Query 044496
Match_columns 142
No_of_seqs 72 out of 74
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 03:46:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044496.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044496hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd04478 RPA2_DBD_D RPA2_DBD_D: 98.5 2.2E-06 4.7E-11 59.6 9.7 85 37-130 2-94 (95)
2 KOG3108 Single-stranded DNA-bi 98.4 2.9E-06 6.3E-11 71.9 9.8 112 11-135 46-167 (265)
3 cd04483 hOBFC1_like hOBFC1_lik 98.3 6.4E-06 1.4E-10 59.0 9.0 64 39-110 2-90 (92)
4 COG3390 Uncharacterized protei 98.3 4.6E-06 1E-10 68.1 9.0 85 5-96 8-110 (196)
5 PF01336 tRNA_anti-codon: OB-f 98.2 1.2E-05 2.5E-10 52.4 7.6 69 37-112 1-75 (75)
6 COG5235 RFA2 Single-stranded D 97.6 0.0013 2.9E-08 55.3 11.9 114 12-134 44-164 (258)
7 PF04076 BOF: Bacterial OB fol 97.6 0.00083 1.8E-08 49.7 8.9 71 31-110 31-102 (103)
8 TIGR00156 conserved hypothetic 97.4 0.0014 2.9E-08 50.4 8.7 68 33-109 56-124 (126)
9 PRK10053 hypothetical protein; 97.3 0.0019 4.2E-08 49.8 8.6 68 33-109 60-128 (130)
10 cd04489 ExoVII_LU_OBF ExoVII_L 96.9 0.017 3.6E-07 38.3 9.2 67 37-110 2-75 (78)
11 cd03524 RPA2_OBF_family RPA2_O 96.9 0.0075 1.6E-07 37.4 7.0 61 39-107 2-71 (75)
12 PF08661 Rep_fac-A_3: Replicat 96.9 0.0097 2.1E-07 43.3 8.3 75 35-120 19-94 (109)
13 cd04492 YhaM_OBF_like YhaM_OBF 96.8 0.0089 1.9E-07 39.3 7.2 55 52-114 22-78 (83)
14 PF10451 Stn1: Telomere regula 96.7 0.03 6.4E-07 47.2 11.3 114 9-133 30-167 (256)
15 COG3111 Periplasmic protein wi 96.6 0.016 3.5E-07 44.9 8.0 66 35-109 58-124 (128)
16 cd04479 RPA3 RPA3: A subfamily 96.3 0.076 1.6E-06 38.4 9.7 67 35-117 16-83 (101)
17 cd04100 Asp_Lys_Asn_RS_N Asp_L 96.1 0.11 2.4E-06 35.5 9.4 68 37-111 2-82 (85)
18 PRK05159 aspC aspartyl-tRNA sy 95.8 0.077 1.7E-06 47.1 9.5 74 35-115 17-100 (437)
19 cd04316 ND_PkAspRS_like_N ND_P 95.8 0.18 3.9E-06 36.2 9.6 74 35-115 13-97 (108)
20 cd04323 AsnRS_cyto_like_N AsnR 95.7 0.3 6.6E-06 33.4 10.2 71 36-113 1-83 (84)
21 cd04317 EcAspRS_like_N EcAspRS 95.6 0.16 3.4E-06 37.7 9.2 73 36-115 16-104 (135)
22 cd04322 LysRS_N LysRS_N: N-ter 95.6 0.18 3.8E-06 36.1 9.2 72 37-115 2-83 (108)
23 cd04485 DnaE_OBF DnaE_OBF: A s 95.3 0.038 8.2E-07 35.7 4.5 55 51-113 21-78 (84)
24 cd04320 AspRS_cyto_N AspRS_cyt 95.3 0.34 7.4E-06 34.2 9.6 72 37-115 2-92 (102)
25 cd04482 RPA2_OBF_like RPA2_OBF 95.0 0.41 8.8E-06 34.0 9.2 65 37-112 1-74 (91)
26 COG4085 Predicted RNA-binding 94.9 0.17 3.7E-06 42.0 8.0 80 31-118 48-139 (204)
27 cd04318 EcAsnRS_like_N EcAsnRS 94.8 0.77 1.7E-05 31.1 10.2 69 37-112 2-80 (82)
28 cd04488 RecG_wedge_OBF RecG_we 94.7 0.29 6.3E-06 31.0 7.2 51 39-96 2-60 (75)
29 TIGR00499 lysS_bact lysyl-tRNA 94.5 0.32 7E-06 44.2 9.6 73 36-115 55-137 (496)
30 PF13742 tRNA_anti_2: OB-fold 94.3 0.31 6.8E-06 35.0 7.4 61 32-100 19-86 (99)
31 TIGR00458 aspS_arch aspartyl-t 94.2 0.46 1E-05 42.2 9.7 74 35-115 13-97 (428)
32 cd04321 ScAspRS_mt_like_N ScAs 94.2 1.1 2.4E-05 30.9 9.7 69 37-112 2-84 (86)
33 cd04319 PhAsnRS_like_N PhAsnRS 93.4 1.6 3.5E-05 30.9 9.7 71 37-114 2-82 (103)
34 TIGR00457 asnS asparaginyl-tRN 93.3 0.66 1.4E-05 41.7 9.2 74 35-115 17-102 (453)
35 PLN02850 aspartate-tRNA ligase 93.3 0.73 1.6E-05 42.4 9.6 74 35-115 82-172 (530)
36 cd04487 RecJ_OBF2_like RecJ_OB 93.3 1.4 3E-05 30.3 8.8 53 37-96 1-58 (73)
37 PLN02502 lysyl-tRNA synthetase 92.9 1 2.2E-05 41.9 9.9 74 35-115 109-194 (553)
38 cd04491 SoSSB_OBF SoSSB_OBF: A 92.9 0.84 1.8E-05 30.9 7.2 48 52-107 26-74 (82)
39 PRK12445 lysyl-tRNA synthetase 92.8 1.1 2.3E-05 41.1 9.8 73 36-115 67-149 (505)
40 PRK00484 lysS lysyl-tRNA synth 92.4 1.3 2.7E-05 40.3 9.7 74 35-115 55-137 (491)
41 PRK03932 asnC asparaginyl-tRNA 91.9 1.6 3.5E-05 39.1 9.7 73 35-114 17-99 (450)
42 cd04490 PolII_SU_OBF PolII_SU_ 91.8 2.7 5.9E-05 29.0 8.9 63 38-110 3-73 (79)
43 PRK02983 lysS lysyl-tRNA synth 91.7 1.5 3.3E-05 43.7 10.1 73 36-115 653-735 (1094)
44 COG1570 XseA Exonuclease VII, 91.5 1.1 2.3E-05 41.0 8.1 64 34-105 23-92 (440)
45 PF01455 HupF_HypC: HupF/HypC 91.3 0.93 2E-05 31.1 5.9 47 39-95 5-51 (68)
46 PTZ00401 aspartyl-tRNA synthet 90.7 1.9 4.1E-05 40.0 9.1 74 35-115 79-169 (550)
47 PRK07373 DNA polymerase III su 90.7 0.98 2.1E-05 40.8 7.1 72 35-114 281-362 (449)
48 TIGR00459 aspS_bact aspartyl-t 90.5 2.3 5E-05 39.8 9.6 73 36-115 17-104 (583)
49 COG1107 Archaea-specific RecJ- 90.3 0.7 1.5E-05 44.1 6.0 71 35-114 214-290 (715)
50 PRK00476 aspS aspartyl-tRNA sy 90.0 2.4 5.1E-05 39.6 9.2 73 36-115 19-106 (588)
51 PLN02221 asparaginyl-tRNA synt 89.7 2.1 4.6E-05 40.0 8.6 73 35-114 51-136 (572)
52 PF07076 DUF1344: Protein of u 89.7 1 2.3E-05 30.9 5.0 44 39-92 5-48 (61)
53 COG0017 AsnS Aspartyl/asparagi 88.7 4.7 0.0001 36.9 9.8 73 35-114 17-99 (435)
54 PRK06386 replication factor A; 88.2 2.7 5.7E-05 37.3 7.8 68 37-116 120-198 (358)
55 PF15490 Ten1_2: Telomere-capp 87.3 11 0.00024 28.6 10.0 71 36-114 23-98 (118)
56 PRK04036 DNA polymerase II sma 87.0 6.2 0.00013 35.9 9.7 54 35-95 154-215 (504)
57 PTZ00385 lysyl-tRNA synthetase 86.9 5.9 0.00013 37.9 9.8 72 36-114 109-191 (659)
58 PRK07218 replication factor A; 86.9 3.1 6.7E-05 37.6 7.6 68 35-112 173-251 (423)
59 PLN02903 aminoacyl-tRNA ligase 85.9 7.4 0.00016 37.2 9.9 74 35-115 73-163 (652)
60 PRK12820 bifunctional aspartyl 85.8 6 0.00013 38.1 9.3 74 35-115 19-110 (706)
61 PF03100 CcmE: CcmE; InterPro 85.2 11 0.00023 28.4 8.7 63 35-109 51-119 (131)
62 PRK13150 cytochrome c-type bio 84.8 10 0.00022 30.3 8.8 64 35-110 58-127 (159)
63 PRK13165 cytochrome c-type bio 84.7 11 0.00024 30.1 8.9 64 35-110 58-127 (160)
64 PLN02603 asparaginyl-tRNA synt 83.6 10 0.00022 35.6 9.5 74 35-115 108-193 (565)
65 PRK10413 hydrogenase 2 accesso 83.3 4.8 0.0001 28.8 5.8 50 39-95 5-56 (82)
66 TIGR00237 xseA exodeoxyribonuc 82.8 6.3 0.00014 35.1 7.6 64 34-105 17-86 (432)
67 PRK13480 3'-5' exoribonuclease 82.3 18 0.00039 31.4 10.0 51 52-110 36-88 (314)
68 TIGR00074 hypC_hupF hydrogenas 81.7 5.5 0.00012 28.0 5.5 44 40-95 6-49 (76)
69 PRK07218 replication factor A; 81.5 7 0.00015 35.4 7.5 67 35-112 69-146 (423)
70 PRK00286 xseA exodeoxyribonucl 81.3 9.2 0.0002 33.6 8.0 68 34-109 23-98 (438)
71 PRK05672 dnaE2 error-prone DNA 80.7 5.6 0.00012 39.7 7.1 71 36-114 955-1033(1046)
72 PRK07217 replication factor A; 80.6 11 0.00024 33.1 8.1 80 27-114 73-160 (311)
73 PRK08402 replication factor A; 80.3 8.4 0.00018 34.0 7.4 71 35-112 73-159 (355)
74 PRK13254 cytochrome c-type bio 80.3 18 0.00039 28.3 8.5 64 35-110 52-120 (148)
75 PRK06826 dnaE DNA polymerase I 79.8 6.1 0.00013 39.9 7.1 73 35-114 992-1074(1151)
76 PRK05673 dnaE DNA polymerase I 79.4 6 0.00013 39.8 6.9 72 35-114 978-1059(1135)
77 PRK06461 single-stranded DNA-b 78.6 10 0.00022 28.4 6.4 54 52-114 43-100 (129)
78 PRK06386 replication factor A; 78.6 6.2 0.00013 35.1 6.1 58 52-116 266-347 (358)
79 PF13567 DUF4131: Domain of un 78.6 15 0.00033 25.9 7.1 56 35-98 76-145 (176)
80 PTZ00417 lysine-tRNA ligase; P 78.5 20 0.00043 33.8 9.6 73 36-115 134-219 (585)
81 PRK14699 replication factor A; 77.9 12 0.00026 34.4 7.8 74 26-107 57-148 (484)
82 PRK10409 hydrogenase assembly 77.8 9.2 0.0002 27.9 5.8 48 39-95 5-55 (90)
83 cd04484 polC_OBF polC_OBF: A s 75.3 24 0.00052 24.3 8.3 65 37-108 2-78 (82)
84 PRK07374 dnaE DNA polymerase I 74.1 10 0.00022 38.4 6.8 72 35-114 1001-1082(1170)
85 COG1200 RecG RecG-like helicas 71.5 33 0.00071 33.2 9.2 55 35-96 61-123 (677)
86 cd04486 YhcR_OBF_like YhcR_OBF 71.4 31 0.00066 23.8 7.5 58 39-107 2-69 (78)
87 PRK06920 dnaE DNA polymerase I 70.5 13 0.00028 37.6 6.6 71 36-114 945-1025(1107)
88 PF07210 DUF1416: Protein of u 69.9 7.9 0.00017 28.3 3.8 30 37-66 8-39 (85)
89 PRK14699 replication factor A; 69.1 21 0.00046 32.8 7.2 56 34-96 286-355 (484)
90 PRK12366 replication factor A; 69.0 28 0.00062 32.8 8.2 76 36-118 410-497 (637)
91 COG1571 Predicted DNA-binding 68.6 17 0.00037 33.2 6.5 73 34-113 266-347 (421)
92 PRK13159 cytochrome c-type bio 68.2 23 0.00049 28.2 6.4 63 35-110 52-120 (155)
93 TIGR00643 recG ATP-dependent D 65.1 21 0.00046 33.1 6.5 54 36-96 34-95 (630)
94 KOG3416 Predicted nucleic acid 64.9 42 0.00091 26.4 7.1 69 10-96 5-76 (134)
95 PF12483 GIDE: E3 Ubiquitin li 64.7 25 0.00054 26.6 5.9 16 49-64 27-42 (160)
96 PRK10917 ATP-dependent DNA hel 63.6 24 0.00052 33.1 6.6 55 35-96 60-122 (681)
97 PRK07211 replication factor A; 61.5 52 0.0011 30.6 8.2 65 35-106 172-250 (485)
98 COG1190 LysU Lysyl-tRNA synthe 61.5 96 0.0021 29.1 10.0 91 37-134 64-167 (502)
99 PRK15491 replication factor A; 61.1 39 0.00084 29.9 7.2 55 35-96 68-138 (374)
100 PRK12366 replication factor A; 59.7 43 0.00093 31.6 7.6 55 35-96 292-359 (637)
101 PF14001 YdfZ: YdfZ protein 58.5 9 0.00019 26.7 2.2 33 74-118 9-41 (64)
102 PRK15491 replication factor A; 54.1 96 0.0021 27.5 8.4 63 36-105 178-256 (374)
103 PRK07211 replication factor A; 53.5 49 0.0011 30.7 6.7 44 37-95 432-475 (485)
104 COG3065 Slp Starvation-inducib 51.2 69 0.0015 26.6 6.5 57 32-96 51-123 (191)
105 cd05793 S1_IF1A S1_IF1A: Trans 51.2 59 0.0013 22.6 5.4 45 39-91 2-48 (77)
106 PRK06763 F0F1 ATP synthase sub 50.8 30 0.00066 29.0 4.5 46 36-93 39-86 (213)
107 PRK07279 dnaE DNA polymerase I 49.4 73 0.0016 32.2 7.6 55 52-114 910-967 (1034)
108 KOG3818 DNA polymerase epsilon 48.8 27 0.00059 32.7 4.3 57 31-96 173-230 (525)
109 smart00652 eIF1a eukaryotic tr 48.5 70 0.0015 22.6 5.5 44 39-90 7-52 (83)
110 PTZ00425 asparagine-tRNA ligas 47.7 60 0.0013 30.8 6.4 55 35-96 82-146 (586)
111 PF03843 Slp: Outer membrane l 46.8 1E+02 0.0022 24.1 6.7 55 35-96 35-105 (160)
112 TIGR03318 YdfZ_fam putative se 46.7 12 0.00026 26.1 1.3 30 74-115 10-39 (65)
113 COG1838 FumA Tartrate dehydrat 46.5 3.7 8E-05 33.7 -1.4 41 86-129 119-159 (184)
114 PF15057 DUF4537: Domain of un 45.4 62 0.0013 24.2 5.1 46 38-91 14-65 (124)
115 cd04474 RPA1_DBD_A RPA1_DBD_A: 45.0 89 0.0019 22.2 5.7 55 35-96 10-80 (104)
116 PF02237 BPL_C: Biotin protein 44.0 77 0.0017 19.7 4.7 28 39-67 15-42 (48)
117 PRK00448 polC DNA polymerase I 44.0 1.4E+02 0.0031 31.2 8.9 55 35-96 237-303 (1437)
118 PF01176 eIF-1a: Translation i 43.7 91 0.002 20.6 5.2 45 39-91 5-51 (65)
119 PRK07217 replication factor A; 43.4 19 0.00041 31.7 2.3 17 52-68 220-236 (311)
120 PF15072 DUF4539: Domain of un 42.9 1.2E+02 0.0027 21.6 6.8 40 39-78 7-51 (86)
121 PF11948 DUF3465: Protein of u 42.8 1.6E+02 0.0035 23.0 7.4 51 39-96 41-100 (131)
122 COG0298 HypC Hydrogenase matur 42.0 1.2E+02 0.0026 22.0 5.9 47 40-95 6-52 (82)
123 PLN02532 asparagine-tRNA synth 41.4 99 0.0021 29.7 6.9 56 52-114 137-200 (633)
124 COG2332 CcmE Cytochrome c-type 41.4 1.6E+02 0.0035 23.6 7.1 64 35-110 52-121 (153)
125 PF13296 T6SS_Vgr: Putative ty 40.1 23 0.0005 26.5 2.1 61 49-117 8-78 (109)
126 PF10949 DUF2777: Protein of u 38.7 35 0.00076 28.0 3.1 41 35-78 14-60 (185)
127 COG1471 RPS4A Ribosomal protei 38.4 93 0.002 26.7 5.6 35 40-93 191-230 (241)
128 PRK09838 periplasmic copper-bi 38.2 1.7E+02 0.0037 21.9 6.9 64 34-109 40-113 (115)
129 cd04456 S1_IF1A_like S1_IF1A_l 37.7 1.1E+02 0.0024 21.4 5.1 43 40-90 3-47 (78)
130 PF03079 ARD: ARD/ARD' family; 37.3 46 0.00099 26.2 3.4 52 50-109 94-148 (157)
131 cd04466 S1_YloQ_GTPase S1_YloQ 37.3 1.1E+02 0.0023 19.4 5.1 44 39-91 1-47 (68)
132 cd04475 RPA1_DBD_B RPA1_DBD_B: 36.4 1.1E+02 0.0024 21.1 5.0 58 52-117 30-89 (101)
133 TIGR00752 slp outer membrane l 34.1 1.1E+02 0.0023 24.9 5.2 56 33-96 47-118 (182)
134 PRK00098 GTPase RsgA; Reviewed 33.6 1.1E+02 0.0023 25.7 5.3 44 39-91 1-47 (298)
135 TIGR00523 eIF-1A eukaryotic/ar 33.1 1.6E+02 0.0034 21.6 5.5 44 39-90 21-66 (99)
136 KOG0641 WD40 repeat protein [G 32.1 1E+02 0.0022 27.1 5.0 48 41-95 243-294 (350)
137 KOG0556 Aspartyl-tRNA syntheta 30.8 3.9E+02 0.0085 25.2 8.7 74 34-114 82-174 (533)
138 COG1588 POP4 RNase P/RNase MRP 30.7 57 0.0012 24.3 2.8 57 37-103 31-87 (95)
139 TIGR00723 ttdB_fumA_fumB hydro 30.0 7 0.00015 31.5 -2.2 42 86-129 110-151 (168)
140 PRK04012 translation initiatio 29.6 2E+02 0.0042 21.2 5.5 45 39-91 23-69 (100)
141 PRK06842 fumarate hydratase; P 27.9 13 0.00029 30.4 -1.0 41 86-129 119-159 (185)
142 PF02294 7kD_DNA_binding: 7kD 27.8 46 0.00099 22.7 1.7 25 34-65 19-46 (62)
143 PF12658 Ten1: Telomere cappin 27.5 2.7E+02 0.0059 21.0 10.8 73 35-114 26-113 (124)
144 PF15491 CTC1_2: CST, telomere 27.2 62 0.0013 28.4 2.9 24 34-58 255-278 (291)
145 CHL00010 infA translation init 26.9 2.2E+02 0.0047 19.7 7.4 45 39-91 9-56 (78)
146 cd05792 S1_eIF1AD_like S1_eIF1 26.7 1.5E+02 0.0033 20.9 4.3 37 47-90 9-47 (78)
147 PF12869 tRNA_anti-like: tRNA_ 26.6 2.5E+02 0.0054 20.3 5.7 54 36-96 69-131 (144)
148 PF00313 CSD: 'Cold-shock' DNA 26.0 1.8E+02 0.004 18.5 9.0 60 39-110 1-64 (66)
149 KOG0555 Asparaginyl-tRNA synth 26.0 1E+02 0.0022 29.0 4.1 57 33-96 122-184 (545)
150 cd04458 CSP_CDS Cold-Shock Pro 26.0 1.6E+02 0.0034 18.8 4.1 40 39-78 1-44 (65)
151 PRK08395 fumarate hydratase; P 25.9 14 0.00031 29.6 -1.1 41 86-129 106-147 (162)
152 PRK00276 infA translation init 25.9 2.1E+02 0.0046 19.2 5.8 47 37-91 7-56 (72)
153 PRK08228 L(+)-tartrate dehydra 25.8 14 0.0003 30.7 -1.2 28 102-129 136-163 (204)
154 TIGR01405 polC_Gram_pos DNA po 24.0 5E+02 0.011 26.9 8.8 55 35-96 8-74 (1213)
155 PF14481 Fimbrial_PilY2: Type 23.8 1.7E+02 0.0037 22.5 4.4 62 39-114 32-99 (118)
156 PF09998 DUF2239: Uncharacteri 23.5 1E+02 0.0022 25.5 3.3 18 49-66 33-51 (187)
157 cd03703 aeIF5B_II aeIF5B_II: T 23.5 72 0.0016 24.0 2.3 21 39-59 1-26 (110)
158 KOG2732 DNA polymerase delta, 23.2 2.8E+02 0.0061 25.7 6.4 37 50-94 110-146 (435)
159 COG4138 BtuD ABC-type cobalami 22.9 1.2E+02 0.0027 25.7 3.8 54 4-58 96-158 (248)
160 PRK06043 fumarate hydratase; P 22.7 18 0.00038 29.8 -1.2 42 86-129 120-161 (192)
161 KOG2104 Nuclear transport fact 22.6 1.1E+02 0.0023 24.0 3.1 30 86-117 80-109 (126)
162 cd04451 S1_IF1 S1_IF1: Transla 22.6 2.2E+02 0.0049 18.3 6.0 45 39-91 3-50 (64)
163 PF09870 DUF2097: Uncharacteri 22.0 1.5E+02 0.0032 21.6 3.6 34 31-66 26-63 (86)
164 PF01330 RuvA_N: RuvA N termin 21.5 2.2E+02 0.0047 18.3 4.1 28 37-67 3-31 (61)
165 PF06918 DUF1280: Protein of u 20.8 2.1E+02 0.0046 23.7 4.8 46 50-105 148-194 (224)
166 PF05683 Fumerase_C: Fumarase 20.8 18 0.00039 30.0 -1.5 40 86-128 146-185 (205)
167 PF07039 DUF1325: SGF29 tudor- 20.8 1.5E+02 0.0032 22.5 3.6 49 36-91 17-81 (130)
168 cd01210 EPS8 Epidermal growth 20.5 1.4E+02 0.003 23.1 3.4 74 36-118 38-116 (127)
No 1
>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=98.48 E-value=2.2e-06 Score=59.63 Aligned_cols=85 Identities=24% Similarity=0.279 Sum_probs=66.2
Q ss_pred EEEEEEEEeeeCC--CCcEEEEcCCeeEEEEe-cccc-----ccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496 37 VWLQGVLVSPPDD--DGRLLLDDGTGVVQIYL-SGDF-----RIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK 108 (142)
Q Consensus 37 VWlQG~vv~~~~~--~~~~~LdDgTG~~~v~~-~~~~-----~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K 108 (142)
|-+.|.|.++... .-++.|+|+||.+++.. .... ....++.| +||.|.|.+.. .+..+-|++.+
T Consensus 2 v~~vG~V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g-------~~v~v~G~v~~-~~g~~ql~i~~ 73 (95)
T cd04478 2 VTLVGVVRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEG-------TYVRVFGNLKS-FQGKKSIMAFS 73 (95)
T ss_pred EEEEEEEEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccC-------CEEEEEEEEcc-cCCeeEEEEEE
Confidence 5578999999654 34899999999999987 3222 22359999 99999999977 77888888887
Q ss_pred EeeCCCCcCccchhHHHHHHHH
Q 044496 109 IVDLSAFPDREAMWYLEVMEAY 130 (142)
Q Consensus 109 ~~DLS~~p~re~mW~lEV~e~~ 130 (142)
+.-+. +|+.-.+=.|||..+|
T Consensus 74 i~~v~-d~ne~~~h~l~~~~~~ 94 (95)
T cd04478 74 IRPVT-DFNEVTYHLLEVIYVH 94 (95)
T ss_pred EEEeC-CccHHHHhHhhhhhhh
Confidence 77554 5777777788888776
No 2
>KOG3108 consensus Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [Replication, recombination and repair]
Probab=98.37 E-value=2.9e-06 Score=71.86 Aligned_cols=112 Identities=21% Similarity=0.299 Sum_probs=82.5
Q ss_pred HHHHHhhccCCCCCCceeecCeEEeEEEEEEEEEeeeCC--CCcEEEEcCCeeEEEEe-cc---ccccc-cccCCccccc
Q 044496 11 LCVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDD--DGRLLLDDGTGVVQIYL-SG---DFRIR-RWNTGVFFFD 83 (142)
Q Consensus 11 f~~QL~~a~~~~s~~~~~l~gl~~~~VWlQG~vv~~~~~--~~~~~LdDgTG~~~v~~-~~---~~~~~-~~~~G~~~~~ 83 (142)
=++||-++...... .|.++|+++++|-+.|.|...... +-.+.|+||||++++.. .. ..... ++.+|
T Consensus 46 ti~qi~s~~~~~~~-~~~i~~~~v~~v~~VGivr~~e~~~t~i~y~I~D~tg~id~r~W~~~~~~~~e~~~l~~~----- 119 (265)
T KOG3108|consen 46 TIKQILSSTQDDDS-VFKIGGVEVSAVSIVGIVRNIEKSATNITYEIEDGTGQIDVRQWFHDNAESEEMPALETG----- 119 (265)
T ss_pred ceeeeccccccccc-cEEEccEEEEEEEEEEEEEeceecCcceEEEEecCcccEEEEEeccccchhhhCcccccC-----
Confidence 34566666655433 888999999999999999998644 55899999999999987 22 22233 59999
Q ss_pred ceeEEEEEeeEeeccCCCceEEEEEEe---eCCCCcCccchhHHHHHHHHHHHhh
Q 044496 84 FWMYVMVVGGFVIRTDDIPVIKVHKIV---DLSAFPDREAMWYLEVMEAYKLFYQ 135 (142)
Q Consensus 84 ~~~YVmViG~~~~~~~~~p~i~a~K~~---DLS~~p~re~mW~lEV~e~~~~~y~ 135 (142)
+||.|.|.++. -+..-.|.+.|+. |.++.-.| .||++++|..+=+
T Consensus 120 --~yVkv~G~Lk~-f~Gk~sl~~fkI~pv~D~Nevt~h----~LE~i~~hl~~s~ 167 (265)
T KOG3108|consen 120 --TYVKVYGHLKP-FQGKKSLQVFKIRPVEDFNEVTTH----FLEVINAHLSLSK 167 (265)
T ss_pred --cEEEeeecccC-CCCceeEEEEeeeeeecCCceeEE----eehhhHHHHHhhh
Confidence 99999999976 4445566666654 44444444 5899999876543
No 3
>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=98.31 E-value=6.4e-06 Score=59.04 Aligned_cols=64 Identities=22% Similarity=0.183 Sum_probs=49.9
Q ss_pred EEEEEEeeeCC--CCcEEEEcCCeeEEEEe-cccc---------------------ccc-cccCCcccccceeEEEEEee
Q 044496 39 LQGVLVSPPDD--DGRLLLDDGTGVVQIYL-SGDF---------------------RIR-RWNTGVFFFDFWMYVMVVGG 93 (142)
Q Consensus 39 lQG~vv~~~~~--~~~~~LdDgTG~~~v~~-~~~~---------------------~~~-~~~~G~~~~~~~~YVmViG~ 93 (142)
+.|+|+++.+. .-.|.||||||.+++.. .... +.. .+++| +||.|.|.
T Consensus 2 ivG~V~sv~~~~~~~~~tLdDgTG~Ie~~~W~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~G-------~vvrV~G~ 74 (92)
T cd04483 2 ILGTVVSRRERETFYSFGVDDGTGVVNCVCWKNLSYAEVSSRSDAARILKSALMALKQAKVLEIG-------DLLRVRGS 74 (92)
T ss_pred eEEEEEEEEecCCeEEEEEecCCceEEEEEEcCcCcccccccccccccccccccccccccccCCC-------CEEEEEEE
Confidence 57999999655 44899999999999987 2111 222 48999 99999999
Q ss_pred EeeccCCCceEEEEEEe
Q 044496 94 FVIRTDDIPVIKVHKIV 110 (142)
Q Consensus 94 ~~~~~~~~p~i~a~K~~ 110 (142)
+.. ....+-+++.+|.
T Consensus 75 i~~-frg~~ql~i~~~~ 90 (92)
T cd04483 75 IRT-YRGEREINASVVY 90 (92)
T ss_pred Eec-cCCeeEEEEEEEE
Confidence 977 7778888887764
No 4
>COG3390 Uncharacterized protein conserved in archaea [Function unknown]
Probab=98.30 E-value=4.6e-06 Score=68.13 Aligned_cols=85 Identities=20% Similarity=0.277 Sum_probs=64.2
Q ss_pred chHHHHHHHHHhhccCCCCC-------C-ceeecCeEEeEEEEEEEEEeeeCCC--C---cEEEEcCCeeEEEEe-cccc
Q 044496 5 LAALKLLCVQLKDARESPSQ-------N-AVTLGGILFQRVWLQGVLVSPPDDD--G---RLLLDDGTGVVQIYL-SGDF 70 (142)
Q Consensus 5 ~pa~Kvf~~QL~~a~~~~s~-------~-~~~l~gl~~~~VWlQG~vv~~~~~~--~---~~~LdDgTG~~~v~~-~~~~ 70 (142)
.+|-.+|++-|+++.-+-++ + ..+.-|+.++|+.+.|+|+++...+ + ++.++|+||.|-+.- -..|
T Consensus 8 eva~rVFa~El~e~~~s~~e~~e~~sp~yliTPlG~k~nRifivGtltek~~i~ed~~~~R~rVvDpTGsF~Vyag~yqP 87 (196)
T COG3390 8 EVAYRVFAKELRESKFSKKEEDEERSPNYLITPLGLKVNRIFIVGTLTEKEGIGEDREYWRIRVVDPTGSFYVYAGQYQP 87 (196)
T ss_pred hHHHHHHHHHHhhcceeccccccccCCcEEechhhhheeEEEEEEEEEeccCcCCcccEEEEEEecCCceEEEEcCCCCh
Confidence 57889999999998654321 1 3445599999999999999995443 3 899999999999953 2222
Q ss_pred cc----ccccCCcccccceeEEEEEeeEee
Q 044496 71 RI----RRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 71 ~~----~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
.. .....+ .+|||+|++..
T Consensus 88 Ea~a~l~~ve~~-------~~VaViGKi~~ 110 (196)
T COG3390 88 EAKAFLEDVEVP-------DLVAVIGKIRT 110 (196)
T ss_pred HHHHHHHhccCC-------ceEEEecccce
Confidence 22 147889 99999999977
No 5
>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=98.20 E-value=1.2e-05 Score=52.35 Aligned_cols=69 Identities=28% Similarity=0.260 Sum_probs=53.0
Q ss_pred EEEEEEEEeee-CCCC--cEEEEcCCeeEEEEecc--ccccc-cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEe
Q 044496 37 VWLQGVLVSPP-DDDG--RLLLDDGTGVVQIYLSG--DFRIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIV 110 (142)
Q Consensus 37 VWlQG~vv~~~-~~~~--~~~LdDgTG~~~v~~~~--~~~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~ 110 (142)
|++.|+|.+++ .... .+.|+|+||.+++..-. ..+.. .+++| +.|.|.|.+....+.++.|.+.++.
