Query 032704
Match_columns 135
No_of_seqs 128 out of 1169
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 04:53:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032704.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032704hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1708 Mitochondrial/chloropl 100.0 3.2E-31 7E-36 215.2 6.5 134 1-134 1-137 (236)
2 PRK12281 rplX 50S ribosomal pr 99.9 3.8E-26 8.2E-31 159.2 7.3 68 66-133 3-70 (76)
3 CHL00141 rpl24 ribosomal prote 99.9 2.3E-24 4.9E-29 152.3 7.3 68 66-133 5-72 (83)
4 PRK00004 rplX 50S ribosomal pr 99.9 4.1E-24 8.9E-29 156.2 7.3 67 67-133 2-68 (105)
5 TIGR01079 rplX_bact ribosomal 99.9 7.5E-24 1.6E-28 155.0 7.2 67 67-133 1-68 (104)
6 COG0198 RplX Ribosomal protein 99.9 1.8E-23 3.9E-28 153.9 6.7 65 67-133 2-66 (104)
7 PRK01191 rpl24p 50S ribosomal 99.7 5.7E-18 1.2E-22 127.5 5.9 64 53-133 35-98 (120)
8 PTZ00194 60S ribosomal protein 99.7 6.6E-18 1.4E-22 130.4 5.1 64 53-133 36-99 (143)
9 TIGR01080 rplX_A_E ribosomal p 99.7 4.4E-17 9.4E-22 121.5 5.6 71 46-133 24-94 (114)
10 PF00467 KOW: KOW motif; Inte 98.9 3E-09 6.5E-14 62.6 4.5 32 72-103 1-32 (32)
11 smart00739 KOW KOW (Kyprides, 98.0 9.4E-06 2E-10 44.9 3.7 26 70-95 2-27 (28)
12 KOG3401 60S ribosomal protein 97.8 1.6E-05 3.4E-10 62.1 2.7 48 54-107 39-87 (145)
13 TIGR00405 L26e_arch ribosomal 97.4 0.00036 7.8E-09 52.2 5.1 38 70-107 87-124 (145)
14 PRK05609 nusG transcription an 97.3 0.00038 8.2E-09 53.2 5.0 36 68-103 125-160 (181)
15 TIGR00922 nusG transcription t 97.3 0.00047 1E-08 52.5 4.9 36 68-103 118-153 (172)
16 PRK08559 nusG transcription an 97.2 0.00053 1.1E-08 52.4 4.9 42 69-110 94-135 (153)
17 COG0250 NusG Transcription ant 97.1 0.00094 2E-08 53.0 4.7 38 66-103 120-157 (178)
18 TIGR01955 RfaH transcriptional 96.8 0.0024 5.1E-08 47.8 4.5 35 68-103 107-141 (159)
19 PRK09014 rfaH transcriptional 96.6 0.0032 7E-08 47.6 4.4 33 70-103 110-142 (162)
20 TIGR01956 NusG_myco NusG famil 96.4 0.0069 1.5E-07 51.1 5.2 36 68-103 204-239 (258)
21 PRK04333 50S ribosomal protein 94.7 0.074 1.6E-06 37.8 4.7 36 69-105 3-38 (84)
22 KOG1999 RNA polymerase II tran 91.5 0.21 4.6E-06 49.0 3.8 29 68-96 458-486 (1024)
23 PTZ00065 60S ribosomal protein 90.9 0.59 1.3E-05 36.0 5.1 35 70-105 8-42 (130)
24 PRK04313 30S ribosomal protein 87.9 0.94 2E-05 37.9 4.6 41 66-106 168-212 (237)
25 KOG1999 RNA polymerase II tran 86.4 1.9 4.2E-05 42.6 6.4 60 69-130 407-487 (1024)
26 PTZ00471 60S ribosomal protein 85.9 1.4 3.1E-05 34.2 4.3 41 70-110 5-51 (134)
27 COG2163 RPL14A Ribosomal prote 84.8 1.7 3.6E-05 33.2 4.2 34 70-104 5-38 (125)
28 COG5164 SPT5 Transcription elo 84.1 0.82 1.8E-05 42.3 2.6 29 69-97 139-167 (607)
29 PF09953 DUF2187: Uncharacteri 83.3 2.7 5.8E-05 28.4 4.2 27 71-103 5-31 (57)
30 PRK06531 yajC preprotein trans 82.2 3.9 8.4E-05 30.7 5.2 31 69-103 36-66 (113)
31 PF03144 GTP_EFTU_D2: Elongati 80.5 3.3 7.2E-05 26.7 3.8 31 68-99 11-44 (74)
32 PLN00036 40S ribosomal protein 77.9 4.5 9.7E-05 34.4 4.8 39 66-104 171-212 (261)
33 COG1862 YajC Preprotein transl 77.7 5.4 0.00012 29.2 4.6 40 69-113 43-82 (97)
34 PTZ00223 40S ribosomal protein 77.6 3.9 8.4E-05 35.0 4.3 39 66-104 168-209 (273)
35 PRK02749 photosystem I reactio 77.0 4.5 9.8E-05 28.4 3.8 29 69-97 2-32 (71)
36 COG1532 Predicted RNA-binding 75.6 5.8 0.00013 26.8 3.9 35 70-104 21-57 (57)
37 PTZ00118 40S ribosomal protein 75.5 5.4 0.00012 34.0 4.6 39 66-104 171-212 (262)
38 CHL00125 psaE photosystem I su 74.8 4.6 0.0001 27.9 3.3 28 70-97 2-31 (64)
39 COG1471 RPS4A Ribosomal protei 74.5 5.5 0.00012 33.7 4.4 40 67-106 171-214 (241)
40 PF01157 Ribosomal_L21e: Ribos 74.2 3.1 6.8E-05 30.6 2.6 29 69-97 32-70 (99)
41 PRK05585 yajC preprotein trans 74.1 5.4 0.00012 29.3 3.8 30 68-103 51-80 (106)
42 COG3700 AphA Acid phosphatase 73.8 0.87 1.9E-05 37.9 -0.5 65 66-132 123-190 (237)
43 TIGR00739 yajC preprotein tran 69.9 8.2 0.00018 27.1 3.8 29 69-103 37-65 (84)
44 PF12701 LSM14: Scd6-like Sm d 69.0 13 0.00028 27.0 4.8 35 72-106 7-41 (96)
45 PF05641 Agenet: Agenet domain 68.6 16 0.00034 24.2 4.8 33 70-103 1-37 (68)
46 PF02699 YajC: Preprotein tran 68.0 1.7 3.7E-05 30.3 0.0 30 68-103 35-64 (82)
47 PF08206 OB_RNB: Ribonuclease 67.5 4.4 9.6E-05 26.1 1.9 25 69-93 31-58 (58)
48 PF11623 DUF3252: Protein of u 67.5 17 0.00036 24.3 4.6 40 70-109 2-43 (53)
49 PRK00409 recombination and DNA 67.4 8.5 0.00018 36.7 4.5 37 68-107 635-672 (782)
50 PLN00045 photosystem I reactio 67.3 7.8 0.00017 28.8 3.3 28 69-96 39-68 (101)
51 PF02427 PSI_PsaE: Photosystem 67.0 6.8 0.00015 26.8 2.8 28 70-97 1-30 (61)
52 PRK05886 yajC preprotein trans 66.7 9.8 0.00021 28.4 3.8 29 69-103 38-66 (109)
53 cd03692 mtIF2_IVc mtIF2_IVc: t 62.0 15 0.00033 25.0 3.8 33 68-100 25-57 (84)
54 PF04452 Methyltrans_RNA: RNA 60.7 12 0.00025 29.8 3.5 37 67-103 14-50 (225)
55 PLN00190 60S ribosomal protein 59.8 14 0.0003 29.5 3.7 47 69-115 33-99 (158)
56 cd05689 S1_RPS1_repeat_ec4 S1_ 58.8 27 0.00058 22.3 4.4 24 68-101 47-70 (72)
57 TIGR01069 mutS2 MutS2 family p 58.8 15 0.00032 35.1 4.4 33 71-107 626-660 (771)
58 PF00924 MS_channel: Mechanose 58.8 11 0.00024 28.6 3.0 59 69-132 60-126 (206)
59 cd04717 BAH_polybromo BAH, or 58.5 29 0.00063 25.0 5.0 35 69-103 3-40 (121)
60 PRK04306 50S ribosomal protein 57.8 21 0.00046 26.2 4.2 39 69-107 34-82 (98)
61 smart00743 Agenet Tudor-like d 55.1 42 0.00091 21.1 4.8 33 69-102 2-35 (61)
62 cd05793 S1_IF1A S1_IF1A: Trans 54.8 15 0.00032 25.5 2.8 31 67-97 36-66 (77)
63 PF11717 Tudor-knot: RNA bindi 53.3 33 0.00071 21.8 4.1 29 70-98 1-29 (55)
64 cd04471 S1_RNase_R S1_RNase_R: 52.9 55 0.0012 21.0 5.2 25 68-102 56-80 (83)
65 smart00652 eIF1a eukaryotic tr 52.0 19 0.00042 25.2 3.1 31 67-97 41-71 (83)
66 PF01426 BAH: BAH domain; Int 52.0 23 0.00049 24.5 3.4 29 69-97 2-32 (119)
67 cd04456 S1_IF1A_like S1_IF1A_l 51.4 21 0.00045 24.8 3.2 31 67-97 36-67 (78)
68 PRK10334 mechanosensitive chan 51.4 49 0.0011 27.8 5.9 39 69-112 129-175 (286)
69 COG2139 RPL21A Ribosomal prote 50.0 41 0.00088 25.0 4.6 41 69-109 32-82 (98)
70 cd04715 BAH_Orc1p_like BAH, or 49.9 46 0.00099 26.0 5.2 30 68-97 28-57 (159)
71 COG0361 InfA Translation initi 49.7 28 0.00061 24.5 3.6 30 66-95 43-72 (75)
72 PTZ00189 60S ribosomal protein 49.6 24 0.00052 28.2 3.6 47 69-115 33-99 (160)
73 PF14505 DUF4438: Domain of un 49.6 38 0.00082 29.0 4.9 32 72-103 60-91 (258)
74 cd05688 S1_RPS1_repeat_ec3 S1_ 48.9 37 0.00081 20.8 3.8 25 68-102 43-67 (68)
75 PF01079 Hint: Hint module; I 48.2 25 0.00053 28.7 3.6 39 67-105 103-153 (217)
76 KOG3418 60S ribosomal protein 48.0 32 0.0007 26.9 4.0 40 70-109 5-50 (136)
77 cd03698 eRF3_II_like eRF3_II_l 48.0 35 0.00076 22.9 3.8 27 68-97 25-51 (83)
78 cd03695 CysN_NodQ_II CysN_NodQ 47.6 43 0.00093 22.6 4.2 30 68-100 25-54 (81)
79 COG1193 Mismatch repair ATPase 47.3 21 0.00046 34.4 3.5 34 67-104 610-643 (753)
80 smart00439 BAH Bromo adjacent 47.1 40 0.00086 23.2 4.1 29 70-98 2-32 (120)
81 cd05708 S1_Rrp5_repeat_sc12 S1 47.1 47 0.001 21.0 4.2 26 68-103 46-71 (77)
82 cd05698 S1_Rrp5_repeat_hs6_sc5 46.5 39 0.00086 21.3 3.7 24 69-102 44-67 (70)
83 TIGR00046 RNA methyltransferas 46.4 35 0.00076 27.5 4.2 37 66-102 28-64 (240)
84 PRK11281 hypothetical protein; 46.0 50 0.0011 33.3 5.9 61 67-132 936-1004(1113)
85 PRK11713 16S ribosomal RNA met 45.9 36 0.00078 27.3 4.2 32 66-97 26-57 (234)
86 cd05707 S1_Rrp5_repeat_sc11 S1 45.8 33 0.00073 21.7 3.3 24 69-102 44-67 (68)
87 cd05695 S1_Rrp5_repeat_hs3 S1_ 45.8 35 0.00076 22.0 3.4 24 69-102 42-65 (66)
88 cd04721 BAH_plant_1 BAH, or Br 45.7 49 0.0011 24.8 4.6 30 68-97 6-35 (130)
89 cd04714 BAH_BAHCC1 BAH, or Bro 45.5 48 0.001 24.2 4.5 34 69-102 3-39 (121)
90 cd05697 S1_Rrp5_repeat_hs5 S1_ 45.2 47 0.001 21.1 3.9 24 69-102 44-67 (69)
91 cd03696 selB_II selB_II: this 45.0 36 0.00077 22.7 3.5 28 69-99 26-53 (83)
92 PRK10929 putative mechanosensi 44.7 57 0.0012 32.9 6.1 38 67-109 933-978 (1109)
93 PF00018 SH3_1: SH3 domain; I 44.2 31 0.00067 20.8 2.8 17 66-82 12-28 (48)
94 PF01176 eIF-1a: Translation i 44.2 31 0.00067 22.7 3.0 27 66-92 38-64 (65)
95 TIGR00523 eIF-1A eukaryotic/ar 43.7 18 0.00039 26.3 1.9 32 66-97 54-86 (99)
96 cd04466 S1_YloQ_GTPase S1_YloQ 43.6 46 0.00099 21.0 3.7 29 70-100 38-66 (68)
97 cd04461 S1_Rrp5_repeat_hs8_sc7 42.8 44 0.00096 22.1 3.6 26 67-102 56-81 (83)
98 cd04090 eEF2_II_snRNP Loc2 eEF 42.1 95 0.0021 21.3 5.3 28 68-95 26-59 (94)
99 cd03693 EF1_alpha_II EF1_alpha 41.6 38 0.00083 23.2 3.3 30 67-99 28-57 (91)
100 cd01736 LSm14_N LSm14 (also kn 41.5 70 0.0015 22.5 4.6 37 71-107 4-40 (74)
101 cd04719 BAH_Orc1p_animal BAH, 41.4 44 0.00095 25.3 3.8 31 68-98 2-33 (128)
102 COG1162 Predicted GTPases [Gen 41.4 39 0.00084 29.3 3.9 30 68-100 43-72 (301)
103 cd00164 S1_like S1_like: Ribos 41.1 53 0.0011 19.3 3.5 24 68-101 40-63 (65)
104 cd05703 S1_Rrp5_repeat_hs12_sc 40.9 50 0.0011 21.8 3.7 25 69-103 46-70 (73)
105 cd05690 S1_RPS1_repeat_ec5 S1_ 40.4 52 0.0011 20.5 3.5 23 69-101 45-67 (69)
106 PF00575 S1: S1 RNA binding do 40.3 66 0.0014 20.4 4.1 25 68-102 47-71 (74)
107 cd04452 S1_IF2_alpha S1_IF2_al 39.3 72 0.0016 20.2 4.1 24 69-102 49-72 (76)
108 cd04089 eRF3_II eRF3_II: domai 38.8 55 0.0012 21.9 3.6 27 68-97 24-50 (82)
109 COG5164 SPT5 Transcription elo 38.8 46 0.001 31.3 4.2 34 71-104 353-386 (607)
110 smart00316 S1 Ribosomal protei 38.6 87 0.0019 18.6 4.3 25 69-103 46-70 (72)
111 cd05706 S1_Rrp5_repeat_sc10 S1 38.2 69 0.0015 20.4 3.9 23 70-102 48-70 (73)
112 KOG4315 G-patch nucleic acid b 38.0 16 0.00034 33.5 1.1 35 70-104 394-428 (455)
113 cd05696 S1_Rrp5_repeat_hs4 S1_ 37.8 65 0.0014 21.0 3.8 24 69-102 46-69 (71)
114 PF05257 CHAP: CHAP domain; I 37.2 51 0.0011 23.3 3.4 37 69-106 62-100 (124)
115 CHL00010 infA translation init 37.1 82 0.0018 21.6 4.3 29 68-96 45-73 (78)
116 PRK04012 translation initiatio 36.9 42 0.0009 24.5 3.0 31 66-96 56-86 (100)
117 cd05685 S1_Tex S1_Tex: The C-t 36.9 63 0.0014 19.6 3.4 22 70-101 45-66 (68)
118 cd03694 GTPBP_II Domain II of 36.8 57 0.0012 22.2 3.5 33 67-99 24-57 (87)
119 PF02211 NHase_beta: Nitrile h 36.6 31 0.00066 28.5 2.5 29 66-94 131-169 (222)
120 PF02941 FeThRed_A: Ferredoxin 36.2 43 0.00093 23.3 2.7 25 72-96 1-39 (67)
121 cd00174 SH3 Src homology 3 dom 36.2 36 0.00078 19.5 2.1 17 66-82 14-30 (54)
122 PLN02661 Putative thiazole syn 35.9 23 0.00051 31.2 1.8 17 17-33 25-41 (357)
123 cd03697 EFTU_II EFTU_II: Elong 35.8 51 0.0011 22.3 3.1 31 68-99 25-55 (87)
124 CHL00084 rpl19 ribosomal prote 35.7 1.7E+02 0.0037 22.1 6.2 28 69-96 22-56 (117)
125 KOG3482 Small nuclear ribonucl 35.7 28 0.0006 24.9 1.8 58 44-105 20-77 (79)
126 cd05792 S1_eIF1AD_like S1_eIF1 35.2 90 0.0019 21.9 4.3 31 67-97 36-67 (78)
127 cd04451 S1_IF1 S1_IF1: Transla 35.2 58 0.0013 21.0 3.2 21 70-90 41-61 (64)
128 cd04716 BAH_plantDCM_I BAH, or 34.8 86 0.0019 23.4 4.4 27 70-96 4-31 (122)
129 cd01854 YjeQ_engC YjeQ/EngC. 34.8 86 0.0019 25.9 4.9 30 69-100 34-63 (287)
130 COG3109 ProQ Activator of osmo 34.8 50 0.0011 27.3 3.4 48 56-104 148-195 (208)
131 PF06701 MIB_HERC2: Mib_herc2; 34.8 52 0.0011 22.5 3.0 20 84-103 19-43 (68)
132 cd05687 S1_RPS1_repeat_ec1_hs1 34.6 79 0.0017 19.9 3.7 23 70-102 45-67 (70)
133 TIGR00358 3_prime_RNase VacB a 34.5 71 0.0015 29.8 4.7 36 68-103 49-87 (654)
134 cd04709 BAH_MTA BAH, or Bromo 34.4 84 0.0018 24.7 4.5 29 70-98 4-33 (164)
135 cd04370 BAH BAH, or Bromo Adja 34.1 99 0.0022 21.0 4.4 30 69-98 3-36 (123)
136 PF07653 SH3_2: Variant SH3 do 33.4 31 0.00066 21.4 1.6 14 66-79 14-27 (55)
137 PF09926 DUF2158: Uncharacteri 33.3 24 0.00052 23.1 1.1 21 70-93 1-21 (53)
138 cd05691 S1_RPS1_repeat_ec6 S1_ 32.8 98 0.0021 19.3 3.9 25 69-103 44-68 (73)
139 COG1385 Uncharacterized protei 32.0 73 0.0016 26.4 4.0 36 67-102 31-66 (246)
140 PRK00276 infA translation init 30.9 1.1E+02 0.0023 20.5 4.0 23 69-91 46-68 (72)
141 smart00326 SH3 Src homology 3 30.9 47 0.001 19.1 2.1 16 67-82 18-33 (58)
142 PRK00049 elongation factor Tu; 30.6 1E+02 0.0022 26.7 4.8 34 66-100 235-268 (396)
143 PRK05352 Na(+)-translocating N 30.3 67 0.0014 29.0 3.7 30 66-95 42-82 (448)
144 cd03691 BipA_TypA_II BipA_TypA 30.2 86 0.0019 20.8 3.5 27 67-93 24-50 (86)
145 PRK05338 rplS 50S ribosomal pr 30.1 2.1E+02 0.0045 21.6 5.8 28 69-96 18-52 (116)
146 PRK12442 translation initiatio 30.1 1E+02 0.0022 22.4 4.0 26 66-91 43-68 (87)
147 PRK07252 hypothetical protein; 30.1 95 0.0021 22.9 4.0 25 69-103 47-71 (120)
148 PRK11642 exoribonuclease R; Pr 29.6 87 0.0019 30.4 4.6 35 69-103 117-154 (813)
149 COG1726 NqrA Na+-transporting 29.6 72 0.0016 29.1 3.8 41 63-103 38-89 (447)
150 smart00357 CSP Cold shock prot 29.6 81 0.0018 18.9 3.1 24 70-93 37-63 (64)
151 TIGR03170 flgA_cterm flagella 29.6 95 0.0021 22.0 3.8 29 66-94 62-102 (122)
152 KOG4225 Sorbin and SH3 domain- 29.5 61 0.0013 30.0 3.4 47 36-90 223-277 (489)
153 PF02887 PK_C: Pyruvate kinase 29.4 27 0.00059 24.8 1.0 20 69-88 89-108 (117)
154 TIGR00219 mreC rod shape-deter 28.6 71 0.0015 26.8 3.4 33 68-104 142-176 (283)
155 cd04091 mtEFG1_II_like mtEFG1_ 28.4 97 0.0021 20.5 3.5 13 68-80 24-36 (81)
156 TIGR02594 conserved hypothetic 28.2 1.3E+02 0.0029 22.4 4.5 35 71-106 75-109 (129)
157 TIGR00008 infA translation ini 28.2 82 0.0018 21.6 3.1 24 67-90 42-65 (68)
158 cd04713 BAH_plant_3 BAH, or Br 28.2 1.3E+02 0.0029 22.7 4.6 30 68-97 19-49 (146)
159 PF13437 HlyD_3: HlyD family s 28.1 1.3E+02 0.0027 20.3 4.1 28 68-95 48-78 (105)
160 PRK10708 hypothetical protein; 27.6 83 0.0018 21.5 3.0 28 71-98 2-29 (62)
161 PF11948 DUF3465: Protein of u 27.5 38 0.00083 26.2 1.5 18 62-79 77-95 (131)
162 PF01245 Ribosomal_L19: Riboso 27.4 78 0.0017 23.5 3.1 27 70-96 19-52 (113)
163 PF05972 APC_15aa: APC 15 resi 27.4 17 0.00038 18.9 -0.3 9 126-134 2-10 (16)
164 COG2002 AbrB Regulators of sta 27.2 43 0.00092 23.3 1.6 22 65-86 23-44 (89)
165 cd05686 S1_pNO40 S1_pNO40: pNO 27.0 1E+02 0.0022 20.0 3.4 19 69-97 48-66 (73)
166 PF07497 Rho_RNA_bind: Rho ter 26.8 58 0.0013 22.9 2.2 18 64-81 37-54 (78)
167 PRK07018 flgA flagellar basal 26.8 95 0.0021 25.1 3.8 35 66-100 173-220 (235)
168 PRK08577 hypothetical protein; 26.6 50 0.0011 24.3 2.0 24 65-88 22-45 (136)
169 PF04085 MreC: rod shape-deter 25.9 94 0.002 23.4 3.4 29 69-101 23-51 (152)
170 PF04717 Phage_base_V: Phage-r 25.8 98 0.0021 20.5 3.1 16 88-103 1-16 (79)
171 PRK12289 GTPase RsgA; Reviewed 25.8 1E+02 0.0022 26.8 4.0 32 70-101 52-83 (352)
172 PRK06437 hypothetical protein; 25.8 51 0.0011 21.8 1.7 15 66-80 48-62 (67)
173 cd05705 S1_Rrp5_repeat_hs14 S1 25.7 1.2E+02 0.0025 20.1 3.5 24 69-102 50-73 (74)
174 PRK12618 flgA flagellar basal 25.4 1.2E+02 0.0027 23.0 3.9 34 67-100 79-125 (141)
175 PRK04950 ProP expression regul 24.8 1.2E+02 0.0026 25.2 4.0 46 58-104 155-200 (213)
176 PF10781 DSRB: Dextransucrase 24.4 98 0.0021 21.2 2.9 28 71-98 2-29 (62)
177 KOG3421 60S ribosomal protein 24.3 89 0.0019 24.4 3.0 35 70-105 7-41 (136)
178 cd01342 Translation_Factor_II_ 24.3 1.7E+02 0.0036 17.4 4.3 28 68-96 25-52 (83)
179 PF09356 Phage_BR0599: Phage c 24.2 59 0.0013 22.5 1.9 17 69-85 40-56 (80)
180 PF07076 DUF1344: Protein of u 24.2 81 0.0017 21.5 2.4 22 86-107 5-26 (61)
181 smart00333 TUDOR Tudor domain. 24.1 1.7E+02 0.0038 17.6 4.6 27 70-96 3-29 (57)
182 PLN00208 translation initiatio 24.1 1.1E+02 0.0025 23.9 3.6 31 67-97 68-98 (145)
183 cd04472 S1_PNPase S1_PNPase: P 23.9 1.2E+02 0.0026 18.5 3.1 23 69-102 44-66 (68)
184 PRK08515 flgA flagellar basal 23.6 1.2E+02 0.0026 24.5 3.8 35 66-100 162-208 (222)
185 PF10133 RNA_bind_2: Predicted 23.5 2.3E+02 0.0051 18.9 5.2 33 71-103 26-60 (61)
186 TIGR00485 EF-Tu translation el 23.3 1.4E+02 0.0031 25.6 4.4 32 67-99 234-265 (394)
187 KOG4792 Crk family adapters [S 23.1 1.4E+02 0.003 25.9 4.2 45 35-80 212-258 (293)
188 cd04088 EFG_mtEFG_II EFG_mtEFG 23.0 1.2E+02 0.0026 19.8 3.2 25 67-94 24-48 (83)
189 PF11604 CusF_Ec: Copper bindi 23.0 1.2E+02 0.0026 20.2 3.1 16 88-103 1-16 (70)
190 PF14604 SH3_9: Variant SH3 do 22.5 66 0.0014 19.8 1.7 16 66-81 11-26 (49)
191 PRK05054 exoribonuclease II; P 22.4 1.6E+02 0.0034 27.7 4.7 34 69-102 53-87 (644)
192 PTZ00329 eukaryotic translatio 22.3 1.3E+02 0.0029 23.8 3.7 31 67-97 68-98 (155)
193 TIGR02768 TraA_Ti Ti-type conj 22.3 1.7E+02 0.0036 27.9 5.0 35 67-103 605-644 (744)
194 TIGR02063 RNase_R ribonuclease 22.2 1.4E+02 0.0031 28.0 4.5 36 68-103 101-140 (709)
195 PRK10220 hypothetical protein; 22.2 2E+02 0.0044 21.8 4.5 27 69-95 51-83 (111)
196 TIGR02062 RNase_B exoribonucle 22.2 1.6E+02 0.0035 27.6 4.8 35 69-103 50-85 (639)
197 PF13550 Phage-tail_3: Putativ 22.0 1.5E+02 0.0032 21.3 3.7 28 66-94 136-163 (164)
198 TIGR01024 rplS_bact ribosomal 22.0 3.5E+02 0.0075 20.3 6.4 27 70-96 19-52 (113)
199 PF06003 SMN: Survival motor n 21.9 1.8E+02 0.0039 24.3 4.6 35 69-103 68-103 (264)
200 PF02470 MCE: mce related prot 21.8 1.4E+02 0.0029 19.7 3.2 37 70-111 15-53 (81)
201 cd06462 Peptidase_S24_S26 The 21.7 2.2E+02 0.0047 17.9 4.4 34 70-106 29-64 (84)
202 PRK08059 general stress protei 21.5 1.7E+02 0.0037 21.3 3.9 25 69-103 51-75 (123)
203 COG2053 RPS28A Ribosomal prote 21.5 78 0.0017 22.1 2.0 13 75-87 27-39 (69)
204 PF04351 PilP: Pilus assembly 20.9 2E+02 0.0044 21.7 4.4 45 75-131 102-147 (149)
205 PF11910 NdhO: Cyanobacterial 20.8 44 0.00095 23.3 0.6 16 70-85 1-16 (67)
206 TIGR01945 rnfC electron transp 20.6 1.2E+02 0.0026 26.8 3.5 31 66-96 43-84 (435)
207 TIGR00157 ribosome small subun 20.4 1.7E+02 0.0037 23.6 4.1 35 71-107 2-39 (245)
208 cd06552 ASCH_yqfb_like ASC-1 h 20.3 1.2E+02 0.0025 20.8 2.7 26 69-94 28-53 (100)
209 PRK06005 flgA flagellar basal 20.3 1.6E+02 0.0034 22.8 3.7 30 66-95 97-138 (160)
210 PF07154 DUF1392: Protein of u 20.2 2.1E+02 0.0046 22.8 4.4 80 19-98 15-116 (150)
No 1
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=3.2e-31 Score=215.23 Aligned_cols=134 Identities=42% Similarity=0.543 Sum_probs=124.4
Q ss_pred Chhhhhhhhhcceeeecc-ccccCccc-CCCCCCC-ccccCCCCceeeeeeeeeeeeeecCCCCCcccccceeeeCCEEE
Q 032704 1 MAAMAALQSSMTSLSISS-NSFFGQRL-SFPSLSP-ITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVK 77 (135)
Q Consensus 1 ~~~~~~~~~~~~~l~~~~-~~f~g~~l-~~~~~~~-~~~~~~~~~~~~~~~~k~wer~~~k~~~lp~~~k~~I~kGD~V~ 77 (135)
|+.|+||||++++||++- ..|.+|.+ +|.++.+ .+.+..+++|+.....++|+|+.|.++..+...+|+++.||+|+
T Consensus 1 M~ts~aL~s~l~s~s~lPs~y~er~y~isP~~~~~~~pr~~adk~~~~~qk~~~w~rrr~~~~e~i~d~dw~ff~GDtVe 80 (236)
T KOG1708|consen 1 MRTSSALASSLTSLSLLPSSYFERQYLISPISLSVTSPRKVADKRCLVLQKNKPWERRRCVPVEPIIDEDWHFFFGDTVE 80 (236)
T ss_pred CchHHHHHHHhhhhhcCCHHHhhceeeeccccccccCCCChhhhhhhHHhhcCccccccCCCCCCccccceeEecCCEEE
Confidence 889999999999999865 66778888 5767774 44788899999999999999999999999999999999999999
Q ss_pred EEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEEe
Q 032704 78 VIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYFI 134 (135)
Q Consensus 78 VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S~ 134 (135)
||.|+||||+|+|++|++++|+|+|+|+|.+.+|++...++.+|.|+..|+|||+|-
T Consensus 81 VlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk 137 (236)
T KOG1708|consen 81 VLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSK 137 (236)
T ss_pred EEecccCCccceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCceecc
Confidence 999999999999999999999999999999999999998999999999999999984
No 2
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=99.93 E-value=3.8e-26 Score=159.21 Aligned_cols=68 Identities=35% Similarity=0.520 Sum_probs=65.8
