Query 033011
Match_columns 129
No_of_seqs 121 out of 665
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 08:42:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033011.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033011hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2659 LisH motif-containing 100.0 9.7E-35 2.1E-39 215.6 12.7 127 2-128 56-183 (228)
2 PF10607 CLTH: CTLH/CRA C-term 100.0 1.9E-33 4.1E-38 196.9 11.7 117 10-128 1-120 (145)
3 KOG0396 Uncharacterized conser 99.9 7.2E-24 1.6E-28 165.6 11.5 121 5-127 147-268 (389)
4 KOG2817 Predicted E3 ubiquitin 99.8 9.8E-18 2.1E-22 132.4 11.6 116 8-125 153-272 (394)
5 smart00757 CRA CT11-RanBPM. pr 99.7 4.1E-17 8.9E-22 107.1 7.1 66 63-128 1-68 (99)
6 smart00668 CTLH C-terminal to 99.6 1.6E-15 3.4E-20 90.6 5.9 55 11-65 2-56 (58)
7 KOG1477 SPRY domain-containing 98.4 6.3E-08 1.4E-12 79.7 0.5 106 24-129 312-427 (469)
8 KOG0293 WD40 repeat-containing 97.3 0.00079 1.7E-08 54.7 6.7 84 13-100 52-136 (519)
9 PF14559 TPR_19: Tetratricopep 90.6 1.7 3.7E-05 25.3 6.1 56 20-80 1-56 (68)
10 PF04494 TFIID_90kDa: WD40 ass 88.5 1.5 3.4E-05 30.4 5.3 48 45-94 38-85 (142)
11 cd08044 TAF5_NTD2 TAF5_NTD2 is 81.0 3.4 7.3E-05 28.3 4.2 50 46-97 28-77 (133)
12 PF14276 DUF4363: Domain of un 78.0 5.3 0.00011 26.7 4.4 47 12-58 30-76 (121)
13 PF10607 CLTH: CTLH/CRA C-term 77.6 11 0.00023 25.7 5.9 92 7-112 37-136 (145)
14 PRK10564 maltose regulon perip 77.6 3 6.5E-05 32.9 3.4 42 13-62 260-301 (303)
15 KOG0275 Conserved WD40 repeat- 77.1 14 0.00029 30.0 6.9 111 6-124 36-150 (508)
16 PF12895 Apc3: Anaphase-promot 76.1 3.3 7.2E-05 25.4 2.8 52 16-73 31-82 (84)
17 COG3071 HemY Uncharacterized e 75.0 25 0.00055 28.8 8.1 73 15-99 268-340 (400)
18 KOG2910 Uncharacterized conser 73.4 19 0.00041 26.7 6.4 53 12-64 41-106 (209)
19 PTZ00196 60S ribosomal protein 73.1 7.8 0.00017 25.6 4.0 45 49-93 48-92 (98)
20 PF13838 Clathrin_H_link: Clat 72.7 5.8 0.00013 24.3 3.1 39 50-90 7-47 (66)
21 smart00668 CTLH C-terminal to 72.7 14 0.00031 20.8 4.8 28 52-79 4-31 (58)
22 PF14689 SPOB_a: Sensor_kinase 67.5 18 0.00038 21.5 4.4 35 9-43 22-56 (62)
23 COG5109 Uncharacterized conser 66.8 19 0.0004 28.9 5.5 91 4-98 132-224 (396)
24 COG5443 FlbT Flagellar biosynt 64.2 13 0.00028 25.9 3.8 33 7-39 91-123 (148)
25 PF01158 Ribosomal_L36e: Ribos 64.0 12 0.00026 24.7 3.5 44 49-92 48-91 (98)
26 KOG0396 Uncharacterized conser 63.5 40 0.00086 27.5 6.9 84 13-99 119-205 (389)
27 KOG1156 N-terminal acetyltrans 58.4 96 0.0021 27.3 8.7 77 13-94 188-264 (700)
28 PF12854 PPR_1: PPR repeat 58.2 17 0.00038 18.6 2.9 24 12-35 9-32 (34)
29 PRK00794 flbT flagellar biosyn 57.7 25 0.00055 24.3 4.3 31 8-38 91-121 (132)
30 COG0268 RpsT Ribosomal protein 57.4 20 0.00043 23.2 3.5 28 15-42 33-60 (88)
31 PF07035 Mic1: Colon cancer-as 57.3 30 0.00064 24.9 4.8 59 17-75 52-115 (167)
32 TIGR01470 cysG_Nterm siroheme 57.3 39 0.00084 24.8 5.6 64 12-76 135-204 (205)
33 PF07721 TPR_4: Tetratricopept 57.0 15 0.00033 17.5 2.4 17 18-34 9-25 (26)
34 PF13934 ELYS: Nuclear pore co 57.0 56 0.0012 24.4 6.5 56 16-78 114-169 (226)
35 PF04121 Nup84_Nup100: Nuclear 56.9 14 0.00031 32.2 3.6 27 10-36 133-159 (697)
36 PF14973 TINF2_N: TERF1-intera 56.7 51 0.0011 23.2 5.8 77 16-96 46-130 (145)
37 PF07378 FlbT: Flagellar prote 55.2 29 0.00063 23.8 4.3 33 6-38 87-119 (126)
38 COG5051 RPL36A Ribosomal prote 50.9 56 0.0012 21.2 4.7 45 49-96 50-94 (97)
39 TIGR00756 PPR pentatricopeptid 50.2 28 0.00062 16.6 2.9 23 15-37 5-27 (35)
40 TIGR00083 ribF riboflavin kina 50.2 18 0.00038 28.3 2.9 25 14-38 146-170 (288)
41 PF10827 DUF2552: Protein of u 50.1 12 0.00025 23.4 1.5 16 25-40 60-75 (79)
42 PRK07143 hypothetical protein; 50.1 12 0.00026 29.1 2.0 25 14-38 152-176 (279)
43 PF05791 Bacillus_HBL: Bacillu 49.2 37 0.0008 24.6 4.3 61 2-66 33-106 (184)
44 cd02064 FAD_synthetase_N FAD s 49.0 13 0.00029 26.6 1.9 24 14-37 148-171 (180)
45 PF12931 Sec16_C: Sec23-bindin 49.0 21 0.00045 27.6 3.1 20 16-35 1-20 (284)
46 PF14691 Fer4_20: Dihydroprymi 48.6 28 0.00061 23.2 3.4 28 49-76 38-65 (111)
47 PF14691 Fer4_20: Dihydroprymi 47.9 29 0.00063 23.2 3.3 24 15-38 43-66 (111)
48 PF15391 DUF4614: Domain of un 47.4 25 0.00055 25.7 3.1 49 27-75 113-178 (181)
49 KOG2235 Uncharacterized conser 46.7 58 0.0013 28.6 5.5 41 86-126 87-128 (776)
50 PRK00239 rpsT 30S ribosomal pr 46.3 38 0.00082 21.8 3.5 28 15-42 33-60 (88)
51 TIGR03338 phnR_burk phosphonat 46.0 48 0.001 23.8 4.6 25 52-76 182-206 (212)
52 PF12793 SgrR_N: Sugar transpo 45.6 37 0.00081 22.8 3.6 23 14-36 74-96 (115)
53 PF13371 TPR_9: Tetratricopept 45.6 59 0.0013 18.7 5.8 53 20-77 5-57 (73)
54 PF10075 PCI_Csn8: COP9 signal 45.1 77 0.0017 21.5 5.3 102 15-122 9-118 (143)
55 COG0264 Tsf Translation elonga 44.6 31 0.00068 27.2 3.5 40 23-62 31-97 (296)
56 KOG2659 LisH motif-containing 44.4 87 0.0019 23.8 5.7 70 4-76 22-91 (228)
57 PF07208 DUF1414: Protein of u 44.2 31 0.00067 19.4 2.5 18 110-127 24-41 (44)
58 KOG3452 60S ribosomal protein 43.8 74 0.0016 21.0 4.6 32 49-80 50-81 (102)
59 PF00627 UBA: UBA/TS-N domain; 43.7 20 0.00042 18.8 1.6 18 16-33 18-37 (37)
60 PF14498 Glyco_hyd_65N_2: Glyc 43.4 18 0.0004 26.9 2.0 32 6-37 50-81 (236)
61 PF13812 PPR_3: Pentatricopept 43.4 40 0.00088 16.2 2.9 22 15-36 6-27 (34)
62 PRK04984 fatty acid metabolism 42.7 58 0.0013 23.9 4.6 24 53-76 193-216 (239)
63 PF04157 EAP30: EAP30/Vps36 fa 42.1 1.4E+02 0.003 22.1 7.0 60 67-126 41-103 (223)
64 PRK05627 bifunctional riboflav 41.7 22 0.00049 27.9 2.3 25 14-38 163-187 (305)
65 PRK11534 DNA-binding transcrip 41.1 56 0.0012 23.8 4.3 26 52-77 186-211 (224)
66 PF01535 PPR: PPR repeat; Int 40.5 38 0.00082 15.8 2.4 21 16-36 6-26 (31)
67 KOG3060 Uncharacterized conser 40.2 1.5E+02 0.0032 23.3 6.4 65 23-92 99-163 (289)
68 PF12862 Apc5: Anaphase-promot 39.8 95 0.0021 19.5 6.2 28 18-45 6-33 (94)
69 PF12569 NARP1: NMDA receptor- 39.5 1.7E+02 0.0037 24.9 7.3 72 20-96 14-85 (517)
70 PRK12791 flbT flagellar biosyn 39.0 68 0.0015 22.2 4.1 28 11-38 91-118 (131)
71 PF13041 PPR_2: PPR repeat fam 38.6 49 0.0011 17.9 2.9 23 15-37 8-30 (50)
72 PF01649 Ribosomal_S20p: Ribos 38.4 59 0.0013 20.6 3.5 28 15-42 32-59 (84)
73 PF13424 TPR_12: Tetratricopep 38.0 85 0.0018 18.3 4.9 56 21-76 16-73 (78)
74 PF12169 DNA_pol3_gamma3: DNA 37.9 99 0.0021 20.7 4.9 44 12-61 16-59 (143)
75 TIGR02812 fadR_gamma fatty aci 37.6 78 0.0017 23.2 4.6 26 53-78 192-217 (235)
76 TIGR00029 S20 ribosomal protei 37.3 63 0.0014 20.7 3.5 28 15-42 33-60 (87)
77 PRK10225 DNA-binding transcrip 35.6 71 0.0015 23.8 4.2 26 53-78 201-226 (257)
78 KOG2817 Predicted E3 ubiquitin 35.6 2.4E+02 0.0053 23.2 7.3 85 14-99 121-208 (394)
79 PF04136 Sec34: Sec34-like fam 35.3 1.5E+02 0.0033 20.8 5.6 67 26-96 68-138 (157)
80 PRK03837 transcriptional regul 35.2 98 0.0021 22.6 4.8 26 12-37 201-226 (241)
81 PRK10421 DNA-binding transcrip 35.0 96 0.0021 23.1 4.8 27 11-37 191-217 (253)
82 TIGR00116 tsf translation elon 34.8 34 0.00074 26.8 2.3 40 23-62 30-94 (290)
83 PRK13689 hypothetical protein; 34.4 42 0.00092 21.0 2.2 18 110-127 49-66 (75)
84 PRK09377 tsf elongation factor 34.3 35 0.00075 26.8 2.3 40 23-62 31-95 (290)
85 PRK09464 pdhR transcriptional 33.9 74 0.0016 23.6 4.0 25 15-39 203-227 (254)
86 TIGR03504 FimV_Cterm FimV C-te 33.7 64 0.0014 17.8 2.8 20 18-37 7-26 (44)
87 TIGR03362 VI_chp_7 type VI sec 32.9 1.3E+02 0.0029 23.6 5.4 62 10-73 213-274 (301)
88 PF12510 Smoothelin: Smootheli 32.8 40 0.00087 19.8 1.8 16 8-23 34-49 (54)
89 PF01877 RNA_binding: RNA bind 32.4 1.1E+02 0.0023 20.6 4.2 44 9-57 56-100 (120)
90 cd00194 UBA Ubiquitin Associat 31.9 38 0.00083 17.4 1.6 21 14-34 15-37 (38)
91 PF10475 DUF2450: Protein of u 31.7 2.4E+02 0.0052 21.7 7.7 30 12-41 129-158 (291)
92 KOG3380 Actin-related protein 31.3 75 0.0016 22.6 3.4 59 14-73 39-99 (152)
93 PF07729 FCD: FCD domain; Int 30.7 77 0.0017 19.7 3.3 24 53-76 100-123 (125)
94 PF12729 4HB_MCP_1: Four helix 30.7 1.6E+02 0.0036 19.5 6.3 32 49-80 121-152 (181)
95 PF13428 TPR_14: Tetratricopep 30.4 76 0.0016 16.7 2.7 18 18-35 9-26 (44)
96 PF11251 DUF3050: Protein of u 30.0 1.6E+02 0.0034 22.5 5.1 98 15-126 100-222 (232)
97 KOG2027 Spindle pole body prot 30.0 1.3E+02 0.0029 24.6 5.1 26 11-36 18-43 (388)
98 PF04699 P16-Arc: ARP2/3 compl 30.0 48 0.001 23.5 2.3 25 14-38 40-64 (152)
99 COG3947 Response regulator con 30.0 3E+02 0.0064 22.2 7.6 74 3-77 222-307 (361)
100 PF08625 Utp13: Utp13 specific 29.9 1.8E+02 0.0039 20.2 5.1 59 15-74 2-72 (141)
101 smart00165 UBA Ubiquitin assoc 29.0 45 0.00097 17.1 1.6 11 23-33 26-36 (37)
102 PF06910 MEA1: Male enhanced a 28.9 1.3E+02 0.0028 21.9 4.3 39 82-120 123-161 (174)
103 PF07079 DUF1347: Protein of u 28.4 73 0.0016 27.0 3.3 49 15-63 133-189 (549)
104 PF02607 B12-binding_2: B12 bi 28.3 62 0.0013 19.4 2.3 25 13-37 4-28 (79)
105 PRK11414 colanic acid/biofilm 28.0 1.2E+02 0.0026 22.0 4.2 25 53-77 185-209 (221)
106 COG4105 ComL DNA uptake lipopr 27.7 2.9E+02 0.0063 21.4 8.7 61 14-80 38-102 (254)
107 TIGR02552 LcrH_SycD type III s 27.7 1.7E+02 0.0037 18.7 5.5 22 15-36 22-43 (135)
108 PF03398 Ist1: Regulator of Vp 27.6 61 0.0013 23.1 2.5 29 9-37 21-49 (165)
109 PF13432 TPR_16: Tetratricopep 27.3 1.2E+02 0.0026 16.9 6.6 55 17-76 4-58 (65)
110 PRK04964 hypothetical protein; 27.1 52 0.0011 19.9 1.7 24 64-87 22-45 (66)
111 TIGR02120 GspF general secreti 26.8 2.6E+02 0.0057 22.3 6.3 23 14-36 67-90 (399)
112 PF07719 TPR_2: Tetratricopept 26.3 86 0.0019 14.9 2.3 16 20-35 11-26 (34)
113 KOG0989 Replication factor C, 26.3 3.5E+02 0.0076 21.9 6.9 59 20-78 218-284 (346)
114 KOG1539 WD repeat protein [Gen 25.5 1.3E+02 0.0029 27.2 4.5 39 18-62 785-838 (910)
115 PRK07535 methyltetrahydrofolat 25.5 99 0.0021 23.7 3.4 23 14-36 12-34 (261)
116 PRK11523 DNA-binding transcrip 25.3 1.5E+02 0.0033 22.0 4.5 26 53-78 195-220 (253)
117 PF05047 L51_S25_CI-B8: Mitoch 24.9 37 0.0008 19.0 0.8 24 30-53 2-25 (52)
118 PF06786 UPF0253: Uncharacteri 24.6 59 0.0013 19.7 1.6 22 64-85 22-43 (66)
119 KOG1854 Mitochondrial inner me 24.5 1.5E+02 0.0033 26.0 4.6 56 6-61 586-645 (657)
120 PRK12332 tsf elongation factor 24.4 60 0.0013 24.0 2.0 15 23-37 30-44 (198)
121 PF14591 AF0941-like: AF0941-l 24.1 62 0.0013 22.3 1.9 77 16-96 8-88 (127)
122 PRK09990 DNA-binding transcrip 23.9 1.6E+02 0.0036 21.7 4.4 27 52-78 201-227 (251)
123 PLN03088 SGT1, suppressor of 23.9 3.7E+02 0.008 21.3 7.0 36 61-96 82-117 (356)
124 COG1802 GntR Transcriptional r 23.2 1.5E+02 0.0033 21.6 4.0 30 10-39 184-213 (230)
125 TIGR01159 DRP1 density-regulat 23.1 76 0.0016 23.0 2.3 21 23-43 20-40 (173)
126 PF08283 Gemini_AL1_M: Geminiv 22.8 89 0.0019 20.8 2.4 24 16-39 8-31 (106)
127 CHL00102 rps20 ribosomal prote 22.8 1.5E+02 0.0032 19.3 3.4 28 15-42 33-67 (93)
128 PF10003 DUF2244: Integral mem 22.7 72 0.0016 22.0 2.1 22 105-126 119-140 (140)
129 CHL00098 tsf elongation factor 22.7 67 0.0015 23.8 2.0 16 22-37 26-41 (200)
130 PRK09591 celC cellobiose phosp 22.5 1.1E+02 0.0023 20.2 2.8 34 18-52 28-61 (104)
131 PF10414 CysG_dimeriser: Siroh 21.8 1.7E+02 0.0037 16.8 3.3 27 9-35 22-57 (60)
132 PF09976 TPR_21: Tetratricopep 21.8 2.6E+02 0.0055 18.7 7.4 66 6-74 44-110 (145)
133 PRK08570 rpl19e 50S ribosomal 21.4 75 0.0016 22.6 1.9 23 5-27 29-51 (150)
134 COG1410 MetH Methionine syntha 21.1 2.3E+02 0.0051 25.6 5.1 63 53-119 41-112 (842)
135 PF13176 TPR_7: Tetratricopept 20.9 1.3E+02 0.0027 15.2 2.3 16 20-35 9-24 (36)
136 PF10602 RPN7: 26S proteasome 20.8 3.2E+02 0.0069 19.4 7.6 27 14-40 40-66 (177)
137 KOG3341 RNA polymerase II tran 20.7 70 0.0015 24.3 1.7 52 50-101 25-78 (249)
138 PF10552 ORF6C: ORF6C domain; 20.6 67 0.0015 21.3 1.5 21 19-39 88-108 (116)
139 PRK11534 DNA-binding transcrip 20.6 2.3E+02 0.005 20.5 4.5 18 86-103 184-201 (224)
140 PRK10573 type IV pilin biogene 20.5 4.2E+02 0.0091 21.2 6.3 22 15-36 66-88 (399)
141 PRK11788 tetratricopeptide rep 20.1 4.1E+02 0.0089 20.4 6.1 16 61-76 192-207 (389)
142 cd00481 Ribosomal_L19e Ribosom 20.1 80 0.0017 22.3 1.8 23 5-27 26-48 (145)
143 COG3898 Uncharacterized membra 20.1 4.8E+02 0.01 22.1 6.4 63 7-74 117-179 (531)
No 1
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=100.00 E-value=9.7e-35 Score=215.58 Aligned_cols=127 Identities=43% Similarity=0.614 Sum_probs=123.6
Q ss_pred CCCcccHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCC
Q 033011 2 KQPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK 81 (129)
Q Consensus 2 ~~p~~d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~ 81 (129)
.+|..|++++++|.+|+++|..|+|+.|++.+++++|.++++|.+|.|.|++|+||||||.|..++||+|||++++|++.
T Consensus 56 ~~~~~d~~~~~eR~~Ir~~I~~G~Ie~Aie~in~l~PeiLd~n~~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~~a~ 135 (228)
T KOG2659|consen 56 KPPSIDLDSMDERLQIRRAIEEGQIEEAIEKVNQLNPEILDTNRELFFHLQQLHLIELIREGKTEEALEFAQTKLAPFAE 135 (228)
T ss_pred CCccCchhhHhHHHHHHHHHHhccHHHHHHHHHHhChHHHccchhHHHHHHHHHHHHHHHhhhHHHHHHHHHHHcccccc
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred -chhHHHHHHHHHhHhccCCCCCCchhhhCCHHHHHHHHHHHHHHHhc
Q 033011 82 -VQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEYRQHVADNLNRAILG 128 (129)
Q Consensus 82 -~~~~~~~l~~~~~lLay~~~~~sp~~~Ll~~~~r~~la~~vn~aiL~ 128 (129)
++.++++++++|++|+|++|..||+++|++.++|+++|+.||+|||.
T Consensus 136 e~~~~~~elE~~l~lLvf~~~~~sp~~~l~~~s~R~kvA~~vN~aiL~ 183 (228)
T KOG2659|consen 136 ENPKKMEELERTLALLVFELSQESPSAELLSQSLRQKVASEVNSAILA 183 (228)
T ss_pred ccHHHHHHHHHHHHHHHcCCcccCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 77999999999999999999999999999999999999999999996
No 2
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=100.00 E-value=1.9e-33 Score=196.90 Aligned_cols=117 Identities=39% Similarity=0.642 Sum_probs=112.0
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHH
Q 033011 10 DMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKL 89 (129)
Q Consensus 10 ~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l 89 (129)
++.+|+.|+++|++|++++|++|+++++|.+++.++.++|.|++|+|||||+.|++.+||+|||++++++. ..+.+++
T Consensus 1 ~~~~r~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~~~~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l~~~~--~~~~~~l 78 (145)
T PF10607_consen 1 SFKERKKIRQAILNGDIDPAIEWLNENFPELLKRNSSLEFELRCQQFIELLREGDIMEAIEYARKHLSPFN--DEFLEEL 78 (145)
T ss_pred CHHHHHHHHHHHHcCCHHHHHHHHHHcCHHHHhcCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhhH--HHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999997776 5799999
Q ss_pred HHHHhHhccCCCCC---CchhhhCCHHHHHHHHHHHHHHHhc
Q 033011 90 EDFMALLAYEEPEK---SPMFHLLSLEYRQHVADNLNRAILG 128 (129)
Q Consensus 90 ~~~~~lLay~~~~~---sp~~~Ll~~~~r~~la~~vn~aiL~ 128 (129)
+++|++|+|++|.+ +||++++++++|+.||+.||++|+.
