Query psy3603
Match_columns 264
No_of_seqs 135 out of 448
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 20:50:43 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3603.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3603hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3416|consensus 100.0 2.9E-30 6.3E-35 214.8 12.1 107 31-137 3-109 (134)
2 PRK06461 single-stranded DNA-b 99.9 8.4E-23 1.8E-27 168.5 15.4 114 30-149 2-118 (129)
3 PRK07218 replication factor A; 99.7 8.8E-16 1.9E-20 149.1 12.4 97 29-127 55-153 (423)
4 PRK08402 replication factor A; 99.6 6.9E-16 1.5E-20 146.9 10.6 116 10-125 35-164 (355)
5 cd04491 SoSSB_OBF SoSSB_OBF: A 99.6 7.4E-15 1.6E-19 110.7 11.4 77 46-122 1-81 (82)
6 PRK06386 replication factor A; 99.6 5.4E-15 1.2E-19 141.1 13.3 113 31-144 1-118 (358)
7 PRK06386 replication factor A; 99.6 8.9E-15 1.9E-19 139.6 12.8 99 24-125 99-199 (358)
8 PRK12366 replication factor A; 99.6 1.7E-14 3.7E-19 145.7 11.1 115 29-143 60-185 (637)
9 PRK15491 replication factor A; 99.5 2.5E-14 5.4E-19 136.8 10.6 106 17-125 43-158 (374)
10 PRK07211 replication factor A; 99.5 4.9E-14 1.1E-18 139.0 12.7 95 31-125 160-261 (485)
11 PRK07217 replication factor A; 99.5 6.3E-14 1.4E-18 131.7 12.6 109 13-126 55-164 (311)
12 PRK14699 replication factor A; 99.5 3.6E-14 7.9E-19 139.8 11.5 113 31-144 56-177 (484)
13 PRK07218 replication factor A; 99.5 6.3E-14 1.4E-18 136.2 12.8 95 30-125 160-256 (423)
14 PRK13480 3'-5' exoribonuclease 99.5 1E-13 2.2E-18 130.1 11.0 103 33-146 3-108 (314)
15 PRK14699 replication factor A; 99.5 1.7E-13 3.6E-18 135.1 12.7 94 32-125 166-268 (484)
16 PRK15491 replication factor A; 99.5 2.6E-13 5.5E-18 129.9 12.4 95 31-125 165-268 (374)
17 PRK12366 replication factor A; 99.3 6.1E-12 1.3E-16 127.3 12.4 95 29-123 392-494 (637)
18 PRK07211 replication factor A; 99.3 9.2E-12 2E-16 123.1 12.1 92 33-125 270-367 (485)
19 cd04475 RPA1_DBD_B RPA1_DBD_B: 99.1 1.2E-09 2.7E-14 85.1 10.1 79 45-124 2-88 (101)
20 cd04474 RPA1_DBD_A RPA1_DBD_A: 99.1 9.6E-10 2.1E-14 87.3 9.6 73 34-106 1-81 (104)
21 cd04478 RPA2_DBD_D RPA2_DBD_D: 98.9 9.8E-09 2.1E-13 78.7 9.7 72 45-126 2-80 (95)
22 cd04497 hPOT1_OB1_like hPOT1_O 98.9 2E-08 4.4E-13 83.5 10.4 85 31-116 2-95 (138)
23 COG1599 RFA1 Single-stranded D 98.8 8.3E-09 1.8E-13 99.1 8.2 117 28-144 45-167 (407)
24 cd04483 hOBFC1_like hOBFC1_lik 98.8 3.5E-08 7.5E-13 77.7 8.6 64 46-116 1-88 (92)
25 cd04492 YhaM_OBF_like YhaM_OBF 98.7 1.1E-07 2.4E-12 69.6 9.5 73 47-124 2-77 (83)
26 PF01336 tRNA_anti-codon: OB-f 98.7 3.4E-08 7.3E-13 71.0 6.6 66 45-116 1-71 (75)
27 TIGR00617 rpa1 replication fac 98.6 2.2E-07 4.7E-12 94.2 9.2 95 31-125 179-287 (608)
28 cd04485 DnaE_OBF DnaE_OBF: A s 98.5 3.7E-07 8.1E-12 65.8 6.0 68 47-116 2-73 (84)
29 TIGR00617 rpa1 replication fac 98.5 7.7E-07 1.7E-11 90.3 9.8 93 29-122 295-397 (608)
30 PF02765 POT1: Telomeric singl 98.3 6.4E-06 1.4E-10 69.0 9.6 80 37-117 8-101 (146)
31 cd03524 RPA2_OBF_family RPA2_O 98.3 7.6E-06 1.7E-10 56.5 8.4 66 47-116 2-72 (75)
32 cd04489 ExoVII_LU_OBF ExoVII_L 98.2 2E-05 4.4E-10 57.9 9.7 66 45-116 2-73 (78)
33 cd04488 RecG_wedge_OBF RecG_we 98.2 1.8E-05 3.9E-10 56.1 8.5 67 47-116 2-71 (75)
34 PRK05673 dnaE DNA polymerase I 97.8 2.9E-05 6.3E-10 84.0 6.2 80 40-125 976-1059(1135)
35 PRK07373 DNA polymerase III su 97.6 0.00015 3.2E-09 71.7 6.7 114 2-125 242-362 (449)
36 cd04484 polC_OBF polC_OBF: A s 97.4 0.0022 4.8E-08 49.3 10.2 71 44-116 1-78 (82)
37 cd04490 PolII_SU_OBF PolII_SU_ 97.3 0.0024 5.2E-08 48.9 8.7 55 45-105 2-62 (79)
38 cd04481 RPA1_DBD_B_like RPA1_D 97.3 0.0011 2.4E-08 52.4 7.0 70 46-115 1-83 (106)
39 cd04487 RecJ_OBF2_like RecJ_OB 97.2 0.005 1.1E-07 46.7 9.7 63 47-116 3-69 (73)
40 PRK07374 dnaE DNA polymerase I 96.9 0.002 4.4E-08 70.3 6.7 80 40-125 999-1082(1170)
41 PRK05672 dnaE2 error-prone DNA 96.6 0.0031 6.7E-08 68.2 5.9 81 37-125 949-1033(1046)
42 cd04482 RPA2_OBF_like RPA2_OBF 96.6 0.029 6.4E-07 43.9 9.7 56 61-125 15-76 (91)
43 PRK10917 ATP-dependent DNA hel 96.5 0.011 2.5E-07 60.6 9.1 83 29-116 47-133 (681)
44 COG4085 Predicted RNA-binding 96.5 0.0083 1.8E-07 54.2 7.0 74 45-123 54-136 (204)
45 PRK06826 dnaE DNA polymerase I 96.5 0.0049 1.1E-07 67.3 6.6 74 40-116 990-1068(1151)
46 COG3481 Predicted HD-superfami 96.5 0.001 2.2E-08 62.8 1.2 59 59-118 15-76 (287)
47 TIGR00643 recG ATP-dependent D 96.4 0.021 4.5E-07 58.1 9.9 81 32-116 23-106 (630)
48 PF13742 tRNA_anti_2: OB-fold 96.3 0.04 8.7E-07 43.7 9.1 68 43-116 22-96 (99)
49 PRK06920 dnaE DNA polymerase I 96.2 0.0078 1.7E-07 65.6 5.9 108 2-116 906-1019(1107)
50 COG5235 RFA2 Single-stranded D 96.0 0.036 7.7E-07 51.2 8.3 74 44-127 68-147 (258)
51 PRK07279 dnaE DNA polymerase I 96.0 0.012 2.7E-07 63.7 6.1 107 2-116 850-961 (1034)
52 cd04480 RPA1_DBD_A_like RPA1_D 95.9 0.023 5E-07 43.2 5.7 60 47-107 2-66 (86)
53 COG1107 Archaea-specific RecJ- 95.7 0.029 6.3E-07 58.0 7.1 81 28-116 198-284 (715)
54 KOG3108|consensus 95.6 0.046 1E-06 51.2 7.6 72 45-126 71-148 (265)
55 TIGR00237 xseA exodeoxyribonuc 95.6 0.075 1.6E-06 52.2 9.3 73 43-124 18-96 (432)
56 PRK00448 polC DNA polymerase I 95.5 0.075 1.6E-06 59.6 10.0 85 30-116 224-316 (1437)
57 COG1200 RecG RecG-like helicas 95.4 0.091 2E-06 54.9 9.7 89 24-116 43-134 (677)
58 PRK00286 xseA exodeoxyribonucl 95.1 0.15 3.2E-06 49.6 9.6 73 43-124 24-102 (438)
59 PRK02801 primosomal replicatio 95.0 0.11 2.4E-06 41.5 7.2 63 42-105 2-80 (101)
60 PRK07459 single-stranded DNA-b 95.0 0.079 1.7E-06 43.7 6.4 61 43-104 4-75 (121)
61 PRK06751 single-stranded DNA-b 94.9 1.1 2.5E-05 39.4 13.7 62 43-105 3-79 (173)
62 PRK06863 single-stranded DNA-b 94.7 0.81 1.8E-05 40.2 12.2 63 42-105 4-84 (168)
63 PRK05733 single-stranded DNA-b 94.6 0.24 5.1E-06 43.6 8.7 64 41-105 4-85 (172)
64 cd04316 ND_PkAspRS_like_N ND_P 94.4 0.5 1.1E-05 37.4 9.4 75 40-125 11-96 (108)
65 cd04496 SSB_OBF SSB_OBF: A sub 94.2 0.14 3.1E-06 38.6 5.7 60 45-105 1-76 (100)
66 cd04498 hPOT1_OB2 hPOT1_OB2: A 94.1 0.12 2.5E-06 43.5 5.5 38 77-114 61-109 (123)
67 PRK08182 single-stranded DNA-b 94.0 0.57 1.2E-05 40.0 9.6 60 44-104 4-85 (148)
68 PRK09010 single-stranded DNA-b 94.0 0.43 9.4E-06 42.2 9.1 64 41-105 5-86 (177)
69 TIGR00621 ssb single stranded 93.8 0.18 3.9E-06 43.4 6.3 63 42-105 4-83 (164)
70 TIGR00458 aspS_arch aspartyl-t 93.8 0.37 8.1E-06 47.3 9.3 75 40-125 11-96 (428)
71 KOG4757|consensus 93.8 0.21 4.6E-06 50.2 7.4 83 28-111 5-96 (522)
72 TIGR01405 polC_Gram_pos DNA po 93.7 0.42 9.1E-06 53.0 10.3 78 37-116 2-87 (1213)
73 PRK06752 single-stranded DNA-b 93.7 0.18 3.9E-06 40.6 5.7 61 43-104 3-78 (112)
74 PRK07274 single-stranded DNA-b 93.7 0.22 4.7E-06 41.5 6.3 62 43-105 3-79 (131)
75 cd04322 LysRS_N LysRS_N: N-ter 93.6 0.76 1.6E-05 36.3 9.1 72 45-125 2-82 (108)
76 cd04320 AspRS_cyto_N AspRS_cyt 93.5 1.2 2.6E-05 34.8 9.9 72 45-125 2-91 (102)
77 PRK05159 aspC aspartyl-tRNA sy 93.5 0.4 8.7E-06 47.1 8.9 82 33-125 5-99 (437)
78 PRK13732 single-stranded DNA-b 93.5 0.47 1E-05 41.9 8.4 63 41-104 5-85 (175)
79 PF10451 Stn1: Telomere regula 93.4 0.37 7.9E-06 44.9 8.0 72 45-125 69-149 (256)
80 PF00436 SSB: Single-strand bi 93.4 0.11 2.3E-06 39.7 3.8 62 43-105 2-80 (104)
81 PRK08486 single-stranded DNA-b 93.2 1.2 2.6E-05 39.5 10.5 60 44-104 4-80 (182)
82 cd04317 EcAspRS_like_N EcAspRS 93.2 0.98 2.1E-05 36.9 9.4 75 40-125 13-103 (135)
83 PRK08763 single-stranded DNA-b 93.1 0.31 6.7E-06 42.6 6.7 64 41-105 4-84 (164)
84 cd04100 Asp_Lys_Asn_RS_N Asp_L 93.0 1.6 3.4E-05 32.9 9.7 65 45-116 2-79 (85)
85 PF04076 BOF: Bacterial OB fol 93.0 1 2.2E-05 36.7 9.1 71 35-116 28-100 (103)
86 cd04323 AsnRS_cyto_like_N AsnR 92.7 2.1 4.5E-05 32.3 9.9 65 45-116 2-78 (84)
87 cd04321 ScAspRS_mt_like_N ScAs 92.6 0.74 1.6E-05 35.1 7.4 52 63-116 15-80 (86)
88 PRK07275 single-stranded DNA-b 92.6 0.34 7.4E-06 42.1 6.2 61 43-104 3-78 (162)
89 PRK06293 single-stranded DNA-b 92.5 0.35 7.6E-06 42.3 6.1 61 43-104 2-74 (161)
90 TIGR00499 lysS_bact lysyl-tRNA 91.9 0.66 1.4E-05 46.7 8.1 72 45-125 56-136 (496)
91 PLN02502 lysyl-tRNA synthetase 91.7 0.7 1.5E-05 47.3 8.1 72 45-125 111-193 (553)
92 PRK06958 single-stranded DNA-b 91.7 0.5 1.1E-05 42.1 6.2 63 42-105 4-84 (182)
93 KOG3056|consensus 91.6 0.64 1.4E-05 47.9 7.6 82 44-125 187-277 (578)
94 PRK00484 lysS lysyl-tRNA synth 91.5 1.7 3.7E-05 43.7 10.5 73 44-125 56-136 (491)
95 PF02760 HIN: HIN-200/IF120x d 91.5 0.44 9.6E-06 42.2 5.6 60 33-99 102-165 (170)
96 PRK12445 lysyl-tRNA synthetase 91.5 0.84 1.8E-05 46.1 8.3 72 45-125 68-148 (505)
97 PTZ00401 aspartyl-tRNA synthet 91.2 1.7 3.7E-05 44.6 10.3 87 30-126 63-169 (550)
98 COG1599 RFA1 Single-stranded D 91.0 0.94 2E-05 44.1 7.9 62 48-113 173-238 (407)
99 PRK07772 single-stranded DNA-b 91.0 0.64 1.4E-05 41.5 6.2 62 42-104 4-84 (186)
100 PRK07135 dnaE DNA polymerase I 91.0 0.31 6.8E-06 52.9 5.0 65 33-100 889-956 (973)
101 cd04318 EcAsnRS_like_N EcAsnRS 90.9 3.4 7.5E-05 30.8 9.3 65 45-116 2-76 (82)
102 PLN02850 aspartate-tRNA ligase 90.7 1.8 4E-05 44.0 9.9 85 30-125 67-171 (530)
103 PRK02983 lysS lysyl-tRNA synth 90.6 0.89 1.9E-05 50.0 8.1 82 34-125 641-734 (1094)
104 COG1570 XseA Exonuclease VII, 90.2 1.3 2.7E-05 44.6 8.1 72 43-123 24-101 (440)
105 PRK05813 single-stranded DNA-b 90.2 1.2 2.6E-05 40.6 7.4 63 42-105 109-179 (219)
106 PRK06642 single-stranded DNA-b 89.9 1.1 2.5E-05 38.3 6.6 62 42-104 5-85 (152)
107 cd04486 YhcR_OBF_like YhcR_OBF 89.2 0.96 2.1E-05 34.6 5.1 29 87-116 42-70 (78)
108 cd04494 BRCA2DBD_OB2 BRCA2DBD_ 89.1 1.2 2.5E-05 41.8 6.5 64 62-125 162-237 (251)
109 PTZ00385 lysyl-tRNA synthetase 88.5 3.9 8.4E-05 43.0 10.5 72 44-125 109-191 (659)
110 cd04319 PhAsnRS_like_N PhAsnRS 87.6 5.6 0.00012 31.1 8.7 71 45-125 2-82 (103)
111 TIGR00156 conserved hypothetic 87.3 3.5 7.6E-05 34.9 7.7 68 37-115 53-122 (126)
112 PF15072 DUF4539: Domain of un 87.2 2.8 6.1E-05 33.2 6.7 62 47-116 7-75 (86)
113 PRK03932 asnC asparaginyl-tRNA 86.6 4.7 0.0001 40.0 9.4 75 40-125 15-99 (450)
114 COG0017 AsnS Aspartyl/asparagi 86.3 3.6 7.8E-05 41.3 8.4 84 32-125 4-99 (435)
115 PRK08402 replication factor A; 86.2 1.2 2.6E-05 43.2 5.0 58 30-87 182-267 (355)
116 TIGR00457 asnS asparaginyl-tRN 86.0 4.2 9.1E-05 40.5 8.7 75 40-125 15-101 (453)
117 TIGR00459 aspS_bact aspartyl-t 85.5 4 8.7E-05 42.2 8.6 74 40-124 14-102 (583)
118 PF02721 DUF223: Domain of unk 84.6 1.8 3.9E-05 33.6 4.4 43 69-111 2-49 (95)
119 PRK06341 single-stranded DNA-b 84.5 3.2 7E-05 36.4 6.4 62 42-104 5-85 (166)
120 TIGR00594 polc DNA-directed DN 84.2 1.5 3.1E-05 48.0 5.0 43 40-83 980-1022(1022)
121 PTZ00417 lysine-tRNA ligase; P 84.0 3.2 7E-05 42.9 7.2 72 45-124 135-217 (585)
122 COG2176 PolC DNA polymerase II 84.0 3.7 8E-05 46.1 7.9 113 30-144 227-353 (1444)
123 PLN02603 asparaginyl-tRNA synt 83.7 6.4 0.00014 40.7 9.0 84 32-126 89-193 (565)
124 PRK05813 single-stranded DNA-b 83.4 10 0.00022 34.7 9.4 62 45-107 11-79 (219)
125 PF11325 DUF3127: Domain of un 81.2 14 0.00029 29.4 8.2 65 47-111 2-75 (84)
126 COG1571 Predicted DNA-binding 80.9 6.1 0.00013 39.6 7.5 73 34-116 259-337 (421)
127 PLN02903 aminoacyl-tRNA ligase 80.2 13 0.00029 39.1 10.0 74 41-125 72-162 (652)
128 PRK00476 aspS aspartyl-tRNA sy 78.1 12 0.00025 38.8 8.8 75 40-125 16-105 (588)
129 PLN02221 asparaginyl-tRNA synt 77.3 19 0.0004 37.4 9.9 106 4-125 10-136 (572)
130 PRK12820 bifunctional aspartyl 76.8 15 0.00033 39.0 9.3 74 41-125 18-109 (706)
131 COG1190 LysU Lysyl-tRNA synthe 76.2 12 0.00026 38.4 8.0 68 45-118 64-140 (502)
132 COG0587 DnaE DNA polymerase II 74.7 5.6 0.00012 44.3 5.7 70 34-105 968-1042(1139)
133 COG3390 Uncharacterized protei 71.6 17 0.00036 33.2 7.0 61 45-109 48-114 (196)
134 PF08646 Rep_fac-A_C: Replicat 70.9 1.5 3.2E-05 36.4 0.2 22 65-86 54-75 (146)
135 PRK10053 hypothetical protein; 69.5 9.9 0.00022 32.4 4.9 58 36-104 56-115 (130)
136 cd04476 RPA1_DBD_C RPA1_DBD_C: 66.1 3.6 7.8E-05 34.7 1.6 22 66-87 69-90 (166)
137 COG0629 Ssb Single-stranded DN 64.7 21 0.00047 30.5 6.1 63 43-106 4-84 (167)
138 PRK04036 DNA polymerase II sma 63.4 25 0.00054 35.5 7.2 62 33-100 144-212 (504)
139 COG3111 Periplasmic protein wi 63.1 23 0.0005 30.3 5.9 69 37-116 53-123 (128)
140 PRK05853 hypothetical protein; 62.2 13 0.00028 32.5 4.4 30 74-104 41-74 (161)
141 PF02760 HIN: HIN-200/IF120x d 60.1 1E+02 0.0022 27.7 9.5 67 47-115 5-76 (170)
142 PLN02532 asparagine-tRNA synth 58.8 42 0.0009 35.4 8.0 61 61-125 130-200 (633)
143 PF09104 BRCA-2_OB3: BRCA2, ol 58.1 1.2E+02 0.0026 26.4 9.5 58 39-101 15-78 (143)
144 cd06555 ASCH_PF0470_like ASC-1 56.0 16 0.00034 30.2 3.6 59 77-142 19-77 (109)
145 PF03100 CcmE: CcmE; InterPro 50.8 1.2E+02 0.0026 25.2 8.2 58 40-100 49-106 (131)
146 PF08696 Dna2: DNA replication 46.6 67 0.0015 28.7 6.4 32 69-100 2-35 (209)
147 PRK13254 cytochrome c-type bio 44.5 1.6E+02 0.0034 25.5 8.1 56 43-101 52-107 (148)
148 COG2332 CcmE Cytochrome c-type 44.3 95 0.0021 27.4 6.8 58 40-101 50-108 (153)
149 PRK13150 cytochrome c-type bio 42.6 1.5E+02 0.0033 26.1 7.8 57 41-101 57-114 (159)
150 PF05113 DUF693: Protein of un 42.5 49 0.0011 32.0 5.1 39 60-99 38-87 (314)
151 PF04057 Rep-A_N: Replication 40.8 1.5E+02 0.0033 23.6 7.0 73 44-116 16-95 (101)
152 PF12869 tRNA_anti-like: tRNA_ 40.7 55 0.0012 26.5 4.6 59 43-106 68-132 (144)
153 PRK00036 primosomal replicatio 40.3 1.4E+02 0.0031 24.7 6.9 77 44-123 3-96 (107)
154 COG4043 Preprotein translocase 39.9 30 0.00064 28.9 2.8 47 77-133 21-67 (111)
155 cd04477 RPA1N RPA1N: A subfami 39.1 51 0.0011 26.3 4.1 70 46-115 17-91 (97)
156 COG0173 AspS Aspartyl-tRNA syn 39.0 1.6E+02 0.0036 31.0 8.5 68 41-116 15-99 (585)
157 PRK13165 cytochrome c-type bio 38.1 2.2E+02 0.0048 25.1 8.1 57 41-101 57-114 (160)
158 COG0361 InfA Translation initi 37.1 1E+02 0.0022 24.1 5.3 46 44-99 6-56 (75)
159 PF13567 DUF4131: Domain of un 37.1 2E+02 0.0044 22.4 8.6 55 41-99 75-138 (176)
160 cd04454 S1_Rrp4_like S1_Rrp4_l 35.3 1.8E+02 0.0039 21.4 6.6 60 46-116 9-76 (82)
161 cd03703 aeIF5B_II aeIF5B_II: T 34.9 2.1E+02 0.0044 23.8 7.1 36 48-100 2-37 (110)
162 PTZ00425 asparagine-tRNA ligas 32.6 3.1E+02 0.0067 28.9 9.5 55 45-105 84-146 (586)
163 PF04775 Bile_Hydr_Trans: Acyl 31.4 89 0.0019 25.8 4.4 46 28-81 2-49 (126)
164 cd03702 IF2_mtIF2_II This fami 31.0 1.9E+02 0.004 23.0 6.0 47 49-99 3-65 (95)
165 cd05706 S1_Rrp5_repeat_sc10 S1 30.3 2E+02 0.0044 20.4 6.6 27 88-114 46-72 (73)
166 PRK09919 anti-adapter protein 30.0 82 0.0018 26.5 4.0 39 77-115 26-64 (114)
167 PRK12442 translation initiatio 29.7 2.2E+02 0.0048 23.0 6.2 51 44-107 6-61 (87)
168 cd05694 S1_Rrp5_repeat_hs2_sc2 29.4 2.3E+02 0.0049 21.1 6.0 69 37-115 1-69 (74)
169 KOG1885|consensus 28.9 1.6E+02 0.0034 30.7 6.5 66 45-116 107-183 (560)
170 PRK00147 queA S-adenosylmethio 28.1 1.6E+02 0.0034 29.0 6.2 35 69-103 28-63 (342)
171 PF11948 DUF3465: Protein of u 28.0 3.7E+02 0.0079 23.2 7.6 56 45-102 39-98 (131)
172 PF07712 SURNod19: Stress up-r 27.6 40 0.00087 33.6 2.0 27 196-223 212-239 (381)
173 TIGR00008 infA translation ini 27.5 1.9E+02 0.0041 22.2 5.2 42 45-99 5-54 (68)
174 PF11183 PmrD: Polymyxin resis 27.4 60 0.0013 25.9 2.6 36 66-101 16-52 (82)
175 PRK13159 cytochrome c-type bio 26.4 4.5E+02 0.0098 23.1 8.7 56 43-101 52-108 (155)
176 PF09926 DUF2158: Uncharacteri 26.2 43 0.00094 24.3 1.5 12 90-101 1-12 (53)
177 PF02547 Queuosine_synth: Queu 26.0 2.3E+02 0.005 27.8 6.8 52 67-120 26-77 (341)
178 PRK10220 hypothetical protein; 25.8 2.2E+02 0.0047 24.0 5.7 41 38-82 52-95 (111)
179 cd05704 S1_Rrp5_repeat_hs13 S1 25.8 1.3E+02 0.0029 21.9 4.1 25 88-114 47-71 (72)
180 COG4013 Uncharacterized protei 23.7 2.2E+02 0.0048 23.1 5.2 28 89-116 20-54 (91)
181 cd03446 MaoC_like MoaC_like 22.3 2.9E+02 0.0063 21.8 5.8 47 31-80 84-132 (140)
182 cd00586 4HBT 4-hydroxybenzoyl- 22.1 2.9E+02 0.0064 19.5 6.1 44 30-80 57-100 (110)
183 KOG0851|consensus 22.0 3.7E+02 0.008 23.2 6.8 73 32-105 4-81 (246)
184 PRK04012 translation initiatio 21.7 3.2E+02 0.007 22.2 5.9 46 39-99 17-69 (100)
185 cd03452 MaoC_C MaoC_C The C-t 21.5 2.7E+02 0.0058 22.7 5.5 48 31-80 82-130 (142)
186 COG1917 Uncharacterized conser 21.1 89 0.0019 24.9 2.6 37 67-106 66-102 (131)
187 PF13585 CHU_C: C-terminal dom 20.8 3.1E+02 0.0067 21.0 5.4 68 38-112 7-87 (87)
188 PF10648 Gmad2: Immunoglobulin 20.7 2.1E+02 0.0045 22.4 4.5 53 92-145 14-66 (88)
189 smart00739 KOW KOW (Kyprides, 20.5 83 0.0018 18.4 1.8 12 90-101 2-13 (28)
190 TIGR00686 phnA alkylphosphonat 20.5 2.6E+02 0.0056 23.5 5.2 41 38-82 51-94 (109)
No 1
>KOG3416|consensus
Probab=99.97 E-value=2.9e-30 Score=214.83 Aligned_cols=107 Identities=53% Similarity=0.945 Sum_probs=104.6
Q ss_pred cccccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeeeEEEEECCEE
Q psy3603 31 MDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKCYAQIWRNCL 110 (264)
Q Consensus 31 ~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ngyVs~frG~L 110 (264)
+.++|+||+|+++|++++|+|++.+..+.||+|+.|+.+.+||+||+|.+.+|||.+++|+|||||++.+||++.|+|+|
T Consensus 3 ~~i~ikdi~P~~kN~~v~fIvl~~g~~tkTkdg~~v~~~kVaD~TgsI~isvW~e~~~~~~PGDIirLt~Gy~Si~qg~L 82 (134)
T KOG3416|consen 3 IMIFIKDIKPGLKNINVTFIVLEYGRATKTKDGHEVRSCKVADETGSINISVWDEEGCLIQPGDIIRLTGGYASIFQGCL 82 (134)
T ss_pred cchhHhhcChhhhcceEEEEEEeeceeeeccCCCEEEEEEEecccceEEEEEecCcCcccCCccEEEecccchhhhcCce
Confidence 45789999999999999999999999988999999999999999999999999999999999999999999999999999
Q ss_pred EEEEcCCceEEEecCceeeecCCCCCC
Q psy3603 111 TLYSSKSGLIEKIGEFCMVFNENLDMS 137 (264)
Q Consensus 111 qL~Igr~G~IekVgEf~~~fnE~pNiS 137 (264)
.|++||.|+++|+|||+|+|+|.||+|
T Consensus 83 tL~~GK~Ge~~KiGef~~vf~etpn~S 109 (134)
T KOG3416|consen 83 TLYVGKGGEVQKIGEFCMVFSETPNIS 109 (134)
T ss_pred EEEecCCceEeEeeeeEEeeecCCCcc
Confidence 999999999999999999999999999
No 2
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=99.90 E-value=8.4e-23 Score=168.46 Aligned_cols=114 Identities=29% Similarity=0.459 Sum_probs=97.4
Q ss_pred ccccccccccccccceEEEEEEEecCCcee--ecCC-cEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeeeEEEEE
Q psy3603 30 AMDVYIKDLHVGIKNVNVTCIVLDISPRVT--LKEN-REVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKCYAQIW 106 (264)
Q Consensus 30 ~~~ikIkDLkpG~knVnv~fiVle~~~~r~--TKdG-g~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ngyVs~f 106 (264)
++..+|+||+|++++|+++|+|+++.++++ +|++ +.|++++|+|+||+|.+++|++.++.|++||+|+|.||++++|
T Consensus 2 ~~~~kI~dL~~g~~~v~~~~~V~~i~~~~~~~~k~~~~~v~~~~l~D~TG~I~~tlW~~~a~~l~~GdvV~I~na~v~~f 81 (129)
T PRK06461 2 EMITKIKDLKPGMERVNVTVRVLEVGEPKVIQTKGGPRTISEAVVGDETGRVKLTLWGEQAGSLKEGEVVEIENAWTTLY 81 (129)
T ss_pred CCceEHHHcCCCCCceEEEEEEEEcCCceEEEeCCCceEEEEEEEECCCCEEEEEEeCCccccCCCCCEEEEECcEEeee
Confidence 457899999999888999999999987654 4555 5699999999999999999999988999999999999999999
Q ss_pred CCEEEEEEcCCceEEEecCceeeecCCCCCCCCCCCCCCCCCC
Q psy3603 107 RNCLTLYSSKSGLIEKIGEFCMVFNENLDMSIPIPNLPVNAPQ 149 (264)
Q Consensus 107 rG~LqL~Igr~G~IekVgEf~~~fnE~pNiSe~~Pe~~~~~~~ 149 (264)
+|++||+++++|.|+++++. ++|.++++|++.+..|.
T Consensus 82 ~G~lqL~i~~~~~i~~~~~~------~v~~~~~i~~~~~~~~~ 118 (129)
T PRK06461 82 RGKVQLNVGKYGSISESDDE------EVPEAEEIPEETPEAPG 118 (129)
T ss_pred CCEEEEEECCCEEEEECCcc------ccCCCCccCccCccccc
Confidence 99999999999999999884 45555555555554433
No 3
>PRK07218 replication factor A; Provisional
Probab=99.65 E-value=8.8e-16 Score=149.08 Aligned_cols=97 Identities=27% Similarity=0.342 Sum_probs=87.2
Q ss_pred cccccccccccccccceEEEEEEEecCCceeecCC--cEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeeeEEEEE
Q psy3603 29 EAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKEN--REVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKCYAQIW 106 (264)
Q Consensus 29 ~~~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdG--g~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ngyVs~f 106 (264)
.....+|+||.+++++|+++++|+++.++..+++| +.+.+++|+|+||+|++++|++.+ |++||+|+|.||++++|
T Consensus 55 ~~~~~kI~Di~~~~~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~~~~--l~~Gdvv~I~na~vre~ 132 (423)
T PRK07218 55 TPSSKDIKELSTDDKNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWKDFG--LSPGDTVTIGNAGVREW 132 (423)
T ss_pred CCCCccHhhCCCCCceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCeEEEEEECCCC--CCCCCEEEEeccEeecc
Confidence 34568999999999999999999999885446677 689999999999999999999764 99999999999999999
Q ss_pred CCEEEEEEcCCceEEEecCce
Q psy3603 107 RNCLTLYSSKSGLIEKIGEFC 127 (264)
Q Consensus 107 rG~LqL~Igr~G~IekVgEf~ 127 (264)
+|.++|++++.+.|...++..
T Consensus 133 ~g~~el~ig~~t~I~~~de~~ 153 (423)
T PRK07218 133 DGRPELNIGESTTVSLLDDSS 153 (423)
T ss_pred CCceEEeccCcceEEEcCccc
Confidence 999999999999999887643
No 4
>PRK08402 replication factor A; Reviewed
Probab=99.64 E-value=6.9e-16 Score=146.88 Aligned_cols=116 Identities=24% Similarity=0.269 Sum_probs=95.8
Q ss_pred CCCcccc---eeeeeeccccc--CcccccccccccccccceEEEEEEEecCCcee--ecCC--cEEEEEEEEeCCCeEEE
Q psy3603 10 HPEKNHG---MRAERKEINRK--KEAMDVYIKDLHVGIKNVNVTCIVLDISPRVT--LKEN--REVRTLKVADSTACINL 80 (264)
Q Consensus 10 ~~~~~h~---~~~e~~~i~~~--~~~~~ikIkDLkpG~knVnv~fiVle~~~~r~--TKdG--g~V~tL~LADeTGsI~l 80 (264)
.+..+|+ |.|.+..+... .+....+|+||.||+++|+++++|+++..+++ +|+| ++|++++|+|+||.|++
T Consensus 35 ~~~~e~~A~~~ia~e~G~~~~~~~~~~~~kI~dl~~g~~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~ir~ 114 (355)
T PRK08402 35 EGISEHAAALLLAEELGVNLEGEEEAPLMHISDLVPGMRGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARV 114 (355)
T ss_pred cCCCHHHHHHHHHHHhCCCccCCCccCccCHHHccCCCceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCeEEE
Confidence 4455655 55666666443 23346899999999999999999999987765 4677 78999999999999999
Q ss_pred EEecCCCC----CCCCCCEEEEeeeEEEEE-CCEEEEEEcCCceEEEecC
Q psy3603 81 SLWDEPGA----LLHPGDIVRLTKCYAQIW-RNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 81 tLWdd~ad----~Ik~GDIIrI~ngyVs~f-rG~LqL~Igr~G~IekVgE 125 (264)
++|++.++ .+++||+|+|.||+|+.| +|.++|++++.|.|...++
T Consensus 115 TlW~~~a~~~~~~l~~Gdvi~I~~a~V~e~~~G~~eLsvg~~s~i~~~pd 164 (355)
T PRK08402 115 VLWDAKVAKYYNKINVGDVIKVIDAQVRESLSGLPELHINFRARIILNPD 164 (355)
T ss_pred EEechhhhhhcccCCCCCEEEEECCEEeecCCCcEEEEECCCceEEeCCC
Confidence 99998864 489999999999999985 8999999999999987655
No 5
>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=99.61 E-value=7.4e-15 Score=110.74 Aligned_cols=77 Identities=35% Similarity=0.528 Sum_probs=68.8
Q ss_pred EEEEEEEecCCcee-ecCC--cEEEEEEEEeCCCeEEEEEecCC-CCCCCCCCEEEEeeeEEEEECCEEEEEEcCCceEE
Q psy3603 46 NVTCIVLDISPRVT-LKEN--REVRTLKVADSTACINLSLWDEP-GALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIE 121 (264)
Q Consensus 46 nv~fiVle~~~~r~-TKdG--g~V~tL~LADeTGsI~ltLWdd~-ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr~G~Ie 121 (264)
+++++|++++++++ +++| ++|++++|+|+||+|++++|++. .+.+++||+|+|.||+++.|+|.+||++++.|.|+
T Consensus 1 ~v~~~V~~~~~~~~~~~~g~~~~~~~~~l~D~TG~i~~~~W~~~~~~~~~~G~vv~i~~~~v~~~~g~~ql~i~~~~~i~ 80 (82)
T cd04491 1 SVEGKVLSISEPREFTRDGSEGKVQSGLVGDETGTIRFTLWDEKAADDLEPGDVVRIENAYVREFNGRLELSVGKNSEIE 80 (82)
T ss_pred CEEEEEEEccCCeEeccCCCeeEEEEEEEECCCCEEEEEEECchhcccCCCCCEEEEEeEEEEecCCcEEEEeCCceEEE
Confidence 47899999998876 3444 78999999999999999999977 56699999999999999999999999999999887
Q ss_pred E
Q psy3603 122 K 122 (264)
Q Consensus 122 k 122 (264)
+
T Consensus 81 ~ 81 (82)
T cd04491 81 K 81 (82)
T ss_pred E
Confidence 5
No 6
>PRK06386 replication factor A; Reviewed
Probab=99.61 E-value=5.4e-15 Score=141.08 Aligned_cols=113 Identities=15% Similarity=0.261 Sum_probs=90.7
Q ss_pred cccccccccccccceEEEEEEEecCCcee-ecCC-cEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeeeEEEEECC
Q psy3603 31 MDVYIKDLHVGIKNVNVTCIVLDISPRVT-LKEN-REVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKCYAQIWRN 108 (264)
Q Consensus 31 ~~ikIkDLkpG~knVnv~fiVle~~~~r~-TKdG-g~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ngyVs~frG 108 (264)
|..+|+||.|++++|+++++|+++.++.. +++| ..+...+|+|+||.|++++|+. .+.+++||+|+|.||++++|+|
T Consensus 1 ~~~kI~DI~~~~~~V~v~akVl~~~~r~i~~~~g~~~~~~gllgDeTG~I~fT~W~~-~~~l~~Gd~v~i~na~v~~~~G 79 (358)
T PRK06386 1 MLSKISDINAARQNVDLKVKVLSLNKRTIKNDRGETIYYYGIIGDETGTVPFTAWEF-PDAVKSGDVIEIKYCYSKEYNG 79 (358)
T ss_pred CCcchhhcCCCCCcEEEEEEEEEccceEEecCCCCeEEEEEEEECCcceEEEEecCC-cccCCCCCEEEEEeEEEeeECC
Confidence 45789999999999999999999985433 4666 5567889999999999999994 4568999999999999999999
Q ss_pred EEEEEEcCCceEEEecCceeeecCC---CCCCCCCCCCC
Q psy3603 109 CLTLYSSKSGLIEKIGEFCMVFNEN---LDMSIPIPNLP 144 (264)
Q Consensus 109 ~LqL~Igr~G~IekVgEf~~~fnE~---pNiSe~~Pe~~ 144 (264)
.++|++++.+.|....+....+++. .+++|+.|...
