Query 046914
Match_columns 90
No_of_seqs 113 out of 1024
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 05:47:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046914.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046914hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02739 5_3_exonuc_N: 5'-3' e 100.0 1.2E-30 2.6E-35 181.2 2.5 82 2-88 29-112 (169)
2 PRK09482 flap endonuclease-lik 100.0 4.5E-29 9.8E-34 183.2 6.9 81 2-88 26-110 (256)
3 smart00475 53EXOc 5'-3' exonuc 100.0 1.2E-28 2.7E-33 180.7 7.2 82 2-88 27-110 (259)
4 PRK14976 5'-3' exonuclease; Pr 99.9 6.8E-28 1.5E-32 178.5 7.9 82 2-88 33-116 (281)
5 cd00008 53EXOc 5'-3' exonuclea 99.9 1.1E-26 2.3E-31 168.4 7.6 82 2-88 28-111 (240)
6 TIGR00593 pola DNA polymerase 99.9 2.1E-26 4.5E-31 190.7 6.3 82 2-88 27-110 (887)
7 PHA00439 exonuclease 99.9 1E-25 2.3E-30 167.5 6.6 81 2-88 39-123 (286)
8 PRK05755 DNA polymerase I; Pro 99.9 6.5E-25 1.4E-29 181.3 8.1 82 2-88 29-112 (880)
9 PHA02567 rnh RnaseH; Provision 99.9 3.6E-23 7.9E-28 154.9 7.6 83 2-88 38-133 (304)
10 COG0258 Exo 5'-3' exonuclease 99.8 5.2E-21 1.1E-25 142.5 5.5 83 1-88 37-122 (310)
11 PRK03980 flap endonuclease-1; 99.5 8E-15 1.7E-19 109.4 2.8 79 2-88 5-108 (292)
12 PTZ00217 flap endonuclease-1; 99.4 6E-14 1.3E-18 108.4 3.7 79 2-88 60-163 (393)
13 TIGR03674 fen_arch flap struct 99.3 3.2E-13 6.9E-18 102.4 2.2 80 2-89 52-156 (338)
14 cd00128 XPG Xeroderma pigmento 99.1 5.7E-11 1.2E-15 88.6 2.3 79 2-88 50-153 (316)
15 KOG2519 5'-3' exonuclease [Rep 94.0 0.089 1.9E-06 42.0 4.3 80 2-89 54-158 (449)
16 COG0420 SbcD DNA repair exonuc 89.3 1.4 2.9E-05 33.7 5.9 57 12-86 29-86 (390)
17 PRK05628 coproporphyrinogen II 81.8 5.6 0.00012 30.3 6.0 74 2-83 168-245 (375)
18 TIGR00600 rad2 DNA excision re 81.1 1.3 2.8E-05 38.8 2.6 26 62-88 772-797 (1034)
19 PHA02546 47 endonuclease subun 79.3 15 0.00032 27.8 7.5 52 16-84 33-85 (340)
20 KOG2520 5'-3' exonuclease [Rep 78.5 1.8 3.9E-05 37.0 2.6 43 44-88 448-491 (815)
21 PRK06294 coproporphyrinogen II 76.0 10 0.00023 29.0 5.9 75 1-83 162-240 (370)
22 PTZ00349 dehydrodolichyl dipho 75.1 4.3 9.4E-05 31.3 3.6 57 16-81 12-69 (322)
23 PRK10966 exonuclease subunit S 71.4 21 0.00046 27.9 6.8 66 16-82 33-108 (407)
24 PRK05799 coproporphyrinogen II 68.9 17 0.00037 27.5 5.6 74 2-83 159-236 (374)
25 PRK09058 coproporphyrinogen II 68.4 17 0.00038 28.5 5.7 75 2-83 223-301 (449)
26 PRK07379 coproporphyrinogen II 67.4 23 0.0005 27.4 6.2 74 2-83 175-252 (400)
27 PF08984 DUF1858: Domain of un 66.6 2.3 5.1E-05 24.3 0.4 26 58-83 8-33 (59)
28 cd07384 MPP_Cdc1_like Saccharo 66.4 38 0.00083 23.0 6.6 53 16-84 39-96 (171)
29 KOG1056 Glutamate-gated metabo 65.6 6.7 0.00014 34.0 3.1 34 55-90 174-207 (878)
30 PF12813 XPG_I_2: XPG domain c 64.2 5.7 0.00012 29.0 2.2 25 64-89 6-33 (246)
31 PRK06582 coproporphyrinogen II 64.0 20 0.00043 27.8 5.2 75 1-83 169-247 (390)
32 PRK13397 3-deoxy-7-phosphohept 63.4 9.9 0.00021 28.2 3.3 21 62-82 66-86 (250)
33 PRK05904 coproporphyrinogen II 63.3 34 0.00073 26.1 6.3 73 2-86 163-237 (353)
34 PRK14836 undecaprenyl pyrophos 63.1 9.9 0.00022 28.2 3.3 57 16-81 7-64 (253)
35 PRK09057 coproporphyrinogen II 62.6 16 0.00034 28.1 4.4 72 2-81 163-238 (380)
36 cd00475 CIS_IPPS Cis (Z)-Isopr 62.4 7.1 0.00015 28.3 2.3 49 24-81 1-50 (221)
37 PRK14830 undecaprenyl pyrophos 61.0 14 0.00031 27.3 3.8 56 17-81 16-72 (251)
38 PF14582 Metallophos_3: Metall 60.8 17 0.00036 27.2 4.0 69 16-89 26-102 (255)
39 PRK14839 undecaprenyl pyrophos 60.5 13 0.00028 27.5 3.4 51 22-81 8-59 (239)
40 PRK14828 undecaprenyl pyrophos 60.2 30 0.00065 25.6 5.4 57 16-81 19-77 (256)
41 PRK13347 coproporphyrinogen II 60.0 30 0.00065 27.2 5.6 76 2-83 212-288 (453)
42 TIGR00619 sbcd exonuclease Sbc 58.5 54 0.0012 23.7 6.4 22 16-38 33-54 (253)
43 PRK14833 undecaprenyl pyrophos 57.7 11 0.00023 27.7 2.6 50 23-81 4-54 (233)
44 PRK14829 undecaprenyl pyrophos 57.4 9.1 0.0002 28.2 2.2 52 22-82 13-65 (243)
45 PRK14831 undecaprenyl pyrophos 57.0 16 0.00036 26.9 3.5 52 22-82 19-71 (249)
46 PRK14841 undecaprenyl pyrophos 57.0 17 0.00038 26.5 3.6 50 23-81 3-53 (233)
47 cd07402 MPP_GpdQ Enterobacter 56.5 63 0.0014 22.3 6.3 47 16-85 32-80 (240)
48 cd08165 MPP_MPPE1 human MPPE1 56.0 45 0.00098 22.2 5.3 54 16-85 32-86 (156)
49 cd08163 MPP_Cdc1 Saccharomyces 55.6 44 0.00096 24.4 5.6 52 17-84 40-93 (257)
50 TIGR00583 mre11 DNA repair pro 55.3 50 0.0011 26.0 6.1 24 16-40 36-59 (405)
51 TIGR00853 pts-lac PTS system, 54.5 19 0.00041 22.5 3.1 27 57-83 57-83 (95)
52 PF00411 Ribosomal_S11: Riboso 54.5 20 0.00042 23.1 3.2 42 40-81 25-66 (110)
53 PRK13398 3-deoxy-7-phosphohept 54.0 14 0.0003 27.4 2.7 22 61-82 77-98 (266)
54 COG0635 HemN Coproporphyrinoge 53.8 46 0.00099 26.2 5.7 74 2-83 197-273 (416)
55 PRK14838 undecaprenyl pyrophos 53.8 19 0.0004 26.6 3.3 51 22-81 9-60 (242)
56 PRK14837 undecaprenyl pyrophos 53.6 24 0.00053 25.8 3.9 51 22-81 5-56 (230)
57 PRK05660 HemN family oxidoredu 53.5 68 0.0015 24.6 6.5 72 2-83 167-240 (378)
58 COG1908 FrhD Coenzyme F420-red 53.4 5.1 0.00011 27.1 0.3 41 23-77 53-93 (132)
59 KOG1602 Cis-prenyltransferase 53.2 31 0.00067 26.1 4.4 56 17-81 30-86 (271)
60 cd08166 MPP_Cdc1_like_1 unchar 52.5 71 0.0015 22.7 6.1 53 16-84 36-89 (195)
61 PRK14834 undecaprenyl pyrophos 52.1 28 0.00061 25.8 4.1 52 22-82 13-65 (249)
62 PRK14832 undecaprenyl pyrophos 51.9 12 0.00026 27.8 2.1 51 22-81 17-68 (253)
63 PF07131 DUF1382: Protein of u 51.9 24 0.00053 20.8 3.0 34 52-88 2-35 (61)
64 TIGR03190 benz_CoA_bzdN benzoy 51.3 14 0.00031 28.3 2.5 24 65-88 333-356 (377)
65 PRK13366 protocatechuate 4,5-d 50.6 87 0.0019 23.5 6.5 66 11-83 36-120 (284)
66 PRK14842 undecaprenyl pyrophos 50.0 17 0.00037 26.8 2.7 52 22-82 7-59 (241)
67 PRK14840 undecaprenyl pyrophos 49.4 16 0.00034 27.1 2.4 57 16-81 11-72 (250)
68 TIGR00539 hemN_rel putative ox 49.1 63 0.0014 24.4 5.7 72 2-83 160-233 (360)
69 COG2877 KdsA 3-deoxy-D-manno-o 48.7 22 0.00049 26.8 3.1 32 50-81 59-94 (279)
70 KOG3120 Predicted haloacid deh 48.6 17 0.00038 27.1 2.5 46 24-75 11-67 (256)
71 PRK08207 coproporphyrinogen II 48.2 42 0.00091 27.0 4.8 71 2-79 329-400 (488)
72 smart00707 RPEL Repeat in Dros 48.1 9.9 0.00021 18.8 0.8 11 52-63 9-19 (26)
73 PRK14827 undecaprenyl pyrophos 47.7 10 0.00023 28.8 1.2 52 22-82 66-118 (296)
74 cd07185 OmpA_C-like Peptidogly 45.6 54 0.0012 19.6 4.1 40 49-89 6-45 (106)
75 PF02274 Amidinotransf: Amidin 44.6 28 0.00061 25.1 3.1 32 52-83 22-53 (281)
76 TIGR03632 bact_S11 30S ribosom 43.8 58 0.0012 20.9 4.1 36 46-81 31-66 (108)
77 PRK14835 undecaprenyl pyrophos 43.1 36 0.00079 25.5 3.5 51 22-81 40-91 (275)
78 cd05564 PTS_IIB_chitobiose_lic 42.3 33 0.00072 21.2 2.8 28 56-83 52-79 (96)
79 PRK09590 celB cellobiose phosp 42.2 33 0.00072 21.9 2.8 32 56-90 56-87 (104)
80 PRK10802 peptidoglycan-associa 41.3 67 0.0014 22.2 4.4 41 49-90 73-113 (173)
81 CHL00041 rps11 ribosomal prote 41.1 66 0.0014 20.9 4.1 36 46-81 44-79 (116)
82 PF08373 RAP: RAP domain; Int 41.1 28 0.00062 19.1 2.1 19 65-83 21-39 (58)
83 PF13521 AAA_28: AAA domain; P 40.9 26 0.00057 23.0 2.3 32 53-84 127-159 (163)
84 PRK08208 coproporphyrinogen II 40.7 1.5E+02 0.0032 23.2 6.7 72 1-83 200-272 (430)
85 cd07386 MPP_DNA_pol_II_small_a 40.7 98 0.0021 21.8 5.3 53 23-84 35-90 (243)
86 PRK08599 coproporphyrinogen II 40.4 1.1E+02 0.0023 23.3 5.7 74 2-83 160-237 (377)
87 PRK08156 type III secretion sy 40.2 75 0.0016 24.8 4.9 41 23-82 257-304 (361)
88 cd07396 MPP_Nbla03831 Homo sap 40.0 1.4E+02 0.003 21.4 6.8 51 16-86 34-84 (267)
89 PF08285 DPM3: Dolichol-phosph 40.0 35 0.00076 21.5 2.6 22 56-77 69-90 (91)
90 TIGR02536 eut_hyp ethanolamine 39.4 45 0.00098 24.0 3.4 33 54-87 107-139 (207)
91 cd07400 MPP_YydB Bacillus subt 38.6 1E+02 0.0022 19.4 5.6 46 16-84 29-77 (144)
92 KOG2518 5'-3' exonuclease [Rep 38.4 94 0.002 25.8 5.4 21 67-88 133-153 (556)
93 TIGR01404 FlhB_rel_III type II 38.2 86 0.0019 24.1 5.0 41 23-82 261-308 (342)
94 TIGR03358 VI_chp_5 type VI sec 38.0 29 0.00064 24.1 2.2 20 54-73 99-118 (159)
95 PRK13109 flhB flagellar biosyn 37.8 80 0.0017 24.5 4.8 41 23-82 271-318 (358)
96 PRK01816 hypothetical protein; 37.5 52 0.0011 22.6 3.3 28 52-79 86-113 (143)
97 COG0065 LeuC 3-isopropylmalate 37.5 1.1E+02 0.0023 24.7 5.4 41 22-80 54-94 (423)
98 PRK05309 30S ribosomal protein 37.2 79 0.0017 21.0 4.1 36 46-81 48-83 (128)
99 KOG4366 Predicted thioesterase 36.6 17 0.00038 26.3 0.9 26 43-68 169-194 (213)
100 PF00586 AIRS: AIR synthase re 36.3 58 0.0013 19.6 3.2 25 56-80 69-93 (96)
101 PRK05198 2-dehydro-3-deoxyphos 36.2 53 0.0012 24.7 3.4 30 51-80 53-86 (264)
102 PRK09108 type III secretion sy 36.1 91 0.002 24.2 4.8 41 23-82 264-311 (353)
103 PF02120 Flg_hook: Flagellar h 36.1 34 0.00074 20.1 2.1 33 50-82 43-75 (85)
104 cd08164 MPP_Ted1 Saccharomyces 35.9 1.6E+02 0.0035 20.9 5.9 21 16-37 38-58 (193)
105 PRK00143 mnmA tRNA-specific 2- 35.6 54 0.0012 25.0 3.5 41 47-88 85-128 (346)
106 PF04019 DUF359: Protein of un 35.4 85 0.0018 20.7 4.0 24 64-88 51-74 (121)
107 PRK06298 type III secretion sy 35.3 94 0.002 24.1 4.8 41 23-82 263-310 (356)
108 PF01930 Cas_Cas4: Domain of u 35.2 55 0.0012 21.6 3.1 34 45-79 68-101 (162)
109 PRK12773 flhB flagellar biosyn 34.9 93 0.002 26.4 4.9 41 23-82 561-608 (646)
110 TIGR00421 ubiX_pad polyprenyl 34.6 47 0.001 23.1 2.8 24 52-77 151-174 (181)
111 PRK04036 DNA polymerase II sma 34.1 2.2E+02 0.0048 22.9 6.9 54 22-84 283-339 (504)
112 PLN03033 2-dehydro-3-deoxyphos 33.9 61 0.0013 24.8 3.5 31 50-80 58-92 (290)
113 TIGR03191 benz_CoA_bzdO benzoy 33.8 40 0.00088 26.6 2.6 22 66-87 382-403 (430)
114 PF05711 TylF: Macrocin-O-meth 33.5 31 0.00067 25.5 1.8 70 16-87 94-168 (248)
115 COG2885 OmpA Outer membrane pr 33.5 76 0.0017 21.6 3.7 32 58-90 96-127 (190)
116 TIGR01362 KDO8P_synth 3-deoxy- 33.1 66 0.0014 24.1 3.5 31 50-80 44-78 (258)
117 COG5458 Uncharacterized conser 33.1 35 0.00076 23.1 1.9 19 49-67 123-141 (144)
118 PTZ00081 enolase; Provisional 33.0 73 0.0016 25.4 3.9 33 52-88 278-310 (439)
119 PF09572 RE_XamI: XamI restric 33.0 75 0.0016 23.8 3.7 40 43-82 80-144 (251)
120 PRK12721 secretion system appa 33.0 1.1E+02 0.0024 23.7 4.8 41 23-82 262-309 (349)
121 PRK09249 coproporphyrinogen II 32.8 1.8E+02 0.0039 22.8 6.1 73 2-82 211-286 (453)
122 PF03135 CagE_TrbE_VirB: CagE, 32.1 58 0.0012 22.5 2.9 29 54-82 157-185 (205)
123 COG3516 Predicted component of 32.1 41 0.00089 23.7 2.1 18 56-73 106-123 (169)
124 cd00840 MPP_Mre11_N Mre11 nucl 32.0 1.6E+02 0.0035 19.7 6.3 49 16-85 35-86 (223)
125 PRK09967 putative outer membra 31.7 1.1E+02 0.0024 20.8 4.2 36 54-90 61-96 (160)
126 PRK12772 bifunctional flagella 31.6 1.1E+02 0.0023 25.5 4.8 41 23-82 525-572 (609)
127 PF09413 DUF2007: Domain of un 31.5 58 0.0013 18.3 2.5 21 63-83 11-31 (67)
128 PF02037 SAP: SAP domain; Int 31.2 49 0.0011 16.8 1.9 15 64-78 6-20 (35)
129 cd05565 PTS_IIB_lactose PTS_II 31.0 49 0.0011 21.0 2.2 26 58-83 55-80 (99)
130 COG3494 Uncharacterized protei 31.0 1.5E+02 0.0033 22.5 5.1 62 16-84 62-132 (279)
131 PF11510 FA_FANCE: Fanconi Ana 30.7 34 0.00073 25.6 1.6 23 53-75 5-27 (263)
132 COG0482 TrmU Predicted tRNA(5- 30.6 67 0.0015 25.2 3.3 41 45-86 83-126 (356)
133 KOG4313 Thiamine pyrophosphoki 30.5 21 0.00046 27.1 0.5 18 37-54 98-115 (306)
134 PRK12457 2-dehydro-3-deoxyphos 30.5 75 0.0016 24.1 3.5 31 50-80 58-92 (281)
135 PF03054 tRNA_Me_trans: tRNA m 30.3 35 0.00075 26.5 1.7 48 38-86 71-126 (356)
136 COG0100 RpsK Ribosomal protein 30.3 1.2E+02 0.0025 20.5 4.0 43 39-81 42-84 (129)
137 PF13986 DUF4224: Domain of un 30.1 63 0.0014 17.7 2.3 20 63-82 16-35 (47)
138 PF01661 Macro: Macro domain; 29.9 1.3E+02 0.0029 18.1 5.0 50 38-87 55-105 (118)
139 PF05591 DUF770: Protein of un 29.9 48 0.001 22.9 2.2 18 56-73 100-117 (157)
140 smart00857 Resolvase Resolvase 29.5 64 0.0014 20.6 2.7 21 59-79 16-36 (148)
141 PRK08898 coproporphyrinogen II 29.2 2.1E+02 0.0045 22.1 5.8 72 2-83 181-254 (394)
142 PF08722 Tn7_Tnp_TnsA_N: TnsA 29.0 79 0.0017 18.9 2.9 53 23-81 34-86 (88)
143 PHA02595 tk.4 hypothetical pro 29.0 1.8E+02 0.004 19.5 5.9 41 44-84 80-121 (154)
144 PF04009 DUF356: Protein of un 28.9 44 0.00095 21.9 1.7 16 16-32 73-88 (107)
145 PRK05702 flhB flagellar biosyn 28.6 1.4E+02 0.0031 23.1 4.8 41 23-82 269-316 (359)
146 PTZ00378 hypothetical protein; 28.5 1.6E+02 0.0035 24.3 5.2 66 17-89 271-358 (518)
147 TIGR02802 Pal_lipo peptidoglyc 28.3 1.4E+02 0.0031 18.0 4.4 33 56-89 11-43 (104)
148 cd02908 Macro_Appr_pase_like M 28.0 1.6E+02 0.0035 19.7 4.5 48 43-90 73-120 (165)
149 PF03979 Sigma70_r1_1: Sigma-7 27.1 56 0.0012 19.7 1.9 22 61-82 38-59 (82)
150 PF04217 DUF412: Protein of un 26.7 1E+02 0.0022 21.2 3.3 27 52-78 87-113 (143)
151 PRK12468 flhB flagellar biosyn 26.6 1.6E+02 0.0035 23.2 4.8 41 23-82 269-316 (386)
152 smart00513 SAP Putative DNA-bi 26.6 66 0.0014 16.1 1.9 15 64-78 6-20 (35)
153 PRK11148 cyclic 3',5'-adenosin 26.4 2.5E+02 0.0054 20.2 6.6 41 23-85 55-95 (275)
154 PRK03094 hypothetical protein; 26.2 80 0.0017 19.6 2.5 26 62-88 8-33 (80)
155 PF06069 PerC: PerC transcript 26.2 1.1E+02 0.0024 19.3 3.2 30 49-78 48-78 (90)
156 PF14451 Ub-Mut7C: Mut7-C ubiq 26.2 46 0.00099 20.4 1.4 16 65-80 33-48 (81)
157 COG3048 DsdA D-serine dehydrat 25.8 51 0.0011 26.1 1.9 22 65-90 196-217 (443)
158 COG1440 CelA Phosphotransferas 25.8 80 0.0017 20.5 2.5 27 57-83 55-81 (102)
159 cd03770 SR_TndX_transposase Se 25.7 93 0.002 20.2 2.9 22 58-79 18-39 (140)
160 PF07807 RED_C: RED-like prote 25.4 43 0.00093 22.3 1.2 33 43-75 44-101 (118)
161 COG4792 EscU Type III secretor 25.2 1.5E+02 0.0033 23.1 4.4 43 23-81 263-309 (349)
162 PF00875 DNA_photolyase: DNA p 25.2 1E+02 0.0022 20.3 3.1 26 59-84 50-75 (165)
163 PLN00061 photosystem II protei 25.1 48 0.001 23.0 1.5 19 45-64 124-142 (150)
164 COG2908 Uncharacterized protei 24.9 2.9E+02 0.0063 20.5 6.4 53 17-84 22-76 (237)
165 PHA02754 hypothetical protein; 24.7 77 0.0017 18.8 2.1 25 56-80 12-36 (67)
166 PF03469 XH: XH domain; Inter 24.7 57 0.0012 22.1 1.8 15 48-62 105-119 (132)
167 COG3033 TnaA Tryptophanase [Am 24.6 89 0.0019 25.2 3.0 25 61-85 333-357 (471)
168 COG4572 ChaB Putative cation t 24.3 81 0.0018 19.3 2.2 21 49-70 3-23 (76)
169 TIGR01854 lipid_A_lpxH UDP-2,3 24.2 2.6E+02 0.0056 19.6 5.4 48 23-84 30-77 (231)
170 TIGR02260 benz_CoA_red_B benzo 24.1 91 0.002 24.5 3.1 26 63-88 369-394 (413)
171 TIGR00328 flhB flagellar biosy 24.1 2E+02 0.0043 22.2 4.9 41 23-82 262-309 (347)
172 TIGR00758 UDG_fam4 uracil-DNA 24.0 1.4E+02 0.0031 20.2 3.7 33 51-83 76-108 (173)
173 PRK00754 signal recognition pa 23.9 1.2E+02 0.0026 19.2 3.1 38 42-80 6-53 (95)
174 cd07383 MPP_Dcr2 Saccharomyces 23.9 2.4E+02 0.0051 19.1 5.8 20 16-36 35-54 (199)
175 TIGR00055 uppS undecaprenyl di 23.8 1.1E+02 0.0025 22.2 3.3 48 25-81 1-49 (226)
176 PRK14646 hypothetical protein; 23.5 1.3E+02 0.0028 20.5 3.4 27 56-82 1-28 (155)
177 PF08443 RimK: RimK-like ATP-g 23.5 1.5E+02 0.0033 20.1 3.8 40 40-82 113-152 (190)
178 PRK08446 coproporphyrinogen II 23.3 2.7E+02 0.0058 21.0 5.4 69 2-83 158-228 (350)
179 TIGR00538 hemN oxygen-independ 23.3 2.7E+02 0.0058 21.8 5.5 75 2-83 211-287 (455)
180 PLN00191 enolase 23.2 1.3E+02 0.0028 24.1 3.8 33 52-88 292-324 (457)
181 PF03698 UPF0180: Uncharacteri 23.2 90 0.002 19.2 2.3 26 62-88 8-33 (80)
182 COG2069 CdhD CO dehydrogenase/ 22.4 86 0.0019 24.6 2.5 16 23-38 119-134 (403)
183 PF05043 Mga: Mga helix-turn-h 22.3 1.1E+02 0.0023 18.1 2.5 27 59-85 46-76 (87)
184 PF02755 RPEL: RPEL repeat; I 22.3 34 0.00074 16.7 0.2 10 52-62 9-18 (26)
185 PF08992 QH-AmDH_gamma: Quinoh 22.2 14 0.0003 22.8 -1.4 15 75-90 21-35 (78)
186 PF06050 HGD-D: 2-hydroxygluta 22.1 77 0.0017 23.2 2.2 24 64-87 305-329 (349)
187 TIGR02263 benz_CoA_red_C benzo 22.0 95 0.0021 23.9 2.7 18 65-82 341-358 (380)
188 PF15513 DUF4651: Domain of un 21.9 1.2E+02 0.0026 17.9 2.6 22 64-85 8-30 (62)
189 PF13297 Telomere_Sde2_2: Telo 21.8 85 0.0018 18.5 1.9 19 61-79 14-32 (60)
190 TIGR03044 PS_II_psb27 photosys 21.8 74 0.0016 21.7 1.9 17 46-64 105-121 (135)
191 COG5135 Uncharacterized conser 21.7 56 0.0012 24.0 1.3 31 53-83 178-213 (245)
192 PF00691 OmpA: OmpA family; I 21.7 1.9E+02 0.004 17.0 3.9 33 55-89 8-42 (97)
193 PF13382 Adenine_deam_C: Adeni 21.6 99 0.0021 21.5 2.6 22 56-77 116-137 (171)
194 COG0020 UppS Undecaprenyl pyro 21.5 1.7E+02 0.0038 21.5 3.9 51 23-82 16-67 (245)
195 PRK03745 signal recognition pa 21.2 1.1E+02 0.0024 19.7 2.5 27 56-82 23-52 (100)
196 PF14772 NYD-SP28: Sperm tail 21.0 78 0.0017 19.7 1.8 21 53-73 49-69 (104)
197 PF00128 Alpha-amylase: Alpha 20.9 98 0.0021 21.6 2.5 24 59-86 5-28 (316)
198 TIGR03350 type_VI_ompA type VI 20.7 2.4E+02 0.0051 18.1 4.1 39 49-89 34-72 (137)
199 PRK12569 hypothetical protein; 20.7 2E+02 0.0044 21.4 4.1 25 58-82 89-113 (245)
200 cd06390 PBP1_iGluR_AMPA_GluR1 20.6 1.2E+02 0.0025 23.1 3.0 26 63-90 104-129 (364)
201 PTZ00129 40S ribosomal protein 20.5 2.3E+02 0.0049 19.6 4.1 44 39-82 52-96 (149)
202 TIGR03398 plc_access_R phospho 20.4 88 0.0019 21.3 2.0 22 41-63 1-22 (141)
203 PF10865 DUF2703: Domain of un 20.4 1.1E+02 0.0024 20.2 2.5 25 56-80 21-45 (120)
204 PRK13381 peptidase T; Provisio 20.4 1.9E+02 0.0042 21.8 4.1 30 52-81 22-51 (404)
205 PF13279 4HBT_2: Thioesterase- 20.3 51 0.0011 20.2 0.8 12 53-64 110-121 (121)
206 PF03461 TRCF: TRCF domain; I 20.2 1.8E+02 0.0039 18.1 3.4 29 55-83 48-78 (101)
No 1
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=99.96 E-value=1.2e-30 Score=181.17 Aligned_cols=82 Identities=35% Similarity=0.668 Sum_probs=77.4
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|+|||||+ ||+++ ++++. ..|+|++|||| +++++|||++||+||+||+++|++|..|++.++++|+++||+++
T Consensus 29 G~~t~ai~-g~~~~l~~l~~~-~~p~~~vv~fD---~~~~~fR~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~ 103 (169)
T PF02739_consen 29 GEPTNAIY-GFLRMLLKLLKD-FKPDYVVVAFD---SKGPTFRKELYPEYKANRKPMPEELIPQLPYIKELLEALGIPVL 103 (169)
T ss_dssp SEB-HHHH-HHHHHHHHHHHH-TTEEEEEEEEE---BSSCHHHHHCCTTTTHHHHHHHHHHHHHHHHHHHHHHHTTSEEE
T ss_pred CCChHHHH-HHHHHHHHHHHH-cCCceEEEEec---CCCcchHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEe
Confidence 88999999 99999 89999 79999999999 77779999999999999999999999999999999999999999
Q ss_pred Eeccccccc
Q 046914 80 EVNVMYEDA 88 (90)
Q Consensus 80 ~~~g~eeD~ 88 (90)
+.+|.||||
T Consensus 104 ~~~g~EADD 112 (169)
T PF02739_consen 104 EVPGYEADD 112 (169)
T ss_dssp EETTB-HHH
T ss_pred cCCCCcHHH
Confidence 999999997
No 2
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.95 E-value=4.5e-29 Score=183.19 Aligned_cols=81 Identities=21% Similarity=0.321 Sum_probs=77.2
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCc--cccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCc
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMN--FRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t--~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~ 77 (90)
|. ||||+ ||+++ +++++ ++|+|++|||| .++++ |||++||+||+||++||++|..|++.|+++|+++||+
T Consensus 26 g~-t~av~-gf~~~l~~ll~~-~~p~~i~v~fD---~~~~~~~fR~~l~p~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~ 99 (256)
T PRK09482 26 DI-NACVE-TCQHALDKLIRH-SQPTHAVAVFD---GDARSSGWRHQLLPDYKAGRKPMPEALQQGLPAIRAAFEELGID 99 (256)
T ss_pred Cc-chHHH-HHHHHHHHHHHH-cCCCEEEEEEe---CCCCCcccHHHHhHHHhcCCCCCcHHHHHHHHHHHHHHHhCCCC
Confidence 55 89999 99999 99999 79999999999 66666 9999999999999999999999999999999999999
Q ss_pred eEEeccccccc
Q 046914 78 VIEVNVMYEDA 88 (90)
Q Consensus 78 ~~~~~g~eeD~ 88 (90)
+++.+|.||||
T Consensus 100 ~~~~~g~EADD 110 (256)
T PRK09482 100 SWHADGNEADD 110 (256)
T ss_pred EeccCCcCHHH
Confidence 99999999997
No 3
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.95 E-value=1.2e-28 Score=180.74 Aligned_cols=82 Identities=37% Similarity=0.628 Sum_probs=79.4
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|||||+ ||+++ ++++. +.|+|+++||| .++++|||++||+||+||++||++|..|++.++++|+++||+++
T Consensus 27 G~~t~a~~-g~~~~l~~l~~~-~~p~~~~~~fD---~~~~~~R~~l~p~YKa~R~~~pe~L~~q~~~~~~~l~~~gi~~i 101 (259)
T smart00475 27 GEPTNAVY-GFLRMLLKLIKE-EKPTYVAVVFD---AKGKTFRHELYPEYKANRPKTPDELLEQIPLIKELLDALGIPVL 101 (259)
T ss_pred CCcccHHH-HHHHHHHHHHHH-cCCCeEEEEEe---CCCCccccchhHHHHhCCCCCCHHHHHHHHHHHHHHHHCCCCEE
Confidence 78999999 99999 89999 79999999999 77899999999999999999999999999999999999999999
Q ss_pred Eeccccccc
Q 046914 80 EVNVMYEDA 88 (90)
Q Consensus 80 ~~~g~eeD~ 88 (90)
+.+|.||||
T Consensus 102 ~~~g~EADD 110 (259)
T smart00475 102 EVEGYEADD 110 (259)
T ss_pred eeCCcCHHH
Confidence 999999997
No 4
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.95 E-value=6.8e-28 Score=178.52 Aligned_cols=82 Identities=29% Similarity=0.393 Sum_probs=79.4
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|||||+ ||+++ ++++. ++|+|++|||| .++++|||++||+||+||+++|++|..|++.++++|+++||+++
T Consensus 33 G~~t~a~~-gf~~~l~~ll~~-~~p~~~~v~fD---~~~~~~R~~l~p~YKanR~~~p~~l~~q~~~i~~~l~~~gi~~~ 107 (281)
T PRK14976 33 GLPTNAIH-TFLTMIFKILKK-LNPSYILIAFD---AGRKTFRHQLYDEYKQGRKKTPESLISQIPLLKKILKLAGIKWE 107 (281)
T ss_pred CCCchHHH-HHHHHHHHHHHh-cCCCEEEEEEE---CCCCcccccccHHHhcCCCCCCHHHHHHHHHHHHHHHHCCCCEE
Confidence 78999999 99999 89999 79999999999 77899999999999999999999999999999999999999999
Q ss_pred Eeccccccc
Q 046914 80 EVNVMYEDA 88 (90)
Q Consensus 80 ~~~g~eeD~ 88 (90)
+.+|.||||
T Consensus 108 ~~~g~EADD 116 (281)
T PRK14976 108 EQPGYEADD 116 (281)
T ss_pred ecCCcCHHH
Confidence 999999996
No 5
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=99.94 E-value=1.1e-26 Score=168.43 Aligned_cols=82 Identities=32% Similarity=0.585 Sum_probs=79.0
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.||||++ ||+++ ++++. ..|+|+++||| .++++|||++||+||+||+++|++|..|++.++++|+++||+++
T Consensus 28 g~~t~ai~-g~~~~l~~~~~~-~~p~~~~~~fD---~~~~~~R~~l~p~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~i 102 (240)
T cd00008 28 GLPTNAVY-GFLNMLLKLIKE-YKPTYVAVVFD---AGGKTFRHELYPEYKANRKKMPEELREQIPLIKELLEALGIPVL 102 (240)
T ss_pred CcCchHHH-HHHHHHHHHHHh-cCCCeEEEEEe---CCCCcccccccHHHHcCCCCCCHHHHHHHHHHHHHHHHCCCCEE
Confidence 78999999 99999 89999 79999999999 67799999999999999999999999999999999999999999
Q ss_pred Eeccccccc
Q 046914 80 EVNVMYEDA 88 (90)
Q Consensus 80 ~~~g~eeD~ 88 (90)
..+|.||||
T Consensus 103 ~~~~~EADD 111 (240)
T cd00008 103 EIEGYEADD 111 (240)
