Query psy11827
Match_columns 336
No_of_seqs 248 out of 1733
Neff 6.5
Searched_HMMs 46136
Date Fri Aug 16 20:00:00 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11827.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11827hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2518|consensus 100.0 6.2E-77 1.4E-81 585.6 22.3 284 1-294 60-343 (556)
2 PTZ00217 flap endonuclease-1; 100.0 8.5E-52 1.9E-56 408.0 25.4 225 1-239 70-298 (393)
3 cd00128 XPG Xeroderma pigmento 100.0 1E-50 2.2E-55 390.9 22.5 245 1-252 60-308 (316)
4 PRK03980 flap endonuclease-1; 100.0 2.6E-50 5.7E-55 383.6 21.6 242 2-270 16-270 (292)
5 TIGR03674 fen_arch flap struct 100.0 3.8E-46 8.2E-51 362.1 21.9 212 2-233 63-287 (338)
6 KOG2519|consensus 100.0 6.9E-39 1.5E-43 313.2 13.1 230 2-244 65-299 (449)
7 TIGR00600 rad2 DNA excision re 100.0 2.1E-32 4.6E-37 292.7 14.5 166 60-233 763-948 (1034)
8 PF00867 XPG_I: XPG I-region; 99.9 4.6E-27 9.9E-32 188.6 3.6 84 79-167 1-94 (94)
9 COG0258 Exo 5'-3' exonuclease 99.9 1E-25 2.3E-30 216.8 13.6 190 12-233 61-255 (310)
10 smart00475 53EXOc 5'-3' exonuc 99.9 6.3E-25 1.4E-29 206.3 14.6 124 72-202 87-219 (259)
11 cd00008 53EXOc 5'-3' exonuclea 99.9 2.2E-24 4.8E-29 200.7 15.7 158 12-201 51-215 (240)
12 KOG2520|consensus 99.9 3.6E-24 7.8E-29 223.4 8.8 121 63-188 460-581 (815)
13 PRK14976 5'-3' exonuclease; Pr 99.9 8.5E-23 1.8E-27 194.0 16.0 166 7-202 50-224 (281)
14 PRK05755 DNA polymerase I; Pro 99.8 8.9E-21 1.9E-25 204.9 15.0 124 71-202 88-220 (880)
15 TIGR00593 pola DNA polymerase 99.8 4.7E-20 1E-24 198.3 16.8 125 71-202 86-218 (887)
16 smart00484 XPGI Xeroderma pigm 99.8 5.6E-20 1.2E-24 140.8 5.6 63 80-142 2-68 (73)
17 PRK09482 flap endonuclease-lik 99.8 4.2E-18 9.1E-23 159.5 17.7 120 72-201 87-214 (256)
18 cd00080 HhH2_motif Helix-hairp 99.4 1.1E-12 2.4E-17 101.1 6.7 51 149-201 2-54 (75)
19 PHA00439 exonuclease 99.3 7E-11 1.5E-15 112.1 12.9 100 71-186 99-206 (286)
20 smart00279 HhH2 Helix-hairpin- 99.0 7.6E-10 1.6E-14 73.4 3.9 33 154-187 1-36 (36)
21 PF00752 XPG_N: XPG N-terminal 98.9 6.9E-10 1.5E-14 89.7 4.1 40 1-40 62-101 (101)
22 smart00485 XPGN Xeroderma pigm 98.9 1.6E-09 3.6E-14 87.3 4.1 39 1-39 60-98 (99)
23 TIGR00600 rad2 DNA excision re 98.7 1.3E-08 2.8E-13 110.7 5.0 89 1-90 59-151 (1034)
24 PF12813 XPG_I_2: XPG domain c 98.5 1.3E-07 2.8E-12 88.7 6.6 51 69-120 4-57 (246)
25 PHA02567 rnh RnaseH; Provision 98.5 6.5E-07 1.4E-11 85.7 11.1 90 72-174 110-207 (304)
26 PF01367 5_3_exonuc: 5'-3' exo 98.4 3.4E-09 7.4E-14 86.2 -6.0 48 152-201 1-50 (101)
27 COG5366 Protein involved in pr 98.1 8.2E-07 1.8E-11 88.1 0.1 109 74-185 134-243 (531)
28 PF02739 5_3_exonuc_N: 5'-3' e 97.9 3.3E-05 7.1E-10 68.5 6.9 50 72-121 89-143 (169)
29 PHA03065 Hypothetical protein; 97.5 0.001 2.3E-08 66.0 11.2 184 2-199 57-274 (438)
30 PF04599 Pox_G5: Poxvirus G5 p 97.4 0.0026 5.5E-08 63.5 12.7 187 2-199 55-272 (425)
31 PF03159 XRN_N: XRN 5'-3' exon 96.9 0.0034 7.4E-08 58.7 7.4 106 14-120 80-223 (237)
32 PF12247 MKT1_N: Temperature d 96.2 0.0027 5.8E-08 50.6 2.1 33 251-285 1-33 (90)
33 KOG2045|consensus 95.9 0.1 2.2E-06 56.6 12.4 183 16-204 83-323 (1493)
34 COG5049 XRN1 5'-3' exonuclease 95.8 0.048 1E-06 57.5 9.4 105 15-120 80-227 (953)
35 KOG2044|consensus 94.7 0.26 5.6E-06 52.8 10.7 106 14-120 98-241 (931)
36 PF00633 HHH: Helix-hairpin-he 86.3 0.63 1.4E-05 29.4 2.1 15 171-185 15-29 (30)
37 PF12826 HHH_2: Helix-hairpin- 86.2 0.69 1.5E-05 34.2 2.7 26 171-198 7-32 (64)
38 PRK00116 ruvA Holliday junctio 79.8 1.5 3.2E-05 39.7 2.6 19 171-189 77-95 (192)
39 smart00278 HhH1 Helix-hairpin- 77.9 1.8 4E-05 26.0 1.9 18 169-186 3-20 (26)
40 PF02371 Transposase_20: Trans 72.5 3.2 7E-05 32.3 2.5 24 166-189 1-24 (87)
41 PF10391 DNA_pol_lambd_f: Fing 72.1 4.6 9.9E-05 28.8 3.0 24 171-195 6-29 (52)
42 TIGR00084 ruvA Holliday juncti 71.9 2.7 5.8E-05 38.0 2.1 43 149-200 59-102 (191)
43 PRK14601 ruvA Holliday junctio 71.4 3 6.5E-05 37.5 2.4 36 151-187 92-128 (183)
44 PRK14605 ruvA Holliday junctio 70.4 3.3 7.1E-05 37.5 2.4 35 149-189 60-95 (194)
45 PRK13844 recombination protein 70.2 6.9 0.00015 35.8 4.4 49 170-239 18-66 (200)
46 PRK13901 ruvA Holliday junctio 69.5 3.5 7.6E-05 37.5 2.4 37 151-188 91-128 (196)
47 PRK14604 ruvA Holliday junctio 67.7 4 8.8E-05 37.0 2.4 37 151-188 92-129 (195)
48 TIGR00615 recR recombination p 67.4 8.8 0.00019 34.9 4.5 47 170-237 14-60 (195)
49 PRK14606 ruvA Holliday junctio 67.0 4.3 9.3E-05 36.6 2.4 36 151-187 92-128 (188)
50 PRK00076 recR recombination pr 65.9 9.8 0.00021 34.7 4.5 48 170-238 14-61 (196)
51 PRK14603 ruvA Holliday junctio 65.3 4.8 0.0001 36.6 2.4 37 151-188 91-128 (197)
52 PF01927 Mut7-C: Mut7-C RNAse 64.8 6.8 0.00015 33.7 3.2 47 69-116 7-53 (147)
53 PRK14600 ruvA Holliday junctio 64.3 6.3 0.00014 35.5 2.9 36 151-188 92-128 (186)
54 PF14520 HHH_5: Helix-hairpin- 63.0 8.1 0.00017 27.8 2.8 25 171-197 9-34 (60)
55 PRK14602 ruvA Holliday junctio 62.6 5.6 0.00012 36.3 2.3 42 149-199 61-103 (203)
56 PRK14600 ruvA Holliday junctio 62.2 4.7 0.0001 36.4 1.7 42 149-199 60-102 (186)
57 COG0632 RuvA Holliday junction 61.9 8.5 0.00019 35.2 3.4 38 151-188 92-129 (201)
58 PRK14603 ruvA Holliday junctio 61.3 5.1 0.00011 36.4 1.8 26 171-199 76-101 (197)
59 PRK14602 ruvA Holliday junctio 61.3 6.3 0.00014 36.0 2.4 37 151-188 93-130 (203)
60 PRK14669 uvrC excinuclease ABC 61.1 6.5 0.00014 41.9 2.8 27 170-198 555-581 (624)
61 PF07719 TPR_2: Tetratricopept 60.9 6.4 0.00014 24.0 1.7 27 42-68 6-32 (34)
62 PRK14606 ruvA Holliday junctio 59.7 5.7 0.00012 35.9 1.8 34 149-188 60-94 (188)
63 PRK13901 ruvA Holliday junctio 59.2 6.1 0.00013 36.0 1.9 34 149-188 59-93 (196)
64 cd08556 GDPD Glycerophosphodie 58.6 15 0.00034 31.6 4.4 40 71-111 149-188 (189)
65 PRK14601 ruvA Holliday junctio 58.1 6.4 0.00014 35.4 1.8 34 149-188 60-94 (183)
66 PF05991 NYN_YacP: YacP-like N 57.4 20 0.00043 31.5 4.8 35 81-115 66-106 (166)
67 PRK14604 ruvA Holliday junctio 57.3 6.5 0.00014 35.7 1.7 42 149-199 60-102 (195)
68 COG1569 Predicted nucleic acid 56.2 21 0.00046 30.8 4.6 47 73-119 65-119 (142)
69 TIGR00084 ruvA Holliday juncti 56.1 9.9 0.00021 34.3 2.7 37 151-187 91-127 (191)
70 PRK14667 uvrC excinuclease ABC 54.9 10 0.00023 39.9 3.1 28 169-198 516-543 (567)
71 TIGR00194 uvrC excinuclease AB 54.9 9.7 0.00021 40.2 2.8 25 170-196 544-568 (574)
72 PF11798 IMS_HHH: IMS family H 53.7 9.8 0.00021 24.2 1.7 14 171-184 15-28 (32)
73 PRK14670 uvrC excinuclease ABC 53.0 12 0.00026 39.6 3.1 30 168-199 515-544 (574)
74 PF00515 TPR_1: Tetratricopept 52.6 9.9 0.00021 23.4 1.6 27 42-68 6-32 (34)
75 TIGR00305 probable toxin-antit 51.6 9.2 0.0002 30.9 1.7 29 89-117 85-113 (114)
76 PRK02515 psbU photosystem II c 49.8 18 0.00039 30.9 3.1 26 171-196 65-90 (132)
77 PRK14671 uvrC excinuclease ABC 47.7 17 0.00036 38.9 3.2 24 170-195 572-595 (621)
78 PRK14605 ruvA Holliday junctio 47.6 12 0.00026 33.9 1.9 37 151-188 92-129 (194)
79 COG5366 Protein involved in pr 47.0 15 0.00031 37.7 2.5 56 72-128 34-92 (531)
80 PRK14672 uvrC excinuclease ABC 46.9 27 0.00058 37.7 4.6 29 169-199 610-638 (691)
81 cd00141 NT_POLXc Nucleotidyltr 46.8 22 0.00048 34.4 3.7 27 171-198 89-115 (307)
82 PF13432 TPR_16: Tetratricopep 46.6 36 0.00079 23.9 4.0 41 42-82 2-45 (65)
83 COG0353 RecR Recombinational D 45.9 19 0.00041 32.8 2.8 17 169-185 14-30 (198)
84 cd01422 MGS Methylglyoxal synt 45.6 33 0.00072 28.2 4.1 34 76-109 38-75 (115)
85 TIGR00114 lumazine-synth 6,7-d 45.3 43 0.00094 28.7 4.8 45 65-109 13-64 (138)
86 PF00885 DMRL_synthase: 6,7-di 45.2 47 0.001 28.6 5.1 45 65-109 16-67 (144)
87 PRK12419 riboflavin synthase s 45.2 39 0.00084 29.8 4.6 45 65-109 23-74 (158)
88 PRK14668 uvrC excinuclease ABC 45.2 17 0.00036 38.5 2.8 30 168-199 526-555 (577)
89 smart00483 POLXc DNA polymeras 44.9 21 0.00045 35.1 3.2 28 170-198 92-119 (334)
90 TIGR00596 rad1 DNA repair prot 43.7 13 0.00028 40.9 1.8 29 167-197 757-785 (814)
91 PRK00558 uvrC excinuclease ABC 43.4 18 0.00039 38.4 2.7 26 170-197 546-571 (598)
92 PRK12766 50S ribosomal protein 43.2 21 0.00046 33.3 2.8 28 169-198 5-33 (232)
93 PRK09454 ugpQ cytoplasmic glyc 42.7 31 0.00067 31.9 3.9 44 72-116 199-242 (249)
94 PF13414 TPR_11: TPR repeat; P 42.3 45 0.00097 23.6 4.0 28 41-68 7-34 (69)
95 cd08568 GDPD_TmGDE_like Glycer 42.3 35 0.00075 31.0 4.1 42 72-115 184-225 (226)
96 PF03009 GDPD: Glycerophosphor 41.1 30 0.00065 30.9 3.5 41 73-114 213-255 (256)
97 KOG0547|consensus 40.8 23 0.0005 36.7 2.9 43 27-69 105-147 (606)
98 PRK14666 uvrC excinuclease ABC 40.3 22 0.00047 38.4 2.7 28 170-199 640-667 (694)
99 COG0632 RuvA Holliday junction 39.5 17 0.00038 33.2 1.6 42 149-199 60-102 (201)
100 cd00532 MGS-like MGS-like doma 39.1 37 0.00081 27.5 3.4 35 76-110 36-74 (112)
101 PF13181 TPR_8: Tetratricopept 39.0 25 0.00053 21.4 1.8 27 42-68 6-32 (34)
102 COG1948 MUS81 ERCC4-type nucle 38.4 28 0.00061 33.0 2.9 26 171-198 186-211 (254)
103 PF13428 TPR_14: Tetratricopep 38.3 31 0.00067 22.8 2.4 28 42-69 6-33 (44)
104 cd08575 GDPD_GDE4_like Glycero 37.7 42 0.0009 31.5 4.0 43 72-115 221-263 (264)
105 cd08567 GDPD_SpGDE_like Glycer 37.4 54 0.0012 30.2 4.6 42 72-114 221-262 (263)
106 PF01850 PIN: PIN domain; Int 37.3 30 0.00065 27.1 2.6 47 64-116 70-116 (121)
107 PF02677 DUF208: Uncharacteriz 34.8 1.4E+02 0.003 26.8 6.5 56 3-96 14-69 (176)
108 cd08561 GDPD_cytoplasmic_ScUgp 34.5 33 0.00072 31.6 2.7 44 72-116 202-245 (249)
109 PLN02404 6,7-dimethyl-8-ribity 33.9 81 0.0018 27.2 4.8 45 65-109 20-71 (141)
110 cd08562 GDPD_EcUgpQ_like Glyce 33.6 63 0.0014 29.0 4.3 40 72-112 189-228 (229)
111 cd08582 GDPD_like_2 Glyceropho 33.2 68 0.0015 29.1 4.5 41 72-113 191-231 (233)
112 smart00028 TPR Tetratricopepti 33.1 35 0.00075 18.7 1.8 25 43-67 7-31 (34)
113 PRK05234 mgsA methylglyoxal sy 32.7 52 0.0011 28.2 3.4 34 76-109 43-80 (142)
114 PF11731 Cdd1: Pathogenicity l 32.5 30 0.00064 27.8 1.7 17 170-186 15-31 (93)
115 TIGR01448 recD_rel helicase, p 32.5 37 0.0008 36.9 3.0 33 152-190 75-107 (720)
116 TIGR01259 comE comEA protein. 32.4 28 0.00062 28.9 1.7 17 171-187 72-88 (120)
117 TIGR00288 conserved hypothetic 31.9 48 0.001 29.2 3.1 46 73-118 70-121 (160)
118 PRK08609 hypothetical protein; 31.8 57 0.0012 34.4 4.2 27 171-197 92-118 (570)
119 cd08601 GDPD_SaGlpQ_like Glyce 31.8 39 0.00085 31.2 2.7 44 72-116 208-251 (256)
120 cd01424 MGS_CPS_II Methylglyox 31.6 81 0.0017 25.2 4.2 35 76-110 37-73 (110)
121 PRK00061 ribH 6,7-dimethyl-8-r 30.8 89 0.0019 27.3 4.6 46 65-110 25-77 (154)
122 cd06167 LabA_like LabA_like pr 30.3 89 0.0019 26.0 4.5 49 70-118 53-115 (149)
123 cd08555 PI-PLCc_GDPD_SF Cataly 29.5 80 0.0017 27.6 4.2 39 72-111 139-178 (179)
124 KOG0967|consensus 29.5 40 0.00086 36.0 2.5 97 14-120 460-568 (714)
125 cd08564 GDPD_GsGDE_like Glycer 28.6 53 0.0012 30.6 3.0 45 71-116 212-260 (265)
126 cd08563 GDPD_TtGDE_like Glycer 28.5 86 0.0019 28.4 4.4 39 72-111 190-228 (230)
127 PF12482 DUF3701: Phage integr 28.4 55 0.0012 26.4 2.6 35 153-187 36-70 (96)
128 PF09868 DUF2095: Uncharacteri 28.4 49 0.0011 27.8 2.3 32 57-88 84-115 (128)
129 KOG4234|consensus 28.2 74 0.0016 29.7 3.7 48 34-81 92-139 (271)
130 PF07219 HemY_N: HemY protein 27.6 78 0.0017 25.5 3.5 34 31-64 53-86 (108)
131 PTZ00134 40S ribosomal protein 27.1 74 0.0016 27.9 3.4 34 155-188 9-51 (154)
132 PRK04053 rps13p 30S ribosomal 26.0 94 0.002 27.1 3.9 35 154-188 3-46 (149)
133 PF13374 TPR_10: Tetratricopep 26.0 46 0.001 20.8 1.5 25 43-67 8-32 (42)
134 COG0529 CysC Adenylylsulfate k 25.8 1.4E+02 0.003 27.2 4.9 26 73-98 86-114 (197)
135 COG1555 ComEA DNA uptake prote 25.8 45 0.00099 28.9 1.9 16 171-186 101-116 (149)
136 smart00851 MGS MGS-like domain 25.6 84 0.0018 24.1 3.2 35 76-110 24-61 (90)
137 cd08579 GDPD_memb_like Glycero 25.6 1.1E+02 0.0023 27.6 4.4 39 72-111 180-218 (220)
138 TIGR02766 crypt_chrom_pln cryp 25.3 2.3E+02 0.0051 28.8 7.3 35 70-104 75-117 (475)
139 PF06792 UPF0261: Uncharacteri 25.3 1.5E+02 0.0033 30.0 5.7 45 65-109 194-240 (403)
140 TIGR03252 uncharacterized HhH- 25.3 37 0.0008 30.4 1.2 16 170-185 118-133 (177)
141 cd00316 Oxidoreductase_nitroge 25.1 2.7E+02 0.0058 27.2 7.5 17 5-21 173-189 (399)
142 PF03683 UPF0175: Uncharacteri 24.7 2E+02 0.0043 21.8 5.1 45 41-92 23-69 (76)
143 PF13174 TPR_6: Tetratricopept 24.7 76 0.0016 18.7 2.3 24 41-64 4-27 (33)
144 PRK00124 hypothetical protein; 24.4 1.1E+02 0.0024 26.7 4.0 85 89-185 54-138 (151)
145 cd08580 GDPD_Rv2277c_like Glyc 24.3 99 0.0021 29.2 4.0 43 72-115 219-262 (263)
146 cd08609 GDPD_GDE3 Glycerophosp 24.3 69 0.0015 31.2 3.0 43 72-115 235-277 (315)
147 PRK10674 deoxyribodipyrimidine 24.2 3E+02 0.0064 28.2 7.8 18 71-88 85-102 (472)
148 PF14635 HHH_7: Helix-hairpin- 23.6 59 0.0013 26.6 2.0 33 155-187 26-70 (104)
149 PRK00116 ruvA Holliday junctio 23.3 59 0.0013 29.2 2.2 21 168-188 109-129 (192)
150 PF14559 TPR_19: Tetratricopep 23.3 90 0.0019 21.8 2.8 29 41-69 29-57 (68)
151 COG0322 UvrC Nuclease subunit 23.2 69 0.0015 34.0 3.0 27 170-198 533-559 (581)
152 PF13176 TPR_7: Tetratricopept 23.1 68 0.0015 20.2 1.9 24 44-67 6-29 (36)
153 KOG4648|consensus 22.9 90 0.002 31.3 3.5 28 41-68 101-128 (536)
154 cd08612 GDPD_GDE4 Glycerophosp 22.9 70 0.0015 30.6 2.8 44 72-116 251-294 (300)
155 PRK13766 Hef nuclease; Provisi 22.7 78 0.0017 34.3 3.4 27 169-197 717-743 (773)
156 PF08588 DUF1769: Protein of u 22.4 68 0.0015 23.3 1.9 31 162-192 4-37 (56)
157 PF10087 DUF2325: Uncharacteri 22.2 1.7E+02 0.0037 22.9 4.4 25 65-89 58-82 (97)
158 cd08574 GDPD_GDE_2_3_6 Glycero 22.0 1.3E+02 0.0028 28.0 4.3 38 73-111 214-251 (252)
159 PF01399 PCI: PCI domain; Int 22.0 3.6E+02 0.0077 20.4 6.5 30 90-119 75-104 (105)
160 COG1059 Thermostable 8-oxoguan 21.9 2.6E+02 0.0057 25.6 5.9 22 171-192 125-146 (210)
161 TIGR00575 dnlj DNA ligase, NAD 21.8 85 0.0018 33.8 3.3 24 171-196 502-525 (652)
162 PRK01229 N-glycosylase/DNA lya 21.7 62 0.0013 29.7 2.0 15 171-185 123-137 (208)
163 PRK14351 ligA NAD-dependent DN 21.6 87 0.0019 34.0 3.4 24 171-196 532-555 (689)
164 PRK13600 putative ribosomal pr 21.6 1E+02 0.0022 24.2 3.0 27 64-90 37-63 (84)
165 COG0054 RibH Riboflavin syntha 21.3 1.9E+02 0.0042 25.3 4.8 46 65-110 25-77 (152)
166 KOG4175|consensus 21.3 2.2E+02 0.0048 26.4 5.4 38 64-101 130-169 (268)
167 PF03979 Sigma70_r1_1: Sigma-7 21.2 1.7E+02 0.0038 22.3 4.2 34 54-88 25-58 (82)
168 COG0177 Nth Predicted EndoIII- 21.2 46 0.00099 30.7 1.0 18 171-188 113-131 (211)
169 PF14716 HHH_8: Helix-hairpin- 21.1 74 0.0016 23.4 2.0 15 170-184 50-64 (68)
170 cd08606 GDPD_YPL110cp_fungi Gl 20.9 86 0.0019 29.5 2.9 44 72-116 235-280 (286)
171 PF05687 DUF822: Plant protein 20.7 4.6E+02 0.0099 22.9 6.9 16 23-38 7-22 (150)
172 TIGR00426 competence protein C 20.7 82 0.0018 23.1 2.2 15 172-186 22-36 (69)
173 PRK02399 hypothetical protein; 20.5 2.1E+02 0.0045 29.1 5.6 45 65-109 195-241 (406)
174 PF07721 TPR_4: Tetratricopept 20.4 1.3E+02 0.0027 17.6 2.6 20 42-61 6-25 (26)
175 PRK14812 hypothetical protein; 20.1 66 0.0014 27.0 1.7 35 76-110 11-45 (119)
No 1
>KOG2518|consensus
Probab=100.00 E-value=6.2e-77 Score=585.57 Aligned_cols=284 Identities=41% Similarity=0.683 Sum_probs=267.5
Q ss_pred ChHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHH
Q psy11827 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRA 80 (336)
Q Consensus 1 mk~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~ 80 (336)
||+|++|+++||+||+||||.++|+|++|+.+||++|+++++.|.+++++|+..+|+++|++|++|||+|++.+|++||.
T Consensus 60 ik~v~lL~~~gikPilVFDG~~LP~K~~te~~Rr~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~ 139 (556)
T KOG2518|consen 60 IKRVKLLLSYGIKPILVFDGDPLPSKKETERKRRERRKKNLDAAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRS 139 (556)
T ss_pred HHHHHHHHhcCCeEEEEecCCCcccccccchHHHHHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCCCCeeeeccccccccccCCcCCCCHHHHHHH
Q psy11827 81 RGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYM 160 (336)
Q Consensus 81 ~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~g~~~~i~~~~l~~~~~~~~~~lt~~qf~~~ 160 (336)
+||+|||||||||||||||++.|+|||||||||||++|||++||||||..|++.+++...+.....+ ..+|+.++|+.|
T Consensus 140 ~nVe~IVAPyEADAQlayL~~~~~i~~IITEDSDLl~fGc~~vifK~d~~G~~le~~~~~l~~~~~l-~~~~~~ekfr~m 218 (556)
T KOG2518|consen 140 QNVEYIVAPYEADAQLAYLEREGIVDAIITEDSDLLVFGCKKVIFKMDSFGNGLEINRSKLPECKPL-GDKFTEEKFRRM 218 (556)
T ss_pred cCCceEecCccccchhHHHHhcCcceEEEeccccccccCchhheeeccCCCCcccccHhhhhhcccc-ccccCHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999998888876554 367999999999
Q ss_pred HHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcccCcccccchhHHHHHHhHhhhhccCceecCCCCcee
Q psy11827 161 CILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPVYDPVSKEVV 240 (336)
Q Consensus 161 ~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k~~~~~~~~~~y~~~f~~A~~~F~~~~V~dP~~~~~~ 240 (336)
|||+||||++||||||++||+++|++|.+ .+.++..+.. + +++.+|++|++.|.+|..||+||+||||..++++
T Consensus 219 ciLSGCDYl~slpGvGl~tA~k~l~k~~~--~d~vi~~~~~--~--~~l~Vpd~y~~~F~~A~~tF~hQrVydP~~k~~~ 292 (556)
T KOG2518|consen 219 CILSGCDYLSSLPGVGLATAHKLLSKYNT--PDRVIISHLL--K--KKLTVPDDYIENFERANLTFLHQRVYDPIEKKLI 292 (556)
T ss_pred HHhcCCcccccCccccHHHHHHHHHhcCc--HHHHHHHHHh--c--cCCcCCHHHHHHHHHHHHhhhhhheeCchHhhhh
Confidence 99999999999999999999999999974 5666633322 2 4578999999999999999999999999999999
Q ss_pred ECCCCCCCCCccchhhhcccCCCCCHHHHHHHHcCCCCcccccccccCCCCCCC
Q psy11827 241 PLNPLESEMRDEVFSQLSLKELELPKDQAFQLALGNLDPFSLEEMDQWNPDSEE 294 (336)
Q Consensus 241 ~L~~~~~~~~~~~~~~~~~G~~~l~~~~~~~ia~G~~~p~t~~~~~~~~p~~~~ 294 (336)
||+|++..++++++.+ +|.. .+++.+..+|.|+.+|.|++.+++|.|.+.+
T Consensus 293 ~L~~~~~~l~~~~~~~--~g~~-~~~~~av~~a~g~~~~~t~~~~~~~~~~~~~ 343 (556)
T KOG2518|consen 293 HLNPIEDELDNEDLEF--LGPL-KDPSVAVEIALGNKDPITFKRIDDHKPHTAP 343 (556)
T ss_pred cCCchhhhcchhhHhh--cccc-cCcchhhhhhhccCCccchhhhhhcccccCC
Confidence 9999999998899999 9998 9999999999999999999999999999655
No 2
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=8.5e-52 Score=408.01 Aligned_cols=225 Identities=26% Similarity=0.367 Sum_probs=204.9
Q ss_pred ChHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHH
Q psy11827 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRA 80 (336)
Q Consensus 1 mk~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~ 80 (336)
|+++.+|+++||+|||||||.+++.|..+..+|+++|+++.+...++.+.|+.++|+++++++++||++|+..++++|+.