T Consensus 80 ~~~Lnv~~~t~v~~~~d~~iev~~~~~~~KI~DL~~g~~ 118 (358)
T PRK06386 80 KIRIYFDSRSEVMLKPDENIEVKRTYKLVKIRDLSLVTP 118 (358)
T ss_pred EEEEEEcCceEEEecCccccccccccCccEeEeccCCCC
Confidence 9999999999886554332333333 35666666544
No 7
>PRK06386 replication factor A; Reviewed
Probab=99.60 E-value=8.9e-15 Score=139.62 Aligned_cols=99 Identities=18% Similarity=0.235 Sum_probs=86.5
Q ss_pred ccccCcccccccccccccccceEEEEEEEecCCceeecCC--cEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeee
Q psy3603 24 INRKKEAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKEN--REVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKC 101 (264)
Q Consensus 24 i~~~~~~~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdG--g~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ng 101 (264)
|.....+...+|+||.|++..|+++++|+++.++...++| +.+.++.|+|+||+|++++|++ .+++||+|+|.|+
T Consensus 99 iev~~~~~~~KI~DL~~g~~~v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTGrIr~TlW~~---~l~eGd~v~i~na 175 (358)
T PRK06386 99 IEVKRTYKLVKIRDLSLVTPYVSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTARVRISSFGK---PLEDNRFVRIENA 175 (358)
T ss_pred cccccccCccEeEeccCCCCceEEEEEEEEccCceEecCCCccEEEEEEEEcCCCeEEEEEccc---cccCCCEEEEeee
Confidence 4444445567999999999999999999999876545444 7899999999999999999997 4899999999999
Q ss_pred EEEEECCEEEEEEcCCceEEEecC
Q psy3603 102 YAQIWRNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 102 yVs~frG~LqL~Igr~G~IekVgE 125 (264)
++++|+|.++|++++.+.|+.+++
T Consensus 176 ~v~e~~G~~el~v~~~t~I~~~~~ 199 (358)
T PRK06386 176 RVSQYNGYIEISVGNKSVIKEVES 199 (358)
T ss_pred EEEccCCeEEEEeCCeEEEEECCC
Confidence 999999999999999999998765
No 8
>PRK12366 replication factor A; Reviewed
Probab=99.55 E-value=1.7e-14 Score=145.68 Aligned_cols=115 Identities=30% Similarity=0.540 Sum_probs=97.7
Q ss_pred cccccccccccccccceEEEEEEEecCCcee--ecCC--cEEEEEEEEeCCCeEEEEEecCCCCC---CCCCCEEEEeee
Q psy3603 29 EAMDVYIKDLHVGIKNVNVTCIVLDISPRVT--LKEN--REVRTLKVADSTACINLSLWDEPGAL---LHPGDIVRLTKC 101 (264)
Q Consensus 29 ~~~~ikIkDLkpG~knVnv~fiVle~~~~r~--TKdG--g~V~tL~LADeTGsI~ltLWdd~ad~---Ik~GDIIrI~ng 101 (264)
+....+|+||.|++.+++++++|++++++++ +++| +++.++.|+|+||+|++++|++.++. |++||+|+|.+|
T Consensus 60 ~~~~~~I~dl~p~~~~v~i~arV~~~~~~r~~~~~~G~eGkv~~~~v~DetG~Ir~t~W~~~~~~~~~le~G~v~~i~~~ 139 (637)
T PRK12366 60 EEEDFKISDIEEGQINVEITGRIIEISNIKTFTRKDGSTGKLANITIADNTGTIRLTLWNDNAKLLKGLKEGDVIKIENA 139 (637)
T ss_pred ccceeEHHHCcCCCcceEEEEEEEEccCCeEEECCCCCccEEEEEEEEcCCCEEEEEEEchhhhhhccCCCCCEEEEecc
Confidence 4567899999999999999999999999886 4566 89999999999999999999988655 899999999999
Q ss_pred EEEEECCEEEEEEcCCceEEEecCc----eeeecCCCCCCCCCCCC
Q psy3603 102 YAQIWRNCLTLYSSKSGLIEKIGEF----CMVFNENLDMSIPIPNL 143 (264)
Q Consensus 102 yVs~frG~LqL~Igr~G~IekVgEf----~~~fnE~pNiSe~~Pe~ 143 (264)
+++.|+|.++|+++..+.|.++++. .+......+++++.+..
T Consensus 140 ~v~~~~~~~el~~~~~t~I~~~~~~d~~~i~~~~~~~~I~el~~g~ 185 (637)
T PRK12366 140 RSRKWNNDVELNSGSETRIDKLEKYDESRYPIIKENYDIPELEPNL 185 (637)
T ss_pred EecccCCceEEEcCCcceEEEccccccccCCcccccccccccCCCC
Confidence 9999999999999999999988632 12333446777776644
No 9
>PRK15491 replication factor A; Provisional
Probab=99.54 E-value=2.5e-14 Score=136.76 Aligned_cols=106 Identities=23% Similarity=0.309 Sum_probs=87.1
Q ss_pred eeeeeecccccCcccccccccccccccceEEEEEEEecCCcee--ecCC--cEEEEEEEEeCCCeEEEEEecCCCC----
Q psy3603 17 MRAERKEINRKKEAMDVYIKDLHVGIKNVNVTCIVLDISPRVT--LKEN--REVRTLKVADSTACINLSLWDEPGA---- 88 (264)
Q Consensus 17 ~~~e~~~i~~~~~~~~ikIkDLkpG~knVnv~fiVle~~~~r~--TKdG--g~V~tL~LADeTGsI~ltLWdd~ad---- 88 (264)
|.|.+-.|... +....+|+||.|++.+++++++|++++++++ +++| +++.+++|+|+||+|++++|++.++
T Consensus 43 lva~elgv~~~-~~~~~kI~dL~~~~~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~ir~tlW~~~a~~~~~ 121 (374)
T PRK15491 43 LVAHDLGVTDT-GVDTTKIADINESSSNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDLADLIKT 121 (374)
T ss_pred HHhhhcCCCcc-ccccccHHHCCCCCCceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCeEEEEEECchhhhhcc
Confidence 44455454443 3456799999999999999999999988886 4577 7999999999999999999998864
Q ss_pred -CCCCCCEEEEeeeEEE-EECCEEEEEEcCCceEEEecC
Q psy3603 89 -LLHPGDIVRLTKCYAQ-IWRNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 89 -~Ik~GDIIrI~ngyVs-~frG~LqL~Igr~G~IekVgE 125 (264)
.|++||+|+|.++ ++ .|+| ++|++++.+.|.+.++
T Consensus 122 ~~le~G~v~~I~~~-~~~~y~g-~Ei~i~~~~~i~~~~~ 158 (374)
T PRK15491 122 GDIEVGKSLNISGY-AKEGYSG-IEVNIGRYGGISESDE 158 (374)
T ss_pred CCcCCCCEEEEeee-eccCccc-EEEEeCCCceeeeccc
Confidence 3778999999854 55 5767 8999999999988754
No 10
>PRK07211 replication factor A; Reviewed
Probab=99.54 E-value=4.9e-14 Score=139.02 Aligned_cols=95 Identities=27% Similarity=0.486 Sum_probs=86.6
Q ss_pred cccccccccccccceEEEEEEEecCCcee-e-cCC--cEEEEEEEEeCCCeEEEEEecCCCCC---CCCCCEEEEeeeEE
Q psy3603 31 MDVYIKDLHVGIKNVNVTCIVLDISPRVT-L-KEN--REVRTLKVADSTACINLSLWDEPGAL---LHPGDIVRLTKCYA 103 (264)
Q Consensus 31 ~~ikIkDLkpG~knVnv~fiVle~~~~r~-T-KdG--g~V~tL~LADeTGsI~ltLWdd~ad~---Ik~GDIIrI~ngyV 103 (264)
.+.+|++|.|++.+++++++|++++++++ . ++| +++++++|+|+||+|++++|++.++. |++||+|+|.+|++
T Consensus 160 ~~~~I~dL~~~~~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG~IR~TlW~d~Ad~~~~le~G~Vv~I~~a~V 239 (485)
T PRK07211 160 DTYTVEDLSLGLSDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETGRVRVTLWDDRADLAEELDAGESVEIVDGYV 239 (485)
T ss_pred CCccHHHcCCCCCceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCCeEEEEEechhhhhhccCCCCCEEEEEeeEE
Confidence 56799999999999999999999999876 3 466 68999999999999999999988754 78999999999999
Q ss_pred EEECCEEEEEEcCCceEEEecC
Q psy3603 104 QIWRNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 104 s~frG~LqL~Igr~G~IekVgE 125 (264)
+.|+|.++|+++..+.|++.++
T Consensus 240 re~~g~~ELsl~~~s~I~~~~d 261 (485)
T PRK07211 240 RERDGSLELHVGDRGAVEEVDE 261 (485)
T ss_pred EecCCcEEEEECCCceEEECCc
Confidence 9999999999999999999765
No 11
>PRK07217 replication factor A; Reviewed
Probab=99.54 E-value=6.3e-14 Score=131.73 Aligned_cols=109 Identities=17% Similarity=0.194 Sum_probs=89.2
Q ss_pred cccceeeeeecccccCcccccccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecC-CCCCCC
Q psy3603 13 KNHGMRAERKEINRKKEAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDE-PGALLH 91 (264)
Q Consensus 13 ~~h~~~~e~~~i~~~~~~~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd-~ad~Ik 91 (264)
++||+..+++.= ....+..+|+||.++.++|+++++|++..+++ ++.......|+|+||+|++++|+. ....|+
T Consensus 55 ~k~g~~~~~~~~--~~~~~~~kI~Di~~~~~~VsV~aKVl~l~e~~---~~si~qvGllgDETG~IkfT~W~~s~~~~le 129 (311)
T PRK07217 55 KEAGIDRDELSG--GGGSELVNIADIDEPEQWVDVTAKVVQLWEPS---SDSIAQVGLLGDETGTIKFTKWAKSDLPELE 129 (311)
T ss_pred HHhCCCcccccc--CCCCCceeeeecCCCCCcEEEEEEEEEecCCC---CCceEEEEEEEcCCceEEEEEccCCCCCccc
Confidence 566665443221 13445679999999988999999999998764 444555578999999999999997 445599
Q ss_pred CCCEEEEeeeEEEEECCEEEEEEcCCceEEEecCc
Q psy3603 92 PGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGEF 126 (264)
Q Consensus 92 ~GDIIrI~ngyVs~frG~LqL~Igr~G~IekVgEf 126 (264)
+||+|+|.|+++++|+|.++|++++++.|..+++-
T Consensus 130 eGd~~rI~na~v~ey~G~~~lnlg~~t~I~~~de~ 164 (311)
T PRK07217 130 EGKSYLLKNVVTDEYQGRFSVKLNRTTSIEELDED 164 (311)
T ss_pred CCCEEEEEeEEEeeECCEEEEEeCCceEEEeCCCC
Confidence 99999999999999999999999999999998763
No 12
>PRK14699 replication factor A; Provisional
Probab=99.54 E-value=3.6e-14 Score=139.77 Aligned_cols=113 Identities=19% Similarity=0.254 Sum_probs=92.4
Q ss_pred cccccccccccccceEEEEEEEecCCcee--ecCC--cEEEEEEEEeCCCeEEEEEecCCCCC-----CCCCCEEEEeee
Q psy3603 31 MDVYIKDLHVGIKNVNVTCIVLDISPRVT--LKEN--REVRTLKVADSTACINLSLWDEPGAL-----LHPGDIVRLTKC 101 (264)
Q Consensus 31 ~~ikIkDLkpG~knVnv~fiVle~~~~r~--TKdG--g~V~tL~LADeTGsI~ltLWdd~ad~-----Ik~GDIIrI~ng 101 (264)
...+|+||.|++.+|+++++|++++++++ +++| +++.+++|+|+||+|++++|++.+++ |++||+|+|.|
T Consensus 56 ~~~kI~di~~~~~~v~i~~rVl~i~~~r~f~r~dG~~g~v~~~~iaDeTG~ir~tlW~~~a~~~~~g~l~~GDvv~I~~- 134 (484)
T PRK14699 56 DSVKIENITPESGPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNMADLIKAGKIKAGQTLQISG- 134 (484)
T ss_pred ccccHhHccCCCceEEEEEEEEEecCceEEecCCCCceEEEEEEEecCCCeEEEEEecCccchhhhcCCCCCCEEEEcc-
Confidence 44799999999999999999999997776 3466 78999999999999999999988864 99999999986
Q ss_pred EEEEECCEEEEEEcCCceEEEecCceeeecCCCCCCCCCCCCC
Q psy3603 102 YAQIWRNCLTLYSSKSGLIEKIGEFCMVFNENLDMSIPIPNLP 144 (264)
Q Consensus 102 yVs~frG~LqL~Igr~G~IekVgEf~~~fnE~pNiSe~~Pe~~ 144 (264)
+++.+++.++|++++.+.|++.++...+-....+++++.|...
T Consensus 135 ~~r~~~~g~el~~~~~~~i~~~~~~i~v~~~~~~I~dL~~~~~ 177 (484)
T PRK14699 135 YAKQGYSGVEVNIGNNGVLTESEEEIDVAANSQKIKDIKDGMG 177 (484)
T ss_pred eeccCCCCceEEeCCCceeeccCcccccCCCCcchhhcCCCCC
Confidence 6877666699999998889887554433223467887777543
No 13
>PRK07218 replication factor A; Provisional
Probab=99.53 E-value=6.3e-14 Score=136.23 Aligned_cols=95 Identities=22% Similarity=0.324 Sum_probs=83.9
Q ss_pred ccccccccccccccceEEEEEEEecCCceee-cCC-cEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeeeEEEEEC
Q psy3603 30 AMDVYIKDLHVGIKNVNVTCIVLDISPRVTL-KEN-REVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKCYAQIWR 107 (264)
Q Consensus 30 ~~~ikIkDLkpG~knVnv~fiVle~~~~r~T-KdG-g~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ngyVs~fr 107 (264)
+...+|.||.+++.+|++.++|+++.++..+ ++| +.+.+++|+|+||+|++++|++.+ .|++||+|+|.|||+++|+
T Consensus 160 ~~~~kI~DL~~g~~~V~v~g~Vl~~~~r~f~~~dg~~~v~~giigDeTG~Ir~tlW~~~~-~l~~Gd~v~I~na~v~e~~ 238 (423)
T PRK07218 160 GGDKKLIDLGPGDRGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDPLP-EIEIGASIRIEDAYVREFR 238 (423)
T ss_pred cCccchhhccCCCCceEEEEEEEEecceeEEcCCCCeEEEEEEEECCCceEEEEEecccc-cCCCCCEEEEeeeEEeccC
Confidence 3455899999999999999999999764434 566 578999999999999999999865 4899999999999999999
Q ss_pred CEEEEEEcCCceEEEecC
Q psy3603 108 NCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 108 G~LqL~Igr~G~IekVgE 125 (264)
|.++|++++.+.|..+++
T Consensus 239 G~~elnv~~~t~I~~~d~ 256 (423)
T PRK07218 239 GVPSVNVSEFTTVEALDR 256 (423)
T ss_pred CeEEEEECCceEEEECCC
Confidence 999999999999999865
No 14
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=99.50 E-value=1e-13 Score=130.13 Aligned_cols=103 Identities=21% Similarity=0.266 Sum_probs=89.5
Q ss_pred cccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC---CCCCCCCCEEEEeeeEEEEECCE
Q psy3603 33 VYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP---GALLHPGDIVRLTKCYAQIWRNC 109 (264)
Q Consensus 33 ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~---ad~Ik~GDIIrI~ngyVs~frG~ 109 (264)
.+|+||++|++ |+..|+|.++... ++|+|++|+.++|+|+||+|.+++|+.. ...|++|++|+|. |.+..|+|.
T Consensus 3 ~~i~~l~~g~~-v~~~~lv~~~~~~-~~knG~~yl~l~l~D~tG~I~ak~W~~~~~~~~~~~~g~vv~v~-G~v~~y~g~ 79 (314)
T PRK13480 3 KGIEELEVGEQ-VDHFLLIKSATKG-VASNGKPFLTLILQDKSGDIEAKLWDVSPEDEATYVPETIVHVK-GDIINYRGR 79 (314)
T ss_pred chHhhcCCCCE-eeEEEEEEEceee-ecCCCCeEEEEEEEcCCcEEEEEeCCCChhhHhhcCCCCEEEEE-EEEEEECCc
Confidence 48999999996 9999999998754 6899999999999999999999999954 3459999999999 689999999
Q ss_pred EEEEEcCCceEEEecCceeeecCCCCCCCCCCCCCCC
Q psy3603 110 LTLYSSKSGLIEKIGEFCMVFNENLDMSIPIPNLPVN 146 (264)
Q Consensus 110 LqL~Igr~G~IekVgEf~~~fnE~pNiSe~~Pe~~~~ 146 (264)
+||+|.+ |+.+.+. +.+|++++.|..+..
T Consensus 80 ~Ql~i~~---i~~~~~~-----e~~d~~dfvp~s~~~ 108 (314)
T PRK13480 80 KQLKVNQ---IRLATEE-----DGVKISDFVEKAPLS 108 (314)
T ss_pred ceEEEEE---eEECCCC-----CcCCHHHcCCCCCCC
Confidence 9999997 8776552 468999999988764
No 15
>PRK14699 replication factor A; Provisional
Probab=99.50 E-value=1.7e-13 Score=135.14 Aligned_cols=94 Identities=30% Similarity=0.473 Sum_probs=83.6
Q ss_pred ccccccccccccceEEEEEEEecCCcee--ecCC--cEEEEEEEEeCCCeEEEEEecCCCCC---CCCCCEEEEeeeEEE
Q psy3603 32 DVYIKDLHVGIKNVNVTCIVLDISPRVT--LKEN--REVRTLKVADSTACINLSLWDEPGAL---LHPGDIVRLTKCYAQ 104 (264)
Q Consensus 32 ~ikIkDLkpG~knVnv~fiVle~~~~r~--TKdG--g~V~tL~LADeTGsI~ltLWdd~ad~---Ik~GDIIrI~ngyVs 104 (264)
..+|+||.|++..|++.++|+++.++++ +++| +++.++.|+|+||+|++++|++.++. |++||+|+|.|||++
T Consensus 166 ~~~I~dL~~~~~~V~i~gkVl~~~~~R~f~~~dG~~g~v~~~~igDeTG~ir~tlW~~~a~~~~~l~~Gd~v~I~~a~vr 245 (484)
T PRK14699 166 SQKIKDIKDGMGDLNLTGKVLEISEIRTFQRKDGTSGKVGNLLLGDETGTLRVTLWDDKTDFLNQIEYGDTVELINAYAR 245 (484)
T ss_pred CcchhhcCCCCCceEEEEEEEeccCceEEecCCCCceEEEEEEEEcCCceEEEEEECcccccccccCCCCEEEEecceEe
Confidence 3689999999999999999999999876 4577 68999999999999999999997655 899999999999997
Q ss_pred E--ECCEEEEEEcCCceEEEecC
Q psy3603 105 I--WRNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 105 ~--frG~LqL~Igr~G~IekVgE 125 (264)
. |+|.++|++++.+.|...++
T Consensus 246 ~~~~~~~~el~~~~~s~i~~~~~ 268 (484)
T PRK14699 246 ENAFTQKVELQVGNRSIIRKSEK 268 (484)
T ss_pred ecccCCceEEEecCceEeecccc
Confidence 5 78999999999888877653
No 16
>PRK15491 replication factor A; Provisional
Probab=99.49 E-value=2.6e-13 Score=129.85 Aligned_cols=95 Identities=28% Similarity=0.436 Sum_probs=84.4
Q ss_pred cccccccccccccceEEEEEEEecCCcee--ecCC--cEEEEEEEEeCCCeEEEEEecCCCC---CCCCCCEEEEeeeEE
Q psy3603 31 MDVYIKDLHVGIKNVNVTCIVLDISPRVT--LKEN--REVRTLKVADSTACINLSLWDEPGA---LLHPGDIVRLTKCYA 103 (264)
Q Consensus 31 ~~ikIkDLkpG~knVnv~fiVle~~~~r~--TKdG--g~V~tL~LADeTGsI~ltLWdd~ad---~Ik~GDIIrI~ngyV 103 (264)
.+.+|+||.+++.+|+++++|++++++++ +++| ++++++.|+|+||.|++++|++.++ .|++||+|+|.+||+
T Consensus 165 ~~~~I~dl~~~~~~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG~Ir~t~W~~~a~~~~~l~~Gd~V~i~~~~~ 244 (374)
T PRK15491 165 NSQKISDIKDGDSDINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETGKIRVTLWDGKTDLADKLENGDSVEIINGYA 244 (374)
T ss_pred CcccHHHcCCCCccEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCCeEEEEEecchhcccccCCCCCEEEEEeceE
Confidence 45789999999988999999999998776 4677 5899999999999999999998876 488999999999998
Q ss_pred EE--ECCEEEEEEcCCceEEEecC
Q psy3603 104 QI--WRNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 104 s~--frG~LqL~Igr~G~IekVgE 125 (264)
+. |+|.++|++++.+.|.+.++
T Consensus 245 r~~~~~g~~El~~~~~s~I~~~~~ 268 (374)
T PRK15491 245 RTNNYSQEVEIQIGNHGSLRKTDR 268 (374)
T ss_pred EEeccCCCEEEEeCCCceEEECCc
Confidence 75 57999999999999998754
No 17
>PRK12366 replication factor A; Reviewed
Probab=99.35 E-value=6.1e-12 Score=127.30 Aligned_cols=95 Identities=26% Similarity=0.402 Sum_probs=82.7
Q ss_pred ccccccccccc---ccccceEEEEEEEecCCcee--ecCC--cEEEEEEEEeCCCeEEEEEecCCCCC-CCCCCEEEEee
Q psy3603 29 EAMDVYIKDLH---VGIKNVNVTCIVLDISPRVT--LKEN--REVRTLKVADSTACINLSLWDEPGAL-LHPGDIVRLTK 100 (264)
Q Consensus 29 ~~~~ikIkDLk---pG~knVnv~fiVle~~~~r~--TKdG--g~V~tL~LADeTGsI~ltLWdd~ad~-Ik~GDIIrI~n 100 (264)
.+.+.+|++|. ++...|++.++|+++.++++ +++| ..+++++|+|+||+|+++||++.++. +.+||+|.|+|
T Consensus 392 ~~~~~~i~dI~~~~~~~~~VdVig~V~~v~~~~~i~~k~G~~~~~r~i~l~D~TG~I~vtlWg~~a~~~~~~G~vi~i~~ 471 (637)
T PRK12366 392 EEKIYKIKDILNLEEDDNDITVIARVVEDYPVNEFERSDGSKGKVRNIELADGTGSIRLTLWDDDAEIEIKEGDAIKILH 471 (637)
T ss_pred eeccccHHHhhcccCCCcEEEEEEEEEEccCceEEEecCCCEeEEEEEEEEeCCCEEEEEEeccccccCCCCCCEEEEEe
Confidence 34567888886 34446999999999999876 4677 46899999999999999999998875 88999999999
Q ss_pred eEEEEECCEEEEEEcCCceEEEe
Q psy3603 101 CYAQIWRNCLTLYSSKSGLIEKI 123 (264)
Q Consensus 101 gyVs~frG~LqL~Igr~G~IekV 123 (264)
++|+.|+|.++|++++.|.|+..
T Consensus 472 ~~V~~~~g~~~Ls~~~~s~i~~~ 494 (637)
T PRK12366 472 PYVKENGDYLDLSIGRYGRIEIN 494 (637)
T ss_pred eEEEeCCCeeEEEecCcceEEEC
Confidence 99999999999999999998764
No 18
>PRK07211 replication factor A; Reviewed
Probab=99.33 E-value=9.2e-12 Score=123.07 Aligned_cols=92 Identities=23% Similarity=0.346 Sum_probs=83.5
Q ss_pred cccccccccccceEEEEEEEecCCcee-e-cCC--cEEEEEEEEeCCCeEEEEEecCCCCC-CCCCCEEEEeeeEEEEEC
Q psy3603 33 VYIKDLHVGIKNVNVTCIVLDISPRVT-L-KEN--REVRTLKVADSTACINLSLWDEPGAL-LHPGDIVRLTKCYAQIWR 107 (264)
Q Consensus 33 ikIkDLkpG~knVnv~fiVle~~~~r~-T-KdG--g~V~tL~LADeTGsI~ltLWdd~ad~-Ik~GDIIrI~ngyVs~fr 107 (264)
.+|.+|.+++. |++.++|+++.++++ + ++| ..+++++|+|+||+|+++||++.++. +.+||+|+|+|++++.|.
T Consensus 270 ~~I~dl~~g~~-vdV~GvV~~v~~~rtf~r~dG~~~~vr~l~l~D~TG~IrvTLWg~~A~~~i~~GdvV~Ikg~~V~dg~ 348 (485)
T PRK07211 270 TPIESLEIDET-VDIAGVVRSADPKRTFDRDDGSEGQVRNVRIQDDTGDIRVALWGEKADLDIGPGDEVVAADVEIQDGW 348 (485)
T ss_pred ccHhhcCCCCc-eeEEEEEEEccCcEEEEcCCCCEeEEEEEEEEcCCCcEEEEEeCccccCCCCCCCEEEEEccEEEecC
Confidence 67888999995 999999999999987 4 467 47899999999999999999999865 899999999999999986
Q ss_pred -CEEEEEEcCCceEEEecC
Q psy3603 108 -NCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 108 -G~LqL~Igr~G~IekVgE 125 (264)
|.++|++++.+.|..+++
T Consensus 349 ~ggleLS~g~~s~i~~~~~ 367 (485)
T PRK07211 349 QDDLEASAGWQSTVVVLDD 367 (485)
T ss_pred CCCEEEEecCCceEEEccc
Confidence 999999999999988766
No 19
>cd04475 RPA1_DBD_B RPA1_DBD_B: A subfamily of OB folds corresponding to the third OB fold, the ssDNA-binding domain (DBD)-B, 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-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of human RPA (hRPA) and Saccharomyces cerevisiae RPA (ScRPA) is associated with RPA1 DBD-A and DBD-B. 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 functiona
Probab=99.07 E-value=1.2e-09 Score=85.08 Aligned_cols=79 Identities=20% Similarity=0.344 Sum_probs=67.8
Q ss_pred eEEEEEEEecCCcee--ecC-C--cEEEEEEEEeCCC-eEEEEEecCCCCCCCC--CCEEEEeeeEEEEECCEEEEEEcC
Q psy3603 45 VNVTCIVLDISPRVT--LKE-N--REVRTLKVADSTA-CINLSLWDEPGALLHP--GDIVRLTKCYAQIWRNCLTLYSSK 116 (264)
Q Consensus 45 Vnv~fiVle~~~~r~--TKd-G--g~V~tL~LADeTG-sI~ltLWdd~ad~Ik~--GDIIrI~ngyVs~frG~LqL~Igr 116 (264)
|++.++|++++++++ +|+ | ...++++|+|+|| +|.++||++.++.+.. |++|.|.+++++.|+ ...|+.+.
T Consensus 2 vDvig~V~~v~~~~~i~~k~~g~~~~~r~v~i~D~t~~~i~vtLWg~~a~~~~~~~~~vv~~~~~~i~~~~-~~~l~~~~ 80 (101)
T cd04475 2 VDVIGVVKSVGPVTTITTKSTGRELDKREITLVDESGHSVELTLWGEQAELFDGSENPVIAIKGVKVSEFN-GKSLSTGS 80 (101)
T ss_pred EeEEEEEeEccCcEEEEEecCCCceeEEEEEEEeCCCCEEEEEEEHHHhhhcccCCCCEEEEEeeEEEecC-CeEEeecC
Confidence 799999999999876 455 6 5679999999999 9999999998877543 999999999999999 57999998
Q ss_pred CceEEEec
Q psy3603 117 SGLIEKIG 124 (264)
Q Consensus 117 ~G~IekVg 124 (264)
.+.|..-.
T Consensus 81 ~s~i~~np 88 (101)
T cd04475 81 SSTIIINP 88 (101)
T ss_pred ceeEEECC
Confidence 77776533
No 20
>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=99.07 E-value=9.6e-10 Score=87.28 Aligned_cols=73 Identities=15% Similarity=0.175 Sum_probs=63.8
Q ss_pred ccccccccccceEEEEEEEecCCceeecC---CcEEEEEEEEeC-CCeEEEEEecCCCC----CCCCCCEEEEeeeEEEE
Q psy3603 34 YIKDLHVGIKNVNVTCIVLDISPRVTLKE---NREVRTLKVADS-TACINLSLWDEPGA----LLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 34 kIkDLkpG~knVnv~fiVle~~~~r~TKd---Gg~V~tL~LADe-TGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs~ 105 (264)
+|++|.|++.++.+.++|+.+++.+.-++ .+++..+.|.|+ +|+|++++|++.++ .|++|+++.|.++.|+.
T Consensus 1 pI~~L~p~~~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG~vy~i~~~~V~~ 80 (104)
T cd04474 1 PISSLNPYQNKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVGKVYYISKGSVKV 80 (104)
T ss_pred ChhHccCCCCcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccccccEEEEeccEEee
Confidence 58999999999999999999998876322 378999999999 99999999997654 69999999999998876
Q ss_pred E
Q psy3603 106 W 106 (264)
Q Consensus 106 f 106 (264)
-
T Consensus 81 a 81 (104)
T cd04474 81 A 81 (104)
T ss_pred c
Confidence 5
No 21
>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=98.92 E-value=9.8e-09 Score=78.72 Aligned_cols=72 Identities=17% Similarity=0.314 Sum_probs=61.1
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC-------CCCCCCCEEEEeeeEEEEECCEEEEEEcCC
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG-------ALLHPGDIVRLTKCYAQIWRNCLTLYSSKS 117 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a-------d~Ik~GDIIrI~ngyVs~frG~LqL~Igr~ 117 (264)
|.++|+|.++... ..+++++|.|+||+|.+.+|+... +.+++|++|+|. |.++.|+|.+||.+.+
T Consensus 2 v~~vG~V~~~~~~------~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~-G~v~~~~g~~ql~i~~- 73 (95)
T cd04478 2 VTLVGVVRNVEEQ------STNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVF-GNLKSFQGKKSIMAFS- 73 (95)
T ss_pred EEEEEEEEeeeEc------ccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEE-EEEcccCCeeEEEEEE-
Confidence 7889999997643 478999999999999999998442 338999999999 6899999999999986
Q ss_pred ceEEEecCc
Q psy3603 118 GLIEKIGEF 126 (264)
Q Consensus 118 G~IekVgEf 126 (264)
|+++.++
T Consensus 74 --i~~v~d~ 80 (95)
T cd04478 74 --IRPVTDF 80 (95)
T ss_pred --EEEeCCc
Confidence 8877654
No 22
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=98.87 E-value=2e-08 Score=83.50 Aligned_cols=85 Identities=22% Similarity=0.253 Sum_probs=71.2
Q ss_pred ccccccccc--ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCe----EEEEEecCCCCC---CCCCCEEEEeee
Q psy3603 31 MDVYIKDLH--VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTAC----INLSLWDEPGAL---LHPGDIVRLTKC 101 (264)
Q Consensus 31 ~~ikIkDLk--pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGs----I~ltLWdd~ad~---Ik~GDIIrI~ng 101 (264)
.++.|++|. .++. |+++++|+++.++..++.....++++|.|.|+. |.+++|.+..+. +++||||.+++.
T Consensus 2 ~f~~i~~~~~~~~~~-v~vigVV~~~~~p~~s~g~d~~~tl~i~D~S~~~~~~l~v~~F~~~~~~LP~v~~GDVIll~~~ 80 (138)
T cd04497 2 KYTPLSSALKESGGS-VNVIGVVVDAGPPVRSKGTDYCCTLTITDPSLANSDGLTVKLFRPNEESLPIVKVGDIILLRRV 80 (138)
T ss_pred ceEeHHHHHhccCCe-EEEEEEEeecCCCcccCCCcEEEEEEEECCCCCCCCcEEEEEECCChhhCCCCCCCCEEEEEEE
Confidence 467888886 5665 999999999998865543356789999999874 999999976433 688999999999
Q ss_pred EEEEECCEEEEEEcC
Q psy3603 102 YAQIWRNCLTLYSSK 116 (264)
Q Consensus 102 yVs~frG~LqL~Igr 116 (264)
.++.|+|+.++....
T Consensus 81 kv~~~~g~~~~~~~~ 95 (138)
T cd04497 81 KIQSYNGKPQGISND 95 (138)
T ss_pred EEEEECCceEEEECC
Confidence 999999999998876
No 23
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=98.84 E-value=8.3e-09 Score=99.14 Aligned_cols=117 Identities=23% Similarity=0.295 Sum_probs=97.7
Q ss_pred CcccccccccccccccceEEEEEEEecCCcee--ecCC--cEEEEEEEEeCCCeEEE-EEecCCCC-CCCCCCEEEEeee
Q psy3603 28 KEAMDVYIKDLHVGIKNVNVTCIVLDISPRVT--LKEN--REVRTLKVADSTACINL-SLWDEPGA-LLHPGDIVRLTKC 101 (264)
Q Consensus 28 ~~~~~ikIkDLkpG~knVnv~fiVle~~~~r~--TKdG--g~V~tL~LADeTGsI~l-tLWdd~ad-~Ik~GDIIrI~ng 101 (264)
..++..+|.++.+++.++++++.|++...+.. ++.| +.+.+.+++|+||++.+ ++|...+. .+++||+++|.++
T Consensus 45 ~~~~~~~i~~~~~~~~~~~v~~~V~~~~e~~~~~~k~g~~~~l~~~~v~Detg~v~~~~~~~~~a~~~~e~Gdv~~i~~~ 124 (407)
T COG1599 45 AMESIGKISDISEASSRVNVTGRVLSIGEKKTFDRKRGAEGKLAEVLVGDETGSVKTVTLWNIAALEKLEPGDVIRIRNA 124 (407)
T ss_pred chhhcccccccchhhccccEEEEECccccceeeecccccccceEEEEEecCCCCEEEEeeccccccccCCccceEEecCc
Confidence 45566899999999989999999999997763 4555 68899999999999999 79998876 6899999999999
Q ss_pred EEEEECCEEEEEEcCCceEEEecCceeeecCCCCCCCCCCCCC
Q psy3603 102 YAQIWRNCLTLYSSKSGLIEKIGEFCMVFNENLDMSIPIPNLP 144 (264)
Q Consensus 102 yVs~frG~LqL~Igr~G~IekVgEf~~~fnE~pNiSe~~Pe~~ 144 (264)
++..|+|..++++++.+.+..++++.+...+..+..+..+...
T Consensus 125 ~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~i~~~~~ 167 (407)
T COG1599 125 YTSLYRGGKRLSVGRVGSVADVDDEEDEARESEDAREIGEESL 167 (407)
T ss_pred ccccccCceeeecccccccccCchhhccccccccccccccccc
Confidence 9999999999999999999998887655555544444444443
No 24
>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=98.78 E-value=3.5e-08 Score=77.67 Aligned_cols=64 Identities=20% Similarity=0.345 Sum_probs=53.9
Q ss_pred EEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC------------------------CCCCCCCEEEEeee
Q psy3603 46 NVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG------------------------ALLHPGDIVRLTKC 101 (264)
Q Consensus 46 nv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a------------------------d~Ik~GDIIrI~ng 101 (264)
+++++|.++.+. .+++.++|.|.||+|.+++|.... +.|++|++|+|+ |
T Consensus 1 ~ivG~V~sv~~~------~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G~vvrV~-G 73 (92)
T cd04483 1 DILGTVVSRRER------ETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIGDLLRVR-G 73 (92)
T ss_pred CeEEEEEEEEec------CCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCCCEEEEE-E
Confidence 467888887644 368999999999999999998442 238999999999 6
Q ss_pred EEEEECCEEEEEEcC
Q psy3603 102 YAQIWRNCLTLYSSK 116 (264)
Q Consensus 102 yVs~frG~LqL~Igr 116 (264)
.++.|+|.+||++..
T Consensus 74 ~i~~frg~~ql~i~~ 88 (92)
T cd04483 74 SIRTYRGEREINASV 88 (92)
T ss_pred EEeccCCeeEEEEEE
Confidence 899999999999874
No 25
>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=98.73 E-value=1.1e-07 Score=69.59 Aligned_cols=73 Identities=26% Similarity=0.383 Sum_probs=59.9
Q ss_pred EEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC---CCCCCCCEEEEeeeEEEEECCEEEEEEcCCceEEEe
Q psy3603 47 VTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG---ALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKI 123 (264)
Q Consensus 47 v~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a---d~Ik~GDIIrI~ngyVs~frG~LqL~Igr~G~IekV 123 (264)
..|+|.++... .+|+|++++.++|.|.||.|.+++|++.. ..+++|.+|.|. |.++.|+|.++|.+.+ |..+
T Consensus 2 ~~~~v~~~~~~-~tk~g~~~~~~~l~D~tg~i~~~~f~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~~~---i~~l 76 (83)
T cd04492 2 GFFLIKSKELR-TAKNGKPYLALTLQDKTGEIEAKLWDASEEDEEKFKPGDIVHVK-GRVEEYRGRLQLKIQR---IRLV 76 (83)
T ss_pred cEEEEEEeeee-cccCCCcEEEEEEEcCCCeEEEEEcCCChhhHhhCCCCCEEEEE-EEEEEeCCceeEEEEE---EEEC
Confidence 45778887644 57888899999999999999999999553 459999999999 6899899999998875 5554
Q ss_pred c
Q psy3603 124 G 124 (264)
Q Consensus 124 g 124 (264)
.
T Consensus 77 ~ 77 (83)
T cd04492 77 T 77 (83)
T ss_pred C
Confidence 4
No 26
>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=98.73 E-value=3.4e-08 Score=71.01 Aligned_cols=66 Identities=26% Similarity=0.374 Sum_probs=55.5
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC----CCCCCCCCEEEEeeeEEEEECCE-EEEEEcC
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP----GALLHPGDIVRLTKCYAQIWRNC-LTLYSSK 116 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~----ad~Ik~GDIIrI~ngyVs~frG~-LqL~Igr 116 (264)
|.+.++|.++. +.++++..++|.|+||+|.+.+|++. .+.|++||+|+|+ |.++.|++. ++|.+.+
T Consensus 1 V~v~G~V~~~~-----~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~~l~~~~ 71 (75)
T PF01336_consen 1 VTVEGRVTSIR-----RSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVR-GKVKRYNGGELELIVPK 71 (75)
T ss_dssp EEEEEEEEEEE-----EEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEE-EEEEEETTSSEEEEEEE
T ss_pred CEEEEEEEEEE-----cCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEE-EEEEEECCccEEEEECE
Confidence 56788888876 44578999999999999999999932 3559999999999 789999987 9999886
No 27
>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=98.57 E-value=2.2e-07 Score=94.19 Aligned_cols=95 Identities=14% Similarity=0.138 Sum_probs=81.5
Q ss_pred cccccccccccccceEEEEEEEecCCcee--ecCC-cEEEEEEEEeCCCeEEEEEecCCC----CCCCCCCEEEEeeeEE
Q psy3603 31 MDVYIKDLHVGIKNVNVTCIVLDISPRVT--LKEN-REVRTLKVADSTACINLSLWDEPG----ALLHPGDIVRLTKCYA 103 (264)
Q Consensus 31 ~~ikIkDLkpG~knVnv~fiVle~~~~r~--TKdG-g~V~tL~LADeTGsI~ltLWdd~a----d~Ik~GDIIrI~ngyV 103 (264)
...+|++|.|++.+..+.++|+.+.+.+. ..+| +++.++.|.|++|.|++++|++.+ +.|++|+++.|.++.+
T Consensus 179 ~~~pI~~L~py~~~wtIkaRV~~Ks~ir~~~~~~gegkvfsv~L~Degg~Irat~f~~~~dkf~~~l~eG~VY~Is~~~V 258 (608)
T TIGR00617 179 RVMPIASLSPYQNKWTIKARVTNKSEIRTWSNARGEGKLFNVELLDESGEIRATAFNEQADKFYDIIQEGKVYYISKGSL 258 (608)
T ss_pred ceEEHHHCCCCCCceEEEEEEEeccccceecCCCCCceeeEEEEecCCCeEEEEECchHHHHHhhhcccCCEEEECceEE
Confidence 57899999999989999999999998876 2344 689999999999999999999865 4589999999999999
Q ss_pred EEEC-------CEEEEEEcCCceEEEecC
Q psy3603 104 QIWR-------NCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 104 s~fr-------G~LqL~Igr~G~IekVgE 125 (264)
+..+ ...+|.+++++.|++..+
T Consensus 259 k~an~~y~~~~~~yei~f~~~T~I~~~~d 287 (608)
T TIGR00617 259 KPANKQFTNLGNDYEMTLDRDTVIEECED 287 (608)
T ss_pred EEccccccCCCCCEEEEECCCeEEEECCC
Confidence 8653 468999999999988643
No 28
>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=98.47 E-value=3.7e-07 Score=65.81 Aligned_cols=68 Identities=16% Similarity=0.245 Sum_probs=56.1
Q ss_pred EEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC----CCCCCCCCEEEEeeeEEEEECCEEEEEEcC
Q psy3603 47 VTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP----GALLHPGDIVRLTKCYAQIWRNCLTLYSSK 116 (264)
Q Consensus 47 v~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~----ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr 116 (264)
+.++|.++.. +.+|+|++++.++|.|.||.+.+++|++. .+.+++|.+|.|. |.+..|+|.++|.+.+
T Consensus 2 i~g~v~~~~~-~~~k~g~~~~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g~~v~v~-G~v~~~~~~~~l~~~~ 73 (84)
T cd04485 2 VAGLVTSVRR-RRTKKGKRMAFVTLEDLTGSIEVVVFPETYEKYRDLLKEDALLLVE-GKVERRDGGLRLIAER 73 (84)
T ss_pred EEEEEEEeEE-EEcCCCCEEEEEEEEeCCCeEEEEECHHHHHHHHHHhcCCCEEEEE-EEEEecCCceEEEeec
Confidence 4566776543 35678889999999999999999999854 2458999999999 6899999999999875
No 29
>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=98.45 E-value=7.7e-07 Score=90.26 Aligned_cols=93 Identities=19% Similarity=0.266 Sum_probs=74.9
Q ss_pred ccccccccccccc--ccceEEEEEEEecCCcee-e-c-CCc--EEEEEEEEeCCC-eEEEEEecCCCCC--CCCCCEEEE
Q psy3603 29 EAMDVYIKDLHVG--IKNVNVTCIVLDISPRVT-L-K-ENR--EVRTLKVADSTA-CINLSLWDEPGAL--LHPGDIVRL 98 (264)
Q Consensus 29 ~~~~ikIkDLkpG--~knVnv~fiVle~~~~r~-T-K-dGg--~V~tL~LADeTG-sI~ltLWdd~ad~--Ik~GDIIrI 98 (264)
.+.+++|.||... ...|+++++|.++++..+ + | +|. ..++++|.|.|| +|+++||++.+.. ..+|+||.|
T Consensus 295 ~~~f~~i~dI~~~~~~~~VDVIGvV~~v~~~~~i~~k~~g~~~~kR~i~L~D~sg~sI~vTLWG~~A~~~~~~~~~Vva~ 374 (608)
T TIGR00617 295 QFNFVKIDDIGGYEGNSLVDVIGIVQSVSPTQTITSRKNNKEFPKRDITLVDDSGKSVRVTLWGDDATKFDVSVQPVIAI 374 (608)
T ss_pred cccceEHHHhhhhcCCCCccEEEEEeEecCceEEEEcCCCCeeeeEEEEEEeCCCCEEEEEEEhhhhhhcCCCCCCEEEE
Confidence 4567888998543 235999999999998876 2 3 553 558999999999 6999999998755 458999999
Q ss_pred eeeEEEEECCEEEEEEcCCceEEE
Q psy3603 99 TKCYAQIWRNCLTLYSSKSGLIEK 122 (264)
Q Consensus 99 ~ngyVs~frG~LqL~Igr~G~Iek 122 (264)
++++++.|+| +.|+.+..+.|..
