Query 045338
Match_columns 134
No_of_seqs 116 out of 264
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 12:14:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045338.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045338hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00255 60S ribosomal protein 100.0 4.6E-50 9.9E-55 289.5 8.5 90 43-132 1-90 (90)
2 TIGR00280 L37a ribosomal prote 100.0 5.6E-50 1.2E-54 289.6 8.9 91 43-134 1-91 (91)
3 PF01780 Ribosomal_L37ae: Ribo 100.0 4.9E-50 1.1E-54 289.3 7.8 90 44-133 1-90 (90)
4 PRK03976 rpl37ae 50S ribosomal 100.0 2.7E-49 5.9E-54 285.5 8.4 90 43-132 1-90 (90)
5 KOG0402 60S ribosomal protein 100.0 4.3E-49 9.3E-54 284.9 5.5 92 43-134 1-92 (92)
6 COG1997 RPL43A Ribosomal prote 100.0 1.6E-42 3.4E-47 250.4 7.4 89 43-132 1-89 (89)
7 PF12760 Zn_Tnp_IS1595: Transp 97.0 0.00061 1.3E-08 42.8 2.4 28 78-105 18-46 (46)
8 TIGR03655 anti_R_Lar restricti 97.0 0.00091 2E-08 43.1 3.1 40 80-128 3-49 (53)
9 PRK09710 lar restriction allev 96.1 0.0063 1.4E-07 42.3 3.3 25 80-104 8-35 (64)
10 PRK00432 30S ribosomal protein 95.8 0.0051 1.1E-07 40.1 1.6 26 80-106 22-47 (50)
11 PF14354 Lar_restr_allev: Rest 95.7 0.018 3.8E-07 37.1 3.6 46 79-128 4-57 (61)
12 COG4888 Uncharacterized Zn rib 95.5 0.0085 1.8E-07 45.1 1.9 46 75-120 19-70 (104)
13 PHA00626 hypothetical protein 95.4 0.011 2.4E-07 40.6 2.2 33 80-112 2-39 (59)
14 PF08271 TF_Zn_Ribbon: TFIIB z 95.1 0.019 4.2E-07 35.4 2.3 31 79-109 1-32 (43)
15 PRK00464 nrdR transcriptional 94.7 0.019 4.2E-07 44.9 1.9 26 79-108 1-40 (154)
16 PF07282 OrfB_Zn_ribbon: Putat 94.7 0.022 4.8E-07 37.3 1.9 27 80-106 30-56 (69)
17 PF01807 zf-CHC2: CHC2 zinc fi 94.7 0.02 4.3E-07 40.7 1.8 52 78-131 33-88 (97)
18 PRK00398 rpoP DNA-directed RNA 94.2 0.035 7.7E-07 34.6 1.9 30 77-106 2-31 (46)
19 smart00400 ZnF_CHCC zinc finge 93.5 0.046 1E-06 35.0 1.6 31 79-112 3-37 (55)
20 smart00661 RPOL9 RNA polymeras 93.4 0.063 1.4E-06 33.3 2.1 32 80-111 2-35 (52)
21 PF05129 Elf1: Transcription e 93.0 0.079 1.7E-06 37.4 2.3 46 74-119 18-69 (81)
22 PF08273 Prim_Zn_Ribbon: Zinc- 93.0 0.057 1.2E-06 34.1 1.4 28 80-108 5-37 (40)
23 COG0675 Transposase and inacti 92.9 0.063 1.4E-06 41.8 1.9 22 80-106 311-332 (364)
24 PF08646 Rep_fac-A_C: Replicat 92.3 0.096 2.1E-06 38.7 2.1 32 80-112 20-53 (146)
25 COG1998 RPS31 Ribosomal protei 92.1 0.077 1.7E-06 35.6 1.1 30 77-106 18-47 (51)
26 TIGR03831 YgiT_finger YgiT-typ 91.3 0.14 2.9E-06 30.6 1.6 15 93-107 29-43 (46)
27 PF11781 RRN7: RNA polymerase 91.2 0.13 2.7E-06 31.6 1.4 26 79-105 9-34 (36)
28 PF09986 DUF2225: Uncharacteri 90.6 0.33 7E-06 39.0 3.6 37 77-113 4-65 (214)
29 PRK05667 dnaG DNA primase; Val 90.3 0.16 3.4E-06 46.5 1.8 48 79-129 37-89 (580)
30 PRK00423 tfb transcription ini 90.2 0.19 4.1E-06 42.1 2.1 37 71-107 4-41 (310)
31 PHA02942 putative transposase; 90.2 0.16 3.5E-06 44.1 1.6 26 80-106 327-352 (383)
32 smart00778 Prim_Zn_Ribbon Zinc 89.5 0.21 4.6E-06 31.1 1.4 26 79-104 4-33 (37)
33 TIGR01391 dnaG DNA primase, ca 89.5 0.23 5E-06 43.2 2.1 31 79-112 35-69 (415)
34 TIGR03830 CxxCG_CxxCG_HTH puta 89.4 0.35 7.6E-06 34.2 2.6 16 93-108 28-43 (127)
35 PRK12366 replication factor A; 89.1 0.18 3.9E-06 46.5 1.2 24 80-105 534-557 (637)
36 PRK14892 putative transcriptio 88.2 0.16 3.4E-06 37.4 0.2 33 73-106 16-52 (99)
37 cd04476 RPA1_DBD_C RPA1_DBD_C: 87.7 0.28 6E-06 36.9 1.2 26 80-106 36-61 (166)
38 smart00659 RPOLCX RNA polymera 87.6 0.41 8.8E-06 30.4 1.8 29 78-107 2-30 (44)
39 smart00531 TFIIE Transcription 87.4 0.4 8.8E-06 36.2 2.0 32 75-106 96-133 (147)
40 PHA02540 61 DNA primase; Provi 87.0 0.47 1E-05 41.3 2.4 27 78-105 27-64 (337)
41 PF13465 zf-H2C2_2: Zinc-finge 86.8 0.43 9.4E-06 26.6 1.4 15 73-87 9-23 (26)
42 smart00440 ZnF_C2C2 C2C2 Zinc 86.3 0.6 1.3E-05 28.8 2.0 29 79-107 1-39 (40)
43 PF05605 zf-Di19: Drought indu 86.3 0.33 7.2E-06 30.9 0.8 10 78-87 2-11 (54)
44 PF03811 Zn_Tnp_IS1: InsA N-te 85.9 0.55 1.2E-05 28.9 1.7 23 80-102 7-35 (36)
45 PF03604 DNA_RNApol_7kD: DNA d 85.8 0.3 6.4E-06 29.5 0.4 27 79-106 1-27 (32)
46 PRK11823 DNA repair protein Ra 85.4 0.37 8E-06 42.4 1.0 25 75-103 4-28 (446)
47 TIGR01384 TFS_arch transcripti 84.8 0.48 1E-05 33.3 1.2 27 80-108 2-28 (104)
48 smart00834 CxxC_CXXC_SSSS Puta 84.6 0.76 1.7E-05 27.0 1.8 28 78-105 5-35 (41)
49 PRK14890 putative Zn-ribbon RN 84.5 0.72 1.6E-05 31.6 1.9 16 76-91 23-38 (59)
50 PF09538 FYDLN_acid: Protein o 84.3 0.41 8.9E-06 35.6 0.7 29 77-108 8-38 (108)
51 TIGR00244 transcriptional regu 84.3 0.57 1.2E-05 37.0 1.5 28 80-107 2-39 (147)
52 COG1571 Predicted DNA-binding 84.2 0.36 7.7E-06 43.6 0.3 30 80-110 352-381 (421)
53 COG1594 RPB9 DNA-directed RNA 84.0 0.86 1.9E-05 33.8 2.2 28 80-107 4-33 (113)
54 TIGR00416 sms DNA repair prote 82.8 0.55 1.2E-05 41.6 1.0 25 75-103 4-28 (454)
55 PF14353 CpXC: CpXC protein 82.8 1.3 2.7E-05 32.2 2.7 13 95-107 37-49 (128)
56 COG1405 SUA7 Transcription ini 82.6 1.1 2.4E-05 38.1 2.6 30 79-108 2-32 (285)
57 PF07191 zinc-ribbons_6: zinc- 82.5 1.4 3.1E-05 31.0 2.8 33 80-114 3-35 (70)
58 COG3677 Transposase and inacti 82.4 1.9 4.1E-05 32.6 3.6 30 79-108 31-65 (129)
59 PF08772 NOB1_Zn_bind: Nin one 82.3 0.79 1.7E-05 32.2 1.4 21 76-96 22-42 (73)
60 PF01096 TFIIS_C: Transcriptio 82.0 2.7 5.9E-05 25.7 3.6 27 80-106 2-38 (39)
61 PF02150 RNA_POL_M_15KD: RNA p 81.3 1.7 3.6E-05 26.3 2.4 29 80-108 3-32 (35)
62 COG2956 Predicted N-acetylgluc 80.7 0.96 2.1E-05 40.6 1.7 37 63-104 340-376 (389)
63 PF11672 DUF3268: Protein of u 80.6 1.9 4.1E-05 32.0 3.0 52 78-130 2-64 (102)
64 PF08792 A2L_zn_ribbon: A2L zi 80.4 2.2 4.9E-05 25.7 2.7 30 78-107 3-32 (33)
65 PRK08402 replication factor A; 80.3 1.1 2.4E-05 39.1 1.9 26 79-104 213-238 (355)
66 cd01121 Sms Sms (bacterial rad 79.9 0.89 1.9E-05 39.4 1.2 21 79-103 1-21 (372)
67 PF10571 UPF0547: Uncharacteri 79.8 0.7 1.5E-05 26.6 0.4 24 80-107 2-25 (26)
68 PF04606 Ogr_Delta: Ogr/Delta- 79.6 3.6 7.8E-05 25.9 3.6 30 80-109 1-40 (47)
69 PF06689 zf-C4_ClpX: ClpX C4-t 79.5 0.76 1.6E-05 28.5 0.5 24 79-102 2-30 (41)
70 PF03119 DNA_ligase_ZBD: NAD-d 78.6 1.3 2.8E-05 25.7 1.2 21 80-100 1-21 (28)
71 COG1779 C4-type Zn-finger prot 78.6 1.6 3.5E-05 36.1 2.2 30 78-107 14-54 (201)
72 PF09855 DUF2082: Nucleic-acid 78.2 2.1 4.5E-05 29.4 2.4 10 79-88 1-10 (64)
73 PRK09678 DNA-binding transcrip 77.9 2.8 6.1E-05 29.4 3.0 30 79-108 2-41 (72)
74 PF09862 DUF2089: Protein of u 77.7 2.4 5.3E-05 32.0 2.8 24 81-109 1-25 (113)
75 COG1645 Uncharacterized Zn-fin 77.6 1.8 3.8E-05 33.7 2.1 28 78-107 28-55 (131)
76 KOG3214 Uncharacterized Zn rib 77.0 1.1 2.3E-05 34.2 0.7 47 74-120 19-71 (109)
77 PF13453 zf-TFIIB: Transcripti 77.0 3.5 7.6E-05 25.0 2.9 24 80-103 1-26 (41)
78 PF08274 PhnA_Zn_Ribbon: PhnA 76.9 2.3 5.1E-05 25.4 2.0 26 80-106 4-29 (30)
79 COG2888 Predicted Zn-ribbon RN 76.8 1.3 2.9E-05 30.7 1.1 16 76-91 25-40 (61)
80 PHA00732 hypothetical protein 76.6 1.4 3E-05 30.9 1.2 10 98-107 29-38 (79)
81 PF01927 Mut7-C: Mut7-C RNAse 76.5 2.3 5E-05 32.0 2.4 31 80-110 93-138 (147)
82 TIGR02159 PA_CoA_Oxy4 phenylac 76.3 0.78 1.7E-05 35.4 -0.2 28 79-106 106-140 (146)
83 PF14471 DUF4428: Domain of un 76.1 0.46 1E-05 30.9 -1.2 34 80-114 1-38 (51)
84 TIGR01384 TFS_arch transcripti 75.9 4.3 9.4E-05 28.5 3.6 33 78-110 62-104 (104)
85 COG1592 Rubrerythrin [Energy p 75.9 1.5 3.2E-05 35.0 1.3 36 63-103 121-156 (166)
86 smart00731 SprT SprT homologue 75.7 2.9 6.2E-05 31.2 2.8 66 38-106 62-143 (146)
87 PF04981 NMD3: NMD3 family ; 75.2 3.1 6.7E-05 33.6 3.0 22 93-114 32-53 (236)
88 PF01599 Ribosomal_S27: Riboso 74.1 3 6.5E-05 27.3 2.2 28 77-105 17-47 (47)
89 TIGR00340 zpr1_rel ZPR1-relate 73.0 2.8 6E-05 33.1 2.2 33 81-113 1-49 (163)
90 COG1327 Predicted transcriptio 73.0 1.2 2.6E-05 35.7 0.2 28 80-107 2-39 (156)
91 TIGR02098 MJ0042_CXXC MJ0042 f 72.4 2.7 5.9E-05 24.7 1.6 30 78-107 2-36 (38)
92 PF03367 zf-ZPR1: ZPR1 zinc-fi 71.3 5.2 0.00011 31.2 3.3 35 80-114 3-52 (161)
93 cd00729 rubredoxin_SM Rubredox 71.0 3 6.6E-05 24.9 1.6 15 96-110 2-16 (34)
94 TIGR00617 rpa1 replication fac 71.0 1.8 3.9E-05 40.0 0.8 27 80-107 476-504 (608)
95 PF08996 zf-DNA_Pol: DNA Polym 70.7 5 0.00011 31.5 3.1 27 78-104 18-53 (188)
96 PF07754 DUF1610: Domain of un 70.6 2.8 6E-05 24.1 1.2 10 76-85 14-23 (24)
97 KOG2593 Transcription initiati 70.1 3.7 8E-05 37.5 2.6 30 75-104 125-161 (436)
98 COG2075 RPL24A Ribosomal prote 69.7 2.9 6.2E-05 29.4 1.4 26 79-104 4-38 (66)
99 TIGR02300 FYDLN_acid conserved 69.2 2.1 4.5E-05 33.4 0.7 27 77-106 8-36 (129)
100 PF09723 Zn-ribbon_8: Zinc rib 69.0 3 6.6E-05 25.7 1.3 17 76-92 24-40 (42)
101 TIGR00382 clpX endopeptidase C 68.0 1.8 4E-05 38.3 0.2 25 79-103 8-36 (413)
102 PRK00241 nudC NADH pyrophospha 67.4 3.9 8.4E-05 33.7 2.0 26 80-105 101-126 (256)
103 PHA02768 hypothetical protein; 67.0 2.1 4.5E-05 28.8 0.3 10 79-88 6-15 (55)
104 smart00507 HNHc HNH nucleases. 67.0 2.8 6E-05 24.2 0.8 13 75-88 8-20 (52)
105 PF13240 zinc_ribbon_2: zinc-r 66.6 1.8 3.8E-05 24.1 -0.1 22 80-105 1-22 (23)
106 PRK08173 DNA topoisomerase III 66.5 5.5 0.00012 38.5 3.0 26 79-106 625-650 (862)
107 PF14803 Nudix_N_2: Nudix N-te 65.4 6.5 0.00014 23.9 2.2 26 80-105 2-31 (34)
108 PF10058 DUF2296: Predicted in 65.3 3.6 7.8E-05 27.1 1.2 49 32-86 4-52 (54)
109 TIGR00311 aIF-2beta translatio 64.7 8.8 0.00019 29.4 3.3 43 62-105 80-127 (133)
110 PRK08665 ribonucleotide-diphos 64.0 7.6 0.00017 37.0 3.5 24 80-105 726-749 (752)
111 PRK04023 DNA polymerase II lar 63.8 3.4 7.3E-05 41.5 1.1 53 78-130 626-696 (1121)
112 COG2158 Uncharacterized protei 63.4 12 0.00026 28.7 3.8 31 88-125 52-84 (112)
113 PF00096 zf-C2H2: Zinc finger, 63.4 5.2 0.00011 20.7 1.4 11 97-107 1-11 (23)
114 PHA00616 hypothetical protein 63.3 2.5 5.4E-05 27.3 0.1 10 78-87 1-10 (44)
115 KOG2462 C2H2-type Zn-finger pr 63.3 3.7 8E-05 35.6 1.1 40 69-108 177-227 (279)
116 PF01396 zf-C4_Topoisom: Topoi 63.2 10 0.00022 23.2 2.8 27 80-106 3-34 (39)
117 COG1592 Rubrerythrin [Energy p 63.0 3.6 7.8E-05 32.9 1.0 13 96-108 134-146 (166)
118 TIGR02605 CxxC_CxxC_SSSS putat 62.9 5.6 0.00012 24.7 1.7 27 78-104 5-34 (52)
119 PRK03988 translation initiatio 61.4 10 0.00022 29.2 3.2 41 65-105 88-132 (138)
120 COG3091 SprT Zn-dependent meta 61.4 5.2 0.00011 32.1 1.6 49 55-105 95-149 (156)
121 cd00350 rubredoxin_like Rubred 60.8 5.1 0.00011 23.5 1.1 14 96-109 1-14 (33)
122 PF13894 zf-C2H2_4: C2H2-type 60.0 6.5 0.00014 19.6 1.3 11 97-107 1-11 (24)
123 PF13719 zinc_ribbon_5: zinc-r 59.8 6.9 0.00015 23.6 1.6 28 80-107 4-36 (37)
124 PF09297 zf-NADH-PPase: NADH p 59.4 10 0.00022 21.9 2.2 26 80-105 5-30 (32)
125 TIGR01385 TFSII transcription 59.3 7.4 0.00016 33.3 2.3 33 74-106 254-296 (299)
126 PF13248 zf-ribbon_3: zinc-rib 59.0 3.3 7.2E-05 23.2 0.1 23 79-105 3-25 (26)
127 PF12773 DZR: Double zinc ribb 58.6 3 6.6E-05 25.6 -0.1 29 80-109 14-42 (50)
128 PHA00733 hypothetical protein 58.2 2.9 6.3E-05 31.3 -0.3 37 71-107 66-110 (128)
129 KOG1873 Ubiquitin-specific pro 57.8 6 0.00013 38.8 1.7 38 77-114 65-111 (877)
130 COG4640 Predicted membrane pro 57.1 4.4 9.5E-05 37.2 0.6 31 80-114 3-33 (465)
131 PRK14715 DNA polymerase II lar 56.7 11 0.00024 39.2 3.3 48 77-130 673-721 (1627)
132 PRK05342 clpX ATP-dependent pr 56.6 3.5 7.6E-05 36.3 -0.1 25 78-102 9-37 (412)
133 PRK14890 putative Zn-ribbon RN 55.7 6.5 0.00014 27.0 1.1 31 75-105 4-34 (59)
134 COG1996 RPC10 DNA-directed RNA 55.1 7 0.00015 25.8 1.2 29 77-106 5-34 (49)
135 PF04071 zf-like: Cysteine-ric 55.0 8.6 0.00019 27.9 1.7 12 92-103 45-58 (86)
136 COG1656 Uncharacterized conser 54.9 4.9 0.00011 32.4 0.5 28 80-107 99-141 (165)
137 PF01873 eIF-5_eIF-2B: Domain 54.6 14 0.0003 28.0 2.8 41 64-105 78-123 (125)
138 TIGR00686 phnA alkylphosphonat 54.5 9.3 0.0002 29.1 1.9 30 80-110 4-33 (109)
139 PF13597 NRDD: Anaerobic ribon 54.2 11 0.00023 34.5 2.5 39 62-105 467-513 (546)
140 PRK12336 translation initiatio 53.6 16 0.00035 29.3 3.3 48 64-112 83-135 (201)
141 PRK05978 hypothetical protein; 53.3 5.7 0.00012 31.2 0.6 40 73-112 28-74 (148)
142 PF13717 zinc_ribbon_4: zinc-r 53.3 9.2 0.0002 23.1 1.4 28 79-106 3-35 (36)
143 PRK00420 hypothetical protein; 53.1 10 0.00022 28.6 1.9 29 78-107 23-51 (112)
144 TIGR00310 ZPR1_znf ZPR1 zinc f 53.1 13 0.00028 30.0 2.6 35 80-114 2-52 (192)
145 PF06044 DRP: Dam-replacing fa 53.1 16 0.00034 31.4 3.3 37 76-112 29-82 (254)
146 PRK04351 hypothetical protein; 53.0 10 0.00022 29.4 1.9 30 77-106 111-142 (149)
147 COG1066 Sms Predicted ATP-depe 52.6 6 0.00013 36.4 0.7 23 77-103 6-28 (456)
148 PRK04860 hypothetical protein; 51.6 5.1 0.00011 31.4 0.1 30 77-107 118-154 (160)
149 PRK07218 replication factor A; 51.4 6.5 0.00014 35.3 0.7 21 79-105 298-318 (423)
150 PF06676 DUF1178: Protein of u 51.3 9 0.00019 30.1 1.4 23 70-92 23-46 (148)
151 PF04216 FdhE: Protein involve 51.3 11 0.00024 31.1 2.0 11 93-103 235-245 (290)
152 COG3877 Uncharacterized protei 50.8 16 0.00034 28.3 2.6 37 78-118 6-46 (122)
153 TIGR02827 RNR_anaer_Bdell anae 50.3 11 0.00025 35.1 2.2 36 62-104 509-554 (586)
154 KOG2907 RNA polymerase I trans 49.7 11 0.00023 29.1 1.6 30 78-107 74-113 (116)
155 PF11023 DUF2614: Protein of u 49.7 5.8 0.00013 30.4 0.2 24 78-105 69-94 (114)
156 KOG3993 Transcription factor ( 49.5 3 6.6E-05 38.5 -1.6 21 93-113 353-373 (500)
157 PF09779 Ima1_N: Ima1 N-termin 49.3 7.3 0.00016 29.3 0.6 24 80-103 2-27 (131)
158 PF12677 DUF3797: Domain of un 49.1 10 0.00022 25.3 1.2 12 79-90 13-25 (49)
159 PRK03681 hypA hydrogenase nick 48.9 8.3 0.00018 28.3 0.8 27 76-103 68-94 (114)
160 PF12874 zf-met: Zinc-finger o 48.8 13 0.00028 19.5 1.4 12 97-108 1-12 (25)
161 PRK08270 anaerobic ribonucleos 48.1 13 0.00029 34.9 2.2 40 61-105 601-648 (656)
162 PRK07562 ribonucleotide-diphos 47.8 21 0.00045 36.5 3.6 42 63-105 1175-1216(1220)
163 PRK06266 transcription initiat 47.7 8.7 0.00019 30.4 0.8 54 75-131 114-168 (178)
164 PRK03824 hypA hydrogenase nick 47.7 9.6 0.00021 28.8 1.0 14 75-88 67-80 (135)
165 PF04423 Rad50_zn_hook: Rad50 46.6 13 0.00029 23.5 1.4 11 77-87 19-29 (54)
166 PRK11788 tetratricopeptide rep 46.4 19 0.00041 28.8 2.6 35 64-103 341-375 (389)
167 PRK08271 anaerobic ribonucleos 46.4 15 0.00033 34.6 2.3 38 62-104 543-588 (623)
168 KOG2462 C2H2-type Zn-finger pr 46.4 4.2 9E-05 35.2 -1.2 38 75-112 212-259 (279)
169 PRK13945 formamidopyrimidine-D 46.3 16 0.00034 30.4 2.2 27 77-103 253-281 (282)
170 PRK14714 DNA polymerase II lar 46.1 16 0.00035 37.5 2.6 31 79-109 668-705 (1337)
171 PF10263 SprT-like: SprT-like 45.8 15 0.00033 26.8 1.9 68 37-106 62-153 (157)
172 COG4643 Uncharacterized protei 45.8 7.4 0.00016 34.9 0.2 28 76-103 30-61 (366)
173 PF04438 zf-HIT: HIT zinc fing 45.8 8.2 0.00018 22.7 0.3 12 76-87 11-22 (30)
174 PRK12495 hypothetical protein; 45.5 11 0.00023 31.9 1.1 30 77-108 41-70 (226)
175 COG2051 RPS27A Ribosomal prote 44.9 26 0.00055 24.7 2.7 28 80-107 21-49 (67)
176 smart00653 eIF2B_5 domain pres 44.8 29 0.00063 25.7 3.2 39 65-104 66-109 (110)
177 TIGR00354 polC DNA polymerase, 44.1 10 0.00022 38.1 0.9 47 77-130 624-672 (1095)
178 PRK06386 replication factor A; 43.7 10 0.00022 33.5 0.7 20 79-104 237-256 (358)
179 smart00355 ZnF_C2H2 zinc finge 43.7 11 0.00025 18.7 0.7 8 99-106 3-10 (26)
180 PF00569 ZZ: Zinc finger, ZZ t 43.4 18 0.00039 22.5 1.7 25 76-103 2-26 (46)
181 PF14690 zf-ISL3: zinc-finger 43.4 13 0.00029 22.3 1.0 14 78-91 2-15 (47)
182 PF02945 Endonuclease_7: Recom 43.3 11 0.00024 26.6 0.8 29 55-86 2-30 (81)
183 PF03833 PolC_DP2: DNA polymer 42.3 8.3 0.00018 38.1 0.0 33 77-109 654-693 (900)
184 PRK06450 threonine synthase; V 42.1 10 0.00022 32.2 0.5 25 78-105 3-27 (338)
185 PRK07220 DNA topoisomerase I; 41.6 23 0.00049 33.6 2.7 27 78-104 635-665 (740)
186 PRK10220 hypothetical protein; 41.5 18 0.0004 27.6 1.7 30 80-110 5-34 (111)
187 PF02591 DUF164: Putative zinc 41.4 30 0.00065 22.0 2.5 46 40-86 5-54 (56)
188 PRK01103 formamidopyrimidine/5 40.8 24 0.00051 29.1 2.4 27 78-104 245-273 (274)
189 smart00709 Zpr1 Duplicated dom 40.7 24 0.00052 27.6 2.3 35 80-114 2-51 (160)
190 COG3809 Uncharacterized protei 40.6 27 0.00058 25.8 2.4 27 80-106 3-31 (88)
191 TIGR01206 lysW lysine biosynth 40.3 27 0.0006 23.2 2.2 29 78-106 2-32 (54)
192 COG4332 Uncharacterized protei 39.4 24 0.00052 29.5 2.2 33 80-112 19-65 (203)
193 PF05899 Cupin_3: Protein of u 39.3 22 0.00047 23.8 1.7 16 92-107 7-22 (74)
194 PF05741 zf-nanos: Nanos RNA b 39.2 12 0.00026 25.2 0.4 12 77-88 32-43 (55)
195 COG1326 Uncharacterized archae 39.1 17 0.00036 30.3 1.3 33 75-107 3-41 (201)
196 PRK14811 formamidopyrimidine-D 38.8 25 0.00055 29.1 2.3 27 78-104 235-263 (269)
197 PF14311 DUF4379: Domain of un 37.9 19 0.00041 22.8 1.1 11 97-107 29-39 (55)
198 TIGR00577 fpg formamidopyrimid 37.6 26 0.00056 29.0 2.2 25 78-102 245-271 (272)
199 PRK10445 endonuclease VIII; Pr 37.4 29 0.00062 28.6 2.4 29 75-103 232-262 (263)
200 PRK05638 threonine synthase; V 37.3 15 0.00033 32.0 0.8 23 78-104 1-23 (442)
201 KOG3576 Ovo and related transc 37.3 3.9 8.4E-05 35.0 -2.7 34 75-108 142-185 (267)
202 PRK14891 50S ribosomal protein 37.2 18 0.0004 28.3 1.2 26 78-103 4-38 (131)
203 CHL00174 accD acetyl-CoA carbo 37.2 6 0.00013 34.1 -1.6 29 78-106 38-67 (296)
204 PRK04023 DNA polymerase II lar 37.1 21 0.00047 36.1 1.9 31 77-107 637-674 (1121)
205 PF09082 DUF1922: Domain of un 37.0 29 0.00063 24.4 2.0 51 79-131 4-56 (68)
206 PRK05654 acetyl-CoA carboxylas 36.7 7 0.00015 33.3 -1.3 29 78-106 27-56 (292)
207 TIGR00515 accD acetyl-CoA carb 36.4 6.4 0.00014 33.5 -1.6 29 78-106 26-55 (285)
208 PF02977 CarbpepA_inh: Carboxy 36.2 7.2 0.00016 25.7 -1.0 33 83-115 7-41 (46)
209 PF14255 Cys_rich_CPXG: Cystei 36.0 18 0.00039 23.8 0.9 10 79-88 1-10 (52)
210 PF00412 LIM: LIM domain; Int 35.9 22 0.00048 21.7 1.2 32 81-112 1-42 (58)
211 KOG4215 Hepatocyte nuclear fac 35.8 14 0.00031 33.7 0.4 38 56-103 30-78 (432)
212 PF14206 Cys_rich_CPCC: Cystei 35.7 26 0.00056 24.9 1.6 32 78-109 1-33 (78)
213 smart00290 ZnF_UBP Ubiquitin C 35.3 29 0.00062 21.1 1.6 24 80-109 1-24 (50)
214 KOG4623 Uncharacterized conser 35.3 16 0.00035 34.6 0.7 43 61-103 10-54 (611)
215 PF08209 Sgf11: Sgf11 (transcr 34.9 21 0.00046 21.7 1.0 18 97-114 5-22 (33)
216 cd06956 NR_DBD_RXR DNA-binding 34.9 20 0.00043 24.6 0.9 24 79-103 1-24 (77)
217 PRK06260 threonine synthase; V 34.7 15 0.00033 31.5 0.4 23 79-103 4-26 (397)
218 PF00641 zf-RanBP: Zn-finger i 34.6 25 0.00053 19.9 1.2 12 94-105 2-13 (30)
219 PHA02998 RNA polymerase subuni 34.6 36 0.00079 28.3 2.6 31 77-107 142-182 (195)
220 PF06054 CoiA: Competence prot 34.6 60 0.0013 28.3 4.0 52 76-127 28-80 (375)
221 PRK08197 threonine synthase; V 34.6 16 0.00035 31.3 0.6 23 78-103 7-29 (394)
222 PF13824 zf-Mss51: Zinc-finger 34.5 19 0.00041 24.3 0.8 13 75-87 11-23 (55)
223 PRK11088 rrmA 23S rRNA methylt 34.4 21 0.00046 28.6 1.2 25 79-106 3-27 (272)
224 COG0777 AccD Acetyl-CoA carbox 33.8 12 0.00026 32.7 -0.3 28 80-107 30-58 (294)
225 TIGR03844 cysteate_syn cysteat 33.7 17 0.00036 31.8 0.5 23 78-103 2-24 (398)
226 PF00105 zf-C4: Zinc finger, C 33.5 19 0.00042 23.6 0.7 23 80-103 2-24 (70)
227 PF01921 tRNA-synt_1f: tRNA sy 33.5 33 0.00071 30.5 2.3 82 23-107 105-210 (360)
228 PF14447 Prok-RING_4: Prokaryo 33.2 19 0.00041 24.4 0.6 8 80-87 41-48 (55)
229 PRK00415 rps27e 30S ribosomal 33.1 35 0.00077 23.3 1.9 28 80-107 13-41 (59)
230 PRK14873 primosome assembly pr 33.1 18 0.00038 34.1 0.6 18 80-103 412-429 (665)
231 cd02341 ZZ_ZZZ3 Zinc finger, Z 32.7 38 0.00082 21.8 1.9 23 79-104 1-23 (48)
232 PF13909 zf-H2C2_5: C2H2-type 32.7 18 0.0004 19.0 0.4 7 79-85 1-7 (24)
233 PF03833 PolC_DP2: DNA polymer 32.5 15 0.00032 36.4 0.0 51 79-130 668-725 (900)
234 PF06677 Auto_anti-p27: Sjogre 32.5 39 0.00085 21.2 1.9 24 79-103 18-41 (41)
235 COG1198 PriA Primosomal protei 32.4 31 0.00068 33.2 2.1 26 80-105 446-471 (730)
236 COG1675 TFA1 Transcription ini 32.2 35 0.00075 27.5 2.0 65 64-131 98-164 (176)
237 PF04032 Rpr2: RNAse P Rpr2/Rp 31.9 34 0.00074 22.7 1.7 49 56-104 21-85 (85)
238 PF14205 Cys_rich_KTR: Cystein 31.8 23 0.0005 24.1 0.8 27 79-105 5-37 (55)
239 PRK14810 formamidopyrimidine-D 31.7 37 0.0008 28.1 2.2 26 77-103 243-271 (272)
240 PF13912 zf-C2H2_6: C2H2-type 31.6 36 0.00077 18.1 1.4 11 97-107 2-12 (27)
241 PF13913 zf-C2HC_2: zinc-finge 31.5 24 0.00052 19.6 0.8 8 80-87 4-11 (25)
242 PRK07111 anaerobic ribonucleos 31.4 20 0.00043 34.2 0.7 37 62-104 657-701 (735)
243 PRK12380 hydrogenase nickel in 31.3 24 0.00051 25.9 0.9 25 77-103 69-93 (113)
244 PF08790 zf-LYAR: LYAR-type C2 31.2 47 0.001 19.7 2.0 19 98-116 2-20 (28)
245 PRK07591 threonine synthase; V 31.1 18 0.00039 31.6 0.3 24 78-104 18-41 (421)
246 cd06968 NR_DBD_ROR DNA-binding 30.9 26 0.00057 25.1 1.1 25 78-103 5-29 (95)
247 KOG1597 Transcription initiati 30.8 36 0.00077 30.0 2.0 28 80-107 2-32 (308)
248 PLN03086 PRLI-interacting fact 30.3 37 0.0008 31.9 2.2 35 75-111 475-519 (567)
249 PRK00807 50S ribosomal protein 29.9 41 0.00089 21.9 1.8 25 79-103 2-35 (52)
250 KOG3507 DNA-directed RNA polym 29.9 20 0.00043 25.0 0.3 31 74-106 16-47 (62)
251 PF09180 ProRS-C_1: Prolyl-tRN 29.8 31 0.00068 23.1 1.2 18 75-92 45-62 (68)
252 PF05191 ADK_lid: Adenylate ki 29.8 39 0.00085 20.5 1.6 10 97-106 2-11 (36)
253 PF01155 HypA: Hydrogenase exp 29.8 25 0.00055 25.6 0.8 25 77-104 69-94 (113)
254 PRK02935 hypothetical protein; 29.7 29 0.00062 26.6 1.1 22 79-104 71-94 (110)
255 PF10588 NADH-G_4Fe-4S_3: NADH 29.6 44 0.00096 20.5 1.8 22 65-87 1-22 (41)
256 TIGR03829 YokU_near_AblA uncha 29.5 57 0.0012 23.9 2.6 27 80-106 1-45 (89)
257 PRK00564 hypA hydrogenase nick 29.1 19 0.00041 26.6 0.1 27 76-103 69-95 (117)
258 TIGR00100 hypA hydrogenase nic 29.0 29 0.00063 25.4 1.1 25 77-103 69-93 (115)
259 PF05876 Terminase_GpA: Phage 28.6 64 0.0014 29.5 3.4 12 95-106 228-239 (557)
260 PRK08329 threonine synthase; V 28.5 30 0.00065 29.2 1.2 22 79-104 2-23 (347)
261 TIGR02443 conserved hypothetic 28.3 59 0.0013 22.3 2.4 27 80-106 11-41 (59)
262 PF01246 Ribosomal_L24e: Ribos 28.2 23 0.0005 24.7 0.4 23 78-100 3-33 (71)
263 smart00547 ZnF_RBZ Zinc finger 28.1 23 0.0005 19.1 0.3 10 95-104 1-10 (26)
264 PF14319 Zn_Tnp_IS91: Transpos 27.8 34 0.00073 25.1 1.2 42 63-104 22-68 (111)
265 PF06397 Desulfoferrod_N: Desu 27.6 40 0.00087 20.9 1.3 12 95-106 5-16 (36)
266 cd00085 HNHc HNH nucleases; HN 27.4 43 0.00094 19.4 1.5 10 79-88 12-21 (57)
267 TIGR01057 topA_arch DNA topois 27.3 76 0.0016 29.3 3.6 24 79-102 590-615 (618)
268 PF00935 Ribosomal_L44: Riboso 27.0 43 0.00093 23.9 1.6 22 76-101 51-72 (77)
269 PRK14714 DNA polymerase II lar 26.9 27 0.00058 36.1 0.7 34 97-131 710-743 (1337)
270 cd06960 NR_DBD_HNF4A DNA-bindi 26.8 37 0.0008 23.0 1.2 25 81-106 1-25 (76)
271 KOG1247 Methionyl-tRNA synthet 26.7 18 0.00039 33.9 -0.4 22 80-106 154-175 (567)
272 PRK05582 DNA topoisomerase I; 26.7 83 0.0018 29.2 3.8 28 78-105 571-603 (650)
273 TIGR01051 topA_bact DNA topois 26.7 73 0.0016 29.4 3.4 23 79-101 575-599 (610)
274 PF05180 zf-DNL: DNL zinc fing 26.4 65 0.0014 22.3 2.3 28 77-104 3-37 (66)
275 PRK08173 DNA topoisomerase III 26.3 61 0.0013 31.5 2.9 28 77-106 725-759 (862)
276 cd00472 Ribosomal_L24e_L24 Rib 26.2 44 0.00095 22.2 1.4 22 79-100 4-33 (54)
277 PRK07956 ligA NAD-dependent DN 26.2 50 0.0011 31.2 2.3 24 77-100 403-426 (665)
278 PRK07220 DNA topoisomerase I; 26.1 62 0.0013 30.7 2.9 23 79-101 590-615 (740)
279 PRK00762 hypA hydrogenase nick 26.1 31 0.00067 25.7 0.8 12 79-90 93-104 (124)
280 PRK08579 anaerobic ribonucleos 26.1 48 0.001 31.2 2.2 38 62-104 545-590 (625)
281 cd07169 NR_DBD_GCNF_like DNA-b 26.1 33 0.00071 24.4 0.9 27 77-104 5-31 (90)
282 TIGR00575 dnlj DNA ligase, NAD 26.1 54 0.0012 30.8 2.5 26 78-103 392-419 (652)
283 PF09526 DUF2387: Probable met 26.1 70 0.0015 22.2 2.5 28 80-107 10-41 (71)
284 PRK14906 DNA-directed RNA poly 25.6 33 0.00072 35.7 1.1 27 78-107 59-85 (1460)
285 PRK00566 DNA-directed RNA poly 25.6 30 0.00066 35.1 0.8 28 77-107 56-83 (1156)
286 PRK12286 rpmF 50S ribosomal pr 25.5 43 0.00094 22.3 1.3 23 76-103 25-47 (57)
287 TIGR02387 rpoC1_cyan DNA-direc 25.4 31 0.00067 32.9 0.8 8 98-105 78-85 (619)
288 COG1499 NMD3 NMD protein affec 25.3 37 0.0008 30.0 1.2 21 93-113 40-60 (355)
289 PF01363 FYVE: FYVE zinc finge 25.3 47 0.001 21.4 1.4 26 79-108 10-37 (69)
290 PRK02625 rpoC1 DNA-directed RN 25.3 31 0.00066 33.0 0.7 24 79-105 69-92 (627)
291 PRK05569 flavodoxin; Provision 24.9 1.3E+02 0.0029 21.3 3.8 50 15-67 53-103 (141)
292 cd06963 NR_DBD_GR_like The DNA 24.8 40 0.00086 22.9 1.0 22 81-103 1-22 (73)
293 COG4469 CoiA Competence protei 24.6 47 0.001 29.7 1.7 21 78-98 25-46 (342)
294 KOG2463 Predicted RNA-binding 24.4 50 0.0011 29.8 1.9 42 77-118 256-305 (376)
295 PF01412 ArfGap: Putative GTPa 24.4 41 0.00089 24.3 1.1 29 75-103 10-40 (116)
296 PF02891 zf-MIZ: MIZ/SP-RING z 24.1 34 0.00073 21.8 0.6 8 79-86 42-49 (50)
297 cd06964 NR_DBD_RAR DNA-binding 24.0 54 0.0012 22.9 1.6 27 79-106 5-31 (85)
298 PF00130 C1_1: Phorbol esters/ 23.9 70 0.0015 19.4 2.0 27 77-106 10-38 (53)
299 KOG0704 ADP-ribosylation facto 23.8 65 0.0014 29.3 2.4 29 75-103 16-46 (386)
300 COG3024 Uncharacterized protei 23.8 36 0.00077 23.9 0.7 14 77-90 6-19 (65)
301 PF01428 zf-AN1: AN1-like Zinc 23.7 48 0.001 20.3 1.2 11 98-108 15-25 (43)
302 PF12171 zf-C2H2_jaz: Zinc-fin 23.6 43 0.00094 18.2 0.9 8 79-86 2-9 (27)
303 PLN03086 PRLI-interacting fact 23.4 39 0.00085 31.8 1.1 28 80-107 435-464 (567)