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF 133 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S 133 (135)
.+|+|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+||++++++|+|+++|+|||+|
T Consensus 3 ~~~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~kkh~kp~~~~~~G~i~~~e~pI~~S 70 (76)
T PRK12281 3 VKLKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMPIHIS 70 (76)
T ss_pred ccccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCCccCCCCCEEEEEcCcCHH
Confidence 56899999999999999999999999999999999999999999999999888899999999999997
No 3
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=99.91 E-value=2.3e-24 Score=152.29 Aligned_cols=68 Identities=50% Similarity=0.757 Sum_probs=65.3
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF 133 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S 133 (135)
.+++|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+|++++++.|+++++|+|||+|
T Consensus 5 ~~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~~k~~k~~~~~~~g~i~~~e~pI~~S 72 (83)
T CHL00141 5 KKMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHSS 72 (83)
T ss_pred eeCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCHH
Confidence 46789999999999999999999999999999999999999999999999888899999999999987
No 4
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=99.90 E-value=4.1e-24 Score=156.23 Aligned_cols=67 Identities=43% Similarity=0.594 Sum_probs=65.3
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF 133 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S 133 (135)
+|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|+|+++++++|+|++.|+|||||
T Consensus 2 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~S 68 (105)
T PRK00004 2 MMKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHIS 68 (105)
T ss_pred CCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHH
Confidence 6899999999999999999999999999999999999999999999999888999999999999997
No 5
>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=99.90 E-value=7.5e-24 Score=155.01 Aligned_cols=67 Identities=45% Similarity=0.650 Sum_probs=64.1
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccC-CceEEEEeeeeeEE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEE-QGQIIKVYSLICYF 133 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~-~GgIi~~E~PIh~S 133 (135)
+++|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+||+++++ +|+|+++|+|||||
T Consensus 1 ~~~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~S 68 (104)
T TIGR01079 1 KMKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHIS 68 (104)
T ss_pred CCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHH
Confidence 35899999999999999999999999999999999999999999999998777 89999999999997
No 6
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.89 E-value=1.8e-23 Score=153.91 Aligned_cols=65 Identities=48% Similarity=0.661 Sum_probs=62.6
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeEE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICYF 133 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~S 133 (135)
+++|++||+|.||+|+|||++|+|++|++++ |+|||||+.++|.||+++++.|||+++|+|||+|
T Consensus 2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~S 66 (104)
T COG0198 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVEGVNVVKKHIKPSQENPEGGIINKEAPIHIS 66 (104)
T ss_pred CcceecCCEEEEEecCCCCcceEEEEEecCe--EEEECcEEEEecCCCCCcCCCCceeeeeecccHH
Confidence 5789999999999999999999999999998 9999999999999988888889999999999997
No 7
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=99.72 E-value=5.7e-18 Score=127.47 Aligned_cols=64 Identities=30% Similarity=0.373 Sum_probs=56.2
Q ss_pred eeeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeE
Q 032704 53 ERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICY 132 (135)
Q Consensus 53 er~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~ 132 (135)
.|++|+.+. |+|++||+|+||+|+|||++|+|++|++++++|+|||||+.+. +| +++|+|||+
T Consensus 35 Lr~~y~ir~------~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~---------~G--~~~e~pIh~ 97 (120)
T PRK01191 35 LREKYGIRS------LPVRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKA---------DG--TEVPRPIHP 97 (120)
T ss_pred HHHHhCCcc------ceEeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECC---------CC--eEEEcccch
Confidence 466776554 5699999999999999999999999999999999999999872 35 689999999
Q ss_pred E
Q 032704 133 F 133 (135)
Q Consensus 133 S 133 (135)
|
T Consensus 98 S 98 (120)
T PRK01191 98 S 98 (120)
T ss_pred h
Confidence 7
No 8
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=99.71 E-value=6.6e-18 Score=130.36 Aligned_cols=64 Identities=27% Similarity=0.380 Sum_probs=58.5
Q ss_pred eeeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeE
Q 032704 53 ERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICY 132 (135)
Q Consensus 53 er~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~ 132 (135)
.|.+|+.++++ |++||+|+||+|+|||++|+|++|++++++|+|||||+.++|.++ .|+|||+
T Consensus 36 Lr~k~~~Rs~~------IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~-----------~e~PIh~ 98 (143)
T PTZ00194 36 LRAKYNVRSMP------VRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEP-----------VQIGIHP 98 (143)
T ss_pred HHHHhCCccce------eecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCE-----------eecCcCc
Confidence 46778877764 899999999999999999999999999999999999999999875 6999998
Q ss_pred E
Q 032704 133 F 133 (135)
Q Consensus 133 S 133 (135)
|
T Consensus 99 S 99 (143)
T PTZ00194 99 S 99 (143)
T ss_pred h
Confidence 7
No 9
>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=99.68 E-value=4.4e-17 Score=121.51 Aligned_cols=71 Identities=24% Similarity=0.297 Sum_probs=62.0
Q ss_pred eeeeeeeeeeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEE
Q 032704 46 VVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIK 125 (135)
Q Consensus 46 ~~~~k~wer~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~ 125 (135)
...+-+|.|++|+++.. +|++||+|+||+|+|||++|+|++|++++++|+|||||+.+ ++ | ++
T Consensus 24 ~a~ls~elr~~y~~r~~------~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k----~~-----G--~~ 86 (114)
T TIGR01080 24 SAPLSKELREKYGKRAL------PVRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEK----VN-----G--TE 86 (114)
T ss_pred ecccCHHHHHHcCcccc------eeecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEEC----CC-----C--eE
Confidence 34566788999986665 58999999999999999999999999999999999999987 22 4 78
Q ss_pred EeeeeeEE
Q 032704 126 VYSLICYF 133 (135)
Q Consensus 126 ~E~PIh~S 133 (135)
.|+|||+|
T Consensus 87 ~e~pIh~S 94 (114)
T TIGR01080 87 VPVPIHPS 94 (114)
T ss_pred EEeeechH
Confidence 99999987
No 10
>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=98.89 E-value=3e-09 Score=62.63 Aligned_cols=32 Identities=53% Similarity=0.709 Sum_probs=30.8
Q ss_pred eCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 72 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 72 kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
+||.|+|++|+++|++|+|++|++++++|+||
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 59999999999999999999999999999986
No 11
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=98.01 E-value=9.4e-06 Score=44.87 Aligned_cols=26 Identities=50% Similarity=0.704 Sum_probs=24.4
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEc
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFR 95 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r 95 (135)
+.+||.|+|+.|+++|++|+|.+++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57999999999999999999999975
No 12
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=97.78 E-value=1.6e-05 Score=62.06 Aligned_cols=48 Identities=27% Similarity=0.632 Sum_probs=42.7
Q ss_pred eeecCCCCCcccccceeeeCCEEEEEecCCCC-eEeEEEEEEccCCEEEEeccce
Q 032704 54 RKECKPNSLPVLHKMHVKAGDTVKVIAGCDKG-KIGEITKVFRHNSTVMVKDINL 107 (135)
Q Consensus 54 r~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKG-K~G~V~~V~r~~~~ViVegvN~ 107 (135)
|.+++-.++| |+.+|+|.|..|.++| ++|+|++|++++..+++|.|..
T Consensus 39 R~~y~vrs~p------ir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~ 87 (145)
T KOG3401|consen 39 RQKYNVRSMP------IRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQR 87 (145)
T ss_pred HHHhCccccc------eeeccEEEEEeccccccccceehhhhhhhheeeeEeEEE
Confidence 6667766665 8999999999999999 9999999999999999998765
No 13
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=97.37 E-value=0.00036 Score=52.17 Aligned_cols=38 Identities=29% Similarity=0.434 Sum_probs=34.7
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccce
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINL 107 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~ 107 (135)
+.+||.|.|++|+++|..|+|.+++.++..|.|+-.+.
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~~ 124 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIEA 124 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEEc
Confidence 78999999999999999999999999888998886553
No 14
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=97.34 E-value=0.00038 Score=53.15 Aligned_cols=36 Identities=25% Similarity=0.288 Sum_probs=32.5
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
..+++||+|.|++|+++|.+|+|.+++++++++.|.
T Consensus 125 ~~~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~ 160 (181)
T PRK05609 125 VDFEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVL 160 (181)
T ss_pred cCCCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEE
Confidence 447899999999999999999999999888888765
No 15
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=97.28 E-value=0.00047 Score=52.46 Aligned_cols=36 Identities=22% Similarity=0.282 Sum_probs=32.2
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
..+++||+|.|+.|+++|.+|+|.+++++++++.|.
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~ 153 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVS 153 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEE
Confidence 347899999999999999999999999888887765
No 16
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=97.25 E-value=0.00053 Score=52.44 Aligned_cols=42 Identities=29% Similarity=0.381 Sum_probs=38.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTK 110 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kk 110 (135)
.+.+||.|.|++|+++|..|.|.+++.+++++.|+-++...+
T Consensus 94 ~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~~~ 135 (153)
T PRK08559 94 GIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAVP 135 (153)
T ss_pred CCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCcce
Confidence 479999999999999999999999999999999997776544
No 17
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=97.06 E-value=0.00094 Score=52.96 Aligned_cols=38 Identities=24% Similarity=0.366 Sum_probs=34.9
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
.+..+.+||.|.|++|+++|-.|+|.+|+.+++++.|+
T Consensus 120 ~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~ 157 (178)
T COG0250 120 PKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVE 157 (178)
T ss_pred ccccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEE
Confidence 45678999999999999999999999999999988776
No 18
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=96.75 E-value=0.0024 Score=47.84 Aligned_cols=35 Identities=17% Similarity=0.102 Sum_probs=29.6
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
..+.+||+|.|+.|+++|-.|.|.+++ .++++.|.
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~-~~~r~~v~ 141 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPD-GEKRSMLL 141 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEEC-CCceEEEE
Confidence 447899999999999999999999998 45576553
No 19
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=96.61 E-value=0.0032 Score=47.64 Aligned_cols=33 Identities=21% Similarity=0.198 Sum_probs=28.4
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
+.+||+|.|+.|+++|.+|+|.+++ .++++.|.
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~-~~~r~~v~ 142 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPD-GEARSILL 142 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeC-CCeEEEEe
Confidence 6899999999999999999999998 55565543
No 20
>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=96.35 E-value=0.0069 Score=51.11 Aligned_cols=36 Identities=28% Similarity=0.508 Sum_probs=32.5
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
..+.+||.|.|+.|+++|..|+|.+++.+++++.|.
T Consensus 204 ~~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~Vl 239 (258)
T TIGR01956 204 SKFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVE 239 (258)
T ss_pred cCCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEE
Confidence 457899999999999999999999999888888775
No 21
>PRK04333 50S ribosomal protein L14e; Validated
Probab=94.69 E-value=0.074 Score=37.84 Aligned_cols=36 Identities=19% Similarity=0.310 Sum_probs=32.2
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEecc
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegv 105 (135)
.+..|-.|.+..|+|+|+...|+.+.. .++|+|+|-
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d-~~~vlVdg~ 38 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIID-KNFVLVTGP 38 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEec-CCEEEEECC
Confidence 478899999999999999999999875 589999887
No 22
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=91.45 E-value=0.21 Score=48.97 Aligned_cols=29 Identities=38% Similarity=0.505 Sum_probs=26.9
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~ 96 (135)
-.|+.||-|+||+|+++|..|.|++|.+.
T Consensus 458 KyF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 458 KYFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred hhccCCCeEEEEeccccCCcceEEEEeCC
Confidence 46899999999999999999999999984
No 23
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=90.93 E-value=0.59 Score=36.03 Aligned_cols=35 Identities=26% Similarity=0.369 Sum_probs=31.9
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEecc
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegv 105 (135)
+-.|=.|.|..|+++||...|..|.- .|+|+|+|=
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID-~nRvLVDGP 42 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVT-PTRVLVDGA 42 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEc-CCeEEEeCC
Confidence 67888899999999999999999986 579999997
No 24
>PRK04313 30S ribosomal protein S4e; Validated
Probab=87.86 E-value=0.94 Score=37.94 Aligned_cols=41 Identities=20% Similarity=0.393 Sum_probs=34.8
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccC----CEEEEeccc
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKDIN 106 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~----~~ViVegvN 106 (135)
.-.++..|-.|.|+.|++-|.+|+|.++.+.. +.|.|++-+
T Consensus 168 ~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~ 212 (237)
T PRK04313 168 DHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKD 212 (237)
T ss_pred EEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCC
Confidence 45678899999999999999999999998655 678888644
No 25
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=86.45 E-value=1.9 Score=42.58 Aligned_cols=60 Identities=30% Similarity=0.402 Sum_probs=41.6
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe----ccc---------ee--------EEEecCCCccCCceEEEEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK----DIN---------LK--------TKHVKKREEEEQGQIIKVY 127 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe----gvN---------~~--------kkhvK~~~e~~~GgIi~~E 127 (135)
.|.+||.|.|+.|..+|-.|+|..|+-. .|++. +++ ++ -|-+...-|+..|-|++.|
T Consensus 407 ~F~~GD~VeV~~Gel~glkG~ve~vdg~--~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvrVe 484 (1024)
T KOG1999|consen 407 LFSPGDAVEVIVGELKGLKGKVESVDGT--IVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVRVE 484 (1024)
T ss_pred ccCCCCeEEEeeeeeccceeEEEeccCc--eEEEeeccccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEEEe
Confidence 3899999999999999999999999854 33322 111 11 1223334567889998888
Q ss_pred eee
Q 032704 128 SLI 130 (135)
Q Consensus 128 ~PI 130 (135)
.-+
T Consensus 485 ~~~ 487 (1024)
T KOG1999|consen 485 QGD 487 (1024)
T ss_pred CCe
Confidence 743
No 26
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=85.90 E-value=1.4 Score=34.17 Aligned_cols=41 Identities=27% Similarity=0.359 Sum_probs=35.4
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccC------CEEEEeccceeEE
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLKTK 110 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~------~~ViVegvN~~kk 110 (135)
+++|-.|.|++|++.|+...|++.+.++ +.++|-||....+
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP~ 51 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYPK 51 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccch
Confidence 6789999999999999999999988776 6899999776443
No 27
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=84.80 E-value=1.7 Score=33.23 Aligned_cols=34 Identities=32% Similarity=0.401 Sum_probs=31.2
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEec
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVeg 104 (135)
+.+|=.|.|.+|++.|+...|+++.-++ .+++.|
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~g 38 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITG 38 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCC-EEEEeC
Confidence 6789999999999999999999999877 888887
No 28
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=84.12 E-value=0.82 Score=42.35 Aligned_cols=29 Identities=31% Similarity=0.444 Sum_probs=26.4
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
.+++||.|+||.|.+++.+|.|..|+.++
T Consensus 139 ~f~~gD~vkVI~g~~~~d~g~V~rI~~~~ 167 (607)
T COG5164 139 GFYKGDLVKVIEGGEMVDIGTVPRIDGEK 167 (607)
T ss_pred ccccCCeEEEeccccccccceEEEecCce
Confidence 47899999999999999999999998763
No 29
>PF09953 DUF2187: Uncharacterized protein conserved in bacteria (DUF2187); InterPro: IPR018690 This family consists of various hypothetical bacterial proteins with known function. It includes the uncharacterised YkvS protein from Bacillus subtilis.
Probab=83.28 E-value=2.7 Score=28.36 Aligned_cols=27 Identities=33% Similarity=0.665 Sum_probs=22.9
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
..||.+.. .+|-+|+|.+|+ .|+|+|+
T Consensus 5 ~vGdiIef----k~g~~G~V~kv~--eNSVIVd 31 (57)
T PF09953_consen 5 KVGDIIEF----KDGFTGIVEKVY--ENSVIVD 31 (57)
T ss_pred ccCcEEEE----cCCcEEEEEEEe--cCcEEEE
Confidence 57999986 358999999999 7889987
No 30
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=82.21 E-value=3.9 Score=30.68 Aligned_cols=31 Identities=26% Similarity=0.472 Sum_probs=26.3
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
.+++||+|.-+. |-.|+|.+|..+.+.|.++
T Consensus 36 sLk~GD~VvT~G----Gi~G~V~~I~~~~~~v~le 66 (113)
T PRK06531 36 AIQKGDEVVTIG----GLYGTVDEVDTEAKTIVLD 66 (113)
T ss_pred hcCCCCEEEECC----CcEEEEEEEecCCCEEEEE
Confidence 579999998765 5689999999888889886
No 31
>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=80.48 E-value=3.3 Score=26.68 Aligned_cols=31 Identities=32% Similarity=0.490 Sum_probs=25.4
Q ss_pred ceeeeCCEEEEEecCCCCeE---eEEEEEEccCCE
Q 032704 68 MHVKAGDTVKVIAGCDKGKI---GEITKVFRHNST 99 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~---G~V~~V~r~~~~ 99 (135)
=.|++||+|.++. .+.++. .+|.+++...+.
