Query psy13182
Match_columns 194
No_of_seqs 191 out of 1294
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 22:14:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13182.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13182hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0556|consensus 100.0 2.3E-37 5E-42 273.0 15.1 169 4-173 9-183 (533)
2 PLN02850 aspartate-tRNA ligase 100.0 1.3E-30 2.8E-35 241.4 17.9 168 3-174 8-181 (530)
3 PTZ00401 aspartyl-tRNA synthet 100.0 2.5E-29 5.4E-34 233.4 17.3 165 6-173 8-177 (550)
4 cd04316 ND_PkAspRS_like_N ND_P 99.8 4.3E-18 9.4E-23 127.2 12.0 103 68-172 2-104 (108)
5 cd04320 AspRS_cyto_N AspRS_cyt 99.7 2.5E-17 5.3E-22 121.8 11.5 94 80-173 1-100 (102)
6 KOG0555|consensus 99.7 1.2E-16 2.6E-21 141.8 10.0 166 6-182 54-226 (545)
7 PLN02502 lysyl-tRNA synthetase 99.6 7.3E-15 1.6E-19 137.1 16.1 168 1-171 1-200 (553)
8 cd04317 EcAspRS_like_N EcAspRS 99.6 2.6E-15 5.7E-20 116.2 10.8 104 67-174 3-112 (135)
9 cd04319 PhAsnRS_like_N PhAsnRS 99.6 5.4E-15 1.2E-19 109.6 11.6 89 80-172 1-89 (103)
10 cd04323 AsnRS_cyto_like_N AsnR 99.6 3.7E-15 8E-20 106.5 9.9 75 80-159 1-75 (84)
11 cd04100 Asp_Lys_Asn_RS_N Asp_L 99.6 4.7E-15 1E-19 106.1 9.8 76 80-159 1-76 (85)
12 cd04322 LysRS_N LysRS_N: N-ter 99.6 7.9E-15 1.7E-19 109.5 11.4 90 80-172 1-90 (108)
13 COG0017 AsnS Aspartyl/asparagi 99.6 7.3E-15 1.6E-19 132.7 12.2 109 66-177 4-112 (435)
14 PRK05159 aspC aspartyl-tRNA sy 99.6 2.1E-14 4.5E-19 130.9 12.6 107 65-174 3-109 (437)
15 TIGR00458 aspS_arch aspartyl-t 99.6 2.6E-14 5.7E-19 130.0 12.1 104 68-173 2-105 (428)
16 PRK12820 bifunctional aspartyl 99.6 3.1E-14 6.6E-19 135.7 12.0 108 66-175 6-119 (706)
17 COG0173 AspS Aspartyl-tRNA syn 99.5 5.8E-14 1.3E-18 129.1 11.1 108 66-176 3-116 (585)
18 PLN02903 aminoacyl-tRNA ligase 99.5 1.1E-13 2.3E-18 130.9 11.3 107 66-174 60-172 (652)
19 PRK03932 asnC asparaginyl-tRNA 99.5 7.4E-13 1.6E-17 121.2 12.4 103 67-172 4-107 (450)
20 cd04318 EcAsnRS_like_N EcAsnRS 99.5 1E-12 2.2E-17 93.3 10.4 70 81-159 2-73 (82)
21 KOG0556|consensus 99.5 2E-13 4.3E-18 121.7 8.2 90 78-194 66-156 (533)
22 PRK00476 aspS aspartyl-tRNA sy 99.4 5.7E-13 1.2E-17 125.4 11.7 103 66-173 5-113 (588)
23 TIGR00459 aspS_bact aspartyl-t 99.4 1.4E-12 3.1E-17 122.4 12.1 104 66-174 3-112 (583)
24 cd04321 ScAspRS_mt_like_N ScAs 99.4 4.8E-12 1E-16 90.9 10.4 75 80-159 1-77 (86)
25 TIGR00457 asnS asparaginyl-tRN 99.3 1.2E-11 2.6E-16 113.3 12.1 96 75-173 13-111 (453)
26 PRK00484 lysS lysyl-tRNA synth 99.3 1.1E-11 2.4E-16 114.7 10.1 90 79-172 55-144 (491)
27 PLN02221 asparaginyl-tRNA synt 99.3 1.4E-11 3.1E-16 115.5 10.3 100 65-172 31-145 (572)
28 PLN02603 asparaginyl-tRNA synt 99.2 1.6E-10 3.4E-15 108.4 12.1 103 65-172 88-200 (565)
29 TIGR00499 lysS_bact lysyl-tRNA 99.2 1.6E-10 3.5E-15 107.0 11.4 92 77-172 52-144 (496)
30 PRK12445 lysyl-tRNA synthetase 99.1 3.6E-10 7.8E-15 104.9 11.8 92 77-172 64-156 (505)
31 PRK02983 lysS lysyl-tRNA synth 99.1 2.4E-10 5.2E-15 114.1 11.3 103 66-171 639-741 (1094)
32 PTZ00385 lysyl-tRNA synthetase 99.1 4.4E-10 9.6E-15 106.7 11.6 86 78-166 107-193 (659)
33 KOG1885|consensus 99.0 1.4E-09 3.1E-14 98.7 10.5 142 3-146 3-174 (560)
34 PTZ00425 asparagine-tRNA ligas 99.0 2.6E-09 5.7E-14 100.4 10.3 81 75-159 78-165 (586)
35 PTZ00417 lysine-tRNA ligase; P 98.8 2.9E-08 6.4E-13 93.6 11.6 92 78-172 132-226 (585)
36 PF01336 tRNA_anti-codon: OB-f 98.8 1.2E-07 2.5E-12 64.8 10.4 61 81-146 1-62 (75)
37 PTZ00401 aspartyl-tRNA synthet 98.7 5.9E-08 1.3E-12 91.1 7.4 142 5-193 3-149 (550)
38 PLN02850 aspartate-tRNA ligase 98.6 9.9E-08 2.2E-12 89.2 8.8 87 80-194 67-154 (530)
39 COG1190 LysU Lysyl-tRNA synthe 98.2 6.4E-06 1.4E-10 75.9 9.6 89 80-172 63-152 (502)
40 KOG2411|consensus 98.1 9.2E-06 2E-10 74.8 8.4 105 67-173 36-146 (628)
41 PLN02532 asparagine-tRNA synth 97.8 4.9E-05 1.1E-09 72.5 7.5 76 90-172 129-209 (633)
42 KOG0554|consensus 97.3 0.00055 1.2E-08 61.7 6.2 62 74-144 16-79 (446)
43 cd04489 ExoVII_LU_OBF ExoVII_L 96.3 0.048 1.1E-06 37.3 8.5 59 81-144 2-61 (78)
44 PF13742 tRNA_anti_2: OB-fold 96.2 0.041 8.9E-07 40.4 8.1 61 78-144 21-84 (99)
45 TIGR00617 rpa1 replication fac 96.1 0.073 1.6E-06 51.0 11.2 118 64-188 178-322 (608)
46 cd04474 RPA1_DBD_A RPA1_DBD_A: 96.0 0.074 1.6E-06 39.2 8.7 84 69-159 2-95 (104)
47 cd04487 RecJ_OBF2_like RecJ_OB 95.9 0.048 1.1E-06 37.9 6.8 58 81-143 1-58 (73)
48 cd04316 ND_PkAspRS_like_N ND_P 95.5 0.058 1.2E-06 39.9 6.5 68 93-190 11-79 (108)
49 cd04482 RPA2_OBF_like RPA2_OBF 95.2 0.093 2E-06 37.9 6.6 62 81-145 1-64 (91)
50 COG1107 Archaea-specific RecJ- 95.0 0.035 7.6E-07 52.6 4.7 77 64-146 200-276 (715)
51 cd04483 hOBFC1_like hOBFC1_lik 94.8 0.17 3.7E-06 36.7 7.0 62 83-144 2-78 (92)
52 cd03524 RPA2_OBF_family RPA2_O 94.6 0.45 9.8E-06 30.7 8.4 57 83-144 2-62 (75)
53 cd04320 AspRS_cyto_N AspRS_cyt 94.2 0.18 3.9E-06 36.7 6.0 29 163-191 42-70 (102)
54 cd04322 LysRS_N LysRS_N: N-ter 94.1 0.16 3.4E-06 37.4 5.8 28 163-190 40-67 (108)
55 cd04478 RPA2_DBD_D RPA2_DBD_D: 93.3 0.6 1.3E-05 33.2 7.4 62 81-144 2-63 (95)
56 PRK12366 replication factor A; 93.0 1.6 3.6E-05 42.1 12.0 74 64-143 277-359 (637)
57 TIGR00458 aspS_arch aspartyl-t 92.6 0.27 5.9E-06 45.1 5.9 68 92-189 10-78 (428)
58 cd04485 DnaE_OBF DnaE_OBF: A s 92.1 1.6 3.5E-05 29.2 8.0 47 93-144 16-63 (84)
59 cd04492 YhaM_OBF_like YhaM_OBF 91.3 1.9 4.1E-05 29.2 7.7 45 93-143 16-61 (83)
60 PRK07211 replication factor A; 91.1 3.3 7.2E-05 38.8 11.3 116 66-189 53-184 (485)
61 PRK07373 DNA polymerase III su 91.0 1.1 2.4E-05 41.5 8.1 72 68-144 270-346 (449)
62 cd04323 AsnRS_cyto_like_N AsnR 90.8 0.73 1.6E-05 32.2 5.3 24 168-191 42-65 (84)
63 PRK05159 aspC aspartyl-tRNA sy 90.3 0.69 1.5E-05 42.5 6.0 67 93-190 15-82 (437)
64 PRK12366 replication factor A; 90.1 4.9 0.00011 38.9 11.8 118 64-189 61-197 (637)
65 cd04490 PolII_SU_OBF PolII_SU_ 90.0 3.7 8.1E-05 28.7 8.3 57 81-143 2-62 (79)
66 cd04100 Asp_Lys_Asn_RS_N Asp_L 89.4 1 2.3E-05 31.4 5.2 25 166-190 41-65 (85)
67 cd04318 EcAsnRS_like_N EcAsnRS 89.2 1.1 2.5E-05 31.0 5.2 23 168-190 43-65 (82)
68 PRK14699 replication factor A; 88.9 4.4 9.6E-05 37.9 10.3 112 65-189 275-408 (484)
69 PRK12820 bifunctional aspartyl 88.3 0.93 2E-05 44.3 5.5 69 91-189 15-84 (706)
70 PF08661 Rep_fac-A_3: Replicat 88.2 3.7 8.1E-05 30.3 7.6 67 66-145 7-73 (109)
71 PRK05672 dnaE2 error-prone DNA 88.0 1.9 4.1E-05 44.0 7.7 70 69-144 944-1017(1046)
72 PRK07211 replication factor A; 87.6 8.2 0.00018 36.2 11.0 110 65-190 160-292 (485)
73 COG1570 XseA Exonuclease VII, 87.2 2.1 4.5E-05 39.6 6.8 61 79-144 24-85 (440)
74 cd04319 PhAsnRS_like_N PhAsnRS 86.1 2.7 5.9E-05 30.5 5.8 21 170-190 45-65 (103)
75 PRK15491 replication factor A; 86.1 12 0.00026 33.9 11.0 73 64-143 55-138 (374)
76 PRK07374 dnaE DNA polymerase I 85.9 3.3 7.1E-05 42.8 8.1 71 69-144 991-1066(1170)
77 TIGR00156 conserved hypothetic 85.8 4.8 0.0001 31.1 7.2 68 66-144 45-113 (126)
78 PF04076 BOF: Bacterial OB fol 85.7 4.6 0.0001 30.0 6.9 67 67-144 23-90 (103)
79 PRK05673 dnaE DNA polymerase I 85.1 3.7 8.1E-05 42.3 8.1 72 68-144 967-1043(1135)
80 PRK06826 dnaE DNA polymerase I 83.9 6.9 0.00015 40.5 9.3 63 77-144 990-1057(1151)
81 COG3111 Periplasmic protein wi 83.4 7.8 0.00017 29.9 7.3 73 62-144 41-113 (128)
82 cd04479 RPA3 RPA3: A subfamily 83.4 8.2 0.00018 28.2 7.3 56 74-144 11-67 (101)
83 PF12869 tRNA_anti-like: tRNA_ 83.2 6.2 0.00013 30.0 6.9 67 74-144 63-132 (144)
84 PRK00286 xseA exodeoxyribonucl 83.0 5.1 0.00011 36.6 7.4 62 78-144 23-85 (438)
85 PRK06920 dnaE DNA polymerase I 82.9 6.9 0.00015 40.3 8.9 71 68-144 934-1009(1107)
86 COG0017 AsnS Aspartyl/asparagi 82.8 3.5 7.6E-05 38.1 6.2 64 95-189 17-81 (435)
87 PRK03932 asnC asparaginyl-tRNA 82.3 3.4 7.4E-05 38.2 6.0 69 91-190 13-82 (450)
88 COG4085 Predicted RNA-binding 82.2 5.1 0.00011 33.2 6.3 67 76-145 49-120 (204)
89 PRK10917 ATP-dependent DNA hel 82.1 9.8 0.00021 36.9 9.3 62 76-143 57-122 (681)
90 PRK10053 hypothetical protein; 81.8 7.7 0.00017 30.1 6.9 67 67-144 50-117 (130)
91 TIGR00457 asnS asparaginyl-tRN 80.3 3.8 8.3E-05 37.9 5.6 67 93-189 15-83 (453)
92 TIGR00237 xseA exodeoxyribonuc 79.9 7.4 0.00016 35.8 7.3 60 80-144 19-79 (432)
93 cd04317 EcAspRS_like_N EcAspRS 79.9 5.4 0.00012 30.3 5.5 22 168-189 57-78 (135)
94 PF10451 Stn1: Telomere regula 77.6 11 0.00023 32.5 7.2 61 79-142 67-133 (256)
95 PF15072 DUF4539: Domain of un 76.0 23 0.0005 25.4 7.4 58 82-144 6-63 (86)
96 PLN02903 aminoacyl-tRNA ligase 75.8 5.5 0.00012 38.7 5.4 67 91-188 69-136 (652)
97 cd04488 RecG_wedge_OBF RecG_we 75.4 19 0.00041 23.3 8.3 44 95-144 18-61 (75)
98 PRK07279 dnaE DNA polymerase I 74.6 15 0.00032 37.7 8.2 69 68-144 877-951 (1034)
99 COG1571 Predicted DNA-binding 73.2 11 0.00024 34.7 6.4 64 79-145 267-332 (421)
100 PRK06461 single-stranded DNA-b 72.2 27 0.00059 26.5 7.6 68 65-143 3-80 (129)
101 cd04480 RPA1_DBD_A_like RPA1_D 72.0 30 0.00065 24.0 7.8 72 83-159 7-79 (86)
102 PRK00484 lysS lysyl-tRNA synth 71.8 9.5 0.00021 35.7 5.8 23 168-190 99-121 (491)
103 PRK15491 replication factor A; 71.1 37 0.0008 30.7 9.3 70 65-142 165-245 (374)
104 PRK00476 aspS aspartyl-tRNA sy 68.3 13 0.00028 35.7 6.0 64 93-189 16-80 (588)
105 TIGR00643 recG ATP-dependent D 68.0 40 0.00086 32.4 9.3 62 76-144 30-96 (630)
106 PLN02502 lysyl-tRNA synthetase 66.4 17 0.00036 34.8 6.3 70 94-190 108-178 (553)
107 PRK06386 replication factor A; 66.0 34 0.00075 30.9 7.9 66 65-144 106-179 (358)
108 PRK07135 dnaE DNA polymerase I 64.4 39 0.00085 34.5 8.7 64 77-146 896-963 (973)
109 TIGR00499 lysS_bact lysyl-tRNA 63.9 15 0.00033 34.4 5.5 67 94-190 53-121 (496)
110 COG5235 RFA2 Single-stranded D 63.6 40 0.00086 28.5 7.2 62 80-144 68-129 (258)
111 PLN02221 asparaginyl-tRNA synt 62.8 13 0.00028 35.6 4.9 66 90-189 46-115 (572)
112 KOG3360|consensus 62.5 20 0.00044 26.4 4.8 64 80-158 33-97 (98)
113 PLN02603 asparaginyl-tRNA synt 60.2 23 0.0005 33.9 6.0 66 94-190 107-175 (565)
114 PRK04036 DNA polymerase II sma 59.6 45 0.00097 31.3 7.8 65 77-144 152-217 (504)
115 PRK02983 lysS lysyl-tRNA synth 56.9 30 0.00064 35.8 6.5 70 92-190 649-719 (1094)
116 PTZ00385 lysyl-tRNA synthetase 55.5 31 0.00066 33.8 6.0 65 96-189 109-175 (659)
117 cd04484 polC_OBF polC_OBF: A s 54.8 70 0.0015 22.2 7.7 59 81-144 2-66 (82)
118 TIGR00459 aspS_bact aspartyl-t 51.7 33 0.00071 33.0 5.5 22 168-189 57-78 (583)
119 PRK13480 3'-5' exoribonuclease 51.0 89 0.0019 27.6 7.8 47 92-144 29-76 (314)
120 PRK14699 replication factor A; 49.9 2.3E+02 0.0049 26.7 11.0 71 65-143 56-138 (484)
121 TIGR00594 polc DNA-directed DN 49.2 37 0.00079 34.9 5.7 37 77-113 980-1022(1022)
122 PRK12445 lysyl-tRNA synthetase 41.6 59 0.0013 30.6 5.5 18 172-189 115-132 (505)
123 cd04321 ScAspRS_mt_like_N ScAs 40.3 33 0.00071 23.9 2.8 18 172-189 47-64 (86)
124 KOG3108|consensus 38.1 1.2E+02 0.0025 26.4 6.4 62 80-145 70-132 (265)
125 PRK02801 primosomal replicatio 37.0 1.1E+02 0.0023 22.2 5.2 37 102-143 44-80 (101)
126 PF11736 DUF3299: Protein of u 36.5 55 0.0012 25.7 3.8 70 72-145 49-125 (146)
127 COG1200 RecG RecG-like helicas 35.1 3.3E+02 0.0072 26.9 9.5 65 74-144 56-124 (677)
128 PF03459 TOBE: TOBE domain; I 34.0 1.3E+02 0.0028 19.2 6.1 33 82-114 6-39 (64)
129 PRK08402 replication factor A; 33.3 1.7E+02 0.0036 26.4 6.8 72 65-143 61-143 (355)
130 PRK07218 replication factor A; 33.2 4E+02 0.0086 24.7 10.1 67 68-146 164-238 (423)
131 PF03100 CcmE: CcmE; InterPro 32.8 2.2E+02 0.0048 21.6 9.6 69 66-143 36-110 (131)
132 PRK07218 replication factor A; 29.8 2.8E+02 0.006 25.7 7.8 68 64-144 56-131 (423)
133 PRK00036 primosomal replicatio 27.3 1.7E+02 0.0037 21.8 5.0 36 102-143 43-78 (107)
134 cd04491 SoSSB_OBF SoSSB_OBF: A 27.2 2E+02 0.0044 19.4 7.2 44 93-144 21-65 (82)
135 cd04496 SSB_OBF SSB_OBF: A sub 27.1 2.1E+02 0.0046 19.6 7.9 53 102-159 40-93 (100)
136 PF04874 Mak16: Mak16 protein 26.7 35 0.00075 25.3 1.1 12 46-57 35-46 (101)
137 PF01835 A2M_N: MG2 domain; I 26.3 2E+02 0.0044 19.9 5.1 31 77-107 13-48 (99)
138 PF04057 Rep-A_N: Replication 25.3 2.7E+02 0.0058 20.2 6.5 46 95-144 38-83 (101)
139 PF00436 SSB: Single-strand bi 24.6 2.4E+02 0.0053 19.5 5.6 48 107-159 49-97 (104)
140 PF13452 MaoC_dehydrat_N: N-te 24.1 1.5E+02 0.0034 21.6 4.3 31 74-104 87-120 (132)
141 TIGR00621 ssb single stranded 22.6 3.6E+02 0.0078 21.2 6.4 51 104-159 49-100 (164)
142 PF08496 Peptidase_S49_N: Pept 22.3 1.1E+02 0.0024 24.3 3.3 24 7-30 62-85 (155)
143 PRK06751 single-stranded DNA-b 22.2 4.2E+02 0.0091 21.3 10.0 48 107-159 48-96 (173)
144 PRK14441 acylphosphatase; Prov 20.5 2.2E+02 0.0048 20.3 4.4 30 104-133 41-70 (93)
No 1
>KOG0556|consensus
Probab=100.00 E-value=2.3e-37 Score=273.04 Aligned_cols=169 Identities=37% Similarity=0.538 Sum_probs=152.1
Q ss_pred cccccCHHHHHHHHHHHHHHHHHHHHHHhhcchhcCCCccchhhhccCCccccccCCCCCCceEEcccccccCCCcEEEE
Q psy13182 4 EAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSARLYGKTPLIMSEKDVDRDFVPIRQLNKDYVDKTVWV 83 (194)
Q Consensus 4 ~~~~~sk~alkK~~K~~~k~~kka~k~a~~~~~a~~~~~~d~~~~~Yg~~~l~qs~~~~~~~~~~i~~L~~~~~g~~V~v 83 (194)
+..++||+++||.+|+++|..++.++...++.+..++ ++|.++++||+++++||++.+++.|+.+.||+.+..|+.|||
T Consensus 9 E~gk~SKK~~kk~a~~~eK~~~k~e~~~~~~~a~~~~-~ed~~~~~yg~~~l~~s~~~~~~~~~~v~dl~~~~~~~~V~v 87 (533)
T KOG0556|consen 9 EDGKLSKKALKKLAKKLEKLRKKQEREETAAKAREAE-AEDYAKERYGDLSLIQSQSKEGRELTDVSDLDESNDGSEVLV 87 (533)
T ss_pred ccccccHHHHHHHHHHHHHHHhhhhhhhhhhhhhhhh-hhhHHhhhcCcccccccccccccceeehhhhhhhcCCceEEE
Confidence 3334999999999999999999877654322222222 568899999999999999999999999999999999999999
Q ss_pred EEEEEeeecCCCeEEEEEEecceEEEEEEecccc--ccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeec--
Q psy13182 84 RGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDT--VSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVG-- 159 (194)
Q Consensus 84 rgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~--~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~-- 159 (194)
|||||+.|..||+|||+||++..++||+++.+++ ++++|++|+.+|++||+|+|+|+|.+++.||+|||++++|||
T Consensus 88 RgrVhtsr~~GK~~FlvLRq~~~tVQ~~~~~~~~~~isk~Mvkf~~~is~ESiV~v~g~v~k~~~~i~scT~qdvEi~v~ 167 (533)
T KOG0556|consen 88 RGRVHTSRLKGKLCFLVLRQQGSTVQCLVAVNEDGTISKQMVKFAGSISKESIVDVRGVVVKVKEPIKSCTVQDVEIHVR 167 (533)
T ss_pred EEEEeeccccceEEEEEEeccCceEEEEEEcCCCchHHHHHHHHHhhcCcceEEEEEEEEecCCCcccccccceeEEEEE
Confidence 9999999999999999999999999999988754 999999999999999999999999999999999999999999
Q ss_pred --cccchhhcccccCC
Q psy13182 160 --DTVSKQMIKYVSQI 173 (194)
Q Consensus 160 --~~is~~~~~~~~~l 173 (194)
++||.+..++|.++
T Consensus 168 ~iyviS~a~~~LPl~v 183 (533)
T KOG0556|consen 168 KIYVISIALPNLPLQV 183 (533)
T ss_pred EEEEEecccccCCeee
Confidence 68999999999886
No 2
>PLN02850 aspartate-tRNA ligase
Probab=99.97 E-value=1.3e-30 Score=241.44 Aligned_cols=168 Identities=32% Similarity=0.488 Sum_probs=145.0
Q ss_pred ccccccCHHHHHHHHHHHHHHHHHHHHHHhhcchhcCCCccchhhhccCCccccccCC-CCCCceEEcccccccCCCcEE
Q psy13182 3 SEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSARLYGKTPLIMSEK-DVDRDFVPIRQLNKDYVDKTV 81 (194)
Q Consensus 3 ~~~~~~sk~alkK~~K~~~k~~kka~k~a~~~~~a~~~~~~d~~~~~Yg~~~l~qs~~-~~~~~~~~i~~L~~~~~g~~V 81 (194)
..+.++||+++||++|+++|+++++++++++ ++.++ ++|.++++||++||+||+. +++++|+.|++|++++.|+.|
T Consensus 8 ~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~-~~~~~--~~~~~~~~yg~~~~~~~~~~~~~~~~~~i~~l~~~~~g~~V 84 (530)
T PLN02850 8 ESGEKISKKAAKKAAAKAEKLRREATAKAAA-ASLED--EDDPLASNYGDVPLEELQSKVTGREWTDVSDLGEELAGSEV 84 (530)
T ss_pred ccCCCcCHHHHHHHHHHHHHHHHHHHHHHHH-hhhcc--ccchhhccCCcccccccccccCCceEeEhhhcchhhCCCEE
Confidence 3466799999999999999998876644321 11112 3588899999999999997 788899999999999999999
Q ss_pred EEEEEEEeeecCCCeEEEEEEecceEEEEEEeccc-cccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeec-
Q psy13182 82 WVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGD-TVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVG- 159 (194)
Q Consensus 82 ~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~-~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~- 159 (194)
+|+||||++|.+|+++|++|||+++++|||+.... .++++|++|+..|++||+|.|+|+|..++.++.+||+ ++||+
T Consensus 85 ~v~Grv~~~R~~gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~t~-~~El~~ 163 (530)
T PLN02850 85 LIRGRVHTIRGKGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQLSRESVVDVEGVVSVPKKPVKGTTQ-QVEIQV 163 (530)
T ss_pred EEEEEEEEEccCCCeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCCCCCCEEEEEEEEEccCcCCCCCCc-cEEEEE
Confidence 99999999999999999999999999999997654 3789999999999999999999999999999999997 89998
Q ss_pred ---cccchhhcccccCCC
Q psy13182 160 ---DTVSKQMIKYVSQIP 174 (194)
Q Consensus 160 ---~~is~~~~~~~~~l~ 174 (194)
.++|++...+|+++.
T Consensus 164 ~~i~vls~a~~~lP~~~~ 181 (530)
T PLN02850 164 RKIYCVSKALATLPFNVE 181 (530)
T ss_pred eEEEEEeCCCCCCCCChh
Confidence 457888778887764
No 3
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=99.96 E-value=2.5e-29 Score=233.43 Aligned_cols=165 Identities=28% Similarity=0.449 Sum_probs=141.8
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHhhcchhcCCCccchhhhccCCccccccCCCCCCceEEcccccccC-CCcEEEEE
Q psy13182 6 QKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSARLYGKTPLIMSEKDVDRDFVPIRQLNKDY-VDKTVWVR 84 (194)
Q Consensus 6 ~~~sk~alkK~~K~~~k~~kka~k~a~~~~~a~~~~~~d~~~~~Yg~~~l~qs~~~~~~~~~~i~~L~~~~-~g~~V~vr 84 (194)
...+|+++||++|+++|+++++++++.++..++ ++|.++++||.+||+||+.++++.|+.|.+|+.++ .|+.|+|+
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~g~~~~~~~~~~~~~~~~~i~~l~~~~~~g~~V~v~ 84 (550)
T PTZ00401 8 AGAPAVEKKQSDKEARKAARLAEEKARAAEKAA---LVEKYKDVFGAAPMVQSTTYKSRTFIPVAVLSKPELVDKTVLIR 84 (550)
T ss_pred cCcchhhHHHHHHHHHhHHHHHHHHHHHHhhhh---ccchhhccCCccccccccccCCCceEEHHHCCccccCCCEEEEE
Confidence 345778888888888888887776554221111 34888999999999999988999999999998777 89999999
Q ss_pred EEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeec----c
Q psy13182 85 GRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVG----D 160 (194)
Q Consensus 85 grv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~----~ 160 (194)
||||++|.+|+++||.|||+++++|+|+......+++|++|+..|+.||+|.|+|+|..++.++.+|+.+++||+ .
T Consensus 85 Grv~~~R~~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l~~esiV~V~G~v~~~~~~~~~~~~~~~El~v~~i~ 164 (550)
T PTZ00401 85 ARVSTTRKKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIPTESIVDVEATVCKVEQPITSTSHSDIELKVKKIH 164 (550)
T ss_pred EEEEEEecCCCeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcCCCCCEEEEEEEEEecCccCCCCCCccEEEEeeEEE
Confidence 999999999999999999999999999876545789999999999999999999999999999999999999999 4
Q ss_pred ccchhhcccccCC
Q psy13182 161 TVSKQMIKYVSQI 173 (194)
Q Consensus 161 ~is~~~~~~~~~l 173 (194)
++|++...+|+++
T Consensus 165 vls~a~~~lP~~~ 177 (550)
T PTZ00401 165 TVTESLRTLPFTL 177 (550)
T ss_pred EEeCCCCCCCCCc
Confidence 5787777788765
No 4
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=99.77 E-value=4.3e-18 Score=127.24 Aligned_cols=103 Identities=19% Similarity=0.284 Sum_probs=83.4
Q ss_pred EcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcc
Q psy13182 68 PIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTI 147 (194)
Q Consensus 68 ~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~ 147 (194)
++.+|...+.|+.|+++|||++.|..|+++|+.|||+++.+|+++... ..+++|++++..|+.||+|.|+|++...+.+
T Consensus 2 ~~~~l~~~~~g~~V~v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~-~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~ 80 (108)
T cd04316 2 YSAEITPELDGEEVTVAGWVHEIRDLGGIKFVILRDREGIVQVTAPKK-KVDKELFKTVRKLSRESVISVTGTVKAEPKA 80 (108)
T ss_pred ChhhCchhhCCCEEEEEEEEEeeeccCCeEEEEEecCCeeEEEEEeCC-CCCHHHHHHHhCCCCcCEEEEEEEEEeCCCC
Confidence 466777677899999999999999999999999999999999998743 3567799999999999999999999998876
Q ss_pred cCCCceeeeeeccccchhhcccccC
Q psy13182 148 VESLPMSILSVGDTVSKQMIKYVSQ 172 (194)
Q Consensus 148 i~~~t~~~~El~~~is~~~~~~~~~ 172 (194)
..+.+++--++. .++++...||+.
