Query psy15553
Match_columns 489
No_of_seqs 289 out of 719
Neff 5.1
Searched_HMMs 46136
Date Sat Aug 17 00:14:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15553.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15553hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2767|consensus 100.0 3E-117 6E-122 887.3 22.9 388 2-433 1-396 (400)
2 PF01873 eIF-5_eIF-2B: Domain 100.0 9.1E-45 2E-49 324.8 10.7 121 3-130 4-124 (125)
3 smart00653 eIF2B_5 domain pres 100.0 5.9E-44 1.3E-48 313.2 12.6 110 14-129 1-110 (110)
4 TIGR00311 aIF-2beta translatio 100.0 1.2E-42 2.6E-47 314.0 12.3 113 14-134 20-132 (133)
5 PRK03988 translation initiatio 100.0 3.9E-42 8.5E-47 312.4 13.1 115 12-134 23-137 (138)
6 PRK12336 translation initiatio 100.0 9.3E-41 2E-45 320.9 12.8 118 10-135 17-134 (201)
7 KOG2768|consensus 100.0 1.5E-32 3.3E-37 261.6 5.4 113 15-134 104-216 (231)
8 COG1601 GCD7 Translation initi 99.9 5.4E-29 1.2E-33 229.0 4.6 111 16-133 29-139 (151)
9 PF02020 W2: eIF4-gamma/eIF5/e 99.9 3.4E-22 7.3E-27 167.3 9.1 83 349-433 1-83 (84)
10 smart00515 eIF5C Domain at the 99.8 9.4E-19 2E-23 145.9 9.0 81 340-426 3-83 (83)
11 KOG2297|consensus 99.6 5.3E-16 1.2E-20 156.4 7.4 92 334-431 321-412 (412)
12 KOG1461|consensus 99.5 4.9E-14 1.1E-18 152.4 9.8 100 330-433 573-672 (673)
13 COG1326 Uncharacterized archae 92.8 0.034 7.3E-07 54.0 0.2 36 96-132 5-42 (201)
14 PF12677 DUF3797: Domain of un 92.7 0.11 2.4E-06 39.9 2.8 32 94-128 10-46 (49)
15 PRK00464 nrdR transcriptional 91.5 0.17 3.6E-06 47.7 3.2 34 99-132 2-40 (154)
16 PF01253 SUI1: Translation ini 91.4 0.42 9.2E-06 40.0 5.3 73 18-94 3-79 (83)
17 TIGR02443 conserved hypothetic 91.4 0.13 2.9E-06 41.0 2.0 39 92-132 5-43 (59)
18 PF09526 DUF2387: Probable met 91.0 0.15 3.1E-06 42.2 2.0 41 92-134 4-44 (71)
19 PF01921 tRNA-synt_1f: tRNA sy 87.0 0.6 1.3E-05 49.6 3.7 54 82-135 150-214 (360)
20 PF14205 Cys_rich_KTR: Cystein 86.8 0.21 4.6E-06 39.2 0.2 50 96-146 3-53 (55)
21 smart00440 ZnF_C2C2 C2C2 Zinc 86.6 0.8 1.7E-05 33.6 3.1 31 99-129 2-37 (40)
22 PF14354 Lar_restr_allev: Rest 86.0 0.71 1.5E-05 36.0 2.8 28 99-128 5-37 (61)
23 TIGR03655 anti_R_Lar restricti 85.5 0.96 2.1E-05 34.9 3.2 34 99-132 3-38 (53)
24 TIGR00244 transcriptional regu 85.1 0.81 1.8E-05 42.9 3.1 34 99-132 2-40 (147)
25 PF01096 TFIIS_C: Transcriptio 85.1 0.95 2.1E-05 33.0 2.8 32 98-129 1-37 (39)
26 PF14803 Nudix_N_2: Nudix N-te 84.2 0.69 1.5E-05 33.0 1.7 30 99-129 2-31 (34)
27 PRK09710 lar restriction allev 84.1 1.3 2.8E-05 36.0 3.4 34 99-134 8-41 (64)
28 cd00674 LysRS_core_class_I cat 83.2 1.1 2.4E-05 47.4 3.6 93 40-134 89-206 (353)
29 COG1997 RPL43A Ribosomal prote 82.4 2.2 4.7E-05 36.7 4.4 58 62-131 7-64 (89)
30 TIGR01159 DRP1 density-regulat 78.0 4.3 9.4E-05 39.0 5.3 73 17-93 86-162 (173)
31 PRK14892 putative transcriptio 77.7 1.4 3E-05 38.7 1.8 36 95-132 19-54 (99)
32 PHA02998 RNA polymerase subuni 77.6 2.6 5.6E-05 40.8 3.7 84 39-131 86-182 (195)
33 COG1384 LysS Lysyl-tRNA synthe 77.5 3 6.4E-05 46.2 4.6 52 83-135 148-209 (521)
34 PF08271 TF_Zn_Ribbon: TFIIB z 76.2 1.7 3.6E-05 32.0 1.6 27 99-129 2-28 (43)
35 smart00661 RPOL9 RNA polymeras 75.5 1.9 4.1E-05 32.4 1.8 32 99-133 2-33 (52)
36 PF12760 Zn_Tnp_IS1595: Transp 74.8 3 6.5E-05 31.2 2.7 28 98-129 19-46 (46)
37 TIGR00467 lysS_arch lysyl-tRNA 73.6 3.7 7.9E-05 45.7 4.1 73 59-134 113-204 (515)
38 PRK00750 lysK lysyl-tRNA synth 73.4 2.8 6.1E-05 46.4 3.2 93 41-135 85-214 (510)
39 COG2051 RPS27A Ribosomal prote 72.7 2.3 5E-05 34.8 1.7 29 97-129 19-47 (67)
40 PF09090 MIF4G_like_2: MIF4G l 70.8 33 0.00072 34.4 9.9 55 340-398 81-135 (253)
41 cd00474 SUI1_eIF1 The SUI1/eIF 69.5 10 0.00023 31.6 5.0 59 23-87 3-62 (77)
42 PRK00415 rps27e 30S ribosomal 68.6 3.3 7.1E-05 33.2 1.7 30 97-130 11-40 (59)
43 PHA00626 hypothetical protein 66.6 4.5 9.8E-05 32.2 2.1 36 99-134 2-37 (59)
44 COG0023 SUI1 Translation initi 65.5 19 0.0004 32.1 6.0 82 2-90 3-92 (104)
45 PF13719 zinc_ribbon_5: zinc-r 65.4 3.2 7E-05 29.8 1.0 31 97-131 2-36 (37)
46 TIGR00340 zpr1_rel ZPR1-relate 65.3 5.2 0.00011 38.1 2.7 32 100-131 1-39 (163)
47 TIGR01384 TFS_arch transcripti 64.4 8 0.00017 33.3 3.5 34 97-130 62-100 (104)
48 COG1327 Predicted transcriptio 64.2 4.6 0.0001 38.1 2.1 32 99-131 2-39 (156)
49 PRK00939 translation initiatio 64.0 14 0.0003 32.5 4.9 63 22-91 26-89 (99)
50 COG1779 C4-type Zn-finger prot 63.8 5.4 0.00012 39.2 2.5 34 97-131 14-54 (201)
51 smart00709 Zpr1 Duplicated dom 63.0 6.7 0.00015 37.2 3.0 32 99-131 2-40 (160)
52 PRK08665 ribonucleotide-diphos 62.1 8.6 0.00019 44.7 4.2 42 82-130 687-750 (752)
53 PF02150 RNA_POL_M_15KD: RNA p 61.5 5.4 0.00012 28.5 1.6 31 99-133 3-33 (35)
54 TIGR02159 PA_CoA_Oxy4 phenylac 61.2 3.9 8.4E-05 38.2 1.0 31 98-129 106-139 (146)
55 TIGR01158 SUI1_rel translation 61.0 18 0.00039 31.8 5.1 59 22-86 26-86 (101)
56 PF01396 zf-C4_Topoisom: Topoi 59.7 12 0.00026 27.3 3.1 33 98-133 2-37 (39)
57 KOG2703|consensus 59.3 5.7 0.00012 42.8 2.0 32 99-131 260-298 (460)
58 TIGR00310 ZPR1_znf ZPR1 zinc f 59.1 8.7 0.00019 37.5 3.1 32 99-131 2-41 (192)
59 PF11331 DUF3133: Protein of u 59.1 4.3 9.3E-05 31.0 0.7 33 97-131 6-42 (46)
60 PF03367 zf-ZPR1: ZPR1 zinc-fi 59.1 6 0.00013 37.4 1.9 33 98-131 2-41 (161)
61 PF13453 zf-TFIIB: Transcripti 59.0 12 0.00025 27.3 3.0 28 99-129 1-28 (41)
62 PRK00241 nudC NADH pyrophospha 58.0 9.7 0.00021 38.5 3.3 40 89-133 91-130 (256)
63 COG4888 Uncharacterized Zn rib 57.1 8.3 0.00018 34.1 2.3 38 94-133 19-59 (104)
64 TIGR01385 TFSII transcription 57.0 10 0.00022 39.4 3.4 56 74-129 206-295 (299)
65 KOG2906|consensus 56.8 11 0.00024 33.2 3.0 32 99-133 3-34 (105)
66 PRK00398 rpoP DNA-directed RNA 56.4 9.5 0.00021 28.4 2.2 36 98-138 4-39 (46)
67 COG3478 Predicted nucleic-acid 56.1 12 0.00027 30.6 2.9 36 97-132 4-52 (68)
68 PRK00420 hypothetical protein; 56.1 14 0.00031 33.2 3.7 41 88-134 14-54 (112)
69 cd00202 ZnF_GATA Zinc finger D 56.0 4.4 9.6E-05 31.6 0.4 32 99-132 1-33 (54)
70 COG2835 Uncharacterized conser 55.7 6.6 0.00014 31.6 1.3 33 96-133 7-39 (60)
71 smart00401 ZnF_GATA zinc finge 54.7 6.4 0.00014 30.4 1.1 33 98-132 4-37 (52)
72 PF14353 CpXC: CpXC protein 54.3 12 0.00026 33.5 2.9 36 98-133 2-51 (128)
73 PF05129 Elf1: Transcription e 53.7 11 0.00023 31.9 2.3 40 94-133 19-59 (81)
74 COG1594 RPB9 DNA-directed RNA 53.6 11 0.00023 33.8 2.5 46 99-147 4-49 (113)
75 PRK00423 tfb transcription ini 53.4 9.8 0.00021 39.4 2.5 29 97-129 11-39 (310)
76 PLN00209 ribosomal protein S27 52.5 10 0.00022 32.6 2.0 30 97-130 36-65 (86)
77 PF09855 DUF2082: Nucleic-acid 51.7 14 0.0003 30.0 2.6 34 99-132 2-48 (64)
78 PRK03954 ribonuclease P protei 50.8 13 0.00029 33.8 2.6 34 98-133 65-106 (121)
79 PRK05667 dnaG DNA primase; Val 50.0 27 0.00059 39.5 5.5 32 99-132 38-69 (580)
80 PF01667 Ribosomal_S27e: Ribos 48.8 7.8 0.00017 30.7 0.7 29 97-129 7-35 (55)
81 PTZ00083 40S ribosomal protein 48.0 13 0.00029 31.9 2.1 30 97-130 35-64 (85)
82 PF09297 zf-NADH-PPase: NADH p 47.9 4.2 9.2E-05 28.1 -0.8 28 97-129 3-30 (32)
83 TIGR01206 lysW lysine biosynth 47.6 15 0.00033 28.9 2.2 32 99-133 4-35 (54)
84 PF13717 zinc_ribbon_4: zinc-r 47.3 10 0.00022 27.2 1.0 29 97-129 2-34 (36)
85 TIGR00100 hypA hydrogenase nic 47.2 16 0.00034 32.6 2.5 28 48-78 38-65 (115)
86 PF00320 GATA: GATA zinc finge 47.2 8.7 0.00019 27.4 0.7 29 100-129 1-29 (36)
87 smart00834 CxxC_CXXC_SSSS Puta 46.9 13 0.00027 26.4 1.5 28 99-128 7-34 (41)
88 PF06107 DUF951: Bacterial pro 46.8 18 0.00039 28.9 2.5 37 101-140 14-50 (57)
89 TIGR01391 dnaG DNA primase, ca 46.8 32 0.00068 37.1 5.2 33 98-132 35-67 (415)
90 PRK00564 hypA hydrogenase nick 45.9 18 0.00039 32.4 2.7 28 48-78 38-66 (117)
91 COG1594 RPB9 DNA-directed RNA 45.6 15 0.00032 32.9 2.1 34 97-130 72-110 (113)
92 PF04216 FdhE: Protein involve 45.1 15 0.00032 37.6 2.3 36 98-133 173-210 (290)
93 COG1645 Uncharacterized Zn-fin 44.5 16 0.00034 33.8 2.1 26 99-131 30-55 (131)
94 PF05315 ICEA: ICEA Protein; 44.2 12 0.00025 37.2 1.3 69 48-116 45-120 (230)
95 PHA02540 61 DNA primase; Provi 43.7 21 0.00045 37.8 3.2 44 98-147 28-76 (337)
96 PRK00432 30S ribosomal protein 43.7 15 0.00033 28.3 1.6 28 97-130 20-47 (50)
97 PRK11827 hypothetical protein; 43.1 16 0.00034 29.4 1.7 36 93-133 4-39 (60)
98 PRK07451 translation initiatio 42.9 42 0.00091 30.4 4.5 58 24-87 44-101 (115)
99 cd04762 HTH_MerR-trunc Helix-T 42.7 43 0.00094 23.5 3.9 46 39-90 2-47 (49)
100 PRK03824 hypA hydrogenase nick 41.5 20 0.00044 32.9 2.4 47 41-104 31-77 (135)
101 PRK03681 hypA hydrogenase nick 41.2 21 0.00045 31.9 2.3 28 48-78 38-65 (114)
102 COG1405 SUA7 Transcription ini 40.8 19 0.00041 37.3 2.3 28 99-130 3-30 (285)
103 PF01927 Mut7-C: Mut7-C RNAse 40.7 36 0.00078 31.4 3.9 58 75-132 63-136 (147)
104 PF04032 Rpr2: RNAse P Rpr2/Rp 40.4 23 0.0005 29.0 2.4 31 98-128 47-85 (85)
105 COG3529 Predicted nucleic-acid 40.3 4.6 0.0001 32.6 -1.7 38 91-130 5-42 (66)
106 PRK05580 primosome assembly pr 40.0 20 0.00043 41.1 2.5 50 97-148 381-452 (679)
107 PRK00762 hypA hydrogenase nick 39.6 25 0.00055 31.8 2.7 28 48-78 38-65 (124)
108 COG0777 AccD Acetyl-CoA carbox 39.5 10 0.00023 39.1 0.2 43 97-143 28-70 (294)
109 PRK12380 hydrogenase nickel in 39.5 23 0.00051 31.5 2.4 28 48-78 38-65 (113)
110 PF09723 Zn-ribbon_8: Zinc rib 39.4 18 0.00039 26.6 1.4 29 99-129 7-35 (42)
111 PRK12286 rpmF 50S ribosomal pr 38.9 22 0.00047 28.2 1.8 26 94-129 24-49 (57)
112 PF01807 zf-CHC2: CHC2 zinc fi 38.1 24 0.00053 30.3 2.2 33 98-132 34-66 (97)
113 PF10058 DUF2296: Predicted in 37.9 22 0.00048 27.8 1.8 31 98-129 23-53 (54)
114 PRK07562 ribonucleotide-diphos 36.3 26 0.00056 42.9 2.8 40 85-132 1180-1219(1220)
115 PF04760 IF2_N: Translation in 35.8 19 0.0004 27.5 1.0 27 39-65 5-31 (54)
116 COG1096 Predicted RNA-binding 35.4 27 0.00058 34.2 2.3 27 97-130 149-175 (188)
117 COG1198 PriA Primosomal protei 34.5 27 0.00059 40.6 2.5 36 97-134 435-476 (730)
118 COG3741 HutG N-formylglutamate 34.4 12 0.00027 38.3 -0.2 68 32-100 62-132 (272)
119 TIGR02098 MJ0042_CXXC MJ0042 f 34.4 17 0.00037 25.7 0.6 31 97-130 2-35 (38)
120 TIGR03826 YvyF flagellar opero 34.2 32 0.0007 31.9 2.5 44 38-106 47-90 (137)
121 PF09862 DUF2089: Protein of u 33.8 33 0.00071 31.0 2.4 49 208-263 60-108 (113)
122 KOG2907|consensus 33.8 21 0.00047 32.2 1.2 34 99-132 76-114 (116)
123 cd03031 GRX_GRX_like Glutaredo 33.8 34 0.00074 31.9 2.6 52 81-132 81-145 (147)
124 smart00531 TFIIE Transcription 32.9 57 0.0012 30.1 4.0 96 38-133 16-136 (147)
125 PRK05654 acetyl-CoA carboxylas 32.8 10 0.00022 39.3 -1.2 43 97-143 27-69 (292)
126 PF05046 Img2: Mitochondrial l 32.6 1.1E+02 0.0024 26.0 5.4 61 20-83 14-76 (87)
127 TIGR00515 accD acetyl-CoA carb 32.6 10 0.00022 39.2 -1.2 43 97-143 26-68 (285)
128 PF08535 KorB: KorB domain; I 31.2 22 0.00048 30.1 0.9 19 41-59 7-25 (93)
129 PF06044 DRP: Dam-replacing fa 31.1 39 0.00084 34.4 2.6 56 79-135 12-68 (254)
130 PF08274 PhnA_Zn_Ribbon: PhnA 30.8 17 0.00038 25.3 0.1 27 97-129 2-28 (30)
131 PF06677 Auto_anti-p27: Sjogre 30.7 68 0.0015 23.9 3.2 35 87-127 7-41 (41)
132 PRK06319 DNA topoisomerase I/S 30.5 56 0.0012 38.8 4.2 33 99-133 594-629 (860)
133 COG1571 Predicted DNA-binding 30.4 24 0.00052 38.4 1.1 36 93-134 346-381 (421)
134 PF03811 Zn_Tnp_IS1: InsA N-te 30.2 42 0.00091 24.3 2.0 29 97-126 5-35 (36)
135 PF03966 Trm112p: Trm112p-like 29.8 48 0.001 26.6 2.6 14 120-133 53-66 (68)
136 PRK08332 ribonucleotide-diphos 29.7 46 0.001 42.3 3.5 43 87-132 1695-1738(1740)
137 KOG3507|consensus 29.5 13 0.00029 29.9 -0.7 32 98-135 21-52 (62)
138 PF14599 zinc_ribbon_6: Zinc-r 29.4 14 0.00031 29.7 -0.6 31 96-131 29-59 (61)
139 COG2023 RPR2 RNase P subunit R 29.3 52 0.0011 29.4 2.9 35 99-133 58-95 (105)
140 TIGR01160 SUI1_MOF2 translatio 29.1 65 0.0014 28.9 3.5 65 22-92 28-97 (110)
141 TIGR02609 doc_partner putative 29.0 1.3E+02 0.0028 24.6 5.1 47 51-97 15-65 (74)
142 PF07282 OrfB_Zn_ribbon: Putat 28.5 37 0.0008 26.9 1.7 30 99-133 30-59 (69)
143 CHL00174 accD acetyl-CoA carbo 28.4 13 0.00029 38.6 -1.1 43 97-143 38-80 (296)
144 COG1996 RPC10 DNA-directed RNA 28.3 19 0.00041 27.9 -0.0 35 99-138 8-42 (49)
145 PRK11823 DNA repair protein Ra 28.2 32 0.00069 37.5 1.6 27 99-134 9-35 (446)
146 TIGR00595 priA primosomal prot 27.6 41 0.00088 37.3 2.4 44 100-148 225-284 (505)
147 PF03604 DNA_RNApol_7kD: DNA d 26.9 20 0.00043 25.3 -0.1 28 99-132 2-29 (32)
148 smart00659 RPOLCX RNA polymera 26.9 44 0.00095 25.1 1.7 31 99-135 4-34 (44)
149 PF11781 RRN7: RNA polymerase 26.8 50 0.0011 23.8 1.9 26 99-130 10-35 (36)
150 smart00647 IBR In Between Ring 26.8 1E+02 0.0022 23.4 3.9 41 88-131 6-51 (64)
151 PF05180 zf-DNL: DNL zinc fing 26.7 32 0.0007 28.2 1.0 40 99-138 6-47 (66)
152 PF14768 RPA_interact_C: Repli 26.5 1.1E+02 0.0025 25.5 4.4 51 81-132 32-82 (82)
153 TIGR01031 rpmF_bact ribosomal 26.5 43 0.00092 26.3 1.6 25 95-129 24-48 (55)
154 COG0375 HybF Zn finger protein 26.4 54 0.0012 29.7 2.5 49 58-112 46-101 (115)
155 TIGR00416 sms DNA repair prote 26.2 38 0.00083 37.1 1.8 27 99-134 9-35 (454)
156 PRK03564 formate dehydrogenase 26.2 54 0.0012 34.4 2.8 36 97-132 187-224 (309)
157 PRK00378 nucleoid-associated p 25.8 1.7E+02 0.0036 30.5 6.4 50 24-95 283-332 (334)
158 COG1499 NMD3 NMD protein affec 25.7 48 0.001 35.4 2.4 33 99-132 23-55 (355)
159 PF04502 DUF572: Family of unk 25.4 35 0.00076 35.7 1.3 25 119-143 76-100 (324)
160 cd02983 P5_C P5 family, C-term 25.3 82 0.0018 28.4 3.5 44 53-96 70-117 (130)
161 TIGR03830 CxxCG_CxxCG_HTH puta 25.1 62 0.0014 28.2 2.7 32 100-131 1-42 (127)
162 PF15494 SRCR_2: Scavenger rec 25.0 47 0.001 28.3 1.8 15 116-130 84-98 (98)
163 COG2093 DNA-directed RNA polym 24.9 35 0.00076 27.8 0.9 11 99-109 20-30 (64)
164 PF04810 zf-Sec23_Sec24: Sec23 24.7 53 0.0012 23.9 1.8 33 98-134 3-38 (40)
165 smart00778 Prim_Zn_Ribbon Zinc 24.7 53 0.0011 24.0 1.7 31 97-128 3-33 (37)
166 PF13936 HTH_38: Helix-turn-he 24.3 39 0.00084 24.9 1.0 22 38-59 21-42 (44)
167 cd01121 Sms Sms (bacterial rad 24.2 44 0.00094 35.7 1.7 27 99-134 2-28 (372)
168 PRK06556 vitamin B12-dependent 24.1 63 0.0014 38.9 3.1 46 80-132 907-952 (953)
169 PRK09019 translation initiatio 24.1 2.2E+02 0.0049 25.5 5.9 49 33-87 46-94 (108)
170 PF06573 Churchill: Churchill 23.8 53 0.0012 29.5 1.9 37 93-129 23-67 (112)
171 smart00400 ZnF_CHCC zinc finge 23.7 72 0.0016 24.4 2.4 32 99-132 4-35 (55)
172 PF13597 NRDD: Anaerobic ribon 23.6 42 0.00091 37.6 1.6 53 80-143 463-526 (546)
173 TIGR03829 YokU_near_AblA uncha 22.8 60 0.0013 28.2 2.0 24 117-140 32-56 (89)
174 TIGR01566 ZF_HD_prot_N ZF-HD h 22.5 38 0.00081 26.6 0.6 17 117-133 33-49 (53)