T Consensus 11 G~l~~gd~v~~~~-~~~~~~~~~~~I~~i~~~~~~ 44 (74)
T PF03144_consen 11 GTLKKGDKVRVLP-NGTGKKGQVVKIKSIFMFNGD 44 (74)
T ss_dssp SEEETTEEEEEES-TTTTEECEEEEEEEEEETTEE
T ss_pred eEEcCCCEEEECc-cCCcceeeeeecccccccccC
Confidence 3689999999998 666555 999999998764
No 32
>PLN00036 40S ribosomal protein S4; Provisional
Probab=77.85 E-value=4.5 Score=34.43 Aligned_cols=39 Identities=28% Similarity=0.525 Sum_probs=33.0
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccC---CEEEEec
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVKD 104 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~---~~ViVeg 104 (135)
.-.++..|-.|.|+.|++-|.+|+|.++..+. +.|.|++
T Consensus 171 ~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d 212 (261)
T PLN00036 171 DFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKD 212 (261)
T ss_pred eEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe
Confidence 45678899999999999999999999999553 4688886
No 33
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=77.67 E-value=5.4 Score=29.20 Aligned_cols=40 Identities=33% Similarity=0.389 Sum_probs=27.5
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccceeEEEec
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVK 113 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~~kkhvK 113 (135)
.+++||+|.-+. |-.|+|++|..+.-.|.+. -|..-+..|
T Consensus 43 sL~kGD~VvT~g----Gi~G~V~~v~d~~v~I~l~-~~~~i~~~k 82 (97)
T COG1862 43 SLKKGDEVVTIG----GIVGTVTKVGDDTVEIELG-DGTKIKFEK 82 (97)
T ss_pred hccCCCEEEEcC----CeEEEEEEEecCcEEEEEC-CCeEEEEEH
Confidence 479999998876 4689999999877333333 455444444
No 34
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=77.62 E-value=3.9 Score=35.04 Aligned_cols=39 Identities=33% Similarity=0.604 Sum_probs=32.7
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccC---CEEEEec
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVKD 104 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~---~~ViVeg 104 (135)
.-.++..|-.|.|+.|++-|.+|+|.++..+. +.|.+++
T Consensus 168 ~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d 209 (273)
T PTZ00223 168 DLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKD 209 (273)
T ss_pred EEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEe
Confidence 45678899999999999999999999996553 4677875
No 35
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=76.97 E-value=4.5 Score=28.42 Aligned_cols=29 Identities=17% Similarity=0.341 Sum_probs=25.6
Q ss_pred eeeeCCEEEEEecC--CCCeEeEEEEEEccC
Q 032704 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (135)
Q Consensus 69 ~I~kGD~V~VI~Gk--dKGK~G~V~~V~r~~ 97 (135)
-|.+||+|.|++=. .-..+|+|.+|++..
T Consensus 2 ~i~rGskVrIlR~ESYWyn~vGtV~svD~sg 32 (71)
T PRK02749 2 AISRGDKVRILRPESYWYNEVGTVASVDKSG 32 (71)
T ss_pred ccccCCEEEEccccceeecCcceEEEEccCC
Confidence 37899999999986 678999999999985
No 36
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=75.64 E-value=5.8 Score=26.80 Aligned_cols=35 Identities=14% Similarity=0.201 Sum_probs=29.9
Q ss_pred eeeCCEEEE--EecCCCCeEeEEEEEEccCCEEEEec
Q 032704 70 VKAGDTVKV--IAGCDKGKIGEITKVFRHNSTVMVKD 104 (135)
Q Consensus 70 I~kGD~V~V--I~GkdKGK~G~V~~V~r~~~~ViVeg 104 (135)
...||.|+. |-|..|--.|+|++|+-+.++|++|+
T Consensus 21 ev~~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE~ 57 (57)
T COG1532 21 EVTEEGVVARDILGDEKEFEGQVKRIDLDEHKIELEG 57 (57)
T ss_pred EEecCcEEEEeccCCceEecceEEEEEccccEEEecC
Confidence 467888776 45889999999999999999999986
No 37
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=75.50 E-value=5.4 Score=33.97 Aligned_cols=39 Identities=26% Similarity=0.494 Sum_probs=32.3
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccC---CEEEEec
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVKD 104 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~---~~ViVeg 104 (135)
.-.++..|-.|.|+.|++-|.+|+|.++..+. +.|.|++
T Consensus 171 ~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d 212 (262)
T PTZ00118 171 EFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKD 212 (262)
T ss_pred eEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEe
Confidence 45678899999999999999999999977654 4677876
No 38
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=74.83 E-value=4.6 Score=27.87 Aligned_cols=28 Identities=25% Similarity=0.355 Sum_probs=24.6
Q ss_pred eeeCCEEEEEecC--CCCeEeEEEEEEccC
Q 032704 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (135)
Q Consensus 70 I~kGD~V~VI~Gk--dKGK~G~V~~V~r~~ 97 (135)
|.+||+|.|++-. .-..+|+|.+|+..+
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~g 31 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSG 31 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCC
Confidence 6899999999986 678899999999974
No 39
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=74.55 E-value=5.5 Score=33.67 Aligned_cols=40 Identities=25% Similarity=0.423 Sum_probs=32.9
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccC----CEEEEeccc
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKDIN 106 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~----~~ViVegvN 106 (135)
-.++..|-.|.|..|++-|.+|+|.+|.... |.|.+|+-+
T Consensus 171 ~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~ 214 (241)
T COG1471 171 HIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEE 214 (241)
T ss_pred EeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCC
Confidence 3566788888999999999999999999774 678888733
No 40
>PF01157 Ribosomal_L21e: Ribosomal protein L21e; InterPro: IPR001147 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 [, ]. L21E family contains proteins from a number of eukaryotic and archaebacterial organisms which include; mammalian L2, Entamoeba histolytica L21, Caenorhabditis elegans L21 (C14B9.7), Saccharomyces cerevisiae (Baker's yeast) L21E (URP1) and Haloarcula marismortui HL31.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZR_U 1S1I_Q 3O58_T 3IZS_U 3O5H_T 1Q82_R 1KQS_P 3CCJ_Q 3CCQ_Q 1VQ5_Q ....
Probab=74.24 E-value=3.1 Score=30.55 Aligned_cols=29 Identities=28% Similarity=0.381 Sum_probs=17.7
Q ss_pred eeeeCCEEEEEecC----------CCCeEeEEEEEEccC
Q 032704 69 HVKAGDTVKVIAGC----------DKGKIGEITKVFRHN 97 (135)
Q Consensus 69 ~I~kGD~V~VI~Gk----------dKGK~G~V~~V~r~~ 97 (135)
.++.||.|-|.--. +-|++|+|..|.+..
T Consensus 32 ~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~ 70 (99)
T PF01157_consen 32 EYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGA 70 (99)
T ss_dssp ---TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSC
T ss_pred HccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCc
Confidence 57899999986432 679999999888764
No 41
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=74.10 E-value=5.4 Score=29.29 Aligned_cols=30 Identities=33% Similarity=0.496 Sum_probs=24.1
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
-.+++||+|.-++| -.|+|.+|+. +.|.||
T Consensus 51 ~~Lk~Gd~VvT~gG----i~G~Vv~i~~--~~v~le 80 (106)
T PRK05585 51 SSLAKGDEVVTNGG----IIGKVTKVSE--DFVIIE 80 (106)
T ss_pred HhcCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 35899999988775 6899999975 677776
No 42
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=73.75 E-value=0.87 Score=37.90 Aligned_cols=65 Identities=22% Similarity=0.334 Sum_probs=43.8
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccc---eeEEEecCCCccCCceEEEEeeeeeE
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN---LKTKHVKKREEEEQGQIIKVYSLICY 132 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN---~~kkhvK~~~e~~~GgIi~~E~PIh~ 132 (135)
-.||.++||.|.-++|+-.||+-+|.+...++..+ ++-| ..--.-||.|-+..--|++.-.-|||
T Consensus 123 I~MHq~RGD~i~FvTGRt~gk~d~vsk~Lak~F~i--~~m~pv~f~Gdk~k~~qy~Kt~~i~~~~~~IhY 190 (237)
T COG3700 123 IDMHQRRGDAIYFVTGRTPGKTDTVSKTLAKNFHI--TNMNPVIFAGDKPKPGQYTKTQWIQDKNIRIHY 190 (237)
T ss_pred HHHHHhcCCeEEEEecCCCCcccccchhHHhhccc--CCCcceeeccCCCCcccccccHHHHhcCceEEe
Confidence 45899999999999999999999999998887665 2221 11111133333333345666677777
No 43
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=69.89 E-value=8.2 Score=27.15 Aligned_cols=29 Identities=38% Similarity=0.678 Sum_probs=22.9
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
.+++||+|.-+.| -.|+|.+|+. +.+.||
T Consensus 37 ~L~~Gd~VvT~gG----i~G~V~~i~d--~~v~ve 65 (84)
T TIGR00739 37 SLKKGDKVLTIGG----IIGTVTKIAE--NTIVIE 65 (84)
T ss_pred hCCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 5899999988764 6899999985 466665
No 44
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=68.99 E-value=13 Score=26.98 Aligned_cols=35 Identities=20% Similarity=0.344 Sum_probs=32.2
Q ss_pred eCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccc
Q 032704 72 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 106 (135)
Q Consensus 72 kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN 106 (135)
-|-+|-+|+..+..-+|.+..|+..+++|.++++-
T Consensus 7 IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr 41 (96)
T PF12701_consen 7 IGSKISLISKSDIRYEGILYSIDTEDSTITLKNVR 41 (96)
T ss_dssp TTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEE
T ss_pred cCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeee
Confidence 58899999999999999999999999999998754
No 45
>PF05641 Agenet: Agenet domain; InterPro: IPR008395 This domain is related to the TUDOR domain IPR008191 from INTERPRO []. The function of the agenet domain is unknown. This signature matches one of the two Agenet domains in the FMR proteins [].; GO: 0003723 RNA binding; PDB: 2BKD_N 3O8V_A 3KUF_A 3H8Z_A.
Probab=68.65 E-value=16 Score=24.17 Aligned_cols=33 Identities=27% Similarity=0.355 Sum_probs=20.0
Q ss_pred eeeCCEEEEEecCC--CC--eEeEEEEEEccCCEEEEe
Q 032704 70 VKAGDTVKVIAGCD--KG--KIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 70 I~kGD~V~VI~Gkd--KG--K~G~V~~V~r~~~~ViVe 103 (135)
|++||.|.|.+-.+ .| -.++|++...++ ++.|+
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~-~~~V~ 37 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD-KYLVE 37 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT--EEEEE
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc-EEEEE
Confidence 58999999998542 33 357899988875 66555
No 46
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=68.04 E-value=1.7 Score=30.29 Aligned_cols=30 Identities=30% Similarity=0.591 Sum_probs=0.4
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
-.+++||+|.-.+| -.|+|.++ +++.|.+|
T Consensus 35 ~~Lk~Gd~VvT~gG----i~G~V~~i--~~~~v~le 64 (82)
T PF02699_consen 35 ASLKPGDEVVTIGG----IYGTVVEI--DDDTVVLE 64 (82)
T ss_dssp G-----------------------------------
T ss_pred HcCCCCCEEEECCc----EEEEEEEE--eCCEEEEE
Confidence 35899999998875 57899998 55666665
No 47
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=67.55 E-value=4.4 Score=26.13 Aligned_cols=25 Identities=36% Similarity=0.412 Sum_probs=16.0
Q ss_pred eeeeCCEEEE-Eec--CCCCeEeEEEEE
Q 032704 69 HVKAGDTVKV-IAG--CDKGKIGEITKV 93 (135)
Q Consensus 69 ~I~kGD~V~V-I~G--kdKGK~G~V~~V 93 (135)
.-.-||+|.| +.. +.+..+|+|++|
T Consensus 31 ~A~~gD~V~v~i~~~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 31 GAMDGDKVLVRITPPSRGKRPEGEVVEV 58 (58)
T ss_dssp TS-TT-EEEEEEEESSSEEEEEEEEEE-
T ss_pred CCCCCCEEEEEEecCCCCCCCCEEEEeC
Confidence 4567999988 444 456778888876
No 48
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=67.52 E-value=17 Score=24.31 Aligned_cols=40 Identities=23% Similarity=0.237 Sum_probs=29.9
Q ss_pred eeeCCEEEEEecC--CCCeEeEEEEEEccCCEEEEeccceeE
Q 032704 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHNSTVMVKDINLKT 109 (135)
Q Consensus 70 I~kGD~V~VI~Gk--dKGK~G~V~~V~r~~~~ViVegvN~~k 109 (135)
|.+|-.|.|+.-+ +-|-+|.|..|...+--|+.||-|--|
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~G~VQRvsdgkaaVLFEGGnWdK 43 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYEGFVQRVSDGKAAVLFEGGNWDK 43 (53)
T ss_dssp --TT-EEEE--TTSTTTT-EEEEEEEETTEEEEEEEETTEEE
T ss_pred ccCCCEEEEeCCCCccchheEEEEEeeCCeEEEEecCCCceE
Confidence 6789999999986 789999999999998899999988643
No 49
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=67.35 E-value=8.5 Score=36.73 Aligned_cols=37 Identities=24% Similarity=0.394 Sum_probs=26.7
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCC-EEEEeccce
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNS-TVMVKDINL 107 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~-~ViVegvN~ 107 (135)
..+++||+|.|.+ -|+.|+|++|..++. .|.+.++.+
T Consensus 635 ~~~~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g~~k~ 672 (782)
T PRK00409 635 EELKVGDEVKYLS---LGQKGEVLSIPDDKEAIVQAGIMKM 672 (782)
T ss_pred cCCCCCCEEEEcc---CCceEEEEEEcCCCeEEEEECCEEE
Confidence 4589999999965 678999999975332 345555554
No 50
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=67.26 E-value=7.8 Score=28.84 Aligned_cols=28 Identities=21% Similarity=0.248 Sum_probs=25.0
Q ss_pred eeeeCCEEEEEecC--CCCeEeEEEEEEcc
Q 032704 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRH 96 (135)
Q Consensus 69 ~I~kGD~V~VI~Gk--dKGK~G~V~~V~r~ 96 (135)
-+.+||+|+|++-. .-..+|+|..|+..
T Consensus 39 g~~RGskVrIlR~ESYWyn~vGtVvsVDq~ 68 (101)
T PLN00045 39 GPKRGSKVKILRPESYWFNDVGKVVAVDQD 68 (101)
T ss_pred ccCCCCEEEEccccceeecCcceEEEEeCC
Confidence 37999999999986 67889999999998
No 51
>PF02427 PSI_PsaE: Photosystem I reaction centre subunit IV / PsaE; InterPro: IPR003375 PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains []. This subunit may form complexes with ferredoxin and ferredoxin-oxidoreductase in the photosystem I reaction centre.; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 1PSF_A 1PSE_A 2WSF_E 2WSC_E 2O01_E 2WSE_E 1GXI_E 1JB0_E 3PCQ_E 1QP2_A ....
Probab=66.97 E-value=6.8 Score=26.84 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=23.1
Q ss_pred eeeCCEEEEEecC--CCCeEeEEEEEEccC
Q 032704 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (135)
Q Consensus 70 I~kGD~V~VI~Gk--dKGK~G~V~~V~r~~ 97 (135)
+.+||+|+|++=. .-..+|+|..|++..
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~ 30 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSG 30 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSS
T ss_pred CCCCCEEEEccccceeecccceEEEEccCC
Confidence 4689999999986 779999999999886
No 52
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=66.65 E-value=9.8 Score=28.37 Aligned_cols=29 Identities=24% Similarity=0.368 Sum_probs=23.4
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
.+++||+|.-+. |-.|+|.+|.. +.|.||
T Consensus 38 ~Lk~GD~VvT~g----Gi~G~V~~I~d--~~v~le 66 (109)
T PRK05886 38 SLQPGDRVHTTS----GLQATIVGITD--DTVDLE 66 (109)
T ss_pred hcCCCCEEEECC----CeEEEEEEEeC--CEEEEE
Confidence 589999998776 46899999974 578776
No 53
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=61.95 E-value=15 Score=25.04 Aligned_cols=33 Identities=21% Similarity=0.264 Sum_probs=25.2
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEE
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~V 100 (135)
=.+++||+|.|+.+..-=..|+|.++.+.++.|
T Consensus 25 G~l~~g~~v~vlr~~~~~~~g~i~sl~~~~~~v 57 (84)
T cd03692 25 GKIKRNAKVRVLRNGEVIYEGKISSLKRFKDDV 57 (84)
T ss_pred CEEeCCCEEEEEcCCCEEEEEEEEEEEEcCccc
Confidence 358999999999985222568888888877665
No 54
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=60.68 E-value=12 Score=29.83 Aligned_cols=37 Identities=24% Similarity=0.416 Sum_probs=27.7
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
-++++.||.|.|..|...--.++|+++.++.-.+.+.
T Consensus 14 VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 14 VLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRIL 50 (225)
T ss_dssp TST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEE
T ss_pred hcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEe
Confidence 4578999999999999888899999999876555444
No 55
>PLN00190 60S ribosomal protein L21; Provisional
Probab=59.79 E-value=14 Score=29.48 Aligned_cols=47 Identities=26% Similarity=0.379 Sum_probs=31.9
Q ss_pred eeeeCCEEEEEec----------CCCCeEeEEEEEEccCCEEE----------EeccceeEEEecCC
Q 032704 69 HVKAGDTVKVIAG----------CDKGKIGEITKVFRHNSTVM----------VKDINLKTKHVKKR 115 (135)
Q Consensus 69 ~I~kGD~V~VI~G----------kdKGK~G~V~~V~r~~~~Vi----------VegvN~~kkhvK~~ 115 (135)
.++.||.|-|..- .+-|+.|+|..+..+.--|+ .+-+|+..-|+|++
T Consensus 33 ~yk~GD~VdIk~~~svqKGMPhk~YHGkTG~V~nv~~~A~gV~V~K~vggr~~~Kri~vriEHlk~s 99 (158)
T PLN00190 33 TFKVGDYVDIKVNGAIHKGMPHKFYHGRTGIVWNVTKRAVGVEVNKQVGNRIIRKRIHVRVEHVQPS 99 (158)
T ss_pred HhcCCCEEEEEecCCeecCCCcccccCCCeEEEeecCcEEEEEEEEeeCCeEeeEEEEeCHHHccCc
Confidence 4678999988743 37899999988766544444 44455555666664
No 56
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=58.78 E-value=27 Score=22.29 Aligned_cols=24 Identities=21% Similarity=0.333 Sum_probs=18.4
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~Vi 101 (135)
..++.||+|.|. |.+++.++.++.
T Consensus 47 ~~~~~Gd~v~v~----------v~~id~~~~~i~ 70 (72)
T cd05689 47 KVVSLGDEVEVM----------VLDIDEERRRIS 70 (72)
T ss_pred cEeCCCCEEEEE----------EEEeeCCcCEEe
Confidence 448999999994 777887776664
No 57
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=58.77 E-value=15 Score=35.14 Aligned_cols=33 Identities=27% Similarity=0.507 Sum_probs=24.4
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCE--EEEeccce
Q 032704 71 KAGDTVKVIAGCDKGKIGEITKVFRHNST--VMVKDINL 107 (135)
Q Consensus 71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~~--ViVegvN~ 107 (135)
++||+|.|. .-|+.|+|+++.. ++. |.+.++.+
T Consensus 626 ~~Gd~V~v~---~~~~~g~v~~i~~-~~~~~V~~g~~k~ 660 (771)
T TIGR01069 626 KIGDKVRIR---YFGQKGKIVQILG-GNKWNVTVGGMRM 660 (771)
T ss_pred CCCCEEEEc---cCCceEEEEEEcC-CCeEEEEECCEEE
Confidence 899999994 5788999999975 444 44445554
No 58
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=58.76 E-value=11 Score=28.61 Aligned_cols=59 Identities=15% Similarity=0.227 Sum_probs=29.5
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEc--------cCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFR--------HNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICY 132 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r--------~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~ 132 (135)
+++.||.|+|= |..|+|.+|.- ++..+++-+-.+.+.-+.--..+.++..+..+.+++|
T Consensus 60 pf~vGD~I~i~-----~~~G~V~~I~l~~t~l~~~~g~~v~IPNs~l~~~~i~N~s~~~~~~~~~v~~~v~~ 126 (206)
T PF00924_consen 60 PFKVGDRIEIG-----GVEGRVEEIGLRSTRLRTWDGEIVIIPNSKLISSPIVNYSRSSPYRRVVVEIPVDY 126 (206)
T ss_dssp SS-TT-EEESS-----S-EEEEEEE-SSEEEEEETTS-EEEEEHHHHHCS-EEETTT-SSEEEEEEEEEE-T
T ss_pred CccCCCEEEEE-----EeehHHHhcCcceeeeecCCCCEEEEEchheeeEEEEEeeccCCceeeeeeeeEec
Confidence 47999998875 88899988753 3335556655544332221111234555666665554
No 59
>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=58.52 E-value=29 Score=24.97 Aligned_cols=35 Identities=20% Similarity=0.239 Sum_probs=27.3
Q ss_pred eeeeCCEEEEEecC--CCCeEeEEEEEEccC-CEEEEe
Q 032704 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN-STVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI~Gk--dKGK~G~V~~V~r~~-~~ViVe 103 (135)
.++.||-|.|.+.. .+-.+|.|.++.... +...+.
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~ 40 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFF 40 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEE
Confidence 47999999999865 667799999999876 444444
No 60
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=57.81 E-value=21 Score=26.24 Aligned_cols=39 Identities=26% Similarity=0.280 Sum_probs=29.1
Q ss_pred eeeeCCEEEEEec----------CCCCeEeEEEEEEccCCEEEEeccce
Q 032704 69 HVKAGDTVKVIAG----------CDKGKIGEITKVFRHNSTVMVKDINL 107 (135)
Q Consensus 69 ~I~kGD~V~VI~G----------kdKGK~G~V~~V~r~~~~ViVegvN~ 107 (135)
.++.||.|-|.-- .+-|+.|+|..+..+---|+|..-|.
