Query 037395
Match_columns 121
No_of_seqs 106 out of 218
Neff 1.9
Searched_HMMs 46136
Date Fri Mar 29 11:47:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037395.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037395hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK03976 rpl37ae 50S ribosomal 99.8 9.1E-22 2E-26 139.5 2.5 53 65-121 16-68 (90)
2 PF01780 Ribosomal_L37ae: Ribo 99.8 6E-22 1.3E-26 140.4 1.2 52 66-121 16-67 (90)
3 TIGR00280 L37a ribosomal prote 99.8 1.2E-21 2.6E-26 139.3 2.4 53 65-121 15-67 (91)
4 PTZ00255 60S ribosomal protein 99.8 1.4E-21 3.1E-26 138.5 2.3 53 65-121 16-68 (90)
5 KOG0402 60S ribosomal protein 99.8 5.6E-20 1.2E-24 132.3 -0.2 52 66-121 17-68 (92)
6 COG1997 RPL43A Ribosomal prote 99.7 9.4E-18 2E-22 119.9 1.3 52 66-121 16-67 (89)
7 PF12760 Zn_Tnp_IS1595: Transp 96.8 0.00096 2.1E-08 40.7 2.3 32 85-116 14-46 (46)
8 TIGR03655 anti_R_Lar restricti 96.3 0.0032 7E-08 39.3 2.4 27 91-117 3-36 (53)
9 PRK00432 30S ribosomal protein 95.0 0.013 2.7E-07 37.4 1.2 27 90-117 21-47 (50)
10 PF07282 OrfB_Zn_ribbon: Putat 94.7 0.024 5.1E-07 35.8 2.0 28 90-117 29-56 (69)
11 PRK00398 rpoP DNA-directed RNA 93.2 0.065 1.4E-06 32.4 1.9 29 89-117 3-31 (46)
12 PRK09710 lar restriction allev 93.2 0.066 1.4E-06 36.7 2.0 28 90-117 7-37 (64)
13 PHA00626 hypothetical protein 92.9 0.078 1.7E-06 36.2 2.1 29 91-119 2-35 (59)
14 PF08271 TF_Zn_Ribbon: TFIIB z 92.9 0.051 1.1E-06 32.5 1.1 29 90-118 1-30 (43)
15 COG0675 Transposase and inacti 92.7 0.076 1.6E-06 38.9 1.9 23 90-117 310-332 (364)
16 smart00661 RPOL9 RNA polymeras 92.2 0.11 2.4E-06 30.9 1.9 28 91-118 2-31 (52)
17 PF08273 Prim_Zn_Ribbon: Zinc- 92.2 0.1 2.2E-06 32.4 1.7 26 90-115 4-34 (40)
18 PF08646 Rep_fac-A_C: Replicat 91.0 0.12 2.5E-06 36.6 1.3 27 90-117 19-47 (146)
19 PF14354 Lar_restr_allev: Rest 90.1 0.18 3.8E-06 31.2 1.4 26 90-115 4-37 (61)
20 PHA02942 putative transposase; 89.5 0.19 4.1E-06 42.1 1.5 27 90-117 326-352 (383)
21 COG1998 RPS31 Ribosomal protei 88.0 0.25 5.5E-06 32.9 1.0 28 90-117 20-47 (51)
22 PRK14892 putative transcriptio 87.1 0.42 9E-06 34.4 1.8 39 73-116 9-51 (99)
23 COG4888 Uncharacterized Zn rib 86.5 0.77 1.7E-05 34.2 3.0 30 89-118 22-57 (104)
24 PF06689 zf-C4_ClpX: ClpX C4-t 86.3 0.15 3.3E-06 30.9 -0.7 25 89-113 1-30 (41)
25 COG3677 Transposase and inacti 86.1 0.43 9.4E-06 34.9 1.5 36 83-118 23-64 (129)
26 PF11781 RRN7: RNA polymerase 85.7 0.5 1.1E-05 28.4 1.4 26 91-117 10-35 (36)
27 cd04476 RPA1_DBD_C RPA1_DBD_C: 85.0 0.4 8.7E-06 34.4 0.9 27 90-117 35-61 (166)
28 PF05129 Elf1: Transcription e 84.4 1.6 3.6E-05 29.9 3.6 29 90-118 23-57 (81)
29 TIGR03831 YgiT_finger YgiT-typ 84.3 0.75 1.6E-05 26.3 1.6 15 104-118 29-43 (46)
30 PRK12366 replication factor A; 84.0 0.4 8.7E-06 42.6 0.6 26 89-116 532-557 (637)
31 smart00834 CxxC_CXXC_SSSS Puta 83.6 0.97 2.1E-05 25.6 1.9 27 90-116 6-35 (41)
32 PF09538 FYDLN_acid: Protein o 82.6 0.47 1E-05 34.3 0.4 27 88-117 8-36 (108)
33 PF03811 Zn_Tnp_IS1: InsA N-te 81.2 1.1 2.3E-05 27.2 1.5 24 90-113 6-35 (36)
34 COG1571 Predicted DNA-binding 80.9 0.45 9.8E-06 41.8 -0.3 28 90-118 351-378 (421)
35 TIGR01384 TFS_arch transcripti 80.2 3.1 6.8E-05 28.1 3.7 32 90-121 63-104 (104)
36 smart00440 ZnF_C2C2 C2C2 Zinc 79.2 4.3 9.2E-05 24.4 3.7 29 90-118 1-39 (40)
37 PF04606 Ogr_Delta: Ogr/Delta- 79.2 2 4.3E-05 26.3 2.3 29 91-119 1-39 (47)
38 smart00778 Prim_Zn_Ribbon Zinc 77.2 1.4 3.1E-05 26.9 1.2 26 90-115 4-33 (37)
39 PF10571 UPF0547: Uncharacteri 76.9 0.93 2E-05 25.8 0.3 24 91-118 2-25 (26)
40 PF05605 zf-Di19: Drought indu 74.6 1.3 2.8E-05 27.3 0.6 9 89-97 2-10 (54)
41 PF08792 A2L_zn_ribbon: A2L zi 74.4 4.4 9.6E-05 24.0 2.8 29 90-118 4-32 (33)
42 PF02150 RNA_POL_M_15KD: RNA p 74.1 1.7 3.6E-05 25.8 0.9 28 91-118 3-31 (35)
43 PF08772 NOB1_Zn_bind: Nin one 74.0 1.6 3.6E-05 30.0 1.0 20 88-107 23-42 (73)
44 smart00400 ZnF_CHCC zinc finge 73.6 2.8 6.1E-05 25.8 1.9 26 90-115 3-31 (55)
45 PRK00423 tfb transcription ini 73.5 2 4.3E-05 34.6 1.5 29 90-118 12-41 (310)
46 PF03604 DNA_RNApol_7kD: DNA d 72.7 0.64 1.4E-05 27.6 -1.1 26 90-117 1-27 (32)
47 TIGR01391 dnaG DNA primase, ca 72.7 2.5 5.4E-05 35.4 1.9 26 90-115 35-63 (415)
48 PF13453 zf-TFIIB: Transcripti 72.6 5.1 0.00011 23.6 2.8 27 91-117 1-29 (41)
49 PRK09678 DNA-binding transcrip 72.1 3.8 8.2E-05 28.1 2.4 29 90-118 2-40 (72)
50 cd00729 rubredoxin_SM Rubredox 72.0 3 6.4E-05 24.5 1.6 14 107-120 2-15 (34)
51 PF01096 TFIIS_C: Transcriptio 69.8 11 0.00024 22.5 3.8 27 91-117 2-38 (39)
52 PF01529 zf-DHHC: DHHC palmito 69.5 3.9 8.5E-05 28.6 2.1 37 78-118 37-73 (174)
53 PRK08402 replication factor A; 69.4 2.3 5E-05 35.9 1.1 28 88-115 211-238 (355)
54 PF01807 zf-CHC2: CHC2 zinc fi 69.2 4.1 8.8E-05 27.9 2.1 26 90-115 34-62 (97)
55 PF01599 Ribosomal_S27: Riboso 69.1 4.5 9.8E-05 26.1 2.1 27 90-116 19-47 (47)
56 COG2888 Predicted Zn-ribbon RN 68.6 1.9 4.1E-05 29.6 0.3 13 89-101 27-39 (61)
57 TIGR02098 MJ0042_CXXC MJ0042 f 68.5 3.2 7E-05 23.7 1.3 29 90-118 3-36 (38)
58 PF09723 Zn-ribbon_8: Zinc rib 67.8 3.5 7.6E-05 24.8 1.4 15 89-103 26-40 (42)
59 PRK05667 dnaG DNA primase; Val 67.0 4 8.8E-05 36.2 2.1 26 90-115 37-65 (580)
60 COG2956 Predicted N-acetylgluc 66.4 3.8 8.2E-05 36.3 1.8 25 87-115 352-376 (389)
61 PF01927 Mut7-C: Mut7-C RNAse 66.2 5.5 0.00012 28.8 2.4 31 90-120 92-137 (147)
62 PF01396 zf-C4_Topoisom: Topoi 65.3 6.7 0.00015 23.5 2.2 28 90-117 2-34 (39)
63 COG1592 Rubrerythrin [Energy p 64.7 3.5 7.5E-05 32.1 1.1 13 107-119 134-146 (166)
64 PF00096 zf-C2H2: Zinc finger, 64.6 5.2 0.00011 20.1 1.5 11 108-118 1-11 (23)
65 PF13894 zf-C2H2_4: C2H2-type 64.4 4.8 0.0001 19.5 1.3 10 108-117 1-10 (24)
66 PRK00241 nudC NADH pyrophospha 64.3 5.2 0.00011 31.8 2.1 28 90-117 100-127 (256)
67 COG2331 Uncharacterized protei 64.1 1.8 3.9E-05 31.2 -0.5 29 78-107 22-52 (82)
68 smart00659 RPOLCX RNA polymera 63.5 5.6 0.00012 24.7 1.7 27 89-117 2-29 (44)
69 COG1645 Uncharacterized Zn-fin 62.0 5.5 0.00012 30.3 1.8 38 78-118 18-55 (131)
70 PF13248 zf-ribbon_3: zinc-rib 61.8 2.3 5.1E-05 23.4 -0.2 23 90-116 3-25 (26)
71 PF07191 zinc-ribbons_6: zinc- 61.8 6.5 0.00014 27.2 2.0 26 90-117 2-27 (70)
72 cd00350 rubredoxin_like Rubred 61.1 5.1 0.00011 23.0 1.1 13 107-119 1-13 (33)
73 PF03119 DNA_ligase_ZBD: NAD-d 60.4 2.7 5.9E-05 24.0 -0.1 21 91-111 1-21 (28)
74 PRK11788 tetratricopeptide rep 60.0 6.5 0.00014 29.8 1.8 29 83-115 348-376 (389)
75 PRK14890 putative Zn-ribbon RN 59.9 4.2 9.2E-05 27.5 0.8 14 89-102 25-38 (59)
76 TIGR02605 CxxC_CxxC_SSSS putat 59.8 7.5 0.00016 23.3 1.8 13 91-103 28-40 (52)
77 PF13240 zinc_ribbon_2: zinc-r 59.6 2.9 6.4E-05 22.9 -0.0 21 92-116 2-22 (23)
78 TIGR00617 rpa1 replication fac 59.2 3.6 7.8E-05 36.6 0.4 28 89-117 474-503 (608)
79 PLN03086 PRLI-interacting fact 59.1 5.9 0.00013 36.0 1.7 50 68-118 410-464 (567)
80 PRK06294 coproporphyrinogen II 58.8 3.2 7E-05 33.8 0.1 28 69-100 1-28 (370)
81 COG1779 C4-type Zn-finger prot 58.0 10 0.00022 30.9 2.7 31 88-118 13-54 (201)
82 PF12773 DZR: Double zinc ribb 57.3 3 6.4E-05 24.8 -0.3 30 90-120 13-42 (50)
83 smart00531 TFIIE Transcription 55.9 3.8 8.3E-05 29.7 0.0 32 86-117 96-133 (147)
84 PF14803 Nudix_N_2: Nudix N-te 55.6 7.2 0.00016 23.3 1.2 26 91-116 2-31 (34)
85 PF07754 DUF1610: Domain of un 55.1 7.8 0.00017 22.1 1.2 7 90-96 17-23 (24)
86 PRK05342 clpX ATP-dependent pr 52.8 4 8.7E-05 34.6 -0.3 25 90-114 10-38 (412)
87 COG2075 RPL24A Ribosomal prote 52.0 12 0.00025 26.0 1.9 26 90-115 4-38 (66)
88 COG1996 RPC10 DNA-directed RNA 51.5 9.9 0.00021 24.8 1.4 27 90-116 7-33 (49)
89 PRK07562 ribonucleotide-diphos 50.1 10 0.00022 37.6 1.8 27 90-117 1191-1217(1220)
90 PF09297 zf-NADH-PPase: NADH p 48.8 9.8 0.00021 21.5 1.0 26 91-116 5-30 (32)
91 TIGR02159 PA_CoA_Oxy4 phenylac 48.8 4.5 9.7E-05 30.3 -0.6 28 90-117 106-140 (146)
92 PF13719 zinc_ribbon_5: zinc-r 47.7 12 0.00027 21.9 1.3 29 90-118 3-36 (37)
93 PF11672 DUF3268: Protein of u 46.6 13 0.00029 26.9 1.6 26 91-116 4-40 (102)
94 PRK04023 DNA polymerase II lar 46.2 8.9 0.00019 37.8 0.8 23 90-117 639-661 (1121)
95 PRK08173 DNA topoisomerase III 44.8 12 0.00026 34.9 1.4 26 90-117 625-650 (862)
96 PF13717 zinc_ribbon_4: zinc-r 44.3 14 0.00029 21.8 1.1 28 90-117 3-35 (36)
97 PF14471 DUF4428: Domain of un 44.1 2.6 5.7E-05 26.8 -2.1 27 91-118 1-31 (51)
98 PHA00732 hypothetical protein 44.0 11 0.00023 25.7 0.7 10 109-118 29-38 (79)
99 PRK07218 replication factor A; 43.9 11 0.00023 32.8 0.9 21 90-116 298-318 (423)
100 PF09180 ProRS-C_1: Prolyl-tRN 43.4 16 0.00035 23.8 1.5 21 86-106 45-65 (68)
101 PHA02540 61 DNA primase; Provi 42.8 22 0.00048 30.2 2.6 26 90-115 28-63 (337)
102 PF12874 zf-met: Zinc-finger o 42.4 21 0.00045 18.2 1.5 12 108-119 1-12 (25)
103 PRK08665 ribonucleotide-diphos 42.3 10 0.00022 34.9 0.5 25 91-117 726-750 (752)
104 PRK07220 DNA topoisomerase I; 41.5 20 0.00044 32.6 2.3 27 89-115 635-665 (740)
105 PRK04351 hypothetical protein; 41.2 24 0.00053 26.5 2.3 29 89-117 112-142 (149)
106 PF08274 PhnA_Zn_Ribbon: PhnA 41.1 16 0.00034 21.5 1.1 26 91-117 4-29 (30)
107 PF14353 CpXC: CpXC protein 40.9 15 0.00033 25.5 1.1 10 90-99 39-48 (128)
108 PF14311 DUF4379: Domain of un 40.3 18 0.00038 22.3 1.2 11 108-118 29-39 (55)
109 PF06676 DUF1178: Protein of u 40.1 17 0.00037 27.8 1.4 14 90-103 33-46 (148)
110 PRK14811 formamidopyrimidine-D 40.1 23 0.0005 28.3 2.2 25 91-116 237-264 (269)
111 PF04071 zf-like: Cysteine-ric 40.0 18 0.00038 25.7 1.4 13 103-115 45-59 (86)
112 PF08996 zf-DNA_Pol: DNA Polym 39.9 19 0.00041 27.2 1.6 28 90-117 19-55 (188)
113 COG1656 Uncharacterized conser 39.9 9.9 0.00022 30.0 0.1 29 89-117 97-140 (165)
114 PF13465 zf-H2C2_2: Zinc-finge 39.5 22 0.00047 19.2 1.4 9 90-98 15-23 (26)
115 PF00130 C1_1: Phorbol esters/ 39.5 24 0.00052 20.8 1.7 25 90-117 12-38 (53)
116 PF03956 DUF340: Membrane prot 39.3 4.9 0.00011 31.1 -1.7 19 41-59 162-180 (191)
117 KOG3576 Ovo and related transc 38.7 4.2 9.1E-05 34.4 -2.3 76 43-118 76-184 (267)
118 smart00290 ZnF_UBP Ubiquitin C 38.4 25 0.00053 20.6 1.6 23 91-119 1-23 (50)
119 COG2158 Uncharacterized protei 38.4 19 0.00041 27.3 1.4 26 90-115 43-70 (112)
120 smart00731 SprT SprT homologue 38.0 32 0.00069 24.6 2.4 29 89-117 112-143 (146)
121 PRK03681 hypA hydrogenase nick 37.7 18 0.00038 25.7 1.1 25 90-115 71-95 (114)
122 TIGR01385 TFSII transcription 37.1 26 0.00056 29.1 2.1 29 89-117 258-296 (299)
123 PF10263 SprT-like: SprT-like 37.0 27 0.00058 24.3 1.9 29 89-117 123-153 (157)
124 PRK14810 formamidopyrimidine-D 35.4 30 0.00066 27.6 2.2 23 91-114 246-271 (272)
125 PHA00733 hypothetical protein 35.2 9.5 0.00021 27.6 -0.6 30 89-118 73-110 (128)
126 PRK08208 coproporphyrinogen II 33.7 12 0.00026 31.2 -0.4 20 79-99 41-60 (430)
127 PRK06386 replication factor A; 33.5 18 0.0004 30.9 0.7 21 90-116 237-257 (358)
128 PRK00420 hypothetical protein; 33.5 26 0.00055 25.8 1.4 27 90-117 24-50 (112)
129 PF09082 DUF1922: Domain of un 33.4 21 0.00046 24.7 0.9 25 91-117 5-29 (68)
130 PRK04860 hypothetical protein; 32.6 16 0.00035 27.8 0.2 29 89-118 119-154 (160)
131 PHA02998 RNA polymerase subuni 32.6 45 0.00098 27.3 2.7 31 88-118 142-182 (195)
132 smart00355 ZnF_C2H2 zinc finge 32.4 20 0.00042 17.1 0.4 9 90-98 1-9 (26)
133 COG1594 RPB9 DNA-directed RNA 32.4 49 0.0011 23.8 2.7 29 89-117 72-110 (113)
134 PF01249 Ribosomal_S21e: Ribos 31.9 8.9 0.00019 27.2 -1.2 34 34-69 11-44 (81)
135 PF02892 zf-BED: BED zinc fing 31.8 25 0.00054 20.2 0.9 10 70-79 2-11 (45)
136 PF01363 FYVE: FYVE zinc finge 31.5 35 0.00075 21.2 1.6 10 88-97 24-33 (69)
137 COG3809 Uncharacterized protei 31.4 41 0.0009 24.6 2.1 28 91-118 3-32 (88)
138 PHA00616 hypothetical protein 31.4 15 0.00031 23.4 -0.2 10 90-99 2-11 (44)
139 PF03107 C1_2: C1 domain; Int 31.3 47 0.001 18.6 1.9 23 91-116 2-24 (30)
140 KOG2462 C2H2-type Zn-finger pr 31.3 27 0.00058 29.7 1.3 41 75-118 116-172 (279)
141 PF11023 DUF2614: Protein of u 31.2 20 0.00044 27.0 0.5 25 88-116 68-94 (114)
142 KOG1311 DHHC-type Zn-finger pr 31.2 21 0.00045 28.0 0.6 24 90-117 114-137 (299)
143 PF14205 Cys_rich_KTR: Cystein 30.9 25 0.00053 23.7 0.8 27 90-116 5-37 (55)
144 cd06956 NR_DBD_RXR DNA-binding 30.7 22 0.00049 23.5 0.6 24 90-114 1-24 (77)
145 COG2051 RPS27A Ribosomal prote 30.7 56 0.0012 22.8 2.6 29 90-118 20-49 (67)
146 COG1379 PHP family phosphoeste 30.4 9.4 0.0002 34.0 -1.5 40 77-120 238-278 (403)
147 PF13597 NRDD: Anaerobic ribon 29.8 31 0.00067 30.4 1.5 23 89-116 491-513 (546)
148 PF06397 Desulfoferrod_N: Desu 29.7 38 0.00082 20.7 1.4 12 106-117 5-16 (36)
149 PF05191 ADK_lid: Adenylate ki 28.9 41 0.00089 20.1 1.5 10 108-117 2-11 (36)
150 PLN02459 probable adenylate ki 28.7 4.5 9.7E-05 32.9 -3.6 16 52-67 109-124 (261)
151 PRK01103 formamidopyrimidine/5 28.7 45 0.00097 26.4 2.1 24 91-115 247-273 (274)
152 PRK13945 formamidopyrimidine-D 28.6 38 0.00081 27.1 1.7 23 91-114 256-281 (282)
153 PF06061 Baculo_ME53: Baculovi 28.3 27 0.00058 29.7 0.8 36 80-116 251-286 (327)
154 PRK00415 rps27e 30S ribosomal 28.3 51 0.0011 22.2 2.0 30 89-118 11-41 (59)
155 PF00641 zf-RanBP: Zn-finger i 28.2 24 0.00052 19.4 0.4 11 106-116 3-13 (30)
156 smart00729 Elp3 Elongator prot 28.1 16 0.00036 24.4 -0.4 18 82-99 5-22 (216)
157 PRK05799 coproporphyrinogen II 27.9 18 0.00038 29.0 -0.3 21 79-100 5-25 (374)
158 KOG2463 Predicted RNA-binding 27.8 43 0.00092 29.8 2.0 19 89-107 257-275 (376)
159 KOG2593 Transcription initiati 27.8 27 0.00059 31.3 0.8 27 89-115 128-161 (436)
160 PF13912 zf-C2H2_6: C2H2-type 27.7 40 0.00086 17.4 1.2 9 109-117 3-11 (27)
161 PF09986 DUF2225: Uncharacteri 27.2 32 0.0007 26.6 1.0 42 49-97 13-56 (214)
162 PRK12286 rpmF 50S ribosomal pr 27.2 48 0.001 21.6 1.7 20 90-114 28-47 (57)
163 TIGR00100 hypA hydrogenase nic 27.1 96 0.0021 22.0 3.4 23 90-115 71-94 (115)
164 PF01753 zf-MYND: MYND finger; 27.1 51 0.0011 18.7 1.6 19 92-117 1-19 (37)
165 TIGR03830 CxxCG_CxxCG_HTH puta 27.0 56 0.0012 21.8 2.1 26 91-118 17-42 (127)
