Query 029417
Match_columns 193
No_of_seqs 222 out of 1416
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 12:34:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029417.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029417hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1708 Mitochondrial/chloropl 100.0 1.3E-43 2.9E-48 300.0 10.0 191 1-191 1-202 (236)
2 TIGR01079 rplX_bact ribosomal 100.0 2.1E-38 4.5E-43 243.9 12.1 103 67-169 1-104 (104)
3 PRK00004 rplX 50S ribosomal pr 100.0 2.3E-38 5E-43 243.8 12.3 104 67-170 2-105 (105)
4 COG0198 RplX Ribosomal protein 100.0 1.2E-35 2.5E-40 229.0 11.0 102 67-170 2-104 (104)
5 PTZ00194 60S ribosomal protein 100.0 7E-30 1.5E-34 206.3 6.4 100 19-148 14-113 (143)
6 PRK01191 rpl24p 50S ribosomal 100.0 2.8E-29 6.1E-34 197.8 7.6 92 40-148 22-113 (120)
7 CHL00141 rpl24 ribosomal prote 100.0 3E-28 6.4E-33 180.9 8.4 77 67-143 6-82 (83)
8 PRK12281 rplX 50S ribosomal pr 99.9 1E-27 2.2E-32 175.5 7.7 74 65-138 2-75 (76)
9 TIGR01080 rplX_A_E ribosomal p 99.9 7.3E-27 1.6E-31 182.8 8.2 91 40-147 18-108 (114)
10 KOG3401 60S ribosomal protein 99.7 3.8E-17 8.1E-22 132.3 3.8 92 35-143 20-112 (145)
11 PF00467 KOW: KOW motif; Inte 98.7 1.8E-08 3.8E-13 62.2 4.6 32 72-103 1-32 (32)
12 smart00739 KOW KOW (Kyprides, 97.7 6.1E-05 1.3E-09 43.8 3.7 26 70-95 2-27 (28)
13 PRK08559 nusG transcription an 97.4 0.00075 1.6E-08 54.7 7.5 62 44-108 72-133 (153)
14 TIGR00405 L26e_arch ribosomal 97.3 0.00074 1.6E-08 53.7 6.3 59 45-106 65-123 (145)
15 PRK05609 nusG transcription an 96.7 0.0027 5.9E-08 51.6 4.9 36 68-103 125-160 (181)
16 TIGR00922 nusG transcription t 96.7 0.0028 6.2E-08 51.3 4.9 34 70-103 120-153 (172)
17 COG0250 NusG Transcription ant 96.4 0.005 1.1E-07 51.7 4.8 38 66-103 120-157 (178)
18 TIGR01955 RfaH transcriptional 95.8 0.013 2.9E-07 46.6 4.5 34 69-103 108-141 (159)
19 PRK09014 rfaH transcriptional 95.6 0.019 4E-07 46.3 4.3 33 70-103 110-142 (162)
20 TIGR01956 NusG_myco NusG famil 95.2 0.034 7.5E-07 49.5 5.0 34 70-103 206-239 (258)
21 PRK04333 50S ribosomal protein 93.4 0.17 3.7E-06 37.8 4.7 37 68-105 2-38 (84)
22 KOG1999 RNA polymerase II tran 86.0 0.84 1.8E-05 47.3 3.9 28 69-96 459-486 (1024)
23 PTZ00065 60S ribosomal protein 85.5 1.9 4E-05 35.0 5.0 35 70-105 8-42 (130)
24 PTZ00471 60S ribosomal protein 82.9 2.1 4.6E-05 34.9 4.3 40 70-109 5-50 (134)
25 COG2163 RPL14A Ribosomal prote 78.7 3.4 7.3E-05 33.2 4.1 36 70-106 5-40 (125)
26 COG5164 SPT5 Transcription elo 76.8 1.6 3.5E-05 42.4 2.1 53 41-97 115-167 (607)
27 TIGR01024 rplS_bact ribosomal 76.1 36 0.00079 26.9 9.2 86 56-161 10-109 (113)
28 PRK04313 30S ribosomal protein 75.9 4.2 9.2E-05 35.9 4.3 37 68-104 170-210 (237)
29 PRK06531 yajC preprotein trans 75.3 4.9 0.00011 31.7 4.1 31 69-103 36-66 (113)
30 PF09953 DUF2187: Uncharacteri 74.7 6.4 0.00014 27.7 4.1 27 71-103 5-31 (57)
31 COG1862 YajC Preprotein transl 72.5 5.9 0.00013 30.5 3.8 29 69-103 43-71 (97)
32 KOG1999 RNA polymerase II tran 72.1 2.5 5.4E-05 44.0 2.1 30 67-96 579-608 (1024)
33 PRK05585 yajC preprotein trans 68.8 8.5 0.00018 29.8 4.0 29 69-103 52-80 (106)
34 COG1532 Predicted RNA-binding 68.4 11 0.00024 26.6 4.1 35 70-104 21-57 (57)
35 PF03144 GTP_EFTU_D2: Elongati 65.8 10 0.00022 25.9 3.6 30 69-99 12-44 (74)
36 TIGR00739 yajC preprotein tran 63.5 14 0.0003 27.4 4.1 29 69-103 37-65 (84)
37 PRK05886 yajC preprotein trans 62.4 14 0.0003 29.1 4.1 29 69-103 38-66 (109)
38 PF05641 Agenet: Agenet domain 61.8 21 0.00045 24.9 4.6 33 70-103 1-37 (68)
39 COG3700 AphA Acid phosphatase 60.1 2.1 4.6E-05 37.2 -0.8 34 67-100 124-157 (237)
40 PTZ00223 40S ribosomal protein 59.9 14 0.0003 33.5 4.2 74 67-162 169-245 (273)
41 PLN00036 40S ribosomal protein 59.8 16 0.00035 32.8 4.6 36 68-103 173-211 (261)
42 PRK05338 rplS 50S ribosomal pr 59.0 90 0.0019 24.8 9.0 82 60-161 14-109 (116)
43 PF02699 YajC: Preprotein tran 58.0 3.3 7.2E-05 30.4 0.0 29 69-103 36-64 (82)
44 PTZ00118 40S ribosomal protein 56.7 19 0.0004 32.4 4.5 36 68-103 173-211 (262)
45 COG1471 RPS4A Ribosomal protei 56.4 19 0.0004 32.1 4.3 36 69-104 173-212 (241)
46 COG2002 AbrB Regulators of sta 54.5 17 0.00036 26.9 3.3 27 49-86 18-44 (89)
47 PF08206 OB_RNB: Ribonuclease 52.8 11 0.00023 25.7 1.9 24 70-93 32-58 (58)
48 CHL00084 rpl19 ribosomal prote 51.6 1.2E+02 0.0026 24.1 10.2 87 55-161 13-113 (117)
49 PRK02749 photosystem I reactio 50.1 33 0.00071 25.2 4.1 29 69-97 2-32 (71)
50 PF01245 Ribosomal_L19: Riboso 48.6 1.2E+02 0.0026 23.8 7.4 56 69-137 18-82 (113)
51 smart00743 Agenet Tudor-like d 48.1 55 0.0012 21.8 4.8 34 69-103 2-36 (61)
52 cd05793 S1_IF1A S1_IF1A: Trans 46.6 21 0.00046 26.0 2.7 28 70-97 39-66 (77)
53 cd03692 mtIF2_IVc mtIF2_IVc: t 45.4 40 0.00086 24.3 4.0 31 69-99 26-56 (84)
54 COG0361 InfA Translation initi 44.7 33 0.00072 25.3 3.5 30 67-96 44-73 (75)
55 PRK00409 recombination and DNA 44.5 33 0.00071 34.9 4.5 38 68-108 635-673 (782)
56 TIGR00523 eIF-1A eukaryotic/ar 44.0 17 0.00036 28.0 1.9 27 69-97 57-86 (99)
57 KOG4315 G-patch nucleic acid b 43.8 20 0.00043 34.5 2.7 46 53-104 383-428 (455)
58 PF12353 eIF3g: Eukaryotic tra 43.0 42 0.00091 26.7 4.1 28 139-166 8-35 (128)
59 CHL00125 psaE photosystem I su 42.4 43 0.00094 24.1 3.6 28 70-97 2-31 (64)
60 PF01157 Ribosomal_L21e: Ribos 41.7 35 0.00075 26.4 3.3 29 69-97 32-70 (99)
61 PF12701 LSM14: Scd6-like Sm d 41.1 69 0.0015 24.4 4.9 37 71-107 6-42 (96)
62 cd04456 S1_IF1A_like S1_IF1A_l 40.8 34 0.00074 25.0 3.0 28 70-97 39-67 (78)
63 smart00652 eIF1a eukaryotic tr 39.5 35 0.00076 25.2 3.0 28 70-97 44-71 (83)
64 KOG3418 60S ribosomal protein 39.4 47 0.001 27.2 3.9 39 70-108 5-49 (136)
65 PRK13264 3-hydroxyanthranilate 39.3 2.4E+02 0.0052 24.0 8.6 56 117-172 100-170 (177)
66 cd05792 S1_eIF1AD_like S1_eIF1 39.2 42 0.00092 24.8 3.3 29 69-97 38-67 (78)
67 PLN00045 photosystem I reactio 38.5 54 0.0012 25.5 3.9 27 70-96 40-68 (101)
68 COG5164 SPT5 Transcription elo 38.3 39 0.00085 33.2 3.8 33 71-103 353-385 (607)
69 PRK04306 50S ribosomal protein 37.9 54 0.0012 25.4 3.8 34 70-103 35-78 (98)
70 PRK00750 lysK lysyl-tRNA synth 37.6 57 0.0012 31.5 4.8 52 127-178 166-233 (510)
71 PF11623 DUF3252: Protein of u 37.2 67 0.0014 22.4 3.8 40 70-109 2-43 (53)
72 PF01079 Hint: Hint module; I 36.9 49 0.0011 28.6 3.9 28 68-95 104-132 (217)
73 TIGR01069 mutS2 MutS2 family p 36.5 54 0.0012 33.3 4.7 34 71-108 626-661 (771)
74 PF14505 DUF4438: Domain of un 36.1 72 0.0016 28.7 4.8 33 71-103 59-91 (258)
75 PF01176 eIF-1a: Translation i 35.8 45 0.00097 23.2 2.9 23 70-92 42-64 (65)
76 PF02427 PSI_PsaE: Photosystem 34.7 45 0.00097 23.9 2.7 28 70-97 1-30 (61)
77 cd04717 BAH_polybromo BAH, or 34.3 1.1E+02 0.0024 23.2 5.2 37 69-105 3-42 (121)
78 PRK08577 hypothetical protein; 33.8 50 0.0011 25.7 3.2 28 49-87 17-44 (136)
79 cd04466 S1_YloQ_GTPase S1_YloQ 33.2 79 0.0017 21.1 3.7 29 70-100 38-66 (68)
80 TIGR03170 flgA_cterm flagella 32.3 78 0.0017 23.8 4.0 33 68-100 64-109 (122)
81 COG1465 Predicted alternative 31.2 3.3E+02 0.0072 25.6 8.4 24 70-93 281-304 (376)
82 COG1193 Mismatch repair ATPase 30.3 54 0.0012 33.5 3.5 34 66-103 609-642 (753)
83 cd05707 S1_Rrp5_repeat_sc11 S1 29.3 85 0.0018 21.0 3.4 23 70-102 45-67 (68)
84 PF14604 SH3_9: Variant SH3 do 29.2 39 0.00085 22.0 1.6 14 67-80 12-25 (49)
85 PRK04012 translation initiatio 29.2 59 0.0013 25.0 2.8 28 70-97 60-87 (100)
86 PF04452 Methyltrans_RNA: RNA 29.1 70 0.0015 27.0 3.5 34 70-103 17-50 (225)
87 cd05695 S1_Rrp5_repeat_hs3 S1_ 29.1 87 0.0019 21.3 3.5 23 70-102 43-65 (66)
88 KOG0122 Translation initiation 28.9 62 0.0013 29.3 3.2 54 129-185 17-77 (270)
89 PF01426 BAH: BAH domain; Int 28.8 74 0.0016 23.3 3.3 29 69-97 2-32 (119)
90 cd05703 S1_Rrp5_repeat_hs12_sc 28.5 1E+02 0.0022 21.5 3.7 24 70-103 47-70 (73)
91 cd04090 eEF2_II_snRNP Loc2 eEF 28.3 1.6E+02 0.0036 21.3 5.0 13 69-81 27-39 (94)
92 cd05698 S1_Rrp5_repeat_hs6_sc5 28.2 1E+02 0.0023 20.5 3.7 24 70-103 45-68 (70)
93 cd05697 S1_Rrp5_repeat_hs5 S1_ 28.1 1.2E+02 0.0025 20.3 4.0 23 70-102 45-67 (69)
94 cd05688 S1_RPS1_repeat_ec3 S1_ 27.9 1.1E+02 0.0024 19.8 3.7 24 69-102 44-67 (68)
95 cd04461 S1_Rrp5_repeat_hs8_sc7 27.1 1.1E+02 0.0023 21.5 3.7 25 68-102 57-81 (83)
96 cd05708 S1_Rrp5_repeat_sc12 S1 26.9 1.4E+02 0.0029 20.0 4.1 25 69-103 47-71 (77)
97 PF05257 CHAP: CHAP domain; I 26.7 95 0.0021 23.3 3.6 37 70-107 63-101 (124)
98 cd04721 BAH_plant_1 BAH, or Br 26.3 1.8E+02 0.0039 22.9 5.3 30 68-97 6-35 (130)
99 cd04715 BAH_Orc1p_like BAH, or 26.3 1.6E+02 0.0035 24.3 5.1 28 70-97 30-57 (159)
100 cd00674 LysRS_core_class_I cat 26.0 1.2E+02 0.0027 28.0 4.8 42 127-168 160-201 (353)
101 PF06701 MIB_HERC2: Mib_herc2; 26.0 80 0.0017 22.7 2.9 20 84-103 19-43 (68)
102 COG2139 RPL21A Ribosomal prote 25.9 1.3E+02 0.0028 23.4 4.2 39 70-108 33-81 (98)
103 PLN00190 60S ribosomal protein 25.8 1.2E+02 0.0026 25.5 4.2 32 70-101 34-75 (158)
104 cd05696 S1_Rrp5_repeat_hs4 S1_ 25.7 1.3E+02 0.0027 20.8 3.8 23 70-102 47-69 (71)
105 KOG0171 Mitochondrial inner me 25.5 1.5E+02 0.0033 25.3 4.8 39 71-109 91-132 (176)
106 cd01854 YjeQ_engC YjeQ/EngC. 25.0 1.1E+02 0.0023 26.9 4.1 29 70-100 35-63 (287)
107 PRK07018 flgA flagellar basal 24.8 1.1E+02 0.0023 26.4 3.9 33 68-100 175-220 (235)
108 cd04714 BAH_BAHCC1 BAH, or Bro 24.1 2.1E+02 0.0045 22.1 5.1 34 70-103 4-40 (121)
109 smart00439 BAH Bromo adjacent 24.1 1.4E+02 0.0031 21.7 4.1 29 70-98 2-32 (120)
110 PRK12442 translation initiatio 23.7 1.3E+02 0.0029 22.8 3.8 26 69-94 46-71 (87)
111 cd03698 eRF3_II_like eRF3_II_l 23.5 1.3E+02 0.0028 21.3 3.6 11 70-80 27-37 (83)
112 PRK08515 flgA flagellar basal 23.2 1.2E+02 0.0026 26.0 4.0 33 68-100 164-208 (222)
113 cd00164 S1_like S1_like: Ribos 23.1 1.4E+02 0.003 18.6 3.4 23 69-101 41-63 (65)
114 PF02887 PK_C: Pyruvate kinase 23.1 45 0.00098 25.1 1.2 19 70-88 90-108 (117)
115 PF00575 S1: S1 RNA binding do 23.1 1.7E+02 0.0038 19.5 4.1 25 69-103 48-72 (74)
116 PF00018 SH3_1: SH3 domain; I 22.6 95 0.0021 19.6 2.5 16 67-82 13-28 (48)
117 PF15276 PP1_bind: Protein pho 22.3 62 0.0013 23.4 1.7 39 41-85 4-42 (64)
