Query 034603
Match_columns 89
No_of_seqs 111 out of 205
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 04:33:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034603.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034603hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0293 WD40 repeat-containing 99.3 2.2E-12 4.9E-17 102.6 5.6 80 2-83 54-134 (519)
2 smart00668 CTLH C-terminal to 99.2 1.2E-11 2.6E-16 71.7 3.3 52 1-53 5-56 (58)
3 KOG2659 LisH motif-containing 99.2 3.7E-11 8E-16 89.0 5.7 79 3-84 70-150 (228)
4 PF10607 CLTH: CTLH/CRA C-term 99.2 5.3E-11 1.2E-15 80.0 5.2 83 2-86 6-89 (145)
5 KOG0396 Uncharacterized conser 98.2 3.3E-06 7.1E-11 66.5 5.3 84 2-86 157-240 (389)
6 KOG0275 Conserved WD40 repeat- 96.6 0.0057 1.2E-07 48.7 5.5 76 3-85 46-124 (508)
7 PF14559 TPR_19: Tetratricopep 96.1 0.018 3.8E-07 33.1 4.5 67 7-80 1-67 (68)
8 KOG2817 Predicted E3 ubiquitin 94.8 0.044 9.6E-07 43.8 4.2 79 2-82 160-242 (394)
9 KOG3060 Uncharacterized conser 92.1 0.43 9.4E-06 36.8 5.4 65 10-81 99-163 (289)
10 PF13432 TPR_16: Tetratricopep 91.0 0.3 6.5E-06 27.7 2.8 54 5-64 5-58 (65)
11 smart00757 CRA CT11-RanBPM. pr 89.9 0.43 9.3E-06 29.5 3.1 36 51-86 1-39 (99)
12 PF13429 TPR_15: Tetratricopep 88.4 0.98 2.1E-05 32.7 4.5 72 6-82 119-190 (280)
13 PF12895 Apc3: Anaphase-promot 86.9 0.71 1.5E-05 27.7 2.6 47 8-61 36-82 (84)
14 PF13371 TPR_9: Tetratricopept 84.9 5.3 0.00011 22.7 5.6 62 6-74 4-65 (73)
15 KOG0624 dsRNA-activated protei 83.6 3.7 8.1E-05 33.4 5.8 73 3-82 161-233 (504)
16 PF13428 TPR_14: Tetratricopep 78.4 4 8.8E-05 21.8 3.2 33 47-80 11-43 (44)
17 TIGR02795 tol_pal_ybgF tol-pal 78.1 11 0.00025 22.6 5.6 55 6-64 11-66 (119)
18 PF14559 TPR_19: Tetratricopep 77.5 3.7 8E-05 23.1 3.0 35 47-82 1-35 (68)
19 PLN03088 SGT1, suppressor of 77.5 7.9 0.00017 29.8 5.7 69 5-80 10-78 (356)
20 PHA00425 DNA packaging protein 75.4 7.6 0.00016 25.0 4.2 41 43-87 8-48 (88)
21 PF10602 RPN7: 26S proteasome 74.6 8.1 0.00018 27.1 4.7 84 2-86 78-171 (177)
22 PF14276 DUF4363: Domain of un 73.4 6.2 0.00014 25.7 3.6 56 2-58 33-98 (121)
23 PF04053 Coatomer_WDAD: Coatom 72.9 4.5 9.8E-05 32.6 3.4 68 3-80 267-355 (443)
24 PRK11788 tetratricopeptide rep 72.5 13 0.00028 27.5 5.6 55 8-64 152-207 (389)
25 PRK15359 type III secretion sy 71.8 17 0.00037 24.1 5.6 67 7-80 34-100 (144)
26 KOG1538 Uncharacterized conser 70.9 4.2 9.1E-05 35.5 2.9 72 7-81 783-859 (1081)
27 TIGR02552 LcrH_SycD type III s 70.1 15 0.00032 23.1 4.8 17 7-23 27-43 (135)
28 PRK12370 invasion protein regu 69.5 20 0.00043 29.1 6.4 70 7-82 382-451 (553)
29 PF11123 DNA_Packaging_2: DNA 67.7 14 0.0003 23.6 4.1 42 42-87 5-46 (82)
30 PRK10747 putative protoheme IX 67.4 26 0.00057 27.1 6.5 33 47-80 163-195 (398)
31 PF12870 Lumazine_bd: Lumazine 66.2 5 0.00011 24.4 1.9 22 2-23 14-35 (111)
32 KOG3452 60S ribosomal protein 66.0 9.2 0.0002 25.4 3.2 46 37-83 50-95 (102)
33 PF14691 Fer4_20: Dihydroprymi 65.7 8 0.00017 25.5 2.9 29 38-67 39-67 (111)
34 PRK14574 hmsH outer membrane p 65.3 17 0.00037 31.6 5.5 58 7-71 112-169 (822)
35 PF09976 TPR_21: Tetratricopep 65.3 34 0.00073 22.4 5.9 53 6-62 57-110 (145)
36 PRK10747 putative protoheme IX 64.8 23 0.0005 27.4 5.7 66 5-77 161-226 (398)
37 KOG3616 Selective LIM binding 64.4 24 0.00052 31.8 6.2 73 4-88 1299-1377(1636)
38 PF13512 TPR_18: Tetratricopep 64.1 15 0.00032 25.6 4.1 59 5-72 18-81 (142)
39 TIGR00756 PPR pentatricopeptid 63.7 7.3 0.00016 18.5 1.9 21 4-24 7-27 (35)
40 PF13281 DUF4071: Domain of un 63.7 30 0.00065 27.6 6.2 63 11-75 155-220 (374)
41 PF13812 PPR_3: Pentatricopept 63.5 7.3 0.00016 18.8 1.9 21 4-24 8-28 (34)
42 cd05804 StaR_like StaR_like; a 61.7 27 0.00059 25.5 5.4 56 8-65 159-214 (355)
43 cd02064 FAD_synthetase_N FAD s 61.1 8.1 0.00018 26.9 2.4 22 2-23 149-170 (180)
44 PF01535 PPR: PPR repeat; Int 60.8 7.6 0.00016 18.3 1.6 20 4-23 7-26 (31)
45 PRK10803 tol-pal system protei 60.3 23 0.0005 26.4 4.9 66 10-79 156-224 (263)
46 cd00189 TPR Tetratricopeptide 59.9 25 0.00054 18.7 5.4 66 7-79 10-75 (100)
47 PF07721 TPR_4: Tetratricopept 59.4 12 0.00025 18.0 2.2 15 7-21 11-25 (26)
48 PF14445 Prok-RING_2: Prokaryo 59.2 4.7 0.0001 23.9 0.8 15 2-16 20-34 (57)
49 cd00736 bacteriophage_lambda_l 56.9 7.3 0.00016 27.4 1.6 60 7-67 68-127 (151)
50 TIGR02561 HrpB1_HrpK type III 56.5 7.7 0.00017 27.5 1.6 61 7-67 54-123 (153)
51 PF13414 TPR_11: TPR repeat; P 56.1 13 0.00029 20.8 2.4 52 7-64 13-65 (69)
52 PF14498 Glyco_hyd_65N_2: Glyc 56.1 5.1 0.00011 29.0 0.7 23 1-23 58-80 (236)
53 COG1729 Uncharacterized protei 54.2 53 0.0012 25.0 5.9 59 6-68 150-209 (262)
54 PF09613 HrpB1_HrpK: Bacterial 53.9 8.3 0.00018 27.4 1.5 55 6-61 53-117 (160)
55 PF13525 YfiO: Outer membrane 53.4 21 0.00045 25.0 3.5 60 5-68 13-73 (203)
56 PF10414 CysG_dimeriser: Siroh 53.2 14 0.0003 21.3 2.2 20 3-22 38-57 (60)
57 PF12854 PPR_1: PPR repeat 53.0 11 0.00023 19.4 1.5 18 6-23 16-33 (34)
58 PRK15174 Vi polysaccharide exp 51.7 47 0.001 27.7 5.7 64 8-78 87-150 (656)
59 TIGR00540 hemY_coli hemY prote 51.6 52 0.0011 25.4 5.7 49 7-61 163-211 (409)
60 PRK11447 cellulose synthase su 51.2 54 0.0012 29.1 6.3 73 8-81 314-394 (1157)
61 PF13176 TPR_7: Tetratricopept 50.6 14 0.00031 18.8 1.8 15 8-22 10-24 (36)
62 PF13838 Clathrin_H_link: Clat 50.6 22 0.00047 21.7 2.8 23 39-61 8-30 (66)
63 PLN03079 Uncharacterized prote 50.6 26 0.00057 22.8 3.3 34 35-69 49-82 (91)
64 COG3877 Uncharacterized protei 50.2 23 0.00049 24.1 3.0 52 10-62 57-122 (122)
65 TIGR00990 3a0801s09 mitochondr 49.8 57 0.0012 26.5 5.9 74 8-82 478-552 (615)
66 TIGR03504 FimV_Cterm FimV C-te 49.3 45 0.00098 18.5 3.8 34 46-82 8-41 (44)
67 TIGR00990 3a0801s09 mitochondr 49.1 63 0.0014 26.2 6.0 67 9-82 343-409 (615)
68 COG5051 RPL36A Ribosomal prote 49.0 29 0.00062 22.7 3.3 44 38-82 51-94 (97)
69 PRK10049 pgaA outer membrane p 48.8 88 0.0019 26.5 7.0 75 7-82 320-403 (765)
70 PF13174 TPR_6: Tetratricopept 47.6 7.4 0.00016 18.6 0.3 16 8-23 11-26 (33)
71 PRK15174 Vi polysaccharide exp 47.5 35 0.00077 28.4 4.4 72 4-82 49-120 (656)
72 PF10579 Rapsyn_N: Rapsyn N-te 47.2 48 0.001 21.1 4.0 38 45-83 14-51 (80)
73 PF08283 Gemini_AL1_M: Geminiv 46.5 23 0.0005 23.5 2.6 25 42-67 7-31 (106)
74 PLN03088 SGT1, suppressor of 46.0 72 0.0016 24.5 5.7 66 7-79 46-111 (356)
75 PF07729 FCD: FCD domain; Int 45.7 27 0.00059 21.0 2.8 24 41-64 100-123 (125)
76 PF04494 TFIID_90kDa: WD40 ass 44.1 42 0.0009 22.6 3.7 45 34-78 39-83 (142)
77 PF07719 TPR_2: Tetratricopept 43.8 11 0.00025 18.1 0.7 16 8-23 12-27 (34)
78 PF12729 4HB_MCP_1: Four helix 43.3 61 0.0013 20.6 4.3 32 37-68 121-152 (181)
79 PF02259 FAT: FAT domain; Int 43.3 32 0.00068 25.1 3.2 77 5-84 6-84 (352)
80 cd02577 PSTD1 PSTD1: Pseudouri 42.8 59 0.0013 25.1 4.8 18 5-22 157-174 (319)
81 TIGR00540 hemY_coli hemY prote 41.4 1.4E+02 0.003 23.1 6.6 31 49-80 165-195 (409)
82 PRK11788 tetratricopeptide rep 41.2 1.2E+02 0.0026 22.3 6.1 12 51-62 121-132 (389)
83 PRK05627 bifunctional riboflav 40.7 25 0.00054 27.0 2.4 22 2-23 164-185 (305)
84 PRK12810 gltD glutamate syntha 40.3 31 0.00067 27.3 2.9 33 35-68 58-90 (471)
85 PRK07143 hypothetical protein; 40.2 27 0.00058 26.6 2.5 22 2-23 153-174 (279)
86 KOG2376 Signal recognition par 39.8 57 0.0012 28.0 4.5 62 7-68 185-255 (652)
87 PF01158 Ribosomal_L36e: Ribos 39.1 43 0.00093 22.0 3.0 46 36-82 47-92 (98)
88 PF07219 HemY_N: HemY protein 38.9 19 0.00041 23.1 1.3 20 7-26 69-88 (108)
89 PRK02603 photosystem I assembl 38.8 1.2E+02 0.0026 20.3 5.6 71 7-81 45-115 (172)
90 TIGR02521 type_IV_pilW type IV 38.7 1.1E+02 0.0024 19.8 6.1 17 49-65 181-197 (234)
91 smart00544 MA3 Domain in DAP-5 38.3 43 0.00093 21.0 2.9 76 4-82 9-103 (113)
92 TIGR02917 PEP_TPR_lipo putativ 38.3 91 0.002 24.8 5.3 13 49-61 443-455 (899)
93 TIGR03302 OM_YfiO outer membra 38.0 93 0.002 21.4 4.8 58 6-67 42-100 (235)
94 PF02334 RTP: Replication term 35.9 32 0.0007 23.4 2.1 47 35-81 9-64 (122)
95 PF12862 Apc5: Anaphase-promot 35.9 45 0.00097 20.6 2.7 22 43-64 4-25 (94)
96 PRK10049 pgaA outer membrane p 35.5 82 0.0018 26.7 4.9 55 7-63 282-336 (765)
97 PF13041 PPR_2: PPR repeat fam 35.5 35 0.00075 18.3 1.9 21 4-24 10-30 (50)
98 PRK09782 bacteriophage N4 rece 35.2 1E+02 0.0022 27.5 5.5 51 8-64 55-105 (987)
99 cd08044 TAF5_NTD2 TAF5_NTD2 is 34.9 28 0.0006 23.2 1.6 47 34-80 28-74 (133)
100 PF14689 SPOB_a: Sensor_kinase 34.3 27 0.00059 20.4 1.4 19 5-23 31-49 (62)
101 TIGR02917 PEP_TPR_lipo putativ 34.0 1.4E+02 0.0031 23.8 5.7 12 50-61 138-149 (899)
102 KOG2376 Signal recognition par 33.5 50 0.0011 28.3 3.2 57 3-65 18-74 (652)
103 PF04006 Mpp10: Mpp10 protein; 33.2 46 0.00099 27.8 3.0 77 3-87 397-485 (600)
104 TIGR01470 cysG_Nterm siroheme 32.8 49 0.0011 23.6 2.8 55 10-65 145-205 (205)
105 PF04097 Nic96: Nup93/Nic96; 32.4 30 0.00065 28.8 1.8 26 2-27 510-535 (613)
106 PF12162 STAT1_TAZ2bind: STAT1 32.2 40 0.00087 16.7 1.5 18 62-82 5-22 (23)
107 PF12793 SgrR_N: Sugar transpo 31.8 64 0.0014 21.3 3.0 33 28-61 57-94 (115)
108 PF02847 MA3: MA3 domain; Int 31.6 60 0.0013 20.2 2.7 18 45-62 10-27 (113)
109 PF01649 Ribosomal_S20p: Ribos 31.3 37 0.00081 21.4 1.7 22 2-23 32-53 (84)
110 PF03704 BTAD: Bacterial trans 31.3 1.2E+02 0.0026 19.5 4.2 35 47-82 72-106 (146)
111 TIGR00083 ribF riboflavin kina 31.1 44 0.00096 25.4 2.4 21 2-22 147-167 (288)
112 PF11817 Foie-gras_1: Foie gra 31.0 75 0.0016 23.1 3.5 19 5-23 186-204 (247)
113 PHA02608 67 prohead core prote 30.9 47 0.001 21.1 2.1 23 1-23 1-23 (80)
114 PRK12831 putative oxidoreducta 30.8 54 0.0012 26.1 2.9 32 35-67 54-85 (464)
115 PRK15363 pathogenicity island 30.5 84 0.0018 22.1 3.5 22 9-30 47-68 (157)
116 PRK00239 rpsT 30S ribosomal pr 30.4 44 0.00096 21.3 1.9 22 2-23 33-54 (88)
117 COG4105 ComL DNA uptake lipopr 29.9 1.1E+02 0.0024 23.3 4.3 56 6-68 43-102 (254)
118 PRK10866 outer membrane biogen 29.7 69 0.0015 23.4 3.2 59 5-67 40-99 (243)
119 PF05400 FliT: Flagellar prote 29.2 59 0.0013 19.0 2.3 18 5-22 2-19 (84)
120 COG0268 RpsT Ribosomal protein 28.7 48 0.001 21.4 1.9 22 2-23 33-54 (88)
121 PF14854 LURAP: Leucine rich a 28.6 56 0.0012 22.3 2.3 32 51-85 18-49 (121)
122 PTZ00196 60S ribosomal protein 28.5 77 0.0017 20.9 2.9 33 36-68 47-79 (98)
123 COG1410 MetH Methionine syntha 28.5 47 0.001 29.3 2.3 20 2-21 42-61 (842)
124 TIGR03338 phnR_burk phosphonat 28.4 64 0.0014 22.3 2.7 26 41-66 183-208 (212)
125 cd07921 PCA_45_Doxase_A_like S 28.3 50 0.0011 22.0 2.0 16 5-20 50-65 (106)
126 PLN02789 farnesyltranstransfer 28.2 1.3E+02 0.0027 23.1 4.5 71 1-77 40-111 (320)
127 TIGR01318 gltD_gamma_fam gluta 28.0 62 0.0013 25.7 2.8 33 35-68 54-86 (467)
128 PRK12771 putative glutamate sy 27.7 64 0.0014 26.2 2.9 63 1-68 23-85 (564)
129 PRK12370 invasion protein regu 27.5 1.9E+02 0.004 23.5 5.5 51 8-64 349-399 (553)
130 TIGR00029 S20 ribosomal protei 26.7 55 0.0012 20.8 1.9 22 2-23 33-54 (87)
131 PRK10316 hypothetical protein; 26.7 96 0.0021 23.0 3.4 75 4-78 61-177 (209)
132 PRK10564 maltose regulon perip 26.4 56 0.0012 25.5 2.2 25 3-27 263-287 (303)
133 PF03008 DUF234: Archaea bacte 26.3 1.1E+02 0.0023 19.3 3.2 34 44-80 8-41 (100)
134 PF07743 HSCB_C: HSCB C-termin 26.1 62 0.0013 19.3 2.0 21 3-23 46-66 (78)
135 TIGR01316 gltA glutamate synth 26.0 75 0.0016 25.0 2.9 32 35-67 42-73 (449)
136 PF08544 GHMP_kinases_C: GHMP 25.6 75 0.0016 18.4 2.3 20 4-23 1-20 (85)
137 cd02069 methionine_synthase_B1 25.6 61 0.0013 23.4 2.2 22 2-23 3-24 (213)
138 PF12569 NARP1: NMDA receptor- 25.4 2.1E+02 0.0046 23.6 5.5 67 9-82 16-82 (517)
139 PRK12814 putative NADPH-depend 25.1 76 0.0016 26.5 2.9 33 35-68 108-140 (652)
140 PF12169 DNA_pol3_gamma3: DNA 25.1 1.2E+02 0.0026 19.6 3.4 19 43-61 20-38 (143)
141 PRK14574 hmsH outer membrane p 24.7 3.2E+02 0.0069 24.0 6.7 29 49-78 114-142 (822)
142 COG3483 TDO2 Tryptophan 2,3-di 24.6 2.3E+02 0.005 21.6 5.1 49 11-61 7-69 (262)
143 CHL00033 ycf3 photosystem I as 23.9 2.2E+02 0.0048 18.7 6.0 69 8-80 46-114 (168)
144 PF00515 TPR_1: Tetratricopept 23.7 80 0.0017 15.1 1.9 19 47-65 11-29 (34)
145 PRK11447 cellulose synthase su 23.4 2.3E+02 0.0049 25.3 5.6 63 5-74 36-98 (1157)
146 PF13181 TPR_8: Tetratricopept 23.3 87 0.0019 14.8 2.0 18 47-64 11-28 (34)
147 PF04053 Coatomer_WDAD: Coatom 23.3 2.3E+02 0.0051 22.8 5.3 49 2-61 323-371 (443)
148 PF08463 EcoEI_R_C: EcoEI R pr 23.1 1.6E+02 0.0035 19.7 3.8 40 39-82 5-45 (164)
149 PRK11749 dihydropyrimidine deh 23.1 90 0.0019 24.5 2.9 32 36-68 55-86 (457)
150 PRK09782 bacteriophage N4 rece 23.1 1.6E+02 0.0036 26.3 4.7 66 5-81 86-151 (987)
151 COG3898 Uncharacterized membra 22.7 64 0.0014 26.8 2.0 47 4-51 195-244 (531)
152 PF07304 SRA1: Steroid recepto 22.1 58 0.0013 22.6 1.5 23 1-23 94-116 (157)
153 PF08542 Rep_fac_C: Replicatio 21.7 57 0.0012 19.5 1.2 22 2-23 9-30 (89)
154 PF07720 TPR_3: Tetratricopept 21.5 45 0.00097 17.6 0.6 13 9-21 13-25 (36)
155 PF02607 B12-binding_2: B12 bi 21.5 1.2E+02 0.0027 17.6 2.7 23 42-64 6-28 (79)
156 PF11464 Rbsn: Rabenosyn Rab b 21.3 1.2E+02 0.0026 17.0 2.4 22 2-23 10-31 (42)
157 TIGR00823 EIIA-LAC phosphotran 21.2 83 0.0018 20.3 2.0 17 6-22 26-42 (99)
158 COG4922 Uncharacterized protei 21.1 87 0.0019 21.5 2.1 19 3-21 14-32 (129)
159 PF00959 Phage_lysozyme: Phage 21.1 1.2E+02 0.0025 18.9 2.7 22 2-23 72-93 (110)
160 PF10825 DUF2752: Protein of u 20.8 1.1E+02 0.0024 17.4 2.2 16 4-19 20-35 (52)
161 cd07923 Gallate_dioxygenase_C 20.8 77 0.0017 20.7 1.7 15 5-19 42-56 (94)
162 PRK09591 celC cellobiose phosp 20.7 86 0.0019 20.5 2.0 17 6-22 29-45 (104)
163 PF13374 TPR_10: Tetratricopep 20.5 1E+02 0.0022 15.0 1.9 19 48-66 13-31 (42)
164 PF02828 L27: L27 domain; Int 20.5 1.7E+02 0.0037 16.4 3.0 31 54-85 3-33 (56)
165 PF05254 UPF0203: Uncharacteri 20.2 1.2E+02 0.0027 18.4 2.5 29 35-63 40-68 (68)
166 PF04733 Coatomer_E: Coatomer 20.1 74 0.0016 23.9 1.8 19 5-23 209-227 (290)
167 PRK05907 hypothetical protein; 20.0 71 0.0015 24.5 1.7 38 4-43 211-249 (311)
No 1
>KOG0293 consensus WD40 repeat-containing protein [Function unknown]
Probab=99.32 E-value=2.2e-12 Score=102.56 Aligned_cols=80 Identities=29% Similarity=0.339 Sum_probs=70.4
Q ss_pred hhHHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHH-Hh
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEA-SL 80 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l-~~ 80 (89)
+.|.++|++|+|+.++..+..+...++..++ ++.|++.||+|||++..|++..|+.+||++..|+. .|.+.|++| |.
T Consensus 54 klf~q~vlqg~w~q~v~~~~~i~~~de~~~~-ea~fLv~kQ~fLEf~k~~~is~al~~l~~~~~~lr-~~~kk~~el~~s 131 (519)
T KOG0293|consen 54 KLFDQQVLQGQWDQQVMSLVRISFEDERNRK-EAMFLVNKQIFLEFLKTGSISHALPVLRNPVLYLR-KNKKKFHELASS 131 (519)
T ss_pred HHHHHHHHcccHHHHHHHHhhccCcchhhhH-HHHHHHHHHHHHHHHhhccHhhhhHhhhcchhhhh-hhHHHHHHHHHH
Confidence 5799999999999999999999877788888 69999999999999999999999999999999998 456666666 44
Q ss_pred hhc
Q 034603 81 LLP 83 (89)
Q Consensus 81 llt 83 (89)
++.
T Consensus 132 ll~ 134 (519)
T KOG0293|consen 132 LLV 134 (519)
T ss_pred Hhc
Confidence 443
No 2
>smart00668 CTLH C-terminal to LisH motif. Alpha-helical motif of unknown function.
