Query 031394
Match_columns 160
No_of_seqs 129 out of 1262
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 13:29:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031394.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031394hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01079 rplX_bact ribosomal 100.0 3.8E-38 8.2E-43 234.8 12.5 102 35-136 2-104 (104)
2 PRK00004 rplX 50S ribosomal pr 100.0 4.6E-38 1E-42 234.4 12.6 104 34-137 2-105 (105)
3 KOG1708 Mitochondrial/chloropl 100.0 5.8E-36 1.3E-40 245.3 9.0 140 3-142 39-179 (236)
4 COG0198 RplX Ribosomal protein 100.0 1.9E-34 4.1E-39 215.0 11.1 102 34-137 2-104 (104)
5 PRK01191 rpl24p 50S ribosomal 100.0 3.8E-29 8.2E-34 190.7 7.9 94 5-115 20-113 (120)
6 PTZ00194 60S ribosomal protein 100.0 6.7E-29 1.5E-33 194.1 7.1 93 5-115 21-113 (143)
7 CHL00141 rpl24 ribosomal prote 100.0 3.4E-28 7.4E-33 174.9 8.7 78 33-110 5-82 (83)
8 PRK12281 rplX 50S ribosomal pr 99.9 1.6E-27 3.4E-32 169.0 7.9 74 32-105 2-75 (76)
9 TIGR01080 rplX_A_E ribosomal p 99.9 1.9E-26 4.2E-31 174.5 8.2 93 5-114 16-108 (114)
10 KOG3401 60S ribosomal protein 99.6 2.1E-15 4.5E-20 118.1 3.4 89 4-109 22-111 (145)
11 PF00467 KOW: KOW motif; Inte 98.8 1.4E-08 3.1E-13 60.6 4.8 32 39-70 1-32 (32)
12 smart00739 KOW KOW (Kyprides, 97.8 3E-05 6.5E-10 43.6 3.9 26 37-62 2-27 (28)
13 PRK08559 nusG transcription an 97.4 0.00043 9.3E-09 54.3 6.1 61 11-74 72-132 (153)
14 TIGR00405 L26e_arch ribosomal 97.4 0.00052 1.1E-08 52.8 6.3 59 12-73 65-123 (145)
15 PRK05609 nusG transcription an 97.0 0.0014 3E-08 51.6 5.5 36 35-70 125-160 (181)
16 TIGR00922 nusG transcription t 96.9 0.0017 3.7E-08 50.9 5.0 36 35-70 118-153 (172)
17 COG0250 NusG Transcription ant 96.9 0.0018 3.8E-08 52.5 4.8 38 33-70 120-157 (178)
18 TIGR01955 RfaH transcriptional 96.4 0.0066 1.4E-07 46.8 5.1 35 35-70 107-141 (159)
19 PRK09014 rfaH transcriptional 95.9 0.012 2.6E-07 45.8 4.5 34 36-70 109-142 (162)
20 TIGR01956 NusG_myco NusG famil 95.8 0.016 3.5E-07 49.8 5.2 35 36-70 205-239 (258)
21 PRK04333 50S ribosomal protein 93.3 0.2 4.3E-06 36.2 4.8 36 36-72 3-38 (84)
22 KOG1999 RNA polymerase II tran 90.0 0.43 9.4E-06 47.6 4.6 28 36-63 459-486 (1024)
23 PTZ00471 60S ribosomal protein 89.2 0.68 1.5E-05 36.4 4.3 40 37-76 5-50 (134)
24 PTZ00065 60S ribosomal protein 86.1 1.6 3.4E-05 34.2 4.7 35 37-72 8-42 (130)
25 COG2163 RPL14A Ribosomal prote 82.9 2.2 4.8E-05 33.1 4.2 35 37-72 5-39 (125)
26 PRK04313 30S ribosomal protein 77.4 4.1 8.9E-05 34.7 4.5 41 31-71 166-210 (237)
27 KOG1999 RNA polymerase II tran 77.3 2.2 4.7E-05 42.9 3.1 26 37-62 408-433 (1024)
28 COG5164 SPT5 Transcription elo 76.4 2.2 4.7E-05 40.1 2.7 28 37-64 140-167 (607)
29 PRK06531 yajC preprotein trans 75.4 5.4 0.00012 30.3 4.2 31 36-70 36-66 (113)
30 COG1862 YajC Preprotein transl 72.1 6.8 0.00015 29.0 4.0 29 36-70 43-71 (97)
31 PF09953 DUF2187: Uncharacteri 70.6 10 0.00022 25.8 4.2 27 38-70 5-31 (57)
32 PRK05585 yajC preprotein trans 68.1 10 0.00022 28.3 4.2 29 36-70 52-80 (106)
33 PRK04306 50S ribosomal protein 67.9 6.1 0.00013 29.5 2.9 53 15-70 15-78 (98)
34 COG1471 RPS4A Ribosomal protei 67.4 9.8 0.00021 32.6 4.4 41 31-71 168-212 (241)
35 PTZ00223 40S ribosomal protein 64.0 11 0.00025 32.7 4.3 40 31-70 166-208 (273)
36 PLN00036 40S ribosomal protein 63.9 14 0.0003 32.0 4.8 39 32-70 170-211 (261)
37 TIGR00739 yajC preprotein tran 61.5 18 0.00038 25.9 4.3 29 36-70 37-65 (84)
38 PRK05886 yajC preprotein trans 61.1 17 0.00036 27.5 4.2 29 36-70 38-66 (109)
39 PTZ00118 40S ribosomal protein 61.0 16 0.00035 31.7 4.6 32 32-63 170-201 (262)
40 PF05641 Agenet: Agenet domain 59.0 26 0.00056 23.5 4.6 33 37-70 1-37 (68)
41 COG1532 Predicted RNA-binding 57.7 23 0.0005 24.0 4.0 34 38-71 22-57 (57)
42 PF03144 GTP_EFTU_D2: Elongati 56.9 19 0.0004 23.7 3.6 30 36-66 12-44 (74)
43 PRK00409 recombination and DNA 56.8 19 0.00042 35.3 4.9 38 35-75 635-673 (782)
44 KOG3418 60S ribosomal protein 56.7 19 0.00041 28.4 4.0 39 37-75 5-49 (136)
45 PLN00190 60S ribosomal protein 55.4 11 0.00024 30.4 2.6 51 16-69 15-76 (158)
46 PF02699 YajC: Preprotein tran 54.0 4.2 9.2E-05 28.8 0.0 30 35-70 35-64 (82)
47 PF12701 LSM14: Scd6-like Sm d 53.1 36 0.00078 25.1 4.8 36 38-73 6-41 (96)
48 PF12353 eIF3g: Eukaryotic tra 51.4 28 0.00061 26.7 4.2 27 107-133 9-35 (128)
49 PF08206 OB_RNB: Ribonuclease 49.5 14 0.00029 24.2 1.9 24 37-60 32-58 (58)
50 COG2002 AbrB Regulators of sta 48.9 27 0.00058 24.8 3.5 27 16-53 18-44 (89)
51 PTZ00189 60S ribosomal protein 48.0 18 0.00038 29.3 2.6 52 15-69 14-76 (160)
52 PF01157 Ribosomal_L21e: Ribos 47.1 37 0.00081 25.2 4.1 36 30-65 25-71 (99)
53 TIGR01069 mutS2 MutS2 family p 46.5 31 0.00068 33.8 4.6 34 38-75 626-661 (771)
54 PF09526 DUF2387: Probable met 43.9 42 0.00092 23.4 3.8 36 105-141 10-45 (71)
55 PF11623 DUF3252: Protein of u 43.1 57 0.0012 21.8 4.0 40 37-76 2-43 (53)
56 COG0361 InfA Translation initi 42.7 40 0.00086 24.0 3.5 30 33-62 43-72 (75)
57 COG2139 RPL21A Ribosomal prote 42.3 56 0.0012 24.5 4.4 39 36-74 32-80 (98)
58 PF14505 DUF4438: Domain of un 42.1 55 0.0012 28.4 4.9 32 39-70 60-91 (258)
59 cd05703 S1_Rrp5_repeat_hs12_sc 41.3 53 0.0011 22.1 3.9 25 36-70 46-70 (73)
60 KOG4315 G-patch nucleic acid b 39.5 20 0.00043 33.3 1.9 46 20-71 383-428 (455)
61 cd04466 S1_YloQ_GTPase S1_YloQ 39.2 61 0.0013 20.9 3.9 28 38-67 39-66 (68)
62 PRK02749 photosystem I reactio 38.3 39 0.00084 23.9 2.8 29 36-64 2-32 (71)
63 COG5164 SPT5 Transcription elo 37.9 34 0.00073 32.5 3.2 34 38-71 353-386 (607)
64 cd05707 S1_Rrp5_repeat_sc11 S1 37.2 60 0.0013 21.0 3.6 23 37-69 45-67 (68)
65 CHL00125 psaE photosystem I su 37.1 39 0.00085 23.4 2.7 28 37-64 2-31 (64)
66 PF01079 Hint: Hint module; I 37.1 55 0.0012 27.2 4.1 37 36-72 105-153 (217)
67 cd05695 S1_Rrp5_repeat_hs3 S1_ 36.8 62 0.0013 21.3 3.6 24 36-69 42-65 (66)
68 KOG2192 PolyC-binding hnRNP-K 35.8 23 0.0005 31.4 1.7 44 18-62 146-189 (390)
69 smart00743 Agenet Tudor-like d 35.7 1.1E+02 0.0024 19.5 4.6 27 36-62 2-29 (61)
70 KOG0122 Translation initiation 35.5 45 0.00098 29.0 3.4 39 109-147 27-72 (270)
71 cd04717 BAH_polybromo BAH, or 35.2 1.1E+02 0.0024 22.5 5.1 36 37-72 4-42 (121)
72 PF02427 PSI_PsaE: Photosystem 34.5 55 0.0012 22.5 3.0 28 37-64 1-30 (61)
73 cd05698 S1_Rrp5_repeat_hs6_sc5 34.1 79 0.0017 20.3 3.8 23 37-69 45-67 (70)
74 cd05696 S1_Rrp5_repeat_hs4 S1_ 34.0 85 0.0018 20.9 4.0 24 36-69 46-69 (71)
75 TIGR03170 flgA_cterm flagella 34.0 70 0.0015 23.3 3.8 35 33-67 62-109 (122)
76 COG3700 AphA Acid phosphatase 33.9 15 0.00032 31.0 0.2 33 35-67 125-157 (237)
77 cd05697 S1_Rrp5_repeat_hs5 S1_ 33.8 94 0.002 20.1 4.1 24 36-69 44-67 (69)
78 PF00575 S1: S1 RNA binding do 33.1 1.1E+02 0.0023 19.9 4.3 26 35-70 47-72 (74)
79 PF04452 Methyltrans_RNA: RNA 33.0 62 0.0013 26.4 3.8 35 36-70 16-50 (225)
80 COG1162 Predicted GTPases [Gen 32.8 55 0.0012 28.9 3.6 30 35-67 43-72 (301)
81 cd05793 S1_IF1A S1_IF1A: Trans 32.8 47 0.001 23.3 2.6 29 36-64 38-66 (77)
82 COG1193 Mismatch repair ATPase 32.8 47 0.001 32.8 3.4 38 29-70 605-642 (753)
83 cd05708 S1_Rrp5_repeat_sc12 S1 32.8 1E+02 0.0022 19.9 4.2 25 36-70 47-71 (77)
84 cd03692 mtIF2_IVc mtIF2_IVc: t 32.3 87 0.0019 21.6 3.9 32 35-66 25-56 (84)
85 cd01854 YjeQ_engC YjeQ/EngC. 32.2 76 0.0017 26.9 4.3 28 38-67 36-63 (287)
86 cd05688 S1_RPS1_repeat_ec3 S1_ 32.0 92 0.002 19.4 3.8 24 36-69 44-67 (68)
87 PF01176 eIF-1a: Translation i 31.6 75 0.0016 21.2 3.4 24 36-59 41-64 (65)
88 cd04451 S1_IF1 S1_IF1: Transla 31.6 50 0.0011 21.7 2.5 21 37-57 41-61 (64)
89 TIGR00523 eIF-1A eukaryotic/ar 31.6 34 0.00074 25.3 1.8 27 35-63 56-85 (99)
90 PLN00045 photosystem I reactio 31.4 96 0.0021 23.3 4.1 28 36-63 39-68 (101)
91 PF05257 CHAP: CHAP domain; I 31.3 78 0.0017 23.0 3.7 37 36-73 62-100 (124)
92 PRK12618 flgA flagellar basal 31.2 76 0.0017 24.6 3.8 34 33-66 78-124 (141)
93 PF00018 SH3_1: SH3 domain; I 30.1 69 0.0015 19.5 2.8 18 32-49 11-28 (48)
94 PF07076 DUF1344: Protein of u 29.8 1.9E+02 0.0041 19.9 6.2 20 53-72 5-24 (61)
95 PF02887 PK_C: Pyruvate kinase 29.6 32 0.00069 25.0 1.4 19 37-55 90-108 (117)
96 CHL00010 infA translation init 29.3 97 0.0021 21.6 3.7 26 37-62 47-72 (78)
97 PRK08577 hypothetical protein; 29.3 72 0.0015 24.0 3.3 29 15-54 16-44 (136)
98 cd04461 S1_Rrp5_repeat_hs8_sc7 29.1 1E+02 0.0022 20.7 3.8 24 36-69 58-81 (83)
99 cd05705 S1_Rrp5_repeat_hs14 S1 29.0 98 0.0021 20.9 3.7 24 36-69 50-73 (74)
100 PRK07018 flgA flagellar basal 28.9 83 0.0018 26.1 3.9 35 33-67 173-220 (235)
101 cd04456 S1_IF1A_like S1_IF1A_l 28.4 74 0.0016 22.4 3.0 29 36-64 38-67 (78)
102 cd05685 S1_Tex S1_Tex: The C-t 27.9 1.1E+02 0.0024 18.9 3.6 23 37-69 45-67 (68)
103 cd00164 S1_like S1_like: Ribos 27.7 1.1E+02 0.0024 18.4 3.5 23 36-68 41-63 (65)
104 PF01426 BAH: BAH domain; Int 27.6 82 0.0018 22.2 3.2 29 36-64 2-32 (119)
105 PF04014 Antitoxin-MazE: Antid 27.6 67 0.0014 19.9 2.4 25 14-49 9-33 (47)
106 cd04714 BAH_BAHCC1 BAH, or Bro 27.4 1.8E+02 0.004 21.5 5.2 35 36-70 3-40 (121)
107 cd04715 BAH_Orc1p_like BAH, or 26.9 1.6E+02 0.0035 23.3 5.1 29 36-64 29-57 (159)
108 PF02211 NHase_beta: Nitrile h 26.9 78 0.0017 26.6 3.4 29 32-60 130-168 (222)
109 cd00174 SH3 Src homology 3 dom 26.5 73 0.0016 18.6 2.4 15 34-48 15-29 (54)
110 cd04721 BAH_plant_1 BAH, or Br 26.4 1.9E+02 0.0041 22.0 5.2 29 36-64 7-35 (130)
111 cd05706 S1_Rrp5_repeat_sc10 S1 26.4 1.4E+02 0.0031 19.3 4.0 23 37-69 48-70 (73)
112 PRK12289 GTPase RsgA; Reviewed 26.0 1.1E+02 0.0025 27.0 4.4 31 38-68 53-83 (352)
113 cd05690 S1_RPS1_repeat_ec5 S1_ 25.9 1.2E+02 0.0027 19.2 3.6 23 36-68 45-67 (69)
114 smart00652 eIF1a eukaryotic tr 25.7 82 0.0018 22.4 2.9 29 36-64 43-71 (83)
115 CHL00084 rpl19 ribosomal prote 25.1 3.2E+02 0.0069 20.9 8.6 80 36-128 22-113 (117)
116 PRK12442 translation initiatio 24.9 1.3E+02 0.0029 22.0 3.8 29 34-62 44-72 (87)
117 cd04452 S1_IF2_alpha S1_IF2_al 24.3 1.8E+02 0.0038 18.8 4.2 23 37-69 50-72 (76)
118 PRK08515 flgA flagellar basal 23.9 1.1E+02 0.0025 25.2 3.8 35 33-67 162-208 (222)