T Consensus 34 ~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~vg~k 82 (98)
T PRK04306 34 EFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVKDGGK 82 (98)
T ss_pred hccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEEECCc
Confidence 4678999987643 26799999999988877777644443
No 61
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=55.07 E-value=42 Score=21.08 Aligned_cols=33 Identities=27% Similarity=0.379 Sum_probs=22.8
Q ss_pred eeeeCCEEEEEecCCCC-eEeEEEEEEccCCEEEE
Q 032704 69 HVKAGDTVKVIAGCDKG-KIGEITKVFRHNSTVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKG-K~G~V~~V~r~~~~ViV 102 (135)
.+++||.|.+..=.+.+ -.|+|+++.. +++..|
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V 35 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLV 35 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC-CCEEEE
Confidence 47899999999743222 4588999988 334433
No 62
>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=54.81 E-value=15 Score=25.48 Aligned_cols=31 Identities=16% Similarity=0.210 Sum_probs=22.4
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
+..|+.||.|.|=-=++--..|.|+..+.++
T Consensus 36 ~iwI~~GD~V~Ve~~~~d~~kg~Iv~r~~~~ 66 (77)
T cd05793 36 RVWINEGDIVLVAPWDFQDDKADIIYKYTPD 66 (77)
T ss_pred cEEEcCCCEEEEEeccccCCEEEEEEEcCHH
Confidence 4569999999994444456788888777653
No 63
>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=53.31 E-value=33 Score=21.82 Aligned_cols=29 Identities=14% Similarity=0.075 Sum_probs=23.5
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCC
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNS 98 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~ 98 (135)
|..|++|.+..+...-..++|+++..+++
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~ 29 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNG 29 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTT
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCC
Confidence 46899999999888888999999988764
No 64
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=52.86 E-value=55 Score=21.04 Aligned_cols=25 Identities=24% Similarity=0.275 Sum_probs=18.0
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
-.++.||+|.|. |..++..+.++.+
T Consensus 56 ~~~~~gd~v~v~----------v~~vd~~~~~i~~ 80 (83)
T cd04471 56 KVFRLGDKVKVR----------VVRVDLDRRKIDF 80 (83)
T ss_pred CEEcCCCEEEEE----------EEEeccccCEEEE
Confidence 457899999984 6777766666554
No 65
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=51.98 E-value=19 Score=25.21 Aligned_cols=31 Identities=19% Similarity=0.192 Sum_probs=22.7
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
...|+.||.|.|=--++--..|.|+.++.++
T Consensus 41 ~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 71 (83)
T smart00652 41 KVWIRRGDIVLVDPWDFQDVKADIIYKYTKD 71 (83)
T ss_pred cEEEcCCCEEEEEecCCCCCEEEEEEEeCHH
Confidence 4559999999996555445778887777654
No 66
>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=51.96 E-value=23 Score=24.45 Aligned_cols=29 Identities=21% Similarity=0.307 Sum_probs=24.8
Q ss_pred eeeeCCEEEEEecC--CCCeEeEEEEEEccC
Q 032704 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (135)
Q Consensus 69 ~I~kGD~V~VI~Gk--dKGK~G~V~~V~r~~ 97 (135)
.++.||-|.|..+. ..-.+|.|.+|....
T Consensus 2 ~~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~ 32 (119)
T PF01426_consen 2 TYKVGDFVYVKPDDPPEPPYVARIEEIWEDK 32 (119)
T ss_dssp EEETTSEEEEECTSTTSEEEEEEEEEEEEET
T ss_pred EEeCCCEEEEeCCCCCCCCEEEEEEEEEcCC
Confidence 47899999999998 667899999998654
No 67
>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=51.41 E-value=21 Score=24.81 Aligned_cols=31 Identities=19% Similarity=0.238 Sum_probs=23.3
Q ss_pred cceeeeCCEEEEEecCC-CCeEeEEEEEEccC
Q 032704 67 KMHVKAGDTVKVIAGCD-KGKIGEITKVFRHN 97 (135)
Q Consensus 67 k~~I~kGD~V~VI~Gkd-KGK~G~V~~V~r~~ 97 (135)
..-|+.||.|.|--=++ .-..|.|+.++.++
T Consensus 36 ~iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~ 67 (78)
T cd04456 36 NIWIKRGDFLIVDPIEEGEDVKADIIFVYCKD 67 (78)
T ss_pred CEEEcCCCEEEEEecccCCCceEEEEEEeCHH
Confidence 35599999999976555 45778888777654
No 68
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=51.41 E-value=49 Score=27.80 Aligned_cols=39 Identities=15% Similarity=0.337 Sum_probs=27.6
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEE--------ccCCEEEEeccceeEEEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVF--------RHNSTVMVKDINLKTKHV 112 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~--------r~~~~ViVegvN~~kkhv 112 (135)
+++.||.|++ .|..|+|.+|. .++..|+|-+-.+.+..+
T Consensus 129 pf~vGD~I~i-----~~~~G~V~~I~~r~T~i~t~d~~~v~IPNs~~~~~~i 175 (286)
T PRK10334 129 PFRAGEYVDL-----GGVAGTVLSVQIFSTTMRTADGKIIVIPNGKIIAGNI 175 (286)
T ss_pred CCCCCCEEEE-----CCEEEEEEEEEeEEEEEEcCCCCEEEEcchHhcCCee
Confidence 4799999998 38899998885 344566676655544433
No 69
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=50.05 E-value=41 Score=25.00 Aligned_cols=41 Identities=29% Similarity=0.268 Sum_probs=30.7
Q ss_pred eeeeCCEEEEEec----------CCCCeEeEEEEEEccCCEEEEeccceeE
Q 032704 69 HVKAGDTVKVIAG----------CDKGKIGEITKVFRHNSTVMVKDINLKT 109 (135)
Q Consensus 69 ~I~kGD~V~VI~G----------kdKGK~G~V~~V~r~~~~ViVegvN~~k 109 (135)
.+..||.|-|.-- .+-|+.|+|.-+--+...|.|.+=|..+
T Consensus 32 ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k~K 82 (98)
T COG2139 32 EYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNKEK 82 (98)
T ss_pred hccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCceE
Confidence 4689999988653 3789999998877777777776655533
No 70
>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=49.95 E-value=46 Score=25.99 Aligned_cols=30 Identities=27% Similarity=0.369 Sum_probs=26.7
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
..++.||-|.|-++..+--+|+|.++....
T Consensus 28 ~~y~lGD~Vlv~s~~~~~yIgkI~~iwe~~ 57 (159)
T cd04715 28 VEYRLYDDVYVHNGDSEPYIGKIIKIYETA 57 (159)
T ss_pred EEEeCCCEEEEeCCCCCCEEEEEEEEEEcC
Confidence 348999999999999889999999999865
No 71
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=49.68 E-value=28 Score=24.50 Aligned_cols=30 Identities=20% Similarity=0.265 Sum_probs=22.9
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEc
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFR 95 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r 95 (135)
++..|.+||.|.|--=++--..|.|+--++
T Consensus 43 ~~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~ 72 (75)
T COG0361 43 NRIRILPGDVVLVELSPYDLTKGRIVYRYK 72 (75)
T ss_pred eeEEeCCCCEEEEEecccccccccEEEEec
Confidence 467799999999988877777777754443
No 72
>PTZ00189 60S ribosomal protein L21; Provisional
Probab=49.62 E-value=24 Score=28.18 Aligned_cols=47 Identities=28% Similarity=0.538 Sum_probs=32.2
Q ss_pred eeeeCCEEEEEe------c----CCCCeEeEEEEEEccC----------CEEEEeccceeEEEecCC
Q 032704 69 HVKAGDTVKVIA------G----CDKGKIGEITKVFRHN----------STVMVKDINLKTKHVKKR 115 (135)
Q Consensus 69 ~I~kGD~V~VI~------G----kdKGK~G~V~~V~r~~----------~~ViVegvN~~kkhvK~~ 115 (135)
.++.||.|-|.. | .+-|+.|+|..+..+- |+++.+-||+..-|+|++
T Consensus 33 ~yk~GD~VdIk~d~svqkGMPhk~YHGkTG~V~nv~~~A~gViV~k~vg~ki~~Kri~vr~EHlk~s 99 (160)
T PTZ00189 33 TFKVGDYVDIVVDSAVHKGMPYKYYHGRTGRVFNVTPRAVGVIVNKRVRGRIVRKRIHVRIEHVRKS 99 (160)
T ss_pred HccCCCEEEEEecCCeecCCCcccccCCCeEEEeecCeEEEEEEEEEECCEEeeeEEecCHhHcCCc
Confidence 467899998764 3 2679999998765544 444455566666677765
No 73
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=49.59 E-value=38 Score=29.03 Aligned_cols=32 Identities=31% Similarity=0.432 Sum_probs=23.8
Q ss_pred eCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 72 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 72 kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
.|.+..|++|.-||..|.|+-=.---+.|+|+
T Consensus 60 iGN~A~VvSG~AKG~~G~VtGkHGGieHVlV~ 91 (258)
T PF14505_consen 60 IGNEAKVVSGDAKGAKGVVTGKHGGIEHVLVD 91 (258)
T ss_dssp BT-EEEE-SSTTTT-EEEEEEEETTTTEEEEE
T ss_pred cCceeEEeecccCCCcCeEecccCCeeeEEEE
Confidence 69999999999999999998766555677664
No 74
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=48.87 E-value=37 Score=20.78 Aligned_cols=25 Identities=24% Similarity=0.372 Sum_probs=19.0
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
-.++.||+|++. |.+++.+++++.+
T Consensus 43 ~~~~~Gd~v~v~----------i~~vd~~~~~i~l 67 (68)
T cd05688 43 EVVNVGDEVEVK----------VLKIDKERKRISL 67 (68)
T ss_pred HEECCCCEEEEE----------EEEEECCCCEEec
Confidence 458999999984 7778877776653
No 75
>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=48.19 E-value=25 Score=28.73 Aligned_cols=39 Identities=26% Similarity=0.367 Sum_probs=23.8
Q ss_pred cceeeeCCEEEE-EecCCCCeEeEEEEEEc-----------cCCEEEEecc
Q 032704 67 KMHVKAGDTVKV-IAGCDKGKIGEITKVFR-----------HNSTVMVKDI 105 (135)
Q Consensus 67 k~~I~kGD~V~V-I~GkdKGK~G~V~~V~r-----------~~~~ViVegv 105 (135)
--.+++||.|.+ -.+..+-+.-+|++|.. ..++++|+|+
T Consensus 103 A~~V~~Gd~v~~~~~~~~~~~~~~V~~v~~~~~~G~yAPLT~~GtivVdgV 153 (217)
T PF01079_consen 103 ASDVRVGDCVLVSDEGGGKLRPSRVVRVSTVEKRGVYAPLTSHGTIVVDGV 153 (217)
T ss_dssp GGG--TT-EEEEE-TTT--EEEEEEEEEEEEEEEEEEEEEESSSEEEETTE
T ss_pred hhhCCCCCEEEEEEcCCCcEEEEEEEEEEEEEEeeEEcCccCcceEEECCE
Confidence 346899999999 45567777778877754 3556777776
No 76
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=47.98 E-value=32 Score=26.87 Aligned_cols=40 Identities=25% Similarity=0.353 Sum_probs=33.5
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccC------CEEEEeccceeE
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLKT 109 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~------~~ViVegvN~~k 109 (135)
+++|-.|.|++|.+.|+-..|++-.-+. +.++|+||....
T Consensus 5 lkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~ryP 50 (136)
T KOG3418|consen 5 LKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDRYP 50 (136)
T ss_pred ccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhhcc
Confidence 6789999999999999999998887765 378999987643
No 77
>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=47.98 E-value=35 Score=22.85 Aligned_cols=27 Identities=19% Similarity=0.388 Sum_probs=20.1
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
=.+++||+|.+.-. ++..+|.+|..++
T Consensus 25 G~i~~Gd~v~i~P~---~~~~~V~si~~~~ 51 (83)
T cd03698 25 GSIQKGDTLLVMPS---KESVEVKSIYVDD 51 (83)
T ss_pred eEEeCCCEEEEeCC---CcEEEEEEEEECC
Confidence 35889999998865 3567888877664
No 78
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=47.59 E-value=43 Score=22.60 Aligned_cols=30 Identities=20% Similarity=0.429 Sum_probs=23.0
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEE
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~V 100 (135)
=.+++||+|.++-. +...+|.+|..++..+
T Consensus 25 G~v~~Gd~v~~~P~---~~~~~V~si~~~~~~~ 54 (81)
T cd03695 25 GSIRVGDEVVVLPS---GKTSRVKSIETFDGEL 54 (81)
T ss_pred ceEECCCEEEEcCC---CCeEEEEEEEECCcEe
Confidence 35899999999865 5678888888776554
No 79
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=47.34 E-value=21 Score=34.37 Aligned_cols=34 Identities=32% Similarity=0.522 Sum_probs=27.5
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEec
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVeg 104 (135)
.-.++.||.|.+++ |..|.|++|....+.+.|+-
T Consensus 610 ~~~l~~gDev~~~t----~e~G~~~~i~a~~~e~~v~~ 643 (753)
T COG1193 610 KRKLKLGDEVEVIT----GEPGAVVKIIAGILEALVQS 643 (753)
T ss_pred ccCceecceeEeec----CCccceeeeeccCceeEEec
Confidence 55789999999999 67788888887777776663
No 80
>smart00439 BAH Bromo adjacent homology domain.
Probab=47.14 E-value=40 Score=23.17 Aligned_cols=29 Identities=28% Similarity=0.431 Sum_probs=24.0
Q ss_pred eeeCCEEEEEecC--CCCeEeEEEEEEccCC
Q 032704 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHNS 98 (135)
Q Consensus 70 I~kGD~V~VI~Gk--dKGK~G~V~~V~r~~~ 98 (135)
++.||.|.|.... ..=-+|.|.++....+
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~ 32 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRIEEIFETKK 32 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEEEEEEECCC
Confidence 6899999999886 3567999999988664
No 81
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=47.11 E-value=47 Score=20.98 Aligned_cols=26 Identities=15% Similarity=0.278 Sum_probs=20.5
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
-.++.||.|.+. |.+++.+++++.++
T Consensus 46 ~~~~~Gd~v~v~----------i~~vd~~~~~i~ls 71 (77)
T cd05708 46 KLFRVGDKVRAK----------VLKIDAEKKRISLG 71 (77)
T ss_pred HeecCCCEEEEE----------EEEEeCCCCEEEEE
Confidence 457999999984 78888888777655
No 82
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=46.50 E-value=39 Score=21.28 Aligned_cols=24 Identities=21% Similarity=0.440 Sum_probs=19.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
.++.||+|.+ +|++++++++++.+
T Consensus 44 ~~~~G~~i~v----------~v~~~d~~~~~i~l 67 (70)
T cd05698 44 HFRVGQVVKV----------KVLSCDPEQQRLLL 67 (70)
T ss_pred cccCCCEEEE----------EEEEEcCCCCEEEE
Confidence 4789999998 47788887777765
No 83
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=46.37 E-value=35 Score=27.54 Aligned_cols=37 Identities=22% Similarity=0.248 Sum_probs=25.4
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
.-++++.||.|.|..|...=-.++|..+.++.-.+.|
T Consensus 28 ~VlR~~~Gd~v~v~~g~g~~~~a~i~~~~~~~~~~~i 64 (240)
T TIGR00046 28 RVLRLKKGDKLKLLDGDGFIYHCEIKKISKKFVKCEL 64 (240)
T ss_pred HcccCCCCCEEEEEeCCCCEEEEEEEEEcCCeEEEEE
Confidence 3467899999999999533244678887766444433
No 84
>PRK11281 hypothetical protein; Provisional
Probab=45.99 E-value=50 Score=33.27 Aligned_cols=61 Identities=20% Similarity=0.281 Sum_probs=35.3
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEE--------ccCCEEEEeccceeEEEecCCCccCCceEEEEeeeeeE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVF--------RHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLICY 132 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~--------r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh~ 132 (135)
.-+++.||.|.| | |..|+|.+|. .++..|+|-+-.+.+..+.-......-..+..+.+|.|
T Consensus 936 eRPfrIGD~I~I--~---~~~G~V~~I~lRsT~Irt~D~~~ViIPNs~~~t~~IiN~S~~~~~~Rv~i~vgV~Y 1004 (1113)
T PRK11281 936 ERPVRIGDTVTI--G---TFSGTVSKIRIRATTITDFDRKEVIVPNKAFVTERLINWSLSDTVTRVVIKVGVAY 1004 (1113)
T ss_pred cCCcCCCCEEEE--C---CEEEEEEEEEeEEEEEEcCCCCEEEEechhhhcCceEeCCCCCcceEEEEEEEeCC
Confidence 345899999998 3 5788888875 34556777766655544331111111123555566655
No 85
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=45.95 E-value=36 Score=27.33 Aligned_cols=32 Identities=22% Similarity=0.435 Sum_probs=24.4
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
.-++++.||.|.|..|...=-.|+|+.+.++.
T Consensus 26 ~VlR~~~Gd~i~v~~g~g~~~~~~i~~i~~~~ 57 (234)
T PRK11713 26 RVLRLKEGDELRLFDGDGGEYLAEITEIGKKE 57 (234)
T ss_pred hhccCCCCCEEEEEeCCCCEEEEEEEEecCcE
Confidence 44678999999999997533457898887643
No 86
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=45.84 E-value=33 Score=21.69 Aligned_cols=24 Identities=25% Similarity=0.329 Sum_probs=19.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
.++.||.|++ +|++++++++++.+
T Consensus 44 ~~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (68)
T cd05707 44 RFKVGQLVKG----------KIVSIDPDNGRIEM 67 (68)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEec
Confidence 3799999998 57888888777754
No 87
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=45.81 E-value=35 Score=22.04 Aligned_cols=24 Identities=25% Similarity=0.234 Sum_probs=19.5
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
.++.||+|.+ +|+.+++++.+|.+
T Consensus 42 ~~~~G~~i~~----------kVi~id~~~~~i~L 65 (66)
T cd05695 42 TYKEGQKVRA----------RILYVDPSTKVVGL 65 (66)
T ss_pred CcCCCCEEEE----------EEEEEeCCCCEEec
Confidence 3789999987 68999998887654
No 88
>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=45.71 E-value=49 Score=24.76 Aligned_cols=30 Identities=13% Similarity=0.273 Sum_probs=24.7
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
..|+.||.|.|.+-..+=-+|.|.++..+.
T Consensus 6 ~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~ 35 (130)
T cd04721 6 VTISVHDFVYVLSEEEDRYVAYIEDLYEDK 35 (130)
T ss_pred EEEECCCEEEEeCCCCCcEEEEEEEEEEcC
Confidence 458999999999755555699999999875
No 89
>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=45.48 E-value=48 Score=24.20 Aligned_cols=34 Identities=15% Similarity=0.264 Sum_probs=26.0
Q ss_pred eeeeCCEEEEEecC--CCCeEeEEEEEEccC-CEEEE
Q 032704 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN-STVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI~Gk--dKGK~G~V~~V~r~~-~~ViV 102 (135)
.++.||-|.|.+.. ++--+|+|.++..+. +...+
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~ 39 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVV 39 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEE
Confidence 47899999999865 456799999998865 33444
No 90
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=45.23 E-value=47 Score=21.06 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=20.1
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
.++.||++.+ +|++++++++++.+
T Consensus 44 ~~~~Gd~i~~----------~V~~id~~~~~i~l 67 (69)
T cd05697 44 KFKPGLKVKC----------RVLSVEPERKRLVL 67 (69)
T ss_pred cCCCCCEEEE----------EEEEEECCCCEEEE
Confidence 4799999998 58889998888765
No 91
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=44.99 E-value=36 Score=22.69 Aligned_cols=28 Identities=21% Similarity=0.336 Sum_probs=21.4
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNST 99 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ 99 (135)
.+++||+|.+.-+. ..++|.+|..++..
T Consensus 26 ~i~~g~~v~~~p~~---~~~~V~sI~~~~~~ 53 (83)
T cd03696 26 SVKVGDKVEILPLG---EETRVRSIQVHGKD 53 (83)
T ss_pred EEeCCCEEEECCCC---ceEEEEEEEECCcC
Confidence 58899999988754 67888888766543
No 92
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=44.67 E-value=57 Score=32.92 Aligned_cols=38 Identities=24% Similarity=0.448 Sum_probs=27.3
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEc--------cCCEEEEeccceeE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFR--------HNSTVMVKDINLKT 109 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r--------~~~~ViVegvN~~k 109 (135)
.-+++.||.|.| .|..|+|.+|.- ++..|+|-+-.+.+
T Consensus 933 erPfrVGD~I~I-----~~~~GtV~~I~lRsT~Irt~Dg~~IiIPNs~~it 978 (1109)
T PRK10929 933 EKPIRIGDTVTI-----RDLTGSVTKINTRATTISDWDRKEIIVPNKAFIT 978 (1109)
T ss_pred hCCCCCCCEEEE-----CCEEEEEEEEeeeEEEEEeCCCCEEEEEChhhhc
Confidence 345899999997 368899988864 55567777665544
No 93
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. The crystal structure of the SH3 domain of the cytoskeletal protein spectrin, and the solution structures of SH3 domains of phospholipase C (PLC-y) and phosphatidylinositol 3-kinase p85 alpha-subunit, have been determined [, , ]. In spite of relatively limited sequence similarity, their overall structures are similar. The domains belong to the alpha+beta structural class, with 5 to 8 beta-strands forming 2 tightly-packed, anti-parallel beta-sheets arranged in a barrel-like structure, and intervening loops sometimes forming helices. Conserved aliphatic and aromatic residues form a hydrophobic core (A11, L23, A29, V34, W42, L52 and V59 in PLC-y []) and a hydrophobic pocket on the molecular surface (L12, F13, W53 and P55 in PLC-y). The conserved core is believed to stabilise the fold, while the pocket is thought to serve as a binding site for target proteins. Conserved carboxylic amino acids located in the loops, on the periphery of the pocket (D14 and E22), may be involved in protein-protein interactions via proline-rich regions. The N- and C-termini are packed in close proximity, indicating that they are independent structural modules.; GO: 0005515 protein binding; PDB: 1UHF_A 1W1F_A 1WA7_A 1SEM_A 1KFZ_A 2SEM_B 1K76_A 3SEM_B 1X2Q_A 2J06_B ....
Probab=44.22 E-value=31 Score=20.77 Aligned_cols=17 Identities=24% Similarity=0.536 Sum_probs=12.7
Q ss_pred ccceeeeCCEEEEEecC
Q 032704 66 HKMHVKAGDTVKVIAGC 82 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~Gk 82 (135)
..+.+++||.+.|+.=.
T Consensus 12 ~eLs~~~Gd~i~v~~~~ 28 (48)
T PF00018_consen 12 DELSFKKGDIIEVLEKS 28 (48)
T ss_dssp TBSEB-TTEEEEEEEES
T ss_pred CEEeEECCCEEEEEEec
Confidence 45678999999998744
No 94
>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=44.18 E-value=31 Score=22.73 Aligned_cols=27 Identities=26% Similarity=0.255 Sum_probs=17.7
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEE
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITK 92 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~ 92 (135)
.+..|+.||.|.|---.+--..|.|+.
T Consensus 38 ~~iwI~~GD~V~V~~~~~d~~kG~Ii~ 64 (65)
T PF01176_consen 38 KRIWIKRGDFVLVEPSPYDKVKGRIIY 64 (65)
T ss_dssp TCC---TTEEEEEEESTTCTTEEEEEE
T ss_pred eeEecCCCCEEEEEecccCCCeEEEEE
Confidence 455699999999986665577777753
No 95
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=43.73 E-value=18 Score=26.34 Aligned_cols=32 Identities=16% Similarity=0.226 Sum_probs=19.5
Q ss_pred ccceeeeCCEEEEEecC-CCCeEeEEEEEEccC
Q 032704 66 HKMHVKAGDTVKVIAGC-DKGKIGEITKVFRHN 97 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~Gk-dKGK~G~V~~V~r~~ 97 (135)
.+..|+.||.|.|--=. .....|.|+..+..+
T Consensus 54 k~iwI~~GD~VlVsp~d~~~~~kg~Iv~r~~~~ 86 (99)
T TIGR00523 54 KRIWIREGDVVIVKPWEFQGDDKCDIVWRYTKT 86 (99)
T ss_pred ccEEecCCCEEEEEEccCCCCccEEEEEEcCHH
Confidence 45679999999992101 112248887776543
No 96
>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=43.62 E-value=46 Score=20.99 Aligned_cols=29 Identities=21% Similarity=0.302 Sum_probs=19.8
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEE
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~V 100 (135)
+..||.|.+-. .+ +..+.|.+|.+.++.+
T Consensus 38 ~~VGD~V~~~~-~~-~~~~~I~~vl~R~s~l 66 (68)
T cd04466 38 PAVGDRVEFEP-ED-DGEGVIEEILPRKNLL 66 (68)
T ss_pred CCCCcEEEEEE-CC-CCcEEEEEEeccceEE
Confidence 58999998732 22 2347788888877644
No 97
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in S. cerevisiae Rrp5 and 14 S1 repeats in H. sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=42.83 E-value=44 Score=22.10 Aligned_cols=26 Identities=19% Similarity=0.359 Sum_probs=19.9
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
.-.++.||+|.| +|.+++.+++++.+
T Consensus 56 ~~~~~~Gd~v~v----------kV~~id~~~~~i~l 81 (83)
T cd04461 56 SFGFKKGQSVTA----------KVTSVDEEKQRFLL 81 (83)
T ss_pred HHhcCCCCEEEE----------EEEEEcCCCCEEEE
Confidence 345899999998 47778877777765
No 98
>cd04090 eEF2_II_snRNP Loc2 eEF2_C_snRNP, cd01514/C terminal domain:eEF2_C_snRNP: This family includes C-terminal portion of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart Snu114p. This domain is homologous to domain II of the eukaryotic translational elongation factor EF-2. Yeast Snu114p is essential for cell viability and for splicing in vivo. U5-116 kD binds GTP. Experiments suggest that GTP binding and probably GTP hydrolysis is important for the function of the U5-116 kD/Snu114p. In complex with GTP, EF-2 promotes the translocation step of translation. During translocation the peptidyl-tRNA is moved from the A site to the P site, the uncharged tRNA from the P site to the E-site and, the mRNA is shifted one codon relative to the ribosome.