118 cd03695 CysN_NodQ_II CysN_NodQ 22.2 1.7E+02 0.0037 20.8 4.0 10 70-79 27-36 (81)
119 CHL00010 infA translation init 21.9 1.4E+02 0.003 21.6 3.5 27 70-96 47-73 (78)
120 cd00174 SH3 Src homology 3 dom 21.6 87 0.0019 18.9 2.1 14 68-81 16-29 (54)
121 PF04014 Antitoxin-MazE: Antid 21.6 88 0.0019 20.1 2.2 25 47-82 9-33 (47)
122 cd03693 EF1_alpha_II EF1_alpha 21.6 1.3E+02 0.0027 21.8 3.3 19 90-108 36-54 (91)
123 cd03696 selB_II selB_II: this 21.5 1.3E+02 0.0029 21.0 3.4 24 70-96 27-50 (83)
124 PF00924 MS_channel: Mechanose 21.4 60 0.0013 26.2 1.7 21 70-95 61-81 (206)
125 PRK12617 flgA flagellar basal 21.4 1.4E+02 0.003 25.8 4.0 28 68-95 154-193 (214)
126 cd05685 S1_Tex S1_Tex: The C-t 21.4 1.6E+02 0.0034 18.9 3.4 22 70-101 45-66 (68)
127 PF13234 rRNA_proc-arch: rRNA- 21.2 1.7E+02 0.0036 25.3 4.5 28 70-97 73-100 (268)
128 cd04451 S1_IF1 S1_IF1: Transla 21.1 90 0.002 21.2 2.3 21 70-90 41-61 (64)
129 TIGR00467 lysS_arch lysyl-tRNA 21.1 1.5E+02 0.0032 29.0 4.5 41 127-168 159-199 (515)
130 KOG2192 PolyC-binding hnRNP-K 21.1 56 0.0012 30.1 1.5 45 50-95 145-189 (390)
131 PF07076 DUF1344: Protein of u 20.9 3.2E+02 0.0069 19.5 6.1 52 86-159 5-56 (61)
132 cd05690 S1_RPS1_repeat_ec5 S1_ 20.9 1.6E+02 0.0035 19.3 3.5 22 70-101 46-67 (69)
133 PF14001 YdfZ: YdfZ protein 20.7 1.7E+02 0.0038 21.1 3.7 34 70-106 10-52 (64)
134 PF09526 DUF2387: Probable met 20.4 1.6E+02 0.0035 21.3 3.6 36 138-174 10-45 (71)
135 cd04452 S1_IF2_alpha S1_IF2_al 20.4 2.2E+02 0.0047 19.1 4.1 23 70-102 50-72 (76)
136 TIGR00358 3_prime_RNase VacB a 20.3 1.6E+02 0.0035 29.2 4.7 35 69-103 50-87 (654)
137 PRK06005 flgA flagellar basal 20.3 1.6E+02 0.0035 24.1 4.0 38 67-104 98-147 (160)
138 PRK11713 16S ribosomal RNA met 20.3 1.6E+02 0.0035 25.1 4.1 27 70-96 30-56 (234)
139 cd05706 S1_Rrp5_repeat_sc10 S1 20.2 2E+02 0.0043 19.3 3.9 23 70-102 48-70 (73)
140 PRK12289 GTPase RsgA; Reviewed 20.1 1.6E+02 0.0035 27.1 4.3 32 70-101 52-83 (352)
No 1
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-43 Score=300.01 Aligned_cols=191 Identities=42% Similarity=0.597 Sum_probs=171.8
Q ss_pred Chhhhhhhhhcccccccc-cccccccc-CCCCCCC-cccCCCCcceEEecCCCHHHHHhhCCCCCCcccccceeeCCEEE
Q 029417 1 MAAMAALQSSMTSLSISS-NSFFGQRL-SFPSLSP-ITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVK 77 (193)
Q Consensus 1 ~~~~~~~~~~~~~l~~~~-~~~~~~~~-~~~~~~~-~~~~~~~~~~~~~~~l~k~lR~k~~~rs~p~~~k~~IkkGD~V~ 77 (193)
|+.|+||||++++||+.- ..|.++.+ +|.++.+ .+.+..+++|+.-..+..|+|..+.+...+..++|+++.||+|+
T Consensus 1 M~ts~aL~s~l~s~s~lPs~y~er~y~isP~~~~~~~pr~~adk~~~~~qk~~~w~rrr~~~~e~i~d~dw~ff~GDtVe 80 (236)
T KOG1708|consen 1 MRTSSALASSLTSLSLLPSSYFERQYLISPISLSVTSPRKVADKRCLVLQKNKPWERRRCVPVEPIIDEDWHFFFGDTVE 80 (236)
T ss_pred CchHHHHHHHhhhhhcCCHHHhhceeeeccccccccCCCChhhhhhhHHhhcCccccccCCCCCCccccceeEecCCEEE
Confidence 889999999999999865 56668887 4666664 34777888999999999999999999998889999999999999
Q ss_pred EeecCCCCeeeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceeEEEeecCcCCC-eeeeecCCCCeeeEEEEEccCC
Q 029417 78 VIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSN-VMLYSKEMEVASRVGHKVLDDG 156 (193)
Q Consensus 78 VI~GkdKGK~GkV~~V~~~~n~ViVEGvN~~kkhvK~~~~~~~GgIi~~E~PIh~SN-V~Lv~p~~~kptRVg~r~~edG 156 (193)
||.|+||||+|+|++|++++|+|+|+|+|...+|++...+|.+|.|+..|+|||.|| |||+||++.+||+++|+++++|
T Consensus 81 VlvGkDkGkqG~Vtqv~r~~s~VvV~gln~k~r~~gsekeg~pgtivk~EaPlhvsk~VmLvdp~d~q~te~~wr~~e~G 160 (236)
T KOG1708|consen 81 VLVGKDKGKQGEVTQVIRHRSWVVVKGLNTKYRHMGSEKEGEPGTIVKSEAPLHVSKQVMLVDPEDDQPTEVEWRFTEDG 160 (236)
T ss_pred EEecccCCccceEEEEeecCceEEEcccchhhhhhcccccCCCceEEeecCCceecceeEEECccccCCceeeEEEcCCC
Confidence 999999999999999999999999999999999999998899999999999999999 9999999999999999999999
Q ss_pred cEEEEEcccCcccccchhh-----h--hhhcccccceeeecc
Q 029417 157 TRVRYLIKTGEIIDSAENW-----K--KLKEANRQEKTEVAT 191 (193)
Q Consensus 157 kKvRv~kksg~~I~~Pe~~-----k--~~~k~~~~~~~~~~~ 191 (193)
++|||+.+||++||.||.| + -+.+...|.+.++|+
T Consensus 161 ekVRvstrSG~iIpipe~~t~dy~~pe~yiE~e~KdTp~~av 202 (236)
T KOG1708|consen 161 EKVRVSTRSGRIIPIPEKWTADYIKPELYIEAEDKDTPQVAV 202 (236)
T ss_pred cEEEEEecccccccCcccccccccCchheeecccCCCcHhhh
Confidence 9999999999999999999 3 444445455555554
No 2
>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=2.1e-38 Score=243.95 Aligned_cols=103 Identities=51% Similarity=0.781 Sum_probs=99.1
Q ss_pred ccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEeceeeeeeeecCCcccC-CceeEEEeecCcCCCeeeeecCCCCe
Q 029417 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEE-QGQIIKIEAPIHSSNVMLYSKEMEVA 145 (193)
Q Consensus 67 k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN~~kkhvK~~~~~~-~GgIi~~E~PIh~SNV~Lv~p~~~kp 145 (193)
+++|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|+||++.++ +|+|+++|+|||+|||+|+||.+++|
T Consensus 1 ~~~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~lv~p~~~k~ 80 (104)
T TIGR01079 1 KMKIKKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVMLFDPKTGKA 80 (104)
T ss_pred CCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHHHeEEEcCcCCCC
Confidence 35799999999999999999999999999999999999999999999988776 89999999999999999999999999
Q ss_pred eeEEEEEccCCcEEEEEcccCccc
Q 029417 146 SRVGHKVLDDGTRVRYLIKTGEII 169 (193)
Q Consensus 146 tRVg~r~~edGkKvRv~kksg~~I 169 (193)
+||+|++++||+++|||++||++|
T Consensus 81 ~rv~~~~~~~g~kvRv~k~~g~~i 104 (104)
T TIGR01079 81 TRVGIRFEEDGKKVRVFKKTGEII 104 (104)
T ss_pred eEEEEEEccCCcEEEEEeccCCcC
Confidence 999999999999999999999876
No 3
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=100.00 E-value=2.3e-38 Score=243.75 Aligned_cols=104 Identities=50% Similarity=0.731 Sum_probs=101.0
Q ss_pred ccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceeEEEeecCcCCCeeeeecCCCCee
Q 029417 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVAS 146 (193)
Q Consensus 67 k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN~~kkhvK~~~~~~~GgIi~~E~PIh~SNV~Lv~p~~~kpt 146 (193)
+|+|++||+|+||+|+|||++|+|++|++++++|+|||+|+.++|+|+++++.+|+|+++|+|||+|||+|+||.+++|+
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 67899999999999999999999999999999999999999999999998888999999999999999999999999999
Q ss_pred eEEEEEccCCcEEEEEcccCcccc
Q 029417 147 RVGHKVLDDGTRVRYLIKTGEIID 170 (193)
Q Consensus 147 RVg~r~~edGkKvRv~kksg~~I~ 170 (193)
||+|++++||+++|||++||+.|+
T Consensus 82 rv~~~~~~~g~kvRv~k~~g~~i~ 105 (105)
T PRK00004 82 RVGFKFLEDGKKVRVAKKSGEVID 105 (105)
T ss_pred EEEEEEccCCcEEEEEecCCCCcC
Confidence 999999999999999999999874
No 4
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-35 Score=228.98 Aligned_cols=102 Identities=51% Similarity=0.749 Sum_probs=97.3
Q ss_pred ccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceeEEEeecCcCCCeeeeec-CCCCe
Q 029417 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSK-EMEVA 145 (193)
Q Consensus 67 k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN~~kkhvK~~~~~~~GgIi~~E~PIh~SNV~Lv~p-~~~kp 145 (193)
+|+|++||+|.||+|+|||++|+|++|++++ |+|||||++++|++|.++++.|||+++|+|||+|||||+|+ .++++
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 4679999999999999999999999999998 99999999999999888888899999999999999999999 79999
Q ss_pred eeEEEEEccCCcEEEEEcccCcccc
Q 029417 146 SRVGHKVLDDGTRVRYLIKTGEIID 170 (193)
Q Consensus 146 tRVg~r~~edGkKvRv~kksg~~I~ 170 (193)
+|++|++.+||+++||+++||+.|+
T Consensus 80 ~Rv~~~~~~~~kkvr~~Kk~g~~i~ 104 (104)
T COG0198 80 TRVGYKVEEDGKKVRVAKKSGEVID 104 (104)
T ss_pred ceEEEEEecCCcEEEEEeccCcccC
Confidence 9999999789999999999999875
No 5
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=99.96 E-value=7e-30 Score=206.31 Aligned_cols=100 Identities=24% Similarity=0.400 Sum_probs=91.2
Q ss_pred ccccccccCCCCCCCcccCCCCcceEEecCCCHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCCeeeEEEEEEccCC
Q 029417 19 NSFFGQRLSFPSLSPITVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNS 98 (193)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n 98 (193)
.++|.++++.+. .+|+++||+|||++|++|++| |++||+|+||+|+|||++|+|++|+++++
T Consensus 14 Ka~~~Ap~h~r~------------k~msa~LSkeLr~k~~~Rs~~------IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~ 75 (143)
T PTZ00194 14 KAHFTAPSHLRR------------KLMSAPLSKELRAKYNVRSMP------VRKDDEVMVVRGHHKGREGKVTAVYRKKW 75 (143)
T ss_pred HHhhcCcHHHHH------------HHhcCccCHHHHHHhCCccce------eecCCEEEEecCCCCCCceEEEEEEcCCC
Confidence 567777777644 899999999999999999998 99999999999999999999999999999
Q ss_pred EEEEeceeeeeeeecCCcccCCceeEEEeecCcCCCeeeeecCCCCeeeE
Q 029417 99 TVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVASRV 148 (193)
Q Consensus 99 ~ViVEGvN~~kkhvK~~~~~~~GgIi~~E~PIh~SNV~Lv~p~~~kptRV 148 (193)
+|+|||||+.++|.++ +|+|||+|||+|+|+..++. |.
T Consensus 76 ~ViVEgvn~~Kk~gk~-----------~e~PIh~SNV~iv~l~l~~~-R~ 113 (143)
T PTZ00194 76 VIHIEKITREKANGEP-----------VQIGIHPSNVIITKLKLNKD-RK 113 (143)
T ss_pred EEEEeCeEEEecCCCE-----------eecCcCchheEEEccccCch-HH
Confidence 9999999999988654 68999999999999988776 53
No 6
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=99.96 E-value=2.8e-29 Score=197.83 Aligned_cols=92 Identities=32% Similarity=0.463 Sum_probs=84.2
Q ss_pred CcceEEecCCCHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEeceeeeeeeecCCcccC
Q 029417 40 DKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEE 119 (193)
Q Consensus 40 ~~~~~~~~~l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN~~kkhvK~~~~~~ 119 (193)
+++.+|+++||+|||++|+.++++ |++||+|+||+|+|||++|+|++|++++++|+|||||+++.
T Consensus 22 ~r~k~msa~LSkeLr~~y~ir~~~------IkkGD~V~VisG~~KGk~GkV~~V~~~~~~V~VeGvn~~k~--------- 86 (120)
T PRK01191 22 LRQKLMSAPLSKELREKYGIRSLP------VRKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYVEGVTVKKA--------- 86 (120)
T ss_pred HHHHHhcCccCHHHHHHhCCccce------EeCCCEEEEeecCCCCceEEEEEEEcCCCEEEEeCcEEECC---------
Confidence 356999999999999999999988 99999999999999999999999999999999999999882
Q ss_pred CceeEEEeecCcCCCeeeeecCCCCeeeE
Q 029417 120 QGQIIKIEAPIHSSNVMLYSKEMEVASRV 148 (193)
Q Consensus 120 ~GgIi~~E~PIh~SNV~Lv~p~~~kptRV 148 (193)
+| +++|+|||+|||+|+|+..+...|.
