLFPKAAAAAGIEFSQLV 308 (315)
T ss_pred CEEEEEeeCCCCCCCccHHHHHHHHcCCCHHHHH
Confidence 5779999965554 4578899999999998864
No 82
>PRK05498 rplF 50S ribosomal protein L6; Validated
Probab=25.31 E-value=1e+02 Score=22.60 Aligned_cols=28 Identities=21% Similarity=0.510 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCcccee
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYR 59 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayR 59 (105)
.+.+.+..|++.+.. +.|-+|.||-|-|
T Consensus 136 ~dke~Vg~~AA~Ir~---------~r~pe~YkgkGi~ 163 (178)
T PRK05498 136 IDKQLVGQVAAEIRS---------YRPPEPYKGKGIR 163 (178)
T ss_pred CCHHHHHHHHHHHhc---------cCCCCCccCCcEe
Confidence 688999999999876 7889999999976
No 83
>PF03789 ELK: ELK domain ; InterPro: IPR005539 This domain is required for the nuclear localisation of these proteins []. All of these proteins are members of the Tale/Knox homeodomain family, a subfamily, containing homeobox IPR001356 from INTERPRO.; GO: 0003677 DNA binding, 0005634 nucleus
Probab=25.29 E-value=26 Score=17.67 Aligned_cols=12 Identities=17% Similarity=0.285 Sum_probs=8.1
Q ss_pred HHHHHHhhcCCC
Q psy11249 35 LAELLNDRFANH 46 (105)
Q Consensus 35 L~~~L~~ry~~H 46 (105)
|...|..+|.+|
T Consensus 2 LK~~LlrkY~g~ 13 (22)
T PF03789_consen 2 LKHQLLRKYSGY 13 (22)
T ss_pred HHHHHHHHHhHh
Confidence 566677777664
No 84
>COG0108 RibB 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]
Probab=25.09 E-value=1.3e+02 Score=23.03 Aligned_cols=40 Identities=28% Similarity=0.376 Sum_probs=28.0
Q ss_pred CccceeEEEecCCCCCCHHHHHHHHHhCCCCccc----CCCCccEEEEcCCce
Q psy11249 54 RGQGYRCIRLNKNVKKDTILENAAKAVGMSYEDM----RLPVELTLWVDPHEV 102 (105)
Q Consensus 54 rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l----~lP~e~tlWvDPgeV 102 (105)
.|+|+=|+.+. ...|++-||++--- .....||+|||..++
T Consensus 51 ~a~GliC~~lt---------~e~~~~L~Lp~Mv~~n~~~~~taFtVsVd~~~t 94 (203)
T COG0108 51 HASGLICVALT---------EERAKRLGLPPMVDNNTDAHGTAFTVSVDARET 94 (203)
T ss_pred hCCeeEEEeCC---------HHHHHhCCCccccccCCCCCCCceEEEEecccC
Confidence 47788888874 34566666654221 378999999999875
No 85
>KOG2781|consensus
Probab=24.96 E-value=58 Score=26.09 Aligned_cols=44 Identities=27% Similarity=0.363 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHHHhCCC
Q psy11249 22 SCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMS 83 (105)
Q Consensus 22 ~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~ 83 (105)
+=|..++..|+.+|.-.+ |+ .-++|+++..=+.|.+||++.|+.
T Consensus 91 R~PSsrL~~FaKelkLvf---------PN---------aqr~nRG~~~~~~lv~a~ra~~~T 134 (290)
T KOG2781|consen 91 RDPSSRLKMFAKELKLVF---------PN---------AQRLNRGNYVVGELVDAARANGVT 134 (290)
T ss_pred CCchHHHHHHHHhheEec---------cC---------hhhhcccceeHHHHHHHHHHCCCc
Confidence 457789999999987543 21 235677888889999999999984
No 86
>KOG3853|consensus
Probab=24.74 E-value=37 Score=27.59 Aligned_cols=13 Identities=38% Similarity=0.997 Sum_probs=10.4
Q ss_pred CCccEEEEcCCce
Q psy11249 90 PVELTLWVDPHEV 102 (105)
Q Consensus 90 P~e~tlWvDPgeV 102 (105)
-+..|+||||-..
T Consensus 154 a~dVtVwvDPLDA 166 (350)
T KOG3853|consen 154 ASDVTVWVDPLDA 166 (350)
T ss_pred ceeeEEEeccchh
Confidence 5678999999753
No 87
>KOG3021|consensus
Probab=24.57 E-value=43 Score=26.91 Aligned_cols=36 Identities=25% Similarity=0.451 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEE
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIR 62 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIr 62 (105)
+++|.. .-|-+.|--.+.-+|-+||+ .=||+||.=.
T Consensus 265 k~ipka--~G~eqR~~LYqLyhyLNHwN----hFGs~YRs~s 300 (313)
T KOG3021|consen 265 KKIPKA--PGFEQRLLLYQLYHYLNHWN----HFGSGYRSSS 300 (313)
T ss_pred hhcCCC--CcHHHHHHHHHHHHHhhhhh----hhccccccch
Confidence 466655 56888888888899999998 4799999433
No 88
>PRK13689 hypothetical protein; Provisional
Probab=24.54 E-value=2e+02 Score=18.72 Aligned_cols=32 Identities=22% Similarity=0.243 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhh
Q psy11249 8 AVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDR 42 (105)
Q Consensus 8 av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~r 42 (105)
+=|-++.+|. ..+++.|....++++.++|..-
T Consensus 37 LGN~vTnlln---~~V~~~qR~~iAe~Fa~AL~~S 68 (75)
T PRK13689 37 LGNMVTNLLN---TSVAPAQRQAIAESFARALQSS 68 (75)
T ss_pred HHHHHHHHHh---hcCCHHHHHHHHHHHHHHHHHH
Confidence 3466777777 5688888766666666666543
No 89
>PF07137 VDE: Violaxanthin de-epoxidase (VDE); InterPro: IPR010788 This family represents a conserved region approximately 350 residues long within plant violaxanthin de-epoxidase (VDE). In higher plants, violaxanthin de-epoxidase forms part of a conserved system that dissipates excess energy as heat in the light-harvesting complexes of photosystem II (PSII), thus protecting them from photo-inhibitory damage [].; GO: 0046422 violaxanthin de-epoxidase activity, 0055114 oxidation-reduction process, 0009507 chloroplast; PDB: 3CQN_B 3CQR_A.
