Query psy10530
Match_columns 141
No_of_seqs 205 out of 1206
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 20:40:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10530hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00194 60S ribosomal protein 100.0 6.8E-53 1.5E-57 324.0 9.2 124 16-140 1-124 (143)
2 PRK01191 rpl24p 50S ribosomal 100.0 9.9E-50 2.1E-54 299.1 9.5 117 19-136 3-120 (120)
3 KOG3401|consensus 100.0 3E-50 6.5E-55 309.0 5.2 128 14-141 1-128 (145)
4 TIGR01080 rplX_A_E ribosomal p 100.0 8.6E-47 1.9E-51 281.0 10.0 113 21-134 1-114 (114)
5 COG0198 RplX Ribosomal protein 99.9 3.4E-22 7.4E-27 147.1 5.8 72 58-132 1-85 (104)
6 PRK00004 rplX 50S ribosomal pr 99.8 2E-21 4.2E-26 142.6 5.1 74 59-133 2-89 (105)
7 CHL00141 rpl24 ribosomal prote 99.8 5.9E-21 1.3E-25 135.1 7.3 66 59-125 6-82 (83)
8 TIGR01079 rplX_bact ribosomal 99.8 6.7E-21 1.4E-25 139.8 4.9 74 60-134 2-90 (104)
9 PRK12281 rplX 50S ribosomal pr 99.8 4.8E-20 1E-24 128.7 6.2 61 59-120 4-75 (76)
10 KOG1708|consensus 99.4 2.2E-13 4.9E-18 111.0 5.7 86 32-126 51-148 (236)
11 PF00467 KOW: KOW motif; Inte 98.7 1.9E-08 4E-13 59.2 4.6 32 64-96 1-32 (32)
12 smart00739 KOW KOW (Kyprides, 97.7 6.2E-05 1.3E-09 41.6 3.6 27 61-88 1-27 (28)
13 PRK08559 nusG transcription an 97.6 0.0003 6.4E-09 54.1 7.6 73 42-121 72-149 (153)
14 TIGR00405 L26e_arch ribosomal 97.6 0.00033 7.2E-09 52.7 7.0 74 43-121 65-141 (145)
15 PRK05609 nusG transcription an 97.0 0.0014 3E-08 50.5 5.0 37 59-96 124-160 (181)
16 TIGR00922 nusG transcription t 97.0 0.0014 3E-08 50.3 4.9 36 60-96 118-153 (172)
17 COG0250 NusG Transcription ant 96.9 0.0024 5.3E-08 50.8 5.7 36 60-96 122-157 (178)
18 TIGR01955 RfaH transcriptional 96.2 0.0096 2.1E-07 44.9 5.0 35 60-96 107-141 (159)
19 TIGR01956 NusG_myco NusG famil 96.2 0.012 2.7E-07 49.6 5.7 54 59-117 203-256 (258)
20 PRK09014 rfaH transcriptional 96.1 0.011 2.4E-07 45.0 4.7 51 61-117 109-159 (162)
21 KOG1999|consensus 92.5 0.14 3E-06 50.2 3.9 34 48-89 453-486 (1024)
22 COG5164 SPT5 Transcription elo 90.6 0.67 1.5E-05 42.8 6.0 84 43-137 335-419 (607)
23 KOG3401|consensus 88.7 0.085 1.8E-06 41.3 -1.0 63 18-83 81-143 (145)
24 PRK04333 50S ribosomal protein 88.4 1 2.2E-05 32.0 4.4 60 60-125 2-61 (84)
25 PTZ00471 60S ribosomal protein 81.2 2.9 6.2E-05 32.4 4.3 38 62-100 5-48 (134)
26 COG2002 AbrB Regulators of sta 80.5 2.1 4.6E-05 30.0 3.1 29 46-79 17-45 (89)
27 TIGR01024 rplS_bact ribosomal 80.4 15 0.00032 27.6 7.7 78 49-128 5-92 (113)
28 PTZ00065 60S ribosomal protein 79.8 3.9 8.4E-05 31.5 4.6 57 62-124 8-64 (130)
29 CHL00084 rpl19 ribosomal prote 79.1 8.2 0.00018 29.1 6.1 79 47-128 7-96 (117)
30 PF04014 Antitoxin-MazE: Antid 76.6 2.4 5.3E-05 26.1 2.2 25 45-74 9-33 (47)
31 PF05641 Agenet: Agenet domain 76.0 8.7 0.00019 25.4 4.9 39 62-101 1-42 (68)
32 PRK06531 yajC preprotein trans 75.7 5.3 0.00011 29.9 4.2 30 62-96 37-66 (113)
33 PF15276 PP1_bind: Protein pho 73.7 2.3 4.9E-05 29.2 1.6 38 38-75 3-40 (64)
34 COG2163 RPL14A Ribosomal prote 73.7 5.6 0.00012 30.3 3.9 35 62-98 5-39 (125)
35 PLN00190 60S ribosomal protein 73.2 9.4 0.0002 30.3 5.2 44 44-96 24-77 (158)
36 COG1862 YajC Preprotein transl 69.5 7.7 0.00017 28.3 3.7 28 62-96 44-71 (97)
37 KOG1999|consensus 68.9 3.8 8.3E-05 40.6 2.5 29 61-90 581-609 (1024)
38 PRK04313 30S ribosomal protein 68.4 9.2 0.0002 32.1 4.4 56 58-121 168-227 (237)
39 PRK05585 yajC preprotein trans 68.1 9.6 0.00021 28.0 4.0 28 62-96 53-80 (106)
40 KOG1728|consensus 67.4 3.4 7.3E-05 32.6 1.6 26 37-70 101-126 (156)
41 PRK04306 50S ribosomal protein 66.2 12 0.00026 27.4 4.2 43 44-95 25-77 (98)
42 PF08922 DUF1905: Domain of un 66.2 4.7 0.0001 27.8 1.9 22 45-71 58-79 (80)
43 PF12701 LSM14: Scd6-like Sm d 66.1 15 0.00032 26.6 4.6 52 64-116 7-58 (96)
44 TIGR00739 yajC preprotein tran 64.6 13 0.00029 26.1 4.0 29 61-96 37-65 (84)
45 COG1532 Predicted RNA-binding 63.9 8 0.00017 25.9 2.6 34 63-97 22-57 (57)
46 PRK05886 yajC preprotein trans 63.3 14 0.0003 27.6 4.0 28 62-96 39-66 (109)
47 COG5164 SPT5 Transcription elo 62.5 6.6 0.00014 36.5 2.7 31 62-93 140-170 (607)
48 PRK02749 photosystem I reactio 60.5 15 0.00032 25.7 3.5 30 60-90 1-32 (71)
49 smart00743 Agenet Tudor-like d 59.1 24 0.00052 22.3 4.2 35 61-96 2-36 (61)
50 COG2139 RPL21A Ribosomal prote 58.0 18 0.00039 26.7 3.8 44 44-96 23-76 (98)
51 PF02699 YajC: Preprotein tran 57.4 3.5 7.5E-05 28.7 0.0 29 61-96 36-64 (82)
52 PTZ00118 40S ribosomal protein 57.1 46 0.00099 28.4 6.7 71 58-136 171-253 (262)
53 PTZ00189 60S ribosomal protein 56.1 27 0.00059 27.8 4.9 44 44-96 24-77 (160)
54 PLN00036 40S ribosomal protein 56.0 42 0.0009 28.6 6.2 71 58-136 171-253 (261)
55 PRK08577 hypothetical protein; 56.0 54 0.0012 24.2 6.3 29 46-79 16-44 (136)
56 PRK05338 rplS 50S ribosomal pr 55.9 60 0.0013 24.4 6.4 65 61-128 18-92 (116)
57 PF09953 DUF2187: Uncharacteri 54.7 28 0.00061 23.3 4.0 27 63-96 5-31 (57)
58 PF11623 DUF3252: Protein of u 53.3 30 0.00065 22.9 3.9 40 62-102 2-43 (53)
59 PF01245 Ribosomal_L19: Riboso 53.3 91 0.002 23.2 7.5 71 50-122 6-85 (113)
60 PLN00045 photosystem I reactio 53.3 21 0.00046 26.4 3.6 33 56-89 34-68 (101)
61 cd05792 S1_eIF1AD_like S1_eIF1 53.0 25 0.00054 24.7 3.8 33 58-90 35-67 (78)
62 PTZ00223 40S ribosomal protein 52.4 25 0.00055 30.1 4.4 55 58-120 168-225 (273)
63 COG1471 RPS4A Ribosomal protei 52.2 26 0.00057 29.6 4.4 40 57-97 169-212 (241)
64 TIGR01439 lp_hng_hel_AbrB loop 51.9 19 0.00041 21.0 2.6 25 45-74 9-33 (43)
65 PF04452 Methyltrans_RNA: RNA 51.7 55 0.0012 26.1 6.1 42 54-96 9-50 (225)
66 PRK00409 recombination and DNA 51.5 21 0.00046 34.3 4.2 37 61-101 636-673 (782)
67 CHL00125 psaE photosystem I su 50.0 18 0.0004 24.7 2.6 28 62-90 2-31 (64)
68 PF14505 DUF4438: Domain of un 49.8 34 0.00075 29.2 4.7 31 64-95 60-90 (258)
69 cd01736 LSm14_N LSm14 (also kn 48.0 65 0.0014 22.6 5.2 53 64-117 5-58 (74)
70 cd04456 S1_IF1A_like S1_IF1A_l 47.0 28 0.0006 24.2 3.2 40 45-90 27-67 (78)
71 PF08206 OB_RNB: Ribonuclease 46.8 26 0.00055 22.5 2.9 25 62-86 32-58 (58)
72 cd05791 S1_CSL4 S1_CSL4: CSL4, 46.7 23 0.00049 24.9 2.8 45 63-119 5-49 (92)
73 PF00924 MS_channel: Mechanose 46.4 23 0.0005 27.0 3.1 23 61-89 60-82 (206)
74 cd03692 mtIF2_IVc mtIF2_IVc: t 45.8 39 0.00084 23.0 3.8 30 61-91 26-55 (84)
75 cd05793 S1_IF1A S1_IF1A: Trans 44.6 23 0.00049 24.5 2.5 41 44-90 26-66 (77)
76 PF02427 PSI_PsaE: Photosystem 43.2 30 0.00065 23.5 2.8 28 62-90 1-30 (61)
77 TIGR01448 recD_rel helicase, p 42.9 64 0.0014 30.7 5.9 42 47-89 562-618 (720)
78 TIGR01069 mutS2 MutS2 family p 42.8 36 0.00078 32.7 4.3 35 63-101 626-661 (771)
79 PF14242 DUF4342: Domain of un 41.8 24 0.00052 25.0 2.3 21 49-69 23-43 (84)
80 smart00652 eIF1a eukaryotic tr 41.5 42 0.00091 23.5 3.5 41 44-90 31-71 (83)
81 TIGR02609 doc_partner putative 39.8 32 0.0007 23.3 2.6 26 44-74 11-36 (74)
82 PRK11509 hydrogenase-1 operon 38.7 33 0.00072 26.2 2.8 32 42-73 74-109 (132)
83 PF01157 Ribosomal_L21e: Ribos 38.3 63 0.0014 23.7 4.1 37 45-90 24-70 (99)
84 PRK10334 mechanosensitive chan 38.1 85 0.0018 26.4 5.4 23 61-89 129-151 (286)
85 PF01176 eIF-1a: Translation i 37.7 43 0.00093 22.0 2.9 27 58-85 38-64 (65)
86 TIGR00523 eIF-1A eukaryotic/ar 37.4 24 0.00052 25.7 1.8 42 44-90 45-86 (99)
87 KOG3418|consensus 36.6 60 0.0013 25.3 3.9 38 62-100 5-48 (136)
88 PF00408 PGM_PMM_IV: Phosphogl 36.4 15 0.00033 24.3 0.6 14 5-18 40-53 (73)
89 cd02786 MopB_CT_3 The MopB_CT_ 35.4 65 0.0014 22.4 3.7 26 44-74 32-57 (116)
90 COG1193 Mismatch repair ATPase 35.3 42 0.0009 32.5 3.4 33 59-96 610-642 (753)
91 COG0361 InfA Translation initi 35.1 53 0.0011 23.0 3.1 41 44-89 33-73 (75)
92 COG1385 Uncharacterized protei 34.5 1.2E+02 0.0026 25.2 5.7 50 47-98 20-69 (246)
93 cd05703 S1_Rrp5_repeat_hs12_sc 34.1 71 0.0015 21.1 3.6 24 62-96 47-70 (73)
94 PF03144 GTP_EFTU_D2: Elongati 33.9 88 0.0019 19.9 3.9 30 61-92 12-44 (74)
95 PF05257 CHAP: CHAP domain; I 33.8 70 0.0015 22.8 3.7 40 58-99 59-100 (124)
96 TIGR00046 RNA methyltransferas 33.7 78 0.0017 25.6 4.4 47 46-95 17-64 (240)
97 TIGR00008 infA translation ini 33.2 40 0.00086 23.1 2.2 37 43-84 30-66 (68)
98 cd02785 MopB_CT_4 The MopB_CT_ 33.1 60 0.0013 23.1 3.3 29 44-79 33-61 (124)
99 cd04717 BAH_polybromo BAH, or 31.4 1.3E+02 0.0029 21.5 4.9 40 61-100 3-44 (121)
100 PRK04012 translation initiatio 31.4 48 0.001 24.2 2.6 41 44-90 47-87 (100)
101 cd02790 MopB_CT_Formate-Dh_H F 31.3 76 0.0017 21.9 3.5 25 45-74 37-61 (116)
102 KOG4315|consensus 30.7 26 0.00056 32.1 1.2 37 60-97 392-428 (455)
103 cd05696 S1_Rrp5_repeat_hs4 S1_ 30.5 94 0.002 20.3 3.7 24 61-95 46-69 (71)
104 cd02779 MopB_CT_Arsenite-Ox Th 30.4 83 0.0018 22.2 3.6 25 45-74 35-59 (115)
105 cd02781 MopB_CT_Acetylene-hydr 30.3 91 0.002 22.1 3.9 29 44-79 34-62 (130)
106 smart00439 BAH Bromo adjacent 29.7 1E+02 0.0022 21.2 3.9 30 62-91 2-32 (120)
107 PF07653 SH3_2: Variant SH3 do 29.6 38 0.00083 21.0 1.6 13 59-71 15-27 (55)
108 cd02794 MopB_CT_DmsA-EC The Mo 29.6 92 0.002 22.0 3.8 25 45-74 32-56 (121)
109 PHA00653 mtd major tropism det 29.4 1.1E+02 0.0024 27.4 4.9 58 61-122 6-70 (381)
110 cd00174 SH3 Src homology 3 dom 29.2 54 0.0012 18.8 2.1 19 59-77 15-33 (54)
111 PRK13922 rod shape-determining 29.1 1.1E+02 0.0024 25.0 4.6 40 51-91 204-247 (276)
112 TIGR02851 spore_V_T stage V sp 29.1 45 0.00097 26.4 2.2 23 46-73 16-38 (180)
113 PF11910 NdhO: Cyanobacterial 28.1 30 0.00064 24.0 0.9 18 62-79 1-18 (67)
114 cd02787 MopB_CT_ydeP The MopB_ 27.7 64 0.0014 22.5 2.6 25 45-74 33-57 (112)
115 PF11717 Tudor-knot: RNA bindi 27.7 63 0.0014 20.5 2.3 28 62-90 1-28 (55)
116 PF01426 BAH: BAH domain; Int 27.3 1.2E+02 0.0025 21.0 3.9 30 61-90 2-32 (119)
117 PRK10929 putative mechanosensi 27.2 1.2E+02 0.0027 30.7 5.3 23 61-89 935-957 (1109)
118 cd04454 S1_Rrp4_like S1_Rrp4_l 27.1 84 0.0018 20.8 3.0 22 63-95 5-26 (82)
119 cd03065 PDI_b_Calsequestrin_N 27.1 60 0.0013 24.0 2.5 19 43-61 71-89 (120)
120 PF13452 MaoC_dehydrat_N: N-te 27.1 2E+02 0.0043 20.3 5.2 39 61-108 87-129 (132)
121 PF04085 MreC: rod shape-deter 26.8 1.9E+02 0.0042 21.8 5.3 34 57-91 89-126 (152)
122 COG1792 MreC Cell shape-determ 26.4 88 0.0019 26.4 3.7 42 49-91 200-245 (284)
123 PF02887 PK_C: Pyruvate kinase 26.3 43 0.00093 23.9 1.5 18 62-79 90-107 (117)
124 cd03450 NodN NodN (nodulation 26.3 2E+02 0.0042 21.7 5.2 44 61-114 97-142 (149)
125 cd02791 MopB_CT_Nitrate-R-NapA 26.2 67 0.0014 22.4 2.5 26 44-74 36-61 (122)
126 cd02954 DIM1 Dim1 family; Dim1 26.2 72 0.0016 23.6 2.7 32 43-74 52-87 (114)
127 COG0335 RplS Ribosomal protein 26.1 1.9E+02 0.0042 21.9 5.0 65 62-128 21-94 (115)
128 TIGR03170 flgA_cterm flagella 26.0 1.1E+02 0.0025 21.7 3.7 14 61-74 65-78 (122)
129 PF07449 HyaE: Hydrogenase-1 e 26.0 60 0.0013 24.0 2.2 39 35-73 58-100 (107)
130 cd04721 BAH_plant_1 BAH, or Br 25.9 2.1E+02 0.0045 21.4 5.2 38 59-97 5-43 (130)
131 COG0668 MscS Small-conductance 25.8 1.1E+02 0.0025 24.5 4.1 26 60-90 146-171 (316)
132 TIGR02594 conserved hypothetic 25.8 1.8E+02 0.004 21.6 4.9 40 54-95 66-105 (129)
133 PRK11713 16S ribosomal RNA met 25.7 1.1E+02 0.0023 24.7 3.9 48 46-95 15-62 (234)
134 TIGR03784 marine_sortase sorta 25.5 2.5E+02 0.0054 22.0 5.9 44 61-117 108-151 (174)
135 CHL00010 infA translation init 25.5 98 0.0021 21.2 3.1 42 42-88 31-72 (78)
136 smart00326 SH3 Src homology 3 25.5 69 0.0015 18.5 2.1 20 58-77 17-36 (58)
137 PF10844 DUF2577: Protein of u 25.1 96 0.0021 22.1 3.2 12 61-72 76-87 (100)
138 PF02470 MCE: mce related prot 25.1 1.1E+02 0.0023 20.3 3.2 30 62-96 15-46 (81)
139 cd04451 S1_IF1 S1_IF1: Transla 24.7 59 0.0013 20.9 1.9 24 59-83 38-61 (64)
140 cd03688 eIF2_gamma_II eIF2_gam 24.7 1.9E+02 0.0041 21.8 4.8 19 61-79 39-57 (113)
141 COG1153 FwdD Formylmethanofura 24.6 67 0.0015 24.8 2.4 37 26-74 21-57 (128)
142 cd03452 MaoC_C MaoC_C The C-t 24.4 2.9E+02 0.0062 20.2 6.0 38 61-108 88-129 (142)
143 PF01079 Hint: Hint module; I 24.1 1E+02 0.0022 25.2 3.5 29 59-88 103-132 (217)
144 PTZ00051 thioredoxin; Provisio 24.1 96 0.0021 20.4 2.9 26 48-73 60-89 (98)
145 cd00508 MopB_CT_Fdh-Nap-like T 23.9 1.1E+02 0.0024 21.1 3.2 25 45-74 37-61 (120)
146 PF01568 Molydop_binding: Moly 23.2 66 0.0014 22.0 2.0 26 44-74 31-56 (110)
147 cd03698 eRF3_II_like eRF3_II_l 23.0 1.3E+02 0.0028 20.1 3.4 12 62-73 27-38 (83)
148 cd02792 MopB_CT_Formate-Dh-Na- 22.7 1.2E+02 0.0025 21.2 3.2 25 45-74 37-61 (122)
149 PLN00208 translation initiatio 22.5 1.1E+02 0.0023 24.0 3.2 32 59-91 68-99 (145)
150 TIGR01553 formate-DH-alph form 22.4 1.7E+02 0.0037 29.2 5.2 27 43-74 913-939 (1009)
151 PF11302 DUF3104: Protein of u 22.1 1.5E+02 0.0032 20.9 3.5 28 60-87 4-37 (75)
152 PRK12617 flgA flagellar basal 22.0 1.4E+02 0.003 24.4 3.9 15 61-75 155-169 (214)
153 cd05705 S1_Rrp5_repeat_hs14 S1 22.0 1.4E+02 0.003 19.8 3.3 23 62-95 51-73 (74)
154 cd03693 EF1_alpha_II EF1_alpha 22.0 1.2E+02 0.0027 20.6 3.2 12 62-73 31-42 (91)
155 PRK07018 flgA flagellar basal 22.0 1.3E+02 0.0027 24.5 3.7 15 60-74 175-189 (235)
156 PF01191 RNA_pol_Rpb5_C: RNA p 21.5 66 0.0014 22.3 1.7 35 40-74 12-61 (74)
157 PRK07696 sulfur carrier protei 21.4 63 0.0014 21.3 1.5 14 59-72 49-62 (67)
158 KOG4792|consensus 21.3 83 0.0018 27.0 2.5 30 54-83 240-269 (293)
159 cd02778 MopB_CT_Thiosulfate-R- 21.2 1E+02 0.0022 21.6 2.6 26 44-74 31-56 (123)
160 PF11160 DUF2945: Protein of u 21.0 2.4E+02 0.0052 18.8 4.3 32 65-100 1-32 (62)
161 COG2100 Predicted Fe-S oxidore 21.0 1.1E+02 0.0024 27.6 3.3 46 49-99 322-387 (414)
162 cd05697 S1_Rrp5_repeat_hs5 S1_ 20.9 2.2E+02 0.0049 17.9 4.1 24 61-95 44-67 (69)
163 cd02788 MopB_CT_NDH-1_NuoG2-N7 20.8 1.1E+02 0.0023 21.1 2.6 25 45-74 31-55 (96)
164 KOG2996|consensus 20.7 79 0.0017 30.7 2.4 13 60-72 822-834 (865)
165 PRK11281 hypothetical protein; 20.6 1.3E+02 0.0029 30.4 4.1 23 61-89 938-960 (1113)
166 COG3700 AphA Acid phosphatase 20.6 37 0.0008 28.3 0.2 94 31-127 75-196 (237)
167 PF08605 Rad9_Rad53_bind: Fung 20.6 59 0.0013 24.8 1.4 18 56-73 54-71 (131)
168 PF09926 DUF2158: Uncharacteri 20.3 64 0.0014 21.0 1.3 14 63-76 2-15 (53)
169 cd05706 S1_Rrp5_repeat_sc10 S1 20.3 2.1E+02 0.0045 18.1 3.8 24 62-96 48-71 (73)
170 cd04714 BAH_BAHCC1 BAH, or Bro 20.0 3.1E+02 0.0067 19.9 5.1 35 61-96 3-40 (121)
No 1
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=100.00 E-value=6.8e-53 Score=324.04 Aligned_cols=124 Identities=68% Similarity=1.052 Sum_probs=120.6
Q ss_pred ecccccCCcccccccccCCCCccceeeeeccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEE
Q psy10530 16 LNKLVTSSRRKNRKRHFNAPSHIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYI 95 (141)
Q Consensus 16 ~~~~vss~~rKqRK~~~nAp~h~r~k~msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~V 95 (141)
+||+||+|||||||++||||+|.|+++|+||||+|||++||+|+++|++||+|+||+|+|||++ |+|++|++++++|+|
T Consensus 1 ~n~~~S~~prKqRKa~~~Ap~h~r~k~msa~LSkeLr~k~~~Rs~~IkkGD~V~Vi~Gk~KGk~-GkV~~V~~k~~~ViV 79 (143)
T PTZ00194 1 FNSIVSSSRRKARKAHFTAPSHLRRKLMSAPLSKELRAKYNVRSMPVRKDDEVMVVRGHHKGRE-GKVTAVYRKKWVIHI 79 (143)
T ss_pred CCccccCCchHHHHHhhcCcHHHHHHHhcCccCHHHHHHhCCccceeecCCEEEEecCCCCCCc-eEEEEEEcCCCEEEE
Confidence 5899999999999999999999999999999999999999999999999999999999999999 999999999999999
Q ss_pred eeeeEeccCCcEEEecccccceEEEeCCCChhHHHHhhhhhhccc
Q psy10530 96 EKIQRDKVNGATVYVGIHPSKCVIVKLKMDKDRKKIIERRAKGRA 140 (141)
Q Consensus 96 Egvn~~K~~G~~v~~pIhpSNV~i~~l~ldk~R~k~Le~k~~~~~ 140 (141)
||||+.|.+|.++|+|||||||+||||++|++|.++||+++.+++
T Consensus 80 Egvn~~Kk~gk~~e~PIh~SNV~iv~l~l~~~R~~~l~~k~~~~~ 124 (143)
T PTZ00194 80 EKITREKANGEPVQIGIHPSNVIITKLKLNKDRKAILERKARSTK 124 (143)
T ss_pred eCeEEEecCCCEeecCcCchheEEEccccCchHHHHHhhhhhhhh
Confidence 999999999999999999999999999999999999999876653
No 2
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=100.00 E-value=9.9e-50 Score=299.09 Aligned_cols=117 Identities=51% Similarity=0.834 Sum_probs=113.4
Q ss_pred cccCCcccccccccCCCCccceeeeeccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeee
Q psy10530 19 LVTSSRRKNRKRHFNAPSHIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKI 98 (141)
Q Consensus 19 ~vss~~rKqRK~~~nAp~h~r~k~msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgv 98 (141)