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 34 5999999999999999988766654
No 7
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=99.95 E-value=3e-28 Score=180.93 Aligned_cols=77 Identities=60% Similarity=0.940 Sum_probs=73.9
Q ss_pred ccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceeEEEeecCcCCCeeeeecCCC
Q 029417 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEME 143 (193)
Q Consensus 67 k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN~~kkhvK~~~~~~~GgIi~~E~PIh~SNV~Lv~p~~~ 143 (193)
+++|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|++|+.++..|+++++|+|||+|||+|+||+|+
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Vegvn~~~k~~k~~~~~~~g~i~~~e~pI~~SnV~lvdp~~~ 82 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHSSNVMLYNEESN 82 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCHHHEEEeCcccC
Confidence 46799999999999999999999999999999999999999999999998888999999999999999999999875
No 8
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=99.95 E-value=1e-27 Score=175.49 Aligned_cols=74 Identities=41% Similarity=0.605 Sum_probs=70.6
Q ss_pred ccccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceeEEEeecCcCCCeeee
Q 029417 65 LHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLY 138 (193)
Q Consensus 65 ~~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN~~kkhvK~~~~~~~GgIi~~E~PIh~SNV~Lv 138 (193)
+.+|+|++||+|+||+|+||||+|+|++|++++++|+|||+|+.++|+||++++.+|+|+++|+|||+|||+|+
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=99.94 E-value=7.3e-27 Score=182.75 Aligned_cols=91 Identities=27% Similarity=0.450 Sum_probs=83.1
Q ss_pred CcceEEecCCCHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEeceeeeeeeecCCcccC
Q 029417 40 DKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLKTKHVKKREEEE 119 (193)
Q Consensus 40 ~~~~~~~~~l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN~~kkhvK~~~~~~ 119 (193)
.+..+|+++|++|||++|++++++ |++||+|+||+|+|||++|+|++|++++++|+|||||+++ +
T Consensus 18 ~r~~~~~a~ls~elr~~y~~r~~~------IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~Vegvn~~k----~----- 82 (114)
T TIGR01080 18 VRRKLMSAPLSKELREKYGKRALP------VRKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYVEGVTKEK----V----- 82 (114)
T ss_pred hhhheeecccCHHHHHHcCcccce------eecCCEEEEecCCCCCCEEEEEEEEcCCCEEEEcCeEEEC----C-----
Confidence 355999999999999999999988 9999999999999999999999999999999999999998 1
Q ss_pred CceeEEEeecCcCCCeeeeecCCCCeee
Q 029417 120 QGQIIKIEAPIHSSNVMLYSKEMEVASR 147 (193)
Q Consensus 120 ~GgIi~~E~PIh~SNV~Lv~p~~~kptR 147 (193)
.| +++|+|||+|||+|+|+..+...|
T Consensus 83 ~G--~~~e~pIh~SnV~l~~l~l~~~~R 108 (114)
T TIGR01080 83 NG--TEVPVPIHPSNVMITKLNLDDEKR 108 (114)
T ss_pred CC--eEEEeeechHHeEEEeccCChHHH
Confidence 24 599999999999999998876544
No 10
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=99.66 E-value=3.8e-17 Score=132.25 Aligned_cols=92 Identities=20% Similarity=0.421 Sum_probs=82.1
Q ss_pred ccCCCCcceEEecCCCHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCC-eeeEEEEEEccCCEEEEeceeeeeeeec
Q 029417 35 TVKPTDKPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKG-KIGEITKVFRHNSTVMVKDINLKTKHVK 113 (193)
Q Consensus 35 ~~~~~~~~~~~~~~l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKG-K~GkV~~V~~~~n~ViVEGvN~~kkhvK 113 (193)
.+.|..++.+||++||+|||++|+.+++| |+.+|+|+|.+|.++| ++|+|++|++++..+++|.|...|
T Consensus 20 ~aps~~rR~i~sa~ls~eLR~~y~vrs~p------ir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK---- 89 (145)
T KOG3401|consen 20 NAPSHIRRKIMSAPLSKELRQKYNVRSMP------IRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREK---- 89 (145)
T ss_pred CCcHHHHHHHhcchhhHHHHHHhCccccc------eeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEee----
Confidence 34567789999999999999999999999 9999999999999999 999999999999999999987666
Q ss_pred CCcccCCceeEEEeecCcCCCeeeeecCCC
Q 029417 114 KREEEEQGQIIKIEAPIHSSNVMLYSKEME 143 (193)
Q Consensus 114 ~~~~~~~GgIi~~E~PIh~SNV~Lv~p~~~ 143 (193)
.+| . .+++|||+|+|.++.|..+
T Consensus 90 --~nG---t--~v~vgihPsK~~iTkl~lD 112 (145)
T KOG3401|consen 90 --ANG---T--TVPVGIHPSKVVITKLKLD 112 (145)
T ss_pred --ccC---c--ccccccCccceeecccchh
Confidence 333 3 8899999999999987654
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=98.74 E-value=1.8e-08 Score=62.22 Aligned_cols=32 Identities=53% Similarity=0.709 Sum_probs=30.8
Q ss_pred eCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 72 AGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 72 kGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
+||.|.|++|+++|+.|+|.+|++++++|+||
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEEC
Confidence 59999999999999999999999999999986
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.69 E-value=6.1e-05 Score=43.79 Aligned_cols=26 Identities=50% Similarity=0.704 Sum_probs=24.2
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEc
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFR 95 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~ 95 (193)
+..||.|+|+.|+++|++|.|.+++.
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 57999999999999999999999875
No 13
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=97.39 E-value=0.00075 Score=54.71 Aligned_cols=62 Identities=23% Similarity=0.242 Sum_probs=47.6
Q ss_pred EEecCCCHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEeceeee
Q 029417 44 LIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINLK 108 (193)
Q Consensus 44 ~~~~~l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN~~ 108 (193)
++..+|+.++-+.+-.+. + ....+..||.|.|+.|+++|..|.|.+++.+++++.|+-++..
T Consensus 72 ~lg~~l~~~Ei~~il~~~-~--~~~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~~ 133 (153)
T PRK08559 72 VVPGEISFEEVEHFLKPK-P--IVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAA 133 (153)
T ss_pred eCCCCCCHHHHHHHHhcc-C--cccCCCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECCc
Confidence 333468888877664321 1 1234889999999999999999999999999999999876543
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=97.28 E-value=0.00074 Score=53.65 Aligned_cols=59 Identities=20% Similarity=0.267 Sum_probs=45.5
Q ss_pred EecCCCHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEecee
Q 029417 45 IVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 106 (193)
Q Consensus 45 ~~~~l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN 106 (193)
+...++.++-..+.... ... -.++.||.|.|+.|+++|-.|.|.+++.++..|.|+-++
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 34568888887774221 111 127899999999999999999999999888889888665
No 15
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=96.71 E-value=0.0027 Score=51.64 Aligned_cols=36 Identities=25% Similarity=0.288 Sum_probs=32.5
Q ss_pred cceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 68 ~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
..+++||.|.|+.|+++|..|.|.++++.++++.|+
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 347899999999999999999999999888888876
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=96.69 E-value=0.0028 Score=51.31 Aligned_cols=34 Identities=24% Similarity=0.270 Sum_probs=31.6
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
++.||+|.|+.|+.+|-+|.|.+++++++++.|.
T Consensus 120 ~~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~ 153 (172)
T TIGR00922 120 FEVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVS 153 (172)
T ss_pred CCCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEE
Confidence 7899999999999999999999999888888776
No 17
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=96.43 E-value=0.005 Score=51.66 Aligned_cols=38 Identities=24% Similarity=0.366 Sum_probs=35.0
Q ss_pred cccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 66 ~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
.+..+.+||.|.|+.|+++|-.|+|.+|+.+++++.|+
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 45568999999999999999999999999999998887
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=95.85 E-value=0.013 Score=46.61 Aligned_cols=34 Identities=18% Similarity=0.115 Sum_probs=29.3
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
.+.+||+|.|+.|+.+|-.|.|.+++. ++++.|.
T Consensus 108 ~~~~G~~V~V~~GPf~g~~g~v~~~~~-~~r~~v~ 141 (159)
T TIGR01955 108 LPYKGDKVRITDGAFAGFEAIFLEPDG-EKRSMLL 141 (159)
T ss_pred CCCCCCEEEEeccCCCCcEEEEEEECC-CceEEEE
Confidence 478999999999999999999999984 4576664
No 19
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=95.57 E-value=0.019 Score=46.28 Aligned_cols=33 Identities=21% Similarity=0.198 Sum_probs=28.5
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
+++||+|.|+.|+.+|-+|.|.+++ .++++.|.
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~-~~~r~~v~ 142 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPD-GEARSILL 142 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeC-CCeEEEEe
Confidence 6799999999999999999999998 45566654
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=95.18 E-value=0.034 Score=49.46 Aligned_cols=34 Identities=29% Similarity=0.546 Sum_probs=31.7
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
+..||.|.|+.|+++|-.|.|.+++.+++++.|.
T Consensus 206 f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~Vl 239 (258)
T TIGR01956 206 FRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVE 239 (258)
T ss_pred CCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEE
Confidence 7899999999999999999999999888888876
No 21
>PRK04333 50S ribosomal protein L14e; Validated
Probab=93.36 E-value=0.17 Score=37.84 Aligned_cols=37 Identities=19% Similarity=0.278 Sum_probs=32.4
Q ss_pred cceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEece
Q 029417 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (193)
Q Consensus 68 ~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGv 105 (193)
+.+..|-.|.+..|+|+|+...|+.+.-+ ++|+|.|-
T Consensus 2 ~~v~~GrvV~~~~Grd~gk~~vIv~i~d~-~~vlVdg~ 38 (84)
T PRK04333 2 PAIEVGRVCVKTAGREAGRKCVIVDIIDK-NFVLVTGP 38 (84)
T ss_pred CcccccEEEEEeccCCCCCEEEEEEEecC-CEEEEECC
Confidence 34789999999999999999999998764 79999875
No 22
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=85.97 E-value=0.84 Score=47.28 Aligned_cols=28 Identities=39% Similarity=0.540 Sum_probs=26.0
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEcc
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~ 96 (193)
.++.||-|.||+|++.|.+|-|++|...
T Consensus 459 yF~~GDhVKVi~G~~eG~tGlVvrVe~~ 486 (1024)
T KOG1999|consen 459 YFEPGDHVKVIAGRYEGDTGLVVRVEQG 486 (1024)
T ss_pred hccCCCeEEEEeccccCCcceEEEEeCC
Confidence 3789999999999999999999999884
No 23
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=85.50 E-value=1.9 Score=35.00 Aligned_cols=35 Identities=26% Similarity=0.367 Sum_probs=31.1
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEece
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDI 105 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGv 105 (193)
+-.|=-|.|..|+|+||...|..|.-. |+|+|+|=
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~-nRvLVDGP 42 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTP-TRVLVDGA 42 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcC-CeEEEeCC
Confidence 678888888899999999999999875 69999974
No 24
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=82.87 E-value=2.1 Score=34.88 Aligned_cols=40 Identities=25% Similarity=0.341 Sum_probs=34.7
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccC------CEEEEeceeeee
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLKT 109 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~------n~ViVEGvN~~k 109 (193)
+++|--|.|++|++.|+...|++.+.+. +..+|-|+...-
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~~ddgt~drpy~halVaGIdryP 50 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQNFDTASKERPYGHALVAGIKKYP 50 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEeecCCCCccCcCceEEEEeecccc
Confidence 6789999999999999999999988775 689999987653
No 25
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=78.72 E-value=3.4 Score=33.24 Aligned_cols=36 Identities=31% Similarity=0.362 Sum_probs=31.8
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEecee
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDIN 106 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN 106 (193)
+.+|=-|.|++|++.|+...|+++.-++ .|++-|--
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~i~gp~ 40 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVLITGPK 40 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEccCC-EEEEeCCc
Confidence 6789999999999999999999998876 89888743
No 26
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=76.78 E-value=1.6 Score=42.36 Aligned_cols=53 Identities=23% Similarity=0.194 Sum_probs=38.2
Q ss_pred cceEEecCCCHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCCeeeEEEEEEccC
Q 029417 41 KPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (193)
Q Consensus 41 ~~~~~~~~l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~ 97 (193)
+--++.+.++.++|-..-.+.|. -...+||.|.||.|.+++.+|.|..|+.++
T Consensus 115 ~~~I~tm~~~~~~rl~~p~~~lR----k~f~~gD~vkVI~g~~~~d~g~V~rI~~~~ 167 (607)
T COG5164 115 KEMIETMTYHFEQRLCGPWGRLR----KGFYKGDLVKVIEGGEMVDIGTVPRIDGEK 167 (607)
T ss_pred ccceeeeeeccCceeecchhhhh----cccccCCeEEEeccccccccceEEEecCce
Confidence 34455566666666554434333 225799999999999999999999998764
No 27
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=76.12 E-value=36 Score=26.86 Aligned_cols=86 Identities=23% Similarity=0.246 Sum_probs=45.5
Q ss_pred hhCCCCCCcccccceeeCCEEEEee---cCCCC----eeeEEEEEEccC--CEEEEeceeeeeeeecCCcccCCceeEEE
Q 029417 56 ECKPNSLPVLHKMHVKAGDTVKVIA---GCDKG----KIGEITKVFRHN--STVMVKDINLKTKHVKKREEEEQGQIIKI 126 (193)
Q Consensus 56 k~~~rs~p~~~k~~IkkGD~V~VI~---GkdKG----K~GkV~~V~~~~--n~ViVEGvN~~kkhvK~~~~~~~GgIi~~ 126 (193)
++-.+.+| .++.||+|.|-. ..+|. -+|.|+++.... ..++|..+ ..|.=++.
T Consensus 10 ~~~~~~ip-----~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i-------------~~gvGVEr 71 (113)
T TIGR01024 10 EQLKKDLP-----DFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKI-------------SYGVGVER 71 (113)
T ss_pred HHhhcCCC-----ccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEe-------------ccCccEEE
Confidence 33345677 489999999843 21232 358887776443 12333322 12333577
Q ss_pred eecCcCC---CeeeeecCCCCeee--EEEEEccCCcEEEE
Q 029417 127 EAPIHSS---NVMLYSKEMEVASR--VGHKVLDDGTRVRY 161 (193)
Q Consensus 127 E~PIh~S---NV~Lv~p~~~kptR--Vg~r~~edGkKvRv 161 (193)
-.|+|.. +|.++.. ++..| .-|--..-|+.-|+
T Consensus 72 ~fpl~SP~I~~IeVl~~--~kvrRaKLyYLR~~~gK~ari 109 (113)
T TIGR01024 72 IFPLHSPNIDSIEVVRR--GKVRRAKLYYLRERRGKAARI 109 (113)
T ss_pred EEEcCCCccceEEEEEe--CccchhheeeeccCcchhhee
Confidence 7888854 4555543 34333 33433345555554
No 28
>PRK04313 30S ribosomal protein S4e; Validated
Probab=75.93 E-value=4.2 Score=35.92 Aligned_cols=37 Identities=22% Similarity=0.425 Sum_probs=29.6
Q ss_pred cceeeCCEEEEeecCCCCeeeEEEEEEccC----CEEEEec
Q 029417 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKD 104 (193)
Q Consensus 68 ~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~----n~ViVEG 104 (193)
.++..|-.|.|+.|+.-|.+|+|.++.+.. +.|.||+
T Consensus 170 i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d 210 (237)
T PRK04313 170 IPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLED 210 (237)
T ss_pred EecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEc
Confidence 447789999999999999999999887544 5677774
No 29
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=75.26 E-value=4.9 Score=31.69 Aligned_cols=31 Identities=26% Similarity=0.472 Sum_probs=26.0
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
.+++||+|+-+.| -.|+|.+|..+.+.|.+|
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 3789999987765 789999999877888886
No 30
>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=74.75 E-value=6.4 Score=27.74 Aligned_cols=27 Identities=33% Similarity=0.665 Sum_probs=22.7
Q ss_pred eeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 71 kkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
..||.+.. ..|-+|+|.+|+ .|+|+|+
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 5799998
No 31
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=72.48 E-value=5.9 Score=30.48 Aligned_cols=29 Identities=38% Similarity=0.566 Sum_probs=23.0
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
.+++||+|.-+.| -.|+|++|..+. +.|+
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 3789999988765 789999998766 5544
No 32
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=72.08 E-value=2.5 Score=43.98 Aligned_cols=30 Identities=40% Similarity=0.687 Sum_probs=27.4
Q ss_pred ccceeeCCEEEEeecCCCCeeeEEEEEEcc
Q 029417 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (193)
Q Consensus 67 k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~ 96 (193)
.-.|+.+|+|.||.|+.+|++|.|+.|++-
T Consensus 579 ~n~I~~kD~Vkvi~Gp~~g~~G~v~~i~r~ 608 (1024)
T KOG1999|consen 579 GNEIRVKDTVKVIGGPSKGREGEVLHIYRP 608 (1024)
T ss_pred CCeecccceEEEecCCCCCccCccceeecc
Confidence 456999999999999999999999999874
No 33
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=68.81 E-value=8.5 Score=29.81 Aligned_cols=29 Identities=34% Similarity=0.529 Sum_probs=23.8
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
.+++||+|+-+.| -.|+|.+|+. +.|.||
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 3899999998876 7899999965 577776
No 34
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=68.39 E-value=11 Score=26.55 Aligned_cols=35 Identities=11% Similarity=0.140 Sum_probs=29.9
Q ss_pred eeeCCEEEEe--ecCCCCeeeEEEEEEccCCEEEEec
Q 029417 70 VKAGDTVKVI--AGCDKGKIGEITKVFRHNSTVMVKD 104 (193)
Q Consensus 70 IkkGD~V~VI--~GkdKGK~GkV~~V~~~~n~ViVEG 104 (193)
...||.|... -|..|--.|+|.+|+-..++|++||
T Consensus 21 ev~~e~V~a~Dilgd~ke~~G~vkriDldehkI~lE~ 57 (57)
T COG1532 21 EVTEEGVVARDILGDEKEFEGQVKRIDLDEHKIELEG 57 (57)
T ss_pred EEecCcEEEEeccCCceEecceEEEEEccccEEEecC
Confidence 3578877764 6888989999999999999999986
No 35
>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=65.85 E-value=10 Score=25.92 Aligned_cols=30 Identities=33% Similarity=0.545 Sum_probs=24.1
Q ss_pred ceeeCCEEEEeecCCCCee---eEEEEEEccCCE
Q 029417 69 HVKAGDTVKVIAGCDKGKI---GEITKVFRHNST 99 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~---GkV~~V~~~~n~ 99 (193)
.|++||+|.++. .+.++. ++|.+++...+.
