Query 030413
Match_columns 177
No_of_seqs 114 out of 906
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 13:21:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030413.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030413hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd04713 BAH_plant_3 BAH, or Br 100.0 1.1E-33 2.5E-38 212.2 15.3 131 10-143 2-136 (146)
2 cd04717 BAH_polybromo BAH, or 100.0 4.3E-33 9.4E-38 203.0 12.2 117 29-145 2-121 (121)
3 cd04716 BAH_plantDCM_I BAH, or 100.0 1.6E-32 3.4E-37 199.7 13.5 116 29-145 2-122 (122)
4 cd04714 BAH_BAHCC1 BAH, or Bro 100.0 1.4E-32 3E-37 200.4 10.6 112 29-140 2-119 (121)
5 PF01426 BAH: BAH domain; Int 100.0 2.6E-31 5.6E-36 191.9 12.2 114 29-144 1-119 (119)
6 smart00439 BAH Bromo adjacent 100.0 6.4E-31 1.4E-35 190.0 12.8 115 30-144 1-120 (120)
7 cd04370 BAH BAH, or Bromo Adja 100.0 1.5E-30 3.3E-35 188.1 11.9 115 29-143 2-122 (123)
8 cd04709 BAH_MTA BAH, or Bromo 100.0 8.2E-30 1.8E-34 193.8 12.1 115 29-144 2-140 (164)
9 cd04721 BAH_plant_1 BAH, or Br 100.0 2.7E-29 5.8E-34 184.9 10.4 108 29-138 6-119 (130)
10 cd04715 BAH_Orc1p_like BAH, or 100.0 1.6E-28 3.5E-33 186.1 13.7 112 3-121 7-127 (159)
11 cd04710 BAH_fungalPHD BAH, or 100.0 1.6E-28 3.5E-33 181.6 12.1 112 28-141 9-134 (135)
12 cd04708 BAH_plantDCM_II BAH, o 100.0 3E-28 6.5E-33 189.7 11.8 122 22-145 1-147 (202)
13 cd04712 BAH_DCM_I BAH, or Brom 99.9 1.1E-26 2.4E-31 171.0 14.1 112 29-144 4-129 (130)
14 cd04718 BAH_plant_2 BAH, or Br 99.9 1.3E-28 2.9E-33 182.5 1.9 97 46-143 51-147 (148)
15 cd04760 BAH_Dnmt1_I BAH, or Br 99.9 3.7E-26 8E-31 165.7 10.4 111 29-141 2-124 (124)
16 cd04720 BAH_Orc1p_Yeast BAH, o 99.9 3.5E-25 7.5E-30 171.2 14.1 115 28-143 50-177 (179)
17 cd04711 BAH_Dnmt1_II BAH, or B 99.9 5.2E-24 1.1E-28 155.4 7.9 112 34-145 13-137 (137)
18 cd04719 BAH_Orc1p_animal BAH, 99.9 1.2E-23 2.5E-28 154.0 9.5 109 29-138 2-123 (128)
19 KOG1886 BAH domain proteins [T 99.9 1.1E-22 2.3E-27 174.0 7.6 156 14-173 35-207 (464)
20 KOG1827 Chromatin remodeling c 99.7 2.9E-17 6.4E-22 145.4 7.3 127 22-150 184-315 (629)
21 KOG3554 Histone deacetylase co 99.3 9.8E-14 2.1E-18 118.5 -2.0 114 30-144 5-164 (693)
22 PF00628 PHD: PHD-finger; Int 97.4 4.5E-05 9.8E-10 46.6 0.8 21 151-173 15-35 (51)
23 KOG1973 Chromatin remodeling p 97.3 6.1E-05 1.3E-09 62.1 0.5 28 144-171 219-254 (274)
24 smart00249 PHD PHD zinc finger 96.8 0.00042 9E-09 40.8 0.4 20 151-172 15-34 (47)
25 COG5034 TNG2 Chromatin remodel 96.1 0.0017 3.8E-08 52.4 0.6 28 144-171 221-256 (271)
26 KOG1632 Uncharacterized PHD Zn 92.4 0.059 1.3E-06 45.9 1.2 82 88-172 3-97 (345)
27 KOG4323 Polycomb-like PHD Zn-f 92.0 0.046 1E-06 48.0 0.1 22 151-174 186-207 (464)
28 COG5076 Transcription factor i 91.2 0.028 6.2E-07 48.2 -2.1 96 21-118 269-364 (371)
29 PF09926 DUF2158: Uncharacteri 89.9 0.59 1.3E-05 28.9 3.6 40 31-74 1-40 (53)
30 PRK10708 hypothetical protein; 87.0 2.8 6.1E-05 26.2 5.2 45 32-78 2-53 (62)
31 PF10781 DSRB: Dextransucrase 86.8 3.3 7.2E-05 25.9 5.4 46 32-79 2-54 (62)
32 PF10383 Clr2: Transcription-s 86.7 4.5 9.8E-05 29.9 7.2 53 17-71 1-70 (139)
33 PF08940 DUF1918: Domain of un 84.0 1.8 4E-05 27.2 3.4 40 32-72 4-43 (58)
34 cd05834 HDGF_related The PWWP 83.4 2.1 4.6E-05 28.8 3.8 44 30-75 2-45 (83)
35 PF07154 DUF1392: Protein of u 82.6 4 8.7E-05 30.4 5.2 50 15-75 74-123 (150)
36 PF09871 DUF2098: Uncharacteri 82.2 4 8.6E-05 28.2 4.8 43 30-78 2-47 (91)
37 PF11302 DUF3104: Protein of u 80.8 3.3 7.2E-05 27.5 3.9 31 30-60 5-40 (75)
38 KOG1568 Mitochondrial inner me 80.3 15 0.00032 28.2 7.7 88 16-112 56-148 (174)
39 cd06080 MUM1_like Mutated mela 78.7 3.8 8.2E-05 27.5 3.7 39 31-74 1-39 (80)
40 cd05835 Dnmt3b_related The PWW 78.4 2.9 6.4E-05 28.3 3.2 41 31-73 1-44 (87)
41 COG4014 Uncharacterized protei 78.4 5.9 0.00013 27.1 4.6 41 32-77 10-53 (97)
42 cd03703 aeIF5B_II aeIF5B_II: T 74.4 9.2 0.0002 27.3 4.9 45 10-60 8-53 (110)
43 PTZ00112 origin recognition co 74.0 7.5 0.00016 37.7 5.6 119 16-136 440-603 (1164)
44 PF11717 Tudor-knot: RNA bindi 73.2 12 0.00026 22.9 4.7 35 31-68 1-35 (55)
45 PF13832 zf-HC5HC2H_2: PHD-zin 72.7 1.2 2.6E-05 31.2 0.0 25 146-170 58-88 (110)
46 cd05162 PWWP The PWWP domain, 71.8 6.4 0.00014 26.3 3.5 40 31-72 1-46 (87)
47 TIGR02227 sigpep_I_bact signal 68.8 47 0.001 24.9 8.6 42 30-71 51-96 (163)
48 PF00467 KOW: KOW motif; Inte 68.8 13 0.00028 20.1 3.7 26 33-60 1-26 (32)
49 smart00293 PWWP domain with co 67.0 8.1 0.00018 24.3 3.1 40 31-72 1-47 (63)
50 cd05840 SPBC215_ISWI_like The 64.6 8.2 0.00018 26.5 2.9 40 31-72 1-49 (93)
51 smart00739 KOW KOW (Kyprides, 64.2 13 0.00028 18.8 3.1 26 31-58 2-27 (28)
52 PRK13251 transcription attenua 63.2 28 0.00061 22.8 5.0 48 66-113 19-66 (75)
53 KOG0957 PHD finger protein [Ge 62.8 2.9 6.3E-05 37.4 0.5 19 151-171 560-578 (707)
54 PF07496 zf-CW: CW-type Zinc F 62.4 2.7 5.9E-05 25.4 0.1 13 151-165 4-16 (50)
55 PF02081 TrpBP: Tryptophan RNA 62.0 21 0.00045 23.4 4.2 48 66-113 19-66 (75)
56 COG3257 GlxB Uncharacterized p 60.6 34 0.00075 27.6 6.1 48 23-81 97-144 (264)
57 PF00855 PWWP: PWWP domain; I 59.7 7.5 0.00016 25.6 2.0 40 31-72 1-43 (86)
58 PF15057 DUF4537: Domain of un 59.5 17 0.00037 26.3 3.9 42 30-71 55-97 (124)
59 PF14446 Prok-RING_1: Prokaryo 57.7 3.4 7.3E-05 25.7 -0.0 16 151-168 22-37 (54)
60 COG5475 Uncharacterized small 57.5 45 0.00097 20.9 5.0 49 30-91 4-52 (60)
61 KOG2133 Transcriptional corepr 55.8 8.9 0.00019 37.0 2.4 113 29-142 144-282 (1229)
62 PF07494 Reg_prop: Two compone 54.8 18 0.00038 18.2 2.5 15 52-66 6-20 (24)
63 PF03144 GTP_EFTU_D2: Elongati 53.4 27 0.00059 22.0 3.8 31 30-60 12-42 (74)
64 cd03701 IF2_IF5B_II IF2_IF5B_I 53.4 40 0.00086 23.1 4.8 41 11-60 9-49 (95)
65 KOG0383 Predicted helicase [Ge 51.7 4.3 9.3E-05 37.9 -0.3 25 146-172 50-79 (696)
66 cd03702 IF2_mtIF2_II This fami 50.7 36 0.00078 23.4 4.3 42 11-61 9-50 (95)
67 PF11793 FANCL_C: FANCL C-term 50.4 7.2 0.00016 25.3 0.6 19 151-169 21-39 (70)
68 PRK12281 rplX 50S ribosomal pr 48.6 37 0.00081 22.4 3.9 29 30-60 6-34 (76)
69 COG1370 Prefoldin, molecular c 48.1 13 0.00029 27.9 1.8 40 12-53 93-132 (155)
70 CHL00141 rpl24 ribosomal prote 47.2 38 0.00083 22.8 3.8 29 30-60 8-36 (83)
71 PF00645 zf-PARP: Poly(ADP-rib 46.8 4.9 0.00011 26.6 -0.6 14 158-171 37-50 (82)
72 PF11926 DUF3444: Domain of un 46.1 53 0.0011 26.2 5.1 42 29-72 26-67 (217)
73 KOG0825 PHD Zn-finger protein 45.2 8.5 0.00018 36.4 0.5 19 151-171 231-250 (1134)
74 PF13550 Phage-tail_3: Putativ 42.7 39 0.00086 24.6 3.8 34 21-57 130-163 (164)
75 cd05836 N_Pac_NP60 The PWWP do 41.4 36 0.00079 22.9 3.1 42 31-74 1-46 (86)
76 KOG0955 PHD finger protein BR1 41.2 7.1 0.00015 38.1 -0.7 48 33-80 29-93 (1051)
77 PF13771 zf-HC5HC2H: PHD-like 41.2 8 0.00017 25.8 -0.2 20 151-170 50-69 (90)
78 PRK00004 rplX 50S ribosomal pr 40.9 50 0.0011 23.2 3.8 29 30-60 4-32 (105)
79 PF09378 HAS-barrel: HAS barre 40.4 35 0.00076 22.4 2.9 36 21-59 14-49 (91)
80 PF13922 PHD_3: PHD domain of 39.6 15 0.00032 23.8 0.8 29 141-171 30-62 (69)
81 KOG1512 PHD Zn-finger protein 39.2 12 0.00026 31.2 0.5 20 151-172 330-349 (381)
82 PF07883 Cupin_2: Cupin domain 38.9 42 0.00091 20.6 3.0 21 23-43 33-53 (71)
83 TIGR01079 rplX_bact ribosomal 36.9 63 0.0014 22.7 3.8 29 30-60 3-31 (104)
84 COG0662 {ManC} Mannose-6-phosp 35.4 50 0.0011 23.6 3.2 23 22-44 70-92 (127)
85 PRK01191 rpl24p 50S ribosomal 34.5 1E+02 0.0023 22.3 4.7 37 29-68 44-80 (120)
86 cd06530 S26_SPase_I The S26 Ty 34.3 70 0.0015 20.7 3.6 26 30-55 31-56 (85)
87 TIGR03214 ura-cupin putative a 33.8 1.5E+02 0.0032 24.1 6.1 46 23-79 94-139 (260)
88 PF06940 DUF1287: Domain of un 33.8 55 0.0012 25.0 3.2 42 22-66 98-139 (164)
89 cd05837 MSH6_like The PWWP dom 33.7 54 0.0012 23.0 3.1 43 30-74 2-53 (110)
90 COG0250 NusG Transcription ant 33.4 97 0.0021 23.9 4.7 46 29-77 122-167 (178)
91 smart00743 Agenet Tudor-like d 33.1 56 0.0012 19.9 2.8 28 30-58 2-29 (61)
92 PF10844 DUF2577: Protein of u 32.6 36 0.00079 23.5 2.0 19 30-48 76-94 (100)
93 PF13831 PHD_2: PHD-finger; PD 32.5 11 0.00023 21.2 -0.6 21 151-173 5-25 (36)
94 PF08921 DUF1904: Domain of un 31.8 23 0.0005 25.1 0.9 18 62-79 54-71 (108)
95 PF11012 DUF2850: Protein of u 31.8 1.1E+02 0.0024 20.4 4.1 32 12-43 27-58 (79)
96 cd05793 S1_IF1A S1_IF1A: Trans 31.8 73 0.0016 21.0 3.3 28 29-58 37-64 (77)
97 PF02559 CarD_CdnL_TRCF: CarD- 31.8 59 0.0013 22.0 3.0 24 31-60 2-25 (98)
98 KOG1244 Predicted transcriptio 31.5 19 0.0004 29.9 0.4 18 151-170 297-314 (336)
99 smart00652 eIF1a eukaryotic tr 31.3 81 0.0018 21.1 3.5 28 29-58 42-69 (83)
100 PF05899 Cupin_3: Protein of u 31.0 66 0.0014 20.7 3.0 19 25-43 42-60 (74)
101 PF01176 eIF-1a: Translation i 29.9 53 0.0012 20.7 2.3 25 29-55 40-64 (65)
102 PF14444 S1-like: S1-like 29.6 57 0.0012 20.5 2.3 30 15-46 20-49 (58)
103 cd04466 S1_YloQ_GTPase S1_YloQ 29.1 66 0.0014 19.8 2.6 26 30-59 37-62 (68)
104 PF11132 SplA: Transcriptional 28.6 40 0.00088 22.2 1.5 25 30-55 5-29 (75)
105 KOG4656 Copper chaperone for s 28.5 1.7E+02 0.0036 23.5 5.2 65 86-150 165-230 (247)
106 PF04322 DUF473: Protein of un 28.1 1.3E+02 0.0028 21.8 4.2 42 17-58 20-71 (119)
107 PTZ00194 60S ribosomal protein 28.0 1.6E+02 0.0034 22.1 4.8 37 29-68 45-81 (143)
108 cd04456 S1_IF1A_like S1_IF1A_l 27.6 97 0.0021 20.5 3.3 29 29-58 37-65 (78)
109 KOG2752 Uncharacterized conser 27.2 27 0.00057 29.6 0.6 23 151-175 149-172 (345)
110 PF00667 FAD_binding_1: FAD bi 26.6 79 0.0017 24.7 3.3 24 21-44 32-55 (219)
111 COG1917 Uncharacterized conser 25.9 82 0.0018 22.3 3.0 21 23-43 78-98 (131)
112 PF02311 AraC_binding: AraC-li 25.7 2.1E+02 0.0045 19.2 5.1 21 23-43 37-57 (136)
113 PF01079 Hint: Hint module; I 25.6 88 0.0019 24.9 3.3 28 30-58 105-132 (217)
114 PRK03187 tgl transglutaminase; 25.6 49 0.0011 27.3 1.9 19 23-43 160-178 (272)
115 PF13341 RAG2_PHD: RAG2 PHD do 25.3 32 0.00069 22.5 0.6 24 151-175 31-54 (78)
116 COG0198 RplX Ribosomal protein 25.1 1.7E+02 0.0036 20.7 4.3 29 30-60 4-32 (104)
117 PF12503 CMV_1a_C: Cucumber mo 24.9 66 0.0014 21.7 2.1 31 64-96 34-71 (85)
118 TIGR01080 rplX_A_E ribosomal p 24.8 2E+02 0.0044 20.5 4.8 38 29-69 40-77 (114)
119 COG3450 Predicted enzyme of th 24.4 71 0.0015 23.0 2.3 18 26-43 81-98 (116)
120 PF07649 C1_3: C1-like domain; 24.0 20 0.00044 18.9 -0.4 15 151-167 16-30 (30)
121 TIGR00218 manA mannose-6-phosp 23.2 1E+02 0.0022 25.5 3.4 33 29-62 153-185 (302)
122 PRK09943 DNA-binding transcrip 23.2 1.1E+02 0.0023 23.2 3.3 21 23-43 142-162 (185)
123 COG4127 Uncharacterized conser 23.0 56 0.0012 27.3 1.7 41 30-71 72-117 (318)
124 TIGR01956 NusG_myco NusG famil 22.8 1.9E+02 0.004 23.9 4.7 45 30-77 205-249 (258)
125 PRK04012 translation initiatio 21.9 1.4E+02 0.003 20.8 3.3 27 29-57 58-84 (100)
126 KOG1844 PHD Zn-finger proteins 21.5 37 0.00079 30.1 0.5 27 143-171 85-120 (508)
127 cd05792 S1_eIF1AD_like S1_eIF1 21.3 2E+02 0.0043 19.1 3.8 14 30-43 38-51 (78)
128 KOG1740 Predicted mitochondria 21.1 59 0.0013 22.8 1.3 28 17-44 36-63 (107)
129 cd03698 eRF3_II_like eRF3_II_l 20.9 2.4E+02 0.0052 18.2 4.3 25 30-59 26-50 (83)
130 PRK11171 hypothetical protein; 20.8 4.3E+02 0.0093 21.4 6.6 21 23-43 97-117 (266)
No 1
>cd04713 BAH_plant_3 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=100.00 E-value=1.1e-33 Score=212.17 Aligned_cols=131 Identities=28% Similarity=0.451 Sum_probs=116.8
Q ss_pred CCCCCCceeeeEEEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCccc---ccCC
Q 030413 10 TKTKTGKRDLESYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRR---QFHG 86 (177)
Q Consensus 10 ~k~~~~~~~y~~~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~---~~~~ 86 (177)
+|++..+.+|++|+++|. +|++||+|||.++++ .++|||+|++||++.+|.++++|+|||||+|+..... ...+
T Consensus 2 ~~~~~~~~~y~s~~~dg~--~y~vgD~Vlv~~~~~-~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~~~~~~~~ 78 (146)
T cd04713 2 GKGKKKKCHYTSFEKDGN--KYRLEDCVLLVPEDD-QKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKGGNWKAED 78 (146)
T ss_pred CCCccceeeeeeEEECCE--EEECCCEEEEeCCCC-CCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccccccccCC
Confidence 367788999999999997 999999999999874 8999999999999988999999999999999986432 2346
Q ss_pred CCeEEEeCCCcccccceEEeeeEEEeeecccccCCC-CCceEEEEeEeecCCCceeeC
Q 030413 87 AKELFLSDHYDVQSAHTIEGKCIVHSFKNYTKLENV-GAEDYYCRFEYKAASGGFTQT 143 (177)
Q Consensus 87 ~~ELf~S~~~d~i~~~~I~gkc~V~~~~~~~~~~~~-~~~~Ffcr~~yd~~~~~f~~~ 143 (177)
+||||+|++.|.+|+++|+|||.|++.+++.+++.. ..++||||+.||+..++|..+
T Consensus 79 ~~ElF~S~~~d~~~~~~I~gkc~V~~~~~~~~~~~~~~~~~F~cr~~yD~~~~~~~~~ 136 (146)
T cd04713 79 PRELFYSFHRDEVPAESVLHPCKVAFVPKGKQIPLRKGHSGFIVRRVYDNVNKKLWKL 136 (146)
T ss_pred CCeEEEeCCCCcCCHHHCcceeEEEECCccccCCccCCCCeEEEEEEEcCCCCcEeec
Confidence 899999999999999999999999999998887754 578999999999999998765
No 2
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. 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=100.00 E-value=4.3e-33 Score=203.05 Aligned_cols=117 Identities=28% Similarity=0.497 Sum_probs=108.0
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcccccCCCCeEEEeCCCcccccceEEeee
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQSAHTIEGKC 108 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~~~~I~gkc 108 (177)
..|++||+|||.+++++.+++||+|.+||++.+|.++++|+|||||+||.++....+.+||||+|++.|++|+++|+|||
T Consensus 2 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~~~~Evfls~~~d~~~~~~I~~kc 81 (121)
T cd04717 2 LQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEVFKSPLYETVPVEEIVGKC 81 (121)
T ss_pred CEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccccccCceEEcCccccccHHHhcCee
Confidence 48999999999998865889999999999999999999999999999999877667899999999999999999999999
Q ss_pred EEEeeecccccCCC---CCceEEEEeEeecCCCceeeCcc
Q 030413 109 IVHSFKNYTKLENV---GAEDYYCRFEYKAASGGFTQTEL 145 (177)
Q Consensus 109 ~V~~~~~~~~~~~~---~~~~Ffcr~~yd~~~~~f~~~~~ 145 (177)
.|++.++|.+.++. ..++||||+.||+..+.|.+++.