T Consensus 79 ~~~~~lL~~~~~~~~~~s~~~~l~~~~~~~~la~~~~~~~l~ 120 (145)
T PF10607_consen 79 KKLMSLLAYPDPEEPLPSPYKELLSPERREELAEEFNSAILK 120 (145)
T ss_pred HHHHHHHHcCCcccccchHHHHHhChHHHHHHHHHHHHHHHH
Confidence 99999999999987 8999999999999999999999985
No 3
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.91 E-value=7.2e-24 Score=165.61 Aligned_cols=121 Identities=22% Similarity=0.284 Sum_probs=114.0
Q ss_pred cccHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchh
Q 033011 5 ANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQK 84 (129)
Q Consensus 5 ~~d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~ 84 (129)
-+|.+-++.-..|+++|+.|++.+|+.||++|.-.|.+.++.++|.++.|+|||||+.++..+||+|+|+||+|++ .+
T Consensus 147 lvD~Dv~~~~~~I~~sll~~~l~~~Lswc~ehk~~LkK~~S~lEf~lRlQefIELi~~~~~~~Ai~~akk~f~~~~--~~ 224 (389)
T KOG0396|consen 147 LVDSDVYKRAYGIRDSLLAGELEPALSWCKEHKVELKKEESSLEFQLRLQEFIELIKVDNYDKAIAFAKKHFAPWA--KS 224 (389)
T ss_pred hHhHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhccchhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhhhh--hh
Confidence 3788999999999999999999999999999999999999999999999999999999999999999999999999 79
Q ss_pred HHHHHHHHHhHhccCC-CCCCchhhhCCHHHHHHHHHHHHHHHh
Q 033011 85 YVEKLEDFMALLAYEE-PEKSPMFHLLSLEYRQHVADNLNRAIL 127 (129)
Q Consensus 85 ~~~~l~~~~~lLay~~-~~~sp~~~Ll~~~~r~~la~~vn~aiL 127 (129)
+.++++.+||+|||+. ++.|+|..|++..||+.+++.|-+..+
T Consensus 225 ~~~~Lk~a~g~laF~~~t~~sky~~l~~~~rw~~l~~lF~s~a~ 268 (389)
T KOG0396|consen 225 HKSDLKLAMGLLAFPKYTSSSKYLNLLTADRWSVLADLFLSEAL 268 (389)
T ss_pred hHHHHHHHHHhhcCccccCcccccCcccHHHHHHHHHHhhHHHH
Confidence 9999999999999975 555789999999999999999877654
No 4
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=99.75 E-value=9.8e-18 Score=132.40 Aligned_cols=116 Identities=30% Similarity=0.448 Sum_probs=107.5
Q ss_pred HHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChH--HHHHHHHHhcCCcCCchhH
Q 033011 8 LEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCT--EALEFAQTKLTPFGKVQKY 85 (129)
Q Consensus 8 ~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~--~Ai~~ar~~l~~~~~~~~~ 85 (129)
...+-+.++|.++|..||+++|++|+..+...|.+.++.|+|.|+.++|+++++.|.-. +||.|||++++||+ ..+
T Consensus 153 ~~~F~el~~Iv~~lke~Dl~~aLeWa~~~~~~L~~~~s~LE~~Lh~l~fl~l~~~g~~~~~eAl~Yar~~~~~F~--~~~ 230 (394)
T KOG2817|consen 153 RTEFVELNQIVEALKERDLEPALEWAESNRQKLKEKSSSLEFKLHSLHFLSLIRGGKSDQREALRYARTHFAPFV--ADH 230 (394)
T ss_pred hhhHHHHHHHHHHHHhccchhHHHHHHHhhhhhccccccHHHHHHHHHHHHHHhcCCcCcHHHHHHHHHhcCccc--cch
Confidence 45577889999999999999999999999999999999999999999999999999766 99999999999999 667
Q ss_pred HHHHHHHHhHhcc--CCCCCCchhhhCCHHHHHHHHHHHHHH
Q 033011 86 VEKLEDFMALLAY--EEPEKSPMFHLLSLEYRQHVADNLNRA 125 (129)
Q Consensus 86 ~~~l~~~~~lLay--~~~~~sp~~~Ll~~~~r~~la~~vn~a 125 (129)
..+++..|++|.| ...++|||.+.+++..|..++..|.+.
T Consensus 231 ~~eIQklm~sl~~l~~gl~~spy~~~ls~~~w~~~~~~f~r~ 272 (394)
T KOG2817|consen 231 LREIQKLMGSLLYLRNGLEKSPYSEILSPKLWKELTEEFTRE 272 (394)
T ss_pred HHHHHHHHHHHHHHHcCCCCCChHHHhCHHHHHHHHHHHHHH
Confidence 9999999999999 347899999999999999999998764
No 5
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=99.70 E-value=4.1e-17 Score=107.14 Aligned_cols=66 Identities=48% Similarity=0.715 Sum_probs=60.6
Q ss_pred CChHHHHHHHHHhcCCcCC-chhHHHHHHHHHhHhccCCC-CCCchhhhCCHHHHHHHHHHHHHHHhc
Q 033011 63 RKCTEALEFAQTKLTPFGK-VQKYVEKLEDFMALLAYEEP-EKSPMFHLLSLEYRQHVADNLNRAILG 128 (129)
Q Consensus 63 ~~~~~Ai~~ar~~l~~~~~-~~~~~~~l~~~~~lLay~~~-~~sp~~~Ll~~~~r~~la~~vn~aiL~ 128 (129)
+++.+||+|||+++++|.. ++.+.++++++||+|||++| +.|||++++++++|+.+|+.||++||.
T Consensus 1 ~~~~eAi~yar~~l~~~~~~~~~~~~el~~~m~llaf~~~~~~sp~~~ll~~~~~~~la~~~n~~~l~ 68 (99)
T smart00757 1 GKIEEALAYARELLAPFAKEHEKFLKELEKTMALLAYPDPTEPSPYKELLSPSQREKLAEELNSAILE 68 (99)
T ss_pred CcHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHhcCCCCCCccHHHHCCHHHHHHHHHHHHHHHHH
Confidence 3578999999999999986 45558899999999999999 899999999999999999999999985
No 6
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=99.61 E-value=1.6e-15 Score=90.60 Aligned_cols=55 Identities=38% Similarity=0.534 Sum_probs=52.6
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCCh
Q 033011 11 MEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKC 65 (129)
Q Consensus 11 ~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~ 65 (129)
+.+|..|+++|+.|+|++|++|+++++|.+.+.++.+.|.|++|+||||++.|+.
T Consensus 2 ~~~~~~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~~l~f~L~~q~~lell~~~~~ 56 (58)
T smart00668 2 FDERKRIRELILKGDWDEALEWLSSLKPPLLERNSKLEFELRKQKFLELVRQGKL 56 (58)
T ss_pred hHHHHHHHHHHHcCCHHHHHHHHHHcCHHHhccCCCchhHHHHHHHHHHHHcCCc
Confidence 5689999999999999999999999999999999999999999999999998864
No 7
>KOG1477 consensus SPRY domain-containing proteins [General function prediction only]
Probab=98.40 E-value=6.3e-08 Score=79.69 Aligned_cols=106 Identities=25% Similarity=0.134 Sum_probs=88.6
Q ss_pred CCHHHHHHHHHhhchHHHc-------cCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCC---chhHHHHHHHHH
Q 033011 24 GNALKAIELTEELAQDLLE-------KNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK---VQKYVEKLEDFM 93 (129)
Q Consensus 24 G~i~~Ai~~~~~~~p~ll~-------~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~---~~~~~~~l~~~~ 93 (129)
|.+..+.+.+.+..+.... ..+...+.+.|+.+|++.+-|.+...+++.+.++++.-. +.....+++.++
T Consensus 312 ~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~g~v~~e~~~~k~~l~~~~g~~~~~~~~~~~~~s~ 391 (469)
T KOG1477|consen 312 GQFTRNGAYNAALIPTYRKVGQVFEVDYPQRGAKDPCGLHVNLGRAGFVFIEANAKKWELAKDYGIKKNSAAVGMLSDSS 391 (469)
T ss_pred ceeechhhhcccccccccccceeecccccchhhccchhhhhhHHHHHHHHHHHHHHHHhhhhhhCcCccccccccccchH
Confidence 3334444444444444433 456788999999999999999999999999999988764 678889999999
Q ss_pred hHhccCCCCCCchhhhCCHHHHHHHHHHHHHHHhcC
Q 033011 94 ALLAYEEPEKSPMFHLLSLEYRQHVADNLNRAILGL 129 (129)
Q Consensus 94 ~lLay~~~~~sp~~~Ll~~~~r~~la~~vn~aiL~~ 129 (129)
+||+|.+|.+||..+++++.+|+.+|+.+|.+||.+
T Consensus 392 ~Llays~p~~s~~g~~~~~~~~e~v~~~~n~~il~t 427 (469)
T KOG1477|consen 392 SLLAYSDPEESPVGYLLDPIQREPVAEALNSAILET 427 (469)
T ss_pred HHHHhcCcccCccccccCcccchhHHhhhccccccc
Confidence 999999999999999999999999999999999964
No 8
>KOG0293 consensus WD40 repeat-containing protein [Function unknown]
Probab=97.32 E-value=0.00079 Score=54.71 Aligned_cols=84 Identities=15% Similarity=0.153 Sum_probs=67.9
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHhh-chHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHHHH
Q 033011 13 MRKRILHFALEGNALKAIELTEEL-AQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLED 91 (129)
Q Consensus 13 ~R~~I~~~I~~G~i~~Ai~~~~~~-~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~ 91 (129)
+-+.+.++++.|+|+.++..+... ++. .+......|.+.+|.|+|..+.|++..|+...|..+.+.. ...+.+.+
T Consensus 52 t~klf~q~vlqg~w~q~v~~~~~i~~~d-e~~~~ea~fLv~kQ~fLEf~k~~~is~al~~l~~~~~~lr---~~~kk~~e 127 (519)
T KOG0293|consen 52 TTKLFDQQVLQGQWDQQVMSLVRISFED-ERNRKEAMFLVNKQIFLEFLKTGSISHALPVLRNPVLYLR---KNKKKFHE 127 (519)
T ss_pred hHHHHHHHHHcccHHHHHHHHhhccCcc-hhhhHHHHHHHHHHHHHHHHhhccHhhhhHhhhcchhhhh---hhHHHHHH
Confidence 345678999999999999988877 555 4555779999999999999999999999999997676664 44556677
Q ss_pred HHhHhccCC
Q 033011 92 FMALLAYEE 100 (129)
Q Consensus 92 ~~~lLay~~ 100 (129)
+...|.+++
T Consensus 128 l~~sll~sn 136 (519)
T KOG0293|consen 128 LASSLLVSN 136 (519)
T ss_pred HHHHHhccc
Confidence 777777764
No 9
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=90.63 E-value=1.7 Score=25.27 Aligned_cols=56 Identities=23% Similarity=0.153 Sum_probs=35.3
Q ss_pred HHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcC
Q 033011 20 FALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFG 80 (129)
Q Consensus 20 ~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~ 80 (129)
++..|+++.|++.+++.... ...++.+.+ .--.=+++.|+.++|.....+.+....
T Consensus 1 ll~~~~~~~A~~~~~~~l~~-~p~~~~~~~----~la~~~~~~g~~~~A~~~l~~~~~~~~ 56 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQR-NPDNPEARL----LLAQCYLKQGQYDEAEELLERLLKQDP 56 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHHH-TTTSHHHHH----HHHHHHHHTT-HHHHHHHHHCCHGGGT
T ss_pred ChhccCHHHHHHHHHHHHHH-CCCCHHHHH----HHHHHHHHcCCHHHHHHHHHHHHHHCc
Confidence 57899999999999876421 111223333 223335678999999999886555443
No 10
>PF04494 TFIID_90kDa: WD40 associated region in TFIID subunit; InterPro: IPR007582 This region, possibly a domain is found in subunits of transcription factor TFIID. The function of this region is unknown.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2J4B_D 2J49_A 2NXP_F.
Probab=88.46 E-value=1.5 Score=30.41 Aligned_cols=48 Identities=19% Similarity=0.297 Sum_probs=38.1
Q ss_pred cccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHHHHHHh
Q 033011 45 KDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMA 94 (129)
Q Consensus 45 ~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~~~~ 94 (129)
..+.|=+.+.-|++||.+|...+|..|-.++-..+. ..+.+.+++..+
T Consensus 38 ~~lLyPvFvh~YL~Lv~~~~~~~A~~F~~kf~~~~~--~~~~~~i~~L~~ 85 (142)
T PF04494_consen 38 SRLLYPVFVHSYLDLVSKGHPEEAKSFLEKFSPDFE--DSHQEDIEKLSS 85 (142)
T ss_dssp GGGHHHHHHHHHHHHHHTT-HHHHHHHHHHHGGGGH--GHGHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHh--HHHHHHHHHHHh
Confidence 457899999999999999999999999998777766 556666666654
No 11
>cd08044 TAF5_NTD2 TAF5_NTD2 is the second conserved N-terminal region of TATA Binding Protein (TBP) Associated Factor 5 (TAF5), involved in forming Transcription Factor IID (TFIID). The TATA Binding Protein (TBP) Associated Factor 5 (TAF5) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TAF5 contains three domains, two conserved sequence motifs at the N-terminal and one at the C-terminal region. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the preinitiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. In yeast and human cells, TAFs have been found as components of other complexes besides TFIID. TAF5 may play a major role in forming TFIID and its related complexes. TAFs from various
Probab=80.96 E-value=3.4 Score=28.34 Aligned_cols=50 Identities=18% Similarity=0.310 Sum_probs=38.7
Q ss_pred ccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHHHHHHhHhc
Q 033011 46 DLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALLA 97 (129)
Q Consensus 46 ~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~~~~lLa 97 (129)
.+.|=+.+--|++||.+|...+|..|-.+.-..+. +.+.+.++...++.-
T Consensus 28 ~lLyPiFvh~yL~lv~~~~~~~A~~F~~~f~~~~~--~~~~~~i~~L~~i~~ 77 (133)
T cd08044 28 QLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFE--DSHSEDIKKLSSITT 77 (133)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhHhhH--HHHHHHHHHHHccCC
Confidence 37788889999999999999999999987666554 566666766655443
No 12
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=78.00 E-value=5.3 Score=26.72 Aligned_cols=47 Identities=19% Similarity=0.078 Sum_probs=41.5
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHH
Q 033011 12 EMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVE 58 (129)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIE 58 (129)
+.-..+.+.|.+++|+.|.+.+.+....-.+..+.+.|.+..+++=+
T Consensus 30 ~~l~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~~~~~~~~h~eid~ 76 (121)
T PF14276_consen 30 EQLEQIEEAIENEDWEKAYKETEELEKEWDKNKKRWSILIEHQEIDN 76 (121)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHhhchheeeeecHHHHHH
Confidence 45778999999999999999999998888888888999999998855
No 13
>PF10607 CLTH: CTLH/CRA C-terminal to LisH motif domain; InterPro: IPR019589 This entry represents the CRA (or CT11-RanBPM) domain, which is a protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi) and which is found in Ran-binding proteins such as Ran-binding protein 9 (RanBP9 or RanBPM) and RanBP10. RanBPM is a scaffolding protein important in regulating cellular function in both the immune system and the nervous system, and may act as an adapter protein to couple membrane receptors to intracellular signaling pathways. This domain is at the C terminus of the proteins and is the binding domain for the CRA motif, which is comprised of approximately 100 amino acids at the C-terminal of RanBPM. It was found to be important for the interaction of RanBPM with fragile X mental retardation protein (FMRP), but its functional significance has yet to be determined [].
Probab=77.59 E-value=11 Score=25.69 Aligned_cols=92 Identities=21% Similarity=0.320 Sum_probs=52.0
Q ss_pred cHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhc---CCcCC--
Q 033011 7 CLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKL---TPFGK-- 81 (129)
Q Consensus 7 d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l---~~~~~-- 81 (129)
++..--.+++..+.|+.|++.+|+++++++....-+ .+.+.++ ++..++.|....- +|+..
T Consensus 37 ~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l~~~~~------------~~~~~l~--~~~~lL~~~~~~~~~~s~~~~l~ 102 (145)
T PF10607_consen 37 SLEFELRCQQFIELLREGDIMEAIEYARKHLSPFND------------EFLEELK--KLMSLLAYPDPEEPLPSPYKELL 102 (145)
T ss_pred chhHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhhHH------------HHHHHHH--HHHHHHHcCCcccccchHHHHHh
Confidence 445555678899999999999999999996531111 3444443 2455555555332 34442
Q ss_pred chhHHHHHHHHHhHh---ccCCCCCCchhhhCCH
Q 033011 82 VQKYVEKLEDFMALL---AYEEPEKSPMFHLLSL 112 (129)
Q Consensus 82 ~~~~~~~l~~~~~lL---ay~~~~~sp~~~Ll~~ 112 (129)
++....++-+.+.-. .|+-|..||+...+..
T Consensus 103 ~~~~~~~la~~~~~~~l~~~~~~~~s~L~~~~~~ 136 (145)
T PF10607_consen 103 SPERREELAEEFNSAILKSYGLPKESPLEVILKA 136 (145)
T ss_pred ChHHHHHHHHHHHHHHHHHhCcCCCCHHHHHHHH
Confidence 333334333333221 1356777886555543
No 14
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=77.59 E-value=3 Score=32.92 Aligned_cols=42 Identities=21% Similarity=0.237 Sum_probs=30.8
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhc
Q 033011 13 MRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCS 62 (129)
Q Consensus 13 ~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~ 62 (129)
-.+.|++++..|||+.|+.++++-.- |=+.=-++-||.-|+.
T Consensus 260 y~~aI~~AVk~gDi~KAL~LldEAe~--------LG~~~Ar~tFik~V~~ 301 (303)
T PRK10564 260 FNQAIKQAVKKGDVDKALKLLDEAER--------LGSTSARSTFISSVKG 301 (303)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHH--------hCCchHHHHHHHHhhc
Confidence 46899999999999999999988642 1222236667776654
No 15
>KOG0275 consensus Conserved WD40 repeat-containing protein [General function prediction only]
Probab=77.12 E-value=14 Score=30.00 Aligned_cols=111 Identities=15% Similarity=0.156 Sum_probs=67.4
Q ss_pred ccHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCC----
Q 033011 6 NCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK---- 81 (129)
Q Consensus 6 ~d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~---- 81 (129)
+.+.+.+.--.....|-+|.|+..+..+....-- ..-...|+.|-.+|||.-..+..|-..+|+. .|...
T Consensus 36 VSLNTVDSvd~Fv~dI~sG~WD~VL~~vqsLKLP-----~kkL~dLYEqivlEliELREL~tAR~~lRQT-dpM~~lKQ~ 109 (508)
T KOG0275|consen 36 VSLNTVDSVDGFVNDINSGHWDTVLKTVQSLKLP-----DKKLIDLYEQIVLELIELRELGTARSLLRQT-DPMIMLKQI 109 (508)
T ss_pred cceeechhHHHHHHhcccCchHHHHHHHHhccCc-----hhHHHHHHHHHHHHHHHHHhhhHHHHHHhcc-Cceehhhcc
Confidence 3344455555677889999999999888776521 1234678899999999877777776667642 23221
Q ss_pred chhHHHHHHHHHhHhccCCCCCCchhhhCCHHHHHHHHHHHHH
Q 033011 82 VQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEYRQHVADNLNR 124 (129)
Q Consensus 82 ~~~~~~~l~~~~~lLay~~~~~sp~~~Ll~~~~r~~la~~vn~ 124 (129)
.|+-.-.++.... -.|-||.+ .|++---+.||..+|+++..
T Consensus 110 ~peRy~~lE~ll~-R~YFDp~E-aY~dssKEkrRa~IAQ~ls~ 150 (508)
T KOG0275|consen 110 QPERYIRLENLLN-RSYFDPRE-AYGDSSKEKRRAVIAQALSG 150 (508)
T ss_pred ChHHHHHHHHHhc-ccccChhh-hcCcchHHHHHHHHHHHhcC
Confidence 2333333433222 23555543 25553345577888877643
No 16
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=76.12 E-value=3.3 Score=25.37 Aligned_cols=52 Identities=27% Similarity=0.340 Sum_probs=29.8
Q ss_pred HHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHH
Q 033011 16 RILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQ 73 (129)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar 73 (129)
.-.-....|+++.|+.+++. ......+....+.+ -+-++++ |+.++|++.-.