Probab=42.05 E-value=95 Score=21.25 Aligned_cols=28 Identities=25% Similarity=0.367 Sum_probs=17.2
Q ss_pred ceeeeCCEEEEEecC------CCCeEeEEEEEEc
Q 032704 68 MHVKAGDTVKVIAGC------DKGKIGEITKVFR 95 (135)
Q Consensus 68 ~~I~kGD~V~VI~Gk------dKGK~G~V~~V~r 95 (135)
=.|++||+|.++.-+ +..+..+|.+++.
T Consensus 26 Gtl~~g~~v~~~~~~~~~~~~~~~~~~~i~~l~~ 59 (94)
T cd04090 26 GTIKKGQKVKVLGENYSLDDEEDMTICTIGRLWI 59 (94)
T ss_pred CeEcCCCEEEEECCCCCCccCCcEEEEEEeEEEE
Confidence 358899999887543 2233455555553
No 99
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=41.65 E-value=38 Score=23.16 Aligned_cols=30 Identities=27% Similarity=0.337 Sum_probs=21.9
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNST 99 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ 99 (135)
.=.|++||+|.++-. +...+|.+|..++..
T Consensus 28 ~G~i~~gd~v~i~P~---~~~~~V~sI~~~~~~ 57 (91)
T cd03693 28 TGVLKPGMVVTFAPA---GVTGEVKSVEMHHEP 57 (91)
T ss_pred cceeecCCEEEECCC---CcEEEEEEEEECCcC
Confidence 345789999888865 367888888766543
No 100
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=41.50 E-value=70 Score=22.52 Aligned_cols=37 Identities=19% Similarity=0.300 Sum_probs=33.4
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccce
Q 032704 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINL 107 (135)
Q Consensus 71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN~ 107 (135)
.-|.++-+|+=.|.--+|..-.|+.++++|.+++|-.
T Consensus 4 ~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~ 40 (74)
T cd01736 4 YIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRS 40 (74)
T ss_pred ccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEe
Confidence 4689999999999999999999999999999998543
No 101
>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=41.41 E-value=44 Score=25.32 Aligned_cols=31 Identities=16% Similarity=0.356 Sum_probs=26.0
Q ss_pred ceeeeCCEEEEEecC-CCCeEeEEEEEEccCC
Q 032704 68 MHVKAGDTVKVIAGC-DKGKIGEITKVFRHNS 98 (135)
Q Consensus 68 ~~I~kGD~V~VI~Gk-dKGK~G~V~~V~r~~~ 98 (135)
..|++||-|.|.... +.--+|+|.+++...+
T Consensus 2 ~~i~vGd~VlI~~~d~~~~yVAkI~~i~e~~~ 33 (128)
T cd04719 2 LTIEVGDFVLIEGEDADGPDVARILHLYEDGN 33 (128)
T ss_pred eEEecCCEEEEECCCCCCCcEeeehhhhcccc
Confidence 368999999999887 7778999999888753
No 102
>COG1162 Predicted GTPases [General function prediction only]
Probab=41.35 E-value=39 Score=29.31 Aligned_cols=30 Identities=20% Similarity=0.339 Sum_probs=25.6
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEE
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~V 100 (135)
....+||+|.+-.+... |.|.+|...+|..
T Consensus 43 ~~~vVGD~V~~~~~~~~---g~I~~i~~Rkn~L 72 (301)
T COG1162 43 LKPVVGDRVVFEDENNN---GVIEKILPRKNVL 72 (301)
T ss_pred ccccccCeEEEecCCCc---ceEEEEecccCce
Confidence 44689999999999876 9999999988764
No 103
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=41.15 E-value=53 Score=19.29 Aligned_cols=24 Identities=25% Similarity=0.333 Sum_probs=17.2
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~Vi 101 (135)
-.++.||+|.+ +|.+++++++.+.
T Consensus 40 ~~~~~G~~v~~----------~v~~~d~~~~~i~ 63 (65)
T cd00164 40 EVFKVGDEVEV----------KVLEVDPEKGRIS 63 (65)
T ss_pred hEeCCCCEEEE----------EEEEEcCCcCEEe
Confidence 34899999987 4677777666554
No 104
>cd05703 S1_Rrp5_repeat_hs12_sc9 S1_Rrp5_repeat_hs12_sc9: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 12 (hs12) and S. cerevisiae S1 repeat 9 (sc9). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=40.90 E-value=50 Score=21.76 Aligned_cols=25 Identities=12% Similarity=0.264 Sum_probs=20.5
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
.++.||.|++ +|+.|++++.+|.+.
T Consensus 46 ~~~vG~~v~~----------kV~~id~~~~~i~Ls 70 (73)
T cd05703 46 KFPIGQALKA----------KVVGVDKEHKLLRLS 70 (73)
T ss_pred hCCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 4799999975 599999999888764
No 105
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=40.39 E-value=52 Score=20.50 Aligned_cols=23 Identities=13% Similarity=0.238 Sum_probs=18.5
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~Vi 101 (135)
.++.||+|.|. |.+|+.++.++.
T Consensus 45 ~~~~G~~v~v~----------v~~id~~~~~i~ 67 (69)
T cd05690 45 IYKKGQEVEAV----------VLNIDVERERIS 67 (69)
T ss_pred EECCCCEEEEE----------EEEEECCcCEEe
Confidence 47999999984 788888877764
No 106
>PF00575 S1: S1 RNA binding domain; InterPro: IPR003029 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S1 domain was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site []. The structure of the S1 domain is very similar to that of cold shock proteins. This suggests that they may both be derived from an ancient nucleic acid-binding protein []. More information about these proteins can be found at Protein of the Month: RNA Exosomes []. This entry does not include translation initiation factor IF-1 S1 domains.; GO: 0003723 RNA binding; PDB: 3L7Z_F 2JE6_I 2JEA_I 2JEB_I 1E3P_A 2Y0S_E 1WI5_A 2BH8_A 2CQO_A 2EQS_A ....
Probab=40.32 E-value=66 Score=20.39 Aligned_cols=25 Identities=28% Similarity=0.356 Sum_probs=21.1
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
-.++.||+|.+. |++++++++++.+
T Consensus 47 ~~~~~G~~v~v~----------v~~vd~~~~~i~l 71 (74)
T PF00575_consen 47 EVYKIGQTVRVK----------VIKVDKEKGRIRL 71 (74)
T ss_dssp GTCETTCEEEEE----------EEEEETTTTEEEE
T ss_pred cccCCCCEEEEE----------EEEEECCCCeEEE
Confidence 358999999885 8999999998876
No 107
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=39.30 E-value=72 Score=20.23 Aligned_cols=24 Identities=21% Similarity=0.242 Sum_probs=17.7
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
.++.||.|.+. |.+++..++++.+
T Consensus 49 ~~~~Gd~v~vk----------v~~~d~~~~~i~l 72 (76)
T cd04452 49 LVKVGRKEVVK----------VIRVDKEKGYIDL 72 (76)
T ss_pred eeCCCCEEEEE----------EEEEECCCCEEEE
Confidence 37999999983 6777776666554
No 108
>cd04089 eRF3_II eRF3_II: 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 is a non-pathogenic prion-li
Probab=38.83 E-value=55 Score=21.89 Aligned_cols=27 Identities=19% Similarity=0.374 Sum_probs=19.1
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
=.+++||+|.+.-. |+..+|.+|..++
T Consensus 24 G~i~~G~~v~i~P~---~~~~~V~si~~~~ 50 (82)
T cd04089 24 GTIKKGDKLLVMPN---KTQVEVLSIYNED 50 (82)
T ss_pred eEEecCCEEEEeCC---CcEEEEEEEEECC
Confidence 35789999888754 4567777776554
No 109
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=38.83 E-value=46 Score=31.27 Aligned_cols=34 Identities=29% Similarity=0.445 Sum_probs=28.9
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEec
Q 032704 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104 (135)
Q Consensus 71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVeg 104 (135)
.-|-+|.|-+|.+||.-|.|..|++..-+|-+--
T Consensus 353 aigktVrIr~g~yKG~lGVVKdv~~~~arVeLhs 386 (607)
T COG5164 353 AIGKTVRIRCGEYKGHLGVVKDVDRNIARVELHS 386 (607)
T ss_pred ccCceEEEeecccccccceeeeccCceEEEEEec
Confidence 5678999999999999999999998876665543
No 110
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=38.56 E-value=87 Score=18.65 Aligned_cols=25 Identities=28% Similarity=0.476 Sum_probs=19.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
.++.||+|.+ .|.+++.+++++.+.
T Consensus 46 ~~~~G~~v~~----------~V~~~~~~~~~i~ls 70 (72)
T smart00316 46 VLKVGDEVKV----------KVLSVDEEKGRIILS 70 (72)
T ss_pred eecCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 4899999988 477788777776653
No 111
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=38.20 E-value=69 Score=20.38 Aligned_cols=23 Identities=22% Similarity=0.241 Sum_probs=18.0
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
++.||+|.+ +|++++++++++.+
T Consensus 48 ~~~Gd~v~~----------~V~~~d~~~~~i~l 70 (73)
T cd05706 48 FKKNDIVRA----------CVLSVDVPNKKIAL 70 (73)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 689999987 47778887777655
No 112
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=38.04 E-value=16 Score=33.46 Aligned_cols=35 Identities=26% Similarity=0.345 Sum_probs=30.2
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEec
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVeg 104 (135)
=+-||+|.|++|+.+|+.|--++=++.+.+..|..
T Consensus 394 r~~Ge~vmvv~gkhkg~~g~llskd~~Ke~~~v~~ 428 (455)
T KOG4315|consen 394 RRGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVRL 428 (455)
T ss_pred cccCceeEEEecccccchhhhhhhhhhhhhcceec
Confidence 47899999999999999999988888877776654
No 113
>cd05696 S1_Rrp5_repeat_hs4 S1_Rrp5_repeat_hs4: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 4 (hs4). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=37.84 E-value=65 Score=21.00 Aligned_cols=24 Identities=25% Similarity=0.217 Sum_probs=19.3
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
+++.||.|.+ +|+.+++++.++.+
T Consensus 46 ~~~vG~~v~~----------kV~~id~~~~~i~l 69 (71)
T cd05696 46 PFKAGTTHKA----------RIIGYSPMDGLLQL 69 (71)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 4799999976 48889988887765
No 114
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism [, ]. The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands [, ]. Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigenes putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2LRJ_A 2VPM_B 2VOB_B 2VPS_A 2K3A_A 2IO9_A 2IO8_A 2IOB_A 2IOA_B 2IO7_B ....
Probab=37.16 E-value=51 Score=23.35 Aligned_cols=37 Identities=24% Similarity=0.286 Sum_probs=24.9
Q ss_pred eeeeCCEEEE--EecCCCCeEeEEEEEEccCCEEEEeccc
Q 032704 69 HVKAGDTVKV--IAGCDKGKIGEITKVFRHNSTVMVKDIN 106 (135)
Q Consensus 69 ~I~kGD~V~V--I~GkdKGK~G~V~~V~r~~~~ViVegvN 106 (135)
..++||.|.. -.+..-|-+|.|++|.. ++.|.+-+-|
T Consensus 62 ~P~~Gdivv~~~~~~~~~GHVaIV~~v~~-~~~i~v~e~N 100 (124)
T PF05257_consen 62 TPQPGDIVVWDSGSGGGYGHVAIVESVND-GGTITVIEQN 100 (124)
T ss_dssp ---TTEEEEEEECTTTTT-EEEEEEEE-T-TSEEEEEECS
T ss_pred ccccceEEEeccCCCCCCCeEEEEEEECC-CCEEEEEECC
Confidence 3489999887 35568899999999944 4677766666
No 115
>CHL00010 infA translation initiation factor 1
Probab=37.09 E-value=82 Score=21.61 Aligned_cols=29 Identities=28% Similarity=0.282 Sum_probs=17.8
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~ 96 (135)
..+..||.|.|--=.+-...|.|+.=++.
T Consensus 45 i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 45 IRILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred cccCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 44689999999743333445677544433
No 116
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=36.91 E-value=42 Score=24.52 Aligned_cols=31 Identities=19% Similarity=0.257 Sum_probs=21.7
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~ 96 (135)
.+..|+.||.|.|--=++--..|.|+..+..
T Consensus 56 k~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 86 (100)
T PRK04012 56 KRMWIREGDVVIVAPWDFQDEKADIIWRYTK 86 (100)
T ss_pred ccEEecCCCEEEEEecccCCCEEEEEEEcCH
Confidence 3566999999999654433556888777754
No 117
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=36.90 E-value=63 Score=19.58 Aligned_cols=22 Identities=23% Similarity=0.371 Sum_probs=16.9
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~Vi 101 (135)
++.||.|.+. |.+++..+.++.
T Consensus 45 ~~~Gd~v~v~----------i~~vd~~~~~i~ 66 (68)
T cd05685 45 VSVGDIVEVK----------VISIDEERGRIS 66 (68)
T ss_pred cCCCCEEEEE----------EEEEECCCCEEe
Confidence 7899999984 777777766664
No 118
>cd03694 GTPBP_II Domain II of the GP-1 family of GTPase. This group includes proteins similar to GTPBP1 and GTPBP2. GTPB1 is structurally, related to elongation factor 1 alpha, a key component of protein biosynthesis machinery. Immunohistochemical analyses on mouse tissues revealed that GTPBP1 is expressed in some neurons and smooth muscle cells of various organs as well as macrophages. Immunofluorescence analyses revealed that GTPBP1 is localized exclusively in cytoplasm and shows a diffuse granular network forming a gradient from the nucleus to the periphery of the cells in smooth muscle cell lines and macrophages. No significant difference was observed in the immune response to protein antigen between mutant mice and wild-type mice, suggesting normal function of antigen-presenting cells of the mutant mice. The absence of an eminent phenotype in GTPBP1-deficient mice may be due to functional compensation by GTPBP2, which is similar to GTPBP1 in structure and tissue distribution.
Probab=36.77 E-value=57 Score=22.16 Aligned_cols=33 Identities=21% Similarity=0.226 Sum_probs=22.5
Q ss_pred cceeeeCCEEEEEecCC-CCeEeEEEEEEccCCE
Q 032704 67 KMHVKAGDTVKVIAGCD-KGKIGEITKVFRHNST 99 (135)
Q Consensus 67 k~~I~kGD~V~VI~Gkd-KGK~G~V~~V~r~~~~ 99 (135)
.=.+++||+|.+.-..+ +.+..+|.+|..++..
T Consensus 24 ~G~v~~g~~v~~~P~~~g~~~~~~V~sI~~~~~~ 57 (87)
T cd03694 24 KGVIRLGDTLLLGPDQDGSFRPVTVKSIHRNRSP 57 (87)
T ss_pred cCEEeCCCEEEECCCCCCCEeEEEEEEEEECCeE
Confidence 34589999998765432 2368888888766543
No 119
>PF02211 NHase_beta: Nitrile hydratase beta subunit; InterPro: IPR024690 Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit []. This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.; GO: 0018822 nitrile hydratase activity; PDB: 2DXB_H 2DD5_K 2DD4_H 2ZZD_B 2DXC_H 1AHJ_F 2ZPE_B 2ZCF_B 2D0Q_B 2CZ7_B ....
Probab=36.62 E-value=31 Score=28.49 Aligned_cols=29 Identities=31% Similarity=0.374 Sum_probs=16.8
Q ss_pred ccceeeeCCEEEEEecC----------CCCeEeEEEEEE
Q 032704 66 HKMHVKAGDTVKVIAGC----------DKGKIGEITKVF 94 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~Gk----------dKGK~G~V~~V~ 94 (135)
..-.+.+||+|.|..-. -+||+|+|..+.
T Consensus 131 ~~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~~ 169 (222)
T PF02211_consen 131 APPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERVH 169 (222)
T ss_dssp SS-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEEE
T ss_pred CCCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEEe
Confidence 44568999999998643 589999998554
No 120
>PF02941 FeThRed_A: Ferredoxin thioredoxin reductase variable alpha chain; InterPro: IPR004207 Ferredoxin thioredoxin reductase is a [4FE-4S] protein which plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit a and subunit b. Subunit a is the variable subunit, and b is the catalytic chain. This family is the alpha chain.; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0015979 photosynthesis, 0009536 plastid; PDB: 2PUK_B 2PVO_B 2PVG_B 1DJ7_B 2PVD_B 2PU9_B 2PUO_B.
Probab=36.20 E-value=43 Score=23.32 Aligned_cols=25 Identities=36% Similarity=0.510 Sum_probs=14.2
Q ss_pred eCCEEEEEe-----------c---CCCCeEeEEEEEEcc
Q 032704 72 AGDTVKVIA-----------G---CDKGKIGEITKVFRH 96 (135)
Q Consensus 72 kGD~V~VI~-----------G---kdKGK~G~V~~V~r~ 96 (135)
.||+|.|.+ + .-+|.+|+|.++..+
T Consensus 1 vGdrVrV~~sv~Vyh~P~hr~~~fDl~G~EGev~~~v~~ 39 (67)
T PF02941_consen 1 VGDRVRVKASVVVYHHPEHRNPPFDLKGMEGEVKQIVTD 39 (67)
T ss_dssp TT-EEEE-S--EES--TTSTTS-EE-TT-EEEEEEE-SE
T ss_pred CCCeEEEeeeEEEEeCCcccCCCccccCCEEEEEEEEee
Confidence 377777764 2 257999999988754
No 121
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=36.18 E-value=36 Score=19.48 Aligned_cols=17 Identities=24% Similarity=0.536 Sum_probs=13.4
Q ss_pred ccceeeeCCEEEEEecC
Q 032704 66 HKMHVKAGDTVKVIAGC 82 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~Gk 82 (135)
..+.+.+||.|.|+...
T Consensus 14 ~~l~~~~Gd~v~v~~~~ 30 (54)
T cd00174 14 DELSFKKGDIIEVLEKS 30 (54)
T ss_pred CCCCCCCCCEEEEEEcC
Confidence 34568999999999773
No 122
>PLN02661 Putative thiazole synthesis
Probab=35.91 E-value=23 Score=31.15 Aligned_cols=17 Identities=47% Similarity=0.563 Sum_probs=12.7
Q ss_pred ccccccCcccCCCCCCC
Q 032704 17 SSNSFFGQRLSFPSLSP 33 (135)
Q Consensus 17 ~~~~f~g~~l~~~~~~~ 33 (135)
|++||.|.||.+...+|
T Consensus 25 ~~~~~~~~~~~~~~~~~ 41 (357)
T PLN02661 25 SSSSFAGVRLVTSVRAP 41 (357)
T ss_pred ccccccCccccccccCC
Confidence 56999999997644444
No 123
>cd03697 EFTU_II EFTU_II: Elongation factor Tu domain II. Elongation factors Tu (EF-Tu) are three-domain GTPases with an essential function in the elongation phase of mRNA translation. The GTPase center of EF-Tu is in the N-terminal domain (domain I), also known as the catalytic or G-domain. The G-domain is composed of about 200 amino acid residues, arranged into a predominantly parallel six-stranded beta-sheet core surrounded by seven a-helices. Non-catalytic domains II and III are beta-barrels of seven and six, respectively, antiparallel beta-strands that share an extended interface. Either non-catalytic domain is composed of about 100 amino acid residues. EF-Tu proteins exist in two principal conformations: in a compact one, EF-Tu*GTP, with tight interfaces between all three domains and a high affinity for aminoacyl-tRNA, and in an open one, EF-Tu*GDP, with essentially no G-domain-domain II interactions and a low affinity for aminoacyl-tRNA. EF-Tu has approximately a 100-fold higher
Probab=35.83 E-value=51 Score=22.32 Aligned_cols=31 Identities=19% Similarity=0.189 Sum_probs=21.8
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEccCCE
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNST 99 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ 99 (135)
=.+++||+|.++-.. .+...+|.+|..+...
T Consensus 25 G~v~~gd~v~~~p~~-~~~~~~V~si~~~~~~ 55 (87)
T cd03697 25 GTIKVGDEVEIVGFG-ETLKTTVTGIEMFRKT 55 (87)
T ss_pred CCCccCCEEEEeCCC-CCceEEEEEEEECCcC
Confidence 357899999987642 2567888888766543
No 124
>CHL00084 rpl19 ribosomal protein L19
Probab=35.74 E-value=1.7e+02 Score=22.10 Aligned_cols=28 Identities=29% Similarity=0.266 Sum_probs=18.8
Q ss_pred eeeeCCEEEEEe---cCCC----CeEeEEEEEEcc
Q 032704 69 HVKAGDTVKVIA---GCDK----GKIGEITKVFRH 96 (135)
Q Consensus 69 ~I~kGD~V~VI~---GkdK----GK~G~V~~V~r~ 96 (135)
.+++||+|.|-. ..+| --+|.|.++...
T Consensus 22 ~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~ 56 (117)
T CHL00084 22 KIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNS 56 (117)
T ss_pred ccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCC
Confidence 389999999854 2222 357888887543
No 125
>KOG3482 consensus Small nuclear ribonucleoprotein (snRNP) SMF [RNA processing and modification]
Probab=35.73 E-value=28 Score=24.90 Aligned_cols=58 Identities=28% Similarity=0.578 Sum_probs=41.8
Q ss_pred eeeeeeeeeeeeecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEecc
Q 032704 44 LIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (135)
Q Consensus 44 ~~~~~~k~wer~~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegv 105 (135)
++..++| |- .+|+---.-.-..+++.-+..=..+.|...|..|+| ..|=+|-.+|.|+
T Consensus 20 ~V~vkLK-wg-~eYkG~LvsvD~YmNlqL~~~eE~idG~~~g~lGEi--lIRCNNvlyi~gv 77 (79)
T KOG3482|consen 20 PVLVKLK-WG-QEYKGTLVSVDNYMNLQLANAEEYIDGVSTGNLGEI--LIRCNNVLYIRGV 77 (79)
T ss_pred eEEEEEe-cC-cEEEEEEEEecchhheehhhhhhhhcccccccceeE--EEEeccEEEEecC
Confidence 3556666 84 677644333335678888888889999999999999 4566777777664
No 126
>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=35.22 E-value=90 Score=21.90 Aligned_cols=31 Identities=26% Similarity=0.313 Sum_probs=22.9
Q ss_pred cceeeeCCEEEEEecCCCC-eEeEEEEEEccC
Q 032704 67 KMHVKAGDTVKVIAGCDKG-KIGEITKVFRHN 97 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKG-K~G~V~~V~r~~ 97 (135)
..=|+.||-|.|-.-.+-. -.|+|..++.+.