T Consensus 1 V~v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g-------~~v~v~G~v~~~~~~~~~l~~~~i~ 73 (75)
T PF01336_consen 1 VTVEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEG-------DIVRVRGKVKRYNGGELELIVPKIE 73 (75)
T ss_dssp EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TT-------SEEEEEEEEEEETTSSEEEEEEEEE
T ss_pred CEEEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCC-------eEEEEEEEEEEECCccEEEEECEEE
Confidence 68999999994 2222 88999999999999833 33333 59999 9999999998844445999999987
Q ss_pred eC
Q 044496 111 DL 112 (142)
Q Consensus 111 DL 112 (142)
+|
T Consensus 74 ~l 75 (75)
T PF01336_consen 74 IL 75 (75)
T ss_dssp EE
T ss_pred EC
Confidence 65
No 6
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=97.61 E-value=0.0013 Score=55.30 Aligned_cols=114 Identities=15% Similarity=0.278 Sum_probs=79.8
Q ss_pred HHHHhhccCCCCCCceeecCeEEeEEEEEEEEEeeeCC--CCcEEEEcCCeeEEEEe-cccc---c-cccccCCcccccc
Q 044496 12 CVQLKDARESPSQNAVTLGGILFQRVWLQGVLVSPPDD--DGRLLLDDGTGVVQIYL-SGDF---R-IRRWNTGVFFFDF 84 (142)
Q Consensus 12 ~~QL~~a~~~~s~~~~~l~gl~~~~VWlQG~vv~~~~~--~~~~~LdDgTG~~~v~~-~~~~---~-~~~~~~G~~~~~~ 84 (142)
++|+-.|.+-.....|..++.|+.+|-..|+|.+.... +--+.|-||||.++|+. +.+. . .+....|
T Consensus 44 IKQIl~~~qd~~d~~f~vd~~Ev~~V~fVGvvrni~~~ttn~~~~iEDGTG~Ievr~W~~~~~~~e~~~d~~~~------ 117 (258)
T COG5235 44 IKQILSCDQDETDSTFLVDSAEVTNVQFVGVVRNIKTSTTNSMFVIEDGTGSIEVRFWPGNSYEEEQCKDLEEQ------ 117 (258)
T ss_pred HHHhhcccccccCCceeecceEEeeEEEEEEEEeeeecccceEEEEecCCceEEEEecCCCchHHHhccccccc------
Confidence 67888888766555899999999999999999998543 66899999999999997 3332 2 3348889
Q ss_pred eeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHHHHHHh
Q 044496 85 WMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLFY 134 (142)
Q Consensus 85 ~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~~~~~y 134 (142)
.||.|.|.++. -+...-|.+-.|.-+-+ .+-=.--.||++-.|..+=
T Consensus 118 -~yvkV~G~lk~-F~GK~~I~~~~i~~I~d-~NeV~~HfLe~I~~Hl~~t 164 (258)
T COG5235 118 -NYVKVNGSLKT-FNGKRSISASHISAIED-SNEVTYHFLECIYQHLFYT 164 (258)
T ss_pred -cEEEEecceee-eCCeeEEehhheeeccc-cchhHHHHHHHHHHHHHHH
Confidence 99999999976 44444444333322222 1111234688887775543
No 7
>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=97.56 E-value=0.00083 Score=49.67 Aligned_cols=71 Identities=21% Similarity=0.197 Sum_probs=53.5
Q ss_pred CeEEeEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496 31 GILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI 109 (142)
Q Consensus 31 gl~~~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~ 109 (142)
.-.=+.|-|.|.|++. -+++.+++.|+||.+.|.. +....++++.++ .=|.+.|.+-+ ....+.|.+.+|
T Consensus 31 ~~Dd~~V~L~G~Iv~~-l~~d~Y~F~D~TG~I~VeId~~~w~g~~vt~~-------~~Vri~GeVDk-~~~~~~IdV~~I 101 (103)
T PF04076_consen 31 AKDDTPVTLEGNIVKQ-LGDDKYLFRDATGEIEVEIDDDVWRGQTVTPD-------DKVRISGEVDK-DWNKTEIDVDRI 101 (103)
T ss_dssp S-SSEEEEEEEEEEEE-EETTEEEEEETTEEEEEE--GGGSTT----TT-------SEEEEEEEEEE-ETTEEEEEEEEE
T ss_pred CcCCCeEEEEEEEEEE-ecCCEEEEECCCCcEEEEEChhhcCCcccCCC-------CEEEEEEEEeC-CCCceEEEEEEE
Confidence 3444678899999995 4789999999999999999 555778889999 99999999987 445688887776
Q ss_pred e
Q 044496 110 V 110 (142)
Q Consensus 110 ~ 110 (142)
.
T Consensus 102 ~ 102 (103)
T PF04076_consen 102 E 102 (103)
T ss_dssp E
T ss_pred E
Confidence 3
No 8
>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=97.40 E-value=0.0014 Score=50.41 Aligned_cols=68 Identities=19% Similarity=0.243 Sum_probs=55.5
Q ss_pred EEeEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496 33 LFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI 109 (142)
Q Consensus 33 ~~~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~ 109 (142)
+=+.|-|+|.|++. -+++.++..|+||.+.|.. +...++.++.++ .=|.+.|.+-+. -..+.|-+.+|
T Consensus 56 Ddt~V~L~G~Iv~~-l~~d~Y~F~D~TG~I~VeId~~~w~G~~v~p~-------d~V~I~GeVDk~-~~~~~IdV~~I 124 (126)
T TIGR00156 56 DGASVTLRGNIISH-IGDDRYVFRDKSGEINVVIPAAVWNGREVQPK-------DMVNISGSLDKK-SAPAEVDVTHI 124 (126)
T ss_pred CCCEEEEEEEEEEE-eCCceEEEECCCCCEEEEECHHHcCCCcCCCC-------CEEEEEEEECCC-CCCeEEEEEEE
Confidence 34678899999995 5788999999999999999 556688899999 999999999873 33466666665
No 9
>PRK10053 hypothetical protein; Provisional
Probab=97.31 E-value=0.0019 Score=49.77 Aligned_cols=68 Identities=21% Similarity=0.353 Sum_probs=55.9
Q ss_pred EEeEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496 33 LFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI 109 (142)
Q Consensus 33 ~~~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~ 109 (142)
.=+.|-|+|.|++ +-+++..+..|+||.+.|.. ....++.++.+. .-|.+.|.+-+. -..+.|.+.+|
T Consensus 60 Dd~~V~L~G~Iv~-~lg~d~Y~F~D~tG~I~VeID~~~w~G~~v~p~-------~kV~I~GevDk~-~~~~~IdV~~i 128 (130)
T PRK10053 60 DGATVSLRGNLID-HKGDDRYVFRDKSGEINVIIPAAVFDGREVQPD-------QMININGSLDKK-SAPPVVRVTHL 128 (130)
T ss_pred CCCeEEEEEEEEE-EeCCceEEEECCCCcEEEEeCHHHcCCCcCCCC-------CEEEEEEEECCC-CCCeEEEEEEE
Confidence 3456889999999 46788999999999999999 556788899999 999999999873 33457766665
No 10
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=96.93 E-value=0.017 Score=38.33 Aligned_cols=67 Identities=21% Similarity=0.343 Sum_probs=51.1
Q ss_pred EEEEEEEEeeeC-CCC--cEEEEcCCeeEEEEe-ccccc-cc-cccCCcccccceeEEEEEeeEeecc-CCCceEEEEEE
Q 044496 37 VWLQGVLVSPPD-DDG--RLLLDDGTGVVQIYL-SGDFR-IR-RWNTGVFFFDFWMYVMVVGGFVIRT-DDIPVIKVHKI 109 (142)
Q Consensus 37 VWlQG~vv~~~~-~~~--~~~LdDgTG~~~v~~-~~~~~-~~-~~~~G~~~~~~~~YVmViG~~~~~~-~~~p~i~a~K~ 109 (142)
+|+.|.|.+... ..| .+.|.|+||.+++.. +...+ .+ .+++| +-|.+.|.+.... +..+.+.+.++
T Consensus 2 ~~v~g~v~~i~~tk~g~~~~~L~D~~~~i~~~~f~~~~~~~~~~l~~g-------~~v~v~g~v~~~~~~~~~~l~v~~i 74 (78)
T cd04489 2 VWVEGEISNLKRPSSGHLYFTLKDEDASIRCVMWRSNARRLGFPLEEG-------MEVLVRGKVSFYEPRGGYQLIVEEI 74 (78)
T ss_pred EEEEEEEecCEECCCcEEEEEEEeCCeEEEEEEEcchhhhCCCCCCCC-------CEEEEEEEEEEECCCCEEEEEEEEE
Confidence 699999999864 333 788999999999986 44333 23 38999 9999999998632 45678888877
Q ss_pred e
Q 044496 110 V 110 (142)
Q Consensus 110 ~ 110 (142)
.
T Consensus 75 ~ 75 (78)
T cd04489 75 E 75 (78)
T ss_pred E
Confidence 4
No 11
>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=96.90 E-value=0.0075 Score=37.37 Aligned_cols=61 Identities=20% Similarity=0.207 Sum_probs=45.9
Q ss_pred EEEEEEeeeCCC-----CcEEEEcCC-eeEEEEe-cccccc--ccccCCcccccceeEEEEEeeEeeccCCCceEEEE
Q 044496 39 LQGVLVSPPDDD-----GRLLLDDGT-GVVQIYL-SGDFRI--RRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVH 107 (142)
Q Consensus 39 lQG~vv~~~~~~-----~~~~LdDgT-G~~~v~~-~~~~~~--~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~ 107 (142)
++|+|+++.... ..+.|+|+| |.+.+.. +..... ..++.| +++.+.|.+.. .+..+.+.+.
T Consensus 2 v~g~v~~~~~~~~~~~~~~~~l~D~~~~~i~~~~~~~~~~~~~~~~~~g-------~~v~v~g~v~~-~~~~~~l~~~ 71 (75)
T cd03524 2 IVGIVVAVEEIRTEGKVLIFTLTDGTGGTIRVTLFGELAEELENLLKEG-------QVVYIKGKVKK-FRGRLQLIVE 71 (75)
T ss_pred eEEEEEeecccccCCeEEEEEEEcCCCCEEEEEEEchHHHHHHhhccCC-------CEEEEEEEEEe-cCCeEEEEee
Confidence 689999986544 589999999 9999987 333322 248999 99999999976 4555666655
No 12
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=96.86 E-value=0.0097 Score=43.25 Aligned_cols=75 Identities=21% Similarity=0.225 Sum_probs=47.0
Q ss_pred eEEEEEEEEEeeeCCCCcEEEEcCC-eeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCC
Q 044496 35 QRVWLQGVLVSPPDDDGRLLLDDGT-GVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLS 113 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~~~~LdDgT-G~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS 113 (142)
++|.+-|+|.+.+.+++++++.-+. |.++|.++... .+..+ .||-|+|.+.. .+....|++...++++
T Consensus 19 k~VrivGkv~~~~~~g~~~~l~~~d~~~V~v~l~~~~---~~~~~-------~~vEviG~V~~-~~~~~~i~~~~~~~~g 87 (109)
T PF08661_consen 19 KTVRIVGKVESVDPDGGSATLSTSDGGQVTVSLNPPS---DEELS-------KYVEVIGKVND-DGTVLSIRYFSFTDFG 87 (109)
T ss_dssp SEEEEEEEEEEE-TTSSEEEEE-TTS-EEEEEESS-----SS----------SEEEEEEEE-T-TS-EEEEEEEE---SS
T ss_pred CeEEEEEEEeeEcCCCCEEEEEcCCCCEEEEEeCCCC---CCCCC-------CEEEEEEEEcC-CCCceEEEEEEeccCC
Confidence 3688999999998779999999654 45888876532 34567 99999999965 3333499999999999
Q ss_pred CCcCccc
Q 044496 114 AFPDREA 120 (142)
Q Consensus 114 ~~p~re~ 120 (142)
++-+-+.
T Consensus 88 ~~~D~~~ 94 (109)
T PF08661_consen 88 DDFDMDL 94 (109)
T ss_dssp S---HHH
T ss_pred CCcCHHH
Confidence 9766543
No 13
>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=96.82 E-value=0.0089 Score=39.34 Aligned_cols=55 Identities=22% Similarity=0.240 Sum_probs=44.8
Q ss_pred cEEEEcCCeeEEEEe-ccccccc-cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCC
Q 044496 52 RLLLDDGTGVVQIYL-SGDFRIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSA 114 (142)
Q Consensus 52 ~~~LdDgTG~~~v~~-~~~~~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~ 114 (142)
.+.|.|+||.+++.. +..+... .++.| .+|.+.|.+.. .+..+.+.+.++..|.+
T Consensus 22 ~~~l~D~tg~i~~~~f~~~~~~~~~l~~g-------~~v~v~G~v~~-~~~~~~l~~~~i~~l~~ 78 (83)
T cd04492 22 ALTLQDKTGEIEAKLWDASEEDEEKFKPG-------DIVHVKGRVEE-YRGRLQLKIQRIRLVTE 78 (83)
T ss_pred EEEEEcCCCeEEEEEcCCChhhHhhCCCC-------CEEEEEEEEEE-eCCceeEEEEEEEECCc
Confidence 789999999999987 5444333 59999 99999999976 56678888999988875
No 14
>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=96.72 E-value=0.03 Score=47.21 Aligned_cols=114 Identities=21% Similarity=0.170 Sum_probs=71.5
Q ss_pred HHHHHHHhhccC-C----------CCCCceeecCeEEeEEEEEEEEEeeeC------CCCcEEEEcCCe--eEEEEecc-
Q 044496 9 KLLCVQLKDARE-S----------PSQNAVTLGGILFQRVWLQGVLVSPPD------DDGRLLLDDGTG--VVQIYLSG- 68 (142)
Q Consensus 9 Kvf~~QL~~a~~-~----------~s~~~~~l~gl~~~~VWlQG~vv~~~~------~~~~~~LdDgTG--~~~v~~~~- 68 (142)
.+|++-|..+-+ + ..++.+..++-.++.|-+.|+|++... +.-.+.|||+|| .+.+..+.
T Consensus 30 PlfI~DI~~~~~~Sr~~~~~y~~~~~~~~~f~~NhPI~~v~i~G~Vv~~~~~~~~~~~~~~l~iDD~Sg~~~i~~~~~~~ 109 (256)
T PF10451_consen 30 PLFISDIHKRLKQSRKVCENYYAPQQQNIYFYNNHPIRWVRIVGVVVGIDYKWIENEDRIILTIDDSSGANTIECKCSKS 109 (256)
T ss_dssp E--HHHHCT----C--THHHHGGGG-TT-EEETTEEE-EEEEEEEEEEEEEEE-BBTCEEEEEEE-SSCS-EEEEEEEHH
T ss_pred cEEHHHhhhhcccccchhhhhhhhccCCEEEECCcccEEEEEEEEEEEEEEEeecccceEEEEEeCCCCceeEEEEEEcc
Confidence 677777776322 1 234567788999999999999999963 334789999999 77776522
Q ss_pred -cccc---ccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHHHHHH
Q 044496 69 -DFRI---RRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEAYKLF 133 (142)
Q Consensus 69 -~~~~---~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~~~~~ 133 (142)
.... -.-..| +-|-|-|.+. .+...+.+.+|.-+. +.+.|--.=-|..+.-+.+
T Consensus 110 ~~~~~~l~~~~~~G-------~~V~VkG~vs---r~~~ql~ve~i~~~~-~l~~Ei~fW~~~~~~R~~L 167 (256)
T PF10451_consen 110 SYLSMGLPINDLIG-------KVVEVKGTVS---RNERQLDVERIELVR-DLNAEIEFWKERMRFRKEL 167 (256)
T ss_dssp HHHCCCHHCTT-TT--------EEEEEEEEE---SSSEEEEEEEEEEET-SCCHHHHHHHHHHHHHHHC
T ss_pred cccccCCCccCCCC-------cEEEEEEEEc---cCcEEEEEEEEEccC-ChHHHHHHHHHHHHHHHHc
Confidence 1111 122389 9999999996 567778888887554 4666655555666654443
No 15
>COG3111 Periplasmic protein with OB-fold [Function unknown]
Probab=96.57 E-value=0.016 Score=44.90 Aligned_cols=66 Identities=20% Similarity=0.202 Sum_probs=54.3
Q ss_pred eEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496 35 QRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI 109 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~ 109 (142)
..|-|+|.+++ .-+++++...|+||.+.|.. +....++.++|- .-|.+-|.+-+ .-..|.|.+-.+
T Consensus 58 a~V~l~GnIv~-qi~~D~y~FrD~sGeI~VeIdd~~w~g~tv~P~-------dkV~I~GevDk-~~~~~eIdV~~I 124 (128)
T COG3111 58 AWVSLEGNIVR-QIGDDRYVFRDASGEINVDIDDKVWNGQTVTPK-------DKVRIQGEVDK-DWNSVEIDVKHI 124 (128)
T ss_pred CeEEEEeeEEE-eeCCceEEEEcCCccEEEEecccccCCcccCcc-------cEEEEEeEEcC-CCccceeEhhhe
Confidence 46779999999 57899999999999999998 667788889999 99999999977 344566655444
No 16
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=96.29 E-value=0.076 Score=38.43 Aligned_cols=67 Identities=22% Similarity=0.220 Sum_probs=52.7
Q ss_pred eEEEEEEEEEeeeCCCCcEEEEcCCe-eEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCC
Q 044496 35 QRVWLQGVLVSPPDDDGRLLLDDGTG-VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLS 113 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~~~~LdDgTG-~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS 113 (142)
++|.+-|+|.+.+ ++.+.+.++-| .++|.++... ....| .||-|+|.+.. .-.|++.-.+|+.
T Consensus 16 k~V~ivGkV~~~~--~~~~~~~~~Dg~~v~v~l~~~~---~~~~~-------~~vEViG~V~~----~~~I~~~~~~~~g 79 (101)
T cd04479 16 KTVRIVGKVEKVD--GDSLTLISSDGVNVTVELNRPL---DLPIS-------GYVEVIGKVSP----DLTIRVLSYIDFG 79 (101)
T ss_pred CEEEEEEEEEEec--CCeEEEEcCCCCEEEEEeCCCC---CcccC-------CEEEEEEEECC----CCeEEEEEEEECC
Confidence 5799999999984 34788888777 7888876533 46778 99999998854 4789999999999
Q ss_pred CCcC
Q 044496 114 AFPD 117 (142)
Q Consensus 114 ~~p~ 117 (142)
++=+
T Consensus 80 ~~~D 83 (101)
T cd04479 80 DDFD 83 (101)
T ss_pred CccC
Confidence 8633
No 17
>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=96.12 E-value=0.11 Score=35.51 Aligned_cols=68 Identities=26% Similarity=0.312 Sum_probs=47.6
Q ss_pred EEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecccc-----c-cccccCCcccccceeEEEEEeeEeecc-----CCCce
Q 044496 37 VWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDF-----R-IRRWNTGVFFFDFWMYVMVVGGFVIRT-----DDIPV 103 (142)
Q Consensus 37 VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~-----~-~~~~~~G~~~~~~~~YVmViG~~~~~~-----~~~p~ 103 (142)
|+++|.|.++..-+. =+.|.|+||.+++..+... + ...++.| ++|.|-|.+..+. .....
T Consensus 2 V~i~Gwv~~~R~~g~~~Fi~Lrd~~~~iQ~v~~~~~~~~~~~~~~~l~~~-------s~V~v~G~~~~~~~~~~~~~~~E 74 (85)
T cd04100 2 VTLAGWVHSRRDHGGLIFIDLRDGSGIVQVVVNKEELGEFFEEAEKLRTE-------SVVGVTGTVVKRPEGNLATGEIE 74 (85)
T ss_pred EEEEEEEehhccCCCEEEEEEEeCCeeEEEEEECCcChHHHHHHhCCCCC-------CEEEEEeEEEECCCCCCCCCCEE
Confidence 789999999854333 3678999999999873321 1 2358999 9999999998732 33456
Q ss_pred EEEEEEee
Q 044496 104 IKVHKIVD 111 (142)
Q Consensus 104 i~a~K~~D 111 (142)
|.+.++.=
T Consensus 75 l~~~~i~i 82 (85)
T cd04100 75 LQAEELEV 82 (85)
T ss_pred EEEeEEEE
Confidence 66665543
No 18
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=95.82 E-value=0.077 Score=47.08 Aligned_cols=74 Identities=23% Similarity=0.281 Sum_probs=55.0
Q ss_pred eEEEEEEEEEeeeCCCCc--EEEEcCCeeEEEEeccc-----c-ccccccCCcccccceeEEEEEeeEeeccC--CCceE
Q 044496 35 QRVWLQGVLVSPPDDDGR--LLLDDGTGVVQIYLSGD-----F-RIRRWNTGVFFFDFWMYVMVVGGFVIRTD--DIPVI 104 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~~--~~LdDgTG~~~v~~~~~-----~-~~~~~~~G~~~~~~~~YVmViG~~~~~~~--~~p~i 104 (142)
+.|++.|+|.++..-++. +.|.|++|.+++..+.. . ....++.| ..|.|.|.+..+.. .+..|
T Consensus 17 ~~V~i~GrV~~~R~~gk~~Fl~LrD~~g~iQ~v~~~~~~~~~~~~~~~L~~g-------s~V~v~G~v~~~~~~~~~~el 89 (437)
T PRK05159 17 EEVTLAGWVHEIRDLGGIAFLILRDRSGIIQVVVKKKVDEELFETIKKLKRE-------SVVSVTGTVKANPKAPGGVEV 89 (437)
T ss_pred CEEEEEEEeEeeecCCCeEEEEEEcCCcEEEEEEeCCccHHHHHHHhCCCCC-------cEEEEEEEEEcCCCCCCCEEE
Confidence 458899999999654432 67999999999987432 1 12358999 99999999987322 45678
Q ss_pred EEEEEeeCCCC
Q 044496 105 KVHKIVDLSAF 115 (142)
Q Consensus 105 ~a~K~~DLS~~ 115 (142)
++.++.=||.+
T Consensus 90 ~~~~i~vls~a 100 (437)
T PRK05159 90 IPEEIEVLNKA 100 (437)
T ss_pred EEeEEEEEeCC
Confidence 88888777764
No 19
>cd04316 ND_PkAspRS_like_N ND_PkAspRS_like_N: N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS). This domain is a beta-barrel domain (OB fold) involved in binding the tRNA anticodon stem-loop. P. kodakaraensis AspRS is a class 2b aaRS. aaRSs catalyze the specific attachment of amino acids (AAs) to their cognate tRNAs during protein biosynthesis. This 2-step reaction involves i) the activation the AA by ATP in the presence of magnesium ions, followed by ii) the transfer of the activated AA to the terminal ribose of tRNA. In the case of the class2b aaRSs, the activated AA is attached to the 3'OH of the terminal ribose. P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn. Some of the enzymes in this group may be discriminating, based on the presence of homologs of asparaginyl-tRNA synthetase (AsnRS) in their completed genomes.
Probab=95.77 E-value=0.18 Score=36.17 Aligned_cols=74 Identities=22% Similarity=0.210 Sum_probs=52.5
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--c-----ccccccCCcccccceeEEEEEeeEeeccC--CCce
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--F-----RIRRWNTGVFFFDFWMYVMVVGGFVIRTD--DIPV 103 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~-----~~~~~~~G~~~~~~~~YVmViG~~~~~~~--~~p~ 103 (142)
+.|++.|.|.++..-++ =+.|+|+||.+++..+.. . ..+.+..| ..|-|.|.+..+.. ....
T Consensus 13 ~~V~v~Gwv~~~R~~g~~~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~~~E 85 (108)
T cd04316 13 EEVTVAGWVHEIRDLGGIKFVILRDREGIVQVTAPKKKVDKELFKTVRKLSRE-------SVISVTGTVKAEPKAPNGVE 85 (108)
T ss_pred CEEEEEEEEEeeeccCCeEEEEEecCCeeEEEEEeCCCCCHHHHHHHhCCCCc-------CEEEEEEEEEeCCCCCCCEE
Confidence 45899999999864433 467899999999887432 1 11358899 99999999877322 1356
Q ss_pred EEEEEEeeCCCC
Q 044496 104 IKVHKIVDLSAF 115 (142)
Q Consensus 104 i~a~K~~DLS~~ 115 (142)
|.+.++.=||..
T Consensus 86 i~~~~i~il~~~ 97 (108)
T cd04316 86 IIPEEIEVLSEA 97 (108)
T ss_pred EEEeEEEEEeCC
Confidence 777777777764
No 20
>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=95.71 E-value=0.3 Score=33.39 Aligned_cols=71 Identities=23% Similarity=0.195 Sum_probs=47.9
Q ss_pred EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecccc-----ccccccCCcccccceeEEEEEeeEeecc-----CCCce
Q 044496 36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDF-----RIRRWNTGVFFFDFWMYVMVVGGFVIRT-----DDIPV 103 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~-----~~~~~~~G~~~~~~~~YVmViG~~~~~~-----~~~p~ 103 (142)
.|++.|.|-++..-++ =+.|.|+||.+++..+... ....+..| ..|.|-|.+..+. .....
T Consensus 1 ~V~v~Gwv~~~R~~g~~~Fi~LrD~~~~iQ~v~~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~~~~~~E 73 (84)
T cd04323 1 RVKVFGWVHRLRSQKKLMFLVLRDGTGFLQCVLSKKLVTEFYDAKSLTQE-------SSVEVTGEVKEDPRAKQAPGGYE 73 (84)
T ss_pred CEEEEEEEEEEecCCCcEEEEEEcCCeEEEEEEcCCcchhHHHHhcCCCc-------CEEEEEEEEEECCcccCCCCCEE
Confidence 3789999999864432 4568999999998774321 12358889 9999999997721 11235
Q ss_pred EEEEEEeeCC
Q 044496 104 IKVHKIVDLS 113 (142)
Q Consensus 104 i~a~K~~DLS 113 (142)
|.+.++.=||
T Consensus 74 i~~~~i~vl~ 83 (84)
T cd04323 74 LQVDYLEIIG 83 (84)
T ss_pred EEEEEEEEEc
Confidence 6666655443
No 21
>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=95.64 E-value=0.16 Score=37.69 Aligned_cols=73 Identities=21% Similarity=0.235 Sum_probs=53.5
Q ss_pred EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc----c-ccccccCCcccccceeEEEEEeeEeecc---------C
Q 044496 36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD----F-RIRRWNTGVFFFDFWMYVMVVGGFVIRT---------D 99 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~----~-~~~~~~~G~~~~~~~~YVmViG~~~~~~---------~ 99 (142)
.|.+.|.|.++..-++ =+.|.||||.+++..+.. . ..+.+..| .+|.|-|.+..+. .
T Consensus 16 ~V~i~Gwv~~~R~~gk~~Fi~LrD~~g~~Q~v~~~~~~~~~~~~~~l~~g-------s~V~V~G~~~~~~~~~~~~~~~~ 88 (135)
T cd04317 16 EVTLCGWVQRRRDHGGLIFIDLRDRYGIVQVVFDPEEAPEFELAEKLRNE-------SVIQVTGKVRARPEGTVNPKLPT 88 (135)
T ss_pred EEEEEEeEehhcccCCEEEEEEecCCeeEEEEEeCCchhHHHHHhCCCCc-------cEEEEEEEEECCCccccCCCCCC
Confidence 4889999999854333 456899999999887432 1 12358899 9999999988632 2
Q ss_pred CCceEEEEEEeeCCCC
Q 044496 100 DIPVIKVHKIVDLSAF 115 (142)
Q Consensus 100 ~~p~i~a~K~~DLS~~ 115 (142)
.+..|.+.++.-||.+
T Consensus 89 ~~~El~~~~i~vl~~~ 104 (135)
T cd04317 89 GEIEVVASELEVLNKA 104 (135)
T ss_pred CcEEEEEeEEEEEECC
Confidence 2468888888888865
No 22
>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=95.63 E-value=0.18 Score=36.11 Aligned_cols=72 Identities=22% Similarity=0.230 Sum_probs=52.4
Q ss_pred EEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc---cc----ccc-ccCCcccccceeEEEEEeeEeeccCCCceEEE
Q 044496 37 VWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD---FR----IRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKV 106 (142)
Q Consensus 37 VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~---~~----~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a 106 (142)
|++.|.|-++..-++ =+.|.||||.+++..+.. +. -.. ++.| +.|.|.|.+..+...+-.|.+
T Consensus 2 v~v~GwV~~~R~~g~~~Fi~lrd~~~~lQ~v~~~~~~~~~~~~~~~~~l~~g-------~~V~v~G~v~~~~~g~~El~~ 74 (108)
T cd04322 2 VSVAGRIMSKRGSGKLSFADLQDESGKIQVYVNKDDLGEEEFEDFKKLLDLG-------DIIGVTGTPFKTKTGELSIFV 74 (108)
T ss_pred EEEEEEEEEEecCCCeEEEEEEECCeEEEEEEECCCCCHHHHHHHHhcCCCC-------CEEEEEEEEEecCCCCEEEEe
Confidence 789999999864433 356899999999876321 11 124 8899 999999999875555667777
Q ss_pred EEEeeCCCC
Q 044496 107 HKIVDLSAF 115 (142)
Q Consensus 107 ~K~~DLS~~ 115 (142)
.++.=||.+
T Consensus 75 ~~~~ils~~ 83 (108)
T cd04322 75 KEFTLLSKS 83 (108)
T ss_pred CEeEEeecc
Confidence 777666663
No 23
>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=95.34 E-value=0.038 Score=35.68 Aligned_cols=55 Identities=20% Similarity=0.294 Sum_probs=41.7
Q ss_pred CcEEEEcCCeeEEEEe-cccc-ccc-cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCC
Q 044496 51 GRLLLDDGTGVVQIYL-SGDF-RIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLS 113 (142)
Q Consensus 51 ~~~~LdDgTG~~~v~~-~~~~-~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS 113 (142)
-.+.|.|+||.+.+.. +... +.+ .+++| .+|.+.|.+.. .+..+.+.+.++.+|.
T Consensus 21 ~~~~l~D~tg~~~~~~f~~~~~~~~~~l~~g-------~~v~v~G~v~~-~~~~~~l~~~~i~~~~ 78 (84)
T cd04485 21 AFVTLEDLTGSIEVVVFPETYEKYRDLLKED-------ALLLVEGKVER-RDGGLRLIAERIEDLE 78 (84)
T ss_pred EEEEEEeCCCeEEEEECHHHHHHHHHHhcCC-------CEEEEEEEEEe-cCCceEEEeeccccHH
Confidence 4789999999999987 4332 233 48999 99999999976 5566788877776553
No 24
>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=95.29 E-value=0.34 Score=34.22 Aligned_cols=72 Identities=15% Similarity=0.086 Sum_probs=51.1
Q ss_pred EEEEEEEEeeeCCC-C--cEEEEcCCeeEEEEeccc----ccc-----ccccCCcccccceeEEEEEeeEeeccC-----
Q 044496 37 VWLQGVLVSPPDDD-G--RLLLDDGTGVVQIYLSGD----FRI-----RRWNTGVFFFDFWMYVMVVGGFVIRTD----- 99 (142)
Q Consensus 37 VWlQG~vv~~~~~~-~--~~~LdDgTG~~~v~~~~~----~~~-----~~~~~G~~~~~~~~YVmViG~~~~~~~----- 99 (142)
|.+.|.|.++..-+ + =+.|.|+||.+++..+.. ... +.+..| ..|.|.|.+..+..
T Consensus 2 V~i~Gwv~~~R~~g~k~~Fi~LrD~sg~iQ~v~~~~~~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~~~ 74 (102)
T cd04320 2 VLIRARVHTSRAQGAKLAFLVLRQQGYTIQGVLAASAEGVSKQMVKWAGSLSKE-------SIVDVEGTVKKPEEPIKSC 74 (102)
T ss_pred EEEEEEEEEeecCCCceEEEEEecCCceEEEEEeCCcccCCHHHHHHHhcCCCc-------cEEEEEEEEECCCCcccCC
Confidence 77999999986433 2 567999999999988422 111 247899 99999999976311
Q ss_pred --CCceEEEEEEeeCCCC
Q 044496 100 --DIPVIKVHKIVDLSAF 115 (142)
Q Consensus 100 --~~p~i~a~K~~DLS~~ 115 (142)
.+-.|.+.++.=||.+
T Consensus 75 ~~~~~El~~~~i~il~~~ 92 (102)
T cd04320 75 TQQDVELHIEKIYVVSEA 92 (102)
T ss_pred CcCcEEEEEEEEEEEecC
Confidence 3457777777666654
No 25
>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=94.96 E-value=0.41 Score=34.00 Aligned_cols=65 Identities=22% Similarity=0.301 Sum_probs=45.5
Q ss_pred EEEEEEEEeeeC--CC--CcEEEEcCCeeEEEEe-ccc--c-cc-ccccCCcccccceeEEEEEeeEeeccCCCceEEEE
Q 044496 37 VWLQGVLVSPPD--DD--GRLLLDDGTGVVQIYL-SGD--F-RI-RRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVH 107 (142)
Q Consensus 37 VWlQG~vv~~~~--~~--~~~~LdDgTG~~~v~~-~~~--~-~~-~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~ 107 (142)
.|+.|.|.+... .. -.|.|.|+++.+.+.. ... . +. ..+++| +-|.|.|.+.. .. .|.+-
T Consensus 1 ~~v~GeVs~~~~~~~sGH~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~G-------d~V~v~G~v~~-y~---ql~ve 69 (91)
T cd04482 1 YRVTGKVVEEPRTIEGGHVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPG-------DEVTVYGSVRP-GT---TLNLE 69 (91)
T ss_pred CEEEEEEeCCeecCCCCCEEEEEECCCcEEEEEEECcccccccccCCCCCC-------CEEEEEEEEec-CC---EEEEE
Confidence 489999998743 33 4788999999988864 322 2 22 249999 99999999977 33 45555
Q ss_pred EEeeC
Q 044496 108 KIVDL 112 (142)
Q Consensus 108 K~~DL 112 (142)
+|.-+
T Consensus 70 ~l~~~ 74 (91)
T cd04482 70 KLRVI 74 (91)
T ss_pred EEEEC
Confidence 54433
No 26
>COG4085 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=94.90 E-value=0.17 Score=41.96 Aligned_cols=80 Identities=25% Similarity=0.311 Sum_probs=59.5
Q ss_pred CeEEeEEEEEEEEEeeeCC--CC--cEEEEcCCeeEEEEecccc-------cccc-ccCCcccccceeEEEEEeeEeecc
Q 044496 31 GILFQRVWLQGVLVSPPDD--DG--RLLLDDGTGVVQIYLSGDF-------RIRR-WNTGVFFFDFWMYVMVVGGFVIRT 98 (142)
Q Consensus 31 gl~~~~VWlQG~vv~~~~~--~~--~~~LdDgTG~~~v~~~~~~-------~~~~-~~~G~~~~~~~~YVmViG~~~~~~ 98 (142)
|....-|-+.|.|++.... .| ++.|+||||++++..+.-+ +.++ ..+| +||-|.|.+.- .