+||||||||||++|+||+|+|+++||||||+|||++||+|+++|++||+|+|++|+|||++ |+|++|++++++|+||||
T Consensus 3 ~~s~~~rK~Rk~~f~a~~~~r~k~msa~LSkeLr~~y~ir~~~IkkGD~V~VisG~~KGk~-GkV~~V~~~~~~V~VeGv 81 (120)
T PRK01191 3 TMSKQPRKQRKALYNAPLHLRQKLMSAPLSKELREKYGIRSLPVRKGDTVKVMRGDFKGEE-GKVVEVDLKRGRIYVEGV 81 (120)
T ss_pred cccCCchHHHHHhhcCCHHHHHHHhcCccCHHHHHHhCCccceEeCCCEEEEeecCCCCce-EEEEEEEcCCCEEEEeCc
Confidence 5899999999999999999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred eEeccCCcEEEecccccceEEEeCCC-ChhHHHHhhhhh
Q psy10530 99 QRDKVNGATVYVGIHPSKCVIVKLKM-DKDRKKIIERRA 136 (141)
Q Consensus 99 n~~K~~G~~v~~pIhpSNV~i~~l~l-dk~R~k~Le~k~ 136 (141)
|+.+++|.++|+|||+|||+|+||+| |++|++.|++++
T Consensus 82 n~~k~~G~~~e~pIh~SNV~l~~l~l~~~~R~~~l~~~~ 120 (120)
T PRK01191 82 TVKKADGTEVPRPIHPSNVMITKLDLSDERREKILERRA 120 (120)
T ss_pred EEECCCCeEEEcccchhHeEEEeCccCCHHHHHHhhccC
Confidence 99999999999999999999999999 558999998764
No 3
>KOG3401|consensus
Probab=100.00 E-value=3e-50 Score=309.04 Aligned_cols=128 Identities=78% Similarity=1.172 Sum_probs=124.7
Q ss_pred eeecccccCCcccccccccCCCCccceeeeeccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccCCEE
Q psy10530 14 MKLNKLVTSSRRKNRKRHFNAPSHIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVI 93 (141)
Q Consensus 14 mk~~~~vss~~rKqRK~~~nAp~h~r~k~msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V 93 (141)
|||||||||+||||||+||+||+|+||++||||||+|||++||+|+|||+.+|+|.|.+|.++|.++|+|++||++++.|
T Consensus 1 mk~np~vtS~r~k~rK~hF~aps~~rR~i~sa~ls~eLR~~y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~i 80 (145)
T KOG3401|consen 1 MKFNPFVTSDRRKNRKAHFNAPSHIRRKIMSAPLSKELRQKYNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVI 80 (145)
T ss_pred CCCCcccccchhhhhHhhcCCcHHHHHHHhcchhhHHHHHHhCccccceeeccEEEEEeccccccccceehhhhhhhhee
Confidence 89999999999999999999999999999999999999999999999999999999999999994449999999999999
Q ss_pred EEeeeeEeccCCcEEEecccccceEEEeCCCChhHHHHhhhhhhcccC
Q psy10530 94 YIEKIQRDKVNGATVYVGIHPSKCVIVKLKMDKDRKKIIERRAKGRAA 141 (141)
Q Consensus 94 ~VEgvn~~K~~G~~v~~pIhpSNV~i~~l~ldk~R~k~Le~k~~~~~~ 141 (141)
+||.|..+|+||+.+++|||||+|+||.|.||+||+++||++++++|+
T Consensus 81 yie~v~~eK~nGt~v~vgihPsK~~iTkl~lDkdrkkl~erk~k~~qv 128 (145)
T KOG3401|consen 81 YIERVQREKANGTTVPVGIHPSKVVITKLKLDKDRKKLLERKAKSRQV 128 (145)
T ss_pred eeEeEEEeeccCcccccccCccceeecccchhhHHHHHHHHHHhhhhh
Confidence 999999999999999999999999999999999999999999998864
No 4
>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=100.00 E-value=8.6e-47 Score=281.02 Aligned_cols=113 Identities=54% Similarity=0.917 Sum_probs=110.4
Q ss_pred cCCcccccccccCCCCccceeeeeccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeE
Q psy10530 21 TSSRRKNRKRHFNAPSHIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQR 100 (141)
Q Consensus 21 ss~~rKqRK~~~nAp~h~r~k~msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~ 100 (141)
|||||||||++|+||+|+|+++|+||||+|||++|++++++|++||+|+|++|+|||++ |+|++|++++++|+|||||+
T Consensus 1 s~~~rK~Rk~~~~a~~~~r~~~~~a~ls~elr~~y~~r~~~IkkGD~V~Vi~Gk~KGk~-GkV~~V~~~~~~V~Vegvn~ 79 (114)
T TIGR01080 1 SKQPRKQRKALFTAPLHVRRKLMSAPLSKELREKYGKRALPVRKGDKVRIMRGDFKGHE-GKVSKVDLKRYRIYVEGVTK 79 (114)
T ss_pred CCCchhhHHHhhcCcHhhhhheeecccCHHHHHHcCcccceeecCCEEEEecCCCCCCE-EEEEEEEcCCCEEEEcCeEE
Confidence 78999999999999999999999999999999999999999999999999999999999 99999999999999999999
Q ss_pred eccCCcEEEecccccceEEEeCCCChh-HHHHhhh
Q psy10530 101 DKVNGATVYVGIHPSKCVIVKLKMDKD-RKKIIER 134 (141)
Q Consensus 101 ~K~~G~~v~~pIhpSNV~i~~l~ldk~-R~k~Le~ 134 (141)
.|++|.++|+|||||||+|+||+||++ |++.||+
T Consensus 80 ~k~~G~~~e~pIh~SnV~l~~l~l~~~~R~~~l~~ 114 (114)
T TIGR01080 80 EKVNGTEVPVPIHPSNVMITKLNLDDEKRKKIIER 114 (114)
T ss_pred ECCCCeEEEeeechHHeEEEeccCChHHHHHHhcC
Confidence 999999999999999999999999986 8998874
No 5
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=99.86 E-value=3.4e-22 Score=147.07 Aligned_cols=72 Identities=32% Similarity=0.395 Sum_probs=62.6
Q ss_pred cccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCc-----------EEEecccccceEEEeC-CCC
Q psy10530 58 RSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGA-----------TVYVGIHPSKCVIVKL-KMD 125 (141)
Q Consensus 58 rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~-----------~v~~pIhpSNV~i~~l-~ld 125 (141)
++++|++||+|.||+|+|||++ |+|++|+++. |+|||||+.+.++. +.|+|||||||||+++ .++
T Consensus 1 ~~~~IrkGD~V~Vi~GkdKGk~-GkVl~v~~k~--V~VEGvnv~kkh~k~~~~~~~ggii~~EapIh~SnV~i~~~~~~~ 77 (104)
T COG0198 1 MKMKVKKGDTVKVIAGKDKGKE-GKVLKVLPKK--VVVEGVNVVKKHIKPSQENPEGGIINKEAPIHISNVAIIDPNKTG 77 (104)
T ss_pred CCcceecCCEEEEEecCCCCcc-eEEEEEecCe--EEEECcEEEEecCCCCCcCCCCceeeeeecccHHHeEEeccccCC
Confidence 4689999999999999999999 9999999998 99999999987654 4569999999999999 455
Q ss_pred h-hHHHHh
Q psy10530 126 K-DRKKII 132 (141)
Q Consensus 126 k-~R~k~L 132 (141)
+ +|..+.
T Consensus 78 ~~~Rv~~~ 85 (104)
T COG0198 78 KPTRVGYK 85 (104)
T ss_pred CcceEEEE
Confidence 5 674443
No 6
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=99.84 E-value=2e-21 Score=142.56 Aligned_cols=74 Identities=34% Similarity=0.443 Sum_probs=65.0
Q ss_pred ccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEecc---------CC--cEEEecccccceEEEeCCCCh-
Q psy10530 59 SMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKV---------NG--ATVYVGIHPSKCVIVKLKMDK- 126 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~---------~G--~~v~~pIhpSNV~i~~l~ldk- 126 (141)
.++|++||+|+||+|+|||++ |+|++|++++++|+|||||+.+. .| .+.|+|||+|||+|+++.+.+
T Consensus 2 ~~~i~kGD~V~Vi~G~dKGk~-G~V~~V~~~~~~V~Vegvn~~k~h~k~~~~~~~G~i~~~e~pI~~SnV~lv~p~~~~~ 80 (105)
T PRK00004 2 MMKIKKGDTVIVIAGKDKGKR-GKVLKVLPKKNKVIVEGVNIVKKHQKPNQENPQGGIIEKEAPIHISNVALVDPKTGKA 80 (105)
T ss_pred CCcccCCCEEEEeEcCCCCcE-EEEEEEEcCCCEEEEcCcEEEEEecCCCCCCCCCceEEEECCcCHHHEEEEeCcCCCC
Confidence 468999999999999999999 99999999999999999999853 24 478999999999999999976
Q ss_pred hH--HHHhh
Q psy10530 127 DR--KKIIE 133 (141)
Q Consensus 127 ~R--~k~Le 133 (141)
.| .+++|
T Consensus 81 ~rv~~~~~~ 89 (105)
T PRK00004 81 TRVGFKFLE 89 (105)
T ss_pred eEEEEEEcc
Confidence 66 45444
No 7
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=99.84 E-value=5.9e-21 Score=135.13 Aligned_cols=66 Identities=23% Similarity=0.349 Sum_probs=59.2
Q ss_pred ccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEec---------cCC--cEEEecccccceEEEeCCCC
Q psy10530 59 SMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDK---------VNG--ATVYVGIHPSKCVIVKLKMD 125 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K---------~~G--~~v~~pIhpSNV~i~~l~ld 125 (141)
+++|++||+|+|++|+|||++ |+|++|++++++|+|||||+.+ ..| .+.|+|||+|||+|+|+++.
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 KMHVKIGDTVKIISGSDKGKI-GEVLKIIKKSNKVIVKGINIKFKHIKPNKENEVGEIKQFEAPIHSSNVMLYNEESN 82 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcE-EEEEEEEcCCCEEEEcCcEEEEEEcCCccCCCCCCEEEEECCCCHHHEEEeCcccC
Confidence 458999999999999999999 9999999999999999999965 124 35799999999999999874
No 8
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=99.82 E-value=6.7e-21 Score=139.80 Aligned_cols=74 Identities=30% Similarity=0.425 Sum_probs=64.8
Q ss_pred cceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEecc----------CC--cEEEecccccceEEEeCCCCh-
Q psy10530 60 MPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKV----------NG--ATVYVGIHPSKCVIVKLKMDK- 126 (141)
Q Consensus 60 ~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~----------~G--~~v~~pIhpSNV~i~~l~ldk- 126 (141)
++|++||+|+||+|+|||++ |+|++|++++++|+|||+|+.+. .| .+.|+|||+|||+|+++.+++
T Consensus 2 ~~ikkGD~V~Vi~G~dKGK~-G~V~~V~~~~~~V~VegvN~~kkh~k~~~~~~~~g~i~~~e~pI~~SnV~lv~p~~~k~ 80 (104)
T TIGR01079 2 MKIKKGDTVKVISGKDKGKR-GKVLKVLPKTNKVIVEGVNMVKKHVKPKPTQRSQGGIIEKEAPIHISNVMLFDPKTGKA 80 (104)
T ss_pred CcccCCCEEEEeEcCCCCcE-EEEEEEEcCCCEEEECCcEEEEEecCcccCCCCCCceEEEEccCCHHHeEEEcCcCCCC
Confidence 58999999999999999999 99999999999999999999753 23 468999999999999999987
Q ss_pred hH--HHHhhh
Q psy10530 127 DR--KKIIER 134 (141)
Q Consensus 127 ~R--~k~Le~ 134 (141)
.| .+++|+
T Consensus 81 ~rv~~~~~~~ 90 (104)
T TIGR01079 81 TRVGIRFEED 90 (104)
T ss_pred eEEEEEEccC
Confidence 56 555543
No 9
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=99.81 E-value=4.8e-20 Score=128.66 Aligned_cols=61 Identities=34% Similarity=0.452 Sum_probs=54.8
Q ss_pred ccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEec---------cCCc--EEEecccccceEEE
Q psy10530 59 SMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDK---------VNGA--TVYVGIHPSKCVIV 120 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K---------~~G~--~v~~pIhpSNV~i~ 120 (141)
.|+|++||+|+|++|+|||++ |+|++|++++++|+|||||+.+ .+|. +.|+|||+|||+++
T Consensus 4 ~~~I~kGD~V~Vi~G~dKGK~-G~V~~V~~~~~~V~Vegvn~~kkh~kp~~~~~~G~i~~~e~pI~~SnV~l~ 75 (76)
T PRK12281 4 KLKVKKGDMVKVIAGDDKGKT-GKVLAVLPKKNRVIVEGVKIAKKAIKPSQKNPNGGFIEKEMPIHISNVKKV 75 (76)
T ss_pred cccccCCCEEEEeEcCCCCcE-EEEEEEEcCCCEEEEcCcEEEEEEcCCCccCCCCCEEEEEcCcCHHHceec
Confidence 368999999999999999999 9999999999999999999964 2464 45999999999986
No 10
>KOG1708|consensus
Probab=99.42 E-value=2.2e-13 Score=111.02 Aligned_cols=86 Identities=27% Similarity=0.336 Sum_probs=75.1
Q ss_pred cCCCCccceeeeeccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEecc--------
Q psy10530 32 FNAPSHIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKV-------- 103 (141)
Q Consensus 32 ~nAp~h~r~k~msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~-------- 103 (141)
-|-|...|+...++|.+.|-|. +.-||+|+|+.|+|||++ |+|++|.+.+++|+|+|+|....
T Consensus 51 k~~~w~rrr~~~~e~i~d~dw~--------ff~GDtVeVlvGkDkGkq-G~Vtqv~r~~s~VvV~gln~k~r~~gsekeg 121 (236)
T KOG1708|consen 51 KNKPWERRRCVPVEPIIDEDWH--------FFFGDTVEVLVGKDKGKQ-GEVTQVIRHRSWVVVKGLNTKYRHMGSEKEG 121 (236)
T ss_pred hcCccccccCCCCCCcccccee--------EecCCEEEEEecccCCcc-ceEEEEeecCceEEEcccchhhhhhcccccC
Confidence 4667788899999999987776 999999999999999999 99999999999999999998631
Q ss_pred -CCc--EEEecccccc-eEEEeCCCCh
Q psy10530 104 -NGA--TVYVGIHPSK-CVIVKLKMDK 126 (141)
Q Consensus 104 -~G~--~v~~pIhpSN-V~i~~l~ldk 126 (141)
.|+ ..|+|||.|| |+|++++-+.
T Consensus 122 ~pgtivk~EaPlhvsk~VmLvdp~d~q 148 (236)
T KOG1708|consen 122 EPGTIVKSEAPLHVSKQVMLVDPEDDQ 148 (236)
T ss_pred CCceEEeecCCceecceeEEECccccC
Confidence 244 4589999999 9999998766
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=98.75 E-value=1.9e-08 Score=59.21 Aligned_cols=32 Identities=38% Similarity=0.642 Sum_probs=30.5
Q ss_pred cCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 64 KDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 64 kGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
+||.|.|++|+|+|.. |+|++|++++.+|+||
T Consensus 1 ~Gd~V~V~~G~~~G~~-G~I~~i~~~~~~V~ve 32 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKI-GKIVEIDRSKVRVTVE 32 (32)
T ss_dssp TTSEEEESSSTTTTEE-EEEEEEETTTTEEEES
T ss_pred CCCEEEEeEcCCCCce-EEEEEEECCCCEEEEC
Confidence 5999999999999999 9999999999999986
No 12
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.69 E-value=6.2e-05 Score=41.62 Aligned_cols=27 Identities=33% Similarity=0.569 Sum_probs=24.5
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEc
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYR 88 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~r 88 (141)
++..||.|+|+.|.|+|.. |.|++++.
T Consensus 1 ~~~~G~~V~I~~G~~~g~~-g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKV-GKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcE-EEEEEEcC
Confidence 3678999999999999999 99999875
No 13
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=97.62 E-value=0.0003 Score=54.12 Aligned_cols=73 Identities=22% Similarity=0.340 Sum_probs=51.7
Q ss_pred eeeccCCHHHHHhhCC---cccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEE--ecccccc
Q psy10530 42 IMSAPLSKELRQKYNV---RSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVY--VGIHPSK 116 (141)
Q Consensus 42 ~msapLSkeLr~ky~~---rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~--~pIhpSN 116 (141)
++..||+.+--+..-- ....++.||.|.|+.|.|+|.. |.|..++..+..+.|+-+ |..++ +-|+.+-
T Consensus 72 ~lg~~l~~~Ei~~il~~~~~~~~~~~G~~V~I~~Gpf~g~~-g~V~~vd~~k~~v~v~ll------~~~~~~pv~v~~~~ 144 (153)
T PRK08559 72 VVPGEISFEEVEHFLKPKPIVEGIKEGDIVELIAGPFKGEK-ARVVRVDESKEEVTVELL------EAAVPIPVTVRGDQ 144 (153)
T ss_pred eCCCCCCHHHHHHHHhccCcccCCCCCCEEEEeccCCCCce-EEEEEEcCCCCEEEEEEE------CCcceeeEEEeccE
Confidence 3345777765443321 2356899999999999999999 999999999999999988 44333 4444444
Q ss_pred eEEEe
Q psy10530 117 CVIVK 121 (141)
Q Consensus 117 V~i~~ 121 (141)
|.+++
T Consensus 145 ~~~~~ 149 (153)
T PRK08559 145 VRVVK 149 (153)
T ss_pred EEEec
Confidence 54443
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=97.55 E-value=0.00033 Score=52.74 Aligned_cols=74 Identities=19% Similarity=0.363 Sum_probs=50.8
Q ss_pred eeccCCHHHHHhhCCc-c--cceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEEecccccceEE
Q psy10530 43 MSAPLSKELRQKYNVR-S--MPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKCVI 119 (141)
Q Consensus 43 msapLSkeLr~ky~~r-s--~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~~pIhpSNV~i 119 (141)
+.++|+.+.-+..-.. . -.++.||.|.|++|.|+|-+ |.|..++..+..+.|+-++. +...++-+..+.|..
T Consensus 65 v~~~i~~~ei~~l~~~~~~~~~~~~Gd~V~I~~GPf~G~~-g~v~~~d~~k~~v~v~l~~~----~~~~~v~v~~~~l~~ 139 (145)
T TIGR00405 65 VEGEIDFEEIERFLTPKKIIESIKKGDIVEIISGPFKGER-AKVIRVDESKEEVTLELIEA----AVPIPVTVKGDQVRI 139 (145)
T ss_pred cCCCCCHHHHHHHhcccccccccCCCCEEEEeecCCCCCe-EEEEEEcCCCCEEEEEEEEc----CccceEEEeeeEEEE
Confidence 3466777654444211 1 23789999999999999999 99999998888999987743 333333444555544
Q ss_pred Ee
Q psy10530 120 VK 121 (141)
Q Consensus 120 ~~ 121 (141)
.+
T Consensus 140 ~~ 141 (145)
T TIGR00405 140 IQ 141 (145)
T ss_pred ec
Confidence 43
No 15
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=96.98 E-value=0.0014 Score=50.48 Aligned_cols=37 Identities=16% Similarity=0.230 Sum_probs=32.4
Q ss_pred ccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 59 SMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
+..++.||.|.|+.|.++|-+ |.|.++++.+.++.|+
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~-g~v~~i~~~~~r~~v~ 160 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFN-GTVEEVDYEKSKLKVL 160 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCE-EEEEEEeCCCCEEEEE
Confidence 456889999999999999999 9999999877777664
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=96.97 E-value=0.0014 Score=50.29 Aligned_cols=36 Identities=17% Similarity=0.253 Sum_probs=31.8
Q ss_pred cceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 60 MPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 60 ~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
..++.||.|.|+.|.++|-+ |.|.+++..+.++.|.
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~-g~v~~~~~~~~r~~V~ 153 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFT-GTVEEVDYEKSKLKVS 153 (172)
T ss_pred cCCCCCCEEEEeecCCCCcE-EEEEEEcCCCCEEEEE
Confidence 45889999999999999999 9999999877777665
No 17
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=96.89 E-value=0.0024 Score=50.79 Aligned_cols=36 Identities=22% Similarity=0.359 Sum_probs=33.6
Q ss_pred cceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 60 MPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 60 ~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
.-+..||.|.|++|.|+|-. |+|..||.++.++.|+
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~-g~V~evd~ek~~~~v~ 157 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFK-AKVEEVDEEKGKLKVE 157 (178)
T ss_pred ccCCCCCEEEEeccCCCCcc-EEEEEEcCcCcEEEEE
Confidence 56899999999999999999 9999999999988876
No 18
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=96.22 E-value=0.0096 Score=44.92 Aligned_cols=35 Identities=14% Similarity=0.184 Sum_probs=29.2
Q ss_pred cceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 60 MPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 60 ~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
..++.||.|.|+.|.++|-+ |.|.+++.+ .++.|.