304 COG5189 SFP1 Putative transcri 23.4 30 0.00066 31.4 0.3 13 75-87 395-407 (423)
305 cd06969 NR_DBD_NGFI-B DNA-bind 23.2 53 0.0011 22.3 1.4 26 80-106 2-27 (75)
306 PRK09521 exosome complex RNA-b 23.2 61 0.0013 25.2 1.9 25 80-105 151-175 (189)
307 PRK14724 DNA topoisomerase III 23.0 45 0.00098 32.9 1.4 26 79-106 644-676 (987)
308 KOG0703 Predicted GTPase-activ 23.0 71 0.0015 27.8 2.5 40 63-103 11-52 (287)
309 PF06827 zf-FPG_IleRS: Zinc fi 23.0 82 0.0018 17.6 2.0 24 80-103 3-28 (30)
310 PF09151 DUF1936: Domain of un 23.0 37 0.0008 21.2 0.5 13 78-90 1-13 (36)
311 cd00974 DSRD Desulforedoxin (D 22.9 66 0.0014 18.7 1.6 13 95-107 3-15 (34)
312 PRK14704 anaerobic ribonucleos 22.9 35 0.00076 32.0 0.6 37 62-104 536-580 (618)
313 PRK06921 hypothetical protein; 22.9 75 0.0016 26.1 2.5 12 78-89 32-43 (266)
314 PRK14724 DNA topoisomerase III 22.8 64 0.0014 31.9 2.4 21 78-101 755-776 (987)
315 PF03107 C1_2: C1 domain; Int 22.7 30 0.00065 19.8 0.1 24 79-105 1-24 (30)
316 PRK14559 putative protein seri 22.7 31 0.00066 32.7 0.2 31 80-114 29-59 (645)
317 TIGR00373 conserved hypothetic 22.6 41 0.00088 25.9 0.8 9 77-85 108-116 (158)
318 COG1379 PHP family phosphoeste 22.5 18 0.00038 32.8 -1.3 30 80-109 248-278 (403)
319 PF09706 Cas_CXXC_CXXC: CRISPR 22.4 41 0.00089 22.8 0.7 13 75-87 2-14 (69)
320 smart00532 LIGANc Ligase N fam 22.3 73 0.0016 28.7 2.5 24 77-100 398-421 (441)
321 PF02593 dTMP_synthase: Thymid 22.3 1.2E+02 0.0026 25.1 3.5 63 16-85 49-114 (217)
322 COG3464 Transposase and inacti 22.3 32 0.00068 30.3 0.2 29 79-107 39-88 (402)
323 KOG2879 Predicted E3 ubiquitin 22.2 38 0.00081 29.8 0.6 19 77-95 238-256 (298)
324 PRK07219 DNA topoisomerase I; 22.2 65 0.0014 30.9 2.2 29 78-106 602-636 (822)
325 cd07172 NR_DBD_GR_PR DNA-bindi 22.2 42 0.00092 23.1 0.8 23 80-103 4-26 (78)
326 cd07156 NR_DBD_VDR_like The DN 22.2 45 0.00099 22.4 0.9 22 81-103 1-22 (72)
327 cd07162 NR_DBD_PXR DNA-binding 22.1 41 0.00089 23.5 0.7 23 80-103 1-23 (87)
328 KOG4317 Predicted Zn-finger pr 22.1 38 0.00081 30.6 0.6 14 74-87 15-28 (383)
329 cd06966 NR_DBD_CAR DNA-binding 22.0 50 0.0011 23.6 1.2 26 80-106 2-27 (94)
330 PF03884 DUF329: Domain of unk 22.0 40 0.00086 22.7 0.6 13 78-90 2-14 (57)
331 KOG1311 DHHC-type Zn-finger pr 22.0 33 0.00071 28.1 0.2 26 77-106 112-137 (299)
332 TIGR02487 NrdD anaerobic ribon 21.9 39 0.00084 31.2 0.7 38 62-105 501-547 (579)
333 cd07179 2DBD_NR_DBD2 The secon 21.9 44 0.00095 22.7 0.8 22 81-103 1-22 (74)
334 TIGR00319 desulf_FeS4 desulfof 21.9 72 0.0016 18.5 1.6 14 94-107 5-18 (34)
335 smart00746 TRASH metallochaper 21.8 43 0.00093 16.9 0.6 8 81-88 1-8 (39)
336 cd00674 LysRS_core_class_I cat 21.7 98 0.0021 27.1 3.1 25 80-105 171-201 (353)
337 COG1601 GCD7 Translation initi 21.6 29 0.00063 27.4 -0.1 37 67-104 94-134 (151)
338 PRK14351 ligA NAD-dependent DN 21.6 66 0.0014 30.6 2.2 22 77-100 422-443 (689)
339 cd07157 2DBD_NR_DBD1 The first 21.5 57 0.0012 22.9 1.3 26 80-106 2-27 (86)
340 PF02892 zf-BED: BED zinc fing 21.5 62 0.0013 19.2 1.3 17 93-109 13-29 (45)
341 COG1096 Predicted RNA-binding 21.5 71 0.0015 26.3 2.1 24 80-105 151-174 (188)
342 COG1773 Rubredoxin [Energy pro 21.4 58 0.0013 22.0 1.3 12 96-107 3-14 (55)
343 KOG4218 Nuclear hormone recept 21.2 43 0.00093 30.8 0.8 26 77-103 14-39 (475)
344 PF07295 DUF1451: Protein of u 21.2 37 0.00081 26.4 0.4 28 77-104 111-138 (146)
345 cd07163 NR_DBD_TLX DNA-binding 21.1 62 0.0014 23.0 1.5 26 80-106 8-33 (92)
346 cd06916 NR_DBD_like DNA-bindin 21.0 62 0.0013 21.7 1.4 25 81-106 1-25 (72)
347 PF09237 GAGA: GAGA factor; I 20.9 37 0.00081 23.1 0.3 13 75-87 21-33 (54)
348 cd01675 RNR_III Class III ribo 20.8 42 0.0009 30.8 0.7 41 61-105 494-541 (555)
349 TIGR00595 priA primosomal prot 20.8 68 0.0015 28.9 2.0 28 80-107 224-251 (505)
350 PF01667 Ribosomal_S27e: Ribos 20.7 79 0.0017 21.2 1.8 28 80-107 9-37 (55)
351 PF13695 zf-3CxxC: Zinc-bindin 20.7 76 0.0016 22.5 1.9 26 77-102 4-44 (98)
352 PHA00689 hypothetical protein 20.3 41 0.0009 23.1 0.4 15 79-93 18-32 (62)
353 COG2824 PhnA Uncharacterized Z 20.3 76 0.0016 24.4 1.9 29 80-109 5-33 (112)
354 cd07173 NR_DBD_AR DNA-binding 20.2 39 0.00085 23.6 0.3 23 80-103 5-27 (82)
355 PF14951 DUF4503: Domain of un 20.2 43 0.00094 30.4 0.6 28 80-107 276-305 (389)
356 cd06957 NR_DBD_PNR_like_2 DNA- 20.1 70 0.0015 22.1 1.5 24 81-105 1-24 (82)
No 1
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=100.00 E-value=4.6e-50 Score=289.50 Aligned_cols=90 Identities=76% Similarity=1.211 Sum_probs=88.7
Q ss_pred hhccceeeeeccCCccccCchhhHhHHHHHHhhhcccccCCCCceeeEEeeeeeeeeCCCCeeEeccccccccchHHHHH
Q 045338 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVR 122 (134)
Q Consensus 43 MakrTKKVgi~GkfGtRYGaslRK~vkkIE~sqhakY~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~p~T~~~~tvk 122 (134)
|++|||||||+||||+|||++|||+|+|||++||++|+|||||+++|+|.++|||+|++|+++||||||+|+||++.++.
T Consensus 1 MakrtkkvG~~GrfG~RYG~slRK~v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~ 80 (90)
T PTZ00255 1 MAKRTKKVGITGKYGTRYGASLRKQIKKIEISQHAKYFCPFCGKHAVKRQAVGIWRCKGCKKTVAGGAWTLSTPAASTVR 80 (90)
T ss_pred CCCcCceeeecCCCcCccCHHHHHHHHHHHHHHhCCccCCCCCCCceeeeeeEEEEcCCCCCEEeCCccccccchhHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhh
Q 045338 123 STIRRLREQT 132 (134)
Q Consensus 123 ~~Irrl~e~~ 132 (134)
++|+||+|++
T Consensus 81 ~~irr~~e~~ 90 (90)
T PTZ00255 81 STIRRLRKLK 90 (90)
T ss_pred HHHHHHHhcC
Confidence 9999999974
No 2
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=100.00 E-value=5.6e-50 Score=289.63 Aligned_cols=91 Identities=56% Similarity=1.017 Sum_probs=89.2
Q ss_pred hhccceeeeeccCCccccCchhhHhHHHHHHhhhcccccCCCCceeeEEeeeeeeeeCCCCeeEeccccccccchHHHHH
Q 045338 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVR 122 (134)
Q Consensus 43 MakrTKKVgi~GkfGtRYGaslRK~vkkIE~sqhakY~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~p~T~~~~tvk 122 (134)
|+ |||||||+||||+|||++|||+|+|||++||++|+|||||+++|+|.++|||+|++|+++||||||+|+||++.++.
T Consensus 1 ma-rtkkvG~~GrfG~RYG~slRK~v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~p~T~~~~t~~ 79 (91)
T TIGR00280 1 MK-RTKKVGITGRFGPRYGLKLRRQVKKIEIQQKAKYVCPFCGKKTVKRGSTGIWTCRKCGAKFAGGAYTPVTPAGKTVR 79 (91)
T ss_pred CC-CCceeeecCCCcCccCHHHHHHHHHHHHHHhcCccCCCCCCCceEEEeeEEEEcCCCCCEEeCCccccccchhHHHH
Confidence 67 89999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcC
Q 045338 123 STIRRLREQTES 134 (134)
Q Consensus 123 ~~Irrl~e~~e~ 134 (134)
++|+||+|++|+
T Consensus 80 ~~irrl~e~~~~ 91 (91)
T TIGR00280 80 KTIRRIVEMKEA 91 (91)
T ss_pred HHHHHHHHhhcC
Confidence 999999999985
No 3
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=100.00 E-value=4.9e-50 Score=289.32 Aligned_cols=90 Identities=69% Similarity=1.130 Sum_probs=83.2
Q ss_pred hccceeeeeccCCccccCchhhHhHHHHHHhhhcccccCCCCceeeEEeeeeeeeeCCCCeeEeccccccccchHHHHHH
Q 045338 44 TKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRS 123 (134)
Q Consensus 44 akrTKKVgi~GkfGtRYGaslRK~vkkIE~sqhakY~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~p~T~~~~tvk~ 123 (134)
|+|||||||+||||+|||++|||+|++||++||++|+|||||+++|+|+++|||+|++|+++||||||+|+||++.++++
T Consensus 1 a~rtkkvgi~GkyG~RYG~slRK~vkkie~~q~~ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~ 80 (90)
T PF01780_consen 1 AKRTKKVGIAGKYGTRYGASLRKRVKKIEISQHAKYTCPFCGKTSVKRVATGIWKCKKCGKKFAGGAYTPSTPAAKTVKR 80 (90)
T ss_dssp -S-SSS-TTGGGGTTSSTHHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHH
T ss_pred CCCCceeeecCcCcCCcCHHHHHHHHHHHHHHhCCCcCCCCCCceeEEeeeEEeecCCCCCEEeCCCccccchHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhc
Q 045338 124 TIRRLREQTE 133 (134)
Q Consensus 124 ~Irrl~e~~e 133 (134)
+|+||+|++|
T Consensus 81 ~i~rl~e~~e 90 (90)
T PF01780_consen 81 AIRRLRELKE 90 (90)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHhcC
Confidence 9999999987
No 4
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=100.00 E-value=2.7e-49 Score=285.46 Aligned_cols=90 Identities=44% Similarity=0.834 Sum_probs=87.9
Q ss_pred hhccceeeeeccCCccccCchhhHhHHHHHHhhhcccccCCCCceeeEEeeeeeeeeCCCCeeEeccccccccchHHHHH
Q 045338 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVR 122 (134)
Q Consensus 43 MakrTKKVgi~GkfGtRYGaslRK~vkkIE~sqhakY~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~p~T~~~~tvk 122 (134)
|++|||||||+||||+|||++|||+|+|||++||++|+|||||+++|+|.++|||+|++|+++||||||+|+||++.++.
T Consensus 1 m~~rtkkvGi~Gr~G~RYG~slRK~v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~ 80 (90)
T PRK03976 1 MMSRTKKVGSAGRFGARYGRKIRKRVADIEEKMRAKHVCPVCGRPKVKRVGTGIWECRKCGAKFAGGAYTPETPAGKTVT 80 (90)
T ss_pred CCCcCceEeecCCCcCccCHHHHHHHHHHHHHHhcCccCCCCCCCceEEEEEEEEEcCCCCCEEeCCccccccchhhhHH
Confidence 78899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhh
Q 045338 123 STIRRLREQT 132 (134)
Q Consensus 123 ~~Irrl~e~~ 132 (134)
++|+||+|.+
T Consensus 81 ~~irr~~~~~ 90 (90)
T PRK03976 81 RAIRRAVEEK 90 (90)
T ss_pred HHHHHHhhcC
Confidence 9999999853
No 5
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.3e-49 Score=284.87 Aligned_cols=92 Identities=74% Similarity=1.178 Sum_probs=90.8
Q ss_pred hhccceeeeeccCCccccCchhhHhHHHHHHhhhcccccCCCCceeeEEeeeeeeeeCCCCeeEeccccccccchHHHHH
Q 045338 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVR 122 (134)
Q Consensus 43 MakrTKKVgi~GkfGtRYGaslRK~vkkIE~sqhakY~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~p~T~~~~tvk 122 (134)
|++|||||||+|+||+|||+||||||++||++||++|+|+||||..|||.++|||.|++|++++|||||+++|++|.+++
T Consensus 1 m~krtKKVgI~gkyGtrYGaSLrk~vKkiei~Qhaky~CsfCGK~~vKR~AvGiW~C~~C~kv~agga~~~~t~aa~t~r 80 (92)
T KOG0402|consen 1 MAKRTKKVGIVGKYGTRYGASLRKMVKKIEIQQHAKYTCSFCGKKTVKRKAVGIWKCGSCKKVVAGGAYTVTTAAAATVR 80 (92)
T ss_pred CCcccceeeeeecccchhhHHHHHHHHHHHHHHhhhhhhhhcchhhhhhhceeEEecCCccceeccceEEeccchhHHHH
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhhcC
Q 045338 123 STIRRLREQTES 134 (134)
Q Consensus 123 ~~Irrl~e~~e~ 134 (134)
++|+||+|++|.
T Consensus 81 s~irrlre~~e~ 92 (92)
T KOG0402|consen 81 STIRRLRELVEQ 92 (92)
T ss_pred HHHHHHHHHhcC
Confidence 999999999874
No 6
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-42 Score=250.36 Aligned_cols=89 Identities=51% Similarity=0.930 Sum_probs=86.8
Q ss_pred hhccceeeeeccCCccccCchhhHhHHHHHHhhhcccccCCCCceeeEEeeeeeeeeCCCCeeEeccccccccchHHHHH
Q 045338 43 MTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVR 122 (134)
Q Consensus 43 MakrTKKVgi~GkfGtRYGaslRK~vkkIE~sqhakY~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~p~T~~~~tvk 122 (134)
|++ ||||||+||||+|||++||++|++||+.|+++|.||+||++.|+|+++|||.|++||.+||||||+|.|+++++++
T Consensus 1 M~~-TkkvG~aGrfGpRYG~~~Rrrv~~ie~~~~~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGgay~P~t~~~k~~~ 79 (89)
T COG1997 1 MAK-TKKVGIAGRFGPRYGSKLRRRVKEIEAQQRAKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGAYTPVTPAGKAVK 79 (89)
T ss_pred CCc-cceeccCcccccccchHHHHHHHHHHHHHhcCCcCCCCCCcceeeeccCeEEcCCCCCeeccccccccchHHHHHH
Confidence 777 9999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhh
Q 045338 123 STIRRLREQT 132 (134)
Q Consensus 123 ~~Irrl~e~~ 132 (134)
++|+|+.|.+
T Consensus 80 ~~i~r~~e~k 89 (89)
T COG1997 80 RTIRREVEMK 89 (89)
T ss_pred HHHHHHhccC
Confidence 9999998864
No 7
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=96.98 E-value=0.00061 Score=42.76 Aligned_cols=28 Identities=32% Similarity=0.749 Sum_probs=24.0
Q ss_pred ccccCCCCceeeEEeee-eeeeeCCCCee
Q 045338 78 KYFCEFCGKYAVKRKAV-GIWGCKDCGKV 105 (134)
Q Consensus 78 kY~CpfCGk~~VKR~av-GIW~CkkCgkt 105 (134)
-+.||.||...+.+... +.|+|++|++.
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 36799999998887777 99999999863
No 8
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=96.95 E-value=0.00091 Score=43.11 Aligned_cols=40 Identities=25% Similarity=0.498 Sum_probs=27.3
Q ss_pred ccCCCCceee-EE------eeeeeeeeCCCCeeEeccccccccchHHHHHHHHHHH
Q 045338 80 FCEFCGKYAV-KR------KAVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRRL 128 (134)
Q Consensus 80 ~CpfCGk~~V-KR------~avGIW~CkkCgkt~AGGAy~p~T~~~~tvk~~Irrl 128 (134)
.|||||...+ .| ...|+|.|..||... +.+.+...||...
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~---------~~~~~~~~Ai~~W 49 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASG---------PVEEDEAEAIEAW 49 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCc---------ccccCHHHHHHHH
Confidence 5999998765 55 367899999997653 3355555555443
No 9
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=96.14 E-value=0.0063 Score=42.27 Aligned_cols=25 Identities=36% Similarity=0.723 Sum_probs=18.4
Q ss_pred ccCCCCceeeEEeeee---eeeeCCCCe
Q 045338 80 FCEFCGKYAVKRKAVG---IWGCKDCGK 104 (134)
Q Consensus 80 ~CpfCGk~~VKR~avG---IW~CkkCgk 104 (134)
.|||||.+++.=.+.| .|.|.+|+.
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA 35 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCES 35 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCc
Confidence 5999999875544443 457999987
No 10
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=95.82 E-value=0.0051 Score=40.07 Aligned_cols=26 Identities=31% Similarity=0.870 Sum_probs=22.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
.||.||.. +-....+.|+|.+||.+.
T Consensus 22 fCP~Cg~~-~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG-FMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc-hheccCCcEECCCcCCEE
Confidence 79999997 666677999999999875
No 11
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=95.65 E-value=0.018 Score=37.08 Aligned_cols=46 Identities=28% Similarity=0.489 Sum_probs=27.1
Q ss_pred cccCCCCceeeEEe-eee------ee-eeCCCCeeEeccccccccchHHHHHHHHHHH
Q 045338 79 YFCEFCGKYAVKRK-AVG------IW-GCKDCGKVKAGGAYTLNTASAVTVRSTIRRL 128 (134)
Q Consensus 79 Y~CpfCGk~~VKR~-avG------IW-~CkkCgkt~AGGAy~p~T~~~~tvk~~Irrl 128 (134)
..|||||...+.-. ..+ .+ .|..||. +-....++.....+.||...
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga----~~~~~~~~~~~~~~~Ai~~W 57 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA----DDSTSEEPWADDEAEAIEAW 57 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC----ccccccccchHHHHHHHHHH
Confidence 46999997764333 222 11 3888977 33444555556666666654
No 12
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=95.50 E-value=0.0085 Score=45.08 Aligned_cols=46 Identities=24% Similarity=0.393 Sum_probs=34.5
Q ss_pred hhcccccCCCCcee-----eE-EeeeeeeeeCCCCeeEeccccccccchHHH
Q 045338 75 QHSKYFCEFCGKYA-----VK-RKAVGIWGCKDCGKVKAGGAYTLNTASAVT 120 (134)
Q Consensus 75 qhakY~CpfCGk~~-----VK-R~avGIW~CkkCgkt~AGGAy~p~T~~~~t 120 (134)
-...|+|||||..+ || -...|.=+|+.||..+.--+=.+.+|.-+.
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~vDvY 70 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPVDVY 70 (104)
T ss_pred CCceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccchhHH
Confidence 45678999999876 33 346788999999999887766666665443
No 13
>PHA00626 hypothetical protein
Probab=95.43 E-value=0.011 Score=40.58 Aligned_cols=33 Identities=24% Similarity=0.527 Sum_probs=26.8
Q ss_pred ccCCCCceeeEEe-----eeeeeeeCCCCeeEeccccc
Q 045338 80 FCEFCGKYAVKRK-----AVGIWGCKDCGKVKAGGAYT 112 (134)
Q Consensus 80 ~CpfCGk~~VKR~-----avGIW~CkkCgkt~AGGAy~ 112 (134)
.||-||...+-|- -...+.|+.||+.|+-.|+-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~ 39 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFG 39 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhhhh
Confidence 5999999765553 35789999999999987764
No 14
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=95.09 E-value=0.019 Score=35.37 Aligned_cols=31 Identities=29% Similarity=0.513 Sum_probs=23.5
Q ss_pred cccCCCCcee-eEEeeeeeeeeCCCCeeEecc
Q 045338 79 YFCEFCGKYA-VKRKAVGIWGCKDCGKVKAGG 109 (134)
Q Consensus 79 Y~CpfCGk~~-VKR~avGIW~CkkCgkt~AGG 109 (134)
|.||.||.+. +-=.+.|-..|..||.++.-.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEEN 32 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-T
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeecc
Confidence 6899999986 344578999999999987644
No 15
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.70 E-value=0.019 Score=44.88 Aligned_cols=26 Identities=35% Similarity=0.837 Sum_probs=19.7
Q ss_pred cccCCCCcee--------------eEEeeeeeeeeCCCCeeEec
Q 045338 79 YFCEFCGKYA--------------VKRKAVGIWGCKDCGKVKAG 108 (134)
Q Consensus 79 Y~CpfCGk~~--------------VKR~avGIW~CkkCgkt~AG 108 (134)
+.||+||.+. |+|. .+|..||++|.+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~----~~c~~c~~~f~~ 40 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRR----RECLACGKRFTT 40 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeee----eeccccCCcceE
Confidence 4799999644 3332 799999999975
No 16
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=94.70 E-value=0.022 Score=37.34 Aligned_cols=27 Identities=30% Similarity=0.717 Sum_probs=23.9
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
+||.||....++...-+|.|..||..+
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCcccccccccccceEEcCCCCCEE
Confidence 599999988777888899999999874
No 17
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=94.67 E-value=0.02 Score=40.71 Aligned_cols=52 Identities=17% Similarity=0.456 Sum_probs=28.4
Q ss_pred ccccCCCCcee--eE-EeeeeeeeeCCCCeeEeccccccc-cchHHHHHHHHHHHHhh
Q 045338 78 KYFCEFCGKYA--VK-RKAVGIWGCKDCGKVKAGGAYTLN-TASAVTVRSTIRRLREQ 131 (134)
Q Consensus 78 kY~CpfCGk~~--VK-R~avGIW~CkkCgkt~AGGAy~p~-T~~~~tvk~~Irrl~e~ 131 (134)
.+.||||+... +. -...|+|+|-.||. .|.+..+- .--+.+.+.|++.|.+.
T Consensus 33 ~~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~--~Gd~i~~v~~~~~~~f~eAv~~l~~~ 88 (97)
T PF01807_consen 33 RCLCPFHDDKTPSFSINPDKNRFKCFGCGK--GGDVIDFVMKYEGCSFKEAVKWLAEE 88 (97)
T ss_dssp EE--SSS--SS--EEEETTTTEEEETTT----EE-HHHHHHHHHT--HHHHHHHHHHH
T ss_pred EEECcCCCCCCCceEEECCCCeEEECCCCC--CCcHHhHHHHHhCCCHHHHHHHHHHH
Confidence 46799999642 22 12458999999995 56666652 34456777788887663
No 18
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=94.19 E-value=0.035 Score=34.56 Aligned_cols=30 Identities=23% Similarity=0.396 Sum_probs=23.3
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
..|.||.||..-.--...+.++|..||..+
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeE
Confidence 368999999986554555589999998655
No 19
>smart00400 ZnF_CHCC zinc finger.
Probab=93.49 E-value=0.046 Score=34.97 Aligned_cols=31 Identities=26% Similarity=0.629 Sum_probs=21.2
Q ss_pred cccCCCCcee----eEEeeeeeeeeCCCCeeEeccccc
Q 045338 79 YFCEFCGKYA----VKRKAVGIWGCKDCGKVKAGGAYT 112 (134)
Q Consensus 79 Y~CpfCGk~~----VKR~avGIW~CkkCgkt~AGGAy~ 112 (134)
..|||++... |. ...++|+|-.||+ .|++-.
T Consensus 3 ~~cPfh~d~~pSf~v~-~~kn~~~Cf~cg~--gGd~i~ 37 (55)
T smart00400 3 GLCPFHGEKTPSFSVS-PDKQFFHCFGCGA--GGNVIS 37 (55)
T ss_pred ccCcCCCCCCCCEEEE-CCCCEEEEeCCCC--CCCHHH
Confidence 4699999753 32 3459999999984 444433
No 20
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=93.44 E-value=0.063 Score=33.26 Aligned_cols=32 Identities=22% Similarity=0.594 Sum_probs=25.6
Q ss_pred ccCCCCceeeEEeee--eeeeeCCCCeeEecccc
Q 045338 80 FCEFCGKYAVKRKAV--GIWGCKDCGKVKAGGAY 111 (134)
Q Consensus 80 ~CpfCGk~~VKR~av--GIW~CkkCgkt~AGGAy 111 (134)
.||.||.....+... -.|.|..||+.+.-.++
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEECCCc
Confidence 599999987655443 38999999999887776
No 21
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=93.03 E-value=0.079 Score=37.36 Aligned_cols=46 Identities=22% Similarity=0.552 Sum_probs=21.9
Q ss_pred hhhcccccCCCC-cee----eEE-eeeeeeeeCCCCeeEeccccccccchHH
Q 045338 74 SQHSKYFCEFCG-KYA----VKR-KAVGIWGCKDCGKVKAGGAYTLNTASAV 119 (134)
Q Consensus 74 sqhakY~CpfCG-k~~----VKR-~avGIW~CkkCgkt~AGGAy~p~T~~~~ 119 (134)
.....+.||||| +.+ +.+ ..+|+=.|..||..+.=-.-.++.|.=+
T Consensus 18 ~l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L~epiDV 69 (81)
T PF05129_consen 18 KLPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPLSEPIDV 69 (81)
T ss_dssp --SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS--TTHH
T ss_pred CCCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCccCcccch
Confidence 455788999999 544 222 3789999999998886554444444433
No 22
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=92.97 E-value=0.057 Score=34.07 Aligned_cols=28 Identities=36% Similarity=1.006 Sum_probs=14.2
Q ss_pred ccCCCCcee-eE----EeeeeeeeeCCCCeeEec
Q 045338 80 FCEFCGKYA-VK----RKAVGIWGCKDCGKVKAG 108 (134)
Q Consensus 80 ~CpfCGk~~-VK----R~avGIW~CkkCgkt~AG 108 (134)
.||.||-.. .. +...|-|.|..|+. .+|
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C~~-~~G 37 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQCGG-DAG 37 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTTTB-E--
T ss_pred CCCCCcCccccccCcCcccCCCEECCCCCC-cCC
Confidence 699999654 33 23569999999955 444
No 23
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.94 E-value=0.063 Score=41.77 Aligned_cols=22 Identities=32% Similarity=0.850 Sum_probs=19.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
+||-||. ...+.|.|..||.++
T Consensus 311 ~C~~cg~-----~~~r~~~C~~cg~~~ 332 (364)
T COG0675 311 TCPCCGH-----LSGRLFKCPRCGFVH 332 (364)
T ss_pred cccccCC-----ccceeEECCCCCCee
Confidence 5999999 668899999999874
No 24
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=92.30 E-value=0.096 Score=38.70 Aligned_cols=32 Identities=25% Similarity=0.611 Sum_probs=21.9
Q ss_pred ccC--CCCceeeEEeeeeeeeeCCCCeeEeccccc
Q 045338 80 FCE--FCGKYAVKRKAVGIWGCKDCGKVKAGGAYT 112 (134)
Q Consensus 80 ~Cp--fCGk~~VKR~avGIW~CkkCgkt~AGGAy~ 112 (134)
-|| .|+|.... .+.|.|.|.+|++.+.---|.
T Consensus 20 aC~~~~C~kKv~~-~~~~~y~C~~C~~~~~~~~~r 53 (146)
T PF08646_consen 20 ACPNEKCNKKVTE-NGDGSYRCEKCNKTVENPKYR 53 (146)
T ss_dssp E-TSTTTS-B-EE-ETTTEEEETTTTEEESS-EEE
T ss_pred CCCCccCCCEeec-CCCcEEECCCCCCcCCCeeEE
Confidence 599 99986444 477999999999998554443
No 25
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=92.05 E-value=0.077 Score=35.61 Aligned_cols=30 Identities=27% Similarity=0.712 Sum_probs=18.4
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
.+-.||.||--.+==.---=|.|.+||+|-
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgyTe 47 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGYTE 47 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccceE
Confidence 345799999532110111149999999873
No 26
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=91.33 E-value=0.14 Score=30.63 Aligned_cols=15 Identities=27% Similarity=0.503 Sum_probs=12.1
Q ss_pred eeeeeeeCCCCeeEe
Q 045338 93 AVGIWGCKDCGKVKA 107 (134)
Q Consensus 93 avGIW~CkkCgkt~A 107 (134)
.+-.|.|..||+.+-
T Consensus 29 ~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 29 NVPALVCPQCGEEYL 43 (46)
T ss_pred CCCccccccCCCEee
Confidence 557799999998764
No 27
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=91.21 E-value=0.13 Score=31.58 Aligned_cols=26 Identities=27% Similarity=0.600 Sum_probs=22.7
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
..|+.||.. .-+...|-|.|.+||.+
T Consensus 9 ~~C~~C~~~-~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSR-WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCe-EeEccCCEEEhhhCceE
Confidence 349999999 77789999999999965
No 28
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.60 E-value=0.33 Score=39.03 Aligned_cols=37 Identities=27% Similarity=0.609 Sum_probs=27.1
Q ss_pred cccccCCCCcee-eEEe------------------------eeeeeeeCCCCeeEecccccc
Q 045338 77 SKYFCEFCGKYA-VKRK------------------------AVGIWGCKDCGKVKAGGAYTL 113 (134)
Q Consensus 77 akY~CpfCGk~~-VKR~------------------------avGIW~CkkCgkt~AGGAy~p 113 (134)
.+++||+|++.- .+++ ---||.|.+||+.+.-.-+.-
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~ 65 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDFEK 65 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccccccc
Confidence 578999999862 2222 125899999999988877663
No 29
>PRK05667 dnaG DNA primase; Validated
Probab=90.27 E-value=0.16 Score=46.51 Aligned_cols=48 Identities=17% Similarity=0.399 Sum_probs=29.0
Q ss_pred cccCCCCcee----eEEeeeeeeeeCCCCeeEeccccccccch-HHHHHHHHHHHH
Q 045338 79 YFCEFCGKYA----VKRKAVGIWGCKDCGKVKAGGAYTLNTAS-AVTVRSTIRRLR 129 (134)
Q Consensus 79 Y~CpfCGk~~----VKR~avGIW~CkkCgkt~AGGAy~p~T~~-~~tvk~~Irrl~ 129 (134)
..||||+... |. ...|+|+|-.||. .|.+..+-.-. +.+...|++.|.
T Consensus 37 ~~CPfH~ektpSf~V~-~~k~~~~CF~Cg~--~Gd~i~fv~~~~~~sf~eAv~~La 89 (580)
T PRK05667 37 GLCPFHDEKTPSFTVS-PDKQFYHCFGCGA--GGDVIKFLMEYEGLSFVEAVEELA 89 (580)
T ss_pred ecCCCCCCCCCceEEE-CCCCeEEECCCCC--CCCHHHHHHHHhCCCHHHHHHHHH
Confidence 4699999653 43 4679999999997 35554432111 223444555543
No 30
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=90.24 E-value=0.19 Score=42.12 Aligned_cols=37 Identities=27% Similarity=0.533 Sum_probs=29.0
Q ss_pred HHHhhhcccccCCCCcee-eEEeeeeeeeeCCCCeeEe
Q 045338 71 MEVSQHSKYFCEFCGKYA-VKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 71 IE~sqhakY~CpfCGk~~-VKR~avGIW~CkkCgkt~A 107 (134)
.+........||.||.+. |.-...|-.-|..||.++.
T Consensus 4 ~~~~~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 4 LVLEEEEKLVCPECGSDKLIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred hhhhcccCCcCcCCCCCCeeEECCCCeEeecccCCccc
Confidence 455566778899999854 5556899999999998764
No 31
>PHA02942 putative transposase; Provisional
Probab=90.17 E-value=0.16 Score=44.12 Aligned_cols=26 Identities=27% Similarity=0.572 Sum_probs=20.9
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
+||.||... ++.+..+|.|..||...