119 cd05689 S1_RPS1_repeat_ec4 S1_ 23.9 1.3E+02 0.0028 19.4 3.4 24 35-68 47-70 (72)
120 cd05687 S1_RPS1_repeat_ec1_hs1 23.8 1.7E+02 0.0037 18.7 4.0 23 37-69 45-67 (70)
121 smart00439 BAH Bromo adjacent 23.8 1.6E+02 0.0035 20.6 4.2 29 37-65 2-32 (120)
122 PF09926 DUF2158: Uncharacteri 23.5 51 0.0011 21.7 1.3 13 37-49 1-13 (53)
123 smart00316 S1 Ribosomal protei 23.5 1.8E+02 0.004 17.6 4.2 24 36-69 46-69 (72)
124 PF07653 SH3_2: Variant SH3 do 23.4 64 0.0014 20.3 1.8 14 33-46 14-27 (55)
125 PF02938 GAD: GAD domain; Int 23.3 47 0.001 23.6 1.3 28 16-50 61-88 (95)
126 PRK11713 16S ribosomal RNA met 23.1 1.4E+02 0.0031 24.5 4.2 32 36-67 29-60 (234)
127 smart00326 SH3 Src homology 3 23.0 91 0.002 18.3 2.4 16 34-49 18-33 (58)
128 PRK00276 infA translation init 22.9 1.3E+02 0.0027 20.5 3.3 22 37-58 47-68 (72)
129 cd05792 S1_eIF1AD_like S1_eIF1 22.9 1.1E+02 0.0024 21.7 3.1 30 35-64 37-67 (78)
130 PF13437 HlyD_3: HlyD family s 22.9 1.7E+02 0.0036 20.2 4.1 27 36-62 49-78 (105)
131 PF15276 PP1_bind: Protein pho 22.9 65 0.0014 22.4 1.8 39 8-52 4-42 (64)
132 TIGR01448 recD_rel helicase, p 22.8 1.4E+02 0.003 29.0 4.7 50 14-63 560-618 (720)
133 cd01736 LSm14_N LSm14 (also kn 22.7 2.2E+02 0.0048 20.2 4.5 37 38-74 4-40 (74)
134 cd04709 BAH_MTA BAH, or Bromo 22.7 2.5E+02 0.0053 22.5 5.4 33 37-69 4-38 (164)
135 cd05691 S1_RPS1_repeat_ec6 S1_ 22.3 1.9E+02 0.0042 18.3 4.0 25 36-70 44-68 (73)
136 PF11717 Tudor-knot: RNA bindi 22.2 1.2E+02 0.0027 19.4 3.0 29 37-65 1-29 (55)
137 cd04471 S1_RNase_R S1_RNase_R: 22.1 1.7E+02 0.0036 19.2 3.8 24 36-69 57-80 (83)
138 KOG4225 Sorbin and SH3 domain- 22.1 98 0.0021 29.1 3.3 37 20-57 233-277 (489)
139 PRK10708 hypothetical protein; 21.9 1.3E+02 0.0028 20.6 3.1 27 38-64 2-28 (62)
140 PF02941 FeThRed_A: Ferredoxin 21.8 1.1E+02 0.0024 21.4 2.8 24 39-62 1-38 (67)
141 cd04090 eEF2_II_snRNP Loc2 eEF 21.4 2.9E+02 0.0063 19.2 5.1 13 36-48 27-39 (94)
142 PRK09510 tolA cell envelope in 21.3 1.5E+02 0.0033 27.0 4.3 26 109-134 324-349 (387)
143 TIGR02594 conserved hypothetic 20.9 2E+02 0.0044 21.8 4.4 33 38-71 75-107 (129)
144 PRK06005 flgA flagellar basal 20.7 1.5E+02 0.0032 23.5 3.7 39 33-71 97-147 (160)
145 PRK07252 hypothetical protein; 20.6 1.8E+02 0.004 21.8 4.1 25 36-70 47-71 (120)
No 1
>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=100.00 E-value=3.8e-38 Score=234.81 Aligned_cols=102 Identities=51% Similarity=0.779 Sum_probs=98.4
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceeeeeEEecCCcccc-CceeEEEeecCcCCCeeeeecCCCCee
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEE-QGQIIKIEAPIHSSNVMLYSKEMEVAS 113 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~-~ggiv~~e~PI~iSnV~Lv~p~~~~pt 113 (160)
++|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|++|++.++ +|+++++|+|||+|||+|+||.+++||
T Consensus 2 ~~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~lv~p~~~k~~ 81 (104)
T TIGR01079 2 MKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVMLFDPKTGKAT 81 (104)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHHHeEEEcCcCCCCe
Confidence 4789999999999999999999999999999999999999999999998776 899999999999999999999999999
Q ss_pred eEEEEEccCCcEEEEEeccCCcc
Q 031394 114 RVGHKVLDDGTRVRYLIKTGEII 136 (160)
Q Consensus 114 Rv~~~~~edG~kvRv~kksg~~i 136 (160)
|++|++++||+++|+|++||+.|
T Consensus 82 rv~~~~~~~g~kvRv~k~~g~~i 104 (104)
T TIGR01079 82 RVGIRFEEDGKKVRVFKKTGEII 104 (104)
T ss_pred EEEEEEccCCcEEEEEeccCCcC
Confidence 99999999999999999999875
No 2
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=100.00 E-value=4.6e-38 Score=234.44 Aligned_cols=104 Identities=50% Similarity=0.731 Sum_probs=100.6
Q ss_pred ccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceeeeeEEecCCccccCceeEEEeecCcCCCeeeeecCCCCee
Q 031394 34 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVAS 113 (160)
Q Consensus 34 k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggiv~~e~PI~iSnV~Lv~p~~~~pt 113 (160)
+|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|++|++++.+|+++++|+|||+|||+|+||.+++|+
T Consensus 2 ~~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~lv~p~~~~~~ 81 (105)
T PRK00004 2 MMKIKKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHISNVALVDPKTGKAT 81 (105)
T ss_pred CCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHHHEEEEeCcCCCCe
Confidence 67899999999999999999999999999999999999999999999998788899999999999999999999999999
Q ss_pred eEEEEEccCCcEEEEEeccCCccc
Q 031394 114 RVGHKVLDDGTRVRYLIKTGEIID 137 (160)
Q Consensus 114 Rv~~~~~edG~kvRv~kksg~~i~ 137 (160)
|++|++++||+++|+|++||+.|+
T Consensus 82 rv~~~~~~~g~kvRv~k~~g~~i~ 105 (105)
T PRK00004 82 RVGFKFLEDGKKVRVAKKSGEVID 105 (105)
T ss_pred EEEEEEccCCcEEEEEecCCCCcC
Confidence 999999999999999999999874
No 3
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.8e-36 Score=245.28 Aligned_cols=140 Identities=42% Similarity=0.687 Sum_probs=135.1
Q ss_pred CCCCCcceeeeccCCHHHHHhcCCCCCccccccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceeeeeEEecCC
Q 031394 3 VKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKR 82 (160)
Q Consensus 3 ~~~~~~~~~~s~~l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~ 82 (160)
.+.+|++||.-..+..|.|..+.+...++.+.|+++.||+|+||.|+||||+|.|++|++.+++|+|+|+|...+|+...
T Consensus 39 r~~adk~~~~~qk~~~w~rrr~~~~e~i~d~dw~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gse 118 (236)
T KOG1708|consen 39 RKVADKRCLVLQKNKPWERRRCVPVEPIIDEDWHFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSE 118 (236)
T ss_pred CChhhhhhhHHhhcCccccccCCCCCCccccceeEecCCEEEEEecccCCccceEEEEeecCceEEEcccchhhhhhccc
Confidence 46789999999999999999999998888899999999999999999999999999999999999999999999999888
Q ss_pred ccccCceeEEEeecCcCCC-eeeeecCCCCeeeEEEEEccCCcEEEEEeccCCcccchhhh
Q 031394 83 EEEEQGQIIKIEAPIHSSN-VMLYSKEMEVASRVGHKVLDDGTRVRYLIKTGEIIDSAENW 142 (160)
Q Consensus 83 ~~~~~ggiv~~e~PI~iSn-V~Lv~p~~~~ptRv~~~~~edG~kvRv~kksg~~i~~p~~~ 142 (160)
.++..|.|+..|+|||+|| |||+||++.+||+++|+++++|++||||.+||++||+|+.|
T Consensus 119 keg~pgtivk~EaPlhvsk~VmLvdp~d~q~te~~wr~~e~GekVRvstrSG~iIpipe~~ 179 (236)
T KOG1708|consen 119 KEGEPGTIVKSEAPLHVSKQVMLVDPEDDQPTEVEWRFTEDGEKVRVSTRSGRIIPIPEKW 179 (236)
T ss_pred ccCCCceEEeecCCceecceeEEECccccCCceeeEEEcCCCcEEEEEecccccccCcccc
Confidence 7888999999999999999 99999999999999999999999999999999999999988
No 4
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-34 Score=215.03 Aligned_cols=102 Identities=51% Similarity=0.749 Sum_probs=96.8
Q ss_pred ccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceeeeeEEecCCccccCceeEEEeecCcCCCeeeeec-CCCCe
Q 031394 34 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSK-EMEVA 112 (160)
Q Consensus 34 k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggiv~~e~PI~iSnV~Lv~p-~~~~p 112 (160)
.|+|++||+|.||+|+|||++|+|++|+++. |+|||+|++++|.+|++.+++|||+++|+|||+|||||++| .++++
T Consensus 2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i~~~~~~~~~ 79 (104)
T COG0198 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVEGVNVVKKHIKPSQENPEGGIINKEAPIHISNVAIIDPNKTGKP 79 (104)
T ss_pred CcceecCCEEEEEecCCCCcceEEEEEecCe--EEEECcEEEEecCCCCCcCCCCceeeeeecccHHHeEEeccccCCCc
Confidence 4678999999999999999999999999999 99999999999999887888899999999999999999999 68999
Q ss_pred eeEEEEEccCCcEEEEEeccCCccc
Q 031394 113 SRVGHKVLDDGTRVRYLIKTGEIID 137 (160)
Q Consensus 113 tRv~~~~~edG~kvRv~kksg~~i~ 137 (160)
+|++|++.+||+++|++++||+.|+
T Consensus 80 ~Rv~~~~~~~~kkvr~~Kk~g~~i~ 104 (104)
T COG0198 80 TRVGYKVEEDGKKVRVAKKSGEVID 104 (104)
T ss_pred ceEEEEEecCCcEEEEEeccCcccC
Confidence 9999998779999999999999874
No 5
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=99.96 E-value=3.8e-29 Score=190.66 Aligned_cols=94 Identities=31% Similarity=0.444 Sum_probs=85.9
Q ss_pred CCCcceeeeccCCHHHHHhcCCCCCccccccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceeeeeEEecCCcc
Q 031394 5 PTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE 84 (160)
Q Consensus 5 ~~~~~~~~s~~l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~ 84 (160)
..+|+++||++||+|||++|+++++++ ++||.|+||+|+|||++|+|++|+++.++|+|||||+.+ +
T Consensus 20 ~~~r~k~msa~LSkeLr~~y~ir~~~I------kkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k----~--- 86 (120)
T PRK01191 20 LHLRQKLMSAPLSKELREKYGIRSLPV------RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKK----A--- 86 (120)
T ss_pred HHHHHHHhcCccCHHHHHHhCCccceE------eCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEEC----C---
Confidence 457899999999999999999999987 999999999999999999999999999999999999987 2
Q ss_pred ccCceeEEEeecCcCCCeeeeecCCCCeeeE
Q 031394 85 EEQGQIIKIEAPIHSSNVMLYSKEMEVASRV 115 (160)
Q Consensus 85 ~~~ggiv~~e~PI~iSnV~Lv~p~~~~ptRv 115 (160)
+| .++|+|||+|||+|+|+..+...|.
T Consensus 87 --~G--~~~e~pIh~SNV~l~~l~l~~~~R~ 113 (120)
T PRK01191 87 --DG--TEVPRPIHPSNVMITKLDLSDERRE 113 (120)
T ss_pred --CC--eEEEcccchhHeEEEeCccCCHHHH
Confidence 24 5999999999999999988766554
No 6
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=99.95 E-value=6.7e-29 Score=194.08 Aligned_cols=93 Identities=25% Similarity=0.404 Sum_probs=86.3
Q ss_pred CCCcceeeeccCCHHHHHhcCCCCCccccccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceeeeeEEecCCcc
Q 031394 5 PTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE 84 (160)
Q Consensus 5 ~~~~~~~~s~~l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~ 84 (160)
..+|+++|||+||+|||.+|++|++++ ++||+|+||+|+|||++|+|++|+++.++|+|||||+.++|.+|
T Consensus 21 ~h~r~k~msa~LSkeLr~k~~~Rs~~I------kkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~--- 91 (143)
T PTZ00194 21 SHLRRKLMSAPLSKELRAKYNVRSMPV------RKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEP--- 91 (143)
T ss_pred HHHHHHHhcCccCHHHHHHhCCcccee------ecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCE---
Confidence 357899999999999999999999987 99999999999999999999999999999999999999987653
Q ss_pred ccCceeEEEeecCcCCCeeeeecCCCCeeeE
Q 031394 85 EEQGQIIKIEAPIHSSNVMLYSKEMEVASRV 115 (160)
Q Consensus 85 ~~~ggiv~~e~PI~iSnV~Lv~p~~~~ptRv 115 (160)
.|+|||+|||+|+++..+.+ |.