T Consensus 31 la~~~~~~~~y~~A~~~~~~--~~~~~~~~~~~~l~-a~~~~~l---~~y~eAi~~l~ 82 (84)
T PF12895_consen 31 LAQCYFQQGKYEEAIELLQK--LKLDPSNPDIHYLL-ARCLLKL---GKYEEAIKALE 82 (84)
T ss_dssp HHHHHHHTTHHHHHHHHHHC--HTHHHCHHHHHHHH-HHHHHHT---T-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHHH--hCCCCCCHHHHHHH-HHHHHHh---CCHHHHHHHHh
Confidence 34456677888888888877 33333333444433 4445554 67777776654
No 17
>COG3071 HemY Uncharacterized enzyme of heme biosynthesis [Coenzyme metabolism]
Probab=75.01 E-value=25 Score=28.81 Aligned_cols=73 Identities=12% Similarity=0.050 Sum_probs=54.0
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHHHHHHh
Q 033011 15 KRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMA 94 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~~~~ 94 (129)
.-+.++|..|+-++|.+|+.+..+.-...+ ...||.-++-++...-++-+.+-+.....+| .+-.+.|
T Consensus 268 ~~a~~li~l~~~~~A~~~i~~~Lk~~~D~~--------L~~~~~~l~~~d~~~l~k~~e~~l~~h~~~p----~L~~tLG 335 (400)
T COG3071 268 AYAERLIRLGDHDEAQEIIEDALKRQWDPR--------LCRLIPRLRPGDPEPLIKAAEKWLKQHPEDP----LLLSTLG 335 (400)
T ss_pred HHHHHHHHcCChHHHHHHHHHHHHhccChh--------HHHHHhhcCCCCchHHHHHHHHHHHhCCCCh----hHHHHHH
Confidence 356789999999999999999887766653 5567788888887777777777666555444 4556677
Q ss_pred HhccC
Q 033011 95 LLAYE 99 (129)
Q Consensus 95 lLay~ 99 (129)
-|||.
T Consensus 336 ~L~~k 340 (400)
T COG3071 336 RLALK 340 (400)
T ss_pred HHHHH
Confidence 77774
No 18
>KOG2910 consensus Uncharacterized conserved protein predicted to be involved in protein sorting [General function prediction only]
Probab=73.41 E-value=19 Score=26.71 Aligned_cols=53 Identities=17% Similarity=0.213 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHhhc--hHHHc-----------cCcccchhhHHHHHHHHHhcCC
Q 033011 12 EMRKRILHFALEGNALKAIELTEELA--QDLLE-----------KNKDLHFDLLSLHFVELVCSRK 64 (129)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~~~~~~--p~ll~-----------~~~~l~F~L~~q~fIELir~~~ 64 (129)
.+|+..|++|+.|+=+.|+-++.... ..|+. .-++++|.....++++=++.|+
T Consensus 41 ~Er~~Ar~lird~rKdrAlllLKkKryQE~Ll~qt~~qL~nlEqmvsdiEft~vqk~V~~gLk~GN 106 (209)
T KOG2910|consen 41 AERQLARDLIRDGRKDRALLLLKKKRYQEELLTQTDNQLINLEQMVSDIEFTQVQKKVMEGLKQGN 106 (209)
T ss_pred HHHHHHHHHHHhChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46888999999999999998886532 23333 3368999999999999999983
No 19
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=73.14 E-value=7.8 Score=25.57 Aligned_cols=45 Identities=18% Similarity=0.344 Sum_probs=32.7
Q ss_pred hhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHHHHHH
Q 033011 49 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFM 93 (129)
Q Consensus 49 F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~~~ 93 (129)
|-=+....+||++.|.--.|+.|+++.+..+..-....++++.+.
T Consensus 48 faPYErr~mELLkv~kdKrAlKfaKkRlGth~RaK~Kreel~~vl 92 (98)
T PTZ00196 48 FSPYERRMIELLKVGKDKRALKYAKKRLGTHKRAKAKRDEIQEAL 92 (98)
T ss_pred ccHHHHHHHHHHHhcchHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 555678889999999999999999999977652223334444443
No 20
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=72.72 E-value=5.8 Score=24.27 Aligned_cols=39 Identities=26% Similarity=0.454 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHhcCChHHHHHHHHHhcCCcC--CchhHHHHHH
Q 033011 50 DLLSLHFVELVCSRKCTEALEFAQTKLTPFG--KVQKYVEKLE 90 (129)
Q Consensus 50 ~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~--~~~~~~~~l~ 90 (129)
.|..++|-+++..|+..+|-..|-. +|-+ .+++....++
T Consensus 7 ~l~~~~F~~l~~~g~y~eAA~~AA~--sP~giLRt~~Ti~rFk 47 (66)
T PF13838_consen 7 DLYVQQFNELFSQGQYEEAAKVAAN--SPRGILRTPETINRFK 47 (66)
T ss_dssp HHHHHHHHHHHHTT-HHHHHHHHHH--SGGGTT-SHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHh--CccchhcCHHHHHHHH
Confidence 4678999999999999999988874 3432 2556666665
No 21
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=72.69 E-value=14 Score=20.75 Aligned_cols=28 Identities=25% Similarity=0.305 Sum_probs=23.4
Q ss_pred HHHHHHHHHhcCChHHHHHHHHHhcCCc
Q 033011 52 LSLHFVELVCSRKCTEALEFAQTKLTPF 79 (129)
Q Consensus 52 ~~q~fIELir~~~~~~Ai~~ar~~l~~~ 79 (129)
...++.+.|..|++.+|+++..++-...
T Consensus 4 ~~~~i~~~i~~g~~~~a~~~~~~~~~~l 31 (58)
T smart00668 4 ERKRIRELILKGDWDEALEWLSSLKPPL 31 (58)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHcCHHH
Confidence 3577899999999999999999766544
No 22
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=67.50 E-value=18 Score=21.47 Aligned_cols=35 Identities=23% Similarity=0.242 Sum_probs=26.4
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHcc
Q 033011 9 EDMEMRKRILHFALEGNALKAIELTEELAQDLLEK 43 (129)
Q Consensus 9 ~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~ 43 (129)
+-+...+-|...+..|+++.|.+.+++....+...
T Consensus 22 D~~NhLqvI~gllqlg~~~~a~eYi~~~~~~~~~~ 56 (62)
T PF14689_consen 22 DFLNHLQVIYGLLQLGKYEEAKEYIKELSKDLQQE 56 (62)
T ss_dssp HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34566778889999999999999998877655443
No 23
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=66.77 E-value=19 Score=28.92 Aligned_cols=91 Identities=20% Similarity=0.264 Sum_probs=65.6
Q ss_pred CcccHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcc--cchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCC
Q 033011 4 PANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKD--LHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK 81 (129)
Q Consensus 4 p~~d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~--l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~ 81 (129)
|..-.+-+..-+.|.+.|.+.+...-++|. +...-+-+.++. +...+....++-++-. ++++|+.+-++.++.|.
T Consensus 132 ~~~~~~~f~~lK~v~~gI~~k~~~l~iE~~-Qi~gyl~kgdtesel~l~~~~~esl~l~hk-~~~~a~r~c~t~~a~f~- 208 (396)
T COG5109 132 IIKIRDGFVKLKKVISGISEKSTFLLIEFL-QIEGYLSKGDTESELELYLVSHESLLLIHK-RYDEALRLCFTKLASFV- 208 (396)
T ss_pred hhhHHHHHHHHHHHHHhhccchhHhHHHHH-HhcCccccCCchhhhHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH-
Confidence 344456667778888889999999999998 333334444444 4455555566655554 79999999999999998
Q ss_pred chhHHHHHHHHHhHhcc
Q 033011 82 VQKYVEKLEDFMALLAY 98 (129)
Q Consensus 82 ~~~~~~~l~~~~~lLay 98 (129)
+.+...++..+-.+.+
T Consensus 209 -~kh~~dv~~~~~~l~n 224 (396)
T COG5109 209 -PKHIQDVKPLLRFLVN 224 (396)
T ss_pred -HHhccchHHHHHHHHc
Confidence 7778888888877776
No 24
>COG5443 FlbT Flagellar biosynthesis regulator FlbT [Cell motility and secretion]
Probab=64.24 E-value=13 Score=25.92 Aligned_cols=33 Identities=24% Similarity=0.216 Sum_probs=29.6
Q ss_pred cHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchH
Q 033011 7 CLEDMEMRKRILHFALEGNALKAIELTEELAQD 39 (129)
Q Consensus 7 d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ 39 (129)
|-+-+...++|-.++.+|.+-+|++.+...||-
T Consensus 91 ~~eil~~lk~Id~lV~~~~~feALkaiR~lyp~ 123 (148)
T COG5443 91 DAEILAALKRIDGLVMAGRAFEALKAIRGLYPI 123 (148)
T ss_pred CHHHHHHHHHHHHHHhccHHHHHHHHHhhhchh
Confidence 556788899999999999999999999999983
No 25
>PF01158 Ribosomal_L36e: Ribosomal protein L36e; InterPro: IPR000509 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 [, ]. A number of eukaryotic ribosomal proteins can be grouped on the basis of sequence similarities. The L36E ribosomal family consists of mammalian, Caenorhabditis elegans and Drosophila L36, Candida albicans L39, and yeast YL39 ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1B_Q 4A1D_Q 4A19_Q 4A18_Q 3IZS_k 3IZR_k.
Probab=64.04 E-value=12 Score=24.68 Aligned_cols=44 Identities=25% Similarity=0.321 Sum_probs=31.9
Q ss_pred hhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHHHHH
Q 033011 49 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDF 92 (129)
Q Consensus 49 F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~~ 92 (129)
|-=+-.+-+||++.|..-.|+.|+++.+..+..-....+++..+
T Consensus 48 faPYEkr~mELlkv~kdKrAlKf~KKRlGth~RAKrKrEel~~v 91 (98)
T PF01158_consen 48 FAPYEKRAMELLKVSKDKRALKFAKKRLGTHIRAKRKREELSNV 91 (98)
T ss_dssp HCHHHHHHHHHHHHCCHHHHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred CChHHHHHHHHHhcchhHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 55567889999999999999999999997664222333444443
No 26
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=63.51 E-value=40 Score=27.53 Aligned_cols=84 Identities=14% Similarity=0.154 Sum_probs=62.9
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCC---chhHHHHH
Q 033011 13 MRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK---VQKYVEKL 89 (129)
Q Consensus 13 ~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~---~~~~~~~l 89 (129)
+|--+.+++++|.+++|..++++..-. +-.++.+..+-+.-..-+..|.+..|+.|-.+|=..+.+ .-++.-.+
T Consensus 119 ~r~vvdhmlr~gy~~~A~~L~K~s~le---dlvD~Dv~~~~~~I~~sll~~~l~~~Lswc~ehk~~LkK~~S~lEf~lRl 195 (389)
T KOG0396|consen 119 DRFVVDHMLRNGYFGAAVLLGKKSQLE---DLVDSDVYKRAYGIRDSLLAGELEPALSWCKEHKVELKKEESSLEFQLRL 195 (389)
T ss_pred HHHHHHHHHHcCchhHHHHHHHhhhhh---hhHhHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhccchhhhHHHH
Confidence 466677899999999999998775532 224566777778888889999999999999887766653 23566677
Q ss_pred HHHHhHhccC
Q 033011 90 EDFMALLAYE 99 (129)
Q Consensus 90 ~~~~~lLay~ 99 (129)
|+...|+=-+
T Consensus 196 QefIELi~~~ 205 (389)
T KOG0396|consen 196 QEFIELIKVD 205 (389)
T ss_pred HHHHHHHHhc
Confidence 7777776543
No 27
>KOG1156 consensus N-terminal acetyltransferase [Chromatin structure and dynamics]
Probab=58.40 E-value=96 Score=27.30 Aligned_cols=77 Identities=18% Similarity=0.170 Sum_probs=57.8
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHHHHH
Q 033011 13 MRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDF 92 (129)
Q Consensus 13 ~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~~ 92 (129)
-.-+++-.+.+|..+.|++.+..+-|.+.+. +.|....-.+.. +.++.++|+...+..+.+...|-.+...++.+
T Consensus 188 ~Ly~n~i~~E~g~~q~ale~L~~~e~~i~Dk---la~~e~ka~l~~--kl~~lEeA~~~y~~Ll~rnPdn~~Yy~~l~~~ 262 (700)
T KOG1156|consen 188 LLYQNQILIEAGSLQKALEHLLDNEKQIVDK---LAFEETKADLLM--KLGQLEEAVKVYRRLLERNPDNLDYYEGLEKA 262 (700)
T ss_pred HHHHHHHHHHcccHHHHHHHHHhhhhHHHHH---HHHhhhHHHHHH--HHhhHHhHHHHHHHHHhhCchhHHHHHHHHHH
Confidence 3567788999999999999999999988877 445555554433 45679999999998888876544555566666
Q ss_pred Hh
Q 033011 93 MA 94 (129)
Q Consensus 93 ~~ 94 (129)
+|
T Consensus 263 lg 264 (700)
T KOG1156|consen 263 LG 264 (700)
T ss_pred HH
Confidence 65
No 28
>PF12854 PPR_1: PPR repeat
Probab=58.23 E-value=17 Score=18.58 Aligned_cols=24 Identities=25% Similarity=0.270 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHh
Q 033011 12 EMRKRILHFALEGNALKAIELTEE 35 (129)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~~~~ 35 (129)
.--..|.-.-++|++++|++++++
T Consensus 9 ty~~lI~~~Ck~G~~~~A~~l~~~ 32 (34)
T PF12854_consen 9 TYNTLIDGYCKAGRVDEAFELFDE 32 (34)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHh
Confidence 334567888899999999998875
No 29
>PRK00794 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=57.66 E-value=25 Score=24.35 Aligned_cols=31 Identities=16% Similarity=0.078 Sum_probs=25.5
Q ss_pred HHhHHHHHHHHHHHHcCCHHHHHHHHHhhch
Q 033011 8 LEDMEMRKRILHFALEGNALKAIELTEELAQ 38 (129)
Q Consensus 8 ~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p 38 (129)
.+....-..|.++|.+|++-.|++.+....|
T Consensus 91 p~~~~~l~~i~~~V~~g~~y~ALk~lR~L~~ 121 (132)
T PRK00794 91 PDILAGLKAIDELVEAGRYYEALKALRGLYP 121 (132)
T ss_pred HHHHHHHHHHHHHHHCCcHHHHHHHHHHhhH
Confidence 4455667788899999999999999988877
No 30
>COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]
Probab=57.38 E-value=20 Score=23.22 Aligned_cols=28 Identities=14% Similarity=0.096 Sum_probs=24.0
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhchHHHc
Q 033011 15 KRILHFALEGNALKAIELTEELAQDLLE 42 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~p~ll~ 42 (129)
+.++.+|..||.+.|.+.+...+|.+..
T Consensus 33 Kk~~~ai~~gd~~~A~~~l~~a~~~idk 60 (88)
T COG0268 33 KKVEAAIEAGDKEAAKAALKEAQKKIDK 60 (88)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 4577899999999999999999987754
No 31
>PF07035 Mic1: Colon cancer-associated protein Mic1-like; InterPro: IPR009755 This entry represents the C terminus (approximately 160 residues) of a number of proteins that resemble colon cancer-associated protein Mic1.
Probab=57.30 E-value=30 Score=24.94 Aligned_cols=59 Identities=17% Similarity=0.116 Sum_probs=34.1
Q ss_pred HHHHHHcCCHHHHHHHHHh--hchHHHccCcccchhhH--HHHHHH-HHhcCChHHHHHHHHHh
Q 033011 17 ILHFALEGNALKAIELTEE--LAQDLLEKNKDLHFDLL--SLHFVE-LVCSRKCTEALEFAQTK 75 (129)
Q Consensus 17 I~~~I~~G~i~~Ai~~~~~--~~p~ll~~~~~l~F~L~--~q~fIE-Lir~~~~~~Ai~~ar~~ 75 (129)
|+..+..-...-|..++.- .+|...+-.-++...|. ...-+| |+..|++-+|+.|+|+.
T Consensus 52 lq~~Vi~DSk~lA~~LLs~~~~~~~~~Ql~lDMLkRL~~~~~~iievLL~~g~vl~ALr~ar~~ 115 (167)
T PF07035_consen 52 LQYHVIPDSKPLACQLLSLGNQYPPAYQLGLDMLKRLGTAYEEIIEVLLSKGQVLEALRYARQY 115 (167)
T ss_pred HhhcccCCcHHHHHHHHHhHccChHHHHHHHHHHHHhhhhHHHHHHHHHhCCCHHHHHHHHHHc
Confidence 3333333344444444433 44555444444444444 444556 77889999999999974
No 32
>TIGR01470 cysG_Nterm siroheme synthase, N-terminal domain. This model represents a subfamily of CysG N-terminal region-related sequences. All sequences in the seed alignment for this model are N-terminal regions of known or predicted siroheme synthases. The C-terminal region of each is uroporphyrin-III C-methyltransferase (EC 2.1.1.107), which catalyzes the first step committed to the biosynthesis of either siroheme or cobalamin (vitamin B12) rather than protoheme (heme). The region represented by this model completes the process of oxidation and iron insertion to yield siroheme. Siroheme is a cofactor for nitrite and sulfite reductases, so siroheme synthase is CysG of cysteine biosynthesis in some organisms.
Probab=57.29 E-value=39 Score=24.82 Aligned_cols=64 Identities=16% Similarity=0.137 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcc------cchhhHHHHHHHHHhcCChHHHHHHHHHhc
Q 033011 12 EMRKRILHFALEGNALKAIELTEELAQDLLEKNKD------LHFDLLSLHFVELVCSRKCTEALEFAQTKL 76 (129)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~------l~F~L~~q~fIELir~~~~~~Ai~~ar~~l 76 (129)
.-|.+|...+-. .++.-++++.+....+.+..++ +...+..-.|.++++.|+..+|.+.+.+.+
T Consensus 135 ~lr~~ie~~l~~-~~~~~~~~~~~~R~~~k~~~~~~~~r~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~ 204 (205)
T TIGR01470 135 LLRERIETLLPP-SLGDLATLAATWRDAVKKRLPNGAARRRFWEKFFDGAFAERVLAGREEQAERVLATRL 204 (205)
T ss_pred HHHHHHHHhcch-hHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHhccHHHHHHHcCCHHHHHHHHHHhh
Confidence 346667766643 5567777777777777654332 333444456889999999999998887654
No 33
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=56.99 E-value=15 Score=17.51 Aligned_cols=17 Identities=18% Similarity=0.155 Sum_probs=13.5
Q ss_pred HHHHHcCCHHHHHHHHH
Q 033011 18 LHFALEGNALKAIELTE 34 (129)
Q Consensus 18 ~~~I~~G~i~~Ai~~~~ 34 (129)
+-+...|++++|..++.
T Consensus 9 ~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 9 RALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHcCCHHHHHHHHh
Confidence 45678899999988875
No 34
>PF13934 ELYS: Nuclear pore complex assembly
Probab=56.96 E-value=56 Score=24.40 Aligned_cols=56 Identities=13% Similarity=0.109 Sum_probs=36.6
Q ss_pred HHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCC
Q 033011 16 RILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTP 78 (129)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~ 78 (129)
-|+-++..|+..-|+..+....|.+-.. --..-++..+.+|.+.||..|.|++-.+
T Consensus 114 Il~~L~~~~~~~lAL~y~~~~~p~l~s~-------~~~~~~~~~La~~~v~EAf~~~R~~~~~ 169 (226)
T PF13934_consen 114 ILQALLRRGDPKLALRYLRAVGPPLSSP-------EALTLYFVALANGLVTEAFSFQRSYPDE 169 (226)
T ss_pred HHHHHHHCCChhHHHHHHHhcCCCCCCH-------HHHHHHHHHHHcCCHHHHHHHHHhCchh
Confidence 3445555788888888887777655444 1122334446678899999999976654
No 35
>PF04121 Nup84_Nup100: Nuclear pore protein 84 / 107 ; InterPro: IPR007252 Nup84p forms a complex with five proteins, including Nup120p, Nup85p, Sec13p, and a Sec13p homolog. This Nup84p complex in conjunction with Sec13-type proteins is required for correct nuclear pore biogenesis [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 3CQC_A 3CQG_A 3I4R_A 3IKO_I 3JRO_C.
Probab=56.86 E-value=14 Score=32.21 Aligned_cols=27 Identities=26% Similarity=0.272 Sum_probs=21.2
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHhh
Q 033011 10 DMEMRKRILHFALEGNALKAIELTEEL 36 (129)
Q Consensus 10 ~~~~R~~I~~~I~~G~i~~Ai~~~~~~ 36 (129)
.-.--+.|-.+|++|++++|.+||.+.
T Consensus 133 e~~~~~~i~~llR~G~~~eA~~lc~~~ 159 (697)
T PF04121_consen 133 ERALLKYIFELLRAGRIEEAQELCRER 159 (697)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHC
Confidence 334456788999999999999999883
No 36
>PF14973 TINF2_N: TERF1-interacting nuclear factor 2 N-terminus
Probab=56.72 E-value=51 Score=23.20 Aligned_cols=77 Identities=17% Similarity=0.272 Sum_probs=45.5
Q ss_pred HHHHHHHcCCHHHHHHHHHhhchHHHccC-----cccchhhHHHHHHHHHhc--CChHHHHHHHHHhcC-CcCCchhHHH
Q 033011 16 RILHFALEGNALKAIELTEELAQDLLEKN-----KDLHFDLLSLHFVELVCS--RKCTEALEFAQTKLT-PFGKVQKYVE 87 (129)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~-----~~l~F~L~~q~fIELir~--~~~~~Ai~~ar~~l~-~~~~~~~~~~ 87 (129)
.|-++++.|.... +..++.++|.+ ..+ ++..-.--...|..+|++ .+..+--.|-|+.|. .|+ +.+..
T Consensus 46 lILELc~~~~~~d-l~~I~~Hl~~~-~~~~~~~~~D~~~~~~~~~F~~LV~~Ll~dp~~r~~f~qe~f~~eYG--~~f~~ 121 (145)
T PF14973_consen 46 LILELCRQERPWD-LKAIQPHLPRI-PQDPNATSKDHKMEEAHENFCQLVQNLLEDPEERENFFQEVFPQEYG--EPFDA 121 (145)
T ss_pred HHHHHHhCCCCch-HHHHHHhcccc-cccccccccHHHHHHHHHHHHHHHHHHHhChHHHHHHHHHHHHHHHC--hHHHH
Confidence 3556777655444 99999999998 222 233334445566666654 245555566766663 344 56666
Q ss_pred HHHHHHhHh
Q 033011 88 KLEDFMALL 96 (129)
Q Consensus 88 ~l~~~~~lL 96 (129)
.+++.+.=.