T Consensus 81 ~~~~Ei~~~~i~-il~~~~~~~P~~ 104 (108)
T cd04316 81 PNGVEIIPEEIE-VLSEAKTPLPLD 104 (108)
T ss_pred CCCEEEEEeEEE-EEeCCCCCCCcC
Confidence 554444444444 567665566654
No 5
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=99.74 E-value=2.5e-17 Score=121.80 Aligned_cols=94 Identities=37% Similarity=0.563 Sum_probs=79.1
Q ss_pred EEEEEEEEEeeecCC-CeEEEEEEecceEEEEEEecccc-ccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeee
Q psy13182 80 TVWVRGRLHTSRAKG-KQCFVVIREQNFTIQGILSVGDT-VSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILS 157 (194)
Q Consensus 80 ~V~vrgrv~~~R~~G-k~~Fl~lRd~~~~vQ~v~~~~~~-~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~E 157 (194)
.|+++|||++.|..| +++|+.|||+++.+|+++..... .+.+|++++..|+.||+|.|+|++..++.++.+|+.+++|
T Consensus 1 ~V~i~Gwv~~~R~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~~~~~~~E 80 (102)
T cd04320 1 EVLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEGTVKKPEEPIKSCTQQDVE 80 (102)
T ss_pred CEEEEEEEEEeecCCCceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEEEEECCCCcccCCCcCcEE
Confidence 388999999999999 99999999999999999975432 4678999999999999999999999988877778888888
Q ss_pred ec----cccchhhcccccCC
Q psy13182 158 VG----DTVSKQMIKYVSQI 173 (194)
Q Consensus 158 l~----~~is~~~~~~~~~l 173 (194)
|+ ..++++...+|+.+
T Consensus 81 l~~~~i~il~~~~~~~P~~~ 100 (102)
T cd04320 81 LHIEKIYVVSEAAEPLPFQL 100 (102)
T ss_pred EEEEEEEEEecCCCCCCCCC
Confidence 88 24566555566554
No 6
>KOG0555|consensus
Probab=99.69 E-value=1.2e-16 Score=141.75 Aligned_cols=166 Identities=19% Similarity=0.167 Sum_probs=112.7
Q ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHhhc-ch-hcCCCccchhhhccCCccccccCCCCCCceEEcccccccCCCcEEEE
Q psy13182 6 QKVSKKALKKQAKEQEKKEKKDQRKSAQQ-NV-EESEPVEDVSARLYGKTPLIMSEKDVDRDFVPIRQLNKDYVDKTVWV 83 (194)
Q Consensus 6 ~~~sk~alkK~~K~~~k~~kka~k~a~~~-~~-a~~~~~~d~~~~~Yg~~~l~qs~~~~~~~~~~i~~L~~~~~g~~V~v 83 (194)
++.||++|||++|.-..+.+|.+++.+.+ .+ ++.+++.+.++ ++.+....+.|.++.++|.+.. .+.|++|.+
T Consensus 54 e~~sk~~Lkk~~kg~~~~~~k~~k~~~~ea~~~ek~~~~le~a~----ki~ised~slp~ak~iki~~s~-~~r~qrVkv 128 (545)
T KOG0555|consen 54 EPISKSALKKIKKGWVRECKKSAKASQKEAEASEKREKNLEEAK----KITISEDKSLPAAKKIKIYDST-ENRGQRVKV 128 (545)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhHHhhh----cccccCCCCCchhheeeecccc-cccCceEEe
Confidence 58899999999998888777776654311 11 11110111122 4455555566777788888874 478999999
Q ss_pred EEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCc-----eeeeee
Q psy13182 84 RGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLP-----MSILSV 158 (194)
Q Consensus 84 rgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t-----~~~~El 158 (194)
.||||+.|.+.++.||+|||+++.+|||+......+ ..+-.|+.||.|+|+|++.+.|.-....- +.-+||
T Consensus 129 ~gWVhrlR~qk~l~FivLrdg~gflqCVl~~kl~~~----yd~~~Ls~essv~vYG~i~~~p~GK~apgghEl~vdy~Ei 204 (545)
T KOG0555|consen 129 FGWVHRLRRQKSLIFIVLRDGTGFLQCVLSDKLCQS----YDALTLSTESSVTVYGTIKKLPEGKSAPGGHELNVDYWEI 204 (545)
T ss_pred ehhhHhhhhcCceEEEEEecCCceEEEEEcchhhhh----hccccccccceEEEEEEEecCcCCCCCCCCceEEeeeeee
Confidence 999999999999999999999999999997542222 23456789999999999999976443322 333333
Q ss_pred ccccchhhcccccCCCCCceEeEE
Q psy13182 159 GDTVSKQMIKYVSQIPKESILDIQ 182 (194)
Q Consensus 159 ~~~is~~~~~~~~~l~~esi~~~~ 182 (194)
-. -.+..-+..-||.+|=+|+.
T Consensus 205 ig--~Apag~~~n~lne~s~~~~~ 226 (545)
T KOG0555|consen 205 IG--LAPAGGFDNPLNEESDVDVL 226 (545)
T ss_pred ec--ccCCCcccccccccCCcceE
Confidence 31 11222334458888877764
No 7
>PLN02502 lysyl-tRNA synthetase
Probab=99.63 E-value=7.3e-15 Score=137.10 Aligned_cols=168 Identities=22% Similarity=0.237 Sum_probs=108.3
Q ss_pred CCccccccCHHHHHHHHHHHHHHHHHHHHHHhhcc-h--h--------cCCCccchhhhccCCccc---c---cc--CCC
Q psy13182 1 MESEAQKVSKKALKKQAKEQEKKEKKDQRKSAQQN-V--E--------ESEPVEDVSARLYGKTPL---I---MS--EKD 61 (194)
Q Consensus 1 ~~~~~~~~sk~alkK~~K~~~k~~kka~k~a~~~~-~--a--------~~~~~~d~~~~~Yg~~~l---~---qs--~~~ 61 (194)
+++.+.++||+++||++|..+++++++++.++++. + + ..+..++.....|....+ . .. .++
T Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~l~~~g~~py 80 (553)
T PLN02502 1 AESNGEPLSKNALKKRLKAKQAEEEKAAKEEAKAAAAAAAAKGRSRKSAAADDETMDPTQYRANRLKKVEALRAKGVEPY 80 (553)
T ss_pred CCCCcccccHHHHHHHHhhhhhhHHHhhhHhhcccccccccCccccccccccccccCHHHHHHHHHHHHHHHHHcCCCCC
Confidence 46778999999999999999999988877654111 0 0 000001111122322211 0 01 134
Q ss_pred CCC--ceEEcccc-------c--ccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccc--cHHHHHHHhc
Q psy13182 62 VDR--DFVPIRQL-------N--KDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTV--SKQMIKYVSQ 128 (194)
Q Consensus 62 ~~~--~~~~i~~L-------~--~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~--s~~m~k~~~~ 128 (194)
|+. ..+.+.++ . .++.|+.|+|+|||++.|.+|+++|+.|||+++.+|+++...... ...|..+...
T Consensus 81 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~v~GrV~~~R~~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~ 160 (553)
T PLN02502 81 PYKFDVTHTAPELQEKYGSLENGEELEDVSVSVAGRIMAKRAFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSL 160 (553)
T ss_pred CCCCCCCccHHHHHHHhhccccccccCCCEEEEEEEEEEEecCCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhC
Confidence 432 11334333 1 235678899999999999999999999999999999998754211 1336666678
Q ss_pred CCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhccccc
Q psy13182 129 IPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYVS 171 (194)
Q Consensus 129 l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~~ 171 (194)
|.+|++|.|.|++.+++. ...++..-++. .+|+..-.+|.
T Consensus 161 l~~gdiV~V~G~~~~t~~--gelel~~~~i~-vLs~~l~plP~ 200 (553)
T PLN02502 161 VDRGDIVGVTGTPGKTKK--GELSIFPTSFE-VLTKCLLMLPD 200 (553)
T ss_pred CCCCcEEEEEEEEEecCC--CCEEEEEeEEE-EEeccCCCCCc
Confidence 999999999999999864 34444444444 56766544554
No 8
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=99.63 E-value=2.6e-15 Score=116.15 Aligned_cols=104 Identities=19% Similarity=0.310 Sum_probs=79.5
Q ss_pred EEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCc
Q psy13182 67 VPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPT 146 (194)
Q Consensus 67 ~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~ 146 (194)
+.+.++.+.+.|+.|+|+|||+++|.+|+++|+.|||+++.+|+|+..... .. ++++..|+.||+|.|+|++..++.
T Consensus 3 ~~~~~~~~~~~g~~V~i~Gwv~~~R~~gk~~Fi~LrD~~g~~Q~v~~~~~~--~~-~~~~~~l~~gs~V~V~G~~~~~~~ 79 (135)
T cd04317 3 HYCGELRESHVGQEVTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEA--PE-FELAEKLRNESVIQVTGKVRARPE 79 (135)
T ss_pred eehhhCChhHCCCEEEEEEeEehhcccCCEEEEEEecCCeeEEEEEeCCch--hH-HHHHhCCCCccEEEEEEEEECCCc
Confidence 346777667789999999999999999999999999999999999864321 22 678899999999999999998654
Q ss_pred c-cC-CCceeeeeec----cccchhhcccccCCC
Q psy13182 147 I-VE-SLPMSILSVG----DTVSKQMIKYVSQIP 174 (194)
Q Consensus 147 ~-i~-~~t~~~~El~----~~is~~~~~~~~~l~ 174 (194)
. +. .+..+++||+ ..++++ ..+|+.+.
T Consensus 80 ~~~~~~~~~~~~El~~~~i~vl~~~-~~lP~~~~ 112 (135)
T cd04317 80 GTVNPKLPTGEIEVVASELEVLNKA-KTLPFEID 112 (135)
T ss_pred cccCCCCCCCcEEEEEeEEEEEECC-CCCCCccc
Confidence 2 21 1223456666 246766 67777654
No 9
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=99.63 E-value=5.4e-15 Score=109.58 Aligned_cols=89 Identities=17% Similarity=0.250 Sum_probs=70.8
Q ss_pred EEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeec
Q psy13182 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVG 159 (194)
Q Consensus 80 ~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~ 159 (194)
+|+++|||++.|..|+++|+.|||+++.+|+++... .++++++.+..|+.||+|.|+|++...+.+..+.+++--.+.
T Consensus 1 ~V~v~Gwv~~~R~~gk~~Fi~lrD~~g~iQ~v~~~~--~~~~~~~~~~~l~~~s~v~V~G~v~~~~~~~~~~Ei~~~~i~ 78 (103)
T cd04319 1 KVTLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKD--LNEEAYREAKKVGIESSVIVEGAVKADPRAPGGAEVHGEKLE 78 (103)
T ss_pred CEEEEEEEEeEEcCCCeEEEEEecCCeeEEEEEeCC--CCHHHHHHHhCCCCCCEEEEEEEEEECCCCCCCEEEEEEEEE
Confidence 389999999999999999999999999999998753 456788888999999999999999998876655444333333
Q ss_pred cccchhhcccccC
Q psy13182 160 DTVSKQMIKYVSQ 172 (194)
Q Consensus 160 ~~is~~~~~~~~~ 172 (194)
.++.+. .+|.+
T Consensus 79 -vl~~a~-~~pi~ 89 (103)
T cd04319 79 -IIQNVE-FFPIT 89 (103)
T ss_pred -EEecCC-CCccC
Confidence 456653 56654
No 10
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=99.62 E-value=3.7e-15 Score=106.53 Aligned_cols=75 Identities=21% Similarity=0.251 Sum_probs=64.9
Q ss_pred EEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeec
Q psy13182 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVG 159 (194)
Q Consensus 80 ~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~ 159 (194)
+|+++|||++.|..|+++|+.|||+++.+|+++..... .. ++++..|+.||+|.|+|++..++.++ ++.+++||+
T Consensus 1 ~V~v~Gwv~~~R~~g~~~Fi~LrD~~~~iQ~v~~~~~~--~~-~~~~~~l~~es~V~V~G~v~~~~~~~--~~~~~~Ei~ 75 (84)
T cd04323 1 RVKVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLV--TE-FYDAKSLTQESSVEVTGEVKEDPRAK--QAPGGYELQ 75 (84)
T ss_pred CEEEEEEEEEEecCCCcEEEEEEcCCeEEEEEEcCCcc--hh-HHHHhcCCCcCEEEEEEEEEECCccc--CCCCCEEEE
Confidence 38999999999999999999999999999998864321 22 67889999999999999999988776 777788888
No 11
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=99.61 E-value=4.7e-15 Score=106.06 Aligned_cols=76 Identities=17% Similarity=0.299 Sum_probs=65.3
Q ss_pred EEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeec
Q psy13182 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVG 159 (194)
Q Consensus 80 ~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~ 159 (194)
.|+++|||++.|..|+++|+.|||+++.+|+++.... ..+|++++..|+.||+|.|+|.+..++.++ +..+++||+
T Consensus 1 ~V~i~Gwv~~~R~~g~~~Fi~Lrd~~~~iQ~v~~~~~--~~~~~~~~~~l~~~s~V~v~G~~~~~~~~~--~~~~~~El~ 76 (85)
T cd04100 1 EVTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEE--LGEFFEEAEKLRTESVVGVTGTVVKRPEGN--LATGEIELQ 76 (85)
T ss_pred CEEEEEEEehhccCCCEEEEEEEeCCeeEEEEEECCc--ChHHHHHHhCCCCCCEEEEEeEEEECCCCC--CCCCCEEEE
Confidence 3899999999999999999999999999999987542 233889999999999999999999987655 445778877
No 12
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=99.61 E-value=7.9e-15 Score=109.49 Aligned_cols=90 Identities=19% Similarity=0.249 Sum_probs=67.8
Q ss_pred EEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeec
Q psy13182 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVG 159 (194)
Q Consensus 80 ~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~ 159 (194)
.|+++|||+++|..|+++|+.|||+++.+|+|+......+..|.++...|++||+|.|+|++..++. .+.++..-.+.
T Consensus 1 ~v~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~--g~~El~~~~~~ 78 (108)
T cd04322 1 EVSVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKT--GELSIFVKEFT 78 (108)
T ss_pred CEEEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCC--CCEEEEeCEeE
Confidence 3789999999999999999999999999999987543334556666666999999999999999865 33433333333
Q ss_pred cccchhhcccccC
Q psy13182 160 DTVSKQMIKYVSQ 172 (194)
Q Consensus 160 ~~is~~~~~~~~~ 172 (194)
.+|++..++|..
T Consensus 79 -ils~~~~plP~~ 90 (108)
T cd04322 79 -LLSKSLRPLPEK 90 (108)
T ss_pred -EeeccCCCCCCC
Confidence 467665445543
No 13
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=99.60 E-value=7.3e-15 Score=132.74 Aligned_cols=109 Identities=21% Similarity=0.317 Sum_probs=90.5
Q ss_pred eEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 66 FVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 66 ~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
.+.+.++.+...+++|+|+||||+.|.+|+++||.|||+++.+|||+... ...+++++ +..|+.||+|.|.|+|.+.+
T Consensus 4 ~~~i~di~~~~~~~~V~v~GWV~~~R~~g~i~Fi~lrDgsg~iQ~v~~~~-~~~~~~~~-~~~L~~es~v~V~G~v~~~~ 81 (435)
T COG0017 4 RTYIKDIKPHVGGQEVTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKN-KVYEELFK-AKKLTLESSVVVTGIVKASP 81 (435)
T ss_pred eeeHHhhhccCCCcEEEEEEEeeeecccCCeEEEEEEcCCcEEEEEEECC-CCcHHHhh-hhcCCCccEEEEEEEEEcCC
Confidence 46778887655569999999999999999999999999999999999864 33677888 99999999999999999999
Q ss_pred cccCCCceeeeeeccccchhhcccccCCCCCc
Q psy13182 146 TIVESLPMSILSVGDTVSKQMIKYVSQIPKES 177 (194)
Q Consensus 146 ~~i~~~t~~~~El~~~is~~~~~~~~~l~~es 177 (194)
....+.+++.-.|. +++.+-.++|.+....+
T Consensus 82 ~a~~g~El~v~~i~-Vl~~a~~~~Pi~~~~~~ 112 (435)
T COG0017 82 KAPQGFELQVEKIE-VLGEADPPYPIDKKEHS 112 (435)
T ss_pred CCCCCEEEEEEEEE-EeeccCCCCCcCccccc
Confidence 98888777766666 56777446676655544
No 14
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=99.58 E-value=2.1e-14 Score=130.94 Aligned_cols=107 Identities=16% Similarity=0.255 Sum_probs=89.3
Q ss_pred ceEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 65 DFVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 65 ~~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
..+.|.+|+..+.|++|+|+|||++.|.+|+++|+.|||+++.+|+++..... ++|++++..|+.||+|.|+|++..+
T Consensus 3 ~~~~~~~l~~~~~g~~V~i~GrV~~~R~~gk~~Fl~LrD~~g~iQ~v~~~~~~--~~~~~~~~~L~~gs~V~v~G~v~~~ 80 (437)
T PRK05159 3 KRHLTSELTPELDGEEVTLAGWVHEIRDLGGIAFLILRDRSGIIQVVVKKKVD--EELFETIKKLKRESVVSVTGTVKAN 80 (437)
T ss_pred ceeEhhhCChhhCCCEEEEEEEeEeeecCCCeEEEEEEcCCcEEEEEEeCCcc--HHHHHHHhCCCCCcEEEEEEEEEcC
Confidence 35789999988899999999999999999999999999999999999875422 6789999999999999999999998
Q ss_pred CcccCCCceeeeeeccccchhhcccccCCC
Q psy13182 145 PTIVESLPMSILSVGDTVSKQMIKYVSQIP 174 (194)
Q Consensus 145 ~~~i~~~t~~~~El~~~is~~~~~~~~~l~ 174 (194)
+....+.+++.-.+. ++|++...+|..+.
T Consensus 81 ~~~~~~~el~~~~i~-vls~a~~~~P~~~~ 109 (437)
T PRK05159 81 PKAPGGVEVIPEEIE-VLNKAEEPLPLDIS 109 (437)
T ss_pred CCCCCCEEEEEeEEE-EEeCCCCCCCCCcc
Confidence 765555555555554 67877767776554
No 15
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=99.56 E-value=2.6e-14 Score=129.97 Aligned_cols=104 Identities=16% Similarity=0.206 Sum_probs=83.0
Q ss_pred EcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcc
Q psy13182 68 PIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTI 147 (194)
Q Consensus 68 ~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~ 147 (194)
.+.+|+.++.|+.|+|+|||+++|.+|+++|+.|||+++++|+++... ..+++|++++..|+.||+|.|.|+|...+..
T Consensus 2 ~~~~l~~~~~g~~v~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~-~~~~~~~~~~~~l~~~s~v~v~G~v~~~~~~ 80 (428)
T TIGR00458 2 YSADIKPEMDGQEVTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAK-KVSKNLFKWAKKLNLESVVAVRGIVKIKEKA 80 (428)
T ss_pred chhhCchhhCCCEEEEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECC-cCCHHHHHHHhCCCCCcEEEEEEEEEecCCC
Confidence 467888788999999999999999999999999999999999998754 3567899999999999999999999976543
Q ss_pred cCCCceeeeeeccccchhhcccccCC
Q psy13182 148 VESLPMSILSVGDTVSKQMIKYVSQI 173 (194)
Q Consensus 148 i~~~t~~~~El~~~is~~~~~~~~~l 173 (194)
..+.++..-.+. ++|++...+|..+
T Consensus 81 ~~~~el~~~~i~-vl~~~~~~lP~~~ 105 (428)
T TIGR00458 81 PGGFEIIPTKIE-VINEAKEPLPLDP 105 (428)
T ss_pred CCcEEEEEeEEE-EEecCCCCCCCCc
Confidence 333333333333 5777765677654
No 16
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=99.55 E-value=3.1e-14 Score=135.69 Aligned_cols=108 Identities=18% Similarity=0.181 Sum_probs=88.2
Q ss_pred eEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 66 FVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 66 ~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
.++|++|+.++.|+.|+|+|||++.|.+|+++|+.|||+++.+|+|+... ..+.++++++..|++||+|.|+|+|..++
T Consensus 6 ~~~cg~l~~~~~g~~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~-~~~~~~~~~~~~L~~EsvV~V~G~v~~r~ 84 (706)
T PRK12820 6 RSFCGHLSLDDTGREVCLAGWVDAFRDHGELLFIHLRDRNGFIQAVFSPE-AAPADVYELAASLRAEFCVALQGEVQKRL 84 (706)
T ss_pred ccccccCChhhCCCEEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCC-cCCHHHHHHHhcCCCCCEEEEEeEEeccC
Confidence 47899999999999999999999999999999999999999999998753 34577899999999999999999999976
Q ss_pred cccCCCc--eeeeeec----cccchhhcccccCCCC
Q psy13182 146 TIVESLP--MSILSVG----DTVSKQMIKYVSQIPK 175 (194)
Q Consensus 146 ~~i~~~t--~~~~El~----~~is~~~~~~~~~l~~ 175 (194)
....++. .+++||. .+++++. .+|+.++.
T Consensus 85 ~~~~n~~~~tg~iEl~~~~i~iL~~a~-~lP~~i~~ 119 (706)
T PRK12820 85 EETENPHIETGDIEVFVRELSILAASE-ALPFAISD 119 (706)
T ss_pred ccccCCCCCCCcEEEEeeEEEEEecCC-CCCCCCcc
Confidence 5554443 3667777 2456553 56776654
No 17
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=99.53 E-value=5.8e-14 Score=129.15 Aligned_cols=108 Identities=22% Similarity=0.297 Sum_probs=91.8
Q ss_pred eEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 66 FVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 66 ~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
.++|++|..++.|++|++.||||+.|.+|+++||.|||++|.+|+|+.. ..+.+.++.+..|+.|++|.|.|+|...+
T Consensus 3 t~~cg~l~~~~vG~~V~L~GWV~r~Rd~GgliFiDLRDr~GivQvv~~~--~~~~~~~~~a~~lr~E~vi~V~G~V~~R~ 80 (585)
T COG0173 3 THYCGELRESHVGQTVTLSGWVHRRRDHGGLIFIDLRDREGIVQVVFDP--EDSPEAFEVASRLRNEFVIQVTGTVRARP 80 (585)
T ss_pred ceeccccCHHHCCCEEEEEeeeeeccccCCeEEEEcccCCCeEEEEECC--ccCHHHHHHHHhcCceEEEEEEEEEEecC
Confidence 4789999999999999999999999999999999999999999999864 36788999999999999999999999998
Q ss_pred c--ccCCCceeeeeecc----ccchhhcccccCCCCC
Q psy13182 146 T--IVESLPMSILSVGD----TVSKQMIKYVSQIPKE 176 (194)
Q Consensus 146 ~--~i~~~t~~~~El~~----~is~~~~~~~~~l~~e 176 (194)
+ .+.......+||+. +++ .--.+|+.|..+
T Consensus 81 e~~~N~~l~TGeiEv~a~~i~vln-~s~~lPf~i~d~ 116 (585)
T COG0173 81 EGTINPNLPTGEIEVLAEEIEVLN-ASKTLPFQIEDE 116 (585)
T ss_pred ccccCCCCCcceEEEEeeeEEEEe-cCCCCCcCCCCC
Confidence 7 56666777888872 234 445667777655
No 18
>PLN02903 aminoacyl-tRNA ligase
Probab=99.50 E-value=1.1e-13 Score=130.94 Aligned_cols=107 Identities=13% Similarity=0.150 Sum_probs=85.8
Q ss_pred eEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 66 FVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 66 ~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
.++|++|+..+.|++|+|+|||++.|.+|+++|+.|||+++.+|+|+.... +.++++++..|+.||+|.|+|+|..++
T Consensus 60 t~~cg~l~~~~~gk~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~--~~~~~~~~~~L~~esvV~V~G~V~~r~ 137 (652)
T PLN02903 60 SHLCGALSVNDVGSRVTLCGWVDLHRDMGGLTFLDVRDHTGIVQVVTLPDE--FPEAHRTANRLRNEYVVAVEGTVRSRP 137 (652)
T ss_pred CCchhhcchhhCCCEEEEEEEEEEEecCCCcEEEEEEcCCccEEEEEeCCc--cHHHHHHHhcCCCCCEEEEEEEEEeCC
Confidence 468999999999999999999999999999999999999999999986432 467889999999999999999999875
Q ss_pred c-ccC-CCceeeeeec----cccchhhcccccCCC
Q psy13182 146 T-IVE-SLPMSILSVG----DTVSKQMIKYVSQIP 174 (194)
Q Consensus 146 ~-~i~-~~t~~~~El~----~~is~~~~~~~~~l~ 174 (194)
. ++. .+..+++||. .++++....+|+.+.
T Consensus 138 ~~~~n~~~~tGeiEl~~~~i~VL~~a~~~lPf~i~ 172 (652)
T PLN02903 138 QESPNKKMKTGSVEVVAESVDILNVVTKSLPFLVT 172 (652)
T ss_pred CcCcCCCCCCCCEEEEEeEEEEEecCCCCCCcccc
Confidence 3 222 2223567776 246766556676654
No 19
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=99.45 E-value=7.4e-13 Score=121.21 Aligned_cols=103 Identities=19% Similarity=0.321 Sum_probs=82.3
Q ss_pred EEcccc-cccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 67 VPIRQL-NKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 67 ~~i~~L-~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
+.|.++ ..++.|+.|+|+|||+++|.+|+++|++|||+++.+|+++.... +..+++++..|+.||+|.|.|++..++
T Consensus 4 ~~~~~~~~~~~~~~~V~i~G~v~~~R~~g~~~Fi~lrD~~g~iq~~~~~~~--~~~~~~~~~~l~~~s~v~v~G~v~~~~ 81 (450)
T PRK03932 4 VSIKDILKGKYVGQEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDN--GEEYFEEIKKLTTGSSVIVTGTVVESP 81 (450)
T ss_pred EEHHHhcccccCCCEEEEEEEEEEEEeCCCeEEEEEECCCCcEEEEEEcCC--ChHHHHHHhcCCCCcEEEEEEEEEcCC
Confidence 456666 56788999999999999999999999999999999999886543 567899999999999999999999987
Q ss_pred cccCCCceeeeeeccccchhhcccccC
Q psy13182 146 TIVESLPMSILSVGDTVSKQMIKYVSQ 172 (194)
Q Consensus 146 ~~i~~~t~~~~El~~~is~~~~~~~~~ 172 (194)
....+.+++.-++. ++++....+|..
T Consensus 82 ~~~~~~el~~~~i~-vl~~~~~~~p~~ 107 (450)
T PRK03932 82 RAGQGYELQATKIE-VIGEDPEDYPIQ 107 (450)
T ss_pred CCCCCEEEEEEEEE-EccCCCCCCCCC
Confidence 65555555555554 567654455544
No 20
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=99.45 E-value=1e-12 Score=93.32 Aligned_cols=70 Identities=16% Similarity=0.233 Sum_probs=59.2
Q ss_pred EEEEEEEEeeecCCCeEEEEEEecceE--EEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeee
Q psy13182 81 VWVRGRLHTSRAKGKQCFVVIREQNFT--IQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSV 158 (194)
Q Consensus 81 V~vrgrv~~~R~~Gk~~Fl~lRd~~~~--vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El 158 (194)
|+++||+++.|.+|+++|+.|||+++. +|+++..... .++++..|+.||+|.|.|++..++.+ .+++||
T Consensus 2 v~v~Gwv~~~R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~----~~~~~~~l~~gs~V~v~G~v~~~~~~-----~~~~El 72 (82)
T cd04318 2 VTVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDKELT----NFKEILKLSTGSSIRVEGVLVKSPGA-----KQPFEL 72 (82)
T ss_pred EEEEEeEEEEEcCCcEEEEEEECCCCccCEEEEEeCccc----CHHHHhcCCCceEEEEEEEEEeCCCC-----CCCEEE
Confidence 789999999999999999999999985 9999875421 15778899999999999999998765 246666
Q ss_pred c
Q psy13182 159 G 159 (194)
Q Consensus 159 ~ 159 (194)
+
T Consensus 73 ~ 73 (82)
T cd04318 73 Q 73 (82)
T ss_pred E
Confidence 6
No 21
>KOG0556|consensus
Probab=99.45 E-value=2e-13 Score=121.74 Aligned_cols=90 Identities=22% Similarity=0.266 Sum_probs=79.8
Q ss_pred CcEEEEEEEEEeeecCCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeee
Q psy13182 78 DKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSIL 156 (194)
Q Consensus 78 g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~ 156 (194)
....|+..+..+....|+.+|++.|.++.+.|+ ++|.. +|++..+||+.+..+..