175 PF05876 Terminase_GpA: Phage 22.4 55 0.0012 36.8 2.2 50 97-146 200-258 (557)
176 PRK14973 DNA topoisomerase I; 22.3 53 0.0012 39.4 2.1 22 374-395 886-907 (936)
177 COG1066 Sms Predicted ATP-depe 22.3 45 0.00097 36.6 1.4 29 97-134 7-35 (456)
178 COG0675 Transposase and inacti 22.3 49 0.0011 32.9 1.6 24 98-131 310-333 (364)
179 PRK03824 hypA hydrogenase nick 22.3 34 0.00073 31.4 0.4 43 83-133 41-83 (135)
180 PF05379 Peptidase_C23: Carlav 22.2 57 0.0012 28.0 1.7 69 40-118 7-76 (89)
181 PF14255 Cys_rich_CPXG: Cystei 22.0 71 0.0015 25.0 2.1 34 98-132 1-36 (52)
182 PF12172 DUF35_N: Rubredoxin-l 21.9 54 0.0012 23.1 1.3 17 115-131 6-22 (37)
183 PF00123 Hormone_2: Peptide ho 21.9 63 0.0014 22.2 1.6 11 414-424 17-27 (28)
184 TIGR01051 topA_bact DNA topois 21.6 86 0.0019 35.7 3.5 30 99-131 576-608 (610)
185 COG3058 FdhE Uncharacterized p 21.6 49 0.0011 34.4 1.4 32 98-129 186-220 (308)
186 COG3677 Transposase and inacti 21.4 1.2E+02 0.0025 27.8 3.7 41 93-134 26-67 (129)
187 KOG2691|consensus 21.1 91 0.002 28.1 2.8 60 71-130 39-111 (113)
188 PHA02942 putative transposase; 21.0 46 0.00099 35.7 1.1 31 98-134 326-356 (383)
189 PF05077 DUF678: Protein of un 21.0 52 0.0011 27.6 1.2 13 117-129 54-66 (74)
190 PF00165 HTH_AraC: Bacterial r 20.9 69 0.0015 22.8 1.7 28 38-65 9-36 (42)
191 PRK02935 hypothetical protein; 20.8 58 0.0013 29.2 1.5 30 98-134 71-100 (110)
192 TIGR01562 FdhE formate dehydro 20.7 53 0.0011 34.4 1.5 37 97-133 184-223 (305)
193 cd04761 HTH_MerR-SF Helix-Turn 20.6 1.4E+02 0.003 21.3 3.4 45 39-89 2-46 (49)
194 PF04161 Arv1: Arv1-like famil 20.5 50 0.0011 32.3 1.2 32 99-130 2-34 (208)
195 TIGR03831 YgiT_finger YgiT-typ 20.5 1.1E+02 0.0024 21.8 2.8 9 122-130 34-42 (46)
196 PTZ00073 60S ribosomal protein 20.5 47 0.001 28.9 0.9 25 96-128 15-39 (91)
No 1
>KOG2767|consensus
Probab=100.00 E-value=2.7e-117 Score=887.28 Aligned_cols=388 Identities=55% Similarity=0.916 Sum_probs=339.8
Q ss_pred ceeccCCCCCCccccccCCCcEEEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEecc
Q psy15553 2 ATVNVNRNVTDAFYRYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSH 81 (489)
Q Consensus 2 ~~iNi~~~~~D~~yRykmP~~~~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~ 81 (489)
|+|||||++.|+|||||||++++||||+||||||+|+||.|||+||+|||.|++|||||||||||+||.+++||||||+|
T Consensus 1 a~iNInrsn~D~FYRYKMPrl~aKvEGKGNGIKTvIvNm~eIakAL~RPp~Y~tKyFGcELGAQT~fd~kn~ryiVNG~H 80 (400)
T KOG2767|consen 1 ASININRSNRDPFYRYKMPRLQAKVEGKGNGIKTVIVNMVEIAKALGRPPLYPTKYFGCELGAQTKFDVKNGRYIVNGAH 80 (400)
T ss_pred CcccccccccchhhhhccchhhhhccccCCCeeeeeecHHHHHHHhCCCCCcccccceeeccccccccccCCeeeecccc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chHHHHHHHHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccccchhhhhhhhhcCCCCCCCCCCCCccccc
Q psy15553 82 DVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFNHKLNTFILKNPPNLNPAVQGSSLTEG 161 (489)
Q Consensus 82 ~~~~lq~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl~~~i~kn~p~~~~~~~g~k~~k~ 161 (489)
++.+||+||++||++|||||+|+||||.|+++ +++++.++|+|||+++.+++||||++|||||||++.+++.+ |++..
T Consensus 81 d~~KLqdlLdgFIkKFVlC~~C~NPETel~it-k~q~i~~~CkACG~r~~~d~rhKLs~fIlKNPP~~~~~s~~-kk~~~ 158 (400)
T KOG2767|consen 81 EASKLQDLLDGFIKKFVLCPSCENPETELIIT-KKQTISLKCKACGFRSDMDLRHKLSTFILKNPPEQKDSSKD-KKKAE 158 (400)
T ss_pred cHHHHHHHHHHHHHHheeCcCCCCCceeEEec-ccchhhhHHHHcCCcccccchhhhcceeecCCcccccchhh-hHHHH
Confidence 99999999999999999999999999999995 58999999999999999999999999999999987764322 11111
Q ss_pred CCc-ccchhhhccCCCCCC-CCCCC----CCCCCCCcccccccCCCCCCCcccchHHHHHHHHhccccccccccccchhh
Q psy15553 162 KRP-KRISKKQESNGDMTK-SDEES----DPTVVAPEKVADEVNDDDGGWLADVSEEAVRARALDLSSGVKGLTISEDLE 235 (489)
Q Consensus 162 ~~~-~~~~k~~~~~~~~~~-~~~~~----~~~~~~~~~~~~~~~~~d~~W~~DtSeeA~~~R~~~L~~~~~~l~~~~d~e 235 (489)
++. +++. +++..+.+++ ++..+ ..++++.....+..++||++|++|||+||+|+||++|+++++.|++..|++
T Consensus 159 ~k~R~~K~-k~k~~g~~s~~~~~~~~~~~~~~i~~~a~~~t~e~~DDddW~~Dtseea~r~R~~~Ls~~~~~~~~~sd~e 237 (400)
T KOG2767|consen 159 KKERKGKS-KDKKDGSKSSKNETSPDDSLSREIDPAAPLETAEEDDDDDWAVDTSEEAIRARMQELSANAKEMLLLSDLE 237 (400)
T ss_pred HHHhhhhc-ccccccccCCccCCCcccccccccccccCcccccccccccccccchHHHHHHHHHHHhhhhhhhhhhhhhh
Confidence 111 1111 2333333333 11111 122232221223445666679999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHhhCCC--ChHHHHHHHHhcCcCcchhHHHHHhhcCCCCcchHHHhhhhcccccCcccccccc
Q psy15553 236 KTEKERMDIFYTCVKTALEKNNV--DAKELLSEAERLEVKTKAPLILAELLFADEDKIPIQAKKHRILFFGSNQFTWRSV 313 (489)
Q Consensus 236 ~~~~~~~~~~~~~v~~~~~~~~~--~~~ei~~ea~~l~v~~k~~~vl~e~lF~~~~~i~~qi~k~~~ll~~~~~~~~~s~ 313 (489)
++++++.+++++++...++++.+ +++||+.+|++|++.+++|+||+++||++. |+++|.+|++||
T Consensus 238 ~~E~~~~~~~~d~~~~~~~en~~~~~~kEi~~~a~~l~i~~k~p~vl~~~Lf~e~--ivkei~k~~~~l----------- 304 (400)
T KOG2767|consen 238 KSEEEREDILYDFVKKKKEENVPDKSDKEIVKEAERLDIKNKAPLVLAEVLFDEK--IVKEILKHRALL----------- 304 (400)
T ss_pred hhHHHHHHHHHHhhhhcccccCCCccHHHHHHHHHHHhhcccchHHHHHHHhhhH--HHHHHHHHHHHH-----------
Confidence 99999999999999999887765 469999999999999999999999999999 999999999999
Q ss_pred hhhHHHHHHHHHHHhHHHHHHhhhhhhhhcccccchHHHHHHHHHHHHHHHhhhhHHHhhHHHHHHHHhhccCcchHHHH
Q psy15553 314 GFYRRQINTIATLINQCQLILLDKQSTVLRFTHEDIKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLL 393 (489)
Q Consensus 314 ~~~rali~~i~~~~aq~~~~l~~~~~~L~~fv~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DILeEE~Il 393 (489)
++|+++++++|++||++||+||..++..+++.+++||+.|||+|||+|++|+
T Consensus 305 ----------------------------~k~~~~~~k~qr~LLggiE~~~~~~~~el~~kva~ilk~lYd~DI~~e~vi~ 356 (400)
T KOG2767|consen 305 ----------------------------LKFCTNNEKAQRYLLGGIERFVEKHEAELISKVAGILKELYDEDILEEEVII 356 (400)
T ss_pred ----------------------------HHHHhccHHHHHHHHhHHHHHHHhhHHHHHHHHHHHHHHHHhhhhhhHHHHH
Confidence 9999988999999999999999998999999999999999999999999999
Q ss_pred HHHhhccccccchHHHHHHHHHHHHHHHHHccccccCCCC
Q psy15553 394 EWAEKTSKKYVSKELSAEIRSRAEPFIKWLREAEEEDSDS 433 (489)
Q Consensus 394 ~W~ek~skk~v~ke~~kkvrk~a~pFIeWLkEAEEEsded 433 (489)
.|++++|++||+++.+++|++.++|||+||++||+|++++
T Consensus 357 ~w~~K~skk~vsk~~sk~i~e~a~Pfi~WL~~AESe~eeE 396 (400)
T KOG2767|consen 357 KWGEKPSKKYVSKEKSKKIRENAKPFIEWLKNAESEDEEE 396 (400)
T ss_pred HHHhcccccccchhhhhhhHhhhhHHHHHHHhcccccccc
Confidence 9999999999999999999999999999999996655543
No 2
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=100.00 E-value=9.1e-45 Score=324.85 Aligned_cols=121 Identities=49% Similarity=0.839 Sum_probs=113.1
Q ss_pred eeccCCCCCCccccccCCCcEEEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccc
Q psy15553 3 TVNVNRNVTDAFYRYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHD 82 (489)
Q Consensus 3 ~iNi~~~~~D~~yRykmP~~~~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~ 82 (489)
..|+++.++|.+ ||+||+|++++||+ +||+|+||.|||++|||+|+||+|||++||||+|+||. ++||||||+|+
T Consensus 4 ~~np~~~~~~~~-R~kmP~~~v~~eG~---~KTvi~Nf~dI~~~L~R~p~~~~ky~~~ELgt~~~id~-~~~lii~G~~~ 78 (125)
T PF01873_consen 4 EKNPERSNSDKF-RYKMPPPQVKIEGK---KKTVIVNFVDICKALNRDPEHVLKYFGKELGTQGSIDG-KGRLIINGRFS 78 (125)
T ss_dssp CSSTTTSCSSSS-S-CCCT--EEEETS---TEEEETTHHHHHHHHTSSHHHHHHHHHHHSSSEEEEET-TTEEEEESSSS
T ss_pred HhCcCcccCCCc-ceecCCCeEEEEcc---ceeeeecHHHHHHHHCCCHHHHHHHHHHHHCCceEECC-CCEEEEEEecC
Confidence 689998888887 99999999999997 69999999999999999999999999999999999994 49999999999
Q ss_pred hHHHHHHHHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcc
Q psy15553 83 VVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHG 130 (489)
Q Consensus 83 ~~~lq~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~ 130 (489)
+++||++|++||++||+|++|+||||.|++ ++++++++|.|||+++
T Consensus 79 ~~~i~~~L~~fI~~yVlC~~C~spdT~l~k--~~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 79 SKQIQDLLDKFIKEYVLCPECGSPDTELIK--EGRLIFLKCKACGASR 124 (125)
T ss_dssp CCHHHHHHHHHHCHHSSCTSTSSSSEEEEE--ETTCCEEEETTTSCEE
T ss_pred HHHHHHHHHHHHHHEEEcCCCCCCccEEEE--cCCEEEEEecccCCcC
Confidence 999999999999999999999999999999 7999999999999986
No 3
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=100.00 E-value=5.9e-44 Score=313.17 Aligned_cols=110 Identities=50% Similarity=0.874 Sum_probs=106.7
Q ss_pred cccccCCCcEEEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHHHHH
Q psy15553 14 FYRYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLDGF 93 (489)
Q Consensus 14 ~yRykmP~~~~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~~f 93 (489)
||||+||+|++++||+| ||+|+||.|||++|||+|+||+|||++||||+|++|. ++|+||||+|++.+||++|++|
T Consensus 1 ~~R~~~p~~~v~~eG~~---kTvi~Nf~~I~~~L~R~p~hv~kyl~~ELgt~g~id~-~~rlii~G~~~~~~i~~~l~~y 76 (110)
T smart00653 1 FYRFKMPPPQVLREGKG---KTVIVNFADIAKALNRPPDHVLKFLLAELGTQGSIDG-KGRLIVNGRFTPKKLQDLLRRY 76 (110)
T ss_pred CCccccCCCeEEEEcCC---eEEEEcHHHHHHHHCCCHHHHHHHHHHHhCCceeECC-CCeEEEEEeeCHHHHHHHHHHH
Confidence 69999999999999995 9999999999999999999999999999999999994 5999999999999999999999
Q ss_pred HhhcccCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 94 IRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 94 I~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
|++||+|++|+||||.|++ ++++++++|.|||++
T Consensus 77 I~~yVlC~~C~spdT~l~k--~~r~~~l~C~aCGa~ 110 (110)
T smart00653 77 IKEYVLCPECGSPDTELIK--ENRLFFLKCEACGAR 110 (110)
T ss_pred HHhcEECCCCCCCCcEEEE--eCCeEEEEccccCCC
Confidence 9999999999999999999 799999999999985
No 4
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=100.00 E-value=1.2e-42 Score=313.98 Aligned_cols=113 Identities=32% Similarity=0.620 Sum_probs=109.5
Q ss_pred cccccCCCcEEEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHHHHH
Q psy15553 14 FYRYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLDGF 93 (489)
Q Consensus 14 ~yRykmP~~~~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~~f 93 (489)
-+||+||+|++++||+ ||+|+||.+||++|||+|+||+|||++||||+|++| ++|+||||+|++.+||++|++|
T Consensus 20 ~~R~~mP~~~v~~eG~----kTvi~Nf~~Ia~~L~R~~~~v~ky~~~ELgt~g~i~--~~rlii~G~~~~~~i~~~L~~y 93 (133)
T TIGR00311 20 TKRFEVPKAYIVIEGN----RTIIQNFREVAKALNRDEQHLLKYLLKELGTAGNLE--GGRLILQGKFTHFLLNERIEDY 93 (133)
T ss_pred CccccCCCceEEEEcC----cEEEecHHHHHHHHCCCHHHHHHHHHHHhCCCceec--CCEEEEEeecCHHHHHHHHHHH
Confidence 5899999999999998 999999999999999999999999999999999997 6899999999999999999999
Q ss_pred HhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 94 IRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 94 I~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
|++||+|++|+||||.|++ ++++++++|.|||++++|..
T Consensus 94 I~~yVlC~~C~sPdT~l~k--~~r~~~l~C~ACGa~~~v~~ 132 (133)
T TIGR00311 94 VRKYVICRECNRPDTRIIK--EGRVSLLKCEACGAKAPLRN 132 (133)
T ss_pred HhheEECCCCCCCCcEEEE--eCCeEEEecccCCCCCccCc
Confidence 9999999999999999999 79999999999999999963
No 5
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=100.00 E-value=3.9e-42 Score=312.41 Aligned_cols=115 Identities=27% Similarity=0.591 Sum_probs=110.8
Q ss_pred CccccccCCCcEEEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHHH
Q psy15553 12 DAFYRYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLD 91 (489)
Q Consensus 12 D~~yRykmP~~~~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~ 91 (489)
...+||+||+|++++||+ ||+|+||.+||++|||+|+||+|||++||||+|+++ +||+||||+|++.+|+++|+
T Consensus 23 ~~~~R~~~p~~~v~~eG~----kTvi~Nf~~I~~~L~R~~~hv~ky~~~ELgt~g~i~--~~~lii~G~~~~~~i~~~L~ 96 (138)
T PRK03988 23 FKESRFEVPKPDVRIEGN----RTIIRNFKEIADRLNRDPKHVAKFLLKELGTAGNIE--GGRLILQGKFSPRVINEKID 96 (138)
T ss_pred CCCcceeCCCCeEEEEcC----cEEEecHHHHHHHHCCCHHHHHHHHHHHhCCceeec--CCEEEEEEeeCHHHHHHHHH
Confidence 456899999999999998 999999999999999999999999999999999994 79999999999999999999
Q ss_pred HHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 92 GFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 92 ~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
+||++||+|++|+||||.|++ ++++++++|.|||++++|+.
T Consensus 97 ~yI~~yVlC~~C~spdT~l~k--~~r~~~l~C~ACGa~~~V~~ 137 (138)
T PRK03988 97 RYVKEYVICPECGSPDTKLIK--EGRIWVLKCEACGAETPVKP 137 (138)
T ss_pred HHHHhcEECCCCCCCCcEEEE--cCCeEEEEcccCCCCCcCCc
Confidence 999999999999999999999 89999999999999999964
No 6
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=100.00 E-value=9.3e-41 Score=320.88 Aligned_cols=118 Identities=30% Similarity=0.588 Sum_probs=113.2
Q ss_pred CCCccccccCCCcEEEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHH
Q psy15553 10 VTDAFYRYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDL 89 (489)
Q Consensus 10 ~~D~~yRykmP~~~~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~ 89 (489)
..+..|||+||+|++++||+ ||+|+||.+||++|||+|+||+|||++||||+++++ ++|+||||+|++.+||++
T Consensus 17 ~~~~~~R~~~p~~~v~~eG~----kT~i~N~~~i~~~l~R~~~~~~ky~~~ELgt~~~~~--~~~~ii~G~~~~~~i~~~ 90 (201)
T PRK12336 17 PTKSGERFSIPEPKIFIEGK----TTILTNFGEIADALNRDPDHLMKFLQRELGTAGKIE--GGRAVFNGKFTEEDIQAA 90 (201)
T ss_pred ccCCccceecCCceEEEEcC----cEEEecHHHHHHHHCCCHHHHHHHHHHHhCCcceec--CCEEEEEeeeCHHHHHHH
Confidence 45778999999999999998 999999999999999999999999999999999997 689999999999999999
Q ss_pred HHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccccch
Q psy15553 90 LDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFN 135 (489)
Q Consensus 90 L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~ 135 (489)
|++||++||+|++|+||||.|++ ++++++++|.|||++++|+.+
T Consensus 91 l~~yi~~yV~C~~C~~pdT~l~k--~~~~~~l~C~aCGa~~~v~~~ 134 (201)
T PRK12336 91 IDAYVDEYVICSECGLPDTRLVK--EDRVLMLRCDACGAHRPVKKR 134 (201)
T ss_pred HHHHHHheEECCCCCCCCcEEEE--cCCeEEEEcccCCCCcccccc
Confidence 99999999999999999999999 789999999999999999843
No 7
>KOG2768|consensus
Probab=99.97 E-value=1.5e-32 Score=261.56 Aligned_cols=113 Identities=27% Similarity=0.541 Sum_probs=109.1
Q ss_pred ccccCCCcEEEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHHHHHH
Q psy15553 15 YRYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLDGFI 94 (489)
Q Consensus 15 yRykmP~~~~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~~fI 94 (489)
-||.|++|+|.+||+ ||+++||.|||+.|||.|+||++|++.||||.|++| +++||+|+|+|.+++||++|++||
T Consensus 104 ~k~v~~PPqvlRegk----kT~f~Nf~Dick~mhR~pdHv~~FLlAELgTsGSid-g~~rLviKGrfq~kq~e~VLRrYI 178 (231)
T KOG2768|consen 104 RKFVMKPPQVLREGK----KTVFVNFADICKTMHRSPDHVMQFLLAELGTSGSID-GQQRLVIKGRFQQKQFENVLRRYI 178 (231)
T ss_pred cceeeCCHHHHhhcc----ceeeeeHHHHHHHhccChHHHHHHHHHHhccccccC-CCceEEEeccccHHHHHHHHHHHH
Confidence 369999999999997 999999999999999999999999999999999999 899999999999999999999999
Q ss_pred hhcccCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 95 RKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 95 ~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
..||.|..|+||||.|.+ ++|++||+|..||.+++|..