T Consensus 122 ~Le~L~~ef 130 (145)
T PF14973_consen 122 ALEKLLWEF 130 (145)
T ss_pred HHHHHHHHH
Confidence 666655433
No 37
>PF07378 FlbT: Flagellar protein FlbT; InterPro: IPR009967 This family consists of several FlbT proteins. FlbT is a post-transcriptional repressor function in flagellum biogenesis. FlbT is associated with the 5' untranslated region (UTR) of fljK (25 kDa flagellin) mRNA and that this association requires a predicted loop structure in the transcript. Mutations within this loop abolish FlbT association and result in increased mRNA stability. It is therefore thought that FlbT promotes the degradation of flagellin mRNA by associating with the 5' UTR [].; GO: 0048027 mRNA 5'-UTR binding, 0006402 mRNA catabolic process, 0045718 negative regulation of flagellum assembly
Probab=55.22 E-value=29 Score=23.82 Aligned_cols=33 Identities=15% Similarity=0.063 Sum_probs=27.8
Q ss_pred ccHHhHHHHHHHHHHHHcCCHHHHHHHHHhhch
Q 033011 6 NCLEDMEMRKRILHFALEGNALKAIELTEELAQ 38 (129)
Q Consensus 6 ~d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p 38 (129)
.+.+....-..+.++|.+|++-.|++.+....|
T Consensus 87 ~~p~~~~~l~~~~~~v~~g~~y~ALk~~R~L~~ 119 (126)
T PF07378_consen 87 ADPDAREGLDEANELVEAGRYYKALKALRKLIP 119 (126)
T ss_pred cCHHHHHHHHHHHHHHHCCcHHHHHHHHHHhHH
Confidence 355667777889999999999999999998876
No 38
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=50.89 E-value=56 Score=21.18 Aligned_cols=45 Identities=16% Similarity=0.309 Sum_probs=33.1
Q ss_pred hhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHHHHHHhHh
Q 033011 49 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALL 96 (129)
Q Consensus 49 F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~~~~lL 96 (129)
|.=+..+.||||++.+-..|-..+++.|..+. .....+++.-..|
T Consensus 50 lsPyErr~i~Lirns~~krArKlakKRLGs~k---RAkaKvEel~~~i 94 (97)
T COG5051 50 LSPYERRVIELIRNSQDKRARKLAKKRLGSLK---RAKAKVEELTSVI 94 (97)
T ss_pred CCHHHHHHHHHHHhcccHHHHHHHHHHhhhHH---HHHHHHHHHHHHH
Confidence 33456789999999999999999999998874 4445555554443
No 39
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=50.22 E-value=28 Score=16.58 Aligned_cols=23 Identities=26% Similarity=0.281 Sum_probs=18.5
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhc
Q 033011 15 KRILHFALEGNALKAIELTEELA 37 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~ 37 (129)
..|......|++++|.+++++..
T Consensus 5 ~li~~~~~~~~~~~a~~~~~~M~ 27 (35)
T TIGR00756 5 TLIDGLCKAGRVEEALELFKEML 27 (35)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHH
Confidence 35677889999999999987754
No 40
>TIGR00083 ribF riboflavin kinase/FMN adenylyltransferase. multifunctional enzyme: riboflavin kinase (EC 2.7.1.26) (flavokinase) / FMN adenylyltransferase (EC 2.7.7.2) (FAD pyrophosphorylase) (FAD synthetase).
Probab=50.18 E-value=18 Score=28.30 Aligned_cols=25 Identities=16% Similarity=-0.047 Sum_probs=22.4
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhch
Q 033011 14 RKRILHFALEGNALKAIELTEELAQ 38 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~~p 38 (129)
-..||++|..|+++.|-+++-..|.
T Consensus 146 ST~IR~~l~~G~i~~A~~lLGr~y~ 170 (288)
T TIGR00083 146 SSAIRQALKNGDLELANKLLGRPYF 170 (288)
T ss_pred HHHHHHHHHcCCHHHHHHhhhhhhc
Confidence 4689999999999999999988765
No 41
>PF10827 DUF2552: Protein of unknown function (DUF2552) ; InterPro: IPR020157 This entry contains proteins with no known function.
Probab=50.12 E-value=12 Score=23.37 Aligned_cols=16 Identities=19% Similarity=0.034 Sum_probs=14.0
Q ss_pred CHHHHHHHHHhhchHH
Q 033011 25 NALKAIELTEELAQDL 40 (129)
Q Consensus 25 ~i~~Ai~~~~~~~p~l 40 (129)
-++.|++|+.++.|.+
T Consensus 60 tld~Ai~Wi~e~M~~i 75 (79)
T PF10827_consen 60 TLDLAIAWIGEHMPHI 75 (79)
T ss_pred cHHHHHHHHHhcccch
Confidence 4789999999999875
No 42
>PRK07143 hypothetical protein; Provisional
Probab=50.05 E-value=12 Score=29.09 Aligned_cols=25 Identities=12% Similarity=-0.133 Sum_probs=21.7
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhch
Q 033011 14 RKRILHFALEGNALKAIELTEELAQ 38 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~~p 38 (129)
-..||++|.+|+++.|-+++-..|.
T Consensus 152 ST~IR~~l~~G~i~~A~~lLGr~y~ 176 (279)
T PRK07143 152 TSLLKEFIEFGDIELLNSLLLYNYS 176 (279)
T ss_pred HHHHHHHHHcCCHHHHHHHcCCCcE
Confidence 4689999999999999999877664
No 43
>PF05791 Bacillus_HBL: Bacillus haemolytic enterotoxin (HBL); InterPro: IPR008414 This family consists of several Bacillus haemolytic enterotoxins (HblC, HblD, HblA, NheA, and NheB), which can cause food poisoning in humans []. Haemolysin BL (encoded by HBL) and non-haemolytic enterotoxin (encoded by NHE), represent the major enterotoxins produced by Bacillus cereus. Most of the cytotoxic activity of B. cereus isolates has been attributed to the level of Nhe, which may indicate a highly diarrheic potential []. The exact mechanism by which B. cereus causes diarrhoea is unknown. Hbl, cytotoxin K (CytK) and Nhe are all putative causes. Both Hbl and Nhe are three-component cytotoxins and maximal cytotoxicity of Nhe against epithelia is dependent on all three components. Nhe has haemolytic activity against erythrocytes from a variety of species. It is possible that the common structural and functional properties of these toxins indicate that the Hbl/Nhe and ClyA families of toxins constitute a superfamily of pore-forming cytotoxins []. The high virulence of some strains is thought to be due to the greater cytotoxic activity of CytK-1 compared to CytK-2, and to a high level of cytK expression []. Haemolysin BL and non-haemolytic enterotoxin production are both influenced by pH and micro []. This entry is found in cytotoxic proteins that form part of the enterotoxin complex and bind to erythrocytes. HblA is composed of a binding component, B, and two lytic components, L1 and L2. All three subunits act synergically to cause hemolysis.; GO: 0009405 pathogenesis, 0016020 membrane; PDB: 2NRJ_A.
Probab=49.22 E-value=37 Score=24.57 Aligned_cols=61 Identities=16% Similarity=0.183 Sum_probs=35.2
Q ss_pred CCCcccHHhHH--------HHHHHHHHHHcCCHHHHHHHHHhhchHHHccCccc-----chhhHHHHHHHHHhcCChH
Q 033011 2 KQPANCLEDME--------MRKRILHFALEGNALKAIELTEELAQDLLEKNKDL-----HFDLLSLHFVELVCSRKCT 66 (129)
Q Consensus 2 ~~p~~d~~~~~--------~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l-----~F~L~~q~fIELir~~~~~ 66 (129)
++|.++++.+. .-..-....+ ..|..|....+|.+...++++ .|.-+-...+++|-.++.+
T Consensus 33 ~Qp~v~~s~i~~~~~~l~~~l~~~q~~ak----~ha~~w~d~~~P~ii~~~~~I~~Y~~~f~syY~~L~~~id~~~~~ 106 (184)
T PF05791_consen 33 QQPDVNFSGIPSKLSDLQKDLVQHQKTAK----EHAKEWLDTIKPQIIDLNQDIINYNTTFQSYYDTLVEAIDQKDKE 106 (184)
T ss_dssp HS-----SS--TT-TTHHHHHHHHHHHHH----HHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HH
T ss_pred cCCCCCCccCcccchhHHHHHHHHHHHHH----HHHHHHHHHhcHHHHHHHHHHHHHHHHHHHHHHHHHHHHCcccHH
Confidence 57888888777 3333333333 468999999999999987763 3566666677777555433
No 44
>cd02064 FAD_synthetase_N FAD synthetase, N-terminal domain of the bifunctional enzyme. FAD synthetase_N. N-terminal domain of the bifunctional riboflavin biosynthesis protein riboflavin kinase/FAD synthetase. These enzymes have both ATP:riboflavin 5'-phosphotransferase and ATP:FMN-adenylyltransferase activities. The N-terminal domain is believed to play a role in the adenylylation reaction of FAD synthetases. The C-terminal domain is thought to have kinase activity. FAD synthetase is present among all kingdoms of life. However, the bifunctional enzyme is not found in mammals, which use separate enzymes for FMN and FAD formation.
Probab=48.97 E-value=13 Score=26.55 Aligned_cols=24 Identities=29% Similarity=0.151 Sum_probs=20.2
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhc
Q 033011 14 RKRILHFALEGNALKAIELTEELA 37 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~~ 37 (129)
-..||++|.+|+++.|-+++-..|
T Consensus 148 ST~IR~~i~~G~i~~an~lLg~~y 171 (180)
T cd02064 148 STRIREALAEGDVELANELLGRPY 171 (180)
T ss_pred HHHHHHHHHhCCHHHHHHHcCCCc
Confidence 468999999999999998876544
No 45
>PF12931 Sec16_C: Sec23-binding domain of Sec16; PDB: 3MZK_C.
Probab=48.97 E-value=21 Score=27.62 Aligned_cols=20 Identities=35% Similarity=0.517 Sum_probs=13.7
Q ss_pred HHHHHHHcCCHHHHHHHHHh
Q 033011 16 RILHFALEGNALKAIELTEE 35 (129)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~~~~ 35 (129)
+|+++++.|+.++|+++|-+
T Consensus 1 ~I~~~Ll~G~~~~Av~~al~ 20 (284)
T PF12931_consen 1 KIQQLLLVGNREEAVELALD 20 (284)
T ss_dssp HHHHHHHTT-HHHHHHHHHH
T ss_pred CHHHHHhCCCHHHHHHHHHH
Confidence 46777777777777777754
No 46
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=48.59 E-value=28 Score=23.21 Aligned_cols=28 Identities=14% Similarity=0.189 Sum_probs=20.7
Q ss_pred hhhHHHHHHHHHhcCChHHHHHHHHHhc
Q 033011 49 FDLLSLHFVELVCSRKCTEALEFAQTKL 76 (129)
Q Consensus 49 F~L~~q~fIELir~~~~~~Ai~~ar~~l 76 (129)
..+..+.||.+|+.|+..+|++..++..
T Consensus 38 ~~~dip~~i~~i~~g~~~~A~~~i~~~n 65 (111)
T PF14691_consen 38 AHIDIPEYIRLIREGNFKEAYELIREDN 65 (111)
T ss_dssp T---HHHHHHHHHCT-HHHHHHHHHHH-
T ss_pred CCCcHHHHHHHHHCCCHHHHHHHHHHhC
Confidence 4566799999999999999999999543
No 47
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=47.89 E-value=29 Score=23.17 Aligned_cols=24 Identities=29% Similarity=0.286 Sum_probs=19.1
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhch
Q 033011 15 KRILHFALEGNALKAIELTEELAQ 38 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~p 38 (129)
....++|..|++.+|++++.+..|
T Consensus 43 p~~i~~i~~g~~~~A~~~i~~~np 66 (111)
T PF14691_consen 43 PEYIRLIREGNFKEAYELIREDNP 66 (111)
T ss_dssp HHHHHHHHCT-HHHHHHHHHHH-T
T ss_pred HHHHHHHHCCCHHHHHHHHHHhCC
Confidence 456789999999999999998766
No 48
>PF15391 DUF4614: Domain of unknown function (DUF4614)
Probab=47.38 E-value=25 Score=25.75 Aligned_cols=49 Identities=27% Similarity=0.287 Sum_probs=36.6
Q ss_pred HHHHHHHHhhchHHHccCcccchhh-HHHHHHHHHhcC----------------ChHHHHHHHHHh
Q 033011 27 LKAIELTEELAQDLLEKNKDLHFDL-LSLHFVELVCSR----------------KCTEALEFAQTK 75 (129)
Q Consensus 27 ~~Ai~~~~~~~p~ll~~~~~l~F~L-~~q~fIELir~~----------------~~~~Ai~~ar~~ 75 (129)
.+||+-+....|.++..|..|.=+| ..|+|||.-|.- .++++-+|-|.|
T Consensus 113 ~dAiEALTaYSPA~lALnDMLkQQL~LTqqFve~sr~LH~Sll~SL~~~~~hY~TLEetKeyIr~h 178 (181)
T PF15391_consen 113 ADAIEALTAYSPAVLALNDMLKQQLSLTQQFVEASRHLHQSLLQSLDADSFHYHTLEETKEYIRRH 178 (181)
T ss_pred HHHHHHHhccChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcceeeHHHHHHHHHHc
Confidence 4689999999999999987766544 579999987652 266666666654
No 49
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.73 E-value=58 Score=28.58 Aligned_cols=41 Identities=15% Similarity=0.295 Sum_probs=33.7
Q ss_pred HHHHHHHHhHhccCCCCC-CchhhhCCHHHHHHHHHHHHHHH
Q 033011 86 VEKLEDFMALLAYEEPEK-SPMFHLLSLEYRQHVADNLNRAI 126 (129)
Q Consensus 86 ~~~l~~~~~lLay~~~~~-sp~~~Ll~~~~r~~la~~vn~ai 126 (129)
...++.....+.-.|++- --.+.+.+++.|.++|+++|.-+
T Consensus 87 l~hIEk~a~dIv~~d~~v~Lv~geiide~Y~d~iaeEinekL 128 (776)
T KOG2235|consen 87 LDHIEKTARDIVSTDDEVTLVLGEIIDEEYVDRIAEEINEKL 128 (776)
T ss_pred HHHHHHHHHHHhhcCCceEEehhhhhhHHHHHHHHHHHHHHH
Confidence 446788888888888775 45799999999999999999754
No 50
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=46.34 E-value=38 Score=21.77 Aligned_cols=28 Identities=14% Similarity=0.093 Sum_probs=22.0
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhchHHHc
Q 033011 15 KRILHFALEGNALKAIELTEELAQDLLE 42 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~p~ll~ 42 (129)
+.+..+|..|+.++|.+.+...++.|.+
T Consensus 33 Kk~~~ai~~~~~~~a~~~~~~a~s~iDk 60 (88)
T PRK00239 33 KKVEAAIAAGDKEAAEEALKAAQSKIDK 60 (88)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHHHH
Confidence 4567788889999999998888876543
No 51
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=45.99 E-value=48 Score=23.83 Aligned_cols=25 Identities=12% Similarity=0.133 Sum_probs=14.2
Q ss_pred HHHHHHHHHhcCChHHHHHHHHHhc
Q 033011 52 LSLHFVELVCSRKCTEALEFAQTKL 76 (129)
Q Consensus 52 ~~q~fIELir~~~~~~Ai~~ar~~l 76 (129)
..++.++.|+.|+.+.|....+.|+
T Consensus 182 ~H~~i~~ai~~~d~~~A~~~~~~Hl 206 (212)
T TIGR03338 182 EHRAIVDAIASGDAERAGALMRAHV 206 (212)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 3455555565666555555555554
No 52
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=45.62 E-value=37 Score=22.76 Aligned_cols=23 Identities=13% Similarity=0.121 Sum_probs=19.8
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhh
Q 033011 14 RKRILHFALEGNALKAIELTEEL 36 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~ 36 (129)
...++++|..|+++.|++++...
T Consensus 74 ~~~~~~~l~~g~~~~a~~ll~~~ 96 (115)
T PF12793_consen 74 EQQAEELLEQGKYEQALQLLDFD 96 (115)
T ss_pred HHHHHHHHHcCCHHHHHHHHHhC
Confidence 46788999999999999999843
No 53
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=45.57 E-value=59 Score=18.69 Aligned_cols=53 Identities=23% Similarity=0.166 Sum_probs=35.8
Q ss_pred HHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcC
Q 033011 20 FALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLT 77 (129)
Q Consensus 20 ~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~ 77 (129)
++..|+++.|++.++..- +.+|+ ...++...=.=+...|+..+|++...+-+.
T Consensus 5 ~~~~~~~~~A~~~~~~~l----~~~p~-~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~ 57 (73)
T PF13371_consen 5 YLQQEDYEEALEVLERAL----ELDPD-DPELWLQRARCLFQLGRYEEALEDLERALE 57 (73)
T ss_pred HHhCCCHHHHHHHHHHHH----HhCcc-cchhhHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 578899999999886643 33343 334444444445667889999888886653
No 54
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=45.07 E-value=77 Score=21.54 Aligned_cols=102 Identities=11% Similarity=0.166 Sum_probs=57.6
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHH-----hcCCcCCchhHHHHH
Q 033011 15 KRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQT-----KLTPFGKVQKYVEKL 89 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~-----~l~~~~~~~~~~~~l 89 (129)
..+-.++.++++.+|.-.....-+.+...++.+......-++++ +|+..+.-..+++ .+.++. +.+.+.+
T Consensus 9 ~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~---~~~~~~~~~~~~~~~~~~~~~~~v--~~~~~~i 83 (143)
T PF10075_consen 9 LILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALW---EGDYSKFWQALRSNPWSPDYKPFV--PGFEDTI 83 (143)
T ss_dssp HHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHH---TT-HHHHHHHS-TT----HHHHTS--TTHHHHH
T ss_pred HHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHH---CCCHHHHHHHHHhccchHHHHHHH--HHHHHHH
Confidence 34567888999999988888888888887777766655555444 5666666665553 233333 3344433
Q ss_pred HHHHhH---hccCCCCCCchhhhCCHHHHHHHHHHH
Q 033011 90 EDFMAL---LAYEEPEKSPMFHLLSLEYRQHVADNL 122 (129)
Q Consensus 90 ~~~~~l---Lay~~~~~sp~~~Ll~~~~r~~la~~v 122 (129)
++-..- .+|.....+-++.+++-+ -+++.+.+
T Consensus 84 R~~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~ 118 (143)
T PF10075_consen 84 RERIAHLISKAYSSISLSDLAEMLGLS-EEELEKFI 118 (143)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHH
T ss_pred HHHHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHH
Confidence 333222 347766656667777655 54554444
No 55
>COG0264 Tsf Translation elongation factor Ts [Translation, ribosomal structure and biogenesis]
Probab=44.57 E-value=31 Score=27.18 Aligned_cols=40 Identities=33% Similarity=0.338 Sum_probs=31.8
Q ss_pred cCCHHHHHHHHHhhchH---------------------------HHccCcccchhhHHHHHHHHHhc
Q 033011 23 EGNALKAIELTEELAQD---------------------------LLEKNKDLHFDLLSLHFVELVCS 62 (129)
Q Consensus 23 ~G~i~~Ai~~~~~~~p~---------------------------ll~~~~~l~F~L~~q~fIELir~ 62 (129)
+||++.|++|+++..-. +.+-|+.-.|.=+-..|.++++.
T Consensus 31 ~Gd~EkAie~LR~kG~akA~KKa~R~AaEGli~~~~~~~~~~av~vEvN~ETDFVAkN~~F~~l~~~ 97 (296)
T COG0264 31 NGDIEKAIEWLREKGIAKAAKKAGRIAAEGLIAAKVDGDGKKAVLVEVNCETDFVAKNAEFQELANK 97 (296)
T ss_pred CCCHHHHHHHHHHhchHhhhhhcCcchhcceEEEEEcCCCcEEEEEEEeccccceeCChhHHHHHHH
Confidence 79999999999984432 34456677899999999999874
No 56
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=44.38 E-value=87 Score=23.82 Aligned_cols=70 Identities=19% Similarity=0.093 Sum_probs=45.6
Q ss_pred CcccHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhc
Q 033011 4 PANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKL 76 (129)
Q Consensus 4 p~~d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l 76 (129)
+.++-+++. |--+-..+-.|..+.|..-.++.. +.....++.+.=.+-+-.++|+.|++++||+...+..
T Consensus 22 ~~~~~~d~n-~LVmnylv~eg~~EaA~~Fa~e~~--i~~~~~d~~~~~eR~~Ir~~I~~G~Ie~Aie~in~l~ 91 (228)
T KOG2659|consen 22 VSVMREDLN-RLVMNYLVHEGYVEAAEKFAKESG--IKPPSIDLDSMDERLQIRRAIEEGQIEEAIEKVNQLN 91 (228)
T ss_pred cCcchhhHH-HHHHHHHHhccHHHHHHHhccccC--CCCccCchhhHhHHHHHHHHHHhccHHHHHHHHHHhC
Confidence 344455554 455556666777776665554432 1111355667667778888899999999999999544
No 57
>PF07208 DUF1414: Protein of unknown function (DUF1414); InterPro: IPR009857 This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown.; PDB: 2JPQ_A 2JUZ_B 2JUW_B 2QTI_A 2OTA_A 2JR2_A 2JRX_A.