T Consensus 70 ~~r~~~Ll~~gikPv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~ 149 (393)
T PTZ00217 70 FNRTIRLLEAGIKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRL 149 (393)
T ss_pred HHHHHHHHHCCCCEEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHH
Confidence 46788899999999999999999999999999999999999988899999999999999999999999999999999999
Q ss_pred cCCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCCCC---e-eeeccccccccccCCcCCCCHHH
Q psy11827 81 RGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGN---C-CFMDREKLPSALKMPLAKFTDAK 156 (336)
Q Consensus 81 ~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~g~---~-~~i~~~~l~~~~~~~~~~lt~~q 156 (336)
+||+||+||||||||||||++.|+||+|+|+|+|+|+||+++||++++..++ . .+++.+.+.+ .++++++|
T Consensus 150 ~Gip~i~AP~EAdaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~-----~~gl~~~q 224 (393)
T PTZ00217 150 MGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLE-----ELGLSMDQ 224 (393)
T ss_pred cCCceEECCcCHHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHH-----HhCCCHHH
Confidence 9999999999999999999999999999999999999999999999986432 2 3566666654 78999999
Q ss_pred HHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcccCcccccchhHHHHHHhHhhhhccCceecCCC
Q psy11827 157 FRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPVYDPVS 236 (336)
Q Consensus 157 f~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k~~~~~~~~~~y~~~f~~A~~~F~~~~V~dP~~ 236 (336)
|+|+|+|+||||+|||||||+|||++||++|+ +++++++++... +..+|++|. |.+|+.+|+|+.|+||.+
T Consensus 225 ~id~~iL~G~Dy~pgi~GIG~ktA~~Li~~~g--sle~il~~~~~~-----k~~~p~~~~--~~~~~~~f~~p~V~~~~~ 295 (393)
T PTZ00217 225 FIDLCILCGCDYCDTIKGIGPKTAYKLIKKYK--SIEEILEHLDKT-----KYPVPENFD--YKEARELFLNPEVTPAEE 295 (393)
T ss_pred HHHHHHHhCCCCCCCCCCccHHHHHHHHHHcC--CHHHHHHHHHhc-----CCCCCCCCC--hHHHHHHhcCCCcCCCCC
Confidence 99999999999999999999999999999997 799999988752 256899997 999999999999999865
Q ss_pred Cce
Q psy11827 237 KEV 239 (336)
Q Consensus 237 ~~~ 239 (336)
-++
T Consensus 296 ~~l 298 (393)
T PTZ00217 296 IDL 298 (393)
T ss_pred CCC
Confidence 443
No 3
>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=100.00 E-value=1e-50 Score=390.92 Aligned_cols=245 Identities=32% Similarity=0.379 Sum_probs=216.1
Q ss_pred ChHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHH
Q psy11827 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRA 80 (336)
Q Consensus 1 mk~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~ 80 (336)
++++.+|+++||+|||||||.+++.|.++..+|+++|.++.+++..+.++|+.+++.++++++..++++++..++++|+.
T Consensus 60 ~~rl~~L~~~~i~pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~ 139 (316)
T cd00128 60 FYRTCRLLELGIKPVFVFDGKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRL 139 (316)
T ss_pred HHHHHHHHHCCCEEEEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHH
Confidence 46888999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCCC--CeeeeccccccccccCCcCCCCHHHHH
Q psy11827 81 RGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSG--NCCFMDREKLPSALKMPLAKFTDAKFR 158 (336)
Q Consensus 81 ~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~g--~~~~i~~~~l~~~~~~~~~~lt~~qf~ 158 (336)
+||+|++||||||||||||+++|.||+|+|+|||+|+||+++|+++++..+ ....++.+.+.+ .++++++||+
T Consensus 140 ~gi~~i~ap~EAdaq~a~l~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~-----~lgl~~~q~i 214 (316)
T cd00128 140 MGIPYIVAPYEAEAQCAYLAKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGAKPVEEIDLEKILK-----ELGLTREKLI 214 (316)
T ss_pred cCCCEEECCcCHHHHHHHHHhCCCeeEEEecCCCeeeecCceEEEecccCCCCceEEEEHHHHHH-----HcCCCHHHHH
Confidence 999999999999999999999999999999999999999999999998766 445788777765 7899999999
Q ss_pred HHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcccCcccccchhHHHHHH--hHhhhhccCceecCCC
Q psy11827 159 YMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFH--NTNLMFLYQPVYDPVS 236 (336)
Q Consensus 159 ~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k~~~~~~~~~~y~~~f~--~A~~~F~~~~V~dP~~ 236 (336)
++|+|+||||+|||||||+|||++||++|+ ++++++.++.+....-...-.++++.+.|. .+..+|.|+.+++|..
T Consensus 215 d~~~L~G~Dy~~gv~giG~k~A~~li~~~~--~~~~~~~~l~~~~~~~~~~~~~~~~~~~f~~p~~~~~~~~~~~~~p~~ 292 (316)
T cd00128 215 DLAILLGCDYTEGIPGIGPVTALKLIKKYG--DIEKDIERLKKKLYRSPEDFPLKEAREFFLNPEVTDDFIDLRWRDPDE 292 (316)
T ss_pred HHHHhcCCCCCCCCCCccHHHHHHHHHHcC--ChHHHHHHHHHhCccCCCcCChHHHHHHHcCCCCCCCCCceeecCCCH
Confidence 999999999999999999999999999998 688888888764320000112456778888 5567799999999999
Q ss_pred CceeECCCCCCCCCcc
Q psy11827 237 KEVVPLNPLESEMRDE 252 (336)
Q Consensus 237 ~~~~~L~~~~~~~~~~ 252 (336)
..++++.+.+.+.+++
T Consensus 293 ~~l~~~~~~~~~~~~~ 308 (316)
T cd00128 293 EGIIEFLCKEHGFNED 308 (316)
T ss_pred HHHHHHccCCCCCCHH
Confidence 9999999877665543
No 4
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=2.6e-50 Score=383.63 Aligned_cols=242 Identities=27% Similarity=0.361 Sum_probs=202.3
Q ss_pred hHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHHc
Q psy11827 2 KYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRAR 81 (336)
Q Consensus 2 k~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~~ 81 (336)
.++-.|+++||+|||||||.+++.|..+..+|+++|+++.+.+.++.+.|+.++|++++++++.||++|+..++++|+.+
T Consensus 16 ~r~~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~~~~~~~k~lL~~~ 95 (292)
T PRK03980 16 YRTINLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTDEIVEDSKKLLDLM 95 (292)
T ss_pred HHHHHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHC
Confidence 45666789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCCCCe-------------eeeccccccccccCC
Q psy11827 82 GVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNC-------------CFMDREKLPSALKMP 148 (336)
Q Consensus 82 gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~g~~-------------~~i~~~~l~~~~~~~ 148 (336)
||||++||||||||||||+++|+||+|+|+|+|+|+||+++||++++..++. ..++.+.+.+
T Consensus 96 GIp~i~AP~EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~e~~~~~~vl~----- 170 (292)
T PRK03980 96 GIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPELIELEEVLK----- 170 (292)
T ss_pred CCCEEecCchHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCccccccccccceeeeHHHHHH-----
Confidence 9999999999999999999999999999999999999999999998876531 1344444443
Q ss_pred cCCCCHHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcccCcccccchhHHHHHHhHhhhhcc
Q psy11827 149 LAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLY 228 (336)
Q Consensus 149 ~~~lt~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k~~~~~~~~~~y~~~f~~A~~~F~~ 228 (336)
.++++++||+|+|+|+||||+|||||||+|||++||++|+ +++++++++.. .+| .|.+++.+|++
T Consensus 171 ~lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~--sle~i~~~~~~--------~~~-----~~~~~r~~f~~ 235 (292)
T PRK03980 171 ELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHG--DLEKVLEERGF--------EIE-----NYDEIREFFLN 235 (292)
T ss_pred HhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCC--CHHHHHHhccC--------CCC-----CHHHHHHHhcC
Confidence 7899999999999999999999999999999999999997 69999885431 222 46789999999
Q ss_pred CceecCCCCceeECCCCCCCCCccchhhhcccCCCCCHHHHH
Q psy11827 229 QPVYDPVSKEVVPLNPLESEMRDEVFSQLSLKELELPKDQAF 270 (336)
Q Consensus 229 ~~V~dP~~~~~~~L~~~~~~~~~~~~~~~~~G~~~l~~~~~~ 270 (336)
+.|-+ +-.+.+=.|.. +....|+ ++...++++-..
T Consensus 236 p~v~~--~~~~~~~~pd~----~~l~~fl-~~e~~f~~~rv~ 270 (292)
T PRK03980 236 PPVTD--DYELKWKEPDK----EGIIEFL-VEEHDFSEERVK 270 (292)
T ss_pred CCCCC--CCCccCCCCCH----HHHHHHH-hccCCCCHHHHH
Confidence 99986 33332222211 2334554 555446655443
No 5
>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=100.00 E-value=3.8e-46 Score=362.14 Aligned_cols=212 Identities=31% Similarity=0.415 Sum_probs=188.2
Q ss_pred hHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHHc
Q psy11827 2 KYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRAR 81 (336)
Q Consensus 2 k~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~~ 81 (336)
+++..|+++||+|||||||.+++.|..+..+|++.|+++.+.+.++.+.|+.++|+++++++..+|++|+..++++|+.+
T Consensus 63 ~~~~~ll~~~i~Pv~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~ 142 (338)
T TIGR03674 63 YRTINLLENGIKPVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLM 142 (338)
T ss_pred HHHHHHHHCCCeEEEEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHc
Confidence 56677889999999999999999999999999999999988888889999999999999999999999999999999999
Q ss_pred CCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCCCCe-------------eeeccccccccccCC
Q psy11827 82 GVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNC-------------CFMDREKLPSALKMP 148 (336)
Q Consensus 82 gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~g~~-------------~~i~~~~l~~~~~~~ 148 (336)
||||++||||||||||||++.|.||+|+|+|+|+|+||+++|+++++..++. ..++.+.+.+
T Consensus 143 Gip~i~AP~EAeaq~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~----- 217 (338)
T TIGR03674 143 GIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLS----- 217 (338)
T ss_pred CCeEEECCccHHHHHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHH-----
Confidence 9999999999999999999999999999999999999999999998765531 1244444443
Q ss_pred cCCCCHHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcccCcccccchhHHHHHHhHhhhhcc
Q psy11827 149 LAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLY 228 (336)
Q Consensus 149 ~~~lt~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k~~~~~~~~~~y~~~f~~A~~~F~~ 228 (336)
.++++++||+|+|+|+||||++||||||+|||++||++|+ +++++++++.. .+. + +.+++.+|.+
T Consensus 218 ~lgl~~~q~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~g--sie~il~~~~~--------~~~-~----~~~~~~~f~~ 282 (338)
T TIGR03674 218 ELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHG--DLEKVLKARGE--------DIE-N----YDEIREFFLN 282 (338)
T ss_pred HhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcC--CHHHHHHhhcC--------CCC-C----HHHHHHHhCC
Confidence 7899999999999999999999999999999999999997 79999987642 121 2 4688999999
Q ss_pred Cceec
Q psy11827 229 QPVYD 233 (336)
Q Consensus 229 ~~V~d 233 (336)
+.|-+
T Consensus 283 ~~v~~ 287 (338)
T TIGR03674 283 PPVTD 287 (338)
T ss_pred CCCCC
Confidence 87755
No 6
>KOG2519|consensus
Probab=100.00 E-value=6.9e-39 Score=313.22 Aligned_cols=230 Identities=27% Similarity=0.307 Sum_probs=196.4
Q ss_pred hHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHHc
Q psy11827 2 KYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRAR 81 (336)
Q Consensus 2 k~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~~ 81 (336)
+|...|.++||+|||||||.+|+.|.++..+|..+|.++.+.-....+.|...+..+++++-+.||.+...++..+|..+
T Consensus 65 ~Rt~~l~~~gi~Pv~VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lm 144 (449)
T KOG2519|consen 65 YRTIRLIENGIKPVYVFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLM 144 (449)
T ss_pred HHHHHHHHcCCcEEEEECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHc
Confidence 46677889999999999999999999999999999987777767777888888899999999999999999999999999
Q ss_pred CCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCC-CCe--e-eeccccccccccCCcCCCCHHHH
Q psy11827 82 GVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLS-GNC--C-FMDREKLPSALKMPLAKFTDAKF 157 (336)
Q Consensus 82 gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~-g~~--~-~i~~~~l~~~~~~~~~~lt~~qf 157 (336)
||+|+.||+||+||||+|+++|.|++++|+|||.+.||.+.+++++..+ +.. + +++...+.+ .++++.++|
T Consensus 145 GIp~i~ap~EAEAqCA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~-----~l~l~~~~f 219 (449)
T KOG2519|consen 145 GIPVLDAPGEAEAQCAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILE-----GLGLSRESF 219 (449)
T ss_pred CCeeecCCchHHHHHHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHH-----HhcccHHHH
Confidence 9999999999999999999999999999999999999999888776542 222 2 455555544 899999999
Q ss_pred HHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcccCcccccchhHHHHHHhHhhhhccCceecCCCC
Q psy11827 158 RYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPVYDPVSK 237 (336)
Q Consensus 158 ~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k~~~~~~~~~~y~~~f~~A~~~F~~~~V~dP~~~ 237 (336)
+|+|+|+|||||++|.|||+++|++||++++ |++++++-...+ ..+.+|++|. |..|+..|.-+-|-++...
T Consensus 220 idL~lLlGCDYc~~I~Gig~~~al~lir~~~--~i~~ile~~~~~----~~~~ip~~w~--~~~~r~~f~~p~~~~~~~~ 291 (449)
T KOG2519|consen 220 IDLCLLLGCDYCPTIRGIGPKKALKLIRQHG--DIENILEINSDL----KEYPIPEDWS--YKLARKLFLEPEFPNPESI 291 (449)
T ss_pred HHHHHHhcCcccccccccChHHHHHHHHHhc--CHHHHhhhccch----hhcCCCCCcc--HHHHHHHhcCcccCCccce
Confidence 9999999999999999999999999999998 788888722122 2467999994 7789999999999997773
Q ss_pred -ceeECCC
Q psy11827 238 -EVVPLNP 244 (336)
Q Consensus 238 -~~~~L~~ 244 (336)
.+...+|
T Consensus 292 ~~i~w~~p 299 (449)
T KOG2519|consen 292 LDLKWKTP 299 (449)
T ss_pred eecccCCC
Confidence 3333344
No 7
>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=99.98 E-value=2.1e-32 Score=292.68 Aligned_cols=166 Identities=25% Similarity=0.305 Sum_probs=137.6
Q ss_pred hhhcccchHHHHHHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCCCCee-eecc
Q psy11827 60 LRQSVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCC-FMDR 138 (336)
Q Consensus 60 f~~~~~it~~m~~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~g~~~-~i~~ 138 (336)
-+++..||++|+..++++|+.+|||||+||||||||||||++.|+||+|+|+|||+|+||+++||+++...++.+ .|+.
T Consensus 763 ~r~~~~vt~~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~~~~~ve~~~~ 842 (1034)
T TIGR00600 763 KRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQY 842 (1034)
T ss_pred ccccccCCHHHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccCCCCceEEeeH
Confidence 567789999999999999999999999999999999999999999999999999999999999999987655544 3455
Q ss_pred ccccccccCCcCCCCHHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcc---c----------
Q psy11827 139 EKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGK---I---------- 205 (336)
Q Consensus 139 ~~l~~~~~~~~~~lt~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k---~---------- 205 (336)
..+.. .+++++++|+++|||+||||++||||||++||++||+.|+..+++.++.. ..|.. .
T Consensus 843 ~~i~~-----~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f-~~w~~~~~~~~~~~~~~~~ 916 (1034)
T TIGR00600 843 VDIHN-----QLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKF-KEWWHEAQKDKKKRENPND 916 (1034)
T ss_pred HHHHH-----HhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHH-HHHHHHhhhccccccccch
Confidence 55544 68999999999999999999999999999999999999986556665532 11110 0
Q ss_pred ------CcccccchhHHHHHHhHhhhhccCceec
Q psy11827 206 ------GSYVKITKEFLTSFHNTNLMFLYQPVYD 233 (336)
Q Consensus 206 ------~~~~~~~~~y~~~f~~A~~~F~~~~V~d 233 (336)
...+.+|++|- +..++.+|.++.|-+
T Consensus 917 ~~~~~~~~~~~lp~~FP--~~~V~~~yl~P~V~~ 948 (1034)
T TIGR00600 917 TKVKKKLRLLQLTPGFP--NPAVADAYLRPVVDD 948 (1034)
T ss_pred hhhhhcccccccCCCCC--cHHHHHHhcCCCCCC
Confidence 01235677774 468999999998865
No 8
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave 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. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=99.93 E-value=4.6e-27 Score=188.63 Aligned_cols=84 Identities=52% Similarity=0.820 Sum_probs=68.5
Q ss_pred HHcCCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecC-CC-CCe--------eeeccccccccccCC
Q psy11827 79 RARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLD-LS-GNC--------CFMDREKLPSALKMP 148 (336)
Q Consensus 79 ~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~-~~-g~~--------~~i~~~~l~~~~~~~ 148 (336)
|.+||||++||||||||||||+++|+||+|+|+|||+|+|||++||++++ .. +++ ..++...+.+
T Consensus 1 ~~~gv~~i~AP~EAeAq~A~L~~~g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~----- 75 (94)
T PF00867_consen 1 RLMGVPYIVAPYEAEAQCAYLERNGLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVIDLDDILK----- 75 (94)
T ss_dssp HHHT-EEEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEEHHHHHH-----
T ss_pred CCCCCeEEEcCchHHHHHHHHHHhcceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEEHHHHHH-----
Confidence 57899999999999999999999999999999999999999999999997 33 322 2455555554
Q ss_pred cCCCCHHHHHHHHHHhCCC
Q psy11827 149 LAKFTDAKFRYMCILSGCD 167 (336)
Q Consensus 149 ~~~lt~~qf~~~~iL~GcD 167 (336)
.+++|++||+++|+|+|||
T Consensus 76 ~l~l~~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 76 ELGLTREQFIDLCILCGCD 94 (94)
T ss_dssp HHTTSHHHHHHHHHHHHET
T ss_pred HcCCCHHHHHHHheecCCC
Confidence 6789999999999999998
No 9
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.93 E-value=1e-25 Score=216.78 Aligned_cols=190 Identities=21% Similarity=0.246 Sum_probs=150.2
Q ss_pred CEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHHcCCceecCccc
Q psy11827 12 IKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRARGVDCIVAPFE 91 (336)
Q Consensus 12 I~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~~gV~~ivAPyE 91 (336)
++|++||||.++..|.++..+|++.|++ +.+.++..+...|++.+....+.+|+.+|+| +.+|.+
T Consensus 61 ~~~~~vFD~~~~tfR~~~~~~yK~~R~~--------------~~p~~l~~q~~~i~~~~~~~~~~~l~~~G~e-add~i~ 125 (310)
T COG0258 61 THPVVVFDGKPPTFRHELLEEYKANREK--------------EMPDELAPQIPILTELLVALGIPLLELMGIE-ADDPIE 125 (310)
T ss_pred CcEEEEEcCCCCcchHHHHHHHHhCCCc--------------cCHHHHHHHHHHHHHHHHHhCcHhhhcCCCC-cchhHH
Confidence 9999999998887888888888887775 3456677788888999999999999999999 899999
Q ss_pred hHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCCCCee-eeccccccccccCCcC-CCCHHHHHHHHHHhC--CC
Q psy11827 92 ADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCC-FMDREKLPSALKMPLA-KFTDAKFRYMCILSG--CD 167 (336)
Q Consensus 92 ADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~g~~~-~i~~~~l~~~~~~~~~-~lt~~qf~~~~iL~G--cD 167 (336)
+.||+|+ +.|.+++|+|+|+|+++|+++++.......+... +++...+.+ .+ +++++||+|+++|+| ||
T Consensus 126 t~A~~a~--~~g~~~~I~S~DkD~lql~~~~~~~~~~~~~~~~~~~~~~~~~e-----~~~g~~p~qliD~~~L~Gd~sD 198 (310)
T COG0258 126 TLAQKAY--KKGDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKFLDLEEVEE-----KFKGLTPEQLIDLKALVGDSSD 198 (310)
T ss_pred HHHHHHH--hcCCeEEEEeCCcchhhhcCCCcEEEeccCCCCcccCCHHHHHH-----HHcCCCHHHHHHHHHHhCCccc
Confidence 9999999 9999999999999999999998644333333222 345555554 45 999999999999999 99
Q ss_pred CCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcccCcccccchhHHHHHHhHhhhhcc-Cceec
Q psy11827 168 YWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLY-QPVYD 233 (336)
Q Consensus 168 y~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k~~~~~~~~~~y~~~f~~A~~~F~~-~~V~d 233 (336)
|+|||+|||+|||++|+++|+ +++.++.++.... ......-......+|.+ ++|-+
T Consensus 199 nipGV~GIG~ktA~~Ll~~~g--s~e~i~~~~~~~~--------~~~~~~l~~~~~~afl~~~l~t~ 255 (310)
T COG0258 199 NIPGVKGIGPKTALKLLQEYG--SLEGLYENLDIIK--------KKTREKLLEDKEKAFLSKPLATI 255 (310)
T ss_pred CCCCCCCcCHHHHHHHHHHhC--CHHHHHHhhhhhc--------chhhHHHHHHHHHHhcCcccccc
Confidence 999999999999999999998 6888887764211 11112224566777777 34433
No 10
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.92 E-value=6.3e-25 Score=206.35 Aligned_cols=124 Identities=22% Similarity=0.274 Sum_probs=106.2
Q ss_pred HHHHHHHHHcCCceecCc-cchHHHHHHHHHc----CCeEEEecCCCceEeecccEEE-EecCCC-CCeeeecccccccc
Q psy11827 72 LNVIQACRARGVDCIVAP-FEADAQMAYLNIA----GYADYVITEDSDLLVFGAKKII-YKLDLS-GNCCFMDREKLPSA 144 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAP-yEADAQlA~L~~~----g~vdaViT~DSDll~fg~~~vi-~kl~~~-g~~~~i~~~~l~~~ 144 (336)
..++++|+.+||+++.+| ||||++||+|++. |....|+|+|+|++++++++|. ++.... +....++.+.+.+
T Consensus 87 ~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~~v~~- 165 (259)
T smart00475 87 PLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENVIE- 165 (259)
T ss_pred HHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEeccCCCCccEEEcHHHHHH-
Confidence 678889999999999877 7999999999884 7888999999999999988763 443321 1234677777765
Q ss_pred ccCCcCCCCHHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhh
Q psy11827 145 LKMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVY 202 (336)
Q Consensus 145 ~~~~~~~lt~~qf~~~~iL~G--cDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~ 202 (336)
.+|++++||+++|+|+| |||+||+||||+|||.+|+++|+ +++++++++...
T Consensus 166 ----~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~yg--sle~i~~~~~~~ 219 (259)
T smart00475 166 ----KYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFG--SLENILENLDKL 219 (259)
T ss_pred ----HhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhC--CHHHHHHHHHHH
Confidence 68999999999999999 99999999999999999999998 799999988763
No 11
>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=99.92 E-value=2.2e-24 Score=200.70 Aligned_cols=158 Identities=20% Similarity=0.238 Sum_probs=121.2
Q ss_pred CEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHHcCCceecCc-c
Q psy11827 12 IKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRARGVDCIVAP-F 90 (336)
Q Consensus 12 I~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~~gV~~ivAP-y 90 (336)
..+++||||....-+.....+.+..|.. .. + .+ ......++++|+.+||+++.+| |
T Consensus 51 ~~~~~~fD~~~~~~R~~l~p~YK~~R~~----~p--------~----~l-------~~q~~~~~~~l~~~gi~~i~~~~~ 107 (240)
T cd00008 51 TYVAVVFDAGGKTFRHELYPEYKANRKK----MP--------E----EL-------REQIPLIKELLEALGIPVLEIEGY 107 (240)
T ss_pred CeEEEEEeCCCCcccccccHHHHcCCCC----CC--------H----HH-------HHHHHHHHHHHHHCCCCEEecCCc
Confidence 6899999998543344433333333321 00 0 01 1345678899999999999997 8
Q ss_pred chHHHHHHHHH----cCCeEEEecCCCceEeecccEEEEecCCCCCeeeeccccccccccCCcCCCCHHHHHHHHHHhC-
Q psy11827 91 EADAQMAYLNI----AGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSG- 165 (336)
Q Consensus 91 EADAQlA~L~~----~g~vdaViT~DSDll~fg~~~vi~kl~~~g~~~~i~~~~l~~~~~~~~~~lt~~qf~~~~iL~G- 165 (336)
|||++||+|++ .|...+|+|+|+|++++..++|..... .+..+++.+.+.+ .++++++||+++|+|+|
T Consensus 108 EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~~~~--~~~~~i~~~~v~~-----~~g~~p~q~~d~~~L~GD 180 (240)
T cd00008 108 EADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVSP--MKKKLVTEENVIE-----KYGVTPAQIIDYKALMGD 180 (240)
T ss_pred CHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEEEeC--CCceEEeHHHHHH-----HhCcCHHHHHHHHHHcCC
Confidence 99999999986 678889999999999998777643221 1234566666654 68999999999999999
Q ss_pred -CCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhh
Q psy11827 166 -CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 201 (336)
Q Consensus 166 -cDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~ 201 (336)
|||+|||||||+|||.+|+++|+ +++++++++..