Probab=99.21 E-value=1.2e-11 Score=71.73 Aligned_cols=52 Identities=37% Similarity=0.493 Sum_probs=44.3
Q ss_pred ChhHHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCH
Q 034603 1 MKHFEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHER 53 (89)
Q Consensus 1 ~~~fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~ 53 (89)
+..++++|++|+|++|++.++..........+ .+.|.|++|+|+|+++.|+.
T Consensus 5 ~~~i~~~i~~g~~~~a~~~~~~~~~~l~~~~~-~l~f~L~~q~~lell~~~~~ 56 (58)
T smart00668 5 RKRIRELILKGDWDEALEWLSSLKPPLLERNS-KLEFELRKQKFLELVRQGKL 56 (58)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHcCHHHhccCC-CchhHHHHHHHHHHHHcCCc
Confidence 35789999999999999999998655444455 59999999999999998875
No 3
>KOG2659 consensus LisH motif-containing protein [Cytoskeleton]
Probab=99.18 E-value=3.7e-11 Score=88.98 Aligned_cols=79 Identities=18% Similarity=0.345 Sum_probs=71.9
Q ss_pred hHHHHHhcCCHHHHHHHhccc--ccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 3 HFEDMVLAGKLDEAEKYLSGF--TQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 3 ~fr~~Vl~G~Wd~a~~~L~~l--~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
..|.+|..|+.++|++.++.+ +.++++. .+.|.+++|+++|+++.|.+.+||+++|.+++|++..+++.++++..
T Consensus 70 ~Ir~~I~~G~Ie~Aie~in~l~PeiLd~n~---~l~F~Lq~q~lIEliR~~~~eeal~F~q~~LA~~a~e~~~~~~elE~ 146 (228)
T KOG2659|consen 70 QIRRAIEEGQIEEAIEKVNQLNPEILDTNR---ELFFHLQQLHLIELIREGKTEEALEFAQTKLAPFAEENPKKMEELER 146 (228)
T ss_pred HHHHHHHhccHHHHHHHHHHhChHHHccch---hHHHHHHHHHHHHHHHhhhHHHHHHHHHHHccccccccHHHHHHHHH
Confidence 578999999999999999999 3666555 68999999999999999999999999999999999999999999988
Q ss_pred hhcC
Q 034603 81 LLPL 84 (89)
Q Consensus 81 lltl 84 (89)
.|++
T Consensus 147 ~l~l 150 (228)
T KOG2659|consen 147 TLAL 150 (228)
T ss_pred HHHH
Confidence 8765
No 4
>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=99.16 E-value=5.3e-11 Score=80.04 Aligned_cols=83 Identities=27% Similarity=0.372 Sum_probs=68.9
Q ss_pred hhHHHHHhcCCHHHHHHHhcccc-cccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGFT-QVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l~-~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
...+++|.+|++++|++.++... .+.+. .+ .+.|.++.|+|+|++..|++.+|+...|++++|.+....+.++++..
T Consensus 6 ~~I~~~I~~g~i~~Ai~w~~~~~~~l~~~-~~-~L~f~L~~q~fiell~~~~~~~Ai~y~r~~l~~~~~~~~~~l~~~~~ 83 (145)
T PF10607_consen 6 KKIRQAILNGDIDPAIEWLNENFPELLKR-NS-SLEFELRCQQFIELLREGDIMEAIEYARKHLSPFNDEFLEELKKLMS 83 (145)
T ss_pred HHHHHHHHcCCHHHHHHHHHHcCHHHHhc-CC-chhHHHHHHHHHHHHHHHhHHHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 56889999999999999999873 22212 23 58999999999999999999999999999998887545677888888
Q ss_pred hhcCCC
Q 034603 81 LLPLEN 86 (89)
Q Consensus 81 lltl~~ 86 (89)
+|+.++
T Consensus 84 lL~~~~ 89 (145)
T PF10607_consen 84 LLAYPD 89 (145)
T ss_pred HHHcCC
Confidence 887765
No 5
>KOG0396 consensus Uncharacterized conserved protein [Function unknown]
Probab=98.17 E-value=3.3e-06 Score=66.55 Aligned_cols=84 Identities=24% Similarity=0.271 Sum_probs=69.7
Q ss_pred hhHHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhh
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLL 81 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~l 81 (89)
...++++++|+...|...++.=+..-...-+ .+-|-++.|+|+|+++.+++.+|+.+.+++++|....+.+..+.+..+
T Consensus 157 ~~I~~sll~~~l~~~Lswc~ehk~~LkK~~S-~lEf~lRlQefIELi~~~~~~~Ai~~akk~f~~~~~~~~~~Lk~a~g~ 235 (389)
T KOG0396|consen 157 YGIRDSLLAGELEPALSWCKEHKVELKKEES-SLEFQLRLQEFIELIKVDNYDKAIAFAKKHFAPWAKSHKSDLKLAMGL 235 (389)
T ss_pred HHHHHHHHhcchHHHHHHHHHHHHHHHhccc-hhhhHHHHHHHHHHHHhccHHHHHHHHHHHHhhhhhhhHHHHHHHHHh
Confidence 3568899999999999999876322222233 489999999999999999999999999999999998888888888888
Q ss_pred hcCCC
Q 034603 82 LPLEN 86 (89)
Q Consensus 82 ltl~~ 86 (89)
|+.+-
T Consensus 236 laF~~ 240 (389)
T KOG0396|consen 236 LAFPK 240 (389)
T ss_pred hcCcc
Confidence 87654
No 6
>KOG0275 consensus Conserved WD40 repeat-containing protein [General function prediction only]
Probab=96.56 E-value=0.0057 Score=48.74 Aligned_cols=76 Identities=18% Similarity=0.210 Sum_probs=62.9
Q ss_pred hHHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhccc---ccCCCHHHHHHHH
Q 034603 3 HFEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKA---FSTYNEEVFKEAS 79 (89)
Q Consensus 3 ~fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~p---l~~~~~~~~~~l~ 79 (89)
-|-+.|-+|+||.+...++.++..+.. .--+++|--||++|-++...|-.+|| .-.| +.+..|++|-.|+
T Consensus 46 ~Fv~dI~sG~WD~VL~~vqsLKLP~kk------L~dLYEqivlEliELREL~tAR~~lR-QTdpM~~lKQ~~peRy~~lE 118 (508)
T KOG0275|consen 46 GFVNDINSGHWDTVLKTVQSLKLPDKK------LIDLYEQIVLELIELRELGTARSLLR-QTDPMIMLKQIQPERYIRLE 118 (508)
T ss_pred HHHHhcccCchHHHHHHHHhccCchhH------HHHHHHHHHHHHHHHHhhhHHHHHHh-ccCceehhhccChHHHHHHH
Confidence 477889999999999999999776622 23489999999999999999999999 4444 5667799999999
Q ss_pred hhhcCC
Q 034603 80 LLLPLE 85 (89)
Q Consensus 80 ~lltl~ 85 (89)
.||.=+
T Consensus 119 ~ll~R~ 124 (508)
T KOG0275|consen 119 NLLNRS 124 (508)
T ss_pred HHhccc
Confidence 988643
No 7
>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=96.06 E-value=0.018 Score=33.08 Aligned_cols=67 Identities=18% Similarity=0.122 Sum_probs=43.1
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
++..|+|++|++++..+-..+.++ ..+.+.+-+ . ++..|+..+|..+|. .+....++++..+.-++.
T Consensus 1 ll~~~~~~~A~~~~~~~l~~~p~~--~~~~~~la~-~---~~~~g~~~~A~~~l~-~~~~~~~~~~~~~~l~a~ 67 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQRNPDN--PEARLLLAQ-C---YLKQGQYDEAEELLE-RLLKQDPDNPEYQQLLAQ 67 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHHHTTTS--HHHHHHHHH-H---HHHTT-HHHHHHHHH-CCHGGGTTHHHHHHHHHH
T ss_pred ChhccCHHHHHHHHHHHHHHCCCC--HHHHHHHHH-H---HHHcCCHHHHHHHHH-HHHHHCcCHHHHHHHHhc
Confidence 467899999999999974333222 135554322 2 356799999999999 555556566665554443
No 8
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=94.82 E-value=0.044 Score=43.78 Aligned_cols=79 Identities=19% Similarity=0.234 Sum_probs=57.6
Q ss_pred hhHHHHHhcCCHHHHHHHhcccc-cccccccccceehhhhhhHHHHHHhcCCHH--HHHHHHHhhcccccCCC-HHHHHH
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGFT-QVHENMLSTKTYFELRRQKFLEALDKHERV--KALDILMKDIKAFSTYN-EEVFKE 77 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l~-~~~~~~~~~~~~FlI~kQKfLElL~~~~~~--~AL~~Lr~eL~pl~~~~-~~~~~~ 77 (89)
.+.-+++-.||-.-|++.+..-. .+.+.. + .+.|.+..+.|++++..|... +||.-.|+.++|+..+. ++.-+-
T Consensus 160 ~~Iv~~lke~Dl~~aLeWa~~~~~~L~~~~-s-~LE~~Lh~l~fl~l~~~g~~~~~eAl~Yar~~~~~F~~~~~~eIQkl 237 (394)
T KOG2817|consen 160 NQIVEALKERDLEPALEWAESNRQKLKEKS-S-SLEFKLHSLHFLSLIRGGKSDQREALRYARTHFAPFVADHLREIQKL 237 (394)
T ss_pred HHHHHHHHhccchhHHHHHHHhhhhhcccc-c-cHHHHHHHHHHHHHHhcCCcCcHHHHHHHHHhcCccccchHHHHHHH
Confidence 45567788888888888887642 333222 2 599999999999999999888 99999999999997544 333333
Q ss_pred HHhhh
Q 034603 78 ASLLL 82 (89)
Q Consensus 78 l~~ll 82 (89)
++.|+
T Consensus 238 m~sl~ 242 (394)
T KOG2817|consen 238 MGSLL 242 (394)
T ss_pred HHHHH
Confidence 34443
No 9
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.10 E-value=0.43 Score=36.75 Aligned_cols=65 Identities=18% Similarity=0.310 Sum_probs=49.3
Q ss_pred cCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhh
Q 034603 10 AGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLL 81 (89)
Q Consensus 10 ~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~l 81 (89)
.|+|++|+++...+ +.+++ --+.|+|-|--=+.-.|+..+|++-|-+-+..|-.+ ++..++||.+
T Consensus 99 ~~~~~~A~e~y~~l--L~ddp----t~~v~~KRKlAilka~GK~l~aIk~ln~YL~~F~~D-~EAW~eLaei 163 (289)
T KOG3060|consen 99 TGNYKEAIEYYESL--LEDDP----TDTVIRKRKLAILKAQGKNLEAIKELNEYLDKFMND-QEAWHELAEI 163 (289)
T ss_pred hhchhhHHHHHHHH--hccCc----chhHHHHHHHHHHHHcCCcHHHHHHHHHHHHHhcCc-HHHHHHHHHH
Confidence 69999999999997 33333 235678888877778888889998888888888644 6667777654
No 10
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=90.99 E-value=0.3 Score=27.74 Aligned_cols=54 Identities=15% Similarity=0.169 Sum_probs=35.2
Q ss_pred HHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhc
Q 034603 5 EDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDI 64 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL 64 (89)
+..+-.|+|++|++.+..+...+.++. .+.|.+=.- +...|+..+|+..+++-+
T Consensus 5 ~~~~~~g~~~~A~~~~~~~l~~~P~~~--~a~~~lg~~----~~~~g~~~~A~~~~~~a~ 58 (65)
T PF13432_consen 5 RALYQQGDYDEAIAAFEQALKQDPDNP--EAWYLLGRI----LYQQGRYDEALAYYERAL 58 (65)
T ss_dssp HHHHHCTHHHHHHHHHHHHHCCSTTHH--HHHHHHHHH----HHHTT-HHHHHHHHHHHH
T ss_pred HHHHHcCCHHHHHHHHHHHHHHCCCCH--HHHHHHHHH----HHHcCCHHHHHHHHHHHH
Confidence 456789999999999999854442221 244433222 236799999999998543
No 11
>smart00757 CRA CT11-RanBPM. protein-protein interaction domain present in crown eukaryotes (plants, animals, fungi)
Probab=89.90 E-value=0.43 Score=29.55 Aligned_cols=36 Identities=17% Similarity=0.197 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHhhcccccCCCHH---HHHHHHhhhcCCC
Q 034603 51 HERVKALDILMKDIKAFSTYNEE---VFKEASLLLPLEN 86 (89)
Q Consensus 51 ~~~~~AL~~Lr~eL~pl~~~~~~---~~~~l~~lltl~~ 86 (89)
+++.+|++..|++++|+...++. .++++..+|..++
T Consensus 1 ~~~~eAi~yar~~l~~~~~~~~~~~~el~~~m~llaf~~ 39 (99)
T smart00757 1 GKIEEALAYARELLAPFAKEHEKFLKELEKTMALLAYPD 39 (99)
T ss_pred CcHHHHHHHHHHHHhhhcccCHHHHHHHHHHHHHHhcCC
Confidence 36789999999999999988754 4444455555543
No 12
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=88.40 E-value=0.98 Score=32.67 Aligned_cols=72 Identities=22% Similarity=0.178 Sum_probs=45.0
Q ss_pred HHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 6 DMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
-....|+|++++..+..+........+ ..|+...-.+.+ ..|+..+|+.++++-+.- .|.+++....+..++
T Consensus 119 ~~~~~~~~~~~~~~l~~~~~~~~~~~~--~~~~~~~a~~~~--~~G~~~~A~~~~~~al~~-~P~~~~~~~~l~~~l 190 (280)
T PF13429_consen 119 LYYRLGDYDEAEELLEKLEELPAAPDS--ARFWLALAEIYE--QLGDPDKALRDYRKALEL-DPDDPDARNALAWLL 190 (280)
T ss_dssp -HHHTT-HHHHHHHHHHHHH-T---T---HHHHHHHHHHHH--HCCHHHHHHHHHHHHHHH--TT-HHHHHHHHHHH
T ss_pred HHHHHhHHHHHHHHHHHHHhccCCCCC--HHHHHHHHHHHH--HcCCHHHHHHHHHHHHHc-CCCCHHHHHHHHHHH
Confidence 456779999999999998643322222 445444444433 579999999999976654 557788777776554
No 13
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=86.95 E-value=0.71 Score=27.69 Aligned_cols=47 Identities=19% Similarity=0.244 Sum_probs=23.1
Q ss_pred HhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHH
Q 034603 8 VLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILM 61 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr 61 (89)
...|+|++|+.++... ..++.. . .+.+++ =+.|++ .|+..+|+.+|.
T Consensus 36 ~~~~~y~~A~~~~~~~-~~~~~~-~-~~~~l~-a~~~~~---l~~y~eAi~~l~ 82 (84)
T PF12895_consen 36 FQQGKYEEAIELLQKL-KLDPSN-P-DIHYLL-ARCLLK---LGKYEEAIKALE 82 (84)
T ss_dssp HHTTHHHHHHHHHHCH-THHHCH-H-HHHHHH-HHHHHH---TT-HHHHHHHHH
T ss_pred HHCCCHHHHHHHHHHh-CCCCCC-H-HHHHHH-HHHHHH---hCCHHHHHHHHh
Confidence 4456666666666662 222211 1 244433 444443 366667766665
No 14
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=84.90 E-value=5.3 Score=22.72 Aligned_cols=62 Identities=15% Similarity=0.078 Sum_probs=39.3
Q ss_pred HHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHH
Q 034603 6 DMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEV 74 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~ 74 (89)
-++-.|+|++|.+.+...-..+..+. ..+..+- .=+...|+..+|+.++.+-++- ++++++.
T Consensus 4 ~~~~~~~~~~A~~~~~~~l~~~p~~~----~~~~~~a--~~~~~~g~~~~A~~~l~~~l~~-~p~~~~~ 65 (73)
T PF13371_consen 4 IYLQQEDYEEALEVLERALELDPDDP----ELWLQRA--RCLFQLGRYEEALEDLERALEL-SPDDPDA 65 (73)
T ss_pred HHHhCCCHHHHHHHHHHHHHhCcccc----hhhHHHH--HHHHHhccHHHHHHHHHHHHHH-CCCcHHH
Confidence 35678999999999998855543332 2222221 2234558899999999966643 4455543
No 15
>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]
Probab=83.62 E-value=3.7 Score=33.38 Aligned_cols=73 Identities=19% Similarity=0.180 Sum_probs=56.6
Q ss_pred hHHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 3 HFEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 3 ~fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
++.+++-+||...|++++..+--+ ..+ .+.+-+.+-|++ +..|+...|++=|| ..+.|+++|++.+-+++.|+
T Consensus 161 ql~s~~~~GD~~~ai~~i~~llEi---~~W-da~l~~~Rakc~--i~~~e~k~AI~Dlk-~askLs~DnTe~~ykis~L~ 233 (504)
T KOG0624|consen 161 QLKSASGSGDCQNAIEMITHLLEI---QPW-DASLRQARAKCY--IAEGEPKKAIHDLK-QASKLSQDNTEGHYKISQLL 233 (504)
T ss_pred HHHHHhcCCchhhHHHHHHHHHhc---Ccc-hhHHHHHHHHHH--HhcCcHHHHHHHHH-HHHhccccchHHHHHHHHHH
Confidence 456778899999999999886322 244 367777777764 45789999999999 77888999988888887765
No 16
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=78.36 E-value=4 Score=21.77 Aligned_cols=33 Identities=9% Similarity=0.070 Sum_probs=26.0
Q ss_pred HHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 47 ALDKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 47 lL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
+.+.|+..+|..++++-++- .++|++....|..
T Consensus 11 ~~~~G~~~~A~~~~~~~l~~-~P~~~~a~~~La~ 43 (44)
T PF13428_consen 11 YRRLGQPDEAERLLRRALAL-DPDDPEAWRALAQ 43 (44)
T ss_pred HHHcCCHHHHHHHHHHHHHH-CcCCHHHHHHhhh
Confidence 45779999999999976664 6688888777664
No 17
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=78.05 E-value=11 Score=22.58 Aligned_cols=55 Identities=11% Similarity=0.132 Sum_probs=30.1
Q ss_pred HHHhcCCHHHHHHHhcccccccc-cccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhc
Q 034603 6 DMVLAGKLDEAEKYLSGFTQVHE-NMLSTKTYFELRRQKFLEALDKHERVKALDILMKDI 64 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~l~~~~~-~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL 64 (89)
.....|+|++|++++..+..... +.....+.|.+-.- +...|+..+|+..+++=+
T Consensus 11 ~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~~~~l~~~----~~~~~~~~~A~~~~~~~~ 66 (119)
T TIGR02795 11 LVLKAGDYADAIQAFQAFLKKYPKSTYAPNAHYWLGEA----YYAQGKYADAAKAFLAVV 66 (119)
T ss_pred HHHHcCCHHHHHHHHHHHHHHCCCccccHHHHHHHHHH----HHhhccHHHHHHHHHHHH
Confidence 34567888888888877743322 11111233332221 445577777877777433
No 18
>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=77.53 E-value=3.7 Score=23.06 Aligned_cols=35 Identities=17% Similarity=0.128 Sum_probs=26.3
Q ss_pred HHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 47 ALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 47 lL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
++..|+..+|+..+.+-+. ..+.+++..-.++.++
T Consensus 1 ll~~~~~~~A~~~~~~~l~-~~p~~~~~~~~la~~~ 35 (68)
T PF14559_consen 1 LLKQGDYDEAIELLEKALQ-RNPDNPEARLLLAQCY 35 (68)
T ss_dssp HHHTTHHHHHHHHHHHHHH-HTTTSHHHHHHHHHHH
T ss_pred ChhccCHHHHHHHHHHHHH-HCCCCHHHHHHHHHHH
Confidence 5778999999999996554 4557787777776554
No 19
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=77.49 E-value=7.9 Score=29.79 Aligned_cols=69 Identities=12% Similarity=0.102 Sum_probs=37.8
Q ss_pred HHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 5 EDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
+.+..+|+|++|+..+...-..+.++. .+. ..+=+ =++..|+..+|+..+++-+. +.+.++..|..++.
T Consensus 10 ~~a~~~~~~~~Ai~~~~~Al~~~P~~~--~a~-~~~a~---~~~~~g~~~eAl~~~~~Al~-l~P~~~~a~~~lg~ 78 (356)
T PLN03088 10 KEAFVDDDFALAVDLYTQAIDLDPNNA--ELY-ADRAQ---ANIKLGNFTEAVADANKAIE-LDPSLAKAYLRKGT 78 (356)
T ss_pred HHHHHcCCHHHHHHHHHHHHHhCCCCH--HHH-HHHHH---HHHHcCCHHHHHHHHHHHHH-hCcCCHHHHHHHHH
Confidence 456778888888888776533332221 111 11112 23345777777777774433 34455666655543
No 20
>PHA00425 DNA packaging protein, small subunit
Probab=75.43 E-value=7.6 Score=25.03 Aligned_cols=41 Identities=32% Similarity=0.434 Sum_probs=30.5
Q ss_pred HHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhhcCCCC
Q 034603 43 KFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLLPLENF 87 (89)
Q Consensus 43 KfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~lltl~~~ 87 (89)
||||.|+ ++.|-..|. +|+-=...+|.+|+-+..||.=-.|
T Consensus 8 k~LemlD---TE~a~~mL~-DL~ddekRtPQLYnAIgKlL~RHkF 48 (88)
T PHA00425 8 KFLEMLD---TEMAQRMLA-DLKDDEKRTPQLYNAIGKLLDRHKF 48 (88)
T ss_pred HHHHHHh---HHHHHHHHH-HhcCccccChHHHHHHHHHHHHhcc
Confidence 7888886 666766666 6766677789999999998854333
No 21
>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=74.64 E-value=8.1 Score=27.09 Aligned_cols=84 Identities=14% Similarity=0.220 Sum_probs=54.4
Q ss_pred hhHHHHHhcCCHHHHHHHhccccccccc-ccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccC---------CC
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGFTQVHEN-MLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFST---------YN 71 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l~~~~~~-~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~---------~~ 71 (89)
.-+|-+|.-|||..+..++.......+. ... ..+--+.=-.-|-.|..++..+|-..+-.-++-+.. .+
T Consensus 78 ~~irv~i~~~d~~~v~~~i~ka~~~~~~~~d~-~~~nrlk~~~gL~~l~~r~f~~AA~~fl~~~~t~~~~~~~el~s~~d 156 (177)
T PF10602_consen 78 NVIRVAIFFGDWSHVEKYIEKAESLIEKGGDW-ERRNRLKVYEGLANLAQRDFKEAAELFLDSLSTFTSLQYTELISYND 156 (177)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHHhccchH-HHHHHHHHHHHHHHHHhchHHHHHHHHHccCcCCCCCchhhhcCHHH
Confidence 4568889999999999999988543322 212 122223334456678889999988887755544432 11
Q ss_pred HHHHHHHHhhhcCCC
Q 034603 72 EEVFKEASLLLPLEN 86 (89)
Q Consensus 72 ~~~~~~l~~lltl~~ 86 (89)
-..|=-||.|.|++.
T Consensus 157 ~a~Y~~l~aLat~~R 171 (177)
T PF10602_consen 157 FAIYGGLCALATLDR 171 (177)
T ss_pred HHHHHHHHHHHhCCH
Confidence 256677788888763
No 22
>PF14276 DUF4363: Domain of unknown function (DUF4363)
Probab=73.37 E-value=6.2 Score=25.70 Aligned_cols=56 Identities=9% Similarity=0.153 Sum_probs=34.8
Q ss_pred hhHHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHH----------HHHHhcCCHHHHHH
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKF----------LEALDKHERVKALD 58 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKf----------LElL~~~~~~~AL~ 58 (89)
...+++|-+++|++|.+....+...=+.... .+.|.+-.|.+ -.+++.++..+|+.