Probab=44.20 E-value=31 Score=19.38 Aligned_cols=18 Identities=22% Similarity=0.373 Sum_probs=15.1
Q ss_pred CCHHHHHHHHHHHHHHHh
Q 033011 110 LSLEYRQHVADNLNRAIL 127 (129)
Q Consensus 110 l~~~~r~~la~~vn~aiL 127 (129)
..+++|+.+|+.|..|+.
T Consensus 24 V~~~qR~~iAe~Fa~AL~ 41 (44)
T PF07208_consen 24 VPPAQRQAIAEKFAQALK 41 (44)
T ss_dssp S-HHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 468999999999999875
No 58
>KOG3452 consensus 60S ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=43.79 E-value=74 Score=21.02 Aligned_cols=32 Identities=22% Similarity=0.238 Sum_probs=27.1
Q ss_pred hhhHHHHHHHHHhcCChHHHHHHHHHhcCCcC
Q 033011 49 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFG 80 (129)
Q Consensus 49 F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~ 80 (129)
|-=+..+-+||++.++-..|+.++++.+..+.
T Consensus 50 ~aPyErr~meLlkvskdkrA~K~lKkRlGth~ 81 (102)
T KOG3452|consen 50 FAPYERRAMELLKVSKDKRALKLLKKRLGTHK 81 (102)
T ss_pred CChHHHHHHHHHHHcccHHHHHHHHHHhhHHH
Confidence 44456788999999999999999999998774
No 59
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=43.73 E-value=20 Score=18.76 Aligned_cols=18 Identities=17% Similarity=0.200 Sum_probs=12.6
Q ss_pred HHHHHHH--cCCHHHHHHHH
Q 033011 16 RILHFAL--EGNALKAIELT 33 (129)
Q Consensus 16 ~I~~~I~--~G~i~~Ai~~~ 33 (129)
..++++. +|+++.|++|+
T Consensus 18 ~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 18 QAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHhC
Confidence 4445544 47999999986
No 60
>PF14498 Glyco_hyd_65N_2: Glycosyl hydrolase family 65, N-terminal domain; PDB: 2EAE_A 2EAB_B 2EAC_A 2EAD_B 2RDY_A.
Probab=43.43 E-value=18 Score=26.92 Aligned_cols=32 Identities=28% Similarity=0.223 Sum_probs=24.6
Q ss_pred ccHHhHHHHHHHHHHHHcCCHHHHHHHHHhhc
Q 033011 6 NCLEDMEMRKRILHFALEGNALKAIELTEELA 37 (129)
Q Consensus 6 ~d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~ 37 (129)
..........+||++|.+|+..+|-+++.++.
T Consensus 50 ~~~~~~~~L~~iR~l~~~g~~~~A~~l~~~~~ 81 (236)
T PF14498_consen 50 TPPDAAEYLPEIRELLFEGDYEEAEELAEENF 81 (236)
T ss_dssp SSHHHHHHHHHHHHHHHTT-CCHHHHHHCCS-
T ss_pred cCccHHHHHHHHHHHHHcCChhHHHHHHHHhc
Confidence 33446777889999999999999999987655
No 61
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=43.36 E-value=40 Score=16.20 Aligned_cols=22 Identities=23% Similarity=0.292 Sum_probs=17.7
Q ss_pred HHHHHHHHcCCHHHHHHHHHhh
Q 033011 15 KRILHFALEGNALKAIELTEEL 36 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~ 36 (129)
..|......|+++.|..++++.
T Consensus 6 ~ll~a~~~~g~~~~a~~~~~~M 27 (34)
T PF13812_consen 6 ALLRACAKAGDPDAALQLFDEM 27 (34)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
Confidence 4577788899999999888764
No 62
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=42.72 E-value=58 Score=23.91 Aligned_cols=24 Identities=8% Similarity=-0.068 Sum_probs=13.1
Q ss_pred HHHHHHHHhcCChHHHHHHHHHhc
Q 033011 53 SLHFVELVCSRKCTEALEFAQTKL 76 (129)
Q Consensus 53 ~q~fIELir~~~~~~Ai~~ar~~l 76 (129)
..+.++.|+.|+.+.|.+..++|+
T Consensus 193 H~~I~~Ai~~~D~~~a~~~~~~H~ 216 (239)
T PRK04984 193 YHKLSALCEEGNHDQVPECVRQYG 216 (239)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHH
Confidence 445555555555555555555555
No 63
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=42.13 E-value=1.4e+02 Score=22.07 Aligned_cols=60 Identities=12% Similarity=0.060 Sum_probs=43.1
Q ss_pred HHHHHHHHhcCCcCCchhHHHHHHHHHhHhccCCCCCCc-hhhhC-CHHHH-HHHHHHHHHHH
Q 033011 67 EALEFAQTKLTPFGKVQKYVEKLEDFMALLAYEEPEKSP-MFHLL-SLEYR-QHVADNLNRAI 126 (129)
Q Consensus 67 ~Ai~~ar~~l~~~~~~~~~~~~l~~~~~lLay~~~~~sp-~~~Ll-~~~~r-~~la~~vn~ai 126 (129)
-+-+|+++|-.....+|++..+|+..|.-|--++|...+ +...+ +.+.+ .+||-++-.-.
T Consensus 41 ~l~~fa~k~~~~i~~~~~~r~~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~c 103 (223)
T PF04157_consen 41 LLENFARKHKSEIKSDPEFRSQFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEVC 103 (223)
T ss_dssp HHHHHHHHHCCCCCCSHHHHHHHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhhccccCCchHHHHHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHHH
Confidence 456788888887777899999999999999998887666 34455 55554 78887765443
No 64
>PRK05627 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed
Probab=41.68 E-value=22 Score=27.91 Aligned_cols=25 Identities=20% Similarity=0.038 Sum_probs=22.1
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhch
Q 033011 14 RKRILHFALEGNALKAIELTEELAQ 38 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~~p 38 (129)
-..||++|.+|+++.|-.++-..|.
T Consensus 163 ST~IR~~I~~G~i~~A~~lLg~~y~ 187 (305)
T PRK05627 163 STAIRQALAEGDLELANKLLGRPYS 187 (305)
T ss_pred hHHHHHHHHcCCHHHHHhhhcCCCc
Confidence 3679999999999999999988765
No 65
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=41.13 E-value=56 Score=23.77 Aligned_cols=26 Identities=15% Similarity=0.201 Sum_probs=17.3
Q ss_pred HHHHHHHHHhcCChHHHHHHHHHhcC
Q 033011 52 LSLHFVELVCSRKCTEALEFAQTKLT 77 (129)
Q Consensus 52 ~~q~fIELir~~~~~~Ai~~ar~~l~ 77 (129)
..+..++.|+.|+.+.|....+.|+.
T Consensus 186 eH~~Il~Ai~~~D~~~A~~~~~~Hi~ 211 (224)
T PRK11534 186 QHQTLTAAILARDTARASELMRQHLL 211 (224)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHH
Confidence 35666677777777777777777763
No 66
>PF01535 PPR: PPR repeat; InterPro: IPR002885 This entry represents the PPR repeat. Pentatricopeptide repeat (PPR) proteins are characterised by tandem repeats of a degenerate 35 amino acid motif []. Most of PPR proteins have roles in mitochondria or plastid []. PPR repeats were discovered while screening Arabidopsis proteins for those predicted to be targeted to mitochondria or chloroplast [, ]. Some of these proteins have been shown to play a role in post-transcriptional processes within organelles and they are thought to be sequence-specific RNA-binding proteins [, , ]. Plant genomes have between one hundred to five hundred PPR genes per genome whereas non-plant genomes encode two to six PPR proteins. Although no PPR structures are yet known, the motif is predicted to fold into a helix-turn-helix structure similar to those found in the tetratricopeptide repeat (TPR) family (see PDOC50005 from PROSITEDOC) []. The plant PPR protein family has been divided in two subfamilies on the basis of their motif content and organisation [, ]. Examples of PPR repeat-containing proteins include PET309 P32522 from SWISSPROT, which may be involved in RNA stabilisation [], and crp1, which is involved in RNA processing []. The repeat is associated with a predicted plant protein O49549 from SWISSPROT that has a domain organisation similar to the human BRCA1 protein.
Probab=40.47 E-value=38 Score=15.84 Aligned_cols=21 Identities=24% Similarity=0.330 Sum_probs=16.7
Q ss_pred HHHHHHHcCCHHHHHHHHHhh
Q 033011 16 RILHFALEGNALKAIELTEEL 36 (129)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~~~~~ 36 (129)
-|.-....|++++|.++.++.
T Consensus 6 li~~~~~~~~~~~a~~~~~~M 26 (31)
T PF01535_consen 6 LISGYCKMGQFEEALEVFDEM 26 (31)
T ss_pred HHHHHHccchHHHHHHHHHHH
Confidence 466777889999999888764
No 67
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.17 E-value=1.5e+02 Score=23.34 Aligned_cols=65 Identities=26% Similarity=0.228 Sum_probs=46.5
Q ss_pred cCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHHHHH
Q 033011 23 EGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDF 92 (129)
Q Consensus 23 ~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~~ 92 (129)
.|++++|++..+ .+++++ ...|-.+..+..=+--.|+..+||+-.-+++..|-.|.+...++.++
T Consensus 99 ~~~~~~A~e~y~----~lL~dd-pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~~D~EAW~eLaei 163 (289)
T KOG3060|consen 99 TGNYKEAIEYYE----SLLEDD-PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFMNDQEAWHELAEI 163 (289)
T ss_pred hhchhhHHHHHH----HHhccC-cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCcHHHHHHHHHH
Confidence 477777776553 455664 56777788887777777888889888888888887666666665554
No 68
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=39.81 E-value=95 Score=19.48 Aligned_cols=28 Identities=14% Similarity=0.127 Sum_probs=22.7
Q ss_pred HHHHHcCCHHHHHHHHHhhchHHHccCc
Q 033011 18 LHFALEGNALKAIELTEELAQDLLEKNK 45 (129)
Q Consensus 18 ~~~I~~G~i~~Ai~~~~~~~p~ll~~~~ 45 (129)
-.++..||+..|++.+...+-.-...+.
T Consensus 6 ~~~~~~~dy~~A~d~L~~~fD~~~~~~~ 33 (94)
T PF12862_consen 6 LNALRSGDYSEALDALHRYFDYAKQSNN 33 (94)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHhhccc
Confidence 4689999999999999998876555544
No 69
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=39.47 E-value=1.7e+02 Score=24.88 Aligned_cols=72 Identities=18% Similarity=0.147 Sum_probs=47.0
Q ss_pred HHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCchhHHHHHHHHHhHh
Q 033011 20 FALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALL 96 (129)
Q Consensus 20 ~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~~~~lL 96 (129)
....|+.+.|++.+.++...+...- .+.-.+-++ +++.|..++|-..-+..+.....|..+..-+..+.|+-
T Consensus 14 l~e~g~~~~AL~~L~~~~~~I~Dk~---~~~E~rA~l--l~kLg~~~eA~~~y~~Li~rNPdn~~Yy~~L~~~~g~~ 85 (517)
T PF12569_consen 14 LEEAGDYEEALEHLEKNEKQILDKL---AVLEKRAEL--LLKLGRKEEAEKIYRELIDRNPDNYDYYRGLEEALGLQ 85 (517)
T ss_pred HHHCCCHHHHHHHHHhhhhhCCCHH---HHHHHHHHH--HHHcCCHHHHHHHHHHHHHHCCCcHHHHHHHHHHHhhh
Confidence 3667999999999999887777662 222222222 34557888888888876655444555666666666433
No 70
>PRK12791 flbT flagellar biosynthesis repressor FlbT; Reviewed
Probab=38.99 E-value=68 Score=22.22 Aligned_cols=28 Identities=21% Similarity=0.277 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhch
Q 033011 11 MEMRKRILHFALEGNALKAIELTEELAQ 38 (129)
Q Consensus 11 ~~~R~~I~~~I~~G~i~~Ai~~~~~~~p 38 (129)
...-..|.++|.+|++-.|++.+....|
T Consensus 91 ~~~l~~~~~~v~~g~~Y~ALK~~R~Li~ 118 (131)
T PRK12791 91 WPIIEAINNHILNGDLYKALKELRKLIA 118 (131)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHhHH
Confidence 3445567778888888888888877766
No 71
>PF13041 PPR_2: PPR repeat family
Probab=38.60 E-value=49 Score=17.92 Aligned_cols=23 Identities=22% Similarity=0.303 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhc
Q 033011 15 KRILHFALEGNALKAIELTEELA 37 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~ 37 (129)
..|.-..+.|++++|.++.++..
T Consensus 8 ~li~~~~~~~~~~~a~~l~~~M~ 30 (50)
T PF13041_consen 8 TLISGYCKAGKFEEALKLFKEMK 30 (50)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHH
Confidence 35677888999999999888765
No 72
>PF01649 Ribosomal_S20p: Ribosomal protein S20; InterPro: IPR002583 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 [, ]. This family consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein S20. Bacterial ribosomal protein S20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1I94_T 1FJG_T 4DH9_T 3KNJ_T 3TVG_W 3UYF_W 3V28_T 3KIS_t 3HUY_T 1HNX_T ....
Probab=38.38 E-value=59 Score=20.64 Aligned_cols=28 Identities=18% Similarity=0.129 Sum_probs=21.9
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhchHHHc
Q 033011 15 KRILHFALEGNALKAIELTEELAQDLLE 42 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~p~ll~ 42 (129)
..++.+|..|+-+.|.+.+...++.|..
T Consensus 32 Kk~~~ai~~~~~~~a~~~l~~a~s~iDk 59 (84)
T PF01649_consen 32 KKFREAIEAGDKEEAKELLRKAYSAIDK 59 (84)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccChHHHHHHHHHHHHHHHH
Confidence 4677888999999999999888876643
No 73
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=37.99 E-value=85 Score=18.34 Aligned_cols=56 Identities=20% Similarity=0.028 Sum_probs=31.1
Q ss_pred HHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHH--HHHHhcCChHHHHHHHHHhc
Q 033011 21 ALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHF--VELVCSRKCTEALEFAQTKL 76 (129)
Q Consensus 21 I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~f--IELir~~~~~~Ai~~ar~~l 76 (129)
...|+++.|+++.++--......+++-.....+-.= .=..+.|+.++|+++.++-+
T Consensus 16 ~~~~~~~~A~~~~~~al~~~~~~~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al 73 (78)
T PF13424_consen 16 RELGRYDEALDYYEKALDIEEQLGDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL 73 (78)
T ss_dssp HHTT-HHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred HHcCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 478999999999988776622222211111111111 11234578889988887643
No 74
>PF12169 DNA_pol3_gamma3: DNA polymerase III subunits gamma and tau domain III; InterPro: IPR022754 This domain is found in bacteria and eukaryotes, and is approximately 110 amino acids in length. It is found in association with PF00004 from PFAM. This domain is also present in the tau subunit before it undergoes cleavage. Domains I-III are shared between the tau and the gamma subunits, while most of the DnaB-binding Domain IV and all of the alpha-interacting Domain V are unique to tau. ; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 1NJF_B 3GLG_G 1XXH_I 1NJG_A 3GLF_B 3GLI_G.
Probab=37.94 E-value=99 Score=20.69 Aligned_cols=44 Identities=27% Similarity=0.307 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHh
Q 033011 12 EMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVC 61 (129)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir 61 (129)
+.-..+-++|.+||..+|+..+++.+- .+..+.-....+++.+|
T Consensus 16 ~~i~~l~~ai~~~d~~~~l~~~~~l~~------~G~d~~~~l~~L~~~~R 59 (143)
T PF12169_consen 16 EQIFELLDAILEGDAAEALELLNELLE------QGKDPKQFLDDLIEYLR 59 (143)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHH------CT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHH------hCCCHHHHHHHHHHHHH
Confidence 345577889999999999999988663 22333334444555544
No 75
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=37.59 E-value=78 Score=23.20 Aligned_cols=26 Identities=8% Similarity=-0.073 Sum_probs=14.6
Q ss_pred HHHHHHHHhcCChHHHHHHHHHhcCC
Q 033011 53 SLHFVELVCSRKCTEALEFAQTKLTP 78 (129)
Q Consensus 53 ~q~fIELir~~~~~~Ai~~ar~~l~~ 78 (129)
.++.++.|+.|+.+.|-...+.|+..
T Consensus 192 H~~I~~Ai~~~d~~~A~~~m~~H~~~ 217 (235)
T TIGR02812 192 YKELQALCKAGNHDEVPDCIRQYGIE 217 (235)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 34555555556655555555555543
No 76
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=37.34 E-value=63 Score=20.72 Aligned_cols=28 Identities=29% Similarity=0.247 Sum_probs=21.8
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhchHHHc
Q 033011 15 KRILHFALEGNALKAIELTEELAQDLLE 42 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~p~ll~ 42 (129)
+.+..+|..|+.+.|.+.+...++.|.+
T Consensus 33 Kk~~~ai~~~d~~~a~~~l~~a~s~iDk 60 (87)
T TIGR00029 33 KKVYAAIAAGDKDKAQEAFKEAAKKLDR 60 (87)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4567788889999998888887776544
No 77
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=35.60 E-value=71 Score=23.81 Aligned_cols=26 Identities=8% Similarity=0.005 Sum_probs=18.2
Q ss_pred HHHHHHHHhcCChHHHHHHHHHhcCC
Q 033011 53 SLHFVELVCSRKCTEALEFAQTKLTP 78 (129)
Q Consensus 53 ~q~fIELir~~~~~~Ai~~ar~~l~~ 78 (129)
..+.++.|++|+.+.|.+..++|+..
T Consensus 201 H~~I~~Ai~~~D~~~A~~~m~~Hi~~ 226 (257)
T PRK10225 201 HKQILAALIKKDARAAKLAMWQHLEN 226 (257)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 45667777777777777777777743
No 78
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.55 E-value=2.4e+02 Score=23.23 Aligned_cols=85 Identities=19% Similarity=0.180 Sum_probs=54.0
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCC---chhHHHHHH
Q 033011 14 RKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGK---VQKYVEKLE 90 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~---~~~~~~~l~ 90 (129)
-.-+.+..+.|..+-|..++++-.-..-...+.=.| +.-.+-++-++.|++..|++||-.+-..+.. +-++.-.=.
T Consensus 121 ~ai~~h~~rqGm~dv~~~l~~Ea~~~~~~~~~~~~F-~el~~Iv~~lke~Dl~~aLeWa~~~~~~L~~~~s~LE~~Lh~l 199 (394)
T KOG2817|consen 121 EAIVYHFYRQGMDDVGECLIKEAGLSEDESKSRTEF-VELNQIVEALKERDLEPALEWAESNRQKLKEKSSSLEFKLHSL 199 (394)
T ss_pred HHHHHHHHHcCchHHHHHHHHHhcCCCcchhhhhhH-HHHHHHHHHHHhccchhHHHHHHHhhhhhccccccHHHHHHHH
Confidence 344567788999999999999876433211121222 3445677779999999999999877655442 223333334
Q ss_pred HHHhHhccC
Q 033011 91 DFMALLAYE 99 (129)
Q Consensus 91 ~~~~lLay~ 99 (129)
..+.++..+
T Consensus 200 ~fl~l~~~g 208 (394)
T KOG2817|consen 200 HFLSLIRGG 208 (394)
T ss_pred HHHHHHhcC
Confidence 455555554
No 79
>PF04136 Sec34: Sec34-like family ; InterPro: IPR007265 Sec34 and Sec35 form a sub-complex in a seven-protein complex that includes Dor1. This complex is thought to be important for tethering vesicles to the Golgi [].; GO: 0006886 intracellular protein transport, 0005801 cis-Golgi network, 0016020 membrane
Probab=35.32 E-value=1.5e+02 Score=20.84 Aligned_cols=67 Identities=19% Similarity=0.235 Sum_probs=39.5
Q ss_pred HHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhcCCcCCc----hhHHHHHHHHHhHh
Q 033011 26 ALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKLTPFGKV----QKYVEKLEDFMALL 96 (129)
Q Consensus 26 i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~~~----~~~~~~l~~~~~lL 96 (129)
|..=+.......|--..-++. .+.+....|++++. .+++.|.|..+|- .|... .++..-+.++++|+
T Consensus 68 I~~~L~yF~~Ld~itr~Ln~p-~~sV~~~~F~~~L~--~LD~cl~Fl~~h~-~fkea~~Y~~rf~q~ltRAl~lI 138 (157)
T PF04136_consen 68 ISEKLQYFEELDPITRRLNSP-GSSVNSDSFKPMLS--RLDECLEFLEEHP-NFKEAEVYLIRFRQCLTRALTLI 138 (157)
T ss_pred HHHHhHHHhhHHHHHHHHcCC-CCcccchHHHHHHH--HHHHHHHHHHHhh-hhhhhHHHHHHHHHHHHHHHHHH
Confidence 344444444455443333332 24466888999887 4889999998764 34322 34555566666665
No 80
>PRK03837 transcriptional regulator NanR; Provisional
Probab=35.23 E-value=98 Score=22.63 Aligned_cols=26 Identities=8% Similarity=-0.098 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHhhc
Q 033011 12 EMRKRILHFALEGNALKAIELTEELA 37 (129)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~~~~~~ 37 (129)
.+-..|.++|..||.+.|.+.+..+.
T Consensus 201 ~~H~~i~~Ai~~~d~~~a~~~~~~H~ 226 (241)
T PRK03837 201 QEHIAIVDAIRAHDPDEADRALQSHL 226 (241)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 33334444444444444444444443
No 81
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=35.01 E-value=96 Score=23.08 Aligned_cols=27 Identities=19% Similarity=0.154 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhhc
Q 033011 11 MEMRKRILHFALEGNALKAIELTEELA 37 (129)
Q Consensus 11 ~~~R~~I~~~I~~G~i~~Ai~~~~~~~ 37 (129)
+.+=..|.++|.+||.+.|..++.++.