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 589999999998 666555 999998887654
No 36
>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=63.50 E-value=14 Score=27.41 Aligned_cols=29 Identities=38% Similarity=0.678 Sum_probs=23.0
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
++++||+|.-..| -.|+|.+|+. +.+.||
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 3889999988775 7899999975 466666
No 37
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=62.44 E-value=14 Score=29.06 Aligned_cols=29 Identities=24% Similarity=0.368 Sum_probs=23.6
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
.+++||+|+-+.| -.|+|.+|.. +.|.||
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 3789999988765 7899999974 578877
No 38
>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=61.77 E-value=21 Score=24.90 Aligned_cols=33 Identities=24% Similarity=0.292 Sum_probs=20.7
Q ss_pred eeeCCEEEEeecC--CCCe--eeEEEEEEccCCEEEEe
Q 029417 70 VKAGDTVKVIAGC--DKGK--IGEITKVFRHNSTVMVK 103 (193)
Q Consensus 70 IkkGD~V~VI~Gk--dKGK--~GkV~~V~~~~n~ViVE 103 (193)
+++||.|+|.+-. +.|- .++|++...+. ++.|+
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 4799999999844 3443 58999998875 77776
No 39
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=60.09 E-value=2.1 Score=37.21 Aligned_cols=34 Identities=26% Similarity=0.537 Sum_probs=30.0
Q ss_pred ccceeeCCEEEEeecCCCCeeeEEEEEEccCCEE
Q 029417 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (193)
Q Consensus 67 k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~V 100 (193)
.||.++||.|.-++|+-.||+-+|.+...++-.+
T Consensus 124 ~MHq~RGD~i~FvTGRt~gk~d~vsk~Lak~F~i 157 (237)
T COG3700 124 DMHQRRGDAIYFVTGRTPGKTDTVSKTLAKNFHI 157 (237)
T ss_pred HHHHhcCCeEEEEecCCCCcccccchhHHhhccc
Confidence 4899999999999999999999999988776544
No 40
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=59.94 E-value=14 Score=33.45 Aligned_cols=74 Identities=27% Similarity=0.472 Sum_probs=45.1
Q ss_pred ccceeeCCEEEEeecCCCCeeeEEEEEEccC---CEEEEeceeeeeeeecCCcccCCceeEEEeecCcCCCeeeeecCCC
Q 029417 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEME 143 (193)
Q Consensus 67 k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~---n~ViVEGvN~~kkhvK~~~~~~~GgIi~~E~PIh~SNV~Lv~p~~~ 143 (193)
-.++..|-.|.|+.|+.-|.+|+|.++.... +.|.+++- .|. +.-...+||.++....+
T Consensus 169 ~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~--------------~g~----~F~T~~~~VfvIG~~~~ 230 (273)
T PTZ00223 169 LIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDA--------------SGH----EFATRAANIFVIGKDMN 230 (273)
T ss_pred EEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeC--------------CCC----eEEEEeeeEEEEeCCCC
Confidence 3457789999999999999999998885443 34556531 121 12334578888874423
Q ss_pred CeeeEEEEEccCCcEEEEE
Q 029417 144 VASRVGHKVLDDGTRVRYL 162 (193)
Q Consensus 144 kptRVg~r~~edGkKvRv~ 162 (193)
+|. +. +..|+-+|..
T Consensus 231 kp~---Is-Lp~~kgi~~~ 245 (273)
T PTZ00223 231 SVP---VT-LPKQQGLRIN 245 (273)
T ss_pred Ccc---eE-CcCCCCcccc
Confidence 432 11 2556666654
No 41
>PLN00036 40S ribosomal protein S4; Provisional
Probab=59.79 E-value=16 Score=32.78 Aligned_cols=36 Identities=28% Similarity=0.552 Sum_probs=27.3
Q ss_pred cceeeCCEEEEeecCCCCeeeEEEEEEccC---CEEEEe
Q 029417 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVK 103 (193)
Q Consensus 68 ~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~---n~ViVE 103 (193)
.++..|-.|.|+.|+.-|.+|+|.++.... +.|.||
T Consensus 173 ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~ 211 (261)
T PLN00036 173 IKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVK 211 (261)
T ss_pred EecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEE
Confidence 446788889999999999999998887443 345555
No 42
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=58.97 E-value=90 Score=24.77 Aligned_cols=82 Identities=22% Similarity=0.261 Sum_probs=43.7
Q ss_pred CCCCcccccceeeCCEEEEee---cCCCC----eeeEEEEEEccCC--EEEEeceeeeeeeecCCcccCCceeEEEeecC
Q 029417 60 NSLPVLHKMHVKAGDTVKVIA---GCDKG----KIGEITKVFRHNS--TVMVKDINLKTKHVKKREEEEQGQIIKIEAPI 130 (193)
Q Consensus 60 rs~p~~~k~~IkkGD~V~VI~---GkdKG----K~GkV~~V~~~~n--~ViVEGvN~~kkhvK~~~~~~~GgIi~~E~PI 130 (193)
..+| .++.||+|.|-. ..+|. -+|.|+++....- .++|..+ ..|-=++.-.|+
T Consensus 14 ~~~p-----~f~~GD~V~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvRki-------------~~gvGVEr~fpl 75 (116)
T PRK05338 14 KDIP-----EFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKI-------------SYGVGVERTFPL 75 (116)
T ss_pred cCCC-----CcCCCCEEEEEEEEccCCceEeccEEEEEEEEeCCCCCceEEEEEc-------------ccCccEEEEecC
Confidence 4566 489999999843 22333 3688887764431 2333322 123224777888
Q ss_pred cCC---CeeeeecCCCCeee--EEEEEccCCcEEEE
Q 029417 131 HSS---NVMLYSKEMEVASR--VGHKVLDDGTRVRY 161 (193)
Q Consensus 131 h~S---NV~Lv~p~~~kptR--Vg~r~~edGkKvRv 161 (193)
|.. +|.++.. ++..| .-|--+.-|+.-|+
T Consensus 76 ~SP~I~~IeV~r~--gkvRRAKLyYLR~~~gK~ari 109 (116)
T PRK05338 76 HSPRIDSIEVVRR--GKVRRAKLYYLRELRGKAARI 109 (116)
T ss_pred CCCcccEEEEEEe--cccchhheeeeccCcchhhee
Confidence 854 4555543 44433 33432344555554
No 43
>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=57.98 E-value=3.3 Score=30.39 Aligned_cols=29 Identities=31% Similarity=0.619 Sum_probs=0.0
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
.+++||+|.-.+| -.|+|.++ +++.|.+|
T Consensus 36 ~Lk~Gd~VvT~gG----i~G~V~~i--~~~~v~le 64 (82)
T PF02699_consen 36 SLKPGDEVVTIGG----IYGTVVEI--DDDTVVLE 64 (82)
T ss_dssp -----------------------------------
T ss_pred cCCCCCEEEECCc----EEEEEEEE--eCCEEEEE
Confidence 4899999998876 67899998 55677776
No 44
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=56.72 E-value=19 Score=32.41 Aligned_cols=36 Identities=25% Similarity=0.518 Sum_probs=26.5
Q ss_pred cceeeCCEEEEeecCCCCeeeEEEEEEccC---CEEEEe
Q 029417 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN---STVMVK 103 (193)
Q Consensus 68 ~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~---n~ViVE 103 (193)
.++..|-.|.|+.|+.-|.+|+|.++.... +.|.||
T Consensus 173 ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~ 211 (262)
T PTZ00118 173 LKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVK 211 (262)
T ss_pred EecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEE
Confidence 446788888999999999999988765443 345555
No 45
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=56.41 E-value=19 Score=32.10 Aligned_cols=36 Identities=28% Similarity=0.458 Sum_probs=28.9
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccC----CEEEEec
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHN----STVMVKD 104 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~----n~ViVEG 104 (193)
++..|-.|.|..|++-|..|+|.+|.... |-|.+|+
T Consensus 173 ~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 173 KFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred ccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence 36788899999999999999999988654 4566664
No 46
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=54.55 E-value=17 Score=26.85 Aligned_cols=27 Identities=26% Similarity=0.495 Sum_probs=23.4
Q ss_pred CCHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCCe
Q 029417 49 LKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGK 86 (193)
Q Consensus 49 l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKGK 86 (193)
+.+++|+.++ |+.||.|.++...|.|+
T Consensus 18 IPkeiR~~lg-----------i~~Gd~lei~~~~~~~~ 44 (89)
T COG2002 18 IPKEIREALG-----------IKEGDVLEIIVDGDGGR 44 (89)
T ss_pred ecHHHHHHhC-----------CCCCCEEEEEEeCCCCE
Confidence 5688999986 57999999999998887
No 47
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=52.82 E-value=11 Score=25.65 Aligned_cols=24 Identities=38% Similarity=0.441 Sum_probs=14.4
Q ss_pred eeeCCEEEE-eecCC--CCeeeEEEEE
Q 029417 70 VKAGDTVKV-IAGCD--KGKIGEITKV 93 (193)
Q Consensus 70 IkkGD~V~V-I~Gkd--KGK~GkV~~V 93 (193)
-.-||+|.| +..+. +..+|+|.+|
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 467999988 44433 4457999876
No 48
>CHL00084 rpl19 ribosomal protein L19
Probab=51.63 E-value=1.2e+02 Score=24.08 Aligned_cols=87 Identities=23% Similarity=0.262 Sum_probs=45.1
Q ss_pred HhhCCCCCCcccccceeeCCEEEEee---cCCCC----eeeEEEEEEccC--CEEEEeceeeeeeeecCCcccCCceeEE
Q 029417 55 KECKPNSLPVLHKMHVKAGDTVKVIA---GCDKG----KIGEITKVFRHN--STVMVKDINLKTKHVKKREEEEQGQIIK 125 (193)
Q Consensus 55 ~k~~~rs~p~~~k~~IkkGD~V~VI~---GkdKG----K~GkV~~V~~~~--n~ViVEGvN~~kkhvK~~~~~~~GgIi~ 125 (193)
+++-...+| .+++||+|.|-. ..+|. -+|.|+++.... ..++|..+ ..|-=++
T Consensus 13 ~~~~~~~~p-----~f~~GDtV~V~~~i~eg~k~R~q~F~GvvI~~r~~G~~~tftvRki-------------~~gvGVE 74 (117)
T CHL00084 13 SEFLKKNLP-----KIRVGDTVKVGVLIQEGNKERVQFYEGTVIAKKNSGLNTTITVRKV-------------FQGIGVE 74 (117)
T ss_pred HHHhhcCCC-----ccCCCCEEEEEEEEecCCeeEeceEEEEEEEEeCCCCCeeEEEEEe-------------ccCccEE
Confidence 333344566 489999999843 22332 368888875432 12333322 1222257
Q ss_pred EeecCcCCC---eeeeecCCCCeee--EEEEEccCCcEEEE
Q 029417 126 IEAPIHSSN---VMLYSKEMEVASR--VGHKVLDDGTRVRY 161 (193)
Q Consensus 126 ~E~PIh~SN---V~Lv~p~~~kptR--Vg~r~~edGkKvRv 161 (193)
.-.|+|..+ |.++.. ++..| .-|--..-|+.-|+
T Consensus 75 r~fpl~SP~I~~IeV~r~--gkvRRAKLyYLR~~~gKaari 113 (117)
T CHL00084 75 RVFLLHSPKLASIEVLRR--SKVRRAKLYYLRNRVGKAARL 113 (117)
T ss_pred EEEecCCCccceEEEEEe--CccchheeEEeccCcChhhee
Confidence 778999544 555543 34433 33433344555444
No 49
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=50.09 E-value=33 Score=25.19 Aligned_cols=29 Identities=17% Similarity=0.341 Sum_probs=24.4
Q ss_pred ceeeCCEEEEeecC--CCCeeeEEEEEEccC
Q 029417 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (193)
Q Consensus 69 ~IkkGD~V~VI~Gk--dKGK~GkV~~V~~~~ 97 (193)
-|++||.|.|++=. .-..+|+|..|+...
T Consensus 2 ~i~rGskVrIlR~ESYWyn~vGtV~svD~sg 32 (71)
T PRK02749 2 AISRGDKVRILRPESYWYNEVGTVASVDKSG 32 (71)
T ss_pred ccccCCEEEEccccceeecCcceEEEEccCC
Confidence 38999999999865 557889999999875
No 50
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=48.62 E-value=1.2e+02 Score=23.77 Aligned_cols=56 Identities=25% Similarity=0.331 Sum_probs=32.5
Q ss_pred ceeeCCEEEEee---cCCCCe----eeEEEEEEccC--CEEEEeceeeeeeeecCCcccCCceeEEEeecCcCCCeee
Q 029417 69 HVKAGDTVKVIA---GCDKGK----IGEITKVFRHN--STVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVML 137 (193)
Q Consensus 69 ~IkkGD~V~VI~---GkdKGK----~GkV~~V~~~~--n~ViVEGvN~~kkhvK~~~~~~~GgIi~~E~PIh~SNV~L 137 (193)
.++.||.|.|-. ...|.+ +|.|+++.... ..++|.++ ..|.=++.-.|+|--.|.=
T Consensus 18 ~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~-------------~~g~gVE~~f~l~SP~I~~ 82 (113)
T PF01245_consen 18 EFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNI-------------SQGVGVERVFPLYSPLIKS 82 (113)
T ss_dssp SSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEE-------------ETTEEEEEEEETTSTTEEE
T ss_pred CcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEE-------------ecCccEEEEEEcCCCCeEE
Confidence 389999998853 233332 47776666542 13333322 2343367888999765543
No 51
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=48.09 E-value=55 Score=21.76 Aligned_cols=34 Identities=26% Similarity=0.394 Sum_probs=24.1
Q ss_pred ceeeCCEEEEeecCCCC-eeeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVIAGCDKG-KIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKG-K~GkV~~V~~~~n~ViVE 103 (193)
.+++||.|.+..=.+.+ -.|+|+++.. .++..|.
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V~ 36 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLVR 36 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC-CCEEEEE
Confidence 47899999999744333 4699999988 4454444
No 52
>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=46.59 E-value=21 Score=26.04 Aligned_cols=28 Identities=18% Similarity=0.191 Sum_probs=20.7
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccC
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~ 97 (193)
|+.||.|.|--=++--..|.|+..+..+
T Consensus 39 I~~GD~V~Ve~~~~d~~kg~Iv~r~~~~ 66 (77)
T cd05793 39 INEGDIVLVAPWDFQDDKADIIYKYTPD 66 (77)
T ss_pred EcCCCEEEEEeccccCCEEEEEEEcCHH
Confidence 8999999994333445678898887654
No 53
>cd03692 mtIF2_IVc mtIF2_IVc: this family represents the C2 subdomain of domain IV of mitochondrial translation initiation factor 2 (mtIF2) which adopts a beta-barrel fold displaying a high degree of structural similarity with domain II of the translation elongation factor EF-Tu. The C-terminal part of mtIF2 contains the entire fMet-tRNAfmet binding site of IF-2 and is resistant to proteolysis. This C-terminal portion consists of two domains, IF2 C1 and IF2 C2. IF2 C2 been shown to contain all molecular determinants necessary and sufficient for the recognition and binding of fMet-tRNAfMet. Like IF2 from certain prokaryotes such as Thermus thermophilus, mtIF2lacks domain II which is thought to be involved in binding of E.coli IF-2 to 30S subunits.
Probab=45.35 E-value=40 Score=24.28 Aligned_cols=31 Identities=19% Similarity=0.282 Sum_probs=20.9
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCE
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNST 99 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ 99 (193)
.|++||.|.|+.+..-=..|+|.++.+.++.
T Consensus 26 ~l~~g~~v~vlr~~~~~~~g~i~sl~~~~~~ 56 (84)
T cd03692 26 KIKRNAKVRVLRNGEVIYEGKISSLKRFKDD 56 (84)
T ss_pred EEeCCCEEEEEcCCCEEEEEEEEEEEEcCcc
Confidence 5889999999988411145677777665543
No 54
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=44.67 E-value=33 Score=25.33 Aligned_cols=30 Identities=20% Similarity=0.258 Sum_probs=22.3
Q ss_pred ccceeeCCEEEEeecCCCCeeeEEEEEEcc
Q 029417 67 KMHVKAGDTVKVIAGCDKGKIGEITKVFRH 96 (193)
Q Consensus 67 k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~ 96 (193)
+..|.+||.|.|--=++--..|.|+.-+..
T Consensus 44 ~i~I~~GD~V~Ve~~~~d~~kg~I~~Ry~~ 73 (75)
T COG0361 44 RIRILPGDVVLVELSPYDLTKGRIVYRYKK 73 (75)
T ss_pred eEEeCCCCEEEEEecccccccccEEEEecC
Confidence 345899999999877777777777655544
No 55
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=44.53 E-value=33 Score=34.89 Aligned_cols=38 Identities=26% Similarity=0.412 Sum_probs=27.3
Q ss_pred cceeeCCEEEEeecCCCCeeeEEEEEEccCC-EEEEeceeee
Q 029417 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNS-TVMVKDINLK 108 (193)
Q Consensus 68 ~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n-~ViVEGvN~~ 108 (193)
..++.||.|.|.+ -|+.|+|++|..+++ .|.+.++.+.