T Consensus 33 ~~i~~~i~~~dW~~A~~~~~~l~~~W~k~~~-~~~~~~~h~eid~i~~sl~rl~~~i~~~dk~~~l~ 98 (121)
T PF14276_consen 33 EQIEEAIENEDWEKAYKETEELEKEWDKNKK-RWSILIEHQEIDNIDISLARLKGYIEAKDKSESLA 98 (121)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHHHhhch-heeeeecHHHHHHHHHHHHHHHHHHHCCCHHHHHH
Confidence 3467899999999999999988543222222 25555554433 23455566555544
No 23
>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.
Probab=72.86 E-value=4.5 Score=32.57 Aligned_cols=68 Identities=22% Similarity=0.301 Sum_probs=37.9
Q ss_pred hHHHHHhcCCHHHH------HHHhcccccccccccccceehhhhhhHHHH---------------HHhcCCHHHHHHHHH
Q 034603 3 HFEDMVLAGKLDEA------EKYLSGFTQVHENMLSTKTYFELRRQKFLE---------------ALDKHERVKALDILM 61 (89)
Q Consensus 3 ~fr~~Vl~G~Wd~a------~~~L~~l~~~~~~~~~~~~~FlI~kQKfLE---------------lL~~~~~~~AL~~Lr 61 (89)
.|+.+|+.||+++| .++++.+ +.+....-++|+- +|.|-| +|+-|+...|+++++
T Consensus 267 ~fk~av~~~d~~~v~~~i~~~~ll~~i---~~~~~~~i~~fL~-~~G~~e~AL~~~~D~~~rFeLAl~lg~L~~A~~~a~ 342 (443)
T PF04053_consen 267 EFKTAVLRGDFEEVLRMIAASNLLPNI---PKDQGQSIARFLE-KKGYPELALQFVTDPDHRFELALQLGNLDIALEIAK 342 (443)
T ss_dssp HHHHHHHTT-HHH-----HHHHTGGG-----HHHHHHHHHHHH-HTT-HHHHHHHSS-HHHHHHHHHHCT-HHHHHHHCC
T ss_pred HHHHHHHcCChhhhhhhhhhhhhcccC---ChhHHHHHHHHHH-HCCCHHHHHhhcCChHHHhHHHHhcCCHHHHHHHHH
Confidence 58999999999995 4444433 2222221255543 344444 366688888888776
Q ss_pred hhcccccCCCHHHHHHHHh
Q 034603 62 KDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 62 ~eL~pl~~~~~~~~~~l~~ 80 (89)
++ .++..++.|+.
T Consensus 343 -~~-----~~~~~W~~Lg~ 355 (443)
T PF04053_consen 343 -EL-----DDPEKWKQLGD 355 (443)
T ss_dssp -CC-----STHHHHHHHHH
T ss_pred -hc-----CcHHHHHHHHH
Confidence 22 35666777654
No 24
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=72.51 E-value=13 Score=27.53 Aligned_cols=55 Identities=15% Similarity=0.091 Sum_probs=25.5
Q ss_pred HhcCCHHHHHHHhccccccccccccc-ceehhhhhhHHHHHHhcCCHHHHHHHHHhhc
Q 034603 8 VLAGKLDEAEKYLSGFTQVHENMLST-KTYFELRRQKFLEALDKHERVKALDILMKDI 64 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l~~~~~~~~~~-~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL 64 (89)
...|+|++|++.+..+...+..+... ...| +-.-=.-+++.|+..+|+..+++-+
T Consensus 152 ~~~g~~~~A~~~~~~~~~~~~~~~~~~~~~~--~~~la~~~~~~~~~~~A~~~~~~al 207 (389)
T PRK11788 152 QQEKDWQKAIDVAERLEKLGGDSLRVEIAHF--YCELAQQALARGDLDAARALLKKAL 207 (389)
T ss_pred HHhchHHHHHHHHHHHHHhcCCcchHHHHHH--HHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34677777777766653222111110 0111 0011112345677777777777544
No 25
>PRK15359 type III secretion system chaperone protein SscB; Provisional
Probab=71.83 E-value=17 Score=24.11 Aligned_cols=67 Identities=9% Similarity=-0.031 Sum_probs=32.3
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
....|++++|..++.....++..+. .++.. .=.=+...|+..+|+.+.++-++ +.+.+++.+..++.
T Consensus 34 ~~~~g~~~~A~~~~~~al~~~P~~~----~a~~~--lg~~~~~~g~~~~A~~~y~~Al~-l~p~~~~a~~~lg~ 100 (144)
T PRK15359 34 SWQEGDYSRAVIDFSWLVMAQPWSW----RAHIA--LAGTWMMLKEYTTAINFYGHALM-LDASHPEPVYQTGV 100 (144)
T ss_pred HHHcCCHHHHHHHHHHHHHcCCCcH----HHHHH--HHHHHHHHhhHHHHHHHHHHHHh-cCCCCcHHHHHHHH
Confidence 3456777777777766533332221 11111 11112334566666666665554 24444555555544
No 26
>KOG1538 consensus Uncharacterized conserved protein WDR10, contains WD40 repeats [General function prediction only]
Probab=70.93 E-value=4.2 Score=35.53 Aligned_cols=72 Identities=17% Similarity=0.206 Sum_probs=54.2
Q ss_pred HHhcCCHHHHHHHhccccc-ccccccccceehhhhhhHHHHH----HhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhh
Q 034603 7 MVLAGKLDEAEKYLSGFTQ-VHENMLSTKTYFELRRQKFLEA----LDKHERVKALDILMKDIKAFSTYNEEVFKEASLL 81 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~-~~~~~~~~~~~FlI~kQKfLEl----L~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~l 81 (89)
+|-.|+|++|-++-..... +++--.- -++|+--.-.|.|+ ...|+..+|.++|. +|+-=. .++++|.+.++.
T Consensus 783 Hve~~~W~eAFalAe~hPe~~~dVy~p-yaqwLAE~DrFeEAqkAfhkAGr~~EA~~vLe-QLtnna-v~E~Rf~DA~y~ 859 (1081)
T KOG1538|consen 783 HVETQRWDEAFALAEKHPEFKDDVYMP-YAQWLAENDRFEEAQKAFHKAGRQREAVQVLE-QLTNNA-VAESRFNDAAYY 859 (1081)
T ss_pred eeecccchHhHhhhhhCccccccccch-HHHHhhhhhhHHHHHHHHHHhcchHHHHHHHH-Hhhhhh-hhhhhhccchhH
Confidence 5778999999999888743 3433333 47777777788775 46699999999998 777643 568889888766
No 27
>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=70.12 E-value=15 Score=23.06 Aligned_cols=17 Identities=29% Similarity=0.395 Sum_probs=10.2
Q ss_pred HHhcCCHHHHHHHhccc
Q 034603 7 MVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l 23 (89)
.+..|+.++|...+..+
T Consensus 27 ~~~~~~~~~A~~~~~~~ 43 (135)
T TIGR02552 27 LYQQGRYDEALKLFQLL 43 (135)
T ss_pred HHHcccHHHHHHHHHHH
Confidence 34456666666666555
No 28
>PRK12370 invasion protein regulator; Provisional
Probab=69.51 E-value=20 Score=29.05 Aligned_cols=70 Identities=13% Similarity=0.099 Sum_probs=37.9
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
....|++++|+..+...-.++..+.. ..+. ...-+...|+..+|+..+++-+....++++..+..++.++
T Consensus 382 l~~~G~~~eAi~~~~~Al~l~P~~~~--~~~~----~~~~~~~~g~~eeA~~~~~~~l~~~~p~~~~~~~~la~~l 451 (553)
T PRK12370 382 LFMAGQLEEALQTINECLKLDPTRAA--AGIT----KLWITYYHTGIDDAIRLGDELRSQHLQDNPILLSMQVMFL 451 (553)
T ss_pred HHHCCCHHHHHHHHHHHHhcCCCChh--hHHH----HHHHHHhccCHHHHHHHHHHHHHhccccCHHHHHHHHHHH
Confidence 34568888888877776444333211 1111 1112444577888888887665433344565555554443
No 29
>PF11123 DNA_Packaging_2: DNA packaging protein ; InterPro: IPR024345 This entry represents Gp18 (gene 18 product), also known as DNA maturase A, from T7-like bacteriophages. In Bacteriophage T3, this protein is required for DNA packaging and functions in a complex with Gp19 [].
Probab=67.68 E-value=14 Score=23.55 Aligned_cols=42 Identities=26% Similarity=0.406 Sum_probs=30.5
Q ss_pred hHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhhcCCCC
Q 034603 42 QKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLLPLENF 87 (89)
Q Consensus 42 QKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~lltl~~~ 87 (89)
+||||+|+ ++.|-..|. +|.-=...+|.+|+-+..+|.=-+|
T Consensus 5 ~klLemlD---tEmA~~mL~-DLr~dekRsPQLYnAI~k~L~RHkF 46 (82)
T PF11123_consen 5 EKLLEMLD---TEMAQQMLA-DLRDDEKRSPQLYNAIGKLLDRHKF 46 (82)
T ss_pred HHHHHHHH---HHHHHHHHH-HhcchhhcChHHHHHHHHHHHHccc
Confidence 58899987 566655555 6665566779999999998865444
No 30
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=67.40 E-value=26 Score=27.06 Aligned_cols=33 Identities=18% Similarity=0.155 Sum_probs=19.4
Q ss_pred HHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 47 ALDKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 47 lL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
++..|+..+|+..++ ++....+.|+..+.-+..
T Consensus 163 ~l~~g~~~~Al~~l~-~~~~~~P~~~~al~ll~~ 195 (398)
T PRK10747 163 QLARNENHAARHGVD-KLLEVAPRHPEVLRLAEQ 195 (398)
T ss_pred HHHCCCHHHHHHHHH-HHHhcCCCCHHHHHHHHH
Confidence 345577777777776 444445566655555543
No 31
>PF12870 Lumazine_bd: Lumazine-binding domain; InterPro: IPR024267 This entry represents a lumazine-binding domain found in a family of putative lipoproteins from bacteria. Lumazine is a fluorescent accessory protein having 6,7-dimethyl-8-(1'-D-ribityl) lumazine (DMRL) as its authentic chromophore; it modulates the emission of bacterial luciferase to shorter wavelengths with increasing luminous strength.; PDB: 3K7C_C.
Probab=66.17 E-value=5 Score=24.42 Aligned_cols=22 Identities=36% Similarity=0.451 Sum_probs=15.9
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+.|-.++.+|||++|.+++.+=
T Consensus 14 ~~f~~al~~gd~~~a~~~~~~~ 35 (111)
T PF12870_consen 14 KNFFDALKNGDYEKAYAYLSPE 35 (111)
T ss_dssp HHHHHHHCTT-HHHHHHTB--T
T ss_pred HHHHHHHHcCCHHHHHHhhCcc
Confidence 4577889999999999998853
No 32
>KOG3452 consensus 60S ribosomal protein L36 [Translation, ribosomal structure and biogenesis]
Probab=65.99 E-value=9.2 Score=25.38 Aligned_cols=46 Identities=22% Similarity=0.273 Sum_probs=35.1
Q ss_pred hhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhhc
Q 034603 37 FELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLLP 83 (89)
Q Consensus 37 FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~llt 83 (89)
|-=++-+-+|+|+.++...|+.+|++.|..+-. ...--++|+..|+
T Consensus 50 ~aPyErr~meLlkvskdkrA~K~lKkRlGth~R-Ak~KrEELsnvl~ 95 (102)
T KOG3452|consen 50 FAPYERRAMELLKVSKDKRALKLLKKRLGTHKR-AKRKREELSNVLA 95 (102)
T ss_pred CChHHHHHHHHHHHcccHHHHHHHHHHhhHHHH-HHHHHHHHHHHHH
Confidence 555788999999999999999999999866542 2344566766654
No 33
>PF14691 Fer4_20: Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster; PDB: 2VDC_G 1H7X_C 1H7W_A 1GT8_A 1GTE_B 1GTH_B.
Probab=65.73 E-value=8 Score=25.52 Aligned_cols=29 Identities=7% Similarity=0.261 Sum_probs=20.8
Q ss_pred hhhhhHHHHHHhcCCHHHHHHHHHhhcccc
Q 034603 38 ELRRQKFLEALDKHERVKALDILMKDIKAF 67 (89)
Q Consensus 38 lI~kQKfLElL~~~~~~~AL~~Lr~eL~pl 67 (89)
.+-=+.|+.++..|+..+|++++++ =.||
T Consensus 39 ~~dip~~i~~i~~g~~~~A~~~i~~-~np~ 67 (111)
T PF14691_consen 39 HIDIPEYIRLIREGNFKEAYELIRE-DNPF 67 (111)
T ss_dssp ---HHHHHHHHHCT-HHHHHHHHHH-H-TT
T ss_pred CCcHHHHHHHHHCCCHHHHHHHHHH-hCCC
Confidence 3445789999999999999999994 3444
No 34
>PRK14574 hmsH outer membrane protein; Provisional
Probab=65.29 E-value=17 Score=31.61 Aligned_cols=58 Identities=7% Similarity=-0.083 Sum_probs=38.6
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCC
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYN 71 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~ 71 (89)
....|+|++|++++..+-..+.++. .+.+ .-.+.+++.++..+|+..+. .+.|..+.+
T Consensus 112 y~~~gdyd~Aiely~kaL~~dP~n~--~~l~----gLa~~y~~~~q~~eAl~~l~-~l~~~dp~~ 169 (822)
T PRK14574 112 YRNEKRWDQALALWQSSLKKDPTNP--DLIS----GMIMTQADAGRGGVVLKQAT-ELAERDPTV 169 (822)
T ss_pred HHHcCCHHHHHHHHHHHHhhCCCCH--HHHH----HHHHHHhhcCCHHHHHHHHH-HhcccCcch
Confidence 3456999999999998854443331 2443 22666777788888888888 566655443
No 35
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=65.27 E-value=34 Score=22.37 Aligned_cols=53 Identities=21% Similarity=0.164 Sum_probs=29.6
Q ss_pred HHHhcCCHHHHHHHhccccccc-ccccccceehhhhhhHHHHHHhcCCHHHHHHHHHh
Q 034603 6 DMVLAGKLDEAEKYLSGFTQVH-ENMLSTKTYFELRRQKFLEALDKHERVKALDILMK 62 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~l~~~~-~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~ 62 (89)
..+-.|+.++|.+.+..+..-. +.....-+++-+- .+ ++..|+..+|+..|..
T Consensus 57 ~~~~~g~~~~A~~~l~~~~~~~~d~~l~~~a~l~LA---~~-~~~~~~~d~Al~~L~~ 110 (145)
T PF09976_consen 57 AAYEQGDYDEAKAALEKALANAPDPELKPLARLRLA---RI-LLQQGQYDEALATLQQ 110 (145)
T ss_pred HHHHCCCHHHHHHHHHHHHhhCCCHHHHHHHHHHHH---HH-HHHcCCHHHHHHHHHh
Confidence 4566788888888888763221 1111101222221 11 2466888888888864
No 36
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=64.75 E-value=23 Score=27.36 Aligned_cols=66 Identities=14% Similarity=0.006 Sum_probs=38.7
Q ss_pred HHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHH
Q 034603 5 EDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKE 77 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~ 77 (89)
+-+...|++++|.+++..+...+.++. .+..++. + -++..|+..+|+.+|. .+.-....+++...+
T Consensus 161 ~l~l~~g~~~~Al~~l~~~~~~~P~~~--~al~ll~-~---~~~~~gdw~~a~~~l~-~l~k~~~~~~~~~~~ 226 (398)
T PRK10747 161 RIQLARNENHAARHGVDKLLEVAPRHP--EVLRLAE-Q---AYIRTGAWSSLLDILP-SMAKAHVGDEEHRAM 226 (398)
T ss_pred HHHHHCCCHHHHHHHHHHHHhcCCCCH--HHHHHHH-H---HHHHHHhHHHHHHHHH-HHHHcCCCCHHHHHH
Confidence 456778999999999998754443322 1222222 2 2245589999997776 333333334554553
No 37
>KOG3616 consensus Selective LIM binding factor [Transcription]
Probab=64.43 E-value=24 Score=31.78 Aligned_cols=73 Identities=14% Similarity=0.139 Sum_probs=49.1
Q ss_pred HHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHH-----HHHhcCCHHHHHHHHHhhcccccCCCHHHHHHH
Q 034603 4 FEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFL-----EALDKHERVKALDILMKDIKAFSTYNEEVFKEA 78 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfL-----ElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l 78 (89)
+--.|-+|+||+|+.+-..- + |--.=.||. -++..|+...||.+|.+.=+|-++.|=..|+.+
T Consensus 1299 idl~ien~qwdk~idtak~q------n------ykpil~kyva~yaa~li~~~d~aq~lal~~q~ga~anpanfniyk~i 1366 (1636)
T KOG3616|consen 1299 IDLMIENDQWDKAIDTAKKQ------N------YKPILDKYVALYAAHLIHEGDLAQALALLEQHGAPANPANFNIYKLI 1366 (1636)
T ss_pred HHHHHhcccHHHHHHHHHhc------c------cHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHhCCCCCcccccHHHHH
Confidence 34578899999999876432 1 111112333 356779999999999999999888777777765
Q ss_pred -HhhhcCCCCC
Q 034603 79 -SLLLPLENFS 88 (89)
Q Consensus 79 -~~lltl~~~r 88 (89)
+-.++-|.-|
T Consensus 1367 ~ed~lakpgt~ 1377 (1636)
T KOG3616|consen 1367 FEDMLAKPGTN 1377 (1636)
T ss_pred HHHHhcCCCcc
Confidence 4455555333
No 38
>PF13512 TPR_18: Tetratricopeptide repeat
Probab=64.11 E-value=15 Score=25.57 Aligned_cols=59 Identities=14% Similarity=0.160 Sum_probs=39.0
Q ss_pred HHHHhcCCHHHHHHHhcccc-cccccccccceehhhhhhHHHHHH----hcCCHHHHHHHHHhhcccccCCCH
Q 034603 5 EDMVLAGKLDEAEKYLSGFT-QVHENMLSTKTYFELRRQKFLEAL----DKHERVKALDILMKDIKAFSTYNE 72 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l~-~~~~~~~~~~~~FlI~kQKfLElL----~~~~~~~AL~~Lr~eL~pl~~~~~ 72 (89)
.+++-+|+|++|++.+..|. ..+-+..+ +|--|++. ..|+..+|+..+.+ +--|.+.+|
T Consensus 18 ~~~l~~~~Y~~A~~~le~L~~ryP~g~ya--------~qAqL~l~yayy~~~~y~~A~a~~~r-FirLhP~hp 81 (142)
T PF13512_consen 18 QEALQKGNYEEAIKQLEALDTRYPFGEYA--------EQAQLDLAYAYYKQGDYEEAIAAYDR-FIRLHPTHP 81 (142)
T ss_pred HHHHHhCCHHHHHHHHHHHHhcCCCCccc--------HHHHHHHHHHHHHccCHHHHHHHHHH-HHHhCCCCC
Confidence 45778999999999999984 33434444 35555554 35889999988874 333333443
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=63.70 E-value=7.3 Score=18.51 Aligned_cols=21 Identities=19% Similarity=0.425 Sum_probs=16.9
Q ss_pred HHHHHhcCCHHHHHHHhcccc
Q 034603 4 FEDMVLAGKLDEAEKYLSGFT 24 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l~ 24 (89)
++-.+..|+|++|.+++..+.
T Consensus 7 i~~~~~~~~~~~a~~~~~~M~ 27 (35)
T TIGR00756 7 IDGLCKAGRVEEALELFKEML 27 (35)
T ss_pred HHHHHHCCCHHHHHHHHHHHH
Confidence 455678899999999998773
No 40
>PF13281 DUF4071: Domain of unknown function (DUF4071)
Probab=63.68 E-value=30 Score=27.61 Aligned_cols=63 Identities=14% Similarity=0.155 Sum_probs=44.3
Q ss_pred CCHHHHHHHhcccccccccccccceehhhhhhHHHHHHh---cCCHHHHHHHHHhhcccccCCCHHHH
Q 034603 11 GKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALD---KHERVKALDILMKDIKAFSTYNEEVF 75 (89)
Q Consensus 11 G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~---~~~~~~AL~~Lr~eL~pl~~~~~~~~ 75 (89)
-+||.-++++..+..++..+.. -.=.|.+|.=+=+-+ .|+..+|++++..-+.+-...+++.|
T Consensus 155 qdydamI~Lve~l~~~p~~~~~--~~~~i~~~yafALnRrn~~gdre~Al~il~~~l~~~~~~~~d~~ 220 (374)
T PF13281_consen 155 QDYDAMIKLVETLEALPTCDVA--NQHNIKFQYAFALNRRNKPGDREKALQILLPVLESDENPDPDTL 220 (374)
T ss_pred hhHHHHHHHHHHhhccCccchh--cchHHHHHHHHHHhhcccCCCHHHHHHHHHHHHhccCCCChHHH
Confidence 4799999999998766544322 233455555555556 59999999999977888776777644
No 41
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=63.49 E-value=7.3 Score=18.83 Aligned_cols=21 Identities=19% Similarity=0.249 Sum_probs=17.2
Q ss_pred HHHHHhcCCHHHHHHHhcccc
Q 034603 4 FEDMVLAGKLDEAEKYLSGFT 24 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l~ 24 (89)
++.+.-.|+|+.|..+++.+.
T Consensus 8 l~a~~~~g~~~~a~~~~~~M~ 28 (34)
T PF13812_consen 8 LRACAKAGDPDAALQLFDEMK 28 (34)
T ss_pred HHHHHHCCCHHHHHHHHHHHH
Confidence 466778999999999998763
No 42
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=61.72 E-value=27 Score=25.55 Aligned_cols=56 Identities=16% Similarity=0.146 Sum_probs=34.1
Q ss_pred HhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcc
Q 034603 8 VLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIK 65 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~ 65 (89)
...|+|++|+.++...-.....+ . ......+-..=.=++..|+..+|+.++++-+.
T Consensus 159 ~~~g~~~eA~~~l~~~l~~~~~~-~-~~~~~~~~~la~~~~~~G~~~~A~~~~~~~~~ 214 (355)
T cd05804 159 EMQGRFKEGIAFMESWRDTWDCS-S-MLRGHNWWHLALFYLERGDYEAALAIYDTHIA 214 (355)
T ss_pred HHcCCHHHHHHHHHhhhhccCCC-c-chhHHHHHHHHHHHHHCCCHHHHHHHHHHHhc
Confidence 35699999999988763332211 1 12222222222236788999999999997553
No 43
>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=61.06 E-value=8.1 Score=26.87 Aligned_cols=22 Identities=14% Similarity=0.268 Sum_probs=19.5
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+..|++|.+|++++|.++|..-
T Consensus 149 T~IR~~i~~G~i~~an~lLg~~ 170 (180)
T cd02064 149 TRIREALAEGDVELANELLGRP 170 (180)
T ss_pred HHHHHHHHhCCHHHHHHHcCCC
Confidence 4689999999999999999754
No 44
>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=60.80 E-value=7.6 Score=18.29 Aligned_cols=20 Identities=15% Similarity=0.297 Sum_probs=16.0
Q ss_pred HHHHHhcCCHHHHHHHhccc
Q 034603 4 FEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l 23 (89)
++-....|+|++|.+.+..+
T Consensus 7 i~~~~~~~~~~~a~~~~~~M 26 (31)
T PF01535_consen 7 ISGYCKMGQFEEALEVFDEM 26 (31)
T ss_pred HHHHHccchHHHHHHHHHHH
Confidence 45567789999999988876
No 45
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=60.29 E-value=23 Score=26.43 Aligned_cols=66 Identities=12% Similarity=0.173 Sum_probs=44.0
Q ss_pred cCCHHHHHHHhcccc-cccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcc--cccCCCHHHHHHHH
Q 034603 10 AGKLDEAEKYLSGFT-QVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIK--AFSTYNEEVFKEAS 79 (89)
Q Consensus 10 ~G~Wd~a~~~L~~l~-~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~--pl~~~~~~~~~~l~ 79 (89)
.|+|++|+..+..+. .-+++.....+.|++=+-.| ..|+..+|+..+++=++ |-++..++.+-.+.