T Consensus 191 ~~~H~~I~~AI~~~D~~~A~~~~~~H~ 217 (253)
T PRK10421 191 TEQHQAVMDAILAGDAEGARKAMMAHL 217 (253)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 444455555555555555555555544
No 82
>TIGR00116 tsf translation elongation factor Ts. This protein is found in Bacteria, mitochondria, and chloroplasts.
Probab=34.76 E-value=34 Score=26.85 Aligned_cols=40 Identities=25% Similarity=0.267 Sum_probs=29.5
Q ss_pred cCCHHHHHHHHHhhchH-------------------------HHccCcccchhhHHHHHHHHHhc
Q 033011 23 EGNALKAIELTEELAQD-------------------------LLEKNKDLHFDLLSLHFVELVCS 62 (129)
Q Consensus 23 ~G~i~~Ai~~~~~~~p~-------------------------ll~~~~~l~F~L~~q~fIELir~ 62 (129)
+||++.|++|+++..-. +.+-|..-.|.-+-..|++++..
T Consensus 30 ~gDiekAi~~LRkkG~akA~Kk~~R~a~EG~V~~~~~~~~~~ivElncETDFVArne~F~~l~~~ 94 (290)
T TIGR00116 30 NGDFEKAIKNLRESGIAKAAKKADRVAAEGVIVLKSDGNKAVIVEVNSETDFVAKNAGFKEFANK 94 (290)
T ss_pred CCCHHHHHHHHHHhchhHHHHhcccccCCcEEEEEEcCCEEEEEEEecCCccccCChHHHHHHHH
Confidence 59999999999985532 23334566788888888888653
No 83
>PRK13689 hypothetical protein; Provisional
Probab=34.39 E-value=42 Score=20.99 Aligned_cols=18 Identities=28% Similarity=0.457 Sum_probs=15.6
Q ss_pred CCHHHHHHHHHHHHHHHh
Q 033011 110 LSLEYRQHVADNLNRAIL 127 (129)
Q Consensus 110 l~~~~r~~la~~vn~aiL 127 (129)
..+++|..+|+.|-.|+.
T Consensus 49 V~~~qR~~iAe~Fa~AL~ 66 (75)
T PRK13689 49 VAPAQRQAIAESFARALQ 66 (75)
T ss_pred CCHHHHHHHHHHHHHHHH
Confidence 368999999999999875
No 84
>PRK09377 tsf elongation factor Ts; Provisional
Probab=34.30 E-value=35 Score=26.83 Aligned_cols=40 Identities=28% Similarity=0.317 Sum_probs=29.3
Q ss_pred cCCHHHHHHHHHhhchH-------------------------HHccCcccchhhHHHHHHHHHhc
Q 033011 23 EGNALKAIELTEELAQD-------------------------LLEKNKDLHFDLLSLHFVELVCS 62 (129)
Q Consensus 23 ~G~i~~Ai~~~~~~~p~-------------------------ll~~~~~l~F~L~~q~fIELir~ 62 (129)
+||++.|++|+.+..-. +.+-|..-.|.-+-..|+.++..
T Consensus 31 ~gD~ekAi~~Lrk~G~akA~Kk~~R~a~EG~I~~~~~~~~~~~vElncETDFVArne~F~~l~~~ 95 (290)
T PRK09377 31 DGDIEKAIEWLRKKGLAKAAKKAGRVAAEGLVAAKVDGNKGVLVEVNSETDFVAKNEDFQALANE 95 (290)
T ss_pred CCCHHHHHHHHHHhchhhHHHhcCccccceEEEEEeCCCEEEEEEEecCCccccCChHHHHHHHH
Confidence 59999999999985432 23334566788888888887653
No 85
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=33.91 E-value=74 Score=23.63 Aligned_cols=25 Identities=24% Similarity=0.194 Sum_probs=19.7
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhchH
Q 033011 15 KRILHFALEGNALKAIELTEELAQD 39 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~p~ 39 (129)
..|-++|.+||.+.|...+.+|...
T Consensus 203 ~~I~~Ai~~~D~~~A~~~~~~Hl~~ 227 (254)
T PRK09464 203 ARIFEAIVAGKPEKAREASHRHLAF 227 (254)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 4788888888888888888877643
No 86
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=33.66 E-value=64 Score=17.84 Aligned_cols=20 Identities=30% Similarity=0.247 Sum_probs=14.3
Q ss_pred HHHHHcCCHHHHHHHHHhhc
Q 033011 18 LHFALEGNALKAIELTEELA 37 (129)
Q Consensus 18 ~~~I~~G~i~~Ai~~~~~~~ 37 (129)
+..|..|+.+.|.+++++.-
T Consensus 7 ~ayie~Gd~e~Ar~lL~evl 26 (44)
T TIGR03504 7 RAYIEMGDLEGARELLEEVI 26 (44)
T ss_pred HHHHHcCChHHHHHHHHHHH
Confidence 45677788888888776643
No 87
>TIGR03362 VI_chp_7 type VI secretion-associated protein, VC_A0119 family. This protein family is one of two related families in type VI secretion systems that contain an ImpA-related N-terminal domain (pfam06812).
Probab=32.91 E-value=1.3e+02 Score=23.58 Aligned_cols=62 Identities=21% Similarity=0.224 Sum_probs=43.6
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHH
Q 033011 10 DMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQ 73 (129)
Q Consensus 10 ~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar 73 (129)
..+.....+.++.+|.++.|+.|+++..+...+....++..|..-+..+- .|...-|..+.+
T Consensus 213 ~~~~~~eA~~l~~~~gl~~Al~~L~~~~~~~~s~R~rf~~rL~~A~l~~~--~g~~~lA~~ll~ 274 (301)
T TIGR03362 213 WEELREEARALAAEGGLEAALQRLQQRLAQAREPRERFHWRLLLARLLEQ--AGKAELAQQLYA 274 (301)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHhhcccCCChHHHHHHHHHHHHHHHH--cCCHHHHHHHHH
Confidence 34556778999999999999999999877666665556666666666553 455455555444
No 88
>PF12510 Smoothelin: Smoothelin cytoskeleton protein; InterPro: IPR022189 This domain family is found in eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00307 from PFAM. Smoothelin is a cytoskeletal protein specifically expressed in differentiated smooth muscle cells and has been shown to co-localize with smooth muscle alpha actin.
Probab=32.78 E-value=40 Score=19.79 Aligned_cols=16 Identities=38% Similarity=0.337 Sum_probs=12.8
Q ss_pred HHhHHHHHHHHHHHHc
Q 033011 8 LEDMEMRKRILHFALE 23 (129)
Q Consensus 8 ~~~~~~R~~I~~~I~~ 23 (129)
..++++|+.||.+|+.
T Consensus 34 ~~dyeeRr~IRaaiR~ 49 (54)
T PF12510_consen 34 TTDYEERRRIRAAIRE 49 (54)
T ss_pred hccHHHHHHHHHHHHH
Confidence 3578899999998864
No 89
>PF01877 RNA_binding: RNA binding; InterPro: IPR002739 The proteins in this entry are functionally uncharacterised.; PDB: 2WNY_B 2NWU_A 2NRQ_A 2OGK_A 3D7A_B 3C9G_B 2PZZ_D.
Probab=32.40 E-value=1.1e+02 Score=20.58 Aligned_cols=44 Identities=16% Similarity=0.090 Sum_probs=35.6
Q ss_pred HhHHHHHHHHHHHHcCCH-HHHHHHHHhhchHHHccCcccchhhHHHHHH
Q 033011 9 EDMEMRKRILHFALEGNA-LKAIELTEELAQDLLEKNKDLHFDLLSLHFV 57 (129)
Q Consensus 9 ~~~~~R~~I~~~I~~G~i-~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fI 57 (129)
...+.-..+.+.+...++ +.|...+.+..- +..++|.|.+|...
T Consensus 56 ~~~~~l~~l~~~l~~~~i~d~~~~~l~~~~~-----~~~~~~rl~KQaA~ 100 (120)
T PF01877_consen 56 EALKSLKKLHELLRDQEILDTARSELEKRVD-----GNKLYFRLDKQAAY 100 (120)
T ss_dssp HHHHHHHHHHHHHHHTTHHHHHHHHHHHTBE-----TSEEEEEEEHHHHH
T ss_pred cHHHHHHHHHHHHhhhhhhhHHHHHHHhccc-----CCEEEEEEchhHhh
Confidence 355667789999999999 888888876652 67899999999876
No 90
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=31.93 E-value=38 Score=17.41 Aligned_cols=21 Identities=19% Similarity=0.137 Sum_probs=14.3
Q ss_pred HHHHHHHH--HcCCHHHHHHHHH
Q 033011 14 RKRILHFA--LEGNALKAIELTE 34 (129)
Q Consensus 14 R~~I~~~I--~~G~i~~Ai~~~~ 34 (129)
+..++.++ ..||++.|+.|+-
T Consensus 15 ~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 15 REEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHh
Confidence 44455554 3589999999873
No 91
>PF10475 DUF2450: Protein of unknown function N-terminal domain (DUF2450) ; InterPro: IPR019515 This entry represents Vacuolar protein sorting-associated protein 54, and is thought to be involved in retrograde transport from early and late endosomes to late Golgi found in eukaryotes, but its function is not known.
Probab=31.70 E-value=2.4e+02 Score=21.70 Aligned_cols=30 Identities=30% Similarity=0.340 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHcCCHHHHHHHHHhhchHHH
Q 033011 12 EMRKRILHFALEGNALKAIELTEELAQDLL 41 (129)
Q Consensus 12 ~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll 41 (129)
+....|+.++.+||+..|++++.+....+-
T Consensus 129 ~~~~~l~~ll~~~dy~~Al~li~~~~~~l~ 158 (291)
T PF10475_consen 129 QTQSRLQELLEEGDYPGALDLIEECQQLLE 158 (291)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHHHH
Confidence 346788899999999999999998877653
No 92
>KOG3380 consensus Actin-related protein Arp2/3 complex, subunit ARPC5 [Cytoskeleton]
Probab=31.32 E-value=75 Score=22.59 Aligned_cols=59 Identities=10% Similarity=0.057 Sum_probs=37.1
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhchHHHccCc--ccchhhHHHHHHHHHhcCChHHHHHHHH
Q 033011 14 RKRILHFALEGNALKAIELTEELAQDLLEKNK--DLHFDLLSLHFVELVCSRKCTEALEFAQ 73 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~--~l~F~L~~q~fIELir~~~~~~Ai~~ar 73 (129)
-.+|+.++..|+...|+..+-.+-|- ..++. .=....-..+-+--+|+.+++.+|+-.-
T Consensus 39 ~~ev~sll~qg~~~~AL~~aL~~~P~-~t~~q~vK~~a~~~v~~vL~~ik~adI~~~v~~Ls 99 (152)
T KOG3380|consen 39 EREVRSLLTQGKSLEALQTALLNPPY-GTKDQEVKDRALNVVLKVLTSIKQADIEAAVKKLS 99 (152)
T ss_pred hHHHHHHHHcccHHHHHHHHHhCCCC-CCccHHHHHHHHHHHHHHHHHHHHHhHHHHHHHhh
Confidence 46899999999999999998877661 11111 0112233344555567777777765443
No 93
>PF07729 FCD: FCD domain; InterPro: IPR011711 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector binding or oligomerisation domain at the C terminus. The winged-helix DNA-binding domain is well conserved in structure for the whole of the GntR family (IPR000524 from INTERPRO), and is similar in structure to other transcriptional regulator families. The C-terminal effector-binding and oligomerisation domains are more variable and are consequently used to define the subfamilies. Based on the sequence and structure of the C-terminal domains, the GtnR family can be divided into four major groups, as represented by FadR (IPR008920 from INTERPRO), HutC, MocR and YtrA, as well as some minor groups such as those represented by AraR and PlmA []. This entry represents the C-terminal ligand binding domain of many members of the GntR family. This domain probably binds to a range of effector molecules that regulate the transcription of genes through the action of the N-terminal DNA-binding domain. This domain is found in P45427 from SWISSPROT and P31460 from SWISSPROT that are regulators of sugar biosynthesis operons.; PDB: 3SXK_A 3SXY_A 3SXM_B 3SXZ_A 3FMS_A 2DI3_B 2HS5_A 3IHU_B 3C7J_A.
Probab=30.72 E-value=77 Score=19.73 Aligned_cols=24 Identities=8% Similarity=0.101 Sum_probs=18.2
Q ss_pred HHHHHHHHhcCChHHHHHHHHHhc
Q 033011 53 SLHFVELVCSRKCTEALEFAQTKL 76 (129)
Q Consensus 53 ~q~fIELir~~~~~~Ai~~ar~~l 76 (129)
....++.|+.|+.+.|.+..+.|+
T Consensus 100 h~~i~~ai~~~d~~~a~~~~~~h~ 123 (125)
T PF07729_consen 100 HREIIDAIRAGDPEAAREALRQHI 123 (125)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHh
Confidence 456778888888888888888776
No 94
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=30.65 E-value=1.6e+02 Score=19.47 Aligned_cols=32 Identities=22% Similarity=0.156 Sum_probs=25.1
Q ss_pred hhhHHHHHHHHHhcCChHHHHHHHHHhcCCcC
Q 033011 49 FDLLSLHFVELVCSRKCTEALEFAQTKLTPFG 80 (129)
Q Consensus 49 F~L~~q~fIELir~~~~~~Ai~~ar~~l~~~~ 80 (129)
|.=..++++++++.|+..+|..+......|..
T Consensus 121 y~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~ 152 (181)
T PF12729_consen 121 YRKLRDQVIELAKSGDNDEARAILNGEARPAF 152 (181)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHhHHHHH
Confidence 45556888999999999999888887776554
No 95
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=30.45 E-value=76 Score=16.74 Aligned_cols=18 Identities=17% Similarity=0.093 Sum_probs=11.5
Q ss_pred HHHHHcCCHHHHHHHHHh
Q 033011 18 LHFALEGNALKAIELTEE 35 (129)
Q Consensus 18 ~~~I~~G~i~~Ai~~~~~ 35 (129)
+-....|+.+.|++++++
T Consensus 9 ~~~~~~G~~~~A~~~~~~ 26 (44)
T PF13428_consen 9 RAYRRLGQPDEAERLLRR 26 (44)
T ss_pred HHHHHcCCHHHHHHHHHH
Confidence 345566777777776654
No 96
>PF11251 DUF3050: Protein of unknown function (DUF3050); InterPro: IPR024423 This family of proteins has no known function.
Probab=30.04 E-value=1.6e+02 Score=22.53 Aligned_cols=98 Identities=20% Similarity=0.350 Sum_probs=54.4
Q ss_pred HHHHHHHHcC-CHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCC---hHHHHHHHHHhcCCcCCchhHHHHHH
Q 033011 15 KRILHFALEG-NALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRK---CTEALEFAQTKLTPFGKVQKYVEKLE 90 (129)
Q Consensus 15 ~~I~~~I~~G-~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~---~~~Ai~~ar~~l~~~~~~~~~~~~l~ 90 (129)
....+.+.+| ++..|+..+.--- +.-.|.=... +.|..|+ +..|..|||+.+-|-- +..-++
T Consensus 100 ~~fl~~~~~g~~v~~Al~~~~~p~-------~~~~Fv~~Tf---~~i~~~~~H~iAAaFtfGREdlIP~M----F~~il~ 165 (232)
T PF11251_consen 100 DRFLSLLREGTSVFEALQQADVPE-------PAKRFVRFTF---EIIAEGKPHEIAAAFTFGREDLIPDM----FRSILK 165 (232)
T ss_pred HHHHHHHHcCCCHHHHHHhcCCCH-------HHHHHHHHHH---HHHhcCCHHHHHHHHHhccccchHHH----HHHHHH
Confidence 4566778888 8998887653211 1122333333 3455564 7789999999886621 111111
Q ss_pred H------HHhHhcc--------CCCCCCchh-----hhC--CHHHHHHHHHHHHHHH
Q 033011 91 D------FMALLAY--------EEPEKSPMF-----HLL--SLEYRQHVADNLNRAI 126 (129)
Q Consensus 91 ~------~~~lLay--------~~~~~sp~~-----~Ll--~~~~r~~la~~vn~ai 126 (129)
+ -+..+.| +.-+-+|.+ .|- |+.+|+++......|+
T Consensus 166 ~~~~~~~~~~~f~yYL~RHIElDgdeHgPlA~~ml~~Lcg~D~~kw~ea~~aa~~AL 222 (232)
T PF11251_consen 166 DLNIPPGQLPTFRYYLERHIELDGDEHGPLAMQMLEELCGDDPQKWQEAEQAAKEAL 222 (232)
T ss_pred HhcCCccccHHHHHHHHhhhhcCCCcchHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 1 1222222 223345643 333 6788988888777765
No 97
>KOG2027 consensus Spindle pole body protein [Cytoskeleton]
Probab=30.01 E-value=1.3e+02 Score=24.63 Aligned_cols=26 Identities=23% Similarity=0.287 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHcCCHHHHHHHHHhh
Q 033011 11 MEMRKRILHFALEGNALKAIELTEEL 36 (129)
Q Consensus 11 ~~~R~~I~~~I~~G~i~~Ai~~~~~~ 36 (129)
-..|+.|-++|.+|+-..|.--+...
T Consensus 18 kq~RrdIA~lL~sg~~~~A~~RvE~l 43 (388)
T KOG2027|consen 18 KQLRRDIADLLKSGQDERARIRVEHL 43 (388)
T ss_pred HHHHHHHHHHHHcCCchhhHHHHHHH
Confidence 35689999999999999998766543
No 98
>PF04699 P16-Arc: ARP2/3 complex 16 kDa subunit (p16-Arc); InterPro: IPR006789 The Arp2/3 protein complex has been implicated in the control of actin polymerisation. The human complex consists of seven subunits which include the actin related proteins Arp2 and Arp3, and five others referred to as p41-Arc, p34-Arc, p21-Arc, p20-Arc, and p16-Arc. The precise function of p16-Arc is currently unknown. Its structure consists of a single domain containing a bundle of seven alpha helices [, ].; GO: 0030833 regulation of actin filament polymerization, 0005856 cytoskeleton; PDB: 3DWL_G 1TYQ_G 1U2V_G 2P9U_G 2P9L_G 1K8K_G 3DXM_G 2P9N_G 3DXK_G 2P9I_G ....
Probab=29.96 E-value=48 Score=23.52 Aligned_cols=25 Identities=12% Similarity=0.202 Sum_probs=19.9
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhch
Q 033011 14 RKRILHFALEGNALKAIELTEELAQ 38 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~~p 38 (129)
-.+|+.++..|+..+|+..+=++-|
T Consensus 40 ~~qvr~ll~~g~~~~ALk~aL~npP 64 (152)
T PF04699_consen 40 EQQVRQLLSSGDNEEALKAALENPP 64 (152)
T ss_dssp HHHHHHHHHCT-HHHHHHHHTSS--
T ss_pred HHHHHHHHhCCCHHHHHHHhccCCC
Confidence 5679999999999999999988766
No 99
>COG3947 Response regulator containing CheY-like receiver and SARP domains [Signal transduction mechanisms]
Probab=29.95 E-value=3e+02 Score=22.22 Aligned_cols=74 Identities=22% Similarity=0.172 Sum_probs=44.5
Q ss_pred CCcccHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccC------------cccchhhHHHHHHHHHhcCChHHHHH
Q 033011 3 QPANCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKN------------KDLHFDLLSLHFVELVCSRKCTEALE 70 (129)
Q Consensus 3 ~p~~d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~------------~~l~F~L~~q~fIELir~~~~~~Ai~ 70 (129)
.|..|......-.+=...|- -.++++-+++.......+..+ +.++.++.--.--+....|...+|++
T Consensus 222 ~~k~Dv~e~es~~rqi~~in-ltide~kelv~~ykgdyl~e~~y~Waedererle~ly~kllgkva~~yle~g~~neAi~ 300 (361)
T COG3947 222 LPKYDVQEYESLARQIEAIN-LTIDELKELVGQYKGDYLPEADYPWAEDERERLEQLYMKLLGKVARAYLEAGKPNEAIQ 300 (361)
T ss_pred CccccHHHHHHHhhhhhccc-cCHHHHHHHHHHhcCCcCCccccccccchHHHHHHHHHHHHHHHHHHHHHcCChHHHHH
Confidence 45666666555444334444 567788777777655554442 12333443333444556799999999
Q ss_pred HHHHhcC
Q 033011 71 FAQTKLT 77 (129)
Q Consensus 71 ~ar~~l~ 77 (129)
+.|.-++
T Consensus 301 l~qr~lt 307 (361)
T COG3947 301 LHQRALT 307 (361)
T ss_pred HHHHHhh
Confidence 9996553
No 100
>PF08625 Utp13: Utp13 specific WD40 associated domain; InterPro: IPR013934 A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA - the small-subunit (SSU) processome [, ]. This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties: They are nucleolar. They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome). They are required for 18S rRNA biogenesis. There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble []. From electron microscopy the SSU processome may correspond to the terminal knobs visualized at the 5' ends of nascent 18S rRNA. Utp13 is a nucleolar protein and component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA []. Upt13 is also a component of the Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome []. Components of the Pwp2 complex are: Utp1 (Pwp2), Utp6, Utp12 (Dip2), Utp13, Utp18, and Utp21. The relationship between the Pwp2 complex and the t-Utps complex [] that also associates with the 5' end of nascent pre-18S rRNA is unclear. ; GO: 0006364 rRNA processing, 0032040 small-subunit processome
Probab=29.89 E-value=1.8e+02 Score=20.20 Aligned_cols=59 Identities=15% Similarity=0.191 Sum_probs=35.4
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhc-h--------HHH---ccCcccchhhHHHHHHHHHhcCChHHHHHHHHH
Q 033011 15 KRILHFALEGNALKAIELTEELA-Q--------DLL---EKNKDLHFDLLSLHFVELVCSRKCTEALEFAQT 74 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~-p--------~ll---~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~ 74 (129)
|.+..++..|++.+|+.++=+.. | .+. +..... ..-.....|.-+...++...+.|.|+
T Consensus 2 Q~L~N~l~~~~y~~Al~LAl~L~~P~~ll~i~~~~~~~~~~~~~~-g~~~l~~~i~~L~~~~l~~LL~~ir~ 72 (141)
T PF08625_consen 2 QELSNLLRQKDYKEALRLALKLDHPFRLLKILKDLLETEEDEDSI-GSEELDEVIKKLDDEQLEKLLRFIRD 72 (141)
T ss_pred chHHHHHHhhhHHHHHHHHHhcCCcHHHHHHHHHHHhcccccccc-hHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 46788999999999999885533 3 122 111112 22334455555555566677777774
No 101
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=29.03 E-value=45 Score=17.06 Aligned_cols=11 Identities=36% Similarity=0.462 Sum_probs=9.4
Q ss_pred cCCHHHHHHHH
Q 033011 23 EGNALKAIELT 33 (129)
Q Consensus 23 ~G~i~~Ai~~~ 33 (129)
.||++.|+.|+
T Consensus 26 ~~d~~~A~~~L 36 (37)
T smart00165 26 NGNVERAAEYL 36 (37)
T ss_pred CCCHHHHHHHH
Confidence 58899999886
No 102
>PF06910 MEA1: Male enhanced antigen 1 (MEA1); InterPro: IPR009685 This family consists of several mammalian male enhanced antigen 1 (MEA1) proteins. The Mea-1 gene is found to be localised in primary and secondary spermatocytes and spermatids, but the protein products are detected only in spermatids. Intensive transcription of Mea-1 gene and specific localisation of the gene product suggest that Mea-1 may play a important role in the late stage of spermatogenesis [].; GO: 0007283 spermatogenesis
Probab=28.93 E-value=1.3e+02 Score=21.90 Aligned_cols=39 Identities=18% Similarity=0.065 Sum_probs=32.8
Q ss_pred chhHHHHHHHHHhHhccCCCCCCchhhhCCHHHHHHHHH
Q 033011 82 VQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEYRQHVAD 120 (129)
Q Consensus 82 ~~~~~~~l~~~~~lLay~~~~~sp~~~Ll~~~~r~~la~ 120 (129)
++.+.+.++++|+-+.-+....-..+.-.+.++|..+..