T Consensus 375 kg~~V~~f~g-~sLs~~~~S~i~i 397 (608)
T TIGR00617 375 KGVRVSDFGG-KSLSTGGSSTIIV 397 (608)
T ss_pred EeEEEEecCC-ceEeccCCceEEE
Confidence 9999999955 6899888777654
No 30
>PF02765 POT1: Telomeric single stranded DNA binding POT1/CDC13; InterPro: IPR011564 This entry represents a domain that binds single stranded telomeric DNA and adopts an OB fold []. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping [, , ]. ; GO: 0003677 DNA binding, 0000723 telomere maintenance, 0000784 nuclear chromosome, telomeric region; PDB: 1S40_A 1KXL_A 1PH7_A 1PH9_A 1PH2_A 1OTC_A 1PHJ_A 1JB7_A 1PA6_A 1PH1_A ....
Probab=98.27 E-value=6.4e-06 Score=68.96 Aligned_cols=80 Identities=23% Similarity=0.336 Sum_probs=65.5
Q ss_pred cccccccceEEEEEEEecCCc--eeecCCcEEEEEEEEeCC--------CeEEEEEecCCC---CCCCC-CCEEEEeeeE
Q psy3603 37 DLHVGIKNVNVTCIVLDISPR--VTLKENREVRTLKVADST--------ACINLSLWDEPG---ALLHP-GDIVRLTKCY 102 (264)
Q Consensus 37 DLkpG~knVnv~fiVle~~~~--r~TKdGg~V~tL~LADeT--------GsI~ltLWdd~a---d~Ik~-GDIIrI~ngy 102 (264)
..+.+.. +++.++|++...+ ..+|....+++++|.|+| -.|.+.++-... ..++. ||||++++..
T Consensus 8 ~~~~~~~-vnvigVV~~~~~p~~~~t~g~D~~~tl~i~D~S~~~~~~~~~~l~v~iF~~~~~~LP~v~~~GDii~l~r~k 86 (146)
T PF02765_consen 8 KEKFGKF-VNVIGVVVDFSPPNPKKTRGTDYMCTLTITDPSLNDSNQKLSGLTVNIFRPHKESLPNVKSVGDIIRLRRVK 86 (146)
T ss_dssp CTTSSEE-EEEEEEEEEEEEECTEEESSSCEEEEEEEEBTTCSCSSCCCCEEEEEEEESSHHHSCTTCSTTHEEEEEEEE
T ss_pred hhcCCCE-EEEEEEEEEccCCcceEcCCCcEEEEEEEECCCCCccccccCCEEEEEECCCHHHCCCCCCCCCEEEEEEEE
Confidence 4455665 9999999999988 666666778999999997 479999996442 23555 9999999999
Q ss_pred EEEECCEEEEEEcCC
Q psy3603 103 AQIWRNCLTLYSSKS 117 (264)
Q Consensus 103 Vs~frG~LqL~Igr~ 117 (264)
++.|+|++++..+..
T Consensus 87 v~~~~~~~~~~~~~~ 101 (146)
T PF02765_consen 87 VQSYNGKPQGLSNST 101 (146)
T ss_dssp EEEETTEEEEEEECE
T ss_pred EEEECCEEEEEecCC
Confidence 999999999988763
No 31
>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=98.27 E-value=7.6e-06 Score=56.51 Aligned_cols=66 Identities=23% Similarity=0.352 Sum_probs=55.2
Q ss_pred EEEEEEecCCceeecCCcEEEEEEEEeCC-CeEEEEEecCCC----CCCCCCCEEEEeeeEEEEECCEEEEEEcC
Q psy3603 47 VTCIVLDISPRVTLKENREVRTLKVADST-ACINLSLWDEPG----ALLHPGDIVRLTKCYAQIWRNCLTLYSSK 116 (264)
Q Consensus 47 v~fiVle~~~~r~TKdGg~V~tL~LADeT-GsI~ltLWdd~a----d~Ik~GDIIrI~ngyVs~frG~LqL~Igr 116 (264)
+.+.|.++.... + |+.+..++|.|.| |+|.+.+|.+.. ..+++|++|.|. |.++.+++.++|.+.+
T Consensus 2 v~g~v~~~~~~~-~--~~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g~~v~v~-g~v~~~~~~~~l~~~~ 72 (75)
T cd03524 2 IVGIVVAVEEIR-T--EGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEGQVVYIK-GKVKKFRGRLQLIVES 72 (75)
T ss_pred eEEEEEeecccc-c--CCeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCCCEEEEE-EEEEecCCeEEEEeee
Confidence 578888887553 2 6789999999999 999999998654 348999999999 7899999999998763
No 32
>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=98.19 E-value=2e-05 Score=57.90 Aligned_cols=66 Identities=17% Similarity=0.185 Sum_probs=53.7
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC----CCCCCCCEEEEeeeEEEEE--CCEEEEEEcC
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG----ALLHPGDIVRLTKCYAQIW--RNCLTLYSSK 116 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a----d~Ik~GDIIrI~ngyVs~f--rG~LqL~Igr 116 (264)
+-+.+.|.++.. +|.| +.-++|.|.+|+|.+.+|.+.. +.+++|++|.|+ |.+..+ +|.++|.+.+
T Consensus 2 ~~v~g~v~~i~~---tk~g--~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g~~v~v~-g~v~~~~~~~~~~l~v~~ 73 (78)
T cd04489 2 VWVEGEISNLKR---PSSG--HLYFTLKDEDASIRCVMWRSNARRLGFPLEEGMEVLVR-GKVSFYEPRGGYQLIVEE 73 (78)
T ss_pred EEEEEEEecCEE---CCCc--EEEEEEEeCCeEEEEEEEcchhhhCCCCCCCCCEEEEE-EEEEEECCCCEEEEEEEE
Confidence 456777887653 5666 9999999999999999998643 458999999999 678877 4889999875
No 33
>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=98.15 E-value=1.8e-05 Score=56.13 Aligned_cols=67 Identities=21% Similarity=0.368 Sum_probs=52.4
Q ss_pred EEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEec-CC--CCCCCCCCEEEEeeeEEEEECCEEEEEEcC
Q psy3603 47 VTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWD-EP--GALLHPGDIVRLTKCYAQIWRNCLTLYSSK 116 (264)
Q Consensus 47 v~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWd-d~--ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr 116 (264)
+.++|.++...+ ++ +..++.+++.|++|.|.++.|+ .. ...+++|+.+.+. |.++.|+|.+||.--+
T Consensus 2 i~~~V~~~~~~~-~~-~~~~~~~~~~D~~g~i~~~~F~~~~~~~~~~~~G~~~~v~-Gkv~~~~~~~qi~~P~ 71 (75)
T cd04488 2 VEGTVVSVEVVP-RR-GRRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPGTRVRVS-GKVKRFRGGLQIVHPE 71 (75)
T ss_pred EEEEEEEEEecc-CC-CccEEEEEEEcCCCEEEEEEECCCHHHHhcCCCCCEEEEE-EEEeecCCeeEEeCCc
Confidence 456677764332 23 5679999999999999999998 32 3459999999999 6899999999987553
No 34
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=97.81 E-value=2.9e-05 Score=84.03 Aligned_cols=80 Identities=21% Similarity=0.286 Sum_probs=66.7
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC----CCCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP----GALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~----ad~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
.+.. |.+.++|.++... .||+|.++..++|.|.||+|.+++|.+. .+.|++|.+|.|. |.+..+++.++|.+.
T Consensus 976 ~g~~-V~v~G~I~~vk~~-~TKkG~~mafltLeD~TG~iEvviFp~~ye~~~~~L~~g~iV~V~-GkVe~~~~~~qlii~ 1052 (1135)
T PRK05673 976 GGSV-VTVAGLVVSVRRR-VTKRGNKMAIVTLEDLSGRIEVMLFSEALEKYRDLLEEDRIVVVK-GQVSFDDGGLRLTAR 1052 (1135)
T ss_pred cCce-EEEEEEEEEEEec-ccCCCCeEEEEEEEeCCCcEEEEECHHHHHHHHHHhccCCEEEEE-EEEEecCCeEEEEEe
Confidence 4554 9999999998755 5788999999999999999999999855 2458999999999 678888899999988
Q ss_pred CCceEEEecC
Q psy3603 116 KSGLIEKIGE 125 (264)
Q Consensus 116 r~G~IekVgE 125 (264)
+ |..+.+
T Consensus 1053 ~---I~~L~~ 1059 (1135)
T PRK05673 1053 E---VMDLEE 1059 (1135)
T ss_pred e---cccHHH
Confidence 6 555443
No 35
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=97.57 E-value=0.00015 Score=71.65 Aligned_cols=114 Identities=15% Similarity=0.168 Sum_probs=77.5
Q ss_pred hhhhhhccCCCcccceeeeeecccccCcccccccccc---cccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeE
Q psy3603 2 WEKKLAGSHPEKNHGMRAERKEINRKKEAMDVYIKDL---HVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACI 78 (264)
Q Consensus 2 ~~~~~~~~~~~~~h~~~~e~~~i~~~~~~~~ikIkDL---kpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI 78 (264)
||||+-|.. .+.|=|..-+..+..- ....+.+| ..+. .|.+.++|.++... .||.|.++.-++|.|.||.|
T Consensus 242 ~EkE~LGfy-lS~HPl~~~~~~l~~~---~~~~~~~l~~~~~~~-~v~vaG~I~~ik~~-~TKkG~~maf~~leD~tG~i 315 (449)
T PRK07373 242 LEKELLGFY-VSEHPLKSIRRPARLL---SPINLSELEEQKEKT-KVSAVVMLNEVKKI-VTKKGDPMAFLQLEDLSGQS 315 (449)
T ss_pred HHHHHhccc-cCcCchHHHHHHHHHc---CCcCHHHHhcccCCC-EEEEEEEEEEeEec-ccCCCCEEEEEEEEECCCCE
Confidence 567766643 3444433222222111 11234444 3455 49999999998755 57889999999999999999
Q ss_pred EEEEecCCC----CCCCCCCEEEEeeeEEEEECCEEEEEEcCCceEEEecC
Q psy3603 79 NLSLWDEPG----ALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 79 ~ltLWdd~a----d~Ik~GDIIrI~ngyVs~frG~LqL~Igr~G~IekVgE 125 (264)
.+++|.+.. +.+++|.+|.|. |.+....+.++|.+.+ |..+.+
T Consensus 316 e~vvFp~~y~~~~~~l~~~~~v~v~-G~v~~~~~~~~liv~~---i~~l~~ 362 (449)
T PRK07373 316 EAVVFPKSYERISELLQVDARLIIW-GKVDRRDDQVQLIVED---AEPIEE 362 (449)
T ss_pred EEEECHHHHHHHHHHhccCCEEEEE-EEEEecCCeEEEEEeE---eecHhh
Confidence 999997543 458999999999 5787645778888876 555444
No 36
>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=97.42 E-value=0.0022 Score=49.28 Aligned_cols=71 Identities=31% Similarity=0.356 Sum_probs=56.6
Q ss_pred ceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecC-CC---CCCC-CCCEEEEeeeEEEE--ECCEEEEEEcC
Q psy3603 44 NVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDE-PG---ALLH-PGDIVRLTKCYAQI--WRNCLTLYSSK 116 (264)
Q Consensus 44 nVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd-~a---d~Ik-~GDIIrI~ngyVs~--frG~LqL~Igr 116 (264)
+|.+.|.|-.+.. +++|.|+.++++.|.|.|++|.+++|.. .. +.|+ +|+.|+++| .+.. |.+++.|.+..
T Consensus 1 ~v~i~G~Vf~~e~-re~k~g~~i~~~~itD~t~Si~~K~F~~~~~~~~~~ik~~G~~v~v~G-~v~~D~f~~e~~~~i~~ 78 (82)
T cd04484 1 NVVVEGEVFDLEI-RELKSGRKILTFKVTDYTSSITVKKFLRKDEKDKEELKSKGDWVRVRG-KVQYDTFSKELVLMIND 78 (82)
T ss_pred CEEEEEEEEEEEE-EEecCCCEEEEEEEEcCCCCEEEEEeccCChhHHhhcccCCCEEEEEE-EEEEccCCCceEEEeee
Confidence 3678888888764 4788999999999999999999999983 21 3488 999999994 5653 55888887764
No 37
>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=97.27 E-value=0.0024 Score=48.95 Aligned_cols=55 Identities=16% Similarity=0.297 Sum_probs=46.0
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCC------CCCCCCEEEEeeeEEEE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGA------LLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad------~Ik~GDIIrI~ngyVs~ 105 (264)
+.+.++|.++. .||+|++ .++|.|.||++.+.+|.+..+ .+++|.+|.|+ |.+..
T Consensus 2 v~i~GiI~~v~---~TK~g~~--~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d~~v~v~-g~v~~ 62 (79)
T cd04490 2 VSIIGMVNDVR---STKNGHR--IVELEDTTGRITVLLTKDKEELFEEAEDILPDEVIGVS-GTVSK 62 (79)
T ss_pred EEEEEEEeEEE---EcCCCCE--EEEEECCCCEEEEEEeCchhhhhhhhhhccCCCEEEEE-EEEec
Confidence 66788999987 5688877 999999999999999986655 58999999999 46654
No 38
>cd04481 RPA1_DBD_B_like RPA1_DBD_B_like: A subgroup of uncharacterized, plant OB folds with similarity to the third OB fold, the ssDNA-binding domain (DBD)-B, 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-B, RPA1 contains three other OB folds: DBD-A, DBD-C, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change.
Probab=97.26 E-value=0.0011 Score=52.45 Aligned_cols=70 Identities=17% Similarity=0.278 Sum_probs=53.8
Q ss_pred EEEEEEEecCCceee-cCC--cEEEEEEEEeCCC-eEEEEEecCCCCC--------CCCCCEEEEee-eEEEEECCEEEE
Q psy3603 46 NVTCIVLDISPRVTL-KEN--REVRTLKVADSTA-CINLSLWDEPGAL--------LHPGDIVRLTK-CYAQIWRNCLTL 112 (264)
Q Consensus 46 nv~fiVle~~~~r~T-KdG--g~V~tL~LADeTG-sI~ltLWdd~ad~--------Ik~GDIIrI~n-gyVs~frG~LqL 112 (264)
++.+.|.++++.... ..| ...+.+.|.|.+| ++.++||++.|.. .+.+=||-|.. ++++.|+|..-|
T Consensus 1 DviG~i~~v~~~~~~~~~~~~~~kr~~~i~D~~~~~l~~tlwG~~A~~f~~~~~~~~~~~~VVav~~~~rV~~~~g~~~l 80 (106)
T cd04481 1 DVIGVIVDVGPLEELPPVNKPSRKLDFEIRDLSDERLKCTLWGEYAEEFDAKFQSAGNGEPVVAVLRFWKIKEYKGPKSL 80 (106)
T ss_pred CeeEEEEEecceEecccCCccceEEEEEEEeCCCCEEEEEEEHHHHHHHHHHHHHhCCCCcEEEEEEeEEEEEEcCCcEE
Confidence 578999999987652 224 5679999999997 7999999987644 24566787765 999999996666
Q ss_pred EEc
Q psy3603 113 YSS 115 (264)
Q Consensus 113 ~Ig 115 (264)
.-+
T Consensus 81 s~~ 83 (106)
T cd04481 81 SNS 83 (106)
T ss_pred EcC
Confidence 655
No 39
>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=97.19 E-value=0.005 Score=46.67 Aligned_cols=63 Identities=21% Similarity=0.277 Sum_probs=46.6
Q ss_pred EEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC----CCCCCCCEEEEeeeEEEEECCEEEEEEcC
Q psy3603 47 VTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG----ALLHPGDIVRLTKCYAQIWRNCLTLYSSK 116 (264)
Q Consensus 47 v~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a----d~Ik~GDIIrI~ngyVs~frG~LqL~Igr 116 (264)
+.+.|.+... +.|+-|. +|.|++++|.+.+|.... ..+++||-|.+.| .+...+|++||.+.+
T Consensus 3 v~GeVs~~~~----~~GHvyf--sLkD~~a~i~cv~f~~~~~~~~~~l~~Gd~V~v~G-~v~~~~G~~ql~v~~ 69 (73)
T cd04487 3 IEGEVVQIKQ----TSGPTIF--TLRDETGTVWAAAFEEAGVRAYPEVEVGDIVRVTG-EVEPRDGQLQIEVES 69 (73)
T ss_pred EEEEEecccc----CCCCEEE--EEEcCCEEEEEEEEchhccCCcCCCCCCCEEEEEE-EEecCCeEEEEEEee
Confidence 4555555431 4556555 458999999999997543 2378999999995 687788999999886
No 40
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=96.86 E-value=0.002 Score=70.32 Aligned_cols=80 Identities=10% Similarity=0.121 Sum_probs=64.5
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC----CCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG----ALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a----d~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
.+. .|.+.+.|.++..+ .||+|.++.-++|.|.||.+.+++|.+.. ..+++|.+|.|. |.+..-.+.++|.+.
T Consensus 999 ~~~-~v~v~g~i~~~k~~-~Tk~G~~maf~~leD~tg~~e~vvFp~~y~~~~~~l~~~~~~~v~-g~v~~~~~~~~~~~~ 1075 (1170)
T PRK07374 999 DKA-KVSAIAMIPEMKQV-TTRKGDRMAILQLEDLTGSCEAVVFPKSYERLSDHLMTDTRLLVW-AKVDRRDDRVQLIID 1075 (1170)
T ss_pred CCC-EEEEEEEEEEeEec-ccCCCCEEEEEEEEECCCCEEEEECHHHHHHHHHHhccCCEEEEE-EEEEecCCeEEEEEe
Confidence 455 49999999998755 57889999999999999999999997542 458999999998 578765588899887
Q ss_pred CCceEEEecC
Q psy3603 116 KSGLIEKIGE 125 (264)
Q Consensus 116 r~G~IekVgE 125 (264)
+ |..+.+
T Consensus 1076 ~---i~~l~~ 1082 (1170)
T PRK07374 1076 D---CREIDD 1082 (1170)
T ss_pred e---eecHhh
Confidence 6 555443
No 41
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=96.62 E-value=0.0031 Score=68.23 Aligned_cols=81 Identities=17% Similarity=0.206 Sum_probs=62.2
Q ss_pred cccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC----CCCCCCCEEEEeeeEEEEECCEEEE
Q psy3603 37 DLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG----ALLHPGDIVRLTKCYAQIWRNCLTL 112 (264)
Q Consensus 37 DLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a----d~Ik~GDIIrI~ngyVs~frG~LqL 112 (264)
++..+.. |.+.++|..+..+ .||+| +.-++|.|.||.+.+++|.+.. ..+++|.++.|. |.++..++.++|
T Consensus 949 ~~~~~~~-v~v~g~i~~~~~~-~TkkG--maf~~leD~~g~~e~~ifp~~~~~~~~~l~~~~~~~v~-g~v~~~~~~~~~ 1023 (1046)
T PRK05672 949 DVEDGRR-VRVAGVVTHRQRP-GTASG--VTFLTLEDETGMVNVVVWPGLWERQRREALGARLLLVR-GRVQNAEGVRHL 1023 (1046)
T ss_pred hccCCCE-EEEEEEEEEEEEe-cCCCc--eEEEEEecCCCCEEEEECHHHHHHHHHHhccCCEEEEE-EEEEecCCeEEE
Confidence 4455664 8888888887644 46777 8999999999999999998643 458999999998 578766777888
Q ss_pred EEcCCceEEEecC
Q psy3603 113 YSSKSGLIEKIGE 125 (264)
Q Consensus 113 ~Igr~G~IekVgE 125 (264)
.+.+ |..+++
T Consensus 1024 ~~~~---i~~~~~ 1033 (1046)
T PRK05672 1024 VADR---LEDLSP 1033 (1046)
T ss_pred EEee---eechHH
Confidence 8775 544433
No 42
>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=96.58 E-value=0.029 Score=43.94 Aligned_cols=56 Identities=23% Similarity=0.211 Sum_probs=42.4
Q ss_pred cCCcEEEEEEEEeCCCeEEEEEecCC--C----CCCCCCCEEEEeeeEEEEECCEEEEEEcCCceEEEecC
Q psy3603 61 KENREVRTLKVADSTACINLSLWDEP--G----ALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 61 KdGg~V~tL~LADeTGsI~ltLWdd~--a----d~Ik~GDIIrI~ngyVs~frG~LqL~Igr~G~IekVgE 125 (264)
+.|+.|.+ |.|+++.|.+.+|... . ..+++||.|.+. |.++.|. ||++.+ |+..+.
T Consensus 15 ~sGH~yFt--lkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~-G~v~~y~---ql~ve~---l~~~gl 76 (91)
T cd04482 15 EGGHVFFK--ISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVY-GSVRPGT---TLNLEK---LRVIRL 76 (91)
T ss_pred CCCCEEEE--EECCCcEEEEEEECcccccccccCCCCCCCEEEEE-EEEecCC---EEEEEE---EEECCC
Confidence 45665555 5699999999999765 2 237899999999 5688887 888886 666544
No 43
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=96.53 E-value=0.011 Score=60.63 Aligned_cols=83 Identities=23% Similarity=0.232 Sum_probs=65.8
Q ss_pred cccccccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEec--CC--CCCCCCCCEEEEeeeEEE
Q psy3603 29 EAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWD--EP--GALLHPGDIVRLTKCYAQ 104 (264)
Q Consensus 29 ~~~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWd--d~--ad~Ik~GDIIrI~ngyVs 104 (264)
.....+|.++.+|+. +.+.+.|.+..... + +..++.+.+.|+||.|.++.|. .. ...|++|+.+.|+ |.++
T Consensus 47 ~~~~~~i~~l~~g~~-vtv~g~V~~~~~~~--~-~~~~~~v~l~D~tg~i~l~~F~~n~~~~~~~l~~G~~~~v~-Gkv~ 121 (681)
T PRK10917 47 RTRLKPIAELRPGEK-VTVEGEVLSAEVVF--G-KRRRLTVTVSDGTGNLTLRFFNFNQPYLKKQLKVGKRVAVY-GKVK 121 (681)
T ss_pred cCCcCCHHHCCCCCE-EEEEEEEEEEEEcc--C-CceEEEEEEEECCeEEEEEEEccCcHHHHhhCCCCCEEEEE-EEEE
Confidence 333468889999996 99999999874332 2 5678999999999999999993 33 3559999999999 5788
Q ss_pred EECCEEEEEEcC
Q psy3603 105 IWRNCLTLYSSK 116 (264)
Q Consensus 105 ~frG~LqL~Igr 116 (264)
.++|.+|+.--.
T Consensus 122 ~~~~~~qm~~P~ 133 (681)
T PRK10917 122 RGKYGLEMVHPE 133 (681)
T ss_pred ecCCeEEEEcCE
Confidence 888888886554
No 44
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=96.52 E-value=0.0083 Score=54.22 Aligned_cols=74 Identities=16% Similarity=0.148 Sum_probs=57.5
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCC---------CCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGA---------LLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad---------~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
+.+++.|++... ..|.-+..+.+-|.||+|.+.+....++ .+.+|++|.|. |.+++|||..++.+.
T Consensus 54 v~vkg~V~~~~n----~~~~gi~~l~lndgtGti~vva~~~tee~l~~n~~~p~~~eGe~veVt-Grv~~yrG~~eVkvn 128 (204)
T COG4085 54 VTVKGEVTADQN----AIGGGIESLVLNDGTGTITVVASRSTEETLELNEGMPVTVEGEIVEVT-GRVEEYRGSSEVKVN 128 (204)
T ss_pred ceeeeEEEeeec----ccccceEEEEEECCCCcEEEEEecChhHhHhhcCCCCccccCcEEEEE-EEEEEeCCCceeecc
Confidence 456666666543 3567789999999999999999975432 36799999999 689999999999998
Q ss_pred CCceEEEe
Q psy3603 116 KSGLIEKI 123 (264)
Q Consensus 116 r~G~IekV 123 (264)
.--.++..
T Consensus 129 q~~d~~~l 136 (204)
T COG4085 129 QPNDSRPL 136 (204)
T ss_pred Cccccccc
Confidence 74444443
No 45
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=96.51 E-value=0.0049 Score=67.31 Aligned_cols=74 Identities=16% Similarity=0.238 Sum_probs=60.4
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC----CCCCCCCCEEEEeeeEEEEE-CCEEEEEE
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP----GALLHPGDIVRLTKCYAQIW-RNCLTLYS 114 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~----ad~Ik~GDIIrI~ngyVs~f-rG~LqL~I 114 (264)
.+. .|.+.++|.++... .||.|.++..++|.|.||.+.+++|.+. ...+++|.+|.|. |.+... ++.++|.+
T Consensus 990 ~~~-~v~v~g~i~~~~~~-~tk~G~~maf~~leD~~g~~e~~vfp~~~~~~~~~l~~~~~~~v~-g~v~~~~~~~~~~~~ 1066 (1151)
T PRK06826 990 DGD-KVIIGGIITEVKRK-TTRNNEMMAFLTLEDLYGTVEVIVFPKVYEKYRSLLNEDNIVLIK-GRVSLREDEEPKLIC 1066 (1151)
T ss_pred CCc-EEEEEEEEEEeEee-ccCCCCeEEEEEEEECCCcEEEEECHHHHHHHHHHhccCCEEEEE-EEEEecCCCceEEEE
Confidence 455 48899999998754 5788999999999999999999999854 2458999999999 578754 56788887
Q ss_pred cC
Q psy3603 115 SK 116 (264)
Q Consensus 115 gr 116 (264)
.+
T Consensus 1067 ~~ 1068 (1151)
T PRK06826 1067 EE 1068 (1151)
T ss_pred ee
Confidence 75
No 46
>COG3481 Predicted HD-superfamily hydrolase [General function prediction only]
Probab=96.50 E-value=0.001 Score=62.83 Aligned_cols=59 Identities=19% Similarity=0.313 Sum_probs=51.4
Q ss_pred eecCCcEEEEEEEEeCCCeEEEEEecCC---CCCCCCCCEEEEeeeEEEEECCEEEEEEcCCc
Q psy3603 59 TLKENREVRTLKVADSTACINLSLWDEP---GALLHPGDIVRLTKCYAQIWRNCLTLYSSKSG 118 (264)
Q Consensus 59 ~TKdGg~V~tL~LADeTGsI~ltLWdd~---ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr~G 118 (264)
.++.|..++.+++.|+||.|++.+||-. .+.|.+|-||.+. |....|++..|+++-+.+
T Consensus 15 ~~~~~~~~l~l~~~d~~gei~~~~wd~~~~~~~~~~~~~Vv~~~-g~~~~~~~~~q~ki~~~r 76 (287)
T COG3481 15 IASNGKDKLKLTLQDKTGEIEAKLWDALKNDEEAFKPGMVVHVE-GVKEVYRGRKQHKIIRIR 76 (287)
T ss_pred HHhcCChhheeeeccccceecccccccccccHhhhCcCceeccc-cceecccccchheeeecc
Confidence 3578899999999999999999999943 3459999999998 679999999999998733
No 47
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=96.39 E-value=0.021 Score=58.12 Aligned_cols=81 Identities=16% Similarity=0.103 Sum_probs=64.7
Q ss_pred ccccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEe-CCCeEEEEEecCC--CCCCCCCCEEEEeeeEEEEECC
Q psy3603 32 DVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVAD-STACINLSLWDEP--GALLHPGDIVRLTKCYAQIWRN 108 (264)
Q Consensus 32 ~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LAD-eTGsI~ltLWdd~--ad~Ik~GDIIrI~ngyVs~frG 108 (264)
..+|.++.+|+. +.+.+.|++... ..+.+..++.+.+.| .+|.+.++.|+.. ...|++|+.+.|+ |.++.++|
T Consensus 23 ~~~i~~~~~g~~-~~~~~~v~~~~~--~~~~~~~~~~~~~~d~~~~~~~~~~F~~~~~~~~~~~g~~~~~~-Gk~~~~~~ 98 (630)
T TIGR00643 23 LQTIGELLPGER-ATIVGEVLSHCI--FGFKRRKVLKLRLKDGGYKKLELRFFNRAFLKKKFKVGSKVVVY-GKVKSSKF 98 (630)
T ss_pred ccCHHHcCCCCE-EEEEEEEEEeEe--ccCCCCceEEEEEEECCCCEEEEEEECCHHHHhhCCCCCEEEEE-EEEEeeCC
Confidence 457999999997 999999987521 113335689999999 9999999999843 2559999999999 68999999
Q ss_pred EEEEEEcC
Q psy3603 109 CLTLYSSK 116 (264)
Q Consensus 109 ~LqL~Igr 116 (264)
.+|+..-.
T Consensus 99 ~~~~~~p~ 106 (630)
T TIGR00643 99 KAYLIHPE 106 (630)
T ss_pred EEEEECCE
Confidence 99887554
No 48
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=96.30 E-value=0.04 Score=43.66 Aligned_cols=68 Identities=19% Similarity=0.241 Sum_probs=52.8
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC-----CCCCCCCEEEEeeeEEEEE--CCEEEEEEc
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG-----ALLHPGDIVRLTKCYAQIW--RNCLTLYSS 115 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a-----d~Ik~GDIIrI~ngyVs~f--rG~LqL~Ig 115 (264)
.+|-+.+-|.+.... +.|+ +-++|.|+..+|.+++|.... ..++.||-|.+. |.++.| +|+++|.+.
T Consensus 22 ~~vwV~GEIs~~~~~---~~gh--~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G~~V~v~-g~~~~y~~~G~~sl~v~ 95 (99)
T PF13742_consen 22 PNVWVEGEISNLKRH---SSGH--VYFTLKDEEASISCVIFRSRARRIRGFDLKDGDKVLVR-GRVSFYEPRGSLSLIVE 95 (99)
T ss_pred CCEEEEEEEeecEEC---CCce--EEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCCCEEEEE-EEEEEECCCcEEEEEEE
Confidence 568888888877532 3444 555678899999999998332 358899999999 689999 589999987
Q ss_pred C
Q psy3603 116 K 116 (264)
Q Consensus 116 r 116 (264)
+
T Consensus 96 ~ 96 (99)
T PF13742_consen 96 D 96 (99)
T ss_pred E
Confidence 5
No 49
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=96.18 E-value=0.0078 Score=65.57 Aligned_cols=108 Identities=11% Similarity=0.039 Sum_probs=74.0
Q ss_pred hhhhhhccCCCcccceeeeeecccccCccccccccccc--ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEE
Q psy3603 2 WEKKLAGSHPEKNHGMRAERKEINRKKEAMDVYIKDLH--VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACIN 79 (264)
Q Consensus 2 ~~~~~~~~~~~~~h~~~~e~~~i~~~~~~~~ikIkDLk--pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ 79 (264)
|||++-|.. .+.|=|..-+..+.. .....+.+|. .+. .|.+.++|..+... .||.|..+.-++|.|.||.+.
T Consensus 906 ~E~e~lG~y-ls~HPl~~~~~~l~~---~~~~~~~~l~~~~~~-~v~v~g~i~~~~~~-~tk~g~~maf~~leD~tg~~e 979 (1107)
T PRK06920 906 KEKEVLGFY-LSSYPTAQYVKLAKE---LEIPSLAQAMRHKKK-VQRAIVYITSVKVI-RTKKGQKMAFITFCDQNDEME 979 (1107)
T ss_pred HHHHHHCcc-cCcCchHHHHHHHHH---hCCcCHHHHhhcCCC-EEEEEEEEEEeEee-cCCCCCeEEEEEEeeCCCcEE
Confidence 466665532 444544332222221 1112444443 344 48999999998754 578899999999999999999
Q ss_pred EEEecCC----CCCCCCCCEEEEeeeEEEEECCEEEEEEcC
Q psy3603 80 LSLWDEP----GALLHPGDIVRLTKCYAQIWRNCLTLYSSK 116 (264)
Q Consensus 80 ltLWdd~----ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr 116 (264)
+++|.+. .+.+.+|.+|.|. |.+...++.++|.+.+
T Consensus 980 ~~vFp~~y~~~~~~l~~~~~~~v~-G~v~~~~~~~~~~~~~ 1019 (1107)
T PRK06920 980 AVVFPETYIHFSDKLQEGAIVLVD-GTIELRNHKLQWIVNG 1019 (1107)
T ss_pred EEECHHHHHHHHHHhccCCEEEEE-EEEEecCCcEEEEEee
Confidence 9999754 3458999999998 5787666778888775
No 50
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=95.98 E-value=0.036 Score=51.15 Aligned_cols=74 Identities=18% Similarity=0.263 Sum_probs=55.1
Q ss_pred ceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC------CCCCCCCCEEEEeeeEEEEECCEEEEEEcCC
Q psy3603 44 NVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP------GALLHPGDIVRLTKCYAQIWRNCLTLYSSKS 117 (264)
Q Consensus 44 nVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~------ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr~ 117 (264)
+|.+++.|..+... ..-..++|.|.||.|.++.|... +.-.++|..|+|. |..+.|.|+..+...-
T Consensus 68 ~V~fVGvvrni~~~------ttn~~~~iEDGTG~Ievr~W~~~~~~~e~~~d~~~~~yvkV~-G~lk~F~GK~~I~~~~- 139 (258)
T COG5235 68 NVQFVGVVRNIKTS------TTNSMFVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQNYVKVN-GSLKTFNGKRSISASH- 139 (258)
T ss_pred eEEEEEEEEeeeec------ccceEEEEecCCceEEEEecCCCchHHHhccccccccEEEEe-cceeeeCCeeEEehhh-
Confidence 46666766665422 23356789999999999999744 2337889999998 5699999999887765
Q ss_pred ceEEEecCce
Q psy3603 118 GLIEKIGEFC 127 (264)
Q Consensus 118 G~IekVgEf~ 127 (264)
|+.++++.
T Consensus 140 --i~~I~d~N 147 (258)
T COG5235 140 --ISAIEDSN 147 (258)
T ss_pred --eeeccccc
Confidence 77776653
No 51
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=95.97 E-value=0.012 Score=63.74 Aligned_cols=107 Identities=19% Similarity=0.201 Sum_probs=73.9
Q ss_pred hhhhhhccCCCcccceeeeeecccccCcccccccccccccccceEEEEEEEecCCceeec-CCcEEEEEEEEeCCCeEEE
Q psy3603 2 WEKKLAGSHPEKNHGMRAERKEINRKKEAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLK-ENREVRTLKVADSTACINL 80 (264)
Q Consensus 2 ~~~~~~~~~~~~~h~~~~e~~~i~~~~~~~~ikIkDLkpG~knVnv~fiVle~~~~r~TK-dGg~V~tL~LADeTGsI~l 80 (264)
||||+-|.. .+.|-|..-+..+.. ....+.+|..+. .+.+.+.|.++... .|| .|..+..++|.|.||.|.+
T Consensus 850 ~E~e~lG~y-ls~HPl~~~~~~~~~----~~~~~~~l~~~~-~~~~~~~i~~~~~~-~tk~~g~~maf~~leD~~g~ie~ 922 (1034)
T PRK07279 850 LEQELLGVG-VSKHPLQAIAEKSSR----PFTPISQLVKNS-EATILVQIQSIRVI-RTKTKGQQMAFLSVTDTKKKLDV 922 (1034)
T ss_pred HHHHHhCcc-cccCchHHHHHHHHh----cCccHHHHhcCC-cceEEEEEEEEEEE-EEcCCCCeEEEEEEeeCCCcEEE
Confidence 466666542 445544322211211 223566665554 37888888887654 456 8889999999999999999
Q ss_pred EEecCC----CCCCCCCCEEEEeeeEEEEECCEEEEEEcC
Q psy3603 81 SLWDEP----GALLHPGDIVRLTKCYAQIWRNCLTLYSSK 116 (264)
Q Consensus 81 tLWdd~----ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr 116 (264)
++|.+. .+.+++|.+|.|. |.++.-++.++|.+.+
T Consensus 923 ~vFp~~y~~~~~~l~~~~~~~v~-G~v~~~~~~~~l~~~~ 961 (1034)
T PRK07279 923 TLFPETYRQYKDELKEGKFYYLK-GKIQERDGRLQMVLQQ 961 (1034)
T ss_pred EECHHHHHHHHHHhccCCEEEEE-EEEEecCCeeEEEEee
Confidence 999854 3458999999999 5787767778887765
No 52
>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=95.88 E-value=0.023 Score=43.20 Aligned_cols=60 Identities=13% Similarity=0.094 Sum_probs=45.8
Q ss_pred EEEEEEecCCceeecCCcEEEEEEEEeCCC-eEEEEEecCCC----CCCCCCCEEEEeeeEEEEEC
Q psy3603 47 VTCIVLDISPRVTLKENREVRTLKVADSTA-CINLSLWDEPG----ALLHPGDIVRLTKCYAQIWR 107 (264)
Q Consensus 47 v~fiVle~~~~r~TKdGg~V~tL~LADeTG-sI~ltLWdd~a----d~Ik~GDIIrI~ngyVs~fr 107 (264)
+.++|+.+-...... .+..+.+.|.|+.| .|.++++.+.+ +.|++|.+..|.+..+..-.