T Consensus 156 ~~~y~~Ai~af~~fl~~yP~s~~a~~A~y~LG~~y~----~~g~~~~A~~~f~~vv~~yP~s~~~~dAl~klg 224 (263)
T PRK10803 156 KSRQDDAIVAFQNFVKKYPDSTYQPNANYWLGQLNY----NKGKKDDAAYYFASVVKNYPKSPKAADAMFKVG 224 (263)
T ss_pred cCCHHHHHHHHHHHHHHCcCCcchHHHHHHHHHHHH----HcCCHHHHHHHHHHHHHHCCCCcchhHHHHHHH
Confidence 699999999998874 33444443247777665543 56899999999887664 54444555554443
No 46
>cd00189 TPR Tetratricopeptide repeat domain; typically contains 34 amino acids [WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found in a variety of organisms including bacteria, cyanobacteria, yeast, fungi, plants, and humans in various subcellular locations; involved in a variety of functions including protein-protein interactions, but common features in the interaction partners have not been defined; involved in chaperone, cell-cycle, transciption, and protein transport complexes; the number of TPR motifs varies among proteins (1,3-11,13 15,16,19); 5-6 tandem repeats generate a right-handed helical structure with an amphipathic channel that is thought to accomodate an alpha-helix of a target protein; it has been proposed that TPR proteins preferably interact with WD-40 repeat proteins, but in many instances several TPR-proteins seem to aggregate to multi-protein complexes; examples of TPR-proteins include, Cdc16p, Cdc23p and C
Probab=59.92 E-value=25 Score=18.67 Aligned_cols=66 Identities=15% Similarity=0.154 Sum_probs=36.4
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHH
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEAS 79 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~ 79 (89)
....|+|++|+..+...-....+.. .+.+ ..-.-+...|+..+|+.++.+-+.... .++..+..++
T Consensus 10 ~~~~~~~~~A~~~~~~~~~~~~~~~--~~~~----~~~~~~~~~~~~~~a~~~~~~~~~~~~-~~~~~~~~~~ 75 (100)
T cd00189 10 YYKLGDYDEALEYYEKALELDPDNA--DAYY----NLAAAYYKLGKYEEALEDYEKALELDP-DNAKAYYNLG 75 (100)
T ss_pred HHHHhcHHHHHHHHHHHHhcCCccH--HHHH----HHHHHHHHHHHHHHHHHHHHHHHhCCC-cchhHHHHHH
Confidence 3457999999999987633332221 1111 111122334888899998886555432 3344444443
No 47
>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=59.45 E-value=12 Score=17.99 Aligned_cols=15 Identities=40% Similarity=0.640 Sum_probs=9.5
Q ss_pred HHhcCCHHHHHHHhc
Q 034603 7 MVLAGKLDEAEKYLS 21 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~ 21 (89)
+...|++++|+..+.
T Consensus 11 ~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 11 LLAQGDPDEAERLLR 25 (26)
T ss_pred HHHcCCHHHHHHHHh
Confidence 455677777776553
No 48
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=59.21 E-value=4.7 Score=23.94 Aligned_cols=15 Identities=20% Similarity=0.352 Sum_probs=12.7
Q ss_pred hhHHHHHhcCCHHHH
Q 034603 2 KHFEDMVLAGKLDEA 16 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a 16 (89)
+.+||.|+.|+|.=+
T Consensus 20 ~~LRQCvlCGRWaC~ 34 (57)
T PF14445_consen 20 SELRQCVLCGRWACN 34 (57)
T ss_pred HHHHHHhhhchhhhh
Confidence 578999999999744
No 49
>cd00736 bacteriophage_lambda_lysozyme The lysozyme from bacteriophage lambda hydrolyses the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), as do other lysozymes. But unlike other lysozymes, bacteriophage lambda does not produce a reducing end upon cleavage of the peptidoglycan but rather uses the 6-OH of the same MurNAc residue to produce a 1,6-anhydromuramic acid terminal residue and is therefore a lytic transglycosylase. An identical 1,6-anhydro bond is formed in bacterial peptidoglycans by the action of the lytic transglycosylases of E. coli. However, they differ structurally.
Probab=56.92 E-value=7.3 Score=27.41 Aligned_cols=60 Identities=13% Similarity=0.039 Sum_probs=42.4
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccc
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAF 67 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl 67 (89)
+++..-|+....-+.. ..........-+.++|.+.+.|..+.+|++.+|++.|+++=+-|
T Consensus 68 Qfl~~Tw~~~~~~~gl-~~F~P~~QD~~A~~Li~~~gal~~i~~G~~~~a~~~La~~WASL 127 (151)
T cd00736 68 QFLSRTWDAYAKQYGL-YDFSPESQDLVAYQLIRERGALPDILAGRIEQAIAKLSNIWASL 127 (151)
T ss_pred hccHHHHHHHHHHcCC-CCCCHHHHHHHHHHHHHHcCcHHHHHcCCHHHHHHHHHhhccCC
Confidence 4556668766554432 22211111223889999999999999999999999999998888
No 50
>TIGR02561 HrpB1_HrpK type III secretion protein HrpB1/HrpK. This gene is found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Probab=56.47 E-value=7.7 Score=27.47 Aligned_cols=61 Identities=16% Similarity=0.160 Sum_probs=39.8
Q ss_pred HHhcCCHHHHHHHhccccccccc-ccccc-eehhh-------hhhHHHHHHhcCCHHHHHHHHHhhcccc
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHEN-MLSTK-TYFEL-------RRQKFLEALDKHERVKALDILMKDIKAF 67 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~-~~~~~-~~FlI-------~kQKfLElL~~~~~~~AL~~Lr~eL~pl 67 (89)
+|-.|+|++|..+++.+..-..+ ++.+. +-|.+ +++.=-|.|+.+...+|+...|.=..++
T Consensus 54 ~i~rg~w~eA~rvlr~l~~~~~~~p~~kAL~A~CL~al~Dp~Wr~~A~~~le~~~~~~a~~Lv~al~g~~ 123 (153)
T TIGR02561 54 LIARGNYDEAARILRELLSSAGAPPYGKALLALCLNAKGDAEWHVHADEVLARDADADAVALVRALLGAQ 123 (153)
T ss_pred HHHcCCHHHHHHHHHhhhccCCCchHHHHHHHHHHHhcCChHHHHHHHHHHHhCCCHhHHHHHHHHhccc
Confidence 68899999999999998543322 32211 11221 4555667888888888888888544443
No 51
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=56.15 E-value=13 Score=20.78 Aligned_cols=52 Identities=19% Similarity=0.331 Sum_probs=31.9
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcC-CHHHHHHHHHhhc
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKH-ERVKALDILMKDI 64 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~-~~~~AL~~Lr~eL 64 (89)
....|+|++|+.++...-.++.+... +.+.+- +=+...| +..+|+..+.+-|
T Consensus 13 ~~~~~~~~~A~~~~~~ai~~~p~~~~--~~~~~g----~~~~~~~~~~~~A~~~~~~al 65 (69)
T PF13414_consen 13 YFQQGDYEEAIEYFEKAIELDPNNAE--AYYNLG----LAYMKLGKDYEEAIEDFEKAL 65 (69)
T ss_dssp HHHTTHHHHHHHHHHHHHHHSTTHHH--HHHHHH----HHHHHTTTHHHHHHHHHHHHH
T ss_pred HHHcCCHHHHHHHHHHHHHcCCCCHH--HHHHHH----HHHHHhCccHHHHHHHHHHHH
Confidence 56789999999999987555533311 222221 1233446 5788888777543
No 52
>PF14498 Glyco_hyd_65N_2: Glycosyl hydrolase family 65, N-terminal domain; PDB: 2EAE_A 2EAB_B 2EAC_A 2EAD_B 2RDY_A.
Probab=56.10 E-value=5.1 Score=28.98 Aligned_cols=23 Identities=17% Similarity=0.421 Sum_probs=19.1
Q ss_pred ChhHHHHHhcCCHHHHHHHhccc
Q 034603 1 MKHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 1 ~~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
|...|+++++|++.+|.+++...
T Consensus 58 L~~iR~l~~~g~~~~A~~l~~~~ 80 (236)
T PF14498_consen 58 LPEIRELLFEGDYEEAEELAEEN 80 (236)
T ss_dssp HHHHHHHHHTT-CCHHHHHHCCS
T ss_pred HHHHHHHHHcCChhHHHHHHHHh
Confidence 35789999999999999998765
No 53
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.19 E-value=53 Score=25.05 Aligned_cols=59 Identities=19% Similarity=0.362 Sum_probs=43.4
Q ss_pred HHHhcCCHHHHHHHhccc-ccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhccccc
Q 034603 6 DMVLAGKLDEAEKYLSGF-TQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~l-~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~ 68 (89)
+++++|++++|+.-+..+ +..+.+.+...+.||+-+--| .+|+..+|-.+..+-..-+.
T Consensus 150 ~~~ksgdy~~A~~~F~~fi~~YP~s~~~~nA~yWLGe~~y----~qg~y~~Aa~~f~~~~k~~P 209 (262)
T COG1729 150 DLYKSGDYAEAEQAFQAFIKKYPNSTYTPNAYYWLGESLY----AQGDYEDAAYIFARVVKDYP 209 (262)
T ss_pred HHHHcCCHHHHHHHHHHHHHcCCCCcccchhHHHHHHHHH----hcccchHHHHHHHHHHHhCC
Confidence 579999999999988776 566777776579999887544 56777777666655555443
No 54
>PF09613 HrpB1_HrpK: Bacterial type III secretion protein (HrpB1_HrpK); InterPro: IPR013394 This family of proteins is encoded by genes found within type III secretion operons in a limited range of species including Xanthomonas, Ralstonia and Burkholderia.
Probab=53.88 E-value=8.3 Score=27.36 Aligned_cols=55 Identities=18% Similarity=0.167 Sum_probs=32.6
Q ss_pred HHHhcCCHHHHHHHhcccccccc-ccccccee--hhh-------hhhHHHHHHhcCCHHHHHHHHH
Q 034603 6 DMVLAGKLDEAEKYLSGFTQVHE-NMLSTKTY--FEL-------RRQKFLEALDKHERVKALDILM 61 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~l~~~~~-~~~~~~~~--FlI-------~kQKfLElL~~~~~~~AL~~Lr 61 (89)
-+|-.|+|++|+.+|+.+..-.. +... ++. |.+ +++.=-|.++.+....|+...+
T Consensus 53 l~i~r~~w~dA~rlLr~l~~~~~~~p~~-kALlA~CL~~~~D~~Wr~~A~evle~~~d~~a~~Lv~ 117 (160)
T PF09613_consen 53 LHIVRGDWDDALRLLRELEERAPGFPYA-KALLALCLYALGDPSWRRYADEVLESGADPDARALVR 117 (160)
T ss_pred HHHHhCCHHHHHHHHHHHhccCCCChHH-HHHHHHHHHHcCChHHHHHHHHHHhcCCChHHHHHHH
Confidence 47889999999999999843322 2222 121 222 3334456777775555555554
No 55
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=53.45 E-value=21 Score=25.02 Aligned_cols=60 Identities=13% Similarity=0.198 Sum_probs=40.4
Q ss_pred HHHHhcCCHHHHHHHhcccc-cccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhccccc
Q 034603 5 EDMVLAGKLDEAEKYLSGFT-QVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l~-~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~ 68 (89)
.+..-.|+|++|++.+..+. .-+.+....++.|.+-.-.| ..|+..+|...+.+=+.-.+
T Consensus 13 ~~~~~~g~y~~Ai~~f~~l~~~~P~s~~a~~A~l~la~a~y----~~~~y~~A~~~~~~fi~~yP 73 (203)
T PF13525_consen 13 LEALQQGDYEEAIKLFEKLIDRYPNSPYAPQAQLMLAYAYY----KQGDYEEAIAAYERFIKLYP 73 (203)
T ss_dssp HHHHHCT-HHHHHHHHHHHHHH-TTSTTHHHHHHHHHHHHH----HTT-HHHHHHHHHHHHHH-T
T ss_pred HHHHHCCCHHHHHHHHHHHHHHCCCChHHHHHHHHHHHHHH----HcCCHHHHHHHHHHHHHHCC
Confidence 45678999999999999985 33445555457777766544 55889999988886555443
No 56
>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=53.15 E-value=14 Score=21.31 Aligned_cols=20 Identities=45% Similarity=0.677 Sum_probs=14.9
Q ss_pred hHHHHHhcCCHHHHHHHhcc
Q 034603 3 HFEDMVLAGKLDEAEKYLSG 22 (89)
Q Consensus 3 ~fr~~Vl~G~Wd~a~~~L~~ 22 (89)
.+.+.|.+|++++|+..+..
T Consensus 38 ~~~~~~~~g~~~~A~~~l~~ 57 (60)
T PF10414_consen 38 PFAELVLAGDEEEAEALLEQ 57 (60)
T ss_dssp HHHHHHHTT-HHHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHHH
Confidence 35678899999999888754
No 57
>PF12854 PPR_1: PPR repeat
Probab=53.05 E-value=11 Score=19.38 Aligned_cols=18 Identities=28% Similarity=0.420 Sum_probs=13.8
Q ss_pred HHHhcCCHHHHHHHhccc
Q 034603 6 DMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~l 23 (89)
-..-.|++++|.+++..+
T Consensus 16 ~~Ck~G~~~~A~~l~~~M 33 (34)
T PF12854_consen 16 GYCKAGRVDEAFELFDEM 33 (34)
T ss_pred HHHHCCCHHHHHHHHHhC
Confidence 345689999999988764
No 58
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=51.73 E-value=47 Score=27.68 Aligned_cols=64 Identities=11% Similarity=0.046 Sum_probs=27.6
Q ss_pred HhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHH
Q 034603 8 VLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEA 78 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l 78 (89)
+..|++++|+..+..+...+.+... +.+ ..=.-+...|+..+|+..+++-+.- .+.++..+..+
T Consensus 87 l~~g~~~~A~~~l~~~l~~~P~~~~--a~~----~la~~l~~~g~~~~Ai~~l~~Al~l-~P~~~~a~~~l 150 (656)
T PRK15174 87 LASSQPDAVLQVVNKLLAVNVCQPE--DVL----LVASVLLKSKQYATVADLAEQAWLA-FSGNSQIFALH 150 (656)
T ss_pred hhcCCHHHHHHHHHHHHHhCCCChH--HHH----HHHHHHHHcCCHHHHHHHHHHHHHh-CCCcHHHHHHH
Confidence 3456666666666655333222211 111 1112234445555566555544332 33444444443
No 59
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=51.57 E-value=52 Score=25.43 Aligned_cols=49 Identities=8% Similarity=0.011 Sum_probs=23.6
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHH
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILM 61 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr 61 (89)
++..|+|++|.+.+..+.....++. .+ ++.-..=++..|+..+|+..+.
T Consensus 163 ~l~~~~~~~Al~~l~~l~~~~P~~~--~~----l~ll~~~~~~~~d~~~a~~~l~ 211 (409)
T TIGR00540 163 LLAQNELHAARHGVDKLLEMAPRHK--EV----LKLAEEAYIRSGAWQALDDIID 211 (409)
T ss_pred HHHCCCHHHHHHHHHHHHHhCCCCH--HH----HHHHHHHHHHHhhHHHHHHHHH
Confidence 4446666666666666533221111 11 2222222355566666666655
No 60
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=51.23 E-value=54 Score=29.08 Aligned_cols=73 Identities=10% Similarity=-0.030 Sum_probs=43.0
Q ss_pred HhcCCHHHHHHHhccccccccccccc--------ceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHH
Q 034603 8 VLAGKLDEAEKYLSGFTQVHENMLST--------KTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEAS 79 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l~~~~~~~~~~--------~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~ 79 (89)
...|++++|+.++...-..+.+.... ...|.+.-+.--.++..|+..+|+..+++-+.- .+.++..+..++
T Consensus 314 ~~~g~~~eA~~~l~~Al~~~p~~~~~~~~~~ll~~~~~~~~~~~g~~~~~~g~~~eA~~~~~~Al~~-~P~~~~a~~~Lg 392 (1157)
T PRK11447 314 SQQGDRARAVAQFEKALALDPHSSNRDKWESLLKVNRYWLLIQQGDAALKANNLAQAERLYQQARQV-DNTDSYAVLGLG 392 (1157)
T ss_pred HHcCCHHHHHHHHHHHHHhCCCccchhHHHHHHHhhhHHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHH
Confidence 45788999988887763332221110 124555545555567788888888888865554 345555555554
Q ss_pred hh
Q 034603 80 LL 81 (89)
Q Consensus 80 ~l 81 (89)
.+
T Consensus 393 ~~ 394 (1157)
T PRK11447 393 DV 394 (1157)
T ss_pred HH
Confidence 43
No 61
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=50.64 E-value=14 Score=18.83 Aligned_cols=15 Identities=20% Similarity=0.337 Sum_probs=8.7
Q ss_pred HhcCCHHHHHHHhcc
Q 034603 8 VLAGKLDEAEKYLSG 22 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~ 22 (89)
.-.|+|++|+++...
T Consensus 10 ~~~g~~~~Ai~~y~~ 24 (36)
T PF13176_consen 10 RQQGDYEKAIEYYEQ 24 (36)
T ss_dssp HHCT-HHHHHHHHHH
T ss_pred HHcCCHHHHHHHHHH
Confidence 345777777766654
No 62
>PF13838 Clathrin_H_link: Clathrin-H-link; PDB: 2XZG_A 3GD1_I 1BPO_C 1C9I_B 1C9L_A.
Probab=50.61 E-value=22 Score=21.74 Aligned_cols=23 Identities=22% Similarity=0.226 Sum_probs=19.2
Q ss_pred hhhhHHHHHHhcCCHHHHHHHHH
Q 034603 39 LRRQKFLEALDKHERVKALDILM 61 (89)
Q Consensus 39 I~kQKfLElL~~~~~~~AL~~Lr 61 (89)
++.|+|=|++..|++.+|-.+.-
T Consensus 8 l~~~~F~~l~~~g~y~eAA~~AA 30 (66)
T PF13838_consen 8 LYVQQFNELFSQGQYEEAAKVAA 30 (66)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHH
Confidence 57899999999999999887765
No 63
>PLN03079 Uncharacterized protein At4g33100; Provisional
Probab=50.60 E-value=26 Score=22.82 Aligned_cols=34 Identities=12% Similarity=0.160 Sum_probs=30.6
Q ss_pred eehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccC
Q 034603 35 TYFELRRQKFLEALDKHERVKALDILMKDIKAFST 69 (89)
Q Consensus 35 ~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~ 69 (89)
-.|..++++..+.|....+...|+..|++ .|+++
T Consensus 49 ~~w~~Yq~Cv~~aL~ek~I~~lLe~ar~~-~p~~~ 82 (91)
T PLN03079 49 AEWHKYRACLSEHLEDKHLSQILEVDGTS-APYKQ 82 (91)
T ss_pred HHHHHHHHHHHHHHHHcChHHHHHHHhhc-CCcCC
Confidence 56899999999999999999999999966 78874
No 64
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.25 E-value=23 Score=24.05 Aligned_cols=52 Identities=27% Similarity=0.358 Sum_probs=35.8
Q ss_pred cCCHHHHHHHhcc--------c----ccccccccccceehhhhhhHHHHHHhcCCH--HHHHHHHHh
Q 034603 10 AGKLDEAEKYLSG--------F----TQVHENMLSTKTYFELRRQKFLEALDKHER--VKALDILMK 62 (89)
Q Consensus 10 ~G~Wd~a~~~L~~--------l----~~~~~~~~~~~~~FlI~kQKfLElL~~~~~--~~AL~~Lr~ 62 (89)
.|+..+++.+++- + ....=++.+ .+.--|-+.|-+..|+.|++ .+|+..|++
T Consensus 57 RGnlKEvEr~lg~sYptvR~kld~vlramgy~p~~-e~~~~i~~~~i~~qle~Gei~peeA~~~L~k 122 (122)
T COG3877 57 RGNLKEVERELGISYPTVRTKLDEVLRAMGYNPDS-ENSVNIGKKKIIDQLEKGEISPEEAIKMLNK 122 (122)
T ss_pred ccCHHHHHHHHCCccHHHHHHHHHHHHHcCCCCCC-CChhhhhHHHHHHHHHcCCCCHHHHHHHhcC
Confidence 5788888887751 1 111112233 46667899999999999987 589998874
No 65
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=49.77 E-value=57 Score=26.52 Aligned_cols=74 Identities=15% Similarity=0.074 Sum_probs=37.5
Q ss_pred HhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHH-hcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 8 VLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEAL-DKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL-~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
.-.|+|++|++++...-.++............+-.+..-+. ..|+..+|+..+++-+. +.+.+...+..++.++
T Consensus 478 ~~~g~~~~A~~~~~~Al~l~p~~~~~~~~~~~l~~~a~~~~~~~~~~~eA~~~~~kAl~-l~p~~~~a~~~la~~~ 552 (615)
T TIGR00990 478 LDQNKFDEAIEKFDTAIELEKETKPMYMNVLPLINKALALFQWKQDFIEAENLCEKALI-IDPECDIAVATMAQLL 552 (615)
T ss_pred HHccCHHHHHHHHHHHHhcCCccccccccHHHHHHHHHHHHHHhhhHHHHHHHHHHHHh-cCCCcHHHHHHHHHHH
Confidence 34688999988887643332211110011111111111122 24788889888886443 3445555566665544
No 66
>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=49.35 E-value=45 Score=18.48 Aligned_cols=34 Identities=24% Similarity=0.201 Sum_probs=23.9
Q ss_pred HHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 46 EALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 46 ElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
.+++.|+...|..+|.+-+. ..++..-.+...||
T Consensus 8 ayie~Gd~e~Ar~lL~evl~---~~~~~q~~eA~~LL 41 (44)
T TIGR03504 8 AYIEMGDLEGARELLEEVIE---EGDEAQRQEARALL 41 (44)
T ss_pred HHHHcCChHHHHHHHHHHHH---cCCHHHHHHHHHHH
Confidence 36788999999999995552 35566666665554
No 67
>TIGR00990 3a0801s09 mitochondrial precursor proteins import receptor (72 kDa mitochondrial outermembrane protein) (mitochondrial import receptor for the ADP/ATP carrier) (translocase of outermembrane tom70).
Probab=49.10 E-value=63 Score=26.24 Aligned_cols=67 Identities=22% Similarity=0.218 Sum_probs=34.1
Q ss_pred hcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 9 LAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 9 l~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
..|+|++|+..+...-.++.+... ..+ .+= .=+...|+..+|+..+++-+.. .+.+++.+..++.+.
T Consensus 343 ~~g~~~eA~~~~~kal~l~P~~~~--~~~-~la---~~~~~~g~~~eA~~~~~~al~~-~p~~~~~~~~lg~~~ 409 (615)
T TIGR00990 343 LKGKHLEALADLSKSIELDPRVTQ--SYI-KRA---SMNLELGDPDKAEEDFDKALKL-NSEDPDIYYHRAQLH 409 (615)
T ss_pred HcCCHHHHHHHHHHHHHcCCCcHH--HHH-HHH---HHHHHCCCHHHHHHHHHHHHHh-CCCCHHHHHHHHHHH
Confidence 467888888877765333322111 111 111 1123456777777777655443 345566666555443
No 68
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=48.97 E-value=29 Score=22.72 Aligned_cols=44 Identities=9% Similarity=0.191 Sum_probs=34.6
Q ss_pred hhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 38 ELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 38 lI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
-=++-+-+|+|+..+...|-.++++.|..+..- ..-..+|+.++
T Consensus 51 sPyErr~i~Lirns~~krArKlakKRLGs~kRA-kaKvEel~~~i 94 (97)
T COG5051 51 SPYERRVIELIRNSQDKRARKLAKKRLGSLKRA-KAKVEELTSVI 94 (97)
T ss_pred CHHHHHHHHHHHhcccHHHHHHHHHHhhhHHHH-HHHHHHHHHHH
Confidence 347889999999999999999999999887532 44566776655
No 69
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=48.78 E-value=88 Score=26.47 Aligned_cols=75 Identities=8% Similarity=-0.060 Sum_probs=41.9
Q ss_pred HHhcCCHHHHHHHhcccccccccccc---------cceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHH
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLS---------TKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKE 77 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~---------~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~ 77 (89)
..-.|++++|..++..+......... ..-....+.-.--=+...|+..+|+.++++ +....+.+++.+-.