T Consensus 181 ~sDnipGv~GiG~ktA~~Ll~~~g--sle~i~~~~~~ 215 (240)
T cd00008 181 SSDNIPGVPGIGEKTAAKLLKEYG--SLEGILENLDK 215 (240)
T ss_pred cccCCCCCCccCHHHHHHHHHHhC--CHHHHHHhHHH
Confidence 99999999999999999999998 79999998865
No 12
>KOG2520|consensus
Probab=99.90 E-value=3.6e-24 Score=223.42 Aligned_cols=121 Identities=26% Similarity=0.389 Sum_probs=111.4
Q ss_pred cccchHHHHHHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCCCCee-eeccccc
Q psy11827 63 SVDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCC-FMDREKL 141 (336)
Q Consensus 63 ~~~it~~m~~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~g~~~-~i~~~~l 141 (336)
+-.+|++|+.+++.+|+.+|||||+||.|||||||.|++.++||+|||.|||+++||+.+|+++|...++.+ .+....+
T Consensus 460 ~~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~knk~ve~y~~~di 539 (815)
T KOG2520|consen 460 ADEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFNKNKYVEKYQLDDI 539 (815)
T ss_pred CchhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhhcCccceeeehHHH
Confidence 345899999999999999999999999999999999999999999999999999999999999998777665 3555555
Q ss_pred cccccCCcCCCCHHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 142 PSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 142 ~~~~~~~~~~lt~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.+ .+++++..++.+|.|+||||+.|++|||+.+|+.+|..|+
T Consensus 540 ~k-----el~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp 581 (815)
T KOG2520|consen 540 EK-----ELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFP 581 (815)
T ss_pred HH-----HHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcC
Confidence 44 7899999999999999999999999999999999999998
No 13
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.90 E-value=8.5e-23 Score=194.05 Aligned_cols=166 Identities=17% Similarity=0.201 Sum_probs=122.8
Q ss_pred HHhCC-CEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHHcCCce
Q psy11827 7 LLAHK-IKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRARGVDC 85 (336)
Q Consensus 7 L~~~g-I~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~~gV~~ 85 (336)
++.++ -.+++||||....-+.+....++..|...- ++ + ......++++|+.+||++
T Consensus 50 l~~~~p~~~~v~fD~~~~~~R~~l~p~YKanR~~~p------------~~----l-------~~q~~~i~~~l~~~gi~~ 106 (281)
T PRK14976 50 LKKLNPSYILIAFDAGRKTFRHQLYDEYKQGRKKTP------------ES----L-------ISQIPLLKKILKLAGIKW 106 (281)
T ss_pred HHhcCCCEEEEEEECCCCcccccccHHHhcCCCCCC------------HH----H-------HHHHHHHHHHHHHCCCCE
Confidence 33444 478999999754334444444433332110 00 0 022456778999999999
Q ss_pred ecCc-cchHHHHHHHHH----cCCeEEEecCCCceEeecccEEE-EecCCCCCeeeeccccccccccCCcCCCCHHHHHH
Q psy11827 86 IVAP-FEADAQMAYLNI----AGYADYVITEDSDLLVFGAKKII-YKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRY 159 (336)
Q Consensus 86 ivAP-yEADAQlA~L~~----~g~vdaViT~DSDll~fg~~~vi-~kl~~~g~~~~i~~~~l~~~~~~~~~~lt~~qf~~ 159 (336)
+.+| ||||++||+|++ .|.-..|+|+|.|++++..++|. +......+...++.+.+.. .+|++++||++
T Consensus 107 ~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~v~~-----~~gv~p~q~~d 181 (281)
T PRK14976 107 EEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLKKKGTSHFILNTNNFFE-----LYGIEPKQIID 181 (281)
T ss_pred EecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCeEEEEecCCCCcEEEcHHHHHH-----HhCcCHHHHHH
Confidence 9999 799999999987 46666799999999999987653 2222111124577777665 78999999999
Q ss_pred HHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhh
Q psy11827 160 MCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVY 202 (336)
Q Consensus 160 ~~iL~G--cDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~ 202 (336)
+++|+| ||++||+||||+|||.+||++|+ |++++++++.+.
T Consensus 182 ~~aL~GD~sDnipGVpGIG~KtA~~LL~~~g--sle~i~~~~~~~ 224 (281)
T PRK14976 182 YKGLVGDSSDNIKGVKGIGPKTAIKLLNKYG--NIENIYENIDKI 224 (281)
T ss_pred HHHHhCCccCCCCCCCcccHHHHHHHHHHcC--CHHHHHHhHHHH
Confidence 999999 99999999999999999999998 799999988663
No 14
>PRK05755 DNA polymerase I; Provisional
Probab=99.85 E-value=8.9e-21 Score=204.92 Aligned_cols=124 Identities=22% Similarity=0.293 Sum_probs=105.2
Q ss_pred HHHHHHHHHHcCCceecCc-cchHHHHHHHHH----cCCeEEEecCCCceEeecccEE-EE-ecCCCCCeeeeccccccc
Q psy11827 71 ALNVIQACRARGVDCIVAP-FEADAQMAYLNI----AGYADYVITEDSDLLVFGAKKI-IY-KLDLSGNCCFMDREKLPS 143 (336)
Q Consensus 71 ~~~l~~~L~~~gV~~ivAP-yEADAQlA~L~~----~g~vdaViT~DSDll~fg~~~v-i~-kl~~~g~~~~i~~~~l~~ 143 (336)
...++++|+.+||+++.+| ||||++||+|++ .|....|+|+|+|++++++++| ++ .++. ++...++.+.+..
T Consensus 88 ~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~~~~~~~-~~~~~~~~~~v~~ 166 (880)
T PRK05755 88 IPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLLDTMGV-SKNEELDPEEVVE 166 (880)
T ss_pred HHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEEeeccCC-CCCeEEcHHHHHH
Confidence 4567889999999999999 799999999985 5889999999999999998766 22 2221 2334577777655
Q ss_pred cccCCcCCCCHHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhh
Q psy11827 144 ALKMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVY 202 (336)
Q Consensus 144 ~~~~~~~~lt~~qf~~~~iL~G--cDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~ 202 (336)
.+|++++||+|+|+|+| ||++|||||||+|||.+||++|+ +++++++++...
T Consensus 167 -----~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~g--sle~i~~~~~~~ 220 (880)
T PRK05755 167 -----KYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYG--SLEGLYENLDEI 220 (880)
T ss_pred -----HHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcC--CHHHHHHhHHHh
Confidence 68999999999999999 89999999999999999999998 799999988753
No 15
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.83 E-value=4.7e-20 Score=198.26 Aligned_cols=125 Identities=22% Similarity=0.250 Sum_probs=105.0
Q ss_pred HHHHHHHHHHcCCceecCc-cchHHHHHHHHH----cCCeEEEecCCCceEeecccEEE-EecCCCCCeeeecccccccc
Q psy11827 71 ALNVIQACRARGVDCIVAP-FEADAQMAYLNI----AGYADYVITEDSDLLVFGAKKII-YKLDLSGNCCFMDREKLPSA 144 (336)
Q Consensus 71 ~~~l~~~L~~~gV~~ivAP-yEADAQlA~L~~----~g~vdaViT~DSDll~fg~~~vi-~kl~~~g~~~~i~~~~l~~~ 144 (336)
...++++|+.+||+++.+| ||||++||+|++ .|+...|+|+|.|++++..++|. ++.....+...++.+.+.+
T Consensus 86 ~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~~~~~~~~~~~~~~~~~v~~- 164 (887)
T TIGR00593 86 IPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIPKGKTSFTEITPEYVVE- 164 (887)
T ss_pred HHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEEEeccCCCCceEEcHHHHHH-
Confidence 3568889999999999888 899999999987 48888999999999999988763 3321111223567666654
Q ss_pred ccCCcCCCCHHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhh
Q psy11827 145 LKMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINVY 202 (336)
Q Consensus 145 ~~~~~~~lt~~qf~~~~iL~G--cDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~ 202 (336)
.+|++++||+|+++|+| ||++||+||||+|||.+|+++|+ |+++++.++...
T Consensus 165 ----~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~yg--sle~i~~~~~~i 218 (887)
T TIGR00593 165 ----KYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFG--SLENIYENLDQI 218 (887)
T ss_pred ----HhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcC--CHHHHHHHHHHh
Confidence 78999999999999999 79999999999999999999998 799999998763
No 16
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.80 E-value=5.6e-20 Score=140.77 Aligned_cols=63 Identities=48% Similarity=0.706 Sum_probs=55.2
Q ss_pred HcCCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCCCC---ee-eecccccc
Q psy11827 80 ARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGN---CC-FMDREKLP 142 (336)
Q Consensus 80 ~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~g~---~~-~i~~~~l~ 142 (336)
.+||||++||||||||||||+++|+||+|+|+|+|+|+||+++||++++..++ .+ .++...+.
T Consensus 2 ~~gi~~i~AP~eAeAq~A~L~~~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl 68 (73)
T smart00484 2 LMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVL 68 (73)
T ss_pred cCCCeEEEcCCcHHHHHHHHHhCCCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHH
Confidence 58999999999999999999999999999999999999999999999998775 22 45544443
No 17
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.79 E-value=4.2e-18 Score=159.50 Aligned_cols=120 Identities=20% Similarity=0.239 Sum_probs=99.7
Q ss_pred HHHHHHHHHcCCceecCc-cchHHHHHHHHH----cCCeEEEecCCCceEeecccEE-EEecCCCCCeeeeccccccccc
Q psy11827 72 LNVIQACRARGVDCIVAP-FEADAQMAYLNI----AGYADYVITEDSDLLVFGAKKI-IYKLDLSGNCCFMDREKLPSAL 145 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAP-yEADAQlA~L~~----~g~vdaViT~DSDll~fg~~~v-i~kl~~~g~~~~i~~~~l~~~~ 145 (336)
..++++|..+||+++..| ||||+.+|.|++ .|.--.|+|.|.|+++.-.++| ++.. . +..+++.+.+.+
T Consensus 87 ~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~~--~-~~~~~~~~~v~~-- 161 (256)
T PRK09482 87 PAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDY--F-QKRWLDAPFIEQ-- 161 (256)
T ss_pred HHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEEEec--c-ccccCCHHHHHH--
Confidence 567889999999999998 799999999986 4555568999999998876665 3332 1 122466666654
Q ss_pred cCCcCCCCHHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhh
Q psy11827 146 KMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 201 (336)
Q Consensus 146 ~~~~~~lt~~qf~~~~iL~G--cDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~ 201 (336)
.+|++++|++|+++|+| +|++||+||||+|||.+|+++|+ +++++++++..
T Consensus 162 ---~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~g--sle~i~~~~~~ 214 (256)
T PRK09482 162 ---EFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFR--SLENIYESLDA 214 (256)
T ss_pred ---HhCCCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhC--CHHHHHHhHHH
Confidence 78999999999999999 99999999999999999999998 79999988765
No 18
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=99.37 E-value=1.1e-12 Score=101.06 Aligned_cols=51 Identities=27% Similarity=0.391 Sum_probs=47.1
Q ss_pred cCCCCHHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhh
Q psy11827 149 LAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 201 (336)
Q Consensus 149 ~~~lt~~qf~~~~iL~G--cDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~ 201 (336)
.++++++||+++|+|+| |||+||+||||+|||.+++++|+ ++++++.++..
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~--~~~~~~~~~~~ 54 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYG--SLENLLENLDK 54 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhC--CHHHHHHHHHH
Confidence 47899999999999999 99999999999999999999997 68888887754
No 19
>PHA00439 exonuclease
Probab=99.25 E-value=7e-11 Score=112.12 Aligned_cols=100 Identities=18% Similarity=0.321 Sum_probs=75.7
Q ss_pred HHHHHHHHHHcCCceecCc-cchHHHHHHHHH----cCC-eEEEecCCCceEeecccEEEEecCCCCCeeeecccccccc
Q psy11827 71 ALNVIQACRARGVDCIVAP-FEADAQMAYLNI----AGY-ADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSA 144 (336)
Q Consensus 71 ~~~l~~~L~~~gV~~ivAP-yEADAQlA~L~~----~g~-vdaViT~DSDll~fg~~~vi~kl~~~g~~~~i~~~~l~~~ 144 (336)
...+.+++..+|++++..| ||||.-+|.|++ .|+ --.|+|.|.|++++....++.. ..++.+.++ .
T Consensus 99 ~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv~~~~~~~--~~~~~~~~~-----~- 170 (286)
T PHA00439 99 RKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIPNCDFLWC--TTGNILTQT-----P- 170 (286)
T ss_pred HHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcCcceEEEc--cCCceEEcC-----c-
Confidence 3456677888999999877 999999999986 455 4578999999999854333321 112111111 0
Q ss_pred ccCCcCCCCHHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHH
Q psy11827 145 LKMPLAKFTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFS 186 (336)
Q Consensus 145 ~~~~~~~lt~~qf~~~~iL~G--cDy~~~ipgiG~ktA~kli~~ 186 (336)
. .+++|.++-.|+| +|..||+|||| |||.+||++
T Consensus 171 ----~---~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 171 ----E---TADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred ----c---cHHHHHhhhhcccccccCCCCCCCcC-HHHHHHHhC
Confidence 1 3899999999999 99999999999 999999998
No 20
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.95 E-value=7.6e-10 Score=73.35 Aligned_cols=33 Identities=33% Similarity=0.515 Sum_probs=30.3
Q ss_pred HHHHHHHHHHhCCCCCC---CCCCCCHHHHHHHHHHc
Q psy11827 154 DAKFRYMCILSGCDYWT---GIKGMGLKKAKDYVFSI 187 (336)
Q Consensus 154 ~~qf~~~~iL~GcDy~~---~ipgiG~ktA~kli~~~ 187 (336)
++||+++|+|+| ||++ |+||||+|||.+|+++|
T Consensus 1 p~q~~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhC-cCCCCCCCCCcccHHHHHHHHHhC
Confidence 479999999999 8887 89999999999999875
No 21
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=98.94 E-value=6.9e-10 Score=89.66 Aligned_cols=40 Identities=43% Similarity=0.656 Sum_probs=34.6
Q ss_pred ChHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhh
Q psy11827 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSH 40 (336)
Q Consensus 1 mk~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~ 40 (336)
++++..|+++||+|||||||.++|.|..|..+|+++|+++
T Consensus 62 ~~r~~~L~~~gI~PifVFDG~~~~~K~~~~~~R~~~r~~~ 101 (101)
T PF00752_consen 62 FSRLCRLLEHGIKPIFVFDGKPPPLKRETIQKRRKRREEA 101 (101)
T ss_dssp HHHHHHHHHTTEEEEEEE--STTGGCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCEEEEEECCCCchhhHHHHHHHHHHHhcC
Confidence 4688999999999999999999999999999999988763
No 22
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=98.87 E-value=1.6e-09 Score=87.26 Aligned_cols=39 Identities=38% Similarity=0.546 Sum_probs=36.0
Q ss_pred ChHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhh
Q psy11827 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDS 39 (336)
Q Consensus 1 mk~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~ 39 (336)
+++++.|+++||+|||||||.++|.|..|..+|+++|++
T Consensus 60 ~~rl~~L~~~~I~PifVFDG~~~~~K~~t~~~R~~~r~~ 98 (99)
T smart00485 60 FYRTCRLLEFGIKPIFVFDGKPPPLKSETLAKRRERREE 98 (99)
T ss_pred HHHHHHHHHCCCeEEEEECCCCchhhHHHHHHHHHHHhc
Confidence 467899999999999999999999999999999988875
No 23
>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=98.69 E-value=1.3e-08 Score=110.74 Aligned_cols=89 Identities=26% Similarity=0.254 Sum_probs=64.1
Q ss_pred ChHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhhHHHH----HHHHhhcchHHHHHhhhhcccchHHHHHHHHH
Q psy11827 1 MKYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKA----AELLILDRGSEAQSHLRQSVDVTHKMALNVIQ 76 (336)
Q Consensus 1 mk~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a----~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~ 76 (336)
|+|+++|+.+||+|||||||.+|+.|+.|..+|+++|+++.+.| ..++..+...+|.+.+.++...++++......
T Consensus 59 f~Ri~~Ll~~gI~PVfVFDG~~p~lK~~t~~~R~~rR~~a~~~a~~~~~~ll~~~~~~~a~~~~~~~~~~~~~~~~~~~~ 138 (1034)
T TIGR00600 59 FHRLCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGASEDARKTAEKLLATFLKRQAIKTAFNSKKSTPEALPSVQQ 138 (1034)
T ss_pred HHHHHHHHHCCCeEEEEECCCCchHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCccccccccc
Confidence 58999999999999999999999999999999999998776544 45666676677777666655555544333222
Q ss_pred HHHHcCCceecCcc
Q psy11827 77 ACRARGVDCIVAPF 90 (336)
Q Consensus 77 ~L~~~gV~~ivAPy 90 (336)
++...-.|...|.
T Consensus 139 -~~~~~d~y~lp~l 151 (1034)
T TIGR00600 139 -VPRPQDLYVLPPL 151 (1034)
T ss_pred -ccccCCCccCCCC
Confidence 2223455665544
No 24
>PF12813 XPG_I_2: XPG domain containing
Probab=98.55 E-value=1.3e-07 Score=88.67 Aligned_cols=51 Identities=33% Similarity=0.344 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHc---CCceecCccchHHHHHHHHHcCCeEEEecCCCceEeecc
Q psy11827 69 KMALNVIQACRAR---GVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFGA 120 (336)
Q Consensus 69 ~m~~~l~~~L~~~---gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg~ 120 (336)
-|+..+++.|++. |+++++.|+|||..||.++++.-+ +|+|+|||+++|+.
T Consensus 4 f~~~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dl 57 (246)
T PF12813_consen 4 FLVPAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDL 57 (246)
T ss_pred chHHHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEecc
Confidence 4667789999999 999999999999999999997666 99999999999987
No 25
>PHA02567 rnh RnaseH; Provisional
Probab=98.53 E-value=6.5e-07 Score=85.74 Aligned_cols=90 Identities=18% Similarity=0.104 Sum_probs=66.2
Q ss_pred HHHHHHHHHcCCceecCc-cchHHHHHHHHH----cCCeEEEecCCCceEeecc-cEEEEecCCCCCeeeeccccccccc
Q psy11827 72 LNVIQACRARGVDCIVAP-FEADAQMAYLNI----AGYADYVITEDSDLLVFGA-KKIIYKLDLSGNCCFMDREKLPSAL 145 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAP-yEADAQlA~L~~----~g~vdaViT~DSDll~fg~-~~vi~kl~~~g~~~~i~~~~l~~~~ 145 (336)
..+.+++..+|++++..| ||||.-+|.|++ .|.--.|+|+|.|+++.-. ++|- .++. ++...+..
T Consensus 110 ~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~QLv~~~~v~-~~~~------~~~~~V~~-- 180 (304)
T PHA02567 110 KIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHKYPGVK-QWSP------MQKKWVKP-- 180 (304)
T ss_pred HHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCCCChhhccCCCCeE-Eeec------CCHHHHHH--
Confidence 345667788899999877 899999999887 5666689999999999853 4441 1111 11222322
Q ss_pred cCCcCCCCHHHHHHHHHHhC--CCCCCCCCC
Q psy11827 146 KMPLAKFTDAKFRYMCILSG--CDYWTGIKG 174 (336)
Q Consensus 146 ~~~~~~lt~~qf~~~~iL~G--cDy~~~ipg 174 (336)
.+| .++|++++-+|+| +|..||+|-
T Consensus 181 ---k~G-~P~q~iD~kaL~GDsSDNIPGVp~ 207 (304)
T PHA02567 181 ---KYG-SPEKDLMTKIIKGDKKDGVASIKV 207 (304)
T ss_pred ---HhC-CHHHHHHHHHhCCcccCCcCCCCC
Confidence 466 5999999999999 999888874
No 26
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=98.44 E-value=3.4e-09 Score=86.17 Aligned_cols=48 Identities=23% Similarity=0.321 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHHhC--CCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhh
Q psy11827 152 FTDAKFRYMCILSG--CDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKINV 201 (336)
Q Consensus 152 lt~~qf~~~~iL~G--cDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~ 201 (336)
++++|++|+..|+| +|.+||+||||+|||.+|+++|+ ++++++.++..
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~yg--sle~i~~~~~~ 50 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYG--SLENILANLDE 50 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHT--SCHCCCCC-SS
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcC--CHHHHHHhHHh
Confidence 36899999999999 99999999999999999999998 68888877654
No 27
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=98.07 E-value=8.2e-07 Score=88.13 Aligned_cols=109 Identities=24% Similarity=0.379 Sum_probs=80.8
Q ss_pred HHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCceEeec-ccEEEEecCCCCCeeeeccccccccccCCcCCC
Q psy11827 74 VIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLLVFG-AKKIIYKLDLSGNCCFMDREKLPSALKMPLAKF 152 (336)
Q Consensus 74 l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll~fg-~~~vi~kl~~~g~~~~i~~~~l~~~~~~~~~~l 152 (336)
.-+++.+.||.|+++||-|++|||||....+|+++. +.+|.+++. ++++|..|.+..+.-.++...+.+.++ ..-.
T Consensus 134 ~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~~-gp~d~l~ld~vdr~il~m~fg~d~Ppl~~~~vp~~le--m~l~ 210 (531)
T COG5366 134 ASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYAF-GPSDILLLDGVDRIILDMSFGSDKPPLDVFHVPRFLE--MFLL 210 (531)
T ss_pred ccccccccceEEEehhhHHHHHHHHHHHHHHHHhcC-CchHhHHHhhhhhheeecccCCCCCCCcccccchHHH--hccc
Confidence 345778899999999999999999999999999999 999999995 699998887644333444444444221 2223
Q ss_pred CHHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHH
Q psy11827 153 TDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVF 185 (336)
Q Consensus 153 t~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~ 185 (336)
+..-|...-.|.|||+|++++..-..-+..+.+
T Consensus 211 s~~lFya~~ll~~c~~~s~~~~C~~da~f~l~q 243 (531)
T COG5366 211 SSRLFYALGLLLGCDFCSTIPRCATDADFSLNQ 243 (531)
T ss_pred ccchhhhhcccccccccccccccccchhHHHHH
Confidence 566788888899999999999753322444433
No 28
>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=97.88 E-value=3.3e-05 Score=68.50 Aligned_cols=50 Identities=26% Similarity=0.426 Sum_probs=42.1
Q ss_pred HHHHHHHHHcCCceecCc-cchHHHHHHHHH----cCCeEEEecCCCceEeeccc
Q psy11827 72 LNVIQACRARGVDCIVAP-FEADAQMAYLNI----AGYADYVITEDSDLLVFGAK 121 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAP-yEADAQlA~L~~----~g~vdaViT~DSDll~fg~~ 121 (336)
..++++|..+|++++..| ||||..+|.|++ .|.--.|+|+|.|+++.-.+
T Consensus 89 ~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~ 143 (169)
T PF02739_consen 89 PYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDE 143 (169)
T ss_dssp HHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS
T ss_pred HHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCC
Confidence 457788999999999887 999999999987 56667889999999999887
No 29
>PHA03065 Hypothetical protein; Provisional
Probab=97.48 E-value=0.001 Score=65.97 Aligned_cols=184 Identities=19% Similarity=0.275 Sum_probs=95.0
Q ss_pred hHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhhHHHHH-------HHHh--hc---chHHHHHhhh--------
Q psy11827 2 KYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAA-------ELLI--LD---RGSEAQSHLR-------- 61 (336)
Q Consensus 2 k~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~-------~~~~--~g---~~~~a~~~f~-------- 61 (336)
++|+.+.+..=+.++..|-+..+-|....++||+......++=. .... .. -.+|.+...+
T Consensus 57 ~~iq~w~~~~gkVtlFvDRG~I~IK~~lReKRr~a~~~~~kRK~~ei~~l~~~i~~ld~~d~~yEEikt~~~lrI~Kl~F 136 (438)
T PHA03065 57 EYVQQWVKKAGKVTLFVDRGSIPIKQSLREKRRKASKNTIKRKREEIEKLEDDIKNLDVDDEMYEEIKTDLELKIDKLSF 136 (438)
T ss_pred HHHHHHHhcCCcEEEEEecCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHH
Confidence 57888855556667777888899999888877755332221111 1111 00 0123222111
Q ss_pred -hcccchHHHHHHHHHHHHHc--CCceecCc-cchHHHHHHHH-----HcCCeEEEecCCCceEeeccc----EEEEecC
Q psy11827 62 -QSVDVTHKMALNVIQACRAR--GVDCIVAP-FEADAQMAYLN-----IAGYADYVITEDSDLLVFGAK----KIIYKLD 128 (336)
Q Consensus 62 -~~~~it~~m~~~l~~~L~~~--gV~~ivAP-yEADAQlA~L~-----~~g~vdaViT~DSDll~fg~~----~vi~kl~ 128 (336)
-...=...+-..+-..|... +|+++..- -.|+-.|..=+ ++|.--.++|.|-|.|+|.|- ++|..+.
T Consensus 137 ~~fLa~~~nlk~~l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~KiI~t~~ 216 (438)
T PHA03065 137 QLFLANSNNLKRLLESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKIIKTAN 216 (438)
T ss_pred HHHHcchhhHHHHHHHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHHHHhHH
Confidence 00000112222233446556 78888764 56775555433 379999999999999999752 3332221
Q ss_pred CCCCeeeeccccccccccCCcCCCCHHHHHHHHHHhCCCCCCCCCCCCHH-HHHHHHHHcCCCcHHHHHHHH
Q psy11827 129 LSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGLK-KAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 129 ~~g~~~~i~~~~l~~~~~~~~~~lt~~qf~~~~iL~GcDy~~~ipgiG~k-tA~kli~~~~~~si~~vl~~~ 199 (336)
....+- -...|.---...++.-||||.||+-|+.+- +-++-++-+.+.+++++++.+
T Consensus 217 ---~~Y~~~-----------P~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dFt~~Nv~~SL 274 (438)
T PHA03065 217 ---QLYKFI-----------PCAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDFTIDNVVRSL 274 (438)
T ss_pred ---HHheeC-----------CChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhhhHHHHHHHH
Confidence 111110 011122222334556689999999998531 112222223333455555544
No 30
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=97.38 E-value=0.0026 Score=63.53 Aligned_cols=187 Identities=18% Similarity=0.240 Sum_probs=101.4
Q ss_pred hHHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhh-----c--c-----hHHHH---------Hhh
Q psy11827 2 KYIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLIL-----D--R-----GSEAQ---------SHL 60 (336)
Q Consensus 2 k~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~-----g--~-----~~~a~---------~~f 60 (336)
++|+.+.+.+=+.++..|-+..+-|....++||+.-....++=.+..++ . + .+|-+ ..|
T Consensus 55 ~~i~~w~~~~~~VtlFvDRG~I~iK~~lReKRr~a~k~~~~RK~~~i~~l~~~~~~ld~~d~~yeEikt~~~lki~K~~F 134 (425)
T PF04599_consen 55 EYIQQWIKNNGKVTLFVDRGSINIKEPLREKRRKALKNTIKRKREEIENLEDCIKNLDVDDEFYEEIKTDLELKIQKLSF 134 (425)
T ss_pred HHHHHHHhcCCeEEEEEecCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccHHHHHHHHHHHHHHHHHHHH
Confidence 5788887777788888899999999988888765432221111111111 0 0 11111 112
Q ss_pred hhcccchHHHHHHHHHHHHH--cCCceecCc-cchHHHHHHHHH-----cCCeEEEecCCCceEeecccEEEEecCCCCC
Q psy11827 61 RQSVDVTHKMALNVIQACRA--RGVDCIVAP-FEADAQMAYLNI-----AGYADYVITEDSDLLVFGAKKIIYKLDLSGN 132 (336)
Q Consensus 61 ~~~~~it~~m~~~l~~~L~~--~gV~~ivAP-yEADAQlA~L~~-----~g~vdaViT~DSDll~fg~~~vi~kl~~~g~ 132 (336)
+-...-...+-..+..+|.. .+|.++..- ..|+-.|.+=++ +|.--.++|.|-|.|+|.+-.-.-|+-...+
T Consensus 135 ~~fla~~~n~k~~l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t~~ 214 (425)
T PF04599_consen 135 QLFLANSNNLKTILESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKTMN 214 (425)
T ss_pred HHHhcchhhHHHHHHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHhHH
Confidence 21121122222223344444 478888764 778877665443 7999999999999999986322222211111
Q ss_pred -eeeeccccccccccCCcCCCCHHHHHHHHHHhCCCCCCCCCCCCH-HHHHHHHHHcCCCcHHHHHHHH
Q psy11827 133 -CCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDYWTGIKGMGL-KKAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 133 -~~~i~~~~l~~~~~~~~~~lt~~qf~~~~iL~GcDy~~~ipgiG~-ktA~kli~~~~~~si~~vl~~~ 199 (336)
...+-+ ...|.---...++.-||||.||+-|+.+ ++-++-++-|.+.+++++++.+
T Consensus 215 ~~Y~~~P-----------~~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~i~LF~dFti~Ni~~SL 272 (425)
T PF04599_consen 215 QLYKFIP-----------CSKSRYLSKLTALVNGCDFFPGLYGISITKKSLNRIKLFEDFTIDNILQSL 272 (425)
T ss_pred hHeeecC-----------CchHHHHHHHHHHHhcccccCCcceeEechhhccceeccccccHHHHHHHH
Confidence 111111 1112222234566679999999999853 1122224445555677777655
No 31
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=96.86 E-value=0.0034 Score=58.66 Aligned_cols=106 Identities=16% Similarity=0.223 Sum_probs=52.7
Q ss_pred EEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHh-h-------cch---HHHHHhhhhcccchH--HHHHHHHHHHHH
Q psy11827 14 VIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLI-L-------DRG---SEAQSHLRQSVDVTH--KMALNVIQACRA 80 (336)
Q Consensus 14 PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~-~-------g~~---~~a~~~f~~~~~it~--~m~~~l~~~L~~ 80 (336)
.++.+||.+|-+|-.+..+||-+.....+....... . |.. ......|. +..||| +.+..+.+.|+.