166 PRK08898 coproporphyrinogen II 27.0 25 0.00054 29.0 0.4 22 78-100 20-41 (394)
167 PRK07111 anaerobic ribonucleos 26.8 30 0.00065 31.9 1.0 21 90-115 681-701 (735)
168 PRK03824 hypA hydrogenase nick 26.8 95 0.0021 22.6 3.4 10 90-99 71-80 (135)
169 PF00569 ZZ: Zinc finger, ZZ t 26.5 54 0.0012 19.8 1.7 22 90-114 5-26 (46)
170 smart00547 ZnF_RBZ Zinc finger 26.5 22 0.00048 18.7 0.0 11 106-116 1-11 (26)
171 PF01783 Ribosomal_L32p: Ribos 26.3 22 0.00047 22.6 -0.0 20 90-114 27-46 (56)
172 PF13353 Fer4_12: 4Fe-4S singl 26.1 15 0.00033 24.4 -0.8 15 84-98 11-25 (139)
173 PF12677 DUF3797: Domain of un 26.0 34 0.00074 22.6 0.8 10 91-100 15-24 (49)
174 COG1096 Predicted RNA-binding 25.5 43 0.00093 27.0 1.5 24 91-116 151-174 (188)
175 cd00974 DSRD Desulforedoxin (D 25.4 58 0.0013 18.5 1.7 13 106-118 3-15 (34)
176 KOG3507 DNA-directed RNA polym 25.0 25 0.00055 24.3 0.1 26 90-117 21-47 (62)
177 PRK09058 coproporphyrinogen II 24.9 20 0.00042 30.3 -0.5 22 77-99 61-82 (449)
178 PRK05904 coproporphyrinogen II 24.9 20 0.00044 29.4 -0.5 21 79-100 8-28 (353)
179 TIGR01206 lysW lysine biosynth 24.8 50 0.0011 21.5 1.5 28 90-117 3-32 (54)
180 TIGR00311 aIF-2beta translatio 24.7 75 0.0016 23.7 2.6 25 91-116 99-127 (133)
181 TIGR00319 desulf_FeS4 desulfof 24.4 64 0.0014 18.2 1.7 13 106-118 6-18 (34)
182 cd01198 INT_ASSRA_C Archaeal s 24.1 29 0.00062 24.0 0.3 14 44-57 126-139 (186)
183 KOG1873 Ubiquitin-specific pro 24.0 32 0.00069 33.4 0.6 31 90-120 67-106 (877)
184 PRK07591 threonine synthase; V 23.4 38 0.00082 28.4 0.9 24 89-115 18-41 (421)
185 PF05741 zf-nanos: Nanos RNA b 23.3 31 0.00068 22.8 0.3 10 90-99 34-43 (55)
186 PRK08599 coproporphyrinogen II 23.2 24 0.00052 28.4 -0.3 19 80-99 4-22 (377)
187 PF07295 DUF1451: Protein of u 23.2 37 0.00081 25.6 0.7 28 89-116 112-139 (146)
188 PF13913 zf-C2HC_2: zinc-finge 23.2 43 0.00092 18.3 0.8 8 110-117 5-12 (25)
189 PF14319 Zn_Tnp_IS91: Transpos 23.1 46 0.001 23.6 1.1 27 90-116 43-69 (111)
190 PF05899 Cupin_3: Protein of u 23.1 47 0.001 21.4 1.1 16 102-117 6-21 (74)
191 COG3091 SprT Zn-dependent meta 22.9 54 0.0012 25.9 1.6 28 89-117 117-150 (156)
192 TIGR00354 polC DNA polymerase, 22.7 47 0.001 33.0 1.4 23 88-116 624-646 (1095)
193 PF00935 Ribosomal_L44: Riboso 22.5 66 0.0014 22.5 1.8 28 73-112 45-72 (77)
194 COG4643 Uncharacterized protei 22.5 33 0.00072 30.3 0.4 26 89-114 32-61 (366)
195 PHA02768 hypothetical protein; 22.2 34 0.00073 22.6 0.3 29 90-118 6-42 (55)
196 PF14447 Prok-RING_4: Prokaryo 22.2 40 0.00087 22.5 0.6 8 91-98 41-48 (55)
197 PF00412 LIM: LIM domain; Int 22.1 69 0.0015 18.6 1.6 10 110-119 29-38 (58)
198 PRK03988 translation initiatio 22.0 86 0.0019 23.5 2.4 26 91-116 104-132 (138)
199 KOG3486 40S ribosomal protein 21.8 63 0.0014 23.4 1.6 45 34-80 11-55 (83)
200 cd06968 NR_DBD_ROR DNA-binding 21.8 44 0.00096 23.3 0.8 24 90-114 6-29 (95)
201 PRK07220 DNA topoisomerase I; 21.6 85 0.0018 28.7 2.8 27 90-116 590-622 (740)
202 PRK14714 DNA polymerase II lar 21.6 43 0.00094 33.8 1.0 22 91-117 681-702 (1337)
203 PF01586 Basic: Myogenic Basic 21.5 32 0.0007 24.6 0.1 11 107-117 72-82 (86)
204 cd06960 NR_DBD_HNF4A DNA-bindi 21.5 46 0.001 21.8 0.8 22 92-114 1-22 (76)
205 PRK05654 acetyl-CoA carboxylas 21.3 17 0.00038 29.9 -1.5 27 90-116 28-55 (292)
206 TIGR03829 YokU_near_AblA uncha 20.9 1.1E+02 0.0024 21.9 2.7 18 91-108 1-19 (89)
207 PF03884 DUF329: Domain of unk 20.9 50 0.0011 21.8 0.9 13 89-101 2-14 (57)
208 PRK13347 coproporphyrinogen II 20.7 29 0.00062 29.2 -0.4 20 79-99 52-71 (453)
209 PF14206 Cys_rich_CPCC: Cystei 20.5 50 0.0011 23.0 0.8 26 89-114 1-27 (78)
210 PF01921 tRNA-synt_1f: tRNA sy 20.4 76 0.0017 27.4 2.1 28 90-117 175-209 (360)
211 PRK08270 anaerobic ribonucleos 20.2 43 0.00094 30.5 0.6 61 51-116 584-648 (656)
212 PRK14559 putative protein seri 20.2 42 0.00092 30.7 0.6 7 92-98 30-36 (645)
213 TIGR00515 accD acetyl-CoA carb 20.1 18 0.00039 29.8 -1.7 27 90-116 27-54 (285)
214 PRK10954 periplasmic protein d 20.1 22 0.00047 26.4 -1.0 17 77-97 38-54 (207)
215 CHL00174 accD acetyl-CoA carbo 20.1 18 0.00038 30.5 -1.7 27 90-116 39-66 (296)
216 TIGR00577 fpg formamidopyrimid 20.1 65 0.0014 25.6 1.5 22 91-113 247-271 (272)
No 1
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=99.83 E-value=9.1e-22 Score=139.52 Aligned_cols=53 Identities=26% Similarity=0.346 Sum_probs=51.0
Q ss_pred ccccccccccccchhhhhhhhhcceeecccCCCcceEEeEEEEeeeCCCCceEecCC
Q 037395 65 DQEGMNCWKPFVNPALMFYFVFACVAWGSWNYKYAIKRKVVGIWSCKYCGKVKAGGA 121 (121)
Q Consensus 65 ~~~g~~~~k~~~~~~lm~~~~~~~~htCPFCGK~kVKR~AVGIWkCkkCgktfAGGA 121 (121)
-.-|.++||+++++|.-||++ |+|||||+++|||.++|||+|++|+++|||||
T Consensus 16 ~RYG~slRK~v~kie~~q~a~----y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 16 ARYGRKIRKRVADIEEKMRAK----HVCPVCGRPKVKRVGTGIWECRKCGAKFAGGA 68 (90)
T ss_pred CccCHHHHHHHHHHHHHHhcC----ccCCCCCCCceEEEEEEEEEcCCCCCEEeCCc
Confidence 356999999999999999999 99999999999999999999999999999998
No 2
>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=99.83 E-value=6e-22 Score=140.44 Aligned_cols=52 Identities=33% Similarity=0.438 Sum_probs=48.7
Q ss_pred cccccccccccchhhhhhhhhcceeecccCCCcceEEeEEEEeeeCCCCceEecCC
Q 037395 66 QEGMNCWKPFVNPALMFYFVFACVAWGSWNYKYAIKRKVVGIWSCKYCGKVKAGGA 121 (121)
Q Consensus 66 ~~g~~~~k~~~~~~lm~~~~~~~~htCPFCGK~kVKR~AVGIWkCkkCgktfAGGA 121 (121)
.-|+++||+++++|..||.+ |+|||||+++|||+++|||+|++|+++|||||
T Consensus 16 RYG~slRK~vkkie~~q~~k----y~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGGA 67 (90)
T PF01780_consen 16 RYGASLRKRVKKIEISQHAK----YTCPFCGKTSVKRVATGIWKCKKCGKKFAGGA 67 (90)
T ss_dssp SSTHHHHHHHHHHHHHHHS-----BEESSSSSSEEEEEETTEEEETTTTEEEE-BS
T ss_pred CcCHHHHHHHHHHHHHHhCC----CcCCCCCCceeEEeeeEEeecCCCCCEEeCCC
Confidence 56999999999999999999 99999999999999999999999999999998
No 3
>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=99.83 E-value=1.2e-21 Score=139.31 Aligned_cols=53 Identities=26% Similarity=0.432 Sum_probs=51.0
Q ss_pred ccccccccccccchhhhhhhhhcceeecccCCCcceEEeEEEEeeeCCCCceEecCC
Q 037395 65 DQEGMNCWKPFVNPALMFYFVFACVAWGSWNYKYAIKRKVVGIWSCKYCGKVKAGGA 121 (121)
Q Consensus 65 ~~~g~~~~k~~~~~~lm~~~~~~~~htCPFCGK~kVKR~AVGIWkCkkCgktfAGGA 121 (121)
..-|.++||.++++|..||++ |+|||||+++|||.++|||+|++|+++|||||
T Consensus 15 ~RYG~slRK~v~kie~~q~a~----y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 15 PRYGLKLRRQVKKIEIQQKAK----YVCPFCGKKTVKRGSTGIWTCRKCGAKFAGGA 67 (91)
T ss_pred CccCHHHHHHHHHHHHHHhcC----ccCCCCCCCceEEEeeEEEEcCCCCCEEeCCc
Confidence 356999999999999999999 99999999999999999999999999999998
No 4
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=99.83 E-value=1.4e-21 Score=138.50 Aligned_cols=53 Identities=34% Similarity=0.490 Sum_probs=50.9
Q ss_pred ccccccccccccchhhhhhhhhcceeecccCCCcceEEeEEEEeeeCCCCceEecCC
Q 037395 65 DQEGMNCWKPFVNPALMFYFVFACVAWGSWNYKYAIKRKVVGIWSCKYCGKVKAGGA 121 (121)
Q Consensus 65 ~~~g~~~~k~~~~~~lm~~~~~~~~htCPFCGK~kVKR~AVGIWkCkkCgktfAGGA 121 (121)
..-|.++||+++++|.-||++ |+|||||+++|||.++|||+|++|+++|||||
T Consensus 16 ~RYG~slRK~v~kie~~q~a~----y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 16 TRYGASLRKQIKKIEISQHAK----YFCPFCGKHAVKRQAVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred CccCHHHHHHHHHHHHHHhCC----ccCCCCCCCceeeeeeEEEEcCCCCCEEeCCc
Confidence 356999999999999999999 99999999999999999999999999999997
No 5
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=99.76 E-value=5.6e-20 Score=132.32 Aligned_cols=52 Identities=37% Similarity=0.458 Sum_probs=50.4
Q ss_pred cccccccccccchhhhhhhhhcceeecccCCCcceEEeEEEEeeeCCCCceEecCC
Q 037395 66 QEGMNCWKPFVNPALMFYFVFACVAWGSWNYKYAIKRKVVGIWSCKYCGKVKAGGA 121 (121)
Q Consensus 66 ~~g~~~~k~~~~~~lm~~~~~~~~htCPFCGK~kVKR~AVGIWkCkkCgktfAGGA 121 (121)
.-|.||+|+.++++.-||++ |+|+||||..|||.|||||.|++|++++||||
T Consensus 17 rYGaSLrk~vKkiei~Qhak----y~CsfCGK~~vKR~AvGiW~C~~C~kv~agga 68 (92)
T KOG0402|consen 17 RYGASLRKMVKKIEIQQHAK----YTCSFCGKKTVKRKAVGIWKCGSCKKVVAGGA 68 (92)
T ss_pred hhhHHHHHHHHHHHHHHhhh----hhhhhcchhhhhhhceeEEecCCccceeccce
Confidence 46899999999999999999 99999999999999999999999999999997
No 6
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=99.67 E-value=9.4e-18 Score=119.93 Aligned_cols=52 Identities=25% Similarity=0.389 Sum_probs=49.9
Q ss_pred cccccccccccchhhhhhhhhcceeecccCCCcceEEeEEEEeeeCCCCceEecCC
Q 037395 66 QEGMNCWKPFVNPALMFYFVFACVAWGSWNYKYAIKRKVVGIWSCKYCGKVKAGGA 121 (121)
Q Consensus 66 ~~g~~~~k~~~~~~lm~~~~~~~~htCPFCGK~kVKR~AVGIWkCkkCgktfAGGA 121 (121)
.-|+.+++..+.+|.-++.+ |.||+||++.|||.++|||.|++||++|||||
T Consensus 16 RYG~~~Rrrv~~ie~~~~~~----~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGga 67 (89)
T COG1997 16 RYGSKLRRRVKEIEAQQRAK----HVCPFCGRTTVKRIATGIWKCRKCGAKFAGGA 67 (89)
T ss_pred ccchHHHHHHHHHHHHHhcC----CcCCCCCCcceeeeccCeEEcCCCCCeecccc
Confidence 46899999999999999999 99999999999999999999999999999997
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=96.83 E-value=0.00096 Score=40.66 Aligned_cols=32 Identities=19% Similarity=0.101 Sum_probs=25.9
Q ss_pred hhcceeecccCCCcceEEeEE-EEeeeCCCCce
Q 037395 85 VFACVAWGSWNYKYAIKRKVV-GIWSCKYCGKV 116 (121)
Q Consensus 85 ~~~~~htCPFCGK~kVKR~AV-GIWkCkkCgkt 116 (121)
...--.+||.||...+.+... +.|+|+.|+++
T Consensus 14 RW~~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 14 RWPDGFVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred cCCCCCCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 333446799999998888877 99999999874
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=96.34 E-value=0.0032 Score=39.32 Aligned_cols=27 Identities=15% Similarity=0.268 Sum_probs=21.7
Q ss_pred ecccCCCcce-EE------eEEEEeeeCCCCceE
Q 037395 91 WGSWNYKYAI-KR------KVVGIWSCKYCGKVK 117 (121)
Q Consensus 91 tCPFCGK~kV-KR------~AVGIWkCkkCgktf 117 (121)
.|||||...+ .| ...|+|.|..|+...
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCc
Confidence 6999998865 55 467899999999764
No 9
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=94.96 E-value=0.013 Score=37.36 Aligned_cols=27 Identities=15% Similarity=0.341 Sum_probs=22.6
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
-.||.||.. +-....+.|+|.+||++.
T Consensus 21 ~fCP~Cg~~-~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPRCGSG-FMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred CcCcCCCcc-hheccCCcEECCCcCCEE
Confidence 379999997 666666999999999985
No 10
>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=94.68 E-value=0.024 Score=35.77 Aligned_cols=28 Identities=18% Similarity=0.219 Sum_probs=25.0
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
-+||.||....++....+|.|..||.++
T Consensus 29 q~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 29 QTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred cCccCcccccccccccceEEcCCCCCEE
Confidence 5899999998888888999999999874
No 11
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.24 E-value=0.065 Score=32.38 Aligned_cols=29 Identities=14% Similarity=-0.019 Sum_probs=22.4
Q ss_pred eeecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 89 VAWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 89 ~htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
.|.|+-||.....-..++.++|..||..+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeE
Confidence 48899999986555555588999998754
No 12
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=93.20 E-value=0.066 Score=36.71 Aligned_cols=28 Identities=11% Similarity=0.065 Sum_probs=20.2
Q ss_pred eecccCCCcceEEeEEE---EeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVG---IWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVG---IWkCkkCgktf 117 (121)
-.|||||...+.=.+.+ +|.|.+|+...
T Consensus 7 KPCPFCG~~~~~v~~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 7 KPCPFCGCPSVTVKAISGYYRAKCNGCESRT 37 (64)
T ss_pred cCCCCCCCceeEEEecCceEEEEcCCCCcCc
Confidence 46999999975544443 46799998753
No 13
>PHA00626 hypothetical protein
Probab=92.94 E-value=0.078 Score=36.23 Aligned_cols=29 Identities=14% Similarity=0.071 Sum_probs=23.2
Q ss_pred ecccCCCcceEEeE-----EEEeeeCCCCceEec
Q 037395 91 WGSWNYKYAIKRKV-----VGIWSCKYCGKVKAG 119 (121)
Q Consensus 91 tCPFCGK~kVKR~A-----VGIWkCkkCgktfAG 119 (121)
.||.||...+.|-+ ..-+.|+.||+.++-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 59999997666633 478999999999864
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=92.90 E-value=0.051 Score=32.50 Aligned_cols=29 Identities=17% Similarity=0.081 Sum_probs=22.8
Q ss_pred eecccCCCcc-eEEeEEEEeeeCCCCceEe
Q 037395 90 AWGSWNYKYA-IKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 90 htCPFCGK~k-VKR~AVGIWkCkkCgktfA 118 (121)
++||.||... +--.+.|-..|+.||.++.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEee
Confidence 5799999986 4455789999999998764
No 15
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.70 E-value=0.076 Score=38.86 Aligned_cols=23 Identities=17% Similarity=0.224 Sum_probs=19.7
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
-+||-||. ...+.|.|..||.++
T Consensus 310 ~~C~~cg~-----~~~r~~~C~~cg~~~ 332 (364)
T COG0675 310 KTCPCCGH-----LSGRLFKCPRCGFVH 332 (364)
T ss_pred ccccccCC-----ccceeEECCCCCCee
Confidence 57999999 667889999999864
No 16
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=92.19 E-value=0.11 Score=30.94 Aligned_cols=28 Identities=14% Similarity=0.258 Sum_probs=21.4
Q ss_pred ecccCCCcceEEeEEE--EeeeCCCCceEe
Q 037395 91 WGSWNYKYAIKRKVVG--IWSCKYCGKVKA 118 (121)
Q Consensus 91 tCPFCGK~kVKR~AVG--IWkCkkCgktfA 118 (121)
.||.||.....+..-+ .|.|..||+.+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEE
Confidence 5999999876654432 899999998764
No 17
>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=92.18 E-value=0.1 Score=32.38 Aligned_cols=26 Identities=19% Similarity=0.412 Sum_probs=14.3
Q ss_pred eecccCCCc-ceE----EeEEEEeeeCCCCc
Q 037395 90 AWGSWNYKY-AIK----RKVVGIWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~-kVK----R~AVGIWkCkkCgk 115 (121)
-.||.||-. ..+ +...|-|.|+.|+.