T Consensus 320 ~~~~g~~~eA~~~l~~~~~~~P~~~~~~~~~~~~p~~~~~~a~~~~a~~l~~~g~~~eA~~~l~~-al~~~P~n~~l~~~ 398 (765)
T PRK10049 320 LLESENYPGALTVTAHTINNSPPFLRLYGSPTSIPNDDWLQGQSLLSQVAKYSNDLPQAEMRARE-LAYNAPGNQGLRID 398 (765)
T ss_pred HHhcccHHHHHHHHHHHhhcCCceEeecCCCCCCCCchHHHHHHHHHHHHHHcCCHHHHHHHHHH-HHHhCCCCHHHHHH
Confidence 35568999999888876432211000 000011111122233466889999999884 44555677777777
Q ss_pred HHhhh
Q 034603 78 ASLLL 82 (89)
Q Consensus 78 l~~ll 82 (89)
++.++
T Consensus 399 lA~l~ 403 (765)
T PRK10049 399 YASVL 403 (765)
T ss_pred HHHHH
Confidence 76655
No 70
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=47.62 E-value=7.4 Score=18.62 Aligned_cols=16 Identities=31% Similarity=0.478 Sum_probs=13.4
Q ss_pred HhcCCHHHHHHHhccc
Q 034603 8 VLAGKLDEAEKYLSGF 23 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l 23 (89)
...|+|++|.+++..+
T Consensus 11 ~~~g~~~~A~~~~~~~ 26 (33)
T PF13174_consen 11 YKLGDYDEAIEYFQRL 26 (33)
T ss_dssp HHHCHHHHHHHHHHHH
T ss_pred HHccCHHHHHHHHHHH
Confidence 3469999999999876
No 71
>PRK15174 Vi polysaccharide export protein VexE; Provisional
Probab=47.50 E-value=35 Score=28.40 Aligned_cols=72 Identities=14% Similarity=-0.043 Sum_probs=47.6
Q ss_pred HHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 4 FEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
..++...|++++|...+..+-........ ....+..-+ +..|+..+|+..+++- .-+.+.+++.+..++.++
T Consensus 49 ~~~~~~~g~~~~A~~l~~~~l~~~p~~~~-~l~~l~~~~-----l~~g~~~~A~~~l~~~-l~~~P~~~~a~~~la~~l 120 (656)
T PRK15174 49 AIACLRKDETDVGLTLLSDRVLTAKNGRD-LLRRWVISP-----LASSQPDAVLQVVNKL-LAVNVCQPEDVLLVASVL 120 (656)
T ss_pred HHHHHhcCCcchhHHHhHHHHHhCCCchh-HHHHHhhhH-----hhcCCHHHHHHHHHHH-HHhCCCChHHHHHHHHHH
Confidence 45678899999999999987333222222 133333222 4589999999999954 445667787777776553
No 72
>PF10579 Rapsyn_N: Rapsyn N-terminal myristoylation and linker region; InterPro: IPR019568 Neuromuscular junction formation relies upon the clustering of acetylcholine receptors and other proteins in the muscle membrane. Rapsyn is a peripheral membrane protein that is selectively concentrated at the neuromuscular junction and is essential for the formation of synaptic acetylcholine receptor aggregates. Acetylcholine receptors fail to aggregate beneath nerve terminals in mice where rapsyn has been knocked out. The N-terminal six amino acids of rapsyn are its myristoylation site, and myristoylation is necessary for the targeting of the protein to the membrane []. ; GO: 0008270 zinc ion binding, 0033130 acetylcholine receptor binding, 0007268 synaptic transmission, 0005856 cytoskeleton, 0030054 cell junction, 0045211 postsynaptic membrane
Probab=47.23 E-value=48 Score=21.06 Aligned_cols=38 Identities=21% Similarity=0.332 Sum_probs=31.5
Q ss_pred HHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhhc
Q 034603 45 LEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLLP 83 (89)
Q Consensus 45 LElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~llt 83 (89)
|-+=..++..+||++-++-|.-.+ .+++.|.-|.+|.+
T Consensus 14 lkLY~~~~~~~Al~~W~~aL~k~~-~~~~rf~~lG~l~q 51 (80)
T PF10579_consen 14 LKLYHQNETQQALQKWRKALEKIT-DREDRFRVLGYLIQ 51 (80)
T ss_pred HHHhccchHHHHHHHHHHHHhhcC-ChHHHHHHHHHHHH
Confidence 445577889999999999998877 57899999988865
No 73
>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=46.54 E-value=23 Score=23.48 Aligned_cols=25 Identities=16% Similarity=0.361 Sum_probs=21.1
Q ss_pred hHHHHHHhcCCHHHHHHHHHhhcccc
Q 034603 42 QKFLEALDKHERVKALDILMKDIKAF 67 (89)
Q Consensus 42 QKfLElL~~~~~~~AL~~Lr~eL~pl 67 (89)
-.|-+.|..|..++||.++| +..|.
T Consensus 7 Da~a~aina~sk~EaL~iik-e~~P~ 31 (106)
T PF08283_consen 7 DAYARAINAGSKEEALSIIK-ELAPK 31 (106)
T ss_pred HHHHHHHhcCCHHHHHHHHH-hcCch
Confidence 45788899999999999999 66664
No 74
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=45.97 E-value=72 Score=24.50 Aligned_cols=66 Identities=15% Similarity=0.133 Sum_probs=42.5
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHH
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEAS 79 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~ 79 (89)
++..|++++|+..+...-.++.+.. .+.|.+ =+- +...|+..+|+..+++-+. +.+.+++...-+.
T Consensus 46 ~~~~g~~~eAl~~~~~Al~l~P~~~--~a~~~l-g~~---~~~lg~~~eA~~~~~~al~-l~P~~~~~~~~l~ 111 (356)
T PLN03088 46 NIKLGNFTEAVADANKAIELDPSLA--KAYLRK-GTA---CMKLEEYQTAKAALEKGAS-LAPGDSRFTKLIK 111 (356)
T ss_pred HHHcCCHHHHHHHHHHHHHhCcCCH--HHHHHH-HHH---HHHhCCHHHHHHHHHHHHH-hCCCCHHHHHHHH
Confidence 4567999999999998755543321 233322 222 2346999999999996665 4556666555443
No 75
>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=45.68 E-value=27 Score=20.99 Aligned_cols=24 Identities=17% Similarity=0.317 Sum_probs=19.0
Q ss_pred hhHHHHHHhcCCHHHHHHHHHhhc
Q 034603 41 RQKFLEALDKHERVKALDILMKDI 64 (89)
Q Consensus 41 kQKfLElL~~~~~~~AL~~Lr~eL 64 (89)
-+..+++|..||...|-.+++..+
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 356788899999999999998765
No 76
>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=44.09 E-value=42 Score=22.60 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=32.7
Q ss_pred ceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHH
Q 034603 34 KTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEA 78 (89)
Q Consensus 34 ~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l 78 (89)
.+.|=|+=+.||+++..|...+|-.++.+--.-+.....+..+.|
T Consensus 39 ~lLyPvFvh~YL~Lv~~~~~~~A~~F~~kf~~~~~~~~~~~i~~L 83 (142)
T PF04494_consen 39 RLLYPVFVHSYLDLVSKGHPEEAKSFLEKFSPDFEDSHQEDIEKL 83 (142)
T ss_dssp GGHHHHHHHHHHHHHHTT-HHHHHHHHHHHGGGGHGHGHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHhHHHHHHHHHH
Confidence 478888999999999999999999999965555543333333333
No 77
>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=43.82 E-value=11 Score=18.10 Aligned_cols=16 Identities=25% Similarity=0.362 Sum_probs=11.4
Q ss_pred HhcCCHHHHHHHhccc
Q 034603 8 VLAGKLDEAEKYLSGF 23 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l 23 (89)
-..|+|++|++.+...
T Consensus 12 ~~~~~~~~A~~~~~~a 27 (34)
T PF07719_consen 12 YQLGNYEEAIEYFEKA 27 (34)
T ss_dssp HHTT-HHHHHHHHHHH
T ss_pred HHhCCHHHHHHHHHHH
Confidence 4578889988887765
No 78
>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=43.34 E-value=61 Score=20.64 Aligned_cols=32 Identities=16% Similarity=0.182 Sum_probs=28.1
Q ss_pred hhhhhhHHHHHHhcCCHHHHHHHHHhhccccc
Q 034603 37 FELRRQKFLEALDKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 37 FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~ 68 (89)
|.=..++.+++...|+..+|...+..+..|..
T Consensus 121 y~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~ 152 (181)
T PF12729_consen 121 YRKLRDQVIELAKSGDNDEARAILNGEARPAF 152 (181)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHhHHHHH
Confidence 55566889999999999999999999999875
No 79
>PF02259 FAT: FAT domain; InterPro: IPR003151 The FAT domain is a domain present in the PIK-related kinases. Members of the family of PIK-related kinases may act as intracellular sensors that govern radial and horizontal pathways [].; GO: 0005515 protein binding
Probab=43.27 E-value=32 Score=25.09 Aligned_cols=77 Identities=25% Similarity=0.293 Sum_probs=43.2
Q ss_pred HHHHhcCCHHHHHHHhccccccc-ccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCC-HHHHHHHHhhh
Q 034603 5 EDMVLAGKLDEAEKYLSGFTQVH-ENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYN-EEVFKEASLLL 82 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l~~~~-~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~-~~~~~~l~~ll 82 (89)
+.+---|+||...+++.....-. +.... ++...|.+.+|=+.-. -+.+|...+-.+++++...+ ...|..+..|.
T Consensus 6 eaaWrl~~Wd~l~~~~~~~~~~~~~~~~~-~al~~l~~~~~~~~~~--~i~~~r~~~~~~l~~~~~~s~~~~y~~l~~lq 82 (352)
T PF02259_consen 6 EAAWRLGDWDLLEEYLSQSNEDSPEYSFY-RALLALRQGDYDEAKK--YIEKARQLLLDELSALSSESYQRAYPSLVKLQ 82 (352)
T ss_pred HHHHhcCChhhHHHHHhhccCCChhHHHH-HHHHHHhCccHHHHHH--HHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 34556799999888888764211 11222 2334444444443322 24566677777777765433 55566666655
Q ss_pred cC
Q 034603 83 PL 84 (89)
Q Consensus 83 tl 84 (89)
.|
T Consensus 83 ~L 84 (352)
T PF02259_consen 83 QL 84 (352)
T ss_pred HH
Confidence 44
No 80
>cd02577 PSTD1 PSTD1: Pseudouridine synthase, a subgroup of the TruD family. This group consists of several hypothetical archeal pseudouridine synthases assigned to the TruD family of psuedouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). The TruD family is comprised of proteins related to Escherichia coli TruD.
Probab=42.82 E-value=59 Score=25.14 Aligned_cols=18 Identities=28% Similarity=0.436 Sum_probs=15.0
Q ss_pred HHHHhcCCHHHHHHHhcc
Q 034603 5 EDMVLAGKLDEAEKYLSG 22 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~ 22 (89)
=.+|+.|+|++|...+-.
T Consensus 157 G~~ll~gd~~~Av~~il~ 174 (319)
T cd02577 157 GKLILEGDYEEAAKTYLT 174 (319)
T ss_pred HHHHHccCHHHHHHHHhc
Confidence 368999999999988654
No 81
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=41.37 E-value=1.4e+02 Score=23.08 Aligned_cols=31 Identities=19% Similarity=0.111 Sum_probs=18.9
Q ss_pred hcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 49 DKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 49 ~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
..|+...|+..++ ++....|.++....-+..
T Consensus 165 ~~~~~~~Al~~l~-~l~~~~P~~~~~l~ll~~ 195 (409)
T TIGR00540 165 AQNELHAARHGVD-KLLEMAPRHKEVLKLAEE 195 (409)
T ss_pred HCCCHHHHHHHHH-HHHHhCCCCHHHHHHHHH
Confidence 3577777777777 444445666665554443
No 82
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=41.17 E-value=1.2e+02 Score=22.35 Aligned_cols=12 Identities=8% Similarity=0.135 Sum_probs=6.0
Q ss_pred CCHHHHHHHHHh
Q 034603 51 HERVKALDILMK 62 (89)
Q Consensus 51 ~~~~~AL~~Lr~ 62 (89)
|+..+|+.++.+
T Consensus 121 g~~~~A~~~~~~ 132 (389)
T PRK11788 121 GLLDRAEELFLQ 132 (389)
T ss_pred CCHHHHHHHHHH
Confidence 445555555443
No 83
>PRK05627 bifunctional riboflavin kinase/FMN adenylyltransferase; Reviewed
Probab=40.74 E-value=25 Score=26.95 Aligned_cols=22 Identities=23% Similarity=0.283 Sum_probs=19.6
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+..|++|.+|++++|-++|..-
T Consensus 164 T~IR~~I~~G~i~~A~~lLg~~ 185 (305)
T PRK05627 164 TAIRQALAEGDLELANKLLGRP 185 (305)
T ss_pred HHHHHHHHcCCHHHHHhhhcCC
Confidence 5789999999999999999753
No 84
>PRK12810 gltD glutamate synthase subunit beta; Reviewed
Probab=40.25 E-value=31 Score=27.33 Aligned_cols=33 Identities=9% Similarity=0.015 Sum_probs=27.1
Q ss_pred eehhhhhhHHHHHHhcCCHHHHHHHHHhhccccc
Q 034603 35 TYFELRRQKFLEALDKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 35 ~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~ 68 (89)
.--.+-.+.|+.++..|+..+|+.++++.. ||.
T Consensus 58 CP~~~~~~~~~~~~~~~~~~~a~~~~~~~~-p~~ 90 (471)
T PRK12810 58 CPVHNYIPEWNDLVYRGRWEEAAERLHQTN-NFP 90 (471)
T ss_pred CCCCCcHHHHHHHHHCCCHHHHHHHHHHhC-Chh
Confidence 344567799999999999999999999665 663
No 85
>PRK07143 hypothetical protein; Provisional
Probab=40.19 E-value=27 Score=26.57 Aligned_cols=22 Identities=9% Similarity=0.125 Sum_probs=19.7
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+..|++|.+|+.++|.++|..-
T Consensus 153 T~IR~~l~~G~i~~A~~lLGr~ 174 (279)
T PRK07143 153 SLLKEFIEFGDIELLNSLLLYN 174 (279)
T ss_pred HHHHHHHHcCCHHHHHHHcCCC
Confidence 4789999999999999999854
No 86
>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.83 E-value=57 Score=27.99 Aligned_cols=62 Identities=16% Similarity=0.131 Sum_probs=41.3
Q ss_pred HHhcCCHHHHHHHhccc-----ccccccccc-cce---ehhhhhhHHHHHHhcCCHHHHHHHHHhhccccc
Q 034603 7 MVLAGKLDEAEKYLSGF-----TQVHENMLS-TKT---YFELRRQKFLEALDKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l-----~~~~~~~~~-~~~---~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~ 68 (89)
.|-.|+|++|++.|..- +.+.+.+.+ ..+ .=.|+=|.+.=+.-.|++.+|..+...-|+-..
T Consensus 185 ~i~~gky~qA~elL~kA~~~~~e~l~~~d~~eEeie~el~~IrvQlayVlQ~~Gqt~ea~~iy~~~i~~~~ 255 (652)
T KOG2376|consen 185 LIENGKYNQAIELLEKALRICREKLEDEDTNEEEIEEELNPIRVQLAYVLQLQGQTAEASSIYVDIIKRNP 255 (652)
T ss_pred HHhcccHHHHHHHHHHHHHHHHHhhcccccchhhHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhcC
Confidence 46789999999999854 333333222 001 125777888888888999999997765555443
No 87
>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=39.14 E-value=43 Score=22.01 Aligned_cols=46 Identities=20% Similarity=0.178 Sum_probs=34.3
Q ss_pred ehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 36 YFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 36 ~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
-|-=++.+-+|+|..++...||.++.+.|--... ...-.++|+.+|
T Consensus 47 GfaPYEkr~mELlkv~kdKrAlKf~KKRlGth~R-AKrKrEel~~vl 92 (98)
T PF01158_consen 47 GFAPYEKRAMELLKVSKDKRALKFAKKRLGTHIR-AKRKREELSNVL 92 (98)
T ss_dssp HHCHHHHHHHHHHHHCCHHHHHHHHHHHHCHHHH-HHHHHHHHHHHH
T ss_pred CCChHHHHHHHHHhcchhHHHHHHHHHHhhhhHH-HHHHHHHHHHHH
Confidence 3666889999999999999999999998866542 133455555554
No 88
>PF07219 HemY_N: HemY protein N-terminus; InterPro: IPR010817 This entry represents the N terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. These are membrane protein involved in a late step of protoheme IX synthesis [].
Probab=38.89 E-value=19 Score=23.12 Aligned_cols=20 Identities=25% Similarity=0.375 Sum_probs=16.4
Q ss_pred HHhcCCHHHHHHHhcccccc
Q 034603 7 MVLAGKLDEAEKYLSGFTQV 26 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~ 26 (89)
++.+|||..|++.+..-...
T Consensus 69 al~~G~~~~A~k~~~~a~~~ 88 (108)
T PF07219_consen 69 ALAEGDWQRAEKLLAKAAKL 88 (108)
T ss_pred HHHCCCHHHHHHHHHHHHhc
Confidence 57899999999999887433
No 89
>PRK02603 photosystem I assembly protein Ycf3; Provisional
Probab=38.83 E-value=1.2e+02 Score=20.27 Aligned_cols=71 Identities=11% Similarity=0.084 Sum_probs=40.3
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhh
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLL 81 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~l 81 (89)
....|++++|..++...-....+... . -.++...=.-+...|+..+|+..+++-+.- .+.+...+..++.+
T Consensus 45 ~~~~g~~~~A~~~~~~al~~~~~~~~-~--~~~~~~la~~~~~~g~~~~A~~~~~~al~~-~p~~~~~~~~lg~~ 115 (172)
T PRK02603 45 AQADGEYAEALENYEEALKLEEDPND-R--SYILYNMGIIYASNGEHDKALEYYHQALEL-NPKQPSALNNIAVI 115 (172)
T ss_pred HHHcCCHHHHHHHHHHHHHHhhccch-H--HHHHHHHHHHHHHcCCHHHHHHHHHHHHHh-CcccHHHHHHHHHH
Confidence 34579999999998866322222111 0 012222223344569999999999877664 33445555555444
No 90
>TIGR02521 type_IV_pilW type IV pilus biogenesis/stability protein PilW. Members of this family are designated PilF in ref (PubMed:8973346) and PilW in ref (PubMed:15612916). This outer membrane protein is required both for pilus stability and for pilus function such as adherence to human cells. Members of this family contain copies of the TPR (tetratricopeptide repeat) domain.
Probab=38.69 E-value=1.1e+02 Score=19.79 Aligned_cols=17 Identities=12% Similarity=-0.062 Sum_probs=9.7
Q ss_pred hcCCHHHHHHHHHhhcc
Q 034603 49 DKHERVKALDILMKDIK 65 (89)
Q Consensus 49 ~~~~~~~AL~~Lr~eL~ 65 (89)
..|+..+|+..+++-+.
T Consensus 181 ~~~~~~~A~~~~~~~~~ 197 (234)
T TIGR02521 181 LRGQYKDARAYLERYQQ 197 (234)
T ss_pred HcCCHHHHHHHHHHHHH
Confidence 34666666666664433
No 91
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=38.33 E-value=43 Score=20.98 Aligned_cols=76 Identities=20% Similarity=0.237 Sum_probs=44.2
Q ss_pred HHHHHhcCCHHHHHHHhcccccccccccccceehhh----------hhhHH---HHHHh------cCCHHHHHHHHHhhc
Q 034603 4 FEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFEL----------RRQKF---LEALD------KHERVKALDILMKDI 64 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI----------~kQKf---LElL~------~~~~~~AL~~Lr~eL 64 (89)
+.+..-.||+++|..-+..+... +.. . ++-+.+ .+..| ++.|. ......|+.-+-+.+
T Consensus 9 l~ey~~~~D~~ea~~~l~~L~~~-~~~-~-~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~l 85 (113)
T smart00544 9 IEEYLSSGDTDEAVHCLLELKLP-EQH-H-EVVKVLLTCALEEKRTYREMYSVLLSRLCQANVISTKQFEKGFWRLLEDI 85 (113)
T ss_pred HHHHHHcCCHHHHHHHHHHhCCC-cch-H-HHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhC
Confidence 34566789999999999988543 111 1 111111 11112 22222 134466777777777
Q ss_pred ccccCCCHHHHHHHHhhh
Q 034603 65 KAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 65 ~pl~~~~~~~~~~l~~ll 82 (89)
.-+..+.|..+..++.++
T Consensus 86 ~dl~~D~P~a~~~la~~~ 103 (113)
T smart00544 86 EDLELDIPNAWRNLAEFV 103 (113)
T ss_pred hhhhcccccHHHHHHHHH
Confidence 777777777777776665
No 92
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=38.25 E-value=91 Score=24.85 Aligned_cols=13 Identities=23% Similarity=-0.000 Sum_probs=6.4
Q ss_pred hcCCHHHHHHHHH
Q 034603 49 DKHERVKALDILM 61 (89)
Q Consensus 49 ~~~~~~~AL~~Lr 61 (89)
..|+..+|+.++.
T Consensus 443 ~~~~~~~A~~~~~ 455 (899)
T TIGR02917 443 RSGQFDKALAAAK 455 (899)
T ss_pred hcCCHHHHHHHHH
Confidence 3444555555554
No 93
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=37.97 E-value=93 Score=21.43 Aligned_cols=58 Identities=14% Similarity=0.192 Sum_probs=36.2
Q ss_pred HHHhcCCHHHHHHHhcccccccc-cccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccc
Q 034603 6 DMVLAGKLDEAEKYLSGFTQVHE-NMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAF 67 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~l~~~~~-~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl 67 (89)
..+..|+|++|+..+..+..... +.....+.|.+- .-+...|+..+|+..+.+-+...
T Consensus 42 ~~~~~~~~~~A~~~~~~~~~~~p~~~~~~~a~~~la----~~~~~~~~~~~A~~~~~~~l~~~ 100 (235)
T TIGR03302 42 EALDSGDYTEAIKYFEALESRYPFSPYAEQAQLDLA----YAYYKSGDYAEAIAAADRFIRLH 100 (235)
T ss_pred HHHHcCCHHHHHHHHHHHHHhCCCchhHHHHHHHHH----HHHHhcCCHHHHHHHHHHHHHHC
Confidence 45678999999999998743332 221111222221 12345699999999999755443
No 94
>PF02334 RTP: Replication terminator protein; InterPro: IPR003432 The bacterial replication terminator protein (RTP) plays a role in the termination of DNA replication by impeding replication fork movement. Two RTP dimers bind to the two inverted repeat regions at the termination site.; GO: 0003677 DNA binding, 0006274 DNA replication termination; PDB: 2DPU_A 2DPD_A 1F4K_A 1J0R_B 2EFW_F 2DQR_B 1BM9_B.