T Consensus 2 I~Vrv~r~W~~~~~~-~~~~~~miL~De~G~~I~a~i~~~~~~~f~~~L~eg~vy~is~f~v~~~~ 66 (86)
T cd04480 2 ICVRVLRLWDVYNNA-SGESLEMVLVDEKGNRIHATIPKRLAAKFRPLLKEGKWYTISNFEVAPNT 66 (86)
T ss_pred EEEEEEEEEcCcCCC-CCcEEEEEEEcCCCCEEEEEECHHHHHhhhhhceeCCEEEEeeEEEEcCC
Confidence 456677765443322 56889999999999 89999998653 55999999999988776543
No 53
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=95.67 E-value=0.029 Score=57.96 Aligned_cols=81 Identities=25% Similarity=0.291 Sum_probs=59.3
Q ss_pred Ccccccccccccc--cccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC----CCCCCCCEEEEeee
Q psy3603 28 KEAMDVYIKDLHV--GIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG----ALLHPGDIVRLTKC 101 (264)
Q Consensus 28 ~~~~~ikIkDLkp--G~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a----d~Ik~GDIIrI~ng 101 (264)
.+.....|.+|.. |.. |.+.+.|+.+... .|-.+ .+|.|+||.|.+..+.+.+ ..+++||||+|. |
T Consensus 198 ke~~r~~i~~id~~ig~t-V~I~GeV~qikqT----~GPTV--FtltDetg~i~aAAFe~aGvRAyP~IevGdiV~Vi-G 269 (715)
T COG1107 198 KELPRTLIDDLDEMIGKT-VRIEGEVTQIKQT----SGPTV--FTLTDETGAIWAAAFEEAGVRAYPEIEVGDIVEVI-G 269 (715)
T ss_pred hhcccccHHHHHhhcCce-EEEEEEEEEEEEc----CCCEE--EEEecCCCceehhhhccCCcccCCCCCCCceEEEE-E
Confidence 3344445666643 343 7788877776422 34334 4688999999999998764 349999999999 5
Q ss_pred EEEEECCEEEEEEcC
Q psy3603 102 YAQIWRNCLTLYSSK 116 (264)
Q Consensus 102 yVs~frG~LqL~Igr 116 (264)
.|+...|+|||.+-.
T Consensus 270 ~V~~r~g~lQiE~~~ 284 (715)
T COG1107 270 EVTRRDGRLQIEIEA 284 (715)
T ss_pred EEeecCCcEEEeehh
Confidence 899999999999887
No 54
>KOG3108|consensus
Probab=95.59 E-value=0.046 Score=51.22 Aligned_cols=72 Identities=22% Similarity=0.316 Sum_probs=57.1
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC------CCCCCCCEEEEeeeEEEEECCEEEEEEcCCc
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG------ALLHPGDIVRLTKCYAQIWRNCLTLYSSKSG 118 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a------d~Ik~GDIIrI~ngyVs~frG~LqL~Igr~G 118 (264)
|.++++|..+... ..-..++|-|.||.|.++.|-... ..|++|-.|++. |..+.|.|...|.+-+
T Consensus 71 v~~VGivr~~e~~------~t~i~y~I~D~tg~id~r~W~~~~~~~~e~~~l~~~~yVkv~-G~Lk~f~Gk~sl~~fk-- 141 (265)
T KOG3108|consen 71 VSIVGIVRNIEKS------ATNITYEIEDGTGQIDVRQWFHDNAESEEMPALETGTYVKVY-GHLKPFQGKKSLQVFK-- 141 (265)
T ss_pred EEEEEEEEeceec------CcceEEEEecCcccEEEEEeccccchhhhCcccccCcEEEee-ecccCCCCceeEEEEe--
Confidence 6777777776543 234677999999999999997442 248999999999 5699999999999887
Q ss_pred eEEEecCc
Q psy3603 119 LIEKIGEF 126 (264)
Q Consensus 119 ~IekVgEf 126 (264)
|..+.++
T Consensus 142 -I~pv~D~ 148 (265)
T KOG3108|consen 142 -IRPVEDF 148 (265)
T ss_pred -eeeeecC
Confidence 8777554
No 55
>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=95.56 E-value=0.075 Score=52.21 Aligned_cols=73 Identities=12% Similarity=0.120 Sum_probs=55.5
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCCC----CCCCCEEEEeeeEEEEE--CCEEEEEEcC
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGAL----LHPGDIVRLTKCYAQIW--RNCLTLYSSK 116 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad~----Ik~GDIIrI~ngyVs~f--rG~LqL~Igr 116 (264)
.+|-+.+-|...... ..|+.|.+| -|+...|++++|...+.. ++.|+-|.+. |+++.| +|.+||++.+
T Consensus 18 ~~v~V~GEisn~~~~---~sGH~YFtL--kD~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~-g~v~~y~~~G~~ql~v~~ 91 (432)
T TIGR00237 18 LQVWIQGEISNFTQP---VSGHWYFTL--KDENAQVRCVMFRGNNNRLKFRPQNGQQVLVR-GGISVYEPRGDYQIICFE 91 (432)
T ss_pred CcEEEEEEecCCeeC---CCceEEEEE--EcCCcEEEEEEEcChhhCCCCCCCCCCEEEEE-EEEEEECCCCcEEEEEEE
Confidence 357777777665422 467777665 699999999999855422 6789999999 689999 5999999987
Q ss_pred CceEEEec
Q psy3603 117 SGLIEKIG 124 (264)
Q Consensus 117 ~G~IekVg 124 (264)
|+..|
T Consensus 92 ---i~~~G 96 (432)
T TIGR00237 92 ---MQPAG 96 (432)
T ss_pred ---eccCC
Confidence 77653
No 56
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=95.48 E-value=0.075 Score=59.58 Aligned_cols=85 Identities=20% Similarity=0.252 Sum_probs=69.8
Q ss_pred ccccccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC------CCCCCCCEEEEeeeEE
Q psy3603 30 AMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG------ALLHPGDIVRLTKCYA 103 (264)
Q Consensus 30 ~~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a------d~Ik~GDIIrI~ngyV 103 (264)
.....|+||...+.+|.+.+.|-.+.. +++|+|+.++++.|.|-|++|.++.|-... +.|+.|+.|+|+ |.+
T Consensus 224 ~~~~~~~~i~~~~~~v~i~G~if~~e~-~~~k~~~~~~~~~~td~~~s~~~k~f~~~~~~~~~~~~~~~g~~v~~~-g~~ 301 (1437)
T PRK00448 224 EEITPMKEINEEERRVVVEGYVFKVEI-KELKSGRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKGDWVKVR-GSV 301 (1437)
T ss_pred cCcccHHHhhccCCeEEEEEEEEEEEE-EeccCCCEEEEEEEEcCCCCEEEEEEecCcchhHHHhcCCCCCEEEEE-EEE
Confidence 356778999888778999999999874 478899999999999999999999997332 348999999999 567
Q ss_pred EE--ECCEEEEEEcC
Q psy3603 104 QI--WRNCLTLYSSK 116 (264)
Q Consensus 104 s~--frG~LqL~Igr 116 (264)
.. |.+.+.+.+..
T Consensus 302 ~~d~~~~~~~~~~~~ 316 (1437)
T PRK00448 302 QNDTFTRDLVMNAQD 316 (1437)
T ss_pred eccCCCCceEEEeee
Confidence 54 66888888765
No 57
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=95.41 E-value=0.091 Score=54.86 Aligned_cols=89 Identities=16% Similarity=0.188 Sum_probs=73.7
Q ss_pred ccccCcccccccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC---CCCCCCCEEEEee
Q psy3603 24 INRKKEAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG---ALLHPGDIVRLTK 100 (264)
Q Consensus 24 i~~~~~~~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a---d~Ik~GDIIrI~n 100 (264)
..-.|......|.++.+|+. +.+.+.|.+..... ..++..+.+.+.|.||.|.++.++-.+ ..+++|..+.++
T Consensus 43 ~~YeD~~~~~~i~~~~~g~~-vti~g~V~~~~~~~--~~~~~~l~v~~~d~~~~l~l~fFn~~~~l~~~~~~G~~v~v~- 118 (677)
T COG1200 43 RRYEDRTLLPGIAEARPGEI-VTIEGTVLSHEKFP--FGKRKLLKVTLSDGTGVLTLVFFNFPAYLKKKLKVGERVIVY- 118 (677)
T ss_pred cchhhccccCChhhcCCCce-EEEEEEEEeeeccC--CCCCceEEEEEecCcEEEEEEEECccHHHHhhCCCCCEEEEE-
Confidence 33446666678889999997 99999999987553 445788999999999999999999763 459999999999
Q ss_pred eEEEEECCEEEEEEcC
Q psy3603 101 CYAQIWRNCLTLYSSK 116 (264)
Q Consensus 101 gyVs~frG~LqL~Igr 116 (264)
|.++.|++.+++.--+
T Consensus 119 Gk~~~~~~~~~~~hpe 134 (677)
T COG1200 119 GKVKRFKGGLQITHPE 134 (677)
T ss_pred EEEeeccCceEEEcce
Confidence 6899999999998664
No 58
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=95.09 E-value=0.15 Score=49.61 Aligned_cols=73 Identities=16% Similarity=0.169 Sum_probs=54.7
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCC----CCCCCCEEEEeeeEEEEE--CCEEEEEEcC
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGA----LLHPGDIVRLTKCYAQIW--RNCLTLYSSK 116 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs~f--rG~LqL~Igr 116 (264)
.+|-+.+-|...... ..|+-| +.|.|++..|++++|..... .++.|+-|.+. |.++.| +|.+||++.+
T Consensus 24 ~~v~v~gEis~~~~~---~sGH~Y--f~Lkd~~a~i~~~~~~~~~~~~~~~~~~G~~v~v~-g~~~~y~~~g~~ql~v~~ 97 (438)
T PRK00286 24 GQVWVRGEISNFTRH---SSGHWY--FTLKDEIAQIRCVMFKGSARRLKFKPEEGMKVLVR-GKVSLYEPRGDYQLIVEE 97 (438)
T ss_pred CcEEEEEEeCCCeeC---CCCeEE--EEEEcCCcEEEEEEEcChhhcCCCCCCCCCEEEEE-EEEEEECCCCCEEEEEEE
Confidence 457777766665422 356555 56789999999999985432 27899999999 689998 5889999987
Q ss_pred CceEEEec
Q psy3603 117 SGLIEKIG 124 (264)
Q Consensus 117 ~G~IekVg 124 (264)
|+..|
T Consensus 98 ---i~~~g 102 (438)
T PRK00286 98 ---IEPAG 102 (438)
T ss_pred ---eeeCC
Confidence 77654
No 59
>PRK02801 primosomal replication protein N; Provisional
Probab=95.05 E-value=0.11 Score=41.49 Aligned_cols=63 Identities=5% Similarity=0.020 Sum_probs=50.3
Q ss_pred ccceEEEEEEEecCCceeecCCcEEEEEEEEeC-----CCe-------EEEEEecCCCC----CCCCCCEEEEeeeEEEE
Q psy3603 42 IKNVNVTCIVLDISPRVTLKENREVRTLKVADS-----TAC-------INLSLWDEPGA----LLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 42 ~knVnv~fiVle~~~~r~TKdGg~V~tL~LADe-----TGs-------I~ltLWdd~ad----~Ik~GDIIrI~ngyVs~ 105 (264)
++.|.+++++.+-.+.+.|..|.++++++|+=+ +|- |++.+|+..++ .++.|+.|.|.| ....
T Consensus 2 mN~v~L~Grl~~dpelr~Tp~G~~v~~f~La~~~~~~ea~~~r~~~~~i~~va~G~~Ae~~~~~l~kGs~v~V~G-~L~~ 80 (101)
T PRK02801 2 TNRLVLSGTVCRTPKRKVSPSGIPHCQFVLEHRSVQEEAGLHRQAWCRMPVIVSGNQFQAITQSITVGSKITVQG-FISC 80 (101)
T ss_pred ccEEEEEEEECcCcceEECCCCCeEEEEEEEEeCeEecCCCceeEEEEEEEEEEcHHHHHHHhhcCCCCEEEEEE-EEEE
Confidence 345899999999888888889999988888654 344 99999997653 388999999995 5554
No 60
>PRK07459 single-stranded DNA-binding protein; Provisional
Probab=95.02 E-value=0.079 Score=43.70 Aligned_cols=61 Identities=16% Similarity=0.264 Sum_probs=48.3
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEE-------eCCCeEEEEEecCCCC----CCCCCCEEEEeeeEEE
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVA-------DSTACINLSLWDEPGA----LLHPGDIVRLTKCYAQ 104 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LA-------DeTGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs 104 (264)
..|.+++.+..-.+.+.+.+|..|+++.|| ++|-=+++++|+..++ .++.|+.|.|.| +.+
T Consensus 4 N~v~LiGrL~~DPelr~t~~G~~v~~fslAv~~~~~~~~t~w~~v~~wg~~Ae~~~~~l~KG~~V~V~G-~l~ 75 (121)
T PRK07459 4 NSVTLVGRAGRDPEVRYFESGSVVCNLTLAVNRRSRDDEPDWFNLEIWGKTAQVAADYVKKGSLIGITG-SLK 75 (121)
T ss_pred cEEEEEEEccCCCEEEEcCCCCEEEEEEEEecccccCCCceEEEEEEehHHHHHHHHHcCCCCEEEEEE-EEE
Confidence 348888888886555567788899999998 5677899999997653 389999999994 554
No 61
>PRK06751 single-stranded DNA-binding protein; Provisional
Probab=94.90 E-value=1.1 Score=39.39 Aligned_cols=62 Identities=16% Similarity=0.197 Sum_probs=47.0
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEE------eC-----CCeEEEEEecCCCC----CCCCCCEEEEeeeEEEE
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVA------DS-----TACINLSLWDEPGA----LLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LA------De-----TGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs~ 105 (264)
..|.++++|..--+.+.+.+|..|+.+.|| ++ |--+.+++|+..++ .++.||.|.|. |+++.
T Consensus 3 N~V~LiGrL~~DpelR~t~sG~~v~~fslAvnr~~~~~~ge~~tdwi~~v~wgk~Ae~~~~~l~KG~~V~Ve-GrL~~ 79 (173)
T PRK06751 3 NRVILVGRLTKDPDLRYTPNGVAVATFTLAVNRAFANQQGEREADFINCVIWRKQAENVANYLKKGSLAGVD-GRLQT 79 (173)
T ss_pred eEEEEEEEECCCCcEEECCCCCEEEEEEEEEccceecCCCCEEEEEEEEEEeCcHHHHHHHHcCCCCEEEEE-EEEEe
Confidence 458888888876666667788889888886 33 33589999997654 38999999999 45654
No 62
>PRK06863 single-stranded DNA-binding protein; Provisional
Probab=94.69 E-value=0.81 Score=40.17 Aligned_cols=63 Identities=16% Similarity=0.174 Sum_probs=45.9
Q ss_pred ccceEEEEEEEecCCceeecCCcEEEEEEEEe------C-CC-------eEEEEEecCCC----CCCCCCCEEEEeeeEE
Q psy3603 42 IKNVNVTCIVLDISPRVTLKENREVRTLKVAD------S-TA-------CINLSLWDEPG----ALLHPGDIVRLTKCYA 103 (264)
Q Consensus 42 ~knVnv~fiVle~~~~r~TKdGg~V~tL~LAD------e-TG-------sI~ltLWdd~a----d~Ik~GDIIrI~ngyV 103 (264)
+..|.+++.|..--+.+.+.+|..++++.|+= + +| -+++++|+..+ +.|+.|+-|.|.| .+
T Consensus 4 ~N~V~LiGrLg~DPElR~t~nG~~va~fsVAvn~~~~d~~~Ge~~e~t~w~~Vv~fgk~AE~v~~~LkKGs~V~VeG-rL 82 (168)
T PRK06863 4 INKVIIVGHLGNDPEIRTMPNGEAVANISVATSESWTDKNTGERREVTEWHRIVFYRRQAEVAGEYLRKGSQVYVEG-RL 82 (168)
T ss_pred ccEEEEEEEcCCCCEEEEcCCCCEEEEEEEEecCcccccCCCcccccceEEEEEEEhHHHHHHHHHCCCCCEEEEEE-EE
Confidence 44588888888765555677888898888872 1 23 47899999654 3489999999995 55
Q ss_pred EE
Q psy3603 104 QI 105 (264)
Q Consensus 104 s~ 105 (264)
+.
T Consensus 83 ~~ 84 (168)
T PRK06863 83 KT 84 (168)
T ss_pred Ee
Confidence 44
No 63
>PRK05733 single-stranded DNA-binding protein; Provisional
Probab=94.60 E-value=0.24 Score=43.65 Aligned_cols=64 Identities=19% Similarity=0.182 Sum_probs=48.1
Q ss_pred cccceEEEEEEEecCCceeecCCcEEEEEEEEe-------CCCe-------EEEEEecCCC----CCCCCCCEEEEeeeE
Q psy3603 41 GIKNVNVTCIVLDISPRVTLKENREVRTLKVAD-------STAC-------INLSLWDEPG----ALLHPGDIVRLTKCY 102 (264)
Q Consensus 41 G~knVnv~fiVle~~~~r~TKdGg~V~tL~LAD-------eTGs-------I~ltLWdd~a----d~Ik~GDIIrI~ngy 102 (264)
++..|.+++.|..--+.+.+.+|..|+++.|+= ++|. +.+++|+..+ +.|+.|+.|.|. |.
T Consensus 4 ~mNkV~LiGrlg~DPElr~t~nG~~va~fsVAv~~~~k~~~~Ge~~e~T~w~~Vv~fgk~Ae~v~~~l~KGs~V~Ve-Gr 82 (172)
T PRK05733 4 GVNKVILVGTCGQDPEVRYLPNGNAVTNLSLATSEQWTDKQSGQKVERTEWHRVSLFGKVAEIAGEYLRKGSQVYIE-GK 82 (172)
T ss_pred cceEEEEEEEecCCCEEEECCCCCEEEEEEEEEcCccccCCCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEE-EE
Confidence 466689999998865565677888898888873 2453 8999999654 348999999999 45
Q ss_pred EEE
Q psy3603 103 AQI 105 (264)
Q Consensus 103 Vs~ 105 (264)
.+.
T Consensus 83 Lr~ 85 (172)
T PRK05733 83 LQT 85 (172)
T ss_pred EEe
Confidence 544
No 64
>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=94.37 E-value=0.5 Score=37.42 Aligned_cols=75 Identities=16% Similarity=0.189 Sum_probs=50.9
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC--------CCCCCCCCEEEEeeeEEEEEC---C
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP--------GALLHPGDIVRLTKCYAQIWR---N 108 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~--------ad~Ik~GDIIrI~ngyVs~fr---G 108 (264)
.|+. |.+.+.|..+. +.+.+.-+.|.|.||.|.+.+=... ...|..|++|.|.| .+..-. +
T Consensus 11 ~g~~-V~v~Gwv~~~R------~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~es~V~V~G-~v~~~~~~~~ 82 (108)
T cd04316 11 DGEE-VTVAGWVHEIR------DLGGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRESVISVTG-TVKAEPKAPN 82 (108)
T ss_pred CCCE-EEEEEEEEeee------ccCCeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCcCEEEEEE-EEEeCCCCCC
Confidence 4665 89999887653 2235888999999999998664332 12488999999996 444432 3
Q ss_pred EEEEEEcCCceEEEecC
Q psy3603 109 CLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 109 ~LqL~Igr~G~IekVgE 125 (264)
.++|.+.+ |+.++.
T Consensus 83 ~~Ei~~~~---i~il~~ 96 (108)
T cd04316 83 GVEIIPEE---IEVLSE 96 (108)
T ss_pred CEEEEEeE---EEEEeC
Confidence 47777665 555554
No 65
>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=94.17 E-value=0.14 Score=38.56 Aligned_cols=60 Identities=15% Similarity=0.117 Sum_probs=42.2
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEE------------eCCCeEEEEEecCCCC----CCCCCCEEEEeeeEEEE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVA------------DSTACINLSLWDEPGA----LLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LA------------DeTGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs~ 105 (264)
+.+++.|......+.+++|..++.++|+ +++=.+.+.+|++.++ .+++||.|.|. |+.+.
T Consensus 1 v~l~G~l~~~p~~~~~~~g~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~g~~a~~~~~~~~kG~~V~v~-G~l~~ 76 (100)
T cd04496 1 VILIGRLGKDPELRYTPSGTPVARFSLAVNRRRKDRDEEEEETDWIRVVAFGKLAENAAKYLKKGDLVYVE-GRLRT 76 (100)
T ss_pred CEEEEEecCCCEEEECCCCCEEEEEEEEEcCceecccccccccEEEEEEEEhHHHHHHHHHhCCCCEEEEE-EEEEe
Confidence 3566777776555556677777766663 2455589999997643 48999999999 56654
No 66
>cd04498 hPOT1_OB2 hPOT1_OB2: A subfamily of OB folds similar to the second OB fold (OB2) of human protection of telomeres 1 protein (hPOT1). POT1 proteins bind to the single-stranded (ss) 3-prime ends of the telomere. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB2) which cooperate to bind telomeric ssDNA. OB1 makes more extensive contact with the ssDNA than OB2. OB2 protects the 3' end of the ssDNA. hPOT1 is implicated in telomere length regulation.
Probab=94.10 E-value=0.12 Score=43.52 Aligned_cols=38 Identities=26% Similarity=0.440 Sum_probs=31.3
Q ss_pred eEEEEEecCCC---CCCCCCCEEEEeeeEEEEECC--------EEEEEE
Q psy3603 77 CINLSLWDEPG---ALLHPGDIVRLTKCYAQIWRN--------CLTLYS 114 (264)
Q Consensus 77 sI~ltLWdd~a---d~Ik~GDIIrI~ngyVs~frG--------~LqL~I 114 (264)
+|.+++||+.+ ..|++||+|+|+|..++..+. .|++.+
T Consensus 61 ti~It~yD~H~~~ar~lK~GdfV~L~NVhiK~~~~~~~~~~~~~Le~~l 109 (123)
T cd04498 61 TIDILVYDNHVELAKSLKPGDFVRIYNVHAKSYSSKNEHDENDHLHFHL 109 (123)
T ss_pred EEEEEEEcchHHHHhhCCCCCEEEEEEEEEEeccCCcccCCcceEEEEE
Confidence 68999999764 339999999999999988877 566665
No 67
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=94.02 E-value=0.57 Score=40.01 Aligned_cols=60 Identities=12% Similarity=0.120 Sum_probs=42.6
Q ss_pred ceEEEEEEEecCCceeecCCcE----EEEEEEE------eCCC--------eEEEEEecCCC----CCCCCCCEEEEeee
Q psy3603 44 NVNVTCIVLDISPRVTLKENRE----VRTLKVA------DSTA--------CINLSLWDEPG----ALLHPGDIVRLTKC 101 (264)
Q Consensus 44 nVnv~fiVle~~~~r~TKdGg~----V~tL~LA------DeTG--------sI~ltLWdd~a----d~Ik~GDIIrI~ng 101 (264)
.|.+++.+..--+.+.+.+|.. |+++.|+ +.+| -+++++|+..+ +.|+.||.|.|.|
T Consensus 4 ~V~LiGrLg~DPElr~t~~G~~~~~~va~fslA~~r~~~~~~Ge~~~~~t~w~~V~~wg~~Ae~v~~~l~KG~~V~V~G- 82 (148)
T PRK08182 4 HFVGEGNIGSAPEYREFPNGNDEPRRLLRLNVYFDNPVPTKDGEYEDRGGFWAPVELWHRDAEHWARLYQKGMRVLVEG- 82 (148)
T ss_pred EEEEEEECCCCCeEEECCCCCeeeeeEEEEEEEecCceECCCCCEEecCcEEEEEEEEhHHHHHHHHhcCCCCEEEEEE-
Confidence 3777787777555555667754 8888886 3444 37899999654 3489999999995
Q ss_pred EEE
Q psy3603 102 YAQ 104 (264)
Q Consensus 102 yVs 104 (264)
...
T Consensus 83 rL~ 85 (148)
T PRK08182 83 RME 85 (148)
T ss_pred EEE
Confidence 443
No 68
>PRK09010 single-stranded DNA-binding protein; Provisional
Probab=93.99 E-value=0.43 Score=42.19 Aligned_cols=64 Identities=16% Similarity=0.176 Sum_probs=46.5
Q ss_pred cccceEEEEEEEecCCceeecCCcEEEEEEEE------eC-CC-------eEEEEEecCCC----CCCCCCCEEEEeeeE
Q psy3603 41 GIKNVNVTCIVLDISPRVTLKENREVRTLKVA------DS-TA-------CINLSLWDEPG----ALLHPGDIVRLTKCY 102 (264)
Q Consensus 41 G~knVnv~fiVle~~~~r~TKdGg~V~tL~LA------De-TG-------sI~ltLWdd~a----d~Ik~GDIIrI~ngy 102 (264)
++..|.+++.|..--+.+.+.+|..|++++|| |+ +| -+++++|+..+ +.|+.|+-|.|.| .
T Consensus 5 ~~N~V~LiGrLg~DPelR~t~nG~~v~~fsVAvn~~~kd~~~Ge~~e~t~w~~V~~fgk~Ae~~~~~L~KGs~V~VeG-r 83 (177)
T PRK09010 5 GVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKQTGEMKEQTEWHRVVLFGKLAEVAGEYLRKGSQVYIEG-Q 83 (177)
T ss_pred CceEEEEEEEeCCCceEEEcCCCCEEEEEEEEEcCccccCcccccccceEEEEEEEehhHHHHHHHhcCCCCEEEEEE-E
Confidence 34458888888876556667788899888887 22 34 36899999654 3499999999994 5
Q ss_pred EEE
Q psy3603 103 AQI 105 (264)
Q Consensus 103 Vs~ 105 (264)
++.
T Consensus 84 L~~ 86 (177)
T PRK09010 84 LRT 86 (177)
T ss_pred EEe
Confidence 543
No 69
>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=93.84 E-value=0.18 Score=43.42 Aligned_cols=63 Identities=11% Similarity=0.130 Sum_probs=46.1
Q ss_pred ccceEEEEEEEecCCceeecCCcEEEEEEEEe-------------CCCeEEEEEecCCCC----CCCCCCEEEEeeeEEE
Q psy3603 42 IKNVNVTCIVLDISPRVTLKENREVRTLKVAD-------------STACINLSLWDEPGA----LLHPGDIVRLTKCYAQ 104 (264)
Q Consensus 42 ~knVnv~fiVle~~~~r~TKdGg~V~tL~LAD-------------eTGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs 104 (264)
+..|.+++.|..--+.+.+.+|..++.++|+= +|--+++++|+..++ .|+.|+.|.|.| +.+
T Consensus 4 ~N~V~L~G~l~~dPe~r~t~~G~~v~~fsvA~~~~~~~~~G~~~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G-~L~ 82 (164)
T TIGR00621 4 VNKVILVGRLTRDPELRYTPSGNAVANFTLATNRRWKDQDGEWKEETEWHDIVIFGRLAEVAAQYLKKGSLVYVEG-RLR 82 (164)
T ss_pred ccEEEEEEEeCCCCEEEECCCCCEEEEEEEEEcCceecCCCCEeccceEEEEEEehHHHHHHHHhCCCCCEEEEEE-EEE
Confidence 34578888888865555667888887777752 345789999997653 489999999994 554
Q ss_pred E
Q psy3603 105 I 105 (264)
Q Consensus 105 ~ 105 (264)
.
T Consensus 83 ~ 83 (164)
T TIGR00621 83 T 83 (164)
T ss_pred e
Confidence 3
No 70
>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=93.84 E-value=0.37 Score=47.31 Aligned_cols=75 Identities=19% Similarity=0.194 Sum_probs=54.3
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC--------CCCCCCCCEEEEeeeEEEEEC---C
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP--------GALLHPGDIVRLTKCYAQIWR---N 108 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~--------ad~Ik~GDIIrI~ngyVs~fr---G 108 (264)
.|+. |.+.+.|..+. +.+++.-+.|.|.+|.|++.+=... ...|..||+|.|.| .+..-+ |
T Consensus 11 ~g~~-v~i~G~v~~~R------~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~s~v~v~G-~v~~~~~~~~ 82 (428)
T TIGR00458 11 DGQE-VTFMGWVHEIR------DLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLESVVAVRG-IVKIKEKAPG 82 (428)
T ss_pred CCCE-EEEEEEEEEEe------cCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCCcEEEEEE-EEEecCCCCC
Confidence 3565 88888887753 2244889999999999999775321 12488999999995 565432 7
Q ss_pred EEEEEEcCCceEEEecC
Q psy3603 109 CLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 109 ~LqL~Igr~G~IekVgE 125 (264)
.++|.+.+ |+.++.
T Consensus 83 ~~el~~~~---i~vl~~ 96 (428)
T TIGR00458 83 GFEIIPTK---IEVINE 96 (428)
T ss_pred cEEEEEeE---EEEEec
Confidence 78888876 666665
No 71
>KOG4757|consensus
Probab=93.78 E-value=0.21 Score=50.20 Aligned_cols=83 Identities=23% Similarity=0.288 Sum_probs=59.4
Q ss_pred Cccccccccc-c-cccccceEEEEEEEecCCceeecCCcEEEEEEEEeC--CCe-EEEEEecCCCCC----CCCCCEEEE
Q psy3603 28 KEAMDVYIKD-L-HVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADS--TAC-INLSLWDEPGAL----LHPGDIVRL 98 (264)
Q Consensus 28 ~~~~~ikIkD-L-kpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADe--TGs-I~ltLWdd~ad~----Ik~GDIIrI 98 (264)
|...+++|.| + +.+. -||+.++|++..+++..+....+.++.|.|. |+. ..+.++....+. -+.||+|.+
T Consensus 5 ds~k~Iri~da~kk~~t-iVNl~GiVkef~pp~qs~g~D~~~tv~IvDp~~ss~gLtv~lfSkt~edLP~Ik~~GDiill 83 (522)
T KOG4757|consen 5 DSLKLIRISDALKKKNT-IVNLIGIVKEFTPPRQSLGKDWVCTVYIVDPDYSSIGLTVHLFSKTGEDLPVIKQVGDIILL 83 (522)
T ss_pred cchheeechHHHHhcCc-EEEEEEEEEeccChhhccCCceEEEEEEeCCCCCCCCcEEEEecCchhhCccccccCcEEEE
Confidence 4555677777 3 4455 4999999999998876554467899999994 333 567777644322 457999999
Q ss_pred eeeEEEEECCEEE
Q psy3603 99 TKCYAQIWRNCLT 111 (264)
Q Consensus 99 ~ngyVs~frG~Lq 111 (264)
+.-.+..|+.+.|
T Consensus 84 hRiKiq~y~~rtq 96 (522)
T KOG4757|consen 84 HRIKIQSYRDRTQ 96 (522)
T ss_pred EEEEEEEhhhhhh
Confidence 9877777875544
No 72
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=93.70 E-value=0.42 Score=53.01 Aligned_cols=78 Identities=18% Similarity=0.227 Sum_probs=62.9
Q ss_pred cccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC------CCCCCCCEEEEeeeEEEE--ECC
Q psy3603 37 DLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG------ALLHPGDIVRLTKCYAQI--WRN 108 (264)
Q Consensus 37 DLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a------d~Ik~GDIIrI~ngyVs~--frG 108 (264)
+|...+.+|.+.+.|-.+.. +++|.|+.++++.|.|-|.+|.++.|.... +.+++|+.|+|+ |.+.. |.+
T Consensus 2 ~~~~~~~~~~~~g~i~~~~~-~~~~~~~~~~~~~~~d~~~s~~~k~f~~~~~~~~~~~~~~~g~~~~~~-g~~~~d~~~~ 79 (1213)
T TIGR01405 2 KINEEENRVKIEGYIFKIEI-KELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIGKWVRAR-GKIELDNFSR 79 (1213)
T ss_pred cccccCCeEEEEEEEEEEEe-EeccCCCEEEEEEEEcCCCCEEEEEecccccchHHHhhcCCCcEEEEE-EEEeccCCCC
Confidence 45556667999999998774 478899999999999999999999998332 348999999999 46653 568
Q ss_pred EEEEEEcC
Q psy3603 109 CLTLYSSK 116 (264)
Q Consensus 109 ~LqL~Igr 116 (264)
.+.+.+..
T Consensus 80 ~~~~~~~~ 87 (1213)
T TIGR01405 80 DLQMIIKD 87 (1213)
T ss_pred ceEEEeee
Confidence 88888876
No 73
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=93.68 E-value=0.18 Score=40.55 Aligned_cols=61 Identities=16% Similarity=0.164 Sum_probs=46.1
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEEeC-----------CCeEEEEEecCCCC----CCCCCCEEEEeeeEEE
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVADS-----------TACINLSLWDEPGA----LLHPGDIVRLTKCYAQ 104 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LADe-----------TGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs 104 (264)
..|.+++.+..-.+.+.+.+|..|..+.||-. |--+++++|+..++ .++.||.|.|.| +.+
T Consensus 3 N~v~liGrl~~dPelr~t~~G~~~~~f~lAv~~~~~~~~g~~~t~~~~v~~wg~~Ae~~~~~l~KG~~V~V~G-~l~ 78 (112)
T PRK06752 3 NRVVLIGRLTKEPELYYTKQGVAYARVCVAVNRGFRNSLGEQQVDFINCVVWRKSAENVTEYCTKGSLVGITG-RIH 78 (112)
T ss_pred eEEEEEEECcCCCEEEECCCCCEEEEEEEEECCCeEcCCCCEEEEEEEEEEehHHHHHHHHhcCCCCEEEEEE-EEE
Confidence 34788888887666666788889988888732 44588999997653 489999999994 544
No 74
>PRK07274 single-stranded DNA-binding protein; Provisional
Probab=93.66 E-value=0.22 Score=41.45 Aligned_cols=62 Identities=15% Similarity=0.272 Sum_probs=46.0
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEE------eCCC-----eEEEEEecCCCC----CCCCCCEEEEeeeEEEE
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVA------DSTA-----CINLSLWDEPGA----LLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LA------DeTG-----sI~ltLWdd~ad----~Ik~GDIIrI~ngyVs~ 105 (264)
..|.+++.+..-.+.+.+.+|..|+.+.|| |+.| -+++++|+..++ .++.|+.|.|. |+++.
T Consensus 3 N~v~LiGrL~~dPelr~t~~g~~~~~fslAv~~~~k~~~g~~~t~w~~v~~fg~~Ae~v~~~l~KG~~V~V~-Grl~~ 79 (131)
T PRK07274 3 NKVILIGRLTATPELVKTANDKSVARVTLAVNRRFKNQNGEREADFINVVLWGKLAETLASYASKGSLISID-GELRT 79 (131)
T ss_pred eEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCceecCCCCEEEEEEEEEEehHHHHHHHHHcCCCCEEEEE-EEEEe
Confidence 347888888876555566788889888887 4444 578999996643 48999999999 45543
No 75
>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=93.63 E-value=0.76 Score=36.30 Aligned_cols=72 Identities=14% Similarity=0.181 Sum_probs=48.1
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC--------CCC-CCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP--------GAL-LHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~--------ad~-Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
|.+.+.|..+. ..+.+.-+.|.|.||.+++.+=... ... |..||+|.|.|-.+..-+|.++|.+.
T Consensus 2 v~v~GwV~~~R------~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g~~V~v~G~v~~~~~g~~El~~~ 75 (108)
T cd04322 2 VSVAGRIMSKR------GSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLGDIIGVTGTPFKTKTGELSIFVK 75 (108)
T ss_pred EEEEEEEEEEe------cCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCCCEEEEEEEEEecCCCCEEEEeC
Confidence 45666666643 2235899999999999999763221 012 88999999996444444577888776
Q ss_pred CCceEEEecC
Q psy3603 116 KSGLIEKIGE 125 (264)
Q Consensus 116 r~G~IekVgE 125 (264)
+ ++.++.
T Consensus 76 ~---~~ils~ 82 (108)
T cd04322 76 E---FTLLSK 82 (108)
T ss_pred E---eEEeec
Confidence 5 555443
No 76
>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=93.53 E-value=1.2 Score=34.77 Aligned_cols=72 Identities=17% Similarity=0.070 Sum_probs=48.4
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC----------CCCCCCCCEEEEeeeEEEEE-C------
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP----------GALLHPGDIVRLTKCYAQIW-R------ 107 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~----------ad~Ik~GDIIrI~ngyVs~f-r------ 107 (264)
|.+.+.|..+. +.|+++.-+.|.|.||.|++.+=... ...|..||+|.|.| .+..- +
T Consensus 2 V~i~Gwv~~~R-----~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V~V~G-~v~~~~~~~~~~~ 75 (102)
T cd04320 2 VLIRARVHTSR-----AQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKESIVDVEG-TVKKPEEPIKSCT 75 (102)
T ss_pred EEEEEEEEEee-----cCCCceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCccEEEEEE-EEECCCCcccCCC
Confidence 55666665542 23437889999999999999885432 12478999999996 45432 1
Q ss_pred -CEEEEEEcCCceEEEecC
Q psy3603 108 -NCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 108 -G~LqL~Igr~G~IekVgE 125 (264)
+.++|.+.+ |+.++.
T Consensus 76 ~~~~El~~~~---i~il~~ 91 (102)
T cd04320 76 QQDVELHIEK---IYVVSE 91 (102)
T ss_pred cCcEEEEEEE---EEEEec
Confidence 567777765 555544
No 77
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=93.52 E-value=0.4 Score=47.10 Aligned_cols=82 Identities=16% Similarity=0.172 Sum_probs=58.2
Q ss_pred cccccccc---cccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC-------CCCCCCCCEEEEeeeE
Q psy3603 33 VYIKDLHV---GIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP-------GALLHPGDIVRLTKCY 102 (264)
Q Consensus 33 ikIkDLkp---G~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~-------ad~Ik~GDIIrI~ngy 102 (264)
..|+||.+ |++ |.+.|.|..+. +.+++.-+.|.|.+|.|++.+=... ...|..||+|.|.| .
T Consensus 5 ~~~~~l~~~~~g~~-V~i~GrV~~~R------~~gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~gs~V~v~G-~ 76 (437)
T PRK05159 5 HLTSELTPELDGEE-VTLAGWVHEIR------DLGGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRESVVSVTG-T 76 (437)
T ss_pred eEhhhCChhhCCCE-EEEEEEeEeee------cCCCeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCCcEEEEEE-E
Confidence 46677654 454 88888887753 2246888999999999999773321 23488999999995 5
Q ss_pred EEEEC---CEEEEEEcCCceEEEecC
Q psy3603 103 AQIWR---NCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 103 Vs~fr---G~LqL~Igr~G~IekVgE 125 (264)
+..-+ |.++|.+.+ |+.++.
T Consensus 77 v~~~~~~~~~~el~~~~---i~vls~ 99 (437)
T PRK05159 77 VKANPKAPGGVEVIPEE---IEVLNK 99 (437)
T ss_pred EEcCCCCCCCEEEEEeE---EEEEeC
Confidence 65543 778888876 666554
No 78
>PRK13732 single-stranded DNA-binding protein; Provisional
Probab=93.50 E-value=0.47 Score=41.91 Aligned_cols=63 Identities=19% Similarity=0.181 Sum_probs=46.9
Q ss_pred cccceEEEEEEEecCCceeecCCcEEEEEEEEe-------CCC-------eEEEEEecCCC----CCCCCCCEEEEeeeE
Q psy3603 41 GIKNVNVTCIVLDISPRVTLKENREVRTLKVAD-------STA-------CINLSLWDEPG----ALLHPGDIVRLTKCY 102 (264)
Q Consensus 41 G~knVnv~fiVle~~~~r~TKdGg~V~tL~LAD-------eTG-------sI~ltLWdd~a----d~Ik~GDIIrI~ngy 102 (264)
++..|.+++.|..--+.+.+.+|..|+++.||- .+| -+++++|+..+ +.|+.||.|.|.| .
T Consensus 5 ~mN~V~LiGrLg~DPElR~t~nG~~va~fslAvn~~~kd~~~Ge~~e~t~w~~Vv~wgk~Ae~v~~~L~KG~~V~VeG-r 83 (175)
T PRK13732 5 GINKVILVGRLGKDPEVRYIPNGGAVANLQVATSESWRDKQTGEMREQTEWHRVVLFGKLAEVAGEYLRKGAQVYIEG-Q 83 (175)
T ss_pred CceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEcCccccCCCCceecceeEEEEEEecHHHHHHHHhcCCCCEEEEEE-E
Confidence 355688888888765565677888999888873 245 35899999654 3489999999995 4
Q ss_pred EE
Q psy3603 103 AQ 104 (264)
Q Consensus 103 Vs 104 (264)
++
T Consensus 84 L~ 85 (175)
T PRK13732 84 LR 85 (175)
T ss_pred EE
Confidence 44
No 79
>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=93.44 E-value=0.37 Score=44.85 Aligned_cols=72 Identities=24% Similarity=0.260 Sum_probs=52.2
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCC--eEEEEEecCC-------CCCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTA--CINLSLWDEP-------GALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTG--sI~ltLWdd~-------ad~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
|.+.|+|+...... .+...+.-++|-|.|| .|.+++|-+. ...+ .|++|+|.| .++ ++..||.+.