Probab=24.19 E-value=58 Score=24.92 Aligned_cols=18 Identities=28% Similarity=0.453 Sum_probs=14.3
Q ss_pred HHHHHHHHHhCCCCcccC
Q psy11249 71 TILENAAKAVGMSYEDMR 88 (105)
Q Consensus 71 p~l~~Aa~~sgl~~~~l~ 88 (105)
|-|.+||+++|++++.+.
T Consensus 165 p~l~~aa~k~G~d~~~F~ 182 (198)
T PF07137_consen 165 PELRRAAKKAGIDFSKFI 182 (198)
T ss_dssp HHHHHHHHHTT--GGGSE
T ss_pred HHHHHHHHHhCCCHHHeE
Confidence 789999999999998875
No 90
>COG5398 Heme oxygenase [Inorganic ion transport and metabolism]
Probab=24.18 E-value=2.2e+02 Score=22.36 Aligned_cols=31 Identities=10% Similarity=0.259 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHH
Q psy11249 3 DQISAAVLFLAKLIERSNTSCDADQLEAFKTKLA 36 (105)
Q Consensus 3 ~EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~ 36 (105)
-++++.|.|+..+|. |.++++....+...+.
T Consensus 15 h~~aEnv~fmkcfLk---g~V~~e~f~kl~~n~y 45 (238)
T COG5398 15 HTVAENVGFMKCFLK---GVVERESFRKLLANLY 45 (238)
T ss_pred HHHHHHHHHHHHHHc---CcccHHHHHHHHHHHH
Confidence 367889999999999 8999987776665543
No 91
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here have anything to do with toluene per-se.
Probab=23.98 E-value=1.7e+02 Score=21.61 Aligned_cols=35 Identities=29% Similarity=0.311 Sum_probs=27.0
Q ss_pred HHHHH-HhhcCCCCHHHHHHHHHHHHHHHHhhcCCC
Q psy11249 12 LAKLI-ERSNTSCDADQLEAFKTKLAELLNDRFANH 46 (105)
Q Consensus 12 l~~~l-~~~~~~l~~~~i~~F~~~L~~~L~~ry~~H 46 (105)
++++. -++..+++++|.+.|.+.+.+.|...|.+.
T Consensus 69 mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~ 104 (198)
T TIGR03481 69 MARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQ 104 (198)
T ss_pred HHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44433 335678999999999999999999888654
No 92
>cd02185 AroH Chorismate mutase (AroH) is one of at least five chorismate-utilizing enzymes present in microorganisms that catalyze the rearrangement of chorismate to prephenic acid, the first committed step in the biosynthesis of aromatic amino acids. In prokaryotes, chorismate mutase may be fused to prephenate dehydratase, prephenate dehydrogenase, or 3-deoxy-D-arabino-heptulosonat-7-phosphate (DAHP) as part of a bifunctional enzyme. The AroH domain forms a homotrimer with three-fold symmetry.
Probab=23.94 E-value=2.1e+02 Score=20.10 Aligned_cols=61 Identities=20% Similarity=0.251 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCHHHHHH--------HHHHHHHHHHhhcCCCC-------CCCCCCCccceeEEEec
Q psy11249 2 QDQISAAVLFLAKLIERSNTSCDADQLEA--------FKTKLAELLNDRFANHW-------FPEAPNRGQGYRCIRLN 64 (105)
Q Consensus 2 ~~EI~~av~Fl~~~l~~~~~~l~~~~i~~--------F~~~L~~~L~~ry~~HW-------~P~~P~rGsayRcIrin 64 (105)
..||.+|+.=|..-+..+ +.+..++|-. .-+.+-.. ..|-.+.| --+-+-.||--||||+=
T Consensus 15 ~e~I~~at~eLl~~i~~~-N~l~~edivSv~FT~T~DL~a~FPA~-aaR~~~~~~~Vplmc~qE~~V~gsL~rcIRvl 90 (117)
T cd02185 15 AEEILEATRELLEEIIER-NNIKPEDIISVIFTVTPDLDAAFPAK-AARELGGWKYVPLMCAQEMDVPGSLPRCIRVL 90 (117)
T ss_pred HHHHHHHHHHHHHHHHHH-cCCCHHHEEEEEEEeCCcccccChHH-HHHhcCCCCCcceeecCcCCCCCCCCceeEEE
Confidence 468888888666555554 5688776521 11111111 22333667 34667899999999873
No 93
>PF13286 HD_assoc: Phosphohydrolase-associated domain; PDB: 2DQB_D.
