Query 022567
Match_columns 295
No_of_seqs 203 out of 662
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 04:32:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022567.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022567hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3026 Splicing factor SPF30 100.0 5.6E-61 1.2E-65 426.0 17.2 257 12-294 1-262 (262)
2 PF06003 SMN: Survival motor n 99.6 1.7E-15 3.6E-20 140.6 6.6 58 95-152 64-123 (264)
3 cd04508 TUDOR Tudor domains ar 99.5 9.7E-15 2.1E-19 100.7 5.5 47 103-149 1-48 (48)
4 smart00333 TUDOR Tudor domain. 99.5 2.6E-14 5.6E-19 102.0 6.2 53 99-152 2-55 (57)
5 smart00743 Agenet Tudor-like d 99.1 1.6E-10 3.4E-15 83.8 6.5 54 99-152 2-58 (61)
6 KOG4327 mRNA splicing protein 99.0 4.6E-10 1E-14 98.6 4.8 56 95-150 63-120 (218)
7 PF00567 TUDOR: Tudor domain; 98.8 1.5E-08 3.3E-13 80.5 6.0 54 99-152 51-105 (121)
8 PF09465 LBR_tudor: Lamin-B re 98.7 1.1E-07 2.3E-12 67.7 7.2 50 98-148 4-55 (55)
9 KOG2185 Predicted RNA-processi 98.7 3.7E-08 8.1E-13 94.9 6.3 119 16-135 1-134 (486)
10 KOG2039 Transcriptional coacti 98.6 3.3E-08 7.2E-13 105.1 6.0 56 97-152 693-749 (875)
11 PF11717 Tudor-knot: RNA bindi 98.3 2E-06 4.3E-11 61.5 6.1 48 100-148 1-54 (55)
12 PF05641 Agenet: Agenet domain 97.9 3.3E-05 7.1E-10 57.4 5.6 53 100-152 1-65 (68)
13 PF15057 DUF4537: Domain of un 97.6 0.00016 3.4E-09 60.1 5.9 48 103-151 1-49 (124)
14 KOG2185 Predicted RNA-processi 97.4 0.00032 7E-09 68.2 6.8 59 91-150 172-230 (486)
15 PF09038 53-BP1_Tudor: Tumour 97.4 0.00044 9.5E-09 57.0 6.3 49 101-150 4-53 (122)
16 PLN00104 MYST -like histone ac 97.2 0.0012 2.6E-08 65.6 7.9 55 95-149 49-113 (450)
17 PF15057 DUF4537: Domain of un 97.2 0.00052 1.1E-08 57.0 4.5 55 97-152 53-114 (124)
18 PF07039 DUF1325: SGF29 tudor- 95.9 0.017 3.6E-07 48.5 5.2 54 95-148 67-126 (130)
19 cd05834 HDGF_related The PWWP 95.6 0.021 4.5E-07 44.2 4.7 53 99-152 2-59 (83)
20 PF00855 PWWP: PWWP domain; I 95.3 0.037 7.9E-07 42.0 5.0 51 100-151 1-59 (86)
21 cd05162 PWWP The PWWP domain, 95.3 0.038 8.3E-07 42.5 5.1 52 100-152 1-63 (87)
22 PF12148 DUF3590: Protein of u 95.1 0.034 7.4E-07 43.3 4.3 46 106-151 2-57 (85)
23 cd06080 MUM1_like Mutated mela 95.0 0.045 9.8E-07 42.2 4.8 51 100-151 1-54 (80)
24 smart00293 PWWP domain with co 95.0 0.062 1.3E-06 39.1 5.1 50 100-150 1-62 (63)
25 cd05841 BS69_related The PWWP 94.6 0.065 1.4E-06 41.6 4.7 52 100-152 7-59 (83)
26 smart00561 MBT Present in Dros 93.3 0.44 9.5E-06 37.8 7.2 56 95-150 23-83 (96)
27 cd05836 N_Pac_NP60 The PWWP do 92.5 0.22 4.9E-06 38.6 4.5 52 100-152 1-61 (86)
28 KOG1150 Predicted molecular ch 92.2 0.2 4.4E-06 45.1 4.4 53 200-257 171-243 (250)
29 cd05840 SPBC215_ISWI_like The 91.8 0.33 7.1E-06 38.3 4.7 51 100-151 1-65 (93)
30 PF14853 Fis1_TPR_C: Fis1 C-te 91.7 0.29 6.3E-06 34.7 3.9 38 14-51 12-49 (53)
31 PF08605 Rad9_Rad53_bind: Fung 91.5 0.37 8.1E-06 40.5 5.0 42 108-151 15-59 (131)
32 cd05835 Dnmt3b_related The PWW 91.2 0.25 5.4E-06 38.4 3.5 51 100-151 1-59 (87)
33 KOG3038 Histone acetyltransfer 90.7 0.47 1E-05 44.0 5.3 44 92-135 191-237 (264)
34 cd05838 WHSC1_related The PWWP 89.1 0.79 1.7E-05 36.2 4.7 50 101-151 2-63 (95)
35 cd05837 MSH6_like The PWWP dom 88.7 0.68 1.5E-05 37.5 4.2 53 99-152 2-69 (110)
36 PF10805 DUF2730: Protein of u 86.4 1.8 3.9E-05 34.9 5.3 46 8-53 36-81 (106)
37 KOG3364 Membrane protein invol 78.4 4.8 0.0001 34.4 5.1 37 14-50 82-118 (149)
38 KOG0644 Uncharacterized conser 77.1 3.2 6.9E-05 44.6 4.4 39 97-135 976-1028(1113)
39 TIGR00293 prefoldin, archaeal 76.8 38 0.00082 27.4 10.1 36 9-50 1-36 (126)
40 KOG1904 Transcription coactiva 76.1 2.5 5.5E-05 42.9 3.4 55 96-151 9-70 (496)
41 cd00584 Prefoldin_alpha Prefol 75.8 41 0.00089 27.3 10.0 39 10-54 2-40 (129)
42 PRK04098 sec-independent trans 75.6 6.2 0.00014 34.2 5.2 59 4-62 51-109 (158)
43 PRK08559 nusG transcription an 71.2 13 0.00027 31.8 6.1 53 98-151 93-149 (153)
44 KOG3038 Histone acetyltransfer 71.0 52 0.0011 30.8 10.3 55 97-151 125-185 (264)
45 PF07106 TBPIP: Tat binding pr 70.7 20 0.00044 30.8 7.3 54 9-62 81-137 (169)
46 COG1730 GIM5 Predicted prefold 70.5 19 0.00042 30.8 7.0 45 6-56 5-49 (145)
47 cd05839 BR140_related The PWWP 69.1 6.9 0.00015 32.0 3.8 51 100-151 1-79 (111)
48 PF15188 CCDC-167: Coiled-coil 68.7 21 0.00045 27.9 6.2 45 9-53 7-52 (85)
49 KOG3548 DNA damage checkpoint 68.4 4.8 0.0001 43.7 3.4 51 100-152 726-778 (1176)
50 PRK14011 prefoldin subunit alp 66.5 80 0.0017 26.9 9.9 36 9-50 5-40 (144)
51 KOG2279 Kinase anchor protein 64.9 4.2 9.2E-05 41.7 2.1 51 98-150 455-508 (608)
52 cd03694 GTPBP_II Domain II of 63.3 15 0.00032 28.0 4.5 50 98-147 25-74 (87)
53 PF02736 Myosin_N: Myosin N-te 61.7 38 0.00082 22.5 5.7 39 106-146 4-42 (42)
54 PF11336 DUF3138: Protein of u 61.7 22 0.00049 35.7 6.3 55 5-60 23-105 (514)
55 PF08863 YolD: YolD-like prote 58.6 32 0.0007 26.0 5.7 49 100-148 39-90 (92)
56 TIGR00046 RNA methyltransferas 58.6 25 0.00053 32.1 5.8 37 98-135 30-66 (240)
57 cd04452 S1_IF2_alpha S1_IF2_al 56.3 21 0.00046 25.7 4.2 37 113-149 3-40 (76)
58 PF02820 MBT: mbt repeat; Int 56.2 30 0.00066 25.5 5.0 37 114-150 12-52 (73)
59 PF07039 DUF1325: SGF29 tudor- 54.2 37 0.00081 28.3 5.7 52 101-152 1-60 (130)
60 PF06657 Cep57_MT_bd: Centroso 51.2 72 0.0016 24.3 6.4 46 9-54 19-67 (79)
61 PF14282 FlxA: FlxA-like prote 50.5 76 0.0017 25.4 6.8 53 8-62 20-72 (106)
62 PRK03947 prefoldin subunit alp 48.9 1.5E+02 0.0033 24.4 11.4 39 6-50 5-43 (140)
63 PRK14639 hypothetical protein; 48.1 60 0.0013 27.4 6.1 49 100-149 85-133 (140)
64 KOG3026 Splicing factor SPF30 47.9 12 0.00025 34.7 1.8 43 109-151 73-119 (262)
65 PF09177 Syntaxin-6_N: Syntaxi 47.7 93 0.002 24.2 6.8 52 11-62 9-60 (97)
66 PF12761 End3: Actin cytoskele 46.5 80 0.0017 28.4 6.9 51 11-61 100-152 (195)
67 cd02421 Peptidase_C39_likeD A 45.6 30 0.00065 27.2 3.7 43 104-149 70-113 (124)
68 PF08169 RBB1NT: RBB1NT (NUC16 45.5 30 0.00064 27.7 3.6 50 102-152 8-67 (96)
69 PF14257 DUF4349: Domain of un 43.0 80 0.0017 28.9 6.7 49 10-58 135-183 (262)
70 PF00575 S1: S1 RNA binding do 42.9 53 0.0012 23.5 4.5 35 114-149 5-39 (74)
71 cd05708 S1_Rrp5_repeat_sc12 S1 42.6 38 0.00082 24.3 3.6 36 114-149 3-38 (77)
72 COG1385 Uncharacterized protei 42.5 54 0.0012 30.3 5.4 36 98-134 32-67 (246)
73 PF14153 Spore_coat_CotO: Spor 42.0 48 0.001 29.5 4.8 49 100-150 132-180 (185)
74 TIGR00405 L26e_arch ribosomal 41.7 66 0.0014 26.8 5.4 52 99-151 86-141 (145)
75 PF04452 Methyltrans_RNA: RNA 41.2 61 0.0013 29.1 5.4 35 99-134 16-50 (225)
76 PF02576 DUF150: Uncharacteris 40.9 93 0.002 25.9 6.2 50 100-149 84-138 (141)
77 PRK00461 rpmC 50S ribosomal pr 40.8 1.7E+02 0.0038 22.8 7.2 52 5-56 6-59 (87)
78 cd01734 YlxS_C YxlS is a Bacil 39.2 1E+02 0.0023 23.2 5.7 50 100-149 22-76 (83)
79 PRK14549 50S ribosomal protein 38.6 1.6E+02 0.0035 21.8 7.1 50 5-54 10-62 (69)
80 PF13234 rRNA_proc-arch: rRNA- 38.4 99 0.0021 28.4 6.5 79 11-125 19-97 (268)
81 TIGR03130 malonate_delta malon 38.1 20 0.00044 28.7 1.6 9 262-270 19-27 (98)
82 PRK14637 hypothetical protein; 37.4 89 0.0019 26.8 5.6 48 100-149 95-142 (151)
83 PF11208 DUF2992: Protein of u 37.3 43 0.00092 28.2 3.5 28 109-137 3-30 (132)
84 PF06696 Strep_SA_rep: Strepto 36.8 65 0.0014 19.4 3.2 21 11-31 2-22 (25)
85 PF03039 IL12: Interleukin-12 36.1 98 0.0021 28.2 5.8 51 5-60 120-170 (219)
86 smart00326 SH3 Src homology 3 35.3 1E+02 0.0023 20.0 4.7 29 95-123 16-44 (58)
87 PRK01203 prefoldin subunit alp 35.2 2.7E+02 0.0059 23.4 8.3 22 103-125 48-69 (130)
88 cd04465 S1_RPS1_repeat_ec2_hs2 35.1 58 0.0013 23.0 3.6 34 114-149 1-34 (67)
89 TIGR01955 RfaH transcriptional 34.8 1.1E+02 0.0024 25.6 5.7 43 98-143 107-152 (159)
90 PRK11713 16S ribosomal RNA met 34.6 1E+02 0.0022 27.9 5.8 35 99-134 29-63 (234)
91 PF11302 DUF3104: Protein of u 34.6 2E+02 0.0043 22.0 6.4 54 97-150 3-70 (75)
92 cd00890 Prefoldin Prefoldin is 34.5 1.3E+02 0.0029 23.9 6.0 39 10-54 2-40 (129)
93 cd05698 S1_Rrp5_repeat_hs6_sc5 34.4 63 0.0014 22.9 3.7 34 114-148 1-34 (70)
94 PRK00409 recombination and DNA 34.2 3.8E+02 0.0082 29.0 10.9 48 98-151 635-683 (782)
95 COG5314 Conjugal transfer/entr 34.0 1.4E+02 0.0031 27.7 6.6 50 7-56 51-102 (252)
96 PF07730 HisKA_3: Histidine ki 33.7 1.6E+02 0.0035 20.5 5.7 50 11-60 12-63 (68)
97 cd05686 S1_pNO40 S1_pNO40: pNO 33.5 87 0.0019 22.7 4.3 36 114-149 4-39 (73)
98 cd05684 S1_DHX8_helicase S1_DH 33.2 88 0.0019 22.9 4.4 36 114-149 1-38 (79)
99 PF13428 TPR_14: Tetratricopep 33.1 55 0.0012 21.2 2.9 33 10-42 8-40 (44)
100 COG3524 KpsE Capsule polysacch 32.6 87 0.0019 30.3 5.1 47 9-60 225-271 (372)
101 cd04471 S1_RNase_R S1_RNase_R: 32.4 74 0.0016 23.1 3.8 35 114-148 2-36 (83)
102 PF02237 BPL_C: Biotin protein 31.5 1.7E+02 0.0036 19.8 6.4 41 102-144 2-42 (48)
103 PF06613 KorB_C: KorB C-termin 31.5 1.1E+02 0.0023 22.4 4.3 40 105-148 10-53 (60)
104 PRK11147 ABC transporter ATPas 31.2 1.7E+02 0.0036 30.6 7.5 48 9-57 570-622 (635)
105 KOG0994 Extracellular matrix g 31.2 1.3E+02 0.0027 34.3 6.5 51 10-60 1235-1290(1758)
106 PF01356 A_amylase_inhib: Alph 31.1 86 0.0019 23.4 3.8 35 101-139 24-58 (68)
107 PF00018 SH3_1: SH3 domain; I 30.9 75 0.0016 21.1 3.3 29 95-123 11-39 (48)
108 TIGR03142 cytochro_ccmI cytoch 29.9 1E+02 0.0022 25.0 4.5 36 13-48 35-71 (117)
109 PRK02001 hypothetical protein; 29.9 1.7E+02 0.0037 25.1 6.1 34 100-134 87-120 (152)
110 PRK04406 hypothetical protein; 29.5 2.5E+02 0.0054 21.2 7.8 25 6-30 3-27 (75)
111 cd00174 SH3 Src homology 3 dom 29.5 1.4E+02 0.0031 19.0 4.6 29 95-123 13-41 (54)
112 PF11623 DUF3252: Protein of u 28.9 1.4E+02 0.003 21.2 4.3 38 100-139 2-41 (53)
113 PF14559 TPR_19: Tetratricopep 28.8 53 0.0011 22.7 2.4 23 18-40 6-28 (68)
114 COG0250 NusG Transcription ant 28.1 1.7E+02 0.0037 25.7 6.0 54 94-150 118-177 (178)
115 TIGR02552 LcrH_SycD type III s 28.0 1E+02 0.0023 24.1 4.3 27 14-40 62-88 (135)
116 PF09953 DUF2187: Uncharacteri 27.9 1.9E+02 0.0041 20.9 5.0 36 100-140 4-39 (57)
117 cd02417 Peptidase_C39_likeA A 27.5 67 0.0015 25.0 3.0 41 105-148 71-111 (121)
118 PRK14633 hypothetical protein; 27.4 1.7E+02 0.0037 24.9 5.7 51 99-150 90-143 (150)
119 CHL00125 psaE photosystem I su 27.3 1.5E+02 0.0032 21.9 4.4 35 100-135 2-42 (64)
120 PHA00728 hypothetical protein 27.2 89 0.0019 26.1 3.7 31 1-33 1-31 (151)
121 cd00890 Prefoldin Prefoldin is 27.0 1.8E+02 0.0038 23.2 5.5 12 112-123 56-67 (129)
122 PHA01809 hypothetical protein 26.9 32 0.0007 24.5 0.9 26 97-124 13-43 (65)
123 TIGR02861 SASP_H small acid-so 26.9 84 0.0018 22.7 3.1 39 106-148 16-57 (58)
124 PF09038 53-BP1_Tudor: Tumour 26.9 93 0.002 25.9 3.8 46 99-147 55-104 (122)
125 KOG1118 Lysophosphatidic acid 26.6 3.9E+02 0.0084 26.0 8.3 38 95-134 320-358 (366)
126 PF08141 SspH: Small acid-solu 26.5 1E+02 0.0022 22.3 3.5 41 104-148 14-57 (58)
127 PF03681 UPF0150: Uncharacteri 26.4 95 0.002 20.7 3.2 21 117-138 2-23 (48)
128 PRK00306 50S ribosomal protein 26.4 2.6E+02 0.0056 20.3 7.2 49 5-54 7-58 (66)
129 cd05697 S1_Rrp5_repeat_hs5 S1_ 26.3 97 0.0021 21.9 3.5 34 114-148 1-34 (69)
130 TIGR00012 L29 ribosomal protei 25.9 2.4E+02 0.0051 19.8 6.4 47 6-52 4-52 (55)
131 PTZ00446 vacuolar sorting prot 25.8 1.9E+02 0.0041 25.9 5.8 43 9-51 132-175 (191)
132 PRK00092 ribosome maturation p 25.5 1.8E+02 0.0039 24.7 5.5 49 99-149 94-147 (154)
133 cd02419 Peptidase_C39C A sub-f 25.5 79 0.0017 24.8 3.1 42 104-149 75-116 (127)
134 PLN00045 photosystem I reactio 25.3 1.7E+02 0.0037 23.4 4.8 40 95-135 35-81 (101)
135 cd05685 S1_Tex S1_Tex: The C-t 25.1 1.2E+02 0.0025 20.8 3.6 34 114-148 1-34 (68)
136 PRK13879 conjugal transfer pro 25.1 2.4E+02 0.0053 26.3 6.7 46 9-54 47-94 (253)
137 PF10781 DSRB: Dextransucrase 25.0 1.5E+02 0.0031 21.6 3.9 38 101-139 2-43 (62)
138 cd05694 S1_Rrp5_repeat_hs2_sc2 24.9 1.2E+02 0.0025 22.4 3.8 34 113-147 4-38 (74)
139 KOG2991 Splicing regulator [RN 24.5 1.3E+02 0.0028 28.4 4.7 43 9-51 145-191 (330)
140 PF00515 TPR_1: Tetratricopept 24.4 66 0.0014 19.2 2.0 26 11-36 9-34 (34)
141 smart00503 SynN Syntaxin N-ter 23.6 3.5E+02 0.0076 20.9 7.3 49 9-59 10-61 (117)
142 cd04472 S1_PNPase S1_PNPase: P 23.5 1.3E+02 0.0029 20.6 3.7 35 114-149 1-35 (68)
143 PRK15326 type III secretion sy 23.3 1.8E+02 0.0038 22.5 4.5 31 10-40 14-44 (80)
144 PRK10708 hypothetical protein; 23.2 1.7E+02 0.0038 21.2 4.1 38 101-139 2-43 (62)
145 smart00316 S1 Ribosomal protei 23.1 1.3E+02 0.0028 20.4 3.6 36 114-150 3-38 (72)
146 PF12945 YcgR_2: Flagellar pro 23.1 2.5E+02 0.0054 20.5 5.3 34 100-133 1-38 (87)
147 PF11691 DUF3288: Protein of u 22.7 1.8E+02 0.004 22.9 4.5 44 19-62 8-70 (90)
148 PF07739 TipAS: TipAS antibiot 22.7 1.5E+02 0.0033 23.0 4.3 42 10-51 28-71 (118)
149 PF13437 HlyD_3: HlyD family s 22.7 3.4E+02 0.0074 20.5 6.2 30 97-126 47-78 (105)
150 PRK09634 nusB transcription an 22.6 2.9E+02 0.0062 25.0 6.4 48 13-60 46-94 (207)
151 PF07719 TPR_2: Tetratricopept 22.6 1.1E+02 0.0023 17.9 2.6 24 13-36 11-34 (34)
152 CHL00154 rpl29 ribosomal prote 22.6 3.2E+02 0.007 20.1 7.0 50 5-54 10-61 (67)
153 PRK14640 hypothetical protein; 22.5 2.3E+02 0.0051 24.1 5.6 49 99-149 93-144 (152)
154 PF13432 TPR_16: Tetratricopep 22.4 1.8E+02 0.004 19.8 4.2 45 14-58 8-59 (65)
155 PF07653 SH3_2: Variant SH3 do 22.4 1.2E+02 0.0026 20.7 3.2 27 95-121 13-40 (55)
156 PF07743 HSCB_C: HSCB C-termin 22.3 2E+02 0.0044 21.1 4.7 41 17-61 11-51 (78)
157 PF14604 SH3_9: Variant SH3 do 22.2 1.4E+02 0.0029 20.2 3.4 27 95-121 10-36 (49)
158 PF14357 DUF4404: Domain of un 21.5 48 0.001 25.6 1.0 32 20-51 3-39 (85)
159 TIGR01215 minE cell division t 21.5 1.7E+02 0.0038 22.4 4.1 33 20-52 19-51 (81)
160 PF12729 4HB_MCP_1: Four helix 21.4 3.2E+02 0.007 21.8 6.2 43 19-61 91-133 (181)
161 TIGR03017 EpsF chain length de 21.3 3.5E+02 0.0075 26.5 7.3 48 10-59 257-304 (444)
162 cd04453 S1_RNase_E S1_RNase_E: 21.0 1.6E+02 0.0034 22.5 3.9 34 113-147 7-42 (88)
163 PRK00034 gatC aspartyl/glutamy 21.0 2.4E+02 0.0051 21.6 5.0 39 20-58 5-43 (95)
164 PF06698 DUF1192: Protein of u 21.0 1.6E+02 0.0035 21.4 3.6 27 5-31 19-45 (59)
165 cd05707 S1_Rrp5_repeat_sc11 S1 20.9 1.5E+02 0.0033 20.8 3.6 34 114-148 1-34 (68)
166 PRK15095 FKBP-type peptidyl-pr 20.8 2.2E+02 0.0048 24.3 5.2 35 99-134 92-126 (156)
167 PRK09039 hypothetical protein; 20.8 1.8E+02 0.0038 28.2 5.0 43 9-51 139-186 (343)
168 smart00745 MIT Microtubule Int 20.8 3.4E+02 0.0073 19.7 6.9 49 12-60 24-72 (77)
169 PF13256 DUF4047: Domain of un 20.7 4.6E+02 0.01 21.9 6.6 47 6-58 56-102 (125)
170 cd05687 S1_RPS1_repeat_ec1_hs1 20.6 1.5E+02 0.0032 20.9 3.5 34 114-148 1-34 (70)
171 cd04461 S1_Rrp5_repeat_hs8_sc7 20.5 1.3E+02 0.0028 22.2 3.3 34 113-147 14-47 (83)
172 cd02259 Peptidase_C39_like Pep 20.4 1.3E+02 0.0027 23.2 3.4 46 101-149 67-112 (122)
173 cd04721 BAH_plant_1 BAH, or Br 20.4 1.2E+02 0.0025 25.2 3.3 27 99-126 7-33 (130)
174 TIGR03185 DNA_S_dndD DNA sulfu 20.3 3.7E+02 0.0079 28.2 7.6 41 9-49 393-433 (650)
175 PRK02103 malonate decarboxylas 20.3 63 0.0014 26.2 1.5 10 261-270 20-29 (105)
176 PRK03598 putative efflux pump 20.1 7.2E+02 0.016 23.2 12.4 39 100-138 225-269 (331)
177 PF15532 Toxin_53: Putative to 20.1 1.8E+02 0.0039 23.5 4.1 37 101-138 20-67 (102)
178 PF07820 TraC: TraC-like prote 20.0 3.2E+02 0.0069 21.7 5.4 44 8-54 3-60 (92)
No 1
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=100.00 E-value=5.6e-61 Score=425.99 Aligned_cols=257 Identities=37% Similarity=0.479 Sum_probs=210.8
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHHhhhcccccccCCCCCCCC---Ccccccccccc
Q 022567 12 LFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLATAKQNAISVSETGTSASAS---PNLLQSKENKT 88 (295)
Q Consensus 12 Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~~~~~~~~~~~~~~~~~~---P~~~~~~~~~~ 88 (295)
|+.+|.+|++||+||++||+.||+|+||++|++||.|||+||+|||.+...++.+.+.+...+.+. |.+...+...