T Consensus 48 G~l~e~v~vkg~V~~~~n~~~~gi~~l~lndgtGti~vva~~~tee~l~~n~~~p~~~eG-------e~veVtGrv~~-y 119 (204)
T COG4085 48 GRLNEEVTVKGEVTADQNAIGGGIESLVLNDGTGTITVVASRSTEETLELNEGMPVTVEG-------EIVEVTGRVEE-Y 119 (204)
T ss_pred ceeeccceeeeEEEeeecccccceEEEEEECCCCcEEEEEecChhHhHhhcCCCCccccC-------cEEEEEEEEEE-e
Confidence 6666668889999998633 22 8999999999997763222 2234 7899 99999998866 7
Q ss_pred CCCceEEEEEEeeCCCCcCc
Q 044496 99 DDIPVIKVHKIVDLSAFPDR 118 (142)
Q Consensus 99 ~~~p~i~a~K~~DLS~~p~r 118 (142)
...+-++.-...|+-..|.+
T Consensus 120 rG~~eVkvnq~~d~~~l~k~ 139 (204)
T COG4085 120 RGSSEVKVNQPNDSRPLPKH 139 (204)
T ss_pred CCCceeeccCcccccccccc
Confidence 77777777777777766655
No 27
>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=94.84 E-value=0.77 Score=31.08 Aligned_cols=69 Identities=25% Similarity=0.315 Sum_probs=47.5
Q ss_pred EEEEEEEEeeeCCCC-c-EEEEcCCee--EEEEeccccc----cccccCCcccccceeEEEEEeeEeeccC--CCceEEE
Q 044496 37 VWLQGVLVSPPDDDG-R-LLLDDGTGV--VQIYLSGDFR----IRRWNTGVFFFDFWMYVMVVGGFVIRTD--DIPVIKV 106 (142)
Q Consensus 37 VWlQG~vv~~~~~~~-~-~~LdDgTG~--~~v~~~~~~~----~~~~~~G~~~~~~~~YVmViG~~~~~~~--~~p~i~a 106 (142)
|++.|.|.++...++ . +.|.||||. +++..+.... ...++.| ..|.|-|.+..+.. ....|.+
T Consensus 2 v~v~Gwv~~~R~~g~~~Fi~LrD~s~~~~lQvv~~~~~~~~~~~~~l~~g-------s~V~v~G~v~~~~~~~~~~El~~ 74 (82)
T cd04318 2 VTVNGWVRSVRDSKKISFIELNDGSCLKNLQVVVDKELTNFKEILKLSTG-------SSIRVEGVLVKSPGAKQPFELQA 74 (82)
T ss_pred EEEEEeEEEEEcCCcEEEEEEECCCCccCEEEEEeCcccCHHHHhcCCCc-------eEEEEEEEEEeCCCCCCCEEEEE
Confidence 689999999865433 3 456699995 8887743221 2358899 99999999987433 3456766
Q ss_pred EEEeeC
Q 044496 107 HKIVDL 112 (142)
Q Consensus 107 ~K~~DL 112 (142)
.++.=|
T Consensus 75 ~~i~il 80 (82)
T cd04318 75 EKIEVL 80 (82)
T ss_pred EEEEEe
Confidence 666443
No 28
>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=94.69 E-value=0.29 Score=30.99 Aligned_cols=51 Identities=24% Similarity=0.261 Sum_probs=37.7
Q ss_pred EEEEEEeeeCC------CCcEEEEcCCeeEEEEe-ccccc-cccccCCcccccceeEEEEEeeEee
Q 044496 39 LQGVLVSPPDD------DGRLLLDDGTGVVQIYL-SGDFR-IRRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 39 lQG~vv~~~~~------~~~~~LdDgTG~~~v~~-~~~~~-~~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
++|+|.++... --++.+.|+||.+++.. +..+. .+.+++| +.+.+.|.+..
T Consensus 2 i~~~V~~~~~~~~~~~~~~~~~~~D~~g~i~~~~F~~~~~~~~~~~~G-------~~~~v~Gkv~~ 60 (75)
T cd04488 2 VEGTVVSVEVVPRRGRRRLKVTLSDGTGTLTLVFFNFQPYLKKQLPPG-------TRVRVSGKVKR 60 (75)
T ss_pred EEEEEEEEEeccCCCccEEEEEEEcCCCEEEEEEECCCHHHHhcCCCC-------CEEEEEEEEee
Confidence 57888776322 12789999999999986 53332 3359999 99999999976
No 29
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=94.54 E-value=0.32 Score=44.23 Aligned_cols=73 Identities=18% Similarity=0.189 Sum_probs=56.0
Q ss_pred EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--cc-----ccc-ccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496 36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--FR-----IRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK 105 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~~-----~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~ 105 (142)
.|.+.|+|.++...++ =+.|.|+||.+++..+.. .. ... +..| +.|.|.|.+......+..|.
T Consensus 55 ~v~v~Grv~~~R~~gk~~F~~l~D~~g~iQ~~~~~~~~~~~~~~~~~~~l~~g-------d~V~v~G~~~~t~~gelel~ 127 (496)
T TIGR00499 55 EVSIAGRIMARRSMGKATFITLQDESGQIQLYVNKDDLPEDFYEFDEYLLDLG-------DIIGVTGYPFKTKTGELSVH 127 (496)
T ss_pred EEEEEEEEEEEecCCCeEEEEEEcCCccEEEEEECCcCcHHHHHHHHhcCCCC-------CEEEEEEEEEECCCCcEEEE
Confidence 4889999999974433 457899999999987321 11 122 6889 99999999988556678999
Q ss_pred EEEEeeCCCC
Q 044496 106 VHKIVDLSAF 115 (142)
Q Consensus 106 a~K~~DLS~~ 115 (142)
|.++.=||.+
T Consensus 128 ~~~i~ilsk~ 137 (496)
T TIGR00499 128 VTELQILTKA 137 (496)
T ss_pred eeEEEEEecC
Confidence 9999888885
No 30
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=94.35 E-value=0.31 Score=34.95 Aligned_cols=61 Identities=21% Similarity=0.322 Sum_probs=47.0
Q ss_pred eEEeEEEEEEEEEeeeC-CCC--cEEEEcCCeeEEEEe--cccccc--ccccCCcccccceeEEEEEeeEeeccCC
Q 044496 32 ILFQRVWLQGVLVSPPD-DDG--RLLLDDGTGVVQIYL--SGDFRI--RRWNTGVFFFDFWMYVMVVGGFVIRTDD 100 (142)
Q Consensus 32 l~~~~VWlQG~vv~~~~-~~~--~~~LdDgTG~~~v~~--~~~~~~--~~~~~G~~~~~~~~YVmViG~~~~~~~~ 100 (142)
..+.++|++|-|.+... ..| -|.|-|+...+.+.. +...+. ..++.| |=|.|.|.+.- ..+
T Consensus 19 ~~~~~vwV~GEIs~~~~~~~gh~YftLkD~~a~i~~~~~~~~~~~i~~~~l~~G-------~~V~v~g~~~~-y~~ 86 (99)
T PF13742_consen 19 PPLPNVWVEGEISNLKRHSSGHVYFTLKDEEASISCVIFRSRARRIRGFDLKDG-------DKVLVRGRVSF-YEP 86 (99)
T ss_pred CCcCCEEEEEEEeecEECCCceEEEEEEcCCcEEEEEEEHHHHhhCCCCCCCCC-------CEEEEEEEEEE-ECC
Confidence 45789999999999976 344 789999988888876 333333 369999 99999999876 444
No 31
>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=94.21 E-value=0.46 Score=42.24 Aligned_cols=74 Identities=26% Similarity=0.206 Sum_probs=54.1
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--cc-----cccccCCcccccceeEEEEEeeEeecc--CCCce
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--FR-----IRRWNTGVFFFDFWMYVMVVGGFVIRT--DDIPV 103 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~~-----~~~~~~G~~~~~~~~YVmViG~~~~~~--~~~p~ 103 (142)
+.|.+.|.|.++..-++ =+.|.|+||.+++..+.. .+ ...++.| ..|.|.|.+..+. ..+..
T Consensus 13 ~~v~i~G~v~~~R~~g~~~Fi~lrd~~g~iQ~v~~~~~~~~~~~~~~~~l~~~-------s~v~v~G~v~~~~~~~~~~e 85 (428)
T TIGR00458 13 QEVTFMGWVHEIRDLGGLIFVLLRDREGLIQITAPAKKVSKNLFKWAKKLNLE-------SVVAVRGIVKIKEKAPGGFE 85 (428)
T ss_pred CEEEEEEEEEEEecCCCcEEEEEEeCCeeEEEEEECCcCCHHHHHHHhCCCCC-------cEEEEEEEEEecCCCCCcEE
Confidence 45889999999965444 367899999999887321 11 1248899 9999999998632 25678
Q ss_pred EEEEEEeeCCCC
Q 044496 104 IKVHKIVDLSAF 115 (142)
Q Consensus 104 i~a~K~~DLS~~ 115 (142)
|.+.++.=||.+
T Consensus 86 l~~~~i~vl~~~ 97 (428)
T TIGR00458 86 IIPTKIEVINEA 97 (428)
T ss_pred EEEeEEEEEecC
Confidence 888777766664
No 32
>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=94.17 E-value=1.1 Score=30.93 Aligned_cols=69 Identities=22% Similarity=0.223 Sum_probs=46.6
Q ss_pred EEEEEEEEeeeC-CCC--cEEEEcCCe-eEEEEecccc---c-cccccCCcccccceeEEEEEeeEeeccC------CCc
Q 044496 37 VWLQGVLVSPPD-DDG--RLLLDDGTG-VVQIYLSGDF---R-IRRWNTGVFFFDFWMYVMVVGGFVIRTD------DIP 102 (142)
Q Consensus 37 VWlQG~vv~~~~-~~~--~~~LdDgTG-~~~v~~~~~~---~-~~~~~~G~~~~~~~~YVmViG~~~~~~~------~~p 102 (142)
|.+.|.|.++.. ..+ =+.|.|||| .+++..+... . ...+..| .-|.|-|.+..+.. ...
T Consensus 2 V~v~Gwv~~~R~~~~~~~Fi~LrD~~g~~iQvv~~~~~~~~~~~~~l~~~-------s~V~V~G~v~~~~~~~~~~~~~~ 74 (86)
T cd04321 2 VTLNGWIDRKPRIVKKLSFADLRDPNGDIIQLVSTAKKDAFSLLKSITAE-------SPVQVRGKLQLKEAKSSEKNDEW 74 (86)
T ss_pred EEEEEeEeeEeCCCCceEEEEEECCCCCEEEEEECCCHHHHHHHhcCCCC-------cEEEEEEEEEeCCCcCCCCCCCE
Confidence 678999999865 222 367899999 6888764321 1 1247889 99999999987321 345
Q ss_pred eEEEEEEeeC
Q 044496 103 VIKVHKIVDL 112 (142)
Q Consensus 103 ~i~a~K~~DL 112 (142)
.|.+.++.=|
T Consensus 75 Ei~~~~i~il 84 (86)
T cd04321 75 ELVVDDIQTL 84 (86)
T ss_pred EEEEEEEEEe
Confidence 6666665433
No 33
>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=93.44 E-value=1.6 Score=30.90 Aligned_cols=71 Identities=23% Similarity=0.228 Sum_probs=48.2
Q ss_pred EEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc-c----c-cccccCCcccccceeEEEEEeeEeecc--CCCceEEE
Q 044496 37 VWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD-F----R-IRRWNTGVFFFDFWMYVMVVGGFVIRT--DDIPVIKV 106 (142)
Q Consensus 37 VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~-~----~-~~~~~~G~~~~~~~~YVmViG~~~~~~--~~~p~i~a 106 (142)
|.+.|.|.++..-++ =+.|.||||.+++..+.. . . ...+..| ..|.|-|.+..+. ...-.|.+
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 VTLAGWVYRKREVGKKAFIVLRDSTGIVQAVFSKDLNEEAYREAKKVGIE-------SSVIVEGAVKADPRAPGGAEVHG 74 (103)
T ss_pred EEEEEEEEeEEcCCCeEEEEEecCCeeEEEEEeCCCCHHHHHHHhCCCCC-------CEEEEEEEEEECCCCCCCEEEEE
Confidence 789999999864332 467899999999887432 1 1 1247889 9999999987621 11235666
Q ss_pred EEEeeCCC
Q 044496 107 HKIVDLSA 114 (142)
Q Consensus 107 ~K~~DLS~ 114 (142)
.++.=||.
T Consensus 75 ~~i~vl~~ 82 (103)
T cd04319 75 EKLEIIQN 82 (103)
T ss_pred EEEEEEec
Confidence 66655554
No 34
>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=93.32 E-value=0.66 Score=41.67 Aligned_cols=74 Identities=24% Similarity=0.311 Sum_probs=53.0
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCC--eeEEEEeccc-c-----ccccccCCcccccceeEEEEEeeEeec--cCCCc
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGT--GVVQIYLSGD-F-----RIRRWNTGVFFFDFWMYVMVVGGFVIR--TDDIP 102 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgT--G~~~v~~~~~-~-----~~~~~~~G~~~~~~~~YVmViG~~~~~--~~~~p 102 (142)
+.|.+.|.|.++...++ =+.|.||| |.+++..+.. . ....++.| +.|.|.|.+..+ ....-
T Consensus 17 ~~v~v~Gwv~~~R~~~~~~F~~lrD~~~~g~iQ~v~~~~~~~~~~~~~~~l~~g-------s~V~v~G~v~~~~~~~~~~ 89 (453)
T TIGR00457 17 DEVTVSGWVRTKRSSKKIIFLELNDGSSLGPIQAVINGEDNPYLFQLLKSLTTG-------SSVSVTGKVVESPGKGQPV 89 (453)
T ss_pred CEEEEEEEeEEEEcCCCeEEEEEECCCCCccEEEEEeCCcChHHHHHHHcCCCC-------cEEEEEEEEEcCCCCCCCE
Confidence 45889999999974333 36789999 9999987432 1 11248999 999999999863 23456
Q ss_pred eEEEEEEeeCCCC
Q 044496 103 VIKVHKIVDLSAF 115 (142)
Q Consensus 103 ~i~a~K~~DLS~~ 115 (142)
.|.+.++.=||.+
T Consensus 90 El~~~~i~vl~~~ 102 (453)
T TIGR00457 90 ELQVKKIEVVGEA 102 (453)
T ss_pred EEEEeEEEEEecC
Confidence 6777777666654
No 35
>PLN02850 aspartate-tRNA ligase
Probab=93.30 E-value=0.73 Score=42.43 Aligned_cols=74 Identities=20% Similarity=0.100 Sum_probs=54.6
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecc----cccc-----ccccCCcccccceeEEEEEeeEee------c
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSG----DFRI-----RRWNTGVFFFDFWMYVMVVGGFVI------R 97 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~----~~~~-----~~~~~G~~~~~~~~YVmViG~~~~------~ 97 (142)
+.||+.|+|.++..-+. =+.|.|++|.+++..+. ..+. ..++.| ..|-|.|.++. .
T Consensus 82 ~~V~v~Grv~~~R~~gk~~Fl~Lrd~~~~iQ~v~~~~~~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~~ 154 (530)
T PLN02850 82 SEVLIRGRVHTIRGKGKSAFLVLRQSGFTVQCVVFVSEVTVSKGMVKYAKQLSRE-------SVVDVEGVVSVPKKPVKG 154 (530)
T ss_pred CEEEEEEEEEEEccCCCeEEEEEEeCCcCEEEEEECCccccCHHHHHHHhCCCCC-------CEEEEEEEEEccCcCCCC
Confidence 67999999999864443 36789999999988732 1222 248999 99999999984 2
Q ss_pred cCCCceEEEEEEeeCCCC
Q 044496 98 TDDIPVIKVHKIVDLSAF 115 (142)
Q Consensus 98 ~~~~p~i~a~K~~DLS~~ 115 (142)
+..+-.|.+.++.=||.+
T Consensus 155 ~t~~~El~~~~i~vls~a 172 (530)
T PLN02850 155 TTQQVEIQVRKIYCVSKA 172 (530)
T ss_pred CCccEEEEEeEEEEEeCC
Confidence 344567888888777664
No 36
>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=93.29 E-value=1.4 Score=30.25 Aligned_cols=53 Identities=26% Similarity=0.280 Sum_probs=39.5
Q ss_pred EEEEEEEEeeeCCCC--cEEEEcCCeeEEEEe-cc-cccc-ccccCCcccccceeEEEEEeeEee
Q 044496 37 VWLQGVLVSPPDDDG--RLLLDDGTGVVQIYL-SG-DFRI-RRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 37 VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~-~~-~~~~-~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
||+.|.|.+.....| -|.|.|+++.+++.. .+ ..+. ..+++| |=|.+.|.+..
T Consensus 1 v~v~GeVs~~~~~~GHvyfsLkD~~a~i~cv~f~~~~~~~~~~l~~G-------d~V~v~G~v~~ 58 (73)
T cd04487 1 VHIEGEVVQIKQTSGPTIFTLRDETGTVWAAAFEEAGVRAYPEVEVG-------DIVRVTGEVEP 58 (73)
T ss_pred CEEEEEEeccccCCCCEEEEEEcCCEEEEEEEEchhccCCcCCCCCC-------CEEEEEEEEec
Confidence 699999997643443 788999999988864 22 2222 248999 99999999864
No 37
>PLN02502 lysyl-tRNA synthetase
Probab=92.92 E-value=1 Score=41.89 Aligned_cols=74 Identities=19% Similarity=0.121 Sum_probs=56.9
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--------cc-c-ccccCCcccccceeEEEEEeeEeeccCCCc
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--------FR-I-RRWNTGVFFFDFWMYVMVVGGFVIRTDDIP 102 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--------~~-~-~~~~~G~~~~~~~~YVmViG~~~~~~~~~p 102 (142)
+.|.+.|+|.++..-++ =+.|.|+||.+++..+.. +. . ..+..| +.|.|.|.+..+...+-
T Consensus 109 ~~V~v~GrV~~~R~~Gk~~F~~LrD~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~g-------diV~V~G~~~~t~~gel 181 (553)
T PLN02502 109 VSVSVAGRIMAKRAFGKLAFYDLRDDGGKIQLYADKKRLDLDEEEFEKLHSLVDRG-------DIVGVTGTPGKTKKGEL 181 (553)
T ss_pred CEEEEEEEEEEEecCCCeEEEEEecCCccEEEEEECccccchhHHHHHHHhCCCCC-------cEEEEEEEEEecCCCCE
Confidence 45889999999965443 457899999999876321 11 1 137889 99999999988666688
Q ss_pred eEEEEEEeeCCCC
Q 044496 103 VIKVHKIVDLSAF 115 (142)
Q Consensus 103 ~i~a~K~~DLS~~ 115 (142)
.|.|.++.=||.+
T Consensus 182 el~~~~i~vLs~~ 194 (553)
T PLN02502 182 SIFPTSFEVLTKC 194 (553)
T ss_pred EEEEeEEEEEecc
Confidence 9999999888885
No 38
>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=92.86 E-value=0.84 Score=30.86 Aligned_cols=48 Identities=19% Similarity=0.210 Sum_probs=34.6
Q ss_pred cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEE
Q 044496 52 RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVH 107 (142)
Q Consensus 52 ~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~ 107 (142)
++.|-|.||.+++.+ +... ...+++| +.|.+.|.........+.|...
T Consensus 26 ~~~l~D~TG~i~~~~W~~~~-~~~~~~G-------~vv~i~~~~v~~~~g~~ql~i~ 74 (82)
T cd04491 26 SGLVGDETGTIRFTLWDEKA-ADDLEPG-------DVVRIENAYVREFNGRLELSVG 74 (82)
T ss_pred EEEEECCCCEEEEEEECchh-cccCCCC-------CEEEEEeEEEEecCCcEEEEeC
Confidence 789999999999998 3322 4459999 9999994444436666666543
No 39
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=92.80 E-value=1.1 Score=41.09 Aligned_cols=73 Identities=16% Similarity=0.205 Sum_probs=55.4
Q ss_pred EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecc--cc----c-c-ccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496 36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSG--DF----R-I-RRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK 105 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~--~~----~-~-~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~ 105 (142)
.|.+.|+|.++..-++ =+.|.|+||.+++..+. .. . . ..+..| +.|.|.|.+......+..|.
T Consensus 67 ~v~v~Grv~~~R~~Gk~~F~~lrD~~g~iQ~~~~~~~~~~~~~~~~~~~l~~G-------d~V~v~G~~~~t~~gelel~ 139 (505)
T PRK12445 67 EVSVAGRMMTRRIMGKASFVTLQDVGGRIQLYVARDSLPEGVYNDQFKKWDLG-------DIIGARGTLFKTQTGELSIH 139 (505)
T ss_pred EEEEEEEEEEEecCCCcEEEEEEeCCccEEEEEECCccchhhHHHHHhcCCCC-------CEEEEEEEEEecCCCcEEEE
Confidence 4889999999964433 45689999999988732 11 1 1 248899 99999999987556688898
Q ss_pred EEEEeeCCCC
Q 044496 106 VHKIVDLSAF 115 (142)
Q Consensus 106 a~K~~DLS~~ 115 (142)
|.++.=||.+
T Consensus 140 ~~~~~llsk~ 149 (505)
T PRK12445 140 CTELRLLTKA 149 (505)
T ss_pred EeEEEEEecC
Confidence 8888877774
No 40
>PRK00484 lysS lysyl-tRNA synthetase; Reviewed
Probab=92.37 E-value=1.3 Score=40.35 Aligned_cols=74 Identities=20% Similarity=0.236 Sum_probs=55.4
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--cc-----cccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--FR-----IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK 105 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~~-----~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~ 105 (142)
..|.+.|+|.++..-++ =+.|.|+||.+++..+.. .. -+.++.| +.|-|.|.+..+...+..|.
T Consensus 55 ~~v~v~G~v~~~R~~g~~~Fi~lrD~~g~iQ~v~~~~~~~~~~~~~~~~l~~g-------~~v~v~G~v~~t~~ge~el~ 127 (491)
T PRK00484 55 IEVSVAGRVMLKRVMGKASFATLQDGSGRIQLYVSKDDVGEEALEAFKKLDLG-------DIIGVEGTLFKTKTGELSVK 127 (491)
T ss_pred cEEEEEEEEEEEecCCceEEEEEEcCCccEEEEEECCcCCHHHHHHHhcCCCC-------CEEEEEEEEEEcCCCcEEEE
Confidence 56899999999964433 367899999999987432 11 1238899 99999999988655678888
Q ss_pred EEEEeeCCCC
Q 044496 106 VHKIVDLSAF 115 (142)
Q Consensus 106 a~K~~DLS~~ 115 (142)
|.++.=||.+
T Consensus 128 ~~~~~vls~~ 137 (491)
T PRK00484 128 ATELTLLTKS 137 (491)
T ss_pred EeEEEEEecc
Confidence 8887777664
No 41
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=91.92 E-value=1.6 Score=39.06 Aligned_cols=73 Identities=26% Similarity=0.331 Sum_probs=54.0
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEe--ccc---cc-cccccCCcccccceeEEEEEeeEeecc--CCCceE
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYL--SGD---FR-IRRWNTGVFFFDFWMYVMVVGGFVIRT--DDIPVI 104 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~--~~~---~~-~~~~~~G~~~~~~~~YVmViG~~~~~~--~~~p~i 104 (142)
+.|.+.|.|.++..-++ =+.|.|+||.+++.. +.. .+ .+.++.| ..|.|-|.+..+. ..+..|
T Consensus 17 ~~V~i~G~v~~~R~~g~~~Fi~lrD~~g~iq~~~~~~~~~~~~~~~~~l~~~-------s~v~v~G~v~~~~~~~~~~el 89 (450)
T PRK03932 17 QEVTVRGWVRTKRDSGKIAFLQLRDGSCFKQLQVVKDNGEEYFEEIKKLTTG-------SSVIVTGTVVESPRAGQGYEL 89 (450)
T ss_pred CEEEEEEEEEEEEeCCCeEEEEEECCCCcEEEEEEcCCChHHHHHHhcCCCC-------cEEEEEEEEEcCCCCCCCEEE
Confidence 56889999999964432 367899999988876 221 11 1248999 9999999998732 246789
Q ss_pred EEEEEeeCCC
Q 044496 105 KVHKIVDLSA 114 (142)
Q Consensus 105 ~a~K~~DLS~ 114 (142)
.|.++.=||.
T Consensus 90 ~~~~i~vl~~ 99 (450)
T PRK03932 90 QATKIEVIGE 99 (450)
T ss_pred EEEEEEEccC
Confidence 9999988886
No 42
>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=91.83 E-value=2.7 Score=29.04 Aligned_cols=63 Identities=17% Similarity=0.170 Sum_probs=43.3
Q ss_pred EEEEEEEeee-CCCC--cEEEEcCCeeEEEEe-ccccc---ccc-ccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496 38 WLQGVLVSPP-DDDG--RLLLDDGTGVVQIYL-SGDFR---IRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI 109 (142)
Q Consensus 38 WlQG~vv~~~-~~~~--~~~LdDgTG~~~v~~-~~~~~---~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~ 109 (142)
-+-|+|.++. ...| .+.|.|.||++++.. +.... .+. +..| .-|+|.|.+.. .+ . .+.+-++
T Consensus 3 ~i~GiI~~v~~TK~g~~~~~leD~~G~~Ev~~F~~~~~~~~~~~~l~~d-------~~v~v~g~v~~-~~-~-~l~~~~I 72 (79)
T cd04490 3 SIIGMVNDVRSTKNGHRIVELEDTTGRITVLLTKDKEELFEEAEDILPD-------EVIGVSGTVSK-DG-G-LIFADEI 72 (79)
T ss_pred EEEEEEeEEEEcCCCCEEEEEECCCCEEEEEEeCchhhhhhhhhhccCC-------CEEEEEEEEec-CC-C-EEEEEEe
Confidence 3556666663 1122 999999999999997 44433 233 8999 99999999955 22 3 6666666
Q ss_pred e
Q 044496 110 V 110 (142)
Q Consensus 110 ~ 110 (142)
.
T Consensus 73 ~ 73 (79)
T cd04490 73 F 73 (79)
T ss_pred E
Confidence 5
No 43
>PRK02983 lysS lysyl-tRNA synthetase; Provisional
Probab=91.70 E-value=1.5 Score=43.73 Aligned_cols=73 Identities=19% Similarity=0.111 Sum_probs=55.5
Q ss_pred EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccccc--------cccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496 36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDFR--------IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK 105 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~~--------~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~ 105 (142)
.|.+.|+|.++..-++ =+.|.|+||.+++..+.... .+.+..| +.|.|.|.+..+...+..|.
T Consensus 653 ~V~v~Grv~~~R~~G~~~F~~lrD~~g~iQ~v~~~~~~~~~~~~~~~~~l~~g-------d~V~v~G~v~~t~~ge~ei~ 725 (1094)
T PRK02983 653 EVSVSGRVLRIRDYGGVLFADLRDWSGELQVLLDASRLEQGSLADFRAAVDLG-------DLVEVTGTMGTSRNGTLSLL 725 (1094)
T ss_pred EEEEEEEEEEEeeCCCeEEEEEEeCCeeEEEEEECCccchhhHHHHHhcCCCC-------CEEEEEEEEEEcCCCCEEEE
Confidence 5889999999965443 45689999999998733211 1237889 99999999988666788888
Q ss_pred EEEEeeCCCC
Q 044496 106 VHKIVDLSAF 115 (142)
Q Consensus 106 a~K~~DLS~~ 115 (142)
+.++.=||.+
T Consensus 726 ~~~i~ll~k~ 735 (1094)
T PRK02983 726 VTSWRLAGKC 735 (1094)
T ss_pred EeEEEEEecc
Confidence 8887767653
No 44
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=91.48 E-value=1.1 Score=41.03 Aligned_cols=64 Identities=19% Similarity=0.330 Sum_probs=49.9
Q ss_pred EeEEEEEEEEEeeeCC-C--CcEEEEcCCeeEEEEe--ccccccc-cccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496 34 FQRVWLQGVLVSPPDD-D--GRLLLDDGTGVVQIYL--SGDFRIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK 105 (142)
Q Consensus 34 ~~~VWlQG~vv~~~~~-~--~~~~LdDgTG~~~v~~--~~~~~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~ 105 (142)
|..||+.|-|...... . -.|.|-|++..+++.. ....+.+ +++.| |.|.|.|.+.. +.|.-..+
T Consensus 23 ~~~V~v~GEISn~t~~~sgH~YFtLKD~~A~i~c~mf~~~~~~l~f~p~eG-------~~V~v~G~is~-Y~~rG~YQ 92 (440)
T COG1570 23 LGQVWVRGEISNFTRPASGHLYFTLKDERAQIRCVMFKGNNRRLKFRPEEG-------MQVLVRGKISL-YEPRGDYQ 92 (440)
T ss_pred CCeEEEEEEecCCccCCCccEEEEEccCCceEEEEEEcCcccccCCCccCC-------CEEEEEEEEEE-EcCCCceE
Confidence 8899999999998633 3 4799999999999986 3334433 59999 99999999977 65554443
No 45
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=91.27 E-value=0.93 Score=31.11 Aligned_cols=47 Identities=28% Similarity=0.365 Sum_probs=35.3
Q ss_pred EEEEEEeeeCCCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEe
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFV 95 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~ 95 (142)
+=|+|+++.++++..+.+-+-.+-++...-.+. .++| +||+|+.++-
T Consensus 5 iP~~Vv~v~~~~~~A~v~~~G~~~~V~~~lv~~---v~~G-------d~VLVHaG~A 51 (68)
T PF01455_consen 5 IPGRVVEVDEDGGMAVVDFGGVRREVSLALVPD---VKVG-------DYVLVHAGFA 51 (68)
T ss_dssp EEEEEEEEETTTTEEEEEETTEEEEEEGTTCTS---B-TT--------EEEEETTEE
T ss_pred ccEEEEEEeCCCCEEEEEcCCcEEEEEEEEeCC---CCCC-------CEEEEecChh
Confidence 458899997778888888886667777666553 8999 9999999874
No 46
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=90.67 E-value=1.9 Score=40.04 Aligned_cols=74 Identities=18% Similarity=0.122 Sum_probs=53.0
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEec---ccccc-----ccccCCcccccceeEEEEEeeEeecc------
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLS---GDFRI-----RRWNTGVFFFDFWMYVMVVGGFVIRT------ 98 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~---~~~~~-----~~~~~G~~~~~~~~YVmViG~~~~~~------ 98 (142)
+.||+.|+|.++..-++ =+.|.|+||.+++..+ ...+. ..++.| ..|.|.|.+..+.
T Consensus 79 ~~V~v~Grv~~~R~~Gk~~Fl~LRd~~~~iQ~v~~~~~~~~~~~~~~~~~l~~e-------siV~V~G~v~~~~~~~~~~ 151 (550)
T PTZ00401 79 KTVLIRARVSTTRKKGKMAFMVLRDGSDSVQAMAAVEGDVPKEMIDFIGQIPTE-------SIVDVEATVCKVEQPITST 151 (550)
T ss_pred CEEEEEEEEEEEecCCCeEEEEEEeCCcCEEEEEECCCccCHHHHHHHhcCCCC-------CEEEEEEEEEecCccCCCC
Confidence 56999999999865443 4678999999998863 12232 248999 9999999988632
Q ss_pred -CCCceEEEEEEeeCCCC
Q 044496 99 -DDIPVIKVHKIVDLSAF 115 (142)
Q Consensus 99 -~~~p~i~a~K~~DLS~~ 115 (142)
...-.|.+.++.=||.+
T Consensus 152 ~~~~~El~v~~i~vls~a 169 (550)
T PTZ00401 152 SHSDIELKVKKIHTVTES 169 (550)
T ss_pred CCccEEEEeeEEEEEeCC
Confidence 22347777777666664
No 47
>PRK07373 DNA polymerase III subunit alpha; Reviewed
Probab=90.66 E-value=0.98 Score=40.85 Aligned_cols=72 Identities=14% Similarity=0.109 Sum_probs=55.7
Q ss_pred eEEEEEEEEEeeeCC----C---CcEEEEcCCeeEEEEe-cccccc-cc-ccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496 35 QRVWLQGVLVSPPDD----D---GRLLLDDGTGVVQIYL-SGDFRI-RR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVI 104 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~----~---~~~~LdDgTG~~~v~~-~~~~~~-~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i 104 (142)
++|.+-|+|.++... + .-+.|.|.||.+++.. +...+. +. ++.| .-|.|-|.+.. ....+.+
T Consensus 281 ~~v~vaG~I~~ik~~~TKkG~~maf~~leD~tG~ie~vvFp~~y~~~~~~l~~~-------~~v~v~G~v~~-~~~~~~l 352 (449)
T PRK07373 281 TKVSAVVMLNEVKKIVTKKGDPMAFLQLEDLSGQSEAVVFPKSYERISELLQVD-------ARLIIWGKVDR-RDDQVQL 352 (449)
T ss_pred CEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHHHHHHHhccC-------CEEEEEEEEEe-cCCeEEE
Confidence 467889999997422 2 2678999999999997 555543 33 8999 99999999976 3456788
Q ss_pred EEEEEeeCCC
Q 044496 105 KVHKIVDLSA 114 (142)
Q Consensus 105 ~a~K~~DLS~ 114 (142)
.+.++.+|.+
T Consensus 353 iv~~i~~l~~ 362 (449)
T PRK07373 353 IVEDAEPIEE 362 (449)
T ss_pred EEeEeecHhh
Confidence 8999998865
No 48
>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=90.52 E-value=2.3 Score=39.82 Aligned_cols=73 Identities=25% Similarity=0.185 Sum_probs=54.1
Q ss_pred EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccccc----cccccCCcccccceeEEEEEeeEeec---------cCC
Q 044496 36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDFR----IRRWNTGVFFFDFWMYVMVVGGFVIR---------TDD 100 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~~----~~~~~~G~~~~~~~~YVmViG~~~~~---------~~~ 100 (142)
.|.+.|.|.++..-++ =+.|.|+||.+++..+.... ...++.| ..|.|.|.+..+ ...