T Consensus 82 ~Vl~~~~y~~~~p~~~~~~dvy~ce~~y~~~~~~~~~~k~ 121 (121)
T cd04717 82 AVMDVKDYIKGRPTEISEEDVYVCESRYNESAKSFKKIKT 121 (121)
T ss_pred EEEehHHHhcCCCCCCCCCCEEEEeEEECcccccEecccC
Confidence 99999999988754 35889999999999999998863
No 3
>cd04716 BAH_plantDCM_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=100.00 E-value=1.6e-32 Score=199.73 Aligned_cols=116 Identities=19% Similarity=0.353 Sum_probs=106.4
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcc-cccCCCCeEEEeCCCcccccceEEee
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGR-RQFHGAKELFLSDHYDVQSAHTIEGK 107 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~-~~~~~~~ELf~S~~~d~i~~~~I~gk 107 (177)
..|++||+|||.+++ ++++|||+|.+||++.+|..+++|+|||||+||..++ ...++++|||+|++.|++|+++|+||
T Consensus 2 ~~~~lgD~V~v~~~~-~~~~yi~rI~~i~e~~~g~~~~~v~WyyRpeet~~~r~~~~~~~rEvFlS~~~D~~pl~~I~~K 80 (122)
T cd04716 2 ITYNLGDDAYVQGGE-GEEPFICKITEFFEGTDGKTYFTAQWFYRAEDTVIERQATNHDKKRVFYSEIKNDNPLDCLISK 80 (122)
T ss_pred cEEEcCCEEEEECCC-CCCCEEEEEEEEEEcCCCceEEEEEEEEcHHHhccccccccCCCceEEEecccCccchhheeee
Confidence 489999999999997 4899999999999999999999999999999999986 45788999999999999999999999
Q ss_pred eEEEeeeccccc----CCCCCceEEEEeEeecCCCceeeCcc
Q 030413 108 CIVHSFKNYTKL----ENVGAEDYYCRFEYKAASGGFTQTEL 145 (177)
Q Consensus 108 c~V~~~~~~~~~----~~~~~~~Ffcr~~yd~~~~~f~~~~~ 145 (177)
|.|++++.+..+ ...+.++|||++.|+....+|..+++
T Consensus 81 c~V~~~~~~~~~~~~~~~~~~~df~c~~~Y~~~~~tF~~~~~ 122 (122)
T cd04716 81 VKILQVPPNVGTKRKKPNSEKCDYYYDMEYCVPYSTFQTLRN 122 (122)
T ss_pred eEEEEeCCCCCcccccccCCCceEEEeeEeccchhheEeCCC
Confidence 999999988876 34568999999999999999998764
No 4
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. 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=100.00 E-value=1.4e-32 Score=200.37 Aligned_cols=112 Identities=50% Similarity=0.903 Sum_probs=103.0
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcccccCCCCeEEEeCCCcccccceEEeee
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQSAHTIEGKC 108 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~~~~I~gkc 108 (177)
++|++||+|+|.++++++++|||+|++||++.+|+++++|+|||||+||.+++++.++++|||+|++.|++|+++|+|||
T Consensus 2 ~~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~~~~~~~EvF~S~~~d~~~~~~I~gkc 81 (121)
T cd04714 2 EIIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRKPNHGEKELFASDHQDENSVQTIEHKC 81 (121)
T ss_pred CEEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCcccccCCCCceEecCCcccccHHHhCccc
Confidence 48999999999998756789999999999998899999999999999999998878999999999999999999999999
Q ss_pred EEEeeecccccCC------CCCceEEEEeEeecCCCce
Q 030413 109 IVHSFKNYTKLEN------VGAEDYYCRFEYKAASGGF 140 (177)
Q Consensus 109 ~V~~~~~~~~~~~------~~~~~Ffcr~~yd~~~~~f 140 (177)
.|+++++|.++.+ .+.++|+|++.||+.+..+
T Consensus 82 ~V~~~~ey~~~~~~~~~~~~~~d~~~Ce~~yn~~~~~~ 119 (121)
T cd04714 82 YVLTFAEYERLARVKKKPQDGVDFYYCAGTYNPDTGML 119 (121)
T ss_pred EEEehhHheecccccCCCCcCCCEEEEeccCCCCcCcc
Confidence 9999999998653 3579999999999997654
No 5
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=99.97 E-value=2.6e-31 Score=191.91 Aligned_cols=114 Identities=39% Similarity=0.763 Sum_probs=102.1
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCc--EEEEEEEEeeccccCCcccccCCCCeEEEeCCCcccccceEEe
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNN--VKVRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQSAHTIEG 106 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~--~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~~~~I~g 106 (177)
++|++||+|||.+++++++++||+|++||++.++. ++++|+|||||+|+..+ ....+||||+|++.+.+|+++|+|
T Consensus 1 ~~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~~~~~~~~~~v~Wf~rp~d~~~~--~~~~~~Elf~s~~~~~~~~~~I~g 78 (119)
T PF01426_consen 1 VTYKVGDFVYVKPDDPPEPPYVARIEEIWEDKDGNKEKMVKVRWFYRPEDTSLG--KTFSPRELFLSDHCDDIPVESIRG 78 (119)
T ss_dssp EEEETTSEEEEECTSTTSEEEEEEEEEEEEETTTSEEEEEEEEEEEEGGGSTTG--GHSCTTEEEEEEEEEEEEGGGEEE
T ss_pred CEEeCCCEEEEeCCCCCCCCEEEEEEEEEcCCCCCEEEEEEEEEeECccccccc--ccCCCCEEEEECcEeEEehhhEEe
Confidence 48999999999999977899999999999998777 99999999999999333 335579999999999999999999
Q ss_pred eeEEEeeecccccCCC---CCceEEEEeEeecCCCceeeCc
Q 030413 107 KCIVHSFKNYTKLENV---GAEDYYCRFEYKAASGGFTQTE 144 (177)
Q Consensus 107 kc~V~~~~~~~~~~~~---~~~~Ffcr~~yd~~~~~f~~~~ 144 (177)
||.|++.+++.+..+. ..++||||+.||+.+++|.++|
T Consensus 79 kc~V~~~~~~~~~~~~~~~~~~~F~cr~~yd~~~~~f~~~~ 119 (119)
T PF01426_consen 79 KCNVLHLEDYEQARPYGKEEPDTFFCRYAYDPQKKRFKKLP 119 (119)
T ss_dssp EEEEEEHHHHTTGCCHCHHTTTEEEEEEEEETTTTEEEE-S
T ss_pred eeEEEECCccccccccccCCCCEEEEEEEEeCCcCEEeCCC
Confidence 9999999999887643 6799999999999999999876
No 6
>smart00439 BAH Bromo adjacent homology domain.
Probab=99.97 E-value=6.4e-31 Score=189.97 Aligned_cols=115 Identities=38% Similarity=0.716 Sum_probs=105.1
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCc-EEEEEEEEeeccccCCcccccCCCCeEEEeCCCcccccceEEeee
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDARNN-VKVRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQSAHTIEGKC 108 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~-~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~~~~I~gkc 108 (177)
.|++||+|||.+++.+++++||+|++||++.+|. ++++|+|||||+||+++....+.+||||+|++.+++|+++|.|||
T Consensus 1 ~~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~~~~~~~~v~Wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~~~~I~~kc 80 (120)
T smart00439 1 TIRVGDFVLVEPDDADEPYYIGRIEEIFETKKNSEKMVRVRWFYRPEETVLEKAALFDKNEVFLSDEYDTVPLSDIIGKC 80 (120)
T ss_pred CcccCCEEEEeCCCCCCCCEEEEEEEEEECCCCCEEEEEEEEEEChhhccccccccCCCcceEEEccCccCChHHeeeEE
Confidence 4789999999999866799999999999999888 999999999999999987767789999999999999999999999
Q ss_pred EEEeeecccccCCC----CCceEEEEeEeecCCCceeeCc
Q 030413 109 IVHSFKNYTKLENV----GAEDYYCRFEYKAASGGFTQTE 144 (177)
Q Consensus 109 ~V~~~~~~~~~~~~----~~~~Ffcr~~yd~~~~~f~~~~ 144 (177)
.|++.+++.+.++. ..++||||+.||+.+++|.+++
T Consensus 81 ~V~~~~~~~~~~~~~~~~~~~~f~cr~~yd~~~~~f~~~~ 120 (120)
T smart00439 81 NVLSKSDYPGLRPEGKIGEPDVFFCESLYDPEKGAFKKLP 120 (120)
T ss_pred EEEEcchhcccccccCCCCCCeEEEEEEEccccCcccCCC
Confidence 99999999876543 3689999999999999998764
No 7
>cd04370 BAH BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in mammalian DNA methyltransferases and the MTA1 subunits of histone deacetylase complexes. A BAH domain is also found in Yeast Sir3p and in the origin receptor complex protein 1 (Orc1p), where it was found to interact with the N-terminal lobe of the silence information regulator 1 protein (Sir1p), confirming the initial hypothesis that BAH plays a role in protein-protein interactions.
Probab=99.97 E-value=1.5e-30 Score=188.07 Aligned_cols=115 Identities=38% Similarity=0.769 Sum_probs=105.2
Q ss_pred eeEEeCCEEEEccCCC--CCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcccccCCCCeEEEeCCCcccccceEEe
Q 030413 29 KIVRVGDCVLMRPSDT--GKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQSAHTIEG 106 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~--~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~~~~I~g 106 (177)
.+|++||+|||.+++. .+++|||+|++||++.+|.++++|+|||||+||+.+....+.+||||+|++.+++|+++|.|
T Consensus 2 ~~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~~~~~~~v~wf~rp~e~~~~~~~~~~~~Elf~s~~~~~i~v~~I~g 81 (123)
T cd04370 2 ITYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTNGSKQVKVRWFYRPEETPKGLSPFALRRELFLSDHLDEIPVESIIG 81 (123)
T ss_pred CEEecCCEEEEecCCcCCCCCCEEEEEeeeeECCCCCEEEEEEEEEchhHhccccccccccceeEEecCccccCHHHhcc
Confidence 4899999999999874 47899999999999999999999999999999999877778999999999999999999999
Q ss_pred eeEEEeeecccccC----CCCCceEEEEeEeecCCCceeeC
Q 030413 107 KCIVHSFKNYTKLE----NVGAEDYYCRFEYKAASGGFTQT 143 (177)
Q Consensus 107 kc~V~~~~~~~~~~----~~~~~~Ffcr~~yd~~~~~f~~~ 143 (177)
+|.|++.+++.+.. ....++||||+.||+.+++|.++
T Consensus 82 kc~V~~~~~~~~~~~~~~~~~~~~f~~r~~yd~~~~~fk~~ 122 (123)
T cd04370 82 KCKVLFVSEFEGLKQRPNKIDTDDFFCRLAYDPTTKEFKAL 122 (123)
T ss_pred ccEEEechHhhccccccccCCCCeEEEEEEECcCcceEEeC
Confidence 99999999998764 23468999999999999999875
No 8
>cd04709 BAH_MTA BAH, or Bromo Adjacent Homology domain, as present in MTA1 and similar proteins. The Metastasis-associated protein MTA1 is part of the NURD (nucleosome remodeling and deacetylating) complex and plays a role in cellular transformation and metastasis. 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=99.97 E-value=8.2e-30 Score=193.83 Aligned_cols=115 Identities=27% Similarity=0.489 Sum_probs=102.0
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCc--------c--------------cccCC
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGG--------R--------------RQFHG 86 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~--------~--------------~~~~~ 86 (177)
..|++||+||+.++. +.+++||+|++|+++.+|.++++|+|||||+|++.. + ...++
T Consensus 2 ~~yrvGD~Vy~~~~~-~~Py~I~rI~e~~~~~~~~~~vkV~wfYRp~DI~~~~~~l~~~~r~~~~~~~~~~~~~~~~~~~ 80 (164)
T cd04709 2 NMYRVGDYVYFESSP-NNPYLIRRIEELNKTARGHVEAKVVCYYRRRDIPDSLYQLADQHRRELEEKSDDLTPKQRHQLR 80 (164)
T ss_pred cEEecCCEEEEECCC-CCCCEEEEEEEEEeCCCCCEEEEEEEEEChhHccchhhhhcccccccccccccccchhhhhccC
Confidence 389999999999984 578999999999999999999999999999998642 0 12468
Q ss_pred CCeEEEeCCCcccccceEEeeeEEEeeecccccCC--CCCceEEEEeEeecCCCceeeCc
Q 030413 87 AKELFLSDHYDVQSAHTIEGKCIVHSFKNYTKLEN--VGAEDYYCRFEYKAASGGFTQTE 144 (177)
Q Consensus 87 ~~ELf~S~~~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~Ffcr~~yd~~~~~f~~~~ 144 (177)
++|||+|+|.|.+|+++|+|||.|++++++.+++. ..+++|||+..||+++++|.+..
T Consensus 81 ~rELF~S~~~d~~p~~~IrGKC~V~~~~d~~~l~~~~~~~d~Ff~~~~YDP~~k~l~~~~ 140 (164)
T cd04709 81 HRELFLSRQVETLPATHIRGKCSVTLLNDTESARSYLAREDTFFYSLVYDPEQKTLLADQ 140 (164)
T ss_pred cceeEEecccccccHHHeeeeEEEEEehhhhhhhhccCCCCEEEEEEEECCCCCeecccc
Confidence 99999999999999999999999999999988764 35799999999999999998764
No 9
>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=99.96 E-value=2.7e-29 Score=184.94 Aligned_cols=108 Identities=26% Similarity=0.432 Sum_probs=97.5
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCccccc-CCCCeEEEeCCCcccccceEEee
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQF-HGAKELFLSDHYDVQSAHTIEGK 107 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~-~~~~ELf~S~~~d~i~~~~I~gk 107 (177)
.++++||+|||.+++ +++|||+|++||++.+|.++++|+||+||+|+.+++++. +.+||||+|++.+++|+++|.||
T Consensus 6 ~~i~vGD~V~v~~~~--~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~~~~~~EvFlS~~~d~i~~~~I~gk 83 (130)
T cd04721 6 VTISVHDFVYVLSEE--EDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPDSVNPREIFLSPNLQVISVECIDGL 83 (130)
T ss_pred EEEECCCEEEEeCCC--CCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCCCCCCCeEEEcCCccccchHHeeee
Confidence 489999999999886 678999999999999999999999999999999876555 89999999999999999999999
Q ss_pred eEEEeeecccccCCC--C---CceEEEEeEeecCCC
Q 030413 108 CIVHSFKNYTKLENV--G---AEDYYCRFEYKAASG 138 (177)
Q Consensus 108 c~V~~~~~~~~~~~~--~---~~~Ffcr~~yd~~~~ 138 (177)
|.|++.++|.++... + .++|+||+.||....
T Consensus 84 ~~Vls~~~y~k~~~~~~~~~~~~~f~C~~~~d~~~~ 119 (130)
T cd04721 84 ATVLTREHYEKFQSVPKNSSELQAYFCYRQIDNNKV 119 (130)
T ss_pred eEECCHHHHhhhhccccCccccccEEEEEEecCCCC
Confidence 999999999986532 2 579999999998743
No 10
>cd04715 BAH_Orc1p_like BAH, or Bromo Adjacent Homology domain, as present in the Schizosaccharomyces pombe homolog of Saccharomyces cerevisiae Orc1p and similar proteins. Orc1 is part of the Yeast Sir1-origin recognition complex, the Orc1p BAH doman functions in epigenetic silencing. 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=99.96 E-value=1.6e-28 Score=186.12 Aligned_cols=112 Identities=28% Similarity=0.383 Sum_probs=95.7
Q ss_pred CCCCCCCCCCCCCceeeeEEEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCC--CcEEEEEEEEeeccccCCc
Q 030413 3 KTRPGIPTKTKTGKRDLESYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDAR--NNVKVRVRWYYRPEESLGG 80 (177)
Q Consensus 3 ~~~~~~~~k~~~~~~~y~~~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~--g~~~v~v~Wfyrp~e~~~~ 80 (177)
|++.|+ .++++.+|++++++|. .|++||+|+|.+++ .++|||+|.+||++.+ |.++++|+|||||+||...
T Consensus 7 ~~g~~~---~~~~~~~Y~s~~~~g~--~y~lGD~Vlv~s~~--~~~yIgkI~~iwe~~~~~g~~~~~v~WfyRp~E~~~~ 79 (159)
T cd04715 7 KRGEGG---KKKDGQFYRSFTYDGV--EYRLYDDVYVHNGD--SEPYIGKIIKIYETAIDSGKKKVKVIWFFRPSEIRME 79 (159)
T ss_pred eccccc---ccCCceEEEEEEECCE--EEeCCCEEEEeCCC--CCCEEEEEEEEEEcCCcCCceEEEEEeeeCHHHhccc
Confidence 455554 4455779999999986 99999999999865 7999999999999865 8999999999999999864
Q ss_pred cc--ccCCCCeEEEeCCC-----cccccceEEeeeEEEeeecccccCC
Q 030413 81 RR--QFHGAKELFLSDHY-----DVQSAHTIEGKCIVHSFKNYTKLEN 121 (177)
Q Consensus 81 ~~--~~~~~~ELf~S~~~-----d~i~~~~I~gkc~V~~~~~~~~~~~ 121 (177)
.. +.+.+||||+|+|. +++|+++|.|||.|+++++|.+..+
T Consensus 80 ~~~~~~~~~nEvFlS~~~d~~~~~~n~l~sI~gKC~Vl~~~ey~~~~~ 127 (159)
T cd04715 80 LKGEPKRHINEVFLACGRGEGLANINLLESIIGKCNVVCISEDFRNPQ 127 (159)
T ss_pred cccCcccCCCcEEEecCcCccccccCcHHHccceeEEEEehHhhhCCC
Confidence 32 45789999999885 6689999999999999999987543
No 11
>cd04710 BAH_fungalPHD BAH, or Bromo Adjacent Homology domain, as present in fungal proteins containing PHD domains. 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=99.96 E-value=1.6e-28 Score=181.62 Aligned_cols=112 Identities=23% Similarity=0.472 Sum_probs=98.8
Q ss_pred eeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCC------------CcEEEEEEEEeeccccCCcccccCCCCeEEEeCC
Q 030413 28 NKIVRVGDCVLMRPSDTGKPPYVARIEKIESDAR------------NNVKVRVRWYYRPEESLGGRRQFHGAKELFLSDH 95 (177)
Q Consensus 28 ~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~------------g~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~ 95 (177)
|..|++||+|||.++++++|++||||++|+...+ +...++|+|||||+|+.... ..+.+|||+|+|
T Consensus 9 g~~~~vgD~Vyv~~~~~~ePyyIgrI~e~~~~~~~~~~~~~~~~~~~~~~vrV~wfYRp~Di~~~~--~~d~relf~S~h 86 (135)
T cd04710 9 GELLKVNDHIYMSSEPPGEPYYIGRIMEFVPKHEFPSGIHARVFPASYFQVRLNWYYRPRDISRRV--VADSRLLYASMH 86 (135)
T ss_pred CeEEeCCCEEEEecCCCCCCCEEEEEEEEEecCCCCccccccccCCCcEEEEEEEEeCHHHcCCcc--cCCceEEEEEee
Confidence 4699999999999998889999999999999642 34799999999999985444 568999999999
Q ss_pred CcccccceEEeeeEEEeeecccccCC--CCCceEEEEeEeecCCCcee
Q 030413 96 YDVQSAHTIEGKCIVHSFKNYTKLEN--VGAEDYYCRFEYKAASGGFT 141 (177)
Q Consensus 96 ~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~Ffcr~~yd~~~~~f~ 141 (177)
.|++|+++|+|||.|.+.+++..++. ..+++|||.+.||+.+++|.
T Consensus 87 ~d~~p~~si~gKC~V~~~~di~~l~~~~~~~~~Fyf~~lyD~~~~r~~ 134 (135)
T cd04710 87 SDICPIGSVRGKCTVRHRDQIPDLEEYKKRPNHFYFDQLFDRYILRYY 134 (135)
T ss_pred EeeechHHEEeEEEEEEecccchhhhhccCCCEEEEEeeeCcchhhcc
Confidence 99999999999999999999877653 35899999999999999885
No 12
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=99.95 E-value=3e-28 Score=189.69 Aligned_cols=122 Identities=22% Similarity=0.422 Sum_probs=105.0
Q ss_pred EEEcCceeeEEeCCEEEEccCC-----------------CCCCCeEEEEeEEEeCCCC------cEEEEEEEEeeccccC
Q 030413 22 YTIRGTNKIVRVGDCVLMRPSD-----------------TGKPPYVARIEKIESDARN------NVKVRVRWYYRPEESL 78 (177)
Q Consensus 22 ~~~~g~~~~~~vGD~V~v~~~~-----------------~~~~~~Ig~I~~i~~~~~g------~~~v~v~Wfyrp~e~~ 78 (177)
|+++|. +|++||+|||.++. +..++.||||.+|+...++ ++.++|+|||||+||.