Probab=35.92 E-value=32 Score=23.44 Aligned_cols=47 Identities=26% Similarity=0.452 Sum_probs=29.9
Q ss_pred eehhhhhhHHHHH-----HhcCC--HHHHHHHHHhhccccc--CCCHHHHHHHHhh
Q 034603 35 TYFELRRQKFLEA-----LDKHE--RVKALDILMKDIKAFS--TYNEEVFKEASLL 81 (89)
Q Consensus 35 ~~FlI~kQKfLEl-----L~~~~--~~~AL~~Lr~eL~pl~--~~~~~~~~~l~~l 81 (89)
--|+|.|--|+-+ ++++. -..-|++||.|.+|++ |...++|+.|-.|
T Consensus 9 ~gFl~kQRaFlKlYiitm~e~~r~Yg~q~Ld~lr~EFk~~Gy~P~hsEvYraLHeL 64 (122)
T PF02334_consen 9 TGFLLKQRAFLKLYIITMVEQERGYGLQLLDELRSEFKPLGYRPNHSEVYRALHEL 64 (122)
T ss_dssp TSSS--HHHHHHHHHHHHHHTT-EBCTCHHHHHHHHHTTTT----HHHHHHHHHHH
T ss_pred cchhHHHHHHHHHHHHhhhhcccchHHHHHHHHHHHhhhcCCCCCHHHHHHHHHHH
Confidence 4588888888764 45443 2578999999999998 3335677666443
No 95
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=35.91 E-value=45 Score=20.57 Aligned_cols=22 Identities=32% Similarity=0.493 Sum_probs=18.6
Q ss_pred HHHHHHhcCCHHHHHHHHHhhc
Q 034603 43 KFLEALDKHERVKALDILMKDI 64 (89)
Q Consensus 43 KfLElL~~~~~~~AL~~Lr~eL 64 (89)
.|++.+..||..+|++-|.+-+
T Consensus 4 ~~~~~~~~~dy~~A~d~L~~~f 25 (94)
T PF12862_consen 4 RYLNALRSGDYSEALDALHRYF 25 (94)
T ss_pred HHHHHHHcCCHHHHHHHHHHHH
Confidence 4888999999999999998544
No 96
>PRK10049 pgaA outer membrane protein PgaA; Provisional
Probab=35.53 E-value=82 Score=26.66 Aligned_cols=55 Identities=15% Similarity=0.097 Sum_probs=33.2
Q ss_pred HHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhh
Q 034603 7 MVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKD 63 (89)
Q Consensus 7 ~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~e 63 (89)
.+..|++++|+..+..+...+.... ........+-|.=+++.|+..+|+..+++-
T Consensus 282 yl~~g~~e~A~~~l~~~l~~~p~~~--~~~~~~~~~L~~a~~~~g~~~eA~~~l~~~ 336 (765)
T PRK10049 282 YLKLHQPEKAQSILTELFYHPETIA--DLSDEELADLFYSLLESENYPGALTVTAHT 336 (765)
T ss_pred HHhcCCcHHHHHHHHHHhhcCCCCC--CCChHHHHHHHHHHHhcccHHHHHHHHHHH
Confidence 3456888888888777532221110 122233444455568889999999988843
No 97
>PF13041 PPR_2: PPR repeat family
Probab=35.49 E-value=35 Score=18.27 Aligned_cols=21 Identities=29% Similarity=0.403 Sum_probs=15.9
Q ss_pred HHHHHhcCCHHHHHHHhcccc
Q 034603 4 FEDMVLAGKLDEAEKYLSGFT 24 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l~ 24 (89)
+.-..-.|+|++|.+++..+.
T Consensus 10 i~~~~~~~~~~~a~~l~~~M~ 30 (50)
T PF13041_consen 10 ISGYCKAGKFEEALKLFKEMK 30 (50)
T ss_pred HHHHHHCcCHHHHHHHHHHHH
Confidence 344567889999999888774
No 98
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=35.19 E-value=1e+02 Score=27.49 Aligned_cols=51 Identities=10% Similarity=-0.095 Sum_probs=27.4
Q ss_pred HhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhc
Q 034603 8 VLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDI 64 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL 64 (89)
-..|+|++|+..+...-.++.+. . .+++.+-+ -++..|+..+|+..+++-+
T Consensus 55 ~~~Gd~~~A~~~l~~Al~~dP~n-~-~~~~~LA~----~yl~~g~~~~A~~~~~kAv 105 (987)
T PRK09782 55 QKNNDEATAIREFEYIHQQVPDN-I-PLTLYLAE----AYRHFGHDDRARLLLEDQL 105 (987)
T ss_pred HhCCCHHHHHHHHHHHHHhCCCC-H-HHHHHHHH----HHHHCCCHHHHHHHHHHHH
Confidence 34588888888777664443333 1 24433322 1344566666666666433
No 99
>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=34.92 E-value=28 Score=23.19 Aligned_cols=47 Identities=13% Similarity=0.147 Sum_probs=32.2
Q ss_pred ceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 34 KTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 34 ~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
.+.|=|.=..||+++.+|...+|-.++++--.-+.....+..+.|+.
T Consensus 28 ~lLyPiFvh~yL~lv~~~~~~~A~~F~~~f~~~~~~~~~~~i~~L~~ 74 (133)
T cd08044 28 QLLYPIFVHSYLDLVASGHLEEAKSFFERFSGDFEDSHSEDIKKLSS 74 (133)
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhHhhHHHHHHHHHHHHc
Confidence 36777888999999999999999999985433333222333444433
No 100
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=34.26 E-value=27 Score=20.44 Aligned_cols=19 Identities=26% Similarity=0.562 Sum_probs=14.6
Q ss_pred HHHHhcCCHHHHHHHhccc
Q 034603 5 EDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l 23 (89)
.-.+..|++++|.+|+..+
T Consensus 31 ~gllqlg~~~~a~eYi~~~ 49 (62)
T PF14689_consen 31 YGLLQLGKYEEAKEYIKEL 49 (62)
T ss_dssp HHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHCCCHHHHHHHHHHH
Confidence 3456789999999999887
No 101
>TIGR02917 PEP_TPR_lipo putative PEP-CTERM system TPR-repeat lipoprotein. This protein family occurs in strictly within a subset of Gram-negative bacterial species with the proposed PEP-CTERM/exosortase system, analogous to the LPXTG/sortase system common in Gram-positive bacteria. This protein occurs in a species if and only if a transmembrane histidine kinase (TIGR02916) and a DNA-binding response regulator (TIGR02915) also occur. The present of tetratricopeptide repeats (TPR) suggests protein-protein interaction, possibly for the regulation of PEP-CTERM protein expression, since many PEP-CTERM proteins in these genomes are preceded by a proposed DNA binding site for the response regulator.
Probab=33.97 E-value=1.4e+02 Score=23.76 Aligned_cols=12 Identities=8% Similarity=-0.288 Sum_probs=6.0
Q ss_pred cCCHHHHHHHHH
Q 034603 50 KHERVKALDILM 61 (89)
Q Consensus 50 ~~~~~~AL~~Lr 61 (89)
.|+..+|...++
T Consensus 138 ~~~~~~A~~~~~ 149 (899)
T TIGR02917 138 LGQLELAQKSYE 149 (899)
T ss_pred cCCHHHHHHHHH
Confidence 344555555554
No 102
>KOG2376 consensus Signal recognition particle, subunit Srp72 [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.51 E-value=50 Score=28.33 Aligned_cols=57 Identities=16% Similarity=0.131 Sum_probs=38.8
Q ss_pred hHHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcc
Q 034603 3 HFEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIK 65 (89)
Q Consensus 3 ~fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~ 65 (89)
.+-.++-+|++++|+..++.+-....++.. .+++|-+-++..+++.+||.+.++..+
T Consensus 18 ~ln~~~~~~e~e~a~k~~~Kil~~~pdd~~------a~~cKvValIq~~ky~~ALk~ikk~~~ 74 (652)
T KOG2376|consen 18 DLNRHGKNGEYEEAVKTANKILSIVPDDED------AIRCKVVALIQLDKYEDALKLIKKNGA 74 (652)
T ss_pred HHHHhccchHHHHHHHHHHHHHhcCCCcHh------hHhhhHhhhhhhhHHHHHHHHHHhcch
Confidence 455678899999999999998544323322 245677777777777777766665543
No 103
>PF04006 Mpp10: Mpp10 protein; InterPro: IPR007151 This family includes proteins related to Mpp10 (M phase phosphoprotein 10). The U3 small nucleolar ribonucleoprotein (snoRNP) is required for three cleavage events that generate the mature 18S rRNA from the pre-rRNA. In Saccharomyces cerevisiae, depletion of Mpp10, a U3 snoRNP-specific protein, halts 18S rRNA production and impairs cleavage at the three U3 snoRNP-dependent sites [].
Probab=33.22 E-value=46 Score=27.84 Aligned_cols=77 Identities=23% Similarity=0.328 Sum_probs=46.3
Q ss_pred hHHHHHhcCCHHHHHHHhcccc---------cccccccccceehhhhhhHHHHHHhcC--CHHHHHHHHHhhcccccCCC
Q 034603 3 HFEDMVLAGKLDEAEKYLSGFT---------QVHENMLSTKTYFELRRQKFLEALDKH--ERVKALDILMKDIKAFSTYN 71 (89)
Q Consensus 3 ~fr~~Vl~G~Wd~a~~~L~~l~---------~~~~~~~~~~~~FlI~kQKfLElL~~~--~~~~AL~~Lr~eL~pl~~~~ 71 (89)
-.++-|++|.||+++.-...-. .+++ ..+.+=.=-||.|.|+.....+ ...+.+.-...+|.-+
T Consensus 397 ~Ik~RI~~~~fDdv~r~~~~~~~~~~~~~~~el~~-~Ksk~sLaeiYe~ey~~~~~~~~~~~~~~~~~~~~ei~~l---- 471 (600)
T PF04006_consen 397 LIKQRIKDQNFDDVVRRRPPDEEPFEYKKRVELDD-EKSKKSLAEIYEQEYLKQTDGAFDEKDEKLDKEHEEIKEL---- 471 (600)
T ss_pred HHHHHHHhccccccccccCCCcccccccccccccc-ccccccHHHHHHHHHHHhhccccccccccchHHHHHHHHH----
Confidence 3688999999999986654221 1111 1221223479999999987652 3455666666666543
Q ss_pred HHHHHHHHhhh-cCCCC
Q 034603 72 EEVFKEASLLL-PLENF 87 (89)
Q Consensus 72 ~~~~~~l~~ll-tl~~~ 87 (89)
|+.||+=| +|.|+
T Consensus 472 ---~~~l~~kLDaLsn~ 485 (600)
T PF04006_consen 472 ---FKKLCYKLDALSNF 485 (600)
T ss_pred ---HHHHHHHhhccccC
Confidence 66666543 44444
No 104
>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=32.78 E-value=49 Score=23.63 Aligned_cols=55 Identities=9% Similarity=0.104 Sum_probs=35.7
Q ss_pred cCCHHHHHHHhcccc-----ccc-ccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcc
Q 034603 10 AGKLDEAEKYLSGFT-----QVH-ENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIK 65 (89)
Q Consensus 10 ~G~Wd~a~~~L~~l~-----~~~-~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~ 65 (89)
.-+|++-.+++..+. ... .+.+. .+...+..-+|.+++..|+..+|...|.+.|+
T Consensus 145 ~~~~~~~~~~~~~~R~~~k~~~~~~~~r~-~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~ 205 (205)
T TIGR01470 145 PPSLGDLATLAATWRDAVKKRLPNGAARR-RFWEKFFDGAFAERVLAGREEQAERVLATRLA 205 (205)
T ss_pred chhHHHHHHHHHHHHHHHHhhCCCHHHHH-HHHHHHhccHHHHHHHcCCHHHHHHHHHHhhC
Confidence 335666666665552 112 12222 34456667789999999999999999987653
No 105
>PF04097 Nic96: Nup93/Nic96; InterPro: IPR007231 Nup93/Nic96 is a component of the nuclear pore complex. It is required for the correct assembly of the nuclear pore complex []. In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1 []. The structure of Nic96 has revealed a mostly alpha helical structure [].; GO: 0006810 transport, 0005643 nuclear pore; PDB: 2QX5_B 2RFO_A.
Probab=32.44 E-value=30 Score=28.84 Aligned_cols=26 Identities=19% Similarity=0.337 Sum_probs=21.2
Q ss_pred hhHHHHHhcCCHHHHHHHhccccccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGFTQVH 27 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l~~~~ 27 (89)
..|+...-+|+|++|.+.+..+..++
T Consensus 510 ~~ff~~~~~g~~~~AL~~i~~L~liP 535 (613)
T PF04097_consen 510 AEFFDLYHAGQYEQALDIIEKLDLIP 535 (613)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHTT-S-
T ss_pred HHHHHHHHcCCHHHHHHHHHhCCCCC
Confidence 56899999999999999999998777
No 106
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=32.17 E-value=40 Score=16.66 Aligned_cols=18 Identities=11% Similarity=0.331 Sum_probs=10.7
Q ss_pred hhcccccCCCHHHHHHHHhhh
Q 034603 62 KDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 62 ~eL~pl~~~~~~~~~~l~~ll 82 (89)
..+-|.+ |+.|.+|+++-
T Consensus 5 dnmmPMS---Pddy~~l~~~V 22 (23)
T PF12162_consen 5 DNMMPMS---PDDYDELERMV 22 (23)
T ss_dssp TS---S----HHHHHHHHHHH
T ss_pred hcccCCC---HHHHHHHHHhh
Confidence 4555665 89999998763
No 107
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=31.77 E-value=64 Score=21.26 Aligned_cols=33 Identities=27% Similarity=0.221 Sum_probs=25.8
Q ss_pred ccccccceehh-----hhhhHHHHHHhcCCHHHHHHHHH
Q 034603 28 ENMLSTKTYFE-----LRRQKFLEALDKHERVKALDILM 61 (89)
Q Consensus 28 ~~~~~~~~~Fl-----I~kQKfLElL~~~~~~~AL~~Lr 61 (89)
...++ .+.|+ ++.+..-++++.|++..|+..|.
T Consensus 57 RG~~S-~L~~l~~~~~~~~~~~~~~l~~g~~~~a~~ll~ 94 (115)
T PF12793_consen 57 RGNRS-QLTFLKSPEELLEQQAEELLEQGKYEQALQLLD 94 (115)
T ss_pred CCCCC-eeEEeeCHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 34455 46664 67788889999999999999987
No 108
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=31.61 E-value=60 Score=20.20 Aligned_cols=18 Identities=17% Similarity=0.261 Sum_probs=14.5
Q ss_pred HHHHhcCCHHHHHHHHHh
Q 034603 45 LEALDKHERVKALDILMK 62 (89)
Q Consensus 45 LElL~~~~~~~AL~~Lr~ 62 (89)
-|++..|+..+|..++++
T Consensus 10 ~ey~~~~d~~ea~~~l~e 27 (113)
T PF02847_consen 10 MEYFSSGDVDEAVECLKE 27 (113)
T ss_dssp HHHHHHT-HHHHHHHHHH
T ss_pred HHHhcCCCHHHHHHHHHH
Confidence 478888999999999984
No 109
>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=31.35 E-value=37 Score=21.36 Aligned_cols=22 Identities=32% Similarity=0.492 Sum_probs=15.0
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+.|+.+|-.|+-++|.+.++..
T Consensus 32 Kk~~~ai~~~~~~~a~~~l~~a 53 (84)
T PF01649_consen 32 KKFREAIEAGDKEEAKELLRKA 53 (84)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHccChHHHHHHHHHH
Confidence 4677777788877777777654
No 110
>PF03704 BTAD: Bacterial transcriptional activator domain; InterPro: IPR005158 Found in the DNRI/REDD/AFSR family of regulators, this region of AFSR (P25941 from SWISSPROT) along with the C-terminal region is capable of independently directing actinorhodin production. It is important for the formation of secondary metabolites.; PDB: 2FF4_B 2FEZ_A.
Probab=31.32 E-value=1.2e+02 Score=19.46 Aligned_cols=35 Identities=26% Similarity=0.391 Sum_probs=24.4
Q ss_pred HHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 47 ALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 47 lL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
+++.|+..+|+..+++ +-.+.|+++..|..+-..+
T Consensus 72 ~~~~~~~~~a~~~~~~-~l~~dP~~E~~~~~lm~~~ 106 (146)
T PF03704_consen 72 LLEAGDYEEALRLLQR-ALALDPYDEEAYRLLMRAL 106 (146)
T ss_dssp HHHTT-HHHHHHHHHH-HHHHSTT-HHHHHHHHHHH
T ss_pred HHhccCHHHHHHHHHH-HHhcCCCCHHHHHHHHHHH
Confidence 4467999999999994 4445668888888775544
No 111
>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=31.11 E-value=44 Score=25.44 Aligned_cols=21 Identities=24% Similarity=0.338 Sum_probs=19.0
Q ss_pred hhHHHHHhcCCHHHHHHHhcc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSG 22 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~ 22 (89)
+..|++|.+|+.++|-++|..
T Consensus 147 T~IR~~l~~G~i~~A~~lLGr 167 (288)
T TIGR00083 147 SAIRQALKNGDLELANKLLGR 167 (288)
T ss_pred HHHHHHHHcCCHHHHHHhhhh
Confidence 578999999999999999974
No 112
>PF11817 Foie-gras_1: Foie gras liver health family 1; InterPro: IPR021773 Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease []. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first []. THe C terminus of this region contains TPR repeats.
Probab=30.99 E-value=75 Score=23.10 Aligned_cols=19 Identities=32% Similarity=0.333 Sum_probs=15.7
Q ss_pred HHHHhcCCHHHHHHHhccc
Q 034603 5 EDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l 23 (89)
+.....|+|++|.+++.++
T Consensus 186 ~ey~~~g~~~~A~~~l~~~ 204 (247)
T PF11817_consen 186 EEYFRLGDYDKALKLLEPA 204 (247)
T ss_pred HHHHHCCCHHHHHHHHHHH
Confidence 3456789999999999988
No 113
>PHA02608 67 prohead core protein; Provisional
Probab=30.94 E-value=47 Score=21.15 Aligned_cols=23 Identities=26% Similarity=0.432 Sum_probs=19.3
Q ss_pred ChhHHHHHhcCCHHHHHHHhccc
Q 034603 1 MKHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 1 ~~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
|..|-++|-+|+.-+|.+....+
T Consensus 1 Me~lIeAIKS~DLV~akK~F~~~ 23 (80)
T PHA02608 1 MEDLIEAIKSGDLVEAKKEFASI 23 (80)
T ss_pred ChHHHHHHhcCcHHHHHHHHHHH
Confidence 78889999999999888877654
No 114
>PRK12831 putative oxidoreductase; Provisional
Probab=30.84 E-value=54 Score=26.09 Aligned_cols=32 Identities=19% Similarity=0.196 Sum_probs=26.6
Q ss_pred eehhhhhhHHHHHHhcCCHHHHHHHHHhhcccc
Q 034603 35 TYFELRRQKFLEALDKHERVKALDILMKDIKAF 67 (89)
Q Consensus 35 ~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl 67 (89)
.--.+-=+.|+.++..|+..+|+.++++.. ||
T Consensus 54 CP~~~~i~~~~~~~~~~~~~~a~~~~~~~n-p~ 85 (464)
T PRK12831 54 CPVSINIPGFISKLKEGDFEEAAKIIAKYN-AL 85 (464)
T ss_pred CCCCCCHHHHHHHHHCCCHHHHHHHHHHhC-Cc
Confidence 455666789999999999999999999654 65
No 115
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=30.54 E-value=84 Score=22.14 Aligned_cols=22 Identities=9% Similarity=-0.026 Sum_probs=15.3
Q ss_pred hcCCHHHHHHHhcccccccccc
Q 034603 9 LAGKLDEAEKYLSGFTQVHENM 30 (89)
Q Consensus 9 l~G~Wd~a~~~L~~l~~~~~~~ 30 (89)
..|++++|+++..-+..+|...
T Consensus 47 ~~G~l~~A~~~f~~L~~~Dp~~ 68 (157)
T PRK15363 47 EVKEFAGAARLFQLLTIYDAWS 68 (157)
T ss_pred HCCCHHHHHHHHHHHHHhCccc
Confidence 4688888888887776666433
No 116
>PRK00239 rpsT 30S ribosomal protein S20; Reviewed
Probab=30.37 E-value=44 Score=21.27 Aligned_cols=22 Identities=32% Similarity=0.392 Sum_probs=16.2
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+.|+.+|-.|+-++|...+...
T Consensus 33 Kk~~~ai~~~~~~~a~~~~~~a 54 (88)
T PRK00239 33 KKVEAAIAAGDKEAAEEALKAA 54 (88)
T ss_pred HHHHHHHHcCCHHHHHHHHHHH
Confidence 4677778888877777777654
No 117
>COG4105 ComL DNA uptake lipoprotein [General function prediction only]
Probab=29.95 E-value=1.1e+02 Score=23.29 Aligned_cols=56 Identities=23% Similarity=0.289 Sum_probs=37.7
Q ss_pred HHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHH----hcCCHHHHHHHHHhhccccc
Q 034603 6 DMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEAL----DKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL----~~~~~~~AL~~Lr~eL~pl~ 68 (89)
..+.+|+|++|++.+..+.... +.+. ..+|--|++. ..++..+|+..+-.=+.-.+
T Consensus 43 ~~L~~gn~~~A~~~fe~l~~~~--p~s~-----~~~qa~l~l~yA~Yk~~~y~~A~~~~drFi~lyP 102 (254)
T COG4105 43 TELQKGNYEEAIKYFEALDSRH--PFSP-----YSEQAQLDLAYAYYKNGEYDLALAYIDRFIRLYP 102 (254)
T ss_pred HHHhcCCHHHHHHHHHHHHHcC--CCCc-----ccHHHHHHHHHHHHhcccHHHHHHHHHHHHHhCC
Confidence 4678999999999999986333 2221 1256666655 34888999988775555443
No 118
>PRK10866 outer membrane biogenesis protein BamD; Provisional
Probab=29.71 E-value=69 Score=23.35 Aligned_cols=59 Identities=12% Similarity=0.060 Sum_probs=35.5
Q ss_pred HHHHhcCCHHHHHHHhcccccccc-cccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccc
Q 034603 5 EDMVLAGKLDEAEKYLSGFTQVHE-NMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAF 67 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l~~~~~-~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl 67 (89)
...+.+|+|++|++.+..+..... +.....+.+.+-. -+...++..+|+...++=+.-.
T Consensus 40 ~~~~~~g~y~~Ai~~f~~l~~~yP~s~~a~~a~l~la~----ayy~~~~y~~A~~~~e~fi~~~ 99 (243)
T PRK10866 40 QQKLQDGNWKQAITQLEALDNRYPFGPYSQQVQLDLIY----AYYKNADLPLAQAAIDRFIRLN 99 (243)
T ss_pred HHHHHCCCHHHHHHHHHHHHHhCCCChHHHHHHHHHHH----HHHhcCCHHHHHHHHHHHHHhC
Confidence 356778999999999999854332 2221112222211 1234688999998888555443
No 119
>PF05400 FliT: Flagellar protein FliT; InterPro: IPR008622 This entry represents the bacterial flagellar FliT family of dual-function proteins. Together with FlgN, FliT has been proposed to act as a substrate-specific export chaperone, facilitating the incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum []. FliT has also been shown to act as a transcriptional regulator in Salmonella typhimurium [].; GO: 0019861 flagellum; PDB: 3A7M_A 3H3M_B 3NKZ_C 2G42_A 2FZT_B.
Probab=29.15 E-value=59 Score=18.98 Aligned_cols=18 Identities=28% Similarity=0.352 Sum_probs=13.1
Q ss_pred HHHHhcCCHHHHHHHhcc
Q 034603 5 EDMVLAGKLDEAEKYLSG 22 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~ 22 (89)
..++-.|+|++....+..