T Consensus 107 ~~~~~G~~V~V~~GPf~g~~-g~v~~~~~~-~r~~v~ 141 (159)
T TIGR01955 107 TLPYKGDKVRITDGAFAGFE-AIFLEPDGE-KRSMLL 141 (159)
T ss_pred cCCCCCCEEEEeccCCCCcE-EEEEEECCC-ceEEEE
Confidence 34789999999999999999 999999844 465553
No 19
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=96.16 E-value=0.012 Score=49.65 Aligned_cols=54 Identities=24% Similarity=0.343 Sum_probs=39.6
Q ss_pred ccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEEecccccce
Q psy10530 59 SMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKC 117 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~~pIhpSNV 117 (141)
.+.+..||.|.|+.|.|+|-+ |.|..++..+.++.|. | .-=|...++-+..+.|
T Consensus 203 ~~~f~vGd~VrI~dGPF~Gfe-G~I~eid~~k~Rv~Vl-V---~IfGR~TpVeL~~~qV 256 (258)
T TIGR01956 203 LSKFRVGNFVKIVDGPFKGIV-GKIKKIDQEKKKAIVE-V---EILGKSVDVDLNFKHL 256 (258)
T ss_pred ccCCCCCCEEEEEecCCCCcE-EEEEEEeCCCCEEEEE-E---EecCCcEEEEEchHHE
Confidence 456889999999999999999 9999999877777765 1 1125544444444444
No 20
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=96.07 E-value=0.011 Score=45.04 Aligned_cols=51 Identities=12% Similarity=0.141 Sum_probs=35.5
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEEecccccce
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKC 117 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~~pIhpSNV 117 (141)
.++.||.|.|+.|.++|-+ |.|.+++. +.++.|. ..-=|..+++-+..++|
T Consensus 109 ~~~~G~~V~I~~Gp~~g~e-g~v~~~~~-~~r~~v~----v~~~gr~~~v~v~~~~~ 159 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQ-AIYTEPDG-EARSILL----LNLLNKQVKHSVDNTQF 159 (162)
T ss_pred CCCCCCEEEEecCCCCCcE-EEEEEeCC-CeEEEEe----ehhhCCcEEEEECHHHe
Confidence 4789999999999999999 99999984 4555543 11114444444445544
No 21
>KOG1999|consensus
Probab=92.52 E-value=0.14 Score=50.20 Aligned_cols=34 Identities=35% Similarity=0.608 Sum_probs=29.6
Q ss_pred CHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEcc
Q psy10530 48 SKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRK 89 (141)
Q Consensus 48 SkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rk 89 (141)
+.|||+. ++.||-|+||+|.|+|.+ |-|++|+..
T Consensus 453 ~~eLrKy-------F~~GDhVKVi~G~~eG~t-GlVvrVe~~ 486 (1024)
T KOG1999|consen 453 ASELRKY-------FEPGDHVKVIAGRYEGDT-GLVVRVEQG 486 (1024)
T ss_pred hHhhhhh-------ccCCCeEEEEeccccCCc-ceEEEEeCC
Confidence 4577663 679999999999999999 999999984
No 22
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=90.59 E-value=0.67 Score=42.79 Aligned_cols=84 Identities=21% Similarity=0.311 Sum_probs=57.7
Q ss_pred eeccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEEecccccceEEEeC
Q psy10530 43 MSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKCVIVKL 122 (141)
Q Consensus 43 msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~~pIhpSNV~i~~l 122 (141)
|--|-+.+|.++-+-|-.- -|-+|+|-+|.|||+- |.|..|++...+|-+. -..+.+-|.-||+.++.-
T Consensus 335 ~~~p~~~~l~r~i~gRd~a--igktVrIr~g~yKG~l-GVVKdv~~~~arVeLh--------s~nK~VTI~K~~l~y~~r 403 (607)
T COG5164 335 LQNPKTNELERKIVGRDPA--IGKTVRIRCGEYKGHL-GVVKDVDRNIARVELH--------SNNKFVTIEKSRLAYLGR 403 (607)
T ss_pred CCCCcchhhhccccccccc--cCceEEEeeccccccc-ceeeeccCceEEEEEe--------cCCceEEeehhheEEecc
Confidence 3456678888877555544 4779999999999999 9999999987666543 233456677778777664
Q ss_pred CCCh-hHHHHhhhhhh
Q psy10530 123 KMDK-DRKKIIERRAK 137 (141)
Q Consensus 123 ~ldk-~R~k~Le~k~~ 137 (141)
.-.- .-.++++|+..
T Consensus 404 eGe~ity~e~vnr~~~ 419 (607)
T COG5164 404 EGEGITYDELVNRRGL 419 (607)
T ss_pred cccccchhhhhhhhcC
Confidence 3321 33556666543
No 23
>KOG3401|consensus
Probab=88.66 E-value=0.085 Score=41.28 Aligned_cols=63 Identities=21% Similarity=0.208 Sum_probs=50.1
Q ss_pred ccccCCcccccccccCCCCccceeeeeccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceE
Q psy10530 18 KLVTSSRRKNRKRHFNAPSHIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKV 83 (141)
Q Consensus 18 ~~vss~~rKqRK~~~nAp~h~r~k~msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV 83 (141)
+..--++-|....++++|.|..-..|+.|+.+++|++...| ..++-+|.+..|.+|+.+++++
T Consensus 81 yie~v~~eK~nGt~v~vgihPsK~~iTkl~lDkdrkkl~er---k~k~~qvg~~~g~~K~~qi~~~ 143 (145)
T KOG3401|consen 81 YIERVQREKANGTTVPVGIHPSKVVITKLKLDKDRKKLLER---KAKSRQVGKEQGKYKFEQIEKM 143 (145)
T ss_pred eeEeEEEeeccCcccccccCccceeecccchhhHHHHHHHH---HHhhhhhhhhcCccchhhhhhc
Confidence 44456778999999999999999999999999999988733 3344456666899999886654
No 24
>PRK04333 50S ribosomal protein L14e; Validated
Probab=88.36 E-value=1 Score=32.02 Aligned_cols=60 Identities=12% Similarity=0.056 Sum_probs=44.4
Q ss_pred cceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEEecccccceEEEeCCCC
Q psy10530 60 MPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKCVIVKLKMD 125 (141)
Q Consensus 60 ~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~~pIhpSNV~i~~l~ld 125 (141)
+.|..|-.|.+..|.|+|+. ..|+.+.- .+.|+|+|--. .| ..+-.++...|.+|+..++
T Consensus 2 ~~v~~GrvV~~~~Grd~gk~-~vIv~i~d-~~~vlVdg~~~---~~-~~rk~kn~khl~lt~~ki~ 61 (84)
T PRK04333 2 PAIEVGRVCVKTAGREAGRK-CVIVDIID-KNFVLVTGPSL---TG-VKRRRCNIKHLEPTDKKVD 61 (84)
T ss_pred CcccccEEEEEeccCCCCCE-EEEEEEec-CCEEEEECCCc---CC-CCCeeechHHEEEeeEEEE
Confidence 35788999999999999999 89998865 47888886522 12 3445677777888776553
No 25
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=81.23 E-value=2.9 Score=32.45 Aligned_cols=38 Identities=21% Similarity=0.414 Sum_probs=32.8
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccC------CEEEEeeeeE
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKK------FVIYIEKIQR 100 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk------~~V~VEgvn~ 100 (141)
++.|-.|.|++|.|.|+. ..|++.+.+. +...|-||..
T Consensus 5 ~kpgkVVivL~GR~AGkK-aVivk~~ddgt~drpy~halVaGIdr 48 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRK-AVIVQNFDTASKERPYGHALVAGIKK 48 (134)
T ss_pred ccCCEEEEEEccccCCcE-EEEEeecCCCCccCcCceEEEEeecc
Confidence 568899999999999999 8998887664 6899999875
No 26
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=80.54 E-value=2.1 Score=30.00 Aligned_cols=29 Identities=17% Similarity=0.415 Sum_probs=25.4
Q ss_pred cCCHHHHHhhCCcccceecCCeEEEeecCCCCee
Q psy10530 46 PLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQ 79 (141)
Q Consensus 46 pLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~ 79 (141)
.+++|+|+.+| |+.||.|.++...+.|..
T Consensus 17 vIPkeiR~~lg-----i~~Gd~lei~~~~~~~~i 45 (89)
T COG2002 17 VIPKEIREALG-----IKEGDVLEIIVDGDGGRI 45 (89)
T ss_pred EecHHHHHHhC-----CCCCCEEEEEEeCCCCEE
Confidence 47899999999 899999999999888763
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=80.39 E-value=15 Score=27.61 Aligned_cols=78 Identities=21% Similarity=0.213 Sum_probs=45.4
Q ss_pred HHHHHhhCCcccc-eecCCeEEEeecC---CCCe---eeceEEEEEccC--CEEEEeeeeEeccCCcEEEecccccceEE
Q psy10530 49 KELRQKYNVRSMP-VRKDDEVQVVRGH---YKGQ---QVGKVVQSYRKK--FVIYIEKIQRDKVNGATVYVGIHPSKCVI 119 (141)
Q Consensus 49 keLr~ky~~rs~~-IrkGD~V~Vi~G~---~KGk---~~GkV~~V~rkk--~~V~VEgvn~~K~~G~~v~~pIhpSNV~i 119 (141)
+++.+++-.+.+| ++.||+|.|-.=- .|.. -.|.|+.+.... ..+.|..+ ...-|.+.-+|+|..++.=
T Consensus 5 ~~~e~~~~~~~ip~f~~GD~v~V~~~i~eg~k~R~q~f~GvvI~~~~~G~~~tftvR~i--~~gvGVEr~fpl~SP~I~~ 82 (113)
T TIGR01024 5 KQIEQEQLKKDLPDFRVGDTVRVHVKIVEGKKERIQVFEGVVIARRGGGIGETFTVRKI--SYGVGVERIFPLHSPNIDS 82 (113)
T ss_pred HHHHHHHhhcCCCccCCCCEEEEEEEEccCCceEcccEEEEEEEEeCCCCceEEEEEEe--ccCccEEEEEEcCCCccce
Confidence 3444555455665 8999999984322 2211 148888886543 24555544 2223567779999988764
Q ss_pred EeC-CCChhH
Q psy10530 120 VKL-KMDKDR 128 (141)
Q Consensus 120 ~~l-~ldk~R 128 (141)
++. ...+.|
T Consensus 83 IeVl~~~kvr 92 (113)
T TIGR01024 83 IEVVRRGKVR 92 (113)
T ss_pred EEEEEeCccc
Confidence 443 335533
No 28
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=79.79 E-value=3.9 Score=31.50 Aligned_cols=57 Identities=12% Similarity=0.116 Sum_probs=42.0
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEEecccccceEEEeCCC
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKCVIVKLKM 124 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~~pIhpSNV~i~~l~l 124 (141)
|..|=.|.|..|+++|+. ..|+.|.- .++|.|+|=. ..|... --|+..++.+|++.+
T Consensus 8 VEiGRVvli~~Gp~~GKL-~vIVDIID-~nRvLVDGP~---~tgV~R-q~i~~k~l~LT~~~v 64 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKL-CFIVDIVT-PTRVLVDGAF---ITGVKR-QSIPLKRLKLTDEKI 64 (130)
T ss_pred eeeceEEEEecCCCCCCE-EEEEEEEc-CCeEEEeCCC---cCCcce-eEEeccceEEccEEE
Confidence 678989999999999999 89999876 4799999751 113111 236667788877766
No 29
>CHL00084 rpl19 ribosomal protein L19
Probab=79.07 E-value=8.2 Score=29.13 Aligned_cols=79 Identities=24% Similarity=0.352 Sum_probs=46.1
Q ss_pred CCHHHHHhhCCcccc-eecCCeEEEee----cCCCCe---eeceEEEEEccC--CEEEEeeeeEeccCCcEEEecccccc
Q psy10530 47 LSKELRQKYNVRSMP-VRKDDEVQVVR----GHYKGQ---QVGKVVQSYRKK--FVIYIEKIQRDKVNGATVYVGIHPSK 116 (141)
Q Consensus 47 LSkeLr~ky~~rs~~-IrkGD~V~Vi~----G~~KGk---~~GkV~~V~rkk--~~V~VEgvn~~K~~G~~v~~pIhpSN 116 (141)
|-.++-+.+-...+| ++.||+|.|-- |. |.. -.|.|+.+.... ..+.|..+ ...-|.+.-+|+|..+
T Consensus 7 ~i~~~~~~~~~~~~p~f~~GDtV~V~~~i~eg~-k~R~q~F~GvvI~~r~~G~~~tftvRki--~~gvGVEr~fpl~SP~ 83 (117)
T CHL00084 7 LVKEIESEFLKKNLPKIRVGDTVKVGVLIQEGN-KERVQFYEGTVIAKKNSGLNTTITVRKV--FQGIGVERVFLLHSPK 83 (117)
T ss_pred HHHHHHHHHhhcCCCccCCCCEEEEEEEEecCC-eeEeceEEEEEEEEeCCCCCeeEEEEEe--ccCccEEEEEecCCCc
Confidence 445555555545564 89999999844 43 211 138888875432 24555544 2223567778999988
Q ss_pred eEEEeC-CCChhH
Q psy10530 117 CVIVKL-KMDKDR 128 (141)
Q Consensus 117 V~i~~l-~ldk~R 128 (141)
+.=++. ...+.|
T Consensus 84 I~~IeV~r~gkvR 96 (117)
T CHL00084 84 LASIEVLRRSKVR 96 (117)
T ss_pred cceEEEEEeCccc
Confidence 864443 334533
No 30
>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=76.62 E-value=2.4 Score=26.14 Aligned_cols=25 Identities=28% Similarity=0.500 Sum_probs=19.3
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
-.|++++++++| |+.||+|.+.--.
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 358899999997 7789999887654
No 31
>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=76.05 E-value=8.7 Score=25.42 Aligned_cols=39 Identities=21% Similarity=0.296 Sum_probs=23.0
Q ss_pred eecCCeEEEeecC--CCCee-eceEEEEEccCCEEEEeeeeEe
Q psy10530 62 VRKDDEVQVVRGH--YKGQQ-VGKVVQSYRKKFVIYIEKIQRD 101 (141)
Q Consensus 62 IrkGD~V~Vi~G~--~KGk~-~GkV~~V~rkk~~V~VEgvn~~ 101 (141)
+++||.|+|.+-. +.|-. .|+|++...+. ++.|+=.+..
T Consensus 1 F~~G~~VEV~s~e~g~~gaWf~a~V~~~~~~~-~~~V~Y~~~~ 42 (68)
T PF05641_consen 1 FKKGDEVEVSSDEDGFRGAWFPATVLKENGDD-KYLVEYDDLP 42 (68)
T ss_dssp --TT-EEEEEE-SBTT--EEEEEEEEEEETT--EEEEEETT-S
T ss_pred CCCCCEEEEEEcCCCCCcEEEEEEEEEeCCCc-EEEEEECCcc
Confidence 5799999999844 45655 68999998874 6666543333
No 32
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=75.74 E-value=5.3 Score=29.92 Aligned_cols=30 Identities=27% Similarity=0.386 Sum_probs=25.1
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
+++||+|.-+.|= .|+|..|+.....|.||
T Consensus 37 Lk~GD~VvT~GGi-----~G~V~~I~~~~~~v~le 66 (113)
T PRK06531 37 IQKGDEVVTIGGL-----YGTVDEVDTEAKTIVLD 66 (113)
T ss_pred cCCCCEEEECCCc-----EEEEEEEecCCCEEEEE
Confidence 7899999888776 39999999877788876
No 33
>PF15276 PP1_bind: Protein phosphatase 1 binding
Probab=73.75 E-value=2.3 Score=29.19 Aligned_cols=38 Identities=18% Similarity=0.116 Sum_probs=30.8
Q ss_pred cceeeeeccCCHHHHHhhCCcccceecCCeEEEeecCC
Q psy10530 38 IRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHY 75 (141)
Q Consensus 38 ~r~k~msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~ 75 (141)
.||.-|..+||.||-.+.---+-|+++|++=.--+...
T Consensus 3 rkRVsFG~~LSPElFD~~LPpnTPlkrG~tP~~~~~~~ 40 (64)
T PF15276_consen 3 RKRVSFGEHLSPELFDKSLPPNTPLKRGATPVRRSDPS 40 (64)
T ss_pred cceeccCCCCCHHHhcccCCCCCCcCCCCCcccccCCC
Confidence 36778899999999999999999999999754444433
No 34
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=73.65 E-value=5.6 Score=30.34 Aligned_cols=35 Identities=17% Similarity=0.283 Sum_probs=29.8
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeee
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKI 98 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgv 98 (141)
+..|-.|.|++|.|.|+. ..|+++.-++ .++|.|-
T Consensus 5 l~~GrVvvv~~GR~aGkk-~VIv~~iDd~-~v~i~gp 39 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKK-VVIVKIIDDN-FVLITGP 39 (125)
T ss_pred ccCCeEEEEecceeCCce-EEEEEEccCC-EEEEeCC
Confidence 678999999999999999 8888887765 8888763
No 35
>PLN00190 60S ribosomal protein L21; Provisional
Probab=73.18 E-value=9.4 Score=30.33 Aligned_cols=44 Identities=25% Similarity=0.423 Sum_probs=33.6
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEee-c---------CCCCeeeceEEEEEccCCEEEEe
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVR-G---------HYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~-G---------~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
..|||.-|+. .+.||.|-|.- | .|-|++ |.|..|...-.-|.|.
T Consensus 24 ~~pls~~l~~--------yk~GD~VdIk~~~svqKGMPhk~YHGkT-G~V~nv~~~A~gV~V~ 77 (158)
T PLN00190 24 YIPLTTYLRT--------FKVGDYVDIKVNGAIHKGMPHKFYHGRT-GIVWNVTKRAVGVEVN 77 (158)
T ss_pred CCcHHHHHHH--------hcCCCEEEEEecCCeecCCCcccccCCC-eEEEeecCcEEEEEEE
Confidence 5899999998 78999987763 2 366898 9999998765555543
No 36
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=69.50 E-value=7.7 Score=28.35 Aligned_cols=28 Identities=32% Similarity=0.452 Sum_probs=21.8
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
+++||+|.-+.|= . |+|++|.... +.|+
T Consensus 44 L~kGD~VvT~gGi----~-G~V~~v~d~~--v~I~ 71 (97)
T COG1862 44 LKKGDEVVTIGGI----V-GTVTKVGDDT--VEIE 71 (97)
T ss_pred ccCCCEEEEcCCe----E-EEEEEEecCc--EEEE
Confidence 7899999888765 4 9999998764 4443
No 37
>KOG1999|consensus
Probab=68.85 E-value=3.8 Score=40.58 Aligned_cols=29 Identities=38% Similarity=0.675 Sum_probs=26.7
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccC
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKK 90 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk 90 (141)
-|+.+|.|+||.|+.+|++ |.|+.+++--
T Consensus 581 ~I~~kD~Vkvi~Gp~~g~~-G~v~~i~r~~ 609 (1024)
T KOG1999|consen 581 EIRVKDTVKVIGGPSKGRE-GEVLHIYRPF 609 (1024)
T ss_pred eecccceEEEecCCCCCcc-Cccceeecce
Confidence 3899999999999999999 9999999863
No 38
>PRK04313 30S ribosomal protein S4e; Validated
Probab=68.38 E-value=9.2 Score=32.09 Aligned_cols=56 Identities=14% Similarity=0.250 Sum_probs=41.5
Q ss_pred cccceecCCeEEEeecCCCCeeeceEEEEEccC----CEEEEeeeeEeccCCcEEEecccccceEEEe
Q psy10530 58 RSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK----FVIYIEKIQRDKVNGATVYVGIHPSKCVIVK 121 (141)
Q Consensus 58 rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk----~~V~VEgvn~~K~~G~~v~~pIhpSNV~i~~ 121 (141)
-.++...|..|.|+.|.+-|.. |+|..+.... +.|+||+ ++|.+++ ...+||+++.
T Consensus 168 ~~i~fe~G~l~~itgG~n~Gri-G~I~~i~~~~~~~~~~V~i~d-----~~G~~F~--T~~~~vfvIG 227 (237)
T PRK04313 168 DHIPFEEGNLAIITGGKHVGEI-GKIKEIEVTKSSKPNIVTLED-----KDGEKFE--TILDYVFVIG 227 (237)
T ss_pred EEEecCCCCEEEEECCeeeeeE-EEEEEEEEccCCCCcEEEEEc-----CCCCEEE--EEeeeEEEEc
Confidence 3568899999999999999999 9999997554 5677763 3565433 3446777765
No 39
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=68.08 E-value=9.6 Score=27.98 Aligned_cols=28 Identities=36% Similarity=0.439 Sum_probs=22.9
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
+++||+|.-+.|= .|+|+.|+. ..|.||
T Consensus 53 Lk~Gd~VvT~gGi-----~G~Vv~i~~--~~v~le 80 (106)
T PRK05585 53 LAKGDEVVTNGGI-----IGKVTKVSE--DFVIIE 80 (106)
T ss_pred cCCCCEEEECCCe-----EEEEEEEeC--CEEEEE
Confidence 7899999999876 399999975 567665
No 40
>KOG1728|consensus
Probab=67.41 E-value=3.4 Score=32.58 Aligned_cols=26 Identities=31% Similarity=0.408 Sum_probs=22.9
Q ss_pred ccceeeeeccCCHHHHHhhCCcccceecCCeEEE
Q psy10530 37 HIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQV 70 (141)
Q Consensus 37 h~r~k~msapLSkeLr~ky~~rs~~IrkGD~V~V 70 (141)
..|++-||+++|+-+|. |..||.|.|
T Consensus 101 ekrHkN~svh~SPcFrd--------i~~gDiVtv 126 (156)
T KOG1728|consen 101 EKRHKNMSVHVSPCFRD--------IQEGDIVTV 126 (156)
T ss_pred HHhccCCccccchhhhc--------cccCCEEEE
Confidence 56889999999999887 999999876
No 41
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=66.22 E-value=12 Score=27.44 Aligned_cols=43 Identities=26% Similarity=0.581 Sum_probs=32.4
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEee-cC---------CCCeeeceEEEEEccCCEEEE
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVR-GH---------YKGQQVGKVVQSYRKKFVIYI 95 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~-G~---------~KGk~~GkV~~V~rkk~~V~V 95 (141)
..|||.-|++ .+.||.|-|.- |. |-|++ |.|..+...-+.|.|
T Consensus 25 ~~~ls~~l~~--------y~~Gd~V~I~~d~sv~kGmPh~~yhGkT-G~V~~v~~~A~~V~v 77 (98)
T PRK04306 25 LSPLSRALQE--------FEEGDKVHIVIDPSVHKGMPHPRFHGKT-GTVVGKRGRAYIVEV 77 (98)
T ss_pred CCcHHHHHHh--------ccCCCEEEEEecCceecCCccccccCCC-EEEEeecCeEEEEEE
Confidence 3679999998 78999887653 22 45888 999999877655555
No 42
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=66.15 E-value=4.7 Score=27.84 Aligned_cols=22 Identities=23% Similarity=0.406 Sum_probs=16.4
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEe
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVV 71 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi 71 (141)
=||++++|++-| +..||+|.|-
T Consensus 58 Lpv~~~vRk~~g-----~~~Gd~V~v~ 79 (80)
T PF08922_consen 58 LPVKAAVRKAIG-----KEAGDTVEVT 79 (80)
T ss_dssp EEE-HHHHHHHT-------TTSEEEEE
T ss_pred EEEcHHHHHHcC-----CCCCCEEEEE
Confidence 589999999877 7899999873
No 43
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=66.14 E-value=15 Score=26.65 Aligned_cols=52 Identities=12% Similarity=0.132 Sum_probs=35.6
Q ss_pred cCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEEecccccc
Q psy10530 64 KDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSK 116 (141)
Q Consensus 64 kGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~~pIhpSN 116 (141)
-|-.|-+++..+-.-+ |.+..|+...++|.+.+|-.--..|-....+|+|++
T Consensus 7 IGs~ISlisk~~iRYe-G~L~~Id~~~sTItL~nVr~~GtE~R~~~~~ipp~~ 58 (96)
T PF12701_consen 7 IGSKISLISKSDIRYE-GILYSIDTEDSTITLKNVRSFGTEGRPTDREIPPSD 58 (96)
T ss_dssp TTCEEEEEETTTEEEE-EEEEEEETTTTEEEEEEEEETTETTSS-SS---C-C
T ss_pred cCCEEEEEECCCcEEE-EEEEEEcCCCCEEEeeeeeecCcCCCCcCcccCCCC
Confidence 4788999999998888 999999999999999987543222222223555554
No 44
>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=64.60 E-value=13 Score=26.07 Aligned_cols=29 Identities=31% Similarity=0.471 Sum_probs=22.6
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
.+++||+|.-..|= .|+|++++- ..+.||
T Consensus 37 ~L~~Gd~VvT~gGi-----~G~V~~i~d--~~v~ve 65 (84)
T TIGR00739 37 SLKKGDKVLTIGGI-----IGTVTKIAE--NTIVIE 65 (84)
T ss_pred hCCCCCEEEECCCe-----EEEEEEEeC--CEEEEE
Confidence 37899999998876 399999985 455555
No 45
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=63.93 E-value=8 Score=25.92 Aligned_cols=34 Identities=21% Similarity=0.222 Sum_probs=27.0
Q ss_pred ecCCeEEE--eecCCCCeeeceEEEEEccCCEEEEee
Q psy10530 63 RKDDEVQV--VRGHYKGQQVGKVVQSYRKKFVIYIEK 97 (141)
Q Consensus 63 rkGD~V~V--i~G~~KGk~~GkV~~V~rkk~~V~VEg 97 (141)
..||.|.- |=|++|--. |+|.++|....+|++||
T Consensus 22 v~~e~V~a~Dilgd~ke~~-G~vkriDldehkI~lE~ 57 (57)
T COG1532 22 VTEEGVVARDILGDEKEFE-GQVKRIDLDEHKIELEG 57 (57)
T ss_pred EecCcEEEEeccCCceEec-ceEEEEEccccEEEecC
Confidence 35565543 458888887 99999999999999986
No 46
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=63.26 E-value=14 Score=27.57 Aligned_cols=28 Identities=18% Similarity=0.237 Sum_probs=22.8
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
+++||+|.-+.|= .|+|++|+- ..|.||
T Consensus 39 Lk~GD~VvT~gGi-----~G~V~~I~d--~~v~le 66 (109)
T PRK05886 39 LQPGDRVHTTSGL-----QATIVGITD--DTVDLE 66 (109)
T ss_pred cCCCCEEEECCCe-----EEEEEEEeC--CEEEEE
Confidence 7899999988876 399999974 577776
No 47
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=62.49 E-value=6.6 Score=36.52 Aligned_cols=31 Identities=26% Similarity=0.236 Sum_probs=27.0
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccCCEE
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVI 93 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V 93 (141)
..+||-|+||.|.+++.. |.|+.|+..+-..