T Consensus 80 l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fd-sn~ITPGT~FM~~l~~~L~~ 158 (237)
T PF03159_consen 80 LYIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPEDQEEKFD-SNCITPGTEFMEKLSDALRY 158 (237)
T ss_dssp EEEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HHHHS-----GGGSSTTSHHHHHHHHHHHH
T ss_pred EEEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHHHhhhhhhccccccccccccccc-cceeccCCHHHHHHHHHHHH
Confidence 368999999988887766665444333222222111 0 100 00012222 234665 444444443331
Q ss_pred ------------cCCceecC----ccchHHHHHHHHH---------cCCeEEEecCCCceEeecc
Q psy11827 81 ------------RGVDCIVA----PFEADAQMAYLNI---------AGYADYVITEDSDLLVFGA 120 (336)
Q Consensus 81 ------------~gV~~ivA----PyEADAQlA~L~~---------~g~vdaViT~DSDll~fg~ 120 (336)
.++.++++ |+|+|--+..+.+ .+..++|++.|+|+++++-
T Consensus 159 ~~~~k~~~~~~~~~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~L 223 (237)
T PF03159_consen 159 YIKKKLNSDPKWQNLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLSL 223 (237)
T ss_dssp HHHHHHHH-GGGCCSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHHH
T ss_pred HHHHHhcCCCCcCceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHHH
Confidence 26778875 8999987776554 3788999999999999873
No 32
>PF12247 MKT1_N: Temperature dependent protein affecting M2 dsRNA replication; InterPro: IPR022040 This domain family is found in eukaryotes, and is typically between 231 and 255 amino acids in length. There is a single completely conserved residue P that may be functionally important. MKT1 is required for maintenance of K2 toxin above 30 degrees C in strains with the L-A-HN variant of the L-A double-stranded RNA virus of Saccharomyces cerevisiae. MKT1 is a 93 kDa protein with serine-rich regions and the retroviral protease signature, DTG. This family is the N-terminal region of MKT1.
Probab=96.24 E-value=0.0027 Score=50.65 Aligned_cols=33 Identities=21% Similarity=0.454 Sum_probs=28.1
Q ss_pred ccchhhhcccCCCCCHHHHHHHHcCCCCccccccc
Q psy11827 251 DEVFSQLSLKELELPKDQAFQLALGNLDPFSLEEM 285 (336)
Q Consensus 251 ~~~~~~~~~G~~~l~~~~~~~ia~G~~~p~t~~~~ 285 (336)
|.|+|.+ +|++ ||+|+|++++.|+|+|..+..+
T Consensus 1 P~D~h~~-iG~r-LP~elYfyls~GLi~~~ll~~l 33 (90)
T PF12247_consen 1 PNDLHEV-IGQR-LPDELYFYLSIGLISPRLLNAL 33 (90)
T ss_pred CCcHHHh-hccC-CCHHHHHHHHccccChHHHhHh
Confidence 4678887 9997 9999999999999999776543
No 33
>KOG2045|consensus
Probab=95.91 E-value=0.1 Score=56.63 Aligned_cols=183 Identities=16% Similarity=0.218 Sum_probs=101.3
Q ss_pred EEecCCCCccchhhHHHHHhhhhhhH-HHHHHHHhhcchHHHHHhhhhcccchH--HHHHHHHHHHHH------------
Q psy11827 16 MVFDGRHLPAKEATEEDRRKKRDSHK-AKAAELLILDRGSEAQSHLRQSVDVTH--KMALNVIQACRA------------ 80 (336)
Q Consensus 16 fVFDG~~~p~K~~t~~~R~~~r~~~~-~~a~~~~~~g~~~~a~~~f~~~~~it~--~m~~~l~~~L~~------------ 80 (336)
+--||..+.+|-....+||=+-.... +.-.++.++|..-.- +-|. +.-||| +.+..+.+-|+.
T Consensus 83 MAVDGvAPRAKMNQQRsRRFrTArdAe~qlaKA~enGe~~p~-erFD-SNcITPGTeFM~rl~~~L~yfIktKistDs~W 160 (1493)
T KOG2045|consen 83 MAVDGVAPRAKMNQQRSRRFRTARDAEQQLAKAAENGELRPH-ERFD-SNCITPGTEFMVRLQEGLRYFIKTKISTDSLW 160 (1493)
T ss_pred EeecccCchhhhhHHHHHhhhhhhhHHHHHHHHHhccccCcc-cccc-cCCCCCcHHHHHHHHHHHHHHHHhccccchhh
Confidence 44599999888866655554322211 122345667765332 3342 334565 444455554443
Q ss_pred cCCceec----CccchHHHHHHHHH---------cCCeEEEecCCCceEeec-cc---E--EEEe---cCCCCCeeeecc
Q psy11827 81 RGVDCIV----APFEADAQMAYLNI---------AGYADYVITEDSDLLVFG-AK---K--IIYK---LDLSGNCCFMDR 138 (336)
Q Consensus 81 ~gV~~iv----APyEADAQlA~L~~---------~g~vdaViT~DSDll~fg-~~---~--vi~k---l~~~g~~~~i~~ 138 (336)
.++.+|. +|+|.+--+--+.+ -+--++++.=|-||+++| |. + +++. +...+....++.
T Consensus 161 q~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLImLGL~tHepHF~lLREEVtFgrrn~~k~leh 240 (1493)
T KOG2045|consen 161 QRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIMLGLCTHEPHFVLLREEVTFGRRNKRKSLEH 240 (1493)
T ss_pred cccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhheeeeccCCcceeeeeeeeecccccccchhhh
Confidence 5788886 59999977665544 256788998899999999 43 1 2221 111111111211
Q ss_pred cc--ccc------cc-----cCC---cCCCCH----HHHHHHHHHhCCCCCCCCCCCCH-HHHHHHHHHcCCCcHHHHHH
Q psy11827 139 EK--LPS------AL-----KMP---LAKFTD----AKFRYMCILSGCDYWTGIKGMGL-KKAKDYVFSIMDPDFENALR 197 (336)
Q Consensus 139 ~~--l~~------~~-----~~~---~~~lt~----~qf~~~~iL~GcDy~~~ipgiG~-ktA~kli~~~~~~si~~vl~ 197 (336)
.+ |.. -+ .|+ ...++. +.|+.++.|.|+||+|.+|++-+ +.|+-|+-+. ..+++-
T Consensus 241 qkFyLLHLsLLREYlelEF~e~rdt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~gAlpllyst----ykkvlp 316 (1493)
T KOG2045|consen 241 QKFYLLHLSLLREYLELEFDELRDTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSGALPLLYST----YKKVLP 316 (1493)
T ss_pred hhhhhhHHHHHHHHHHHHHHHhhhccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCChHHHHHHH----HHHHhc
Confidence 11 110 00 011 223343 45667888889999999999976 3566666542 234555
Q ss_pred HHhhhcc
Q psy11827 198 KINVYGK 204 (336)
Q Consensus 198 ~~~~~~k 204 (336)
.++.|.+
T Consensus 317 t~~GyIN 323 (1493)
T KOG2045|consen 317 TLGGYIN 323 (1493)
T ss_pred cCCcccc
Confidence 5555543
No 34
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=95.81 E-value=0.048 Score=57.52 Aligned_cols=105 Identities=19% Similarity=0.215 Sum_probs=62.6
Q ss_pred EEEecCCCCccchhhHHHHHhhhhhhHHHH-HHHHhhcch--HHH-------------HHhhhhcccchH--HHHHHHHH
Q psy11827 15 IMVFDGRHLPAKEATEEDRRKKRDSHKAKA-AELLILDRG--SEA-------------QSHLRQSVDVTH--KMALNVIQ 76 (336)
Q Consensus 15 ifVFDG~~~p~K~~t~~~R~~~r~~~~~~a-~~~~~~g~~--~~a-------------~~~f~~~~~it~--~m~~~l~~ 76 (336)
++--||..|-+|-.....||=+.......| .++.++|.. +++ .+.|. +..||| ..+..+.+
T Consensus 80 ymAVDGvAPRAKMNQQRaRRFRsAkda~~A~~Kae~~~e~~~e~~~e~g~~id~~~~~kk~fD-SNcITPGTpFMerLak 158 (953)
T COG5049 80 YMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKDEIGNEIDTIDVEKKKFD-SNCITPGTPFMERLAK 158 (953)
T ss_pred EEEecccCchhhhhHHHHHhhhhhhhhHHHHhhccccccccchhccccCCccchhhhhhcccc-ccCCCCCChHHHHHHH
Confidence 456799999888765544443322111111 122222221 111 11232 234565 44555555
Q ss_pred HHHH------------cCCceecC----ccchHHHHHHHHHc---------CCeEEEecCCCceEeecc
Q psy11827 77 ACRA------------RGVDCIVA----PFEADAQMAYLNIA---------GYADYVITEDSDLLVFGA 120 (336)
Q Consensus 77 ~L~~------------~gV~~ivA----PyEADAQlA~L~~~---------g~vdaViT~DSDll~fg~ 120 (336)
.|+- .+|.+|.+ |+|.+--+--+.++ +-.++|++-|-||+.+|-
T Consensus 159 ~L~Y~i~~KlssDp~Wrnl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGL 227 (953)
T COG5049 159 VLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGL 227 (953)
T ss_pred HHHHHHHhhhcCCccceeEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeec
Confidence 5553 58888875 99999888777663 578999999999999994
No 35
>KOG2044|consensus
Probab=94.68 E-value=0.26 Score=52.80 Aligned_cols=106 Identities=20% Similarity=0.242 Sum_probs=63.1
Q ss_pred EEEEecCCCCccchhhHHHHHhhh--hhhHHHHH------HHHhhcch---HHHHHhhhhcccchH--HHHHHHHHHHHH
Q psy11827 14 VIMVFDGRHLPAKEATEEDRRKKR--DSHKAKAA------ELLILDRG---SEAQSHLRQSVDVTH--KMALNVIQACRA 80 (336)
Q Consensus 14 PifVFDG~~~p~K~~t~~~R~~~r--~~~~~~a~------~~~~~g~~---~~a~~~f~~~~~it~--~m~~~l~~~L~~ 80 (336)
.++--||-.|-+|-....+||=+. +.+.+.+. ++.++|.. ++-.+.|. +.-||| ..+..|-++|+-
T Consensus 98 LymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~~~~e~fD-SNcITPGTpFM~~La~aLrY 176 (931)
T KOG2044|consen 98 LYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETFD-SNCITPGTPFMDRLAKALRY 176 (931)
T ss_pred eEEeecccCchhhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCchhhccccc-cCccCCCChHHHHHHHHHHH
Confidence 356789999989886655555332 22111111 12223332 11112232 223555 455556666654
Q ss_pred ------------cCCceecC----ccchHHHHHHHHH---c------CCeEEEecCCCceEeecc
Q psy11827 81 ------------RGVDCIVA----PFEADAQMAYLNI---A------GYADYVITEDSDLLVFGA 120 (336)
Q Consensus 81 ------------~gV~~ivA----PyEADAQlA~L~~---~------g~vdaViT~DSDll~fg~ 120 (336)
.||.+|.+ |+|.+--+-...+ . +-.++++.-|-||+++|-
T Consensus 177 yI~~rLn~DPgWkNikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDADLImLgL 241 (931)
T KOG2044|consen 177 YIHDRLNSDPGWKNIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLIMLGL 241 (931)
T ss_pred HHHHhhcCCccccceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCccceeeec
Confidence 48888874 9999977665554 2 568999999999999994
No 36
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=86.32 E-value=0.63 Score=29.41 Aligned_cols=15 Identities=27% Similarity=0.423 Sum_probs=12.0
Q ss_pred CCCCCCHHHHHHHHH
Q psy11827 171 GIKGMGLKKAKDYVF 185 (336)
Q Consensus 171 ~ipgiG~ktA~kli~ 185 (336)
.+||||++||..++.
T Consensus 15 ~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 15 KLPGIGPKTANAILS 29 (30)
T ss_dssp TSTT-SHHHHHHHHH
T ss_pred hCCCcCHHHHHHHHh
Confidence 699999999988763
No 37
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=86.20 E-value=0.69 Score=34.20 Aligned_cols=26 Identities=31% Similarity=0.364 Sum_probs=19.4
Q ss_pred CCCCCCHHHHHHHHHHcCCCcHHHHHHH
Q psy11827 171 GIKGMGLKKAKDYVFSIMDPDFENALRK 198 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~~si~~vl~~ 198 (336)
||||||.++|..|.+.|+ +++++...
T Consensus 7 GI~~VG~~~ak~L~~~f~--sl~~l~~a 32 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFG--SLEALMNA 32 (64)
T ss_dssp TSTT--HHHHHHHHHCCS--CHHHHCC-
T ss_pred CCCCccHHHHHHHHHHcC--CHHHHHHc
Confidence 899999999999999998 56665443
No 38
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=79.75 E-value=1.5 Score=39.65 Aligned_cols=19 Identities=21% Similarity=0.293 Sum_probs=17.5
Q ss_pred CCCCCCHHHHHHHHHHcCC
Q psy11827 171 GIKGMGLKKAKDYVFSIMD 189 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~ 189 (336)
+|||||+|+|.+++..++.
T Consensus 77 ~i~GIGpk~A~~il~~fg~ 95 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSP 95 (192)
T ss_pred cCCCCCHHHHHHHHHhCCH
Confidence 5999999999999999874
No 39
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=77.95 E-value=1.8 Score=26.04 Aligned_cols=18 Identities=22% Similarity=0.344 Sum_probs=15.2
Q ss_pred CCCCCCCCHHHHHHHHHH
Q psy11827 169 WTGIKGMGLKKAKDYVFS 186 (336)
Q Consensus 169 ~~~ipgiG~ktA~kli~~ 186 (336)
+..+||||.++|.+++..
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 457999999999998863
No 40
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=72.45 E-value=3.2 Score=32.34 Aligned_cols=24 Identities=29% Similarity=0.378 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHcCC
Q psy11827 166 CDYWTGIKGMGLKKAKDYVFSIMD 189 (336)
Q Consensus 166 cDy~~~ipgiG~ktA~kli~~~~~ 189 (336)
|+.+.+|||||+.+|..|+...++
T Consensus 1 ~~~l~sipGig~~~a~~llaeigd 24 (87)
T PF02371_consen 1 AELLTSIPGIGPITAATLLAEIGD 24 (87)
T ss_pred CchhcCCCCccHHHHHHHHHHHcC
Confidence 455679999999999999998865
No 41
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=72.10 E-value=4.6 Score=28.81 Aligned_cols=24 Identities=29% Similarity=0.386 Sum_probs=16.9
Q ss_pred CCCCCCHHHHHHHHHHcCCCcHHHH
Q psy11827 171 GIKGMGLKKAKDYVFSIMDPDFENA 195 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~~si~~v 195 (336)
+|.|||++||.+++.+ |-.+++.+
T Consensus 6 ~I~GVG~~tA~~w~~~-G~rtl~Dl 29 (52)
T PF10391_consen 6 GIWGVGPKTARKWYAK-GIRTLEDL 29 (52)
T ss_dssp TSTT--HHHHHHHHHT-T--SHHHH
T ss_pred hcccccHHHHHHHHHh-CCCCHHHH
Confidence 7899999999999995 44467766
No 42
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=71.88 E-value=2.7 Score=38.03 Aligned_cols=43 Identities=21% Similarity=0.169 Sum_probs=27.8
Q ss_pred cCCCC-HHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHHh
Q psy11827 149 LAKFT-DAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKIN 200 (336)
Q Consensus 149 ~~~lt-~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~~ 200 (336)
.+||. .+.--.|..| -+++|||||+|..++..++ .++++..+.
T Consensus 59 LyGF~~~~Er~lF~~L------~~V~GIGpK~Al~iL~~~~---~~el~~aI~ 102 (191)
T TIGR00084 59 LFGFNTLEERELFKEL------IKVNGVGPKLALAILSNMS---PEEFVYAIE 102 (191)
T ss_pred eeCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHhcCC---HHHHHHHHH
Confidence 67774 3443334443 3799999999999998764 344444443
No 43
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=71.44 E-value=3 Score=37.51 Aligned_cols=36 Identities=19% Similarity=0.280 Sum_probs=22.8
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCCHHHHHHHHHHc
Q psy11827 151 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSI 187 (336)
Q Consensus 151 ~lt~~qf~~~~iL~G-cDy~~~ipgiG~ktA~kli~~~ 187 (336)
.+++++|.. +|..| -..+..+||||.|||-+++-.-
T Consensus 92 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 92 SLDVNSFYK-ALSLGDESVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 456666654 33344 3344578888888888887653
No 44
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.37 E-value=3.3 Score=37.53 Aligned_cols=35 Identities=17% Similarity=0.272 Sum_probs=25.2
Q ss_pred cCCCC-HHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCC
Q psy11827 149 LAKFT-DAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMD 189 (336)
Q Consensus 149 ~~~lt-~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~ 189 (336)
.+||. .+.--.|..| -+++|||||+|+.++..++.
T Consensus 60 LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~ILs~~~~ 95 (194)
T PRK14605 60 LFGFATTEELSLFETL------IDVSGIGPKLGLAMLSAMNA 95 (194)
T ss_pred eeCCCCHHHHHHHHHH------hCCCCCCHHHHHHHHHhCCH
Confidence 67774 3444444444 38999999999999998863
No 45
>PRK13844 recombination protein RecR; Provisional
Probab=70.22 E-value=6.9 Score=35.75 Aligned_cols=49 Identities=10% Similarity=0.019 Sum_probs=34.1
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcccCcccccchhHHHHHHhHhhhhccCceecCCCCce
Q psy11827 170 TGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPVYDPVSKEV 239 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k~~~~~~~~~~y~~~f~~A~~~F~~~~V~dP~~~~~ 239 (336)
..+||||+|+|.+|.-. + +..++++.+.+-+|....+..+.+|+.-+.+
T Consensus 18 ~~LPGIG~KsA~Rla~~--------l-------------L~~~~~~~~~la~~i~~~~~~i~~C~~C~~l 66 (200)
T PRK13844 18 RKLPTIGKKSSQRLALY--------L-------------LDKSPETAIAIANSLLDATANIKKCVYCQAL 66 (200)
T ss_pred HHCCCCCHHHHHHHHHH--------H-------------HcCCHHHHHHHHHHHHHHHHhCCcCCCCCCC
Confidence 47999999999988743 1 1245667777777777777777777554443
No 46
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.45 E-value=3.5 Score=37.53 Aligned_cols=37 Identities=22% Similarity=0.278 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 151 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 151 ~lt~~qf~~~~iL~G-cDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.+++++|..+ |..| -..+..+||||.|||-++|-.-+
T Consensus 91 ~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAeRIIlELk 128 (196)
T PRK13901 91 GIKYNEFRDA-IDREDIELISKVKGIGNKMAGKIFLKLR 128 (196)
T ss_pred CCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 4567766653 3333 34445888888888888886543
No 47
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.69 E-value=4 Score=37.02 Aligned_cols=37 Identities=22% Similarity=0.326 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 151 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 151 ~lt~~qf~~~~iL~G-cDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.++.++|..+ |..| -..+..+||||.|||-+++-.-+
T Consensus 92 ~~~~~el~~a-I~~~D~~~L~kvpGIGkKtAerIilELk 129 (195)
T PRK14604 92 SGTPDELQLA-IAGGDVARLARVPGIGKKTAERIVLELK 129 (195)
T ss_pred CCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 4567766653 2233 34445899999999999987643
No 48
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=67.38 E-value=8.8 Score=34.93 Aligned_cols=47 Identities=17% Similarity=0.104 Sum_probs=31.5
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcccCcccccchhHHHHHHhHhhhhccCceecCCCC
Q psy11827 170 TGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPVYDPVSK 237 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k~~~~~~~~~~y~~~f~~A~~~F~~~~V~dP~~~ 237 (336)
..+||||+|+|.+|.-. + +..++++.+.+-+|....+..+.+++.-+
T Consensus 14 ~~LPGIG~KsA~RlA~~--------l-------------l~~~~~~~~~la~ai~~~~~~i~~C~~C~ 60 (195)
T TIGR00615 14 KKLPGIGPKSAQRLAFH--------L-------------LKRDPSEVLRLAQALLEAKENLRTCSVCG 60 (195)
T ss_pred HHCCCCCHHHHHHHHHH--------H-------------HcCCHHHHHHHHHHHHHHHHcCCcCCCCC
Confidence 47999999999998643 1 12455666666666666666666665444
No 49
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.03 E-value=4.3 Score=36.65 Aligned_cols=36 Identities=19% Similarity=0.233 Sum_probs=20.8
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCCHHHHHHHHHHc
Q psy11827 151 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSI 187 (336)
Q Consensus 151 ~lt~~qf~~~~iL~G-cDy~~~ipgiG~ktA~kli~~~ 187 (336)
.++.++|..+ |..| -..+..+||||.|||-+++-.-
T Consensus 92 ~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 92 NEDAETLVTM-IASQDVEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred CCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 3455555543 2233 3344567777777777777653
No 50
>PRK00076 recR recombination protein RecR; Reviewed
Probab=65.90 E-value=9.8 Score=34.67 Aligned_cols=48 Identities=15% Similarity=0.120 Sum_probs=31.6
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcHHHHHHHHhhhcccCcccccchhHHHHHHhHhhhhccCceecCCCCc
Q psy11827 170 TGIKGMGLKKAKDYVFSIMDPDFENALRKINVYGKIGSYVKITKEFLTSFHNTNLMFLYQPVYDPVSKE 238 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~~~~~si~~vl~~~~~~~k~~~~~~~~~~y~~~f~~A~~~F~~~~V~dP~~~~ 238 (336)
..+||||+|+|.++.-.- +..+++..+.+-+|....+..+.+|+.-+.
T Consensus 14 ~~LPGIG~KsA~Rla~~l---------------------l~~~~~~~~~la~~i~~~~~~i~~C~~C~~ 61 (196)
T PRK00076 14 RKLPGIGPKSAQRLAFHL---------------------LQRDREDVLRLAQALEEAKEKIKHCSVCGN 61 (196)
T ss_pred HHCCCCCHHHHHHHHHHH---------------------HcCCHHHHHHHHHHHHHHHHcCCcCCCCCC
Confidence 479999999999887431 124556666666666666666666654443
No 51
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.31 E-value=4.8 Score=36.57 Aligned_cols=37 Identities=22% Similarity=0.322 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 151 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 151 ~lt~~qf~~~~iL~G-cDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.++.++|..+ |..| -..+..+||||.|||-+++-..+
T Consensus 91 ~~~~~~l~~a-I~~~D~~~L~kvpGIGkKtAerIilELk 128 (197)
T PRK14603 91 ALPPALLARA-LLEGDARLLTSASGVGKKLAERIALELK 128 (197)
T ss_pred CCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 3566766653 2233 22335789999999988887644
No 52
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=64.76 E-value=6.8 Score=33.67 Aligned_cols=47 Identities=23% Similarity=0.186 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCceE
Q psy11827 69 KMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLL 116 (336)
Q Consensus 69 ~m~~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll 116 (336)
.|...+.+.||.+|++.+..+...|..+..++++.-- .|+|-|.+++
T Consensus 7 ~~L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~R-illTrd~~l~ 53 (147)
T PF01927_consen 7 AMLGRLARWLRLLGYDTLYSRDIDDDEILELAREEGR-ILLTRDRDLL 53 (147)
T ss_pred CCHHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCe-EEEECCHHHH
Confidence 4556788999999999999998799999999886443 6889999975
No 53
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.34 E-value=6.3 Score=35.54 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=25.5
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 151 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 151 ~lt~~qf~~~~iL~G-cDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.++.++|..+ |-.| -..+ .+||||.|||-+++-.-+
T Consensus 92 ~~~~~~l~~a-I~~~D~~~L-~vpGIGkKtAerIilELk 128 (186)
T PRK14600 92 KLTPEQLFSA-IVNEDKAAL-KVNGIGEKLINRIITELQ 128 (186)
T ss_pred cCCHHHHHHH-HHcCCHhhe-ECCCCcHHHHHHHHHHHH
Confidence 4677777653 4444 4455 899999999999987643
No 54
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=62.98 E-value=8.1 Score=27.83 Aligned_cols=25 Identities=28% Similarity=0.422 Sum_probs=19.8
Q ss_pred CCCCCCHHHHHHHHHH-cCCCcHHHHHH
Q psy11827 171 GIKGMGLKKAKDYVFS-IMDPDFENALR 197 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~-~~~~si~~vl~ 197 (336)
+|||||+++|.+|... +. +++.+..
T Consensus 9 ~I~Gig~~~a~~L~~~G~~--t~~~l~~ 34 (60)
T PF14520_consen 9 SIPGIGPKRAEKLYEAGIK--TLEDLAN 34 (60)
T ss_dssp TSTTCHHHHHHHHHHTTCS--SHHHHHT
T ss_pred cCCCCCHHHHHHHHhcCCC--cHHHHHc
Confidence 7999999999999988 43 5665544
No 55
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.59 E-value=5.6 Score=36.31 Aligned_cols=42 Identities=19% Similarity=0.178 Sum_probs=28.5
Q ss_pred cCCCC-HHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHH
Q psy11827 149 LAKFT-DAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 149 ~~~lt-~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~ 199 (336)
.+||. .++-..|-.| -+++|||||+|+.++..++ .+.++..+
T Consensus 61 LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~~---~~~l~~aI 103 (203)
T PRK14602 61 LFGFATWDERQTFIVL------ISISKVGAKTALAILSQFR---PDDLRRLV 103 (203)
T ss_pred eeCCCCHHHHHHHHHH------hCCCCcCHHHHHHHHhhCC---HHHHHHHH
Confidence 67774 4444444444 3799999999999999874 34444444
No 56
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.23 E-value=4.7 Score=36.36 Aligned_cols=42 Identities=19% Similarity=0.274 Sum_probs=27.1
Q ss_pred cCCCCH-HHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHH
Q psy11827 149 LAKFTD-AKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 149 ~~~lt~-~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~ 199 (336)
.+||.. +.--.|-.| -++.|||||+|+.++..++ .+.++..+
T Consensus 60 LyGF~~~~Er~lF~~L------isV~GIGpK~Al~iLs~~~---~~~l~~aI 102 (186)
T PRK14600 60 LYGFLNREEQDCLRML------VKVSGVNYKTAMSILSKLT---PEQLFSAI 102 (186)
T ss_pred eeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHccCC---HHHHHHHH
Confidence 677743 333333333 3899999999999999874 34444444
No 57
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=61.92 E-value=8.5 Score=35.18 Aligned_cols=38 Identities=16% Similarity=0.226 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 151 KFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 151 ~lt~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.++.+.|...-...=-.++..+||||.|+|.+++-.-.