T Consensus 69 v~i~G~Vv~~~~~~--~~~~~~~~l~iDD~Sg~~~i~~~~~~~~~~~~~l~~~~~-~G~~V~VkG-~vs--r~~~ql~ve 142 (256)
T PF10451_consen 69 VRIVGVVVGIDYKW--IENEDRIILTIDDSSGANTIECKCSKSSYLSMGLPINDL-IGKVVEVKG-TVS--RNERQLDVE 142 (256)
T ss_dssp EEEEEEEEEEEEEE---BBTCEEEEEEE-SSCS-EEEEEEEHHHHHCCCHHCTT--TT-EEEEEE-EEE--SSSEEEEEE
T ss_pred EEEEEEEEEEEEEe--ecccceEEEEEeCCCCceeEEEEEEcccccccCCCccCC-CCcEEEEEE-EEc--cCcEEEEEE
Confidence 88999999986432 2224578889999999 8999999642 2224 899999995 577 999999998
Q ss_pred CCceEEEecC
Q psy3603 116 KSGLIEKIGE 125 (264)
Q Consensus 116 r~G~IekVgE 125 (264)
+ |..+..
T Consensus 143 ~---i~~~~~ 149 (256)
T PF10451_consen 143 R---IELVRD 149 (256)
T ss_dssp E---EEEETS
T ss_pred E---EEccCC
Confidence 7 666643
No 80
>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=93.44 E-value=0.11 Score=39.74 Aligned_cols=62 Identities=19% Similarity=0.190 Sum_probs=41.1
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEEeC-------------CCeEEEEEecCCCC----CCCCCCEEEEeeeEEEE
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVADS-------------TACINLSLWDEPGA----LLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LADe-------------TGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs~ 105 (264)
..|.+.+.|..--..+.+++|..+..+.|+-. +--+++.+|++.++ .+++||.|.|.| +.+.
T Consensus 2 N~v~l~G~l~~~p~~~~~~~g~~~~~f~la~~~~~~~~~~~~~~~~~~~~v~~~g~~A~~~~~~l~kG~~V~V~G-~l~~ 80 (104)
T PF00436_consen 2 NKVTLIGRLGKDPELRYTKNGTPVARFSLAVNRRFKDDGGEGDEKTDWINVVAWGKLAENVAEYLKKGDRVYVEG-RLRT 80 (104)
T ss_dssp EEEEEEEEESSSEEEEEETTSEEEEEEEEEEEEEEEETTSCEEEEEEEEEEEEEHHHHHHHHHH--TT-EEEEEE-EEEE
T ss_pred cEEEEEEEECCCcEEEECCCCCEEEEEEEEEecEEeeeeccCccceEEEEEEeeeecccccceEEcCCCEEEEEE-EEEe
Confidence 34788888877655555677877876666433 33578999997654 389999999994 5554
No 81
>PRK08486 single-stranded DNA-binding protein; Provisional
Probab=93.19 E-value=1.2 Score=39.53 Aligned_cols=60 Identities=15% Similarity=0.169 Sum_probs=44.6
Q ss_pred ceEEEEEEEecCCceeecCCcEEEEEEEE-------------eCCCeEEEEEecCCCC----CCCCCCEEEEeeeEEE
Q psy3603 44 NVNVTCIVLDISPRVTLKENREVRTLKVA-------------DSTACINLSLWDEPGA----LLHPGDIVRLTKCYAQ 104 (264)
Q Consensus 44 nVnv~fiVle~~~~r~TKdGg~V~tL~LA-------------DeTGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs 104 (264)
.|.+++.|..--+.+.+.+|..|+.++|| ++|--|++++|+..++ .|+.|+-|.|.| +.+
T Consensus 4 ~V~LvGrL~~DPElr~t~sG~~va~fslAv~r~~~~~~Ge~~e~t~fi~v~~fg~~AE~~~~~l~KG~~V~VeG-rL~ 80 (182)
T PRK08486 4 KVILVGNLTRDVELRYLPSGSAIATIGLATSRRFKKQDGEKGEEVCFIDIRLFGRTAEIANQYLSKGSKVLIEG-RLT 80 (182)
T ss_pred EEEEEEEecCCCEEEECCCCCEEEEEEEEEecceecCCCCCcccceEEEEEEEhHHHHHHHHHcCCCCEEEEEE-EEE
Confidence 37788877776556667788888888885 2455689999996543 489999999994 553
No 82
>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=93.19 E-value=0.98 Score=36.95 Aligned_cols=75 Identities=13% Similarity=0.160 Sum_probs=51.5
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC------CCCCCCCEEEEeeeEEEE--------
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG------ALLHPGDIVRLTKCYAQI-------- 105 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a------d~Ik~GDIIrI~ngyVs~-------- 105 (264)
.|+. |.+.|.|..+.. . +.+.-+.|.|.+|.+.+.+=.... ..|..||+|.|.| .+..
T Consensus 13 ~g~~-V~i~Gwv~~~R~-----~-gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~gs~V~V~G-~~~~~~~~~~~~ 84 (135)
T cd04317 13 VGQE-VTLCGWVQRRRD-----H-GGLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNESVIQVTG-KVRARPEGTVNP 84 (135)
T ss_pred CCCE-EEEEEeEehhcc-----c-CCEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCccEEEEEE-EEECCCccccCC
Confidence 4564 899998877532 2 348889999999999987743211 2488999999996 4443
Q ss_pred --ECCEEEEEEcCCceEEEecC
Q psy3603 106 --WRNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 106 --frG~LqL~Igr~G~IekVgE 125 (264)
-.|.++|.+.. |+.++.
T Consensus 85 ~~~~~~~El~~~~---i~vl~~ 103 (135)
T cd04317 85 KLPTGEIEVVASE---LEVLNK 103 (135)
T ss_pred CCCCCcEEEEEeE---EEEEEC
Confidence 13567777765 555554
No 83
>PRK08763 single-stranded DNA-binding protein; Provisional
Probab=93.14 E-value=0.31 Score=42.59 Aligned_cols=64 Identities=13% Similarity=0.160 Sum_probs=46.9
Q ss_pred cccceEEEEEEEecCCceeecCCcEEEEEEEE------eCCC-------eEEEEEecCCCC----CCCCCCEEEEeeeEE
Q psy3603 41 GIKNVNVTCIVLDISPRVTLKENREVRTLKVA------DSTA-------CINLSLWDEPGA----LLHPGDIVRLTKCYA 103 (264)
Q Consensus 41 G~knVnv~fiVle~~~~r~TKdGg~V~tL~LA------DeTG-------sI~ltLWdd~ad----~Ik~GDIIrI~ngyV 103 (264)
++..|.+++.|..--+.+.+.+|..|+++.|| |+.| -+++++|+..++ .++.|+-|.|.| .+
T Consensus 4 ~~Nkv~LiGrLg~DPelr~t~~G~~va~fsVA~~~~~k~~~G~~~e~t~w~~Vv~fgk~Ae~v~~~L~KGs~V~VeG-rL 82 (164)
T PRK08763 4 GINKVILVGNLGNDPDIKYTQSGMTITRISLATTSVRKDREGNTQERTEWHRVKFFGKLGEIAGEYLRKGSQCYIEG-SI 82 (164)
T ss_pred cceEEEEEEEecCCCeEEEcCCCCeEEEEEEEeccceecCCCCeeccceEEEEEEehHHHHHHHHhcCCCCEEEEEE-EE
Confidence 35558888888875555567788899888887 3334 389999996543 489999999994 55
Q ss_pred EE
Q psy3603 104 QI 105 (264)
Q Consensus 104 s~ 105 (264)
+.
T Consensus 83 ~~ 84 (164)
T PRK08763 83 RY 84 (164)
T ss_pred Ee
Confidence 43
No 84
>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=93.05 E-value=1.6 Score=32.86 Aligned_cols=65 Identities=12% Similarity=0.117 Sum_probs=42.8
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC-------CCCCCCCEEEEeeeEEEEE------CCEEE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG-------ALLHPGDIVRLTKCYAQIW------RNCLT 111 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a-------d~Ik~GDIIrI~ngyVs~f------rG~Lq 111 (264)
|.+.+.|..+. +.+++.-+.|.|.||.+++.+=.... ..+..||+|.|.| .+..- ++.++
T Consensus 2 V~i~Gwv~~~R------~~g~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~s~V~v~G-~~~~~~~~~~~~~~~E 74 (85)
T cd04100 2 VTLAGWVHSRR------DHGGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTESVVGVTG-TVVKRPEGNLATGEIE 74 (85)
T ss_pred EEEEEEEehhc------cCCCEEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCCCEEEEEe-EEEECCCCCCCCCCEE
Confidence 45556665432 23458889999999999986643321 2488999999995 55542 45566
Q ss_pred EEEcC
Q psy3603 112 LYSSK 116 (264)
Q Consensus 112 L~Igr 116 (264)
|.+.+
T Consensus 75 l~~~~ 79 (85)
T cd04100 75 LQAEE 79 (85)
T ss_pred EEEeE
Confidence 66553
No 85
>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=93.04 E-value=1 Score=36.65 Aligned_cols=71 Identities=17% Similarity=0.173 Sum_probs=46.2
Q ss_pred cccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC--CCCCCCCCEEEEeeeEEEEECCEEEE
Q psy3603 35 IKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP--GALLHPGDIVRLTKCYAQIWRNCLTL 112 (264)
Q Consensus 35 IkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~--ad~Ik~GDIIrI~ngyVs~frG~LqL 112 (264)
++++..++. |.+.+.|++.- ++.. .++.|.||+|.+-+=++. ...+.++|.|+|. |.+.-.-+..+|
T Consensus 28 a~~~~Dd~~-V~L~G~Iv~~l------~~d~---Y~F~D~TG~I~VeId~~~w~g~~vt~~~~Vri~-GeVDk~~~~~~I 96 (103)
T PF04076_consen 28 AKNAKDDTP-VTLEGNIVKQL------GDDK---YLFRDATGEIEVEIDDDVWRGQTVTPDDKVRIS-GEVDKDWNKTEI 96 (103)
T ss_dssp HTTS-SSEE-EEEEEEEEEEE------ETTE---EEEEETTEEEEEE--GGGSTT----TTSEEEEE-EEEEEETTEEEE
T ss_pred HhhCcCCCe-EEEEEEEEEEe------cCCE---EEEECCCCcEEEEEChhhcCCcccCCCCEEEEE-EEEeCCCCceEE
Confidence 445666665 99999887742 1233 478999999999884432 3458899999999 578755567888
Q ss_pred EEcC
Q psy3603 113 YSSK 116 (264)
Q Consensus 113 ~Igr 116 (264)
.+.+
T Consensus 97 dV~~ 100 (103)
T PF04076_consen 97 DVDR 100 (103)
T ss_dssp EEEE
T ss_pred EEEE
Confidence 7765
No 86
>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=92.67 E-value=2.1 Score=32.28 Aligned_cols=65 Identities=17% Similarity=0.072 Sum_probs=42.0
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC------CCCCCCCEEEEeeeEEEEEC------CEEEE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG------ALLHPGDIVRLTKCYAQIWR------NCLTL 112 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a------d~Ik~GDIIrI~ngyVs~fr------G~LqL 112 (264)
|.+.+.|..+ |+.+.+.-+.|.|.+|.+++.+=.... ..+..|++|.|.| .+..-. +.++|
T Consensus 2 V~v~Gwv~~~------R~~g~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~es~V~V~G-~v~~~~~~~~~~~~~Ei 74 (84)
T cd04323 2 VKVFGWVHRL------RSQKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQESSVEVTG-EVKEDPRAKQAPGGYEL 74 (84)
T ss_pred EEEEEEEEEE------ecCCCcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCcCEEEEEE-EEEECCcccCCCCCEEE
Confidence 4555666543 233567888999999999986643221 2378999999995 565532 23566
Q ss_pred EEcC
Q psy3603 113 YSSK 116 (264)
Q Consensus 113 ~Igr 116 (264)
.+.+
T Consensus 75 ~~~~ 78 (84)
T cd04323 75 QVDY 78 (84)
T ss_pred EEEE
Confidence 5543
No 87
>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=92.62 E-value=0.74 Score=35.14 Aligned_cols=52 Identities=12% Similarity=0.069 Sum_probs=36.7
Q ss_pred CcEEEEEEEEeCCC-eEEEEEecCC------CCCCCCCCEEEEeeeEEEEEC-------CEEEEEEcC
Q psy3603 63 NREVRTLKVADSTA-CINLSLWDEP------GALLHPGDIVRLTKCYAQIWR-------NCLTLYSSK 116 (264)
Q Consensus 63 Gg~V~tL~LADeTG-sI~ltLWdd~------ad~Ik~GDIIrI~ngyVs~fr-------G~LqL~Igr 116 (264)
++.+.-+.|.|.|| .+++.+ +.. ...+..||+|.|.| .+..-+ |.++|.+.+
T Consensus 15 ~~~~~Fi~LrD~~g~~iQvv~-~~~~~~~~~~~~l~~~s~V~V~G-~v~~~~~~~~~~~~~~Ei~~~~ 80 (86)
T cd04321 15 VKKLSFADLRDPNGDIIQLVS-TAKKDAFSLLKSITAESPVQVRG-KLQLKEAKSSEKNDEWELVVDD 80 (86)
T ss_pred CCceEEEEEECCCCCEEEEEE-CCCHHHHHHHhcCCCCcEEEEEE-EEEeCCCcCCCCCCCEEEEEEE
Confidence 56788899999999 588754 422 13478999999995 555532 667776654
No 88
>PRK07275 single-stranded DNA-binding protein; Provisional
Probab=92.61 E-value=0.34 Score=42.14 Aligned_cols=61 Identities=20% Similarity=0.233 Sum_probs=46.7
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEE------e-----CCCeEEEEEecCCCC----CCCCCCEEEEeeeEEE
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVA------D-----STACINLSLWDEPGA----LLHPGDIVRLTKCYAQ 104 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LA------D-----eTGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs 104 (264)
..|.+++++..--+.+.|.+|..|+.++|| + +|--|.+++|+..++ .++.|+.|.|.| +++
T Consensus 3 N~v~LiGrL~~DPElr~t~sG~~v~~ftlAv~r~~~~~~ge~~tdfi~vv~wgk~Ae~~~~~l~KG~~V~VeG-rl~ 78 (162)
T PRK07275 3 NNVVLVGRMTRDAELRYTPSNVAVATFTLAVNRTFKSQNGEREADFINCVIWRQQAENLANWAKKGALIGVTG-RIQ 78 (162)
T ss_pred eEEEEEEEECCCCeEEECCCCCEEEEEEEEEcCceecCCCCEeeeEEEEEEEcHHHHHHHHHcCCCCEEEEEE-EEE
Confidence 347888888876666677889899988887 3 355589999997654 489999999994 553
No 89
>PRK06293 single-stranded DNA-binding protein; Provisional
Probab=92.49 E-value=0.35 Score=42.27 Aligned_cols=61 Identities=13% Similarity=0.101 Sum_probs=46.8
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEE--------eCCCeEEEEEecCCCC----CCCCCCEEEEeeeEEE
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVA--------DSTACINLSLWDEPGA----LLHPGDIVRLTKCYAQ 104 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LA--------DeTGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs 104 (264)
..|.+++.+..--+.+.+.+|..|++++|| ++|-=+++++|+..++ .|+.|+.|.|.| ..+
T Consensus 2 N~V~LiGrLg~DPElR~t~sG~~v~~FsLAvn~~~~~~~~T~wi~v~awg~~Ae~v~~yL~KG~~V~VeG-rL~ 74 (161)
T PRK06293 2 MFGYIVGRLGADPEERMTSKGKRVVVLRLGVKSRVGSKDETVWCRCNIWGNRYDKMLPYLKKGSGVIVAG-EMS 74 (161)
T ss_pred eEEEEEEEecCCCeEEEcCCCCEEEEEEEEEeCCCCCccceEEEEEEEEhHHHHHHHHhCCCCCEEEEEE-EEE
Confidence 357888888876555567788899999998 3466789999996543 389999999995 444
No 90
>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=91.95 E-value=0.66 Score=46.67 Aligned_cols=72 Identities=15% Similarity=0.200 Sum_probs=52.9
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC-C--------CCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP-G--------ALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~-a--------d~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
|.+.|.|..+. ..+++.-+.|.|.||.|++.+=.+. . ..+..||+|.|.|--.+.-.|.++|.+.
T Consensus 56 v~v~Grv~~~R------~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~gd~V~v~G~~~~t~~gelel~~~ 129 (496)
T TIGR00499 56 VSIAGRIMARR------SMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLGDIIGVTGYPFKTKTGELSVHVT 129 (496)
T ss_pred EEEEEEEEEEe------cCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCCCEEEEEEEEEECCCCcEEEEee
Confidence 88888887753 3467899999999999999774321 1 1378999999997544445688999988
Q ss_pred CCceEEEecC
Q psy3603 116 KSGLIEKIGE 125 (264)
Q Consensus 116 r~G~IekVgE 125 (264)
+ |+.++.
T Consensus 130 ~---i~ilsk 136 (496)
T TIGR00499 130 E---LQILTK 136 (496)
T ss_pred E---EEEEec
Confidence 7 655544
No 91
>PLN02502 lysyl-tRNA synthetase
Probab=91.72 E-value=0.7 Score=47.30 Aligned_cols=72 Identities=18% Similarity=0.217 Sum_probs=51.5
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC-----------CCCCCCCEEEEeeeEEEEECCEEEEE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG-----------ALLHPGDIVRLTKCYAQIWRNCLTLY 113 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a-----------d~Ik~GDIIrI~ngyVs~frG~LqL~ 113 (264)
|.+.+.|..+. .-|++.-+.|.|.+|.|++.+=.+.. ..|..||+|.|.|--.+.-+|.++|.
T Consensus 111 V~v~GrV~~~R------~~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~gdiV~V~G~~~~t~~gelel~ 184 (553)
T PLN02502 111 VSVAGRIMAKR------AFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRGDIVGVTGTPGKTKKGELSIF 184 (553)
T ss_pred EEEEEEEEEEe------cCCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCCcEEEEEEEEEecCCCCEEEE
Confidence 77777777653 22478899999999999997642211 23789999999965444456999999
Q ss_pred EcCCceEEEecC
Q psy3603 114 SSKSGLIEKIGE 125 (264)
Q Consensus 114 Igr~G~IekVgE 125 (264)
+.+ |+.++.
T Consensus 185 ~~~---i~vLs~ 193 (553)
T PLN02502 185 PTS---FEVLTK 193 (553)
T ss_pred EeE---EEEEec
Confidence 886 655544
No 92
>PRK06958 single-stranded DNA-binding protein; Provisional
Probab=91.66 E-value=0.5 Score=42.14 Aligned_cols=63 Identities=14% Similarity=0.159 Sum_probs=46.9
Q ss_pred ccceEEEEEEEecCCceeecCCcEEEEEEEE------e--------CCCeEEEEEecCCCC----CCCCCCEEEEeeeEE
Q psy3603 42 IKNVNVTCIVLDISPRVTLKENREVRTLKVA------D--------STACINLSLWDEPGA----LLHPGDIVRLTKCYA 103 (264)
Q Consensus 42 ~knVnv~fiVle~~~~r~TKdGg~V~tL~LA------D--------eTGsI~ltLWdd~ad----~Ik~GDIIrI~ngyV 103 (264)
+..|.+++.|..-.+.+.+.+|..|+++.|| | .|--+++++|+..++ .|++|+.|.|.+ .+
T Consensus 4 ~N~V~LiGrLg~DPElr~t~nG~~va~fsVAv~~~~kdk~sGe~~e~T~w~~V~~fGk~AE~v~~~LkKGs~V~VeG-rL 82 (182)
T PRK06958 4 VNKVILVGNLGADPEVRYLPSGDAVANIRLATTDRYKDKASGEFKEATEWHRVAFFGRLAEIVGEYLKKGSSVYIEG-RI 82 (182)
T ss_pred ccEEEEEEEecCCCeEEEcCCCCEEEEEEEEeccccccccCCcccccceEEEEEEehHHHHHHHHHhCCCCEEEEEE-EE
Confidence 3458888888886555567788889888886 2 244588999997653 489999999994 55
Q ss_pred EE
Q psy3603 104 QI 105 (264)
Q Consensus 104 s~ 105 (264)
+.
T Consensus 83 ~~ 84 (182)
T PRK06958 83 RT 84 (182)
T ss_pred Ee
Confidence 53
No 93
>KOG3056|consensus
Probab=91.59 E-value=0.64 Score=47.86 Aligned_cols=82 Identities=17% Similarity=0.176 Sum_probs=67.4
Q ss_pred ceEEEEEEEecCCceeecCCcEEEEEEEEeCCC--eEEEEEecCCCCC---CCCCCEEEEeeeEEEEEC----CEEEEEE
Q psy3603 44 NVNVTCIVLDISPRVTLKENREVRTLKVADSTA--CINLSLWDEPGAL---LHPGDIVRLTKCYAQIWR----NCLTLYS 114 (264)
Q Consensus 44 nVnv~fiVle~~~~r~TKdGg~V~tL~LADeTG--sI~ltLWdd~ad~---Ik~GDIIrI~ngyVs~fr----G~LqL~I 114 (264)
+--..++|++++.++.+..|.+|..+.|.|=-+ +|.+=|+++.... ++.|+||-|-|+.+-..+ +..-|.|
T Consensus 187 ~Wvt~GvI~~K~~~K~t~~G~~y~iwkL~dLk~~q~vslfLFG~a~k~~wk~k~GtVialLNp~v~k~~~gs~~~f~LsI 266 (578)
T KOG3056|consen 187 NWVTMGVIVEKSDPKFTSNGNPYSIWKLTDLKDHQTVSLFLFGKAHKRYWKIKLGTVIALLNPEVLKDRPGSRKSFSLSI 266 (578)
T ss_pred CeEEEEEEeecCCcccccCCCceEEEEeeecCccceeEEEEecHHHHHHhhhccCcEEEEeCccccCCCCCCcceEEEEe
Confidence 456889999999998899999999999999988 8999999986432 889999999999887765 3577777
Q ss_pred cCCceEEEecC
Q psy3603 115 SKSGLIEKIGE 125 (264)
Q Consensus 115 gr~G~IekVgE 125 (264)
...-.|..+|+
T Consensus 267 ds~~~ileiG~ 277 (578)
T KOG3056|consen 267 DSSKKILEIGQ 277 (578)
T ss_pred cCccceEEeec
Confidence 77666666654
No 94
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=91.54 E-value=1.7 Score=43.66 Aligned_cols=73 Identities=16% Similarity=0.187 Sum_probs=52.5
Q ss_pred ceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC-C-------CCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 44 NVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP-G-------ALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 44 nVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~-a-------d~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
.|.+.|.|..+.. . |++.-+.|.|.+|.|++.+=.+. . ..|..||+|.|.|--+..-.|.++|.+.
T Consensus 56 ~v~v~G~v~~~R~-----~-g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~g~~v~v~G~v~~t~~ge~el~~~ 129 (491)
T PRK00484 56 EVSVAGRVMLKRV-----M-GKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLGDIIGVEGTLFKTKTGELSVKAT 129 (491)
T ss_pred EEEEEEEEEEEec-----C-CceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCCCEEEEEEEEEEcCCCcEEEEEe
Confidence 3788888877532 2 47899999999999999774321 1 1388999999996444445688999988
Q ss_pred CCceEEEecC
Q psy3603 116 KSGLIEKIGE 125 (264)
Q Consensus 116 r~G~IekVgE 125 (264)
+ |+.++.
T Consensus 130 ~---~~vls~ 136 (491)
T PRK00484 130 E---LTLLTK 136 (491)
T ss_pred E---EEEEec
Confidence 7 555543
No 95
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.
Probab=91.52 E-value=0.44 Score=42.23 Aligned_cols=60 Identities=22% Similarity=0.264 Sum_probs=42.8
Q ss_pred cccccccc---cccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCCC-CCCCCEEEEe
Q psy3603 33 VYIKDLHV---GIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGAL-LHPGDIVRLT 99 (264)
Q Consensus 33 ikIkDLkp---G~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad~-Ik~GDIIrI~ 99 (264)
.+|.+|.. |. -|+..|.|..+... .......|.|.||.+.+.+-+..... .++||-+++.
T Consensus 102 pKI~~L~~q~~Gt-~V~G~F~v~KK~v~------~~~~~YeI~DnTG~MeVvv~G~~~ni~CEeGDKLrL~ 165 (170)
T PF02760_consen 102 PKINDLQKQASGT-FVNGLFTVHKKTVN------KKNTIYEIQDNTGKMEVVVYGKWHNIKCEEGDKLRLF 165 (170)
T ss_dssp --HHHHTTSSTTE-EEEEEEEEEEEEEE------SSEEEEEEEETTEEEEEEEEGGGCGCC--TT-EEEEE
T ss_pred CchhHHhcCCCCc-EEeEEEEEEEEEEc------CCeEEEEEecCCCcEEEEEeccCcccccCCCCeEEEE
Confidence 56777743 44 39999999887643 24667789999999999998876554 7899999987
No 96
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=91.48 E-value=0.84 Score=46.09 Aligned_cols=72 Identities=13% Similarity=0.101 Sum_probs=52.3
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC---------CCCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP---------GALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~---------ad~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
|.+.|.|..+.. . |++.-+.|.|.+|.|++.+=.+. ...+..||+|.|.|--.+.-.|+++|.+.
T Consensus 68 v~v~Grv~~~R~-----~-Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~Gd~V~v~G~~~~t~~gelel~~~ 141 (505)
T PRK12445 68 VSVAGRMMTRRI-----M-GKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLGDIIGARGTLFKTQTGELSIHCT 141 (505)
T ss_pred EEEEEEEEEEec-----C-CCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCCCEEEEEEEEEecCCCcEEEEEe
Confidence 888888877632 2 46788999999999998764221 12378999999996544445799999988
Q ss_pred CCceEEEecC
Q psy3603 116 KSGLIEKIGE 125 (264)
Q Consensus 116 r~G~IekVgE 125 (264)
+ |+.++.
T Consensus 142 ~---~~llsk 148 (505)
T PRK12445 142 E---LRLLTK 148 (505)
T ss_pred E---EEEEec
Confidence 7 655544
No 97
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=91.25 E-value=1.7 Score=44.55 Aligned_cols=87 Identities=13% Similarity=0.059 Sum_probs=61.0
Q ss_pred ccccccccccccc---cceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEe--cCCC-------CCCCCCCEEE
Q psy3603 30 AMDVYIKDLHVGI---KNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLW--DEPG-------ALLHPGDIVR 97 (264)
Q Consensus 30 ~~~ikIkDLkpG~---knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLW--dd~a-------d~Ik~GDIIr 97 (264)
...+.|+||.+.. +.|.+.+.|..+.. .| +++-+.|.|.+|.|++.+= ++.. ..|..||+|.
T Consensus 63 ~~~~~i~~l~~~~~~g~~V~v~Grv~~~R~-----~G-k~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l~~esiV~ 136 (550)
T PTZ00401 63 RTFIPVAVLSKPELVDKTVLIRARVSTTRK-----KG-KMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIPTESIVD 136 (550)
T ss_pred CceEEHHHCCccccCCCEEEEEEEEEEEec-----CC-CeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcCCCCCEEE
Confidence 4568899985332 34888888876532 23 5789999999999999873 2211 2488999999
Q ss_pred EeeeEEEE--------ECCEEEEEEcCCceEEEecCc
Q psy3603 98 LTKCYAQI--------WRNCLTLYSSKSGLIEKIGEF 126 (264)
Q Consensus 98 I~ngyVs~--------frG~LqL~Igr~G~IekVgEf 126 (264)
|.| .+.. -.+.++|.+.+ |..++..
T Consensus 137 V~G-~v~~~~~~~~~~~~~~~El~v~~---i~vls~a 169 (550)
T PTZ00401 137 VEA-TVCKVEQPITSTSHSDIELKVKK---IHTVTES 169 (550)
T ss_pred EEE-EEEecCccCCCCCCccEEEEeeE---EEEEeCC
Confidence 995 5554 25678888887 6666553
No 98
>COG1599 RFA1 Single-stranded DNA-binding replication protein A (RPA), large (70 kD) subunit and related ssDNA-binding proteins [DNA replication, recombination, and repair]
Probab=91.01 E-value=0.94 Score=44.05 Aligned_cols=62 Identities=18% Similarity=0.158 Sum_probs=50.1
Q ss_pred EEEEEecCCcee-ec-CC-cEEEEEEEEeCC-CeEEEEEecCCCCCCCCCCEEEEeeeEEEEECCEEEEE
Q psy3603 48 TCIVLDISPRVT-LK-EN-REVRTLKVADST-ACINLSLWDEPGALLHPGDIVRLTKCYAQIWRNCLTLY 113 (264)
Q Consensus 48 ~fiVle~~~~r~-TK-dG-g~V~tL~LADeT-GsI~ltLWdd~ad~Ik~GDIIrI~ngyVs~frG~LqL~ 113 (264)
...|+.....+. .. +| +.+....|.|.| |.+.++.|++. +.|++..+.++++..|++...++
T Consensus 173 ~~~v~~g~~ik~~~~~~ge~~~~~~~~~d~~~~~~~~~~~~~~----~~g~~~~ie~~~v~~~~~~~~~~ 238 (407)
T COG1599 173 KARVVVGSEIKTFDNQGGESKVFSNELEDEERGVIVFTDWDPS----QDGDVYRIEGARVKTKNKQPEEN 238 (407)
T ss_pred eEEEEecccceeEecCCCccceEeeeecccceeEEEeccCccc----ccceeeeecCcEEEEeccccccc
Confidence 667777776765 22 33 567888999987 99999999975 78999999999999998888875
No 99
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=90.98 E-value=0.64 Score=41.49 Aligned_cols=62 Identities=16% Similarity=0.139 Sum_probs=46.5
Q ss_pred ccceEEEEEEEecCCceeecCCcEEEEEEEEe---------------CCCeEEEEEecCCC----CCCCCCCEEEEeeeE
Q psy3603 42 IKNVNVTCIVLDISPRVTLKENREVRTLKVAD---------------STACINLSLWDEPG----ALLHPGDIVRLTKCY 102 (264)
Q Consensus 42 ~knVnv~fiVle~~~~r~TKdGg~V~tL~LAD---------------eTGsI~ltLWdd~a----d~Ik~GDIIrI~ngy 102 (264)
+..|.+++.+..--+.+.+.+|..|++++|+- +|--|++++|+..+ +.|+.||.|.|.+ +
T Consensus 4 ~~~VtLiGrL~~DPElR~t~sG~~va~FrVAv~~r~~~~~~g~~~d~~t~fi~V~~Wg~~Ae~va~~L~KGd~V~V~G-r 82 (186)
T PRK07772 4 DTTITVVGNLTADPELRFTPSGAAVANFTVASTPRTFDRQTNEWKDGEALFLRCSIWRQAAENVAESLTKGMRVIVTG-R 82 (186)
T ss_pred cCEEEEEEEeCCCCeEEEcCCCCEEEEEEEEecCcceecCCCcEeccCceEEEEEEecHHHHHHHHhcCCCCEEEEEE-E
Confidence 44588888888876666678888898888882 12257899999764 3489999999995 4
Q ss_pred EE
Q psy3603 103 AQ 104 (264)
Q Consensus 103 Vs 104 (264)
.+
T Consensus 83 L~ 84 (186)
T PRK07772 83 LK 84 (186)
T ss_pred EE
Confidence 44
No 100
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=90.98 E-value=0.31 Score=52.89 Aligned_cols=65 Identities=22% Similarity=0.313 Sum_probs=51.9
Q ss_pred cccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC---CCCCCCCEEEEee
Q psy3603 33 VYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG---ALLHPGDIVRLTK 100 (264)
Q Consensus 33 ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a---d~Ik~GDIIrI~n 100 (264)
..|.+|..+. .+.+.+.|.++...+ |.|.++..+++.|.||+|.+++|.+.. ..+.+|+++.|.+
T Consensus 889 ~~~~~l~~~~-~~~v~g~i~~~~~~~--K~g~~maf~~~eD~~~~~e~~~F~~~~~~~~~l~~~~~~~~~~ 956 (973)
T PRK07135 889 IRLKDLRINT-EYRLAIEVKNVKRLR--KANKEYKKVILSDDSVEITIFVNDNDYLLFETLKKGDIYEFLI 956 (973)
T ss_pred hhHHHhcCCC-eEEEEEEEEEEEEEe--eCCCeEEEEEEEECCCcEEEEEcHHHHHHHHHhhcCCEEEEEE
Confidence 3577775555 488999999987554 788999999999999999999997542 2378899999874
No 101
>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=90.91 E-value=3.4 Score=30.81 Aligned_cols=65 Identities=15% Similarity=0.204 Sum_probs=42.8
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCe--EEEEEecCC-----CCCCCCCCEEEEeeeEEEEE-C--CEEEEEE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTAC--INLSLWDEP-----GALLHPGDIVRLTKCYAQIW-R--NCLTLYS 114 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGs--I~ltLWdd~-----ad~Ik~GDIIrI~ngyVs~f-r--G~LqL~I 114 (264)
|.+.+.|..+ |+.+.+.-+.|.|.||. +++.+=.+. ...+..||+|.|.| .+..- + +.++|.+
T Consensus 2 v~v~Gwv~~~------R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~gs~V~v~G-~v~~~~~~~~~~El~~ 74 (82)
T cd04318 2 VTVNGWVRSV------RDSKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTGSSIRVEG-VLVKSPGAKQPFELQA 74 (82)
T ss_pred EEEEEeEEEE------EcCCcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCceEEEEEE-EEEeCCCCCCCEEEEE
Confidence 4455666543 22345788899999994 999764332 23488999999996 45443 2 5677776
Q ss_pred cC
Q psy3603 115 SK 116 (264)
Q Consensus 115 gr 116 (264)
.+
T Consensus 75 ~~ 76 (82)
T cd04318 75 EK 76 (82)
T ss_pred EE
Confidence 64
No 102
>PLN02850 aspartate-tRNA ligase
Probab=90.69 E-value=1.8 Score=43.98 Aligned_cols=85 Identities=14% Similarity=0.099 Sum_probs=59.6
Q ss_pred ccccccccccc---cccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC----------CCCCCCCCEE
Q psy3603 30 AMDVYIKDLHV---GIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP----------GALLHPGDIV 96 (264)
Q Consensus 30 ~~~ikIkDLkp---G~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~----------ad~Ik~GDII 96 (264)
...+.|++|.+ |+. |.+.+.|..+.. .| ++.-+.|.|.+|+|++.+=... +..|..||+|
T Consensus 67 ~~~~~i~~l~~~~~g~~-V~v~Grv~~~R~-----~g-k~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~es~V 139 (530)
T PLN02850 67 REWTDVSDLGEELAGSE-VLIRGRVHTIRG-----KG-KSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQLSRESVV 139 (530)
T ss_pred ceEeEhhhcchhhCCCE-EEEEEEEEEEcc-----CC-CeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCCCCCCEE
Confidence 35678888854 554 888888877532 23 4789999999999999885432 2348899999
Q ss_pred EEeeeEEEE-------ECCEEEEEEcCCceEEEecC
Q psy3603 97 RLTKCYAQI-------WRNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 97 rI~ngyVs~-------frG~LqL~Igr~G~IekVgE 125 (264)
.|.| .+.. -.+.++|.+.+ |..++.
T Consensus 140 ~V~G-~v~~~~~~~~~~t~~~El~~~~---i~vls~ 171 (530)
T PLN02850 140 DVEG-VVSVPKKPVKGTTQQVEIQVRK---IYCVSK 171 (530)
T ss_pred EEEE-EEEccCcCCCCCCccEEEEEeE---EEEEeC
Confidence 9995 5652 12457887776 655544
No 103
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=90.62 E-value=0.89 Score=49.99 Aligned_cols=82 Identities=21% Similarity=0.204 Sum_probs=58.2
Q ss_pred cccccc---ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC---------CCCCCCCEEEEeee
Q psy3603 34 YIKDLH---VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG---------ALLHPGDIVRLTKC 101 (264)
Q Consensus 34 kIkDLk---pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a---------d~Ik~GDIIrI~ng 101 (264)
.|+++. .|++ |.+.+.|..+. +.+++.-+.|.|.||.|++.+=.+.. ..|+.||+|.|+|-
T Consensus 641 ~~~~~~~~~~~~~-V~v~Grv~~~R------~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~gd~V~v~G~ 713 (1094)
T PRK02983 641 TVAEALDAPTGEE-VSVSGRVLRIR------DYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLGDLVEVTGT 713 (1094)
T ss_pred CHHHHHHhcCCCE-EEEEEEEEEEe------eCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCCCEEEEEEE
Confidence 355553 4554 88888887763 23478999999999999997743321 23789999999975
Q ss_pred EEEEECCEEEEEEcCCceEEEecC
Q psy3603 102 YAQIWRNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 102 yVs~frG~LqL~Igr~G~IekVgE 125 (264)
-.+.-+|+++|.+.+ |+.++.
T Consensus 714 v~~t~~ge~ei~~~~---i~ll~k 734 (1094)
T PRK02983 714 MGTSRNGTLSLLVTS---WRLAGK 734 (1094)
T ss_pred EEEcCCCCEEEEEeE---EEEEec
Confidence 555556889988876 655543
No 104
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=90.23 E-value=1.3 Score=44.59 Aligned_cols=72 Identities=13% Similarity=0.107 Sum_probs=53.6
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCCC----CCCCCEEEEeeeEEEEE--CCEEEEEEcC
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGAL----LHPGDIVRLTKCYAQIW--RNCLTLYSSK 116 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad~----Ik~GDIIrI~ngyVs~f--rG~LqL~Igr 116 (264)
.+|-+.+-|-.+..+ ..| -..+.|.|+.+.|++++|.-.... .++|+-|.|. |.++.| +|..||++..
T Consensus 24 ~~V~v~GEISn~t~~---~sg--H~YFtLKD~~A~i~c~mf~~~~~~l~f~p~eG~~V~v~-G~is~Y~~rG~YQi~~~~ 97 (440)
T COG1570 24 GQVWVRGEISNFTRP---ASG--HLYFTLKDERAQIRCVMFKGNNRRLKFRPEEGMQVLVR-GKISLYEPRGDYQIVAES 97 (440)
T ss_pred CeEEEEEEecCCccC---CCc--cEEEEEccCCceEEEEEEcCcccccCCCccCCCEEEEE-EEEEEEcCCCceEEEEec
Confidence 447777766665433 355 445578899999999999854322 6689999999 689999 7999999986
Q ss_pred CceEEEe
Q psy3603 117 SGLIEKI 123 (264)
Q Consensus 117 ~G~IekV 123 (264)
|+..
T Consensus 98 ---~~p~ 101 (440)
T COG1570 98 ---MEPA 101 (440)
T ss_pred ---CCcC
Confidence 6554
No 105
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=90.21 E-value=1.2 Score=40.65 Aligned_cols=63 Identities=19% Similarity=0.164 Sum_probs=48.1
Q ss_pred ccceEEEEEEEecCCceeecCCcEEEEEEEEe-----CCCeEEEEEecCCCC---CCCCCCEEEEeeeEEEE
Q psy3603 42 IKNVNVTCIVLDISPRVTLKENREVRTLKVAD-----STACINLSLWDEPGA---LLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 42 ~knVnv~fiVle~~~~r~TKdGg~V~tL~LAD-----eTGsI~ltLWdd~ad---~Ik~GDIIrI~ngyVs~ 105 (264)
+..|.+.+.+..-.+.+.+..|..+..+.||= +|--|++++|+..++ .++.||-|.|.| ..+.