T Consensus 36 ~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~~ 67 (78)
T cd05792 36 NIWIKRGDFVLVEPIEEGDKVKAEIVKILTRD 67 (78)
T ss_pred cEEEEeCCEEEEEecccCCceEEEEEEEECHH
Confidence 3349999999997655443 488898888764
No 127
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=35.22 E-value=58 Score=20.95 Aligned_cols=21 Identities=33% Similarity=0.289 Sum_probs=13.4
Q ss_pred eeeCCEEEEEecCCCCeEeEE
Q 032704 70 VKAGDTVKVIAGCDKGKIGEI 90 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V 90 (135)
+..||.|.+--..+.+..|.|
T Consensus 41 ~~vGD~V~~~~~~~~~~~g~I 61 (64)
T cd04451 41 ILPGDRVKVELSPYDLTKGRI 61 (64)
T ss_pred cCCCCEEEEEEeecCCCEEEE
Confidence 689999988744322334555
No 128
>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=34.82 E-value=86 Score=23.38 Aligned_cols=27 Identities=30% Similarity=0.364 Sum_probs=23.1
Q ss_pred eeeCCEEEEEecC-CCCeEeEEEEEEcc
Q 032704 70 VKAGDTVKVIAGC-DKGKIGEITKVFRH 96 (135)
Q Consensus 70 I~kGD~V~VI~Gk-dKGK~G~V~~V~r~ 96 (135)
++.||-|.|.++. ..--+|+|.++...
T Consensus 4 ~~lgD~V~v~~~~~~~~yi~rI~~i~e~ 31 (122)
T cd04716 4 YNLGDDAYVQGGEGEEPFICKITEFFEG 31 (122)
T ss_pred EEcCCEEEEECCCCCCCEEEEEEEEEEc
Confidence 6889999999986 55679999999975
No 129
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=34.78 E-value=86 Score=25.86 Aligned_cols=30 Identities=23% Similarity=0.252 Sum_probs=22.7
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~V 100 (135)
.+.+||.|.+-.-. +..|.|.+|.+.+|.+
T Consensus 34 ~~~vGD~V~~~~~~--~~~~~i~~i~~R~~~l 63 (287)
T cd01854 34 KPVVGDWVEVEPDD--DGEGVIVRVLPRKNLL 63 (287)
T ss_pred CccCCCEEEEEecC--CCcEEEEEEECCCceE
Confidence 36899999885322 4578999999887754
No 130
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=34.76 E-value=50 Score=27.29 Aligned_cols=48 Identities=17% Similarity=0.223 Sum_probs=37.3
Q ss_pred ecCCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEec
Q 032704 56 ECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104 (135)
Q Consensus 56 ~~k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVeg 104 (135)
+.++...|...-..+.+||.|+|-.|+. .+-.+|++|.+++-+|.+++
T Consensus 148 ~~~~~~~~~~~~s~l~~g~~~kVk~G~~-a~~AtvlEv~Kd~vRVqL~~ 195 (208)
T COG3109 148 PREEVHTPVSDISALTVGQALKVKAGQN-AMDATVLEITKDGVRVQLNS 195 (208)
T ss_pred CCCCccccHHHHHhhhccceeeeccccc-cccceEEEEeccceEEeecC
Confidence 3345556666667789999999999974 45678999999988887764
No 131
>PF06701 MIB_HERC2: Mib_herc2; InterPro: IPR010606 Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in []and usually the protein also contains an E3 ligase domain (either Ring or Hect).; GO: 0004842 ubiquitin-protein ligase activity, 0046872 metal ion binding, 0016567 protein ubiquitination; PDB: 2DK3_A 3DKM_A.
Probab=34.75 E-value=52 Score=22.55 Aligned_cols=20 Identities=20% Similarity=0.469 Sum_probs=11.2
Q ss_pred CCeEeEEEEE-----EccCCEEEEe
Q 032704 84 KGKIGEITKV-----FRHNSTVMVK 103 (135)
Q Consensus 84 KGK~G~V~~V-----~r~~~~ViVe 103 (135)
.|..|+|++| ...++.|.|.
T Consensus 19 ~g~~GtV~~i~~~~~~~~~~~v~V~ 43 (68)
T PF06701_consen 19 EGHVGTVVSIRDWSSESPDGWVVVQ 43 (68)
T ss_dssp TT--EEE-S--------BTTEEEEE
T ss_pred CCcceEEEecccccccCCCCeEEEE
Confidence 4899999998 6667788776
No 132
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=34.63 E-value=79 Score=19.92 Aligned_cols=23 Identities=35% Similarity=0.550 Sum_probs=16.8
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
+++||+|.+. |++++++++++.+
T Consensus 45 ~~~Gd~i~~~----------i~~~~~~~~~i~l 67 (70)
T cd05687 45 VKVGDEVEVY----------VLRVEDEEGNVVL 67 (70)
T ss_pred CCCCCEEEEE----------EEEEECCCCeEEE
Confidence 7899999876 6777766655554
No 133
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=34.47 E-value=71 Score=29.83 Aligned_cols=36 Identities=22% Similarity=0.346 Sum_probs=24.9
Q ss_pred ceeeeCCEEEEE-ecC-CCCe-EeEEEEEEccCCEEEEe
Q 032704 68 MHVKAGDTVKVI-AGC-DKGK-IGEITKVFRHNSTVMVK 103 (135)
Q Consensus 68 ~~I~kGD~V~VI-~Gk-dKGK-~G~V~~V~r~~~~ViVe 103 (135)
.....||+|.|. ... .+|+ +|+|.+|......-+|-
T Consensus 49 ~~a~~GD~V~v~i~~~~~~~~~~g~v~~il~r~~~~~vG 87 (654)
T TIGR00358 49 KKVMHGDLVEACPLSQPQRGRFEAEVERILEPALTRFVG 87 (654)
T ss_pred CcCCCCCEEEEEEeecCCCCCceEEEEEEeccCCCEEEE
Confidence 346779999774 333 3444 89999999887665554
No 134
>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=34.37 E-value=84 Score=24.72 Aligned_cols=29 Identities=17% Similarity=0.149 Sum_probs=24.0
Q ss_pred eeeCCEEEEEecCC-CCeEeEEEEEEccCC
Q 032704 70 VKAGDTVKVIAGCD-KGKIGEITKVFRHNS 98 (135)
Q Consensus 70 I~kGD~V~VI~Gkd-KGK~G~V~~V~r~~~ 98 (135)
+++||-|.+.++.. -..+|.|.++....+
T Consensus 4 yrvGD~Vy~~~~~~~Py~I~rI~e~~~~~~ 33 (164)
T cd04709 4 YRVGDYVYFESSPNNPYLIRRIEELNKTAR 33 (164)
T ss_pred EecCCEEEEECCCCCCCEEEEEEEEEeCCC
Confidence 78999999998864 478999999887553
No 135
>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=34.07 E-value=99 Score=20.95 Aligned_cols=30 Identities=20% Similarity=0.287 Sum_probs=24.5
Q ss_pred eeeeCCEEEEEecCC----CCeEeEEEEEEccCC
Q 032704 69 HVKAGDTVKVIAGCD----KGKIGEITKVFRHNS 98 (135)
Q Consensus 69 ~I~kGD~V~VI~Gkd----KGK~G~V~~V~r~~~ 98 (135)
.++.||.|.|-...+ .=-+|.|.++....+
T Consensus 3 ~y~vgd~V~v~~~~~~~~~~~~i~~I~~i~~~~~ 36 (123)
T cd04370 3 TYEVGDSVYVEPDDSIKSDPPYIARIEELWEDTN 36 (123)
T ss_pred EEecCCEEEEecCCcCCCCCCEEEEEeeeeECCC
Confidence 478999999999874 456999999998754
No 136
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=33.41 E-value=31 Score=21.39 Aligned_cols=14 Identities=29% Similarity=0.688 Sum_probs=10.3
Q ss_pred ccceeeeCCEEEEE
Q 032704 66 HKMHVKAGDTVKVI 79 (135)
Q Consensus 66 ~k~~I~kGD~V~VI 79 (135)
..+.+++||.|.|+
T Consensus 14 ~~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 14 DELSFKKGDVIEVL 27 (55)
T ss_dssp TB-EB-TTEEEEEE
T ss_pred CceEEecCCEEEEE
Confidence 34679999999999
No 137
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=33.33 E-value=24 Score=23.06 Aligned_cols=21 Identities=33% Similarity=0.441 Sum_probs=14.6
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEE
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKV 93 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V 93 (135)
++.||.|+..+|- ..=+|..|
T Consensus 1 f~~GDvV~LKSGG---p~MTV~~v 21 (53)
T PF09926_consen 1 FKIGDVVQLKSGG---PRMTVTEV 21 (53)
T ss_pred CCCCCEEEEccCC---CCeEEEEc
Confidence 4689999999994 33345444
No 138
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=32.80 E-value=98 Score=19.31 Aligned_cols=25 Identities=36% Similarity=0.533 Sum_probs=19.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
.++.||.|.+ +|.+++++++.+.+.
T Consensus 44 ~~~~Gd~v~~----------~v~~~d~~~~~i~ls 68 (73)
T cd05691 44 RFKVGDEVEA----------KITNVDRKNRKISLS 68 (73)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 4789999988 488888877766543
No 139
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.98 E-value=73 Score=26.38 Aligned_cols=36 Identities=22% Similarity=0.450 Sum_probs=28.7
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
-++++.||++.+..|.+.=-.++|.++.++.-.+.+
T Consensus 31 VlRl~~gd~l~l~~g~g~~~~a~i~~~~kk~~~~~i 66 (246)
T COG1385 31 VLRLKEGDELRLFDGSGGEFLAEITKIGKKEALLKI 66 (246)
T ss_pred eeecCCCCEEEEEeCCCcEEEEEEeecCCCceEEEE
Confidence 467899999999999987777789888877544443
No 140
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=30.93 E-value=1.1e+02 Score=20.52 Aligned_cols=23 Identities=30% Similarity=0.268 Sum_probs=15.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEIT 91 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~ 91 (135)
.+..||.|.|---.+-...|.|+
T Consensus 46 ~i~vGD~V~ve~~~~~~~~g~Iv 68 (72)
T PRK00276 46 RILPGDKVTVELSPYDLTKGRIT 68 (72)
T ss_pred ccCCCCEEEEEEcccCCCeEEEE
Confidence 36899999988444334446663
No 141
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=30.87 E-value=47 Score=19.10 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=12.9
Q ss_pred cceeeeCCEEEEEecC
Q 032704 67 KMHVKAGDTVKVIAGC 82 (135)
Q Consensus 67 k~~I~kGD~V~VI~Gk 82 (135)
.+.+++||.|.|+...
T Consensus 18 ~l~~~~Gd~v~v~~~~ 33 (58)
T smart00326 18 ELSFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCCCEEEEEEcC
Confidence 3458999999999774
No 142
>PRK00049 elongation factor Tu; Reviewed
Probab=30.55 E-value=1e+02 Score=26.67 Aligned_cols=34 Identities=18% Similarity=0.222 Sum_probs=25.8
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEE
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~V 100 (135)
..=.|++||+|.++..++ ++..+|.+|..++..+
T Consensus 235 ~~G~i~~gd~v~i~p~~~-~~~~~VksI~~~~~~~ 268 (396)
T PRK00049 235 ERGIIKVGEEVEIVGIRD-TQKTTVTGVEMFRKLL 268 (396)
T ss_pred eeeEEecCCEEEEeecCC-CceEEEEEEEECCcEe
Confidence 344689999999887644 7889999998776543
No 143
>PRK05352 Na(+)-translocating NADH-quinone reductase subunit A; Provisional
Probab=30.26 E-value=67 Score=28.97 Aligned_cols=30 Identities=40% Similarity=0.419 Sum_probs=23.1
Q ss_pred ccceeeeCCEEEE--EecCCCCe---------EeEEEEEEc
Q 032704 66 HKMHVKAGDTVKV--IAGCDKGK---------IGEITKVFR 95 (135)
Q Consensus 66 ~k~~I~kGD~V~V--I~GkdKGK---------~G~V~~V~r 95 (135)
.+..+++||+|+. .-+.++|- -|+|++|.+
T Consensus 42 ~~~~V~~GD~V~~Gq~I~~~~~~~s~~~hspvSGtV~~I~~ 82 (448)
T PRK05352 42 PKMKVKEGDKVKKGQPLFEDKKNPGVKFTSPASGTVVAINR 82 (448)
T ss_pred CceEeCcCCEEcCCCEeEecCCCceEEEEcCCCeEEEEEcc
Confidence 4667999999987 55666664 499999963
No 144
>cd03691 BipA_TypA_II BipA_TypA_II: domain II of BipA (also called TypA) having homology to domain II of the elongation factors (EFs) EF-G and EF-Tu. BipA is a highly conserved protein with global regulatory properties in Escherichia coli. BipA is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways. BipA functions as a translation factor that is required specifically for the expression of the transcriptional modulator Fis. BipA binds to ribosomes at a site that coincides with that of EF-G and has a GTPase activity that is sensitive to high GDP:GTP ratios and, is stimulated by 70S ribosomes programmed with mRNA and aminoacylated tRNAs. The growth rate-dependent induction of BipA allows the efficient expression of Fis, thereby modulating a range of downstream processes, including DNA metabolism and type III secretion.
Probab=30.20 E-value=86 Score=20.76 Aligned_cols=27 Identities=33% Similarity=0.361 Sum_probs=16.4
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKV 93 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V 93 (135)
.=.+++||+|.+..-.++.+.-+|.++
T Consensus 24 sG~l~~g~~v~~~~~~~~~~~~~v~~l 50 (86)
T cd03691 24 RGTVKVGQQVAVVKRDGKIEKAKITKL 50 (86)
T ss_pred eCEEcCCCEEEEEcCCCCEEEEEEeeE
Confidence 446899999988766433333334443
No 145
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=30.10 E-value=2.1e+02 Score=21.56 Aligned_cols=28 Identities=25% Similarity=0.274 Sum_probs=19.1
Q ss_pred eeeeCCEEEEEe----cC---CCCeEeEEEEEEcc
Q 032704 69 HVKAGDTVKVIA----GC---DKGKIGEITKVFRH 96 (135)
Q Consensus 69 ~I~kGD~V~VI~----Gk---dKGK~G~V~~V~r~ 96 (135)
.+++||+|.|-. |. -.--+|.|.++...
T Consensus 18 ~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~ 52 (116)
T PRK05338 18 EFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGR 52 (116)
T ss_pred CcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCC
Confidence 389999999843 32 12357888888755
No 146
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=30.09 E-value=1e+02 Score=22.38 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=19.8
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEE
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEIT 91 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~ 91 (135)
+...|..||+|.|---++-=..|.|+
T Consensus 43 ~rIrIl~GD~V~VE~spYDltkGRIi 68 (87)
T PRK12442 43 HRIRILAGDRVTLELSPYDLTKGRIN 68 (87)
T ss_pred eeEEecCCCEEEEEECcccCCceeEE
Confidence 35679999999998777666667773
No 147
>PRK07252 hypothetical protein; Provisional
Probab=30.09 E-value=95 Score=22.90 Aligned_cols=25 Identities=16% Similarity=0.239 Sum_probs=20.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
.++.||.|.| +|++++.+++++.+.
T Consensus 47 ~~~vGD~V~V----------kI~~iD~~~~ri~lS 71 (120)
T PRK07252 47 LLKVGEEVLV----------QVVDFDEYTGKASLS 71 (120)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 4799999998 477888888887654
No 148
>PRK11642 exoribonuclease R; Provisional
Probab=29.62 E-value=87 Score=30.38 Aligned_cols=35 Identities=23% Similarity=0.317 Sum_probs=24.7
Q ss_pred eeeeCCEEEEE-ecCC--CCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVI-AGCD--KGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI-~Gkd--KGK~G~V~~V~r~~~~ViVe 103 (135)
+..-||+|.|. .+.+ +..+|+|++|....+.-+|-
T Consensus 117 ~A~~GD~V~v~i~~~~~~~r~eg~Vv~IleR~~~~~vG 154 (813)
T PRK11642 117 TCIHGDQVLAQPLGADRKGRREARIVRVLVPKTSQIVG 154 (813)
T ss_pred cCCCCCEEEEEEccCCCCCCcEEEEEEEEecCCCEEEE
Confidence 45669999775 3422 33599999999888766554
No 149
>COG1726 NqrA Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrA [Energy production and conversion]
Probab=29.61 E-value=72 Score=29.15 Aligned_cols=41 Identities=27% Similarity=0.413 Sum_probs=27.7
Q ss_pred cccccceeeeCCEEEE---EecC--CCC------eEeEEEEEEccCCEEEEe
Q 032704 63 PVLHKMHVKAGDTVKV---IAGC--DKG------KIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 63 p~~~k~~I~kGD~V~V---I~Gk--dKG------K~G~V~~V~r~~~~ViVe 103 (135)
++...|+++.||.|+- +.-. +-| --|+|++|.|-..||.-+
T Consensus 38 gmrp~mkV~~gD~VkkGq~LfEdKknpgv~~Tap~sG~V~aI~RG~KRvLqs 89 (447)
T COG1726 38 GMRPSMKVREGDAVKKGQVLFEDKKNPGVVFTAPVSGKVTAIHRGEKRVLQS 89 (447)
T ss_pred CCCCcceeccCCeeeccceeeecccCCCeEEeccCCceEEEeecccceeeee
Confidence 5668999999999962 2211 112 248899999987776544
No 150
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=29.60 E-value=81 Score=18.95 Aligned_cols=24 Identities=17% Similarity=0.080 Sum_probs=16.6
Q ss_pred eeeCCEEEEEec---CCCCeEeEEEEE
Q 032704 70 VKAGDTVKVIAG---CDKGKIGEITKV 93 (135)
Q Consensus 70 I~kGD~V~VI~G---kdKGK~G~V~~V 93 (135)
+..||+|.+-.- +.++.++.|.+|
T Consensus 37 ~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 37 LREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred CCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 678999988642 345667777665
No 151
>TIGR03170 flgA_cterm flagella basal body P-ring formation protein FlgA. This model describes a conserved C-terminal region of the flagellar basal body P-ring formation protein FlgA. This sequence region contains a SAF domain, now described by Pfam model pfam08666.
Probab=29.58 E-value=95 Score=21.99 Aligned_cols=29 Identities=41% Similarity=0.549 Sum_probs=20.8
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEE
Q 032704 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVF 94 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~Gk------------dKGK~G~V~~V~ 94 (135)
..+-|++||.|.|+.-. .-|..|+..+|.
T Consensus 62 ~~~~V~~G~~V~i~~~~~~~~i~~~g~Al~~g~~G~~I~V~ 102 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARGGGLSVTTEGKALEDGAVGDQIRVR 102 (122)
T ss_pred CccEEcCCCEEEEEEecCCEEEEEEEEEccccCCCCEEEEE
Confidence 45669999999997643 456666666666
No 152
>KOG4225 consensus Sorbin and SH3 domain-containing protein [Signal transduction mechanisms]
Probab=29.50 E-value=61 Score=30.02 Aligned_cols=47 Identities=21% Similarity=0.391 Sum_probs=30.1
Q ss_pred ccCCCCceeeeeeeeeeeeeecCCCCCcccccceeeeCCEEEEEe--------cCCCCeEeEE
Q 032704 36 VKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIA--------GCDKGKIGEI 90 (135)
Q Consensus 36 ~~~~~~~~~~~~~~k~wer~~~k~~~lp~~~k~~I~kGD~V~VI~--------GkdKGK~G~V 90 (135)
-..++++|....++ +.+++... ..+.+.+||.|.|+. |.+-|.+|.+
T Consensus 223 r~~~~~~~~~aral-----f~F~~qt~---kEL~~~kGDIVyI~rkvD~nWyeGEhhGr~Gif 277 (489)
T KOG4225|consen 223 RRKTEKPKRAARAL-----FDFEAQTP---KELPFNKGDIVYILRKVDQNWYEGEHHGRVGIF 277 (489)
T ss_pred CCCCccccchhhhe-----eccccCCc---cccccCCCCEEEEEeeccCceeeeeecceecce
Confidence 45566666653322 33333331 456689999999975 7788888865
No 153
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=29.38 E-value=27 Score=24.77 Aligned_cols=20 Identities=45% Similarity=0.630 Sum_probs=14.3
Q ss_pred eeeeCCEEEEEecCCCCeEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIG 88 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G 88 (135)
.+.+||.|.++.|.--|..|
T Consensus 89 ~~~~gd~vVv~~g~~~~~~g 108 (117)
T PF02887_consen 89 LLKPGDKVVVVAGMPFGTPG 108 (117)
T ss_dssp SS-TTSEEEEEEESSTTTTS
T ss_pred CCCCCCEEEEEeCCCCCCCC
Confidence 37999999999995444444
No 154
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=28.57 E-value=71 Score=26.81 Aligned_cols=33 Identities=30% Similarity=0.366 Sum_probs=26.4
Q ss_pred ceeeeCCEEEEEecCC-CCeEeEEEEEEccCCEEE-Eec
Q 032704 68 MHVKAGDTVKVIAGCD-KGKIGEITKVFRHNSTVM-VKD 104 (135)
Q Consensus 68 ~~I~kGD~V~VI~Gkd-KGK~G~V~~V~r~~~~Vi-Veg 104 (135)
--|++||-|.- + +|-+|.|++|.+...+|. +-+
T Consensus 142 dGV~~g~~Vi~----~~~GLVG~V~~V~~~~S~V~litd 176 (283)
T TIGR00219 142 DGVYKDMPVIA----DGKGLVGKVVSVGSNTSRVLLLTD 176 (283)
T ss_pred cCCCCCCEEEc----CCCceEEEEEEECCCeEEEEEEEc
Confidence 34788998875 5 899999999999998874 444
No 155
>cd04091 mtEFG1_II_like mtEFG1_C: C-terminus of mitochondrial Elongation factor G1 (mtEFG1)-like proteins found in eukaryotes. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more complex than that in prokaryotes, with both cytoplasmic and mitochondrial elongation factors and multiple isoforms being expressed in certain species. Eukaryotic EF-2 operates in the cytosolic protein synthesis machinery of eukaryotes, EF-Gs in protein synthesis in bacteria. Eukaryotic mtEFG1 proteins show significant homology to bacterial EF-Gs. Mutants in yeast mtEFG1 have impaired mitochondrial protein synthesis, respiratory defects and a tendency to lose mitochondrial DNA. There are two forms of mtEFG present in mammals
Probab=28.42 E-value=97 Score=20.50 Aligned_cols=13 Identities=31% Similarity=0.432 Sum_probs=10.5
Q ss_pred ceeeeCCEEEEEe
Q 032704 68 MHVKAGDTVKVIA 80 (135)
Q Consensus 68 ~~I~kGD~V~VI~ 80 (135)
=.|++||+|....