T ss_pred ecCCcCHHH
Confidence 999999997
No 6
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.93 E-value=2.1e-26 Score=190.72 Aligned_cols=82 Identities=27% Similarity=0.507 Sum_probs=79.7
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|||||+ ||+++ +++++ ..|+|++|||| .+++||||++||+||+||++||++|..|++.|+++|++|||+++
T Consensus 27 G~~t~av~-Gf~~~l~~ll~~-~~p~~i~v~FD---~~~~tfR~~~~~~YKa~R~~~Pe~l~~Q~~~i~~~l~~~gi~~i 101 (887)
T TIGR00593 27 GEPTNAVY-GFTKMLLKLLKE-EKPTYVAVAFD---SGTPTFRHEAYAEYKANRAPTPEELIEQIPLIKELLDALGIPIL 101 (887)
T ss_pred CCEecHHH-HHHHHHHHHHHh-cCCCEEEEEEc---CCCCcchHHHHHHHHhCCCCChHHHHHHHHHHHHHHHHCCCcEE
Confidence 89999999 99999 89999 79999999999 78899999999999999999999999999999999999999999
Q ss_pred Eeccccccc
Q 046914 80 EVNVMYEDA 88 (90)
Q Consensus 80 ~~~g~eeD~ 88 (90)
+.+|.||||
T Consensus 102 ~~~g~EADD 110 (887)
T TIGR00593 102 EVEGYEADD 110 (887)
T ss_pred eeCCccHHH
Confidence 999999997
No 7
>PHA00439 exonuclease
Probab=99.92 E-value=1e-25 Score=167.53 Aligned_cols=81 Identities=15% Similarity=0.119 Sum_probs=75.4
Q ss_pred CcchHHHHHHHHhh--hhhhcc--CCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCc
Q 046914 2 GESYGLLWRGFLSY--NIRHDT--YMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~--~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~ 77 (90)
|.||||++ ||+++ +++++. +.|+|++|||| +++||||++||+|||||++||++ ..|++.++++++++||+
T Consensus 39 G~~t~A~~-gf~~~L~kl~~~~k~~~p~~i~vaFD----~~~tfR~elyp~YKanR~~~p~~-~~~~~~i~el~~~~gi~ 112 (286)
T PHA00439 39 CDHAKARQ-ILEDSIKSYKTRKKAWKDAPIVLAFT----DSVNWRKEVVPTYKANRKAKRKP-VGYRKFLEELMAREEWK 112 (286)
T ss_pred CeeccHHH-HHHHHHHHHHHhhccCCCCeEEEEEC----CCCChHhhhhhHhcCCCCCCCCc-hhhHHHHHHHHHhCCCC
Confidence 78999999 99999 777651 48999999999 47899999999999999999999 89999999999999999
Q ss_pred eEEeccccccc
Q 046914 78 VIEVNVMYEDA 88 (90)
Q Consensus 78 ~~~~~g~eeD~ 88 (90)
+++.+|.||||
T Consensus 113 ~i~~~G~EADD 123 (286)
T PHA00439 113 SILEPGLEGDD 123 (286)
T ss_pred EEeeCCccHHH
Confidence 99999999997
No 8
>PRK05755 DNA polymerase I; Provisional
Probab=99.91 E-value=6.5e-25 Score=181.26 Aligned_cols=82 Identities=30% Similarity=0.605 Sum_probs=79.4
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|||||+ ||+++ ++++. +.|+|++|||| .++++|||++||+||+||+++|++|..|++.|+++|+++||+++
T Consensus 29 g~~~~a~~-g~~~~l~~~~~~-~~p~~~~v~fD---~~~~~~R~~~~~~YK~~R~~~p~~l~~q~~~~~~~l~~~gi~~~ 103 (880)
T PRK05755 29 GLPTGAVY-GFLNMLLKLLKE-EKPTHVAVAFD---AKGKTFRHELYPEYKANRPPMPEDLREQIPLIRELLRALGIPLL 103 (880)
T ss_pred CCcccHHH-HHHHHHHHHHHh-cCCCEEEEEEE---CCCCccccccCHHHhCCCCCCcHHHHHHHHHHHHHHHHCCCCEE
Confidence 78999999 99999 89998 79999999999 77899999999999999999999999999999999999999999
Q ss_pred Eeccccccc
Q 046914 80 EVNVMYEDA 88 (90)
Q Consensus 80 ~~~g~eeD~ 88 (90)
+.+|.||||
T Consensus 104 ~~~g~EADD 112 (880)
T PRK05755 104 ELEGYEADD 112 (880)
T ss_pred eeCCccHHH
Confidence 999999997
No 9
>PHA02567 rnh RnaseH; Provisional
Probab=99.89 E-value=3.6e-23 Score=154.91 Aligned_cols=83 Identities=13% Similarity=0.087 Sum_probs=72.6
Q ss_pred CcchHHHHHHHHhh--hhhhccC--CCCeEEEeeeCCCCCC-CccccccCccccCCCCCCchhHHHhH--------HHHH
Q 046914 2 GESYGLLWRGFLSY--NIRHDTY--MTDITLDVHDLYGACG-MNFRHTLYPSYKNNRPPTPDTIVQGL--------QYLK 68 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~--~p~~i~v~fD~fD~~~-~t~R~~~yp~YKa~R~~~P~~L~~Ql--------~~i~ 68 (90)
|.+||||+.+|+++ ++++. + .++|++|||| .++ ++|||++||+|||||+++|++|..|+ +.++
T Consensus 38 ~~~~~~ir~~v~nsL~~~v~~-~k~~~~~i~vaFD---~~~~~tfR~elyp~YKAnR~~~Peel~~q~~~l~~~l~~ii~ 113 (304)
T PHA02567 38 KINEAMVRHLVLNSIRYNVKK-FKEEYPEIVLAFD---NSKSGYWRRDIAWYYKKNRKKDREESPWDWEGLFEAINKIVD 113 (304)
T ss_pred CCcHHHHHHHHHHHHHHHHHH-hcCCCCeEEEEEe---CCCCCCchhhhhhHhhcCCCCCChHHHHHHHHhhhhHHHHHH
Confidence 78999996469998 55554 3 4577999999 554 89999999999999999999988887 7889
Q ss_pred HHHHHcCCceEEeccccccc
Q 046914 69 ASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 69 ~~l~~lGi~~~~~~g~eeD~ 88 (90)
+++++|||++++.+|.||||
T Consensus 114 el~~~~gi~~l~~~g~EADD 133 (304)
T PHA02567 114 EIKENMPYKVMKIDKAEADD 133 (304)
T ss_pred HHHHHCCCCEEEeCCccHHH
Confidence 99999999999999999997
No 10
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.83 E-value=5.2e-21 Score=142.55 Aligned_cols=83 Identities=27% Similarity=0.411 Sum_probs=79.7
Q ss_pred CCcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCC-CchhHHHhHHHHHHHHHHcCCc
Q 046914 1 MGESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPP-TPDTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 1 ~G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~-~P~~L~~Ql~~i~~~l~~lGi~ 77 (90)
.|.||||++ ||.++ ++++. .+|.|+++||| .+.++||+++|++||++|.+ +|++|..|++.|++++.++|++
T Consensus 37 ~g~~~~~~~-~~~~~l~~~~~~-~~~~~~~~vFD---~~~~tfR~~~~~~yK~~R~~~~p~~l~~q~~~i~~~~~~~~~~ 111 (310)
T COG0258 37 LGDPTGAVS-GFLGMLYRLIRL-LEPTHPVVVFD---GKPPTFRHELLEEYKANREKEMPDELAPQIPILTELLVALGIP 111 (310)
T ss_pred CCCCccHHH-HHHHHHHHHHHh-cCCCcEEEEEc---CCCCcchHHHHHHHHhCCCccCHHHHHHHHHHHHHHHHHhCcH
Confidence 378999999 99999 89998 79999999999 78899999999999999999 9999999999999999999999
Q ss_pred eEEeccccccc
Q 046914 78 VIEVNVMYEDA 88 (90)
Q Consensus 78 ~~~~~g~eeD~ 88 (90)
+++.+|.||||
T Consensus 112 ~l~~~G~eadd 122 (310)
T COG0258 112 LLELMGIEADD 122 (310)
T ss_pred hhhcCCCCcch
Confidence 99999999997
No 11
>PRK03980 flap endonuclease-1; Provisional
Probab=99.50 E-value=8e-15 Score=109.44 Aligned_cols=79 Identities=14% Similarity=0.119 Sum_probs=71.5
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHH-----------------
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQ----------------- 62 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~----------------- 62 (90)
|.||++++ ||+.. ++++.+..| ++||| ...+++|++.+++||++|.++|+++..
T Consensus 5 G~~Ts~l~-g~~~r~~~ll~~gi~P---vfVFD---G~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~ 77 (292)
T PRK03980 5 GRITSHLS-GIFYRTINLLENGIKP---VYVFD---GKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRS 77 (292)
T ss_pred CcCcHHHH-HHHHHHHHHHHCCCEE---EEEEC---CCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhcc
Confidence 89999999 99999 888764455 88899 788999999999999999999999977
Q ss_pred ------hHHHHHHHHHHcCCceEEeccccccc
Q 046914 63 ------GLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 63 ------Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
|++.++++|++|||+++..|+ ||+|
T Consensus 78 ~~vt~~~~~~~k~lL~~~GIp~i~AP~-EAEA 108 (292)
T PRK03980 78 SRLTDEIVEDSKKLLDLMGIPYVQAPS-EGEA 108 (292)
T ss_pred ccCCHHHHHHHHHHHHHCCCCEEecCc-hHHH
Confidence 999999999999999999998 7665
No 12
>PTZ00217 flap endonuclease-1; Provisional
Probab=99.44 E-value=6e-14 Score=108.35 Aligned_cols=79 Identities=16% Similarity=0.193 Sum_probs=71.2
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhH-------------------
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTI------------------- 60 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L------------------- 60 (90)
|.+|++|+ ||++. ++++.+..| ++||| ...+++|++.++.||++|.++|++|
T Consensus 60 G~~t~~l~-g~~~r~~~Ll~~gikP---v~VFD---G~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~ 132 (393)
T PTZ00217 60 GEVTSHIS-GLFNRTIRLLEAGIKP---VYVFD---GKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRT 132 (393)
T ss_pred CCccHHHH-HHHHHHHHHHHCCCCE---EEEEc---CCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhc
Confidence 78999999 99998 788753455 57888 7778999999999999999999999
Q ss_pred ----HHhHHHHHHHHHHcCCceEEeccccccc
Q 046914 61 ----VQGLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 61 ----~~Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
..|++.++++|+.|||+++..|+ ||||
T Consensus 133 ~~vt~~~~~~~~~lL~~~Gip~i~AP~-EAda 163 (393)
T PTZ00217 133 VRVTKEQNEDAKKLLRLMGIPVIEAPC-EAEA 163 (393)
T ss_pred ccCCHHHHHHHHHHHHHcCCceEECCc-CHHH
Confidence 78999999999999999999998 9997
No 13
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=99.34 E-value=3.2e-13 Score=102.37 Aligned_cols=80 Identities=14% Similarity=0.141 Sum_probs=69.4
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHh----------------
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQG---------------- 63 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Q---------------- 63 (90)
|.||++|+ ||++. ++++.+..| ++||| ...+++|++.++++|+.|.++++++..|
T Consensus 52 G~~t~~l~-g~~~~~~~ll~~~i~P---v~VFD---G~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~ 124 (338)
T TIGR03674 52 GRITSHLS-GLFYRTINLLENGIKP---VYVFD---GKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRS 124 (338)
T ss_pred CCCcHHHH-HHHHHHHHHHHCCCeE---EEEEC---CCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhc
Confidence 88999999 99998 777653344 88999 7788999999999999998888877644
Q ss_pred -------HHHHHHHHHHcCCceEEecccccccc
Q 046914 64 -------LQYLKASIKAMSIKVIEVNVMYEDAY 89 (90)
Q Consensus 64 -------l~~i~~~l~~lGi~~~~~~g~eeD~~ 89 (90)
++.++++|++|||+++.+|+ |||+.
T Consensus 125 ~~~~~~~~~~~k~lL~~~Gip~i~AP~-EAeaq 156 (338)
T TIGR03674 125 SRLTSEIVESSKKLLDLMGIPYVQAPS-EGEAQ 156 (338)
T ss_pred CCCCHHHHHHHHHHHHHcCCeEEECCc-cHHHH
Confidence 99999999999999999998 99873
No 14
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=99.07 E-value=5.7e-11 Score=88.63 Aligned_cols=79 Identities=18% Similarity=0.099 Sum_probs=66.6
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCcc-------ccccCccccCCCCCCch--------------
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNF-------RHTLYPSYKNNRPPTPD-------------- 58 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~-------R~~~yp~YKa~R~~~P~-------------- 58 (90)
|.|+++|+ ||++. ++++. . -+.++||| ....++ |++..++||++|.++|+
T Consensus 50 g~~~~~l~-~~~~rl~~L~~~--~-i~pvfVFD---G~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~ 122 (316)
T cd00128 50 GETTSHLQ-GFFYRTCRLLEL--G-IKPVFVFD---GKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRA 122 (316)
T ss_pred CCCcHHHH-HHHHHHHHHHHC--C-CEEEEEEc---CCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhcc
Confidence 78999999 99998 55544 3 47788899 555555 99999999999998887
Q ss_pred --hHHHhHHHHHHHHHHcCCceEEeccccccc
Q 046914 59 --TIVQGLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 59 --~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
....|++.++++|+++||+++..++ ||||
T Consensus 123 ~~~~~~~~~~~~~lL~~~gi~~i~ap~-EAda 153 (316)
T cd00128 123 VRVTPQMIEEAKELLRLMGIPYIVAPY-EAEA 153 (316)
T ss_pred CcCCHHHHHHHHHHHHHcCCCEEECCc-CHHH
Confidence 3478999999999999999999996 9997
No 15
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=94.02 E-value=0.089 Score=41.95 Aligned_cols=80 Identities=18% Similarity=0.168 Sum_probs=46.5
Q ss_pred CcchHHHHHHHHhh--hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCC-----CCCc-------hhH-------
Q 046914 2 GESYGLLWRGFLSY--NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNR-----PPTP-------DTI------- 60 (90)
Q Consensus 2 G~pt~ai~~gf~~~--~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R-----~~~P-------~~L------- 60 (90)
|.+|.=|. |++.. ++++. . -..++||| ...+....+.+..=..-| .-.| ..+
T Consensus 54 ~~~~~HL~-g~f~Rt~~l~~~--g-i~Pv~VfD---G~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~ 126 (449)
T KOG2519|consen 54 GEPTSHLM-GMFYRTIRLIEN--G-IKPVYVFD---GKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRL 126 (449)
T ss_pred CCchHHHH-HHHHHHHHHHHc--C-CcEEEEEC---CCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHH
Confidence 56888888 88777 67743 3 44677888 433333222222211111 1111 111
Q ss_pred ----HHhHHHHHHHHHHcCCceEEecccccccc
Q 046914 61 ----VQGLQYLKASIKAMSIKVIEVNVMYEDAY 89 (90)
Q Consensus 61 ----~~Ql~~i~~~l~~lGi~~~~~~g~eeD~~ 89 (90)
.++-..++.+|+.|||+++..++ ||-|+
T Consensus 127 vkvtk~~~dEak~LL~lmGIp~i~ap~-EAEAq 158 (449)
T KOG2519|consen 127 VKVTKQHNDEAKRLLSLMGIPVLDAPG-EAEAQ 158 (449)
T ss_pred hhhcchhhHHHHHHHHHcCCeeecCCc-hHHHH
Confidence 11223789999999999999997 87664
No 16
>COG0420 SbcD DNA repair exonuclease [DNA replication, recombination, and repair]
Probab=89.29 E-value=1.4 Score=33.66 Aligned_cols=57 Identities=21% Similarity=0.277 Sum_probs=40.4
Q ss_pred HHhh-hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEeccccc
Q 046914 12 FLSY-NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYE 86 (90)
Q Consensus 12 f~~~-~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~ee 86 (90)
|... .+.++ .+.|.|++|=|+||+.. |.|..+..-+..++.+.+ .|||++.+.|+-.
T Consensus 29 f~~~l~~a~~-~~vD~vliAGDlFd~~~----------------Ps~~a~~~~~~~l~~l~~-~~Ipv~~I~GNHD 86 (390)
T COG0420 29 FDELLEIAKE-EKVDFVLIAGDLFDTNN----------------PSPRALKLFLEALRRLKD-AGIPVVVIAGNHD 86 (390)
T ss_pred HHHHHHHHHH-ccCCEEEEccccccCCC----------------CCHHHHHHHHHHHHHhcc-CCCcEEEecCCCC
Confidence 3344 67777 58999999999999753 445555555555554444 8999999998643
No 17
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=81.76 E-value=5.6 Score=30.25 Aligned_cols=74 Identities=14% Similarity=0.064 Sum_probs=49.0
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCCc--hhHHHhHHHHHHHHHHcCCc
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPTP--DTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~P--~~L~~Ql~~i~~~l~~lGi~ 77 (90)
|.|....- .|.++ +.+.. ..|+|+.+- +-+ ...| .++..++.+.-+.| +.+..++..+.+.|++.|..
T Consensus 168 GlPgqt~~-~~~~tl~~~~~-l~~~~i~~y~l~~---~~gT---~l~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~G~~ 239 (375)
T PRK05628 168 GTPGESDD-DWRASLDAALE-AGVDHVSAYALIV---EDGT---ALARRVRRGELPAPDDDVLADRYELADARLSAAGFD 239 (375)
T ss_pred cCCCCCHH-HHHHHHHHHHh-cCCCEEEeeeeec---CCCC---hHHHHhhcCCCCCCChHHHHHHHHHHHHHHHHcCCC
Confidence 56666666 67777 77777 589988532 221 1111 23445555544444 45889999999999999998
Q ss_pred eEEecc
Q 046914 78 VIEVNV 83 (90)
Q Consensus 78 ~~~~~g 83 (90)
.+++..
T Consensus 240 ~ye~s~ 245 (375)
T PRK05628 240 WYEVSN 245 (375)
T ss_pred eeeecc
Confidence 887764
No 18
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=81.10 E-value=1.3 Score=38.79 Aligned_cols=26 Identities=15% Similarity=0.116 Sum_probs=22.5
Q ss_pred HhHHHHHHHHHHcCCceEEeccccccc
Q 046914 62 QGLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 62 ~Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
..+..++++|+.|||+++..|+ ||+|
T Consensus 772 ~m~~~~~~LL~~~GIP~i~AP~-EAEA 797 (1034)
T TIGR00600 772 QMILESQELLRLFGIPYIVAPM-EAEA 797 (1034)
T ss_pred HHHHHHHHHHHHCCCCeeeCCc-cHHH
Confidence 3467789999999999999996 9986
No 19
>PHA02546 47 endonuclease subunit; Provisional
Probab=79.33 E-value=15 Score=27.83 Aligned_cols=52 Identities=6% Similarity=-0.015 Sum_probs=33.1
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhH-HHHHHHHHHcCCceEEeccc
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGL-QYLKASIKAMSIKVIEVNVM 84 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql-~~i~~~l~~lGi~~~~~~g~ 84 (90)
...++ .+++.++++=|+||... +.+......+ ..+.+.|...|++++.+.|+
T Consensus 33 ~~a~~-~~vD~VliaGDlfD~~~----------------~~~~~~~~~~~~~l~~~L~~~gi~v~~I~GN 85 (340)
T PHA02546 33 EYSKA-HGITTWIQLGDTFDVRK----------------AITQNTMNFVREKIFDLLKEAGITLHVLVGN 85 (340)
T ss_pred HHHHH-cCCCEEEECCcccCCCC----------------CCCHHHHHHHHHHHHHHHHHCCCeEEEEccC
Confidence 56667 59999999999988521 1111111112 12445566789999999885
No 20
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=78.54 E-value=1.8 Score=37.04 Aligned_cols=43 Identities=16% Similarity=0.217 Sum_probs=32.4
Q ss_pred ccCc-cccCCCCCCchhHHHhHHHHHHHHHHcCCceEEeccccccc
Q 046914 44 TLYP-SYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 44 ~~yp-~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
+++. .|+.-|-... -.-.-+..++++|+.+|||+|.+|+ ||.|
T Consensus 448 el~~ek~~~~r~~~e-vt~~m~~e~QElL~~fGIPyI~APm-EAEA 491 (815)
T KOG2520|consen 448 ELLSEKYIQSRGADE-VTSDMFKELQELLRLFGIPYIIAPM-EAEA 491 (815)
T ss_pred HHHHHHHHHhccCch-hHHHHHHHHHHHHHHcCCceecccc-cHHH
Confidence 3444 6777776555 4445578899999999999999995 8865
No 21
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=76.03 E-value=10 Score=28.96 Aligned_cols=75 Identities=9% Similarity=0.002 Sum_probs=48.4
Q ss_pred CCcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCC--chhHHHhHHHHHHHHHHcCC
Q 046914 1 MGESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPT--PDTIVQGLQYLKASIKAMSI 76 (90)
Q Consensus 1 ~G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~--P~~L~~Ql~~i~~~l~~lGi 76 (90)
+|.|...+- .|.+. +.+.. ..|+|+-+- +.+ .++. .+|...+....+. +++...++..+.+.|.+.|.
T Consensus 162 ~GlPgqt~~-~~~~~l~~~~~-l~~~~is~y~l~~--~~gT----~l~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~Gy 233 (370)
T PRK06294 162 YGLPTQSLS-DFIVDLHQAIT-LPITHISLYNLTI--DPHT----SFYKHRKRLLPSIADEEILAEMSLAAEELLTSQGF 233 (370)
T ss_pred cCCCCCCHH-HHHHHHHHHHc-cCCCeEEEeeeEe--cCCC----hHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHcCC
Confidence 467777777 77777 76666 588888642 221 0121 1233344444444 45678899999999999999
Q ss_pred ceEEecc
Q 046914 77 KVIEVNV 83 (90)
Q Consensus 77 ~~~~~~g 83 (90)
..+++..
T Consensus 234 ~~yeis~ 240 (370)
T PRK06294 234 TRYELAS 240 (370)
T ss_pred Ceeeeee
Confidence 8887764
No 22
>PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional
Probab=75.10 E-value=4.3 Score=31.26 Aligned_cols=57 Identities=14% Similarity=0.059 Sum_probs=37.2
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
++++.+..|.||+|..| |...| |+.-.+-...||.. ...+..+-++|..+||.++++
T Consensus 12 ~~l~~g~iP~HVAiIMD----GNrRwAk~~gl~~~~GH~~G-----~~~l~~il~~c~~lGIk~lTl 69 (322)
T PTZ00349 12 SLLRDFINIKHISIIMD----GNRRFAKEKGLHSAIGHFMG-----SKALIQIIEICIKLKIKILSV 69 (322)
T ss_pred HHhhcCCCCCcEEEEcC----CCHHHHHHCCCCHHHHHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 56666568999999999 55555 23223444444432 334555667788899999875
No 23
>PRK10966 exonuclease subunit SbcD; Provisional
Probab=71.44 E-value=21 Score=27.86 Aligned_cols=66 Identities=12% Similarity=0.197 Sum_probs=37.2
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCC-ccccccCccc--cCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGM-NFRHTLYPSY--KNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~-t~R~~~yp~Y--Ka~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+++.. .+|+.++++=|+||...+ .+..+++... +-.+...| =|-...+...+++++..||.++..+
T Consensus 33 ~~i~~-~~~D~viIaGDifD~~~p~~~a~~~~~~~l~~L~~~~~~v~~I~GNHD~~~~l~~~~~~l~~~gi~vl~~~ 108 (407)
T PRK10966 33 EQVQE-HQVDAIIVAGDIFDTGSPPSYARELYNRFVVNLQQTGCQLVVLAGNHDSVATLNESRDLLAFLNTTVIASA 108 (407)
T ss_pred HHHHh-cCCCEEEECCccccCCCCcHHHHHHHHHHHHHHHhcCCcEEEEcCCCCChhhhhhHHHHHHHCCcEEEecc
Confidence 66677 699999999999997543 2222221111 00111122 0112335566788888888877554
No 24
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=68.93 E-value=17 Score=27.54 Aligned_cols=74 Identities=12% Similarity=0.068 Sum_probs=47.4
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEE-eeeCCCCCCCccccccCccccCCCCCC--chhHHHhHHHHHHHHHHcCCc
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLD-VHDLYGACGMNFRHTLYPSYKNNRPPT--PDTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v-~fD~fD~~~~t~R~~~yp~YKa~R~~~--P~~L~~Ql~~i~~~l~~lGi~ 77 (90)
|.|-...- .|.+. +.+.+ ..|+|+.+ .+-+ .++ ..++..++.++-+. +++....+..+.+.|.+.|..
T Consensus 159 GlPgqt~e-~~~~~l~~~~~-l~~~~is~y~l~~--~pg----T~l~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~Gy~ 230 (374)
T PRK05799 159 GLPNQTLE-DWKETLEKVVE-LNPEHISCYSLII--EEG----TPFYNLYENGKLKLPDEEEEREMYHYTIEFLKEKGYH 230 (374)
T ss_pred CCCCCCHH-HHHHHHHHHHh-cCCCEEEEeccEe--cCC----CHHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHcCCc
Confidence 45555555 56666 66666 58888743 2331 122 23444566665443 456778889999999999999
Q ss_pred eEEecc
Q 046914 78 VIEVNV 83 (90)
Q Consensus 78 ~~~~~g 83 (90)
.+++..
T Consensus 231 ~ye~~~ 236 (374)
T PRK05799 231 QYEISN 236 (374)
T ss_pred EEeeee
Confidence 888764
No 25
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=68.40 E-value=17 Score=28.54 Aligned_cols=75 Identities=12% Similarity=-0.047 Sum_probs=49.9
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCc---hhHHHhHHHHHHHHHHcCCc
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP---DTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P---~~L~~Ql~~i~~~l~~lGi~ 77 (90)
|.|....- .|.+. +.+.+ ..|+|+.+ +.. -....| .++..++.++-+.| ++-...+..+.+.|.+.|..
T Consensus 223 GlPgqT~e-~~~~~l~~~~~-l~~~~is~-y~L-~~~pgT---~l~~~~~~g~l~~~~~~~~~~~my~~~~~~L~~~Gy~ 295 (449)
T PRK09058 223 GLPGQTPE-IWQQDLAIVRD-LGLDGVDL-YAL-NLLPGT---PLAKAVEKGKLPPPATPAERADMYAYGVEFLAKAGWR 295 (449)
T ss_pred eCCCCCHH-HHHHHHHHHHh-cCCCEEEE-ecc-ccCCCC---HHHHHHHcCCCCCCCCHHHHHHHHHHHHHHHHHCCCe
Confidence 66666666 67777 66666 58888753 221 011122 34556777775544 67788899999999999999
Q ss_pred eEEecc
Q 046914 78 VIEVNV 83 (90)
Q Consensus 78 ~~~~~g 83 (90)
.+++..
T Consensus 296 ~yeis~ 301 (449)
T PRK09058 296 QLSNSH 301 (449)
T ss_pred EEeeee
Confidence 887753
No 26
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=67.35 E-value=23 Score=27.38 Aligned_cols=74 Identities=11% Similarity=0.047 Sum_probs=49.3
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCC--chhHHHhHHHHHHHHHHcCCc
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPT--PDTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~--P~~L~~Ql~~i~~~l~~lGi~ 77 (90)
|.|....- .+.++ +.+.+ ..|+|+.+- +-+ .++. .++..|+.++.+. +++...++..+.+.|.+.|..
T Consensus 175 GlPgqt~e-~~~~tl~~~~~-l~p~~is~y~L~~--~pgT----~l~~~~~~g~~~~~~~~~~~~~~~~~~~~L~~~Gy~ 246 (400)
T PRK07379 175 GLPHQTLE-DWQASLEAAIA-LNPTHLSCYDLVL--EPGT----AFGKQYQPGKAPLPSDETTAAMYRLAQEILTQAGYE 246 (400)
T ss_pred CCCCCCHH-HHHHHHHHHHc-CCCCEEEEeccee--cCCc----hhHHHhhcCCCCCCCHHHHHHHHHHHHHHHHHcCCc
Confidence 66666666 66677 76666 588888643 111 0222 2445566666544 456678899999999999999
Q ss_pred eEEecc
Q 046914 78 VIEVNV 83 (90)
Q Consensus 78 ~~~~~g 83 (90)
.+++..
T Consensus 247 ~yeisn 252 (400)
T PRK07379 247 HYEISN 252 (400)
T ss_pred eeeeeh
Confidence 888764
No 27
>PF08984 DUF1858: Domain of unknown function (DUF1858); InterPro: IPR015077 This protein has no known function. It is found in various hypothetical bacterial proteins. ; PDB: 2K53_A 2K5E_A 2FI0_A.
Probab=66.56 E-value=2.3 Score=24.26 Aligned_cols=26 Identities=8% Similarity=0.078 Sum_probs=22.2
Q ss_pred hhHHHhHHHHHHHHHHcCCceEEecc
Q 046914 58 DTIVQGLQYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 58 ~~L~~Ql~~i~~~l~~lGi~~~~~~g 83 (90)
-+|..|.|.+.++|..+|+.++.-+.