T Consensus 123 D~~~ve~Vk~~Ma~i~LP~~~vP~WA~~IseeqWk~~l~ 161 (174)
T PF06910_consen 123 DAEHVELVKRTMAGITLPSSAVPEWAKEISEEQWKDVLQ 161 (174)
T ss_pred CHHHHHHHHHHHhcccCCCCCCcHHHhhCCHHHHHHHHH
Confidence 678899999999999988877777899999999966443
No 103
>PF07079 DUF1347: Protein of unknown function (DUF1347); InterPro: IPR010764 This family consists of several hypothetical bacterial proteins of around 610 residues in length. Members of this family are highly conserved and seem to be specific to Chlamydia species. The function of this family is unknown.
Probab=28.45 E-value=73 Score=27.05 Aligned_cols=49 Identities=16% Similarity=0.116 Sum_probs=40.6
Q ss_pred HHHHHHHHcCCHHHHHHHHHhhchHHHccCc--------ccchhhHHHHHHHHHhcC
Q 033011 15 KRILHFALEGNALKAIELTEELAQDLLEKNK--------DLHFDLLSLHFVELVCSR 63 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~--------~l~F~L~~q~fIELir~~ 63 (129)
..+-.+|..|...++...+|+..|.++++.. .+...|-+-.|+|++...
T Consensus 133 i~a~sLIe~g~f~EgR~iLn~i~~~llkrE~~w~~d~yd~~vlmlsrSYfLEl~e~~ 189 (549)
T PF07079_consen 133 IEAHSLIETGRFSEGRAILNRIIERLLKRECEWNSDMYDRAVLMLSRSYFLELKESM 189 (549)
T ss_pred HHHHHHHhcCCcchHHHHHHHHHHHHhhhhhcccHHHHHHHHHHHhHHHHHHHHHhc
Confidence 4566789999999999999999999999532 355688889999997765
No 104
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=28.34 E-value=62 Score=19.37 Aligned_cols=25 Identities=32% Similarity=0.380 Sum_probs=17.0
Q ss_pred HHHHHHHHHHcCCHHHHHHHHHhhc
Q 033011 13 MRKRILHFALEGNALKAIELTEELA 37 (129)
Q Consensus 13 ~R~~I~~~I~~G~i~~Ai~~~~~~~ 37 (129)
-..++.+++.+||.+.+.+++++..
T Consensus 4 ~~~~l~~al~~~d~~~~~~~~~~~l 28 (79)
T PF02607_consen 4 LIERLLDALLAGDEEEAEALLEEAL 28 (79)
T ss_dssp HHHHHHHHHHTT-CCHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 3566777777777777777776654
No 105
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=28.05 E-value=1.2e+02 Score=21.97 Aligned_cols=25 Identities=0% Similarity=-0.087 Sum_probs=16.0
Q ss_pred HHHHHHHHhcCChHHHHHHHHHhcC
Q 033011 53 SLHFVELVCSRKCTEALEFAQTKLT 77 (129)
Q Consensus 53 ~q~fIELir~~~~~~Ai~~ar~~l~ 77 (129)
..+.++.|+.|+.+.|-+..+.|+.
T Consensus 185 H~~I~~Ai~~~D~~~A~~~~~~hl~ 209 (221)
T PRK11414 185 YRLLLAALKAKDKEGCRHCLAEIMQ 209 (221)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHH
Confidence 4466666666666666666666664
No 106
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=27.74 E-value=2.9e+02 Score=21.37 Aligned_cols=61 Identities=16% Similarity=0.136 Sum_probs=45.6
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHH----hcCChHHHHHHHHHhcCCcC
Q 033011 14 RKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELV----CSRKCTEALEFAQTKLTPFG 80 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELi----r~~~~~~Ai~~ar~~l~~~~ 80 (129)
=.+....+..|+++.|++..+... ..++.-.+. .|--|+++ +.++..+|+.++-..+.-+.
T Consensus 38 Y~~g~~~L~~gn~~~A~~~fe~l~----~~~p~s~~~--~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP 102 (254)
T COG4105 38 YNEGLTELQKGNYEEAIKYFEALD----SRHPFSPYS--EQAQLDLAYAYYKNGEYDLALAYIDRFIRLYP 102 (254)
T ss_pred HHHHHHHHhcCCHHHHHHHHHHHH----HcCCCCccc--HHHHHHHHHHHHhcccHHHHHHHHHHHHHhCC
Confidence 467889999999999998876544 566655554 67777776 56788999988887666554
No 107
>TIGR02552 LcrH_SycD type III secretion low calcium response chaperone LcrH/SycD. ScyD/LcrH contains three central tetratricopeptide-like repeats that are predicted to fold into an all-alpha-helical array.
Probab=27.73 E-value=1.7e+02 Score=18.74 Aligned_cols=22 Identities=18% Similarity=0.164 Sum_probs=16.0
Q ss_pred HHHHHHHHcCCHHHHHHHHHhh
Q 033011 15 KRILHFALEGNALKAIELTEEL 36 (129)
Q Consensus 15 ~~I~~~I~~G~i~~Ai~~~~~~ 36 (129)
......+..|+.++|+.++...
T Consensus 22 ~~a~~~~~~~~~~~A~~~~~~~ 43 (135)
T TIGR02552 22 ALAYNLYQQGRYDEALKLFQLL 43 (135)
T ss_pred HHHHHHHHcccHHHHHHHHHHH
Confidence 3445677789999998887664
No 108
>PF03398 Ist1: Regulator of Vps4 activity in the MVB pathway; InterPro: IPR005061 This is a eukaryotic protein family of unknown function.; PDB: 3GGZ_B 3GGY_B 3FRR_A 3FRS_A.
Probab=27.63 E-value=61 Score=23.08 Aligned_cols=29 Identities=24% Similarity=0.237 Sum_probs=22.8
Q ss_pred HhHHHHHHHHHHHHcCCHHHHHHHHHhhc
Q 033011 9 EDMEMRKRILHFALEGNALKAIELTEELA 37 (129)
Q Consensus 9 ~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~ 37 (129)
..-..|+.|-++|..|+.+.|.-.+...-
T Consensus 21 ~~~~~rkdIa~LL~~g~~~~Ar~rvE~li 49 (165)
T PF03398_consen 21 QAKQARKDIAQLLKNGKEESARIRVEQLI 49 (165)
T ss_dssp HHHHHHHHHHHHHCCT-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34567999999999999999998886543
No 109
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=27.33 E-value=1.2e+02 Score=16.92 Aligned_cols=55 Identities=22% Similarity=0.174 Sum_probs=32.6
Q ss_pred HHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHHhc
Q 033011 17 ILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQTKL 76 (129)
Q Consensus 17 I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l 76 (129)
-...+..|+++.|++.+++ +++.++. .-..+...-.=+...|+..+|+.+-++-+
T Consensus 4 a~~~~~~g~~~~A~~~~~~----~l~~~P~-~~~a~~~lg~~~~~~g~~~~A~~~~~~a~ 58 (65)
T PF13432_consen 4 ARALYQQGDYDEAIAAFEQ----ALKQDPD-NPEAWYLLGRILYQQGRYDEALAYYERAL 58 (65)
T ss_dssp HHHHHHCTHHHHHHHHHHH----HHCCSTT-HHHHHHHHHHHHHHTT-HHHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHH----HHHHCCC-CHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 4567889999999988755 3445443 11111111112236689999998888644
No 110
>PRK04964 hypothetical protein; Provisional
Probab=27.08 E-value=52 Score=19.93 Aligned_cols=24 Identities=17% Similarity=0.127 Sum_probs=15.5
Q ss_pred ChHHHHHHHHHhcCCcCCchhHHH
Q 033011 64 KCTEALEFAQTKLTPFGKVQKYVE 87 (129)
Q Consensus 64 ~~~~Ai~~ar~~l~~~~~~~~~~~ 87 (129)
-+..||..+-+-|...+.++....
T Consensus 22 YiP~Ai~ca~k~L~~IAad~~Lp~ 45 (66)
T PRK04964 22 YVPDALGCVLKALNEIAADEALPE 45 (66)
T ss_pred cCcHHHHHHHHHHHHHhccccCCH
Confidence 377888888877766654443333
No 111
>TIGR02120 GspF general secretion pathway protein F. This membrane protein is a component of the terminal branch complex of the general secretion pathway (GSP), also known as the"Type II" secretion pathway. The GSP transports proteins (generally virulence-associated cell wall hydrolases) across the outer membrase of the bacterial cell. Transport across the inner membrane is often, but not exclusively handled by the Sec system. This model was constructed from the broader subfamily model, pfam00482 which includes components of pilin complexes (PilC) as well as other related genes. GspF is nearly always gene clustered with other GSP subunits. Some genes from Xylella and Xanthomonas strains score below the trusted cutoff due to excessive divergence from the family such that a sequence from Deinococcus which does not appear to be GspF scores higher.
Probab=26.83 E-value=2.6e+02 Score=22.31 Aligned_cols=23 Identities=13% Similarity=0.096 Sum_probs=14.3
Q ss_pred HHHHHHHHHcC-CHHHHHHHHHhh
Q 033011 14 RKRILHFALEG-NALKAIELTEEL 36 (129)
Q Consensus 14 R~~I~~~I~~G-~i~~Ai~~~~~~ 36 (129)
-+++-.++.+| .+.+|++.+.+.
T Consensus 67 ~~~La~ll~sGi~l~~aL~~l~~~ 90 (399)
T TIGR02120 67 TRQLATLLGAGLPLEEALAALLEQ 90 (399)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHh
Confidence 44556666666 567777766554
No 112
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=26.35 E-value=86 Score=14.92 Aligned_cols=16 Identities=38% Similarity=0.370 Sum_probs=10.8
Q ss_pred HHHcCCHHHHHHHHHh
Q 033011 20 FALEGNALKAIELTEE 35 (129)
Q Consensus 20 ~I~~G~i~~Ai~~~~~ 35 (129)
....|+++.|++.+++
T Consensus 11 ~~~~~~~~~A~~~~~~ 26 (34)
T PF07719_consen 11 YYQLGNYEEAIEYFEK 26 (34)
T ss_dssp HHHTT-HHHHHHHHHH
T ss_pred HHHhCCHHHHHHHHHH
Confidence 4567888888887765
No 113
>KOG0989 consensus Replication factor C, subunit RFC4 [Replication, recombination and repair]
Probab=26.28 E-value=3.5e+02 Score=21.87 Aligned_cols=59 Identities=15% Similarity=0.091 Sum_probs=42.8
Q ss_pred HHHcCCHHHHHHHHHhhchHHHccC-c-------ccchhhHHHHHHHHHhcCChHHHHHHHHHhcCC
Q 033011 20 FALEGNALKAIELTEELAQDLLEKN-K-------DLHFDLLSLHFVELVCSRKCTEALEFAQTKLTP 78 (129)
Q Consensus 20 ~I~~G~i~~Ai~~~~~~~p~ll~~~-~-------~l~F~L~~q~fIELir~~~~~~Ai~~ar~~l~~ 78 (129)
.+-.|+.-.|+..++...+.-.... + .+.-.-..-.++|+.++++..+-++++|+.+..
T Consensus 218 ~~S~GdLR~Ait~Lqsls~~gk~It~~~~~e~~~GvVp~~~l~~lle~a~S~d~~~~v~~~Rei~~s 284 (346)
T KOG0989|consen 218 KISDGDLRRAITTLQSLSLLGKRITTSLVNEELAGVVPDEKLLDLLELALSADTPNTVKRVREIMRS 284 (346)
T ss_pred HHcCCcHHHHHHHHHHhhccCcccchHHHHHHHhccCCHHHHHHHHHHHHccChHHHHHHHHHHHHh
Confidence 3557999999999999998221111 1 123334467899999999999999999976643
No 114
>KOG1539 consensus WD repeat protein [General function prediction only]
Probab=25.49 E-value=1.3e+02 Score=27.23 Aligned_cols=39 Identities=23% Similarity=0.428 Sum_probs=26.2
Q ss_pred HHHHHc----CCHHHHHHHHHhhchHHHccCcccchhhHHH-----------HHHHHHhc
Q 033011 18 LHFALE----GNALKAIELTEELAQDLLEKNKDLHFDLLSL-----------HFVELVCS 62 (129)
Q Consensus 18 ~~~I~~----G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q-----------~fIELir~ 62 (129)
-.++++ .+...|.+.+..+.| +.+.|.++.. .||.|+..
T Consensus 785 ~~~Lre~~~s~~~~~~~~~L~~~~p------saiD~eiRsL~d~~~~~~~~~~Fi~~l~~ 838 (910)
T KOG1539|consen 785 TTLLREGKDSKDFLDAFALLKNLSP------SAIDFEIRSLNDAGETIEEMVIFIKMLTQ 838 (910)
T ss_pred HHHHhhccccccHHHHHHHHHhcCc------chheeehhhhhccCcchHHHHHHHHHHHH
Confidence 445554 468999999999888 4455555554 67766654
No 115
>PRK07535 methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase; Validated
Probab=25.47 E-value=99 Score=23.68 Aligned_cols=23 Identities=22% Similarity=0.059 Sum_probs=21.2
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhh
Q 033011 14 RKRILHFALEGNALKAIELTEEL 36 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~ 36 (129)
++.++++|.+|+++.+++.+.+.
T Consensus 12 ~~~~~~~~~~~d~~~i~~~A~~~ 34 (261)
T PRK07535 12 RKSIAEAIEAKDAAFIQKLALKQ 34 (261)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHH
Confidence 89999999999999999998774
No 116
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=25.33 E-value=1.5e+02 Score=21.96 Aligned_cols=26 Identities=8% Similarity=-0.055 Sum_probs=14.3
Q ss_pred HHHHHHHHhcCChHHHHHHHHHhcCC
Q 033011 53 SLHFVELVCSRKCTEALEFAQTKLTP 78 (129)
Q Consensus 53 ~q~fIELir~~~~~~Ai~~ar~~l~~ 78 (129)
.+..++.|+.|+.+.|....+.|+..
T Consensus 195 H~~I~~Ai~~~D~~~A~~~~~~Hi~~ 220 (253)
T PRK11523 195 HDQILKALIRKDPHAAKLAMWQHLEN 220 (253)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 44555555555555555555555543
No 117
>PF05047 L51_S25_CI-B8: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain ; InterPro: IPR007741 Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) 1.6.5.3 from EC. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.; PDB: 1S3A_A.
Probab=24.95 E-value=37 Score=18.98 Aligned_cols=24 Identities=13% Similarity=0.206 Sum_probs=17.5
Q ss_pred HHHHHhhchHHHccCcccchhhHH
Q 033011 30 IELTEELAQDLLEKNKDLHFDLLS 53 (129)
Q Consensus 30 i~~~~~~~p~ll~~~~~l~F~L~~ 53 (129)
-+.+..+.|.+...|+.+.|.++.
T Consensus 2 R~F~~~~lp~l~~~NP~v~~~v~~ 25 (52)
T PF05047_consen 2 RDFLKNNLPTLKYHNPQVQFEVRR 25 (52)
T ss_dssp HHHHHHTHHHHHHHSTT--EEEE-
T ss_pred HhHHHHhHHHHHHHCCCcEEEEEE
Confidence 456788899999999999998766
No 118
>PF06786 UPF0253: Uncharacterised protein family (UPF0253); InterPro: IPR009624 This is a group of proteins of unknown function.
Probab=24.56 E-value=59 Score=19.68 Aligned_cols=22 Identities=14% Similarity=0.116 Sum_probs=14.6
Q ss_pred ChHHHHHHHHHhcCCcCCchhH
Q 033011 64 KCTEALEFAQTKLTPFGKVQKY 85 (129)
Q Consensus 64 ~~~~Ai~~ar~~l~~~~~~~~~ 85 (129)
-+..||..+-+-|...+.++..
T Consensus 22 YiP~Ai~calk~Ln~iAad~~L 43 (66)
T PF06786_consen 22 YIPDAIGCALKTLNDIAADEAL 43 (66)
T ss_pred cCcHHHHHHHHHHHHHHccccc
Confidence 3778888888777666544333
No 119
>KOG1854 consensus Mitochondrial inner membrane protein (mitofilin) [Cell wall/membrane/envelope biogenesis]
Probab=24.46 E-value=1.5e+02 Score=26.01 Aligned_cols=56 Identities=20% Similarity=0.167 Sum_probs=39.5
Q ss_pred ccHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccC----cccchhhHHHHHHHHHh
Q 033011 6 NCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKN----KDLHFDLLSLHFVELVC 61 (129)
Q Consensus 6 ~d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~----~~l~F~L~~q~fIELir 61 (129)
.+.++++...+.++++..||.+.|+..++.....=..-- .+..-.|-.|+.+|++.
T Consensus 586 ~~~d~~~iLsrA~~~~~~gdl~~Avr~v~lLkG~pr~va~dWi~daRr~lE~qql~eiL~ 645 (657)
T KOG1854|consen 586 NITDTYKILSRARYHLLKGDLDDAVRVVNLLKGWPRKVARDWIKDARRRLETQQLVEILK 645 (657)
T ss_pred ccccHHHHHHHHHHHHhcccHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678889999999999999999999999887654211110 12344566666666654
No 120
>PRK12332 tsf elongation factor Ts; Reviewed
Probab=24.38 E-value=60 Score=23.99 Aligned_cols=15 Identities=40% Similarity=0.441 Sum_probs=13.3
Q ss_pred cCCHHHHHHHHHhhc
Q 033011 23 EGNALKAIELTEELA 37 (129)
Q Consensus 23 ~G~i~~Ai~~~~~~~ 37 (129)
+||++.|++|+.+..
T Consensus 30 ~gd~~~A~~~lr~~g 44 (198)
T PRK12332 30 NGDMEKAIEWLREKG 44 (198)
T ss_pred CCCHHHHHHHHHHhh
Confidence 599999999999854
No 121
>PF14591 AF0941-like: AF0941-like; PDB: 1YOZ_B.
Probab=24.15 E-value=62 Score=22.32 Aligned_cols=77 Identities=19% Similarity=0.198 Sum_probs=43.3
Q ss_pred HHHHHHHcCCHHHHHHHHHhhchHHHccCc--ccchhhHHHHHHHHHhcCCh--HHHHHHHHHhcCCcCCchhHHHHHHH
Q 033011 16 RILHFALEGNALKAIELTEELAQDLLEKNK--DLHFDLLSLHFVELVCSRKC--TEALEFAQTKLTPFGKVQKYVEKLED 91 (129)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~--~l~F~L~~q~fIELir~~~~--~~Ai~~ar~~l~~~~~~~~~~~~l~~ 91 (129)
++.+++.+--|..+.+-+.+.+|.|..... .+ |.-.++..++...+|++ ++|.+... .|..++ +.....+.+
T Consensus 8 kL~ELi~~~vI~d~~e~leei~~~L~~~e~I~em-Fr~D~e~Il~~~~~Gdi~eEEA~~ll~-eL~~~a--sqL~~~~~~ 83 (127)
T PF14591_consen 8 KLGELIRNSVIPDVEEDLEEIFESLADKEEIEEM-FRSDLEDILEDYKSGDIDEEEALQLLD-ELKSYA--SQLQEHYFR 83 (127)
T ss_dssp HHHHHHT------TSS-GGGHHH-HT-HHHHHHH-HHHHHHHHHHHHHTTSS-HHHHHHHHH-HHHHHH--HTHHHHHHH
T ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHcCHHHHHHH-HHHHHHHHHHHHHcCCCCHHHHHHHHH-HHHHHH--HHHHHHHHH
Confidence 455566666777777777777886664422 24 99999999999999964 46776665 454554 344444444
Q ss_pred HHhHh
Q 033011 92 FMALL 96 (129)
Q Consensus 92 ~~~lL 96 (129)
+--+|
T Consensus 84 ~~e~l 88 (127)
T PF14591_consen 84 VRELL 88 (127)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 44444
No 122
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=23.93 E-value=1.6e+02 Score=21.68 Aligned_cols=27 Identities=15% Similarity=0.095 Sum_probs=19.8
Q ss_pred HHHHHHHHHhcCChHHHHHHHHHhcCC
Q 033011 52 LSLHFVELVCSRKCTEALEFAQTKLTP 78 (129)
Q Consensus 52 ~~q~fIELir~~~~~~Ai~~ar~~l~~ 78 (129)
..+..++.|+.|+.+.|....+.|+..