T Consensus 140 f~~gD~vkVI~g~~~~d~-g~V~rI~~~~vtF 170 (607)
T COG5164 140 FYKGDLVKVIEGGEMVDI-GTVPRIDGEKVTF 170 (607)
T ss_pred cccCCeEEEecccccccc-ceEEEecCceeEE
Confidence 679999999999999999 9999998765433
No 48
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=60.53 E-value=15 Score=25.70 Aligned_cols=30 Identities=20% Similarity=0.450 Sum_probs=23.9
Q ss_pred cceecCCeEEEeecC--CCCeeeceEEEEEccC
Q psy10530 60 MPVRKDDEVQVVRGH--YKGQQVGKVVQSYRKK 90 (141)
Q Consensus 60 ~~IrkGD~V~Vi~G~--~KGk~~GkV~~V~rkk 90 (141)
|-|++||.|.|+|=. +=... |+|..||...
T Consensus 1 m~i~rGskVrIlR~ESYWyn~v-GtV~svD~sg 32 (71)
T PRK02749 1 MAISRGDKVRILRPESYWYNEV-GTVASVDKSG 32 (71)
T ss_pred CccccCCEEEEccccceeecCc-ceEEEEccCC
Confidence 458999999999976 33444 9999999874
No 49
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=59.09 E-value=24 Score=22.27 Aligned_cols=35 Identities=14% Similarity=0.071 Sum_probs=23.5
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
.+++||.|.+..=.+.+=-.|+|+++.. .++..|.
T Consensus 2 ~~~~G~~Ve~~~~~~~~W~~a~V~~~~~-~~~~~V~ 36 (61)
T smart00743 2 DFKKGDRVEVFSKEEDSWWEAVVTKVLG-DGKYLVR 36 (61)
T ss_pred CcCCCCEEEEEECCCCEEEEEEEEEECC-CCEEEEE
Confidence 4689999999974433322599999988 3334443
No 50
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=58.00 E-value=18 Score=26.72 Aligned_cols=44 Identities=23% Similarity=0.447 Sum_probs=33.1
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeec----------CCCCeeeceEEEEEccCCEEEEe
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRG----------HYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G----------~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
.+|||.-|++ .+.||.|-|.-- .|-|++ |.|+.+--.-+.|.|.
T Consensus 23 ~~plsr~l~e--------y~~Gd~V~I~IdpSv~kGmPh~rf~G~T-G~Vvg~~g~ay~V~v~ 76 (98)
T COG2139 23 LSPLSRYLQE--------YKVGDKVHIDIDPSVHKGMPHPRFQGKT-GTVVGVRGRAYKVEVY 76 (98)
T ss_pred CcchhhHHhh--------ccCCCEEEEEeCcccccCCCCccccCcc-eEEEeccCCEEEEEEe
Confidence 6789998888 789999977532 366898 9999887665555554
No 51
>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=57.42 E-value=3.5 Score=28.74 Aligned_cols=29 Identities=28% Similarity=0.441 Sum_probs=0.0
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
.+++||+|.-.+|= .|+|+++ +++.+.+|
T Consensus 36 ~Lk~Gd~VvT~gGi-----~G~V~~i--~~~~v~le 64 (82)
T PF02699_consen 36 SLKPGDEVVTIGGI-----YGTVVEI--DDDTVVLE 64 (82)
T ss_dssp ------------------------------------
T ss_pred cCCCCCEEEECCcE-----EEEEEEE--eCCEEEEE
Confidence 47899999999887 3999999 44566665
No 52
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=57.09 E-value=46 Score=28.41 Aligned_cols=71 Identities=21% Similarity=0.340 Sum_probs=44.9
Q ss_pred cccceecCCeEEEeecCCCCeeeceEEEEEccC---CEEEEeeeeEeccCCcEEEecccccceEEEeC--------CCCh
Q psy10530 58 RSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK---FVIYIEKIQRDKVNGATVYVGIHPSKCVIVKL--------KMDK 126 (141)
Q Consensus 58 rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk---~~V~VEgvn~~K~~G~~v~~pIhpSNV~i~~l--------~ldk 126 (141)
-.+++..|..|.|+.|.+-|.. |+|.++.... +.|+||. ++|.+++- ..+||+++.- --++
T Consensus 171 ~~ikfe~G~l~~vtgG~n~Gri-G~I~~~~~~~~~~~~V~i~d-----~~g~~F~T--~~~~vfvIG~~~kp~islp~~k 242 (262)
T PTZ00118 171 EFLKFEVGNLVMITGGHNVGRV-GTIVSKEKHPGSFDLIHVKD-----SRGKTFAT--RLSNVFVIGVGTKPYVSLPRER 242 (262)
T ss_pred eEEecCCCCEEEEECCeeceeE-EEEEEEEecCCCCcEEEEEe-----CCCCeEEE--EeeeEEEEccCCCeeEeCcCCC
Confidence 3568899999999999999999 9998866543 3555553 45643321 2234444421 2233
Q ss_pred -hHHHHhhhhh
Q psy10530 127 -DRKKIIERRA 136 (141)
Q Consensus 127 -~R~k~Le~k~ 136 (141)
-|..++|.+.
T Consensus 243 gi~~~~~e~~~ 253 (262)
T PTZ00118 243 GIKKDIIEERR 253 (262)
T ss_pred CccccHHHHHH
Confidence 3667777654
No 53
>PTZ00189 60S ribosomal protein L21; Provisional
Probab=56.08 E-value=27 Score=27.78 Aligned_cols=44 Identities=25% Similarity=0.419 Sum_probs=33.0
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEee------c----CCCCeeeceEEEEEccCCEEEEe
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVR------G----HYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~------G----~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
..|||.-|+. .+.||.|-|.- | .|-|++ |.|..|...-.-|+|+
T Consensus 24 ~~pls~~l~~--------yk~GD~VdIk~d~svqkGMPhk~YHGkT-G~V~nv~~~A~gViV~ 77 (160)
T PTZ00189 24 VPSLSTYLTT--------FKVGDYVDIVVDSAVHKGMPYKYYHGRT-GRVFNVTPRAVGVIVN 77 (160)
T ss_pred CCcHHHHHHH--------ccCCCEEEEEecCCeecCCCcccccCCC-eEEEeecCeEEEEEEE
Confidence 4789999998 78999987653 2 245888 9999998765555554
No 54
>PLN00036 40S ribosomal protein S4; Provisional
Probab=56.02 E-value=42 Score=28.64 Aligned_cols=71 Identities=17% Similarity=0.229 Sum_probs=45.9
Q ss_pred cccceecCCeEEEeecCCCCeeeceEEEEEccC---CEEEEeeeeEeccCCcEEEecccccceEEEeC--------CCCh
Q psy10530 58 RSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK---FVIYIEKIQRDKVNGATVYVGIHPSKCVIVKL--------KMDK 126 (141)
Q Consensus 58 rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk---~~V~VEgvn~~K~~G~~v~~pIhpSNV~i~~l--------~ldk 126 (141)
-.++...|..|.|+.|.+-|.. |+|..+.... +.|+|| .++|.+++- ..+||+++.- .-++
T Consensus 171 ~~ikfe~G~l~~vtgG~n~Grv-G~I~~i~~~~~~~~iV~i~-----d~~g~~F~T--~~~~vfvIG~~~kp~isLp~~~ 242 (261)
T PLN00036 171 DFIKFDVGNLVMVTGGRNRGRV-GVIKNREKHKGSFEIIHVK-----DATGHEFAT--RLGNVFVIGKGTKPWISLPKGK 242 (261)
T ss_pred eEEecCCCCEEEEECCeeceeE-EEEEEEEecCCCCCEEEEE-----eCCCCeEEE--EeeeEEEEccCCCeeEeCcCCC
Confidence 3568899999999999999999 9999988443 355655 345644322 2344544422 2233
Q ss_pred -hHHHHhhhhh
Q psy10530 127 -DRKKIIERRA 136 (141)
Q Consensus 127 -~R~k~Le~k~ 136 (141)
-|..++|.+.
T Consensus 243 gi~~~~~e~r~ 253 (261)
T PLN00036 243 GIKLSIIEEAR 253 (261)
T ss_pred CcccchHHHHH
Confidence 3667777654
No 55
>PRK08577 hypothetical protein; Provisional
Probab=56.02 E-value=54 Score=24.18 Aligned_cols=29 Identities=17% Similarity=0.259 Sum_probs=25.1
Q ss_pred cCCHHHHHhhCCcccceecCCeEEEeecCCCCee
Q psy10530 46 PLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQ 79 (141)
Q Consensus 46 pLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~ 79 (141)
.+++|+|+++| |+.||.|.+..-.++|..
T Consensus 16 ~ip~~~r~~l~-----~~~g~~~~~~~~~~~~~~ 44 (136)
T PRK08577 16 TIPLEIREALG-----IREGMYVLLIADTDKKEI 44 (136)
T ss_pred EecHHHHHHcC-----cCCCCEEEEEEECCCCEE
Confidence 57899999888 899999999988778866
No 56
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=55.88 E-value=60 Score=24.44 Aligned_cols=65 Identities=22% Similarity=0.227 Sum_probs=39.0
Q ss_pred ceecCCeEEEee----cCCCCe---eeceEEEEEccC--CEEEEeeeeEeccCCcEEEecccccceEEEeCC-CChhH
Q psy10530 61 PVRKDDEVQVVR----GHYKGQ---QVGKVVQSYRKK--FVIYIEKIQRDKVNGATVYVGIHPSKCVIVKLK-MDKDR 128 (141)
Q Consensus 61 ~IrkGD~V~Vi~----G~~KGk---~~GkV~~V~rkk--~~V~VEgvn~~K~~G~~v~~pIhpSNV~i~~l~-ldk~R 128 (141)
.++.||+|.|-- |. |.. -.|.|+.+.... ..+.|..+ ...-|.+.-+|+|..+|.=++.- .++.|
T Consensus 18 ~f~~GD~V~V~~~i~eg~-k~R~q~f~GvvI~~~~~G~~~tftvRki--~~gvGVEr~fpl~SP~I~~IeV~r~gkvR 92 (116)
T PRK05338 18 EFRPGDTVRVHVKVVEGN-KERIQAFEGVVIARRGRGLNETFTVRKI--SYGVGVERTFPLHSPRIDSIEVVRRGKVR 92 (116)
T ss_pred CcCCCCEEEEEEEEccCC-ceEeccEEEEEEEEeCCCCCceEEEEEc--ccCccEEEEecCCCCcccEEEEEEecccc
Confidence 489999999843 32 221 148888887543 24555544 22235677789999887644432 34533
No 57
>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=54.72 E-value=28 Score=23.33 Aligned_cols=27 Identities=19% Similarity=0.377 Sum_probs=21.1
Q ss_pred ecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 63 RKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 63 rkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
..||.++.- .|-+ |+|.+|+ .+.|+|+
T Consensus 5 ~vGdiIefk----~g~~-G~V~kv~--eNSVIVd 31 (57)
T PF09953_consen 5 KVGDIIEFK----DGFT-GIVEKVY--ENSVIVD 31 (57)
T ss_pred ccCcEEEEc----CCcE-EEEEEEe--cCcEEEE
Confidence 479999862 4677 9999998 4778887
No 58
>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=53.34 E-value=30 Score=22.91 Aligned_cols=40 Identities=25% Similarity=0.269 Sum_probs=28.9
Q ss_pred eecCCeEEEeecC--CCCeeeceEEEEEccCCEEEEeeeeEec
Q psy10530 62 VRKDDEVQVVRGH--YKGQQVGKVVQSYRKKFVIYIEKIQRDK 102 (141)
Q Consensus 62 IrkGD~V~Vi~G~--~KGk~~GkV~~V~rkk~~V~VEgvn~~K 102 (141)
|-.|-.|.|+.-. |-|-+ |.|.+|...+--|..||=|+.|
T Consensus 2 ilPG~~V~V~n~~~~Y~~y~-G~VQRvsdgkaaVLFEGGnWdK 43 (53)
T PF11623_consen 2 ILPGSTVRVKNPNDIYYGYE-GFVQRVSDGKAAVLFEGGNWDK 43 (53)
T ss_dssp --TT-EEEE--TTSTTTT-E-EEEEEEETTEEEEEEEETTEEE
T ss_pred ccCCCEEEEeCCCCccchhe-EEEEEeeCCeEEEEecCCCceE
Confidence 5678899998776 67998 9999999988889999877654
No 59
>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=53.33 E-value=91 Score=23.15 Aligned_cols=71 Identities=15% Similarity=0.168 Sum_probs=42.2
Q ss_pred HHHHhhCCccc-ceecCCeEEEeec---CCCCe---eeceEEEEEccC--CEEEEeeeeEeccCCcEEEecccccceEEE
Q psy10530 50 ELRQKYNVRSM-PVRKDDEVQVVRG---HYKGQ---QVGKVVQSYRKK--FVIYIEKIQRDKVNGATVYVGIHPSKCVIV 120 (141)
Q Consensus 50 eLr~ky~~rs~-~IrkGD~V~Vi~G---~~KGk---~~GkV~~V~rkk--~~V~VEgvn~~K~~G~~v~~pIhpSNV~i~ 120 (141)
++.+.+-...+ .++.||.|.|.-= ..|.. -.|.|+.+.... ..+.|-++ ....|.+.-+|+|...|.=+
T Consensus 6 ~~e~~~~~~~~p~f~~GD~v~V~~~i~e~~k~r~q~f~GvvIa~~~~g~~ssftlR~~--~~g~gVE~~f~l~SP~I~~I 83 (113)
T PF01245_consen 6 EVEREQIKKDIPEFRVGDTVRVTYKISEGNKERIQVFEGVVIARRRRGLNSSFTLRNI--SQGVGVERVFPLYSPLIKSI 83 (113)
T ss_dssp HHHHTTCSSSSSSSSSSSEEEEEEEEESSSSEEEEEEEEEEEEEEBSSTSSEEEEEEE--ETTEEEEEEEETTSTTEEEE
T ss_pred HHHHHHhhcCCCCcCCCCEEEEEEEEecCCCceeEEEEEEEEEEECCCCCeeEEEEEE--ecCccEEEEEEcCCCCeEEE
Confidence 34444333344 5899999988542 22332 148888887754 35555543 22234566789999988654
Q ss_pred eC
Q psy10530 121 KL 122 (141)
Q Consensus 121 ~l 122 (141)
+.
T Consensus 84 eV 85 (113)
T PF01245_consen 84 EV 85 (113)
T ss_dssp EE
T ss_pred EE
Confidence 43
No 60
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=53.33 E-value=21 Score=26.37 Aligned_cols=33 Identities=18% Similarity=0.338 Sum_probs=25.6
Q ss_pred CCcccceecCCeEEEeecC--CCCeeeceEEEEEcc
Q psy10530 56 NVRSMPVRKDDEVQVVRGH--YKGQQVGKVVQSYRK 89 (141)
Q Consensus 56 ~~rs~~IrkGD~V~Vi~G~--~KGk~~GkV~~V~rk 89 (141)
...-+-+++||.|.|+|-. +=... |+|+.||..
T Consensus 34 kpp~ig~~RGskVrIlR~ESYWyn~v-GtVvsVDq~ 68 (101)
T PLN00045 34 KPPPIGPKRGSKVKILRPESYWFNDV-GKVVAVDQD 68 (101)
T ss_pred CCCCcccCCCCEEEEccccceeecCc-ceEEEEeCC
Confidence 3445568999999999976 23444 999999998
No 61
>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=53.02 E-value=25 Score=24.66 Aligned_cols=33 Identities=12% Similarity=0.147 Sum_probs=26.3
Q ss_pred cccceecCCeEEEeecCCCCeeeceEEEEEccC
Q psy10530 58 RSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK 90 (141)
Q Consensus 58 rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk 90 (141)
+++=|+.||-|.|-.-++-.+..|.|+.++.+.
T Consensus 35 k~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~~ 67 (78)
T cd05792 35 KNIWIKRGDFVLVEPIEEGDKVKAEIVKILTRD 67 (78)
T ss_pred ccEEEEeCCEEEEEecccCCceEEEEEEEECHH
Confidence 366799999999998777655559999988764
No 62
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=52.38 E-value=25 Score=30.12 Aligned_cols=55 Identities=16% Similarity=0.285 Sum_probs=38.6
Q ss_pred cccceecCCeEEEeecCCCCeeeceEEEEEccC---CEEEEeeeeEeccCCcEEEecccccceEEE
Q psy10530 58 RSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK---FVIYIEKIQRDKVNGATVYVGIHPSKCVIV 120 (141)
Q Consensus 58 rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk---~~V~VEgvn~~K~~G~~v~~pIhpSNV~i~ 120 (141)
-.++...|..|.|+.|.+-|.. |+|..+.... +.|+++. ++|.+++ ...+||+++
T Consensus 168 ~~ikfe~G~l~~vtgG~n~Gri-G~I~~i~~~~~~~~iv~i~d-----~~g~~F~--T~~~~VfvI 225 (273)
T PTZ00223 168 DLIKNRNGKVVMVTGGANRGRI-GEIVSIERHPGAFDIARLKD-----ASGHEFA--TRAANIFVI 225 (273)
T ss_pred EEEecCCCCEEEEECCeeceeE-EEEEEEEecCCCCCEEEEEe-----CCCCeEE--EEeeeEEEE
Confidence 3678899999999999999999 9999985443 3566653 4554432 234556555
No 63
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=52.21 E-value=26 Score=29.59 Aligned_cols=40 Identities=20% Similarity=0.302 Sum_probs=32.7
Q ss_pred CcccceecCCeEEEeecCCCCeeeceEEEEEccC----CEEEEee
Q psy10530 57 VRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK----FVIYIEK 97 (141)
Q Consensus 57 ~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk----~~V~VEg 97 (141)
+-.+++..|-.|.|+.|.+-|.. |+|..+.... +.|.+|+
T Consensus 169 ~~~i~fe~g~~~~vtgG~h~G~~-G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 169 VEHIKFEEGALVYVTGGRHVGRV-GTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred eeEeccCCCcEEEEECCccccce-EEEEEEEEecCCCccEEEEec
Confidence 34678889999999999999999 9999998764 4666663
No 64
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=51.87 E-value=19 Score=20.95 Aligned_cols=25 Identities=28% Similarity=0.573 Sum_probs=20.4
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
-.|++++++.++ +..||.+.+....
T Consensus 9 i~iP~~~r~~l~-----~~~gd~~~i~~~~ 33 (43)
T TIGR01439 9 IVIPKEIREKLG-----LKEGDRLEVIRVE 33 (43)
T ss_pred EEecHHHHHHcC-----cCCCCEEEEEEeC
Confidence 458899999888 7899999988653
No 65
>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=51.68 E-value=55 Score=26.11 Aligned_cols=42 Identities=14% Similarity=0.245 Sum_probs=29.2
Q ss_pred hhCCcccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 54 KYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 54 ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
.|=++-++++.||.|.|.-|.-.--. ++|..+..+.-.+.+.
T Consensus 9 ~Hl~~VlR~k~Gd~i~v~dg~g~~~~-a~i~~i~~~~~~~~i~ 50 (225)
T PF04452_consen 9 HHLVKVLRLKEGDSIEVFDGDGGEYR-AEITEISKKSATLRIL 50 (225)
T ss_dssp HHHHTTST--TT-EEEEEESSSEEEE-EEEEEEESSEEEEEEE
T ss_pred HHHHHhcCCCCCCEEEEEECCCCEEE-EEEEECcCcEEEEEEe
Confidence 34457789999999999998755455 8999999876655554
No 66
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=51.51 E-value=21 Score=34.25 Aligned_cols=37 Identities=19% Similarity=0.324 Sum_probs=27.2
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEcc-CCEEEEeeeeEe
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRK-KFVIYIEKIQRD 101 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rk-k~~V~VEgvn~~ 101 (141)
+++.||.|.|.+ -|+. |+|++|..+ ...|.+.++.+.
T Consensus 636 ~~~~Gd~V~v~~---~~~~-g~v~~i~~~~~~~V~~g~~k~~ 673 (782)
T PRK00409 636 ELKVGDEVKYLS---LGQK-GEVLSIPDDKEAIVQAGIMKMK 673 (782)
T ss_pred CCCCCCEEEEcc---CCce-EEEEEEcCCCeEEEEECCEEEE
Confidence 489999999976 4677 999999753 335666666653
No 67
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=49.98 E-value=18 Score=24.73 Aligned_cols=28 Identities=18% Similarity=0.400 Sum_probs=22.3
Q ss_pred eecCCeEEEeecC--CCCeeeceEEEEEccC
Q psy10530 62 VRKDDEVQVVRGH--YKGQQVGKVVQSYRKK 90 (141)
Q Consensus 62 IrkGD~V~Vi~G~--~KGk~~GkV~~V~rkk 90 (141)
|++||.|.|+|-. +=... |+|..||...