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTTTB
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCCCC
Confidence 479999755 455 34569999999965
No 18
>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=91.02 E-value=0.12 Score=36.60 Aligned_cols=27 Identities=19% Similarity=0.254 Sum_probs=19.5
Q ss_pred eecc--cCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGS--WNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCP--FCGK~kVKR~AVGIWkCkkCgktf 117 (121)
.-|| .|+|. |...+.|.|.|.+|++.+
T Consensus 19 ~aC~~~~C~kK-v~~~~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 19 PACPNEKCNKK-VTENGDGSYRCEKCNKTV 47 (146)
T ss_dssp EE-TSTTTS-B--EEETTTEEEETTTTEEE
T ss_pred CCCCCccCCCE-eecCCCcEEECCCCCCcC
Confidence 5699 99886 444477899999999886
No 19
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=90.12 E-value=0.18 Score=31.18 Aligned_cols=26 Identities=15% Similarity=0.296 Sum_probs=16.3
Q ss_pred eecccCCCcceEEeE-EE------Ee-eeCCCCc
Q 037395 90 AWGSWNYKYAIKRKV-VG------IW-SCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~kVKR~A-VG------IW-kCkkCgk 115 (121)
..|||||...+.-.. .+ .+ .|..||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 469999987643332 22 11 2888886
No 20
>PHA02942 putative transposase; Provisional
Probab=89.49 E-value=0.19 Score=42.05 Aligned_cols=27 Identities=11% Similarity=0.052 Sum_probs=21.4
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
-+||.||... ++.+..+|.|..||.+.
T Consensus 326 q~Cs~CG~~~-~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 326 VSCPKCGHKM-VEIAHRYFHCPSCGYEN 352 (383)
T ss_pred ccCCCCCCcc-CcCCCCEEECCCCCCEe
Confidence 5799999764 45566789999999864
No 21
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=88.00 E-value=0.25 Score=32.91 Aligned_cols=28 Identities=14% Similarity=0.285 Sum_probs=17.3
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
-.||.||--.+==.----|.|.+||+|-
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCgyTe 47 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCGYTE 47 (51)
T ss_pred ccCCCCCCcchhhhcCceeEeccccceE
Confidence 5799999422110001139999999984
No 22
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=87.05 E-value=0.42 Score=34.38 Aligned_cols=39 Identities=23% Similarity=0.307 Sum_probs=25.2
Q ss_pred ccccchhhhhhhhhcceeecccCCCcce----EEeEEEEeeeCCCCce
Q 037395 73 KPFVNPALMFYFVFACVAWGSWNYKYAI----KRKVVGIWSCKYCGKV 116 (121)
Q Consensus 73 k~~~~~~lm~~~~~~~~htCPFCGK~kV----KR~AVGIWkCkkCgkt 116 (121)
|+.++..+--.-. .+||+||..+| .| .++.=.|..||.-
T Consensus 9 k~~~k~k~klpt~----f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~y 51 (99)
T PRK14892 9 KKIIRPKPKLPKI----FECPRCGKVSISVKIKK-NIAIITCGNCGLY 51 (99)
T ss_pred CCCcccccCCCcE----eECCCCCCeEeeeecCC-CcceEECCCCCCc
Confidence 3444444433333 68999996554 23 6778889999964
No 23
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=86.53 E-value=0.77 Score=34.20 Aligned_cols=30 Identities=17% Similarity=0.115 Sum_probs=23.5
Q ss_pred eeecccCCCcce-----E-EeEEEEeeeCCCCceEe
Q 037395 89 VAWGSWNYKYAI-----K-RKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 89 ~htCPFCGK~kV-----K-R~AVGIWkCkkCgktfA 118 (121)
..+|||||+.++ | -...|.=.|+.||..+.
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 368999999863 3 44788899999998764
No 24
>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=86.26 E-value=0.15 Score=30.94 Aligned_cols=25 Identities=20% Similarity=0.392 Sum_probs=13.1
Q ss_pred eeecccCCCcc--eEEeEE---EEeeeCCC
Q 037395 89 VAWGSWNYKYA--IKRKVV---GIWSCKYC 113 (121)
Q Consensus 89 ~htCPFCGK~k--VKR~AV---GIWkCkkC 113 (121)
+..|+||||.. +.+.-. |+.-|..|
T Consensus 1 ~~~CSFCgr~~~~v~~li~g~~~~~IC~~C 30 (41)
T PF06689_consen 1 EKRCSFCGRPESEVGRLISGPNGAYICDEC 30 (41)
T ss_dssp --B-TTT--BTTTSSSEEEES-SEEEEHHH
T ss_pred CCCccCCCCCHHHHhceecCCCCcEECHHH
Confidence 46899999984 666554 34666655
No 25
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=86.10 E-value=0.43 Score=34.95 Aligned_cols=36 Identities=11% Similarity=0.097 Sum_probs=25.8
Q ss_pred hhhhcce-eecccCCCcceEEeE-----EEEeeeCCCCceEe
Q 037395 83 YFVFACV-AWGSWNYKYAIKRKV-----VGIWSCKYCGKVKA 118 (121)
Q Consensus 83 ~~~~~~~-htCPFCGK~kVKR~A-----VGIWkCkkCgktfA 118 (121)
++.++.. -.||+|+...++|.+ .-=|.|++|+++|.
T Consensus 23 ~~~~~~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 23 AIRMQITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred HHhhhcccCcCCCCCccceeeECCccccccccccCCcCccee
Confidence 3444444 789999988865554 33589999999984
No 26
>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=85.69 E-value=0.5 Score=28.39 Aligned_cols=26 Identities=15% Similarity=0.105 Sum_probs=22.7
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
.|+.||.. .-+..-|-|.|..||.+.
T Consensus 10 ~C~~C~~~-~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSR-WFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCe-EeEccCCEEEhhhCceEc
Confidence 39999999 888889999999999753
No 27
>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=85.05 E-value=0.4 Score=34.45 Aligned_cols=27 Identities=19% Similarity=0.204 Sum_probs=19.8
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
.-||-|.|.. .-...|.|.|.+|++++
T Consensus 35 ~aC~~C~kkv-~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 35 PACPGCNKKV-VEEGNGTYRCEKCNKSV 61 (166)
T ss_pred ccccccCccc-EeCCCCcEECCCCCCcC
Confidence 3488898864 33333899999999875
No 28
>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=84.36 E-value=1.6 Score=29.86 Aligned_cols=29 Identities=24% Similarity=0.478 Sum_probs=16.4
Q ss_pred eecccCC-Ccc--eE---EeEEEEeeeCCCCceEe
Q 037395 90 AWGSWNY-KYA--IK---RKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 90 htCPFCG-K~k--VK---R~AVGIWkCkkCgktfA 118 (121)
.+||||+ +.+ ++ ...+|+=.|+.|+..+.
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQ 57 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEESSS--EEE
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEE
Confidence 5799999 544 22 24799999999998763
No 29
>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=84.27 E-value=0.75 Score=26.29 Aligned_cols=15 Identities=27% Similarity=0.454 Sum_probs=11.3
Q ss_pred EEEEeeeCCCCceEe
Q 037395 104 VVGIWSCKYCGKVKA 118 (121)
Q Consensus 104 AVGIWkCkkCgktfA 118 (121)
.+--|.|..||..+.
T Consensus 29 ~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 29 NVPALVCPQCGEEYL 43 (46)
T ss_pred CCCccccccCCCEee
Confidence 346688999998764
No 30
>PRK12366 replication factor A; Reviewed
Probab=84.00 E-value=0.4 Score=42.62 Aligned_cols=26 Identities=27% Similarity=0.479 Sum_probs=20.7
Q ss_pred eeecccCCCcceEEeEEEEeeeCCCCce
Q 037395 89 VAWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 89 ~htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
-.-||-|.|.-+. .-|.|.|.+|+++
T Consensus 532 y~aCp~CnkKv~~--~~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCPNCRKRVEE--VDGEYICEFCGEV 557 (637)
T ss_pred EecccccCeEeEc--CCCcEECCCCCCC
Confidence 3569999886553 5699999999986
No 31
>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=83.62 E-value=0.97 Score=25.63 Aligned_cols=27 Identities=11% Similarity=-0.102 Sum_probs=17.4
Q ss_pred eecccCCCcceEEeE---EEEeeeCCCCce
Q 037395 90 AWGSWNYKYAIKRKV---VGIWSCKYCGKV 116 (121)
Q Consensus 90 htCPFCGK~kVKR~A---VGIWkCkkCgkt 116 (121)
|.|+.||+.--.... ..+..|..||..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 788888885432232 346778888863
No 32
>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=82.64 E-value=0.47 Score=34.27 Aligned_cols=27 Identities=11% Similarity=0.030 Sum_probs=19.6
Q ss_pred ceeecccCCCcc--eEEeEEEEeeeCCCCceE
Q 037395 88 CVAWGSWNYKYA--IKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 88 ~~htCPFCGK~k--VKR~AVGIWkCkkCgktf 117 (121)
-|++||.||+.- +.|.= =.|.+||..|
T Consensus 8 tKR~Cp~CG~kFYDLnk~P---ivCP~CG~~~ 36 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDP---IVCPKCGTEF 36 (108)
T ss_pred CcccCCCCcchhccCCCCC---ccCCCCCCcc
Confidence 468999999873 55532 2499999876
No 33
>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=81.20 E-value=1.1 Score=27.17 Aligned_cols=24 Identities=17% Similarity=0.273 Sum_probs=19.1
Q ss_pred eecccCCCcc-eEEeEE-----EEeeeCCC
Q 037395 90 AWGSWNYKYA-IKRKVV-----GIWSCKYC 113 (121)
Q Consensus 90 htCPFCGK~k-VKR~AV-----GIWkCkkC 113 (121)
-.||+|+.+. |+|.+. =-|.|+.|
T Consensus 6 v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 4799999998 999754 35778777
No 34
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=80.88 E-value=0.45 Score=41.78 Aligned_cols=28 Identities=18% Similarity=0.153 Sum_probs=19.7
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceEe
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktfA 118 (121)
-.||+||.. ||=.+-+=|+|++||+++.
T Consensus 351 p~Cp~Cg~~-m~S~G~~g~rC~kCg~~~~ 378 (421)
T COG1571 351 PVCPRCGGR-MKSAGRNGFRCKKCGTRAR 378 (421)
T ss_pred CCCCccCCc-hhhcCCCCcccccccccCC
Confidence 379999876 3323332599999999764
No 35
>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=80.17 E-value=3.1 Score=28.06 Aligned_cols=32 Identities=13% Similarity=0.007 Sum_probs=25.1
Q ss_pred eecccCCCcceEE----------eEEEEeeeCCCCceEecCC
Q 037395 90 AWGSWNYKYAIKR----------KVVGIWSCKYCGKVKAGGA 121 (121)
Q Consensus 90 htCPFCGK~kVKR----------~AVGIWkCkkCgktfAGGA 121 (121)
..||.||...+-- -.+=++.|.+|+++|..++
T Consensus 63 ~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~~ 104 (104)
T TIGR01384 63 VECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREYE 104 (104)
T ss_pred CCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeCc
Confidence 6899999987422 2567899999999997653
No 36
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=79.23 E-value=4.3 Score=24.45 Aligned_cols=29 Identities=17% Similarity=0.156 Sum_probs=21.5
Q ss_pred eecccCCCcceE------E----eEEEEeeeCCCCceEe
Q 037395 90 AWGSWNYKYAIK------R----KVVGIWSCKYCGKVKA 118 (121)
Q Consensus 90 htCPFCGK~kVK------R----~AVGIWkCkkCgktfA 118 (121)
+.||.||...+- | ..+=++.|.+|+++|.
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 479999987532 2 2367999999999874
No 37
>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=79.20 E-value=2 Score=26.33 Aligned_cols=29 Identities=17% Similarity=0.135 Sum_probs=21.4
Q ss_pred ecccCCCcceEEeEEE--------EeeeCC--CCceEec
Q 037395 91 WGSWNYKYAIKRKVVG--------IWSCKY--CGKVKAG 119 (121)
Q Consensus 91 tCPFCGK~kVKR~AVG--------IWkCkk--CgktfAG 119 (121)
+||.||.....|.+.- ..+|.. ||.+|..
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVA 39 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEE
Confidence 5999999987776543 367877 8888753
No 38
>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=77.17 E-value=1.4 Score=26.90 Aligned_cols=26 Identities=19% Similarity=0.362 Sum_probs=18.5
Q ss_pred eecccCCCc-ceE---EeEEEEeeeCCCCc
Q 037395 90 AWGSWNYKY-AIK---RKVVGIWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~-kVK---R~AVGIWkCkkCgk 115 (121)
-.||.||-. ..+ +...|-|.|..|+.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 469999754 332 33569999999974
No 39
>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=76.90 E-value=0.93 Score=25.76 Aligned_cols=24 Identities=13% Similarity=-0.137 Sum_probs=17.1
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCceEe
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgktfA 118 (121)
+||.|++.. .+..=.|..||+.|.
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 688898764 344457888888764
No 40
>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=74.56 E-value=1.3 Score=27.27 Aligned_cols=9 Identities=11% Similarity=-0.252 Sum_probs=7.7
Q ss_pred eeecccCCC
Q 037395 89 VAWGSWNYK 97 (121)
Q Consensus 89 ~htCPFCGK 97 (121)
.++|||||+
T Consensus 2 ~f~CP~C~~ 10 (54)
T PF05605_consen 2 SFTCPYCGK 10 (54)
T ss_pred CcCCCCCCC
Confidence 378999998
No 41
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=74.36 E-value=4.4 Score=23.99 Aligned_cols=29 Identities=21% Similarity=0.104 Sum_probs=23.7
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceEe
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktfA 118 (121)
..|+.||...+--..-++-.|..|+.++.
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEee
Confidence 47888999887767778899999998763
No 42
>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=74.11 E-value=1.7 Score=25.78 Aligned_cols=28 Identities=11% Similarity=0.169 Sum_probs=18.4
Q ss_pred ecccCCCcceEEeEEEEe-eeCCCCceEe
Q 037395 91 WGSWNYKYAIKRKVVGIW-SCKYCGKVKA 118 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIW-kCkkCgktfA 118 (121)
.||.||...+-+....-. .|+.|++..-
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccC
Confidence 599999987544432211 6999999864
No 43
>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=73.98 E-value=1.6 Score=29.95 Aligned_cols=20 Identities=15% Similarity=0.076 Sum_probs=9.6
Q ss_pred ceeecccCCCcceEEeEEEE
Q 037395 88 CVAWGSWNYKYAIKRKVVGI 107 (121)
Q Consensus 88 ~~htCPFCGK~kVKR~AVGI 107 (121)
-+..||.||...++|+++-+
T Consensus 23 ~k~FCp~CGn~TL~rvsvsv 42 (73)
T PF08772_consen 23 TKQFCPKCGNATLKRVSVSV 42 (73)
T ss_dssp S--S-SSS--S--EEEE-B-
T ss_pred CceeCcccCCCcceEEEEEE
Confidence 35779999999999999754
No 44
>smart00400 ZnF_CHCC zinc finger.
Probab=73.59 E-value=2.8 Score=25.78 Aligned_cols=26 Identities=12% Similarity=0.254 Sum_probs=17.9
Q ss_pred eecccCCCcc--eE-EeEEEEeeeCCCCc
Q 037395 90 AWGSWNYKYA--IK-RKVVGIWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~k--VK-R~AVGIWkCkkCgk 115 (121)
..|||++... ++ ....++|+|-.|++
T Consensus 3 ~~cPfh~d~~pSf~v~~~kn~~~Cf~cg~ 31 (55)
T smart00400 3 GLCPFHGEKTPSFSVSPDKQFFHCFGCGA 31 (55)
T ss_pred ccCcCCCCCCCCEEEECCCCEEEEeCCCC
Confidence 4699997553 21 22458999999984
No 45
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=73.47 E-value=2 Score=34.63 Aligned_cols=29 Identities=21% Similarity=0.045 Sum_probs=24.1
Q ss_pred eecccCCCcc-eEEeEEEEeeeCCCCceEe
Q 037395 90 AWGSWNYKYA-IKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 90 htCPFCGK~k-VKR~AVGIWkCkkCgktfA 118 (121)
..||.||.+. |.-...|-.-|..||.++.
T Consensus 12 ~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 12 LVCPECGSDKLIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred CcCcCCCCCCeeEECCCCeEeecccCCccc
Confidence 4799999854 5677899999999998764
No 46
>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=72.73 E-value=0.64 Score=27.63 Aligned_cols=26 Identities=19% Similarity=0.069 Sum_probs=14.5
Q ss_pred eecccCCCcc-eEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYA-IKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~k-VKR~AVGIWkCkkCgktf 117 (121)
|.|..||+.. ++. .-.| +|+.||..+
T Consensus 1 Y~C~~Cg~~~~~~~-~~~i-rC~~CG~RI 27 (32)
T PF03604_consen 1 YICGECGAEVELKP-GDPI-RCPECGHRI 27 (32)
T ss_dssp EBESSSSSSE-BST-SSTS-SBSSSS-SE
T ss_pred CCCCcCCCeeEcCC-CCcE-ECCcCCCeE
Confidence 5677777764 332 2223 777777643
No 47
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=72.66 E-value=2.5 Score=35.41 Aligned_cols=26 Identities=12% Similarity=0.238 Sum_probs=19.0
Q ss_pred eecccCCCcc---eEEeEEEEeeeCCCCc
Q 037395 90 AWGSWNYKYA---IKRKVVGIWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~k---VKR~AVGIWkCkkCgk 115 (121)
..||||+... .--...|+|+|-+||.
T Consensus 35 ~~CPfh~ek~pSf~v~~~k~~~~Cf~Cg~ 63 (415)
T TIGR01391 35 GLCPFHHEKTPSFSVSPEKQFYHCFGCGA 63 (415)
T ss_pred eeCCCCCCCCCeEEEEcCCCcEEECCCCC
Confidence 5699997642 2233578999999996
No 48
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=72.61 E-value=5.1 Score=23.64 Aligned_cols=27 Identities=19% Similarity=0.046 Sum_probs=19.2
Q ss_pred ecccCCCcce--EEeEEEEeeeCCCCceE
Q 037395 91 WGSWNYKYAI--KRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 91 tCPFCGK~kV--KR~AVGIWkCkkCgktf 117 (121)
.||.|+.... +-..+=|+.|.+|+-.|
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeEE
Confidence 4999987532 22356799999998765
No 49
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=72.08 E-value=3.8 Score=28.10 Aligned_cols=29 Identities=14% Similarity=0.092 Sum_probs=21.3
Q ss_pred eecccCCCcceEEeEE--------EEeeeC--CCCceEe
Q 037395 90 AWGSWNYKYAIKRKVV--------GIWSCK--YCGKVKA 118 (121)
Q Consensus 90 htCPFCGK~kVKR~AV--------GIWkCk--kCgktfA 118 (121)
..||+||..+.-|.+- =.++|. .||.+|.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence 3699999988555432 347898 9999885
No 50
>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=71.99 E-value=3 Score=24.48 Aligned_cols=14 Identities=36% Similarity=1.227 Sum_probs=11.2
Q ss_pred EeeeCCCCceEecC
Q 037395 107 IWSCKYCGKVKAGG 120 (121)
Q Consensus 107 IWkCkkCgktfAGG 120 (121)
+|.|..||+++.|.
T Consensus 2 ~~~C~~CG~i~~g~ 15 (34)
T cd00729 2 VWVCPVCGYIHEGE 15 (34)
T ss_pred eEECCCCCCEeECC
Confidence 59999999887763
No 51
>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=69.80 E-value=11 Score=22.47 Aligned_cols=27 Identities=11% Similarity=0.006 Sum_probs=17.7
Q ss_pred ecccCCCcceE-E---------eEEEEeeeCCCCceE
Q 037395 91 WGSWNYKYAIK-R---------KVVGIWSCKYCGKVK 117 (121)
Q Consensus 91 tCPFCGK~kVK-R---------~AVGIWkCkkCgktf 117 (121)
+||.||....- . ..+=+..|..|+++|
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 69999987532 2 237789999999887
No 52
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=69.47 E-value=3.9 Score=28.59 Aligned_cols=37 Identities=11% Similarity=-0.048 Sum_probs=26.9
Q ss_pred hhhhhhhhhcceeecccCCCcceEEeEEEEeeeCCCCceEe
Q 037395 78 PALMFYFVFACVAWGSWNYKYAIKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 78 ~~lm~~~~~~~~htCPFCGK~kVKR~AVGIWkCkkCgktfA 118 (121)
..........-...|+.|...+--|. .+|+.|++-+.