T Consensus 201 ~H~~I~~Ai~~~D~~~A~~~~~~Hi~~ 227 (251)
T PRK09990 201 QHARLYNAVLQRLPEQAQRAARDHIRT 227 (251)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 456777777777777777777777743
No 123
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=23.86 E-value=3.7e+02 Score=21.28 Aligned_cols=36 Identities=3% Similarity=-0.049 Sum_probs=16.8
Q ss_pred hcCChHHHHHHHHHhcCCcCCchhHHHHHHHHHhHh
Q 033011 61 CSRKCTEALEFAQTKLTPFGKVQKYVEKLEDFMALL 96 (129)
Q Consensus 61 r~~~~~~Ai~~ar~~l~~~~~~~~~~~~l~~~~~lL 96 (129)
..|+..+|+.+.++-+.-...++.....+..+-.-|
T Consensus 82 ~lg~~~eA~~~~~~al~l~P~~~~~~~~l~~~~~kl 117 (356)
T PLN03088 82 KLEEYQTAKAALEKGASLAPGDSRFTKLIKECDEKI 117 (356)
T ss_pred HhCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHH
Confidence 346666666666644432222344444444443333
No 124
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=23.18 E-value=1.5e+02 Score=21.64 Aligned_cols=30 Identities=17% Similarity=0.132 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHhhchH
Q 033011 10 DMEMRKRILHFALEGNALKAIELTEELAQD 39 (129)
Q Consensus 10 ~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ 39 (129)
.+++=..|.++|.+||.+.|.+.+.++.-.
T Consensus 184 ~~~eH~~il~Ai~~~d~~~A~~~m~~Hl~~ 213 (230)
T COG1802 184 AIDEHRAILEALEARDAEAAAEAMRQHLRR 213 (230)
T ss_pred hHHHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 466777788888888888888888776543
No 125
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=23.08 E-value=76 Score=23.04 Aligned_cols=21 Identities=29% Similarity=0.284 Sum_probs=18.1
Q ss_pred cCCHHHHHHHHHhhchHHHcc
Q 033011 23 EGNALKAIELTEELAQDLLEK 43 (129)
Q Consensus 23 ~G~i~~Ai~~~~~~~p~ll~~ 43 (129)
.|.+..+-+|+.+|+|.+...
T Consensus 20 ~~~~~kCk~WL~~n~p~l~~~ 40 (173)
T TIGR01159 20 SGDLKRCKVWLSENAPDLYAK 40 (173)
T ss_pred CCCHHHHHHHHHHhChHHHHH
Confidence 478899999999999988754
No 126
>PF08283 Gemini_AL1_M: Geminivirus rep protein central domain; InterPro: IPR022692 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name []. Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) [, ]. Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants. Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship [, , ]. Amino acid sequence alignments of Potato yellow mosaic virus (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions []. Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus [] and Miscanthus streak virus (MiSV) [], reveal high levels of similarity. This is the central region of the geminivirus rep proteins []. It is found C-terminal to PF00799 from PFAM and is thought to be responsible for oligomerisation.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters
Probab=22.80 E-value=89 Score=20.82 Aligned_cols=24 Identities=21% Similarity=0.232 Sum_probs=20.6
Q ss_pred HHHHHHHcCCHHHHHHHHHhhchH
Q 033011 16 RILHFALEGNALKAIELTEELAQD 39 (129)
Q Consensus 16 ~I~~~I~~G~i~~Ai~~~~~~~p~ 39 (129)
..-++|-+|.-++|+..+++.+|.
T Consensus 8 a~a~aina~sk~EaL~iike~~P~ 31 (106)
T PF08283_consen 8 AYARAINAGSKEEALSIIKELAPK 31 (106)
T ss_pred HHHHHHhcCCHHHHHHHHHhcCch
Confidence 345678999999999999999985
No 127
>CHL00102 rps20 ribosomal protein S20
Probab=22.79 E-value=1.5e+02 Score=19.26 Aligned_cols=28 Identities=18% Similarity=0.124 Sum_probs=21.4
Q ss_pred HHHHHHHHc-------CCHHHHHHHHHhhchHHHc
Q 033011 15 KRILHFALE-------GNALKAIELTEELAQDLLE 42 (129)
Q Consensus 15 ~~I~~~I~~-------G~i~~Ai~~~~~~~p~ll~ 42 (129)
+.+..+|.. |+.+.|.+++...++.|.+
T Consensus 33 Kk~~~ai~~~~~~~~~~d~~~a~~~l~~a~s~iDk 67 (93)
T CHL00102 33 KKYLKNLEDYKTSPNSNNKKKVQETLSSVYSKIDK 67 (93)
T ss_pred HHHHHHHHhhcccCCcccHHHHHHHHHHHHHHHHH
Confidence 456677777 8999999988888776644
No 128
>PF10003 DUF2244: Integral membrane protein (DUF2244); InterPro: IPR019253 This entry consists of various bacterial putative membrane proteins with no known function.
Probab=22.74 E-value=72 Score=21.96 Aligned_cols=22 Identities=32% Similarity=0.436 Sum_probs=19.5
Q ss_pred chhhhCCHHHHHHHHHHHHHHH
Q 033011 105 PMFHLLSLEYRQHVADNLNRAI 126 (129)
Q Consensus 105 p~~~Ll~~~~r~~la~~vn~ai 126 (129)
.++..++++.|..+|.++.+++
T Consensus 119 eiG~fL~~~eR~~la~~L~~aL 140 (140)
T PF10003_consen 119 EIGRFLNPEEREELARELRRAL 140 (140)
T ss_pred EEccCCCHHHHHHHHHHHHhhC
Confidence 4688999999999999999874
No 129
>CHL00098 tsf elongation factor Ts
Probab=22.73 E-value=67 Score=23.80 Aligned_cols=16 Identities=25% Similarity=0.262 Sum_probs=13.8
Q ss_pred HcCCHHHHHHHHHhhc
Q 033011 22 LEGNALKAIELTEELA 37 (129)
Q Consensus 22 ~~G~i~~Ai~~~~~~~ 37 (129)
-+||++.|++|+.+..
T Consensus 26 ~~gd~~~A~~~Lr~~g 41 (200)
T CHL00098 26 ANGDFEKALESLRQKG 41 (200)
T ss_pred cCCCHHHHHHHHHHhh
Confidence 3699999999999864
No 130
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=22.53 E-value=1.1e+02 Score=20.23 Aligned_cols=34 Identities=26% Similarity=0.224 Sum_probs=24.8
Q ss_pred HHHHHcCCHHHHHHHHHhhchHHHccCcccchhhH
Q 033011 18 LHFALEGNALKAIELTEELAQDLLEKNKDLHFDLL 52 (129)
Q Consensus 18 ~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~ 52 (129)
.++.++||++.|-+.+.+-.-.+.+- ..+++.|.
T Consensus 28 l~~ak~gdf~~A~~~l~eA~~~l~~A-H~~qt~li 61 (104)
T PRK09591 28 FAAMREGNFDLAEQKLNQSNEELLEA-HHAQTKLL 61 (104)
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHH-HHHHHHHH
Confidence 35667899999999999988777666 33444444
No 131
>PF10414 CysG_dimeriser: Sirohaem synthase dimerisation region; InterPro: IPR019478 Bacterial sulphur metabolism depends on the iron-containing porphinoid sirohaem. CysG is a multi-functional enzyme with S-adenosyl-L-methionine (SAM)-dependent bismethyltransferase, dehydrogenase and ferrochelatase activities. CysG synthesizes sirohaem from uroporphyrinogen III via reactions which encompass two branchpoint intermediates in tetrapyrrole biosynthesis, diverting flux first from protoporphyrin IX biosynthesis and then from cobalamin (vitamin B12) biosynthesis. CysG is a dimer. Its dimerisation region is 74 residues long, and acts to hold the two structurally similar protomers held together asymmetrically through a number of salt-bridges across complementary residues within the dimerisation region []. CysG dimerisation produces a series of active sites, accounting for CysG's multi-functionality, catalysing four diverse reactions: Two SAM-dependent methylations NAD+-dependent tetrapyrrole dehydrogenation Metal chelation ; GO: 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 1PJT_A 1PJS_A 1PJQ_A.
Probab=21.85 E-value=1.7e+02 Score=16.80 Aligned_cols=27 Identities=30% Similarity=0.465 Sum_probs=15.3
Q ss_pred HhHHHHHHHH---------HHHHcCCHHHHHHHHHh
Q 033011 9 EDMEMRKRIL---------HFALEGNALKAIELTEE 35 (129)
Q Consensus 9 ~~~~~R~~I~---------~~I~~G~i~~Ai~~~~~ 35 (129)
.++..|+.+. +++..|+.+.|...+..
T Consensus 22 ~~~~~RR~FWe~~~~g~~~~~~~~g~~~~A~~~l~~ 57 (60)
T PF10414_consen 22 PDFAERRRFWERFFDGPFAELVLAGDEEEAEALLEQ 57 (60)
T ss_dssp SSHHHHHHHHHHHT-HHHHHHHHTT-HHHHHHHHHH
T ss_pred CCchHHHHHHHHHHcCHHHHHHHCCCHHHHHHHHHH
Confidence 3455555544 55666777777766654
No 132
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=21.80 E-value=2.6e+02 Score=18.66 Aligned_cols=66 Identities=15% Similarity=0.028 Sum_probs=38.8
Q ss_pred ccHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhH-HHHHHHHHhcCChHHHHHHHHH
Q 033011 6 NCLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLL-SLHFVELVCSRKCTEALEFAQT 74 (129)
Q Consensus 6 ~d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~-~q~fIELir~~~~~~Ai~~ar~ 74 (129)
.....+-.-..-...+..|+.+.|++.++..--.- .++.+.-..+ +.-.| ++..|+.++|+...++
T Consensus 44 s~ya~~A~l~lA~~~~~~g~~~~A~~~l~~~~~~~--~d~~l~~~a~l~LA~~-~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 44 SPYAALAALQLAKAAYEQGDYDEAKAALEKALANA--PDPELKPLARLRLARI-LLQQGQYDEALATLQQ 110 (145)
T ss_pred ChHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhhC--CCHHHHHHHHHHHHHH-HHHcCCHHHHHHHHHh
Confidence 33444455555667788999999999887744321 1122221111 11112 2466889999999976
No 133
>PRK08570 rpl19e 50S ribosomal protein L19e; Reviewed
Probab=21.43 E-value=75 Score=22.59 Aligned_cols=23 Identities=17% Similarity=0.133 Sum_probs=19.3
Q ss_pred cccHHhHHHHHHHHHHHHcCCHH
Q 033011 5 ANCLEDMEMRKRILHFALEGNAL 27 (129)
Q Consensus 5 ~~d~~~~~~R~~I~~~I~~G~i~ 27 (129)
-.+++....|..|+.+|.+|-|-
T Consensus 29 ~~eI~~A~tR~dIR~LI~~G~I~ 51 (150)
T PRK08570 29 LEDVAEAITREDIRELIKEGVIK 51 (150)
T ss_pred HHHHHHHhhHHHHHHHHHCCCee
Confidence 45778888999999999999763
No 134
>COG1410 MetH Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]
Probab=21.08 E-value=2.3e+02 Score=25.56 Aligned_cols=63 Identities=19% Similarity=0.250 Sum_probs=42.1
Q ss_pred HHHHHHHHhcCChHHHHHHHHHhcCCcCC---------chhHHHHHHHHHhHhccCCCCCCchhhhCCHHHHHHHH
Q 033011 53 SLHFVELVCSRKCTEALEFAQTKLTPFGK---------VQKYVEKLEDFMALLAYEEPEKSPMFHLLSLEYRQHVA 119 (129)
Q Consensus 53 ~q~fIELir~~~~~~Ai~~ar~~l~~~~~---------~~~~~~~l~~~~~lLay~~~~~sp~~~Ll~~~~r~~la 119 (129)
.-+|-+++..|+.++|+..||++...=++ ...-...+.+...++++... +.-.+|.+.|+-+-
T Consensus 41 skkf~~li~~~~y~~~l~iAr~Qv~~GA~ilDvn~d~~~~D~~~~m~~~l~~~a~~~~----vPlMIDSs~~eviE 112 (842)
T COG1410 41 SKKFRRLIIAEDYDEALDVARQQVENGAQILDVNVDYVGRDGVADMVELLNLLANEPT----VPLMIDSSEWEVIE 112 (842)
T ss_pred hHHHHHHHHcccHHHHHHHHHHHHhcCCEEEEeeccccccccHHHHHHHHHHhccCCC----CceEEehhHHHHHH
Confidence 45788888888999999999987765442 12334556777778887533 33456777776553
No 135
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=20.86 E-value=1.3e+02 Score=15.19 Aligned_cols=16 Identities=38% Similarity=0.522 Sum_probs=10.6
Q ss_pred HHHcCCHHHHHHHHHh
Q 033011 20 FALEGNALKAIELTEE 35 (129)
Q Consensus 20 ~I~~G~i~~Ai~~~~~ 35 (129)
....|+++.|++...+
T Consensus 9 ~~~~g~~~~Ai~~y~~ 24 (36)
T PF13176_consen 9 YRQQGDYEKAIEYYEQ 24 (36)
T ss_dssp HHHCT-HHHHHHHHHH
T ss_pred HHHcCCHHHHHHHHHH
Confidence 3456888888877765
No 136
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=20.80 E-value=3.2e+02 Score=19.41 Aligned_cols=27 Identities=11% Similarity=0.069 Sum_probs=15.6
Q ss_pred HHHHHHHHHcCCHHHHHHHHHhhchHH
Q 033011 14 RKRILHFALEGNALKAIELTEELAQDL 40 (129)
Q Consensus 14 R~~I~~~I~~G~i~~Ai~~~~~~~p~l 40 (129)
+..-.....-||.+.|++...+.....
T Consensus 40 ~~l~~~~~~~Gd~~~A~k~y~~~~~~~ 66 (177)
T PF10602_consen 40 EDLADHYCKIGDLEEALKAYSRARDYC 66 (177)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHHhhhc
Confidence 344455566666666666666655443
No 137
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=20.74 E-value=70 Score=24.34 Aligned_cols=52 Identities=15% Similarity=0.248 Sum_probs=36.2
Q ss_pred hhHHHHHHHHHhcCC-h-HHHHHHHHHhcCCcCCchhHHHHHHHHHhHhccCCC
Q 033011 50 DLLSLHFVELVCSRK-C-TEALEFAQTKLTPFGKVQKYVEKLEDFMALLAYEEP 101 (129)
Q Consensus 50 ~L~~q~fIELir~~~-~-~~Ai~~ar~~l~~~~~~~~~~~~l~~~~~lLay~~~ 101 (129)
.|.-++..++-.+=. . +.-.+||++|-+...+|+++..++++.|+.+--++.
T Consensus 25 ~l~e~Ql~q~~~Ql~~f~~~LeeFA~kH~~ei~knsqFR~~Fq~Mca~IGvDPl 78 (249)
T KOG3341|consen 25 ELAEQQLVQMSKQLEVFQEALEEFARKHKTEIRKNSQFRNQFQEMCASIGVDPL 78 (249)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHcCCCcc
Confidence 344556666544321 1 234579999988888899999999999988876654
No 138
>PF10552 ORF6C: ORF6C domain; InterPro: IPR018878 This entry represents the carboxy-terminal domain from ORF6 (Q9B012 from SWISSPROT), an antirepressor protein from Lactococcus phage bIL285 [].
Probab=20.60 E-value=67 Score=21.32 Aligned_cols=21 Identities=10% Similarity=0.018 Sum_probs=17.8
Q ss_pred HHHHcCCHHHHHHHHHhhchH
Q 033011 19 HFALEGNALKAIELTEELAQD 39 (129)
Q Consensus 19 ~~I~~G~i~~Ai~~~~~~~p~ 39 (129)
..|...+.+.|++.++.+.|.
T Consensus 88 ~~I~~kdfd~A~~~I~~W~p~ 108 (116)
T PF10552_consen 88 KDIPRKDFDEALEFINNWEPS 108 (116)
T ss_pred HhhhHHHHHHHHHHHHHcCCC
Confidence 567788999999999999884
No 139
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=20.58 E-value=2.3e+02 Score=20.45 Aligned_cols=18 Identities=6% Similarity=0.185 Sum_probs=10.3
Q ss_pred HHHHHHHHhHhccCCCCC
Q 033011 86 VEKLEDFMALLAYEEPEK 103 (129)
Q Consensus 86 ~~~l~~~~~lLay~~~~~ 103 (129)
..+-+.++..+.=.|++.
T Consensus 184 ~~eH~~Il~Ai~~~D~~~ 201 (224)
T PRK11534 184 HDQHQTLTAAILARDTAR 201 (224)
T ss_pred HHHHHHHHHHHHhCCHHH
Confidence 345566666666666543
No 140
>PRK10573 type IV pilin biogenesis protein; Provisional
Probab=20.52 E-value=4.2e+02 Score=21.17 Aligned_cols=22 Identities=14% Similarity=0.274 Sum_probs=12.7
Q ss_pred HHHHHHHHcC-CHHHHHHHHHhh
Q 033011 15 KRILHFALEG-NALKAIELTEEL 36 (129)
Q Consensus 15 ~~I~~~I~~G-~i~~Ai~~~~~~ 36 (129)
+++-.++.+| .+.+|++.+.+.
T Consensus 66 ~~L~~ll~~G~~l~~aL~~l~~~ 88 (399)
T PRK10573 66 RQLATLLQAGLPLSEGLQLLAEQ 88 (399)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhc
Confidence 4555566666 456666666544
No 141
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=20.15 E-value=4.1e+02 Score=20.41 Aligned_cols=16 Identities=13% Similarity=0.096 Sum_probs=8.7
Q ss_pred hcCChHHHHHHHHHhc
Q 033011 61 CSRKCTEALEFAQTKL 76 (129)
Q Consensus 61 r~~~~~~Ai~~ar~~l 76 (129)
+.|+..+|+.+.++-+
T Consensus 192 ~~~~~~~A~~~~~~al 207 (389)
T PRK11788 192 ARGDLDAARALLKKAL 207 (389)
T ss_pred hCCCHHHHHHHHHHHH
Confidence 4455666665555433
No 142
>cd00481 Ribosomal_L19e Ribosomal protein L19e. L19e is found in the large ribosomal subunit of eukaryotes and archaea. L19e is distinct from the ribosomal subunit L19, which is found in prokaryotes. It consists of two small globular domains connected by an extended segment. It is located toward the surface of the large subunit, with one exposed end involved in forming the intersubunit bridge with the small subunit. The other exposed end is involved in forming the translocon binding site, along with L22, L23, L24, L29, and L31e subunits.
Probab=20.06 E-value=80 Score=22.32 Aligned_cols=23 Identities=13% Similarity=0.244 Sum_probs=19.1
Q ss_pred cccHHhHHHHHHHHHHHHcCCHH
Q 033011 5 ANCLEDMEMRKRILHFALEGNAL 27 (129)
Q Consensus 5 ~~d~~~~~~R~~I~~~I~~G~i~ 27 (129)
-.+++....|..|+.+|.+|-|-
T Consensus 26 ~~eI~~A~tR~dIR~LIkdG~I~ 48 (145)
T cd00481 26 LEEIANANTREDIRKLIKDGLII 48 (145)
T ss_pred HHHHHHhhhHHHHHHHHHCCCee
Confidence 35778888899999999998763
No 143
>COG3898 Uncharacterized membrane-bound protein [Function unknown]
Probab=20.05 E-value=4.8e+02 Score=22.06 Aligned_cols=63 Identities=16% Similarity=0.031 Sum_probs=43.6
Q ss_pred cHHhHHHHHHHHHHHHcCCHHHHHHHHHhhchHHHccCcccchhhHHHHHHHHHhcCChHHHHHHHHH
Q 033011 7 CLEDMEMRKRILHFALEGNALKAIELTEELAQDLLEKNKDLHFDLLSLHFVELVCSRKCTEALEFAQT 74 (129)
Q Consensus 7 d~~~~~~R~~I~~~I~~G~i~~Ai~~~~~~~p~ll~~~~~l~F~L~~q~fIELir~~~~~~Ai~~ar~ 74 (129)
|-+-+-+--.-+.++..|+.+.|.+..+..- .. +.....=.+--|||--+.|..+.|..||-+
T Consensus 117 DqepLIhlLeAQaal~eG~~~~Ar~kfeAMl----~d-PEtRllGLRgLyleAqr~GareaAr~yAe~ 179 (531)
T COG3898 117 DQEPLIHLLEAQAALLEGDYEDARKKFEAML----DD-PETRLLGLRGLYLEAQRLGAREAARHYAER 179 (531)
T ss_pred cchHHHHHHHHHHHHhcCchHHHHHHHHHHh----cC-hHHHHHhHHHHHHHHHhcccHHHHHHHHHH
Confidence 4444555566678899999999998877643 22 332222234457899999999999999874
Done!