T Consensus 1 ma~eL~sYK~QLqqVeaaL~~dP~NeEllkLe~DLkEvIsLTedLlqT~~ee~~sss~a~~ssq~~h~s~~~~~~~~~~- 79 (262)
T KOG3026|consen 1 MAKELASYKLQLQQVEAALQGDPENEELLKLEKDLKEVISLTEDLLQTQKEEDKSSSDAFVSSQPTHSSFTPRWVSGDY- 79 (262)
T ss_pred ChhHHHHHHHHHHHHHHHHccCCccHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccccccccCccccCCCchhhhhhhh-
Confidence 567899999999999999999999999999999999999999999999987755433221111111 1111111111
Q ss_pred cCCCCCCCCCCCCCCCeEEEEEcCCCcEEEEEEeeEeC-Cc-eEEEEecCCCEEEEcCCCcccCCchhHHHHHHhhhhhh
Q 022567 89 ESGSISDNQEKLAVGTKVQAVYSEDGEWYDATIEAITP-NG-YYVTYDSWGNKEEVDPANVRPVNLLVEAEKVAEATKLA 166 (295)
Q Consensus 89 ~~~~~~~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~-~~-~~V~F~~Ygn~e~V~~~~lrp~~~~~~~~~~~~~~~~~ 166 (295)
..-+.+.+...|.||++|+|.|++||.||.|+|+.|+. .+ +.|.|.+|++...+...++|++.....+
T Consensus 80 l~~~~~i~a~~w~vg~K~~A~~~ddg~~y~AtIe~ita~~~~~ai~f~s~~~a~~t~~a~lr~~e~~~s~---------- 149 (262)
T KOG3026|consen 80 LFYPSRITAVGWKVGDKVQAVFSDDGQIYDATIEHITAMEGTVAIIFASYGTAPSTYAARLRSPEEKSSA---------- 149 (262)
T ss_pred ccccccchhcccccCCEEEEeecCCCceEEeehhhccCCCCceeEEEeeccccccccHhhccCcchhhhh----------
Confidence 11223344558999999999999999999999999997 45 9999999999999999999987432111
Q ss_pred hhhhhhhhhhccccccCcCcccCCCCCCcHHHHHHHHHHHHHhhhhhhHHHHHHHHhHHhhhhHhHhhhcCccccccccc
Q 022567 167 IKRKIEQAAASDFQSKSLPAKLHINPDDPEDVKAAKRKKIHAFKSKMRFEQLEVTQNKRQNAWQQFQTTKGKTKKVGFFS 246 (295)
Q Consensus 167 ~k~~i~~aa~~~~~~~~~P~~l~i~p~d~e~~k~~k~KK~ka~Kk~~R~~ele~e~~~kkn~Wq~F~~Kk~kkkk~g~~~ 246 (295)
.+.....|-.+.+-|+++|..+.++|||+|++||+||+++||.+++..||+||+|++++.+++++|
T Consensus 150 -----------~~~~~n~P~~~k~~~~~pe~~~~~e~~k~~a~KKqQr~kele~~~e~~kn~WqqFntr~~kk~kvG--- 215 (262)
T KOG3026|consen 150 -----------AYTANNKPIQNKHVSTLPEISPIKERKKKKALKKQQRQKELEAEREASKNSWQQFNTRAVKKGKVG--- 215 (262)
T ss_pred -----------hcccCCCcchhccCCCCcccccccccccchhHHHHHHHHhHHHHHhhhhhHHHHHHHHhhhccccc---
Confidence 111223466667888999999999999999999999999999999999999999999988888887
Q ss_pred CCcccccccCCCCCCcceeeccCCCCCCccccccceeeccCCCccCCC
Q 022567 247 GRKRESIFKSPDDPYGKVGVTGSGKGLTDFQKREKHLHLKGGGIADTD 294 (295)
Q Consensus 247 g~kk~SiF~tPd~~~grVGv~GsGk~MT~~~~r~kh~~~~~~~~~~~~ 294 (295)
|+++.|||+|||++.|||||+|||+ ++.++.|.+|+|.+.|+.++++
T Consensus 216 g~k~~SIFkSped~~Grvgvg~~G~-ia~~~~~e~~~~~k~g~~d~l~ 262 (262)
T KOG3026|consen 216 GIKKSSIFKSPEDVPGRVGVGGCGN-IADSGMREKHIYNKRGDRDSLF 262 (262)
T ss_pred ceeeeccccCCCCCCcccCCCCccc-ccccccceehhhhhccccccCC
Confidence 8999999999999999999999999 9999999999999999887664
No 2
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=99.59 E-value=1.7e-15 Score=140.61 Aligned_cols=58 Identities=43% Similarity=0.733 Sum_probs=47.9
Q ss_pred CCCCCCCCCCeEEEEEcCCCcEEEEEEeeEeCC-c-eEEEEecCCCEEEEcCCCcccCCc
Q 022567 95 DNQEKLAVGTKVQAVYSEDGEWYDATIEAITPN-G-YYVTYDSWGNKEEVDPANVRPVNL 152 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~-~-~~V~F~~Ygn~e~V~~~~lrp~~~ 152 (295)
.+...|+|||.|+|+||+||+||+|+|++|+.+ + |+|+|++|||+|+|.+.+|+|+..
T Consensus 64 ~~~~~WkvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~f~gYgn~e~v~l~dL~~~~~ 123 (264)
T PF06003_consen 64 APNKKWKVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVVFTGYGNEEEVNLSDLKPSEG 123 (264)
T ss_dssp TTTT---TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEEETTTTEEEEEEGGGEEETT-
T ss_pred CcccCCCCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEEEcccCCeEeeehhhhccccc
Confidence 345689999999999999999999999999964 5 999999999999999999999854
No 3
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=99.54 E-value=9.7e-15 Score=100.72 Aligned_cols=47 Identities=40% Similarity=0.738 Sum_probs=44.1
Q ss_pred CCeEEEEEcCCCcEEEEEEeeEeCCc-eEEEEecCCCEEEEcCCCccc
Q 022567 103 GTKVQAVYSEDGEWYDATIEAITPNG-YYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 103 Gd~C~A~~s~Dg~wY~A~I~~i~~~~-~~V~F~~Ygn~e~V~~~~lrp 149 (295)
|+.|+|+|++||.||||+|.++..++ |.|.|+||||+++|+.++|||
T Consensus 1 G~~c~a~~~~d~~wyra~V~~~~~~~~~~V~f~DyG~~~~v~~~~l~~ 48 (48)
T cd04508 1 GDLCLAKYSDDGKWYRAKITSILSDGKVEVFFVDYGNTEVVPLSDLRP 48 (48)
T ss_pred CCEEEEEECCCCeEEEEEEEEECCCCcEEEEEEcCCCcEEEeHHHcCC
Confidence 78999999989999999999998666 999999999999999999885
No 4
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=99.51 E-value=2.6e-14 Score=101.97 Aligned_cols=53 Identities=42% Similarity=0.746 Sum_probs=49.6
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEeCCc-eEEEEecCCCEEEEcCCCcccCCc
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAITPNG-YYVTYDSWGNKEEVDPANVRPVNL 152 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~-~~V~F~~Ygn~e~V~~~~lrp~~~ 152 (295)
.|++|+.|+|+| .||.||||+|.++++++ |.|.|+|||+.++|+.++||+++.
T Consensus 2 ~~~~G~~~~a~~-~d~~wyra~I~~~~~~~~~~V~f~D~G~~~~v~~~~l~~l~~ 55 (57)
T smart00333 2 TFKVGDKVAARW-EDGEWYRARIIKVDGEQLYEVFFIDYGNEEVVPPSDLRPLPE 55 (57)
T ss_pred CCCCCCEEEEEe-CCCCEEEEEEEEECCCCEEEEEEECCCccEEEeHHHeecCCC
Confidence 489999999999 89999999999999756 999999999999999999999854
No 5
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=99.12 E-value=1.6e-10 Score=83.79 Aligned_cols=54 Identities=28% Similarity=0.521 Sum_probs=50.3
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEeCCc-eEEEEec--CCCEEEEcCCCcccCCc
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAITPNG-YYVTYDS--WGNKEEVDPANVRPVNL 152 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~-~~V~F~~--Ygn~e~V~~~~lrp~~~ 152 (295)
.|++|+.|.|.|+.||.||+|+|+++.++. |.|.|.+ +++.++|+..+|||+++
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~~~~~~V~~~~~~~~~~e~v~~~~LRp~~~ 58 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLGDGKYLVRYLTESEPLKETVDWSDLRPHPP 58 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECCCCEEEEEECCCCcccEEEEeHHHcccCCC
Confidence 489999999999889999999999999855 9999999 99999999999999854
No 6
>KOG4327 consensus mRNA splicing protein SMN (survival motor neuron) [RNA processing and modification]
Probab=98.98 E-value=4.6e-10 Score=98.55 Aligned_cols=56 Identities=38% Similarity=0.565 Sum_probs=50.7
Q ss_pred CCCCCCCCCCeEEEEEcCCCcEEEEEEeeEeC-Cc-eEEEEecCCCEEEEcCCCcccC
Q 022567 95 DNQEKLAVGTKVQAVYSEDGEWYDATIEAITP-NG-YYVTYDSWGNKEEVDPANVRPV 150 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~-~~-~~V~F~~Ygn~e~V~~~~lrp~ 150 (295)
.....|+||+.|+|.|++||.+|+|+|..|+. .+ |+|+|.+|||.++|.+.+|.+-
T Consensus 63 ~~~~~wKVgdkc~A~Y~e~g~~ypatidsi~~~~~tcvv~ylgygnr~Ev~lsDLl~~ 120 (218)
T KOG4327|consen 63 ASLQQWKVGDKCSAIYSEDGCIYPATIDSIDFKRETCVVVYLGYGNREEVNLSDLLSP 120 (218)
T ss_pred cchhhheecceeeeeeecCcccccceecccccccCceEEEEEeecchhhhhHHHhccc
Confidence 45578999999999999999999999999993 34 9999999999999999999875
No 7
>PF00567 TUDOR: Tudor domain; InterPro: IPR008191 There are multiple copies of this domain in the Drosophila melanogaster tudor protein and it has been identified in several RNA-binding proteins []. Although the function of this domain is unknown, in Drosophila melanogaster the tudor protein is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation [].; PDB: 3NTI_A 3NTK_B 3NTH_A 2DIQ_A 3FDR_A 3PNW_O 3S6W_A 3PMT_A 2WAC_A 2O4X_A ....
Probab=98.76 E-value=1.5e-08 Score=80.47 Aligned_cols=54 Identities=33% Similarity=0.548 Sum_probs=44.2
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEeCCc-eEEEEecCCCEEEEcCCCcccCCc
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAITPNG-YYVTYDSWGNKEEVDPANVRPVNL 152 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~-~~V~F~~Ygn~e~V~~~~lrp~~~ 152 (295)
.+.+|..|++.++.||.||||+|....+++ |.|.|+|||+++.|+.++|++++.
T Consensus 51 ~~~~~~~~~~~~~~~~~w~Ra~I~~~~~~~~~~V~~iD~G~~~~v~~~~l~~l~~ 105 (121)
T PF00567_consen 51 ESNPGEGCLCVVSEDGRWYRAVITVDIDENQYKVFLIDYGNTEKVSASDLRPLPP 105 (121)
T ss_dssp T--TTEEEEEEETTTSEEEEEEEEEEECTTEEEEEETTTTEEEEEEGGGEEE--H
T ss_pred ccccCCEEEEEEecCCceeeEEEEEecccceeEEEEEecCceEEEcHHHhhhhCH
Confidence 467899999999999999999994333555 999999999999999999999863
No 8
>PF09465 LBR_tudor: Lamin-B receptor of TUDOR domain; InterPro: IPR019023 The Lamin-B receptor is a chromatin and lamin binding protein in the inner nuclear membrane. It is one of the integral inner nuclear envelope membrane proteins responsible for targeting nuclear membranes to chromatin, being a downstream effector of Ran, a small Ras-like nuclear GTPase which regulates NE assembly. Lamin-B receptor interacts with importin beta, a Ran-binding protein, thereby directly contributing to the fusion of membrane vesicles and the formation of the nuclear envelope []. ; PDB: 2L8D_A 2DIG_A.
Probab=98.66 E-value=1.1e-07 Score=67.73 Aligned_cols=50 Identities=20% Similarity=0.490 Sum_probs=40.3
Q ss_pred CCCCCCCeEEEEEcCCCcEEEEEEeeEeCCc--eEEEEecCCCEEEEcCCCcc
Q 022567 98 EKLAVGTKVQAVYSEDGEWYDATIEAITPNG--YYVTYDSWGNKEEVDPANVR 148 (295)
Q Consensus 98 ~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~--~~V~F~~Ygn~e~V~~~~lr 148 (295)
..|..|+.|+++|.++..||+|+|++++... |.|.|.+ |+..+|+..||+
T Consensus 4 ~k~~~Ge~V~~rWP~s~lYYe~kV~~~d~~~~~y~V~Y~D-Gtel~lke~dik 55 (55)
T PF09465_consen 4 RKFAIGEVVMVRWPGSSLYYEGKVLSYDSKSDRYTVLYED-GTELELKENDIK 55 (55)
T ss_dssp SSS-SS-EEEEE-TTTS-EEEEEEEEEETTTTEEEEEETT-S-EEEEECCCEE
T ss_pred ccccCCCEEEEECCCCCcEEEEEEEEecccCceEEEEEcC-CCEEEecccccC
Confidence 5799999999999999999999999998643 9999999 888899988875
No 9
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=98.65 E-value=3.7e-08 Score=94.85 Aligned_cols=119 Identities=22% Similarity=0.229 Sum_probs=73.2
Q ss_pred HHHHHHHHHHHHHHhcc---CCCChhHHHHHHHHHHHHHHHHHHHHHhhhcccccc-----c-CCCCCCCCCcccccccc
Q 022567 16 LSTYKEQLQQVRELLVH---DPGNSEYADMEKELSEVIALTEELLATAKQNAISVS-----E-TGTSASASPNLLQSKEN 86 (295)
Q Consensus 16 L~~Yk~QL~qVe~aL~~---DP~N~ELl~Lk~dL~EvI~Lt~ell~~~~~~~~~~~-----~-~~~~~~~~P~~~~~~~~ 86 (295)
|++|+.||.+|+++|.. +.+..||+.|+.||.|+|+||+++++........+. . .+..+..+..-+.+...
T Consensus 1 lEny~aQll~veqaieq~~d~s~r~ellqlk~dl~ELlsLteellaaide~p~D~l~de~re~~~E~~D~~aag~~~~s~ 80 (486)
T KOG2185|consen 1 LENYDAQLLLVEQAIEQKEDLSSRDELLQLKPDLPELLSLTEELLAAIDEVPDDGLLDEKRERLLEEADIVAAGLNHDSG 80 (486)
T ss_pred CcchHHHHHHHHHHHHhhcchhHHHHHHHhCCcHHHHHHHHHHHHHhhhcCCCcchHHHHHHHHhhhhhhhhccccCCcc
Confidence 46899999999999964 677889999999999999999999987753221100 0 00000000000000000
Q ss_pred c--ccCCCCCCCCCCCCCCCeEEEEEcCCCcE-E--EEEEeeEeCCc-eEEEEec
Q 022567 87 K--TESGSISDNQEKLAVGTKVQAVYSEDGEW-Y--DATIEAITPNG-YYVTYDS 135 (295)
Q Consensus 87 ~--~~~~~~~~~~~~~kvGd~C~A~~s~Dg~w-Y--~A~I~~i~~~~-~~V~F~~ 135 (295)
. .+..+.......--+|.+|+|+|. ++.| | .|+|.++.+.. +.|.|..
T Consensus 81 t~p~~e~~e~~e~~~~L~GsKcsaph~-ss~gl~yHna~I~g~E~sarvRVlfl~ 134 (486)
T KOG2185|consen 81 TKPEHEEPEKTEEKKDLDGSKCSAPHT-SSRGLYYHNARIIGFEGSARVRVLFLT 134 (486)
T ss_pred cCcccccchhcchhhhccCCccccccc-CCccceecceeEEeeccccceEEEeec
Confidence 0 001111112233468999999994 3333 4 99999998665 9999863
No 10
>KOG2039 consensus Transcriptional coactivator p100 [Transcription]
Probab=98.64 E-value=3.3e-08 Score=105.10 Aligned_cols=56 Identities=29% Similarity=0.425 Sum_probs=51.3
Q ss_pred CCCCCCCCeEEEEEcCCCcEEEEEEeeEeC-CceEEEEecCCCEEEEcCCCcccCCc
Q 022567 97 QEKLAVGTKVQAVYSEDGEWYDATIEAITP-NGYYVTYDSWGNKEEVDPANVRPVNL 152 (295)
Q Consensus 97 ~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~-~~~~V~F~~Ygn~e~V~~~~lrp~~~ 152 (295)
....++|+.|+|+|+-||+||||.|.+|.+ ..+.|.|++|||+|+|++.+|+++++
T Consensus 693 ~~~p~~gd~c~A~y~~D~qwyRa~i~~V~~~~~~~V~yiDygn~E~lp~~~l~~lp~ 749 (875)
T KOG2039|consen 693 SYTPKRGDLCVAKYSLDGQWYRALIVEVLDPESMEVFYIDYGNIETLPFVRLKPLPP 749 (875)
T ss_pred CCCCCCCCeeeeeeccccceeeeeeeeeccCcceeEEEEecCcccccccccccCCCh
Confidence 346799999999999999999999999976 55999999999999999999999965
No 11
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=98.29 E-value=2e-06 Score=61.48 Aligned_cols=48 Identities=42% Similarity=0.867 Sum_probs=41.0
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeCC---c-eEEEEecCCCE--EEEcCCCcc
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITPN---G-YYVTYDSWGNK--EEVDPANVR 148 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~~---~-~~V~F~~Ygn~--e~V~~~~lr 148 (295)
+.||+.|+|.| .+|.||+|+|.++... . |.|.|.||+.+ |.|+.++|+
T Consensus 1 ~~vG~~v~~~~-~~~~~y~A~I~~~r~~~~~~~YyVHY~g~nkR~DeWV~~~~i~ 54 (55)
T PF11717_consen 1 FEVGEKVLCKY-KDGQWYEAKILDIREKNGEPEYYVHYQGWNKRLDEWVPESRIR 54 (55)
T ss_dssp --TTEEEEEEE-TTTEEEEEEEEEEEECTTCEEEEEEETTSTGCC-EEEETTTEE
T ss_pred CCcCCEEEEEE-CCCcEEEEEEEEEEecCCCEEEEEEcCCCCCCceeeecHHHcc
Confidence 47999999999 6999999999999832 2 99999999976 899999886
No 12
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=97.87 E-value=3.3e-05 Score=57.42 Aligned_cols=53 Identities=32% Similarity=0.534 Sum_probs=37.4
Q ss_pred CCCCCeEEEEEcC---CCcEEEEEEeeEeCC-ceEEEEecCC------C--EEEEcCCCcccCCc
Q 022567 100 LAVGTKVQAVYSE---DGEWYDATIEAITPN-GYYVTYDSWG------N--KEEVDPANVRPVNL 152 (295)
Q Consensus 100 ~kvGd~C~A~~s~---Dg~wY~A~I~~i~~~-~~~V~F~~Yg------n--~e~V~~~~lrp~~~ 152 (295)
|++|+.|....-. .|.||+|+|.+...+ .|.|.|.++. + .|+|....|||.++
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~~~~V~Y~~~~~~~~~~~~l~e~V~~~~iRP~pP 65 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDDKYLVEYDDLPDEDGESPPLKEWVDARRIRPCPP 65 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT-EEEEEETT-SS--------EEEEEGGGEEE---
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCcEEEEEECCcccccccccccEEEechheEECcCc
Confidence 5789999999744 378999999999988 5999996554 2 58999999999865
No 13
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=97.56 E-value=0.00016 Score=60.14 Aligned_cols=48 Identities=29% Similarity=0.531 Sum_probs=42.2
Q ss_pred CCeEEEEEcCCCcEEEEEEeeEeCCc-eEEEEecCCCEEEEcCCCcccCC
Q 022567 103 GTKVQAVYSEDGEWYDATIEAITPNG-YYVTYDSWGNKEEVDPANVRPVN 151 (295)
Q Consensus 103 Gd~C~A~~s~Dg~wY~A~I~~i~~~~-~~V~F~~Ygn~e~V~~~~lrp~~ 151 (295)
|..|+|+|..||.||+|+|.+....+ |.|.| ..+..+.|+..+|-++.
T Consensus 1 g~~VlAR~~~DG~YY~GtV~~~~~~~~~lV~f-~~~~~~~v~~~~iI~~~ 49 (124)
T PF15057_consen 1 GQKVLARREEDGFYYPGTVKKCVSSGQFLVEF-DDGDTQEVPISDIIALS 49 (124)
T ss_pred CCeEEEeeCCCCcEEeEEEEEccCCCEEEEEE-CCCCEEEeChHHeEEcc
Confidence 78999999999999999999988666 99999 67788889988887763
No 14
>KOG2185 consensus Predicted RNA-processing protein, contains G-patch domain [RNA processing and modification]
Probab=97.42 E-value=0.00032 Score=68.17 Aligned_cols=59 Identities=22% Similarity=0.237 Sum_probs=44.2
Q ss_pred CCCCCCCCCCCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcccC
Q 022567 91 GSISDNQEKLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRPV 150 (295)
Q Consensus 91 ~~~~~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp~ 150 (295)
.+++|..+.+.+|..|+|+. +|+.|..|+|++|+..-++|.|.--|....+..-|..++
T Consensus 172 ~yq~pD~s~L~~gs~vlak~-~sdiWh~ari~~vd~~~q~vkv~~~g~~~s~kegD~~~~ 230 (486)
T KOG2185|consen 172 NYQQPDWSQLMVGSKVLAKS-GSDIWHKARIESVDDELQVVKVVFRGDKSSAKEGDSLAL 230 (486)
T ss_pred cCCCccHHHHhhcCeeeeec-cchhhhhhheeeeccceeEEEEEeccchhhhhcccccCc
Confidence 35678888899999999995 699999999999975446666655565555555566555
No 15
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=97.40 E-value=0.00044 Score=57.01 Aligned_cols=49 Identities=22% Similarity=0.330 Sum_probs=35.8
Q ss_pred CCCCeEEEEEcCCCcEEEEEEeeEeCCc-eEEEEecCCCEEEEcCCCcccC
Q 022567 101 AVGTKVQAVYSEDGEWYDATIEAITPNG-YYVTYDSWGNKEEVDPANVRPV 150 (295)
Q Consensus 101 kvGd~C~A~~s~Dg~wY~A~I~~i~~~~-~~V~F~~Ygn~e~V~~~~lrp~ 150 (295)
-||-+|+|+||.++-||+++|..-..++ |.|.|.|- ..-.|...+|-..
T Consensus 4 ~iG~rV~AkWS~n~yyY~G~I~~~~~~~kykv~FdDG-~~~~v~~~div~~ 53 (122)
T PF09038_consen 4 FIGLRVFAKWSDNGYYYPGKITSDKGKNKYKVLFDDG-YECRVLGKDIVVC 53 (122)
T ss_dssp STT-EEEEESSTTSEEEEEEEEEEETTTEEEEEETTS--EEEEECCCEEEE
T ss_pred ccccEEEEEEccCCcccCceEeecCCCCeEEEEecCC-ccceeccCcEEEE
Confidence 4799999999966667999999865666 99999763 2335677776554
No 16
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=97.19 E-value=0.0012 Score=65.62 Aligned_cols=55 Identities=24% Similarity=0.356 Sum_probs=47.6
Q ss_pred CCCCCCCCCCeEEEEEcCCCcEEEEEEeeEeC-C-------ceEEEEecCCCE--EEEcCCCccc
Q 022567 95 DNQEKLAVGTKVQAVYSEDGEWYDATIEAITP-N-------GYYVTYDSWGNK--EEVDPANVRP 149 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~-~-------~~~V~F~~Ygn~--e~V~~~~lrp 149 (295)
.....+.||++|+|.|+.||.||.|+|.++.. . .|.|.|.+++.+ |.|+.++|..
T Consensus 49 ~~~~~~~VGekVla~~~~Dg~~~~A~VI~~R~~~~~~~~~~~YYVHY~g~nrRlDEWV~~~rLdl 113 (450)
T PLN00104 49 GVMLPLEVGTRVMCRWRFDGKYHPVKVIERRRGGSGGPNDYEYYVHYTEFNRRLDEWVKLEQLDL 113 (450)
T ss_pred CccceeccCCEEEEEECCCCCEEEEEEEEEeccCCCCCCCceEEEEEecCCccHhhccCHhhccc
Confidence 44567999999999998899999999999884 1 299999999998 8999998864
No 17
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=97.18 E-value=0.00052 Score=57.04 Aligned_cols=55 Identities=25% Similarity=0.366 Sum_probs=43.5
Q ss_pred CCCCCCCCeEEEEE-cCCCcEEEEEEee-----EeCCc-eEEEEecCCCEEEEcCCCcccCCc
Q 022567 97 QEKLAVGTKVQAVY-SEDGEWYDATIEA-----ITPNG-YYVTYDSWGNKEEVDPANVRPVNL 152 (295)
Q Consensus 97 ~~~~kvGd~C~A~~-s~Dg~wY~A~I~~-----i~~~~-~~V~F~~Ygn~e~V~~~~lrp~~~ 152 (295)
...+++||.|+|+| ..+..|+||+|.. ...+. |+|.|.+ |.+..|+...+..+++
T Consensus 53 ~~~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~n-g~~~~vp~~~~~~I~~ 114 (124)
T PF15057_consen 53 RHSLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFYN-GKTAKVPRGEVIWISP 114 (124)
T ss_pred cCcCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEEC-CCCCccchhhEEECCH
Confidence 56799999999999 5567799999997 44455 9999954 3347888888888854
No 18
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=95.85 E-value=0.017 Score=48.49 Aligned_cols=54 Identities=28% Similarity=0.427 Sum_probs=36.3
Q ss_pred CCCCCCCCCCeEEEEEcCCCcEEEEEEeeEe--CCc-eEEEEecCCCE---EEEcCCCcc
Q 022567 95 DNQEKLAVGTKVQAVYSEDGEWYDATIEAIT--PNG-YYVTYDSWGNK---EEVDPANVR 148 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~--~~~-~~V~F~~Ygn~---e~V~~~~lr 148 (295)
.....|..|+.|||+|-+==.||+|+|.+.. ..+ |.|.|.|-... ..|+...+-
T Consensus 67 ~~~~~f~~g~~VLAlYP~TT~FY~A~V~~~p~~~~~~y~l~Fedd~~~~~~~~V~~r~Vv 126 (130)
T PF07039_consen 67 DPLAEFPKGTKVLALYPDTTCFYPATVVSPPKKKSGEYKLKFEDDEDADGYREVPQRYVV 126 (130)
T ss_dssp -GGGS--TT-EEEEE-TTSSEEEEEEEEEE-SSTTS-EEEEECTTTSTTSBEEE-GGGEE
T ss_pred CchhhCCCCCEEEEECCCCceEEEEEEEeCCCCCCCcEEEEEeCCCCcCCcEEEccceEE
Confidence 3456799999999999766889999999983 445 99999997764 355544443
No 19
>cd05834 HDGF_related The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, HPR2, HPR3, HPR4, respectively) and lens epithelium-derived growth factor, LEDGF. Members of the HDGF family have been linked to human diseases, and HDGF is a prognostic factor in several types of cancer. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=95.64 E-value=0.021 Score=44.17 Aligned_cols=53 Identities=15% Similarity=0.139 Sum_probs=45.2
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEeC----Cc-eEEEEecCCCEEEEcCCCcccCCc
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAITP----NG-YYVTYDSWGNKEEVDPANVRPVNL 152 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~~----~~-~~V~F~~Ygn~e~V~~~~lrp~~~ 152 (295)
.+++||.|.|+.. .--|.||+|..... .+ |.|.|.|.++...|+..+|.|+..
T Consensus 2 ~f~~GdlVwaK~k-Gyp~WPa~I~~~~~~~~~~~~~~V~FfGt~~~a~v~~~~l~pf~~ 59 (83)
T cd05834 2 QFKAGDLVFAKVK-GYPAWPARVDEPEDWKPPGKKYPVYFFGTHETAFLKPEDLFPYTE 59 (83)
T ss_pred CCCCCCEEEEecC-CCCCCCEEEecccccCCCCCEEEEEEeCCCCEeEECHHHceeccc
Confidence 4899999999985 45677999998874 34 999999988889999999999853
No 20
>PF00855 PWWP: PWWP domain; InterPro: IPR000313 Upon characterisation of WHSC1, a gene mapping to the Wolf-Hirschhornsyndrome critical region and at its C terminus similar to the Drosophila melanogaster ASH1/trithorax group proteins, a novel protein domain designated PWWP domain was identified []. The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. It is present in proteins of nuclear origin and plays a role in cell growth and differentiation. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present it has been suggested that the domain is involved in protein-protein interactions [].; PDB: 3LYI_B 2L89_A 2NLU_A 1RI0_A 1KHC_A 3QKJ_C 2DAQ_A 1N27_A 3PFS_B 3QJ6_A ....