T Consensus 37 ~~~~~~~~~~~~~~C~~C~~~kp~Rs----~HC~~C~~CV~ 73 (174)
T PF01529_consen 37 IDSPEDDENGELKYCSTCKIIKPPRS----HHCRVCNRCVL 73 (174)
T ss_pred hhhhccccCCCCEECcccCCcCCCcc----eeccccccccc
Confidence 33334445556689999998888886 89999997654
No 53
>PRK08402 replication factor A; Reviewed
Probab=69.39 E-value=2.3 Score=35.90 Aligned_cols=28 Identities=11% Similarity=0.075 Sum_probs=22.1
Q ss_pred ceeecccCCCcceEEeEEEEeeeCCCCc
Q 037395 88 CVAWGSWNYKYAIKRKVVGIWSCKYCGK 115 (121)
Q Consensus 88 ~~htCPFCGK~kVKR~AVGIWkCkkCgk 115 (121)
+-..||-|.|.-+.-...|-|.|..|++
T Consensus 211 ~y~aCp~CnKkv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 211 VYDACPECRRKVDYDPATDTWICPEHGE 238 (355)
T ss_pred eEecCCCCCeEEEEecCCCCEeCCCCCC
Confidence 4467999988655566779999999985
No 54
>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=69.22 E-value=4.1 Score=27.87 Aligned_cols=26 Identities=15% Similarity=0.291 Sum_probs=13.3
Q ss_pred eecccCCCcc--eE-EeEEEEeeeCCCCc
Q 037395 90 AWGSWNYKYA--IK-RKVVGIWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~k--VK-R~AVGIWkCkkCgk 115 (121)
..||||+-.. +. -...|+|+|-.||.
T Consensus 34 ~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp E--SSS--SS--EEEETTTTEEEETTT--
T ss_pred EECcCCCCCCCceEEECCCCeEEECCCCC
Confidence 5699998542 11 12347999999995
No 55
>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=69.08 E-value=4.5 Score=26.11 Aligned_cols=27 Identities=11% Similarity=-0.024 Sum_probs=17.3
Q ss_pred eecc--cCCCcceEEeEEEEeeeCCCCce
Q 037395 90 AWGS--WNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 90 htCP--FCGK~kVKR~AVGIWkCkkCgkt 116 (121)
-.|| .||.-..==.-..=|.|.+|+.|
T Consensus 19 k~CP~~~CG~GvFMA~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 19 KECPSPRCGAGVFMAEHKDRHYCGKCGYT 47 (47)
T ss_dssp EE-TSTTTTSSSEEEE-SSEEEETTTSS-
T ss_pred hcCCCcccCCceEeeecCCCccCCCcccC
Confidence 6799 99986422222356999999976
No 56
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=68.61 E-value=1.9 Score=29.60 Aligned_cols=13 Identities=8% Similarity=-0.457 Sum_probs=9.5
Q ss_pred eeecccCCCcceE
Q 037395 89 VAWGSWNYKYAIK 101 (121)
Q Consensus 89 ~htCPFCGK~kVK 101 (121)
++.||-||...+.
T Consensus 27 ~F~CPnCGe~~I~ 39 (61)
T COG2888 27 KFPCPNCGEVEIY 39 (61)
T ss_pred EeeCCCCCceeee
Confidence 4789999976543
No 57
>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=68.52 E-value=3.2 Score=23.66 Aligned_cols=29 Identities=17% Similarity=0.051 Sum_probs=18.3
Q ss_pred eecccCCCcc-eE----EeEEEEeeeCCCCceEe
Q 037395 90 AWGSWNYKYA-IK----RKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 90 htCPFCGK~k-VK----R~AVGIWkCkkCgktfA 118 (121)
.+||.|+..- +. ...-+-=.|.+|+.+|-
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 6799999842 22 11222457999998874
No 58
>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=67.78 E-value=3.5 Score=24.77 Aligned_cols=15 Identities=7% Similarity=-0.250 Sum_probs=12.8
Q ss_pred eeecccCCCcceEEe
Q 037395 89 VAWGSWNYKYAIKRK 103 (121)
Q Consensus 89 ~htCPFCGK~kVKR~ 103 (121)
...||.||...++|+
T Consensus 26 ~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 26 PVPCPECGSTEVRRV 40 (42)
T ss_pred CCcCCCCCCCceEEe
Confidence 468999999888886
No 59
>PRK05667 dnaG DNA primase; Validated
Probab=66.98 E-value=4 Score=36.18 Aligned_cols=26 Identities=12% Similarity=0.233 Sum_probs=19.3
Q ss_pred eecccCCCcc---eEEeEEEEeeeCCCCc
Q 037395 90 AWGSWNYKYA---IKRKVVGIWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~k---VKR~AVGIWkCkkCgk 115 (121)
..||||+-.. .-....|+|+|-+||.
T Consensus 37 ~~CPfH~ektpSf~V~~~k~~~~CF~Cg~ 65 (580)
T PRK05667 37 GLCPFHDEKTPSFTVSPDKQFYHCFGCGA 65 (580)
T ss_pred ecCCCCCCCCCceEEECCCCeEEECCCCC
Confidence 5799997552 2234679999999996
No 60
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=66.45 E-value=3.8 Score=36.25 Aligned_cols=25 Identities=16% Similarity=0.037 Sum_probs=19.7
Q ss_pred cceeecccCCCcceEEeEEEEeeeCCCCc
Q 037395 87 ACVAWGSWNYKYAIKRKVVGIWSCKYCGK 115 (121)
Q Consensus 87 ~~~htCPFCGK~kVKR~AVGIWkCkkCgk 115 (121)
.-.|+|..||-.+-+ =-|+|++|++
T Consensus 352 ~~~YRC~~CGF~a~~----l~W~CPsC~~ 376 (389)
T COG2956 352 KPRYRCQNCGFTAHT----LYWHCPSCRA 376 (389)
T ss_pred cCCceecccCCccee----eeeeCCCccc
Confidence 445999999987643 3599999985
No 61
>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=66.22 E-value=5.5 Score=28.84 Aligned_cols=31 Identities=23% Similarity=0.431 Sum_probs=22.5
Q ss_pred eecccCCCcc--eEEeEE-------------EEeeeCCCCceEecC
Q 037395 90 AWGSWNYKYA--IKRKVV-------------GIWSCKYCGKVKAGG 120 (121)
Q Consensus 90 htCPFCGK~k--VKR~AV-------------GIWkCkkCgktfAGG 120 (121)
-.|+.|+... |.+..+ -.|.|.+||+.+=.|
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~G 137 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEG 137 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEeccc
Confidence 4799998863 333322 389999999988665
No 62
>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=65.31 E-value=6.7 Score=23.47 Aligned_cols=28 Identities=11% Similarity=0.037 Sum_probs=19.8
Q ss_pred eecccCCCcceEEeEE--EEeeeCC---CCceE
Q 037395 90 AWGSWNYKYAIKRKVV--GIWSCKY---CGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AV--GIWkCkk---Cgktf 117 (121)
..||.||...+.|.+- =.|.|.. |.++.
T Consensus 2 ~~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~ 34 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKGKFLGCSNYPECKYTE 34 (39)
T ss_pred cCCCCCCceeEEEECCCCCEEECCCCCCcCCeE
Confidence 4799999887766643 3678865 76654
No 63
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=64.74 E-value=3.5 Score=32.12 Aligned_cols=13 Identities=38% Similarity=1.262 Sum_probs=11.6
Q ss_pred EeeeCCCCceEec
Q 037395 107 IWSCKYCGKVKAG 119 (121)
Q Consensus 107 IWkCkkCgktfAG 119 (121)
+|.|+.||+++.|
T Consensus 134 ~~vC~vCGy~~~g 146 (166)
T COG1592 134 VWVCPVCGYTHEG 146 (166)
T ss_pred EEEcCCCCCcccC
Confidence 8999999999887
No 64
>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=64.56 E-value=5.2 Score=20.13 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=6.8
Q ss_pred eeeCCCCceEe
Q 037395 108 WSCKYCGKVKA 118 (121)
Q Consensus 108 WkCkkCgktfA 118 (121)
|.|..|+++|.
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 45666666654
No 65
>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=64.42 E-value=4.8 Score=19.45 Aligned_cols=10 Identities=40% Similarity=1.032 Sum_probs=4.6
Q ss_pred eeeCCCCceE
Q 037395 108 WSCKYCGKVK 117 (121)
Q Consensus 108 WkCkkCgktf 117 (121)
|.|..|++++
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 5566666555
No 66
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=64.30 E-value=5.2 Score=31.76 Aligned_cols=28 Identities=11% Similarity=0.040 Sum_probs=22.4
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
-.||.||.....+.+--.-.|.+|+...
T Consensus 100 ~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 100 RFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred ccccccCCCCeecCCceeEECCCCCCEE
Confidence 3799999987766666678899999754
No 67
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.05 E-value=1.8 Score=31.23 Aligned_cols=29 Identities=14% Similarity=-0.056 Sum_probs=23.9
Q ss_pred hhhhhhhhhcceeecccCCCcceEEe--EEEE
Q 037395 78 PALMFYFVFACVAWGSWNYKYAIKRK--VVGI 107 (121)
Q Consensus 78 ~~lm~~~~~~~~htCPFCGK~kVKR~--AVGI 107 (121)
-++||++..+-.-+||.||. .+||+ ++||
T Consensus 22 ~dvvq~~~ddplt~ce~c~a-~~kk~l~~vgi 52 (82)
T COG2331 22 FDVVQAMTDDPLTTCEECGA-RLKKLLNAVGI 52 (82)
T ss_pred HHHHHhcccCccccChhhCh-HHHHhhccceE
Confidence 36899999888899999998 77775 6665
No 68
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=63.54 E-value=5.6 Score=24.68 Aligned_cols=27 Identities=19% Similarity=0.192 Sum_probs=18.7
Q ss_pred eeecccCCCcc-eEEeEEEEeeeCCCCceE
Q 037395 89 VAWGSWNYKYA-IKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 89 ~htCPFCGK~k-VKR~AVGIWkCkkCgktf 117 (121)
.|.|..||... ++ ..+-=+|+.||..+
T Consensus 2 ~Y~C~~Cg~~~~~~--~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK--SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC--CCCceECCCCCceE
Confidence 48889998874 44 23446888888754
No 69
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=62.01 E-value=5.5 Score=30.35 Aligned_cols=38 Identities=13% Similarity=0.012 Sum_probs=28.9
Q ss_pred hhhhhhhhhcceeecccCCCcceEEeEEEEeeeCCCCceEe
Q 037395 78 PALMFYFVFACVAWGSWNYKYAIKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 78 ~~lm~~~~~~~~htCPFCGK~kVKR~AVGIWkCkkCgktfA 118 (121)
..|++=++- =.+.||.||-+.++ =.|==.|.-|++++.
T Consensus 18 ~lLl~GAkM-L~~hCp~Cg~PLF~--KdG~v~CPvC~~~~~ 55 (131)
T COG1645 18 ELLLQGAKM-LAKHCPKCGTPLFR--KDGEVFCPVCGYREV 55 (131)
T ss_pred HHHHhhhHH-HHhhCcccCCccee--eCCeEECCCCCceEE
Confidence 456665553 34789999999999 667789999997653
No 70
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=61.84 E-value=2.3 Score=23.39 Aligned_cols=23 Identities=17% Similarity=0.147 Sum_probs=14.6
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCce
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
.+||.||+. +. .+-=.|..||..
T Consensus 3 ~~Cp~Cg~~-~~---~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAE-ID---PDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCc-CC---cccccChhhCCC
Confidence 468888883 32 233567777764
No 71
>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=61.76 E-value=6.5 Score=27.23 Aligned_cols=26 Identities=15% Similarity=0.188 Sum_probs=14.8
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
-.||.|... |.+.. |.++|..|.+-+
T Consensus 2 ~~CP~C~~~-L~~~~-~~~~C~~C~~~~ 27 (70)
T PF07191_consen 2 NTCPKCQQE-LEWQG-GHYHCEACQKDY 27 (70)
T ss_dssp -B-SSS-SB-EEEET-TEEEETTT--EE
T ss_pred CcCCCCCCc-cEEeC-CEEECccccccc
Confidence 368888776 55555 778888887654
No 72
>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=61.09 E-value=5.1 Score=23.01 Aligned_cols=13 Identities=31% Similarity=0.874 Sum_probs=9.7
Q ss_pred EeeeCCCCceEec
Q 037395 107 IWSCKYCGKVKAG 119 (121)
Q Consensus 107 IWkCkkCgktfAG 119 (121)
+|.|+.||++.-+
T Consensus 1 ~~~C~~CGy~y~~ 13 (33)
T cd00350 1 KYVCPVCGYIYDG 13 (33)
T ss_pred CEECCCCCCEECC
Confidence 4888888887654
No 73
>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=60.42 E-value=2.7 Score=23.97 Aligned_cols=21 Identities=5% Similarity=-0.198 Sum_probs=12.6
Q ss_pred ecccCCCcceEEeEEEEeeeC
Q 037395 91 WGSWNYKYAIKRKVVGIWSCK 111 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCk 111 (121)
+||.||...++-..--+|+|.
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 599999999877665578774
No 74
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=60.02 E-value=6.5 Score=29.76 Aligned_cols=29 Identities=14% Similarity=-0.019 Sum_probs=23.2
Q ss_pred hhhhcceeecccCCCcceEEeEEEEeeeCCCCc
Q 037395 83 YFVFACVAWGSWNYKYAIKRKVVGIWSCKYCGK 115 (121)
Q Consensus 83 ~~~~~~~htCPFCGK~kVKR~AVGIWkCkkCgk 115 (121)
..+..-.+.|+.||-+.-+.. |.|.+|+-
T Consensus 348 ~~~~~p~~~c~~cg~~~~~~~----~~c~~c~~ 376 (389)
T PRK11788 348 QLKRKPRYRCRNCGFTARTLY----WHCPSCKA 376 (389)
T ss_pred HHhCCCCEECCCCCCCCccce----eECcCCCC
Confidence 345556789999999988777 89999973
No 75
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=59.89 E-value=4.2 Score=27.53 Aligned_cols=14 Identities=14% Similarity=-0.230 Sum_probs=10.1
Q ss_pred eeecccCCCcceEE
Q 037395 89 VAWGSWNYKYAIKR 102 (121)
Q Consensus 89 ~htCPFCGK~kVKR 102 (121)
+..||.||+..+.|
T Consensus 25 ~F~CPnCG~~~I~R 38 (59)
T PRK14890 25 KFLCPNCGEVIIYR 38 (59)
T ss_pred EeeCCCCCCeeEee
Confidence 36799999875543
No 76
>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=59.81 E-value=7.5 Score=23.28 Aligned_cols=13 Identities=8% Similarity=-0.286 Sum_probs=7.8
Q ss_pred ecccCCCcceEEe
Q 037395 91 WGSWNYKYAIKRK 103 (121)
Q Consensus 91 tCPFCGK~kVKR~ 103 (121)
.||.||...++|.
T Consensus 28 ~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 28 TCPECGGEKLRRL 40 (52)
T ss_pred CCCCCCCCceeEE
Confidence 4666666555554
No 77
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=59.64 E-value=2.9 Score=22.92 Aligned_cols=21 Identities=14% Similarity=0.060 Sum_probs=10.6
Q ss_pred cccCCCcceEEeEEEEeeeCCCCce
Q 037395 92 GSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 92 CPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
||.||+..-.-.. -|..||..
T Consensus 2 Cp~CG~~~~~~~~----fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIEDDAK----FCPNCGTP 22 (23)
T ss_pred CcccCCCCCCcCc----chhhhCCc
Confidence 6666665432221 26666643
No 78
>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=59.17 E-value=3.6 Score=36.63 Aligned_cols=28 Identities=18% Similarity=0.171 Sum_probs=20.4
Q ss_pred eeeccc--CCCcceEEeEEEEeeeCCCCceE
Q 037395 89 VAWGSW--NYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 89 ~htCPF--CGK~kVKR~AVGIWkCkkCgktf 117 (121)
-.-||- |.|. |....-|.|.|.+|++++
T Consensus 474 Y~ACp~~~CnKK-V~~~~~g~~~CekC~~~~ 503 (608)
T TIGR00617 474 YRACPSEDCNKK-VVDQGDGTYRCEKCNKNF 503 (608)
T ss_pred eccCChhhCCCc-cccCCCCCEECCCCCCCC
Confidence 355766 8775 444556999999999764
No 79
>PLN03086 PRLI-interacting factor K; Provisional
Probab=59.13 E-value=5.9 Score=35.99 Aligned_cols=50 Identities=12% Similarity=0.148 Sum_probs=41.6
Q ss_pred cccccccccchhhhhhhhhccee---eccc--CCCcceEEeEEEEeeeCCCCceEe
Q 037395 68 GMNCWKPFVNPALMFYFVFACVA---WGSW--NYKYAIKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 68 g~~~~k~~~~~~lm~~~~~~~~h---tCPF--CGK~kVKR~AVGIWkCkkCgktfA 118 (121)
=.||-..+..-.|+-|-.+ |.+ .||. ||..-.++.----|+|..|++.|.
T Consensus 410 C~NC~~~i~l~~l~lHe~~-C~r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~ 464 (567)
T PLN03086 410 CRNCKHYIPSRSIALHEAY-CSRHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ 464 (567)
T ss_pred CCCCCCccchhHHHHHHhh-CCCcceeCCcccccceeeccccccCccCCCCCCccc
Confidence 4578889999999999864 876 4885 999888888888999999998763
No 80
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=58.78 E-value=3.2 Score=33.79 Aligned_cols=28 Identities=32% Similarity=0.458 Sum_probs=19.8
Q ss_pred ccccccccchhhhhhhhhcceeecccCCCcce
Q 037395 69 MNCWKPFVNPALMFYFVFACVAWGSWNYKYAI 100 (121)
Q Consensus 69 ~~~~k~~~~~~lm~~~~~~~~htCPFCGK~kV 100 (121)
||-++|+ .|-.|.-| |.+.|+||+-.++
T Consensus 1 ~~~~~~~---~lYiHIPF-C~~~C~yC~f~~~ 28 (370)
T PRK06294 1 MNGKSPL---ALYIHIPF-CTKKCHYCSFYTI 28 (370)
T ss_pred CCCCCce---EEEEEeCC-ccCcCCCCcCccc
Confidence 4555543 56667666 9999999986654
No 81
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=58.01 E-value=10 Score=30.91 Aligned_cols=31 Identities=10% Similarity=0.016 Sum_probs=23.3
Q ss_pred ceeecccCCCcc-----------eEEeEEEEeeeCCCCceEe
Q 037395 88 CVAWGSWNYKYA-----------IKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 88 ~~htCPFCGK~k-----------VKR~AVGIWkCkkCgktfA 118 (121)
-.-.||.||.+- .+++..--|.|++||+..+
T Consensus 13 ~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 13 TRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 347899999842 2456667799999999764
No 82
>PF12773 DZR: Double zinc ribbon
Probab=57.34 E-value=3 Score=24.79 Aligned_cols=30 Identities=10% Similarity=0.008 Sum_probs=20.1
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceEecC
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVKAGG 120 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktfAGG 120 (121)
..|+.||.... +.....+.|.+|+..+..+
T Consensus 13 ~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 13 KFCPHCGTPLP-PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cCChhhcCChh-hccCCCCCCcCCcCCCcCC
Confidence 46888887765 3344458888888776543
No 83
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=55.86 E-value=3.8 Score=29.73 Aligned_cols=32 Identities=13% Similarity=0.072 Sum_probs=21.0
Q ss_pred hcceeecccCCCcceEEe------EEEEeeeCCCCceE
Q 037395 86 FACVAWGSWNYKYAIKRK------VVGIWSCKYCGKVK 117 (121)
Q Consensus 86 ~~~~htCPFCGK~kVKR~------AVGIWkCkkCgktf 117 (121)
..=.|.||.||+.---=. -.|-..|..||..+
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 334699999997521111 14558999999865
No 84
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=55.60 E-value=7.2 Score=23.34 Aligned_cols=26 Identities=19% Similarity=0.208 Sum_probs=14.8
Q ss_pred ecccCCCcceEEeEEE----EeeeCCCCce
Q 037395 91 WGSWNYKYAIKRKVVG----IWSCKYCGKV 116 (121)
Q Consensus 91 tCPFCGK~kVKR~AVG----IWkCkkCgkt 116 (121)
.||.||.....|+-.| =|.|..||..
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 3789999875
No 85
>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=55.08 E-value=7.8 Score=22.09 Aligned_cols=7 Identities=0% Similarity=-0.866 Sum_probs=3.6
Q ss_pred eecccCC
Q 037395 90 AWGSWNY 96 (121)
Q Consensus 90 htCPFCG 96 (121)
|.||.||
T Consensus 17 f~CPnCG 23 (24)
T PF07754_consen 17 FPCPNCG 23 (24)
T ss_pred EeCCCCC
Confidence 4555554
No 86
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=52.81 E-value=4 Score=34.64 Aligned_cols=25 Identities=20% Similarity=0.533 Sum_probs=18.7
Q ss_pred eecccCCCcc--eEEeEE--EEeeeCCCC
Q 037395 90 AWGSWNYKYA--IKRKVV--GIWSCKYCG 114 (121)
Q Consensus 90 htCPFCGK~k--VKR~AV--GIWkCkkCg 114 (121)
..|+|||+.. +.+.-. |.+-|..|-
T Consensus 10 ~~CSFCGr~~~ev~~li~g~~~~IC~~Ci 38 (412)
T PRK05342 10 LYCSFCGKSQHEVRKLIAGPGVYICDECI 38 (412)
T ss_pred cccCCCCCChhhccccccCCCCcccchHH
Confidence 4899999974 666433 468899884
No 87
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=52.05 E-value=12 Score=26.04 Aligned_cols=26 Identities=19% Similarity=0.197 Sum_probs=20.1
Q ss_pred eecccCCCcc--------eEEeEEEEeeeC-CCCc
Q 037395 90 AWGSWNYKYA--------IKRKVVGIWSCK-YCGK 115 (121)
Q Consensus 90 htCPFCGK~k--------VKR~AVGIWkCk-kCgk 115 (121)
++|+|||+.. |++-+.=.|-|. ||.+
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 7899999863 788888888884 4544
No 88
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=51.48 E-value=9.9 Score=24.78 Aligned_cols=27 Identities=15% Similarity=0.101 Sum_probs=12.3
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCce
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
|.|..||+.--.=....-=.|..||..