T Consensus 17 ~V~l~GwV~~~R~~Gkl~Fi~LrD~sg~iQvv~~~~~~~~~~~~~L~~e-------svV~V~G~v~~r~~~~~n~~~~tg 89 (583)
T TIGR00459 17 TVTLAGWVNRRRDLGGLIFIDLRDRSGIVQVVCDPDADALKLAKGLRNE-------DVVQVKGKVSARPEGNINRNLDTG 89 (583)
T ss_pred EEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCCHHHHHHHhcCCCC-------CEEEEEEEEEeCCccccCccCCCC
Confidence 5889999999864443 35689999999998743311 1258899 999999999752 234
Q ss_pred CceEEEEEEeeCCCC
Q 044496 101 IPVIKVHKIVDLSAF 115 (142)
Q Consensus 101 ~p~i~a~K~~DLS~~ 115 (142)
+..|.|.++.-||.+
T Consensus 90 ~iEl~~~~i~iL~~a 104 (583)
T TIGR00459 90 EIEILAESITLLNKS 104 (583)
T ss_pred cEEEEEeEEEEeecC
Confidence 678888888888764
No 49
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=90.30 E-value=0.7 Score=44.11 Aligned_cols=71 Identities=21% Similarity=0.261 Sum_probs=50.4
Q ss_pred eEEEEEEEEEeee--CCCCcEEEEcCCeeEEEEe---cccccccc-ccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496 35 QRVWLQGVLVSPP--DDDGRLLLDDGTGVVQIYL---SGDFRIRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK 108 (142)
Q Consensus 35 ~~VWlQG~vv~~~--~~~~~~~LdDgTG~~~v~~---~~~~~~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K 108 (142)
..|.+.|-|+++. .+-..|+|.|+||.+...- .+. |-.| ++.| ++|.|+|.+..+.+ .--|....
T Consensus 214 ~tV~I~GeV~qikqT~GPTVFtltDetg~i~aAAFe~aGv-RAyP~IevG-------diV~ViG~V~~r~g-~lQiE~~~ 284 (715)
T COG1107 214 KTVRIEGEVTQIKQTSGPTVFTLTDETGAIWAAAFEEAGV-RAYPEIEVG-------DIVEVIGEVTRRDG-RLQIEIEA 284 (715)
T ss_pred ceEEEEEEEEEEEEcCCCEEEEEecCCCceehhhhccCCc-ccCCCCCCC-------ceEEEEEEEeecCC-cEEEeehh
Confidence 4688999999984 4456999999999988864 332 2234 9999 99999999976433 33444555
Q ss_pred EeeCCC
Q 044496 109 IVDLSA 114 (142)
Q Consensus 109 ~~DLS~ 114 (142)
|..|+-
T Consensus 285 me~L~G 290 (715)
T COG1107 285 MEKLTG 290 (715)
T ss_pred hHHhhC
Confidence 555543
No 50
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=89.96 E-value=2.4 Score=39.62 Aligned_cols=73 Identities=22% Similarity=0.252 Sum_probs=52.4
Q ss_pred EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc---cc-cccccCCcccccceeEEEEEeeEeecc---------CC
Q 044496 36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD---FR-IRRWNTGVFFFDFWMYVMVVGGFVIRT---------DD 100 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~---~~-~~~~~~G~~~~~~~~YVmViG~~~~~~---------~~ 100 (142)
.|.+.|.|.++..-++ =+.|.|+||.+++..+.. ++ ...++.| ..|.|.|.+..+. ..
T Consensus 19 ~V~l~GwV~~~R~~g~l~Fi~LrD~~g~iQ~v~~~~~~~~~~~~~l~~e-------s~V~V~G~v~~~~~~~~n~~~~~g 91 (588)
T PRK00476 19 TVTLCGWVHRRRDHGGLIFIDLRDREGIVQVVFDPDAEAFEVAESLRSE-------YVIQVTGTVRARPEGTVNPNLPTG 91 (588)
T ss_pred EEEEEEEEEEEEeCCCeEEEEEEeCCceEEEEEeCCHHHHHHHhCCCCC-------CEEEEEEEEEecCCcccCccCCCC
Confidence 4889999999864433 456899999999987542 11 1358899 9999999998732 22
Q ss_pred CceEEEEEEeeCCCC
Q 044496 101 IPVIKVHKIVDLSAF 115 (142)
Q Consensus 101 ~p~i~a~K~~DLS~~ 115 (142)
+..|.|.++.=||.+
T Consensus 92 ~~El~~~~i~il~~a 106 (588)
T PRK00476 92 EIEVLASELEVLNKS 106 (588)
T ss_pred cEEEEEeEEEEEecC
Confidence 457777777766664
No 51
>PLN02221 asparaginyl-tRNA synthetase
Probab=89.70 E-value=2.1 Score=40.03 Aligned_cols=73 Identities=21% Similarity=0.329 Sum_probs=51.3
Q ss_pred eEEEEEEEEEeeeCCCC----cEEEEcCC--eeEEEEeccc-cc-cccccCCcccccceeEEEEEeeEeecc-----CCC
Q 044496 35 QRVWLQGVLVSPPDDDG----RLLLDDGT--GVVQIYLSGD-FR-IRRWNTGVFFFDFWMYVMVVGGFVIRT-----DDI 101 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~----~~~LdDgT--G~~~v~~~~~-~~-~~~~~~G~~~~~~~~YVmViG~~~~~~-----~~~ 101 (142)
+.|++.|-|-++..-++ =+.|.||| |.+++..+.. .. ...++.| .-|.|.|.++.+. ...
T Consensus 51 ~~V~I~GWV~~iR~~Gk~~i~Fl~LRDgs~~g~iQvVv~~~~~~~~~~L~~E-------S~V~V~G~V~~~~~~~~~~~~ 123 (572)
T PLN02221 51 QKVRIGGWVKTGREQGKGTFAFLEVNDGSCPANLQVMVDSSLYDLSTLVATG-------TCVTVDGVLKVPPEGKGTKQK 123 (572)
T ss_pred CEEEEEEEEEehhhCCCceEEEEEEeCCcccccEEEEEcCchhhHHhcCCCc-------eEEEEEEEEEeCCccCCCCcc
Confidence 57999999999965543 36789999 8999987432 21 1147889 9999999997632 123
Q ss_pred ceEEEEEEeeCCC
Q 044496 102 PVIKVHKIVDLSA 114 (142)
Q Consensus 102 p~i~a~K~~DLS~ 114 (142)
-.|.+-++.=||.
T Consensus 124 iEl~v~~i~vl~~ 136 (572)
T PLN02221 124 IELSVEKVIDVGT 136 (572)
T ss_pred EEEEEeEEEEEec
Confidence 4666666666664
No 52
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=89.70 E-value=1 Score=30.93 Aligned_cols=44 Identities=27% Similarity=0.409 Sum_probs=35.1
Q ss_pred EEEEEEeeeCCCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEe
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVG 92 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG 92 (142)
.+|+|.+++...-++.||||.- -.++..+.-..+++| |=|+|.=
T Consensus 5 veG~I~~id~~~~titLdDGks---y~lp~ef~~~~L~~G-------~kV~V~y 48 (61)
T PF07076_consen 5 VEGTIKSIDPETMTITLDDGKS---YKLPEEFDFDGLKPG-------MKVVVFY 48 (61)
T ss_pred ceEEEEEEcCCceEEEecCCCE---EECCCcccccccCCC-------CEEEEEE
Confidence 6899999988888999999974 345666766679999 8877753
No 53
>COG0017 AsnS Aspartyl/asparaginyl-tRNA synthetases [Translation, ribosomal structure and biogenesis]
Probab=88.65 E-value=4.7 Score=36.86 Aligned_cols=73 Identities=23% Similarity=0.261 Sum_probs=50.9
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecc--cc----ccccccCCcccccceeEEEEEeeEeecc--CCCceE
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSG--DF----RIRRWNTGVFFFDFWMYVMVVGGFVIRT--DDIPVI 104 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~--~~----~~~~~~~G~~~~~~~~YVmViG~~~~~~--~~~p~i 104 (142)
+.|-++|-|-++.+-++ =+.|.||||.+++..+. .. +-+.++.+ ..|.|-|.+.++. ...-.|
T Consensus 17 ~~V~v~GWV~~~R~~g~i~Fi~lrDgsg~iQ~v~~~~~~~~~~~~~~~L~~e-------s~v~V~G~v~~~~~a~~g~El 89 (435)
T COG0017 17 QEVTVRGWVHNKRDLGKIIFLVLRDGSGFIQAVVPKNKVYEELFKAKKLTLE-------SSVVVTGIVKASPKAPQGFEL 89 (435)
T ss_pred cEEEEEEEeeeecccCCeEEEEEEcCCcEEEEEEECCCCcHHHhhhhcCCCc-------cEEEEEEEEEcCCCCCCCEEE
Confidence 88999999999865555 35789999999998732 21 22358999 9999999998732 223355
Q ss_pred EEEEEeeCCC
Q 044496 105 KVHKIVDLSA 114 (142)
Q Consensus 105 ~a~K~~DLS~ 114 (142)
++.++-=||.
T Consensus 90 ~v~~i~Vl~~ 99 (435)
T COG0017 90 QVEKIEVLGE 99 (435)
T ss_pred EEEEEEEeec
Confidence 5555444443
No 54
>PRK06386 replication factor A; Reviewed
Probab=88.23 E-value=2.7 Score=37.34 Aligned_cols=68 Identities=15% Similarity=0.118 Sum_probs=52.9
Q ss_pred EEEEEEEEeeeC----C-CC-----cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496 37 VWLQGVLVSPPD----D-DG-----RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK 105 (142)
Q Consensus 37 VWlQG~vv~~~~----~-~~-----~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~ 105 (142)
|=+.|+|++..+ . ++ +.+|-|.||++++.+ .. .++.| +.+.+.+.+....+..|.|.
T Consensus 120 v~V~akVle~~e~e~~~~g~~~~v~sg~lgDeTGrIr~TlW~~-----~l~eG-------d~v~i~na~v~e~~G~~el~ 187 (358)
T PRK06386 120 VSVIGKITGITKKEYDSDGTSKIVYQGYIEDDTARVRISSFGK-----PLEDN-------RFVRIENARVSQYNGYIEIS 187 (358)
T ss_pred eEEEEEEEEccCceEecCCCccEEEEEEEEcCCCeEEEEEccc-----cccCC-------CEEEEeeeEEEccCCeEEEE
Confidence 446888887744 2 33 799999999999998 33 48899 99999999988777888888
Q ss_pred EEEEeeCCCCc
Q 044496 106 VHKIVDLSAFP 116 (142)
Q Consensus 106 a~K~~DLS~~p 116 (142)
+-+.+-+...|
T Consensus 188 v~~~t~I~~~~ 198 (358)
T PRK06386 188 VGNKSVIKEVE 198 (358)
T ss_pred eCCeEEEEECC
Confidence 87777666543
No 55
>PF15490 Ten1_2: Telomere-capping, CST complex subunit
Probab=87.33 E-value=11 Score=28.59 Aligned_cols=71 Identities=15% Similarity=0.060 Sum_probs=55.2
Q ss_pred EEEEEEEEEeeeCCCCcEEE----EcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeec-cCCCceEEEEEEe
Q 044496 36 RVWLQGVLVSPPDDDGRLLL----DDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIR-TDDIPVIKVHKIV 110 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~~~~L----dDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~-~~~~p~i~a~K~~ 110 (142)
.|..-|++.+-+.....++| .|+.-.+.|..... +.-+.+.| ++++++|-+... .+..++|+|--..
T Consensus 23 svR~~GrL~~yD~~~~~a~l~~~~~~~~~~l~V~t~~l-~~~~~~~g-------slyq~iGEl~~~~~~~~~~L~ARV~r 94 (118)
T PF15490_consen 23 SVRTFGRLQSYDVATSRATLTAQHESDQHSLKVDTKLL-EPFQARVG-------SLYQFIGELEHQPQDGGIVLKARVLR 94 (118)
T ss_pred eEEEEEEEEEEeccCCEEEEEeeccCCCcEEEEEeeEc-cccccCCC-------CEEEEEEEEEEEcCCCcEEEEEEEEE
Confidence 46788999999888999999 88877777776442 11246899 999999999986 5678899988777
Q ss_pred eCCC
Q 044496 111 DLSA 114 (142)
Q Consensus 111 DLS~ 114 (142)
....
T Consensus 95 ~VdG 98 (118)
T PF15490_consen 95 CVDG 98 (118)
T ss_pred ecCC
Confidence 6655
No 56
>PRK04036 DNA polymerase II small subunit; Validated
Probab=87.03 E-value=6.2 Score=35.92 Aligned_cols=54 Identities=19% Similarity=0.222 Sum_probs=38.6
Q ss_pred eEEEEEEEEEeeeCC-CC--cEEEEcCCeeEEEEecccc---cc--ccccCCcccccceeEEEEEeeEe
Q 044496 35 QRVWLQGVLVSPPDD-DG--RLLLDDGTGVVQIYLSGDF---RI--RRWNTGVFFFDFWMYVMVVGGFV 95 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~-~~--~~~LdDgTG~~~v~~~~~~---~~--~~~~~G~~~~~~~~YVmViG~~~ 95 (142)
..+|+-|+|.++.+. +| .+.|-|.||++.+.++... .. ..+-+| .-|.|.|.+.
T Consensus 154 ~~~~viG~v~~~~~~~~g~~~~~LED~sgrv~l~~~~~~~~~~~~~~~lvtg-------~vv~v~G~~~ 215 (504)
T PRK04036 154 EEVSIIGMVSDIRSTKNGHKIVELEDTTGTFPVLIMKDREDLAELADELLLD-------EVIGVEGTLS 215 (504)
T ss_pred ceEEEEEEEEEeecccCCceEEEEECCCCeEEEEeecchhhhhhhhhcccCc-------eEEEEEEEEc
Confidence 568999999988522 33 5899999999999874321 11 246777 7778888754
No 57
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=86.92 E-value=5.9 Score=37.89 Aligned_cols=72 Identities=14% Similarity=0.027 Sum_probs=54.1
Q ss_pred EEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc---cc------cccccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496 36 RVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD---FR------IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVI 104 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~---~~------~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i 104 (142)
.|++.|+|.++..-++ =+.|.|+||.+++..+.. .+ ...+..| +.|-|-|.+......+..|
T Consensus 109 ~V~vaGrV~~~R~~Gk~~F~~LrD~~G~IQvv~~~~~~~~~~~~~~~~~~l~~g-------diV~V~G~v~~t~~GeleI 181 (659)
T PTZ00385 109 TVRVAGRVTSVRDIGKIIFVTIRSNGNELQVVGQVGEHFTREDLKKLKVSLRVG-------DIIGADGVPCRMQRGELSV 181 (659)
T ss_pred EEEEEEEEEeeeccCCeEEEEEEECCceEEEEEECCccCCHHHHHHHHhCCCCC-------CEEEEEEEEEecCCceEEE
Confidence 4999999999864444 356789999999987321 11 1247888 9999999988744567888
Q ss_pred EEEEEeeCCC
Q 044496 105 KVHKIVDLSA 114 (142)
Q Consensus 105 ~a~K~~DLS~ 114 (142)
.|.++.=||.
T Consensus 182 ~~~~i~lLsk 191 (659)
T PTZ00385 182 AASRMLILSP 191 (659)
T ss_pred EeeEEEEech
Confidence 8888887776
No 58
>PRK07218 replication factor A; Provisional
Probab=86.89 E-value=3.1 Score=37.59 Aligned_cols=68 Identities=16% Similarity=0.224 Sum_probs=50.9
Q ss_pred eEEEEEEEEEeeeC-----CCC-----cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCce
Q 044496 35 QRVWLQGVLVSPPD-----DDG-----RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPV 103 (142)
Q Consensus 35 ~~VWlQG~vv~~~~-----~~~-----~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~ 103 (142)
..|-+-|+|+++.+ +++ +.+|-|+||++++.+ ...+ .+++| +.|.+.+.+....+..|.
T Consensus 173 ~~V~v~g~Vl~~~~r~f~~~dg~~~v~~giigDeTG~Ir~tlW~~~~---~l~~G-------d~v~I~na~v~e~~G~~e 242 (423)
T PRK07218 173 RGVNVEARVLELEHREIDGRDGETTILSGVLADETGRLPFTDWDPLP---EIEIG-------ASIRIEDAYVREFRGVPS 242 (423)
T ss_pred CceEEEEEEEEecceeEEcCCCCeEEEEEEEECCCceEEEEEecccc---cCCCC-------CEEEEeeeEEeccCCeEE
Confidence 34667888888733 122 678999999999998 4322 48999 999999999887788898
Q ss_pred EEEEEEeeC
Q 044496 104 IKVHKIVDL 112 (142)
Q Consensus 104 i~a~K~~DL 112 (142)
|.+.+-+.+
T Consensus 243 lnv~~~t~I 251 (423)
T PRK07218 243 VNVSEFTTV 251 (423)
T ss_pred EEECCceEE
Confidence 888744433
No 59
>PLN02903 aminoacyl-tRNA ligase
Probab=85.91 E-value=7.4 Score=37.16 Aligned_cols=74 Identities=27% Similarity=0.238 Sum_probs=51.4
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc-cc-----cccccCCcccccceeEEEEEeeEeecc--------
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD-FR-----IRRWNTGVFFFDFWMYVMVVGGFVIRT-------- 98 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~-~~-----~~~~~~G~~~~~~~~YVmViG~~~~~~-------- 98 (142)
+.|.+.|.|-++..-++ =+.|.|+||.++|..+.. .. ...++.| ..|.|.|.+..+.
T Consensus 73 k~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~L~~e-------svV~V~G~V~~r~~~~~n~~~ 145 (652)
T PLN02903 73 SRVTLCGWVDLHRDMGGLTFLDVRDHTGIVQVVTLPDEFPEAHRTANRLRNE-------YVVAVEGTVRSRPQESPNKKM 145 (652)
T ss_pred CEEEEEEEEEEEecCCCcEEEEEEcCCccEEEEEeCCccHHHHHHHhcCCCC-------CEEEEEEEEEeCCCcCcCCCC
Confidence 35889999999865443 456899999999887422 11 1248899 9999999998631
Q ss_pred -CCCceEEEEEEeeCCCC
Q 044496 99 -DDIPVIKVHKIVDLSAF 115 (142)
Q Consensus 99 -~~~p~i~a~K~~DLS~~ 115 (142)
..+-.|.|.++.=||.+
T Consensus 146 ~tGeiEl~~~~i~VL~~a 163 (652)
T PLN02903 146 KTGSVEVVAESVDILNVV 163 (652)
T ss_pred CCCCEEEEEeEEEEEecC
Confidence 12346666666655553
No 60
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=85.82 E-value=6 Score=38.05 Aligned_cols=74 Identities=20% Similarity=0.174 Sum_probs=52.3
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccc--cc-----cccccCCcccccceeEEEEEeeEeecc----C--
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGD--FR-----IRRWNTGVFFFDFWMYVMVVGGFVIRT----D-- 99 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~--~~-----~~~~~~G~~~~~~~~YVmViG~~~~~~----~-- 99 (142)
+.|.+.|.|.++..-++ =+.|.|+||.+++..+.. .. ...++.| ..|.|.|.++.+. +
T Consensus 19 ~~V~l~GWV~~~R~~G~l~FidLRD~~G~iQvV~~~~~~~~~~~~~~~~L~~E-------svV~V~G~v~~r~~~~~n~~ 91 (706)
T PRK12820 19 REVCLAGWVDAFRDHGELLFIHLRDRNGFIQAVFSPEAAPADVYELAASLRAE-------FCVALQGEVQKRLEETENPH 91 (706)
T ss_pred CEEEEEEEEEEEEcCCCcEEEEEEeCCccEEEEEeCCcCCHHHHHHHhcCCCC-------CEEEEEeEEeccCccccCCC
Confidence 45889999999865444 456899999999987321 11 1248999 9999999998731 1
Q ss_pred ---CCceEEEEEEeeCCCC
Q 044496 100 ---DIPVIKVHKIVDLSAF 115 (142)
Q Consensus 100 ---~~p~i~a~K~~DLS~~ 115 (142)
.+-.|.|.++.=||.+
T Consensus 92 ~~tg~iEl~~~~i~iL~~a 110 (706)
T PRK12820 92 IETGDIEVFVRELSILAAS 110 (706)
T ss_pred CCCCcEEEEeeEEEEEecC
Confidence 2346777777766664
No 61
>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=85.22 E-value=11 Score=28.40 Aligned_cols=63 Identities=21% Similarity=0.302 Sum_probs=40.0
Q ss_pred eEEEEEEEEE--eeeC--C--CCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496 35 QRVWLQGVLV--SPPD--D--DGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK 108 (142)
Q Consensus 35 ~~VWlQG~vv--~~~~--~--~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K 108 (142)
+++.+-|.|+ ++.- + .-+|.|.|+...+.|.+.+... ..++.| .-|.|.|.+.. .-.+.|-+
T Consensus 51 ~~vrv~G~V~~gSv~~~~~~~~~~F~i~D~~~~i~V~Y~G~~P-d~F~eg-------~~VVv~G~~~~----~g~F~A~~ 118 (131)
T PF03100_consen 51 RKVRVGGLVVEGSVEYDPDGNTLTFTITDGGKEIPVVYTGPLP-DLFREG-------QGVVVEGRLGE----DGVFEATE 118 (131)
T ss_dssp SEEEEEEEEECTTEEE-TTSSEEEEEEE-SS-EEEEEEES--C-TT--TT-------SEEEEEEEECC----TSEEEEEE
T ss_pred ceEEEeeEEccCCEEEcCCCCEEEEEEEECCcEEEEEECCCCC-ccccCC-------CeEEEEEEECC----CCEEEEEE
Confidence 4566788887 3322 2 3399999999999999866432 248899 99999998833 34677766
Q ss_pred E
Q 044496 109 I 109 (142)
Q Consensus 109 ~ 109 (142)
+
T Consensus 119 l 119 (131)
T PF03100_consen 119 L 119 (131)
T ss_dssp E
T ss_pred E
Confidence 5
No 62
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=84.80 E-value=10 Score=30.31 Aligned_cols=64 Identities=22% Similarity=0.291 Sum_probs=44.5
Q ss_pred eEEEEEEEEE--eeeC-C---CCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496 35 QRVWLQGVLV--SPPD-D---DGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK 108 (142)
Q Consensus 35 ~~VWlQG~vv--~~~~-~---~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K 108 (142)
+++.+-|.|+ |+.- + .-+|.+.|+.+.+.|.+.+... --++.| .=|.+.|.+.. .-++.|.+
T Consensus 58 ~~iRvgG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~GilP-DlFrEG-------~gVVveG~~~~----~g~F~A~e 125 (159)
T PRK13150 58 QRLRVGGMVMPGSVRRDPDSLKVNFSLYDAEGSVTVSYEGILP-DLFREG-------QGVVVQGTLEK----GNHVLAHE 125 (159)
T ss_pred CEEEEeeEEeCCcEEECCCCcEEEEEEEcCCcEEEEEEeccCC-ccccCC-------CeEEEEEEECC----CCEEEEeE
Confidence 5566777776 4422 2 2399999999999999866431 027788 88999998854 34677777
Q ss_pred Ee
Q 044496 109 IV 110 (142)
Q Consensus 109 ~~ 110 (142)
+.
T Consensus 126 vL 127 (159)
T PRK13150 126 VL 127 (159)
T ss_pred EE
Confidence 64
No 63
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=84.67 E-value=11 Score=30.13 Aligned_cols=64 Identities=20% Similarity=0.287 Sum_probs=44.2
Q ss_pred eEEEEEEEEE--eee-CCC---CcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496 35 QRVWLQGVLV--SPP-DDD---GRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK 108 (142)
Q Consensus 35 ~~VWlQG~vv--~~~-~~~---~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K 108 (142)
+++.+-|.|+ |+. +++ -+|.+-|+...+.|.+.+... -.++.| .=|.+.|.+.. .-++.|.+
T Consensus 58 ~~iRvgG~V~~GSi~r~~~~l~v~F~vtD~~~~v~V~Y~GilP-DlFrEG-------~gVVveG~~~~----~g~F~A~~ 125 (160)
T PRK13165 58 QRLRVGGMVMPGSVQRDPNSLKVSFTLYDAGGSVTVTYEGILP-DLFREG-------QGIVAQGVLEE----GNHIEAKE 125 (160)
T ss_pred CEEEEeeEEeCCcEEECCCCeEEEEEEEcCCeEEEEEEcccCC-ccccCC-------CeEEEEEEECC----CCeEEEEE
Confidence 5666777777 443 223 389999999999999865431 027778 88999998854 34677766
Q ss_pred Ee
Q 044496 109 IV 110 (142)
Q Consensus 109 ~~ 110 (142)
+.
T Consensus 126 vL 127 (160)
T PRK13165 126 VL 127 (160)
T ss_pred EE
Confidence 63
No 64
>PLN02603 asparaginyl-tRNA synthetase
Probab=83.65 E-value=10 Score=35.56 Aligned_cols=74 Identities=22% Similarity=0.229 Sum_probs=51.7
Q ss_pred eEEEEEEEEEeeeCCCC--cEEEEcCCee--EEEEeccccc------cccccCCcccccceeEEEEEeeEeeccCC--Cc
Q 044496 35 QRVWLQGVLVSPPDDDG--RLLLDDGTGV--VQIYLSGDFR------IRRWNTGVFFFDFWMYVMVVGGFVIRTDD--IP 102 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~--~~~LdDgTG~--~~v~~~~~~~------~~~~~~G~~~~~~~~YVmViG~~~~~~~~--~p 102 (142)
+.|.+.|.|-++...++ =+.|.||||. +++..+.... ...+..| ..|.|-|.+..+.+. .-
T Consensus 108 ~~V~v~GwV~~iR~~g~~~Fi~l~Dgs~~~~lQ~v~~~~~~~~~~l~~~~l~~g-------s~V~V~G~v~~~~~~~~~~ 180 (565)
T PLN02603 108 KTLNVMGWVRTLRAQSSVTFIEVNDGSCLSNMQCVMTPDAEGYDQVESGLITTG-------ASVLVQGTVVSSQGGKQKV 180 (565)
T ss_pred CEEEEEEEEEEEEeCCCeEEEEEECCCCCEeEEEEEECcHHHHHHHhhcCCCCC-------CEEEEEEEEEecCCCCccE
Confidence 57889999999864433 3568999985 7777633211 1137889 999999999873222 35
Q ss_pred eEEEEEEeeCCCC
Q 044496 103 VIKVHKIVDLSAF 115 (142)
Q Consensus 103 ~i~a~K~~DLS~~ 115 (142)
.|++.++.=|+.+
T Consensus 181 EL~v~~i~vlg~a 193 (565)
T PLN02603 181 ELKVSKIVVVGKS 193 (565)
T ss_pred EEEEeEEEEEECC
Confidence 7888888777764
No 65
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=83.31 E-value=4.8 Score=28.78 Aligned_cols=50 Identities=14% Similarity=0.050 Sum_probs=34.7
Q ss_pred EEEEEEeeeCCC-CcEEEEcCCeeEEEEeccccccc-cccCCcccccceeEEEEEeeEe
Q 044496 39 LQGVLVSPPDDD-GRLLLDDGTGVVQIYLSGDFRIR-RWNTGVFFFDFWMYVMVVGGFV 95 (142)
Q Consensus 39 lQG~vv~~~~~~-~~~~LdDgTG~~~v~~~~~~~~~-~~~~G~~~~~~~~YVmViG~~~ 95 (142)
+=|.|+++.++. ...+.+.+-.+-+|++.-.+... ..++| +||+|+-++-
T Consensus 5 iP~kVi~i~~~~~~~A~vd~~Gv~r~V~l~Lv~~~~~~~~vG-------DyVLVHaGfA 56 (82)
T PRK10413 5 VPGQVLAVGEDIHQLAQVEVCGIKRDVNIALICEGNPADLLG-------QWVLVHVGFA 56 (82)
T ss_pred cceEEEEECCCCCcEEEEEcCCeEEEEEeeeeccCCcccccC-------CEEEEecchh
Confidence 347899985442 56778877666666655444333 48999 9999998873
No 66
>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=82.84 E-value=6.3 Score=35.14 Aligned_cols=64 Identities=25% Similarity=0.412 Sum_probs=48.2
Q ss_pred EeEEEEEEEEEeeeC-CC--CcEEEEcCCeeEEEEe-cccc-ccc-cccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496 34 FQRVWLQGVLVSPPD-DD--GRLLLDDGTGVVQIYL-SGDF-RIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK 105 (142)
Q Consensus 34 ~~~VWlQG~vv~~~~-~~--~~~~LdDgTG~~~v~~-~~~~-~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~ 105 (142)
|.+||++|-|.+... .. -.|.|-|....+.+.. .+.. +.. .++.| |=|.|.|.+.. ..+.-.++
T Consensus 17 ~~~v~V~GEisn~~~~~sGH~YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G-------~~V~v~g~v~~-y~~~G~~q 86 (432)
T TIGR00237 17 FLQVWIQGEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNNNRLKFRPQNG-------QQVLVRGGISV-YEPRGDYQ 86 (432)
T ss_pred CCcEEEEEEecCCeeCCCceEEEEEEcCCcEEEEEEEcChhhCCCCCCCCC-------CEEEEEEEEEE-ECCCCcEE
Confidence 679999999999853 23 3899999999998875 3333 222 48999 99999999977 66654443
No 67
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=82.31 E-value=18 Score=31.38 Aligned_cols=51 Identities=22% Similarity=0.238 Sum_probs=39.0
Q ss_pred cEEEEcCCeeEEEEe-ccccccc-cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEe
Q 044496 52 RLLLDDGTGVVQIYL-SGDFRIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIV 110 (142)
Q Consensus 52 ~~~LdDgTG~~~v~~-~~~~~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~ 110 (142)
+++|-|.||.++... +...... .+++| ++|.|-|.+.. .+..+-++...+.
T Consensus 36 ~l~l~D~tG~I~ak~W~~~~~~~~~~~~g-------~vv~v~G~v~~-y~g~~Ql~i~~i~ 88 (314)
T PRK13480 36 TLILQDKSGDIEAKLWDVSPEDEATYVPE-------TIVHVKGDIIN-YRGRKQLKVNQIR 88 (314)
T ss_pred EEEEEcCCcEEEEEeCCCChhhHhhcCCC-------CEEEEEEEEEE-ECCcceEEEEEeE
Confidence 789999999999988 4433433 59999 99999999987 6666656555443
No 68
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=81.71 E-value=5.5 Score=28.04 Aligned_cols=44 Identities=25% Similarity=0.204 Sum_probs=32.7
Q ss_pred EEEEEeeeCCCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEe
Q 044496 40 QGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFV 95 (142)
Q Consensus 40 QG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~ 95 (142)
=|+|+++ +++..+.+.+-.+-++++.-.+ +.++| +||+|+-++-
T Consensus 6 P~~V~~i--~~~~A~v~~~G~~~~v~l~lv~---~~~vG-------D~VLVH~G~A 49 (76)
T TIGR00074 6 PGQVVEI--DENIALVEFCGIKRDVSLDLVG---EVKVG-------DYVLVHVGFA 49 (76)
T ss_pred ceEEEEE--cCCEEEEEcCCeEEEEEEEeeC---CCCCC-------CEEEEecChh
Confidence 4788887 3467888888666666665543 58899 9999998873
No 69
>PRK07218 replication factor A; Provisional
Probab=81.49 E-value=7 Score=35.36 Aligned_cols=67 Identities=21% Similarity=0.288 Sum_probs=48.9
Q ss_pred eEEEEEEEEEeeeCC----CC------cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCce
Q 044496 35 QRVWLQGVLVSPPDD----DG------RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPV 103 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~----~~------~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~ 103 (142)
.+|-+-|+|+++.+. ++ ..+|-|.||++++.+ . +. ++++| +.+.+.+.+.......|.
T Consensus 69 ~~V~v~~kVl~i~~rt~r~dg~~g~v~~~~igDeTG~Ir~tlW~-~~---~l~~G-------dvv~I~na~vre~~g~~e 137 (423)
T PRK07218 69 KNVTVTGRVLTIGERSIRYQGDDHVIYEGILADETGTISYTAWK-DF---GLSPG-------DTVTIGNAGVREWDGRPE 137 (423)
T ss_pred ceeEEEEEEEEecceeEecCCCceEEEEEEEECCCCeEEEEEEC-CC---CCCCC-------CEEEEeccEeeccCCceE
Confidence 677889999998532 12 789999999999998 5 22 49999 999999877665555666
Q ss_pred EEEEEEeeC
Q 044496 104 IKVHKIVDL 112 (142)
Q Consensus 104 i~a~K~~DL 112 (142)
+.+.+-+-+
T Consensus 138 l~ig~~t~I 146 (423)
T PRK07218 138 LNIGESTTV 146 (423)
T ss_pred EeccCcceE
Confidence 665444333
No 70
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=81.33 E-value=9.2 Score=33.62 Aligned_cols=68 Identities=22% Similarity=0.427 Sum_probs=50.0
Q ss_pred EeEEEEEEEEEeeeCC-CC--cEEEEcCCeeEEEEe-cccc-ccc-cccCCcccccceeEEEEEeeEeeccCCCc--eEE
Q 044496 34 FQRVWLQGVLVSPPDD-DG--RLLLDDGTGVVQIYL-SGDF-RIR-RWNTGVFFFDFWMYVMVVGGFVIRTDDIP--VIK 105 (142)
Q Consensus 34 ~~~VWlQG~vv~~~~~-~~--~~~LdDgTG~~~v~~-~~~~-~~~-~~~~G~~~~~~~~YVmViG~~~~~~~~~p--~i~ 105 (142)
+.+||++|-|...... .| .|.|-|.+..+.+.. .+.. +.. .++.| |=|.|.|.+.. ..+.- -+.