T Consensus 109 ~N~V~LiGrL~~DPelR~t~~G~~va~f~lAvnr~~~~td~i~~v~wg~~Ae~~~~l~KG~~V~V~G-rL~s 179 (219)
T PRK05813 109 PNEIFLDGYICKEPVYRTTPFGREIADLLLAVNRPYNKSDYIPCIAWGRNARFCKTLEVGDNIRVWG-RVQS 179 (219)
T ss_pred ccEEEEEEEccCCCeEEECCCCCEEEEEEEEEcCCCCCceEEEEEEEhHHhHHHhhCCCCCEEEEEE-EEEe
Confidence 44577788777766666678899999999983 266799999996653 389999999995 4543
No 106
>PRK06642 single-stranded DNA-binding protein; Provisional
Probab=89.91 E-value=1.1 Score=38.34 Aligned_cols=62 Identities=18% Similarity=0.140 Sum_probs=46.1
Q ss_pred ccceEEEEEEEecCCceeecCCcEEEEEEEE------eC--------CCeEEEEEecC-CC----CCCCCCCEEEEeeeE
Q psy3603 42 IKNVNVTCIVLDISPRVTLKENREVRTLKVA------DS--------TACINLSLWDE-PG----ALLHPGDIVRLTKCY 102 (264)
Q Consensus 42 ~knVnv~fiVle~~~~r~TKdGg~V~tL~LA------De--------TGsI~ltLWdd-~a----d~Ik~GDIIrI~ngy 102 (264)
+..|.+++.|..-.+.+.+.+|..|+.+.|| |+ |-=+++++|+. .+ +.++.||.|.|.| .
T Consensus 5 ~N~V~LiGrLg~DPElr~t~~G~~v~~fslAv~~~~k~~~~G~~~~~T~w~~v~~~g~~~Ae~~~~~l~KG~~V~V~G-r 83 (152)
T PRK06642 5 LNKVILIGNVGRDPEIRTTGEGKKIINLSLATTETWKDRITSERKERTEWHRVVIFSEGLVSVVERYVTKGSKLYIEG-S 83 (152)
T ss_pred ceEEEEEEEccCCceEEECCCCCEEEEEEEEeccccccccCCccccceeEEEEEEeChHHHHHHHHhCCCCCEEEEEE-E
Confidence 4458888888876555567788899999998 32 33578999996 43 3489999999994 5
Q ss_pred EE
Q psy3603 103 AQ 104 (264)
Q Consensus 103 Vs 104 (264)
.+
T Consensus 84 L~ 85 (152)
T PRK06642 84 LQ 85 (152)
T ss_pred EE
Confidence 44
No 107
>cd04486 YhcR_OBF_like YhcR_OBF_like: A subfamily of OB-fold domains similar to the OB folds of Bacillus subtilis YhcR. YhcR is a sugar-nonspecific nuclease, which is active in the presence of Ca2+ and Mn2+. It cleaves RNA endonucleolytically, producing 3'-monophosphate nucleosides. YhcR appears to be the major Ca2+ activated nuclease of B. subtilis. YhcR may be localized in the cell wall.
Probab=89.18 E-value=0.96 Score=34.64 Aligned_cols=29 Identities=28% Similarity=0.305 Sum_probs=24.9
Q ss_pred CCCCCCCCEEEEeeeEEEEECCEEEEEEcC
Q psy3603 87 GALLHPGDIVRLTKCYAQIWRNCLTLYSSK 116 (264)
Q Consensus 87 ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr 116 (264)
...+++||.|+|. |.+++|+|..||....
T Consensus 42 ~~~~~~Gd~V~vt-G~v~ey~g~tql~~~~ 70 (78)
T cd04486 42 GADVAVGDLVRVT-GTVTEYYGLTQLTAVS 70 (78)
T ss_pred CCCCCCCCEEEEE-EEEEeeCCeEEEccCC
Confidence 4458999999998 7899999999988754
No 108
>cd04494 BRCA2DBD_OB2 BRCA2DBD_OB2: A subfamily of OB folds corresponding to the second OB fold (OB2) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA).
Probab=89.10 E-value=1.2 Score=41.78 Aligned_cols=64 Identities=20% Similarity=0.218 Sum_probs=52.2
Q ss_pred CCcEEEEEEEEeCC----CeEEEEEecCCCC---CCCCCCEEEEeeeEEEEECC-----EEEEEEcCCceEEEecC
Q psy3603 62 ENREVRTLKVADST----ACINLSLWDEPGA---LLHPGDIVRLTKCYAQIWRN-----CLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 62 dGg~V~tL~LADeT----GsI~ltLWdd~ad---~Ik~GDIIrI~ngyVs~frG-----~LqL~Igr~G~IekVgE 125 (264)
+=.+++.|+|.|-. .+..+++|+...+ .|++|-.++|+|-.++..++ .++|..++.+.-+.+..
T Consensus 162 dVtp~~klRV~d~~~~~~~~~~LTIWrPtedl~s~L~EG~ry~i~~L~~s~~k~~~~~~~vqLtatk~Tr~~~l~~ 237 (251)
T cd04494 162 DVTPVWKLRVTDYRSKPEKSGLLSIWRPTEDLRSLLTEGKRYRIYGLATSNSKKRSGNEEVQLTATKKTRYQPLPV 237 (251)
T ss_pred cceeEEEEEEeecccCCCceEEEEEeCCCHHHHhhhcCCcEEEEEeccccCCCCCCCcceEEEEecCcccceECCH
Confidence 33688999999987 8899999996654 59999999999877777655 89999999887776543
No 109
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=88.54 E-value=3.9 Score=43.03 Aligned_cols=72 Identities=14% Similarity=0.090 Sum_probs=51.7
Q ss_pred ceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC--C--------CCCCCCCEEEEeeeEEEE-ECCEEEE
Q psy3603 44 NVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP--G--------ALLHPGDIVRLTKCYAQI-WRNCLTL 112 (264)
Q Consensus 44 nVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~--a--------d~Ik~GDIIrI~ngyVs~-frG~LqL 112 (264)
.|.+.+.|..+.. - |++.-+.|.|.||.|++.+=.+. . ..+..||+|.|.| .+.. -.|+++|
T Consensus 109 ~V~vaGrV~~~R~-----~-Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~gdiV~V~G-~v~~t~~GeleI 181 (659)
T PTZ00385 109 TVRVAGRVTSVRD-----I-GKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVGDIIGADG-VPCRMQRGELSV 181 (659)
T ss_pred EEEEEEEEEeeec-----c-CCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCCCEEEEEE-EEEecCCceEEE
Confidence 3888888877532 2 45788889999999999885321 1 2478999999996 4544 3699999
Q ss_pred EEcCCceEEEecC
Q psy3603 113 YSSKSGLIEKIGE 125 (264)
Q Consensus 113 ~Igr~G~IekVgE 125 (264)
.+.+ |+.+..
T Consensus 182 ~~~~---i~lLsk 191 (659)
T PTZ00385 182 AASR---MLILSP 191 (659)
T ss_pred EeeE---EEEech
Confidence 8887 555543
No 110
>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=87.57 E-value=5.6 Score=31.13 Aligned_cols=71 Identities=14% Similarity=0.059 Sum_probs=45.3
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC-------CCCCCCCCEEEEeeeEEEEEC---CEEEEEE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP-------GALLHPGDIVRLTKCYAQIWR---NCLTLYS 114 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~-------ad~Ik~GDIIrI~ngyVs~fr---G~LqL~I 114 (264)
|.+.|.|..+ |+.+++.-+.|.|.||.+++.+=.+. ...+..||+|.|.| .+..-. +.++|.+
T Consensus 2 V~v~Gwv~~~------R~~gk~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~l~~~s~v~V~G-~v~~~~~~~~~~Ei~~ 74 (103)
T cd04319 2 VTLAGWVYRK------REVGKKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIESSVIVEG-AVKADPRAPGGAEVHG 74 (103)
T ss_pred EEEEEEEEeE------EcCCCeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCCCEEEEEE-EEEECCCCCCCEEEEE
Confidence 4455555543 33345788899999999998664321 12378899999995 455432 3466666
Q ss_pred cCCceEEEecC
Q psy3603 115 SKSGLIEKIGE 125 (264)
Q Consensus 115 gr~G~IekVgE 125 (264)
.+ |+.+++
T Consensus 75 ~~---i~vl~~ 82 (103)
T cd04319 75 EK---LEIIQN 82 (103)
T ss_pred EE---EEEEec
Confidence 54 555554
No 111
>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=87.31 E-value=3.5 Score=34.93 Aligned_cols=68 Identities=15% Similarity=0.180 Sum_probs=43.6
Q ss_pred cccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecC--CCCCCCCCCEEEEeeeEEEEECCEEEEEE
Q psy3603 37 DLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDE--PGALLHPGDIVRLTKCYAQIWRNCLTLYS 114 (264)
Q Consensus 37 DLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd--~ad~Ik~GDIIrI~ngyVs~frG~LqL~I 114 (264)
+++++.. |.+.+.|++.- ++.. .++.|.||+|.+-+=++ ....+.|+|-|+|. |.+..--...+|.+
T Consensus 53 ~~~Ddt~-V~L~G~Iv~~l------~~d~---Y~F~D~TG~I~VeId~~~w~G~~v~p~d~V~I~-GeVDk~~~~~~IdV 121 (126)
T TIGR00156 53 SMHDGAS-VTLRGNIISHI------GDDR---YVFRDKSGEINVVIPAAVWNGREVQPKDMVNIS-GSLDKKSAPAEVDV 121 (126)
T ss_pred hCCCCCE-EEEEEEEEEEe------CCce---EEEECCCCCEEEEECHHHcCCCcCCCCCEEEEE-EEECCCCCCeEEEE
Confidence 3556665 88888887642 1222 47899999999988222 23458999999999 45653212344444
Q ss_pred c
Q psy3603 115 S 115 (264)
Q Consensus 115 g 115 (264)
.
T Consensus 122 ~ 122 (126)
T TIGR00156 122 T 122 (126)
T ss_pred E
Confidence 3
No 112
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=87.20 E-value=2.8 Score=33.16 Aligned_cols=62 Identities=21% Similarity=0.299 Sum_probs=43.2
Q ss_pred EEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEec----CCCCCCCCCCEEEEeeeEEEEEC---CEEEEEEcC
Q psy3603 47 VTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWD----EPGALLHPGDIVRLTKCYAQIWR---NCLTLYSSK 116 (264)
Q Consensus 47 v~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWd----d~ad~Ik~GDIIrI~ngyVs~fr---G~LqL~Igr 116 (264)
+.++|.++... +. =..+++.|.||+|.+++-. +..+.|.+|-++-+++ |..|. ..-.|+|..
T Consensus 7 l~v~Iks~~~~-----~~-D~~v~l~DpTG~i~~tiH~~v~~~y~~~l~~GavLlLk~--V~Vf~ps~~~~yLnIt~ 75 (86)
T PF15072_consen 7 LVVIIKSIVPS-----SE-DAFVVLKDPTGEIRGTIHRKVLEEYGDELSPGAVLLLKD--VTVFSPSPRSHYLNITL 75 (86)
T ss_pred EEEEEEEeecc-----CC-CeEEEEECCCCcEEEEEeHHHHhhcCCccccCEEEEEee--eeEEecCCCccEEEEeh
Confidence 44555555432 22 3478999999999999986 3456799999999994 77774 344555553
No 113
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=86.60 E-value=4.7 Score=39.98 Aligned_cols=75 Identities=25% Similarity=0.234 Sum_probs=53.5
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC-------CCCCCCCCEEEEeeeEEEEE---CCE
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP-------GALLHPGDIVRLTKCYAQIW---RNC 109 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~-------ad~Ik~GDIIrI~ngyVs~f---rG~ 109 (264)
.|+. |.+.|.|..+.. -+++.-+.|.|.||.|++.+=-+. ...|..||+|.|.| .+..- .+.
T Consensus 15 ~~~~-V~i~G~v~~~R~------~g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~s~v~v~G-~v~~~~~~~~~ 86 (450)
T PRK03932 15 VGQE-VTVRGWVRTKRD------SGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTGSSVIVTG-TVVESPRAGQG 86 (450)
T ss_pred CCCE-EEEEEEEEEEEe------CCCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCCcEEEEEE-EEEcCCCCCCC
Confidence 3554 999999987642 256888999999999988774321 12388999999995 56543 257
Q ss_pred EEEEEcCCceEEEecC
Q psy3603 110 LTLYSSKSGLIEKIGE 125 (264)
Q Consensus 110 LqL~Igr~G~IekVgE 125 (264)
++|.+.+ |+.++.
T Consensus 87 ~el~~~~---i~vl~~ 99 (450)
T PRK03932 87 YELQATK---IEVIGE 99 (450)
T ss_pred EEEEEEE---EEEccC
Confidence 8888876 666654
No 114
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=86.27 E-value=3.6 Score=41.34 Aligned_cols=84 Identities=23% Similarity=0.235 Sum_probs=61.0
Q ss_pred ccccccccccc--cceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecC-C------CCCCCCCCEEEEeeeE
Q psy3603 32 DVYIKDLHVGI--KNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDE-P------GALLHPGDIVRLTKCY 102 (264)
Q Consensus 32 ~ikIkDLkpG~--knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd-~------ad~Ik~GDIIrI~ngy 102 (264)
...|+||.+.. +.|.+.+=|.++. +-+.+.-+.|.|.||.|++++=.. . +..|.-+++|.|.| .
T Consensus 4 ~~~i~di~~~~~~~~V~v~GWV~~~R------~~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~es~v~V~G-~ 76 (435)
T COG0017 4 RTYIKDIKPHVGGQEVTVRGWVHNKR------DLGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLESSVVVTG-I 76 (435)
T ss_pred eeeHHhhhccCCCcEEEEEEEeeeec------ccCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCccEEEEEE-E
Confidence 46778876532 3488888887764 225699999999999999999731 1 22478899999995 4
Q ss_pred EEEE---CCEEEEEEcCCceEEEecC
Q psy3603 103 AQIW---RNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 103 Vs~f---rG~LqL~Igr~G~IekVgE 125 (264)
++.- .+.++|.+.+ |+.+++
T Consensus 77 v~~~~~a~~g~El~v~~---i~Vl~~ 99 (435)
T COG0017 77 VKASPKAPQGFELQVEK---IEVLGE 99 (435)
T ss_pred EEcCCCCCCCEEEEEEE---EEEeec
Confidence 6554 3778888887 766655
No 115
>PRK08402 replication factor A; Reviewed
Probab=86.24 E-value=1.2 Score=43.25 Aligned_cols=58 Identities=16% Similarity=0.178 Sum_probs=43.7
Q ss_pred ccccccccccccccceEEEEEEEecCCc-----------eee-c----------CC------cEEEEEEEEeCCCeEEEE
Q psy3603 30 AMDVYIKDLHVGIKNVNVTCIVLDISPR-----------VTL-K----------EN------REVRTLKVADSTACINLS 81 (264)
Q Consensus 30 ~~~ikIkDLkpG~knVnv~fiVle~~~~-----------r~T-K----------dG------g~V~tL~LADeTGsI~lt 81 (264)
+....|.+|.+|...|++.+.|+.+... +.+ . .| ..++++.|.|.||.+.++
T Consensus 182 ~~~k~I~ei~~gd~~v~v~g~Iv~i~~~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG~~~vt 261 (355)
T PRK08402 182 YTRKKIGELEGGERFVEVRGTIAKVYRVLVYDACPECRRKVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTGYIRVT 261 (355)
T ss_pred ccccCHHHcccCCcEEEEEEEEEEEecCeeEecCCCCCeEEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCCcEEEE
Confidence 4457889999988779999999998761 112 1 12 123688999999999999
Q ss_pred EecCCC
Q psy3603 82 LWDEPG 87 (264)
Q Consensus 82 LWdd~a 87 (264)
+|++.+
T Consensus 262 ~f~e~a 267 (355)
T PRK08402 262 LFGDDA 267 (355)
T ss_pred EecHHH
Confidence 999875
No 116
>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=85.96 E-value=4.2 Score=40.47 Aligned_cols=75 Identities=25% Similarity=0.229 Sum_probs=53.9
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCC--CeEEEEEecCC-------CCCCCCCCEEEEeeeEEEE---EC
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADST--ACINLSLWDEP-------GALLHPGDIVRLTKCYAQI---WR 107 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeT--GsI~ltLWdd~-------ad~Ik~GDIIrI~ngyVs~---fr 107 (264)
.|+. |.+.|.|.++. .++++.-+.|.|.| |.|++.+=... ...|..||+|.|.| .+.. -.
T Consensus 15 ~g~~-v~v~Gwv~~~R------~~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~gs~V~v~G-~v~~~~~~~ 86 (453)
T TIGR00457 15 VGDE-VTVSGWVRTKR------SSKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTGSSVSVTG-KVVESPGKG 86 (453)
T ss_pred CCCE-EEEEEEeEEEE------cCCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCCcEEEEEE-EEEcCCCCC
Confidence 3554 99999987763 34578888999999 99999774431 12488999999995 5554 24
Q ss_pred CEEEEEEcCCceEEEecC
Q psy3603 108 NCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 108 G~LqL~Igr~G~IekVgE 125 (264)
+.++|.+.+ |+.++.
T Consensus 87 ~~~El~~~~---i~vl~~ 101 (453)
T TIGR00457 87 QPVELQVKK---IEVVGE 101 (453)
T ss_pred CCEEEEEeE---EEEEec
Confidence 678888875 666654
No 117
>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=85.53 E-value=4 Score=42.22 Aligned_cols=74 Identities=11% Similarity=0.116 Sum_probs=51.0
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC-----CCCCCCCCEEEEeeeEEEE---------
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP-----GALLHPGDIVRLTKCYAQI--------- 105 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~-----ad~Ik~GDIIrI~ngyVs~--------- 105 (264)
.|++ |.+.+.|..+. +-+++.-+.|.|.||.|++.+=.+. ...+..||+|.|.| .+..
T Consensus 14 ~g~~-V~l~GwV~~~R------~~Gkl~Fi~LrD~sg~iQvv~~~~~~~~~~~~~L~~esvV~V~G-~v~~r~~~~~n~~ 85 (583)
T TIGR00459 14 LGQT-VTLAGWVNRRR------DLGGLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNEDVVQVKG-KVSARPEGNINRN 85 (583)
T ss_pred CCCE-EEEEEEEEEEE------cCCCcEEEEEEeCCccEEEEEeCCHHHHHHHhcCCCCCEEEEEE-EEEeCCccccCcc
Confidence 3565 88888887653 2245889999999999999764321 23488999999995 5653
Q ss_pred -ECCEEEEEEcCCceEEEec
Q psy3603 106 -WRNCLTLYSSKSGLIEKIG 124 (264)
Q Consensus 106 -frG~LqL~Igr~G~IekVg 124 (264)
-.|.++|.+.+ |+.++
T Consensus 86 ~~tg~iEl~~~~---i~iL~ 102 (583)
T TIGR00459 86 LDTGEIEILAES---ITLLN 102 (583)
T ss_pred CCCCcEEEEEeE---EEEee
Confidence 24667777665 44443
No 118
>PF02721 DUF223: Domain of unknown function DUF223; InterPro: IPR003871 The function of this domain has not been characterised, but may be involved in nucleic acid or nucleotide binding.
Probab=84.56 E-value=1.8 Score=33.61 Aligned_cols=43 Identities=12% Similarity=0.071 Sum_probs=33.8
Q ss_pred EEEEeCCCe-EEEEEecCCC----CCCCCCCEEEEeeeEEEEECCEEE
Q psy3603 69 LKVADSTAC-INLSLWDEPG----ALLHPGDIVRLTKCYAQIWRNCLT 111 (264)
Q Consensus 69 L~LADeTGs-I~ltLWdd~a----d~Ik~GDIIrI~ngyVs~frG~Lq 111 (264)
|+|+|+.|. |.++++.+.. ..|++|.+..|.+-.|....|...
T Consensus 2 mvL~De~G~~I~A~I~~~~~~~f~~~l~Eg~~y~i~~F~V~~~~~~yr 49 (95)
T PF02721_consen 2 MVLVDEKGDKIQATIPKELVDKFKDSLKEGSWYTISNFTVSPNSGSYR 49 (95)
T ss_pred EEEEecCCCEEEEEECHHHHHHHHhhcccCCEEEeEeEEEEeCCCcee
Confidence 789999997 9999998653 459999999999876665444443
No 119
>PRK06341 single-stranded DNA-binding protein; Provisional
Probab=84.53 E-value=3.2 Score=36.43 Aligned_cols=62 Identities=16% Similarity=0.185 Sum_probs=44.6
Q ss_pred ccceEEEEEEEecCCceeecCCcEEEEEEEEeC-------CC-------eEEEEEecC-CC----CCCCCCCEEEEeeeE
Q psy3603 42 IKNVNVTCIVLDISPRVTLKENREVRTLKVADS-------TA-------CINLSLWDE-PG----ALLHPGDIVRLTKCY 102 (264)
Q Consensus 42 ~knVnv~fiVle~~~~r~TKdGg~V~tL~LADe-------TG-------sI~ltLWdd-~a----d~Ik~GDIIrI~ngy 102 (264)
+..|.+++.|..--+.+.+.+|..|+++.||=. +| -+++++|++ .+ +.|+.|+.|.|.+ .
T Consensus 5 mN~V~LiGrLg~DPElR~t~sG~~v~~fsVAvn~~~kd~~~Ge~~e~T~w~~Vv~fg~~~Ae~~~~~LkKG~~V~VeG-r 83 (166)
T PRK06341 5 VNKVILIGNLGADPEIRRTQDGRPIANLRIATSETWRDRNSGERKEKTEWHRVVIFNEGLCKVAEQYLKKGAKVYIEG-Q 83 (166)
T ss_pred ceEEEEEEEecCCCEEEEcCCCCEEEEEEEEEccceecCCCCcccccceEEEEEEeChHHHHHHHHhcCCCCEEEEEE-E
Confidence 445888888887545555778888988888652 34 358999996 33 3489999999994 4
Q ss_pred EE
Q psy3603 103 AQ 104 (264)
Q Consensus 103 Vs 104 (264)
++
T Consensus 84 L~ 85 (166)
T PRK06341 84 LQ 85 (166)
T ss_pred EE
Confidence 43
No 120
>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=84.21 E-value=1.5 Score=48.01 Aligned_cols=43 Identities=16% Similarity=0.268 Sum_probs=35.3
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEe
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLW 83 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLW 83 (264)
.+.. +.+.+.|..+.....||.|..+.-++|.|.||.|.+++|
T Consensus 980 ~g~~-v~v~G~i~~~~~~~~tkkG~~maf~tleD~tg~ie~viF 1022 (1022)
T TIGR00594 980 NDSQ-VRTLGGLNSVKKKITTKNGKPMAFLQLEDETGSIEVVVF 1022 (1022)
T ss_pred CCCE-EEEEEEEEEEEEecccCCCCEEEEEEEEECCCcEEEEeC
Confidence 4453 888888887764435688989999999999999999987
No 121
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=84.05 E-value=3.2 Score=42.90 Aligned_cols=72 Identities=17% Similarity=0.193 Sum_probs=50.3
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC-----------CCCCCCCCEEEEeeeEEEEECCEEEEE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP-----------GALLHPGDIVRLTKCYAQIWRNCLTLY 113 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~-----------ad~Ik~GDIIrI~ngyVs~frG~LqL~ 113 (264)
|.+.|.|..+. .-|+++.-+.|.|.+|.|++.+=.+. ...+..||+|.|.|.-.+.-.|+++|.
T Consensus 135 v~v~Grv~~~R-----~~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~Gd~V~V~G~~~~t~~gel~i~ 209 (585)
T PTZ00417 135 LNVTGRIMRVS-----ASGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRGDIVGIVGFPGKSKKGELSIF 209 (585)
T ss_pred EEEEEEEEeee-----cCCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCCCEEEEEeEEcCCCCceEEEE
Confidence 67777776653 23446788888999999999885221 124789999999975333346899988
Q ss_pred EcCCceEEEec
Q psy3603 114 SSKSGLIEKIG 124 (264)
Q Consensus 114 Igr~G~IekVg 124 (264)
+.+ |+.++
T Consensus 210 ~~~---i~lls 217 (585)
T PTZ00417 210 PKE---TIILS 217 (585)
T ss_pred EEE---EEEEe
Confidence 886 54443
No 122
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=84.03 E-value=3.7 Score=46.08 Aligned_cols=113 Identities=19% Similarity=0.122 Sum_probs=79.1
Q ss_pred ccccccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC------CCCCCCCCEEEEeeeEE
Q psy3603 30 AMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP------GALLHPGDIVRLTKCYA 103 (264)
Q Consensus 30 ~~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~------ad~Ik~GDIIrI~ngyV 103 (264)
++...+-++.+.+.+|.+.+.|-++... ++|.|+..+++.|.|-|-++.+..|-.. .+.|+.|+-|+++| .+
T Consensus 227 ~~i~~~~~i~~~~~~v~v~G~IF~~e~~-~~ksGr~l~~i~vTD~t~Sl~~k~f~~~~ed~~~~~~ik~g~wvk~~g-~v 304 (1444)
T COG2176 227 EEIKPLIKINEEETRVKVEGYIFKIEIK-ELKSGRTLLNIKVTDYTSSLILKKFLRDEEDEKKFDGIKKGMWVKARG-NV 304 (1444)
T ss_pred cceeehhhccccccceEEEEEEEEEeee-ecccCcEEEEEEEecCchheeehhhccccccHHHHhhcccCcEEEEEE-EE
Confidence 4455666677777779999999987633 6789999999999999999999999742 24499999999994 56
Q ss_pred EE--ECCEEEEEEcCCceEEEe------cCceeeecCCCCCCCCCCCCC
Q psy3603 104 QI--WRNCLTLYSSKSGLIEKI------GEFCMVFNENLDMSIPIPNLP 144 (264)
Q Consensus 104 s~--frG~LqL~Igr~G~IekV------gEf~~~fnE~pNiSe~~Pe~~ 144 (264)
.. |-+.+++.+..-.+|+.. .|-+.++.--.+||...--+.
T Consensus 305 ~~d~f~~~l~m~i~~I~ei~~~~r~D~~~eKRVELh~HTkMS~mDai~s 353 (1444)
T COG2176 305 QLDTFTRDLTMIINDINEIENAKRKDLAKEKRVELHFHTKMSQMDAITS 353 (1444)
T ss_pred EecccccceEEEhhhhhhhhcccccccCccceEEEEeccchhhhcccCC
Confidence 65 458888888873333221 122223333466776554443
No 123
>PLN02603 asparaginyl-tRNA synthetase
Probab=83.65 E-value=6.4 Score=40.65 Aligned_cols=84 Identities=20% Similarity=0.218 Sum_probs=56.4
Q ss_pred ccccccccc---------cccceEEEEEEEecCCceeecCCcEEEEEEEEeCCC--eEEEEEecCCC-----C--CCCCC
Q psy3603 32 DVYIKDLHV---------GIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTA--CINLSLWDEPG-----A--LLHPG 93 (264)
Q Consensus 32 ~ikIkDLkp---------G~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTG--sI~ltLWdd~a-----d--~Ik~G 93 (264)
.+.|++|.+ |++ |.+.+.|.++. +.+.+.-+.|.|.|| .|++.+=.+.. . .|..|
T Consensus 89 ~~~~~~~~~~~~~~~~~~g~~-V~v~GwV~~iR------~~g~~~Fi~l~Dgs~~~~lQ~v~~~~~~~~~~l~~~~l~~g 161 (565)
T PLN02603 89 KLRIADVKGGEDEGLARVGKT-LNVMGWVRTLR------AQSSVTFIEVNDGSCLSNMQCVMTPDAEGYDQVESGLITTG 161 (565)
T ss_pred ceEhhhcccccccccccCCCE-EEEEEEEEEEE------eCCCeEEEEEECCCCCEeEEEEEECcHHHHHHHhhcCCCCC
Confidence 356777652 454 88888887653 335688899999997 48887732211 1 27899
Q ss_pred CEEEEeeeEEEEE-C--CEEEEEEcCCceEEEecCc
Q psy3603 94 DIVRLTKCYAQIW-R--NCLTLYSSKSGLIEKIGEF 126 (264)
Q Consensus 94 DIIrI~ngyVs~f-r--G~LqL~Igr~G~IekVgEf 126 (264)
|+|.|.| .+..- . +.++|.+.+ |+.++..
T Consensus 162 s~V~V~G-~v~~~~~~~~~~EL~v~~---i~vlg~a 193 (565)
T PLN02603 162 ASVLVQG-TVVSSQGGKQKVELKVSK---IVVVGKS 193 (565)
T ss_pred CEEEEEE-EEEecCCCCccEEEEEeE---EEEEECC
Confidence 9999996 45443 2 338888876 7766654
No 124
>PRK05813 single-stranded DNA-binding protein; Provisional
Probab=83.42 E-value=10 Score=34.69 Aligned_cols=62 Identities=15% Similarity=0.068 Sum_probs=49.9
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEE-----eCCCeEEEEEecCCCCC--CCCCCEEEEeeeEEEEEC
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVA-----DSTACINLSLWDEPGAL--LHPGDIVRLTKCYAQIWR 107 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LA-----DeTGsI~ltLWdd~ad~--Ik~GDIIrI~ngyVs~fr 107 (264)
|.+++++.+--+-+.+..|..|.++.|+ |++--|++++|+..++. ++.|+.|.|. |..+.|+
T Consensus 11 V~L~Grl~~d~e~~~~~~G~~~~~f~laV~R~s~~~D~i~v~v~~rlae~~~l~kG~~v~Ve-Gqlrsy~ 79 (219)
T PRK05813 11 VYLEGKVVSELEFSHEMYGEGFYNFKLEVPRLSDSKDILPVTVSERLLAGMDLKVGTLVIVE-GQLRSYN 79 (219)
T ss_pred EEEEEEEcCCceEEEEeCCeEEEEEEEEeeccCCCccEEEEEEEhhhhhhhcccCCCEEEEE-EEEEEec
Confidence 8888888876655556778777777765 88999999999977654 8899999999 5788774
No 125
>PF11325 DUF3127: Domain of unknown function (DUF3127); InterPro: IPR021474 This bacterial family of proteins has no known function.
Probab=81.24 E-value=14 Score=29.40 Aligned_cols=65 Identities=17% Similarity=0.346 Sum_probs=40.9
Q ss_pred EEEEEEecCCcee--ecCCcEEEEEEEEeC---CCeEEEEEecCCCCC---CCCCCEEEEe-eeEEEEECCEEE
Q psy3603 47 VTCIVLDISPRVT--LKENREVRTLKVADS---TACINLSLWDEPGAL---LHPGDIVRLT-KCYAQIWRNCLT 111 (264)
Q Consensus 47 v~fiVle~~~~r~--TKdGg~V~tL~LADe---TGsI~ltLWdd~ad~---Ik~GDIIrI~-ngyVs~frG~Lq 111 (264)
+.++|+.+.+... .++|=+-+.++|--. --.|.+.+|+|.++. +++||.|+|+ +-..++|+|.--
T Consensus 2 i~Gkii~~l~~~~g~s~~Gw~Kre~Vlet~~qYP~~i~f~~~~dk~~~l~~~~~Gd~V~Vsf~i~~RE~~gr~f 75 (84)
T PF11325_consen 2 ITGKIIKVLPEQQGVSKNGWKKREFVLETEEQYPQKICFEFWGDKIDLLDNFQVGDEVKVSFNIEGREWNGRWF 75 (84)
T ss_pred cccEEEEEecCcccCcCCCcEEEEEEEeCCCcCCceEEEEEEcchhhhhccCCCCCEEEEEEEeeccEecceEe
Confidence 4566655554443 356622345555522 245999999988754 8899999987 344566765543
No 126
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=80.91 E-value=6.1 Score=39.60 Aligned_cols=73 Identities=18% Similarity=0.122 Sum_probs=51.5
Q ss_pred ccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCC------CCCCCCCEEEEeeeEEEEEC
Q psy3603 34 YIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPG------ALLHPGDIVRLTKCYAQIWR 107 (264)
Q Consensus 34 kIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~a------d~Ik~GDIIrI~ngyVs~fr 107 (264)
+|+|+.+..+ ..+.++|.+.... ..|+ ..-+.+.|++|.|.+.++-... ..|.+||.|.+.|+ ++...
T Consensus 259 ~l~d~~~~~~-~~v~g~v~~~p~~---ieGg-hv~v~i~d~~G~I~~~A~eptk~fr~~a~~L~pGD~i~~~G~-~~~~~ 332 (421)
T COG1571 259 KLNDIEDYSK-YRVVGRVEAEPRA---IEGG-HVVVEITDGEGEIGAVAFEPTKEFRELARKLIPGDEITVYGS-VKPGT 332 (421)
T ss_pred hhhhhhhccc-eEEEEEEecccEE---eeCC-EEEEEecCCCceEEEEEecccccchHHHHhcCCCCEEEEecC-ccccc
Confidence 3678888876 8888888775422 3444 3446889999999999987443 34889999999975 44333
Q ss_pred CEEEEEEcC
Q psy3603 108 NCLTLYSSK 116 (264)
Q Consensus 108 G~LqL~Igr 116 (264)
|++.+
T Consensus 333 ----~n~ek 337 (421)
T COG1571 333 ----LNLEK 337 (421)
T ss_pred ----eeEEE
Confidence 55554
No 127
>PLN02903 aminoacyl-tRNA ligase
Probab=80.20 E-value=13 Score=39.13 Aligned_cols=74 Identities=12% Similarity=0.127 Sum_probs=51.5
Q ss_pred cccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC-------CCCCCCCCEEEEeeeEEEEE-------
Q psy3603 41 GIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP-------GALLHPGDIVRLTKCYAQIW------- 106 (264)
Q Consensus 41 G~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~-------ad~Ik~GDIIrI~ngyVs~f------- 106 (264)
|++ |.+.|.|..+. +-+.+.-+.|.|.+|.|++.+=.+. ...|..|++|.|.| .+..-
T Consensus 72 gk~-V~l~GWV~~~R------~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~L~~esvV~V~G-~V~~r~~~~~n~ 143 (652)
T PLN02903 72 GSR-VTLCGWVDLHR------DMGGLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNEYVVAVEG-TVRSRPQESPNK 143 (652)
T ss_pred CCE-EEEEEEEEEEe------cCCCcEEEEEEcCCccEEEEEeCCccHHHHHHHhcCCCCCEEEEEE-EEEeCCCcCcCC
Confidence 444 88888887653 2235888999999999999774321 13488999999995 56542
Q ss_pred ---CCEEEEEEcCCceEEEecC
Q psy3603 107 ---RNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 107 ---rG~LqL~Igr~G~IekVgE 125 (264)
.|.++|.+.+ |+.++.
T Consensus 144 ~~~tGeiEl~~~~---i~VL~~ 162 (652)
T PLN02903 144 KMKTGSVEVVAES---VDILNV 162 (652)
T ss_pred CCCCCCEEEEEeE---EEEEec
Confidence 2668887776 555544
No 128
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=78.10 E-value=12 Score=38.78 Aligned_cols=75 Identities=12% Similarity=0.183 Sum_probs=52.4
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecC-----CCCCCCCCCEEEEeeeEEEEE--------
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDE-----PGALLHPGDIVRLTKCYAQIW-------- 106 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd-----~ad~Ik~GDIIrI~ngyVs~f-------- 106 (264)
.|++ |.+.+.|..+. +-+.+.-+.|.|.+|.|++.+=.. ....+..|++|.|.| .+..-
T Consensus 16 ~g~~-V~l~GwV~~~R------~~g~l~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~l~~es~V~V~G-~v~~~~~~~~n~~ 87 (588)
T PRK00476 16 VGQT-VTLCGWVHRRR------DHGGLIFIDLRDREGIVQVVFDPDAEAFEVAESLRSEYVIQVTG-TVRARPEGTVNPN 87 (588)
T ss_pred CCCE-EEEEEEEEEEE------eCCCeEEEEEEeCCceEEEEEeCCHHHHHHHhCCCCCCEEEEEE-EEEecCCcccCcc
Confidence 3554 88888887653 223688999999999999876321 123488999999995 56542
Q ss_pred --CCEEEEEEcCCceEEEecC
Q psy3603 107 --RNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 107 --rG~LqL~Igr~G~IekVgE 125 (264)
.|.++|.+.+ |+.++.
T Consensus 88 ~~~g~~El~~~~---i~il~~ 105 (588)
T PRK00476 88 LPTGEIEVLASE---LEVLNK 105 (588)
T ss_pred CCCCcEEEEEeE---EEEEec
Confidence 4568888776 555554
No 129
>PLN02221 asparaginyl-tRNA synthetase
Probab=77.27 E-value=19 Score=37.42 Aligned_cols=106 Identities=17% Similarity=0.223 Sum_probs=66.8
Q ss_pred hhhhccCCCcccceeeeeecccccCccccccccccc---------ccccceEEEEEEEecCCceeecCCc-EEEEEEEEe
Q psy3603 4 KKLAGSHPEKNHGMRAERKEINRKKEAMDVYIKDLH---------VGIKNVNVTCIVLDISPRVTLKENR-EVRTLKVAD 73 (264)
Q Consensus 4 ~~~~~~~~~~~h~~~~e~~~i~~~~~~~~ikIkDLk---------pG~knVnv~fiVle~~~~r~TKdGg-~V~tL~LAD 73 (264)
..||++.++-+-.. +-.........|++|- .|+ .|.+.|-|.++.. .|+ .+.-+.|.|
T Consensus 10 ~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~g~-~V~I~GWV~~iR~-----~Gk~~i~Fl~LRD 77 (572)
T PLN02221 10 NQLAAVSLENDGST------VQKAQFSDRVLIRSILDRPDGGAGLAGQ-KVRIGGWVKTGRE-----QGKGTFAFLEVND 77 (572)
T ss_pred HhhhheeccCCCcc------cccccccCceEHHHHhccccCChhcCCC-EEEEEEEEEehhh-----CCCceEEEEEEeC
Confidence 45666666544331 1112233556777763 133 3777887777532 343 478899999
Q ss_pred CC--CeEEEEEecCCC---CCCCCCCEEEEeeeEEEEE------CCEEEEEEcCCceEEEecC
Q psy3603 74 ST--ACINLSLWDEPG---ALLHPGDIVRLTKCYAQIW------RNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 74 eT--GsI~ltLWdd~a---d~Ik~GDIIrI~ngyVs~f------rG~LqL~Igr~G~IekVgE 125 (264)
.| |.|++++=.... +.+..|++|.|.| .+..- .+.++|.+.+ |+.++.
T Consensus 78 gs~~g~iQvVv~~~~~~~~~~L~~ES~V~V~G-~V~~~~~~~~~~~~iEl~v~~---i~vl~~ 136 (572)
T PLN02221 78 GSCPANLQVMVDSSLYDLSTLVATGTCVTVDG-VLKVPPEGKGTKQKIELSVEK---VIDVGT 136 (572)
T ss_pred CcccccEEEEEcCchhhHHhcCCCceEEEEEE-EEEeCCccCCCCccEEEEEeE---EEEEec
Confidence 99 999997743211 2478899999995 56543 2468888876 766664
No 130
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=76.84 E-value=15 Score=39.00 Aligned_cols=74 Identities=16% Similarity=0.161 Sum_probs=51.0
Q ss_pred cccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC--------CCCCCCCCEEEEeeeEEEEE------
Q psy3603 41 GIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP--------GALLHPGDIVRLTKCYAQIW------ 106 (264)
Q Consensus 41 G~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~--------ad~Ik~GDIIrI~ngyVs~f------ 106 (264)
|+. |.+.+.|..+. +-+.+.-+.|.|.+|.|++.+=... ...|..|++|.|.| .+..-
T Consensus 18 g~~-V~l~GWV~~~R------~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~~L~~EsvV~V~G-~v~~r~~~~~n 89 (706)
T PRK12820 18 GRE-VCLAGWVDAFR------DHGELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAEFCVALQG-EVQKRLEETEN 89 (706)
T ss_pred CCE-EEEEEEEEEEE------cCCCcEEEEEEeCCccEEEEEeCCcCCHHHHHHHhcCCCCCEEEEEe-EEeccCccccC
Confidence 454 88888887653 2235889999999999999774322 13488999999995 56552
Q ss_pred ----CCEEEEEEcCCceEEEecC
Q psy3603 107 ----RNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 107 ----rG~LqL~Igr~G~IekVgE 125 (264)
.|.++|.+.+ |+.++.