Probab=23.94 E-value=1.9e+02 Score=18.01 Aligned_cols=37 Identities=11% Similarity=0.106 Sum_probs=24.5
Q ss_pred CHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHH
Q psy11249 1 MQDQISAAVLFLAKLIERSNTSCDADQLEAFKTKLAELL 39 (105)
Q Consensus 1 M~~EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L 39 (105)
|-.|+.++++-|.++++. .-+...++..+...-...|
T Consensus 3 ~s~~~~~~~~~Lk~f~~~--~Iy~~~~v~~~~~~~~~ii 39 (92)
T PF13286_consen 3 FSPEVKEAIKELKKFNYE--NIYQSPRVVEEEEKGRRII 39 (92)
T ss_dssp -HHHHHHHHHHHHHHHHH--HTTTSHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHH--HccCCHHHHHHHHHHHHHH
Confidence 457888999999999986 4566666655544444433
No 94
>PRK13289 bifunctional nitric oxide dioxygenase/dihydropteridine reductase 2; Provisional
Probab=23.73 E-value=2e+02 Score=22.87 Aligned_cols=42 Identities=2% Similarity=0.066 Sum_probs=30.7
Q ss_pred HHHHHHHHHHhhc-CCCCHHHHHHHHHHHHHHHHhhcCCCCCC
Q psy11249 8 AVLFLAKLIERSN-TSCDADQLEAFKTKLAELLNDRFANHWFP 49 (105)
Q Consensus 8 av~Fl~~~l~~~~-~~l~~~~i~~F~~~L~~~L~~ry~~HW~P 49 (105)
...+|.++-.+|. -.++++.-..|++.|-..|.+.+..+|.|
T Consensus 74 l~~~l~~L~~~H~~~gV~~~~f~~~~~~ll~~l~~~~~~~~t~ 116 (399)
T PRK13289 74 LLPAVERIAQKHVSLQIKPEHYPIVGEHLLAAIREVLGDAATD 116 (399)
T ss_pred HHHHHHHHHHHHHHcCCChHHhHHHHHHHHHHHHHHhCCCCCH
Confidence 3455555555532 35888889999999999999988877754
No 95
>PF02337 Gag_p10: Retroviral GAG p10 protein; InterPro: IPR003322 Retroviral matrix proteins (or major core proteins) are components of envelope-associated capsids, which line the inner surface of virus envelopes and are associated with viral membranes []. Matrix proteins are produced as part of Gag precursor polyproteins. During viral maturation, the Gag polyprotein is cleaved into major structural proteins by the viral protease, yielding the matrix (MA), capsid (CA), nucleocapsid (NC), and some smaller peptides. Gag-derived proteins govern the entire assembly and release of the virus particles, with matrix proteins playing key roles in Gag stability, capsid assembly, transport and budding. Although matrix proteins from different retroviruses appear to perform similar functions and can have similar structural folds, their primary sequences can be very different. This entry represents matrix proteins from beta-retroviruses such as Mason-Pfizer monkey virus (MPMV) (Simian Mason-Pfizer virus) and Mouse mammary tumor virus (MMTV) [, ]. This entry also identifies matrix proteins from several eukaryotic endogenous retroviruses, which arise when one or more copies of the retroviral genome becomes integrated into the host genome [].; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 2F77_X 2F76_X.
Probab=23.71 E-value=1.5e+02 Score=19.76 Aligned_cols=39 Identities=23% Similarity=0.437 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCC
Q psy11249 8 AVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFANHWFPEAP 52 (105)
Q Consensus 8 av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P 52 (105)
-|..|.++|..++=++..+++..|-..+... .=|||++-
T Consensus 10 fv~~Lk~lLk~rGi~v~~~~L~~f~~~i~~~------~PWF~~eG 48 (90)
T PF02337_consen 10 FVSILKHLLKERGIRVKKKDLINFLSFIDKV------CPWFPEEG 48 (90)
T ss_dssp HHHHHHHHHHCCT----HHHHHHHHHHHHHH------TT-SS--S
T ss_pred HHHHHHHHHHHcCeeecHHHHHHHHHHHHHh------CCCCCCCC
Confidence 4667788888777788999999998888652 45887653
No 96
>PF06519 TolA: TolA C-terminal; InterPro: IPR014161 TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cut-offs are based largely on conserved operon structure. The Tol-Pal complex is required for maintaining outer membrane integrity, and is also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins OmpC, PhoE and LamB.; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2X9A_D 3QDP_A 3QDR_A 1TOL_A 1S62_A.
Probab=23.44 E-value=1.8e+02 Score=19.33 Aligned_cols=52 Identities=19% Similarity=0.369 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCCCCCCCCcccee-EEEecCCCC--------CCHHHHHHHHHh
Q psy11249 25 ADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYR-CIRLNKNVK--------KDTILENAAKAV 80 (105)
Q Consensus 25 ~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayR-cIrin~~~~--------~Dp~l~~Aa~~s 80 (105)
...++.++......+ +.+|+.+.-.+|+-=+ -|++.+++. =|+.|.+||..+
T Consensus 10 ~~ev~~Y~~~I~~~I----q~~l~~~~~y~GK~C~v~i~l~~dG~v~~v~~~~GD~~lC~aa~~A 70 (96)
T PF06519_consen 10 GSEVSRYAAQIKQAI----QRNLYDDESYKGKECRVRIRLAPDGLVLSVTVESGDPALCRAAKSA 70 (96)
T ss_dssp CHHHHHHHHHHHHHH----HTTTTTGGGGTT--EEEEEEEETTSEEEEEEEEEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHH----HHhcCCccccCCCEEEEEEEECCCCcEEEeeecCCCHHHHHHHHHH
Confidence 345566666555544 5566777888886543 234443322 299999999887
No 97
>COG4196 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.20 E-value=73 Score=28.29 Aligned_cols=17 Identities=24% Similarity=0.558 Sum_probs=11.9
Q ss_pred HHHHHHHHhCCCCcccC
Q psy11249 72 ILENAAKAVGMSYEDMR 88 (105)
Q Consensus 72 ~l~~Aa~~sgl~~~~l~ 88 (105)
+|..+|...||+.+.+.
T Consensus 149 vL~~iA~~LGl~~~~v~ 165 (808)
T COG4196 149 VLAGIADGLGLPISQVR 165 (808)
T ss_pred HHHHhhcccCCChHHhc
Confidence 66777777888776553
No 98
>cd06941 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily. The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors ha
Probab=23.00 E-value=1e+02 Score=22.26 Aligned_cols=31 Identities=10% Similarity=0.266 Sum_probs=23.6
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPEAPNR 54 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~r 54 (105)
-++++|+...+.+.++|.+..... +|+.|.+
T Consensus 122 ~~~~~Ve~lq~~~~~aL~~~i~~~-~p~~~~r 152 (195)
T cd06941 122 SEPKKVAILQDRVLEALKVQVSRN-RPAEAQL 152 (195)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhh-CCCcccH
Confidence 467889999999999999877544 5655553
No 99
>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors. The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of prom
Probab=22.91 E-value=94 Score=23.17 Aligned_cols=31 Identities=26% Similarity=0.462 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCC
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPEAPNR 54 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~r 54 (105)
-++..|+.+.+.+.++|.+.... .||+.|.|
T Consensus 153 ~~~~~Ve~~Q~~~~~aL~~y~~~-~~p~~p~r 183 (221)
T cd06936 153 KDKEAVEKLQEPLLDLLQKFCKL-YHPEDPQH 183 (221)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHh-hCCCchhH
Confidence 46889999999999999987654 47887764
No 100
>PF08153 NGP1NT: NGP1NT (NUC091) domain; InterPro: IPR012971 This N-terminal domain is found in a subfamily of hypothetical nucleolar GTP-binding proteins similar to human NGP1 [].