T Consensus 23 ~~~v~v~gEis~~~~~~sGH~Yf~Lkd~~a~i~~~~~~~~~~~~~~~~~~G-------~~v~v~g~~~~-y~~~g~~ql~ 94 (438)
T PRK00286 23 LGQVWVRGEISNFTRHSSGHWYFTLKDEIAQIRCVMFKGSARRLKFKPEEG-------MKVLVRGKVSL-YEPRGDYQLI 94 (438)
T ss_pred CCcEEEEEEeCCCeeCCCCeEEEEEEcCCcEEEEEEEcChhhcCCCCCCCC-------CEEEEEEEEEE-ECCCCCEEEE
Confidence 7899999999998533 33 889999999999886 3333 322 48999 99999999986 55544 444
Q ss_pred EEEE
Q 044496 106 VHKI 109 (142)
Q Consensus 106 a~K~ 109 (142)
+.+|
T Consensus 95 v~~i 98 (438)
T PRK00286 95 VEEI 98 (438)
T ss_pred EEEe
Confidence 4444
No 71
>PRK05672 dnaE2 error-prone DNA polymerase; Validated
Probab=80.68 E-value=5.6 Score=39.69 Aligned_cols=71 Identities=25% Similarity=0.368 Sum_probs=54.4
Q ss_pred EEEEEEEEEeeeCC---C--CcEEEEcCCeeEEEEe-cccccc-cc-ccCCcccccceeEEEEEeeEeeccCCCceEEEE
Q 044496 36 RVWLQGVLVSPPDD---D--GRLLLDDGTGVVQIYL-SGDFRI-RR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVH 107 (142)
Q Consensus 36 ~VWlQG~vv~~~~~---~--~~~~LdDgTG~~~v~~-~~~~~~-~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~ 107 (142)
.|++-|+|.++... . .-+.|.|.||.+++.. +...+. +. ++.| ..+.|-|.+.. .++...+.|.
T Consensus 955 ~v~v~g~i~~~~~~~TkkGmaf~~leD~~g~~e~~ifp~~~~~~~~~l~~~-------~~~~v~g~v~~-~~~~~~~~~~ 1026 (1046)
T PRK05672 955 RVRVAGVVTHRQRPGTASGVTFLTLEDETGMVNVVVWPGLWERQRREALGA-------RLLLVRGRVQN-AEGVRHLVAD 1026 (1046)
T ss_pred EEEEEEEEEEEEEecCCCceEEEEEecCCCCEEEEECHHHHHHHHHHhccC-------CEEEEEEEEEe-cCCeEEEEEe
Confidence 48889999887432 2 3588999999999997 555433 33 8999 99999999986 4556788899
Q ss_pred EEeeCCC
Q 044496 108 KIVDLSA 114 (142)
Q Consensus 108 K~~DLS~ 114 (142)
++.+|..
T Consensus 1027 ~i~~~~~ 1033 (1046)
T PRK05672 1027 RLEDLSP 1033 (1046)
T ss_pred eeechHH
Confidence 9988854
No 72
>PRK07217 replication factor A; Reviewed
Probab=80.60 E-value=11 Score=33.11 Aligned_cols=80 Identities=15% Similarity=0.109 Sum_probs=55.4
Q ss_pred eeecCeE--EeEEEEEEEEEeeeCCCC-----cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeecc
Q 044496 27 VTLGGIL--FQRVWLQGVLVSPPDDDG-----RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRT 98 (142)
Q Consensus 27 ~~l~gl~--~~~VWlQG~vv~~~~~~~-----~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~ 98 (142)
..+..+. =++|-+-|+|++..++.. .-+|-|.||++++.. .. .....++.| +-+.+-+.+....
T Consensus 73 ~kI~Di~~~~~~VsV~aKVl~l~e~~~~si~qvGllgDETG~IkfT~W~~-s~~~~leeG-------d~~rI~na~v~ey 144 (311)
T PRK07217 73 VNIADIDEPEQWVDVTAKVVQLWEPSSDSIAQVGLLGDETGTIKFTKWAK-SDLPELEEG-------KSYLLKNVVTDEY 144 (311)
T ss_pred eeeeecCCCCCcEEEEEEEEEecCCCCCceEEEEEEEcCCceEEEEEccC-CCCCcccCC-------CEEEEEeEEEeeE
Confidence 3455443 456778999999854422 347999999999998 32 112248899 8888888887777
Q ss_pred CCCceEEEEEEeeCCC
Q 044496 99 DDIPVIKVHKIVDLSA 114 (142)
Q Consensus 99 ~~~p~i~a~K~~DLS~ 114 (142)
+..|.|...+-+-++.
T Consensus 145 ~G~~~lnlg~~t~I~~ 160 (311)
T PRK07217 145 QGRFSVKLNRTTSIEE 160 (311)
T ss_pred CCEEEEEeCCceEEEe
Confidence 7778777666555544
No 73
>PRK08402 replication factor A; Reviewed
Probab=80.34 E-value=8.4 Score=34.00 Aligned_cols=71 Identities=20% Similarity=0.329 Sum_probs=46.0
Q ss_pred eEEEEEEEEEeeeCC------CC------cEEEEcCCeeEEEEe-ccccc--cccccCCcccccceeEEEEEeeEeec-c
Q 044496 35 QRVWLQGVLVSPPDD------DG------RLLLDDGTGVVQIYL-SGDFR--IRRWNTGVFFFDFWMYVMVVGGFVIR-T 98 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~------~~------~~~LdDgTG~~~v~~-~~~~~--~~~~~~G~~~~~~~~YVmViG~~~~~-~ 98 (142)
..|-+.|+|+++.+. +| +++|-|.||.+++.+ +.... ...+++| .-|.+.|..... .
T Consensus 73 ~~V~v~~rVl~~~~~r~f~rrdG~~~~V~~i~l~DeTG~ir~TlW~~~a~~~~~~l~~G-------dvi~I~~a~V~e~~ 145 (355)
T PRK08402 73 RGVNIVGRVLRKYPPREYTKKDGSTGRVASLIIYDDTGRARVVLWDAKVAKYYNKINVG-------DVIKVIDAQVRESL 145 (355)
T ss_pred ceeeEEEEEEEccCCceeeccCCCcceEEEEEEEcCCCeEEEEEechhhhhhcccCCCC-------CEEEEECCEEeecC
Confidence 567789999998542 33 289999999999988 33221 1247888 777777666553 2
Q ss_pred CCCceEEEEEEeeC
Q 044496 99 DDIPVIKVHKIVDL 112 (142)
Q Consensus 99 ~~~p~i~a~K~~DL 112 (142)
+..|.|..-.-+-+
T Consensus 146 ~G~~eLsvg~~s~i 159 (355)
T PRK08402 146 SGLPELHINFRARI 159 (355)
T ss_pred CCcEEEEECCCceE
Confidence 55555554433333
No 74
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=80.27 E-value=18 Score=28.29 Aligned_cols=64 Identities=20% Similarity=0.316 Sum_probs=44.0
Q ss_pred eEEEEEEEEEe--ee--CC-CCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEE
Q 044496 35 QRVWLQGVLVS--PP--DD-DGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKI 109 (142)
Q Consensus 35 ~~VWlQG~vv~--~~--~~-~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~ 109 (142)
+++.+-|.|+. +. ++ .-+|.|.|+...+.|.+.+... -.++.| .-|.+.|.+.. .-.+.|.++
T Consensus 52 ~~vrvgG~V~~gSi~~~~~~~~~F~ltD~~~~i~V~Y~G~lP-d~F~eg-------~~VVv~G~~~~----~g~F~A~~v 119 (148)
T PRK13254 52 RRFRLGGLVEKGSVQRGDGLTVRFVVTDGNATVPVVYTGILP-DLFREG-------QGVVAEGRLQD----GGVFVADEV 119 (148)
T ss_pred CeEEEeEEEecCcEEeCCCCEEEEEEEeCCeEEEEEECCCCC-ccccCC-------CEEEEEEEECC----CCeEEEEEE
Confidence 45666677653 21 22 3499999999999999865421 137889 99999999954 236777776
Q ss_pred e
Q 044496 110 V 110 (142)
Q Consensus 110 ~ 110 (142)
.
T Consensus 120 L 120 (148)
T PRK13254 120 L 120 (148)
T ss_pred E
Confidence 4
No 75
>PRK06826 dnaE DNA polymerase III DnaE; Reviewed
Probab=79.83 E-value=6.1 Score=39.85 Aligned_cols=73 Identities=22% Similarity=0.379 Sum_probs=56.2
Q ss_pred eEEEEEEEEEeeeCC---CC----cEEEEcCCeeEEEEe-ccccc-ccc-ccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496 35 QRVWLQGVLVSPPDD---DG----RLLLDDGTGVVQIYL-SGDFR-IRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVI 104 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~---~~----~~~LdDgTG~~~v~~-~~~~~-~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i 104 (142)
..|.+-|+|.++... .| -+.|.|.||.+++.. +...+ -+. +..| .-|.|-|.+..+.++.+.+
T Consensus 992 ~~v~v~g~i~~~~~~~tk~G~~maf~~leD~~g~~e~~vfp~~~~~~~~~l~~~-------~~~~v~g~v~~~~~~~~~~ 1064 (1151)
T PRK06826 992 DKVIIGGIITEVKRKTTRNNEMMAFLTLEDLYGTVEVIVFPKVYEKYRSLLNED-------NIVLIKGRVSLREDEEPKL 1064 (1151)
T ss_pred cEEEEEEEEEEeEeeccCCCCeEEEEEEEECCCcEEEEECHHHHHHHHHHhccC-------CEEEEEEEEEecCCCceEE
Confidence 357889999987422 23 578999999999997 55443 233 8999 9999999997644556889
Q ss_pred EEEEEeeCCC
Q 044496 105 KVHKIVDLSA 114 (142)
Q Consensus 105 ~a~K~~DLS~ 114 (142)
.|.++.+|..
T Consensus 1065 ~~~~~~~l~~ 1074 (1151)
T PRK06826 1065 ICEEIEPLVI 1074 (1151)
T ss_pred EEeeeecHhh
Confidence 9999999876
No 76
>PRK05673 dnaE DNA polymerase III subunit alpha; Validated
Probab=79.44 E-value=6 Score=39.80 Aligned_cols=72 Identities=24% Similarity=0.351 Sum_probs=55.5
Q ss_pred eEEEEEEEEEeeeCC---CC----cEEEEcCCeeEEEEe-cccc-cccc-ccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496 35 QRVWLQGVLVSPPDD---DG----RLLLDDGTGVVQIYL-SGDF-RIRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVI 104 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~---~~----~~~LdDgTG~~~v~~-~~~~-~~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i 104 (142)
..|.+-|+|.++... .| .+.|.|.||.+++.. +... +.+. ++.| ..|.|-|.+.. .++.+.+
T Consensus 978 ~~V~v~G~I~~vk~~~TKkG~~mafltLeD~TG~iEvviFp~~ye~~~~~L~~g-------~iV~V~GkVe~-~~~~~ql 1049 (1135)
T PRK05673 978 SVVTVAGLVVSVRRRVTKRGNKMAIVTLEDLSGRIEVMLFSEALEKYRDLLEED-------RIVVVKGQVSF-DDGGLRL 1049 (1135)
T ss_pred ceEEEEEEEEEEEecccCCCCeEEEEEEEeCCCcEEEEECHHHHHHHHHHhccC-------CEEEEEEEEEe-cCCeEEE
Confidence 357889999988432 33 488999999999997 5543 3334 8999 99999999976 4457888
Q ss_pred EEEEEeeCCC
Q 044496 105 KVHKIVDLSA 114 (142)
Q Consensus 105 ~a~K~~DLS~ 114 (142)
.+.++.+|.+
T Consensus 1050 ii~~I~~L~~ 1059 (1135)
T PRK05673 1050 TAREVMDLEE 1059 (1135)
T ss_pred EEeecccHHH
Confidence 8998888865
No 77
>PRK06461 single-stranded DNA-binding protein; Reviewed
Probab=78.62 E-value=10 Score=28.42 Aligned_cols=54 Identities=19% Similarity=0.209 Sum_probs=38.9
Q ss_pred cEEEEcCCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE---EeeCCC
Q 044496 52 RLLLDDGTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK---IVDLSA 114 (142)
Q Consensus 52 ~~~LdDgTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K---~~DLS~ 114 (142)
.++|-|.||.+.+.+ .... ..+++| +.|.|.+.........+.|.+.+ |..+++
T Consensus 43 ~~~l~D~TG~I~~tlW~~~a--~~l~~G-------dvV~I~na~v~~f~G~lqL~i~~~~~i~~~~~ 100 (129)
T PRK06461 43 EAVVGDETGRVKLTLWGEQA--GSLKEG-------EVVEIENAWTTLYRGKVQLNVGKYGSISESDD 100 (129)
T ss_pred EEEEECCCCEEEEEEeCCcc--ccCCCC-------CEEEEECcEEeeeCCEEEEEECCCEEEEECCc
Confidence 379999999999988 4321 148899 99999976655467777888774 444443
No 78
>PRK06386 replication factor A; Reviewed
Probab=78.61 E-value=6.2 Score=35.07 Aligned_cols=58 Identities=21% Similarity=0.244 Sum_probs=38.7
Q ss_pred cEEEEcCCeeEEEEecccc------------c-----------cccccCCcccccceeEEEEEeeEeec-cCCCceEEEE
Q 044496 52 RLLLDDGTGVVQIYLSGDF------------R-----------IRRWNTGVFFFDFWMYVMVVGGFVIR-TDDIPVIKVH 107 (142)
Q Consensus 52 ~~~LdDgTG~~~v~~~~~~------------~-----------~~~~~~G~~~~~~~~YVmViG~~~~~-~~~~p~i~a~ 107 (142)
.++||||||.+.+.+..+. + .+.--.| .|..|-|.+..+ .+-....+.+
T Consensus 266 k~vLDDGtg~~~~~l~~e~~e~l~G~~lee~~~~a~~~~~~~~i~~~llG-------r~~~v~G~~~~~~~~~~~~~~~~ 338 (358)
T PRK06386 266 YFTISDGTGFVTCYANKDSFLPYININENEFARKASSMNPNMLIKKNLLG-------KCFSVTGDLRKKDDEIDMNVISA 338 (358)
T ss_pred EEEEECCCCeEEEEEChHHhHHHhCCCHHHHHHHhhccCHHHHhhhhhcc-------cEEEEEcceEeccCCeEEEEEEe
Confidence 4799999999999983321 1 0122468 999999999873 2224555666
Q ss_pred EEeeCCCCc
Q 044496 108 KIVDLSAFP 116 (142)
Q Consensus 108 K~~DLS~~p 116 (142)
+.+|.++..
T Consensus 339 ~~~~~~~~~ 347 (358)
T PRK06386 339 KSITADEIK 347 (358)
T ss_pred eeccchhhh
Confidence 667766643
No 79
>PF13567 DUF4131: Domain of unknown function (DUF4131)
Probab=78.58 E-value=15 Score=25.95 Aligned_cols=56 Identities=29% Similarity=0.376 Sum_probs=36.4
Q ss_pred eEEEEEEEEEeeeCC--CC-cEEEEc-----------CCeeEEEEeccccccccccCCcccccceeEEEEEeeEeecc
Q 044496 35 QRVWLQGVLVSPPDD--DG-RLLLDD-----------GTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRT 98 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~--~~-~~~LdD-----------gTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~ 98 (142)
+.+.++|+|.+.... ++ ++.+.. -+|++.+....+... .+.+| +++.+-|.+....
T Consensus 76 ~~~~v~g~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~-~l~~G-------d~i~~~g~l~~~~ 145 (176)
T PF13567_consen 76 KEVTVQGTVESVPQIDGRGQRFTLRVERVLAGGNWIPVSGKILLYLPKDSQP-RLQPG-------DRIRVRGKLKPPS 145 (176)
T ss_pred ceEEEEEEEcccccccCceEEEEEEEEEeeccccccccceeeEEEecccccc-ccCCC-------CEEEEEEEEecCC
Confidence 456699999998533 22 456541 155555555433322 58999 9999999998743
No 80
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=78.49 E-value=20 Score=33.81 Aligned_cols=73 Identities=16% Similarity=0.069 Sum_probs=52.7
Q ss_pred EEEEEEEEEeeeCCCC--cE-EEEcCCeeEEEEecccc--------cc--ccccCCcccccceeEEEEEeeEeeccCCCc
Q 044496 36 RVWLQGVLVSPPDDDG--RL-LLDDGTGVVQIYLSGDF--------RI--RRWNTGVFFFDFWMYVMVVGGFVIRTDDIP 102 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~--~~-~LdDgTG~~~v~~~~~~--------~~--~~~~~G~~~~~~~~YVmViG~~~~~~~~~p 102 (142)
.|-+.|+|.++..-+. .| .|.|.+|.++|..+... .. ..+..| +.|-|.|.+......+.
T Consensus 134 ~v~v~Grv~~~R~~G~k~~F~~L~d~~g~iQv~~~~~~~~~~~~~~~~~~~~l~~G-------d~V~V~G~~~~t~~gel 206 (585)
T PTZ00417 134 ILNVTGRIMRVSASGQKLRFFDLVGDGAKIQVLANFAFHDHTKSNFAECYDKIRRG-------DIVGIVGFPGKSKKGEL 206 (585)
T ss_pred eEEEEEEEEeeecCCCCCEEEEEEeCCeeEEEEEECCccCCCHHHHHHHHhcCCCC-------CEEEEEeEEcCCCCceE
Confidence 3778999999965542 34 45588899998874321 11 247788 99999999876435578
Q ss_pred eEEEEEEeeCCCC
Q 044496 103 VIKVHKIVDLSAF 115 (142)
Q Consensus 103 ~i~a~K~~DLS~~ 115 (142)
.|.|.++.=||.+
T Consensus 207 ~i~~~~i~llsk~ 219 (585)
T PTZ00417 207 SIFPKETIILSPC 219 (585)
T ss_pred EEEEEEEEEEecC
Confidence 8899999888864
No 81
>PRK14699 replication factor A; Provisional
Probab=77.94 E-value=12 Score=34.39 Aligned_cols=74 Identities=20% Similarity=0.205 Sum_probs=47.7
Q ss_pred ceeecCeE--EeEEEEEEEEEeeeCC------CC------cEEEEcCCeeEEEEe-ccccc---cccccCCcccccceeE
Q 044496 26 AVTLGGIL--FQRVWLQGVLVSPPDD------DG------RLLLDDGTGVVQIYL-SGDFR---IRRWNTGVFFFDFWMY 87 (142)
Q Consensus 26 ~~~l~gl~--~~~VWlQG~vv~~~~~------~~------~~~LdDgTG~~~v~~-~~~~~---~~~~~~G~~~~~~~~Y 87 (142)
.+.+..+. =.+|-+.|+|+++.+. +| ++.|-|.||++++.+ +.... ...+++| +.
T Consensus 57 ~~kI~di~~~~~~v~i~~rVl~i~~~r~f~r~dG~~g~v~~~~iaDeTG~ir~tlW~~~a~~~~~g~l~~G-------Dv 129 (484)
T PRK14699 57 SVKIENITPESGPVNFIARVVSVFDTKEFTRNDGTIGRVGNLIVGDETGKIKLTLWDNMADLIKAGKIKAG-------QT 129 (484)
T ss_pred cccHhHccCCCceEEEEEEEEEecCceEEecCCCCceEEEEEEEecCCCeEEEEEecCccchhhhcCCCCC-------CE
Confidence 34444333 2457789999998521 12 678999999999999 43322 1248999 99
Q ss_pred EEEEeeEeeccCCCceEEEE
Q 044496 88 VMVVGGFVIRTDDIPVIKVH 107 (142)
Q Consensus 88 VmViG~~~~~~~~~p~i~a~ 107 (142)
|-+-|.++...+ .+.|.+.
T Consensus 130 v~I~~~~r~~~~-g~el~~~ 148 (484)
T PRK14699 130 LQISGYAKQGYS-GVEVNIG 148 (484)
T ss_pred EEEcceeccCCC-CceEEeC
Confidence 999886544232 3555544
No 82
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=77.81 E-value=9.2 Score=27.87 Aligned_cols=48 Identities=19% Similarity=0.120 Sum_probs=34.5
Q ss_pred EEEEEEeeeCCCCcEEEEcCCeeEEEEeccccc---cccccCCcccccceeEEEEEeeEe
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFR---IRRWNTGVFFFDFWMYVMVVGGFV 95 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~---~~~~~~G~~~~~~~~YVmViG~~~ 95 (142)
+=|+|+++ +++..+.|-+..+-+|++.-.+. ..+.++| +||+|+-++-
T Consensus 5 iP~kVv~i--~~~~A~vd~~Gv~reV~l~Lv~~~~~~~~~~vG-------DyVLVHaGfA 55 (90)
T PRK10409 5 VPGQIRTI--DGNQAKVDVCGIQRDVDLTLVGSCDENGQPRVG-------QWVLVHVGFA 55 (90)
T ss_pred cceEEEEE--cCCeEEEEcCCeEEEEEEeeecccCCCCccCCC-------CEEEEecChH
Confidence 34789997 34578888887776777644432 2368999 9999999873
No 83
>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=75.34 E-value=24 Score=24.35 Aligned_cols=65 Identities=17% Similarity=0.169 Sum_probs=44.3
Q ss_pred EEEEEEEEeeeCC---CC----cEEEEcCCeeEEEEe-c-ccccc-cccc-CCcccccceeEEEEEeeEeec-cCCCceE
Q 044496 37 VWLQGVLVSPPDD---DG----RLLLDDGTGVVQIYL-S-GDFRI-RRWN-TGVFFFDFWMYVMVVGGFVIR-TDDIPVI 104 (142)
Q Consensus 37 VWlQG~vv~~~~~---~~----~~~LdDgTG~~~v~~-~-~~~~~-~~~~-~G~~~~~~~~YVmViG~~~~~-~~~~p~i 104 (142)
|-++|.|..+... .| ++-+-|.|+.+.+.. . ...+. ..++ .| ++|.+-|.+.-. ...+.++
T Consensus 2 v~i~G~Vf~~e~re~k~g~~i~~~~itD~t~Si~~K~F~~~~~~~~~~ik~~G-------~~v~v~G~v~~D~f~~e~~~ 74 (82)
T cd04484 2 VVVEGEVFDLEIRELKSGRKILTFKVTDYTSSITVKKFLRKDEKDKEELKSKG-------DWVRVRGKVQYDTFSKELVL 74 (82)
T ss_pred EEEEEEEEEEEEEEecCCCEEEEEEEEcCCCCEEEEEeccCChhHHhhcccCC-------CEEEEEEEEEEccCCCceEE
Confidence 5689999988542 33 567889999998886 3 22222 2488 99 999999998752 2345555
Q ss_pred EEEE
Q 044496 105 KVHK 108 (142)
Q Consensus 105 ~a~K 108 (142)
.+-.
T Consensus 75 ~i~~ 78 (82)
T cd04484 75 MIND 78 (82)
T ss_pred Eeee
Confidence 4433
No 84
>PRK07374 dnaE DNA polymerase III subunit alpha; Validated
Probab=74.14 E-value=10 Score=38.45 Aligned_cols=72 Identities=15% Similarity=0.149 Sum_probs=55.3
Q ss_pred eEEEEEEEEEeeeCC---CC----cEEEEcCCeeEEEEe-cccccc-cc-ccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496 35 QRVWLQGVLVSPPDD---DG----RLLLDDGTGVVQIYL-SGDFRI-RR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVI 104 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~---~~----~~~LdDgTG~~~v~~-~~~~~~-~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i 104 (142)
++|.+-|.|.++... .| -+.|.|.||.+++.. +...+. +. ++.| .-+.|-|.+.. .++.+.+
T Consensus 1001 ~~v~v~g~i~~~k~~~Tk~G~~maf~~leD~tg~~e~vvFp~~y~~~~~~l~~~-------~~~~v~g~v~~-~~~~~~~ 1072 (1170)
T PRK07374 1001 AKVSAIAMIPEMKQVTTRKGDRMAILQLEDLTGSCEAVVFPKSYERLSDHLMTD-------TRLLVWAKVDR-RDDRVQL 1072 (1170)
T ss_pred CEEEEEEEEEEeEecccCCCCEEEEEEEEECCCCEEEEECHHHHHHHHHHhccC-------CEEEEEEEEEe-cCCeEEE
Confidence 468899999987322 22 589999999999997 555443 33 8999 99999999976 4456788
Q ss_pred EEEEEeeCCC
Q 044496 105 KVHKIVDLSA 114 (142)
Q Consensus 105 ~a~K~~DLS~ 114 (142)
.+.++.+|.+
T Consensus 1073 ~~~~i~~l~~ 1082 (1170)
T PRK07374 1073 IIDDCREIDD 1082 (1170)
T ss_pred EEeeeecHhh
Confidence 8899988865
No 85
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=71.47 E-value=33 Score=33.24 Aligned_cols=55 Identities=25% Similarity=0.385 Sum_probs=42.4
Q ss_pred eEEEEEEEEEeeeCC-CC-----cEEEEcCCeeEEEEe-ccc-cccccccCCcccccceeEEEEEeeEee
Q 044496 35 QRVWLQGVLVSPPDD-DG-----RLLLDDGTGVVQIYL-SGD-FRIRRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~-~~-----~~~LdDgTG~~~v~~-~~~-~~~~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
..|.++|+|.+.... ++ ++.+-||||.+.+.. +.. .-.+.++.| .=|++.|.+..
T Consensus 61 ~~vti~g~V~~~~~~~~~~~~~l~v~~~d~~~~l~l~fFn~~~~l~~~~~~G-------~~v~v~Gk~~~ 123 (677)
T COG1200 61 EIVTIEGTVLSHEKFPFGKRKLLKVTLSDGTGVLTLVFFNFPAYLKKKLKVG-------ERVIVYGKVKR 123 (677)
T ss_pred ceEEEEEEEEeeeccCCCCCceEEEEEecCcEEEEEEEECccHHHHhhCCCC-------CEEEEEEEEee
Confidence 467799999887533 11 788999999999986 443 233458999 99999999976
No 86
>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=71.41 E-value=31 Score=23.81 Aligned_cols=58 Identities=17% Similarity=0.243 Sum_probs=37.4
Q ss_pred EEEEEEeeeCCC--CcEEEEcCCe--------eEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEE
Q 044496 39 LQGVLVSPPDDD--GRLLLDDGTG--------VVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVH 107 (142)
Q Consensus 39 lQG~vv~~~~~~--~~~~LdDgTG--------~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~ 107 (142)
++|+|....... +-|-|-|.++ -+-+..++ ...+++| +-|.|-|.+.. ......|.+.
T Consensus 2 v~GvVTa~~~~~~~~GffiQd~~~d~~~~ts~gifV~~~~---~~~~~~G-------d~V~vtG~v~e-y~g~tql~~~ 69 (78)
T cd04486 2 VEGVVTAVFSGGGLGGFYIQDEDGDGDPATSEGIFVYTGS---GADVAVG-------DLVRVTGTVTE-YYGLTQLTAV 69 (78)
T ss_pred eEEEEEEEcCCCCcCEEEEEcCCCCCCCcccceEEEecCC---CCCCCCC-------CEEEEEEEEEe-eCCeEEEccC
Confidence 689999986553 5666777632 23333332 2348999 99999999966 5444444443
No 87
>PRK06920 dnaE DNA polymerase III DnaE; Reviewed
Probab=70.49 E-value=13 Score=37.57 Aligned_cols=71 Identities=13% Similarity=0.099 Sum_probs=54.6
Q ss_pred EEEEEEEEEeeeC---CCC----cEEEEcCCeeEEEEe-ccccc-ccc-ccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496 36 RVWLQGVLVSPPD---DDG----RLLLDDGTGVVQIYL-SGDFR-IRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK 105 (142)
Q Consensus 36 ~VWlQG~vv~~~~---~~~----~~~LdDgTG~~~v~~-~~~~~-~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~ 105 (142)
.|.+-|.|+++.. ..| -+.|.|.||.+++.. +...+ -+. +..| .-+.|-|.+.. .++.+.+.
T Consensus 945 ~v~v~g~i~~~~~~~tk~g~~maf~~leD~tg~~e~~vFp~~y~~~~~~l~~~-------~~~~v~G~v~~-~~~~~~~~ 1016 (1107)
T PRK06920 945 VQRAIVYITSVKVIRTKKGQKMAFITFCDQNDEMEAVVFPETYIHFSDKLQEG-------AIVLVDGTIEL-RNHKLQWI 1016 (1107)
T ss_pred EEEEEEEEEEeEeecCCCCCeEEEEEEeeCCCcEEEEECHHHHHHHHHHhccC-------CEEEEEEEEEe-cCCcEEEE
Confidence 5889999998732 122 589999999999997 55443 233 8999 99999999976 45677888
Q ss_pred EEEEeeCCC
Q 044496 106 VHKIVDLSA 114 (142)
Q Consensus 106 a~K~~DLS~ 114 (142)
+-++.+|..
T Consensus 1017 ~~~i~~l~~ 1025 (1107)
T PRK06920 1017 VNGLYPLEE 1025 (1107)
T ss_pred EeecccHHH
Confidence 889988864
No 88
>PF07210 DUF1416: Protein of unknown function (DUF1416); InterPro: IPR010814 This family consists of several hypothetical bacterial proteins of around 100 residues in length. Members of this family appear to be Actinomycete specific. The function of this family is unknown.
Probab=69.85 E-value=7.9 Score=28.26 Aligned_cols=30 Identities=13% Similarity=0.169 Sum_probs=23.3
Q ss_pred EEEEEEEEeeeC--CCCcEEEEcCCeeEEEEe
Q 044496 37 VWLQGVLVSPPD--DDGRLLLDDGTGVVQIYL 66 (142)
Q Consensus 37 VWlQG~vv~~~~--~~~~~~LdDgTG~~~v~~ 66 (142)
.-+||+|..--+ .+...+|-|+||.|....
T Consensus 8 ~VItG~V~~~G~Pv~gAyVRLLD~sgEFtaEv 39 (85)
T PF07210_consen 8 TVITGRVTRDGEPVGGAYVRLLDSSGEFTAEV 39 (85)
T ss_pred EEEEEEEecCCcCCCCeEEEEEcCCCCeEEEE
Confidence 449999994311 267899999999998886
No 89
>PRK14699 replication factor A; Provisional
Probab=69.07 E-value=21 Score=32.76 Aligned_cols=56 Identities=21% Similarity=0.379 Sum_probs=40.1
Q ss_pred EeEEEEEEEEEeeeC------CCC------cEEEEcCCeeEEEEe-cccccc-ccccCCcccccceeEEEEEeeEee
Q 044496 34 FQRVWLQGVLVSPPD------DDG------RLLLDDGTGVVQIYL-SGDFRI-RRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 34 ~~~VWlQG~vv~~~~------~~~------~~~LdDgTG~~~v~~-~~~~~~-~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
-+.+-+.|+|+++.+ ++| +++|.|+||++++.+ +..... ..++.| .++-+.+.+..
T Consensus 286 ~~~v~I~grV~~~~~~r~~~~~~Gseg~v~~~~l~DeTG~Ir~T~W~~~a~~~~~i~~G-------d~v~i~~~y~~ 355 (484)
T PRK14699 286 MNNINISGRVLDISEVRTFEKKDGSPGRVGNLLLGDSTGKIRLTLWDEKTNFLDEIDFD-------ETVEVLNAYSR 355 (484)
T ss_pred CceeEEEEEEEEcCCCeEEEcCCCCeeEEEEEEEECCCCeEEEEEeCcccccccccCCC-------ceEEEEeEEEE
Confidence 367889999998854 122 689999999999998 322222 247788 88887777765
No 90
>PRK12366 replication factor A; Reviewed
Probab=69.00 E-value=28 Score=32.76 Aligned_cols=76 Identities=18% Similarity=0.235 Sum_probs=48.7
Q ss_pred EEEEEEEEEeeeCC------CC------cEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCce
Q 044496 36 RVWLQGVLVSPPDD------DG------RLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPV 103 (142)
Q Consensus 36 ~VWlQG~vv~~~~~------~~------~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~ 103 (142)
.|=+-|+|.++.+. +| .++|-|+||++++.+=++.....+.+| ..+.+.|.....-+..+.
T Consensus 410 ~VdVig~V~~v~~~~~i~~k~G~~~~~r~i~l~D~TG~I~vtlWg~~a~~~~~~G-------~vi~i~~~~V~~~~g~~~ 482 (637)
T PRK12366 410 DITVIARVVEDYPVNEFERSDGSKGKVRNIELADGTGSIRLTLWDDDAEIEIKEG-------DAIKILHPYVKENGDYLD 482 (637)
T ss_pred EEEEEEEEEEccCceEEEecCCCEeEEEEEEEEeCCCEEEEEEeccccccCCCCC-------CEEEEEeeEEEeCCCeeE
Confidence 45567888876332 12 577999999999998222223357889 888888877764555555
Q ss_pred EEEEEEeeCCCCcCc
Q 044496 104 IKVHKIVDLSAFPDR 118 (142)
Q Consensus 104 i~a~K~~DLS~~p~r 118 (142)
|..-.-+.+.-+|+.
T Consensus 483 Ls~~~~s~i~~~p~~ 497 (637)
T PRK12366 483 LSIGRYGRIEINPEG 497 (637)
T ss_pred EEecCcceEEECCCC
Confidence 655444444445543
No 91
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=68.64 E-value=17 Score=33.20 Aligned_cols=73 Identities=21% Similarity=0.337 Sum_probs=47.7
Q ss_pred EeEEEEEEEEEeee--CCCC--cEEEEcCCeeEEEEe---cccccc--ccccCCcccccceeEEEEEeeEeeccCCCceE
Q 044496 34 FQRVWLQGVLVSPP--DDDG--RLLLDDGTGVVQIYL---SGDFRI--RRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVI 104 (142)
Q Consensus 34 ~~~VWlQG~vv~~~--~~~~--~~~LdDgTG~~~v~~---~~~~~~--~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i 104 (142)
.+..-++|+|+... ..+| -+.+-||+|.+.+-- -..++. +.+.+| +.|-++|.+....=+.--+
T Consensus 266 ~~~~~v~g~v~~~p~~ieGghv~v~i~d~~G~I~~~A~eptk~fr~~a~~L~pG-------D~i~~~G~~~~~~~n~ek~ 338 (421)
T COG1571 266 YSKYRVVGRVEAEPRAIEGGHVVVEITDGEGEIGAVAFEPTKEFRELARKLIPG-------DEITVYGSVKPGTLNLEKF 338 (421)
T ss_pred ccceEEEEEEecccEEeeCCEEEEEecCCCceEEEEEecccccchHHHHhcCCC-------CEEEEecCccccceeEEEE
Confidence 56788999998863 2344 455667999776653 333333 359999 9999999997744223344
Q ss_pred EEEEEeeCC
Q 044496 105 KVHKIVDLS 113 (142)
Q Consensus 105 ~a~K~~DLS 113 (142)
+++|+.+..