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCcE
Confidence 556666555411122223355555554
No 89
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=50.15 E-value=10 Score=37.56 Aligned_cols=27 Identities=19% Similarity=0.272 Sum_probs=23.4
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
-.||.||...|.|.+ +-|+|..||-|-
T Consensus 1191 ~~c~~cg~~~~vrng-tc~~c~~cg~t~ 1217 (1220)
T PRK07562 1191 EACSECGNFTLVRNG-TCLKCDTCGSTT 1217 (1220)
T ss_pred CcCCCcCCeEEEeCC-eeeeccccCCCC
Confidence 459999999999998 579999999763
No 90
>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=48.79 E-value=9.8 Score=21.45 Aligned_cols=26 Identities=12% Similarity=0.008 Sum_probs=13.9
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCce
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
.|+.||.....-.+---=.|..|+..
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 48889888766655434578888865
No 91
>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=48.79 E-value=4.5 Score=30.30 Aligned_cols=28 Identities=7% Similarity=0.076 Sum_probs=22.1
Q ss_pred eecccCCCcceEEeE-------EEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKV-------VGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~A-------VGIWkCkkCgktf 117 (121)
-.||.||....++.+ --+|+|..|..-|
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 589999999888775 3589999987543
No 92
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=47.75 E-value=12 Score=21.92 Aligned_cols=29 Identities=14% Similarity=-0.012 Sum_probs=19.5
Q ss_pred eecccCCCcc-eE----EeEEEEeeeCCCCceEe
Q 037395 90 AWGSWNYKYA-IK----RKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 90 htCPFCGK~k-VK----R~AVGIWkCkkCgktfA 118 (121)
-+||.|+..- |- +.+-+.=+|.+|+.+|.
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 4799998762 22 23445668999998873
No 93
>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=46.57 E-value=13 Score=26.89 Aligned_cols=26 Identities=12% Similarity=0.042 Sum_probs=18.4
Q ss_pred ecccCCCcceEEeE----------EE-EeeeCCCCce
Q 037395 91 WGSWNYKYAIKRKV----------VG-IWSCKYCGKV 116 (121)
Q Consensus 91 tCPFCGK~kVKR~A----------VG-IWkCkkCgkt 116 (121)
.||+||...+-+.+ .. +|.|..|+.-
T Consensus 4 ~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~Ay 40 (102)
T PF11672_consen 4 ICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAY 40 (102)
T ss_pred ccCCCCCeeEEcccchhcCccCCCCceeEECCCCCce
Confidence 69999998754431 23 4999999753
No 94
>PRK04023 DNA polymerase II large subunit; Validated
Probab=46.20 E-value=8.9 Score=37.83 Aligned_cols=23 Identities=13% Similarity=0.247 Sum_probs=15.3
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
..||.||.. ...||.|.+|+...
T Consensus 639 frCP~CG~~-----Te~i~fCP~CG~~~ 661 (1121)
T PRK04023 639 RRCPFCGTH-----TEPVYRCPRCGIEV 661 (1121)
T ss_pred ccCCCCCCC-----CCcceeCccccCcC
Confidence 357777766 45677777776654
No 95
>PRK08173 DNA topoisomerase III; Validated
Probab=44.78 E-value=12 Score=34.87 Aligned_cols=26 Identities=8% Similarity=-0.038 Sum_probs=18.6
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
..||.||+..+++ -+-|.|..|+.++
T Consensus 625 ~~CP~Cg~~~~~~--~~~~~Cs~C~f~~ 650 (862)
T PRK08173 625 TPCPNCGGVVKEN--YRRFACTKCDFSI 650 (862)
T ss_pred ccCCccccccccc--CceeEcCCCCccc
Confidence 5799999865433 3349999998553
No 96
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=44.31 E-value=14 Score=21.85 Aligned_cols=28 Identities=18% Similarity=0.004 Sum_probs=17.8
Q ss_pred eecccCCCcc-e----EEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYA-I----KRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~k-V----KR~AVGIWkCkkCgktf 117 (121)
-+||-|++.- | -+.....=+|++|+.+|
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 4688887652 1 22333456899998876
No 97
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=44.10 E-value=2.6 Score=26.78 Aligned_cols=27 Identities=30% Similarity=0.235 Sum_probs=19.1
Q ss_pred ecccCCCcc--eEE--eEEEEeeeCCCCceEe
Q 037395 91 WGSWNYKYA--IKR--KVVGIWSCKYCGKVKA 118 (121)
Q Consensus 91 tCPFCGK~k--VKR--~AVGIWkCkkCgktfA 118 (121)
.|+.||+.. ++| ..=| |-|+.|.++..
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl~ 31 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKLS 31 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHhc
Confidence 489998874 442 4556 99999987653
No 98
>PHA00732 hypothetical protein
Probab=44.05 E-value=11 Score=25.69 Aligned_cols=10 Identities=30% Similarity=0.710 Sum_probs=5.4
Q ss_pred eeCCCCceEe
Q 037395 109 SCKYCGKVKA 118 (121)
Q Consensus 109 kCkkCgktfA 118 (121)
.|..|+++++
T Consensus 29 ~C~~CgKsF~ 38 (79)
T PHA00732 29 KCPVCNKSYR 38 (79)
T ss_pred ccCCCCCEeC
Confidence 4555555554
No 99
>PRK07218 replication factor A; Provisional
Probab=43.94 E-value=11 Score=32.81 Aligned_cols=21 Identities=19% Similarity=0.091 Sum_probs=16.6
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCce
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
..||.|++..-+ |.|+.||++
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 479999877633 999999975
No 100
>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=43.35 E-value=16 Score=23.82 Aligned_cols=21 Identities=14% Similarity=-0.352 Sum_probs=12.3
Q ss_pred hcceeecccCCCcceEEeEEE
Q 037395 86 FACVAWGSWNYKYAIKRKVVG 106 (121)
Q Consensus 86 ~~~~htCPFCGK~kVKR~AVG 106 (121)
....-+|.+|||.+.++.-+|
T Consensus 45 ~~~~~~Ci~cgk~a~~~~~fa 65 (68)
T PF09180_consen 45 EPEGGKCIVCGKPAKKWVLFA 65 (68)
T ss_dssp EBTT-B-TTT-SB-SCEEEEE
T ss_pred CCCCCeeecCCChhhEEEEEE
Confidence 345678999999988877543
No 101
>PHA02540 61 DNA primase; Provisional
Probab=42.80 E-value=22 Score=30.17 Aligned_cols=26 Identities=19% Similarity=0.348 Sum_probs=17.8
Q ss_pred eecccCCCcc----eEEeEE------EEeeeCCCCc
Q 037395 90 AWGSWNYKYA----IKRKVV------GIWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~k----VKR~AV------GIWkCkkCgk 115 (121)
..|||||-.. -.|-.| +||+|=.||+
T Consensus 28 ~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa 63 (337)
T PHA02540 28 FRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGY 63 (337)
T ss_pred ecCCCCCCccccCcCCcEEEeccCCceEEEecCCCC
Confidence 6799998632 112222 4999999996
No 102
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=42.44 E-value=21 Score=18.20 Aligned_cols=12 Identities=25% Similarity=0.703 Sum_probs=9.2
Q ss_pred eeeCCCCceEec
Q 037395 108 WSCKYCGKVKAG 119 (121)
Q Consensus 108 WkCkkCgktfAG 119 (121)
|.|.-|++++..
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 788888887753
No 103
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=42.33 E-value=10 Score=34.95 Aligned_cols=25 Identities=20% Similarity=0.245 Sum_probs=19.8
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
.||.||. .+.+.. |=..|+.||+.-
T Consensus 726 ~Cp~Cg~-~l~~~~-GC~~C~~CG~sk 750 (752)
T PRK08665 726 ACPECGS-ILEHEE-GCVVCHSCGYSK 750 (752)
T ss_pred CCCCCCc-ccEECC-CCCcCCCCCCCC
Confidence 5999995 566555 889999999864
No 104
>PRK07220 DNA topoisomerase I; Validated
Probab=41.46 E-value=20 Score=32.60 Aligned_cols=27 Identities=15% Similarity=-0.015 Sum_probs=19.2
Q ss_pred eeecccCCCcceEEeEEE----EeeeCCCCc
Q 037395 89 VAWGSWNYKYAIKRKVVG----IWSCKYCGK 115 (121)
Q Consensus 89 ~htCPFCGK~kVKR~AVG----IWkCkkCgk 115 (121)
...||.||...++...-| .|.|..|.+
T Consensus 635 ~~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~ 665 (740)
T PRK07220 635 DKVCEAHGLNHIRIINGGKRPWDLGCPQCNF 665 (740)
T ss_pred CCCCCCCCCceEEEEecCCccceeeCCCCCC
Confidence 368999997655444333 689999985
No 105
>PRK04351 hypothetical protein; Provisional
Probab=41.23 E-value=24 Score=26.45 Aligned_cols=29 Identities=10% Similarity=-0.010 Sum_probs=22.5
Q ss_pred eeecccCCCc--ceEEeEEEEeeeCCCCceE
Q 037395 89 VAWGSWNYKY--AIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 89 ~htCPFCGK~--kVKR~AVGIWkCkkCgktf 117 (121)
.|.|.-||.. ..+|..+--..|+.|+-+.
T Consensus 112 ~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L 142 (149)
T PRK04351 112 LYECQSCGQQYLRKRRINTKRYRCGKCRGKL 142 (149)
T ss_pred EEECCCCCCEeeeeeecCCCcEEeCCCCcEe
Confidence 4899889975 4677777789999998653
No 106
>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=41.06 E-value=16 Score=21.51 Aligned_cols=26 Identities=12% Similarity=-0.027 Sum_probs=13.3
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
.||.|+..-.- .--.|+.|..|+..|
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 58888877544 444678888888765
No 107
>PF14353 CpXC: CpXC protein
Probab=40.89 E-value=15 Score=25.51 Aligned_cols=10 Identities=0% Similarity=-0.672 Sum_probs=8.9
Q ss_pred eecccCCCcc
Q 037395 90 AWGSWNYKYA 99 (121)
Q Consensus 90 htCPFCGK~k 99 (121)
++||.||+..
T Consensus 39 ~~CP~Cg~~~ 48 (128)
T PF14353_consen 39 FTCPSCGHKF 48 (128)
T ss_pred EECCCCCCce
Confidence 8999999874
No 108
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=40.29 E-value=18 Score=22.27 Aligned_cols=11 Identities=36% Similarity=1.090 Sum_probs=8.8
Q ss_pred eeeCCCCceEe
Q 037395 108 WSCKYCGKVKA 118 (121)
Q Consensus 108 WkCkkCgktfA 118 (121)
|+|.+||..+-
T Consensus 29 W~C~~Cgh~w~ 39 (55)
T PF14311_consen 29 WKCPKCGHEWK 39 (55)
T ss_pred EECCCCCCeeE
Confidence 99999987653
No 109
>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=40.10 E-value=17 Score=27.84 Aligned_cols=14 Identities=0% Similarity=-0.223 Sum_probs=12.3
Q ss_pred eecccCCCcceEEe
Q 037395 90 AWGSWNYKYAIKRK 103 (121)
Q Consensus 90 htCPFCGK~kVKR~ 103 (121)
-+||+||.+.|.|.
T Consensus 33 v~CP~Cgs~~V~K~ 46 (148)
T PF06676_consen 33 VSCPVCGSTEVSKA 46 (148)
T ss_pred ccCCCCCCCeEeee
Confidence 58999999998875
No 110
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=40.06 E-value=23 Score=28.27 Aligned_cols=25 Identities=20% Similarity=0.190 Sum_probs=18.0
Q ss_pred ecccCCCcceEEeEE---EEeeeCCCCce
Q 037395 91 WGSWNYKYAIKRKVV---GIWSCKYCGKV 116 (121)
Q Consensus 91 tCPFCGK~kVKR~AV---GIWkCkkCgkt 116 (121)
.||.||.+. +|..+ +.|.|..|-+.
T Consensus 237 pC~~Cg~~I-~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 237 PCPRCGTPI-EKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred CCCcCCCee-EEEEECCCCcEECCCCcCC
Confidence 799999664 44433 48999999653
No 111
>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=39.98 E-value=18 Score=25.73 Aligned_cols=13 Identities=31% Similarity=0.966 Sum_probs=9.8
Q ss_pred eEEE--EeeeCCCCc
Q 037395 103 KVVG--IWSCKYCGK 115 (121)
Q Consensus 103 ~AVG--IWkCkkCgk 115 (121)
...| ||.|..|..
T Consensus 45 ~~~G~~vw~C~~C~~ 59 (86)
T PF04071_consen 45 TKNGSKVWDCSDCTL 59 (86)
T ss_pred cCCCCeeeECccCCC
Confidence 3445 999999964
No 112
>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=39.91 E-value=19 Score=27.21 Aligned_cols=28 Identities=7% Similarity=-0.212 Sum_probs=15.2
Q ss_pred eecccCCCcceE---------EeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIK---------RKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVK---------R~AVGIWkCkkCgktf 117 (121)
.+||.|++...= ......|.|.+|+..+
T Consensus 19 ~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~ 55 (188)
T PF08996_consen 19 LTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPL 55 (188)
T ss_dssp EE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B-
T ss_pred eECCCCCCCccccccccCCccccccCcCcCCCCCCcC
Confidence 678999887522 2344589999998754
No 113
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=39.89 E-value=9.9 Score=29.98 Aligned_cols=29 Identities=17% Similarity=0.305 Sum_probs=21.1
Q ss_pred eeecccCCCcc--eE-------------EeEEEEeeeCCCCceE
Q 037395 89 VAWGSWNYKYA--IK-------------RKVVGIWSCKYCGKVK 117 (121)
Q Consensus 89 ~htCPFCGK~k--VK-------------R~AVGIWkCkkCgktf 117 (121)
.-.||.|+-.. |. +.+.-.|.|.+||+.+
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 36899998763 33 4444589999999875
No 114
>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=39.53 E-value=22 Score=19.19 Aligned_cols=9 Identities=11% Similarity=-0.281 Sum_probs=5.4
Q ss_pred eecccCCCc
Q 037395 90 AWGSWNYKY 98 (121)
Q Consensus 90 htCPFCGK~ 98 (121)
|.|+.|++.
T Consensus 15 ~~C~~C~k~ 23 (26)
T PF13465_consen 15 YKCPYCGKS 23 (26)
T ss_dssp EEESSSSEE
T ss_pred CCCCCCcCe
Confidence 566666653
No 115
>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=39.45 E-value=24 Score=20.84 Aligned_cols=25 Identities=20% Similarity=0.549 Sum_probs=17.4
Q ss_pred eecccCCCcc--eEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYA--IKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~k--VKR~AVGIWkCkkCgktf 117 (121)
..|..|++.. +.+.+ ++|..|+.++
T Consensus 12 ~~C~~C~~~i~g~~~~g---~~C~~C~~~~ 38 (53)
T PF00130_consen 12 TYCDVCGKFIWGLGKQG---YRCSWCGLVC 38 (53)
T ss_dssp EB-TTSSSBECSSSSCE---EEETTTT-EE
T ss_pred CCCcccCcccCCCCCCe---EEECCCCChH
Confidence 5788998887 45555 8999998764
No 116
>PF03956 DUF340: Membrane protein of unknown function (DUF340); InterPro: IPR005642 Members of this family contain a conserved core of four predicted transmembrane segments. Some members have an additional pair of N-terminal transmembrane helices. The functions of the proteins in this family are unknown.
Probab=39.29 E-value=4.9 Score=31.08 Aligned_cols=19 Identities=42% Similarity=0.705 Sum_probs=16.5
Q ss_pred ccccccCccccccceeecc
Q 037395 41 SCANRITPHAFDHGFILSG 59 (121)
Q Consensus 41 ~~~~~~~~~~~~~~~~~~~ 59 (121)
+|.++..|+||-|||||+=
T Consensus 162 ~~g~~~~~~a~~~G~iltl 180 (191)
T PF03956_consen 162 YCGEEYVPIAFISGFILTL 180 (191)
T ss_pred HcCCceeHHHHHHHHHHHH
Confidence 4778999999999999873
No 117
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=38.68 E-value=4.2 Score=34.37 Aligned_cols=76 Identities=25% Similarity=0.359 Sum_probs=44.0
Q ss_pred ccccCccccc----cceeecccccc------------ccccccccc---ccccchh-hhhhhh---hcceeecccCCCc-
Q 037395 43 ANRITPHAFD----HGFILSGFAEK------------DDQEGMNCW---KPFVNPA-LMFYFV---FACVAWGSWNYKY- 98 (121)
Q Consensus 43 ~~~~~~~~~~----~~~~~~~~~~~------------~~~~g~~~~---k~~~~~~-lm~~~~---~~~~htCPFCGK~- 98 (121)
+...+||..| +|+..|-|.+- .||.-..|+ |-|.--. |-.|.+ ..-.|-|.||||-
T Consensus 76 ~~~~~p~~~d~~~p~g~lass~~~i~~ss~k~t~gsssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgf 155 (267)
T KOG3576|consen 76 AVEFVPGGYDVKNPLGPLASSFESISTSSPKSTIGSSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGF 155 (267)
T ss_pred chhccCCCCCCCCCCccchhccccccccCCcccccCCCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcc
Confidence 4456788888 88888855432 122223333 4443222 222333 1124889999985
Q ss_pred ----ceE---EeEEEE--eeeCCCCceEe
Q 037395 99 ----AIK---RKVVGI--WSCKYCGKVKA 118 (121)
Q Consensus 99 ----kVK---R~AVGI--WkCkkCgktfA 118 (121)
.+| |+-+|| ++|.-|+|.|+
T Consensus 156 ndtfdlkrh~rthtgvrpykc~~c~kaft 184 (267)
T KOG3576|consen 156 NDTFDLKRHTRTHTGVRPYKCSLCEKAFT 184 (267)
T ss_pred cchhhhhhhhccccCccccchhhhhHHHH
Confidence 244 455665 79999998764
No 118
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=38.44 E-value=25 Score=20.61 Aligned_cols=23 Identities=30% Similarity=0.601 Sum_probs=16.7
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCceEec
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKVKAG 119 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgktfAG 119 (121)
.|..|+... .+|.|-.|++...|
T Consensus 1 ~C~~C~~~~------~l~~CL~C~~~~c~ 23 (50)
T smart00290 1 RCSVCGTIE------NLWLCLTCGQVGCG 23 (50)
T ss_pred CcccCCCcC------CeEEecCCCCcccC
Confidence 377887544 39999999876543
No 119
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=38.35 E-value=19 Score=27.29 Aligned_cols=26 Identities=19% Similarity=0.184 Sum_probs=16.9
Q ss_pred eecccCCCcceEEeEEE--EeeeCCCCc
Q 037395 90 AWGSWNYKYAIKRKVVG--IWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~kVKR~AVG--IWkCkkCgk 115 (121)
|.|--++--..++..-| +|.|..|.-
T Consensus 43 Ypc~~~~~gewi~~~~G~~VwSC~dC~~ 70 (112)
T COG2158 43 YPCENEELGEWISDSNGRKVWSCSDCHW 70 (112)
T ss_pred ccccccccCceeEcCCCCEEeeccccce
Confidence 55555654444555555 999999953
No 120
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=38.01 E-value=32 Score=24.63 Aligned_cols=29 Identities=14% Similarity=0.131 Sum_probs=21.5
Q ss_pred eeecccCCCcc--eEEeEE-EEeeeCCCCceE
Q 037395 89 VAWGSWNYKYA--IKRKVV-GIWSCKYCGKVK 117 (121)
Q Consensus 89 ~htCPFCGK~k--VKR~AV-GIWkCkkCgktf 117 (121)
.|.|.-||... .+|.-. .-+.|++|+-.+
T Consensus 112 ~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCceEccccCcceEEcCCCCCEE
Confidence 58998899764 455433 789999998765
No 121
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=37.66 E-value=18 Score=25.74 Aligned_cols=25 Identities=16% Similarity=0.376 Sum_probs=15.0
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCc
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgk 115 (121)
..|+-||... .-....++.|++||.