T Consensus 327 ~Cs~CG~~~-~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 327 SCPKCGHKM-VEIAHRYFHCPSCGYEN 352 (383)
T ss_pred cCCCCCCcc-CcCCCCEEECCCCCCEe
Confidence 699999754 34566799999999876
No 32
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=89.51 E-value=0.21 Score=31.06 Aligned_cols=26 Identities=31% Similarity=0.751 Sum_probs=18.8
Q ss_pred cccCCCCcee-e---EEeeeeeeeeCCCCe
Q 045338 79 YFCEFCGKYA-V---KRKAVGIWGCKDCGK 104 (134)
Q Consensus 79 Y~CpfCGk~~-V---KR~avGIW~CkkCgk 104 (134)
-.||.||... . .+...|-|.|..|+.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 3699999654 3 233569999999974
No 33
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=89.49 E-value=0.23 Score=43.20 Aligned_cols=31 Identities=26% Similarity=0.559 Sum_probs=22.2
Q ss_pred cccCCCCcee----eEEeeeeeeeeCCCCeeEeccccc
Q 045338 79 YFCEFCGKYA----VKRKAVGIWGCKDCGKVKAGGAYT 112 (134)
Q Consensus 79 Y~CpfCGk~~----VKR~avGIW~CkkCgkt~AGGAy~ 112 (134)
..||||+... |. ...|+|+|-.||. .|.+..
T Consensus 35 ~~CPfh~ek~pSf~v~-~~k~~~~Cf~Cg~--~Gd~i~ 69 (415)
T TIGR01391 35 GLCPFHHEKTPSFSVS-PEKQFYHCFGCGA--GGDAIK 69 (415)
T ss_pred eeCCCCCCCCCeEEEE-cCCCcEEECCCCC--CCCHHH
Confidence 4799998643 33 3579999999997 455544
No 34
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=89.44 E-value=0.35 Score=34.17 Aligned_cols=16 Identities=31% Similarity=0.684 Sum_probs=12.8
Q ss_pred eeeeeeeCCCCeeEec
Q 045338 93 AVGIWGCKDCGKVKAG 108 (134)
Q Consensus 93 avGIW~CkkCgkt~AG 108 (134)
.+..|.|..||..+..
T Consensus 28 ~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 28 GVPGWYCPACGEELLD 43 (127)
T ss_pred eeeeeECCCCCCEEEc
Confidence 5688999999987643
No 35
>PRK12366 replication factor A; Reviewed
Probab=89.11 E-value=0.18 Score=46.51 Aligned_cols=24 Identities=33% Similarity=0.733 Sum_probs=20.6
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
.||-|.|.-+. .-|.|.|.+|+++
T Consensus 534 aCp~CnkKv~~--~~g~~~C~~c~~~ 557 (637)
T PRK12366 534 LCPNCRKRVEE--VDGEYICEFCGEV 557 (637)
T ss_pred cccccCeEeEc--CCCcEECCCCCCC
Confidence 69999887664 6799999999987
No 36
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=88.18 E-value=0.16 Score=37.45 Aligned_cols=33 Identities=27% Similarity=0.656 Sum_probs=23.8
Q ss_pred HhhhcccccCCCCceee----EEeeeeeeeeCCCCeeE
Q 045338 73 VSQHSKYFCEFCGKYAV----KRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 73 ~sqhakY~CpfCGk~~V----KR~avGIW~CkkCgkt~ 106 (134)
..-..-++||+||...+ .| ..+.=.|..||.-+
T Consensus 16 ~klpt~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~y~ 52 (99)
T PRK14892 16 PKLPKIFECPRCGKVSISVKIKK-NIAIITCGNCGLYT 52 (99)
T ss_pred cCCCcEeECCCCCCeEeeeecCC-CcceEECCCCCCcc
Confidence 33567789999996554 23 56777999998654
No 37
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=87.69 E-value=0.28 Score=36.89 Aligned_cols=26 Identities=31% Similarity=0.710 Sum_probs=20.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
-||-|.|.... ...|.|.|.+|+..+
T Consensus 36 aC~~C~kkv~~-~~~~~~~C~~C~~~~ 61 (166)
T cd04476 36 ACPGCNKKVVE-EGNGTYRCEKCNKSV 61 (166)
T ss_pred cccccCcccEe-CCCCcEECCCCCCcC
Confidence 59999987443 344899999999886
No 38
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.62 E-value=0.41 Score=30.44 Aligned_cols=29 Identities=24% Similarity=0.612 Sum_probs=20.5
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCeeEe
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCgkt~A 107 (134)
.|.|..||.+---....+| .|+.||..+-
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~i-rC~~CG~rIl 30 (44)
T smart00659 2 IYICGECGRENEIKSKDVV-RCRECGYRIL 30 (44)
T ss_pred EEECCCCCCEeecCCCCce-ECCCCCceEE
Confidence 5899999987433334444 9999997653
No 39
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=87.40 E-value=0.4 Score=36.18 Aligned_cols=32 Identities=22% Similarity=0.481 Sum_probs=21.7
Q ss_pred hhcccccCCCCceeeEEe------eeeeeeeCCCCeeE
Q 045338 75 QHSKYFCEFCGKYAVKRK------AVGIWGCKDCGKVK 106 (134)
Q Consensus 75 qhakY~CpfCGk~~VKR~------avGIW~CkkCgkt~ 106 (134)
.+.-|.||.||..-.-=. ..|--.|..||..+
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 456789999996531101 24558999999775
No 40
>PHA02540 61 DNA primase; Provisional
Probab=87.00 E-value=0.47 Score=41.31 Aligned_cols=27 Identities=22% Similarity=0.806 Sum_probs=18.4
Q ss_pred ccccCCCCcee---------eEEeeee--eeeeCCCCee
Q 045338 78 KYFCEFCGKYA---------VKRKAVG--IWGCKDCGKV 105 (134)
Q Consensus 78 kY~CpfCGk~~---------VKR~avG--IW~CkkCgkt 105 (134)
+..|||||... |- ..-| +|||-.||+.
T Consensus 27 ~~~CPf~~ds~~~~~kpsF~V~-p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 27 NFRCPICGDSQKDKNKARGWIY-EKKDGGVFKCHNCGYH 64 (337)
T ss_pred EecCCCCCCccccCcCCcEEEe-ccCCceEEEecCCCCC
Confidence 44799999732 21 1234 9999999963
No 41
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=86.80 E-value=0.43 Score=26.63 Aligned_cols=15 Identities=33% Similarity=0.853 Sum_probs=11.5
Q ss_pred HhhhcccccCCCCce
Q 045338 73 VSQHSKYFCEFCGKY 87 (134)
Q Consensus 73 ~sqhakY~CpfCGk~ 87 (134)
-+...+|.||.|++.
T Consensus 9 H~~~k~~~C~~C~k~ 23 (26)
T PF13465_consen 9 HTGEKPYKCPYCGKS 23 (26)
T ss_dssp HSSSSSEEESSSSEE
T ss_pred cCCCCCCCCCCCcCe
Confidence 445678999999875
No 42
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=86.31 E-value=0.6 Score=28.84 Aligned_cols=29 Identities=24% Similarity=0.533 Sum_probs=21.0
Q ss_pred cccCCCCceeeE------Ee----eeeeeeeCCCCeeEe
Q 045338 79 YFCEFCGKYAVK------RK----AVGIWGCKDCGKVKA 107 (134)
Q Consensus 79 Y~CpfCGk~~VK------R~----avGIW~CkkCgkt~A 107 (134)
+.||.||...+- |. .+=++.|.+|++.|.
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 479999977522 21 356899999998763
No 43
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=86.30 E-value=0.33 Score=30.94 Aligned_cols=10 Identities=40% Similarity=1.212 Sum_probs=8.7
Q ss_pred ccccCCCCce
Q 045338 78 KYFCEFCGKY 87 (134)
Q Consensus 78 kY~CpfCGk~ 87 (134)
.|+|||||+.
T Consensus 2 ~f~CP~C~~~ 11 (54)
T PF05605_consen 2 SFTCPYCGKG 11 (54)
T ss_pred CcCCCCCCCc
Confidence 6899999993
No 44
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=85.94 E-value=0.55 Score=28.90 Aligned_cols=23 Identities=35% Similarity=0.810 Sum_probs=18.7
Q ss_pred ccCCCCcee-eEEeee-----eeeeeCCC
Q 045338 80 FCEFCGKYA-VKRKAV-----GIWGCKDC 102 (134)
Q Consensus 80 ~CpfCGk~~-VKR~av-----GIW~CkkC 102 (134)
.||+|+.+. |+|.+- =-|.|+.|
T Consensus 7 ~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 7 HCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 599999998 998743 36888887
No 45
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=85.82 E-value=0.3 Score=29.48 Aligned_cols=27 Identities=30% Similarity=0.691 Sum_probs=17.8
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
|.|..||.+..-.....| .|+.||..+
T Consensus 1 Y~C~~Cg~~~~~~~~~~i-rC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPI-RCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BSTSSTS-SBSSSS-SE
T ss_pred CCCCcCCCeeEcCCCCcE-ECCcCCCeE
Confidence 789999987533334455 899998654
No 46
>PRK11823 DNA repair protein RadA; Provisional
Probab=85.37 E-value=0.37 Score=42.43 Aligned_cols=25 Identities=32% Similarity=0.812 Sum_probs=21.2
Q ss_pred hhcccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 75 QHSKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 75 qhakY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.+..|.|..||-..-+.. |+|..|+
T Consensus 4 ~~~~y~C~~Cg~~~~~~~----g~Cp~C~ 28 (446)
T PRK11823 4 KKTAYVCQECGAESPKWL----GRCPECG 28 (446)
T ss_pred CCCeEECCcCCCCCcccC----eeCcCCC
Confidence 356799999999988764 8999996
No 47
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=84.79 E-value=0.48 Score=33.34 Aligned_cols=27 Identities=33% Similarity=0.866 Sum_probs=22.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEec
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKAG 108 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~AG 108 (134)
.||.||..-..+ .+.+.|..|+++..-
T Consensus 2 fC~~Cg~~l~~~--~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK--NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC--CCeEECcCCCCcccc
Confidence 699999988653 478999999988654
No 48
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=84.64 E-value=0.76 Score=27.01 Aligned_cols=28 Identities=29% Similarity=0.566 Sum_probs=19.2
Q ss_pred ccccCCCCceeeEEee---eeeeeeCCCCee
Q 045338 78 KYFCEFCGKYAVKRKA---VGIWGCKDCGKV 105 (134)
Q Consensus 78 kY~CpfCGk~~VKR~a---vGIW~CkkCgkt 105 (134)
.|.|+.||+.--...+ ..+..|..||..
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 5789999995422222 457789999863
No 49
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=84.48 E-value=0.72 Score=31.65 Aligned_cols=16 Identities=31% Similarity=0.823 Sum_probs=10.9
Q ss_pred hcccccCCCCceeeEE
Q 045338 76 HSKYFCEFCGKYAVKR 91 (134)
Q Consensus 76 hakY~CpfCGk~~VKR 91 (134)
..+|.||.||+..+.|
T Consensus 23 ~~~F~CPnCG~~~I~R 38 (59)
T PRK14890 23 AVKFLCPNCGEVIIYR 38 (59)
T ss_pred cCEeeCCCCCCeeEee
Confidence 4677888888765443
No 50
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=84.31 E-value=0.41 Score=35.56 Aligned_cols=29 Identities=28% Similarity=0.622 Sum_probs=21.7
Q ss_pred cccccCCCCce--eeEEeeeeeeeeCCCCeeEec
Q 045338 77 SKYFCEFCGKY--AVKRKAVGIWGCKDCGKVKAG 108 (134)
Q Consensus 77 akY~CpfCGk~--~VKR~avGIW~CkkCgkt~AG 108 (134)
.|++||.||+. .+.|.. | .|.+||..|--
T Consensus 8 tKR~Cp~CG~kFYDLnk~P--i-vCP~CG~~~~~ 38 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDP--I-VCPKCGTEFPP 38 (108)
T ss_pred CcccCCCCcchhccCCCCC--c-cCCCCCCccCc
Confidence 57899999986 466644 3 69999877643
No 51
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=84.31 E-value=0.57 Score=37.02 Aligned_cols=28 Identities=29% Similarity=0.597 Sum_probs=18.7
Q ss_pred ccCCCCcee--eE--Ee---eeee---eeeCCCCeeEe
Q 045338 80 FCEFCGKYA--VK--RK---AVGI---WGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~--VK--R~---avGI---W~CkkCgkt~A 107 (134)
.|||||.+. |. |. +..| =.|..||+.|+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 599999854 21 11 2234 47999999886
No 52
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=84.19 E-value=0.36 Score=43.56 Aligned_cols=30 Identities=27% Similarity=0.548 Sum_probs=20.6
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEeccc
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGA 110 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~AGGA 110 (134)
.||+||..- |=.+-+=|+|++||+++..-.
T Consensus 352 ~Cp~Cg~~m-~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 352 VCPRCGGRM-KSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCccCCch-hhcCCCCcccccccccCCccc
Confidence 699999752 212333599999999876543
No 53
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=83.97 E-value=0.86 Score=33.82 Aligned_cols=28 Identities=32% Similarity=0.751 Sum_probs=23.2
Q ss_pred ccCCCCceeeEEe--eeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYAVKRK--AVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~VKR~--avGIW~CkkCgkt~A 107 (134)
.||-||..-+-+. ..+.+.|++||+..-
T Consensus 4 FCp~Cgsll~p~~~~~~~~l~C~kCgye~~ 33 (113)
T COG1594 4 FCPKCGSLLYPKKDDEGGKLVCRKCGYEEE 33 (113)
T ss_pred ccCCccCeeEEeEcCCCcEEECCCCCcchh
Confidence 5999999987776 467999999997653
No 54
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=82.84 E-value=0.55 Score=41.59 Aligned_cols=25 Identities=32% Similarity=0.760 Sum_probs=21.0
Q ss_pred hhcccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 75 QHSKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 75 qhakY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.+..|.|..||-+.-+.. |+|..|+
T Consensus 4 ~~~~y~C~~Cg~~~~~~~----g~Cp~C~ 28 (454)
T TIGR00416 4 AKSKFVCQHCGADSPKWQ----GKCPACH 28 (454)
T ss_pred CCCeEECCcCCCCCcccc----EECcCCC
Confidence 355799999999988764 9999995
No 55
>PF14353 CpXC: CpXC protein
Probab=82.80 E-value=1.3 Score=32.22 Aligned_cols=13 Identities=23% Similarity=0.513 Sum_probs=9.7
Q ss_pred eeeeeCCCCeeEe
Q 045338 95 GIWGCKDCGKVKA 107 (134)
Q Consensus 95 GIW~CkkCgkt~A 107 (134)
-.+.|.+||..+.
T Consensus 37 ~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 37 FSFTCPSCGHKFR 49 (128)
T ss_pred CEEECCCCCCcee
Confidence 3678888887764
No 56
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=82.57 E-value=1.1 Score=38.07 Aligned_cols=30 Identities=30% Similarity=0.543 Sum_probs=24.6
Q ss_pred cccCCCCceeeEE-eeeeeeeeCCCCeeEec
Q 045338 79 YFCEFCGKYAVKR-KAVGIWGCKDCGKVKAG 108 (134)
Q Consensus 79 Y~CpfCGk~~VKR-~avGIW~CkkCgkt~AG 108 (134)
+.||.||.+.+-. ..-|=|.|..||-.+--
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~ 32 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLVLED 32 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCEEecc
Confidence 5799999996544 47899999999987754
No 57
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=82.55 E-value=1.4 Score=30.97 Aligned_cols=33 Identities=21% Similarity=0.516 Sum_probs=20.8
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEeccccccc
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLN 114 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~p~ 114 (134)
.||.|+.. +.+.+ |.++|..|.+-|.==|+-|+
T Consensus 3 ~CP~C~~~-L~~~~-~~~~C~~C~~~~~~~a~CPd 35 (70)
T PF07191_consen 3 TCPKCQQE-LEWQG-GHYHCEACQKDYKKEAFCPD 35 (70)
T ss_dssp B-SSS-SB-EEEET-TEEEETTT--EEEEEEE-TT
T ss_pred cCCCCCCc-cEEeC-CEEECccccccceecccCCC
Confidence 69999988 55555 88999999987766555554
No 58
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=82.44 E-value=1.9 Score=32.62 Aligned_cols=30 Identities=23% Similarity=0.442 Sum_probs=19.9
Q ss_pred cccCCCCceeeEEee-----eeeeeeCCCCeeEec
Q 045338 79 YFCEFCGKYAVKRKA-----VGIWGCKDCGKVKAG 108 (134)
Q Consensus 79 Y~CpfCGk~~VKR~a-----vGIW~CkkCgkt~AG 108 (134)
=.||+|+...+.+.+ .-=|.|++|+++|.=
T Consensus 31 ~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 31 VNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred CcCCCCCccceeeECCccccccccccCCcCcceee
Confidence 568888877644442 334788888888753
No 59
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=82.33 E-value=0.79 Score=32.21 Aligned_cols=21 Identities=38% Similarity=0.789 Sum_probs=10.3
Q ss_pred hcccccCCCCceeeEEeeeee
Q 045338 76 HSKYFCEFCGKYAVKRKAVGI 96 (134)
Q Consensus 76 hakY~CpfCGk~~VKR~avGI 96 (134)
-.+..||.||...++|+++.+
T Consensus 22 ~~k~FCp~CGn~TL~rvsvsv 42 (73)
T PF08772_consen 22 MTKQFCPKCGNATLKRVSVSV 42 (73)
T ss_dssp SS--S-SSS--S--EEEE-B-
T ss_pred CCceeCcccCCCcceEEEEEE
Confidence 357889999999999998765
No 60
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=82.03 E-value=2.7 Score=25.70 Aligned_cols=27 Identities=22% Similarity=0.426 Sum_probs=17.8
Q ss_pred ccCCCCceeeEEe----------eeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRK----------AVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~----------avGIW~CkkCgkt~ 106 (134)
.||.||....--. .+=+..|..||++|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 6999998752211 46789999999987
No 61
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=81.31 E-value=1.7 Score=26.28 Aligned_cols=29 Identities=24% Similarity=0.613 Sum_probs=18.6
Q ss_pred ccCCCCceeeEEeeeeee-eeCCCCeeEec
Q 045338 80 FCEFCGKYAVKRKAVGIW-GCKDCGKVKAG 108 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW-~CkkCgkt~AG 108 (134)
.||.||..-.-+.+..-. .|+.|++..--
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~ 32 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEPI 32 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE-
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccCC
Confidence 599999986554432211 69999988653
No 62
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=80.68 E-value=0.96 Score=40.58 Aligned_cols=37 Identities=27% Similarity=0.676 Sum_probs=26.9
Q ss_pred hhhHhHHHHHHhhhcccccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 63 SLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 63 slRK~vkkIE~sqhakY~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
.||++|-. -+.+...|.|..||-..- +=-|+|++|.+
T Consensus 340 ~lr~mvge-~l~~~~~YRC~~CGF~a~----~l~W~CPsC~~ 376 (389)
T COG2956 340 LLRDMVGE-QLRRKPRYRCQNCGFTAH----TLYWHCPSCRA 376 (389)
T ss_pred HHHHHHHH-HHhhcCCceecccCCcce----eeeeeCCCccc
Confidence 35666654 456788999999997642 23499999974
No 63
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=80.64 E-value=1.9 Score=32.01 Aligned_cols=52 Identities=17% Similarity=0.360 Sum_probs=30.3
Q ss_pred ccccCCCCceeeEEe----------eee-eeeeCCCCeeEeccccccccchHHHHHHHHHHHHh
Q 045338 78 KYFCEFCGKYAVKRK----------AVG-IWGCKDCGKVKAGGAYTLNTASAVTVRSTIRRLRE 130 (134)
Q Consensus 78 kY~CpfCGk~~VKR~----------avG-IW~CkkCgkt~AGGAy~p~T~~~~tvk~~Irrl~e 130 (134)
+=.||+||....-+. ... +|.|..|+.=|-==. .-+.|.|.-+...+|.+|.
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~H~-~t~~PlGtLAd~~lR~~R~ 64 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVGCHP-GTDIPLGTLADAELRRARK 64 (102)
T ss_pred CcccCCCCCeeEEcccchhcCccCCCCceeEECCCCCceeeeeC-CCCCcCcccCCHHHHHHHH
Confidence 347999999874433 124 499999964332111 1145666666666665554
No 64
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=80.37 E-value=2.2 Score=25.67 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=24.2
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCeeEe
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCgkt~A 107 (134)
...|+.||.+.+--..-++-.|..|+.++.
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcEee
Confidence 357999999887656778899999998763
No 65
>PRK08402 replication factor A; Reviewed
Probab=80.28 E-value=1.1 Score=39.13 Aligned_cols=26 Identities=23% Similarity=0.501 Sum_probs=21.2
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
..||-|.|.-+.-...|-|.|..|++
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGE 238 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCC
Confidence 36999998666456779999999985
No 66
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=79.93 E-value=0.89 Score=39.42 Aligned_cols=21 Identities=38% Similarity=0.888 Sum_probs=18.7
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
|.|..||-...|.. |+|..|+
T Consensus 1 ~~c~~cg~~~~~~~----g~cp~c~ 21 (372)
T cd01121 1 YVCSECGYVSPKWL----GKCPECG 21 (372)
T ss_pred CCCCCCCCCCCCcc----EECcCCC
Confidence 88999999988864 8999997
No 67
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=79.83 E-value=0.7 Score=26.62 Aligned_cols=24 Identities=25% Similarity=0.423 Sum_probs=17.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~A 107 (134)
+||.|++.. ....=.|..||+.|.
T Consensus 2 ~CP~C~~~V----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEV----PESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCc----hhhcCcCCCCCCCCc
Confidence 599999874 333347999998774
No 68
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=79.60 E-value=3.6 Score=25.87 Aligned_cols=30 Identities=27% Similarity=0.546 Sum_probs=22.6
Q ss_pred ccCCCCceeeEEeee--------eeeeeCC--CCeeEecc
Q 045338 80 FCEFCGKYAVKRKAV--------GIWGCKD--CGKVKAGG 109 (134)
Q Consensus 80 ~CpfCGk~~VKR~av--------GIW~Ckk--Cgkt~AGG 109 (134)
.||.||.....|.+. =...|.. ||.+|..-
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEE
Confidence 599999988777643 3467887 99888654
No 69
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=79.53 E-value=0.76 Score=28.52 Aligned_cols=24 Identities=38% Similarity=0.920 Sum_probs=13.7
Q ss_pred cccCCCCcee--eEEe--ee-eeeeeCCC
Q 045338 79 YFCEFCGKYA--VKRK--AV-GIWGCKDC 102 (134)
Q Consensus 79 Y~CpfCGk~~--VKR~--av-GIW~CkkC 102 (134)
..|+|||++. +.+. +. |+.-|..|
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~C 30 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDEC 30 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHH
Confidence 4799999975 3333 33 77888887
No 70
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=78.56 E-value=1.3 Score=25.74 Aligned_cols=21 Identities=24% Similarity=0.495 Sum_probs=13.1
Q ss_pred ccCCCCceeeEEeeeeeeeeC
Q 045338 80 FCEFCGKYAVKRKAVGIWGCK 100 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~Ck 100 (134)
+||.||...++-..-=+|.|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 599999999976666688885
No 71
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=78.56 E-value=1.6 Score=36.15 Aligned_cols=30 Identities=20% Similarity=0.464 Sum_probs=22.0
Q ss_pred ccccCCCCcee-----------eEEeeeeeeeeCCCCeeEe
Q 045338 78 KYFCEFCGKYA-----------VKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 78 kY~CpfCGk~~-----------VKR~avGIW~CkkCgkt~A 107 (134)
.-.||.||.+- ..++-.--|.|++||+..+
T Consensus 14 ~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 14 RIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 34799999853 3344556799999998765
No 72
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=78.19 E-value=2.1 Score=29.36 Aligned_cols=10 Identities=40% Similarity=0.946 Sum_probs=8.1
Q ss_pred cccCCCCcee
Q 045338 79 YFCEFCGKYA 88 (134)
Q Consensus 79 Y~CpfCGk~~ 88 (134)
|.||-||.+.
T Consensus 1 y~C~KCg~~~ 10 (64)
T PF09855_consen 1 YKCPKCGNEE 10 (64)
T ss_pred CCCCCCCCcc
Confidence 7899999764
No 73
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=77.88 E-value=2.8 Score=29.36 Aligned_cols=30 Identities=20% Similarity=0.544 Sum_probs=22.2
Q ss_pred cccCCCCceeeEEee--------eeeeeeC--CCCeeEec
Q 045338 79 YFCEFCGKYAVKRKA--------VGIWGCK--DCGKVKAG 108 (134)
Q Consensus 79 Y~CpfCGk~~VKR~a--------vGIW~Ck--kCgkt~AG 108 (134)
..||+||..+.-|.+ -=-+.|. .||.+|.-
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFIT 41 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEE
Confidence 479999988754442 2457898 99999864
No 74
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=77.71 E-value=2.4 Score=32.00 Aligned_cols=24 Identities=38% Similarity=0.861 Sum_probs=19.5
Q ss_pred cCCCCcee-eEEeeeeeeeeCCCCeeEecc
Q 045338 81 CEFCGKYA-VKRKAVGIWGCKDCGKVKAGG 109 (134)
Q Consensus 81 CpfCGk~~-VKR~avGIW~CkkCgkt~AGG 109 (134)
||.||.+- |.| -+|.+|+-++-|.
T Consensus 1 CPvCg~~l~vt~-----l~C~~C~t~i~G~ 25 (113)
T PF09862_consen 1 CPVCGGELVVTR-----LKCPSCGTEIEGE 25 (113)
T ss_pred CCCCCCceEEEE-----EEcCCCCCEEEee
Confidence 99999874 444 4899999999885
No 75
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=77.57 E-value=1.8 Score=33.71 Aligned_cols=28 Identities=25% Similarity=0.452 Sum_probs=24.0
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCeeEe
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCgkt~A 107 (134)
.+.||.||-+.++ -.|==.|.-|++++-
T Consensus 28 ~~hCp~Cg~PLF~--KdG~v~CPvC~~~~~ 55 (131)
T COG1645 28 AKHCPKCGTPLFR--KDGEVFCPVCGYREV 55 (131)
T ss_pred HhhCcccCCccee--eCCeEECCCCCceEE
Confidence 4689999999999 778789999997654
No 76
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=76.99 E-value=1.1 Score=34.18 Aligned_cols=47 Identities=17% Similarity=0.405 Sum_probs=36.0
Q ss_pred hhhcccccCCCCcee-----eEE-eeeeeeeeCCCCeeEeccccccccchHHH
Q 045338 74 SQHSKYFCEFCGKYA-----VKR-KAVGIWGCKDCGKVKAGGAYTLNTASAVT 120 (134)
Q Consensus 74 sqhakY~CpfCGk~~-----VKR-~avGIW~CkkCgkt~AGGAy~p~T~~~~t 120 (134)
.....|+||||.-.+ |.+ ..+|-=.|+-|+..|+--+=.+++|.-+.
T Consensus 19 ~ldt~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFqt~it~LsepIDVY 71 (109)
T KOG3214|consen 19 PLDTQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQTTITALSEPIDVY 71 (109)
T ss_pred chheeeccCccccccceeeeehhhcCcceeeeeehhhhhccchHhhccchHHH
Confidence 345678999999764 333 37899999999999998777777776554
No 77
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=76.97 E-value=3.5 Score=25.02 Aligned_cols=24 Identities=38% Similarity=0.679 Sum_probs=17.4
Q ss_pred ccCCCCcee--eEEeeeeeeeeCCCC
Q 045338 80 FCEFCGKYA--VKRKAVGIWGCKDCG 103 (134)
Q Consensus 80 ~CpfCGk~~--VKR~avGIW~CkkCg 103 (134)
.||.|+..- +.-..+=|+.|.+|+
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCC
Confidence 599999853 222356799999994
No 78
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=76.85 E-value=2.3 Score=25.37 Aligned_cols=26 Identities=23% Similarity=0.557 Sum_probs=15.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
.||.|+.+-.- ....++.|..|+..|
T Consensus 4 ~Cp~C~se~~y-~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTY-EDGELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----E-E-SSSEEETTTTEEE
T ss_pred CCCCCCCccee-ccCCEEeCCcccccC
Confidence 59999988655 677899999999765
No 79
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=76.84 E-value=1.3 Score=30.66 Aligned_cols=16 Identities=31% Similarity=0.719 Sum_probs=10.5
Q ss_pred hcccccCCCCceeeEE
Q 045338 76 HSKYFCEFCGKYAVKR 91 (134)
Q Consensus 76 hakY~CpfCGk~~VKR 91 (134)
..+|.||-||+..+.|
T Consensus 25 ~v~F~CPnCGe~~I~R 40 (61)
T COG2888 25 AVKFPCPNCGEVEIYR 40 (61)
T ss_pred eeEeeCCCCCceeeeh
Confidence 4567888888655433
No 80
>PHA00732 hypothetical protein
Probab=76.55 E-value=1.4 Score=30.87 Aligned_cols=10 Identities=30% Similarity=0.610 Sum_probs=5.4
Q ss_pred eeCCCCeeEe
Q 045338 98 GCKDCGKVKA 107 (134)
Q Consensus 98 ~CkkCgkt~A 107 (134)
.|..|++.|+
T Consensus 29 ~C~~CgKsF~ 38 (79)
T PHA00732 29 KCPVCNKSYR 38 (79)
T ss_pred ccCCCCCEeC
Confidence 4555555554
No 81
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=76.50 E-value=2.3 Score=32.01 Aligned_cols=31 Identities=32% Similarity=0.772 Sum_probs=22.9
Q ss_pred ccCCCCcee--eEEeee-------------eeeeeCCCCeeEeccc
Q 045338 80 FCEFCGKYA--VKRKAV-------------GIWGCKDCGKVKAGGA 110 (134)
Q Consensus 80 ~CpfCGk~~--VKR~av-------------GIW~CkkCgkt~AGGA 110 (134)
-||.|+..- +....+ =.|.|.+||+.+=.|.
T Consensus 93 RC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~Gs 138 (147)
T PF01927_consen 93 RCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGS 138 (147)
T ss_pred ccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccc
Confidence 699999864 333322 3899999999987775
No 82
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=76.30 E-value=0.78 Score=35.43 Aligned_cols=28 Identities=18% Similarity=0.522 Sum_probs=23.0
Q ss_pred cccCCCCceeeEEee-------eeeeeeCCCCeeE
Q 045338 79 YFCEFCGKYAVKRKA-------VGIWGCKDCGKVK 106 (134)
Q Consensus 79 Y~CpfCGk~~VKR~a-------vGIW~CkkCgkt~ 106 (134)
-.||.||.....+.+ --+|.|..|.+-|
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcH
Confidence 579999999888774 2799999998755
No 83
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=76.12 E-value=0.46 Score=30.95 Aligned_cols=34 Identities=38% Similarity=0.620 Sum_probs=24.1
Q ss_pred ccCCCCcee--eEE--eeeeeeeeCCCCeeEeccccccc
Q 045338 80 FCEFCGKYA--VKR--KAVGIWGCKDCGKVKAGGAYTLN 114 (134)
Q Consensus 80 ~CpfCGk~~--VKR--~avGIW~CkkCgkt~AGGAy~p~ 114 (134)
.|+.||+.. +.| ..-| |-|+.|.++..++-+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~~~~~~~~ 38 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLSGFFSDVK 38 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhcCcccchh
Confidence 499999874 332 4667 999999988855544333
No 84
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=75.92 E-value=4.3 Score=28.48 Aligned_cols=33 Identities=24% Similarity=0.536 Sum_probs=24.9
Q ss_pred ccccCCCCceeeE------Ee----eeeeeeeCCCCeeEeccc
Q 045338 78 KYFCEFCGKYAVK------RK----AVGIWGCKDCGKVKAGGA 110 (134)
Q Consensus 78 kY~CpfCGk~~VK------R~----avGIW~CkkCgkt~AGGA 110 (134)
...||.||...+- |. .+=++.|.+|+++|..++
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~~ 104 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREYE 104 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeCc
Confidence 5689999988742 21 456899999999987653
No 85
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=75.90 E-value=1.5 Score=35.03 Aligned_cols=36 Identities=22% Similarity=0.494 Sum_probs=20.3
Q ss_pred hhhHhHHHHHHhhhcccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 63 SLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 63 slRK~vkkIE~sqhakY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
-+++..+.++..+ -|.||.||-+-.. --.|.|+.||
T Consensus 121 ~~~~~Le~~~~~~--~~vC~vCGy~~~g---e~P~~CPiCg 156 (166)
T COG1592 121 MFRGLLERLEEGK--VWVCPVCGYTHEG---EAPEVCPICG 156 (166)
T ss_pred HHHHHHHhhhcCC--EEEcCCCCCcccC---CCCCcCCCCC
Confidence 4566666666555 5666666655433 3345666665
No 86
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=75.72 E-value=2.9 Score=31.24 Aligned_cols=66 Identities=18% Similarity=0.398 Sum_probs=40.5
Q ss_pred HhhhhhhccceeeeeccCCccccCchhhHhHHHHHHhh-------------hcccccCCCCcee--eEEeee-eeeeeCC
Q 045338 38 VCFCKMTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQ-------------HSKYFCEFCGKYA--VKRKAV-GIWGCKD 101 (134)
Q Consensus 38 ~~~~~MakrTKKVgi~GkfGtRYGaslRK~vkkIE~sq-------------hakY~CpfCGk~~--VKR~av-GIW~Ckk 101 (134)
+.++||+== .+.+.|+ +..-|...+..+.++.... .-.|.|.-||... .+|... .-+.|.+
T Consensus 62 ~l~HEm~H~--~~~~~g~-~~~Hg~~f~~~~~~~~~~~~~~~h~~~~~~~~~~~y~C~~C~~~~~~~rr~~~~~~y~C~~ 138 (146)
T smart00731 62 TLLHELCHA--ALYLFGR-GYGHGDEWKRWMRQVNGLFPERCHTFLIESVKKYPYRCTGCGQRYLRVRRSNNVSRYRCGK 138 (146)
T ss_pred hHHHHHHHH--HHHHhCC-CCCcCHHHHHHHHHHcCCCcceEcCCcccccceEEEECCCCCCCCceEccccCcceEEcCC
Confidence 566777531 2333343 3366777777777775542 3367888888753 444433 7788888
Q ss_pred CCeeE
Q 045338 102 CGKVK 106 (134)
Q Consensus 102 Cgkt~ 106 (134)
|+-.+
T Consensus 139 C~g~l 143 (146)
T smart00731 139 CGGKL 143 (146)
T ss_pred CCCEE
Confidence 87654
No 87
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=75.18 E-value=3.1 Score=33.56 Aligned_cols=22 Identities=23% Similarity=0.631 Sum_probs=19.3
Q ss_pred eeeeeeeCCCCeeEeccccccc
Q 045338 93 AVGIWGCKDCGKVKAGGAYTLN 114 (134)
Q Consensus 93 avGIW~CkkCgkt~AGGAy~p~ 114 (134)
.+-|=.|+.||..+-+|.|...
T Consensus 32 ~i~v~~C~~Cg~~~~~~~W~~~ 53 (236)
T PF04981_consen 32 RIEVTICPKCGRYRIGGRWVDP 53 (236)
T ss_pred ccCceECCCCCCEECCCEeeec
Confidence 3567789999999999999987
No 88
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=74.15 E-value=3 Score=27.32 Aligned_cols=28 Identities=21% Similarity=0.428 Sum_probs=17.8
Q ss_pred cccccC--CCCcee-eEEeeeeeeeeCCCCee
Q 045338 77 SKYFCE--FCGKYA-VKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 77 akY~Cp--fCGk~~-VKR~avGIW~CkkCgkt 105 (134)
..-.|| .||.-. |- .-..=|.|.+|+.|
T Consensus 17 ~rk~CP~~~CG~GvFMA-~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMA-EHKDRHYCGKCGYT 47 (47)
T ss_dssp SSEE-TSTTTTSSSEEE-E-SSEEEETTTSS-
T ss_pred hhhcCCCcccCCceEee-ecCCCccCCCcccC
Confidence 345699 999854 33 22356999999975
No 89
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=73.03 E-value=2.8 Score=33.11 Aligned_cols=33 Identities=21% Similarity=0.471 Sum_probs=22.0
Q ss_pred cCCCCceeeEEe------------eeeeeeeCCCCee----Eecccccc
Q 045338 81 CEFCGKYAVKRK------------AVGIWGCKDCGKV----KAGGAYTL 113 (134)
Q Consensus 81 CpfCGk~~VKR~------------avGIW~CkkCgkt----~AGGAy~p 113 (134)
||.||...++.. =.=-+.|.+||++ ..||+..|
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~~~~~p 49 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRSTDVYQLEEKEP 49 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchhheeEcCCcCC
Confidence 999998754442 1223899999965 45666554
No 90
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=72.97 E-value=1.2 Score=35.66 Aligned_cols=28 Identities=39% Similarity=0.797 Sum_probs=17.7
Q ss_pred ccCCCCceeeE----Eeee---ee---eeeCCCCeeEe
Q 045338 80 FCEFCGKYAVK----RKAV---GI---WGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~VK----R~av---GI---W~CkkCgkt~A 107 (134)
.||||+....+ |.+- -| =.|..||.-|+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccc
Confidence 59999976421 1111 11 37999998886
No 91
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=72.39 E-value=2.7 Score=24.71 Aligned_cols=30 Identities=27% Similarity=0.437 Sum_probs=19.0
Q ss_pred ccccCCCCcee-eEE----eeeeeeeeCCCCeeEe
Q 045338 78 KYFCEFCGKYA-VKR----KAVGIWGCKDCGKVKA 107 (134)
Q Consensus 78 kY~CpfCGk~~-VKR----~avGIW~CkkCgkt~A 107 (134)
...||.||..- +.- ...+-=.|.+|+..|-
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 36799999853 221 1122348999998873
No 92
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=71.25 E-value=5.2 Score=31.20 Aligned_cols=35 Identities=29% Similarity=0.665 Sum_probs=19.7
Q ss_pred ccCCCCceeeEEe-ee----------eeeeeCCCCee----Eeccccccc
Q 045338 80 FCEFCGKYAVKRK-AV----------GIWGCKDCGKV----KAGGAYTLN 114 (134)
Q Consensus 80 ~CpfCGk~~VKR~-av----------GIW~CkkCgkt----~AGGAy~p~ 114 (134)
.||.||+...-|. -+ =-+.|.+||++ ..||+..|.