Probab=95.31 E-value=0.037 Score=42.04 Aligned_cols=51 Identities=22% Similarity=0.337 Sum_probs=42.2
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeC-------Cc-eEEEEecCCCEEEEcCCCcccCC
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITP-------NG-YYVTYDSWGNKEEVDPANVRPVN 151 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~-------~~-~~V~F~~Ygn~e~V~~~~lrp~~ 151 (295)
|.+||.|.|+.. .--|.||+|..... .+ |.|.|.|-.+...|+.++|+|+.
T Consensus 1 f~~GdlVWaK~~-g~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg~~~~~wv~~~~i~~f~ 59 (86)
T PF00855_consen 1 FRPGDLVWAKLK-GYPWWPARVCDPDEKSKKKRKDGHVLVRFFGDNDYAWVKPSNIKPFS 59 (86)
T ss_dssp -STTEEEEEEET-TSEEEEEEEEECCHCTSCSSSSTEEEEEETTTTEEEEEEGGGEEECC
T ss_pred CCCCCEEEEEeC-CCCCCceEEeecccccccCCCCCEEEEEecCCCCEEEECHHHhhChh
Confidence 578999999995 55699999998852 34 99999887777899999999985
No 21
>cd05162 PWWP The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes. The function of the PWWP domain is still not known precisely; however, based on the fact that other regions of PWWP-domain proteins are responsible for nuclear localization and DNA-binding, is likely that the PWWP domain acts as a site for protein-protein binding interactions, influencing chromatin remodeling and thereby regulating transcriptional processes. Some PWWP-domain proteins have been linked to cancer or other diseases; some are known to function as growth factors.
Probab=95.28 E-value=0.038 Score=42.50 Aligned_cols=52 Identities=17% Similarity=0.179 Sum_probs=43.0
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeC----------Cc-eEEEEecCCCEEEEcCCCcccCCc
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITP----------NG-YYVTYDSWGNKEEVDPANVRPVNL 152 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~----------~~-~~V~F~~Ygn~e~V~~~~lrp~~~ 152 (295)
|++||.|.|++. .--|+||+|..... .+ |.|.|.|=.+...|+.++|.|+..
T Consensus 1 f~~GdlVwaK~~-g~pwWPa~V~~~~~~~~~~~~~~~~~~~~V~Ffg~~~~~wv~~~~l~pf~~ 63 (87)
T cd05162 1 FRPGDLVWAKMK-GYPWWPALVVDPPKDSKKAKKKAKEGKVLVLFFGDKTFAWVGAERLKPFTE 63 (87)
T ss_pred CCCCCEEEEeCC-CCCCCCEEEccccccchhhhccCCCCEEEEEEeCCCcEEEeCccceeeccc
Confidence 578999999996 34688999998874 24 999998866668999999999854
No 22
>PF12148 DUF3590: Protein of unknown function (DUF3590); InterPro: IPR021991 This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with PF00097 from PFAM, PF02182 from PFAM, PF00628 from PFAM, PF00240 from PFAM. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed. ; PDB: 3DB4_A 3ASK_A 3DB3_A 2L3R_A.
Probab=95.13 E-value=0.034 Score=43.30 Aligned_cols=46 Identities=30% Similarity=0.613 Sum_probs=33.5
Q ss_pred EEEEEcCCCcEEEEEEeeEeC------Cc--eEEEEecCCCE--EEEcCCCcccCC
Q 022567 106 VQAVYSEDGEWYDATIEAITP------NG--YYVTYDSWGNK--EEVDPANVRPVN 151 (295)
Q Consensus 106 C~A~~s~Dg~wY~A~I~~i~~------~~--~~V~F~~Ygn~--e~V~~~~lrp~~ 151 (295)
+=|+-...|.|+.|.|..|+. +. |.|+|++|.+. ..|+..+|||..
T Consensus 2 vD~~d~~~gAWfEa~i~~i~~~~~~~~e~viYhIkyddype~gvv~~~~~~iRpRA 57 (85)
T PF12148_consen 2 VDARDRNMGAWFEAQIVTITKKCMSDDEDVIYHIKYDDYPENGVVEMRSKDIRPRA 57 (85)
T ss_dssp EEEE-TTT-EEEEEEEEEEEES-SSSSTTEEEEEEETT-GGG-EEEEEGGGEEE--
T ss_pred cccccCCCcceEEEEEEEeeccCCCCCCCEEEEEEeccCCCcCceeccccccccee
Confidence 346666789999999999982 23 99999999954 678899999973
No 23
>cd06080 MUM1_like Mutated melanoma-associated antigen 1 (MUM-1) is a melanoma-associated antigen (MAA). MUM-1 belongs to the mutated or aberrantly expressed type of MAAs, along with antigens such as CDK4, beta-catenin, gp100-in4, p15, and N-acetylglucosaminyltransferase V. It is highly expressed in several types of human cancers. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=95.05 E-value=0.045 Score=42.20 Aligned_cols=51 Identities=18% Similarity=0.138 Sum_probs=42.3
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeC-Cc-eEEEEecCC-CEEEEcCCCcccCC
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITP-NG-YYVTYDSWG-NKEEVDPANVRPVN 151 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~-~~-~~V~F~~Yg-n~e~V~~~~lrp~~ 151 (295)
|.+||.|-|+.. .--|.||+|.++.. .+ |.|.|.|=+ +...+..++|+|..
T Consensus 1 f~~gdlVWaK~~-g~P~WPa~I~~~~~~~~k~~V~FfG~~~~~a~~~~~~l~p~~ 54 (80)
T cd06080 1 FEKNDLVWAKIQ-GYPWWPAVIKSISRKKQKARVNFIGDNMQSEKKGIRVVKRWL 54 (80)
T ss_pred CCCCCEEEEeCC-CCCCCCEEEeeecCCCCEEEEEEeCCCCceeccchhhccccc
Confidence 578999999986 45677999999984 34 999999877 66888999998863
No 24
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=94.97 E-value=0.062 Score=39.13 Aligned_cols=50 Identities=16% Similarity=0.220 Sum_probs=41.0
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeC-----------Cc-eEEEEecCCCEEEEcCCCcccC
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITP-----------NG-YYVTYDSWGNKEEVDPANVRPV 150 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~-----------~~-~~V~F~~Ygn~e~V~~~~lrp~ 150 (295)
+++||.|.|+.. .--|.||+|..-.. .+ |.|.|.|=++...|+.++|+|+
T Consensus 1 f~~GdlVwaK~~-G~p~WPa~V~~~~~~~~~~~~~~~~~~~~~V~Ffg~~~~awv~~~~l~p~ 62 (63)
T smart00293 1 FKPGDLVWAKMK-GFPWWPALVVSPKETPDNIRKRKRFENLYPVLFFGDKDTAWISSSKLFPL 62 (63)
T ss_pred CCCCCEEEEECC-CCCCCCeEEcCcccCChhHhhccCCCCEEEEEEeCCCCEEEECccceeeC
Confidence 578999999985 34688999986641 34 9999988888889999999986
No 25
>cd05841 BS69_related The PWWP domain is part of BS69 protein, a nuclear protein that specifically binds adenoviral E1A and Epstein-Barr viral EBNA2 proteins, suppressing their transactivation functions. BS69 is a multi-domain protein, containing bromo, PHD, PWWP, and MYND domains. The specific role of the PWWP domain within BS69 is not clearly identified, but BS69 functions in chromatin remodeling, consistent with other PWWP-containing proteins. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=94.65 E-value=0.065 Score=41.62 Aligned_cols=52 Identities=13% Similarity=0.139 Sum_probs=43.5
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEec-CCCEEEEcCCCcccCCc
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDS-WGNKEEVDPANVRPVNL 152 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~-Ygn~e~V~~~~lrp~~~ 152 (295)
.++||.|.|+..+ =-|.||+|...+++.|.|.|-| -.++..|+..+|.|+..
T Consensus 7 ~~p~dLVwAK~kG-yp~WPAkV~~~~~~~~~V~FFG~t~~~a~v~~~~i~~~~~ 59 (83)
T cd05841 7 RPPHELVWAKLKG-FPYWPAKVMRVEDNQVDVRFFGGQHDRAWIPSNNIQPIST 59 (83)
T ss_pred CCCCCEEEEeCCC-CCCCCEEEeecCCCeEEEEEcCCCCCeEEEehHHeeehhh
Confidence 5789999999964 3456999999876669999988 77889999999999843
No 26
>smart00561 MBT Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. Present in Drosophila Scm, l(3)mbt, and vertebrate SCML2. These proteins are involved in transcriptional regulation.
Probab=93.27 E-value=0.44 Score=37.82 Aligned_cols=56 Identities=23% Similarity=0.395 Sum_probs=43.5
Q ss_pred CCCCCCCCCCeEEEEEcCC-CcEEEEEEeeEeCCceEEEEecCCCE--EE--EcCCCcccC
Q 022567 95 DNQEKLAVGTKVQAVYSED-GEWYDATIEAITPNGYYVTYDSWGNK--EE--VDPANVRPV 150 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~D-g~wY~A~I~~i~~~~~~V~F~~Ygn~--e~--V~~~~lrp~ 150 (295)
+....|++|.++.|.-..+ ..+..|+|.+|.+..+.|.|+|+++. .. +.-.+|+|+
T Consensus 23 ~~~~~F~vGmkLEavD~~~~~~i~vAtV~~v~g~~l~v~~dg~~~~~D~W~~~~S~~I~Pv 83 (96)
T smart00561 23 SPPNGFKVGMKLEAVDPRNPSLICVATVVEVKGYRLLLHFDGWDDKYDFWCDADSPDIHPV 83 (96)
T ss_pred CccCcccCCCEEEEECCCCCceEEEEEEEEEECCEEEEEEccCCCcCCEEEECCCCCcccC
Confidence 4456799999999996322 56889999999865699999999877 44 444577776
No 27
>cd05836 N_Pac_NP60 The PWWP domain is an essential part of the cytokine-like nuclear factor n-pac protein, or NP60, which enhances the activity of MAP2K4 and MAP2K6 kinases to phosphorylate p38-alpha. In a variety of cell lines, NP60 has been shown to localize to the nucleus. In addition to the PWWP domain, NP60 also contains an AT-hook and a C-terminal NAD-binding domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
Probab=92.50 E-value=0.22 Score=38.64 Aligned_cols=52 Identities=17% Similarity=0.172 Sum_probs=42.3
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEe-------C-Cc-eEEEEecCCCEEEEcCCCcccCCc
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAIT-------P-NG-YYVTYDSWGNKEEVDPANVRPVNL 152 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~-------~-~~-~~V~F~~Ygn~e~V~~~~lrp~~~ 152 (295)
+++||.|.|+.. .--|.||+|.... . .+ |.|.|.|-++...|...+|.|...
T Consensus 1 f~~GDlVwaK~~-g~P~WPa~V~~~~~~~~~~~~~~~~~~V~FFG~~~~~wv~~~~l~pF~~ 61 (86)
T cd05836 1 LKLGDLVWAKMK-GFPPWPGRIVKPPKDLKKPRGKAKCFFVFFFGSENHAWIKEENIKPYHE 61 (86)
T ss_pred CCCCCEEEEeCC-CCCCCCEEEechhhhcccccCCCCeEEEEEeCCCCEEEECHHhCeechh
Confidence 579999999986 4557799998643 1 24 999999988889999999999843
No 28
>KOG1150 consensus Predicted molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=92.23 E-value=0.2 Score=45.07 Aligned_cols=53 Identities=26% Similarity=0.540 Sum_probs=30.8
Q ss_pred HHHHHHHHH----hhhhhhHHHHHHH----------------HhHHhhhhHhHhhhcCcccccccccCCcccccccCC
Q 022567 200 AAKRKKIHA----FKSKMRFEQLEVT----------------QNKRQNAWQQFQTTKGKTKKVGFFSGRKRESIFKSP 257 (295)
Q Consensus 200 ~~k~KK~ka----~Kk~~R~~ele~e----------------~~~kkn~Wq~F~~Kk~kkkk~g~~~g~kk~SiF~tP 257 (295)
+++|++.-+ .++.+|..+++.+ +..+-++|++|+++.+ |++. +++-.-+|+-|
T Consensus 171 erkRk~~e~r~~~eRkr~re~eIeaeek~Kr~~E~qKnfEEsRd~Rv~sWrnFq~~t~-K~kk----~Kknk~~~~pP 243 (250)
T KOG1150|consen 171 ERKRKELEARANEERKRQREEEIEAEEKRKREREWQKNFEESRDGRVGSWRNFQAKTK-KGKK----EKKNKTFLRPP 243 (250)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHhcccccchHHHHHHhhh-cchh----hhhcccccCCC
Confidence 445554422 4566666666654 3345679999999643 3332 33445677755
No 29
>cd05840 SPBC215_ISWI_like The PWWP domain is a component of the S. pombe hypothetical protein SPBC215, as well as ISWI complex protein 4. The ISWI (imitation switch) proteins are ATPases responsible for chromatin remodeling in eukaryotes, and SPBC215 is proposed to also bind chromatin. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=91.79 E-value=0.33 Score=38.33 Aligned_cols=51 Identities=18% Similarity=0.168 Sum_probs=41.2
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEe-------------CCc-eEEEEecCCCEEEEcCCCcccCC
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAIT-------------PNG-YYVTYDSWGNKEEVDPANVRPVN 151 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~-------------~~~-~~V~F~~Ygn~e~V~~~~lrp~~ 151 (295)
|++||.|.|+-. .--|.||+|..-. ..+ |.|.|.+=++.-.|...+|.|+.
T Consensus 1 f~~GDlVwaK~~-GyPwWPA~V~~~~~~p~~~l~~~~~~~~~~~~V~FFg~~~~~Wv~~~~l~pl~ 65 (93)
T cd05840 1 FQPGDRVLAKVK-GFPAWPAIVVPEEMLPDSVLKGKKKKNKRTYPVMFFPDGDYYWVPNKDLKPLT 65 (93)
T ss_pred CCCCCEEEEeCC-CCCCCCEEECChHHCCHHHHhcccCCCCCeEEEEEeCCCcEEEEChhhcccCC
Confidence 578999999985 4568899997621 234 99999887777899999999995
No 30
>PF14853 Fis1_TPR_C: Fis1 C-terminal tetratricopeptide repeat; PDB: 1IYG_A 1PC2_A 1NZN_A 3UUX_C 1Y8M_A 2PQR_A 2PQN_A 3O48_A.
Probab=91.75 E-value=0.29 Score=34.68 Aligned_cols=38 Identities=18% Similarity=0.338 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHH
Q 022567 14 SNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIA 51 (295)
Q Consensus 14 ~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~ 51 (295)
-.|.+|..-+.-|+.+|..+|+|..-+.|+.-+++-|.
T Consensus 12 ykl~~Y~~A~~~~~~lL~~eP~N~Qa~~L~~~i~~~i~ 49 (53)
T PF14853_consen 12 YKLGEYEKARRYCDALLEIEPDNRQAQSLKELIEDKIQ 49 (53)
T ss_dssp HHTT-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHH
T ss_pred HHhhhHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHHh
Confidence 46778999999999999999999999999998887764
No 31
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=91.50 E-value=0.37 Score=40.52 Aligned_cols=42 Identities=19% Similarity=0.271 Sum_probs=33.8
Q ss_pred EEE-cCCCcEEEEEEeeEeCCc--eEEEEecCCCEEEEcCCCcccCC
Q 022567 108 AVY-SEDGEWYDATIEAITPNG--YYVTYDSWGNKEEVDPANVRPVN 151 (295)
Q Consensus 108 A~~-s~Dg~wY~A~I~~i~~~~--~~V~F~~Ygn~e~V~~~~lrp~~ 151 (295)
|.| .-+-.||||+|.+...+. |.|.|.+.. ..|...+|+.+.
T Consensus 15 avW~~~~~~yYPa~~~~~~~~~~~~~V~Fedg~--~~i~~~dv~~LD 59 (131)
T PF08605_consen 15 AVWAGYNLKYYPATCVGSGVDRDRSLVRFEDGT--YEIKNEDVKYLD 59 (131)
T ss_pred ceeecCCCeEeeEEEEeecCCCCeEEEEEecCc--eEeCcccEeeee
Confidence 444 227899999999997554 999999977 788889898874
No 32
>cd05835 Dnmt3b_related The PWWP domain is an essential component of DNA methyltransferase 3 B (Dnmt3b) which is responsible for establishing DNA methylation patterns during embryogenesis and gametogenesis. In tumorigenesis, DNA methylation by Dnmt3b is known to play a role in the inactivation of tumor suppressor genes. In addition, a point mutation in the PWWP domain of Dnmt3b has been identified in patients with ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies), a rare autosomal recessive disorder characterized by hypomethylation of classical satellite DNA. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=91.24 E-value=0.25 Score=38.35 Aligned_cols=51 Identities=25% Similarity=0.371 Sum_probs=41.4
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeC-------Cc-eEEEEecCCCEEEEcCCCcccCC
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITP-------NG-YYVTYDSWGNKEEVDPANVRPVN 151 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~-------~~-~~V~F~~Ygn~e~V~~~~lrp~~ 151 (295)
+.+||.|-|+-.+ --|.||+|..... .+ +.|.|-|-++...|..++|.|..
T Consensus 1 f~vGDlVWaK~kg-~pwWP~~V~~~~~~~~~~~~~~~~~V~fFGs~~~a~v~~~~l~pf~ 59 (87)
T cd05835 1 FNVGDLVWGKIKG-FPWWPGRVVSITVTSKRPPVVGMRWVTWFGSGTFSEVSVDKLSPFS 59 (87)
T ss_pred CCCCCEEEEecCC-CCCCCeEEechhhcccccCCCCeEEEEEeCCCCEeEECHHHCcChh
Confidence 5789999999853 4477999998753 23 99999887777899999999984
No 33
>KOG3038 consensus Histone acetyltransferase SAGA associated factor SGF29 [General function prediction only]
Probab=90.73 E-value=0.47 Score=44.01 Aligned_cols=44 Identities=27% Similarity=0.421 Sum_probs=36.2
Q ss_pred CCCCCCCCCCCCCeEEEEEcCCCcEEEEEEeeEeCC--c-eEEEEec
Q 022567 92 SISDNQEKLAVGTKVQAVYSEDGEWYDATIEAITPN--G-YYVTYDS 135 (295)
Q Consensus 92 ~~~~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~--~-~~V~F~~ 135 (295)
..+++...|.+|..|+|+|-+-=+||+|+|.+--.+ + |.|.|.|
T Consensus 191 p~p~p~~~fpp~~~VLA~YP~TTcFY~aiVh~tp~d~s~~y~vlffD 237 (264)
T KOG3038|consen 191 PIPPPTALFPPGTIVLAVYPGTTCFYKAIVHSTPRDGSCDYYVLFFD 237 (264)
T ss_pred CCCCCccCCCCCCEEEEEcCCcceeeeeEeecCCCCCCCcceeeeec
Confidence 356677889999999999988889999999987644 3 8888854
No 34
>cd05838 WHSC1_related The PWWP domain was first identified in the WHSC1 (Wolf-Hirschhorn syndrome candidate 1) protein, a protein implicated in Wolf-Hirschhorn syndrome (WHS). When translocated, WHSC1 plays a role in lymphoid multiple myeloma (MM) disease, also known as plasmacytoma. WHCS1 proteins typically contain two copies of the PWWP domain. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding, proteins that function as transcription factors regulating a variety of developmental processes.
Probab=89.10 E-value=0.79 Score=36.20 Aligned_cols=50 Identities=22% Similarity=0.174 Sum_probs=41.6
Q ss_pred CCCCeEEEEEcCCCcEEEEEEeeEe-----------CCc-eEEEEecCCCEEEEcCCCcccCC
Q 022567 101 AVGTKVQAVYSEDGEWYDATIEAIT-----------PNG-YYVTYDSWGNKEEVDPANVRPVN 151 (295)
Q Consensus 101 kvGd~C~A~~s~Dg~wY~A~I~~i~-----------~~~-~~V~F~~Ygn~e~V~~~~lrp~~ 151 (295)
.+||.|.|++.+ --|.||+|..-. ..+ |.|.|-|..+...|...+|.|..
T Consensus 2 ~~GdlVWaK~~g-~pwWPa~V~~~~~~p~~~~~~~~~~~~~~V~Ffgs~~y~Wv~~~~l~pf~ 63 (95)
T cd05838 2 LYGDIVWAKLGN-FRWWPAIICDPREVPPNIQVLRHCIGEFCVMFFGTHDYYWVHRGRVFPYQ 63 (95)
T ss_pred CcCCEEEEECCC-CCCCCeEEcChhhcChhHhhccCCCCeEEEEEeCCCCEEEeccccccchh
Confidence 689999999964 678899998632 124 99999999899999999999984
No 35
>cd05837 MSH6_like The PWWP domain is present in MSH6, a mismatch repair protein homologous to bacterial MutS. The PWWP domain of histone-lysine N-methyltransferase, also known as Nuclear SET domain-containing protein 3, is also included. Mutations in MSH6 have been linked to increased cancer susceptibility, particularly in hereditary nonpolyposis colorectal cancer in humans. The role of the PWWP domain in MSH6 is not clear; MSH6 orthologs found in S. cerevisiae, Caenorhabditis elegans and Arabidopsis thaliana lack the PWWP domain. Histone methyltransferases (HMTases) induce the posttranslational methylation of lysine residues in histones and play a role in apoptosis. In the HMTase Whistle, the PWWP domain is necessary for HMTase activity. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain pro
Probab=88.65 E-value=0.68 Score=37.52 Aligned_cols=53 Identities=19% Similarity=0.229 Sum_probs=41.9
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEe-------------CCc-eEEEEecC-CCEEEEcCCCcccCCc
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAIT-------------PNG-YYVTYDSW-GNKEEVDPANVRPVNL 152 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~-------------~~~-~~V~F~~Y-gn~e~V~~~~lrp~~~ 152 (295)
.|.+||.|-|+.. ---|+||+|..-. ..+ |.|.|.|- ++...|+..+|.|+..
T Consensus 2 ~~~~GdlVWaK~~-g~PwWPa~V~~~~~~~~~~~~~~~~~~~~~~~V~FFG~~~~~aWv~~~~l~pf~~ 69 (110)
T cd05837 2 KYQVGDLVWAKVS-GYPWWPCMVCSDPLLGTYTKTKRNKRKPRQYHVQFFGDNPERAWISEKSLKPFKG 69 (110)
T ss_pred CCCCCCEEEEeCC-CCCCCCEEEecccccchhhhhhhccCCCCeEEEEEcCCCCCEEEecHHHccccCC
Confidence 4899999999986 3569999999521 124 99999875 4678999999999954
No 36
>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins. The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.
Probab=86.36 E-value=1.8 Score=34.91 Aligned_cols=46 Identities=28% Similarity=0.352 Sum_probs=41.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHH
Q 022567 8 SIEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALT 53 (295)
Q Consensus 8 s~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt 53 (295)
.++.|++.+......|++||.-|..=|+..++..|+-+|.++=--.
T Consensus 36 ~~~~l~~~~~~~~~Rl~~lE~~l~~LPt~~dv~~L~l~l~el~G~~ 81 (106)
T PF10805_consen 36 DIEKLEERLDEHDRRLQALETKLEHLPTRDDVHDLQLELAELRGEL 81 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHhHH
Confidence 3678999999999999999999999999999999999998875333
No 37
>KOG3364 consensus Membrane protein involved in organellar division [Cell wall/membrane/envelope biogenesis]
Probab=78.41 E-value=4.8 Score=34.40 Aligned_cols=37 Identities=24% Similarity=0.477 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHH
Q 022567 14 SNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVI 50 (295)
Q Consensus 14 ~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI 50 (295)
..|.+|..-|.-|..+|..+|+|.+-+.||+-++.-|
T Consensus 82 yRlkeY~~s~~yvd~ll~~e~~n~Qa~~Lk~~ied~i 118 (149)
T KOG3364|consen 82 YRLKEYSKSLRYVDALLETEPNNRQALELKETIEDKI 118 (149)
T ss_pred HHHhhHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHH
Confidence 6789999999999999999999999999998887765
No 38
>KOG0644 consensus Uncharacterized conserved protein, contains WD40 repeat and BROMO domains [General function prediction only]
Probab=77.08 E-value=3.2 Score=44.60 Aligned_cols=39 Identities=31% Similarity=0.698 Sum_probs=31.1
Q ss_pred CCCCCCCCeEEEEE----cCCCcEEEEEEeeEeC-------Cc---eEEEEec
Q 022567 97 QEKLAVGTKVQAVY----SEDGEWYDATIEAITP-------NG---YYVTYDS 135 (295)
Q Consensus 97 ~~~~kvGd~C~A~~----s~Dg~wY~A~I~~i~~-------~~---~~V~F~~ 135 (295)
..+|+.+|+|...| -+||.|+.++|.++.. .. |.|+|+.
T Consensus 976 QrnW~~~d~crvwwrda~~e~g~WWeG~ils~~pksp~fpdSpwery~v~~~~ 1028 (1113)
T KOG0644|consen 976 QRNWTCRDKCRVWWRDAGEEDGAWWEGRILSVKPKSPDFPDSPWERYIVRYDN 1028 (1113)
T ss_pred hhccccccceeEEEccCCCcCCceeeeeeeeccCCCCCCCCCcceeEEEEecC
Confidence 36899999999999 3468899999999872 22 7888753
No 39
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=76.78 E-value=38 Score=27.44 Aligned_cols=36 Identities=17% Similarity=0.365 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVI 50 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI 50 (295)
+++|.+.++.|+.|++.+.+.+ .+|.....++..++
T Consensus 1 ~qql~~q~~ql~~~i~~l~~~i------~~l~~~i~e~~~~~ 36 (126)
T TIGR00293 1 LQQLAAELQILQQQVESLQAQI------AALRALIAELETAI 36 (126)
T ss_pred CHhHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHH
Confidence 3577888889999988888777 34555555554444
No 40
>KOG1904 consensus Transcription coactivator [Transcription]
Probab=76.06 E-value=2.5 Score=42.90 Aligned_cols=55 Identities=18% Similarity=0.216 Sum_probs=45.2
Q ss_pred CCCCCCCCCeEEEEEcCCCcEEEEEEeeEeCC------c-eEEEEecCCCEEEEcCCCcccCC
Q 022567 96 NQEKLAVGTKVQAVYSEDGEWYDATIEAITPN------G-YYVTYDSWGNKEEVDPANVRPVN 151 (295)
Q Consensus 96 ~~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~------~-~~V~F~~Ygn~e~V~~~~lrp~~ 151 (295)
..+.+++||.|+|+-.+=--| +|+|....+. . |.|.|.|-..+..|...+|.|..