T Consensus 179 ~eyV~C~~CkSpdt~L~k--enRLfFL~C~~cgs~~sv~~ 216 (231)
T KOG2768|consen 179 KEYVTCKTCKSPDTILQK--ENRLFFLRCEKCGSRCSVAS 216 (231)
T ss_pred HHheEeeecCChhHHhhh--hcceEEEEecCCCCeeeeee
Confidence 999999999999999999 79999999999999988753
No 8
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=5.4e-29 Score=228.99 Aligned_cols=111 Identities=28% Similarity=0.621 Sum_probs=107.8
Q ss_pred cccCCCcEEEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHHHHHHh
Q psy15553 16 RYKMPKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLDGFIR 95 (489)
Q Consensus 16 RykmP~~~~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~~fI~ 95 (489)
||.||.|.+.++|+ +|+|.||.+||++|+|+|+|+.+||..||||.|++| +.+|+|++|.|+.+.|++.|+.||.
T Consensus 29 R~~ip~~~i~~~g~----~Ti~~Nf~dia~~l~rDp~h~~k~l~kel~t~g~~d-~~~rlvl~g~f~~~~i~~~i~~yi~ 103 (151)
T COG1601 29 RFRIPEPEINREGN----RTIIRNFGDIAEALNRDPEHLVKFLKKELGTAGSID-GKGRLVLQGKFSDSEIVNEIERYIA 103 (151)
T ss_pred ceecCCcceecccc----hhHHHhHHHHHHHhcCCHHHHHHHHHHHhccccccC-CcceEEEEecccHHHHHHHHHHHHH
Confidence 99999999999998 999999999999999999999999999999999999 4599999999999999999999999
Q ss_pred hcccCCCCCCCCceEEEeccCCeEeeecccccCccccc
Q psy15553 96 KFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 96 ~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
.||.|+.|++|||.|++ .+|.++++|.|||+.+||.
T Consensus 104 ~yv~C~~c~s~dt~l~~--~~R~~~l~c~acGa~~pv~ 139 (151)
T COG1601 104 EYVKCKECGSPDTELIK--EERLLFLKCEACGAIRPVK 139 (151)
T ss_pred heeEeccCCCCchhhhh--hhhhHhhHHHHhCCcccch
Confidence 99999999999999999 7999999999999999995
No 9
>PF02020 W2: eIF4-gamma/eIF5/eIF2-epsilon; InterPro: IPR003307 This entry represents the W2 domain (two invariant tryptophans) and is a region of ~165 amino acids which is found in the C terminus of the following eIFs [, , , ]: Eukaryotic translation initiation factor 2B epsilon (eIF-2B-epsilon) Eukaryotic translation initiation factor 4 gamma (eIF-4-gamma) Eukaryotic translation initiation factor 5 (eIF-5), a GTPase-activating protein (GAP) specific for eIF2 Translation initiation is a sophisticated, well regulated and highly coordinated cellular process in eukaryotes, in which at least 11 eukayrotic initiation factors (eIFs) are included []. The W2 domain has a globular fold and is exclusively composed out of alpha-helices [, , ]. The structure can be divided into a structural C-terminal core onto which the two N-terminal helices are attached. The core contains two aromatic/acidic residue-rich regions (AA boxes), which are important for mediating protein-protein interactions. For example, the W2 domain of H. sapiens eIF5 binds eIF2-beta, eIF3 and eIF1 [], and therefore plays an important role in multifactor complex assembly. The entry covers the entire W2 domain.; GO: 0005488 binding; PDB: 3D3M_A 3L6A_A 1PAQ_A 2FUL_D 2IU1_A 1UG3_B 3JUI_A.
Probab=99.87 E-value=3.4e-22 Score=167.29 Aligned_cols=83 Identities=45% Similarity=0.722 Sum_probs=68.6
Q ss_pred hHHHHHHHHHHHHHHHhhhhHHHhhHHHHHHHHhhccCcchHHHHHHHhhccccccchHHHHHHHHHHHHHHHHHccccc
Q psy15553 349 IKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKKYVSKELSAEIRSRAEPFIKWLREAEE 428 (489)
Q Consensus 349 ~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DILeEE~Il~W~ek~skk~v~ke~~kkvrk~a~pFIeWLkEAEE 428 (489)
+++|+++|.+||.|| .+++.+++.|+.||+.|||.|||+|++|++||++ ++++++.+..+++|++++|||+||++|||
T Consensus 1 ~~~Q~~~L~ale~~~-~~~~~~~~~~~~il~~LYd~Dil~Eeail~W~~~-~~~~~~~~~~~~~r~~~~~fi~WL~eaee 78 (84)
T PF02020_consen 1 EDDQVDLLNALEEFC-AENPNLMPLFPKILQQLYDEDILEEEAILEWYED-SKPAVDGEGRAKVRKQAQPFIEWLEEAEE 78 (84)
T ss_dssp HHHHHHHHHHHHHHH-HHTCGHGGHHHHHHHHHHHTTSS-HHHHHHHHHC--SSSSCHHHHHHHHHHHHHHHHHHHHCC-
T ss_pred CHHHHHHHHHHHHHH-HhCccHHHHHHHHHHHHhhhhhccHHHHHHHHHc-CCccccchhHHHHHHHHHHHHHHHhccCc
Confidence 368999999999999 6688999999999999999999999999999998 65555666678899999999999999999
Q ss_pred cCCCC
Q psy15553 429 EDSDS 433 (489)
Q Consensus 429 Esded 433 (489)
|||++
T Consensus 79 E~~ee 83 (84)
T PF02020_consen 79 ESDEE 83 (84)
T ss_dssp -----
T ss_pred cCCCC
Confidence 88764
No 10
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=99.77 E-value=9.4e-19 Score=145.87 Aligned_cols=81 Identities=41% Similarity=0.653 Sum_probs=69.9
Q ss_pred hhhcccccchHHHHHHHHHHHHHHHhhhhHHHhhHHHHHHHHhhccCcchHHHHHHHhhccccccchHHHHHHHHHHHHH
Q psy15553 340 TVLRFTHEDIKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKKYVSKELSAEIRSRAEPF 419 (489)
Q Consensus 340 ~L~~fv~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DILeEE~Il~W~ek~skk~v~ke~~kkvrk~a~pF 419 (489)
+|.+|+. +.++|+++|++||.+|.. ++...+.|+.||+.|||.|||+||+|++||++.+. .+..++++++++||
T Consensus 3 ll~~~~~-~~~~q~~~L~ale~~~~~-~~~~~~~~~~il~~LYd~dileEe~il~W~~~~~~----~~~~~~~~~~~~~f 76 (83)
T smart00515 3 LLKFLAK-DEEEQIDLLYAIEEFCVE-LEKLIKLLPKILKSLYDADILEEEAILKWYEKAVS----AEGKKKVRKNAKPF 76 (83)
T ss_pred HHHHHHC-ChHHHHHHHHHHHHHHHH-cchHHHHHHHHHHHHhhhccccHHHHHHHHHcCCC----hHHHHHHHHHHhHH
Confidence 4577777 479999999999999964 34477999999999999999999999999998753 34578899999999
Q ss_pred HHHHccc
Q psy15553 420 IKWLREA 426 (489)
Q Consensus 420 IeWLkEA 426 (489)
|+||++|
T Consensus 77 v~WL~eA 83 (83)
T smart00515 77 VTWLQEA 83 (83)
T ss_pred HHHHHcC
Confidence 9999987
No 11
>KOG2297|consensus
Probab=99.62 E-value=5.3e-16 Score=156.35 Aligned_cols=92 Identities=23% Similarity=0.433 Sum_probs=80.9
Q ss_pred HhhhhhhhhcccccchHHHHHHHHHHHHHHHhhhhHHHhhHHHHHHHHhhccCcchHHHHHHHhhccccccchHHHHHHH
Q psy15553 334 LLDKQSTVLRFTHEDIKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKKYVSKELSAEIR 413 (489)
Q Consensus 334 l~~~~~~L~~fv~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DILeEE~Il~W~ek~skk~v~ke~~kkvr 413 (489)
|+++-++|..||+. ..+++.||+.+|.+| +++.++|+.|+.|+..||..|||+||.||+||.+++. +++ ...+.
T Consensus 321 lK~yaPLL~af~s~-g~sEL~Ll~KvQe~C-Yen~~fMKaFqkiV~lfYk~dVLsEe~IL~Wyk~gh~---~KG-k~~Fl 394 (412)
T KOG2297|consen 321 LKQYAPLLAAFCSQ-GQSELELLLKVQEYC-YENIHFMKAFQKIVVLFYKADVLSEETILKWYKEGHV---AKG-KSVFL 394 (412)
T ss_pred HHhhhHHHHHHhcC-ChHHHHHHHHHHHHH-HhhHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccc---ccc-HHHHH
Confidence 34444455899986 589999999999999 8899999999999999999999999999999998773 555 67899
Q ss_pred HHHHHHHHHHccccccCC
Q psy15553 414 SRAEPFIKWLREAEEEDS 431 (489)
Q Consensus 414 k~a~pFIeWLkEAEEEsd 431 (489)
++++|||+||++|||||+
T Consensus 395 eqmkkFVeWL~~AEEEsE 412 (412)
T KOG2297|consen 395 EQMKKFVEWLQNAEEESE 412 (412)
T ss_pred HHHHHHHHHHHhhhhccC
Confidence 999999999999999874
No 12
>KOG1461|consensus
Probab=99.50 E-value=4.9e-14 Score=152.44 Aligned_cols=100 Identities=26% Similarity=0.445 Sum_probs=82.6
Q ss_pred HHHHHhhhhhhhhcccccchHHHHHHHHHHHHHHHhhhhHHHhhHHHHHHHHhhccCcchHHHHHHHhhccccccchHHH
Q psy15553 330 CQLILLDKQSTVLRFTHEDIKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEKTSKKYVSKELS 409 (489)
Q Consensus 330 ~~~~l~~~~~~L~~fv~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DILeEE~Il~W~ek~skk~v~ke~~ 409 (489)
+...+.++|+.|..+...+++.|+++|.+||.+|. .+..+.+.+.++++.||+.|||+|++|++||...+ .+.+..
T Consensus 573 ~~~~~~~~w~~l~~~y~ks~deqid~l~~led~~~-e~~~~~~~~~~~v~~lY~~dil~EdaI~~W~~~~~---~~~~~~ 648 (673)
T KOG1461|consen 573 AALKVFTQWGPLLGNYIKSEDEQIDLLLALEDKCV-ESEELGPKAAKLVHYLYDYDILQEDAILSWSSQKA---GDDEED 648 (673)
T ss_pred HHHHHHHHhhHHhhhhhhhHHHHHHHHHHHHHHHH-hcccchHHHHHHHHHHHHHhHhhHHHHHHhhhccc---cchHHH
Confidence 34567889997665554358999999999999994 45777889999999999999999999999998733 244556
Q ss_pred HHHHHHHHHHHHHHccccccCCCC
Q psy15553 410 AEIRSRAEPFIKWLREAEEEDSDS 433 (489)
Q Consensus 410 kkvrk~a~pFIeWLkEAEEEsded 433 (489)
+..++++++||+||++|+||||+|
T Consensus 649 ~~~~~~~k~fv~WL~easeE~~~e 672 (673)
T KOG1461|consen 649 AVYNQQLKKFVDWLKEASEEEESE 672 (673)
T ss_pred HHHHHHHHHHHHHHhhcccccccC
Confidence 778899999999999999888764
No 13
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=92.80 E-value=0.034 Score=53.96 Aligned_cols=36 Identities=19% Similarity=0.544 Sum_probs=30.2
Q ss_pred hcccCCCCCCCCc--eEEEeccCCeEeeecccccCcccc
Q psy15553 96 KFVLCPECDNPET--DLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 96 ~yVlC~~C~~PeT--~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
.|..||+|++-+| .+++. +++-..++|..||...+.
T Consensus 5 iy~~Cp~Cg~eev~hEVik~-~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 5 IYIECPSCGSEEVSHEVIKE-RGREPLVRCEECGTVHPA 42 (201)
T ss_pred EEEECCCCCcchhhHHHHHh-cCCceEEEccCCCcEeec
Confidence 4789999999999 88872 466789999999999854
No 14
>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=92.72 E-value=0.11 Score=39.89 Aligned_cols=32 Identities=44% Similarity=1.047 Sum_probs=27.0
Q ss_pred HhhcccCCCCCC-----CCceEEEeccCCeEeeecccccC
Q psy15553 94 IRKFVLCPECDN-----PETDLVVSAKKGTIQQVCKACGF 128 (489)
Q Consensus 94 I~~yVlC~~C~~-----PeT~l~~~~k~~~~~l~C~ACG~ 128 (489)
..+|+.||.|+| -|-.|++ +..++...|+ ||.
T Consensus 10 ~~kY~~Cp~CGN~~vGngEG~liV--~edtfkRtCk-CGf 46 (49)
T PF12677_consen 10 SNKYCKCPKCGNDKVGNGEGTLIV--EEDTFKRTCK-CGF 46 (49)
T ss_pred hhhhccCcccCCcEeecCcceEEE--eccceeeeec-ccc
Confidence 566999999986 4778888 7889999998 885
No 15
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.47 E-value=0.17 Score=47.68 Aligned_cols=34 Identities=32% Similarity=0.662 Sum_probs=25.0
Q ss_pred cCCCCCCCCceEEEec---cCCeE--eeecccccCcccc
Q psy15553 99 LCPECDNPETDLVVSA---KKGTI--QQVCKACGFHGML 132 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~---k~~~~--~l~C~ACG~~~~v 132 (489)
.||.|++|+|.++-.. ++..+ +..|..||.+..-
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 6999999999988632 22123 4899999998543
No 16
>PF01253 SUI1: Translation initiation factor SUI1; InterPro: IPR001950 In Saccharomyces cerevisiae (Baker's yeast), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation []. SUI1 is a protein of 108 residues. Close homologs of SUI1 have been found [] in mammals, insects and plants. SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2OGH_A 1D1R_A 2IF1_A 2XZN_F 2XZM_F.
Probab=91.41 E-value=0.42 Score=40.00 Aligned_cols=73 Identities=15% Similarity=0.172 Sum_probs=49.8
Q ss_pred cCCCcEEEEeccCCC-eeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeec---CCCeEEEEeccchHHHHHHHHHH
Q psy15553 18 KMPKLIAKVEGKGNG-IKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDH---KNDRFIVNGSHDVVKLQDLLDGF 93 (489)
Q Consensus 18 kmP~~~~kieGkgng-iKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~---~~~r~iinG~~~~~~lq~~L~~f 93 (489)
..|.+.+.++-+++| .=|+|.||. .-.=++.-+.+.|...+|+.+++.+ ++..+.|+|.|...-.+=|+..|
T Consensus 3 ~~~~I~I~~e~r~~~K~vT~V~gl~----~~~~d~~~lak~lkk~~ac~~sv~~~~~k~~~I~iQGd~~~~i~~~L~~~~ 78 (83)
T PF01253_consen 3 EPPKIHIRVEKRRGRKFVTIVSGLE----LFGIDLKELAKELKKKFACGGSVTKDPGKGEEIQIQGDHRDEIKDLLVEKG 78 (83)
T ss_dssp -TTCEEEEEEESSSSEEEEEEES------STTSHHHHHHHHHHHHHTS-EEEEE-TTTSSEEEEESS-HHHHHHHHHHHC
T ss_pred CCCEEEEEEEeCcCCeEEEEEECCc----ccccCHHHHHHHHHHhccCceEEeecCCCCCEEEECCcHHHHHHHHHHHhC
Confidence 367888888844323 447788887 3444677889999999999999953 35569999999888666666655
Q ss_pred H
Q psy15553 94 I 94 (489)
Q Consensus 94 I 94 (489)
+
T Consensus 79 ~ 79 (83)
T PF01253_consen 79 G 79 (83)
T ss_dssp S
T ss_pred C
Confidence 3
No 17
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=91.35 E-value=0.13 Score=40.99 Aligned_cols=39 Identities=23% Similarity=0.555 Sum_probs=31.8
Q ss_pred HHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 92 GFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 92 ~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
+||-- ..||.|+..||...-. +++.-...|-.||++-..
T Consensus 5 RFIAG-A~CP~C~~~Dtl~~~~-e~~~e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 5 RFIAG-AVCPACSAQDTLAMWK-ENNIELVECVECGYQEQQ 43 (59)
T ss_pred eEecc-ccCCCCcCccEEEEEE-eCCceEEEeccCCCcccc
Confidence 45544 6799999999998873 788889999999998654
No 18
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=90.99 E-value=0.15 Score=42.20 Aligned_cols=41 Identities=24% Similarity=0.553 Sum_probs=33.1
Q ss_pred HHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 92 GFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 92 ~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
+||-- ..||.|+.-||...-. +++.-.+.|-+||++-..+.
T Consensus 4 rFIAG-a~CP~C~~~D~i~~~~-e~~ve~vECV~CGy~e~~~~ 44 (71)
T PF09526_consen 4 RFIAG-AVCPKCQAMDTIMMWR-ENGVEYVECVECGYTERQPD 44 (71)
T ss_pred eEecC-ccCCCCcCccEEEEEE-eCCceEEEecCCCCeeccCC
Confidence 45544 6799999999988763 67889999999999877643
No 19
>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=87.01 E-value=0.6 Score=49.57 Aligned_cols=54 Identities=20% Similarity=0.602 Sum_probs=35.1
Q ss_pred chHHHHHHHHHHHhh---------cccCCCCCCCCceEEEe--ccCCeEeeecccccCcccccch
Q psy15553 82 DVVKLQDLLDGFIRK---------FVLCPECDNPETDLVVS--AKKGTIQQVCKACGFHGMLQFN 135 (489)
Q Consensus 82 ~~~~lq~~L~~fI~~---------yVlC~~C~~PeT~l~~~--~k~~~~~l~C~ACG~~~~v~~~ 135 (489)
....|.++|..|..+ .++|+.|+.-+|+-+.. .+...+.-+|..||+...++.+
T Consensus 150 ~~~~I~~Il~~~~~~~~~~~y~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~ 214 (360)
T PF01921_consen 150 NRDEIREILNEYRGRERPETYSPFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDIT 214 (360)
T ss_dssp THHHHHHHHHHHHHHT--TT--SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETT
T ss_pred hHHHHHHHHHHhcCcCCCCCeeeeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecC
Confidence 356788888888544 48999999966554443 3488999999999999999753
No 20
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=86.82 E-value=0.21 Score=39.23 Aligned_cols=50 Identities=20% Similarity=0.547 Sum_probs=34.5
Q ss_pred hcccCCCCCCCC-ceEEEeccCCeEeeecccccCcccccchhhhhhhhhcCC
Q psy15553 96 KFVLCPECDNPE-TDLVVSAKKGTIQQVCKACGFHGMLQFNHKLNTFILKNP 146 (489)
Q Consensus 96 ~yVlC~~C~~Pe-T~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl~~~i~kn~ 146 (489)
+.++||.|+|.- +.+..|+.=+.+-+-|.-|-..+.++.. .|.--++|.|
T Consensus 3 ~Wi~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v~-~~~i~vikep 53 (55)
T PF14205_consen 3 EWILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDVK-QLKITVIKEP 53 (55)
T ss_pred eEEECCCCCCccceeeecCceeccccccCCCCCceEEEEee-ccEEEEEeCC
Confidence 578999999863 4444433335688999999999999754 4544455544
No 21
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=86.56 E-value=0.8 Score=33.56 Aligned_cols=31 Identities=32% Similarity=0.716 Sum_probs=24.6
Q ss_pred cCCCCCCCCceEEEec-----cCCeEeeecccccCc
Q psy15553 99 LCPECDNPETDLVVSA-----KKGTIQQVCKACGFH 129 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~-----k~~~~~l~C~ACG~~ 129 (489)
.||.|++.+..+...+ +.-++|..|..||++
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 6999999999986421 134689999999985
No 22
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=85.98 E-value=0.71 Score=36.01 Aligned_cols=28 Identities=25% Similarity=0.609 Sum_probs=21.5
Q ss_pred cCCCCCCCCceEEEeccCCe-----EeeecccccC
Q psy15553 99 LCPECDNPETDLVVSAKKGT-----IQQVCKACGF 128 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~-----~~l~C~ACG~ 128 (489)
-||-|+++...+.. .... +++.|..||+
T Consensus 5 PCPFCG~~~~~~~~--~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQ--DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeec--ccCCCCCCEEEEEcCCCCC
Confidence 59999777777765 2222 8899999999
No 23
>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=85.45 E-value=0.96 Score=34.85 Aligned_cols=34 Identities=24% Similarity=0.460 Sum_probs=23.5
Q ss_pred cCCCCCCCCceEEE--eccCCeEeeecccccCcccc
Q psy15553 99 LCPECDNPETDLVV--SAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 99 lC~~C~~PeT~l~~--~~k~~~~~l~C~ACG~~~~v 132 (489)
-||-|++.+-.+.. +..+...+..|..||+..++
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 49999997665541 11233334499999999987
No 24
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=85.14 E-value=0.81 Score=42.86 Aligned_cols=34 Identities=24% Similarity=0.477 Sum_probs=24.4
Q ss_pred cCCCCCCCCceEEEe--ccCCeE---eeecccccCcccc
Q psy15553 99 LCPECDNPETDLVVS--AKKGTI---QQVCKACGFHGML 132 (489)
Q Consensus 99 lC~~C~~PeT~l~~~--~k~~~~---~l~C~ACG~~~~v 132 (489)
.||-|++++|.++=. ++.+.. -..|.+||.+.+-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTT 40 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTT 40 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccce
Confidence 699999999999842 123333 3579999988543
No 25
>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=85.06 E-value=0.95 Score=32.96 Aligned_cols=32 Identities=28% Similarity=0.642 Sum_probs=22.6
Q ss_pred ccCCCCCCCCceEEEec-----cCCeEeeecccccCc
Q psy15553 98 VLCPECDNPETDLVVSA-----KKGTIQQVCKACGFH 129 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~-----k~~~~~l~C~ACG~~ 129 (489)
+.||.|++.++...-.+ +.-++|..|..||++
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 46999999999888532 134689999999975
No 26
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=84.23 E-value=0.69 Score=33.03 Aligned_cols=30 Identities=33% Similarity=0.880 Sum_probs=16.4
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
.||.|+.| +.+.+-..+...-+.|.+||..