T Consensus 92 --------~e~PIh~SNV~iv~l~l~~~-R~ 113 (143)
T PTZ00194 92 --------VQIGIHPSNVIITKLKLNKD-RK 113 (143)
T ss_pred --------eecCcCchheEEEccccCch-HH
Confidence 69999999999999988776 54
No 7
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=99.95 E-value=3.4e-28 Score=174.85 Aligned_cols=78 Identities=59% Similarity=0.930 Sum_probs=74.1
Q ss_pred cccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceeeeeEEecCCccccCceeEEEeecCcCCCeeeeecCCC
Q 031394 33 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEME 110 (160)
Q Consensus 33 ~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggiv~~e~PI~iSnV~Lv~p~~~ 110 (160)
.+++|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|++|+..+.+|+++++|+|||+|||+|+||+++
T Consensus 5 ~~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~~k~~k~~~~~~~g~i~~~e~pI~~SnV~lvdp~~~ 82 (83)
T CHL00141 5 KKMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHSSNVMLYNEESN 82 (83)
T ss_pred eeCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCHHHEEEeCcccC
Confidence 456889999999999999999999999999999999999999999999988788899999999999999999999874
No 8
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=99.94 E-value=1.6e-27 Score=168.98 Aligned_cols=74 Identities=41% Similarity=0.605 Sum_probs=70.5
Q ss_pred ccccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceeeeeEEecCCccccCceeEEEeecCcCCCeeee
Q 031394 32 LHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLY 105 (160)
Q Consensus 32 ~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggiv~~e~PI~iSnV~Lv 105 (160)
+.+|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|++|++++.+|+++++|+|||+|||+|+
T Consensus 2 ~~~~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~kkh~kp~~~~~~G~i~~~e~pI~~SnV~l~ 75 (76)
T PRK12281 2 KVKLKVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMPIHISNVKKV 75 (76)
T ss_pred CccccccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCCccCCCCCEEEEEcCcCHHHceec
Confidence 35678999999999999999999999999999999999999999999999988888999999999999999996
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=99.93 E-value=1.9e-26 Score=174.54 Aligned_cols=93 Identities=27% Similarity=0.429 Sum_probs=85.0
Q ss_pred CCCcceeeeccCCHHHHHhcCCCCCccccccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceeeeeEEecCCcc
Q 031394 5 PTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREE 84 (160)
Q Consensus 5 ~~~~~~~~s~~l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~ 84 (160)
..+|+++||++||+|||++|+++++++ ++||+|+||+|+|||++|+|++|++++++|+|||+|+.+ |+
T Consensus 16 ~~~r~~~~~a~ls~elr~~y~~r~~~I------kkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k----~~-- 83 (114)
T TIGR01080 16 LHVRRKLMSAPLSKELREKYGKRALPV------RKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEK----VN-- 83 (114)
T ss_pred HhhhhheeecccCHHHHHHcCccccee------ecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEEC----CC--
Confidence 467999999999999999999999987 999999999999999999999999999999999999987 32
Q ss_pred ccCceeEEEeecCcCCCeeeeecCCCCeee
Q 031394 85 EEQGQIIKIEAPIHSSNVMLYSKEMEVASR 114 (160)
Q Consensus 85 ~~~ggiv~~e~PI~iSnV~Lv~p~~~~ptR 114 (160)
| .++|+|||+|||+|+|+..+...|
T Consensus 84 ---G--~~~e~pIh~SnV~l~~l~l~~~~R 108 (114)
T TIGR01080 84 ---G--TEVPVPIHPSNVMITKLNLDDEKR 108 (114)
T ss_pred ---C--eEEEeeechHHeEEEeccCChHHH
Confidence 4 599999999999999998776544
No 10
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=99.55 E-value=2.1e-15 Score=118.09 Aligned_cols=89 Identities=21% Similarity=0.449 Sum_probs=79.3
Q ss_pred CCCCcceeeeccCCHHHHHhcCCCCCccccccceecCCEEEEeecCCCC-eeeEEEEEEccCCeEEEeceeeeeEEecCC
Q 031394 4 KPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKG-KIGEITKVFRHNSTVMVKDINLKTKHVKKR 82 (160)
Q Consensus 4 ~~~~~~~~~s~~l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKG-K~G~V~~V~~~~~~V~VeGvN~~kkh~k~~ 82 (160)
.+.+++++|||+||+|||++|+.++||+ +.+|.|.|..|.++| ++|.|++|++++..+++|.|...+ .
T Consensus 22 ps~~rR~i~sa~ls~eLR~~y~vrs~pi------r~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK----~- 90 (145)
T KOG3401|consen 22 PSHIRRKIMSAPLSKELRQKYNVRSMPI------RKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREK----A- 90 (145)
T ss_pred cHHHHHHHhcchhhHHHHHHhCccccce------eeccEEEEEeccccccccceehhhhhhhheeeeEeEEEee----c-
Confidence 3567899999999999999999999999 999999999999999 999999999999999999976544 1
Q ss_pred ccccCceeEEEeecCcCCCeeeeecCC
Q 031394 83 EEEEQGQIIKIEAPIHSSNVMLYSKEM 109 (160)
Q Consensus 83 ~~~~~ggiv~~e~PI~iSnV~Lv~p~~ 109 (160)
.|. ..+.|||+|++.+..|..
T Consensus 91 ----nGt--~v~vgihPsK~~iTkl~l 111 (145)
T KOG3401|consen 91 ----NGT--TVPVGIHPSKVVITKLKL 111 (145)
T ss_pred ----cCc--ccccccCccceeecccch
Confidence 233 789999999999988754
No 11
>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=98.78 E-value=1.4e-08 Score=60.59 Aligned_cols=32 Identities=53% Similarity=0.709 Sum_probs=30.8
Q ss_pred cCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 39 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 39 kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
+||.|.|++|+++|++|+|++|++++++|+||
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 69999999999999999999999999999986
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.84 E-value=3e-05 Score=43.64 Aligned_cols=26 Identities=50% Similarity=0.704 Sum_probs=24.2
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEc
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFR 62 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~ 62 (160)
+.+||.|.|+.|+++|..|.|++++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 47999999999999999999999975
No 13
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=97.40 E-value=0.00043 Score=54.28 Aligned_cols=61 Identities=23% Similarity=0.248 Sum_probs=46.6
Q ss_pred eeeccCCHHHHHhcCCCCCccccccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceee
Q 031394 11 LIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINL 74 (160)
Q Consensus 11 ~~s~~l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~ 74 (160)
++..+|+.++-..+-... + ....+.+||.|.|+.|+++|..|.|.+++.+++.+.|+-++.
T Consensus 72 ~lg~~l~~~Ei~~il~~~-~--~~~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~ 132 (153)
T PRK08559 72 VVPGEISFEEVEHFLKPK-P--IVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEA 132 (153)
T ss_pred eCCCCCCHHHHHHHHhcc-C--cccCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECC
Confidence 444567777766654221 1 123479999999999999999999999999999999987753
No 14
>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=97.38 E-value=0.00052 Score=52.77 Aligned_cols=59 Identities=20% Similarity=0.267 Sum_probs=45.5
Q ss_pred eeccCCHHHHHhcCCCCCccccccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEecee
Q 031394 12 IVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 73 (160)
Q Consensus 12 ~s~~l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN 73 (160)
+...|+.++-..+.... ... -.+.+||.|.|++|+++|-.|.|.+++..+..|.|+-.+
T Consensus 65 v~~~i~~~ei~~l~~~~-~~~--~~~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~ 123 (145)
T TIGR00405 65 VEGEIDFEEIERFLTPK-KII--ESIKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIE 123 (145)
T ss_pred cCCCCCHHHHHHHhccc-ccc--cccCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEE
Confidence 44568887777764321 111 237899999999999999999999999888899988665
No 15
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=97.04 E-value=0.0014 Score=51.63 Aligned_cols=36 Identities=25% Similarity=0.288 Sum_probs=32.4
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
..+.+||+|.|++|+++|..|.|.++++.++++.|.
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 446899999999999999999999999888888776
No 16
>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=96.91 E-value=0.0017 Score=50.93 Aligned_cols=36 Identities=22% Similarity=0.282 Sum_probs=32.2
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
..+.+||+|.|++|+++|-.|.|.++++.++++.|.
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 346899999999999999999999999888888776
No 17
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=96.86 E-value=0.0018 Score=52.52 Aligned_cols=38 Identities=24% Similarity=0.366 Sum_probs=35.0
Q ss_pred cccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 33 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 33 ~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
....+.+||.|.|++|+++|-.|+|..|+.+++++.|+
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 44578999999999999999999999999999998887
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=96.42 E-value=0.0066 Score=46.83 Aligned_cols=35 Identities=17% Similarity=0.106 Sum_probs=29.4
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
..+.+||+|.|+.|+++|-.|.|.+++. .+++.|.
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~g~v~~~~~-~~r~~v~ 141 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFEAIFLEPDG-EKRSMLL 141 (159)
T ss_pred cCCCCCCEEEEeccCCCCcEEEEEEECC-CceEEEE
Confidence 3478999999999999999999999984 4566554
No 19
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=95.94 E-value=0.012 Score=45.78 Aligned_cols=34 Identities=21% Similarity=0.189 Sum_probs=28.6
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.+.+||+|.|+.|+++|-.|.|.+++ ..+++.|.
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~-~~~r~~v~ 142 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPD-GEARSILL 142 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeC-CCeEEEEe
Confidence 36899999999999999999999998 45555544
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=95.85 E-value=0.016 Score=49.77 Aligned_cols=35 Identities=29% Similarity=0.536 Sum_probs=32.1
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.+..||.|.|+.|+++|..|.|.+++...+++.|.
T Consensus 205 ~f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~Vl 239 (258)
T TIGR01956 205 KFRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVE 239 (258)
T ss_pred CCCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEE
Confidence 46899999999999999999999999888888776
No 21
>PRK04333 50S ribosomal protein L14e; Validated
Probab=93.29 E-value=0.2 Score=36.20 Aligned_cols=36 Identities=19% Similarity=0.310 Sum_probs=31.4
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEece
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 72 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGv 72 (160)
.+..|-.|.+.+|+|+|+...|+.+.- .++|+|+|-
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 458899999999999999999999854 589999874
No 22
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=89.98 E-value=0.43 Score=47.62 Aligned_cols=28 Identities=39% Similarity=0.540 Sum_probs=25.6
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEcc
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRH 63 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~ 63 (160)
.|.+||-|.||+|++.|.+|.|.+|...
T Consensus 459 yF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 459 YFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred hccCCCeEEEEeccccCCcceEEEEeCC
Confidence 3589999999999999999999999873
No 23
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=89.22 E-value=0.68 Score=36.36 Aligned_cols=40 Identities=25% Similarity=0.341 Sum_probs=34.9
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccC------CeEEEeceeeee
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLKT 76 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~------~~V~VeGvN~~k 76 (160)
+++|--|.|++|.+.|+...|++.+.+. +.++|-|+..-.
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP 50 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYP 50 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccc
Confidence 5789999999999999999999988776 689999987643
No 24
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=86.14 E-value=1.6 Score=34.18 Aligned_cols=35 Identities=26% Similarity=0.368 Sum_probs=30.6
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccCCeEEEece
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 72 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGv 72 (160)
+..|=-|.|..|+|+||...|..|. +.|+|+|+|=
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDII-D~nRvLVDGP 42 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIV-TPTRVLVDGA 42 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEE-cCCeEEEeCC
Confidence 4678888888999999999999996 5789999983
No 25
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=82.94 E-value=2.2 Score=33.06 Aligned_cols=35 Identities=31% Similarity=0.365 Sum_probs=31.2
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccCCeEEEece
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 72 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGv 72 (160)
+.+|=-|+|++|.++|+...|+++.-++ .+++.|-
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp 39 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGP 39 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCC
Confidence 5789999999999999999999997766 8888884
No 26
>PRK04313 30S ribosomal protein S4e; Validated
Probab=77.39 E-value=4.1 Score=34.73 Aligned_cols=41 Identities=20% Similarity=0.432 Sum_probs=32.2
Q ss_pred cccccceecCCEEEEeecCCCCeeeEEEEEEccC----CeEEEec
Q 031394 31 VLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKD 71 (160)
Q Consensus 31 ~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~----~~V~VeG 71 (160)
+....++..|-.|.|+.|..-|.+|+|..+.+.. +.|.+++
T Consensus 166 I~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d 210 (237)
T PRK04313 166 IVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLED 210 (237)
T ss_pred eeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEc
Confidence 3445677899999999999999999999987444 5677774
No 27
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=77.29 E-value=2.2 Score=42.90 Aligned_cols=26 Identities=38% Similarity=0.494 Sum_probs=24.7
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEc
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFR 62 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~ 62 (160)
|.+||.|+|+.|..+|-.|+|.+|+-
T Consensus 408 F~~GD~VeV~~Gel~glkG~ve~vdg 433 (1024)
T KOG1999|consen 408 FSPGDAVEVIVGELKGLKGKVESVDG 433 (1024)
T ss_pred cCCCCeEEEeeeeeccceeEEEeccC
Confidence 78999999999999999999999975
No 28
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=76.44 E-value=2.2 Score=40.08 Aligned_cols=28 Identities=32% Similarity=0.476 Sum_probs=25.4
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccC
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHN 64 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 64 (160)
+.+||.|.||.|.+++.+|.|..|+.+.
T Consensus 140 f~~gD~vkVI~g~~~~d~g~V~rI~~~~ 167 (607)
T COG5164 140 FYKGDLVKVIEGGEMVDIGTVPRIDGEK 167 (607)
T ss_pred cccCCeEEEeccccccccceEEEecCce
Confidence 4799999999999999999999998743
No 29
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=75.42 E-value=5.4 Score=30.33 Aligned_cols=31 Identities=26% Similarity=0.472 Sum_probs=26.4
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.+++||+|+-+.| -.|+|.+|+.+.+.|.++
T Consensus 36 sLk~GD~VvT~GG----i~G~V~~I~~~~~~v~le 66 (113)
T PRK06531 36 AIQKGDEVVTIGG----LYGTVDEVDTEAKTIVLD 66 (113)
T ss_pred hcCCCCEEEECCC----cEEEEEEEecCCCEEEEE
Confidence 5799999987765 789999999877888886
No 30
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=72.11 E-value=6.8 Score=29.05 Aligned_cols=29 Identities=38% Similarity=0.566 Sum_probs=23.3
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.+++||+|.-++| -.|+|.+|..+. +.|+
T Consensus 43 sL~kGD~VvT~gG----i~G~V~~v~d~~--v~I~ 71 (97)
T COG1862 43 SLKKGDEVVTIGG----IVGTVTKVGDDT--VEIE 71 (97)
T ss_pred hccCCCEEEEcCC----eEEEEEEEecCc--EEEE
Confidence 5799999998875 789999998866 4444
No 31
>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=70.55 E-value=10 Score=25.77 Aligned_cols=27 Identities=33% Similarity=0.665 Sum_probs=22.7
Q ss_pred ecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 38 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 38 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
..||.+.. -.|-+|+|.+|+ .|+|+|+
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 358999999998 5899988
No 32
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=68.05 E-value=10 Score=28.35 Aligned_cols=29 Identities=34% Similarity=0.529 Sum_probs=23.9
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.+++||+|.-++| -.|+|.+|+. +.|.+|
T Consensus 52 ~Lk~Gd~VvT~gG----i~G~Vv~i~~--~~v~le 80 (106)
T PRK05585 52 SLAKGDEVVTNGG----IIGKVTKVSE--DFVIIE 80 (106)
T ss_pred hcCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 5799999998876 6899999975 677776
No 33
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=67.90 E-value=6.1 Score=29.46 Aligned_cols=53 Identities=23% Similarity=0.316 Sum_probs=35.0
Q ss_pred cCCHHHHHhcCCCCCcccccc-ceecCCEEEEeecC----------CCCeeeEEEEEEccCCeEEEe
Q 031394 15 RLKRWERKECKPNSLPVLHKM-HVKAGDTVKVIAGC----------DKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 15 ~l~~~lR~k~~~~~~~~~~k~-~I~kGD~V~Vi~Gk----------dKGK~G~V~~V~~~~~~V~Ve 70 (160)
.|++..|+. |. .|+..++ .++.||.|-|..=+ +-|++|+|..+....-.|.|.