T Consensus 66 ~~~~~~~v~dl~~~~~~~~V~vRgrVhtsr~~GK~~Flv--------------LRq~~~tVQ~~~~~~~~---------- 121 (533)
T KOG0556|consen 66 EGRELTDVSDLDESNDGSEVLVRGRVHTSRLKGKLCFLV--------------LRQQGSTVQCLVAVNED---------- 121 (533)
T ss_pred cccceeehhhhhhhcCCceEEEEEEEeeccccceEEEEE--------------EeccCceEEEEEEcCCC----------
Confidence 445677777777778889999999999999998 77876 89999999999988754
Q ss_pred eeccccchhhcccccCCCCCceEeEEEEEecCCccccC
Q psy13182 157 SVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVES 194 (194)
Q Consensus 157 El~~~is~~~~~~~~~l~~esi~~~~~~~~~~~~~~~~ 194 (194)
.++|++|++|..+|++||||||+|+|.+++.||+|
T Consensus 122 ---~~isk~Mvkf~~~is~ESiV~v~g~v~k~~~~i~s 156 (533)
T KOG0556|consen 122 ---GTISKQMVKFAGSISKESIVDVRGVVVKVKEPIKS 156 (533)
T ss_pred ---chHHHHHHHHHhhcCcceEEEEEEEEecCCCcccc
Confidence 46999999999999999999999999999999986
No 22
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=99.45 E-value=5.7e-13 Score=125.40 Aligned_cols=103 Identities=19% Similarity=0.271 Sum_probs=83.2
Q ss_pred eEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 66 FVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 66 ~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
.+.+++|...+.|++|+++|||+++|.+|+++|+.|||+++.+|+|+.. . ..+++++..|+.||+|.|+|+|..++
T Consensus 5 ~~~~~~l~~~~~g~~V~l~GwV~~~R~~g~l~Fi~LrD~~g~iQ~v~~~---~-~~~~~~~~~l~~es~V~V~G~v~~~~ 80 (588)
T PRK00476 5 THYCGELRESHVGQTVTLCGWVHRRRDHGGLIFIDLRDREGIVQVVFDP---D-AEAFEVAESLRSEYVIQVTGTVRARP 80 (588)
T ss_pred ceeHHHhhHHhCCCEEEEEEEEEEEEeCCCeEEEEEEeCCceEEEEEeC---C-HHHHHHHhCCCCCCEEEEEEEEEecC
Confidence 4668888888899999999999999999999999999999999999864 2 56889999999999999999999876
Q ss_pred cccC--CCceeeeeec----cccchhhcccccCC
Q psy13182 146 TIVE--SLPMSILSVG----DTVSKQMIKYVSQI 173 (194)
Q Consensus 146 ~~i~--~~t~~~~El~----~~is~~~~~~~~~l 173 (194)
.... ....+++||. ..++++. .+|+.+
T Consensus 81 ~~~~n~~~~~g~~El~~~~i~il~~a~-~lP~~~ 113 (588)
T PRK00476 81 EGTVNPNLPTGEIEVLASELEVLNKSK-TLPFPI 113 (588)
T ss_pred CcccCccCCCCcEEEEEeEEEEEecCC-CCCCcc
Confidence 4322 2224556666 2467666 677766
No 23
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=99.42 E-value=1.4e-12 Score=122.39 Aligned_cols=104 Identities=17% Similarity=0.232 Sum_probs=81.9
Q ss_pred eEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 66 FVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 66 ~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
.++|++|+..+.|+.|+++|||++.|.+|+++|+.|||+++.+|+++... .++++++..|+.||+|.|.|+|..++
T Consensus 3 t~~~~~l~~~~~g~~V~l~GwV~~~R~~Gkl~Fi~LrD~sg~iQvv~~~~----~~~~~~~~~L~~esvV~V~G~v~~r~ 78 (583)
T TIGR00459 3 THYCGQLRTEHLGQTVTLAGWVNRRRDLGGLIFIDLRDRSGIVQVVCDPD----ADALKLAKGLRNEDVVQVKGKVSARP 78 (583)
T ss_pred ceeHhhcchhhCCCEEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCC----HHHHHHHhcCCCCCEEEEEEEEEeCC
Confidence 36788998788999999999999999999999999999999999998653 56778899999999999999999865
Q ss_pred c-ccCC-Cceeeeeec----cccchhhcccccCCC
Q psy13182 146 T-IVES-LPMSILSVG----DTVSKQMIKYVSQIP 174 (194)
Q Consensus 146 ~-~i~~-~t~~~~El~----~~is~~~~~~~~~l~ 174 (194)
. ++.. ...+++||. ..++++ ..+|..+.
T Consensus 79 ~~~~n~~~~tg~iEl~~~~i~iL~~a-~~~P~~~~ 112 (583)
T TIGR00459 79 EGNINRNLDTGEIEILAESITLLNKS-KTPPLIIE 112 (583)
T ss_pred ccccCccCCCCcEEEEEeEEEEeecC-CCCCCccc
Confidence 2 2221 234556666 245655 35666553
No 24
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=99.39 E-value=4.8e-12 Score=90.93 Aligned_cols=75 Identities=17% Similarity=0.163 Sum_probs=58.9
Q ss_pred EEEEEEEEEeeec-CCCeEEEEEEecce-EEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeee
Q psy13182 80 TVWVRGRLHTSRA-KGKQCFVVIREQNF-TIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILS 157 (194)
Q Consensus 80 ~V~vrgrv~~~R~-~Gk~~Fl~lRd~~~-~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~E 157 (194)
+|++.|||++.|. .|+++|+.|||+++ .+|+++... .+.+..+..|+.||+|.|+|.+...+.... ...+.+|
T Consensus 1 ~V~v~Gwv~~~R~~~~~~~Fi~LrD~~g~~iQvv~~~~----~~~~~~~~~l~~~s~V~V~G~v~~~~~~~~-~~~~~~E 75 (86)
T cd04321 1 KVTLNGWIDRKPRIVKKLSFADLRDPNGDIIQLVSTAK----KDAFSLLKSITAESPVQVRGKLQLKEAKSS-EKNDEWE 75 (86)
T ss_pred CEEEEEeEeeEeCCCCceEEEEEECCCCCEEEEEECCC----HHHHHHHhcCCCCcEEEEEEEEEeCCCcCC-CCCCCEE
Confidence 3789999999998 68999999999999 699987543 235566778999999999999999875431 1224456
Q ss_pred ec
Q psy13182 158 VG 159 (194)
Q Consensus 158 l~ 159 (194)
|+
T Consensus 76 i~ 77 (86)
T cd04321 76 LV 77 (86)
T ss_pred EE
Confidence 55
No 25
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=99.33 E-value=1.2e-11 Score=113.33 Aligned_cols=96 Identities=17% Similarity=0.264 Sum_probs=74.2
Q ss_pred cCCCcEEEEEEEEEeeecCCCeEEEEEEecc--eEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCc
Q psy13182 75 DYVDKTVWVRGRLHTSRAKGKQCFVVIREQN--FTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLP 152 (194)
Q Consensus 75 ~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~--~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t 152 (194)
.+.|++|+|+|||+++|.+|+++|++|||++ +.+|+|+... .+.++++++..|+.||+|.|+|+|.+++....+.+
T Consensus 13 ~~~g~~v~v~Gwv~~~R~~~~~~F~~lrD~~~~g~iQ~v~~~~--~~~~~~~~~~~l~~gs~V~v~G~v~~~~~~~~~~E 90 (453)
T TIGR00457 13 KFVGDEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGE--DNPYLFQLLKSLTTGSSVSVTGKVVESPGKGQPVE 90 (453)
T ss_pred hcCCCEEEEEEEeEEEEcCCCeEEEEEECCCCCccEEEEEeCC--cChHHHHHHHcCCCCcEEEEEEEEEcCCCCCCCEE
Confidence 5679999999999999999999999999999 9999998754 35678899999999999999999998754333333
Q ss_pred eeeeeeccccchhh-cccccCC
Q psy13182 153 MSILSVGDTVSKQM-IKYVSQI 173 (194)
Q Consensus 153 ~~~~El~~~is~~~-~~~~~~l 173 (194)
+..-.+. +++++. ..+|..+
T Consensus 91 l~~~~i~-vl~~~~~~~~P~~~ 111 (453)
T TIGR00457 91 LQVKKIE-VVGEAEPDDYPLQK 111 (453)
T ss_pred EEEeEEE-EEecCCccCCCCCc
Confidence 3333333 456654 3455543
No 26
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=99.30 E-value=1.1e-11 Score=114.68 Aligned_cols=90 Identities=19% Similarity=0.265 Sum_probs=70.5
Q ss_pred cEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeee
Q psy13182 79 KTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSV 158 (194)
Q Consensus 79 ~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El 158 (194)
+.|+|+|||+++|.+|+++|+.|||+++.+|+++... ..+.++++++..|..||+|.|.|+|..++. ...++..-++
T Consensus 55 ~~v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~-~~~~~~~~~~~~l~~g~~v~v~G~v~~t~~--ge~el~~~~~ 131 (491)
T PRK00484 55 IEVSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKD-DVGEEALEAFKKLDLGDIIGVEGTLFKTKT--GELSVKATEL 131 (491)
T ss_pred cEEEEEEEEEEEecCCceEEEEEEcCCccEEEEEECC-cCCHHHHHHHhcCCCCCEEEEEEEEEEcCC--CcEEEEEeEE
Confidence 6799999999999999999999999999999998754 345677888888999999999999998753 3333333333
Q ss_pred ccccchhhcccccC
Q psy13182 159 GDTVSKQMIKYVSQ 172 (194)
Q Consensus 159 ~~~is~~~~~~~~~ 172 (194)
. .+|++.-.+|..
T Consensus 132 ~-vls~~~~plP~~ 144 (491)
T PRK00484 132 T-LLTKSLRPLPDK 144 (491)
T ss_pred E-EEeccCCCCCcc
Confidence 3 567665555654
No 27
>PLN02221 asparaginyl-tRNA synthetase
Probab=99.29 E-value=1.4e-11 Score=115.46 Aligned_cols=100 Identities=16% Similarity=0.237 Sum_probs=74.2
Q ss_pred ceEEccccc------ccCCCcEEEEEEEEEeeecCCC--eEEEEEEecc--eEEEEEEeccccccHHHHHHHhcCCCccE
Q psy13182 65 DFVPIRQLN------KDYVDKTVWVRGRLHTSRAKGK--QCFVVIREQN--FTIQGILSVGDTVSKQMIKYVSQIPKESI 134 (194)
Q Consensus 65 ~~~~i~~L~------~~~~g~~V~vrgrv~~~R~~Gk--~~Fl~lRd~~--~~vQ~v~~~~~~~s~~m~k~~~~l~rESi 134 (194)
.+..|.++. .++.|+.|+|+||||++|.+|+ ++||.|||++ +.+|||+..... .....|+.||+
T Consensus 31 ~~~~~~~~~~~~~~~~~~~g~~V~I~GWV~~iR~~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~------~~~~~L~~ES~ 104 (572)
T PLN02221 31 DRVLIRSILDRPDGGAGLAGQKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSSLY------DLSTLVATGTC 104 (572)
T ss_pred CceEHHHHhccccCChhcCCCEEEEEEEEEehhhCCCceEEEEEEeCCcccccEEEEEcCchh------hHHhcCCCceE
Confidence 456677753 5788999999999999999996 7999999999 789999864310 11235889999
Q ss_pred EEEEEEEEecCcccCCCceeeeeec----cccchhh-cccccC
Q psy13182 135 LDIQAHVQATPTIVESLPMSILSVG----DTVSKQM-IKYVSQ 172 (194)
Q Consensus 135 V~V~G~V~~~~~~i~~~t~~~~El~----~~is~~~-~~~~~~ 172 (194)
|.|.|+|..++. ..++++ .+||+ .++|.+- .+||++
T Consensus 105 V~V~G~V~~~~~-~~~~~~-~iEl~v~~i~vl~~a~~~~~Pi~ 145 (572)
T PLN02221 105 VTVDGVLKVPPE-GKGTKQ-KIELSVEKVIDVGTVDPTKYPLP 145 (572)
T ss_pred EEEEEEEEeCCc-cCCCCc-cEEEEEeEEEEEecCCCCCCCCC
Confidence 999999998876 344444 78877 2456553 345554
No 28
>PLN02603 asparaginyl-tRNA synthetase
Probab=99.20 E-value=1.6e-10 Score=108.37 Aligned_cols=103 Identities=18% Similarity=0.211 Sum_probs=73.5
Q ss_pred ceEEccccc------ccCCCcEEEEEEEEEeeecCCCeEEEEEEecce--EEEEEEeccccccHHHHHHHh--cCCCccE
Q psy13182 65 DFVPIRQLN------KDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNF--TIQGILSVGDTVSKQMIKYVS--QIPKESI 134 (194)
Q Consensus 65 ~~~~i~~L~------~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~--~vQ~v~~~~~~~s~~m~k~~~--~l~rESi 134 (194)
..++|.++. ..+.|++|+|+|||+++|.+|+++|+.|||+++ .+|||+.... ..++.+. .|+.||+
T Consensus 88 ~~~~~~~~~~~~~~~~~~~g~~V~v~GwV~~iR~~g~~~Fi~l~Dgs~~~~lQ~v~~~~~----~~~~~l~~~~l~~gs~ 163 (565)
T PLN02603 88 KKLRIADVKGGEDEGLARVGKTLNVMGWVRTLRAQSSVTFIEVNDGSCLSNMQCVMTPDA----EGYDQVESGLITTGAS 163 (565)
T ss_pred CceEhhhcccccccccccCCCEEEEEEEEEEEEeCCCeEEEEEECCCCCEeEEEEEECcH----HHHHHHhhcCCCCCCE
Confidence 346677764 256799999999999999999999999999986 5999986531 1223333 4999999
Q ss_pred EEEEEEEEecCcccCCCceeeeeeccccchhhcccccC
Q psy13182 135 LDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYVSQ 172 (194)
Q Consensus 135 V~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~~~ 172 (194)
|.|+|++..++....+.+++.-+|. .+++...++|.+
T Consensus 164 V~V~G~v~~~~~~~~~~EL~v~~i~-vlg~a~~~~Pi~ 200 (565)
T PLN02603 164 VLVQGTVVSSQGGKQKVELKVSKIV-VVGKSDPSYPIQ 200 (565)
T ss_pred EEEEEEEEecCCCCccEEEEEeEEE-EEECCCCCCCCc
Confidence 9999999987653322333333332 466665566654
No 29
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=99.18 E-value=1.6e-10 Score=107.05 Aligned_cols=92 Identities=15% Similarity=0.267 Sum_probs=71.7
Q ss_pred CCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhc-CCCccEEEEEEEEEecCcccCCCceee
Q psy13182 77 VDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQ-IPKESILDIQAHVQATPTIVESLPMSI 155 (194)
Q Consensus 77 ~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~-l~rESiV~V~G~V~~~~~~i~~~t~~~ 155 (194)
.|+.|+|+|||++.|..||++|+.|||+++.+|+++... ..+.+++++... |..||+|.|.|++.+++. ...+++.
T Consensus 52 ~~~~v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~-~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~--gelel~~ 128 (496)
T TIGR00499 52 KNIEVSIAGRIMARRSMGKATFITLQDESGQIQLYVNKD-DLPEDFYEFDEYLLDLGDIIGVTGYPFKTKT--GELSVHV 128 (496)
T ss_pred CCCEEEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECC-cCcHHHHHHHHhcCCCCCEEEEEEEEEECCC--CcEEEEe
Confidence 477899999999999999999999999999999998754 345667777764 899999999999988753 3344444
Q ss_pred eeeccccchhhcccccC
Q psy13182 156 LSVGDTVSKQMIKYVSQ 172 (194)
Q Consensus 156 ~El~~~is~~~~~~~~~ 172 (194)
-++. .+|++.-++|..
T Consensus 129 ~~i~-ilsk~~~plP~k 144 (496)
T TIGR00499 129 TELQ-ILTKALRPLPDK 144 (496)
T ss_pred eEEE-EEecCCCCCCcc
Confidence 4443 567776555543
No 30
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=99.15 E-value=3.6e-10 Score=104.92 Aligned_cols=92 Identities=18% Similarity=0.241 Sum_probs=69.4
Q ss_pred CCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHH-HHHhcCCCccEEEEEEEEEecCcccCCCceee
Q psy13182 77 VDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMI-KYVSQIPKESILDIQAHVQATPTIVESLPMSI 155 (194)
Q Consensus 77 ~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~-k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~ 155 (194)
.|+.|+|+|||+++|.+|+++|+.|||+++++|+++.... .....+ .....|..||+|.|.|++.+++. ...++..
T Consensus 64 ~~~~v~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~-~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~--gelel~~ 140 (505)
T PRK12445 64 LNIEVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDS-LPEGVYNDQFKKWDLGDIIGARGTLFKTQT--GELSIHC 140 (505)
T ss_pred CCCEEEEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCc-cchhhHHHHHhcCCCCCEEEEEEEEEecCC--CcEEEEE
Confidence 4778999999999999999999999999999999987532 222333 34577999999999999998752 3444444
Q ss_pred eeeccccchhhcccccC
Q psy13182 156 LSVGDTVSKQMIKYVSQ 172 (194)
Q Consensus 156 ~El~~~is~~~~~~~~~ 172 (194)
-++. .+|++.-++|..
T Consensus 141 ~~~~-llsk~~~plP~~ 156 (505)
T PRK12445 141 TELR-LLTKALRPLPDK 156 (505)
T ss_pred eEEE-EEecCCCCCCcc
Confidence 4444 578776556653
No 31
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=99.14 E-value=2.4e-10 Score=114.15 Aligned_cols=103 Identities=13% Similarity=0.160 Sum_probs=78.6
Q ss_pred eEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 66 FVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 66 ~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
.+.+.++...+.|++|+|+|||+++|.+|+++|+.|||+++.+|+++.........|..|...|..||+|.|+|++.+++
T Consensus 639 ~~~~~~~~~~~~~~~V~v~Grv~~~R~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~v~~t~ 718 (1094)
T PRK02983 639 THTVAEALDAPTGEEVSVSGRVLRIRDYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGTMGTSR 718 (1094)
T ss_pred ccCHHHHHHhcCCCEEEEEEEEEEEeeCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEEcC
Confidence 35677776667899999999999999999999999999999999998764322344666777899999999999999976
Q ss_pred cccCCCceeeeeeccccchhhccccc
Q psy13182 146 TIVESLPMSILSVGDTVSKQMIKYVS 171 (194)
Q Consensus 146 ~~i~~~t~~~~El~~~is~~~~~~~~ 171 (194)
. .+.++..-++. .+++...++|.
T Consensus 719 ~--ge~ei~~~~i~-ll~k~~~plP~ 741 (1094)
T PRK02983 719 N--GTLSLLVTSWR-LAGKCLRPLPD 741 (1094)
T ss_pred C--CCEEEEEeEEE-EEeccCcCCCC
Confidence 4 34444433343 45666545554
No 32
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=99.13 E-value=4.4e-10 Score=106.66 Aligned_cols=86 Identities=22% Similarity=0.272 Sum_probs=68.1
Q ss_pred CcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHH-hcCCCccEEEEEEEEEecCcccCCCceeee
Q psy13182 78 DKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYV-SQIPKESILDIQAHVQATPTIVESLPMSIL 156 (194)
Q Consensus 78 g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~-~~l~rESiV~V~G~V~~~~~~i~~~t~~~~ 156 (194)
+..|+|+|||++.|.+||++|+.|||+++++|+++...+..+++++++. ..|..||+|.|+|+|...+ ..+.++..-
T Consensus 107 ~~~V~vaGrV~~~R~~Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~v~~t~--~GeleI~~~ 184 (659)
T PTZ00385 107 QATVRVAGRVTSVRDIGKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADGVPCRMQ--RGELSVAAS 184 (659)
T ss_pred CCEEEEEEEEEeeeccCCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEEEEEecC--CceEEEEee
Confidence 4469999999999999999999999999999999986533356677666 5799999999999999864 345565555
Q ss_pred eeccccchhh
Q psy13182 157 SVGDTVSKQM 166 (194)
Q Consensus 157 El~~~is~~~ 166 (194)
++. .+|++.
T Consensus 185 ~i~-lLska~ 193 (659)
T PTZ00385 185 RML-ILSPYV 193 (659)
T ss_pred EEE-Eechhh
Confidence 554 567643
No 33
>KOG1885|consensus
Probab=99.04 E-value=1.4e-09 Score=98.67 Aligned_cols=142 Identities=20% Similarity=0.277 Sum_probs=96.8
Q ss_pred ccccccCHHHHHHHHHHHHHHHHHHHHHHh-hcc-h-------hcCCCccchhhhccCCccc------ccc--CCCCCC-
Q psy13182 3 SEAQKVSKKALKKQAKEQEKKEKKDQRKSA-QQN-V-------EESEPVEDVSARLYGKTPL------IMS--EKDVDR- 64 (194)
Q Consensus 3 ~~~~~~sk~alkK~~K~~~k~~kka~k~a~-~~~-~-------a~~~~~~d~~~~~Yg~~~l------~qs--~~~~~~- 64 (194)
+-..++||+.|||+.+..+++..++.+++. ++. . ...+ ++.....|.++.. ..+ .++|+.
T Consensus 3 ~ss~~~sk~~lkrr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e--~~~d~~qy~~~R~r~i~~l~~s~~~Pyphkf 80 (560)
T KOG1885|consen 3 ESSEMLSKNELKRRSLAKQKALEKAKKASSKAAAPSVAAAKSVSKSE--ETSDPEQYFKIRSRAIEELRASGLNPYPHKF 80 (560)
T ss_pred cchhhhhHHHHHHhHHHhhHHHHHHHhhhhccCCCcccccccccccc--ccCCHHHHHHHHHHHHHHHhhcCCCCCcchh
Confidence 334688999999999988887777666544 111 0 1111 2223355544432 112 133331
Q ss_pred -------ce-EEcccc-c-ccCCCcEEEEEEEEEeeecCC-CeEEEEEEecceEEEEEEeccc-cccHHHHHHHhcCCCc
Q psy13182 65 -------DF-VPIRQL-N-KDYVDKTVWVRGRLHTSRAKG-KQCFVVIREQNFTIQGILSVGD-TVSKQMIKYVSQIPKE 132 (194)
Q Consensus 65 -------~~-~~i~~L-~-~~~~g~~V~vrgrv~~~R~~G-k~~Fl~lRd~~~~vQ~v~~~~~-~~s~~m~k~~~~l~rE 132 (194)
.| .++..| + .+..+..+.|.||||..|.+| |++|++||.++..+|+|+.... ..+.++......|.++
T Consensus 81 ~vs~si~~fieky~~l~~ge~~~n~~~svaGRI~s~R~sGsKL~Fydl~~~g~klQvm~~~~~~~~~~~F~~~~~~lkrG 160 (560)
T KOG1885|consen 81 HVSISIPDFIEKYLHLATGEHLDNEIVSVAGRIHSKRESGSKLVFYDLHGDGVKLQVMANAKKITSEEDFEQLHKFLKRG 160 (560)
T ss_pred hccccHHHHHHHhcCcccccccccceeeeeeeEeeeeccCCceEEEEEecCCeEEEEEEehhhcCCHHHHHHHHhhhhcc
Confidence 11 112233 1 334556799999999999999 8999999999999999998875 4556778888999999
Q ss_pred cEEEEEEEEEecCc
Q psy13182 133 SILDIQAHVQATPT 146 (194)
Q Consensus 133 SiV~V~G~V~~~~~ 146 (194)
++|.+.|.+.++..
T Consensus 161 Diig~~G~pgrt~~ 174 (560)
T KOG1885|consen 161 DIIGVSGYPGRTKS 174 (560)
T ss_pred CEEeeecCCCcCCC
Confidence 99999999988754
No 34
>PTZ00425 asparagine-tRNA ligase; Provisional
Probab=98.98 E-value=2.6e-09 Score=100.40 Aligned_cols=81 Identities=16% Similarity=0.264 Sum_probs=65.0
Q ss_pred cCCCcEEEEEEEEEeeecCCC--eEEEEEEecce--EEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcc---
Q psy13182 75 DYVDKTVWVRGRLHTSRAKGK--QCFVVIREQNF--TIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTI--- 147 (194)
Q Consensus 75 ~~~g~~V~vrgrv~~~R~~Gk--~~Fl~lRd~~~--~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~--- 147 (194)
.+.|+.|+|.|||+++|.+|+ ++||.|||+++ .+|+|+... ...+..+.+|+.||+|.|+|+|...+..
T Consensus 78 ~~~g~~Vtl~GWv~~iR~~g~~~~~Fv~lrDgsg~~~iQiVv~~~----~~~~~~l~~l~~gs~v~v~G~v~~~~~~~~n 153 (586)
T PTZ00425 78 KYIDQIITVCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIVDQS----IENYEKLLKCGVGCCFRFTGKLIISPVQNEN 153 (586)
T ss_pred ccCCCEEEEEEEEeehhhcCCceEEEEEEECCCCCcceEEEECCc----hHHHHHHhcCCCccEEEEEEEEEcCCccccC
Confidence 467999999999999999984 89999999998 599988532 2234566789999999999999987654
Q ss_pred cCCCceeeeeec
Q psy13182 148 VESLPMSILSVG 159 (194)
Q Consensus 148 i~~~t~~~~El~ 159 (194)
..|+..+++||.
T Consensus 154 ~~g~~~~~~El~ 165 (586)
T PTZ00425 154 KKGLLKENVELA 165 (586)
T ss_pred cCCCCCccEEEE
Confidence 345556677775
No 35
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=98.83 E-value=2.9e-08 Score=93.57 Aligned_cols=92 Identities=17% Similarity=0.135 Sum_probs=68.8
Q ss_pred CcEEEEEEEEEeeecCC-CeEEEEEEecceEEEEEEeccc-cccHHHH-HHHhcCCCccEEEEEEEEEecCcccCCCcee
Q psy13182 78 DKTVWVRGRLHTSRAKG-KQCFVVIREQNFTIQGILSVGD-TVSKQMI-KYVSQIPKESILDIQAHVQATPTIVESLPMS 154 (194)
Q Consensus 78 g~~V~vrgrv~~~R~~G-k~~Fl~lRd~~~~vQ~v~~~~~-~~s~~m~-k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~ 154 (194)
+..|.|.|||+++|.+| +++|+.|||.++++|+++.... ......+ .+...|.+|++|.|.|++.++. ....++.
T Consensus 132 ~~~v~v~Grv~~~R~~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~t~--~gel~i~ 209 (585)
T PTZ00417 132 DTILNVTGRIMRVSASGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKSK--KGELSIF 209 (585)
T ss_pred CCeEEEEEEEEeeecCCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcCCC--CceEEEE
Confidence 45699999999999999 7999999999999999987542 1222333 3467899999999999988764 2345555
Q ss_pred eeeeccccchhhcccccC
Q psy13182 155 ILSVGDTVSKQMIKYVSQ 172 (194)
Q Consensus 155 ~~El~~~is~~~~~~~~~ 172 (194)
.-++. .+|++...+|..
T Consensus 210 ~~~i~-llsk~l~~lP~~ 226 (585)
T PTZ00417 210 PKETI-ILSPCLHMLPMK 226 (585)
T ss_pred EEEEE-EEecCCCCCCcc
Confidence 55554 567776667765
No 36
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=98.79 E-value=1.2e-07 Score=64.84 Aligned_cols=61 Identities=20% Similarity=0.347 Sum_probs=53.9
Q ss_pred EEEEEEEEee-ecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCc
Q psy13182 81 VWVRGRLHTS-RAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPT 146 (194)
Q Consensus 81 V~vrgrv~~~-R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~ 146 (194)
|+|.|||++. +..+++.|+.|+|+++.+|++++. ..+..+...|..+++|.|.|.+...+.
T Consensus 1 V~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~-----~~~~~~~~~l~~g~~v~v~G~v~~~~~ 62 (75)
T PF01336_consen 1 VTVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFN-----EEYERFREKLKEGDIVRVRGKVKRYNG 62 (75)
T ss_dssp EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET-----HHHHHHHHTS-TTSEEEEEEEEEEETT
T ss_pred CEEEEEEEEEEcCCCCEEEEEEEECCccEEEEEcc-----HHhhHHhhcCCCCeEEEEEEEEEEECC
Confidence 7899999999 777799999999999999999996 356788899999999999999999854
No 37
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=98.65 E-value=5.9e-08 Score=91.05 Aligned_cols=142 Identities=16% Similarity=0.191 Sum_probs=94.6
Q ss_pred ccccCHHHHHHHHHHHHHHHHHHHHHHhhcchhcCCCccchhhhccCCccccccCCCCCCceEEcccc---cccCCCcEE
Q psy13182 5 AQKVSKKALKKQAKEQEKKEKKDQRKSAQQNVEESEPVEDVSARLYGKTPLIMSEKDVDRDFVPIRQL---NKDYVDKTV 81 (194)
Q Consensus 5 ~~~~sk~alkK~~K~~~k~~kka~k~a~~~~~a~~~~~~d~~~~~Yg~~~l~qs~~~~~~~~~~i~~L---~~~~~g~~V 81 (194)
+...||++.|+..|+++++++|++++++ .+++.+ + ..+...+. . -.++++ .+.....+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~-~-~~~~~~~~----------~----~~~g~~~~~~~~~~~~~~ 64 (550)
T PTZ00401 3 SNHADAGAPAVEKKQSDKEARKAARLAE--EKARAA-E-KAALVEKY----------K----DVFGAAPMVQSTTYKSRT 64 (550)
T ss_pred ccccccCcchhhHHHHHHHHHhHHHHHH--HHHHHH-h-hhhccchh----------h----ccCCccccccccccCCCc
Confidence 3467888999999999988888777653 222222 1 11111000 0 122332 111122345
Q ss_pred EEEEEEEeeec-CCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeec
Q psy13182 82 WVRGRLHTSRA-KGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVG 159 (194)
Q Consensus 82 ~vrgrv~~~R~-~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~ 159 (194)
|+...-++... .|+.+.|+.|.++.+.++ ++|.. .|+..-.||+++...