T Consensus 2 i~rGskVrIlR~ESYWyn~v-GtV~svd~~g 31 (64)
T CHL00125 2 VKRGSKVRILRKESYWYNEI-GTVATVDQSG 31 (64)
T ss_pred cccCCEEEEccccceeecCc-ceEEEEcCCC
Confidence 7899999999976 23444 9999999873
No 68
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=49.79 E-value=34 Score=29.17 Aligned_cols=31 Identities=26% Similarity=0.315 Sum_probs=22.0
Q ss_pred cCCeEEEeecCCCCeeeceEEEEEccCCEEEE
Q psy10530 64 KDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYI 95 (141)
Q Consensus 64 kGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~V 95 (141)
.|.+..|++|+-||.. |.|+.=-=--+.|+|
T Consensus 60 iGN~A~VvSG~AKG~~-G~VtGkHGGieHVlV 90 (258)
T PF14505_consen 60 IGNEAKVVSGDAKGAK-GVVTGKHGGIEHVLV 90 (258)
T ss_dssp BT-EEEE-SSTTTT-E-EEEEEEETTTTEEEE
T ss_pred cCceeEEeecccCCCc-CeEecccCCeeeEEE
Confidence 6899999999999999 999875544445555
No 69
>cd01736 LSm14_N LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.
Probab=48.02 E-value=65 Score=22.59 Aligned_cols=53 Identities=11% Similarity=0.103 Sum_probs=39.9
Q ss_pred cCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEEec-ccccce
Q psy10530 64 KDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVG-IHPSKC 117 (141)
Q Consensus 64 kGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~~p-IhpSNV 117 (141)
.|..+.+|+=.+---+ |..-.|+..+.+|...+|..--..|-....| |.||+=
T Consensus 5 IG~~isLISk~~iRYe-GiL~~In~~~sTi~L~nVr~fGTEgR~~~~~~ipp~~~ 58 (74)
T cd01736 5 IGSKISLISKSDIRYE-GILYTINTEDSTIALKNVRSFGTEGRPTDGPEIPPSDE 58 (74)
T ss_pred cCceEEEEecCCcEEE-EEEEeeccccCEEEeeeeEeecccCCCCCCCccCCCCc
Confidence 4778888888888888 9999999999999999886544444333344 777764
No 70
>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=46.99 E-value=28 Score=24.17 Aligned_cols=40 Identities=15% Similarity=0.236 Sum_probs=28.5
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeecCC-CCeeeceEEEEEccC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRGHY-KGQQVGKVVQSYRKK 90 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~-KGk~~GkV~~V~rkk 90 (141)
+.++--+|. + +-|+.||.|.|-.=+| .-.. |.|+.++.+.
T Consensus 27 ~~i~gK~Rk----~-iwI~~GD~VlV~~~~~~~~~k-g~Iv~r~~~~ 67 (78)
T cd04456 27 VSIPGKLRK----N-IWIKRGDFLIVDPIEEGEDVK-ADIIFVYCKD 67 (78)
T ss_pred EEEchhhcc----C-EEEcCCCEEEEEecccCCCce-EEEEEEeCHH
Confidence 455554553 3 8899999999987776 3344 8898888764
No 71
>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=46.81 E-value=26 Score=22.52 Aligned_cols=25 Identities=24% Similarity=0.294 Sum_probs=13.1
Q ss_pred eecCCeEEE-eec-CCCCeeeceEEEE
Q psy10530 62 VRKDDEVQV-VRG-HYKGQQVGKVVQS 86 (141)
Q Consensus 62 IrkGD~V~V-i~G-~~KGk~~GkV~~V 86 (141)
.--||+|.| +.. ...+...|+|++|
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 457998877 333 3333334888876
No 72
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=46.69 E-value=23 Score=24.87 Aligned_cols=45 Identities=9% Similarity=-0.054 Sum_probs=30.2
Q ss_pred ecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEEecccccceEE
Q psy10530 63 RKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKCVI 119 (141)
Q Consensus 63 rkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~~pIhpSNV~i 119 (141)
+.||.| .|+|+.|....+.+-|-.++-. +-......-||.|++.-
T Consensus 5 ~~GDiV-----------ig~V~~v~~~~~~v~I~~v~~~-~l~~~~~g~l~~~dv~~ 49 (92)
T cd05791 5 KVGSIV-----------IARVTRINPRFAKVDILCVGGR-PLKESFRGVIRKEDIRA 49 (92)
T ss_pred CCCCEE-----------EEEEEEEcCCEEEEEEEEecCe-ecCCCcccEEEHHHccc
Confidence 788887 3999999888777777655421 11234456688888753
No 73
>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=46.37 E-value=23 Score=27.02 Aligned_cols=23 Identities=22% Similarity=0.472 Sum_probs=16.1
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEcc
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRK 89 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rk 89 (141)
|++.||.|+|= |.. |.|.++..-
T Consensus 60 pf~vGD~I~i~-----~~~-G~V~~I~l~ 82 (206)
T PF00924_consen 60 PFKVGDRIEIG-----GVE-GRVEEIGLR 82 (206)
T ss_dssp SS-TT-EEESS-----S-E-EEEEEE-SS
T ss_pred CccCCCEEEEE-----Eee-hHHHhcCcc
Confidence 79999998876 787 999999764
No 74
>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=45.79 E-value=39 Score=23.03 Aligned_cols=30 Identities=23% Similarity=0.267 Sum_probs=19.8
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCC
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKF 91 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~ 91 (141)
.|++|+.|.|+++..--.+ |+|.++.+.+.
T Consensus 26 ~l~~g~~v~vlr~~~~~~~-g~i~sl~~~~~ 55 (84)
T cd03692 26 KIKRNAKVRVLRNGEVIYE-GKISSLKRFKD 55 (84)
T ss_pred EEeCCCEEEEEcCCCEEEE-EEEEEEEEcCc
Confidence 5788999999998411134 67777665543
No 75
>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=44.59 E-value=23 Score=24.53 Aligned_cols=41 Identities=12% Similarity=0.289 Sum_probs=28.0
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccC
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK 90 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk 90 (141)
-|.+|--+|. .+.|+.||.|.|--=+|--.. |.|+..+..+
T Consensus 26 la~i~gK~rk-----~iwI~~GD~V~Ve~~~~d~~k-g~Iv~r~~~~ 66 (77)
T cd05793 26 LCRIRGKMRK-----RVWINEGDIVLVAPWDFQDDK-ADIIYKYTPD 66 (77)
T ss_pred EEEEchhhcc-----cEEEcCCCEEEEEeccccCCE-EEEEEEcCHH
Confidence 3556655553 488999999999444443444 8998887654
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=43.19 E-value=30 Score=23.52 Aligned_cols=28 Identities=14% Similarity=0.404 Sum_probs=20.8
Q ss_pred eecCCeEEEeecC--CCCeeeceEEEEEccC
Q psy10530 62 VRKDDEVQVVRGH--YKGQQVGKVVQSYRKK 90 (141)
Q Consensus 62 IrkGD~V~Vi~G~--~KGk~~GkV~~V~rkk 90 (141)
|.+||.|.|+|=. +=... |+|..||...
T Consensus 1 i~rgskVrIlR~ESYWyn~v-GtV~svdqs~ 30 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEV-GTVASVDQSG 30 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSE-EEEEEETTSS
T ss_pred CCCCCEEEEccccceeeccc-ceEEEEccCC
Confidence 5789999999976 34555 9999999874
No 77
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=42.87 E-value=64 Score=30.68 Aligned_cols=42 Identities=26% Similarity=0.365 Sum_probs=31.6
Q ss_pred CCHHHHHhhCC----------cccceecCCeEEEeecCC-----CCeeeceEEEEEcc
Q psy10530 47 LSKELRQKYNV----------RSMPVRKDDEVQVVRGHY-----KGQQVGKVVQSYRK 89 (141)
Q Consensus 47 LSkeLr~ky~~----------rs~~IrkGD~V~Vi~G~~-----KGk~~GkV~~V~rk 89 (141)
|...|++.+|. ....++.||.|+.++=++ -|.. |.|+.++..
T Consensus 562 lN~~lq~~lnp~~~~~~~~~~~~~~~~~GDkVm~~~N~~~~~v~NGdi-G~I~~i~~~ 618 (720)
T TIGR01448 562 LNQHLQALLNPYQKGQGGIEIAEGEYRKGDRVMQTKNDYNNEIFNGDL-GMIVKIEGA 618 (720)
T ss_pred HHHHHHHHhCccCCCCceeecCCceecCCCEEEEeeecchhccccCCe-eEEEecccc
Confidence 55666776664 245789999999998664 5787 999999764
No 78
>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=42.83 E-value=36 Score=32.74 Aligned_cols=35 Identities=26% Similarity=0.431 Sum_probs=25.4
Q ss_pred ecCCeEEEeecCCCCeeeceEEEEEc-cCCEEEEeeeeEe
Q psy10530 63 RKDDEVQVVRGHYKGQQVGKVVQSYR-KKFVIYIEKIQRD 101 (141)
Q Consensus 63 rkGD~V~Vi~G~~KGk~~GkV~~V~r-kk~~V~VEgvn~~ 101 (141)
+.||.|.|.+ -|+. |+|+++.. +...|.+.++.+.
T Consensus 626 ~~Gd~V~v~~---~~~~-g~v~~i~~~~~~~V~~g~~k~~ 661 (771)
T TIGR01069 626 KIGDKVRIRY---FGQK-GKIVQILGGNKWNVTVGGMRMK 661 (771)
T ss_pred CCCCEEEEcc---CCce-EEEEEEcCCCeEEEEECCEEEE
Confidence 7899999955 5777 99999975 2334666666653
No 79
>PF14242 DUF4342: Domain of unknown function (DUF4342)
Probab=41.76 E-value=24 Score=24.98 Aligned_cols=21 Identities=43% Similarity=0.537 Sum_probs=18.3
Q ss_pred HHHHHhhCCcccceecCCeEE
Q psy10530 49 KELRQKYNVRSMPVRKDDEVQ 69 (141)
Q Consensus 49 keLr~ky~~rs~~IrkGD~V~ 69 (141)
|||.+|=|++.+.|+++|++.
T Consensus 23 K~li~kGNv~Ri~Ikk~~~tl 43 (84)
T PF14242_consen 23 KELIKKGNVTRIIIKKDDKTL 43 (84)
T ss_pred HHHHHhcCeEEEEEEcCCeEE
Confidence 688999999999999999654
No 80
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=41.54 E-value=42 Score=23.49 Aligned_cols=41 Identities=20% Similarity=0.346 Sum_probs=29.3
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccC
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK 90 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk 90 (141)
-|.++--+|+ .+-|+.||.|.|---+|--.. |.|+.++.+.
T Consensus 31 la~ipgK~Rk-----~iwI~~GD~VlVe~~~~~~~k-g~Iv~r~~~~ 71 (83)
T smart00652 31 LARIPGKMRK-----KVWIRRGDIVLVDPWDFQDVK-ADIIYKYTKD 71 (83)
T ss_pred EEEEchhhcc-----cEEEcCCCEEEEEecCCCCCE-EEEEEEeCHH
Confidence 4556655563 688999999999766664344 8888887654
No 81
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=39.84 E-value=32 Score=23.26 Aligned_cols=26 Identities=19% Similarity=0.299 Sum_probs=20.8
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
.-.|++++.+++| +..||+|.|....
T Consensus 11 ~vtIPk~i~~~lg-----l~~Gd~v~v~~~~ 36 (74)
T TIGR02609 11 VVTLPKEVLESLG-----LKEGDTLYVDEEE 36 (74)
T ss_pred EEEECHHHHHHcC-----cCCCCEEEEEEEC
Confidence 4578999999888 7799999876543
No 82
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=38.67 E-value=33 Score=26.15 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=23.2
Q ss_pred eeeccCCHHHHHhhCCcccc----eecCCeEEEeec
Q psy10530 42 IMSAPLSKELRQKYNVRSMP----VRKDDEVQVVRG 73 (141)
Q Consensus 42 ~msapLSkeLr~ky~~rs~~----IrkGD~V~Vi~G 73 (141)
.+..--..+|..+||++++| ++-|..|-.+.|
T Consensus 74 kVDiD~~~~LA~~fgV~siPTLl~FkdGk~v~~i~G 109 (132)
T PRK11509 74 IADLEQSEAIGDRFGVFRFPATLVFTGGNYRGVLNG 109 (132)
T ss_pred EEECCCCHHHHHHcCCccCCEEEEEECCEEEEEEeC
Confidence 34445678999999999998 566666666655
No 83
>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=38.27 E-value=63 Score=23.65 Aligned_cols=37 Identities=27% Similarity=0.504 Sum_probs=21.6
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeec----------CCCCeeeceEEEEEccC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRG----------HYKGQQVGKVVQSYRKK 90 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G----------~~KGk~~GkV~~V~rkk 90 (141)
.|||.-|+. .+.||.|-|.-- .|-|++ |.|..|.+..
T Consensus 24 ~~ls~~l~~--------yk~GD~V~I~id~sv~kGmPh~~yHGkT-G~V~~v~~~~ 70 (99)
T PF01157_consen 24 IPLSTYLQE--------YKVGDKVDIKIDPSVHKGMPHKRYHGKT-GRVFNVTKGA 70 (99)
T ss_dssp --CHHHH------------TT-EEEE---TTSSSSS--GGGTTEE-EEEEEE-SSC
T ss_pred CcHHHHHHH--------ccCCCEEEEEecCccccCCCcceECCCc-eeEEEeCCCc
Confidence 479999987 789999987632 245898 9999998765
No 84
>PRK10334 mechanosensitive channel MscS; Provisional
Probab=38.09 E-value=85 Score=26.44 Aligned_cols=23 Identities=26% Similarity=0.374 Sum_probs=19.1
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEcc
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRK 89 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rk 89 (141)
|++.||.|++ .|.+ |.|.++..-
T Consensus 129 pf~vGD~I~i-----~~~~-G~V~~I~~r 151 (286)
T PRK10334 129 PFRAGEYVDL-----GGVA-GTVLSVQIF 151 (286)
T ss_pred CCCCCCEEEE-----CCEE-EEEEEEEeE
Confidence 7899999998 3677 999998654
No 85
>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=37.66 E-value=43 Score=22.03 Aligned_cols=27 Identities=19% Similarity=0.397 Sum_probs=17.7
Q ss_pred cccceecCCeEEEeecCCCCeeeceEEE
Q psy10530 58 RSMPVRKDDEVQVVRGHYKGQQVGKVVQ 85 (141)
Q Consensus 58 rs~~IrkGD~V~Vi~G~~KGk~~GkV~~ 85 (141)
+.+.|+.||.|.|---.+--.. |.|+.
T Consensus 38 ~~iwI~~GD~V~V~~~~~d~~k-G~Ii~ 64 (65)
T PF01176_consen 38 KRIWIKRGDFVLVEPSPYDKVK-GRIIY 64 (65)
T ss_dssp TCC---TTEEEEEEESTTCTTE-EEEEE
T ss_pred eeEecCCCCEEEEEecccCCCe-EEEEE
Confidence 5778999999999866655555 77753
No 86
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=37.43 E-value=24 Score=25.66 Aligned_cols=42 Identities=21% Similarity=0.344 Sum_probs=25.9
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccC
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK 90 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk 90 (141)
-|.++--+|. .+.|+.||.|.|-.=++-+...|.|+..+...
T Consensus 45 la~i~GK~Rk-----~iwI~~GD~VlVsp~d~~~~~kg~Iv~r~~~~ 86 (99)
T TIGR00523 45 LGRIPGKLKK-----RIWIREGDVVIVKPWEFQGDDKCDIVWRYTKT 86 (99)
T ss_pred EEEEchhhcc-----cEEecCCCEEEEEEccCCCCccEEEEEEcCHH
Confidence 3555555552 78899999999932222212227888777653
No 87
>KOG3418|consensus
Probab=36.61 E-value=60 Score=25.29 Aligned_cols=38 Identities=18% Similarity=0.373 Sum_probs=28.6
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccC------CEEEEeeeeE
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKK------FVIYIEKIQR 100 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk------~~V~VEgvn~ 100 (141)
++.|-.|.|++|.|.|+. ..|++-..+. +...|+||..
T Consensus 5 lkPgkvv~v~sG~yAg~K-aVivk~~Ddg~~d~p~~h~LvAgi~r 48 (136)
T KOG3418|consen 5 LKPGKVVLVLSGRYAGKK-AVIVKNIDDGTEDKPYGHALVAGVDR 48 (136)
T ss_pred ccCCcEEEeecccccCcc-EEEEeecccCCccCCCceeeeeehhh
Confidence 578899999999999988 5665544332 3788888865
No 88
>PF00408 PGM_PMM_IV: Phosphoglucomutase/phosphomannomutase, C-terminal domain; InterPro: IPR005843 The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) []. PGM (5.4.2.2 from EC) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose []. PGM/PMM (5.4.2.2 from EC; 5.4.2.8 from EC) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate [, ]. Both PNGM (5.4.2.3 from EC) and PAGM (5.4.2.10 from EC) are involved in the biosynthesis of UDP-N-acetylglucosamine [, ]. Despite differences in substrate specificity, these enzymes share a similar catalytic mechanism, converting 1-phospho-sugars to 6-phospho-sugars via a biphosphorylated 1,6-phospho-sugar. The active enzyme is phosphorylated at a conserved serine residue and binds one magnesium ion; residues around the active site serine are well conserved among family members. The reaction mechanism involves phosphoryl transfer from the phosphoserine to the substrate to create a biophosphorylated sugar, followed by a phosphoryl transfer from the substrate back to the enzyme []. The structures of PGM and PGM/PMM have been determined, and were found to be very similar in topology. These enzymes are both composed of four domains and a large central active site cleft, where each domain contains residues essential for catalysis and/or substrate recognition. Domain I contains the catalytic phosphoserine, domain II contains a metal-binding loop to coordinate the magnesium ion, domain III contains the sugar-binding loop that recognises the two different binding orientations of the 1- and 6-phospho-sugars, and domain IV contains a phosphate-binding site required for orienting the incoming phospho-sugar substrate. This entry represents the C-terminal domain alpha-D-phosphohexomutase enzymes.; GO: 0016868 intramolecular transferase activity, phosphotransferases, 0005975 carbohydrate metabolic process; PDB: 1KFQ_B 1KFI_A 3PDK_B 2F7L_A 1TUO_A 2FKM_X 3C04_A 1K2Y_X 1P5G_X 2H4L_X ....
Probab=36.40 E-value=15 Score=24.25 Aligned_cols=14 Identities=43% Similarity=0.603 Sum_probs=11.5
Q ss_pred ccccCceeeeeecc
Q psy10530 5 TRSSGTEVKMKLNK 18 (141)
Q Consensus 5 ~~~~~~~~~mk~~~ 18 (141)
-|.|||++++++.-
T Consensus 40 vR~SgTEP~iRv~~ 53 (73)
T PF00408_consen 40 VRPSGTEPKIRVYV 53 (73)
T ss_dssp EEEESSSSEEEEEE
T ss_pred EECCCCCceEEEEE
Confidence 58999999988753
No 89
>cd02786 MopB_CT_3 The MopB_CT_3 CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=35.38 E-value=65 Score=22.40 Aligned_cols=26 Identities=12% Similarity=0.064 Sum_probs=21.9
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
..-++.+.-+++| |+.||.|.|-+..
T Consensus 32 ~v~i~p~dA~~lg-----i~~Gd~V~v~s~~ 57 (116)
T cd02786 32 TLLIHPADAAARG-----IADGDLVVVFNDR 57 (116)
T ss_pred EEEECHHHHHHcC-----CCCCCEEEEEcCC
Confidence 3567889999999 7789999999776
No 90
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=35.29 E-value=42 Score=32.51 Aligned_cols=33 Identities=24% Similarity=0.409 Sum_probs=25.0
Q ss_pred ccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 59 SMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
.-.++.||+|.+++ |+. |.|+++.-+...+.|+
T Consensus 610 ~~~l~~gDev~~~t----~e~-G~~~~i~a~~~e~~v~ 642 (753)
T COG1193 610 KRKLKLGDEVEVIT----GEP-GAVVKIIAGILEALVQ 642 (753)
T ss_pred ccCceecceeEeec----CCc-cceeeeeccCceeEEe
Confidence 34689999999999 666 8999998555555543
No 91
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=35.12 E-value=53 Score=23.04 Aligned_cols=41 Identities=27% Similarity=0.421 Sum_probs=30.2
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEcc
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRK 89 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rk 89 (141)
-|++|--+|. ..+.|..||.|.|--=+|--+. |-|+-=+.+
T Consensus 33 ~ahI~GKmr~----~~i~I~~GD~V~Ve~~~~d~~k-g~I~~Ry~~ 73 (75)
T COG0361 33 LAHISGKMRK----NRIRILPGDVVLVELSPYDLTK-GRIVYRYKK 73 (75)
T ss_pred EEEccCcchh----eeEEeCCCCEEEEEeccccccc-ccEEEEecC
Confidence 4667766665 4678999999999888887666 777655443
No 92
>COG1385 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.50 E-value=1.2e+02 Score=25.15 Aligned_cols=50 Identities=14% Similarity=0.209 Sum_probs=37.1
Q ss_pred CCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeee
Q psy10530 47 LSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKI 98 (141)
Q Consensus 47 LSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgv 98 (141)
|+.+ .-.|=.|-++++.||++.+.-|...=-. +.|.++..+.-.+.+...
T Consensus 20 l~~~-~~~Hl~~VlRl~~gd~l~l~~g~g~~~~-a~i~~~~kk~~~~~i~~~ 69 (246)
T COG1385 20 LTGD-EAHHLKRVLRLKEGDELRLFDGSGGEFL-AEITKIGKKEALLKIVEQ 69 (246)
T ss_pred ECch-hhhhHHheeecCCCCEEEEEeCCCcEEE-EEEeecCCCceEEEEEee
Confidence 3444 6777788899999999999999854444 688888887666655544
No 93
>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=34.13 E-value=71 Score=21.06 Aligned_cols=24 Identities=13% Similarity=0.198 Sum_probs=19.9
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
++.||+|+ ++|+.+++++.+|.+.
T Consensus 47 ~~vG~~v~-----------~kV~~id~~~~~i~Ls 70 (73)
T cd05703 47 FPIGQALK-----------AKVVGVDKEHKLLRLS 70 (73)
T ss_pred CCCCCEEE-----------EEEEEEeCCCCEEEEE
Confidence 67899975 7899999999888763
No 94
>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=33.86 E-value=88 Score=19.94 Aligned_cols=30 Identities=23% Similarity=0.231 Sum_probs=21.1
Q ss_pred ceecCCeEEEeecCCCC---eeeceEEEEEccCCE
Q psy10530 61 PVRKDDEVQVVRGHYKG---QQVGKVVQSYRKKFV 92 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KG---k~~GkV~~V~rkk~~ 92 (141)
.|++||+|.++. ..-+ .. ++|..++.....
T Consensus 12 ~l~~gd~v~~~~-~~~~~~~~~-~~I~~i~~~~~~ 44 (74)
T PF03144_consen 12 TLKKGDKVRVLP-NGTGKKGQV-VKIKSIFMFNGD 44 (74)
T ss_dssp EEETTEEEEEES-TTTTEECEE-EEEEEEEETTEE
T ss_pred EEcCCCEEEECc-cCCcceeee-eecccccccccC
Confidence 589999999988 4433 34 677777766543
No 95
>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=33.78 E-value=70 Score=22.75 Aligned_cols=40 Identities=15% Similarity=-0.040 Sum_probs=24.1
Q ss_pred cccceecCCeEEE--eecCCCCeeeceEEEEEccCCEEEEeeee
Q psy10530 58 RSMPVRKDDEVQV--VRGHYKGQQVGKVVQSYRKKFVIYIEKIQ 99 (141)
Q Consensus 58 rs~~IrkGD~V~V--i~G~~KGk~~GkV~~V~rkk~~V~VEgvn 99 (141)
.....+.||.|.. -.+..-|+. |.|++|... +.|.|-.=|
T Consensus 59 ~~~~P~~Gdivv~~~~~~~~~GHV-aIV~~v~~~-~~i~v~e~N 100 (124)
T PF05257_consen 59 TGSTPQPGDIVVWDSGSGGGYGHV-AIVESVNDG-GTITVIEQN 100 (124)
T ss_dssp ECS---TTEEEEEEECTTTTT-EE-EEEEEE-TT-SEEEEEECS
T ss_pred cCcccccceEEEeccCCCCCCCeE-EEEEEECCC-CEEEEEECC
Confidence 3445789998776 466677898 999999554 555554443
No 96
>TIGR00046 RNA methyltransferase, RsmE family. Members of this protein family, previously called conserved hypothetical protein TIGR00046, include the YggJ protein of E. coli, which has now been shown to methylate U1498 in 16S rRNA.