T Consensus 8 ~el~~~yP~~~~il~~~gf~~l~~p~ 33 (59)
T PF08984_consen 8 YELLEQYPELIEILVSYGFHCLGNPV 33 (59)
T ss_dssp HHHHHH-GGGHHHHHHTTGGGGGSCC
T ss_pred HHHHHHCHHHHHHHHHcCCcccCCcH
Confidence 58899999999999999999987764
No 28
>cd07384 MPP_Cdc1_like Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain. Cdc1 (also known as XlCdc1 in Xenopus laevis) is an endoplasmic reticulum-localized transmembrane lipid phosphatase with a metallophosphatase domain facing the ER lumen. In budding yeast, the gene encoding CDC1 is essential while nonlethal mutations cause defects in Golgi inheritance and actin polarization. Cdc1 mutant cells accumulate an unidentified phospholipid, suggesting that Cdc1 is a lipid phosphatase. Cdc1 mutant cells also have highly elevated intracellular calcium levels suggesting a possible role for Cdc1 in calcium regulation. The 5' flanking region of Cdc1 is a regulatory region with conserved binding site motifs for AP1, AP2, Sp1, NF-1 and CREB. DNA polymerase delta consists of at least four subunits - Pol3, Cdc1, Cdc27, and Cdm1. This group also contains Saccharomyces cerevisiae TED1 (Trafficking of Emp24p/Erv25p-dependent cargo disrupted 1), which acts together wit
Probab=66.44 E-value=38 Score=23.01 Aligned_cols=53 Identities=15% Similarity=0.066 Sum_probs=35.5
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHH-----cCCceEEeccc
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKA-----MSIKVIEVNVM 84 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~-----lGi~~~~~~g~ 84 (90)
++++. .+|+.+++.=|.||.+...-+ ++....+..+++++.. .+++++.++|+
T Consensus 39 ~~i~~-~~pd~vi~lGDl~d~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~GN 96 (171)
T cd07384 39 TALQR-LKPDVVLFLGDLFDGGRIADS---------------EEWEEYVKRFKKIFFLPSNGLEDIPVYYVPGN 96 (171)
T ss_pred HHHHh-cCCCEEEEeccccCCcEeCCH---------------HHHHHHHHHHHHHhcccccccCCceEEEECCc
Confidence 56677 699999999999886443211 3444455555565543 27888888884
No 29
>KOG1056 consensus Glutamate-gated metabotropic ion channel receptor subunit GRM2 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=65.62 E-value=6.7 Score=34.00 Aligned_cols=34 Identities=18% Similarity=0.287 Sum_probs=29.8
Q ss_pred CCchhHHHhHHHHHHHHHHcCCceEEeccccccccC
Q 046914 55 PTPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDAYG 90 (90)
Q Consensus 55 ~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~~~ 90 (90)
-.|.|- -|-..+-++++.+|+.+++..+ .||+||
T Consensus 174 tVP~D~-~Qa~Am~~il~~f~W~yVstv~-s~~dYG 207 (878)
T KOG1056|consen 174 TVPSDV-FQAQAMVDILKKFNWNYVSTVA-SEGDYG 207 (878)
T ss_pred ecCChH-HHHHHHHHHHHHhCeeEeeehh-cCccch
Confidence 366666 7888899999999999999997 999998
No 30
>PF12813 XPG_I_2: XPG domain containing
Probab=64.24 E-value=5.7 Score=29.05 Aligned_cols=25 Identities=8% Similarity=0.137 Sum_probs=21.3
Q ss_pred HHHHHHHHHHc---CCceEEecccccccc
Q 046914 64 LQYLKASIKAM---SIKVIEVNVMYEDAY 89 (90)
Q Consensus 64 l~~i~~~l~~l---Gi~~~~~~g~eeD~~ 89 (90)
.+.+.+.|..+ |+.+...+| |||.|
T Consensus 6 ~~~~~e~L~~~~~~~~~~~~~~~-EAD~~ 33 (246)
T PF12813_consen 6 VPAFIEALRESWRYGVPVVQCPG-EADRE 33 (246)
T ss_pred HHHHHHHHHHHhhcCCcEEEcCc-cchHH
Confidence 35678888888 999999998 99975
No 31
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=63.98 E-value=20 Score=27.76 Aligned_cols=75 Identities=12% Similarity=0.081 Sum_probs=48.7
Q ss_pred CCcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCCc--hhHHHhHHHHHHHHHHcCC
Q 046914 1 MGESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPTP--DTIVQGLQYLKASIKAMSI 76 (90)
Q Consensus 1 ~G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~P--~~L~~Ql~~i~~~l~~lGi 76 (90)
+|.|-..+- .+.+. +.+.. ..|+|+-+- +.+ .++ ..++..|+.++-..| ++....+..+.+.|++.|.
T Consensus 169 ~GlPgqt~e-~~~~~l~~~~~-l~p~his~y~L~i--~~g----T~l~~~~~~g~~~~p~~~~~~~~~~~~~~~L~~~Gy 240 (390)
T PRK06582 169 YARSGQTLK-DWQEELKQAMQ-LATSHISLYQLTI--EKG----TPFYKLFKEGNLILPHSDAAAEMYEWTNHYLESKKY 240 (390)
T ss_pred cCCCCCCHH-HHHHHHHHHHh-cCCCEEEEecCEE--ccC----ChHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHcCC
Confidence 366666665 56666 55555 488887643 121 122 224455666665444 5678889999999999999
Q ss_pred ceEEecc
Q 046914 77 KVIEVNV 83 (90)
Q Consensus 77 ~~~~~~g 83 (90)
..+++..
T Consensus 241 ~~yeis~ 247 (390)
T PRK06582 241 FRYEISN 247 (390)
T ss_pred ceeecee
Confidence 8888764
No 32
>PRK13397 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=63.44 E-value=9.9 Score=28.20 Aligned_cols=21 Identities=19% Similarity=0.409 Sum_probs=19.1
Q ss_pred HhHHHHHHHHHHcCCceEEec
Q 046914 62 QGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 62 ~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
++++++++.++.+||++++-.
T Consensus 66 ~gl~~L~~~~~~~Gl~~~Tev 86 (250)
T PRK13397 66 QGIRYLHEVCQEFGLLSVSEI 86 (250)
T ss_pred HHHHHHHHHHHHcCCCEEEee
Confidence 599999999999999999765
No 33
>PRK05904 coproporphyrinogen III oxidase; Provisional
Probab=63.25 E-value=34 Score=26.15 Aligned_cols=73 Identities=14% Similarity=0.035 Sum_probs=47.3
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|....- .|.++ +.+.+ ..|+|+.+- +.+ ..+.+-++. .+.+.+++-.+.+..+.+.|+..|...+
T Consensus 163 GlPgqt~e-~~~~tl~~~~~-l~p~~is~y~L~~-~~gT~l~~~--------~~~~~~~~~~~~~~~~~~~L~~~Gy~~y 231 (353)
T PRK05904 163 CLPILKLK-DLDEVFNFILK-HKINHISFYSLEI-KEGSILKKY--------HYTIDEDKEAEQLNYIKAKFNKLNYKRY 231 (353)
T ss_pred cCCCCCHH-HHHHHHHHHHh-cCCCEEEEEeeEe-cCCChHhhc--------CCCCChHHHHHHHHHHHHHHHHcCCcEE
Confidence 56666666 67777 77777 688887543 221 012222222 2234456678889999999999999999
Q ss_pred Eeccccc
Q 046914 80 EVNVMYE 86 (90)
Q Consensus 80 ~~~g~ee 86 (90)
++.. ++
T Consensus 232 eisn-fa 237 (353)
T PRK05904 232 EVSN-WT 237 (353)
T ss_pred echh-hc
Confidence 8874 54
No 34
>PRK14836 undecaprenyl pyrophosphate synthase; Provisional
Probab=63.07 E-value=9.9 Score=28.17 Aligned_cols=57 Identities=11% Similarity=0.088 Sum_probs=37.0
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
.+++....|.||+|..| +...| |+.-.+-...+|. -..-+..+-++|..+||..+++
T Consensus 7 ~~~~~~~~P~HVAiImD----GNrRwA~~~gl~~~~GH~~-----G~~~~~~iv~~c~~~gI~~lTv 64 (253)
T PRK14836 7 MIPANENIPRHIAIIMD----GNGRWAKRRGKPRVEGHRA-----GVRAVRRTIEFCLEKGIEMLTL 64 (253)
T ss_pred cccccCCCCCeEEEecC----CcHHHHHHCCCchhhhHHH-----HHHHHHHHHHHHHHcCCCEEeh
Confidence 34454357999999999 54444 3333344445543 3445666777888899998875
No 35
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=62.58 E-value=16 Score=28.05 Aligned_cols=72 Identities=11% Similarity=0.034 Sum_probs=46.0
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCCc--hhHHHhHHHHHHHHHHcCCc
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPTP--DTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~P--~~L~~Ql~~i~~~l~~lGi~ 77 (90)
|.|-..+- .+.+. +.+.. ..|+|+.+- +-+ .++ ..+|..++.++-..| ++....+..+.++|+..|..
T Consensus 163 GlPgqt~~-~~~~~l~~~~~-l~p~~is~y~L~~--~~g----T~l~~~~~~g~~~~~~~~~~~~~~~~~~~~L~~~G~~ 234 (380)
T PRK09057 163 ARPGQTLA-AWRAELKEALS-LAADHLSLYQLTI--EEG----TAFYGLHAAGKLILPDEDLAADLYELTQEITAAAGLP 234 (380)
T ss_pred CCCCCCHH-HHHHHHHHHHh-cCCCeEEeeccee--cCC----ChHHHHHhcCCCCCCChHHHHHHHHHHHHHHHHcCCc
Confidence 66666666 66666 44445 488888643 111 011 234556776665554 56678899999999999997
Q ss_pred eEEe
Q 046914 78 VIEV 81 (90)
Q Consensus 78 ~~~~ 81 (90)
.+++
T Consensus 235 ~ye~ 238 (380)
T PRK09057 235 AYEI 238 (380)
T ss_pred hhhh
Confidence 6653
No 36
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=62.36 E-value=7.1 Score=28.32 Aligned_cols=49 Identities=6% Similarity=0.076 Sum_probs=31.9
Q ss_pred CCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 24 TDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 24 p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
|.||+|..| |...| |+.-.+...++|.. ...+..+-++|..+||.++++
T Consensus 1 P~HvaiImD----GNrRwA~~~gl~~~~GH~~G-----~~~~~~i~~~~~~~gI~~lTv 50 (221)
T cd00475 1 PKHVAFIMD----GNRRWAKQRGMDRIEGHKAG-----AEKLRDILRWCLELGVKEVTL 50 (221)
T ss_pred CCeEEEecC----CCHHHHHHCCCChhHhHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 789999999 55544 33333545555532 334556667788899999876
No 37
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=60.99 E-value=14 Score=27.27 Aligned_cols=56 Identities=7% Similarity=0.178 Sum_probs=36.0
Q ss_pred hhhccCCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 17 IRHDTYMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 17 l~~~~~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
+++....|.||+|..| +...| |+.-.+....+| .-...+..+-++|..+||..+++
T Consensus 16 ~~~~~~~P~HVAiImD----GNrRwAk~~gl~~~~Gh~-----~G~~~l~~~l~~c~~~GI~~vTv 72 (251)
T PRK14830 16 ELDKGNIPKHIAIIMD----GNGRWAKKRMLPRIAGHK-----AGMDTVKKITKAASELGVKVLTL 72 (251)
T ss_pred ccCCCCCCCeEEEEec----CchHHHHHCCCchhhhHH-----HHHHHHHHHHHHHHHcCCCEEEE
Confidence 4443347999999999 55444 332233334444 33456677778888999998875
No 38
>PF14582 Metallophos_3: Metallophosphoesterase, calcineurin superfamily; PDB: 1UF3_B 2YVT_A.
Probab=60.82 E-value=17 Score=27.25 Aligned_cols=69 Identities=19% Similarity=0.165 Sum_probs=38.3
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCccccccCc-cccCCCCCCchhH----HHh---HHHHHHHHHHcCCceEEecccccc
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRHTLYP-SYKNNRPPTPDTI----VQG---LQYLKASIKAMSIKVIEVNVMYED 87 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp-~YKa~R~~~P~~L----~~Q---l~~i~~~l~~lGi~~~~~~g~eeD 87 (90)
+++.+ ..||.++++=| --..+-|.+-|. .-.++|.|.=+++ ..| +...-..|..+|+|++.+|| --|
T Consensus 26 ~~~~e-~~~D~~v~~G~---~~~~~a~~~e~~~a~~~~r~p~k~~i~~e~~~~~e~~~~ff~~L~~~~~p~~~vPG-~~D 100 (255)
T PF14582_consen 26 EVIPE-KGPDAVVFVGD---LLKAEARSDEYERAQEEQREPDKSEINEEECYDSEALDKFFRILGELGVPVFVVPG-NMD 100 (255)
T ss_dssp HHHHH-HT-SEEEEES----SS-TCHHHHHHHHHHHTT----THHHHHHHHHHHHHHHHHHHHHHCC-SEEEEE---TTS
T ss_pred hhccc-cCCCEEEEecc---ccccchhhhHHHHHhhhccCcchhhhhhhhhhhHHHHHHHHHHHHhcCCcEEEecC-CCC
Confidence 57777 49999999999 444555665554 4446666533222 333 44555667889999999998 667
Q ss_pred cc
Q 046914 88 AY 89 (90)
Q Consensus 88 ~~ 89 (90)
++
T Consensus 101 ap 102 (255)
T PF14582_consen 101 AP 102 (255)
T ss_dssp -S
T ss_pred ch
Confidence 64
No 39
>PRK14839 undecaprenyl pyrophosphate synthase; Provisional
Probab=60.55 E-value=13 Score=27.47 Aligned_cols=51 Identities=10% Similarity=0.096 Sum_probs=34.3
Q ss_pred CCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 22 YMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
..|.||+|..| |...| |+.-.+...++|.. ...+..+-++|..+||..+++
T Consensus 8 ~~P~HVAiImD----GNrRwAk~~gl~~~~GH~~G-----~~~l~~i~~~c~~~GI~~lTv 59 (239)
T PRK14839 8 RSGLHVAIIMD----GNGRWATARGLPRLAGHRAG-----VEAIRRVVEAAPDLGIGTLTL 59 (239)
T ss_pred CCCCEEEEEcC----CCHHHHHHCCCCHHHHHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 48999999999 55555 44444555555532 334555666778899998875
No 40
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=60.23 E-value=30 Score=25.65 Aligned_cols=57 Identities=5% Similarity=0.040 Sum_probs=32.9
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCcccc-ccCccc-cCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRH-TLYPSY-KNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~-~~yp~Y-Ka~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
..++.+.-|.||+|..| +...|-+ .-.+.. .++|.. ..-+..+-+.|..+||..+++
T Consensus 19 ~~~~~~~~P~HvAiImD----GNrRwA~~~gl~~~~~GH~~G-----~~~l~~~~~~~~~~gIk~lTv 77 (256)
T PRK14828 19 GELDGAQVPGHVGIIVD----GNRRWARKAGFTDVSQGHRAG-----AAKIGEFLGWCDETDVNVVTL 77 (256)
T ss_pred hhcccCCCCCEEEEEec----CChHHHHHcCCCchHHHHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 34443247999999999 5555532 222333 333321 233444556677899998876
No 41
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=60.03 E-value=30 Score=27.19 Aligned_cols=76 Identities=9% Similarity=-0.015 Sum_probs=45.3
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEE
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIE 80 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~ 80 (90)
|.|-...- .|... +.+.. ..|+++.+- . -...-+.+..-..-+....|.+++...++..+.+.|.+.|...++
T Consensus 212 GlPgqt~e-~~~~tl~~~~~-l~p~~i~~y-~---l~~~p~~~~~~~~~~~~~lp~~~~~~~~~~~~~~~L~~~Gy~~~~ 285 (453)
T PRK13347 212 GLPHQTVE-SFRETLDKVIA-LSPDRIAVF-G---YAHVPSRRKNQRLIDEAALPDAEERLRQARAVADRLLAAGYVPIG 285 (453)
T ss_pred eCCCCCHH-HHHHHHHHHHh-cCCCEEEEe-c---cccccchhhHHhcCCccCCcCHHHHHHHHHHHHHHHHHCCCEEEe
Confidence 55555566 67777 76677 588887632 2 111111110000001223355678889999999999999998887
Q ss_pred ecc
Q 046914 81 VNV 83 (90)
Q Consensus 81 ~~g 83 (90)
+..
T Consensus 286 ~~~ 288 (453)
T PRK13347 286 LDH 288 (453)
T ss_pred ccc
Confidence 763
No 42
>TIGR00619 sbcd exonuclease SbcD. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=58.50 E-value=54 Score=23.66 Aligned_cols=22 Identities=14% Similarity=0.197 Sum_probs=17.9
Q ss_pred hhhhccCCCCeEEEeeeCCCCCC
Q 046914 16 NIRHDTYMTDITLDVHDLYGACG 38 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~ 38 (90)
.++.+ .+++.++++=|+||...
T Consensus 33 ~~~~~-~~~D~lli~GDi~d~~~ 54 (253)
T TIGR00619 33 EFAKA-EQIDALLVAGDVFDTAN 54 (253)
T ss_pred HHHHH-cCCCEEEECCccCCCCC
Confidence 56666 58999999999999654
No 43
>PRK14833 undecaprenyl pyrophosphate synthase; Provisional
Probab=57.70 E-value=11 Score=27.70 Aligned_cols=50 Identities=6% Similarity=0.002 Sum_probs=34.3
Q ss_pred CCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 23 MTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
.|.||+|..| |...| |+.-.+...+||.. ...+..+-+.|..+||..+++
T Consensus 4 ~P~HVaiImD----GNrRwA~~~gl~~~~GH~~G-----~~~l~~~~~~c~~~gI~~lTv 54 (233)
T PRK14833 4 TLKHLAIIMD----GNGRWAKLRGKARAAGHKKG-----VKTLREITIWCANHKLECLTL 54 (233)
T ss_pred CCCeEEEEcc----CCHHHHHHCCCChhhhHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 6899999999 55555 44445556666542 334555666778899998875
No 44
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=57.37 E-value=9.1 Score=28.15 Aligned_cols=52 Identities=8% Similarity=-0.031 Sum_probs=34.4
Q ss_pred CCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEec
Q 046914 22 YMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
..|.||+|..| |...| |+.-.+...++|.. ..-+..+-++|..+||+.+++=
T Consensus 13 ~~P~HvaiImD----GNrRwAk~~g~~~~~GH~~G-----~~~l~~iv~~c~~~gI~~vTvY 65 (243)
T PRK14829 13 KLPRHIAVVMD----GNGRWATQRGLKRTEGHKAG-----EPVLFDVVAGAIEAGVPYLSLY 65 (243)
T ss_pred CCCCeEEEecC----CCHHHHHHCCCChhHHHHHH-----HHHHHHHHHHHHHcCCCEEEEe
Confidence 47999999999 55555 33333444444432 3345566678889999998763
No 45
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=57.02 E-value=16 Score=26.93 Aligned_cols=52 Identities=15% Similarity=0.149 Sum_probs=34.6
Q ss_pred CCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEec
Q 046914 22 YMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
.-|.||+|..| |...| |+.-.+-..++|.. ...+..+-+.|..+||.++++=
T Consensus 19 ~~P~HVaiImD----GNrRwA~~~gl~~~~GH~~G-----~~~l~~i~~~c~~~GI~~vT~y 71 (249)
T PRK14831 19 RLPKHVAVIMD----GNGRWAKRRGLPRIMGHRRG-----VDALKDLLRCCKDWGIGALTAY 71 (249)
T ss_pred CCCCeEEEecC----CcHHHHHHCCCchhhhHHHH-----HHHHHHHHHHHHHcCCCEEEEe
Confidence 47999999999 55555 33334555555532 3345566677888999998763
No 46
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=56.96 E-value=17 Score=26.55 Aligned_cols=50 Identities=12% Similarity=0.100 Sum_probs=32.8
Q ss_pred CCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 23 MTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
.|.||+|..| |...| |+.-.+...+++.. ..-+..+-+.|..+||.++++
T Consensus 3 ~P~HVaiImD----GNrRwAk~~g~~~~~GH~~G-----~~~l~~i~~~~~~lgIk~lTv 53 (233)
T PRK14841 3 IPQHVAIIMD----GNGRWAKKRGLPRIKGHQRG-----AEVLHNTVKWSLELGIKYLTA 53 (233)
T ss_pred CCCEEEEEcc----CCHHHHHHCCCchhhhHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 5899999999 55555 33334555555432 233555666778899999875
No 47
>cd07402 MPP_GpdQ Enterobacter aerogenes GpdQ and related proteins, metallophosphatase domain. GpdQ (glycerophosphodiesterase Q, also known as Rv0805 in Mycobacterium tuberculosis) is a binuclear metallophosphoesterase from Enterobacter aerogenes that catalyzes the hydrolysis of mono-, di-, and triester substrates, including some organophosphate pesticides and products of the degradation of nerve agents. The GpdQ homolog, Rv0805, has 2',3'-cyclic nucleotide phosphodiesterase activity. GpdQ and Rv0805 belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosa
Probab=56.50 E-value=63 Score=22.26 Aligned_cols=47 Identities=19% Similarity=0.181 Sum_probs=33.3
Q ss_pred hhhhccC--CCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEecccc
Q 046914 16 NIRHDTY--MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMY 85 (90)
Q Consensus 16 ~l~~~~~--~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~e 85 (90)
+.++. . +|+.++++=|+.+.+. + .+...+.++++.++++++.++|.-
T Consensus 32 ~~i~~-~~~~~d~vi~~GDl~~~~~------------------~----~~~~~~~~~l~~~~~p~~~v~GNH 80 (240)
T cd07402 32 AHINA-LHPRPDLVLVTGDLTDDGS------------------P----ESYERLRELLAALPIPVYLLPGNH 80 (240)
T ss_pred HHHHh-cCCCCCEEEECccCCCCCC------------------H----HHHHHHHHHHhhcCCCEEEeCCCC
Confidence 44444 3 7899999999654321 1 245567778888899999999854
No 48
>cd08165 MPP_MPPE1 human MPPE1 and related proteins, metallophosphatase domain. MPPE1 is a functionally uncharacterized metallophosphatase domain-containing protein. The MPPE1 gene is located on chromosome 18 and is a candidate susceptibility gene for Bipolar disorder. MPPE1 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to
Probab=55.96 E-value=45 Score=22.25 Aligned_cols=54 Identities=9% Similarity=-0.011 Sum_probs=33.6
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHH-cCCceEEecccc
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKA-MSIKVIEVNVMY 85 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~-lGi~~~~~~g~e 85 (90)
+++.. .+|+.+++.=|+||.+....+ ++....+..+++++.. .+++++.+.|+-
T Consensus 32 ~~i~~-~~pd~vv~~GDl~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~i~~v~GNH 86 (156)
T cd08165 32 TSLWL-LQPDVVFVLGDLFDEGKWSTD---------------EEWEDYVERFKKMFGHPPDLPLHVVVGNH 86 (156)
T ss_pred HHHHh-cCCCEEEECCCCCCCCccCCH---------------HHHHHHHHHHHHHhccCCCCeEEEEcCCC
Confidence 56777 699999999998765332111 2333334445555544 378888888743
No 49
>cd08163 MPP_Cdc1 Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain. Cdc1 (also known as XlCdc1 in Xenopus laevis) is an endoplasmic reticulum-localized transmembrane lipid phosphatase with a metallophosphatase domain facing the ER lumen. In budding yeast, the gene encoding CDC1 is essential while nonlethal mutations cause defects in Golgi inheritance and actin polarization. Cdc1 mutant cells accumulate an unidentified phospholipid, suggesting that Cdc1 is a lipid phosphatase. Cdc1 mutant cells also have highly elevated intracellular calcium levels suggesting a possible role for Cdc1 in calcium regulation. The 5' flanking region of Cdc1 is a regulatory region with conserved binding site motifs for AP1, AP2, Sp1, NF-1 and CREB. DNA polymerase delta consists of at least four subunits - Pol3, Cdc1, Cdc27, and Cdm1. Cdc1 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site
Probab=55.62 E-value=44 Score=24.38 Aligned_cols=52 Identities=10% Similarity=0.001 Sum_probs=34.4
Q ss_pred hhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHc--CCceEEeccc
Q 046914 17 IRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAM--SIKVIEVNVM 84 (90)
Q Consensus 17 l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~l--Gi~~~~~~g~ 84 (90)
+.+. .+|+.+++.=|.||.+.. ...++..+.+..+++++... .++++.++|.
T Consensus 40 ~~~~-l~PD~vv~lGDL~d~G~~---------------~~~~~~~~~~~rf~~i~~~~~~~~pv~~VpGN 93 (257)
T cd08163 40 MQKQ-LKPDSTIFLGDLFDGGRD---------------WADEYWKKEYNRFMRIFDPSPGRKMVESLPGN 93 (257)
T ss_pred HHHh-cCCCEEEEecccccCCee---------------CcHHHHHHHHHHHHHHhcCCCccceEEEeCCC
Confidence 4455 589999999998885321 22255555566667776554 3778888873
No 50
>TIGR00583 mre11 DNA repair protein (mre11). All proteins in this family for which functions are known are subunits of a nuclease complex made up of multiple proteins including MRE11 and RAD50 homologs. The functions of this nuclease complex include recombinational repair and non-homolgous end joining. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). The proteins in this family are distantly related to proteins in the SbcCD complex of bacteria.
Probab=55.28 E-value=50 Score=26.00 Aligned_cols=24 Identities=21% Similarity=0.177 Sum_probs=19.5
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCc
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMN 40 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t 40 (90)
++... .++|.|+++=|+||...++
T Consensus 36 ~~a~~-~~vD~VLiaGDLFd~~~Ps 59 (405)
T TIGR00583 36 QIAKE-QDVDMILLGGDLFHENKPS 59 (405)
T ss_pred HHHHH-cCCCEEEECCccCCCCCCC
Confidence 56666 5899999999999976655
No 51
>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Lac family includes several sequenced lactose (b-galactoside) permeases of Gram-positive bacteria as well as those in E. coli. While the Lac family usually consists of two polypeptide components IIA and IICB, the Chb permease of E. coli consists of three IIA, IIB and IIC. This family is specific for the IIB subunit of the Lac PTS family.
Probab=54.53 E-value=19 Score=22.46 Aligned_cols=27 Identities=22% Similarity=0.124 Sum_probs=23.3
Q ss_pred chhHHHhHHHHHHHHHHcCCceEEecc
Q 046914 57 PDTIVQGLQYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 57 P~~L~~Ql~~i~~~l~~lGi~~~~~~g 83 (90)
-+.+...++.+++.++..|+|+..++.
T Consensus 57 ~pqi~~~~~~i~~~~~~~~ipv~~I~~ 83 (95)
T TIGR00853 57 APQVAYMLPDLKKETDKKGIPVEVING 83 (95)
T ss_pred CchHHHHHHHHHHHhhhcCCCEEEeCh
Confidence 357788899999999999999998875
No 52
>PF00411 Ribosomal_S11: Ribosomal protein S11; InterPro: IPR001971 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S11 [] plays an essential role in selecting the correct tRNA in protein biosynthesis. It is located on the large lobe of the small ribosomal subunit. On the basis of sequence similarities, S11 belongs to a family of bacterial, archaeal and eukaryotic ribosomal proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2YKR_K 3U5C_O 3O2Z_H 3IZB_K 3U5G_O 3O30_H 1S1H_K 3BBN_K 2XZN_K 2XZM_K ....
Probab=54.50 E-value=20 Score=23.08 Aligned_cols=42 Identities=21% Similarity=0.275 Sum_probs=34.0
Q ss_pred ccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 40 NFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 40 t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
.|..-=--.||..|+.+|..-..-.+.+-+.+..+||..+.+
T Consensus 25 ~~~S~G~~gfK~~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v 66 (110)
T PF00411_consen 25 FWSSAGSLGFKGARKSTPYAAQQAAEKIAKKAKELGIKTVRV 66 (110)
T ss_dssp EEEETTTSSTTTTCGSSHHHHHHHHHHHHHHHHCTTEEEEEE
T ss_pred EEEeccccccccccccCHHHHHHHHHHHHHHHHHcCCeEEEE
Confidence 455555578999999999988888888888888899987765
No 53
>PRK13398 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=53.98 E-value=14 Score=27.40 Aligned_cols=22 Identities=23% Similarity=0.277 Sum_probs=19.8
Q ss_pred HHhHHHHHHHHHHcCCceEEec
Q 046914 61 VQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 61 ~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
..++..++++++.+||++++-.
T Consensus 77 ~~gl~~l~~~~~~~Gl~~~te~ 98 (266)
T PRK13398 77 EEGLKILKEVGDKYNLPVVTEV 98 (266)
T ss_pred HHHHHHHHHHHHHcCCCEEEee
Confidence 7889999999999999998765
No 54
>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]
Probab=53.83 E-value=46 Score=26.18 Aligned_cols=74 Identities=8% Similarity=-0.083 Sum_probs=47.6
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCC-CCCchhHHHhHHHHHHHHHHcCCce
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNR-PPTPDTIVQGLQYLKASIKAMSIKV 78 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R-~~~P~~L~~Ql~~i~~~l~~lGi~~ 78 (90)
|.|.+.+- .|.+. +...+ ..|+|+.+= +- ....+.= +...+... .|.+++...+...+.+.|+..|...
T Consensus 197 glP~QT~~-~~~~~l~~a~~-l~pdhis~y~L~---~~p~t~~---~~~~~~~~~lP~~d~~~~~~~~~~e~L~~~Gy~~ 268 (416)
T COG0635 197 GLPGQTLE-SLKEDLEQALE-LGPDHLSLYSLA---IEPGTKF---AQRKIKGKALPDEDEKADMYELVEELLEKAGYRQ 268 (416)
T ss_pred CCCCCCHH-HHHHHHHHHHh-CCCCEEEEeeee---cCCCchh---hhhcccCCCCcChHHHHHHHHHHHHHHHHCCCcE
Confidence 66777777 67777 66666 589998632 11 1122211 12222222 3455677999999999999999999
Q ss_pred EEecc
Q 046914 79 IEVNV 83 (90)
Q Consensus 79 ~~~~g 83 (90)
++++.