T Consensus 15 ~fsk~~R~~-G~--~~ls~~l~~y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~ 78 (98)
T PRK04306 15 KLSKSPRER-GL--SPLSRALQEFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVK 78 (98)
T ss_pred hhCcCcccc-CC--CcHHHHHHhccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEE
Confidence 355555554 32 3344444 56789999887433 679999999887766666653
No 34
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=67.37 E-value=9.8 Score=32.60 Aligned_cols=41 Identities=24% Similarity=0.470 Sum_probs=32.2
Q ss_pred cccccceecCCEEEEeecCCCCeeeEEEEEEccC----CeEEEec
Q 031394 31 VLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKD 71 (160)
Q Consensus 31 ~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~----~~V~VeG 71 (160)
+....++..|-.|.|+.|..-|.+|+|..|.... +.|.+|+
T Consensus 168 I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 168 IVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred heeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence 3455667889999999999999999999988653 5666665
No 35
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=63.99 E-value=11 Score=32.74 Aligned_cols=40 Identities=33% Similarity=0.593 Sum_probs=29.0
Q ss_pred cccccceecCCEEEEeecCCCCeeeEEEEEEccC---CeEEEe
Q 031394 31 VLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVK 70 (160)
Q Consensus 31 ~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~---~~V~Ve 70 (160)
+....++..|-.|.|+.|..-|.+|+|..+.... +.|.++
T Consensus 166 I~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~ 208 (273)
T PTZ00223 166 VVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLK 208 (273)
T ss_pred eeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEE
Confidence 3445677888999999999999999998884332 345554
No 36
>PLN00036 40S ribosomal protein S4; Provisional
Probab=63.94 E-value=14 Score=32.03 Aligned_cols=39 Identities=26% Similarity=0.500 Sum_probs=28.7
Q ss_pred ccccceecCCEEEEeecCCCCeeeEEEEEEccC---CeEEEe
Q 031394 32 LHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVK 70 (160)
Q Consensus 32 ~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~---~~V~Ve 70 (160)
....++..|-.|.|+.|..-|.+|+|..+.... +.|.|+
T Consensus 170 ~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~ 211 (261)
T PLN00036 170 VDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVK 211 (261)
T ss_pred eeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEE
Confidence 345677888889999999999999988887432 344554
No 37
>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=61.49 E-value=18 Score=25.85 Aligned_cols=29 Identities=38% Similarity=0.678 Sum_probs=23.2
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.+++||+|.-.+| -.|+|.+++. +.+.+|
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 6799999998876 6899999975 466665
No 38
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=61.06 E-value=17 Score=27.54 Aligned_cols=29 Identities=24% Similarity=0.368 Sum_probs=23.8
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.+++||+|.-++| -.|+|.+|.- +.|.||
T Consensus 38 ~Lk~GD~VvT~gG----i~G~V~~I~d--~~v~le 66 (109)
T PRK05886 38 SLQPGDRVHTTSG----LQATIVGITD--DTVDLE 66 (109)
T ss_pred hcCCCCEEEECCC----eEEEEEEEeC--CEEEEE
Confidence 5799999988875 6899999974 677776
No 39
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=60.98 E-value=16 Score=31.67 Aligned_cols=32 Identities=25% Similarity=0.525 Sum_probs=24.8
Q ss_pred ccccceecCCEEEEeecCCCCeeeEEEEEEcc
Q 031394 32 LHKMHVKAGDTVKVIAGCDKGKIGEITKVFRH 63 (160)
Q Consensus 32 ~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~ 63 (160)
....++..|-.|.|+.|..-|.+|+|..+...
T Consensus 170 ~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~ 201 (262)
T PTZ00118 170 LEFLKFEVGNLVMITGGHNVGRVGTIVSKEKH 201 (262)
T ss_pred eeEEecCCCCEEEEECCeeceeEEEEEEEEec
Confidence 34567788888888999999999988775543
No 40
>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=59.00 E-value=26 Score=23.51 Aligned_cols=33 Identities=27% Similarity=0.355 Sum_probs=19.8
Q ss_pred eecCCEEEEeecCC--CC--eeeEEEEEEccCCeEEEe
Q 031394 37 VKAGDTVKVIAGCD--KG--KIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 37 I~kGD~V~Vi~Gkd--KG--K~G~V~~V~~~~~~V~Ve 70 (160)
|++||.|+|.+-.+ .| -.|+|++...+. ++.|+
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 57999999998432 23 348999998875 66665
No 41
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=57.73 E-value=23 Score=23.97 Aligned_cols=34 Identities=12% Similarity=0.163 Sum_probs=29.1
Q ss_pred ecCCEEEEe--ecCCCCeeeEEEEEEccCCeEEEec
Q 031394 38 KAGDTVKVI--AGCDKGKIGEITKVFRHNSTVMVKD 71 (160)
Q Consensus 38 ~kGD~V~Vi--~GkdKGK~G~V~~V~~~~~~V~VeG 71 (160)
..||.|... -|..|--.|+|.+|+-..+++++||
T Consensus 22 v~~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE~ 57 (57)
T COG1532 22 VTEEGVVARDILGDEKEFEGQVKRIDLDEHKIELEG 57 (57)
T ss_pred EecCcEEEEeccCCceEecceEEEEEccccEEEecC
Confidence 567777764 6888888999999999999999986
No 42
>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=56.93 E-value=19 Score=23.67 Aligned_cols=30 Identities=33% Similarity=0.545 Sum_probs=23.8
Q ss_pred ceecCCEEEEeecCCCCee---eEEEEEEccCCe
Q 031394 36 HVKAGDTVKVIAGCDKGKI---GEITKVFRHNST 66 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~---G~V~~V~~~~~~ 66 (160)
.|++||+|.++. .+.++. ++|.++....+.
T Consensus 12 ~l~~gd~v~~~~-~~~~~~~~~~~I~~i~~~~~~ 44 (74)
T PF03144_consen 12 TLKKGDKVRVLP-NGTGKKGQVVKIKSIFMFNGD 44 (74)
T ss_dssp EEETTEEEEEES-TTTTEECEEEEEEEEEETTEE
T ss_pred EEcCCCEEEECc-cCCcceeeeeecccccccccC
Confidence 579999999998 666555 889888877653
No 43
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=56.80 E-value=19 Score=35.26 Aligned_cols=38 Identities=26% Similarity=0.412 Sum_probs=27.9
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCC-eEEEeceeee
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNS-TVMVKDINLK 75 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~-~V~VeGvN~~ 75 (160)
..|+.||.|.|.+ -|+.|+|++|..++. .|.+.++.+.
T Consensus 635 ~~~~~Gd~V~v~~---~~~~g~v~~i~~~~~~~V~~g~~k~~ 673 (782)
T PRK00409 635 EELKVGDEVKYLS---LGQKGEVLSIPDDKEAIVQAGIMKMK 673 (782)
T ss_pred cCCCCCCEEEEcc---CCceEEEEEEcCCCeEEEEECCEEEE
Confidence 5589999999966 578899999975332 3555566664
No 44
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=56.68 E-value=19 Score=28.40 Aligned_cols=39 Identities=26% Similarity=0.361 Sum_probs=31.6
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccC------CeEEEeceeee
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLK 75 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~------~~V~VeGvN~~ 75 (160)
+++|--|.|++|.+.|+...|++-.-+. +.++|+|+...
T Consensus 5 lkPgkvv~v~sG~yAg~KaVivk~~Ddg~~d~p~~h~LvAgi~ry 49 (136)
T KOG3418|consen 5 LKPGKVVLVLSGRYAGKKAVIVKNIDDGTEDKPYGHALVAGVDRY 49 (136)
T ss_pred ccCCcEEEeecccccCccEEEEeecccCCccCCCceeeeeehhhc
Confidence 5899999999999999998887765444 47889988654
No 45
>PLN00190 60S ribosomal protein L21; Provisional
Probab=55.35 E-value=11 Score=30.39 Aligned_cols=51 Identities=27% Similarity=0.374 Sum_probs=33.0
Q ss_pred CCHHHHHhcCCCCCcccccc-ceecCCEEEEee-cC---------CCCeeeEEEEEEccCCeEEE
Q 031394 16 LKRWERKECKPNSLPVLHKM-HVKAGDTVKVIA-GC---------DKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 16 l~~~lR~k~~~~~~~~~~k~-~I~kGD~V~Vi~-Gk---------dKGK~G~V~~V~~~~~~V~V 69 (160)
||+..|+. | ..|+..++ .++.||.|-|.. |. +-|++|.|..|....-.|+|
T Consensus 15 fsk~~R~~-G--~~pls~~l~~yk~GD~VdIk~~~svqKGMPhk~YHGkTG~V~nv~~~A~gV~V 76 (158)
T PLN00190 15 FARPFRKK-G--YIPLTTYLRTFKVGDYVDIKVNGAIHKGMPHKFYHGRTGIVWNVTKRAVGVEV 76 (158)
T ss_pred hCcccccc-C--CCcHHHHHHHhcCCCEEEEEecCCeecCCCcccccCCCeEEEeecCcEEEEEE
Confidence 45555544 3 34444555 568899999874 32 77999999888765544443
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=54.03 E-value=4.2 Score=28.77 Aligned_cols=30 Identities=30% Similarity=0.591 Sum_probs=0.4
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
-.+++||+|.-.+| -.|+|.++ +.+.+.+|
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 36799999998886 57999888 55666666
No 47
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=53.13 E-value=36 Score=25.06 Aligned_cols=36 Identities=19% Similarity=0.315 Sum_probs=33.1
Q ss_pred ecCCEEEEeecCCCCeeeEEEEEEccCCeEEEecee
Q 031394 38 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 73 (160)
Q Consensus 38 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN 73 (160)
.-|-+|-+++..+-.-+|.+..|+...++|.+.++-
T Consensus 6 ~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr 41 (96)
T PF12701_consen 6 YIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVR 41 (96)
T ss_dssp CTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEE
T ss_pred ccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeee
Confidence 369999999999999999999999999999999864
No 48
>PF12353 eIF3g: Eukaryotic translation initiation factor 3 subunit G ; InterPro: IPR024675 At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding []. eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700 kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied. Subunit G is required for eIF3 integrity. This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain PF00076 from PFAM.
Probab=51.36 E-value=28 Score=26.71 Aligned_cols=27 Identities=26% Similarity=0.308 Sum_probs=21.3
Q ss_pred cCCCCeeeEEEEEccCCcEEEEEeccC
Q 031394 107 KEMEVASRVGHKVLDDGTRVRYLIKTG 133 (160)
Q Consensus 107 p~~~~ptRv~~~~~edG~kvRv~kksg 133 (160)
..+|..+=+.|++++||+++.|.++--
T Consensus 9 ~~~G~KtViey~~n~dGkkvKvtk~~k 35 (128)
T PF12353_consen 9 DEDGIKTVIEYKFNDDGKKVKVTKKIK 35 (128)
T ss_pred CCCCcEEEEEEEECCCCCEEEEEEEEE
Confidence 456788899999999998888775544
No 49
>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=49.45 E-value=14 Score=24.24 Aligned_cols=24 Identities=38% Similarity=0.436 Sum_probs=14.5
Q ss_pred eecCCEEEE-eecC--CCCeeeEEEEE
Q 031394 37 VKAGDTVKV-IAGC--DKGKIGEITKV 60 (160)
Q Consensus 37 I~kGD~V~V-i~Gk--dKGK~G~V~~V 60 (160)
-.-||+|.| +..+ .+...|+|.+|
T Consensus 32 A~~gD~V~v~i~~~~~~~~~eg~vv~V 58 (58)
T PF08206_consen 32 AMDGDKVLVRITPPSRGKRPEGEVVEV 58 (58)
T ss_dssp S-TT-EEEEEEEESSSEEEEEEEEEE-
T ss_pred CCCCCEEEEEEecCCCCCCCCEEEEeC
Confidence 368999998 4543 34556888775
No 50
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=48.86 E-value=27 Score=24.79 Aligned_cols=27 Identities=26% Similarity=0.495 Sum_probs=22.8
Q ss_pred CCHHHHHhcCCCCCccccccceecCCEEEEeecCCCCe
Q 031394 16 LKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGK 53 (160)
Q Consensus 16 l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKGK 53 (160)
+|+++|..+| |+.||.|.+....|.|+
T Consensus 18 IPkeiR~~lg-----------i~~Gd~lei~~~~~~~~ 44 (89)
T COG2002 18 IPKEIREALG-----------IKEGDVLEIIVDGDGGR 44 (89)
T ss_pred ecHHHHHHhC-----------CCCCCEEEEEEeCCCCE
Confidence 6788888875 47899999999998887
No 51
>PTZ00189 60S ribosomal protein L21; Provisional
Probab=47.99 E-value=18 Score=29.30 Aligned_cols=52 Identities=21% Similarity=0.312 Sum_probs=33.2
Q ss_pred cCCHHHHHhcCCCCCcccccc-ceecCCEEEEeecC----------CCCeeeEEEEEEccCCeEEE
Q 031394 15 RLKRWERKECKPNSLPVLHKM-HVKAGDTVKVIAGC----------DKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 15 ~l~~~lR~k~~~~~~~~~~k~-~I~kGD~V~Vi~Gk----------dKGK~G~V~~V~~~~~~V~V 69 (160)
.||+..|+. | ..|+..++ .++.||.|-|..=+ +-|++|.|..+....-.|+|
T Consensus 14 ~fsk~~R~~-G--~~pls~~l~~yk~GD~VdIk~d~svqkGMPhk~YHGkTG~V~nv~~~A~gViV 76 (160)
T PTZ00189 14 KFAKPFRKH-G--VPSLSTYLTTFKVGDYVDIVVDSAVHKGMPYKYYHGRTGRVFNVTPRAVGVIV 76 (160)
T ss_pred hhCcccccc-C--CCcHHHHHHHccCCCEEEEEecCCeecCCCcccccCCCeEEEeecCeEEEEEE
Confidence 355566655 3 34444555 56789999887432 67999999887665443444
No 52
>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=47.09 E-value=37 Score=25.23 Aligned_cols=36 Identities=25% Similarity=0.376 Sum_probs=20.8
Q ss_pred cccccc-ceecCCEEEEeecC----------CCCeeeEEEEEEccCC
Q 031394 30 PVLHKM-HVKAGDTVKVIAGC----------DKGKIGEITKVFRHNS 65 (160)
Q Consensus 30 ~~~~k~-~I~kGD~V~Vi~Gk----------dKGK~G~V~~V~~~~~ 65 (160)
|+..++ .++.||.|-|..=+ +-|++|.|..|.+..-
T Consensus 25 ~ls~~l~~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~~ 71 (99)
T PF01157_consen 25 PLSTYLQEYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGAR 71 (99)
T ss_dssp -CHHHH----TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSCE
T ss_pred cHHHHHHHccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCce
Confidence 444444 57899999987433 6799999999988653
No 53
>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=46.47 E-value=31 Score=33.80 Aligned_cols=34 Identities=29% Similarity=0.523 Sum_probs=25.3
Q ss_pred ecCCEEEEeecCCCCeeeEEEEEEccCCe--EEEeceeee
Q 031394 38 KAGDTVKVIAGCDKGKIGEITKVFRHNST--VMVKDINLK 75 (160)
Q Consensus 38 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~--V~VeGvN~~ 75 (160)
+.||.|.|. .-|+.|+|+++.. .+. |.+.++.+.
T Consensus 626 ~~Gd~V~v~---~~~~~g~v~~i~~-~~~~~V~~g~~k~~ 661 (771)
T TIGR01069 626 KIGDKVRIR---YFGQKGKIVQILG-GNKWNVTVGGMRMK 661 (771)
T ss_pred CCCCEEEEc---cCCceEEEEEEcC-CCeEEEEECCEEEE
Confidence 799999995 4678899999974 344 555566654
No 54
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=43.91 E-value=42 Score=23.39 Aligned_cols=36 Identities=6% Similarity=0.051 Sum_probs=28.5
Q ss_pred eecCCCCeeeEEEEEccCCcEEEEEeccCCcccchhh
Q 031394 105 YSKEMEVASRVGHKVLDDGTRVRYLIKTGEIIDSAEN 141 (160)
Q Consensus 105 v~p~~~~ptRv~~~~~edG~kvRv~kksg~~i~~p~~ 141 (160)
++|.++.-.++.+- .+||...|-|.+||+.--.|..