Probab=22.72 E-value=66 Score=23.00 Aligned_cols=22 Identities=23% Similarity=0.531 Sum_probs=18.3
Q ss_pred CCCHHHHHHHHHHHHHHHHhhc
Q psy11249 22 SCDADQLEAFKTKLAELLNDRF 43 (105)
Q Consensus 22 ~l~~~~i~~F~~~L~~~L~~ry 43 (105)
-|++++++.|.++|++...+=|
T Consensus 43 vI~Q~~L~~FReem~~~~~DPy 64 (130)
T PF08153_consen 43 VISQEALEKFREEMGEKVKDPY 64 (130)
T ss_pred EECHHHHHHHHHHHHHhhcCCc
Confidence 4789999999999998766544
No 101
>cd06940 NR_LBD_REV_ERB The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily. The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of
Probab=22.61 E-value=86 Score=22.76 Aligned_cols=32 Identities=22% Similarity=0.364 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCC
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFPEAPN 53 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~ 53 (105)
+--++++|+.+++.+.++|.+....+ ||+.|.
T Consensus 130 ~L~~~~~Ve~lq~~~~~aL~~~~~~~-~p~~~~ 161 (189)
T cd06940 130 GLENVNLVEALQETLIRALRTLIAKN-HPNEPS 161 (189)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHh-CCCCcc
Confidence 44568899999999999998776643 677665
No 102
>COG5502 Uncharacterized conserved protein [Function unknown]
Probab=22.26 E-value=2e+02 Score=20.76 Aligned_cols=33 Identities=12% Similarity=0.139 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCC
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFPEAPN 53 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~ 53 (105)
.+||.+....|+.+|-..|..-|.+-|.+..|.
T Consensus 41 drL~~eea~~~aaqLP~~ir~~~~~~p~~~~~~ 73 (135)
T COG5502 41 DRLPGEEAADFAAQLPMEIRDILVDGPDLGPPK 73 (135)
T ss_pred HHcChhHHHHHHHhCCHHHHHHHhcCCcCCCCC
Confidence 579999999999999999999999988877665
No 103
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=22.11 E-value=1.3e+02 Score=15.82 Aligned_cols=27 Identities=15% Similarity=0.167 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHHHH
Q psy11249 6 SAAVLFLAKLIERSNTSCDADQLEAFKTKL 35 (105)
Q Consensus 6 ~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L 35 (105)
+.+|+++..+|. .+-..++|..+.++.
T Consensus 8 ~~~v~~i~~~l~---~~~t~~~I~~~l~~~ 34 (39)
T PF05184_consen 8 KFVVKEIEKLLK---NNKTEEEIKKALEKA 34 (39)
T ss_dssp HHHHHHHHHHHH---STCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH---cCccHHHHHHHHHHH
Confidence 457888888887 346777776666554
No 104
>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=22.09 E-value=1.4e+02 Score=22.84 Aligned_cols=31 Identities=6% Similarity=0.190 Sum_probs=22.0
Q ss_pred CHHHHHHHHH---------HHHHHHHhhcCCCCHHHHHHHHHH
Q psy11249 1 MQDQISAAVL---------FLAKLIERSNTSCDADQLEAFKTK 34 (105)
Q Consensus 1 M~~EI~~av~---------Fl~~~l~~~~~~l~~~~i~~F~~~ 34 (105)
||.+|..++. .|.+||. ++++++..+.+...
T Consensus 14 lk~~l~~~LG~~~~~~Y~~~l~~fl~---~klsk~Efd~~~~~ 53 (252)
T PF12767_consen 14 LKSQLQKRLGPDRWKKYFQSLKRFLS---GKLSKEEFDKECRR 53 (252)
T ss_pred HHHHHHHHHChHHHHHHHHHHHHHHH---hccCHHHHHHHHHH
Confidence 3566666664 6788888 78999887766543
No 105
>PF14941 OAF: Transcriptional regulator, Out at first
Probab=22.06 E-value=37 Score=26.63 Aligned_cols=15 Identities=33% Similarity=1.041 Sum_probs=11.4
Q ss_pred CCC-------CCCCCccceeEE
Q psy11249 47 WFP-------EAPNRGQGYRCI 61 (105)
Q Consensus 47 W~P-------~~P~rGsayRcI 61 (105)
||| .++.||+-|||=
T Consensus 195 WYPCgLKYCkgkd~k~ssYrCG 216 (240)
T PF14941_consen 195 WYPCGLKYCKGKDQKPSSYRCG 216 (240)
T ss_pred eEccchhhccCCCCCCCccccc
Confidence 777 356689999984
No 106
>PRK07179 hypothetical protein; Provisional
Probab=21.99 E-value=2.2e+02 Score=22.60 Aligned_cols=48 Identities=19% Similarity=0.277 Sum_probs=33.8
Q ss_pred HHHHHHHHHhhcCCCCCCCC--CCCccceeEEEecCCCCCC----HHHHHHHHH
Q psy11249 32 KTKLAELLNDRFANHWFPEA--PNRGQGYRCIRLNKNVKKD----TILENAAKA 79 (105)
Q Consensus 32 ~~~L~~~L~~ry~~HW~P~~--P~rGsayRcIrin~~~~~D----p~l~~Aa~~ 79 (105)
.+++.....+++..+|.+-. ..||.|...|.+..+..+| |.+.+|..+
T Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~YL~l~~~p~v~~a~~~ 79 (407)
T PRK07179 26 EERLDKYIEERVNKNWNGKHLVLGKTPGPDAIILQSNDYLNLSGHPDIIKAQIA 79 (407)
T ss_pred HHHHHHHHHHhhccCcCCceEEeecCCCCcEEEeecCCccCCCCCHHHHHHHHH
Confidence 35566667777888886655 4667888888887665554 778777765
No 107
>PF09371 Tex_N: Tex-like protein N-terminal domain; InterPro: IPR018974 This presumed domain is found at the N terminus of Q45388 from SWISSPROT. This protein defines a novel family of prokaryotic transcriptional accessory factors []. ; PDB: 2OCE_A 3BZK_A 3BZC_A.