T Consensus 1 f~~~Gv--~Y~vgD~VYv~p~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k~~~~~~~~~~~vrVrwFYRPEdt~ 78 (202)
T cd04708 1 FVYDGV--TYSVGDFLYVSPDAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEKESKQADVASTQVKVRRFYRPEDVS 78 (202)
T ss_pred CcCCCE--EEecCCeEEECcccccccccccccccccccCCCCCcEEEEEEEEEecccCCCCCCcceEEEEEEEechhhcC
Confidence 456675 99999999999991 1358999999999986543 6899999999999986
Q ss_pred CcccccCCCCeEEEeCCCcccccceEEeeeEEEeeecccccCC--CCCceEEEEeEeecCCCceeeCcc
Q 030413 79 GGRRQFHGAKELFLSDHYDVQSAHTIEGKCIVHSFKNYTKLEN--VGAEDYYCRFEYKAASGGFTQTEL 145 (177)
Q Consensus 79 ~~~~~~~~~~ELf~S~~~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~Ffcr~~yd~~~~~f~~~~~ 145 (177)
.......+.+|||+|++.+++|+++|.|||.|....++.++.. ..++.|||+..||+.++.|+.+|.
T Consensus 79 ~~~~y~sd~rely~Sde~~~~~~~~I~GKC~V~~~~d~~~~~~~~~~~~~Ffc~~~Yd~~tg~f~~lP~ 147 (202)
T cd04708 79 PEKAYASDIREVYYSEDTLTVPVEAVEGKCEVRKKSDLPDSDAPVIFEHVFFCELLYDPAKGSLKQLPP 147 (202)
T ss_pred cccceecCceeEEEeccceeechhHcceEEEEEecCcchhhhccccCCCceEEEEEEcCCCCccCCCCc
Confidence 6434456899999999999999999999999999999887653 468999999999999999999875
No 13
>cd04712 BAH_DCM_I BAH, or Bromo Adjacent Homology domain, as present in DNA (Cytosine-5)-methyltransferases (DCM) 1. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=99.95 E-value=1.1e-26 Score=171.04 Aligned_cols=112 Identities=23% Similarity=0.314 Sum_probs=97.8
Q ss_pred eeEEeCCEEEEccCCCC----------CCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcccccCCCCeEEEeCCCcc
Q 030413 29 KIVRVGDCVLMRPSDTG----------KPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAKELFLSDHYDV 98 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~----------~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~ 98 (177)
..|++||+|+|.+++++ .+++|++|+.|+++.+|.+|++++|||||+||.+++ .+.+||||+|+|++.
T Consensus 4 ~~i~vGD~V~v~~d~~~~~~~~~~~~~~~~~i~~V~~~~e~~~g~~~~h~~W~yrp~eTv~g~--~~~~~ElFLSd~c~~ 81 (130)
T cd04712 4 LTIRVGDVVSVERDDADSTTKWNDDHRWLPLVQFVEYMKKGSDGSKMFHGRWLYRGCDTVLGN--YANERELFLTNECTC 81 (130)
T ss_pred CEEeCCCEEEEcCCCCCccccccccccccceEEEEEEeeecCCCceEEEEEEEEcchhccccc--cCCCceEEEeccccc
Confidence 48999999999999865 489999999999999999999999999999999998 588999999999999
Q ss_pred cccc----eEEeeeEEEeeecccccCCCCCceEEEEeEeecCCCceeeCc
Q 030413 99 QSAH----TIEGKCIVHSFKNYTKLENVGAEDYYCRFEYKAASGGFTQTE 144 (177)
Q Consensus 99 i~~~----~I~gkc~V~~~~~~~~~~~~~~~~Ffcr~~yd~~~~~f~~~~ 144 (177)
+|++ .|.+||.|........ ...++.|||+..|+++++.|+.+|
T Consensus 82 ~~~~~~~~~I~~k~~V~~~~~~~~--~~~~~~F~r~syy~~e~~~F~~l~ 129 (130)
T cd04712 82 LELDLLSTEIKGVHKVDWSGTPWG--KGLPEFFVRQSYYWPERGAFTSLK 129 (130)
T ss_pred cccccccceeEEEEEEEEecCcCC--cCCCCEEEEEEEECccCCceEcCC
Confidence 9999 9999999997766532 113456777777778999999886
No 14
>cd04718 BAH_plant_2 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=99.94 E-value=1.3e-28 Score=182.47 Aligned_cols=97 Identities=27% Similarity=0.494 Sum_probs=93.3
Q ss_pred CCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcccccCCCCeEEEeCCCcccccceEEeeeEEEeeecccccCCCCCc
Q 030413 46 KPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQSAHTIEGKCIVHSFKNYTKLENVGAE 125 (177)
Q Consensus 46 ~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~~~~I~gkc~V~~~~~~~~~~~~~~~ 125 (177)
.++|||||++||++. |+.+++|+|||||+||.+++++.+.++|||+|++.|++|+++|+|||.|+++++|.++++.+.|
T Consensus 51 ~~~~vArIekiW~~~-G~~~~~grWy~rPEET~~gr~~~~~~kEvFlS~~~d~~~~~~I~gkC~V~~~keY~k~e~~g~D 129 (148)
T cd04718 51 GDLWLARIEKLWEEN-GTYWYAARWYTLPEETHMGRQPHNLRRELYLTNDFADIEMECILRHCSVKCPKEFRDASNDGDD 129 (148)
T ss_pred CchHHHHHHHHHhcc-CceEEEEEEEeCchhccCccccccccceeeeccccccccHHHHhcccEEcCHHHcccccCCCCc
Confidence 579999999999986 9999999999999999999999999999999999999999999999999999999999988999
Q ss_pred eEEEEeEeecCCCceeeC
Q 030413 126 DYYCRFEYKAASGGFTQT 143 (177)
Q Consensus 126 ~Ffcr~~yd~~~~~f~~~ 143 (177)
+|||++.||..++.|..+
T Consensus 130 vy~Ce~~Yd~~~~~Fkr~ 147 (148)
T cd04718 130 VFLCEYEYDVHWQSFKRL 147 (148)
T ss_pred eEEEEEEEhhhcCceeec
Confidence 999999999999999864
No 15
>cd04760 BAH_Dnmt1_I BAH, or Bromo Adjacent Homology domain, first copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=99.94 E-value=3.7e-26 Score=165.74 Aligned_cols=111 Identities=23% Similarity=0.438 Sum_probs=97.3
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcccccCCCCeEEEeCCCcccccceEEeee
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQSAHTIEGKC 108 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~~~~I~gkc 108 (177)
.+|.+||+|+|.+++++.+++||+|+.||++.+|.+|++++|||||+||.+++. ++++|||+|++++.+++++|.+||
T Consensus 2 ~~i~vGD~V~v~~~~~~~p~~I~rV~~mfe~~~g~k~~h~rWf~Rg~dTVlG~~--~~~kEvFlsd~c~d~~l~~I~~Kv 79 (124)
T cd04760 2 EELEAGDCVSVKPDDPTKPLYIARVTYMWKDSIGGKMFHAHWFCRGSDTVLGET--SDPLELFLVDECEDMALSSIHGKV 79 (124)
T ss_pred CEEecCCEEEEecCCCCCCcEEEEEhhheecCCCCcEEEEEEEEECCccccccc--CCCcEEEeecccCCcchHHheeee
Confidence 489999999999988788999999999999999999999999999999999986 779999999999999999999999
Q ss_pred EEEeeeccccc------C-C-----CCCceEEEEeEeecCCCcee
Q 030413 109 IVHSFKNYTKL------E-N-----VGAEDYYCRFEYKAASGGFT 141 (177)
Q Consensus 109 ~V~~~~~~~~~------~-~-----~~~~~Ffcr~~yd~~~~~f~ 141 (177)
.|...+.-... + + .+-++|||+.-||++..+|.
T Consensus 80 ~V~~~~p~~~w~~~~g~~~~~~~~~ddg~tffyq~~yd~~~arf~ 124 (124)
T cd04760 80 NVIYKAPSENWSMEGGMDEEDEIFEDDGKTFFYQKWYDPECARFE 124 (124)
T ss_pred EEEEeCCCcchhhhcCCCCccccccCCCCeEEEEEeeChhhhccC
Confidence 99997753211 1 1 12379999999999887774
No 16
>cd04720 BAH_Orc1p_Yeast BAH, or Bromo Adjacent Homology domain, as present in Orc1p, which again is part of the Saccharomyces cerevisiae Sir1-origin recognition complex, and as present in Sir3p. The Orc1p BAH doman functions in epigenetic silencing. 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=99.93 E-value=3.5e-25 Score=171.24 Aligned_cols=115 Identities=24% Similarity=0.373 Sum_probs=101.2
Q ss_pred eeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCC-CcEEEEEEEEeeccccCCccc--c-------cCCCCeEEEeCCCc
Q 030413 28 NKIVRVGDCVLMRPSDTGKPPYVARIEKIESDAR-NNVKVRVRWYYRPEESLGGRR--Q-------FHGAKELFLSDHYD 97 (177)
Q Consensus 28 ~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~-g~~~v~v~Wfyrp~e~~~~~~--~-------~~~~~ELf~S~~~d 97 (177)
++++++||+|+|.+++. .++|||.|.+|+.+.. +.+.+.|+|||||.|+..++. + ...+||||+|.|.+
T Consensus 50 ~~~~~vGD~Vlik~~~~-~~~~V~iI~ei~~~~~~~~v~i~v~Wy~r~~Ei~~~~~~~~~~~~~~~~~~~nElflT~~~d 128 (179)
T cd04720 50 GLELSVGDTILVKDDVA-NSPSVYLIHEIRLNTLNNEVELWVMWFLRWFEINPARYYKQFDPEFRSESNKNELYLTAELS 128 (179)
T ss_pred CeEEeCCCEEEEeCCCC-CCCEEEEEEEEEeCCCCCEEEEEEEEcCCHHHcccccccccccchhcccCCCceEEEecccc
Confidence 57999999999999874 7999999999999865 568999999999999987542 2 23479999999999
Q ss_pred ccccceEEeeeEEEeeecccccCCC---CCceEEEEeEeecCCCceeeC
Q 030413 98 VQSAHTIEGKCIVHSFKNYTKLENV---GAEDYYCRFEYKAASGGFTQT 143 (177)
Q Consensus 98 ~i~~~~I~gkc~V~~~~~~~~~~~~---~~~~Ffcr~~yd~~~~~f~~~ 143 (177)
.+++.+|+++|.|++.++|.++.+. +..+||||++||+.++.|.++
T Consensus 129 ~i~l~~Ii~k~~Vls~~ef~~~~~~~~~~~~~F~cR~~~d~~~~~F~~~ 177 (179)
T cd04720 129 EIKLKDIIDKANVLSESEFNDLSTDDKNGERTFFCRYACEPDGEEFVWI 177 (179)
T ss_pred eEEhhheeeeEEEecHHHhhhhcccccCCCceEEEEEEEeCCCCeEccc
Confidence 9999999999999999999987543 578999999999999999874
No 17
>cd04711 BAH_Dnmt1_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases from Bilateria, Dnmt1 and similar proteins. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=99.90 E-value=5.2e-24 Score=155.42 Aligned_cols=112 Identities=22% Similarity=0.432 Sum_probs=93.1
Q ss_pred CCEEEEccCCCCCCCeEEEEeEEEeCCCC-------cEEEEEEEEeeccccCCcccc-c-CCCCeEEEeCCCcccccceE
Q 030413 34 GDCVLMRPSDTGKPPYVARIEKIESDARN-------NVKVRVRWYYRPEESLGGRRQ-F-HGAKELFLSDHYDVQSAHTI 104 (177)
Q Consensus 34 GD~V~v~~~~~~~~~~Ig~I~~i~~~~~g-------~~~v~v~Wfyrp~e~~~~~~~-~-~~~~ELf~S~~~d~i~~~~I 104 (177)
+|.|-=.+-+.++|++||||++|....++ +++++|+|||||+|+..++.. + .+.||||+|+|.+++|+++|
T Consensus 13 ~~~~~~~~~d~~ePy~VgrI~eI~~~k~~~~k~~~~~ikvrV~~fYRPEdi~~g~~~ayhsDirevy~Sd~~~~~~~~~I 92 (137)
T cd04711 13 SDYIKGSNLDAPEPFRIGRIKEIFCAKRSNGKPNESDIKLRINKFYRPENTHKGFKATYHADINMLYWSDEEATVDFSAV 92 (137)
T ss_pred ccccccccCCCCCCcEEEEEEEEecCCCCCCCCCccceEEEEEEEecccccccccccccccceeeEEeecceeecChhhc
Confidence 55555556666789999999999886532 479999999999999997543 3 44599999999999999999
Q ss_pred EeeeEEEeeecccc-cC---CCCCceEEEEeEeecCCCceeeCcc
Q 030413 105 EGKCIVHSFKNYTK-LE---NVGAEDYYCRFEYKAASGGFTQTEL 145 (177)
Q Consensus 105 ~gkc~V~~~~~~~~-~~---~~~~~~Ffcr~~yd~~~~~f~~~~~ 145 (177)
.|||.|.+..+... +. ..+++.|||+.+||.++|.|+.+|+
T Consensus 93 ~GKC~V~~~~di~~s~~~y~~~gpd~Fyf~~~Y~a~t~~F~d~p~ 137 (137)
T cd04711 93 QGRCTVEYGEDLPESVQEYSGGGPDRFYFLEAYNAKTKSFEDPPN 137 (137)
T ss_pred cceEEEEeccccchhHHHHhcCCCcceEEhhhhccccCcccCCCC
Confidence 99999998877653 32 3578999999999999999999874
No 18
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. 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=99.90 E-value=1.2e-23 Score=154.00 Aligned_cols=109 Identities=25% Similarity=0.356 Sum_probs=93.2
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCC---cEEEEEEEEeeccccCCcc----cccCCCCeEEEeCCCc---c
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARN---NVKVRVRWYYRPEESLGGR----RQFHGAKELFLSDHYD---V 98 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g---~~~v~v~Wfyrp~e~~~~~----~~~~~~~ELf~S~~~d---~ 98 (177)
.++++||+|+|.++++ +++|||+|++|+++.+| ...++|||||||+|++... ....+++|||+|++.+ .
T Consensus 2 ~~i~vGd~VlI~~~d~-~~~yVAkI~~i~e~~~~~~~~~~~~VqWy~R~~Ev~~~~~~~~~~~~~~~EvF~~~~~~~~~~ 80 (128)
T cd04719 2 LTIEVGDFVLIEGEDA-DGPDVARILHLYEDGNEDDDPKRAIVQWFSRPSEVPKNKRKLLGREPHSQEVFFYSRSSCDND 80 (128)
T ss_pred eEEecCCEEEEECCCC-CCCcEeeehhhhccccCCcccceEEEEcccChHHccccchhhccCCCCCcEEEEecCccccCc
Confidence 4799999999999985 78899999999998766 5799999999999997432 1346899999999874 8
Q ss_pred cccceEEeeeEEEeeecccccCCC---CCceEEEEeEeecCCC
Q 030413 99 QSAHTIEGKCIVHSFKNYTKLENV---GAEDYYCRFEYKAASG 138 (177)
Q Consensus 99 i~~~~I~gkc~V~~~~~~~~~~~~---~~~~Ffcr~~yd~~~~ 138 (177)
+++++|.|+|.|+++++|.+++.. ...+||.|+.++.+..
T Consensus 81 i~~etI~gkc~V~~~~~y~~l~~~~~~~~~~~F~r~~~~~k~~ 123 (128)
T cd04719 81 IDAETIIGKVRVEPVEPKTDLPETKKKTGGPLFVKRYWDTKTF 123 (128)
T ss_pred EeHHHcccEEEEEEcCCccchhhhccccCceEEEEEEeccccc
Confidence 999999999999999999988732 3578999999998743
No 19
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=99.87 E-value=1.1e-22 Score=174.01 Aligned_cols=156 Identities=38% Similarity=0.556 Sum_probs=137.7
Q ss_pred CCceeeeEEEEcCceeeEEe-CCEEEEccCCCCCCCeEEEEeEEEeCCC-CcEEEEEEEEeeccccCCccc---ccCCCC
Q 030413 14 TGKRDLESYTIRGTNKIVRV-GDCVLMRPSDTGKPPYVARIEKIESDAR-NNVKVRVRWYYRPEESLGGRR---QFHGAK 88 (177)
Q Consensus 14 ~~~~~y~~~~~~g~~~~~~v-GD~V~v~~~~~~~~~~Ig~I~~i~~~~~-g~~~v~v~Wfyrp~e~~~~~~---~~~~~~ 88 (177)
..+.||+++.+.|. .+.. ||.|.+.+++++.++|||+|+.|+.+.. +++.+.|+|||||+|+..+.. .....+
T Consensus 35 ~k~~h~~t~~~~~g--~~~~~~d~vllvped~~~pPyvaii~~i~a~~~g~~~k~ev~W~YrPee~~~~~~~~~~a~~~r 112 (464)
T KOG1886|consen 35 VKSLHFETFIYRGG--RYINYGDSVLLVPEDPGKPPYVAIIEDIYAQERGGNVKVEVQWFYRPEESEGGGSGKWGAKQPR 112 (464)
T ss_pred cccccccceeeccC--cccccCcceeecCCCCCCCCeeEEEeeeeccccCCCcceecccccCCCccCCCCCCCcccCCCc
Confidence 34789999999875 5555 9999999999899999999999999876 689999999999999997743 345567
Q ss_pred eEEEeCCCcccccceEEeeeEEEeeecccccCC-CCCceEEEEeEeecCCCceeeCcc--ccccc---------cccCcc
Q 030413 89 ELFLSDHYDVQSAHTIEGKCIVHSFKNYTKLEN-VGAEDYYCRFEYKAASGGFTQTEL--LCTAN---------VRCLIT 156 (177)
Q Consensus 89 ELf~S~~~d~i~~~~I~gkc~V~~~~~~~~~~~-~~~~~Ffcr~~yd~~~~~f~~~~~--~C~c~---------~~C~~~ 156 (177)
|||+|.|.|++++++|.++|.|.++..+.+++. .+.+.|+||..||..+++|..+.- +|.|+ .+| .
T Consensus 113 elF~SfH~De~~A~ti~~rC~V~fvp~~kqlp~~~~~~~f~~r~vYd~~~~~~~~~~~~~~~~~~k~e~d~~~~kt~--~ 190 (464)
T KOG1886|consen 113 ELFLSFHEDEAFAETILHRCKVHFVPAYKQLPNRVGHESFICRRVYDAVTSKLRKLRDGDFGDGQKLEIDMLVPKTG--P 190 (464)
T ss_pred cccccccccchhhhhhcccceeeeccccccccccCCCCCcccccccccccccccCccccchhcccccCCccchhhhc--c
Confidence 999999999999999999999999999999886 678999999999999999998764 88888 889 9
Q ss_pred chhcccccccccchhhh
Q 030413 157 RMISWYNVRGARTGIIL 173 (177)
Q Consensus 157 ~c~~wyH~~C~~~~~~~ 173 (177)
.|..|+|.+|+....+.