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 4489999999966 578899999975332 3445566554
No 56
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=43.98 E-value=17 Score=27.95 Aligned_cols=27 Identities=19% Similarity=0.141 Sum_probs=18.2
Q ss_pred ceeeCCEEEEeecCCCC---eeeEEEEEEccC
Q 029417 69 HVKAGDTVKVIAGCDKG---KIGEITKVFRHN 97 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKG---K~GkV~~V~~~~ 97 (193)
.|+.||.|.| .++-- ..|.|+.++...
T Consensus 57 wI~~GD~VlV--sp~d~~~~~kg~Iv~r~~~~ 86 (99)
T TIGR00523 57 WIREGDVVIV--KPWEFQGDDKCDIVWRYTKT 86 (99)
T ss_pred EecCCCEEEE--EEccCCCCccEEEEEEcCHH
Confidence 3899999999 22111 248888877654
No 57
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=43.82 E-value=20 Score=34.49 Aligned_cols=46 Identities=28% Similarity=0.380 Sum_probs=35.6
Q ss_pred HHHhhCCCCCCcccccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEec
Q 029417 53 ERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKD 104 (193)
Q Consensus 53 lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEG 104 (193)
+|++.---.+| =.-|++|.|++|+.+|+.|--+.-++.+.+..|..
T Consensus 383 irq~~lET~~p------r~~Ge~vmvv~gkhkg~~g~llskd~~Ke~~~v~~ 428 (455)
T KOG4315|consen 383 IRQELLETALP------RRGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVRL 428 (455)
T ss_pred hHHHHHhhhcc------cccCceeEEEecccccchhhhhhhhhhhhhcceec
Confidence 45544444556 57899999999999999999988888777766654
No 58
>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=42.96 E-value=42 Score=26.72 Aligned_cols=28 Identities=25% Similarity=0.302 Sum_probs=21.9
Q ss_pred ecCCCCeeeEEEEEccCCcEEEEEcccC
Q 029417 139 SKEMEVASRVGHKVLDDGTRVRYLIKTG 166 (193)
Q Consensus 139 ~p~~~kptRVg~r~~edGkKvRv~kksg 166 (193)
...+|..+=+.|++++||++|.+.++--
T Consensus 8 ~~~~G~KtViey~~n~dGkkvKvtk~~k 35 (128)
T PF12353_consen 8 PDEDGIKTVIEYKFNDDGKKVKVTKKIK 35 (128)
T ss_pred cCCCCcEEEEEEEECCCCCEEEEEEEEE
Confidence 3456778889999999998888776544
No 59
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=42.38 E-value=43 Score=24.12 Aligned_cols=28 Identities=25% Similarity=0.355 Sum_probs=23.4
Q ss_pred eeeCCEEEEeecC--CCCeeeEEEEEEccC
Q 029417 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (193)
Q Consensus 70 IkkGD~V~VI~Gk--dKGK~GkV~~V~~~~ 97 (193)
|++||.|.|++=. .-..+|+|..|+...
T Consensus 2 i~rGskVrIlR~ESYWyn~vGtV~svd~~g 31 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEIGTVATVDQSG 31 (64)
T ss_pred cccCCEEEEccccceeecCcceEEEEcCCC
Confidence 7899999999865 456789999999864
No 60
>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=41.74 E-value=35 Score=26.38 Aligned_cols=29 Identities=28% Similarity=0.391 Sum_probs=17.7
Q ss_pred ceeeCCEEEEeec----------CCCCeeeEEEEEEccC
Q 029417 69 HVKAGDTVKVIAG----------CDKGKIGEITKVFRHN 97 (193)
Q Consensus 69 ~IkkGD~V~VI~G----------kdKGK~GkV~~V~~~~ 97 (193)
..+.||.|-|.-- .+-|++|+|..|.+..
T Consensus 32 ~yk~GD~V~I~id~sv~kGmPh~~yHGkTG~V~~v~~~~ 70 (99)
T PF01157_consen 32 EYKVGDKVDIKIDPSVHKGMPHKRYHGKTGRVFNVTKGA 70 (99)
T ss_dssp ---TT-EEEE---TTSSSSS--GGGTTEEEEEEEE-SSC
T ss_pred HccCCCEEEEEecCccccCCCcceECCCceeEEEeCCCc
Confidence 3689999998743 2669999999888765
No 61
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=41.13 E-value=69 Score=24.44 Aligned_cols=37 Identities=19% Similarity=0.288 Sum_probs=33.1
Q ss_pred eeCCEEEEeecCCCCeeeEEEEEEccCCEEEEeceee
Q 029417 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVKDINL 107 (193)
Q Consensus 71 kkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVEGvN~ 107 (193)
.-|-+|-+++..+-.-+|.+..|+...+.|.+++|-.
T Consensus 6 ~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL~nVr~ 42 (96)
T PF12701_consen 6 YIGSKISLISKSDIRYEGILYSIDTEDSTITLKNVRS 42 (96)
T ss_dssp CTTCEEEEEETTTEEEEEEEEEEETTTTEEEEEEEEE
T ss_pred ccCCEEEEEECCCcEEEEEEEEEcCCCCEEEeeeeee
Confidence 3688999999999999999999999999999997643
No 62
>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=40.76 E-value=34 Score=25.02 Aligned_cols=28 Identities=21% Similarity=0.234 Sum_probs=21.4
Q ss_pred eeeCCEEEEeecCC-CCeeeEEEEEEccC
Q 029417 70 VKAGDTVKVIAGCD-KGKIGEITKVFRHN 97 (193)
Q Consensus 70 IkkGD~V~VI~Gkd-KGK~GkV~~V~~~~ 97 (193)
|+.||.|.|--=++ .-..|.|+.++.+.
T Consensus 39 I~~GD~VlV~~~~~~~~~kg~Iv~r~~~~ 67 (78)
T cd04456 39 IKRGDFLIVDPIEEGEDVKADIIFVYCKD 67 (78)
T ss_pred EcCCCEEEEEecccCCCceEEEEEEeCHH
Confidence 99999999976555 34568888887664
No 63
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=39.55 E-value=35 Score=25.22 Aligned_cols=28 Identities=18% Similarity=0.165 Sum_probs=20.3
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccC
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~ 97 (193)
|+.||.|.|---++--..|.|+.++.++
T Consensus 44 I~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 71 (83)
T smart00652 44 IRRGDIVLVDPWDFQDVKADIIYKYTKD 71 (83)
T ss_pred EcCCCEEEEEecCCCCCEEEEEEEeCHH
Confidence 8999999996444433568888877654
No 64
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=39.35 E-value=47 Score=27.23 Aligned_cols=39 Identities=26% Similarity=0.361 Sum_probs=30.4
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccC------CEEEEeceeee
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN------STVMVKDINLK 108 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~------n~ViVEGvN~~ 108 (193)
+++|--|.|++|.+.|+.-.|++-.-+. +.++|+||-..
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 6899999999999999988877665443 36788887543
No 65
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=39.27 E-value=2.4e+02 Score=23.96 Aligned_cols=56 Identities=16% Similarity=0.204 Sum_probs=38.5
Q ss_pred ccCCceeEEEeecCc-CCCeeeeecCCCC-eeeEEEEEcc-------------CCcEEEEEcccCcccccc
Q 029417 117 EEEQGQIIKIEAPIH-SSNVMLYSKEMEV-ASRVGHKVLD-------------DGTRVRYLIKTGEIIDSA 172 (193)
Q Consensus 117 ~~~~GgIi~~E~PIh-~SNV~Lv~p~~~k-ptRVg~r~~e-------------dGkKvRv~kksg~~I~~P 172 (193)
++..|-+++...+.. ...++-+|++|+. -.++.+...+ ..+.-|-|++||.+-+.+
T Consensus 100 ~~tv~LviE~~r~~~~~d~~~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~e~rtC~~CG~v~~~~ 170 (177)
T PRK13264 100 AGSIGLVIERKRPEGELDGFQWYCDECNHKVHEVEVQLTDIETDLPPVFAAFYASEELRTCDNCGTVHPGK 170 (177)
T ss_pred CCeEEEEEEeCCCCCCccceEEECCCCCCeEEEEEEEecChhhhhHHHHHHHhcCHhhccCCcCCcccCcc
Confidence 444566677777666 5678889988765 4556555432 225689999999998765
No 66
>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=39.16 E-value=42 Score=24.77 Aligned_cols=29 Identities=31% Similarity=0.353 Sum_probs=21.9
Q ss_pred ceeeCCEEEEeecCCCCe-eeEEEEEEccC
Q 029417 69 HVKAGDTVKVIAGCDKGK-IGEITKVFRHN 97 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK-~GkV~~V~~~~ 97 (193)
-|+.||-|.|-.-.+-.| .|.|..++.+.
T Consensus 38 WIkrGd~VlV~p~~~~~kvkgeIv~i~~~~ 67 (78)
T cd05792 38 WIKRGDFVLVEPIEEGDKVKAEIVKILTRD 67 (78)
T ss_pred EEEeCCEEEEEecccCCceEEEEEEEECHH
Confidence 489999999976554334 68898888765
No 67
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=38.54 E-value=54 Score=25.53 Aligned_cols=27 Identities=22% Similarity=0.274 Sum_probs=23.5
Q ss_pred eeeCCEEEEeecC--CCCeeeEEEEEEcc
Q 029417 70 VKAGDTVKVIAGC--DKGKIGEITKVFRH 96 (193)
Q Consensus 70 IkkGD~V~VI~Gk--dKGK~GkV~~V~~~ 96 (193)
+++||.|.|++=. .-..+|+|..|+..
T Consensus 40 ~~RGskVrIlR~ESYWyn~vGtVvsVDq~ 68 (101)
T PLN00045 40 PKRGSKVKILRPESYWFNDVGKVVAVDQD 68 (101)
T ss_pred cCCCCEEEEccccceeecCcceEEEEeCC
Confidence 7999999999865 55778999999987
No 68
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=38.27 E-value=39 Score=33.20 Aligned_cols=33 Identities=30% Similarity=0.454 Sum_probs=28.4
Q ss_pred eeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 71 kkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
.-|-+|+|-+|.+||.-|.|..|++..-+|-+-
T Consensus 353 aigktVrIr~g~yKG~lGVVKdv~~~~arVeLh 385 (607)
T COG5164 353 AIGKTVRIRCGEYKGHLGVVKDVDRNIARVELH 385 (607)
T ss_pred ccCceEEEeecccccccceeeeccCceEEEEEe
Confidence 468899999999999999999999877666554
No 69
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=37.90 E-value=54 Score=25.36 Aligned_cols=34 Identities=26% Similarity=0.332 Sum_probs=25.0
Q ss_pred eeeCCEEEEeec----------CCCCeeeEEEEEEccCCEEEEe
Q 029417 70 VKAGDTVKVIAG----------CDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 70 IkkGD~V~VI~G----------kdKGK~GkV~~V~~~~n~ViVE 103 (193)
.+.||.|-|.-- .+-|++|+|..+...---|+|.
T Consensus 35 y~~Gd~V~I~~d~sv~kGmPh~~yhGkTG~V~~v~~~A~~V~v~ 78 (98)
T PRK04306 35 FEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRGRAYIVEVK 78 (98)
T ss_pred ccCCCEEEEEecCceecCCccccccCCCEEEEeecCeEEEEEEE
Confidence 568999988743 2668999999887765555553
No 70
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=37.59 E-value=57 Score=31.46 Aligned_cols=52 Identities=15% Similarity=0.133 Sum_probs=34.6
Q ss_pred eecCcCCCeeeeecCCCCeeeEEE-EEccCCcEEEEEcccCcc---------------cccchhhhhh
Q 029417 127 EAPIHSSNVMLYSKEMEVASRVGH-KVLDDGTRVRYLIKTGEI---------------IDSAENWKKL 178 (193)
Q Consensus 127 E~PIh~SNV~Lv~p~~~kptRVg~-r~~edGkKvRv~kksg~~---------------I~~Pe~~k~~ 178 (193)
+.+=.++=...+|++||+-+-+.. .++.+...|+|.-.||.. +|||..|.-+
T Consensus 166 ~~~~~~~P~~pic~~cg~~~~~~~~~~d~~~~~v~y~~~cG~~~~~~~~~g~~KL~Wr~dW~~rW~~l 233 (510)
T PRK00750 166 ERQATYSPFLPICPKCGKVLTTPVISYDAEAGTVTYDCECGHEGEVPVTGGHGKLQWKVDWPMRWAAL 233 (510)
T ss_pred ccCCCeeeeeeeCCCCCccceEEEEEEeCCCCEEEEEcCCCCEEEEecCCCCcccCCCCCcHHHHHHc
Confidence 445556778889999998654443 455555578887667765 3567777644
No 71
>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=37.22 E-value=67 Score=22.39 Aligned_cols=40 Identities=23% Similarity=0.237 Sum_probs=29.2
Q ss_pred eeeCCEEEEeecC--CCCeeeEEEEEEccCCEEEEeceeeee
Q 029417 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHNSTVMVKDINLKT 109 (193)
Q Consensus 70 IkkGD~V~VI~Gk--dKGK~GkV~~V~~~~n~ViVEGvN~~k 109 (193)
|.+|-+|.|+.-. +-|-+|.|.+|...+--|+.||=|-.|
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 6789999999764 779999999999988889999977654
No 72
>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=36.85 E-value=49 Score=28.56 Aligned_cols=28 Identities=29% Similarity=0.329 Sum_probs=14.8
Q ss_pred cceeeCCEEEE-eecCCCCeeeEEEEEEc
Q 029417 68 MHVKAGDTVKV-IAGCDKGKIGEITKVFR 95 (193)
Q Consensus 68 ~~IkkGD~V~V-I~GkdKGK~GkV~~V~~ 95 (193)
-.++.||.|.+ -.+..+-+.-+|++|..
T Consensus 104 ~~V~~Gd~v~~~~~~~~~~~~~~V~~v~~ 132 (217)
T PF01079_consen 104 SDVRVGDCVLVSDEGGGKLRPSRVVRVST 132 (217)
T ss_dssp GG--TT-EEEEE-TTT--EEEEEEEEEEE
T ss_pred hhCCCCCEEEEEEcCCCcEEEEEEEEEEE
Confidence 35899999999 34445555667766653
No 73
>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=36.55 E-value=54 Score=33.35 Aligned_cols=34 Identities=29% Similarity=0.523 Sum_probs=25.0
Q ss_pred eeCCEEEEeecCCCCeeeEEEEEEccCCE--EEEeceeee
Q 029417 71 KAGDTVKVIAGCDKGKIGEITKVFRHNST--VMVKDINLK 108 (193)
Q Consensus 71 kkGD~V~VI~GkdKGK~GkV~~V~~~~n~--ViVEGvN~~ 108 (193)
+.||.|.|. .-|+.|+|+++.. ++. |.+.++.+.
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 4678999999975 344 445566554
No 74
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=36.10 E-value=72 Score=28.69 Aligned_cols=33 Identities=30% Similarity=0.391 Sum_probs=23.8
Q ss_pred eeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 71 KAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 71 kkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
-.|.+..|++|.-||..|.|+-=.---+.|+|.
T Consensus 59 CiGN~A~VvSG~AKG~~G~VtGkHGGieHVlV~ 91 (258)
T PF14505_consen 59 CIGNEAKVVSGDAKGAKGVVTGKHGGIEHVLVD 91 (258)
T ss_dssp -BT-EEEE-SSTTTT-EEEEEEEETTTTEEEEE
T ss_pred ecCceeEEeecccCCCcCeEecccCCeeeEEEE
Confidence 479999999999999999998765555677765
No 75
>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=35.83 E-value=45 Score=23.17 Aligned_cols=23 Identities=30% Similarity=0.226 Sum_probs=15.5
Q ss_pred eeeCCEEEEeecCCCCeeeEEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITK 92 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~ 92 (193)
|+.||.|.|---.+--..|.|..
T Consensus 42 I~~GD~V~V~~~~~d~~kG~Ii~ 64 (65)
T PF01176_consen 42 IKRGDFVLVEPSPYDKVKGRIIY 64 (65)
T ss_dssp --TTEEEEEEESTTCTTEEEEEE
T ss_pred cCCCCEEEEEecccCCCeEEEEE
Confidence 89999999985554466777754
No 76
>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=34.68 E-value=45 Score=23.86 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=21.9
Q ss_pred eeeCCEEEEeecC--CCCeeeEEEEEEccC
Q 029417 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (193)
Q Consensus 70 IkkGD~V~VI~Gk--dKGK~GkV~~V~~~~ 97 (193)
|.+||.|.|++=. .-..+|+|..|+...