Probab=21.98 E-value=1.6e+02 Score=22.07 Aligned_cols=32 Identities=22% Similarity=0.291 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHH
Q psy11249 7 AAVLFLAKLIERSNTSCDADQLEAFKTKLAEL 38 (105)
Q Consensus 7 ~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~ 38 (105)
.+|=||+||=+-.-|.++..++..|.+.+...
T Consensus 23 ~TvPFIARYRKe~TG~Lde~~lR~i~~~~~~~ 54 (193)
T PF09371_consen 23 NTVPFIARYRKEMTGGLDEVQLREIQDRYEYL 54 (193)
T ss_dssp --HHHHHHH-HHHHTS--HHHHHHHHHHHHHH
T ss_pred CCcchhhhhhhhhhCCCCHHHHHHHHHHHHHH
Confidence 46789999977655789999999888877654
No 108
>cd06945 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily. The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as
Probab=21.96 E-value=2.2e+02 Score=21.54 Aligned_cols=33 Identities=24% Similarity=0.564 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCCCCC--CCCCC
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANHWFP--EAPNR 54 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~HW~P--~~P~r 54 (105)
+--++++|+.+++++.++|.++...+ || +.|.|
T Consensus 158 gL~~~~~Ve~lQe~~~~aL~~y~~~~-~p~~~~~~r 192 (239)
T cd06945 158 GLKEPKKVEELQNKIISCLRDHVTSN-YPGQDKPNR 192 (239)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHh-CCCcccccH
Confidence 44578899999999999999988776 57 66543
No 109
>cd06950 NR_LBD_Tlx_PNR_like The ligand binding domain of Tailless-like proteins, orphan nuclear receptors. The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX and PNR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge
Probab=21.58 E-value=1e+02 Score=22.59 Aligned_cols=29 Identities=28% Similarity=0.563 Sum_probs=22.3
Q ss_pred CHHHHHHHHHHHHHHHHhhcCCCCCCCCCC
Q psy11249 24 DADQLEAFKTKLAELLNDRFANHWFPEAPN 53 (105)
Q Consensus 24 ~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~ 53 (105)
+..+|+.+++++.++|.+....| ||+.|.
T Consensus 147 ~~~~Ve~lq~~~~~aL~~y~~~~-~~~~~~ 175 (206)
T cd06950 147 DPAQVEALQDQAQLMLNKHIRTR-YPTQPA 175 (206)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHh-CCCccc
Confidence 46789999999999998877655 565554
No 110
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=21.54 E-value=1.8e+02 Score=20.97 Aligned_cols=37 Identities=19% Similarity=0.315 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecC
Q psy11249 26 DQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNK 65 (105)
Q Consensus 26 ~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~ 65 (105)
+.+.++++..+..|.-+.+....|. ...|..+|.||+
T Consensus 23 ~~lGRlAs~IAk~L~GKhKp~y~p~---~d~Gd~VvViNa 59 (144)
T PRK09216 23 KVLGRLASEVASILRGKHKPTFTPH---VDTGDFVIVINA 59 (144)
T ss_pred CchHHHHHHHHHHHhccCCCCcCCC---CCCCCEEEEEeC
Confidence 5578999999999999999997764 478899999984
No 111
>PF09492 Pec_lyase: Pectic acid lyase; InterPro: IPR012669 Members of this family are isozymes of pectate lyase (4.2.2.2 from EC), also called polygalacturonic transeliminase and alpha-1,4-D-endopolygalacturonic acid lyase.; PDB: 1R76_A 1GXM_B 1GXN_A 1GXO_A.
Probab=21.50 E-value=1.9e+02 Score=23.17 Aligned_cols=55 Identities=31% Similarity=0.418 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCC-CCCCCCCCCccceeEEEec
Q psy11249 7 AAVLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFAN-HWFPEAPNRGQGYRCIRLN 64 (105)
Q Consensus 7 ~av~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~-HW~P~~P~rGsayRcIrin 64 (105)
..+.||++..... =+.+=.+.|..-|.-+|..+|.+ -|-=--|.+|+=++.|.+|
T Consensus 43 ~ei~fLa~~y~~t---~d~~y~~A~~kgl~ylL~aQypnGGWPQ~yP~~~~Y~~~ITfN 98 (289)
T PF09492_consen 43 TEIRFLARVYQAT---KDPRYREAFLKGLDYLLKAQYPNGGWPQFYPLRGGYHDHITFN 98 (289)
T ss_dssp HHHHHHHHHHHHC---G-HHHHHHHHHHHHHHHHHS-TTS--BSECS--SGGGGSEE-G
T ss_pred HHHHHHHHHHHHh---CChHHHHHHHHHHHHHHHhhCCCCCCCccCCCCCCCCCceEEc
Confidence 4678999998863 34566689999999999999954 4766678888888899998
No 112
>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=21.47 E-value=62 Score=18.31 Aligned_cols=29 Identities=28% Similarity=0.436 Sum_probs=16.2
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCcccee
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYR 59 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayR 59 (105)
++++.|..=.+.|.+.+ ++=.-.+|.|||
T Consensus 27 vS~rTi~~~i~~L~~~~--------~~I~~~~~~GY~ 55 (55)
T PF08279_consen 27 VSRRTIRRDIKELREWG--------IPIESKRGKGYR 55 (55)
T ss_dssp S-HHHHHHHHHHHHHTT---------EEEEETTTEE-
T ss_pred CCHHHHHHHHHHHHHCC--------CeEEeeCCCCcC
Confidence 66777766666666655 344445666765
No 113
>TIGR01066 rplM_bact ribosomal protein L13, bacterial type. This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts.