T Consensus 92 ~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk 129 (201)
T COG0632 92 NLDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELK 129 (201)
T ss_pred CCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHh
Confidence 44666666544333344566899999999999998654
No 58
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.27 E-value=5.1 Score=36.42 Aligned_cols=26 Identities=23% Similarity=0.281 Sum_probs=19.9
Q ss_pred CCCCCCHHHHHHHHHHcCCCcHHHHHHHH
Q psy11827 171 GIKGMGLKKAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~~si~~vl~~~ 199 (336)
++.|||||+|+.++..++ .++++..+
T Consensus 76 ~V~GIGpK~AL~iLs~~~---~~~l~~aI 101 (197)
T PRK14603 76 GVSGVGPKLALALLSALP---PALLARAL 101 (197)
T ss_pred CcCCcCHHHHHHHHcCCC---HHHHHHHH
Confidence 799999999999999764 34444444
No 59
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.26 E-value=6.3 Score=35.98 Aligned_cols=37 Identities=19% Similarity=0.384 Sum_probs=27.0
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 151 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 151 ~lt~~qf~~~~iL~G-cDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.++.++|..+ |..| -.-+..+||||.|||-+++-.-+
T Consensus 93 ~~~~~~l~~a-I~~~D~~~L~~ipGIGkKtAerIilELk 130 (203)
T PRK14602 93 QFRPDDLRRL-VAEEDVAALTRVSGIGKKTAQHIFLELK 130 (203)
T ss_pred hCCHHHHHHH-HHhCCHHHHhcCCCcCHHHHHHHHHHHH
Confidence 4677777653 4444 44456899999999999997644
No 60
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=61.08 E-value=6.5 Score=41.92 Aligned_cols=27 Identities=19% Similarity=0.231 Sum_probs=22.8
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcHHHHHHH
Q psy11827 170 TGIKGMGLKKAKDYVFSIMDPDFENALRK 198 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~~~~~si~~vl~~ 198 (336)
.+|||||++++.+|++.|+ |++++...
T Consensus 555 ~~IpGIG~kr~~~LL~~Fg--Si~~I~~A 581 (624)
T PRK14669 555 LEIPGVGAKTVQRLLKHFG--SLERVRAA 581 (624)
T ss_pred hcCCCCCHHHHHHHHHHcC--CHHHHHhC
Confidence 5899999999999999998 57666543
No 61
>PF07719 TPR_2: Tetratricopeptide repeat; InterPro: IPR013105 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. This repeat includes outlying Tetratricopeptide-like repeats (TPR) that are not matched by IPR001440 from INTERPRO.; PDB: 1XNF_B 3Q15_A 4ABN_A 1OUV_A 3U4T_A 3MA5_C 2KCV_A 2KCL_A 2XEV_A 3NF1_A ....
Probab=60.86 E-value=6.4 Score=23.99 Aligned_cols=27 Identities=11% Similarity=0.089 Sum_probs=21.4
Q ss_pred HHHHHHHhhcchHHHHHhhhhcccchH
Q psy11827 42 AKAAELLILDRGSEAQSHLRQSVDVTH 68 (336)
Q Consensus 42 ~~a~~~~~~g~~~~a~~~f~~~~~it~ 68 (336)
..|..++..|+.++|+++|.+++.+.|
T Consensus 6 ~lg~~~~~~~~~~~A~~~~~~al~l~p 32 (34)
T PF07719_consen 6 YLGQAYYQLGNYEEAIEYFEKALELDP 32 (34)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHCc
Confidence 456778899999999999999886654
No 62
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.70 E-value=5.7 Score=35.87 Aligned_cols=34 Identities=24% Similarity=0.232 Sum_probs=24.4
Q ss_pred cCCCC-HHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 149 LAKFT-DAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 149 ~~~lt-~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.+||. .++-..|..| -++.|||||+|+.++..+.
T Consensus 60 LyGF~~~~Er~lF~~L------i~V~GIGpK~AL~iLs~~~ 94 (188)
T PRK14606 60 LYGFSNERKKELFLSL------TKVSRLGPKTALKIISNED 94 (188)
T ss_pred eeCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCCC
Confidence 67774 4444444444 2799999999999998764
No 63
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.22 E-value=6.1 Score=35.97 Aligned_cols=34 Identities=24% Similarity=0.308 Sum_probs=24.6
Q ss_pred cCCCC-HHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 149 LAKFT-DAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 149 ~~~lt-~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.+||. .+.--.|-.| -+++|||||+|+.++..+.
T Consensus 59 LYGF~t~~Er~lF~~L------isVsGIGPK~ALaILs~~~ 93 (196)
T PRK13901 59 LFGFLNSSEREVFEEL------IGVDGIGPRAALRVLSGIK 93 (196)
T ss_pred eeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCCC
Confidence 67774 4444444444 3799999999999998874
No 64
>cd08556 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcoho
Probab=58.61 E-value=15 Score=31.57 Aligned_cols=40 Identities=23% Similarity=0.297 Sum_probs=33.4
Q ss_pred HHHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecC
Q psy11827 71 ALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITE 111 (336)
Q Consensus 71 ~~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~ 111 (336)
-..+++.++..|+++.+-.....+++.++.+.| ||+|+|.
T Consensus 149 ~~~~i~~~~~~g~~v~~wtvn~~~~~~~~~~~G-VdgI~TD 188 (189)
T cd08556 149 TPELVRAAHAAGLKVYVWTVNDPEDARRLLALG-VDGIITD 188 (189)
T ss_pred CHHHHHHHHHcCCEEEEEcCCCHHHHHHHHHCC-CCEEecC
Confidence 356788899999999988777778888888888 8999975
No 65
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=58.10 E-value=6.4 Score=35.43 Aligned_cols=34 Identities=21% Similarity=0.281 Sum_probs=24.4
Q ss_pred cCCCC-HHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 149 LAKFT-DAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 149 ~~~lt-~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.+||. .+.--.|-.| -++.|||||+|+.++..+.
T Consensus 60 LyGF~~~~Er~lF~~L------i~VsGIGpK~Al~ILs~~~ 94 (183)
T PRK14601 60 LYGFLDKDEQKMFEML------LKVNGIGANTAMAVCSSLD 94 (183)
T ss_pred eeCCCCHHHHHHHHHH------hccCCccHHHHHHHHcCCC
Confidence 67774 4444444444 3799999999999998864
No 66
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=57.38 E-value=20 Score=31.52 Aligned_cols=35 Identities=20% Similarity=0.252 Sum_probs=24.0
Q ss_pred cCCceecCc--cchHHHHHHHHH---c-CCeEEEecCCCce
Q psy11827 81 RGVDCIVAP--FEADAQMAYLNI---A-GYADYVITEDSDL 115 (336)
Q Consensus 81 ~gV~~ivAP--yEADAQlA~L~~---~-g~vdaViT~DSDl 115 (336)
.||.++.++ -.||.-+--++. . +.--.|+|.|..+
T Consensus 66 ~gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~i 106 (166)
T PF05991_consen 66 GGIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREI 106 (166)
T ss_pred CceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHH
Confidence 467788776 579987777665 2 4455788877764
No 67
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=57.27 E-value=6.5 Score=35.70 Aligned_cols=42 Identities=26% Similarity=0.300 Sum_probs=27.3
Q ss_pred cCCCC-HHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHH
Q psy11827 149 LAKFT-DAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 149 ~~~lt-~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~ 199 (336)
.+||. .+.--.|..| -++.|||||+|+.++..+. .++++..+
T Consensus 60 LyGF~~~~Er~lF~~L------i~V~GIGpK~Al~iLs~~~---~~el~~aI 102 (195)
T PRK14604 60 LYGFSTPAQRQLFELL------IGVSGVGPKAALNLLSSGT---PDELQLAI 102 (195)
T ss_pred eeCCCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCCC---HHHHHHHH
Confidence 67774 3333333333 3799999999999999764 34444444
No 68
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=56.21 E-value=21 Score=30.79 Aligned_cols=47 Identities=28% Similarity=0.391 Sum_probs=31.7
Q ss_pred HHHHHHHHcCCceecCccc--------hHHHHHHHHHcCCeEEEecCCCceEeec
Q psy11827 73 NVIQACRARGVDCIVAPFE--------ADAQMAYLNIAGYADYVITEDSDLLVFG 119 (336)
Q Consensus 73 ~l~~~L~~~gV~~ivAPyE--------ADAQlA~L~~~g~vdaViT~DSDll~fg 119 (336)
+....+.+.+--+.+-|-+ -|+-+-.++-+|.+|+++|+|.|+|...
T Consensus 65 ~~v~~l~~~~~~i~I~p~~~f~~~RDp~Dn~~L~~A~~~kA~~lvTgD~dLL~lr 119 (142)
T COG1569 65 ELVLVLFESVSLIAINPLEKFNICRDPKDNKLLALAYESKADYLVTGDQDLLVLR 119 (142)
T ss_pred HHHHHHHHhheeEeecccccccccCCchHHHHHHHHHhccCCEEEEcchhhheec
Confidence 3334444444333355544 4777777888999999999999999664
No 69
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=56.06 E-value=9.9 Score=34.34 Aligned_cols=37 Identities=19% Similarity=0.333 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHc
Q psy11827 151 KFTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSI 187 (336)
Q Consensus 151 ~lt~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~ 187 (336)
.++.++|...+.--=-..+..+||||.|||-+++-..
T Consensus 91 ~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileL 127 (191)
T TIGR00084 91 NMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLEL 127 (191)
T ss_pred cCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHH
Confidence 4577777776552212344589999999999998543
No 70
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=54.92 E-value=10 Score=39.91 Aligned_cols=28 Identities=21% Similarity=0.214 Sum_probs=23.0
Q ss_pred CCCCCCCCHHHHHHHHHHcCCCcHHHHHHH
Q psy11827 169 WTGIKGMGLKKAKDYVFSIMDPDFENALRK 198 (336)
Q Consensus 169 ~~~ipgiG~ktA~kli~~~~~~si~~vl~~ 198 (336)
+..|||||+++..+|++.|+ |++++-.+
T Consensus 516 Ld~I~GiG~kr~~~Ll~~Fg--s~~~ik~A 543 (567)
T PRK14667 516 LDKIKGIGEVKKEIIYRNFK--TLYDFLKA 543 (567)
T ss_pred cccCCCCCHHHHHHHHHHhC--CHHHHHhC
Confidence 35899999999999999998 56665544
No 71
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=54.89 E-value=9.7 Score=40.23 Aligned_cols=25 Identities=16% Similarity=0.219 Sum_probs=21.4
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcHHHHH
Q psy11827 170 TGIKGMGLKKAKDYVFSIMDPDFENAL 196 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~~~~~si~~vl 196 (336)
..|||||+++..+|++.|+ |++++-
T Consensus 544 d~I~GIG~kr~~~LL~~Fg--s~~~i~ 568 (574)
T TIGR00194 544 LKIPGVGEKRVQKLLKYFG--SLKGIK 568 (574)
T ss_pred hcCCCCCHHHHHHHHHHcC--CHHHHH
Confidence 5899999999999999998 566553
No 72
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=53.66 E-value=9.8 Score=24.19 Aligned_cols=14 Identities=36% Similarity=0.411 Sum_probs=11.1
Q ss_pred CCCCCCHHHHHHHH
Q psy11827 171 GIKGMGLKKAKDYV 184 (336)
Q Consensus 171 ~ipgiG~ktA~kli 184 (336)
.++|||.+|+.+|-
T Consensus 15 ~~~GIG~kt~~kL~ 28 (32)
T PF11798_consen 15 KFWGIGKKTAKKLN 28 (32)
T ss_dssp GSTTS-HHHHHHHH
T ss_pred hhCCccHHHHHHHH
Confidence 69999999998863
No 73
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=52.97 E-value=12 Score=39.58 Aligned_cols=30 Identities=37% Similarity=0.452 Sum_probs=24.1
Q ss_pred CCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHH
Q psy11827 168 YWTGIKGMGLKKAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 168 y~~~ipgiG~ktA~kli~~~~~~si~~vl~~~ 199 (336)
-+..|||||+++..+|++.|+ |++++-.+-
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fg--s~~~I~~As 544 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLG--TYKDILLLN 544 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhC--CHHHHHhCC
Confidence 445899999999999999998 577665443
No 74
>PF00515 TPR_1: Tetratricopeptide repeat; InterPro: IPR001440 The tetratrico peptide repeat (TPR) is a structural motif present in a wide range of proteins [, , ]. It mediates protein-protein interactions and the assembly of multiprotein complexes []. The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding. The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel alpha-helices []. The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees; within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B. ; GO: 0005515 protein binding; PDB: 3SF4_C 2LNI_A 1ELW_A 2C0M_A 1FCH_B 3R9A_B 2J9Q_A 2C0L_A 1KT1_A 3FWV_A ....
Probab=52.65 E-value=9.9 Score=23.38 Aligned_cols=27 Identities=11% Similarity=0.121 Sum_probs=21.6
Q ss_pred HHHHHHHhhcchHHHHHhhhhcccchH
Q psy11827 42 AKAAELLILDRGSEAQSHLRQSVDVTH 68 (336)
Q Consensus 42 ~~a~~~~~~g~~~~a~~~f~~~~~it~ 68 (336)
..|..+...|+.++|..+|++++.+.|
T Consensus 6 ~~g~~~~~~~~~~~A~~~~~~al~~~p 32 (34)
T PF00515_consen 6 NLGNAYFQLGDYEEALEYYQRALELDP 32 (34)
T ss_dssp HHHHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred HHHHHHHHhCCchHHHHHHHHHHHHCc
Confidence 457778889999999999999887655
No 75
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=51.59 E-value=9.2 Score=30.93 Aligned_cols=29 Identities=34% Similarity=0.357 Sum_probs=23.7
Q ss_pred ccchHHHHHHHHHcCCeEEEecCCCceEe
Q psy11827 89 PFEADAQMAYLNIAGYADYVITEDSDLLV 117 (336)
Q Consensus 89 PyEADAQlA~L~~~g~vdaViT~DSDll~ 117 (336)
|-..|+-...++..+-+|+++|+|.|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 45567777778889999999999999864
No 76
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=49.81 E-value=18 Score=30.86 Aligned_cols=26 Identities=23% Similarity=0.103 Sum_probs=18.5
Q ss_pred CCCCCCHHHHHHHHHHcCCCcHHHHH
Q psy11827 171 GIKGMGLKKAKDYVFSIMDPDFENAL 196 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~~si~~vl 196 (336)
.+|||||++|.++|+.-+-.+++.++
T Consensus 65 ~lpGigP~~A~~IV~nGpf~sveDL~ 90 (132)
T PRK02515 65 QFPGMYPTLAGKIVKNAPYDSVEDVL 90 (132)
T ss_pred HCCCCCHHHHHHHHHCCCCCCHHHHH
Confidence 59999999999999642223555543
No 77
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=47.73 E-value=17 Score=38.85 Aligned_cols=24 Identities=29% Similarity=0.374 Sum_probs=20.5
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcHHHH
Q psy11827 170 TGIKGMGLKKAKDYVFSIMDPDFENA 195 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~~~~~si~~v 195 (336)
.+|||||+++|..|++.|+ |++++
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fg--s~~~i 595 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFG--SVEKV 595 (621)
T ss_pred hcCCCcCHHHHHHHHHHcC--CHHHH
Confidence 5899999999999999998 45544
No 78
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.64 E-value=12 Score=33.86 Aligned_cols=37 Identities=24% Similarity=0.425 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCCHHHHHHHHHHcC
Q psy11827 151 KFTDAKFRYMCILSG-CDYWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 151 ~lt~~qf~~~~iL~G-cDy~~~ipgiG~ktA~kli~~~~ 188 (336)
.++.++|+.. |..+ -.-+..+||||.|||-+++-.-+
T Consensus 92 ~~~~~~l~~a-I~~~D~~~L~~vpGIGkKtAerIilELk 129 (194)
T PRK14605 92 AMNAEALASA-IISGNAELLSTIPGIGKKTASRIVLELK 129 (194)
T ss_pred hCCHHHHHHH-HHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 4677776543 3233 22234899999999999987643
No 79
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=47.02 E-value=15 Score=37.70 Aligned_cols=56 Identities=4% Similarity=-0.197 Sum_probs=45.3
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHH---cCCeEEEecCCCceEeecccEEEEecC
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNI---AGYADYVITEDSDLLVFGAKKIIYKLD 128 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~---~g~vdaViT~DSDll~fg~~~vi~kl~ 128 (336)
......|+..||.++++||-+.+|+++... .-+.+++. +-+|++++++.+.+..+.
T Consensus 34 d~~~fyld~~~v~~~~~~~~~~~~l~if~~~~~~p~f~~~~-g~t~~~l~~~~~f~~~~~ 92 (531)
T COG5366 34 DGNWFYLDYVDVSSICRGLVFGMELVIFEPLLKLPEFKDEN-GVTMIWLWDGIGFNKLQG 92 (531)
T ss_pred cchHHHHHhcCchhhhHHHHhhccHHhhcCcccCceEEccC-Cccceeeecccceeeecc
Confidence 456678999999999999999999999654 66677776 777888999988776543
No 80
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=46.94 E-value=27 Score=37.72 Aligned_cols=29 Identities=10% Similarity=0.171 Sum_probs=23.5
Q ss_pred CCCCCCCCHHHHHHHHHHcCCCcHHHHHHHH
Q psy11827 169 WTGIKGMGLKKAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 169 ~~~ipgiG~ktA~kli~~~~~~si~~vl~~~ 199 (336)
+..|||||++++.+|++.|+ |+.++-.+-
T Consensus 610 L~~IpGiG~kr~~~LL~~Fg--S~~~i~~As 638 (691)
T PRK14672 610 FERLPHVGKVRAHRLLAHFG--SFRSLQSAT 638 (691)
T ss_pred cccCCCCCHHHHHHHHHHhc--CHHHHHhCC
Confidence 35899999999999999998 566655443
No 81
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=46.75 E-value=22 Score=34.36 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=22.4
Q ss_pred CCCCCCHHHHHHHHHHcCCCcHHHHHHH
Q psy11827 171 GIKGMGLKKAKDYVFSIMDPDFENALRK 198 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~~si~~vl~~ 198 (336)
+|||||++||.++. ..+-.+++.+..+
T Consensus 89 ~i~GiGpk~a~~l~-~lGi~sl~dL~~a 115 (307)
T cd00141 89 RVPGVGPKTARKLY-ELGIRTLEDLRKA 115 (307)
T ss_pred cCCCCCHHHHHHHH-HcCCCCHHHHHHH
Confidence 69999999999999 7676677776664
No 82
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=46.56 E-value=36 Score=23.89 Aligned_cols=41 Identities=17% Similarity=0.049 Sum_probs=26.1
Q ss_pred HHHHHHHhhcchHHHHHhhhhcccchH---HHHHHHHHHHHHcC
Q psy11827 42 AKAAELLILDRGSEAQSHLRQSVDVTH---KMALNVIQACRARG 82 (336)
Q Consensus 42 ~~a~~~~~~g~~~~a~~~f~~~~~it~---~m~~~l~~~L~~~g 82 (336)
..|..++..|+.++|.++|.+.+...| +....+-.++...|
T Consensus 2 ~~a~~~~~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~~~~~~g 45 (65)
T PF13432_consen 2 ALARALYQQGDYDEAIAAFEQALKQDPDNPEAWYLLGRILYQQG 45 (65)
T ss_dssp HHHHHHHHCTHHHHHHHHHHHHHCCSTTHHHHHHHHHHHHHHTT
T ss_pred hHHHHHHHcCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHcC
Confidence 356777888888888888888776655 22333444444444
No 83
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=45.93 E-value=19 Score=32.81 Aligned_cols=17 Identities=29% Similarity=0.530 Sum_probs=14.0
Q ss_pred CCCCCCCCHHHHHHHHH
Q psy11827 169 WTGIKGMGLKKAKDYVF 185 (336)
Q Consensus 169 ~~~ipgiG~ktA~kli~ 185 (336)
+..+||||+|+|.++.-
T Consensus 14 l~kLPGvG~KsA~R~Af 30 (198)
T COG0353 14 LKKLPGVGPKSAQRLAF 30 (198)
T ss_pred HhhCCCCChhHHHHHHH
Confidence 35799999999988764
No 84
>cd01422 MGS Methylglyoxal synthase catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The first part of the catalytic mechanism is believed to be similar to TIM (triosephosphate isomerase) in that both enzymes utilize DHAP to form an ene-diolate phosphate intermediate. In MGS, the second catalytic step is characterized by the elimination of phosphate and collapse of the enediolate to form methylglyoxal instead of reprotonation to form the isomer glyceraldehyde 3-phosphate, as in TIM. This is the first reaction in the methylglyoxal bypass of the Embden-Myerhoff glycolytic pathway and is believed to provide physiological benefits under non-ideal growth conditions in bacteria.
Probab=45.65 E-value=33 Score=28.17 Aligned_cols=34 Identities=26% Similarity=0.327 Sum_probs=27.1
Q ss_pred HHHHH-cCCcee---cCccchHHHHHHHHHcCCeEEEe
Q psy11827 76 QACRA-RGVDCI---VAPFEADAQMAYLNIAGYADYVI 109 (336)
Q Consensus 76 ~~L~~-~gV~~i---vAPyEADAQlA~L~~~g~vdaVi 109 (336)
+.|++ .|+++- +.|.|.+.+++.+.++|.+|+||
T Consensus 38 ~~L~~~~Gi~v~~vk~~~~~g~~~i~~~i~~g~i~~VI 75 (115)
T cd01422 38 LLIQEATGLTVNRMKSGPLGGDQQIGALIAEGEIDAVI 75 (115)
T ss_pred HHHHHhhCCcEEEEecCCCCchhHHHHHHHcCceeEEE
Confidence 34566 788764 33479999999999999999996
No 85
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=45.30 E-value=43 Score=28.72 Aligned_cols=45 Identities=31% Similarity=0.399 Sum_probs=35.1
Q ss_pred cchHHHHHHHHHHHHHcCCc-----eecCc--cchHHHHHHHHHcCCeEEEe
Q psy11827 65 DVTHKMALNVIQACRARGVD-----CIVAP--FEADAQMAYLNIAGYADYVI 109 (336)
Q Consensus 65 ~it~~m~~~l~~~L~~~gV~-----~ivAP--yEADAQlA~L~~~g~vdaVi 109 (336)
.|+..|....++.|+..|+. .+.-| ||-=..+..|.++|-.|+|+
T Consensus 13 ~i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI 64 (138)
T TIGR00114 13 DITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVI 64 (138)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEE
Confidence 46778888899999999875 44466 67666677788888889887
No 86
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=45.25 E-value=47 Score=28.60 Aligned_cols=45 Identities=27% Similarity=0.429 Sum_probs=36.0
Q ss_pred cchHHHHHHHHHHHHHcCC-----ceecCc--cchHHHHHHHHHcCCeEEEe
Q psy11827 65 DVTHKMALNVIQACRARGV-----DCIVAP--FEADAQMAYLNIAGYADYVI 109 (336)
Q Consensus 65 ~it~~m~~~l~~~L~~~gV-----~~ivAP--yEADAQlA~L~~~g~vdaVi 109 (336)
.|+..|.....+.|+..|+ +.+.-| ||-=..+..|.+++.+|+|+
T Consensus 16 ~i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi 67 (144)
T PF00885_consen 16 EITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVI 67 (144)
T ss_dssp HHHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEE
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEE
Confidence 4567888889999999987 555556 77777888899999999987
No 87
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=45.21 E-value=39 Score=29.76 Aligned_cols=45 Identities=24% Similarity=0.366 Sum_probs=35.7
Q ss_pred cchHHHHHHHHHHHHHcC-----CceecCc--cchHHHHHHHHHcCCeEEEe
Q psy11827 65 DVTHKMALNVIQACRARG-----VDCIVAP--FEADAQMAYLNIAGYADYVI 109 (336)
Q Consensus 65 ~it~~m~~~l~~~L~~~g-----V~~ivAP--yEADAQlA~L~~~g~vdaVi 109 (336)
.||..|..-..+.|+..| |..+.-| ||-=..+..|.++|..|+||
T Consensus 23 ~It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiI 74 (158)
T PRK12419 23 DIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIV 74 (158)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEE
Confidence 567788888899999988 4566567 77777777788888888887
No 88
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=45.16 E-value=17 Score=38.48 Aligned_cols=30 Identities=13% Similarity=0.152 Sum_probs=24.5
Q ss_pred CCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHH
Q psy11827 168 YWTGIKGMGLKKAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 168 y~~~ipgiG~ktA~kli~~~~~~si~~vl~~~ 199 (336)
-+..|||||++++.+|++.++ |++++..+-
T Consensus 526 ~L~~IpGIG~kr~~~LL~~FG--S~~~I~~As 555 (577)
T PRK14668 526 VLDDVPGVGPETRKRLLRRFG--SVEGVREAS 555 (577)
T ss_pred HHhcCCCCCHHHHHHHHHHcC--CHHHHHhCC
Confidence 346899999999999999998 577776543
No 89
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=44.88 E-value=21 Score=35.05 Aligned_cols=28 Identities=21% Similarity=0.207 Sum_probs=23.1
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcHHHHHHH
Q psy11827 170 TGIKGMGLKKAKDYVFSIMDPDFENALRK 198 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~~~~~si~~vl~~ 198 (336)
-.|||||++||.+|.+ .|-.+++.+.++
T Consensus 92 ~~i~GiGpk~a~~l~~-lGi~tl~eL~~a 119 (334)
T smart00483 92 TNVFGVGPKTAAKWYR-KGIRTLEELKKN 119 (334)
T ss_pred HccCCcCHHHHHHHHH-hCCCCHHHHHhc
Confidence 3799999999999999 777778777554
No 90
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=43.74 E-value=13 Score=40.89 Aligned_cols=29 Identities=10% Similarity=0.234 Sum_probs=24.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHcCCCcHHHHHH
Q psy11827 167 DYWTGIKGMGLKKAKDYVFSIMDPDFENALR 197 (336)
Q Consensus 167 Dy~~~ipgiG~ktA~kli~~~~~~si~~vl~ 197 (336)
+|+.+|||||++.|..|+.+++ ++++++.
T Consensus 757 ~~L~~lPgI~~~~a~~ll~~f~--si~~l~~ 785 (814)
T TIGR00596 757 DFLLKLPGVTKKNYRNLRKKVK--SIRELAK 785 (814)
T ss_pred HHHHHCCCCCHHHHHHHHHHcC--CHHHHHh
Confidence 4455899999999999999998 5776655
No 91
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=43.44 E-value=18 Score=38.39 Aligned_cols=26 Identities=19% Similarity=0.281 Sum_probs=22.2
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcHHHHHH
Q psy11827 170 TGIKGMGLKKAKDYVFSIMDPDFENALR 197 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~~~~~si~~vl~ 197 (336)
.+|||||++++.+|++.|+ |+.++..
T Consensus 546 ~~IpGIG~k~~k~Ll~~Fg--S~~~i~~ 571 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFG--SLKAIKE 571 (598)
T ss_pred hhCCCcCHHHHHHHHHHcC--CHHHHHh
Confidence 5899999999999999998 5666654
No 92
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=43.23 E-value=21 Score=33.32 Aligned_cols=28 Identities=21% Similarity=0.240 Sum_probs=22.2
Q ss_pred CCCCCCCCHHHHHHHHHH-cCCCcHHHHHHH
Q psy11827 169 WTGIKGMGLKKAKDYVFS-IMDPDFENALRK 198 (336)
Q Consensus 169 ~~~ipgiG~ktA~kli~~-~~~~si~~vl~~ 198 (336)
+..|||||.++|.+|+.. |+ |++.+..+
T Consensus 5 L~~IpGIG~krakkLl~~GF~--Sve~Ik~A 33 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFE--SVEDVRAA 33 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCC--CHHHHHhC
Confidence 347999999999999998 76 56665443
No 93
>PRK09454 ugpQ cytoplasmic glycerophosphodiester phosphodiesterase; Provisional
Probab=42.72 E-value=31 Score=31.94 Aligned_cols=44 Identities=25% Similarity=0.280 Sum_probs=30.9
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCceE
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLL 116 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll 116 (336)
..+++.+++.|+++.+-----..++.+|.+.| ||+|+|+.-|++
T Consensus 199 ~~~v~~~~~~g~~v~~WTvn~~~~~~~l~~~G-VdgIiTD~p~~~ 242 (249)
T PRK09454 199 EARVAALKAAGLRILVYTVNDPARARELLRWG-VDCICTDRIDLI 242 (249)
T ss_pred HHHHHHHHHCCCEEEEEeCCCHHHHHHHHHcC-CCEEEeCChHhc
Confidence 45777788888888776544455666777776 788888777754
No 94
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=42.30 E-value=45 Score=23.62 Aligned_cols=28 Identities=7% Similarity=0.017 Sum_probs=23.9
Q ss_pred HHHHHHHHhhcchHHHHHhhhhcccchH
Q psy11827 41 KAKAAELLILDRGSEAQSHLRQSVDVTH 68 (336)
Q Consensus 41 ~~~a~~~~~~g~~~~a~~~f~~~~~it~ 68 (336)
...|..++..|+.++|..+|.+++.+.|
T Consensus 7 ~~~g~~~~~~~~~~~A~~~~~~ai~~~p 34 (69)
T PF13414_consen 7 YNLGQIYFQQGDYEEAIEYFEKAIELDP 34 (69)
T ss_dssp HHHHHHHHHTTHHHHHHHHHHHHHHHST
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHcCC
Confidence 4567778899999999999999988876
No 95
>cd08568 GDPD_TmGDE_like Glycerophosphodiester phosphodiesterase domain of Thermotoga maritime and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermotoga maritime glycerophosphodiester phosphodiesterase (TmGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. TmGDE exists as a monomer that might be the biologically relevant form.