T Consensus 10 ~CP~C~~~D~i~~~-~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 10 VCPKCQAMDTIMMW-RENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred cCCCCcCccEEEEE-EeCCceEEEecCCCCeeccCCc
Confidence 57888888888764 4888999999999998665543
No 55
>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=43.06 E-value=57 Score=21.84 Aligned_cols=40 Identities=23% Similarity=0.237 Sum_probs=29.5
Q ss_pred eecCCEEEEeecC--CCCeeeEEEEEEccCCeEEEeceeeee
Q 031394 37 VKAGDTVKVIAGC--DKGKIGEITKVFRHNSTVMVKDINLKT 76 (160)
Q Consensus 37 I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~~~V~VeGvN~~k 76 (160)
|.+|-.|.|+.-. +-|-+|.|.+|.-.+--|+.||-|--|
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 4799999999775 689999999999988899999977544
No 56
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=42.67 E-value=40 Score=23.99 Aligned_cols=30 Identities=20% Similarity=0.265 Sum_probs=22.2
Q ss_pred cccceecCCEEEEeecCCCCeeeEEEEEEc
Q 031394 33 HKMHVKAGDTVKVIAGCDKGKIGEITKVFR 62 (160)
Q Consensus 33 ~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~ 62 (160)
++..|.+||.|.|--=++--..|.|..-+.
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 355779999999987777777777755443
No 57
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=42.31 E-value=56 Score=24.47 Aligned_cols=39 Identities=31% Similarity=0.262 Sum_probs=27.8
Q ss_pred ceecCCEEEEeecC----------CCCeeeEEEEEEccCCeEEEeceee
Q 031394 36 HVKAGDTVKVIAGC----------DKGKIGEITKVFRHNSTVMVKDINL 74 (160)
Q Consensus 36 ~I~kGD~V~Vi~Gk----------dKGK~G~V~~V~~~~~~V~VeGvN~ 74 (160)
.+..||.|-|..-+ +-|++|+|.-+--....|.|..=|.
T Consensus 32 ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k 80 (98)
T COG2139 32 EYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNK 80 (98)
T ss_pred hccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCc
Confidence 46899999987544 7899999977665555555554443
No 58
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=42.06 E-value=55 Score=28.37 Aligned_cols=32 Identities=31% Similarity=0.432 Sum_probs=24.3
Q ss_pred cCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 39 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 39 kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.|....|+||.-||..|.|+-=.---+.|+|+
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 59999999999999999998766655677775
No 59
>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=41.34 E-value=53 Score=22.10 Aligned_cols=25 Identities=12% Similarity=0.264 Sum_probs=20.4
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.+..||.|.+ +|+.+++++.++.+.
T Consensus 46 ~~~vG~~v~~----------kV~~id~~~~~i~Ls 70 (73)
T cd05703 46 KFPIGQALKA----------KVVGVDKEHKLLRLS 70 (73)
T ss_pred hCCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 3588999875 899999999888764
No 60
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=39.49 E-value=20 Score=33.26 Aligned_cols=46 Identities=28% Similarity=0.380 Sum_probs=36.5
Q ss_pred HHHhcCCCCCccccccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEec
Q 031394 20 ERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 71 (160)
Q Consensus 20 lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeG 71 (160)
+|+..---.+|- .-|++|.|++|+.+|+-|--++-+..+.+.+|.-
T Consensus 383 irq~~lET~~pr------~~Ge~vmvv~gkhkg~~g~llskd~~Ke~~~v~~ 428 (455)
T KOG4315|consen 383 IRQELLETALPR------RGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVRL 428 (455)
T ss_pred hHHHHHhhhccc------ccCceeEEEecccccchhhhhhhhhhhhhcceec
Confidence 555554455665 7899999999999999999999888887776653
No 61
>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=39.24 E-value=61 Score=20.86 Aligned_cols=28 Identities=21% Similarity=0.311 Sum_probs=19.1
Q ss_pred ecCCEEEEeecCCCCeeeEEEEEEccCCeE
Q 031394 38 KAGDTVKVIAGCDKGKIGEITKVFRHNSTV 67 (160)
Q Consensus 38 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V 67 (160)
..||.|.+- ..+ +-.|.|.+|.+.++.+
T Consensus 39 ~VGD~V~~~-~~~-~~~~~I~~vl~R~s~l 66 (68)
T cd04466 39 AVGDRVEFE-PED-DGEGVIEEILPRKNLL 66 (68)
T ss_pred CCCcEEEEE-ECC-CCcEEEEEEeccceEE
Confidence 699999873 222 2347788888877654
No 62
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=38.33 E-value=39 Score=23.86 Aligned_cols=29 Identities=17% Similarity=0.341 Sum_probs=24.4
Q ss_pred ceecCCEEEEeecC--CCCeeeEEEEEEccC
Q 031394 36 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN 64 (160)
Q Consensus 36 ~I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~ 64 (160)
-|.+||.|.|+.=. .-..+|+|.+|+...
T Consensus 2 ~i~rGskVrIlR~ESYWyn~vGtV~svD~sg 32 (71)
T PRK02749 2 AISRGDKVRILRPESYWYNEVGTVASVDKSG 32 (71)
T ss_pred ccccCCEEEEccccceeecCcceEEEEccCC
Confidence 36899999999765 568889999999875
No 63
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=37.88 E-value=34 Score=32.47 Aligned_cols=34 Identities=29% Similarity=0.445 Sum_probs=29.3
Q ss_pred ecCCEEEEeecCCCCeeeEEEEEEccCCeEEEec
Q 031394 38 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 71 (160)
Q Consensus 38 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeG 71 (160)
.-|-+|.|-+|.+||.-|.|..|++...+|.+..
T Consensus 353 aigktVrIr~g~yKG~lGVVKdv~~~~arVeLhs 386 (607)
T COG5164 353 AIGKTVRIRCGEYKGHLGVVKDVDRNIARVELHS 386 (607)
T ss_pred ccCceEEEeecccccccceeeeccCceEEEEEec
Confidence 4689999999999999999999998777666553
No 64
>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=37.24 E-value=60 Score=20.98 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=18.6
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
+..||.|.+ +|++++++++++.+
T Consensus 45 ~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (68)
T cd05707 45 FKVGQLVKG----------KIVSIDPDNGRIEM 67 (68)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEec
Confidence 589999988 78888888877754
No 65
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=37.15 E-value=39 Score=23.41 Aligned_cols=28 Identities=25% Similarity=0.355 Sum_probs=23.4
Q ss_pred eecCCEEEEeecC--CCCeeeEEEEEEccC
Q 031394 37 VKAGDTVKVIAGC--DKGKIGEITKVFRHN 64 (160)
Q Consensus 37 I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~ 64 (160)
|.+||.|.|+.=. .-..+|+|.+|+...
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~g 31 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSG 31 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCC
Confidence 5799999999765 567889999999864
No 66
>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=37.09 E-value=55 Score=27.23 Aligned_cols=37 Identities=27% Similarity=0.403 Sum_probs=21.6
Q ss_pred ceecCCEEEE-eecCCCCeeeEEEEEEc-----------cCCeEEEece
Q 031394 36 HVKAGDTVKV-IAGCDKGKIGEITKVFR-----------HNSTVMVKDI 72 (160)
Q Consensus 36 ~I~kGD~V~V-i~GkdKGK~G~V~~V~~-----------~~~~V~VeGv 72 (160)
.++.||.|.+ -.+....+.-+|.+|.. ..+.++|+|+
T Consensus 105 ~V~~Gd~v~~~~~~~~~~~~~~V~~v~~~~~~G~yAPLT~~GtivVdgV 153 (217)
T PF01079_consen 105 DVRVGDCVLVSDEGGGKLRPSRVVRVSTVEKRGVYAPLTSHGTIVVDGV 153 (217)
T ss_dssp G--TT-EEEEE-TTT--EEEEEEEEEEEEEEEEEEEEEESSSEEEETTE
T ss_pred hCCCCCEEEEEEcCCCcEEEEEEEEEEEEEEeeEEcCccCcceEEECCE
Confidence 6799999999 45556666678877753 3455666665
No 67
>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=36.81 E-value=62 Score=21.26 Aligned_cols=24 Identities=25% Similarity=0.234 Sum_probs=19.4
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
.++.||.|.+ +|+.+++++.++.+
T Consensus 42 ~~~~G~~i~~----------kVi~id~~~~~i~L 65 (66)
T cd05695 42 TYKEGQKVRA----------RILYVDPSTKVVGL 65 (66)
T ss_pred CcCCCCEEEE----------EEEEEeCCCCEEec
Confidence 4688999877 89999998887654
No 68
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=35.80 E-value=23 Score=31.44 Aligned_cols=44 Identities=18% Similarity=0.228 Sum_probs=28.3
Q ss_pred HHHHHhcCCCCCccccccceecCCEEEEeecCCCCeeeEEEEEEc
Q 031394 18 RWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFR 62 (160)
Q Consensus 18 ~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~ 62 (160)
++||+||..|-.- .+.-.----|+|++++|+-|--.|.|..|..
T Consensus 146 kelrekcsarlki-ft~c~p~stdrv~l~~g~~k~v~~~i~~il~ 189 (390)
T KOG2192|consen 146 KELREKCSARLKI-FTECCPHSTDRVVLIGGKPKRVVECIKIILD 189 (390)
T ss_pred HHHHHhhhhhhhh-hhccCCCCcceEEEecCCcchHHHHHHHHHH
Confidence 7899999544321 1122222349999999998877776655443
No 69
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=35.69 E-value=1.1e+02 Score=19.48 Aligned_cols=27 Identities=30% Similarity=0.367 Sum_probs=20.1
Q ss_pred ceecCCEEEEeecCCCC-eeeEEEEEEc
Q 031394 36 HVKAGDTVKVIAGCDKG-KIGEITKVFR 62 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKG-K~G~V~~V~~ 62 (160)
.+.+||.|.+..=.+.+ -.|+|+++..
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~ 29 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG 29 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC
Confidence 46899999999633322 4599999987
No 70
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=35.49 E-value=45 Score=29.03 Aligned_cols=39 Identities=21% Similarity=0.342 Sum_probs=26.5
Q ss_pred CCCeeeEEEEEccCCcEEEEE---eccCCcccchh----hhhHhhh
Q 031394 109 MEVASRVGHKVLDDGTRVRYL---IKTGEIIDSAE----NWKKLKE 147 (160)
Q Consensus 109 ~~~ptRv~~~~~edG~kvRv~---kksg~~i~~p~----~~~~~~~ 147 (160)
+|..+-++|++++||+|+-|- +.....++... +|.+|-.
T Consensus 27 ~g~ktvieyk~n~dgkK~Kvt~~~kv~k~~v~K~vaeRknW~KFG~ 72 (270)
T KOG0122|consen 27 DGTKTVIEYKINEDGKKVKVTRTFKVEKRAVPKAVAERKNWVKFGD 72 (270)
T ss_pred CCcEEEEEEEEcCCCcEEEEEEEEEEEEEeccHHHHhhccchhhcc
Confidence 678899999999999775443 44444455432 6777654
No 71
>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=35.23 E-value=1.1e+02 Score=22.45 Aligned_cols=36 Identities=19% Similarity=0.212 Sum_probs=27.5
Q ss_pred eecCCEEEEeecC--CCCeeeEEEEEEccC-CeEEEece
Q 031394 37 VKAGDTVKVIAGC--DKGKIGEITKVFRHN-STVMVKDI 72 (160)
Q Consensus 37 I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~-~~V~VeGv 72 (160)
++.||-|.|.+.. ..--+|.|.++.... +...+.+.
T Consensus 4 ~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~ 42 (121)
T cd04717 4 YRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGC 42 (121)
T ss_pred EECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEE
Confidence 5899999999765 566799999998865 55555543
No 72
>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=34.54 E-value=55 Score=22.53 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=22.1
Q ss_pred eecCCEEEEeecC--CCCeeeEEEEEEccC
Q 031394 37 VKAGDTVKVIAGC--DKGKIGEITKVFRHN 64 (160)
Q Consensus 37 I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~ 64 (160)
|.+|+.|.|+.=. .-..+|+|.+|+...
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 4789999999765 578899999999875
No 73
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=34.15 E-value=79 Score=20.32 Aligned_cols=23 Identities=17% Similarity=0.372 Sum_probs=18.4
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
+..||.+.+ +|++++++.+++.+
T Consensus 45 ~~~G~~i~v----------~v~~~d~~~~~i~l 67 (70)
T cd05698 45 FRVGQVVKV----------KVLSCDPEQQRLLL 67 (70)
T ss_pred ccCCCEEEE----------EEEEEcCCCCEEEE
Confidence 588999988 67888887777765
No 74
>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=34.03 E-value=85 Score=20.85 Aligned_cols=24 Identities=25% Similarity=0.217 Sum_probs=19.2
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
+++.||.|.+ +|+.++++.+++.+
T Consensus 46 ~~~vG~~v~~----------kV~~id~~~~~i~l 69 (71)
T cd05696 46 PFKAGTTHKA----------RIIGYSPMDGLLQL 69 (71)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 4688999876 78889998887765
No 75
>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=34.02 E-value=70 Score=23.28 Aligned_cols=35 Identities=34% Similarity=0.475 Sum_probs=24.5
Q ss_pred cccceecCCEEEEeecC------------CCCeeeEEEEEE-ccCCeE
Q 031394 33 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVF-RHNSTV 67 (160)
Q Consensus 33 ~k~~I~kGD~V~Vi~Gk------------dKGK~G~V~~V~-~~~~~V 67 (160)
..+-+++||.|.|+.-. .-|..|..++|. ..++++
T Consensus 62 ~~~~V~~G~~V~i~~~~~~~~i~~~g~Al~~g~~G~~I~V~N~~s~k~ 109 (122)
T TIGR03170 62 PPWLVKRGDTVTVIARGGGLSVTTEGKALEDGAVGDQIRVRNLSSGKI 109 (122)
T ss_pred CccEEcCCCEEEEEEecCCEEEEEEEEEccccCCCCEEEEEECCCCCE
Confidence 44678999999998544 557777777776 344443
No 76
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=33.90 E-value=15 Score=30.98 Aligned_cols=33 Identities=27% Similarity=0.548 Sum_probs=28.8
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCCeE
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 67 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V 67 (160)
||.++||.+.-++|.-.|++-.|.....+.-.+
T Consensus 125 MHq~RGD~i~FvTGRt~gk~d~vsk~Lak~F~i 157 (237)
T COG3700 125 MHQRRGDAIYFVTGRTPGKTDTVSKTLAKNFHI 157 (237)
T ss_pred HHHhcCCeEEEEecCCCCcccccchhHHhhccc
Confidence 688999999999999999999998887766544
No 77
>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=33.80 E-value=94 Score=20.07 Aligned_cols=24 Identities=21% Similarity=0.282 Sum_probs=19.9
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
.+..||.+.+ +|++++++++++.+
T Consensus 44 ~~~~Gd~i~~----------~V~~id~~~~~i~l 67 (69)
T cd05697 44 KFKPGLKVKC----------RVLSVEPERKRLVL 67 (69)
T ss_pred cCCCCCEEEE----------EEEEEECCCCEEEE
Confidence 4688999988 78899998888765
No 78
>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=33.13 E-value=1.1e+02 Score=19.89 Aligned_cols=26 Identities=27% Similarity=0.386 Sum_probs=21.0
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
..+..||+|.+ .|++++++++++.+.
T Consensus 47 ~~~~~G~~v~v----------~v~~vd~~~~~i~lS 72 (74)
T PF00575_consen 47 EVYKIGQTVRV----------KVIKVDKEKGRIRLS 72 (74)
T ss_dssp GTCETTCEEEE----------EEEEEETTTTEEEEE
T ss_pred cccCCCCEEEE----------EEEEEECCCCeEEEE
Confidence 35689999987 789999999888763
No 79
>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=32.96 E-value=62 Score=26.35 Aligned_cols=35 Identities=26% Similarity=0.429 Sum_probs=26.7
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.++.||.|.|..|...--.++|..+.++.-.+.+.