T Consensus 9 ~~~~~~~GDLV~AKlkgyp~W-ParI~~~~~~~~kp~pkky~V~FfGT~e~Afl~p~dlqpy~ 70 (496)
T KOG1904|consen 9 AAGNFKCGDLVFAKLKGYPPW-PARIRNGPDGAVKPPPKKYTVFFFGTKETAFLKPKDLQPYM 70 (496)
T ss_pred ccCCCCCCceeeecccCCCCC-cccccCcccccccCCCceeEEEEeccCcccccchhhccchh
Confidence 346799999999998655556 9999877644 4 99999888888899999999974
No 41
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=75.81 E-value=41 Score=27.35 Aligned_cols=39 Identities=15% Similarity=0.300 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHH
Q 022567 10 EELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTE 54 (295)
Q Consensus 10 e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ 54 (295)
++|...++.|+.+++.+.+.+ ..|..-..|+..+|+..+
T Consensus 2 ~~l~~~~~~l~~~i~~l~~~~------~~l~~~~~e~~~~~~~l~ 40 (129)
T cd00584 2 EQLAAQLQVLQQEIEELQQEL------ARLNEAIAEYEQAKETLE 40 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHH
Confidence 567888888888888888776 235555555555554444
No 42
>PRK04098 sec-independent translocase; Provisional
Probab=75.55 E-value=6.2 Score=34.25 Aligned_cols=59 Identities=24% Similarity=0.313 Sum_probs=50.0
Q ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHHhhh
Q 022567 4 GEELSIEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLATAKQ 62 (295)
Q Consensus 4 ~e~~s~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~~~ 62 (295)
++++.+++|..++..|+.+|++....|..+-+=+||..+..++.+.+.-..+++...+.
T Consensus 51 ~~Ei~~~elk~e~~k~k~~l~~~~~~l~~~~~~eel~~~~~~~~~~~~~~~~~~~~~~~ 109 (158)
T PRK04098 51 DKEINIEEIKEEALKYKKEFESAVESLKKKLKFEELDDLKITAENEIKSIQDLLQDYKK 109 (158)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHHHHHhccChHHHHHHhhhhhhcchhHHHHHhhhhh
Confidence 35667889999999999999999999988656669999999999988888888877653
No 43
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=71.23 E-value=13 Score=31.76 Aligned_cols=53 Identities=17% Similarity=0.068 Sum_probs=44.3
Q ss_pred CCCCCCCeEEEEEcCCCcEEEEEEeeEeCC-c-eEEEEecCCCE--EEEcCCCcccCC
Q 022567 98 EKLAVGTKVQAVYSEDGEWYDATIEAITPN-G-YYVTYDSWGNK--EEVDPANVRPVN 151 (295)
Q Consensus 98 ~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~-~-~~V~F~~Ygn~--e~V~~~~lrp~~ 151 (295)
..+.+|+.+... ++.-.=|.|+|..++.. . +.|.+.+.... .+|++++|+++.
T Consensus 93 ~~~~~G~~V~I~-~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~~pv~v~~~~~~~~~ 149 (153)
T PRK08559 93 EGIKEGDIVELI-AGPFKGEKARVVRVDESKEEVTVELLEAAVPIPVTVRGDQVRVVK 149 (153)
T ss_pred cCCCCCCEEEEe-ccCCCCceEEEEEEcCCCCEEEEEEECCcceeeEEEeccEEEEec
Confidence 459999999998 34445589999999854 4 99999999988 999999999874
No 44
>KOG3038 consensus Histone acetyltransferase SAGA associated factor SGF29 [General function prediction only]
Probab=70.97 E-value=52 Score=30.81 Aligned_cols=55 Identities=22% Similarity=0.254 Sum_probs=39.4
Q ss_pred CCCCCCCCeEEEEE---cCCCcEEEEEEeeEeCCc-eEEEEecCCC--EEEEcCCCcccCC
Q 022567 97 QEKLAVGTKVQAVY---SEDGEWYDATIEAITPNG-YYVTYDSWGN--KEEVDPANVRPVN 151 (295)
Q Consensus 97 ~~~~kvGd~C~A~~---s~Dg~wY~A~I~~i~~~~-~~V~F~~Ygn--~e~V~~~~lrp~~ 151 (295)
....-+||.|-|++ ++||.|.-|.|..++.++ |.+.=.|=.- .+.....+|.|++
T Consensus 125 ~~~~~~gd~VAa~v~~~~~dg~WIlaeVv~~~~~~~ye~ev~D~Epk~d~~g~r~~~yklp 185 (264)
T KOG3038|consen 125 DYVLLKGDEVAARVKAVSEDGDWILAEVVKVSSETRYEFEVVDPEPKKDEVGNRGQLYKLP 185 (264)
T ss_pred CccccCCceeeeeeeeccCCCCEEEEEEEEEecCCceEeEecCCCccccccccccceeccc
Confidence 35678899999998 789999999999999887 6554444322 3445555555553
No 45
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=70.71 E-value=20 Score=30.76 Aligned_cols=54 Identities=30% Similarity=0.391 Sum_probs=39.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh---ccCCCChhHHHHHHHHHHHHHHHHHHHHHhhh
Q 022567 9 IEELFSNLSTYKEQLQQVRELL---VHDPGNSEYADMEKELSEVIALTEELLATAKQ 62 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL---~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~~~ 62 (295)
|.+|+++|.+.+.++..+++-| ...|.|+||...-..|.+=|.-.++-|..++.
T Consensus 81 i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~ 137 (169)
T PF07106_consen 81 IKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLEKLRS 137 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455555555555555555433 56999999999999999999998888888764
No 46
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=70.55 E-value=19 Score=30.76 Aligned_cols=45 Identities=22% Similarity=0.341 Sum_probs=37.5
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHH
Q 022567 6 ELSIEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEEL 56 (295)
Q Consensus 6 ~~s~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~el 56 (295)
..++++|.++|+.|+.|++-+.+-+ ..|..+..+|.++|...+.+
T Consensus 5 ~~~le~l~a~lq~l~~qie~L~~~i------~~l~~~~~e~~~~~~tl~~l 49 (145)
T COG1730 5 QQELEELAAQLQILQSQIESLQAQI------AALNAAISELQTAIETLENL 49 (145)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999999888 56888888888888766544
No 47
>cd05839 BR140_related The PWWP domain is found in the BR140 family, which includes peregrin and BR140-like proteins 1 and 2. BR140 is the only family to contain the PWWP domain at the C terminus, with PHD and bromo domains in the N-terminal region. In myeloid leukemias, BR140 is disrupted by chromosomal translocations, similar to translocations of WHSC1 in lymphoid multiple myeloma. The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins seem to be nuclear, often DNA-binding proteins, that function as transcription factors regulating a variety of developmental processes.
Probab=69.06 E-value=6.9 Score=32.01 Aligned_cols=51 Identities=20% Similarity=0.067 Sum_probs=38.7
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEe--------------------------CCc-eEEEEecC-CCEEEEcCCCcccCC
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAIT--------------------------PNG-YYVTYDSW-GNKEEVDPANVRPVN 151 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~--------------------------~~~-~~V~F~~Y-gn~e~V~~~~lrp~~ 151 (295)
+.+||.|-|+.+ .--||||+|..-+ +.. |.|.|.+= .+...|+..+|+|+.
T Consensus 1 ~~pg~lVwaK~~-g~P~wPa~iidp~~~~~~~~~~~~p~~~l~~~~~~~~~~~~~~~lV~FFd~~~s~~Wv~~~~l~pl~ 79 (111)
T cd05839 1 LEPLTLVWAKCR-GYPSYPALIIDPKMPRDGVFHNGVPPDVLTLGEARAQNADERLYLVLFFDNKRTWQWLPGDKLEPLG 79 (111)
T ss_pred CCCcCEeeeeec-CCCCCCeEeeCCCCCCcccccCCCCchhhhHHHHHhccCCCcEEEEEEecCCCcceecCHHHCcccc
Confidence 357999999985 4569999998643 122 88888663 555789999999984
No 48
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=68.73 E-value=21 Score=27.87 Aligned_cols=45 Identities=24% Similarity=0.315 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcc-CCCChhHHHHHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELLVH-DPGNSEYADMEKELSEVIALT 53 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~~-DP~N~ELl~Lk~dL~EvI~Lt 53 (295)
|+.|++.|.+|+.+|+.|+.-|.. ....+.-..|.+|+.+|-...
T Consensus 7 Id~lEekl~~cr~~le~ve~rL~~~eLs~e~R~~lE~E~~~l~~~l 52 (85)
T PF15188_consen 7 IDGLEEKLAQCRRRLEAVESRLRRRELSPEARRSLEKELNELKEKL 52 (85)
T ss_pred HhhHHHHHHHHHHHHHHHHHHHcccCCChHHHHHHHHHHHHHHHHh
Confidence 778999999999999999999965 344445566666666554443
No 49
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=68.36 E-value=4.8 Score=43.72 Aligned_cols=51 Identities=20% Similarity=0.328 Sum_probs=42.9
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeC-Cc-eEEEEecCCCEEEEcCCCcccCCc
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITP-NG-YYVTYDSWGNKEEVDPANVRPVNL 152 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~-~~-~~V~F~~Ygn~e~V~~~~lrp~~~ 152 (295)
--.|=.|.|.|+ -++|++.+.+..+ .| |.|.|..|.--.-+...+|+|+.+
T Consensus 726 ~i~gl~v~a~w~--~~fyp~s~ls~rd~~gr~~~fft~~~~~kdi~~~diiplda 778 (1176)
T KOG3548|consen 726 HIPGLRVYAVWQ--KMFYPASVLSERDGLGRYKVFFTVDNVIKDIPNSDIIPLDA 778 (1176)
T ss_pred CCCceEEEEEee--ccCCCcccceeecCCCcEEEEEeccccccccccccceeccc
Confidence 567889999995 7899999998874 45 999999888778899999999854
No 50
>PRK14011 prefoldin subunit alpha; Provisional
Probab=66.54 E-value=80 Score=26.91 Aligned_cols=36 Identities=31% Similarity=0.458 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVI 50 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI 50 (295)
++++...|+.|+.|++.+...|. .|.....++.+.|
T Consensus 5 lq~~~~~l~~~~~qie~L~~si~------~L~~a~~e~~~~i 40 (144)
T PRK14011 5 LQNQFMALEVYNQQVQKLQEELS------SIDMMKMELLKSI 40 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHH
Confidence 67888999999999999998884 3566666665555
No 51
>KOG2279 consensus Kinase anchor protein AKAP149, contains KH and Tudor RNA-binding domains [Signal transduction mechanisms]
Probab=64.90 E-value=4.2 Score=41.66 Aligned_cols=51 Identities=14% Similarity=0.167 Sum_probs=41.6
Q ss_pred CCCCCCCeEEEEEcCCCcEEEEEEeeEeCCc---eEEEEecCCCEEEEcCCCcccC
Q 022567 98 EKLAVGTKVQAVYSEDGEWYDATIEAITPNG---YYVTYDSWGNKEEVDPANVRPV 150 (295)
Q Consensus 98 ~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~---~~V~F~~Ygn~e~V~~~~lrp~ 150 (295)
..+..+-.|-|. .+++-|.+|.+..-.++. +-|.|++|| .-.+..++||++
T Consensus 455 ~P~~~t~~sAAp-~g~~awpra~lvd~~det~l~I~~~~VdyG-Y~~~~~ddlrqi 508 (608)
T KOG2279|consen 455 KPLVATISSAAP-TGISAWPRAYLVDTSDETKLDIGLELVDYG-YAIELPDDLRQI 508 (608)
T ss_pred cchhhceeeecc-cCCCCccceEEEeccCcccchhhheeeccc-ccccchhhhhhh
Confidence 445677778888 579999999998776543 899999999 778888999886
No 52
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=63.33 E-value=15 Score=28.03 Aligned_cols=50 Identities=16% Similarity=0.201 Sum_probs=36.7
Q ss_pred CCCCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCc
Q 022567 98 EKLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 147 (295)
Q Consensus 98 ~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~l 147 (295)
..+++||.|+..=+.+|.|+.++|.+|.-+...|.+..=|+.-.+.+..|
T Consensus 25 G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~~~~a~aGd~v~l~l~~i 74 (87)
T cd03694 25 GVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSPVRVVRAGQSASLALKKI 74 (87)
T ss_pred CEEeCCCEEEECCCCCCCEeEEEEEEEEECCeECCEECCCCEEEEEEcCC
Confidence 46899999998765558899999999985555555555666666665544
No 53
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=61.69 E-value=38 Score=22.48 Aligned_cols=39 Identities=13% Similarity=0.084 Sum_probs=30.3
Q ss_pred EEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCC
Q 022567 106 VQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPAN 146 (295)
Q Consensus 106 C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~ 146 (295)
|-..- ....|-.|.|.++.++.++|...+ |.+.+|+.++
T Consensus 4 vWvpD-~~egfv~g~I~~~~g~~vtV~~~~-G~~~tv~~dd 42 (42)
T PF02736_consen 4 VWVPD-PKEGFVKGEIIEEEGDKVTVKTED-GKEVTVKKDD 42 (42)
T ss_dssp EEEEE-SSSSEEEEEEEEEESSEEEEEETT-TEEEEEEGGG
T ss_pred EEEeC-CcccEEEEEEEEEcCCEEEEEECC-CCEEEeCCCC
Confidence 44443 356799999999987779999999 8888887543
No 54
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=61.66 E-value=22 Score=35.67 Aligned_cols=55 Identities=24% Similarity=0.390 Sum_probs=44.9
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHhcc--------------------CC--------CChhHHHHHHHHHHHHHHHHHH
Q 022567 5 EELSIEELFSNLSTYKEQLQQVRELLVH--------------------DP--------GNSEYADMEKELSEVIALTEEL 56 (295)
Q Consensus 5 e~~s~e~Le~~L~~Yk~QL~qVe~aL~~--------------------DP--------~N~ELl~Lk~dL~EvI~Lt~el 56 (295)
....|+.|+++|+..+.|..++++.|.. +| +|+++..++.++.. +.|--|.
T Consensus 23 ~a~~i~~L~~ql~aLq~~v~eL~~~laa~~~aa~~gA~~~~~~~a~~~aP~~~a~~~~T~d~~~~~~qqiAn-~~lKv~~ 101 (514)
T PF11336_consen 23 TADQIKALQAQLQALQDQVNELRAKLAAKPAAAPGGAAIGPAATAAAAAPSSDAQAGLTNDDATEMRQQIAN-AQLKVES 101 (514)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCccccccccccccccCCCcccccccChHHHHHHHHHHHh-hhhhHHH
Confidence 4455789999999999999999999964 23 38999999999999 6777777
Q ss_pred HHHh
Q 022567 57 LATA 60 (295)
Q Consensus 57 l~~~ 60 (295)
|...
T Consensus 102 l~da 105 (514)
T PF11336_consen 102 LEDA 105 (514)
T ss_pred HhhH
Confidence 7654
No 55
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=58.61 E-value=32 Score=25.98 Aligned_cols=49 Identities=20% Similarity=0.254 Sum_probs=35.4
Q ss_pred CCCCCeEEEEEcCCCcE--EEEEEeeEeCCceEEEEec-CCCEEEEcCCCcc
Q 022567 100 LAVGTKVQAVYSEDGEW--YDATIEAITPNGYYVTYDS-WGNKEEVDPANVR 148 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~w--Y~A~I~~i~~~~~~V~F~~-Ygn~e~V~~~~lr 148 (295)
+.-+..|...|..+|.+ +.++|..|+...-.|.+.+ .+++..+++++|.
T Consensus 39 ~~~~~~v~ity~~~g~~~~~~G~I~~id~~~~~l~~~~~~~~~~~I~~~~I~ 90 (92)
T PF08863_consen 39 YQENQPVTITYYEDGYYQSVTGTIHKIDEINRTLKLKDEDGETEKIPFDDII 90 (92)
T ss_pred hcCCCEEEEEEEECCeeEEEEEEEEEEcCCCCEEEEEeCCCCEEEEEhhhEE
Confidence 45578888888777743 4577888876654444444 6888999999885
No 56
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=58.61 E-value=25 Score=32.10 Aligned_cols=37 Identities=22% Similarity=0.221 Sum_probs=29.7
Q ss_pred CCCCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEec
Q 022567 98 EKLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDS 135 (295)
Q Consensus 98 ~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~ 135 (295)
...++||.+.+.. ++|..|.|+|..++.+.+.+.+..
T Consensus 30 lR~~~Gd~v~v~~-g~g~~~~a~i~~~~~~~~~~~i~~ 66 (240)
T TIGR00046 30 LRLKKGDKLKLLD-GDGFIYHCEIKKISKKFVKCELLE 66 (240)
T ss_pred ccCCCCCEEEEEe-CCCCEEEEEEEEEcCCeEEEEEEe
Confidence 3578999999975 589999999999987766665543
No 57
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=56.33 E-value=21 Score=25.72 Aligned_cols=37 Identities=22% Similarity=0.335 Sum_probs=29.0
Q ss_pred CCcEEEEEEeeEeCCceEEEEecCC-CEEEEcCCCccc
Q 022567 113 DGEWYDATIEAITPNGYYVTYDSWG-NKEEVDPANVRP 149 (295)
Q Consensus 113 Dg~wY~A~I~~i~~~~~~V~F~~Yg-n~e~V~~~~lrp 149 (295)
-|..|.|+|.++...++.|.+.+|+ -.-.|+.++|..
T Consensus 3 ~G~~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s~l~~ 40 (76)
T cd04452 3 EGELVVVTVKSIADMGAYVSLLEYGNIEGMILLSELSR 40 (76)
T ss_pred CCCEEEEEEEEEEccEEEEEEcCCCCeEEEEEhHHcCC
Confidence 3789999999999888999998875 445677776653
No 58
>PF02820 MBT: mbt repeat; InterPro: IPR004092 The function of the malignant brain tumor (MBT) repeat is unknown, but is found in a number of nuclear proteins involved in transcriptional repression. The repeat contains a completely conserved glutamate at its amino terminus that may be important for function. The crystal structure of the two MBT repeats of human SCM-like 2 protein has been reported. Each repeat consists of an extended "arm" and a globular core. The arm of the first repeat packs against the core of the second repeat and vice versa. The structure of the core-interacting part of each arm consists of an N-terminal alpha-helix and a turn of 310 helix connected by a short beta-strand. The core consists of an Src homology 3-like five-stranded beta-barrel followed by a C-terminal alpha-helix and another short beta-strand. Each arm interacts with its partner core in a similar way, with the orientation of the N-terminal helix relative to the barrel varying slightly. There are also extensive interactions between the two barrels [].; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2P0K_A 3F70_B 3CEY_A 2VYT_A 2BIV_A 1OI1_A 3OQ5_A 2RJE_B 2RJD_A 2RI3_A ....
Probab=56.19 E-value=30 Score=25.54 Aligned_cols=37 Identities=22% Similarity=0.296 Sum_probs=28.4
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCE--EEEcC--CCcccC
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNK--EEVDP--ANVRPV 150 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~--e~V~~--~~lrp~ 150 (295)
..++.|+|..|.+..+.|.|+||.+. ..+.. .+|.|+
T Consensus 12 ~~~~vAtV~~v~g~~l~v~~dg~~~~~d~w~~~~S~~i~Pv 52 (73)
T PF02820_consen 12 SLICVATVVKVCGGRLLVRYDGWDDDYDFWCHIDSPRIFPV 52 (73)
T ss_dssp CEEEEEEEEEEETTEEEEEETTSTGGGEEEEETTSTTEEET
T ss_pred CeEEEEEEEEEeCCEEEEEEcCCCCCccEEEECCCCCeeec
Confidence 56789999999877799999999974 34444 456666
No 59
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=54.20 E-value=37 Score=28.31 Aligned_cols=52 Identities=21% Similarity=0.323 Sum_probs=40.0
Q ss_pred CCCCeEEEEEc---CCCcEEEEEEeeEeCCc--eEEEEecCC---CEEEEcCCCcccCCc
Q 022567 101 AVGTKVQAVYS---EDGEWYDATIEAITPNG--YYVTYDSWG---NKEEVDPANVRPVNL 152 (295)
Q Consensus 101 kvGd~C~A~~s---~Dg~wY~A~I~~i~~~~--~~V~F~~Yg---n~e~V~~~~lrp~~~ 152 (295)
++|+.|-|+-. +++.|--|+|.++..++ |.|.=.+-+ +.-.++..+|-||+.
T Consensus 1 q~G~~VAak~~~~~~~~~WIla~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP~ 60 (130)
T PF07039_consen 1 QPGDQVAAKVKQGNEEEEWILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLPK 60 (130)
T ss_dssp -TT-EEEEEECTTTTTCEEEEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-S
T ss_pred CCCCEEEEEcCCCCCCCCEEEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECCC
Confidence 57999999873 57899999999999765 988877765 346788888888865
No 60
>PF06657 Cep57_MT_bd: Centrosome microtubule-binding domain of Cep57; InterPro: IPR010597 This entry is thought to represent a centrosomal protein of 57 kDa (Cep57-related protein). It is required for spindle microtubule attachment to both kinetochores and centrosomes and functions to tether minus-ends of spindle microtubules to centrosomes. It may act by forming ring-like structures around microtubules, or by serving as a cross-linker or scaffold at the attachment site [].
Probab=51.23 E-value=72 Score=24.34 Aligned_cols=46 Identities=22% Similarity=0.346 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhc---cCCCChhHHHHHHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELLV---HDPGNSEYADMEKELSEVIALTE 54 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~---~DP~N~ELl~Lk~dL~EvI~Lt~ 54 (295)
|..|+.+|..++.+++.+.+.+. .-.+...-..|..+|.++|..-+
T Consensus 19 l~~LqDE~~hm~~e~~~L~~~~~~~d~s~~~~~R~~L~~~l~~lv~~mE 67 (79)
T PF06657_consen 19 LKALQDEFGHMKMEHQELQDEYKQMDPSLGRRKRRDLEQELEELVKRME 67 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcccccChHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999966664 34444556788888888776544
No 61
>PF14282 FlxA: FlxA-like protein
Probab=50.53 E-value=76 Score=25.39 Aligned_cols=53 Identities=21% Similarity=0.235 Sum_probs=41.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHHhhh
Q 022567 8 SIEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLATAKQ 62 (295)
Q Consensus 8 s~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~~~ 62 (295)
-|+.|+.+|...+.||..|..- .+.+.++-......|..=|...+.-|..+..
T Consensus 20 ~I~~L~~Qi~~Lq~ql~~l~~~--~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq~ 72 (106)
T PF14282_consen 20 QIEQLQKQIKQLQEQLQELSQD--SDLDAEQKQQQIQLLQAQIQQLQAQIAQLQS 72 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHcc--cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3678888888888888877664 3335567788888899999999988887753
No 62
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=48.88 E-value=1.5e+02 Score=24.39 Aligned_cols=39 Identities=26% Similarity=0.364 Sum_probs=27.2
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHH
Q 022567 6 ELSIEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVI 50 (295)
Q Consensus 6 ~~s~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI 50 (295)
...+++|...++.|+.+++.+...+ .+|.....++..+|
T Consensus 5 ~~~l~~l~~~~~~l~~~~~~l~~~~------~~l~~~~~e~~~~~ 43 (140)
T PRK03947 5 EQELEELAAQLQALQAQIEALQQQL------EELQASINELDTAK 43 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHH
Confidence 3457888899999999998888776 23555555555444
No 63
>PRK14639 hypothetical protein; Provisional
Probab=48.06 E-value=60 Score=27.40 Aligned_cols=49 Identities=10% Similarity=0.195 Sum_probs=36.5
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCccc
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp 149 (295)
--+|..|..... ++..|.++|.+++++++++....-+.+..+++++|+-
T Consensus 85 r~~G~~v~v~l~-~~~~~~G~L~~~~~~~i~l~~~~~~~~~~i~~~~I~k 133 (140)
T PRK14639 85 KSIGELVKITTN-EKEKFEGKIVSVDDENITLENLENKEKTTINFNDIKK 133 (140)
T ss_pred HhCCCEEEEEEC-CCcEEEEEEEEEeCCEEEEEEccCCcEEEEEhHHeee
Confidence 467999999875 7899999999998877666443223446788877764
No 64
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=47.93 E-value=12 Score=34.69 Aligned_cols=43 Identities=14% Similarity=0.224 Sum_probs=34.6
Q ss_pred EE-cCCCcEEEEEEeeEe---CCceEEEEecCCCEEEEcCCCcccCC
Q 022567 109 VY-SEDGEWYDATIEAIT---PNGYYVTYDSWGNKEEVDPANVRPVN 151 (295)
Q Consensus 109 ~~-s~Dg~wY~A~I~~i~---~~~~~V~F~~Ygn~e~V~~~~lrp~~ 151 (295)
.| ++|-.+|+-+|..+. ++.|.+.|.+||....+.+++|.+++
T Consensus 73 ~~~~~~~l~~~~~i~a~~w~vg~K~~A~~~ddg~~y~AtIe~ita~~ 119 (262)
T KOG3026|consen 73 RWVSGDYLFYPSRITAVGWKVGDKVQAVFSDDGQIYDATIEHITAME 119 (262)
T ss_pred hhhhhhhccccccchhcccccCCEEEEeecCCCceEEeehhhccCCC
Confidence 45 678889999998875 22399999999999999999998863
No 65
>PF09177 Syntaxin-6_N: Syntaxin 6, N-terminal; InterPro: IPR015260 Members of this entry, which are found in the amino terminus of various SNARE proteins, adopt a structure consisting of an antiparallel three-helix bundle. Their exact function has not been determined, though it is known that they regulate the SNARE motif, as well as mediate various protein-protein interactions involved in membrane-transport []. ; GO: 0048193 Golgi vesicle transport, 0016020 membrane; PDB: 1LVF_B 2C5I_T 2C5J_A 2C5K_T 4DND_A.
Probab=47.70 E-value=93 Score=24.20 Aligned_cols=52 Identities=17% Similarity=0.191 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHHhhh
Q 022567 11 ELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLATAKQ 62 (295)
Q Consensus 11 ~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~~~ 62 (295)
+.+..|..-+.-+..-...+...+.+.|+..++.||...|.-.+.-|..+..
T Consensus 9 ev~~sl~~l~~~~~~~~~~~~~~~~~~e~~~~~~eL~~~l~~ie~~L~DL~~ 60 (97)
T PF09177_consen 9 EVQSSLDRLESLYRRWQRLRSDTSSSEELKWLKRELRNALQSIEWDLEDLEE 60 (97)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTHCC-HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhcccCCCcHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444444444444445557889999999999999999998888753
No 66
>PF12761 End3: Actin cytoskeleton-regulatory complex protein END3
Probab=46.53 E-value=80 Score=28.39 Aligned_cols=51 Identities=20% Similarity=0.279 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhcc--CCCChhHHHHHHHHHHHHHHHHHHHHHhh
Q 022567 11 ELFSNLSTYKEQLQQVRELLVH--DPGNSEYADMEKELSEVIALTEELLATAK 61 (295)
Q Consensus 11 ~Le~~L~~Yk~QL~qVe~aL~~--DP~N~ELl~Lk~dL~EvI~Lt~ell~~~~ 61 (295)
-|+-+|++....|..|+..-.. .+.+....-+|.+|+.++.--+..|..+.