T Consensus 269 yeisn 273 (416)
T COG0635 269 YEISN 273 (416)
T ss_pred Eeech
Confidence 98875
No 55
>PRK14838 undecaprenyl pyrophosphate synthase; Provisional
Probab=53.79 E-value=19 Score=26.58 Aligned_cols=51 Identities=4% Similarity=0.067 Sum_probs=32.2
Q ss_pred CCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 22 YMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
..|.||+|..| |...| |+.-.+....+|.. ..-+..+-+.|..+||..+++
T Consensus 9 ~~P~HVAiImD----GNrRwA~~~gl~~~~GH~~G-----~~~l~~i~~~~~~~gI~~lT~ 60 (242)
T PRK14838 9 RIPQHIAIIMD----GNGRWAKERGKERSFGHQAG-----AETVHIITEEAARLGVKFLTL 60 (242)
T ss_pred CCCCEEEEecc----CCHHHHHHCCCCHHHHHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 47999999999 55555 33333444444421 233455556777899998875
No 56
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=53.60 E-value=24 Score=25.84 Aligned_cols=51 Identities=6% Similarity=0.069 Sum_probs=33.2
Q ss_pred CCCCeEEEeeeCCCCCCCccc-cccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 22 YMTDITLDVHDLYGACGMNFR-HTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~R-~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
..|.||+|..| |...|- +.-.|-...||.. ...+..+-+.|..+||.++++
T Consensus 5 ~~P~HVAiImD----GNrRwAk~~gl~~~~GH~~G-----~~~~~~i~~~c~~~GI~~lT~ 56 (230)
T PRK14837 5 SLPSHVGIIMD----GNRRWALKKGLSFFEGHKEG-----LKRAKEIVKHSLKLGIKYLSL 56 (230)
T ss_pred CCCCeEEEEcc----CCHHHHHHCCCchhhhHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 36899999999 555552 2223444444432 344556667778899999876
No 57
>PRK05660 HemN family oxidoreductase; Provisional
Probab=53.53 E-value=68 Score=24.58 Aligned_cols=72 Identities=11% Similarity=-0.070 Sum_probs=45.0
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|...+- .+.+. +.+.+ ..|+|+.+- +.+ .++.-+-++ ..+.+.+++....+..+.+.|++.|...+
T Consensus 167 Glpgqt~~-~~~~~l~~~~~-l~p~~is~y~l~~--~~gT~l~~~------~~~~~~~~~~~~~~~~~~~~L~~~Gy~~y 236 (378)
T PRK05660 167 GLPDQSLE-EALDDLRQAIA-LNPPHLSWYQLTI--EPNTLFGSR------PPVLPDDDALWDIFEQGHQLLTAAGYQQY 236 (378)
T ss_pred CCCCCCHH-HHHHHHHHHHh-cCCCeEEeeccEe--ccCCccccc------CCCCcCHHHHHHHHHHHHHHHHHcCCcEe
Confidence 55555555 66666 66666 588888532 221 122222111 12234456778999999999999999988
Q ss_pred Eecc
Q 046914 80 EVNV 83 (90)
Q Consensus 80 ~~~g 83 (90)
++..
T Consensus 237 ei~~ 240 (378)
T PRK05660 237 ETSA 240 (378)
T ss_pred eccc
Confidence 8774
No 58
>COG1908 FrhD Coenzyme F420-reducing hydrogenase, delta subunit [Energy production and conversion]
Probab=53.44 E-value=5.1 Score=27.06 Aligned_cols=41 Identities=27% Similarity=0.314 Sum_probs=29.2
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCc
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~ 77 (90)
..|-|+|+== .-+. =|=.+-+||++|. ++.++++|+.+||-
T Consensus 53 GaDGV~v~GC---~~ge--CHy~~GN~ka~rR---------~~~lke~l~elgie 93 (132)
T COG1908 53 GADGVLVAGC---KIGE--CHYISGNYKAKRR---------MELLKELLKELGIE 93 (132)
T ss_pred CCCeEEEecc---cccc--eeeeccchHHHHH---------HHHHHHHHHHhCCC
Confidence 4566666533 2222 4566788999986 88899999999974
No 59
>KOG1602 consensus Cis-prenyltransferase [Lipid transport and metabolism]
Probab=53.19 E-value=31 Score=26.07 Aligned_cols=56 Identities=13% Similarity=0.107 Sum_probs=36.8
Q ss_pred hhhccCCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 17 IRHDTYMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 17 l~~~~~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
.+..+..|.||++..| |...| |+.-.+.-+.|++ =..++-.|-++|-.+||..+++
T Consensus 30 ~~~~g~~P~HVaFIMD----GNRR~AKk~~L~~~~GH~a-----Gf~~l~~ile~C~~lGI~~vT~ 86 (271)
T KOG1602|consen 30 LLARGPMPRHVAFIMD----GNRRYAKKRGLETSEGHEA-----GFEALKEILELCKELGIKEVTV 86 (271)
T ss_pred HHhcCCCcceeEEEec----CchHHHHhcCCCcccchHH-----HHHHHHHHHHHHHHcCCcEEEE
Confidence 4553368999999999 44444 4444444445543 2455666677778899998875
No 60
>cd08166 MPP_Cdc1_like_1 uncharacterized subgroup related to Saccharomyces cerevisiae CDC1, metallophosphatase domain. A functionally uncharacterized subgroup related to the metallophosphatase domain of Saccharomyces cerevisiae Cdc1, S. cerevisiae Ted1 and human MPPE1. Cdc1 is an endoplasmic reticulum-localized transmembrane lipid phosphatase and is a subunit of DNA polymerase delta. TED1 (trafficking of Emp24p/Erv25p-dependent cargo disrupted 1), acts together with Emp24p and Erv25p in cargo exit from the ER. The MPPE1 gene is a candidate susceptibility gene for Bipolar disorder. Proteins in this uncharacterized subgroup belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like R
Probab=52.49 E-value=71 Score=22.73 Aligned_cols=53 Identities=15% Similarity=0.018 Sum_probs=37.4
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHH-HcCCceEEeccc
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIK-AMSIKVIEVNVM 84 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~-~lGi~~~~~~g~ 84 (90)
..+.. .+|+.++++=|.||.+. ....++..+|+..+++++. .-+++++.++|.
T Consensus 36 ~a~~~-l~PD~Vi~lGDL~D~G~---------------~~~~~e~~e~l~Rf~~If~~~~~~~~~~VpGN 89 (195)
T cd08166 36 LALNF-VQPDIVIFLGDLMDEGS---------------IANDDEYYSYVQRFINIFEVPNGTKIIYLPGD 89 (195)
T ss_pred HHHhc-cCCCEEEEeccccCCCC---------------CCCHHHHHHHHHHHHHHhcCCCCCcEEEECCC
Confidence 35556 69999999999988753 1224566777777776654 357888888873
No 61
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=52.06 E-value=28 Score=25.76 Aligned_cols=52 Identities=12% Similarity=0.125 Sum_probs=33.4
Q ss_pred CCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEec
Q 046914 22 YMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
..|.||+|..| +...| |+.-.+....+|.. ..-+..+-++|..+||.++++=
T Consensus 13 ~~P~HVAiImD----GNrRwAk~~g~~~~~GH~~G-----~~~l~~i~~~c~~lgI~~lTvY 65 (249)
T PRK14834 13 SVPRHVAIIMD----GNGRWAKARGLPRAAGHRAG-----VEALRRVVRAAGELGIGYLTLF 65 (249)
T ss_pred CCCCeEEEEec----CchHHHHHCCCchhhhHHHH-----HHHHHHHHHHHHHcCCCEEEEE
Confidence 57999999999 55555 22223444444432 3345556677888999988753
No 62
>PRK14832 undecaprenyl pyrophosphate synthase; Provisional
Probab=51.87 E-value=12 Score=27.79 Aligned_cols=51 Identities=16% Similarity=0.145 Sum_probs=33.4
Q ss_pred CCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 22 YMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
.-|.||+|..| |...| |+.-.+...+||.. ...+..+-+.|..+||..+++
T Consensus 17 ~iP~HVAiImD----GNrRwAk~~gl~~~~GH~~G-----~~~l~~i~~~c~~~gI~~lTv 68 (253)
T PRK14832 17 KIPQHIAVIMD----GNGRWATSQGLPRIAGHRQG-----ARTLKELLRCCKDWGIKALTA 68 (253)
T ss_pred CCCCEEEEECC----CCHHHHHHCCCCHHHHHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 47999999999 55555 33333444444432 344556667778899998875
No 63
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=51.87 E-value=24 Score=20.84 Aligned_cols=34 Identities=21% Similarity=0.453 Sum_probs=27.2
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCceEEeccccccc
Q 046914 52 NRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 52 ~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
|| ..|-+|+..|+... .|...||..+-+| +..|+
T Consensus 2 nr-asPv~LR~~lE~A~-~La~~GIRFVpiP-v~~de 35 (61)
T PF07131_consen 2 NR-ASPVDLRKALEMAH-SLAHIGIRFVPIP-VVTDE 35 (61)
T ss_pred CC-ccHHHHHHHHHHHH-HHHHcCceeeccc-cccHH
Confidence 44 46888999999887 8999999999888 36554
No 64
>TIGR03190 benz_CoA_bzdN benzoyl-CoA reductase, bzd-type, N subunit. Members of this family are the N subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=51.33 E-value=14 Score=28.32 Aligned_cols=24 Identities=17% Similarity=0.166 Sum_probs=20.1
Q ss_pred HHHHHHHHHcCCceEEeccccccc
Q 046914 65 QYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 65 ~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
+.|++.|+..|||++.+++-+.|.
T Consensus 333 ~~lk~~l~e~GIP~L~iE~D~~~~ 356 (377)
T TIGR03190 333 PDLKRHLEANGIPTLFLEFDITNP 356 (377)
T ss_pred HHHHHHHHHCCCCEEEEecCCCCc
Confidence 468899999999999999877654
No 65
>PRK13366 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=50.56 E-value=87 Score=23.47 Aligned_cols=66 Identities=15% Similarity=0.250 Sum_probs=41.8
Q ss_pred HHHhh-hhhhccCCCCeEEEeeeCCCCCCCccccccCcccc-------------CCCCCCc-----hhHHHhHHHHHHHH
Q 046914 11 GFLSY-NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYK-------------NNRPPTP-----DTIVQGLQYLKASI 71 (90)
Q Consensus 11 gf~~~-~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YK-------------a~R~~~P-----~~L~~Ql~~i~~~l 71 (90)
||-.. +.+++ .+||.++|..| .....|+-+..|.+. -+..++| ++|..+| .+.+
T Consensus 36 a~~~i~~~i~~-~~PDvvVii~~---dH~~~f~~d~~P~f~Ig~~~~~~~~~~~~g~~~v~~~~g~~eLA~~i---~~~l 108 (284)
T PRK13366 36 GYEFSKQWEKE-EKPDVIFLVYN---DHATAFSLDIIPTFAIGTAAEYQPADEGWGPRPVPKVIGHPDLAAHI---AQSV 108 (284)
T ss_pred HHHHHHHHHHH-hCCCEEEEEcC---CcHHhhcccCCCceEEeeCceecCcccccCCCCCCCCCCCHHHHHHH---HHHH
Confidence 55555 67777 69999998866 455667765555554 1223455 6776554 4566
Q ss_pred HHcCCceEEecc
Q 046914 72 KAMSIKVIEVNV 83 (90)
Q Consensus 72 ~~lGi~~~~~~g 83 (90)
..-||.+.....
T Consensus 109 ~~~g~~~~~~~~ 120 (284)
T PRK13366 109 IQDDFDLTIVNK 120 (284)
T ss_pred HHCCCCEeecCC
Confidence 677888765543
No 66
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional
Probab=50.05 E-value=17 Score=26.76 Aligned_cols=52 Identities=10% Similarity=0.044 Sum_probs=34.0
Q ss_pred CCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEec
Q 046914 22 YMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
..|.||+|..| +...| |+.-.+-...+|.. ...+..+-++|..+||..+++=
T Consensus 7 ~~P~HVaiImD----GNrRwAk~~gl~~~~GH~~G-----~~~l~~i~~~c~~lgI~~vTvY 59 (241)
T PRK14842 7 TIPAHIAVIMD----GNGRWAESQGKKRSEGHREG-----ANAIDRLMDASLEYGLKNISLY 59 (241)
T ss_pred CCCCeEEEEcC----CCHHHHHHCCCChhHhHHHH-----HHHHHHHHHHHHHcCCCEEEEE
Confidence 47999999999 55555 33333555555532 3345556667888999998763
No 67
>PRK14840 undecaprenyl pyrophosphate synthase; Provisional
Probab=49.43 E-value=16 Score=27.11 Aligned_cols=57 Identities=9% Similarity=0.054 Sum_probs=36.7
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCcccccc-----CccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRHTL-----YPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~-----yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
+.++....|.||+|..| |...|-++. .+-..++|.. ..-+..+-+.|..+||..+++
T Consensus 11 ~~~~~~~~P~HVaiImD----GNrRwAk~~~~~~gl~~~~GH~~G-----~~~l~~v~~~c~~~GIk~lTv 72 (250)
T PRK14840 11 NFPSLQSLPRHVAIIMD----GNRRWYRKHEQFCQKRAISGHYYG-----AKSLPQIVDTALHLGIEVLTL 72 (250)
T ss_pred hhcccCCCCCeEEEEcC----CChHHHhhCCCccCCCHHHHHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 44444358999999999 666664432 2545555532 233555666777899998875
No 68
>TIGR00539 hemN_rel putative oxygen-independent coproporphyrinogen III oxidase. Experimentally determined examples of oxygen-independent coproporphyrinogen III oxidase, an enzyme that replaces HemF function under anaerobic conditions, belong to a family of proteins described by the model hemN. This model, hemN_rel, models a closely related protein, shorter at the amino end and lacking the region containing the motif PYRT[SC]YP found in members of the hemN family. Several species, including E. coli, Helicobacter pylori, Aquifex aeolicus, and Chlamydia trachomatis, have members of both this family and the E. coli hemN family. The member of this family from Bacillus subtilis was shown to complement an hemF/hemN double mutant of Salmonella typimurium and to prevent accumulation of coproporphyrinogen III under anaerobic conditions, but the exact role of this protein is still uncertain. It is found in a number of species that do not synthesize heme de novo.
Probab=49.11 E-value=63 Score=24.43 Aligned_cols=72 Identities=14% Similarity=0.142 Sum_probs=45.2
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|...+- .+.++ +.+.+ ..|+|+.+- +-+ .++.-+. ..++ +.+.+++....+..+.+.|+..|...+
T Consensus 160 GlPgqt~~-~~~~~l~~~~~-l~~~~is~y~l~~--~~gT~~~----~~~~--~~~~~~~~~~~~~~~~~~L~~~Gy~~y 229 (360)
T TIGR00539 160 GLPLQTLN-SLKEELKLAKE-LPINHLSAYALSV--EPNTNFE----KNAK--KLPDDDSCAHFDEVVREILEGFGFKQY 229 (360)
T ss_pred CCCCCCHH-HHHHHHHHHHc-cCCCEEEeecceE--cCCChhh----hhhh--cCcCHHHHHHHHHHHHHHHHHcCCcee
Confidence 55666666 66667 66667 588887543 221 1221121 1111 235567788889999999999999988
Q ss_pred Eecc
Q 046914 80 EVNV 83 (90)
Q Consensus 80 ~~~g 83 (90)
++..
T Consensus 230 ei~~ 233 (360)
T TIGR00539 230 EVSN 233 (360)
T ss_pred ehhh
Confidence 7764
No 69
>COG2877 KdsA 3-deoxy-D-manno-octulosonic acid (KDO) 8-phosphate synthase [Cell envelope biogenesis, outer membrane]
Probab=48.69 E-value=22 Score=26.76 Aligned_cols=32 Identities=19% Similarity=0.347 Sum_probs=25.0
Q ss_pred cCCCCCC----chhHHHhHHHHHHHHHHcCCceEEe
Q 046914 50 KNNRPPT----PDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 50 Ka~R~~~----P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
||||... -+.|-+.++.++++=+.+|+++++-
T Consensus 59 KANRsSi~s~RGpGLeeglki~~~vK~efgv~ilTD 94 (279)
T COG2877 59 KANRSSIHSYRGPGLEEGLKILQEVKEEFGVPILTD 94 (279)
T ss_pred cccccccccccCCCHHHHHHHHHHHHHHcCCceeec
Confidence 5566543 2578889999999999999998863
No 70
>KOG3120 consensus Predicted haloacid dehalogenase-like hydrolase [General function prediction only]
Probab=48.62 E-value=17 Score=27.08 Aligned_cols=46 Identities=13% Similarity=0.145 Sum_probs=29.4
Q ss_pred CCeEEEeeeCCCC-----CCCccccccCccccCCCCCCchhHHHhHH------HHHHHHHHcC
Q 046914 24 TDITLDVHDLYGA-----CGMNFRHTLYPSYKNNRPPTPDTIVQGLQ------YLKASIKAMS 75 (90)
Q Consensus 24 p~~i~v~fD~fD~-----~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~------~i~~~l~~lG 75 (90)
...++++|| ||. ...+|=.+..|. ...|.+|..++| .+.++++.||
T Consensus 11 ~~ril~~FD-FD~TIid~dSD~wVv~~lp~-----~~l~~qL~~t~p~~~Wne~M~rv~k~Lh 67 (256)
T KOG3120|consen 11 SPRILLVFD-FDRTIIDQDSDNWVVDELPT-----TDLFNQLRDTYPKGFWNELMDRVFKELH 67 (256)
T ss_pred CCcEEEEEe-cCceeecCCcchHHHHhccc-----chhHHHHHHhcccchHHHHHHHHHHHHH
Confidence 356888999 663 345776666666 556777777777 4445555444
No 71
>PRK08207 coproporphyrinogen III oxidase; Provisional
Probab=48.19 E-value=42 Score=26.97 Aligned_cols=71 Identities=7% Similarity=-0.098 Sum_probs=46.0
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|....- .|.++ +.+.. ..|+++-+-.=.. .+++.+.++ +..| ..+.+++....+..+.+.|.++|...+
T Consensus 329 GLPgEt~e-d~~~tl~~l~~-L~pd~isv~~L~i-~~gT~l~~~-~~~~---~~~~~~~~~~m~~~a~~~l~~~Gy~~Y 400 (488)
T PRK08207 329 GLPGEGLE-EVKHTLEEIEK-LNPESLTVHTLAI-KRASRLTEN-KEKY---KVADREEIEKMMEEAEEWAKELGYVPY 400 (488)
T ss_pred CCCCCCHH-HHHHHHHHHHh-cCcCEEEEEeceE-cCCChHHHh-cCcC---CCcCHHHHHHHHHHHHHHHHHcCCHhh
Confidence 56666666 67777 77777 5888876542210 133333222 2333 345677888999999999999999876
No 72
>smart00707 RPEL Repeat in Drosophila CG10860, human KIAA0680 and C. elegans F26H9.2.
Probab=48.09 E-value=9.9 Score=18.79 Aligned_cols=11 Identities=27% Similarity=0.570 Sum_probs=8.0
Q ss_pred CCCCCchhHHHh
Q 046914 52 NRPPTPDTIVQG 63 (90)
Q Consensus 52 ~R~~~P~~L~~Q 63 (90)
+| |.|++|+.+
T Consensus 9 ~R-P~~eeLv~r 19 (26)
T smart00707 9 QR-PTREELEER 19 (26)
T ss_pred cC-CCHHHHHHc
Confidence 45 789998764
No 73
>PRK14827 undecaprenyl pyrophosphate synthase; Provisional
Probab=47.68 E-value=10 Score=28.78 Aligned_cols=52 Identities=8% Similarity=0.010 Sum_probs=33.2
Q ss_pred CCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEec
Q 046914 22 YMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
..|.||+|..| |+..| |+.-.+-..+||.. ..-+..+-+.|..+||..+++=
T Consensus 66 ~iP~HVAiIMD----GNrRwAk~~gl~~~~GH~~G-----~~~l~~v~~~c~~lGI~~lTvY 118 (296)
T PRK14827 66 RLPNHVAIVMD----GNGRWATQRGLARTEGHKMG-----EAVVIDIACGAIELGIKWLSLY 118 (296)
T ss_pred CCCCeEEEecc----CchHHHHHCCCCHhHHHHHH-----HHHHHHHHHHHHHcCCCEEEEe
Confidence 57899999999 55555 33333555555532 2224455566778999998764
No 74
>cd07185 OmpA_C-like Peptidoglycan binding domains similar to the C-terminal domain of outer-membrane protein OmpA. OmpA-like domains (named after the C-terminal domain of Escherichia coli OmpA protein) have been shown to non-covalently associate with peptidoglycan, a network of glycan chains composed of disaccharides, which are crosslinked via short peptide bridges. Well-studied members of this family include the Escherichia coli outer membrane protein OmpA, the Escherichia coli lipoprotein PAL, Neisseria meningitdis RmpM, which interact with the outer membrane, as well as the Escherichia coli motor protein MotB, and the Vibrio flagellar motor proteins PomB and MotY, which interact with the inner membrane.
Probab=45.61 E-value=54 Score=19.59 Aligned_cols=40 Identities=13% Similarity=0.032 Sum_probs=27.8
Q ss_pred ccCCCCCCchhHHHhHHHHHHHHHHcCCceEEecccccccc
Q 046914 49 YKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDAY 89 (90)
Q Consensus 49 YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~~ 89 (90)
++.+.....++...+|..+...+....-..+.+.| ++|.-
T Consensus 6 F~~~~~~l~~~~~~~l~~~~~~l~~~~~~~v~v~g-~a~~~ 45 (106)
T cd07185 6 FDFGSAELTPEAKPLLDKLAEVLKKNPDAKIRIEG-HTDSR 45 (106)
T ss_pred cCCCchhcCHHHHHHHHHHHHHHHHCCCceEEEEE-EeCCC
Confidence 34444555666778888888888887766788886 77653
No 75
>PF02274 Amidinotransf: Amidinotransferase; InterPro: IPR003198 This family contains glycine and inosamine amidinotransferases, enzymes which are involved in creatine and streptomycin biosynthesis respectively. This family also includes arginine deiminases, which catalyse the reversible reaction: arginine + H2O = citrulline + NH3 The Streptococcus anti-tumour glycoprotein is also found in this family [].; GO: 0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines, 0005737 cytoplasm; PDB: 2CI7_A 2CI1_A 2CI4_A 2CI3_A 2CI5_A 2C6Z_A 2CI6_A 3I4A_B 3I2E_B 2JAI_A ....
Probab=44.59 E-value=28 Score=25.06 Aligned_cols=32 Identities=22% Similarity=0.456 Sum_probs=25.8
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCceEEecc
Q 046914 52 NRPPTPDTIVQGLQYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 52 ~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g 83 (90)
+.+..++....|...+.++|+..|+.++..+.
T Consensus 22 ~~~~~~~~a~~e~~~l~~~L~~~Gv~V~~~~~ 53 (281)
T PF02274_consen 22 SDPPDPEKAREEHDALVEALRSNGVEVIELPP 53 (281)
T ss_dssp SS---HHHHHHHHHHHHHHHHTTT-EEEEEHH
T ss_pred cCcchHHHHHHHHHHHHHHHHhCCcEEEEeCC
Confidence 56778899999999999999999999999885
No 76
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=43.79 E-value=58 Score=20.89 Aligned_cols=36 Identities=17% Similarity=0.262 Sum_probs=28.2
Q ss_pred CccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 46 YPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 46 yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
-..||..|+.+|-.-...-+.+-+.+..+||..+.+
T Consensus 31 ~~gfkg~rk~t~~Aa~~~a~~~~~~~~~~gi~~v~v 66 (108)
T TIGR03632 31 AVGFKGSKKSTPYAAQLAAEDAAKKAKEFGMKTVDV 66 (108)
T ss_pred ceeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEE
Confidence 457999999999776666667777888899988765
No 77
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=43.05 E-value=36 Score=25.55 Aligned_cols=51 Identities=12% Similarity=-0.036 Sum_probs=32.6
Q ss_pred CCCCeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 22 YMTDITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
.-|.||+|..| +...| |+.-.+...++|.. ..-+..+-++|..+||..+++
T Consensus 40 ~~P~HVAiImD----GNrRwAk~~g~~~~~GH~~G-----~~~l~~i~~~c~~lGIk~lTv 91 (275)
T PRK14835 40 KLPRHLGLILD----GNRRFARALGLQREMGHEFG-----VQKAYEVLEWCLELGIPTVTI 91 (275)
T ss_pred CCCCEEEEEec----CchHHHHHCCCCHHHHHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 47899999999 55555 33333444444321 233455666777899998876
No 78
>cd05564 PTS_IIB_chitobiose_lichenan PTS_IIB_chitobiose_lichenan: subunit IIB of enzyme II (EII) of the N,N-diacetylchitobiose-specific and lichenan-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In these systems, EII is either a lichenan- or an N,N-diacetylchitobiose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. In the chitobiose system, these subunits are expressed as separate proteins from chbA, chbB, and chbC of the chb operon (formerly the cel (cellulose) operon). In the lichenan system, these subunits are expressed from licA, licB, and licC of the lic operon. The lic operon of Bacillus subtilis is required for the transport and degradation of oligomeric beta-glucosides, which are produced by extracellular enzymes on substrates such as lichenan or barley glucan. The lic operon is transcribed from a gammaA-dependent promoter and is inducible by lichenan, lichenan hydrolysate, and cellobiose. The IIB d
Probab=42.33 E-value=33 Score=21.24 Aligned_cols=28 Identities=14% Similarity=0.112 Sum_probs=23.5
Q ss_pred CchhHHHhHHHHHHHHHHcCCceEEecc
Q 046914 56 TPDTIVQGLQYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 56 ~P~~L~~Ql~~i~~~l~~lGi~~~~~~g 83 (90)
+-+.+..+++.+++.+...++|+..++.
T Consensus 52 ~~Pqv~~~~~~i~~~~~~~~~pv~~I~~ 79 (96)
T cd05564 52 LGPQVRYMLDEVKKKAAEYGIPVAVIDM 79 (96)
T ss_pred EChhHHHHHHHHHHHhccCCCcEEEcCh
Confidence 3467888899999988899999988875
No 79
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=42.21 E-value=33 Score=21.90 Aligned_cols=32 Identities=9% Similarity=0.082 Sum_probs=25.5
Q ss_pred CchhHHHhHHHHHHHHHHcCCceEEeccccccccC
Q 046914 56 TPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDAYG 90 (90)
Q Consensus 56 ~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~~~ 90 (90)
.-+.+.-+++.+++.++..|+|+..++. ++||
T Consensus 56 l~PQi~~~~~~i~~~~~~~~ipv~~I~~---~~Y~ 87 (104)
T PRK09590 56 VSPQTKMYFKQFEEAGAKVGKPVVQIPP---QAYI 87 (104)
T ss_pred EChHHHHHHHHHHHHhhhcCCCEEEeCH---HHcC
Confidence 3467788888999999999999988775 4554
No 80
>PRK10802 peptidoglycan-associated outer membrane lipoprotein; Provisional
Probab=41.29 E-value=67 Score=22.16 Aligned_cols=41 Identities=12% Similarity=0.090 Sum_probs=32.8
Q ss_pred ccCCCCCCchhHHHhHHHHHHHHHHcCCceEEeccccccccC
Q 046914 49 YKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDAYG 90 (90)
Q Consensus 49 YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~~~ 90 (90)
+.-+.....++-..+|..+.++|.......+.+.| +.|..|
T Consensus 73 F~~d~~~l~~~~~~~L~~~a~~L~~~p~~~v~I~G-htD~~G 113 (173)
T PRK10802 73 FDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEG-HADERG 113 (173)
T ss_pred ecCCCccCCHHHHHHHHHHHHHHHhCCCceEEEEE-ecCCCC
Confidence 44455567788888899999999998877788998 898765
No 81
>CHL00041 rps11 ribosomal protein S11
Probab=41.09 E-value=66 Score=20.94 Aligned_cols=36 Identities=19% Similarity=0.160 Sum_probs=27.1
Q ss_pred CccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 46 YPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 46 yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
-..||..|+.+|-.-...-+.+-+.+..+|+..+.+
T Consensus 44 ~~gfKg~rK~T~~Aa~~~a~~~~~~~~~~gi~~v~I 79 (116)
T CHL00041 44 ACGFKGARKGTPFAAQTAAENAIRTVIDQGMKRAEV 79 (116)
T ss_pred ceeeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEE
Confidence 358999999999666555566777777788887764
No 82
>PF08373 RAP: RAP domain; InterPro: IPR013584 The ~60-residue RAP (an acronym for RNA-binding domain abundant in Apicomplexans) domain is found in various proteins in eukaryotes. It is particularly abundant in apicomplexans and might mediate a range of cellular functions through its potential interactions with RNA []. The RAP domain consists of multiple blocks of charged and aromatics residues and is predicted to be composed of alpha helical and beta strand structures. Two predicted loop regions that are dominated by glycine and tryptophan residues are found before and after the central beta sheet []. Some proteins known to contain a RAP domain are listed below: Human hypothetical protein MGC5297, Mammalian FAST kinase domain-containing proteins (FASTKDs), Chlamydomonas reinhardtii chloroplastic trans-splicing factor Raa3.
Probab=41.07 E-value=28 Score=19.08 Aligned_cols=19 Identities=26% Similarity=0.387 Sum_probs=15.1
Q ss_pred HHHHHHHHHcCCceEEecc
Q 046914 65 QYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 65 ~~i~~~l~~lGi~~~~~~g 83 (90)
..=..+|+++|..++.++-
T Consensus 21 ~lk~r~L~~~G~~Vi~Ip~ 39 (58)
T PF08373_consen 21 KLKHRHLKALGYKVISIPY 39 (58)
T ss_pred HHHHHHHHHCCCEEEEecH
Confidence 3345689999999999883
No 83
>PF13521 AAA_28: AAA domain; PDB: 1LW7_A.
Probab=40.86 E-value=26 Score=22.97 Aligned_cols=32 Identities=25% Similarity=0.243 Sum_probs=17.6
Q ss_pred CCCCchhHHHhHHHHHHHHHHcCCceEEe-ccc
Q 046914 53 RPPTPDTIVQGLQYLKASIKAMSIKVIEV-NVM 84 (90)
Q Consensus 53 R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~-~g~ 84 (90)
|...|++-..--..++++++.+|++++.+ .|-
T Consensus 127 R~~~~~~r~~~~~~~~~~l~~~~~~~~~v~~gs 159 (163)
T PF13521_consen 127 RPEDPEERERIDELLKELLERHGIPYIIVPSGS 159 (163)
T ss_dssp ------SHHHHHHHHHHHHHGGG---EEEE-SS
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCeEEEeCCCC
Confidence 44456666666677899999999999998 553
No 84
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=40.70 E-value=1.5e+02 Score=23.19 Aligned_cols=72 Identities=7% Similarity=-0.030 Sum_probs=45.7
Q ss_pred CCcchHHHHHHHHhh-hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 1 MGESYGLLWRGFLSY-NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 1 ~G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
+|.|....- .|.++ +.+.+ ..|+|+.+--=. ....| .++ +..+ +.+++....+..+.+.|.+.|...+
T Consensus 200 ~GlP~qt~e-~~~~~l~~~~~-l~~~~is~y~L~--~~~~T---~l~---~~~~-~~~~~~~~m~~~~~~~L~~~Gy~~y 268 (430)
T PRK08208 200 YGIPGQTHA-SWMESLDQALV-YRPEELFLYPLY--VRPLT---GLG---RRAR-AWDDQRLSLYRLARDLLLEAGYTQT 268 (430)
T ss_pred cCCCCCCHH-HHHHHHHHHHh-CCCCEEEEcccc--ccCCC---ccc---hhcC-CCHHHHHHHHHHHHHHHHHcCCeEE
Confidence 366666666 67777 66666 588877644210 11111 122 2212 2457888999999999999999888
Q ss_pred Eecc
Q 046914 80 EVNV 83 (90)
Q Consensus 80 ~~~g 83 (90)
++..
T Consensus 269 ei~~ 272 (430)
T PRK08208 269 SMRM 272 (430)
T ss_pred eecc
Confidence 7764
No 85
>cd07386 MPP_DNA_pol_II_small_archeal_C archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain. The small subunit of the archeal DNA polymerase II contains a C-terminal metallophosphatase domain. This domain is thought to be functionally active because the active site residues required for phosphoesterase activity in other members of this superfamily are intact. The archeal replicative DNA polymerases are thought to possess intrinsic phosphatase activity that hydrolyzes the pyrophosphate released during nucleotide polymerization. This domain belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiestera
Probab=40.68 E-value=98 Score=21.84 Aligned_cols=53 Identities=15% Similarity=0.142 Sum_probs=34.8
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCC-CchhHHHhHHHHHHHHHHc--CCceEEeccc
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPP-TPDTIVQGLQYLKASIKAM--SIKVIEVNVM 84 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~-~P~~L~~Ql~~i~~~l~~l--Gi~~~~~~g~ 84 (90)
+++.++++=|+||.... |..+... ....+..++..+.++|..+ +++++.++|.