Probab=33.72 E-value=78 Score=25.65 Aligned_cols=47 Identities=19% Similarity=0.293 Sum_probs=30.8
Q ss_pred cCCHHHHHhhCCcccceecCCeEEEeecCCCCee-eceEEEEEccCCEEEE
Q psy10530 46 PLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQ-VGKVVQSYRKKFVIYI 95 (141)
Q Consensus 46 pLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~-~GkV~~V~rkk~~V~V 95 (141)
.|+.+ ...|=++-++++.||.|.|.-|. |.. .++|..+..+.-.+.|
T Consensus 17 ~l~~~-~~~Hl~~VlR~~~Gd~v~v~~g~--g~~~~a~i~~~~~~~~~~~i 64 (240)
T TIGR00046 17 SLTEE-EAHHLVRVLRLKKGDKLKLLDGD--GFIYHCEIKKISKKFVKCEL 64 (240)
T ss_pred EEChH-HHhHHHHcccCCCCCEEEEEeCC--CCEEEEEEEEEcCCeEEEEE
Confidence 34543 33444578899999999999984 443 3678777765444433
No 97
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=33.24 E-value=40 Score=23.12 Aligned_cols=37 Identities=22% Similarity=0.364 Sum_probs=27.1
Q ss_pred eeccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEE
Q psy10530 43 MSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVV 84 (141)
Q Consensus 43 msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~ 84 (141)
.-|.+|-.||. +.+.|..||.|.|--=+|--.. |.|+
T Consensus 30 vla~i~GKmr~----~rI~I~~GD~V~Ve~spyd~tk-grIi 66 (68)
T TIGR00008 30 VLAHISGKIRM----HYIRILPGDKVKVELSPYDLTR-GRIT 66 (68)
T ss_pred EEEEecCcchh----ccEEECCCCEEEEEECcccCCc-EeEE
Confidence 34777776665 5788999999999877775554 6553
No 98
>cd02785 MopB_CT_4 The MopB_CT_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=33.06 E-value=60 Score=23.10 Aligned_cols=29 Identities=14% Similarity=0.139 Sum_probs=24.1
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecCCCCee
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQ 79 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~ 79 (141)
..-++.+.-+++| |.-||.|.|-++. |+.
T Consensus 33 ~v~i~p~dA~~~g-----i~~Gd~V~v~s~~--G~i 61 (124)
T cd02785 33 RVKINPIDAAARG-----IAHGDLVEVYNDR--GSV 61 (124)
T ss_pred eEEECHHHHHHcC-----CCCCCEEEEEeCC--CEE
Confidence 4678999999999 6789999999886 554
No 99
>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=31.42 E-value=1.3e+02 Score=21.54 Aligned_cols=40 Identities=10% Similarity=-0.027 Sum_probs=27.7
Q ss_pred ceecCCeEEEeecCC-CCeeeceEEEEEccC-CEEEEeeeeE
Q psy10530 61 PVRKDDEVQVVRGHY-KGQQVGKVVQSYRKK-FVIYIEKIQR 100 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~-KGk~~GkV~~V~rkk-~~V~VEgvn~ 100 (141)
.++.||-|.|.+... ..-.+|.|.++.... +...+.+.=.
T Consensus 3 ~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf 44 (121)
T cd04717 3 QYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWF 44 (121)
T ss_pred EEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEE
Confidence 478999999998764 322349999988865 5555554433
No 100
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=31.39 E-value=48 Score=24.15 Aligned_cols=41 Identities=17% Similarity=0.362 Sum_probs=28.6
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccC
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK 90 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk 90 (141)
-|.++--+|. .+.|+.||.|.|--=.|--.. |.|+..+.+.
T Consensus 47 la~i~GK~Rk-----~IwI~~GD~VlVe~~~~~~~k-g~Iv~r~~~~ 87 (100)
T PRK04012 47 MGRIPGKMKK-----RMWIREGDVVIVAPWDFQDEK-ADIIWRYTKP 87 (100)
T ss_pred EEEEchhhcc-----cEEecCCCEEEEEecccCCCE-EEEEEEcCHH
Confidence 4555555553 588999999999765554445 8888887653
No 101
>cd02790 MopB_CT_Formate-Dh_H Formate dehydrogenase H (Formate-Dh-H) catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. It is a component of the anaerobic formate hydrogen lyase complex. The E. coli formate dehydrogenase H (Fdh-H) is a monomer composed of a single polypeptide chain with a Mo active site region and a [4Fe-4S] center. This CD (MopB_CT_Formate-Dh_H) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=31.25 E-value=76 Score=21.85 Aligned_cols=25 Identities=12% Similarity=0.282 Sum_probs=20.7
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
.-++.+.-+++| |+.||.|.|.++.
T Consensus 37 v~in~~dA~~lg-----i~~Gd~V~v~~~~ 61 (116)
T cd02790 37 VEINPEDAKRLG-----IEDGEKVRVSSRR 61 (116)
T ss_pred EEECHHHHHHcC-----CCCCCEEEEEcCC
Confidence 456778888888 8899999999875
No 102
>KOG4315|consensus
Probab=30.74 E-value=26 Score=32.06 Aligned_cols=37 Identities=27% Similarity=0.342 Sum_probs=30.7
Q ss_pred cceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEee
Q psy10530 60 MPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEK 97 (141)
Q Consensus 60 ~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEg 97 (141)
+|=+-|+.|.|++|+++|+- |--+.=++.+.+..|..
T Consensus 392 ~pr~~Ge~vmvv~gkhkg~~-g~llskd~~Ke~~~v~~ 428 (455)
T KOG4315|consen 392 LPRRGGEKVMVVSGKHKGVY-GSLLSKDLDKETGVVRL 428 (455)
T ss_pred cccccCceeEEEecccccch-hhhhhhhhhhhhcceec
Confidence 46678899999999999998 98888888877766653
No 103
>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=30.47 E-value=94 Score=20.25 Aligned_cols=24 Identities=4% Similarity=0.180 Sum_probs=19.2
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCCEEEE
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYI 95 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~V 95 (141)
.++.||+|. .+|+.+++++.++.+
T Consensus 46 ~~~vG~~v~-----------~kV~~id~~~~~i~l 69 (71)
T cd05696 46 PFKAGTTHK-----------ARIIGYSPMDGLLQL 69 (71)
T ss_pred ccCCCCEEE-----------EEEEEEeCCCCEEEE
Confidence 478899875 688999998887765
No 104
>cd02779 MopB_CT_Arsenite-Ox This CD contains the molybdopterin_binding C-terminal (MopB_CT) region of Arsenite oxidase (Arsenite-Ox) and related proteins. Arsenite oxidase oxidizes arsenite to the less toxic arsenate; it transfers the electrons obtained from the oxidation of arsenite towards the soluble periplasmic electron carriers cytochrome c and/or amicyanin.
Probab=30.44 E-value=83 Score=22.16 Aligned_cols=25 Identities=16% Similarity=0.197 Sum_probs=21.6
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
.-|+.+.-+++| |..||.|.|.++.
T Consensus 35 v~in~~dA~~lg-----i~~Gd~V~v~s~~ 59 (115)
T cd02779 35 IEVNPEDAKREG-----LKNGDLVEVYNDY 59 (115)
T ss_pred EEECHHHHHHcC-----CCCCCEEEEEeCC
Confidence 567888888888 8899999999887
No 105
>cd02781 MopB_CT_Acetylene-hydratase The MopB_CT_Acetylene-hydratase CD contains acetylene hydratase (Ahy) and other related proteins. The acetylene hydratase of Pelobacter acetylenicus is a tungsten iron-sulfur protein involved in the fermentation of acetylene to ethanol and acetate. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=30.31 E-value=91 Score=22.10 Aligned_cols=29 Identities=24% Similarity=0.249 Sum_probs=23.4
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecCCCCee
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQ 79 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~ 79 (141)
..-++.+.-+++| |+.||.|.|.++. |..
T Consensus 34 ~v~inp~dA~~~g-----i~~Gd~V~v~s~~--G~~ 62 (130)
T cd02781 34 VAEINPETAAKLG-----IADGDWVWVETPR--GRA 62 (130)
T ss_pred EEEECHHHHHHcC-----CCCCCEEEEECCC--CEE
Confidence 3567888889888 7889999999887 544
No 106
>smart00439 BAH Bromo adjacent homology domain.
Probab=29.70 E-value=1e+02 Score=21.23 Aligned_cols=30 Identities=20% Similarity=0.249 Sum_probs=23.1
Q ss_pred eecCCeEEEeecC-CCCeeeceEEEEEccCC
Q psy10530 62 VRKDDEVQVVRGH-YKGQQVGKVVQSYRKKF 91 (141)
Q Consensus 62 IrkGD~V~Vi~G~-~KGk~~GkV~~V~rkk~ 91 (141)
++.||.|.|.... .+.-.+|+|..++....
T Consensus 2 ~~vgd~V~v~~~~~~~~~~i~~I~~i~~~~~ 32 (120)
T smart00439 2 IRVGDFVLVEPDDADEPYYIGRIEEIFETKK 32 (120)
T ss_pred cccCCEEEEeCCCCCCCCEEEEEEEEEECCC
Confidence 6789999999887 33334599999988654
No 107
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues [, ]. They are found in a great variety of intracellular or membrane-associated proteins [, , ] for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices []. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes []. This entry represents a variant of the SH3 domain.; PDB: 1I1J_B 1K0X_A 1HJD_A 2KEA_A 1KJW_A 1JXM_A 1JXO_B 2EBP_A 2DL3_A 2EYX_A ....
Probab=29.63 E-value=38 Score=20.97 Aligned_cols=13 Identities=23% Similarity=0.572 Sum_probs=9.9
Q ss_pred ccceecCCeEEEe
Q psy10530 59 SMPVRKDDEVQVV 71 (141)
Q Consensus 59 s~~IrkGD~V~Vi 71 (141)
-+.+++||.|.|+
T Consensus 15 ~Ls~~~Gd~i~v~ 27 (55)
T PF07653_consen 15 ELSFKKGDVIEVL 27 (55)
T ss_dssp B-EB-TTEEEEEE
T ss_pred ceEEecCCEEEEE
Confidence 3779999999999
No 108
>cd02794 MopB_CT_DmsA-EC The MopB_CT_DmsA-EC CD includes the DmsA enzyme of the dmsABC operon encoding the anaerobic dimethylsulfoxide reductase (DMSOR) of Escherichia coli and other related DMSOR-like enzymes. Unlike other DMSOR-like enzymes, this group has a predicted N-terminal iron-sulfur [4Fe-4S] cluster binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=29.56 E-value=92 Score=22.02 Aligned_cols=25 Identities=12% Similarity=0.090 Sum_probs=21.6
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
.-++.+.-+++| |..||.|.|.++.
T Consensus 32 v~i~p~~A~~~g-----i~~Gd~V~v~s~~ 56 (121)
T cd02794 32 VWINPLDAAARG-----IKDGDRVLVFNDR 56 (121)
T ss_pred EEECHHHHHHcC-----CCCCCEEEEEcCC
Confidence 457899999999 7889999999877
No 109
>PHA00653 mtd major tropism determinant
Probab=29.44 E-value=1.1e+02 Score=27.37 Aligned_cols=58 Identities=10% Similarity=0.137 Sum_probs=38.8
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEec------cCC-cEEEecccccceEEEeC
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDK------VNG-ATVYVGIHPSKCVIVKL 122 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K------~~G-~~v~~pIhpSNV~i~~l 122 (141)
.+|.|-+-++- .|+|-+ |+|+ |+..+++++|.+..-.- .|- .+...-.+||||.|+.-
T Consensus 6 ~~r~gt~~~~a--sf~ga~-~ei~-~~t~~~~l~v~Dgtt~gg~~L~kl~~~~~~~~~~~~s~~~~~~t 70 (381)
T PHA00653 6 QFRGGTTAQHA--TFTGAA-REIT-VDTDKNTVVVHDGATAGGFPLARHDLVKTAFIKADKSAVAFTRT 70 (381)
T ss_pred EEccCccccee--eecccc-eeEE-EccCCceEEEecCcccCCceeeccccccceeeeecccceeEEec
Confidence 34555555543 488998 8875 78888999998774321 111 24456778999998864
No 110
>cd00174 SH3 Src homology 3 domains; SH3 domains bind to proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs; they play a role in the regulation of enzymes by intramolecular interactions, changing the subcellular localization of signal pathway components and mediate multiprotein complex assemblies.
Probab=29.18 E-value=54 Score=18.78 Aligned_cols=19 Identities=21% Similarity=0.438 Sum_probs=14.4
Q ss_pred ccceecCCeEEEeecCCCC
Q psy10530 59 SMPVRKDDEVQVVRGHYKG 77 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~~KG 77 (141)
.+.+.+||.|.|+.....|
T Consensus 15 ~l~~~~Gd~v~v~~~~~~~ 33 (54)
T cd00174 15 ELSFKKGDIIEVLEKSDDG 33 (54)
T ss_pred CCCCCCCCEEEEEEcCCCC
Confidence 4568899999999874433
No 111
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=29.14 E-value=1.1e+02 Score=24.99 Aligned_cols=40 Identities=30% Similarity=0.418 Sum_probs=29.1
Q ss_pred HHHhhCCcccceecCCeEEEeecC----CCCeeeceEEEEEccCC
Q psy10530 51 LRQKYNVRSMPVRKDDEVQVVRGH----YKGQQVGKVVQSYRKKF 91 (141)
Q Consensus 51 Lr~ky~~rs~~IrkGD~V~Vi~G~----~KGk~~GkV~~V~rkk~ 91 (141)
|.=.|=.+..+|++||+ .|.+|- .+|-..|+|.+|.+..+
T Consensus 204 l~l~~i~~~~~i~~GD~-VvTSGl~g~fP~Gi~VG~V~~v~~~~~ 247 (276)
T PRK13922 204 LKLEFIPRSADIKVGDL-VVTSGLGGIFPAGLPVGKVTSVERDDY 247 (276)
T ss_pred eEEEecCCCCCCCCCCE-EEECCCCCcCCCCCEEEEEEEEEeCCC
Confidence 34445455678999999 577886 35777899999977654
No 112
>TIGR02851 spore_V_T stage V sporulation protein T. Members of this protein family are the stage V sporulation protein T (SpoVT), a protein of the sporulation/germination program in Bacillus subtilis and related species. The amino-terminal 50 amino acids are nearly perfectly conserved across all endospore-forming bacteria. SpoVT is a DNA-binding transcriptional regulator related to AbrB (See PFAM model pfam04014).
Probab=29.11 E-value=45 Score=26.43 Aligned_cols=23 Identities=22% Similarity=0.544 Sum_probs=18.5
Q ss_pred cCCHHHHHhhCCcccceecCCeEEEeec
Q psy10530 46 PLSKELRQKYNVRSMPVRKDDEVQVVRG 73 (141)
Q Consensus 46 pLSkeLr~ky~~rs~~IrkGD~V~Vi~G 73 (141)
.+++|+|+.+| |+.||.|.+..-
T Consensus 16 ~iP~~iR~~l~-----i~~gd~~~~~~~ 38 (180)
T TIGR02851 16 VIPKEIRRTLR-----IREGDPLEIFTD 38 (180)
T ss_pred EEeHHHHHHcC-----CCCCCeEEEEEe
Confidence 47899999877 889999988653
No 113
>PF11910 NdhO: Cyanobacterial and plant NDH-1 subunit O; InterPro: IPR020905 NAD(P)H-quinone oxidoreductase (NDH-1) shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in this species is believed to be plastoquinone. It couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. Cyanobacterial NDH-1 also plays a role in inorganic carbon-concentration. NDH-1 can be composed of about 15 different subunits, although different subcomplexes with different compositions have been identified which probably have different functions. This entry represents subunit O. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process, 0005886 plasma membrane
Probab=28.11 E-value=30 Score=23.96 Aligned_cols=18 Identities=28% Similarity=0.447 Sum_probs=15.1
Q ss_pred eecCCeEEEeecCCCCee
Q psy10530 62 VRKDDEVQVVRGHYKGQQ 79 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~ 79 (141)
|+||+.|.|++.++-|..
T Consensus 1 lKKG~lVrv~re~~~nSl 18 (67)
T PF11910_consen 1 LKKGSLVRVNREKYENSL 18 (67)
T ss_pred CCcceEEEeehHhhcCch
Confidence 589999999999988743
No 114
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=27.71 E-value=64 Score=22.54 Aligned_cols=25 Identities=8% Similarity=0.166 Sum_probs=21.9
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
.-++.|.-+++| |+.||.|.|.+..
T Consensus 33 v~i~p~dA~~lg-----I~dGd~V~v~s~~ 57 (112)
T cd02787 33 VFMNPDDIARLG-----LKAGDRVDLESAF 57 (112)
T ss_pred EEECHHHHHHhC-----CCCCCEEEEEecC
Confidence 567889999999 8899999999877
No 115
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=27.67 E-value=63 Score=20.48 Aligned_cols=28 Identities=11% Similarity=0.052 Sum_probs=20.8
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccC
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKK 90 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk 90 (141)
|..|+.|.+..+...-.. ++|+++..+.
T Consensus 1 ~~vG~~v~~~~~~~~~y~-A~I~~~r~~~ 28 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYE-AKILDIREKN 28 (55)
T ss_dssp --TTEEEEEEETTTEEEE-EEEEEEEECT
T ss_pred CCcCCEEEEEECCCcEEE-EEEEEEEecC
Confidence 467999999995555556 8999998876
No 116
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=27.29 E-value=1.2e+02 Score=20.97 Aligned_cols=30 Identities=17% Similarity=0.151 Sum_probs=22.6
Q ss_pred ceecCCeEEEeecCCCC-eeeceEEEEEccC
Q psy10530 61 PVRKDDEVQVVRGHYKG-QQVGKVVQSYRKK 90 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KG-k~~GkV~~V~rkk 90 (141)
.++.||-|.|..+...+ -.+|.|..+....
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 47899999999999433 3368888887543
No 117
>PRK10929 putative mechanosensitive channel protein; Provisional
Probab=27.18 E-value=1.2e+02 Score=30.69 Aligned_cols=23 Identities=26% Similarity=0.531 Sum_probs=18.8
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEcc
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRK 89 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rk 89 (141)
|++.||.|.| .|.. |.|.+|.-.
T Consensus 935 PfrVGD~I~I-----~~~~-GtV~~I~lR 957 (1109)
T PRK10929 935 PIRIGDTVTI-----RDLT-GSVTKINTR 957 (1109)
T ss_pred CCCCCCEEEE-----CCEE-EEEEEEeee
Confidence 7999999998 2566 999988763
No 118
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=27.13 E-value=84 Score=20.76 Aligned_cols=22 Identities=23% Similarity=0.292 Sum_probs=15.5
Q ss_pred ecCCeEEEeecCCCCeeeceEEEEEccCCEEEE
Q psy10530 63 RKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYI 95 (141)
Q Consensus 63 rkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~V 95 (141)
+.||.| .|+|++|..+.+.|-+
T Consensus 5 ~~GdiV-----------~G~V~~v~~~~~~V~i 26 (82)
T cd04454 5 DVGDIV-----------IGIVTEVNSRFWKVDI 26 (82)
T ss_pred CCCCEE-----------EEEEEEEcCCEEEEEe
Confidence 577776 3999999776555544
No 119
>cd03065 PDI_b_Calsequestrin_N PDIb family, Calsequestrin subfamily, N-terminal TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca2
Probab=27.06 E-value=60 Score=23.96 Aligned_cols=19 Identities=5% Similarity=0.127 Sum_probs=14.5
Q ss_pred eeccCCHHHHHhhCCcccc
Q psy10530 43 MSAPLSKELRQKYNVRSMP 61 (141)
Q Consensus 43 msapLSkeLr~ky~~rs~~ 61 (141)
+-+.=..+|.++||++++|
T Consensus 71 VD~d~~~~La~~~~I~~iP 89 (120)
T cd03065 71 VDSKKDAKVAKKLGLDEED 89 (120)
T ss_pred EeCCCCHHHHHHcCCcccc
Confidence 3444567889999999887
No 120
>PF13452 MaoC_dehydrat_N: N-terminal half of MaoC dehydratase; PDB: 3HMJ_H 2UV8_I 2VKZ_G 1S9C_K 3OML_A 3KHP_A.
Probab=27.05 E-value=2e+02 Score=20.26 Aligned_cols=39 Identities=21% Similarity=0.454 Sum_probs=22.4
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCC---EEEEe-eeeEeccCCcEE
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKF---VIYIE-KIQRDKVNGATV 108 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~---~V~VE-gvn~~K~~G~~v 108 (141)
||+.||+|.+ ..+|..|..+.+ ..+|+ .......+|..+
T Consensus 87 Pl~~Gd~l~~---------~~~v~~v~~k~g~G~~~~v~~~~~~~~~~Ge~v 129 (132)
T PF13452_consen 87 PLRPGDTLTA---------TSRVTDVYDKRGAGKGVFVTVETEYTDQDGELV 129 (132)
T ss_dssp --BSSEEEEE---------EEEEEEEEEES-TTSEEEEEEEEEEE-CTTEEE
T ss_pred CCCCCCEEEE---------EEEEEEEEEecCCCCEEEEEEEEEEECCCCCEE
Confidence 7999999876 278888888742 33333 233334667543
No 121
>PF04085 MreC: rod shape-determining protein MreC; InterPro: IPR007221 MreC (murein formation C) is involved in the rod shape determination in Escherichia coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped.; GO: 0008360 regulation of cell shape; PDB: 2J5U_B 2QF4_B 2QF5_A.
Probab=26.82 E-value=1.9e+02 Score=21.79 Aligned_cols=34 Identities=26% Similarity=0.261 Sum_probs=22.0
Q ss_pred CcccceecCCeEEEeecCC----CCeeeceEEEEEccCC
Q psy10530 57 VRSMPVRKDDEVQVVRGHY----KGQQVGKVVQSYRKKF 91 (141)
Q Consensus 57 ~rs~~IrkGD~V~Vi~G~~----KGk~~GkV~~V~rkk~ 91 (141)
....+|++||.|. .+|-. +|-..|+|.+|.+...
T Consensus 89 ~~~~~i~~GD~V~-TSG~~~~fP~Gi~VG~V~~v~~~~~ 126 (152)
T PF04085_consen 89 PKDADIKKGDIVV-TSGLGGIFPPGIPVGTVSSVEPDKS 126 (152)
T ss_dssp CTTS---TT-EEE-EE-TTSSS-CCEEEEEEEEEECTTT
T ss_pred CCCCCCCCCCEEE-ECCCCCcCCCCCEEEEEEEEEeCCC
Confidence 3566799999966 56643 5777899999999876
No 122
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=26.42 E-value=88 Score=26.44 Aligned_cols=42 Identities=21% Similarity=0.256 Sum_probs=32.6
Q ss_pred HHHHHhhCCcccceecCCeEEEeecCC----CCeeeceEEEEEccCC
Q psy10530 49 KELRQKYNVRSMPVRKDDEVQVVRGHY----KGQQVGKVVQSYRKKF 91 (141)
Q Consensus 49 keLr~ky~~rs~~IrkGD~V~Vi~G~~----KGk~~GkV~~V~rkk~ 91 (141)
.+|.-.|-..+-.|+.|| ..|.+|-. .|-..|+|.+|..+++
T Consensus 200 ~~l~~~~~~~~~~i~~GD-~vvTSGlgg~fP~Gl~Vg~V~~v~~~~~ 245 (284)
T COG1792 200 DLLLLVYLPPNSDIKEGD-LVVTSGLGGVFPAGLPVGEVSSVKLDDY 245 (284)
T ss_pred CceeeeeccCCCCccCCC-EEEecCCCCcCCCCcEEEEEEEEEeCCC
Confidence 344445677788899999 68888875 5777799999998874
No 123
>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=26.34 E-value=43 Score=23.87 Aligned_cols=18 Identities=33% Similarity=0.432 Sum_probs=13.9
Q ss_pred eecCCeEEEeecCCCCee
Q psy10530 62 VRKDDEVQVVRGHYKGQQ 79 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~ 79 (141)
+..||.|.|+.|..-|..