T Consensus 16 R~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 16 RLKEGDSIEVFDGDGGEYRAEITEISKKSATLRIL 50 (225)
T ss_dssp T--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEE
T ss_pred CCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEe
Confidence 45999999999999888889999999876655555
No 80
>COG1162 Predicted GTPases [General function prediction only]
Probab=32.82 E-value=55 Score=28.87 Aligned_cols=30 Identities=20% Similarity=0.339 Sum_probs=25.5
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCCeE
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 67 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V 67 (160)
.....||+|.+-.+... |.|.+|.+.+|.+
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 34479999999999877 9999999988854
No 81
>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=32.79 E-value=47 Score=23.28 Aligned_cols=29 Identities=17% Similarity=0.176 Sum_probs=20.2
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccC
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHN 64 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 64 (160)
.|++||.|.|--=++--..|.|+..+...
T Consensus 38 wI~~GD~V~Ve~~~~d~~kg~Iv~r~~~~ 66 (77)
T cd05793 38 WINEGDIVLVAPWDFQDDKADIIYKYTPD 66 (77)
T ss_pred EEcCCCEEEEEeccccCCEEEEEEEcCHH
Confidence 45899999994334445678888776543
No 82
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=32.79 E-value=47 Score=32.77 Aligned_cols=38 Identities=34% Similarity=0.543 Sum_probs=29.7
Q ss_pred CccccccceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 29 LPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 29 ~~~~~k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
+|-...-.++.||.|.+++ |..|.|++|....+.+.|+
T Consensus 605 ~~~~~~~~l~~gDev~~~t----~e~G~~~~i~a~~~e~~v~ 642 (753)
T COG1193 605 LPEAKKRKLKLGDEVEVIT----GEPGAVVKIIAGILEALVQ 642 (753)
T ss_pred CccccccCceecceeEeec----CCccceeeeeccCceeEEe
Confidence 3333366889999999999 7888999998777777666
No 83
>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=32.78 E-value=1e+02 Score=19.89 Aligned_cols=25 Identities=16% Similarity=0.352 Sum_probs=19.9
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.++.||.|.+ +|++++.+.+++.+.
T Consensus 47 ~~~~Gd~v~v----------~i~~vd~~~~~i~ls 71 (77)
T cd05708 47 LFRVGDKVRA----------KVLKIDAEKKRISLG 71 (77)
T ss_pred eecCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 4689999988 588888888877654
No 84
>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=32.25 E-value=87 Score=21.64 Aligned_cols=32 Identities=19% Similarity=0.237 Sum_probs=20.9
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCCe
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNST 66 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~ 66 (160)
=.|.+|+.|.|+.+..-=..|+|.++.+..+.
T Consensus 25 G~l~~g~~v~vlr~~~~~~~g~i~sl~~~~~~ 56 (84)
T cd03692 25 GKIKRNAKVRVLRNGEVIYEGKISSLKRFKDD 56 (84)
T ss_pred CEEeCCCEEEEEcCCCEEEEEEEEEEEEcCcc
Confidence 46789999999987421145677776655443
No 85
>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=32.18 E-value=76 Score=26.88 Aligned_cols=28 Identities=25% Similarity=0.284 Sum_probs=21.6
Q ss_pred ecCCEEEEeecCCCCeeeEEEEEEccCCeE
Q 031394 38 KAGDTVKVIAGCDKGKIGEITKVFRHNSTV 67 (160)
Q Consensus 38 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V 67 (160)
..||.|.+-.-. +..|.|.+|.+.+|.+
T Consensus 36 ~vGD~V~~~~~~--~~~~~i~~i~~R~~~l 63 (287)
T cd01854 36 VVGDWVEVEPDD--DGEGVIVRVLPRKNLL 63 (287)
T ss_pred cCCCEEEEEecC--CCcEEEEEEECCCceE
Confidence 699999885322 4579999999888754
No 86
>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=31.99 E-value=92 Score=19.44 Aligned_cols=24 Identities=25% Similarity=0.461 Sum_probs=18.2
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
.+..||+|.+ .|++++++++++.+
T Consensus 44 ~~~~Gd~v~v----------~i~~vd~~~~~i~l 67 (68)
T cd05688 44 VVNVGDEVEV----------KVLKIDKERKRISL 67 (68)
T ss_pred EECCCCEEEE----------EEEEEECCCCEEec
Confidence 4689999988 57778877776653
No 87
>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=31.63 E-value=75 Score=21.21 Aligned_cols=24 Identities=29% Similarity=0.206 Sum_probs=16.0
Q ss_pred ceecCCEEEEeecCCCCeeeEEEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITK 59 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~ 59 (160)
.|+.||.|.|---++--..|.|..
T Consensus 41 wI~~GD~V~V~~~~~d~~kG~Ii~ 64 (65)
T PF01176_consen 41 WIKRGDFVLVEPSPYDKVKGRIIY 64 (65)
T ss_dssp ---TTEEEEEEESTTCTTEEEEEE
T ss_pred ecCCCCEEEEEecccCCCeEEEEE
Confidence 469999999986655567777754
No 88
>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=31.61 E-value=50 Score=21.67 Aligned_cols=21 Identities=33% Similarity=0.289 Sum_probs=13.1
Q ss_pred eecCCEEEEeecCCCCeeeEE
Q 031394 37 VKAGDTVKVIAGCDKGKIGEI 57 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V 57 (160)
+..||.|.+---.+-+.+|.|
T Consensus 41 ~~vGD~V~~~~~~~~~~~g~I 61 (64)
T cd04451 41 ILPGDRVKVELSPYDLTKGRI 61 (64)
T ss_pred cCCCCEEEEEEeecCCCEEEE
Confidence 379999988744322334555
No 89
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=31.57 E-value=34 Score=25.28 Aligned_cols=27 Identities=19% Similarity=0.165 Sum_probs=17.0
Q ss_pred cceecCCEEEEeecCCCC---eeeEEEEEEcc
Q 031394 35 MHVKAGDTVKVIAGCDKG---KIGEITKVFRH 63 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKG---K~G~V~~V~~~ 63 (160)
..|++||.|.| .++-- ..|.|+.++..
T Consensus 56 iwI~~GD~VlV--sp~d~~~~~kg~Iv~r~~~ 85 (99)
T TIGR00523 56 IWIREGDVVIV--KPWEFQGDDKCDIVWRYTK 85 (99)
T ss_pred EEecCCCEEEE--EEccCCCCccEEEEEEcCH
Confidence 45689999998 33222 24777776654
No 90
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=31.43 E-value=96 Score=23.26 Aligned_cols=28 Identities=21% Similarity=0.248 Sum_probs=23.9
Q ss_pred ceecCCEEEEeecC--CCCeeeEEEEEEcc
Q 031394 36 HVKAGDTVKVIAGC--DKGKIGEITKVFRH 63 (160)
Q Consensus 36 ~I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~ 63 (160)
-+.+||.|.|+.=. .-..+|+|.+|+..
T Consensus 39 g~~RGskVrIlR~ESYWyn~vGtVvsVDq~ 68 (101)
T PLN00045 39 GPKRGSKVKILRPESYWFNDVGKVVAVDQD 68 (101)
T ss_pred ccCCCCEEEEccccceeecCcceEEEEeCC
Confidence 35899999999765 56788999999987
No 91
>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=31.31 E-value=78 Score=22.96 Aligned_cols=37 Identities=24% Similarity=0.286 Sum_probs=24.7
Q ss_pred ceecCCEEEE--eecCCCCeeeEEEEEEccCCeEEEecee
Q 031394 36 HVKAGDTVKV--IAGCDKGKIGEITKVFRHNSTVMVKDIN 73 (160)
Q Consensus 36 ~I~kGD~V~V--i~GkdKGK~G~V~~V~~~~~~V~VeGvN 73 (160)
..++||.|+. -.+..-|-+|.|.+|.. .+.|++-.-|
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 4579999887 45667899999999944 4566666555
No 92
>PRK12618 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=31.20 E-value=76 Score=24.60 Aligned_cols=34 Identities=18% Similarity=0.238 Sum_probs=24.8
Q ss_pred cccceecCCEEEEeecC------------CCCeeeEEEEEE-ccCCe
Q 031394 33 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVF-RHNST 66 (160)
Q Consensus 33 ~k~~I~kGD~V~Vi~Gk------------dKGK~G~V~~V~-~~~~~ 66 (160)
..|-|.+||.|.|++.. .-|..|..+.|- ..+++
T Consensus 78 ~p~lV~rG~~V~i~~~~ggl~i~~~G~AL~~G~~Gd~IrV~N~~S~r 124 (141)
T PRK12618 78 PPAIVDRNQLVPLAYRLGGLEIRTEGRALSRGGVGDEIRVMNLSSRT 124 (141)
T ss_pred CccEEeCCCEEEEEEecCCEEEEEEEEEcccCCCCCEEEEEECCCCC
Confidence 34678999999999654 568888888884 34444
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=30.06 E-value=69 Score=19.53 Aligned_cols=18 Identities=22% Similarity=0.464 Sum_probs=12.4
Q ss_pred ccccceecCCEEEEeecC
Q 031394 32 LHKMHVKAGDTVKVIAGC 49 (160)
Q Consensus 32 ~~k~~I~kGD~V~Vi~Gk 49 (160)
...+.+.+||.+.|+.=.
T Consensus 11 ~~eLs~~~Gd~i~v~~~~ 28 (48)
T PF00018_consen 11 PDELSFKKGDIIEVLEKS 28 (48)
T ss_dssp TTBSEB-TTEEEEEEEES
T ss_pred CCEEeEECCCEEEEEEec
Confidence 345677999999998633
No 94
>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=29.82 E-value=1.9e+02 Score=19.86 Aligned_cols=20 Identities=20% Similarity=0.185 Sum_probs=17.4
Q ss_pred eeeEEEEEEccCCeEEEece
Q 031394 53 KIGEITKVFRHNSTVMVKDI 72 (160)
Q Consensus 53 K~G~V~~V~~~~~~V~VeGv 72 (160)
-+|+|.+|+++.-.+++++=
T Consensus 5 veG~I~~id~~~~titLdDG 24 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDG 24 (61)
T ss_pred ceEEEEEEcCCceEEEecCC
Confidence 46999999999999999854
No 95
>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=29.59 E-value=32 Score=25.03 Aligned_cols=19 Identities=47% Similarity=0.697 Sum_probs=14.3
Q ss_pred eecCCEEEEeecCCCCeee
Q 031394 37 VKAGDTVKVIAGCDKGKIG 55 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G 55 (160)
+.+||.|++++|.--|..|
T Consensus 90 ~~~gd~vVv~~g~~~~~~g 108 (117)
T PF02887_consen 90 LKPGDKVVVVAGMPFGTPG 108 (117)
T ss_dssp S-TTSEEEEEEESSTTTTS
T ss_pred CCCCCEEEEEeCCCCCCCC
Confidence 5899999999996555555
No 96
>CHL00010 infA translation initiation factor 1
Probab=29.31 E-value=97 Score=21.59 Aligned_cols=26 Identities=31% Similarity=0.259 Sum_probs=15.8
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEc
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFR 62 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~ 62 (160)
+..||.|.|--=.+-...|.|+.-+.
T Consensus 47 ~~vGD~V~ve~~~~~~~~g~Ii~r~~ 72 (78)
T CHL00010 47 ILPGDRVKVELSPYDLTKGRIIYRLR 72 (78)
T ss_pred cCCCCEEEEEEcccCCCeEEEEEEec
Confidence 37999999873333344567754443
No 97
>PRK08577 hypothetical protein; Provisional
Probab=29.28 E-value=72 Score=23.99 Aligned_cols=29 Identities=28% Similarity=0.286 Sum_probs=22.0
Q ss_pred cCCHHHHHhcCCCCCccccccceecCCEEEEeecCCCCee
Q 031394 15 RLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKI 54 (160)
Q Consensus 15 ~l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKGK~ 54 (160)
-+|+++|.++| |.+||.|.+..=.|+|.+
T Consensus 16 ~ip~~~r~~l~-----------~~~g~~~~~~~~~~~~~~ 44 (136)
T PRK08577 16 TIPLEIREALG-----------IREGMYVLLIADTDKKEI 44 (136)
T ss_pred EecHHHHHHcC-----------cCCCCEEEEEEECCCCEE
Confidence 36778887763 478999999977777765
No 98
>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=29.07 E-value=1e+02 Score=20.75 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=19.0
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
.+..||.|.| +|++++.+++++.+
T Consensus 58 ~~~~Gd~v~v----------kV~~id~~~~~i~l 81 (83)
T cd04461 58 GFKKGQSVTA----------KVTSVDEEKQRFLL 81 (83)
T ss_pred hcCCCCEEEE----------EEEEEcCCCCEEEE
Confidence 4688999988 77888887777765
No 99
>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=28.97 E-value=98 Score=20.89 Aligned_cols=24 Identities=13% Similarity=0.196 Sum_probs=19.1
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
.+..||.|.+ +|++|+++++++.+
T Consensus 50 ~~~~G~~v~~----------kVl~id~~~~~i~L 73 (74)
T cd05705 50 YLPEGKLLTA----------KVLSVNSEKNLVEL 73 (74)
T ss_pred ccCCCCEEEE----------EEEEEECCCCEEec
Confidence 4588999875 89999998887654
No 100
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=28.92 E-value=83 Score=26.07 Aligned_cols=35 Identities=29% Similarity=0.391 Sum_probs=25.7
Q ss_pred cccceecCCEEEEeecC------------CCCeeeEEEEEE-ccCCeE
Q 031394 33 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVF-RHNSTV 67 (160)
Q Consensus 33 ~k~~I~kGD~V~Vi~Gk------------dKGK~G~V~~V~-~~~~~V 67 (160)
..|-|++||.|.|+... .-|..|..++|- ..++++
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 44678999999999654 567888888887 555544
No 101
>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=28.37 E-value=74 Score=22.38 Aligned_cols=29 Identities=21% Similarity=0.217 Sum_probs=21.0
Q ss_pred ceecCCEEEEeecCC-CCeeeEEEEEEccC
Q 031394 36 HVKAGDTVKVIAGCD-KGKIGEITKVFRHN 64 (160)
Q Consensus 36 ~I~kGD~V~Vi~Gkd-KGK~G~V~~V~~~~ 64 (160)
.|++||.|.|--=++ .-..|.|..++.+.
T Consensus 38 wI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~ 67 (78)
T cd04456 38 WIKRGDFLIVDPIEEGEDVKADIIFVYCKD 67 (78)
T ss_pred EEcCCCEEEEEecccCCCceEEEEEEeCHH
Confidence 459999999976555 34668887776654
No 102
>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=27.88 E-value=1.1e+02 Score=18.91 Aligned_cols=23 Identities=22% Similarity=0.429 Sum_probs=17.2
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
++.||.|.+ +|++++++++++.+
T Consensus 45 ~~~Gd~v~v----------~i~~vd~~~~~i~l 67 (68)
T cd05685 45 VSVGDIVEV----------KVISIDEERGRISL 67 (68)
T ss_pred cCCCCEEEE----------EEEEEECCCCEEec
Confidence 588999988 57778777666643
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=27.65 E-value=1.1e+02 Score=18.37 Aligned_cols=23 Identities=26% Similarity=0.377 Sum_probs=16.6
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 68 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~ 68 (160)
.++.||+|.+ +|++++++++.+.