T Consensus 2 fC~~CG~~-l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGP-LERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B--EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccCh-hhhhcCCCCCccceECCCCCCE
Confidence 49999999 4444412356678999999975
No 27
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=84.06 E-value=1.3 Score=36.03 Aligned_cols=34 Identities=21% Similarity=0.421 Sum_probs=27.8
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
-||-|+-..-.+.- .++-++..|..||+..+...
T Consensus 8 PCPFCG~~~~~v~~--~~g~~~v~C~~CgA~~~~~~ 41 (64)
T PRK09710 8 PCPFCGCPSVTVKA--ISGYYRAKCNGCESRTGYGG 41 (64)
T ss_pred CCCCCCCceeEEEe--cCceEEEEcCCCCcCccccc
Confidence 49999988777765 67888899999999877654
No 28
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=83.17 E-value=1.1 Score=47.40 Aligned_cols=93 Identities=19% Similarity=0.431 Sum_probs=58.0
Q ss_pred hHHHHHHhCCCCChhhhHH------HHhhcCceeeecCCCeEEEEeccch---------HHHHHHHHHHHhh--------
Q psy15553 40 MADVAKAIGRPPTYPTKYF------GCELGAQTKLDHKNDRFIVNGSHDV---------VKLQDLLDGFIRK-------- 96 (489)
Q Consensus 40 ~~dIakaL~R~p~~~~kyf------~~ELGa~~~~d~~~~r~iinG~~~~---------~~lq~~L~~fI~~-------- 96 (489)
+..|+.-.+.+|+|.-.|. ...||..-.+= ..-..--+|.++. ..|.++|..|...
T Consensus 89 i~~ip~p~g~~~~~~d~~~~~f~~~l~~lgi~~d~~-~~T~~y~~g~~~~~i~~~L~~~~~I~~i~~~~~~~~~~~~~~P 167 (353)
T cd00674 89 LSSVPDPFGCCESYAEHFERPFEESLEKLGIEVEFI-SQSQMYKSGLYDENILIALEKRDEIMAILNEYRGRELQETWYP 167 (353)
T ss_pred chhchhhcCCCHHHHHHHHHHHHHHHHHcCCeeeee-ecCCchhhchHHHHHHHHHHHCChHHHHHHHhcCCccCCCcee
Confidence 4455555555566655552 34566654432 1223345666654 4567777777765
Q ss_pred -cccCCCCCCCCceEE-EeccCCeEeeecccccCcccccc
Q psy15553 97 -FVLCPECDNPETDLV-VSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 97 -yVlC~~C~~PeT~l~-~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
.++|+.|+.-.|.++ .+.+.+.+.-+|. ||+...++.
T Consensus 168 ~~p~c~~cg~~~~~v~~~d~~~~~v~y~c~-cG~~g~~~~ 206 (353)
T cd00674 168 FMPYCEKCGKDTTTVEAYDAKAGTVTYKCE-CGHEETVDI 206 (353)
T ss_pred eeeecCCcCcceeEEEEEeCCCCeEEEEcC-CCCEEEEee
Confidence 479999996555553 5555677888996 999999874
No 29
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=82.43 E-value=2.2 Score=36.75 Aligned_cols=58 Identities=22% Similarity=0.452 Sum_probs=36.3
Q ss_pred hcCceeeecCCCeEEEEeccchHHHHHHHHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCccc
Q psy15553 62 LGAQTKLDHKNDRFIVNGSHDVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGM 131 (489)
Q Consensus 62 LGa~~~~d~~~~r~iinG~~~~~~lq~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~ 131 (489)
.|..|.|. -|| |.--.....++...-..+| .||.|+.+ |.-.+ ..+ +-.|.-||+...
T Consensus 7 vG~aGrfG---pRY---G~~~Rrrv~~ie~~~~~~~-~Cp~C~~~-~VkR~--a~G--IW~C~kCg~~fA 64 (89)
T COG1997 7 VGIAGRFG---PRY---GSKLRRRVKEIEAQQRAKH-VCPFCGRT-TVKRI--ATG--IWKCRKCGAKFA 64 (89)
T ss_pred eccCcccc---ccc---chHHHHHHHHHHHHHhcCC-cCCCCCCc-ceeee--ccC--eEEcCCCCCeec
Confidence 35556553 244 5555556666666655555 59999999 44333 344 567999998753
No 30
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=77.96 E-value=4.3 Score=39.03 Aligned_cols=73 Identities=12% Similarity=0.107 Sum_probs=54.3
Q ss_pred ccCCCcEEEEeccCCCe-eEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeec---CCCeEEEEeccchHHHHHHHHH
Q psy15553 17 YKMPKLIAKVEGKGNGI-KTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDH---KNDRFIVNGSHDVVKLQDLLDG 92 (489)
Q Consensus 17 ykmP~~~~kieGkgngi-KTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~---~~~r~iinG~~~~~~lq~~L~~ 92 (489)
=..+++.++++-|+.|+ =|+|.+|.. .+-++.-+.|+|...+++.+++.. +++.++|+|.|.....+=|+..
T Consensus 86 ~~~~~V~I~~~~R~krK~VT~V~GLe~----f~idlk~laK~lkkkfacG~SV~k~~~~~~eI~IQGD~~~~v~e~L~~~ 161 (173)
T TIGR01159 86 KLPQKVTIKREPRTKRKFVTVIKGLET----FDIDLKKASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEK 161 (173)
T ss_pred CCCCeEEEEEEecCCCceEEEEeCCcC----CCcCHHHHHHHHHHHhCCCCccccCCCCCCEEEecCCHHHHHHHHHHHH
Confidence 35677888888876443 478888874 245678899999999999976631 4678999999988777666665
Q ss_pred H
Q psy15553 93 F 93 (489)
Q Consensus 93 f 93 (489)
|
T Consensus 162 ~ 162 (173)
T TIGR01159 162 W 162 (173)
T ss_pred c
Confidence 5
No 31
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=77.67 E-value=1.4 Score=38.71 Aligned_cols=36 Identities=25% Similarity=0.579 Sum_probs=26.8
Q ss_pred hhcccCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 95 RKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 95 ~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
..++.||.|+++--.+.+ .++...+.|..||....-
T Consensus 19 pt~f~CP~Cge~~v~v~~--~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGKVSISVKI--KKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCCeEeeeec--CCCcceEECCCCCCccCE
Confidence 467899999975333334 567889999999998654
No 32
>PHA02998 RNA polymerase subunit; Provisional
Probab=77.56 E-value=2.6 Score=40.77 Aligned_cols=84 Identities=18% Similarity=0.354 Sum_probs=48.9
Q ss_pred chHHHHHHhCC---CCChhhhHHHHhh-----cCceeeecCCCeEEEEeccchHHHHHHHHHHHhhcccCCCCCCCCceE
Q psy15553 39 NMADVAKAIGR---PPTYPTKYFGCEL-----GAQTKLDHKNDRFIVNGSHDVVKLQDLLDGFIRKFVLCPECDNPETDL 110 (489)
Q Consensus 39 N~~dIakaL~R---~p~~~~kyf~~EL-----Ga~~~~d~~~~r~iinG~~~~~~lq~~L~~fI~~yVlC~~C~~PeT~l 110 (489)
-..+||..++- -...+++||++-+ |+.-.||. + -.|+-..-=.++.. +.-|.||.|++.++..
T Consensus 86 ~y~~lc~~ir~tng~eke~lry~lfgikcv~~~veydid~----~---~d~~y~~yfnvlpk--kt~v~CPkCg~~~A~f 156 (195)
T PHA02998 86 EYKDLCDMIRGTNGTEKEILRYLLFGIKCIKKGVEYDIDK----I---PDVDYDDYFNVLDE--KYNTPCPNCKSKNTTP 156 (195)
T ss_pred cHHHHHHHHHhcCCchHHHHHHHHHHHHHHhcCCccchhh----c---ccccchhheeccCc--ccCCCCCCCCCCceEE
Confidence 36788877643 3456888988654 23333321 1 01121221122221 1358999999999985
Q ss_pred EEec-----cCCeEeeecccccCccc
Q psy15553 111 VVSA-----KKGTIQQVCKACGFHGM 131 (489)
Q Consensus 111 ~~~~-----k~~~~~l~C~ACG~~~~ 131 (489)
..-+ +-.+.|.+|..||++-.
T Consensus 157 ~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 157 MMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred EEEeeccCCCCceEEEEcCCCCCccC
Confidence 5321 13478999999999753
No 33
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=77.48 E-value=3 Score=46.22 Aligned_cols=52 Identities=21% Similarity=0.560 Sum_probs=39.7
Q ss_pred hHHHHHHHHHHHhh---------cccCCCCCCCCceEEEeccC-CeEeeecccccCcccccch
Q psy15553 83 VVKLQDLLDGFIRK---------FVLCPECDNPETDLVVSAKK-GTIQQVCKACGFHGMLQFN 135 (489)
Q Consensus 83 ~~~lq~~L~~fI~~---------yVlC~~C~~PeT~l~~~~k~-~~~~l~C~ACG~~~~v~~~ 135 (489)
...|+++|..|-.. -++|+.|+.-.|+=+++-.. ..+.-+|. ||+.+.|+.+
T Consensus 148 rdeI~~il~~~~~~~~~e~~~P~~piC~kcGri~~t~v~~~d~~~~v~Y~Ce-~Gh~g~v~ir 209 (521)
T COG1384 148 RDEIMEILNEYRGRELEEDWSPFMPICEKCGRILTTPVIEWDGEGTVEYRCE-CGHEGEVDIR 209 (521)
T ss_pred HHHHHHHHHHhcCCcccCCceeccccccccCCcceeEEEEecCCceEEEEec-CCccceeecc
Confidence 35788888888777 37899999955444443334 48999998 9999999975
No 34
>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=76.24 E-value=1.7 Score=32.04 Aligned_cols=27 Identities=37% Similarity=1.026 Sum_probs=19.0
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
.||.|++.. ++.|...+ .+.|..||..
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g--~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERG--ELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE--EEEETTTT--EEEETTT-BB
T ss_pred CCcCCcCCc--eEEcCCCC--eEECCCCCCE
Confidence 599999966 55543344 5699999976
No 35
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=75.46 E-value=1.9 Score=32.36 Aligned_cols=32 Identities=31% Similarity=0.840 Sum_probs=20.2
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
.||.|++. |......+.....|..||+...+.
T Consensus 2 FCp~Cg~~---l~~~~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGNM---LIPKEGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCc---cccccCCCCCEEECCcCCCeEECC
Confidence 49999983 332111122377899999876664
No 36
>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=74.78 E-value=3 Score=31.17 Aligned_cols=28 Identities=29% Similarity=0.669 Sum_probs=20.5
Q ss_pred ccCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 98 VLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
+.||.|++. ....+ ++ ....+|++|+++
T Consensus 19 ~~CP~Cg~~-~~~~~--~~-~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGST-KHYRL--KT-RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCe-eeEEe--CC-CCeEECCCCCCc
Confidence 449999998 44444 23 567899999974
No 37
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=73.62 E-value=3.7 Score=45.69 Aligned_cols=73 Identities=16% Similarity=0.374 Sum_probs=47.5
Q ss_pred HHhhcCceeeecCCCeEEEEeccch---------HHHHHHHHHHHhh---------cccCCCCCCCCceEE-EeccCCeE
Q psy15553 59 GCELGAQTKLDHKNDRFIVNGSHDV---------VKLQDLLDGFIRK---------FVLCPECDNPETDLV-VSAKKGTI 119 (489)
Q Consensus 59 ~~ELGa~~~~d~~~~r~iinG~~~~---------~~lq~~L~~fI~~---------yVlC~~C~~PeT~l~-~~~k~~~~ 119 (489)
.-+||..-.+- .+..+.=+|.|+. .+|.++|..|... .++|+.|+.-.|.++ .+.+. .+
T Consensus 113 l~~~gi~~e~~-s~te~Y~sG~~~~~i~~~L~~~~~I~~il~~~~~~~~~~~~~P~~pic~~cGrv~~~~~~~~~~~-~v 190 (515)
T TIGR00467 113 LPVLGINPEFI-RASKQYTSGLYASQIKIALDHRKEISEILNEYRTSKLEENWYPISVFCENCGRDTTTVNNYDNEY-SI 190 (515)
T ss_pred HHHcCCeEEEE-EHHHhhhcCChHHHHHHHHHhHHHHHHHHHHhcCCccCCCceeeeeecCCcCccCceEEEecCCc-eE
Confidence 34566654443 2233444666654 5677788887743 479999999877555 32223 57
Q ss_pred eeecccccCcccccc
Q psy15553 120 QQVCKACGFHGMLQF 134 (489)
Q Consensus 120 ~l~C~ACG~~~~v~~ 134 (489)
.-+|. ||+...++.
T Consensus 191 ~Y~c~-cG~~g~~~~ 204 (515)
T TIGR00467 191 EYSCE-CGNQESVDI 204 (515)
T ss_pred EEEcC-CCCEEEEee
Confidence 77997 999999875
No 38
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=73.38 E-value=2.8 Score=46.38 Aligned_cols=93 Identities=22% Similarity=0.498 Sum_probs=57.3
Q ss_pred HHHHHHhCCC-----------CChhhhH------HHHhhcCceeeecCCCeEEEEeccch---------HHHHHHHHHHH
Q psy15553 41 ADVAKAIGRP-----------PTYPTKY------FGCELGAQTKLDHKNDRFIVNGSHDV---------VKLQDLLDGFI 94 (489)
Q Consensus 41 ~dIakaL~R~-----------p~~~~ky------f~~ELGa~~~~d~~~~r~iinG~~~~---------~~lq~~L~~fI 94 (489)
..+++.|+.| .+|...| +...+|..-.+= ....+.=+|.|.. ..|.++|..|.
T Consensus 85 ~~~~~~~G~pl~~~p~p~G~~~~~~~~~~~~~~~~~~~~gi~~d~~-~~t~~y~~g~~~~~i~~~l~~~~~i~~il~~~~ 163 (510)
T PRK00750 85 EMLEEYLGKPLTEIPDPFGCHESYAEHFNAPLREFLDRFGIEYEFI-SATECYKSGRYDEAILTALENRDEIMEILLPYL 163 (510)
T ss_pred HHHHHhcCcccccCCCCCCCchHHHHHHHHHHHHHHHHcCCceEEE-ehhhhhccCchHHHHHHHHHhHHHHHHHHHHhc
Confidence 3577888887 3444444 334456544322 1112223555543 45566666664
Q ss_pred hh---------cccCCCCCCCCceEE--EeccCCeEeeecccccCcccccch
Q psy15553 95 RK---------FVLCPECDNPETDLV--VSAKKGTIQQVCKACGFHGMLQFN 135 (489)
Q Consensus 95 ~~---------yVlC~~C~~PeT~l~--~~~k~~~~~l~C~ACG~~~~v~~~ 135 (489)
.. .++|+.|+.-.|..+ .+.+.+.+.-.|. ||+...++.+
T Consensus 164 ~~~~~~~~~P~~pic~~cg~~~~~~~~~~d~~~~~v~y~~~-cG~~~~~~~~ 214 (510)
T PRK00750 164 GEERQATYSPFLPICPKCGKVLTTPVISYDAEAGTVTYDCE-CGHEGEVPVT 214 (510)
T ss_pred CCccCCCeeeeeeeCCCCCccceEEEEEEeCCCCEEEEEcC-CCCEEEEecC
Confidence 33 478999999998776 4445667777897 9999988765
No 39
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=72.69 E-value=2.3 Score=34.82 Aligned_cols=29 Identities=28% Similarity=0.665 Sum_probs=23.3
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
+|.||.|+|--|.+- .-....+|..||..
T Consensus 19 ~VkCpdC~N~q~vFs----hast~V~C~~CG~~ 47 (67)
T COG2051 19 RVKCPDCGNEQVVFS----HASTVVTCLICGTT 47 (67)
T ss_pred EEECCCCCCEEEEec----cCceEEEecccccE
Confidence 699999999766664 44568899999986
No 40
>PF09090 MIF4G_like_2: MIF4G like; InterPro: IPR015174 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 2", and is found in nuclear cap-binding proteins and eIF4G. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA.; GO: 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A.
Probab=70.84 E-value=33 Score=34.39 Aligned_cols=55 Identities=16% Similarity=0.311 Sum_probs=41.5
Q ss_pred hhhcccccchHHHHHHHHHHHHHHHhhhhHHHhhHHHHHHHHhhccCcchHHHHHHHhh
Q psy15553 340 TVLRFTHEDIKAQRYLLNGIEQVIALHKEKLLSMVPGILKLFYDYDILEEKVLLEWAEK 398 (489)
Q Consensus 340 ~L~~fv~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DILeEE~Il~W~ek 398 (489)
.|+.+...++..|..+|.++=+|. .++|. ....|+..|-...||+-.+|+.|.=.
T Consensus 81 ~Lk~l~~~~~~~q~~il~~v~~~W-~~~~q---~~~li~dkll~~~ii~~~~Vv~w~f~ 135 (253)
T PF09090_consen 81 VLKELEAESEEAQFWILDAVFRFW-KNNPQ---MGFLIIDKLLNYGIISPSAVVNWVFS 135 (253)
T ss_dssp HHHHH-TSSHHHHHHHHHHHHHHH-TT-HH---HHHHHHHHHHHTTSS-HHHHHHHHTS
T ss_pred HHHHhccCChHHHHHHHHHHHHHH-hcCCc---eehHHHHHHHhcCCCCHHHHHHHHcC
Confidence 336662335789999999999988 45666 35788999999999999999999743
No 41
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=69.45 E-value=10 Score=31.63 Aligned_cols=59 Identities=7% Similarity=0.049 Sum_probs=43.7
Q ss_pred EEEEeccCCC-eeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHH
Q psy15553 23 IAKVEGKGNG-IKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQ 87 (489)
Q Consensus 23 ~~kieGkgng-iKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq 87 (489)
.++++-++.| .=|+|.+|..-.. ++.-+.+.|...+|+.|++. ++.+.|+|.|...-.+
T Consensus 3 ~I~~e~R~~~K~VT~I~Gl~~~~~----dlk~l~k~lKk~~~cggtv~--~~~I~lQGD~r~~v~~ 62 (77)
T cd00474 3 RIRIQQRNGGKTVTTVQGLDLEYA----DLKKLAKELKKKCACGGTVK--DEVIELQGDQRKKIKE 62 (77)
T ss_pred EEEEEECCCCccEEEEECCCCchH----hHHHHHHHHHHHcCCCcEEe--cCEEEEeCcHHHHHHH
Confidence 4555655444 4578888863221 67789999999999999996 5899999999766543
No 42
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=68.63 E-value=3.3 Score=33.22 Aligned_cols=30 Identities=27% Similarity=0.540 Sum_probs=23.8
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCcc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFHG 130 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~ 130 (489)
-|.||.|+|.-|.+.. -.....|..||..=
T Consensus 11 ~VkCp~C~n~q~vFsh----a~t~V~C~~Cg~~L 40 (59)
T PRK00415 11 KVKCPDCGNEQVVFSH----ASTVVRCLVCGKTL 40 (59)
T ss_pred EEECCCCCCeEEEEec----CCcEEECcccCCCc
Confidence 4899999998777754 35688999999763
No 43
>PHA00626 hypothetical protein
Probab=66.62 E-value=4.5 Score=32.22 Aligned_cols=36 Identities=19% Similarity=0.465 Sum_probs=23.4
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
.||.|++-+-..-..-.+..-.-+|.-||+..+-|.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhh
Confidence 699999865443211012234568999999987763
No 44
>COG0023 SUI1 Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=65.46 E-value=19 Score=32.10 Aligned_cols=82 Identities=12% Similarity=0.013 Sum_probs=53.1
Q ss_pred ceeccCCCCCCccccc---cCCC----cEEEEeccCCC-eeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCC
Q psy15553 2 ATVNVNRNVTDAFYRY---KMPK----LIAKVEGKGNG-IKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKND 73 (489)
Q Consensus 2 ~~iNi~~~~~D~~yRy---kmP~----~~~kieGkgng-iKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~ 73 (489)
+...+++. .+|+..+ .+|+ +.++++-+.-| --|+|.+|..- .-++.-+.++|-..+|+.|++ +++
T Consensus 3 ~~~~~~~~-~~p~e~~~~~~~k~~~~~V~I~~e~rr~gK~VTiI~Gld~~----~~dlk~Lak~LKk~cacGGtv--k~~ 75 (104)
T COG0023 3 YSTICGRI-GLPKELTCEEVAKEGDQIVRIRRETRRKGKTVTIIEGLDLK----DIDLKKLAKELKKKCACGGTV--KDG 75 (104)
T ss_pred ccccCCCC-CCchHHhhhhcccccCCeEEEEEEeecCCcEEEEEeCcccc----hhhHHHHHHHHHHHcCCCcee--cCC
Confidence 33444332 5666655 5555 45555655333 35777887752 223556788888899999999 588
Q ss_pred eEEEEeccchHHHHHHH
Q psy15553 74 RFIVNGSHDVVKLQDLL 90 (489)
Q Consensus 74 r~iinG~~~~~~lq~~L 90 (489)
...|+|.|......=|+
T Consensus 76 ~IeiQGdhr~~v~~~L~ 92 (104)
T COG0023 76 EIEIQGDHRDKVKELLI 92 (104)
T ss_pred EEEEeChHHHHHHHHHH
Confidence 99999999876554443
No 45
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=65.37 E-value=3.2 Score=29.80 Aligned_cols=31 Identities=29% Similarity=0.747 Sum_probs=21.4
Q ss_pred cccCCCCCC----CCceEEEeccCCeEeeecccccCccc
Q psy15553 97 FVLCPECDN----PETDLVVSAKKGTIQQVCKACGFHGM 131 (489)
Q Consensus 97 yVlC~~C~~----PeT~l~~~~k~~~~~l~C~ACG~~~~ 131 (489)
.+.||.|+. |++.|-. ....++|..||+.-.