T Consensus 90 ~~~gd~vVv~~g~~~~~~ 107 (117)
T PF02887_consen 90 LKPGDKVVVVAGMPFGTP 107 (117)
T ss_dssp S-TTSEEEEEEESSTTTT
T ss_pred CCCCCEEEEEeCCCCCCC
Confidence 899999999999655544
No 124
>cd03450 NodN NodN (nodulation factor N) contains a single hot dog fold similar to those of the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. Rhizobium and related species form nodules on the roots of their legume hosts, a symbiotic process that requires production of Nod factors, which are signal molecules involved in root hair deformation and meristematic cell division. The nodulation gene products, including NodN, are involved in producing the Nod factors, however the role played by NodN is unclear.
Probab=26.28 E-value=2e+02 Score=21.74 Aligned_cols=44 Identities=11% Similarity=0.076 Sum_probs=25.7
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCCE-EEEe-eeeEeccCCcEEEecccc
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFV-IYIE-KIQRDKVNGATVYVGIHP 114 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~-V~VE-gvn~~K~~G~~v~~pIhp 114 (141)
|+..||+|.+. ++|.++..+... +.|. .+. ..-.|+..|+++--
T Consensus 97 PV~~GDtl~~~---------~~V~~~~~~~~~~~~~~~~~~-~~~~~~~~p~~~~~ 142 (149)
T cd03450 97 PVPVGSRVRGR---------FTLLSVEELKGGGVQVTLEVT-VEIEGEDKPACVAE 142 (149)
T ss_pred ceeCCcEEEEE---------EEEEEEEEcCCCeEEEEEEEE-EEEeCCCCceEEEE
Confidence 78899988763 678888777753 2222 221 22346555555543
No 125
>cd02791 MopB_CT_Nitrate-R-NapA-like Nitrate reductases, NapA (Nitrate-R-NapA), NasA, and NarB catalyze the reduction of nitrate to nitrite. Monomeric Nas is located in the cytoplasm and participates in nitrogen assimilation. Dimeric Nap is located in the periplasm and is coupled to quinol oxidation via a membrane-anchored tetraheme cytochrome. This CD (MopB_CT_Nitrate-R-Nap) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs
Probab=26.25 E-value=67 Score=22.43 Aligned_cols=26 Identities=15% Similarity=0.220 Sum_probs=22.0
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
..-++.+.-+++| |+.||.|.|.++.
T Consensus 36 ~v~in~~dA~~lg-----i~~Gd~V~v~~~~ 61 (122)
T cd02791 36 YVEIHPEDAARLG-----LKEGDLVRVTSRR 61 (122)
T ss_pred EEEECHHHHHHcC-----CCCCCEEEEEcCC
Confidence 3567888889888 7899999999877
No 126
>cd02954 DIM1 Dim1 family; Dim1 is also referred to as U5 small nuclear ribonucleoprotein particle (snRNP)-specific 15kD protein. It is a component of U5 snRNP, which pre-assembles with U4/U6 snRNPs to form a [U4/U6:U5] tri-snRNP complex required for pre-mRNA splicing. Dim1 interacts with multiple splicing-associated proteins, suggesting that it functions at multiple control points in the splicing of pre-mRNA as part of a large spliceosomal complex involving many protein-protein interactions. U5 snRNP contains seven core proteins (common to all snRNPs) and nine U5-specific proteins, one of which is Dim1. Dim1 adopts a thioredoxin fold but does not contain the redox active CXXC motif. It is essential for G2/M phase transition, as a consequence to its role in pre-mRNA splicing.
Probab=26.24 E-value=72 Score=23.57 Aligned_cols=32 Identities=9% Similarity=0.270 Sum_probs=25.6
Q ss_pred eeccCCHHHHHhhCCcccc----eecCCeEEEeecC
Q psy10530 43 MSAPLSKELRQKYNVRSMP----VRKDDEVQVVRGH 74 (141)
Q Consensus 43 msapLSkeLr~ky~~rs~~----IrkGD~V~Vi~G~ 74 (141)
+-.--..+|-++||++++| ++.|..|..+.|.
T Consensus 52 VDvD~~~~la~~~~V~~iPTf~~fk~G~~v~~~~G~ 87 (114)
T cd02954 52 VDIDEVPDFNKMYELYDPPTVMFFFRNKHMKIDLGT 87 (114)
T ss_pred EECCCCHHHHHHcCCCCCCEEEEEECCEEEEEEcCC
Confidence 3444567899999999998 7888888888885
No 127
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=26.05 E-value=1.9e+02 Score=21.90 Aligned_cols=65 Identities=23% Similarity=0.260 Sum_probs=32.7
Q ss_pred eecCCeEEE----eecCCCCee--eceEEEEEccC--CEEEEeeeeEeccCCcEEEecccccceEEEeC-CCChhH
Q psy10530 62 VRKDDEVQV----VRGHYKGQQ--VGKVVQSYRKK--FVIYIEKIQRDKVNGATVYVGIHPSKCVIVKL-KMDKDR 128 (141)
Q Consensus 62 IrkGD~V~V----i~G~~KGk~--~GkV~~V~rkk--~~V~VEgvn~~K~~G~~v~~pIhpSNV~i~~l-~ldk~R 128 (141)
++.||+|.| +-|.-.--+ .|.|+.+.... ..+.|..+ ...-|.+.-+|+|..+|.=++. .-++-|
T Consensus 21 f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRki--s~G~GVEr~Fp~~SP~Ie~IeV~rrGkVR 94 (115)
T COG0335 21 FRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKI--SYGVGVERVFPLHSPLIESIEVVRRGKVR 94 (115)
T ss_pred CCCCCEEEEEEEEEeCCeEEEeeeeEEEEEECCCCccceEEEEEe--ecCceEEEEeecCCCceeEEEEEecCcee
Confidence 688998764 333311111 25555554321 13333322 1112456668999999974443 335544
No 128
>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=26.00 E-value=1.1e+02 Score=21.68 Aligned_cols=14 Identities=29% Similarity=0.432 Sum_probs=10.9
Q ss_pred ceecCCeEEEeecC
Q psy10530 61 PVRKDDEVQVVRGH 74 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~ 74 (141)
-|++||.|.|+.-.
T Consensus 65 ~V~~G~~V~i~~~~ 78 (122)
T TIGR03170 65 LVKRGDTVTVIARG 78 (122)
T ss_pred EEcCCCEEEEEEec
Confidence 48999999887643
No 129
>PF07449 HyaE: Hydrogenase-1 expression protein HyaE; InterPro: IPR010893 This family contains bacterial hydrogenase-1 expression proteins approximately 120 residues long. This includes the Escherichia coli protein HyaE, and the homologous proteins HoxO of Ralstonia eutropha (Alcaligenes eutrophus) and HupG of Rhizobium leguminosarum. Deletion of the hoxO gene in R. eutropha led to complete loss of the uptake [NiFe] hydrogenase activity, suggesting that it has a critical role in hydrogenase assembly [].; PDB: 2QSI_B 2ES7_A 2GZP_A 2JZT_A 2HFD_A 2QGV_G.
Probab=25.98 E-value=60 Score=23.96 Aligned_cols=39 Identities=21% Similarity=0.507 Sum_probs=29.2
Q ss_pred CCccceeeeeccCCHHHHHhhCCcccc----eecCCeEEEeec
Q psy10530 35 PSHIRRRIMSAPLSKELRQKYNVRSMP----VRKDDEVQVVRG 73 (141)
Q Consensus 35 p~h~r~k~msapLSkeLr~ky~~rs~~----IrkGD~V~Vi~G 73 (141)
|...+.-.+....+.+|+..||++.+| +|-|+.+-+|.|
T Consensus 58 ~~~~~~avv~~~~e~~L~~r~gv~~~PaLvf~R~g~~lG~i~g 100 (107)
T PF07449_consen 58 PGRFRGAVVARAAERALAARFGVRRWPALVFFRDGRYLGAIEG 100 (107)
T ss_dssp TTSEEEEEEEHHHHHHHHHHHT-TSSSEEEEEETTEEEEEEES
T ss_pred hCccceEEECchhHHHHHHHhCCccCCeEEEEECCEEEEEecC
Confidence 444556667778899999999999887 677777777766
No 130
>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=25.86 E-value=2.1e+02 Score=21.39 Aligned_cols=38 Identities=16% Similarity=0.175 Sum_probs=26.3
Q ss_pred ccceecCCeEEEeecCCCCeeeceEEEEEccC-CEEEEee
Q psy10530 59 SMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK-FVIYIEK 97 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk-~~V~VEg 97 (141)
.+.|+.||.|.|.+-. .....|.|.+++... +...|.+
T Consensus 5 ~~~i~vGD~V~v~~~~-~~~~va~Ie~i~ed~~g~~~v~v 43 (130)
T cd04721 5 GVTISVHDFVYVLSEE-EDRYVAYIEDLYEDKKGSKMVKV 43 (130)
T ss_pred CEEEECCCEEEEeCCC-CCcEEEEEEEEEEcCCCCEEEEE
Confidence 4669999999999755 333358999988864 4444443
No 131
>COG0668 MscS Small-conductance mechanosensitive channel [Cell envelope biogenesis, outer membrane]
Probab=25.85 E-value=1.1e+02 Score=24.45 Aligned_cols=26 Identities=19% Similarity=0.292 Sum_probs=20.0
Q ss_pred cceecCCeEEEeecCCCCeeeceEEEEEccC
Q psy10530 60 MPVRKDDEVQVVRGHYKGQQVGKVVQSYRKK 90 (141)
Q Consensus 60 ~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk 90 (141)
-|++.||-|++-. |-+ |.|..+.-..
T Consensus 146 ~~f~vGD~I~i~~----~~~-G~V~~i~~~~ 171 (316)
T COG0668 146 RPFKVGDWIEIGS----GVE-GTVEDIGLRS 171 (316)
T ss_pred cCcCcCCEEEECC----Cce-EEEEEEEEEE
Confidence 3678999999866 666 8888887653
No 132
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=25.80 E-value=1.8e+02 Score=21.64 Aligned_cols=40 Identities=20% Similarity=0.178 Sum_probs=29.1
Q ss_pred hhCCcccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEE
Q psy10530 54 KYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYI 95 (141)
Q Consensus 54 ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~V 95 (141)
.+|.+--.-+.||.|..-+|. .|+. |.|+..+..++.|++
T Consensus 66 ~~G~~v~~p~~GDiv~f~~~~-~~HV-Gi~~g~~~~~g~i~~ 105 (129)
T TIGR02594 66 RYGTKLSKPAYGCIAVKRRGG-GGHV-GFVVGKDKQTGTIIV 105 (129)
T ss_pred HcCCcCCCCCccEEEEEECCC-CCEE-EEEEeEcCCCCEEEE
Confidence 456543345899999776654 7888 999999887666665
No 133
>PRK11713 16S ribosomal RNA methyltransferase RsmE; Provisional
Probab=25.70 E-value=1.1e+02 Score=24.70 Aligned_cols=48 Identities=21% Similarity=0.320 Sum_probs=32.1
Q ss_pred cCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEccCCEEEE
Q psy10530 46 PLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYI 95 (141)
Q Consensus 46 pLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~V 95 (141)
.|+++.. .|=.+-++++.||.|.|.-|.- +.-.|+|..++++...+.+
T Consensus 15 ~l~~~~~-~Hl~~VlR~~~Gd~i~v~~g~g-~~~~~~i~~i~~~~~~~~i 62 (234)
T PRK11713 15 ILDGEEA-HHLVRVLRLKEGDELRLFDGDG-GEYLAEITEIGKKEVELEI 62 (234)
T ss_pred EEChHHH-hHHHhhccCCCCCEEEEEeCCC-CEEEEEEEEecCcEEEEEE
Confidence 4555433 4546778999999999998863 3234788888765444434
No 134
>TIGR03784 marine_sortase sortase, marine proteobacterial type. Members of this protein family are sortase enzymes, cysteine transpeptidases involved in protein sorting activities. Members of this family tend to be found in proteobacteria, rather than in Gram-positive bacteria where sortases attach proteins to the Gram-positive cell wall or participate in pilin cross-linking. Many species with this sortase appear to contain a signal target sequence, a protein with a Vault protein inter-alpha-trypsin domain (pfam08487) and a von Willebrand factor type A domain (pfam00092), encoded by an adjacent gene. These sortases are designated subfamily 6 according to Comfort and Clubb (2004).
Probab=25.51 E-value=2.5e+02 Score=22.05 Aligned_cols=44 Identities=11% Similarity=0.074 Sum_probs=24.2
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeEeccCCcEEEecccccce
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQRDKVNGATVYVGIHPSKC 117 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~~K~~G~~v~~pIhpSNV 117 (141)
.+++||+|.|...+ |+. ..-.|.++.++.++...+..|-....+
T Consensus 108 ~L~~GD~I~v~~~~--g~~-----------~~Y~V~~~~iV~~~d~~v~~~~~~~~L 151 (174)
T TIGR03784 108 ELRPGDVIRLQTPD--GQW-----------QSYQVTATRVVDESETGLDLPADDSQL 151 (174)
T ss_pred hCCCCCEEEEEECC--CeE-----------EEEEEeEEEEECCccceeccCCCCCEE
Confidence 38899999887764 332 123355555555554444444333333
No 135
>CHL00010 infA translation initiation factor 1
Probab=25.50 E-value=98 Score=21.21 Aligned_cols=42 Identities=21% Similarity=0.366 Sum_probs=25.8
Q ss_pred eeeccCCHHHHHhhCCcccceecCCeEEEeecCCCCeeeceEEEEEc
Q psy10530 42 IMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGHYKGQQVGKVVQSYR 88 (141)
Q Consensus 42 ~msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV~~V~r 88 (141)
...+.+.--||. +.+.+..||.|.|--=.+-... |.|+-=+.
T Consensus 31 ~~~c~~rGklr~----~~i~~~vGD~V~ve~~~~~~~~-g~Ii~r~~ 72 (78)
T CHL00010 31 QVLGYISGKIRR----NSIRILPGDRVKVELSPYDLTK-GRIIYRLR 72 (78)
T ss_pred EEEEEeccceec----CCcccCCCCEEEEEEcccCCCe-EEEEEEec
Confidence 445555555552 4677889999999744443444 66654443
No 136
>smart00326 SH3 Src homology 3 domains. Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.
Probab=25.50 E-value=69 Score=18.49 Aligned_cols=20 Identities=20% Similarity=0.383 Sum_probs=15.0
Q ss_pred cccceecCCeEEEeecCCCC
Q psy10530 58 RSMPVRKDDEVQVVRGHYKG 77 (141)
Q Consensus 58 rs~~IrkGD~V~Vi~G~~KG 77 (141)
..+.+++||.|.|+....-|
T Consensus 17 ~~l~~~~Gd~v~v~~~~~~~ 36 (58)
T smart00326 17 DELSFKKGDIITVLEKSDDG 36 (58)
T ss_pred CCCCCCCCCEEEEEEcCCCC
Confidence 34568999999999876433
No 137
>PF10844 DUF2577: Protein of unknown function (DUF2577); InterPro: IPR022555 This family of proteins has no known function
Probab=25.12 E-value=96 Score=22.07 Aligned_cols=12 Identities=25% Similarity=0.482 Sum_probs=10.9
Q ss_pred ceecCCeEEEee
Q psy10530 61 PVRKDDEVQVVR 72 (141)
Q Consensus 61 ~IrkGD~V~Vi~ 72 (141)
.++.||+|.+++
T Consensus 76 ~Lk~GD~V~ll~ 87 (100)
T PF10844_consen 76 GLKVGDKVLLLR 87 (100)
T ss_pred CCcCCCEEEEEE
Confidence 578999999999
No 138
>PF02470 MCE: mce related protein; InterPro: IPR003399 This domain is found in all 24 mce genes associated with the four mammalian cell entry (mce) operons of Mycobacterium tuberculosis and their homologs in other Actinomycetales [, ]. The archetype (mce1A, Rv0169), was isolated as being necessary for colonisation of, and survival within, the macrophage []. The domain is also found in: Chloroplast Ycf22 and related cyanobacterial homologs, the majority of which have an N-terminal transmembrane domain and are putative ABC transporters. Proteobacterial homologs, which include YrbD, YebT, VpsC and Ttg2C, the latter being annotated as a toluene tolerance proteins, belong to the periplasmic substrate-binding ABC transporter superfamily.
Probab=25.08 E-value=1.1e+02 Score=20.26 Aligned_cols=30 Identities=23% Similarity=0.358 Sum_probs=21.7
Q ss_pred eecCCeEEEeecCCCCeeeceEEEE--EccCCEEEEe
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQS--YRKKFVIYIE 96 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V--~rkk~~V~VE 96 (141)
|..|..|. ++|-+.|+|.+| +...+.|.|+
T Consensus 15 L~~gs~V~-----~~Gv~VG~V~~i~l~~~~~~v~v~ 46 (81)
T PF02470_consen 15 LSVGSPVR-----YRGVEVGKVTSIELDPDGNRVRVT 46 (81)
T ss_pred CCCcCEEE-----ECCEEEEEEEEEEEcCCCCEEEEE
Confidence 55666665 468888999999 6666776664
No 139
>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=24.74 E-value=59 Score=20.94 Aligned_cols=24 Identities=21% Similarity=0.369 Sum_probs=15.5
Q ss_pred ccceecCCeEEEeecCCCCeeeceE
Q psy10530 59 SMPVRKDDEVQVVRGHYKGQQVGKV 83 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~~KGk~~GkV 83 (141)
..++..||.|.+-.-.+-+.+ |-|
T Consensus 38 ~~~~~vGD~V~~~~~~~~~~~-g~I 61 (64)
T cd04451 38 YIRILPGDRVKVELSPYDLTK-GRI 61 (64)
T ss_pred CcccCCCCEEEEEEeecCCCE-EEE
Confidence 455889999988755443334 544
No 140
>cd03688 eIF2_gamma_II eIF2_gamma_II: this subfamily represents the domain II of the gamma subunit of eukaryotic translation initiation factor 2 (eIF2-gamma) found in Eukaryota and Archaea. eIF2 is a G protein that delivers the methionyl initiator tRNA to the small ribosomal subunit and releases it upon GTP hydrolysis after the recognition of the initiation codon. eIF2 is composed three subunits, alpha, beta and gamma. Subunit gamma shows strongest conservation, and it confers both tRNA binding and GTP/GDP binding.
Probab=24.72 E-value=1.9e+02 Score=21.77 Aligned_cols=19 Identities=16% Similarity=0.309 Sum_probs=13.9
Q ss_pred ceecCCeEEEeecCCCCee
Q psy10530 61 PVRKDDEVQVVRGHYKGQQ 79 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~ 79 (141)
.++.||+|+|..|-..-+.
T Consensus 39 ~lkvgdeIEIrpg~~~~~~ 57 (113)
T cd03688 39 VLKVGDEIEIRPGIVVKDE 57 (113)
T ss_pred EEeCCCEEEEeeceeeecC
Confidence 3789999999988544333
No 141
>COG1153 FwdD Formylmethanofuran dehydrogenase subunit D [Energy production and conversion]
Probab=24.65 E-value=67 Score=24.76 Aligned_cols=37 Identities=24% Similarity=0.264 Sum_probs=26.1
Q ss_pred cccccccCCCCccceeeeeccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 26 KNRKRHFNAPSHIRRRIMSAPLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 26 KqRK~~~nAp~h~r~k~msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
|--+-+|||-. .+-++.+..+++| +..||.|+|.+-.
T Consensus 21 K~~~~Y~~a~a-------~~~inp~D~~~Lg-----v~EGD~VkVkse~ 57 (128)
T COG1153 21 KFTDEYFNACA-------VCEINPEDMKQLG-----VSEGDKVKVKSEF 57 (128)
T ss_pred cchhhhhhhee-------EEEECHHHHHHhC-----CCcCCeEEEEecC
Confidence 33444555543 4567888888888 8899999998743
No 142
>cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=24.40 E-value=2.9e+02 Score=20.17 Aligned_cols=38 Identities=24% Similarity=0.235 Sum_probs=24.1
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCC----EEEEeeeeEeccCCcEE
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKF----VIYIEKIQRDKVNGATV 108 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~----~V~VEgvn~~K~~G~~v 108 (141)
|+..||++.+. ++|+.+..++. .|.+ .+...+.+|..+
T Consensus 88 PV~~GDtl~~~---------~~V~~~~~~~~~~~~~v~~-~~~~~nq~g~~V 129 (142)
T cd03452 88 PVYPGDTIQVR---------LTCKRKIPRDGQDYGVVRW-DAEVTNQNGELV 129 (142)
T ss_pred CCCCCCEEEEE---------EEEEEEeecCCCCcEEEEE-EEEEEecCCCEE
Confidence 78899998763 67887765432 3444 455556677654
No 143
>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=24.10 E-value=1e+02 Score=25.16 Aligned_cols=29 Identities=28% Similarity=0.155 Sum_probs=14.7
Q ss_pred ccceecCCeEEEeecC-CCCeeeceEEEEEc
Q psy10530 59 SMPVRKDDEVQVVRGH-YKGQQVGKVVQSYR 88 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~-~KGk~~GkV~~V~r 88 (141)
.-.|+.||.|.+..+. ..... -+|+.|..
T Consensus 103 A~~V~~Gd~v~~~~~~~~~~~~-~~V~~v~~ 132 (217)
T PF01079_consen 103 ASDVRVGDCVLVSDEGGGKLRP-SRVVRVST 132 (217)
T ss_dssp GGG--TT-EEEEE-TTT--EEE-EEEEEEEE
T ss_pred hhhCCCCCEEEEEEcCCCcEEE-EEEEEEEE
Confidence 3369999999994443 33344 66776654
No 144
>PTZ00051 thioredoxin; Provisional
Probab=24.08 E-value=96 Score=20.39 Aligned_cols=26 Identities=31% Similarity=0.496 Sum_probs=18.6
Q ss_pred CHHHHHhhCCcccc----eecCCeEEEeec
Q psy10530 48 SKELRQKYNVRSMP----VRKDDEVQVVRG 73 (141)
Q Consensus 48 SkeLr~ky~~rs~~----IrkGD~V~Vi~G 73 (141)
..++.++|+++++| ++.|..|..+.|
T Consensus 60 ~~~~~~~~~v~~~Pt~~~~~~g~~~~~~~G 89 (98)
T PTZ00051 60 LSEVAEKENITSMPTFKVFKNGSVVDTLLG 89 (98)
T ss_pred hHHHHHHCCCceeeEEEEEeCCeEEEEEeC
Confidence 46789999999988 455555555555
No 145
>cd00508 MopB_CT_Fdh-Nap-like This CD includes formate dehydrogenases (Fdh) H and N; nitrate reductases, Nap and Nas; and other related proteins. Formate dehydrogenase H is a component of the anaerobic formate hydrogen lyase complex and catalyzes the reversible oxidation of formate to CO2 with the release of a proton and two electrons. Formate dehydrogenase N (alpha subunit) is the major electron donor to the bacterial nitrate respiratory chain and nitrate reductases, Nap and Nas, catalyze the reduction of nitrate to nitrite. This CD (MopB_CT_Fdh-Nap-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=23.88 E-value=1.1e+02 Score=21.05 Aligned_cols=25 Identities=16% Similarity=0.248 Sum_probs=20.7
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
.-++.+.-+++| |..||.|.|-++.