T Consensus 339 ~v~~l~~~~ 347 (421)
T COG1571 339 QVLKLARYE 347 (421)
T ss_pred EEEEeeeeE
Confidence 556665533
No 92
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=68.23 E-value=23 Score=28.23 Aligned_cols=63 Identities=16% Similarity=0.205 Sum_probs=41.9
Q ss_pred eEEEEEEEEE--eee--CC--CCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496 35 QRVWLQGVLV--SPP--DD--DGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK 108 (142)
Q Consensus 35 ~~VWlQG~vv--~~~--~~--~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K 108 (142)
+++.+=|.|+ |+. .+ .-+|.+-|+...+.|.+++... --++.| .=|.+.|.+. + -+..|.+
T Consensus 52 ~~~RlGG~V~~GSv~r~~~~~~v~F~vtD~~~~v~V~Y~GilP-DlFrEG-------qgVVaeG~~~---~--g~F~A~~ 118 (155)
T PRK13159 52 QQFRLGGMVKAGSIQRAADSLKVSFTVIDKNAATQVEYTGILP-DLFRDN-------QSVIANGRMQ---G--GRFVANE 118 (155)
T ss_pred CeEEEccEEecCcEEEcCCCcEEEEEEEcCCcEEEEEEccCCC-ccccCC-------CeEEEEEEEc---C--CEEEEeE
Confidence 5666666666 442 22 2399999999999999866431 026777 7788888884 1 3666666
Q ss_pred Ee
Q 044496 109 IV 110 (142)
Q Consensus 109 ~~ 110 (142)
+.
T Consensus 119 vL 120 (155)
T PRK13159 119 VL 120 (155)
T ss_pred EE
Confidence 53
No 93
>TIGR00643 recG ATP-dependent DNA helicase RecG.
Probab=65.07 E-value=21 Score=33.06 Aligned_cols=54 Identities=22% Similarity=0.270 Sum_probs=39.3
Q ss_pred EEEEEEEEEeeeC--CC----CcEEEEc-CCeeEEEEe-ccccccccccCCcccccceeEEEEEeeEee
Q 044496 36 RVWLQGVLVSPPD--DD----GRLLLDD-GTGVVQIYL-SGDFRIRRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 36 ~VWlQG~vv~~~~--~~----~~~~LdD-gTG~~~v~~-~~~~~~~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
.+-++|+|++... .. -.+.+.| +||.+.+.. +...-.+.+++| ..+++.|.+..
T Consensus 34 ~~~~~~~v~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~F~~~~~~~~~~~g-------~~~~~~Gk~~~ 95 (630)
T TIGR00643 34 RATIVGEVLSHCIFGFKRRKVLKLRLKDGGYKKLELRFFNRAFLKKKFKVG-------SKVVVYGKVKS 95 (630)
T ss_pred EEEEEEEEEEeEeccCCCCceEEEEEEECCCCEEEEEEECCHHHHhhCCCC-------CEEEEEEEEEe
Confidence 4667888876421 11 2789999 999998886 532223459999 99999999965
No 94
>KOG3416 consensus Predicted nucleic acid binding protein [General function prediction only]
Probab=64.92 E-value=42 Score=26.39 Aligned_cols=69 Identities=17% Similarity=0.206 Sum_probs=45.2
Q ss_pred HHHHHHhhccCCCCCCceeecCeEEeE-EEEEEEEEeeeCCCC--cEEEEcCCeeEEEEeccccccccccCCccccccee
Q 044496 10 LLCVQLKDARESPSQNAVTLGGILFQR-VWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWM 86 (142)
Q Consensus 10 vf~~QL~~a~~~~s~~~~~l~gl~~~~-VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~ 86 (142)
+|+++|+.+.+. +.+.. |-.-|+..++.+++. ++.+-|.||.+.+..=.+ .+..+++| +
T Consensus 5 i~ikdi~P~~kN----------~~v~fIvl~~g~~tkTkdg~~v~~~kVaD~TgsI~isvW~e-~~~~~~PG-------D 66 (134)
T KOG3416|consen 5 IFIKDIKPGLKN----------INVTFIVLEYGRATKTKDGHEVRSCKVADETGSINISVWDE-EGCLIQPG-------D 66 (134)
T ss_pred hhHhhcChhhhc----------ceEEEEEEeeceeeeccCCCEEEEEEEecccceEEEEEecC-cCcccCCc-------c
Confidence 566677666332 22222 334577777644433 788999999999998332 23468999 8
Q ss_pred EEEEEeeEee
Q 044496 87 YVMVVGGFVI 96 (142)
Q Consensus 87 YVmViG~~~~ 96 (142)
.+..-|++.+
T Consensus 67 IirLt~Gy~S 76 (134)
T KOG3416|consen 67 IIRLTGGYAS 76 (134)
T ss_pred EEEecccchh
Confidence 8888888765
No 95
>PF12483 GIDE: E3 Ubiquitin ligase; InterPro: IPR022170 This domain family is found in bacteria, archaea and eukaryotes, and is typically between 150 and 163 amino acids in length. There is a single completely conserved residue E that may be functionally important. GIDE is an E3 ubiquitin ligase which is involved in inducing apoptosis. ; GO: 0016881 acid-amino acid ligase activity
Probab=64.65 E-value=25 Score=26.64 Aligned_cols=16 Identities=38% Similarity=0.711 Sum_probs=12.9
Q ss_pred CCCcEEEEcCCeeEEE
Q 044496 49 DDGRLLLDDGTGVVQI 64 (142)
Q Consensus 49 ~~~~~~LdDgTG~~~v 64 (142)
....|.|+|+||.+.|
T Consensus 27 ~~vPF~L~D~tg~v~V 42 (160)
T PF12483_consen 27 SEVPFYLEDGTGRVRV 42 (160)
T ss_pred eEcCEEEECCceEEEE
Confidence 4567888888888888
No 96
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=63.63 E-value=24 Score=33.12 Aligned_cols=55 Identities=20% Similarity=0.256 Sum_probs=40.5
Q ss_pred eEEEEEEEEEeeeCC-----CCcEEEEcCCeeEEEEe-c-cccc-cccccCCcccccceeEEEEEeeEee
Q 044496 35 QRVWLQGVLVSPPDD-----DGRLLLDDGTGVVQIYL-S-GDFR-IRRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~-----~~~~~LdDgTG~~~v~~-~-~~~~-~~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
+.|.+.|+|++.... --.+.+.||||.+.+.. + +-+- .+.+++| .-+.|.|.+..
T Consensus 60 ~~vtv~g~V~~~~~~~~~~~~~~v~l~D~tg~i~l~~F~~n~~~~~~~l~~G-------~~~~v~Gkv~~ 122 (681)
T PRK10917 60 EKVTVEGEVLSAEVVFGKRRRLTVTVSDGTGNLTLRFFNFNQPYLKKQLKVG-------KRVAVYGKVKR 122 (681)
T ss_pred CEEEEEEEEEEEEEccCCceEEEEEEEECCeEEEEEEEccCcHHHHhhCCCC-------CEEEEEEEEEe
Confidence 467789999887322 13789999999988875 3 2232 2358999 99999999965
No 97
>PRK07211 replication factor A; Reviewed
Probab=61.53 E-value=52 Score=30.56 Aligned_cols=65 Identities=31% Similarity=0.467 Sum_probs=44.4
Q ss_pred eEEEEEEEEEeeeC------CCC------cEEEEcCCeeEEEEe-cccccc-ccccCCcccccceeEEEEEeeEeeccCC
Q 044496 35 QRVWLQGVLVSPPD------DDG------RLLLDDGTGVVQIYL-SGDFRI-RRWNTGVFFFDFWMYVMVVGGFVIRTDD 100 (142)
Q Consensus 35 ~~VWlQG~vv~~~~------~~~------~~~LdDgTG~~~v~~-~~~~~~-~~~~~G~~~~~~~~YVmViG~~~~~~~~ 100 (142)
++|-+-|+|.++.+ ++| ++.|-|.||++++.+ +..... ..+++| +.+.+.+........
T Consensus 172 ~~v~I~grV~~v~~iRtf~r~dGseGkv~sv~L~DeTG~IR~TlW~d~Ad~~~~le~G-------~Vv~I~~a~Vre~~g 244 (485)
T PRK07211 172 SDVTLVGVVLDTDSVRTFDRDDGSEGRVSNLTVGDETGRVRVTLWDDRADLAEELDAG-------ESVEIVDGYVRERDG 244 (485)
T ss_pred CceEEEEEEEEcCCCeEEECCCCCeeEEEEEEEEcCCCeEEEEEechhhhhhccCCCC-------CEEEEEeeEEEecCC
Confidence 45678899997743 232 789999999999998 432222 238899 888888766554445
Q ss_pred CceEEE
Q 044496 101 IPVIKV 106 (142)
Q Consensus 101 ~p~i~a 106 (142)
.+.|..
T Consensus 245 ~~ELsl 250 (485)
T PRK07211 245 SLELHV 250 (485)
T ss_pred cEEEEE
Confidence 665543
No 98
>COG1190 LysU Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=61.48 E-value=96 Score=29.13 Aligned_cols=91 Identities=22% Similarity=0.277 Sum_probs=64.6
Q ss_pred EEEEEEEEeeeCCC--CcEEEEcCCeeEEEEecccc------c--cccccCCcccccceeEEEEEeeEeeccCCCceEEE
Q 044496 37 VWLQGVLVSPPDDD--GRLLLDDGTGVVQIYLSGDF------R--IRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKV 106 (142)
Q Consensus 37 VWlQG~vv~~~~~~--~~~~LdDgTG~~~v~~~~~~------~--~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a 106 (142)
|-+-|+|+....-+ .=+.|.|++|.+++..+.+. . .+-|..| ++|=|-|.+-.....+-.+.|
T Consensus 64 v~vAGRi~~~R~~GK~~F~~i~d~~gkiQ~yi~k~~~~~~~~~~~~~~~dlG-------Diigv~G~~~~T~~GelSv~v 136 (502)
T COG1190 64 VSVAGRIMTIRNMGKASFADLQDGSGKIQLYVNKDEVGEEVFEALFKKLDLG-------DIIGVEGPLFKTKTGELSVSV 136 (502)
T ss_pred eEEecceeeecccCceeEEEEecCCceEEEEEeccccchhhHHHHHhccccC-------CEEeeeeeeeecCCCceEEEE
Confidence 77889999985332 36789999999999985432 1 1136789 999999999885568999999
Q ss_pred EEEeeCCCC--cCccchhHH-HHHHHHHHHh
Q 044496 107 HKIVDLSAF--PDREAMWYL-EVMEAYKLFY 134 (142)
Q Consensus 107 ~K~~DLS~~--p~re~mW~l-EV~e~~~~~y 134 (142)
-.+.-||.+ |.-|..=.| +++--||.=|
T Consensus 137 ~~~~lLsKsL~pLPeK~hgL~D~E~RyR~Ry 167 (502)
T COG1190 137 EELRLLSKSLRPLPEKFHGLTDKEIRYRQRY 167 (502)
T ss_pred EEEeeecccCCCCChhhcCCccHHHHHHHHH
Confidence 999999985 555544433 2333344433
No 99
>PRK15491 replication factor A; Provisional
Probab=61.06 E-value=39 Score=29.89 Aligned_cols=55 Identities=20% Similarity=0.243 Sum_probs=39.9
Q ss_pred eEEEEEEEEEeeeCC------CC------cEEEEcCCeeEEEEe-cccccc---ccccCCcccccceeEEEEEeeEee
Q 044496 35 QRVWLQGVLVSPPDD------DG------RLLLDDGTGVVQIYL-SGDFRI---RRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~------~~------~~~LdDgTG~~~v~~-~~~~~~---~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
++|-+.|+|+++.+. +| +++|-|.||.+++.+ +..... ..+++| +.+.+-|....
T Consensus 68 ~~v~i~arVl~~~~~R~f~r~dGs~g~v~~~~v~DeTG~ir~tlW~~~a~~~~~~~le~G-------~v~~I~~~~~~ 138 (374)
T PRK15491 68 SNVNFTAKVVSIFEPKEFNRNDGTTGRVGNIIVADETGSIRLTLWDDLADLIKTGDIEVG-------KSLNISGYAKE 138 (374)
T ss_pred CceEEEEEEeeccCCeeeecCCCCceEEEEEEEEcCCCeEEEEEECchhhhhccCCcCCC-------CEEEEeeeecc
Confidence 678899999998321 22 668999999999998 433221 238899 88888887654
No 100
>PRK12366 replication factor A; Reviewed
Probab=59.72 E-value=43 Score=31.59 Aligned_cols=55 Identities=24% Similarity=0.316 Sum_probs=39.3
Q ss_pred eEEEEEEEEEeeeCC------C--C---cEEEEcCCeeEEEEe-ccc-cccccccCCcccccceeEEEEEeeEee
Q 044496 35 QRVWLQGVLVSPPDD------D--G---RLLLDDGTGVVQIYL-SGD-FRIRRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~------~--~---~~~LdDgTG~~~v~~-~~~-~~~~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
.++.+.|+|+++.+- + | ++.|-|+||.+++.. +.. .+--+++.| +++.+.+....
T Consensus 292 ~~~~I~grV~~~~~~R~f~~~~g~gkv~s~~l~D~tG~IR~t~w~~~~d~~~~l~~G-------~vy~is~~~vk 359 (637)
T PRK12366 292 EEVDVKGRIIAISDKREVERDDRTAEVQDIELADGTGRVRVSFWGEKAKILENLKEG-------DAVKIENCKVR 359 (637)
T ss_pred CEEEEEEEEEecCCceEEEcCCCcEEEEEEEEEcCCCeEEEEEeCchhhhhcccCCC-------CEEEEecCEEe
Confidence 378899999999531 1 2 788999999999987 321 122246789 88888876665
No 101
>PF14001 YdfZ: YdfZ protein
Probab=58.48 E-value=9 Score=26.66 Aligned_cols=33 Identities=36% Similarity=0.323 Sum_probs=27.7
Q ss_pred cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCCCcCc
Q 044496 74 RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDR 118 (142)
Q Consensus 74 ~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~r 118 (142)
++.+| ..||+-| ++..-+|+|+.--+|++...|
T Consensus 9 ~i~~G-------~rVMiag-----tG~~gvikAih~~gl~~eq~r 41 (64)
T PF14001_consen 9 AITTG-------SRVMIAG-----TGATGVIKAIHADGLTAEQIR 41 (64)
T ss_pred cCCCC-------CEEEEcC-----CCcccEEeeeecCCCCHHHhh
Confidence 59999 9999988 777889999999999884443
No 102
>PRK15491 replication factor A; Provisional
Probab=54.08 E-value=96 Score=27.47 Aligned_cols=63 Identities=21% Similarity=0.388 Sum_probs=42.1
Q ss_pred EEEEEEEEEeeeC------CCC------cEEEEcCCeeEEEEe-cccc-ccccccCCcccccceeEEEEEeeEee--ccC
Q 044496 36 RVWLQGVLVSPPD------DDG------RLLLDDGTGVVQIYL-SGDF-RIRRWNTGVFFFDFWMYVMVVGGFVI--RTD 99 (142)
Q Consensus 36 ~VWlQG~vv~~~~------~~~------~~~LdDgTG~~~v~~-~~~~-~~~~~~~G~~~~~~~~YVmViG~~~~--~~~ 99 (142)
.|=+.|+|+++.+ ++| ++.|-|.||++++.+ +... .-..+++| +.|.+.+.... ..+
T Consensus 178 ~V~I~g~V~~~~~~r~~~~~~G~~~~v~~~~l~DetG~Ir~t~W~~~a~~~~~l~~G-------d~V~i~~~~~r~~~~~ 250 (374)
T PRK15491 178 DINIVGKVLDISDVRTFQKKDGSQGRVRNITIGDETGKIRVTLWDGKTDLADKLENG-------DSVEIINGYARTNNYS 250 (374)
T ss_pred cEEEEEEEEEccCceEEEecCCCeEEEEEEEEECCCCeEEEEEecchhcccccCCCC-------CEEEEEeceEEEeccC
Confidence 4778899998854 233 478999999999988 3211 12358999 89988776432 233
Q ss_pred CCceEE
Q 044496 100 DIPVIK 105 (142)
Q Consensus 100 ~~p~i~ 105 (142)
..+.|.
T Consensus 251 g~~El~ 256 (374)
T PRK15491 251 QEVEIQ 256 (374)
T ss_pred CCEEEE
Confidence 456555
No 103
>PRK07211 replication factor A; Reviewed
Probab=53.52 E-value=49 Score=30.68 Aligned_cols=44 Identities=25% Similarity=0.354 Sum_probs=35.3
Q ss_pred EEEEEEEEeeeCCCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEe
Q 044496 37 VWLQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFV 95 (142)
Q Consensus 37 VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~ 95 (142)
|-..|+|+.. ++-+.||||+++..+.... .+..| +-|-|-|.++
T Consensus 432 ~~~~g~v~~~---~~~~~ld~g~~~~~~~~~~-----~~~~g-------~~v~~~g~~~ 475 (485)
T PRK07211 432 VEFTGTVVQA---GDPVVLDDGEETMSVETDA-----DVRLG-------EEVTVRGSLR 475 (485)
T ss_pred EEEEEEEEeC---CCCeEEeCCCeEEEEecCC-----cCCCC-------CEEEEEEeec
Confidence 4467999996 5678999999999988754 35678 8899998774
No 104
>COG3065 Slp Starvation-inducible outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=51.18 E-value=69 Score=26.57 Aligned_cols=57 Identities=26% Similarity=0.350 Sum_probs=38.2
Q ss_pred eEEeEEEEEEEEEeeeCCCCcEE-------EEc---------CCeeEEEEeccccccccccCCcccccceeEEEEEeeEe
Q 044496 32 ILFQRVWLQGVLVSPPDDDGRLL-------LDD---------GTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFV 95 (142)
Q Consensus 32 l~~~~VWlQG~vv~~~~~~~~~~-------LdD---------gTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~ 95 (142)
---|.|.+=|+|+++....++-. ||- .+|||-.+.++.-.--.++ | -||-|+|.+.
T Consensus 51 ~~gq~aR~GGkVvnv~n~~~rTrlEi~slPldS~arP~l~~~~qGRfiAy~~GFlDPv~~~-g-------r~vTv~G~i~ 122 (191)
T COG3065 51 YVGQQARFGGKVVNVINQKGRTRLEIASLPLDSGARPDLEAESQGRFIAYVNGFLDPVNFR-G-------RLVTVVGTIA 122 (191)
T ss_pred cccceeeeCcEEEEEecCCCcEEEEEEeeccCcccCCCcCCCCCceEEEEcccccChhhhc-C-------cEEEEEeeec
Confidence 34577889999999976544322 222 2577766666644333455 8 9999999997
Q ss_pred e
Q 044496 96 I 96 (142)
Q Consensus 96 ~ 96 (142)
.
T Consensus 123 g 123 (191)
T COG3065 123 G 123 (191)
T ss_pred c
Confidence 6
No 105
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=51.16 E-value=59 Score=22.62 Aligned_cols=45 Identities=27% Similarity=0.241 Sum_probs=31.0
Q ss_pred EEEEEEeeeCCCCcEEEEcCCeeE-EEEeccccccc-cccCCcccccceeEEEEE
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTGVV-QIYLSGDFRIR-RWNTGVFFFDFWMYVMVV 91 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG~~-~v~~~~~~~~~-~~~~G~~~~~~~~YVmVi 91 (142)
+.|+|++. -+++.+.+....|.- .+..++-++.+ -++.| +||.|-
T Consensus 2 ~~g~V~~~-~g~~~~~V~~~~g~~~la~i~gK~rk~iwI~~G-------D~V~Ve 48 (77)
T cd05793 2 EYGQVEKM-LGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEG-------DIVLVA 48 (77)
T ss_pred EEEEEEEE-cCCCEEEEEECCCCEEEEEEchhhcccEEEcCC-------CEEEEE
Confidence 56888886 467777777666653 34456666654 37999 999885
No 106
>PRK06763 F0F1 ATP synthase subunit alpha; Validated
Probab=50.76 E-value=30 Score=29.04 Aligned_cols=46 Identities=17% Similarity=0.242 Sum_probs=25.8
Q ss_pred EEEEEEEEEeeeCCCCcEEEE--cCCeeEEEEeccccccccccCCcccccceeEEEEEee
Q 044496 36 RVWLQGVLVSPPDDDGRLLLD--DGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGG 93 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~~~~Ld--DgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~ 93 (142)
.-.+||+|+++. ++.|.+- -.+..++|..++.+ ..+.| +||-+-|.
T Consensus 39 ~~tiEGrVvEV~--~~~i~iesk~yn~~v~i~~d~~~---nvKVG-------D~VKaTG~ 86 (213)
T PRK06763 39 FSTIEGRVVEVD--NGVIVIKSKQYEEPVSVYIDSLS---NVKVG-------DEVKATGS 86 (213)
T ss_pred cceeeeEEEEEe--CCEEEEEeccCCCceEEEecCCC---CcccC-------cEEEEchH
Confidence 347899999994 4434332 33445666653322 24555 55555543
No 107
>PRK07279 dnaE DNA polymerase III DnaE; Reviewed
Probab=49.40 E-value=73 Score=32.25 Aligned_cols=55 Identities=18% Similarity=0.291 Sum_probs=44.0
Q ss_pred cEEEEcCCeeEEEEe-ccccc-ccc-ccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCC
Q 044496 52 RLLLDDGTGVVQIYL-SGDFR-IRR-WNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSA 114 (142)
Q Consensus 52 ~~~LdDgTG~~~v~~-~~~~~-~~~-~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~ 114 (142)
-+.|.|.||.+++.. +...+ -+. +..| .-+.|-|.+..+ +....+.+.++.+|..
T Consensus 910 f~~leD~~g~ie~~vFp~~y~~~~~~l~~~-------~~~~v~G~v~~~-~~~~~l~~~~i~~l~~ 967 (1034)
T PRK07279 910 FLSVTDTKKKLDVTLFPETYRQYKDELKEG-------KFYYLKGKIQER-DGRLQMVLQQIQEASS 967 (1034)
T ss_pred EEEEeeCCCcEEEEECHHHHHHHHHHhccC-------CEEEEEEEEEec-CCeeEEEEeeeecccc
Confidence 589999999999997 54433 333 8899 999999999873 5577888999988865
No 108
>KOG3818 consensus DNA polymerase epsilon, subunit B [Replication, recombination and repair]
Probab=48.83 E-value=27 Score=32.70 Aligned_cols=57 Identities=28% Similarity=0.411 Sum_probs=46.4
Q ss_pred CeEEeEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEecccccccc-ccCCcccccceeEEEEEeeEee
Q 044496 31 GILFQRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRR-WNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 31 gl~~~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~-~~~G~~~~~~~~YVmViG~~~~ 96 (142)
|-..+.+-+=|.+... .+|.+-|-|.||.+++.++..+.+-. +-+| -.|.|-|.+..
T Consensus 173 t~~~~~~lvLGlLTq~--k~G~~~lEDpsgsVqlDlsqa~fh~glf~eg-------C~VL~EG~f~~ 230 (525)
T KOG3818|consen 173 TRALQSFLVLGLLTQL--KEGKFHLEDPSGSVQLDLSQAKFHHGLFCEG-------CFVLVEGTFES 230 (525)
T ss_pred cccccceeeeehhhhc--cCCcEEEeCCCCcEEEeecccccccceeccc-------eEEEEeeeeec
Confidence 6668888888988875 78999999999999999988555554 7888 88888887653
No 109
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=48.51 E-value=70 Score=22.56 Aligned_cols=44 Identities=23% Similarity=0.274 Sum_probs=31.2
Q ss_pred EEEEEEeeeCCCCcEEEEcCCeeEEE-Eeccccccc-cccCCcccccceeEEEE
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTGVVQI-YLSGDFRIR-RWNTGVFFFDFWMYVMV 90 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG~~~v-~~~~~~~~~-~~~~G~~~~~~~~YVmV 90 (142)
+.|+|++. -+++.+.+....|.-.+ ..++-++.+ -++.| +||.|
T Consensus 7 ~~g~V~~~-lG~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~G-------D~VlV 52 (83)
T smart00652 7 EIAQVVKM-LGNGRLEVMCADGKERLARIPGKMRKKVWIRRG-------DIVLV 52 (83)
T ss_pred EEEEEEEE-cCCCEEEEEECCCCEEEEEEchhhcccEEEcCC-------CEEEE
Confidence 56888885 46788887777776444 456656644 37999 99988
No 110
>PTZ00425 asparagine-tRNA ligase; Provisional
Probab=47.71 E-value=60 Score=30.78 Aligned_cols=55 Identities=20% Similarity=0.310 Sum_probs=40.4
Q ss_pred eEEEEEEEEEeeeCCCC----cEEEEcCCee--EEEEecccc----ccccccCCcccccceeEEEEEeeEee
Q 044496 35 QRVWLQGVLVSPPDDDG----RLLLDDGTGV--VQIYLSGDF----RIRRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~----~~~LdDgTG~--~~v~~~~~~----~~~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
+.|.+.|-|-++..-++ =+.|.||||. ++|..+... ....+..| .-|.|.|.++.
T Consensus 82 ~~Vtl~GWv~~iR~~g~~~~~Fv~lrDgsg~~~iQiVv~~~~~~~~~l~~l~~g-------s~v~v~G~v~~ 146 (586)
T PTZ00425 82 QIITVCGWSKAVRKQGGGRFCFVNLNDGSCHLNLQIIVDQSIENYEKLLKCGVG-------CCFRFTGKLII 146 (586)
T ss_pred CEEEEEEEEeehhhcCCceEEEEEEECCCCCcceEEEECCchHHHHHHhcCCCc-------cEEEEEEEEEc
Confidence 46999999999865443 4678999995 777663321 12247889 99999999976
No 111
>PF03843 Slp: Outer membrane lipoprotein Slp family; InterPro: IPR004658 Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli (which also contains a close paralog), Haemophilus influenzae and Pasteurella multocida and Vibrio cholerae. The known members of the family to date share a motif LX[GA]C near the N terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N terminus. Slp from E. coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.; GO: 0019867 outer membrane
Probab=46.79 E-value=1e+02 Score=24.12 Aligned_cols=55 Identities=29% Similarity=0.307 Sum_probs=34.9
Q ss_pred eEEEEEEEEEeeeCC-CCcEE------E---------EcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEee
Q 044496 35 QRVWLQGVLVSPPDD-DGRLL------L---------DDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~-~~~~~------L---------dDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
+.|.+=|+|+++... +.+.+ | +.+.|+|.+..++.-.-....+| ..|-|+|.+..
T Consensus 35 ~~VrwGG~I~~v~n~~~~T~leV~~~PLd~~grP~~~~~s~GRFla~~~gFLDP~~y~~G-------r~vTV~G~v~g 105 (160)
T PF03843_consen 35 QQVRWGGVIVNVRNLPDQTELEVVQYPLDSSGRPQTDDPSQGRFLARVPGFLDPAIYAPG-------RLVTVVGTVTG 105 (160)
T ss_pred CEEEECCEEEEEEECCCceEEEEEEccCCCCCCcCCCCCCCCEEEEEeCCCcCHHHcCCC-------CEEEEEEEecc
Confidence 456667777776433 22111 2 33478888877664443347899 99999999976
No 112
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=46.65 E-value=12 Score=26.11 Aligned_cols=30 Identities=37% Similarity=0.368 Sum_probs=26.0
Q ss_pred cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCCC
Q 044496 74 RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAF 115 (142)
Q Consensus 74 ~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~ 115 (142)
++.+| .+||+.| ++..-+|+|+.--.||+.
T Consensus 10 ait~G-------~rVMia~-----tG~tgvikaIh~dglt~~ 39 (65)
T TIGR03318 10 AITTG-------SRVMIAG-----TGHTGVIKAIHTEGLTAE 39 (65)
T ss_pred ccCCC-------cEEEEec-----CCccceeehhhhCCCCHH
Confidence 49999 9999988 677889999998888883
No 113
>COG1838 FumA Tartrate dehydratase beta subunit/Fumarate hydratase class I, C-terminal domain [Energy production and conversion]
Probab=46.48 E-value=3.7 Score=33.70 Aligned_cols=41 Identities=29% Similarity=0.413 Sum_probs=25.6
Q ss_pred eEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHH
Q 044496 86 MYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEA 129 (142)
Q Consensus 86 ~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~ 129 (142)
-|.+.+|+- + .=-.-.||-++.+...+-.. |++|.|||+|.
T Consensus 119 vyl~~~gGa-A-~L~a~~IK~~~~v~~~dLGm-EAiw~leVe~f 159 (184)
T COG1838 119 VYLVAPGGA-A-ALAAKSIKSVRCVAYEDLGM-EAIWELEVEDF 159 (184)
T ss_pred EEEEccchH-H-HHHHHhhhheeeEeecccCh-hheeEEEeccc
Confidence 788888872 1 11122344455555555455 99999999985
No 114
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=45.40 E-value=62 Score=24.24 Aligned_cols=46 Identities=17% Similarity=0.180 Sum_probs=32.8
Q ss_pred EEEEEEEeeeCCCCcEEEEcCCeeEEEEec------cccccccccCCcccccceeEEEEE
Q 044496 38 WLQGVLVSPPDDDGRLLLDDGTGVVQIYLS------GDFRIRRWNTGVFFFDFWMYVMVV 91 (142)
Q Consensus 38 WlQG~vv~~~~~~~~~~LdDgTG~~~v~~~------~~~~~~~~~~G~~~~~~~~YVmVi 91 (142)
+=.|+|.+.. +++.+++.+..|..+.... ++....++++| +||.+-
T Consensus 14 YY~GtV~~~~-~~~~~lV~f~~~~~~~v~~~~iI~~~~~~~~~L~~G-------D~VLA~ 65 (124)
T PF15057_consen 14 YYPGTVKKCV-SSGQFLVEFDDGDTQEVPISDIIALSDAMRHSLQVG-------DKVLAP 65 (124)
T ss_pred EEeEEEEEcc-CCCEEEEEECCCCEEEeChHHeEEccCcccCcCCCC-------CEEEEe
Confidence 4578999865 8889999997777666541 12333369999 888776
No 115
>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=45.02 E-value=89 Score=22.17 Aligned_cols=55 Identities=13% Similarity=0.167 Sum_probs=34.4
Q ss_pred eEEEEEEEEEeeeCC--------CC---cEEEEcC-CeeEEEEeccc--ccccc-ccCCcccccceeEEEEEe-eEee
Q 044496 35 QRVWLQGVLVSPPDD--------DG---RLLLDDG-TGVVQIYLSGD--FRIRR-WNTGVFFFDFWMYVMVVG-GFVI 96 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~--------~~---~~~LdDg-TG~~~v~~~~~--~~~~~-~~~G~~~~~~~~YVmViG-~~~~ 96 (142)
++.-+.|+|+++.+- ++ .+.|.|+ +|.+++..-+. .+-.+ ++.| +.+-+-+ .++.
T Consensus 10 ~~~~I~~rV~~k~~~~~f~~~~~~g~~~~~~l~De~~~~I~~t~~~~~~~~f~~~l~eG-------~vy~i~~~~V~~ 80 (104)
T cd04474 10 NKWTIKARVTNKSDIRTWSNARGEGKLFSFDLLDEDGGEIRATFFNDAVDKFYDLLEVG-------KVYYISKGSVKV 80 (104)
T ss_pred CcEEEEEEEeeccccccccCCCCCcEEEEEEEEECCCCEEEEEEehHHHHHhhcccccc-------cEEEEeccEEee
Confidence 456688999876321 13 6788888 99999987322 22223 8899 6554444 4444
No 116
>PF02237 BPL_C: Biotin protein ligase C terminal domain; InterPro: IPR003142 This C-terminal domain has an SH3-like barrel fold, the function of which is unknown. It is found associated with prokaryotic bifunctional transcriptional repressors [] and eukaryotic enzymes involved in biotin utilization [, ]. In Escherichia coli the biotin operon repressor (BirA) is a bifunctional protein. BirA acts both as the acetyl-coA carboxylase biotin holoenzyme synthetase (6.3.4.15 from EC) and as the biotin operon repressor. DNA sequence analysis of mutations indicates that the helix-turn-helix DNA binding region is located at the N terminus while mutations affecting enzyme function, although mapping over a large region, are found mainly in the central part of the protein's primary sequence [].; GO: 0006464 protein modification process; PDB: 3RUX_A 2CGH_A 3L1A_B 3L2Z_A 1HXD_A 1BIB_A 2EWN_B 1BIA_A 2EJ9_A 3FJP_A ....