Probab=42.30 E-value=35 Score=30.99 Aligned_cols=42 Identities=19% Similarity=0.273 Sum_probs=30.7
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCce
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDL 115 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDl 115 (336)
..+.+.+++.|+++.+---.-..++..|. .+ ||+|+|++-|.
T Consensus 184 ~~~v~~~~~~G~~v~~WTvn~~~~~~~l~-~~-vdgiiTD~p~~ 225 (226)
T cd08568 184 VELLRLLRKLGLKIVLWTVNDPELVPKLK-GL-VDGVITDDVEK 225 (226)
T ss_pred HHHHHHHHHCCCEEEEEcCCCHHHHHHHH-hh-CCEEEccCccc
Confidence 46778889999999886533335555665 46 99999987764
No 96
>PF03009 GDPD: Glycerophosphoryl diester phosphodiesterase family; InterPro: IPR004129 Glycerophosphoryl diester phosphodiesterases display broad specificity for glycerophosphodiesters; glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol, and bis(glycerophosphoglycerol) all of which are are hydrolysed by this enzyme.; GO: 0008889 glycerophosphodiester phosphodiesterase activity, 0006071 glycerol metabolic process; PDB: 3I10_A 2P76_H 2OOG_F 3KS6_D 3KS5_A 2PZ0_B 1YDY_B 1T8Q_A 1O1Z_A 3L12_B ....
Probab=41.08 E-value=30 Score=30.89 Aligned_cols=41 Identities=24% Similarity=0.289 Sum_probs=28.7
Q ss_pred HHHHHHHHcCCceecCccchH--HHHHHHHHcCCeEEEecCCCc
Q psy11827 73 NVIQACRARGVDCIVAPFEAD--AQMAYLNIAGYADYVITEDSD 114 (336)
Q Consensus 73 ~l~~~L~~~gV~~ivAPyEAD--AQlA~L~~~g~vdaViT~DSD 114 (336)
.+++.++..|+.+.+.-..-+ +++.+|.+.| ||+|+|++-|
T Consensus 213 ~~v~~~~~~g~~v~~wtvn~~~~~~~~~l~~~g-vdgIiTD~P~ 255 (256)
T PF03009_consen 213 RLVQEAHKAGLKVYVWTVNDPDVEDMKRLLDLG-VDGIITDFPD 255 (256)
T ss_dssp HHHHHHHHTT-EEEEBSB-SHSHHHHHHHHHHT--SEEEES-HH
T ss_pred HHHHHHHHCCCEEEEEecCCcHHHHHHHHHhCC-CCEEEEcCCC
Confidence 478888999999988765544 7777777776 8899987643
No 97
>KOG0547|consensus
Probab=40.81 E-value=23 Score=36.74 Aligned_cols=43 Identities=19% Similarity=0.205 Sum_probs=34.5
Q ss_pred hhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHH
Q psy11827 27 EATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHK 69 (336)
Q Consensus 27 ~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~ 69 (336)
..+-++|.+.......++..++++|+.++|.++|.+++...|.
T Consensus 105 a~~~e~~~k~A~~lK~~GN~~f~~kkY~eAIkyY~~AI~l~p~ 147 (606)
T KOG0547|consen 105 AMLKEERLKYAAALKTKGNKFFRNKKYDEAIKYYTQAIELCPD 147 (606)
T ss_pred ccChHHHHHHHHHHHhhhhhhhhcccHHHHHHHHHHHHhcCCC
Confidence 3455667666677778888999999999999999999877664
No 98
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=40.27 E-value=22 Score=38.39 Aligned_cols=28 Identities=11% Similarity=0.059 Sum_probs=23.7
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcHHHHHHHH
Q psy11827 170 TGIKGMGLKKAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~~~~~si~~vl~~~ 199 (336)
..|||||++++.+|++.|+ |++++...-
T Consensus 640 ~~IPGIGpkr~k~LL~~FG--Sle~I~~AS 667 (694)
T PRK14666 640 QRVEGIGPATARLLWERFG--SLQAMAAAG 667 (694)
T ss_pred hhCCCCCHHHHHHHHHHhC--CHHHHHhcC
Confidence 4799999999999999998 677776643
No 99
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=39.50 E-value=17 Score=33.17 Aligned_cols=42 Identities=21% Similarity=0.252 Sum_probs=26.7
Q ss_pred cCCCCHH-HHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCCcHHHHHHHH
Q psy11827 149 LAKFTDA-KFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDPDFENALRKI 199 (336)
Q Consensus 149 ~~~lt~~-qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~si~~vl~~~ 199 (336)
.+||... .=..|..| -++.|||||+|+.++.... ...+...+
T Consensus 60 LyGF~~~~ER~lF~~L------isVnGIGpK~ALaiLs~~~---~~~l~~aI 102 (201)
T COG0632 60 LYGFLTEEERELFRLL------ISVNGIGPKLALAILSNLD---PEELAQAI 102 (201)
T ss_pred HcCCCCHHHHHHHHHH------HccCCccHHHHHHHHcCCC---HHHHHHHH
Confidence 6787533 22233333 3799999999999998753 44444444
No 100
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=39.10 E-value=37 Score=27.47 Aligned_cols=35 Identities=17% Similarity=0.172 Sum_probs=27.3
Q ss_pred HHHHHcCCcee--cCccc-hHHHHHHHHHc-CCeEEEec
Q psy11827 76 QACRARGVDCI--VAPFE-ADAQMAYLNIA-GYADYVIT 110 (336)
Q Consensus 76 ~~L~~~gV~~i--vAPyE-ADAQlA~L~~~-g~vdaViT 110 (336)
+.|++.||++. ..+.| .+.|+..+.++ |.+|.||.
T Consensus 36 ~~L~~~Gi~~~~v~~~~~~g~~~i~~~i~~~g~idlVIn 74 (112)
T cd00532 36 RVLADAGIPVRAVSKRHEDGEPTVDAAIAEKGKFDVVIN 74 (112)
T ss_pred HHHHHcCCceEEEEecCCCCCcHHHHHHhCCCCEEEEEE
Confidence 34567898875 34667 68999999999 99999984
No 101
>PF13181 TPR_8: Tetratricopeptide repeat; PDB: 3GW4_B 3MA5_C 2KCV_A 2KCL_A 3FP3_A 3LCA_A 3FP4_A 3FP2_A 1W3B_B 1ELW_A ....
Probab=39.00 E-value=25 Score=21.39 Aligned_cols=27 Identities=11% Similarity=0.044 Sum_probs=20.9
Q ss_pred HHHHHHHhhcchHHHHHhhhhcccchH
Q psy11827 42 AKAAELLILDRGSEAQSHLRQSVDVTH 68 (336)
Q Consensus 42 ~~a~~~~~~g~~~~a~~~f~~~~~it~ 68 (336)
..|..+...|+.++|.++|.+++.+.|
T Consensus 6 ~lg~~y~~~~~~~~A~~~~~~a~~~~~ 32 (34)
T PF13181_consen 6 NLGKIYEQLGDYEEALEYFEKALELNP 32 (34)
T ss_dssp HHHHHHHHTTSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHhhCC
Confidence 345566778999999999998876544
No 102
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=38.41 E-value=28 Score=32.97 Aligned_cols=26 Identities=27% Similarity=0.355 Sum_probs=22.5
Q ss_pred CCCCCCHHHHHHHHHHcCCCcHHHHHHH
Q psy11827 171 GIKGMGLKKAKDYVFSIMDPDFENALRK 198 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~~si~~vl~~ 198 (336)
++||||.+.|..+++.++ |+.+++..
T Consensus 186 s~pgig~~~a~~ll~~fg--S~~~~~ta 211 (254)
T COG1948 186 SIPGIGPKLAERLLKKFG--SVEDVLTA 211 (254)
T ss_pred cCCCccHHHHHHHHHHhc--CHHHHhhc
Confidence 799999999999999998 57776654
No 103
>PF13428 TPR_14: Tetratricopeptide repeat
Probab=38.25 E-value=31 Score=22.79 Aligned_cols=28 Identities=25% Similarity=0.259 Sum_probs=23.1
Q ss_pred HHHHHHHhhcchHHHHHhhhhcccchHH
Q psy11827 42 AKAAELLILDRGSEAQSHLRQSVDVTHK 69 (336)
Q Consensus 42 ~~a~~~~~~g~~~~a~~~f~~~~~it~~ 69 (336)
.-|..+.+.|+.++|.+.|++++...|+
T Consensus 6 ~la~~~~~~G~~~~A~~~~~~~l~~~P~ 33 (44)
T PF13428_consen 6 ALARAYRRLGQPDEAERLLRRALALDPD 33 (44)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 4566788899999999999998877663
No 104
>cd08575 GDPD_GDE4_like Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE4 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1)) and similar proteins. Mammalian GDE4 is a transmembrane protein whose cellular function is not elucidated. It is expressed widely, including in placenta, liver, kidney, pancreas, spleen, thymus, ovary, small intestine and peripheral blood leukocytes. It is also expressed in the growth cones in neuroblastoma Neuro2a cells, which suggests mammalian GDE4 may play some distinct role from other members of mammalian GDEs family. Also included in this subfamily are uncharacterized mammalian glycerophosphodiester phosphodiesterase domain-containing protein 3 (GDPD3) and similar proteins which display very high sequence homology to mammalian GDE4.
Probab=37.67 E-value=42 Score=31.45 Aligned_cols=43 Identities=21% Similarity=0.262 Sum_probs=33.5
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCce
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDL 115 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDl 115 (336)
..+++.++..|+++.+---.-..++..|.+.| ||+|+|..-|.
T Consensus 221 ~~~v~~~~~~G~~v~vWTVNd~~~~~~l~~~G-VdgIiTD~P~~ 263 (264)
T cd08575 221 PNLFDHLRKRGIQVYLWVLNDEEDFEEAFDLG-ADGVMTDSPTK 263 (264)
T ss_pred HHHHHHHHhcCCcEEEEEECCHHHHHHHHhcC-CCEEEeCCccc
Confidence 35677788899998886655566777888887 99999987764
No 105
>cd08567 GDPD_SpGDE_like Glycerophosphodiester phosphodiesterase domain of putative Silicibacter pomeroyi glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46) and similar proteins. The prototype of this CD is a putative GP-GDE from Silicibacter pomeroyi (SpGDE). It shows high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=37.37 E-value=54 Score=30.17 Aligned_cols=42 Identities=24% Similarity=0.292 Sum_probs=29.6
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCc
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSD 114 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSD 114 (336)
..+++.+++.|+++.+-.-.-..++.+|...| ||+|+|..-|
T Consensus 221 ~~~i~~~~~~G~~v~vwtvn~~~~~~~~~~~G-vdgi~TD~P~ 262 (263)
T cd08567 221 KELVDEAHALGLKVVPWTVNDPEDMARLIDLG-VDGIITDYPD 262 (263)
T ss_pred HHHHHHHHHCCCEEEEecCCCHHHHHHHHHcC-CCEEEcCCCC
Confidence 45777888889888875544344666666665 8899887655
No 106
>PF01850 PIN: PIN domain; InterPro: IPR002716 The PilT protein, N-terminal domain (PIN) is a compact domain of about 100 amino acids. The domain has two nearly invariant aspartates and forms a coiled-coil with other monomer units to polymerise a pilus fibre []. The function of the PIN domain is unknown but a role in signalling appears likely given the presence of this domain in some bacterial plasmid stability proteins and Dis3 from yeast that is implicated in mitotic control [].; PDB: 3TND_G 2H1O_B 2BSQ_B 2H1C_A 2FE1_A 3ZVK_C 1V8P_F 1V8O_C 3H87_A 1O4W_A ....
Probab=37.26 E-value=30 Score=27.13 Aligned_cols=47 Identities=26% Similarity=0.152 Sum_probs=36.0
Q ss_pred ccchHHHHHHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCceE
Q psy11827 64 VDVTHKMALNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLL 116 (336)
Q Consensus 64 ~~it~~m~~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll 116 (336)
..++.+......++....+ ..-+|+.++.+++..-++.|+|.|.|+.
T Consensus 70 ~~~~~~~~~~~~~~~~~~~------~~~~Da~~~a~A~~~~~~~v~T~D~~f~ 116 (121)
T PF01850_consen 70 LPITSEVFERAAELMRKYG------LDFADALIAATAKENGAPLVVTFDKDFR 116 (121)
T ss_dssp EEBCHHHHHHHHHHHHHHH------SSHHHHHHHHHHHHHT-EEE-ESSHHHH
T ss_pred ccchhHHHHHHHHHHHhcc------CChhHHHHHHHHHHcCCEEEEECCcCHH
Confidence 4566777777777777776 5679999999999888888889999853
No 107
>PF02677 DUF208: Uncharacterized BCR, COG1636; InterPro: IPR003828 This entry describes proteins of unknown function.
Probab=34.78 E-value=1.4e+02 Score=26.82 Aligned_cols=56 Identities=14% Similarity=0.158 Sum_probs=37.8
Q ss_pred HHHHHHhCCCEEEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHHcC
Q psy11827 3 YIHMLLAHKIKVIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRARG 82 (336)
Q Consensus 3 ~i~~L~~~gI~PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~~g 82 (336)
-|+.|++.|++|...|=.+..--.. +..+|+ .+++++.+.+|
T Consensus 14 ~~~~L~~~g~~vt~~fyNPNIhP~~-Ey~~R~-------------------------------------~~~~~~~~~~~ 55 (176)
T PF02677_consen 14 PLERLREEGFDVTGYFYNPNIHPYE-EYERRL-------------------------------------EELKRFAEKLG 55 (176)
T ss_pred HHHHHHHCCCCeEEEEeCCCCCcHH-HHHHHH-------------------------------------HHHHHHHHHcC
Confidence 3678999999999888887763211 122221 23555667779
Q ss_pred CceecCccchHHHH
Q psy11827 83 VDCIVAPFEADAQM 96 (336)
Q Consensus 83 V~~ivAPyEADAQl 96 (336)
|++|+++|.-+.=+
T Consensus 56 i~~i~~~Y~~~~w~ 69 (176)
T PF02677_consen 56 IPLIEGDYDPEEWL 69 (176)
T ss_pred CCEEecCCCHHHHH
Confidence 99999999866533
No 108
>cd08561 GDPD_cytoplasmic_ScUgpQ2_like Glycerophosphodiester phosphodiesterase domain of Streptomyces coelicolor cytoplasmic phosphodiesterases UgpQ2 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized cytoplasmic phosphodiesterases which predominantly exist in bacteria. The prototype of this family is a putative cytoplasmic phosphodiesterase encoded by gene ulpQ2 (SCO1419) in the Streptomyces coelicolor genome. It is distantly related to the Escherichia coli cytoplasmic phosphodiesterases UgpQ that catalyzes the hydrolysis of glycerophosphodiesters at the inner side of the cytoplasmic membrane to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=34.54 E-value=33 Score=31.58 Aligned_cols=44 Identities=32% Similarity=0.390 Sum_probs=32.2
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCceE
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLL 116 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll 116 (336)
..+++.++..|+++.+.--.-.+++..|.+.| ||+|+|...+.+
T Consensus 202 ~~~v~~~~~~G~~v~vWTVN~~~~~~~l~~~g-VdgIiTD~p~~~ 245 (249)
T cd08561 202 PRFVRAAHAAGLEVHVWTVNDPAEMRRLLDLG-VDGIITDRPDLL 245 (249)
T ss_pred HHHHHHHHHCCCEEEEEecCCHHHHHHHHhcC-CCEEEcCCHHHH
Confidence 46777888889988887655566666666665 789998776643
No 109
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=33.93 E-value=81 Score=27.21 Aligned_cols=45 Identities=18% Similarity=0.283 Sum_probs=34.3
Q ss_pred cchHHHHHHHHHHHHHcCCc-----eecCc--cchHHHHHHHHHcCCeEEEe
Q psy11827 65 DVTHKMALNVIQACRARGVD-----CIVAP--FEADAQMAYLNIAGYADYVI 109 (336)
Q Consensus 65 ~it~~m~~~l~~~L~~~gV~-----~ivAP--yEADAQlA~L~~~g~vdaVi 109 (336)
.|+..|..-..+.|+..|++ .+.-| ||-=..+..|.++|..|+|+
T Consensus 20 ~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~~~DavI 71 (141)
T PLN02404 20 IITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAIL 71 (141)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcCCCCEEE
Confidence 46778888889999999874 44456 67666677788888888886
No 110
>cd08562 GDPD_EcUgpQ_like Glycerophosphodiester phosphodiesterase domain in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase UgpQ and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Escherichia coli cytosolic glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46), UgpQ, and similar proteins. GP-GDE plays an essential role in the metabolic pathway of E. coli. It catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols, which are major sources of carbon and phosphate. E. coli possesses two major G3P uptake systems: Glp and Ugp, which contain genes coding for two distinct GP-GDEs. UgpQ gene from the E. coli ugp operon codes for a cytosolic phosphodiesterase GlpQ, which is the prototype of this family. Various glycerophosphodiesters, such as glycerophosphocholine (GPC), glycerophosphoethanolanmine (GPE), glycerophosphoglycerol (GPG)
Probab=33.57 E-value=63 Score=29.03 Aligned_cols=40 Identities=23% Similarity=0.238 Sum_probs=29.4
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCC
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITED 112 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~D 112 (336)
..+++.++..|+++.+.---..+++.+|.+.| ||+|+|..
T Consensus 189 ~~~v~~~~~~g~~v~~wTvn~~~~~~~~~~~g-VdgiiTD~ 228 (229)
T cd08562 189 EEQVKALKDAGYKLLVYTVNDPARAAELLEWG-VDAIFTDR 228 (229)
T ss_pred HHHHHHHHHCCCEEEEEeCCCHHHHHHHHHCC-CCEEEcCC
Confidence 45777888888888876555566777777776 88888753
No 111
>cd08582 GDPD_like_2 Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in a group of uncharacterized bacterial glycerophosphodiester phosphodiesterase and similar proteins. They show high sequence similarity to Escherichia coli glycerophosphodiester phosphodiesterase, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=33.20 E-value=68 Score=29.12 Aligned_cols=41 Identities=22% Similarity=0.207 Sum_probs=27.4
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCC
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDS 113 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DS 113 (336)
..+++.++..|+++.+-.---.+++.+|.+.| ||+|+|..-
T Consensus 191 ~~~v~~~~~~G~~v~~wTvn~~~~~~~l~~~G-Vdgi~TD~p 231 (233)
T cd08582 191 PAFIKALRDAGLKLNVWTVDDAEDAKRLIELG-VDSITTNRP 231 (233)
T ss_pred HHHHHHHHHCCCEEEEEeCCCHHHHHHHHHCC-CCEEEcCCC
Confidence 35666777788887765444456667777666 778887654
No 112
>smart00028 TPR Tetratricopeptide repeats. Repeats present in 4 or more copies in proteins. Contain a minimum of 34 amino acids each and self-associate via a "knobs and holes" mechanism.
Probab=33.15 E-value=35 Score=18.66 Aligned_cols=25 Identities=16% Similarity=0.162 Sum_probs=18.2
Q ss_pred HHHHHHhhcchHHHHHhhhhcccch
Q psy11827 43 KAAELLILDRGSEAQSHLRQSVDVT 67 (336)
Q Consensus 43 ~a~~~~~~g~~~~a~~~f~~~~~it 67 (336)
.|..+...|+.++|..+|++++.+.
T Consensus 7 ~a~~~~~~~~~~~a~~~~~~~~~~~ 31 (34)
T smart00028 7 LGNAYLKLGDYDEALEYYEKALELD 31 (34)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHccC
Confidence 4556667788888888888776554
No 113
>PRK05234 mgsA methylglyoxal synthase; Validated
Probab=32.69 E-value=52 Score=28.22 Aligned_cols=34 Identities=24% Similarity=0.236 Sum_probs=25.7
Q ss_pred HHHHHc-CCceecCccc---hHHHHHHHHHcCCeEEEe
Q psy11827 76 QACRAR-GVDCIVAPFE---ADAQMAYLNIAGYADYVI 109 (336)
Q Consensus 76 ~~L~~~-gV~~ivAPyE---ADAQlA~L~~~g~vdaVi 109 (336)
+.|++. |+++..-.++ .+.|++.+.++|.+|+||
T Consensus 43 ~~L~~~~Gi~v~~vi~~~~gg~~~i~~~I~~g~i~lVI 80 (142)
T PRK05234 43 GLIQEATGLDVTRLLSGPLGGDQQIGALIAEGKIDMLI 80 (142)
T ss_pred HHHHhccCCeeEEEEcCCCCCchhHHHHHHcCceeEEE
Confidence 456677 8876432445 789999999999999987
No 114
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=32.52 E-value=30 Score=27.82 Aligned_cols=17 Identities=29% Similarity=0.380 Sum_probs=15.1
Q ss_pred CCCCCCCHHHHHHHHHH
Q psy11827 170 TGIKGMGLKKAKDYVFS 186 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~ 186 (336)
..|||||+.+|.+|..-
T Consensus 15 ~~iP~IG~a~a~DL~~L 31 (93)
T PF11731_consen 15 TDIPNIGKATAEDLRLL 31 (93)
T ss_pred hcCCCccHHHHHHHHHc
Confidence 47999999999999965
No 115
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=32.49 E-value=37 Score=36.86 Aligned_cols=33 Identities=24% Similarity=0.200 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHcCCC
Q psy11827 152 FTDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSIMDP 190 (336)
Q Consensus 152 lt~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~~~~ 190 (336)
-+.+.++.+.. +| .|||||+++|.+++..||..
T Consensus 75 ~~~~~i~~yL~-s~-----~~~GIG~~~A~~iv~~fg~~ 107 (720)
T TIGR01448 75 TSKEGIVAYLS-SR-----SIKGVGKKLAQRIVKTFGEA 107 (720)
T ss_pred CCHHHHHHHHh-cC-----CCCCcCHHHHHHHHHHhCHh
Confidence 35666666432 22 49999999999999999854
No 116
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=32.37 E-value=28 Score=28.92 Aligned_cols=17 Identities=29% Similarity=0.362 Sum_probs=15.7
Q ss_pred CCCCCCHHHHHHHHHHc
Q psy11827 171 GIKGMGLKKAKDYVFSI 187 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~ 187 (336)
.+||||+++|.++|..+
T Consensus 72 ~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 72 ALPGIGPAKAKAIIEYR 88 (120)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 69999999999999875
No 117
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=31.90 E-value=48 Score=29.23 Aligned_cols=46 Identities=26% Similarity=0.389 Sum_probs=33.1
Q ss_pred HHHHHHHHcCCceecCccchHHHHHH--H--HHcCCeEE--EecCCCceEee
Q psy11827 73 NVIQACRARGVDCIVAPFEADAQMAY--L--NIAGYADY--VITEDSDLLVF 118 (336)
Q Consensus 73 ~l~~~L~~~gV~~ivAPyEADAQlA~--L--~~~g~vda--ViT~DSDll~f 118 (336)
.+++.|+..|++.+...+..|-.|+- | .-++.+|. ++|+|||+.-.
T Consensus 70 ~l~~~l~~~Gf~pv~~kG~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~L 121 (160)
T TIGR00288 70 KLIEAVVNQGFEPIIVAGDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPV 121 (160)
T ss_pred HHHHHHHHCCceEEEecCcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHH
Confidence 56889999999987666788877764 2 22465554 58999997543
No 118
>PRK08609 hypothetical protein; Provisional
Probab=31.79 E-value=57 Score=34.44 Aligned_cols=27 Identities=22% Similarity=0.148 Sum_probs=21.1
Q ss_pred CCCCCCHHHHHHHHHHcCCCcHHHHHH
Q psy11827 171 GIKGMGLKKAKDYVFSIMDPDFENALR 197 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~~si~~vl~ 197 (336)
.|||||||||.++-+..|-.+++.+-.
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~ 118 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKE 118 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHH
Confidence 799999999999998776555555443
No 119
>cd08601 GDPD_SaGlpQ_like Glycerophosphodiester phosphodiesterase domain of Staphylococcus aureus and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized glycerophosphodiester phosphodiesterase (GP-GDE, EC 3.1.4.46) from Staphylococcus aureus, Bacillus subtilis and similar proteins. Members in this family show very high sequence similarity to Escherichia coli periplasmic phosphodiesterase GlpQ, which catalyzes the Ca2+-dependent degradation of periplasmic glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=31.77 E-value=39 Score=31.22 Aligned_cols=44 Identities=20% Similarity=0.136 Sum_probs=32.4
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCceE
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLL 116 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll 116 (336)
..+++.++..|+++.+-.-.-.+++..|...| ||+|+|...|++
T Consensus 208 ~~~v~~~~~~g~~v~~wTvn~~~~~~~l~~~G-vd~IiTD~p~~~ 251 (256)
T cd08601 208 PWMVHLIHKKGLLVHPYTVNEKADMIRLINWG-VDGMFTNYPDRL 251 (256)
T ss_pred HHHHHHHHHCCCEEEEEecCCHHHHHHHHhcC-CCEEEeCCHHHH
Confidence 45777888889888876655566677777776 889998777644
No 120
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=31.60 E-value=81 Score=25.17 Aligned_cols=35 Identities=17% Similarity=0.127 Sum_probs=27.3
Q ss_pred HHHHHcCCcee--cCccchHHHHHHHHHcCCeEEEec
Q psy11827 76 QACRARGVDCI--VAPFEADAQMAYLNIAGYADYVIT 110 (336)
Q Consensus 76 ~~L~~~gV~~i--vAPyEADAQlA~L~~~g~vdaViT 110 (336)
+.|+..|+++- ..+.+++.++..+.++|.+|.|+.