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~----~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPA----GGRKVRCPKCGHVFR 36 (37)
T ss_pred EEECCCCCceEEcCHHHccc----CCcEEECCCCCcEee
Confidence 478999973 4555433 234899999998754
No 46
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=65.25 E-value=5.2 Score=38.09 Aligned_cols=32 Identities=19% Similarity=0.605 Sum_probs=20.5
Q ss_pred CCCCCCC-CceEEEecc----CCe--EeeecccccCccc
Q psy15553 100 CPECDNP-ETDLVVSAK----KGT--IQQVCKACGFHGM 131 (489)
Q Consensus 100 C~~C~~P-eT~l~~~~k----~~~--~~l~C~ACG~~~~ 131 (489)
||.|+.+ .+.+....+ +.+ ....|..||++..
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchh
Confidence 9999997 344222111 233 3678999999964
No 47
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=64.41 E-value=8 Score=33.32 Aligned_cols=34 Identities=26% Similarity=0.496 Sum_probs=26.4
Q ss_pred cccCCCCCCCCceEEEec-----cCCeEeeecccccCcc
Q psy15553 97 FVLCPECDNPETDLVVSA-----KKGTIQQVCKACGFHG 130 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~-----k~~~~~l~C~ACG~~~ 130 (489)
.+.||.|++.+..+...+ +.-++|-.|..||++-
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w 100 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVW 100 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCee
Confidence 589999999998766321 2467899999999863
No 48
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=64.16 E-value=4.6 Score=38.11 Aligned_cols=32 Identities=28% Similarity=0.717 Sum_probs=23.1
Q ss_pred cCCCCCCCCceEEEecc---CC-eE--eeecccccCccc
Q psy15553 99 LCPECDNPETDLVVSAK---KG-TI--QQVCKACGFHGM 131 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k---~~-~~--~l~C~ACG~~~~ 131 (489)
.||.|+.++|.++= +. .+ .| -..|..||.+.+
T Consensus 2 ~CPfC~~~~tkViD-SR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVID-SRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeee-cccccccchhhhhhcccccccccc
Confidence 69999999999973 21 11 22 457999998754
No 49
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=63.97 E-value=14 Score=32.46 Aligned_cols=63 Identities=19% Similarity=0.199 Sum_probs=43.3
Q ss_pred cEEEEeccCCC-eeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHHH
Q psy15553 22 LIAKVEGKGNG-IKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLD 91 (489)
Q Consensus 22 ~~~kieGkgng-iKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~ 91 (489)
+.++++-+..| .=|+|.||..- .=++.-+.+.|...+|+.|++. ++.+.|+|.|..... ++|.
T Consensus 26 i~I~~ekr~~gK~VTiI~Gl~~~----~~~lk~l~k~lKk~~gcGgsvk--~~~I~iQGD~r~~v~-~~L~ 89 (99)
T PRK00939 26 IKIKVDKRRYGKEVTIIEGIDPK----DIDLKELAKKLKSKLACGGTVK--DGRIELQGDHRERVK-ELLI 89 (99)
T ss_pred EEEEEEecCCCceEEEEeCCCCc----chhHHHHHHHHHHHhCCCceEE--CCEEEEeCcHHHHHH-HHHH
Confidence 44455543323 45788888631 1136678899999999999995 678999999976544 4443
No 50
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=63.78 E-value=5.4 Score=39.17 Aligned_cols=34 Identities=21% Similarity=0.509 Sum_probs=21.5
Q ss_pred cccCCCCCCCCceEEEecc-----CCe--EeeecccccCccc
Q psy15553 97 FVLCPECDNPETDLVVSAK-----KGT--IQQVCKACGFHGM 131 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k-----~~~--~~l~C~ACG~~~~ 131 (489)
-+-||.|++ .-.++-..- +++ ....|..||+++.
T Consensus 14 ~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 14 RIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 367999999 322222100 233 4789999999965
No 51
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=63.03 E-value=6.7 Score=37.15 Aligned_cols=32 Identities=22% Similarity=0.718 Sum_probs=21.1
Q ss_pred cCCCCCCCCc-eEEEecc----CCe--EeeecccccCccc
Q psy15553 99 LCPECDNPET-DLVVSAK----KGT--IQQVCKACGFHGM 131 (489)
Q Consensus 99 lC~~C~~PeT-~l~~~~k----~~~--~~l~C~ACG~~~~ 131 (489)
+||.|+.+=| .+.. .+ +.+ ....|..||++..
T Consensus 2 ~Cp~C~~~~~~~~~~-~~IP~F~evii~sf~C~~CGyk~~ 40 (160)
T smart00709 2 DCPSCGGNGTTRMLL-TSIPYFREVIIMSFECEHCGYRNN 40 (160)
T ss_pred cCCCCCCCCEEEEEE-ecCCCcceEEEEEEECCCCCCccc
Confidence 6999996644 3333 12 222 3679999999954
No 52
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=62.11 E-value=8.6 Score=44.73 Aligned_cols=42 Identities=26% Similarity=0.530 Sum_probs=29.5
Q ss_pred chHHHHHHHHHHHhhc----------------------ccCCCCCCCCceEEEeccCCeEeeecccccCcc
Q psy15553 82 DVVKLQDLLDGFIRKF----------------------VLCPECDNPETDLVVSAKKGTIQQVCKACGFHG 130 (489)
Q Consensus 82 ~~~~lq~~L~~fI~~y----------------------VlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~ 130 (489)
-+..|-..|..++..- ..||+|+. | |+. ..+ ...|..||+..
T Consensus 687 cpDaI~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~--~-l~~--~~G--C~~C~~CG~sk 750 (752)
T PRK08665 687 CPDAIAKVLEKHYLGGGKDVGAGNGTGSAGIEAPAPERGACPECGS--I-LEH--EEG--CVVCHSCGYSK 750 (752)
T ss_pred HHHHHHHHHHHHHHhccccccccccccccccccccCCCCCCCCCCc--c-cEE--CCC--CCcCCCCCCCC
Confidence 3567777887776540 35999984 3 665 455 56999999964
No 53
>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=61.55 E-value=5.4 Score=28.49 Aligned_cols=31 Identities=29% Similarity=0.795 Sum_probs=18.3
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
-||.|+|.=. ....+.... .|..||+..+++
T Consensus 3 FCp~C~nlL~--p~~~~~~~~--~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 3 FCPECGNLLY--PKEDKEKRV--ACRTCGYEEPIS 33 (35)
T ss_dssp BETTTTSBEE--EEEETTTTE--EESSSS-EEE-S
T ss_pred eCCCCCccce--EcCCCccCc--CCCCCCCccCCC
Confidence 5999998532 221122223 999999987764
No 54
>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=61.22 E-value=3.9 Score=38.17 Aligned_cols=31 Identities=29% Similarity=0.557 Sum_probs=23.0
Q ss_pred ccCCCCCCCCceEEEeccCCe---EeeecccccCc
Q psy15553 98 VLCPECDNPETDLVVSAKKGT---IQQVCKACGFH 129 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~---~~l~C~ACG~~ 129 (489)
|.||.|+|.+|.++-. =+.+ -..+|.+|...
T Consensus 106 ~~cp~c~s~~t~~~s~-fg~t~cka~~~c~~c~ep 139 (146)
T TIGR02159 106 VQCPRCGSADTTITSI-FGPTACKALYRCRACKEP 139 (146)
T ss_pred CcCCCCCCCCcEeecC-CCChhhHHHhhhhhhCCc
Confidence 8999999999999851 1222 35688888753
No 55
>TIGR01158 SUI1_rel translation initation factor SUI1, putative, prokaryotic. This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met.
Probab=60.97 E-value=18 Score=31.76 Aligned_cols=59 Identities=14% Similarity=0.080 Sum_probs=42.6
Q ss_pred cEEEEeccC--CCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHH
Q psy15553 22 LIAKVEGKG--NGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKL 86 (489)
Q Consensus 22 ~~~kieGkg--ngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~l 86 (489)
+.+.++-+| +-.=|+|.||..-. -++.-+.|+|...+|+.|++. ++.+.|+|.|...-.
T Consensus 26 i~i~~e~rgr~gK~VTvV~Gl~~~~----~~l~~l~k~LKk~~gcGgtvk--~~~IeiQGD~~~~v~ 86 (101)
T TIGR01158 26 VRIQRETRGRKGKGVTIIEGLDLSD----IDLKELAKELKSKCGCGGTVK--DGVIEIQGDHRDRVK 86 (101)
T ss_pred EEEEEEEecCCCCEEEEEeCCcCch----hhHHHHHHHHHHHhcCCeeEe--CCEEEEeCcHHHHHH
Confidence 445555443 33558899986322 245678899999999999994 789999999976544
No 56
>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=59.74 E-value=12 Score=27.26 Aligned_cols=33 Identities=30% Similarity=0.650 Sum_probs=21.7
Q ss_pred ccCCCCCCCCceEEEeccCCeEeeeccc---ccCccccc
Q psy15553 98 VLCPECDNPETDLVVSAKKGTIQQVCKA---CGFHGMLQ 133 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~~l~C~A---CG~~~~v~ 133 (489)
+.||.|+++ -+.+.++.+ .|+-|.. |.+...++
T Consensus 2 ~~CP~Cg~~--lv~r~~k~g-~F~~Cs~yP~C~~~~~~~ 37 (39)
T PF01396_consen 2 EKCPKCGGP--LVLRRGKKG-KFLGCSNYPECKYTEPLP 37 (39)
T ss_pred cCCCCCCce--eEEEECCCC-CEEECCCCCCcCCeEeCC
Confidence 579999932 333333344 8899987 87776654
No 57
>KOG2703|consensus
Probab=59.29 E-value=5.7 Score=42.77 Aligned_cols=32 Identities=38% Similarity=0.972 Sum_probs=23.9
Q ss_pred cCCCCCCC-CceEEEecc----CCeE--eeecccccCccc
Q psy15553 99 LCPECDNP-ETDLVVSAK----KGTI--QQVCKACGFHGM 131 (489)
Q Consensus 99 lC~~C~~P-eT~l~~~~k----~~~~--~l~C~ACG~~~~ 131 (489)
-||+|..| ||.|... + +.+| ...|.+||+++.
T Consensus 260 ~Cp~C~~pcet~Mk~~-~IPhFkeVIiMst~Cd~CGyksn 298 (460)
T KOG2703|consen 260 TCPSCTAPCETNMKLT-DIPHFKEVIIMSTVCDRCGYKSN 298 (460)
T ss_pred CCCCCCCchhccceec-cCCcceeEEEEeecccccCCccc
Confidence 59999999 8988762 2 2333 568999999864
No 58
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=59.11 E-value=8.7 Score=37.49 Aligned_cols=32 Identities=25% Similarity=0.695 Sum_probs=21.6
Q ss_pred cCCCCCCC-CceEEEecc-----CCe--EeeecccccCccc
Q psy15553 99 LCPECDNP-ETDLVVSAK-----KGT--IQQVCKACGFHGM 131 (489)
Q Consensus 99 lC~~C~~P-eT~l~~~~k-----~~~--~~l~C~ACG~~~~ 131 (489)
-||.|+.+ .|.+.. .+ +.+ ....|..||++..
T Consensus 2 ~Cp~C~~~~~~~~~~-~~~IP~F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 2 DCPSCGGECETVMKT-VNDIPYFGEVLETSTICEHCGYRSN 41 (192)
T ss_pred cCCCCCCCCEEEEEE-EcCCCCcceEEEEEEECCCCCCccc
Confidence 59999976 554544 22 222 3679999999954
No 59
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=59.11 E-value=4.3 Score=31.01 Aligned_cols=33 Identities=30% Similarity=0.466 Sum_probs=26.0
Q ss_pred cccCCCCC----CCCceEEEeccCCeEeeecccccCccc
Q psy15553 97 FVLCPECD----NPETDLVVSAKKGTIQQVCKACGFHGM 131 (489)
Q Consensus 97 yVlC~~C~----~PeT~l~~~~k~~~~~l~C~ACG~~~~ 131 (489)
||.|++|. -|...... +++...++|-+|...-.
T Consensus 6 Fv~C~~C~~lLqlP~~~~~~--~k~~~klrCGaCs~vl~ 42 (46)
T PF11331_consen 6 FVVCSSCFELLQLPAKFSLS--KKNQQKLRCGACSEVLS 42 (46)
T ss_pred EeECccHHHHHcCCCccCCC--ccceeEEeCCCCceeEE
Confidence 89999996 57766665 56688999999987644
No 60
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=59.10 E-value=6 Score=37.42 Aligned_cols=33 Identities=27% Similarity=0.788 Sum_probs=17.7
Q ss_pred ccCCCCCCCC-ceEEEecc----CCe--EeeecccccCccc
Q psy15553 98 VLCPECDNPE-TDLVVSAK----KGT--IQQVCKACGFHGM 131 (489)
Q Consensus 98 VlC~~C~~Pe-T~l~~~~k----~~~--~~l~C~ACG~~~~ 131 (489)
.+||.|+.+- |.+.. .+ +.+ ....|..||+++.
T Consensus 2 s~Cp~C~~~~~~~~~~-~~IP~F~evii~sf~C~~CGyk~~ 41 (161)
T PF03367_consen 2 SLCPNCGENGTTRILL-TDIPYFKEVIIMSFECEHCGYKNN 41 (161)
T ss_dssp EE-TTTSSCCEEEEEE-EEETTTEEEEEEEEE-TTT--EEE
T ss_pred CcCCCCCCCcEEEEEE-EcCCCCceEEEEEeECCCCCCEee
Confidence 4799999885 44432 11 222 3568999999864
No 61
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=59.02 E-value=12 Score=27.28 Aligned_cols=28 Identities=25% Similarity=0.531 Sum_probs=20.6
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
.||.|+++=.... -..+..-.|.+||-.
T Consensus 1 ~CP~C~~~l~~~~---~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVR---LGDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEE---ECCEEEEECCCCCeE
Confidence 4999999533333 366888899999965
No 62
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=57.97 E-value=9.7 Score=38.47 Aligned_cols=40 Identities=23% Similarity=0.414 Sum_probs=30.6
Q ss_pred HHHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCccccc
Q psy15553 89 LLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 89 ~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
.|-.|-..+-.|+.|+.| |... .....+.|.+||......
T Consensus 91 ~l~~w~~~~~fC~~CG~~-~~~~----~~~~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 91 QLAEFYRSHRFCGYCGHP-MHPS----KTEWAMLCPHCRERYYPR 130 (256)
T ss_pred HHHHHhhcCccccccCCC-Ceec----CCceeEECCCCCCEECCC
Confidence 467888999999999998 4432 344678999999876654
No 63
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=57.14 E-value=8.3 Score=34.10 Aligned_cols=38 Identities=21% Similarity=0.470 Sum_probs=28.8
Q ss_pred HhhcccCCCCCCCCce---EEEeccCCeEeeecccccCccccc
Q psy15553 94 IRKFVLCPECDNPETD---LVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 94 I~~yVlC~~C~~PeT~---l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
+.++--||-|+.---. +.+ .....++.|..||.+....
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk--~~~~g~~~Cg~CGls~e~e 59 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKK--TVNIGTAVCGNCGLSFECE 59 (104)
T ss_pred CCceEecCccCCeeeeEEEEEe--cCceeEEEcccCcceEEEe
Confidence 3456789999865444 555 6777899999999987764
No 64
>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=57.01 E-value=10 Score=39.39 Aligned_cols=56 Identities=16% Similarity=0.328 Sum_probs=38.8
Q ss_pred eEEEEeccchHHHH-------------HHHHHHHhh----------------cccCCCCCCCCceEEEecc-----CCeE
Q psy15553 74 RFIVNGSHDVVKLQ-------------DLLDGFIRK----------------FVLCPECDNPETDLVVSAK-----KGTI 119 (489)
Q Consensus 74 r~iinG~~~~~~lq-------------~~L~~fI~~----------------yVlC~~C~~PeT~l~~~~k-----~~~~ 119 (489)
+-|++|.+++.+|- .....+.++ -+.|+.|++.++.+...+- .-+.
T Consensus 206 ~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~ke~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~ 285 (299)
T TIGR01385 206 HNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQTRSADEPMTT 285 (299)
T ss_pred HHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHHHHHHHHHhhhhhcCCcccccCCCCCCccceEEEecccCCCCCCeE
Confidence 45788998887653 333333332 4799999999998765211 2368
Q ss_pred eeecccccCc
Q psy15553 120 QQVCKACGFH 129 (489)
Q Consensus 120 ~l~C~ACG~~ 129 (489)
|..|..||++
T Consensus 286 f~~C~~Cg~~ 295 (299)
T TIGR01385 286 FVTCEECGNR 295 (299)
T ss_pred EEEcCCCCCe
Confidence 9999999986
No 65
>KOG2906|consensus
Probab=56.79 E-value=11 Score=33.25 Aligned_cols=32 Identities=25% Similarity=0.662 Sum_probs=24.5
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
.||.|+| .|++.......-+.|..|++..++.
T Consensus 3 FCP~Cgn---~Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGN---MLIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCC---EEEEecCCeEeeEEcCCCCceeeEe
Confidence 5999998 4666323344789999999999885
No 66
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=56.37 E-value=9.5 Score=28.35 Aligned_cols=36 Identities=14% Similarity=0.442 Sum_probs=23.7
Q ss_pred ccCCCCCCCCceEEEeccCCeEeeecccccCcccccchhhh
Q psy15553 98 VLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFNHKL 138 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl 138 (489)
..|+.|+. .+..+ ......+|.-||+.-....+.++
T Consensus 4 y~C~~CG~---~~~~~--~~~~~~~Cp~CG~~~~~~~~~~~ 39 (46)
T PRK00398 4 YKCARCGR---EVELD--EYGTGVRCPYCGYRILFKERPPV 39 (46)
T ss_pred EECCCCCC---EEEEC--CCCCceECCCCCCeEEEccCCCc
Confidence 46999987 34442 22227899999988776554443
No 67
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=56.13 E-value=12 Score=30.60 Aligned_cols=36 Identities=25% Similarity=0.681 Sum_probs=23.4
Q ss_pred cccCCCCCCCCce---EEE---------e-ccCCeEeeecccccCcccc
Q psy15553 97 FVLCPECDNPETD---LVV---------S-AKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 97 yVlC~~C~~PeT~---l~~---------~-~k~~~~~l~C~ACG~~~~v 132 (489)
+-.||.|+|.+-. |.- + ..++-+...|+.||+.-.-
T Consensus 4 ~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY 52 (68)
T COG3478 4 AFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFY 52 (68)
T ss_pred cccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhhe
Confidence 3459999987532 111 1 1355678899999997544
No 68
>PRK00420 hypothetical protein; Validated
Probab=56.10 E-value=14 Score=33.17 Aligned_cols=41 Identities=29% Similarity=0.412 Sum_probs=28.7
Q ss_pred HHHHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 88 DLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 88 ~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
-+|.++-=.--.||.|+.|=+.+ + ++ ...|..||..-.|..