T Consensus 100 rLkrELa~Le~~l~~~~~~~~~~~~~~~~~~~lvk~e~EqLL~YK~~ql~~~~ 152 (195)
T PF12761_consen 100 RLKRELAELEEKLSKVEQAAESRRSDTDSKPALVKREFEQLLDYKERQLRELE 152 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCcchHHHHHHHHHHHHHHHHHHHHhhh
Confidence 4999999999999999998886 55567788889999999998888887764
No 67
>cd02421 Peptidase_C39_likeD A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this sub-family.
Probab=45.57 E-value=30 Score=27.24 Aligned_cols=43 Identities=7% Similarity=0.074 Sum_probs=29.7
Q ss_pred CeEEEEEcCCCcEEEEEEeeEeCCceEEEEec-CCCEEEEcCCCccc
Q 022567 104 TKVQAVYSEDGEWYDATIEAITPNGYYVTYDS-WGNKEEVDPANVRP 149 (295)
Q Consensus 104 d~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~-Ygn~e~V~~~~lrp 149 (295)
-.|++.|. ||.| ++|.+++++.+.|...+ -++.+.++.+++..
T Consensus 70 lP~i~~~~-~g~~--~Vl~~~~~~~~~i~dp~~~~~~~~~~~~el~~ 113 (124)
T cd02421 70 LPAILLLK-NGRA--CVLLGVDDGHARILDPESGGGEVEISLEELEE 113 (124)
T ss_pred CCEEEEEc-CCCE--EEEEEecCCeEEEEccCCCCCcEEEcHHHHHh
Confidence 45999885 7887 78888877556665554 45556777766654
No 68
>PF08169 RBB1NT: RBB1NT (NUC162) domain; InterPro: IPR012603 This domain is found N-terminal to the ARID/BRIGHT domain in DNA-binding proteins of the Retinoblastoma-binding protein 1 family [].; PDB: 2YRV_A.
Probab=45.55 E-value=30 Score=27.66 Aligned_cols=50 Identities=20% Similarity=0.353 Sum_probs=26.2
Q ss_pred CCCeEEEEE-cCCCcEEEEEEeeEeCC--------ceEEE-EecCCCEEEEcCCCcccCCc
Q 022567 102 VGTKVQAVY-SEDGEWYDATIEAITPN--------GYYVT-YDSWGNKEEVDPANVRPVNL 152 (295)
Q Consensus 102 vGd~C~A~~-s~Dg~wY~A~I~~i~~~--------~~~V~-F~~Ygn~e~V~~~~lrp~~~ 152 (295)
+|-.|+.-- ...+.||||.|.+-+.+ .|.|+ |.+ |---+|...+|+.+..
T Consensus 8 lGkVV~V~~~~~k~~W~PALVVsPsc~ddv~VkKD~~lVRSFkD-~KfysV~rkd~~e~~~ 67 (96)
T PF08169_consen 8 LGKVVCVESTKKKTSWFPALVVSPSCNDDVTVKKDQCLVRSFKD-GKFYSVARKDVREFDI 67 (96)
T ss_dssp TTSEEEEE-SS-SS-EEEEEEE--SS-SS----TT-EEEEESSS---EEEE-TTTEE---S
T ss_pred cCcEEEEEcCCCCCceeeEEEEcCCccceeeeccceEEEEEecc-CceEEEEhhhhhhccc
Confidence 688877755 33468999999976632 24443 444 4446899999988754
No 69
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=43.04 E-value=80 Score=28.93 Aligned_cols=49 Identities=24% Similarity=0.308 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHH
Q 022567 10 EELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLA 58 (295)
Q Consensus 10 e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~ 58 (295)
-++++.|+..+.+.+.+.++|..-.+-+|++.+..+|.++=.=.+.+-.
T Consensus 135 ~D~~arl~~l~~~~~rl~~ll~ka~~~~d~l~ie~~L~~v~~eIe~~~~ 183 (262)
T PF14257_consen 135 VDLEARLKNLEAEEERLLELLEKAKTVEDLLEIERELSRVRSEIEQLEG 183 (262)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4899999999999999999998777888999999999887554444433
No 70
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 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 [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=42.93 E-value=53 Score=23.49 Aligned_cols=35 Identities=11% Similarity=0.254 Sum_probs=29.4
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCccc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp 149 (295)
|.-|.|+|.+|+..++.|.+. ++-.-.|+.++|-.
T Consensus 5 G~iv~g~V~~v~~~g~~V~l~-~~~~g~ip~~~l~~ 39 (74)
T PF00575_consen 5 GDIVEGKVTSVEDFGVFVDLG-NGIEGFIPISELSD 39 (74)
T ss_dssp TSEEEEEEEEEETTEEEEEES-TSSEEEEEGGGSSS
T ss_pred CCEEEEEEEEEECCEEEEEEC-CcEEEEEEeehhcC
Confidence 667899999999988999998 67777888888764
No 71
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=42.64 E-value=38 Score=24.27 Aligned_cols=36 Identities=14% Similarity=0.269 Sum_probs=27.5
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCccc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp 149 (295)
|.-|.|+|..|...++.|.+.+.+-.-.++.+++.+
T Consensus 3 g~~v~g~V~~i~~~g~~v~l~~~~~~g~i~~~~l~~ 38 (77)
T cd05708 3 GQKIDGTVRRVEDYGVFIDIDGTNVSGLCHKSEISD 38 (77)
T ss_pred CCEEEEEEEEEEcceEEEEECCCCeEEEEEHHHCCC
Confidence 677999999999888888887655555667666654
No 72
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.51 E-value=54 Score=30.31 Aligned_cols=36 Identities=17% Similarity=0.144 Sum_probs=28.3
Q ss_pred CCCCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEe
Q 022567 98 EKLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYD 134 (295)
Q Consensus 98 ~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~ 134 (295)
...++||.+.... ++|.+|.|.|..++...+.+.+.
T Consensus 32 lRl~~gd~l~l~~-g~g~~~~a~i~~~~kk~~~~~i~ 67 (246)
T COG1385 32 LRLKEGDELRLFD-GSGGEFLAEITKIGKKEALLKIV 67 (246)
T ss_pred eecCCCCEEEEEe-CCCcEEEEEEeecCCCceEEEEE
Confidence 3578999999986 68889999999998776444443
No 73
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=41.98 E-value=48 Score=29.48 Aligned_cols=49 Identities=10% Similarity=0.054 Sum_probs=36.0
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcccC
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRPV 150 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp~ 150 (295)
+-+--.|+..- ++.=|+++|.+..++-+.|.=.+-++..+|++++|.-+
T Consensus 132 ~lp~i~C~i~t--~~~~Y~G~I~~~~~~~v~i~~~~~~~~~~i~~~~I~sI 180 (185)
T PF14153_consen 132 HLPPIKCEIET--KDKSYRGIILSYDEGEVSIMPFNQGEEIEIPIDDITSI 180 (185)
T ss_pred cCCCCceEEEe--CCceEEEEEEeccCCEEEEeccCCCcceEeehhheeee
Confidence 34456788884 78899999999865545555444567789999998765
No 74
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=41.65 E-value=66 Score=26.76 Aligned_cols=52 Identities=12% Similarity=0.017 Sum_probs=42.0
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEeCCc--eEEEEecCCCE--EEEcCCCcccCC
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAITPNG--YYVTYDSWGNK--EEVDPANVRPVN 151 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~--~~V~F~~Ygn~--e~V~~~~lrp~~ 151 (295)
.+++||.+...- +-=.=+.|+|..++... +.|.+.+++.. .+|+.++|+.+.
T Consensus 86 ~~~~Gd~V~I~~-GPf~G~~g~v~~~d~~k~~v~v~l~~~~~~~~v~v~~~~l~~~~ 141 (145)
T TIGR00405 86 SIKKGDIVEIIS-GPFKGERAKVIRVDESKEEVTLELIEAAVPIPVTVKGDQVRIIQ 141 (145)
T ss_pred ccCCCCEEEEee-cCCCCCeEEEEEEcCCCCEEEEEEEEcCccceEEEeeeEEEEec
Confidence 489999999983 22234799999998544 99999999988 899999998763
No 75
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=41.21 E-value=61 Score=29.10 Aligned_cols=35 Identities=23% Similarity=0.300 Sum_probs=26.4
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEe
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYD 134 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~ 134 (295)
..++||.+...- ++|..|.|+|+.++...+.+...
T Consensus 16 R~k~Gd~i~v~d-g~g~~~~a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 16 RLKEGDSIEVFD-GDGGEYRAEITEISKKSATLRIL 50 (225)
T ss_dssp T--TT-EEEEEE-SSSEEEEEEEEEEESSEEEEEEE
T ss_pred CCCCCCEEEEEE-CCCCEEEEEEEECcCcEEEEEEe
Confidence 478999999886 68999999999998776655554
No 76
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=40.93 E-value=93 Score=25.89 Aligned_cols=50 Identities=10% Similarity=0.241 Sum_probs=33.7
Q ss_pred CCCCCeEEEEEc---CCCcEEEEEEeeEeCCceEEEEecCC--CEEEEcCCCccc
Q 022567 100 LAVGTKVQAVYS---EDGEWYDATIEAITPNGYYVTYDSWG--NKEEVDPANVRP 149 (295)
Q Consensus 100 ~kvGd~C~A~~s---~Dg~wY~A~I~~i~~~~~~V~F~~Yg--n~e~V~~~~lrp 149 (295)
.-+|..+...+. ....+|.++|.+++++.+++.+.+-+ ....+++++|+-
T Consensus 84 ~~iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~i~l~~~~~~~~~~~~I~~~~I~k 138 (141)
T PF02576_consen 84 RFIGRKVKVKLKQPVNGRKEFEGKLLEVDEDEITLEVEGKGKKKEVEIPFSDIKK 138 (141)
T ss_dssp HH-SEEEEEE-SS-SSS-SEEEEEEEEEETTEEEEEEE-SS-EEEEEE-SS--SS
T ss_pred HhcCCeEEEEEeccCCCcEEEEEEEEEEeCCEEEEEECCccceEEEEEEHHHCce
Confidence 357999999983 34579999999999887888887765 256888888864
No 77
>PRK00461 rpmC 50S ribosomal protein L29; Reviewed
Probab=40.80 E-value=1.7e+02 Score=22.81 Aligned_cols=52 Identities=17% Similarity=0.243 Sum_probs=39.1
Q ss_pred cccCHHHHHHHHHHHHHHHHHHH--HHhccCCCChhHHHHHHHHHHHHHHHHHH
Q 022567 5 EELSIEELFSNLSTYKEQLQQVR--ELLVHDPGNSEYADMEKELSEVIALTEEL 56 (295)
Q Consensus 5 e~~s~e~Le~~L~~Yk~QL~qVe--~aL~~DP~N~ELl~Lk~dL~EvI~Lt~el 56 (295)
-++|.++|...|.+.+..|-+.. .+...-.+-..+..+|.++--+.....+-
T Consensus 6 R~lS~eEL~e~L~elkkELf~LR~q~atgql~n~~~ir~iRR~IARilTvl~Ek 59 (87)
T PRK00461 6 RKKSVEELEKLVIELKAELFTLRFKNATGSLDQTHKIKEIRKDIARILTILNER 59 (87)
T ss_pred HhCCHHHHHHHHHHHHHHHHHHHHHHHhCcccccHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998887 44443223357899999988877766554
No 78
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=39.20 E-value=1e+02 Score=23.24 Aligned_cols=50 Identities=16% Similarity=0.212 Sum_probs=34.8
Q ss_pred CCCCCeEEEEEc---CCCcEEEEEEeeEeCCceEEEEecC--CCEEEEcCCCccc
Q 022567 100 LAVGTKVQAVYS---EDGEWYDATIEAITPNGYYVTYDSW--GNKEEVDPANVRP 149 (295)
Q Consensus 100 ~kvGd~C~A~~s---~Dg~wY~A~I~~i~~~~~~V~F~~Y--gn~e~V~~~~lrp 149 (295)
.-+|..|...+. ++...|.++|.+++++.+++....- +....+++++|+-
T Consensus 22 r~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~v~l~~~~~~~~~~~~i~~~~I~k 76 (83)
T cd01734 22 RAVGKYVHVKLYQPIDGQKEFEGTLLGVDDDTVTLEVDIKTRGKTVEIPLDKIAK 76 (83)
T ss_pred HhCCCEEEEEEEcccCCeEEEEEEEEeEeCCEEEEEEecCCCCeEEEEEhHHeeE
Confidence 467998888763 2345899999999887766664311 3456777777764
No 79
>PRK14549 50S ribosomal protein L29P; Provisional
Probab=38.60 E-value=1.6e+02 Score=21.77 Aligned_cols=50 Identities=20% Similarity=0.337 Sum_probs=38.0
Q ss_pred cccCHHHHHHHHHHHHHHHHHHH--HHhccCCCCh-hHHHHHHHHHHHHHHHH
Q 022567 5 EELSIEELFSNLSTYKEQLQQVR--ELLVHDPGNS-EYADMEKELSEVIALTE 54 (295)
Q Consensus 5 e~~s~e~Le~~L~~Yk~QL~qVe--~aL~~DP~N~-ELl~Lk~dL~EvI~Lt~ 54 (295)
-++|.++|...|.+.+.+|-... .+...-++|. .+..++.|+--|-....
T Consensus 10 r~ls~~eL~~~l~elk~eLf~LR~q~~~~~~l~n~~~ir~~Rk~IARi~Tvl~ 62 (69)
T PRK14549 10 REMSPEEREEKLEELKLELLKERAQAAMGGAPENPGRIREIRRTIARILTIQR 62 (69)
T ss_pred HhCCHHHHHHHHHHHHHHHHHHHHHHHhCcCccccHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999988 3333326665 78899999877765544
No 80
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=38.40 E-value=99 Score=28.42 Aligned_cols=79 Identities=23% Similarity=0.253 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHHhhhcccccccCCCCCCCCCcccccccccccC
Q 022567 11 ELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLATAKQNAISVSETGTSASASPNLLQSKENKTES 90 (295)
Q Consensus 11 ~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~~~~~~~~~~~~~~~~~~P~~~~~~~~~~~~ 90 (295)
+|+.+|.+.+.+|..+.. ...++=.++-.|+.+|.++-. ++...... |.
T Consensus 19 ~~~~~~~~~e~~~~~i~~--~~~~~v~~y~~l~~~l~~~~~---~~~~~i~~---------------p~----------- 67 (268)
T PF13234_consen 19 ELEKKLKELEEELDAIKI--EDEEDVEEYYDLRQELEELRK---ELRKIITS---------------PK----------- 67 (268)
T ss_dssp HHHHHHHHHHHHHHCS----TTCTCCHHHHHHHHHHHHHHH---HHHHHHCT---------------CC-----------
T ss_pred HHHHHHHHHHHHHHhccc--ccHhHHHHHHHHHHHHHHHHH---HHHHHHhC---------------cH-----------
Confidence 344444444444444443 335666778888887776444 44333210 00
Q ss_pred CCCCCCCCCCCCCCeEEEEEcCCCcEEEEEEeeEe
Q 022567 91 GSISDNQEKLAVGTKVQAVYSEDGEWYDATIEAIT 125 (295)
Q Consensus 91 ~~~~~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~ 125 (295)
-....+++|..|.... ++..|..|+|..+.
T Consensus 68 ----~~~~fL~~GRlV~v~~-~~~~~~wgvvv~~~ 97 (268)
T PF13234_consen 68 ----YCLPFLQPGRLVVVRD-GDRDFGWGVVVNFA 97 (268)
T ss_dssp ----CHHHHS-TTEEEEEEE-TTCEEEEEEEEEEE
T ss_pred ----HHHHhCCCCCEEEEec-CCCccceeEEEecc
Confidence 0112378899888886 58899999999886
No 81
>TIGR03130 malonate_delta malonate decarboxylase acyl carrier protein. Members of this protein family are the acyl carrier protein, also called the delta subunit, of malonate decarboxylase. This subunit has the same covalently bound prosthetic group, derived from and similar to coenzyme A, as does citrate lyase, although this protein and the acyl carrier protein of citrate lyase do not show significant sequence similarity. Both malonyl and acetyl groups are transferred to the prosthetic group for catalysis.
Probab=38.12 E-value=20 Score=28.67 Aligned_cols=9 Identities=67% Similarity=1.007 Sum_probs=8.0
Q ss_pred cceeeccCC
Q 022567 262 GKVGVTGSG 270 (295)
Q Consensus 262 grVGv~GsG 270 (295)
..|||+|||
T Consensus 19 ~lvGVVGSG 27 (98)
T TIGR03130 19 ALVGVVGSG 27 (98)
T ss_pred EEEEEEccC
Confidence 569999999
No 82
>PRK14637 hypothetical protein; Provisional
Probab=37.42 E-value=89 Score=26.76 Aligned_cols=48 Identities=21% Similarity=0.291 Sum_probs=36.3
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCccc
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp 149 (295)
--+|..|...+.+++.|+.++|.+++++.+.+. .-+....+++++|+.
T Consensus 95 r~~G~~V~V~l~~~~~~~~G~L~~~~d~~v~l~--~~~~~~~i~~~~I~k 142 (151)
T PRK14637 95 IFVGETVKVWFECTGQWQVGTIAEADETCLVLT--SDGVPVTIPYVQITK 142 (151)
T ss_pred HhCCCEEEEEECCCCcEEEEEEEEEeCCEEEEE--ECCEEEEEEHHHeee
Confidence 468999999885578888999999987765554 235566778877764
No 83
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=37.31 E-value=43 Score=28.22 Aligned_cols=28 Identities=29% Similarity=0.495 Sum_probs=19.3
Q ss_pred EEcCCCcEEEEEEeeEeCCceEEEEecCC
Q 022567 109 VYSEDGEWYDATIEAITPNGYYVTYDSWG 137 (295)
Q Consensus 109 ~~s~Dg~wY~A~I~~i~~~~~~V~F~~Yg 137 (295)
+|- ||.||-|+++.++++.|.|.=.-||
T Consensus 3 V~F-dg~FWvGv~E~~~~~~~~v~rv~FG 30 (132)
T PF11208_consen 3 VYF-DGPFWVGVFERHEDGKYKVARVTFG 30 (132)
T ss_pred EEe-cCCcEEEEEEEEECCEEEEEEEeeC
Confidence 454 9999999999998766433333334
No 84
>PF06696 Strep_SA_rep: Streptococcal surface antigen repeat; InterPro: IPR009578 This family consists of a number of ~25 residue long repeats found commonly in Streptococcal surface antigens although one copy is present in the HPSR2-heavy chain potential motor protein of Giardia lamblia (Giardia intestinalis) (Q24984 from SWISSPROT). This family is often found in conjunction with IPR001899 from INTERPRO.; PDB: 3IOX_A 3IPK_A 2WD6_B 1JMM_A.
Probab=36.76 E-value=65 Score=19.45 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhc
Q 022567 11 ELFSNLSTYKEQLQQVRELLV 31 (295)
Q Consensus 11 ~Le~~L~~Yk~QL~qVe~aL~ 31 (295)
+.++.|..|+..|..|...+.
T Consensus 2 ~Yqakla~YqaeLa~vqk~na 22 (25)
T PF06696_consen 2 DYQAKLAQYQAELARVQKANA 22 (25)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHhh
Confidence 457889999999999887663
No 85
>PF03039 IL12: Interleukin-12 alpha subunit; InterPro: IPR004281 Interleukin 12 (IL-12) is a disulphide-bonded heterodimer consisting of a 35kDa alpha subunit and a 40kDa beta subunit. It is involved in the stimulation and maintenance of Th1 cellular immune responses, including the normal host defence against various intracellular pathogens, such as Leishmania, Toxoplasma, Measles virus and Human immunodeficiency virus 1 (HIV). IL-12 also has an important role in pathological Th1 responses, such as in inflammatory bowel disease and multiple sclerosis. Suppression of IL-12 activity in such diseases may have therapeutic benefit. On the other hand, administration of recombinant IL-12 may have therapeutic benefit in conditions associated with pathological Th2 responses [, ].; GO: 0005143 interleukin-12 receptor binding, 0008083 growth factor activity, 0006955 immune response, 0005576 extracellular region; PDB: 3HMX_B 1F45_B.
Probab=36.13 E-value=98 Score=28.23 Aligned_cols=51 Identities=18% Similarity=0.451 Sum_probs=34.7
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHHh
Q 022567 5 EELSIEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLATA 60 (295)
Q Consensus 5 e~~s~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~ 60 (295)
++..+..+-++|.-|+..++.+.+.|..||+++=++ -.. ++.-.++++..+
T Consensus 120 ~tlCLssIyEDLk~Y~~efka~~~~ll~~p~~qi~L--d~~---mL~aIdeLmQaL 170 (219)
T PF03039_consen 120 MTLCLSSIYEDLKMYQAEFKAINKKLLMDPERQISL--DQN---MLAAIDELMQAL 170 (219)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHCCSTT---SH--HHH---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHhhcCchhhhhh--hHH---HHHHHHHHHHHc
Confidence 344566678999999999999999999999988776 233 444444555444
No 86
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=35.30 E-value=1e+02 Score=19.95 Aligned_cols=29 Identities=10% Similarity=0.369 Sum_probs=22.3
Q ss_pred CCCCCCCCCCeEEEEEcCCCcEEEEEEee
Q 022567 95 DNQEKLAVGTKVQAVYSEDGEWYDATIEA 123 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~ 123 (295)
+....+.+||.+...-..++.|+.++...
T Consensus 16 ~~~l~~~~Gd~v~v~~~~~~~w~~~~~~~ 44 (58)
T smart00326 16 PDELSFKKGDIITVLEKSDDGWWKGRLGR 44 (58)
T ss_pred CCCCCCCCCCEEEEEEcCCCCeEEEEeCC
Confidence 44567899999988875578898887654
No 87
>PRK01203 prefoldin subunit alpha; Provisional
Probab=35.22 E-value=2.7e+02 Score=23.38 Aligned_cols=22 Identities=14% Similarity=0.190 Sum_probs=15.8
Q ss_pred CCeEEEEEcCCCcEEEEEEeeEe
Q 022567 103 GTKVQAVYSEDGEWYDATIEAIT 125 (295)
Q Consensus 103 Gd~C~A~~s~Dg~wY~A~I~~i~ 125 (295)
|..++.+-. -|.|-+|+|....
T Consensus 48 ~~eiLVPLg-~slYV~gki~d~~ 69 (130)
T PRK01203 48 SKELLISIG-SGIFADGNIKKDK 69 (130)
T ss_pred CCeEEEEcc-CCceEeEEecCCC
Confidence 566777764 6888899887543
No 88
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=35.09 E-value=58 Score=23.02 Aligned_cols=34 Identities=18% Similarity=0.225 Sum_probs=26.0
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCccc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp 149 (295)
|.-|.|+|..+.+.|+.|.| .|-.--++.++|-+
T Consensus 1 G~iv~g~V~~v~~~G~~v~l--~g~~gfip~s~~~~ 34 (67)
T cd04465 1 GEIVEGKVTEKVKGGLIVDI--EGVRAFLPASQVDL 34 (67)
T ss_pred CCEEEEEEEEEECCeEEEEE--CCEEEEEEHHHCCC
Confidence 56789999999988899999 35455777766643
No 89
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=34.82 E-value=1.1e+02 Score=25.60 Aligned_cols=43 Identities=19% Similarity=0.254 Sum_probs=32.6
Q ss_pred CCCCCCCeEEEEEcCCCcE--EEEEEeeEeCCc-eEEEEecCCCEEEEc
Q 022567 98 EKLAVGTKVQAVYSEDGEW--YDATIEAITPNG-YYVTYDSWGNKEEVD 143 (295)
Q Consensus 98 ~~~kvGd~C~A~~s~Dg~w--Y~A~I~~i~~~~-~~V~F~~Ygn~e~V~ 143 (295)
..+.+||.+... +|-| |.+.|..+++.. +.|.+.-+|..-.|.
T Consensus 107 ~~~~~G~~V~V~---~GPf~g~~g~v~~~~~~~r~~v~l~~~gr~~~v~ 152 (159)
T TIGR01955 107 TLPYKGDKVRIT---DGAFAGFEAIFLEPDGEKRSMLLLNMIGKQIKVS 152 (159)
T ss_pred cCCCCCCEEEEe---ccCCCCcEEEEEEECCCceEEEEEhhhCCceEEE
Confidence 458999999888 4555 999999998665 777777777654333
No 90
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=34.65 E-value=1e+02 Score=27.95 Aligned_cols=35 Identities=23% Similarity=0.216 Sum_probs=27.8
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEe
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYD 134 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~ 134 (295)
..++||.+...- ++|..|.|+|..++.+.+.+...
T Consensus 29 R~~~Gd~i~v~~-g~g~~~~~~i~~i~~~~~~~~i~ 63 (234)
T PRK11713 29 RLKEGDELRLFD-GDGGEYLAEITEIGKKEVELEIL 63 (234)
T ss_pred cCCCCCEEEEEe-CCCCEEEEEEEEecCcEEEEEEE
Confidence 578999998875 58899999999997655655554
No 91
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=34.63 E-value=2e+02 Score=21.96 Aligned_cols=54 Identities=15% Similarity=0.162 Sum_probs=41.5
Q ss_pred CCCCCCCCeEEEEEcC------CCcEEEEEEeeEeC-------Cc-eEEEEecCCCEEEEcCCCcccC
Q 022567 97 QEKLAVGTKVQAVYSE------DGEWYDATIEAITP-------NG-YYVTYDSWGNKEEVDPANVRPV 150 (295)
Q Consensus 97 ~~~~kvGd~C~A~~s~------Dg~wY~A~I~~i~~-------~~-~~V~F~~Ygn~e~V~~~~lrp~ 150 (295)
+-.++.||.++..-.. |+.|+=|.|..+.+ .. +.|.-++-|-...|..+.+.-+
T Consensus 3 FL~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggaR~P~~~tlFQVadVDtG~I~wVnaD~Vt~I 70 (75)
T PF11302_consen 3 FLSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGARDPKVPTLFQVADVDTGVIRWVNADEVTHI 70 (75)
T ss_pred ccccCCCCEEEEecCccccccCCCCcEEEEEEEEeccccCCCCCceEEEEEccCCeEEEEEchheeee
Confidence 3457899999887643 57899999998873 23 7888888888888888776543
No 92
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=34.49 E-value=1.3e+02 Score=23.87 Aligned_cols=39 Identities=21% Similarity=0.285 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHH
Q 022567 10 EELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTE 54 (295)
Q Consensus 10 e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ 54 (295)
++|...++.|+.+|+.+.+.+ ..|.....++..++...+
T Consensus 2 ~~l~~~~~~l~~~i~~l~~~~------~~l~~~~~e~~~~~~~l~ 40 (129)
T cd00890 2 QELAAQLQQLQQQLEALQQQL------QKLEAQLTEYEKAKETLE 40 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHH
Confidence 566777777777777776665 334555555555544433
No 93
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=34.40 E-value=63 Score=22.86 Aligned_cols=34 Identities=24% Similarity=0.319 Sum_probs=24.7
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 148 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lr 148 (295)
|.-|.|+|..|.+.|+.|.|.+ +-.-.++.++|.