T Consensus 191 ~~~~~~~p~~~~t~~~~ 207 (464)
T KOG1886|consen 191 RRGTLPDPKKVQTLNAA 207 (464)
T ss_pred cCCCCCCcccccccccc
Confidence 99999999999887643
No 20
>KOG1827 consensus Chromatin remodeling complex RSC, subunit RSC1/Polybromo and related proteins [Chromatin structure and dynamics; Transcription]
Probab=99.69 E-value=2.9e-17 Score=145.45 Aligned_cols=127 Identities=24% Similarity=0.349 Sum_probs=116.2
Q ss_pred EEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcccccCCCCeEEEeCCCccccc
Q 030413 22 YTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQSA 101 (177)
Q Consensus 22 ~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~~ 101 (177)
+.++|. .|.+||.||+.+..+..++.|++|.++|.+.+|..|..+.|||||++|.+--.+.+.++|+|.|......++
T Consensus 184 ~~i~~~--~~~~gd~vlv~~~~d~~~p~v~~Ier~w~~~dg~k~~~~~w~~rP~~T~H~a~r~F~k~Evfkt~~~~~~~~ 261 (629)
T KOG1827|consen 184 VEIDGT--KYIVGDYVLVQNPADNLKPIVAQIERLWKLPDGEKWPQGCWIYRPEETVHRADRKFYKQEVFKTSLYRDDLV 261 (629)
T ss_pred ccccCc--ccccCceeeecCcccccCCceeeecccccCcccccccceeEeeCCccCccccccchhcccceecccccccHH
Confidence 678876 999999999999987789999999999999999999999999999999987666688999999999999999
Q ss_pred ceEEeeeEEEeeecccccCCC---CCceEEEEeEeecCCCceeeCcc--ccccc
Q 030413 102 HTIEGKCIVHSFKNYTKLENV---GAEDYYCRFEYKAASGGFTQTEL--LCTAN 150 (177)
Q Consensus 102 ~~I~gkc~V~~~~~~~~~~~~---~~~~Ffcr~~yd~~~~~f~~~~~--~C~c~ 150 (177)
+.|+|+|.|+.+.+|...++. ..+.|+|.+.|++..+.|.++++ .|+.+
T Consensus 262 q~l~g~c~v~~~~~yi~~~p~~ls~~dv~lcesRyn~~~K~f~kirsw~~~~p~ 315 (629)
T KOG1827|consen 262 QRLLGKCYVMKPTEYISGDPENLSEEDVFLCESRYNEQLKKFNKIRSWKAFLPR 315 (629)
T ss_pred HHhhcceEEeehhHhhhcCcccccccceeeEEeeeccchhhhccccCchhcCcc
Confidence 999999999999999998874 46899999999999999999887 55544
No 21
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=99.32 E-value=9.8e-14 Score=118.54 Aligned_cols=114 Identities=27% Similarity=0.464 Sum_probs=96.9
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCc---------c-------------------
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGG---------R------------------- 81 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~---------~------------------- 81 (177)
.|++||+||+..... .++.|-+|+++..+.+|++.++|..|||..|++.. +
T Consensus 5 ~y~vgd~vYf~~sss-~PYliRrIEELnKTa~GnVeAkvVc~~RRRDIs~~L~~lAD~~ar~~~~y~a~~~a~~~~e~e~ 83 (693)
T KOG3554|consen 5 MYRVGDYVYFENSSS-NPYLIRRIEELNKTANGNVEAKVVCYLRRRDISSHLLKLADKHARRFDNYAAPEAAPEATEAEI 83 (693)
T ss_pred cceecceEEEecCCC-ChHHHHHHHHHhccccCCcceEEEEEEEccchHHHHHHHHHHHhhhcccccCcccCcccchhhh
Confidence 789999999999874 58889999999999999999999999999987510 0
Q ss_pred ----------------cccCCCCeEEEeCCCcccccceEEeeeEEEeeecccccCC--CCCceEEEEeEeecCCCceeeC
Q 030413 82 ----------------RQFHGAKELFLSDHYDVQSAHTIEGKCIVHSFKNYTKLEN--VGAEDYYCRFEYKAASGGFTQT 143 (177)
Q Consensus 82 ----------------~~~~~~~ELf~S~~~d~i~~~~I~gkc~V~~~~~~~~~~~--~~~~~Ffcr~~yd~~~~~f~~~ 143 (177)
+.....+|||+|.+.+.+|+..|+|||.|..+.+-+.+.. ..+|+||+...|||..+.+...
T Consensus 84 EEe~e~p~~vdlt~~qrhqLrhrElFlsRQ~EsLPAthIRGKCsV~LLnete~~~~YL~~eDtFfySLVyDP~~kTLLAD 163 (693)
T KOG3554|consen 84 EEESECPAPVDLTEKQRHQLRHRELFLSRQSESLPATHIRGKCSVTLLNETESLQSYLEKEDTFFYSLVYDPNQKTLLAD 163 (693)
T ss_pred hhhccCCCcCCCCHHHHHHHHHHHHHHhhhhccCchhhhccceeEEEecChHHHHhhccccceeEEEeeeccchhhhhcc
Confidence 0114469999999999999999999999999998776654 3589999999999998887655
Q ss_pred c
Q 030413 144 E 144 (177)
Q Consensus 144 ~ 144 (177)
+
T Consensus 164 k 164 (693)
T KOG3554|consen 164 K 164 (693)
T ss_pred C
Confidence 4
No 22
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=97.44 E-value=4.5e-05 Score=46.64 Aligned_cols=21 Identities=14% Similarity=0.377 Sum_probs=19.2
Q ss_pred cccCccchhcccccccccchhhh
Q 030413 151 VRCLITRMISWYNVRGARTGIIL 173 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~~~~~~~ 173 (177)
|+| +.|..|||+.|++++...
T Consensus 15 i~C--~~C~~~~H~~C~~~~~~~ 35 (51)
T PF00628_consen 15 IQC--DSCNRWYHQECVGPPEKA 35 (51)
T ss_dssp EEB--STTSCEEETTTSTSSHSH
T ss_pred EEc--CCCChhhCcccCCCChhh
Confidence 999 999999999999998653
No 23
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=97.33 E-value=6.1e-05 Score=62.11 Aligned_cols=28 Identities=14% Similarity=0.364 Sum_probs=24.2
Q ss_pred ccccccc-------cccCccchh-cccccccccchh
Q 030413 144 ELLCTAN-------VRCLITRMI-SWYNVRGARTGI 171 (177)
Q Consensus 144 ~~~C~c~-------~~C~~~~c~-~wyH~~C~~~~~ 171 (177)
+++|+|+ |.|-++.|. .|||+.|||++.
T Consensus 219 ~~yC~Cnqvsyg~Mi~CDn~~C~~eWFH~~CVGL~~ 254 (274)
T KOG1973|consen 219 PTYCICNQVSYGKMIGCDNPGCPIEWFHFTCVGLKT 254 (274)
T ss_pred CEEEEecccccccccccCCCCCCcceEEEecccccc
Confidence 4599999 999666699 899999999983
No 24
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.14 E-value=0.0017 Score=52.42 Aligned_cols=28 Identities=21% Similarity=0.453 Sum_probs=24.8
Q ss_pred ccccccc-------cccCccchhc-ccccccccchh
Q 030413 144 ELLCTAN-------VRCLITRMIS-WYNVRGARTGI 171 (177)
Q Consensus 144 ~~~C~c~-------~~C~~~~c~~-wyH~~C~~~~~ 171 (177)
.++|.|+ |-|-++.|+- |||++|+|+..
T Consensus 221 ~lYCfCqqvSyGqMVaCDn~nCkrEWFH~~CVGLk~ 256 (271)
T COG5034 221 ELYCFCQQVSYGQMVACDNANCKREWFHLECVGLKE 256 (271)
T ss_pred eeEEEecccccccceecCCCCCchhheeccccccCC
Confidence 4599999 9998889987 99999999864
No 26
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=92.39 E-value=0.059 Score=45.95 Aligned_cols=82 Identities=12% Similarity=0.071 Sum_probs=58.9
Q ss_pred CeEEEeCCCcccccceEEeeeEEEeeecccccCCCCCceEEEEeEeecCCCceeeCcc--ccccc---------cccCcc
Q 030413 88 KELFLSDHYDVQSAHTIEGKCIVHSFKNYTKLENVGAEDYYCRFEYKAASGGFTQTEL--LCTAN---------VRCLIT 156 (177)
Q Consensus 88 ~ELf~S~~~d~i~~~~I~gkc~V~~~~~~~~~~~~~~~~Ffcr~~yd~~~~~f~~~~~--~C~c~---------~~C~~~ 156 (177)
.+.+++.++.--....+.+++.......+... +....+.++...+....+.+.+-.. .|.|. ++| +
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~~~~~~~~a~~~~~~~~~~~~~p~~~~~~c--d 79 (345)
T KOG1632|consen 3 KIPKTSKTFSKTESDRRAPIAQKTTKPPKEPV-PIERPVPDVFRGRKGRRGGLLKALTQRYCKCYKPCDPDDLMEQC--D 79 (345)
T ss_pred CcccccceecccccccccccccccccCCcCCC-CCCCCCcccccccccccccccHhhhhchhhcccccCchhhhhcc--c
Confidence 34556666666666677777777666665544 4456677788888888777776443 77776 888 9
Q ss_pred chhccccccc--ccchhh
Q 030413 157 RMISWYNVRG--ARTGII 172 (177)
Q Consensus 157 ~c~~wyH~~C--~~~~~~ 172 (177)
.|..|||.+| +|++..
T Consensus 80 ~C~~~~~~ec~~v~~~~~ 97 (345)
T KOG1632|consen 80 LCEDWYHGECWEVGTAEK 97 (345)
T ss_pred cccccccccccccCchhh
Confidence 9999999999 988754
No 27
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=92.03 E-value=0.046 Score=48.03 Aligned_cols=22 Identities=18% Similarity=0.380 Sum_probs=18.9
Q ss_pred cccCccchhcccccccccchhhhh
Q 030413 151 VRCLITRMISWYNVRGARTGIILL 174 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~~~~~~~~ 174 (177)
++| ++|..|||..|....+...
T Consensus 186 lqC--~~C~~~fHq~Chqp~i~~~ 207 (464)
T KOG4323|consen 186 LQC--DKCRQWYHQACHQPLIKDE 207 (464)
T ss_pred eee--cccccHHHHHhccCCCCHh
Confidence 999 9999999999987765544
No 28
>COG5076 Transcription factor involved in chromatin remodeling, contains bromodomain [Chromatin structure and dynamics / Transcription]
Probab=91.15 E-value=0.028 Score=48.19 Aligned_cols=96 Identities=16% Similarity=0.108 Sum_probs=81.9
Q ss_pred EEEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcccccCCCCeEEEeCCCcccc
Q 030413 21 SYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQS 100 (177)
Q Consensus 21 ~~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~ 100 (177)
+..+.+. ..++|+.+.+.+..+.+.+.++.+...|.+.++..+.-+.|||+|+++.......+..+++......+.++
T Consensus 269 ~~~i~~~--~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 346 (371)
T COG5076 269 SVLITNS--QAHVGAWPFLRPVSDEEVPDYYKDIRDPMDLSTKELKLRNNYYRPEETFVRDAKLFFDNCVMYNGEVTDYY 346 (371)
T ss_pred hhccccc--ccccccccccccCCcccccchhhhhhcccccccchhhhhcccCCCccccccccchhhhcccccchhhhhhh
Confidence 4455554 78999999999998888999999999999988888889999999997777666667889999999999999
Q ss_pred cceEEeeeEEEeeecccc
Q 030413 101 AHTIEGKCIVHSFKNYTK 118 (177)
Q Consensus 101 ~~~I~gkc~V~~~~~~~~ 118 (177)
.....+.|.|....++..
T Consensus 347 ~~~~~~~~~~~~~~~~~~ 364 (371)
T COG5076 347 KNANVLEDFVIKKTRLIR 364 (371)
T ss_pred hhccchhhhHhhhhhhhh
Confidence 999999998887766543
No 29
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=89.85 E-value=0.59 Score=28.93 Aligned_cols=40 Identities=15% Similarity=0.313 Sum_probs=26.7
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeec
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRP 74 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp 74 (177)
|++||.|.+.++.+ ..-|..|..- .....-++..+||---
T Consensus 1 f~~GDvV~LKSGGp--~MTV~~v~~~--~~~~~~~v~C~WFd~~ 40 (53)
T PF09926_consen 1 FKIGDVVQLKSGGP--RMTVTEVGPN--AGASGGWVECQWFDGH 40 (53)
T ss_pred CCCCCEEEEccCCC--CeEEEEcccc--ccCCCCeEEEEeCCCC
Confidence 57899999999984 4444444332 1233468999999643
No 30
>PRK10708 hypothetical protein; Provisional
Probab=87.03 E-value=2.8 Score=26.23 Aligned_cols=45 Identities=13% Similarity=0.271 Sum_probs=34.3
Q ss_pred EeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEE-------EEEEEeeccccC
Q 030413 32 RVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKV-------RVRWYYRPEESL 78 (177)
Q Consensus 32 ~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v-------~v~Wfyrp~e~~ 78 (177)
+++|.|.|+.+. .+...|.|..+..=..|.+++ .+.||+.-.+-.
T Consensus 2 kvnD~VtVKTDG--~~rR~G~iLavE~F~EG~MyLvaL~dYP~GiWFFNE~~~~ 53 (62)
T PRK10708 2 KVNDRVTVKTDG--GPRRPGVVLAVEEFSEGTMYLVSLEDYPLGIWFFNEAGHQ 53 (62)
T ss_pred ccccEEEEecCC--CccccceEEEEeeccCcEEEEEEcCcCCCceEEEeccCCC
Confidence 589999999986 688899999988866776554 467887655443
No 31
>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=86.79 E-value=3.3 Score=25.90 Aligned_cols=46 Identities=17% Similarity=0.320 Sum_probs=34.7
Q ss_pred EeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEE-------EEEEEeeccccCC
Q 030413 32 RVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKV-------RVRWYYRPEESLG 79 (177)
Q Consensus 32 ~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v-------~v~Wfyrp~e~~~ 79 (177)
+++|.|.|+.+. .+..-|.|..+..=..|-+++ .+.||+.-.+-+.
T Consensus 2 kvnD~VtVKTDG--~~rR~G~ilavE~F~EG~MYLvaL~dYP~GiWFFNE~~~~d 54 (62)
T PF10781_consen 2 KVNDRVTVKTDG--GPRREGVILAVEPFNEGTMYLVALEDYPAGIWFFNEKDSPD 54 (62)
T ss_pred ccccEEEEecCC--cccccceEEEEeeccCcEEEEEEcCcCCcceEEEecCCCCC
Confidence 589999999986 688899999888866776554 4678877655443
No 32
>PF10383 Clr2: Transcription-silencing protein Clr2 ; InterPro: IPR018839 Clr2 (cryptic loci regulator) is a chromatin silencing protein, one of a quartet of proteins forming the core of SHREC, a multienzyme effector complex that mediates hetero-chromatic transcriptional gene silencing in fission yeast []. Clr2 does not have any obvious well-conserved domains but, along with the other core proteins, binds to the histone deacetylase Clr3, and on its own might also have a role in chromatin organisation at the cnt domain, the site of kinetochore assembly.
Probab=86.65 E-value=4.5 Score=29.93 Aligned_cols=53 Identities=23% Similarity=0.327 Sum_probs=38.5
Q ss_pred eeeeEEEEcCceeeEEeCCEEEEccCC----------CCCCCeEEEEeEEEeCCCC-------cEEEEEEEE
Q 030413 17 RDLESYTIRGTNKIVRVGDCVLMRPSD----------TGKPPYVARIEKIESDARN-------NVKVRVRWY 71 (177)
Q Consensus 17 ~~y~~~~~~g~~~~~~vGD~V~v~~~~----------~~~~~~Ig~I~~i~~~~~g-------~~~v~v~Wf 71 (177)
.||+.+.+.- +.+.+||.|-|.+.. .++.-.|..|.+|...... .+++++.-|
T Consensus 1 i~y~GiflGA--E~I~vGD~VRl~~~~~~~~~~~~~~~~~~tdvMvI~~I~~~~~~~~~~~~~~v~~~G~lY 70 (139)
T PF10383_consen 1 IYYRGIFLGA--EMIWVGDAVRLKPLNASPSPNQSDGNPDVTDVMVIDEIQLRLINCDPDSPSTVRFRGDLY 70 (139)
T ss_pred CeECeEEEee--EEEEeCCEEEECccCCCcccccccCCCCceeEEEEeEEEEecccCCCCCCceEEEEeEec
Confidence 4788888854 699999999995432 2356679999999886422 477877655
No 33
>PF08940 DUF1918: Domain of unknown function (DUF1918); InterPro: IPR015035 This domain is found in various hypothetical bacterial proteins, and has no known function. ; PDB: 2A7Y_A.
Probab=84.00 E-value=1.8 Score=27.23 Aligned_cols=40 Identities=23% Similarity=0.392 Sum_probs=27.2
Q ss_pred EeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEe
Q 030413 32 RVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYY 72 (177)
Q Consensus 32 ~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfy 72 (177)
++||.+.+.....+.+...|.|.++... +|..=..|+|--
T Consensus 4 ~vGD~lvv~g~~vg~~~r~GeIveV~g~-dG~PPY~VRw~D 43 (58)
T PF08940_consen 4 SVGDRLVVHGRTVGQPDRHGEIVEVRGP-DGSPPYLVRWDD 43 (58)
T ss_dssp -TTEEEEES-TTTS--EEEEEEEE-S-S-SS-S-EEEEETT
T ss_pred CCCCEEEEcCCcCCCCCcEeEEEEEECC-CCCCCEEEEecC
Confidence 6899999999887789999999999985 676677888853
No 34
>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=83.40 E-value=2.1 Score=28.83 Aligned_cols=44 Identities=23% Similarity=0.315 Sum_probs=34.7
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeecc
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPE 75 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~ 75 (177)
.+++||.|.-.-.. -++|-|+|.+.-+.......+.|+||-..+
T Consensus 2 ~f~~GdlVwaK~kG--yp~WPa~I~~~~~~~~~~~~~~V~FfGt~~ 45 (83)
T cd05834 2 QFKAGDLVFAKVKG--YPAWPARVDEPEDWKPPGKKYPVYFFGTHE 45 (83)
T ss_pred CCCCCCEEEEecCC--CCCCCEEEecccccCCCCCEEEEEEeCCCC
Confidence 57899999999865 699999999987653445668899987543
No 35
>PF07154 DUF1392: Protein of unknown function (DUF1392); InterPro: IPR009824 This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length, which seem to be specific to Anabaena species. The function of this family is unknown.
Probab=82.62 E-value=4 Score=30.44 Aligned_cols=50 Identities=30% Similarity=0.428 Sum_probs=36.6
Q ss_pred CceeeeEEEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeecc
Q 030413 15 GKRDLESYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPE 75 (177)
Q Consensus 15 ~~~~y~~~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~ 75 (177)
|...+++.++... .|++||.|.+...+ +.+-.-.|..|.- ++-.|||--+
T Consensus 74 ~tg~~q~~tv~kp--~F~LGd~V~~~f~~--~~pkqRlIlGv~l-------v~~~W~Y~VE 123 (150)
T PF07154_consen 74 GTGQLQSLTVQKP--AFRLGDRVEFRFYS--DGPKQRLILGVFL-------VNNSWFYAVE 123 (150)
T ss_pred ecCccceeeccCC--ceecCCEEEEEecC--CCCceEEEEEEEE-------ecCceEEEEE
Confidence 4566777788776 89999999999964 3566777777766 4555888655
No 36
>PF09871 DUF2098: Uncharacterized protein conserved in archaea (DUF2098); InterPro: IPR019209 This family of proteins have no known function.
Probab=82.24 E-value=4 Score=28.15 Aligned_cols=43 Identities=23% Similarity=0.364 Sum_probs=33.5
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEE---EEEeeccccC
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRV---RWYYRPEESL 78 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v---~Wfyrp~e~~ 78 (177)
.+.+|++|--.+.. -+|+|.+|-. .+|..|+.+ .-||||+-+.
T Consensus 2 ~I~vGs~VRY~~TG-----T~G~V~diK~-ed~~~wv~LD~t~L~Yr~~~Le 47 (91)
T PF09871_consen 2 PIKVGSYVRYINTG-----TVGKVVDIKE-EDGETWVLLDSTDLYYRPDYLE 47 (91)
T ss_pred cceeCCEEEECCCC-----eEEEEEEEEE-eCCCeEEEEccCCceeecceeE
Confidence 57899999766654 2999999955 578889888 6788888655
No 37
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=80.81 E-value=3.3 Score=27.46 Aligned_cols=31 Identities=23% Similarity=0.375 Sum_probs=24.9
Q ss_pred eEEeCCEEEEccCC-----CCCCCeEEEEeEEEeCC
Q 030413 30 IVRVGDCVLMRPSD-----TGKPPYVARIEKIESDA 60 (177)
Q Consensus 30 ~~~vGD~V~v~~~~-----~~~~~~Ig~I~~i~~~~ 60 (177)
-++.||+|.|..+. .+...|+|+|+..-...
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gga 40 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGA 40 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccc
Confidence 35899999999976 24689999999887753
No 38
>KOG1568 consensus Mitochondrial inner membrane protease, subunit IMP2 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=80.34 E-value=15 Score=28.20 Aligned_cols=88 Identities=20% Similarity=0.312 Sum_probs=53.1
Q ss_pred ceeeeEEEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccC---Ccc-c-ccCCCCeE
Q 030413 16 KRDLESYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESL---GGR-R-QFHGAKEL 90 (177)
Q Consensus 16 ~~~y~~~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~---~~~-~-~~~~~~EL 90 (177)
......+-+.. ..+..||.|.+.++.++++.+|-||..+--+ .+.. +-++++.. .|. . .-....+=
T Consensus 56 ~Vll~k~~v~n--~~~~rGDiVvl~sP~~p~~~~iKRv~alegd----~~~t---~~~k~~~v~vpkghcWVegDn~~hs 126 (174)
T KOG1568|consen 56 TVLLRKWNVKN--RKVSRGDIVVLKSPNDPDKVIIKRVAALEGD----IMVT---EDEKEEPVVVPKGHCWVEGDNQKHS 126 (174)
T ss_pred EEEEEeecccc--ceeccCCEEEEeCCCChhheeeeeeeccccc----Eecc---CCCCCCceecCCCcEEEecCCcccc
Confidence 34444554443 3678999999999988889999999877554 1111 22222221 110 0 00223445
Q ss_pred EEeCCCcccccceEEeeeEEEe
Q 030413 91 FLSDHYDVQSAHTIEGKCIVHS 112 (177)
Q Consensus 91 f~S~~~d~i~~~~I~gkc~V~~ 112 (177)
+=|+.+--+++..|.|++.-..
T Consensus 127 ~DSntFGPVS~gli~grai~il 148 (174)
T KOG1568|consen 127 YDSNTFGPVSTGLIVGRAIYIL 148 (174)
T ss_pred cccCccCCcchhheeeeEEEEE
Confidence 5567777888899999886544
No 39
>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=78.66 E-value=3.8 Score=27.52 Aligned_cols=39 Identities=23% Similarity=0.228 Sum_probs=31.2
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeec
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRP 74 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp 74 (177)
|.+||.|.-.-.. -|.|.|+|.++... ...+.|.||=..