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~~ 52 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQPK 52 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-SS
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCCC
Confidence 5999999863333 22 33899999975 457776654
No 93
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=71.03 E-value=3 Score=24.93 Aligned_cols=15 Identities=33% Similarity=1.055 Sum_probs=12.8
Q ss_pred eeeeCCCCeeEeccc
Q 045338 96 IWGCKDCGKVKAGGA 110 (134)
Q Consensus 96 IW~CkkCgkt~AGGA 110 (134)
+|.|..||+++.|..
T Consensus 2 ~~~C~~CG~i~~g~~ 16 (34)
T cd00729 2 VWVCPVCGYIHEGEE 16 (34)
T ss_pred eEECCCCCCEeECCc
Confidence 599999999988764
No 94
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=71.02 E-value=1.8 Score=39.96 Aligned_cols=27 Identities=33% Similarity=0.685 Sum_probs=20.6
Q ss_pred ccCC--CCceeeEEeeeeeeeeCCCCeeEe
Q 045338 80 FCEF--CGKYAVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~Cpf--CGk~~VKR~avGIW~CkkCgkt~A 107 (134)
-||. |.|..+ -...|.|.|.+|++.+.
T Consensus 476 ACp~~~CnKKV~-~~~~g~~~CekC~~~~~ 504 (608)
T TIGR00617 476 ACPSEDCNKKVV-DQGDGTYRCEKCNKNFA 504 (608)
T ss_pred cCChhhCCCccc-cCCCCCEECCCCCCCCC
Confidence 5877 887644 35669999999998764
No 95
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=70.66 E-value=5 Score=31.50 Aligned_cols=27 Identities=22% Similarity=0.474 Sum_probs=15.2
Q ss_pred ccccCCCCceee-----E----EeeeeeeeeCCCCe
Q 045338 78 KYFCEFCGKYAV-----K----RKAVGIWGCKDCGK 104 (134)
Q Consensus 78 kY~CpfCGk~~V-----K----R~avGIW~CkkCgk 104 (134)
..+||.|+.... . -.....|.|.+|+.
T Consensus 18 ~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~ 53 (188)
T PF08996_consen 18 KLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST 53 (188)
T ss_dssp EEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred EeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence 458999998751 1 23456899999987
No 96
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=70.61 E-value=2.8 Score=24.11 Aligned_cols=10 Identities=30% Similarity=0.830 Sum_probs=5.6
Q ss_pred hcccccCCCC
Q 045338 76 HSKYFCEFCG 85 (134)
Q Consensus 76 hakY~CpfCG 85 (134)
-..|.||.||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 4455566555
No 97
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=70.13 E-value=3.7 Score=37.48 Aligned_cols=30 Identities=27% Similarity=0.690 Sum_probs=21.9
Q ss_pred hhcccccCCCCcee-------eEEeeeeeeeeCCCCe
Q 045338 75 QHSKYFCEFCGKYA-------VKRKAVGIWGCKDCGK 104 (134)
Q Consensus 75 qhakY~CpfCGk~~-------VKR~avGIW~CkkCgk 104 (134)
..+-|.||+|.++- +-=-..|-.+|.-|+-
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGG 161 (436)
T ss_pred ccccccCCccccchhhhHHHHhhcccCceEEEecCCC
Confidence 56789999999872 1112468899999973
No 98
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=69.73 E-value=2.9 Score=29.36 Aligned_cols=26 Identities=35% Similarity=0.767 Sum_probs=20.5
Q ss_pred cccCCCCcee--------eEEeeeeeeeeC-CCCe
Q 045338 79 YFCEFCGKYA--------VKRKAVGIWGCK-DCGK 104 (134)
Q Consensus 79 Y~CpfCGk~~--------VKR~avGIW~Ck-kCgk 104 (134)
++|.|||++. |++.+.=.|-|. +|.+
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v~~FcssKc~k 38 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKVLRFCSSKCEK 38 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeEEEEechhHHH
Confidence 5799999875 888888889886 4554
No 99
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=69.25 E-value=2.1 Score=33.38 Aligned_cols=27 Identities=19% Similarity=0.202 Sum_probs=20.4
Q ss_pred cccccCCCCcee--eEEeeeeeeeeCCCCeeE
Q 045338 77 SKYFCEFCGKYA--VKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 77 akY~CpfCGk~~--VKR~avGIW~CkkCgkt~ 106 (134)
.|++||.||+.- +.|.. =.|.+||..+
T Consensus 8 tKr~Cp~cg~kFYDLnk~p---~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRP---AVSPYTGEQF 36 (129)
T ss_pred ccccCCCcCccccccCCCC---ccCCCcCCcc
Confidence 588999999863 55543 2899998875
No 100
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=68.98 E-value=3 Score=25.69 Aligned_cols=17 Identities=29% Similarity=0.548 Sum_probs=13.5
Q ss_pred hcccccCCCCceeeEEe
Q 045338 76 HSKYFCEFCGKYAVKRK 92 (134)
Q Consensus 76 hakY~CpfCGk~~VKR~ 92 (134)
...-.||.||.+.++|+
T Consensus 24 ~~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 24 DDPVPCPECGSTEVRRV 40 (42)
T ss_pred CCCCcCCCCCCCceEEe
Confidence 45668999999888875
No 101
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=68.00 E-value=1.8 Score=38.35 Aligned_cols=25 Identities=36% Similarity=1.065 Sum_probs=18.7
Q ss_pred cccCCCCcee--eEEeee--eeeeeCCCC
Q 045338 79 YFCEFCGKYA--VKRKAV--GIWGCKDCG 103 (134)
Q Consensus 79 Y~CpfCGk~~--VKR~av--GIW~CkkCg 103 (134)
..|+|||+.. |.+.-. |.+-|..|-
T Consensus 8 ~~c~fc~~~~~~~~~~~~~~~~~ic~~c~ 36 (413)
T TIGR00382 8 LYCSFCGKSQDEVRKLIAGPGVYICDECI 36 (413)
T ss_pred eecCCCCCChhhcccccCCCCCcCCCchH
Confidence 3799999964 665533 489999993
No 102
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=67.39 E-value=3.9 Score=33.73 Aligned_cols=26 Identities=27% Similarity=0.611 Sum_probs=19.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
.||.||.....+.+.-.-.|.+|+..
T Consensus 101 fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 101 FCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred cccccCCCCeecCCceeEECCCCCCE
Confidence 69999988766555556789999854
No 103
>PHA02768 hypothetical protein; Provisional
Probab=67.03 E-value=2.1 Score=28.84 Aligned_cols=10 Identities=40% Similarity=1.075 Sum_probs=6.0
Q ss_pred cccCCCCcee
Q 045338 79 YFCEFCGKYA 88 (134)
Q Consensus 79 Y~CpfCGk~~ 88 (134)
|.||.||+.-
T Consensus 6 y~C~~CGK~F 15 (55)
T PHA02768 6 YECPICGEIY 15 (55)
T ss_pred cCcchhCCee
Confidence 5666666653
No 104
>smart00507 HNHc HNH nucleases.
Probab=66.97 E-value=2.8 Score=24.24 Aligned_cols=13 Identities=38% Similarity=0.912 Sum_probs=10.2
Q ss_pred hhcccccCCCCcee
Q 045338 75 QHSKYFCEFCGKYA 88 (134)
Q Consensus 75 qhakY~CpfCGk~~ 88 (134)
.+. |.|++||...
T Consensus 8 ~r~-~~C~~C~~~~ 20 (52)
T smart00507 8 HRD-GVCAYCGKPA 20 (52)
T ss_pred HHC-CCCcCCcCCC
Confidence 455 8999999874
No 105
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=66.60 E-value=1.8 Score=24.15 Aligned_cols=22 Identities=27% Similarity=0.696 Sum_probs=12.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
.||.||+..-.-. =-|..||..
T Consensus 1 ~Cp~CG~~~~~~~----~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDA----KFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcC----cchhhhCCc
Confidence 3777877643211 137777653
No 106
>PRK08173 DNA topoisomerase III; Validated
Probab=66.47 E-value=5.5 Score=38.46 Aligned_cols=26 Identities=19% Similarity=0.441 Sum_probs=19.1
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
-.||.||+..++ .-+-|.|..|+.++
T Consensus 625 ~~CP~Cg~~~~~--~~~~~~Cs~C~f~~ 650 (862)
T PRK08173 625 TPCPNCGGVVKE--NYRRFACTKCDFSI 650 (862)
T ss_pred ccCCcccccccc--cCceeEcCCCCccc
Confidence 469999986543 23449999998765
No 107
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=65.42 E-value=6.5 Score=23.90 Aligned_cols=26 Identities=35% Similarity=0.751 Sum_probs=14.8
Q ss_pred ccCCCCceeeEEeeee----eeeeCCCCee
Q 045338 80 FCEFCGKYAVKRKAVG----IWGCKDCGKV 105 (134)
Q Consensus 80 ~CpfCGk~~VKR~avG----IW~CkkCgkt 105 (134)
.||.||.....++..| =|.|..||..
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCE
Confidence 4999999876665533 4789999875
No 108
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=65.30 E-value=3.6 Score=27.14 Aligned_cols=49 Identities=22% Similarity=0.339 Sum_probs=28.3
Q ss_pred hHhhHhHhhhhhhccceeeeeccCCccccCchhhHhHHHHHHhhhcccccCCCCc
Q 045338 32 RFLEFLVCFCKMTKRTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFCEFCGK 86 (134)
Q Consensus 32 ~~~~~~~~~~~MakrTKKVgi~GkfGtRYGaslRK~vkkIE~sqhakY~CpfCGk 86 (134)
|+++++.-.+.++-..+..=|..+=..+-|..+ .|.-..-.|.||+||.
T Consensus 4 ki~d~L~G~d~~~~~~r~aLIC~~C~~hNGla~------~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 4 KILDVLLGDDPTSPSNRYALICSKCFSHNGLAP------KEEFEEIQYRCPYCGA 52 (54)
T ss_pred HHHHHHhCCCCccccCceeEECcccchhhcccc------cccCCceEEEcCCCCC
Confidence 344444444444445556666777677777665 2333445777777774
No 109
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=64.66 E-value=8.8 Score=29.40 Aligned_cols=43 Identities=16% Similarity=0.352 Sum_probs=26.9
Q ss_pred chhhHhHHHHHHhhhccc-ccCCCCcee--eEEeeeeee--eeCCCCee
Q 045338 62 ASLRKQIKKMEVSQHSKY-FCEFCGKYA--VKRKAVGIW--GCKDCGKV 105 (134)
Q Consensus 62 aslRK~vkkIE~sqhakY-~CpfCGk~~--VKR~avGIW--~CkkCgkt 105 (134)
+---+.+.++-..=-.+| .||.|+.+. +.+. ..+| +|..||..
T Consensus 80 ~~~~~~i~~~L~~yI~~yVlC~~C~sPdT~l~k~-~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 80 KFTHFLLNERIEDYVRKYVICRECNRPDTRIIKE-GRVSLLKCEACGAK 127 (133)
T ss_pred ecCHHHHHHHHHHHHhheEECCCCCCCCcEEEEe-CCeEEEecccCCCC
Confidence 333455555555555567 699999864 3333 3455 89999754
No 110
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=64.02 E-value=7.6 Score=36.98 Aligned_cols=24 Identities=29% Similarity=0.728 Sum_probs=18.6
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
.||.||.+ +.++ -|=..|+.||+.
T Consensus 726 ~Cp~Cg~~-l~~~-~GC~~C~~CG~s 749 (752)
T PRK08665 726 ACPECGSI-LEHE-EGCVVCHSCGYS 749 (752)
T ss_pred CCCCCCcc-cEEC-CCCCcCCCCCCC
Confidence 49999954 5544 488899999975
No 111
>PRK04023 DNA polymerase II large subunit; Validated
Probab=63.76 E-value=3.4 Score=41.50 Aligned_cols=53 Identities=21% Similarity=0.381 Sum_probs=27.1
Q ss_pred ccccCCCCceeeEEe-------eeeeeeeCCCCeeEec------cccc-----cccchHHHHHHHHHHHHh
Q 045338 78 KYFCEFCGKYAVKRK-------AVGIWGCKDCGKVKAG------GAYT-----LNTASAVTVRSTIRRLRE 130 (134)
Q Consensus 78 kY~CpfCGk~~VKR~-------avGIW~CkkCgkt~AG------GAy~-----p~T~~~~tvk~~Irrl~e 130 (134)
...||.||....... ...||.|..|+..... |+=. ..-+....+.+|+.+|.+
T Consensus 626 ~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~~s~~~i~l~~~~~~A~~~lg~ 696 (1121)
T PRK04023 626 RRKCPSCGKETFYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTPYSKRKIDLKELYDRALENLGE 696 (1121)
T ss_pred CccCCCCCCcCCcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCccceEEecHHHHHHHHHHHhCC
Confidence 345666666543322 2357777777665431 1111 123445566666666654
No 112
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=63.42 E-value=12 Score=28.70 Aligned_cols=31 Identities=19% Similarity=0.553 Sum_probs=19.9
Q ss_pred eeEEeeee--eeeeCCCCeeEeccccccccchHHHHHHHH
Q 045338 88 AVKRKAVG--IWGCKDCGKVKAGGAYTLNTASAVTVRSTI 125 (134)
Q Consensus 88 ~VKR~avG--IW~CkkCgkt~AGGAy~p~T~~~~tvk~~I 125 (134)
...+...| +|.|..|- |...-..+.-+.+.|
T Consensus 52 ewi~~~~G~~VwSC~dC~-------~iH~ke~~~~ilr~l 84 (112)
T COG2158 52 EWISDSNGRKVWSCSDCH-------WIHRKEGAEEILREL 84 (112)
T ss_pred ceeEcCCCCEEeeccccc-------eecccchHHHHHHHH
Confidence 34555667 99999994 555555555555444
No 113
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=63.36 E-value=5.2 Score=20.72 Aligned_cols=11 Identities=36% Similarity=0.854 Sum_probs=7.6
Q ss_pred eeeCCCCeeEe
Q 045338 97 WGCKDCGKVKA 107 (134)
Q Consensus 97 W~CkkCgkt~A 107 (134)
|.|..|++.|.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 56777777764
No 114
>PHA00616 hypothetical protein
Probab=63.28 E-value=2.5 Score=27.31 Aligned_cols=10 Identities=40% Similarity=0.853 Sum_probs=8.0
Q ss_pred ccccCCCCce
Q 045338 78 KYFCEFCGKY 87 (134)
Q Consensus 78 kY~CpfCGk~ 87 (134)
+|.||.||+.
T Consensus 1 pYqC~~CG~~ 10 (44)
T PHA00616 1 MYQCLRCGGI 10 (44)
T ss_pred CCccchhhHH
Confidence 5889999875
No 115
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=63.25 E-value=3.7 Score=35.56 Aligned_cols=40 Identities=35% Similarity=0.663 Sum_probs=28.7
Q ss_pred HHHHHhhhc-ccccCCCCcee--------eEEeeee--eeeeCCCCeeEec
Q 045338 69 KKMEVSQHS-KYFCEFCGKYA--------VKRKAVG--IWGCKDCGKVKAG 108 (134)
Q Consensus 69 kkIE~sqha-kY~CpfCGk~~--------VKR~avG--IW~CkkCgkt~AG 108 (134)
.++.|.-|. .+.|++|||.- =-|.-+| =..|..|++-||.
T Consensus 177 LkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFAD 227 (279)
T KOG2462|consen 177 LKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFAD 227 (279)
T ss_pred HhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcc
Confidence 456666676 88899999864 2355555 3788889888885
No 116
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=63.18 E-value=10 Score=23.22 Aligned_cols=27 Identities=30% Similarity=0.663 Sum_probs=19.3
Q ss_pred ccCCCCceeeEEeee--eeeeeCC---CCeeE
Q 045338 80 FCEFCGKYAVKRKAV--GIWGCKD---CGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~av--GIW~Ckk---Cgkt~ 106 (134)
.||.||..-+.|.+- =.|-|.. |..+.
T Consensus 3 ~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~ 34 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGKKGKFLGCSNYPECKYTE 34 (39)
T ss_pred CCCCCCceeEEEECCCCCEEECCCCCCcCCeE
Confidence 699999887777643 3678876 66553
No 117
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=63.01 E-value=3.6 Score=32.88 Aligned_cols=13 Identities=38% Similarity=1.158 Sum_probs=12.7
Q ss_pred eeeeCCCCeeEec
Q 045338 96 IWGCKDCGKVKAG 108 (134)
Q Consensus 96 IW~CkkCgkt~AG 108 (134)
+|.|..||+++.|
T Consensus 134 ~~vC~vCGy~~~g 146 (166)
T COG1592 134 VWVCPVCGYTHEG 146 (166)
T ss_pred EEEcCCCCCcccC
Confidence 9999999999999
No 118
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=62.93 E-value=5.6 Score=24.68 Aligned_cols=27 Identities=33% Similarity=0.750 Sum_probs=14.6
Q ss_pred ccccCCCCcee-eEEe-e-eeeeeeCCCCe
Q 045338 78 KYFCEFCGKYA-VKRK-A-VGIWGCKDCGK 104 (134)
Q Consensus 78 kY~CpfCGk~~-VKR~-a-vGIW~CkkCgk 104 (134)
.|.|+.||..- +.+. + .....|..||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 46777777632 2211 1 24556777774
No 119
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=61.39 E-value=10 Score=29.21 Aligned_cols=41 Identities=20% Similarity=0.480 Sum_probs=25.2
Q ss_pred hHhHHHHHHhhhccc-ccCCCCcee--eEEe-eeeeeeeCCCCee
Q 045338 65 RKQIKKMEVSQHSKY-FCEFCGKYA--VKRK-AVGIWGCKDCGKV 105 (134)
Q Consensus 65 RK~vkkIE~sqhakY-~CpfCGk~~--VKR~-avGIW~CkkCgkt 105 (134)
-+.+.++-..=-..| .||.||.+. +.+. .+=+=+|..||..
T Consensus 88 ~~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 88 PRVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred HHHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 345555555555666 699999864 3332 2234489999753
No 120
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=61.35 E-value=5.2 Score=32.11 Aligned_cols=49 Identities=18% Similarity=0.539 Sum_probs=34.3
Q ss_pred CCccccCchhhHhHHHHHHhhhcccccCCCCce--eeEEeeee----eeeeCCCCee
Q 045338 55 KYGTRYGASLRKQIKKMEVSQHSKYFCEFCGKY--AVKRKAVG----IWGCKDCGKV 105 (134)
Q Consensus 55 kfGtRYGaslRK~vkkIE~sqhakY~CpfCGk~--~VKR~avG----IW~CkkCgkt 105 (134)
=||.||-.++-.-++.+-- ..-.|.|. |+.. .++|...- ++.|++|+-+
T Consensus 95 V~~l~~~~~h~~~~~~v~~-~~~~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gk 149 (156)
T COG3091 95 VLGLRFCRTHQFEVQSVRR-TTYPYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGK 149 (156)
T ss_pred hCCCCCCccchHHHhhccc-cceeEEee-cCCccchhhhcccccccceEEeccCCce
Confidence 3788888887776664432 34468999 9975 35555444 5999999855
No 121
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=60.84 E-value=5.1 Score=23.54 Aligned_cols=14 Identities=29% Similarity=0.695 Sum_probs=11.2
Q ss_pred eeeeCCCCeeEecc
Q 045338 96 IWGCKDCGKVKAGG 109 (134)
Q Consensus 96 IW~CkkCgkt~AGG 109 (134)
+|.|..||++..+.
T Consensus 1 ~~~C~~CGy~y~~~ 14 (33)
T cd00350 1 KYVCPVCGYIYDGE 14 (33)
T ss_pred CEECCCCCCEECCC
Confidence 58999999887765
No 122
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=60.04 E-value=6.5 Score=19.64 Aligned_cols=11 Identities=36% Similarity=0.791 Sum_probs=5.6
Q ss_pred eeeCCCCeeEe
Q 045338 97 WGCKDCGKVKA 107 (134)
Q Consensus 97 W~CkkCgkt~A 107 (134)
|.|..|+++|.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 56667766654
No 123
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=59.83 E-value=6.9 Score=23.56 Aligned_cols=28 Identities=25% Similarity=0.403 Sum_probs=19.3
Q ss_pred ccCCCCcee-eE----EeeeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYA-VK----RKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~-VK----R~avGIW~CkkCgkt~A 107 (134)
+||.|+..- |. +.+.+.=+|.+|+.+|.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 699999752 22 13445668999998873
No 124
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=59.39 E-value=10 Score=21.94 Aligned_cols=26 Identities=27% Similarity=0.567 Sum_probs=13.9
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
.||.||.....-.+---=.|..|+..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 59999988766444333379999864
No 125
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=59.32 E-value=7.4 Score=33.34 Aligned_cols=33 Identities=18% Similarity=0.472 Sum_probs=23.8
Q ss_pred hhhcccccCCCCceee------EEe----eeeeeeeCCCCeeE
Q 045338 74 SQHSKYFCEFCGKYAV------KRK----AVGIWGCKDCGKVK 106 (134)
Q Consensus 74 sqhakY~CpfCGk~~V------KR~----avGIW~CkkCgkt~ 106 (134)
.....+.||.||...+ -|. -+-++.|..||..|
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRW 296 (299)
T ss_pred CCcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCee
Confidence 3445699999998763 121 36788999999875
No 126
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=58.99 E-value=3.3 Score=23.21 Aligned_cols=23 Identities=30% Similarity=0.730 Sum_probs=15.2
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
..||.||+. + ..+-=.|..||..
T Consensus 3 ~~Cp~Cg~~-~---~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAE-I---DPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCc-C---CcccccChhhCCC
Confidence 469999984 2 2333478888764
No 127
>PF12773 DZR: Double zinc ribbon
Probab=58.62 E-value=3 Score=25.63 Aligned_cols=29 Identities=24% Similarity=0.527 Sum_probs=19.0
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEecc
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGG 109 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~AGG 109 (134)
.||.||.... ......+.|.+||..+..+
T Consensus 14 fC~~CG~~l~-~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 14 FCPHCGTPLP-PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred CChhhcCChh-hccCCCCCCcCCcCCCcCC
Confidence 5888887655 3344457888888765543
No 128
>PHA00733 hypothetical protein
Probab=58.19 E-value=2.9 Score=31.32 Aligned_cols=37 Identities=24% Similarity=0.328 Sum_probs=24.5
Q ss_pred HHHhhhcccccCCCCceeeE--------EeeeeeeeeCCCCeeEe
Q 045338 71 MEVSQHSKYFCEFCGKYAVK--------RKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 71 IE~sqhakY~CpfCGk~~VK--------R~avGIW~CkkCgkt~A 107 (134)
+......+|.|+.||+.--. +....-..|..|++.|.
T Consensus 66 ~~~~~~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~ 110 (128)
T PHA00733 66 LTSKAVSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFR 110 (128)
T ss_pred cccCCCCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccC
Confidence 34445678999999986311 11134579999998774
No 129
>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=57.79 E-value=6 Score=38.80 Aligned_cols=38 Identities=21% Similarity=0.405 Sum_probs=30.1
Q ss_pred cccccCCCCceeeEEe---------eeeeeeeCCCCeeEeccccccc
Q 045338 77 SKYFCEFCGKYAVKRK---------AVGIWGCKDCGKVKAGGAYTLN 114 (134)
Q Consensus 77 akY~CpfCGk~~VKR~---------avGIW~CkkCgkt~AGGAy~p~ 114 (134)
..|.|..|-.....+. ..-||-|=+||+.+-|+-=.++
T Consensus 65 ~~~~C~eC~e~~~~k~g~s~~~~~~~~~iWLCLkCG~q~CG~~~~~~ 111 (877)
T KOG1873|consen 65 LWIKCSECNEEVKVKDGGSSDQFEFDNAIWLCLKCGYQGCGRNSESQ 111 (877)
T ss_pred HHHHHHHhhhcceeccCCCccccccccceeeecccCCeeeCCCcccc
Confidence 6788999998864444 5689999999999999854443
No 130
>COG4640 Predicted membrane protein [Function unknown]
Probab=57.05 E-value=4.4 Score=37.18 Aligned_cols=31 Identities=26% Similarity=0.554 Sum_probs=23.6
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEeccccccc
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLN 114 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~p~ 114 (134)
.||-||+.... +--.|+.||..|.++-=..+
T Consensus 3 fC~kcG~qk~E----d~~qC~qCG~~~t~~~sqan 33 (465)
T COG4640 3 FCPKCGSQKAE----DDVQCTQCGHKFTSRQSQAN 33 (465)
T ss_pred ccccccccccc----ccccccccCCcCCchhhhhh
Confidence 59999977643 33469999999999865554
No 131
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=56.70 E-value=11 Score=39.21 Aligned_cols=48 Identities=19% Similarity=0.322 Sum_probs=35.3
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCeeEecccccc-ccchHHHHHHHHHHHHh
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTL-NTASAVTVRSTIRRLRE 130 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~p-~T~~~~tvk~~Irrl~e 130 (134)
+.+.||.||+.... +.|..||..+--..|.- .-+......+|+.+|.+
T Consensus 673 ~~~~Cp~Cg~~~~~------~~Cp~CG~~~~~~~~~~~~i~~~~~~~~A~~~v~~ 721 (1627)
T PRK14715 673 AFFKCPKCGKVGLY------HVCPFCGTRVELKPYARREIPPKDYWYAALENLKI 721 (1627)
T ss_pred EeeeCCCCCCcccc------ccCcccCCcccCCCccceecCHHHHHHHHHHHhCC
Confidence 45689999999887 78999997755555543 45566777778777754
No 132
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=56.61 E-value=3.5 Score=36.32 Aligned_cols=25 Identities=36% Similarity=1.089 Sum_probs=18.6
Q ss_pred ccccCCCCcee--eEEe--eeeeeeeCCC
Q 045338 78 KYFCEFCGKYA--VKRK--AVGIWGCKDC 102 (134)
Q Consensus 78 kY~CpfCGk~~--VKR~--avGIW~CkkC 102 (134)
...|+|||+.. +.+. +-|.+-|..|
T Consensus 9 ~~~CSFCGr~~~ev~~li~g~~~~IC~~C 37 (412)
T PRK05342 9 LLYCSFCGKSQHEVRKLIAGPGVYICDEC 37 (412)
T ss_pred ccccCCCCCChhhccccccCCCCcccchH
Confidence 44799999975 5543 3467999999
No 133
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=55.65 E-value=6.5 Score=26.99 Aligned_cols=31 Identities=26% Similarity=0.503 Sum_probs=19.4
Q ss_pred hhcccccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 75 QHSKYFCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 75 qhakY~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
+..+..|..||....-+.-.-...|..||+.
T Consensus 4 ~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 4 MMEPPKCTSCGIEIAPREKAVKFLCPNCGEV 34 (59)
T ss_pred cccCccccCCCCcccCCCccCEeeCCCCCCe
Confidence 4567789999998876662233444444443
No 134
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=55.07 E-value=7 Score=25.83 Aligned_cols=29 Identities=31% Similarity=0.668 Sum_probs=19.0
Q ss_pred cccccCCCCceeeEE-eeeeeeeeCCCCeeE
Q 045338 77 SKYFCEFCGKYAVKR-KAVGIWGCKDCGKVK 106 (134)
Q Consensus 77 akY~CpfCGk~~VKR-~avGIW~CkkCgkt~ 106 (134)
..|.|..||+.--.= ...|| .|..||..+
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~i-rCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREVELDQETRGI-RCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCeeehhhccCce-eCCCCCcEE
Confidence 468888888875211 23444 888888765
No 135
>PF04071 zf-like: Cysteine-rich small domain; InterPro: IPR007212 This is a probable metal-binding domain. It is found in a probable precorrin-3B C17-methyltransferase from Methanobacterium thermoautotrophicum, that catalyses the methylation of C-17 in precorrin-3B to form precorrin-4.
Probab=55.05 E-value=8.6 Score=27.88 Aligned_cols=12 Identities=42% Similarity=1.337 Sum_probs=9.7
Q ss_pred eeee--eeeeCCCC
Q 045338 92 KAVG--IWGCKDCG 103 (134)
Q Consensus 92 ~avG--IW~CkkCg 103 (134)
.+.| ||.|..|.
T Consensus 45 ~~~G~~vw~C~~C~ 58 (86)
T PF04071_consen 45 TKNGSKVWDCSDCT 58 (86)
T ss_pred cCCCCeeeECccCC
Confidence 4566 99999994
No 136
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=54.92 E-value=4.9 Score=32.39 Aligned_cols=28 Identities=29% Similarity=0.585 Sum_probs=20.3
Q ss_pred ccCCCCcee--eE-------------EeeeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYA--VK-------------RKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~--VK-------------R~avGIW~CkkCgkt~A 107 (134)
.||.|+..- |. +...-.|.|.+||+.+=
T Consensus 99 RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 99 RCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred cCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccccc
Confidence 599999864 22 33344899999998753
No 137
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=54.60 E-value=14 Score=27.98 Aligned_cols=41 Identities=27% Similarity=0.532 Sum_probs=26.1
Q ss_pred hhHhHHHHHHhhhccc-ccCCCCcee--eEEeeeeee--eeCCCCee
Q 045338 64 LRKQIKKMEVSQHSKY-FCEFCGKYA--VKRKAVGIW--GCKDCGKV 105 (134)
Q Consensus 64 lRK~vkkIE~sqhakY-~CpfCGk~~--VKR~avGIW--~CkkCgkt 105 (134)
-.+.+.++-..=-.+| .||.|+.+. +.+. .++| +|..||..
T Consensus 78 ~~~~i~~~L~~fI~~yVlC~~C~spdT~l~k~-~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 78 SSKQIQDLLDKFIKEYVLCPECGSPDTELIKE-GRLIFLKCKACGAS 123 (125)
T ss_dssp SCCHHHHHHHHHHCHHSSCTSTSSSSEEEEEE-TTCCEEEETTTSCE
T ss_pred CHHHHHHHHHHHHHHEEEcCCCCCCccEEEEc-CCEEEEEecccCCc
Confidence 3445555555555666 699999864 3333 4444 79999864
No 138
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=54.46 E-value=9.3 Score=29.07 Aligned_cols=30 Identities=13% Similarity=0.091 Sum_probs=23.1
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEeccc
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGA 110 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~AGGA 110 (134)
.||.|+..-+- +.-.+|-|..|+.-|+-.+
T Consensus 4 ~CP~C~seytY-~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYTY-HDGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcceE-ecCCeeECccccccccccc
Confidence 59999988766 3446899999988776554
No 139
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=54.16 E-value=11 Score=34.53 Aligned_cols=39 Identities=23% Similarity=0.405 Sum_probs=22.5
Q ss_pred chhhHhHHHHHHhhhccc--------ccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 62 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 62 aslRK~vkkIE~sqhakY--------~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
..+++.|+++.....-.| .|+.||.... +-|.|.+||..
T Consensus 467 ~al~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~~-----~~~~CP~CGs~ 513 (546)
T PF13597_consen 467 EALEKLVRYAMENTGIPYFTINPPIDICPDCGYIGG-----EGDKCPKCGSE 513 (546)
T ss_dssp HHHHHHHHHHHH--H-SEEEEE--EEEETTT---S-------EEE-CCC---
T ss_pred HHHHHHHHHHHHhCCCCeEEEecCcccccCCCcCCC-----CCCCCCCCCCc
Confidence 678888888888666676 5999997543 37999999987
No 140
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=53.63 E-value=16 Score=29.27 Aligned_cols=48 Identities=17% Similarity=0.374 Sum_probs=29.7
Q ss_pred hhHhHHHHHHhhhccc-ccCCCCcee--eEEeeeeee--eeCCCCeeEeccccc
Q 045338 64 LRKQIKKMEVSQHSKY-FCEFCGKYA--VKRKAVGIW--GCKDCGKVKAGGAYT 112 (134)
Q Consensus 64 lRK~vkkIE~sqhakY-~CpfCGk~~--VKR~avGIW--~CkkCgkt~AGGAy~ 112 (134)
-.+.+.++-..=-..| .||.|+.+. +.+. ..+| +|..||..-.=.+..
T Consensus 83 ~~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~-~~~~~l~C~aCGa~~~v~~~~ 135 (201)
T PRK12336 83 TEEDIQAAIDAYVDEYVICSECGLPDTRLVKE-DRVLMLRCDACGAHRPVKKRK 135 (201)
T ss_pred CHHHHHHHHHHHHHheEECCCCCCCCcEEEEc-CCeEEEEcccCCCCccccccc
Confidence 3455555555555667 699999864 3333 3454 799998654444433
No 141
>PRK05978 hypothetical protein; Provisional
Probab=53.32 E-value=5.7 Score=31.17 Aligned_cols=40 Identities=23% Similarity=0.301 Sum_probs=24.9
Q ss_pred HhhhcccccCCCCceeeEEe-eeeeeeeCCCCeeE------eccccc
Q 045338 73 VSQHSKYFCEFCGKYAVKRK-AVGIWGCKDCGKVK------AGGAYT 112 (134)
Q Consensus 73 ~sqhakY~CpfCGk~~VKR~-avGIW~CkkCgkt~------AGGAy~ 112 (134)
+..-.+-.||.||+-++=+. -.=-=+|..||..+ -|+||.
T Consensus 28 ~~rGl~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~~~~a~DgpAy~ 74 (148)
T PRK05978 28 MWRGFRGRCPACGEGKLFRAFLKPVDHCAACGEDFTHHRADDLPAYL 74 (148)
T ss_pred HHHHHcCcCCCCCCCcccccccccCCCccccCCccccCCccccCcch
Confidence 33556678999999876221 00002799999654 466764
No 142
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=53.30 E-value=9.2 Score=23.05 Aligned_cols=28 Identities=21% Similarity=0.368 Sum_probs=18.1
Q ss_pred cccCCCCcee-e----EEeeeeeeeeCCCCeeE
Q 045338 79 YFCEFCGKYA-V----KRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 79 Y~CpfCGk~~-V----KR~avGIW~CkkCgkt~ 106 (134)
-+||-|+..- + -+....-=+|.+|+.+|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 3699998753 1 11233345899999887
No 143
>PRK00420 hypothetical protein; Validated
Probab=53.13 E-value=10 Score=28.62 Aligned_cols=29 Identities=28% Similarity=0.364 Sum_probs=21.8
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCeeEe
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCgkt~A 107 (134)
...||.||-+-++ .-.|-=.|..||..+-
T Consensus 23 ~~~CP~Cg~pLf~-lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCGLPLFE-LKDGEVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCCCccee-cCCCceECCCCCCeee
Confidence 3689999987776 2456678999997554
No 144
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=53.08 E-value=13 Score=30.02 Aligned_cols=35 Identities=31% Similarity=0.423 Sum_probs=21.8
Q ss_pred ccCCCCceeeEE-eeee-----------eeeeCCCCee----Eeccccccc
Q 045338 80 FCEFCGKYAVKR-KAVG-----------IWGCKDCGKV----KAGGAYTLN 114 (134)
Q Consensus 80 ~CpfCGk~~VKR-~avG-----------IW~CkkCgkt----~AGGAy~p~ 114 (134)
.||.||+...-| .-+- -+.|.+||++ ..||+..|.