Probab=44.04 E-value=77 Score=19.68 Aligned_cols=28 Identities=32% Similarity=0.557 Sum_probs=21.6
Q ss_pred EEEEEEeeeCCCCcEEEEcCCeeEEEEec
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTGVVQIYLS 67 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG~~~v~~~ 67 (142)
++|++..+ +++|.+++.+..|......+
T Consensus 15 ~~G~~~gI-d~~G~L~v~~~~g~~~~i~s 42 (48)
T PF02237_consen 15 IEGIAEGI-DDDGALLVRTEDGSIRTISS 42 (48)
T ss_dssp EEEEEEEE-ETTSEEEEEETTEEEEEESS
T ss_pred EEEEEEEE-CCCCEEEEEECCCCEEEEEE
Confidence 48999987 57899999999995544433
No 117
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=44.04 E-value=1.4e+02 Score=31.25 Aligned_cols=55 Identities=22% Similarity=0.250 Sum_probs=41.6
Q ss_pred eEEEEEEEEEeeeCC---CC----cEEEEcCCeeEEEEe-cccc---cc-ccccCCcccccceeEEEEEeeEee
Q 044496 35 QRVWLQGVLVSPPDD---DG----RLLLDDGTGVVQIYL-SGDF---RI-RRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~---~~----~~~LdDgTG~~~v~~-~~~~---~~-~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
.+|.++|.|...... .| +|-+-|.|+.+.+.. .... +. ..++.| +||.|-|.+.-
T Consensus 237 ~~v~i~G~if~~e~~~~k~~~~~~~~~~td~~~s~~~k~f~~~~~~~~~~~~~~~g-------~~v~~~g~~~~ 303 (1437)
T PRK00448 237 RRVVVEGYVFKVEIKELKSGRHILTFKITDYTSSIIVKKFSRDKEDLKKFDEIKKG-------DWVKVRGSVQN 303 (1437)
T ss_pred CeEEEEEEEEEEEEEeccCCCEEEEEEEEcCCCCEEEEEEecCcchhHHHhcCCCC-------CEEEEEEEEec
Confidence 579999999998542 44 677889999999886 2111 11 249999 99999999975
No 118
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=43.68 E-value=91 Score=20.64 Aligned_cols=45 Identities=20% Similarity=0.276 Sum_probs=27.9
Q ss_pred EEEEEEeeeCCCCcEEEEcCCee-EEEEeccccccc-cccCCcccccceeEEEEE
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTGV-VQIYLSGDFRIR-RWNTGVFFFDFWMYVMVV 91 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG~-~~v~~~~~~~~~-~~~~G~~~~~~~~YVmVi 91 (142)
+.|+|++. -+++.|.+....|. +.+.+++-++.+ .++.| +||.|-
T Consensus 5 ~~~~V~~~-lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~G-------D~V~V~ 51 (65)
T PF01176_consen 5 VIGRVTEM-LGNNLFEVECEDGEERLARIPGKFRKRIWIKRG-------DFVLVE 51 (65)
T ss_dssp EEEEEEEE-ESSSEEEEEETTSEEEEEEE-HHHHTCC---TT-------EEEEEE
T ss_pred EEEEEEEE-CCCCEEEEEeCCCCEEEEEeccceeeeEecCCC-------CEEEEE
Confidence 46888886 46777777777777 444455545555 37999 999653
No 119
>PRK07217 replication factor A; Reviewed
Probab=43.41 E-value=19 Score=31.68 Aligned_cols=17 Identities=29% Similarity=0.532 Sum_probs=14.6
Q ss_pred cEEEEcCCeeEEEEecc
Q 044496 52 RLLLDDGTGVVQIYLSG 68 (142)
Q Consensus 52 ~~~LdDgTG~~~v~~~~ 68 (142)
.++||||||+..+.++.
T Consensus 220 k~vlDDGt~~~~~~~~~ 236 (311)
T PRK07217 220 KGVLDDGEEVQEVIFNR 236 (311)
T ss_pred EEEEECCCCeEEEEECh
Confidence 68999999999998743
No 120
>PF15072 DUF4539: Domain of unknown function (DUF4539)
Probab=42.85 E-value=1.2e+02 Score=21.61 Aligned_cols=40 Identities=20% Similarity=0.225 Sum_probs=27.5
Q ss_pred EEEEEEeee--CCCCcEEEEcCCeeEEEEe-ccccccc--cccCC
Q 044496 39 LQGVLVSPP--DDDGRLLLDDGTGVVQIYL-SGDFRIR--RWNTG 78 (142)
Q Consensus 39 lQG~vv~~~--~~~~~~~LdDgTG~~~v~~-~~~~~~~--~~~~G 78 (142)
|-|.|-+.. ..|-.++|-|+||.++... ..+..+. .+.+|
T Consensus 7 l~v~Iks~~~~~~D~~v~l~DpTG~i~~tiH~~v~~~y~~~l~~G 51 (86)
T PF15072_consen 7 LVVIIKSIVPSSEDAFVVLKDPTGEIRGTIHRKVLEEYGDELSPG 51 (86)
T ss_pred EEEEEEEeeccCCCeEEEEECCCCcEEEEEeHHHHhhcCCccccC
Confidence 445565553 3377999999999999887 4444433 48888
No 121
>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=42.78 E-value=1.6e+02 Score=22.98 Aligned_cols=51 Identities=25% Similarity=0.246 Sum_probs=36.5
Q ss_pred EEEEEEeeeCCCC------cEEEEcCCee-EEEEeccc--cccccccCCcccccceeEEEEEeeEee
Q 044496 39 LQGVLVSPPDDDG------RLLLDDGTGV-VQIYLSGD--FRIRRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 39 lQG~vv~~~~~~~------~~~LdDgTG~-~~v~~~~~--~~~~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
-+|+|+.+-++++ +|+|+=++|. +.|.-+-+ |+.-.++.| +.|-+.|.+.-
T Consensus 41 g~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDlaprip~l~~G-------D~V~f~GeYe~ 100 (131)
T PF11948_consen 41 GCGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLAPRIPWLQKG-------DQVEFYGEYEW 100 (131)
T ss_pred ccEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCccccCcCcCCC-------CEEEEEEEEEE
Confidence 3899999954422 7888878776 55544444 333349999 99999999965
No 122
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=42.00 E-value=1.2e+02 Score=22.04 Aligned_cols=47 Identities=26% Similarity=0.292 Sum_probs=26.7
Q ss_pred EEEEEeeeCCCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEe
Q 044496 40 QGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFV 95 (142)
Q Consensus 40 QG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~ 95 (142)
-|.|++..+.++..++|=|-=.=+++++-... ..+.| +||.|+-++.
T Consensus 6 PgqI~~I~~~~~~A~Vd~gGvkreV~l~Lv~~--~v~~G-------dyVLVHvGfA 52 (82)
T COG0298 6 PGQIVEIDDNNHLAIVDVGGVKREVNLDLVGE--EVKVG-------DYVLVHVGFA 52 (82)
T ss_pred ccEEEEEeCCCceEEEEeccEeEEEEeeeecC--ccccC-------CEEEEEeeEE
Confidence 47788875444434443331112233322222 68899 9999998884
No 123
>PLN02532 asparagine-tRNA synthetase
Probab=41.40 E-value=99 Score=29.70 Aligned_cols=56 Identities=21% Similarity=0.391 Sum_probs=39.0
Q ss_pred cEEEEcCCee--EEEEecccc--ccccccCCcccccceeEEEEEeeEeeccC----CCceEEEEEEeeCCC
Q 044496 52 RLLLDDGTGV--VQIYLSGDF--RIRRWNTGVFFFDFWMYVMVVGGFVIRTD----DIPVIKVHKIVDLSA 114 (142)
Q Consensus 52 ~~~LdDgTG~--~~v~~~~~~--~~~~~~~G~~~~~~~~YVmViG~~~~~~~----~~p~i~a~K~~DLS~ 114 (142)
=+.|.||||. ++|..++.. ....+..| .-|.|.|.++.+.. ..-.|.|.++.=|+.
T Consensus 137 FI~LrDGSg~~~lQvVv~~~~~~~~~~L~~E-------s~V~V~G~V~~~~~~~~~g~iEl~v~~i~VLg~ 200 (633)
T PLN02532 137 YLLISDGSCVASLQVVVDSALAPLTQLMATG-------TCILAEGVLKLPLPAQGKHVIELEVEKILHIGT 200 (633)
T ss_pred EEEEECCCCccceEEEEeCCcccHhhcCCCc-------eEEEEEEEEEecCCCCCCCcEEEEeeEEEEEec
Confidence 4679999999 888774321 12358899 99999999987411 123677777766664
No 124
>COG2332 CcmE Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]
Probab=41.39 E-value=1.6e+02 Score=23.65 Aligned_cols=64 Identities=19% Similarity=0.303 Sum_probs=41.0
Q ss_pred eEEEEEEEEEeee----CC--CCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEEEEE
Q 044496 35 QRVWLQGVLVSPP----DD--DGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHK 108 (142)
Q Consensus 35 ~~VWlQG~vv~~~----~~--~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K 108 (142)
+|+.+-|.|..-+ .+ .-+|.+.|+-..++|.+.++.. --++.| .=|.+.|.++. + ..+.|.+
T Consensus 52 ~rlR~GGlV~~GSv~R~~~~~~v~F~vtD~~~~v~V~Y~GiLP-DLFREG-------QgVVa~G~~~~---~-~~f~A~~ 119 (153)
T COG2332 52 QRLRLGGLVEAGSVQRDPGSLKVSFVVTDGNKSVTVSYEGILP-DLFREG-------QGVVAEGQLQG---G-GVFEAKE 119 (153)
T ss_pred cEEEEeeeEeeceEEecCCCcEEEEEEecCCceEEEEEeccCc-hhhhcC-------CeEEEEEEecC---C-CEEEeee
Confidence 4555666665432 11 3489999999999999855431 016677 77888888854 2 5666665
Q ss_pred Ee
Q 044496 109 IV 110 (142)
Q Consensus 109 ~~ 110 (142)
+.
T Consensus 120 vL 121 (153)
T COG2332 120 VL 121 (153)
T ss_pred hh
Confidence 53
No 125
>PF13296 T6SS_Vgr: Putative type VI secretion system Rhs element Vgr
Probab=40.12 E-value=23 Score=26.54 Aligned_cols=61 Identities=26% Similarity=0.352 Sum_probs=38.3
Q ss_pred CCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEE-e---------eEeeccCCCceEEEEEEeeCCCCcC
Q 044496 49 DDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVV-G---------GFVIRTDDIPVIKVHKIVDLSAFPD 117 (142)
Q Consensus 49 ~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmVi-G---------~~~~~~~~~p~i~a~K~~DLS~~p~ 117 (142)
+.|.+++||.+|.+++.++++...-.++.| |..=. + ++.-+++..-.|||-|=.=||..+.
T Consensus 8 g~Nql~~DDt~gQ~~~qL~S~~~~SqLnLG--------~l~~~~~~~R~~~RG~GfELrTD~~gavRa~~GlliSt~~~ 78 (109)
T PF13296_consen 8 GYNQLVFDDTPGQIRAQLSSDHGASQLNLG--------HLVDQRDNGRGAPRGEGFELRTDAWGAVRAGKGLLISTEAR 78 (109)
T ss_pred CCCEEEEecCCCcceEEEecccchhhhhcc--------cccCcccccccCccccceEEecchhhhhhcccEEEEEcCCC
Confidence 368999999999999999776533347777 22222 1 1222345555777777666666433
No 126
>PF10949 DUF2777: Protein of unknown function (DUF2777); InterPro: IPR024488 This family of proteins with unknown function appears to be restricted to Bacillaceae.
Probab=38.75 E-value=35 Score=28.00 Aligned_cols=41 Identities=27% Similarity=0.528 Sum_probs=29.5
Q ss_pred eEEEEEEEEEeeeCCCCcEEEEcCCeeEEEEe--ccc----cccccccCC
Q 044496 35 QRVWLQGVLVSPPDDDGRLLLDDGTGVVQIYL--SGD----FRIRRWNTG 78 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~--~~~----~~~~~~~~G 78 (142)
.|.|++|+| -+ .++.+.+||++|.+..-= ... .+...|.+|
T Consensus 14 ~r~~~~Gtv-~i--~~~w~ffddE~~Eallle~~~~~~iei~~~~~W~~g 60 (185)
T PF10949_consen 14 PRAYIYGTV-YI--NDEWIFFDDEEGEALLLEELPFEEIEIFRDGRWMKG 60 (185)
T ss_pred ccceEEEEE-EE--eCcEEEEEcCCCceechhhCCCCcEEEEECCcEEEE
Confidence 478999999 44 788999999999876542 221 233468888
No 127
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=38.40 E-value=93 Score=26.66 Aligned_cols=35 Identities=26% Similarity=0.357 Sum_probs=22.5
Q ss_pred EEEEEeeeC----CCCcEEEEcCCee-EEEEeccccccccccCCcccccceeEEEEEee
Q 044496 40 QGVLVSPPD----DDGRLLLDDGTGV-VQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGG 93 (142)
Q Consensus 40 QG~vv~~~~----~~~~~~LdDgTG~-~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~ 93 (142)
.|+|++++. ..+...+.|+.|. |+-.. +||+|||.
T Consensus 191 ~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~-------------------~yVfvIG~ 230 (241)
T COG1471 191 VGTIVEIEIQESSKPNLVTVEDEEGNTFQTIK-------------------DYVFVIGE 230 (241)
T ss_pred eEEEEEEEEecCCCccEEEEecCCCCceEEee-------------------eEEEEEcC
Confidence 377777732 2556777777662 33322 89999995
No 128
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=38.16 E-value=1.7e+02 Score=21.93 Aligned_cols=64 Identities=14% Similarity=0.066 Sum_probs=37.9
Q ss_pred EeEEEEEEEEEeeeCCCCcEEEEcC----------CeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCce
Q 044496 34 FQRVWLQGVLVSPPDDDGRLLLDDG----------TGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPV 103 (142)
Q Consensus 34 ~~~VWlQG~vv~~~~~~~~~~LdDg----------TG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~ 103 (142)
-+.+|-+|+|.+++.+.+.+.|.=+ |=.|.+. .......+++| +.|..-=. . .++..+
T Consensus 40 ~~~~~~~G~V~~vd~~~~~iti~H~pIp~l~wPaMTM~F~v~--~~~~l~~lk~G-------~~V~F~~~--~-~~~~~~ 107 (115)
T PRK09838 40 PQVISGTGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTIT--PQTKMSEIKTG-------DKVAFNFV--Q-QGNLSL 107 (115)
T ss_pred CceEEEEEEEEEEeCCCCEEEEeecccccCCCCCccccccCC--ChhhhccCCCC-------CEEEEEEE--E-cCCcEE
Confidence 4779999999998666666666544 1111111 11112248999 88876432 2 455667
Q ss_pred EEEEEE
Q 044496 104 IKVHKI 109 (142)
Q Consensus 104 i~a~K~ 109 (142)
|..+|.
T Consensus 108 i~~i~~ 113 (115)
T PRK09838 108 LQDIKV 113 (115)
T ss_pred EEEEee
Confidence 777664
No 129
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=37.69 E-value=1.1e+02 Score=21.36 Aligned_cols=43 Identities=14% Similarity=0.224 Sum_probs=29.9
Q ss_pred EEEEEeeeCCCCcEEEEcCCeeEEE-Eeccccccc-cccCCcccccceeEEEE
Q 044496 40 QGVLVSPPDDDGRLLLDDGTGVVQI-YLSGDFRIR-RWNTGVFFFDFWMYVMV 90 (142)
Q Consensus 40 QG~vv~~~~~~~~~~LdDgTG~~~v-~~~~~~~~~-~~~~G~~~~~~~~YVmV 90 (142)
-|+|++. -+++.+.+....|...+ ..++-++.+ -++.| +||.|
T Consensus 3 i~~V~~~-lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~G-------D~VlV 47 (78)
T cd04456 3 IVRVLRM-LGNNRHEVECADGQRRLVSIPGKLRKNIWIKRG-------DFLIV 47 (78)
T ss_pred EEEEEEE-CCCCEEEEEECCCCEEEEEEchhhccCEEEcCC-------CEEEE
Confidence 3777774 56788887766676444 456666644 37999 99988
No 130
>PF03079 ARD: ARD/ARD' family; InterPro: IPR004313 The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence Q9ZFE7 from SWISSPROT, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+ []. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions []. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels [, ]. This family also contains other proteins, whose functions are not well characterised.; GO: 0010309 acireductone dioxygenase [iron(II)-requiring] activity, 0055114 oxidation-reduction process; PDB: 1VR3_A 1ZRR_A 2HJI_A.
Probab=37.34 E-value=46 Score=26.16 Aligned_cols=52 Identities=25% Similarity=0.379 Sum_probs=32.6
Q ss_pred CCcEEEEcCCeeEEEEeccccccc-cccCCcccccceeEEEEEeeEee--ccCCCceEEEEEE
Q 044496 50 DGRLLLDDGTGVVQIYLSGDFRIR-RWNTGVFFFDFWMYVMVVGGFVI--RTDDIPVIKVHKI 109 (142)
Q Consensus 50 ~~~~~LdDgTG~~~v~~~~~~~~~-~~~~G~~~~~~~~YVmViG~~~~--~~~~~p~i~a~K~ 109 (142)
+.++ +-||+|.|.+....+.-.| ...+| +++.|=-++.. ..++.|.++|+..
T Consensus 94 EvR~-i~~G~g~Fdvr~~~~~wiri~~e~G-------Dli~vP~g~~HrF~~~~~~~i~aiRl 148 (157)
T PF03079_consen 94 EVRY-IVDGSGYFDVRDGDDVWIRILCEKG-------DLIVVPAGTYHRFTLGESPYIKAIRL 148 (157)
T ss_dssp EEEE-EEECEEEEEEE-TTCEEEEEEEETT-------CEEEE-TT--EEEEESTTSSEEEEEE
T ss_pred eEEE-EeCcEEEEEEEcCCCEEEEEEEcCC-------CEEecCCCCceeEEcCCCCcEEEEEe
Confidence 3354 4499999999965444333 47888 88777655554 2567788888765
No 131
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=37.27 E-value=1.1e+02 Score=19.37 Aligned_cols=44 Identities=18% Similarity=0.311 Sum_probs=27.8
Q ss_pred EEEEEEeeeCCCCcEEEEcC-CeeEEEEecccccc-c-cccCCcccccceeEEEEE
Q 044496 39 LQGVLVSPPDDDGRLLLDDG-TGVVQIYLSGDFRI-R-RWNTGVFFFDFWMYVMVV 91 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDg-TG~~~v~~~~~~~~-~-~~~~G~~~~~~~~YVmVi 91 (142)
+.|+|++.. .+.+.+.++ .+.+.+..++..+. . .+-.| ++|.+-
T Consensus 1 ~~grVv~~~--~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~VG-------D~V~~~ 47 (68)
T cd04466 1 MEGLIIKAI--GGFYYVETEDGKIYECRLRGKFRKDKNPPAVG-------DRVEFE 47 (68)
T ss_pred CCEEEEEEE--CCEEEEEeCCCeEEEEEEccccccCCCCCCCC-------cEEEEE
Confidence 368888863 455666655 46777776543332 2 37899 999763
No 132
>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=36.43 E-value=1.1e+02 Score=21.12 Aligned_cols=58 Identities=17% Similarity=0.169 Sum_probs=32.0
Q ss_pred cEEEEcCCe-eEEEEeccc-cccccccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeCCCCcC
Q 044496 52 RLLLDDGTG-VVQIYLSGD-FRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPD 117 (142)
Q Consensus 52 ~~~LdDgTG-~~~v~~~~~-~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~ 117 (142)
.+.|.|+|| .+.+.+=++ ...-....| +.+.+.|.-....+ .-.+..-.-+.+--+|+
T Consensus 30 ~v~i~D~t~~~i~vtLWg~~a~~~~~~~~-------~vv~~~~~~i~~~~-~~~l~~~~~s~i~~np~ 89 (101)
T cd04475 30 EITLVDESGHSVELTLWGEQAELFDGSEN-------PVIAIKGVKVSEFN-GKSLSTGSSSTIIINPD 89 (101)
T ss_pred EEEEEeCCCCEEEEEEEHHHhhhcccCCC-------CEEEEEeeEEEecC-CeEEeecCceeEEECCC
Confidence 788999999 799988222 211112227 77777775544222 33344433344444555
No 133
>TIGR00752 slp outer membrane lipoprotein, Slp family. Slp superfamily members are present in the Gram-negative gamma proteobacteria Escherichia coli, which also contains a close paralog, Haemophilus influenzae and Pasteurella multocida and Vibrio cholera. The known members of the family to date share a motif LX[GA]C near the N-terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N-terminus. Slp from Escherichia coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation.
Probab=34.15 E-value=1.1e+02 Score=24.89 Aligned_cols=56 Identities=23% Similarity=0.236 Sum_probs=36.2
Q ss_pred EEeEEEEEEEEEeeeCCCC-------cEEEE---------cCCeeEEEEeccccccccccCCcccccceeEEEEEeeEee
Q 044496 33 LFQRVWLQGVLVSPPDDDG-------RLLLD---------DGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 33 ~~~~VWlQG~vv~~~~~~~-------~~~Ld---------DgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
.=+.|.+=|+|+++....+ .+-|| .+.|||-+..++.-.-... .| .+|-|+|.+..
T Consensus 47 ~G~~Vr~GG~I~~v~N~~~~T~lEVv~~PLd~~grP~~~~~s~GRFla~~~gFLDP~~y-~G-------r~VTVvG~i~G 118 (182)
T TIGR00752 47 VGQTARFGGKVVNVTNLANQTKLEIASLPLDSIAKPFVELQSDGRFIAYFNGFLDPVNL-RE-------RYVTVGGQIAG 118 (182)
T ss_pred CCCEEEECCEEEEEEECCCceEEEEEEcccCCCCCcCCCCCCCCEEEEEeCCCcChhhc-CC-------CEEEEEEEecc
Confidence 3467778888888853322 11122 3367887777664443346 59 99999999975
No 134
>PRK00098 GTPase RsgA; Reviewed
Probab=33.63 E-value=1.1e+02 Score=25.73 Aligned_cols=44 Identities=23% Similarity=0.331 Sum_probs=27.4
Q ss_pred EEEEEEeeeCCCCcEEEEcCCe-eEEEEecccccc-c-cccCCcccccceeEEEEE
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTG-VVQIYLSGDFRI-R-RWNTGVFFFDFWMYVMVV 91 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG-~~~v~~~~~~~~-~-~~~~G~~~~~~~~YVmVi 91 (142)
|+|+|++. .++...+.+++| .+.+...+-.+. + .+-.| ++|.+-
T Consensus 1 ~~g~v~~~--~~~~~~v~~~~~~~~~~~~~g~~~~~~~~~~vG-------D~V~~~ 47 (298)
T PRK00098 1 MEGLIIKA--LGGFYYVESEDGQVYQCRARGKFRKKTNTPAVG-------DRVEFS 47 (298)
T ss_pred CeEEEEEE--ECCEEEEEECCCCEEEEEeccccccCCCCcCCC-------CEEEEE
Confidence 68999986 345555555544 577776544432 2 36788 888773
No 135
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=33.09 E-value=1.6e+02 Score=21.58 Aligned_cols=44 Identities=23% Similarity=0.243 Sum_probs=30.6
Q ss_pred EEEEEEeeeCCCCcEEEEcCCee-EEEEeccccccc-cccCCcccccceeEEEE
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTGV-VQIYLSGDFRIR-RWNTGVFFFDFWMYVMV 90 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG~-~~v~~~~~~~~~-~~~~G~~~~~~~~YVmV 90 (142)
+.|+|++. -+++.|.+....|. +.+..++-++.+ -++.| +||.|
T Consensus 21 ~~g~V~~~-lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~G-------D~VlV 66 (99)
T TIGR00523 21 ILGVIEQM-LGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREG-------DVVIV 66 (99)
T ss_pred EEEEEEEE-cCCCEEEEEeCCCCEEEEEEchhhcccEEecCC-------CEEEE
Confidence 67888885 46777776655565 334456656644 37999 99998
No 136
>KOG0641 consensus WD40 repeat protein [General function prediction only]
Probab=32.08 E-value=1e+02 Score=27.12 Aligned_cols=48 Identities=25% Similarity=0.316 Sum_probs=30.4
Q ss_pred EEEEeeeCCCCcEEEEcCCeeEEEEe----ccccccccccCCcccccceeEEEEEeeEe
Q 044496 41 GVLVSPPDDDGRLLLDDGTGVVQIYL----SGDFRIRRWNTGVFFFDFWMYVMVVGGFV 95 (142)
Q Consensus 41 G~vv~~~~~~~~~~LdDgTG~~~v~~----~~~~~~~~~~~G~~~~~~~~YVmViG~~~ 95 (142)
|+++..-..+.+++|.|=-|-=-|+. +.+-|--++.|| .|-|.-|.+-
T Consensus 243 grll~sg~~dssc~lydirg~r~iq~f~phsadir~vrfsp~-------a~yllt~syd 294 (350)
T KOG0641|consen 243 GRLLASGHADSSCMLYDIRGGRMIQRFHPHSADIRCVRFSPG-------AHYLLTCSYD 294 (350)
T ss_pred cceeeeccCCCceEEEEeeCCceeeeeCCCccceeEEEeCCC-------ceEEEEeccc
Confidence 55555434466777777666544443 333344468999 9999988764
No 137
>KOG0556 consensus Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=30.83 E-value=3.9e+02 Score=25.23 Aligned_cols=74 Identities=22% Similarity=0.119 Sum_probs=50.1
Q ss_pred EeEEEEEEEEEeeeCCC--CcEEEEcCCeeEEEEe--ccc---cccc-----cccCCcccccceeEEEEEeeEeeccCC-
Q 044496 34 FQRVWLQGVLVSPPDDD--GRLLLDDGTGVVQIYL--SGD---FRIR-----RWNTGVFFFDFWMYVMVVGGFVIRTDD- 100 (142)
Q Consensus 34 ~~~VWlQG~vv~~~~~~--~~~~LdDgTG~~~v~~--~~~---~~~~-----~~~~G~~~~~~~~YVmViG~~~~~~~~- 100 (142)
=+.||+-|+|-.-...+ .-++|.++..++++.. +.+ .+++ .++.- .||-|.|.+.+...+
T Consensus 82 ~~~V~vRgrVhtsr~~GK~~FlvLRq~~~tVQ~~~~~~~~~~isk~Mvkf~~~is~E-------SiV~v~g~v~k~~~~i 154 (533)
T KOG0556|consen 82 GSEVLVRGRVHTSRLKGKLCFLVLRQQGSTVQCLVAVNEDGTISKQMVKFAGSISKE-------SIVDVRGVVVKVKEPI 154 (533)
T ss_pred CceEEEEEEEeeccccceEEEEEEeccCceEEEEEEcCCCchHHHHHHHHHhhcCcc-------eEEEEEEEEecCCCcc
Confidence 36799999998753222 2568899988888876 333 2333 36777 999999999873222
Q ss_pred ------CceEEEEEEeeCCC
Q 044496 101 ------IPVIKVHKIVDLSA 114 (142)
Q Consensus 101 ------~p~i~a~K~~DLS~ 114 (142)
.-.|.+-||-=+|.
T Consensus 155 ~scT~qdvEi~v~~iyviS~ 174 (533)
T KOG0556|consen 155 KSCTVQDVEIHVRKIYVISI 174 (533)
T ss_pred cccccceeEEEEEEEEEEec
Confidence 33566667666665
No 138
>COG1588 POP4 RNase P/RNase MRP subunit p29 [Translation, ribosomal structure and biogenesis]
Probab=30.72 E-value=57 Score=24.28 Aligned_cols=57 Identities=19% Similarity=0.200 Sum_probs=37.8
Q ss_pred EEEEEEEEeeeCCCCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCce
Q 044496 37 VWLQGVLVSPPDDDGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPV 103 (142)
Q Consensus 37 VWlQG~vv~~~~~~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~ 103 (142)
+=+.|.||. +-.|.+.+++++|...|-....-..-....| .||-|=|.+.. ..|+-.
T Consensus 31 vGI~G~VVd--ETkNtLvi~t~~~~~~VpK~~~vfef~~~~G-------~~vkVdG~lL~-~rPE~R 87 (95)
T COG1588 31 VGIEGRVVD--ETKNTLVIDTGSREKVVPKDGAVFEFEGPDG-------EKVKVDGRLLL-GRPEDR 87 (95)
T ss_pred cceeEEEEe--eeccEEEEECCCceEEEecCcEEEEEEcCCC-------cEEEEcchhhh-cCHHHH
Confidence 346788875 4689999999998887765332222234458 88888887765 444433
No 139
>TIGR00723 ttdB_fumA_fumB hydro-lyases, Fe-S type, tartrate/fumarate subfamily, beta region. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase. This model represents a subset of closely related proteins or modules, including the E. coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of archaeal proteins in this subfamily has not been established.
Probab=30.01 E-value=7 Score=31.47 Aligned_cols=42 Identities=26% Similarity=0.343 Sum_probs=27.1
Q ss_pred eEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHH
Q 044496 86 MYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEA 129 (142)
Q Consensus 86 ~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~ 129 (142)
-|...+|+.-+--+ -.|+.++.+...+--..|++|.+||++.
T Consensus 110 VYl~~~GGaaAlla--~~Ik~~~~v~~~dLGmpEAi~~leVedf 151 (168)
T TIGR00723 110 VYLAFPGGCAALLA--QSVKKVEGVAWEDLGMPEAIWELEVEDF 151 (168)
T ss_pred EEEEcCcHHHHHHH--hcccEEEEEeecCCCCccEEEEEEEecc
Confidence 56666665433111 2377777777776223599999999875
No 140
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=29.59 E-value=2e+02 Score=21.17 Aligned_cols=45 Identities=22% Similarity=0.215 Sum_probs=29.7
Q ss_pred EEEEEEeeeCCCCcEEEEcCCee-EEEEeccccccc-cccCCcccccceeEEEEE
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTGV-VQIYLSGDFRIR-RWNTGVFFFDFWMYVMVV 91 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG~-~~v~~~~~~~~~-~~~~G~~~~~~~~YVmVi 91 (142)
+-|+|++. -+++.|.+....|. ..+..++-++.+ -++.| +||.|-
T Consensus 23 ~~g~V~~~-lG~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~G-------D~VlVe 69 (100)
T PRK04012 23 VFGVVEQM-LGANRVRVRCMDGVERMGRIPGKMKKRMWIREG-------DVVIVA 69 (100)
T ss_pred EEEEEEEE-cCCCEEEEEeCCCCEEEEEEchhhcccEEecCC-------CEEEEE
Confidence 56788885 46777776655555 334456656555 37999 999874
No 141
>PRK06842 fumarate hydratase; Provisional
Probab=27.89 E-value=13 Score=30.35 Aligned_cols=41 Identities=24% Similarity=0.340 Sum_probs=26.2
Q ss_pred eEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHH
Q 044496 86 MYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEA 129 (142)
Q Consensus 86 ~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~ 129 (142)
-|...+|+.-+--+ ..|+-++.+..-+-- .|++|.+||++.
T Consensus 119 VYl~~~GGaaAlla--~~Ik~v~~v~~~dLG-~EAi~~l~V~df 159 (185)
T PRK06842 119 VYFGAIGGAAALIA--KSIKKSEVIAYEDLG-AEAIRKLEVKDF 159 (185)
T ss_pred EEEEcCChHHHHHH--hheeeEeEEeccccC-ccEEEEEEEecC
Confidence 56666665533111 266666666665422 699999999874
No 142
>PF02294 7kD_DNA_binding: 7kD DNA-binding domain; InterPro: IPR003212 This family contains members of the hyperthermophilic archaebacterium 7kDa DNA-binding/endoribonuclease P2 family. There are five 7kDa DNA-binding proteins, 7a-7e, found as monomers in the cell. Protein 7e shows the tightest DNA-binding ability.; GO: 0003677 DNA binding, 0004521 endoribonuclease activity; PDB: 1SSO_A 2CVR_A 1B4O_A 2XIW_B 1WTV_A 1WTQ_A 1BF4_A 1WVL_B 1WTR_A 1WTP_B ....
Probab=27.79 E-value=46 Score=22.72 Aligned_cols=25 Identities=40% Similarity=0.719 Sum_probs=17.5
Q ss_pred EeEEEEEEEEEeeeCCCCcEEEEcC---CeeEEEE
Q 044496 34 FQRVWLQGVLVSPPDDDGRLLLDDG---TGVVQIY 65 (142)
Q Consensus 34 ~~~VWlQG~vv~~~~~~~~~~LdDg---TG~~~v~ 65 (142)
+..||=.|..+| |+.||| ||+=-+.
T Consensus 19 ikkvwrvgkmvs-------ftyddgngktgrgavs 46 (62)
T PF02294_consen 19 IKKVWRVGKMVS-------FTYDDGNGKTGRGAVS 46 (62)
T ss_dssp EEEEEECSSEEE-------EEEECSSSSEEEEEEE
T ss_pred HHHHHhhcceEE-------EEEecCCCcccccccc
Confidence 668999888877 678887 4554443
No 143
>PF12658 Ten1: Telomere capping, CST complex subunit; InterPro: IPR024222 Stn1 and Ten1 are DNA-binding proteins with specificity for telomeric DNA substrates and both protect chromosome termini from unregulated resection and regulate telomere length. Stn1 complexes with Ten1 and Cdc13 to function as a telomere-specific replication protein A (RPA)-like complex []. These three interacting proteins associate with the telomeric overhang in budding yeast, whereas a single protein known as Pot1 (protection of telomeres-1) performs this function in fission yeast, and a two-subunit complex consisting of POT1 and TPP1 associates with telomeric ssDNA in humans. S.pombe has Stn1- and Ten1-like proteins that are essential for chromosome end protection. Stn1 orthologues exist in all species that have Pot1, whereas Ten1-like proteins can be found in all fungi. Fission yeast Stn1 and Ten1 localise at telomeres in a manner that correlates with the length of the ssDNA overhang, suggesting that they specifically associate with the telomeric ssDNA. Two separate protein complexes are required for chromosome end protection in fission yeast. Protection of telomeres by multiple proteins with OB-fold domains is conserved in eukaryotic evolution [].; PDB: 3KF8_D 3KF6_B 3K0X_A.
Probab=27.46 E-value=2.7e+02 Score=20.99 Aligned_cols=73 Identities=18% Similarity=0.174 Sum_probs=46.5
Q ss_pred eEEEEEEEEEeeeCCCCcEEEEcCCe--------eEEEEecccc---ccccccCCcccccceeEEEEEeeEeecc----C
Q 044496 35 QRVWLQGVLVSPPDDDGRLLLDDGTG--------VVQIYLSGDF---RIRRWNTGVFFFDFWMYVMVVGGFVIRT----D 99 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~~~~~~LdDgTG--------~~~v~~~~~~---~~~~~~~G~~~~~~~~YVmViG~~~~~~----~ 99 (142)
.+|.+=|-|.+-....+.++|...-- .+.+..+..- ....++.| ..|.|+|.+.... .