T Consensus 14 ~Ll~Ga~ml~~~CP~Cg~pLf~l-k---~g--~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 14 LLLKGAKMLSKHCPVCGLPLFEL-K---DG--EVVCPVHGKVYIVKS 54 (112)
T ss_pred HHHhHHHHccCCCCCCCCcceec-C---CC--ceECCCCCCeeeecc
Confidence 34444444456899999998887 3 33 567999999766653
No 69
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=56.03 E-value=4.4 Score=31.63 Aligned_cols=32 Identities=25% Similarity=0.484 Sum_probs=24.7
Q ss_pred cCCCCCCCCceEEEeccCC-eEeeecccccCcccc
Q psy15553 99 LCPECDNPETDLVVSAKKG-TIQQVCKACGFHGML 132 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~-~~~l~C~ACG~~~~v 132 (489)
.|..|+..+|-+-+ ++. .-..-|.|||-....
T Consensus 1 ~C~~C~~~~Tp~WR--~g~~~~~~LCNaCgl~~~k 33 (54)
T cd00202 1 ACSNCGTTTTPLWR--RGPSGGSTLCNACGLYWKK 33 (54)
T ss_pred CCCCCCCCCCcccc--cCCCCcchHHHHHHHHHHh
Confidence 49999999999988 432 446789999976543
No 70
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=55.74 E-value=6.6 Score=31.64 Aligned_cols=33 Identities=27% Similarity=0.739 Sum_probs=25.8
Q ss_pred hcccCCCCCCCCceEEEeccCCeEeeecccccCccccc
Q psy15553 96 KFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 96 ~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
+-+-||.|+.| |..+..++ .+.|..||-..++.
T Consensus 7 eiLaCP~~kg~---L~~~~~~~--~L~c~~~~~aYpI~ 39 (60)
T COG2835 7 EILACPVCKGP---LVYDEEKQ--ELICPRCKLAYPIR 39 (60)
T ss_pred eeeeccCcCCc---ceEeccCC--EEEecccCceeecc
Confidence 45789999999 55533444 89999999998875
No 71
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=54.73 E-value=6.4 Score=30.40 Aligned_cols=33 Identities=27% Similarity=0.517 Sum_probs=24.6
Q ss_pred ccCCCCCCCCceEEEeccCCeE-eeecccccCcccc
Q psy15553 98 VLCPECDNPETDLVVSAKKGTI-QQVCKACGFHGML 132 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~-~l~C~ACG~~~~v 132 (489)
..|..|+..+|.+-+ .+..- .+-|.|||-....
T Consensus 4 ~~C~~C~~~~T~~WR--~g~~g~~~LCnaCgl~~~k 37 (52)
T smart00401 4 RSCSNCGTTETPLWR--RGPSGNKTLCNACGLYYKK 37 (52)
T ss_pred CCcCCCCCCCCCccc--cCCCCCCcEeecccHHHHH
Confidence 369999999999987 33222 4889999976544
No 72
>PF14353 CpXC: CpXC protein
Probab=54.28 E-value=12 Score=33.46 Aligned_cols=36 Identities=25% Similarity=0.543 Sum_probs=24.6
Q ss_pred ccCCCCCCCCceEE---Eec-----------cCCeEeeecccccCccccc
Q psy15553 98 VLCPECDNPETDLV---VSA-----------KKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 98 VlC~~C~~PeT~l~---~~~-----------k~~~~~l~C~ACG~~~~v~ 133 (489)
+.||.|+.+-..-+ +++ .+......|..||+...++
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecC
Confidence 57999997733211 111 2455689999999999885
No 73
>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=53.70 E-value=11 Score=31.94 Aligned_cols=40 Identities=25% Similarity=0.452 Sum_probs=22.1
Q ss_pred HhhcccCCCCCCCCceEEE-eccCCeEeeecccccCccccc
Q psy15553 94 IRKFVLCPECDNPETDLVV-SAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 94 I~~yVlC~~C~~PeT~l~~-~~k~~~~~l~C~ACG~~~~v~ 133 (489)
+.++-.||-|+...|.-+. +.+.+.-.+.|..||......
T Consensus 19 l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 19 LPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp -SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred CCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 3456789999988776554 345678899999999986553
No 74
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=53.63 E-value=11 Score=33.77 Aligned_cols=46 Identities=17% Similarity=0.411 Sum_probs=28.7
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccccchhhhhhhhhcCCC
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFNHKLNTFILKNPP 147 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl~~~i~kn~p 147 (489)
-||.|+|- |+...++....+.|..||+...+.....-..++..+-|
T Consensus 4 FCp~Cgsl---l~p~~~~~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~ 49 (113)
T COG1594 4 FCPKCGSL---LYPKKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVE 49 (113)
T ss_pred ccCCccCe---eEEeEcCCCcEEECCCCCcchhccccceeEEEEeeccC
Confidence 59999973 44321223449999999999998754333333343433
No 75
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=53.37 E-value=9.8 Score=39.39 Aligned_cols=29 Identities=31% Similarity=0.769 Sum_probs=21.8
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
-..||.|++ |.++.|. ..-.+.|.-||..
T Consensus 11 ~~~Cp~Cg~--~~iv~d~--~~Ge~vC~~CG~V 39 (310)
T PRK00423 11 KLVCPECGS--DKLIYDY--ERGEIVCADCGLV 39 (310)
T ss_pred CCcCcCCCC--CCeeEEC--CCCeEeecccCCc
Confidence 357999997 4677753 3448899999984
No 76
>PLN00209 ribosomal protein S27; Provisional
Probab=52.54 E-value=10 Score=32.64 Aligned_cols=30 Identities=27% Similarity=0.308 Sum_probs=23.8
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCcc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFHG 130 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~ 130 (489)
-|.||.|.|.-|.... -.....|..||..=
T Consensus 36 ~VkCp~C~n~q~VFSh----A~t~V~C~~Cg~~L 65 (86)
T PLN00209 36 DVKCQGCFNITTVFSH----SQTVVVCGSCQTVL 65 (86)
T ss_pred EEECCCCCCeeEEEec----CceEEEccccCCEe
Confidence 4899999998777753 45688999999753
No 77
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=51.68 E-value=14 Score=30.04 Aligned_cols=34 Identities=26% Similarity=0.619 Sum_probs=22.6
Q ss_pred cCCCCCCCCceEEE------------e-ccCCeEeeecccccCcccc
Q psy15553 99 LCPECDNPETDLVV------------S-AKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 99 lC~~C~~PeT~l~~------------~-~k~~~~~l~C~ACG~~~~v 132 (489)
.||.|++-+.+.-. + ..++-+...|..||+.-.-
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y 48 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFY 48 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEE
Confidence 49999997765321 1 1234467899999997543
No 78
>PRK03954 ribonuclease P protein component 4; Validated
Probab=50.77 E-value=13 Score=33.81 Aligned_cols=34 Identities=15% Similarity=0.427 Sum_probs=24.0
Q ss_pred ccCCCCCCC-----CceEEEeccCC---eEeeecccccCccccc
Q psy15553 98 VLCPECDNP-----ETDLVVSAKKG---TIQQVCKACGFHGMLQ 133 (489)
Q Consensus 98 VlC~~C~~P-----eT~l~~~~k~~---~~~l~C~ACG~~~~v~ 133 (489)
-+|..|.+| ...+.+ .++ .+...|..||+..-.+
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi--~~~~~~~vvitCl~CG~~kR~P 106 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRL--RQKRMPHVVITCLECGHIMRYP 106 (121)
T ss_pred HHhhcCCCeeecCCceEEEE--ecCCcceEEEECccCCCEEeec
Confidence 469999877 344444 333 5789999999986543
No 79
>PRK05667 dnaG DNA primase; Validated
Probab=50.02 E-value=27 Score=39.48 Aligned_cols=32 Identities=34% Similarity=0.586 Sum_probs=24.0
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
+||-|.--..++.+++.++ +-+|-+||..+.+
T Consensus 38 ~CPfH~ektpSf~V~~~k~--~~~CF~Cg~~Gd~ 69 (580)
T PRK05667 38 LCPFHDEKTPSFTVSPDKQ--FYHCFGCGAGGDV 69 (580)
T ss_pred cCCCCCCCCCceEEECCCC--eEEECCCCCCCCH
Confidence 7999986555888865554 5789999987654
No 80
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=48.77 E-value=7.8 Score=30.67 Aligned_cols=29 Identities=31% Similarity=0.552 Sum_probs=18.2
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
-|.||.|.|.-|.. ..-.....|..||..
T Consensus 7 ~VkCp~C~~~q~vF----Sha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 7 DVKCPGCYNIQTVF----SHAQTVVKCVVCGTV 35 (55)
T ss_dssp EEE-TTT-SEEEEE----TT-SS-EE-SSSTSE
T ss_pred EEECCCCCCeeEEE----ecCCeEEEcccCCCE
Confidence 38999999876654 355568899999976
No 81
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=48.02 E-value=13 Score=31.86 Aligned_cols=30 Identities=23% Similarity=0.437 Sum_probs=23.7
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCcc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFHG 130 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~ 130 (489)
-|.||.|.|.-|.... -.....|..||..=
T Consensus 35 ~VkCp~C~n~q~VFSh----A~t~V~C~~Cg~~L 64 (85)
T PTZ00083 35 DVKCPGCSQITTVFSH----AQTVVLCGGCSSQL 64 (85)
T ss_pred EEECCCCCCeeEEEec----CceEEEccccCCEe
Confidence 4899999998877754 35678999999753
No 82
>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=47.91 E-value=4.2 Score=28.08 Aligned_cols=28 Identities=25% Similarity=0.705 Sum_probs=15.7
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
.-.|+.|++|-+ + ...-+.+.|.+||..
T Consensus 3 ~rfC~~CG~~t~-~----~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTK-P----APGGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEE-E-----SSSS-EEESSSS-E
T ss_pred CcccCcCCcccc-C----CCCcCEeECCCCcCE
Confidence 346999999833 2 234589999999975
No 83
>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=47.59 E-value=15 Score=28.85 Aligned_cols=32 Identities=19% Similarity=0.523 Sum_probs=22.1
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
.||.|+. .|.+...-....+.|..||+.--|-
T Consensus 4 ~CP~CG~---~iev~~~~~GeiV~Cp~CGaeleVv 35 (54)
T TIGR01206 4 ECPDCGA---EIELENPELGELVICDECGAELEVV 35 (54)
T ss_pred CCCCCCC---EEecCCCccCCEEeCCCCCCEEEEE
Confidence 7999997 4444212223467999999997774
No 84
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.28 E-value=10 Score=27.21 Aligned_cols=29 Identities=21% Similarity=0.670 Sum_probs=19.1
Q ss_pred cccCCCCCC----CCceEEEeccCCeEeeecccccCc
Q psy15553 97 FVLCPECDN----PETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 97 yVlC~~C~~----PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
.+.||.|+. ||..|- .+...++|..||+.
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip----~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIP----PKGRKVRCSKCGHV 34 (36)
T ss_pred EEECCCCCCEEeCCHHHCC----CCCcEEECCCCCCE
Confidence 467999973 333322 34458999999975
No 85
>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=47.19 E-value=16 Score=32.61 Aligned_cols=28 Identities=11% Similarity=0.152 Sum_probs=16.1
Q ss_pred CCCCChhhhHHHHhhcCceeeecCCCeEEEE
Q psy15553 48 GRPPTYPTKYFGCELGAQTKLDHKNDRFIVN 78 (489)
Q Consensus 48 ~R~p~~~~kyf~~ELGa~~~~d~~~~r~iin 78 (489)
+-.|+.+.-.| ++-+.+++- .+-++.|+
T Consensus 38 ~V~p~~L~faf--~~~~~~t~~-ega~L~I~ 65 (115)
T TIGR00100 38 CVNPSQLQFAF--EVVREGTVA-EGAKLNIE 65 (115)
T ss_pred ccCHHHHHHHH--HHHhCCCcc-CCCEEEEE
Confidence 34566665544 445666654 46677764
No 86
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=47.19 E-value=8.7 Score=27.39 Aligned_cols=29 Identities=31% Similarity=0.778 Sum_probs=17.3
Q ss_pred CCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 100 CPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 100 C~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
|..|+..+|.+-+....+. ..-|.|||-.
T Consensus 1 C~~C~tt~t~~WR~~~~g~-~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGN-RTLCNACGLY 29 (36)
T ss_dssp -TTT--ST-SSEEEETTSE-E-EEHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCC-CHHHHHHHHH
Confidence 8899999999998433332 3389999954
No 87
>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=46.87 E-value=13 Score=26.43 Aligned_cols=28 Identities=21% Similarity=0.427 Sum_probs=20.7
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccC
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGF 128 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~ 128 (489)
.|+.|+..=+.+.. -...-...|-.||+
T Consensus 7 ~C~~Cg~~fe~~~~--~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQK--ISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEe--cCCCCCCCCCCCCC
Confidence 69999997666654 22256778999998
No 88
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=46.83 E-value=18 Score=28.90 Aligned_cols=37 Identities=24% Similarity=0.435 Sum_probs=29.8
Q ss_pred CCCCCCCceEEEeccCCeEeeecccccCcccccchhhhhh
Q psy15553 101 PECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFNHKLNT 140 (489)
Q Consensus 101 ~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl~~ 140 (489)
.-|++-+=.+++ -+--+-++|..||..=.+ +|.+|-.
T Consensus 14 HPCG~~~Wei~R--~GaDikikC~gCg~~iml-pR~~feK 50 (57)
T PF06107_consen 14 HPCGSNEWEIIR--IGADIKIKCLGCGRQIML-PRSKFEK 50 (57)
T ss_pred CCCCCCEEEEEE--ccCcEEEEECCCCCEEEE-eHHHHHH
Confidence 358888888888 677799999999999888 4776644
No 89
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=46.76 E-value=32 Score=37.14 Aligned_cols=33 Identities=30% Similarity=0.458 Sum_probs=24.9
Q ss_pred ccCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 98 VLCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
.+||-|.--...+.+++.++ +-+|-+||..+.+
T Consensus 35 ~~CPfh~ek~pSf~v~~~k~--~~~Cf~Cg~~Gd~ 67 (415)
T TIGR01391 35 GLCPFHHEKTPSFSVSPEKQ--FYHCFGCGAGGDA 67 (415)
T ss_pred eeCCCCCCCCCeEEEEcCCC--cEEECCCCCCCCH
Confidence 48999986556888865555 5789999997654
No 90
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.86 E-value=18 Score=32.42 Aligned_cols=28 Identities=14% Similarity=0.059 Sum_probs=16.2
Q ss_pred CCCCChhhhHHHHhhcCcee-eecCCCeEEEE
Q psy15553 48 GRPPTYPTKYFGCELGAQTK-LDHKNDRFIVN 78 (489)
Q Consensus 48 ~R~p~~~~kyf~~ELGa~~~-~d~~~~r~iin 78 (489)
+-.|+.+.-.| ++-++++ +- .+-++.|.
T Consensus 38 ~V~pe~L~faf--~~~~~~T~~~-ega~L~Ie 66 (117)
T PRK00564 38 GMDKSLFVSAF--ETFREESLVC-KDAILDIV 66 (117)
T ss_pred CcCHHHHHHHH--HHHhcCCccc-CCCEEEEE
Confidence 44566665555 3445566 54 46677775
No 91
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=45.56 E-value=15 Score=32.88 Aligned_cols=34 Identities=26% Similarity=0.456 Sum_probs=25.6
Q ss_pred cccCCCCCCCCceEEEecc-----CCeEeeecccccCcc
Q psy15553 97 FVLCPECDNPETDLVVSAK-----KGTIQQVCKACGFHG 130 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k-----~~~~~l~C~ACG~~~ 130 (489)
-+.||.|++-+-.+...+. .-+.|-+|..||++-
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 3789999999877765321 235799999999873
No 92
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=45.10 E-value=15 Score=37.56 Aligned_cols=36 Identities=25% Similarity=0.496 Sum_probs=17.9
Q ss_pred ccCCCCCCCCceEEEeccC--CeEeeecccccCccccc
Q psy15553 98 VLCPECDNPETDLVVSAKK--GTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~--~~~~l~C~ACG~~~~v~ 133 (489)
-.||.||++=+-=++.... +.-++.|.-||..-...
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~ 210 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFV 210 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeec
Confidence 4899999875444443333 56899999999986653
No 93
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=44.52 E-value=16 Score=33.80 Aligned_cols=26 Identities=35% Similarity=1.020 Sum_probs=18.8
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGM 131 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~ 131 (489)
-||.|+.|= .+ +++ .+.|..||++-.
T Consensus 30 hCp~Cg~PL---F~--KdG--~v~CPvC~~~~~ 55 (131)
T COG1645 30 HCPKCGTPL---FR--KDG--EVFCPVCGYREV 55 (131)
T ss_pred hCcccCCcc---ee--eCC--eEECCCCCceEE
Confidence 599999994 43 455 456999998433
No 94
>PF05315 ICEA: ICEA Protein; InterPro: IPR007979 This family consists of several ICEA proteins from Helicobacter pylori, infection of which causes gastritis and peptic ulcer disease, and the bacteria is classified as a definite carcinogen of gastric cancer. ICEA1 is speculated to be associated with peptic ulcer disease and may have endonuclease activity [].
Probab=44.24 E-value=12 Score=37.16 Aligned_cols=69 Identities=19% Similarity=0.270 Sum_probs=50.7
Q ss_pred CCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHHHHHHhhc------ccCCCCCCC-CceEEEeccC
Q psy15553 48 GRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLDGFIRKF------VLCPECDNP-ETDLVVSAKK 116 (489)
Q Consensus 48 ~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~~fI~~y------VlC~~C~~P-eT~l~~~~k~ 116 (489)
.|...++.|+|-.|++-.-+-.-+=+|+.+||--+...+..-|+.=|+.| |+|..|++. .|.|.+|.++
T Consensus 45 cR~~SsLak~y~lEfdk~~~~gnsId~IRLnG~n~~~~fnq~Ir~dIk~~yk~q~Cvm~g~~g~sent~ieiDHKd 120 (230)
T PF05315_consen 45 CRSSSSLAKEYILEFDKRQTSGNSIDRIRLNGFNTEKVFNQNIRQDIKNYYKQQCCVMCGVRGNSENTKIEIDHKD 120 (230)
T ss_pred cCCchHHHHHhhcccccccCCCccHHHHHHcCcCchhhhhhHHHHHHHHHHHhcCeeeecccCCCccceeeecccc
Confidence 58888999999998874432111123788999988888888888888776 788888866 5677776543
No 95
>PHA02540 61 DNA primase; Provisional
Probab=43.69 E-value=21 Score=37.81 Aligned_cols=44 Identities=25% Similarity=0.563 Sum_probs=32.9
Q ss_pred ccCCCCCCCC-----ceEEEeccCCeEeeecccccCcccccchhhhhhhhhcCCC
Q psy15553 98 VLCPECDNPE-----TDLVVSAKKGTIQQVCKACGFHGMLQFNHKLNTFILKNPP 147 (489)
Q Consensus 98 VlC~~C~~Pe-----T~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl~~~i~kn~p 147 (489)
-+||-|+=-. ++..+.+.++..+-+|-.||+.+.+ .+|+...-+
T Consensus 28 ~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~Gd~------i~Flme~e~ 76 (337)
T PHA02540 28 FRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYHRPF------GNFLKDYEP 76 (337)
T ss_pred ecCCCCCCccccCcCCcEEEeccCCceEEEecCCCCCCCH------HHHHHHhcC
Confidence 3799999522 3577766777788999999999976 467776554
No 96
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=43.67 E-value=15 Score=28.29 Aligned_cols=28 Identities=21% Similarity=0.568 Sum_probs=19.5
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCcc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFHG 130 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~ 130 (489)
+-.||.|++- -|.. .. -.+.|..||..-
T Consensus 20 ~~fCP~Cg~~--~m~~--~~--~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSG--FMAE--HL--DRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcc--hhec--cC--CcEECCCcCCEE
Confidence 5579999984 4443 22 366899999864
No 97
>PRK11827 hypothetical protein; Provisional
Probab=43.12 E-value=16 Score=29.43 Aligned_cols=36 Identities=19% Similarity=0.350 Sum_probs=24.7
Q ss_pred HHhhcccCCCCCCCCceEEEeccCCeEeeecccccCccccc
Q psy15553 93 FIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 93 fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
.+-+.+-||.|+.|=. +.. .. -.+.|.+||-..+|.