T Consensus 65 ~~~i~~l~~~~~~g~~V~v~Grv~~~R~~Gk~~Fl~--------------LRd~~~~iQ~v~~~~--------------- 115 (550)
T PTZ00401 65 FIPVAVLSKPELVDKTVLIRARVSTTRKKGKMAFMV--------------LRDGSDSVQAMAAVE--------------- 115 (550)
T ss_pred eEEHHHCCccccCCCEEEEEEEEEEEecCCCeEEEE--------------EEeCCcCEEEEEECC---------------
Confidence 66666665555 688899999999999887 67765 455555899888654
Q ss_pred cccchhhcccccCCCCCceEeEEEEEecCCcccc
Q psy13182 160 DTVSKQMIKYVSQIPKESILDIQAHVQATPTIVE 193 (194)
Q Consensus 160 ~~is~~~~~~~~~l~~esi~~~~~~~~~~~~~~~ 193 (194)
..++++|.+|..+|+.||||+|+|+|.+++.||.
T Consensus 116 ~~~~~~~~~~~~~l~~esiV~V~G~v~~~~~~~~ 149 (550)
T PTZ00401 116 GDVPKEMIDFIGQIPTESIVDVEATVCKVEQPIT 149 (550)
T ss_pred CccCHHHHHHHhcCCCCCEEEEEEEEEecCccCC
Confidence 2367899999999999999999999999877764
No 38
>PLN02850 aspartate-tRNA ligase
Probab=98.65 E-value=9.9e-08 Score=89.22 Aligned_cols=87 Identities=23% Similarity=0.292 Sum_probs=69.7
Q ss_pred EEEEEEEEEeeecCCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeee
Q psy13182 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSV 158 (194)
Q Consensus 80 ~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El 158 (194)
..|+..+-.+....|+.+.|+.|.++.+.|+ ++|.. .|+..-.||+++....
T Consensus 67 ~~~~~i~~l~~~~~g~~V~v~Grv~~~R~~gk~~Fl~--------------Lrd~~~~iQ~v~~~~~------------- 119 (530)
T PLN02850 67 REWTDVSDLGEELAGSEVLIRGRVHTIRGKGKSAFLV--------------LRQSGFTVQCVVFVSE------------- 119 (530)
T ss_pred ceEeEhhhcchhhCCCEEEEEEEEEEEccCCCeEEEE--------------EEeCCcCEEEEEECCc-------------
Confidence 4566666666667789999999999999887 77776 5666668999886652
Q ss_pred ccccchhhcccccCCCCCceEeEEEEEecCCccccC
Q psy13182 159 GDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVES 194 (194)
Q Consensus 159 ~~~is~~~~~~~~~l~~esi~~~~~~~~~~~~~~~~ 194 (194)
..+|+.|.+|..+|+.||||+|+|+|.+++.||++
T Consensus 120 -~~~~~~~~~~~~~l~~es~V~V~G~v~~~~~~~~~ 154 (530)
T PLN02850 120 -VTVSKGMVKYAKQLSRESVVDVEGVVSVPKKPVKG 154 (530)
T ss_pred -cccCHHHHHHHhCCCCCCEEEEEEEEEccCcCCCC
Confidence 23788999999999999999999999998877653
No 39
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=98.24 E-value=6.4e-06 Score=75.91 Aligned_cols=89 Identities=20% Similarity=0.297 Sum_probs=72.3
Q ss_pred EEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHH-HHhcCCCccEEEEEEEEEecCcccCCCceeeeee
Q psy13182 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIK-YVSQIPKESILDIQAHVQATPTIVESLPMSILSV 158 (194)
Q Consensus 80 ~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k-~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El 158 (194)
.|.+.||+...|.+||.+|+.+.|.++.+|.++.... ...+.+. +...+..+++|.|.|.+.++. .+..|+..-++
T Consensus 63 ~v~vAGRi~~~R~~GK~~F~~i~d~~gkiQ~yi~k~~-~~~~~~~~~~~~~dlGDiigv~G~~~~T~--~GelSv~v~~~ 139 (502)
T COG1190 63 EVSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDE-VGEEVFEALFKKLDLGDIIGVEGPLFKTK--TGELSVSVEEL 139 (502)
T ss_pred eeEEecceeeecccCceeEEEEecCCceEEEEEeccc-cchhhHHHHHhccccCCEEeeeeeeeecC--CCceEEEEEEE
Confidence 3999999999999999999999999999999988653 3333444 677788999999999999986 35567777777
Q ss_pred ccccchhhcccccC
Q psy13182 159 GDTVSKQMIKYVSQ 172 (194)
Q Consensus 159 ~~~is~~~~~~~~~ 172 (194)
. .+|+..-++|.-
T Consensus 140 ~-lLsKsL~pLPeK 152 (502)
T COG1190 140 R-LLSKSLRPLPEK 152 (502)
T ss_pred e-eecccCCCCChh
Confidence 6 678888777753
No 40
>KOG2411|consensus
Probab=98.14 E-value=9.2e-06 Score=74.80 Aligned_cols=105 Identities=18% Similarity=0.222 Sum_probs=73.5
Q ss_pred EEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCc
Q psy13182 67 VPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPT 146 (194)
Q Consensus 67 ~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~ 146 (194)
..|++|....+|++|.+.||+.-.|.++.+.|+.|||.+|.+|..+....- . ..-+....++.|++|.|.|+|...|.
T Consensus 36 ~~~~el~~~~vg~kv~l~GWl~~~~~~k~~~F~~LRD~~G~vq~lls~~s~-~-l~~~~~~~v~~e~vv~v~gtvv~Rp~ 113 (628)
T KOG2411|consen 36 SLCGELSVNDVGKKVVLCGWLELHRVHKMLTFFNLRDAYGIVQQLLSPDSF-P-LAQKLENDVPLEDVVQVEGTVVSRPN 113 (628)
T ss_pred ccchhhccCccCCEEEEeeeeeeeeccccceEEEeeccCcceEEEecchhh-h-HHhcccCCCChhheEeeeeeEecccc
Confidence 678888877899999999999988888889999999999999988764310 0 01122344688999999999988753
Q ss_pred c--cCCCceeeeeec----cccchhhcccccCC
Q psy13182 147 I--VESLPMSILSVG----DTVSKQMIKYVSQI 173 (194)
Q Consensus 147 ~--i~~~t~~~~El~----~~is~~~~~~~~~l 173 (194)
. +.....+++|+. ...+..--++|+.+
T Consensus 114 ~sin~km~tg~vev~~e~~~vln~~~~~~p~~v 146 (628)
T KOG2411|consen 114 ESINSKMKTGFVEVVAEKVEVLNPVNKKLPFEV 146 (628)
T ss_pred cccCccccccceEEEeeeeEEecCccCCCccch
Confidence 2 223345566665 12333444445443
No 41
>PLN02532 asparagine-tRNA synthetase
Probab=97.83 E-value=4.9e-05 Score=72.45 Aligned_cols=76 Identities=5% Similarity=0.085 Sum_probs=51.1
Q ss_pred eecCCCeEEEEEEecceE--EEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcc--cCCCceeeeeeccccchh
Q psy13182 90 SRAKGKQCFVVIREQNFT--IQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTI--VESLPMSILSVGDTVSKQ 165 (194)
Q Consensus 90 ~R~~Gk~~Fl~lRd~~~~--vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~--i~~~t~~~~El~~~is~~ 165 (194)
.|..|+++||.|||+++. +|||+..... .....|+.|++|.|+|+|..++.+ ..+.++..-+|. .++.+
T Consensus 129 ~r~~g~i~FI~LrDGSg~~~lQvVv~~~~~------~~~~~L~~Es~V~V~G~V~~~~~~~~~g~iEl~v~~i~-VLg~a 201 (633)
T PLN02532 129 APPPPSVAYLLISDGSCVASLQVVVDSALA------PLTQLMATGTCILAEGVLKLPLPAQGKHVIELEVEKIL-HIGTV 201 (633)
T ss_pred cccCCCcEEEEEECCCCccceEEEEeCCcc------cHhhcCCCceEEEEEEEEEecCCCCCCCcEEEEeeEEE-EEecC
Confidence 688999999999999998 9999864311 112678999999999999987332 233333333333 35543
Q ss_pred h-cccccC
Q psy13182 166 M-IKYVSQ 172 (194)
Q Consensus 166 ~-~~~~~~ 172 (194)
- .+||.+
T Consensus 202 ~~~p~Pi~ 209 (633)
T PLN02532 202 DPEKYPLS 209 (633)
T ss_pred CCCCCccc
Confidence 2 345543
No 42
>KOG0554|consensus
Probab=97.29 E-value=0.00055 Score=61.75 Aligned_cols=62 Identities=11% Similarity=0.204 Sum_probs=53.1
Q ss_pred ccCCCcEEEEEEEEEeeecCCCeEEEEEEecce--EEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 74 KDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNF--TIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 74 ~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~--~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
....|+.+.+.||+.++|..|+.+|+.+.||+. .+|+|+... ....+..++.|.+.|.+..+
T Consensus 16 ~~~~g~~~~i~GWvKsvr~~~~~~Fl~i~DGs~~~~lQvVv~~~---------~~q~la~Gt~i~~~g~l~~~ 79 (446)
T KOG0554|consen 16 HPRAGDTISIGGWVKSVRKLKKVTFLDINDGSCPSPLQVVVDSE---------QSQLLATGTCISAEGVLKVS 79 (446)
T ss_pred CCCCCCceeecchhhhcccccceEEEEecCCCCCcceEEEechH---------HhhhccccceEEEEeeEEec
Confidence 446789999999999999999999999999986 489998652 34556789999999999887
No 43
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=96.30 E-value=0.048 Score=37.33 Aligned_cols=59 Identities=10% Similarity=0.276 Sum_probs=44.6
Q ss_pred EEEEEEEEeeec-CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 81 VWVRGRLHTSRA-KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 81 V~vrgrv~~~R~-~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
+|+.|-|.+.|. .+.++|+.|.|.++.+.|++|... ..+.-..|..+..|.|+|.+...
T Consensus 2 ~~v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~~-----~~~~~~~l~~g~~v~v~g~v~~~ 61 (78)
T cd04489 2 VWVEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRSN-----ARRLGFPLEEGMEVLVRGKVSFY 61 (78)
T ss_pred EEEEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcch-----hhhCCCCCCCCCEEEEEEEEEEE
Confidence 577888877764 334999999999999999998641 11223456778999999999864
No 44
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=96.20 E-value=0.041 Score=40.36 Aligned_cols=61 Identities=10% Similarity=0.281 Sum_probs=48.7
Q ss_pred CcEEEEEEEEEeeec-CCCeEEEEEEecceEEEEEEeccccccHHHHHHH--hcCCCccEEEEEEEEEec
Q psy13182 78 DKTVWVRGRLHTSRA-KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYV--SQIPKESILDIQAHVQAT 144 (194)
Q Consensus 78 g~~V~vrgrv~~~R~-~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~--~~l~rESiV~V~G~V~~~ 144 (194)
-..+||+|-|.+.+. .++-+|+.|+|+...+.|+++... ...+ ..+..+.-|.|.|.+.--
T Consensus 21 ~~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~------~~~i~~~~l~~G~~V~v~g~~~~y 84 (99)
T PF13742_consen 21 LPNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSR------ARRIRGFDLKDGDKVLVRGRVSFY 84 (99)
T ss_pred cCCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHH------HhhCCCCCCCCCCEEEEEEEEEEE
Confidence 367999999999998 567899999999999999999752 1112 346778999999988764
No 45
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.06 E-value=0.073 Score=50.97 Aligned_cols=118 Identities=16% Similarity=0.126 Sum_probs=76.8
Q ss_pred CceEEcccccccCCCcEEEEEEEEEee---e------cCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccE
Q psy13182 64 RDFVPIRQLNKDYVDKTVWVRGRLHTS---R------AKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESI 134 (194)
Q Consensus 64 ~~~~~i~~L~~~~~g~~V~vrgrv~~~---R------~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESi 134 (194)
+.++.|.+|++- .+ .++|+|||.+. | ..|++.-+.|.|.++.|.+.+|.. ..-+|...|..+.+
T Consensus 178 ~~~~pI~~L~py-~~-~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~Degg~Irat~f~~-----~~dkf~~~l~eG~V 250 (608)
T TIGR00617 178 RRVMPIASLSPY-QN-KWTIKARVTNKSEIRTWSNARGEGKLFNVELLDESGEIRATAFNE-----QADKFYDIIQEGKV 250 (608)
T ss_pred cceEEHHHCCCC-CC-ceEEEEEEEeccccceecCCCCCceeeEEEEecCCCeEEEEECch-----HHHHHhhhcccCCE
Confidence 368899999873 33 48999999642 2 236788889999999999998854 23366777888999
Q ss_pred EEEEEEEEecCcccCCCceeeeeeccc----cch-----hhccccc---------CCCCCceEeEEEEEecC
Q psy13182 135 LDIQAHVQATPTIVESLPMSILSVGDT----VSK-----QMIKYVS---------QIPKESILDIQAHVQAT 188 (194)
Q Consensus 135 V~V~G~V~~~~~~i~~~t~~~~El~~~----is~-----~~~~~~~---------~l~~esi~~~~~~~~~~ 188 (194)
+.|.+--.++..+.-..+-+++||... |.. ..+++.+ +....++|||-|+|...
T Consensus 251 Y~Is~~~Vk~an~~y~~~~~~yei~f~~~T~I~~~~d~~~iP~~~~~f~~i~dI~~~~~~~~VDVIGvV~~v 322 (608)
T TIGR00617 251 YYISKGSLKPANKQFTNLGNDYEMTLDRDTVIEECEDETAIPKIQFNFVKIDDIGGYEGNSLVDVIGIVQSV 322 (608)
T ss_pred EEECceEEEEccccccCCCCCEEEEECCCeEEEECCCcccCCcccccceEHHHhhhhcCCCCccEEEEEeEe
Confidence 998664333333333345566777611 110 1111111 12567899999999865
No 46
>cd04474 RPA1_DBD_A RPA1_DBD_A: A subfamily of OB folds corresponding to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change. Although ScRPA and the hRPA have similar ssDNA-binding properties, they differ funct
Probab=96.00 E-value=0.074 Score=39.18 Aligned_cols=84 Identities=12% Similarity=0.059 Sum_probs=62.9
Q ss_pred cccccccCCCcEEEEEEEEEe---ee---c---CCCeEEEEEEec-ceEEEEEEeccccccHHHHHHHhcCCCccEEEEE
Q psy13182 69 IRQLNKDYVDKTVWVRGRLHT---SR---A---KGKQCFVVIREQ-NFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQ 138 (194)
Q Consensus 69 i~~L~~~~~g~~V~vrgrv~~---~R---~---~Gk~~Fl~lRd~-~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~ 138 (194)
|.+|++.. ..+.|+|||.+ .| . .|++..+.|+|. ++.+.|.++.. ..-+|...|..+.++.|.
T Consensus 2 I~~L~p~~--~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~-----~~~~f~~~l~eG~vy~i~ 74 (104)
T cd04474 2 ISSLNPYQ--NKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFND-----AVDKFYDLLEVGKVYYIS 74 (104)
T ss_pred hhHccCCC--CcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehH-----HHHHhhcccccccEEEEe
Confidence 55676533 35889999864 22 2 367889999999 88999998853 233567778889999999
Q ss_pred EEEEecCcccCCCceeeeeec
Q psy13182 139 AHVQATPTIVESLPMSILSVG 159 (194)
Q Consensus 139 G~V~~~~~~i~~~t~~~~El~ 159 (194)
+--..+..+.-..+.+++||.
T Consensus 75 ~~~V~~a~~~y~~~~~~yeI~ 95 (104)
T cd04474 75 KGSVKVANKKFNTLKNDYEIT 95 (104)
T ss_pred ccEEeeccccCCCCCCcEEEE
Confidence 977777767777778888887
No 47
>cd04487 RecJ_OBF2_like RecJ_OBF2_like: A subfamily of OB folds corresponding to the second OB fold (OBF2) of archaeal-specific proteins with similarity to eubacterial RecJ. RecJ is an ssDNA-specific exonuclease. Although the overall sequence similarity of these proteins to eubacterial RecJ proteins is marginal, they appear to carry motifs, which have been shown to be essential for nuclease function in Escherichia coli RecJ. In addition to this OB fold, most proteins in this subfamily contain: i) an N-terminal OB fold belonging to a different domain family (the ribosomal S1-like RNA-binding family); and ii) a domain, C-terminal to OBF2, characteristic of DHH family proteins. DHH family proteins include E. coli RecJ, and are predicted to have a phosphoesterase function.
Probab=95.86 E-value=0.048 Score=37.89 Aligned_cols=58 Identities=10% Similarity=0.204 Sum_probs=43.9
Q ss_pred EEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEe
Q psy13182 81 VWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQA 143 (194)
Q Consensus 81 V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~ 143 (194)
||++|-|.+.+..|.-+|+.|+|....+.|+++.... ......+..+.-|.+.|.+..
T Consensus 1 v~v~GeVs~~~~~~GHvyfsLkD~~a~i~cv~f~~~~-----~~~~~~l~~Gd~V~v~G~v~~ 58 (73)
T cd04487 1 VHIEGEVVQIKQTSGPTIFTLRDETGTVWAAAFEEAG-----VRAYPEVEVGDIVRVTGEVEP 58 (73)
T ss_pred CEEEEEEeccccCCCCEEEEEEcCCEEEEEEEEchhc-----cCCcCCCCCCCEEEEEEEEec
Confidence 5899999876546667999999999999999886421 111234567899999999874
No 48
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=95.51 E-value=0.058 Score=39.86 Aligned_cols=68 Identities=22% Similarity=0.284 Sum_probs=46.1
Q ss_pred CCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhccccc
Q psy13182 93 KGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYVS 171 (194)
Q Consensus 93 ~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~~ 171 (194)
.|+.+.+..|.++.|.++ ++|.. .+...-.+|.++... ..+..|.++..
T Consensus 11 ~g~~V~v~Gwv~~~R~~g~~~Fi~--------------LrD~~g~iQ~v~~~~----------------~~~~~~~~~~~ 60 (108)
T cd04316 11 DGEEVTVAGWVHEIRDLGGIKFVI--------------LRDREGIVQVTAPKK----------------KVDKELFKTVR 60 (108)
T ss_pred CCCEEEEEEEEEeeeccCCeEEEE--------------EecCCeeEEEEEeCC----------------CCCHHHHHHHh
Confidence 466777777777777655 55654 233334577766532 23445666667
Q ss_pred CCCCCceEeEEEEEecCCc
Q psy13182 172 QIPKESILDIQAHVQATPT 190 (194)
Q Consensus 172 ~l~~esi~~~~~~~~~~~~ 190 (194)
+|+.||+|.|+|.+...+.
T Consensus 61 ~l~~es~V~V~G~v~~~~~ 79 (108)
T cd04316 61 KLSRESVISVTGTVKAEPK 79 (108)
T ss_pred CCCCcCEEEEEEEEEeCCC
Confidence 8999999999999988754
No 49
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=95.21 E-value=0.093 Score=37.92 Aligned_cols=62 Identities=13% Similarity=0.131 Sum_probs=47.1
Q ss_pred EEEEEEEEeeec--CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 81 VWVRGRLHTSRA--KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 81 V~vrgrv~~~R~--~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
.||+|.|.+.+. .|.=+|+.|+|.++.+.|++|.... .+-.....|..+..|.|.|.+..-+
T Consensus 1 ~~v~GeVs~~~~~~~sGH~yFtlkD~~~~i~cv~f~~~g---~~~~~~~~l~~Gd~V~v~G~v~~y~ 64 (91)
T cd04482 1 YRVTGKVVEEPRTIEGGHVFFKISDGTGEIDCAAYEPTK---EFRDVVRLLIPGDEVTVYGSVRPGT 64 (91)
T ss_pred CEEEEEEeCCeecCCCCCEEEEEECCCcEEEEEEECccc---ccccccCCCCCCCEEEEEEEEecCC
Confidence 379999998764 5677999999999999999986521 1113345577899999999987764
No 50
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=94.97 E-value=0.035 Score=52.60 Aligned_cols=77 Identities=14% Similarity=0.172 Sum_probs=61.8
Q ss_pred CceEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEe
Q psy13182 64 RDFVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQA 143 (194)
Q Consensus 64 ~~~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~ 143 (194)
.+++.+.+|+. +.|+.|.|+|-|..++..+.-.-++|+|+++.++|-+|....+ +..-.|..+.+|.|.|.|..
T Consensus 200 ~~r~~i~~id~-~ig~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGv-----RAyP~IevGdiV~ViG~V~~ 273 (715)
T COG1107 200 LPRTLIDDLDE-MIGKTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGV-----RAYPEIEVGDIVEVIGEVTR 273 (715)
T ss_pred cccccHHHHHh-hcCceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCc-----ccCCCCCCCceEEEEEEEee
Confidence 34566788865 8999999999999999998887889999999999988874321 22234678999999999988
Q ss_pred cCc
Q psy13182 144 TPT 146 (194)
Q Consensus 144 ~~~ 146 (194)
...
T Consensus 274 r~g 276 (715)
T COG1107 274 RDG 276 (715)
T ss_pred cCC
Confidence 743
No 51
>cd04483 hOBFC1_like hOBFC1_like: A subfamily of OB folds similar to that found in human OB fold containing protein 1 (hOBFC1). Members of this group belong to the Replication protein A subunit 2 (RPA2) family of OB folds. RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The OB fold domain of RPA2 has dual roles in ssDNA binding and trimerization.
Probab=94.78 E-value=0.17 Score=36.68 Aligned_cols=62 Identities=8% Similarity=0.129 Sum_probs=46.5
Q ss_pred EEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccH--------------HH-HHHHhcCCCccEEEEEEEEEec
Q psy13182 83 VRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSK--------------QM-IKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 83 vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~--------------~m-~k~~~~l~rESiV~V~G~V~~~ 144 (194)
|-|+|.+.+.......+.|.|+++.+-|.+........ .| .+....|..+++|.|+|.+..-
T Consensus 2 ivG~V~sv~~~~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~G~i~~f 78 (92)
T cd04483 2 ILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVRGSIRTY 78 (92)
T ss_pred eEEEEEEEEecCCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEEEEEecc
Confidence 56899999888888899999999999997775422110 01 1345668899999999999874
No 52
>cd03524 RPA2_OBF_family RPA2_OBF_family: A family of oligonucleotide binding (OB) folds with similarity to the OB fold of the single strand (ss) DNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA contains six OB folds, which are involved in ssDNA binding and in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. This family also includes OB folds similar to those found in Escherichia coli SSB, the wedge domain of E. coli RecG (a branched-DNA-specific helicase), E. coli ssDNA specific exodeoxyribonuclease VII large subunit, Pyroco
Probab=94.65 E-value=0.45 Score=30.71 Aligned_cols=57 Identities=12% Similarity=0.070 Sum_probs=42.0
Q ss_pred EEEEEEeeecCC---CeEEEEEEecc-eEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 83 VRGRLHTSRAKG---KQCFVVIREQN-FTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 83 vrgrv~~~R~~G---k~~Fl~lRd~~-~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
+.|.|...+... .+.|+.|.|.+ +.+.++++.. ....+...+..+..+.|+|.+...
T Consensus 2 v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~-----~~~~~~~~~~~g~~v~v~g~v~~~ 62 (75)
T cd03524 2 IVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGE-----LAEELENLLKEGQVVYIKGKVKKF 62 (75)
T ss_pred eEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEch-----HHHHHHhhccCCCEEEEEEEEEec
Confidence 456666665443 67999999999 9999998864 222334567889999999999764
No 53
>cd04320 AspRS_cyto_N AspRS_cyto_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae and human cytoplasmic aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis.
Probab=94.15 E-value=0.18 Score=36.71 Aligned_cols=29 Identities=38% Similarity=0.605 Sum_probs=23.6
Q ss_pred chhhcccccCCCCCceEeEEEEEecCCcc
Q psy13182 163 SKQMIKYVSQIPKESILDIQAHVQATPTI 191 (194)
Q Consensus 163 s~~~~~~~~~l~~esi~~~~~~~~~~~~~ 191 (194)
+..|.++...|+.||+|.|.|+|..++.+
T Consensus 42 ~~~~~~~~~~l~~es~V~V~G~v~~~~~~ 70 (102)
T cd04320 42 SKQMVKWAGSLSKESIVDVEGTVKKPEEP 70 (102)
T ss_pred CHHHHHHHhcCCCccEEEEEEEEECCCCc
Confidence 44566777789999999999999987654
No 54
>cd04322 LysRS_N LysRS_N: N-terminal, anticodon recognition domain of lysyl-tRNA synthetases (LysRS). These enzymes are homodimeric class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Included in this group are E. coli LysS and LysU. These two isoforms of LysRS are encoded by distinct genes which are differently regulated. Eukaryotes contain 2 sets of aaRSs, both of which encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein
Probab=94.15 E-value=0.16 Score=37.44 Aligned_cols=28 Identities=11% Similarity=0.168 Sum_probs=22.2
Q ss_pred chhhcccccCCCCCceEeEEEEEecCCc
Q psy13182 163 SKQMIKYVSQIPKESILDIQAHVQATPT 190 (194)
Q Consensus 163 s~~~~~~~~~l~~esi~~~~~~~~~~~~ 190 (194)
+..|.++...|+.+|+|.|.|.+..++.
T Consensus 40 ~~~~~~~~~~l~~g~~V~v~G~v~~~~~ 67 (108)
T cd04322 40 EEEFEDFKKLLDLGDIIGVTGTPFKTKT 67 (108)
T ss_pred HHHHHHHHhcCCCCCEEEEEEEEEecCC
Confidence 3466666666999999999999987654
No 55
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=93.26 E-value=0.6 Score=33.17 Aligned_cols=62 Identities=13% Similarity=0.100 Sum_probs=47.2
Q ss_pred EEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 81 VWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 81 V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
|.+-|+|.+....+...-+.|.|+++++-|.+........ ......+..+..|.|.|.+..-
T Consensus 2 v~~vG~V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~--~~~~~~~~~g~~v~v~G~v~~~ 63 (95)
T cd04478 2 VTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDD--SSEVEPIEEGTYVRVFGNLKSF 63 (95)
T ss_pred EEEEEEEEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcc--cccccccccCCEEEEEEEEccc
Confidence 6788999999998888899999999999997765422100 0123456778999999999775
No 56
>PRK12366 replication factor A; Reviewed
Probab=92.97 E-value=1.6 Score=42.08 Aligned_cols=74 Identities=11% Similarity=0.056 Sum_probs=54.8
Q ss_pred CceEEcccccccCCCcEEEEEEEEEeeec---------CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccE
Q psy13182 64 RDFVPIRQLNKDYVDKTVWVRGRLHTSRA---------KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESI 134 (194)
Q Consensus 64 ~~~~~i~~L~~~~~g~~V~vrgrv~~~R~---------~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESi 134 (194)
..+..|.+|++-..|..+.|+|||.+... .|++.-+.|.|.++++.++++.... -+| ..|..+.+
T Consensus 277 ~~~~pI~~L~~~~~g~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D~tG~IR~t~w~~~~-----d~~-~~l~~G~v 350 (637)
T PRK12366 277 LEIVNIEELTEFEDGEEVDVKGRIIAISDKREVERDDRTAEVQDIELADGTGRVRVSFWGEKA-----KIL-ENLKEGDA 350 (637)
T ss_pred cCceeHHHCCcccCCCEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCCCeEEEEEeCchh-----hhh-cccCCCCE
Confidence 45688999976326789999999987632 3678888999999999999986411 012 23567999
Q ss_pred EEEEEEEEe
Q psy13182 135 LDIQAHVQA 143 (194)
Q Consensus 135 V~V~G~V~~ 143 (194)
+.|.+...+
T Consensus 351 y~is~~~vk 359 (637)
T PRK12366 351 VKIENCKVR 359 (637)
T ss_pred EEEecCEEe
Confidence 999886666
No 57
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=92.62 E-value=0.27 Score=45.11 Aligned_cols=68 Identities=19% Similarity=0.227 Sum_probs=48.7
Q ss_pred cCCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhcccc
Q psy13182 92 AKGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYV 170 (194)
Q Consensus 92 ~~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~ 170 (194)
..|+.+-|..|.+..+.++ ++|.. .+...-.||.++... .++..|.++.
T Consensus 10 ~~g~~v~i~G~v~~~R~~g~~~Fi~--------------lrd~~g~iQ~v~~~~----------------~~~~~~~~~~ 59 (428)
T TIGR00458 10 MDGQEVTFMGWVHEIRDLGGLIFVL--------------LRDREGLIQITAPAK----------------KVSKNLFKWA 59 (428)
T ss_pred hCCCEEEEEEEEEEEecCCCcEEEE--------------EEeCCeeEEEEEECC----------------cCCHHHHHHH
Confidence 3467788888888877776 66655 333334688877654 2455677777
Q ss_pred cCCCCCceEeEEEEEecCC
Q psy13182 171 SQIPKESILDIQAHVQATP 189 (194)
Q Consensus 171 ~~l~~esi~~~~~~~~~~~ 189 (194)
..|+.||+|.|.|+|....