T Consensus 35 ~~d~lvi~GDl~d~~~~---------~~~~~~~~~~~~~~~~~~~~~~~l~~L~~~~~v~~ipGN 90 (243)
T cd07386 35 RVKYLIIAGDLVDGIGV---------YPGQEEELEILDIYEQYEEAAEYLSDVPSHIKIIIIPGN 90 (243)
T ss_pred CccEEEEeCCccccccc---------CCcchhhhhhhhHHHHHHHHHHHHHhcccCCeEEEeCCC
Confidence 56999999998886321 1111111 2345666677788888777 5889989984
No 86
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=40.41 E-value=1.1e+02 Score=23.29 Aligned_cols=74 Identities=11% Similarity=0.009 Sum_probs=43.8
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCCc--hhHHHhHHHHHHHHHHcCCc
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPTP--DTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~P--~~L~~Ql~~i~~~l~~lGi~ 77 (90)
|.|....- .|.+. +.+.+ ..++|+.+- +- ....| .++..++.++.+.| +.....+..+.+.|...|..
T Consensus 160 GlPgqt~~-~~~~~l~~~~~-l~~~~i~~y~l~---~~pgT---~~~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~Gy~ 231 (377)
T PRK08599 160 ALPGQTIE-DFKESLAKALA-LDIPHYSAYSLI---LEPKT---VFYNLMRKGKLRLPGEDLEAEMYEYLMDEMEAHGFH 231 (377)
T ss_pred CCCCCCHH-HHHHHHHHHHc-cCCCEEeeecee---ecCCC---hhHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHcCCc
Confidence 55555555 56666 66666 578876321 11 11111 12334555665433 44455678899999999998
Q ss_pred eEEecc
Q 046914 78 VIEVNV 83 (90)
Q Consensus 78 ~~~~~g 83 (90)
.+++..
T Consensus 232 ~~~~~~ 237 (377)
T PRK08599 232 QYEISN 237 (377)
T ss_pred Eeeeee
Confidence 887764
No 87
>PRK08156 type III secretion system protein SpaS; Validated
Probab=40.19 E-value=75 Score=24.78 Aligned_cols=41 Identities=10% Similarity=0.061 Sum_probs=29.4
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|.+||.- |..++.+.| +++.. .|+++-+..|||+++-+
T Consensus 257 NPTH~AVALk----------------Yd~~~~~AP~VvAKG~d~~A~---~IreiA~e~~VPiven~ 304 (361)
T PRK08156 257 NPTHIAIGIY----------------FNPELAPIPFISVRETNQRAL---AVRAYAEKVGVPVVRDI 304 (361)
T ss_pred CCCeEEEEEE----------------ecCCCCCCCEEEEecCcHHHH---HHHHHHHHCCCCEeeCH
Confidence 7999999987 334444555 44443 37889999999998754
No 88
>cd07396 MPP_Nbla03831 Homo sapiens Nbla03831 and related proteins, metallophosphatase domain. Nbla03831 (also known as LOC56985) is an uncharacterized Homo sapiens protein with a domain that belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.
Probab=40.01 E-value=1.4e+02 Score=21.42 Aligned_cols=51 Identities=12% Similarity=0.036 Sum_probs=35.3
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEeccccc
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYE 86 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~ee 86 (90)
+.++. ..|+.++++=|..+.+... =..++..+.+.++.++++++.++|.-+
T Consensus 34 ~~i~~-~~~d~vv~~GDlv~~~~~~-------------------~~~~~~~~~~~l~~l~~p~~~v~GNHD 84 (267)
T cd07396 34 EEWNR-ESLDFVVQLGDIIDGDNAR-------------------AEEALDAVLAILDRLKGPVHHVLGNHD 84 (267)
T ss_pred HHHHc-CCCCEEEECCCeecCCCch-------------------HHHHHHHHHHHHHhcCCCEEEecCccc
Confidence 45555 4799999998953322110 224566788899999999999999654
No 89
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=39.95 E-value=35 Score=21.47 Aligned_cols=22 Identities=9% Similarity=0.267 Sum_probs=19.5
Q ss_pred CchhHHHhHHHHHHHHHHcCCc
Q 046914 56 TPDTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 56 ~P~~L~~Ql~~i~~~l~~lGi~ 77 (90)
.-+||..||...|+-|++-|+.
T Consensus 69 A~~eL~~eI~eAK~dLr~kGv~ 90 (91)
T PF08285_consen 69 AAKELQKEIKEAKADLRKKGVD 90 (91)
T ss_pred HHHHHHHHHHHHHHHHHHcCCC
Confidence 3469999999999999999986
No 90
>TIGR02536 eut_hyp ethanolamine utilization protein. This family of proteins is found in operons for the polyhedral organelle-based degradation of ethanolamine. This family is not found in proteobacterial species which otherwise have the same suite of genes in the eut operon. Proteobacteria have two genes that are not found in non-proteobacteria which may complement this genes function, a phosphotransacetylase (pfam01515) and the EutJ protein (TIGR02529) of unknown function.
Probab=39.41 E-value=45 Score=23.99 Aligned_cols=33 Identities=18% Similarity=0.339 Sum_probs=27.5
Q ss_pred CCCchhHHHhHHHHHHHHHHcCCceEEecccccc
Q 046914 54 PPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYED 87 (90)
Q Consensus 54 ~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD 87 (90)
...|..|..-+..-.+.|..+||..+.... ++|
T Consensus 107 ~~~p~~l~~~~~~y~~kL~sfGIk~~~~~~-~~~ 139 (207)
T TIGR02536 107 NTAPYALKQKFQEYEEKLQSFGIEFIDSEN-YIT 139 (207)
T ss_pred ccCCHHHHHHHHHHHHHHHHcCeEEeccch-hhh
Confidence 456999999999999999999999887764 544
No 91
>cd07400 MPP_YydB Bacillus subtilis YydB and related proteins, metallophosphatase domain. YydB (BSU40220) is an uncharacterized Bacillus subtilis protein that belongs to the following Bacillus subtilis gene cluster yydB-yydC-yydD-yydG-yydH-yydI-yydJ. YydB belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productiv
Probab=38.57 E-value=1e+02 Score=19.45 Aligned_cols=46 Identities=13% Similarity=0.016 Sum_probs=29.7
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCC---ceEEeccc
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSI---KVIEVNVM 84 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi---~~~~~~g~ 84 (90)
..+.. ..++.++++=|++|.+.. .++..+.++++.+.. +++.++|.
T Consensus 29 ~~~~~-~~~d~vi~~GDl~~~~~~----------------------~~~~~~~~~~~~l~~~~~~~~~v~GN 77 (144)
T cd07400 29 AEIKA-LDPDLVVITGDLTQRGLP----------------------EEFEEAREFLDALPAPLEPVLVVPGN 77 (144)
T ss_pred HHHhc-cCCCEEEECCCCCCCCCH----------------------HHHHHHHHHHHHccccCCcEEEeCCC
Confidence 55666 589999999997664321 223344555555554 78888874
No 92
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=38.43 E-value=94 Score=25.81 Aligned_cols=21 Identities=19% Similarity=0.240 Sum_probs=17.3
Q ss_pred HHHHHHHcCCceEEeccccccc
Q 046914 67 LKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 67 i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
|-+.|...||.++..| .|||+
T Consensus 133 lI~~~r~~nVe~IVAP-yEADA 153 (556)
T KOG2518|consen 133 LIQYLRSQNVEYIVAP-YEADA 153 (556)
T ss_pred HHHHHHHcCCceEecC-ccccc
Confidence 4457788899999999 59997
No 93
>TIGR01404 FlhB_rel_III type III secretion protein, YscU/HrpY family. This model represents one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, flagellar biosynthetic protein FlhB (TIGRFAMs model TIGR00328). This model may not identify all type III secretion system FlhB homologs.
Probab=38.24 E-value=86 Score=24.13 Aligned_cols=41 Identities=20% Similarity=0.133 Sum_probs=28.8
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|.+||.. |..+..+.| +++.. .|+++-+..|||+++-+
T Consensus 261 NPTH~AVAL~----------------Yd~~~~~AP~VvAKG~d~~A~---~Ir~iA~e~~VPiven~ 308 (342)
T TIGR01404 261 NPTHIAIGIY----------------YKPGETPLPLIICKGTDAQAL---AVRAYAEEAGIPVVRDI 308 (342)
T ss_pred CCceeEEEeE----------------ECCCCCCCCEEEEeeCcHHHH---HHHHHHHHcCCCEeeCH
Confidence 7899999987 333334455 44543 37888999999998754
No 94
>TIGR03358 VI_chp_5 type VI secretion protein, VC_A0107 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PubMed:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al.
Probab=38.01 E-value=29 Score=24.13 Aligned_cols=20 Identities=25% Similarity=0.395 Sum_probs=17.0
Q ss_pred CCCchhHHHhHHHHHHHHHH
Q 046914 54 PPTPDTIVQGLQYLKASIKA 73 (90)
Q Consensus 54 ~~~P~~L~~Ql~~i~~~l~~ 73 (90)
.=.|+.+..|+|.++++|++
T Consensus 99 DF~Pd~Ia~qVp~L~~Llel 118 (159)
T TIGR03358 99 DFSPDAVAKQVPELKKLLEA 118 (159)
T ss_pred cCCHHHHHHHhHHHHHHHHH
Confidence 34699999999999998875
No 95
>PRK13109 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=37.77 E-value=80 Score=24.53 Aligned_cols=41 Identities=22% Similarity=0.248 Sum_probs=28.5
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|++||.- |..+..+.| +.+.. .|+++-+..|||+++-+
T Consensus 271 NPTH~AVAL~----------------Yd~~~~~aP~VvAKG~d~~A~---~Ir~~A~e~~VPiven~ 318 (358)
T PRK13109 271 NPTHFAIALR----------------YERSENPAPLVVAKGQDLIAL---KIREIAEENGIPVIEDK 318 (358)
T ss_pred CCCceEEEeE----------------eCCCCCCCCEEEEEeCcHHHH---HHHHHHHHcCCCEEeCH
Confidence 7999999987 333334455 34433 37889999999998754
No 96
>PRK01816 hypothetical protein; Provisional
Probab=37.51 E-value=52 Score=22.61 Aligned_cols=28 Identities=7% Similarity=0.228 Sum_probs=24.5
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 52 NRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 52 ~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
.+.+.|+.|......|++-|.+.|+.+-
T Consensus 86 a~tpLPpsL~~Wy~el~~Kl~~~g~~~~ 113 (143)
T PRK01816 86 SVTPLPPALLNWFYEVREKLQEAGQALA 113 (143)
T ss_pred cCCCCChHHHHHHHHHHHHHHHcCCccC
Confidence 3468899999999999999999998764
No 97
>COG0065 LeuC 3-isopropylmalate dehydratase large subunit [Amino acid transport and metabolism]
Probab=37.50 E-value=1.1e+02 Score=24.65 Aligned_cols=41 Identities=12% Similarity=-0.013 Sum_probs=30.1
Q ss_pred CCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEE
Q 046914 22 YMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIE 80 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~ 80 (90)
..|+.++++|| +.-++-.. ....|...+++.++.+||..+.
T Consensus 54 ~~p~k~~~~~D---H~vPt~~~---------------~~a~~~~~lr~~~ke~Gi~~~~ 94 (423)
T COG0065 54 RDPEKTVATFD---HNVPTPDI---------------KAAEQQKELRENAKEFGIVNFY 94 (423)
T ss_pred cCccceEEEec---CCCCCccH---------------HHHHHHHHHHHHHHHhCCeeee
Confidence 47888999999 54333222 2238999999999999987765
No 98
>PRK05309 30S ribosomal protein S11; Validated
Probab=37.17 E-value=79 Score=20.97 Aligned_cols=36 Identities=22% Similarity=0.242 Sum_probs=28.3
Q ss_pred CccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 46 YPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 46 yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
-..||..|+.+|-.-...-+.+-+.+..+||..+.+
T Consensus 48 ~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~~v~v 83 (128)
T PRK05309 48 GLGFKGSRKSTPYAAQVAAEDAAKKAKEHGMKTVEV 83 (128)
T ss_pred ccEeCCCccCCHHHHHHHHHHHHHHHHHcCCcEEEE
Confidence 457999999999877666677777788899987765
No 99
>KOG4366 consensus Predicted thioesterase [General function prediction only]
Probab=36.59 E-value=17 Score=26.31 Aligned_cols=26 Identities=19% Similarity=0.339 Sum_probs=21.8
Q ss_pred cccCccccCCCCCCchhHHHhHHHHH
Q 046914 43 HTLYPSYKNNRPPTPDTIVQGLQYLK 68 (90)
Q Consensus 43 ~~~yp~YKa~R~~~P~~L~~Ql~~i~ 68 (90)
.+++|.|-.+|++.|+++...|....
T Consensus 169 ~e~c~~~~e~~ae~ped~~~~ls~~e 194 (213)
T KOG4366|consen 169 LELCPRTNEKRAEIPEDLLKWLSERE 194 (213)
T ss_pred HHHhhhhccCcccCChHHHhhccccc
Confidence 37899999999999999987776543
No 100
>PF00586 AIRS: AIR synthase related protein, N-terminal domain; InterPro: IPR000728 This family includes Hydrogen expression/formation protein, HypE, which may be involved in the maturation of NifE hydrogenase; AIR synthase and FGAM synthase, which are involved in de novo purine biosynthesis; and selenide, water dikinase, an enzyme which synthesizes selenophosphate from selenide and ATP.; GO: 0003824 catalytic activity; PDB: 3VIU_A 2Z1T_A 2Z1U_A 3C9U_B 3C9S_A 3C9R_A 1VQV_A 3C9T_B 3M84_A 3QTY_A ....
Probab=36.26 E-value=58 Score=19.60 Aligned_cols=25 Identities=8% Similarity=0.337 Sum_probs=20.1
Q ss_pred CchhHHHhHHHHHHHHHHcCCceEE
Q 046914 56 TPDTIVQGLQYLKASIKAMSIKVIE 80 (90)
Q Consensus 56 ~P~~L~~Ql~~i~~~l~~lGi~~~~ 80 (90)
.++.|.+-+.-|.+.++.+|++++.
T Consensus 69 ~~~~l~~~~~Gi~~~~~~~g~~ivG 93 (96)
T PF00586_consen 69 SPEELKEIVKGIAEACREFGIPIVG 93 (96)
T ss_dssp BHHHHHHHHHHHHHHHHHHT-EEEE
T ss_pred CHHHHHHHHHHHHHHHHHhCCcEeC
Confidence 4556888888999999999999874
No 101
>PRK05198 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=36.21 E-value=53 Score=24.71 Aligned_cols=30 Identities=20% Similarity=0.382 Sum_probs=23.6
Q ss_pred CCCCCCc----hhHHHhHHHHHHHHHHcCCceEE
Q 046914 51 NNRPPTP----DTIVQGLQYLKASIKAMSIKVIE 80 (90)
Q Consensus 51 a~R~~~P----~~L~~Ql~~i~~~l~~lGi~~~~ 80 (90)
|+|...- ..|.+.|.+++++=+.+|+++++
T Consensus 53 apRTSp~sFqG~G~eeGL~~L~~vk~~~GlpvvT 86 (264)
T PRK05198 53 ANRSSIHSFRGPGLEEGLKILQEVKETFGVPVLT 86 (264)
T ss_pred CCCCCCCCCCCCChHHHHHHHHHHHHHHCCceEE
Confidence 5776432 25578899999999999999886
No 102
>PRK09108 type III secretion system protein HrcU; Validated
Probab=36.12 E-value=91 Score=24.16 Aligned_cols=41 Identities=17% Similarity=0.189 Sum_probs=28.6
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|++||.- |..+..+.| +++.. .|+++-+..|||+++-+
T Consensus 264 NPTH~AVAL~----------------Y~~~~~~AP~VvAKG~d~~A~---~Ir~~A~e~~VPvven~ 311 (353)
T PRK09108 264 NPTHYAVALR----------------YAPDEHPLPRVIAKGVDDGAL---ALRRHAHALGIPIVGNP 311 (353)
T ss_pred CCCceEEEeE----------------eCCCCCCCCEEEEEeCcHHHH---HHHHHHHHcCCCEEeCH
Confidence 7899999977 333334555 34433 37889999999998754
No 103
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=36.09 E-value=34 Score=20.07 Aligned_cols=33 Identities=24% Similarity=0.441 Sum_probs=24.5
Q ss_pred cCCCCCCchhHHHhHHHHHHHHHHcCCceEEec
Q 046914 50 KNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 50 Ka~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
.+.++.+=+-|..+++.|++.|...|+.+-.+.
T Consensus 43 ~~~~~~~~~~L~~~~~~L~~~L~~~G~~~~~~~ 75 (85)
T PF02120_consen 43 TAENPETKELLRQNLPELKERLQAQGLEVVNLS 75 (85)
T ss_dssp E--SSHHHHHHHHTHHHHHHHHHTTT-EEEEEE
T ss_pred EECCHHHHHHHHHHHHHHHHHHHHCCCCeEEEE
Confidence 344555667899999999999999999876544
No 104
>cd08164 MPP_Ted1 Saccharomyces cerevisiae Ted1 and related proteins, metallophosphatase domain. Saccharomyces cerevisiae Ted1 (trafficking of Emp24p/Erv25p-dependent cargo disrupted 1) is a metallophosphatase domain-containing protein which acts together with Emp24p and Erv25p in cargo exit from the ER. Ted1 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the
Probab=35.90 E-value=1.6e+02 Score=20.90 Aligned_cols=21 Identities=14% Similarity=0.181 Sum_probs=16.6
Q ss_pred hhhhccCCCCeEEEeeeCCCCC
Q 046914 16 NIRHDTYMTDITLDVHDLYGAC 37 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~ 37 (90)
.+... .+|++|+|.=|.||++
T Consensus 38 ~~~~~-l~Pd~V~fLGDLfd~~ 58 (193)
T cd08164 38 MMQFW-LKPDAVVVLGDLFSSQ 58 (193)
T ss_pred HHHHh-cCCCEEEEeccccCCC
Confidence 34555 6999999999998864
No 105
>PRK00143 mnmA tRNA-specific 2-thiouridylase MnmA; Reviewed
Probab=35.63 E-value=54 Score=24.99 Aligned_cols=41 Identities=17% Similarity=0.327 Sum_probs=32.4
Q ss_pred ccccCCCCCCchhHHHh---HHHHHHHHHHcCCceEEeccccccc
Q 046914 47 PSYKNNRPPTPDTIVQG---LQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 47 p~YKa~R~~~P~~L~~Q---l~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
.+|+.++.|.|..+-.. +..+.+....+|...+ +.|.++|+
T Consensus 85 ~~~~~g~tpnpc~~C~r~ik~~~l~~~A~~~g~~~I-ATGH~a~d 128 (346)
T PRK00143 85 DEYKAGRTPNPCVLCNKEIKFKAFLEYARELGADYI-ATGHYARI 128 (346)
T ss_pred HHHHcCCCCCcChhhhHHHHHHHHHHHHHHCCCCEE-Eeeeeccc
Confidence 46899999999887443 4678888899999976 67788886
No 106
>PF04019 DUF359: Protein of unknown function (DUF359); InterPro: IPR007164 This is family of archaebacterial proteins, which are about 170 amino acids in length. They have no known function. The most conserved portion of the protein contains the sequence GEEDL that may be important for its function.
Probab=35.45 E-value=85 Score=20.69 Aligned_cols=24 Identities=25% Similarity=0.232 Sum_probs=17.7
Q ss_pred HHHHHHHHHHcCCceEEeccccccc
Q 046914 64 LQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 64 l~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
+..|++.+..-+=..+.++| |||.
T Consensus 51 ~~ai~~a~~~~~~~~I~V~G-EEDL 74 (121)
T PF04019_consen 51 IEAIKKALESGKPVVIFVDG-EEDL 74 (121)
T ss_pred HHHHHHHHhCCCCEEEEEeC-hHHH
Confidence 66777777665666678887 9984
No 107
>PRK06298 type III secretion system protein; Validated
Probab=35.31 E-value=94 Score=24.14 Aligned_cols=41 Identities=7% Similarity=0.062 Sum_probs=28.7
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|++||.. |..+..+.| +++.. .|+++-+..|||+++-+
T Consensus 263 NPTH~AVALk----------------Yd~~~~~AP~VvAKG~d~~A~---~Ir~iA~e~~VPiven~ 310 (356)
T PRK06298 263 NPKDIAVAIG----------------YMPEKYKAPWIIAMGINLRAK---RIIAEAEKYGVPIMRNV 310 (356)
T ss_pred CCCceEEEeE----------------eCCCCCCCCEEEEeeCcHHHH---HHHHHHHHcCCCEEeCH
Confidence 7999999987 333344555 34433 37888899999998754
No 108
>PF01930 Cas_Cas4: Domain of unknown function DUF83; InterPro: IPR022765 This entry represents an uncharacterised domain found in several proteins, including DNA replication helicase Dna2, clustered regularly interspaced short palindromic repeats (CRISPR)-associated exonuclease Cas4 and putative RecB family exonuclease proteins.
Probab=35.18 E-value=55 Score=21.58 Aligned_cols=34 Identities=18% Similarity=0.197 Sum_probs=28.0
Q ss_pred cCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 45 LYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 45 ~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
.-=+||.+++..... ..|+-.---+|+.+|+++-
T Consensus 68 ~~~E~K~~~~~~~~~-~~Ql~~Y~~lL~~~g~~v~ 101 (162)
T PF01930_consen 68 IPVEIKSGRKPREEH-RMQLAAYALLLEEFGIPVK 101 (162)
T ss_pred EEEEEecCCCCcchh-HHHHHHHHHHHHhcCccce
Confidence 346899999987777 8898888888899998764
No 109
>PRK12773 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=34.91 E-value=93 Score=26.36 Aligned_cols=41 Identities=12% Similarity=0.117 Sum_probs=29.4
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|++||.- |..++.+.| +++.. .|+++-+..|||+++-+
T Consensus 561 NPTHyAVALK----------------Ydp~~~~APiVVAKG~D~lAl---rIReiAeE~gVPIVENp 608 (646)
T PRK12773 561 NPTHFAVALE----------------YKPGIHKAPIVIAKGVDDFAL---LIIRIARENGVPTVEDR 608 (646)
T ss_pred CCCceEEEEE----------------ECCCCCCCCEEEEEeCcHHHH---HHHHHHHHcCCcEEECH
Confidence 7999999987 334444556 44443 37888899999998754
No 110
>TIGR00421 ubiX_pad polyprenyl P-hydroxybenzoate and phenylacrylic acid decarboxylases. In E.coli, the protein UbiX (3-octaprenyl-4-hydroxybenzoate carboxy-lyase) has been shown to be involved in the third step of ubiquinone biosynthesis. It catalyzes the reaction [3-octaprenyl-4-hydroxybenzoate = 2-octaprenylphenol + CO2]. The knockout of the homologous protein in yeast confers sensitivity to phenylacrylic acid. Members are not restricted to ubiquinone-synthesizing species. This family represents a distinct clade within the flavoprotein family of Pfam model pfam02441.
Probab=34.65 E-value=47 Score=23.12 Aligned_cols=24 Identities=13% Similarity=0.408 Sum_probs=20.6
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCc
Q 046914 52 NRPPTPDTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 52 ~R~~~P~~L~~Ql~~i~~~l~~lGi~ 77 (90)
+|+..+++|...+ +.++|+.|||.
T Consensus 151 ~~p~~~~~~~~~i--~~~~l~~lg~~ 174 (181)
T TIGR00421 151 TRPKSVEDMIDFI--VGRVLDQLGIE 174 (181)
T ss_pred CCCCCHHHHHHHH--HHHHHHHcCCC
Confidence 6778888988887 88999999985
No 111
>PRK04036 DNA polymerase II small subunit; Validated
Probab=34.09 E-value=2.2e+02 Score=22.90 Aligned_cols=54 Identities=19% Similarity=0.198 Sum_probs=35.7
Q ss_pred CCCCeEEEeeeCCCCCCCccccccCccccCCCCC-CchhHHHhHHHHHHHHHHc--CCceEEeccc
Q 046914 22 YMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPP-TPDTIVQGLQYLKASIKAM--SIKVIEVNVM 84 (90)
Q Consensus 22 ~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~-~P~~L~~Ql~~i~~~l~~l--Gi~~~~~~g~ 84 (90)
.++++++++=|++|..+. || .+... ...++..|+..+.++|..+ +++++.++|.
T Consensus 283 ~~~d~lVIaGDivd~~~~------~p---~~~~~~~~~~~~~~~~~l~~~L~~L~~~i~V~~ipGN 339 (504)
T PRK04036 283 SRVKYLIIAGDLVDGIGI------YP---GQEEELEIVDIYEQYEAAAEYLKQIPEDIKIIISPGN 339 (504)
T ss_pred hcCCEEEEeCcccccccC------Cc---cchhhccchhhHHHHHHHHHHHHhhhcCCeEEEecCC
Confidence 378999999998775321 22 12111 1345667777777777776 6888889984
No 112
>PLN03033 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=33.93 E-value=61 Score=24.75 Aligned_cols=31 Identities=23% Similarity=0.407 Sum_probs=24.8
Q ss_pred cCCCCCCc----hhHHHhHHHHHHHHHHcCCceEE
Q 046914 50 KNNRPPTP----DTIVQGLQYLKASIKAMSIKVIE 80 (90)
Q Consensus 50 Ka~R~~~P----~~L~~Ql~~i~~~l~~lGi~~~~ 80 (90)
||||...- ..|.+.|.+++++=+.+|+++++
T Consensus 58 KApRTSp~sFrG~G~eeGL~iL~~vk~~~glpvvT 92 (290)
T PLN03033 58 KANRTSSKSFRGPGMAEGLKILEKVKVAYDLPIVT 92 (290)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCceEE
Confidence 46886432 35678999999999999999885
No 113
>TIGR03191 benz_CoA_bzdO benzoyl-CoA reductase, bzd-type, O subunit. Members of this family are the O subunit of one of two related types of four-subunit ATP-dependent benzoyl-CoA reductase. This enzyme system catalyzes the dearomatization of benzoyl-CoA, a common intermediate in pathways for the degradation for a number of different aromatic compounds, such as phenol and toluene.
Probab=33.76 E-value=40 Score=26.59 Aligned_cols=22 Identities=14% Similarity=0.122 Sum_probs=19.6
Q ss_pred HHHHHHHHcCCceEEecccccc
Q 046914 66 YLKASIKAMSIKVIEVNVMYED 87 (90)
Q Consensus 66 ~i~~~l~~lGi~~~~~~g~eeD 87 (90)
.+++.++.+|||++.+++-+.|
T Consensus 382 ~ik~~l~~~GIP~L~ietD~~d 403 (430)
T TIGR03191 382 ENRLAIAKAGIPIMTFEGNMGD 403 (430)
T ss_pred HHHHHHHHcCCCEEEEECCCCC
Confidence 5788899999999999998887
No 114
>PF05711 TylF: Macrocin-O-methyltransferase (TylF); InterPro: IPR008884 This family consists of bacterial macrocin O-methyltransferase (TylF) proteins. TylF is responsible for the methylation of macrocin to produce tylosin. Tylosin is a macrolide antibiotic used in veterinary medicine to treat infections caused by Gram-positive bacteria and as an animal growth promoter in the Sus scrofa (Pig) industry. It is produced by several Streptomyces species. As with other macrolides, the antibiotic activity of tylosin is due to the inhibition of protein biosynthesis by a mechanism that involves the binding of tylosin to the ribosome, preventing the formation of the mRNA-aminoacyl-tRNA-ribosome complex [].; PDB: 3TOS_D 2WK1_A.
Probab=33.54 E-value=31 Score=25.45 Aligned_cols=70 Identities=9% Similarity=0.039 Sum_probs=32.3
Q ss_pred hhhhccCCCCeEEEeeeCCCC-CCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCC---ceEEecccccc
Q 046914 16 NIRHDTYMTDITLDVHDLYGA-CGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSI---KVIEVNVMYED 87 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~-~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi---~~~~~~g~eeD 87 (90)
.+++....++.-+.+||+|+. +..+- .+.....++.++. -+.+..-++.+++.+...|+ .+.-++|..+|
T Consensus 94 ~~l~~~~~~~R~i~lfDSFeG~P~~~~~d~~~d~~~~~~~~--~~~~~~s~e~V~~n~~~~gl~~~~v~~vkG~F~d 168 (248)
T PF05711_consen 94 AVLEAYGNPDRRIYLFDSFEGFPEPDEEDYPADKGWEFHEY--NGYLAVSLEEVRENFARYGLLDDNVRFVKGWFPD 168 (248)
T ss_dssp HHHHCTTTTS--EEEEE-SSSSSS--CCCTCCCCHCTCCGC--CHHCTHHHHHHHHCCCCTTTSSTTEEEEES-HHH
T ss_pred HHHHHhCCCCCEEEEEeCCCCCCCCccccccccchhhhhhc--ccccccCHHHHHHHHHHcCCCcccEEEECCcchh
Confidence 455542245777899999885 22221 1111222222221 12233336667777877776 34456665544
No 115
>COG2885 OmpA Outer membrane protein and related peptidoglycan-associated (lipo)proteins [Cell envelope biogenesis, outer membrane]
Probab=33.49 E-value=76 Score=21.64 Aligned_cols=32 Identities=25% Similarity=0.165 Sum_probs=28.6
Q ss_pred hhHHHhHHHHHHHHHHcCCceEEeccccccccC
Q 046914 58 DTIVQGLQYLKASIKAMSIKVIEVNVMYEDAYG 90 (90)
Q Consensus 58 ~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~~~ 90 (90)
++....|..+.+.|+......+.++| +.|..|
T Consensus 96 p~~~~~L~~~a~~L~~~p~~~i~V~G-HTD~~G 127 (190)
T COG2885 96 PKAQATLDELAKYLKKNPITRILVEG-HTDSTG 127 (190)
T ss_pred HhHHHHHHHHHHHHHhCCCcEEEEEe-cCCCCC
Confidence 37888999999999999999999998 998765
No 116
>TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase. In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide.
Probab=33.11 E-value=66 Score=24.14 Aligned_cols=31 Identities=19% Similarity=0.390 Sum_probs=23.9
Q ss_pred cCCCCCCc----hhHHHhHHHHHHHHHHcCCceEE
Q 046914 50 KNNRPPTP----DTIVQGLQYLKASIKAMSIKVIE 80 (90)
Q Consensus 50 Ka~R~~~P----~~L~~Ql~~i~~~l~~lGi~~~~ 80 (90)
||+|...- ..+.+.|.+++++=+.+|+++++
T Consensus 44 KapRTsp~sFqG~G~eeGL~iL~~vk~~~glpvvT 78 (258)
T TIGR01362 44 KANRSSIHSFRGPGLEEGLKILQKVKEEFGVPILT 78 (258)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHhCCceEE
Confidence 35776432 24568899999999999999986
No 117
>COG5458 Uncharacterized conserved protein [Function unknown]
Probab=33.08 E-value=35 Score=23.12 Aligned_cols=19 Identities=21% Similarity=0.198 Sum_probs=15.7
Q ss_pred ccCCCCCCchhHHHhHHHH
Q 046914 49 YKNNRPPTPDTIVQGLQYL 67 (90)
Q Consensus 49 YKa~R~~~P~~L~~Ql~~i 67 (90)
=|+++..||.+|..++..+
T Consensus 123 g~ag~~~mP~dLrreLaeL 141 (144)
T COG5458 123 GKAGGADMPADLRRELAEL 141 (144)
T ss_pred CCCccccCCHHHHHHHHHh
Confidence 4889999999999887643
No 118
>PTZ00081 enolase; Provisional
Probab=33.00 E-value=73 Score=25.39 Aligned_cols=33 Identities=18% Similarity=0.186 Sum_probs=24.7
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCceEEeccccccc
Q 046914 52 NRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 52 ~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
++..++++| +.+..++++.++|.+++-|= .+||
T Consensus 278 ~~~~s~~el---i~~~~~~l~~y~I~~IEDPl-~~~D 310 (439)
T PTZ00081 278 SNKLTGEEL---VELYLDLVKKYPIVSIEDPF-DQDD 310 (439)
T ss_pred ccccCHHHH---HHHHHHHHhcCCcEEEEcCC-Cccc
Confidence 355667766 77888999999999998774 4444
No 119
>PF09572 RE_XamI: XamI restriction endonuclease; InterPro: IPR019072 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 II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the XamI restriction endonuclease which recognises GTCGAC but cleavage site unknown. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=32.97 E-value=75 Score=23.80 Aligned_cols=40 Identities=15% Similarity=0.184 Sum_probs=31.8
Q ss_pred cccCccccCCCCCCchhHH-------------------------HhHHHHHHHHHHcCCceEEec
Q 046914 43 HTLYPSYKNNRPPTPDTIV-------------------------QGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 43 ~~~yp~YKa~R~~~P~~L~-------------------------~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
.++||=...+|.|+++++. .|+..|+++|++.|...+...