T Consensus 37 v~inp~dA~~lg-----i~~Gd~V~v~~~~ 61 (120)
T cd00508 37 VEIHPEDAARLG-----IKDGDLVRVSSRR 61 (120)
T ss_pred EEECHHHHHHcC-----CCCCCEEEEEeCC
Confidence 457778888888 7999999999865
No 146
>PF01568 Molydop_binding: Molydopterin dinucleotide binding domain; InterPro: IPR006657 A domain in this entry corresponds to the C-terminal domain IV in dimethyl sulphoxide (DMSO)reductase which interacts with the 2-amino pyrimidone ring of both molybdopterin guanine dinucleotide molecules [].; GO: 0016491 oxidoreductase activity, 0030151 molybdenum ion binding, 0055114 oxidation-reduction process; PDB: 2IVF_A 1OGY_G 3ML1_A 3O5A_A 1TI2_G 1VLE_M 1VLD_U 1VLF_O 1TI4_I 1TI6_E ....
Probab=23.17 E-value=66 Score=22.02 Aligned_cols=26 Identities=19% Similarity=0.197 Sum_probs=19.5
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
..-++.+.-+++| |+.||.|.|.+-.
T Consensus 31 ~v~inp~dA~~~G-----i~~Gd~V~v~s~~ 56 (110)
T PF01568_consen 31 FVEINPEDAAKLG-----IKDGDWVRVSSPR 56 (110)
T ss_dssp EEEEEHHHHHHCT-------TTCEEEEEETT
T ss_pred EEEEcHHHHHHhc-----CcCCCEEEEEecc
Confidence 4557788888888 8999999999754
No 147
>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=22.96 E-value=1.3e+02 Score=20.06 Aligned_cols=12 Identities=25% Similarity=0.479 Sum_probs=7.7
Q ss_pred eecCCeEEEeec
Q psy10530 62 VRKDDEVQVVRG 73 (141)
Q Consensus 62 IrkGD~V~Vi~G 73 (141)
|++||+|.+...
T Consensus 27 i~~Gd~v~i~P~ 38 (83)
T cd03698 27 IQKGDTLLVMPS 38 (83)
T ss_pred EeCCCEEEEeCC
Confidence 566666666654
No 148
>cd02792 MopB_CT_Formate-Dh-Na-like Formate dehydrogenase N, alpha subunit (Formate-Dh-Na) is a major component of nitrate respiration in bacteria such as in the E. coli formate dehydrogenase N (Fdh-N). Fdh-N is a membrane protein that is a complex of three different subunits and is the major electron donor to the nitrate respiratory chain. Also included in this CD is the Desulfovibrio gigas tungsten formate dehydrogenase, DgW-FDH. In contrast to Fdh-N, which is a functional heterotrimer, DgW-FDH is a heterodimer. The DgW-FDH complex is composed of a large subunit carrying the W active site and one [4Fe-4S] center, and a small subunit that harbors a series of three [4Fe-4S] clusters as well as a putative vacant binding site for a fourth cluster. The smaller subunit is not included in this alignment. This CD (MopB_CT_Formate-Dh-Na-like) is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=22.70 E-value=1.2e+02 Score=21.19 Aligned_cols=25 Identities=24% Similarity=0.294 Sum_probs=20.9
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
.-++.+.-+++| |..||.|.|.+..
T Consensus 37 v~i~p~dA~~lg-----i~~Gd~V~v~s~~ 61 (122)
T cd02792 37 VEISPELAAERG-----IKNGDMVWVSSPR 61 (122)
T ss_pred EEECHHHHHHcC-----CCCCCEEEEEcCC
Confidence 457888888888 7899999999865
No 149
>PLN00208 translation initiation factor (eIF); Provisional
Probab=22.53 E-value=1.1e+02 Score=24.04 Aligned_cols=32 Identities=16% Similarity=0.206 Sum_probs=23.6
Q ss_pred ccceecCCeEEEeecCCCCeeeceEEEEEccCC
Q psy10530 59 SMPVRKDDEVQVVRGHYKGQQVGKVVQSYRKKF 91 (141)
Q Consensus 59 s~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~ 91 (141)
.+.|+.||.|.|---.|--.. |.|+..+....
T Consensus 68 rIWI~~GD~VlVel~~~d~~K-gdIv~ry~~dq 99 (145)
T PLN00208 68 KVWIAAGDIILVGLRDYQDDK-ADVILKYMPDE 99 (145)
T ss_pred eEEecCCCEEEEEccCCCCCE-EEEEEEcCHHH
Confidence 478999999999555554455 88888877543
No 150
>TIGR01553 formate-DH-alph formate dehydrogenase, alpha subunit, proteobacterial-type. This model is well-defined, with a large, unpopulated trusted/noise gap.
Probab=22.43 E-value=1.7e+02 Score=29.18 Aligned_cols=27 Identities=22% Similarity=0.299 Sum_probs=22.3
Q ss_pred eeccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 43 MSAPLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 43 msapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
|-.-+++||-+++| |+-||.|.|.+=.
T Consensus 913 ~fveI~p~~A~~~G-----I~~Gd~V~v~s~r 939 (1009)
T TIGR01553 913 MFCEISEELATEKG-----IQNGDKVILESVR 939 (1009)
T ss_pred cEEEECHHHHHHcC-----CcCCCEEEEEcCC
Confidence 34568899999999 6789999998866
No 151
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=22.08 E-value=1.5e+02 Score=20.86 Aligned_cols=28 Identities=25% Similarity=0.322 Sum_probs=18.6
Q ss_pred cceecCCeEEEeecCC------CCeeeceEEEEE
Q psy10530 60 MPVRKDDEVQVVRGHY------KGQQVGKVVQSY 87 (141)
Q Consensus 60 ~~IrkGD~V~Vi~G~~------KGk~~GkV~~V~ 87 (141)
+.++.||.|.|-.... +.=.+|.|+.+.
T Consensus 4 L~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ 37 (75)
T PF11302_consen 4 LSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCE 37 (75)
T ss_pred cccCCCCEEEEecCccccccCCCCcEEEEEEEEe
Confidence 4689999999977662 222257776553
No 152
>PRK12617 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.98 E-value=1.4e+02 Score=24.37 Aligned_cols=15 Identities=33% Similarity=0.392 Sum_probs=12.3
Q ss_pred ceecCCeEEEeecCC
Q psy10530 61 PVRKDDEVQVVRGHY 75 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~ 75 (141)
-|++||.|.|+....
T Consensus 155 lV~rG~~V~I~a~~~ 169 (214)
T PRK12617 155 LVRRGDTVPLVSRNG 169 (214)
T ss_pred eEcCCCEEEEEEecC
Confidence 499999999987653
No 153
>cd05705 S1_Rrp5_repeat_hs14 S1_Rrp5_repeat_hs14: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 14 (hs14). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.98 E-value=1.4e+02 Score=19.77 Aligned_cols=23 Identities=13% Similarity=0.212 Sum_probs=18.2
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccCCEEEE
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYI 95 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~V 95 (141)
++.||+|. ++|+.|+.++.+|.+
T Consensus 51 ~~~G~~v~-----------~kVl~id~~~~~i~L 73 (74)
T cd05705 51 LPEGKLLT-----------AKVLSVNSEKNLVEL 73 (74)
T ss_pred cCCCCEEE-----------EEEEEEECCCCEEec
Confidence 67899874 789999998877653
No 154
>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=21.97 E-value=1.2e+02 Score=20.64 Aligned_cols=12 Identities=8% Similarity=0.066 Sum_probs=6.3
Q ss_pred eecCCeEEEeec
Q psy10530 62 VRKDDEVQVVRG 73 (141)
Q Consensus 62 IrkGD~V~Vi~G 73 (141)
|+.||+|.++..
T Consensus 31 i~~gd~v~i~P~ 42 (91)
T cd03693 31 LKPGMVVTFAPA 42 (91)
T ss_pred eecCCEEEECCC
Confidence 455555555543
No 155
>PRK07018 flgA flagellar basal body P-ring biosynthesis protein FlgA; Reviewed
Probab=21.96 E-value=1.3e+02 Score=24.49 Aligned_cols=15 Identities=20% Similarity=0.209 Sum_probs=12.1
Q ss_pred cceecCCeEEEeecC
Q psy10530 60 MPVRKDDEVQVVRGH 74 (141)
Q Consensus 60 ~~IrkGD~V~Vi~G~ 74 (141)
.-|++||.|.|+...
T Consensus 175 ~~V~~G~~V~i~~~~ 189 (235)
T PRK07018 175 WVVCKGQTVSIIARG 189 (235)
T ss_pred cEeCCCCEEEEEEec
Confidence 348999999998764
No 156
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) [, , , ]. This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1EIK_A 2Y0S_Z 1DZF_A 3GTG_E 2VUM_E 3GTP_E 3GTO_E 3S17_E 3S1R_E 1I3Q_E ....
Probab=21.54 E-value=66 Score=22.35 Aligned_cols=35 Identities=31% Similarity=0.538 Sum_probs=17.6
Q ss_pred eeeeeccCCHHHHHhhCCc---------------ccceecCCeEEEeecC
Q psy10530 40 RRIMSAPLSKELRQKYNVR---------------SMPVRKDDEVQVVRGH 74 (141)
Q Consensus 40 ~k~msapLSkeLr~ky~~r---------------s~~IrkGD~V~Vi~G~ 74 (141)
+.+|+.-=-++|-++|++. .+-.+.||.|+|+|=.
T Consensus 12 H~ils~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S 61 (74)
T PF01191_consen 12 HEILSEEEKKELLKKYNIKPEQLPKILSSDPVARYLGAKPGDVVKIIRKS 61 (74)
T ss_dssp EEEE-HHHHHHHHHHTT--TTCSSEEETTSHHHHHTT--TTSEEEEEEEE
T ss_pred eEEcCHHHHHHHHHHhCCChhhCCcccccChhhhhcCCCCCCEEEEEecC
Confidence 4455555556677777763 2335666666666544
No 157
>PRK07696 sulfur carrier protein ThiS; Provisional
Probab=21.41 E-value=63 Score=21.32 Aligned_cols=14 Identities=21% Similarity=0.444 Sum_probs=11.2
Q ss_pred ccceecCCeEEEee
Q psy10530 59 SMPVRKDDEVQVVR 72 (141)
Q Consensus 59 s~~IrkGD~V~Vi~ 72 (141)
+..++.||.|+|++
T Consensus 49 ~~~L~~gD~iEIv~ 62 (67)
T PRK07696 49 DTSVFDGDQIEIVT 62 (67)
T ss_pred ceecCCCCEEEEEE
Confidence 45689999999875
No 158
>KOG4792|consensus
Probab=21.29 E-value=83 Score=27.05 Aligned_cols=30 Identities=23% Similarity=0.446 Sum_probs=22.9
Q ss_pred hhCCcccceecCCeEEEeecCCCCeeeceE
Q psy10530 54 KYNVRSMPVRKDDEVQVVRGHYKGQQVGKV 83 (141)
Q Consensus 54 ky~~rs~~IrkGD~V~Vi~G~~KGk~~GkV 83 (141)
-|..-.+.+.+||.|+|..=.--|+..|++
T Consensus 240 AYDkTaL~levGdiVkVTk~ninGqwegEl 269 (293)
T KOG4792|consen 240 AYDKTALALEVGDIVKVTKKNINGQWEGEL 269 (293)
T ss_pred ccChhhhhhhcCcEEEEEeeccCceeeeee
Confidence 477888999999999998766666654443
No 159
>cd02778 MopB_CT_Thiosulfate-R-like The MopB_CT_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Also included in this CD is the phenylacetyl-CoA:acceptor oxidoreductase, large subunit (PadB2), which has been characterized as a membrane-bound molybdenum-iron-sulfur enzyme involved in anaerobic metabolism of phenylalanine in the denitrifying bacterium Thauera aromatica. The MopB_CT_Thiosulfate-R-like CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=21.15 E-value=1e+02 Score=21.59 Aligned_cols=26 Identities=15% Similarity=0.295 Sum_probs=21.8
Q ss_pred eccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 44 SAPLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 44 sapLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
..-|+.+.-+++| |.-||.|.|.++.
T Consensus 31 ~v~i~p~dA~~~g-----i~~Gd~V~v~s~~ 56 (123)
T cd02778 31 TLWINPETAARLG-----IKDGDRVEVSSAR 56 (123)
T ss_pred eEEECHHHHHHcC-----CCCCCEEEEEeCC
Confidence 4568899999998 6789999999865
No 160
>PF11160 DUF2945: Protein of unknown function (DUF2945); InterPro: IPR021331 This family of proteins has no known function.
Probab=20.97 E-value=2.4e+02 Score=18.85 Aligned_cols=32 Identities=25% Similarity=0.288 Sum_probs=22.9
Q ss_pred CCeEEEeecCCCCeeeceEEEEEccCCEEEEeeeeE
Q psy10530 65 DDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIEKIQR 100 (141)
Q Consensus 65 GD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn~ 100 (141)
||.|.==++. |...|+|.++..+.. .+.|.++
T Consensus 1 GD~V~W~s~~--g~~~G~V~~~~t~~~--~~~G~~v 32 (62)
T PF11160_consen 1 GDKVRWNSGQ--GTTTGTVVEVHTEPT--EIKGRTV 32 (62)
T ss_pred CCEEEEcCCC--CeEEEEEEEEEecce--eECCEEe
Confidence 6777774443 666799999998754 5788765
No 161
>COG2100 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=20.95 E-value=1.1e+02 Score=27.61 Aligned_cols=46 Identities=26% Similarity=0.462 Sum_probs=29.5
Q ss_pred HHHHHhhCCc-----------------ccceecCCeEE---EeecCCCCeeeceEEEEEccCCEEEEeeee
Q psy10530 49 KELRQKYNVR-----------------SMPVRKDDEVQ---VVRGHYKGQQVGKVVQSYRKKFVIYIEKIQ 99 (141)
Q Consensus 49 keLr~ky~~r-----------------s~~IrkGD~V~---Vi~G~~KGk~~GkV~~V~rkk~~V~VEgvn 99 (141)
.||-++||++ ..|.+.||.|. |..|.+||.- +.|.+. -.|.|-+.|
T Consensus 322 relEketg~kpLilkP~~fG~~pRp~lp~PF~rGevv~aevV~~Gr~kGEm----lavArd-RvIav~~~~ 387 (414)
T COG2100 322 RELEKETGVKPLILKPGEFGMHPRPRLPKPFKRGEVVKAEVVLPGRLKGEM----LAVARD-RVIAVINSN 387 (414)
T ss_pred HHHHHHhCCCccccChhhcCCCcCCCCCCccccCcEEEEEEEecceecceE----EEEecc-cEEEEecCc
Confidence 4677788877 45789999764 6789988754 445442 234444443
No 162
>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=20.88 E-value=2.2e+02 Score=17.85 Aligned_cols=24 Identities=8% Similarity=0.146 Sum_probs=18.6
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEccCCEEEE
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYI 95 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~V 95 (141)
.++.||++.+ +|++++..+.++.+
T Consensus 44 ~~~~Gd~i~~-----------~V~~id~~~~~i~l 67 (69)
T cd05697 44 KFKPGLKVKC-----------RVLSVEPERKRLVL 67 (69)
T ss_pred cCCCCCEEEE-----------EEEEEECCCCEEEE
Confidence 4778998864 78888888877765
No 163
>cd02788 MopB_CT_NDH-1_NuoG2-N7 MopB_CT_NDH-1_NuoG2-N7: C-terminal region of the NuoG-like subunit (of the variant with a [4Fe-4S] cluster, N7) of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1) found in various bacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain, is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Unique to this group, compared to the other prokaryotic and eukaryotic groups
Probab=20.78 E-value=1.1e+02 Score=21.11 Aligned_cols=25 Identities=24% Similarity=0.243 Sum_probs=21.1
Q ss_pred ccCCHHHHHhhCCcccceecCCeEEEeecC
Q psy10530 45 APLSKELRQKYNVRSMPVRKDDEVQVVRGH 74 (141)
Q Consensus 45 apLSkeLr~ky~~rs~~IrkGD~V~Vi~G~ 74 (141)
.-++.+.-++|| |.-||.|.|.++.
T Consensus 31 v~inp~dA~~lG-----i~~Gd~V~v~s~~ 55 (96)
T cd02788 31 ARLSPADAARLG-----LADGDLVEFSLGD 55 (96)
T ss_pred EEECHHHHHHcC-----CCCCCEEEEEECC
Confidence 567888999999 6789999998776
No 164
>KOG2996|consensus
Probab=20.75 E-value=79 Score=30.66 Aligned_cols=13 Identities=15% Similarity=0.473 Sum_probs=10.7
Q ss_pred cceecCCeEEEee
Q psy10530 60 MPVRKDDEVQVVR 72 (141)
Q Consensus 60 ~~IrkGD~V~Vi~ 72 (141)
+.++.||.|.+..
T Consensus 822 LSlk~GDvV~i~~ 834 (865)
T KOG2996|consen 822 LSLKEGDVVKIYD 834 (865)
T ss_pred cccccCCEEEEeh
Confidence 4489999999973
No 165
>PRK11281 hypothetical protein; Provisional
Probab=20.57 E-value=1.3e+02 Score=30.44 Aligned_cols=23 Identities=35% Similarity=0.511 Sum_probs=18.3
Q ss_pred ceecCCeEEEeecCCCCeeeceEEEEEcc
Q psy10530 61 PVRKDDEVQVVRGHYKGQQVGKVVQSYRK 89 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~KGk~~GkV~~V~rk 89 (141)
|++.||.|.| | |.. |.|.+|.-.
T Consensus 938 PfrIGD~I~I--~---~~~-G~V~~I~lR 960 (1113)
T PRK11281 938 PVRIGDTVTI--G---TFS-GTVSKIRIR 960 (1113)
T ss_pred CcCCCCEEEE--C---CEE-EEEEEEEeE
Confidence 7899999998 3 466 999888653
No 166
>COG3700 AphA Acid phosphatase (class B) [General function prediction only]
Probab=20.56 E-value=37 Score=28.31 Aligned_cols=94 Identities=26% Similarity=0.315 Sum_probs=59.2
Q ss_pred ccCCCCccceeeeeccCCHHH------HHhhC-------Cc--------ccceecCCeEEEeecCCCCeeeceEEEEEcc
Q psy10530 31 HFNAPSHIRRRIMSAPLSKEL------RQKYN-------VR--------SMPVRKDDEVQVVRGHYKGQQVGKVVQSYRK 89 (141)
Q Consensus 31 ~~nAp~h~r~k~msapLSkeL------r~ky~-------~r--------s~~IrkGD~V~Vi~G~~KGk~~GkV~~V~rk 89 (141)
.|..|.-.|.|---+|=|.|. |++-+ +. .|+.+.||.|..+.|.-.|+. -.|....-+
T Consensus 75 LFsSp~F~~Gk~~~sPgs~DyLknq~FW~~vn~g~D~~SIPKevA~qLI~MHq~RGD~i~FvTGRt~gk~-d~vsk~Lak 153 (237)
T COG3700 75 LFSSPGFWRGKKYFSPGSEDYLKNQVFWEKVNNGWDEFSIPKEVARQLIDMHQRRGDAIYFVTGRTPGKT-DTVSKTLAK 153 (237)
T ss_pred EecccccccCccccCCChHHhhcCHHHHHHHhcCCccccchHHHHHHHHHHHHhcCCeEEEEecCCCCcc-cccchhHHh
Confidence 456666666666666666554 43333 22 578999999999999999998 888888887
Q ss_pred CCEEEEeeeeEe-----cc-CC-cEEEecccccceEEEeCCCChh
Q psy10530 90 KFVIYIEKIQRD-----KV-NG-ATVYVGIHPSKCVIVKLKMDKD 127 (141)
Q Consensus 90 k~~V~VEgvn~~-----K~-~G-~~v~~pIhpSNV~i~~l~ldk~ 127 (141)
.+.| .+.+-+ |+ .+ -+....|.--|+.|.--+.|.|
T Consensus 154 ~F~i--~~m~pv~f~Gdk~k~~qy~Kt~~i~~~~~~IhYGDSD~D 196 (237)
T COG3700 154 NFHI--TNMNPVIFAGDKPKPGQYTKTQWIQDKNIRIHYGDSDND 196 (237)
T ss_pred hccc--CCCcceeeccCCCCcccccccHHHHhcCceEEecCCchh
Confidence 7655 332222 11 01 1333456666777765555443
No 167
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=20.55 E-value=59 Score=24.79 Aligned_cols=18 Identities=28% Similarity=0.379 Sum_probs=14.9
Q ss_pred CCcccceecCCeEEEeec
Q psy10530 56 NVRSMPVRKDDEVQVVRG 73 (141)
Q Consensus 56 ~~rs~~IrkGD~V~Vi~G 73 (141)
.++.+-||.||.|.|=.-
T Consensus 54 dv~~LDlRIGD~Vkv~~~ 71 (131)
T PF08605_consen 54 DVKYLDLRIGDTVKVDGP 71 (131)
T ss_pred cEeeeeeecCCEEEECCC
Confidence 467789999999998763
No 168
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=20.33 E-value=64 Score=20.97 Aligned_cols=14 Identities=29% Similarity=0.342 Sum_probs=11.4
Q ss_pred ecCCeEEEeecCCC
Q psy10530 63 RKDDEVQVVRGHYK 76 (141)
Q Consensus 63 rkGD~V~Vi~G~~K 76 (141)
+.||.|+..+|-.+
T Consensus 2 ~~GDvV~LKSGGp~ 15 (53)
T PF09926_consen 2 KIGDVVQLKSGGPR 15 (53)
T ss_pred CCCCEEEEccCCCC
Confidence 57999999999544
No 169
>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=20.31 E-value=2.1e+02 Score=18.14 Aligned_cols=24 Identities=21% Similarity=0.174 Sum_probs=17.6
Q ss_pred eecCCeEEEeecCCCCeeeceEEEEEccCCEEEEe
Q psy10530 62 VRKDDEVQVVRGHYKGQQVGKVVQSYRKKFVIYIE 96 (141)
Q Consensus 62 IrkGD~V~Vi~G~~KGk~~GkV~~V~rkk~~V~VE 96 (141)
++.||.|. ++|+.+++++..+.+.
T Consensus 48 ~~~Gd~v~-----------~~V~~~d~~~~~i~ls 71 (73)
T cd05706 48 FKKNDIVR-----------ACVLSVDVPNKKIALS 71 (73)
T ss_pred cCCCCEEE-----------EEEEEEeCCCCEEEEE
Confidence 67899875 5788888877766653
No 170
>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=20.03 E-value=3.1e+02 Score=19.95 Aligned_cols=35 Identities=11% Similarity=0.030 Sum_probs=25.2
Q ss_pred ceecCCeEEEeecCC--CCeeeceEEEEEccC-CEEEEe
Q psy10530 61 PVRKDDEVQVVRGHY--KGQQVGKVVQSYRKK-FVIYIE 96 (141)
Q Consensus 61 ~IrkGD~V~Vi~G~~--KGk~~GkV~~V~rkk-~~V~VE 96 (141)
-++.||-|.|.+... +=- +|+|.++.... +..++.
T Consensus 3 ~~~vGD~V~v~~~~~~~~py-IgrI~~i~e~~~g~~~~~ 40 (121)
T cd04714 3 IIRVGDCVLFKSPGRPSLPY-VARIESLWEDPEGNMVVR 40 (121)
T ss_pred EEEcCCEEEEeCCCCCCCCE-EEEEEEEEEcCCCCEEEE
Confidence 378999999998765 233 49999998754 455554
Done!