T Consensus 4 ~LLeILaCP~ckg~L~-~~~--~~--~~Lic~~~~laYPI~ 39 (60)
T PRK11827 4 RLLEIIACPVCNGKLW-YNQ--EK--QELICKLDNLAFPLR 39 (60)
T ss_pred HHHhheECCCCCCcCe-EcC--CC--CeEECCccCeecccc
Confidence 3445688999998633 322 22 257799999999984
No 98
>PRK07451 translation initiation factor Sui1; Validated
Probab=42.87 E-value=42 Score=30.37 Aligned_cols=58 Identities=19% Similarity=0.251 Sum_probs=39.4
Q ss_pred EEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHH
Q psy15553 24 AKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQ 87 (489)
Q Consensus 24 ~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq 87 (489)
....|++.-.=|+|.+|..-... -.-+.|.|-..+|+.|++ +++.+.|+|.|.....+
T Consensus 44 ~~r~gR~GK~VTvV~Gl~~~~~d----lk~LaK~LK~k~gcGGtv--kd~~IelQGD~r~~v~~ 101 (115)
T PRK07451 44 ATRSGRKGKTVTVITGFQHKPET----LAKLLKQLKTQCGSGGTV--KDNTIEIQGDHRQKILE 101 (115)
T ss_pred EEecCCCCCeEEEEeCCCCCHHH----HHHHHHHHHHHhcCCceE--cCCEEEEcCcHHHHHHH
Confidence 33456642256788888622122 235788889999999999 57889999999755443
No 99
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=42.72 E-value=43 Score=23.46 Aligned_cols=46 Identities=13% Similarity=0.126 Sum_probs=32.8
Q ss_pred chHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHH
Q psy15553 39 NMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLL 90 (489)
Q Consensus 39 N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L 90 (489)
++.++|+.|+.++..+-+|........... .++++. |+...|..++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~~~~~~~--~~~~~~----~~~~ei~~~~ 47 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRT--PGGHRR----FPEEDLERLL 47 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCceeC--CCCcee----cCHHHHHHHH
Confidence 678999999999999999988765443322 234443 6777776655
No 100
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.49 E-value=20 Score=32.86 Aligned_cols=47 Identities=9% Similarity=0.107 Sum_probs=27.2
Q ss_pred HHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHHHHHHhhcccCCCCC
Q psy15553 41 ADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLDGFIRKFVLCPECD 104 (489)
Q Consensus 41 ~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~~fI~~yVlC~~C~ 104 (489)
..|.+.=+-.|+.+...|.. + +++++- .+-++.|.- +.-...|+.|+
T Consensus 31 l~IG~ls~V~pe~L~fafe~-l-~~gt~~-ega~L~i~~--------------~p~~~~C~~CG 77 (135)
T PRK03824 31 VVLGELQDVDKEIVEFALNE-L-LKGTIL-EGAEIIFEE--------------EEAVLKCRNCG 77 (135)
T ss_pred hhHhhhhhhhHHHHHHHHHH-H-HcCCcc-cCCEEEEEe--------------cceEEECCCCC
Confidence 34555555567777766643 4 344433 355776653 22457788887
No 101
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=41.22 E-value=21 Score=31.88 Aligned_cols=28 Identities=7% Similarity=0.045 Sum_probs=16.5
Q ss_pred CCCCChhhhHHHHhhcCceeeecCCCeEEEE
Q psy15553 48 GRPPTYPTKYFGCELGAQTKLDHKNDRFIVN 78 (489)
Q Consensus 48 ~R~p~~~~kyf~~ELGa~~~~d~~~~r~iin 78 (489)
+-.|+.+.-.|. +-+++++= .+-++.|.
T Consensus 38 ~V~p~~L~f~f~--~~~~~t~~-egA~L~i~ 65 (114)
T PRK03681 38 CVETSSLAFCFD--LVCRGTVA-EGCKLHLE 65 (114)
T ss_pred ccCHHHHHHHHH--HHhCCCcc-CCCEEEEE
Confidence 445777665554 34555554 46677775
No 102
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=40.77 E-value=19 Score=37.27 Aligned_cols=28 Identities=32% Similarity=0.926 Sum_probs=20.9
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHG 130 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~ 130 (489)
.||.|++. .++.+.+.+ ...|..||..-
T Consensus 3 ~CpeCg~~--~~~~d~~~g--e~VC~~CG~Vi 30 (285)
T COG1405 3 SCPECGST--NIITDYERG--EIVCADCGLVL 30 (285)
T ss_pred CCCCCCCc--cceeeccCC--eEEeccCCEEe
Confidence 59999998 666643434 67899999863
No 103
>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=40.66 E-value=36 Score=31.36 Aligned_cols=58 Identities=19% Similarity=0.390 Sum_probs=39.2
Q ss_pred EEEEeccchHHHHHHHHHHH-----hh-cccCCCCCCCCceEEEec----------cCCeEeeecccccCcccc
Q psy15553 75 FIVNGSHDVVKLQDLLDGFI-----RK-FVLCPECDNPETDLVVSA----------KKGTIQQVCKACGFHGML 132 (489)
Q Consensus 75 ~iinG~~~~~~lq~~L~~fI-----~~-yVlC~~C~~PeT~l~~~~----------k~~~~~l~C~ACG~~~~v 132 (489)
+.|......++|..++..|= +. |-.|+.|++|=..+.+.. ....-|-.|..||...=.
T Consensus 63 ~li~~~~~~~QL~ev~~~~~l~~~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 63 ILIRSDDPEEQLREVLERFGLKLRLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred EEEcCCCHHHHHHHHHHHcCCccccCCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 55677778899999998873 32 789999999543332210 011238999999986433
No 104
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=40.39 E-value=23 Score=29.02 Aligned_cols=31 Identities=26% Similarity=0.729 Sum_probs=17.7
Q ss_pred ccCCCCCC---CC--ceEEEe---ccCCeEeeecccccC
Q psy15553 98 VLCPECDN---PE--TDLVVS---AKKGTIQQVCKACGF 128 (489)
Q Consensus 98 VlC~~C~~---Pe--T~l~~~---~k~~~~~l~C~ACG~ 128 (489)
-+|..|++ |- ..+.+. ...+.+...|..||+
T Consensus 47 ~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 47 TICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp TB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred ccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 57999998 42 233331 126789999999995
No 105
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=40.34 E-value=4.6 Score=32.63 Aligned_cols=38 Identities=26% Similarity=0.566 Sum_probs=30.0
Q ss_pred HHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcc
Q psy15553 91 DGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHG 130 (489)
Q Consensus 91 ~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~ 130 (489)
.+||-- -.||.|.--||--.- .++++-...|-+||+.-
T Consensus 5 KRFIAG-A~CP~C~~~Dtl~mW-~En~ve~vECV~CG~~~ 42 (66)
T COG3529 5 KRFIAG-AVCPACQAQDTLAMW-RENNVEIVECVKCGHHM 42 (66)
T ss_pred hhhhcc-CCCcccchhhHHHHH-HhcCCceEehhhcchHh
Confidence 467766 469999999996433 27889999999999874
No 106
>PRK05580 primosome assembly protein PriA; Validated
Probab=40.05 E-value=20 Score=41.15 Aligned_cols=50 Identities=20% Similarity=0.491 Sum_probs=30.0
Q ss_pred cccCCCCCCC------CceEEEeccCCeEeeecccccCccccc----------------chhhhhhhhhcCCCC
Q psy15553 97 FVLCPECDNP------ETDLVVSAKKGTIQQVCKACGFHGMLQ----------------FNHKLNTFILKNPPN 148 (489)
Q Consensus 97 yVlC~~C~~P------eT~l~~~~k~~~~~l~C~ACG~~~~v~----------------~~~kl~~~i~kn~p~ 148 (489)
||+|..|+.+ +..|+.. ...-.+.|.-||++..++ ...|+...+-++-|.
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h--~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e~~~e~l~~~fp~ 452 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLH--RFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEEELAELFPE 452 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEE--CCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHHHHHHHHhCCC
Confidence 5566666543 2334431 122367888888876542 346888888888774
No 107
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.59 E-value=25 Score=31.76 Aligned_cols=28 Identities=14% Similarity=0.138 Sum_probs=16.0
Q ss_pred CCCCChhhhHHHHhhcCceeeecCCCeEEEE
Q psy15553 48 GRPPTYPTKYFGCELGAQTKLDHKNDRFIVN 78 (489)
Q Consensus 48 ~R~p~~~~kyf~~ELGa~~~~d~~~~r~iin 78 (489)
+-.|+.+.-+|. +-+.+++= ++-.+.|.
T Consensus 38 ~V~pe~L~faf~--~~~~gT~~-egA~L~I~ 65 (124)
T PRK00762 38 MLNPEQLRFMLD--VLAEGTIA-EDADLIVE 65 (124)
T ss_pred ccCHHHHHHHHH--HHhCCCCc-CCCEEEEE
Confidence 334777766664 44556554 35667664
No 108
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=39.52 E-value=10 Score=39.08 Aligned_cols=43 Identities=21% Similarity=0.505 Sum_probs=31.9
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCcccccchhhhhhhhh
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFNHKLNTFIL 143 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl~~~i~ 143 (489)
++.||+|+. +.+.+ +=+.-...|..||+...+..+.++-.++=
T Consensus 28 w~KCp~c~~--~~y~~--eL~~n~~vcp~c~~h~ri~A~~Ri~~llD 70 (294)
T COG0777 28 WTKCPSCGE--MLYRK--ELESNLKVCPKCGHHMRISARERLEALLD 70 (294)
T ss_pred eeECCCccc--eeeHH--HHHhhhhcccccCcccccCHHHHHHHhhC
Confidence 789999984 23332 22334789999999999999988877654
No 109
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=39.51 E-value=23 Score=31.46 Aligned_cols=28 Identities=7% Similarity=-0.015 Sum_probs=16.7
Q ss_pred CCCCChhhhHHHHhhcCceeeecCCCeEEEE
Q psy15553 48 GRPPTYPTKYFGCELGAQTKLDHKNDRFIVN 78 (489)
Q Consensus 48 ~R~p~~~~kyf~~ELGa~~~~d~~~~r~iin 78 (489)
+-.|+.+.-+| ++-+++++= .+-++.|.
T Consensus 38 ~v~pe~L~f~f--~~~~~~T~~-egA~L~I~ 65 (113)
T PRK12380 38 CVEESAVRFSF--EIVCHGTVA-QGCDLHIV 65 (113)
T ss_pred ccCHHHHHHHH--HHHhCCCcc-CCCEEEEE
Confidence 44577776555 445555554 46677775
No 110
>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=39.44 E-value=18 Score=26.56 Aligned_cols=29 Identities=24% Similarity=0.405 Sum_probs=22.0
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
.|..|+..-..+.. -...-...|.+||..
T Consensus 7 ~C~~Cg~~fe~~~~--~~~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 7 RCEECGHEFEVLQS--ISEDDPVPCPECGST 35 (42)
T ss_pred EeCCCCCEEEEEEE--cCCCCCCcCCCCCCC
Confidence 58999988777776 233678899999983
No 111
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=38.87 E-value=22 Score=28.23 Aligned_cols=26 Identities=35% Similarity=0.977 Sum_probs=19.4
Q ss_pred HhhcccCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 94 IRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 94 I~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
+..++.|+.|+++- +-...|..||.-
T Consensus 24 ~~~l~~C~~CG~~~----------~~H~vC~~CG~Y 49 (57)
T PRK12286 24 APGLVECPNCGEPK----------LPHRVCPSCGYY 49 (57)
T ss_pred CCcceECCCCCCcc----------CCeEECCCCCcC
Confidence 56678999999863 236679999964
No 112
>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=38.07 E-value=24 Score=30.31 Aligned_cols=33 Identities=27% Similarity=0.594 Sum_probs=17.6
Q ss_pred ccCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 98 VLCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
.+||-|.--.-.+.+++.++ .-+|-+||+.+.+
T Consensus 34 ~~CPfH~d~~pS~~i~~~k~--~~~Cf~Cg~~Gd~ 66 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPDKN--RFKCFGCGKGGDV 66 (97)
T ss_dssp E--SSS--SS--EEEETTTT--EEEETTT--EE-H
T ss_pred EECcCCCCCCCceEEECCCC--eEEECCCCCCCcH
Confidence 67999985445777765555 5689999988754
No 113
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=37.94 E-value=22 Score=27.82 Aligned_cols=31 Identities=23% Similarity=0.412 Sum_probs=22.3
Q ss_pred ccCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 98 VLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
++|+.|.+..=-.-+ .+...+.-+|..||+.
T Consensus 23 LIC~~C~~hNGla~~-~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPK-EEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhccccc-ccCCceEEEcCCCCCc
Confidence 579999877655522 1566778899999974
No 114
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=36.25 E-value=26 Score=42.87 Aligned_cols=40 Identities=25% Similarity=0.476 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 85 KLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 85 ~lq~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
..+..+.+| +=..|+.|+| ++|++ + .-.++|..||..+-.
T Consensus 1180 ~~~a~~~g~--~g~~c~~cg~--~~~vr---n-gtc~~c~~cg~t~gc 1219 (1220)
T PRK07562 1180 RAEAKMQGY--TGEACSECGN--FTLVR---N-GTCLKCDTCGSTTGC 1219 (1220)
T ss_pred hhHHHhCCC--CCCcCCCcCC--eEEEe---C-CeeeeccccCCCCCC
Confidence 555666777 5577999997 57776 3 348999999998753
No 115
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=35.81 E-value=19 Score=27.48 Aligned_cols=27 Identities=30% Similarity=0.374 Sum_probs=22.7
Q ss_pred chHHHHHHhCCCCChhhhHHHHhhcCc
Q psy15553 39 NMADVAKAIGRPPTYPTKYFGCELGAQ 65 (489)
Q Consensus 39 N~~dIakaL~R~p~~~~kyf~~ELGa~ 65 (489)
-..++|+.|+.++.-|.+.+..++|..
T Consensus 5 ~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred EHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 356999999999999999999999998
No 116
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=35.43 E-value=27 Score=34.15 Aligned_cols=27 Identities=30% Similarity=0.675 Sum_probs=19.5
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCcc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFHG 130 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~ 130 (489)
|-+|+.|+.| |++ +-..|+|.-||+.-
T Consensus 149 ~A~CsrC~~~---L~~----~~~~l~Cp~Cg~tE 175 (188)
T COG1096 149 YARCSRCRAP---LVK----KGNMLKCPNCGNTE 175 (188)
T ss_pred EEEccCCCcc---eEE----cCcEEECCCCCCEE
Confidence 5678888865 554 34588999999863
No 117
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=34.54 E-value=27 Score=40.61 Aligned_cols=36 Identities=28% Similarity=0.653 Sum_probs=24.3
Q ss_pred cccCCCCCCC------CceEEEeccCCeEeeecccccCcccccc
Q psy15553 97 FVLCPECDNP------ETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 97 yVlC~~C~~P------eT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
||+|+.|+.. +..|+. -+..-.+.|.-||+..+++.
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~--H~~~~~L~CH~Cg~~~~~p~ 476 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTL--HKATGQLRCHYCGYQEPIPQ 476 (730)
T ss_pred eeecccCCCcccCCCCCcceEE--ecCCCeeEeCCCCCCCCCCC
Confidence 6888877643 334444 23345899999999987753
No 118
>COG3741 HutG N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=34.44 E-value=12 Score=38.30 Aligned_cols=68 Identities=18% Similarity=0.296 Sum_probs=58.0
Q ss_pred CeeEEEechHHHHHHhCCCCChhhhH---HHHhhcCceeeecCCCeEEEEeccchHHHHHHHHHHHhhcccC
Q psy15553 32 GIKTVIVNMADVAKAIGRPPTYPTKY---FGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLDGFIRKFVLC 100 (489)
Q Consensus 32 giKTvi~N~~dIakaL~R~p~~~~ky---f~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~~fI~~yVlC 100 (489)
|--++..||+-.+=-+||+|.+..-| --..||+++.|| +.+.|+--|+.+...+..-|..|-+=|--|
T Consensus 62 GA~~l~A~fsR~~vDvNR~p~~~~l~~~~~ttGL~~~~~fd-ge~l~~~g~~~~~~e~~~Rle~~~~PYHaa 132 (272)
T COG3741 62 GATLLRANFSRAVVDVNREPDGASLYPGRVTTGLGPVTTFD-GEPLYIYGGAPTPAEALARLETLWKPYHAA 132 (272)
T ss_pred cchhhhccccceeEecCCCCCCCcCccccccCCcccccccc-CccccccCCCCCHHHHHHHHHHhhccHHHH
Confidence 45678889998888999999999999 446799999999 688898889999999999999887777554
No 119
>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=34.39 E-value=17 Score=25.65 Aligned_cols=31 Identities=23% Similarity=0.515 Sum_probs=18.6
Q ss_pred cccCCCCCCCCceEEEecc---CCeEeeecccccCcc
Q psy15553 97 FVLCPECDNPETDLVVSAK---KGTIQQVCKACGFHG 130 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k---~~~~~l~C~ACG~~~ 130 (489)
.+.||.|+.- +.++.. ......+|..||+.-
T Consensus 2 ~~~CP~C~~~---~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKTS---FRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCE---EEeCHHHcCCCCCEEECCCCCCEE
Confidence 3789999862 222110 112378899999864
No 120
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=34.16 E-value=32 Score=31.95 Aligned_cols=44 Identities=11% Similarity=0.273 Sum_probs=35.2
Q ss_pred echHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHHHHHHhhcccCCCCCCC
Q psy15553 38 VNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLDGFIRKFVLCPECDNP 106 (489)
Q Consensus 38 ~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~~fI~~yVlC~~C~~P 106 (489)
.|+.+|+.+++-++.+|.+|+- .||+.|.+. + +-+..|..||-|
T Consensus 47 ati~eV~e~tgVs~~~I~~~Ir------------eGRL~~~~~-~------------nl~~~CE~CG~~ 90 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIR------------EGRLQLKHF-P------------NLGYPCERCGTS 90 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH------------cCCeeccCC-C------------CCcCcccccCCc
Confidence 4889999999999999999984 678877652 1 336889999976
No 121
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=33.83 E-value=33 Score=30.96 Aligned_cols=49 Identities=22% Similarity=0.202 Sum_probs=26.5
Q ss_pred cchHHHHHHHHhccccccccccccchhhhhHHHHHHHHHHHHHHHHhhCCCChHHH
Q psy15553 208 DVSEEAVRARALDLSSGVKGLTISEDLEKTEKERMDIFYTCVKTALEKNNVDAKEL 263 (489)
Q Consensus 208 DtSeeA~~~R~~~L~~~~~~l~~~~d~e~~~~~~~~~~~~~v~~~~~~~~~~~~ei 263 (489)
..|=-.||.|+.+|-.... .....+.. -......|.+..++|.++.+|.
T Consensus 60 giSYPTvR~rLd~ii~~lg---~~~~~~~~----~~~~~~~IL~~L~~GeIs~eeA 108 (113)
T PF09862_consen 60 GISYPTVRNRLDKIIEKLG---YEEDEEEE----EEDERKEILDKLEKGEISVEEA 108 (113)
T ss_pred CCCcHHHHHHHHHHHHHhC---CCCCcccc----cchhHHHHHHHHHcCCCCHHHH
Confidence 5677779999987643332 21111111 1122345666777888875443
No 122
>KOG2907|consensus
Probab=33.82 E-value=21 Score=32.18 Aligned_cols=34 Identities=26% Similarity=0.520 Sum_probs=26.2
Q ss_pred cCCCCCCCCceEE----Eec-cCCeEeeecccccCcccc
Q psy15553 99 LCPECDNPETDLV----VSA-KKGTIQQVCKACGFHGML 132 (489)
Q Consensus 99 lC~~C~~PeT~l~----~~~-k~~~~~l~C~ACG~~~~v 132 (489)
.||.|++++-.+. +.. ++++.|-.|..||++-..
T Consensus 76 kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 76 KCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred cCcccCCchhhhhhhhcccccCCceEEEEcCccceeeec
Confidence 6999999986554 211 478899999999998654
No 123
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=33.79 E-value=34 Score=31.91 Aligned_cols=52 Identities=25% Similarity=0.501 Sum_probs=34.9
Q ss_pred cchHHHHHHHHHHH-------------hhcccCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 81 HDVVKLQDLLDGFI-------------RKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 81 ~~~~~lq~~L~~fI-------------~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
|...+|+.+|..+- -.||.|+.|+.---.+..+......+++|..|...+.|
T Consensus 81 ~e~G~L~~lL~~~~~~~~~~~C~~Cgg~rfv~C~~C~Gs~k~~~~~~~~~~~~~rC~~Cnengl~ 145 (147)
T cd03031 81 NESGELRKLLKGIRARAGGGVCEGCGGARFVPCSECNGSCKVFAENATAAGGFLRCPECNENGLV 145 (147)
T ss_pred HHcCCHHHHHhhcccccCCCCCCCCCCcCeEECCCCCCcceEEeccCcccccEEECCCCCccccc
Confidence 45666777777751 24899999987655554411124678999999876654
No 124
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=32.93 E-value=57 Score=30.08 Aligned_cols=96 Identities=19% Similarity=0.199 Sum_probs=50.1
Q ss_pred echHHHHHHhCCCCChhhhHHH--Hh--hcCc---eeeecCCC-----eEEEEeccchHHHHHHHHHH------------
Q psy15553 38 VNMADVAKAIGRPPTYPTKYFG--CE--LGAQ---TKLDHKND-----RFIVNGSHDVVKLQDLLDGF------------ 93 (489)
Q Consensus 38 ~N~~dIakaL~R~p~~~~kyf~--~E--LGa~---~~~d~~~~-----r~iinG~~~~~~lq~~L~~f------------ 93 (489)
+-=.++|+.|+-++..|-+.+. .| ++.. ...++.++ -|.|+=.+-...|.-.|..-
T Consensus 16 ~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~~~~~L~~~l~~e~ 95 (147)
T smart00531 16 VTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDKMRKRLEDKLEDET 95 (147)
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3457899999999999888654 45 4422 22343333 13355333322222111111
Q ss_pred HhhcccCCCCCCCCceEEEec-cCCeEeeecccccCccccc
Q psy15553 94 IRKFVLCPECDNPETDLVVSA-KKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 94 I~~yVlC~~C~~PeT~l~~~~-k~~~~~l~C~ACG~~~~v~ 133 (489)
-..|..||.|+.-=|.+.... .+-.-...|.-||+.=...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 234788999984333221100 0111228999999875443
No 125
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=32.77 E-value=10 Score=39.33 Aligned_cols=43 Identities=21% Similarity=0.495 Sum_probs=30.9
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCcccccchhhhhhhhh
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFNHKLNTFIL 143 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl~~~i~ 143 (489)
++.||.|+..=..-.. +. -...|..||++..+..|.+|...+=
T Consensus 27 ~~~c~~c~~~~~~~~l--~~--~~~vc~~c~~h~rl~areRi~~L~D 69 (292)
T PRK05654 27 WTKCPSCGQVLYRKEL--EA--NLNVCPKCGHHMRISARERLDLLLD 69 (292)
T ss_pred eeECCCccchhhHHHH--Hh--cCCCCCCCCCCeeCCHHHHHHHHcc
Confidence 7999999974222111 12 2579999999999999988876554
No 126
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 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 proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=32.58 E-value=1.1e+02 Score=25.95 Aligned_cols=61 Identities=16% Similarity=0.223 Sum_probs=42.6
Q ss_pred CCcEEEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhc--CceeeecCCCeEEEEeccch
Q psy15553 20 PKLIAKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELG--AQTKLDHKNDRFIVNGSHDV 83 (489)
Q Consensus 20 P~~~~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELG--a~~~~d~~~~r~iinG~~~~ 83 (489)
=++-.++-..||-+-|+|.++.==..+|.. -+.+||+...+ -.+.+++-.+.++|+|.|..