T Consensus 80 p~~FpWl~~~~~Pt~~Ei~~aA~ivadrL~~avA~piiRnaqErRQe~~i~~~L~~~GYt~~~~~ 144 (251)
T PF09572_consen 80 PDRFPWLGRGRAPTEEEIERAATIVADRLCGAVADPIIRNAQERRQEAAIAEWLEARGYTKVPGG 144 (251)
T ss_pred cccccccCCCCCCCHHHHHHHHHHHHHHHHhhhcchHHHhHHHHHHHHHHHHHHHhcCceEcccc
Confidence 3567888889999887764 489999999999998766543
No 120
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=32.97 E-value=1.1e+02 Score=23.68 Aligned_cols=41 Identities=17% Similarity=0.111 Sum_probs=28.1
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|.+||.. |..++.+.| +++.. .|+++-+..|||+++-+
T Consensus 262 NPTH~AVAL~----------------Yd~~~~~aP~VvAKG~d~~A~---~Ir~iA~e~~VPiven~ 309 (349)
T PRK12721 262 NPTHIAVCLY----------------YHPGETPLPRVLEKGKDAQAL---HIVKLAERNGIPVVENI 309 (349)
T ss_pred cCCceEEEEE----------------eCCCCCCCCEEEEEeCcHHHH---HHHHHHHHcCCCEEeCH
Confidence 7999999987 222334455 34433 47888899999998754
No 121
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=32.78 E-value=1.8e+02 Score=22.82 Aligned_cols=73 Identities=12% Similarity=0.040 Sum_probs=43.9
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEeeeCCCCCCCcc--ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCce
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDVHDLYGACGMNF--RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKV 78 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~fD~fD~~~~t~--R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~ 78 (90)
|.|....- .|.+. +.+.. ..++|+.+- .. ...+.. +....+ | ...+.+++....+..+.+.|.+.|...
T Consensus 211 GlPgqt~e-~~~~~l~~~~~-l~~~~i~~y-~l--~~~p~~~~~~~~~~--~-~~~~~~~~~~~~~~~~~~~L~~~Gy~~ 282 (453)
T PRK09249 211 GLPKQTPE-SFARTLEKVLE-LRPDRLAVF-NY--AHVPWLFKAQRKID--E-ADLPSPEEKLAILQQTIETLTEAGYQY 282 (453)
T ss_pred cCCCCCHH-HHHHHHHHHHh-cCCCEEEEc-cC--ccchhhhhHhcCCC--c-ccCCCHHHHHHHHHHHHHHHHHCCCEE
Confidence 55555566 66677 66667 588888643 11 111111 111111 1 112456777888999999999999988
Q ss_pred EEec
Q 046914 79 IEVN 82 (90)
Q Consensus 79 ~~~~ 82 (90)
+++.
T Consensus 283 ye~s 286 (453)
T PRK09249 283 IGMD 286 (453)
T ss_pred Eecc
Confidence 8775
No 122
>PF03135 CagE_TrbE_VirB: CagE, TrbE, VirB family, component of type IV transporter system; InterPro: IPR018145 This domain is found in (amongst others): the Helicobacter pylori protein CagE (see examples), which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration []. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro []. Similar type IV transport systems are also found in other bacteria. This domain is also found in proteins from the trb and Vir conjugal transfer systems in Agrobacterium tumefaciens and homologues of VirB proteins from other species.; GO: 0005524 ATP binding
Probab=32.13 E-value=58 Score=22.50 Aligned_cols=29 Identities=3% Similarity=0.237 Sum_probs=22.5
Q ss_pred CCCchhHHHhHHHHHHHHHHcCCceEEec
Q 046914 54 PPTPDTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 54 ~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
.+.|++|......+..+|..+|+.+....
T Consensus 157 ~~~~~~l~~~~~~v~~~l~~~G~~~~~e~ 185 (205)
T PF03135_consen 157 ADDPEELDDKVAEVSSALNNLGFVAVRET 185 (205)
T ss_pred cCCHHHHHHHHHHHHHHHHHCCCEEEEec
Confidence 35778888888888888888888776543
No 123
>COG3516 Predicted component of the type VI protein secretion system [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.10 E-value=41 Score=23.73 Aligned_cols=18 Identities=28% Similarity=0.521 Sum_probs=16.4
Q ss_pred CchhHHHhHHHHHHHHHH
Q 046914 56 TPDTIVQGLQYLKASIKA 73 (90)
Q Consensus 56 ~P~~L~~Ql~~i~~~l~~ 73 (90)
-|+.+..|+|.++++|++
T Consensus 106 sP~~Va~qVp~L~kLLea 123 (169)
T COG3516 106 SPDAVARQVPELKKLLEA 123 (169)
T ss_pred CHHHHHHhhHHHHHHHHH
Confidence 689999999999999975
No 124
>cd00840 MPP_Mre11_N Mre11 nuclease, N-terminal metallophosphatase domain. Mre11 (also known as SbcD in Escherichia coli) is a subunit of the MRX protein complex. This complex includes: Mre11, Rad50, and Xrs2/Nbs1, and plays a vital role in several nuclear processes including DNA double-strand break repair, telomere length maintenance, cell cycle checkpoint control, and meiotic recombination, in eukaryotes. During double-strand break repair, the MRX complex is required to hold the two ends of a broken chromosome together. In vitro studies show that Mre11 has 3'-5' exonuclease activity on dsDNA templates and endonuclease activity on dsDNA and ssDNA templates. In addition to the N-terminal phosphatase domain, the eukaryotic MRE11 members of this family have a C-terminal DNA binding domain (not included in this alignment model). MRE11-like proteins are found in prokaryotes and archaea was well as in eukaryotes. Mre11 belongs to the metallophosphatase (MPP) superfamily. MPPs are functi
Probab=31.95 E-value=1.6e+02 Score=19.74 Aligned_cols=49 Identities=18% Similarity=0.301 Sum_probs=31.3
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHc---CCceEEecccc
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAM---SIKVIEVNVMY 85 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~l---Gi~~~~~~g~e 85 (90)
+..++ ..++.++++=|+||....+ +. .+..+.+.+..+ +++++.+.|.-
T Consensus 35 ~~~~~-~~~d~i~~~GD~~~~~~~~----------------~~----~~~~~~~~~~~~~~~~~~v~~~~GNH 86 (223)
T cd00840 35 ELAIE-EKVDFVLIAGDLFDSNNPS----------------PE----ALELLIEALRRLKEAGIPVFIIAGNH 86 (223)
T ss_pred HHHHh-cCCCEEEECCcccCCCCCC----------------HH----HHHHHHHHHHHHHHCCCCEEEecCCC
Confidence 55666 5899999999987754221 11 223344455554 88998888854
No 125
>PRK09967 putative outer membrane lipoprotein; Provisional
Probab=31.66 E-value=1.1e+02 Score=20.79 Aligned_cols=36 Identities=17% Similarity=0.183 Sum_probs=27.9
Q ss_pred CCCchhHHHhHHHHHHHHHHcCCceEEeccccccccC
Q 046914 54 PPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDAYG 90 (90)
Q Consensus 54 ~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~~~ 90 (90)
....++-..+|..+-+.|.......+.+.| +.|..|
T Consensus 61 a~L~~~~~~~L~~ia~~l~~~~~~~v~I~G-hTD~~G 96 (160)
T PRK09967 61 YKLLPESQQQIQTMAAKLASTGLTHARMDG-HTDNYG 96 (160)
T ss_pred cccCHHHHHHHHHHHHHHHhCCCceEEEEE-EcCCCC
Confidence 334556677888888899888877788998 888765
No 126
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=31.60 E-value=1.1e+02 Score=25.53 Aligned_cols=41 Identities=17% Similarity=0.235 Sum_probs=29.0
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|.+||.. |..+..+.| +++.. .|+++-+..|||+++-+
T Consensus 525 NPTH~AVAL~----------------Y~~~~~~aP~VvAKG~d~~A~---~Ir~~A~e~~VPive~~ 572 (609)
T PRK12772 525 NPTHIAVALK----------------YEEGKDEAPKVVAKGADYVAL---KIKEIAKENDVPIIENK 572 (609)
T ss_pred CCCceEEEeE----------------eCCCCCCCCEEEEeeCcHHHH---HHHHHHHHCCCcEEeCH
Confidence 7899999987 344444556 34433 37888999999998754
No 127
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=31.50 E-value=58 Score=18.33 Aligned_cols=21 Identities=14% Similarity=0.147 Sum_probs=13.5
Q ss_pred hHHHHHHHHHHcCCceEEecc
Q 046914 63 GLQYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 63 Ql~~i~~~l~~lGi~~~~~~g 83 (90)
+...++.+|+.-||+++....
T Consensus 11 ea~~i~~~L~~~gI~~~v~~~ 31 (67)
T PF09413_consen 11 EAELIKGLLEENGIPAFVKNE 31 (67)
T ss_dssp HHHHHHHHHHHTT--EE--S-
T ss_pred HHHHHHHHHHhCCCcEEEECC
Confidence 456699999999999987654
No 128
>PF02037 SAP: SAP domain; InterPro: IPR003034 The SAP (after SAF-A/B, Acinus and PIAS) motif is a putative DNA binding domain found in diverse nuclear proteins involved in chromosomal organisation [], including in apoptosis []. In yeast, SAP is found in the most distal N-terminal region of E3 SUMO-protein ligase SIZ1, where it is involved in nuclear localization [].; GO: 0003676 nucleic acid binding; PDB: 2RNN_A 1JEQ_A 2KW9_A 2KVU_A 2DO1_A 1ZBU_B 1ZBH_A 2DO5_A 2RNO_A 1H1J_S ....
Probab=31.18 E-value=49 Score=16.81 Aligned_cols=15 Identities=20% Similarity=0.310 Sum_probs=11.6
Q ss_pred HHHHHHHHHHcCCce
Q 046914 64 LQYLKASIKAMSIKV 78 (90)
Q Consensus 64 l~~i~~~l~~lGi~~ 78 (90)
.+.++++|.+.|+++
T Consensus 6 v~eLk~~l~~~gL~~ 20 (35)
T PF02037_consen 6 VAELKEELKERGLST 20 (35)
T ss_dssp HHHHHHHHHHTTS-S
T ss_pred HHHHHHHHHHCCCCC
Confidence 456899999999985
No 129
>cd05565 PTS_IIB_lactose PTS_IIB_lactose: subunit IIB of enzyme II (EII) of the lactose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS) found in Firmicutes as well as Actinobacteria. In this system, EII is a lactose-specific permease with two cytoplasmic domains (IIA and IIB) and a transmembrane channel IIC domain. The IIC and IIB domains are expressed as a single protein from the lac operon. The IIB domain fold includes a central four-stranded parallel open twisted beta-sheet flanked by alpha-helices on both sides. The seven major PTS systems with this IIB fold include lactose, chitobiose/lichenan, ascorbate, galactitol, mannitol, fructose, and a sensory system with similarity to the bacterial bgl system.
Probab=31.01 E-value=49 Score=20.97 Aligned_cols=26 Identities=15% Similarity=0.198 Sum_probs=22.4
Q ss_pred hhHHHhHHHHHHHHHHcCCceEEecc
Q 046914 58 DTIVQGLQYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 58 ~~L~~Ql~~i~~~l~~lGi~~~~~~g 83 (90)
+.++-+++.+++.++..|+|+..++.
T Consensus 55 PQv~~~~~~i~~~~~~~~ipv~~I~~ 80 (99)
T cd05565 55 PQMASYYDELKKDTDRLGIKLVTTTG 80 (99)
T ss_pred ChHHHHHHHHHHHhhhcCCCEEEeCH
Confidence 56788888899999999999988874
No 130
>COG3494 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.97 E-value=1.5e+02 Score=22.49 Aligned_cols=62 Identities=16% Similarity=0.081 Sum_probs=43.2
Q ss_pred hhhhccCCCCeEEEeeeCCCCCCCccccccCcccc---------CCCCCCchhHHHhHHHHHHHHHHcCCceEEeccc
Q 046914 16 NIRHDTYMTDITLDVHDLYGACGMNFRHTLYPSYK---------NNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVM 84 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~~~~t~R~~~yp~YK---------a~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~ 84 (90)
+++++ +.-++++.+=-| .+++.||+-....+= +-++. +|.| |..+-+++++.|+.++.....
T Consensus 62 k~l~~-~~v~~vVl~G~v--~~Rp~~~~L~~d~~~l~~lp~Iv~~~~~g-DDaL---Lk~vi~~~E~~GfKvigahei 132 (279)
T COG3494 62 KLLKT-EGVDRVVLAGGV--ERRPNFRDLRPDKIGLAVLPKIVEALIRG-DDAL---LKAVIDFIESRGFKVIGAHEI 132 (279)
T ss_pred HHHHH-cCCcEEEEeccc--ccCcchhhcccccchhhHHHHHHHHhccC-cHHH---HHHHHHHHHhcCcEEecHhhh
Confidence 77888 688999888775 457888876533332 12223 6777 566788999999999876543
No 131
>PF11510 FA_FANCE: Fanconi Anaemia group E protein FANCE; InterPro: IPR021025 Fanconi Anaemia (FA) is a cancer predisposition disorder characterised by chromosome fragility and hypersensitivity to genotoxic agents that suggest defects in the molecular mechanisms of DNA damage signalling and repair. In response to DNA damage, the FA core complex monoubiquitinates the FANCD2 protein. This ubiquitination targets FANCD2 to nuclear foci where it interacts with a variety of DNA repair proteins. The FA group E protein (FANCE) has an important role in DNA repair, functioning as the FANCD2-binding protein in the FA core complex []. This entry represents the C-terminal domain of FANCE, which consists predominantly of helices and does not contain any beta-strands. This domain folds in a continuous right-handed solenoidal pattern from its N terminus to its C terminus. ; PDB: 2ILR_A.
Probab=30.68 E-value=34 Score=25.65 Aligned_cols=23 Identities=22% Similarity=0.235 Sum_probs=16.5
Q ss_pred CCCCchhHHHhHHHHHHHHHHcC
Q 046914 53 RPPTPDTIVQGLQYLKASIKAMS 75 (90)
Q Consensus 53 R~~~P~~L~~Ql~~i~~~l~~lG 75 (90)
..+.|++...|++.|+++|+..+
T Consensus 5 ~~~lp~~~~~~~~~lk~ll~~~~ 27 (263)
T PF11510_consen 5 SVELPKHIQDQVPRLKELLETES 27 (263)
T ss_dssp -----HHHHHHHHHHHHHHHHHH
T ss_pred hhhCcHHHHHHHHHHHHHHHHhh
Confidence 45789999999999999998764
No 132
>COG0482 TrmU Predicted tRNA(5-methylaminomethyl-2-thiouridylate) methyltransferase, contains the PP-loop ATPase domain [Translation, ribosomal structure and biogenesis]
Probab=30.56 E-value=67 Score=25.16 Aligned_cols=41 Identities=20% Similarity=0.357 Sum_probs=26.4
Q ss_pred cCccccCCCCCCchhHHHh---HHHHHHHHHHcCCceEEeccccc
Q 046914 45 LYPSYKNNRPPTPDTIVQG---LQYLKASIKAMSIKVIEVNVMYE 86 (90)
Q Consensus 45 ~yp~YKa~R~~~P~~L~~Q---l~~i~~~l~~lGi~~~~~~g~ee 86 (90)
..++||++|.|.|+-+=.+ +..+.+.+..+|-..+ +.|.|+
T Consensus 83 f~~~Y~~G~TPNPci~CN~~iKF~~~l~~a~~lgad~i-ATGHYa 126 (356)
T COG0482 83 FLAEYKAGKTPNPCILCNKEIKFKALLDYAKELGADYI-ATGHYA 126 (356)
T ss_pred HHHHHhCCCCCCcchhcCHHHHHHHHHHHHHHcCCCeE-EEeeeE
Confidence 3479999999999877533 3444455555775543 555553
No 133
>KOG4313 consensus Thiamine pyrophosphokinase [Nucleotide transport and metabolism]
Probab=30.50 E-value=21 Score=27.05 Aligned_cols=18 Identities=33% Similarity=0.748 Sum_probs=15.5
Q ss_pred CCCccccccCccccCCCC
Q 046914 37 CGMNFRHTLYPSYKNNRP 54 (90)
Q Consensus 37 ~~~t~R~~~yp~YKa~R~ 54 (90)
+...||+++|..||..|+
T Consensus 98 ~a~qwrne~Y~v~~~kkp 115 (306)
T KOG4313|consen 98 IADQWRNELYTVYKSKKP 115 (306)
T ss_pred chhcccceeeEEEecCcc
Confidence 567999999999987775
No 134
>PRK12457 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=30.49 E-value=75 Score=24.13 Aligned_cols=31 Identities=23% Similarity=0.328 Sum_probs=23.5
Q ss_pred cCCCCCCc----hhHHHhHHHHHHHHHHcCCceEE
Q 046914 50 KNNRPPTP----DTIVQGLQYLKASIKAMSIKVIE 80 (90)
Q Consensus 50 Ka~R~~~P----~~L~~Ql~~i~~~l~~lGi~~~~ 80 (90)
||||...- ..|.+.|.+++++=+.+|+++++
T Consensus 58 KapRTSp~sFqG~G~eeGL~iL~~vk~~~GlpvvT 92 (281)
T PRK12457 58 KANRSSIHSYRGVGLDEGLRIFEEVKARFGVPVIT 92 (281)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCceEE
Confidence 35665332 35678899999999999999886
No 135
>PF03054 tRNA_Me_trans: tRNA methyl transferase; InterPro: IPR004506 tRNA-specific 2-thiouridylase catalyzes the 2-thiolation of uridine at the wobble position (U34) of tRNA, leading to the formation of s(2)U34.; GO: 0016740 transferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 2DET_A 2DER_A 2DEU_A 2HMA_A.
Probab=30.34 E-value=35 Score=26.50 Aligned_cols=48 Identities=17% Similarity=0.306 Sum_probs=28.7
Q ss_pred CCccccccC----ccccCCCCCCchhHHHh---HHHHHHHHHH-cCCceEEeccccc
Q 046914 38 GMNFRHTLY----PSYKNNRPPTPDTIVQG---LQYLKASIKA-MSIKVIEVNVMYE 86 (90)
Q Consensus 38 ~~t~R~~~y----p~YKa~R~~~P~~L~~Q---l~~i~~~l~~-lGi~~~~~~g~ee 86 (90)
.+.|+++.+ .+|+++|.|.|.-+=.+ +..+.+.... +|+..+ +.|.||
T Consensus 71 ~~~f~~~Vi~~f~~~Y~~G~TPNPcv~CN~~IKF~~l~~~a~~~~g~d~i-ATGHYA 126 (356)
T PF03054_consen 71 REEFWEEVIEPFLDEYRKGRTPNPCVLCNRFIKFGALLEYADEGLGADYI-ATGHYA 126 (356)
T ss_dssp HHHHHHHTHHHHHHHHHTT----HHHHHHHHTTTTHHHHHHHTTTT-SEE-E---SE
T ss_pred HHHHHHHHHHHHHHHHhcCCCCChHHhhchhhhHHHHHHHHHhhcCCCee-ccceeE
Confidence 455665554 49999999999988554 6677777777 999965 677776
No 136
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=30.26 E-value=1.2e+02 Score=20.52 Aligned_cols=43 Identities=21% Similarity=0.202 Sum_probs=31.7
Q ss_pred CccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 39 MNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 39 ~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
-.|+.-=--.+|+.|+.+|=.--..-+.+.+....+||..+++
T Consensus 42 i~wassG~~gfk~~rk~tpyAA~~aa~~aa~~a~e~Gi~~v~v 84 (129)
T COG0100 42 IIWASSGGMGFKGSRKSTPYAAQLAAEDAAKKAKEHGIKSVEV 84 (129)
T ss_pred EEEEecCCceEcCCCCCCHHHHHHHHHHHHHHHHHhCccEEEE
Confidence 4677766778999998888666555556666666699988875
No 137
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=30.06 E-value=63 Score=17.73 Aligned_cols=20 Identities=5% Similarity=-0.119 Sum_probs=14.3
Q ss_pred hHHHHHHHHHHcCCceEEec
Q 046914 63 GLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 63 Ql~~i~~~l~~lGi~~~~~~ 82 (90)
|-..-.+.|..+||+.+.-+
T Consensus 16 ~~~~Q~~~L~~~Gi~~~~~~ 35 (47)
T PF13986_consen 16 RPSKQIRWLRRNGIPFVVRA 35 (47)
T ss_pred CHHHHHHHHHHCCCeeEECC
Confidence 44455678889999987644
No 138
>PF01661 Macro: Macro domain; InterPro: IPR002589 The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose, an NAD metabolite or related ligands. Binding to ADP-ribose could be either covalent or non-covalent []: in certain cases it is believed to bind non-covalently []; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein []. The domain was described originally in association with ADP-ribose 1''-phosphate (Appr-1''-P) processing activity (A1pp) of the yeast YBR022W protein []. The domain is also called Macro domain as it is the C-terminal domain of mammalian core histone macro-H2A [, ]. Macro domain proteins can be found in eukaryotes, in (mostly pathogenic) bacteria, in archaea and in ssRNA viruses, such as coronaviruses, Rubella and Hepatitis E viruses. In vertebrates the domain occurs e.g. in histone macroH2A, in predicted poly-ADP-ribose polymerases (PARPs) and in B aggressive lymphoma (BAL) protein. The macro domain can be associated with catalytic domains, such as PARP, or sirtuin. The Macro domain can recognise ADP-ribose or in some cases poly-ADP-ribose, which can be involved in ADP-ribosylation reactions that occur in important processes, such as chromatin biology, DNA repair and transcription regulation []. The human macroH2A1.1 Macro domain binds an NAD metabolite O-acetyl-ADP-ribose []. The Macro domain has been suggested to play a regulatory role in ADP-ribosylation, which is involved in inter- and intracellular signaling, transcriptional regulation, DNA repair pathways and maintenance of genomic stability, telomere dynamics, cell differentiation and proliferation, and necrosis and apoptosis. The 3D structure of the Macro domain has a mixed alpha/beta fold of a mixed beta sheet sandwiched between four helices. Several Macro domain only domains are shorter than the structure of AF1521 and lack either the first strand or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [, , , ]. ; PDB: 2DX6_A 2XD7_D 3Q71_A 2FAV_B 1SPV_A 3EKE_A 3EJF_A 1YD9_B 3GPG_B 3GPQ_A ....
Probab=29.90 E-value=1.3e+02 Score=18.14 Aligned_cols=50 Identities=12% Similarity=0.135 Sum_probs=36.9
Q ss_pred CCccccccCccccCCC-CCCchhHHHhHHHHHHHHHHcCCceEEecccccc
Q 046914 38 GMNFRHTLYPSYKNNR-PPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYED 87 (90)
Q Consensus 38 ~~t~R~~~yp~YKa~R-~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD 87 (90)
.+..-|-..|.|.... ....+.|..-+..+.+.++..++..+..|-.=..
T Consensus 55 ~~~Iih~v~P~~~~~~~~~~~~~L~~~~~~~l~~a~~~~~~sIa~P~ig~G 105 (118)
T PF01661_consen 55 CKYIIHAVGPTYNSPGEKNSYEALESAYRNALQKAEENGIKSIAFPAIGTG 105 (118)
T ss_dssp SSEEEEEEEEETTTSTSTTHHHHHHHHHHHHHHHHHHTTTSEEEEESTTSS
T ss_pred ccceEEEecceeccccccccHHHHHHHHHHHHHHHHHcCCcccccCcccCC
Confidence 3556677778886443 3456788888898999999999999998864443
No 139
>PF05591 DUF770: Protein of unknown function (DUF770); InterPro: IPR008312 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, these proteins are encoded in type VI secretion loci (including the SCI genomic island in Salmonella enterica and the imp locus in Rhizobium leguminosarum) implicated in pathogenicity and protein secretion [, , [].
Probab=29.88 E-value=48 Score=22.89 Aligned_cols=18 Identities=17% Similarity=0.416 Sum_probs=16.0
Q ss_pred CchhHHHhHHHHHHHHHH
Q 046914 56 TPDTIVQGLQYLKASIKA 73 (90)
Q Consensus 56 ~P~~L~~Ql~~i~~~l~~ 73 (90)
-|+.+..|+|.++++++.
T Consensus 100 ~Pd~v~~qVp~L~~Llel 117 (157)
T PF05591_consen 100 HPDAVAEQVPELRKLLEL 117 (157)
T ss_pred CHHHHHHhhHHHHHHHHH
Confidence 599999999999998864
No 140
>smart00857 Resolvase Resolvase, N terminal domain. The N-terminal domain of the resolvase family contains the active site and the dimer interface. The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase.
Probab=29.51 E-value=64 Score=20.58 Aligned_cols=21 Identities=29% Similarity=0.358 Sum_probs=18.9
Q ss_pred hHHHhHHHHHHHHHHcCCceE
Q 046914 59 TIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 59 ~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
.+..|...+++.+...|+++.
T Consensus 16 s~~~Q~~~~~~~a~~~g~~i~ 36 (148)
T smart00857 16 SLERQLEALRAYAKANGWEVV 36 (148)
T ss_pred CHHHHHHHHHHHHHHCCCEEE
Confidence 688999999999999998864
No 141
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=29.24 E-value=2.1e+02 Score=22.07 Aligned_cols=72 Identities=13% Similarity=-0.006 Sum_probs=43.8
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|-..+- .+.+. +.+.+ ..|+|+-+- +-+ ..+.+-++. +. ..+..+...+....+.+.|.+.|...+
T Consensus 181 GlPgqt~~-~~~~~l~~~~~-l~p~~is~y~l~~-~~gT~l~~~------~~-~~~~~~~~~~~~~~~~~~L~~~Gy~~y 250 (394)
T PRK08898 181 ALPGQTLD-EALADVETALA-FGPPHLSLYHLTL-EPNTLFAKF------PP-ALPDDDASADMQDWIEARLAAAGYAHY 250 (394)
T ss_pred CCCCCCHH-HHHHHHHHHHh-cCCCEEEEeeeEE-CCCChhhhc------cC-CCCChHHHHHHHHHHHHHHHHcCCchh
Confidence 56666666 66666 66666 588887543 221 012222221 11 124456677888899999999999888
Q ss_pred Eecc
Q 046914 80 EVNV 83 (90)
Q Consensus 80 ~~~g 83 (90)
++..
T Consensus 251 e~~~ 254 (394)
T PRK08898 251 EVSA 254 (394)
T ss_pred cccc
Confidence 7764
No 142
>PF08722 Tn7_Tnp_TnsA_N: TnsA endonuclease N terminal; InterPro: IPR014833 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The N-terminal domain of TnsA is catalytic. ; PDB: 1F1Z_B 1T0F_B.
Probab=29.03 E-value=79 Score=18.88 Aligned_cols=53 Identities=13% Similarity=0.072 Sum_probs=31.9
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
-||.++..-| ..++ ...+-+-|....-.-+...+.+...++.+++.|++..-+
T Consensus 34 TpDFlv~~~~---g~~~---~~~~ieVK~~~~l~~~~~~~k~~~~~~y~~~~g~~f~iv 86 (88)
T PF08722_consen 34 TPDFLVTYRD---GNGK---KPVAIEVKPSSELEKPRTKEKLEIEREYWEEQGIPFRIV 86 (88)
T ss_dssp EEEEEEEESS---S--S---SEEEEEE--GGGGGSHHHHHHHHHHHHHHHHCT--EEEE
T ss_pred eccEEEEEcc---CCcc---eEEEEEEccHHHhcChhHHHHHHHHHHHHHHcCCeEEEE
Confidence 4565554444 2222 444556666555555788999999999999999987644
No 143
>PHA02595 tk.4 hypothetical protein; Provisional
Probab=28.99 E-value=1.8e+02 Score=19.47 Aligned_cols=41 Identities=10% Similarity=0.195 Sum_probs=31.4
Q ss_pred ccCccccCCCCCCchhHHHhHHHHHHHHHHcCC-ceEEeccc
Q 046914 44 TLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSI-KVIEVNVM 84 (90)
Q Consensus 44 ~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi-~~~~~~g~ 84 (90)
.++..|+..++...+.|...|..+.+.++..++ ..+.+|..
T Consensus 80 nl~tq~~~~~~~~y~ai~~~l~~l~~~~~~~~~~~sIa~P~I 121 (154)
T PHA02595 80 NLYTQFDPGPNLEYSALMNCFEELNEVFEGTLFKPTIYIPRI 121 (154)
T ss_pred EEeccCCCCCCCcHHHHHHHHHHHHHHHHhcCCCcEEeeCCC
Confidence 455666666555567799999999999999998 77877753
No 144
>PF04009 DUF356: Protein of unknown function (DUF356); InterPro: IPR007154 Members of this family are around 120 amino acids in length and are found in some archaebacteria. The function of this family is unknown. However it contains a conserved motif IHPPAH that may be involved in its function.
Probab=28.93 E-value=44 Score=21.92 Aligned_cols=16 Identities=6% Similarity=-0.016 Sum_probs=13.0
Q ss_pred hhhhccCCCCeEEEeee
Q 046914 16 NIRHDTYMTDITLDVHD 32 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD 32 (90)
++.+= ++|.|++|+-.