T Consensus 24 G~lk~gd~v~~~~ 36 (81)
T cd04091 24 GKLKKGDTIYNVR 36 (81)
T ss_pred CEEcCCCEEEEcC
Confidence 3688999998876
No 156
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=28.24 E-value=1.3e+02 Score=22.38 Aligned_cols=35 Identities=20% Similarity=0.190 Sum_probs=26.7
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEEEEeccc
Q 032704 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 106 (135)
Q Consensus 71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegvN 106 (135)
++||.|..-.+. .|-+|.++..+.++++|++=|=|
T Consensus 75 ~~GDiv~f~~~~-~~HVGi~~g~~~~~g~i~~lgGN 109 (129)
T TIGR02594 75 AYGCIAVKRRGG-GGHVGFVVGKDKQTGTIIVLGGN 109 (129)
T ss_pred CccEEEEEECCC-CCEEEEEEeEcCCCCEEEEeeCC
Confidence 899999776554 78999999988877777654433
No 157
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=28.20 E-value=82 Score=21.65 Aligned_cols=24 Identities=29% Similarity=0.267 Sum_probs=17.2
Q ss_pred cceeeeCCEEEEEecCCCCeEeEE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEI 90 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V 90 (135)
+..|..||+|.|=-=++--..|.|
T Consensus 42 rI~I~~GD~V~Ve~spyd~tkgrI 65 (68)
T TIGR00008 42 YIRILPGDKVKVELSPYDLTRGRI 65 (68)
T ss_pred cEEECCCCEEEEEECcccCCcEeE
Confidence 566999999999766654444555
No 158
>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=28.17 E-value=1.3e+02 Score=22.71 Aligned_cols=30 Identities=17% Similarity=0.274 Sum_probs=24.0
Q ss_pred ceeeeCCEEEEEecC-CCCeEeEEEEEEccC
Q 032704 68 MHVKAGDTVKVIAGC-DKGKIGEITKVFRHN 97 (135)
Q Consensus 68 ~~I~kGD~V~VI~Gk-dKGK~G~V~~V~r~~ 97 (135)
..++.||.|.|..+. .+--+|.|.+|....
T Consensus 19 ~~y~vgD~Vlv~~~~~~~pyI~~I~~i~~~~ 49 (146)
T cd04713 19 NKYRLEDCVLLVPEDDQKPYIAIIKDIYKQE 49 (146)
T ss_pred EEEECCCEEEEeCCCCCCCEEEEEEEEEEcC
Confidence 458999999999765 455599999998654
No 159
>PF13437 HlyD_3: HlyD family secretion protein
Probab=28.11 E-value=1.3e+02 Score=20.32 Aligned_cols=28 Identities=25% Similarity=0.392 Sum_probs=23.5
Q ss_pred ceee-eCCEEEEEe--cCCCCeEeEEEEEEc
Q 032704 68 MHVK-AGDTVKVIA--GCDKGKIGEITKVFR 95 (135)
Q Consensus 68 ~~I~-kGD~V~VI~--GkdKGK~G~V~~V~r 95 (135)
-.|+ .||.|.+.. |.++-..|+|..|.+
T Consensus 48 ~~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 48 ARIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred cceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 3587 999999985 567788999999998
No 160
>PRK10708 hypothetical protein; Provisional
Probab=27.59 E-value=83 Score=21.54 Aligned_cols=28 Identities=21% Similarity=0.208 Sum_probs=23.4
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCC
Q 032704 71 KAGDTVKVIAGCDKGKIGEITKVFRHNS 98 (135)
Q Consensus 71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~ 98 (135)
+.+|+|.|-+.-.--++|.|+.|..-+.
T Consensus 2 kvnD~VtVKTDG~~rR~G~iLavE~F~E 29 (62)
T PRK10708 2 KVNDRVTVKTDGGPRRPGVVLAVEEFSE 29 (62)
T ss_pred ccccEEEEecCCCccccceEEEEeeccC
Confidence 5689999998877888999999987653
No 161
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=27.55 E-value=38 Score=26.24 Aligned_cols=18 Identities=17% Similarity=0.444 Sum_probs=15.1
Q ss_pred Ccccccce-eeeCCEEEEE
Q 032704 62 LPVLHKMH-VKAGDTVKVI 79 (135)
Q Consensus 62 lp~~~k~~-I~kGD~V~VI 79 (135)
++++++|+ +++||+|.+.
T Consensus 77 IDlaprip~l~~GD~V~f~ 95 (131)
T PF11948_consen 77 IDLAPRIPWLQKGDQVEFY 95 (131)
T ss_pred cCccccCcCcCCCCEEEEE
Confidence 67778887 9999999874
No 162
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=27.43 E-value=78 Score=23.54 Aligned_cols=27 Identities=30% Similarity=0.320 Sum_probs=17.1
Q ss_pred eeeCCEEEEEec---CCCC----eEeEEEEEEcc
Q 032704 70 VKAGDTVKVIAG---CDKG----KIGEITKVFRH 96 (135)
Q Consensus 70 I~kGD~V~VI~G---kdKG----K~G~V~~V~r~ 96 (135)
+++||+|.|-.= .+|. -+|.|+++...
T Consensus 19 f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~ 52 (113)
T PF01245_consen 19 FRVGDTVRVTYKISEGNKERIQVFEGVVIARRRR 52 (113)
T ss_dssp SSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBS
T ss_pred cCCCCEEEEEEEEecCCCceeEEEEEEEEEEECC
Confidence 899999998642 2222 35666666654
No 163
>PF05972 APC_15aa: APC 15 residue motif; InterPro: IPR009240 The 15 aa repeat is found in the APC protein family. It is involved in binding beta-catenin [] along with the IPR009223 from INTERPRO repeats. Many human cancer mutations map to the region around these motifs, and may be involved in disrupting their binding of beta-catenin.; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1JPP_C.
Probab=27.38 E-value=17 Score=18.87 Aligned_cols=9 Identities=22% Similarity=0.069 Sum_probs=2.5
Q ss_pred EeeeeeEEe
Q 032704 126 VYSLICYFI 134 (135)
Q Consensus 126 ~E~PIh~S~ 134 (135)
.|.||+||+
T Consensus 2 ~dqP~dyS~ 10 (16)
T PF05972_consen 2 EDQPIDYSL 10 (16)
T ss_dssp ------CCC
T ss_pred Cccccchhh
Confidence 478999996
No 164
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=27.19 E-value=43 Score=23.29 Aligned_cols=22 Identities=27% Similarity=0.576 Sum_probs=18.9
Q ss_pred cccceeeeCCEEEEEecCCCCe
Q 032704 65 LHKMHVKAGDTVKVIAGCDKGK 86 (135)
Q Consensus 65 ~~k~~I~kGD~V~VI~GkdKGK 86 (135)
...+.|+.||.|.++...|.|+
T Consensus 23 R~~lgi~~Gd~lei~~~~~~~~ 44 (89)
T COG2002 23 REALGIKEGDVLEIIVDGDGGR 44 (89)
T ss_pred HHHhCCCCCCEEEEEEeCCCCE
Confidence 3456799999999999998887
No 165
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal. pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=27.00 E-value=1e+02 Score=19.95 Aligned_cols=19 Identities=21% Similarity=0.164 Sum_probs=13.9
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
.++.||+|.|. |.+++..+
T Consensus 48 ~~~~Gd~v~vk----------v~~vd~~~ 66 (73)
T cd05686 48 VVDVGEKVWVK----------VIGREMKD 66 (73)
T ss_pred EECCCCEEEEE----------EEEECCCC
Confidence 47999999984 66666654
No 166
>PF07497 Rho_RNA_bind: Rho termination factor, RNA-binding domain; InterPro: IPR011113 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [].; GO: 0003723 RNA binding, 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=26.83 E-value=58 Score=22.90 Aligned_cols=18 Identities=17% Similarity=0.342 Sum_probs=11.9
Q ss_pred ccccceeeeCCEEEEEec
Q 032704 64 VLHKMHVKAGDTVKVIAG 81 (135)
Q Consensus 64 ~~~k~~I~kGD~V~VI~G 81 (135)
++.++.+|.||.|.-..-
T Consensus 37 qIrrf~LR~GD~V~G~vr 54 (78)
T PF07497_consen 37 QIRRFGLRTGDLVEGQVR 54 (78)
T ss_dssp CCCCTT--TTEEEEEEEE
T ss_pred HHHHcCCCCCCEEEEEEe
Confidence 467889999999984433
No 167
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=26.83 E-value=95 Score=25.11 Aligned_cols=35 Identities=29% Similarity=0.391 Sum_probs=23.8
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEE-ccCCEE
Q 032704 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVF-RHNSTV 100 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~Gk------------dKGK~G~V~~V~-r~~~~V 100 (135)
..+-|++||.|.|+... .-|..|+...|. ...+++
T Consensus 173 ~~~~V~~G~~V~i~~~~g~~~i~~~G~Al~~G~~Gd~IrVrN~~Sgk~ 220 (235)
T PRK07018 173 QAWVVCKGQTVSIIARGDGFSVKTEGEALNDGAVGQQIRVRNMASGQV 220 (235)
T ss_pred CccEeCCCCEEEEEEecCCEEEEEEEEEcCCCCCCCeEEEEECCCCCE
Confidence 35679999999998753 456667666666 444443
No 168
>PRK08577 hypothetical protein; Provisional
Probab=26.59 E-value=50 Score=24.27 Aligned_cols=24 Identities=29% Similarity=0.368 Sum_probs=19.9
Q ss_pred cccceeeeCCEEEEEecCCCCeEe
Q 032704 65 LHKMHVKAGDTVKVIAGCDKGKIG 88 (135)
Q Consensus 65 ~~k~~I~kGD~V~VI~GkdKGK~G 88 (135)
..++.|++||.|.+..-.|+|.+=
T Consensus 22 r~~l~~~~g~~~~~~~~~~~~~~~ 45 (136)
T PRK08577 22 REALGIREGMYVLLIADTDKKEIH 45 (136)
T ss_pred HHHcCcCCCCEEEEEEECCCCEEE
Confidence 467889999999999888877763
No 169
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=25.90 E-value=94 Score=23.45 Aligned_cols=29 Identities=31% Similarity=0.429 Sum_probs=20.1
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~Vi 101 (135)
-|++|+-|.- .+|-+|+|.+|.++..+|.
T Consensus 23 Gi~~g~~Vv~----~~glVG~V~~V~~~~S~V~ 51 (152)
T PF04085_consen 23 GIKPGMPVVS----GGGLVGRVTEVGPNTSRVL 51 (152)
T ss_dssp T--TT-EEEE----TTEEEEEEEEE-SS-EEEE
T ss_pred cCCCCCEEEe----CCCcEEEEEEECCCEEEEE
Confidence 4788888876 7789999999999887774
No 170
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=25.84 E-value=98 Score=20.48 Aligned_cols=16 Identities=31% Similarity=0.395 Sum_probs=14.7
Q ss_pred eEEEEEEccCCEEEEe
Q 032704 88 GEITKVFRHNSTVMVK 103 (135)
Q Consensus 88 G~V~~V~r~~~~ViVe 103 (135)
|+|++|+.++++|.|+
T Consensus 1 G~V~~v~~~~grvrV~ 16 (79)
T PF04717_consen 1 GTVTAVDPDKGRVRVR 16 (79)
T ss_dssp EEEEEEETTTTEEEEE
T ss_pred CeEEEEECCCCEEEEE
Confidence 7899999999999888
No 171
>PRK12289 GTPase RsgA; Reviewed
Probab=25.84 E-value=1e+02 Score=26.76 Aligned_cols=32 Identities=28% Similarity=0.323 Sum_probs=24.4
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEE
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~Vi 101 (135)
+.+||.|.+-.-.+.+..|.|.+|.+.+|.+.
T Consensus 52 ~~vGD~V~~~~~~~~~~~~~I~~vlpR~~~L~ 83 (352)
T PRK12289 52 VMVGDRVIVEEPDWQGQRGAIAEVLPRKTELD 83 (352)
T ss_pred cccCCEEEEeecCCCCCceEEEEEecccccee
Confidence 58999998854333456799999999988664
No 172
>PRK06437 hypothetical protein; Provisional
Probab=25.82 E-value=51 Score=21.79 Aligned_cols=15 Identities=27% Similarity=0.403 Sum_probs=12.0
Q ss_pred ccceeeeCCEEEEEe
Q 032704 66 HKMHVKAGDTVKVIA 80 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~ 80 (135)
....++.||+|.++.
T Consensus 48 ~~~~L~dgD~Veiv~ 62 (67)
T PRK06437 48 EDHNVKKEDDVLILE 62 (67)
T ss_pred CceEcCCCCEEEEEe
Confidence 566789999998874
No 173
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.69 E-value=1.2e+02 Score=20.12 Aligned_cols=24 Identities=13% Similarity=0.196 Sum_probs=19.0
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
.++.||.|.+ +|++|+.+++++.+
T Consensus 50 ~~~~G~~v~~----------kVl~id~~~~~i~L 73 (74)
T cd05705 50 YLPEGKLLTA----------KVLSVNSEKNLVEL 73 (74)
T ss_pred ccCCCCEEEE----------EEEEEECCCCEEec
Confidence 4789999975 48999998887653
No 174
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=25.39 E-value=1.2e+02 Score=23.02 Aligned_cols=34 Identities=18% Similarity=0.249 Sum_probs=23.8
Q ss_pred cceeeeCCEEEEEecC------------CCCeEeEEEEEE-ccCCEE
Q 032704 67 KMHVKAGDTVKVIAGC------------DKGKIGEITKVF-RHNSTV 100 (135)
Q Consensus 67 k~~I~kGD~V~VI~Gk------------dKGK~G~V~~V~-r~~~~V 100 (135)
.+-|.+||.|.|+... .-|..|+...|. ...+++
T Consensus 79 p~lV~rG~~V~i~~~~ggl~i~~~G~AL~~G~~Gd~IrV~N~~S~ri 125 (141)
T PRK12618 79 PAIVDRNQLVPLAYRLGGLEIRTEGRALSRGGVGDEIRVMNLSSRTT 125 (141)
T ss_pred ccEEeCCCEEEEEEecCCEEEEEEEEEcccCCCCCEEEEEECCCCCE
Confidence 4679999999998643 467777777774 344443
No 175
>PRK04950 ProP expression regulator; Provisional
Probab=24.83 E-value=1.2e+02 Score=25.24 Aligned_cols=46 Identities=22% Similarity=0.348 Sum_probs=34.3
Q ss_pred CCCCCcccccceeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEec
Q 032704 58 KPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104 (135)
Q Consensus 58 k~~~lp~~~k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVeg 104 (135)
+|...+...-..+.+|..|.|-.|+. -.-|+|++|.+++=+|.++.
T Consensus 155 ~~~~~~~~~~~~l~~gq~v~vk~g~~-~~~a~i~ei~kd~v~vql~~ 200 (213)
T PRK04950 155 EPQHTPVSDISELTVGQAVKVKAGKS-AMDATVLEITKDDVRVQLDS 200 (213)
T ss_pred CccccccccHHHhccCCEEEEeccCC-CCceEEEEEecCcEEEEcCC
Confidence 33334444556789999999999973 46789999999987776653
No 176
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=24.40 E-value=98 Score=21.19 Aligned_cols=28 Identities=29% Similarity=0.236 Sum_probs=23.4
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCC
Q 032704 71 KAGDTVKVIAGCDKGKIGEITKVFRHNS 98 (135)
Q Consensus 71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~ 98 (135)
+.+|+|.|-+.-.--+.|.|+.|..-+.
T Consensus 2 kvnD~VtVKTDG~~rR~G~ilavE~F~E 29 (62)
T PF10781_consen 2 KVNDRVTVKTDGGPRREGVILAVEPFNE 29 (62)
T ss_pred ccccEEEEecCCcccccceEEEEeeccC
Confidence 5689999998877788999999987654
No 177
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=24.30 E-value=89 Score=24.44 Aligned_cols=35 Identities=29% Similarity=0.379 Sum_probs=30.4
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEecc
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVegv 105 (135)
+-.|-.+.|-.|++.||.--|..|.- .|++.|+|-
T Consensus 7 veVGrva~v~~G~~~GkL~AIVdviD-qnr~lvDGp 41 (136)
T KOG3421|consen 7 VEVGRVALVSFGPDAGKLVAIVDVID-QNRALVDGP 41 (136)
T ss_pred hhcceEEEEEecCCCceEEEEEEeec-chhhhccCc
Confidence 46788899999999999999999885 579999985
No 178
>cd01342 Translation_Factor_II_like Translation_Factor_II_like: Elongation factor Tu (EF-Tu) domain II-like proteins. Elongation factor Tu consists of three structural domains, this family represents the second domain. Domain II adopts a beta barrel structure and is involved in binding to charged tRNA. Domain II is found in other proteins such as elongation factor G and translation initiation factor IF-2. This group also includes the C2 subdomain of domain IV of IF-2 that has the same fold as domain II of (EF-Tu). Like IF-2 from certain prokaryotes such as Thermus thermophilus, mitochondrial IF-2 lacks domain II, which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=24.26 E-value=1.7e+02 Score=17.45 Aligned_cols=28 Identities=32% Similarity=0.478 Sum_probs=17.6
Q ss_pred ceeeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032704 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (135)
Q Consensus 68 ~~I~kGD~V~VI~GkdKGK~G~V~~V~r~ 96 (135)
=.+++||.+.+... ......+|..+...
T Consensus 25 G~l~~g~~v~~~~~-~~~~~~~i~~i~~~ 52 (83)
T cd01342 25 GTLKKGDKVRVGPG-GGGVKGKVKSLKRF 52 (83)
T ss_pred CEEecCCEEEEecC-CceeEEEEeEeEec
Confidence 35789999988874 22344556555544
No 179
>PF09356 Phage_BR0599: Phage conserved hypothetical protein BR0599; InterPro: IPR018964 This entry describes the C-terminal region of a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus (Rhodopseudomonas capsulata) gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.
Probab=24.24 E-value=59 Score=22.52 Aligned_cols=17 Identities=47% Similarity=0.856 Sum_probs=15.1
Q ss_pred eeeeCCEEEEEecCCCC
Q 032704 69 HVKAGDTVKVIAGCDKG 85 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKG 85 (135)
.+..||+|.|..|-||.
T Consensus 40 ~~~~G~~v~l~~GCDkt 56 (80)
T PF09356_consen 40 GLAVGDTVTLYPGCDKT 56 (80)
T ss_pred cCCCCCEEEEEeCCCCC
Confidence 37899999999999984
No 180
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=24.20 E-value=81 Score=21.50 Aligned_cols=22 Identities=18% Similarity=0.149 Sum_probs=19.0
Q ss_pred eEeEEEEEEccCCEEEEeccce
Q 032704 86 KIGEITKVFRHNSTVMVKDINL 107 (135)
Q Consensus 86 K~G~V~~V~r~~~~ViVegvN~ 107 (135)
-+|+|.+|++...++.+++=+-
T Consensus 5 veG~I~~id~~~~titLdDGks 26 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDGKS 26 (61)
T ss_pred ceEEEEEEcCCceEEEecCCCE
Confidence 4799999999999999997553
No 181
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=24.13 E-value=1.7e+02 Score=17.60 Aligned_cols=27 Identities=26% Similarity=0.082 Sum_probs=19.9
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEcc
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRH 96 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~ 96 (135)
+++|+.|.+.-....=-.++|+++..+
T Consensus 3 ~~~G~~~~a~~~d~~wyra~I~~~~~~ 29 (57)
T smart00333 3 FKVGDKVAARWEDGEWYRARIIKVDGE 29 (57)
T ss_pred CCCCCEEEEEeCCCCEEEEEEEEECCC
Confidence 578999998872333457889999874
No 182
>PLN00208 translation initiation factor (eIF); Provisional
Probab=24.12 E-value=1.1e+02 Score=23.95 Aligned_cols=31 Identities=16% Similarity=0.194 Sum_probs=24.1
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
+.-|+.||.|.|---.+.-..|.|+..+...
T Consensus 68 rIWI~~GD~VlVel~~~d~~KgdIv~ry~~d 98 (145)
T PLN00208 68 KVWIAAGDIILVGLRDYQDDKADVILKYMPD 98 (145)
T ss_pred eEEecCCCEEEEEccCCCCCEEEEEEEcCHH
Confidence 4569999999996556667788898877654
No 183
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=23.88 E-value=1.2e+02 Score=18.49 Aligned_cols=23 Identities=30% Similarity=0.414 Sum_probs=15.8
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
.++.||.|.|. |.+++. ++.+.+
T Consensus 44 ~~~~Gd~v~v~----------v~~~d~-~~~i~l 66 (68)
T cd04472 44 VLKVGDEVKVK----------VIEVDD-RGRISL 66 (68)
T ss_pred ccCCCCEEEEE----------EEEECC-CCcEEe
Confidence 47999999984 666666 555543
No 184
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.63 E-value=1.2e+02 Score=24.51 Aligned_cols=35 Identities=14% Similarity=0.333 Sum_probs=23.9
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEEccCCEE
Q 032704 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVFRHNSTV 100 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~Gk------------dKGK~G~V~~V~r~~~~V 100 (135)
..+-|++||.|.|+.-. .-|..|.+..|--..+++
T Consensus 162 ~~~lV~rGd~V~i~~~~gg~~I~~~G~Al~~G~~Gd~IrVrN~Sgki 208 (222)
T PRK08515 162 ALILVRKNDIINGVLKEGGVSIEISLKALQDGNLGDIIQAKNKSNKI 208 (222)
T ss_pred CcceEecCCEEEEEEECCCEEEEEEEEEcccCCCCCEEEEEeCCCCE
Confidence 45679999999998643 456677777666644443
No 185
>PF10133 RNA_bind_2: Predicted RNA-binding protein; InterPro: IPR019300 This entry represents a family of bacterial proteins predicted to have RNA-binding properties, though their exact function has not yet been defined.
Probab=23.48 E-value=2.3e+02 Score=18.86 Aligned_cols=33 Identities=18% Similarity=0.359 Sum_probs=23.4
Q ss_pred eeCCEEEEE--ecCCCCeEeEEEEEEccCCEEEEe
Q 032704 71 KAGDTVKVI--AGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 71 ~kGD~V~VI--~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
..||.|... =|..|=-.|+|.+++--+++|+++
T Consensus 26 ~~~~~i~l~dIfG~~k~v~g~I~~idl~~hkIile 60 (61)
T PF10133_consen 26 PEGDKIRLTDIFGEQKEVEGRIKEIDLVDHKIILE 60 (61)
T ss_pred EeCCEEEEEeccCCeEEEEEEEEEEEccCCEEEEe
Confidence 456665543 367777778888888888888876
No 186
>TIGR00485 EF-Tu translation elongation factor TU. This alignment models orthologs of translation elongation factor EF-Tu in bacteria, mitochondria, and chloroplasts, one of several GTP-binding translation factors found by the more general pfam model GTP_EFTU. The eukaryotic conterpart, eukaryotic translation elongation factor 1 (eEF-1 alpha), is excluded from this model. EF-Tu is one of the most abundant proteins in bacteria, as well as one of the most highly conserved, and in a number of species the gene is duplicated with identical function. When bound to GTP, EF-Tu can form a complex with any (correctly) aminoacylated tRNA except those for initiation and for selenocysteine, in which case EF-Tu is replaced by other factors. Transfer RNA is carried to the ribosome in these complexes for protein translation.
Probab=23.30 E-value=1.4e+02 Score=25.61 Aligned_cols=32 Identities=19% Similarity=0.193 Sum_probs=23.2
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccCCE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNST 99 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ 99 (135)
.=.|++||+|.++..+ .++..+|.+|..++..
T Consensus 234 ~G~l~~gd~v~i~p~~-~~~~~~VksI~~~~~~ 265 (394)
T TIGR00485 234 RGIVKVGEEVEIVGLK-DTRKTTVTGVEMFRKE 265 (394)
T ss_pred eeEEeCCCEEEEecCC-CCcEEEEEEEEECCeE
Confidence 4468999999887543 5677889888766543
No 187
>KOG4792 consensus Crk family adapters [Signal transduction mechanisms]
Probab=23.07 E-value=1.4e+02 Score=25.87 Aligned_cols=45 Identities=27% Similarity=0.390 Sum_probs=28.3
Q ss_pred cccCCCCceeeeeeeeeeeeeecC--CCCCcccccceeeeCCEEEEEe
Q 032704 35 TVKPTDKPCLIVVRLKRWERKECK--PNSLPVLHKMHVKAGDTVKVIA 80 (135)
Q Consensus 35 ~~~~~~~~~~~~~~~k~wer~~~k--~~~lp~~~k~~I~kGD~V~VI~ 80 (135)
...++.+|++...++.-.-|...+ ||.-+. ..+.+.+||.|+|..