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 4689999999865 567899999999875
No 77
>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=34.31 E-value=1.1e+02 Score=23.25 Aligned_cols=37 Identities=19% Similarity=0.217 Sum_probs=27.7
Q ss_pred ceeeCCEEEEeecC--CCCeeeEEEEEEccC-CEEEEece
Q 029417 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN-STVMVKDI 105 (193)
Q Consensus 69 ~IkkGD~V~VI~Gk--dKGK~GkV~~V~~~~-n~ViVEGv 105 (193)
.++.||-|.|.+.. .+--+|.|.++.... +...+.+.
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~ 42 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGC 42 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEE
Confidence 37899999999765 556699999998865 44455543
No 78
>PRK08577 hypothetical protein; Provisional
Probab=33.77 E-value=50 Score=25.75 Aligned_cols=28 Identities=29% Similarity=0.298 Sum_probs=22.4
Q ss_pred CCHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCCee
Q 029417 49 LKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKI 87 (193)
Q Consensus 49 l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKGK~ 87 (193)
+.+++|++++ |+.||.|.+..-.|+|.+
T Consensus 17 ip~~~r~~l~-----------~~~g~~~~~~~~~~~~~~ 44 (136)
T PRK08577 17 IPLEIREALG-----------IREGMYVLLIADTDKKEI 44 (136)
T ss_pred ecHHHHHHcC-----------cCCCCEEEEEEECCCCEE
Confidence 5678888885 679999999987777765
No 79
>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=33.16 E-value=79 Score=21.10 Aligned_cols=29 Identities=21% Similarity=0.302 Sum_probs=19.8
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~V 100 (193)
+..||.|.+-. .+ +-.|.|.+|.+.++.+
T Consensus 38 ~~VGD~V~~~~-~~-~~~~~I~~vl~R~s~l 66 (68)
T cd04466 38 PAVGDRVEFEP-ED-DGEGVIEEILPRKNLL 66 (68)
T ss_pred CCCCcEEEEEE-CC-CCcEEEEEEeccceEE
Confidence 47999998732 22 2357788998877643
No 80
>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=32.35 E-value=78 Score=23.85 Aligned_cols=33 Identities=36% Similarity=0.546 Sum_probs=22.2
Q ss_pred cceeeCCEEEEeecC------------CCCeeeEEEEEEc-cCCEE
Q 029417 68 MHVKAGDTVKVIAGC------------DKGKIGEITKVFR-HNSTV 100 (193)
Q Consensus 68 ~~IkkGD~V~VI~Gk------------dKGK~GkV~~V~~-~~n~V 100 (193)
+-|++||.|.|+.-. +-|..|.+.+|.. ..+++
T Consensus 64 ~~V~~G~~V~i~~~~~~~~i~~~g~Al~~g~~G~~I~V~N~~s~k~ 109 (122)
T TIGR03170 64 WLVKRGDTVTVIARGGGLSVTTEGKALEDGAVGDQIRVRNLSSGKI 109 (122)
T ss_pred cEEcCCCEEEEEEecCCEEEEEEEEEccccCCCCEEEEEECCCCCE
Confidence 348999999998532 4467777777763 44443
No 81
>COG1465 Predicted alternative 3-dehydroquinate synthase [Amino acid transport and metabolism]
Probab=31.22 E-value=3.3e+02 Score=25.58 Aligned_cols=24 Identities=25% Similarity=0.361 Sum_probs=19.8
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKV 93 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V 93 (193)
++.||.|+|+-++-+.+.+.|-++
T Consensus 281 L~aGDeV~iVD~dGr~R~aiVGRv 304 (376)
T COG1465 281 LKAGDEVLIVDFDGRTRSAIVGRV 304 (376)
T ss_pred hcCCCeEEEEecCCceeEEEEEEE
Confidence 689999999999888888877433
No 82
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=30.26 E-value=54 Score=33.52 Aligned_cols=34 Identities=32% Similarity=0.523 Sum_probs=27.5
Q ss_pred cccceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 66 HKMHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 66 ~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
..-+++.||+|.+++ |..|.|++|....+.+.|+
T Consensus 609 ~~~~l~~gDev~~~t----~e~G~~~~i~a~~~e~~v~ 642 (753)
T COG1193 609 KKRKLKLGDEVEVIT----GEPGAVVKIIAGILEALVQ 642 (753)
T ss_pred cccCceecceeEeec----CCccceeeeeccCceeEEe
Confidence 355789999999999 6788899998666676666
No 83
>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=29.26 E-value=85 Score=21.00 Aligned_cols=23 Identities=26% Similarity=0.335 Sum_probs=18.2
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViV 102 (193)
++.||.|.+ +|++++++++++.+
T Consensus 45 ~~~Gd~v~~----------~v~~~d~~~~~i~l 67 (68)
T cd05707 45 FKVGQLVKG----------KIVSIDPDNGRIEM 67 (68)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEec
Confidence 689999988 67888887777654
No 84
>PF14604 SH3_9: Variant SH3 domain; PDB: 2CRE_A 2E5K_A 2CT3_A 2DE0_X 2D8H_A 2DA9_A 2X3X_E 2X3W_D 2KRN_A 2ED0_A ....
Probab=29.20 E-value=39 Score=22.00 Aligned_cols=14 Identities=29% Similarity=0.653 Sum_probs=10.1
Q ss_pred ccceeeCCEEEEee
Q 029417 67 KMHVKAGDTVKVIA 80 (193)
Q Consensus 67 k~~IkkGD~V~VI~ 80 (193)
.+.+++||.|.|+.
T Consensus 12 ELs~~~Gd~i~v~~ 25 (49)
T PF14604_consen 12 ELSFKKGDVITVLE 25 (49)
T ss_dssp B-EB-TTEEEEEEE
T ss_pred EeeEcCCCEEEEEE
Confidence 45689999999984
No 85
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=29.16 E-value=59 Score=25.02 Aligned_cols=28 Identities=18% Similarity=0.192 Sum_probs=19.9
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccC
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~ 97 (193)
|+.||.|.|--=.+--..|.|+..+...
T Consensus 60 I~~GD~VlVe~~~~~~~kg~Iv~r~~~~ 87 (100)
T PRK04012 60 IREGDVVIVAPWDFQDEKADIIWRYTKP 87 (100)
T ss_pred ecCCCEEEEEecccCCCEEEEEEEcCHH
Confidence 8999999996433334568888877644
No 86
>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=29.10 E-value=70 Score=27.02 Aligned_cols=34 Identities=26% Similarity=0.435 Sum_probs=24.5
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
++.||.|.|.-|...--.++|..+.++.-.+.+.
T Consensus 17 ~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 17 LKEGDSIEVFDGDGGEYRAEITEISKKSATLRIL 50 (225)
T ss_dssp --TT-EEEEEESSSEEEEEEEEEEESSEEEEEEE
T ss_pred CCCCCEEEEEECCCCEEEEEEEECcCcEEEEEEe
Confidence 8999999999988777789999998775444444
No 87
>cd05695 S1_Rrp5_repeat_hs3 S1_Rrp5_repeat_hs3: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 3 (hs3). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.10 E-value=87 Score=21.31 Aligned_cols=23 Identities=26% Similarity=0.248 Sum_probs=18.8
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViV 102 (193)
++.||+|.+ +|+.+++++.+|.+
T Consensus 43 ~~~G~~i~~----------kVi~id~~~~~i~L 65 (66)
T cd05695 43 YKEGQKVRA----------RILYVDPSTKVVGL 65 (66)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEec
Confidence 689999887 78999998877654
No 88
>KOG0122 consensus Translation initiation factor 3, subunit g (eIF-3g) [Translation, ribosomal structure and biogenesis]
Probab=28.87 E-value=62 Score=29.25 Aligned_cols=54 Identities=17% Similarity=0.312 Sum_probs=34.2
Q ss_pred cCcCCCeeeeecCCCCeeeEEEEEccCCcEEEEE---cccCcccccc----hhhhhhhcccccc
Q 029417 129 PIHSSNVMLYSKEMEVASRVGHKVLDDGTRVRYL---IKTGEIIDSA----ENWKKLKEANRQE 185 (193)
Q Consensus 129 PIh~SNV~Lv~p~~~kptRVg~r~~edGkKvRv~---kksg~~I~~P----e~~k~~~k~~~~~ 185 (193)
++.+++-.+ ++|..+-+.|++++||+|+-|. +.....++.. .+|+++-....+.
T Consensus 17 ~l~P~~q~i---~~g~ktvieyk~n~dgkK~Kvt~~~kv~k~~v~K~vaeRknW~KFG~~~~~~ 77 (270)
T KOG0122|consen 17 GLLPPKQTI---EDGTKTVIEYKINEDGKKVKVTRTFKVEKRAVPKAVAERKNWVKFGDSKGEP 77 (270)
T ss_pred cCCCcceee---cCCcEEEEEEEEcCCCcEEEEEEEEEEEEEeccHHHHhhccchhhccccCCC
Confidence 444554333 2677899999999999875444 4444444442 2898887665443
No 89
>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=28.78 E-value=74 Score=23.25 Aligned_cols=29 Identities=21% Similarity=0.307 Sum_probs=23.3
Q ss_pred ceeeCCEEEEeecC--CCCeeeEEEEEEccC
Q 029417 69 HVKAGDTVKVIAGC--DKGKIGEITKVFRHN 97 (193)
Q Consensus 69 ~IkkGD~V~VI~Gk--dKGK~GkV~~V~~~~ 97 (193)
.++.||-|.|..+. ..--+|.|.++....
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 37899999999998 444689999998654
No 90
>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=28.53 E-value=1e+02 Score=21.51 Aligned_cols=24 Identities=13% Similarity=0.267 Sum_probs=19.8
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
++.||.|.+ +|+.+++++.+|.+.
T Consensus 47 ~~vG~~v~~----------kV~~id~~~~~i~Ls 70 (73)
T cd05703 47 FPIGQALKA----------KVVGVDKEHKLLRLS 70 (73)
T ss_pred CCCCCEEEE----------EEEEEeCCCCEEEEE
Confidence 679999875 799999999888754
No 91
>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=28.32 E-value=1.6e+02 Score=21.25 Aligned_cols=13 Identities=38% Similarity=0.659 Sum_probs=10.5
Q ss_pred ceeeCCEEEEeec
Q 029417 69 HVKAGDTVKVIAG 81 (193)
Q Consensus 69 ~IkkGD~V~VI~G 81 (193)
.|++||.|.++.-
T Consensus 27 tl~~g~~v~~~~~ 39 (94)
T cd04090 27 TIKKGQKVKVLGE 39 (94)
T ss_pred eEcCCCEEEEECC
Confidence 4889999988753
No 92
>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=28.24 E-value=1e+02 Score=20.49 Aligned_cols=24 Identities=17% Similarity=0.358 Sum_probs=18.5
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
++.||.|.+ +|++++++++++.+.
T Consensus 45 ~~~G~~i~v----------~v~~~d~~~~~i~ls 68 (70)
T cd05698 45 FRVGQVVKV----------KVLSCDPEQQRLLLS 68 (70)
T ss_pred ccCCCEEEE----------EEEEEcCCCCEEEEE
Confidence 689999988 677888877776653
No 93
>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=28.15 E-value=1.2e+02 Score=20.34 Aligned_cols=23 Identities=22% Similarity=0.286 Sum_probs=19.2
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViV 102 (193)
++.||++.+ +|++++++++++.+
T Consensus 45 ~~~Gd~i~~----------~V~~id~~~~~i~l 67 (69)
T cd05697 45 FKPGLKVKC----------RVLSVEPERKRLVL 67 (69)
T ss_pred CCCCCEEEE----------EEEEEECCCCEEEE
Confidence 789999988 78889988887765
No 94
>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=27.86 E-value=1.1e+02 Score=19.79 Aligned_cols=24 Identities=25% Similarity=0.461 Sum_probs=17.7
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEE
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViV 102 (193)
.++.||+|.+ +|.+++.+++++.+
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 4789999988 47777777666543
No 95
>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=27.11 E-value=1.1e+02 Score=21.50 Aligned_cols=25 Identities=20% Similarity=0.372 Sum_probs=19.0
Q ss_pred cceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEE
Q 029417 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (193)
Q Consensus 68 ~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViV 102 (193)
-.++.||+|.| +|.+++.+++++.+
T Consensus 57 ~~~~~Gd~v~v----------kV~~id~~~~~i~l 81 (83)
T cd04461 57 FGFKKGQSVTA----------KVTSVDEEKQRFLL 81 (83)
T ss_pred HhcCCCCEEEE----------EEEEEcCCCCEEEE
Confidence 34789999988 67778777777765
No 96
>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=26.92 E-value=1.4e+02 Score=19.99 Aligned_cols=25 Identities=16% Similarity=0.352 Sum_probs=19.6
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
.++.||.|.+ +|.+++.+++++.++
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 3689999988 578888877777655
No 97
>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=26.67 E-value=95 Score=23.35 Aligned_cols=37 Identities=24% Similarity=0.283 Sum_probs=24.9
Q ss_pred eeeCCEEEE--eecCCCCeeeEEEEEEccCCEEEEeceee
Q 029417 70 VKAGDTVKV--IAGCDKGKIGEITKVFRHNSTVMVKDINL 107 (193)
Q Consensus 70 IkkGD~V~V--I~GkdKGK~GkV~~V~~~~n~ViVEGvN~ 107 (193)
.++||.|.. -.+..-|.+|.|.+|.. .+.|.|-+-|.
T Consensus 63 P~~Gdivv~~~~~~~~~GHVaIV~~v~~-~~~i~v~e~N~ 101 (124)
T PF05257_consen 63 PQPGDIVVWDSGSGGGYGHVAIVESVND-GGTITVIEQNW 101 (124)
T ss_dssp --TTEEEEEEECTTTTT-EEEEEEEE-T-TSEEEEEECSS
T ss_pred cccceEEEeccCCCCCCCeEEEEEEECC-CCEEEEEECCc
Confidence 389998887 35567899999999955 45777665553
No 98
>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=26.33 E-value=1.8e+02 Score=22.93 Aligned_cols=30 Identities=13% Similarity=0.273 Sum_probs=23.5
Q ss_pred cceeeCCEEEEeecCCCCeeeEEEEEEccC
Q 029417 68 MHVKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (193)
Q Consensus 68 ~~IkkGD~V~VI~GkdKGK~GkV~~V~~~~ 97 (193)
..|+.||.|.|.+-..+=-+|.|.++....
T Consensus 6 ~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~ 35 (130)
T cd04721 6 VTISVHDFVYVLSEEEDRYVAYIEDLYEDK 35 (130)
T ss_pred EEEECCCEEEEeCCCCCcEEEEEEEEEEcC
Confidence 459999999999654344589999998865
No 99
>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=26.30 E-value=1.6e+02 Score=24.26 Aligned_cols=28 Identities=29% Similarity=0.371 Sum_probs=25.3
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccC
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~ 97 (193)
++.||-|.|-+|..+--+|+|.++....
T Consensus 30 y~lGD~Vlv~s~~~~~yIgkI~~iwe~~ 57 (159)
T cd04715 30 YRLYDDVYVHNGDSEPYIGKIIKIYETA 57 (159)
T ss_pred EeCCCEEEEeCCCCCCEEEEEEEEEEcC
Confidence 8999999999998778899999999764
No 100
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=26.04 E-value=1.2e+02 Score=27.99 Aligned_cols=42 Identities=14% Similarity=0.057 Sum_probs=25.2
Q ss_pred eecCcCCCeeeeecCCCCeeeEEEEEccCCcEEEEEcccCcc
Q 029417 127 EAPIHSSNVMLYSKEMEVASRVGHKVLDDGTRVRYLIKTGEI 168 (193)
Q Consensus 127 E~PIh~SNV~Lv~p~~~kptRVg~r~~edGkKvRv~kksg~~ 168 (193)
|.+=.++=...+|++||+-+-.-..++.|...|+|.-.||..