T Consensus 60 ~~l~~~s~v~v~G~v~~~~ 78 (428)
T TIGR00458 60 KKLNLESVVAVRGIVKIKE 78 (428)
T ss_pred hCCCCCcEEEEEEEEEecC
Confidence 7899999999999998754
No 58
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=92.09 E-value=1.6 Score=29.18 Aligned_cols=47 Identities=19% Similarity=0.360 Sum_probs=36.3
Q ss_pred CC-CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 93 KG-KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 93 ~G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
.| .+.|+.+.|.++.+.+++|.. ..-+....|..+..+.|.|.+...
T Consensus 16 ~g~~~~~~~l~D~tg~~~~~~f~~-----~~~~~~~~l~~g~~v~v~G~v~~~ 63 (84)
T cd04485 16 KGKRMAFVTLEDLTGSIEVVVFPE-----TYEKYRDLLKEDALLLVEGKVERR 63 (84)
T ss_pred CCCEEEEEEEEeCCCeEEEEECHH-----HHHHHHHHhcCCCEEEEEEEEEec
Confidence 35 479999999999999998843 222345567789999999999764
No 59
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=91.28 E-value=1.9 Score=29.17 Aligned_cols=45 Identities=11% Similarity=0.163 Sum_probs=35.6
Q ss_pred CC-CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEe
Q psy13182 93 KG-KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQA 143 (194)
Q Consensus 93 ~G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~ 143 (194)
.| .+.++.|.|.++.+.+++|... ......|..+..+.|.|.+..
T Consensus 16 ~g~~~~~~~l~D~tg~i~~~~f~~~------~~~~~~l~~g~~v~v~G~v~~ 61 (83)
T cd04492 16 NGKPYLALTLQDKTGEIEAKLWDAS------EEDEEKFKPGDIVHVKGRVEE 61 (83)
T ss_pred CCCcEEEEEEEcCCCeEEEEEcCCC------hhhHhhCCCCCEEEEEEEEEE
Confidence 35 5799999999999999998531 122566788899999999975
No 60
>PRK07211 replication factor A; Reviewed
Probab=91.11 E-value=3.3 Score=38.81 Aligned_cols=116 Identities=10% Similarity=0.090 Sum_probs=70.3
Q ss_pred eEEcccccccCCCcEEEEEEEEEeeec-----------CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccE
Q psy13182 66 FVPIRQLNKDYVDKTVWVRGRLHTSRA-----------KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESI 134 (194)
Q Consensus 66 ~~~i~~L~~~~~g~~V~vrgrv~~~R~-----------~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESi 134 (194)
..+|.+|++.. ..|.|.|||.++-. .|++.=+.|=|.++.+.++++.. ...++...|..+.+
T Consensus 53 ~~~I~dL~pg~--~~vtI~aRV~~~~~~Rt~~~~~~~~eGkv~~v~l~DeTG~Ir~TlW~d-----~ad~~~~~Le~GdV 125 (485)
T PRK07211 53 VNGIADIEPGM--DEVKFLAKVLSIGDLRTFERDGEDEDGRVINVEVADETGSVRVAFWDE-----QAVAAEEELEVGQV 125 (485)
T ss_pred cccHhhCCCCC--CceEEEEEEeEccCceEEEeCCCCCCcEEEEEEEEcCCCeEEEEEech-----HhHhhhcccCCCCE
Confidence 35788887532 45899999876532 46888899999999999999854 22245677889999
Q ss_pred EEEEEEEEecCcccCCCceeeeeecc--ccchhhcc-cccC-C-CCCceEeEEEEEecCC
Q psy13182 135 LDIQAHVQATPTIVESLPMSILSVGD--TVSKQMIK-YVSQ-I-PKESILDIQAHVQATP 189 (194)
Q Consensus 135 V~V~G~V~~~~~~i~~~t~~~~El~~--~is~~~~~-~~~~-l-~~esi~~~~~~~~~~~ 189 (194)
+.|.|.+...-..+ -.++..+|... .++.++-. +|+. | |..+.++|.|.|....
T Consensus 126 ~~I~~~~~~~ys~~-El~i~~ve~~~d~~i~~~~~~~~~I~dL~~~~~~v~I~grV~~v~ 184 (485)
T PRK07211 126 LRIKGRPKDGYNGL-EVSVDKVEPDPDAEIDVQIGDTYTVEDLSLGLSDVTLVGVVLDTD 184 (485)
T ss_pred EEEeceEeccccce-EEEEeeEEEcccccccccccCCccHHHcCCCCCceEEEEEEEEcC
Confidence 99998764221110 11122222210 01111100 1111 2 5678899999887543
No 61
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=91.04 E-value=1.1 Score=41.50 Aligned_cols=72 Identities=13% Similarity=0.130 Sum_probs=53.2
Q ss_pred EcccccccCCCcEEEEEEEEEeeec----CC-CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEE
Q psy13182 68 PIRQLNKDYVDKTVWVRGRLHTSRA----KG-KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQ 142 (194)
Q Consensus 68 ~i~~L~~~~~g~~V~vrgrv~~~R~----~G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~ 142 (194)
.+.+|.....|+.|++.|.|.+++. .| .++|+.|-|.++.+-+++|.. ..-++...|..+.++.|+|.+.
T Consensus 270 ~~~~l~~~~~~~~v~vaG~I~~ik~~~TKkG~~maf~~leD~tG~ie~vvFp~-----~y~~~~~~l~~~~~v~v~G~v~ 344 (449)
T PRK07373 270 NLSELEEQKEKTKVSAVVMLNEVKKIVTKKGDPMAFLQLEDLSGQSEAVVFPK-----SYERISELLQVDARLIIWGKVD 344 (449)
T ss_pred CHHHHhcccCCCEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHH-----HHHHHHHHhccCCEEEEEEEEE
Confidence 3444432235778999999988773 35 479999999999999999853 2334445567789999999997
Q ss_pred ec
Q psy13182 143 AT 144 (194)
Q Consensus 143 ~~ 144 (194)
..
T Consensus 345 ~~ 346 (449)
T PRK07373 345 RR 346 (449)
T ss_pred ec
Confidence 64
No 62
>cd04323 AsnRS_cyto_like_N AsnRS_cyto_like_N: N-terminal, anticodon recognition domain of the type found in human and Saccharomyces cerevisiae cytoplasmic asparaginyl-tRNA synthetase (AsnRS), in Brugia malayai AsnRs and, in various putative bacterial AsnRSs. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, whereas the other exclusively with
Probab=90.78 E-value=0.73 Score=32.25 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=19.7
Q ss_pred ccccCCCCCceEeEEEEEecCCcc
Q psy13182 168 KYVSQIPKESILDIQAHVQATPTI 191 (194)
Q Consensus 168 ~~~~~l~~esi~~~~~~~~~~~~~ 191 (194)
++...|+.||+|.|.|++..++.+
T Consensus 42 ~~~~~l~~es~V~V~G~v~~~~~~ 65 (84)
T cd04323 42 YDAKSLTQESSVEVTGEVKEDPRA 65 (84)
T ss_pred HHHhcCCCcCEEEEEEEEEECCcc
Confidence 344579999999999999987654
No 63
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=90.33 E-value=0.69 Score=42.52 Aligned_cols=67 Identities=16% Similarity=0.232 Sum_probs=45.6
Q ss_pred CCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhccccc
Q psy13182 93 KGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYVS 171 (194)
Q Consensus 93 ~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~~ 171 (194)
.|+.+-|..|.++.+.++ ++|.. .+...-.||.++.... + ..+.++..
T Consensus 15 ~g~~V~i~GrV~~~R~~gk~~Fl~--------------LrD~~g~iQ~v~~~~~----------------~-~~~~~~~~ 63 (437)
T PRK05159 15 DGEEVTLAGWVHEIRDLGGIAFLI--------------LRDRSGIIQVVVKKKV----------------D-EELFETIK 63 (437)
T ss_pred CCCEEEEEEEeEeeecCCCeEEEE--------------EEcCCcEEEEEEeCCc----------------c-HHHHHHHh
Confidence 467778888888777666 55654 2222224788775531 1 34556667
Q ss_pred CCCCCceEeEEEEEecCCc
Q psy13182 172 QIPKESILDIQAHVQATPT 190 (194)
Q Consensus 172 ~l~~esi~~~~~~~~~~~~ 190 (194)
+|+.||+|.|+|+|.+++.
T Consensus 64 ~L~~gs~V~v~G~v~~~~~ 82 (437)
T PRK05159 64 KLKRESVVSVTGTVKANPK 82 (437)
T ss_pred CCCCCcEEEEEEEEEcCCC
Confidence 8999999999999998763
No 64
>PRK12366 replication factor A; Reviewed
Probab=90.12 E-value=4.9 Score=38.88 Aligned_cols=118 Identities=15% Similarity=0.155 Sum_probs=72.8
Q ss_pred CceEEcccccccCCCcEEEEEEEEEee---e----c---CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCcc
Q psy13182 64 RDFVPIRQLNKDYVDKTVWVRGRLHTS---R----A---KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKES 133 (194)
Q Consensus 64 ~~~~~i~~L~~~~~g~~V~vrgrv~~~---R----~---~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rES 133 (194)
.+...|.+|++.. ..|.|.|||.+. | . .|++.-+.+-|.++++.++++.. ...+...|..+.
T Consensus 61 ~~~~~I~dl~p~~--~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~DetG~Ir~t~W~~------~~~~~~~le~G~ 132 (637)
T PRK12366 61 EEDFKISDIEEGQ--INVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTGTIRLTLWND------NAKLLKGLKEGD 132 (637)
T ss_pred cceeEHHHCcCCC--cceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCCEEEEEEEch------hhhhhccCCCCC
Confidence 4578999997632 459999999755 2 2 35678889999999999999864 123346788999
Q ss_pred EEEEEEEEEecCcc---c---CCCceeeeeeccccchhhc--cccc-CCCCCceEeEEEEEecCC
Q psy13182 134 ILDIQAHVQATPTI---V---ESLPMSILSVGDTVSKQMI--KYVS-QIPKESILDIQAHVQATP 189 (194)
Q Consensus 134 iV~V~G~V~~~~~~---i---~~~t~~~~El~~~is~~~~--~~~~-~l~~esi~~~~~~~~~~~ 189 (194)
++.|.+.....-.. + ..+++..++..+..+-+.+ .+++ .|.....|||.|+|....
T Consensus 133 v~~i~~~~v~~~~~~~el~~~~~t~I~~~~~~d~~~i~~~~~~~~I~el~~g~~v~v~G~V~~~~ 197 (637)
T PRK12366 133 VIKIENARSRKWNNDVELNSGSETRIDKLEKYDESRYPIIKENYDIPELEPNLSATIEGEVTKAY 197 (637)
T ss_pred EEEEeccEecccCCceEEEcCCcceEEEccccccccCCcccccccccccCCCCeEEEEEEEEEcc
Confidence 99999976554110 0 0111111111001111111 1222 367778999999998653
No 65
>cd04490 PolII_SU_OBF PolII_SU_OBF: A subfamily of OB folds corresponding to the OB fold found in Pyrococcus abyssi DNA polymerase II (PolII) small subunit. PolII is a family D DNA polymerase, having a 3-prime to 5-prime exonuclease activity. P. abyssi PolII is heterodimeric. The large subunit appears to be the polymerase, and the small subunit may be the exonuclease. The small subunit contains a calcineurin-like phosphatase superfamily domain C-terminal to this OB-fold domain.
Probab=90.01 E-value=3.7 Score=28.70 Aligned_cols=57 Identities=16% Similarity=0.268 Sum_probs=41.3
Q ss_pred EEEEEEEEeee--cCCCeEEEEEEecceEEEEEEeccccccHHHH--HHHhcCCCccEEEEEEEEEe
Q psy13182 81 VWVRGRLHTSR--AKGKQCFVVIREQNFTIQGILSVGDTVSKQMI--KYVSQIPKESILDIQAHVQA 143 (194)
Q Consensus 81 V~vrgrv~~~R--~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~--k~~~~l~rESiV~V~G~V~~ 143 (194)
+.+.|-|...| ..|+. |+.|=|.++++.+++|.. ..- ++...|..+.++.|.|.+..
T Consensus 2 v~i~GiI~~v~~TK~g~~-~~~leD~~G~~Ev~~F~~-----~~~~~~~~~~l~~d~~v~v~g~v~~ 62 (79)
T cd04490 2 VSIIGMVNDVRSTKNGHR-IVELEDTTGRITVLLTKD-----KEELFEEAEDILPDEVIGVSGTVSK 62 (79)
T ss_pred EEEEEEEeEEEEcCCCCE-EEEEECCCCEEEEEEeCc-----hhhhhhhhhhccCCCEEEEEEEEec
Confidence 34555554443 34566 999999999999999964 222 45566778899999999954
No 66
>cd04100 Asp_Lys_Asn_RS_N Asp_Lys_Asn_RS_N: N-terminal, anticodon recognition domain of class 2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. Class 2b aaRSs include the homodimeric aspartyl-, asparaginyl-, and lysyl-tRNA synthetases (AspRS, AsnRS, and LysRS). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Included in this group are archeal and archeal-like A
Probab=89.45 E-value=1 Score=31.42 Aligned_cols=25 Identities=16% Similarity=0.372 Sum_probs=21.1
Q ss_pred hcccccCCCCCceEeEEEEEecCCc
Q psy13182 166 MIKYVSQIPKESILDIQAHVQATPT 190 (194)
Q Consensus 166 ~~~~~~~l~~esi~~~~~~~~~~~~ 190 (194)
|.++...|+.+|+|.|+|.+..++.
T Consensus 41 ~~~~~~~l~~~s~V~v~G~~~~~~~ 65 (85)
T cd04100 41 FFEEAEKLRTESVVGVTGTVVKRPE 65 (85)
T ss_pred HHHHHhCCCCCCEEEEEeEEEECCC
Confidence 5566678999999999999998764
No 67
>cd04318 EcAsnRS_like_N EcAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli asparaginyl-tRNA synthetase (AsnRS) and, in Arabidopsis thaliana and Saccharomyces cerevisiae mitochondrial (mt) AsnRS. This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial
Probab=89.15 E-value=1.1 Score=30.99 Aligned_cols=23 Identities=13% Similarity=0.286 Sum_probs=18.9
Q ss_pred ccccCCCCCceEeEEEEEecCCc
Q psy13182 168 KYVSQIPKESILDIQAHVQATPT 190 (194)
Q Consensus 168 ~~~~~l~~esi~~~~~~~~~~~~ 190 (194)
++...|+.||+|.|.|.+..++.
T Consensus 43 ~~~~~l~~gs~V~v~G~v~~~~~ 65 (82)
T cd04318 43 KEILKLSTGSSIRVEGVLVKSPG 65 (82)
T ss_pred HHHhcCCCceEEEEEEEEEeCCC
Confidence 34457999999999999998765
No 68
>PRK14699 replication factor A; Provisional
Probab=88.95 E-value=4.4 Score=37.94 Aligned_cols=112 Identities=13% Similarity=0.184 Sum_probs=69.1
Q ss_pred ceEEcccccccCCCcEEEEEEEEEeeec----------CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccE
Q psy13182 65 DFVPIRQLNKDYVDKTVWVRGRLHTSRA----------KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESI 134 (194)
Q Consensus 65 ~~~~i~~L~~~~~g~~V~vrgrv~~~R~----------~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESi 134 (194)
++..|.+|++ .+..|.|.|+|.+.-. .|++.-+.|-|.++++.+.++.... ++...|..+..
T Consensus 275 ~~~~I~~L~~--~~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeTG~Ir~T~W~~~a------~~~~~i~~Gd~ 346 (484)
T PRK14699 275 EFTPIEDIKA--DMNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTGKIRLTLWDEKT------NFLDEIDFDET 346 (484)
T ss_pred cccCHHHcCC--CCceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCCeEEEEEeCccc------ccccccCCCce
Confidence 4677888865 3567999999986532 3456668999999999998886411 23344566777
Q ss_pred EEEEEEEEecCcccCCCceeeeeeccc----cchh----hc--c--cccCCCCCceEeEEEEEecCC
Q psy13182 135 LDIQAHVQATPTIVESLPMSILSVGDT----VSKQ----MI--K--YVSQIPKESILDIQAHVQATP 189 (194)
Q Consensus 135 V~V~G~V~~~~~~i~~~t~~~~El~~~----is~~----~~--~--~~~~l~~esi~~~~~~~~~~~ 189 (194)
+.|.+.-.... .-...+||+.. |.+. .. . .-.+|...+.|||.|+|+...
T Consensus 347 v~i~~~y~~~~-----~~~~~~eL~~~~~t~I~~~~~~~e~~~~~~~I~die~~~~vdV~G~V~~v~ 408 (484)
T PRK14699 347 VEVLNAYSREN-----TFSQQVELNLGARGIIQKSEKKVEYREKFTDIADIIPGESYSVQGKVSEIG 408 (484)
T ss_pred EEEEeEEEEec-----cCCccEEEEecCceeEeecCCcceeeeccccHHHccCCCeeEEEEEEEEcC
Confidence 77766554321 11234555511 1000 00 1 123477889999999998653
No 69
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=88.33 E-value=0.93 Score=44.31 Aligned_cols=69 Identities=16% Similarity=0.180 Sum_probs=46.4
Q ss_pred ecCCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhccc
Q psy13182 91 RAKGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKY 169 (194)
Q Consensus 91 R~~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~ 169 (194)
...|+.+-|..|.+..+.++ ++|.. .|...-.||.++... .++..+..+
T Consensus 15 ~~~g~~V~l~GWV~~~R~~G~l~Fid--------------LRD~~G~iQvV~~~~----------------~~~~~~~~~ 64 (706)
T PRK12820 15 DDTGREVCLAGWVDAFRDHGELLFIH--------------LRDRNGFIQAVFSPE----------------AAPADVYEL 64 (706)
T ss_pred hhCCCEEEEEEEEEEEEcCCCcEEEE--------------EEeCCccEEEEEeCC----------------cCCHHHHHH
Confidence 35577777888877777665 66665 333333477766543 133445566
Q ss_pred ccCCCCCceEeEEEEEecCC
Q psy13182 170 VSQIPKESILDIQAHVQATP 189 (194)
Q Consensus 170 ~~~l~~esi~~~~~~~~~~~ 189 (194)
..+|+.||+|.|+|+|...+
T Consensus 65 ~~~L~~EsvV~V~G~v~~r~ 84 (706)
T PRK12820 65 AASLRAEFCVALQGEVQKRL 84 (706)
T ss_pred HhcCCCCCEEEEEeEEeccC
Confidence 67899999999999999854
No 70
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=88.20 E-value=3.7 Score=30.31 Aligned_cols=67 Identities=15% Similarity=0.194 Sum_probs=41.9
Q ss_pred eEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 66 FVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 66 ~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
++.-..| ..+.|+.|++-|++.+....|+.+.+..-|+. .+++.+.... .+..+..|.|.|+|....
T Consensus 7 RVn~~~L-~~~~gk~VrivGkv~~~~~~g~~~~l~~~d~~-~V~v~l~~~~-----------~~~~~~~vEviG~V~~~~ 73 (109)
T PF08661_consen 7 RVNGSML-SQFVGKTVRIVGKVESVDPDGGSATLSTSDGG-QVTVSLNPPS-----------DEELSKYVEVIGKVNDDG 73 (109)
T ss_dssp EE-GGGG-GGGTTSEEEEEEEEEEE-TTSSEEEEE-TTS--EEEEEESS-------------SS---SEEEEEEEE-TTS
T ss_pred eECHHHH-HhhCCCeEEEEEEEeeEcCCCCEEEEEcCCCC-EEEEEeCCCC-----------CCCCCCEEEEEEEEcCCC
Confidence 4444555 46899999999999999988877555544544 6666554321 113578999999998864
No 71
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=87.99 E-value=1.9 Score=44.01 Aligned_cols=70 Identities=14% Similarity=0.167 Sum_probs=52.7
Q ss_pred cccccccCCCcEEEEEEEEEeeecC----CCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 69 IRQLNKDYVDKTVWVRGRLHTSRAK----GKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 69 i~~L~~~~~g~~V~vrgrv~~~R~~----Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
+.+|.....|..|++.|.+...+.. | ++|+.|-|.++.+.+++|.. ..-++...|..++++.|.|.+...
T Consensus 944 ~~~l~~~~~~~~v~v~g~i~~~~~~~TkkG-maf~~leD~~g~~e~~ifp~-----~~~~~~~~l~~~~~~~v~g~v~~~ 1017 (1046)
T PRK05672 944 AAELLDVEDGRRVRVAGVVTHRQRPGTASG-VTFLTLEDETGMVNVVVWPG-----LWERQRREALGARLLLVRGRVQNA 1017 (1046)
T ss_pred HHHHhhccCCCEEEEEEEEEEEEEecCCCc-eEEEEEecCCCCEEEEECHH-----HHHHHHHHhccCCEEEEEEEEEec
Confidence 3344332357789999998766543 5 99999999999999999853 233445667889999999999764
No 72
>PRK07211 replication factor A; Reviewed
Probab=87.56 E-value=8.2 Score=36.24 Aligned_cols=110 Identities=12% Similarity=0.140 Sum_probs=67.8
Q ss_pred ceEEcccccccCCCcEEEEEEEEEeee-------c---CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccE
Q psy13182 65 DFVPIRQLNKDYVDKTVWVRGRLHTSR-------A---KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESI 134 (194)
Q Consensus 65 ~~~~i~~L~~~~~g~~V~vrgrv~~~R-------~---~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESi 134 (194)
++..|.+|++ ....|.|.|+|.+.- . .|++.=+.|=|.++++.+.++... ...+..|..+++
T Consensus 160 ~~~~I~dL~~--~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG~IR~TlW~d~------Ad~~~~le~G~V 231 (485)
T PRK07211 160 DTYTVEDLSL--GLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETGRVRVTLWDDR------ADLAEELDAGES 231 (485)
T ss_pred CCccHHHcCC--CCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCCeEEEEEechh------hhhhccCCCCCE
Confidence 5567777764 245688999998542 2 346777889999999999888541 111245788999
Q ss_pred EEEEE-EEEecCcccCCCceeeeeec-----------cccc-hhhcccccCCCCCceEeEEEEEecCCc
Q psy13182 135 LDIQA-HVQATPTIVESLPMSILSVG-----------DTVS-KQMIKYVSQIPKESILDIQAHVQATPT 190 (194)
Q Consensus 135 V~V~G-~V~~~~~~i~~~t~~~~El~-----------~~is-~~~~~~~~~l~~esi~~~~~~~~~~~~ 190 (194)
|.|.+ .|.... ..+||+ +.++ .+...--..|.....|||.|+|.....
T Consensus 232 v~I~~a~Vre~~--------g~~ELsl~~~s~I~~~~dev~~vp~~~~I~dl~~g~~vdV~GvV~~v~~ 292 (485)
T PRK07211 232 VEIVDGYVRERD--------GSLELHVGDRGAVEEVDEDVEYVPDTTPIESLEIDETVDIAGVVRSADP 292 (485)
T ss_pred EEEEeeEEEecC--------CcEEEEECCCceEEECCcccccccccccHhhcCCCCceeEEEEEEEccC
Confidence 99974 554431 233333 1111 010111223566678999999987643
No 73
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=87.21 E-value=2.1 Score=39.60 Aligned_cols=61 Identities=11% Similarity=0.292 Sum_probs=45.5
Q ss_pred cEEEEEEEEEeeecCCC-eEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 79 KTVWVRGRLHTSRAKGK-QCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 79 ~~V~vrgrv~~~R~~Gk-~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
..|||+|-|.+.+...+ -.|+.|.|....++|++|.... .+.--.+.-+--|.|.|.|..=
T Consensus 24 ~~V~v~GEISn~t~~~sgH~YFtLKD~~A~i~c~mf~~~~-----~~l~f~p~eG~~V~v~G~is~Y 85 (440)
T COG1570 24 GQVWVRGEISNFTRPASGHLYFTLKDERAQIRCVMFKGNN-----RRLKFRPEEGMQVLVRGKISLY 85 (440)
T ss_pred CeEEEEEEecCCccCCCccEEEEEccCCceEEEEEEcCcc-----cccCCCccCCCEEEEEEEEEEE
Confidence 46999999999985543 7999999999999999987521 0111123457889999988764
No 74
>cd04319 PhAsnRS_like_N PhAsnRS_like_N: N-terminal, anticodon recognition domain of the type found in Pyrococcus horikoshii AsnRS asparaginyl-tRNA synthetase (AsnRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The archeal enzymes in this group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose.
Probab=86.09 E-value=2.7 Score=30.50 Aligned_cols=21 Identities=24% Similarity=0.355 Sum_probs=17.8
Q ss_pred ccCCCCCceEeEEEEEecCCc
Q psy13182 170 VSQIPKESILDIQAHVQATPT 190 (194)
Q Consensus 170 ~~~l~~esi~~~~~~~~~~~~ 190 (194)
...|+.||+|.|+|.|...+.
T Consensus 45 ~~~l~~~s~v~V~G~v~~~~~ 65 (103)
T cd04319 45 AKKVGIESSVIVEGAVKADPR 65 (103)
T ss_pred HhCCCCCCEEEEEEEEEECCC
Confidence 347999999999999988754
No 75
>PRK15491 replication factor A; Provisional
Probab=86.09 E-value=12 Score=33.92 Aligned_cols=73 Identities=15% Similarity=0.142 Sum_probs=51.8
Q ss_pred CceEEcccccccCCCcEEEEEEEEEee-------ec---CCCeEEEEEEecceEEEEEEeccccccHHHHHHH-hcCCCc
Q psy13182 64 RDFVPIRQLNKDYVDKTVWVRGRLHTS-------RA---KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYV-SQIPKE 132 (194)
Q Consensus 64 ~~~~~i~~L~~~~~g~~V~vrgrv~~~-------R~---~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~-~~l~rE 132 (194)
++..+|.+|++. ...|.|.|||.+. |. .|++.=+.+=|.++++.++++.... -.+. ..|..+
T Consensus 55 ~~~~kI~dL~~~--~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~ir~tlW~~~a-----~~~~~~~le~G 127 (374)
T PRK15491 55 VDTTKIADINES--SSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDLA-----DLIKTGDIEVG 127 (374)
T ss_pred cccccHHHCCCC--CCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCeEEEEEECchh-----hhhccCCcCCC
Confidence 356789999753 3569999999876 22 3466668899999999999986411 0111 347789
Q ss_pred cEEEEEEEEEe
Q psy13182 133 SILDIQAHVQA 143 (194)
Q Consensus 133 SiV~V~G~V~~ 143 (194)
.++.|.|.+..
T Consensus 128 ~v~~I~~~~~~ 138 (374)
T PRK15491 128 KSLNISGYAKE 138 (374)
T ss_pred CEEEEeeeecc
Confidence 99999997544
No 76
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=85.93 E-value=3.3 Score=42.83 Aligned_cols=71 Identities=10% Similarity=0.133 Sum_probs=52.8
Q ss_pred cccccccCCCcEEEEEEEEEeeec----CC-CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEe
Q psy13182 69 IRQLNKDYVDKTVWVRGRLHTSRA----KG-KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQA 143 (194)
Q Consensus 69 i~~L~~~~~g~~V~vrgrv~~~R~----~G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~ 143 (194)
+.+|.....|..|++.|.|..+|. .| .++|+.+-|.++.+.+++|.. ..-++...|..+.++.|+|.|..
T Consensus 991 ~~~l~~~~~~~~v~v~g~i~~~k~~~Tk~G~~maf~~leD~tg~~e~vvFp~-----~y~~~~~~l~~~~~~~v~g~v~~ 1065 (1170)
T PRK07374 991 LSSLEEQPDKAKVSAIAMIPEMKQVTTRKGDRMAILQLEDLTGSCEAVVFPK-----SYERLSDHLMTDTRLLVWAKVDR 1065 (1170)
T ss_pred HHHHhcccCCCEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHH-----HHHHHHHHhccCCEEEEEEEEEe
Confidence 344432235778999999988763 34 479999999999999999853 23344555778899999999976
Q ss_pred c
Q psy13182 144 T 144 (194)
Q Consensus 144 ~ 144 (194)
.
T Consensus 1066 ~ 1066 (1170)
T PRK07374 1066 R 1066 (1170)
T ss_pred c
Confidence 4
No 77
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=85.76 E-value=4.8 Score=31.06 Aligned_cols=68 Identities=12% Similarity=0.221 Sum_probs=46.8
Q ss_pred eEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHh-cCCCccEEEEEEEEEec
Q psy13182 66 FVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVS-QIPKESILDIQAHVQAT 144 (194)
Q Consensus 66 ~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~-~l~rESiV~V~G~V~~~ 144 (194)
...+.+.-.-..+..|.++|.|-..- |+- -+.+||.++++.+-+... .|.. .+..++-|.|.|.|-+.