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~g~~~p~ 52 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSNDVKTLGAKEPK 52 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccceeEECCCCCCE
Confidence 599998653111 1222 4899999965 456666553
No 145
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=53.06 E-value=16 Score=31.40 Aligned_cols=37 Identities=24% Similarity=0.622 Sum_probs=17.7
Q ss_pred hcccccCCCCceeeEEe----eeeeeeeCCCC-------------eeEeccccc
Q 045338 76 HSKYFCEFCGKYAVKRK----AVGIWGCKDCG-------------KVKAGGAYT 112 (134)
Q Consensus 76 hakY~CpfCGk~~VKR~----avGIW~CkkCg-------------kt~AGGAy~ 112 (134)
.....||-||...+..- .|.=..|..|+ .++++|||.
T Consensus 29 ~~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKSk~~~l~~~I~dGAY~ 82 (254)
T PF06044_consen 29 AENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKSKKKKLSNKINDGAYH 82 (254)
T ss_dssp HHH---TTT--SS-EE--------EEE-TTT--EEEEEEEESS--SEEEEEEHH
T ss_pred HHCCcCCCCCChhHhhccCCCccceeECCCCchHHhhhhhccccCCcccCccHH
Confidence 44556888888754443 44567888886 467889984
No 146
>PRK04351 hypothetical protein; Provisional
Probab=53.00 E-value=10 Score=29.41 Aligned_cols=30 Identities=23% Similarity=0.523 Sum_probs=23.0
Q ss_pred cccccCCCCce--eeEEeeeeeeeeCCCCeeE
Q 045338 77 SKYFCEFCGKY--AVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 77 akY~CpfCGk~--~VKR~avGIW~CkkCgkt~ 106 (134)
-.|.|.-||.. ..+|...--..|+.|+-.+
T Consensus 111 y~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L 142 (149)
T PRK04351 111 YLYECQSCGQQYLRKRRINTKRYRCGKCRGKL 142 (149)
T ss_pred EEEECCCCCCEeeeeeecCCCcEEeCCCCcEe
Confidence 45789999974 4677777889999997543
No 147
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=52.60 E-value=6 Score=36.37 Aligned_cols=23 Identities=30% Similarity=0.832 Sum_probs=20.4
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
..|.|..||....|+.+ +|..||
T Consensus 6 t~f~C~~CG~~s~KW~G----kCp~Cg 28 (456)
T COG1066 6 TAFVCQECGYVSPKWLG----KCPACG 28 (456)
T ss_pred cEEEcccCCCCCccccc----cCCCCC
Confidence 56999999999999766 899996
No 148
>PRK04860 hypothetical protein; Provisional
Probab=51.56 E-value=5.1 Score=31.44 Aligned_cols=30 Identities=23% Similarity=0.763 Sum_probs=21.2
Q ss_pred cccccCCCCceee--EEee-----eeeeeeCCCCeeEe
Q 045338 77 SKYFCEFCGKYAV--KRKA-----VGIWGCKDCGKVKA 107 (134)
Q Consensus 77 akY~CpfCGk~~V--KR~a-----vGIW~CkkCgkt~A 107 (134)
-+|.|+ |++..+ +|.. .....|+.|+..+.
T Consensus 118 ~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 118 FPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 469999 987543 3333 45699999997763
No 149
>PRK07218 replication factor A; Provisional
Probab=51.40 E-value=6.5 Score=35.25 Aligned_cols=21 Identities=33% Similarity=0.632 Sum_probs=17.5
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
+.||.|++.--+ |.|+.||+.
T Consensus 298 ~rCP~C~r~v~~------~~C~~hG~v 318 (423)
T PRK07218 298 ERCPECGRVIQK------GQCRSHGAV 318 (423)
T ss_pred ecCcCccccccC------CcCCCCCCc
Confidence 579999987644 999999975
No 150
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=51.34 E-value=9 Score=30.13 Aligned_cols=23 Identities=22% Similarity=0.465 Sum_probs=16.1
Q ss_pred HHHHhhhcc-cccCCCCceeeEEe
Q 045338 70 KMEVSQHSK-YFCEFCGKYAVKRK 92 (134)
Q Consensus 70 kIE~sqhak-Y~CpfCGk~~VKR~ 92 (134)
..|.++... -+||.||.+.|.|.
T Consensus 23 ~fd~Q~~~glv~CP~Cgs~~V~K~ 46 (148)
T PF06676_consen 23 AFDRQQARGLVSCPVCGSTEVSKA 46 (148)
T ss_pred HHHHHHHcCCccCCCCCCCeEeee
Confidence 344444444 48999999998876
No 151
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=51.32 E-value=11 Score=31.13 Aligned_cols=11 Identities=36% Similarity=0.821 Sum_probs=6.2
Q ss_pred eeeeeeeCCCC
Q 045338 93 AVGIWGCKDCG 103 (134)
Q Consensus 93 avGIW~CkkCg 103 (134)
+.-+=.|.+|+
T Consensus 235 ~~rve~C~~C~ 245 (290)
T PF04216_consen 235 AYRVEVCESCG 245 (290)
T ss_dssp SEEEEEETTTT
T ss_pred cEEEEECCccc
Confidence 34555666665
No 152
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.83 E-value=16 Score=28.35 Aligned_cols=37 Identities=19% Similarity=0.474 Sum_probs=24.7
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCeeEecc----ccccccchH
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGG----AYTLNTASA 118 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCgkt~AGG----Ay~p~T~~~ 118 (134)
.-.||.||+.-+- ---+|+.|+-|+-|- -+.+-|+-.
T Consensus 6 ~~~cPvcg~~~iV----TeL~c~~~etTVrg~F~~s~F~~Lt~d~ 46 (122)
T COG3877 6 INRCPVCGRKLIV----TELKCSNCETTVRGNFKMSKFEYLTSDQ 46 (122)
T ss_pred CCCCCccccccee----EEEecCCCCceEecceecccccccCHhH
Confidence 3469999987532 125999999999883 344445443
No 153
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=50.33 E-value=11 Score=35.11 Aligned_cols=36 Identities=22% Similarity=0.502 Sum_probs=26.4
Q ss_pred chhhHhHHHHHHhhhccc--------ccCCCCceeeEEeeee-e-eeeCCCCe
Q 045338 62 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVG-I-WGCKDCGK 104 (134)
Q Consensus 62 aslRK~vkkIE~sqhakY--------~CpfCGk~~VKR~avG-I-W~CkkCgk 104 (134)
..+++.|+.+... +-.| .|+.||.. .| + |.|..||.
T Consensus 509 ea~~~lv~~~~~~-~i~Y~tin~~~siC~~CGy~------~g~~~~~CP~CGs 554 (586)
T TIGR02827 509 DGYRKLLRVAADT-GCNYFCFNIKITICNDCHHI------DKRTLHRCPVCGS 554 (586)
T ss_pred HHHHHHHHHHHhc-CCceEEeCCCCeecCCCCCc------CCCcCCcCcCCCC
Confidence 5788888888654 5666 59999972 23 3 99999983
No 154
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=49.74 E-value=11 Score=29.07 Aligned_cols=30 Identities=23% Similarity=0.486 Sum_probs=22.9
Q ss_pred ccccCCCCceeeE------Ee----eeeeeeeCCCCeeEe
Q 045338 78 KYFCEFCGKYAVK------RK----AVGIWGCKDCGKVKA 107 (134)
Q Consensus 78 kY~CpfCGk~~VK------R~----avGIW~CkkCgkt~A 107 (134)
++.||-||.+.|- |- .+=-+.|.+|++++.
T Consensus 74 ~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 74 KHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred hccCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 6889999988632 22 345789999999875
No 155
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=49.74 E-value=5.8 Score=30.39 Aligned_cols=24 Identities=29% Similarity=0.678 Sum_probs=18.9
Q ss_pred ccccCCCCcee--eEEeeeeeeeeCCCCee
Q 045338 78 KYFCEFCGKYA--VKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 78 kY~CpfCGk~~--VKR~avGIW~CkkCgkt 105 (134)
...||.|||.. ..|+. .|-.|+..
T Consensus 69 ~V~CP~C~K~TKmLGr~D----~CM~C~~p 94 (114)
T PF11023_consen 69 QVECPNCGKQTKMLGRVD----ACMHCKEP 94 (114)
T ss_pred eeECCCCCChHhhhchhh----ccCcCCCc
Confidence 34699999986 88885 79899854
No 156
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=49.52 E-value=3 Score=38.48 Aligned_cols=21 Identities=38% Similarity=0.749 Sum_probs=18.2
Q ss_pred eeeeeeeCCCCeeEecccccc
Q 045338 93 AVGIWGCKDCGKVKAGGAYTL 113 (134)
Q Consensus 93 avGIW~CkkCgkt~AGGAy~p 113 (134)
..||..|..|+++|---||.=
T Consensus 353 s~gi~~C~~C~KkFrRqAYLr 373 (500)
T KOG3993|consen 353 SSGIFSCHTCGKKFRRQAYLR 373 (500)
T ss_pred cCceeecHHhhhhhHHHHHHH
Confidence 458999999999999888863
No 157
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=49.34 E-value=7.3 Score=29.27 Aligned_cols=24 Identities=33% Similarity=0.879 Sum_probs=17.3
Q ss_pred ccCCCCcee-eEEeeeee-eeeCCCC
Q 045338 80 FCEFCGKYA-VKRKAVGI-WGCKDCG 103 (134)
Q Consensus 80 ~CpfCGk~~-VKR~avGI-W~CkkCg 103 (134)
.|=|||+.+ +......= |.|..|+
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w~C~~C~ 27 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNWTCPHCE 27 (131)
T ss_pred eeccCCCCCCCCCCCCCCeeECCCCC
Confidence 588999765 55444444 9999996
No 158
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=49.08 E-value=10 Score=25.29 Aligned_cols=12 Identities=42% Similarity=0.838 Sum_probs=9.7
Q ss_pred c-ccCCCCceeeE
Q 045338 79 Y-FCEFCGKYAVK 90 (134)
Q Consensus 79 Y-~CpfCGk~~VK 90 (134)
| .||.||.+.|-
T Consensus 13 Y~~Cp~CGN~~vG 25 (49)
T PF12677_consen 13 YCKCPKCGNDKVG 25 (49)
T ss_pred hccCcccCCcEee
Confidence 5 69999998754
No 159
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=48.86 E-value=8.3 Score=28.34 Aligned_cols=27 Identities=22% Similarity=0.678 Sum_probs=17.0
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 76 HSKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 76 hakY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.....|+-||..--. ....+|.|+.||
T Consensus 68 p~~~~C~~Cg~~~~~-~~~~~~~CP~Cg 94 (114)
T PRK03681 68 EAECWCETCQQYVTL-LTQRVRRCPQCH 94 (114)
T ss_pred CcEEEcccCCCeeec-CCccCCcCcCcC
Confidence 455678888864322 233457788887
No 160
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=48.80 E-value=13 Score=19.52 Aligned_cols=12 Identities=25% Similarity=0.559 Sum_probs=9.9
Q ss_pred eeeCCCCeeEec
Q 045338 97 WGCKDCGKVKAG 108 (134)
Q Consensus 97 W~CkkCgkt~AG 108 (134)
|.|.-|+.+|..
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 789999988864
No 161
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=48.11 E-value=13 Score=34.89 Aligned_cols=40 Identities=23% Similarity=0.358 Sum_probs=29.4
Q ss_pred CchhhHhHHHHHHhhhccc--------ccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 61 GASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 61 GaslRK~vkkIE~sqhakY--------~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
...+++.|+++-...+-.| .|+.||... .. .|.|..||..
T Consensus 601 ~~a~~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~-g~----~~~CP~CG~~ 648 (656)
T PRK08270 601 AEACKKLVKKALENYRLPYITITPTFSICPKHGYLS-GE----HEFCPKCGEE 648 (656)
T ss_pred HHHHHHHHHHHHHhCCCceEEeCCCCcccCCCCCcC-CC----CCCCcCCcCc
Confidence 3788999998866545555 599999742 21 4999999864
No 162
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=47.84 E-value=21 Score=36.50 Aligned_cols=42 Identities=17% Similarity=0.445 Sum_probs=28.2
Q ss_pred hhhHhHHHHHHhhhcccccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 63 SLRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 63 slRK~vkkIE~sqhakY~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
....+..+-......--.||.||...|.|.+ +-|+|..||-|
T Consensus 1175 ~~~~~~~~a~~~g~~g~~c~~cg~~~~vrng-tc~~c~~cg~t 1216 (1220)
T PRK07562 1175 VEAERRAEAKMQGYTGEACSECGNFTLVRNG-TCLKCDTCGST 1216 (1220)
T ss_pred hhhhhhhHHHhCCCCCCcCCCcCCeEEEeCC-eeeeccccCCC
Confidence 3334433333333444469999999999876 56899999865
No 163
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=47.74 E-value=8.7 Score=30.35 Aligned_cols=54 Identities=19% Similarity=0.355 Sum_probs=33.0
Q ss_pred hhcccccCCCCcee-eEEeeeeeeeeCCCCeeEeccccccccchHHHHHHHHHHHHhh
Q 045338 75 QHSKYFCEFCGKYA-VKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRRLREQ 131 (134)
Q Consensus 75 qhakY~CpfCGk~~-VKR~avGIW~CkkCgkt~AGGAy~p~T~~~~tvk~~Irrl~e~ 131 (134)
.+.-|.||.|+..- .-=.-..-..|..||...- +.=++......+.-|..|.+.
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~---~~dn~~~~~~l~~~I~~l~~~ 168 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLE---EYDNSELIKELKEQIKELEEE 168 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCe---ecccHHHHHHHHHHHHHHHHH
Confidence 34578999999642 0000113589999986543 234566666666667777654
No 164
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.71 E-value=9.6 Score=28.79 Aligned_cols=14 Identities=21% Similarity=0.468 Sum_probs=10.1
Q ss_pred hhcccccCCCCcee
Q 045338 75 QHSKYFCEFCGKYA 88 (134)
Q Consensus 75 qhakY~CpfCGk~~ 88 (134)
....+.|+.||..-
T Consensus 67 ~p~~~~C~~CG~~~ 80 (135)
T PRK03824 67 EEAVLKCRNCGNEW 80 (135)
T ss_pred cceEEECCCCCCEE
Confidence 34678899999653
No 165
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=46.58 E-value=13 Score=23.54 Aligned_cols=11 Identities=36% Similarity=0.914 Sum_probs=5.1
Q ss_pred cccccCCCCce
Q 045338 77 SKYFCEFCGKY 87 (134)
Q Consensus 77 akY~CpfCGk~ 87 (134)
++-.||.||++
T Consensus 19 ~~~~CPlC~r~ 29 (54)
T PF04423_consen 19 AKGCCPLCGRP 29 (54)
T ss_dssp -SEE-TTT--E
T ss_pred CCCcCCCCCCC
Confidence 33389999976
No 166
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=46.45 E-value=19 Score=28.83 Aligned_cols=35 Identities=29% Similarity=0.705 Sum_probs=24.3
Q ss_pred hhHhHHHHHHhhhcccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 64 LRKQIKKMEVSQHSKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 64 lRK~vkkIE~sqhakY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
++++++++ +.....|.|+.||-..-... |.|.+|+
T Consensus 341 ~~~~~~~~-~~~~p~~~c~~cg~~~~~~~----~~c~~c~ 375 (389)
T PRK11788 341 LRDLVGEQ-LKRKPRYRCRNCGFTARTLY----WHCPSCK 375 (389)
T ss_pred HHHHHHHH-HhCCCCEECCCCCCCCccce----eECcCCC
Confidence 34444433 45566689999998876543 7999996
No 167
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=46.41 E-value=15 Score=34.57 Aligned_cols=38 Identities=26% Similarity=0.492 Sum_probs=27.3
Q ss_pred chhhHhHHHHHHhhhccc--------ccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 62 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 62 aslRK~vkkIE~sqhakY--------~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
..+++.|+.+.. ..-.| .|+.||... ++. .|.|..||.
T Consensus 543 eal~~lv~~~~~-~~i~Yf~in~~~~iC~~CG~~~-~g~---~~~CP~CGs 588 (623)
T PRK08271 543 EGYRKLLNIAAK-TGCNYFAFNVKITICNDCHHID-KRT---GKRCPICGS 588 (623)
T ss_pred HHHHHHHHHHHH-cCCceEEeCCCCccCCCCCCcC-CCC---CcCCcCCCC
Confidence 678888888855 44556 599999752 111 499999985
No 168
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=46.36 E-value=4.2 Score=35.22 Aligned_cols=38 Identities=32% Similarity=0.566 Sum_probs=27.3
Q ss_pred hhcccccCCCCceeeEEe----------eeeeeeeCCCCeeEeccccc
Q 045338 75 QHSKYFCEFCGKYAVKRK----------AVGIWGCKDCGKVKAGGAYT 112 (134)
Q Consensus 75 qhakY~CpfCGk~~VKR~----------avGIW~CkkCgkt~AGGAy~ 112 (134)
..++|.||-|+|---.|- .+==.+|..|+|+||==.|.
T Consensus 212 GEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~SyL 259 (279)
T KOG2462|consen 212 GEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSYL 259 (279)
T ss_pred CCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHHH
Confidence 457999999998643332 34458999999999855443
No 169
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=46.31 E-value=16 Score=30.44 Aligned_cols=27 Identities=22% Similarity=0.447 Sum_probs=19.0
Q ss_pred cccccCCCCceeeEEe--eeeeeeeCCCC
Q 045338 77 SKYFCEFCGKYAVKRK--AVGIWGCKDCG 103 (134)
Q Consensus 77 akY~CpfCGk~~VKR~--avGIW~CkkCg 103 (134)
..-.||.||.+-.+.. +-+.|.|..|-
T Consensus 253 ~g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 253 TGKPCRKCGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CcCCCCcCCCeeEEEEECCCccEECCCCc
Confidence 3457999997654332 34689999994
No 170
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=46.11 E-value=16 Score=37.55 Aligned_cols=31 Identities=23% Similarity=0.559 Sum_probs=16.9
Q ss_pred cccCCCCceeeEEe-------eeeeeeeCCCCeeEecc
Q 045338 79 YFCEFCGKYAVKRK-------AVGIWGCKDCGKVKAGG 109 (134)
Q Consensus 79 Y~CpfCGk~~VKR~-------avGIW~CkkCgkt~AGG 109 (134)
..||.||.....-. ..-.++|.+||..+...
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~d 705 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPPD 705 (1337)
T ss_pred EECCCCCCccccccCcccCCcCCCceeCccCCCccCCC
Confidence 67888776532210 11256777777765443
No 171
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=45.84 E-value=15 Score=26.75 Aligned_cols=68 Identities=18% Similarity=0.334 Sum_probs=40.0
Q ss_pred hHhhhhhhccceeeeec-cCCccccCchhhHhHHHHHHhh---------------------hcccccCCCCceeeEE--e
Q 045338 37 LVCFCKMTKRTKKAGIV-GKYGTRYGASLRKQIKKMEVSQ---------------------HSKYFCEFCGKYAVKR--K 92 (134)
Q Consensus 37 ~~~~~~MakrTKKVgi~-GkfGtRYGaslRK~vkkIE~sq---------------------hakY~CpfCGk~~VKR--~ 92 (134)
.+.+++|+=- -+-+. ++-..-.|...++...+|...- .-.|.|+-||....++ .
T Consensus 62 ~tL~HEm~H~--~~~~~~~~~~~~Hg~~fk~~~~~ig~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~r~~~~ 139 (157)
T PF10263_consen 62 DTLLHEMAHA--AAYVFGGGRRRGHGKEFKQWARRIGASPPRGRPNPTTCHSYEIEGKEYKKYVYRCPSCGREYKRHRRS 139 (157)
T ss_pred HHHHHHHHHH--HhhhccCCCCCCCCHHHHHHHHHHCCcccccccccccccccccccccccceEEEcCCCCCEeeeeccc
Confidence 3566676531 12122 4555566788888888877732 2356788898664222 2
Q ss_pred eeeeeeeCCCCeeE
Q 045338 93 AVGIWGCKDCGKVK 106 (134)
Q Consensus 93 avGIW~CkkCgkt~ 106 (134)
...=+.|+.|+-.+
T Consensus 140 ~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 140 KRKRYRCGRCGGPL 153 (157)
T ss_pred chhhEECCCCCCEE
Confidence 33457888887544
No 172
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.83 E-value=7.4 Score=34.88 Aligned_cols=28 Identities=36% Similarity=0.768 Sum_probs=21.9
Q ss_pred hcccccCCCCcee----eEEeeeeeeeeCCCC
Q 045338 76 HSKYFCEFCGKYA----VKRKAVGIWGCKDCG 103 (134)
Q Consensus 76 hakY~CpfCGk~~----VKR~avGIW~CkkCg 103 (134)
-..|.||.||+.. -.|.+-|-|-|--|+
T Consensus 30 ~~~~~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 30 PGGHPCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred CCCCCCCccCCccccccCCccCCccEEEEeec
Confidence 3445899999764 346689999999998
No 173
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=45.82 E-value=8.2 Score=22.70 Aligned_cols=12 Identities=42% Similarity=0.874 Sum_probs=6.8
Q ss_pred hcccccCCCCce
Q 045338 76 HSKYFCEFCGKY 87 (134)
Q Consensus 76 hakY~CpfCGk~ 87 (134)
.++|+||.|+..
T Consensus 11 ~~kY~Cp~C~~~ 22 (30)
T PF04438_consen 11 PAKYRCPRCGAR 22 (30)
T ss_dssp EESEE-TTT--E
T ss_pred CCEEECCCcCCc
Confidence 568888888764
No 174
>PRK12495 hypothetical protein; Provisional
Probab=45.50 E-value=11 Score=31.91 Aligned_cols=30 Identities=20% Similarity=0.444 Sum_probs=24.7
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCeeEec
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAG 108 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCgkt~AG 108 (134)
..+.|+.||.+..+ . -|.=.|-.|...++.
T Consensus 41 sa~hC~~CG~PIpa-~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 41 TNAHCDECGDPIFR-H-DGQEFCPTCQQPVTE 70 (226)
T ss_pred chhhcccccCcccC-C-CCeeECCCCCCcccc
Confidence 34689999999983 3 788899999988765
No 175
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=44.88 E-value=26 Score=24.73 Aligned_cols=28 Identities=32% Similarity=0.519 Sum_probs=20.8
Q ss_pred ccCCCCcee-eEEeeeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYA-VKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~-VKR~avGIW~CkkCgkt~A 107 (134)
.||-||... |==.+.-.=.|-.||.++|
T Consensus 21 kCpdC~N~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 21 KCPDCGNEQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred ECCCCCCEEEEeccCceEEEecccccEEE
Confidence 799999876 3333444559999999886
No 176
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=44.83 E-value=29 Score=25.72 Aligned_cols=39 Identities=21% Similarity=0.610 Sum_probs=25.3
Q ss_pred hHhHHHHHHhhhccc-ccCCCCcee--eEEeeeeee--eeCCCCe
Q 045338 65 RKQIKKMEVSQHSKY-FCEFCGKYA--VKRKAVGIW--GCKDCGK 104 (134)
Q Consensus 65 RK~vkkIE~sqhakY-~CpfCGk~~--VKR~avGIW--~CkkCgk 104 (134)
.+.+.++-..=-..| .||.|+.+. +.+. .++| +|..||.
T Consensus 66 ~~~i~~~l~~yI~~yVlC~~C~spdT~l~k~-~r~~~l~C~aCGa 109 (110)
T smart00653 66 PKKLQDLLRRYIKEYVLCPECGSPDTELIKE-NRLFFLKCEACGA 109 (110)
T ss_pred HHHHHHHHHHHHHhcEECCCCCCCCcEEEEe-CCeEEEEccccCC
Confidence 455555555555666 699999874 4443 4555 6998985
No 177
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=44.07 E-value=10 Score=38.10 Aligned_cols=47 Identities=23% Similarity=0.382 Sum_probs=32.0
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCeeEecccc--ccccchHHHHHHHHHHHHh
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAY--TLNTASAVTVRSTIRRLRE 130 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy--~p~T~~~~tvk~~Irrl~e 130 (134)
..+.||.||....+ +.|..||... --.| ...-+......+|+.+|.+
T Consensus 624 ~~RKCPkCG~yTlk------~rCP~CG~~T-e~~~pc~~~i~l~~~~~~A~~~lg~ 672 (1095)
T TIGR00354 624 AIRKCPQCGKESFW------LKCPVCGELT-EQLYYGKRKVDLRELYEEAIANLGE 672 (1095)
T ss_pred EEEECCCCCccccc------ccCCCCCCcc-ccccceeEEecHHHHHHHHHHHhCC
Confidence 34689999999998 8999998652 1111 2345566677777777644
No 178
>PRK06386 replication factor A; Reviewed
Probab=43.75 E-value=10 Score=33.48 Aligned_cols=20 Identities=30% Similarity=0.476 Sum_probs=16.9
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
+.||.|++.--+ |.|+.||+
T Consensus 237 ~rCP~C~R~l~~------g~C~~HG~ 256 (358)
T PRK06386 237 TKCSVCNKIIED------GVCKDHPD 256 (358)
T ss_pred ecCcCCCeEccC------CcCCCCCC
Confidence 579999987665 89999997
No 179
>smart00355 ZnF_C2H2 zinc finger.
Probab=43.67 E-value=11 Score=18.67 Aligned_cols=8 Identities=63% Similarity=1.456 Sum_probs=3.5
Q ss_pred eCCCCeeE
Q 045338 99 CKDCGKVK 106 (134)
Q Consensus 99 CkkCgkt~ 106 (134)
|..|++.|
T Consensus 3 C~~C~~~f 10 (26)
T smart00355 3 CPECGKVF 10 (26)
T ss_pred CCCCcchh
Confidence 44444443
No 180
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=43.41 E-value=18 Score=22.47 Aligned_cols=25 Identities=28% Similarity=0.667 Sum_probs=16.6
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 76 HSKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 76 hakY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
|..+.|..|+...+... -|+|..|.
T Consensus 2 h~~~~C~~C~~~~i~g~---Ry~C~~C~ 26 (46)
T PF00569_consen 2 HHGYTCDGCGTDPIIGV---RYHCLVCP 26 (46)
T ss_dssp CSSCE-SSS-SSSEESS---EEEESSSS
T ss_pred CCCeECcCCCCCcCcCC---eEECCCCC
Confidence 67789999998543322 39999995
No 181
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=43.35 E-value=13 Score=22.26 Aligned_cols=14 Identities=36% Similarity=0.688 Sum_probs=10.6
Q ss_pred ccccCCCCceeeEE
Q 045338 78 KYFCEFCGKYAVKR 91 (134)
Q Consensus 78 kY~CpfCGk~~VKR 91 (134)
+..||.||...+.+
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (47)
T PF14690_consen 2 PPRCPHCGSPSVHR 15 (47)
T ss_pred CccCCCcCCCceEC
Confidence 56799999877554
No 182
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=43.32 E-value=11 Score=26.65 Aligned_cols=29 Identities=24% Similarity=0.501 Sum_probs=13.6
Q ss_pred CCccccCchhhHhHHHHHHhhhcccccCCCCc
Q 045338 55 KYGTRYGASLRKQIKKMEVSQHSKYFCEFCGK 86 (134)
Q Consensus 55 kfGtRYGaslRK~vkkIE~sqhakY~CpfCGk 86 (134)
+.+.+||.+....- ++. ..+...||.||+
T Consensus 2 ~~~~~Ygit~~~~~-~l~--~~q~~~C~iC~~ 30 (81)
T PF02945_consen 2 RLKRRYGITPEEYE-ALL--EEQGGRCAICGK 30 (81)
T ss_dssp -----H-HHHHHHH-CCH--HHTTTE-TTT-S
T ss_pred CcccccCCCHHHHH-HHH--HHhCCcCcCCCC
Confidence 35678998887665 332 233448999998
No 183
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=42.34 E-value=8.3 Score=38.08 Aligned_cols=33 Identities=24% Similarity=0.548 Sum_probs=0.0
Q ss_pred cccccCCCCceeeEEee-------eeeeeeCCCCeeEecc
Q 045338 77 SKYFCEFCGKYAVKRKA-------VGIWGCKDCGKVKAGG 109 (134)
Q Consensus 77 akY~CpfCGk~~VKR~a-------vGIW~CkkCgkt~AGG 109 (134)
..+.||.||+....... .=+|.|..|+..+..+
T Consensus 654 ~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~ 693 (900)
T PF03833_consen 654 GRRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVEED 693 (900)
T ss_dssp ----------------------------------------
T ss_pred ecccCcccCCcchhhcCcccCCccccceeccccccccCcc
Confidence 34568888888766542 2467888888776544
No 184
>PRK06450 threonine synthase; Validated
Probab=42.14 E-value=10 Score=32.22 Aligned_cols=25 Identities=36% Similarity=0.640 Sum_probs=17.7
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
++.|+.||++-- ..-.|.|..||-.
T Consensus 3 ~~~C~~Cg~~~~---~~~~~~C~~cg~~ 27 (338)
T PRK06450 3 KEVCMKCGKERE---SIYEIRCKKCGGP 27 (338)
T ss_pred eeEECCcCCcCC---CcccccCCcCCCE
Confidence 478999998852 2335899999743
No 185
>PRK07220 DNA topoisomerase I; Validated
Probab=41.59 E-value=23 Score=33.56 Aligned_cols=27 Identities=26% Similarity=0.484 Sum_probs=18.8
Q ss_pred ccccCCCCceeeEEeeee----eeeeCCCCe
Q 045338 78 KYFCEFCGKYAVKRKAVG----IWGCKDCGK 104 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avG----IW~CkkCgk 104 (134)
...||.||...++...-| .|.|..|.+
T Consensus 635 ~~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~ 665 (740)
T PRK07220 635 DKVCEAHGLNHIRIINGGKRPWDLGCPQCNF 665 (740)
T ss_pred CCCCCCCCCceEEEEecCCccceeeCCCCCC
Confidence 467999997544433333 689999986
No 186
>PRK10220 hypothetical protein; Provisional
Probab=41.49 E-value=18 Score=27.60 Aligned_cols=30 Identities=17% Similarity=0.458 Sum_probs=22.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEeccc
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGA 110 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~AGGA 110 (134)
.||.|+..-+- ..-.+|-|..|+.-|.-++
T Consensus 5 ~CP~C~seytY-~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYTY-EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcceE-cCCCeEECCcccCcCCccc
Confidence 59999987665 3556899999977665443
No 187
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=41.40 E-value=30 Score=22.03 Aligned_cols=46 Identities=20% Similarity=0.389 Sum_probs=20.5
Q ss_pred hhhhhccceeeeeccCCccccC---chhhHhH-HHHHHhhhcccccCCCCc
Q 045338 40 FCKMTKRTKKAGIVGKYGTRYG---ASLRKQI-KKMEVSQHSKYFCEFCGK 86 (134)
Q Consensus 40 ~~~MakrTKKVgi~GkfGtRYG---aslRK~v-kkIE~sqhakY~CpfCGk 86 (134)
..++.++.+.++++.=-+-.=+ ..|..+. .+| .....-..||.||+
T Consensus 5 Y~rl~~~~~g~~va~v~~~~C~gC~~~l~~~~~~~i-~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 5 YERLRKRKGGVAVARVEGGTCSGCHMELPPQELNEI-RKGDEIVFCPNCGR 54 (56)
T ss_pred HHHHHhhcCCcEEEEeeCCccCCCCEEcCHHHHHHH-HcCCCeEECcCCCc
Confidence 3344444445555543332222 2333332 222 22245567777775
No 188
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=40.76 E-value=24 Score=29.12 Aligned_cols=27 Identities=30% Similarity=0.476 Sum_probs=18.7
Q ss_pred ccccCCCCceeeEEe--eeeeeeeCCCCe
Q 045338 78 KYFCEFCGKYAVKRK--AVGIWGCKDCGK 104 (134)
Q Consensus 78 kY~CpfCGk~~VKR~--avGIW~CkkCgk 104 (134)
.-.||.||.+-.+-. +-+.|-|..|-+
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRRCGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCeeEEEEECCCCcEECcCCCC
Confidence 346999997743322 336899999954
No 189
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=40.66 E-value=24 Score=27.65 Aligned_cols=35 Identities=29% Similarity=0.573 Sum_probs=21.7
Q ss_pred ccCCCCceee---EEe--------eeeeeeeCCCCee----Eeccccccc
Q 045338 80 FCEFCGKYAV---KRK--------AVGIWGCKDCGKV----KAGGAYTLN 114 (134)
Q Consensus 80 ~CpfCGk~~V---KR~--------avGIW~CkkCgkt----~AGGAy~p~ 114 (134)
.||.||.... .-. =.=-..|.+||++ ..||+..|.
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~p~ 51 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNNEVKSGGAIEPK 51 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccceEEECcccCCC
Confidence 4999986542 211 2224799999965 456665554
No 190
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.62 E-value=27 Score=25.78 Aligned_cols=27 Identities=33% Similarity=0.574 Sum_probs=21.6
Q ss_pred ccCCCCcee--eEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYA--VKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~--VKR~avGIW~CkkCgkt~ 106 (134)
.||.||-.- +.|.++-|=.|..|.=++
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCccccEe
Confidence 599999875 567788899999996444
No 191
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=40.30 E-value=27 Score=23.15 Aligned_cols=29 Identities=21% Similarity=0.531 Sum_probs=18.8
Q ss_pred ccccCCCCcee-eEEee-eeeeeeCCCCeeE
Q 045338 78 KYFCEFCGKYA-VKRKA-VGIWGCKDCGKVK 106 (134)
Q Consensus 78 kY~CpfCGk~~-VKR~a-vGIW~CkkCgkt~ 106 (134)
.++||.||... +.-.. --|=.|..||..+
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 46899999864 22111 2366999998543
No 192
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.39 E-value=24 Score=29.47 Aligned_cols=33 Identities=24% Similarity=0.421 Sum_probs=23.3
Q ss_pred ccCCCCcee------eEEe-------ee-eeeeeCCCCeeEeccccc
Q 045338 80 FCEFCGKYA------VKRK-------AV-GIWGCKDCGKVKAGGAYT 112 (134)
Q Consensus 80 ~CpfCGk~~------VKR~-------av-GIW~CkkCgkt~AGGAy~ 112 (134)
.|+.||+.. .-|+ .| =|++|..|++++-=+-|+
T Consensus 19 ~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~tWN~~Ife 65 (203)
T COG4332 19 RCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYTWNISIFE 65 (203)
T ss_pred hCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCCccchhhhh
Confidence 599999764 2222 22 588999999998776665
No 193
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=39.30 E-value=22 Score=23.82 Aligned_cols=16 Identities=19% Similarity=0.428 Sum_probs=12.4
Q ss_pred eeeeeeeeCCCCeeEe
Q 045338 92 KAVGIWGCKDCGKVKA 107 (134)
Q Consensus 92 ~avGIW~CkkCgkt~A 107 (134)
...|+|+|......+.
T Consensus 7 ~~~g~w~~~pg~~~~~ 22 (74)
T PF05899_consen 7 FSAGVWECTPGKFPWP 22 (74)
T ss_dssp EEEEEEEEECEEEEEE
T ss_pred EEEEEEEECCceeEee
Confidence 4789999999765554
No 194
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=39.15 E-value=12 Score=25.16 Aligned_cols=12 Identities=42% Similarity=1.088 Sum_probs=4.4
Q ss_pred cccccCCCCcee
Q 045338 77 SKYFCEFCGKYA 88 (134)
Q Consensus 77 akY~CpfCGk~~ 88 (134)
.+|+||.||.+.
T Consensus 32 r~y~Cp~CgAtG 43 (55)
T PF05741_consen 32 RKYVCPICGATG 43 (55)
T ss_dssp GG---TTT---G
T ss_pred hcCcCCCCcCcC
Confidence 468999999763
No 195
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=39.06 E-value=17 Score=30.30 Aligned_cols=33 Identities=24% Similarity=0.547 Sum_probs=22.6
Q ss_pred hhcccccCCCCceee----EEeee--eeeeeCCCCeeEe
Q 045338 75 QHSKYFCEFCGKYAV----KRKAV--GIWGCKDCGKVKA 107 (134)
Q Consensus 75 qhakY~CpfCGk~~V----KR~av--GIW~CkkCgkt~A 107 (134)
++--+.||.||...+ -+... =.-+|..||..+.
T Consensus 3 ~~iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~ 41 (201)
T COG1326 3 EEIYIECPSCGSEEVSHEVIKERGREPLVRCEECGTVHP 41 (201)
T ss_pred ceEEEECCCCCcchhhHHHHHhcCCceEEEccCCCcEee
Confidence 455678999995544 22222 3689999998873
No 196
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=38.84 E-value=25 Score=29.11 Aligned_cols=27 Identities=26% Similarity=0.407 Sum_probs=19.0
Q ss_pred ccccCCCCceeeEEe--eeeeeeeCCCCe
Q 045338 78 KYFCEFCGKYAVKRK--AVGIWGCKDCGK 104 (134)
Q Consensus 78 kY~CpfCGk~~VKR~--avGIW~CkkCgk 104 (134)
.-.||.||.+-.+.. +-+.|-|..|-.