T Consensus 1 f~~gdlVWaK~~g--~P~WPa~I~~~~~~---~~k~~V~FfG~~ 39 (80)
T cd06080 1 FEKNDLVWAKIQG--YPWWPAVIKSISRK---KQKARVNFIGDN 39 (80)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEeeecCC---CCEEEEEEeCCC
Confidence 4689999988876 68999999988543 567889888666
No 40
>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=78.41 E-value=2.9 Score=28.29 Aligned_cols=41 Identities=22% Similarity=0.274 Sum_probs=31.7
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEeCCC---CcEEEEEEEEee
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIESDAR---NNVKVRVRWYYR 73 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~---g~~~v~v~Wfyr 73 (177)
|.+||.|...-.. -+.|-|+|.+...+.. ...++.|+||=.
T Consensus 1 f~vGDlVWaK~kg--~pwWP~~V~~~~~~~~~~~~~~~~~V~fFGs 44 (87)
T cd05835 1 FNVGDLVWGKIKG--FPWWPGRVVSITVTSKRPPVVGMRWVTWFGS 44 (87)
T ss_pred CCCCCEEEEecCC--CCCCCeEEechhhcccccCCCCeEEEEEeCC
Confidence 4689999999875 6899999999876531 235688889863
No 41
>COG4014 Uncharacterized protein conserved in archaea [Function unknown]
Probab=78.38 E-value=5.9 Score=27.13 Aligned_cols=41 Identities=27% Similarity=0.422 Sum_probs=29.9
Q ss_pred EeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEE---EEeecccc
Q 030413 32 RVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVR---WYYRPEES 77 (177)
Q Consensus 32 ~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~---Wfyrp~e~ 77 (177)
.+||.|.--+.+ .+|+|.+|..+.+|++|+.+- -+||+.=+
T Consensus 10 ~VG~avrYvnTg-----TvgrV~dIkkdEdG~~WV~LdstdLwYre~~l 53 (97)
T COG4014 10 KVGDAVRYVNTG-----TVGRVVDIKKDEDGDIWVVLDSTDLWYREHYL 53 (97)
T ss_pred hhcceEEEeecC-----ceeeEEEEEeecCCceEEEEecCCceecccce
Confidence 478876444433 289999999999999999874 35676643
No 42
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=74.39 E-value=9.2 Score=27.27 Aligned_cols=45 Identities=18% Similarity=0.293 Sum_probs=35.0
Q ss_pred CCCCCCceeeeEE-EEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCC
Q 030413 10 TKTKTGKRDLESY-TIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDA 60 (177)
Q Consensus 10 ~k~~~~~~~y~~~-~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~ 60 (177)
+|..+|....-.+ ..+| ++++||.|.+-..+ .|-+++|..|..+.
T Consensus 8 vk~~~G~G~t~dvIl~~G---tL~~GD~Iv~g~~~---Gpi~tkVRaLl~~~ 53 (110)
T cd03703 8 VKEEEGLGTTIDVILYDG---TLREGDTIVVCGLN---GPIVTKVRALLKPQ 53 (110)
T ss_pred EEEcCCCceEEEEEEECC---eEecCCEEEEccCC---CCceEEEeEecCCC
Confidence 3556677777555 5566 89999999998875 57799999999874
No 43
>PTZ00112 origin recognition complex 1 protein; Provisional
Probab=73.96 E-value=7.5 Score=37.74 Aligned_cols=119 Identities=23% Similarity=0.307 Sum_probs=74.2
Q ss_pred ceeeeEEEEcCceeeEEeCCEEEEccCCCCC----------------------CCeEEEEeEEEeCC-CCcEEEEEEEEe
Q 030413 16 KRDLESYTIRGTNKIVRVGDCVLMRPSDTGK----------------------PPYVARIEKIESDA-RNNVKVRVRWYY 72 (177)
Q Consensus 16 ~~~y~~~~~~g~~~~~~vGD~V~v~~~~~~~----------------------~~~Ig~I~~i~~~~-~g~~~v~v~Wfy 72 (177)
-..|+++.+++. .|.+||.|+|.-..++. ..-=|+|.+|+.+. ...+.+.|..||
T Consensus 440 g~iye~~~in~~--~ys~g~dv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~kg~is~fy~~~~~~~~~~e~c~y~ 517 (1164)
T PTZ00112 440 GVIYESIQINDV--EYSIGDDVLIFCTGNGNTYNGKSGTKKNQNNKNIKENIYQLRKGKISSFYKNTNSNQVEAEVCIYY 517 (1164)
T ss_pred ceEEEEEEEcce--eeccCCcEEEEEcCCCCccccccCccccccccchhhhhheecccccchhhhcCCCceeeEEEEEEE
Confidence 467999999986 99999999998765321 12358899999875 457999999999
Q ss_pred eccccCC--------cccccCCCCeEEEeCC-----------CcccccceEEeeeEEEeeecccccC---CCCCceEEEE
Q 030413 73 RPEESLG--------GRRQFHGAKELFLSDH-----------YDVQSAHTIEGKCIVHSFKNYTKLE---NVGAEDYYCR 130 (177)
Q Consensus 73 rp~e~~~--------~~~~~~~~~ELf~S~~-----------~d~i~~~~I~gkc~V~~~~~~~~~~---~~~~~~Ffcr 130 (177)
-..|.+- ..+..-..-|+|+-+. +-.+.+.-|..|..|....+-..-+ ..|.|-|.|-
T Consensus 518 d~~d~~~i~~~~~~~~~rr~~~~f~~~~d~~~~~~~llgni~f~~~~~~~i~kki~~~ne~~~~~~d~~~~~g~~kflc~ 597 (1164)
T PTZ00112 518 DQHDAQYIKELEEKQKSRRCKADFEVFLDDDTKNFYLLGNIHFKILDAKMILKKIYVYNEKELYDEDKTAKQGKDKFLCT 597 (1164)
T ss_pred ccccHHHHHHHHHHHHhhhhhhhhhHhcccccceeEEecceeEEEechHhhhhhheeecchhhcccchhhhcccchhhhh
Confidence 9887541 1111122345555443 2334445566666666544322111 2356777776
Q ss_pred eEeecC
Q 030413 131 FEYKAA 136 (177)
Q Consensus 131 ~~yd~~ 136 (177)
+..-..
T Consensus 598 ~~~k~~ 603 (1164)
T PTZ00112 598 HYLKER 603 (1164)
T ss_pred Hhhhcc
Confidence 554433
No 44
>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=73.18 E-value=12 Score=22.93 Aligned_cols=35 Identities=29% Similarity=0.328 Sum_probs=25.0
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEE
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRV 68 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v 68 (177)
+.+|+.|++.-.+ ...+-|+|+++... +|.....|
T Consensus 1 ~~vG~~v~~~~~~--~~~y~A~I~~~r~~-~~~~~YyV 35 (55)
T PF11717_consen 1 FEVGEKVLCKYKD--GQWYEAKILDIREK-NGEPEYYV 35 (55)
T ss_dssp --TTEEEEEEETT--TEEEEEEEEEEEEC-TTCEEEEE
T ss_pred CCcCCEEEEEECC--CcEEEEEEEEEEec-CCCEEEEE
Confidence 4689999999933 58999999999995 44433333
No 45
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=72.66 E-value=1.2 Score=31.22 Aligned_cols=25 Identities=12% Similarity=0.218 Sum_probs=20.0
Q ss_pred ccccc------cccCccchhcccccccccch
Q 030413 146 LCTAN------VRCLITRMISWYNVRGARTG 170 (177)
Q Consensus 146 ~C~c~------~~C~~~~c~~wyH~~C~~~~ 170 (177)
-.+|+ ++|..++|..+||+.|....
T Consensus 58 C~iC~~~~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 58 CSICGKSGGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred CcCCCCCCceeEEcCCCCCCcCCCHHHHHHC
Confidence 55576 99977779999999998553
No 46
>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=71.80 E-value=6.4 Score=26.28 Aligned_cols=40 Identities=25% Similarity=0.287 Sum_probs=31.0
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEeCCC------CcEEEEEEEEe
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIESDAR------NNVKVRVRWYY 72 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~------g~~~v~v~Wfy 72 (177)
|++||.|...-.. -+.|-|+|.+...... ....+.|++|-
T Consensus 1 f~~GdlVwaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~~~~V~Ffg 46 (87)
T cd05162 1 FRPGDLVWAKMKG--YPWWPALVVDPPKDSKKAKKKAKEGKVLVLFFG 46 (87)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEccccccchhhhccCCCCEEEEEEeC
Confidence 4789999999986 6899999999987531 23567777775
No 47
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=68.78 E-value=47 Score=24.88 Aligned_cols=42 Identities=21% Similarity=0.320 Sum_probs=29.1
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeC----CCCcEEEEEEEE
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESD----ARNNVKVRVRWY 71 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~----~~g~~~v~v~Wf 71 (177)
.++.||.|.+..+.+....+|-||..+--+ .+|.+++.++-.
T Consensus 51 ~~~rGDiVvf~~~~~~~~~~iKRVig~pGd~v~i~~~~l~vNg~~~ 96 (163)
T TIGR02227 51 DPKRGDIVVFKDPDDNKNIYVKRVIGLPGDKVEFRDGKLYINGKKI 96 (163)
T ss_pred CCCCCcEEEEecCCCCCceeEEEEEecCCCEEEEECCEEEECCEEC
Confidence 678899999987654457888888877443 245566665543
No 48
>PF00467 KOW: KOW motif; InterPro: IPR005824 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 KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=68.76 E-value=13 Score=20.09 Aligned_cols=26 Identities=23% Similarity=0.302 Sum_probs=22.0
Q ss_pred eCCEEEEccCCCCCCCeEEEEeEEEeCC
Q 030413 33 VGDCVLMRPSDTGKPPYVARIEKIESDA 60 (177)
Q Consensus 33 vGD~V~v~~~~~~~~~~Ig~I~~i~~~~ 60 (177)
+||.|.|.++. ..-.+|+|.++..+.
T Consensus 1 ~Gd~V~V~~G~--~~G~~G~I~~i~~~~ 26 (32)
T PF00467_consen 1 VGDTVKVISGP--FKGKIGKIVEIDRSK 26 (32)
T ss_dssp TTSEEEESSST--TTTEEEEEEEEETTT
T ss_pred CCCEEEEeEcC--CCCceEEEEEEECCC
Confidence 58999999986 467899999998764
No 49
>smart00293 PWWP domain with conserved PWWP motif. conservation of Pro-Trp-Trp-Pro residues
Probab=66.98 E-value=8.1 Score=24.30 Aligned_cols=40 Identities=15% Similarity=0.107 Sum_probs=29.5
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEeCCC-------CcEEEEEEEEe
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIESDAR-------NNVKVRVRWYY 72 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~-------g~~~v~v~Wfy 72 (177)
|++||.|..+-.. -+.|-|+|.+-..... ....+.|++|-
T Consensus 1 f~~GdlVwaK~~G--~p~WPa~V~~~~~~~~~~~~~~~~~~~~~V~Ffg 47 (63)
T smart00293 1 FKPGDLVWAKMKG--FPWWPALVVSPKETPDNIRKRKRFENLYPVLFFG 47 (63)
T ss_pred CCCCCEEEEECCC--CCCCCeEEcCcccCChhHhhccCCCCEEEEEEeC
Confidence 4789999999986 6899999998876432 23456666664
No 50
>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=64.59 E-value=8.2 Score=26.53 Aligned_cols=40 Identities=23% Similarity=0.289 Sum_probs=29.2
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEe---------CCCCcEEEEEEEEe
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIES---------DARNNVKVRVRWYY 72 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~---------~~~g~~~v~v~Wfy 72 (177)
|++||.|...-.. -+.|-|+|.+-.. ...+...+.|++|-
T Consensus 1 f~~GDlVwaK~~G--yPwWPA~V~~~~~~p~~~l~~~~~~~~~~~~V~FFg 49 (93)
T cd05840 1 FQPGDRVLAKVKG--FPAWPAIVVPEEMLPDSVLKGKKKKNKRTYPVMFFP 49 (93)
T ss_pred CCCCCEEEEeCCC--CCCCCEEECChHHCCHHHHhcccCCCCCeEEEEEeC
Confidence 4789999999986 6999999986321 12344668888883
No 51
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=64.23 E-value=13 Score=18.79 Aligned_cols=26 Identities=19% Similarity=0.281 Sum_probs=20.3
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEe
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIES 58 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~ 58 (177)
+.+||.|.|..+. ..-.+|.|.++..
T Consensus 2 ~~~G~~V~I~~G~--~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGP--FKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECC--CCCcEEEEEEEcC
Confidence 4689999999986 4566899888753
No 52
>PRK13251 transcription attenuation protein MtrB; Provisional
Probab=63.25 E-value=28 Score=22.76 Aligned_cols=48 Identities=19% Similarity=0.152 Sum_probs=38.7
Q ss_pred EEEEEEeeccccCCcccccCCCCeEEEeCCCcccccceEEeeeEEEee
Q 030413 66 VRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQSAHTIEGKCIVHSF 113 (177)
Q Consensus 66 v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~~~~I~gkc~V~~~ 113 (177)
+.|.=+-|..|+..--....+..||......+-.++--|+|++.+++.
T Consensus 19 V~vIgltrg~dtkfhhtEkLDkGEVmiaqftehtsaiKirGkA~I~t~ 66 (75)
T PRK13251 19 VNVIGLTRGKDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEIQTK 66 (75)
T ss_pred eEEEEEecCCCccchhhhhcCCCcEEEEEeecceeEEEEeceEEEEee
Confidence 666677788888644333478999999999999999999999999874
No 53
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=62.82 E-value=2.9 Score=37.42 Aligned_cols=19 Identities=11% Similarity=0.256 Sum_probs=17.6
Q ss_pred cccCccchhcccccccccchh
Q 030413 151 VRCLITRMISWYNVRGARTGI 171 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~~~~~ 171 (177)
++| |.|+..||..|+.+..
T Consensus 560 ~~C--DtC~lhYHlGCL~PPL 578 (707)
T KOG0957|consen 560 TQC--DTCHLHYHLGCLSPPL 578 (707)
T ss_pred hhc--chhhceeeccccCCcc
Confidence 999 9999999999998764
No 54
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=62.36 E-value=2.7 Score=25.45 Aligned_cols=13 Identities=23% Similarity=0.815 Sum_probs=7.1
Q ss_pred cccCccchhcccccc
Q 030413 151 VRCLITRMISWYNVR 165 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~ 165 (177)
||| +.|.||=...
T Consensus 4 VQC--d~C~KWR~lp 16 (50)
T PF07496_consen 4 VQC--DSCLKWRRLP 16 (50)
T ss_dssp EE---TTT--EEEE-
T ss_pred EEC--CCCCceeeCC
Confidence 799 9999995543
No 55
>PF02081 TrpBP: Tryptophan RNA-binding attenuator protein; InterPro: IPR023558 The tryptophan RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in Bacillus sp. by binding to the leader region of the nascent trp operon mRNA []. The crystal structure of the Trp RNA-binding attenuation protein of Bacillus subtilis has been solved []. TRAP forms an oligomeric ring consisting of 11 single-domain subunits, where each subunit adopts a double-stranded beta-helix structure with the appearance of a beta-sandwich of distinct architecture and jelly-roll fold. The 11 subunits are stabilised by 11 inter-subunit strands, forming a beta-wheel with a large central hole. TRAP is activated by binding to tryptophan in clefts between adjacent beta-strands, which induces conformational changes in the protein. Activated TRAP binds an mRNA target sequence consisting of 11 (G/U)AG repeats, separated by 2-3 spacer nucleotides. The spacer nucleotides do not make direct contact with the TRAP protein, but they do influence the conformation of the RNA, which might influence the specificity of TRAP []. This entry represents the structural domain in the TRAP family of proteins.; PDB: 3ZTE_U 1GTN_H 1UTD_D 1GTF_D 1UTF_F 2ZP9_K 1C9S_Q 2EXT_A 3AQD_T 1QAW_C ....
Probab=61.99 E-value=21 Score=23.42 Aligned_cols=48 Identities=19% Similarity=0.118 Sum_probs=35.9
Q ss_pred EEEEEEeeccccCCcccccCCCCeEEEeCCCcccccceEEeeeEEEee
Q 030413 66 VRVRWYYRPEESLGGRRQFHGAKELFLSDHYDVQSAHTIEGKCIVHSF 113 (177)
Q Consensus 66 v~v~Wfyrp~e~~~~~~~~~~~~ELf~S~~~d~i~~~~I~gkc~V~~~ 113 (177)
+.|.=+-|..||..--....+..||......+-.++--|+|++.|++.
T Consensus 19 V~ViGlTRG~dtkfhHtEkLDkGEVmIaQFTehtsaiKiRGkA~I~t~ 66 (75)
T PF02081_consen 19 VTVIGLTRGTDTKFHHTEKLDKGEVMIAQFTEHTSAIKIRGKAEILTK 66 (75)
T ss_dssp EEEEEEESSSSSSEEEEEEE-TT-EEEEE-BSSEEEEEEESSEEEEET
T ss_pred eEEEEEecCCcccchhhhccCCCcEEEEEeecceEEEEEeeeEEEEec
Confidence 666677788887644333477899999999999999999999999874
No 56
>COG3257 GlxB Uncharacterized protein, possibly involved in glyoxylate utilization [General function prediction only]
Probab=60.64 E-value=34 Score=27.58 Aligned_cols=48 Identities=15% Similarity=0.403 Sum_probs=30.6
Q ss_pred EEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcc
Q 030413 23 TIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGR 81 (177)
Q Consensus 23 ~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~ 81 (177)
++.|.....+.|+++|+.++.. | .+... ..--.++.|+-++.+...|.
T Consensus 97 ~~~G~th~l~eggyaylPpgs~----~-----~~~N~--~~~~~rfhw~rk~Y~~VdG~ 144 (264)
T COG3257 97 KAEGKTHALREGGYAYLPPGSG----W-----TLRNA--QKEDSRFHWIRKRYQPVEGV 144 (264)
T ss_pred EEcCeEEEeccCCeEEeCCCCc----c-----eEeec--cCCceEEEEEeecceeecCc
Confidence 3445456678899999998862 1 11211 12337888998888877663
No 57
>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=59.67 E-value=7.5 Score=25.57 Aligned_cols=40 Identities=28% Similarity=0.391 Sum_probs=28.7
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEeCC---CCcEEEEEEEEe
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIESDA---RNNVKVRVRWYY 72 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~---~g~~~v~v~Wfy 72 (177)
|++||.|...-.. -+.|-|+|....... .....+.|+||-
T Consensus 1 f~~GdlVWaK~~g--~pwWPa~V~~~~~~~~~~~~~~~~~V~Ffg 43 (86)
T PF00855_consen 1 FRPGDLVWAKLKG--YPWWPARVCDPDEKSKKKRKDGHVLVRFFG 43 (86)
T ss_dssp -STTEEEEEEETT--SEEEEEEEEECCHCTSCSSSSTEEEEEETT
T ss_pred CCCCCEEEEEeCC--CCCCceEEeecccccccCCCCCEEEEEecC
Confidence 5789999999976 689999999887532 233456666664
No 58
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=59.50 E-value=17 Score=26.30 Aligned_cols=42 Identities=19% Similarity=0.132 Sum_probs=28.9
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCC-CCcEEEEEEEE
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDA-RNNVKVRVRWY 71 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~-~g~~~v~v~Wf 71 (177)
.+++||.|+...+.....+.-|.|+...+.. .....+.|.-+
T Consensus 55 ~L~~GD~VLA~~~~~~~~Y~Pg~V~~~~~~~~~~~~~~~V~f~ 97 (124)
T PF15057_consen 55 SLQVGDKVLAPWEPDDCRYGPGTVIAGPERRASEDKEYTVRFY 97 (124)
T ss_pred cCCCCCEEEEecCcCCCEEeCEEEEECccccccCCceEEEEEE
Confidence 6799999999976644455569999877654 23455555443
No 59
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=57.70 E-value=3.4 Score=25.68 Aligned_cols=16 Identities=19% Similarity=0.119 Sum_probs=14.6
Q ss_pred cccCccchhccccccccc
Q 030413 151 VRCLITRMISWYNVRGAR 168 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~~ 168 (177)
|.| +.|...||.+|-.
T Consensus 22 VvC--p~CgapyHR~C~~ 37 (54)
T PF14446_consen 22 VVC--PECGAPYHRDCWE 37 (54)
T ss_pred EEC--CCCCCcccHHHHh
Confidence 899 9999999999973
No 60
>COG5475 Uncharacterized small protein [Function unknown]
Probab=57.53 E-value=45 Score=20.86 Aligned_cols=49 Identities=16% Similarity=0.288 Sum_probs=29.9
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCCcccccCCCCeEE
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLGGRRQFHGAKELF 91 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~~~~~~~~~~ELf 91 (177)
.++.||.|.|+++.+ . ..|...- .+-|...+||-+-. .....+.++||.