T Consensus 2 l~aa~~~dWe~l~~l~~~ 19 (84)
T PF05400_consen 2 LEAAEAGDWEELEELLDE 19 (84)
T ss_dssp HHHHHCT-HHHHHHHHHH
T ss_pred hHHHhhCcHHHHHHHHHH
Confidence 467789999998887764
No 120
>COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]
Probab=28.65 E-value=48 Score=21.37 Aligned_cols=22 Identities=27% Similarity=0.288 Sum_probs=17.1
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+.|+.+|..||-+.|...+...
T Consensus 33 Kk~~~ai~~gd~~~A~~~l~~a 54 (88)
T COG0268 33 KKVEAAIEAGDKEAAKAALKEA 54 (88)
T ss_pred HHHHHHHHcCCHHHHHHHHHHH
Confidence 5678888888888888877654
No 121
>PF14854 LURAP: Leucine rich adaptor protein
Probab=28.64 E-value=56 Score=22.33 Aligned_cols=32 Identities=19% Similarity=0.161 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHhhcccccCCCHHHHHHHHhhhcCC
Q 034603 51 HERVKALDILMKDIKAFSTYNEEVFKEASLLLPLE 85 (89)
Q Consensus 51 ~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~lltl~ 85 (89)
.....++.+||+|+.-|.. --.+-|++|++++
T Consensus 18 ~~Ld~kl~~Lr~EM~~LRq---lDvkLL~QL~~vN 49 (121)
T PF14854_consen 18 SNLDAKLAFLRKEMAGLRQ---LDVKLLQQLLAVN 49 (121)
T ss_pred cCHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH
Confidence 3456788888888887763 2355666666553
No 122
>PTZ00196 60S ribosomal protein L36; Provisional
Probab=28.54 E-value=77 Score=20.85 Aligned_cols=33 Identities=18% Similarity=0.230 Sum_probs=28.0
Q ss_pred ehhhhhhHHHHHHhcCCHHHHHHHHHhhccccc
Q 034603 36 YFELRRQKFLEALDKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 36 ~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~ 68 (89)
=|-=|+..-+|||..|....||.++.+.|--+.
T Consensus 47 GfaPYErr~mELLkv~kdKrAlKfaKkRlGth~ 79 (98)
T PTZ00196 47 GFSPYERRMIELLKVGKDKRALKYAKKRLGTHK 79 (98)
T ss_pred cccHHHHHHHHHHHhcchHHHHHHHHHHhhhHH
Confidence 366688999999999999999999999886543
No 123
>COG1410 MetH Methionine synthase I, cobalamin-binding domain [Amino acid transport and metabolism]
Probab=28.53 E-value=47 Score=29.32 Aligned_cols=20 Identities=30% Similarity=0.461 Sum_probs=17.8
Q ss_pred hhHHHHHhcCCHHHHHHHhc
Q 034603 2 KHFEDMVLAGKLDEAEKYLS 21 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~ 21 (89)
+.||..|..|||++|.+.-.
T Consensus 42 kkf~~li~~~~y~~~l~iAr 61 (842)
T COG1410 42 KKFRRLIIAEDYDEALDVAR 61 (842)
T ss_pred HHHHHHHHcccHHHHHHHHH
Confidence 57999999999999998764
No 124
>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=28.36 E-value=64 Score=22.32 Aligned_cols=26 Identities=12% Similarity=0.263 Sum_probs=21.8
Q ss_pred hhHHHHHHhcCCHHHHHHHHHhhccc
Q 034603 41 RQKFLEALDKHERVKALDILMKDIKA 66 (89)
Q Consensus 41 kQKfLElL~~~~~~~AL~~Lr~eL~p 66 (89)
-++.++++..||...|...++..+.-
T Consensus 183 H~~i~~ai~~~d~~~A~~~~~~Hl~~ 208 (212)
T TIGR03338 183 HRAIVDAIASGDAERAGALMRAHVAA 208 (212)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 45579999999999999999988753
No 125
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=28.35 E-value=50 Score=22.01 Aligned_cols=16 Identities=13% Similarity=-0.070 Sum_probs=13.6
Q ss_pred HHHHhcCCHHHHHHHh
Q 034603 5 EDMVLAGKLDEAEKYL 20 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L 20 (89)
+++|+++||..-+++=
T Consensus 50 ~~AV~~rD~~~Li~lG 65 (106)
T cd07921 50 KQAVLDRDWLRLLELG 65 (106)
T ss_pred HHHHHhCCHHHHHHhc
Confidence 7899999999887753
No 126
>PLN02789 farnesyltranstransferase
Probab=28.23 E-value=1.3e+02 Score=23.12 Aligned_cols=71 Identities=17% Similarity=0.130 Sum_probs=39.4
Q ss_pred ChhHHHHHh-cCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHH
Q 034603 1 MKHFEDMVL-AGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKE 77 (89)
Q Consensus 1 ~~~fr~~Vl-~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~ 77 (89)
|.+||..+. .|..++|.......-.++... ...+..+...|+.|. .+..+||.++.+-+. ..+.|...++.
T Consensus 40 ~~~~ra~l~~~e~serAL~lt~~aI~lnP~~----ytaW~~R~~iL~~L~-~~l~eeL~~~~~~i~-~npknyqaW~~ 111 (320)
T PLN02789 40 MDYFRAVYASDERSPRALDLTADVIRLNPGN----YTVWHFRRLCLEALD-ADLEEELDFAEDVAE-DNPKNYQIWHH 111 (320)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHCchh----HHHHHHHHHHHHHcc-hhHHHHHHHHHHHHH-HCCcchHHhHH
Confidence 456777776 446777777777654333222 223445556666662 246788888774333 23344434443
No 127
>TIGR01318 gltD_gamma_fam glutamate synthase small subunit family protein, proteobacterial. This model represents one of three built for the NADPH-dependent or NADH-dependent glutamate synthase (EC 1.4.1.13 and 1.4.1.14, respectively) small subunit and homologs. TIGR01317 describes the small subunit (or equivalent region from longer forms) in eukaryotes, Gram-positive bacteria, and some other lineages, both NADH and NADPH-dependent. TIGR01316 describes a protein of similar length, from Archaea and a number of bacterial lineages, that forms glutamate synthase homotetramers without a large subunit. This model describes both glutatate synthase small subunit and closely related paralogs of unknown function from a number of gamma and alpha subdivision Proteobacteria, including E. coli.
Probab=27.96 E-value=62 Score=25.74 Aligned_cols=33 Identities=6% Similarity=0.080 Sum_probs=27.0
Q ss_pred eehhhhhhHHHHHHhcCCHHHHHHHHHhhccccc
Q 034603 35 TYFELRRQKFLEALDKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 35 ~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~ 68 (89)
.-..+==++|+.++..|+..+|+.++++. .||+
T Consensus 54 CP~~~~~~~~~~~~~~g~~~~a~~~~~~~-np~~ 86 (467)
T TIGR01318 54 CPVHNAIPQWLQLVQEGRIDEAAELSHQT-NTLP 86 (467)
T ss_pred CCCCCcHHHHHHHHHCCCHHHHHHHHHHh-CCch
Confidence 45566678999999999999999999954 4764
No 128
>PRK12771 putative glutamate synthase (NADPH) small subunit; Provisional
Probab=27.68 E-value=64 Score=26.20 Aligned_cols=63 Identities=14% Similarity=0.074 Sum_probs=41.1
Q ss_pred ChhHHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhccccc
Q 034603 1 MKHFEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 1 ~~~fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~ 68 (89)
|++|+..+.+|.|+-.. .........-.. ..--.+--++|+.++..|+..+|+.++++.. ||.
T Consensus 23 ~~~~~~~~~~~~~~~~~---~~~~~~~~~C~~-~CP~~~~i~~~~~~~~~g~~~~a~~~~~~~n-p~~ 85 (564)
T PRK12771 23 PDGFSDEIATGPWRHKC---PVYVDQTPPCNA-ACPAGEDIRGWLALVRGGDYEYAWRRLTKDN-PFP 85 (564)
T ss_pred cccchHhhhcccccccc---ccccCCCCcccc-CCCCCCcHHHHHHHHHCCCHHHHHHHHHHhC-Ccc
Confidence 46788888888885332 111111101112 3555667799999999999999999999554 764
No 129
>PRK12370 invasion protein regulator; Provisional
Probab=27.47 E-value=1.9e+02 Score=23.46 Aligned_cols=51 Identities=4% Similarity=-0.076 Sum_probs=29.3
Q ss_pred HhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhc
Q 034603 8 VLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDI 64 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL 64 (89)
...|+|++|+..+...-.++.+... +.+.+ =.=+...|+..+|+..+++-+
T Consensus 349 ~~~g~~~~A~~~~~~Al~l~P~~~~--a~~~l----g~~l~~~G~~~eAi~~~~~Al 399 (553)
T PRK12370 349 TIHSEYIVGSLLFKQANLLSPISAD--IKYYY----GWNLFMAGQLEEALQTINECL 399 (553)
T ss_pred HHccCHHHHHHHHHHHHHhCCCCHH--HHHHH----HHHHHHCCCHHHHHHHHHHHH
Confidence 3568888888888775444333211 22221 111344588888888888643
No 130
>TIGR00029 S20 ribosomal protein S20. This family consists of bacterial (and chloroplast) examples of the bacteria ribosomal small subunit protein S20.
Probab=26.73 E-value=55 Score=20.83 Aligned_cols=22 Identities=23% Similarity=0.267 Sum_probs=15.7
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+.|+.+|-.|+-++|.+.+...
T Consensus 33 Kk~~~ai~~~d~~~a~~~l~~a 54 (87)
T TIGR00029 33 KKVYAAIAAGDKDKAQEAFKEA 54 (87)
T ss_pred HHHHHHHHCCCHHHHHHHHHHH
Confidence 4677777778877777777644
No 131
>PRK10316 hypothetical protein; Provisional
Probab=26.65 E-value=96 Score=23.05 Aligned_cols=75 Identities=9% Similarity=0.120 Sum_probs=45.9
Q ss_pred HHHHHhcCCHHHHHHHhcccc-cccccccc--------------------cceehhhhh------------hHHHHHHhc
Q 034603 4 FEDMVLAGKLDEAEKYLSGFT-QVHENMLS--------------------TKTYFELRR------------QKFLEALDK 50 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l~-~~~~~~~~--------------------~~~~FlI~k------------QKfLElL~~ 50 (89)
=|.+|-+|+-+.|..++..-. .++..... -...|-+-+ .+==+.|..
T Consensus 61 AR~Alf~G~~~~Ak~ll~~A~~~l~~a~~D~~~f~ka~~~~p~~~d~wlPVd~e~~l~ed~~~tp~K~~Ava~AN~~Lk~ 140 (209)
T PRK10316 61 ARLALFHGDPEKAKELTNQASALLSDDSTDWAKFAKPDKKAPVNGDQYIVINASVGISEDYVATPEKEAAIKIANEKMAK 140 (209)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHHHhhhccHHHHHhccccCCCCCCceEEeCCeEEecccccCChhHHHHHHHHHHHHHC
Confidence 378999999999999886431 11111000 001122222 233478899
Q ss_pred CCHHHHHHHHH---------hhcccccCCCHHHHHHH
Q 034603 51 HERVKALDILM---------KDIKAFSTYNEEVFKEA 78 (89)
Q Consensus 51 ~~~~~AL~~Lr---------~eL~pl~~~~~~~~~~l 78 (89)
|+..+|++.|+ ..+.||.+...++++-.
T Consensus 141 Gd~~~A~e~LklAgvdv~~~~al~PL~qT~~~V~~A~ 177 (209)
T PRK10316 141 GDKKGAMEELRLAGVGVMENQYLMPLKQTRNAVADAQ 177 (209)
T ss_pred CCHHHHHHHHHHcCcchhhHhHhcCchhhHHHHHHHH
Confidence 99999999998 56788876655544433
No 132
>PRK10564 maltose regulon periplasmic protein; Provisional
Probab=26.39 E-value=56 Score=25.53 Aligned_cols=25 Identities=24% Similarity=0.312 Sum_probs=21.2
Q ss_pred hHHHHHhcCCHHHHHHHhccccccc
Q 034603 3 HFEDMVLAGKLDEAEKYLSGFTQVH 27 (89)
Q Consensus 3 ~fr~~Vl~G~Wd~a~~~L~~l~~~~ 27 (89)
..+++|-+||.++|.++++.-+.+.
T Consensus 263 aI~~AVk~gDi~KAL~LldEAe~LG 287 (303)
T PRK10564 263 AIKQAVKKGDVDKALKLLDEAERLG 287 (303)
T ss_pred HHHHHHHcCCHHHHHHHHHHHHHhC
Confidence 4688999999999999999876554
No 133
>PF03008 DUF234: Archaea bacterial proteins of unknown function; InterPro: IPR004256 This represents a C-terminal domain of unknown function, usually fused to a prokaryotic putative DEXX-box ATPase domain (IPR011579 from INTERPRO) [].
Probab=26.28 E-value=1.1e+02 Score=19.26 Aligned_cols=34 Identities=6% Similarity=0.131 Sum_probs=25.2
Q ss_pred HHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 44 FLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 44 fLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
+...|+.|....+++..++++..+. ...|.++|+
T Consensus 8 ~~s~ie~g~~~~~~~~i~~~l~~y~---g~~fE~i~r 41 (100)
T PF03008_consen 8 NRSLIERGRGEAVYEKIKPELNQYM---GFAFEEICR 41 (100)
T ss_pred cHHHHHCCCHHHHHHHHHHHHHHHh---hHHHHHHHH
Confidence 4577888998888888887775543 566777765
No 134
>PF07743 HSCB_C: HSCB C-terminal oligomerisation domain; InterPro: IPR009073 This entry represents the C-terminal oligomerisation domain found in HscB (heat shock cognate protein B), which is also known as HSC20 (20K heat shock cognate protein). HscB acts as a co-chaperone to regulate the ATPase activity and peptide-binding specificity of the molecular chaperone HscA, also known as HSC66 (HSP70 class). HscB proteins contain two domains, an N-terminal J-domain, which is involved in interactions with HscA, connected by a short loop to the C-terminal oligomerisation domain; the two domains make contact through a hydrophobic interface. The core of the oligomerisation domain is thought to bind and target proteins to HscA and consists of an open, three-helical bundle []. HscB, along with HscA, has been shown to play a role in the biogenesis of iron-sulphur proteins.; GO: 0006457 protein folding; PDB: 1FPO_C 3BVO_B 3HHO_A 3UO2_B 3UO3_B.
Probab=26.06 E-value=62 Score=19.26 Aligned_cols=21 Identities=19% Similarity=0.243 Sum_probs=15.1
Q ss_pred hHHHHHhcCCHHHHHHHhccc
Q 034603 3 HFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 3 ~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
.+..+.-.++|+.|-..+..+
T Consensus 46 ~l~~~f~~~d~~~A~~~~~kL 66 (78)
T PF07743_consen 46 ELAEAFDAKDWEEAKEALRKL 66 (78)
T ss_dssp HHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHccCcHHHHHHHHHHH
Confidence 466677788888888887766
No 135
>TIGR01316 gltA glutamate synthase (NADPH), homotetrameric. This protein is homologous to the small subunit of NADPH and NADH forms of glutamate synthase as found in eukaryotes and some bacteria. This protein is found in numerous species having no homolog of the glutamate synthase large subunit. The prototype of the family, from Pyrococcus sp. KOD1, was shown to be active as a homotetramer and to require NADPH.
Probab=25.96 E-value=75 Score=25.05 Aligned_cols=32 Identities=13% Similarity=0.224 Sum_probs=26.3
Q ss_pred eehhhhhhHHHHHHhcCCHHHHHHHHHhhcccc
Q 034603 35 TYFELRRQKFLEALDKHERVKALDILMKDIKAF 67 (89)
Q Consensus 35 ~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl 67 (89)
.--.+-=++|+.++..|+..+|+.++++. .||
T Consensus 42 CP~~~~i~~~~~~~~~g~~~~A~~~~~~~-~p~ 73 (449)
T TIGR01316 42 CPVHVPIPEFIAKIQEGDFKGAVDIIKTT-SLL 73 (449)
T ss_pred CCCCCCHHHHHHHHHCCCHHHHHHHHHHh-CCh
Confidence 55566778999999999999999999943 454
No 136
>PF08544 GHMP_kinases_C: GHMP kinases C terminal ; InterPro: IPR013750 This domain is found in homoserine kinases (2.7.1.39 from EC), galactokinases (2.7.1.6 from EC) and mevalonate kinases (2.7.1.36 from EC). These kinases make up the GHMP kinase superfamily of ATP-dependent enzymes []. These enzymes are involved in the biosynthesis of isoprenes and amino acids as well as in carbohydrate metabolism. The C-terminal domain of homoserine kinase has a central alpha-beta plait fold and an insertion of four helices, which, together with the N-terminal fold, create a novel nucleotide binding fold [].; PDB: 2R3V_C 4EMD_A 4DXL_A 4ED4_A 2GS8_A 1K47_E 3GON_A 3K17_B 1PIE_A 2AJ4_A ....
Probab=25.62 E-value=75 Score=18.43 Aligned_cols=20 Identities=10% Similarity=0.157 Sum_probs=15.8
Q ss_pred HHHHHhcCCHHHHHHHhccc
Q 034603 4 FEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+++++.+|||+..-+.+...
T Consensus 1 m~~al~~~d~~~~~~~~~~~ 20 (85)
T PF08544_consen 1 MIKALAEGDLELLGELMNEN 20 (85)
T ss_dssp HHHHHHTTCHHHHHHHHHHH
T ss_pred CHHHHHCcCHHHHHHHHHHh
Confidence 36788899999888888754
No 137
>cd02069 methionine_synthase_B12_BD B12 binding domain of methionine synthase. This domain binds methylcobalamin, which it uses as an intermediate methyl carrier from methyltetrahydrofolate (CH3H4folate) to homocysteine (Hcy).
Probab=25.61 E-value=61 Score=23.39 Aligned_cols=22 Identities=14% Similarity=0.170 Sum_probs=19.8
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+.|.++|++||.+++.+.++..
T Consensus 3 ~~l~~Al~~~D~~~~~~~l~~a 24 (213)
T cd02069 3 ERLKHALVKGIRDGIEEDTEEA 24 (213)
T ss_pred HHHHHHHHhCCHHHHHHHHHHH
Confidence 4689999999999999999865
No 138
>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=25.38 E-value=2.1e+02 Score=23.64 Aligned_cols=67 Identities=21% Similarity=0.209 Sum_probs=46.5
Q ss_pred hcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 9 LAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 9 l~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
-.|+.++|.+.|..-. ..... +..+.-.+-.|+ +.-|+..+|..+.| +|=-.+|+|-+.|+.+...+
T Consensus 16 e~g~~~~AL~~L~~~~---~~I~D-k~~~~E~rA~ll--~kLg~~~eA~~~y~-~Li~rNPdn~~Yy~~L~~~~ 82 (517)
T PF12569_consen 16 EAGDYEEALEHLEKNE---KQILD-KLAVLEKRAELL--LKLGRKEEAEKIYR-ELIDRNPDNYDYYRGLEEAL 82 (517)
T ss_pred HCCCHHHHHHHHHhhh---hhCCC-HHHHHHHHHHHH--HHcCCHHHHHHHHH-HHHHHCCCcHHHHHHHHHHH
Confidence 3699999999997652 11122 344444555554 34478899999999 55556889999999888777
No 139
>PRK12814 putative NADPH-dependent glutamate synthase small subunit; Provisional
Probab=25.13 E-value=76 Score=26.53 Aligned_cols=33 Identities=15% Similarity=0.246 Sum_probs=26.2
Q ss_pred eehhhhhhHHHHHHhcCCHHHHHHHHHhhccccc
Q 034603 35 TYFELRRQKFLEALDKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 35 ~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~ 68 (89)
.--.+==+.|+.++..|+..+|+.++++.. ||.
T Consensus 108 CP~~~~~~~~~~~~~~g~~~~a~~~~~~~~-p~p 140 (652)
T PRK12814 108 CPAGCNIPGFIAAIARGDDREAIRIIKETI-PLP 140 (652)
T ss_pred CCCCCcHHHHHHHHHCCCHHHHHHHHHhhC-Ccc
Confidence 334455689999999999999999999554 663
No 140
>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=25.10 E-value=1.2e+02 Score=19.60 Aligned_cols=19 Identities=26% Similarity=0.492 Sum_probs=13.6
Q ss_pred HHHHHHhcCCHHHHHHHHH
Q 034603 43 KFLEALDKHERVKALDILM 61 (89)
Q Consensus 43 KfLElL~~~~~~~AL~~Lr 61 (89)
++++.+-.||..+|+..++
T Consensus 20 ~l~~ai~~~d~~~~l~~~~ 38 (143)
T PF12169_consen 20 ELLDAILEGDAAEALELLN 38 (143)
T ss_dssp HHHHHHHTT-HHHHHHHHH
T ss_pred HHHHHHHcCCHHHHHHHHH
Confidence 4567777788888888887
No 141
>PRK14574 hmsH outer membrane protein; Provisional
Probab=24.74 E-value=3.2e+02 Score=24.00 Aligned_cols=29 Identities=14% Similarity=0.242 Sum_probs=19.9
Q ss_pred hcCCHHHHHHHHHhhcccccCCCHHHHHHH
Q 034603 49 DKHERVKALDILMKDIKAFSTYNEEVFKEA 78 (89)
Q Consensus 49 ~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l 78 (89)
..|+..+|+.++++=++- .+.|++.+..+
T Consensus 114 ~~gdyd~Aiely~kaL~~-dP~n~~~l~gL 142 (822)
T PRK14574 114 NEKRWDQALALWQSSLKK-DPTNPDLISGM 142 (822)
T ss_pred HcCCHHHHHHHHHHHHhh-CCCCHHHHHHH
Confidence 558888888888854443 55667777654
No 142
>COG3483 TDO2 Tryptophan 2,3-dioxygenase (vermilion) [Amino acid transport and metabolism]
Probab=24.61 E-value=2.3e+02 Score=21.61 Aligned_cols=49 Identities=18% Similarity=0.257 Sum_probs=30.0
Q ss_pred CCHHHHHHHhcccccccccccccceehhhhhhHH--------------HHHHhcCCHHHHHHHHH
Q 034603 11 GKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKF--------------LEALDKHERVKALDILM 61 (89)
Q Consensus 11 G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKf--------------LElL~~~~~~~AL~~Lr 61 (89)
||+-..++.|+.=+.+++. .+ ++.|.|.-|-+ .+++..|++.-|+..|+
T Consensus 7 ~dYl~ldell~aq~p~s~~-hd-E~LFIv~Hqt~ElW~klilhEl~aA~~llr~~~~~pa~kmL~ 69 (262)
T COG3483 7 GDYLKLDELLSAQGPLSDD-HD-EMLFIVQHQTSELWMKLILHELRAARDLLRADDLPPALKMLA 69 (262)
T ss_pred HHHHHHHHHHHccCCCCCC-cc-cceeeehhHHHHHHHHHHHHHHHHHHHHHhcCCCcHHHHHHH
Confidence 5666677777766555422 23 79999888765 34556666555555444
No 143
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=23.95 E-value=2.2e+02 Score=18.73 Aligned_cols=69 Identities=13% Similarity=0.155 Sum_probs=37.2
Q ss_pred HhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHh
Q 034603 8 VLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASL 80 (89)
Q Consensus 8 Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ 80 (89)
...|+|++|+..+...-.+..++... .. ++.--=+=+...|+..+|+..+++-+..- +.+.+.+..++.