T Consensus 235 g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPIEKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred cCCCCcCCCeeEEEEECCCCcEECCCCcC
Confidence 447999997653322 346999999954
No 197
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=37.88 E-value=19 Score=22.84 Aligned_cols=11 Identities=36% Similarity=1.132 Sum_probs=9.0
Q ss_pred eeeCCCCeeEe
Q 045338 97 WGCKDCGKVKA 107 (134)
Q Consensus 97 W~CkkCgkt~A 107 (134)
|.|..||..+-
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 99999987664
No 198
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.64 E-value=26 Score=28.99 Aligned_cols=25 Identities=32% Similarity=0.525 Sum_probs=17.6
Q ss_pred ccccCCCCceeeEEe--eeeeeeeCCC
Q 045338 78 KYFCEFCGKYAVKRK--AVGIWGCKDC 102 (134)
Q Consensus 78 kY~CpfCGk~~VKR~--avGIW~CkkC 102 (134)
.-.||.||.+-.+-. +-+.|-|..|
T Consensus 245 g~pC~~Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEEEECCCCCEECCCC
Confidence 347999997743322 3468999998
No 199
>PRK10445 endonuclease VIII; Provisional
Probab=37.36 E-value=29 Score=28.64 Aligned_cols=29 Identities=24% Similarity=0.517 Sum_probs=19.9
Q ss_pred hhcccccCCCCceeeEEe--eeeeeeeCCCC
Q 045338 75 QHSKYFCEFCGKYAVKRK--AVGIWGCKDCG 103 (134)
Q Consensus 75 qhakY~CpfCGk~~VKR~--avGIW~CkkCg 103 (134)
.+..-.||.||..-.+-. +-+.|-|..|-
T Consensus 232 ~r~g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 232 HRDGEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 344567999997643322 45789999994
No 200
>PRK05638 threonine synthase; Validated
Probab=37.32 E-value=15 Score=32.02 Aligned_cols=23 Identities=30% Similarity=0.417 Sum_probs=16.0
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
|+.|+.||+.-- .. -.|.| .|+-
T Consensus 1 ~l~C~~Cg~~~~--~~-~~~~C-~c~~ 23 (442)
T PRK05638 1 KMKCPKCGREYN--SY-IPPFC-ICGE 23 (442)
T ss_pred CeEeCCCCCCCC--CC-Cceec-CCCC
Confidence 578999998753 12 33999 8973
No 201
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=37.27 E-value=3.9 Score=35.00 Aligned_cols=34 Identities=32% Similarity=0.750 Sum_probs=24.5
Q ss_pred hhcccccCCCCce-----eeEE---eeeee--eeeCCCCeeEec
Q 045338 75 QHSKYFCEFCGKY-----AVKR---KAVGI--WGCKDCGKVKAG 108 (134)
Q Consensus 75 qhakY~CpfCGk~-----~VKR---~avGI--W~CkkCgkt~AG 108 (134)
.-..|.|.||||- ++|| .-+|| ++|.-|++.|+-
T Consensus 142 ~vkr~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftq 185 (267)
T KOG3576|consen 142 DVKRHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQ 185 (267)
T ss_pred HHHHHHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHh
Confidence 3456889999984 2555 34555 899999987753
No 202
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=37.23 E-value=18 Score=28.31 Aligned_cols=26 Identities=15% Similarity=0.440 Sum_probs=20.2
Q ss_pred ccccCCCCcee--------eEEeeeeeeeeC-CCC
Q 045338 78 KYFCEFCGKYA--------VKRKAVGIWGCK-DCG 103 (134)
Q Consensus 78 kY~CpfCGk~~--------VKR~avGIW~Ck-kCg 103 (134)
...|.|||... |++.+.-+|-|. ||.
T Consensus 4 ~e~CsFcG~kIyPG~G~~fVR~DGkvf~FcssKC~ 38 (131)
T PRK14891 4 TRTCDYTGEEIEPGTGTMFVRKDGTVLHFVDSKCE 38 (131)
T ss_pred eeeecCcCCcccCCCCcEEEecCCCEEEEecHHHH
Confidence 45799998764 888888999986 454
No 203
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=37.17 E-value=6 Score=34.15 Aligned_cols=29 Identities=24% Similarity=0.283 Sum_probs=20.9
Q ss_pred ccccCCCCcee-eEEeeeeeeeeCCCCeeE
Q 045338 78 KYFCEFCGKYA-VKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 78 kY~CpfCGk~~-VKR~avGIW~CkkCgkt~ 106 (134)
=..||.|++.. .|......|.|.+|++.+
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 45799999876 333455678999998744
No 204
>PRK04023 DNA polymerase II large subunit; Validated
Probab=37.07 E-value=21 Score=36.09 Aligned_cols=31 Identities=29% Similarity=0.527 Sum_probs=18.6
Q ss_pred cccccCCCCcee--eE-----EeeeeeeeeCCCCeeEe
Q 045338 77 SKYFCEFCGKYA--VK-----RKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 77 akY~CpfCGk~~--VK-----R~avGIW~CkkCgkt~A 107 (134)
....||.||... ++ |...+--.|.+||....
T Consensus 637 ~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~ 674 (1121)
T PRK04023 637 FYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPT 674 (1121)
T ss_pred CcccCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCC
Confidence 345788888751 22 22333367999997654
No 205
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=37.03 E-value=29 Score=24.41 Aligned_cols=51 Identities=24% Similarity=0.496 Sum_probs=31.3
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCeeEeccccc--cccchHHHHHHHHHHHHhh
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYT--LNTASAVTVRSTIRRLREQ 131 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~--p~T~~~~tvk~~Irrl~e~ 131 (134)
+.| -||+...-+..+--=+| -||+++.=.-=. .....+.-+...+++|.+.
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~rIl~~~~~~~eA~eiVrklQ~e 56 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERRILARAENAEEASEIVRKLQEE 56 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEEEE--SSS-BS--SSHHHHHHHHHHHSS-
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCeeeeeeEEEEEecCCHHHHHHHHHHHHHH
Confidence 468 69999988888888899 999987644322 2455566666667777654
No 206
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=36.67 E-value=7 Score=33.30 Aligned_cols=29 Identities=21% Similarity=0.485 Sum_probs=20.7
Q ss_pred ccccCCCCceeeEE-eeeeeeeeCCCCeeE
Q 045338 78 KYFCEFCGKYAVKR-KAVGIWGCKDCGKVK 106 (134)
Q Consensus 78 kY~CpfCGk~~VKR-~avGIW~CkkCgkt~ 106 (134)
=..||.|+...-++ .....+.|.+|++.+
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 45799999876333 344568999999765
No 207
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=36.35 E-value=6.4 Score=33.46 Aligned_cols=29 Identities=17% Similarity=0.343 Sum_probs=21.2
Q ss_pred ccccCCCCceeeEE-eeeeeeeeCCCCeeE
Q 045338 78 KYFCEFCGKYAVKR-KAVGIWGCKDCGKVK 106 (134)
Q Consensus 78 kY~CpfCGk~~VKR-~avGIW~CkkCgkt~ 106 (134)
=..||.|+...-+. ..-..+.|.+||+.+
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 45799999886443 445668999999754
No 208
>PF02977 CarbpepA_inh: Carboxypeptidase A inhibitor; InterPro: IPR004231 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family is represented by the well-characterised metallocarboxypeptidase A inhibitor (MCPI) from potatoes, which belongs to the MEROPS inhibitor family I37, clan IE. It inhibits metallopeptidases belonging to MEROPS peptidase family M14, carboxypeptidase A. In Russet Burbank potatoes, it is a mixture of approximately equal amounts of two polypeptide chains containing 38 or 39 amino acid residues. The chains differ in their amino terminal sequence only [] and are resistant to fragmentation by proteases []. The structure of the complex between bovine carboxypeptidase A and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-A resolution []. The potato inhibitor is synthesised as a precursor, having a 29 residue N-terminal signal peptide, a 27 residue pro-peptide, the 39 residue mature inhibitor region and a 7 residue C-terminal extension. The 7 residue C-terminal extension is involved in inhibitor inactivation and may be required for targeting to the vacuole where the mature active inhibitor accumulates []. The N-terminal region and the mature inhibitor are weakly related to other solananaceous proteins found in this entry, from potato, tomato and henbane, which have been incorrectly described as metallocarboxipeptidase inhibitors [].; GO: 0008191 metalloendopeptidase inhibitor activity; PDB: 4CPA_I 1H20_A 2HLG_A.
Probab=36.17 E-value=7.2 Score=25.73 Aligned_cols=33 Identities=30% Similarity=0.525 Sum_probs=20.0
Q ss_pred CCCce-eeEEeeeeeeeeCCC-CeeEecccccccc
Q 045338 83 FCGKY-AVKRKAVGIWGCKDC-GKVKAGGAYTLNT 115 (134)
Q Consensus 83 fCGk~-~VKR~avGIW~CkkC-gkt~AGGAy~p~T 115 (134)
-|++. ...=.-.|||-|.-| ..+..+|-|+..+
T Consensus 7 tCn~~C~t~sDC~g~tlC~~C~k~~~t~~g~~~~~ 41 (46)
T PF02977_consen 7 TCNKYCNTNSDCSGITLCQWCWKLKKTCGGYVGSA 41 (46)
T ss_dssp TTT-B-SSSCCCTTSSSS-EE-CCCEBCC--EEEE
T ss_pred ccCCccccCccccceeehHHHHhcccCCCCcccce
Confidence 34444 233346799999999 8888888877654
No 209
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=35.99 E-value=18 Score=23.84 Aligned_cols=10 Identities=30% Similarity=0.939 Sum_probs=7.8
Q ss_pred cccCCCCcee
Q 045338 79 YFCEFCGKYA 88 (134)
Q Consensus 79 Y~CpfCGk~~ 88 (134)
+.||+||...
T Consensus 1 i~CPyCge~~ 10 (52)
T PF14255_consen 1 IQCPYCGEPI 10 (52)
T ss_pred CCCCCCCCee
Confidence 4799999764
No 210
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=35.86 E-value=22 Score=21.65 Aligned_cols=32 Identities=31% Similarity=0.757 Sum_probs=21.5
Q ss_pred cCCCCceee----E-Eeeeeeee-----eCCCCeeEeccccc
Q 045338 81 CEFCGKYAV----K-RKAVGIWG-----CKDCGKVKAGGAYT 112 (134)
Q Consensus 81 CpfCGk~~V----K-R~avGIW~-----CkkCgkt~AGGAy~ 112 (134)
|+.|++... . +.....|| |..|+..+.++.|.
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~ 42 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFY 42 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEE
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeE
Confidence 677777642 2 23446775 89999999888643
No 211
>KOG4215 consensus Hepatocyte nuclear factor 4 and similar steroid hormone receptors [Transcription]
Probab=35.84 E-value=14 Score=33.73 Aligned_cols=38 Identities=37% Similarity=0.857 Sum_probs=26.9
Q ss_pred CccccCch--------hhHhHHHHHHhhhcccccCC---CCceeeEEeeeeeeeeCCCC
Q 045338 56 YGTRYGAS--------LRKQIKKMEVSQHSKYFCEF---CGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 56 fGtRYGas--------lRK~vkkIE~sqhakY~Cpf---CGk~~VKR~avGIW~CkkCg 103 (134)
-|.+||++ +|+-|. +.-.|+|-| |-=++-||.+ |+.|-
T Consensus 30 TGKHYGA~SCdGCKGFFRRSVr-----k~~~YtCRF~k~C~VDKdkRNa-----CRyCR 78 (432)
T KOG4215|consen 30 TGKHYGAISCDGCKGFFRRSVR-----KNHQYTCRFNKQCVVDKDKRNA-----CRYCR 78 (432)
T ss_pred cccccceeecCcchHHHHHHHH-----hcceeeeeccccccccchhhhh-----hhHhh
Confidence 47789974 677776 567899977 6666777764 66663
No 212
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=35.74 E-value=26 Score=24.94 Aligned_cols=32 Identities=31% Similarity=0.575 Sum_probs=22.8
Q ss_pred ccccCCCCceeeEEeeee-eeeeCCCCeeEecc
Q 045338 78 KYFCEFCGKYAVKRKAVG-IWGCKDCGKVKAGG 109 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avG-IW~CkkCgkt~AGG 109 (134)
||.||-||...+...+.| -=.|.-|.=.--|-
T Consensus 1 K~~CPCCg~~Tl~~~~~~~ydIC~VC~WEdD~~ 33 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERGEGTYDICPVCFWEDDGV 33 (78)
T ss_pred CccCCCCCcEEeccCCCcCceECCCCCcccCCc
Confidence 689999999887755544 33588887555443
No 213
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=35.28 E-value=29 Score=21.06 Aligned_cols=24 Identities=38% Similarity=1.061 Sum_probs=17.7
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEecc
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGG 109 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~AGG 109 (134)
.|..|+... .+|.|-.|+...-|-
T Consensus 1 ~C~~C~~~~------~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIE------NLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcC------CeEEecCCCCcccCC
Confidence 378888543 499999998777543
No 214
>KOG4623 consensus Uncharacterized conserved protein [Function unknown]
Probab=35.27 E-value=16 Score=34.57 Aligned_cols=43 Identities=26% Similarity=0.539 Sum_probs=33.5
Q ss_pred CchhhHhHHHHHHhhh-cccccCCCCce-eeEEeeeeeeeeCCCC
Q 045338 61 GASLRKQIKKMEVSQH-SKYFCEFCGKY-AVKRKAVGIWGCKDCG 103 (134)
Q Consensus 61 GaslRK~vkkIE~sqh-akY~CpfCGk~-~VKR~avGIW~CkkCg 103 (134)
|+.+=+..+-|-.... +.-+|=||.+. .|.+....-|.|.+|.
T Consensus 10 ~a~l~~ly~~Irsr~k~t~VnCwFCnk~t~vpyq~rNswTCpsCE 54 (611)
T KOG4623|consen 10 GAGLGNLYDGIRSRFKDTTVNCWFCNKKTEVPYQGRNSWTCPSCE 54 (611)
T ss_pred hhcchHHHHHHHhhcCCceEEEEEecCcceeccCCCCCCcCCcHH
Confidence 4555566666666555 67789999976 6999999999999995
No 215
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=34.90 E-value=21 Score=21.66 Aligned_cols=18 Identities=22% Similarity=0.636 Sum_probs=13.1
Q ss_pred eeeCCCCeeEeccccccc
Q 045338 97 WGCKDCGKVKAGGAYTLN 114 (134)
Q Consensus 97 W~CkkCgkt~AGGAy~p~ 114 (134)
-.|..|+..|+.+-|.|.
T Consensus 5 ~~C~nC~R~v~a~RfA~H 22 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAPH 22 (33)
T ss_dssp EE-TTTSSEEEGGGHHHH
T ss_pred EECCCCcCCcchhhhHHH
Confidence 478889999888877653
No 216
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=34.88 E-value=20 Score=24.56 Aligned_cols=24 Identities=33% Similarity=0.931 Sum_probs=18.6
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
+.|..||..... .-.|+|.|..|.
T Consensus 1 ~~C~VC~~~~~g-~hygv~sC~aC~ 24 (77)
T cd06956 1 HICAICGDRASG-KHYGVYSCEGCK 24 (77)
T ss_pred CCCcccCCcCcc-eEECceeehhHH
Confidence 469999987644 467889999885
No 217
>PRK06260 threonine synthase; Validated
Probab=34.71 E-value=15 Score=31.50 Aligned_cols=23 Identities=35% Similarity=0.674 Sum_probs=11.9
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
+.|+.||+.--- ..-.|.|..|+
T Consensus 4 ~~C~~cg~~~~~--~~~~~~Cp~cg 26 (397)
T PRK06260 4 LKCIECGKEYDP--DEIIYTCPECG 26 (397)
T ss_pred EEECCCCCCCCC--CCccccCCCCC
Confidence 566666655311 12246666664
No 218
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=34.62 E-value=25 Score=19.86 Aligned_cols=12 Identities=33% Similarity=0.947 Sum_probs=9.6
Q ss_pred eeeeeeCCCCee
Q 045338 94 VGIWGCKDCGKV 105 (134)
Q Consensus 94 vGIW~CkkCgkt 105 (134)
.|-|.|..|...
T Consensus 2 ~g~W~C~~C~~~ 13 (30)
T PF00641_consen 2 EGDWKCPSCTFM 13 (30)
T ss_dssp SSSEEETTTTEE
T ss_pred CcCccCCCCcCC
Confidence 367999999864
No 219
>PHA02998 RNA polymerase subunit; Provisional
Probab=34.62 E-value=36 Score=28.26 Aligned_cols=31 Identities=23% Similarity=0.394 Sum_probs=22.0
Q ss_pred cccccCCCCceeeE------Ee----eeeeeeeCCCCeeEe
Q 045338 77 SKYFCEFCGKYAVK------RK----AVGIWGCKDCGKVKA 107 (134)
Q Consensus 77 akY~CpfCGk~~VK------R~----avGIW~CkkCgkt~A 107 (134)
..-.||.||....- |. .+--..|..||+.|.
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 33479999987522 21 367789999998764
No 220
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=34.62 E-value=60 Score=28.25 Aligned_cols=52 Identities=17% Similarity=0.202 Sum_probs=32.7
Q ss_pred hcccccCCCCceeeEEe-eeeeeeeCCCCeeEeccccccccchHHHHHHHHHH
Q 045338 76 HSKYFCEFCGKYAVKRK-AVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRR 127 (134)
Q Consensus 76 hakY~CpfCGk~~VKR~-avGIW~CkkCgkt~AGGAy~p~T~~~~tvk~~Irr 127 (134)
..+|.||.||..-+-|. ...+||=.+-...---..+.++|......|..|-.
T Consensus 28 ~~~~~CP~C~~~v~lk~G~~k~~HFAH~~~~~c~~~~~~ES~~Hl~~K~~l~~ 80 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKGKKKIPHFAHKSKSDCPFFSEGESEEHLQGKELLYQ 80 (375)
T ss_pred CCcEECCCCCCeeEEEEcCcccceeeecCCCCCCcccCCchHHHHHHHHHHHH
Confidence 88999999999865444 45788744332221111345677777777766544
No 221
>PRK08197 threonine synthase; Validated
Probab=34.62 E-value=16 Score=31.28 Aligned_cols=23 Identities=26% Similarity=0.462 Sum_probs=16.7
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.+.|+.||+.--- ..-+|.| .||
T Consensus 7 ~~~C~~Cg~~~~~--~~~~~~C-~cg 29 (394)
T PRK08197 7 HLECSKCGETYDA--DQVHNLC-KCG 29 (394)
T ss_pred EEEECCCCCCCCC--CCcceec-CCC
Confidence 4789999987521 2337999 896
No 222
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=34.55 E-value=19 Score=24.30 Aligned_cols=13 Identities=31% Similarity=0.672 Sum_probs=10.3
Q ss_pred hhcccccCCCCce
Q 045338 75 QHSKYFCEFCGKY 87 (134)
Q Consensus 75 qhakY~CpfCGk~ 87 (134)
.+..|+||.||=+
T Consensus 11 ~~v~~~Cp~cGip 23 (55)
T PF13824_consen 11 AHVNFECPDCGIP 23 (55)
T ss_pred cccCCcCCCCCCc
Confidence 4678999999854
No 223
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=34.44 E-value=21 Score=28.63 Aligned_cols=25 Identities=20% Similarity=0.505 Sum_probs=18.0
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
+.||.|+..-.. ...-|.|.. +..|
T Consensus 3 ~~CP~C~~~l~~--~~~~~~C~~-~h~f 27 (272)
T PRK11088 3 YQCPLCHQPLTL--EENSWICPQ-NHQF 27 (272)
T ss_pred ccCCCCCcchhc--CCCEEEcCC-CCCC
Confidence 689999987533 335699977 6666
No 224
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=33.81 E-value=12 Score=32.68 Aligned_cols=28 Identities=21% Similarity=0.593 Sum_probs=21.7
Q ss_pred ccCCCCceeeEEe-eeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYAVKRK-AVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~VKR~-avGIW~CkkCgkt~A 107 (134)
+||.||...-..+ ....|.|.+|++.+-
T Consensus 30 KCp~c~~~~y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 30 KCPSCGEMLYRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred ECCCccceeeHHHHHhhhhcccccCcccc
Confidence 6999998864443 566899999997654
No 225
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=33.71 E-value=17 Score=31.82 Aligned_cols=23 Identities=17% Similarity=0.210 Sum_probs=16.0
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.+.|+.||+.-- .. ..|.|..|+
T Consensus 2 ~l~C~~Cg~~~~--~~-~~~~C~~c~ 24 (398)
T TIGR03844 2 TLRCPGCGEVLP--DH-YTLSCPLDC 24 (398)
T ss_pred EEEeCCCCCccC--Cc-cccCCCCCC
Confidence 357999998752 23 368998776
No 226
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=33.54 E-value=19 Score=23.62 Aligned_cols=23 Identities=30% Similarity=0.769 Sum_probs=18.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.|..||..... .-.|+|.|..|.
T Consensus 2 ~C~VCg~~~~~-~~ygv~sC~~C~ 24 (70)
T PF00105_consen 2 KCKVCGDPASG-YHYGVLSCNACK 24 (70)
T ss_dssp BSTTTSSBESE-EETTEEEEHHHH
T ss_pred CCeECCCccCc-ccccccccccce
Confidence 58999987644 468999999885
No 227
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=33.51 E-value=33 Score=30.49 Aligned_cols=82 Identities=21% Similarity=0.460 Sum_probs=40.1
Q ss_pred hcccchhhhhHhhHhHhhhhhhccceeeeeccCCcc-ccCchhhHhHH------HHHHh-----hhc---cc--ccCCCC
Q 045338 23 SLYSQQQQVRFLEFLVCFCKMTKRTKKAGIVGKYGT-RYGASLRKQIK------KMEVS-----QHS---KY--FCEFCG 85 (134)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~MakrTKKVgi~GkfGt-RYGaslRK~vk------kIE~s-----qha---kY--~CpfCG 85 (134)
.+|+.|-.-.|++++..+-- .-..+-.+--|.. +|-..|++.+. +|... ..+ +| .|+.||
T Consensus 105 ~SyaeH~~~~~~~~L~~~gi---e~e~~s~te~Y~sG~y~~~i~~aL~~~~~I~~Il~~~~~~~~~~~y~Pf~piC~~cG 181 (360)
T PF01921_consen 105 ESYAEHFNAPFEEFLDEFGI---EYEFISQTEMYRSGRYDEQIRTALENRDEIREILNEYRGRERPETYSPFLPICEKCG 181 (360)
T ss_dssp SCHHHHHHHHHHHHHHTTT------EEEECCCCCCTTTTHHHHCHHHHTHHHHHHHHHHHHHHT--TT--SEEEEETTTE
T ss_pred ccHHHHHHHHHHHHHHHcCC---ceEEEeHHHhhhCCchHHHHHHHHHhHHHHHHHHHHhcCcCCCCCeeeeeeeccccC
Confidence 57888888888888775321 1122333344442 56555554433 22221 122 22 599999
Q ss_pred c-eeeEEe------eeeeeeeCCCCeeEe
Q 045338 86 K-YAVKRK------AVGIWGCKDCGKVKA 107 (134)
Q Consensus 86 k-~~VKR~------avGIW~CkkCgkt~A 107 (134)
+ +.+.=. ..=-|.|..||....
T Consensus 182 ri~tt~v~~~d~~~~~v~Y~c~~cG~~g~ 210 (360)
T PF01921_consen 182 RIDTTEVTEYDPEGGTVTYRCEECGHEGE 210 (360)
T ss_dssp E--EEEEEEE--SSSEEEEE--TTS---E
T ss_pred CcccceeeEeecCCCEEEEEecCCCCEEE
Confidence 9 432212 233699999997643
No 228
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=33.17 E-value=19 Score=24.38 Aligned_cols=8 Identities=50% Similarity=1.161 Sum_probs=6.6
Q ss_pred ccCCCCce
Q 045338 80 FCEFCGKY 87 (134)
Q Consensus 80 ~CpfCGk~ 87 (134)
-|||||+.
T Consensus 41 gCPfC~~~ 48 (55)
T PF14447_consen 41 GCPFCGTP 48 (55)
T ss_pred CCCCCCCc
Confidence 49999975
No 229
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=33.11 E-value=35 Score=23.33 Aligned_cols=28 Identities=36% Similarity=0.567 Sum_probs=20.8
Q ss_pred ccCCCCcee-eEEeeeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYA-VKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~-VKR~avGIW~CkkCgkt~A 107 (134)
.||-|++.. |==.+.-.=.|..||.+.|
T Consensus 13 kCp~C~n~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 13 KCPDCGNEQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred ECCCCCCeEEEEecCCcEEECcccCCCcc
Confidence 699999986 3333555569999998873
No 230
>PRK14873 primosome assembly protein PriA; Provisional
Probab=33.11 E-value=18 Score=34.09 Aligned_cols=18 Identities=44% Similarity=1.366 Sum_probs=0.0
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.|..||....- |.|.+||
T Consensus 412 ~Ch~CG~~~~p------~~Cp~Cg 429 (665)
T PRK14873 412 RCRWCGRAAPD------WRCPRCG 429 (665)
T ss_pred ECCCCcCCCcC------ccCCCCc
No 231
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=32.72 E-value=38 Score=21.76 Aligned_cols=23 Identities=22% Similarity=0.798 Sum_probs=16.1
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
|.|..|+..-+.-. =|+|..|..
T Consensus 1 y~Cd~C~~~pI~G~---R~~C~~C~~ 23 (48)
T cd02341 1 FKCDSCGIEPIPGT---RYHCSECDD 23 (48)
T ss_pred CCCCCCCCCccccc---eEECCCCCC
Confidence 78999998443311 299999974
No 232
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=32.65 E-value=18 Score=18.99 Aligned_cols=7 Identities=43% Similarity=1.298 Sum_probs=3.0
Q ss_pred cccCCCC
Q 045338 79 YFCEFCG 85 (134)
Q Consensus 79 Y~CpfCG 85 (134)
|.|++|.
T Consensus 1 y~C~~C~ 7 (24)
T PF13909_consen 1 YKCPHCS 7 (24)
T ss_dssp EE-SSSS
T ss_pred CCCCCCC
Confidence 4455554
No 233
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=32.53 E-value=15 Score=36.42 Aligned_cols=51 Identities=18% Similarity=0.244 Sum_probs=0.0
Q ss_pred cccCCCCceee-EE------eeeeeeeeCCCCeeEeccccccccchHHHHHHHHHHHHh
Q 045338 79 YFCEFCGKYAV-KR------KAVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRRLRE 130 (134)
Q Consensus 79 Y~CpfCGk~~V-KR------~avGIW~CkkCgkt~AGGAy~p~T~~~~tvk~~Irrl~e 130 (134)
..||+||.... .+ ..+.-=.|.+|+.....=. .-.-+......+|+.+|.+
T Consensus 668 ~~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~~~~-~~~i~l~~~~~~A~e~lg~ 725 (900)
T PF03833_consen 668 NRCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETTSYS-KQKIDLKEEYDRALENLGE 725 (900)
T ss_dssp -----------------------------------------------------------
T ss_pred hcCcccCCccccceeccccccccCccccccccccCcccc-eeecCHHHHHHHHHHhhcc
Confidence 36888887631 11 0111128999987643322 2233444445555555543
No 234
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=32.50 E-value=39 Score=21.25 Aligned_cols=24 Identities=29% Similarity=0.642 Sum_probs=17.1
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCC
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
-.||.||-+-++ .-.|-=.|-.|+
T Consensus 18 ~~Cp~C~~PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMR-DKDGKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEE-ecCCCEECCCCC
Confidence 369999988888 334445787774
No 235
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=32.39 E-value=31 Score=33.20 Aligned_cols=26 Identities=31% Similarity=0.543 Sum_probs=21.1
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
.||+|+..-+-=...|.=.|..||+.
T Consensus 446 ~Cp~Cd~~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 446 ECPNCDSPLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred cCCCCCcceEEecCCCeeEeCCCCCC
Confidence 58888877666667788999999976
No 236
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=32.16 E-value=35 Score=27.54 Aligned_cols=65 Identities=20% Similarity=0.340 Sum_probs=39.9
Q ss_pred hhHhHHHHH-HhhhcccccCCCCce-eeEEeeeeeeeeCCCCeeEeccccccccchHHHHHHHHHHHHhh
Q 045338 64 LRKQIKKME-VSQHSKYFCEFCGKY-AVKRKAVGIWGCKDCGKVKAGGAYTLNTASAVTVRSTIRRLREQ 131 (134)
Q Consensus 64 lRK~vkkIE-~sqhakY~CpfCGk~-~VKR~avGIW~CkkCgkt~AGGAy~p~T~~~~tvk~~Irrl~e~ 131 (134)
+.+...++| ...+.-|.||-|.-. +....-.=-..|..||...- |.=+++.-.-..+.|++|.+.
T Consensus 98 le~Lk~~le~~~~~~~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~---~~d~s~~i~~l~~~i~~l~~~ 164 (176)
T COG1675 98 LEKLKRKLEKETENNYYVCPNCHVKYSFDEAMELGFTCPKCGEDLE---EYDSSEEIEELESELDELEEE 164 (176)
T ss_pred HHHHHHHHHhhccCCceeCCCCCCcccHHHHHHhCCCCCCCCchhh---hccchHHHHHHHHHHHHHHHH
Confidence 444455556 567778899988743 33222111279999987652 344555556667777777765
No 237
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=31.89 E-value=34 Score=22.69 Aligned_cols=49 Identities=24% Similarity=0.600 Sum_probs=26.6
Q ss_pred CccccCchhhHhHHHHHHhhhc---ccccCCCCcee---------eEE----eeeeeeeeCCCCe
Q 045338 56 YGTRYGASLRKQIKKMEVSQHS---KYFCEFCGKYA---------VKR----KAVGIWGCKDCGK 104 (134)
Q Consensus 56 fGtRYGaslRK~vkkIE~sqha---kY~CpfCGk~~---------VKR----~avGIW~CkkCgk 104 (134)
...+|+..+++..++-++.... .-.|..||..- +++ ...=+|.|..||.
T Consensus 21 lsr~y~~~~~~i~~k~~~~l~~~~kr~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 21 LSRHYMKLMRKISKKTRIRLPPEIKRTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp HHHHHHHHHHHHHHHCT---STTCCCTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred HHHHHHHHHHHHHHHhCCCCChHHhcccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 3456777777777766665433 33699998743 331 3567899999974
No 238
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=31.80 E-value=23 Score=24.10 Aligned_cols=27 Identities=26% Similarity=0.608 Sum_probs=15.7
Q ss_pred cccCCCCc-eeeE-Eeee----eeeeeCCCCee
Q 045338 79 YFCEFCGK-YAVK-RKAV----GIWGCKDCGKV 105 (134)
Q Consensus 79 Y~CpfCGk-~~VK-R~av----GIW~CkkCgkt 105 (134)
..||.||. +.+| |..+ =.-.|.+|...
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E 37 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQE 37 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCce
Confidence 36999994 4332 2222 23478888753
No 239
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=31.70 E-value=37 Score=28.14 Aligned_cols=26 Identities=19% Similarity=0.333 Sum_probs=18.1
Q ss_pred cccccCCCCceeeEEe---eeeeeeeCCCC
Q 045338 77 SKYFCEFCGKYAVKRK---AVGIWGCKDCG 103 (134)
Q Consensus 77 akY~CpfCGk~~VKR~---avGIW~CkkCg 103 (134)
..-.||.||..- .|. +-+.|-|..|-
T Consensus 243 ~g~pCprCG~~I-~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 243 TGEPCLNCKTPI-RRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCCcCCCCCCee-EEEEECCCccEECcCCc
Confidence 344799999654 444 34689999994
No 240
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=31.55 E-value=36 Score=18.10 Aligned_cols=11 Identities=36% Similarity=1.108 Sum_probs=7.1
Q ss_pred eeeCCCCeeEe
Q 045338 97 WGCKDCGKVKA 107 (134)
Q Consensus 97 W~CkkCgkt~A 107 (134)
-.|..|+++|.
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 35777777664
No 241
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=31.47 E-value=24 Score=19.62 Aligned_cols=8 Identities=38% Similarity=1.119 Sum_probs=4.3
Q ss_pred ccCCCCce
Q 045338 80 FCEFCGKY 87 (134)
Q Consensus 80 ~CpfCGk~ 87 (134)
.||.||+.
T Consensus 4 ~C~~CgR~ 11 (25)
T PF13913_consen 4 PCPICGRK 11 (25)
T ss_pred cCCCCCCE
Confidence 45655543
No 242
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.38 E-value=20 Score=34.19 Aligned_cols=37 Identities=27% Similarity=0.579 Sum_probs=24.5
Q ss_pred chhhHhHHHHHHhhhccc--------ccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 62 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 62 aslRK~vkkIE~sqhakY--------~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
..+.+.|+.+. ...-.| .|+.||-.... -|.|..||.
T Consensus 657 eal~~lvk~~~-~~~i~Y~sin~~~~~C~~CG~~~~~-----~~~CP~CG~ 701 (735)
T PRK07111 657 EAFEIIVKAMK-NTNIGYGSINHPVDRCPVCGYLGVI-----EDKCPKCGS 701 (735)
T ss_pred HHHHHHHHHHH-hCCCceEEeCCCCeecCCCCCCCCc-----CccCcCCCC
Confidence 46777777643 334455 59999954432 199999984
No 243
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=31.32 E-value=24 Score=25.89 Aligned_cols=25 Identities=16% Similarity=0.345 Sum_probs=13.8
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
....|+.||..--.. .-.|.|..||
T Consensus 69 ~~~~C~~Cg~~~~~~--~~~~~CP~Cg 93 (113)
T PRK12380 69 AQAWCWDCSQVVEIH--QHDAQCPHCH 93 (113)
T ss_pred cEEEcccCCCEEecC--CcCccCcCCC
Confidence 445677787543221 1235577776
No 244
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=31.20 E-value=47 Score=19.70 Aligned_cols=19 Identities=37% Similarity=0.728 Sum_probs=14.4
Q ss_pred eeCCCCeeEeccccccccc
Q 045338 98 GCKDCGKVKAGGAYTLNTA 116 (134)
Q Consensus 98 ~CkkCgkt~AGGAy~p~T~ 116 (134)
.|=-|+++|.|..|.-.|.
T Consensus 2 sCiDC~~~F~~~~y~~Ht~ 20 (28)
T PF08790_consen 2 SCIDCSKDFDGDSYKSHTS 20 (28)
T ss_dssp EETTTTEEEEGGGTTT---
T ss_pred eeecCCCCcCcCCcCCCCc
Confidence 5889999999999987664
No 245
>PRK07591 threonine synthase; Validated
Probab=31.14 E-value=18 Score=31.60 Aligned_cols=24 Identities=25% Similarity=0.454 Sum_probs=16.4
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
.+.|+.||+.--- . ..|.|..||-
T Consensus 18 ~l~C~~Cg~~~~~--~-~~~~C~~cg~ 41 (421)
T PRK07591 18 ALKCRECGAEYPL--G-PIHVCEECFG 41 (421)
T ss_pred EEEeCCCCCcCCC--C-CCccCCCCCC
Confidence 4789999987432 1 2289988963
No 246
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=30.92 E-value=26 Score=25.14 Aligned_cols=25 Identities=24% Similarity=0.654 Sum_probs=19.5
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.-.|..||....- .-.|.|.|..|.
T Consensus 5 ~~~C~VCg~~~~g-~hyGv~sC~aC~ 29 (95)
T cd06968 5 VIPCKICGDKSSG-IHYGVITCEGCK 29 (95)
T ss_pred ccCCcccCCcCcc-eEECceeehhhH
Confidence 3469999987655 358999999996
No 247
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=30.83 E-value=36 Score=30.04 Aligned_cols=28 Identities=29% Similarity=0.568 Sum_probs=23.1
Q ss_pred ccCCCCce---eeEEeeeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKY---AVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~---~VKR~avGIW~CkkCgkt~A 107 (134)
+||.|... .|.....|.=.|..||-++-
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~ 32 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVLE 32 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeeec
Confidence 58888765 48888999999999998763
No 248
>PLN03086 PRLI-interacting factor K; Provisional
Probab=30.29 E-value=37 Score=31.92 Aligned_cols=35 Identities=23% Similarity=0.622 Sum_probs=24.8
Q ss_pred hhcccccCCCCceeeEEe----------eeeeeeeCCCCeeEecccc
Q 045338 75 QHSKYFCEFCGKYAVKRK----------AVGIWGCKDCGKVKAGGAY 111 (134)
Q Consensus 75 qhakY~CpfCGk~~VKR~----------avGIW~CkkCgkt~AGGAy 111 (134)
.|.+|.|| ||+.. .|. ..-+..|.-|++.|.-|-.