Probab=21.47 E-value=1.7e+02 Score=20.99 Aligned_cols=37 Identities=22% Similarity=0.336 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecC
Q psy11249 26 DQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNK 65 (105)
Q Consensus 26 ~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~ 65 (105)
..+.++++..+..|.-+.+....|. -..|..+|.||+
T Consensus 21 ~~lGRLAs~iAk~L~GKhKp~y~p~---~d~Gd~VvViNa 57 (140)
T TIGR01066 21 KTLGRLASEVARLLRGKHKPTYTPH---VDCGDYVIVINA 57 (140)
T ss_pred CchHHHHHHHHHHHhccCCCccCCC---ccCCCEEEEEec
Confidence 5678999999999999999998775 478899999984
No 114
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=21.41 E-value=30 Score=18.67 Aligned_cols=17 Identities=41% Similarity=0.530 Sum_probs=11.7
Q ss_pred HHHHHHHHhCCCCcccC
Q psy11249 72 ILENAAKAVGMSYEDMR 88 (105)
Q Consensus 72 ~l~~Aa~~sgl~~~~l~ 88 (105)
.|.+-|.++||+.++++
T Consensus 7 ~Li~eA~~~Gls~eeir 23 (30)
T PF08671_consen 7 ELIKEAKESGLSKEEIR 23 (30)
T ss_dssp HHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHcCCCHHHHH
Confidence 36778999999988764
No 115
>PF13558 SbcCD_C: Putative exonuclease SbcCD, C subunit; PDB: 3QG5_B 3QF7_A 3THO_A 3EUK_H 3EUJ_A 3AV0_B 3AUY_B 3AUX_A.
Probab=21.34 E-value=2.3e+02 Score=17.99 Aligned_cols=49 Identities=20% Similarity=0.158 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecC-CCCCCHHHHHHHHH
Q psy11249 26 DQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNK-NVKKDTILENAAKA 79 (105)
Q Consensus 26 ~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~-~~~~Dp~l~~Aa~~ 79 (105)
++...+.-.|...|...|..+. .++.++|.|.++. ..++|+.-.+.+.+
T Consensus 37 Ek~~~~~l~l~aal~~~~~~~~-----~~~~~~~~l~lDEaF~~lD~~~~~~~~~ 86 (90)
T PF13558_consen 37 EKQFPFYLALAAALAALYSSSS-----GRGDSPRLLFLDEAFSKLDEENIERLMD 86 (90)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTS-----TS-TTBSEEEEESTTTTCGHHHHHHHHH
T ss_pred HhHHHHHHHHHHHHHHHHhhhc-----CCCCCcCEEEEeCCCCcCCHHHHHHHHH
Confidence 3347888899999999998872 2788899999995 58999887776643
No 116
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=21.24 E-value=28 Score=23.37 Aligned_cols=77 Identities=19% Similarity=0.274 Sum_probs=50.8
Q ss_pred HHHHHHHHHHhhcC-CCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHHHhCCCCcc
Q psy11249 8 AVLFLAKLIERSNT-SCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMSYED 86 (105)
Q Consensus 8 av~Fl~~~l~~~~~-~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~ 86 (105)
+..+|...|..... .-....+..|+..+++.|...|.+ .+..--+-+|+|..|=...-.|.|..--..-.|++.+
T Consensus 9 ~~~~L~~~l~~~~~~~~~~~~~~~lA~~IE~~lf~~~~~----~~~~Y~~k~Rsl~~NLkd~~N~~L~~~il~g~i~p~~ 84 (115)
T PF07500_consen 9 ARKLLYKALQKRSDEQDDPEDAKELAKEIEEALFDKFGS----TSKKYKQKFRSLMFNLKDPKNPDLRRRILSGEISPEE 84 (115)
T ss_dssp HHHHHHHHHHHCCCCCCCTCCHHHHHHHHHHHHHHHHTS----TSHHHHHHHHHHHHHHCSSTTCCHHHHHHHSSSTTCH
T ss_pred HHHHHHHHHHhcCccccchhHHHHHHHHHHHHHHHHHcc----CcHHHHHHHHHHHHHhccCCcHHHHHHHHcCCCCHHH
Confidence 45667777765211 115677899999999999999932 3344445667888874444566666666666666666
Q ss_pred cC
Q psy11249 87 MR 88 (105)
Q Consensus 87 l~ 88 (105)
|.
T Consensus 85 lv 86 (115)
T PF07500_consen 85 LV 86 (115)
T ss_dssp HH
T ss_pred Hh
Confidence 54
No 117
>cd03123 alpha_CA_VI_IX_XII_XIV Carbonic anhydrase alpha, isozymes VI, IX, XII and XIV. Carbonic anhydrases (CAs) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism: a nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide, followed by the regeneration of the active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. They are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionary distinct groups - alpha, beta and gamma carbonic anhydrases - which show no significant sequence identity or structural similarity. Alpha CAs are mostly monomeric enzymes. The zinc ion is complexed by three histidine residues. This sub-family comprises the secreted CA VI, which is found in saliva, for example, and the membrane proteins CA IX, XII, and XIV.
Probab=21.23 E-value=1.3e+02 Score=23.01 Aligned_cols=39 Identities=23% Similarity=0.434 Sum_probs=27.9
Q ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEe
Q psy11249 22 SCDADQLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRL 63 (105)
Q Consensus 22 ~l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIri 63 (105)
.++++|++.|...|...-...+.+.-.|-.|..| |.|+.
T Consensus 208 ~iS~~Ql~~fr~~l~~~~~~~~~~N~Rp~Qpln~---R~V~~ 246 (248)
T cd03123 208 TLSKEQLETLENTLMDTHNKTLQNNYRATQPLNG---RVVEA 246 (248)
T ss_pred ecCHHHHHHHHHHhhccCCCcccCCCCCCCCCCC---CEEEe
Confidence 4899999999987654333445666777888877 67664
No 118
>cd01783 DAGK_delta_RA Ubiquitin-like domain of Diacylgylcerol kinase (DAGK). DAGK_delta_RA Diacylgylcerol kinase (DAGK) phosphorylates the second messenger diacylglycerol to phosphatidic acid as part of a protein kinase C pathway. Nine mammalian DAGK isotypes have been identified, which are classified into five subgroups according to their domain architecture and the DAGK-delta and -theta isozymes, which fall into one such group, contain an RA (Ras-associated) domain. DAGKs also contain a conserved catalytic domain (DAGKc), an assesory domain (DAGKa), and an array of conserved motifs that are likely to play a role in lipid-protein and protein-protein interactions in various DAG/PA-dependent signalling pathways.