T Consensus 160 ~~~~~~~P~~p~c~~cg~~~~~v~~~d~~~~~v~y~c~cG~~ 201 (353)
T cd00674 160 ELQETWYPFMPYCEKCGKDTTTVEAYDAKAGTVTYKCECGHE 201 (353)
T ss_pred ccCCCceeeeeecCCcCcceeEEEEEeCCCCeEEEEcCCCCE
Confidence 344445667888999986431112345555667776666654
No 101
>PF06701 MIB_HERC2: Mib_herc2; InterPro: IPR010606 Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in []and usually the protein also contains an E3 ligase domain (either Ring or Hect).; GO: 0004842 ubiquitin-protein ligase activity, 0046872 metal ion binding, 0016567 protein ubiquitination; PDB: 2DK3_A 3DKM_A.
Probab=25.99 E-value=80 Score=22.71 Aligned_cols=20 Identities=20% Similarity=0.469 Sum_probs=8.2
Q ss_pred CCeeeEEEEE-----EccCCEEEEe
Q 029417 84 KGKIGEITKV-----FRHNSTVMVK 103 (193)
Q Consensus 84 KGK~GkV~~V-----~~~~n~ViVE 103 (193)
.|..|+|++| ...++.|.|.
T Consensus 19 ~g~~GtV~~i~~~~~~~~~~~v~V~ 43 (68)
T PF06701_consen 19 EGHVGTVVSIRDWSSESPDGWVVVQ 43 (68)
T ss_dssp TT--EEE-S--------BTTEEEEE
T ss_pred CCcceEEEecccccccCCCCeEEEE
Confidence 3678888876 3334455554
No 102
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=25.92 E-value=1.3e+02 Score=23.40 Aligned_cols=39 Identities=31% Similarity=0.277 Sum_probs=26.5
Q ss_pred eeeCCEEEEeec----------CCCCeeeEEEEEEccCCEEEEeceeee
Q 029417 70 VKAGDTVKVIAG----------CDKGKIGEITKVFRHNSTVMVKDINLK 108 (193)
Q Consensus 70 IkkGD~V~VI~G----------kdKGK~GkV~~V~~~~n~ViVEGvN~~ 108 (193)
...||.|-|.-- .+-|++|+|.-+--....|.|..=|..
T Consensus 33 y~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~~G~k~ 81 (98)
T COG2139 33 YKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVYDGNKE 81 (98)
T ss_pred ccCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEecCCce
Confidence 579999988754 377999999776555545555544443
No 103
>PLN00190 60S ribosomal protein L21; Provisional
Probab=25.82 E-value=1.2e+02 Score=25.45 Aligned_cols=32 Identities=28% Similarity=0.396 Sum_probs=22.5
Q ss_pred eeeCCEEEEee-c---------CCCCeeeEEEEEEccCCEEE
Q 029417 70 VKAGDTVKVIA-G---------CDKGKIGEITKVFRHNSTVM 101 (193)
Q Consensus 70 IkkGD~V~VI~-G---------kdKGK~GkV~~V~~~~n~Vi 101 (193)
.+.||.|-|.. | .+-|++|.|..|...---|+
T Consensus 34 yk~GD~VdIk~~~svqKGMPhk~YHGkTG~V~nv~~~A~gV~ 75 (158)
T PLN00190 34 FKVGDYVDIKVNGAIHKGMPHKFYHGRTGIVWNVTKRAVGVE 75 (158)
T ss_pred hcCCCEEEEEecCCeecCCCcccccCCCeEEEeecCcEEEEE
Confidence 57899998874 2 37799999988766533333
No 104
>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=25.72 E-value=1.3e+02 Score=20.76 Aligned_cols=23 Identities=26% Similarity=0.242 Sum_probs=18.6
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViV 102 (193)
++.||.|.+ +|+.++++++++.+
T Consensus 47 ~~vG~~v~~----------kV~~id~~~~~i~l 69 (71)
T cd05696 47 FKAGTTHKA----------RIIGYSPMDGLLQL 69 (71)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 789999876 68888888877765
No 105
>KOG0171 consensus Mitochondrial inner membrane protease, subunit IMP1 [Posttranslational modification, protein turnover, chaperones]
Probab=25.50 E-value=1.5e+02 Score=25.28 Aligned_cols=39 Identities=23% Similarity=0.074 Sum_probs=29.7
Q ss_pred eeCCEEEEeecCCCCe---eeEEEEEEccCCEEEEeceeeee
Q 029417 71 KAGDTVKVIAGCDKGK---IGEITKVFRHNSTVMVKDINLKT 109 (193)
Q Consensus 71 kkGD~V~VI~GkdKGK---~GkV~~V~~~~n~ViVEGvN~~k 109 (193)
..||-|.|.-|+-.+- ++-++.+.--.+.|.|+|=|..+
T Consensus 91 ~eGD~v~v~~~~~~~n~~~e~~~~~i~VP~GhVfv~GDN~~n 132 (176)
T KOG0171|consen 91 MEGDLVEVHDGPLVVNDLVEKFSTPIRVPEGHVFVEGDNRNN 132 (176)
T ss_pred cCCceEEEecCCcccchhhhhccceeeccCceEEEecCCCCC
Confidence 6899999999987644 44445566667899999988765
No 106
>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=25.03 E-value=1.1e+02 Score=26.89 Aligned_cols=29 Identities=24% Similarity=0.254 Sum_probs=22.0
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTV 100 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~V 100 (193)
+..||.|.+-.-. +..|.|.+|.+.+|.+
T Consensus 35 ~~vGD~V~~~~~~--~~~~~i~~i~~R~~~l 63 (287)
T cd01854 35 PVVGDWVEVEPDD--DGEGVIVRVLPRKNLL 63 (287)
T ss_pred ccCCCEEEEEecC--CCcEEEEEEECCCceE
Confidence 4799999885322 4679999999888744
No 107
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=24.75 E-value=1.1e+02 Score=26.39 Aligned_cols=33 Identities=30% Similarity=0.406 Sum_probs=23.4
Q ss_pred cceeeCCEEEEeecC------------CCCeeeEEEEEE-ccCCEE
Q 029417 68 MHVKAGDTVKVIAGC------------DKGKIGEITKVF-RHNSTV 100 (193)
Q Consensus 68 ~~IkkGD~V~VI~Gk------------dKGK~GkV~~V~-~~~n~V 100 (193)
+-|++||.|.|+... .-|..|...+|. ...+++
T Consensus 175 ~~V~~G~~V~i~~~~g~~~i~~~G~Al~~G~~Gd~IrVrN~~Sgk~ 220 (235)
T PRK07018 175 WVVCKGQTVSIIARGDGFSVKTEGEALNDGAVGQQIRVRNMASGQV 220 (235)
T ss_pred cEeCCCCEEEEEEecCCEEEEEEEEEcCCCCCCCeEEEEECCCCCE
Confidence 458999999998643 457777777776 444444
No 108
>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=24.13 E-value=2.1e+02 Score=22.08 Aligned_cols=34 Identities=15% Similarity=0.304 Sum_probs=25.6
Q ss_pred eeeCCEEEEeecCC--CCeeeEEEEEEccC-CEEEEe
Q 029417 70 VKAGDTVKVIAGCD--KGKIGEITKVFRHN-STVMVK 103 (193)
Q Consensus 70 IkkGD~V~VI~Gkd--KGK~GkV~~V~~~~-n~ViVE 103 (193)
++.||-|.|.+..+ +=-+|+|.++.... +...|.
T Consensus 4 ~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~ 40 (121)
T cd04714 4 IRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVR 40 (121)
T ss_pred EEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEE
Confidence 78999999998654 45689999998754 444454
No 109
>smart00439 BAH Bromo adjacent homology domain.
Probab=24.11 E-value=1.4e+02 Score=21.68 Aligned_cols=29 Identities=28% Similarity=0.431 Sum_probs=23.2
Q ss_pred eeeCCEEEEeecC--CCCeeeEEEEEEccCC
Q 029417 70 VKAGDTVKVIAGC--DKGKIGEITKVFRHNS 98 (193)
Q Consensus 70 IkkGD~V~VI~Gk--dKGK~GkV~~V~~~~n 98 (193)
++.||.|.|.... ..=-+|+|.++....+
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~ 32 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRIEEIFETKK 32 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEEEEEEECCC
Confidence 6899999999876 2456899999987654
No 110
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=23.74 E-value=1.3e+02 Score=22.83 Aligned_cols=26 Identities=23% Similarity=0.146 Sum_probs=19.4
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEE
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVF 94 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~ 94 (193)
+|..||+|.|---++-=..|.|+.-+
T Consensus 46 rIl~GD~V~VE~spYDltkGRIiyR~ 71 (87)
T PRK12442 46 RILAGDRVTLELSPYDLTKGRINFRH 71 (87)
T ss_pred EecCCCEEEEEECcccCCceeEEEEe
Confidence 48899999998777666667775444
No 111
>cd03698 eRF3_II_like eRF3_II_like: domain similar to domain II of the eukaryotic class II release factor (eRF3). In eukaryotes, translation termination is mediated by two interacting release factors, eRF1 and eRF3, which act as class I and II factors, respectively. eRF1 functions as an omnipotent release factor, decoding all three stop codons and triggering the release of the nascent peptide catalyzed by the ribsome. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. Sequence comparison of class II release factors with elongation factors shows that eRF3 is more similar to eEF1alpha whereas prokaryote RF3 is more similar to EF-G, implying that their precise function may differ. Only eukaryote RF3s are found in this group. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM
Probab=23.45 E-value=1.3e+02 Score=21.29 Aligned_cols=11 Identities=36% Similarity=0.724 Sum_probs=6.6
Q ss_pred eeeCCEEEEee
Q 029417 70 VKAGDTVKVIA 80 (193)
Q Consensus 70 IkkGD~V~VI~ 80 (193)
|++||+|.+.-
T Consensus 27 i~~Gd~v~i~P 37 (83)
T cd03698 27 IQKGDTLLVMP 37 (83)
T ss_pred EeCCCEEEEeC
Confidence 56666666654
No 112
>PRK08515 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=23.21 E-value=1.2e+02 Score=26.02 Aligned_cols=33 Identities=15% Similarity=0.382 Sum_probs=22.7
Q ss_pred cceeeCCEEEEeecC------------CCCeeeEEEEEEccCCEE
Q 029417 68 MHVKAGDTVKVIAGC------------DKGKIGEITKVFRHNSTV 100 (193)
Q Consensus 68 ~~IkkGD~V~VI~Gk------------dKGK~GkV~~V~~~~n~V 100 (193)
+-|++||.|.|+.-. .-|..|.+.+|-...+++
T Consensus 164 ~lV~rGd~V~i~~~~gg~~I~~~G~Al~~G~~Gd~IrVrN~Sgki 208 (222)
T PRK08515 164 ILVRKNDIINGVLKEGGVSIEISLKALQDGNLGDIIQAKNKSNKI 208 (222)
T ss_pred ceEecCCEEEEEEECCCEEEEEEEEEcccCCCCCEEEEEeCCCCE
Confidence 448999999998643 456777777776644443
No 113
>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=23.11 E-value=1.4e+02 Score=18.58 Aligned_cols=23 Identities=26% Similarity=0.377 Sum_probs=15.9
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEE
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~Vi 101 (193)
.++.||+|.+ +|.+++++++.+.
T Consensus 41 ~~~~G~~v~~----------~v~~~d~~~~~i~ 63 (65)
T cd00164 41 VFKVGDEVEV----------KVLEVDPEKGRIS 63 (65)
T ss_pred EeCCCCEEEE----------EEEEEcCCcCEEe
Confidence 3789999887 5666666555543
No 114
>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=23.11 E-value=45 Score=25.12 Aligned_cols=19 Identities=47% Similarity=0.697 Sum_probs=14.6
Q ss_pred eeeCCEEEEeecCCCCeee
Q 029417 70 VKAGDTVKVIAGCDKGKIG 88 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~G 88 (193)
+..||.|+++.|.--|..|
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 6899999999996556555
No 115
>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=23.07 E-value=1.7e+02 Score=19.52 Aligned_cols=25 Identities=28% Similarity=0.428 Sum_probs=20.5
Q ss_pred ceeeCCEEEEeecCCCCeeeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViVE 103 (193)
.++.||+|.+ +|++++++++++.+.
T Consensus 48 ~~~~G~~v~v----------~v~~vd~~~~~i~lS 72 (74)
T PF00575_consen 48 VYKIGQTVRV----------KVIKVDKEKGRIRLS 72 (74)
T ss_dssp TCETTCEEEE----------EEEEEETTTTEEEEE
T ss_pred ccCCCCEEEE----------EEEEEECCCCeEEEE
Confidence 4789999987 688999998888763
No 116
>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=22.61 E-value=95 Score=19.62 Aligned_cols=16 Identities=25% Similarity=0.561 Sum_probs=11.2
Q ss_pred ccceeeCCEEEEeecC
Q 029417 67 KMHVKAGDTVKVIAGC 82 (193)
Q Consensus 67 k~~IkkGD~V~VI~Gk 82 (193)
.+.+++||.+.|+.=.
T Consensus 13 eLs~~~Gd~i~v~~~~ 28 (48)
T PF00018_consen 13 ELSFKKGDIIEVLEKS 28 (48)
T ss_dssp BSEB-TTEEEEEEEES
T ss_pred EEeEECCCEEEEEEec
Confidence 3458999999998643
No 117
>PF15276 PP1_bind: Protein phosphatase 1 binding
Probab=22.25 E-value=62 Score=23.37 Aligned_cols=39 Identities=18% Similarity=0.066 Sum_probs=28.7
Q ss_pred cceEEecCCCHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCC
Q 029417 41 KPCLIVVRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKG 85 (193)
Q Consensus 41 ~~~~~~~~l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKG 85 (193)
|++-+..+||.|+-.+.-|.+-| +++|++=.--......
T Consensus 4 kRVsFG~~LSPElFD~~LPpnTP------lkrG~tP~~~~~~~~~ 42 (64)
T PF15276_consen 4 KRVSFGEHLSPELFDKSLPPNTP------LKRGATPVRRSDPSSS 42 (64)
T ss_pred ceeccCCCCCHHHhcccCCCCCC------cCCCCCcccccCCCCC
Confidence 45567889999998888888888 9999975554444333
No 118
>cd03695 CysN_NodQ_II CysN_NodQ_II: This subfamily represents the domain II of the large subunit of ATP sulfurylase (ATPS): CysN or the N-terminal portion of NodQ, found mainly in proteobacteria and homologous to the domain II of EF-Tu. Escherichia coli ATPS consists of CysN and a smaller subunit CysD and CysN. ATPS produces adenosine-5'-phosphosulfate (APS) from ATP and sulfate, coupled with GTP hydrolysis. In the subsequent reaction APS is phosphorylated by an APS kinase (CysC), to produce 3'-phosphoadenosine-5'-phosphosulfate (PAPS) for use in amino acid (aa) biosynthesis. The Rhizobiaceae group (alpha-proteobacteria) appears to carry out the same chemistry for the sufation of a nodulation factor. In Rhizobium meliloti, a the hererodimeric complex comprised of NodP and NodQ appears to possess both ATPS and APS kinase activities. The N and C termini of NodQ correspond to CysN and CysC, respectively. Other eubacteria, Archaea, and eukaryotes use a different ATP sulfurylase, which sho
Probab=22.19 E-value=1.7e+02 Score=20.79 Aligned_cols=10 Identities=40% Similarity=0.833 Sum_probs=4.8
Q ss_pred eeeCCEEEEe
Q 029417 70 VKAGDTVKVI 79 (193)
Q Consensus 70 IkkGD~V~VI 79 (193)
+++||+|.+.
T Consensus 27 v~~Gd~v~~~ 36 (81)
T cd03695 27 IRVGDEVVVL 36 (81)
T ss_pred EECCCEEEEc
Confidence 4445544444
No 119
>CHL00010 infA translation initiation factor 1
Probab=21.88 E-value=1.4e+02 Score=21.61 Aligned_cols=27 Identities=30% Similarity=0.265 Sum_probs=16.8
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEcc
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRH 96 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~ 96 (193)
+..||.|.|--=.+-...|.|+.-++.
T Consensus 47 ~~vGD~V~ve~~~~~~~~g~Ii~r~~~ 73 (78)
T CHL00010 47 ILPGDRVKVELSPYDLTKGRIIYRLRN 73 (78)
T ss_pred cCCCCEEEEEEcccCCCeEEEEEEecC
Confidence 689999998733333345677554443
No 120
>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=21.60 E-value=87 Score=18.93 Aligned_cols=14 Identities=29% Similarity=0.610 Sum_probs=11.7
Q ss_pred cceeeCCEEEEeec
Q 029417 68 MHVKAGDTVKVIAG 81 (193)
Q Consensus 68 ~~IkkGD~V~VI~G 81 (193)
+.+.+||.|.|+..