T Consensus 37 ~~l~~~gi~~~~v~~~~~~~~~i~~~i~~~~id~vIn 73 (110)
T cd01424 37 KYLQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVIN 73 (110)
T ss_pred HHHHHcCCeEEEEeecCCCchhHHHHHHcCCeEEEEE
Confidence 35667888864 345678899999999999999985
No 121
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=30.78 E-value=89 Score=27.28 Aligned_cols=46 Identities=28% Similarity=0.368 Sum_probs=34.3
Q ss_pred cchHHHHHHHHHHHHHcCC-----ceecCc--cchHHHHHHHHHcCCeEEEec
Q psy11827 65 DVTHKMALNVIQACRARGV-----DCIVAP--FEADAQMAYLNIAGYADYVIT 110 (336)
Q Consensus 65 ~it~~m~~~l~~~L~~~gV-----~~ivAP--yEADAQlA~L~~~g~vdaViT 110 (336)
.|+..|....++.|+..|+ ..+.-| ||-=..+..|.+++..|+|++
T Consensus 25 ~i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavIa 77 (154)
T PRK00061 25 FITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIA 77 (154)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEEE
Confidence 4677888889999999884 444456 666666677888888888873
No 122
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=30.29 E-value=89 Score=25.98 Aligned_cols=49 Identities=22% Similarity=0.308 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHcCCceecCcc--------chHHHHHH----HHHcC--CeEEEecCCCceEee
Q psy11827 70 MALNVIQACRARGVDCIVAPF--------EADAQMAY----LNIAG--YADYVITEDSDLLVF 118 (336)
Q Consensus 70 m~~~l~~~L~~~gV~~ivAPy--------EADAQlA~----L~~~g--~vdaViT~DSDll~f 118 (336)
-...+.+.|+..|+.++..|. .+|..|+. ++..+ -+-.++|+|+|+...
T Consensus 53 ~~~~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~ 115 (149)
T cd06167 53 RQRGFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPL 115 (149)
T ss_pred hHHHHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHH
Confidence 456688899999999998772 48888764 22232 244568999997643
No 123
>cd08555 PI-PLCc_GDPD_SF Catalytic domain of phosphoinositide-specific phospholipase C-like phosphodiesterases superfamily. The PI-PLC-like phosphodiesterases superfamily represents the catalytic domains of bacterial phosphatidylinositol-specific phospholipase C (PI-PLC, EC 4.6.1.13), eukaryotic phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11), glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria, as well as their uncharacterized homologs found in organisms ranging from bacteria and archaea to metazoans, plants, and fungi. PI-PLCs are ubiquitous enzymes hydrolyzing the membrane lipid phosphoinositides to yield two important second messengers, inositol phosphates and diacylglycerol (DAG). GP-GDEs play essential roles in glycerol metabolism and catalyze the hydrolysis of glycerophosph
Probab=29.55 E-value=80 Score=27.56 Aligned_cols=39 Identities=15% Similarity=0.179 Sum_probs=30.7
Q ss_pred HHHHHHHHHcCCceecCccch-HHHHHHHHHcCCeEEEecC
Q psy11827 72 LNVIQACRARGVDCIVAPFEA-DAQMAYLNIAGYADYVITE 111 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEA-DAQlA~L~~~g~vdaViT~ 111 (336)
..+++.+++.|.++.+-...- ...+.+|.+.| ||+|+|.
T Consensus 139 ~~~v~~~~~~g~~v~~wtvn~~~~~~~~l~~~G-vd~i~TD 178 (179)
T cd08555 139 TELIASANKLGLLSRIWTVNDNNEIINKFLNLG-VDGLITD 178 (179)
T ss_pred HHHHHHHHHCCCEEEEEeeCChHHHHHHHHHcC-CCEEeCC
Confidence 456777888999999887654 77777888888 9999974
No 124
>KOG0967|consensus
Probab=29.49 E-value=40 Score=36.01 Aligned_cols=97 Identities=22% Similarity=0.249 Sum_probs=53.1
Q ss_pred EEEEecCCCCccchhhHHHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHH---c---C--Cce
Q psy11827 14 VIMVFDGRHLPAKEATEEDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRA---R---G--VDC 85 (336)
Q Consensus 14 PifVFDG~~~p~K~~t~~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~---~---g--V~~ 85 (336)
.|||||+..+....-....=++||+ .+.+..+ +.-.+|+.+..++-.+..++.+.|.+ . | |..
T Consensus 460 cvf~FDily~ng~~Li~~pL~eRR~-------~l~e~f~--e~~g~f~fat~~~tn~~~eiq~Fl~~sv~~~cEGlMvKt 530 (714)
T KOG0967|consen 460 CVFVFDILYLNGESLIQEPLRERRE-------LLHESFK--EIPGEFQFATSLDTNDIDEIQEFLEESVQNSCEGLMVKT 530 (714)
T ss_pred EEEEEeeeeeCChhhhhhhHHHHHH-------HHHhhcc--cCCCceeEeeeeccCCHHHHHHHHHHhhccCcceeEEEe
Confidence 5899999988665432221112221 1122222 22345666666666666666666554 1 1 111
Q ss_pred e--cCccchHHHHHHHHH--cCCeEEEecCCCceEeecc
Q psy11827 86 I--VAPFEADAQMAYLNI--AGYADYVITEDSDLLVFGA 120 (336)
Q Consensus 86 i--vAPyEADAQlA~L~~--~g~vdaViT~DSDll~fg~ 120 (336)
+ -|-||-.--=.++.+ +.|+|+|. ..-||.+.|+
T Consensus 531 Ld~~atYep~kRs~~WlKlKkDYldgvg-dslDLv~iga 568 (714)
T KOG0967|consen 531 LDTNATYEPSKRSNNWLKLKKDYLDGVG-DSLDLVVIGA 568 (714)
T ss_pred eccccccCchhhccchhhhhhhhhcccc-cceeeeeeee
Confidence 1 256665544444444 78999986 6678888776
No 125
>cd08564 GDPD_GsGDE_like Glycerophosphodiester phosphodiesterase domain of putative Galdieria sulphuraria glycerophosphodiester phosphodiesterase and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in putative Galdieria sulphuraria glycerophosphodiester phosphodiesterase (GsGDE, EC 3.1.4.46) and its uncharacterized eukaryotic homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols.
Probab=28.63 E-value=53 Score=30.64 Aligned_cols=45 Identities=13% Similarity=0.211 Sum_probs=32.1
Q ss_pred HHHHHHHHHHcCCceecCc----cchHHHHHHHHHcCCeEEEecCCCceE
Q psy11827 71 ALNVIQACRARGVDCIVAP----FEADAQMAYLNIAGYADYVITEDSDLL 116 (336)
Q Consensus 71 ~~~l~~~L~~~gV~~ivAP----yEADAQlA~L~~~g~vdaViT~DSDll 116 (336)
...+++.++..|+.+.+.- ....+++.+|...| ||+|+|...|++
T Consensus 212 ~~~~v~~~~~~Gl~v~~wT~~~~~n~~~~~~~l~~~G-vdgiiTD~p~~~ 260 (265)
T cd08564 212 TEEFVKKAHENGLKVMTYFDEPVNDNEEDYKVYLELG-VDCICPNDPVLL 260 (265)
T ss_pred hHHHHHHHHHcCCEEEEecCCCCCCCHHHHHHHHHcC-CCEEEcCCHHHH
Confidence 3567778888999877653 23356677777777 789998877654
No 126
>cd08563 GDPD_TtGDE_like Glycerophosphodiester phosphodiesterase domain of Thermoanaerobacter tengcongensis and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Thermoanaerobacter tengcongensis glycerophosphodiester phosphodiesterase (TtGDE, EC 3.1.4.46) and its uncharacterized homologs. Members in this family show high sequence similarity to Escherichia coli GP-GDE, which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Despite the fact that most of GDPD family members exist as the monomer, TtGDE can function as a dimeric unit. Its catalytic mechanism is based on the general base-acid catalysis, which is similar to that of phosphoinositide-specific phospholipases C (PI-PLCs, EC 3.1.4.11). A divalent metal cation is required for the enzyme activity of TtGDE.
Probab=28.46 E-value=86 Score=28.36 Aligned_cols=39 Identities=23% Similarity=0.353 Sum_probs=24.1
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecC
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITE 111 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~ 111 (336)
..+++.+++.|+++.+---.-..++..|.+.| ||+|+|.
T Consensus 190 ~~~i~~~~~~g~~v~~Wtvn~~~~~~~~~~~G-Vdgi~TD 228 (230)
T cd08563 190 EEVVEELKKRGIPVRLWTVNEEEDMKRLKDLG-VDGIITN 228 (230)
T ss_pred HHHHHHHHHCCCEEEEEecCCHHHHHHHHHCC-CCEEeCC
Confidence 45666777777777765444445555566555 5777764
No 127
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=28.43 E-value=55 Score=26.42 Aligned_cols=35 Identities=20% Similarity=0.275 Sum_probs=31.1
Q ss_pred CHHHHHHHHHHhCCCCCCCCCCCCHHHHHHHHHHc
Q psy11827 153 TDAKFRYMCILSGCDYWTGIKGMGLKKAKDYVFSI 187 (336)
Q Consensus 153 t~~qf~~~~iL~GcDy~~~ipgiG~ktA~kli~~~ 187 (336)
|-..+++.+-..|.-...+|||+|.+.|..+..-.
T Consensus 36 TL~dL~~~i~~rg~~Wwr~vpglG~~~A~~I~awL 70 (96)
T PF12482_consen 36 TLADLVDRINRRGGRWWRAVPGLGAAGARRIEAWL 70 (96)
T ss_pred hHHHHHHHHHHccchHHHhCcccchHHHHHHHHHH
Confidence 77899999999998888999999999998887653
No 128
>PF09868 DUF2095: Uncharacterized protein conserved in archaea (DUF2095); InterPro: IPR018662 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=28.38 E-value=49 Score=27.77 Aligned_cols=32 Identities=16% Similarity=0.137 Sum_probs=26.8
Q ss_pred HHhhhhcccchHHHHHHHHHHHHHcCCceecC
Q psy11827 57 QSHLRQSVDVTHKMALNVIQACRARGVDCIVA 88 (336)
Q Consensus 57 ~~~f~~~~~it~~m~~~l~~~L~~~gV~~ivA 88 (336)
.++|.+...||++++..|...|+..||.++..
T Consensus 84 Inylek~GEIt~e~A~eLr~~L~~kGvr~fG~ 115 (128)
T PF09868_consen 84 INYLEKRGEITPEEAKELRSILVKKGVRSFGS 115 (128)
T ss_pred HHHHHHhCCCCHHHHHHHHHHHHHhhHHHhCC
Confidence 45677788899999999999999999987654
No 129
>KOG4234|consensus
Probab=28.17 E-value=74 Score=29.65 Aligned_cols=48 Identities=19% Similarity=0.142 Sum_probs=33.6
Q ss_pred HhhhhhhHHHHHHHHhhcchHHHHHhhhhcccchHHHHHHHHHHHHHc
Q psy11827 34 RKKRDSHKAKAAELLILDRGSEAQSHLRQSVDVTHKMALNVIQACRAR 81 (336)
Q Consensus 34 ~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~~it~~m~~~l~~~L~~~ 81 (336)
..........+.++..+|+.++|.+.|+.++.+.|..-..+..+|-..
T Consensus 92 ~~kad~lK~EGN~~F~ngdyeeA~skY~~Ale~cp~~~~e~rsIly~N 139 (271)
T KOG4234|consen 92 IEKADSLKKEGNELFKNGDYEEANSKYQEALESCPSTSTEERSILYSN 139 (271)
T ss_pred HHHHHHHHHHHHHhhhcccHHHHHHHHHHHHHhCccccHHHHHHHHhh
Confidence 333344455666778889999999999999887776666666665443
No 130
>PF07219 HemY_N: HemY protein N-terminus; InterPro: IPR010817 This entry represents the N terminus (approximately 150 residues) of bacterial HemY porphyrin biosynthesis proteins. These are membrane protein involved in a late step of protoheme IX synthesis [].
Probab=27.58 E-value=78 Score=25.52 Aligned_cols=34 Identities=18% Similarity=0.169 Sum_probs=25.8
Q ss_pred HHHHhhhhhhHHHHHHHHhhcchHHHHHhhhhcc
Q psy11827 31 EDRRKKRDSHKAKAAELLILDRGSEAQSHLRQSV 64 (336)
Q Consensus 31 ~~R~~~r~~~~~~a~~~~~~g~~~~a~~~f~~~~ 64 (336)
..|+++.++++.++...+.+|+.+.|.+...++.
T Consensus 53 ~rr~~ka~~al~~Gl~al~~G~~~~A~k~~~~a~ 86 (108)
T PF07219_consen 53 RRRRRKAQRALSRGLIALAEGDWQRAEKLLAKAA 86 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3344455667788888999999999998887664
No 131
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=27.13 E-value=74 Score=27.89 Aligned_cols=34 Identities=18% Similarity=0.088 Sum_probs=28.6
Q ss_pred HHHHHHHHHhCCCCCC---------CCCCCCHHHHHHHHHHcC
Q psy11827 155 AKFRYMCILSGCDYWT---------GIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 155 ~qf~~~~iL~GcDy~~---------~ipgiG~ktA~kli~~~~ 188 (336)
++|..|.-++|+|.-. .|.|||..+|..++.+.+
T Consensus 9 ~~~~~mvrI~~~~l~~~K~v~~aLt~I~GIG~~~A~~I~~~lg 51 (154)
T PTZ00134 9 DDFQHILRILNTNVDGKRKVPYALTAIKGIGRRFAYLVCKKAG 51 (154)
T ss_pred hhhhhhhhccCccCCCCCEEEEeecccccccHHHHHHHHHHcC
Confidence 5788888888887654 488999999999999876
No 132
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=26.00 E-value=94 Score=27.06 Aligned_cols=35 Identities=29% Similarity=0.576 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhCCCCCC---------CCCCCCHHHHHHHHHHcC
Q psy11827 154 DAKFRYMCILSGCDYWT---------GIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 154 ~~qf~~~~iL~GcDy~~---------~ipgiG~ktA~kli~~~~ 188 (336)
.++|.+|.-++|+|.-. .|-|||..+|..+..+.+
T Consensus 3 ~~~~~~m~rI~~~~i~~~k~i~~aLt~IyGIG~~~a~~Ic~~lg 46 (149)
T PRK04053 3 EEEFKYIVRIAGTDLDGTKPVEYALTGIKGIGRRTARAIARKLG 46 (149)
T ss_pred hhhhhhhHhhcCccCCCCCEEeeeccccccccHHHHHHHHHHcC
Confidence 45777888788877654 378999999999999876
No 133
>PF13374 TPR_10: Tetratricopeptide repeat; PDB: 3CEQ_B 3EDT_H 3NF1_A.
Probab=25.98 E-value=46 Score=20.75 Aligned_cols=25 Identities=20% Similarity=0.185 Sum_probs=18.3
Q ss_pred HHHHHHhhcchHHHHHhhhhcccch
Q psy11827 43 KAAELLILDRGSEAQSHLRQSVDVT 67 (336)
Q Consensus 43 ~a~~~~~~g~~~~a~~~f~~~~~it 67 (336)
-|..+...|+.++|..++.+++.+.
T Consensus 8 la~~~~~~g~~~~A~~~~~~al~~~ 32 (42)
T PF13374_consen 8 LANAYRAQGRYEEALELLEEALEIR 32 (42)
T ss_dssp HHHHHHHCT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHhhhhcchhhHHHHHHHHHH
Confidence 4566778899999999998876443
No 134
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=25.84 E-value=1.4e+02 Score=27.19 Aligned_cols=26 Identities=35% Similarity=0.497 Sum_probs=20.7
Q ss_pred HHHHHHHHcCCceec---CccchHHHHHH
Q psy11827 73 NVIQACRARGVDCIV---APFEADAQMAY 98 (336)
Q Consensus 73 ~l~~~L~~~gV~~iv---APyEADAQlA~ 98 (336)
++-++|-..|+=.|+ +||.+|-|+|.
T Consensus 86 evAkll~daG~iviva~ISP~r~~R~~aR 114 (197)
T COG0529 86 EVAKLLADAGLIVIVAFISPYREDRQMAR 114 (197)
T ss_pred HHHHHHHHCCeEEEEEeeCccHHHHHHHH
Confidence 456677788887776 59999999886
No 135
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=25.78 E-value=45 Score=28.87 Aligned_cols=16 Identities=31% Similarity=0.461 Sum_probs=14.6
Q ss_pred CCCCCCHHHHHHHHHH
Q psy11827 171 GIKGMGLKKAKDYVFS 186 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~ 186 (336)
.+||||+++|.+++.-
T Consensus 101 ~lpgIG~~kA~aIi~y 116 (149)
T COG1555 101 ALPGIGPKKAQAIIDY 116 (149)
T ss_pred HCCCCCHHHHHHHHHH
Confidence 6999999999999974
No 136
>smart00851 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site PUBMED:10526357.
Probab=25.64 E-value=84 Score=24.15 Aligned_cols=35 Identities=20% Similarity=0.150 Sum_probs=24.9
Q ss_pred HHHHHcCCce--ec-CccchHHHHHHHHHcCCeEEEec
Q psy11827 76 QACRARGVDC--IV-APFEADAQMAYLNIAGYADYVIT 110 (336)
Q Consensus 76 ~~L~~~gV~~--iv-APyEADAQlA~L~~~g~vdaViT 110 (336)
+.|++.||++ ++ .+++....+..+.++|.+|+||.
T Consensus 24 ~~L~~~Gi~~~~~~~ki~~~~~~i~~~i~~g~id~VIn 61 (90)
T smart00851 24 KFLREAGLPVKTLHPKVHGGILAILDLIKNGEIDLVIN 61 (90)
T ss_pred HHHHHCCCcceeccCCCCCCCHHHHHHhcCCCeEEEEE
Confidence 4567789986 33 34655445777888999999984
No 137
>cd08579 GDPD_memb_like Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial glycerophosphodiester phosphodiesterases. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized bacterial glycerophosphodiester phosphodiesterases. In addition to a C-terminal GDPD domain, most members in this family have an N-terminus that functions as a membrane anchor.
Probab=25.57 E-value=1.1e+02 Score=27.57 Aligned_cols=39 Identities=21% Similarity=0.242 Sum_probs=29.0
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecC
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITE 111 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~ 111 (336)
..+++.+++.|+++.+--..-.+++..|...| ||+|+|.
T Consensus 180 ~~~v~~~~~~G~~v~~wtvn~~~~~~~~~~~G-vd~i~TD 218 (220)
T cd08579 180 KEFIRQAHQNGKKVYVWTVNDPDDMQRYLAMG-VDGIITD 218 (220)
T ss_pred HHHHHHHHHCCCEEEEEcCCCHHHHHHHHHcC-CCEEeCC
Confidence 45777888899988876655566677777776 8898875
No 138
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=25.35 E-value=2.3e+02 Score=28.83 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHcCCceecC-----ccc--hHHHHHHHHH-cCC
Q psy11827 70 MALNVIQACRARGVDCIVA-----PFE--ADAQMAYLNI-AGY 104 (336)
Q Consensus 70 m~~~l~~~L~~~gV~~ivA-----PyE--ADAQlA~L~~-~g~ 104 (336)
....+.+++++.+|.-|.+ ||| -|.++...++ .|+
T Consensus 75 ~~~~l~~l~~~~~i~~v~~~~~~~~~~~~rd~~v~~~l~~~gi 117 (475)
T TIGR02766 75 TVAALLDCVRSTGATRLFFNHLYDPVSLVRDHRAKEVLTAQGI 117 (475)
T ss_pred HHHHHHHHHHHcCCCEEEEecccCHHHHHHHHHHHHHHHHcCC
Confidence 3455777788889988743 433 3566666555 444
No 139
>PF06792 UPF0261: Uncharacterised protein family (UPF0261); InterPro: IPR008322 The proteins in this entry are functionally uncharacterised.
Probab=25.30 E-value=1.5e+02 Score=30.02 Aligned_cols=45 Identities=22% Similarity=0.174 Sum_probs=39.6
Q ss_pred cchHHHHHHHHHHHHHcCCceec--CccchHHHHHHHHHcCCeEEEe
Q psy11827 65 DVTHKMALNVIQACRARGVDCIV--APFEADAQMAYLNIAGYADYVI 109 (336)
Q Consensus 65 ~it~~m~~~l~~~L~~~gV~~iv--APyEADAQlA~L~~~g~vdaVi 109 (336)
.+|-.-+..+.+.|++.|.+++| |-+-.-.-+-.|.++|.+|+|+
T Consensus 194 GvTTp~V~~~~~~Le~~G~Ev~VFHAtG~GG~aME~Li~~G~~~~Vl 240 (403)
T PF06792_consen 194 GVTTPCVDAIRERLEEEGYEVLVFHATGTGGRAMERLIREGQFDGVL 240 (403)
T ss_pred CCcHHHHHHHHHHHHhcCCeEEEEcCCCCchHHHHHHHHcCCcEEEE
Confidence 45556678899999999999997 8888999999999999999998
No 140
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=25.26 E-value=37 Score=30.45 Aligned_cols=16 Identities=31% Similarity=0.555 Sum_probs=12.6
Q ss_pred CCCCCCCHHHHHHHHH
Q psy11827 170 TGIKGMGLKKAKDYVF 185 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~ 185 (336)
-++||||+|||-=++.
T Consensus 118 l~LpGVG~KTAnvVL~ 133 (177)
T TIGR03252 118 KALPGFGKQKAKIFLA 133 (177)
T ss_pred HcCCCCCHHHHHHHHH
Confidence 4799999999965544
No 141
>cd00316 Oxidoreductase_nitrogenase The nitrogenase enzyme system catalyzes the ATP-dependent reduction of dinitrogen to ammonia. This group contains both alpha and beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase) and, both subunits of Protochlorophyllide (Pchlide) reductase and chlorophyllide (chlide) reductase. The nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized nitrogenase is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers whose alpha and beta subunits are similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molec
Probab=25.12 E-value=2.7e+02 Score=27.21 Aligned_cols=17 Identities=35% Similarity=0.548 Sum_probs=14.8
Q ss_pred HHHHhCCCEEEEEecCC
Q psy11827 5 HMLLAHKIKVIMVFDGR 21 (336)
Q Consensus 5 ~~L~~~gI~PifVFDG~ 21 (336)
++|...|++++.+|++.
T Consensus 173 ~ll~~~G~~v~~~~~~~ 189 (399)
T cd00316 173 RLLEEMGIRVNALFDGG 189 (399)
T ss_pred HHHHHcCCcEEEEcCCC
Confidence 57889999999999983
No 142
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=24.70 E-value=2e+02 Score=21.75 Aligned_cols=45 Identities=16% Similarity=0.085 Sum_probs=28.1
Q ss_pred HHHHHHHHhhcchHH--HHHhhhhcccchHHHHHHHHHHHHHcCCceecCccch
Q psy11827 41 KAKAAELLILDRGSE--AQSHLRQSVDVTHKMALNVIQACRARGVDCIVAPFEA 92 (336)
Q Consensus 41 ~~~a~~~~~~g~~~~--a~~~f~~~~~it~~m~~~l~~~L~~~gV~~ivAPyEA 92 (336)
...|-.+|+.|..+. |.+.. .++ ..++.++|+++||++-...-|.
T Consensus 23 ~~~Ai~lY~~g~iS~gkAAela----g~s---~~eF~~~L~~~gI~~~~~~eel 69 (76)
T PF03683_consen 23 EELAIKLYEEGKISLGKAAELA----GMS---RWEFLELLKERGIPINYDEEEL 69 (76)
T ss_pred HHHHHHHHHcCCCCHHHHHHHh----CCC---HHHHHHHHHHCCCCCCCCHHHH
Confidence 456777889888753 33332 233 2568899999999943333333
No 143
>PF13174 TPR_6: Tetratricopeptide repeat; PDB: 3QKY_A 2XEV_A 3URZ_B 2Q7F_A.
Probab=24.68 E-value=76 Score=18.69 Aligned_cols=24 Identities=17% Similarity=0.007 Sum_probs=18.3
Q ss_pred HHHHHHHHhhcchHHHHHhhhhcc
Q psy11827 41 KAKAAELLILDRGSEAQSHLRQSV 64 (336)
Q Consensus 41 ~~~a~~~~~~g~~~~a~~~f~~~~ 64 (336)
...|+.+...|+.++|.+.|++.+
T Consensus 4 ~~~a~~~~~~g~~~~A~~~~~~~~ 27 (33)
T PF13174_consen 4 YRLARCYYKLGDYDEAIEYFQRLI 27 (33)
T ss_dssp HHHHHHHHHHCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHccCHHHHHHHHHHHH
Confidence 456777788899999998887654
No 144
>PRK00124 hypothetical protein; Validated
Probab=24.41 E-value=1.1e+02 Score=26.74 Aligned_cols=85 Identities=25% Similarity=0.219 Sum_probs=44.8
Q ss_pred ccchHHHHHHHHHcCCeEEEecCCCceEeecccEEEEecCCCCCeeeeccccccccccCCcCCCCHHHHHHHHHHhCCCC
Q psy11827 89 PFEADAQMAYLNIAGYADYVITEDSDLLVFGAKKIIYKLDLSGNCCFMDREKLPSALKMPLAKFTDAKFRYMCILSGCDY 168 (336)
Q Consensus 89 PyEADAQlA~L~~~g~vdaViT~DSDll~fg~~~vi~kl~~~g~~~~i~~~~l~~~~~~~~~~lt~~qf~~~~iL~GcDy 168 (336)
+-.||.-++.+++.| |.|||.|--|-..-..+-.+-++..|. .++.+++...+..+ --.++++. +|. .
T Consensus 54 ~D~AD~~Iv~~~~~g--DiVIT~Di~LAa~~l~Kga~vl~prG~--~yt~~nI~~~L~~R---~~~~~lR~----~G~-~ 121 (151)
T PRK00124 54 FDAADNEIVQLAEKG--DIVITQDYGLAALALEKGAIVLNPRGY--IYTNDNIDQLLAMR---DLMATLRR----SGI-R 121 (151)
T ss_pred CChHHHHHHHhCCCC--CEEEeCCHHHHHHHHHCCCEEECCCCc--CCCHHHHHHHHHHH---HHHHHHHH----cCC-C
Confidence 457888888888888 899999966543333332233443443 35555554321100 00112222 233 4
Q ss_pred CCCCCCCCHHHHHHHHH
Q psy11827 169 WTGIKGMGLKKAKDYVF 185 (336)
Q Consensus 169 ~~~ipgiG~ktA~kli~ 185 (336)
..|-+.++.+.-..+.+
T Consensus 122 t~Gp~~~~~~Dr~~F~~ 138 (151)
T PRK00124 122 TGGPKPFTQEDRSRFEA 138 (151)
T ss_pred CCCCCCCCHHHHHHHHH
Confidence 45666677665555544
No 145
>cd08580 GDPD_Rv2277c_like Glycerophosphodiester phosphodiesterase domain of uncharacterized bacterial protein Rv2277c and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in uncharacterized bacterial protein Rv2277c and similar proteins. Members in this subfamily are bacterial homologous of mammalian GDE4, a transmembrane protein whose cellular function has not yet been elucidated.
Probab=24.32 E-value=99 Score=29.22 Aligned_cols=43 Identities=14% Similarity=0.212 Sum_probs=31.4
Q ss_pred HHHHHHHHHc-CCceecCccchHHHHHHHHHcCCeEEEecCCCce
Q psy11827 72 LNVIQACRAR-GVDCIVAPFEADAQMAYLNIAGYADYVITEDSDL 115 (336)
Q Consensus 72 ~~l~~~L~~~-gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDl 115 (336)
.++.+.+++. |+.+.+-.---.+.+..|..-| ||+|||..-|.