T Consensus 475 ~Hkpv~Cp-Cg~~~-~R~~L~~H~~thCp~Kpi~C~fC~~~v~~g~~ 519 (567)
T PLN03086 475 FHEPLQCP-CGVVL-EKEQMVQHQASTCPLRLITCRFCGDMVQAGGS 519 (567)
T ss_pred cCCCccCC-CCCCc-chhHHHhhhhccCCCCceeCCCCCCccccCcc
Confidence 47899999 99643 322 2356789999999965533
No 249
>PRK00807 50S ribosomal protein L24e; Validated
Probab=29.91 E-value=41 Score=21.88 Aligned_cols=25 Identities=36% Similarity=0.837 Sum_probs=15.7
Q ss_pred cccCCCCcee--------eEEeeeeeeeeC-CCC
Q 045338 79 YFCEFCGKYA--------VKRKAVGIWGCK-DCG 103 (134)
Q Consensus 79 Y~CpfCGk~~--------VKR~avGIW~Ck-kCg 103 (134)
+.|.|||... |+..+.=.+-|. +|-
T Consensus 2 ~~C~fcG~~I~pg~G~~~vr~Dgkv~~Fcs~KC~ 35 (52)
T PRK00807 2 RTCSFCGKEIEPGTGKMYVKKDGTILYFCSSKCE 35 (52)
T ss_pred cccCCCCCeEcCCCCeEEEEeCCcEEEEeCHHHH
Confidence 5799999764 444455556555 553
No 250
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=29.85 E-value=20 Score=25.00 Aligned_cols=31 Identities=29% Similarity=0.725 Sum_probs=23.2
Q ss_pred hhhcccccCCCCce-eeEEeeeeeeeeCCCCeeE
Q 045338 74 SQHSKYFCEFCGKY-AVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 74 sqhakY~CpfCGk~-~VKR~avGIW~CkkCgkt~ 106 (134)
++--.|.|-.||.. .+||.. .-.|+.||+.+
T Consensus 16 ~~~miYiCgdC~~en~lk~~D--~irCReCG~RI 47 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTLKRGD--VIRCRECGYRI 47 (62)
T ss_pred cccEEEEeccccccccccCCC--cEehhhcchHH
Confidence 35567999999975 577544 46999999753
No 251
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=29.82 E-value=31 Score=23.13 Aligned_cols=18 Identities=33% Similarity=0.374 Sum_probs=9.9
Q ss_pred hhcccccCCCCceeeEEe
Q 045338 75 QHSKYFCEFCGKYAVKRK 92 (134)
Q Consensus 75 qhakY~CpfCGk~~VKR~ 92 (134)
....=+|++||++..++.
T Consensus 45 ~~~~~~Ci~cgk~a~~~~ 62 (68)
T PF09180_consen 45 EPEGGKCIVCGKPAKKWV 62 (68)
T ss_dssp EBTT-B-TTT-SB-SCEE
T ss_pred CCCCCeeecCCChhhEEE
Confidence 344557999999887654
No 252
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=29.78 E-value=39 Score=20.51 Aligned_cols=10 Identities=30% Similarity=0.903 Sum_probs=7.7
Q ss_pred eeeCCCCeeE
Q 045338 97 WGCKDCGKVK 106 (134)
Q Consensus 97 W~CkkCgkt~ 106 (134)
|.|.+||.++
T Consensus 2 r~C~~Cg~~Y 11 (36)
T PF05191_consen 2 RICPKCGRIY 11 (36)
T ss_dssp EEETTTTEEE
T ss_pred cCcCCCCCcc
Confidence 7788888765
No 253
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=29.77 E-value=25 Score=25.58 Aligned_cols=25 Identities=24% Similarity=0.638 Sum_probs=12.3
Q ss_pred cccccCCCCcee-eEEeeeeeeeeCCCCe
Q 045338 77 SKYFCEFCGKYA-VKRKAVGIWGCKDCGK 104 (134)
Q Consensus 77 akY~CpfCGk~~-VKR~avGIW~CkkCgk 104 (134)
....|+.||..- +.... ..|+.||.
T Consensus 69 ~~~~C~~Cg~~~~~~~~~---~~CP~Cgs 94 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFD---FSCPRCGS 94 (113)
T ss_dssp -EEEETTTS-EEECHHCC---HH-SSSSS
T ss_pred CcEECCCCCCEEecCCCC---CCCcCCcC
Confidence 445677777663 33222 45777763
No 254
>PRK02935 hypothetical protein; Provisional
Probab=29.71 E-value=29 Score=26.59 Aligned_cols=22 Identities=27% Similarity=0.717 Sum_probs=17.0
Q ss_pred cccCCCCcee--eEEeeeeeeeeCCCCe
Q 045338 79 YFCEFCGKYA--VKRKAVGIWGCKDCGK 104 (134)
Q Consensus 79 Y~CpfCGk~~--VKR~avGIW~CkkCgk 104 (134)
-.||.|+|.. ..|+. -|-.|++
T Consensus 71 V~CP~C~K~TKmLGrvD----~CM~C~~ 94 (110)
T PRK02935 71 VICPSCEKPTKMLGRVD----ACMHCNQ 94 (110)
T ss_pred eECCCCCchhhhcccee----ecCcCCC
Confidence 3799999974 66766 6888875
No 255
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=29.61 E-value=44 Score=20.53 Aligned_cols=22 Identities=23% Similarity=0.551 Sum_probs=12.1
Q ss_pred hHhHHHHHHhhhcccccCCCCce
Q 045338 65 RKQIKKMEVSQHSKYFCEFCGKY 87 (134)
Q Consensus 65 RK~vkkIE~sqhakY~CpfCGk~ 87 (134)
||.+-+..++.| +..||.|.+.
T Consensus 1 Rr~~lelll~~H-~~dC~~C~~~ 22 (41)
T PF10588_consen 1 RRTVLELLLANH-PLDCPTCDKN 22 (41)
T ss_dssp -HHHHHHHHTT-----TTT-TTG
T ss_pred CHHHHHHHHhCC-CCcCcCCCCC
Confidence 566777777777 6789999864
No 256
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=29.50 E-value=57 Score=23.88 Aligned_cols=27 Identities=30% Similarity=0.837 Sum_probs=16.6
Q ss_pred ccCCCCc-eeeEEeeeeee-----------------eeCCCCeeE
Q 045338 80 FCEFCGK-YAVKRKAVGIW-----------------GCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk-~~VKR~avGIW-----------------~CkkCgkt~ 106 (134)
.|+.|+. ....+..+=.| .|..||..+
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y 45 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEY 45 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEe
Confidence 4999954 44444433333 588998765
No 257
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.12 E-value=19 Score=26.57 Aligned_cols=27 Identities=19% Similarity=0.400 Sum_probs=14.4
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 76 HSKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 76 hakY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.....|+.||...-- .......|..||
T Consensus 69 p~~~~C~~Cg~~~~~-~~~~~~~CP~Cg 95 (117)
T PRK00564 69 KVELECKDCSHVFKP-NALDYGVCEKCH 95 (117)
T ss_pred CCEEEhhhCCCcccc-CCccCCcCcCCC
Confidence 345567778754311 122334577776
No 258
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=29.00 E-value=29 Score=25.43 Aligned_cols=25 Identities=20% Similarity=0.549 Sum_probs=13.7
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
....|+.||...---. -.|.|++||
T Consensus 69 ~~~~C~~Cg~~~~~~~--~~~~CP~Cg 93 (115)
T TIGR00100 69 VECECEDCSEEVSPEI--DLYRCPKCH 93 (115)
T ss_pred cEEEcccCCCEEecCC--cCccCcCCc
Confidence 4456777775432111 136777776
No 259
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=28.64 E-value=64 Score=29.53 Aligned_cols=12 Identities=25% Similarity=0.598 Sum_probs=5.8
Q ss_pred eeeeeCCCCeeE
Q 045338 95 GIWGCKDCGKVK 106 (134)
Q Consensus 95 GIW~CkkCgkt~ 106 (134)
-.+.|.+||..+
T Consensus 228 a~y~C~~Cg~~i 239 (557)
T PF05876_consen 228 ARYVCPHCGCEI 239 (557)
T ss_pred eEEECCCCcCCC
Confidence 344555555443
No 260
>PRK08329 threonine synthase; Validated
Probab=28.46 E-value=30 Score=29.25 Aligned_cols=22 Identities=32% Similarity=0.773 Sum_probs=15.6
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
+.|+.||+.--. ... |.| .|+-
T Consensus 2 l~C~~Cg~~~~~--~~~-~~C-~c~~ 23 (347)
T PRK08329 2 LRCTKCGRTYEE--KFK-LRC-DCGG 23 (347)
T ss_pred cCcCCCCCCcCC--CCc-eec-CCCC
Confidence 689999987632 233 999 7963
No 261
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=28.28 E-value=59 Score=22.33 Aligned_cols=27 Identities=19% Similarity=0.617 Sum_probs=18.1
Q ss_pred ccCCCCcee---eEEe-eeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYA---VKRK-AVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~---VKR~-avGIW~CkkCgkt~ 106 (134)
.||.|+... +-+. .+-.=.|-+||++-
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 699999754 2222 23346899999875
No 262
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=28.22 E-value=23 Score=24.72 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=13.2
Q ss_pred ccccCCCCcee--------eEEeeeeeeeeC
Q 045338 78 KYFCEFCGKYA--------VKRKAVGIWGCK 100 (134)
Q Consensus 78 kY~CpfCGk~~--------VKR~avGIW~Ck 100 (134)
...|.|||... |+..+.-+|-|.
T Consensus 3 ~~~C~Fsg~~I~PG~G~~~Vr~DG~v~~F~s 33 (71)
T PF01246_consen 3 TEKCSFSGYKIYPGHGKMYVRNDGKVFYFCS 33 (71)
T ss_dssp SEE-TTT-SEE-SSSSEEEE-TTS-EEEESS
T ss_pred eEEecccCCccCCCCCeEEEecCCCeEEEeC
Confidence 46799999765 666666677664
No 263
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=28.05 E-value=23 Score=19.09 Aligned_cols=10 Identities=40% Similarity=1.129 Sum_probs=8.0
Q ss_pred eeeeeCCCCe
Q 045338 95 GIWGCKDCGK 104 (134)
Q Consensus 95 GIW~CkkCgk 104 (134)
|-|.|..|+.
T Consensus 1 g~W~C~~C~~ 10 (26)
T smart00547 1 GDWECPACTF 10 (26)
T ss_pred CcccCCCCCC
Confidence 5699999964
No 264
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=27.84 E-value=34 Score=25.06 Aligned_cols=42 Identities=21% Similarity=0.448 Sum_probs=27.5
Q ss_pred hhhHhHHHHHHh-----hhcccccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 63 SLRKQIKKMEVS-----QHSKYFCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 63 slRK~vkkIE~s-----qhakY~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
..+|-+.+|+.= ....|.|+-||...+--.+-+==.|.+|+.
T Consensus 22 ~~~k~~~~il~Crt~~~G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 22 YQRKAVEAILACRTEALGFHRYRCEDCGHEKIVYNSCKNRHCPSCQA 68 (111)
T ss_pred HHHHHHHHHHhcCCccCCcceeecCCCCceEEecCcccCcCCCCCCC
Confidence 344555555432 345678999998886666666668888864
No 265
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=27.56 E-value=40 Score=20.88 Aligned_cols=12 Identities=25% Similarity=1.016 Sum_probs=7.0
Q ss_pred eeeeeCCCCeeE
Q 045338 95 GIWGCKDCGKVK 106 (134)
Q Consensus 95 GIW~CkkCgkt~ 106 (134)
.+++|..||..+
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 478899998765
No 266
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=27.44 E-value=43 Score=19.40 Aligned_cols=10 Identities=40% Similarity=1.092 Sum_probs=8.4
Q ss_pred cccCCCCcee
Q 045338 79 YFCEFCGKYA 88 (134)
Q Consensus 79 Y~CpfCGk~~ 88 (134)
|.|++||...
T Consensus 12 ~~C~~c~~~~ 21 (57)
T cd00085 12 GLCPYCGKPG 21 (57)
T ss_pred CcCccCCCcC
Confidence 8999999864
No 267
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=27.30 E-value=76 Score=29.30 Aligned_cols=24 Identities=29% Similarity=0.594 Sum_probs=16.4
Q ss_pred cccCCCCceeeEE-eeee-eeeeCCC
Q 045338 79 YFCEFCGKYAVKR-KAVG-IWGCKDC 102 (134)
Q Consensus 79 Y~CpfCGk~~VKR-~avG-IW~CkkC 102 (134)
..||.||+..+.+ ...| -|-|..+
T Consensus 590 ~~CPkCg~~l~~~~~k~g~f~gCs~y 615 (618)
T TIGR01057 590 GKCPKCGGKLVSKYAKKGRFVGCSNY 615 (618)
T ss_pred CCCCcCCCeeeeeecCCccEEECCCC
Confidence 5699999876633 3334 4999763
No 268
>PF00935 Ribosomal_L44: Ribosomal protein L44; InterPro: IPR000552 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of mammalian [], Trypanosoma brucei, Caenorhabditis elegans and fungal L44, and Haloarcula marismortui LA [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZS_r 1S1I_Z 3O5H_f 3O58_f 3IZR_r 1M1K_4 3CCQ_3 3CCL_3 3CME_3 1K73_4 ....
Probab=27.01 E-value=43 Score=23.86 Aligned_cols=22 Identities=27% Similarity=0.457 Sum_probs=15.2
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCC
Q 045338 76 HSKYFCEFCGKYAVKRKAVGIWGCKD 101 (134)
Q Consensus 76 hakY~CpfCGk~~VKR~avGIW~Ckk 101 (134)
.-+|.|..||+..++. +|.|++
T Consensus 51 ~Lrl~C~~C~~~~~~~----~~R~kk 72 (77)
T PF00935_consen 51 VLRLECTECGKAHMRP----GKRCKK 72 (77)
T ss_dssp EEEEEETTTS-EEEEE-----BBESS
T ss_pred EEEEEeCCCCcccccc----cceeEE
Confidence 4678999999988763 277764
No 269
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.92 E-value=27 Score=36.06 Aligned_cols=34 Identities=15% Similarity=0.177 Sum_probs=20.7
Q ss_pred eeeCCCCeeEeccccccccchHHHHHHHHHHHHhh
Q 045338 97 WGCKDCGKVKAGGAYTLNTASAVTVRSTIRRLREQ 131 (134)
Q Consensus 97 W~CkkCgkt~AGGAy~p~T~~~~tvk~~Irrl~e~ 131 (134)
=.|..||...-.=.+. .-+......+|+.+|.+-
T Consensus 710 ~~CP~CGtplv~~~~~-~i~~~~~~~~A~~~~g~~ 743 (1337)
T PRK14714 710 VECPRCDVELTPYQRR-TINVKEEYRSALENVGER 743 (1337)
T ss_pred ccCCCCCCcccccceE-EecHHHHHHHHHHHhCcc
Confidence 3799998544433322 345666777777777553
No 270
>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is
Probab=26.77 E-value=37 Score=22.96 Aligned_cols=25 Identities=32% Similarity=0.785 Sum_probs=18.0
Q ss_pred cCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 81 CEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 81 CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
|..||..+.. .-.|.|.|..|.-=|
T Consensus 1 C~vCg~~~~~-~hygv~~C~aC~~FF 25 (76)
T cd06960 1 CAVCGDRATG-KHYGVLSCNGCKGFF 25 (76)
T ss_pred CCccCccCcc-cEECcceeeeehhee
Confidence 7788876544 457889999997433
No 271
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=26.73 E-value=18 Score=33.88 Aligned_cols=22 Identities=41% Similarity=1.001 Sum_probs=12.7
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
+|||||-+.-+ |= .|.+||+.+
T Consensus 154 ~cp~C~yd~AR----GD-qcd~cG~l~ 175 (567)
T KOG1247|consen 154 KCPFCGYDDAR----GD-QCDKCGKLV 175 (567)
T ss_pred cCCCCCCcccc----ch-hhhhhhhhc
Confidence 47777766533 22 567776544
No 272
>PRK05582 DNA topoisomerase I; Validated
Probab=26.72 E-value=83 Score=29.22 Aligned_cols=28 Identities=25% Similarity=0.549 Sum_probs=18.3
Q ss_pred ccccCCCCceeeEEe-eee-eeeeCC---CCee
Q 045338 78 KYFCEFCGKYAVKRK-AVG-IWGCKD---CGKV 105 (134)
Q Consensus 78 kY~CpfCGk~~VKR~-avG-IW~Ckk---Cgkt 105 (134)
...||.||+..+.|. ..| .|.|.. |+..
T Consensus 571 ~~~CP~Cg~~l~~~~~k~gkf~~Cs~~~~C~~~ 603 (650)
T PRK05582 571 GEDCPKCGSPMVIKMGRYGKFIACSNFPDCRNT 603 (650)
T ss_pred CCCCCCCCCEeEEEecCCCceeecCCccccccC
Confidence 367999998765433 234 488875 7644
No 273
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=26.68 E-value=73 Score=29.44 Aligned_cols=23 Identities=26% Similarity=0.612 Sum_probs=15.7
Q ss_pred cccCCCCceeeEEe-eeee-eeeCC
Q 045338 79 YFCEFCGKYAVKRK-AVGI-WGCKD 101 (134)
Q Consensus 79 Y~CpfCGk~~VKR~-avGI-W~Ckk 101 (134)
-.||.||++.+.|. ..|- |.|..
T Consensus 575 ~~CP~Cg~~~~~~~~~~gkf~gCs~ 599 (610)
T TIGR01051 575 QDCPLCGRPMVVKLGKYGPFLACSN 599 (610)
T ss_pred CCCCCCCCeeEEEecCCCceeeCCC
Confidence 47999998765333 2344 99977
No 274
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=26.39 E-value=65 Score=22.35 Aligned_cols=28 Identities=29% Similarity=0.584 Sum_probs=19.4
Q ss_pred cccccCCCCceeeEEe-------eeeeeeeCCCCe
Q 045338 77 SKYFCEFCGKYAVKRK-------AVGIWGCKDCGK 104 (134)
Q Consensus 77 akY~CpfCGk~~VKR~-------avGIW~CkkCgk 104 (134)
-.|||.-|+....+.. ++=|=+|..|..
T Consensus 3 l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~ 37 (66)
T PF05180_consen 3 LTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKN 37 (66)
T ss_dssp EEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--
T ss_pred EEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcc
Confidence 3589999998776655 555779999974
No 275
>PRK08173 DNA topoisomerase III; Validated
Probab=26.30 E-value=61 Score=31.52 Aligned_cols=28 Identities=18% Similarity=0.331 Sum_probs=19.6
Q ss_pred cccccCCCCceeeEEeeeeeeeeCC-------CCeeE
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKD-------CGKVK 106 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~Ckk-------Cgkt~ 106 (134)
..-.||.||...+. .-..|.|.. |+.++
T Consensus 725 ~~g~CPkCg~~v~e--~~k~y~Cs~~~~~~~~C~f~i 759 (862)
T PRK08173 725 PVGACPKCGGRVFE--HGMSYVCEKSVGPPKTCDFRS 759 (862)
T ss_pred cccCCCCCCCeeEe--eceEEEeCCCcCCCCCCCeee
Confidence 34579999997554 233699986 77665
No 276
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=26.25 E-value=44 Score=22.19 Aligned_cols=22 Identities=27% Similarity=0.516 Sum_probs=16.6
Q ss_pred cccCCCCcee--------eEEeeeeeeeeC
Q 045338 79 YFCEFCGKYA--------VKRKAVGIWGCK 100 (134)
Q Consensus 79 Y~CpfCGk~~--------VKR~avGIW~Ck 100 (134)
..|.|||... |++.+.-.|-|.
T Consensus 4 ~~C~f~g~~I~PG~G~~~Vr~Dgkv~~F~s 33 (54)
T cd00472 4 EKCSFCGYKIYPGHGKMYVRNDGKVFRFCS 33 (54)
T ss_pred EEecCcCCeecCCCccEEEecCCCEEEEEC
Confidence 5799998765 777777777774
No 277
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=26.19 E-value=50 Score=31.16 Aligned_cols=24 Identities=21% Similarity=0.540 Sum_probs=18.6
Q ss_pred cccccCCCCceeeEEeeeeeeeeC
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCK 100 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~Ck 100 (134)
-+-.||.||...++...--.|.|.
T Consensus 403 ~P~~CP~Cgs~l~~~~~~~~~~C~ 426 (665)
T PRK07956 403 MPTHCPVCGSELVRVEGEAVLRCT 426 (665)
T ss_pred CCCCCCCCCCEeEecCCCeEEECC
Confidence 456899999998875555578895
No 278
>PRK07220 DNA topoisomerase I; Validated
Probab=26.14 E-value=62 Score=30.74 Aligned_cols=23 Identities=26% Similarity=0.657 Sum_probs=14.7
Q ss_pred cccCCCCceeeEEee-e-e-eeeeCC
Q 045338 79 YFCEFCGKYAVKRKA-V-G-IWGCKD 101 (134)
Q Consensus 79 Y~CpfCGk~~VKR~a-v-G-IW~Ckk 101 (134)
..||.||++.+.|.+ . | -|.|..
T Consensus 590 ~~CP~Cg~~l~~r~~r~g~~f~gCs~ 615 (740)
T PRK07220 590 GKCPLCGSDLMVRRSKRGSRFIGCEG 615 (740)
T ss_pred cccccCCCeeeEEecCCCceEEEcCC
Confidence 479999988765433 1 2 466643
No 279
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.13 E-value=31 Score=25.68 Aligned_cols=12 Identities=25% Similarity=0.650 Sum_probs=9.1
Q ss_pred cccCCCCceeeE
Q 045338 79 YFCEFCGKYAVK 90 (134)
Q Consensus 79 Y~CpfCGk~~VK 90 (134)
+.||.||...++
T Consensus 93 ~~CP~Cgs~~~~ 104 (124)
T PRK00762 93 IECPVCGNKRAH 104 (124)
T ss_pred CcCcCCCCCCCE
Confidence 579999976644
No 280
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.12 E-value=48 Score=31.22 Aligned_cols=38 Identities=26% Similarity=0.664 Sum_probs=27.4
Q ss_pred chhhHhHHHHHHhhhccc--------ccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 62 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 62 aslRK~vkkIE~sqhakY--------~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
..+.+.|+.| ....-.| .|+.||... .+. .|.|..||.
T Consensus 545 ~al~~lv~~~-~~~~i~Y~~inp~~~~C~~CG~~~---~g~-~~~CP~CGs 590 (625)
T PRK08579 545 EALAKLTKRI-MNTKLVYWSYTPAITVCNKCGRST---TGL-YTRCPRCGS 590 (625)
T ss_pred HHHHHHHHHH-HhcCCceEEeCCCCccCCCCCCcc---CCC-CCcCcCCCC
Confidence 6788889988 3445555 599999843 111 489999986
No 281
>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=26.09 E-value=33 Score=24.35 Aligned_cols=27 Identities=30% Similarity=0.652 Sum_probs=20.9
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
....|..||..+.- .-.|.|.|..|.-
T Consensus 5 ~~~~C~VCg~~a~g-~hyGv~sC~aCk~ 31 (90)
T cd07169 5 EQRTCLICGDRATG-LHYGIISCEGCKG 31 (90)
T ss_pred cCCCCeecCCcCcc-eEECcceehhhHH
Confidence 44569999987755 4689999999963
No 282
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=26.08 E-value=54 Score=30.83 Aligned_cols=26 Identities=27% Similarity=0.600 Sum_probs=19.7
Q ss_pred ccccCCCCceeeEEeeeeeeeeC--CCC
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCK--DCG 103 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~Ck--kCg 103 (134)
+-.||.||...++...--.|.|. .|-
T Consensus 392 P~~CP~C~s~l~~~~~~~~~~C~n~~C~ 419 (652)
T TIGR00575 392 PTHCPSCGSPLVKIEEEAVIRCPNLNCP 419 (652)
T ss_pred CCCCCCCCCEeEecCCcEEEEECCCCCH
Confidence 56899999998876655678884 463
No 283
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=26.07 E-value=70 Score=22.18 Aligned_cols=28 Identities=25% Similarity=0.590 Sum_probs=19.3
Q ss_pred ccCCCCcee---eEEe-eeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYA---VKRK-AVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~---VKR~-avGIW~CkkCgkt~A 107 (134)
.||-|+..+ +-+. .+-.=.|-+||++-.
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 699999764 2222 344558999998764
No 284
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=25.63 E-value=33 Score=35.74 Aligned_cols=27 Identities=41% Similarity=0.830 Sum_probs=16.9
Q ss_pred ccccCCCCceeeEEeeeeeeeeCCCCeeEe
Q 045338 78 KYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGIW~CkkCgkt~A 107 (134)
.|.| .|||.+-.|. -|+ .|.+||.-++
T Consensus 59 d~eC-~CGKyk~~~~-~g~-~C~~CGVEvt 85 (1460)
T PRK14906 59 DWEC-ACGKYKRIRF-KGI-VCERCGVEVT 85 (1460)
T ss_pred CcEE-eCccccccCc-CCe-EcCCCCcEec
Confidence 5778 5887653332 255 7888876654
No 285
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=25.56 E-value=30 Score=35.09 Aligned_cols=28 Identities=43% Similarity=0.902 Sum_probs=15.9
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCeeEe
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCgkt~A 107 (134)
..|.| .|||.+-.+. -|+ .|.+||.-++
T Consensus 56 kd~eC-~Cgkyk~~~~-~~~-~C~~cgve~~ 83 (1156)
T PRK00566 56 KDYEC-LCGKYKRVRY-KGI-ICERCGVEVT 83 (1156)
T ss_pred cCcEE-eCccccccCc-CCc-CCCCCCceee
Confidence 34677 6776553332 244 6777765554
No 286
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=25.48 E-value=43 Score=22.26 Aligned_cols=23 Identities=26% Similarity=0.614 Sum_probs=15.5
Q ss_pred hcccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 76 HSKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 76 hakY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.+-..||-||...+.= =-|..||
T Consensus 25 ~~l~~C~~CG~~~~~H-----~vC~~CG 47 (57)
T PRK12286 25 PGLVECPNCGEPKLPH-----RVCPSCG 47 (57)
T ss_pred CcceECCCCCCccCCe-----EECCCCC
Confidence 4445799999887652 2477776
No 287
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=25.37 E-value=31 Score=32.92 Aligned_cols=8 Identities=38% Similarity=0.983 Sum_probs=4.0
Q ss_pred eeCCCCee
Q 045338 98 GCKDCGKV 105 (134)
Q Consensus 98 ~CkkCgkt 105 (134)
-|.+||.-
T Consensus 78 ~C~~CgvE 85 (619)
T TIGR02387 78 VCERCGVE 85 (619)
T ss_pred CCCCCCCE
Confidence 45555543
No 288
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=25.34 E-value=37 Score=30.00 Aligned_cols=21 Identities=24% Similarity=0.596 Sum_probs=18.7
Q ss_pred eeeeeeeCCCCeeEecccccc
Q 045338 93 AVGIWGCKDCGKVKAGGAYTL 113 (134)
Q Consensus 93 avGIW~CkkCgkt~AGGAy~p 113 (134)
.+-|=.|.+||..+-||-|.-
T Consensus 40 ~~~v~~C~~Cga~~~~~~W~~ 60 (355)
T COG1499 40 EVNVEVCRHCGAYRIRGRWVD 60 (355)
T ss_pred ceEEEECCcCCCccCCCccee
Confidence 456779999999999999987
No 289
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=25.30 E-value=47 Score=21.36 Aligned_cols=26 Identities=35% Similarity=0.899 Sum_probs=9.7
Q ss_pred cccCCCCcee--eEEeeeeeeeeCCCCeeEec
Q 045338 79 YFCEFCGKYA--VKRKAVGIWGCKDCGKVKAG 108 (134)
Q Consensus 79 Y~CpfCGk~~--VKR~avGIW~CkkCgkt~AG 108 (134)
-.|+.|++.- ++|. =+|+.||..|=.
T Consensus 10 ~~C~~C~~~F~~~~rr----hhCr~CG~~vC~ 37 (69)
T PF01363_consen 10 SNCMICGKKFSLFRRR----HHCRNCGRVVCS 37 (69)
T ss_dssp SB-TTT--B-BSSS-E----EE-TTT--EEEC
T ss_pred CcCcCcCCcCCCceee----EccCCCCCEECC
Confidence 4577777652 2333 266666666544
No 290
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=25.29 E-value=31 Score=32.97 Aligned_cols=24 Identities=46% Similarity=1.028 Sum_probs=10.2
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
|.| .|||.+-.+. -|+ -|.+||.-
T Consensus 69 ~eC-~CGkyk~~~~-~~~-~C~~CgvE 92 (627)
T PRK02625 69 WEC-HCGKYKRVRH-RGI-VCERCGVE 92 (627)
T ss_pred cEE-eCCCccccCc-CCc-CCCCCCcE
Confidence 445 4554432221 133 45555543
No 291
>PRK05569 flavodoxin; Provisional
Probab=24.93 E-value=1.3e+02 Score=21.26 Aligned_cols=50 Identities=24% Similarity=0.332 Sum_probs=29.5
Q ss_pred ccccchhhhc-ccchhhhhHhhHhHhhhhhhccceeeeeccCCccccCchhhHh
Q 045338 15 AFSSATLISL-YSQQQQVRFLEFLVCFCKMTKRTKKAGIVGKYGTRYGASLRKQ 67 (134)
Q Consensus 15 ~~~~~~~~~~-~~~~~~~~~~~~~~~~~~MakrTKKVgi~GkfGtRYGaslRK~ 67 (134)
.|-||+.... .++++--.|++.+ ....-+.|+|++.+-||-.+|..++.+
T Consensus 53 ilgsPty~~~~~~~~~~~~~~~~l---~~~~~~~K~v~~f~t~g~~~~~~~~~~ 103 (141)
T PRK05569 53 AFGSPSMDNNNIEQEEMAPFLDQF---KLTPNENKKCILFGSYGWDNGEFMKLW 103 (141)
T ss_pred EEECCCcCCCcCChHHHHHHHHHh---hccCcCCCEEEEEeCCCCCCCcHHHHH
Confidence 3445554332 2233334455543 333346789999999999988776554
No 292
>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha
Probab=24.77 E-value=40 Score=22.87 Aligned_cols=22 Identities=32% Similarity=0.764 Sum_probs=16.1
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 045338 81 CEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 81 CpfCGk~~VKR~avGIW~CkkCg 103 (134)
|..||..+.. .-.|.|.|..|.
T Consensus 1 C~VCg~~a~~-~hygv~sC~aCk 22 (73)
T cd06963 1 CLICGDEASG-CHYGVLTCGSCK 22 (73)
T ss_pred CcccCccCcc-eEECceeehhhh
Confidence 6778876543 467889998886
No 293
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=24.57 E-value=47 Score=29.67 Aligned_cols=21 Identities=29% Similarity=0.676 Sum_probs=16.3
Q ss_pred ccccCCCCcee-eEEeeeeeee
Q 045338 78 KYFCEFCGKYA-VKRKAVGIWG 98 (134)
Q Consensus 78 kY~CpfCGk~~-VKR~avGIW~ 98 (134)
+|.||.||+.- +|+-..=|||
T Consensus 25 ~ffCPaC~~~l~lK~G~~k~pH 46 (342)
T COG4469 25 RFFCPACGSQLILKQGLIKIPH 46 (342)
T ss_pred ccccCCCCCeeeeecCccccch
Confidence 79999999986 5555556776
No 294
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=24.38 E-value=50 Score=29.84 Aligned_cols=42 Identities=26% Similarity=0.351 Sum_probs=26.9
Q ss_pred cccccCCCCceeeEEeeee-------eeeeCCC-CeeEeccccccccchH
Q 045338 77 SKYFCEFCGKYAVKRKAVG-------IWGCKDC-GKVKAGGAYTLNTASA 118 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avG-------IW~CkkC-gkt~AGGAy~p~T~~~ 118 (134)
.+..||.||-..+.+.+|- +=||++= ...--|--|++-+|-|
T Consensus 256 ~k~FCp~CG~~TL~K~aVsv~~dG~~~~h~k~r~~~n~RG~~YSlp~PkG 305 (376)
T KOG2463|consen 256 PKDFCPSCGHKTLTKCAVSVDEDGNGQTHFKKRFQWNNRGLQYSLPKPKG 305 (376)
T ss_pred chhcccccCCCeeeEEEEEecCCCceeEEeecccccccCcceeecCCCCC
Confidence 3668999999898888774 4455422 1112277777777744
No 295
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=24.35 E-value=41 Score=24.34 Aligned_cols=29 Identities=24% Similarity=0.588 Sum_probs=18.3
Q ss_pred hhcccccCCCCceeeEEee--eeeeeeCCCC
Q 045338 75 QHSKYFCEFCGKYAVKRKA--VGIWGCKDCG 103 (134)
Q Consensus 75 qhakY~CpfCGk~~VKR~a--vGIW~CkkCg 103 (134)
....-.|-.||.......+ .||.-|-.|.
T Consensus 10 ~~~N~~CaDCg~~~p~w~s~~~GiflC~~Ca 40 (116)
T PF01412_consen 10 KPGNKVCADCGAPNPTWASLNYGIFLCLECA 40 (116)
T ss_dssp STTCTB-TTT-SBS--EEETTTTEEE-HHHH
T ss_pred CcCcCcCCCCCCCCCCEEEeecChhhhHHHH
Confidence 4556789999988876665 4899999884
No 296
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=24.10 E-value=34 Score=21.83 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=3.2
Q ss_pred cccCCCCc
Q 045338 79 YFCEFCGK 86 (134)
Q Consensus 79 Y~CpfCGk 86 (134)
+.||.|++
T Consensus 42 W~CPiC~~ 49 (50)
T PF02891_consen 42 WKCPICNK 49 (50)
T ss_dssp -B-TTT--
T ss_pred eECcCCcC
Confidence 67888875
No 297
>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg
Probab=24.01 E-value=54 Score=22.94 Aligned_cols=27 Identities=19% Similarity=0.390 Sum_probs=20.5
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
-.|..||..... .-.|+|.|..|.-=|
T Consensus 5 ~~C~VCg~~~~g-~hyGv~sC~aC~~FF 31 (85)
T cd06964 5 KPCFVCQDKSSG-YHYGVSACEGCKGFF 31 (85)
T ss_pred CCCcccCCcCcc-cEECcceeeeeeeEE
Confidence 369999987654 458999999997443
No 298
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=23.85 E-value=70 Score=19.45 Aligned_cols=27 Identities=30% Similarity=0.914 Sum_probs=17.6
Q ss_pred cccccCCCCcee--eEEeeeeeeeeCCCCeeE
Q 045338 77 SKYFCEFCGKYA--VKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 77 akY~CpfCGk~~--VKR~avGIW~CkkCgkt~ 106 (134)
.+-.|..|++.- +.+.+ ++|..|+..+
T Consensus 10 ~~~~C~~C~~~i~g~~~~g---~~C~~C~~~~ 38 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQG---YRCSWCGLVC 38 (53)
T ss_dssp STEB-TTSSSBECSSSSCE---EEETTTT-EE
T ss_pred CCCCCcccCcccCCCCCCe---EEECCCCChH
Confidence 455799999887 33333 7999998765
No 299
>KOG0704 consensus ADP-ribosylation factor GTPase activator [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport; Cytoskeleton]
Probab=23.85 E-value=65 Score=29.28 Aligned_cols=29 Identities=28% Similarity=0.539 Sum_probs=22.3
Q ss_pred hhcccccCCCCceeeEEe--eeeeeeeCCCC
Q 045338 75 QHSKYFCEFCGKYAVKRK--AVGIWGCKDCG 103 (134)
Q Consensus 75 qhakY~CpfCGk~~VKR~--avGIW~CkkCg 103 (134)
+...-.|=.||..---.+ ..|||-|=.|-
T Consensus 16 ~deNk~CfeC~a~NPQWvSvsyGIfICLECS 46 (386)
T KOG0704|consen 16 QDENKKCFECGAPNPQWVSVSYGIFICLECS 46 (386)
T ss_pred cccCCceeecCCCCCCeEeecccEEEEEecC
Confidence 345668999998865555 55999999995
No 300
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.78 E-value=36 Score=23.92 Aligned_cols=14 Identities=36% Similarity=0.487 Sum_probs=10.7
Q ss_pred cccccCCCCceeeE
Q 045338 77 SKYFCEFCGKYAVK 90 (134)
Q Consensus 77 akY~CpfCGk~~VK 90 (134)
..-.||.|||..+.
T Consensus 6 ~~v~CP~Cgkpv~w 19 (65)
T COG3024 6 ITVPCPTCGKPVVW 19 (65)
T ss_pred ccccCCCCCCcccc
Confidence 34579999998764
No 301
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=23.67 E-value=48 Score=20.25 Aligned_cols=11 Identities=45% Similarity=0.821 Sum_probs=5.2
Q ss_pred eeCCCCeeEec
Q 045338 98 GCKDCGKVKAG 108 (134)
Q Consensus 98 ~CkkCgkt~AG 108 (134)
.|+.|+..|=.