T Consensus 71 ~~C~~Cg~~~-~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYV-TLLTQRVRRCPQCHG 95 (114)
T ss_pred EEcccCCCee-ecCCccCCcCcCcCC
Confidence 5788888543 111223477888884
No 122
>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=37.07 E-value=26 Score=29.12 Aligned_cols=29 Identities=14% Similarity=0.151 Sum_probs=22.4
Q ss_pred eeecccCCCcce------EE----eEEEEeeeCCCCceE
Q 037395 89 VAWGSWNYKYAI------KR----KVVGIWSCKYCGKVK 117 (121)
Q Consensus 89 ~htCPFCGK~kV------KR----~AVGIWkCkkCgktf 117 (121)
.++|+.||+..+ -| ..+-++.|..||..|
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRW 296 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCee
Confidence 489999998864 22 237788999999886
No 123
>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=37.01 E-value=27 Score=24.35 Aligned_cols=29 Identities=14% Similarity=0.106 Sum_probs=19.9
Q ss_pred eeecccCCCcceEEe--EEEEeeeCCCCceE
Q 037395 89 VAWGSWNYKYAIKRK--VVGIWSCKYCGKVK 117 (121)
Q Consensus 89 ~htCPFCGK~kVKR~--AVGIWkCkkCgktf 117 (121)
.|.|+-||....++. .+.=..|+.|+-.+
T Consensus 123 ~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 123 VYRCPSCGREYKRHRRSKRKRYRCGRCGGPL 153 (157)
T ss_pred EEEcCCCCCEeeeecccchhhEECCCCCCEE
Confidence 489999996643322 33457899998665
No 124
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=35.41 E-value=30 Score=27.57 Aligned_cols=23 Identities=26% Similarity=0.225 Sum_probs=16.9
Q ss_pred ecccCCCcceEEeEE---EEeeeCCCC
Q 037395 91 WGSWNYKYAIKRKVV---GIWSCKYCG 114 (121)
Q Consensus 91 tCPFCGK~kVKR~AV---GIWkCkkCg 114 (121)
.||.||. .+.|..+ +.|.|..|-
T Consensus 246 pCprCG~-~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLNCKT-PIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred cCCCCCC-eeEEEEECCCccEECcCCc
Confidence 8999984 4555544 478899884
No 125
>PHA00733 hypothetical protein
Probab=35.19 E-value=9.5 Score=27.61 Aligned_cols=30 Identities=17% Similarity=-0.007 Sum_probs=18.5
Q ss_pred eeecccCCCcceE--------EeEEEEeeeCCCCceEe
Q 037395 89 VAWGSWNYKYAIK--------RKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 89 ~htCPFCGK~kVK--------R~AVGIWkCkkCgktfA 118 (121)
.|+|+.||+.--. |....-..|..|++.|.
T Consensus 73 Py~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~ 110 (128)
T PHA00733 73 PYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFR 110 (128)
T ss_pred CccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccC
Confidence 4788888875221 11134478888888764
No 126
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=33.67 E-value=12 Score=31.18 Aligned_cols=20 Identities=15% Similarity=0.328 Sum_probs=15.1
Q ss_pred hhhhhhhhcceeecccCCCcc
Q 037395 79 ALMFYFVFACVAWGSWNYKYA 99 (121)
Q Consensus 79 ~lm~~~~~~~~htCPFCGK~k 99 (121)
.|-.|.-| |.+.|+||.-.+
T Consensus 41 ~lYvHIPF-C~~~C~yC~~~~ 60 (430)
T PRK08208 41 SLYIHIPF-CEMRCGFCNLFT 60 (430)
T ss_pred EEEEEeCC-ccCcCCCCCCcc
Confidence 45666655 999999998554
No 127
>PRK06386 replication factor A; Reviewed
Probab=33.49 E-value=18 Score=30.92 Aligned_cols=21 Identities=19% Similarity=-0.067 Sum_probs=16.8
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCce
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
..||.|++..-+ |.|+.||++
T Consensus 237 ~rCP~C~R~l~~------g~C~~HG~v 257 (358)
T PRK06386 237 TKCSVCNKIIED------GVCKDHPDA 257 (358)
T ss_pred ecCcCCCeEccC------CcCCCCCCC
Confidence 579999887654 899999973
No 128
>PRK00420 hypothetical protein; Validated
Probab=33.49 E-value=26 Score=25.84 Aligned_cols=27 Identities=19% Similarity=-0.024 Sum_probs=19.9
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
..||.||...++ .-.|-=.|..||..+
T Consensus 24 ~~CP~Cg~pLf~-lk~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLFE-LKDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCccee-cCCCceECCCCCCee
Confidence 689999977766 233567899998754
No 129
>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=33.45 E-value=21 Score=24.71 Aligned_cols=25 Identities=20% Similarity=0.253 Sum_probs=17.9
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
.| -||+..+-+..+--=+| -||+++
T Consensus 5 rC-~Cgr~lya~e~~kTkkC-~CG~~l 29 (68)
T PF09082_consen 5 RC-DCGRYLYAKEGAKTKKC-VCGKTL 29 (68)
T ss_dssp EE-TTS--EEEETT-SEEEE-TTTEEE
T ss_pred Ee-cCCCEEEecCCcceeEe-cCCCee
Confidence 45 49999888888888899 999886
No 130
>PRK04860 hypothetical protein; Provisional
Probab=32.63 E-value=16 Score=27.78 Aligned_cols=29 Identities=14% Similarity=0.366 Sum_probs=20.3
Q ss_pred eeecccCCCcce--EEeE-----EEEeeeCCCCceEe
Q 037395 89 VAWGSWNYKYAI--KRKV-----VGIWSCKYCGKVKA 118 (121)
Q Consensus 89 ~htCPFCGK~kV--KR~A-----VGIWkCkkCgktfA 118 (121)
.|.|+ |++..+ +|-. .....|+.|+..+.
T Consensus 119 ~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~ 154 (160)
T PRK04860 119 PYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLV 154 (160)
T ss_pred EEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeE
Confidence 38898 977543 4433 45699999998763
No 131
>PHA02998 RNA polymerase subunit; Provisional
Probab=32.60 E-value=45 Score=27.31 Aligned_cols=31 Identities=13% Similarity=-0.006 Sum_probs=22.6
Q ss_pred ceeecccCCCcceE------Ee----EEEEeeeCCCCceEe
Q 037395 88 CVAWGSWNYKYAIK------RK----VVGIWSCKYCGKVKA 118 (121)
Q Consensus 88 ~~htCPFCGK~kVK------R~----AVGIWkCkkCgktfA 118 (121)
-.-+||.||....- |. .+--..|..||++|.
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 44689999987543 32 266789999999873
No 132
>smart00355 ZnF_C2H2 zinc finger.
Probab=32.45 E-value=20 Score=17.08 Aligned_cols=9 Identities=11% Similarity=-0.491 Sum_probs=5.1
Q ss_pred eecccCCCc
Q 037395 90 AWGSWNYKY 98 (121)
Q Consensus 90 htCPFCGK~ 98 (121)
|.|+.|++.
T Consensus 1 ~~C~~C~~~ 9 (26)
T smart00355 1 YRCPECGKV 9 (26)
T ss_pred CCCCCCcch
Confidence 356666654
No 133
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=32.41 E-value=49 Score=23.78 Aligned_cols=29 Identities=10% Similarity=0.047 Sum_probs=20.9
Q ss_pred eeecccCCCcceE----Ee------EEEEeeeCCCCceE
Q 037395 89 VAWGSWNYKYAIK----RK------VVGIWSCKYCGKVK 117 (121)
Q Consensus 89 ~htCPFCGK~kVK----R~------AVGIWkCkkCgktf 117 (121)
+-+||.||-..+- ++ .|=...|.+||++|
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~w 110 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRW 110 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEe
Confidence 4679999987532 11 24479999999987
No 134
>PF01249 Ribosomal_S21e: Ribosomal protein S21e ; InterPro: IPR001931 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 ribosomal proteins can be grouped on the basis of sequence similarities. These proteins have 82 to 87 amino acids. The amino termini are all N alpha-acetylated. The N-terminal halves of the protein molecules are highly conserved in contrast to the carboxy-terminal parts [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3U5G_V 3U5C_V 3IZB_T 2XZN_Z 2XZM_Z 3IZ6_T.
Probab=31.88 E-value=8.9 Score=27.20 Aligned_cols=34 Identities=35% Similarity=0.541 Sum_probs=27.9
Q ss_pred CCCCcccccccccCccccccceeecccccccccccc
Q 037395 34 SRVPSICSCANRITPHAFDHGFILSGFAEKDDQEGM 69 (121)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~ 69 (121)
.-+|--||=.|||. +|-||+-|---+++-|.+ |.
T Consensus 11 lYiPRKCS~TnriI-~aKDHaSvQinv~~vd~~-G~ 44 (81)
T PF01249_consen 11 LYIPRKCSATNRII-SAKDHASVQINVADVDEN-GR 44 (81)
T ss_dssp SSHHHCHTTTHHCH-HTTSTTSEEEEEEEE-SS-S-
T ss_pred EeccccccccCCcc-ccCCceeEEEEeeeecCc-cc
Confidence 36899999999986 588999999999988887 64
No 135
>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=31.78 E-value=25 Score=20.23 Aligned_cols=10 Identities=30% Similarity=0.697 Sum_probs=4.3
Q ss_pred cccccccchh
Q 037395 70 NCWKPFVNPA 79 (121)
Q Consensus 70 ~~~k~~~~~~ 79 (121)
..|+-|..+.
T Consensus 2 ~vW~~F~~~~ 11 (45)
T PF02892_consen 2 PVWKHFTKIP 11 (45)
T ss_dssp GCCCCCEE--
T ss_pred CccccEEEcc
Confidence 4565555544
No 136
>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=31.49 E-value=35 Score=21.16 Aligned_cols=10 Identities=0% Similarity=-0.485 Sum_probs=3.7
Q ss_pred ceeecccCCC
Q 037395 88 CVAWGSWNYK 97 (121)
Q Consensus 88 ~~htCPFCGK 97 (121)
=+|.|..||.
T Consensus 24 rrhhCr~CG~ 33 (69)
T PF01363_consen 24 RRHHCRNCGR 33 (69)
T ss_dssp -EEE-TTT--
T ss_pred eeEccCCCCC
Confidence 3466666654
No 137
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.42 E-value=41 Score=24.60 Aligned_cols=28 Identities=21% Similarity=-0.007 Sum_probs=23.4
Q ss_pred ecccCCCcc--eEEeEEEEeeeCCCCceEe
Q 037395 91 WGSWNYKYA--IKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 91 tCPFCGK~k--VKR~AVGIWkCkkCgktfA 118 (121)
.||.|+-.. +-|..|-|=.|.+|.-+|-
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrGVWL 32 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRGVWL 32 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCccccEee
Confidence 599999875 5677888999999987774
No 138
>PHA00616 hypothetical protein
Probab=31.42 E-value=15 Score=23.44 Aligned_cols=10 Identities=0% Similarity=-0.678 Sum_probs=7.9
Q ss_pred eecccCCCcc
Q 037395 90 AWGSWNYKYA 99 (121)
Q Consensus 90 htCPFCGK~k 99 (121)
|+|+.||+.-
T Consensus 2 YqC~~CG~~F 11 (44)
T PHA00616 2 YQCLRCGGIF 11 (44)
T ss_pred CccchhhHHH
Confidence 7899998764
No 139
>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=31.29 E-value=47 Score=18.55 Aligned_cols=23 Identities=13% Similarity=0.235 Sum_probs=13.4
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCce
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
.|..|++..---. ..+|..|+.+
T Consensus 2 ~C~~C~~~~~~~~---~Y~C~~c~f~ 24 (30)
T PF03107_consen 2 WCDVCRRKIDGFY---FYHCSECCFT 24 (30)
T ss_pred CCCCCCCCcCCCE---eEEeCCCCCe
Confidence 5667766543222 5777777744
No 140
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=31.29 E-value=27 Score=29.72 Aligned_cols=41 Identities=24% Similarity=0.157 Sum_probs=29.5
Q ss_pred ccchhhhhhhhhcceeecccCCCcc--eE--------------EeEEEEeeeCCCCceEe
Q 037395 75 FVNPALMFYFVFACVAWGSWNYKYA--IK--------------RKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 75 ~~~~~lm~~~~~~~~htCPFCGK~k--VK--------------R~AVGIWkCkkCgktfA 118 (121)
.-..+.+.++...-.|.|+.|||.- .. +.| -+|+.|+|++.
T Consensus 116 ~~s~~~~~~~~~~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka---~~C~~C~K~Yv 172 (279)
T KOG2462|consen 116 VPSAEATASAAKHPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKA---FSCKYCGKVYV 172 (279)
T ss_pred ccccccccccccCCceeccccccccccccccchhhccccccccccc---ccCCCCCceee
Confidence 3445666777778889999999973 33 333 78999998864
No 141
>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=31.20 E-value=20 Score=27.04 Aligned_cols=25 Identities=16% Similarity=0.052 Sum_probs=19.1
Q ss_pred ceeecccCCCcc--eEEeEEEEeeeCCCCce
Q 037395 88 CVAWGSWNYKYA--IKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 88 ~~htCPFCGK~k--VKR~AVGIWkCkkCgkt 116 (121)
=..+||.|+|.. +.|+ =.|-.|+..
T Consensus 68 v~V~CP~C~K~TKmLGr~----D~CM~C~~p 94 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRV----DACMHCKEP 94 (114)
T ss_pred eeeECCCCCChHhhhchh----hccCcCCCc
Confidence 346899999996 7887 378888753
No 142
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=31.19 E-value=21 Score=27.99 Aligned_cols=24 Identities=17% Similarity=0.278 Sum_probs=21.1
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
+.|+.|.+.+-.|. |||+-|++-+
T Consensus 114 ~~C~~C~~~rPpRs----~HCsvC~~CV 137 (299)
T KOG1311|consen 114 KYCDTCQLYRPPRS----SHCSVCNNCV 137 (299)
T ss_pred EEcCcCcccCCCCc----ccchhhcccc
Confidence 78999999998888 9999998743
No 143
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=30.86 E-value=25 Score=23.74 Aligned_cols=27 Identities=15% Similarity=0.088 Sum_probs=14.8
Q ss_pred eecccCCC-cceE-EeEEE----EeeeCCCCce
Q 037395 90 AWGSWNYK-YAIK-RKVVG----IWSCKYCGKV 116 (121)
Q Consensus 90 htCPFCGK-~kVK-R~AVG----IWkCkkCgkt 116 (121)
..||.||. +.+| |.-+- .-.|.+|.+.
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 4333 22121 2457777653
No 144
>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=30.74 E-value=22 Score=23.54 Aligned_cols=24 Identities=25% Similarity=0.311 Sum_probs=16.9
Q ss_pred eecccCCCcceEEeEEEEeeeCCCC
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCG 114 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCg 114 (121)
|.|..||..+.- .-.|+|.|..|.
T Consensus 1 ~~C~VC~~~~~g-~hygv~sC~aC~ 24 (77)
T cd06956 1 HICAICGDRASG-KHYGVYSCEGCK 24 (77)
T ss_pred CCCcccCCcCcc-eEECceeehhHH
Confidence 468888876543 567888888774
No 145
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=30.74 E-value=56 Score=22.78 Aligned_cols=29 Identities=14% Similarity=0.109 Sum_probs=22.9
Q ss_pred eecccCCCcc-eEEeEEEEeeeCCCCceEe
Q 037395 90 AWGSWNYKYA-IKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 90 htCPFCGK~k-VKR~AVGIWkCkkCgktfA 118 (121)
-+||-||... |=-.|.-.=.|-.||.+.|
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccEEE
Confidence 5899999886 4445666679999999886
No 146
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=30.44 E-value=9.4 Score=33.96 Aligned_cols=40 Identities=25% Similarity=0.439 Sum_probs=26.7
Q ss_pred chhhhhhhhhcceeecccCCCc-ceEEeEEEEeeeCCCCceEecC
Q 037395 77 NPALMFYFVFACVAWGSWNYKY-AIKRKVVGIWSCKYCGKVKAGG 120 (121)
Q Consensus 77 ~~~lm~~~~~~~~htCPFCGK~-kVKR~AVGIWkCkkCgktfAGG 120 (121)
+|.|=-|-. -.|+.|... ++.-.-.+-|.|.+||.++.=|
T Consensus 238 dP~LGKY~~----TAC~rC~t~y~le~A~~~~wrCpkCGg~ikKG 278 (403)
T COG1379 238 DPRLGKYHL----TACSRCYTRYSLEEAKSLRWRCPKCGGKIKKG 278 (403)
T ss_pred CccccchhH----HHHHHhhhccCcchhhhhcccCcccccchhhh
Confidence 477878877 457789743 3332333459999999887543
No 147
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=29.80 E-value=31 Score=30.42 Aligned_cols=23 Identities=13% Similarity=-0.051 Sum_probs=11.6
Q ss_pred eeecccCCCcceEEeEEEEeeeCCCCce
Q 037395 89 VAWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 89 ~htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
.-.|+.||.... +-+.|.+||..
T Consensus 491 ~~~C~~CG~~~~-----~~~~CP~CGs~ 513 (546)
T PF13597_consen 491 IDICPDCGYIGG-----EGDKCPKCGSE 513 (546)
T ss_dssp EEEETTT---S-------EEE-CCC---
T ss_pred cccccCCCcCCC-----CCCCCCCCCCc
Confidence 357999998654 36999999986
No 148
>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=29.68 E-value=38 Score=20.75 Aligned_cols=12 Identities=25% Similarity=0.977 Sum_probs=6.8
Q ss_pred EEeeeCCCCceE
Q 037395 106 GIWSCKYCGKVK 117 (121)
Q Consensus 106 GIWkCkkCgktf 117 (121)
.|++|..||..+
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 478888888776
No 149
>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=28.92 E-value=41 Score=20.06 Aligned_cols=10 Identities=30% Similarity=0.906 Sum_probs=7.1
Q ss_pred eeeCCCCceE
Q 037395 108 WSCKYCGKVK 117 (121)
Q Consensus 108 WkCkkCgktf 117 (121)
|.|.+||+++
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 6777787764
No 150
>PLN02459 probable adenylate kinase
Probab=28.71 E-value=4.5 Score=32.94 Aligned_cols=16 Identities=44% Similarity=0.802 Sum_probs=13.3
Q ss_pred ccceeecccccccccc
Q 037395 52 DHGFILSGFAEKDDQE 67 (121)
Q Consensus 52 ~~~~~~~~~~~~~~~~ 67 (121)
..||||.||-..-+|-
T Consensus 109 ~~g~iLDGFPRt~~Qa 124 (261)
T PLN02459 109 ESGFILDGFPRTVRQA 124 (261)
T ss_pred CceEEEeCCCCCHHHH
Confidence 5899999998877763
No 151
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=28.65 E-value=45 Score=26.44 Aligned_cols=24 Identities=13% Similarity=0.052 Sum_probs=17.7
Q ss_pred ecccCCCcceEEeEE---EEeeeCCCCc
Q 037395 91 WGSWNYKYAIKRKVV---GIWSCKYCGK 115 (121)
Q Consensus 91 tCPFCGK~kVKR~AV---GIWkCkkCgk 115 (121)
.||.||.+. +|..+ +.|.|..|-+
T Consensus 247 pC~~Cg~~I-~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTPI-EKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCee-EEEEECCCCcEECcCCCC
Confidence 699999764 44433 5899999965
No 152
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.60 E-value=38 Score=27.11 Aligned_cols=23 Identities=13% Similarity=-0.064 Sum_probs=17.0
Q ss_pred ecccCCCcceEEeEE---EEeeeCCCC
Q 037395 91 WGSWNYKYAIKRKVV---GIWSCKYCG 114 (121)
Q Consensus 91 tCPFCGK~kVKR~AV---GIWkCkkCg 114 (121)
.||.||.+.. +..+ +.|.|..|-
T Consensus 256 pC~~Cg~~I~-~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 256 PCRKCGTPIE-RIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCcCCCeeE-EEEECCCccEECCCCc
Confidence 8999997644 4433 489999995
No 153
>PF06061 Baculo_ME53: Baculoviridae ME53; InterPro: IPR010336 ME53 is one of the major early-transcribed genes. The ME53 protein is reported to contain a putative zinc finger motif [].; GO: 0003677 DNA binding, 0008270 zinc ion binding
Probab=28.33 E-value=27 Score=29.72 Aligned_cols=36 Identities=19% Similarity=0.373 Sum_probs=29.1
Q ss_pred hhhhhhhcceeecccCCCcceEEeEEEEeeeCCCCce
Q 037395 80 LMFYFVFACVAWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 80 lm~~~~~~~~htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
.+-||...|...|..|-+.++- ..-=|-.|.+||.|
T Consensus 251 yvv~f~~p~~~~C~~Ck~~K~y-k~nPVLyCS~CGFT 286 (327)
T PF06061_consen 251 YVVFFNIPCKRECKYCKKNKLY-KNNPVLYCSKCGFT 286 (327)
T ss_pred eEEEeccccchhhhhcccccee-cCCceEEEcccCCC
Confidence 3445666788889999878877 77789999999987
No 154
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=28.27 E-value=51 Score=22.22 Aligned_cols=30 Identities=17% Similarity=0.098 Sum_probs=23.2
Q ss_pred eeecccCCCcc-eEEeEEEEeeeCCCCceEe
Q 037395 89 VAWGSWNYKYA-IKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 89 ~htCPFCGK~k-VKR~AVGIWkCkkCgktfA 118 (121)
+-.||-|++.. |==.|.-.=.|..||.+.|
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCcc
Confidence 36899999986 5555666778999998874
No 155
>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=28.20 E-value=24 Score=19.44 Aligned_cols=11 Identities=36% Similarity=1.053 Sum_probs=8.8
Q ss_pred EEeeeCCCCce
Q 037395 106 GIWSCKYCGKV 116 (121)
Q Consensus 106 GIWkCkkCgkt 116 (121)
|-|.|..|...