T Consensus 1 g~~~~g~V~~v~~~G~~V~l~~-~~~gli~~s~l~ 34 (70)
T cd05698 1 GLKTHGTIVKVKPNGCIVSFYN-NVKGFLPKSELS 34 (70)
T ss_pred CCEEEEEEEEEecCcEEEEECC-CCEEEEEHHHcC
Confidence 5679999999998888898854 233456665553
No 94
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=34.25 E-value=3.8e+02 Score=29.03 Aligned_cols=48 Identities=21% Similarity=0.255 Sum_probs=36.9
Q ss_pred CCCCCCCeEEEEEcCCCcEEEEEEeeEeCCc-eEEEEecCCCEEEEcCCCcccCC
Q 022567 98 EKLAVGTKVQAVYSEDGEWYDATIEAITPNG-YYVTYDSWGNKEEVDPANVRPVN 151 (295)
Q Consensus 98 ~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~-~~V~F~~Ygn~e~V~~~~lrp~~ 151 (295)
..+++||.|...- -|+ .|+|.+|.+++ +.|.+- +-+-.|++++|.++.
T Consensus 635 ~~~~~Gd~V~v~~--~~~--~g~v~~i~~~~~~~V~~g--~~k~~v~~~~l~~~~ 683 (782)
T PRK00409 635 EELKVGDEVKYLS--LGQ--KGEVLSIPDDKEAIVQAG--IMKMKVPLSDLEKIQ 683 (782)
T ss_pred cCCCCCCEEEEcc--CCc--eEEEEEEcCCCeEEEEEC--CEEEEEeHHHceeCc
Confidence 5699999999874 344 69999997555 788773 345789999998774
No 95
>COG5314 Conjugal transfer/entry exclusion protein [Intracellular trafficking and secretion]
Probab=34.03 E-value=1.4e+02 Score=27.68 Aligned_cols=50 Identities=16% Similarity=0.252 Sum_probs=41.8
Q ss_pred cCHHHHHHHHHHHHHHHHHHHHHhcc--CCCChhHHHHHHHHHHHHHHHHHH
Q 022567 7 LSIEELFSNLSTYKEQLQQVRELLVH--DPGNSEYADMEKELSEVIALTEEL 56 (295)
Q Consensus 7 ~s~e~Le~~L~~Yk~QL~qVe~aL~~--DP~N~ELl~Lk~dL~EvI~Lt~el 56 (295)
.++|..+++|.+|+.|+++..-.|.. -|++--+-.|...|.-++.|..++
T Consensus 51 rsleqVnnQIqqlQnQaq~yqNmlqNta~l~~~iw~Ql~~~l~kl~~l~d~a 102 (252)
T COG5314 51 RSLEQVNNQIQQLQNQAQQYQNMLQNTAALPFYIWGQLSQVLNKLQNLQDQA 102 (252)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCChHHHHHHHHHHHHHHHHHHHH
Confidence 35788889999999999999999864 788888888888888888777655
No 96
>PF07730 HisKA_3: Histidine kinase; InterPro: IPR011712 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 [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This entry represetns the dimerisation and phosphoacceptor domain of a sub-family of histidine kinases. It shares sequence similarity with IPR003661 from INTERPRO and IPR011102 from INTERPRO.; GO: 0000155 two-component sensor activity, 0046983 protein dimerization activity, 0000160 two-component signal transduction system (phosphorelay), 0016021 integral to membrane; PDB: 3GIE_B 3GIG_A 3EHJ_B 3EHH_B 3GIF_B 3EHF_B 3EHG_A.
Probab=33.68 E-value=1.6e+02 Score=20.50 Aligned_cols=50 Identities=22% Similarity=0.340 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCC--ChhHHHHHHHHHHHHHHHHHHHHHh
Q 022567 11 ELFSNLSTYKEQLQQVRELLVHDPG--NSEYADMEKELSEVIALTEELLATA 60 (295)
Q Consensus 11 ~Le~~L~~Yk~QL~qVe~aL~~DP~--N~ELl~Lk~dL~EvI~Lt~ell~~~ 60 (295)
.+-..|..-..+|+.+...+..+|+ .++|..+..-+.+.|.-+..++..+
T Consensus 12 ~v~q~L~~i~~~l~~~~~~~~~~~~~~~~~l~~i~~~~~~~~~~~R~~~~~L 63 (68)
T PF07730_consen 12 GVGQSLTAIKMQLEALRRRLADDPEEAREELEEIRELLREALQELRRIIHEL 63 (68)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHhhhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556777778888888888855543 2233444444444444444444443
No 97
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=33.52 E-value=87 Score=22.70 Aligned_cols=36 Identities=11% Similarity=0.241 Sum_probs=27.1
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCccc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp 149 (295)
|.-|.|+|.+|.+.|+-|.+.+++-.-.|..++|..
T Consensus 4 g~~~~g~V~~i~~fG~fv~l~~~~~eGlvh~sel~~ 39 (73)
T cd05686 4 YQIFKGEVASVTEYGAFVKIPGCRKQGLVHKSHMSS 39 (73)
T ss_pred CCEEEEEEEEEEeeeEEEEECCCCeEEEEEchhhCC
Confidence 678999999999888888886664445666666643
No 98
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide. The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=33.25 E-value=88 Score=22.86 Aligned_cols=36 Identities=17% Similarity=0.315 Sum_probs=27.1
Q ss_pred CcEEEEEEeeEeCCceEEEEecC--CCEEEEcCCCccc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSW--GNKEEVDPANVRP 149 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Y--gn~e~V~~~~lrp 149 (295)
|.-|.|+|..|...++.|.+.++ +-.-.|+.++|.+
T Consensus 1 G~~~~g~V~~v~~~G~fv~l~~~~~~~~gll~~s~l~~ 38 (79)
T cd05684 1 GKIYKGKVTSIMDFGCFVQLEGLKGRKEGLVHISQLSF 38 (79)
T ss_pred CCEEEEEEEEEEeeeEEEEEeCCCCCcEEEEEhHhccC
Confidence 56799999999988888888765 4445667776654
No 99
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=33.15 E-value=55 Score=21.23 Aligned_cols=33 Identities=21% Similarity=0.268 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCChhHHHH
Q 022567 10 EELFSNLSTYKEQLQQVRELLVHDPGNSEYADM 42 (295)
Q Consensus 10 e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~L 42 (295)
.....++-++..=....+.+|..+|+|.+..-.
T Consensus 8 a~~~~~~G~~~~A~~~~~~~l~~~P~~~~a~~~ 40 (44)
T PF13428_consen 8 ARAYRRLGQPDEAERLLRRALALDPDDPEAWRA 40 (44)
T ss_pred HHHHHHcCCHHHHHHHHHHHHHHCcCCHHHHHH
Confidence 344455566677777788899999999987644
No 100
>COG3524 KpsE Capsule polysaccharide export protein [Cell envelope biogenesis, outer membrane]
Probab=32.55 E-value=87 Score=30.30 Aligned_cols=47 Identities=21% Similarity=0.421 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHHh
Q 022567 9 IEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLATA 60 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~ 60 (295)
+..|+++|..-+.||.+|.+- ..|+|++...|+...+. |-++++...
T Consensus 225 vs~Le~eL~~iqaqL~tvks~--m~~~nPqi~~LkarieS---lrkql~qe~ 271 (372)
T COG3524 225 VSKLEDELIVIQAQLDTVKSV--MNPENPQIPGLKARIES---LRKQLLQEK 271 (372)
T ss_pred HHHHHHHHHHHHHHHHHHHHh--cCCCCCcchhHHHHHHH---HHHHHHHHH
Confidence 357899999999999999875 47888999998887664 344444433
No 101
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=32.44 E-value=74 Score=23.11 Aligned_cols=35 Identities=26% Similarity=0.405 Sum_probs=28.1
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 148 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lr 148 (295)
|.-|.|+|.+|.+.|+.|....||-.-.|.++++.
T Consensus 2 g~~~~g~V~~v~~~G~fv~l~~~~~~G~v~~~~l~ 36 (83)
T cd04471 2 GEEFDGVISGVTSFGLFVELDNLTVEGLVHVSTLG 36 (83)
T ss_pred CCEEEEEEEeEEeeeEEEEecCCCEEEEEEEEecC
Confidence 56799999999988888888877766677777664
No 102
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=31.50 E-value=1.7e+02 Score=19.76 Aligned_cols=41 Identities=15% Similarity=0.211 Sum_probs=27.7
Q ss_pred CCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEEEEcC
Q 022567 102 VGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDP 144 (295)
Q Consensus 102 vGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~ 144 (295)
.|..|.... ++..+.+++..|+++|+.+.=.+-|....+..
T Consensus 2 lG~~V~v~~--~~~~~~G~~~gId~~G~L~v~~~~g~~~~i~s 42 (48)
T PF02237_consen 2 LGQEVRVET--GDGEIEGIAEGIDDDGALLVRTEDGSIRTISS 42 (48)
T ss_dssp TTSEEEEEE--TSCEEEEEEEEEETTSEEEEEETTEEEEEESS
T ss_pred CCCEEEEEE--CCeEEEEEEEEECCCCEEEEEECCCCEEEEEE
Confidence 477888887 56677999999999994444344444444443
No 103
>PF06613 KorB_C: KorB C-terminal beta-barrel domain; InterPro: IPR010575 This domain is found in several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This family is found in conjunction with IPR003115 from INTERPRO.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1IGQ_B 1IGU_A.
Probab=31.46 E-value=1.1e+02 Score=22.40 Aligned_cols=40 Identities=30% Similarity=0.418 Sum_probs=27.2
Q ss_pred eEEEEEcCCCcEEEEEEeeE---eCCc-eEEEEecCCCEEEEcCCCcc
Q 022567 105 KVQAVYSEDGEWYDATIEAI---TPNG-YYVTYDSWGNKEEVDPANVR 148 (295)
Q Consensus 105 ~C~A~~s~Dg~wY~A~I~~i---~~~~-~~V~F~~Ygn~e~V~~~~lr 148 (295)
.++..| ||. .|++.-- +..| .+|+|.+-|+..+|.+.++.
T Consensus 10 iv~V~~--d~R--~arllLnrRps~~G~~WiKyED~G~e~E~dl~~v~ 53 (60)
T PF06613_consen 10 IVQVEH--DGR--PARLLLNRRPSSEGLAWIKYEDDGEEFEVDLGSVQ 53 (60)
T ss_dssp EEEEEE--TTE--EEEE-TTB--SSTTEEEEEETTT--EEEEEGGG-E
T ss_pred EEEEEE--CCc--hhhhhhccCCCcCCeEEEEEccCCcEEEEEccceE
Confidence 467777 787 6666422 3457 99999999999999888776
No 104
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=31.22 E-value=1.7e+02 Score=30.55 Aligned_cols=48 Identities=13% Similarity=0.196 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccCC----CCh-hHHHHHHHHHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELLVHDP----GNS-EYADMEKELSEVIALTEELL 57 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~~DP----~N~-ELl~Lk~dL~EvI~Lt~ell 57 (295)
++.|+.+|+..+.++..+++.|. || ++. ++..|-.++.++=...+++.
T Consensus 570 ~~~~e~~i~~le~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 622 (635)
T PRK11147 570 LEQLPQLLEDLEAEIEALQAQVA-DADFFSQPHEQTQKVLADLADAEQELEVAF 622 (635)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc-CchhhcccHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999996 55 223 57777666666555444443
No 105
>KOG0994 consensus Extracellular matrix glycoprotein Laminin subunit beta [Extracellular structures]
Probab=31.15 E-value=1.3e+02 Score=34.33 Aligned_cols=51 Identities=22% Similarity=0.292 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhc-----cCCCChhHHHHHHHHHHHHHHHHHHHHHh
Q 022567 10 EELFSNLSTYKEQLQQVRELLV-----HDPGNSEYADMEKELSEVIALTEELLATA 60 (295)
Q Consensus 10 e~Le~~L~~Yk~QL~qVe~aL~-----~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~ 60 (295)
++|+.+|..-.+-|.|+|+-|. .+-.+.||-.|..+..-|..++++|-..+
T Consensus 1235 ~~lr~~l~~~~e~L~~~E~~Lsdi~~~~~~a~~~LesLq~~~~~l~~~~keL~e~~ 1290 (1758)
T KOG0994|consen 1235 ESLRRQLQALTEDLPQEEETLSDITNSLPLAGKDLESLQREFNGLLTTYKELREQL 1290 (1758)
T ss_pred HHHHHHHHHHHhhhhhhhhhhhhhhhccchhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666666777777776 46677899999999998888888776554
No 106
>PF01356 A_amylase_inhib: Alpha amylase inhibitor; InterPro: IPR000833 Alpha-amylase inhibitor inhibits mammalian alpha-amylases specifically, by forming a tight stoichiometric 1:1 complex with alpha-amylase. The inhibitor has no action on plant and microbial alpha amylases. A crystal structure has been determined for tendamistat, the 74-amino acid inhibitor produced by Streptomyces tendae that targets a wide range of mammalian alpha-amylases []. The binding of tendamistat to alpha-amylase leads to the steric blockage of the active site of the enzyme. The crystal structure of tendamistat revealed an immunoglobulin-like fold that could potentially adopt multiple conformations. Such molecular flexibility could enable an induced-fit type of binding that would both optimise binding and allow broad target specificity. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; GO: 0015066 alpha-amylase inhibitor activity; PDB: 2KER_A 3AIT_A 1BVN_T 1HOE_A 4AIT_A 2AIT_A 1OK0_A.
Probab=31.15 E-value=86 Score=23.38 Aligned_cols=35 Identities=23% Similarity=0.356 Sum_probs=23.5
Q ss_pred CCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCE
Q 022567 101 AVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNK 139 (295)
Q Consensus 101 kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~ 139 (295)
...-.+-..|. ||.|=++++..- |-.++|-|||+.
T Consensus 24 a~tvsVtV~Y~-dG~~~PCrv~~P---G~~~Tf~Gygt~ 58 (68)
T PF01356_consen 24 ADTVSVTVEYT-DGQEVPCRVIPP---GDIATFPGYGTN 58 (68)
T ss_dssp SS-EEEEEEET-TS-CEEEEEE-T---TEEEEEE-TTTT
T ss_pred cccEEEEEEEe-CCCcceeEEeCC---CCEEEecccccC
Confidence 33445777886 999999998642 478899999964
No 107
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=30.86 E-value=75 Score=21.08 Aligned_cols=29 Identities=14% Similarity=0.390 Sum_probs=22.5
Q ss_pred CCCCCCCCCCeEEEEEcCCCcEEEEEEee
Q 022567 95 DNQEKLAVGTKVQAVYSEDGEWYDATIEA 123 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~ 123 (295)
+....++.||.+..+-..|..||.++...
T Consensus 11 ~~eLs~~~Gd~i~v~~~~~~~Ww~~~~~~ 39 (48)
T PF00018_consen 11 PDELSFKKGDIIEVLEKSDDGWWKVRNES 39 (48)
T ss_dssp TTBSEB-TTEEEEEEEESSSSEEEEEETT
T ss_pred CCEEeEECCCEEEEEEecCCCEEEEEECC
Confidence 45567899999999986678899998764
No 108
>TIGR03142 cytochro_ccmI cytochrome c-type biogenesis protein CcmI. This TPR repeat-containing protein is the CcmI protein (also called CycH) of c-type cytochrome biogenesis. CcmI is thought to act as an apo-cytochrome c chaperone. This model describes the N-terminal region of the protein, Members of this protein family
Probab=29.95 E-value=1e+02 Score=24.95 Aligned_cols=36 Identities=22% Similarity=0.323 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHhccC-CCChhHHHHHHHHHH
Q 022567 13 FSNLSTYKEQLQQVRELLVHD-PGNSEYADMEKELSE 48 (295)
Q Consensus 13 e~~L~~Yk~QL~qVe~aL~~D-P~N~ELl~Lk~dL~E 48 (295)
+.++.-|+.||..++.-+... =+.+|+..++.||+.
T Consensus 35 ~~n~~iyr~qL~ELe~d~~~G~l~~~e~~~~~~El~r 71 (117)
T TIGR03142 35 ELNLAVYRDRLAELERDLAEGLLDEAEAEAARAELQR 71 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 467889999999999988752 244678888888764
No 109
>PRK02001 hypothetical protein; Validated
Probab=29.87 E-value=1.7e+02 Score=25.09 Aligned_cols=34 Identities=9% Similarity=0.266 Sum_probs=28.0
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEe
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYD 134 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~ 134 (295)
--+|..|...+. ++..|.++|.+++++++++...
T Consensus 87 r~~G~~v~V~l~-~~~~~~G~L~~~~~~~i~l~~~ 120 (152)
T PRK02001 87 KNIGRELEVLTK-NGKKIEGELKSADENDITLEVK 120 (152)
T ss_pred HhCCCEEEEEEC-CCCEEEEEEEEEeCCEEEEEEc
Confidence 468999999985 7999999999998776666554
No 110
>PRK04406 hypothetical protein; Provisional
Probab=29.55 E-value=2.5e+02 Score=21.18 Aligned_cols=25 Identities=24% Similarity=0.279 Sum_probs=15.5
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHh
Q 022567 6 ELSIEELFSNLSTYKEQLQQVRELL 30 (295)
Q Consensus 6 ~~s~e~Le~~L~~Yk~QL~qVe~aL 30 (295)
+.+++.|++.|...+.+|.--+..+
T Consensus 3 ~~~~~~le~Ri~~LE~~lAfQE~tI 27 (75)
T PRK04406 3 EKTIEQLEERINDLECQLAFQEQTI 27 (75)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456667777777666666555554
No 111
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=29.47 E-value=1.4e+02 Score=19.04 Aligned_cols=29 Identities=10% Similarity=0.404 Sum_probs=21.3
Q ss_pred CCCCCCCCCCeEEEEEcCCCcEEEEEEee
Q 022567 95 DNQEKLAVGTKVQAVYSEDGEWYDATIEA 123 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~ 123 (295)
+....+..||.+...-..++.|+.++...
T Consensus 13 ~~~l~~~~Gd~v~v~~~~~~~w~~~~~~~ 41 (54)
T cd00174 13 PDELSFKKGDIIEVLEKSDDGWWEGRLLG 41 (54)
T ss_pred CCCCCCCCCCEEEEEEcCCCCeEEEEECC
Confidence 34567899999998875467788887543
No 112
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=28.93 E-value=1.4e+02 Score=21.24 Aligned_cols=38 Identities=16% Similarity=0.379 Sum_probs=25.5
Q ss_pred CCCCCeEEEEEcCCCcE--EEEEEeeEeCCceEEEEecCCCE
Q 022567 100 LAVGTKVQAVYSEDGEW--YDATIEAITPNGYYVTYDSWGNK 139 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~w--Y~A~I~~i~~~~~~V~F~~Ygn~ 139 (295)
+-+|..|...-. +..| |.+.|..|++..+.|.|.| ||=
T Consensus 2 ilPG~~V~V~n~-~~~Y~~y~G~VQRvsdgkaaVLFEG-GnW 41 (53)
T PF11623_consen 2 ILPGSTVRVKNP-NDIYYGYEGFVQRVSDGKAAVLFEG-GNW 41 (53)
T ss_dssp --TT-EEEE--T-TSTTTT-EEEEEEEETTEEEEEEEE-TTE
T ss_pred ccCCCEEEEeCC-CCccchheEEEEEeeCCeEEEEecC-CCc
Confidence 356888888853 4444 6899999987779999999 664
No 113
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=28.83 E-value=53 Score=22.66 Aligned_cols=23 Identities=26% Similarity=0.505 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHhccCCCChhHH
Q 022567 18 TYKEQLQQVRELLVHDPGNSEYA 40 (295)
Q Consensus 18 ~Yk~QL~qVe~aL~~DP~N~ELl 40 (295)
.|..=++..+.+|..+|+|.+..
T Consensus 6 ~~~~A~~~~~~~l~~~p~~~~~~ 28 (68)
T PF14559_consen 6 DYDEAIELLEKALQRNPDNPEAR 28 (68)
T ss_dssp HHHHHHHHHHHHHHHTTTSHHHH
T ss_pred CHHHHHHHHHHHHHHCCCCHHHH
Confidence 45666667777777788777753
No 114
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=28.08 E-value=1.7e+02 Score=25.69 Aligned_cols=54 Identities=20% Similarity=0.420 Sum_probs=40.4
Q ss_pred CCCCCCCCCCCeEEEEEcCCCcE--EEEEEeeEeCC-c-eEEEEecCCCE--EEEcCCCcccC
Q 022567 94 SDNQEKLAVGTKVQAVYSEDGEW--YDATIEAITPN-G-YYVTYDSWGNK--EEVDPANVRPV 150 (295)
Q Consensus 94 ~~~~~~~kvGd~C~A~~s~Dg~w--Y~A~I~~i~~~-~-~~V~F~~Ygn~--e~V~~~~lrp~ 150 (295)
+.....+.+||.+... ||-| +.|+|..|+.+ + ..|....+|.. .+|.+++|+.+
T Consensus 118 ~~~~~~~e~Gd~VrI~---~GpFa~f~g~V~evd~ek~~~~v~v~ifgr~tPVel~~~qVek~ 177 (178)
T COG0250 118 KKPKVDFEPGDVVRII---DGPFAGFKAKVEEVDEEKGKLKVEVSIFGRPTPVELEFDQVEKL 177 (178)
T ss_pred CcccccCCCCCEEEEe---ccCCCCccEEEEEEcCcCcEEEEEEEEeCCceEEEEehhhEEEe
Confidence 4556789999999988 4444 78999999976 4 77777777754 56777777643
No 115
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=28.00 E-value=1e+02 Score=24.08 Aligned_cols=27 Identities=19% Similarity=0.240 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHhccCCCChhHH
Q 022567 14 SNLSTYKEQLQQVRELLVHDPGNSEYA 40 (295)
Q Consensus 14 ~~L~~Yk~QL~qVe~aL~~DP~N~ELl 40 (295)
..+.+|..=+...+.++..+|+|.++.
T Consensus 62 ~~~~~~~~A~~~~~~~~~~~p~~~~~~ 88 (135)
T TIGR02552 62 QMLKEYEEAIDAYALAAALDPDDPRPY 88 (135)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCChHHH
Confidence 344445555555556666666665543
No 116
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=27.94 E-value=1.9e+02 Score=20.94 Aligned_cols=36 Identities=22% Similarity=0.326 Sum_probs=26.4
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEE
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKE 140 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e 140 (295)
-.+||.+..+ +| ..++|..+.++.+.|....+++..
T Consensus 4 a~vGdiIefk---~g--~~G~V~kv~eNSVIVdIT~m~~~~ 39 (57)
T PF09953_consen 4 AKVGDIIEFK---DG--FTGIVEKVYENSVIVDITIMENFD 39 (57)
T ss_pred cccCcEEEEc---CC--cEEEEEEEecCcEEEEEEecCCcc
Confidence 3689999853 67 499999999888666665555543
No 117
>cd02417 Peptidase_C39_likeA A sub-family of peptidase C39 which contains Cyclolysin and Hemolysin processing peptidases. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in this
Probab=27.52 E-value=67 Score=24.99 Aligned_cols=41 Identities=12% Similarity=0.091 Sum_probs=27.5
Q ss_pred eEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcc
Q 022567 105 KVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 148 (295)
Q Consensus 105 ~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lr 148 (295)
.|++.+. ||.| ++|.+++++.+.|..-+.+..+.++.+++.
T Consensus 71 P~I~~~~-~g~~--~Vl~~~~~~~~~i~dp~~~~~~~~~~~el~ 111 (121)
T cd02417 71 PALAWDD-DGGH--FILAKLDGQKYLIQDPISQRPEVLSREEFE 111 (121)
T ss_pred CEEEEcc-CCCE--EEEEEEcCCCEEEECCCcCCCeecCHHHHH
Confidence 6999875 7776 678888755577766555655566665554
No 118
>PRK14633 hypothetical protein; Provisional
Probab=27.41 E-value=1.7e+02 Score=24.92 Aligned_cols=51 Identities=18% Similarity=0.311 Sum_probs=36.8
Q ss_pred CCCCCCeEEEEE-c--CCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcccC
Q 022567 99 KLAVGTKVQAVY-S--EDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRPV 150 (295)
Q Consensus 99 ~~kvGd~C~A~~-s--~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp~ 150 (295)
..-+|..|.... . +++..|.+++.+++++.+++...+ |....+++++|+..
T Consensus 90 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~i~l~~~~-~~~~~i~~~~I~ka 143 (150)
T PRK14633 90 QALVGFNVKAVTLAPVGSQTKFKGVLERVEGNNVILNLED-GKEISFDFDELKKL 143 (150)
T ss_pred HHhCCCeEEEEEecccCCcEEEEEEEEEEeCCEEEEEEcC-CcEEEEEhHHeeeE
Confidence 357899988865 2 378999999999987766665432 44557888887753
No 119
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=27.26 E-value=1.5e+02 Score=21.86 Aligned_cols=35 Identities=23% Similarity=0.640 Sum_probs=26.4
Q ss_pred CCCCCeEEEEEcCCCcEEEE--EEeeEeCCc----eEEEEec
Q 022567 100 LAVGTKVQAVYSEDGEWYDA--TIEAITPNG----YYVTYDS 135 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A--~I~~i~~~~----~~V~F~~ 135 (295)
++.|+.|..+= ..--||.- +|-+|+.++ +.|+|..
T Consensus 2 i~rGskVrIlR-~ESYWyn~vGtV~svd~~gi~YPV~VRF~k 42 (64)
T CHL00125 2 VKRGSKVRILR-KESYWYNEIGTVATVDQSGIRYPVLVRFEK 42 (64)
T ss_pred cccCCEEEEcc-ccceeecCcceEEEEcCCCCCccEEEEEee
Confidence 56799998885 47779986 777887554 7888864
No 120
>PHA00728 hypothetical protein
Probab=27.16 E-value=89 Score=26.14 Aligned_cols=31 Identities=19% Similarity=0.307 Sum_probs=24.6
Q ss_pred CCCccccCHHHHHHHHHHHHHHHHHHHHHhccC
Q 022567 1 MQGGEELSIEELFSNLSTYKEQLQQVRELLVHD 33 (295)
Q Consensus 1 m~~~e~~s~e~Le~~L~~Yk~QL~qVe~aL~~D 33 (295)
||- -..+|+|..+-++.+..|+.+++++-.+
T Consensus 1 mak--~teveql~keneelkkkla~leal~nn~ 31 (151)
T PHA00728 1 MAK--LTEVEQLKKENEELKKKLAELEALMNNE 31 (151)
T ss_pred Ccc--hhHHHHHHHhHHHHHHHHHHHHHHHcCC
Confidence 554 3347899999999999999999998764
No 121
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=27.04 E-value=1.8e+02 Score=23.19 Aligned_cols=12 Identities=17% Similarity=0.335 Sum_probs=9.4
Q ss_pred CCCcEEEEEEee
Q 022567 112 EDGEWYDATIEA 123 (295)
Q Consensus 112 ~Dg~wY~A~I~~ 123 (295)
+.+.|.+|.|..