T Consensus 45 ~~tV~~a~~~~Ddt~V~L~G~Iv~~l--~~d-~Y~F~D~TG~I~VeId~~--------~w~G~~v~p~d~V~I~GeVDk~ 113 (126)
T TIGR00156 45 KMTVDFAKSMHDGASVTLRGNIISHI--GDD-RYVFRDKSGEINVVIPAA--------VWNGREVQPKDMVNISGSLDKK 113 (126)
T ss_pred eEeHHHHhhCCCCCEEEEEEEEEEEe--CCc-eEEEECCCCCEEEEECHH--------HcCCCcCCCCCEEEEEEEECCC
Confidence 45565554446788999999986543 322 345699999988755432 2322 45789999999999864
No 78
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=85.72 E-value=4.6 Score=29.97 Aligned_cols=67 Identities=13% Similarity=0.181 Sum_probs=41.4
Q ss_pred EEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHH-hcCCCccEEEEEEEEEec
Q psy13182 67 VPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYV-SQIPKESILDIQAHVQAT 144 (194)
Q Consensus 67 ~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~-~~l~rESiV~V~G~V~~~ 144 (194)
..+.++.....+..|.++|.|-..-..-.. .+||.++.|.+-+... .|. ..+..+.-|.|.|.|-+.
T Consensus 23 ~TV~~a~~~~Dd~~V~L~G~Iv~~l~~d~Y---~F~D~TG~I~VeId~~--------~w~g~~vt~~~~Vri~GeVDk~ 90 (103)
T PF04076_consen 23 TTVAQAKNAKDDTPVTLEGNIVKQLGDDKY---LFRDATGEIEVEIDDD--------VWRGQTVTPDDKVRISGEVDKD 90 (103)
T ss_dssp --HHHHTTS-SSEEEEEEEEEEEEEETTEE---EEEETTEEEEEE--GG--------GSTT----TTSEEEEEEEEEEE
T ss_pred EeHHHHhhCcCCCeEEEEEEEEEEecCCEE---EEECCCCcEEEEEChh--------hcCCcccCCCCEEEEEEEEeCC
Confidence 445555445678899999998664433333 4599999988765432 111 235789999999999865
No 79
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=85.14 E-value=3.7 Score=42.31 Aligned_cols=72 Identities=19% Similarity=0.266 Sum_probs=53.9
Q ss_pred EcccccccCCCcEEEEEEEEEeeecC----C-CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEE
Q psy13182 68 PIRQLNKDYVDKTVWVRGRLHTSRAK----G-KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQ 142 (194)
Q Consensus 68 ~i~~L~~~~~g~~V~vrgrv~~~R~~----G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~ 142 (194)
.+.+|.....|..|.+.|-|..++.. | .++|+.|-|.++.+.+++|.. ..-++...|..+++|.|.|.|.
T Consensus 967 ~~~~l~~~~~g~~V~v~G~I~~vk~~~TKkG~~mafltLeD~TG~iEvviFp~-----~ye~~~~~L~~g~iV~V~GkVe 1041 (1135)
T PRK05673 967 RLADLEPTEGGSVVTVAGLVVSVRRRVTKRGNKMAIVTLEDLSGRIEVMLFSE-----ALEKYRDLLEEDRIVVVKGQVS 1041 (1135)
T ss_pred CHHHHhccccCceEEEEEEEEEEEecccCCCCeEEEEEEEeCCCcEEEEECHH-----HHHHHHHHhccCCEEEEEEEEE
Confidence 34455322347889999988777643 5 479999999999999999853 2335556678899999999997
Q ss_pred ec
Q psy13182 143 AT 144 (194)
Q Consensus 143 ~~ 144 (194)
..
T Consensus 1042 ~~ 1043 (1135)
T PRK05673 1042 FD 1043 (1135)
T ss_pred ec
Confidence 64
No 80
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=83.90 E-value=6.9 Score=40.50 Aligned_cols=63 Identities=17% Similarity=0.222 Sum_probs=50.0
Q ss_pred CCcEEEEEEEEEeeec----CC-CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 77 VDKTVWVRGRLHTSRA----KG-KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 77 ~g~~V~vrgrv~~~R~----~G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
.|..|++.|.|..+|. .| .++|+.|-|.++.+.+++|.. .+-++...|..+.++.|.|.+...
T Consensus 990 ~~~~v~v~g~i~~~~~~~tk~G~~maf~~leD~~g~~e~~vfp~-----~~~~~~~~l~~~~~~~v~g~v~~~ 1057 (1151)
T PRK06826 990 DGDKVIIGGIITEVKRKTTRNNEMMAFLTLEDLYGTVEVIVFPK-----VYEKYRSLLNEDNIVLIKGRVSLR 1057 (1151)
T ss_pred CCcEEEEEEEEEEeEeeccCCCCeEEEEEEEECCCcEEEEECHH-----HHHHHHHHhccCCEEEEEEEEEec
Confidence 4678999999977763 35 479999999999999999853 333555667889999999999753
No 81
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=83.37 E-value=7.8 Score=29.88 Aligned_cols=73 Identities=15% Similarity=0.076 Sum_probs=49.4
Q ss_pred CCCceEEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEE
Q psy13182 62 VDRDFVPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHV 141 (194)
Q Consensus 62 ~~~~~~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V 141 (194)
|++..+.+.+-..-+.+..|.++|-+-. ..|.= -+++||.++.+++-+....-. -..+.++..|.|+|.|
T Consensus 41 p~~~~~TV~~Ak~~~Dda~V~l~GnIv~--qi~~D-~y~FrD~sGeI~VeIdd~~w~-------g~tv~P~dkV~I~Gev 110 (128)
T COG3111 41 PNAKVTTVDQAKTLHDDAWVSLEGNIVR--QIGDD-RYVFRDASGEINVDIDDKVWN-------GQTVTPKDKVRIQGEV 110 (128)
T ss_pred CCcceeEHHHhhccccCCeEEEEeeEEE--eeCCc-eEEEEcCCccEEEEecccccC-------CcccCcccEEEEEeEE
Confidence 4455566665545577889999998854 34422 345699999999866543100 1345789999999999
Q ss_pred Eec
Q psy13182 142 QAT 144 (194)
Q Consensus 142 ~~~ 144 (194)
-+.
T Consensus 111 Dk~ 113 (128)
T COG3111 111 DKD 113 (128)
T ss_pred cCC
Confidence 775
No 82
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=83.37 E-value=8.2 Score=28.20 Aligned_cols=56 Identities=14% Similarity=0.246 Sum_probs=40.3
Q ss_pred ccCCCcEEEEEEEEEeeecCCCeEEEEEEecce-EEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 74 KDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNF-TIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 74 ~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~-~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
+.+.|+.|++-|++...+.. -+.++...+ .+++.+.... .+..+..|.|.|+|...
T Consensus 11 ~~f~gk~V~ivGkV~~~~~~----~~~~~~~Dg~~v~v~l~~~~-----------~~~~~~~vEViG~V~~~ 67 (101)
T cd04479 11 SQFVGKTVRIVGKVEKVDGD----SLTLISSDGVNVTVELNRPL-----------DLPISGYVEVIGKVSPD 67 (101)
T ss_pred HhhCCCEEEEEEEEEEecCC----eEEEEcCCCCEEEEEeCCCC-----------CcccCCEEEEEEEECCC
Confidence 45899999999999988754 244454444 7888776431 23577899999999853
No 83
>PF12869 tRNA_anti-like: tRNA_anti-like; InterPro: IPR024422 The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold [].; PDB: 3F1Z_I.
Probab=83.25 E-value=6.2 Score=29.99 Aligned_cols=67 Identities=19% Similarity=0.234 Sum_probs=36.4
Q ss_pred ccCCCcEEEEEEEEEeeecC-CCeEEEEEEecce--EEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 74 KDYVDKTVWVRGRLHTSRAK-GKQCFVVIREQNF--TIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 74 ~~~~g~~V~vrgrv~~~R~~-Gk~~Fl~lRd~~~--~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
..+.|+.+.|.|.|..++.. ++..|+....... .++|.+..... ..-....|..++.|+|.|++...
T Consensus 63 ~kY~gK~i~vtG~V~~I~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~----~~~~~~~l~~G~~Vti~G~~~g~ 132 (144)
T PF12869_consen 63 KKYKGKIIEVTGTVSSIDKGFGDNYVVLLGTENGFAGVQCYFSNDQE----KRASVAKLKKGQKVTIKGICTGY 132 (144)
T ss_dssp HHHTT-EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGG----GHHHHHH--TTSEEEEEEE----
T ss_pred hhcCCCEEEEEEEEEEEEEcCCCcEEEEccCCCCceeEEEEEccchh----hhhhHhcCCCCCEEEEEEEEEee
Confidence 44679999999999999763 3445666665333 36665554321 11123458999999999988765
No 84
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=83.02 E-value=5.1 Score=36.61 Aligned_cols=62 Identities=13% Similarity=0.245 Sum_probs=47.2
Q ss_pred CcEEEEEEEEEeeecC-CCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 78 DKTVWVRGRLHTSRAK-GKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 78 g~~V~vrgrv~~~R~~-Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
-..|||+|-|.+.+.. +.-+|+.|.|....+-|++|..... +.--.+..+.-|.|.|.|..-
T Consensus 23 ~~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~-----~~~~~~~~G~~v~v~g~~~~y 85 (438)
T PRK00286 23 LGQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSAR-----RLKFKPEEGMKVLVRGKVSLY 85 (438)
T ss_pred CCcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhh-----cCCCCCCCCCEEEEEEEEEEE
Confidence 4579999999998765 4679999999999999999975210 001234678999999998863
No 85
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=82.85 E-value=6.9 Score=40.31 Aligned_cols=71 Identities=14% Similarity=0.255 Sum_probs=53.4
Q ss_pred EcccccccCCCcEEEEEEEEEeeec----CC-CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEE
Q psy13182 68 PIRQLNKDYVDKTVWVRGRLHTSRA----KG-KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQ 142 (194)
Q Consensus 68 ~i~~L~~~~~g~~V~vrgrv~~~R~----~G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~ 142 (194)
.+.+|.. ..|..|++.|.|.++|. .| .++|+.+-|.++.+.+++|.. ..-++...|..+.++.|+|.+.
T Consensus 934 ~~~~l~~-~~~~~v~v~g~i~~~~~~~tk~g~~maf~~leD~tg~~e~~vFp~-----~y~~~~~~l~~~~~~~v~G~v~ 1007 (1107)
T PRK06920 934 SLAQAMR-HKKKVQRAIVYITSVKVIRTKKGQKMAFITFCDQNDEMEAVVFPE-----TYIHFSDKLQEGAIVLVDGTIE 1007 (1107)
T ss_pred CHHHHhh-cCCCEEEEEEEEEEeEeecCCCCCeEEEEEEeeCCCcEEEEECHH-----HHHHHHHHhccCCEEEEEEEEE
Confidence 3444432 35778999999988753 34 579999999999999999853 2334556678899999999997
Q ss_pred ec
Q psy13182 143 AT 144 (194)
Q Consensus 143 ~~ 144 (194)
..
T Consensus 1008 ~~ 1009 (1107)
T PRK06920 1008 LR 1009 (1107)
T ss_pred ec
Confidence 54
No 86
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=82.78 E-value=3.5 Score=38.12 Aligned_cols=64 Identities=25% Similarity=0.238 Sum_probs=42.6
Q ss_pred CeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhcccccCC
Q psy13182 95 KQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYVSQI 173 (194)
Q Consensus 95 k~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~~~l 173 (194)
+.+-|..+.++.+.++ +.|.. |+-+|.+ ||+++.++. ....+.+ ...|
T Consensus 17 ~~V~v~GWV~~~R~~g~i~Fi~-------------lrDgsg~-iQ~v~~~~~----------------~~~~~~~-~~~L 65 (435)
T COG0017 17 QEVTVRGWVHNKRDLGKIIFLV-------------LRDGSGF-IQAVVPKNK----------------VYEELFK-AKKL 65 (435)
T ss_pred cEEEEEEEeeeecccCCeEEEE-------------EEcCCcE-EEEEEECCC----------------CcHHHhh-hhcC
Confidence 4566666666665554 55543 1234444 999988751 2344445 6689
Q ss_pred CCCceEeEEEEEecCC
Q psy13182 174 PKESILDIQAHVQATP 189 (194)
Q Consensus 174 ~~esi~~~~~~~~~~~ 189 (194)
+.||.|.|+|+|.+.+
T Consensus 66 ~~es~v~V~G~v~~~~ 81 (435)
T COG0017 66 TLESSVVVTGIVKASP 81 (435)
T ss_pred CCccEEEEEEEEEcCC
Confidence 9999999999999876
No 87
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=82.27 E-value=3.4 Score=38.16 Aligned_cols=69 Identities=13% Similarity=0.119 Sum_probs=42.8
Q ss_pred ecCCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhccc
Q psy13182 91 RAKGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKY 169 (194)
Q Consensus 91 R~~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~ 169 (194)
...|+.+-|..|.+..+.++ ++|.. .+...-.+|.++... . +..+.++
T Consensus 13 ~~~~~~V~i~G~v~~~R~~g~~~Fi~--------------lrD~~g~iq~~~~~~---------------~--~~~~~~~ 61 (450)
T PRK03932 13 KYVGQEVTVRGWVRTKRDSGKIAFLQ--------------LRDGSCFKQLQVVKD---------------N--GEEYFEE 61 (450)
T ss_pred ccCCCEEEEEEEEEEEEeCCCeEEEE--------------EECCCCcEEEEEEcC---------------C--ChHHHHH
Confidence 34467778888888777665 55554 222222344444332 1 2234455
Q ss_pred ccCCCCCceEeEEEEEecCCc
Q psy13182 170 VSQIPKESILDIQAHVQATPT 190 (194)
Q Consensus 170 ~~~l~~esi~~~~~~~~~~~~ 190 (194)
..+|+.+|+|.|.|+|.+++.
T Consensus 62 ~~~l~~~s~v~v~G~v~~~~~ 82 (450)
T PRK03932 62 IKKLTTGSSVIVTGTVVESPR 82 (450)
T ss_pred HhcCCCCcEEEEEEEEEcCCC
Confidence 568999999999999998753
No 88
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=82.20 E-value=5.1 Score=33.21 Aligned_cols=67 Identities=15% Similarity=0.217 Sum_probs=48.3
Q ss_pred CCCcEEEEEEEEEeee--cCCCeEEEEEEecceEEEEEEeccccccHHHHH---HHhcCCCccEEEEEEEEEecC
Q psy13182 76 YVDKTVWVRGRLHTSR--AKGKQCFVVIREQNFTIQGILSVGDTVSKQMIK---YVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 76 ~~g~~V~vrgrv~~~R--~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k---~~~~l~rESiV~V~G~V~~~~ 145 (194)
...+.+.+.|-+...+ ..+.+.|+++.|+++++-+++|... .+.+. ..--+..+-++.|+|.+..-+
T Consensus 49 ~l~e~v~vkg~V~~~~n~~~~gi~~l~lndgtGti~vva~~~t---ee~l~~n~~~p~~~eGe~veVtGrv~~yr 120 (204)
T COG4085 49 RLNEEVTVKGEVTADQNAIGGGIESLVLNDGTGTITVVASRST---EETLELNEGMPVTVEGEIVEVTGRVEEYR 120 (204)
T ss_pred eeeccceeeeEEEeeecccccceEEEEEECCCCcEEEEEecCh---hHhHhhcCCCCccccCcEEEEEEEEEEeC
Confidence 3456788999887776 3458899999999999999988752 22222 111344789999999887653
No 89
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=82.10 E-value=9.8 Score=36.94 Aligned_cols=62 Identities=11% Similarity=0.102 Sum_probs=47.4
Q ss_pred CCCcEEEEEEEEEeeecC--C-CeEEEEEEecceEEEEEEeccccccHHHHHH-HhcCCCccEEEEEEEEEe
Q psy13182 76 YVDKTVWVRGRLHTSRAK--G-KQCFVVIREQNFTIQGILSVGDTVSKQMIKY-VSQIPKESILDIQAHVQA 143 (194)
Q Consensus 76 ~~g~~V~vrgrv~~~R~~--G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~-~~~l~rESiV~V~G~V~~ 143 (194)
..|+.+++.|.|...+.. + +...+.+.|+++.++++.|... . .| ...|..+..+.|.|.+..
T Consensus 57 ~~g~~vtv~g~V~~~~~~~~~~~~~~v~l~D~tg~i~l~~F~~n---~---~~~~~~l~~G~~~~v~Gkv~~ 122 (681)
T PRK10917 57 RPGEKVTVEGEVLSAEVVFGKRRRLTVTVSDGTGNLTLRFFNFN---Q---PYLKKQLKVGKRVAVYGKVKR 122 (681)
T ss_pred CCCCEEEEEEEEEEEEEccCCceEEEEEEEECCeEEEEEEEccC---c---HHHHhhCCCCCEEEEEEEEEe
Confidence 468899999998776433 3 4678888999999999888310 1 13 466889999999999976
No 90
>PRK10053 hypothetical protein; Provisional
Probab=81.82 E-value=7.7 Score=30.06 Aligned_cols=67 Identities=19% Similarity=0.322 Sum_probs=46.8
Q ss_pred EEcccccccCCCcEEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHh-cCCCccEEEEEEEEEec
Q psy13182 67 VPIRQLNKDYVDKTVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVS-QIPKESILDIQAHVQAT 144 (194)
Q Consensus 67 ~~i~~L~~~~~g~~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~-~l~rESiV~V~G~V~~~ 144 (194)
..+.+...-..+..|.++|.|-.. .|.- -+.+||+++.|++-+... .|.. .+..++-|.|.|.|-+.
T Consensus 50 ~tV~~a~~~~Dd~~V~L~G~Iv~~--lg~d-~Y~F~D~tG~I~VeID~~--------~w~G~~v~p~~kV~I~GevDk~ 117 (130)
T PRK10053 50 MTVEQAKTMHDGATVSLRGNLIDH--KGDD-RYVFRDKSGEINVIIPAA--------VFDGREVQPDQMININGSLDKK 117 (130)
T ss_pred EEHHHhhcCcCCCeEEEEEEEEEE--eCCc-eEEEECCCCcEEEEeCHH--------HcCCCcCCCCCEEEEEEEECCC
Confidence 455555455678899999998553 3432 345699999999765432 2332 46789999999999875
No 91
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=80.34 E-value=3.8 Score=37.91 Aligned_cols=67 Identities=15% Similarity=0.159 Sum_probs=42.8
Q ss_pred CCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccE-EEEEEEEEecCcccCCCceeeeeeccccchhhcccc
Q psy13182 93 KGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESI-LDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYV 170 (194)
Q Consensus 93 ~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESi-V~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~ 170 (194)
.|+.+.|..|.++.+.++ ++|.. |.-++. =.||.++... .+..+.++.
T Consensus 15 ~g~~v~v~Gwv~~~R~~~~~~F~~-------------lrD~~~~g~iQ~v~~~~-----------------~~~~~~~~~ 64 (453)
T TIGR00457 15 VGDEVTVSGWVRTKRSSKKIIFLE-------------LNDGSSLGPIQAVINGE-----------------DNPYLFQLL 64 (453)
T ss_pred CCCEEEEEEEeEEEEcCCCeEEEE-------------EECCCCCccEEEEEeCC-----------------cChHHHHHH
Confidence 367777777777777554 56654 112221 3577666442 123344555
Q ss_pred cCCCCCceEeEEEEEecCC
Q psy13182 171 SQIPKESILDIQAHVQATP 189 (194)
Q Consensus 171 ~~l~~esi~~~~~~~~~~~ 189 (194)
..|+.+|+|.|+|.|.+++
T Consensus 65 ~~l~~gs~V~v~G~v~~~~ 83 (453)
T TIGR00457 65 KSLTTGSSVSVTGKVVESP 83 (453)
T ss_pred HcCCCCcEEEEEEEEEcCC
Confidence 6899999999999999764
No 92
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=79.89 E-value=7.4 Score=35.79 Aligned_cols=60 Identities=10% Similarity=0.318 Sum_probs=45.0
Q ss_pred EEEEEEEEEeeecC-CCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 80 TVWVRGRLHTSRAK-GKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 80 ~V~vrgrv~~~R~~-Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
.|||.|-|.+.+.. +.-+|+.|.|....+.||+|..... .+. -.+.-+.-|.|.|.|.--
T Consensus 19 ~v~V~GEisn~~~~~sGH~YFtLkD~~a~i~~vmf~~~~~---~l~--f~~~~G~~V~v~g~v~~y 79 (432)
T TIGR00237 19 QVWIQGEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNNN---RLK--FRPQNGQQVLVRGGISVY 79 (432)
T ss_pred cEEEEEEecCCeeCCCceEEEEEEcCCcEEEEEEEcChhh---CCC--CCCCCCCEEEEEEEEEEE
Confidence 79999999998754 4579999999999999999975210 000 123568889999988654
No 93
>cd04317 EcAspRS_like_N EcAspRS_like_N: N-terminal, anticodon recognition domain of the type found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. These homodimeric enzymes are class2b aminoacyl-tRNA synthetases (aaRSs). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic synthesis, wh
Probab=79.87 E-value=5.4 Score=30.30 Aligned_cols=22 Identities=23% Similarity=0.564 Sum_probs=17.8
Q ss_pred ccccCCCCCceEeEEEEEecCC
Q psy13182 168 KYVSQIPKESILDIQAHVQATP 189 (194)
Q Consensus 168 ~~~~~l~~esi~~~~~~~~~~~ 189 (194)
.+...|+.+|+|.|+|++...+
T Consensus 57 ~~~~~l~~gs~V~V~G~~~~~~ 78 (135)
T cd04317 57 ELAEKLRNESVIQVTGKVRARP 78 (135)
T ss_pred HHHhCCCCccEEEEEEEEECCC
Confidence 3445799999999999998754
No 94
>PF10451 Stn1: Telomere regulation protein Stn1; InterPro: IPR018856 The budding yeast protein Stn1 is a DNA-binding protein which has specificity for telomeric DNA. Structural profiling has predicted an OB-fold []. This entry represents the N-terminal part of the molecule, which adopts the OB fold. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF6_A 3KF8_A.
Probab=77.55 E-value=11 Score=32.46 Aligned_cols=61 Identities=16% Similarity=0.172 Sum_probs=41.3
Q ss_pred cEEEEEEEEEeeecC----CCeEEEEEEecce--EEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEE
Q psy13182 79 KTVWVRGRLHTSRAK----GKQCFVVIREQNF--TIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQ 142 (194)
Q Consensus 79 ~~V~vrgrv~~~R~~----Gk~~Fl~lRd~~~--~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~ 142 (194)
+.|.|.|.|-...-. .+..|+.+-|+++ .+.|.+......+ +---...+ .+.+|.|.|++.
T Consensus 67 ~~v~i~G~Vv~~~~~~~~~~~~~~l~iDD~Sg~~~i~~~~~~~~~~~--~~l~~~~~-~G~~V~VkG~vs 133 (256)
T PF10451_consen 67 RWVRIVGVVVGIDYKWIENEDRIILTIDDSSGANTIECKCSKSSYLS--MGLPINDL-IGKVVEVKGTVS 133 (256)
T ss_dssp -EEEEEEEEEEEEEEE-BBTCEEEEEEE-SSCS-EEEEEEEHHHHHC--CCHHCTT--TT-EEEEEEEEE
T ss_pred EEEEEEEEEEEEEEEeecccceEEEEEeCCCCceeEEEEEEcccccc--cCCCccCC-CCcEEEEEEEEc
Confidence 468899988887755 6789999999999 8888887541100 00012333 899999999999
No 95
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=76.03 E-value=23 Score=25.39 Aligned_cols=58 Identities=12% Similarity=0.219 Sum_probs=42.5
Q ss_pred EEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 82 WVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 82 ~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
.+.|.+.+.+..+.=+|+.|+|.+|.++|.+... -+-++-..|..++++.++-+-.-.
T Consensus 6 ~l~v~Iks~~~~~~D~~v~l~DpTG~i~~tiH~~-----v~~~y~~~l~~GavLlLk~V~Vf~ 63 (86)
T PF15072_consen 6 CLVVIIKSIVPSSEDAFVVLKDPTGEIRGTIHRK-----VLEEYGDELSPGAVLLLKDVTVFS 63 (86)
T ss_pred EEEEEEEEeeccCCCeEEEEECCCCcEEEEEeHH-----HHhhcCCccccCEEEEEeeeeEEe
Confidence 4677888888887778999999999999987643 111345667788888877654443
No 96
>PLN02903 aminoacyl-tRNA ligase
Probab=75.76 E-value=5.5 Score=38.69 Aligned_cols=67 Identities=7% Similarity=0.071 Sum_probs=40.4
Q ss_pred ecCCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhccc
Q psy13182 91 RAKGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKY 169 (194)
Q Consensus 91 R~~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~ 169 (194)
...|+.+.|..|.+..+.++ ++|.. .|...-.+|.++... . +..+.++
T Consensus 69 ~~~gk~V~l~GWV~~~R~~G~l~Fid--------------LRD~~G~iQvV~~~~----------------~-~~~~~~~ 117 (652)
T PLN02903 69 NDVGSRVTLCGWVDLHRDMGGLTFLD--------------VRDHTGIVQVVTLPD----------------E-FPEAHRT 117 (652)
T ss_pred hhCCCEEEEEEEEEEEecCCCcEEEE--------------EEcCCccEEEEEeCC----------------c-cHHHHHH
Confidence 34566677777776666554 55554 122111256554332 1 2234455
Q ss_pred ccCCCCCceEeEEEEEecC
Q psy13182 170 VSQIPKESILDIQAHVQAT 188 (194)
Q Consensus 170 ~~~l~~esi~~~~~~~~~~ 188 (194)
...|+.||+|.|.|+|...
T Consensus 118 ~~~L~~esvV~V~G~V~~r 136 (652)
T PLN02903 118 ANRLRNEYVVAVEGTVRSR 136 (652)
T ss_pred HhcCCCCCEEEEEEEEEeC
Confidence 6689999999999999875
No 97
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=75.43 E-value=19 Score=23.25 Aligned_cols=44 Identities=11% Similarity=0.105 Sum_probs=33.5
Q ss_pred CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 95 KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 95 k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
+..-+.+.|+++.+.++.|... . .....+..+..+.+.|.+..-
T Consensus 18 ~~~~~~~~D~~g~i~~~~F~~~---~---~~~~~~~~G~~~~v~Gkv~~~ 61 (75)
T cd04488 18 RRLKVTLSDGTGTLTLVFFNFQ---P---YLKKQLPPGTRVRVSGKVKRF 61 (75)
T ss_pred cEEEEEEEcCCCEEEEEEECCC---H---HHHhcCCCCCEEEEEEEEeec
Confidence 5688889999999999888521 1 123557889999999999874
No 98
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=74.63 E-value=15 Score=37.73 Aligned_cols=69 Identities=16% Similarity=0.289 Sum_probs=50.4
Q ss_pred EcccccccCCCcEEEEEEEEEeee----c-CC-CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEE
Q psy13182 68 PIRQLNKDYVDKTVWVRGRLHTSR----A-KG-KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHV 141 (194)
Q Consensus 68 ~i~~L~~~~~g~~V~vrgrv~~~R----~-~G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V 141 (194)
.+.+|. .+..+.+.|+|.+++ . .| .++|+.+-|.++.+.+++|.. .+-++...|..+.++.|+|.|
T Consensus 877 ~~~~l~---~~~~~~~~~~i~~~~~~~tk~~g~~maf~~leD~~g~ie~~vFp~-----~y~~~~~~l~~~~~~~v~G~v 948 (1034)
T PRK07279 877 PISQLV---KNSEATILVQIQSIRVIRTKTKGQQMAFLSVTDTKKKLDVTLFPE-----TYRQYKDELKEGKFYYLKGKI 948 (1034)
T ss_pred cHHHHh---cCCcceEEEEEEEEEEEEEcCCCCeEEEEEEeeCCCcEEEEECHH-----HHHHHHHHhccCCEEEEEEEE
Confidence 444553 255677778776544 2 45 589999999999999999853 333555667889999999999
Q ss_pred Eec
Q psy13182 142 QAT 144 (194)
Q Consensus 142 ~~~ 144 (194)
...
T Consensus 949 ~~~ 951 (1034)
T PRK07279 949 QER 951 (1034)
T ss_pred Eec
Confidence 764
No 99
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=73.18 E-value=11 Score=34.70 Aligned_cols=64 Identities=14% Similarity=0.182 Sum_probs=51.0
Q ss_pred cEEEEEEEEEe--eecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 79 KTVWVRGRLHT--SRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 79 ~~V~vrgrv~~--~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
....+.|++.. .+.-|..+|+.+.|+.+.+-|++|.. .+++-..+..|..++.|.+.|.+....
T Consensus 267 ~~~~v~g~v~~~p~~ieGghv~v~i~d~~G~I~~~A~ep---tk~fr~~a~~L~pGD~i~~~G~~~~~~ 332 (421)
T COG1571 267 SKYRVVGRVEAEPRAIEGGHVVVEITDGEGEIGAVAFEP---TKEFRELARKLIPGDEITVYGSVKPGT 332 (421)
T ss_pred cceEEEEEEecccEEeeCCEEEEEecCCCceEEEEEecc---cccchHHHHhcCCCCEEEEecCccccc
Confidence 35677776633 34568999999999999999999875 345667788999999999999887764
No 100
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=72.18 E-value=27 Score=26.54 Aligned_cols=68 Identities=16% Similarity=0.167 Sum_probs=46.2
Q ss_pred ceEEcccccccCCCcEEEEEEEEEeee------cCC---CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEE
Q psy13182 65 DFVPIRQLNKDYVDKTVWVRGRLHTSR------AKG---KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESIL 135 (194)
Q Consensus 65 ~~~~i~~L~~~~~g~~V~vrgrv~~~R------~~G---k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV 135 (194)
.+.+|.||.+. ...|.+.+.|..+. ..| ...-+.|.|.|+++.+.+-... +..|..+++|
T Consensus 3 ~~~kI~dL~~g--~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~I~~tlW~~~---------a~~l~~GdvV 71 (129)
T PRK06461 3 MITKIKDLKPG--MERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQ---------AGSLKEGEVV 71 (129)
T ss_pred CceEHHHcCCC--CCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCEEEEEEeCCc---------cccCCCCCEE
Confidence 35788888642 25688888887432 123 3567899999999888776431 3456789999
Q ss_pred EEE-EEEEe
Q psy13182 136 DIQ-AHVQA 143 (194)
Q Consensus 136 ~V~-G~V~~ 143 (194)
.|. |.+..