T Consensus 26 ~KVRfLgcV~~Y~~~~~~L~l~h~~p~~~~~~~~~v~VdI~~vL~tv~~~~~rvG-------~WvNV~Gy~~~~~~~~~~ 98 (124)
T PF12658_consen 26 DKVRFLGCVSSYDTSTGTLTLEHNYPRENDSQPSSVSVDINLVLETVSSEELRVG-------EWVNVVGYIRGEKPSQTQ 98 (124)
T ss_dssp EEEEEEEEEEEEECCCTEEEEEETCCC---S----EEEE-TTTTTTS-GGGGSTT--------EEEEEEEEECTT-----
T ss_pred CEEEEEEEEeEEecCccEEEEeecCCCCcCCCCceEEEEHHHHhhhcCccceecc-------eEEEEEEEeccccccccc
Confidence 46778888888777788999988511 2555553332 22359999 9999999998833 2
Q ss_pred CCceEEEEEEeeCCC
Q 044496 100 DIPVIKVHKIVDLSA 114 (142)
Q Consensus 100 ~~p~i~a~K~~DLS~ 114 (142)
+.+.++|+-+-+.+.
T Consensus 99 ~~v~Vqai~i~~ag~ 113 (124)
T PF12658_consen 99 SPVYVQAIMIWSAGP 113 (124)
T ss_dssp ---EEEEEEEEE-TC
T ss_pred ccceEEEEEEEecCc
Confidence 345677887776665
No 144
>PF15491 CTC1_2: CST, telomere maintenance, complex subunit CTC1
Probab=27.16 E-value=62 Score=28.41 Aligned_cols=24 Identities=38% Similarity=0.569 Sum_probs=20.2
Q ss_pred EeEEEEEEEEEeeeCCCCcEEEEcC
Q 044496 34 FQRVWLQGVLVSPPDDDGRLLLDDG 58 (142)
Q Consensus 34 ~~~VWlQG~vv~~~~~~~~~~LdDg 58 (142)
++-|.|||++++.+ ++..++|+|-
T Consensus 255 Vtgvy~qg~~veLD-~~VwLLltdq 278 (291)
T PF15491_consen 255 VTGVYMQGMVVELD-EDVWLLLTDQ 278 (291)
T ss_pred EEEEEEcccEEEEc-ccEEEEEecc
Confidence 67799999999984 5788998885
No 145
>CHL00010 infA translation initiation factor 1
Probab=26.95 E-value=2.2e+02 Score=19.65 Aligned_cols=45 Identities=27% Similarity=0.361 Sum_probs=29.3
Q ss_pred EEEEEEeeeCCCCcEEEEcCCe-eEEEEeccccccc--cccCCcccccceeEEEEE
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTG-VVQIYLSGDFRIR--RWNTGVFFFDFWMYVMVV 91 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG-~~~v~~~~~~~~~--~~~~G~~~~~~~~YVmVi 91 (142)
++|+|++.- +++.+.+.+..| .+.+...+-.+.+ .+.+| ++|.|-
T Consensus 9 ~~G~Vik~l-g~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vG-------D~V~ve 56 (78)
T CHL00010 9 MEGLVTESL-PNGMFRVRLDNGCQVLGYISGKIRRNSIRILPG-------DRVKVE 56 (78)
T ss_pred EEEEEEEEc-CCCEEEEEeCCCCEEEEEeccceecCCcccCCC-------CEEEEE
Confidence 899999973 345565543334 5666666655543 36889 999765
No 146
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=26.73 E-value=1.5e+02 Score=20.94 Aligned_cols=37 Identities=16% Similarity=0.273 Sum_probs=28.2
Q ss_pred eCCCCcEEEEcCCeeEEE-Eecccccccc-ccCCcccccceeEEEE
Q 044496 47 PDDDGRLLLDDGTGVVQI-YLSGDFRIRR-WNTGVFFFDFWMYVMV 90 (142)
Q Consensus 47 ~~~~~~~~LdDgTG~~~v-~~~~~~~~~~-~~~G~~~~~~~~YVmV 90 (142)
..++|.+.+.+..|.-.+ ..++-++.+- ++.| +||.|
T Consensus 9 ~~G~n~~~V~~~dG~~~l~~iP~KfRk~iWIkrG-------d~VlV 47 (78)
T cd05792 9 SKGNNLHEVETPNGSRYLVSMPTKFRKNIWIKRG-------DFVLV 47 (78)
T ss_pred cCCCcEEEEEcCCCCEEEEEechhhcccEEEEeC-------CEEEE
Confidence 357888888888887444 4577777666 7999 99988
No 147
>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=26.59 E-value=2.5e+02 Score=20.28 Aligned_cols=54 Identities=24% Similarity=0.228 Sum_probs=28.0
Q ss_pred EEEEEEEEEeeeC--CCCcEEEEcC---CeeEEEEecccc--ccc--cccCCcccccceeEEEEEeeEee
Q 044496 36 RVWLQGVLVSPPD--DDGRLLLDDG---TGVVQIYLSGDF--RIR--RWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 36 ~VWlQG~vv~~~~--~~~~~~LdDg---TG~~~v~~~~~~--~~~--~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
.+-++|+|.++.. ++..+++.+. .+.+.+..+... ... .++.| +-|-|.|.+..
T Consensus 69 ~i~vtG~V~~I~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~l~~G-------~~Vti~G~~~g 131 (144)
T PF12869_consen 69 IIEVTGTVSSIDKGFGDNYVVLLGTENGFAGVQCYFSNDQEKRASVAKLKKG-------QKVTIKGICTG 131 (144)
T ss_dssp EEEEEEEEEEEEE-STT-EEEEEE-TT-S-S--EEEEEEGGGHHHHHH--TT-------SEEEEEEE---
T ss_pred EEEEEEEEEEEEEcCCCcEEEEccCCCCceeEEEEEccchhhhhhHhcCCCC-------CEEEEEEEEEe
Confidence 3458899999954 3444554433 333566653333 112 39999 99999998865
No 148
>PF00313 CSD: 'Cold-shock' DNA-binding domain; InterPro: IPR002059 When Escherichia coli is exposed to a temperature drop from 37 to 10 degrees centigrade, a 4-5 hour lag phase occurs, after which growth is resumed at a reduced rate []. During the lag phase, the expression of around 13 proteins, which contain specific DNA-binding regions [], is increased 2-10 fold. These so-called 'cold shock' proteins are thought to help the cell to survive in temperatures lower than optimum growth temperature, by contrast with heat shock proteins, which help the cell to survive in temperatures greater than the optimum, possibly by condensation of the chromosome and organisation of the prokaryotic nucleoid []. A conserved domain of about 70 amino acids has been found in prokaryotic and eukaryotic DNA-binding proteins [, , ]. This domain is known as the 'cold-shock domain' (CSD), part of which is highly similar [] to the RNP-1 RNA-binding motif.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1HZC_A 1I5F_A 1HZ9_B 1C9O_B 1HZB_B 1HZA_A 2HAX_B 2L15_A 2LSS_A 3I2Z_B ....
Probab=25.98 E-value=1.8e+02 Score=18.51 Aligned_cols=60 Identities=13% Similarity=0.034 Sum_probs=35.6
Q ss_pred EEEEEEeeeCCCC-cEEEEcCCe-eEEEEeccccccc--cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEe
Q 044496 39 LQGVLVSPPDDDG-RLLLDDGTG-VVQIYLSGDFRIR--RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIV 110 (142)
Q Consensus 39 lQG~vv~~~~~~~-~~~LdDgTG-~~~v~~~~~~~~~--~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~ 110 (142)
|+|+|.+..+..+ -|+-.|+++ .+-+..+...... .++.| +-|..-=.. ..--++|.+|.
T Consensus 1 ~~G~V~~~~~~kgyGFI~~~~~~~diFfh~s~~~~~~~~~l~~G-------~~V~F~~~~-----~~~g~~A~~V~ 64 (66)
T PF00313_consen 1 MTGTVKWFDDEKGYGFITSDDGGEDIFFHISDLSGNGFRSLKEG-------DRVEFEVEE-----GKKGPQAVNVR 64 (66)
T ss_dssp EEEEEEEEETTTTEEEEEETTSSSEEEEEGGGBCSSSSTS--TT-------SEEEEEEEE-----CTTSEEEEEEE
T ss_pred CeEEEEEEECCCCceEEEEcccceeEEeccccccccccccCCCC-------CEEEEEEEE-----CCCCCEEEEEE
Confidence 8999999976544 677777777 4555556655543 58999 666432211 23344666654
No 149
>KOG0555 consensus Asparaginyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=25.98 E-value=1e+02 Score=28.97 Aligned_cols=57 Identities=28% Similarity=0.224 Sum_probs=37.5
Q ss_pred EEeEEEEEEEEEeeeCCCC--cEEEEcCCeeEEEEecccccc-c---cccCCcccccceeEEEEEeeEee
Q 044496 33 LFQRVWLQGVLVSPPDDDG--RLLLDDGTGVVQIYLSGDFRI-R---RWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 33 ~~~~VWlQG~vv~~~~~~~--~~~LdDgTG~~~v~~~~~~~~-~---~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
.=|||-+-|-|-......+ -++|.||||-+++.++..--. . .+..- .-|.|.|.+.+
T Consensus 122 r~qrVkv~gWVhrlR~qk~l~FivLrdg~gflqCVl~~kl~~~yd~~~Ls~e-------ssv~vYG~i~~ 184 (545)
T KOG0555|consen 122 RGQRVKVFGWVHRLRRQKSLIFIVLRDGTGFLQCVLSDKLCQSYDALTLSTE-------SSVTVYGTIKK 184 (545)
T ss_pred cCceEEeehhhHhhhhcCceEEEEEecCCceEEEEEcchhhhhhcccccccc-------ceEEEEEEEec
Confidence 3478888888877643333 357999999999998553211 1 24444 66777777765
No 150
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=25.97 E-value=1.6e+02 Score=18.77 Aligned_cols=40 Identities=20% Similarity=0.160 Sum_probs=26.3
Q ss_pred EEEEEEeeeCC-CCcEEEEcCCee-EEEEecccccc--ccccCC
Q 044496 39 LQGVLVSPPDD-DGRLLLDDGTGV-VQIYLSGDFRI--RRWNTG 78 (142)
Q Consensus 39 lQG~vv~~~~~-~~~~~LdDgTG~-~~v~~~~~~~~--~~~~~G 78 (142)
++|+|.+.+++ +--|+-.|++|. +-+-.+..... +.+++|
T Consensus 1 ~~G~Vk~~~~~kGfGFI~~~~~g~diffh~~~~~~~~~~~~~~G 44 (65)
T cd04458 1 VTGTVKWFDDEKGFGFITPDDGGEDVFVHISALEGDGFRSLEEG 44 (65)
T ss_pred CcEEEEEEECCCCeEEEecCCCCcCEEEEhhHhhccCCCcCCCC
Confidence 58999998765 446777776564 55555555443 458888
No 151
>PRK08395 fumarate hydratase; Provisional
Probab=25.92 E-value=14 Score=29.56 Aligned_cols=41 Identities=27% Similarity=0.289 Sum_probs=25.2
Q ss_pred eEEEEEeeEeeccCCCceEEEEEEeeCCCCcC-ccchhHHHHHHH
Q 044496 86 MYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPD-REAMWYLEVMEA 129 (142)
Q Consensus 86 ~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~-re~mW~lEV~e~ 129 (142)
-|...+|+.-+-- ...|+.++.+...+ .- .|++|.+||++.
T Consensus 106 vYl~~~GGaaal~--~~~Ik~~~~v~~~d-LGm~EAi~~leVedf 147 (162)
T PRK08395 106 VYFAFPGGAGSLA--AKSIKRVRDVYWED-LGMPDAVWELEVEDF 147 (162)
T ss_pred EEEecccHHHHHH--HhcccEEEEEeecC-CCCccEEEEEEEecC
Confidence 4555555432211 23566667777654 44 599999999874
No 152
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=25.86 E-value=2.1e+02 Score=19.20 Aligned_cols=47 Identities=23% Similarity=0.267 Sum_probs=29.6
Q ss_pred EEEEEEEEeeeCCCCcEEEEcCCe-eEEEEecccccc-c-cccCCcccccceeEEEEE
Q 044496 37 VWLQGVLVSPPDDDGRLLLDDGTG-VVQIYLSGDFRI-R-RWNTGVFFFDFWMYVMVV 91 (142)
Q Consensus 37 VWlQG~vv~~~~~~~~~~LdDgTG-~~~v~~~~~~~~-~-~~~~G~~~~~~~~YVmVi 91 (142)
+-|+|+|++.- .++.+.+-+..| .+.+...+-.+. + .+.+| ++|.+-
T Consensus 7 ~~~~G~Vi~~~-~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vG-------D~V~ve 56 (72)
T PRK00276 7 IEMEGTVVEAL-PNAMFRVELENGHEVLAHISGKMRKNYIRILPG-------DKVTVE 56 (72)
T ss_pred EEEEEEEEEEc-CCCEEEEEeCCCCEEEEEEccceeeCCcccCCC-------CEEEEE
Confidence 55899999963 343555543344 466666665553 3 37899 998764
No 153
>PRK08228 L(+)-tartrate dehydratase subunit beta; Validated
Probab=25.82 E-value=14 Score=30.69 Aligned_cols=28 Identities=14% Similarity=0.178 Sum_probs=21.0
Q ss_pred ceEEEEEEeeCCCCcCccchhHHHHHHH
Q 044496 102 PVIKVHKIVDLSAFPDREAMWYLEVMEA 129 (142)
Q Consensus 102 p~i~a~K~~DLS~~p~re~mW~lEV~e~ 129 (142)
-.|+.++.++.-+--..|++|.+||++.
T Consensus 136 ~~Ik~v~~V~~~dLGmpEAv~~l~Vedf 163 (204)
T PRK08228 136 TQVEEIEDAQWRDLGMPETLWVCRVKEF 163 (204)
T ss_pred hhccEEEEeeeccCCCccEEEEEEEeec
Confidence 3677777777775334699999999986
No 154
>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=23.97 E-value=5e+02 Score=26.95 Aligned_cols=55 Identities=16% Similarity=0.175 Sum_probs=40.2
Q ss_pred eEEEEEEEEEeeeCC---CC----cEEEEcCCeeEEEEe-cccccc----ccccCCcccccceeEEEEEeeEee
Q 044496 35 QRVWLQGVLVSPPDD---DG----RLLLDDGTGVVQIYL-SGDFRI----RRWNTGVFFFDFWMYVMVVGGFVI 96 (142)
Q Consensus 35 ~~VWlQG~vv~~~~~---~~----~~~LdDgTG~~~v~~-~~~~~~----~~~~~G~~~~~~~~YVmViG~~~~ 96 (142)
.+|-++|.|..+... .| +|-+-|.|+.+.+.. ....+. ..++.| +||.+-|.+.-
T Consensus 8 ~~~~~~g~i~~~~~~~~~~~~~~~~~~~~d~~~s~~~k~f~~~~~~~~~~~~~~~g-------~~~~~~g~~~~ 74 (1213)
T TIGR01405 8 NRVKIEGYIFKIEIKELKSGRTLLKIKVTDYTDSLILKKFLKSEEDPEKFDGIKIG-------KWVRARGKIEL 74 (1213)
T ss_pred CeEEEEEEEEEEEeEeccCCCEEEEEEEEcCCCCEEEEEecccccchHHHhhcCCC-------cEEEEEEEEec
Confidence 467799999988542 33 567889999998886 221111 248999 99999999875
No 155
>PF14481 Fimbrial_PilY2: Type 4 fimbrial biogenesis protein PilY2; PDB: 3TDQ_A.
Probab=23.82 E-value=1.7e+02 Score=22.52 Aligned_cols=62 Identities=19% Similarity=0.182 Sum_probs=35.4
Q ss_pred EEEEEEeeeCCCCcEEEEcCCeeEEEEe-ccccccc-----cccCCcccccceeEEEEEeeEeeccCCCceEEEEEEeeC
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTGVVQIYL-SGDFRIR-----RWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIKVHKIVDL 112 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG~~~v~~-~~~~~~~-----~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~a~K~~DL 112 (142)
--|+|.++.. ...++.-||.- -.+ +++++++ .+++| +.|..-|.+ ++|.|.|.-+-|..=
T Consensus 32 ~~GvV~~v~~-e~~lv~IDgq~---YrLPn~v~q~~~p~ifqvrpG-------svVS~sGsv---ss~~p~I~si~i~rq 97 (118)
T PF14481_consen 32 GAGVVQEVQP-EKNLVDIDGQH---YRLPNRVAQQGGPVIFQVRPG-------SVVSFSGSV---SSPLPTITSIYILRQ 97 (118)
T ss_dssp EEEEEEEEEG-GGTEEEETTEE---EE--TT-EETTEEGGGT--TT--------EEEEEEE-----SSS-EEEEEEE-HC
T ss_pred ccceEEEeec-ccceEEEcCcE---EeCCchhhhcCCceEEEEcCC-------cEEEEeeee---cCCCcccceEEEEec
Confidence 3477877743 45555566632 112 4444433 46999 999999988 678999998888876
Q ss_pred CC
Q 044496 113 SA 114 (142)
Q Consensus 113 S~ 114 (142)
++
T Consensus 98 ~s 99 (118)
T PF14481_consen 98 MS 99 (118)
T ss_dssp CC
T ss_pred CC
Confidence 65
No 156
>PF09998 DUF2239: Uncharacterized protein conserved in bacteria (DUF2239); InterPro: IPR018715 This family of uncharacterised bacterial proteins has no known function.
Probab=23.50 E-value=1e+02 Score=25.54 Aligned_cols=18 Identities=39% Similarity=0.536 Sum_probs=14.3
Q ss_pred CCCcEEEEcCCee-EEEEe
Q 044496 49 DDGRLLLDDGTGV-VQIYL 66 (142)
Q Consensus 49 ~~~~~~LdDgTG~-~~v~~ 66 (142)
....++.||.||+ +.+.+
T Consensus 33 ~~~vLvFdd~TGr~vD~Dl 51 (187)
T PF09998_consen 33 AAPVLVFDDATGRQVDLDL 51 (187)
T ss_pred CCceEEEECCCCCEEeeeC
Confidence 3567889999998 77776
No 157
>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=23.46 E-value=72 Score=23.96 Aligned_cols=21 Identities=38% Similarity=0.773 Sum_probs=13.1
Q ss_pred EEEEEEeeeCCCC-----cEEEEcCC
Q 044496 39 LQGVLVSPPDDDG-----RLLLDDGT 59 (142)
Q Consensus 39 lQG~vv~~~~~~~-----~~~LdDgT 59 (142)
++|+|.++..+.| .++|.|||
T Consensus 1 ~~gtVlEvk~~~G~G~t~dvIl~~Gt 26 (110)
T cd03703 1 LQGTVLEVKEEEGLGTTIDVILYDGT 26 (110)
T ss_pred CcEEEEEEEEcCCCceEEEEEEECCe
Confidence 3789999865433 45555553
No 158
>KOG2732 consensus DNA polymerase delta, regulatory subunit 55 [Replication, recombination and repair]
Probab=23.15 E-value=2.8e+02 Score=25.74 Aligned_cols=37 Identities=27% Similarity=0.311 Sum_probs=27.5
Q ss_pred CCcEEEEcCCeeEEEEeccccccccccCCcccccceeEEEEEeeE
Q 044496 50 DGRLLLDDGTGVVQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGF 94 (142)
Q Consensus 50 ~~~~~LdDgTG~~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~ 94 (142)
++.+.|-|++|++++.++. .+...+-+| +-|-|.|+.
T Consensus 110 ed~i~LEDe~grV~L~G~~-i~~~~~vTG-------vvvavlG~~ 146 (435)
T KOG2732|consen 110 EDEIVLEDESGRVRLEGSF-ISHAVLVTG-------VVVAVLGKE 146 (435)
T ss_pred cceEEEecCCceEEEEeec-ccccceeee-------EEEEEeccc
Confidence 6699999999999999862 122247888 777777755
No 159
>COG4138 BtuD ABC-type cobalamin transport system, ATPase component [Coenzyme metabolism]
Probab=22.92 E-value=1.2e+02 Score=25.73 Aligned_cols=54 Identities=30% Similarity=0.315 Sum_probs=34.1
Q ss_pred cchHHHHHHHHHhhccCCC--CCC----ceeecCeEEeEEEEEEEEEeeeCC---CCcEEEEcC
Q 044496 4 SLAALKLLCVQLKDARESP--SQN----AVTLGGILFQRVWLQGVLVSPPDD---DGRLLLDDG 58 (142)
Q Consensus 4 ~~pa~Kvf~~QL~~a~~~~--s~~----~~~l~gl~~~~VWlQG~vv~~~~~---~~~~~LdDg 58 (142)
+.|+ |--+++|.+-+..- +.+ .--+.|=|+|||.+-|++..+.++ .+.++|-|.
T Consensus 96 ~qP~-~~~a~~i~~i~~~L~l~DKL~Rs~~qLSGGEWQRVRLAav~LQv~Pd~NP~~~LLllDE 158 (248)
T COG4138 96 HQPD-KTRTELLNDVAGALALDDKLGRSTNQLSGGEWQRVRLAAVVLQITPDANPAGQLLLLDE 158 (248)
T ss_pred cCch-HHHHHHHHHHHhhhcccchhhhhhhhcCcccceeeEEeEEEEEecCCCCccceeEEecC
Confidence 3455 55556665554311 111 112668899999999999999665 566666665
No 160
>PRK06043 fumarate hydratase; Provisional
Probab=22.72 E-value=18 Score=29.81 Aligned_cols=42 Identities=33% Similarity=0.406 Sum_probs=28.8
Q ss_pred eEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHHH
Q 044496 86 MYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVMEA 129 (142)
Q Consensus 86 ~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e~ 129 (142)
-|...+|+.-+-- .-.|+-++++..-+--..|++|.+||++.
T Consensus 120 vYl~~~GGaaALl--~~~Ik~~~~v~~~dLGmpEAi~~leV~df 161 (192)
T PRK06043 120 VYLAYTGGCAALA--AESIKRVKAVHWLDLGMPEAVWVLEVEEF 161 (192)
T ss_pred EEEEeCChHHHHH--HhcccEEEEEeeccCCCccEEEEEEEeec
Confidence 6777777654311 23677777777765334699999999986
No 161
>KOG2104 consensus Nuclear transport factor 2 [Intracellular trafficking, secretion, and vesicular transport]
Probab=22.62 E-value=1.1e+02 Score=23.97 Aligned_cols=30 Identities=27% Similarity=0.509 Sum_probs=25.3
Q ss_pred eEEEEEeeEeeccCCCceEEEEEEeeCCCCcC
Q 044496 86 MYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPD 117 (142)
Q Consensus 86 ~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~ 117 (142)
+-|||.|-++. ...|.++-++|--|..|++
T Consensus 80 ilv~V~G~Lk~--dEd~~~~FsQvF~L~~n~~ 109 (126)
T KOG2104|consen 80 ILVMVVGQLKL--DEDPILRFSQVFLLKPNIQ 109 (126)
T ss_pred EEEEEeeeeee--ccCCccceeeEEEEeEcCC
Confidence 99999999976 3788899999999987653
No 162
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=22.60 E-value=2.2e+02 Score=18.30 Aligned_cols=45 Identities=24% Similarity=0.279 Sum_probs=27.7
Q ss_pred EEEEEEeeeCCCCcEEEEcCCe-eEEEEeccccc-cc-cccCCcccccceeEEEEE
Q 044496 39 LQGVLVSPPDDDGRLLLDDGTG-VVQIYLSGDFR-IR-RWNTGVFFFDFWMYVMVV 91 (142)
Q Consensus 39 lQG~vv~~~~~~~~~~LdDgTG-~~~v~~~~~~~-~~-~~~~G~~~~~~~~YVmVi 91 (142)
|+|+|++.- +++.+.+.+.+| .+.+...+-.+ .+ ++..| ++|.+-
T Consensus 3 ~~G~Vi~~~-~g~~~~V~~~~g~~~~c~~rGklr~~~~~~~vG-------D~V~~~ 50 (64)
T cd04451 3 MEGVVTEAL-PNAMFRVELENGHEVLAHISGKMRMNYIRILPG-------DRVKVE 50 (64)
T ss_pred EEEEEEEEe-CCCEEEEEeCCCCEEEEEECceeecCCcccCCC-------CEEEEE
Confidence 789999863 234555544444 56666655444 23 47899 888554
No 163
>PF09870 DUF2097: Uncharacterized protein conserved in archaea (DUF2097); InterPro: IPR019208 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=21.99 E-value=1.5e+02 Score=21.56 Aligned_cols=34 Identities=41% Similarity=0.623 Sum_probs=23.5
Q ss_pred CeEEeEEEEEEEEEeeeCCCCcEEEE-cCC---eeEEEEe
Q 044496 31 GILFQRVWLQGVLVSPPDDDGRLLLD-DGT---GVVQIYL 66 (142)
Q Consensus 31 gl~~~~VWlQG~vv~~~~~~~~~~Ld-DgT---G~~~v~~ 66 (142)
.+.+.||-+-|+|++.+. +.++|+ ||- |.+++.+
T Consensus 26 EisygRv~vpG~V~~~~~--~~~~l~~~~~~~~g~ve~Dl 63 (86)
T PF09870_consen 26 EISYGRVHVPGEVLSIED--GFLRLQLDGELINGTVEVDL 63 (86)
T ss_pred EEEeeEEEeeeEEEEeee--eEEEEEEcCccccCcEEEEH
Confidence 578999999999999843 444443 333 5566655
No 164
>PF01330 RuvA_N: RuvA N terminal domain; InterPro: IPR013849 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. This entry represents domain I of RuvA, which has an OB-fold structure. This domain forms the RuvA tetramer contacts [].; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1HJP_A 1D8L_B 1CUK_A 1C7Y_A 1IXR_B 2ZTC_A 2ZTD_B 2H5X_A 2ZTE_A 1BVS_E ....
Probab=21.52 E-value=2.2e+02 Score=18.34 Aligned_cols=28 Identities=21% Similarity=0.581 Sum_probs=20.6
Q ss_pred EEEEEEEEeeeCCCCcEEEEcCCee-EEEEec
Q 044496 37 VWLQGVLVSPPDDDGRLLLDDGTGV-VQIYLS 67 (142)
Q Consensus 37 VWlQG~vv~~~~~~~~~~LdDgTG~-~~v~~~ 67 (142)
.++.|+|+++ +.+.++|+-+ |. .+|..+
T Consensus 3 ~~l~G~v~~~--~~~~vvi~~~-GvGy~v~v~ 31 (61)
T PF01330_consen 3 AYLKGKVVEK--NPDYVVIDVN-GVGYEVFVP 31 (61)
T ss_dssp EEEEEEEEEE--ESSEEEEEET-TEEEEEEE-
T ss_pred cEEEEEEEEE--cCCEEEEEEC-CEEEEEEeC
Confidence 3789999998 5567888777 66 666663
No 165
>PF06918 DUF1280: Protein of unknown function (DUF1280); InterPro: IPR009689 This family represents a conserved region approximately 200 residues long within a number of proteins of unknown function that seem to be specific to Caenorhabditis elegans.
Probab=20.83 E-value=2.1e+02 Score=23.75 Aligned_cols=46 Identities=20% Similarity=0.283 Sum_probs=32.9
Q ss_pred CCcEEEEcCCee-EEEEeccccccccccCCcccccceeEEEEEeeEeeccCCCceEE
Q 044496 50 DGRLLLDDGTGV-VQIYLSGDFRIRRWNTGVFFFDFWMYVMVVGGFVIRTDDIPVIK 105 (142)
Q Consensus 50 ~~~~~LdDgTG~-~~v~~~~~~~~~~~~~G~~~~~~~~YVmViG~~~~~~~~~p~i~ 105 (142)
.+.++.|||||- +.|.+.+|.-+... +-++++|-+..+.+|...+.
T Consensus 148 ~~~L~~~~~t~d~I~l~igGDkGg~~t----------Kl~~~i~Nv~~PNs~~~~~~ 194 (224)
T PF06918_consen 148 SGKLIFDDGTGDEIWLGIGGDKGGDET----------KLCLQIENVDKPNSPHNLLL 194 (224)
T ss_pred cCCceeCCCCCCCEEEEEcccCCCCce----------EEEEEEeccCCCCCcCcEEE
Confidence 678999999987 77777665543333 77889998887555555443
No 166
>PF05683 Fumerase_C: Fumarase C-terminus; InterPro: IPR004647 This entry represents various Fe-S type hydro-lyases, including the beta subunit from both L-tartrate dehydratase (TtdB; EC:4.2.1.32) and class 2 fumarate hydratase (FumC; (4.2.1.2 from EC) []. A number of Fe-S cluster-containing hydro-lyases share a conserved motif, including argininosuccinate lyase, adenylosuccinate lyase, aspartase, class I fumarate hydratase (fumarase), and tartrate dehydratase (see IPR000362 from INTERPRO). Proteins in this group represent a subset of closely related proteins or modules, including the Escherichia coli tartrate dehydratase beta chain and the C-terminal region of the class I fumarase (where the N-terminal region is homologous to the tartrate dehydratase alpha chain). The activity of the archaeal proteins in this group is unknown.; GO: 0016836 hydro-lyase activity; PDB: 2ISB_A.
Probab=20.82 E-value=18 Score=30.00 Aligned_cols=40 Identities=30% Similarity=0.424 Sum_probs=25.1
Q ss_pred eEEEEEeeEeeccCCCceEEEEEEeeCCCCcCccchhHHHHHH
Q 044496 86 MYVMVVGGFVIRTDDIPVIKVHKIVDLSAFPDREAMWYLEVME 128 (142)
Q Consensus 86 ~YVmViG~~~~~~~~~p~i~a~K~~DLS~~p~re~mW~lEV~e 128 (142)
-|...+|+- + .=-.-.|+.++.++.-+--- |++|.+||++
T Consensus 146 vYl~~~GGa-a-al~~~~Ik~v~~v~~~eLG~-EAi~~leVed 185 (205)
T PF05683_consen 146 VYLAAPGGA-A-ALLAQCIKSVEVVAWEELGM-EAIWELEVED 185 (205)
T ss_dssp EEEEE-S-S-S-TTGGGGEEEEEEEE-GGG-T-TSEEEEEEEE
T ss_pred EEEEeccHH-H-HHHhcceeEEEEEeccccCc-eEEEEEEEec
Confidence 677777752 2 22245788888888876322 9999999975
No 167
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=20.78 E-value=1.5e+02 Score=22.47 Aligned_cols=49 Identities=14% Similarity=0.204 Sum_probs=30.8
Q ss_pred EEEEEEEEEeeeCCCCcEEEEcC-----CeeEEEEeccc---cc-------cc-cccCCcccccceeEEEEE
Q 044496 36 RVWLQGVLVSPPDDDGRLLLDDG-----TGVVQIYLSGD---FR-------IR-RWNTGVFFFDFWMYVMVV 91 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~~~~LdDg-----TG~~~v~~~~~---~~-------~~-~~~~G~~~~~~~~YVmVi 91 (142)
.-||+++|++...++++.-+.|. .+++.+..+.. |. .. .+..| .-||.+
T Consensus 17 ~~WIla~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP~~~~~~~~~~~~f~~g-------~~VLAl 81 (130)
T PF07039_consen 17 EEWILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLPKKAPPDTDPLAEFPKG-------TKVLAL 81 (130)
T ss_dssp CEEEEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-SB--TTT-GGGS--TT--------EEEEE
T ss_pred CCEEEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECCCccCCCCCchhhCCCC-------CEEEEE
Confidence 57999999999877777777663 35666665331 22 22 37888 777765
No 168
>cd01210 EPS8 Epidermal growth factor receptor kinase substrate (EPS8) Phosphotyrosine-binding (PTB) domain. Epidermal growth factor receptor kinase substrate (EPS8) Phosphotyrosine-binding (PTB) domain. EPS8 is a regulator of Rac signaling. It consists of a PTB and an SH3 domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=20.45 E-value=1.4e+02 Score=23.12 Aligned_cols=74 Identities=18% Similarity=0.083 Sum_probs=39.3
Q ss_pred EEEEEEEEEeeeCCCCcEEEEc-CCee-EEEE-ecccccccc-ccCCcccccceeEEEEEeeEe-eccCCCceEEEEEEe
Q 044496 36 RVWLQGVLVSPPDDDGRLLLDD-GTGV-VQIY-LSGDFRIRR-WNTGVFFFDFWMYVMVVGGFV-IRTDDIPVIKVHKIV 110 (142)
Q Consensus 36 ~VWlQG~vv~~~~~~~~~~LdD-gTG~-~~v~-~~~~~~~~~-~~~G~~~~~~~~YVmViG~~~-~~~~~~p~i~a~K~~ 110 (142)
+||-|+.+..+ +++.++|-| .||. ++-. ++.+.+-+. .+.| .|=-+.=-+. .+..+.|-+-.-+..
T Consensus 38 ~iW~Q~m~lqv--~~~~v~LlD~etk~elE~fpl~~I~~~~a~~~~~-------~ynslL~~vvq~~~~~~~e~hlFQc~ 108 (127)
T cd01210 38 RVWSQKMILRV--RYQWVTLLDYETKEELESYPLSLIQEPTAFTSME-------LYNSILLFVVQEPGGSRTEMHIFQCQ 108 (127)
T ss_pred CccccceEEEE--cCCeEEEEcCCCcChhhcCCHhhccccceecCCC-------CcCceEEEEEeCCCCCCCcEEEEEec
Confidence 79999999998 556555555 4653 2211 244444343 5566 5543332222 223345555555555
Q ss_pred eCCCCcCc
Q 044496 111 DLSAFPDR 118 (142)
Q Consensus 111 DLS~~p~r 118 (142)
+.++...+
T Consensus 109 ~v~A~~i~ 116 (127)
T cd01210 109 RVGAEHLV 116 (127)
T ss_pred cccHHHHH
Confidence 65554443
Done!