T Consensus 4 ~FstgdvV~lKsGGP--~---Mtvs~~s----s~Gmy~C~Wf~g~g----~~~~~F~ed~Lv 52 (60)
T COG5475 4 SFSTGDVVTLKSGGP--R---MTVSGYS----SDGMYECRWFDGYG----VKREAFHEDELV 52 (60)
T ss_pred eeecCcEEEeecCCc--e---EEEeccc----cCCeEEEEEecCCC----ccccccccccee
Confidence 789999999999974 1 1222211 12468899997654 222235566664
No 61
>KOG2133 consensus Transcriptional corepressor Atrophin-1/DRPLA [General function prediction only]
Probab=55.81 E-value=8.9 Score=37.00 Aligned_cols=113 Identities=19% Similarity=0.206 Sum_probs=81.4
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCC-CcEEEEEEEEeeccccC-Cc---c--------------cccCCCCe
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDAR-NNVKVRVRWYYRPEESL-GG---R--------------RQFHGAKE 89 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~-g~~~v~v~Wfyrp~e~~-~~---~--------------~~~~~~~E 89 (177)
..|.++|.|.+....+ .++.|+.|-..-..++ ..+.++...+.|++|++ .+ . .+....+|
T Consensus 144 ~~y~~~~~l~~~v~~~-~p~lia~~~~~~~~Kr~~~~~~k~s~~~r~~d~Pet~y~~~m~pe~Ar~e~~P~~~pq~~sq~ 222 (1229)
T KOG2133|consen 144 TLYDLRDSLFVEVSQP-EPYLIAAICGFKYTKRDDRQVVKLSFYFRADDIPETGYLNLMKPERARLEINPHLCPQPLSQE 222 (1229)
T ss_pred hhhhhhhhhhhhhccC-CccccccccCccccccccccccccccccccccCcccccccccCchhhhhccCCccCCCcchhh
Confidence 4889999999999874 6777877766655553 46777888889999887 22 0 11245689
Q ss_pred EEEeCCC-cccccceEEeeeEEEeeecccccCC------CCCceEEEEeEeecCCCceee
Q 030413 90 LFLSDHY-DVQSAHTIEGKCIVHSFKNYTKLEN------VGAEDYYCRFEYKAASGGFTQ 142 (177)
Q Consensus 90 Lf~S~~~-d~i~~~~I~gkc~V~~~~~~~~~~~------~~~~~Ffcr~~yd~~~~~f~~ 142 (177)
||.+... -.-|.++..|+|.+....+...... ...++||-..++.+-.++..+
T Consensus 223 l~~s~l~~i~qppscp~gk~~~~~skd~~h~~~~n~p~~ld~~i~fk~agglpps~k~a~ 282 (1229)
T KOG2133|consen 223 LFNSELQGITQPPSCPRGKGIAEYSKDVRHGGNTNAPFSLDNDIFFKCAGGLPPSTKPAS 282 (1229)
T ss_pred hhcccccCCCCCCcCCCCCceEEeecccccCCccCCCCcccceeeeecccCCCCCCCCCC
Confidence 9999877 4578999999999997666543321 134677777888887776655
No 62
>PF07494 Reg_prop: Two component regulator propeller; InterPro: IPR011110 A large group of two component regulator proteins appear to have the same N-terminal structure of 14 tandem repeats. These repeats show homology to members of IPR002372 from INTERPRO and IPR001680 from INTERPRO indicating that they are likely to form a beta-propeller. This family has been built with artificially high cut-offs in order to avoid overlaps with other beta-propeller families. The fourteen repeats are likely to form two propellers; it is not clear if these structures are likely to recruit other proteins or interact with DNA.; PDB: 3V9F_D 3VA6_B 3OTT_B 4A2M_D 4A2L_B.
Probab=54.76 E-value=18 Score=18.17 Aligned_cols=15 Identities=27% Similarity=0.319 Sum_probs=11.4
Q ss_pred EEeEEEeCCCCcEEE
Q 030413 52 RIEKIESDARNNVKV 66 (177)
Q Consensus 52 ~I~~i~~~~~g~~~v 66 (177)
.|..|.++++|.+|+
T Consensus 6 ~I~~i~~D~~G~lWi 20 (24)
T PF07494_consen 6 NIYSIYEDSDGNLWI 20 (24)
T ss_dssp CEEEEEE-TTSCEEE
T ss_pred eEEEEEEcCCcCEEE
Confidence 367889999998886
No 63
>PF03144 GTP_EFTU_D2: Elongation factor Tu domain 2; InterPro: IPR004161 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. EF1A (also known as EF-1alpha or EF-Tu) is a G-protein. It forms a ternary complex of EF1A-GTP-aminoacyltRNA. The binding of aminoacyl-tRNA stimulates GTP hydrolysis by EF1A, causing a conformational change in EF1A that causes EF1A-GDP to detach from the ribosome, leaving the aminoacyl-tRNA attached at the A-site. Only the cognate aminoacyl-tRNA can induce the required conformational change in EF1A through its tight anticodon-codon binding [, ]. EF1A-GDP is returned to its active state, EF1A-GTP, through the action of another elongation factor, EF1B (also known as EF-Ts or EF-1beta/gamma/delta). EF1A consists of three structural domains. This entry represents domain 2 of EF2, which adopts a beta-barrel structure, and is involved in binding to both charged tRNA []. This domain is structurally related to the C-terminal domain of EF2 (IPR004160 from INTERPRO), to which it displays weak sequence matches. This domain is also found in other proteins such as translation initiation factor IF-2 and tetracycline-resistance proteins. More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005525 GTP binding; PDB: 3MCA_A 3AGJ_E 1SKQ_B 1JNY_A 1S0U_A 1ZUN_B 3SFS_W 3UOQ_W 2H5E_B 2XEX_A ....
Probab=53.40 E-value=27 Score=22.01 Aligned_cols=31 Identities=32% Similarity=0.364 Sum_probs=23.3
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCC
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDA 60 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~ 60 (177)
.++.||.|++.+.+.+..+..++|.+|+...
T Consensus 12 ~l~~gd~v~~~~~~~~~~~~~~~I~~i~~~~ 42 (74)
T PF03144_consen 12 TLKKGDKVRVLPNGTGKKGQVVKIKSIFMFN 42 (74)
T ss_dssp EEETTEEEEEESTTTTEECEEEEEEEEEETT
T ss_pred EEcCCCEEEECccCCcceeeeeecccccccc
Confidence 8999999999773222345788888888853
No 64
>cd03701 IF2_IF5B_II IF2_IF5B_II: This family represents the domain II of prokaryotic Initiation Factor 2 (IF2) and its archeal and eukaryotic homologue aeIF5B. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of the 60S ribosomal subunit. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains in EF1A, eEF1A and aeIF2gamma.
Probab=53.36 E-value=40 Score=23.06 Aligned_cols=41 Identities=12% Similarity=0.345 Sum_probs=29.7
Q ss_pred CCCCCceeeeEEEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCC
Q 030413 11 KTKTGKRDLESYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDA 60 (177)
Q Consensus 11 k~~~~~~~y~~~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~ 60 (177)
+...|+...-.+.+... ++++||++.+-.. .|+|..++.+.
T Consensus 9 ~~~~g~G~vatviV~~G--tL~~Gd~iv~G~~-------~GkVr~~~d~~ 49 (95)
T cd03701 9 KLDKGRGPVATVIVQNG--TLKKGDVIVAGGT-------YGKIRTMVDEN 49 (95)
T ss_pred EecCCCCeeEEEEEEcC--eEecCCEEEECCc-------cceEEEEECCC
Confidence 44556666666655544 9999999998766 47888888864
No 65
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=51.71 E-value=4.3 Score=37.85 Aligned_cols=25 Identities=4% Similarity=0.061 Sum_probs=21.6
Q ss_pred ccccc-----cccCccchhcccccccccchhh
Q 030413 146 LCTAN-----VRCLITRMISWYNVRGARTGII 172 (177)
Q Consensus 146 ~C~c~-----~~C~~~~c~~wyH~~C~~~~~~ 172 (177)
.|+|. +.| ++|..|||+.|++....
T Consensus 50 c~ic~~~g~~l~c--~tC~~s~h~~cl~~pl~ 79 (696)
T KOG0383|consen 50 CRICADGGELLWC--DTCPASFHASCLGPPLT 79 (696)
T ss_pred hhhhcCCCcEEEe--ccccHHHHHHccCCCCC
Confidence 77888 999 99999999999976543
No 66
>cd03702 IF2_mtIF2_II This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.
Probab=50.69 E-value=36 Score=23.42 Aligned_cols=42 Identities=12% Similarity=0.340 Sum_probs=30.0
Q ss_pred CCCCCceeeeEEEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCC
Q 030413 11 KTKTGKRDLESYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDAR 61 (177)
Q Consensus 11 k~~~~~~~y~~~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~ 61 (177)
+...|+.....+.+... ++++||++..-.. .|+|..|+.+.+
T Consensus 9 ~~~~g~G~vatviV~~G--tL~~Gd~iv~G~~-------~gkVr~l~d~~g 50 (95)
T cd03702 9 KLDKGRGPVATVLVQNG--TLKVGDVLVAGTT-------YGKVRAMFDENG 50 (95)
T ss_pred EecCCCCccEEEEEEcC--eEeCCCEEEEccc-------ccEEEEEECCCC
Confidence 44556666666666433 8999999998765 469999998743
No 67
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=50.37 E-value=7.2 Score=25.29 Aligned_cols=19 Identities=11% Similarity=0.025 Sum_probs=9.0
Q ss_pred cccCccchhcccccccccc
Q 030413 151 VRCLITRMISWYNVRGART 169 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~~~ 169 (177)
+.|+++.|..-||..|+-.
T Consensus 21 ~~C~n~~C~~~fH~~CL~~ 39 (70)
T PF11793_consen 21 VVCPNPSCGKKFHLLCLSE 39 (70)
T ss_dssp B--S-TT----B-SGGGHH
T ss_pred eEcCCcccCCHHHHHHHHH
Confidence 7787889999999999853
No 68
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=48.65 E-value=37 Score=22.42 Aligned_cols=29 Identities=17% Similarity=0.217 Sum_probs=24.2
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCC
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDA 60 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~ 60 (177)
.++.||.|.|.++. +.=-+|.|.++....
T Consensus 6 ~I~kGD~V~Vi~G~--dKGK~G~V~~V~~~~ 34 (76)
T PRK12281 6 KVKKGDMVKVIAGD--DKGKTGKVLAVLPKK 34 (76)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 67899999999987 355689999998863
No 69
>COG1370 Prefoldin, molecular chaperone implicated in de novo protein folding, alpha subunit [Posttranslational modification, protein turnover, chaperones]
Probab=48.11 E-value=13 Score=27.95 Aligned_cols=40 Identities=28% Similarity=0.377 Sum_probs=32.4
Q ss_pred CCCCceeeeEEEEcCceeeEEeCCEEEEccCCCCCCCeEEEE
Q 030413 12 TKTGKRDLESYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARI 53 (177)
Q Consensus 12 ~~~~~~~y~~~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I 53 (177)
.++|+..|.++.+.++ ..++.||-|+|-+++ +...-+|+.
T Consensus 93 ~r~Gk~VFaKfVi~~D-~~iR~~dEvlVVne~-d~LlAvGra 132 (155)
T COG1370 93 VRKGKSVFAKFVIDVD-EEIRAGDEVLVVNED-DELLAVGRA 132 (155)
T ss_pred HHhccchhhhheeccC-cccCCCCeEEEECCC-CcEEEeeeE
Confidence 3678899999999874 799999999999998 356666663
No 70
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=47.21 E-value=38 Score=22.76 Aligned_cols=29 Identities=21% Similarity=0.308 Sum_probs=24.2
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCC
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDA 60 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~ 60 (177)
.++.||.|.|.++.+ .=-+|.|.++....
T Consensus 8 ~I~~GD~V~Vi~G~d--KGK~G~V~~V~~~~ 36 (83)
T CHL00141 8 HVKIGDTVKIISGSD--KGKIGEVLKIIKKS 36 (83)
T ss_pred cccCCCEEEEeEcCC--CCcEEEEEEEEcCC
Confidence 679999999999873 55689999998763
No 71
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=46.83 E-value=4.9 Score=26.56 Aligned_cols=14 Identities=14% Similarity=0.238 Sum_probs=10.2
Q ss_pred hhcccccccccchh
Q 030413 158 MISWYNVRGARTGI 171 (177)
Q Consensus 158 c~~wyH~~C~~~~~ 171 (177)
-..|||.+|.-...
T Consensus 37 ~~~W~H~~C~~~~~ 50 (82)
T PF00645_consen 37 IPKWYHWDCFFKKQ 50 (82)
T ss_dssp EEEEEEHHHHHHTT
T ss_pred CCceECccccccch
Confidence 35799999976543
No 72
>PF11926 DUF3444: Domain of unknown function (DUF3444); InterPro: IPR024593 This entry represents an uncharacterised domain. This domain is found in DnaJ, cytosine-specific methyltransferases, and members from the zinc finger, C3HC4 type family.
Probab=46.15 E-value=53 Score=26.25 Aligned_cols=42 Identities=33% Similarity=0.618 Sum_probs=35.6
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEe
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYY 72 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfy 72 (177)
..+.+|+.=.+..+.++-|.+.|+|.++... +...+++.|+-
T Consensus 26 ~~F~~gQIWAlYd~~D~mPR~Ya~I~kV~~~--~~Fkl~i~wLe 67 (217)
T PF11926_consen 26 EKFQVGQIWALYDDDDGMPRYYARIKKVDSS--NPFKLHITWLE 67 (217)
T ss_pred HhCCCCCEEEEeeCCCCCeeeEEEEEEEecC--CCeEEEEEEcc
Confidence 4789999988998877889999999999885 45679999984
No 73
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=45.21 E-value=8.5 Score=36.45 Aligned_cols=19 Identities=16% Similarity=0.261 Sum_probs=17.3
Q ss_pred cccCccchhcc-cccccccchh
Q 030413 151 VRCLITRMISW-YNVRGARTGI 171 (177)
Q Consensus 151 ~~C~~~~c~~w-yH~~C~~~~~ 171 (177)
+.| ++|..- ||+.||.+.+
T Consensus 231 LLC--DsCN~~~YH~YCLDPdl 250 (1134)
T KOG0825|consen 231 LLC--DSCNKVYYHVYCLDPDL 250 (1134)
T ss_pred eee--cccccceeeccccCccc
Confidence 999 999996 9999999865
No 74
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=42.74 E-value=39 Score=24.59 Aligned_cols=34 Identities=24% Similarity=0.345 Sum_probs=26.0
Q ss_pred EEEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEE
Q 030413 21 SYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIE 57 (177)
Q Consensus 21 ~~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~ 57 (177)
+|++.-.+..+.+||.|.|..+. ..+.+||.+|.
T Consensus 130 ~f~~~~~~~~l~pGDvi~l~~~~---~~~~~RI~~i~ 163 (164)
T PF13550_consen 130 SFTLPPDGLALEPGDVIALSDDG---RDMRFRITEIE 163 (164)
T ss_pred EEEEChhhccCCCCCEEEEEeCC---CceEEEEEEEe
Confidence 45555455688999999999884 58888988874
No 75
>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=41.37 E-value=36 Score=22.86 Aligned_cols=42 Identities=24% Similarity=0.318 Sum_probs=29.1
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEeCC----CCcEEEEEEEEeec
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIESDA----RNNVKVRVRWYYRP 74 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~----~g~~~v~v~Wfyrp 74 (177)
+++||.|.-.-.. -+.|-|+|.+-..+. .......|+||=.+
T Consensus 1 f~~GDlVwaK~~g--~P~WPa~V~~~~~~~~~~~~~~~~~~V~FFG~~ 46 (86)
T cd05836 1 LKLGDLVWAKMKG--FPPWPGRIVKPPKDLKKPRGKAKCFFVFFFGSE 46 (86)
T ss_pred CCCCCEEEEeCCC--CCCCCEEEechhhhcccccCCCCeEEEEEeCCC
Confidence 4789999999875 699999998854331 11245667777544
No 76
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=41.22 E-value=7.1 Score=38.13 Aligned_cols=48 Identities=15% Similarity=0.072 Sum_probs=34.0
Q ss_pred eCCEEEEccCCCCCCCeEEEEeEEEeCCC----------C-----cEEEEE--EEEeeccccCCc
Q 030413 33 VGDCVLMRPSDTGKPPYVARIEKIESDAR----------N-----NVKVRV--RWYYRPEESLGG 80 (177)
Q Consensus 33 vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~----------g-----~~~v~v--~Wfyrp~e~~~~ 80 (177)
.+|.+|+.+....+....|++.++..... + ...+++ .|++.|-++...
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (1051)
T KOG0955|consen 29 RNDRFYAQATRMVELDTEGRVFQISIFPPLGKVNEDLITTEEIFPNKSVHVNKNWERPSFDIQEK 93 (1051)
T ss_pred cCceEEeccccccccccccceeecccCCcccccchhhcccccccccccccccccccCCccchhhh
Confidence 78899999887667888888877766421 1 134444 899999987643
No 77
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=41.18 E-value=8 Score=25.78 Aligned_cols=20 Identities=20% Similarity=0.280 Sum_probs=17.5
Q ss_pred cccCccchhcccccccccch
Q 030413 151 VRCLITRMISWYNVRGARTG 170 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~~~~ 170 (177)
|.|...+|...||+.|....
T Consensus 50 i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 50 IGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred EEEeCCCCCcEEChHHHccC
Confidence 89988899999999998654
No 78
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=40.89 E-value=50 Score=23.20 Aligned_cols=29 Identities=14% Similarity=0.244 Sum_probs=24.3
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCC
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDA 60 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~ 60 (177)
.++.||.|.|.++. +.=-+|.|.++....
T Consensus 4 ~i~kGD~V~Vi~G~--dKGk~G~V~~V~~~~ 32 (105)
T PRK00004 4 KIKKGDTVIVIAGK--DKGKRGKVLKVLPKK 32 (105)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 57899999999987 456699999998763
No 79
>PF09378 HAS-barrel: HAS barrel domain; InterPro: IPR018538 The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family []. ; PDB: 3OAA_I.
Probab=40.40 E-value=35 Score=22.44 Aligned_cols=36 Identities=22% Similarity=0.389 Sum_probs=23.3
Q ss_pred EEEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeC
Q 030413 21 SYTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESD 59 (177)
Q Consensus 21 ~~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~ 59 (177)
.|.+++ ....++||+|.+..++ ...-+|+|.++...
T Consensus 14 ~f~~~~-~~~v~~GeyV~i~~~~--~~~vlG~V~~i~~~ 49 (91)
T PF09378_consen 14 EFIVEP-SKDVRVGEYVVIEYDD--GEKVLGMVTSISRG 49 (91)
T ss_dssp EEEEEE--TT-BTTEEEEES------TTEEEEEEEEES-
T ss_pred EEEEeC-CCCCCcCeEEEEEEec--hhhhhhhhheeEEc
Confidence 344443 1378999999999984 46889999999884
No 80
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=39.60 E-value=15 Score=23.79 Aligned_cols=29 Identities=10% Similarity=0.169 Sum_probs=24.7
Q ss_pred eeCccccccc----cccCccchhcccccccccchh
Q 030413 141 TQTELLCTAN----VRCLITRMISWYNVRGARTGI 171 (177)
Q Consensus 141 ~~~~~~C~c~----~~C~~~~c~~wyH~~C~~~~~ 171 (177)
......|.|. |.| ..|..+-|-+|.+...
T Consensus 30 ~~~~~~C~C~LkAMi~C--q~CGAFCHDDCIgpsk 62 (69)
T PF13922_consen 30 ESTSNKCACSLKAMIMC--QGCGAFCHDDCIGPSK 62 (69)
T ss_pred cccccccccchHHHHHH--hhccchhccccccHHH
Confidence 3445689999 999 9999999999999865
No 81
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=39.15 E-value=12 Score=31.24 Aligned_cols=20 Identities=5% Similarity=-0.182 Sum_probs=18.6
Q ss_pred cccCccchhcccccccccchhh
Q 030413 151 VRCLITRMISWYNVRGARTGII 172 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~~~~~~ 172 (177)
++| |.|..-||.=|+|+.++
T Consensus 330 ~FC--D~CDRG~HT~CVGL~~l 349 (381)
T KOG1512|consen 330 LFC--DVCDRGPHTLCVGLQDL 349 (381)
T ss_pred ecc--ccccCCCCccccccccc
Confidence 999 99999999999999764
No 82
>PF07883 Cupin_2: Cupin domain; InterPro: IPR013096 This family represents the conserved barrel domain of the cupin superfamily [] (cupa is the Latin term for a small barrel). ; PDB: 2OPK_C 3BU7_B 2PHD_D 3NVC_A 3NKT_A 3NJZ_A 3NW4_A 3NST_A 3NL1_A 2H0V_A ....
Probab=38.89 E-value=42 Score=20.57 Aligned_cols=21 Identities=24% Similarity=0.509 Sum_probs=15.6
Q ss_pred EEcCceeeEEeCCEEEEccCC
Q 030413 23 TIRGTNKIVRVGDCVLMRPSD 43 (177)
Q Consensus 23 ~~~g~~~~~~vGD~V~v~~~~ 43 (177)
.++|....++.||.+++.+..