T Consensus 72 ~I~na~v~~ 80 (129)
T PRK06461 72 EIENAWTTL 80 (129)
T ss_pred EEECcEEee
Confidence 999 45443
No 101
>cd04480 RPA1_DBD_A_like RPA1_DBD_A_like: A subgroup of uncharacterized plant OB folds with similarity to the second OB fold, the ssDNA-binding domain (DBD)-A, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-A, RPA1 contains three other OB folds: DBD-B, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with DBD-A and DBD-B of RPA1. RPA1 DBD-C is involved in trimerization. The ssDNA-binding mechanism is believed to be multistep and to involve conformational change.
Probab=71.95 E-value=30 Score=23.98 Aligned_cols=72 Identities=13% Similarity=0.017 Sum_probs=49.8
Q ss_pred EEEEEEeeecCCCeEEEEEEecce-EEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeec
Q psy13182 83 VRGRLHTSRAKGKQCFVVIREQNF-TIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVG 159 (194)
Q Consensus 83 vrgrv~~~R~~Gk~~Fl~lRd~~~-~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~ 159 (194)
+|-|.+.....|...=+.|.|..| .+|+.+... ..-+|...|..+++..+.+.-..+....-..+-++.+|.
T Consensus 7 ~r~W~~~~~~~~~~~~miL~De~G~~I~a~i~~~-----~~~~f~~~L~eg~vy~is~f~v~~~~~~y~~~~~~y~I~ 79 (86)
T cd04480 7 LRLWDVYNNASGESLEMVLVDEKGNRIHATIPKR-----LAAKFRPLLKEGKWYTISNFEVAPNTGSYRPTDHPYKIK 79 (86)
T ss_pred EEEEcCcCCCCCcEEEEEEEcCCCCEEEEEECHH-----HHHhhhhhceeCCEEEEeeEEEEcCCCcccccCCcEEEE
Confidence 566776666677777777888877 899987653 233566677788999999866666554555555666664
No 102
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=71.81 E-value=9.5 Score=35.72 Aligned_cols=23 Identities=13% Similarity=0.226 Sum_probs=18.3
Q ss_pred ccccCCCCCceEeEEEEEecCCc
Q psy13182 168 KYVSQIPKESILDIQAHVQATPT 190 (194)
Q Consensus 168 ~~~~~l~~esi~~~~~~~~~~~~ 190 (194)
++...|+.+|||.|.|.|.+++.
T Consensus 99 ~~~~~l~~g~~v~v~G~v~~t~~ 121 (491)
T PRK00484 99 EAFKKLDLGDIIGVEGTLFKTKT 121 (491)
T ss_pred HHHhcCCCCCEEEEEEEEEEcCC
Confidence 33446999999999999998653
No 103
>PRK15491 replication factor A; Provisional
Probab=71.14 E-value=37 Score=30.74 Aligned_cols=70 Identities=14% Similarity=0.207 Sum_probs=47.1
Q ss_pred ceEEcccccccCCCcEEEEEEEEEeeec-------CC---CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccE
Q psy13182 65 DFVPIRQLNKDYVDKTVWVRGRLHTSRA-------KG---KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESI 134 (194)
Q Consensus 65 ~~~~i~~L~~~~~g~~V~vrgrv~~~R~-------~G---k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESi 134 (194)
+|..|.+|.+ .+..|.|.|+|.+... .| ++.-+.|-|.++++.+.++.... .....|..+..
T Consensus 165 ~~~~I~dl~~--~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG~Ir~t~W~~~a------~~~~~l~~Gd~ 236 (374)
T PRK15491 165 NSQKISDIKD--GDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETGKIRVTLWDGKT------DLADKLENGDS 236 (374)
T ss_pred CcccHHHcCC--CCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCCeEEEEEecchh------cccccCCCCCE
Confidence 4567777754 2345999999988753 34 34558889999999988885411 11245778889
Q ss_pred EEEEEE-EE
Q psy13182 135 LDIQAH-VQ 142 (194)
Q Consensus 135 V~V~G~-V~ 142 (194)
|.|.+. ++
T Consensus 237 V~i~~~~~r 245 (374)
T PRK15491 237 VEIINGYAR 245 (374)
T ss_pred EEEEeceEE
Confidence 988663 44
No 104
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=68.26 E-value=13 Score=35.71 Aligned_cols=64 Identities=11% Similarity=0.179 Sum_probs=39.6
Q ss_pred CCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhccccc
Q psy13182 93 KGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYVS 171 (194)
Q Consensus 93 ~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~~ 171 (194)
.|+.+.|..|.+..|.++ ++|.. .+...-.+|.++... ..+.++..
T Consensus 16 ~g~~V~l~GwV~~~R~~g~l~Fi~--------------LrD~~g~iQ~v~~~~-------------------~~~~~~~~ 62 (588)
T PRK00476 16 VGQTVTLCGWVHRRRDHGGLIFID--------------LRDREGIVQVVFDPD-------------------AEAFEVAE 62 (588)
T ss_pred CCCEEEEEEEEEEEEeCCCeEEEE--------------EEeCCceEEEEEeCC-------------------HHHHHHHh
Confidence 466677777777766655 55554 222222366555320 12334455
Q ss_pred CCCCCceEeEEEEEecCC
Q psy13182 172 QIPKESILDIQAHVQATP 189 (194)
Q Consensus 172 ~l~~esi~~~~~~~~~~~ 189 (194)
.|+.||+|.|.|+|.+.+
T Consensus 63 ~l~~es~V~V~G~v~~~~ 80 (588)
T PRK00476 63 SLRSEYVIQVTGTVRARP 80 (588)
T ss_pred CCCCCCEEEEEEEEEecC
Confidence 799999999999999754
No 105
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=67.96 E-value=40 Score=32.41 Aligned_cols=62 Identities=6% Similarity=-0.023 Sum_probs=45.8
Q ss_pred CCCcEEEEEEEEEeee--cCC--CeEEEEEEe-cceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 76 YVDKTVWVRGRLHTSR--AKG--KQCFVVIRE-QNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 76 ~~g~~V~vrgrv~~~R--~~G--k~~Fl~lRd-~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
..|+.+++.|.|.... ..+ +..-+.+.| +++.+.+++|.. . .....+..+..+.|.|.+...
T Consensus 30 ~~g~~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~F~~----~---~~~~~~~~g~~~~~~Gk~~~~ 96 (630)
T TIGR00643 30 LPGERATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNR----A---FLKKKFKVGSKVVVYGKVKSS 96 (630)
T ss_pred CCCCEEEEEEEEEEeEeccCCCCceEEEEEEECCCCEEEEEEECC----H---HHHhhCCCCCEEEEEEEEEee
Confidence 5688999999986532 122 457788899 999999998843 1 123567899999999999764
No 106
>PLN02502 lysyl-tRNA synthetase
Probab=66.40 E-value=17 Score=34.76 Aligned_cols=70 Identities=13% Similarity=0.014 Sum_probs=41.8
Q ss_pred CCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhcccccC
Q psy13182 94 GKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYVSQ 172 (194)
Q Consensus 94 Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~~~ 172 (194)
|+.+-|..|..+.+.++ ++|.. .+...-.||.++..... . .-...+..+-..
T Consensus 108 ~~~V~v~GrV~~~R~~Gk~~F~~--------------LrD~~g~iQv~~~~~~~------------~-~~~~~~~~~~~~ 160 (553)
T PLN02502 108 DVSVSVAGRIMAKRAFGKLAFYD--------------LRDDGGKIQLYADKKRL------------D-LDEEEFEKLHSL 160 (553)
T ss_pred CCEEEEEEEEEEEecCCCeEEEE--------------EecCCccEEEEEECccc------------c-chhHHHHHHHhC
Confidence 45566777777766665 55554 23333357776654310 0 001124444456
Q ss_pred CCCCceEeEEEEEecCCc
Q psy13182 173 IPKESILDIQAHVQATPT 190 (194)
Q Consensus 173 l~~esi~~~~~~~~~~~~ 190 (194)
|+.+|||.|.|.+.+++.
T Consensus 161 l~~gdiV~V~G~~~~t~~ 178 (553)
T PLN02502 161 VDRGDIVGVTGTPGKTKK 178 (553)
T ss_pred CCCCcEEEEEEEEEecCC
Confidence 999999999999998754
No 107
>PRK06386 replication factor A; Reviewed
Probab=65.97 E-value=34 Score=30.89 Aligned_cols=66 Identities=14% Similarity=0.112 Sum_probs=40.2
Q ss_pred ceEEcccccccCCCcEEEEEEEEEeeec--------CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEE
Q psy13182 65 DFVPIRQLNKDYVDKTVWVRGRLHTSRA--------KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILD 136 (194)
Q Consensus 65 ~~~~i~~L~~~~~g~~V~vrgrv~~~R~--------~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~ 136 (194)
+..+|.||.+. ...|.|.|+|...-. .|.+.=+.|=|.|+++..++ |...|..+.+|.
T Consensus 106 ~~~KI~DL~~g--~~~v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTGrIr~Tl------------W~~~l~eGd~v~ 171 (358)
T PRK06386 106 KLVKIRDLSLV--TPYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTARVRISS------------FGKPLEDNRFVR 171 (358)
T ss_pred CccEeEeccCC--CCceEEEEEEEEccCceEecCCCccEEEEEEEEcCCCeEEEEE------------ccccccCCCEEE
Confidence 45688888653 345778888865421 02233344444444444443 444578899999
Q ss_pred EEEEEEec
Q psy13182 137 IQAHVQAT 144 (194)
Q Consensus 137 V~G~V~~~ 144 (194)
|.+.....
T Consensus 172 i~na~v~e 179 (358)
T PRK06386 172 IENARVSQ 179 (358)
T ss_pred EeeeEEEc
Confidence 99977665
No 108
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=64.41 E-value=39 Score=34.53 Aligned_cols=64 Identities=6% Similarity=0.075 Sum_probs=48.4
Q ss_pred CCcEEEEEEEEEeeec---CC-CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCc
Q psy13182 77 VDKTVWVRGRLHTSRA---KG-KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPT 146 (194)
Q Consensus 77 ~g~~V~vrgrv~~~R~---~G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~ 146 (194)
.+..+++.|.|.++|. .| .++|+.+-|.++.+-+++|.. .+.....|..+.++.|.|....+..
T Consensus 896 ~~~~~~v~g~i~~~~~~~K~g~~maf~~~eD~~~~~e~~~F~~------~~~~~~~l~~~~~~~~~~~~~~~~~ 963 (973)
T PRK07135 896 INTEYRLAIEVKNVKRLRKANKEYKKVILSDDSVEITIFVNDN------DYLLFETLKKGDIYEFLISKSKNNK 963 (973)
T ss_pred CCCeEEEEEEEEEEEEEeeCCCeEEEEEEEECCCcEEEEEcHH------HHHHHHHhhcCCEEEEEEEEcCCCc
Confidence 4667888888876543 36 589999999999999999953 2233345778899999998887743
No 109
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=63.91 E-value=15 Score=34.44 Aligned_cols=67 Identities=12% Similarity=0.066 Sum_probs=40.4
Q ss_pred CCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhccccc-
Q psy13182 94 GKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYVS- 171 (194)
Q Consensus 94 Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~~- 171 (194)
|+.+-|..|....+.++ ++|.. .+...-.||.++... .++..+.++..
T Consensus 53 ~~~v~v~Grv~~~R~~gk~~F~~--------------l~D~~g~iQ~~~~~~----------------~~~~~~~~~~~~ 102 (496)
T TIGR00499 53 NIEVSIAGRIMARRSMGKATFIT--------------LQDESGQIQLYVNKD----------------DLPEDFYEFDEY 102 (496)
T ss_pred CCEEEEEEEEEEEecCCCeEEEE--------------EEcCCccEEEEEECC----------------cCcHHHHHHHHh
Confidence 55556666666666554 55554 222223577777553 12233333333
Q ss_pred CCCCCceEeEEEEEecCCc
Q psy13182 172 QIPKESILDIQAHVQATPT 190 (194)
Q Consensus 172 ~l~~esi~~~~~~~~~~~~ 190 (194)
.|+.+|||.|.|.+.+++.
T Consensus 103 ~l~~gd~V~v~G~~~~t~~ 121 (496)
T TIGR00499 103 LLDLGDIIGVTGYPFKTKT 121 (496)
T ss_pred cCCCCCEEEEEEEEEECCC
Confidence 3899999999999998865
No 110
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=63.59 E-value=40 Score=28.53 Aligned_cols=62 Identities=11% Similarity=0.172 Sum_probs=45.2
Q ss_pred EEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 80 ~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
.|.+-|||.++..+---.|+.+-|+++.+-|-.-... + .....+..+.-+..|.|.|-++.=
T Consensus 68 ~V~fVGvvrni~~~ttn~~~~iEDGTG~Ievr~W~~~--~-~~~e~~~d~~~~~yvkV~G~lk~F 129 (258)
T COG5235 68 NVQFVGVVRNIKTSTTNSMFVIEDGTGSIEVRFWPGN--S-YEEEQCKDLEEQNYVKVNGSLKTF 129 (258)
T ss_pred eEEEEEEEEeeeecccceEEEEecCCceEEEEecCCC--c-hHHHhccccccccEEEEecceeee
Confidence 4889999999998887789999999998876433221 1 112344555667799999988654
No 111
>PLN02221 asparaginyl-tRNA synthetase
Probab=62.77 E-value=13 Score=35.61 Aligned_cols=66 Identities=12% Similarity=0.155 Sum_probs=43.9
Q ss_pred eecCCCeEEEEEEecceEEEE---EEeccccccHHHHHHHhcCCCccEE-EEEEEEEecCcccCCCceeeeeeccccchh
Q psy13182 90 SRAKGKQCFVVIREQNFTIQG---ILSVGDTVSKQMIKYVSQIPKESIL-DIQAHVQATPTIVESLPMSILSVGDTVSKQ 165 (194)
Q Consensus 90 ~R~~Gk~~Fl~lRd~~~~vQ~---v~~~~~~~s~~m~k~~~~l~rESiV-~V~G~V~~~~~~i~~~t~~~~El~~~is~~ 165 (194)
....|+.+.|..|.++.+.++ ++|.. |+-++.+ .+|.++... . ...+
T Consensus 46 ~~~~g~~V~I~GWV~~iR~~Gk~~i~Fl~-------------LRDgs~~g~iQvVv~~~-~-------------~~~~-- 96 (572)
T PLN02221 46 AGLAGQKVRIGGWVKTGREQGKGTFAFLE-------------VNDGSCPANLQVMVDSS-L-------------YDLS-- 96 (572)
T ss_pred hhcCCCEEEEEEEEEehhhCCCceEEEEE-------------EeCCcccccEEEEEcCc-h-------------hhHH--
Confidence 445578889999999888875 66765 2334543 577666432 0 0111
Q ss_pred hcccccCCCCCceEeEEEEEecCC
Q psy13182 166 MIKYVSQIPKESILDIQAHVQATP 189 (194)
Q Consensus 166 ~~~~~~~l~~esi~~~~~~~~~~~ 189 (194)
..|+.||+|.|+|.|...+
T Consensus 97 -----~~L~~ES~V~V~G~V~~~~ 115 (572)
T PLN02221 97 -----TLVATGTCVTVDGVLKVPP 115 (572)
T ss_pred -----hcCCCceEEEEEEEEEeCC
Confidence 1388999999999998765
No 112
>KOG3360|consensus
Probab=62.53 E-value=20 Score=26.39 Aligned_cols=64 Identities=14% Similarity=0.168 Sum_probs=38.5
Q ss_pred EEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEE-EEEEEEEecCcccCCCceeeeee
Q psy13182 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESIL-DIQAHVQATPTIVESLPMSILSV 158 (194)
Q Consensus 80 ~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV-~V~G~V~~~~~~i~~~t~~~~El 158 (194)
..=|+|||.|.+ .+++++.+......-..|.+|+.. ++|-. .|.+.-..+...+.+.+.++.+|
T Consensus 33 ~lGlrGWv~Nt~-------------~GtvkG~leGp~~~vd~mk~wl~~--~gsP~s~I~~~ef~n~kei~~~~y~~F~I 97 (98)
T KOG3360|consen 33 KLGLRGWVMNTS-------------EGTVKGQLEGPPEKVDEMKEWLLT--RGSPVSAIDRAEFSNQKEISRYTYKDFSI 97 (98)
T ss_pred hhcceEEEEecC-------------CceEEEEEeCCHHHHHHHHHHHHh--cCChhHheeeeeecccceecccccceeee
Confidence 344788887753 235667666544445688899874 33322 45555666666666666665554
No 113
>PLN02603 asparaginyl-tRNA synthetase
Probab=60.20 E-value=23 Score=33.89 Aligned_cols=66 Identities=15% Similarity=0.116 Sum_probs=38.9
Q ss_pred CCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccE-EEEEEEEEecCcccCCCceeeeeeccccchhhccccc
Q psy13182 94 GKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESI-LDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYVS 171 (194)
Q Consensus 94 Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESi-V~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~~ 171 (194)
|+.+-|..|..+.+.|+ ++|.. |.-+|. -.||.++.... .... .+..
T Consensus 107 g~~V~v~GwV~~iR~~g~~~Fi~-------------l~Dgs~~~~lQ~v~~~~~---------------~~~~---~l~~ 155 (565)
T PLN02603 107 GKTLNVMGWVRTLRAQSSVTFIE-------------VNDGSCLSNMQCVMTPDA---------------EGYD---QVES 155 (565)
T ss_pred CCEEEEEEEEEEEEeCCCeEEEE-------------EECCCCCEeEEEEEECcH---------------HHHH---HHhh
Confidence 56667777777766665 55554 122333 36666653320 0111 1112
Q ss_pred -CCCCCceEeEEEEEecCCc
Q psy13182 172 -QIPKESILDIQAHVQATPT 190 (194)
Q Consensus 172 -~l~~esi~~~~~~~~~~~~ 190 (194)
.|+.+|+|.|+|+|..++.
T Consensus 156 ~~l~~gs~V~V~G~v~~~~~ 175 (565)
T PLN02603 156 GLITTGASVLVQGTVVSSQG 175 (565)
T ss_pred cCCCCCCEEEEEEEEEecCC
Confidence 4999999999999998753
No 114
>PRK04036 DNA polymerase II small subunit; Validated
Probab=59.62 E-value=45 Score=31.31 Aligned_cols=65 Identities=8% Similarity=0.175 Sum_probs=47.6
Q ss_pred CCcEEEEEEEEEeeecCCCe-EEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 77 VDKTVWVRGRLHTSRAKGKQ-CFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 77 ~g~~V~vrgrv~~~R~~Gk~-~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
.++.++|-|-|..++...+- ..+.|=|.+++++++.... ..+....+..|..+.+|.|.|.+...
T Consensus 152 ~~~~~~viG~v~~~~~~~~g~~~~~LED~sgrv~l~~~~~---~~~~~~~~~~lvtg~vv~v~G~~~~~ 217 (504)
T PRK04036 152 GGEEVSIIGMVSDIRSTKNGHKIVELEDTTGTFPVLIMKD---REDLAELADELLLDEVIGVEGTLSGD 217 (504)
T ss_pred CCceEEEEEEEEEeecccCCceEEEEECCCCeEEEEeecc---hhhhhhhhhcccCceEEEEEEEEcCC
Confidence 56789999999888755432 3678999999999876432 11233445678899999999987654
No 115
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=56.87 E-value=30 Score=35.81 Aligned_cols=70 Identities=10% Similarity=0.164 Sum_probs=42.1
Q ss_pred cCCCeEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhcccc
Q psy13182 92 AKGKQCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYV 170 (194)
Q Consensus 92 ~~Gk~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~ 170 (194)
..|+.+-|..|....+.++ ++|.. .+...-.||.++.... .-+..+..|-
T Consensus 649 ~~~~~V~v~Grv~~~R~~G~~~F~~--------------lrD~~g~iQ~v~~~~~---------------~~~~~~~~~~ 699 (1094)
T PRK02983 649 PTGEEVSVSGRVLRIRDYGGVLFAD--------------LRDWSGELQVLLDASR---------------LEQGSLADFR 699 (1094)
T ss_pred cCCCEEEEEEEEEEEeeCCCeEEEE--------------EEeCCeeEEEEEECCc---------------cchhhHHHHH
Confidence 3455566666666655554 55554 2333345777665531 1122344455
Q ss_pred cCCCCCceEeEEEEEecCCc
Q psy13182 171 SQIPKESILDIQAHVQATPT 190 (194)
Q Consensus 171 ~~l~~esi~~~~~~~~~~~~ 190 (194)
..|+.+|+|.|+|+|.+++.
T Consensus 700 ~~l~~gd~V~v~G~v~~t~~ 719 (1094)
T PRK02983 700 AAVDLGDLVEVTGTMGTSRN 719 (1094)
T ss_pred hcCCCCCEEEEEEEEEEcCC
Confidence 57999999999999988753
No 116
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=55.51 E-value=31 Score=33.75 Aligned_cols=65 Identities=14% Similarity=0.080 Sum_probs=39.7
Q ss_pred eEEEEEEecceEEEE-EEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccCCCceeeeeeccccchhhcccc-cCC
Q psy13182 96 QCFVVIREQNFTIQG-ILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVESLPMSILSVGDTVSKQMIKYV-SQI 173 (194)
Q Consensus 96 ~~Fl~lRd~~~~vQ~-v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~~~t~~~~El~~~is~~~~~~~-~~l 173 (194)
.+-|..|.+..+.++ ++|.. .+...-.||.++.+. ..++..+.++- ..|
T Consensus 109 ~V~vaGrV~~~R~~Gk~~F~~--------------LrD~~G~IQvv~~~~---------------~~~~~~~~~~~~~~l 159 (659)
T PTZ00385 109 TVRVAGRVTSVRDIGKIIFVT--------------IRSNGNELQVVGQVG---------------EHFTREDLKKLKVSL 159 (659)
T ss_pred EEEEEEEEEeeeccCCeEEEE--------------EEECCceEEEEEECC---------------ccCCHHHHHHHHhCC
Confidence 355666666655554 55554 344444777776653 11233333333 369
Q ss_pred CCCceEeEEEEEecCC
Q psy13182 174 PKESILDIQAHVQATP 189 (194)
Q Consensus 174 ~~esi~~~~~~~~~~~ 189 (194)
+.+|||.|.|+|.++.
T Consensus 160 ~~gdiV~V~G~v~~t~ 175 (659)
T PTZ00385 160 RVGDIIGADGVPCRMQ 175 (659)
T ss_pred CCCCEEEEEEEEEecC
Confidence 9999999999998764
No 117
>cd04484 polC_OBF polC_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold nucleic acid binding domain of Bacillus subtilis type C replicative DNA polymerase III alpha subunit (polC). Replication in B. subtilis and Staphylococcus aureus requires two different polymerases, polC and DnaE. The holoenzyme is thought to include the two different polymerases. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=54.80 E-value=70 Score=22.24 Aligned_cols=59 Identities=15% Similarity=0.137 Sum_probs=40.6
Q ss_pred EEEEEEEEeee----cCCC-eEEEEEEecceEEEEEEeccccccHHHHHHHhcCC-CccEEEEEEEEEec
Q psy13182 81 VWVRGRLHTSR----AKGK-QCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIP-KESILDIQAHVQAT 144 (194)
Q Consensus 81 V~vrgrv~~~R----~~Gk-~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~-rESiV~V~G~V~~~ 144 (194)
|.++|-|...- ..|+ +..+.+.|.+..+-|-.|.. . . .+....|. .+..|.|+|.+.-.
T Consensus 2 v~i~G~Vf~~e~re~k~g~~i~~~~itD~t~Si~~K~F~~-~-~---~~~~~~ik~~G~~v~v~G~v~~D 66 (82)
T cd04484 2 VVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLR-K-D---EKDKEELKSKGDWVRVRGKVQYD 66 (82)
T ss_pred EEEEEEEEEEEEEEecCCCEEEEEEEEcCCCCEEEEEecc-C-C---hhHHhhcccCCCEEEEEEEEEEc
Confidence 66788776552 2454 46688889998888866653 1 1 12235678 89999999998764
No 118
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=51.73 E-value=33 Score=33.04 Aligned_cols=22 Identities=23% Similarity=0.517 Sum_probs=17.7
Q ss_pred ccccCCCCCceEeEEEEEecCC
Q psy13182 168 KYVSQIPKESILDIQAHVQATP 189 (194)
Q Consensus 168 ~~~~~l~~esi~~~~~~~~~~~ 189 (194)
++...|+.||+|.|.|+|.+.+
T Consensus 57 ~~~~~L~~esvV~V~G~v~~r~ 78 (583)
T TIGR00459 57 KLAKGLRNEDVVQVKGKVSARP 78 (583)
T ss_pred HHHhcCCCCCEEEEEEEEEeCC
Confidence 3445799999999999998643
No 119
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=51.05 E-value=89 Score=27.63 Aligned_cols=47 Identities=13% Similarity=0.167 Sum_probs=34.9
Q ss_pred cCCC-eEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 92 AKGK-QCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 92 ~~Gk-~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
..|+ ...++|.|.++.+.+.+-... . .....+..+.+|.|+|.+..-
T Consensus 29 knG~~yl~l~l~D~tG~I~ak~W~~~---~---~~~~~~~~g~vv~v~G~v~~y 76 (314)
T PRK13480 29 SNGKPFLTLILQDKSGDIEAKLWDVS---P---EDEATYVPETIVHVKGDIINY 76 (314)
T ss_pred CCCCeEEEEEEEcCCcEEEEEeCCCC---h---hhHhhcCCCCEEEEEEEEEEE
Confidence 4465 588899999999999775431 1 224557889999999999764
No 120
>PRK14699 replication factor A; Provisional
Probab=49.90 E-value=2.3e+02 Score=26.70 Aligned_cols=71 Identities=15% Similarity=0.144 Sum_probs=49.1
Q ss_pred ceEEcccccccCCCcEEEEEEEEEeee-------cCC---CeEEEEEEecceEEEEEEeccccccHHHHHHHh--cCCCc
Q psy13182 65 DFVPIRQLNKDYVDKTVWVRGRLHTSR-------AKG---KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVS--QIPKE 132 (194)
Q Consensus 65 ~~~~i~~L~~~~~g~~V~vrgrv~~~R-------~~G---k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~--~l~rE 132 (194)
...+|.+|.+ .+..|.+.|+|.++- ..| +++-+.+=|.|+++-.++=... ...+. .|..+
T Consensus 56 ~~~kI~di~~--~~~~v~i~~rVl~i~~~r~f~r~dG~~g~v~~~~iaDeTG~ir~tlW~~~------a~~~~~g~l~~G 127 (484)
T PRK14699 56 DSVKIENITP--ESGPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNM------ADLIKAGKIKAG 127 (484)
T ss_pred ccccHhHccC--CCceEEEEEEEEEecCceEEecCCCCceEEEEEEEecCCCeEEEEEecCc------cchhhhcCCCCC
Confidence 3467888865 246799999998873 233 5677789999999887664321 11122 47889
Q ss_pred cEEEEEEEEEe
Q psy13182 133 SILDIQAHVQA 143 (194)
Q Consensus 133 SiV~V~G~V~~ 143 (194)
++|.|.|.++.
T Consensus 128 Dvv~I~~~~r~ 138 (484)
T PRK14699 128 QTLQISGYAKQ 138 (484)
T ss_pred CEEEEcceecc
Confidence 99999997544
No 121
>TIGR00594 polc DNA-directed DNA polymerase III (polc). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.20 E-value=37 Score=34.87 Aligned_cols=37 Identities=19% Similarity=0.346 Sum_probs=30.2
Q ss_pred CCcEEEEEEEEEeeec-----CC-CeEEEEEEecceEEEEEEe
Q psy13182 77 VDKTVWVRGRLHTSRA-----KG-KQCFVVIREQNFTIQGILS 113 (194)
Q Consensus 77 ~g~~V~vrgrv~~~R~-----~G-k~~Fl~lRd~~~~vQ~v~~ 113 (194)
.|..|++.|.|.+.|. .| .++|+.+.|.++.+.+++|
T Consensus 980 ~g~~v~v~G~i~~~~~~~~tkkG~~maf~tleD~tg~ie~viF 1022 (1022)
T TIGR00594 980 NDSQVRTLGGLNSVKKKITTKNGKPMAFLQLEDETGSIEVVVF 1022 (1022)
T ss_pred CCCEEEEEEEEEEEEEecccCCCCEEEEEEEEECCCcEEEEeC
Confidence 4678999999976553 24 4899999999999999875
No 122
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=41.60 E-value=59 Score=30.64 Aligned_cols=18 Identities=11% Similarity=0.104 Sum_probs=15.9
Q ss_pred CCCCCceEeEEEEEecCC
Q psy13182 172 QIPKESILDIQAHVQATP 189 (194)
Q Consensus 172 ~l~~esi~~~~~~~~~~~ 189 (194)
.|+.+|||.|.|.|.++.