T Consensus 41 ~~~~G~~v~~----------~v~~~d~~~~~i~ 63 (65)
T cd00164 41 VFKVGDEVEV----------KVLEVDPEKGRIS 63 (65)
T ss_pred EeCCCCEEEE----------EEEEEcCCcCEEe
Confidence 4689999887 6777777666554
No 104
>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=27.64 E-value=82 Score=22.20 Aligned_cols=29 Identities=21% Similarity=0.307 Sum_probs=23.7
Q ss_pred ceecCCEEEEeecC--CCCeeeEEEEEEccC
Q 031394 36 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN 64 (160)
Q Consensus 36 ~I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~ 64 (160)
.++.||-|.|..+. ..--+|.|.++....
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 36899999999998 556779999997654
No 105
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=27.55 E-value=67 Score=19.87 Aligned_cols=25 Identities=24% Similarity=0.323 Sum_probs=17.5
Q ss_pred ccCCHHHHHhcCCCCCccccccceecCCEEEEeecC
Q 031394 14 VRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGC 49 (160)
Q Consensus 14 ~~l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~Gk 49 (160)
..|++++|+++ .|..||.|.+..-.
T Consensus 9 v~iPk~~~~~l-----------~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 9 VTIPKEIREKL-----------GLKPGDEVEIEVEG 33 (47)
T ss_dssp EEE-HHHHHHT-----------TSSTTTEEEEEEET
T ss_pred EECCHHHHHHc-----------CCCCCCEEEEEEeC
Confidence 35788888887 34789999887543
No 106
>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=27.42 E-value=1.8e+02 Score=21.55 Aligned_cols=35 Identities=14% Similarity=0.275 Sum_probs=26.0
Q ss_pred ceecCCEEEEeecCC--CCeeeEEEEEEccC-CeEEEe
Q 031394 36 HVKAGDTVKVIAGCD--KGKIGEITKVFRHN-STVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~Gkd--KGK~G~V~~V~~~~-~~V~Ve 70 (160)
.++.||-|.|.+..+ +=-+|+|.++.... +...+.
T Consensus 3 ~~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~ 40 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVR 40 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEE
Confidence 368999999998654 55689999998755 444443
No 107
>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=26.90 E-value=1.6e+02 Score=23.32 Aligned_cols=29 Identities=28% Similarity=0.363 Sum_probs=25.7
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccC
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHN 64 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 64 (160)
.++.||-|.|-+|..+--+|+|.++....
T Consensus 29 ~y~lGD~Vlv~s~~~~~yIgkI~~iwe~~ 57 (159)
T cd04715 29 EYRLYDDVYVHNGDSEPYIGKIIKIYETA 57 (159)
T ss_pred EEeCCCEEEEeCCCCCCEEEEEEEEEEcC
Confidence 36999999999999888899999998764
No 108
>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=26.86 E-value=78 Score=26.59 Aligned_cols=29 Identities=31% Similarity=0.329 Sum_probs=16.3
Q ss_pred ccccceecCCEEEEeecC----------CCCeeeEEEEE
Q 031394 32 LHKMHVKAGDTVKVIAGC----------DKGKIGEITKV 60 (160)
Q Consensus 32 ~~k~~I~kGD~V~Vi~Gk----------dKGK~G~V~~V 60 (160)
.....+..||+|.|..-. -+|++|+|..+
T Consensus 130 ~~~~~F~vGd~Vrv~~~~~~~HtR~P~Y~rg~~G~I~~~ 168 (222)
T PF02211_consen 130 DAPPRFAVGDRVRVRNLPPPGHTRLPRYVRGKTGTIERV 168 (222)
T ss_dssp SSS-SS-TT-EEEE-----SS--SS-GGGTT-EEEEEEE
T ss_pred CCCCCCCCCCEEEECCCCCCCcccccHhhCCCeeEEEEE
Confidence 345678999999998654 47999999754
No 109
>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=26.47 E-value=73 Score=18.60 Aligned_cols=15 Identities=27% Similarity=0.596 Sum_probs=12.3
Q ss_pred ccceecCCEEEEeec
Q 031394 34 KMHVKAGDTVKVIAG 48 (160)
Q Consensus 34 k~~I~kGD~V~Vi~G 48 (160)
.+.+.+||.|.|+..
T Consensus 15 ~l~~~~Gd~v~v~~~ 29 (54)
T cd00174 15 ELSFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCCCEEEEEEc
Confidence 456699999999976
No 110
>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=26.41 E-value=1.9e+02 Score=21.98 Aligned_cols=29 Identities=14% Similarity=0.264 Sum_probs=23.0
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccC
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHN 64 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 64 (160)
.|+.||.|.|.+-..+=-+|.|.++..+.
T Consensus 7 ~i~vGD~V~v~~~~~~~~va~Ie~i~ed~ 35 (130)
T cd04721 7 TISVHDFVYVLSEEEDRYVAYIEDLYEDK 35 (130)
T ss_pred EEECCCEEEEeCCCCCcEEEEEEEEEEcC
Confidence 47999999999754444589999998865
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=26.37 E-value=1.4e+02 Score=19.28 Aligned_cols=23 Identities=22% Similarity=0.241 Sum_probs=17.6
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
+..||.|.+ +|++++++++.+.+
T Consensus 48 ~~~Gd~v~~----------~V~~~d~~~~~i~l 70 (73)
T cd05706 48 FKKNDIVRA----------CVLSVDVPNKKIAL 70 (73)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 578999887 67888887776654
No 112
>PRK12289 GTPase RsgA; Reviewed
Probab=25.95 E-value=1.1e+02 Score=27.04 Aligned_cols=31 Identities=26% Similarity=0.297 Sum_probs=23.6
Q ss_pred ecCCEEEEeecCCCCeeeEEEEEEccCCeEE
Q 031394 38 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 68 (160)
Q Consensus 38 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~ 68 (160)
..||.|.+-.-.+.+..|.|.+|.+.++.+.
T Consensus 53 ~vGD~V~~~~~~~~~~~~~I~~vlpR~~~L~ 83 (352)
T PRK12289 53 MVGDRVIVEEPDWQGQRGAIAEVLPRKTELD 83 (352)
T ss_pred ccCCEEEEeecCCCCCceEEEEEecccccee
Confidence 6999998854333456799999999888664
No 113
>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=25.91 E-value=1.2e+02 Score=19.19 Aligned_cols=23 Identities=13% Similarity=0.166 Sum_probs=18.1
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 68 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~ 68 (160)
.+..||.|.| +|++|+.++.++.
T Consensus 45 ~~~~G~~v~v----------~v~~id~~~~~i~ 67 (69)
T cd05690 45 IYKKGQEVEA----------VVLNIDVERERIS 67 (69)
T ss_pred EECCCCEEEE----------EEEEEECCcCEEe
Confidence 3689999988 5888888877764
No 114
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=25.67 E-value=82 Score=22.36 Aligned_cols=29 Identities=17% Similarity=0.150 Sum_probs=19.9
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccC
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHN 64 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 64 (160)
.|+.||.|.|=--++--..|.|..++.+.
T Consensus 43 wI~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 71 (83)
T smart00652 43 WIRRGDIVLVDPWDFQDVKADIIYKYTKD 71 (83)
T ss_pred EEcCCCEEEEEecCCCCCEEEEEEEeCHH
Confidence 45999999996444434567787776543
No 115
>CHL00084 rpl19 ribosomal protein L19
Probab=25.06 E-value=3.2e+02 Score=20.91 Aligned_cols=80 Identities=21% Similarity=0.178 Sum_probs=40.6
Q ss_pred ceecCCEEEEee---cCCC----CeeeEEEEEEccCCeEEEeceeeeeEEecCCccccCceeEEEeecCcCC---Ceeee
Q 031394 36 HVKAGDTVKVIA---GCDK----GKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSS---NVMLY 105 (160)
Q Consensus 36 ~I~kGD~V~Vi~---GkdK----GK~G~V~~V~~~~~~V~VeGvN~~kkh~k~~~~~~~ggiv~~e~PI~iS---nV~Lv 105 (160)
.+++||+|.|-. ..+| --+|.|+++....- =+.+.+.+ + ..|-=++.-.|+|-. ++.++
T Consensus 22 ~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~---~~tftvRk--i------~~gvGVEr~fpl~SP~I~~IeV~ 90 (117)
T CHL00084 22 KIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGL---NTTITVRK--V------FQGIGVERVFLLHSPKLASIEVL 90 (117)
T ss_pred ccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCC---CeeEEEEE--e------ccCccEEEEEecCCCccceEEEE
Confidence 379999999854 2233 24688888754221 11111111 1 112225777888854 45555
Q ss_pred ecCCCCeee--EEEEEccCCcEEEE
Q 031394 106 SKEMEVASR--VGHKVLDDGTRVRY 128 (160)
Q Consensus 106 ~p~~~~ptR--v~~~~~edG~kvRv 128 (160)
.- ++..| .-|--..-|+..|+
T Consensus 91 r~--gkvRRAKLyYLR~~~gKaari 113 (117)
T CHL00084 91 RR--SKVRRAKLYYLRNRVGKAARL 113 (117)
T ss_pred Ee--CccchheeEEeccCcChhhee
Confidence 43 34333 33433344665554
No 116
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=24.87 E-value=1.3e+02 Score=21.97 Aligned_cols=29 Identities=21% Similarity=0.221 Sum_probs=21.1
Q ss_pred ccceecCCEEEEeecCCCCeeeEEEEEEc
Q 031394 34 KMHVKAGDTVKVIAGCDKGKIGEITKVFR 62 (160)
Q Consensus 34 k~~I~kGD~V~Vi~GkdKGK~G~V~~V~~ 62 (160)
+.+|.+||+|.|---++-=..|.|+.-++
T Consensus 44 rIrIl~GD~V~VE~spYDltkGRIiyR~~ 72 (87)
T PRK12442 44 RIRILAGDRVTLELSPYDLTKGRINFRHK 72 (87)
T ss_pred eEEecCCCEEEEEECcccCCceeEEEEec
Confidence 45678999999987777666677755443
No 117
>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=24.32 E-value=1.8e+02 Score=18.83 Aligned_cols=23 Identities=22% Similarity=0.327 Sum_probs=17.1
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
+..||.|.+ +|++++..++.+.+
T Consensus 50 ~~~Gd~v~v----------kv~~~d~~~~~i~l 72 (76)
T cd04452 50 VKVGRKEVV----------KVIRVDKEKGYIDL 72 (76)
T ss_pred eCCCCEEEE----------EEEEEECCCCEEEE
Confidence 689999988 57777776666554
No 118
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.88 E-value=1.1e+02 Score=25.25 Aligned_cols=35 Identities=14% Similarity=0.333 Sum_probs=24.8
Q ss_pred cccceecCCEEEEeecC------------CCCeeeEEEEEEccCCeE
Q 031394 33 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVFRHNSTV 67 (160)
Q Consensus 33 ~k~~I~kGD~V~Vi~Gk------------dKGK~G~V~~V~~~~~~V 67 (160)
..|-+++||.|.|++-. .-|..|.+++|--.++++
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 34568999999998654 567778777776644443
No 119
>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=23.86 E-value=1.3e+02 Score=19.45 Aligned_cols=24 Identities=21% Similarity=0.271 Sum_probs=17.9
Q ss_pred cceecCCEEEEeecCCCCeeeEEEEEEccCCeEE
Q 031394 35 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 68 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~ 68 (160)
..+..||.|.| +|.+++.++.++.
T Consensus 47 ~~~~~Gd~v~v----------~v~~id~~~~~i~ 70 (72)
T cd05689 47 KVVSLGDEVEV----------MVLDIDEERRRIS 70 (72)
T ss_pred cEeCCCCEEEE----------EEEEeeCCcCEEe
Confidence 34688999998 5777887776654
No 120
>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=23.83 E-value=1.7e+02 Score=18.71 Aligned_cols=23 Identities=35% Similarity=0.550 Sum_probs=16.0
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
++.||.+.+. |++++++.+.+.+
T Consensus 45 ~~~Gd~i~~~----------i~~~~~~~~~i~l 67 (70)
T cd05687 45 VKVGDEVEVY----------VLRVEDEEGNVVL 67 (70)
T ss_pred CCCCCEEEEE----------EEEEECCCCeEEE
Confidence 6899998874 6677766555544
No 121
>smart00439 BAH Bromo adjacent homology domain.
Probab=23.80 E-value=1.6e+02 Score=20.63 Aligned_cols=29 Identities=28% Similarity=0.431 Sum_probs=23.4
Q ss_pred eecCCEEEEeecC--CCCeeeEEEEEEccCC
Q 031394 37 VKAGDTVKVIAGC--DKGKIGEITKVFRHNS 65 (160)
Q Consensus 37 I~kGD~V~Vi~Gk--dKGK~G~V~~V~~~~~ 65 (160)
|..||.|.|.+.. ..=-+|.|.++....+
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~ 32 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRIEEIFETKK 32 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEEEEEEECCC
Confidence 5789999999876 3457899999987664
No 122
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=23.52 E-value=51 Score=21.75 Aligned_cols=13 Identities=38% Similarity=0.618 Sum_probs=10.7
Q ss_pred eecCCEEEEeecC
Q 031394 37 VKAGDTVKVIAGC 49 (160)
Q Consensus 37 I~kGD~V~Vi~Gk 49 (160)
++.||.|+..+|-
T Consensus 1 f~~GDvV~LKSGG 13 (53)
T PF09926_consen 1 FKIGDVVQLKSGG 13 (53)
T ss_pred CCCCCEEEEccCC
Confidence 3689999999884
No 123
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=23.46 E-value=1.8e+02 Score=17.64 Aligned_cols=24 Identities=29% Similarity=0.494 Sum_probs=18.0
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
.++.||.|.+ .|++++.+++.+.+
T Consensus 46 ~~~~G~~v~~----------~V~~~~~~~~~i~l 69 (72)
T smart00316 46 VLKVGDEVKV----------KVLSVDEEKGRIIL 69 (72)
T ss_pred eecCCCEEEE----------EEEEEeCCCCEEEE
Confidence 3689999887 67778777666654
No 124
>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=23.38 E-value=64 Score=20.28 Aligned_cols=14 Identities=29% Similarity=0.688 Sum_probs=10.0
Q ss_pred cccceecCCEEEEe
Q 031394 33 HKMHVKAGDTVKVI 46 (160)
Q Consensus 33 ~k~~I~kGD~V~Vi 46 (160)
..+.+.+||.|.|+
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 34667999999999
No 125
>PF02938 GAD: GAD domain; InterPro: IPR004115 This entry represetns an 2 layer alpha/beta insertion domain found in some glutamyl-tRNA amidotransferases and aspartyl tRNA synthetases [, ]. The function of this domain is not yet known.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0005737 cytoplasm; PDB: 1ZQ1_D 1EQR_B 1IL2_B 1C0A_A 1L0W_A 1G51_B 1EFW_B 2D6F_D.
Probab=23.28 E-value=47 Score=23.60 Aligned_cols=28 Identities=29% Similarity=0.404 Sum_probs=20.4
Q ss_pred CCHHHHHhcCCCCCccccccceecCCEEEEeecCC
Q 031394 16 LKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCD 50 (160)
Q Consensus 16 l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~Gkd 50 (160)
|+++.+.++ ...+.+..||.+.+++|+.
T Consensus 61 l~e~~~~~l-------~~~~~a~~GD~ll~~Ag~~ 88 (95)
T PF02938_consen 61 LSEEELKAL-------IERLGAKPGDLLLFVAGKK 88 (95)
T ss_dssp CHHHHHHHH-------HHHTT--TTEEEEEEEESH
T ss_pred CCHHHHHHH-------HHHhCCCCCCEEEEECCCH
Confidence 566667665 6667889999999999974
No 126
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=23.15 E-value=1.4e+02 Score=24.48 Aligned_cols=32 Identities=22% Similarity=0.425 Sum_probs=22.6
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 67 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V 67 (160)
.++.||.+.|..|...=-.|+|..+.++.-.+
T Consensus 29 R~~~Gd~i~v~~g~g~~~~~~i~~i~~~~~~~ 60 (234)
T PRK11713 29 RLKEGDELRLFDGDGGEYLAEITEIGKKEVEL 60 (234)
T ss_pred cCCCCCEEEEEeCCCCEEEEEEEEecCcEEEE
Confidence 44999999999997533447888886643333
No 127
>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=23.02 E-value=91 Score=18.32 Aligned_cols=16 Identities=25% Similarity=0.538 Sum_probs=12.5
Q ss_pred ccceecCCEEEEeecC
Q 031394 34 KMHVKAGDTVKVIAGC 49 (160)
Q Consensus 34 k~~I~kGD~V~Vi~Gk 49 (160)
.+.+.+||.|.|+...