T Consensus 73 ~lrkI-HPPAHIiVis~ 88 (107)
T PF04009_consen 73 RLRKI-HPPAHIIVISP 88 (107)
T ss_pred HHhhc-CCCceEEEECC
Confidence 67777 69999998876
No 145
>PRK05702 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=28.63 E-value=1.4e+02 Score=23.13 Aligned_cols=41 Identities=10% Similarity=0.203 Sum_probs=26.8
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|++||.- |..++.+.| +.+. ..|+++.+..|||+++-+
T Consensus 269 NPTH~AVal~----------------Y~~~~~~aP~vvakg~~~~A---~~i~~~A~~~~vpi~~~~ 316 (359)
T PRK05702 269 NPTHYAVALK----------------YDRGKMAAPVVVAKGVDEVA---LKIREIAREHNVPIVENP 316 (359)
T ss_pred CCCceEEEeE----------------eCCCCCCCCEEEEeeCcHHH---HHHHHHHHHcCCCEEeCH
Confidence 7889998876 222233344 3333 247888889999998754
No 146
>PTZ00378 hypothetical protein; Provisional
Probab=28.48 E-value=1.6e+02 Score=24.31 Aligned_cols=66 Identities=12% Similarity=0.207 Sum_probs=40.0
Q ss_pred hhhccCCC-CeEEEeeeCCCCCCCcc-------------ccc------cCccccCCCCCCchhHHHhHHHHHHHHHHcC-
Q 046914 17 IRHDTYMT-DITLDVHDLYGACGMNF-------------RHT------LYPSYKNNRPPTPDTIVQGLQYLKASIKAMS- 75 (90)
Q Consensus 17 l~~~~~~p-~~i~v~fD~fD~~~~t~-------------R~~------~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lG- 75 (90)
+-+.++.| +-|.+++|+ -.+.| +.. .|.--|..+.-++++| +++.+++++..-
T Consensus 271 i~~aGy~pG~dI~iglD~---AASef~~~~~~~~~~~~y~~~k~~~e~~Y~l~~~~~~~t~~el---ieyy~~li~kYP~ 344 (518)
T PTZ00378 271 LRAVQLTPGTDVCLGLRM---AASTTRVPATAVADGGAWKEAKDDCEVLYSLFPGEPDVTGDQL---SEYVREQLQAVPD 344 (518)
T ss_pred HHHhCCCCCCeEEEEEec---ccccccccccccccchhhccccCCCceeeeecCCCCCCCHHHH---HHHHHHHHHHCCC
Confidence 33333566 469999994 33444 442 2321155554567776 888999999996
Q ss_pred -CceEEecccccccc
Q 046914 76 -IKVIEVNVMYEDAY 89 (90)
Q Consensus 76 -i~~~~~~g~eeD~~ 89 (90)
|..++-+ ..|||+
T Consensus 345 iIvsIEDp-~~E~D~ 358 (518)
T PTZ00378 345 IVVYVEDT-HCDEDT 358 (518)
T ss_pred ceEEEecC-CCchHH
Confidence 6666554 556554
No 147
>TIGR02802 Pal_lipo peptidoglycan-associated lipoprotein. Members of this protein are Pal (also called OprL), the Peptidoglycan-Associated Lipoprotein of the Tol-Pal system. The system appears to be involved both in the maintenance of outer membrane integrity and in the import of certain organic molecules as nutrients. Members of this family contain a hydrodrophobic lipoprotein signal sequence, a conserved N-terminal cleavage and modification site, a poorly conserved low-complexity region, together comprising about 65 amino acids, and a well-conserved C-terminal domain. The seed alignment for this model includes only the conserved C-terminal domain.
Probab=28.33 E-value=1.4e+02 Score=18.04 Aligned_cols=33 Identities=12% Similarity=-0.048 Sum_probs=22.3
Q ss_pred CchhHHHhHHHHHHHHHHcCCceEEecccccccc
Q 046914 56 TPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDAY 89 (90)
Q Consensus 56 ~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~~ 89 (90)
..++-..+|..+.++|....-..+.+.| ++|.-
T Consensus 11 l~~~~~~~L~~~a~~l~~~~~~~i~I~G-htd~~ 43 (104)
T TIGR02802 11 LKSEAQAILDAHAAYLKKNPSVRVTIEG-HTDER 43 (104)
T ss_pred cCHHHHHHHHHHHHHHHHCCCcEEEEEE-ecCCC
Confidence 3455566777777777776665677887 67754
No 148
>cd02908 Macro_Appr_pase_like Macro domain, Appr-1"-pase_like family. The macro domain is a high-affinity ADP-ribose binding module found in a variety of proteins as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Some macro domains recognize poly ADP-ribose as a ligand. Previously identified as displaying an Appr-1"-p (ADP-ribose-1"-monophosphate) processing activity, the macro domain may play roles in distinct ADP-ribose pathways, such as the ADP-ribosylation of proteins, an important post-translational modification which occurs in DNA repair, transcription, chromatin biology, and long-term memory formation, among other processes. This family is composed of uncharacterized proteins that show similarity to Appr-1"-pase, containing conserved putative active site residues. Appr-1"-pase is a phosphatase specific for ADP-ribose-1"-monophosphate.
Probab=27.99 E-value=1.6e+02 Score=19.68 Aligned_cols=48 Identities=13% Similarity=0.276 Sum_probs=34.8
Q ss_pred cccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEeccccccccC
Q 046914 43 HTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDAYG 90 (90)
Q Consensus 43 ~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~~~ 90 (90)
|-.=|.|........+.|..-+..+-+....+|+.++..|..-...+|
T Consensus 73 H~v~P~~~~~~~~~~~~L~~~~~~~L~~a~~~~~~sIa~P~igtG~~g 120 (165)
T cd02908 73 HTVGPVWRGGQHNEAELLASCYRNSLELARENGLRSIAFPAISTGVYG 120 (165)
T ss_pred EEcCCcccCCCCcHHHHHHHHHHHHHHHHHHcCCCEEEECceecCCCC
Confidence 333457766555567788888888888888999999999876554443
No 149
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=27.13 E-value=56 Score=19.66 Aligned_cols=22 Identities=9% Similarity=0.264 Sum_probs=13.9
Q ss_pred HHhHHHHHHHHHHcCCceEEec
Q 046914 61 VQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 61 ~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
..|+..|-..|...||.++...
T Consensus 38 ~e~id~i~~~L~~~gI~Vvd~~ 59 (82)
T PF03979_consen 38 PEQIDEIYDTLEDEGIEVVDEE 59 (82)
T ss_dssp HHHHHHHHHHHHTT----B--S
T ss_pred HHHHHHHHHHHHHCCCEEecCC
Confidence 4689999999999999999854
No 150
>PF04217 DUF412: Protein of unknown function, DUF412; InterPro: IPR007334 This family consists of bacterial uncharacterised proteins.
Probab=26.65 E-value=1e+02 Score=21.18 Aligned_cols=27 Identities=11% Similarity=0.354 Sum_probs=23.7
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCce
Q 046914 52 NRPPTPDTIVQGLQYLKASIKAMSIKV 78 (90)
Q Consensus 52 ~R~~~P~~L~~Ql~~i~~~l~~lGi~~ 78 (90)
.+.+.|+.|......|++-|.+.|+.+
T Consensus 87 a~tpLPp~l~~Wy~ei~~Kl~~~g~~~ 113 (143)
T PF04217_consen 87 ANTPLPPSLLSWYHEIRQKLQEQGIAL 113 (143)
T ss_pred cCCCCCHHHHHHHHHHHHHHHHcCCcc
Confidence 346789999999999999999999875
No 151
>PRK12468 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=26.60 E-value=1.6e+02 Score=23.16 Aligned_cols=41 Identities=10% Similarity=0.135 Sum_probs=28.3
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|++||.- |..+..+.| +++.. .|+++-+..|||+++-+
T Consensus 269 NPTH~AVALk----------------Y~~~~~~AP~VvAKG~d~~A~---~Ir~~A~e~~VPiven~ 316 (386)
T PRK12468 269 NPTHYAVALQ----------------YNESKMSAPKVLAKGAGAVAL---RIRELGAEHRIPLLEAP 316 (386)
T ss_pred CCCceEEEEE----------------eCCCCCCCCEEEEeeCcHHHH---HHHHHHHHcCCcEEeCH
Confidence 7899999987 333334455 34433 37888899999998754
No 152
>smart00513 SAP Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation.
Probab=26.56 E-value=66 Score=16.14 Aligned_cols=15 Identities=20% Similarity=0.304 Sum_probs=12.5
Q ss_pred HHHHHHHHHHcCCce
Q 046914 64 LQYLKASIKAMSIKV 78 (90)
Q Consensus 64 l~~i~~~l~~lGi~~ 78 (90)
...+++.|...|+++
T Consensus 6 ~~~Lk~~l~~~gl~~ 20 (35)
T smart00513 6 VSELKDELKKRGLST 20 (35)
T ss_pred HHHHHHHHHHcCCCC
Confidence 456899999999985
No 153
>PRK11148 cyclic 3',5'-adenosine monophosphate phosphodiesterase; Provisional
Probab=26.37 E-value=2.5e+02 Score=20.15 Aligned_cols=41 Identities=12% Similarity=0.060 Sum_probs=29.9
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEecccc
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMY 85 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~e 85 (90)
+|+.++++=|+.|.+ + .++...+.+.|+.++++++.++|+-
T Consensus 55 ~~D~vvitGDl~~~~--~--------------------~~~~~~~~~~l~~l~~Pv~~v~GNH 95 (275)
T PRK11148 55 EFDLIVATGDLAQDH--S--------------------SEAYQHFAEGIAPLRKPCVWLPGNH 95 (275)
T ss_pred CCCEEEECCCCCCCC--C--------------------HHHHHHHHHHHhhcCCcEEEeCCCC
Confidence 689999999964421 1 1345667788889999999999853
No 154
>PRK03094 hypothetical protein; Provisional
Probab=26.24 E-value=80 Score=19.57 Aligned_cols=26 Identities=23% Similarity=0.376 Sum_probs=20.7
Q ss_pred HhHHHHHHHHHHcCCceEEeccccccc
Q 046914 62 QGLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 62 ~Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
..|..|++.|+.-|-.++.+.. |.|+
T Consensus 8 ~~Ls~i~~~L~~~GYeVv~l~~-~~~~ 33 (80)
T PRK03094 8 QSLTDVQQALKQKGYEVVQLRS-EQDA 33 (80)
T ss_pred cCcHHHHHHHHHCCCEEEecCc-cccc
Confidence 4577899999999999988875 5443
No 155
>PF06069 PerC: PerC transcriptional activator; InterPro: IPR024684 This family includes PerC, which is a transcriptional activator of EaeA/BfpA expression in enteropathogenic bacteria []. It also includes a number of uncharacterised proteins, such as Orf40 from bacteriophage SfV.
Probab=26.21 E-value=1.1e+02 Score=19.32 Aligned_cols=30 Identities=30% Similarity=0.383 Sum_probs=20.7
Q ss_pred ccCCCCCCc-hhHHHhHHHHHHHHHHcCCce
Q 046914 49 YKNNRPPTP-DTIVQGLQYLKASIKAMSIKV 78 (90)
Q Consensus 49 YKa~R~~~P-~~L~~Ql~~i~~~l~~lGi~~ 78 (90)
=|++|++.| +++..-=..+.+....|||..
T Consensus 48 ~kakR~p~~~~~f~~l~~Aa~~T~~~MGi~~ 78 (90)
T PF06069_consen 48 RKAKRPPEPPDNFGDLRKAADRTQKRMGIDQ 78 (90)
T ss_pred HhcccCCCChhHHHHHHHHHHHHHHHcCCCC
Confidence 377787765 455555566778888999963
No 156
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=26.15 E-value=46 Score=20.39 Aligned_cols=16 Identities=19% Similarity=0.306 Sum_probs=12.4
Q ss_pred HHHHHHHHHcCCceEE
Q 046914 65 QYLKASIKAMSIKVIE 80 (90)
Q Consensus 65 ~~i~~~l~~lGi~~~~ 80 (90)
..+++++++||||.=+
T Consensus 33 ~tvkd~IEsLGVP~tE 48 (81)
T PF14451_consen 33 ATVKDVIESLGVPHTE 48 (81)
T ss_pred CcHHHHHHHcCCChHH
Confidence 3589999999998533
No 157
>COG3048 DsdA D-serine dehydratase [Amino acid transport and metabolism]
Probab=25.83 E-value=51 Score=26.06 Aligned_cols=22 Identities=32% Similarity=0.761 Sum_probs=17.8
Q ss_pred HHHHHHHHHcCCceEEeccccccccC
Q 046914 65 QYLKASIKAMSIKVIEVNVMYEDAYG 90 (90)
Q Consensus 65 ~~i~~~l~~lGi~~~~~~g~eeD~~~ 90 (90)
.+=|+.|++.|+++++ ||+|||
T Consensus 196 ~WKKd~LRs~gV~ViE----Ye~DY~ 217 (443)
T COG3048 196 AWKKDKLRSHGVTVVE----YEQDYG 217 (443)
T ss_pred HHHHHHHHhcCceEEE----ecchhh
Confidence 4568899999999984 777876
No 158
>COG1440 CelA Phosphotransferase system cellobiose-specific component IIB [Carbohydrate transport and metabolism]
Probab=25.83 E-value=80 Score=20.50 Aligned_cols=27 Identities=19% Similarity=0.177 Sum_probs=23.6
Q ss_pred chhHHHhHHHHHHHHHHcCCceEEecc
Q 046914 57 PDTIVQGLQYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 57 P~~L~~Ql~~i~~~l~~lGi~~~~~~g 83 (90)
-+.++-+++.+++.++..|||+-.++-
T Consensus 55 GPQv~y~~~~~~~~~~~~giPV~vI~~ 81 (102)
T COG1440 55 GPQVRYMLKQLKEAAEEKGIPVEVIDM 81 (102)
T ss_pred ChHHHHHHHHHHHHhcccCCCeEEeCH
Confidence 477899999999999999999887764
No 159
>cd03770 SR_TndX_transposase Serine Recombinase (SR) family, TndX-like transposase subfamily, catalytic domain; composed of large serine recombinases similar to Clostridium TndX and TnpX transposases. Serine recombinases catalyze site-specific recombination of DNA molecules by a concerted, four-strand cleavage and rejoining mechanism which involves a transient phosphoserine linkage between DNA and the enzyme. They are functionally versatile and include resolvases, invertases, integrases, and transposases. TndX mediates the excision and circularization of the conjugative transposon Tn5397 from Clostridium difficile. TnpX is responsible for the movement of the nonconjugative chloramphenicol resistance elements of the Tn4451/3 family. Mobile genetic elements such as transposons are important vehicles for the transmission of virulence and antibiotic resistance in many microorganisms.
Probab=25.69 E-value=93 Score=20.24 Aligned_cols=22 Identities=18% Similarity=0.187 Sum_probs=19.6
Q ss_pred hhHHHhHHHHHHHHHHcCCceE
Q 046914 58 DTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 58 ~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
..|..|...+++.+...|+.+.
T Consensus 18 ~sle~Q~~~l~~~a~~~g~~i~ 39 (140)
T cd03770 18 NSIENQKAILEEYAKENGLENI 39 (140)
T ss_pred CCHHHHHHHHHHHHHHCCCEEE
Confidence 4789999999999999999864
No 160
>PF07807 RED_C: RED-like protein C-terminal region; InterPro: IPR012492 This family contains sequences that are similar to the C-terminal region of Red protein (Q13123 from SWISSPROT). This and related proteins are thought to be localised to the nucleus, and contain a RED repeat which consists of a number of RE and RD sequence elements []. The region in question has several conserved NLS sequences []. The function of Red protein is unknown, but efficient sequestration to nuclear bodies suggests that its expression may be tightly regulated or that the protein self-aggregates extremely efficiently [].
Probab=25.40 E-value=43 Score=22.31 Aligned_cols=33 Identities=15% Similarity=0.303 Sum_probs=24.6
Q ss_pred cccCccccCCCCCCch-------------------------hHHHhHHHHHHHHHHcC
Q 046914 43 HTLYPSYKNNRPPTPD-------------------------TIVQGLQYLKASIKAMS 75 (90)
Q Consensus 43 ~~~yp~YKa~R~~~P~-------------------------~L~~Ql~~i~~~l~~lG 75 (90)
.|.|..|+.+|..+|- .|-.|+..|..||+.=+
T Consensus 44 ~EEy~~Y~~~kEalPKAAfQyGvKm~dGrKtrk~~~k~ek~kLdre~~kI~~Il~krk 101 (118)
T PF07807_consen 44 EEEYSKYMEQKEALPKAAFQYGVKMADGRKTRKQGEKDEKAKLDREWQKIQKILKKRK 101 (118)
T ss_pred HHHHHHHHhhhhhCcHHHHHhccccccccccccccchhHHHHHhHHHHHHHHHHHHhc
Confidence 4668888888887772 47778888888887654
No 161
>COG4792 EscU Type III secretory pathway, component EscU [Intracellular trafficking and secretion]
Probab=25.22 E-value=1.5e+02 Score=23.09 Aligned_cols=43 Identities=16% Similarity=0.070 Sum_probs=27.9
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCch----hHHHhHHHHHHHHHHcCCceEEe
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPD----TIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~----~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
+|+|++||.= ||-+-.|.|= .=-+|-..|..+-++.|||+++-
T Consensus 263 nPThiaI~l~----------------Y~~gETplPlVi~k~~daqA~~i~~iAe~~~ipVven 309 (349)
T COG4792 263 NPTHIAICLR----------------YKRGETPLPLVIEKGTDAQALQIVKIAEEEGIPVVEN 309 (349)
T ss_pred cCceEEEEEe----------------eccCCCCCCEEEEecCcHHHHHHHHHHHHhCCCeeec
Confidence 6888888876 4444445551 11245556778889999998853
No 162
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=25.19 E-value=1e+02 Score=20.34 Aligned_cols=26 Identities=15% Similarity=0.301 Sum_probs=21.5
Q ss_pred hHHHhHHHHHHHHHHcCCceEEeccc
Q 046914 59 TIVQGLQYLKASIKAMSIKVIEVNVM 84 (90)
Q Consensus 59 ~L~~Ql~~i~~~l~~lGi~~~~~~g~ 84 (90)
=|.+.|..+++-|..+|++.+...|.
T Consensus 50 Fl~~sL~~L~~~L~~~g~~L~v~~g~ 75 (165)
T PF00875_consen 50 FLLESLADLQESLRKLGIPLLVLRGD 75 (165)
T ss_dssp HHHHHHHHHHHHHHHTTS-EEEEESS
T ss_pred HHHHHHHHHHHHHHhcCcceEEEecc
Confidence 46888999999999999998888774
No 163
>PLN00061 photosystem II protein Psb27; Provisional
Probab=25.09 E-value=48 Score=22.98 Aligned_cols=19 Identities=16% Similarity=0.468 Sum_probs=14.2
Q ss_pred cCccccCCCCCCchhHHHhH
Q 046914 45 LYPSYKNNRPPTPDTIVQGL 64 (90)
Q Consensus 45 ~yp~YKa~R~~~P~~L~~Ql 64 (90)
-|..|=.|| |+|++|+..|
T Consensus 124 hYssyGpnr-PLPe~lK~Rl 142 (150)
T PLN00061 124 FYSKAGPSA-PLPEDVKSEI 142 (150)
T ss_pred HHHhcCCCC-CCCHHHHHHH
Confidence 366666667 7999998776
No 164
>COG2908 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.86 E-value=2.9e+02 Score=20.45 Aligned_cols=53 Identities=8% Similarity=0.034 Sum_probs=38.6
Q ss_pred hhhccCCC--CeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEeccc
Q 046914 17 IRHDTYMT--DITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVM 84 (90)
Q Consensus 17 l~~~~~~p--~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~ 84 (90)
+++. ..+ +.+.++=|+||..... - .|+++..|+-.--..+..-|.+|+.++|+
T Consensus 22 Fl~~-~a~~ad~lyilGDifd~w~g~----~----------~~~~~~~~V~~~l~~~a~~G~~v~~i~GN 76 (237)
T COG2908 22 FLRE-EAAQADALYILGDIFDGWIGD----D----------EPPQLHRQVAQKLLRLARKGTRVYYIHGN 76 (237)
T ss_pred HHHh-ccccCcEEEEechhhhhhhcC----C----------cccHHHHHHHHHHHHHHhcCCeEEEecCc
Confidence 4444 344 8999999988853211 0 78888888877777778889999999984
No 165
>PHA02754 hypothetical protein; Provisional
Probab=24.72 E-value=77 Score=18.79 Aligned_cols=25 Identities=12% Similarity=0.159 Sum_probs=20.1
Q ss_pred CchhHHHhHHHHHHHHHHcCCceEE
Q 046914 56 TPDTIVQGLQYLKASIKAMSIKVIE 80 (90)
Q Consensus 56 ~P~~L~~Ql~~i~~~l~~lGi~~~~ 80 (90)
|..++.+.+..++++|+..||.+=.
T Consensus 12 ~eK~Fke~MRelkD~LSe~GiYi~R 36 (67)
T PHA02754 12 MEKDFKEAMRELKDILSEAGIYIDR 36 (67)
T ss_pred HHhHHHHHHHHHHHHHhhCceEEEE
Confidence 4457888999999999999986533
No 166
>PF03469 XH: XH domain; InterPro: IPR005379 The XH (rice gene X Homology) domain is found in a family of plant proteins including Oryza sativa (Rice) Q9SBW2 from SWISSPROT. The molecular function of these proteins is unknown, however these proteins usually contain an XS domain (IPR005380 from INTERPRO) that is also found in the PTGS protein SGS3. As the XS and XH domains are fused in most of these proteins, these two domains may interact. The XH domain is between 124 and 145 residues in length and contains a conserved glutamate residue that may be functionally important [].
Probab=24.66 E-value=57 Score=22.06 Aligned_cols=15 Identities=33% Similarity=0.550 Sum_probs=12.3
Q ss_pred cccCCCCCCchhHHH
Q 046914 48 SYKNNRPPTPDTIVQ 62 (90)
Q Consensus 48 ~YKa~R~~~P~~L~~ 62 (90)
+||.+|+.+..+.+.
T Consensus 105 N~ke~RkAtl~E~v~ 119 (132)
T PF03469_consen 105 NFKEGRKATLKEVVQ 119 (132)
T ss_pred ccccccccCHHHHHH
Confidence 699999999877755
No 167
>COG3033 TnaA Tryptophanase [Amino acid transport and metabolism]
Probab=24.62 E-value=89 Score=25.19 Aligned_cols=25 Identities=16% Similarity=0.284 Sum_probs=22.3
Q ss_pred HHhHHHHHHHHHHcCCceEEecccc
Q 046914 61 VQGLQYLKASIKAMSIKVIEVNVMY 85 (90)
Q Consensus 61 ~~Ql~~i~~~l~~lGi~~~~~~g~e 85 (90)
+.|..++-+.|++.|+|++...|+.
T Consensus 333 v~Qv~YL~~~l~~~GVpi~~paGGH 357 (471)
T COG3033 333 VAQVQYLADGLEEAGVPIVQPAGGH 357 (471)
T ss_pred HHHHHHHHHHHHhcCCeeEecCCCc
Confidence 7899999999999999988877754
No 168
>COG4572 ChaB Putative cation transport regulator [General function prediction only]
Probab=24.28 E-value=81 Score=19.32 Aligned_cols=21 Identities=19% Similarity=0.343 Sum_probs=16.2
Q ss_pred ccCCCCCCchhHHHhHHHHHHH
Q 046914 49 YKNNRPPTPDTIVQGLQYLKAS 70 (90)
Q Consensus 49 YKa~R~~~P~~L~~Ql~~i~~~ 70 (90)
||++- ..|++.+.|||.-.+.
T Consensus 3 yk~~s-dlp~~vr~~lp~haqd 23 (76)
T COG4572 3 YKTKS-DLPEEVRHQLPSHAQD 23 (76)
T ss_pred ccccc-cccHHHHHHhHHHHHH
Confidence 77765 6999999999865443
No 169
>TIGR01854 lipid_A_lpxH UDP-2,3-diacylglucosamine hydrolase. This model represents LpxH, UDP-2,3-diacylglucosamine hydrolase, and essential enzyme in E. coli that catalyzes the fourth step in lipid A biosynthesis. Note that Pseudomonas aeruginosa has both a member of this family that shares this function and a more distant homolog, designated LpxH2, that does not. Many species that produce lipid A lack an lpxH gene in this family; some of those species have an lpxH2 gene instead, although for which the function is unknown.
Probab=24.21 E-value=2.6e+02 Score=19.58 Aligned_cols=48 Identities=13% Similarity=0.113 Sum_probs=26.8
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEeccc
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVM 84 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~ 84 (90)
.|+.++++=|+||..... + . +.....++..+-+.|...|++++.+.|+
T Consensus 30 ~~d~lii~GDi~d~~~~~---------~---~--~~~~~~~~~~~l~~L~~~~~~v~~v~GN 77 (231)
T TIGR01854 30 KADALYILGDLFEAWIGD---------D---D--PSTLARSVAQAIRQVSDQGVPCYFMHGN 77 (231)
T ss_pred cCCEEEEcCceeccccCC---------C---C--CCHHHHHHHHHHHHHHHCCCeEEEEcCC
Confidence 699999999988742110 0 0 1112223322223344557888888774
No 170
>TIGR02260 benz_CoA_red_B benzoyl-CoA reductase, bcr type, subunit B. This model describes B, or beta, subunit of the bcr type of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA.
Probab=24.08 E-value=91 Score=24.49 Aligned_cols=26 Identities=12% Similarity=0.020 Sum_probs=18.5
Q ss_pred hHHHHHHHHHHcCCceEEeccccccc
Q 046914 63 GLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 63 Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
+.+..+.+.+.+|||++.+++-+.|.
T Consensus 369 ~~~~~~~l~e~~GIP~L~iE~D~~d~ 394 (413)
T TIGR02260 369 QLLMMREIEKRTGKPAAFIETDLVDP 394 (413)
T ss_pred hHHHHHHHHHHcCCCEEEEEcCCCCc
Confidence 44445556667999999998866653
No 171
>TIGR00328 flhB flagellar biosynthetic protein FlhB. FlhB and its functionally equivalent orthologs, from among a larger superfamily of proteins involved in type III protein export systems, are specifically involved in flagellar protein export. The seed members are restricted and the trusted cutoff is set high such that the proteins gathered by this model play roles specifically related to flagellar structures. Full-length homologs scoring below the trusted cutoff are involved in peptide export but not necessarily in the creation of flagella.
Probab=24.07 E-value=2e+02 Score=22.24 Aligned_cols=41 Identities=15% Similarity=0.246 Sum_probs=26.9
Q ss_pred CCCeEEEeeeCCCCCCCccccccCccccCCCCCCc-------hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTLYPSYKNNRPPTP-------DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~yp~YKa~R~~~P-------~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+|+|++||.- |..+..+.| +++. ..|+++-+..|||+++-+
T Consensus 262 NPTH~AVal~----------------Y~~~~~~aP~vvakG~~~~A---~~I~~~A~~~~vPi~~~~ 309 (347)
T TIGR00328 262 NPTHYAVALK----------------YDPGKMPAPVVVAKGVDELA---LKIKEIARENNVPIVENP 309 (347)
T ss_pred CCCceEEEeE----------------eCCCCCCCCEEEEeeCcHHH---HHHHHHHHHcCCCEEeCH
Confidence 7888888865 333333445 2332 247888899999998755
No 172
>TIGR00758 UDG_fam4 uracil-DNA glycosylase, family 4. This well-conserved family of proteins is about 200 residues in length and homologous to the N-terminus of the DNA polymerase of phage SPO1 of Bacillus subtilis. The member from Thermus thermophilus HB8 is known to act as uracil-DNA glycosylase, an enzyme of DNA base excision repair. Its appearance as a domain of phage DNA polymerases could be consistent with uracil-DNA glycosylase activity.
Probab=24.01 E-value=1.4e+02 Score=20.25 Aligned_cols=33 Identities=36% Similarity=0.453 Sum_probs=27.4
Q ss_pred CCCCCCchhHHHhHHHHHHHHHHcCCceEEecc
Q 046914 51 NNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 51 a~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g 83 (90)
.||.|+++|+..-.+++.+.++.+.-.++-.=|
T Consensus 76 ~~r~P~~~Ei~~c~~~l~~eI~~v~P~~Iv~lG 108 (173)
T TIGR00758 76 NNRDPTPEEVEACAPYLVKQIELIRPKVIICLG 108 (173)
T ss_pred CCCCcCHHHHHHHHHHHHHHHHhcCCCEEEEEC
Confidence 389999999999999999999998766665544
No 173
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=23.90 E-value=1.2e+02 Score=19.20 Aligned_cols=38 Identities=13% Similarity=0.291 Sum_probs=26.1
Q ss_pred ccccCccccC-------CCCCCchhH---HHhHHHHHHHHHHcCCceEE
Q 046914 42 RHTLYPSYKN-------NRPPTPDTI---VQGLQYLKASIKAMSIKVIE 80 (90)
Q Consensus 42 R~~~yp~YKa-------~R~~~P~~L---~~Ql~~i~~~l~~lGi~~~~ 80 (90)
|.-+||.|=. +| ..|-++ -+.+..|.++|.+||+++..
T Consensus 6 r~vIyP~Y~d~~~tr~eGR-rv~k~~aV~~P~~~EI~~a~~~lgl~~~~ 53 (95)
T PRK00754 6 RIVIWPAYIDSTRSRSEGR-IISRKLAVKEPRLEEIIEAAEKLGLNPEV 53 (95)
T ss_pred cEEEeeccccCCCChhhcC-ccCHHHhccCCCHHHHHHHHHHcCCCeEE
Confidence 3556666633 34 366666 45678889999999999753
No 174
>cd07383 MPP_Dcr2 Saccharomyces cerevisiae DCR2 phosphatase and related proteins, metallophosphatase domain. DCR2 phosphatase (Dosage-dependent Cell Cycle Regulator 2) functions together with DCR1 (Gid8) in a common pathway to accelerate initiation of DNA replication in Saccharomyces cerevisiae. Genetic analysis suggests that DCR1 functions upstream of DCR2. DCR2 interacts with and dephosphorylates Sic1, an inhibitor of mitotic cyclin/cyclin-dependent kinase complexes, which may serve to trigger the initiation of cell division. DCR2 belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAP
Probab=23.86 E-value=2.4e+02 Score=19.05 Aligned_cols=20 Identities=15% Similarity=0.145 Sum_probs=15.6
Q ss_pred hhhhccCCCCeEEEeeeCCCC
Q 046914 16 NIRHDTYMTDITLDVHDLYGA 36 (90)
Q Consensus 16 ~l~~~~~~p~~i~v~fD~fD~ 36 (90)
++++. .+|+.++++=|+++.
T Consensus 35 ~~~~~-~~~d~vv~~GDl~~~ 54 (199)
T cd07383 35 RVLDA-EKPDLVVLTGDLITG 54 (199)
T ss_pred HHHhh-cCCCEEEECCccccC
Confidence 56667 699999999997654
No 175
>TIGR00055 uppS undecaprenyl diphosphate synthase. Alternate name: undecaprenyl pyrophosphate synthetase. Activity has been demonstrated experimentally for members of this family from Micrococcus luteus, E. coli, Haemophilus influenzae, and Streptococcus pneumoniae.
Probab=23.78 E-value=1.1e+02 Score=22.25 Aligned_cols=48 Identities=8% Similarity=0.119 Sum_probs=30.3
Q ss_pred CeEEEeeeCCCCCCCcc-ccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 25 DITLDVHDLYGACGMNF-RHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 25 ~~i~v~fD~fD~~~~t~-R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
.||+|..| |...| |+.-.|-...||.. ...+..+-+.|..+||+.+++
T Consensus 1 ~HVAiImD----GNrRwAk~~gl~~~~GH~~G-----~~~~~~v~~~c~~~GI~~lT~ 49 (226)
T TIGR00055 1 RHVAIIMD----GNGRWAKKKGKPRAYGHKAG-----VKSLRRILRWCANLGVECLTL 49 (226)
T ss_pred CcEEEEcC----CCHHHHHHCCCChhHhHHHH-----HHHHHHHHHHHHHcCCCEEEE
Confidence 48999999 55555 22223444455432 334556667778899998875
No 176
>PRK14646 hypothetical protein; Provisional
Probab=23.55 E-value=1.3e+02 Score=20.53 Aligned_cols=27 Identities=15% Similarity=0.235 Sum_probs=21.1
Q ss_pred CchhHHHhHH-HHHHHHHHcCCceEEec
Q 046914 56 TPDTIVQGLQ-YLKASIKAMSIKVIEVN 82 (90)
Q Consensus 56 ~P~~L~~Ql~-~i~~~l~~lGi~~~~~~ 82 (90)
||..+..|+. .+..+++.+|+..+.++
T Consensus 1 ~~~~~~~~i~~li~p~~~~~G~eLvdve 28 (155)
T PRK14646 1 MNKENKSKLEILLEKVANEFDLKICSLN 28 (155)
T ss_pred CCchHHHHHHHHHHHHHHHcCCEEEEEE
Confidence 6777777776 67788999999887765
No 177
>PF08443 RimK: RimK-like ATP-grasp domain; InterPro: IPR013651 This ATP-grasp domain is found in the ribosomal S6 modification enzyme RimK []. It has an unusual nucleotide-binding fold referred to as palmate, or ATP-grasp fold. This domain is found in a number of enzymes of known structure as well as in urea amidolyase, tubulin-tyrosine ligase, and three enzymes of purine biosynthesis.; PDB: 1UC8_B 1UC9_A.