Probab=21.08 E-value=1.5e+02 Score=20.14 Aligned_cols=40 Identities=23% Similarity=0.346 Sum_probs=32.8
Q ss_pred CCCCCCCccceeEEEecCCCCCCHHHHHHHHHhCCCCccc
Q psy11249 48 FPEAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMSYEDM 87 (105)
Q Consensus 48 ~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l 87 (105)
||..=..+-+|..|.+|......-+|..|-..-|+.-++.
T Consensus 8 Y~G~L~~~~~y~sv~V~~~tt~~dvv~eaL~kfGl~~~~~ 47 (97)
T cd01783 8 YPGWLRVGVAYVSIRVNKDTTVQDVILEVLPLFGLQAECP 47 (97)
T ss_pred ecCccccCcceEEEEecccchHHHHHHHHHHHhCcccCCc
Confidence 4554445788999999999999999999999999987653
No 119
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=21.06 E-value=2.5e+02 Score=18.31 Aligned_cols=38 Identities=13% Similarity=0.256 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHhhcCC--------CCHHHHHHHHHHHHHHHHhhc
Q psy11249 6 SAAVLFLAKLIERSNTS--------CDADQLEAFKTKLAELLNDRF 43 (105)
Q Consensus 6 ~~av~Fl~~~l~~~~~~--------l~~~~i~~F~~~L~~~L~~ry 43 (105)
.+++.++..+|..+.-. .+.+++....+=+.+.+..+|
T Consensus 39 ~~~~~~fk~~l~~~sv~rpp~~~~iFs~~~~~~i~~y~~~t~frHy 84 (101)
T PF14769_consen 39 EDSFKYFKELLLRHSVQRPPFSIGIFSVDQVKAIIDYFHNTYFRHY 84 (101)
T ss_pred HHHHHHHHHHHHHhccCCCCcccCcCCHHHHHHHHHHHHHHHHHHH
Confidence 34444555555443323 344444444444444444444
No 120
>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily. The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=21.05 E-value=1.1e+02 Score=23.17 Aligned_cols=30 Identities=13% Similarity=0.145 Sum_probs=24.0
Q ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCCCCCCC
Q psy11249 23 CDADQLEAFKTKLAELLNDRFANHWFPEAPN 53 (105)
Q Consensus 23 l~~~~i~~F~~~L~~~L~~ry~~HW~P~~P~ 53 (105)
-+...|+.++++..++|.+.... -||+.|.
T Consensus 163 ~~~~~Ve~lQe~~~~aL~~y~~~-~~p~~~~ 192 (237)
T cd07070 163 NNHSLVKDAQEKANAALLDYTLC-HYPHCGD 192 (237)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHh-cCCCcch
Confidence 35778999999999999987664 4787764
No 121
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=21.03 E-value=1.4e+02 Score=21.39 Aligned_cols=27 Identities=19% Similarity=0.043 Sum_probs=23.9
Q ss_pred eeEEEecCCCCCCHHHHHHHHHhCCCC
Q psy11249 58 YRCIRLNKNVKKDTILENAAKAVGMSY 84 (105)
Q Consensus 58 yRcIrin~~~~~Dp~l~~Aa~~sgl~~ 84 (105)
-|.||+-+.+.+||.+..-|-..|++-
T Consensus 30 vRiIrv~CsGrvn~~fvl~Al~~GaDG 56 (132)
T COG1908 30 VRIIRVMCSGRVNPEFVLKALRKGADG 56 (132)
T ss_pred eEEEEeeccCccCHHHHHHHHHcCCCe
Confidence 589999999999999999999888864
No 122
>COG5086 Uncharacterized conserved protein [Function unknown]
Probab=20.75 E-value=63 Score=24.76 Aligned_cols=30 Identities=7% Similarity=0.073 Sum_probs=21.8
Q ss_pred CHHHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHHH
Q psy11249 1 MQDQISAAVLFLAKLIERSNTSCDADQLEAFKTKL 35 (105)
Q Consensus 1 M~~EI~~av~Fl~~~l~~~~~~l~~~~i~~F~~~L 35 (105)
|.+|+...=+|+.+|++++-+ +++.|+.-+
T Consensus 79 MetElERvKFvvrsYirtRl~-----Kidk~~~y~ 108 (218)
T COG5086 79 METELERVKFVVRSYIRTRLK-----KIDKNLYYD 108 (218)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-----HhhhhHHHh
Confidence 889999999999999997433 344554433
No 123
>TIGR02116 toxin_Txe_YoeB toxin-antitoxin system, toxin component, Txe/YoeB family. The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This model describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by matches to TIGR01552 and/or pfam02604.