T Consensus 56 g~~~~~~~~i~~ 67 (129)
T cd00890 56 GAGLFVKAEVKD 67 (129)
T ss_pred CCceEEEEEECC
Confidence 468888998875
No 122
>PHA01809 hypothetical protein
Probab=26.95 E-value=32 Score=24.47 Aligned_cols=26 Identities=27% Similarity=0.525 Sum_probs=17.4
Q ss_pred CCCCCCCCeEEEEEcCCC-----cEEEEEEeeE
Q 022567 97 QEKLAVGTKVQAVYSEDG-----EWYDATIEAI 124 (295)
Q Consensus 97 ~~~~kvGd~C~A~~s~Dg-----~wY~A~I~~i 124 (295)
...|+-|+.|.|+| |. .||..-|..|
T Consensus 13 vfrfkngslcialf--drteneisfydvdidei 43 (65)
T PHA01809 13 VFRFKNGSLCIALF--DRTENEISFYDVDIDEI 43 (65)
T ss_pred EEEecCCcEEEEEe--ccccceeeeEecChHHh
Confidence 34688999999999 32 3555544444
No 123
>TIGR02861 SASP_H small acid-soluble spore protein, H-type. This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of Bacillus subtilis.
Probab=26.91 E-value=84 Score=22.74 Aligned_cols=39 Identities=21% Similarity=0.323 Sum_probs=28.3
Q ss_pred EEEEEcCCCcEEEEEEeeEeCC-c-eEEEEecC-CCEEEEcCCCcc
Q 022567 106 VQAVYSEDGEWYDATIEAITPN-G-YYVTYDSW-GNKEEVDPANVR 148 (295)
Q Consensus 106 C~A~~s~Dg~wY~A~I~~i~~~-~-~~V~F~~Y-gn~e~V~~~~lr 148 (295)
.-..| +|. +-.|..|+++ + ++|.+.+- ++...|++.+|.
T Consensus 16 i~V~Y--~G~--pV~Ie~vde~~~tA~V~~l~~p~~~~~Vpv~~L~ 57 (58)
T TIGR02861 16 INVTY--KGV--PVYIEHVDEQSGTARVYSLDNPGKEQDVPVNDLE 57 (58)
T ss_pred eEEEE--CCE--EEEEEEEcCCCCeEEEEECCCCCcEEEEEHHHcc
Confidence 34455 342 6679999854 4 99999984 777899988774
No 124
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=26.86 E-value=93 Score=25.92 Aligned_cols=46 Identities=24% Similarity=0.421 Sum_probs=32.5
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEeC--Cc--eEEEEecCCCEEEEcCCCc
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAITP--NG--YYVTYDSWGNKEEVDPANV 147 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~~--~~--~~V~F~~Ygn~e~V~~~~l 147 (295)
.+.+|..|+|.+ +|.-|..++|..+.. +. |.|. .+ |++-.+...+|
T Consensus 55 plpl~~eV~A~~-eddY~~~GvV~~h~~~~~e~yY~Ve-~d-G~~~~~~r~~v 104 (122)
T PF09038_consen 55 PLPLGTEVTALS-EDDYFSPGVVKGHKTDSGEVYYCVE-TD-GQRKRYQRKDV 104 (122)
T ss_dssp SS-TTEEEEECC-TTCTSEEEEEEEEEEETTEEEEEEE-ET-TEEEEEEGGGE
T ss_pred ceeccceeEEee-cCCcccccEEEEEEccCCcEEEEEE-EC-CCEEEEEeeeE
Confidence 456788999985 799999999998872 22 6666 55 66666555544
No 125
>KOG1118 consensus Lysophosphatidic acid acyltransferase endophilin/SH3GL, involved in synaptic vesicle formation [Lipid transport and metabolism; Signal transduction mechanisms]
Probab=26.63 E-value=3.9e+02 Score=26.03 Aligned_cols=38 Identities=18% Similarity=0.436 Sum_probs=26.3
Q ss_pred CCCCCCCCCCeEEEEEcCCCcEEEEEEeeEeCCc-eEEEEe
Q 022567 95 DNQEKLAVGTKVQAVYSEDGEWYDATIEAITPNG-YYVTYD 134 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~-~~V~F~ 134 (295)
...-.|+.||.....---|-.||.+.+.+-+ | +-|.|+
T Consensus 320 EgEL~fkeGDlI~l~~QIdenWyeG~~~g~s--G~FPvnYv 358 (366)
T KOG1118|consen 320 EGELDFKEGDLITLTNQIDENWYEGEKHGES--GMFPVNYV 358 (366)
T ss_pred CCccCcccCceeeehhhcCcchhhheecCcc--Ccccccee
Confidence 3445677777777766667889999998764 4 555554
No 126
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=26.53 E-value=1e+02 Score=22.30 Aligned_cols=41 Identities=20% Similarity=0.256 Sum_probs=29.4
Q ss_pred CeEEEEEcCCCcEEEEEEeeEeCC-c-eEEEEe-cCCCEEEEcCCCcc
Q 022567 104 TKVQAVYSEDGEWYDATIEAITPN-G-YYVTYD-SWGNKEEVDPANVR 148 (295)
Q Consensus 104 d~C~A~~s~Dg~wY~A~I~~i~~~-~-~~V~F~-~Ygn~e~V~~~~lr 148 (295)
+..-..| +| -+-.|..|+++ + ++|.+. .-++...|++.+|.
T Consensus 14 ~~i~V~y--~G--~pV~Ie~vde~~~tA~V~~l~~p~~~~~Vpv~~L~ 57 (58)
T PF08141_consen 14 DMIEVTY--NG--VPVWIEHVDEENGTARVHPLDNPEEEQEVPVNDLE 57 (58)
T ss_pred ceEEEEE--CC--EEEEEEEEcCCCCeEEEEECCCCCcEEEEEHHHcc
Confidence 3445566 45 37779999854 4 999999 45566899988774
No 127
>PF03681 UPF0150: Uncharacterised protein family (UPF0150); InterPro: IPR005357 This family of small proteins is uncharacterised. In Q9A3L8 from SWISSPROT this domain is found next to a DNA binding helix-turn-helix domain IPR002145 from INTERPRO, which suggests that this is some kind of ligand binding domain.; PDB: 2DSY_C 2YZT_A 3KWR_A.
Probab=26.38 E-value=95 Score=20.70 Aligned_cols=21 Identities=29% Similarity=0.513 Sum_probs=16.0
Q ss_pred EEEEEeeEeCCc-eEEEEecCCC
Q 022567 117 YDATIEAITPNG-YYVTYDSWGN 138 (295)
Q Consensus 117 Y~A~I~~i~~~~-~~V~F~~Ygn 138 (295)
|+++|.. .+++ |.+.|-++..
T Consensus 2 Y~~~i~~-~~~~~y~~~~pdlpg 23 (48)
T PF03681_consen 2 YPAIIEK-DEDGGYVAYFPDLPG 23 (48)
T ss_dssp EEEEEEE--TSSSEEEEETTCCT
T ss_pred EEEEEEE-CCCCeEEEEeCCccC
Confidence 8999998 5555 9999988753
No 128
>PRK00306 50S ribosomal protein L29; Reviewed
Probab=26.37 E-value=2.6e+02 Score=20.32 Aligned_cols=49 Identities=22% Similarity=0.360 Sum_probs=35.6
Q ss_pred cccCHHHHHHHHHHHHHHHHHHH--HHhccCCCC-hhHHHHHHHHHHHHHHHH
Q 022567 5 EELSIEELFSNLSTYKEQLQQVR--ELLVHDPGN-SEYADMEKELSEVIALTE 54 (295)
Q Consensus 5 e~~s~e~Le~~L~~Yk~QL~qVe--~aL~~DP~N-~ELl~Lk~dL~EvI~Lt~ 54 (295)
-.+|.++|...|.+++.+|-... .+... ++| ..+..+|.++--+-....
T Consensus 7 r~ls~~eL~~~l~~lkkeL~~lR~~~~~~~-~~n~~~i~~~rk~IARi~Tvl~ 58 (66)
T PRK00306 7 RELSVEELNEKLLELKKELFNLRFQKATGQ-LENTHRLREVRRDIARIKTVLR 58 (66)
T ss_pred hhCCHHHHHHHHHHHHHHHHHHHHHHHhCC-CcCcHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998877 33333 444 467888888877665443
No 129
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=26.31 E-value=97 Score=21.94 Aligned_cols=34 Identities=26% Similarity=0.453 Sum_probs=25.2
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 148 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lr 148 (295)
|.-|.|+|..|.+.|+.|.+.. +-.-.|+.++|.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~-~v~g~i~~~~l~ 34 (69)
T cd05697 1 GQVVKGTIRKLRPSGIFVKLSD-HIKGLVPPMHLA 34 (69)
T ss_pred CCEEEEEEEEEeccEEEEEecC-CcEEEEEHHHCC
Confidence 5679999999998888888853 344566666664
No 130
>TIGR00012 L29 ribosomal protein L29. called L29 in prokaryotic (50S) large subunits and L35 in eukaryotic (60S) large subunits.
Probab=25.91 E-value=2.4e+02 Score=19.77 Aligned_cols=47 Identities=19% Similarity=0.292 Sum_probs=33.3
Q ss_pred ccCHHHHHHHHHHHHHHHHHHH--HHhccCCCChhHHHHHHHHHHHHHH
Q 022567 6 ELSIEELFSNLSTYKEQLQQVR--ELLVHDPGNSEYADMEKELSEVIAL 52 (295)
Q Consensus 6 ~~s~e~Le~~L~~Yk~QL~qVe--~aL~~DP~N~ELl~Lk~dL~EvI~L 52 (295)
++|.++|.+.|.+.+.+|-.+. .+...-.+-..+..+|.++--+-.+
T Consensus 4 ~~s~~EL~~~l~~lr~eLf~Lr~~~~~~~~~~~~~i~~~Rk~IARi~Tv 52 (55)
T TIGR00012 4 EKSKEELAKKLDELKKELFELRFQKATGQLAKPHRIRQVRRDIARLLTV 52 (55)
T ss_pred hCCHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHHHH
Confidence 5788999999999999998887 3332222334778888887765443
No 131
>PTZ00446 vacuolar sorting protein SNF7-like; Provisional
Probab=25.78 E-value=1.9e+02 Score=25.89 Aligned_cols=43 Identities=16% Similarity=0.355 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccC-CCChhHHHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELLVHD-PGNSEYADMEKELSEVIA 51 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~~D-P~N~ELl~Lk~dL~EvI~ 51 (295)
+++|..++++..+.=..|..+|... |++.+--.|-.||.++-.
T Consensus 132 Vd~lmDei~E~~e~~~EIseaLs~~~~~~~DEdELe~ELe~Le~ 175 (191)
T PTZ00446 132 VEKIIDTIQENKDIQEEINQALSFNLLNNVDDDEIDKELDLLKE 175 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHHHH
Confidence 5678888888888888999999865 455555666667766543
No 132
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=25.55 E-value=1.8e+02 Score=24.69 Aligned_cols=49 Identities=12% Similarity=0.244 Sum_probs=36.8
Q ss_pred CCCCCCeEEEEE---cCCCcEEEEEEeeEeCCceEEEEecCCC--EEEEcCCCccc
Q 022567 99 KLAVGTKVQAVY---SEDGEWYDATIEAITPNGYYVTYDSWGN--KEEVDPANVRP 149 (295)
Q Consensus 99 ~~kvGd~C~A~~---s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn--~e~V~~~~lrp 149 (295)
..-+|..|...+ -.++..|.++|.+++++.+++... |. ..++++++|+-
T Consensus 94 ~r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~i~l~~~--~~~~~~~i~~~~I~~ 147 (154)
T PRK00092 94 RRFIGREVKVKLYEPIDGRKKFQGILLAVDGETVTLEVE--GKEKEVEIPLDNIAK 147 (154)
T ss_pred HHhCCCeEEEEEEcccCCceEEEEEEEEeeCCEEEEEEC--CCeEEEEEEHHHcce
Confidence 357899999986 257889999999998877665543 34 56778777764
No 133
>cd02419 Peptidase_C39C A sub-family of peptidase family C39. Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is conserved in this sub-family.
Probab=25.52 E-value=79 Score=24.82 Aligned_cols=42 Identities=5% Similarity=0.120 Sum_probs=28.9
Q ss_pred CeEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCccc
Q 022567 104 TKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 104 d~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp 149 (295)
-.|++.|. ||.| ++|.+++++.+.|..-+.| .+.++.+++..
T Consensus 75 lP~i~~~~-~g~~--~Vl~~~~~~~~~i~dp~~~-~~~~~~~el~~ 116 (127)
T cd02419 75 LPCILHWD-MNHF--VVLKKVSRRRIVIHDPALG-KRKLSLEEASR 116 (127)
T ss_pred CCEEEEEC-CCEE--EEEEEEcCCEEEEECCccC-CEEEcHHHHHh
Confidence 47999884 7766 6888886555777666654 55777766654
No 134
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=25.33 E-value=1.7e+02 Score=23.37 Aligned_cols=40 Identities=18% Similarity=0.422 Sum_probs=31.0
Q ss_pred CCCCCCCCCCeEEEEEcCCCcEEEE--EEeeEeCC-c----eEEEEec
Q 022567 95 DNQEKLAVGTKVQAVYSEDGEWYDA--TIEAITPN-G----YYVTYDS 135 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~Dg~wY~A--~I~~i~~~-~----~~V~F~~ 135 (295)
+++..++.|+.|..+- ..--||.- +|.+|+.+ + +.|+|..
T Consensus 35 pp~ig~~RGskVrIlR-~ESYWyn~vGtVvsVDq~~girYPVvVRF~k 81 (101)
T PLN00045 35 PPPIGPKRGSKVKILR-PESYWFNDVGKVVAVDQDPGVRYPVVVRFEK 81 (101)
T ss_pred CCCcccCCCCEEEEcc-ccceeecCcceEEEEeCCCCcccceEEEeee
Confidence 5567899999999985 47789986 77788754 3 7888864
No 135
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=25.11 E-value=1.2e+02 Score=20.79 Aligned_cols=34 Identities=12% Similarity=0.211 Sum_probs=24.0
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 148 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lr 148 (295)
|.-|.|+|.+|...++.|.+.. +-.-.++.+++.
T Consensus 1 g~~~~g~V~~i~~~G~fv~l~~-~~~g~~~~~~l~ 34 (68)
T cd05685 1 GMVLEGVVTNVTDFGAFVDIGV-KQDGLIHISKMA 34 (68)
T ss_pred CCEEEEEEEEEecccEEEEcCC-CCEEEEEHHHCC
Confidence 4569999999998887787753 333456655554
No 136
>PRK13879 conjugal transfer protein TrbJ; Provisional
Probab=25.08 E-value=2.4e+02 Score=26.28 Aligned_cols=46 Identities=15% Similarity=0.395 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcc--CCCChhHHHHHHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELLVH--DPGNSEYADMEKELSEVIALTE 54 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~~--DP~N~ELl~Lk~dL~EvI~Lt~ 54 (295)
++.+...+++|+.|+++.+.-|.. .|....+-.+...|..|+..+.
T Consensus 47 v~q~~~Qi~Qlq~Qiqqy~nql~Nl~~lp~~~w~~~~~~i~~L~~~a~ 94 (253)
T PRK13879 47 VAQTLKQIEQYQTQLQQYENMLQNTMAPAAYIWDQAQSTINGLMNAVD 94 (253)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHHH
Confidence 345567778888888888877754 5777888899999998888764
No 137
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=24.98 E-value=1.5e+02 Score=21.58 Aligned_cols=38 Identities=21% Similarity=0.387 Sum_probs=28.9
Q ss_pred CCCCeEEEEEcCCCcEEEEEEeeEe--CCc--eEEEEecCCCE
Q 022567 101 AVGTKVQAVYSEDGEWYDATIEAIT--PNG--YYVTYDSWGNK 139 (295)
Q Consensus 101 kvGd~C~A~~s~Dg~wY~A~I~~i~--~~~--~~V~F~~Ygn~ 139 (295)
+|+|.|..+- +.|.--.++|..|. ..| |.|...+|-.-
T Consensus 2 kvnD~VtVKT-DG~~rR~G~ilavE~F~EG~MYLvaL~dYP~G 43 (62)
T PF10781_consen 2 KVNDRVTVKT-DGGPRREGVILAVEPFNEGTMYLVALEDYPAG 43 (62)
T ss_pred ccccEEEEec-CCcccccceEEEEeeccCcEEEEEEcCcCCcc
Confidence 6789999884 44556778998887 344 99999999754
No 138
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.90 E-value=1.2e+02 Score=22.43 Aligned_cols=34 Identities=9% Similarity=0.228 Sum_probs=24.9
Q ss_pred CCcEEEEEEeeEeCCceEEEEecCCC-EEEEcCCCc
Q 022567 113 DGEWYDATIEAITPNGYYVTYDSWGN-KEEVDPANV 147 (295)
Q Consensus 113 Dg~wY~A~I~~i~~~~~~V~F~~Ygn-~e~V~~~~l 147 (295)
.|.-+.|.|.+|.+.||.|.| ++++ +--++.+++
T Consensus 4 ~G~~v~g~V~si~d~G~~v~~-g~~gv~Gfl~~~~~ 38 (74)
T cd05694 4 EGMVLSGCVSSVEDHGYILDI-GIPGTTGFLPKKDA 38 (74)
T ss_pred CCCEEEEEEEEEeCCEEEEEe-CCCCcEEEEEHHHC
Confidence 466789999999988899998 6544 445555544
No 139
>KOG2991 consensus Splicing regulator [RNA processing and modification]
Probab=24.50 E-value=1.3e+02 Score=28.41 Aligned_cols=43 Identities=26% Similarity=0.312 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh---ccCCC-ChhHHHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELL---VHDPG-NSEYADMEKELSEVIA 51 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL---~~DP~-N~ELl~Lk~dL~EvI~ 51 (295)
+.++-..+..|+.|++=--..| ..||- |.+++.||.+|++-=.
T Consensus 145 mqe~~sqi~~lK~qq~Ps~~qlR~~llDPAinl~F~rlK~ele~tk~ 191 (330)
T KOG2991|consen 145 MQECTSQIQYLKQQQQPSVAQLRSTLLDPAINLFFLRLKGELEQTKD 191 (330)
T ss_pred HHHHHHHHHHHHHhhCcHHHHHHHHhhChHHHHHHHHHHHHHHHHHH
Confidence 4566677777777765433333 24776 8888999999987433
No 140
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=24.44 E-value=66 Score=19.18 Aligned_cols=26 Identities=31% Similarity=0.507 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCCC
Q 022567 11 ELFSNLSTYKEQLQQVRELLVHDPGN 36 (295)
Q Consensus 11 ~Le~~L~~Yk~QL~qVe~aL~~DP~N 36 (295)
.+--.+..|..=+.-.+.+|+.||+|
T Consensus 9 ~~~~~~~~~~~A~~~~~~al~~~p~~ 34 (34)
T PF00515_consen 9 NAYFQLGDYEEALEYYQRALELDPDN 34 (34)
T ss_dssp HHHHHTT-HHHHHHHHHHHHHHSTTH
T ss_pred HHHHHhCCchHHHHHHHHHHHHCcCC
Confidence 34456677888888888999999975
No 141
>smart00503 SynN Syntaxin N-terminal domain. Three-helix domain that (in Sso1p) slows the rate of its reaction with the SNAP-25 homologue Sec9p
Probab=23.59 E-value=3.5e+02 Score=20.89 Aligned_cols=49 Identities=16% Similarity=0.334 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhc---cCCCChhHHHHHHHHHHHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELLV---HDPGNSEYADMEKELSEVIALTEELLAT 59 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~---~DP~N~ELl~Lk~dL~EvI~Lt~ell~~ 59 (295)
++++...|..+...+.+++.+.. ..++ ....++.+|..++.=+..+...
T Consensus 10 v~~I~~~I~~i~~~v~~l~~l~~~~l~~~~--~~~~~~~~l~~~~~~~~~~~~~ 61 (117)
T smart00503 10 VEEIRANIQKISQNVAELQKLHEELLTPPD--ADKELREKLERLIDDIKRLAKE 61 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccCc--hhHHHHHHHHHHHHHHHHHHHH
Confidence 45667777777766666665443 3333 2234455555555444444433
No 142
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=23.46 E-value=1.3e+02 Score=20.62 Aligned_cols=35 Identities=20% Similarity=0.336 Sum_probs=25.1
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCccc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp 149 (295)
|.-|.|+|..|...++.|.+.+ +-.-.++.++|..
T Consensus 1 g~~~~g~V~~v~~~G~~v~l~~-~~~g~l~~~~l~~ 35 (68)
T cd04472 1 GKIYEGKVVKIKDFGAFVEILP-GKDGLVHISELSD 35 (68)
T ss_pred CCEEEEEEEEEEEeEEEEEeCC-CCEEEEEhHHcCC
Confidence 4678999999998888888753 3445666666653
No 143
>PRK15326 type III secretion system needle complex protein PrgI; Provisional
Probab=23.32 E-value=1.8e+02 Score=22.51 Aligned_cols=31 Identities=10% Similarity=0.246 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCChhHH
Q 022567 10 EELFSNLSTYKEQLQQVRELLVHDPGNSEYA 40 (295)
Q Consensus 10 e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl 40 (295)
+.|+....+.-.+|......|..+|+|+-+|
T Consensus 14 ~~~~~~a~~~~~~l~~Al~~l~~~pdnP~~L 44 (80)
T PRK15326 14 AKFDTGVDNLQTQVTEALDKLAAKPSDPALL 44 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhcCCCCHHHH
Confidence 4677778888889999999999999998754
No 144
>PRK10708 hypothetical protein; Provisional
Probab=23.20 E-value=1.7e+02 Score=21.19 Aligned_cols=38 Identities=18% Similarity=0.345 Sum_probs=28.9
Q ss_pred CCCCeEEEEEcCCCcEEEEEEeeEe--CCc--eEEEEecCCCE
Q 022567 101 AVGTKVQAVYSEDGEWYDATIEAIT--PNG--YYVTYDSWGNK 139 (295)
Q Consensus 101 kvGd~C~A~~s~Dg~wY~A~I~~i~--~~~--~~V~F~~Ygn~ 139 (295)
+|+|+|..+- +.|.--.++|..|. ..| |.|...+|-+-
T Consensus 2 kvnD~VtVKT-DG~~rR~G~iLavE~F~EG~MyLvaL~dYP~G 43 (62)
T PRK10708 2 KVNDRVTVKT-DGGPRRPGVVLAVEEFSEGTMYLVSLEDYPLG 43 (62)
T ss_pred ccccEEEEec-CCCccccceEEEEeeccCcEEEEEEcCcCCCc
Confidence 6789999884 45566788998887 344 99999998754
No 145
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=23.13 E-value=1.3e+02 Score=20.37 Aligned_cols=36 Identities=22% Similarity=0.351 Sum_probs=26.3
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcccC
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRPV 150 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp~ 150 (295)
|.-|.|+|..++..++.|.+. .+-.-.++.+++.+.
T Consensus 3 G~~v~g~V~~v~~~g~~v~i~-~~~~g~l~~~~~~~~ 38 (72)
T smart00316 3 GDVVEGTVTEITPFGAFVDLG-NGVEGLIPISELSDK 38 (72)
T ss_pred CCEEEEEEEEEEccEEEEEeC-CCCEEEEEHHHCCcc
Confidence 778999999999888877774 244456777666653
No 146
>PF12945 YcgR_2: Flagellar protein YcgR; PDB: 2RDE_B 1YLN_A 3KYG_A.
Probab=23.09 E-value=2.5e+02 Score=20.50 Aligned_cols=34 Identities=18% Similarity=0.401 Sum_probs=21.8
Q ss_pred CCCCCeEEEEE-cCCC--cEEEEEEeeEeCCc-eEEEE
Q 022567 100 LAVGTKVQAVY-SEDG--EWYDATIEAITPNG-YYVTY 133 (295)
Q Consensus 100 ~kvGd~C~A~~-s~Dg--~wY~A~I~~i~~~~-~~V~F 133 (295)
+++|+.+.... .++| .+|+++|.++.++. ..|..
T Consensus 1 L~iG~~i~i~i~~~~~~~~~y~S~v~g~~~~~~l~i~~ 38 (87)
T PF12945_consen 1 LKIGQKIEIEITNPTGEKGRYKSRVIGIDDDRYLIISM 38 (87)
T ss_dssp --TT-EEEEEEE-TTS-EEEEEEEEEEEETTTEEEEE-
T ss_pred CCCCCEEEEEEECCCCceEEEEEEEEEECCCCEEEEEc
Confidence 36899988766 3443 46999999999775 55544
No 147
>PF11691 DUF3288: Protein of unknown function (DUF3288); InterPro: IPR021705 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=22.74 E-value=1.8e+02 Score=22.95 Aligned_cols=44 Identities=34% Similarity=0.548 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHhccCCCChhHH----------------HHHHHHHHHHH---HHHHHHHHhhh
Q 022567 19 YKEQLQQVRELLVHDPGNSEYA----------------DMEKELSEVIA---LTEELLATAKQ 62 (295)
Q Consensus 19 Yk~QL~qVe~aL~~DP~N~ELl----------------~Lk~dL~EvI~---Lt~ell~~~~~ 62 (295)
|..--..|+.+|..+|+..+|. .|+.||..|++ ||++.|....+
T Consensus 8 ~~~DR~~vd~Ll~~~p~d~~L~eLARL~iRY~gFPGA~diq~DL~kiL~~W~lteeeLf~kTR 70 (90)
T PF11691_consen 8 YKTDREIVDRLLAGEPTDYNLAELARLRIRYQGFPGARDIQKDLDKILQKWGLTEEELFEKTR 70 (90)
T ss_pred hhhhHHHHHHHHcCCCCchhHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5556678999999999988874 45788888875 68888877654
No 148
>PF07739 TipAS: TipAS antibiotic-recognition domain; InterPro: IPR012925 TipAL is a bacterial transcriptional regulator of the MerR family. The tipA gene can be expressed as a long form, TipAL, and a short form, TipAS, which constitutes the C-terminal part of TipAL. TipAS forms the antibiotic-recognition domain []. This domain, which has an alpha-helical globin-like fold, is also found at the C terminus of other MerR family transcription factors, including Mta, a central regulator of multidrug resistance in Bacillus subtilis [], and SkgA from Caulobacter crescentus []. ; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 1NY9_A 3HH0_A 3QAO_A.