T Consensus 3 g~W~C~~C~~~ 13 (30)
T PF00641_consen 3 GDWKCPSCTFM 13 (30)
T ss_dssp SSEEETTTTEE
T ss_pred cCccCCCCcCC
Confidence 56999999864
No 156
>smart00729 Elp3 Elongator protein 3, MiaB family, Radical SAM. This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.
Probab=28.14 E-value=16 Score=24.38 Aligned_cols=18 Identities=6% Similarity=0.082 Sum_probs=13.4
Q ss_pred hhhhhcceeecccCCCcc
Q 037395 82 FYFVFACVAWGSWNYKYA 99 (121)
Q Consensus 82 ~~~~~~~~htCPFCGK~k 99 (121)
...-..|.+.|.||.-..
T Consensus 5 i~~t~~C~~~C~yC~~~~ 22 (216)
T smart00729 5 YIITRGCPRRCTFCSFPS 22 (216)
T ss_pred EEecCchhccCCcCCcCc
Confidence 344568999999997654
No 157
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=27.87 E-value=18 Score=29.04 Aligned_cols=21 Identities=14% Similarity=0.088 Sum_probs=16.2
Q ss_pred hhhhhhhhcceeecccCCCcce
Q 037395 79 ALMFYFVFACVAWGSWNYKYAI 100 (121)
Q Consensus 79 ~lm~~~~~~~~htCPFCGK~kV 100 (121)
.|-.|.-| |.+.|+||.-.+.
T Consensus 5 ~lYiHiPf-C~~~C~yC~~~~~ 25 (374)
T PRK05799 5 SLYIHIPF-CKQKCLYCDFPSY 25 (374)
T ss_pred EEEEEeCC-ccCCCCCCCCCcc
Confidence 46667766 9999999986554
No 158
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=27.82 E-value=43 Score=29.76 Aligned_cols=19 Identities=5% Similarity=-0.001 Sum_probs=17.1
Q ss_pred eeecccCCCcceEEeEEEE
Q 037395 89 VAWGSWNYKYAIKRKVVGI 107 (121)
Q Consensus 89 ~htCPFCGK~kVKR~AVGI 107 (121)
++.||.||-..++|.||-|
T Consensus 257 k~FCp~CG~~TL~K~aVsv 275 (376)
T KOG2463|consen 257 KDFCPSCGHKTLTKCAVSV 275 (376)
T ss_pred hhcccccCCCeeeEEEEEe
Confidence 6889999999999999865
No 159
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=27.80 E-value=27 Score=31.30 Aligned_cols=27 Identities=19% Similarity=0.236 Sum_probs=18.6
Q ss_pred eeecccCCCc-------ceEEeEEEEeeeCCCCc
Q 037395 89 VAWGSWNYKY-------AIKRKVVGIWSCKYCGK 115 (121)
Q Consensus 89 ~htCPFCGK~-------kVKR~AVGIWkCkkCgk 115 (121)
.|.||+|.|+ .+-=...|-.+|.-|+-
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQLLDNETGEFHCENCGG 161 (436)
T ss_pred cccCCccccchhhhHHHHhhcccCceEEEecCCC
Confidence 4889999887 11122457788988873
No 160
>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=27.68 E-value=40 Score=17.41 Aligned_cols=9 Identities=44% Similarity=1.018 Sum_probs=5.1
Q ss_pred eeCCCCceE
Q 037395 109 SCKYCGKVK 117 (121)
Q Consensus 109 kCkkCgktf 117 (121)
.|..|+++|
T Consensus 3 ~C~~C~~~F 11 (27)
T PF13912_consen 3 ECDECGKTF 11 (27)
T ss_dssp EETTTTEEE
T ss_pred CCCccCCcc
Confidence 455666555
No 161
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=27.20 E-value=32 Score=26.63 Aligned_cols=42 Identities=17% Similarity=0.096 Sum_probs=24.7
Q ss_pred cccccceeeccccc--ccccccccccccccchhhhhhhhhcceeecccCCC
Q 037395 49 HAFDHGFILSGFAE--KDDQEGMNCWKPFVNPALMFYFVFACVAWGSWNYK 97 (121)
Q Consensus 49 ~~~~~~~~~~~~~~--~~~~~g~~~~k~~~~~~lm~~~~~~~~htCPFCGK 97 (121)
+.|.+--|.||+.. +-|.+.. .-+..+.-++|.+ .+||.||-
T Consensus 13 ~~F~~~~vrs~~~r~~~~d~D~~---~~Y~~vnP~~Y~V----~vCP~Cgy 56 (214)
T PF09986_consen 13 KEFKTKKVRSGKIRVIRRDSDFC---PRYKGVNPLFYEV----WVCPHCGY 56 (214)
T ss_pred CeeeeeEEEcCCceEeeecCCCc---cccCCCCCeeeeE----EECCCCCC
Confidence 45777777777763 3333333 3333344567777 77777774
No 162
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=27.20 E-value=48 Score=21.59 Aligned_cols=20 Identities=15% Similarity=0.237 Sum_probs=11.9
Q ss_pred eecccCCCcceEEeEEEEeeeCCCC
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCG 114 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCg 114 (121)
..||.||...+.=. .|..||
T Consensus 28 ~~C~~CG~~~~~H~-----vC~~CG 47 (57)
T PRK12286 28 VECPNCGEPKLPHR-----VCPSCG 47 (57)
T ss_pred eECCCCCCccCCeE-----ECCCCC
Confidence 46777777665533 255555
No 163
>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=27.10 E-value=96 Score=21.98 Aligned_cols=23 Identities=9% Similarity=0.079 Sum_probs=14.8
Q ss_pred eecccCCCcc-eEEeEEEEeeeCCCCc
Q 037395 90 AWGSWNYKYA-IKRKVVGIWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~k-VKR~AVGIWkCkkCgk 115 (121)
..|+.||+.. +... .+.|++||.
T Consensus 71 ~~C~~Cg~~~~~~~~---~~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVSPEID---LYRCPKCHG 94 (115)
T ss_pred EEcccCCCEEecCCc---CccCcCCcC
Confidence 5788888653 2222 377888874
No 164
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 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 MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=27.10 E-value=51 Score=18.70 Aligned_cols=19 Identities=32% Similarity=0.363 Sum_probs=11.3
Q ss_pred cccCCCcceEEeEEEEeeeCCCCceE
Q 037395 92 GSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 92 CPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
|..|++..++ .|..|..++
T Consensus 1 C~~C~~~~~~-------~C~~C~~~~ 19 (37)
T PF01753_consen 1 CAVCGKPALK-------RCSRCKSVY 19 (37)
T ss_dssp -TTTSSCSSE-------EETTTSSSE
T ss_pred CcCCCCCcCC-------cCCCCCCEE
Confidence 5667774443 677776554
No 165
>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=27.03 E-value=56 Score=21.83 Aligned_cols=26 Identities=19% Similarity=0.236 Sum_probs=18.4
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCceEe
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKVKA 118 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgktfA 118 (121)
+=.++|...+- .+-.|.|..||..+.
T Consensus 17 ~~~~~G~~~~v--~~~~~~C~~CGe~~~ 42 (127)
T TIGR03830 17 PYTYKGESITI--GVPGWYCPACGEELL 42 (127)
T ss_pred eEEEcCEEEEE--eeeeeECCCCCCEEE
Confidence 34567765444 778899999998764
No 166
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=26.97 E-value=25 Score=28.96 Aligned_cols=22 Identities=18% Similarity=0.187 Sum_probs=17.0
Q ss_pred hhhhhhhhhcceeecccCCCcce
Q 037395 78 PALMFYFVFACVAWGSWNYKYAI 100 (121)
Q Consensus 78 ~~lm~~~~~~~~htCPFCGK~kV 100 (121)
..|-.|.-| |.+.|+||+-.+.
T Consensus 20 ~~lYiHIPF-C~~~C~yC~f~~~ 41 (394)
T PRK08898 20 LSLYVHFPW-CVRKCPYCDFNSH 41 (394)
T ss_pred eEEEEEeCC-ccCcCCCCCCccc
Confidence 356777776 9999999996544
No 167
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.85 E-value=30 Score=31.89 Aligned_cols=21 Identities=14% Similarity=0.158 Sum_probs=15.3
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCc
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGK 115 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgk 115 (121)
-.|+.||...... |.|..||.
T Consensus 681 ~~C~~CG~~~~~~-----~~CP~CG~ 701 (735)
T PRK07111 681 DRCPVCGYLGVIE-----DKCPKCGS 701 (735)
T ss_pred eecCCCCCCCCcC-----ccCcCCCC
Confidence 5799999654321 99999984
No 168
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.81 E-value=95 Score=22.63 Aligned_cols=10 Identities=0% Similarity=-0.721 Sum_probs=7.7
Q ss_pred eecccCCCcc
Q 037395 90 AWGSWNYKYA 99 (121)
Q Consensus 90 htCPFCGK~k 99 (121)
+.|+.||..-
T Consensus 71 ~~C~~CG~~~ 80 (135)
T PRK03824 71 LKCRNCGNEW 80 (135)
T ss_pred EECCCCCCEE
Confidence 7888888663
No 169
>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=26.54 E-value=54 Score=19.79 Aligned_cols=22 Identities=14% Similarity=-0.005 Sum_probs=14.4
Q ss_pred eecccCCCcceEEeEEEEeeeCCCC
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCG 114 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCg 114 (121)
++|..|+...+... -|+|..|.
T Consensus 5 ~~C~~C~~~~i~g~---Ry~C~~C~ 26 (46)
T PF00569_consen 5 YTCDGCGTDPIIGV---RYHCLVCP 26 (46)
T ss_dssp CE-SSS-SSSEESS---EEEESSSS
T ss_pred eECcCCCCCcCcCC---eEECCCCC
Confidence 78999998554433 39999885
No 170
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=26.54 E-value=22 Score=18.70 Aligned_cols=11 Identities=36% Similarity=1.054 Sum_probs=8.2
Q ss_pred EEeeeCCCCce
Q 037395 106 GIWSCKYCGKV 116 (121)
Q Consensus 106 GIWkCkkCgkt 116 (121)
|-|.|..|+..
T Consensus 1 g~W~C~~C~~~ 11 (26)
T smart00547 1 GDWECPACTFL 11 (26)
T ss_pred CcccCCCCCCc
Confidence 46999999653
No 171
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=26.33 E-value=22 Score=22.62 Aligned_cols=20 Identities=15% Similarity=0.250 Sum_probs=13.0
Q ss_pred eecccCCCcceEEeEEEEeeeCCCC
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCG 114 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCg 114 (121)
-.||.||...+... -|..||
T Consensus 27 ~~c~~cg~~~~~H~-----vc~~cG 46 (56)
T PF01783_consen 27 VKCPNCGEPKLPHR-----VCPSCG 46 (56)
T ss_dssp EESSSSSSEESTTS-----BCTTTB
T ss_pred eeeccCCCEecccE-----eeCCCC
Confidence 57888887665443 366665
No 172
>PF13353 Fer4_12: 4Fe-4S single cluster domain; PDB: 3C8F_A 3CB8_A 3T7V_A 2YX0_A 3CAN_A.
Probab=26.10 E-value=15 Score=24.44 Aligned_cols=15 Identities=13% Similarity=0.341 Sum_probs=7.2
Q ss_pred hhhcceeecccCCCc
Q 037395 84 FVFACVAWGSWNYKY 98 (121)
Q Consensus 84 ~~~~~~htCPFCGK~ 98 (121)
|...|.+.|+||-..
T Consensus 11 ~t~~Cnl~C~yC~~~ 25 (139)
T PF13353_consen 11 FTNGCNLRCKYCFNS 25 (139)
T ss_dssp EEC--SB--TT-TTC
T ss_pred EcCcccccCcCcCCc
Confidence 366799999999644
No 173
>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=25.97 E-value=34 Score=22.63 Aligned_cols=10 Identities=0% Similarity=-0.452 Sum_probs=8.3
Q ss_pred ecccCCCcce
Q 037395 91 WGSWNYKYAI 100 (121)
Q Consensus 91 tCPFCGK~kV 100 (121)
.||.||...|
T Consensus 15 ~Cp~CGN~~v 24 (49)
T PF12677_consen 15 KCPKCGNDKV 24 (49)
T ss_pred cCcccCCcEe
Confidence 6999998765
No 174
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=25.46 E-value=43 Score=27.00 Aligned_cols=24 Identities=21% Similarity=0.381 Sum_probs=12.6
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCce
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
.|+.|+...+++. -.-+|..||.+
T Consensus 151 ~CsrC~~~L~~~~--~~l~Cp~Cg~t 174 (188)
T COG1096 151 RCSRCRAPLVKKG--NMLKCPNCGNT 174 (188)
T ss_pred EccCCCcceEEcC--cEEECCCCCCE
Confidence 4666665555521 23456666654
No 175
>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=25.41 E-value=58 Score=18.45 Aligned_cols=13 Identities=23% Similarity=0.994 Sum_probs=9.8
Q ss_pred EEeeeCCCCceEe
Q 037395 106 GIWSCKYCGKVKA 118 (121)
Q Consensus 106 GIWkCkkCgktfA 118 (121)
.+++|..||..+.
T Consensus 3 ~~ykC~~CGniv~ 15 (34)
T cd00974 3 EVYKCEICGNIVE 15 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 3688888888774
No 176
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=25.05 E-value=25 Score=24.31 Aligned_cols=26 Identities=19% Similarity=0.182 Sum_probs=20.2
Q ss_pred eecccCCCc-ceEEeEEEEeeeCCCCceE
Q 037395 90 AWGSWNYKY-AIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~-kVKR~AVGIWkCkkCgktf 117 (121)
|.|-.||.. .+||.- .-+|+.||+.+
T Consensus 21 YiCgdC~~en~lk~~D--~irCReCG~RI 47 (62)
T KOG3507|consen 21 YICGDCGQENTLKRGD--VIRCRECGYRI 47 (62)
T ss_pred EEeccccccccccCCC--cEehhhcchHH
Confidence 789999876 588764 37999999753
No 177
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=24.89 E-value=20 Score=30.26 Aligned_cols=22 Identities=14% Similarity=0.240 Sum_probs=16.9
Q ss_pred chhhhhhhhhcceeecccCCCcc
Q 037395 77 NPALMFYFVFACVAWGSWNYKYA 99 (121)
Q Consensus 77 ~~~lm~~~~~~~~htCPFCGK~k 99 (121)
+..|-.|.-| |.+.|.||+-.+
T Consensus 61 ~~~lYiHIPF-C~~~C~yC~f~~ 82 (449)
T PRK09058 61 KRLLYIHIPF-CRTHCTFCGFFQ 82 (449)
T ss_pred ceEEEEEeCC-cCCcCCCCCCcC
Confidence 3457777777 999999999543
No 178
>PRK05904 coproporphyrinogen III oxidase; Provisional
Probab=24.85 E-value=20 Score=29.36 Aligned_cols=21 Identities=19% Similarity=0.169 Sum_probs=15.7
Q ss_pred hhhhhhhhcceeecccCCCcce
Q 037395 79 ALMFYFVFACVAWGSWNYKYAI 100 (121)
Q Consensus 79 ~lm~~~~~~~~htCPFCGK~kV 100 (121)
.|-.|.-| |.+.|+||+-.++
T Consensus 8 ~lYiHiPF-C~~kC~yC~f~~~ 28 (353)
T PRK05904 8 HLYIHIPF-CQYICTFCDFKRI 28 (353)
T ss_pred EEEEEeCC-ccCcCCCCCCeec
Confidence 45556666 9999999997654
No 179
>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=24.76 E-value=50 Score=21.49 Aligned_cols=28 Identities=11% Similarity=0.016 Sum_probs=17.2
Q ss_pred eecccCCCcc-eEEeEE-EEeeeCCCCceE
Q 037395 90 AWGSWNYKYA-IKRKVV-GIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK~k-VKR~AV-GIWkCkkCgktf 117 (121)
.+||.||... +.-... -|=.|..||..+
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAEL 32 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCEE
Confidence 4789998863 332221 266888888653
No 180
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=24.66 E-value=75 Score=23.67 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=17.8
Q ss_pred ecccCCCcc--eEEeEEEEe--eeCCCCce
Q 037395 91 WGSWNYKYA--IKRKVVGIW--SCKYCGKV 116 (121)
Q Consensus 91 tCPFCGK~k--VKR~AVGIW--kCkkCgkt 116 (121)
.|+.|+.+- +.+. ..+| +|..||.+
T Consensus 99 lC~~C~sPdT~l~k~-~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 99 ICRECNRPDTRIIKE-GRVSLLKCEACGAK 127 (133)
T ss_pred ECCCCCCCCcEEEEe-CCeEEEecccCCCC
Confidence 799999983 3333 2344 89999975
No 181
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=24.36 E-value=64 Score=18.22 Aligned_cols=13 Identities=23% Similarity=0.979 Sum_probs=10.2
Q ss_pred EEeeeCCCCceEe
Q 037395 106 GIWSCKYCGKVKA 118 (121)
Q Consensus 106 GIWkCkkCgktfA 118 (121)
.+++|..||..+.
T Consensus 6 ~~ykC~~Cgniv~ 18 (34)
T TIGR00319 6 QVYKCEVCGNIVE 18 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 4788888888774
No 182
>cd01198 INT_ASSRA_C Archaeal site-specific recombinase A (ASSRA), DNA breaking-rejoining enzymes, integrase/recombinases, C-terminal catalytic domain. Members of this CD are archael in origin. No biochemical characterization is available for the proteins of this subgroup at this point.
Probab=24.10 E-value=29 Score=23.95 Aligned_cols=14 Identities=43% Similarity=0.747 Sum_probs=11.7
Q ss_pred cccCccccccceee
Q 037395 44 NRITPHAFDHGFIL 57 (121)
Q Consensus 44 ~~~~~~~~~~~~~~ 57 (121)
.+++||.|-|.|.-
T Consensus 126 ~~~~~H~lRHt~at 139 (186)
T cd01198 126 ENFTPHCFRHFFTT 139 (186)
T ss_pred cCcCcccchhHHHH
Confidence 47899999999863
No 183
>KOG1873 consensus Ubiquitin-specific protease [Posttranslational modification, protein turnover, chaperones]
Probab=24.00 E-value=32 Score=33.37 Aligned_cols=31 Identities=23% Similarity=0.267 Sum_probs=25.3
Q ss_pred eecccCCCcceEEe---------EEEEeeeCCCCceEecC
Q 037395 90 AWGSWNYKYAIKRK---------VVGIWSCKYCGKVKAGG 120 (121)
Q Consensus 90 htCPFCGK~kVKR~---------AVGIWkCkkCgktfAGG 120 (121)
|.|..|-.....+. ---||-|-+||+.+.|+
T Consensus 67 ~~C~eC~e~~~~k~g~s~~~~~~~~~iWLCLkCG~q~CG~ 106 (877)
T KOG1873|consen 67 IKCSECNEEVKVKDGGSSDQFEFDNAIWLCLKCGYQGCGR 106 (877)
T ss_pred HHHHHhhhcceeccCCCccccccccceeeecccCCeeeCC
Confidence 88999988754443 46799999999999986
No 184
>PRK07591 threonine synthase; Validated
Probab=23.40 E-value=38 Score=28.39 Aligned_cols=24 Identities=13% Similarity=-0.165 Sum_probs=16.8
Q ss_pred eeecccCCCcceEEeEEEEeeeCCCCc
Q 037395 89 VAWGSWNYKYAIKRKVVGIWSCKYCGK 115 (121)
Q Consensus 89 ~htCPFCGK~kVKR~AVGIWkCkkCgk 115 (121)
.+.|..||+.---- ..|.|..|+-
T Consensus 18 ~l~C~~Cg~~~~~~---~~~~C~~cg~ 41 (421)
T PRK07591 18 ALKCRECGAEYPLG---PIHVCEECFG 41 (421)
T ss_pred EEEeCCCCCcCCCC---CCccCCCCCC
Confidence 48899999875321 2299998973
No 185
>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=23.34 E-value=31 Score=22.79 Aligned_cols=10 Identities=0% Similarity=-0.522 Sum_probs=3.3
Q ss_pred eecccCCCcc
Q 037395 90 AWGSWNYKYA 99 (121)
Q Consensus 90 htCPFCGK~k 99 (121)
|+||.||.+.