T Consensus 90 ~~~~tg~iEl~~~~---i~iL~~ 109 (706)
T PRK12820 90 PHIETGDIEVFVRE---LSILAA 109 (706)
T ss_pred CCCCCCcEEEEeeE---EEEEec
Confidence 2667777765 555443
No 131
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=76.19 E-value=12 Score=38.44 Aligned_cols=68 Identities=16% Similarity=0.151 Sum_probs=49.0
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC---------CCCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP---------GALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~---------ad~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
|.+-++|..+ |.-|+..-+.|.|.+|.|++-+=.+. ...++-||+|.+.|.-.+.-.|+|.|++.
T Consensus 64 v~vAGRi~~~------R~~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlGDiigv~G~~~~T~~GelSv~v~ 137 (502)
T COG1190 64 VSVAGRIMTI------RNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLGDIIGVEGPLFKTKTGELSVSVE 137 (502)
T ss_pred eEEecceeee------cccCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccCCEEeeeeeeeecCCCceEEEEE
Confidence 4555555443 22258889999999999999876442 12366799999997656666799999999
Q ss_pred CCc
Q psy3603 116 KSG 118 (264)
Q Consensus 116 r~G 118 (264)
..-
T Consensus 138 ~~~ 140 (502)
T COG1190 138 ELR 140 (502)
T ss_pred EEe
Confidence 743
No 132
>COG0587 DnaE DNA polymerase III, alpha subunit [DNA replication, recombination, and repair]
Probab=74.73 E-value=5.6 Score=44.31 Aligned_cols=70 Identities=17% Similarity=0.228 Sum_probs=49.3
Q ss_pred ccccccccccceEEEEEEEecCCceeec-CCcEEEEEEEEeCCCeEEEEEecCC----CCCCCCCCEEEEeeeEEEE
Q psy3603 34 YIKDLHVGIKNVNVTCIVLDISPRVTLK-ENREVRTLKVADSTACINLSLWDEP----GALLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 34 kIkDLkpG~knVnv~fiVle~~~~r~TK-dGg~V~tL~LADeTGsI~ltLWdd~----ad~Ik~GDIIrI~ngyVs~ 105 (264)
.+.++.+.....-+.+.|..+... .+| +|.++.-+++.|+||.+.+++|-.. ...+.+|.++.|. |.++.
T Consensus 968 ~~~~~~~~~~~~~~~~~i~~vr~~-~tk~~G~~~~f~tl~D~~g~~e~v~f~~~~~~~~~~l~~~~~~~v~-g~v~~ 1042 (1139)
T COG0587 968 RLLDLVEDGRRVVLAGGIVAVRQR-PTKAKGNKMAFLTLEDETGILEVVVFPSEYERYRRLLLEGRLLIVK-GKVQR 1042 (1139)
T ss_pred chhhhccccceeEEEEEEEEEEEe-eccCCCCEEEEEEEecCCCcEEEEEcHHHHHHHHHHhccCcEEEEE-EEEEe
Confidence 344444433225667777776544 455 7999999999999999999999533 3447788999998 45665
No 133
>COG3390 Uncharacterized protein conserved in archaea [Function unknown]
Probab=71.55 E-value=17 Score=33.21 Aligned_cols=61 Identities=16% Similarity=0.200 Sum_probs=40.7
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEE--ec-CC---CCCCCCCCEEEEeeeEEEEECCE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSL--WD-EP---GALLHPGDIVRLTKCYAQIWRNC 109 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltL--Wd-d~---ad~Ik~GDIIrI~ngyVs~frG~ 109 (264)
|-+++.|.++... ...+.|..++|+|.||++-+=. .. +. .+.++.+|.|-|. |+++.|++.
T Consensus 48 ifivGtltek~~i---~ed~~~~R~rVvDpTGsF~Vyag~yqPEa~a~l~~ve~~~~VaVi-GKi~~y~~d 114 (196)
T COG3390 48 IFIVGTLTEKEGI---GEDREYWRIRVVDPTGSFYVYAGQYQPEAKAFLEDVEVPDLVAVI-GKIRTYRTD 114 (196)
T ss_pred EEEEEEEEeccCc---CCcccEEEEEEecCCceEEEEcCCCChHHHHHHHhccCCceEEEe-cccceeecC
Confidence 4555555554432 1115799999999999987711 11 11 1348899999999 689999854
No 134
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=70.86 E-value=1.5 Score=36.39 Aligned_cols=22 Identities=36% Similarity=0.505 Sum_probs=19.3
Q ss_pred EEEEEEEEeCCCeEEEEEecCC
Q psy3603 65 EVRTLKVADSTACINLSLWDEP 86 (264)
Q Consensus 65 ~V~tL~LADeTGsI~ltLWdd~ 86 (264)
-.+.+.|+|.||++.+++||+.
T Consensus 54 y~l~~~i~D~tg~~~~~~F~~~ 75 (146)
T PF08646_consen 54 YRLSLKISDGTGSIWVTLFDEE 75 (146)
T ss_dssp EEEEEEEEETTEEEEEEEEHHH
T ss_pred EEEEEEEEeCCCeEEEEEEhHH
Confidence 3479999999999999999865
No 135
>PRK10053 hypothetical protein; Provisional
Probab=69.48 E-value=9.9 Score=32.36 Aligned_cols=58 Identities=17% Similarity=0.299 Sum_probs=38.7
Q ss_pred ccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecC--CCCCCCCCCEEEEeeeEEE
Q psy3603 36 KDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDE--PGALLHPGDIVRLTKCYAQ 104 (264)
Q Consensus 36 kDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd--~ad~Ik~GDIIrI~ngyVs 104 (264)
++++.+.. |.+.+.|++.- .+.. .++.|.||+|.+-+=++ ....+.|.|-|+|.| .+.
T Consensus 56 ~~~~Dd~~-V~L~G~Iv~~l------g~d~---Y~F~D~tG~I~VeID~~~w~G~~v~p~~kV~I~G-evD 115 (130)
T PRK10053 56 KTMHDGAT-VSLRGNLIDHK------GDDR---YVFRDKSGEINVIIPAAVFDGREVQPDQMINING-SLD 115 (130)
T ss_pred hcCcCCCe-EEEEEEEEEEe------CCce---EEEECCCCcEEEEeCHHHcCCCcCCCCCEEEEEE-EEC
Confidence 33455554 88888776632 1223 46899999999987332 234589999999995 454
No 136
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, 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-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=66.05 E-value=3.6 Score=34.71 Aligned_cols=22 Identities=41% Similarity=0.504 Sum_probs=19.4
Q ss_pred EEEEEEEeCCCeEEEEEecCCC
Q psy3603 66 VRTLKVADSTACINLSLWDEPG 87 (264)
Q Consensus 66 V~tL~LADeTGsI~ltLWdd~a 87 (264)
.+.+.|+|.||++.+++||+.+
T Consensus 69 ~l~~~i~D~Tg~~~~~~F~~~a 90 (166)
T cd04476 69 ILSLNVADHTGEAWLTLFDEVA 90 (166)
T ss_pred EEEEEEEeCCCCEEEEEehHHH
Confidence 3689999999999999999664
No 137
>COG0629 Ssb Single-stranded DNA-binding protein [DNA replication, recombination, and repair]
Probab=64.69 E-value=21 Score=30.53 Aligned_cols=63 Identities=19% Similarity=0.181 Sum_probs=41.0
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEE-EE-----e--------CCCeEEEEEecCCCC----CCCCCCEEEEeeeEEE
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLK-VA-----D--------STACINLSLWDEPGA----LLHPGDIVRLTKCYAQ 104 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~-LA-----D--------eTGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs 104 (264)
..|-+++.+..-.+.+.+.+|+.+..+. ++ | +|=-|++++|+..++ .+++|+-|.|. |...
T Consensus 4 Nkv~LvG~l~~DPE~r~t~~g~~~v~~~~~a~~r~~~~~~~~~~~~t~~~~vv~wgk~Ae~~~~yl~KG~~V~Ve-G~l~ 82 (167)
T COG0629 4 NKVILVGRLTRDPELRYTPNGGAVVALFSAAVNRRFDNQSGERDEETDWIRVVIWGKLAENAAEYLKKGSLVYVE-GRLQ 82 (167)
T ss_pred ceEEEEeecccCcceeecCCCCeeeEEEEEEeccccccCCcccccccceEEEEEehHHHHHHHHHhcCCCEEEEE-EEEE
Confidence 3477777777766666677665443322 22 2 134589999997754 38999999999 4565
Q ss_pred EE
Q psy3603 105 IW 106 (264)
Q Consensus 105 ~f 106 (264)
..
T Consensus 83 ~~ 84 (167)
T COG0629 83 TR 84 (167)
T ss_pred ee
Confidence 43
No 138
>PRK04036 DNA polymerase II small subunit; Validated
Probab=63.39 E-value=25 Score=35.49 Aligned_cols=62 Identities=18% Similarity=0.297 Sum_probs=44.8
Q ss_pred ccccccc-ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC------CCCCCCCCEEEEee
Q psy3603 33 VYIKDLH-VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP------GALLHPGDIVRLTK 100 (264)
Q Consensus 33 ikIkDLk-pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~------ad~Ik~GDIIrI~n 100 (264)
.+|.+++ .+. .+-++|.|.++. .+++|.. .+.|-|+||.|.+.+=.+. .+.|-+|.+|-|.|
T Consensus 144 ~~l~~~~~~~~-~~~viG~v~~~~---~~~~g~~--~~~LED~sgrv~l~~~~~~~~~~~~~~~lvtg~vv~v~G 212 (504)
T PRK04036 144 ESLKKLKRGGE-EVSIIGMVSDIR---STKNGHK--IVELEDTTGTFPVLIMKDREDLAELADELLLDEVIGVEG 212 (504)
T ss_pred HHHhcCccCCc-eEEEEEEEEEee---cccCCce--EEEEECCCCeEEEEeecchhhhhhhhhcccCceEEEEEE
Confidence 4566777 555 499999998763 4566643 4789999999999874322 23477899999985
No 139
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=63.06 E-value=23 Score=30.34 Aligned_cols=69 Identities=19% Similarity=0.196 Sum_probs=42.2
Q ss_pred cccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC--CCCCCCCCEEEEeeeEEEEECCEEEEEE
Q psy3603 37 DLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP--GALLHPGDIVRLTKCYAQIWRNCLTLYS 114 (264)
Q Consensus 37 DLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~--ad~Ik~GDIIrI~ngyVs~frG~LqL~I 114 (264)
.+..+.. |.+.+-+++- .++. ...+.|.||+|++-+=+.. ...+.|-|-|+|+| .+..-=...+|.+
T Consensus 53 ~~~Dda~-V~l~GnIv~q------i~~D---~y~FrD~sGeI~VeIdd~~w~g~tv~P~dkV~I~G-evDk~~~~~eIdV 121 (128)
T COG3111 53 TLHDDAW-VSLEGNIVRQ------IGDD---RYVFRDASGEINVDIDDKVWNGQTVTPKDKVRIQG-EVDKDWNSVEIDV 121 (128)
T ss_pred ccccCCe-EEEEeeEEEe------eCCc---eEEEEcCCccEEEEecccccCCcccCcccEEEEEe-EEcCCCccceeEh
Confidence 3455555 6666655442 1222 3468899999998764422 34589999999994 4543223455555
Q ss_pred cC
Q psy3603 115 SK 116 (264)
Q Consensus 115 gr 116 (264)
..
T Consensus 122 ~~ 123 (128)
T COG3111 122 KH 123 (128)
T ss_pred hh
Confidence 54
No 140
>PRK05853 hypothetical protein; Validated
Probab=62.18 E-value=13 Score=32.50 Aligned_cols=30 Identities=17% Similarity=0.204 Sum_probs=23.2
Q ss_pred CCCeEEEEEecCCCC----CCCCCCEEEEeeeEEE
Q psy3603 74 STACINLSLWDEPGA----LLHPGDIVRLTKCYAQ 104 (264)
Q Consensus 74 eTGsI~ltLWdd~ad----~Ik~GDIIrI~ngyVs 104 (264)
+|--|.+++|+..++ .|+.|+-|.|.| +..
T Consensus 41 ~T~wi~V~~wg~lAe~v~~~L~KG~~V~V~G-rL~ 74 (161)
T PRK05853 41 NSLFITVNCWGRLVTGVGAALGKGAPVIVVG-HVY 74 (161)
T ss_pred CccEEEEEEEhHHHHHHHHHcCCCCEEEEEE-EEE
Confidence 466789999996543 489999999995 443
No 141
>PF02760 HIN: HIN-200/IF120x domain; InterPro: IPR004021 This domain has no known function. It is found in one or two copies per protein, and is found associated with the PAAD/DAPIN domain IPR004020 from INTERPRO.; PDB: 3RN2_A 3RN5_C 2OQ0_A 3B6Y_A 3RLN_A 3RNU_A 3RLO_A.
Probab=60.08 E-value=1e+02 Score=27.66 Aligned_cols=67 Identities=16% Similarity=0.243 Sum_probs=46.2
Q ss_pred EEEEEEecCCcee--ecC-C-cEEEEEEEEeCCCeEEEEEecCC-CCCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 47 VTCIVLDISPRVT--LKE-N-REVRTLKVADSTACINLSLWDEP-GALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 47 v~fiVle~~~~r~--TKd-G-g~V~tL~LADeTGsI~ltLWdd~-ad~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
....||...++=+ +.. | +.+..++||-+|--.++.++|-. -+.|-+..+|.|++ |. .++|-|+++-.
T Consensus 5 ~~VmVLkaTepF~Ye~~e~gkk~MFHATVATet~fF~VKVfn~~LKeKF~~kkiI~IS~-Y~-~~~gfLEi~~a 76 (170)
T PF02760_consen 5 KTVMVLKATEPFEYESPEEGKKKMFHATVATETEFFRVKVFNINLKEKFIPKKIIAISD-YF-GRNGFLEINEA 76 (170)
T ss_dssp EEEEEEEE---EEEECTTTCEEEEEEEEEE-SS-EEEEEES-GGGCCTCSTTSEEEEES-EE-EETTEEEE-TT
T ss_pred eEEEEEeccCCeEEeCcccCcceEEEEEEeccccEEEEEEecchhHhhcCCCcEEEEeh-hh-cccceEEEeec
Confidence 4567788776643 444 5 67889999999999999999944 56799999999996 44 46888887743
No 142
>PLN02532 asparagine-tRNA synthetase
Probab=58.78 E-value=42 Score=35.45 Aligned_cols=61 Identities=16% Similarity=0.223 Sum_probs=45.4
Q ss_pred cCCcEEEEEEEEeCCCe--EEEEEecCCC---CCCCCCCEEEEeeeEEEEE-----CCEEEEEEcCCceEEEecC
Q psy3603 61 KENREVRTLKVADSTAC--INLSLWDEPG---ALLHPGDIVRLTKCYAQIW-----RNCLTLYSSKSGLIEKIGE 125 (264)
Q Consensus 61 KdGg~V~tL~LADeTGs--I~ltLWdd~a---d~Ik~GDIIrI~ngyVs~f-----rG~LqL~Igr~G~IekVgE 125 (264)
|+-+.+.-+.|.|.||. |++++=.... ..|..|.+|.|.| .+..- .|.++|.+.+ |+.++.
T Consensus 130 r~~g~i~FI~LrDGSg~~~lQvVv~~~~~~~~~~L~~Es~V~V~G-~V~~~~~~~~~g~iEl~v~~---i~VLg~ 200 (633)
T PLN02532 130 PPPPSVAYLLISDGSCVASLQVVVDSALAPLTQLMATGTCILAEG-VLKLPLPAQGKHVIELEVEK---ILHIGT 200 (633)
T ss_pred ccCCCcEEEEEECCCCccceEEEEeCCcccHhhcCCCceEEEEEE-EEEecCCCCCCCcEEEEeeE---EEEEec
Confidence 44467899999999998 9997754322 3488999999995 56654 3568888876 766664
No 143
>PF09104 BRCA-2_OB3: BRCA2, oligonucleotide/oligosaccharide-binding, domain 3; InterPro: IPR015188 This domain assumes an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB3 has a pronounced groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for strong ssDNA binding []. ; PDB: 1IYJ_D 1MIU_A.
Probab=58.13 E-value=1.2e+02 Score=26.42 Aligned_cols=58 Identities=16% Similarity=0.339 Sum_probs=34.2
Q ss_pred cccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCC-eEEEEEecCC-----CCCCCCCCEEEEeee
Q psy3603 39 HVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTA-CINLSLWDEP-----GALLHPGDIVRLTKC 101 (264)
Q Consensus 39 kpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTG-sI~ltLWdd~-----ad~Ik~GDIIrI~ng 101 (264)
+|-=..|+++|.|..+.. +.| ..-.+-|+|+.- -+.++.|.+. .|.+++|.+|-+.|-
T Consensus 15 ~pp~~EvD~VG~VvsV~~----~~~-f~~~vYLsD~~~Nll~Ikfw~~l~~~~~eDilk~~~liA~SNL 78 (143)
T PF09104_consen 15 QPPYGEVDTVGFVVSVSK----KQG-FQPLVYLSDECHNLLAIKFWTGLNQYGYEDILKPGSLIAASNL 78 (143)
T ss_dssp -TCCCEEEEEEEEEEEE------TT-S--EEEEE-TTS-EEEEEESS-------SS---TT-EEEEEEE
T ss_pred CCCccccceEEEEEEEEe----cCC-CceeEEeecCCccEEEEEeccCccccchhhhcCcceEEEEeee
Confidence 443345999999999921 122 222256689977 4788999865 366899999999974
No 144
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=55.96 E-value=16 Score=30.16 Aligned_cols=59 Identities=20% Similarity=0.237 Sum_probs=35.7
Q ss_pred eEEEEEecCCCCCCCCCCEEEEeeeEEEEECCEEEEEEcCCceEEEecCceeeecCCCCCCCCCCC
Q psy3603 77 CINLSLWDEPGALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGEFCMVFNENLDMSIPIPN 142 (264)
Q Consensus 77 sI~ltLWdd~ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr~G~IekVgEf~~~fnE~pNiSe~~Pe 142 (264)
+|.+++=|.....|++||.|.+.+- .. ...+.+.|.. |.+-..|...+.. .++..+.|.
T Consensus 19 tiEiRlnD~kr~~ikvGD~I~f~~~-~~--~~~l~v~V~~---i~~Y~sF~~ll~~-e~~~~~~~~ 77 (109)
T cd06555 19 TIEIRLNDEKRQQIKVGDKILFNDL-DT--GQQLLVKVVD---IRKYDSFRELLEE-EGLEKVGPG 77 (109)
T ss_pred EEEEEecccchhcCCCCCEEEEEEc-CC--CcEEEEEEEE---EEecCCHHHHHHh-cCHhhcCCC
Confidence 3444444445567999999999852 22 4457777765 6666676633333 445555554
No 145
>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=50.83 E-value=1.2e+02 Score=25.17 Aligned_cols=58 Identities=21% Similarity=0.200 Sum_probs=39.4
Q ss_pred ccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEee
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTK 100 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~n 100 (264)
.+. .|.+.+.|.+-+ . ....+..-++..|.|....|.+..=+...+.|++|.-|-+.|
T Consensus 49 ~~~-~vrv~G~V~~gS-v-~~~~~~~~~~F~i~D~~~~i~V~Y~G~~Pd~F~eg~~VVv~G 106 (131)
T PF03100_consen 49 VGR-KVRVGGLVVEGS-V-EYDPDGNTLTFTITDGGKEIPVVYTGPLPDLFREGQGVVVEG 106 (131)
T ss_dssp TTS-EEEEEEEEECTT-E-EE-TTSSEEEEEEE-SS-EEEEEEES--CTT--TTSEEEEEE
T ss_pred CCc-eEEEeeEEccCC-E-EEcCCCCEEEEEEEECCcEEEEEECCCCCccccCCCeEEEEE
Confidence 344 499999998643 2 222234567789999999999999998899999999999996
No 146
>PF08696 Dna2: DNA replication factor Dna2; InterPro: IPR014808 Dna2 is a DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease, (5'-flap endonuclease) and helicase activities. It is required for Okazaki fragment processing and is involved in DNA repair pathways []. ; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication
Probab=46.55 E-value=67 Score=28.69 Aligned_cols=32 Identities=28% Similarity=0.388 Sum_probs=24.4
Q ss_pred EEEEeCCCe-EEEEEecCCCCC-CCCCCEEEEee
Q psy3603 69 LKVADSTAC-INLSLWDEPGAL-LHPGDIVRLTK 100 (264)
Q Consensus 69 L~LADeTGs-I~ltLWdd~ad~-Ik~GDIIrI~n 100 (264)
|++.|.+|. ..+.|||+=.+. +++||+|.|.+
T Consensus 2 l~~~~~~~~~~~v~L~~~W~~t~v~~Gd~I~ii~ 35 (209)
T PF08696_consen 2 LVCSESSGETRTVILRDEWCETPVSPGDIIHIIG 35 (209)
T ss_pred eEeecCCCCeEEEEEeCCcccCCCcCCCEEEEEE
Confidence 455666555 678888876655 99999999995
No 147
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=44.48 E-value=1.6e+02 Score=25.49 Aligned_cols=56 Identities=14% Similarity=0.073 Sum_probs=44.5
Q ss_pred cceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeee
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKC 101 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ng 101 (264)
+.|.+.+.|.+-+.. ++++..++..|.|...+|.+..=+...+.|++|.-|-+.|-
T Consensus 52 ~~vrvgG~V~~gSi~---~~~~~~~~F~ltD~~~~i~V~Y~G~lPd~F~eg~~VVv~G~ 107 (148)
T PRK13254 52 RRFRLGGLVEKGSVQ---RGDGLTVRFVVTDGNATVPVVYTGILPDLFREGQGVVAEGR 107 (148)
T ss_pred CeEEEeEEEecCcEE---eCCCCEEEEEEEeCCeEEEEEECCCCCccccCCCEEEEEEE
Confidence 349999999864322 32456778899999999999888888899999999999953
No 148
>COG2332 CcmE Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]
Probab=44.28 E-value=95 Score=27.43 Aligned_cols=58 Identities=16% Similarity=0.116 Sum_probs=46.8
Q ss_pred ccccceEEEEEEEecCCceeecCC-cEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeee
Q psy3603 40 VGIKNVNVTCIVLDISPRVTLKEN-REVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKC 101 (264)
Q Consensus 40 pG~knVnv~fiVle~~~~r~TKdG-g~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ng 101 (264)
+|++ +.+-++|.+-+.. |++ ..-..+.+.|.-.+|.++.=+...|+|++|.-|...|.
T Consensus 50 ~G~r-lR~GGlV~~GSv~---R~~~~~~v~F~vtD~~~~v~V~Y~GiLPDLFREGQgVVa~G~ 108 (153)
T COG2332 50 TGQR-LRLGGLVEAGSVQ---RDPGSLKVSFVVTDGNKSVTVSYEGILPDLFREGQGVVAEGQ 108 (153)
T ss_pred CCcE-EEEeeeEeeceEE---ecCCCcEEEEEEecCCceEEEEEeccCchhhhcCCeEEEEEE
Confidence 3565 9999999886533 543 44567788899999999999999999999999999863
No 149
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=42.56 E-value=1.5e+02 Score=26.15 Aligned_cols=57 Identities=18% Similarity=0.193 Sum_probs=45.9
Q ss_pred cccceEEEEEEEecCCceeecC-CcEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeee
Q psy3603 41 GIKNVNVTCIVLDISPRVTLKE-NREVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKC 101 (264)
Q Consensus 41 G~knVnv~fiVle~~~~r~TKd-Gg~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ng 101 (264)
+. .|.+-+.|..=+.. |+ ++.-+...|.|..++|.++.=+...|+|++|.-|.+.|.
T Consensus 57 g~-~iRvgG~V~~GSv~---r~~~~~~v~F~vtD~~~~v~V~Y~GilPDlFrEG~gVVveG~ 114 (159)
T PRK13150 57 GQ-RLRVGGMVMPGSVR---RDPDSLKVNFSLYDAEGSVTVSYEGILPDLFREGQGVVVQGT 114 (159)
T ss_pred CC-EEEEeeEEeCCcEE---ECCCCcEEEEEEEcCCcEEEEEEeccCCccccCCCeEEEEEE
Confidence 45 49999999864432 33 355688899999999999999988999999999999953
No 150
>PF05113 DUF693: Protein of unknown function (DUF693); InterPro: IPR007800 This family consists of uncharacterised proteins from Borrelia burgdorferi.
Probab=42.54 E-value=49 Score=32.03 Aligned_cols=39 Identities=18% Similarity=0.454 Sum_probs=27.6
Q ss_pred ecCCcEEEEEEEEeC--------CCeEEEEEecCC---CCCCCCCCEEEEe
Q psy3603 60 LKENREVRTLKVADS--------TACINLSLWDEP---GALLHPGDIVRLT 99 (264)
Q Consensus 60 TKdGg~V~tL~LADe--------TGsI~ltLWdd~---ad~Ik~GDIIrI~ 99 (264)
|++|- -+++.|.+. +-...++||+-+ .+.|++||||+|+
T Consensus 38 TqnGi-~vdI~IsN~yS~~n~i~sKqaki~lwNlPLdFt~~ik~gDIVKIY 87 (314)
T PF05113_consen 38 TQNGI-HVDISISNTYSNYNYISSKQAKIVLWNLPLDFTDNIKTGDIVKIY 87 (314)
T ss_pred ccCCe-EEEEEEeEeecccceeeeeeeEEEEEecCcccccccCcCcEEEEE
Confidence 56664 366666665 334578899944 4569999999997
No 151
>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=40.78 E-value=1.5e+02 Score=23.62 Aligned_cols=73 Identities=19% Similarity=0.164 Sum_probs=42.2
Q ss_pred ceEEEEEEEecCCcee-ecCCcEEEEEEEEeCCCeEEEEEecCC-----CCCCCCCCEEEEeeeEEEEEC-CEEEEEEcC
Q psy3603 44 NVNVTCIVLDISPRVT-LKENREVRTLKVADSTACINLSLWDEP-----GALLHPGDIVRLTKCYAQIWR-NCLTLYSSK 116 (264)
Q Consensus 44 nVnv~fiVle~~~~r~-TKdGg~V~tL~LADeTGsI~ltLWdd~-----ad~Ik~GDIIrI~ngyVs~fr-G~LqL~Igr 116 (264)
..+-+.-|+++..... .-++..-+.+.|.|..=.+.+.+=-.. ...|+.|.+|++..-.+...+ ++--|.+-+
T Consensus 16 ~~~pvlQVl~~k~i~~~~~~~~~RyR~~lSDG~~~~~amLatqln~lv~~g~l~~~siirl~~y~~n~v~~~k~iiiil~ 95 (101)
T PF04057_consen 16 NDNPVLQVLNIKKINSKQGGGSDRYRLVLSDGVHSIQAMLATQLNHLVESGELQKGSIIRLKQYTCNTVKNGKKIIIILD 95 (101)
T ss_dssp S--TEEEEEEEEEE----TTS--EEEEEEESSSEEEEEEESGGGHHHHHTTSSSTT-EEEEEEEEEEESTTSSEEEEEEE
T ss_pred CCCcEEEEEeeEEccCCCCCCCceEEEEEEChHHHHHHHhHHHhHHHHhcCCcccCCEEEEeEEEEeeccCCCEEEEEEe
Confidence 3455666777654322 123356678899999999888664432 346999999999963334445 555555443
No 152
>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=40.65 E-value=55 Score=26.47 Aligned_cols=59 Identities=19% Similarity=0.148 Sum_probs=28.9
Q ss_pred cceEEEEEEEecCCceeecCCcEEE-EEEEEeCCCeEEEEEecCCC-----CCCCCCCEEEEeeeEEEEE
Q psy3603 43 KNVNVTCIVLDISPRVTLKENREVR-TLKVADSTACINLSLWDEPG-----ALLHPGDIVRLTKCYAQIW 106 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdGg~V~-tL~LADeTGsI~ltLWdd~a-----d~Ik~GDIIrI~ngyVs~f 106 (264)
+.|.+.+.|.++.. ..++.+. ...-.+..+.|.+.+=++.. ..|++||.|.|+| .+.-|
T Consensus 68 K~i~vtG~V~~I~~----~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~l~~G~~Vti~G-~~~g~ 132 (144)
T PF12869_consen 68 KIIEVTGTVSSIDK----GFGDNYVVLLGTENGFAGVQCYFSNDQEKRASVAKLKKGQKVTIKG-ICTGY 132 (144)
T ss_dssp -EEEEEEEEEEEEE-----STT-EEEEEE-TT-S-S--EEEEEEGGGHHHHHH--TTSEEEEEE-E----
T ss_pred CEEEEEEEEEEEEE----cCCCcEEEEccCCCCceeEEEEEccchhhhhhHhcCCCCCEEEEEE-EEEee
Confidence 35999999998842 1334442 22222345567766666541 2299999999995 45555
No 153
>PRK00036 primosomal replication protein N; Reviewed
Probab=40.30 E-value=1.4e+02 Score=24.67 Aligned_cols=77 Identities=12% Similarity=0.086 Sum_probs=54.5
Q ss_pred ceEEEEEEEecCCceeecCCcEEEEEEEEeCCCe------------EEEEEecCCC---CCCCCCCEEEEeeeEEEEEC-
Q psy3603 44 NVNVTCIVLDISPRVTLKENREVRTLKVADSTAC------------INLSLWDEPG---ALLHPGDIVRLTKCYAQIWR- 107 (264)
Q Consensus 44 nVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGs------------I~ltLWdd~a---d~Ik~GDIIrI~ngyVs~fr- 107 (264)
.+.+++.|.+....+.|-.|-+++.++|.-+|-. |.+.+-++.+ ..+..|..|++.|--+...+
T Consensus 3 ~l~Ltg~v~~~~~lryTPAGIp~~~~~LeH~S~q~EAG~~Rqv~~~i~ava~G~~a~~~~~l~~Gs~v~v~GFLa~~~~~ 82 (107)
T PRK00036 3 TLELSARVLECGAMRHTPAGLPALELLLVHESEVVEAGHPRRVELTISAVALGDLALLLADTPLGTEMQVQGFLAPARKD 82 (107)
T ss_pred EEEEEEEEeccCccccCCCCCceEEEEEEEeEEeEeCCCcceEEEEEEEEEEhhHHHHhcccCCCCEEEEEEEEEECCCC
Confidence 4789999999887877888988999998666433 4445556444 23889999999964443444
Q ss_pred -CEEEEEEcCCceEEEe
Q psy3603 108 -NCLTLYSSKSGLIEKI 123 (264)
Q Consensus 108 -G~LqL~Igr~G~IekV 123 (264)
.+|.|++.. |+.+
T Consensus 83 ~~~LVLHi~~---Ie~i 96 (107)
T PRK00036 83 SVKVKLHLQQ---ARRI 96 (107)
T ss_pred CCcEEEEhHH---eEEc
Confidence 457777776 6555
No 154
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular trafficking, secretion, and vesicular transport]
Probab=39.88 E-value=30 Score=28.94 Aligned_cols=47 Identities=19% Similarity=0.275 Sum_probs=30.1
Q ss_pred eEEEEEecCCCCCCCCCCEEEEeeeEEEEECCEEEEEEcCCceEEEecCceeeecCC
Q psy3603 77 CINLSLWDEPGALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGEFCMVFNEN 133 (264)
Q Consensus 77 sI~ltLWdd~ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr~G~IekVgEf~~~fnE~ 133 (264)
+|.++|-|++-..+++||.|...+ +.|-+.+.. ++.-+.|...+.|+
T Consensus 21 ~iEvRl~d~krr~ik~GD~IiF~~-------~~l~v~V~~---vr~Y~tF~~mlree 67 (111)
T COG4043 21 KIEVRLADPKRRQIKPGDKIIFNG-------DKLKVEVID---VRVYDTFEEMLREE 67 (111)
T ss_pred eEEEEecCHhhcCCCCCCEEEEcC-------CeeEEEEEE---EeehhHHHHHHHhc
Confidence 355566666666799999998874 455555554 55556666444443
No 155
>cd04477 RPA1N RPA1N: A subfamily of OB folds corresponding to the N-terminal OB-fold domain 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). RPA1N is known to specifically interact with the p53 tumor suppressor, DNA polymerase alpha, and transcription factors. In addition to RPA1N, RPA1 contains three other OB folds: ssDNA-binding domain (DBD)-A, DBD-B, and DBD-C.
Probab=39.12 E-value=51 Score=26.28 Aligned_cols=70 Identities=17% Similarity=0.162 Sum_probs=41.8
Q ss_pred EEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEe---cCCC--CCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 46 NVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLW---DEPG--ALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 46 nv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLW---dd~a--d~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
.-+.-|+++.+.....++..-+.+.|.|..=.+.+.|= ++.. ..|+.|++|+|..-.....+++--|.|-
T Consensus 17 ~PvlQv~~ik~i~~~~~~~~RyRi~lSDG~~~~~amLatqln~~v~~g~l~~~sIirl~~y~~~~i~~k~viiIl 91 (97)
T cd04477 17 KPVLQVLNIKKIDSSNGSSERYRILLSDGVYYVQAMLATQLNPLVESGQLQRGSIIRLKRFICNVIKGKRILIIL 91 (97)
T ss_pred CCEEEEEEEEEccCCCCCcceEEEEEEChhHHHHHHHhhhhhhHHhcCCccCCcEEEECeEEEEEecCcEEEEEE
Confidence 34555666654422222444566789999777765554 3222 3489999999986555555655555444
No 156
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=39.00 E-value=1.6e+02 Score=30.97 Aligned_cols=68 Identities=10% Similarity=0.149 Sum_probs=46.0
Q ss_pred cccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecC-------CCCCCCCCCEEEEeeeEEEEE-------
Q psy3603 41 GIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDE-------PGALLHPGDIVRLTKCYAQIW------- 106 (264)
Q Consensus 41 G~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd-------~ad~Ik~GDIIrI~ngyVs~f------- 106 (264)
|++ |.+.+=|-.. ||-|.++-+.|.|++|-++++.=.+ .++.+..-++|.|.| .|...
T Consensus 15 G~~-V~L~GWV~r~------Rd~GgliFiDLRDr~GivQvv~~~~~~~~~~~~a~~lr~E~vi~V~G-~V~~R~e~~~N~ 86 (585)
T COG0173 15 GQT-VTLSGWVHRR------RDHGGLIFIDLRDREGIVQVVFDPEDSPEAFEVASRLRNEFVIQVTG-TVRARPEGTINP 86 (585)
T ss_pred CCE-EEEEeeeeec------cccCCeEEEEcccCCCeEEEEECCccCHHHHHHHHhcCceEEEEEEE-EEEecCccccCC
Confidence 554 7776665432 4444599999999999888866553 235588899999995 45443
Q ss_pred ---CCEEEEEEcC
Q psy3603 107 ---RNCLTLYSSK 116 (264)
Q Consensus 107 ---rG~LqL~Igr 116 (264)
-|+++|.+.+
T Consensus 87 ~l~TGeiEv~a~~ 99 (585)
T COG0173 87 NLPTGEIEVLAEE 99 (585)
T ss_pred CCCcceEEEEeee
Confidence 1566666665
No 157
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=38.13 E-value=2.2e+02 Score=25.15 Aligned_cols=57 Identities=12% Similarity=0.135 Sum_probs=45.4
Q ss_pred cccceEEEEEEEecCCceeecCC-cEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeee
Q psy3603 41 GIKNVNVTCIVLDISPRVTLKEN-REVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKC 101 (264)
Q Consensus 41 G~knVnv~fiVle~~~~r~TKdG-g~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ng 101 (264)
+. .|.+-+.|.+=+.. |++ +.-...+|.|...+|.++.=+-..|+|++|.-|.+.|.
T Consensus 57 g~-~iRvgG~V~~GSi~---r~~~~l~v~F~vtD~~~~v~V~Y~GilPDlFrEG~gVVveG~ 114 (160)
T PRK13165 57 GQ-RLRVGGMVMPGSVQ---RDPNSLKVSFTLYDAGGSVTVTYEGILPDLFREGQGIVAQGV 114 (160)
T ss_pred CC-EEEEeeEEeCCcEE---ECCCCeEEEEEEEcCCeEEEEEEcccCCccccCCCeEEEEEE
Confidence 45 49999999864432 344 44578899999999999988888999999999999953
No 158
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=37.14 E-value=1e+02 Score=24.11 Aligned_cols=46 Identities=20% Similarity=0.412 Sum_probs=28.4
Q ss_pred ceEEEEEEEecCCcee----ecCCcEEEEEEEEeCCCeEEE-EEecCCCCCCCCCCEEEEe
Q psy3603 44 NVNVTCIVLDISPRVT----LKENREVRTLKVADSTACINL-SLWDEPGALLHPGDIVRLT 99 (264)
Q Consensus 44 nVnv~fiVle~~~~r~----TKdGg~V~tL~LADeTGsI~l-tLWdd~ad~Ik~GDIIrI~ 99 (264)
.+.+.+.|++.-+... .-+| ..+ +|==+|.++. .+| |.|||+|.|.
T Consensus 6 ~~e~~g~V~e~L~~~~f~v~~edg-~~~---~ahI~GKmr~~~i~------I~~GD~V~Ve 56 (75)
T COG0361 6 EIEMEGTVIEMLPNGRFRVELENG-HER---LAHISGKMRKNRIR------ILPGDVVLVE 56 (75)
T ss_pred ccEEEEEEEEecCCCEEEEEecCC-cEE---EEEccCcchheeEE------eCCCCEEEEE
Confidence 3678888888754422 1122 222 2223677777 777 7899999987
No 159
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=37.12 E-value=2e+02 Score=22.44 Aligned_cols=55 Identities=27% Similarity=0.309 Sum_probs=30.9
Q ss_pred cccceEEEEEEEecCCceeecCCcEEEEEEE-----Ee----CCCeEEEEEecCCCCCCCCCCEEEEe
Q psy3603 41 GIKNVNVTCIVLDISPRVTLKENREVRTLKV-----AD----STACINLSLWDEPGALLHPGDIVRLT 99 (264)
Q Consensus 41 G~knVnv~fiVle~~~~r~TKdGg~V~tL~L-----AD----eTGsI~ltLWdd~ad~Ik~GDIIrI~ 99 (264)
+. .+.+.++|.+..... .++ .-..+.+ .+ .+|.|.+.+=.+....+++||.|+++
T Consensus 75 ~~-~~~v~g~V~~~~~~~--~~~-~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~l~~Gd~i~~~ 138 (176)
T PF13567_consen 75 GK-EVTVQGTVESVPQID--GRG-QRFTLRVERVLAGGNWIPVSGKILLYLPKDSQPRLQPGDRIRVR 138 (176)
T ss_pred Cc-eEEEEEEEccccccc--Cce-EEEEEEEEEeeccccccccceeeEEEeccccccccCCCCEEEEE
Confidence 44 388889887765332 122 1122221 11 25666665544443458999999998
No 160
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=35.32 E-value=1.8e+02 Score=21.37 Aligned_cols=60 Identities=22% Similarity=0.238 Sum_probs=35.1
Q ss_pred EEEEEEEecCCceeecCCcEEEEEEE-EeCCCeEEEEEecCC-----CCCCCCCCEEEEeeeEEEEEC--CEEEEEEcC
Q psy3603 46 NVTCIVLDISPRVTLKENREVRTLKV-ADSTACINLSLWDEP-----GALLHPGDIVRLTKCYAQIWR--NCLTLYSSK 116 (264)
Q Consensus 46 nv~fiVle~~~~r~TKdGg~V~tL~L-ADeTGsI~ltLWdd~-----ad~Ik~GDIIrI~ngyVs~fr--G~LqL~Igr 116 (264)
-+.++|.++... .+.+.| +.-.|.+...-.... .+.|++||.|..+ +.... +.+.|++..