Probab=20.68 E-value=2.2e+02 Score=17.56 Aligned_cols=39 Identities=18% Similarity=0.355 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHHhhcCCCCCCCCCCCcc--ceeEEEec
Q psy11249 25 ADQLEAFKTKLAELLNDRFANHWFPEAPNRGQ--GYRCIRLN 64 (105)
Q Consensus 25 ~~~i~~F~~~L~~~L~~ry~~HW~P~~P~rGs--ayRcIrin 64 (105)
+.....|.+.|.+++..=+.++. ..++.+|. ||..+||+
T Consensus 17 ~~~~~~i~~~i~~l~~~P~~~~~-~~~~L~G~~~g~~r~rig 57 (80)
T TIGR02116 17 KKLKKKINELIKDVRRDPFKGKG-KPEPLKGDLSGYWSRRIT 57 (80)
T ss_pred HHHHHHHHHHHHHHHcCCCCCCC-CcccCCCCCCCcEEEEcC
Confidence 34557788888765433222222 23556774 67788884
No 124
>cd07071 NR_LBD_Nurr1 The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors. The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=20.65 E-value=1.2e+02 Score=23.19 Aligned_cols=34 Identities=18% Similarity=0.210 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHhhcCCC-CCCCCCCC
Q psy11249 21 TSCDADQLEAFKTKLAELLNDRFANH-WFPEAPNR 54 (105)
Q Consensus 21 ~~l~~~~i~~F~~~L~~~L~~ry~~H-W~P~~P~r 54 (105)
|--++++|+.+++.+.++|.+....+ =+|+.|.+
T Consensus 157 gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~r 191 (238)
T cd07071 157 GLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNY 191 (238)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccH
Confidence 44678999999999999999876522 25666653
No 125
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=20.65 E-value=1.4e+02 Score=20.92 Aligned_cols=24 Identities=13% Similarity=0.086 Sum_probs=21.0
Q ss_pred CCCCCCHHHHHHHHHhCCCCcccC
Q psy11249 65 KNVKKDTILENAAKAVGMSYEDMR 88 (105)
Q Consensus 65 ~~~~~Dp~l~~Aa~~sgl~~~~l~ 88 (105)
.++++||-..++.++-||+.+...
T Consensus 42 ~g~~~~~~a~~vl~e~Gid~~~~~ 65 (139)
T COG0394 42 PGEPPDPRAVEVLAEHGIDISGHR 65 (139)
T ss_pred CCCCCCHHHHHHHHHcCCCcCCcc
Confidence 378899999999999999998743
No 126
>KOG4231|consensus
Probab=20.38 E-value=2.5e+02 Score=25.21 Aligned_cols=49 Identities=16% Similarity=0.212 Sum_probs=26.8
Q ss_pred HHHHHhhcCCCCHHHHHHHHHHHHHHHHhhc-CCCCCCCCCCCccceeEEEecCC
Q psy11249 13 AKLIERSNTSCDADQLEAFKTKLAELLNDRF-ANHWFPEAPNRGQGYRCIRLNKN 66 (105)
Q Consensus 13 ~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry-~~HW~P~~P~rGsayRcIrin~~ 66 (105)
.+++..|.-.++....-..++.-++...++- + -.|-||+|-|.+.|+.+
T Consensus 376 ~~~i~~~~~~~~~~~~~a~~~~~~~eil~~~~~-----~~~vkg~G~rILSiDGG 425 (763)
T KOG4231|consen 376 MRLIVTPEPRVNKAAARALAILGENEILRRSIK-----GRQVKGQGLRILSIDGG 425 (763)
T ss_pred HHHhcccccccchhhhHHHHHhhhhHHHHhhcc-----ccccCCCceEEEEecCC
Confidence 3444443334444444444433333333332 2 36889999999999943
No 127
>COG4226 HicB Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=20.34 E-value=2.2e+02 Score=19.89 Aligned_cols=57 Identities=19% Similarity=0.128 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHhhcCCCCCCCCCCCccceeEEEecCCCCCCHHHHHHHHHhCCCCccc
Q psy11249 27 QLEAFKTKLAELLNDRFANHWFPEAPNRGQGYRCIRLNKNVKKDTILENAAKAVGMSYEDM 87 (105)
Q Consensus 27 ~i~~F~~~L~~~L~~ry~~HW~P~~P~rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l 87 (105)
.-..|..+|...|..-=..-=-|.+|.. |--.+|| +..+...+..||++.|++...|
T Consensus 43 lk~~~~~s~~~yle~C~~~g~EP~k~~S--Gkf~~Ri--~p~lH~~a~~aAa~qgiSLN~~ 99 (111)
T COG4226 43 LKKEGELSLDDYLEFCKERGIEPRKPYS--GKFNLRI--DPELHEAAALAAAAQGISLNTW 99 (111)
T ss_pred HHHHHHhhHHHHHHHHHHcCCCCccccC--ceeeEec--CHHHHHHHHHHHHHhcCcHHHH
Confidence 3356777777777765555557888886 4557888 5567777788888999987654
No 128
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=20.25 E-value=1.4e+02 Score=19.76 Aligned_cols=37 Identities=24% Similarity=0.223 Sum_probs=23.0
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHHHHHHHhhcCCC
Q psy11249 9 VLFLAKLIERSNTSCDADQLEAFKTKLAELLNDRFANH 46 (105)
Q Consensus 9 v~Fl~~~l~~~~~~l~~~~i~~F~~~L~~~L~~ry~~H 46 (105)
+..+...|..+ +.+.+...+..+..+...|.+.|.|.
T Consensus 11 ~~~i~~~l~~~-g~i~~~~a~~ig~~~~~~L~~~~gG~ 47 (108)
T PF08765_consen 11 ADVIAAELERL-GEIDAELAEIIGEEVALKLCRYFGGQ 47 (108)
T ss_dssp HHHHHHHHHHT-S-S-----TTSHHHHHHHHHHHH-SS
T ss_pred HHHHHHHHHHc-CCcchhHHHHHHHHHHHHHHHHHCCE
Confidence 33445555554 55888889999999999999999886
No 129
>COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis]
Probab=20.16 E-value=1e+02 Score=25.56 Aligned_cols=41 Identities=22% Similarity=0.349 Sum_probs=31.8
Q ss_pred CccceeEEEecCCCCCCHHHHHHHHHhCCCCcccCCCCccEEEEcCC
Q psy11249 54 RGQGYRCIRLNKNVKKDTILENAAKAVGMSYEDMRLPVELTLWVDPH 100 (105)
Q Consensus 54 rGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l~lP~e~tlWvDPg 100 (105)
|-.|-|.|.+ +...=..|+.||.+.++.. .--+-.|+|.||
T Consensus 246 k~~GgRIiaV--GTTs~R~LEsa~~~~~~~~----~sg~T~IFI~PG 286 (348)
T COG0809 246 KARGGRIIAV--GTTSVRTLESAAREAGLKA----FSGWTDIFIYPG 286 (348)
T ss_pred HHcCCeEEEE--cchhHHHHHHHhcccCcCc----CcCcccEEEcCC
Confidence 5667899999 8888899999999988322 334566888887
Done!