T Consensus 34 y~Cp~CgAtG 43 (55)
T PF05741_consen 34 YVCPICGATG 43 (55)
T ss_dssp ---TTT---G
T ss_pred CcCCCCcCcC
Confidence 7899999863
No 186
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=23.23 E-value=24 Score=28.42 Aligned_cols=19 Identities=11% Similarity=0.022 Sum_probs=14.1
Q ss_pred hhhhhhhcceeecccCCCcc
Q 037395 80 LMFYFVFACVAWGSWNYKYA 99 (121)
Q Consensus 80 lm~~~~~~~~htCPFCGK~k 99 (121)
|-.|.-| |.+.|+||.-.+
T Consensus 4 lYihiPf-C~~~C~yC~~~~ 22 (377)
T PRK08599 4 AYIHIPF-CEHICYYCDFNK 22 (377)
T ss_pred EEEEeCC-cCCCCCCCCCee
Confidence 3345566 999999998654
No 187
>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=23.22 E-value=37 Score=25.63 Aligned_cols=28 Identities=11% Similarity=-0.002 Sum_probs=17.5
Q ss_pred eeecccCCCcceEEeEEEEeeeCCCCce
Q 037395 89 VAWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 89 ~htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
.++|..||....--.+.=|=.|.+|+.+
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 4677777776533334457777777754
No 188
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=23.16 E-value=43 Score=18.30 Aligned_cols=8 Identities=38% Similarity=1.082 Sum_probs=4.0
Q ss_pred eCCCCceE
Q 037395 110 CKYCGKVK 117 (121)
Q Consensus 110 CkkCgktf 117 (121)
|..||++|
T Consensus 5 C~~CgR~F 12 (25)
T PF13913_consen 5 CPICGRKF 12 (25)
T ss_pred CCCCCCEE
Confidence 44555544
No 189
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=23.11 E-value=46 Score=23.59 Aligned_cols=27 Identities=11% Similarity=-0.085 Sum_probs=19.2
Q ss_pred eecccCCCcceEEeEEEEeeeCCCCce
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
+.|+-||...+--.+-+==.|.+|+..
T Consensus 43 ~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 43 YRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred eecCCCCceEEecCcccCcCCCCCCCh
Confidence 778888888766555555677777754
No 190
>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=23.10 E-value=47 Score=21.42 Aligned_cols=16 Identities=19% Similarity=0.308 Sum_probs=11.8
Q ss_pred EeEEEEeeeCCCCceE
Q 037395 102 RKVVGIWSCKYCGKVK 117 (121)
Q Consensus 102 R~AVGIWkCkkCgktf 117 (121)
+..+|+|.|......+
T Consensus 6 ~~~~g~w~~~pg~~~~ 21 (74)
T PF05899_consen 6 VFSAGVWECTPGKFPW 21 (74)
T ss_dssp SEEEEEEEEECEEEEE
T ss_pred CEEEEEEEECCceeEe
Confidence 4678999998865443
No 191
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=22.91 E-value=54 Score=25.93 Aligned_cols=28 Identities=18% Similarity=0.208 Sum_probs=20.7
Q ss_pred eeecccCCCc--ceEEeEEEE----eeeCCCCceE
Q 037395 89 VAWGSWNYKY--AIKRKVVGI----WSCKYCGKVK 117 (121)
Q Consensus 89 ~htCPFCGK~--kVKR~AVGI----WkCkkCgktf 117 (121)
.|.|. |+.. +++|.-+-. ..|++|+-+.
T Consensus 117 ~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gkL 150 (156)
T COG3091 117 PYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGKL 150 (156)
T ss_pred eEEee-cCCccchhhhcccccccceEEeccCCceE
Confidence 48999 9976 456655544 9999998653
No 192
>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=22.68 E-value=47 Score=33.02 Aligned_cols=23 Identities=17% Similarity=0.274 Sum_probs=18.0
Q ss_pred ceeecccCCCcceEEeEEEEeeeCCCCce
Q 037395 88 CVAWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 88 ~~htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
....||.||+.+.+ +.|.+||..
T Consensus 624 ~~RKCPkCG~yTlk------~rCP~CG~~ 646 (1095)
T TIGR00354 624 AIRKCPQCGKESFW------LKCPVCGEL 646 (1095)
T ss_pred EEEECCCCCccccc------ccCCCCCCc
Confidence 45789999999887 568888854
No 193
>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=22.51 E-value=66 Score=22.48 Aligned_cols=28 Identities=18% Similarity=-0.046 Sum_probs=17.7
Q ss_pred ccccchhhhhhhhhcceeecccCCCcceEEeEEEEeeeCC
Q 037395 73 KPFVNPALMFYFVFACVAWGSWNYKYAIKRKVVGIWSCKY 112 (121)
Q Consensus 73 k~~~~~~lm~~~~~~~~htCPFCGK~kVKR~AVGIWkCkk 112 (121)
|+-+++.| .++|..|++..++.. |.|++
T Consensus 45 K~TKKi~L--------rl~C~~C~~~~~~~~----~R~kk 72 (77)
T PF00935_consen 45 KTTKKIVL--------RLECTECGKAHMRPG----KRCKK 72 (77)
T ss_dssp -SSEBBEE--------EEEETTTS-EEEEE-----BBESS
T ss_pred cccccEEE--------EEEeCCCCccccccc----ceeEE
Confidence 45556655 489999998877543 77764
No 194
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.47 E-value=33 Score=30.31 Aligned_cols=26 Identities=31% Similarity=0.477 Sum_probs=21.0
Q ss_pred eeecccCCCcc-e---EEeEEEEeeeCCCC
Q 037395 89 VAWGSWNYKYA-I---KRKVVGIWSCKYCG 114 (121)
Q Consensus 89 ~htCPFCGK~k-V---KR~AVGIWkCkkCg 114 (121)
.|.||.||+.- + -|.+-|-|-|..|+
T Consensus 32 ~~~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 32 GHPCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred CCCCCccCCccccccCCccCCccEEEEeec
Confidence 46999998763 3 47789999999997
No 195
>PHA02768 hypothetical protein; Provisional
Probab=22.21 E-value=34 Score=22.63 Aligned_cols=29 Identities=17% Similarity=0.018 Sum_probs=18.2
Q ss_pred eecccCCCcceEEe--------EEEEeeeCCCCceEe
Q 037395 90 AWGSWNYKYAIKRK--------VVGIWSCKYCGKVKA 118 (121)
Q Consensus 90 htCPFCGK~kVKR~--------AVGIWkCkkCgktfA 118 (121)
|.|+.|||.-..+. -+---+|..|++.+.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~ 42 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISL 42 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcCCcccCCcccceec
Confidence 68999999743322 111237888887653
No 196
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=22.17 E-value=40 Score=22.54 Aligned_cols=8 Identities=0% Similarity=-0.446 Sum_probs=6.4
Q ss_pred ecccCCCc
Q 037395 91 WGSWNYKY 98 (121)
Q Consensus 91 tCPFCGK~ 98 (121)
-|||||+.
T Consensus 41 gCPfC~~~ 48 (55)
T PF14447_consen 41 GCPFCGTP 48 (55)
T ss_pred CCCCCCCc
Confidence 49999975
No 197
>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=22.08 E-value=69 Score=18.61 Aligned_cols=10 Identities=40% Similarity=0.890 Sum_probs=4.8
Q ss_pred eCCCCceEec
Q 037395 110 CKYCGKVKAG 119 (121)
Q Consensus 110 CkkCgktfAG 119 (121)
|..|++.+.+
T Consensus 29 C~~C~~~l~~ 38 (58)
T PF00412_consen 29 CSKCGKPLND 38 (58)
T ss_dssp ETTTTCBTTT
T ss_pred cCCCCCccCC
Confidence 5555554443
No 198
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=22.03 E-value=86 Score=23.49 Aligned_cols=26 Identities=19% Similarity=0.202 Sum_probs=18.6
Q ss_pred ecccCCCcc---eEEeEEEEeeeCCCCce
Q 037395 91 WGSWNYKYA---IKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 91 tCPFCGK~k---VKR~AVGIWkCkkCgkt 116 (121)
.|+.||.+- +|..-+=+=+|..||..
T Consensus 104 lC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 104 ICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred ECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 799999983 44333445689999975
No 199
>KOG3486 consensus 40S ribosomal protein S21 [Translation, ribosomal structure and biogenesis]
Probab=21.84 E-value=63 Score=23.43 Aligned_cols=45 Identities=33% Similarity=0.375 Sum_probs=31.4
Q ss_pred CCCCcccccccccCccccccceeecccccccccccccccccccchhh
Q 037395 34 SRVPSICSCANRITPHAFDHGFILSGFAEKDDQEGMNCWKPFVNPAL 80 (121)
Q Consensus 34 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~k~~~~~~l 80 (121)
--||--||=.|||. +|=||--|--.++.-|.. |--.--+|..-||
T Consensus 11 LYvPrKcS~sNriI-~aKDHaSVQ~N~~~vd~~-g~~~~g~~ttyAl 55 (83)
T KOG3486|consen 11 LYVPRKCSATNRII-TAKDHASVQLNIGHVDAE-GGLYTGQFTTYAL 55 (83)
T ss_pred EEecccccccceee-ecccchheeecccccccc-cCccCCceehHHH
Confidence 36899999999996 688999888877776655 4433334443333
No 200
>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=21.81 E-value=44 Score=23.27 Aligned_cols=24 Identities=13% Similarity=0.066 Sum_probs=17.4
Q ss_pred eecccCCCcceEEeEEEEeeeCCCC
Q 037395 90 AWGSWNYKYAIKRKVVGIWSCKYCG 114 (121)
Q Consensus 90 htCPFCGK~kVKR~AVGIWkCkkCg 114 (121)
..|..||..+.- .-.|.|.|..|.
T Consensus 6 ~~C~VCg~~~~g-~hyGv~sC~aC~ 29 (95)
T cd06968 6 IPCKICGDKSSG-IHYGVITCEGCK 29 (95)
T ss_pred cCCcccCCcCcc-eEECceeehhhH
Confidence 468889876644 347888888885
No 201
>PRK07220 DNA topoisomerase I; Validated
Probab=21.62 E-value=85 Score=28.73 Aligned_cols=27 Identities=11% Similarity=0.059 Sum_probs=18.3
Q ss_pred eecccCCCcceEEeE---EEEeeeCC---CCce
Q 037395 90 AWGSWNYKYAIKRKV---VGIWSCKY---CGKV 116 (121)
Q Consensus 90 htCPFCGK~kVKR~A---VGIWkCkk---Cgkt 116 (121)
..||.||+..+.|.+ -.-|.|.. |..+
T Consensus 590 ~~CP~Cg~~l~~r~~r~g~~f~gCs~yp~C~~~ 622 (740)
T PRK07220 590 GKCPLCGSDLMVRRSKRGSRFIGCEGYPECTFS 622 (740)
T ss_pred cccccCCCeeeEEecCCCceEEEcCCCCCCCce
Confidence 479999988765443 23688864 7654
No 202
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.60 E-value=43 Score=33.84 Aligned_cols=22 Identities=14% Similarity=0.142 Sum_probs=12.2
Q ss_pred ecccCCCcceEEeEEEEeeeCCCCceE
Q 037395 91 WGSWNYKYAIKRKVVGIWSCKYCGKVK 117 (121)
Q Consensus 91 tCPFCGK~kVKR~AVGIWkCkkCgktf 117 (121)
.||.||... .-++.|.+||..+
T Consensus 681 fCP~CGs~t-----e~vy~CPsCGaev 702 (1337)
T PRK14714 681 RCPDCGTHT-----EPVYVCPDCGAEV 702 (1337)
T ss_pred cCcccCCcC-----CCceeCccCCCcc
Confidence 455555543 1145777777654
No 203
>PF01586 Basic: Myogenic Basic domain; InterPro: IPR002546 This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding []. With 12 residues of the basic domain involved in DNA binding []. The basic domain forms an extended alpha helix in the structure.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007517 muscle organ development, 0005634 nucleus; PDB: 1MDY_C.
Probab=21.52 E-value=32 Score=24.55 Aligned_cols=11 Identities=36% Similarity=1.274 Sum_probs=0.9
Q ss_pred EeeeCCCCceE
Q 037395 107 IWSCKYCGKVK 117 (121)
Q Consensus 107 IWkCkkCgktf 117 (121)
+|.||-|.++-
T Consensus 72 ~WACKaCKRKt 82 (86)
T PF01586_consen 72 LWACKACKRKT 82 (86)
T ss_dssp -------S---
T ss_pred HHHhHhhhccC
Confidence 59999998874
No 204
>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=21.46 E-value=46 Score=21.79 Aligned_cols=22 Identities=27% Similarity=0.308 Sum_probs=11.7
Q ss_pred cccCCCcceEEeEEEEeeeCCCC
Q 037395 92 GSWNYKYAIKRKVVGIWSCKYCG 114 (121)
Q Consensus 92 CPFCGK~kVKR~AVGIWkCkkCg 114 (121)
|..||..+. -.-.|.|.|..|.
T Consensus 1 C~vCg~~~~-~~hygv~~C~aC~ 22 (76)
T cd06960 1 CAVCGDRAT-GKHYGVLSCNGCK 22 (76)
T ss_pred CCccCccCc-ccEECcceeeeeh
Confidence 455665432 2345666666664
No 205
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=21.33 E-value=17 Score=29.91 Aligned_cols=27 Identities=11% Similarity=0.172 Sum_probs=15.0
Q ss_pred eecccCCCcceEEe-EEEEeeeCCCCce
Q 037395 90 AWGSWNYKYAIKRK-VVGIWSCKYCGKV 116 (121)
Q Consensus 90 htCPFCGK~kVKR~-AVGIWkCkkCgkt 116 (121)
..||.|+....++. ....+.|.+|++-
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h 55 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHH 55 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCC
Confidence 46777776643222 2234677777654
No 206
>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=20.95 E-value=1.1e+02 Score=21.91 Aligned_cols=18 Identities=28% Similarity=0.448 Sum_probs=11.7
Q ss_pred ecccCCC-cceEEeEEEEe
Q 037395 91 WGSWNYK-YAIKRKVVGIW 108 (121)
Q Consensus 91 tCPFCGK-~kVKR~AVGIW 108 (121)
.|++|+. ....+..+=.|
T Consensus 1 ~C~~C~~~~~~~~~tTv~~ 19 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYW 19 (89)
T ss_pred CCcccCCCceecceEEEEE
Confidence 4899944 55666666666
No 207
>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=20.86 E-value=50 Score=21.85 Aligned_cols=13 Identities=8% Similarity=-0.472 Sum_probs=6.8
Q ss_pred eeecccCCCcceE
Q 037395 89 VAWGSWNYKYAIK 101 (121)
Q Consensus 89 ~htCPFCGK~kVK 101 (121)
+.+||.|||...-
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 3689999987654
No 208
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=20.73 E-value=29 Score=29.17 Aligned_cols=20 Identities=15% Similarity=0.149 Sum_probs=16.5
Q ss_pred hhhhhhhhcceeecccCCCcc
Q 037395 79 ALMFYFVFACVAWGSWNYKYA 99 (121)
Q Consensus 79 ~lm~~~~~~~~htCPFCGK~k 99 (121)
.|-.|.-| |.+.|+||+-.+
T Consensus 52 ~LYvHIPf-C~~~C~yC~~~~ 71 (453)
T PRK13347 52 SLYLHVPF-CRSLCWFCGCNT 71 (453)
T ss_pred EEEEEeCC-ccccCCCCCCcC
Confidence 57778777 999999998654
No 209
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=20.48 E-value=50 Score=23.00 Aligned_cols=26 Identities=15% Similarity=0.079 Sum_probs=17.5
Q ss_pred eeecccCCCcceEEeEEEE-eeeCCCC
Q 037395 89 VAWGSWNYKYAIKRKVVGI-WSCKYCG 114 (121)
Q Consensus 89 ~htCPFCGK~kVKR~AVGI-WkCkkCg 114 (121)
||.||-||..++-..+-|. =.|.-|.
T Consensus 1 K~~CPCCg~~Tl~~~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERGEGTYDICPVCF 27 (78)
T ss_pred CccCCCCCcEEeccCCCcCceECCCCC
Confidence 5899999999876665432 2455553
No 210
>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=20.38 E-value=76 Score=27.43 Aligned_cols=28 Identities=11% Similarity=0.126 Sum_probs=15.3
Q ss_pred eecccCCC-cceEEeE------EEEeeeCCCCceE
Q 037395 90 AWGSWNYK-YAIKRKV------VGIWSCKYCGKVK 117 (121)
Q Consensus 90 htCPFCGK-~kVKR~A------VGIWkCkkCgktf 117 (121)
-.|+.||| ..+.=.. +=-++|..||.+.
T Consensus 175 piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g 209 (360)
T PF01921_consen 175 PICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEG 209 (360)
T ss_dssp EEETTTEE--EEEEEEE--SSSEEEEE--TTS---
T ss_pred eeccccCCcccceeeEeecCCCEEEEEecCCCCEE
Confidence 57999999 3433223 3369999999864
No 211
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.22 E-value=43 Score=30.49 Aligned_cols=61 Identities=11% Similarity=0.140 Sum_probs=31.5
Q ss_pred cccceeeccccccc--c-cccccccccccchhhhhhhhh-cceeecccCCCcceEEeEEEEeeeCCCCce
Q 037395 51 FDHGFILSGFAEKD--D-QEGMNCWKPFVNPALMFYFVF-ACVAWGSWNYKYAIKRKVVGIWSCKYCGKV 116 (121)
Q Consensus 51 ~~~~~~~~~~~~~~--~-~~g~~~~k~~~~~~lm~~~~~-~~~htCPFCGK~kVKR~AVGIWkCkkCgkt 116 (121)
++-|+|+--|-..- + +.=+++|+-+-+-.-+.||-+ ----.|+.||... .+ .|.|..||..
T Consensus 584 ~~GG~I~hv~l~e~~~n~~a~~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~-g~----~~~CP~CG~~ 648 (656)
T PRK08270 584 YTGGTVFHLYLGEAISDAEACKKLVKKALENYRLPYITITPTFSICPKHGYLS-GE----HEFCPKCGEE 648 (656)
T ss_pred ecceEEEEEECCCCCCCHHHHHHHHHHHHHhCCCceEEeCCCCcccCCCCCcC-CC----CCCCcCCcCc
Confidence 45677776654311 1 222334443322111333322 2335799999742 22 4999999964
No 212
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=20.17 E-value=42 Score=30.72 Aligned_cols=7 Identities=0% Similarity=-0.600 Sum_probs=3.6
Q ss_pred cccCCCc
Q 037395 92 GSWNYKY 98 (121)
Q Consensus 92 CPFCGK~ 98 (121)
||.||..
T Consensus 30 Cp~CG~~ 36 (645)
T PRK14559 30 CPQCGTE 36 (645)
T ss_pred CCCCCCC
Confidence 5555544
No 213
>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=20.13 E-value=18 Score=29.81 Aligned_cols=27 Identities=7% Similarity=-0.017 Sum_probs=14.9
Q ss_pred eecccCCCcceEE-eEEEEeeeCCCCce
Q 037395 90 AWGSWNYKYAIKR-KVVGIWSCKYCGKV 116 (121)
Q Consensus 90 htCPFCGK~kVKR-~AVGIWkCkkCgkt 116 (121)
..||.|++...++ ..-..+.|.+|++-
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence 4577776664332 23334667777653
No 214
>PRK10954 periplasmic protein disulfide isomerase I; Provisional
Probab=20.13 E-value=22 Score=26.39 Aligned_cols=17 Identities=18% Similarity=0.530 Sum_probs=14.2
Q ss_pred chhhhhhhhhcceeecccCCC
Q 037395 77 NPALMFYFVFACVAWGSWNYK 97 (121)
Q Consensus 77 ~~~lm~~~~~~~~htCPFCGK 97 (121)
+|++..||- |.||+|.+
T Consensus 38 ~~~VvEffd----y~CphC~~ 54 (207)
T PRK10954 38 EPQVLEFFS----FYCPHCYQ 54 (207)
T ss_pred CCeEEEEeC----CCCccHHH
Confidence 677888888 99999976
No 215
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=20.11 E-value=18 Score=30.47 Aligned_cols=27 Identities=19% Similarity=0.152 Sum_probs=16.3
Q ss_pred eecccCCCcce-EEeEEEEeeeCCCCce
Q 037395 90 AWGSWNYKYAI-KRKVVGIWSCKYCGKV 116 (121)
Q Consensus 90 htCPFCGK~kV-KR~AVGIWkCkkCgkt 116 (121)
.+||.|++... |...-..|.|.+|++-
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h 66 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYH 66 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCC
Confidence 56777777653 3333445777777764
No 216
>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=20.07 E-value=65 Score=25.62 Aligned_cols=22 Identities=23% Similarity=0.199 Sum_probs=16.0
Q ss_pred ecccCCCcceEEeEE---EEeeeCCC
Q 037395 91 WGSWNYKYAIKRKVV---GIWSCKYC 113 (121)
Q Consensus 91 tCPFCGK~kVKR~AV---GIWkCkkC 113 (121)
.||.||.. ++|..+ +.|.|..|
T Consensus 247 pC~~Cg~~-I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 247 PCRRCGTP-IEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCe-eEEEEECCCCCEECCCC
Confidence 79999866 444444 47889888
Done!