T Consensus 219 ~~~V~~~h~~~gl~V~~WTVN~~~~~~~l~~~G-VDgIiTD~P~~ 262 (263)
T cd08580 219 PAAVDCFRRNSKVKIVLFGINTADDYRLAKCLG-ADAVMVDSPAA 262 (263)
T ss_pred HHHHHHHHhcCCcEEEEEEeCCHHHHHHHHHcC-CCEEEeCCccc
Confidence 4567778888 9998886644445666777776 89999876664
No 146
>cd08609 GDPD_GDE3 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE3 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE3 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 2 (GDPD2), Osteoblast differentiation promoting factor) and their metazoan homologs. Mammalian GDE3 is a transmembrane protein specifically expressed in bone tissues and spleen. It is a mammalian homolog of bacterial glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), which catalyzes the hydrolysis of various glycerophosphodiesters, and produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. Mammalian GDE3 has been characterized as glycerophosphoinositol inositolphosphodiesterase (EC 3.1.4.43) that selectively hydrolyzes extracellular glycerophosphoinositol (GPI) to generate inositol 1-phosphate (Ins1P) and glycerol. Mammalia
Probab=24.30 E-value=69 Score=31.17 Aligned_cols=43 Identities=19% Similarity=0.112 Sum_probs=29.8
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCce
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDL 115 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDl 115 (336)
..+.+.+++.|+++.+---.-.+++.+|.+.| ||+|+|+.-|+
T Consensus 235 ~~~v~~~~~~G~~v~vWTVNd~~~~~~l~~~G-VDgIiTD~P~~ 277 (315)
T cd08609 235 ALEIKELRKDNVSVNLWVVNEPWLFSLLWCSG-VSSVTTNACQL 277 (315)
T ss_pred HHHHHHHHHCCCEEEEECCCCHHHHHHHHhcC-CCEEEcCCHHH
Confidence 34566677788887776545556677777777 68888877653
No 147
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=24.16 E-value=3e+02 Score=28.22 Aligned_cols=18 Identities=17% Similarity=0.169 Sum_probs=12.4
Q ss_pred HHHHHHHHHHcCCceecC
Q psy11827 71 ALNVIQACRARGVDCIVA 88 (336)
Q Consensus 71 ~~~l~~~L~~~gV~~ivA 88 (336)
...+.+++++.+|..|++
T Consensus 85 ~~vl~~l~~~~~i~~v~~ 102 (472)
T PRK10674 85 VEWLKQFCQQHQVTHLFY 102 (472)
T ss_pred HHHHHHHHHHcCCCEEEE
Confidence 345666677788888764
No 148
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=23.64 E-value=59 Score=26.63 Aligned_cols=33 Identities=21% Similarity=0.253 Sum_probs=22.0
Q ss_pred HHHHHHHHHhCCCCCC------------CCCCCCHHHHHHHHHHc
Q psy11827 155 AKFRYMCILSGCDYWT------------GIKGMGLKKAKDYVFSI 187 (336)
Q Consensus 155 ~qf~~~~iL~GcDy~~------------~ipgiG~ktA~kli~~~ 187 (336)
..|+++--.+|.|-.. =+.|+||.+|..|++..
T Consensus 26 ~~~vd~vN~vGVDIN~a~~~~~~~~~LqfV~GLGPRKA~~Ll~~l 70 (104)
T PF14635_consen 26 RAFVDVVNQVGVDINRAVSHPHLANLLQFVCGLGPRKAQALLKAL 70 (104)
T ss_dssp HHHHHHHHHH-EEHHHHCT-HHHHGGGGGSTT--HHHHHHHHHHH
T ss_pred HHHHHHHHhhCccHHHHhcChHHHhhHhHhcCCChHHHHHHHHHH
Confidence 4577777788866432 37899999999998863
No 149
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=23.33 E-value=59 Score=29.20 Aligned_cols=21 Identities=29% Similarity=0.438 Sum_probs=17.3
Q ss_pred CCCCCCCCCHHHHHHHHHHcC
Q psy11827 168 YWTGIKGMGLKKAKDYVFSIM 188 (336)
Q Consensus 168 y~~~ipgiG~ktA~kli~~~~ 188 (336)
-+..+||||.++|.+++....
T Consensus 109 ~L~~v~Gig~k~A~~I~~~l~ 129 (192)
T PRK00116 109 ALTKVPGIGKKTAERIVLELK 129 (192)
T ss_pred HHHhCCCCCHHHHHHHHHHHH
Confidence 345799999999999997754
No 150
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=23.30 E-value=90 Score=21.83 Aligned_cols=29 Identities=17% Similarity=0.028 Sum_probs=18.3
Q ss_pred HHHHHHHHhhcchHHHHHhhhhcccchHH
Q psy11827 41 KAKAAELLILDRGSEAQSHLRQSVDVTHK 69 (336)
Q Consensus 41 ~~~a~~~~~~g~~~~a~~~f~~~~~it~~ 69 (336)
..-|..+++.|+.++|...+.+.....|+
T Consensus 29 ~~la~~~~~~g~~~~A~~~l~~~~~~~~~ 57 (68)
T PF14559_consen 29 LLLAQCYLKQGQYDEAEELLERLLKQDPD 57 (68)
T ss_dssp HHHHHHHHHTT-HHHHHHHHHCCHGGGTT
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHCcC
Confidence 34555566778888888777776655543
No 151
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=23.21 E-value=69 Score=34.00 Aligned_cols=27 Identities=19% Similarity=0.267 Sum_probs=22.0
Q ss_pred CCCCCCCHHHHHHHHHHcCCCcHHHHHHH
Q psy11827 170 TGIKGMGLKKAKDYVFSIMDPDFENALRK 198 (336)
Q Consensus 170 ~~ipgiG~ktA~kli~~~~~~si~~vl~~ 198 (336)
..|||||+++..+|++.|+ ++..+..+
T Consensus 533 d~I~GiG~~r~~~LL~~Fg--s~~~i~~A 559 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFG--SLKGIKSA 559 (581)
T ss_pred ccCCCcCHHHHHHHHHHhh--CHHHHHhc
Confidence 4799999999999999998 56555444
No 152
>PF13176 TPR_7: Tetratricopeptide repeat; PDB: 3SF4_C 3RO3_A 3RO2_A.
Probab=23.10 E-value=68 Score=20.23 Aligned_cols=24 Identities=8% Similarity=-0.063 Sum_probs=17.1
Q ss_pred HHHHHhhcchHHHHHhhhhcccch
Q psy11827 44 AAELLILDRGSEAQSHLRQSVDVT 67 (336)
Q Consensus 44 a~~~~~~g~~~~a~~~f~~~~~it 67 (336)
|.-+.+.|+.++|.++|.++..+.
T Consensus 6 g~~~~~~g~~~~Ai~~y~~aL~l~ 29 (36)
T PF13176_consen 6 GRIYRQQGDYEKAIEYYEQALALA 29 (36)
T ss_dssp HHHHHHCT-HHHHHHHHHHHHHHH
T ss_pred HHHHHHcCCHHHHHHHHHHHHHhc
Confidence 445667899999999998865443
No 153
>KOG4648|consensus
Probab=22.91 E-value=90 Score=31.33 Aligned_cols=28 Identities=14% Similarity=0.130 Sum_probs=23.4
Q ss_pred HHHHHHHHhhcchHHHHHhhhhcccchH
Q psy11827 41 KAKAAELLILDRGSEAQSHLRQSVDVTH 68 (336)
Q Consensus 41 ~~~a~~~~~~g~~~~a~~~f~~~~~it~ 68 (336)
.+++..+..+|+.+||.+||.+++.+.|
T Consensus 101 KE~GN~yFKQgKy~EAIDCYs~~ia~~P 128 (536)
T KOG4648|consen 101 KERGNTYFKQGKYEEAIDCYSTAIAVYP 128 (536)
T ss_pred HHhhhhhhhccchhHHHHHhhhhhccCC
Confidence 4567778889999999999999987765
No 154
>cd08612 GDPD_GDE4 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE4 and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian GDE4 (also known as glycerophosphodiester phosphodiesterase domain-containing protein 1 (GDPD1)) and similar proteins. Mammalian GDE4 is a transmembrane protein whose cellular function has not yet been elucidated. It is expressed widely, including in placenta, liver, kidney, pancreas, spleen, thymus, ovary, small intestine and peripheral blood leukocytes. It is also expressed in the growth cones in neuroblastoma Neuro2a cells, which suggests GDE4 may play some distinct role from other members of the GDE family.
Probab=22.88 E-value=70 Score=30.56 Aligned_cols=44 Identities=18% Similarity=0.203 Sum_probs=32.6
Q ss_pred HHHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecCCCceE
Q psy11827 72 LNVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITEDSDLL 116 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~DSDll 116 (336)
..+++.++..|+++.+---.-.+++.+|...| ||+|+|..-|.+
T Consensus 251 ~~~v~~~~~~G~~v~vWTVNd~~~~~~l~~~G-VdgIiTD~P~~l 294 (300)
T cd08612 251 PSLFRHLQKRGIQVYGWVLNDEEEFERAFELG-ADGVMTDYPTKL 294 (300)
T ss_pred HHHHHHHHHCCCEEEEeecCCHHHHHHHHhcC-CCEEEeCCHHHH
Confidence 35667788899998876655456777888776 889998776643
No 155
>PRK13766 Hef nuclease; Provisional
Probab=22.66 E-value=78 Score=34.29 Aligned_cols=27 Identities=11% Similarity=0.140 Sum_probs=22.7
Q ss_pred CCCCCCCCHHHHHHHHHHcCCCcHHHHHH
Q psy11827 169 WTGIKGMGLKKAKDYVFSIMDPDFENALR 197 (336)
Q Consensus 169 ~~~ipgiG~ktA~kli~~~~~~si~~vl~ 197 (336)
+.+|||||+++|.+|+..|+ ++.+++.
T Consensus 717 L~~ipgig~~~a~~Ll~~fg--s~~~i~~ 743 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFG--SVEAVMT 743 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHh
Confidence 45799999999999999997 5676654
No 156
>PF08588 DUF1769: Protein of unknown function (DUF1769); InterPro: IPR013897 This entry is found in fungal proteins with unknown function.
Probab=22.36 E-value=68 Score=23.35 Aligned_cols=31 Identities=26% Similarity=0.386 Sum_probs=22.7
Q ss_pred HHhCCCCCCCC---CCCCHHHHHHHHHHcCCCcH
Q psy11827 162 ILSGCDYWTGI---KGMGLKKAKDYVFSIMDPDF 192 (336)
Q Consensus 162 iL~GcDy~~~i---pgiG~ktA~kli~~~~~~si 192 (336)
++-|+||...| ..-|..+|+|+++.+=++++
T Consensus 4 l~FGndFd~pird~lP~g~~~alk~~~w~idP~l 37 (56)
T PF08588_consen 4 LLFGNDFDRPIRDRLPPGFNAALKFFKWFIDPGL 37 (56)
T ss_pred ceecCccCccchhhCCchHHHHHHHHHHHhCCCc
Confidence 45689998765 23479999999997655554
No 157
>PF10087 DUF2325: Uncharacterized protein conserved in bacteria (DUF2325); InterPro: IPR016772 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=22.21 E-value=1.7e+02 Score=22.86 Aligned_cols=25 Identities=24% Similarity=0.332 Sum_probs=23.0
Q ss_pred cchHHHHHHHHHHHHHcCCceecCc
Q psy11827 65 DVTHKMALNVIQACRARGVDCIVAP 89 (336)
Q Consensus 65 ~it~~m~~~l~~~L~~~gV~~ivAP 89 (336)
.|+|.+...+++.++..|+|++.+.
T Consensus 58 ~vsH~~~~~vk~~akk~~ip~~~~~ 82 (97)
T PF10087_consen 58 YVSHNAMWKVKKAAKKYGIPIIYSR 82 (97)
T ss_pred CcChHHHHHHHHHHHHcCCcEEEEC
Confidence 4679999999999999999999987
No 158
>cd08574 GDPD_GDE_2_3_6 Glycerophosphodiester phosphodiesterase domain of mammalian glycerophosphodiester phosphodiesterase GDE2, GDE3, GDE6-like proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in mammalian glycerophosphodiester phosphodiesterase domain-containing protein subtype 5 (GDE2), subtype 2 (GDE3), subtype 1 (GDE6), and their eukaryotic homologs. Mammalian GDE2, GDE3, and GDE6 show very high sequence similarity to each other and have been classified into the same family. Although they are all transmembrane proteins, based on different pattern of tissue distribution, these enzymes might display diverse cellular functions. Mammalian GDE2 is primarily expressed in mature neurons. It selectively hydrolyzes glycerophosphocholine (GPC) and mainly functions in a complex with an antioxidant scavenger peroxiredoxin1 (Prdx1) to control motor neuron differentiation in the spinal cord. Mammalian GDE3 is specifically expressed in bo
Probab=21.97 E-value=1.3e+02 Score=27.97 Aligned_cols=38 Identities=13% Similarity=0.089 Sum_probs=26.3
Q ss_pred HHHHHHHHcCCceecCccchHHHHHHHHHcCCeEEEecC
Q psy11827 73 NVIQACRARGVDCIVAPFEADAQMAYLNIAGYADYVITE 111 (336)
Q Consensus 73 ~l~~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT~ 111 (336)
.+++.+++.|+++.+-.---.+++.+|.+.| ||+|+|.
T Consensus 214 ~~v~~~~~~g~~v~~WTVn~~~~~~~l~~~G-VdgIiTD 251 (252)
T cd08574 214 QEIREYSKANISVNLYVVNEPWLYSLLWCSG-VQSVTTN 251 (252)
T ss_pred HHHHHHHHCCCEEEEEccCCHHHHHHHHHcC-CCEEecC
Confidence 4666777788887776544455666777776 8888863
No 159
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=21.97 E-value=3.6e+02 Score=20.40 Aligned_cols=30 Identities=20% Similarity=0.231 Sum_probs=25.6
Q ss_pred cchHHHHHHHHHcCCeEEEecCCCceEeec
Q psy11827 90 FEADAQMAYLNIAGYADYVITEDSDLLVFG 119 (336)
Q Consensus 90 yEADAQlA~L~~~g~vdaViT~DSDll~fg 119 (336)
-|++.-++.+..+|.+.|-|...+..+.|+
T Consensus 75 ~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~ 104 (105)
T PF01399_consen 75 EEVESILIDLISNGLIKAKIDQVNGVVVFS 104 (105)
T ss_dssp HHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred HHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence 678888888999999999998888888775
No 160
>COG1059 Thermostable 8-oxoguanine DNA glycosylase [DNA replication, recombination, and repair]
Probab=21.94 E-value=2.6e+02 Score=25.57 Aligned_cols=22 Identities=32% Similarity=0.554 Sum_probs=18.9
Q ss_pred CCCCCCHHHHHHHHHHcCCCcH
Q psy11827 171 GIKGMGLKKAKDYVFSIMDPDF 192 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~~si 192 (336)
.|.|||.|.|-.+++--|-.|+
T Consensus 125 nikGiGyKEASHFLRNVG~~D~ 146 (210)
T COG1059 125 NIKGIGYKEASHFLRNVGFEDL 146 (210)
T ss_pred HcccccHHHHHHHHHhcChhHH
Confidence 7999999999999998775454
No 161
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=21.77 E-value=85 Score=33.80 Aligned_cols=24 Identities=21% Similarity=0.277 Sum_probs=16.9
Q ss_pred CCCCCCHHHHHHHHHHcCCCcHHHHH
Q psy11827 171 GIKGMGLKKAKDYVFSIMDPDFENAL 196 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~~si~~vl 196 (336)
||||||.++|..|.+.|+ +++++.
T Consensus 502 gIpgVG~~~ak~L~~~f~--sl~~l~ 525 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFG--TLDKLK 525 (652)
T ss_pred cCCCcCHHHHHHHHHHhC--CHHHHH
Confidence 577788888888887776 455543
No 162
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=21.71 E-value=62 Score=29.72 Aligned_cols=15 Identities=40% Similarity=0.762 Sum_probs=13.8
Q ss_pred CCCCCCHHHHHHHHH
Q psy11827 171 GIKGMGLKKAKDYVF 185 (336)
Q Consensus 171 ~ipgiG~ktA~kli~ 185 (336)
++||||+|||--++.
T Consensus 123 ~lpGIG~KTAd~vL~ 137 (208)
T PRK01229 123 NIKGIGYKEASHFLR 137 (208)
T ss_pred cCCCCcHHHHHHHHH
Confidence 899999999999885
No 163
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=21.65 E-value=87 Score=33.97 Aligned_cols=24 Identities=25% Similarity=0.411 Sum_probs=16.9
Q ss_pred CCCCCCHHHHHHHHHHcCCCcHHHHH
Q psy11827 171 GIKGMGLKKAKDYVFSIMDPDFENAL 196 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~~~~~si~~vl 196 (336)
+|||||.++|.+|.+.|+ +++++.
T Consensus 532 gIpgIG~~~ak~L~~~F~--si~~L~ 555 (689)
T PRK14351 532 GIPEVGPTTARNLAREFG--TFEAIM 555 (689)
T ss_pred CCCCcCHHHHHHHHHHhC--CHHHHH
Confidence 577888888888888776 455443
No 164
>PRK13600 putative ribosomal protein L7Ae-like; Provisional
Probab=21.58 E-value=1e+02 Score=24.17 Aligned_cols=27 Identities=11% Similarity=0.081 Sum_probs=23.0
Q ss_pred ccchHHHHHHHHHHHHHcCCceecCcc
Q psy11827 64 VDVTHKMALNVIQACRARGVDCIVAPF 90 (336)
Q Consensus 64 ~~it~~m~~~l~~~L~~~gV~~ivAPy 90 (336)
-|+.+.++..+..++.+.||||+.-|-
T Consensus 37 ~Da~~~vv~~l~~lceek~Ip~v~V~s 63 (84)
T PRK13600 37 EDVEVYLMTRVLSQINQKNIPVSFFKS 63 (84)
T ss_pred CCCCHHHHHHHHHHHHHcCCCEEEECC
Confidence 466788888999999999999998763
No 165
>COG0054 RibH Riboflavin synthase beta-chain [Coenzyme metabolism]
Probab=21.33 E-value=1.9e+02 Score=25.31 Aligned_cols=46 Identities=26% Similarity=0.405 Sum_probs=33.4
Q ss_pred cchHHHHHHHHHHHHHcCC-----ceecCc--cchHHHHHHHHHcCCeEEEec
Q psy11827 65 DVTHKMALNVIQACRARGV-----DCIVAP--FEADAQMAYLNIAGYADYVIT 110 (336)
Q Consensus 65 ~it~~m~~~l~~~L~~~gV-----~~ivAP--yEADAQlA~L~~~g~vdaViT 110 (336)
+|+..|..-..+.|+..|+ .++.-| ||-=--...|+++|..|||++
T Consensus 25 ~I~d~ll~gA~~~l~~~G~~~~~i~vv~VPGa~EiPl~a~~La~~~~yDAvv~ 77 (152)
T COG0054 25 DITDALLEGAVDALKRHGADVDNIDVVRVPGAFEIPLAAKKLARTGKYDAVVA 77 (152)
T ss_pred HHHHHHHHHHHHHHHHcCCCcccceEEEeCCcchhHHHHHHHHhcCCcceEEE
Confidence 4667777777888888774 455567 666655566999999999873
No 166
>KOG4175|consensus
Probab=21.28 E-value=2.2e+02 Score=26.43 Aligned_cols=38 Identities=29% Similarity=0.406 Sum_probs=32.8
Q ss_pred ccchHHHHHHHHHHHHHcCCcee--cCccchHHHHHHHHH
Q psy11827 64 VDVTHKMALNVIQACRARGVDCI--VAPFEADAQMAYLNI 101 (336)
Q Consensus 64 ~~it~~m~~~l~~~L~~~gV~~i--vAPyEADAQlA~L~~ 101 (336)
++++|+-+..+...++..||.++ +||.--|--|-.|..
T Consensus 130 vDlPpEEa~~~Rne~~k~gislvpLvaPsTtdeRmell~~ 169 (268)
T KOG4175|consen 130 VDLPPEEAETLRNEARKHGISLVPLVAPSTTDERMELLVE 169 (268)
T ss_pred ccCChHHHHHHHHHHHhcCceEEEeeCCCChHHHHHHHHH
Confidence 57889999999999999999988 799988888777654
No 167
>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=21.24 E-value=1.7e+02 Score=22.33 Aligned_cols=34 Identities=12% Similarity=0.225 Sum_probs=17.9
Q ss_pred HHHHHhhhhcccchHHHHHHHHHHHHHcCCceecC
Q psy11827 54 SEAQSHLRQSVDVTHKMALNVIQACRARGVDCIVA 88 (336)
Q Consensus 54 ~~a~~~f~~~~~it~~m~~~l~~~L~~~gV~~ivA 88 (336)
++-.+.+.. ..++++.+..+...|...||.++-.
T Consensus 25 ~eI~~~L~~-~~~~~e~id~i~~~L~~~gI~Vvd~ 58 (82)
T PF03979_consen 25 DEINDALPE-DDLDPEQIDEIYDTLEDEGIEVVDE 58 (82)
T ss_dssp HHHHHH-S--S---HHHHHHHHHHHHTT----B--
T ss_pred HHHHHHcCc-cCCCHHHHHHHHHHHHHCCCEEecC
Confidence 344455552 3478899999999999999999984
No 168
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=21.20 E-value=46 Score=30.71 Aligned_cols=18 Identities=22% Similarity=0.213 Sum_probs=14.7
Q ss_pred CCCCCCHHHHHHHHHH-cC
Q psy11827 171 GIKGMGLKKAKDYVFS-IM 188 (336)
Q Consensus 171 ~ipgiG~ktA~kli~~-~~ 188 (336)
++||+|.|||-=.+.. |+
T Consensus 113 ~LPGVGrKTAnvVL~~a~g 131 (211)
T COG0177 113 SLPGVGRKTANVVLSFAFG 131 (211)
T ss_pred hCCCcchHHHHHHHHhhcC
Confidence 6999999999877765 44
No 169
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=21.13 E-value=74 Score=23.41 Aligned_cols=15 Identities=27% Similarity=0.341 Sum_probs=12.0
Q ss_pred CCCCCCCHHHHHHHH
Q psy11827 170 TGIKGMGLKKAKDYV 184 (336)
Q Consensus 170 ~~ipgiG~ktA~kli 184 (336)
.+|||||.+.|.++-
T Consensus 50 ~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 50 KKLPGIGKSIAKKID 64 (68)
T ss_dssp CTSTTTTHHHHHHHH
T ss_pred hhCCCCCHHHHHHHH
Confidence 689999988887763
No 170
>cd08606 GDPD_YPL110cp_fungi Glycerophosphodiester phosphodiesterase domain of Saccharomyces cerevisiae YPL110cp and similar proteins. This subfamily corresponds to the glycerophosphodiester phosphodiesterase domain (GDPD) present in Saccharomyces cerevisiae YPL110cp and other uncharacterized fungal homologs. The product of S. cerevisiae ORF YPL110c (GDE1), YPL110cp (Gde1p), displays homology to bacterial and mammalian glycerophosphodiester phosphodiesterases (GP-GDE, EC 3.1.4.46), which catalyzes the degradation of glycerophosphodiesters to produce sn-glycerol-3-phosphate (G3P) and the corresponding alcohols. S. cerevisiae YPL110cp has been characterized as a cytoplasmic glycerophosphocholine (GPC)-specific phosphodiesterase that selectively hydrolyzes GPC, not glycerophosphoinositol (GPI), to generate choline and glycerolphosphate. YPL110cp has multi-domain architecture, including not only C-terminal GDPD, but also an SPX N-terminal domain along with several ankyrin repeats, which imp
Probab=20.89 E-value=86 Score=29.49 Aligned_cols=44 Identities=20% Similarity=0.262 Sum_probs=28.3
Q ss_pred HHHHHHHHHcCCceecCcc--chHHHHHHHHHcCCeEEEecCCCceE
Q psy11827 72 LNVIQACRARGVDCIVAPF--EADAQMAYLNIAGYADYVITEDSDLL 116 (336)
Q Consensus 72 ~~l~~~L~~~gV~~ivAPy--EADAQlA~L~~~g~vdaViT~DSDll 116 (336)
..+.+.+++.|+.+.+--. .-.+.+..|.+.| ||+|+|+.-|.+
T Consensus 235 ~~~v~~~~~~Gl~v~~WTv~~n~~~~~~~l~~~G-VdgIiTD~p~~~ 280 (286)
T cd08606 235 PRLIQVVKRSGLVCVSYGVLNNDPENAKTQVKAG-VDAVIVDSVLAI 280 (286)
T ss_pred hHHHHHHHHCCcEEEEECCccCCHHHHHHHHHcC-CCEEEECCHHHH
Confidence 3566677788888776543 3344555666665 778887766644
No 171
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=20.74 E-value=4.6e+02 Score=22.89 Aligned_cols=16 Identities=31% Similarity=0.424 Sum_probs=7.9
Q ss_pred CccchhhHHHHHhhhh
Q psy11827 23 LPAKEATEEDRRKKRD 38 (336)
Q Consensus 23 ~p~K~~t~~~R~~~r~ 38 (336)
+..|..++.+||++|.
T Consensus 7 pt~kErEnnk~RERrR 22 (150)
T PF05687_consen 7 PTWKERENNKRRERRR 22 (150)
T ss_pred ccHhhhHHHHHHHHHH
Confidence 3345555555555543
No 172
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=20.72 E-value=82 Score=23.06 Aligned_cols=15 Identities=47% Similarity=0.662 Sum_probs=14.3
Q ss_pred CCCCCHHHHHHHHHH
Q psy11827 172 IKGMGLKKAKDYVFS 186 (336)
Q Consensus 172 ipgiG~ktA~kli~~ 186 (336)
+||||.++|.+++..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 899999999999987
No 173
>PRK02399 hypothetical protein; Provisional
Probab=20.51 E-value=2.1e+02 Score=29.09 Aligned_cols=45 Identities=24% Similarity=0.206 Sum_probs=38.6
Q ss_pred cchHHHHHHHHHHHHHcCCceec--CccchHHHHHHHHHcCCeEEEe
Q psy11827 65 DVTHKMALNVIQACRARGVDCIV--APFEADAQMAYLNIAGYADYVI 109 (336)
Q Consensus 65 ~it~~m~~~l~~~L~~~gV~~iv--APyEADAQlA~L~~~g~vdaVi 109 (336)
.+|-.-+..+.+.|.+.|.+++| |-+-.-.-+-.|.++|.+++|+
T Consensus 195 GvTtp~v~~~~~~Le~~GyEvlVFHATG~GGraME~Li~~G~~~gVl 241 (406)
T PRK02399 195 GVTTPCVQAAREELEARGYEVLVFHATGTGGRAMEKLIDSGLIAGVL 241 (406)
T ss_pred CCcHHHHHHHHHHHHhCCCeEEEEcCCCCchHHHHHHHHcCCceEEE
Confidence 44555677899999999999987 8888888999999999999998
No 174
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=20.37 E-value=1.3e+02 Score=17.61 Aligned_cols=20 Identities=40% Similarity=0.346 Sum_probs=16.0
Q ss_pred HHHHHHHhhcchHHHHHhhh
Q psy11827 42 AKAAELLILDRGSEAQSHLR 61 (336)
Q Consensus 42 ~~a~~~~~~g~~~~a~~~f~ 61 (336)
..|+.++..|+.++|...+.
T Consensus 6 ~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 6 ALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHcCCHHHHHHHHh
Confidence 45778889999999987764
No 175
>PRK14812 hypothetical protein; Provisional
Probab=20.07 E-value=66 Score=26.98 Aligned_cols=35 Identities=17% Similarity=0.033 Sum_probs=26.0
Q ss_pred HHHHHcCCceecCccchHHHHHHHHHcCCeEEEec
Q psy11827 76 QACRARGVDCIVAPFEADAQMAYLNIAGYADYVIT 110 (336)
Q Consensus 76 ~~L~~~gV~~ivAPyEADAQlA~L~~~g~vdaViT 110 (336)
.+|+..||.+|+|++-|+.=-.-..+.|+.-.+++
T Consensus 11 wAL~~~Gi~aVIA~SFa~IF~~N~~nnGllpi~~~ 45 (119)
T PRK14812 11 WALADYGFKVVIAGSFGDIHYNNELNNGMLPIVQP 45 (119)
T ss_pred HHHHHcCCCEEEEchHHHHHHhHHHHCCCCcccCC
Confidence 46788899999999888876666777887544443
Done!