T Consensus 15 ~C~~C~~~FC~ 25 (43)
T PF01428_consen 15 KCKHCGKSFCL 25 (43)
T ss_dssp E-TTTS-EE-T
T ss_pred ECCCCCcccCc
Confidence 67777776643
No 302
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=23.58 E-value=43 Score=18.19 Aligned_cols=8 Identities=38% Similarity=1.535 Sum_probs=4.1
Q ss_pred cccCCCCc
Q 045338 79 YFCEFCGK 86 (134)
Q Consensus 79 Y~CpfCGk 86 (134)
|.|+.|++
T Consensus 2 ~~C~~C~k 9 (27)
T PF12171_consen 2 FYCDACDK 9 (27)
T ss_dssp CBBTTTTB
T ss_pred CCcccCCC
Confidence 44555554
No 303
>PLN03086 PRLI-interacting factor K; Provisional
Probab=23.41 E-value=39 Score=31.75 Aligned_cols=28 Identities=25% Similarity=0.559 Sum_probs=21.6
Q ss_pred ccCC--CCceeeEEeeeeeeeeCCCCeeEe
Q 045338 80 FCEF--CGKYAVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~Cpf--CGk~~VKR~avGIW~CkkCgkt~A 107 (134)
.||. ||..-.++.----|+|..|++.|.
T Consensus 435 ~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~ 464 (567)
T PLN03086 435 VCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ 464 (567)
T ss_pred eCCcccccceeeccccccCccCCCCCCccc
Confidence 3664 888777777778899999998873
No 304
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=23.38 E-value=30 Score=31.37 Aligned_cols=13 Identities=38% Similarity=0.876 Sum_probs=10.8
Q ss_pred hhcccccCCCCce
Q 045338 75 QHSKYFCEFCGKY 87 (134)
Q Consensus 75 qhakY~CpfCGk~ 87 (134)
..++|.|++|+|.
T Consensus 395 ~~KPYrCevC~KR 407 (423)
T COG5189 395 KDKPYRCEVCDKR 407 (423)
T ss_pred cCCceeccccchh
Confidence 3489999999985
No 305
>cd06969 NR_DBD_NGFI-B DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B. DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcrip
Probab=23.23 E-value=53 Score=22.33 Aligned_cols=26 Identities=27% Similarity=0.718 Sum_probs=19.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
.|..||..+.. .-.|.|.|..|.-=|
T Consensus 2 ~C~VCg~~~~g-~hyGv~sC~aC~~FF 27 (75)
T cd06969 2 LCAVCGDNAAC-QHYGVRTCEGCKGFF 27 (75)
T ss_pred CCeecCCcCcc-eEECcceeeeeeeee
Confidence 48889987655 358999999997443
No 306
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=23.22 E-value=61 Score=25.20 Aligned_cols=25 Identities=28% Similarity=0.707 Sum_probs=18.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
.|+.||..-+.+.-. .=.|..|+..
T Consensus 151 ~~~~~g~~~~~~~~~-~~~c~~~~~~ 175 (189)
T PRK09521 151 MCSRCRTPLVKKGEN-ELKCPNCGNI 175 (189)
T ss_pred EccccCCceEECCCC-EEECCCCCCE
Confidence 499999988775433 3589999854
No 307
>PRK14724 DNA topoisomerase III; Provisional
Probab=23.02 E-value=45 Score=32.93 Aligned_cols=26 Identities=23% Similarity=0.510 Sum_probs=18.2
Q ss_pred cccCCCCceeeEEeeeeeeeeCC-------CCeeE
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKD-------CGKVK 106 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~Ckk-------Cgkt~ 106 (134)
-.||.||...++ .-+-|.|.. |+.++
T Consensus 644 ~~CP~Cg~~~~~--~~~~~~Cs~~~~~~~~C~f~~ 676 (987)
T PRK14724 644 TPCPNCGGVVKE--NYRRYACTGANGAGEGCGFSF 676 (987)
T ss_pred ccCCcccccccc--cCceeecCCCcCCCCCCCccc
Confidence 469999987533 234599984 88664
No 308
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=22.99 E-value=71 Score=27.81 Aligned_cols=40 Identities=15% Similarity=0.509 Sum_probs=27.8
Q ss_pred hhhHhHHHHHHhhhcccccCCCCceeeEEe--eeeeeeeCCCC
Q 045338 63 SLRKQIKKMEVSQHSKYFCEFCGKYAVKRK--AVGIWGCKDCG 103 (134)
Q Consensus 63 slRK~vkkIE~sqhakY~CpfCGk~~VKR~--avGIW~CkkCg 103 (134)
..++.++++--.-. .-.|.-||....++. .-||..|-+|-
T Consensus 11 ~~~~~l~~Ll~~~~-N~~CADC~a~~P~WaSwnlGvFiC~~C~ 52 (287)
T KOG0703|consen 11 RNKRRLRELLREPD-NKVCADCGAKGPRWASWNLGVFICLRCA 52 (287)
T ss_pred hHHHHHHHHHcCcc-cCcccccCCCCCCeEEeecCeEEEeecc
Confidence 33444554433333 557999999988887 45999999994
No 309
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=22.97 E-value=82 Score=17.64 Aligned_cols=24 Identities=21% Similarity=0.546 Sum_probs=12.0
Q ss_pred ccCCCCcee--eEEeeeeeeeeCCCC
Q 045338 80 FCEFCGKYA--VKRKAVGIWGCKDCG 103 (134)
Q Consensus 80 ~CpfCGk~~--VKR~avGIW~CkkCg 103 (134)
.||.|+... +.-.+-.-.-|..|-
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTC
T ss_pred cCccCCCcceEeEecCCCCeECcCCc
Confidence 589999874 332234557787774
No 310
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=22.96 E-value=37 Score=21.22 Aligned_cols=13 Identities=23% Similarity=0.628 Sum_probs=7.2
Q ss_pred ccccCCCCceeeE
Q 045338 78 KYFCEFCGKYAVK 90 (134)
Q Consensus 78 kY~CpfCGk~~VK 90 (134)
+|.||.||--.+.
T Consensus 1 ~hlcpkcgvgvl~ 13 (36)
T PF09151_consen 1 QHLCPKCGVGVLE 13 (36)
T ss_dssp --B-TTTSSSBEE
T ss_pred CccCCccCceEEE
Confidence 4679999865543
No 311
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=22.92 E-value=66 Score=18.68 Aligned_cols=13 Identities=23% Similarity=0.884 Sum_probs=10.4
Q ss_pred eeeeeCCCCeeEe
Q 045338 95 GIWGCKDCGKVKA 107 (134)
Q Consensus 95 GIW~CkkCgkt~A 107 (134)
.+++|..||..+.
T Consensus 3 ~~ykC~~CGniv~ 15 (34)
T cd00974 3 EVYKCEICGNIVE 15 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 4789999998774
No 312
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.90 E-value=35 Score=32.02 Aligned_cols=37 Identities=24% Similarity=0.529 Sum_probs=24.2
Q ss_pred chhhHhHHHHHHhhhccc--------ccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 62 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 62 aslRK~vkkIE~sqhakY--------~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
..+.+.|+.+.- ..-.| .|+.||....- .|.|..||.
T Consensus 536 ~Al~~lvk~~~~-~~i~Y~sin~~~~~C~~CGy~g~~-----~~~CP~CG~ 580 (618)
T PRK14704 536 KALKQIVQAMAE-HGVGYGSINHPVDRCKCCSYHGVI-----GNECPSCGN 580 (618)
T ss_pred HHHHHHHHHHHh-cCCceEEeCCCCeecCCCCCCCCc-----CccCcCCCC
Confidence 567777777543 33444 59999963221 199999985
No 313
>PRK06921 hypothetical protein; Provisional
Probab=22.89 E-value=75 Score=26.07 Aligned_cols=12 Identities=25% Similarity=0.733 Sum_probs=10.0
Q ss_pred ccccCCCCceee
Q 045338 78 KYFCEFCGKYAV 89 (134)
Q Consensus 78 kY~CpfCGk~~V 89 (134)
.|.||.|+.+-.
T Consensus 32 ~~~Cp~C~dtG~ 43 (266)
T PRK06921 32 RYDCPKCKDRGI 43 (266)
T ss_pred CCCCCCCCCCEE
Confidence 589999998853
No 314
>PRK14724 DNA topoisomerase III; Provisional
Probab=22.84 E-value=64 Score=31.91 Aligned_cols=21 Identities=24% Similarity=0.487 Sum_probs=15.9
Q ss_pred ccccCCCCceeeEEeeeee-eeeCC
Q 045338 78 KYFCEFCGKYAVKRKAVGI-WGCKD 101 (134)
Q Consensus 78 kY~CpfCGk~~VKR~avGI-W~Ckk 101 (134)
--.||.||...+. .|- |.|..
T Consensus 755 ~g~CPkCg~~v~e---~gk~y~Cs~ 776 (987)
T PRK14724 755 LGPCPKCGAPVFE---HGSNYVCEK 776 (987)
T ss_pred ccCCCCCCCceEe---ecceEEcCC
Confidence 3579999988654 455 99985
No 315
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=22.73 E-value=30 Score=19.77 Aligned_cols=24 Identities=17% Similarity=0.670 Sum_probs=14.1
Q ss_pred cccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 79 YFCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 79 Y~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
|.|.-|++..-.-. ..+|+.|+.+
T Consensus 1 ~~C~~C~~~~~~~~---~Y~C~~c~f~ 24 (30)
T PF03107_consen 1 FWCDVCRRKIDGFY---FYHCSECCFT 24 (30)
T ss_pred CCCCCCCCCcCCCE---eEEeCCCCCe
Confidence 45777766543311 6778777743
No 316
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=22.65 E-value=31 Score=32.66 Aligned_cols=31 Identities=23% Similarity=0.445 Sum_probs=19.1
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEeccccccc
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGGAYTLN 114 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~AGGAy~p~ 114 (134)
.||.||... ..|-=.|..||....-=.|.+-
T Consensus 29 ~Cp~CG~~~----~~~~~fC~~CG~~~~~~~~~~~ 59 (645)
T PRK14559 29 PCPQCGTEV----PVDEAHCPNCGAETGTIWWAII 59 (645)
T ss_pred cCCCCCCCC----CcccccccccCCcccchhhhhc
Confidence 488888773 2333478888877655444443
No 317
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=22.62 E-value=41 Score=25.93 Aligned_cols=9 Identities=11% Similarity=0.239 Sum_probs=5.4
Q ss_pred cccccCCCC
Q 045338 77 SKYFCEFCG 85 (134)
Q Consensus 77 akY~CpfCG 85 (134)
.-|.||.|+
T Consensus 108 ~~Y~Cp~c~ 116 (158)
T TIGR00373 108 MFFICPNMC 116 (158)
T ss_pred CeEECCCCC
Confidence 446677665
No 318
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=22.55 E-value=18 Score=32.81 Aligned_cols=30 Identities=23% Similarity=0.565 Sum_probs=20.1
Q ss_pred ccCCCCce-eeEEeeeeeeeeCCCCeeEecc
Q 045338 80 FCEFCGKY-AVKRKAVGIWGCKDCGKVKAGG 109 (134)
Q Consensus 80 ~CpfCGk~-~VKR~avGIW~CkkCgkt~AGG 109 (134)
.|..|... +..-.-.+=|.|.+||.++-=|
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg~ikKG 278 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGGKIKKG 278 (403)
T ss_pred HHHHhhhccCcchhhhhcccCcccccchhhh
Confidence 59999843 3332233569999999877654
No 319
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=22.38 E-value=41 Score=22.85 Aligned_cols=13 Identities=46% Similarity=1.078 Sum_probs=10.7
Q ss_pred hhcccccCCCCce
Q 045338 75 QHSKYFCEFCGKY 87 (134)
Q Consensus 75 qhakY~CpfCGk~ 87 (134)
+..+|.|.+||+.
T Consensus 2 ~k~~~~C~~Cg~r 14 (69)
T PF09706_consen 2 SKKKYNCIFCGER 14 (69)
T ss_pred CCCCCcCcCCCCc
Confidence 5678999999944
No 320
>smart00532 LIGANc Ligase N family.
Probab=22.35 E-value=73 Score=28.71 Aligned_cols=24 Identities=21% Similarity=0.360 Sum_probs=19.2
Q ss_pred cccccCCCCceeeEEeeeeeeeeC
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCK 100 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~Ck 100 (134)
.+-.||.||...++...--.|.|.
T Consensus 398 ~P~~CP~C~s~l~~~~~~~~~~C~ 421 (441)
T smart00532 398 MPTHCPSCGSELVREEGEVDIRCP 421 (441)
T ss_pred CCCCCCCCCCEeEecCCceEEEeC
Confidence 356899999998876655689995
No 321
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=22.30 E-value=1.2e+02 Score=25.15 Aligned_cols=63 Identities=24% Similarity=0.277 Sum_probs=44.5
Q ss_pred cccchhhhcccchhhhhHhhHhHhhhhhhc-cceeeeeccCCccccCchhhHhHHHHHHhhhccccc--CCCC
Q 045338 16 FSSATLISLYSQQQQVRFLEFLVCFCKMTK-RTKKAGIVGKYGTRYGASLRKQIKKMEVSQHSKYFC--EFCG 85 (134)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~~~~~~Mak-rTKKVgi~GkfGtRYGaslRK~vkkIE~sqhakY~C--pfCG 85 (134)
+.++.|+=.|.+|..+- ..+.++++ ..-|.=|++...++ ..+|+.++++-.+..-.+.| |||.
T Consensus 49 i~~~Dl~I~y~lHPDl~-----~~l~~~~~e~g~kavIvp~~~~~--~g~~~~lk~~~e~~gi~~~~P~~~Cs 114 (217)
T PF02593_consen 49 IPEADLLIAYGLHPDLT-----YELPEIAKEAGVKAVIVPSESPK--PGLRRQLKKQLEEFGIEVEFPKPFCS 114 (217)
T ss_pred CCCCCEEEEeccCchhH-----HHHHHHHHHcCCCEEEEecCCCc--cchHHHHHHHHHhcCceeecCccccc
Confidence 66778888899998743 23334444 44466678877777 89999999988887655655 5775
No 322
>COG3464 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.25 E-value=32 Score=30.30 Aligned_cols=29 Identities=31% Similarity=0.648 Sum_probs=21.8
Q ss_pred cccCCCCceeeEEee---------------------eeeeeeCCCCeeEe
Q 045338 79 YFCEFCGKYAVKRKA---------------------VGIWGCKDCGKVKA 107 (134)
Q Consensus 79 Y~CpfCGk~~VKR~a---------------------vGIW~CkkCgkt~A 107 (134)
+.||-||....++.+ ..=|+|..|+++++
T Consensus 39 ~~CP~Cg~~~~~~~~~~~~~I~~L~~~~~~~~L~~r~rR~~c~~c~~~~~ 88 (402)
T COG3464 39 HRCPECGQRTIRRHGWRIRKIQDLPLFEVPVYLFLRKRRYKCCRCGKRFA 88 (402)
T ss_pred CCCCCCCCcceeccccceeeeeecccCCeeEEEEeccceeecccCCCCcc
Confidence 899999988655431 24478999999984
No 323
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.25 E-value=38 Score=29.80 Aligned_cols=19 Identities=26% Similarity=0.560 Sum_probs=12.4
Q ss_pred cccccCCCCceeeEEeeee
Q 045338 77 SKYFCEFCGKYAVKRKAVG 95 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avG 95 (134)
.+=+||+||+.-.-..-.|
T Consensus 238 ~~~~C~~Cg~~PtiP~~~~ 256 (298)
T KOG2879|consen 238 SDTECPVCGEPPTIPHVIG 256 (298)
T ss_pred CCceeeccCCCCCCCeeec
Confidence 3457999999865443333
No 324
>PRK07219 DNA topoisomerase I; Validated
Probab=22.22 E-value=65 Score=30.90 Aligned_cols=29 Identities=24% Similarity=0.476 Sum_probs=19.8
Q ss_pred ccccCCCCceeeEEe-eee--eeeeCC---CCeeE
Q 045338 78 KYFCEFCGKYAVKRK-AVG--IWGCKD---CGKVK 106 (134)
Q Consensus 78 kY~CpfCGk~~VKR~-avG--IW~Ckk---Cgkt~ 106 (134)
.-.||.||+..+.|. ..| -|.|.. |..+.
T Consensus 602 ~~~CP~Cg~~l~~r~~~~g~~F~gCs~yp~C~~t~ 636 (822)
T PRK07219 602 IGKCPECGGDLIIIRTDKGSRFVGCSGYPDCRNTF 636 (822)
T ss_pred cCcCCCCCCcceeeeccCCceeeecCCCcCCCCee
Confidence 357999998765433 334 589977 88663
No 325
>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers. DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p
Probab=22.18 E-value=42 Score=23.12 Aligned_cols=23 Identities=26% Similarity=0.642 Sum_probs=18.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.|..||..+.. .-.|.|.|..|.
T Consensus 4 ~C~VCg~~a~g-~hyGv~sC~aC~ 26 (78)
T cd07172 4 ICLVCSDEASG-CHYGVLTCGSCK 26 (78)
T ss_pred CCeecCCcCcc-eEECceeehhhH
Confidence 49999986544 567899999996
No 326
>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi
Probab=22.16 E-value=45 Score=22.42 Aligned_cols=22 Identities=27% Similarity=0.709 Sum_probs=16.0
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 045338 81 CEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 81 CpfCGk~~VKR~avGIW~CkkCg 103 (134)
|..||..... .-.|.|.|..|.
T Consensus 1 C~VC~~~~~g-~hygv~sC~aC~ 22 (72)
T cd07156 1 CGVCGDRATG-YHFNAMTCEGCK 22 (72)
T ss_pred CCccCccCcc-cEECcceehhhh
Confidence 6778876544 467888898886
No 327
>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers. DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding
Probab=22.09 E-value=41 Score=23.54 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=17.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.|..||..... .-.|.|.|..|.
T Consensus 1 ~C~VCg~~~~g-~hygv~sC~aC~ 23 (87)
T cd07162 1 ICRVCGDRATG-YHFNAMTCEGCK 23 (87)
T ss_pred CCcccCCcCcc-eEECcceehhhH
Confidence 38889876654 357889998886
No 328
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=22.09 E-value=38 Score=30.59 Aligned_cols=14 Identities=29% Similarity=0.631 Sum_probs=11.1
Q ss_pred hhhcccccCCCCce
Q 045338 74 SQHSKYFCEFCGKY 87 (134)
Q Consensus 74 sqhakY~CpfCGk~ 87 (134)
.|.+.|+||.|.-.
T Consensus 15 vq~~~YtCPRCn~~ 28 (383)
T KOG4317|consen 15 VQKREYTCPRCNLL 28 (383)
T ss_pred cccccccCCCCCcc
Confidence 36677999999864
No 329
>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian
Probab=22.04 E-value=50 Score=23.57 Aligned_cols=26 Identities=23% Similarity=0.588 Sum_probs=18.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
.|..||..+.. .-.|.|.|..|.-=|
T Consensus 2 ~C~VCg~~a~g-~hyGv~sC~aC~~FF 27 (94)
T cd06966 2 ICGVCGDKALG-YNFNAITCESCKAFF 27 (94)
T ss_pred CCeeCCCcCcc-eEECcceeeeehhee
Confidence 38888876543 367889999887433
No 330
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=22.01 E-value=40 Score=22.74 Aligned_cols=13 Identities=31% Similarity=0.529 Sum_probs=6.7
Q ss_pred ccccCCCCceeeE
Q 045338 78 KYFCEFCGKYAVK 90 (134)
Q Consensus 78 kY~CpfCGk~~VK 90 (134)
+..||.||+...-
T Consensus 2 ~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 2 TVKCPICGKPVEW 14 (57)
T ss_dssp EEE-TTT--EEE-
T ss_pred cccCCCCCCeecc
Confidence 4579999988765
No 331
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=22.00 E-value=33 Score=28.14 Aligned_cols=26 Identities=23% Similarity=0.574 Sum_probs=20.9
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
.-+-|+.|....-.|. |||.-|++=|
T Consensus 112 ~~~~C~~C~~~rPpRs----~HCsvC~~CV 137 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRS----SHCSVCNNCV 137 (299)
T ss_pred ceEEcCcCcccCCCCc----ccchhhcccc
Confidence 3567999999988876 7999998643
No 332
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=21.93 E-value=39 Score=31.19 Aligned_cols=38 Identities=32% Similarity=0.537 Sum_probs=24.1
Q ss_pred chhhHhHHHHHHhhhccc--------ccCCCCceeeEEeeee-eeeeCCCCee
Q 045338 62 ASLRKQIKKMEVSQHSKY--------FCEFCGKYAVKRKAVG-IWGCKDCGKV 105 (134)
Q Consensus 62 aslRK~vkkIE~sqhakY--------~CpfCGk~~VKR~avG-IW~CkkCgkt 105 (134)
..+++.|+.+-..- -.| .|+.||.. +.+ .|.|.+||..
T Consensus 501 eal~~lv~~a~~~~-i~Y~~~n~~~~~C~~CG~~-----g~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 501 EALKDITKKAMKNG-IGYFGINPPVDVCEDCGYT-----GEGLNDKCPKCGSH 547 (579)
T ss_pred HHHHHHHHHHHhcC-CceEEeccCCccCCCCCCC-----CCCCCCcCcCCCCc
Confidence 56777777765432 344 59999862 222 2899999853
No 333
>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers. The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=21.92 E-value=44 Score=22.66 Aligned_cols=22 Identities=27% Similarity=0.744 Sum_probs=16.4
Q ss_pred cCCCCceeeEEeeeeeeeeCCCC
Q 045338 81 CEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 81 CpfCGk~~VKR~avGIW~CkkCg 103 (134)
|..||..+.. .-.|+|.|..|.
T Consensus 1 C~VCg~~~~g-~hygv~sC~aC~ 22 (74)
T cd07179 1 CRVCGGKSSG-FHFGALTCEGCK 22 (74)
T ss_pred CcccCccCcc-eEECceeehhHH
Confidence 6788876644 457889998885
No 334
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=21.87 E-value=72 Score=18.45 Aligned_cols=14 Identities=21% Similarity=0.759 Sum_probs=11.0
Q ss_pred eeeeeeCCCCeeEe
Q 045338 94 VGIWGCKDCGKVKA 107 (134)
Q Consensus 94 vGIW~CkkCgkt~A 107 (134)
..+++|..||..+.
T Consensus 5 ~~~ykC~~Cgniv~ 18 (34)
T TIGR00319 5 GQVYKCEVCGNIVE 18 (34)
T ss_pred CcEEEcCCCCcEEE
Confidence 35889999998774
No 335
>smart00746 TRASH metallochaperone-like domain.
Probab=21.81 E-value=43 Score=16.94 Aligned_cols=8 Identities=63% Similarity=1.514 Sum_probs=6.0
Q ss_pred cCCCCcee
Q 045338 81 CEFCGKYA 88 (134)
Q Consensus 81 CpfCGk~~ 88 (134)
||+||...
T Consensus 1 c~~C~~~~ 8 (39)
T smart00746 1 CSFCGKDI 8 (39)
T ss_pred CCCCCCCc
Confidence 78888765
No 336
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=21.69 E-value=98 Score=27.08 Aligned_cols=25 Identities=36% Similarity=0.903 Sum_probs=16.1
Q ss_pred ccCCCCceeeEEee------eeeeeeCCCCee
Q 045338 80 FCEFCGKYAVKRKA------VGIWGCKDCGKV 105 (134)
Q Consensus 80 ~CpfCGk~~VKR~a------vGIW~CkkCgkt 105 (134)
.||.||+..+.=.+ +=-|.| +||..
T Consensus 171 ~c~~cg~~~~~v~~~d~~~~~v~y~c-~cG~~ 201 (353)
T cd00674 171 YCEKCGKDTTTVEAYDAKAGTVTYKC-ECGHE 201 (353)
T ss_pred ecCCcCcceeEEEEEeCCCCeEEEEc-CCCCE
Confidence 59999976433222 235889 59865
No 337
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=21.64 E-value=29 Score=27.36 Aligned_cols=37 Identities=24% Similarity=0.611 Sum_probs=21.4
Q ss_pred hHHHHHHhhhccc-ccCCCCcee---eEEeeeeeeeeCCCCe
Q 045338 67 QIKKMEVSQHSKY-FCEFCGKYA---VKRKAVGIWGCKDCGK 104 (134)
Q Consensus 67 ~vkkIE~sqhakY-~CpfCGk~~---VKR~avGIW~CkkCgk 104 (134)
.+.+|+. --+.| .|+.||+.. ++..-.=.=+|..||.
T Consensus 94 i~~~i~~-yi~~yv~C~~c~s~dt~l~~~~R~~~l~c~acGa 134 (151)
T COG1601 94 IVNEIER-YIAEYVKCKECGSPDTELIKEERLLFLKCEACGA 134 (151)
T ss_pred HHHHHHH-HHHheeEeccCCCCchhhhhhhhhHhhHHHHhCC
Confidence 3344433 33344 799999875 4443333447888853
No 338
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=21.58 E-value=66 Score=30.64 Aligned_cols=22 Identities=14% Similarity=0.339 Sum_probs=16.4
Q ss_pred cccccCCCCceeeEEeeeeeeeeC
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCK 100 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~Ck 100 (134)
-+-.||.||...++ .++-+| |.
T Consensus 422 ~P~~CP~C~~~l~~-~~~~~~-C~ 443 (689)
T PRK14351 422 FPDTCPVCDSAVER-DGPLAF-CT 443 (689)
T ss_pred CCCCCCCCCCEeee-CCceEE-cC
Confidence 35689999999886 555566 75
No 339
>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers. The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.
Probab=21.54 E-value=57 Score=22.89 Aligned_cols=26 Identities=31% Similarity=0.667 Sum_probs=19.3
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
.|..||..+.. .-.|.|.|..|.-=|
T Consensus 2 ~C~VCg~~a~g-~hyGv~sC~aCk~FF 27 (86)
T cd07157 2 TCQVCGEPAAG-FHHGAYVCEACKKFF 27 (86)
T ss_pred CCcccCCcCcc-cEECcceeeEeeeEE
Confidence 58899977643 467889999997544
No 340
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=21.46 E-value=62 Score=19.16 Aligned_cols=17 Identities=35% Similarity=0.405 Sum_probs=10.1
Q ss_pred eeeeeeeCCCCeeEecc
Q 045338 93 AVGIWGCKDCGKVKAGG 109 (134)
Q Consensus 93 avGIW~CkkCgkt~AGG 109 (134)
......|+.|++.+.++
T Consensus 13 ~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CSS-EEETTTTEE----
T ss_pred CcCeEEeCCCCeEEeeC
Confidence 45678999999999987
No 341
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=21.46 E-value=71 Score=26.31 Aligned_cols=24 Identities=29% Similarity=0.654 Sum_probs=15.5
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
.|+.|+..-++ .--.-.|..||.+
T Consensus 151 ~CsrC~~~L~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 151 RCSRCRAPLVK--KGNMLKCPNCGNT 174 (188)
T ss_pred EccCCCcceEE--cCcEEECCCCCCE
Confidence 47777777766 2234577777754
No 342
>COG1773 Rubredoxin [Energy production and conversion]
Probab=21.43 E-value=58 Score=22.01 Aligned_cols=12 Identities=42% Similarity=1.013 Sum_probs=9.3
Q ss_pred eeeeCCCCeeEe
Q 045338 96 IWGCKDCGKVKA 107 (134)
Q Consensus 96 IW~CkkCgkt~A 107 (134)
-|+|+-||+.+-
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 389999998763
No 343
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=21.25 E-value=43 Score=30.79 Aligned_cols=26 Identities=27% Similarity=0.685 Sum_probs=18.8
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCC
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
..--||.||.. |-----|+-.|.+|.
T Consensus 14 l~ElCPVCGDk-VSGYHYGLLTCESCK 39 (475)
T KOG4218|consen 14 LGELCPVCGDK-VSGYHYGLLTCESCK 39 (475)
T ss_pred cccccccccCc-cccceeeeeehhhhh
Confidence 33469999964 333457999999996
No 344
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=21.16 E-value=37 Score=26.38 Aligned_cols=28 Identities=25% Similarity=0.582 Sum_probs=16.5
Q ss_pred cccccCCCCceeeEEeeeeeeeeCCCCe
Q 045338 77 SKYFCEFCGKYAVKRKAVGIWGCKDCGK 104 (134)
Q Consensus 77 akY~CpfCGk~~VKR~avGIW~CkkCgk 104 (134)
-.|.|.-||....--.+.=|=.|.+||.
T Consensus 111 G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~ 138 (146)
T PF07295_consen 111 GTLVCENCGHEVELTHPERLPPCPKCGH 138 (146)
T ss_pred ceEecccCCCEEEecCCCcCCCCCCCCC
Confidence 4567777776542223444667777764
No 345
>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).
Probab=21.08 E-value=62 Score=22.95 Aligned_cols=26 Identities=31% Similarity=0.782 Sum_probs=20.2
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
.|..||..... .-.|.|.|..|.-=|
T Consensus 8 ~C~VCg~~a~g-~hyGv~sC~aCk~FF 33 (92)
T cd07163 8 PCKVCGDRSSG-KHYGIYACDGCSGFF 33 (92)
T ss_pred CCcccCCcCcc-cEECceeeeeeeeEE
Confidence 59999987655 477899999997443
No 346
>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or hetero
Probab=20.98 E-value=62 Score=21.71 Aligned_cols=25 Identities=28% Similarity=0.683 Sum_probs=17.9
Q ss_pred cCCCCceeeEEeeeeeeeeCCCCeeE
Q 045338 81 CEFCGKYAVKRKAVGIWGCKDCGKVK 106 (134)
Q Consensus 81 CpfCGk~~VKR~avGIW~CkkCgkt~ 106 (134)
|..||.++.. .-.|.|.|..|.-=|
T Consensus 1 C~vC~~~~~~-~hygv~sC~aC~~FF 25 (72)
T cd06916 1 CAVCGDKASG-YHYGVLTCEGCKGFF 25 (72)
T ss_pred CCccCccCcc-cEECcceeeeeeeeE
Confidence 6788876644 457889999997433
No 347
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=20.93 E-value=37 Score=23.09 Aligned_cols=13 Identities=23% Similarity=0.626 Sum_probs=6.0
Q ss_pred hhcccccCCCCce
Q 045338 75 QHSKYFCEFCGKY 87 (134)
Q Consensus 75 qhakY~CpfCGk~ 87 (134)
...+.+||.||..
T Consensus 21 S~~PatCP~C~a~ 33 (54)
T PF09237_consen 21 SEQPATCPICGAV 33 (54)
T ss_dssp TS--EE-TTT--E
T ss_pred cCCCCCCCcchhh
Confidence 4456799999875
No 348
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=20.78 E-value=42 Score=30.75 Aligned_cols=41 Identities=22% Similarity=0.421 Sum_probs=25.3
Q ss_pred CchhhHhHHHHHHhh-------hcccccCCCCceeeEEeeeeeeeeCCCCee
Q 045338 61 GASLRKQIKKMEVSQ-------HSKYFCEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 61 GaslRK~vkkIE~sq-------hakY~CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
-..+.+.|+.+-... .....|+.||.... +. .|.|..||..
T Consensus 494 ~~al~~lv~~a~~~~~~y~~~~~p~~~C~~CG~~~~-~~---~~~CP~CGs~ 541 (555)
T cd01675 494 PEALEALVKKAAKRGVIYFGINTPIDICNDCGYIGE-GE---GFKCPKCGSE 541 (555)
T ss_pred HHHHHHHHHHHHHcCCceEEEecCCccCCCCCCCCc-CC---CCCCcCCCCc
Confidence 356777777765431 11237999997443 11 3999999854
No 349
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.75 E-value=68 Score=28.91 Aligned_cols=28 Identities=25% Similarity=0.494 Sum_probs=15.1
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~A 107 (134)
.||.|+-.-+--...+.=.|..||++..
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCcCC
Confidence 3777775443323444446666665554
No 350
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=20.71 E-value=79 Score=21.22 Aligned_cols=28 Identities=29% Similarity=0.418 Sum_probs=16.3
Q ss_pred ccCCCCceee-EEeeeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYAV-KRKAVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~V-KR~avGIW~CkkCgkt~A 107 (134)
.||-|++..+ ==.+.-.=.|..|+.+.+
T Consensus 9 kCp~C~~~q~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp E-TTT-SEEEEETT-SS-EE-SSSTSEEE
T ss_pred ECCCCCCeeEEEecCCeEEEcccCCCEec
Confidence 6999998763 223445558999998874
No 351
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=20.69 E-value=76 Score=22.51 Aligned_cols=26 Identities=19% Similarity=0.588 Sum_probs=19.3
Q ss_pred cccccCCCCce-eeEEeeeeee--------------eeCCC
Q 045338 77 SKYFCEFCGKY-AVKRKAVGIW--------------GCKDC 102 (134)
Q Consensus 77 akY~CpfCGk~-~VKR~avGIW--------------~CkkC 102 (134)
..|.|+-|++. .-.++.+-|| .|++|
T Consensus 4 grF~C~~C~~~W~S~~v~i~f~~~~~g~v~~rv~~Q~C~~C 44 (98)
T PF13695_consen 4 GRFQCSKCSRGWTSAKVWILFHMYRGGQVNMRVFGQRCKKC 44 (98)
T ss_pred EEEECCCCCCCCccCEEEEEEEEcCCCeEEEEEECCCCCCC
Confidence 46899999765 4555667666 79999
No 352
>PHA00689 hypothetical protein
Probab=20.31 E-value=41 Score=23.07 Aligned_cols=15 Identities=27% Similarity=0.665 Sum_probs=12.3
Q ss_pred cccCCCCceeeEEee
Q 045338 79 YFCEFCGKYAVKRKA 93 (134)
Q Consensus 79 Y~CpfCGk~~VKR~a 93 (134)
-+|..|||+.++.+.
T Consensus 18 vtckrcgktglrwed 32 (62)
T PHA00689 18 VTCKRCGKTGLRWED 32 (62)
T ss_pred eehhhccccCceeec
Confidence 479999999988653
No 353
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=20.29 E-value=76 Score=24.40 Aligned_cols=29 Identities=14% Similarity=0.232 Sum_probs=24.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCCeeEecc
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCGKVKAGG 109 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCgkt~AGG 109 (134)
.||.|...-+-+.+. ...|..|...|+..
T Consensus 5 ~cp~c~sEytYed~~-~~~cpec~~ew~~~ 33 (112)
T COG2824 5 PCPKCNSEYTYEDGG-QLICPECAHEWNEN 33 (112)
T ss_pred CCCccCCceEEecCc-eEeCchhccccccc
Confidence 699999998887766 88999999887744
No 354
>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul
Probab=20.24 E-value=39 Score=23.61 Aligned_cols=23 Identities=30% Similarity=0.642 Sum_probs=18.4
Q ss_pred ccCCCCceeeEEeeeeeeeeCCCC
Q 045338 80 FCEFCGKYAVKRKAVGIWGCKDCG 103 (134)
Q Consensus 80 ~CpfCGk~~VKR~avGIW~CkkCg 103 (134)
.|..||..+.. .-.|.|.|..|.
T Consensus 5 ~C~VCg~~a~g-~hyGv~sC~aCk 27 (82)
T cd07173 5 TCLICGDEASG-CHYGALTCGSCK 27 (82)
T ss_pred CCeecCCcCcc-eEECcchhhhHH
Confidence 59999987654 458999999996
No 355
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=20.17 E-value=43 Score=30.38 Aligned_cols=28 Identities=29% Similarity=0.827 Sum_probs=23.7
Q ss_pred ccCCCCceeeEEe--eeeeeeeCCCCeeEe
Q 045338 80 FCEFCGKYAVKRK--AVGIWGCKDCGKVKA 107 (134)
Q Consensus 80 ~CpfCGk~~VKR~--avGIW~CkkCgkt~A 107 (134)
+|..||..++.+. .-|..+|..|...++
T Consensus 276 vCd~CGn~rLe~~pe~rg~~~C~~Cs~~V~ 305 (389)
T PF14951_consen 276 VCDRCGNGRLEQSPEDRGAFSCGDCSRVVT 305 (389)
T ss_pred cccccCCccceeCccCCCceeccchhhhcc
Confidence 7999999987764 478999999998776
No 356
>cd06957 NR_DBD_PNR_like_2 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers. The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members
Probab=20.06 E-value=70 Score=22.11 Aligned_cols=24 Identities=29% Similarity=0.869 Sum_probs=17.0
Q ss_pred cCCCCceeeEEeeeeeeeeCCCCee
Q 045338 81 CEFCGKYAVKRKAVGIWGCKDCGKV 105 (134)
Q Consensus 81 CpfCGk~~VKR~avGIW~CkkCgkt 105 (134)
|..||..+.. .-.|.|.|..|.-=
T Consensus 1 C~VCg~~~~g-~hyGv~sC~aCk~F 24 (82)
T cd06957 1 CKVCGDKSYG-KHYGVYCCDGCSCF 24 (82)
T ss_pred CCccCccCcc-eEECcceEeeeeeE
Confidence 6778876544 36788889888743
Done!