T Consensus 16 l~~~~Gd~v~v~~~ 29 (54)
T cd00174 16 LSFKKGDIIEVLEK 29 (54)
T ss_pred CCCCCCCEEEEEEc
Confidence 34889999999976
No 121
>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=21.57 E-value=88 Score=20.05 Aligned_cols=25 Identities=24% Similarity=0.327 Sum_probs=17.9
Q ss_pred cCCCHHHHHhhCCCCCCcccccceeeCCEEEEeecC
Q 029417 47 VRLKRWERKECKPNSLPVLHKMHVKAGDTVKVIAGC 82 (193)
Q Consensus 47 ~~l~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~Gk 82 (193)
..|.+++|++++ |..||.|.+..-.
T Consensus 9 v~iPk~~~~~l~-----------l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 9 VTIPKEIREKLG-----------LKPGDEVEIEVEG 33 (47)
T ss_dssp EEE-HHHHHHTT-----------SSTTTEEEEEEET
T ss_pred EECCHHHHHHcC-----------CCCCCEEEEEEeC
Confidence 456788888884 5789999887543
No 122
>cd03693 EF1_alpha_II EF1_alpha_II: this family represents the domain II of elongation factor 1-alpha (EF-1a) that is found in archaea and all eukaryotic lineages. EF-1A is very abundant in the cytosol, where it is involved in the GTP-dependent binding of aminoacyl-tRNAs to the A site of the ribosomes in the second step of translation from mRNAs to proteins. Both domain II of EF1A and domain IV of IF2/eIF5B have been implicated in recognition of the 3'-ends of tRNA. More than 61% of eukaryotic elongation factor 1A (eEF-1A) in cells is estimated to be associated with actin cytoskeleton. The binding of eEF1A to actin is a noncanonical function that may link two distinct cellular processes, cytoskeleton organization and gene expression.
Probab=21.55 E-value=1.3e+02 Score=21.80 Aligned_cols=19 Identities=16% Similarity=0.184 Sum_probs=8.3
Q ss_pred EEEEEccCCEEEEeceeee
Q 029417 90 ITKVFRHNSTVMVKDINLK 108 (193)
Q Consensus 90 V~~V~~~~n~ViVEGvN~~ 108 (193)
-+.+.+.+..+.|.++.+.
T Consensus 36 ~v~i~P~~~~~~V~sI~~~ 54 (91)
T cd03693 36 VVTFAPAGVTGEVKSVEMH 54 (91)
T ss_pred EEEECCCCcEEEEEEEEEC
Confidence 3334444344455555433
No 123
>cd03696 selB_II selB_II: this subfamily represents the domain of elongation factor SelB, homologous to domain II of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=21.52 E-value=1.3e+02 Score=21.05 Aligned_cols=24 Identities=25% Similarity=0.387 Sum_probs=14.2
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEcc
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRH 96 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~ 96 (193)
|++||+|.+.-+. ..++|.+|...
T Consensus 27 i~~g~~v~~~p~~---~~~~V~sI~~~ 50 (83)
T cd03696 27 VKVGDKVEILPLG---EETRVRSIQVH 50 (83)
T ss_pred EeCCCEEEECCCC---ceEEEEEEEEC
Confidence 6777777766542 45666555443
No 124
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=21.45 E-value=60 Score=26.20 Aligned_cols=21 Identities=24% Similarity=0.422 Sum_probs=14.5
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEc
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFR 95 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~ 95 (193)
++.||.|+|= |..|+|.+|.-
T Consensus 61 f~vGD~I~i~-----~~~G~V~~I~l 81 (206)
T PF00924_consen 61 FKVGDRIEIG-----GVEGRVEEIGL 81 (206)
T ss_dssp S-TT-EEESS-----S-EEEEEEE-S
T ss_pred ccCCCEEEEE-----EeehHHHhcCc
Confidence 8999998875 88999988864
No 125
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.40 E-value=1.4e+02 Score=25.78 Aligned_cols=28 Identities=25% Similarity=0.251 Sum_probs=20.7
Q ss_pred cceeeCCEEEEeecC------------CCCeeeEEEEEEc
Q 029417 68 MHVKAGDTVKVIAGC------------DKGKIGEITKVFR 95 (193)
Q Consensus 68 ~~IkkGD~V~VI~Gk------------dKGK~GkV~~V~~ 95 (193)
+-|++||.|.|+... ..|-.|..++|-.
T Consensus 154 ~lV~rG~~V~I~a~~~g~~Vs~~G~AL~~G~~Ge~IrVrN 193 (214)
T PRK12617 154 RLVRRGDTVPLVSRNGGLEVRMSGRALSDAGENERVSVEN 193 (214)
T ss_pred ceEcCCCEEEEEEecCCEEEEEEEEEccCCCCCCEEEEEE
Confidence 458999999999754 3466777777763
No 126
>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=21.36 E-value=1.6e+02 Score=18.91 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=16.3
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~Vi 101 (193)
++.||.|.+ +|.+++.+++++.
T Consensus 45 ~~~Gd~v~v----------~i~~vd~~~~~i~ 66 (68)
T cd05685 45 VSVGDIVEV----------KVISIDEERGRIS 66 (68)
T ss_pred cCCCCEEEE----------EEEEEECCCCEEe
Confidence 689999988 4777777666654
No 127
>PF13234 rRNA_proc-arch: rRNA-processing arch domain; PDB: 4A4K_E 4A4Z_A 2XGJ_B 3L9O_A.
Probab=21.21 E-value=1.7e+02 Score=25.27 Aligned_cols=28 Identities=18% Similarity=0.205 Sum_probs=23.0
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccC
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN 97 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~ 97 (193)
+.+|..|.|-.|.+....|.|+.+.+..
T Consensus 73 L~~GRlV~v~~~~~~~~wgvvv~~~~~~ 100 (268)
T PF13234_consen 73 LQPGRLVVVRDGDRDFGWGVVVNFAKKS 100 (268)
T ss_dssp S-TTEEEEEEETTCEEEEEEEEEEEE--
T ss_pred CCCCCEEEEecCCCccceeEEEeccccc
Confidence 6899999999999999999999998764
No 128
>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=21.12 E-value=90 Score=21.22 Aligned_cols=21 Identities=33% Similarity=0.289 Sum_probs=13.3
Q ss_pred eeeCCEEEEeecCCCCeeeEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEI 90 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV 90 (193)
+..||.|.+---.+-+.+|.|
T Consensus 41 ~~vGD~V~~~~~~~~~~~g~I 61 (64)
T cd04451 41 ILPGDRVKVELSPYDLTKGRI 61 (64)
T ss_pred cCCCCEEEEEEeecCCCEEEE
Confidence 689999988744322334555
No 129
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=21.11 E-value=1.5e+02 Score=28.96 Aligned_cols=41 Identities=5% Similarity=0.073 Sum_probs=23.4
Q ss_pred eecCcCCCeeeeecCCCCeeeEEEEEccCCcEEEEEcccCcc
Q 029417 127 EAPIHSSNVMLYSKEMEVASRVGHKVLDDGTRVRYLIKTGEI 168 (193)
Q Consensus 127 E~PIh~SNV~Lv~p~~~kptRVg~r~~edGkKvRv~kksg~~ 168 (193)
|.+=.++=...+|++||+-+-....++.+. .|+|.-.||..
T Consensus 159 ~~~~~~~P~~pic~~cGrv~~~~~~~~~~~-~v~Y~c~cG~~ 199 (515)
T TIGR00467 159 KLEENWYPISVFCENCGRDTTTVNNYDNEY-SIEYSCECGNQ 199 (515)
T ss_pred ccCCCceeeeeecCCcCccCceEEEecCCc-eEEEEcCCCCE
Confidence 344445567788999987422212333444 57776566654
No 130
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=21.06 E-value=56 Score=30.15 Aligned_cols=45 Identities=18% Similarity=0.193 Sum_probs=28.5
Q ss_pred CHHHHHhhCCCCCCcccccceeeCCEEEEeecCCCCeeeEEEEEEc
Q 029417 50 KRWERKECKPNSLPVLHKMHVKAGDTVKVIAGCDKGKIGEITKVFR 95 (193)
Q Consensus 50 ~k~lR~k~~~rs~p~~~k~~IkkGD~V~VI~GkdKGK~GkV~~V~~ 95 (193)
-++||+||..|-.-| ..-.----|+|+++.|+-|.-.|-|..|..
T Consensus 145 ikelrekcsarlkif-t~c~p~stdrv~l~~g~~k~v~~~i~~il~ 189 (390)
T KOG2192|consen 145 IKELREKCSARLKIF-TECCPHSTDRVVLIGGKPKRVVECIKIILD 189 (390)
T ss_pred HHHHHHhhhhhhhhh-hccCCCCcceEEEecCCcchHHHHHHHHHH
Confidence 379999997653221 111112349999999998887776654443
No 131
>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=20.94 E-value=3.2e+02 Score=19.48 Aligned_cols=52 Identities=19% Similarity=0.094 Sum_probs=31.9
Q ss_pred eeeEEEEEEccCCEEEEeceeeeeeeecCCcccCCceeEEEeecCcCCCeeeeecCCCCeeeEEEEEccCCcEE
Q 029417 86 KIGEITKVFRHNSTVMVKDINLKTKHVKKREEEEQGQIIKIEAPIHSSNVMLYSKEMEVASRVGHKVLDDGTRV 159 (193)
Q Consensus 86 K~GkV~~V~~~~n~ViVEGvN~~kkhvK~~~~~~~GgIi~~E~PIh~SNV~Lv~p~~~kptRVg~r~~edGkKv 159 (193)
-+|+|.+|++..-.|..++=.-.+ .|- +..+=..+.|...+|-|-. .+|+++
T Consensus 5 veG~I~~id~~~~titLdDGksy~------------------lp~---ef~~~~L~~G~kV~V~yd~-~~gk~v 56 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDGKSYK------------------LPE---EFDFDGLKPGMKVVVFYDE-VDGKRV 56 (61)
T ss_pred ceEEEEEEcCCceEEEecCCCEEE------------------CCC---cccccccCCCCEEEEEEEc-cCCcEE
Confidence 369999999999888888432221 221 1223234557777777764 566654
No 132
>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=20.93 E-value=1.6e+02 Score=19.32 Aligned_cols=22 Identities=14% Similarity=0.206 Sum_probs=17.3
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~Vi 101 (193)
++.||+|.| +|.+|+.++.++.
T Consensus 46 ~~~G~~v~v----------~v~~id~~~~~i~ 67 (69)
T cd05690 46 YKKGQEVEA----------VVLNIDVERERIS 67 (69)
T ss_pred ECCCCEEEE----------EEEEEECCcCEEe
Confidence 789999988 4788887777664
No 133
>PF14001 YdfZ: YdfZ protein
Probab=20.67 E-value=1.7e+02 Score=21.08 Aligned_cols=34 Identities=18% Similarity=0.357 Sum_probs=25.1
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccC---------CEEEEecee
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHN---------STVMVKDIN 106 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~---------n~ViVEGvN 106 (193)
|..|-+|+|- .-|.+|.|..|..+. ..|.+||++
T Consensus 10 i~~G~rVMia---gtG~~gvikAih~~gl~~eq~rR~kcVel~g~~ 52 (64)
T PF14001_consen 10 ITTGSRVMIA---GTGATGVIKAIHADGLTAEQIRRAKCVELEGCE 52 (64)
T ss_pred CCCCCEEEEc---CCCcccEEeeeecCCCCHHHhhhccEEEEeCCC
Confidence 8899999874 348999999997554 246677654
No 134
>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=20.45 E-value=1.6e+02 Score=21.28 Aligned_cols=36 Identities=6% Similarity=0.051 Sum_probs=29.3
Q ss_pred eecCCCCeeeEEEEEccCCcEEEEEcccCcccccchh
Q 029417 138 YSKEMEVASRVGHKVLDDGTRVRYLIKTGEIIDSAEN 174 (193)
Q Consensus 138 v~p~~~kptRVg~r~~edGkKvRv~kksg~~I~~Pe~ 174 (193)
+||.|+.-.++-+- .+||...|-|.+||..--.|+.
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 57999888888764 4888999999999998766654
No 135
>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=20.42 E-value=2.2e+02 Score=19.10 Aligned_cols=23 Identities=22% Similarity=0.327 Sum_probs=16.9
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViV 102 (193)
++.||.|.+ +|.+++..++++.+
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 46777776666554
No 136
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=20.30 E-value=1.6e+02 Score=29.22 Aligned_cols=35 Identities=23% Similarity=0.369 Sum_probs=24.7
Q ss_pred ceeeCCEEEEe-ecC-CCCe-eeEEEEEEccCCEEEEe
Q 029417 69 HVKAGDTVKVI-AGC-DKGK-IGEITKVFRHNSTVMVK 103 (193)
Q Consensus 69 ~IkkGD~V~VI-~Gk-dKGK-~GkV~~V~~~~n~ViVE 103 (193)
....||+|.|. ... .+|+ .|+|.+|......-+|-
T Consensus 50 ~a~~GD~V~v~i~~~~~~~~~~g~v~~il~r~~~~~vG 87 (654)
T TIGR00358 50 KVMHGDLVEACPLSQPQRGRFEAEVERILEPALTRFVG 87 (654)
T ss_pred cCCCCCEEEEEEeecCCCCCceEEEEEEeccCCCEEEE
Confidence 45689999764 333 3444 89999999887665554
No 137
>PRK06005 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=20.28 E-value=1.6e+02 Score=24.12 Aligned_cols=38 Identities=26% Similarity=0.424 Sum_probs=24.8
Q ss_pred ccceeeCCEEEEeecC------------CCCeeeEEEEEEccCCEEEEec
Q 029417 67 KMHVKAGDTVKVIAGC------------DKGKIGEITKVFRHNSTVMVKD 104 (193)
Q Consensus 67 k~~IkkGD~V~VI~Gk------------dKGK~GkV~~V~~~~n~ViVEG 104 (193)
.+-|++||.|.|+... +-|..|.+.+|-.-...-+|+|
T Consensus 98 p~~V~rG~~V~i~~~~~g~~i~~~G~Al~~G~~Gd~IrVrN~~Sgkiv~g 147 (160)
T PRK06005 98 PSLVTRGSPVKLVFSAGGLTITAAGTPLQSGAAGDLIRVRNVDSGVIVSG 147 (160)
T ss_pred CcEEeCCCEEEEEEecCCEEEEEEEEEcccCCCCCEEEEEECCCCCEEEE
Confidence 3568999999998643 4577787777764333333443
No 138
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=20.25 E-value=1.6e+02 Score=25.06 Aligned_cols=27 Identities=26% Similarity=0.476 Sum_probs=20.7
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEcc
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRH 96 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~ 96 (193)
++.||.|.|..|...=-.|+|..+.++
T Consensus 30 ~~~Gd~i~v~~g~g~~~~~~i~~i~~~ 56 (234)
T PRK11713 30 LKEGDELRLFDGDGGEYLAEITEIGKK 56 (234)
T ss_pred CCCCCEEEEEeCCCCEEEEEEEEecCc
Confidence 899999999998642234788888654
No 139
>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=20.19 E-value=2e+02 Score=19.28 Aligned_cols=23 Identities=22% Similarity=0.241 Sum_probs=17.3
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVMV 102 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~ViV 102 (193)
++.||.|.+ +|++++++++++.+
T Consensus 48 ~~~Gd~v~~----------~V~~~d~~~~~i~l 70 (73)
T cd05706 48 FKKNDIVRA----------CVLSVDVPNKKIAL 70 (73)
T ss_pred cCCCCEEEE----------EEEEEeCCCCEEEE
Confidence 678999887 67777777766654
No 140
>PRK12289 GTPase RsgA; Reviewed
Probab=20.14 E-value=1.6e+02 Score=27.10 Aligned_cols=32 Identities=28% Similarity=0.323 Sum_probs=23.9
Q ss_pred eeeCCEEEEeecCCCCeeeEEEEEEccCCEEE
Q 029417 70 VKAGDTVKVIAGCDKGKIGEITKVFRHNSTVM 101 (193)
Q Consensus 70 IkkGD~V~VI~GkdKGK~GkV~~V~~~~n~Vi 101 (193)
+..||.|.+-.-.+.+..|.|.+|.+.+|.+.
T Consensus 52 ~~vGD~V~~~~~~~~~~~~~I~~vlpR~~~L~ 83 (352)
T PRK12289 52 VMVGDRVIVEEPDWQGQRGAIAEVLPRKTELD 83 (352)
T ss_pred cccCCEEEEeecCCCCCceEEEEEecccccee
Confidence 47999998854333456799999999987654
Done!