T Consensus 18 ~l~~~~Gd~v~v~~~~ 33 (58)
T smart00326 18 ELSFKKGDIITVLEKS 33 (58)
T ss_pred CCCCCCCCEEEEEEcC
Confidence 3456999999999664
No 128
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=22.92 E-value=1.3e+02 Score=20.50 Aligned_cols=22 Identities=32% Similarity=0.271 Sum_probs=14.2
Q ss_pred eecCCEEEEeecCCCCeeeEEE
Q 031394 37 VKAGDTVKVIAGCDKGKIGEIT 58 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~ 58 (160)
+..||.|.|---.+-...|.|.
T Consensus 47 i~vGD~V~ve~~~~~~~~g~Iv 68 (72)
T PRK00276 47 ILPGDKVTVELSPYDLTKGRIT 68 (72)
T ss_pred cCCCCEEEEEEcccCCCeEEEE
Confidence 4799999987444334446664
No 129
>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=22.91 E-value=1.1e+02 Score=21.69 Aligned_cols=30 Identities=30% Similarity=0.369 Sum_probs=21.4
Q ss_pred cceecCCEEEEeecCCCCe-eeEEEEEEccC
Q 031394 35 MHVKAGDTVKVIAGCDKGK-IGEITKVFRHN 64 (160)
Q Consensus 35 ~~I~kGD~V~Vi~GkdKGK-~G~V~~V~~~~ 64 (160)
.-|+.||-|.|-.-.+-.+ .|.|..++.+.
T Consensus 37 iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~~ 67 (78)
T cd05792 37 IWIKRGDFVLVEPIEEGDKVKAEIVKILTRD 67 (78)
T ss_pred EEEEeCCEEEEEecccCCceEEEEEEEECHH
Confidence 3579999999976554333 68888887654
No 130
>PF13437 HlyD_3: HlyD family secretion protein
Probab=22.87 E-value=1.7e+02 Score=20.23 Aligned_cols=27 Identities=26% Similarity=0.415 Sum_probs=22.1
Q ss_pred cee-cCCEEEEee--cCCCCeeeEEEEEEc
Q 031394 36 HVK-AGDTVKVIA--GCDKGKIGEITKVFR 62 (160)
Q Consensus 36 ~I~-kGD~V~Vi~--GkdKGK~G~V~~V~~ 62 (160)
.|+ .||.|.+.. |.+.--.|+|.+|.+
T Consensus 49 ~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 49 RIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred ceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 456 999999984 666777899999988
No 131
>PF15276 PP1_bind: Protein phosphatase 1 binding
Probab=22.86 E-value=65 Score=22.37 Aligned_cols=39 Identities=18% Similarity=0.066 Sum_probs=30.2
Q ss_pred cceeeeccCCHHHHHhcCCCCCccccccceecCCEEEEeecCCCC
Q 031394 8 KPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKG 52 (160)
Q Consensus 8 ~~~~~s~~l~~~lR~k~~~~~~~~~~k~~I~kGD~V~Vi~GkdKG 52 (160)
|++-+..+||.|+=.+.-+..-|+ ++|++=.--......
T Consensus 4 kRVsFG~~LSPElFD~~LPpnTPl------krG~tP~~~~~~~~~ 42 (64)
T PF15276_consen 4 KRVSFGEHLSPELFDKSLPPNTPL------KRGATPVRRSDPSSS 42 (64)
T ss_pred ceeccCCCCCHHHhcccCCCCCCc------CCCCCcccccCCCCC
Confidence 567788999999999988888888 999876555444433
No 132
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=22.83 E-value=1.4e+02 Score=29.02 Aligned_cols=50 Identities=18% Similarity=0.154 Sum_probs=35.6
Q ss_pred ccCCHHHHHhcCCCCC--cc--ccccceecCCEEEEeec-----CCCCeeeEEEEEEcc
Q 031394 14 VRLKRWERKECKPNSL--PV--LHKMHVKAGDTVKVIAG-----CDKGKIGEITKVFRH 63 (160)
Q Consensus 14 ~~l~~~lR~k~~~~~~--~~--~~k~~I~kGD~V~Vi~G-----kdKGK~G~V~~V~~~ 63 (160)
..|+..++..+++... +. .....++.||+|..+.= =+-|-+|.|..++.+
T Consensus 560 ~~lN~~lq~~lnp~~~~~~~~~~~~~~~~~GDkVm~~~N~~~~~v~NGdiG~I~~i~~~ 618 (720)
T TIGR01448 560 DALNQHLQALLNPYQKGQGGIEIAEGEYRKGDRVMQTKNDYNNEIFNGDLGMIVKIEGA 618 (720)
T ss_pred HHHHHHHHHHhCccCCCCceeecCCceecCCCEEEEeeecchhccccCCeeEEEecccc
Confidence 3477888888876321 11 12347899999999864 357999999999775
No 133
>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=22.74 E-value=2.2e+02 Score=20.18 Aligned_cols=37 Identities=19% Similarity=0.300 Sum_probs=33.6
Q ss_pred ecCCEEEEeecCCCCeeeEEEEEEccCCeEEEeceee
Q 031394 38 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINL 74 (160)
Q Consensus 38 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeGvN~ 74 (160)
.-|.++.+|+=.|.--+|..-.|+.+.++|.+++|-.
T Consensus 4 ~IG~~isLISk~~iRYeGiL~~In~~~sTi~L~nVr~ 40 (74)
T cd01736 4 YIGSKISLISKSDIRYEGILYTINTEDSTIALKNVRS 40 (74)
T ss_pred ccCceEEEEecCCcEEEEEEEeeccccCEEEeeeeEe
Confidence 4699999999999999999999999999999998643
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=22.65 E-value=2.5e+02 Score=22.47 Aligned_cols=33 Identities=18% Similarity=0.143 Sum_probs=25.4
Q ss_pred eecCCEEEEeecCC-CCeeeEEEEEEccCC-eEEE
Q 031394 37 VKAGDTVKVIAGCD-KGKIGEITKVFRHNS-TVMV 69 (160)
Q Consensus 37 I~kGD~V~Vi~Gkd-KGK~G~V~~V~~~~~-~V~V 69 (160)
++.||-|.|.+++. -+.+|.|.++....+ .+.|
T Consensus 4 yrvGD~Vy~~~~~~~Py~I~rI~e~~~~~~~~~~v 38 (164)
T cd04709 4 YRVGDYVYFESSPNNPYLIRRIEELNKTARGHVEA 38 (164)
T ss_pred EecCCEEEEECCCCCCCEEEEEEEEEeCCCCCEEE
Confidence 68999999998865 378999999886553 3443
No 135
>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=22.27 E-value=1.9e+02 Score=18.33 Aligned_cols=25 Identities=36% Similarity=0.533 Sum_probs=18.7
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.+..||.|.+ +|++++++++.+.+.
T Consensus 44 ~~~~Gd~v~~----------~v~~~d~~~~~i~ls 68 (73)
T cd05691 44 RFKVGDEVEA----------KITNVDRKNRKISLS 68 (73)
T ss_pred ccCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 3588999987 688888877766543
No 136
>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=22.19 E-value=1.2e+02 Score=19.41 Aligned_cols=29 Identities=14% Similarity=0.075 Sum_probs=22.9
Q ss_pred eecCCEEEEeecCCCCeeeEEEEEEccCC
Q 031394 37 VKAGDTVKVIAGCDKGKIGEITKVFRHNS 65 (160)
Q Consensus 37 I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~ 65 (160)
|..|++|.+.-+...--.++|+++..+.+
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 46899999999777777899999988664
No 137
>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=22.12 E-value=1.7e+02 Score=19.19 Aligned_cols=24 Identities=25% Similarity=0.344 Sum_probs=16.5
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEE
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 69 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~V 69 (160)
.+..||+|.| +|.+++.++.++.+
T Consensus 57 ~~~~gd~v~v----------~v~~vd~~~~~i~~ 80 (83)
T cd04471 57 VFRLGDKVKV----------RVVRVDLDRRKIDF 80 (83)
T ss_pred EEcCCCEEEE----------EEEEeccccCEEEE
Confidence 4678999988 46667666555543
No 138
>KOG4225 consensus Sorbin and SH3 domain-containing protein [Signal transduction mechanisms]
Probab=22.08 E-value=98 Score=29.09 Aligned_cols=37 Identities=19% Similarity=0.351 Sum_probs=25.8
Q ss_pred HHHhcCCCCCccccccceecCCEEEEee--------cCCCCeeeEE
Q 031394 20 ERKECKPNSLPVLHKMHVKAGDTVKVIA--------GCDKGKIGEI 57 (160)
Q Consensus 20 lR~k~~~~~~~~~~k~~I~kGD~V~Vi~--------GkdKGK~G~V 57 (160)
.|..|++..-- ...+.+.+||.|.|+. |.+-|.+|.+
T Consensus 233 aralf~F~~qt-~kEL~~~kGDIVyI~rkvD~nWyeGEhhGr~Gif 277 (489)
T KOG4225|consen 233 ARALFDFEAQT-PKELPFNKGDIVYILRKVDQNWYEGEHHGRVGIF 277 (489)
T ss_pred hhheeccccCC-ccccccCCCCEEEEEeeccCceeeeeecceecce
Confidence 45556544422 4567789999999974 6677888865
No 139
>PRK10708 hypothetical protein; Provisional
Probab=21.86 E-value=1.3e+02 Score=20.60 Aligned_cols=27 Identities=22% Similarity=0.213 Sum_probs=20.6
Q ss_pred ecCCEEEEeecCCCCeeeEEEEEEccC
Q 031394 38 KAGDTVKVIAGCDKGKIGEITKVFRHN 64 (160)
Q Consensus 38 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~ 64 (160)
+.+|+|.|-+--.--..|.|+.|.+=.
T Consensus 2 kvnD~VtVKTDG~~rR~G~iLavE~F~ 28 (62)
T PRK10708 2 KVNDRVTVKTDGGPRRPGVVLAVEEFS 28 (62)
T ss_pred ccccEEEEecCCCccccceEEEEeecc
Confidence 468999998766666789998887633
No 140
>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=21.78 E-value=1.1e+02 Score=21.37 Aligned_cols=24 Identities=38% Similarity=0.570 Sum_probs=11.4
Q ss_pred cCCEEEEeecC--------------CCCeeeEEEEEEc
Q 031394 39 AGDTVKVIAGC--------------DKGKIGEITKVFR 62 (160)
Q Consensus 39 kGD~V~Vi~Gk--------------dKGK~G~V~~V~~ 62 (160)
.||+|.|.+-- -+|.+|.|.++..
T Consensus 1 vGdrVrV~~sv~Vyh~P~hr~~~fDl~G~EGev~~~v~ 38 (67)
T PF02941_consen 1 VGDRVRVKASVVVYHHPEHRNPPFDLKGMEGEVKQIVT 38 (67)
T ss_dssp TT-EEEE-S--EES--TTSTTS-EE-TT-EEEEEEE-S
T ss_pred CCCeEEEeeeEEEEeCCcccCCCccccCCEEEEEEEEe
Confidence 37888776421 3577777776653
No 141
>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=21.38 E-value=2.9e+02 Score=19.18 Aligned_cols=13 Identities=38% Similarity=0.659 Sum_probs=10.7
Q ss_pred ceecCCEEEEeec
Q 031394 36 HVKAGDTVKVIAG 48 (160)
Q Consensus 36 ~I~kGD~V~Vi~G 48 (160)
.|++||.|.++.-
T Consensus 27 tl~~g~~v~~~~~ 39 (94)
T cd04090 27 TIKKGQKVKVLGE 39 (94)
T ss_pred eEcCCCEEEEECC
Confidence 6899999988753
No 142
>PRK09510 tolA cell envelope integrity inner membrane protein TolA; Provisional
Probab=21.30 E-value=1.5e+02 Score=27.05 Aligned_cols=26 Identities=19% Similarity=0.215 Sum_probs=22.1
Q ss_pred CCCeeeEEEEEccCCcEEEEEeccCC
Q 031394 109 MEVASRVGHKVLDDGTRVRYLIKTGE 134 (160)
Q Consensus 109 ~~~ptRv~~~~~edG~kvRv~kksg~ 134 (160)
.|..|+|.+.+..||.-+.|...||.
T Consensus 324 ~gktc~VrI~LapDG~V~sV~~sSGd 349 (387)
T PRK09510 324 AGKTCTLRIKLAPDGTLLDIKKEGGD 349 (387)
T ss_pred cCceEEEEEEEcCCCcEEeeeeCCCC
Confidence 46789999999999988888877876
No 143
>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=20.90 E-value=2e+02 Score=21.80 Aligned_cols=33 Identities=18% Similarity=0.209 Sum_probs=25.9
Q ss_pred ecCCEEEEeecCCCCeeeEEEEEEccCCeEEEec
Q 031394 38 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 71 (160)
Q Consensus 38 ~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~VeG 71 (160)
++||.|..=.|. .|-.|.++..+.+.+.+++=|
T Consensus 75 ~~GDiv~f~~~~-~~HVGi~~g~~~~~g~i~~lg 107 (129)
T TIGR02594 75 AYGCIAVKRRGG-GGHVGFVVGKDKQTGTIIVLG 107 (129)
T ss_pred CccEEEEEECCC-CCEEEEEEeEcCCCCEEEEee
Confidence 799999886654 789999999888777765544
No 144
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.72 E-value=1.5e+02 Score=23.46 Aligned_cols=39 Identities=26% Similarity=0.417 Sum_probs=26.4
Q ss_pred cccceecCCEEEEeecC------------CCCeeeEEEEEEccCCeEEEec
Q 031394 33 HKMHVKAGDTVKVIAGC------------DKGKIGEITKVFRHNSTVMVKD 71 (160)
Q Consensus 33 ~k~~I~kGD~V~Vi~Gk------------dKGK~G~V~~V~~~~~~V~VeG 71 (160)
..|-+.+||.|.++... +-|..|.++.|---...-+|.|
T Consensus 97 ~p~~V~rG~~V~i~~~~~g~~i~~~G~Al~~G~~Gd~IrVrN~~Sgkiv~g 147 (160)
T PRK06005 97 EPSLVTRGSPVKLVFSAGGLTITAAGTPLQSGAAGDLIRVRNVDSGVIVSG 147 (160)
T ss_pred CCcEEeCCCEEEEEEecCCEEEEEEEEEcccCCCCCEEEEEECCCCCEEEE
Confidence 45678999999998654 5688888888863333333443
No 145
>PRK07252 hypothetical protein; Provisional
Probab=20.57 E-value=1.8e+02 Score=21.77 Aligned_cols=25 Identities=16% Similarity=0.239 Sum_probs=20.7
Q ss_pred ceecCCEEEEeecCCCCeeeEEEEEEccCCeEEEe
Q 031394 36 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 70 (160)
Q Consensus 36 ~I~kGD~V~Vi~GkdKGK~G~V~~V~~~~~~V~Ve 70 (160)
.++.||.|.| +|++++.+.+++.+.
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 3689999998 788899888888765
Done!