T Consensus 33 ~~~~~~~~l~~Gd~~~i~~~~ 53 (71)
T PF07883_consen 33 TVDGERVELKPGDAIYIPPGV 53 (71)
T ss_dssp EETTEEEEEETTEEEEEETTS
T ss_pred EEccEEeEccCCEEEEECCCC
Confidence 455656777888888888875
No 83
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=36.91 E-value=63 Score=22.68 Aligned_cols=29 Identities=14% Similarity=0.201 Sum_probs=24.1
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCC
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDA 60 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~ 60 (177)
.++.||.|.|.++. +.=-+|.|.++....
T Consensus 3 ~ikkGD~V~Vi~G~--dKGK~G~V~~V~~~~ 31 (104)
T TIGR01079 3 KIKKGDTVKVISGK--DKGKRGKVLKVLPKT 31 (104)
T ss_pred cccCCCEEEEeEcC--CCCcEEEEEEEEcCC
Confidence 57899999999987 456699999998763
No 84
>COG0662 {ManC} Mannose-6-phosphate isomerase [Carbohydrate transport and metabolism]
Probab=35.36 E-value=50 Score=23.59 Aligned_cols=23 Identities=30% Similarity=0.447 Sum_probs=18.3
Q ss_pred EEEcCceeeEEeCCEEEEccCCC
Q 030413 22 YTIRGTNKIVRVGDCVLMRPSDT 44 (177)
Q Consensus 22 ~~~~g~~~~~~vGD~V~v~~~~~ 44 (177)
+.++|..+.++.||+++|.++..
T Consensus 70 v~~~~~~~~v~~gd~~~iP~g~~ 92 (127)
T COG0662 70 VTIGGEEVEVKAGDSVYIPAGTP 92 (127)
T ss_pred EEECCEEEEecCCCEEEECCCCc
Confidence 35556668889999999999874
No 85
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=34.45 E-value=1e+02 Score=22.27 Aligned_cols=37 Identities=22% Similarity=0.232 Sum_probs=27.1
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEE
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRV 68 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v 68 (177)
..++.||-|.|.++.+ .=-.|+|.++... .+.+.+.+
T Consensus 44 ~~IkkGD~V~VisG~~--KGk~GkV~~V~~~-~~~V~VeG 80 (120)
T PRK01191 44 LPVRKGDTVKVMRGDF--KGEEGKVVEVDLK-RGRIYVEG 80 (120)
T ss_pred ceEeCCCEEEEeecCC--CCceEEEEEEEcC-CCEEEEeC
Confidence 4789999999999973 4457999999775 33344433
No 86
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=34.26 E-value=70 Score=20.66 Aligned_cols=26 Identities=19% Similarity=0.363 Sum_probs=17.8
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeE
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEK 55 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~ 55 (177)
.++.||.|.+........+++.||..
T Consensus 31 ~~~~GDiv~~~~~~~~~~~~vkRv~~ 56 (85)
T cd06530 31 EPKRGDVVVFKSPGDPGKPIIKRVIG 56 (85)
T ss_pred CCCCCCEEEEeCCCCCCCEEEEEEEE
Confidence 46778888887775324677777776
No 87
>TIGR03214 ura-cupin putative allantoin catabolism protein. This model represents a protein containing a tandem arrangement of cupin domains (N-terminal part of pfam07883 and C-terminal more distantly related to pfam00190). This protein is found in the vicinity of genes involved in the catabolism of allantoin, a breakdown product of urate and sometimes of urate iteslf. The distribution of pathway components in the genomes in which this family is observed suggests that the function is linked to the allantoate catabolism to glyoxylate pathway (GenProp0686) since it is sometimes found in genomes lacking any elements of the xanthine-to-allantoin pathways (e.g. in Enterococcus faecalis).
Probab=33.84 E-value=1.5e+02 Score=24.11 Aligned_cols=46 Identities=15% Similarity=0.261 Sum_probs=25.0
Q ss_pred EEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeeccccCC
Q 030413 23 TIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEESLG 79 (177)
Q Consensus 23 ~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~~~ 79 (177)
+++|....++.||++|+.++.+. .+... ++..+++.|+-++-+...
T Consensus 94 ~~~g~~~~L~~Gd~~y~pa~~~H---------~~~N~--~~~~a~~l~v~k~y~~~~ 139 (260)
T TIGR03214 94 TAEGETHELREGGYAYLPPGSKW---------TLANA--QAEDARFFLYKKRYQPVE 139 (260)
T ss_pred EECCEEEEECCCCEEEECCCCCE---------EEEEC--CCCCEEEEEEEeeeEEcC
Confidence 34444456777888888887521 22222 222366666666555433
No 88
>PF06940 DUF1287: Domain of unknown function (DUF1287); InterPro: IPR009706 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=33.80 E-value=55 Score=25.02 Aligned_cols=42 Identities=19% Similarity=0.086 Sum_probs=29.6
Q ss_pred EEEcCceeeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEE
Q 030413 22 YTIRGTNKIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKV 66 (177)
Q Consensus 22 ~~~~g~~~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v 66 (177)
++++.....++.||-|...-+. ..++||.|.+-... +|..++
T Consensus 98 L~~~~~~~~~q~GDIVtw~l~~--~~~HIgIVSd~r~~-~G~p~v 139 (164)
T PF06940_consen 98 LTTDINPEDWQPGDIVTWRLPG--GLPHIGIVSDRRSK-DGVPLV 139 (164)
T ss_pred ccCCCChhhcCCCCEEEEeCCC--CCCeEEEEeCCcCC-CCCEEE
Confidence 3333333589999999998765 48999999877553 565443
No 89
>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=33.73 E-value=54 Score=23.05 Aligned_cols=43 Identities=19% Similarity=0.203 Sum_probs=31.4
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEe---------CCCCcEEEEEEEEeec
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIES---------DARNNVKVRVRWYYRP 74 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~---------~~~g~~~v~v~Wfyrp 74 (177)
.|.+||.|...-.. -+.|-|.|.+--. .......+.|++|-..
T Consensus 2 ~~~~GdlVWaK~~g--~PwWPa~V~~~~~~~~~~~~~~~~~~~~~~~V~FFG~~ 53 (110)
T cd05837 2 KYQVGDLVWAKVSG--YPWWPCMVCSDPLLGTYTKTKRNKRKPRQYHVQFFGDN 53 (110)
T ss_pred CCCCCCEEEEeCCC--CCCCCEEEecccccchhhhhhhccCCCCeEEEEEcCCC
Confidence 57899999999886 6899999985311 1123467888888754
No 90
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=33.38 E-value=97 Score=23.89 Aligned_cols=46 Identities=22% Similarity=0.372 Sum_probs=37.1
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeecccc
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEES 77 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~ 77 (177)
..+.+||.|-|.++. -..+.|+|+++..+ .+...+.+.-|-|+..+
T Consensus 122 ~~~e~Gd~VrI~~Gp--Fa~f~g~V~evd~e-k~~~~v~v~ifgr~tPV 167 (178)
T COG0250 122 VDFEPGDVVRIIDGP--FAGFKAKVEEVDEE-KGKLKVEVSIFGRPTPV 167 (178)
T ss_pred ccCCCCCEEEEeccC--CCCccEEEEEEcCc-CcEEEEEEEEeCCceEE
Confidence 478999999999986 46789999999886 46677888878776644
No 91
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=33.07 E-value=56 Score=19.89 Aligned_cols=28 Identities=18% Similarity=0.159 Sum_probs=22.8
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEe
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIES 58 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~ 58 (177)
.+++||.|.+...+ +..-|-|+|.++..
T Consensus 2 ~~~~G~~Ve~~~~~-~~~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKE-EDSWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECC-CCEEEEEEEEEECC
Confidence 47899999999865 35788899998865
No 92
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=32.59 E-value=36 Score=23.52 Aligned_cols=19 Identities=32% Similarity=0.391 Sum_probs=14.3
Q ss_pred eEEeCCEEEEccCCCCCCC
Q 030413 30 IVRVGDCVLMRPSDTGKPP 48 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~ 48 (177)
.+++||.|.+.+.+.+..+
T Consensus 76 ~Lk~GD~V~ll~~~~gQ~y 94 (100)
T PF10844_consen 76 GLKVGDKVLLLRVQGGQKY 94 (100)
T ss_pred CCcCCCEEEEEEecCCCEE
Confidence 6799999999996543333
No 93
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=32.48 E-value=11 Score=21.21 Aligned_cols=21 Identities=5% Similarity=-0.096 Sum_probs=13.4
Q ss_pred cccCccchhcccccccccchhhh
Q 030413 151 VRCLITRMISWYNVRGARTGIIL 173 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~~~~~~~ 173 (177)
++| ++|...-|..|-|+....
T Consensus 5 l~C--~~C~v~VH~~CYGv~~~~ 25 (36)
T PF13831_consen 5 LFC--DNCNVAVHQSCYGVSEVP 25 (36)
T ss_dssp EE---SSS--EEEHHHHT-SS--
T ss_pred EEe--CCCCCcCChhhCCcccCC
Confidence 689 999999999999887653
No 94
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=31.85 E-value=23 Score=25.08 Aligned_cols=18 Identities=28% Similarity=0.396 Sum_probs=10.6
Q ss_pred CcEEEEEEEEeeccccCC
Q 030413 62 NNVKVRVRWYYRPEESLG 79 (177)
Q Consensus 62 g~~~v~v~Wfyrp~e~~~ 79 (177)
+-.++.|.||-|+.|+..
T Consensus 54 ~~pfVEV~WF~R~qe~qd 71 (108)
T PF08921_consen 54 GYPFVEVLWFDRGQEVQD 71 (108)
T ss_dssp ---EEEEEES---HHHHH
T ss_pred cceeEEEEEecCCHHHHH
Confidence 346899999999999863
No 95
>PF11012 DUF2850: Protein of unknown function (DUF2850); InterPro: IPR021271 This family of proteins with unknown function appear to be restricted to Vibrionaceae.
Probab=31.83 E-value=1.1e+02 Score=20.44 Aligned_cols=32 Identities=16% Similarity=0.188 Sum_probs=26.7
Q ss_pred CCCCceeeeEEEEcCceeeEEeCCEEEEccCC
Q 030413 12 TKTGKRDLESYTIRGTNKIVRVGDCVLMRPSD 43 (177)
Q Consensus 12 ~~~~~~~y~~~~~~g~~~~~~vGD~V~v~~~~ 43 (177)
.+.|+..-.+|..+|....|++|+-+++..-.
T Consensus 27 ~~ngrlV~T~F~fDG~~l~~~~G~~~~~y~~~ 58 (79)
T PF11012_consen 27 FRNGRLVATSFEFDGKTLEYRTGSGTYRYQIS 58 (79)
T ss_pred EECCCEEeeEEEECCCEEEEEECCeEEEEEEc
Confidence 45678888899999988999999999887744
No 96
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=31.81 E-value=73 Score=21.03 Aligned_cols=28 Identities=29% Similarity=0.179 Sum_probs=19.6
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEe
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIES 58 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~ 58 (177)
.-++.||+|.|...+ ...-=|+|...+.
T Consensus 37 iwI~~GD~V~Ve~~~--~d~~kg~Iv~r~~ 64 (77)
T cd05793 37 VWINEGDIVLVAPWD--FQDDKADIIYKYT 64 (77)
T ss_pred EEEcCCCEEEEEecc--ccCCEEEEEEEcC
Confidence 567899999998765 2455666665544
No 97
>PF02559 CarD_CdnL_TRCF: CarD-like/TRCF domain; InterPro: IPR003711 The bacterium Myxococcus xanthus responds to blue light by producing carotenoids. It also responds to starvation conditions by developing fruiting bodies, where the cells differentiate into myxospores. Each response entails the transcriptional activation of a separate set of genes. A single gene, carD, is required for the activation of both light- and starvation-inducible genes []. The predicted protein contains four repeats of a DNA-binding domain present in mammalian high mobility group I(Y) proteins and other nuclear proteins from animals and plants. Other peptide stretches on CarD also resemble functional domains typical of eukaryotic transcription factors, including a very acidic region and a leucine zipper. High mobility group yI(Y) proteins are known to bind the minor groove of A+T-rich DNA [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3MLQ_H 2EYQ_A.
Probab=31.75 E-value=59 Score=21.99 Aligned_cols=24 Identities=38% Similarity=0.526 Sum_probs=18.3
Q ss_pred EEeCCEEEEccCCCCCCCeEEEEeEEEeCC
Q 030413 31 VRVGDCVLMRPSDTGKPPYVARIEKIESDA 60 (177)
Q Consensus 31 ~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~ 60 (177)
|++||.|.-...+ ||+|..|....
T Consensus 2 f~~GD~VVh~~~G------v~~i~~i~~~~ 25 (98)
T PF02559_consen 2 FKIGDYVVHPNHG------VGRIEGIEEIE 25 (98)
T ss_dssp --TTSEEEETTTE------EEEEEEEEEEE
T ss_pred CCCCCEEEECCCc------eEEEEEEEEEe
Confidence 6899999877665 99999998854
No 98
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=31.55 E-value=19 Score=29.95 Aligned_cols=18 Identities=11% Similarity=0.091 Sum_probs=16.5
Q ss_pred cccCccchhcccccccccch
Q 030413 151 VRCLITRMISWYNVRGARTG 170 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~~~~ 170 (177)
.+| |.|..-|||=|+-+.
T Consensus 297 lfc--ddcdrgyhmyclspp 314 (336)
T KOG1244|consen 297 LFC--DDCDRGYHMYCLSPP 314 (336)
T ss_pred Eee--cccCCceeeEecCCC
Confidence 899 999999999999764
No 99
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=31.27 E-value=81 Score=21.11 Aligned_cols=28 Identities=32% Similarity=0.254 Sum_probs=18.8
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEe
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIES 58 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~ 58 (177)
.-++.||+|.|...+ ...--|.|.....
T Consensus 42 iwI~~GD~VlVe~~~--~~~~kg~Iv~r~~ 69 (83)
T smart00652 42 VWIRRGDIVLVDPWD--FQDVKADIIYKYT 69 (83)
T ss_pred EEEcCCCEEEEEecC--CCCCEEEEEEEeC
Confidence 467899999998765 2245666665554
No 100
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=31.04 E-value=66 Score=20.71 Aligned_cols=19 Identities=16% Similarity=0.312 Sum_probs=14.3
Q ss_pred cCceeeEEeCCEEEEccCC
Q 030413 25 RGTNKIVRVGDCVLMRPSD 43 (177)
Q Consensus 25 ~g~~~~~~vGD~V~v~~~~ 43 (177)
+|...+++.||.|++..+.
T Consensus 42 ~G~~~~~~aGD~~~~p~G~ 60 (74)
T PF05899_consen 42 DGETVTFKAGDAFFLPKGW 60 (74)
T ss_dssp TTEEEEEETTEEEEE-TTE
T ss_pred CCCEEEEcCCcEEEECCCC
Confidence 3555788999999998875
No 101
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=29.91 E-value=53 Score=20.73 Aligned_cols=25 Identities=32% Similarity=0.365 Sum_probs=16.1
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeE
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEK 55 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~ 55 (177)
.-++.||+|.|...+- ..--|+|..
T Consensus 40 iwI~~GD~V~V~~~~~--d~~kG~Ii~ 64 (65)
T PF01176_consen 40 IWIKRGDFVLVEPSPY--DKVKGRIIY 64 (65)
T ss_dssp C---TTEEEEEEESTT--CTTEEEEEE
T ss_pred EecCCCCEEEEEeccc--CCCeEEEEE
Confidence 4578999999998752 366777753
No 102
>PF14444 S1-like: S1-like
Probab=29.57 E-value=57 Score=20.53 Aligned_cols=30 Identities=20% Similarity=0.333 Sum_probs=21.5
Q ss_pred CceeeeEEEEcCceeeEEeCCEEEEccCCCCC
Q 030413 15 GKRDLESYTIRGTNKIVRVGDCVLMRPSDTGK 46 (177)
Q Consensus 15 ~~~~y~~~~~~g~~~~~~vGD~V~v~~~~~~~ 46 (177)
+..+|+.=.+.|. .-++||-|.+....+++
T Consensus 20 e~vFF~~~vv~G~--~P~vGdrV~v~A~~n~~ 49 (58)
T PF14444_consen 20 EDVFFQTDVVKGN--VPKVGDRVLVEAIYNPN 49 (58)
T ss_pred ccEEEEcccEecC--CCccCCEEEEEEEeCCC
Confidence 3567775567775 66999999999865433
No 103
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=29.07 E-value=66 Score=19.84 Aligned_cols=26 Identities=35% Similarity=0.363 Sum_probs=16.7
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeC
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESD 59 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~ 59 (177)
..-+||.|.+...+. + -+.|+++.+.
T Consensus 37 ~~~VGD~V~~~~~~~-~---~~~I~~vl~R 62 (68)
T cd04466 37 PPAVGDRVEFEPEDD-G---EGVIEEILPR 62 (68)
T ss_pred CCCCCcEEEEEECCC-C---cEEEEEEecc
Confidence 357999999976441 2 2556666553
No 104
>PF11132 SplA: Transcriptional regulator protein (SplA); InterPro: IPR022608 The SplA protein functions in trans as a negative regulator of the level of splB-lacZ expression in the developing forespore [].
Probab=28.55 E-value=40 Score=22.21 Aligned_cols=25 Identities=24% Similarity=0.262 Sum_probs=18.9
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeE
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEK 55 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~ 55 (177)
.++.||.|||-=.++ --+.|+.|.+
T Consensus 5 ~~~~GD~VyViYrNP-Ht~~VanIqe 29 (75)
T PF11132_consen 5 PYHAGDIVYVIYRNP-HTQDVANIQE 29 (75)
T ss_pred ccCCCCEEEEEEcCC-CCccccccch
Confidence 789999999988774 3466777654
No 105
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=28.52 E-value=1.7e+02 Score=23.54 Aligned_cols=65 Identities=12% Similarity=0.115 Sum_probs=46.4
Q ss_pred CCCeEEEeCCCcccccceEEeeeEEEeeeccc-ccCCCCCceEEEEeEeecCCCceeeCccccccc
Q 030413 86 GAKELFLSDHYDVQSAHTIEGKCIVHSFKNYT-KLENVGAEDYYCRFEYKAASGGFTQTELLCTAN 150 (177)
Q Consensus 86 ~~~ELf~S~~~d~i~~~~I~gkc~V~~~~~~~-~~~~~~~~~Ffcr~~yd~~~~~f~~~~~~C~c~ 150 (177)
...+-|+|..-+.+++-.|+|...|++..... ...|.+...+..--..-.+.+-|...|+.|-|.
T Consensus 165 ~nGraf~s~~de~LkvwdlIGRsvVi~k~~ddlgg~p~nsge~la~gvIARSAGv~eN~KqiCaCd 230 (247)
T KOG4656|consen 165 KNGRAFFSAPDEKLKVWDLIGRSVVISKSLDDLGGEPGNSGERLACGVIARSAGVWENNKQICACD 230 (247)
T ss_pred cCCcEEEecccccccHhhhhceeEEEeccccccCCCCCCcCcceeEEEeeeccccccCcceeeecC
Confidence 35788999998999999999999999877432 223333333333344455668888888999987
No 106
>PF04322 DUF473: Protein of unknown function (DUF473); InterPro: IPR007417 This is a family of uncharacterised archaeal proteins.
Probab=28.11 E-value=1.3e+02 Score=21.76 Aligned_cols=42 Identities=24% Similarity=0.392 Sum_probs=27.5
Q ss_pred eeeeEEEEcCc-----eeeEEeCCEEEEccCCC-----CCCCeEEEEeEEEe
Q 030413 17 RDLESYTIRGT-----NKIVRVGDCVLMRPSDT-----GKPPYVARIEKIES 58 (177)
Q Consensus 17 ~~y~~~~~~g~-----~~~~~vGD~V~v~~~~~-----~~~~~Ig~I~~i~~ 58 (177)
.++..+.+... -....+||+|++.+... +..=-||+|.++..
T Consensus 20 ~~~RTiEirSa~N~~~~~~~~~Gd~VFlT~~~~~Dl~~Gt~GiIa~V~~~~i 71 (119)
T PF04322_consen 20 NHIRTIEIRSAHNVIALESLDPGDRVFLTSVSLEDLTPGTEGIIAEVKKIEI 71 (119)
T ss_pred CCceEEEEEcchheeeeecCCCCCEEEEecCCHHHCCCCCCeEEEEEEEEEE
Confidence 45556655531 13458999999999762 34556888877655
No 107
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=28.04 E-value=1.6e+02 Score=22.06 Aligned_cols=37 Identities=11% Similarity=0.116 Sum_probs=27.3
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEE
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRV 68 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v 68 (177)
..++.||.|.|.++.+ .=-.|+|.++... ++.+.|.+
T Consensus 45 ~~IkkGD~V~Vi~Gk~--KGk~GkV~~V~~k-~~~ViVEg 81 (143)
T PTZ00194 45 MPVRKDDEVMVVRGHH--KGREGKVTAVYRK-KWVIHIEK 81 (143)
T ss_pred ceeecCCEEEEecCCC--CCCceEEEEEEcC-CCEEEEeC
Confidence 4789999999999974 3346999999775 34444444
No 108
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=27.60 E-value=97 Score=20.50 Aligned_cols=29 Identities=17% Similarity=0.234 Sum_probs=19.0
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEe
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIES 58 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~ 58 (177)
.-++.||+|.|.+.+- +..-=|.|.....