T Consensus 212 a~~s~~~~l~l~~~lPa~Arv~q~RVPnAYDk-TaL~levGdiVkVTk 258 (293)
T KOG4792|consen 212 ASTSSDTPLPLQQNLPAYARVIQKRVPNAYDK-TALALEVGDIVKVTK 258 (293)
T ss_pred CCcccCCcCccccCCChheeeehhcCCCccCh-hhhhhhcCcEEEEEe
Confidence 346677777776665544444433 444332 456789999999964
No 188
>cd04088 EFG_mtEFG_II EFG_mtEFG_II: this subfamily represents the domain II of elongation factor G (EF-G) in bacteria and, the C-terminus of mitochondrial Elongation factor G1 (mtEFG1) and G2 (mtEFG2)_like proteins found in eukaryotes. During the process of peptide synthesis and tRNA site changes, the ribosome is moved along the mRNA a distance equal to one codon with the addition of each amino acid. In bacteria this translocation step is catalyzed by EF-G_GTP, which is hydrolyzed to provide the required energy. Thus, this action releases the uncharged tRNA from the P site and transfers the newly formed peptidyl-tRNA from the A site to the P site. Eukaryotic cells harbor 2 protein synthesis systems: one localized in the cytoplasm, the other in the mitochondria. Most factors regulating mitochondrial protein synthesis are encoded by nuclear genes, translated in the cytoplasm, and then transported to the mitochondria. The eukaryotic system of elongation factor (EF) components is more compl
Probab=23.01 E-value=1.2e+02 Score=19.81 Aligned_cols=25 Identities=28% Similarity=0.383 Sum_probs=15.5
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEE
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVF 94 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~ 94 (135)
.=.+++||.|.++. .++..+|.+++
T Consensus 24 sG~l~~g~~v~~~~---~~~~~~v~~l~ 48 (83)
T cd04088 24 SGTLKAGSTLYNST---KGKKERVGRLL 48 (83)
T ss_pred cCEEcCCCEEEECC---CCcEEEeeEEE
Confidence 34688999998886 23334444443
No 189
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=22.98 E-value=1.2e+02 Score=20.19 Aligned_cols=16 Identities=19% Similarity=0.308 Sum_probs=14.5
Q ss_pred eEEEEEEccCCEEEEe
Q 032704 88 GEITKVFRHNSTVMVK 103 (135)
Q Consensus 88 G~V~~V~r~~~~ViVe 103 (135)
|+|.+|+.+.+.|.|.
T Consensus 1 G~V~~vd~~~~~iti~ 16 (70)
T PF11604_consen 1 GVVKSVDPEAGTITIS 16 (70)
T ss_dssp EEEEEEETTTTEEEEE
T ss_pred CEEEEEecCCCEEEEe
Confidence 7899999999999876
No 190
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=22.51 E-value=66 Score=19.80 Aligned_cols=16 Identities=25% Similarity=0.557 Sum_probs=11.4
Q ss_pred ccceeeeCCEEEEEec
Q 032704 66 HKMHVKAGDTVKVIAG 81 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~G 81 (135)
..+.+++||.|.|+.-
T Consensus 11 dELs~~~Gd~i~v~~~ 26 (49)
T PF14604_consen 11 DELSFKKGDVITVLEK 26 (49)
T ss_dssp TB-EB-TTEEEEEEEE
T ss_pred CEeeEcCCCEEEEEEe
Confidence 4678999999999843
No 191
>PRK05054 exoribonuclease II; Provisional
Probab=22.37 E-value=1.6e+02 Score=27.70 Aligned_cols=34 Identities=21% Similarity=0.221 Sum_probs=23.5
Q ss_pred eeeeCCEEEEE-ecCCCCeEeEEEEEEccCCEEEE
Q 032704 69 HVKAGDTVKVI-AGCDKGKIGEITKVFRHNSTVMV 102 (135)
Q Consensus 69 ~I~kGD~V~VI-~GkdKGK~G~V~~V~r~~~~ViV 102 (135)
....||+|.|. ..+.+++.|+|.+|......-+|
T Consensus 53 ~a~~GD~V~v~i~~~~~r~~g~v~~il~r~~~~~v 87 (644)
T PRK05054 53 KVMHGDRIIAVIHTEKDREIAEPEELIEPFLTRFV 87 (644)
T ss_pred cCCCCCEEEEEEecCCCCcEEEEEEEEecCCCEEE
Confidence 45669999764 55455668999998877654433
No 192
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=22.34 E-value=1.3e+02 Score=23.80 Aligned_cols=31 Identities=10% Similarity=0.190 Sum_probs=24.4
Q ss_pred cceeeeCCEEEEEecCCCCeEeEEEEEEccC
Q 032704 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (135)
Q Consensus 67 k~~I~kGD~V~VI~GkdKGK~G~V~~V~r~~ 97 (135)
+..|+.||.|.|=--++.-..|.|+..+...
T Consensus 68 ~IWI~~GD~VlVel~~yd~~KgdIi~Ry~~d 98 (155)
T PTZ00329 68 RVWINIGDIILVSLRDFQDSKADVILKYTPD 98 (155)
T ss_pred eEEecCCCEEEEeccCCCCCEEEEEEEcCHH
Confidence 4569999999997666777788898777654
No 193
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=22.31 E-value=1.7e+02 Score=27.92 Aligned_cols=35 Identities=17% Similarity=0.416 Sum_probs=26.5
Q ss_pred cceeeeCCEEEEEecC-----CCCeEeEEEEEEccCCEEEEe
Q 032704 67 KMHVKAGDTVKVIAGC-----DKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 67 k~~I~kGD~V~VI~Gk-----dKGK~G~V~~V~r~~~~ViVe 103 (135)
...+++||+|....-. .-|.+|+|+.|.. +.+.|+
T Consensus 605 ~~~~~~GDrV~~~~N~~~~gv~NGd~g~V~~i~~--~~i~v~ 644 (744)
T TIGR02768 605 ERKFAAGDRIVFLENNRDLGVKNGMLGTVEEIED--GRLVVQ 644 (744)
T ss_pred CceecCCCEEEEEecccccCCcCCCEEEEEEecC--CeEEEE
Confidence 3578999999998653 4679999999963 456554
No 194
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=22.21 E-value=1.4e+02 Score=27.97 Aligned_cols=36 Identities=19% Similarity=0.216 Sum_probs=25.9
Q ss_pred ceeeeCCEEEEE-ec---CCCCeEeEEEEEEccCCEEEEe
Q 032704 68 MHVKAGDTVKVI-AG---CDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 68 ~~I~kGD~V~VI-~G---kdKGK~G~V~~V~r~~~~ViVe 103 (135)
.....||+|.|- .. +.+...|+|++|.......+|-
T Consensus 101 ~~a~~GD~Vlv~I~~~~~~~~~~eg~Vv~Il~r~~~~~VG 140 (709)
T TIGR02063 101 NGAMHGDRVLVRITGKPDGGDRFEARVIKILERANDQIVG 140 (709)
T ss_pred CcCCCCCEEEEEEecccCCCCCceEEEEEEEeeCCCEEEE
Confidence 357789999775 32 2456799999999887665554
No 195
>PRK10220 hypothetical protein; Provisional
Probab=22.21 E-value=2e+02 Score=21.78 Aligned_cols=27 Identities=37% Similarity=0.541 Sum_probs=19.1
Q ss_pred eeeeCCEEEEEec-CCCC-----eEeEEEEEEc
Q 032704 69 HVKAGDTVKVIAG-CDKG-----KIGEITKVFR 95 (135)
Q Consensus 69 ~I~kGD~V~VI~G-kdKG-----K~G~V~~V~r 95 (135)
.+.-||.|.||.. +-|| |+|+..+-.|
T Consensus 51 ~L~dGDsV~viKDLkVKGss~~~K~GTkvknIr 83 (111)
T PRK10220 51 LLADGDSVTIVKDLKVKGSSSMLKIGTKVKNIR 83 (111)
T ss_pred CccCCCEEEEEeeccccccccceeCccEEEEEE
Confidence 4789999999987 5565 5566555444
No 196
>TIGR02062 RNase_B exoribonuclease II. This family consists of exoribonuclease II, the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.
Probab=22.17 E-value=1.6e+02 Score=27.59 Aligned_cols=35 Identities=17% Similarity=0.173 Sum_probs=24.8
Q ss_pred eeeeCCEEEEE-ecCCCCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVI-AGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI-~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
....||+|.|. ....+.+.|+|.+|....+.-+|-
T Consensus 50 ~A~~GD~V~v~i~~~~~r~~~~v~~iver~~~~~vG 85 (639)
T TIGR02062 50 KVMHGDKIIAVIHSEKERESAEPEELIEPFLTRFVG 85 (639)
T ss_pred cCCCCCEEEEEEecCCCCcEEEEEEEEccCCCEEEE
Confidence 45679999764 444456689999998777665554
No 197
>PF13550 Phage-tail_3: Putative phage tail protein
Probab=22.02 E-value=1.5e+02 Score=21.30 Aligned_cols=28 Identities=14% Similarity=0.235 Sum_probs=21.5
Q ss_pred ccceeeeCCEEEEEecCCCCeEeEEEEEE
Q 032704 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVF 94 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~GkdKGK~G~V~~V~ 94 (135)
.-+.+.+||.|.|-.. .+.....|.+|.
T Consensus 136 ~~~~l~pGDvi~l~~~-~~~~~~RI~~i~ 163 (164)
T PF13550_consen 136 DGLALEPGDVIALSDD-GRDMRFRITEIE 163 (164)
T ss_pred hhccCCCCCEEEEEeC-CCceEEEEEEEe
Confidence 4467999999997666 777777887764
No 198
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=21.99 E-value=3.5e+02 Score=20.28 Aligned_cols=27 Identities=26% Similarity=0.182 Sum_probs=18.4
Q ss_pred eeeCCEEEEEec---CCC----CeEeEEEEEEcc
Q 032704 70 VKAGDTVKVIAG---CDK----GKIGEITKVFRH 96 (135)
Q Consensus 70 I~kGD~V~VI~G---kdK----GK~G~V~~V~r~ 96 (135)
+++||+|.|-.= .+| --+|.|.++...
T Consensus 19 f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~ 52 (113)
T TIGR01024 19 FRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGG 52 (113)
T ss_pred cCCCCEEEEEEEEccCCceEcccEEEEEEEEeCC
Confidence 899999998442 122 247888877654
No 199
>PF06003 SMN: Survival motor neuron protein (SMN); InterPro: IPR010304 This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus, 0005737 cytoplasm; PDB: 1MHN_A 4A4G_A 3S6N_M 4A4E_A 1G5V_A 4A4H_A 4A4F_A 2D9T_A.
Probab=21.88 E-value=1.8e+02 Score=24.29 Aligned_cols=35 Identities=17% Similarity=0.141 Sum_probs=23.1
Q ss_pred eeeeCCEEEEEec-CCCCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVIAG-CDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI~G-kdKGK~G~V~~V~r~~~~ViVe 103 (135)
..++||++..+-= ...=-.++|.+|+.+++.++|.
T Consensus 68 ~WkvGd~C~A~~s~Dg~~Y~A~I~~i~~~~~~~~V~ 103 (264)
T PF06003_consen 68 KWKVGDKCMAVYSEDGQYYPATIESIDEEDGTCVVV 103 (264)
T ss_dssp ---TT-EEEEE-TTTSSEEEEEEEEEETTTTEEEEE
T ss_pred CCCCCCEEEEEECCCCCEEEEEEEEEcCCCCEEEEE
Confidence 4689999998863 3344589999999988776553
No 200
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=21.75 E-value=1.4e+02 Score=19.66 Aligned_cols=37 Identities=19% Similarity=0.426 Sum_probs=22.9
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEE--EccCCEEEEeccceeEEE
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKV--FRHNSTVMVKDINLKTKH 111 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V--~r~~~~ViVegvN~~kkh 111 (135)
+.+|..|.+ +|- ++|+|.+| ..+.+.|.|+ +.+...+
T Consensus 15 L~~gs~V~~-~Gv---~VG~V~~i~l~~~~~~v~v~-~~i~~~~ 53 (81)
T PF02470_consen 15 LSVGSPVRY-RGV---EVGKVTSIELDPDGNRVRVT-LRIDPDY 53 (81)
T ss_pred CCCcCEEEE-CCE---EEEEEEEEEEcCCCCEEEEE-EEEcCCc
Confidence 566766653 344 57788888 7777777665 3343333
No 201
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=21.71 E-value=2.2e+02 Score=17.85 Aligned_cols=34 Identities=18% Similarity=0.049 Sum_probs=20.2
Q ss_pred eeeCCEEEEEecCCCCeEeEEEEEEccC--CEEEEeccc
Q 032704 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN--STVMVKDIN 106 (135)
Q Consensus 70 I~kGD~V~VI~GkdKGK~G~V~~V~r~~--~~ViVegvN 106 (135)
+..||.|.+..+. -.-.|..+.... +.+.+.+.|
T Consensus 29 ~~~G~iv~~~~~~---~~~~ikrl~~~~~~~~~~l~~~N 64 (84)
T cd06462 29 PKRGDIVVFRLPG---GELTVKRVIGLPGEGHYFLLGDN 64 (84)
T ss_pred CcCCEEEEEEcCC---CcEEEEEEEEECCCCEEEEECCC
Confidence 5667777666644 234455555555 566777666
No 202
>PRK08059 general stress protein 13; Validated
Probab=21.52 E-value=1.7e+02 Score=21.26 Aligned_cols=25 Identities=24% Similarity=0.368 Sum_probs=19.8
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEEccCCEEEEe
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~r~~~~ViVe 103 (135)
.++.||.|.|. |.++++.++++.+.
T Consensus 51 ~~~vGD~I~vk----------I~~id~~~~~i~ls 75 (123)
T PRK08059 51 FLSVGDEVKVK----------VLSVDEEKGKISLS 75 (123)
T ss_pred cCCCCCEEEEE----------EEEEECCCCeEEEE
Confidence 47899999984 78888877777765
No 203
>COG2053 RPS28A Ribosomal protein S28E/S33 [Translation, ribosomal structure and biogenesis]
Probab=21.46 E-value=78 Score=22.14 Aligned_cols=13 Identities=46% Similarity=0.966 Sum_probs=10.8
Q ss_pred EEEEEecCCCCeE
Q 032704 75 TVKVIAGCDKGKI 87 (135)
Q Consensus 75 ~V~VI~GkdKGK~ 87 (135)
+|.++.|+|||.+
T Consensus 27 k~ril~grdkgRi 39 (69)
T COG2053 27 KVRILEGRDKGRI 39 (69)
T ss_pred EEEEeecCCcCcE
Confidence 5889999999864
No 204
>PF04351 PilP: Pilus assembly protein, PilP; InterPro: IPR007446 The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [].; PDB: 2Y4Y_B 2Y4X_A 2IVW_A 2LC4_A.
Probab=20.87 E-value=2e+02 Score=21.68 Aligned_cols=45 Identities=20% Similarity=0.233 Sum_probs=28.0
Q ss_pred EEEEEecCCCCe-EeEEEEEEccCCEEEEeccceeEEEecCCCccCCceEEEEeeeee
Q 032704 75 TVKVIAGCDKGK-IGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKVYSLIC 131 (135)
Q Consensus 75 ~V~VI~GkdKGK-~G~V~~V~r~~~~ViVegvN~~kkhvK~~~e~~~GgIi~~E~PIh 131 (135)
...|-.|.+-|+ .|+|++|..+ .|.|. .. +. +..|+.++++.-|.
T Consensus 102 v~~V~~G~yiG~n~G~I~~Is~~--~I~l~-----E~-v~----d~~G~w~~R~~~l~ 147 (149)
T PF04351_consen 102 VYRVKVGDYIGQNYGRITSISED--SIELV-----EI-VP----DGQGCWQERPATLA 147 (149)
T ss_dssp EEEEETTEEETTTTEEEEEEETT--EEEEE-----EE-EE-----SSSSEEEEEEEEE
T ss_pred EEEecCCCEeccCCCEEEEEeCC--eEEEE-----EE-cc----cCCCCEEEEeEEEe
Confidence 344556777777 7889998854 44333 21 11 34689998887764
No 205
>PF11910 NdhO: Cyanobacterial and plant NDH-1 subunit O; InterPro: IPR020905 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit O. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0005886 plasma membrane
Probab=20.77 E-value=44 Score=23.30 Aligned_cols=16 Identities=25% Similarity=0.246 Sum_probs=13.0
Q ss_pred eeeCCEEEEEecCCCC
Q 032704 70 VKAGDTVKVIAGCDKG 85 (135)
Q Consensus 70 I~kGD~V~VI~GkdKG 85 (135)
++|||.|.|++.+.-|
T Consensus 1 lKKG~lVrv~re~~~n 16 (67)
T PF11910_consen 1 LKKGSLVRVNREKYEN 16 (67)
T ss_pred CCcceEEEeehHhhcC
Confidence 5899999999887654
No 206
>TIGR01945 rnfC electron transport complex, RnfABCDGE type, C subunit. The six subunit complex RnfABCDGE in Rhodobacter capsulatus encodes an apparent NADH oxidoreductase responsible for electron transport to nitrogenase, necessary for nitrogen fixation. A closely related complex in E. coli, RsxABCDGE (Reducer of SoxR), reduces the 2Fe-2S-containing superoxide sensor SoxR, active as a transcription factor when oxidized. This family of putative NADH oxidoreductase complexes exists in many of the same species as the related NQR, a Na(+)-translocating NADH-quinone reductase, but is distinct. This model describes the C subunit.
Probab=20.64 E-value=1.2e+02 Score=26.81 Aligned_cols=31 Identities=23% Similarity=0.247 Sum_probs=22.8
Q ss_pred ccceeeeCCEEEE--EecCCCC---------eEeEEEEEEcc
Q 032704 66 HKMHVKAGDTVKV--IAGCDKG---------KIGEITKVFRH 96 (135)
Q Consensus 66 ~k~~I~kGD~V~V--I~GkdKG---------K~G~V~~V~r~ 96 (135)
.+..+++||+|+. +-+.++| --|+|++|.+.
T Consensus 43 ~~~~V~~Gd~V~~Gq~i~~~~~~~~~~~ha~vsG~V~~i~~~ 84 (435)
T TIGR01945 43 AEPIVKVGDKVLKGQKIAKADGFVSAPIHAPTSGTVVAIEER 84 (435)
T ss_pred CceeeCCCCEECCCCEeccCCCcceeeeecCCCeEEEEeccc
Confidence 4667999999986 4455666 35899999753
No 207
>TIGR00157 ribosome small subunit-dependent GTPase A. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option).
Probab=20.44 E-value=1.7e+02 Score=23.58 Aligned_cols=35 Identities=17% Similarity=0.092 Sum_probs=23.7
Q ss_pred eeCCEEEEEecCCCCeEeEEEEEEccCCEE---EEeccce
Q 032704 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTV---MVKDINL 107 (135)
Q Consensus 71 ~kGD~V~VI~GkdKGK~G~V~~V~r~~~~V---iVegvN~ 107 (135)
.+||.|.+-... +..|.|.+|....+.+ ++.++..
T Consensus 2 ~vGD~V~~~~~~--~~~~~i~~i~eR~~~L~r~~~~n~D~ 39 (245)
T TIGR00157 2 VVGDRVVWEPGN--VVKVYGGAIAERKNELTRPIVANIDQ 39 (245)
T ss_pred CCCcEEEEEecC--CCceEEEEEecccceEECcccccCCE
Confidence 579999985432 2458899998887655 4555443
No 208
>cd06552 ASCH_yqfb_like ASC-1 homology domain, subfamily similar to Escherichia coli Yqfb. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=20.30 E-value=1.2e+02 Score=20.77 Aligned_cols=26 Identities=42% Similarity=0.404 Sum_probs=16.3
Q ss_pred eeeeCCEEEEEecCCCCeEeEEEEEE
Q 032704 69 HVKAGDTVKVIAGCDKGKIGEITKVF 94 (135)
Q Consensus 69 ~I~kGD~V~VI~GkdKGK~G~V~~V~ 94 (135)
++++||.+.+..|...--..+|++|.
T Consensus 28 ~~~~Gd~~~~~~~~~~~~~~~v~~V~ 53 (100)
T cd06552 28 HLKPGDVVEVHTGERIFGEAEITSVE 53 (100)
T ss_pred CCCCCCEEEEEECCEEEEEEEEEEEE
Confidence 36899999888775333333444444
No 209
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.27 E-value=1.6e+02 Score=22.83 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=21.8
Q ss_pred ccceeeeCCEEEEEecC------------CCCeEeEEEEEEc
Q 032704 66 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVFR 95 (135)
Q Consensus 66 ~k~~I~kGD~V~VI~Gk------------dKGK~G~V~~V~r 95 (135)
..+-|++||.|.++... +-|..|++..|-.
T Consensus 97 ~p~~V~rG~~V~i~~~~~g~~i~~~G~Al~~G~~Gd~IrVrN 138 (160)
T PRK06005 97 EPSLVTRGSPVKLVFSAGGLTITAAGTPLQSGAAGDLIRVRN 138 (160)
T ss_pred CCcEEeCCCEEEEEEecCCEEEEEEEEEcccCCCCCEEEEEE
Confidence 45679999999998653 4566677766663
No 210
>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=20.20 E-value=2.1e+02 Score=22.76 Aligned_cols=80 Identities=23% Similarity=0.233 Sum_probs=51.1
Q ss_pred ccccCcccCCCCCC--Ccc-ccCCCC---ceeeeeeeeeeee-eecCCCCCc---------------ccccceeeeCCEE
Q 032704 19 NSFFGQRLSFPSLS--PIT-VKPTDK---PCLIVVRLKRWER-KECKPNSLP---------------VLHKMHVKAGDTV 76 (135)
Q Consensus 19 ~~f~g~~l~~~~~~--~~~-~~~~~~---~~~~~~~~k~wer-~~~k~~~lp---------------~~~k~~I~kGD~V 76 (135)
+-=|||.+.|.... -.. .+++++ +|.+.=....|-= -.|....+. -..|-.++-||+|
T Consensus 15 SPPWG~~ipPl~v~llE~Vylks~~tfGYCcGV~W~~~~W~Y~I~~~~~il~~t~~eii~tg~~q~~tv~kp~F~LGd~V 94 (150)
T PF07154_consen 15 SPPWGQQIPPLEVQLLERVYLKSTRTFGYCCGVQWEEDCWIYAIVCHNEILYATKYEIIGTGQLQSLTVQKPAFRLGDRV 94 (150)
T ss_pred cCCccccCCchhhhhheeeeecCcCcceeeeeeEEcCCcEEEEEEecCceEEeccceEeecCccceeeccCCceecCCEE
Confidence 45689999874433 233 555555 4777655444521 111111100 1367789999999
Q ss_pred EEEecCCCCeEeEEEEEEccCC
Q 032704 77 KVIAGCDKGKIGEITKVFRHNS 98 (135)
Q Consensus 77 ~VI~GkdKGK~G~V~~V~r~~~ 98 (135)
.+-...|.=|+-.|+-|+.-++
T Consensus 95 ~~~f~~~~pkqRlIlGv~lv~~ 116 (150)
T PF07154_consen 95 EFRFYSDGPKQRLILGVFLVNN 116 (150)
T ss_pred EEEecCCCCceEEEEEEEEecC
Confidence 9999999999999998887553
Done!