T Consensus 9 iV~G~V~~v~~~--------~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~---V~~~~~~~~i~LS~~~ 76 (82)
T cd04454 9 IVIGIVTEVNSR--------FWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAK---VISLGDDMNVLLTTAD 76 (82)
T ss_pred EEEEEEEEEcCC--------EEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEE---EEEeCCCCCEEEEECC
Confidence 357778777533 222333 344666666655422 2459999999887 44443 567776553
No 161
>cd03703 aeIF5B_II aeIF5B_II: This family represents the domain II of archeal and eukaryotic aeIF5B. aeIF5B is a homologue of prokaryotic Initiation Factor 2 (IF2). Disruption of the eIF5B gene (FUN12) in yeast causes a severe slow-growth phenotype, associated with a defect in translation. eIF5B has a function analogous to prokaryotic IF2 in mediating the joining of joining of 60S subunits. The eIF5B consists of three N-terminal domains (I, II, II) connected by a long helix to domain IV. Domain I is a G domain, domain II and IV are beta-barrels and domain III has a novel alpha-beta-alpha sandwich fold. The G domain and the beta-barrel domain II display a similar structure and arrangement to the homologous domains of EF1A, eEF1A and aeIF2gamma.
Probab=34.87 E-value=2.1e+02 Score=23.79 Aligned_cols=36 Identities=19% Similarity=0.256 Sum_probs=26.3
Q ss_pred EEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEee
Q psy3603 48 TCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTK 100 (264)
Q Consensus 48 ~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~n 100 (264)
.+.|+|+..- +.-+.++++.|.|.| |++||+|-+-+
T Consensus 2 ~gtVlEvk~~---~G~G~t~dvIl~~Gt--------------L~~GD~Iv~g~ 37 (110)
T cd03703 2 QGTVLEVKEE---EGLGTTIDVILYDGT--------------LREGDTIVVCG 37 (110)
T ss_pred cEEEEEEEEc---CCCceEEEEEEECCe--------------EecCCEEEEcc
Confidence 3567776422 333789999999887 78999998854
No 162
>PTZ00425 asparagine-tRNA ligase; Provisional
Probab=32.65 E-value=3.1e+02 Score=28.85 Aligned_cols=55 Identities=13% Similarity=0.054 Sum_probs=36.2
Q ss_pred eEEEEEEEecCCceeecCCc-EEEEEEEEeCCC--eEEEEEecCC-----CCCCCCCCEEEEeeeEEEE
Q psy3603 45 VNVTCIVLDISPRVTLKENR-EVRTLKVADSTA--CINLSLWDEP-----GALLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg-~V~tL~LADeTG--sI~ltLWdd~-----ad~Ik~GDIIrI~ngyVs~ 105 (264)
|.+.+=|..+. +.|+ .+.-+.|.|.|| .|++++=... ...+..|++|.|.| .+..
T Consensus 84 Vtl~GWv~~iR-----~~g~~~~~Fv~lrDgsg~~~iQiVv~~~~~~~~~l~~l~~gs~v~v~G-~v~~ 146 (586)
T PTZ00425 84 ITVCGWSKAVR-----KQGGGRFCFVNLNDGSCHLNLQIIVDQSIENYEKLLKCGVGCCFRFTG-KLII 146 (586)
T ss_pred EEEEEEEeehh-----hcCCceEEEEEEECCCCCcceEEEECCchHHHHHHhcCCCccEEEEEE-EEEc
Confidence 66666665542 2243 689999999999 4888652221 12377899999995 5654
No 163
>PF04775 Bile_Hydr_Trans: Acyl-CoA thioester hydrolase/BAAT N-terminal region; InterPro: IPR006862 This entry presents the N-termini of acyl-CoA thioester hydrolase and bile acid-CoA:amino acid N-acetyltransferase (BAAT) []. This region is not thought to contain the active site of either enzyme. Thioesterase isoforms have been identified in peroxisomes, cytoplasm and mitochondria, where they are thought to have distinct functions in lipid metabolism []. For example, in peroxisomes, the hydrolase acts on bile-CoA esters [].; GO: 0016290 palmitoyl-CoA hydrolase activity, 0006629 lipid metabolic process; PDB: 3HLK_B 3K2I_B.
Probab=31.38 E-value=89 Score=25.78 Aligned_cols=46 Identities=22% Similarity=0.267 Sum_probs=26.0
Q ss_pred CcccccccccccccccceEEEEEEEecCCceeecCCcEE--EEEEEEeCCCeEEEE
Q psy3603 28 KEAMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREV--RTLKVADSTACINLS 81 (264)
Q Consensus 28 ~~~~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V--~tL~LADeTGsI~lt 81 (264)
|+-..+.|.-|.|++. |.+.+...+- .|..+ ...-.||++|.|.+.
T Consensus 2 De~~~I~v~GL~p~~~-vtl~a~~~~~-------~g~~w~S~A~f~Ad~~G~VDl~ 49 (126)
T PF04775_consen 2 DEPVDIRVSGLPPGQE-VTLRARLTDD-------NGVQWQSYATFRADENGIVDLS 49 (126)
T ss_dssp TS--EEEEES--TT-E-EEEEEEEE-T-------TS-EEEEEEEEE--TTS-EETT
T ss_pred CCCeEEEEeCCCCCCE-EEEEEEEEeC-------CCCEEEEEEEEEcCCCCeEEec
Confidence 5566788999999997 9998888752 23333 345679999999754
No 164
>cd03702 IF2_mtIF2_II This family represents the domain II of bacterial Initiation Factor 2 (IF2) and its eukaryotic mitochondrial homologue mtIF2. IF2, the largest initiation factor is an essential GTP binding protein. In E. coli three natural forms of IF2 exist in the cell, IF2alpha, IF2beta1, and IF2beta2. Bacterial IF-2 is structurally and functionally related to eukaryotic mitochondrial mtIF-2.
Probab=30.99 E-value=1.9e+02 Score=23.02 Aligned_cols=47 Identities=21% Similarity=0.297 Sum_probs=25.6
Q ss_pred EEEEecCCceeecCCcEEEEEEEEeC-------------CCeEEEEEecCCCCC---CCCCCEEEEe
Q psy3603 49 CIVLDISPRVTLKENREVRTLKVADS-------------TACINLSLWDEPGAL---LHPGDIVRLT 99 (264)
Q Consensus 49 fiVle~~~~r~TKdGg~V~tL~LADe-------------TGsI~ltLWdd~ad~---Ik~GDIIrI~ 99 (264)
+.|+|...- +.-+.+++++|.+. .|.|+. |||+.... ..||+.|+|.
T Consensus 3 g~VlE~~~~---~g~G~vatviV~~GtL~~Gd~iv~G~~~gkVr~-l~d~~g~~v~~a~Ps~~V~I~ 65 (95)
T cd03702 3 GVVIESKLD---KGRGPVATVLVQNGTLKVGDVLVAGTTYGKVRA-MFDENGKRVKEAGPSTPVEIL 65 (95)
T ss_pred EEEEEEEec---CCCCccEEEEEEcCeEeCCCEEEEcccccEEEE-EECCCCCCCCEECCCCcEEEc
Confidence 556665322 22256666666554 355554 56655433 4567777775
No 165
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=30.35 E-value=2e+02 Score=20.38 Aligned_cols=27 Identities=19% Similarity=0.112 Sum_probs=17.2
Q ss_pred CCCCCCCEEEEeeeEEEEECCEEEEEE
Q psy3603 88 ALLHPGDIVRLTKCYAQIWRNCLTLYS 114 (264)
Q Consensus 88 d~Ik~GDIIrI~ngyVs~frG~LqL~I 114 (264)
+.+++||.|+++=..+...++.++|.+
T Consensus 46 ~~~~~Gd~v~~~V~~~d~~~~~i~ls~ 72 (73)
T cd05706 46 YKFKKNDIVRACVLSVDVPNKKIALSL 72 (73)
T ss_pred cccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 448999999997322333346666654
No 166
>PRK09919 anti-adapter protein IraM; Provisional
Probab=30.01 E-value=82 Score=26.54 Aligned_cols=39 Identities=21% Similarity=0.314 Sum_probs=25.9
Q ss_pred eEEEEEecCCCCCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 77 CINLSLWDEPGALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 77 sI~ltLWdd~ad~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
.+.+.||-+..-.|.+||+|.+.+.-|-.-+-..+|.|=
T Consensus 26 nlKlilWY~~d~~L~pG~~i~~~~~gvliNdk~~pItIY 64 (114)
T PRK09919 26 NLKLILWYQADIFLPPGSIITPVKSGVLLNDKPYPITIY 64 (114)
T ss_pred cceEEEEEeeeEEeCCCCEEEEcCCeEEECCcEeEEEEE
Confidence 457788875444489999999997655554444555443
No 167
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=29.69 E-value=2.2e+02 Score=22.96 Aligned_cols=51 Identities=18% Similarity=0.229 Sum_probs=32.5
Q ss_pred ceEEEEEEEecCCceee----cCCcEEEEEEEEeCCCeEEE-EEecCCCCCCCCCCEEEEeeeEEEEEC
Q psy3603 44 NVNVTCIVLDISPRVTL----KENREVRTLKVADSTACINL-SLWDEPGALLHPGDIVRLTKCYAQIWR 107 (264)
Q Consensus 44 nVnv~fiVle~~~~r~T----KdGg~V~tL~LADeTGsI~l-tLWdd~ad~Ik~GDIIrI~ngyVs~fr 107 (264)
-|.+.++|++.-+...- -+|.. ++|=-+|.|+. .+| |.+||.|.|. .+-|+
T Consensus 6 ~ie~~G~V~e~Lp~~~frV~LenG~~----vla~isGKmR~~rIr------Il~GD~V~VE---~spYD 61 (87)
T PRK12442 6 LIELDGIVDEVLPDSRFRVTLENGVE----VGAYASGRMRKHRIR------ILAGDRVTLE---LSPYD 61 (87)
T ss_pred eEEEEEEEEEECCCCEEEEEeCCCCE----EEEEeccceeeeeEE------ecCCCEEEEE---ECccc
Confidence 38899999998644221 12222 23444777777 666 6799999997 45554
No 168
>cd05694 S1_Rrp5_repeat_hs2_sc2 S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=29.36 E-value=2.3e+02 Score=21.09 Aligned_cols=69 Identities=12% Similarity=0.079 Sum_probs=38.2
Q ss_pred cccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeeeEEEEECCEEEEEEc
Q psy3603 37 DLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKCYAQIWRNCLTLYSS 115 (264)
Q Consensus 37 DLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ngyVs~frG~LqL~Ig 115 (264)
||+.|+. +.+.|.++.+ .+-++.+-+.+=+|-|..+-=... +.+++|+.+.+.=-.+..-+..+.|.+.
T Consensus 1 dl~~G~~---v~g~V~si~d------~G~~v~~g~~gv~Gfl~~~~~~~~-~~~~~Gq~v~~~V~~vd~~~~~v~ls~k 69 (74)
T cd05694 1 DLVEGMV---LSGCVSSVED------HGYILDIGIPGTTGFLPKKDAGNF-SKLKVGQLLLCVVEKVKDDGRVVSLSAD 69 (74)
T ss_pred CCCCCCE---EEEEEEEEeC------CEEEEEeCCCCcEEEEEHHHCCcc-cccCCCCEEEEEEEEEECCCCEEEEEEe
Confidence 4566653 6677777652 255666533344565553221111 5689999998871122333566666654
No 169
>KOG1885|consensus
Probab=28.93 E-value=1.6e+02 Score=30.72 Aligned_cols=66 Identities=12% Similarity=0.171 Sum_probs=45.7
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEecCC----------CCCCCCCCEEEEeeeEEE-EECCEEEEE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWDEP----------GALLHPGDIVRLTKCYAQ-IWRNCLTLY 113 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWdd~----------ad~Ik~GDIIrI~ngyVs-~frG~LqL~ 113 (264)
+.+-++|.++.. .|.+.+-+.|-++.+.+++.+=-.. .+.++.||||.+.| +.. .-.|+|.|.
T Consensus 107 ~svaGRI~s~R~-----sGsKL~Fydl~~~g~klQvm~~~~~~~~~~~F~~~~~~lkrGDiig~~G-~pgrt~~gELSi~ 180 (560)
T KOG1885|consen 107 VSVAGRIHSKRE-----SGSKLVFYDLHGDGVKLQVMANAKKITSEEDFEQLHKFLKRGDIIGVSG-YPGRTKSGELSII 180 (560)
T ss_pred eeeeeeEeeeec-----cCCceEEEEEecCCeEEEEEEehhhcCCHHHHHHHHhhhhccCEEeeec-CCCcCCCceEEEe
Confidence 666677766532 4778888888888888877654322 13489999999995 554 445877777
Q ss_pred EcC
Q psy3603 114 SSK 116 (264)
Q Consensus 114 Igr 116 (264)
..+
T Consensus 181 ~~~ 183 (560)
T KOG1885|consen 181 PNE 183 (560)
T ss_pred ecc
Confidence 775
No 170
>PRK00147 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional
Probab=28.14 E-value=1.6e+02 Score=28.96 Aligned_cols=35 Identities=26% Similarity=0.374 Sum_probs=23.2
Q ss_pred EEEEe-CCCeEEEEEecCCCCCCCCCCEEEEeeeEE
Q psy3603 69 LKVAD-STACINLSLWDEPGALLHPGDIVRLTKCYA 103 (264)
Q Consensus 69 L~LAD-eTGsI~ltLWdd~ad~Ik~GDIIrI~ngyV 103 (264)
|.|.| ++|.|.=..+.+..+.|++||++.+-+.+|
T Consensus 28 LLV~~r~~~~i~h~~F~dl~~~l~~gDlLV~NdTkV 63 (342)
T PRK00147 28 LLVLDRKTGEIEHRHFRDLPDYLNPGDLLVFNDTRV 63 (342)
T ss_pred EEEEECCCCcEEeeehhhhHhhcCCCCEEEEEcCee
Confidence 33444 477777777777777788888877765433
No 171
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=28.03 E-value=3.7e+02 Score=23.22 Aligned_cols=56 Identities=18% Similarity=0.194 Sum_probs=33.0
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEEEec-CCC---CCCCCCCEEEEeeeE
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVADSTACINLSLWD-EPG---ALLHPGDIVRLTKCY 102 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~ltLWd-d~a---d~Ik~GDIIrI~ngy 102 (264)
|...+.|..+.+...+.......-+.| .+|.--+.+-+ |.+ ..+++||.|.+.|-|
T Consensus 39 v~g~G~V~~vLpdd~~GsrHQ~Fiv~l--~~g~tllIahNIDlaprip~l~~GD~V~f~GeY 98 (131)
T PF11948_consen 39 VSGCGTVVKVLPDDNKGSRHQRFIVRL--SSGQTLLIAHNIDLAPRIPWLQKGDQVEFYGEY 98 (131)
T ss_pred EeccEEEEEECcccCCCCcceEEEEEe--CCCCEEEEEeccCccccCcCcCCCCEEEEEEEE
Confidence 566888888865432212233334444 34554444555 333 338999999999876
No 172
>PF07712 SURNod19: Stress up-regulated Nod 19; InterPro: IPR011692 This family of plant proteins have been implicated in nodule development [] in the legume Medicago truncatula (Barrel medic). MtN-19 was shown by Northern blot to be induced during nodulation []. The molecular function of these proteins is unknown.
Probab=27.56 E-value=40 Score=33.57 Aligned_cols=27 Identities=44% Similarity=0.918 Sum_probs=19.5
Q ss_pred cceEEeec-eeeeeEEEeecCcceeeeec
Q psy3603 196 NTWVTWDQ-LLPVKFQFFSSSSRTLKFSN 223 (264)
Q Consensus 196 ~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 223 (264)
=+||.||+ .+|||+-.|.... ++|.++
T Consensus 212 v~wvdWd~~vvPvkiyi~DvTd-~~~~~~ 239 (381)
T PF07712_consen 212 VKWVDWDECVVPVKIYILDVTD-TLKISN 239 (381)
T ss_pred EEEeccccceeeEEEEEEEccC-chhhcc
Confidence 47999997 6899998887653 344443
No 173
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=27.51 E-value=1.9e+02 Score=22.15 Aligned_cols=42 Identities=17% Similarity=0.357 Sum_probs=25.8
Q ss_pred eEEEEEEEecCCceeecCCcEEEEEEEEe-------CCCeEEE-EEecCCCCCCCCCCEEEEe
Q psy3603 45 VNVTCIVLDISPRVTLKENREVRTLKVAD-------STACINL-SLWDEPGALLHPGDIVRLT 99 (264)
Q Consensus 45 Vnv~fiVle~~~~r~TKdGg~V~tL~LAD-------eTGsI~l-tLWdd~ad~Ik~GDIIrI~ 99 (264)
+.+.++|.+.-+.. ...+.+.| -+|.++. .+| +.+||.|.|.
T Consensus 5 ie~~G~V~e~L~~~-------~f~V~l~ng~~vla~i~GKmr~~rI~------I~~GD~V~Ve 54 (68)
T TIGR00008 5 IEMEGKVTESLPNA-------MFRVELENGHEVLAHISGKIRMHYIR------ILPGDKVKVE 54 (68)
T ss_pred EEEEEEEEEECCCC-------EEEEEECCCCEEEEEecCcchhccEE------ECCCCEEEEE
Confidence 78889998875432 22223322 2455553 444 6799999987
No 174
>PF11183 PmrD: Polymyxin resistance protein PmrD; InterPro: IPR020146 The Salmonella PmrA/PmrB two-component system is required for resistance to the cationic peptide antibiotic olymyxin B, resistance to Fe(3+)-mediated killing, growth in soil, virulence in mice, and infection of chicken macrophages. PmrA-activated genes encode periplasmic and integral membrane proteins as well as cytoplasmic products mediating the modification of the lipopolysaccharide, suggesting a role for the PmrA/PmrB system in remodeling of the Gram-negative envelope. The PmrA/PmrB two-component system of Salmonella enterica is activated by Fe(3+), which is sensed by the PmrB protein, and by low Mg(2+), which is sensed by the PhoQ protein. The low Mg(2+) activation requires pmrD, a PhoPPhoQ-activated gene that activates the response regulator PmrA at a posttranscriptional level. However, under conditions that activate the PmrA protein independently of pmrD, such as exposure to Fe3, lower levels of pmrD transcription occur. It has been demonstrated that PmrA binds to the pmrD promoter, suppressing transcription. Negative regulation of the PhoP/PhoQ-activated pmrD gene by the PmrA/ PmrB system closes a regulatory circuit designed to maintain proper cellular levels of activated PmrA protein, and constitutes a singular example of a multicomponent feedback loop []. ; PDB: 2RQX_A 2JSO_A.
Probab=27.36 E-value=60 Score=25.93 Aligned_cols=36 Identities=17% Similarity=0.216 Sum_probs=27.7
Q ss_pred EEEEEEEeCCCeEEEEEecCCCCCCCCCCEEE-Eeee
Q psy3603 66 VRTLKVADSTACINLSLWDEPGALLHPGDIVR-LTKC 101 (264)
Q Consensus 66 V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIr-I~ng 101 (264)
..-+.+.|.-|.+.+-+|=+..-.+++||.+. |.+|
T Consensus 16 ~~~l~l~~a~g~LkmIAEv~s~~~l~~GD~LtPl~dA 52 (82)
T PF11183_consen 16 CHVLLLCDAGGALKMIAEVTSDFRLQEGDKLTPLQDA 52 (82)
T ss_dssp EEEEEEEETTTTCEEEEEEEESS---TT-EEEESSSS
T ss_pred EEEEEEecCCCCeEEEEEeecCcccCCCCCccccccc
Confidence 66788999999999999987755699999999 8877
No 175
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=26.37 E-value=4.5e+02 Score=23.14 Aligned_cols=56 Identities=13% Similarity=0.036 Sum_probs=43.7
Q ss_pred cceEEEEEEEecCCceeecCC-cEEEEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeee
Q psy3603 43 KNVNVTCIVLDISPRVTLKEN-REVRTLKVADSTACINLSLWDEPGALLHPGDIVRLTKC 101 (264)
Q Consensus 43 knVnv~fiVle~~~~r~TKdG-g~V~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ng 101 (264)
+.+-+-+.|.+=+.. |++ +.-+..+|.|..++|.+..=+-..|+|++|.-|.+.|.
T Consensus 52 ~~~RlGG~V~~GSv~---r~~~~~~v~F~vtD~~~~v~V~Y~GilPDlFrEGqgVVaeG~ 108 (155)
T PRK13159 52 QQFRLGGMVKAGSIQ---RAADSLKVSFTVIDKNAATQVEYTGILPDLFRDNQSVIANGR 108 (155)
T ss_pred CeEEEccEEecCcEE---EcCCCcEEEEEEEcCCcEEEEEEccCCCccccCCCeEEEEEE
Confidence 447777888764433 333 44578899999999999988888999999999999954
No 176
>PF09926 DUF2158: Uncharacterized small protein (DUF2158); InterPro: IPR019226 This entry represents a family of predominantly prokaryotic proteins with no known function.
Probab=26.23 E-value=43 Score=24.33 Aligned_cols=12 Identities=33% Similarity=0.598 Sum_probs=10.1
Q ss_pred CCCCCEEEEeee
Q psy3603 90 LHPGDIVRLTKC 101 (264)
Q Consensus 90 Ik~GDIIrI~ng 101 (264)
|++||+|+++.|
T Consensus 1 f~~GDvV~LKSG 12 (53)
T PF09926_consen 1 FKIGDVVQLKSG 12 (53)
T ss_pred CCCCCEEEEccC
Confidence 679999999865
No 177
>PF02547 Queuosine_synth: Queuosine biosynthesis protein; InterPro: IPR003699 This entry represents the queuosine biosynthesis proteins QueA. Queuosine is a hypermodified nucleoside that usually occurs in the first position of the anticodon of tRNAs specifying the amino acids asparagine, aspartate, histidine, and tyrosine. The hypermodified nucleoside is found in bacteria and eukaryotes []. Queuosine is synthesized de novo exclusively in bacteria; for eukaryotes the compound is a nutrient factor. Queuosine biosynthesis protein, or S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (QueA) catalyses the formation of the 2,3-epoxy-4,5-dihydroxycyclopentane ring of the Q precursor epoxyqueuosine (oQ). S-adenosyl-L-methionine (AdoMet) reacts with 7-aminomethyl-7-deazaguanine of tRNA at position 34 to yield adenine, methionine, and a modified tRNA with oQ at position 34. QueA consists of two domains: domain 1 has 3 layers alpha/beta/alpha, while domain 2 is a closed beta-barrel with Greek-key topology [].; GO: 0016740 transferase activity, 0016853 isomerase activity, 0008616 queuosine biosynthetic process; PDB: 1WDI_A 1VKY_B 1YY3_A.
Probab=26.01 E-value=2.3e+02 Score=27.82 Aligned_cols=52 Identities=17% Similarity=0.266 Sum_probs=32.1
Q ss_pred EEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeeeEEEEECCEEEEEEcCCceE
Q psy3603 67 RTLKVADSTACINLSLWDEPGALLHPGDIVRLTKCYAQIWRNCLTLYSSKSGLI 120 (264)
Q Consensus 67 ~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ngyVs~frG~LqL~Igr~G~I 120 (264)
+-|++-.++|.|.=..+.+..+.|++||++.+-+ +++..-.|.-.-..+|+|
T Consensus 26 RLLVl~r~~~~i~h~~F~~l~~~L~~GDlLV~Nd--TkVipARL~g~k~tG~~v 77 (341)
T PF02547_consen 26 RLLVLDRRSGEIEHRRFRDLPDYLRPGDLLVFND--TKVIPARLFGQKETGGKV 77 (341)
T ss_dssp EEEEEETTTTEEEEEEGGGGGGG--TTEEEEEEE--EEE-SEEEEEEETTS-EE
T ss_pred eEEEEECCCCcEeeeeHhHHHHhhCCCCEEEEeC--CEEEeeEEEEEecCCCEE
Confidence 3445555578998888888888999999999875 444444444444334444
No 178
>PRK10220 hypothetical protein; Provisional
Probab=25.83 E-value=2.2e+02 Score=24.02 Aligned_cols=41 Identities=22% Similarity=0.373 Sum_probs=26.7
Q ss_pred ccccccceEEEEEEEecC---CceeecCCcEEEEEEEEeCCCeEEEEE
Q psy3603 38 LHVGIKNVNVTCIVLDIS---PRVTLKENREVRTLKVADSTACINLSL 82 (264)
Q Consensus 38 LkpG~knVnv~fiVle~~---~~r~TKdGg~V~tL~LADeTGsI~ltL 82 (264)
|..|+. |.+ |.+.. ....-|.|.++++++|.|....|.+++
T Consensus 52 L~dGDs-V~v---iKDLkVKGss~~~K~GTkvknIrL~d~~h~Idcki 95 (111)
T PRK10220 52 LADGDS-VTI---VKDLKVKGSSSMLKIGTKVKNIRLVEGDHNIDCKI 95 (111)
T ss_pred ccCCCE-EEE---EeeccccccccceeCccEEEEEEecCCCceEEEec
Confidence 566665 433 33332 222247889999999998877787755
No 179
>cd05704 S1_Rrp5_repeat_hs13 S1_Rrp5_repeat_hs13: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 13 (hs13). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.80 E-value=1.3e+02 Score=21.89 Aligned_cols=25 Identities=24% Similarity=0.175 Sum_probs=17.8
Q ss_pred CCCCCCCEEEEeeeEEEEECCEEEEEE
Q psy3603 88 ALLHPGDIVRLTKCYAQIWRNCLTLYS 114 (264)
Q Consensus 88 d~Ik~GDIIrI~ngyVs~frG~LqL~I 114 (264)
+.+++||.|+++ .++.-++.++|++
T Consensus 47 ~~~~~Gd~v~~k--V~~~~~~~i~LSl 71 (72)
T cd05704 47 EGFKPGKIVRCC--ILSKKDGKYQLSL 71 (72)
T ss_pred HhCCCCCEEEEE--EEEecCCEEEEEe
Confidence 448999999997 3444447777765
No 180
>COG4013 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.66 E-value=2.2e+02 Score=23.10 Aligned_cols=28 Identities=21% Similarity=0.114 Sum_probs=20.4
Q ss_pred CCCCCCEEEEeeeEE-------EEECCEEEEEEcC
Q psy3603 89 LLHPGDIVRLTKCYA-------QIWRNCLTLYSSK 116 (264)
Q Consensus 89 ~Ik~GDIIrI~ngyV-------s~frG~LqL~Igr 116 (264)
.+++||.|++.=|+| ..-+|.|+|.+.+
T Consensus 20 eV~~gd~vel~~grVhIpG~vv~~n~g~l~l~~es 54 (91)
T COG4013 20 EVDVGDYVELYFGRVHIPGRVVHYNDGLLRLVHES 54 (91)
T ss_pred cCCCCCEEEEEEEEEEeccEEEEeeccEEEEEEec
Confidence 478999988774443 3346889999887
No 181
>cd03446 MaoC_like MoaC_like Similar to the MaoC (monoamine oxidase C) dehydratase regulatory protein but without the N-terminal PutA domain. This protein family has a hot-dog fold similar to that of (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=22.26 E-value=2.9e+02 Score=21.78 Aligned_cols=47 Identities=11% Similarity=0.192 Sum_probs=29.7
Q ss_pred cccccccccccccceEEEEEEEecCCceeecCC-cE-EEEEEEEeCCCeEEE
Q psy3603 31 MDVYIKDLHVGIKNVNVTCIVLDISPRVTLKEN-RE-VRTLKVADSTACINL 80 (264)
Q Consensus 31 ~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdG-g~-V~tL~LADeTGsI~l 80 (264)
...+.+-+.+|+. +.+...|+++.+.. +.+ +. .+.+.+.|..|.+-+
T Consensus 84 ~~~f~~pv~~GD~-l~~~~~v~~~~~~~--~~~~~~v~~~~~~~nq~g~~v~ 132 (140)
T cd03446 84 NLRFLNPVFIGDT-IRAEAEVVEKEEKD--GEDAGVVTRRIEVVNQRGEVVQ 132 (140)
T ss_pred eEEEcCCCCCCCE-EEEEEEEEEecccC--CCCceEEEEEEEEEcCCCCEEE
Confidence 3456677888997 99999999875432 222 22 245666677776543
No 182
>cd00586 4HBT 4-hydroxybenzoyl-CoA thioesterase (4HBT). Catalyzes the final step in the 4-chlorobenzoate degradation pathway in which 4-chlorobenzoate is converted to 4-hydroxybenzoate in certain soil-dwelling bacteria. 4HBT forms a homotetramer with four active sites. There is no evidence to suggest that 4HBT is related to the type I thioesterases functioning in primary or secondary metabolic pathways. Each subunit of the 4HBT tetramer adopts a so-called hot-dog fold similar to those of beta-hydroxydecanoyl-ACP dehydratase, (R)-specific enoyl-CoA hydratase, and type II, thioesterase (TEII).
Probab=22.11 E-value=2.9e+02 Score=19.50 Aligned_cols=44 Identities=14% Similarity=0.141 Sum_probs=28.3
Q ss_pred ccccccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEE
Q psy3603 30 AMDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINL 80 (264)
Q Consensus 30 ~~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~l 80 (264)
....+.+.+.+|++ |.+...|...... ..++...+-+++|.+-+
T Consensus 57 ~~i~~~~~~~~~~~-i~v~~~~~~~~~~------~~~~~~~~~~~~g~~~a 100 (110)
T cd00586 57 LEIDYLRPLRLGDR-LTVETRVLRLGRK------SFTFEQEIFREDGELLA 100 (110)
T ss_pred eEeeEcCccCCCCE-EEEEEEEEecCcE------EEEEEEEEECCCCeEEE
Confidence 34466777888886 8888888886533 23455566555666544
No 183
>KOG0851|consensus
Probab=22.04 E-value=3.7e+02 Score=23.20 Aligned_cols=73 Identities=18% Similarity=0.105 Sum_probs=47.7
Q ss_pred ccccccccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCe-EEEEEecCCC----CCCCCCCEEEEeeeEEEE
Q psy3603 32 DVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTAC-INLSLWDEPG----ALLHPGDIVRLTKCYAQI 105 (264)
Q Consensus 32 ~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGs-I~ltLWdd~a----d~Ik~GDIIrI~ngyVs~ 105 (264)
+..+.+|.|.-.+=.+.+.|+.+-... ...++..+.+.++|++|. |.+++-.... ..+.+|+-+.|.+-.+..
T Consensus 4 ~~~l~~l~~~~t~w~i~~~vl~v~~~~-~~~~~~~~~~il~D~~~~~i~a~i~~~~~~~~~~~l~~~~w~~i~~f~v~~ 81 (246)
T KOG0851|consen 4 FHRLRDLSPSITGWRIQVKVLRVWKKY-SNPNGEELRLVLADEHGVKIEATVGRRLSSKYEDNLIENEWKIITTFGVNP 81 (246)
T ss_pred ccchhhcCcCceeeEEEEEEEEEEEec-CCCCccEEEEEEEecCCcEEEEEcchHHHhhhhhheecceeEEeeeeeecc
Confidence 456777777665555566666665332 222356788889999976 8888876443 347888877777544443
No 184
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=21.71 E-value=3.2e+02 Score=22.16 Aligned_cols=46 Identities=15% Similarity=0.272 Sum_probs=25.8
Q ss_pred cccccceEEEEEEEecCCceeecCCcEEEEEEEEeC-------CCeEEEEEecCCCCCCCCCCEEEEe
Q psy3603 39 HVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADS-------TACINLSLWDEPGALLHPGDIVRLT 99 (264)
Q Consensus 39 kpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADe-------TGsI~ltLWdd~ad~Ik~GDIIrI~ 99 (264)
.|... .+.++|++.-.. -...+.+.|. .|.++-++| |.+||+|.|.
T Consensus 17 ~p~e~--e~~g~V~~~lG~-------~~~~V~~~dG~~~la~i~GK~Rk~Iw------I~~GD~VlVe 69 (100)
T PRK04012 17 MPEEG--EVFGVVEQMLGA-------NRVRVRCMDGVERMGRIPGKMKKRMW------IREGDVVIVA 69 (100)
T ss_pred CCCCC--EEEEEEEEEcCC-------CEEEEEeCCCCEEEEEEchhhcccEE------ecCCCEEEEE
Confidence 44444 567777776322 2233333332 445555555 7899999986
No 185
>cd03452 MaoC_C MaoC_C The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit. MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=21.48 E-value=2.7e+02 Score=22.74 Aligned_cols=48 Identities=13% Similarity=0.092 Sum_probs=30.7
Q ss_pred cccccccccccccceEEEEEEEecCCceeecCCcEE-EEEEEEeCCCeEEE
Q psy3603 31 MDVYIKDLHVGIKNVNVTCIVLDISPRVTLKENREV-RTLKVADSTACINL 80 (264)
Q Consensus 31 ~~ikIkDLkpG~knVnv~fiVle~~~~r~TKdGg~V-~tL~LADeTGsI~l 80 (264)
...+.+-+.+|+. |.+.+.|+++.+. ..++.+.+ +.+.+.|..|.+-+
T Consensus 82 ~~rf~~PV~~GDt-l~~~~~V~~~~~~-~~~~~~~v~~~~~~~nq~g~~V~ 130 (142)
T cd03452 82 NLRFLEPVYPGDT-IQVRLTCKRKIPR-DGQDYGVVRWDAEVTNQNGELVA 130 (142)
T ss_pred eEEECCCCCCCCE-EEEEEEEEEEeec-CCCCcEEEEEEEEEEecCCCEEE
Confidence 3455666788997 9999999988644 21122332 56666777777544
No 186
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=21.06 E-value=89 Score=24.95 Aligned_cols=37 Identities=16% Similarity=0.108 Sum_probs=24.1
Q ss_pred EEEEEEeCCCeEEEEEecCCCCCCCCCCEEEEeeeEEEEE
Q psy3603 67 RTLKVADSTACINLSLWDEPGALLHPGDIVRLTKCYAQIW 106 (264)
Q Consensus 67 ~tL~LADeTGsI~ltLWdd~ad~Ik~GDIIrI~ngyVs~f 106 (264)
..+.|. .|.+.+.++ .....+++||+|.|--+.+..+
T Consensus 66 ~~~~Vl--~G~~~~~~~-g~~~~l~~Gd~i~ip~g~~H~~ 102 (131)
T COG1917 66 QTIYVL--EGEGTVQLE-GEKKELKAGDVIIIPPGVVHGL 102 (131)
T ss_pred eEEEEE--ecEEEEEec-CCceEecCCCEEEECCCCeeee
Confidence 444444 466677777 4555689999999985544433
No 187
>PF13585 CHU_C: C-terminal domain of CHU protein family; PDB: 3EIF_A 1XF1_B.
Probab=20.78 E-value=3.1e+02 Score=20.96 Aligned_cols=68 Identities=18% Similarity=0.196 Sum_probs=30.5
Q ss_pred ccccccceEEEEEEEecCCceeecCCcEEEEEEEEeCCCeEEEE------EecCC--C--CCCCCCCEEEEeee---EEE
Q psy3603 38 LHVGIKNVNVTCIVLDISPRVTLKENREVRTLKVADSTACINLS------LWDEP--G--ALLHPGDIVRLTKC---YAQ 104 (264)
Q Consensus 38 LkpG~knVnv~fiVle~~~~r~TKdGg~V~tL~LADeTGsI~lt------LWdd~--a--d~Ik~GDIIrI~ng---yVs 104 (264)
+.|...+++.++.|.-.. .-.-..+.|-|+-|.+-.. -||-. . ..+..|..+.+... ...
T Consensus 7 fTPNgDg~ND~~~i~~~~-------~~~~~~~~IynrwG~~Vf~~~~~~~~WdG~~~g~g~~~p~G~Y~Y~i~~~~~~~~ 79 (87)
T PF13585_consen 7 FTPNGDGINDTFKIPGIE-------NIPNYSLTIYNRWGELVFESNDYNNGWDGTYNGSGNPLPSGTYFYVIEYNDGNKK 79 (87)
T ss_dssp E--SSSSSS--BEEEESS--------EEEEEEEEE-SSS-EEEE---EEG-B-SB-T-TS-B--SEEEEEEEEESTT---
T ss_pred EeCCCCCcCCEEEEeccc-------ccceeEEEEEeCCCcEEEEECCCCCCCCCEecCCcccCCCceEEEEEEEeCCCCe
Confidence 466655688888887632 1245889999999988665 47733 1 44677877666533 334
Q ss_pred EECCEEEE
Q psy3603 105 IWRNCLTL 112 (264)
Q Consensus 105 ~frG~LqL 112 (264)
.++|.++|
T Consensus 80 ~~~G~i~l 87 (87)
T PF13585_consen 80 EKKGWITL 87 (87)
T ss_dssp EE------
T ss_pred EEeeecCC
Confidence 45555543
No 188
>PF10648 Gmad2: Immunoglobulin-like domain of bacterial spore germination; InterPro: IPR018911 This domain is found linked to IPR019606 from INTERPRO in some bacterial proteins. It is predicted to contain an immunoglobulin-like all-beta fold.
Probab=20.73 E-value=2.1e+02 Score=22.44 Aligned_cols=53 Identities=6% Similarity=-0.034 Sum_probs=33.2
Q ss_pred CCCEEEEeeeEEEEECCEEEEEEcCCceEEEecCceeeecCCCCCCCCCCCCCC
Q psy3603 92 PGDIVRLTKCYAQIWRNCLTLYSSKSGLIEKIGEFCMVFNENLDMSIPIPNLPV 145 (264)
Q Consensus 92 ~GDIIrI~ngyVs~frG~LqL~Igr~G~IekVgEf~~~fnE~pNiSe~~Pe~~~ 145 (264)
.++-|+|+ |+++.|.+.+.+.|...........+.+.-...+....|.-.-.+
T Consensus 14 V~sp~~V~-G~A~~FEgtv~~rv~D~~g~vl~e~~~~a~~g~~~~g~F~~tv~~ 66 (88)
T PF10648_consen 14 VSSPVKVS-GKARVFEGTVNIRVRDGHGEVLAEGFVTATGGAPSWGPFEGTVSF 66 (88)
T ss_pred cCCCEEEE-EEEEEeeeEEEEEEEcCCCcEEEEeeEEeccCCCcccceEEEEEe
Confidence 46679999 689999999999987644322234444433444555555444444
No 189
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=20.55 E-value=83 Score=18.42 Aligned_cols=12 Identities=33% Similarity=0.506 Sum_probs=10.5
Q ss_pred CCCCCEEEEeee
Q psy3603 90 LHPGDIVRLTKC 101 (264)
Q Consensus 90 Ik~GDIIrI~ng 101 (264)
+++||.|+|.+|
T Consensus 2 ~~~G~~V~I~~G 13 (28)
T smart00739 2 FEVGDTVRVIAG 13 (28)
T ss_pred CCCCCEEEEeEC
Confidence 679999999976
No 190
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=20.52 E-value=2.6e+02 Score=23.50 Aligned_cols=41 Identities=15% Similarity=0.392 Sum_probs=28.1
Q ss_pred ccccccceEEEEEEEecC---CceeecCCcEEEEEEEEeCCCeEEEEE
Q psy3603 38 LHVGIKNVNVTCIVLDIS---PRVTLKENREVRTLKVADSTACINLSL 82 (264)
Q Consensus 38 LkpG~knVnv~fiVle~~---~~r~TKdGg~V~tL~LADeTGsI~ltL 82 (264)
|..|++ |. +|.+.. ....-|.|.+|++++|.|....|.+++
T Consensus 51 L~dGDs-V~---liKDLkVKGss~~~K~GTkVknIrL~d~~h~Idckv 94 (109)
T TIGR00686 51 LANGDS-VI---LIKDLKVKGSSLVLKKGTKIKNIRLVNGDHNVDCKI 94 (109)
T ss_pred ccCCCE-EE---EEeeccccCcccceeCccEEEEEEecCCCceEeeEe
Confidence 667775 43 344432 222247899999999999888888887
Done!