Probab=23.53 E-value=1.5e+02 Score=20.09 Aligned_cols=40 Identities=18% Similarity=0.283 Sum_probs=16.5
Q ss_pred ccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEec
Q 046914 40 NFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 40 t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
.||+..-.+-+...-..|+++. ..+.++.+++|+.+..++
T Consensus 113 d~r~n~~~g~~~~~~~l~~e~~---~~a~~~~~~lgl~~~giD 152 (190)
T PF08443_consen 113 DFRTNLSRGGKVEPYDLPEEIK---ELALKAARALGLDFAGID 152 (190)
T ss_dssp ------------EE----HHHH---HHHHHHHHHTT-SEEEEE
T ss_pred cchhhhccCceEEEecCCHHHH---HHHHHHHHHhCCCEEEEE
Confidence 5777765444444445566653 447778899999888776
No 178
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=23.33 E-value=2.7e+02 Score=21.03 Aligned_cols=69 Identities=4% Similarity=0.016 Sum_probs=40.5
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEe-eeCCCCCCCccccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDV-HDLYGACGMNFRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~-fD~fD~~~~t~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|-...- .|.+. +.+.+ ..|+|+.+- +-+ +.+.+-+++ + .+.+.++ .+...+.+.|.+.|...+
T Consensus 158 GlPgqt~~-~~~~~l~~~~~-l~~~~is~y~L~~-~~gT~l~~~-----~--~~~~~~~---~~~~~~~~~l~~~Gy~~y 224 (350)
T PRK08446 158 DTPLDNKK-LLKEELKLAKE-LPINHLSAYSLTI-EENTPFFEK-----N--HKKKDDE---NLAKFFIEQLEELGFKQY 224 (350)
T ss_pred CCCCCCHH-HHHHHHHHHHh-cCCCEEEecccee-cCCChhHHh-----h--hcCCCHH---HHHHHHHHHHHHCCCcEE
Confidence 55666666 66677 66666 588888532 221 012222221 1 1222222 367788999999999999
Q ss_pred Eecc
Q 046914 80 EVNV 83 (90)
Q Consensus 80 ~~~g 83 (90)
++..
T Consensus 225 eis~ 228 (350)
T PRK08446 225 EISN 228 (350)
T ss_pred Eeeh
Confidence 8875
No 179
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.
Probab=23.29 E-value=2.7e+02 Score=21.83 Aligned_cols=75 Identities=12% Similarity=-0.030 Sum_probs=43.3
Q ss_pred CcchHHHHHHHHhh-hhhhccCCCCeEEEeeeCCCCCCCc-cccccCccccCCCCCCchhHHHhHHHHHHHHHHcCCceE
Q 046914 2 GESYGLLWRGFLSY-NIRHDTYMTDITLDVHDLYGACGMN-FRHTLYPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 2 G~pt~ai~~gf~~~-~l~~~~~~p~~i~v~fD~fD~~~~t-~R~~~yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~ 79 (90)
|.|....- .|.++ +.+.. ..|+|+.+ +.. ...+. .+.. ........+.+++....+..+.+.|+..|...+
T Consensus 211 GlPgqt~e-~~~~tl~~~~~-l~~~~is~-y~L--~~~p~~~~~~--~~~~~~~~~~~e~~~~~~~~~~~~L~~~Gy~~~ 283 (455)
T TIGR00538 211 GLPKQTKE-SFAKTLEKVAE-LNPDRLAV-FNY--AHVPWVKPAQ--RKIPEAALPSAEEKLDILQETIAFLTEAGYQFI 283 (455)
T ss_pred eCCCCCHH-HHHHHHHHHHh-cCCCEEEE-ecC--ccccchhHHH--hcccccCCCCHHHHHHHHHHHHHHHHHCCCEEE
Confidence 45555555 66677 76677 58888642 221 01111 0100 001112234567778889999999999999888
Q ss_pred Eecc
Q 046914 80 EVNV 83 (90)
Q Consensus 80 ~~~g 83 (90)
++..
T Consensus 284 ~~~~ 287 (455)
T TIGR00538 284 GMDH 287 (455)
T ss_pred eccc
Confidence 7663
No 180
>PLN00191 enolase
Probab=23.20 E-value=1.3e+02 Score=24.13 Aligned_cols=33 Identities=18% Similarity=0.249 Sum_probs=24.1
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCceEEeccccccc
Q 046914 52 NRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 52 ~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
++..+++++ +..++++++.++|.+++-| ..+|+
T Consensus 292 ~~~~s~~e~---i~~~~~L~~~y~I~~IEDP-l~~~D 324 (457)
T PLN00191 292 SNKKSGDEL---IDLYKEFVSDYPIVSIEDP-FDQDD 324 (457)
T ss_pred ccccCHHHH---HHHHHHHhhcCCcEEEECC-CCccc
Confidence 344466665 7788888999999999888 45544
No 181
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=23.15 E-value=90 Score=19.23 Aligned_cols=26 Identities=19% Similarity=0.442 Sum_probs=21.0
Q ss_pred HhHHHHHHHHHHcCCceEEeccccccc
Q 046914 62 QGLQYLKASIKAMSIKVIEVNVMYEDA 88 (90)
Q Consensus 62 ~Ql~~i~~~l~~lGi~~~~~~g~eeD~ 88 (90)
..|..+++.|+.-|..+..+.. +.|.
T Consensus 8 ~~Ls~v~~~L~~~GyeVv~l~~-~~~~ 33 (80)
T PF03698_consen 8 EGLSNVKEALREKGYEVVDLEN-EQDL 33 (80)
T ss_pred CCchHHHHHHHHCCCEEEecCC-cccc
Confidence 3577899999999999998885 5544
No 182
>COG2069 CdhD CO dehydrogenase/acetyl-CoA synthase delta subunit (corrinoid Fe-S protein) [Energy production and conversion]
Probab=22.43 E-value=86 Score=24.60 Aligned_cols=16 Identities=6% Similarity=0.094 Sum_probs=13.3
Q ss_pred CCCeEEEeeeCCCCCC
Q 046914 23 MTDITLDVHDLYGACG 38 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~ 38 (90)
+|.--+|.|||||.+.
T Consensus 119 qPnppvVtfDVFD~p~ 134 (403)
T COG2069 119 QPNPPVVTFDVFDIPR 134 (403)
T ss_pred CCCCCeeEEEeccCCC
Confidence 6788899999999743
No 183
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=22.30 E-value=1.1e+02 Score=18.07 Aligned_cols=27 Identities=19% Similarity=0.249 Sum_probs=19.1
Q ss_pred hHHHhHHHHHHHHHHcCCce----EEecccc
Q 046914 59 TIVQGLQYLKASIKAMSIKV----IEVNVMY 85 (90)
Q Consensus 59 ~L~~Ql~~i~~~l~~lGi~~----~~~~g~e 85 (90)
.+...+..+++.|+..||.+ +.+.|.|
T Consensus 46 ti~~~i~~l~~~l~~~~l~i~~~~~~l~G~E 76 (87)
T PF05043_consen 46 TIYRDIKKLNKYLKKYGLKISKKGYRLEGDE 76 (87)
T ss_dssp HHHHHHHHHHHHHHCCT-EE-SSEEEEES-H
T ss_pred HHHHHHHHHHHHHHHcCeEEeCCCeEEEeCH
Confidence 46778899999999999987 4444544
No 184
>PF02755 RPEL: RPEL repeat; InterPro: IPR004018 The RPEL repeat is named after four conserved amino acids it contains. The function of the RPEL repeat is unknown however it might be a DNA binding repeat based on the observation that Q9VZY2 from SWISSPROT contains a SAP domain that is also implicated in DNA binding.; PDB: 2YJE_M 2V52_M 2YJF_M 2V51_E.
Probab=22.29 E-value=34 Score=16.71 Aligned_cols=10 Identities=40% Similarity=0.836 Sum_probs=4.7
Q ss_pred CCCCCchhHHH
Q 046914 52 NRPPTPDTIVQ 62 (90)
Q Consensus 52 ~R~~~P~~L~~ 62 (90)
+| |.|++|+.
T Consensus 9 ~R-P~~~eLv~ 18 (26)
T PF02755_consen 9 QR-PTREELVE 18 (26)
T ss_dssp T----HHHHHH
T ss_pred cC-CCHHHHHH
Confidence 44 57777764
No 185
>PF08992 QH-AmDH_gamma: Quinohemoprotein amine dehydrogenase, gamma subunit; InterPro: IPR015084 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the main structural domain of the QHNDH gamma subunit.; GO: 0016638 oxidoreductase activity, acting on the CH-NH2 group of donors, 0055114 oxidation-reduction process; PDB: 1JJU_C 1PBY_C 1JMX_G 1JMZ_G.
Probab=22.17 E-value=14 Score=22.78 Aligned_cols=15 Identities=27% Similarity=0.423 Sum_probs=7.9
Q ss_pred CCceEEeccccccccC
Q 046914 75 SIKVIEVNVMYEDAYG 90 (90)
Q Consensus 75 Gi~~~~~~g~eeD~~~ 90 (90)
|+..+-.| +|+|.||
T Consensus 21 G~a~LCQP-mEaDLYg 35 (78)
T PF08992_consen 21 GVASLCQP-MEADLYG 35 (78)
T ss_dssp SSTTS-SS-CHHCHHH
T ss_pred cHhhccCc-chhhhhc
Confidence 34455555 5666665
No 186
>PF06050 HGD-D: 2-hydroxyglutaryl-CoA dehydratase, D-component ; InterPro: IPR010327 Degradation of glutamate via the hydroxyglutarate pathway involves the syn-elimination of water from 2-hydroxyglutaryl-CoA. This anaerobic process is catalysed by 2-hydroxyglutaryl-CoA dehydratase, an enzyme with two components (A and D) that reversibly associate during reaction cycles. This component contains one non-reducible [4Fe-4S]2+ cluster and a reduced riboflavin 5'-monophosphate [].; PDB: 3O3O_B 3O3N_D 3O3M_D.
Probab=22.14 E-value=77 Score=23.22 Aligned_cols=24 Identities=25% Similarity=0.372 Sum_probs=16.2
Q ss_pred HHHHHHHHHHc-CCceEEecccccc
Q 046914 64 LQYLKASIKAM-SIKVIEVNVMYED 87 (90)
Q Consensus 64 l~~i~~~l~~l-Gi~~~~~~g~eeD 87 (90)
.+.+++.++.. |||++.+++-+.|
T Consensus 305 ~~~l~~~~~~~~gIP~l~le~d~~d 329 (349)
T PF06050_consen 305 QPLLKEALREFLGIPVLFLEGDYVD 329 (349)
T ss_dssp HHHHHHHHHCCHT--EEEEEE-TS-
T ss_pred HHHHHHHHHHhcCCCeEeecccccc
Confidence 56889999999 9999888864443
No 187
>TIGR02263 benz_CoA_red_C benzoyl-CoA reductase, subunit C. This model describes C subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This enzyme acts under anaerobic conditions.
Probab=21.96 E-value=95 Score=23.91 Aligned_cols=18 Identities=28% Similarity=0.250 Sum_probs=15.7
Q ss_pred HHHHHHHHHcCCceEEec
Q 046914 65 QYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 65 ~~i~~~l~~lGi~~~~~~ 82 (90)
+.+++.|+..|||++.++
T Consensus 341 ~~lk~~l~e~GIP~L~id 358 (380)
T TIGR02263 341 PMLAARCKEHGIPQIAFK 358 (380)
T ss_pred HHHHHHHHHCCCCEEEEE
Confidence 568899999999999985
No 188
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=21.92 E-value=1.2e+02 Score=17.91 Aligned_cols=22 Identities=18% Similarity=0.184 Sum_probs=17.8
Q ss_pred HHHHHHHHHHcC-CceEEecccc
Q 046914 64 LQYLKASIKAMS-IKVIEVNVMY 85 (90)
Q Consensus 64 l~~i~~~l~~lG-i~~~~~~g~e 85 (90)
+..|++.++.|| |.++.++..+
T Consensus 8 ~~~iR~~fs~lG~I~vLYvn~~e 30 (62)
T PF15513_consen 8 TAEIRQFFSQLGEIAVLYVNPYE 30 (62)
T ss_pred HHHHHHHHHhcCcEEEEEEcccc
Confidence 456899999999 9999887643
No 189
>PF13297 Telomere_Sde2_2: Telomere stability C-terminal
Probab=21.84 E-value=85 Score=18.49 Aligned_cols=19 Identities=32% Similarity=0.459 Sum_probs=15.9
Q ss_pred HHhHHHHHHHHHHcCCceE
Q 046914 61 VQGLQYLKASIKAMSIKVI 79 (90)
Q Consensus 61 ~~Ql~~i~~~l~~lGi~~~ 79 (90)
.-.++.+|+.|.++|+.|=
T Consensus 14 ~lGldrLK~~L~a~GLKcG 32 (60)
T PF13297_consen 14 ALGLDRLKSALMALGLKCG 32 (60)
T ss_pred HhCHHHHHHHHHHcCCccC
Confidence 4568899999999999873
No 190
>TIGR03044 PS_II_psb27 photosystem II protein Psb27. Members of this family are the Psb27 protein of the cyanobacterial photosynthetic supracomplex, photosystem II. Although most protein components of both cyanobacterial and chloroplast versions of photosystem II are closely related and described together by single model families, this family is strictly bacterial. Some uncharacterized proteins with highly divergent sequences, from Arabidopsis, score between trusted and noise cutoffs for this model but are not at this time assigned as functionally equivalent photosystem II proteins.
Probab=21.83 E-value=74 Score=21.65 Aligned_cols=17 Identities=47% Similarity=0.939 Sum_probs=12.1
Q ss_pred CccccCCCCCCchhHHHhH
Q 046914 46 YPSYKNNRPPTPDTIVQGL 64 (90)
Q Consensus 46 yp~YKa~R~~~P~~L~~Ql 64 (90)
|..| .|| |.|+.++.-|
T Consensus 105 Y~sy-~~r-PlPeklk~Rl 121 (135)
T TIGR03044 105 YKSY-ANR-PLPEKLKERL 121 (135)
T ss_pred hccC-CCC-CCCHHHHHHH
Confidence 7777 587 7998875443
No 191
>COG5135 Uncharacterized conserved protein [Function unknown]
Probab=21.71 E-value=56 Score=24.03 Aligned_cols=31 Identities=26% Similarity=0.504 Sum_probs=25.0
Q ss_pred CCCCch-----hHHHhHHHHHHHHHHcCCceEEecc
Q 046914 53 RPPTPD-----TIVQGLQYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 53 R~~~P~-----~L~~Ql~~i~~~l~~lGi~~~~~~g 83 (90)
|+|.|- +-..||+.++..++.+|+.|+++..
T Consensus 178 ~~P~P~~~~~~e~~~~l~~~~~~~~~F~lv~le~~~ 213 (245)
T COG5135 178 RKPAPGQKLTSETSKQLDKLHAGLENFGLVCLEVDS 213 (245)
T ss_pred ccCCCcccccccChhhHHHHHhhhcceeEEEeecCc
Confidence 556673 4468999999999999999998764
No 192
>PF00691 OmpA: OmpA family; InterPro: IPR006665 This entry represents domain with a beta/alpha/beta/alpha-beta(2) structure found in the C-terminal region of many Gram-negative bacterial outer membrane proteins [], such as porin-like integral membrane proteins (such as ompA) [], small lipid-anchored proteins (such as pal) [], and MotB proton channels []. The N-terminal half is variable although some of the proteins in this group have the OmpA-like transmembrane domain IPR000498 from INTERPRO at the N terminus. OmpA from Escherichia coli is required for pathogenesis, and can interact with host receptor molecules []. MotB (and MotA) serves two functions in E. coli, the MotA(4)-MotB(2) complex attaches to the cell wall via MotB to form the stator of the flagellar motor, and the MotA-MotB complex couples the flow of ions across the cell membrane to movement of the rotor [].; GO: 0009279 cell outer membrane; PDB: 1OAP_A 2W8B_G 2HQS_C 4ERH_A 2ZF8_A 2ZOV_A 2ZVZ_B 2ZVY_A 3TD4_B 3TD5_D ....
Probab=21.67 E-value=1.9e+02 Score=17.01 Aligned_cols=33 Identities=18% Similarity=0.081 Sum_probs=21.8
Q ss_pred CCchhHHHhHHHHHHHHH--HcCCceEEecccccccc
Q 046914 55 PTPDTIVQGLQYLKASIK--AMSIKVIEVNVMYEDAY 89 (90)
Q Consensus 55 ~~P~~L~~Ql~~i~~~l~--~lGi~~~~~~g~eeD~~ 89 (90)
...++-..+|..|.++|. ..-. .+.+.| ++|.-
T Consensus 8 ~l~~~~~~~L~~l~~~l~~~~~~~-~i~I~G-~td~~ 42 (97)
T PF00691_consen 8 ELSPESQEQLDELAKILKYPGNKD-QIEIEG-HTDST 42 (97)
T ss_dssp SBHHHHHHHHHHHHHHHHSTTSTT-EEEEEE-EEESS
T ss_pred eeCHHHHHHHHHHHHHHhCcCCCC-eEEEEE-EEcCc
Confidence 344566677777777787 3334 788887 77754
No 193
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=21.63 E-value=99 Score=21.53 Aligned_cols=22 Identities=9% Similarity=0.350 Sum_probs=18.8
Q ss_pred CchhHHHhHHHHHHHHHHcCCc
Q 046914 56 TPDTIVQGLQYLKASIKAMSIK 77 (90)
Q Consensus 56 ~P~~L~~Ql~~i~~~l~~lGi~ 77 (90)
..+++..|+..+++.+..+|.+
T Consensus 116 ~~eev~~~~~~l~~~~~~lG~~ 137 (171)
T PF13382_consen 116 PAEEVARQLEELEEALRELGCP 137 (171)
T ss_dssp -HHHHHHHHHHHHHHHHTTS-B
T ss_pred CHHHHHHHHHHHHHHHHHcCCC
Confidence 4689999999999999999976
No 194
>COG0020 UppS Undecaprenyl pyrophosphate synthase [Lipid metabolism]
Probab=21.52 E-value=1.7e+02 Score=21.55 Aligned_cols=51 Identities=10% Similarity=0.151 Sum_probs=31.2
Q ss_pred CCCeEEEeeeCCCCCCCcccccc-CccccCCCCCCchhHHHhHHHHHHHHHHcCCceEEec
Q 046914 23 MTDITLDVHDLYGACGMNFRHTL-YPSYKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 23 ~p~~i~v~fD~fD~~~~t~R~~~-yp~YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
.|.|+++..| +...|-++. -+-+..++.. ..-+..+-+.+..+||++++.-
T Consensus 16 ~p~HvaiImD----GN~RwAk~~~~~r~~Gh~~G-----~~~~~~i~~~~~~lgik~ltly 67 (245)
T COG0020 16 LPRHVAIIMD----GNRRWAKKRGLPRIEGHKAG-----AKALREILEWCLELGIKYLTLY 67 (245)
T ss_pred cccceEEEec----CChHHHHhCCCChhHHHHHh-----HHHHHHHHHHHHHcCCCEEEEE
Confidence 6899999999 555553332 3333333322 3335556667777899988753
No 195
>PRK03745 signal recognition particle protein Srp19; Provisional
Probab=21.19 E-value=1.1e+02 Score=19.66 Aligned_cols=27 Identities=30% Similarity=0.518 Sum_probs=19.4
Q ss_pred CchhHH---HhHHHHHHHHHHcCCceEEec
Q 046914 56 TPDTIV---QGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 56 ~P~~L~---~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
.|-++. +-+..|.++|++||++++.++
T Consensus 23 v~k~~aV~~P~~~EI~~a~~~lgl~~~~~E 52 (100)
T PRK03745 23 VPKNLAVERPTLEEIVDAAEALGFKVIEVD 52 (100)
T ss_pred cCHHHcccCCCHHHHHHHHHHcCCCcEeec
Confidence 555553 457778889999999985333
No 196
>PF14772 NYD-SP28: Sperm tail
Probab=20.99 E-value=78 Score=19.74 Aligned_cols=21 Identities=14% Similarity=0.276 Sum_probs=17.5
Q ss_pred CCCCchhHHHhHHHHHHHHHH
Q 046914 53 RPPTPDTIVQGLQYLKASIKA 73 (90)
Q Consensus 53 R~~~P~~L~~Ql~~i~~~l~~ 73 (90)
|...|.+|..+|...+..|+.
T Consensus 49 ~~~~~~eL~~~ie~q~~~~e~ 69 (104)
T PF14772_consen 49 RKKKPQELRKEIEEQKQACER 69 (104)
T ss_pred HHccHHHHHHHHHHHHHHHHH
Confidence 457899999999999888765
No 197
>PF00128 Alpha-amylase: Alpha amylase, catalytic domain; InterPro: IPR006047 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. Enzymes containing this domain, such as alpha-amylase, belong to family 13 (GH13 from CAZY) of the glycosyl hydrolases. The maltogenic alpha-amylase is an enzyme which catalyses hydrolysis of (1-4)-alpha-D-glucosidic linkages in polysaccharides so as to remove successive alpha-maltose residues from the non-reducing ends of the chains in the conversion of starch to maltose. Other enzymes include neopullulanase, which hydrolyses pullulan to panose, and cyclomaltodextrinase, which hydrolyses cyclodextrins. This entry represents the catalytic domain found in several protein members of this family. It has a structure consisting of an 8 stranded alpha/beta barrel that contains the active site, interrupted by a ~70 amino acid calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain []. More information about this protein can be found at Protein of the Month: alpha-Amylase [].; GO: 0003824 catalytic activity, 0043169 cation binding, 0005975 carbohydrate metabolic process; PDB: 3FAX_A 3FAW_A 2DH3_B 2DH2_A 1CIU_A 1A47_A 3BMW_A 3BMV_A 2FH8_A 2FH6_A ....
Probab=20.92 E-value=98 Score=21.56 Aligned_cols=24 Identities=29% Similarity=0.617 Sum_probs=17.5
Q ss_pred hHHHhHHHHHHHHHHcCCceEEeccccc
Q 046914 59 TIVQGLQYLKASIKAMSIKVIEVNVMYE 86 (90)
Q Consensus 59 ~L~~Ql~~i~~~l~~lGi~~~~~~g~ee 86 (90)
.|+++|++|+ .|||..|.+....+
T Consensus 5 gi~~kLdyl~----~lGv~~I~l~Pi~~ 28 (316)
T PF00128_consen 5 GIIDKLDYLK----DLGVNAIWLSPIFE 28 (316)
T ss_dssp HHHHTHHHHH----HHTESEEEESS-EE
T ss_pred HHHHhhHHHH----HcCCCceecccccc
Confidence 5677787666 59999998877655
No 198
>TIGR03350 type_VI_ompA type VI secretion system OmpA/MotB family protein. The flagellar motor protein MotB and the Gram-negative bacterial outer membrane protein OmpA share a region of sequence homology. This model describes a domain found fused to type VI secretion system homologs of the type IV system protein DotU (see model TIGR03349), with OmpA/MotB homology.
Probab=20.71 E-value=2.4e+02 Score=18.15 Aligned_cols=39 Identities=13% Similarity=0.101 Sum_probs=28.2
Q ss_pred ccCCCCCCchhHHHhHHHHHHHHHHcCCceEEecccccccc
Q 046914 49 YKNNRPPTPDTIVQGLQYLKASIKAMSIKVIEVNVMYEDAY 89 (90)
Q Consensus 49 YKa~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~g~eeD~~ 89 (90)
+..+.....++-...|..+-++|.... ..+.+.| +.|..
T Consensus 34 F~~gs~~L~~~~~~~L~~ia~~l~~~~-~~i~I~G-hTD~~ 72 (137)
T TIGR03350 34 FASGSAEVRADFEPLLDRIAKALAAVP-GRITVVG-HTDNV 72 (137)
T ss_pred cCCCccccCHHHHHHHHHHHHHHHhCC-CeEEEEE-ecCCC
Confidence 445555556666777888888888877 5688887 88864
No 199
>PRK12569 hypothetical protein; Provisional
Probab=20.65 E-value=2e+02 Score=21.35 Aligned_cols=25 Identities=16% Similarity=0.305 Sum_probs=20.3
Q ss_pred hhHHHhHHHHHHHHHHcCCceEEec
Q 046914 58 DTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 58 ~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
+.+..|+..++.++.+.|.++-.+.
T Consensus 89 ~~v~yQigaL~~~~~~~g~~l~hVK 113 (245)
T PRK12569 89 NDVLYQLGALREFARAHGVRLQHVK 113 (245)
T ss_pred HHHHHHHHHHHHHHHHcCCeeEEec
Confidence 4558999999999999998865543
No 200
>cd06390 PBP1_iGluR_AMPA_GluR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=20.58 E-value=1.2e+02 Score=23.05 Aligned_cols=26 Identities=15% Similarity=0.091 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHcCCceEEeccccccccC
Q 046914 63 GLQYLKASIKAMSIKVIEVNVMYEDAYG 90 (90)
Q Consensus 63 Ql~~i~~~l~~lGi~~~~~~g~eeD~~~ 90 (90)
|...|.++++.+|+..+..= |+|+||
T Consensus 104 ~~~Ai~diI~~~~W~~v~iI--Yd~d~g 129 (364)
T cd06390 104 LQDALISVIEHYKWQKFVYI--YDADRG 129 (364)
T ss_pred HHHHHHHHHHHcCCcEEEEE--EeCCcc
Confidence 67889999999999998775 677786
No 201
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=20.45 E-value=2.3e+02 Score=19.56 Aligned_cols=44 Identities=20% Similarity=0.202 Sum_probs=32.2
Q ss_pred CccccccCccccCCC-CCCchhHHHhHHHHHHHHHHcCCceEEec
Q 046914 39 MNFRHTLYPSYKNNR-PPTPDTIVQGLQYLKASIKAMSIKVIEVN 82 (90)
Q Consensus 39 ~t~R~~~yp~YKa~R-~~~P~~L~~Ql~~i~~~l~~lGi~~~~~~ 82 (90)
-.|+.-==..+|+.| +.+|=.-...-+.+-+.+..+||..+.+.
T Consensus 52 ~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~~v~V~ 96 (149)
T PTZ00129 52 TLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGINALHIK 96 (149)
T ss_pred EEEEecCcceecccccCCCHHHHHHHHHHHHHHHHHcCCeEEEEE
Confidence 467777678999999 88885554445556666778999887653
No 202
>TIGR03398 plc_access_R phospholipase C accessory protein PlcR. The class of microbial phosphocholine-preferring phospholipase C enzymes described by model TIGR03396 has two members in Pseudomonas aeruginosa, one of which (PlcH) is hemolytic and can hydrolyzes sphingomyelin as well as phosphatidylcholine. This model describes PlcR, an accessory protein for PlcH with which it forms a heterodimer. The member of the family from P. aeruginosa, although not the members from various Burkholderia species, is encoded immediately downstream of phospholipase C.
Probab=20.41 E-value=88 Score=21.29 Aligned_cols=22 Identities=32% Similarity=0.537 Sum_probs=15.2
Q ss_pred cccccCccccCCCCCCchhHHHh
Q 046914 41 FRHTLYPSYKNNRPPTPDTIVQG 63 (90)
Q Consensus 41 ~R~~~yp~YKa~R~~~P~~L~~Q 63 (90)
||.++ .+|-.||..||..=..+
T Consensus 1 fr~ql-~~yg~~r~sm~aaeR~a 22 (141)
T TIGR03398 1 FRDQL-AAYGRNRNSMPAAERAA 22 (141)
T ss_pred ChhHH-HHHhhcccccCHHHHHH
Confidence 34443 78999999999754433
No 203
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=20.41 E-value=1.1e+02 Score=20.18 Aligned_cols=25 Identities=20% Similarity=0.294 Sum_probs=21.9
Q ss_pred CchhHHHhHHHHHHHHHHcCCceEE
Q 046914 56 TPDTIVQGLQYLKASIKAMSIKVIE 80 (90)
Q Consensus 56 ~P~~L~~Ql~~i~~~l~~lGi~~~~ 80 (90)
|-+.|...+..++..|..+||.+..
T Consensus 21 Tg~~L~~av~~l~~~L~~~Giev~l 45 (120)
T PF10865_consen 21 TGETLREAVKELAPVLAPLGIEVRL 45 (120)
T ss_pred HHHHHHHHHHHHHHHHHhCCcEEEE
Confidence 5678999999999999999998653
No 204
>PRK13381 peptidase T; Provisional
Probab=20.36 E-value=1.9e+02 Score=21.82 Aligned_cols=30 Identities=10% Similarity=0.196 Sum_probs=23.3
Q ss_pred CCCCCchhHHHhHHHHHHHHHHcCCceEEe
Q 046914 52 NRPPTPDTIVQGLQYLKASIKAMSIKVIEV 81 (90)
Q Consensus 52 ~R~~~P~~L~~Ql~~i~~~l~~lGi~~~~~ 81 (90)
++-+.|+.-.+...+|++.|+.+|+.....
T Consensus 22 ~~~~~~~~~~~~~~~l~~~l~~~G~~~~~~ 51 (404)
T PRK13381 22 GTLPSTPGQHELAKLLADELRELGLEDIVI 51 (404)
T ss_pred CCCcCChhHHHHHHHHHHHHHHcCCCcEEE
Confidence 555667777788999999999999954433
No 205
>PF13279 4HBT_2: Thioesterase-like superfamily; PDB: 2W3X_E 3CK1_A 2GF6_C 2NUJ_A 2HLJ_A 2XFL_B 2XEM_B 2OIW_B 2HX5_A 2FUJ_A ....
Probab=20.29 E-value=51 Score=20.23 Aligned_cols=12 Identities=33% Similarity=0.673 Sum_probs=7.0
Q ss_pred CCCCchhHHHhH
Q 046914 53 RPPTPDTIVQGL 64 (90)
Q Consensus 53 R~~~P~~L~~Ql 64 (90)
..++|++++++|
T Consensus 110 ~~~~P~~~~~~l 121 (121)
T PF13279_consen 110 SVPIPDELREAL 121 (121)
T ss_dssp E-B--HHHHHHH
T ss_pred cCCCCHHHHhcC
Confidence 467899998875
No 206
>PF03461 TRCF: TRCF domain; InterPro: IPR005118 This domain is found in proteins necessary for strand-specific repair in DNA such as TRCF in Escherichia coli. A lesion in the template strand blocks the RNA polymerase complex (RNAP). The RNAP-DNA-RNA complex is specifically recognised by the transcription-repair-coupling factor (TRCF) which releases RNAP and the truncated transcript.; GO: 0003684 damaged DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0006281 DNA repair; PDB: 2QSR_A 2EYQ_A.
Probab=20.17 E-value=1.8e+02 Score=18.07 Aligned_cols=29 Identities=24% Similarity=0.408 Sum_probs=20.4
Q ss_pred CCchhH--HHhHHHHHHHHHHcCCceEEecc
Q 046914 55 PTPDTI--VQGLQYLKASIKAMSIKVIEVNV 83 (90)
Q Consensus 55 ~~P~~L--~~Ql~~i~~~l~~lGi~~~~~~g 83 (90)
++|++. .--+-.|+-++..+||..+...+
T Consensus 48 ~~P~ev~~L~~~~~lk~~a~~~gi~~i~~~~ 78 (101)
T PF03461_consen 48 PLPEEVENLLELARLKILARKLGIESIKQKG 78 (101)
T ss_dssp S--HHHHHHHHHHHHHHHHHHCTECEEEEET
T ss_pred CCcHHHHHHHHHHHHHHHHHHCCCcEEEecC
Confidence 456655 44556788999999999888765
Done!