Probab=22.72 E-value=1.5e+02 Score=23.02 Aligned_cols=42 Identities=21% Similarity=0.368 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcc--CCCChhHHHHHHHHHHHHH
Q 022567 10 EELFSNLSTYKEQLQQVRELLVH--DPGNSEYADMEKELSEVIA 51 (295)
Q Consensus 10 e~Le~~L~~Yk~QL~qVe~aL~~--DP~N~ELl~Lk~dL~EvI~ 51 (295)
++.+.--.++..=+..+..++.. ||+.++.+.|-.++.++|.
T Consensus 28 ~~~~~~~~~~~~l~~~l~~~~~~g~~p~s~evq~l~~~~~~~~~ 71 (118)
T PF07739_consen 28 EEWQELQKEWDELFAELAALMEEGVDPDSPEVQELAERWMELIN 71 (118)
T ss_dssp -----TTHHHHHHHHHHHHHHHHT--TT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHHHH
Confidence 33333334455555666667776 9999999999999999887
No 149
>PF13437 HlyD_3: HlyD family secretion protein
Probab=22.66 E-value=3.4e+02 Score=20.53 Aligned_cols=30 Identities=17% Similarity=0.320 Sum_probs=23.0
Q ss_pred CCCCC-CCCeEEEEEc-CCCcEEEEEEeeEeC
Q 022567 97 QEKLA-VGTKVQAVYS-EDGEWYDATIEAITP 126 (295)
Q Consensus 97 ~~~~k-vGd~C~A~~s-~Dg~wY~A~I~~i~~ 126 (295)
...++ +|+.+...+. .....|+|+|..|..
T Consensus 47 ~~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 47 IARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred hcceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 34566 9999999985 334699999999983
No 150
>PRK09634 nusB transcription antitermination protein NusB; Provisional
Probab=22.63 E-value=2.9e+02 Score=25.02 Aligned_cols=48 Identities=19% Similarity=0.253 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHHh-ccCCCChhHHHHHHHHHHHHHHHHHHHHHh
Q 022567 13 FSNLSTYKEQLQQVRELL-VHDPGNSEYADMEKELSEVIALTEELLATA 60 (295)
Q Consensus 13 e~~L~~Yk~QL~qVe~aL-~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~ 60 (295)
.+.|++--.+|++-...| .++-.-..|.+.+..|.+.|.+|+..|+..
T Consensus 46 ~~~l~~~~~el~~~~~~l~~s~~~~~~~~~~r~~l~~~~~~~~~~~ng~ 94 (207)
T PRK09634 46 RETLDTAAAELERAQQRLLDSEGDASDLESARTMLQEALTLAETAINRL 94 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHccc
Confidence 355666666676666544 345555779999999999999999999865
No 151
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=22.62 E-value=1.1e+02 Score=17.94 Aligned_cols=24 Identities=29% Similarity=0.573 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHhccCCCC
Q 022567 13 FSNLSTYKEQLQQVRELLVHDPGN 36 (295)
Q Consensus 13 e~~L~~Yk~QL~qVe~aL~~DP~N 36 (295)
--.+.+|+.=+.-.+.+|..+|+|
T Consensus 11 ~~~~~~~~~A~~~~~~al~l~p~~ 34 (34)
T PF07719_consen 11 YYQLGNYEEAIEYFEKALELDPNN 34 (34)
T ss_dssp HHHTT-HHHHHHHHHHHHHHSTTS
T ss_pred HHHhCCHHHHHHHHHHHHHHCcCC
Confidence 345667888888888888888886
No 152
>CHL00154 rpl29 ribosomal protein L29; Validated
Probab=22.58 E-value=3.2e+02 Score=20.13 Aligned_cols=50 Identities=14% Similarity=0.221 Sum_probs=35.7
Q ss_pred cccCHHHHHHHHHHHHHHHHHHH--HHhccCCCChhHHHHHHHHHHHHHHHH
Q 022567 5 EELSIEELFSNLSTYKEQLQQVR--ELLVHDPGNSEYADMEKELSEVIALTE 54 (295)
Q Consensus 5 e~~s~e~Le~~L~~Yk~QL~qVe--~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ 54 (295)
-++|.++|.+.|.+.+.+|-.+. .+...=-+...+..++.|+--|-.+..
T Consensus 10 r~ls~~eL~~~l~elk~elf~LRfq~atgql~n~~~ir~~RrdIARikTil~ 61 (67)
T CHL00154 10 IDLTDSEISEEIIKTKKELFDLRLKKATRQNFKPHLFKHKKHRLAQLLTLLS 61 (67)
T ss_pred HhCCHHHHHHHHHHHHHHHHHHHHHHHhCcccChHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999888877 333222223578889999877765544
No 153
>PRK14640 hypothetical protein; Provisional
Probab=22.46 E-value=2.3e+02 Score=24.08 Aligned_cols=49 Identities=18% Similarity=0.286 Sum_probs=35.1
Q ss_pred CCCCCCeEEEEEc---CCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCccc
Q 022567 99 KLAVGTKVQAVYS---EDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 99 ~~kvGd~C~A~~s---~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp 149 (295)
...+|..|...+. .++..|.++|.+++++++++... |....+++++|+-
T Consensus 93 ~r~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~v~l~~~--~~~~~i~~~~I~k 144 (152)
T PRK14640 93 EKYVGQEAAVTLRMATNNRRKFKGVIKAVQGDMITLTVD--GKDEVLAFTNIQK 144 (152)
T ss_pred HHhCCCeEEEEEecccCCceEEEEEEEEEeCCEEEEEEC--CeEEEEEhHHeee
Confidence 3578999988762 36789999999998776555432 4456677777764
No 154
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=22.44 E-value=1.8e+02 Score=19.76 Aligned_cols=45 Identities=24% Similarity=0.308 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHHHHhccCCCChhHHHHHH-------HHHHHHHHHHHHHH
Q 022567 14 SNLSTYKEQLQQVRELLVHDPGNSEYADMEK-------ELSEVIALTEELLA 58 (295)
Q Consensus 14 ~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~-------dL~EvI~Lt~ell~ 58 (295)
-+...|..=+...+.+|..+|+|.+..-+.- +..+.|.+-+..|.
T Consensus 8 ~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g~~~~A~~~~~~a~~ 59 (65)
T PF13432_consen 8 YQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQGRYDEALAYYERALE 59 (65)
T ss_dssp HHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHH
T ss_pred HHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 3455788888999999999999999665554 44555555555553
No 155
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=22.43 E-value=1.2e+02 Score=20.67 Aligned_cols=27 Identities=11% Similarity=0.347 Sum_probs=19.6
Q ss_pred CCCCCCCCCCeEEEE-EcCCCcEEEEEE
Q 022567 95 DNQEKLAVGTKVQAV-YSEDGEWYDATI 121 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~-~s~Dg~wY~A~I 121 (295)
+....++.||.+... -..++.||.+..
T Consensus 13 ~~~Ls~~~Gd~i~v~~~~~~~~ww~~~~ 40 (55)
T PF07653_consen 13 PDELSFKKGDVIEVLGEKDDDGWWLGEN 40 (55)
T ss_dssp TTB-EB-TTEEEEEEEEECSTSEEEEEE
T ss_pred CCceEEecCCEEEEEEeecCCCEEEEEE
Confidence 455679999999988 445678999887
No 156
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=22.30 E-value=2e+02 Score=21.06 Aligned_cols=41 Identities=27% Similarity=0.334 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHHhh
Q 022567 17 STYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLATAK 61 (295)
Q Consensus 17 ~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~~ 61 (295)
-+++++|+.+... ++. ++|..|..++.+.|.-+...|..+-
T Consensus 11 mE~rE~le~~~~~---~~~-~~L~~l~~~~~~~~~~~~~~l~~~f 51 (78)
T PF07743_consen 11 MELREELEEAQNS---DDE-AELEELKKEIEERIKELIKELAEAF 51 (78)
T ss_dssp HHHHHHHHHHCCC---TSH-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhhcC---CCH-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567777666544 555 8999999999998887777776653
No 157
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=22.16 E-value=1.4e+02 Score=20.21 Aligned_cols=27 Identities=11% Similarity=0.309 Sum_probs=20.0
Q ss_pred CCCCCCCCCCeEEEEEcCCCcEEEEEE
Q 022567 95 DNQEKLAVGTKVQAVYSEDGEWYDATI 121 (295)
Q Consensus 95 ~~~~~~kvGd~C~A~~s~Dg~wY~A~I 121 (295)
+..-.++.||.+......++.|+.++.
T Consensus 10 ~dELs~~~Gd~i~v~~~~~~~W~~g~~ 36 (49)
T PF14604_consen 10 PDELSFKKGDVITVLEKSDDGWWYGRN 36 (49)
T ss_dssp TTB-EB-TTEEEEEEEESSTSEEEEEE
T ss_pred cCEeeEcCCCEEEEEEeCCCCEEEEEE
Confidence 345678999999999866777888874
No 158
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=21.53 E-value=48 Score=25.63 Aligned_cols=32 Identities=19% Similarity=0.485 Sum_probs=14.6
Q ss_pred HHHHHHHHHHhccCCC-Chh----HHHHHHHHHHHHH
Q 022567 20 KEQLQQVRELLVHDPG-NSE----YADMEKELSEVIA 51 (295)
Q Consensus 20 k~QL~qVe~aL~~DP~-N~E----Ll~Lk~dL~EvI~ 51 (295)
+.+|+++.+-|..++. +++ |..|..|++.++.
T Consensus 3 ~~~L~~L~~eL~~~~~ld~~~~~~L~~l~~dIe~~L~ 39 (85)
T PF14357_consen 3 QELLEKLHQELEQNPPLDEETRAELSSLDDDIEAQLA 39 (85)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 4455555555554332 433 3444444444433
No 159
>TIGR01215 minE cell division topological specificity factor MinE. This protein is involved in the process of cell division. This protein prevents the proteins MinC and MinD to inhibit cell division at internal sites, but allows inhibiton at polar sites. This allows for correct cell division at the proper sites.
Probab=21.50 E-value=1.7e+02 Score=22.35 Aligned_cols=33 Identities=21% Similarity=0.230 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhccCCCChhHHHHHHHHHHHHHH
Q 022567 20 KEQLQQVRELLVHDPGNSEYADMEKELSEVIAL 52 (295)
Q Consensus 20 k~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~L 52 (295)
++-|+.|-+.=..+-..+-|-.||.||.+||+=
T Consensus 19 KeRLq~iL~~dR~~~~p~~l~~mk~dil~VIsk 51 (81)
T TIGR01215 19 KDRLKLILAHDRAQLAPEYLEELRKEILEVISK 51 (81)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHH
Confidence 444554433323334445789999999999973
No 160
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=21.39 E-value=3.2e+02 Score=21.84 Aligned_cols=43 Identities=14% Similarity=0.273 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHHhh
Q 022567 19 YKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLATAK 61 (295)
Q Consensus 19 Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~~ 61 (295)
+...|+.++.....+.+.+-+..++..+..........+....
T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~ 133 (181)
T PF12729_consen 91 IDEALEEYEKLILSPEEKQLLEEFKEAWKAYRKLRDQVIELAK 133 (181)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444443333344444567777778888777777776554
No 161
>TIGR03017 EpsF chain length determinant protein EpsF. Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=21.27 E-value=3.5e+02 Score=26.47 Aligned_cols=48 Identities=10% Similarity=0.289 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHH
Q 022567 10 EELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLAT 59 (295)
Q Consensus 10 e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~ 59 (295)
.+|..+|.+-+.||++... .-.|+++.+..|+..|.++-......+..
T Consensus 257 ~~l~~~l~~le~~l~~l~~--~y~~~hP~v~~l~~~i~~l~~~l~~e~~~ 304 (444)
T TIGR03017 257 QNLKTDIARAESKLAELSQ--RLGPNHPQYKRAQAEINSLKSQLNAEIKK 304 (444)
T ss_pred HHHHHHHHHHHHHHHHHHH--HhCCCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555555554432 24788889999998888887776665554
No 162
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=20.99 E-value=1.6e+02 Score=22.55 Aligned_cols=34 Identities=18% Similarity=0.361 Sum_probs=24.6
Q ss_pred CCcEEEEEEeeEeCC--ceEEEEecCCCEEEEcCCCc
Q 022567 113 DGEWYDATIEAITPN--GYYVTYDSWGNKEEVDPANV 147 (295)
Q Consensus 113 Dg~wY~A~I~~i~~~--~~~V~F~~Ygn~e~V~~~~l 147 (295)
=|..|.|+|+.|.+. ++-|.+.+ |..--|++++|
T Consensus 7 ~G~iy~g~V~~i~~~~~GaFV~l~~-g~~Gllh~sei 42 (88)
T cd04453 7 VGNIYLGRVKKIVPGLQAAFVDIGL-GKNGFLHLSDI 42 (88)
T ss_pred CCCEEEEEEEEeccCCcEEEEEeCC-CCEEEEEhHHc
Confidence 477999999999975 67777754 34456666666
No 163
>PRK00034 gatC aspartyl/glutamyl-tRNA amidotransferase subunit C; Reviewed
Probab=20.98 E-value=2.4e+02 Score=21.60 Aligned_cols=39 Identities=15% Similarity=0.360 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHH
Q 022567 20 KEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLA 58 (295)
Q Consensus 20 k~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~ 58 (295)
+..+.-+..+...+.+.+|+-.+..+|..+|...+.+-.
T Consensus 5 ~e~i~~la~La~l~l~~ee~~~~~~~l~~il~~~~~l~~ 43 (95)
T PRK00034 5 REEVKHLAKLARLELSEEELEKFAGQLNKILDFVEQLNE 43 (95)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 345666777778889999999999999999999887654
No 164
>PF06698 DUF1192: Protein of unknown function (DUF1192); InterPro: IPR009579 This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=20.96 E-value=1.6e+02 Score=21.36 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=20.5
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHhc
Q 022567 5 EELSIEELFSNLSTYKEQLQQVRELLV 31 (295)
Q Consensus 5 e~~s~e~Le~~L~~Yk~QL~qVe~aL~ 31 (295)
..+|+++|++.+...+....-+++++.
T Consensus 19 s~lSv~EL~~RIa~L~aEI~R~~~~~~ 45 (59)
T PF06698_consen 19 SLLSVEELEERIALLEAEIARLEAAIA 45 (59)
T ss_pred hhcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567888888888877777777777663
No 165
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.86 E-value=1.5e+02 Score=20.81 Aligned_cols=34 Identities=24% Similarity=0.410 Sum_probs=24.1
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 148 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lr 148 (295)
|.-|.|+|.+|.+.++.|.|.+ +-.-.|+.++|.
T Consensus 1 G~~v~g~V~~v~~~Gv~V~l~~-~~~G~v~~s~l~ 34 (68)
T cd05707 1 GDVVRGFVKNIANNGVFVTLGR-GVDARVRVSELS 34 (68)
T ss_pred CCEEEEEEEEEECccEEEEeCC-CCEEEEEHHHCC
Confidence 5568999999998888888854 233455555553
No 166
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=20.83 E-value=2.2e+02 Score=24.25 Aligned_cols=35 Identities=17% Similarity=0.275 Sum_probs=27.5
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEe
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYD 134 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~ 134 (295)
.+.+|..+.+. ..+|...+++|..|+++.++|-|-
T Consensus 92 ~~~~G~~~~~~-~~~G~~~~~~V~~i~~~~v~vD~N 126 (156)
T PRK15095 92 EPEIGAIMLFT-AMDGSEMPGVIREINGDSITVDFN 126 (156)
T ss_pred CCCCCCEEEEE-CCCCCEEEEEEEEEcCCEEEEECC
Confidence 47899997765 468999999999998766666553
No 167
>PRK09039 hypothetical protein; Validated
Probab=20.80 E-value=1.8e+02 Score=28.23 Aligned_cols=43 Identities=21% Similarity=0.337 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcc-----CCCChhHHHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELLVH-----DPGNSEYADMEKELSEVIA 51 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~~-----DP~N~ELl~Lk~dL~EvI~ 51 (295)
+.-|..+|+..+.||..++++|.. .-....+..|+.+|..+|.
T Consensus 139 V~~L~~qI~aLr~Qla~le~~L~~ae~~~~~~~~~i~~L~~~L~~a~~ 186 (343)
T PRK09039 139 VELLNQQIAALRRQLAALEAALDASEKRDRESQAKIADLGRRLNVALA 186 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788889999999999998853 1222335666666666663
No 168
>smart00745 MIT Microtubule Interacting and Trafficking molecule domain.
Probab=20.79 E-value=3.4e+02 Score=19.67 Aligned_cols=49 Identities=14% Similarity=0.198 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHHHh
Q 022567 12 LFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLATA 60 (295)
Q Consensus 12 Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~~~ 60 (295)
-+.-|.-|+.=++....++..+|+......++.-..+.+.-.+.+...+
T Consensus 24 ~~eAl~~Y~~a~e~l~~~~~~~~~~~~~~~~~~k~~eyl~raE~lk~~~ 72 (77)
T smart00745 24 YEEALELYKKAIEYLLEGIKVESDSKRREAVKAKAAEYLDRAEEIKKSL 72 (77)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567888999999999999999987788899999999999999888765
No 169
>PF13256 DUF4047: Domain of unknown function (DUF4047)
Probab=20.67 E-value=4.6e+02 Score=21.87 Aligned_cols=47 Identities=19% Similarity=0.216 Sum_probs=37.7
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHHHHHHHHHHH
Q 022567 6 ELSIEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEVIALTEELLA 58 (295)
Q Consensus 6 ~~s~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~EvI~Lt~ell~ 58 (295)
.-|++.|+..+..++.+.++|-+-+ +=|+.+..+|+..-.-+.+-+.
T Consensus 56 ~~Sie~leq~~~~w~~~rEki~~e~------eaLQ~IY~eie~~ynq~qe~~k 102 (125)
T PF13256_consen 56 VTSIEELEQAIVEWKQGREKIVAER------EALQNIYTEIEDYYNQIQEELK 102 (125)
T ss_pred hchHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHhc
Confidence 3489999999999999999998776 3478888888887776666654
No 170
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=20.56 E-value=1.5e+02 Score=20.92 Aligned_cols=34 Identities=9% Similarity=0.211 Sum_probs=24.5
Q ss_pred CcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCcc
Q 022567 114 GEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVR 148 (295)
Q Consensus 114 g~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lr 148 (295)
|.-|.|+|.++.+.++.|.. +++..-.++..++.
T Consensus 1 G~iv~g~V~~i~~~~~~v~l-~~~~~g~l~~~e~~ 34 (70)
T cd05687 1 GDIVKGTVVSVDDDEVLVDI-GYKSEGIIPISEFS 34 (70)
T ss_pred CCEEEEEEEEEeCCEEEEEe-CCCceEEEEHHHhC
Confidence 55689999999887777776 44555666666664
No 171
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=20.52 E-value=1.3e+02 Score=22.24 Aligned_cols=34 Identities=21% Similarity=0.317 Sum_probs=23.8
Q ss_pred CCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCc
Q 022567 113 DGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANV 147 (295)
Q Consensus 113 Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~l 147 (295)
-|.-|.|+|..|.+.|+.|.+.+ +-.-.|+.++|
T Consensus 14 ~G~i~~g~V~~v~~~G~fv~l~~-~~~g~v~~~el 47 (83)
T cd04461 14 PGMVVHGYVRNITPYGVFVEFLG-GLTGLAPKSYI 47 (83)
T ss_pred CCCEEEEEEEEEeeceEEEEcCC-CCEEEEEHHHC
Confidence 47788999999998888887753 23345555554
No 172
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=20.44 E-value=1.3e+02 Score=23.17 Aligned_cols=46 Identities=2% Similarity=0.049 Sum_probs=29.9
Q ss_pred CCCCeEEEEEcCCCcEEEEEEeeEeCCceEEEEecCCCEEEEcCCCccc
Q 022567 101 AVGTKVQAVYSEDGEWYDATIEAITPNGYYVTYDSWGNKEEVDPANVRP 149 (295)
Q Consensus 101 kvGd~C~A~~s~Dg~wY~A~I~~i~~~~~~V~F~~Ygn~e~V~~~~lrp 149 (295)
+.+-.|++.+. ||.| ++|.+++++.+.|..-+.+....++.+++..
T Consensus 67 ~~~~P~i~~~~-~~~~--~Vl~~~~~~~~~i~dp~~~~~~~~~~~~l~~ 112 (122)
T cd02259 67 RLQLPALLLWK-QGHF--VILYGADKGQVLIADPLEEGPVTLSESELEE 112 (122)
T ss_pred cCCCCEEEEcC-CCcE--EEEEEEcCCEEEEECCcccCCEEeCHHHHHh
Confidence 44567888864 7775 7888887444666555444445777766654
No 173
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=20.36 E-value=1.2e+02 Score=25.23 Aligned_cols=27 Identities=30% Similarity=0.350 Sum_probs=22.8
Q ss_pred CCCCCCeEEEEEcCCCcEEEEEEeeEeC
Q 022567 99 KLAVGTKVQAVYSEDGEWYDATIEAITP 126 (295)
Q Consensus 99 ~~kvGd~C~A~~s~Dg~wY~A~I~~i~~ 126 (295)
.+++||.|+.+ ++++.-|-|.|+++-.
T Consensus 7 ~i~vGD~V~v~-~~~~~~~va~Ie~i~e 33 (130)
T cd04721 7 TISVHDFVYVL-SEEEDRYVAYIEDLYE 33 (130)
T ss_pred EEECCCEEEEe-CCCCCcEEEEEEEEEE
Confidence 48999999999 5567778999999974
No 174
>TIGR03185 DNA_S_dndD DNA sulfur modification protein DndD. This model describes the DndB protein encoded by an operon associated with a sulfur-containing modification to DNA. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndD is described as a putative ATPase. The small number of examples known so far include species from among the Firmicutes, Actinomycetes, Proteobacteria, and Cyanobacteria.
Probab=20.29 E-value=3.7e+02 Score=28.19 Aligned_cols=41 Identities=24% Similarity=0.397 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCChhHHHHHHHHHHH
Q 022567 9 IEELFSNLSTYKEQLQQVRELLVHDPGNSEYADMEKELSEV 49 (295)
Q Consensus 9 ~e~Le~~L~~Yk~QL~qVe~aL~~DP~N~ELl~Lk~dL~Ev 49 (295)
+.+|..++..-+.+|..++.-|..-|+++++..|..+|.++
T Consensus 393 ~~~~~~~~~~~e~el~~l~~~l~~~~~~e~i~~l~e~l~~l 433 (650)
T TIGR03185 393 KSQLLKELRELEEELAEVDKKISTIPSEEQIAQLLEELGEA 433 (650)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHH
Confidence 45667778888889999999999888877777776666554
No 175
>PRK02103 malonate decarboxylase subunit delta; Provisional
Probab=20.26 E-value=63 Score=26.23 Aligned_cols=10 Identities=50% Similarity=0.630 Sum_probs=8.6
Q ss_pred CcceeeccCC
Q 022567 261 YGKVGVTGSG 270 (295)
Q Consensus 261 ~grVGv~GsG 270 (295)
..-|||+|||
T Consensus 20 ~~lvGVVgSG 29 (105)
T PRK02103 20 AALVGVVASG 29 (105)
T ss_pred ceEEEEEccC
Confidence 4689999998
No 176
>PRK03598 putative efflux pump membrane fusion protein; Provisional
Probab=20.14 E-value=7.2e+02 Score=23.23 Aligned_cols=39 Identities=18% Similarity=0.279 Sum_probs=18.7
Q ss_pred CCCCCeEEEEEcCCCcEEEEEEeeEe-----CCc-eEEEEecCCC
Q 022567 100 LAVGTKVQAVYSEDGEWYDATIEAIT-----PNG-YYVTYDSWGN 138 (295)
Q Consensus 100 ~kvGd~C~A~~s~Dg~wY~A~I~~i~-----~~~-~~V~F~~Ygn 138 (295)
+..|+..+.....+..|-.+.|..-. .+. +.|+|.+|.+
T Consensus 225 V~~G~~l~~I~~~~~~~v~~~V~e~~~~~i~~Gq~v~v~~~~~~~ 269 (331)
T PRK03598 225 LNAGSTVFTLSLTRPVWVRAYVDERNLGQAQPGRKVLLYTDGRPD 269 (331)
T ss_pred cCCCCeEEEEecCCceEEEEEECHHHHhhCCCCCEEEEEEcCCCC
Confidence 34555555555444455455544322 122 5666655543
No 177
>PF15532 Toxin_53: Putative toxin 53
Probab=20.10 E-value=1.8e+02 Score=23.48 Aligned_cols=37 Identities=22% Similarity=0.456 Sum_probs=28.0
Q ss_pred CCCCeEEEEEcCCCcEEEEEEeeEeC---------Cc--eEEEEecCCC
Q 022567 101 AVGTKVQAVYSEDGEWYDATIEAITP---------NG--YYVTYDSWGN 138 (295)
Q Consensus 101 kvGd~C~A~~s~Dg~wY~A~I~~i~~---------~~--~~V~F~~Ygn 138 (295)
.+..-+-.+|..+|.=|+.+|-.++. +| |.|. .++|-
T Consensus 20 ~~~~~~k~kW~~~g~tyrvRvH~~Dp~ap~Gsnaa~G~IyRI~-qg~G~ 67 (102)
T PF15532_consen 20 KVPEGFKFKWTDGGKTYRVRVHPADPTAPAGSNAANGWIYRIS-QGSGW 67 (102)
T ss_pred CccccceEEeecCCceEEEEecCCCCCCCCCCcccCCCEEEEE-eccCc
Confidence 44567889999899999999999884 34 8887 34443
No 178
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=20.03 E-value=3.2e+02 Score=21.68 Aligned_cols=44 Identities=18% Similarity=0.201 Sum_probs=28.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHh--------------ccCCCChhHHHHHHHHHHHHHHHH
Q 022567 8 SIEELFSNLSTYKEQLQQVRELL--------------VHDPGNSEYADMEKELSEVIALTE 54 (295)
Q Consensus 8 s~e~Le~~L~~Yk~QL~qVe~aL--------------~~DP~N~ELl~Lk~dL~EvI~Lt~ 54 (295)
++.+|.++|+..++||.+.+.-. ..|=+|+||. ..+++|+.=..
T Consensus 3 ~~s~I~~eIekLqe~lk~~e~keaERigr~AlKaGL~eieI~d~eL~---~~FeeIa~RFr 60 (92)
T PF07820_consen 3 SSSKIREEIEKLQEQLKQAETKEAERIGRIALKAGLGEIEISDAELQ---AAFEEIAARFR 60 (92)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccccccCCHHHHH---HHHHHHHHHHh
Confidence 57788999999999998877543 2355666654 44555554433
Done!