T Consensus 115 ~l~~Gd~V~v~G~~~~t~ 132 (505)
T PRK12445 115 KWDLGDIIGARGTLFKTQ 132 (505)
T ss_pred cCCCCCEEEEEEEEEecC
Confidence 578999999999999865
No 123
>cd04321 ScAspRS_mt_like_N ScAspRS_mt_like_N: N-terminal, anticodon recognition domain of the type found in Saccharomyces cerevisiae mitochondrial (mt) aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. The enzymes in this fungal group are homodimeric class2b aminoacyl-tRNA synthetases (aaRSs). aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation of the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. Eukaryotes contain 2 sets of aaRSs, both of which are encoded by the nuclear genome. One set concerns with cytoplasmic protein synthesis, whereas the other exclusively with mitochondrial protein synthesis. Mutations in the gene for
Probab=40.30 E-value=33 Score=23.93 Aligned_cols=18 Identities=22% Similarity=0.342 Sum_probs=16.2
Q ss_pred CCCCCceEeEEEEEecCC
Q psy13182 172 QIPKESILDIQAHVQATP 189 (194)
Q Consensus 172 ~l~~esi~~~~~~~~~~~ 189 (194)
.|+.||+|.|.|.+...+
T Consensus 47 ~l~~~s~V~V~G~v~~~~ 64 (86)
T cd04321 47 SITAESPVQVRGKLQLKE 64 (86)
T ss_pred cCCCCcEEEEEEEEEeCC
Confidence 689999999999998765
No 124
>KOG3108|consensus
Probab=38.11 E-value=1.2e+02 Score=26.38 Aligned_cols=62 Identities=11% Similarity=0.090 Sum_probs=47.1
Q ss_pred EEEEEEEEEeeecCCCeEEEEEEecceEEEEEEeccc-cccHHHHHHHhcCCCccEEEEEEEEEecC
Q psy13182 80 TVWVRGRLHTSRAKGKQCFVVIREQNFTIQGILSVGD-TVSKQMIKYVSQIPKESILDIQAHVQATP 145 (194)
Q Consensus 80 ~V~vrgrv~~~R~~Gk~~Fl~lRd~~~~vQ~v~~~~~-~~s~~m~k~~~~l~rESiV~V~G~V~~~~ 145 (194)
.|.+-|||.++-....-+++.|=|+++.+=|-..... ..+. ....|..+..|.|.|.+....
T Consensus 70 ~v~~VGivr~~e~~~t~i~y~I~D~tg~id~r~W~~~~~~~~----e~~~l~~~~yVkv~G~Lk~f~ 132 (265)
T KOG3108|consen 70 AVSIVGIVRNIEKSATNITYEIEDGTGQIDVRQWFHDNAESE----EMPALETGTYVKVYGHLKPFQ 132 (265)
T ss_pred EEEEEEEEEeceecCcceEEEEecCcccEEEEEeccccchhh----hCcccccCcEEEeeecccCCC
Confidence 5789999999999888899999999999776443322 2221 233678899999999998763
No 125
>PRK02801 primosomal replication protein N; Provisional
Probab=36.96 E-value=1.1e+02 Score=22.24 Aligned_cols=37 Identities=19% Similarity=0.199 Sum_probs=25.6
Q ss_pred EecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEe
Q psy13182 102 REQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQA 143 (194)
Q Consensus 102 Rd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~ 143 (194)
|+-...++|+++.. ..-..+..|..+|.|.|+|.+..
T Consensus 44 r~~~~~i~~va~G~-----~Ae~~~~~l~kGs~v~V~G~L~~ 80 (101)
T PRK02801 44 RQAWCRMPVIVSGN-----QFQAITQSITVGSKITVQGFISC 80 (101)
T ss_pred eeEEEEEEEEEEcH-----HHHHHHhhcCCCCEEEEEEEEEE
Confidence 43344588888753 11123446899999999999987
No 126
>PF11736 DUF3299: Protein of unknown function (DUF3299); InterPro: IPR021727 This is a family of bacterial proteins of unknown function.
Probab=36.46 E-value=55 Score=25.75 Aligned_cols=70 Identities=16% Similarity=0.148 Sum_probs=41.2
Q ss_pred ccccCCCcEEEEEEEEEeeecCC-Ce-EEEEEEecceEEEEEEeccccccHHHH--HHHhcCC---CccEEEEEEEEEec
Q psy13182 72 LNKDYVDKTVWVRGRLHTSRAKG-KQ-CFVVIREQNFTIQGILSVGDTVSKQMI--KYVSQIP---KESILDIQAHVQAT 144 (194)
Q Consensus 72 L~~~~~g~~V~vrgrv~~~R~~G-k~-~Fl~lRd~~~~vQ~v~~~~~~~s~~m~--k~~~~l~---rESiV~V~G~V~~~ 144 (194)
....+.|+.|+|.|++.=....+ ++ -||.+..-+.-+-| ...-.++|+ +....+. .-.-|.|+|++...
T Consensus 49 ~v~~L~Gk~V~i~Gf~vPle~~~~~v~eFlLvP~~gaC~h~----PpPppNqiV~V~~~~~~~~~~~~~pv~V~G~l~~~ 124 (146)
T PF11736_consen 49 VVKALDGKQVRIPGFMVPLEQEEGKVTEFLLVPYFGACIHV----PPPPPNQIVHVKMPKPIPVDSLYDPVWVEGTLKVE 124 (146)
T ss_pred hhHHhCCCEEEEeeEEEeeccCCCcEEEEEEeccCCcCcCC----CCCCCccEEEEEeCCCccccccceeEEEEEEEEec
Confidence 34668899999999999888654 44 88888875543211 000011110 0111111 24689999999886
Q ss_pred C
Q psy13182 145 P 145 (194)
Q Consensus 145 ~ 145 (194)
.
T Consensus 125 ~ 125 (146)
T PF11736_consen 125 R 125 (146)
T ss_pred c
Confidence 4
No 127
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=35.10 E-value=3.3e+02 Score=26.87 Aligned_cols=65 Identities=8% Similarity=-0.021 Sum_probs=47.4
Q ss_pred ccCCCcEEEEEEEEEeeecC---C-CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 74 KDYVDKTVWVRGRLHTSRAK---G-KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 74 ~~~~g~~V~vrgrv~~~R~~---G-k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
....|..|++.|.|.+.-.. + +.--+.+.|+++.+-+++|-... .....++.+..+.|.|.+..-
T Consensus 56 ~~~~g~~vti~g~V~~~~~~~~~~~~~l~v~~~d~~~~l~l~fFn~~~------~l~~~~~~G~~v~v~Gk~~~~ 124 (677)
T COG1200 56 EARPGEIVTIEGTVLSHEKFPFGKRKLLKVTLSDGTGVLTLVFFNFPA------YLKKKLKVGERVIVYGKVKRF 124 (677)
T ss_pred hcCCCceEEEEEEEEeeeccCCCCCceEEEEEecCcEEEEEEEECccH------HHHhhCCCCCEEEEEEEEeec
Confidence 33568999999999655444 3 45677788888888888775421 223557899999999999883
No 128
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=33.98 E-value=1.3e+02 Score=19.20 Aligned_cols=33 Identities=9% Similarity=0.099 Sum_probs=28.6
Q ss_pred EEEEEEEeeecCCCeEEEEEEecceE-EEEEEec
Q psy13182 82 WVRGRLHTSRAKGKQCFVVIREQNFT-IQGILSV 114 (194)
Q Consensus 82 ~vrgrv~~~R~~Gk~~Fl~lRd~~~~-vQ~v~~~ 114 (194)
.+.|.|..+...|...++.++-+.+. +-+.+..
T Consensus 6 ~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~ 39 (64)
T PF03459_consen 6 QLPGTVESIENLGSEVEVTLDLGGGETLTARITP 39 (64)
T ss_dssp EEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEH
T ss_pred EEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcH
Confidence 47899999999999999999999988 7776654
No 129
>PRK08402 replication factor A; Reviewed
Probab=33.25 E-value=1.7e+02 Score=26.42 Aligned_cols=72 Identities=17% Similarity=0.259 Sum_probs=48.2
Q ss_pred ceEEcccccccCCCcEEEEEEEEEeeec-------CC---CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccE
Q psy13182 65 DFVPIRQLNKDYVDKTVWVRGRLHTSRA-------KG---KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESI 134 (194)
Q Consensus 65 ~~~~i~~L~~~~~g~~V~vrgrv~~~R~-------~G---k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESi 134 (194)
+..+|.||.+. ...|.+.|+|.+.-. .| ++.=++|-|.|+++..++-... .-++...|..+++
T Consensus 61 ~~~kI~dl~~g--~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~ir~TlW~~~-----a~~~~~~l~~Gdv 133 (355)
T PRK08402 61 PLMHISDLVPG--MRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARVVLWDAK-----VAKYYNKINVGDV 133 (355)
T ss_pred CccCHHHccCC--CceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCeEEEEEechh-----hhhhcccCCCCCE
Confidence 46789999653 256999999987621 24 3444899999999987776431 0112345789999
Q ss_pred EEEEE-EEEe
Q psy13182 135 LDIQA-HVQA 143 (194)
Q Consensus 135 V~V~G-~V~~ 143 (194)
|.|.| .|..
T Consensus 134 i~I~~a~V~e 143 (355)
T PRK08402 134 IKVIDAQVRE 143 (355)
T ss_pred EEEECCEEee
Confidence 99985 4443
No 130
>PRK07218 replication factor A; Provisional
Probab=33.20 E-value=4e+02 Score=24.68 Aligned_cols=67 Identities=13% Similarity=0.027 Sum_probs=41.5
Q ss_pred EcccccccCCCcEEEEEEEEEeeec------CC--CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEE
Q psy13182 68 PIRQLNKDYVDKTVWVRGRLHTSRA------KG--KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQA 139 (194)
Q Consensus 68 ~i~~L~~~~~g~~V~vrgrv~~~R~------~G--k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G 139 (194)
+|.+|.+ .+..|.|.|+|...-. -| .+.-..|-|.|+++..++-.. ...|..+.+|.|.+
T Consensus 164 kI~DL~~--g~~~V~v~g~Vl~~~~r~f~~~dg~~~v~~giigDeTG~Ir~tlW~~----------~~~l~~Gd~v~I~n 231 (423)
T PRK07218 164 KLIDLGP--GDRGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDP----------LPEIEIGASIRIED 231 (423)
T ss_pred chhhccC--CCCceEEEEEEEEecceeEEcCCCCeEEEEEEEECCCceEEEEEecc----------cccCCCCCEEEEee
Confidence 3444433 2345889999986611 12 234445677777777666543 12468899999999
Q ss_pred EEEecCc
Q psy13182 140 HVQATPT 146 (194)
Q Consensus 140 ~V~~~~~ 146 (194)
.....-.
T Consensus 232 a~v~e~~ 238 (423)
T PRK07218 232 AYVREFR 238 (423)
T ss_pred eEEeccC
Confidence 7776543
No 131
>PF03100 CcmE: CcmE; InterPro: IPR004329 CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.; GO: 0017003 protein-heme linkage, 0017004 cytochrome complex assembly, 0005886 plasma membrane; PDB: 1SR3_A 2KCT_A 1J6Q_A 1LM0_A.
Probab=32.82 E-value=2.2e+02 Score=21.59 Aligned_cols=69 Identities=12% Similarity=0.152 Sum_probs=41.1
Q ss_pred eEEccccc--ccCCCcEEEEEEEEE--eeec--CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEE
Q psy13182 66 FVPIRQLN--KDYVDKTVWVRGRLH--TSRA--KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQA 139 (194)
Q Consensus 66 ~~~i~~L~--~~~~g~~V~vrgrv~--~~R~--~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G 139 (194)
|....++. ....|+.+.+.|+|. ++.. .+...-+.+.|....+.++.... .+. .+..+..|.|+|
T Consensus 36 y~t~se~~~~~~~~~~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~--~Pd-------~F~eg~~VVv~G 106 (131)
T PF03100_consen 36 YLTPSELAAEPQKVGRKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGP--LPD-------LFREGQGVVVEG 106 (131)
T ss_dssp EE-TTTTTTTST-TTSEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES----CT-------T--TTSEEEEEE
T ss_pred EcCHHHHhhccccCCceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCC--CCc-------cccCCCeEEEEE
Confidence 45555653 223689999999997 3333 34555566788988888776643 111 125678999999
Q ss_pred EEEe
Q psy13182 140 HVQA 143 (194)
Q Consensus 140 ~V~~ 143 (194)
.+..
T Consensus 107 ~~~~ 110 (131)
T PF03100_consen 107 RLGE 110 (131)
T ss_dssp EECC
T ss_pred EECC
Confidence 8844
No 132
>PRK07218 replication factor A; Provisional
Probab=29.82 E-value=2.8e+02 Score=25.71 Aligned_cols=68 Identities=19% Similarity=0.099 Sum_probs=46.1
Q ss_pred CceEEcccccccCCCcEEEEEEEEEeeec--------CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEE
Q psy13182 64 RDFVPIRQLNKDYVDKTVWVRGRLHTSRA--------KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESIL 135 (194)
Q Consensus 64 ~~~~~i~~L~~~~~g~~V~vrgrv~~~R~--------~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV 135 (194)
++-.+|.||.+. ++.|.|.|+|..+-. .|.+.-+.+=|.|+++..++-.. ..|..+.+|
T Consensus 56 ~~~~kI~Di~~~--~~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~~-----------~~l~~Gdvv 122 (423)
T PRK07218 56 PSSKDIKELSTD--DKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWKD-----------FGLSPGDTV 122 (423)
T ss_pred CCCccHhhCCCC--CceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCeEEEEEECC-----------CCCCCCCEE
Confidence 445789999754 467999999988732 23456666667777766665542 126889999
Q ss_pred EEEEEEEec
Q psy13182 136 DIQAHVQAT 144 (194)
Q Consensus 136 ~V~G~V~~~ 144 (194)
.|.+.....
T Consensus 123 ~I~na~vre 131 (423)
T PRK07218 123 TIGNAGVRE 131 (423)
T ss_pred EEeccEeec
Confidence 999755443
No 133
>PRK00036 primosomal replication protein N; Reviewed
Probab=27.34 E-value=1.7e+02 Score=21.84 Aligned_cols=36 Identities=14% Similarity=0.275 Sum_probs=26.9
Q ss_pred EecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEe
Q psy13182 102 REQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQA 143 (194)
Q Consensus 102 Rd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~ 143 (194)
|+-..++|++++. ++.+....|..++.+.|+|.+..
T Consensus 43 Rqv~~~i~ava~G------~~a~~~~~l~~Gs~v~v~GFLa~ 78 (107)
T PRK00036 43 RRVELTISAVALG------DLALLLADTPLGTEMQVQGFLAP 78 (107)
T ss_pred ceEEEEEEEEEEh------hHHHHhcccCCCCEEEEEEEEEE
Confidence 4444567777764 24455667999999999999997
No 134
>cd04491 SoSSB_OBF SoSSB_OBF: A subfamily of OB folds similar to the OB fold of the crenarchaeote Sulfolobus solfataricus single-stranded (ss) DNA-binding protein (SSoSSB). SSoSSB has a single OB fold, and it physically and functionally interacts with RNA polymerase. In vitro, SSoSSB can substitute for the basal transcription factor TBP, stimulating transcription from promoters under conditions in which TBP is limiting, and supporting transcription when TBP is absent. SSoSSB selectively melts the duplex DNA of promoter sequences. It also relieves transcriptional repression by the chromatin Alba. In addition, SSoSSB activates reverse gyrase activity, which involves DNA binding, DNA cleavage, strand passage and ligation. SSoSSB stimulates all these steps in the presence of the chromatin protein, Sul7d. SSoSSB antagonizes the inhibitory effect of Sul7d on reverse gyrase supercoiling activity. It also physically and functionally interacts with Mini-chromosome Maintenance (MCM), stimulating
Probab=27.20 E-value=2e+02 Score=19.39 Aligned_cols=44 Identities=18% Similarity=0.161 Sum_probs=32.2
Q ss_pred CCCeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEE-EEEEec
Q psy13182 93 KGKQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQ-AHVQAT 144 (194)
Q Consensus 93 ~Gk~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~-G~V~~~ 144 (194)
.++..-+.|.|.++.+.+.+..... ...|..+.+|.+. |.+..-
T Consensus 21 ~~~~~~~~l~D~TG~i~~~~W~~~~--------~~~~~~G~vv~i~~~~v~~~ 65 (82)
T cd04491 21 EGKVQSGLVGDETGTIRFTLWDEKA--------ADDLEPGDVVRIENAYVREF 65 (82)
T ss_pred eeEEEEEEEECCCCEEEEEEECchh--------cccCCCCCEEEEEeEEEEec
Confidence 3467888899999999988775411 3456789999999 666553
No 135
>cd04496 SSB_OBF SSB_OBF: A subfamily of OB folds similar to the OB fold of ssDNA-binding protein (SSB). SSBs bind with high affinity to ssDNA. They bind to and protect ssDNA intermediates during DNA metabolic pathways. All bacterial and eukaryotic SSBs studied to date oligomerize to bring together four OB folds in their active state. The majority (e.g. Escherichia coli SSB) have a single OB fold per monomer, which oligomerize to form a homotetramer. However, Deinococcus and Thermus SSB proteins have two OB folds per monomer, which oligomerize to form a homodimer. Mycobacterium tuberculosis SSB varies in quaternary structure from E. coli SSB. It forms a dimer of dimers having a unique dimer interface, which lends the protein greater stability. Included in this group are OB folds similar to Escherichia coli PriB. E.coli PriB is homodimeric with each monomer having a single OB fold. It does not appear to form higher order oligomers. PriB is an essential protein for the replication restart
Probab=27.12 E-value=2.1e+02 Score=19.56 Aligned_cols=53 Identities=8% Similarity=-0.057 Sum_probs=34.5
Q ss_pred EecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccC-CCceeeeeec
Q psy13182 102 REQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVE-SLPMSILSVG 159 (194)
Q Consensus 102 Rd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~-~~t~~~~El~ 159 (194)
+..+..++|.++.. .. -..+..+..++.|.|.|.+....-... |-+...++|.
T Consensus 40 ~~~~~~~~v~~~g~--~a---~~~~~~~~kG~~V~v~G~l~~~~~~~~~g~~~~~~~i~ 93 (100)
T cd04496 40 EEETDWIRVVAFGK--LA---ENAAKYLKKGDLVYVEGRLRTRSWEDKDGQKRYGTEVV 93 (100)
T ss_pred ccccEEEEEEEEhH--HH---HHHHHHhCCCCEEEEEEEEEeceeECCCCCEEEEEEEE
Confidence 34455677777743 11 134556899999999999988754333 5566666655
No 136
>PF04874 Mak16: Mak16 protein C-terminal region; InterPro: IPR006958 The function of these proteins is unknown. The yeast orthologues have been implicated in cell cycle progression and biogenesis of 60S ribosomal subunits. The Schistosoma mansoni (Blood fluke) Mak16 has been shown to target protein transport to the nucleolus [].
Probab=26.73 E-value=35 Score=25.31 Aligned_cols=12 Identities=25% Similarity=0.545 Sum_probs=8.7
Q ss_pred hhhccCCccccc
Q psy13182 46 SARLYGKTPLIM 57 (194)
Q Consensus 46 ~~~~Yg~~~l~q 57 (194)
..+-||++|++-
T Consensus 35 k~G~Ygd~~yN~ 46 (101)
T PF04874_consen 35 KSGTYGDIPYNF 46 (101)
T ss_pred HcCCcccccccc
Confidence 457799998753
No 137
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) [] are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2B39_B 3KLS_B 3PRX_C 3KM9_B 3PVM_C 3CU7_A 4E0S_A 4A5W_A 4ACQ_C 2P9R_B ....
Probab=26.27 E-value=2e+02 Score=19.93 Aligned_cols=31 Identities=16% Similarity=0.156 Sum_probs=23.5
Q ss_pred CCcEEEEEEEEEeee-----cCCCeEEEEEEecceE
Q psy13182 77 VDKTVWVRGRLHTSR-----AKGKQCFVVIREQNFT 107 (194)
Q Consensus 77 ~g~~V~vrgrv~~~R-----~~Gk~~Fl~lRd~~~~ 107 (194)
.|+.|++++.+.+.. ..+..+.|.++|..+.
T Consensus 13 PGetV~~~~~~~~~~~~~~~~~~~~~~v~i~dp~g~ 48 (99)
T PF01835_consen 13 PGETVHFRAIVRDLDNDFKPPANSPVTVTIKDPSGN 48 (99)
T ss_dssp TTSEEEEEEEEEEECTTCSCESSEEEEEEEEETTSE
T ss_pred CCCEEEEEEEEeccccccccccCCceEEEEECCCCC
Confidence 588999999987765 2234688889988765
No 138
>PF04057 Rep-A_N: Replication factor-A protein 1, N-terminal domain; InterPro: IPR007199 Replication factor-a protein 1 (RPA1) forms a multiprotein complex with RPA2 and RPA3 that binds single-stranded DNA and functions in the recognition of DNA damage for nucleotide excision repair. The complex binds to single-stranded DNA sequences participating in DNA replication in addition to those mediating transcriptional repression and activation, and stimulates the activity of cognate strand exchange protein Sep1. It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the Simian Virus 40 origin of replication [].; GO: 0003677 DNA binding, 0006260 DNA replication, 0005634 nucleus; PDB: 1EWI_A 2B3G_A 2B29_A.
Probab=25.35 E-value=2.7e+02 Score=20.18 Aligned_cols=46 Identities=17% Similarity=0.281 Sum_probs=30.2
Q ss_pred CeEEEEEEecceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEec
Q psy13182 95 KQCFVVIREQNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQAT 144 (194)
Q Consensus 95 k~~Fl~lRd~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~ 144 (194)
.---+.|-||.+.+|+|+...- .+++ .-..|.+.|+|.+.-.....
T Consensus 38 ~RyR~~lSDG~~~~~amLatql---n~lv-~~g~l~~~siirl~~y~~n~ 83 (101)
T PF04057_consen 38 DRYRLVLSDGVHSIQAMLATQL---NHLV-ESGELQKGSIIRLKQYTCNT 83 (101)
T ss_dssp -EEEEEEESSSEEEEEEESGGG---HHHH-HTTSSSTT-EEEEEEEEEEE
T ss_pred ceEEEEEEChHHHHHHHhHHHh---HHHH-hcCCcccCCEEEEeEEEEee
Confidence 3456788999999999886541 1111 23468899999998766544
No 139
>PF00436 SSB: Single-strand binding protein family; InterPro: IPR000424 The Escherichia coli single-strand binding protein [] (gene ssb), also known as the helix-destabilising protein, is a protein of 177 amino acids. It binds tightly, as a homotetramer, to single-stranded DNA (ss-DNA) and plays an important role in DNA replication, recombination and repair. Closely related variants of SSB are encoded in the genome of a variety of large self-transmissible plasmids. SSB has also been characterised in bacteria such as Proteus mirabilis or Serratia marcescens. Eukaryotic mitochondrial proteins that bind ss-DNA and are probably involved in mitochondrial DNA replication are structurally and evolutionary related to prokaryotic SSB.; GO: 0003697 single-stranded DNA binding; PDB: 3UDG_B 1SE8_A 2CWA_A 3ULL_B 1S3O_A 2DUD_A 3AFP_A 3AFQ_A 3VDY_A 3EIV_C ....
Probab=24.62 E-value=2.4e+02 Score=19.47 Aligned_cols=48 Identities=4% Similarity=-0.113 Sum_probs=28.6
Q ss_pred EEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcccC-CCceeeeeec
Q psy13182 107 TIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIVE-SLPMSILSVG 159 (194)
Q Consensus 107 ~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i~-~~t~~~~El~ 159 (194)
.++|.++.. ..-..+..|..++.|.|.|.+....-... |.+...++|.
T Consensus 49 ~~~v~~~g~-----~A~~~~~~l~kG~~V~V~G~l~~~~~~~~~G~~~~~~~i~ 97 (104)
T PF00436_consen 49 WINVVAWGK-----LAENVAEYLKKGDRVYVEGRLRTRTYEDKDGQKRYRVEII 97 (104)
T ss_dssp EEEEEEEHH-----HHHHHHHH--TT-EEEEEEEEEEEEEESTTSSEEEEEEEE
T ss_pred EEEEEeeee-----cccccceEEcCCCEEEEEEEEEeeEEECCCCCEEEEEEEE
Confidence 466766643 11234455889999999999988753333 5666666665
No 140
>PF13452 MaoC_dehydrat_N: N-terminal half of MaoC dehydratase; PDB: 3HMJ_H 2UV8_I 2VKZ_G 1S9C_K 3OML_A 3KHP_A.
Probab=24.09 E-value=1.5e+02 Score=21.60 Aligned_cols=31 Identities=23% Similarity=0.261 Sum_probs=23.5
Q ss_pred ccCCCcEEEEEEEEEeeecC---CCeEEEEEEec
Q psy13182 74 KDYVDKTVWVRGRLHTSRAK---GKQCFVVIREQ 104 (194)
Q Consensus 74 ~~~~g~~V~vrgrv~~~R~~---Gk~~Fl~lRd~ 104 (194)
+-..|++++...+|..++.+ |+..|+..+-.
T Consensus 87 Pl~~Gd~l~~~~~v~~v~~k~g~G~~~~v~~~~~ 120 (132)
T PF13452_consen 87 PLRPGDTLTATSRVTDVYDKRGAGKGVFVTVETE 120 (132)
T ss_dssp --BSSEEEEEEEEEEEEEEES-TTSEEEEEEEEE
T ss_pred CCCCCCEEEEEEEEEEEEEecCCCCEEEEEEEEE
Confidence 44579999999999988876 67888877643
No 141
>TIGR00621 ssb single stranded DNA-binding protein (ssb). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.59 E-value=3.6e+02 Score=21.20 Aligned_cols=51 Identities=6% Similarity=-0.121 Sum_probs=33.3
Q ss_pred cceEEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCccc-CCCceeeeeec
Q psy13182 104 QNFTIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTIV-ESLPMSILSVG 159 (194)
Q Consensus 104 ~~~~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~i-~~~t~~~~El~ 159 (194)
.+..+-|+++.. ..-.++..|.+++.|.|+|.+....-.. .|-+...+||.
T Consensus 49 ~t~~~~v~~wg~-----~Ae~~~~~l~KG~~V~V~G~L~~~~~~~kdG~~~~~~ev~ 100 (164)
T TIGR00621 49 ETEWHDIVIFGR-----LAEVAAQYLKKGSLVYVEGRLRTRKWEDQNGQKRSKTEII 100 (164)
T ss_pred cceEEEEEEehH-----HHHHHHHhCCCCCEEEEEEEEEeceEECCCCcEEEEEEEE
Confidence 344566776643 1224566789999999999998875332 55555555555
No 142
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=22.29 E-value=1.1e+02 Score=24.32 Aligned_cols=24 Identities=33% Similarity=0.421 Sum_probs=15.2
Q ss_pred ccCHHHHHHHHHHHHHHHHHHHHH
Q psy13182 7 KVSKKALKKQAKEQEKKEKKDQRK 30 (194)
Q Consensus 7 ~~sk~alkK~~K~~~k~~kka~k~ 30 (194)
-+++.++|...|..++++|+.+++
T Consensus 62 ll~k~e~K~~~K~~KK~~K~~~K~ 85 (155)
T PF08496_consen 62 LLDKKELKAWEKAEKKEEKAKAKA 85 (155)
T ss_pred hcCHHHHHHHHHHHHHHHHHHhhh
Confidence 457777777776666666654443
No 143
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=22.20 E-value=4.2e+02 Score=21.31 Aligned_cols=48 Identities=13% Similarity=0.076 Sum_probs=33.8
Q ss_pred EEEEEEeccccccHHHHHHHhcCCCccEEEEEEEEEecCcc-cCCCceeeeeec
Q psy13182 107 TIQGILSVGDTVSKQMIKYVSQIPKESILDIQAHVQATPTI-VESLPMSILSVG 159 (194)
Q Consensus 107 ~vQ~v~~~~~~~s~~m~k~~~~l~rESiV~V~G~V~~~~~~-i~~~t~~~~El~ 159 (194)
.+-|+++.. ..-..+..|.+++.|.|+|.|....-. ..|-+...+||.
T Consensus 48 wi~~v~wgk-----~Ae~~~~~l~KG~~V~VeGrL~~r~yedkdG~~~~~~eVv 96 (173)
T PRK06751 48 FINCVIWRK-----QAENVANYLKKGSLAGVDGRLQTRNYEGQDGKRVYVTEVL 96 (173)
T ss_pred EEEEEEeCc-----HHHHHHHHcCCCCEEEEEEEEEeCccCCCCCcEEEEEEEE
Confidence 466777753 223456678999999999999988643 456666666665
No 144
>PRK14441 acylphosphatase; Provisional
Probab=20.51 E-value=2.2e+02 Score=20.26 Aligned_cols=30 Identities=3% Similarity=0.092 Sum_probs=16.7
Q ss_pred cceEEEEEEeccccccHHHHHHHhcCCCcc
Q psy13182 104 QNFTIQGILSVGDTVSKQMIKYVSQIPKES 133 (194)
Q Consensus 104 ~~~~vQ~v~~~~~~~s~~m~k~~~~l~rES 133 (194)
..+++.+++...+..-..|+.++...+.-+
T Consensus 41 ~dG~Vei~~qG~~~~i~~f~~~l~~gp~~a 70 (93)
T PRK14441 41 PDGRVEAEAEGERAAVGALVRWCHAGPPAA 70 (93)
T ss_pred CCCEEEEEEEECHHHHHHHHHHHhhCCCCc
Confidence 334555555544333457778877655544
Done!