T Consensus 46 ~~~g~~~~A~~~~~~al~l~~~~~~~-~~--~~~~lg~~~~~~g~~~eA~~~~~~Al~~~-~~~~~~~~~la~ 114 (168)
T CHL00033 46 QSEGEYAEALQNYYEAMRLEIDPYDR-SY--ILYNIGLIHTSNGEHTKALEYYFQALERN-PFLPQALNNMAV 114 (168)
T ss_pred HHcCCHHHHHHHHHHHHhccccchhh-HH--HHHHHHHHHHHcCCHHHHHHHHHHHHHhC-cCcHHHHHHHHH
Confidence 45699999999888663232222110 00 11111122334588999999998766542 333444444443
No 144
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 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. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=23.74 E-value=80 Score=15.10 Aligned_cols=19 Identities=11% Similarity=0.198 Sum_probs=11.4
Q ss_pred HHhcCCHHHHHHHHHhhcc
Q 034603 47 ALDKHERVKALDILMKDIK 65 (89)
Q Consensus 47 lL~~~~~~~AL~~Lr~eL~ 65 (89)
+...|+..+|+..+++-|+
T Consensus 11 ~~~~~~~~~A~~~~~~al~ 29 (34)
T PF00515_consen 11 YFQLGDYEEALEYYQRALE 29 (34)
T ss_dssp HHHTT-HHHHHHHHHHHHH
T ss_pred HHHhCCchHHHHHHHHHHH
Confidence 3455777777777775443
No 145
>PRK11447 cellulose synthase subunit BcsC; Provisional
Probab=23.41 E-value=2.3e+02 Score=25.28 Aligned_cols=63 Identities=11% Similarity=0.036 Sum_probs=44.9
Q ss_pred HHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHH
Q 034603 5 EDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEV 74 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~ 74 (89)
|-..-.|+.|.|.+.|.++-.++.++.. + +.....=++..|+..+|...++ .+..+.+.+++.
T Consensus 36 ~~~~~~~~~d~a~~~l~kl~~~~p~~p~--~----~~~~~~~~l~~g~~~~A~~~l~-~l~~~~P~~~~~ 98 (1157)
T PRK11447 36 RLGEATHREDLVRQSLYRLELIDPNNPD--V----IAARFRLLLRQGDSDGAQKLLD-RLSQLAPDSNAY 98 (1157)
T ss_pred HHHHhhCChHHHHHHHHHHHccCCCCHH--H----HHHHHHHHHhCCCHHHHHHHHH-HHHhhCCCChHH
Confidence 3344578999999999999777655533 2 2334445588999999999999 666666666653
No 146
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=23.32 E-value=87 Score=14.84 Aligned_cols=18 Identities=17% Similarity=0.126 Sum_probs=12.9
Q ss_pred HHhcCCHHHHHHHHHhhc
Q 034603 47 ALDKHERVKALDILMKDI 64 (89)
Q Consensus 47 lL~~~~~~~AL~~Lr~eL 64 (89)
+...|+..+|+..+++-+
T Consensus 11 y~~~~~~~~A~~~~~~a~ 28 (34)
T PF13181_consen 11 YEQLGDYEEALEYFEKAL 28 (34)
T ss_dssp HHHTTSHHHHHHHHHHHH
T ss_pred HHHcCCHHHHHHHHHHHH
Confidence 345688888888887644
No 147
>PF04053 Coatomer_WDAD: Coatomer WD associated region ; InterPro: IPR006692 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the WD-associated region found in coatomer subunits alpha, beta and beta' subunits. The alpha-subunit (RET1P) of the coatomer complex in Saccharomyces cerevisiae (Baker's yeast), participates in membrane transport between the endoplasmic reticulum and Golgi apparatus. The protein contains six WD-40 repeat motifs in its N-terminal region []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030117 membrane coat; PDB: 3MKQ_B.
Probab=23.31 E-value=2.3e+02 Score=22.84 Aligned_cols=49 Identities=24% Similarity=0.080 Sum_probs=40.2
Q ss_pred hhHHHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHH
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILM 61 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr 61 (89)
.+|.=+|-.|+.+.|.+....+. + -..|+|=-=++|..|+..-|-.|+.
T Consensus 323 ~rFeLAl~lg~L~~A~~~a~~~~-----~------~~~W~~Lg~~AL~~g~~~lAe~c~~ 371 (443)
T PF04053_consen 323 HRFELALQLGNLDIALEIAKELD-----D------PEKWKQLGDEALRQGNIELAEECYQ 371 (443)
T ss_dssp HHHHHHHHCT-HHHHHHHCCCCS-----T------HHHHHHHHHHHHHTTBHHHHHHHHH
T ss_pred HHhHHHHhcCCHHHHHHHHHhcC-----c------HHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 46888999999999999998873 1 1278888889999999999999988
No 148
>PF08463 EcoEI_R_C: EcoEI R protein C-terminal; InterPro: IPR013670 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the C-terminal domain found in both the R subunit of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity [, ]. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=23.10 E-value=1.6e+02 Score=19.74 Aligned_cols=40 Identities=25% Similarity=0.365 Sum_probs=28.2
Q ss_pred hhhhHHHHHHhcC-CHHHHHHHHHhhcccccCCCHHHHHHHHhhh
Q 034603 39 LRRQKFLEALDKH-ERVKALDILMKDIKAFSTYNEEVFKEASLLL 82 (89)
Q Consensus 39 I~kQKfLElL~~~-~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~ll 82 (89)
-+.+++-++|... +...||..+++. .|+. ....++|...+
T Consensus 5 ~y~e~~~~~l~~~~~~~~al~~i~~~-~~~~---~~~L~eL~~~l 45 (164)
T PF08463_consen 5 DYRERFRKYLREHFDDIEALRKIWSN-PPLT---EADLKELEEKL 45 (164)
T ss_pred HHHHHHHHHHHHHhcCHHHHHHHHcC-cccC---HHHHHHHHHhC
Confidence 3566677777766 577899999888 5554 66777776655
No 149
>PRK11749 dihydropyrimidine dehydrogenase subunit A; Provisional
Probab=23.10 E-value=90 Score=24.50 Aligned_cols=32 Identities=6% Similarity=0.163 Sum_probs=25.9
Q ss_pred ehhhhhhHHHHHHhcCCHHHHHHHHHhhccccc
Q 034603 36 YFELRRQKFLEALDKHERVKALDILMKDIKAFS 68 (89)
Q Consensus 36 ~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~ 68 (89)
--.+-=+.|+.++..|+..+|+.++++.. ||.
T Consensus 55 p~~~~~~~~~~~~~~~~~~~a~~~~~~~~-p~~ 86 (457)
T PRK11749 55 PVSIDIPEFIRLIAEGNLKGAAETILETN-PLP 86 (457)
T ss_pred CCcCCHHHHHHHHHCCCHHHHHHHHHHhC-Cch
Confidence 33455689999999999999999999554 764
No 150
>PRK09782 bacteriophage N4 receptor, outer membrane subunit; Provisional
Probab=23.10 E-value=1.6e+02 Score=26.26 Aligned_cols=66 Identities=20% Similarity=0.105 Sum_probs=48.5
Q ss_pred HHHHhcCCHHHHHHHhcccccccccccccceehhhhhhHHHHHHhcCCHHHHHHHHHhhcccccCCCHHHHHHHHhh
Q 034603 5 EDMVLAGKLDEAEKYLSGFTQVHENMLSTKTYFELRRQKFLEALDKHERVKALDILMKDIKAFSTYNEEVFKEASLL 81 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l~~~~~~~~~~~~~FlI~kQKfLElL~~~~~~~AL~~Lr~eL~pl~~~~~~~~~~l~~l 81 (89)
+-.+..|+.++|+.++......+.++ ..+... |-.+ ++..+|..+.. ++.-+.+.|++.+-.++.+
T Consensus 86 ~~yl~~g~~~~A~~~~~kAv~ldP~n----~~~~~~----La~i--~~~~kA~~~ye-~l~~~~P~n~~~~~~la~~ 151 (987)
T PRK09782 86 EAYRHFGHDDRARLLLEDQLKRHPGD----ARLERS----LAAI--PVEVKSVTTVE-ELLAQQKACDAVPTLRCRS 151 (987)
T ss_pred HHHHHCCCHHHHHHHHHHHHhcCccc----HHHHHH----HHHh--ccChhHHHHHH-HHHHhCCCChhHHHHHHHH
Confidence 44577899999999999876555433 223222 2333 78889998888 6777788999999998887
No 151
>COG3898 Uncharacterized membrane-bound protein [Function unknown]
Probab=22.74 E-value=64 Score=26.81 Aligned_cols=47 Identities=21% Similarity=0.249 Sum_probs=30.3
Q ss_pred HHHHHhcCCHHHHHHHhcccc---cccccccccceehhhhhhHHHHHHhcC
Q 034603 4 FEDMVLAGKLDEAEKYLSGFT---QVHENMLSTKTYFELRRQKFLEALDKH 51 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l~---~~~~~~~~~~~~FlI~kQKfLElL~~~ 51 (89)
+.+..-.||||.|++++..=. .++.+.-. .-+=.++--|=.++++.+
T Consensus 195 Le~r~~~gdWd~AlkLvd~~~~~~vie~~~ae-R~rAvLLtAkA~s~ldad 244 (531)
T COG3898 195 LEARCAAGDWDGALKLVDAQRAAKVIEKDVAE-RSRAVLLTAKAMSLLDAD 244 (531)
T ss_pred HHHHHhcCChHHHHHHHHHHHHHHhhchhhHH-HHHHHHHHHHHHHHhcCC
Confidence 556678999999999998542 22222222 244456667777888764
No 152
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=22.15 E-value=58 Score=22.62 Aligned_cols=23 Identities=13% Similarity=0.268 Sum_probs=17.9
Q ss_pred ChhHHHHHhcCCHHHHHHHhccc
Q 034603 1 MKHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 1 ~~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
|..+=+++.+|||+.|.++=..|
T Consensus 94 L~~L~~aL~~~d~~~A~~Ih~~L 116 (157)
T PF07304_consen 94 LHQLAQALQARDYDAADEIHVDL 116 (157)
T ss_dssp HHHHHHHHHHT-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHH
Confidence 34567889999999999988777
No 153
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=21.65 E-value=57 Score=19.52 Aligned_cols=22 Identities=27% Similarity=0.383 Sum_probs=18.8
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
..+-+.+++|+|+++...+..+
T Consensus 9 ~~i~~~~~~~~~~~~~~~~~~l 30 (89)
T PF08542_consen 9 EEILESCLNGDFKEARKKLYEL 30 (89)
T ss_dssp HHHHHHHHHTCHHHHHHHHHHH
T ss_pred HHHHHHHHhCCHHHHHHHHHHH
Confidence 3566788999999999999988
No 154
>PF07720 TPR_3: Tetratricopeptide repeat; InterPro: IPR011716 This entry includes tetratricopeptide-like repeats found in the LcrH/SycD-like chaperones [].; PDB: 3KS2_O 3GZ2_A 3GZ1_A 3GYZ_A 4AM9_A 2VGX_A 2VGY_A.
Probab=21.52 E-value=45 Score=17.60 Aligned_cols=13 Identities=38% Similarity=0.608 Sum_probs=9.6
Q ss_pred hcCCHHHHHHHhc
Q 034603 9 LAGKLDEAEKYLS 21 (89)
Q Consensus 9 l~G~Wd~a~~~L~ 21 (89)
+.|++++|+++.+
T Consensus 13 ~~~ky~~A~~~~~ 25 (36)
T PF07720_consen 13 QKGKYDEAIHFFQ 25 (36)
T ss_dssp HTT-HHHHHHHHH
T ss_pred HHhhHHHHHHHHH
Confidence 5788999998855
No 155
>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=21.46 E-value=1.2e+02 Score=17.56 Aligned_cols=23 Identities=22% Similarity=0.348 Sum_probs=11.6
Q ss_pred hHHHHHHhcCCHHHHHHHHHhhc
Q 034603 42 QKFLEALDKHERVKALDILMKDI 64 (89)
Q Consensus 42 QKfLElL~~~~~~~AL~~Lr~eL 64 (89)
+++++++-++|...|...+.+-+
T Consensus 6 ~~l~~al~~~d~~~~~~~~~~~l 28 (79)
T PF02607_consen 6 ERLLDALLAGDEEEAEALLEEAL 28 (79)
T ss_dssp HHHHHHHHTT-CCHHHHHHHHHH
T ss_pred HHHHHHHHhCCHHHHHHHHHHHH
Confidence 44555555555555555555444
No 156
>PF11464 Rbsn: Rabenosyn Rab binding domain; InterPro: IPR021565 Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively []. Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking []. ; PDB: 1Z0K_B 1YZM_A 1Z0J_B.
Probab=21.31 E-value=1.2e+02 Score=16.96 Aligned_cols=22 Identities=14% Similarity=0.181 Sum_probs=15.6
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
++..+|-.+|++|++..+=..|
T Consensus 10 ~~I~qAk~~~r~dEV~~L~~NL 31 (42)
T PF11464_consen 10 SYIKQAKAARRFDEVATLEENL 31 (42)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHH
T ss_pred HHHHHHHHhcCcHHHHHHHHHH
Confidence 4678888999999997654444
No 157
>TIGR00823 EIIA-LAC phosphotransferase system enzyme II, lactose-specific, factor III. operon. While the Lac permeases consist of two polypeptide chains (IIA and IICB), the Chb permease of E. coli consists of three (IIA, IIB and IIC). In B. subtilis, a PTS permease similar to the Chb permease of E. coli is believed to transport lichenan (a b-1,3;1,4 glucan) degradation products, oligosaccharides of 2-4 glucose units. This model is specific for the IIA subunit of the Lac PTS family.
Probab=21.24 E-value=83 Score=20.35 Aligned_cols=17 Identities=18% Similarity=0.268 Sum_probs=14.0
Q ss_pred HHHhcCCHHHHHHHhcc
Q 034603 6 DMVLAGKLDEAEKYLSG 22 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~ 22 (89)
+..-+|||++|++.|..
T Consensus 26 ~~a~~gdfe~A~~~l~e 42 (99)
T TIGR00823 26 KAAKAGDFAKARALVEQ 42 (99)
T ss_pred HHHHcCCHHHHHHHHHH
Confidence 35678999999999874
No 158
>COG4922 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.08 E-value=87 Score=21.55 Aligned_cols=19 Identities=26% Similarity=0.648 Sum_probs=14.9
Q ss_pred hHHHHHhcCCHHHHHHHhc
Q 034603 3 HFEDMVLAGKLDEAEKYLS 21 (89)
Q Consensus 3 ~fr~~Vl~G~Wd~a~~~L~ 21 (89)
..+.++-+|.|.+|.+++-
T Consensus 14 ~y~~~~~~g~veka~a~~v 32 (129)
T COG4922 14 FYRTLFEAGEVEKADAYLV 32 (129)
T ss_pred HHHHHHHCCCHHHhhhhhh
Confidence 4566777899999998875
No 159
>PF00959 Phage_lysozyme: Phage lysozyme; InterPro: IPR002196 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 24 GH24 from CAZY comprises enzymes with only one known activity; lysozyme (3.2.1.17 from EC). This entry includes Bacteriophage lambda lysozyme and Escherichia coli endolysin []. Lysozyme helps to release mature phage particles from the cell wall by breaking down the peptidoglycan. The enzyme hydrolyses the 1,4-beta linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid in peptidoglycan heteropolymers of prokaryotic cell walls. E. coli endolysin also functions in bacterial cell lysis and acts as a transglycosylase. The Bacteriophage T4 lysozyme structure contains 2 domains, the interface between which forms the active-site cleft. The N terminus of the 2 domains undergoes a 'hinge-bending' motion about an axis passing through the molecular waist [, ]. This mobility is thought to be important in allowing access of substrates to the enzyme active site.; GO: 0003796 lysozyme activity, 0009253 peptidoglycan catabolic process, 0016998 cell wall macromolecule catabolic process; PDB: 1XJT_A 1XJU_A 1K28_A 1WTH_A 2Z6B_A 1AM7_C 3D3D_B 1D9U_B 2ANX_A 2ANV_B ....
Probab=21.05 E-value=1.2e+02 Score=18.92 Aligned_cols=22 Identities=18% Similarity=0.173 Sum_probs=17.3
Q ss_pred hhHHHHHhcCCHHHHHHHhccc
Q 034603 2 KHFEDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 2 ~~fr~~Vl~G~Wd~a~~~L~~l 23 (89)
+.+.++|-.|+|++|-+-+...
T Consensus 72 st~~~~~~~g~~~~a~~~~~~~ 93 (110)
T PF00959_consen 72 STMLKAINAGDWDAACDEMWRW 93 (110)
T ss_dssp HHHHHHHHTTCHHHHHHHGGGS
T ss_pred chHHHHHhcccHHHHHHHHHHH
Confidence 3577899999999988777554
No 160
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=20.79 E-value=1.1e+02 Score=17.36 Aligned_cols=16 Identities=25% Similarity=0.254 Sum_probs=11.7
Q ss_pred HHHHHhcCCHHHHHHH
Q 034603 4 FEDMVLAGKLDEAEKY 19 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~ 19 (89)
-=.+++.|||.+|..+
T Consensus 20 a~~~ll~gd~~~A~~~ 35 (52)
T PF10825_consen 20 AFIALLHGDFAAAFRY 35 (52)
T ss_pred HHHHHHCCCHHHHHHH
Confidence 3456788888888765
No 161
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=20.77 E-value=77 Score=20.65 Aligned_cols=15 Identities=7% Similarity=0.116 Sum_probs=12.8
Q ss_pred HHHHhcCCHHHHHHH
Q 034603 5 EDMVLAGKLDEAEKY 19 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~ 19 (89)
+++|+++||..-+++
T Consensus 42 ~~av~~rD~~~li~~ 56 (94)
T cd07923 42 RTLIRNRDWIGMIRY 56 (94)
T ss_pred HHHHHcchHHHHHHc
Confidence 689999999988765
No 162
>PRK09591 celC cellobiose phosphotransferase system IIA component; Reviewed
Probab=20.73 E-value=86 Score=20.48 Aligned_cols=17 Identities=29% Similarity=0.374 Sum_probs=14.1
Q ss_pred HHHhcCCHHHHHHHhcc
Q 034603 6 DMVLAGKLDEAEKYLSG 22 (89)
Q Consensus 6 ~~Vl~G~Wd~a~~~L~~ 22 (89)
++..+|||++|++.|..
T Consensus 29 ~~ak~gdf~~A~~~l~e 45 (104)
T PRK09591 29 AAMREGNFDLAEQKLNQ 45 (104)
T ss_pred HHHHcCCHHHHHHHHHH
Confidence 45678999999999874
No 163
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=20.48 E-value=1e+02 Score=14.98 Aligned_cols=19 Identities=16% Similarity=0.239 Sum_probs=11.1
Q ss_pred HhcCCHHHHHHHHHhhccc
Q 034603 48 LDKHERVKALDILMKDIKA 66 (89)
Q Consensus 48 L~~~~~~~AL~~Lr~eL~p 66 (89)
...|+..+|+..+++-+.-
T Consensus 13 ~~~g~~~~A~~~~~~al~~ 31 (42)
T PF13374_consen 13 RAQGRYEEALELLEEALEI 31 (42)
T ss_dssp HHCT-HHHHHHHHHHHHHH
T ss_pred HhhhhcchhhHHHHHHHHH
Confidence 3457777777777654443
No 164
>PF02828 L27: L27 domain; InterPro: IPR014775 The L27 domain is found in receptor targeting proteins Lin-2 and Lin-7, as well as some protein kinases and human MPP2 protein.; PDB: 1ZL8_B 1VA8_A 3LRA_A 3UIT_A 1Y74_D 1RSO_B.
Probab=20.46 E-value=1.7e+02 Score=16.42 Aligned_cols=31 Identities=23% Similarity=0.357 Sum_probs=20.0
Q ss_pred HHHHHHHHhhcccccCCCHHHHHHHHhhhcCC
Q 034603 54 VKALDILMKDIKAFSTYNEEVFKEASLLLPLE 85 (89)
Q Consensus 54 ~~AL~~Lr~eL~pl~~~~~~~~~~l~~lltl~ 85 (89)
..|+++|. +|.+....++....+|..+|.=+
T Consensus 3 ~~~~e~L~-~L~~~~~~~~~~~~eL~~lL~~p 33 (56)
T PF02828_consen 3 QRVLELLE-ELQSLSSASQEDAQELQQLLQSP 33 (56)
T ss_dssp HHHHHHHH-HHHHHTSSTHHHHHHHHHHHHSH
T ss_pred HHHHHHHH-HHHhccCCChHHHHHHHHHHcCH
Confidence 45666666 77776666556677777776543
No 165
>PF05254 UPF0203: Uncharacterised protein family (UPF0203); InterPro: IPR007918 This is a family of small highly conserved proteins. In Saccharomyces cerevisiae (Baker's yeast) the gene YKL053C-A (MDM35) O60200 from SWISSPROT is one of the genes essential for maintenance of normal mitochondrial distribution and morphology (MDM) []; wherease in Homo sapiens (Human), p53CSV, O43715 from SWISSPROT is a direct transcriptional target for p53 and appears to be a cell-survival mediator in response to genotoxic stress including low-levels of DNA damage. It is suggested that p53CSV modulates the apoptotic pathway through interaction with HSP70 and Apaf-1 thereby inhibiting activation of procaspase-3 and procaspase-9 [].
Probab=20.22 E-value=1.2e+02 Score=18.35 Aligned_cols=29 Identities=17% Similarity=0.142 Sum_probs=24.9
Q ss_pred eehhhhhhHHHHHHhcCCHHHHHHHHHhh
Q 034603 35 TYFELRRQKFLEALDKHERVKALDILMKD 63 (89)
Q Consensus 35 ~~FlI~kQKfLElL~~~~~~~AL~~Lr~e 63 (89)
-.|..+++...+.|....+.+.|...|++
T Consensus 40 ~~~~~Y~~Cv~~al~~k~i~~~l~~~re~ 68 (68)
T PF05254_consen 40 ELFKEYQQCVQKALKEKGIDELLEEAREE 68 (68)
T ss_pred HHHHHHHHHHHHHHHHcCcHHHHHHhccC
Confidence 46899999999999999999888877753
No 166
>PF04733 Coatomer_E: Coatomer epsilon subunit; InterPro: IPR006822 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the epsilon subunit of the coatomer complex, which is involved in the regulation of intracellular protein trafficking between the endoplasmic reticulum and the Golgi complex []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006890 retrograde vesicle-mediated transport, Golgi to ER, 0030126 COPI vesicle coat; PDB: 3MV2_B 3MV3_F 3MKR_A.
Probab=20.09 E-value=74 Score=23.94 Aligned_cols=19 Identities=26% Similarity=0.254 Sum_probs=15.0
Q ss_pred HHHHhcCCHHHHHHHhccc
Q 034603 5 EDMVLAGKLDEAEKYLSGF 23 (89)
Q Consensus 5 r~~Vl~G~Wd~a~~~L~~l 23 (89)
--.+.-|+|++|++.|..-
T Consensus 209 ~~~l~~~~~~eAe~~L~~a 227 (290)
T PF04733_consen 209 VCHLQLGHYEEAEELLEEA 227 (290)
T ss_dssp HHHHHCT-HHHHHHHHHHH
T ss_pred HHHHHhCCHHHHHHHHHHH
Confidence 3568899999999999874
No 167
>PRK05907 hypothetical protein; Provisional
Probab=20.03 E-value=71 Score=24.46 Aligned_cols=38 Identities=21% Similarity=0.112 Sum_probs=28.5
Q ss_pred HHHHHhcCCHHHHHHHhcccccc-cccccccceehhhhhhH
Q 034603 4 FEDMVLAGKLDEAEKYLSGFTQV-HENMLSTKTYFELRRQK 43 (89)
Q Consensus 4 fr~~Vl~G~Wd~a~~~L~~l~~~-~~~~~~~~~~FlI~kQK 43 (89)
+-.+|..|+-.+|.+.+..+..- .+.+ . .+.++|.+|=
T Consensus 211 L~dai~~~~~~~Al~il~~Ll~~~ge~p-~-~ILall~rQf 249 (311)
T PRK05907 211 LRDALLRRDRVEGHSLLRSLLSDMGEDP-L-GIIAFLRSQC 249 (311)
T ss_pred HHHHHHccCHHHHHHHHHHHHHhcCCCh-H-HHHHHHHHHH
Confidence 56899999999999999999544 4343 3 3666776665
Done!