T Consensus 37 iwI~~GD~VlV~~~~~-~~~~kg~Iv~r~~ 65 (78)
T cd04456 37 IWIKRGDFLIVDPIEE-GEDVKADIIFVYC 65 (78)
T ss_pred EEEcCCCEEEEEeccc-CCCceEEEEEEeC
Confidence 5679999999987651 1344566655544
No 109
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=27.19 E-value=27 Score=29.59 Aligned_cols=23 Identities=13% Similarity=0.348 Sum_probs=17.0
Q ss_pred cccCccchhcccc-cccccchhhhhh
Q 030413 151 VRCLITRMISWYN-VRGARTGIILLV 175 (177)
Q Consensus 151 ~~C~~~~c~~wyH-~~C~~~~~~~~~ 175 (177)
.|| -.|--|+| -.|+--...+..
T Consensus 149 ~QC--~iCEDWFHce~c~~~~~~~~~ 172 (345)
T KOG2752|consen 149 LQC--VICEDWFHCEGCMQAKTFLED 172 (345)
T ss_pred eeE--EeccchhcccccCcccchhhc
Confidence 899 99999999 667655444433
No 110
>PF00667 FAD_binding_1: FAD binding domain; InterPro: IPR003097 This domain is found in sulphite reductase, NADPH cytochrome P450 reductase, nitric oxide synthase and methionine synthase reductase. Flavoprotein pyridine nucleotide cytochrome reductases [] (FPNCR) catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin:NADP+reductases (FNR) [], plant and fungal NAD(P)H:nitrate reductases [, ], NADH:cytochrome b5 reductases [], NADPH:P450 reductases [], NADPH:sulphite reductases [], nitric oxide synthases [], phthalate dioxygenase reductase [], and various other flavoproteins.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3QFR_B 3FJO_A 3QFC_B 3QE2_B 3QFS_A 3QFT_A 2B5O_B 2QTZ_A 2QTL_A 2BPO_B ....
Probab=26.59 E-value=79 Score=24.74 Aligned_cols=24 Identities=13% Similarity=0.236 Sum_probs=14.3
Q ss_pred EEEEcCceeeEEeCCEEEEccCCC
Q 030413 21 SYTIRGTNKIVRVGDCVLMRPSDT 44 (177)
Q Consensus 21 ~~~~~g~~~~~~vGD~V~v~~~~~ 44 (177)
.+.+.+.+..|++||.+-|.+.++
T Consensus 32 eldl~~~~l~Y~pGD~l~V~P~N~ 55 (219)
T PF00667_consen 32 ELDLSDSGLSYQPGDHLGVYPPND 55 (219)
T ss_dssp EEE-TTSTG---TT-EEEEE-SSE
T ss_pred EEEeCCCCCcccCCCEEEEEccCC
Confidence 566666678999999999999983
No 111
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=25.95 E-value=82 Score=22.27 Aligned_cols=21 Identities=24% Similarity=0.627 Sum_probs=16.9
Q ss_pred EEcCceeeEEeCCEEEEccCC
Q 030413 23 TIRGTNKIVRVGDCVLMRPSD 43 (177)
Q Consensus 23 ~~~g~~~~~~vGD~V~v~~~~ 43 (177)
+++|...+++.||++++.++.
T Consensus 78 ~~~g~~~~l~~Gd~i~ip~g~ 98 (131)
T COG1917 78 QLEGEKKELKAGDVIIIPPGV 98 (131)
T ss_pred EecCCceEecCCCEEEECCCC
Confidence 445656788999999999976
No 112
>PF02311 AraC_binding: AraC-like ligand binding domain; InterPro: IPR003313 This entry defines the arabinose-binding and dimerisation domain of the bacterial gene regulatory protein AraC. The crystal structure of the arabinose-binding and dimerization domain of the Escherichia coli gene regulatory protein AraC was determined in the presence and absence of L-arabinose. The arabinose-bound molecule shows that the protein adopts an unusual fold, binding sugar within a beta barrel and completely burying the arabinose with the amino-terminal arm of the protein. Dimer contacts in the presence of arabinose are mediated by an antiparallel coiled-coil. In the uncomplexed protein, the amino-terminal arm is disordered, uncovering the sugar-binding pocket and allowing it to serve as an oligomerization interface [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 1XJA_B 2ARA_A 2AAC_B 2ARC_A.
Probab=25.74 E-value=2.1e+02 Score=19.22 Aligned_cols=21 Identities=29% Similarity=0.529 Sum_probs=11.5
Q ss_pred EEcCceeeEEeCCEEEEccCC
Q 030413 23 TIRGTNKIVRVGDCVLMRPSD 43 (177)
Q Consensus 23 ~~~g~~~~~~vGD~V~v~~~~ 43 (177)
.++|....++.||.+++.++.
T Consensus 37 ~~~~~~~~l~~g~~~li~p~~ 57 (136)
T PF02311_consen 37 HIDGQEYPLKPGDLFLIPPGQ 57 (136)
T ss_dssp EETTEEEEE-TT-EEEE-TTS
T ss_pred EECCEEEEEECCEEEEecCCc
Confidence 445555666777777777765
No 113
>PF01079 Hint: Hint module; InterPro: IPR001767 This domain identifies a group of cysteine peptidases correspond to MEROPS peptidase family C46 (clan CH). The type example is the Hedgehog protein from Drosophila melanogaster (Fruit fly). These are involved in intracellular signalling required for a variety of patterning events during development. The hedgehog family of proteins self process by a cysteine-dependent mechanism, which is a one-time autolytic cleavage. It is differentiated from a typical peptidase reaction by the fact that the newly-formed carboxyl group is esterified with cholesterol, rather than being left free. The three-dimensional structure of the autolytic domain of the hedgehog protein of D. melanogaster shows that it is formed from two divergent copies of a module that also occurs in inteins, called a Hint domain [,].; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3K7H_B 3K7I_B 3K7G_B 1AT0_A 3MXW_A 3M1N_B 3HO5_H 2WFR_A 2WFQ_A 2WG3_B ....
Probab=25.58 E-value=88 Score=24.91 Aligned_cols=28 Identities=36% Similarity=0.624 Sum_probs=16.7
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEe
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIES 58 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~ 58 (177)
.+++||+|++...+ .......+|.++..
T Consensus 105 ~V~~Gd~v~~~~~~-~~~~~~~~V~~v~~ 132 (217)
T PF01079_consen 105 DVRVGDCVLVSDEG-GGKLRPSRVVRVST 132 (217)
T ss_dssp G--TT-EEEEE-TT-T--EEEEEEEEEEE
T ss_pred hCCCCCEEEEEEcC-CCcEEEEEEEEEEE
Confidence 67999999994443 35677888888766
No 114
>PRK03187 tgl transglutaminase; Provisional
Probab=25.58 E-value=49 Score=27.34 Aligned_cols=19 Identities=37% Similarity=0.574 Sum_probs=15.5
Q ss_pred EEcCceeeEEeCCEEEEccCC
Q 030413 23 TIRGTNKIVRVGDCVLMRPSD 43 (177)
Q Consensus 23 ~~~g~~~~~~vGD~V~v~~~~ 43 (177)
+..|. .+-+||+||+++++
T Consensus 160 t~~g~--~~~PGD~vYFkNPd 178 (272)
T PRK03187 160 TKTGG--DFLPGDCVYFKNPD 178 (272)
T ss_pred EecCC--CCCCCcEEEecCCC
Confidence 34454 88999999999987
No 115
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=25.26 E-value=32 Score=22.54 Aligned_cols=24 Identities=13% Similarity=0.227 Sum_probs=15.2
Q ss_pred cccCccchhcccccccccchhhhhh
Q 030413 151 VRCLITRMISWYNVRGARTGIILLV 175 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~~~~~~~~~ 175 (177)
|.|.++ -.-|-|++|..+....++
T Consensus 31 I~cs~~-~GHWvhaqCm~LsE~~L~ 54 (78)
T PF13341_consen 31 IFCSRG-GGHWVHAQCMDLSETMLI 54 (78)
T ss_dssp EEE-ST-T-EEEETGGGT--HHHHH
T ss_pred EEEeCC-CceEeEeecccchHHHHH
Confidence 888444 445999999998876554
No 116
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=25.07 E-value=1.7e+02 Score=20.66 Aligned_cols=29 Identities=17% Similarity=0.187 Sum_probs=23.5
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCC
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDA 60 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~ 60 (177)
.++.||.|+|.++.+ +=--|+|.++....
T Consensus 4 ~IrkGD~V~Vi~Gkd--KGk~GkVl~v~~k~ 32 (104)
T COG0198 4 KVKKGDTVKVIAGKD--KGKEGKVLKVLPKK 32 (104)
T ss_pred ceecCCEEEEEecCC--CCcceEEEEEecCe
Confidence 678999999999974 45578888887764
No 117
>PF12503 CMV_1a_C: Cucumber mosaic virus 1a protein C terminal ; InterPro: IPR022184 This domain family is found in viruses, and is approximately 90 amino acids in length. The family is found in association with PF01443 from PFAM, PF01660 from PFAM. There is a conserved GLG sequence motif. 1a protein is the major virulence factor of the (Cucumber mosaic virus. The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic. The determinant of the pathogenesis of these different strains is the specific amino acid residue at the 461 residue of the 1a protein. ; GO: 0008168 methyltransferase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=24.88 E-value=66 Score=21.72 Aligned_cols=31 Identities=26% Similarity=0.369 Sum_probs=19.3
Q ss_pred EEEEEEEEeeccccC-------CcccccCCCCeEEEeCCC
Q 030413 64 VKVRVRWYYRPEESL-------GGRRQFHGAKELFLSDHY 96 (177)
Q Consensus 64 ~~v~v~Wfyrp~e~~-------~~~~~~~~~~ELf~S~~~ 96 (177)
-...++|+| |.+.. .|..+ -.++|||+-+..
T Consensus 34 Hf~~GrWm~-P~~~~Y~VGyNe~GLGp-K~~~ElyiVnk~ 71 (85)
T PF12503_consen 34 HFPNGRWMY-PEGYEYMVGYNESGLGP-KFDGELYIVNKD 71 (85)
T ss_pred EecCCceec-CCCeEEEeeecCCCCCc-CcCCeEEEEcCc
Confidence 345578999 88764 12122 247999987653
No 118
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=24.81 E-value=2e+02 Score=20.53 Aligned_cols=38 Identities=24% Similarity=0.220 Sum_probs=27.5
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEE
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVR 69 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~ 69 (177)
..++.||-|.|.++.. .=..|.|.++... .+.+.+.+.
T Consensus 40 ~~IkkGD~V~Vi~Gk~--KGk~GkV~~V~~~-~~~V~Vegv 77 (114)
T TIGR01080 40 LPVRKGDKVRIMRGDF--KGHEGKVSKVDLK-RYRIYVEGV 77 (114)
T ss_pred ceeecCCEEEEecCCC--CCCEEEEEEEEcC-CCEEEEcCe
Confidence 3789999999999973 4567999999753 344444443
No 119
>COG3450 Predicted enzyme of the cupin superfamily [General function prediction only]
Probab=24.41 E-value=71 Score=22.98 Aligned_cols=18 Identities=28% Similarity=0.364 Sum_probs=14.9
Q ss_pred CceeeEEeCCEEEEccCC
Q 030413 26 GTNKIVRVGDCVLMRPSD 43 (177)
Q Consensus 26 g~~~~~~vGD~V~v~~~~ 43 (177)
|+..+|+.||.+++.++-
T Consensus 81 Ge~v~~~aGD~~~~~~G~ 98 (116)
T COG3450 81 GEPVEVRAGDSFVFPAGF 98 (116)
T ss_pred CeEEEEcCCCEEEECCCC
Confidence 345788999999999886
No 120
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=23.96 E-value=20 Score=18.93 Aligned_cols=15 Identities=20% Similarity=0.100 Sum_probs=6.8
Q ss_pred cccCccchhcccccccc
Q 030413 151 VRCLITRMISWYNVRGA 167 (177)
Q Consensus 151 ~~C~~~~c~~wyH~~C~ 167 (177)
..| +.|.-.+|.+|+
T Consensus 16 Y~C--~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 16 YRC--SECDFDLHEECA 30 (30)
T ss_dssp EE---TTT-----HHHH
T ss_pred EEC--ccCCCccChhcC
Confidence 468 888889998884
No 121
>TIGR00218 manA mannose-6-phosphate isomerase, class I. The names phosphomannose isomerase and mannose-6-phosphate isomerase are synonomous. This family contains two rather deeply branched groups. One group contains an experimentally determined phosphomannose isomerase of Streptococcus mutans as well as three uncharacterized paralogous proteins of Bacillus subtilis, all at more than 50 % identity to each other, plus a more distant homolog from Archaeoglobus fulgidus. The other group contains members from E. coli, budding yeast, Borrelia burgdorferi, etc.
Probab=23.24 E-value=1e+02 Score=25.54 Aligned_cols=33 Identities=9% Similarity=0.086 Sum_probs=27.1
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCC
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIESDARN 62 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g 62 (177)
..++.||++||.++..+. +-=+.|.+|-+++|.
T Consensus 153 v~v~~Gd~i~ipaGt~HA-~~g~~~~Eiq~~SD~ 185 (302)
T TIGR00218 153 IKLKPGDFFYVPSGTPHA-YKGGLVLEVMQNSDN 185 (302)
T ss_pred cccCCCCEEEeCCCCccc-ccCceEEEEEcCCCc
Confidence 477999999999998776 566778899887664
No 122
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=23.22 E-value=1.1e+02 Score=23.23 Aligned_cols=21 Identities=19% Similarity=0.256 Sum_probs=13.2
Q ss_pred EEcCceeeEEeCCEEEEccCC
Q 030413 23 TIRGTNKIVRVGDCVLMRPSD 43 (177)
Q Consensus 23 ~~~g~~~~~~vGD~V~v~~~~ 43 (177)
.++|....+..||++++.++.
T Consensus 142 ~~~~~~~~l~~Gd~~~~~~~~ 162 (185)
T PRK09943 142 TINGQDYHLVAGQSYAINTGI 162 (185)
T ss_pred EECCEEEEecCCCEEEEcCCC
Confidence 344444566777777777765
No 123
>COG4127 Uncharacterized conserved protein [Function unknown]
Probab=23.01 E-value=56 Score=27.32 Aligned_cols=41 Identities=12% Similarity=0.284 Sum_probs=30.7
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCC----CC-cEEEEEEEE
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDA----RN-NVKVRVRWY 71 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~----~g-~~~v~v~Wf 71 (177)
+++.||-|.+.+.. ...++||+|.+=++-. .| ....+|.|+
T Consensus 72 eI~KGDlvi~y~k~-~r~y~IGkVtsdYEy~p~~~~~i~hTrkVkWL 117 (318)
T COG4127 72 EIQKGDLVITYSKS-NRTYLIGKVTSDYEYHPEWLEGIGHTRKVKWL 117 (318)
T ss_pred HhccCcEEEeeccc-CceEEEEEecCCcccCccccccCchhhHhHHh
Confidence 67999999999987 4789999998876631 11 234567787
No 124
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=22.76 E-value=1.9e+02 Score=23.86 Aligned_cols=45 Identities=22% Similarity=0.300 Sum_probs=36.1
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeCCCCcEEEEEEEEeecccc
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESDARNNVKVRVRWYYRPEES 77 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~~~g~~~v~v~Wfyrp~e~ 77 (177)
.+.+||.|.|..+. -.-+.|.|.++..+ .+...+.+.+|-|..-+
T Consensus 205 ~f~vGd~VrI~dGP--F~GfeG~I~eid~~-k~Rv~VlV~IfGR~TpV 249 (258)
T TIGR01956 205 KFRVGNFVKIVDGP--FKGIVGKIKKIDQE-KKKAIVEVEILGKSVDV 249 (258)
T ss_pred CCCCCCEEEEEecC--CCCcEEEEEEEeCC-CCEEEEEEEecCCcEEE
Confidence 47899999999986 46789999999763 56788888888776543
No 125
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=21.86 E-value=1.4e+02 Score=20.84 Aligned_cols=27 Identities=30% Similarity=0.218 Sum_probs=14.8
Q ss_pred eeEEeCCEEEEccCCCCCCCeEEEEeEEE
Q 030413 29 KIVRVGDCVLMRPSDTGKPPYVARIEKIE 57 (177)
Q Consensus 29 ~~~~vGD~V~v~~~~~~~~~~Ig~I~~i~ 57 (177)
.-+..||+|.|...+- .+-=|+|...+
T Consensus 58 IwI~~GD~VlVe~~~~--~~~kg~Iv~r~ 84 (100)
T PRK04012 58 MWIREGDVVIVAPWDF--QDEKADIIWRY 84 (100)
T ss_pred EEecCCCEEEEEeccc--CCCEEEEEEEc
Confidence 3556777777776542 23345554443
No 126
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=21.48 E-value=37 Score=30.14 Aligned_cols=27 Identities=11% Similarity=0.193 Sum_probs=22.7
Q ss_pred Cccccccc---------cccCccchhcccccccccchh
Q 030413 143 TELLCTAN---------VRCLITRMISWYNVRGARTGI 171 (177)
Q Consensus 143 ~~~~C~c~---------~~C~~~~c~~wyH~~C~~~~~ 171 (177)
....|+|. ++| +-|..|.|.-|.+.-.
T Consensus 85 ~~~~c~c~~~~~~~g~~i~c--~~c~~Wqh~~C~g~~~ 120 (508)
T KOG1844|consen 85 EISRCDCGLEDDMEGLMIQC--DWCGRWQHKICCGSFK 120 (508)
T ss_pred cccccccccccCCCceeeCC--cccCcccCceeeeecC
Confidence 34488887 999 9999999999998754
No 127
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=21.30 E-value=2e+02 Score=19.13 Aligned_cols=14 Identities=36% Similarity=0.724 Sum_probs=11.2
Q ss_pred eEEeCCEEEEccCC
Q 030413 30 IVRVGDCVLMRPSD 43 (177)
Q Consensus 30 ~~~vGD~V~v~~~~ 43 (177)
=++-||+|+|.+-+
T Consensus 38 WIkrGd~VlV~p~~ 51 (78)
T cd05792 38 WIKRGDFVLVEPIE 51 (78)
T ss_pred EEEeCCEEEEEecc
Confidence 46889999997754
No 128
>KOG1740 consensus Predicted mitochondrial/chloroplast ribosomal protein S17 [Translation, ribosomal structure and biogenesis]
Probab=21.11 E-value=59 Score=22.84 Aligned_cols=28 Identities=25% Similarity=0.418 Sum_probs=21.6
Q ss_pred eeeeEEEEcCceeeEEeCCEEEEccCCC
Q 030413 17 RDLESYTIRGTNKIVRVGDCVLMRPSDT 44 (177)
Q Consensus 17 ~~y~~~~~~g~~~~~~vGD~V~v~~~~~ 44 (177)
.+++.+...+++...++||.|-+.+.-+
T Consensus 36 ~~~~kymahD~~n~cnvGD~VrlepsRP 63 (107)
T KOG1740|consen 36 KRTSKYMAHDDKNQCNVGDRVRLEPSRP 63 (107)
T ss_pred HHhhheeecCccccccccceEEeccCCc
Confidence 4566666666566899999999999875
No 129
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=20.94 E-value=2.4e+02 Score=18.24 Aligned_cols=25 Identities=28% Similarity=0.508 Sum_probs=19.8
Q ss_pred eEEeCCEEEEccCCCCCCCeEEEEeEEEeC
Q 030413 30 IVRVGDCVLMRPSDTGKPPYVARIEKIESD 59 (177)
Q Consensus 30 ~~~vGD~V~v~~~~~~~~~~Ig~I~~i~~~ 59 (177)
.+++||.|++.|.+ . .++|.+|...
T Consensus 26 ~i~~Gd~v~i~P~~--~---~~~V~si~~~ 50 (83)
T cd03698 26 SIQKGDTLLVMPSK--E---SVEVKSIYVD 50 (83)
T ss_pred EEeCCCEEEEeCCC--c---EEEEEEEEEC
Confidence 78999999999975 2 4778777654
No 130
>PRK11171 hypothetical protein; Provisional
Probab=20.83 E-value=4.3e+02 Score=21.44 Aligned_cols=21 Identities=19% Similarity=0.463 Sum_probs=13.7
Q ss_pred EEcCceeeEEeCCEEEEccCC
Q 030413 23 TIRGTNKIVRVGDCVLMRPSD 43 (177)
Q Consensus 23 ~~~g~~~~~~vGD~V~v~~~~ 43 (177)
.++|...++..||++++.+..
T Consensus 97 ~~~g~~~~L~~GDsi~~p~~~ 117 (266)
T PRK11171 97 TLEGKTHALSEGGYAYLPPGS 117 (266)
T ss_pred EECCEEEEECCCCEEEECCCC
Confidence 344444566778888877775
Done!