T Consensus 14 LPVY~~~k~~g~~~~T~IrkI~GD~~aL~~---dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~~~ 76 (87)
T PF05046_consen 14 LPVYLDIKNGGNRKITVIRKIEGDIWALKK---DLRKFLGEKPKKKIDVRVNELTGHIEIKGDHVE 76 (87)
T ss_pred ccEEEEEeCCCcEeEEEEEeecCCHHHHHH---HHHHHhhhhcCCCcceEEeecCCEEEEcCccHH
Confidence 336667777788899999987643344432 35566666655 45667778999999999944
No 127
>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=32.57 E-value=10 Score=39.17 Aligned_cols=43 Identities=16% Similarity=0.494 Sum_probs=30.5
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCcccccchhhhhhhhh
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFNHKLNTFIL 143 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl~~~i~ 143 (489)
++.||.|+..=..-.. ++ -+..|..||++..+..|.++...+=
T Consensus 26 ~~~c~~c~~~~~~~~l--~~--~~~vc~~c~~h~rl~areRi~~L~D 68 (285)
T TIGR00515 26 WTKCPKCGQVLYTKEL--ER--NLEVCPKCDHHMRMDARERIESLLD 68 (285)
T ss_pred eeECCCCcchhhHHHH--Hh--hCCCCCCCCCcCcCCHHHHHHHcee
Confidence 7999999964222111 12 2479999999999999988876553
No 128
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=31.23 E-value=22 Score=30.05 Aligned_cols=19 Identities=16% Similarity=0.506 Sum_probs=9.7
Q ss_pred HHHHHHhCCCCChhhhHHH
Q psy15553 41 ADVAKAIGRPPTYPTKYFG 59 (489)
Q Consensus 41 ~dIakaL~R~p~~~~kyf~ 59 (489)
.+||+.|+|++.||.+|+.
T Consensus 7 ~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 7 EEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp HHHHHHTT--HHHHHHHHG
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4555555555555555554
No 129
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=31.09 E-value=39 Score=34.42 Aligned_cols=56 Identities=14% Similarity=0.354 Sum_probs=27.2
Q ss_pred eccchHHH-HHHHHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccccch
Q psy15553 79 GSHDVVKL-QDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFN 135 (489)
Q Consensus 79 G~~~~~~l-q~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~ 135 (489)
|-++.+++ .-+-..++.+-+.||.|++.-..=.-+ ...+--..|..|+...-+..+
T Consensus 12 ~YkS~sQ~aRVltE~Wv~~n~yCP~Cg~~~L~~f~N-N~PVaDF~C~~C~eeyELKSk 68 (254)
T PF06044_consen 12 GYKSNSQIARVLTEDWVAENMYCPNCGSKPLSKFEN-NRPVADFYCPNCNEEYELKSK 68 (254)
T ss_dssp HTTT-TTHHHHHHHHHHHHH---TTT--SS-EE---------EEE-TTT--EEEEEEE
T ss_pred hccChhhhhHHHHHHHHHHCCcCCCCCChhHhhccC-CCccceeECCCCchHHhhhhh
Confidence 33444444 445578999999999999985554432 345568899999999888643
No 130
>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=30.79 E-value=17 Score=25.30 Aligned_cols=27 Identities=30% Similarity=0.578 Sum_probs=13.2
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
+-.||.|++..|-. .+ ..+.|..||+.
T Consensus 2 ~p~Cp~C~se~~y~----D~--~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSEYTYE----DG--ELLVCPECGHE 28 (30)
T ss_dssp S---TTT-----EE-----S--SSEEETTTTEE
T ss_pred CCCCCCCCCcceec----cC--CEEeCCccccc
Confidence 34699999998872 23 36789999974
No 131
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=30.72 E-value=68 Score=23.85 Aligned_cols=35 Identities=34% Similarity=0.780 Sum_probs=22.9
Q ss_pred HHHHHHHHhhcccCCCCCCCCceEEEeccCCeEeeeccccc
Q psy15553 87 QDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACG 127 (489)
Q Consensus 87 q~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG 127 (489)
+-+|.+|-=---.||.|+.|= .++ +++ ...|-+|+
T Consensus 7 ~~LL~G~~ML~~~Cp~C~~PL---~~~-k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 7 EYLLQGWTMLDEHCPDCGTPL---MRD-KDG--KIYCVSCG 41 (41)
T ss_pred HHHHHhHhHhcCccCCCCCee---EEe-cCC--CEECCCCC
Confidence 456677766667899998664 443 333 24688886
No 132
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=30.53 E-value=56 Score=38.76 Aligned_cols=33 Identities=18% Similarity=0.433 Sum_probs=24.6
Q ss_pred cCCCCCCCCceEEEeccCCeEeeeccc---ccCccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKA---CGFHGMLQ 133 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~A---CG~~~~v~ 133 (489)
.||.|+++...+.. .+...|+.|.. |.+..++.
T Consensus 594 ~CP~Cg~~~L~~k~--gr~G~Fl~Cs~yP~C~~t~~~~ 629 (860)
T PRK06319 594 DCPKCHKGKLVKIW--AKNRYFYGCSEYPECDYKTSEE 629 (860)
T ss_pred ccCCCCCcceeEEe--cCCCceeeccCCccccccCCcc
Confidence 59999998777765 34446888976 88877765
No 133
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=30.36 E-value=24 Score=38.44 Aligned_cols=36 Identities=22% Similarity=0.508 Sum_probs=27.2
Q ss_pred HHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 93 FIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 93 fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
|...--+||.|+. .|.- +++. ..+|+.||.+.+-..
T Consensus 346 ~~~~~p~Cp~Cg~---~m~S--~G~~-g~rC~kCg~~~~~~~ 381 (421)
T COG1571 346 YERVNPVCPRCGG---RMKS--AGRN-GFRCKKCGTRARETL 381 (421)
T ss_pred eEEcCCCCCccCC---chhh--cCCC-CcccccccccCCccc
Confidence 5555668999984 5554 6777 999999999876543
No 134
>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=30.22 E-value=42 Score=24.26 Aligned_cols=29 Identities=34% Similarity=0.673 Sum_probs=18.0
Q ss_pred cccCCCCCCCCceEEEecc--CCeEeeecccc
Q psy15553 97 FVLCPECDNPETDLVVSAK--KGTIQQVCKAC 126 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k--~~~~~l~C~AC 126 (489)
.|.||.|.+.+-.. +..+ ++.---+|..|
T Consensus 5 ~v~CP~C~s~~~v~-k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 5 DVHCPRCQSTEGVK-KNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeeCCCCCCCCcce-eCCCCCCCCEeEecCcC
Confidence 47899999876333 3222 34456678777
No 135
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=29.80 E-value=48 Score=26.58 Aligned_cols=14 Identities=21% Similarity=0.650 Sum_probs=12.1
Q ss_pred eeecccccCccccc
Q psy15553 120 QQVCKACGFHGMLQ 133 (489)
Q Consensus 120 ~l~C~ACG~~~~v~ 133 (489)
.+.|..||...+|.
T Consensus 53 ~L~Cp~c~r~YPI~ 66 (68)
T PF03966_consen 53 ELICPECGREYPIR 66 (68)
T ss_dssp EEEETTTTEEEEEE
T ss_pred EEEcCCCCCEEeCC
Confidence 78999999998874
No 136
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=29.71 E-value=46 Score=42.33 Aligned_cols=43 Identities=26% Similarity=0.626 Sum_probs=27.6
Q ss_pred HHHHHHHHhhcccCCCCCCCCceEEEe-ccCCeEeeecccccCcccc
Q psy15553 87 QDLLDGFIRKFVLCPECDNPETDLVVS-AKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 87 q~~L~~fI~~yVlC~~C~~PeT~l~~~-~k~~~~~l~C~ACG~~~~v 132 (489)
..+|..++ .-+-||.|+.++-.|+-- ...+ ...|..||....+
T Consensus 1695 ~~~~~~~~-~~~~cp~c~~~~~~~~~~~~~~g--c~~c~~cg~s~c~ 1738 (1740)
T PRK08332 1695 EEKIRELL-GVVYCPVCYEKEGKLVELRMESG--CATCPVCGWSKCV 1738 (1740)
T ss_pred HHHHHHHh-ccCCCCCCCCCCCcceeeEecCC--ceeCCCCCCcccc
Confidence 44555554 335599999997555421 0344 6799999987653
No 137
>KOG3507|consensus
Probab=29.54 E-value=13 Score=29.86 Aligned_cols=32 Identities=22% Similarity=0.544 Sum_probs=22.3
Q ss_pred ccCCCCCCCCceEEEeccCCeEeeecccccCcccccch
Q psy15553 98 VLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFN 135 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~ 135 (489)
-+|..|+.-.|. ++.-..+|.-||++-...+|
T Consensus 21 YiCgdC~~en~l------k~~D~irCReCG~RIlyKkR 52 (62)
T KOG3507|consen 21 YICGDCGQENTL------KRGDVIRCRECGYRILYKKR 52 (62)
T ss_pred EEeccccccccc------cCCCcEehhhcchHHHHHHH
Confidence 369999876542 22346789999998766555
No 138
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=29.39 E-value=14 Score=29.73 Aligned_cols=31 Identities=23% Similarity=0.585 Sum_probs=13.2
Q ss_pred hcccCCCCCCCCceEEEeccCCeEeeecccccCccc
Q psy15553 96 KFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGM 131 (489)
Q Consensus 96 ~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~ 131 (489)
-.++|.-|+. |.-+ .=-.+.++|..||+-.+
T Consensus 29 v~IlCNDC~~--~s~v---~fH~lg~KC~~C~SYNT 59 (61)
T PF14599_consen 29 VWILCNDCNA--KSEV---PFHFLGHKCSHCGSYNT 59 (61)
T ss_dssp EEEEESSS----EEEE---E--TT----TTTS---E
T ss_pred EEEECCCCCC--ccce---eeeHhhhcCCCCCCccc
Confidence 3678999987 2222 23467899999997543
No 139
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=29.30 E-value=52 Score=29.38 Aligned_cols=35 Identities=26% Similarity=0.616 Sum_probs=25.5
Q ss_pred cCCCCCC---CCceEEEeccCCeEeeecccccCccccc
Q psy15553 99 LCPECDN---PETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 99 lC~~C~~---PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
.|+.|.+ |--...+-.+++.+...|.-||...-.+
T Consensus 58 ~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p 95 (105)
T COG2023 58 ICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYP 95 (105)
T ss_pred hccccCcccccCcceEEEEcCCeEEEEecCCCcEEEec
Confidence 6999999 4444333336777999999999986554
No 140
>TIGR01160 SUI1_MOF2 translation initiation factor SUI1, eukaryotic. Alternate name: MOF2. A similar protein family (see TIGRFAMs model TIGR01158) is found in prokaryotes. The human proteins complements a yeast SUI1 mutatation.
Probab=29.08 E-value=65 Score=28.91 Aligned_cols=65 Identities=11% Similarity=0.129 Sum_probs=44.0
Q ss_pred cEEEEeccCCC--eeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecC---CCeEEEEeccchHHHHHHHHH
Q psy15553 22 LIAKVEGKGNG--IKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHK---NDRFIVNGSHDVVKLQDLLDG 92 (489)
Q Consensus 22 ~~~kieGkgng--iKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~---~~r~iinG~~~~~~lq~~L~~ 92 (489)
+.++++ ..|| .=|+|.+|.+ .=+-.-++|.|...+|+.|++-.. ++-+.|+|.|.....+=|...
T Consensus 28 I~Iri~-qR~grK~VTiI~Gl~~-----~~dlk~l~K~lKkk~~cGGsVk~~~~~~~~IelQGD~re~v~~~L~~~ 97 (110)
T TIGR01160 28 IHIRIQ-QRNGRKTLTTVQGLPK-----EYDLKKIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEFLISQ 97 (110)
T ss_pred EEEEEE-EccCCccEEEEeccCC-----hHHHHHHHHHHHHHhCCCceEEeCCCCCCEEEEeCcHHHHHHHHHHHc
Confidence 666777 3455 3467777762 122345789999999999998632 257889999987665555444
No 141
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=29.04 E-value=1.3e+02 Score=24.64 Aligned_cols=47 Identities=15% Similarity=0.230 Sum_probs=35.3
Q ss_pred CChhhhHHHHhhcCceeeecCCCeEEEEeccc----hHHHHHHHHHHHhhc
Q psy15553 51 PTYPTKYFGCELGAQTKLDHKNDRFIVNGSHD----VVKLQDLLDGFIRKF 97 (489)
Q Consensus 51 p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~----~~~lq~~L~~fI~~y 97 (489)
|.-+..-++..-|....+...+++++|.=.-. ..++..+++..+++|
T Consensus 15 Pk~i~~~lgl~~Gd~v~v~~~~~~iii~~~~~~~~~~~~~~~~~~~~~~~y 65 (74)
T TIGR02609 15 PKEVLESLGLKEGDTLYVDEEEGGLKLKRFDEGKELEKKMQMAVERAMSKY 65 (74)
T ss_pred CHHHHHHcCcCCCCEEEEEEECCEEEEEECCCCccHHHHHHHHHHHHHHHH
Confidence 77777888888888888888888898874444 456666677777766
No 142
>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=28.49 E-value=37 Score=26.90 Aligned_cols=30 Identities=23% Similarity=0.554 Sum_probs=21.4
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
.||.|+.+.-. .. ..+ ...|..||....-|
T Consensus 30 ~C~~CG~~~~~-~~--~~r--~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 30 TCPRCGHRNKK-RR--SGR--VFTCPNCGFEMDRD 59 (69)
T ss_pred CccCccccccc-cc--ccc--eEEcCCCCCEECcH
Confidence 59999988766 11 233 78899999985443
No 143
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=28.37 E-value=13 Score=38.61 Aligned_cols=43 Identities=19% Similarity=0.465 Sum_probs=30.6
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCcccccchhhhhhhhh
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFNHKLNTFIL 143 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl~~~i~ 143 (489)
++.||.|+..=. .+ .=..-+..|..||+...+..|.++...+=
T Consensus 38 w~kc~~C~~~~~--~~--~l~~~~~vcp~c~~h~rltAreRI~~L~D 80 (296)
T CHL00174 38 WVQCENCYGLNY--KK--FLKSKMNICEQCGYHLKMSSSDRIELLID 80 (296)
T ss_pred eeECCCccchhh--HH--HHHHcCCCCCCCCCCcCCCHHHHHHHHcc
Confidence 799999986421 11 11123579999999999999988876554
No 144
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.29 E-value=19 Score=27.90 Aligned_cols=35 Identities=20% Similarity=0.296 Sum_probs=26.4
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccccchhhh
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFNHKL 138 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl 138 (489)
.|..|+..=..+. ..-..+|.-||++-.+.+|++.
T Consensus 8 ~C~~Cg~~~~~~~-----~~~~irCp~Cg~rIl~K~R~~~ 42 (49)
T COG1996 8 KCARCGREVELDQ-----ETRGIRCPYCGSRILVKERPKV 42 (49)
T ss_pred EhhhcCCeeehhh-----ccCceeCCCCCcEEEEeccCCc
Confidence 5899998763333 2457899999999998887765
No 145
>PRK11823 DNA repair protein RadA; Provisional
Probab=28.20 E-value=32 Score=37.49 Aligned_cols=27 Identities=26% Similarity=0.565 Sum_probs=22.5
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
.|.+|+. ....|+-+|.+||+..++..
T Consensus 9 ~C~~Cg~---------~~~~~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 9 VCQECGA---------ESPKWLGRCPECGAWNTLVE 35 (446)
T ss_pred ECCcCCC---------CCcccCeeCcCCCCccceee
Confidence 4999996 35578899999999999865
No 146
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.64 E-value=41 Score=37.29 Aligned_cols=44 Identities=27% Similarity=0.547 Sum_probs=27.5
Q ss_pred CCCCCCCCceEEEeccCCeEeeecccccCccccc----------------chhhhhhhhhcCCCC
Q psy15553 100 CPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ----------------FNHKLNTFILKNPPN 148 (489)
Q Consensus 100 C~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~----------------~~~kl~~~i~kn~p~ 148 (489)
||.|..|=|. ++ ..+ .+.|.-||+..+++ ...++..++-++-|.
T Consensus 225 C~~C~~~l~~-h~--~~~--~l~Ch~Cg~~~~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~ 284 (505)
T TIGR00595 225 CPNCDVSLTY-HK--KEG--KLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPG 284 (505)
T ss_pred CCCCCCceEE-ec--CCC--eEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCC
Confidence 6666665433 22 233 67899998887653 136777777777664
No 147
>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=26.88 E-value=20 Score=25.31 Aligned_cols=28 Identities=25% Similarity=0.544 Sum_probs=17.8
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
+|..|+..-. |. .. -.++|.-||++-..
T Consensus 2 ~C~~Cg~~~~-~~---~~--~~irC~~CG~RIly 29 (32)
T PF03604_consen 2 ICGECGAEVE-LK---PG--DPIRCPECGHRILY 29 (32)
T ss_dssp BESSSSSSE--BS---TS--STSSBSSSS-SEEB
T ss_pred CCCcCCCeeE-cC---CC--CcEECCcCCCeEEE
Confidence 5899997755 22 12 24699999998554
No 148
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=26.87 E-value=44 Score=25.11 Aligned_cols=31 Identities=23% Similarity=0.640 Sum_probs=21.6
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccccch
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFN 135 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~ 135 (489)
.|..|+..- .. + ..-.++|.-||++-....|
T Consensus 4 ~C~~Cg~~~---~~--~-~~~~irC~~CG~rIlyK~R 34 (44)
T smart00659 4 ICGECGREN---EI--K-SKDVVRCRECGYRILYKKR 34 (44)
T ss_pred ECCCCCCEe---ec--C-CCCceECCCCCceEEEEeC
Confidence 699999842 22 2 3457999999998766544
No 149
>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=26.83 E-value=50 Score=23.77 Aligned_cols=26 Identities=27% Similarity=0.698 Sum_probs=18.3
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHG 130 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~ 130 (489)
.|+.|++- .... .++ +.-|..||+..
T Consensus 10 ~C~~C~~~--~~~~--~dG--~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSR--WFYS--DDG--FYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCe--EeEc--cCC--EEEhhhCceEc
Confidence 69999998 3332 455 66799999753
No 150
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=26.79 E-value=1e+02 Score=23.38 Aligned_cols=41 Identities=27% Similarity=0.772 Sum_probs=25.9
Q ss_pred HHHHHHHhh---cccCC--CCCCCCceEEEeccCCeEeeecccccCccc
Q psy15553 88 DLLDGFIRK---FVLCP--ECDNPETDLVVSAKKGTIQQVCKACGFHGM 131 (489)
Q Consensus 88 ~~L~~fI~~---yVlC~--~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~ 131 (489)
-+++.||+. +.-|| .|+.. +......+...+.|..||...-
T Consensus 6 ~~~~~~i~~~~~~~~CP~~~C~~~---~~~~~~~~~~~v~C~~C~~~fC 51 (64)
T smart00647 6 LLLESYVESNPDLKWCPAPDCSAA---IIVTEEEGCNRVTCPKCGFSFC 51 (64)
T ss_pred HHHHHHHhcCCCccCCCCCCCcce---EEecCCCCCCeeECCCCCCeEC
Confidence 456677754 78899 99652 3331012556888988987653
No 151
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=26.71 E-value=32 Score=28.22 Aligned_cols=40 Identities=18% Similarity=0.437 Sum_probs=26.1
Q ss_pred cCCCCCCCCceEEEec--cCCeEeeecccccCcccccchhhh
Q psy15553 99 LCPECDNPETDLVVSA--KKGTIQQVCKACGFHGMLQFNHKL 138 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~--k~~~~~l~C~ACG~~~~v~~~~kl 138 (489)
.|..|+...+..+-.. .+++.+.+|..|..+.-+.-+-++
T Consensus 6 TC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlIaDnLg~ 47 (66)
T PF05180_consen 6 TCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLIADNLGW 47 (66)
T ss_dssp EETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES--SS-S
T ss_pred EcCCCCCccceeeCHHHHhCCeEEEECCCCcceeeehhhhcc
Confidence 5999998888887611 178999999999988777544433
No 152
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=26.54 E-value=1.1e+02 Score=25.53 Aligned_cols=51 Identities=16% Similarity=0.311 Sum_probs=37.0
Q ss_pred cchHHHHHHHHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 81 HDVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 81 ~~~~~lq~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
.+...|+.+|..=+.+.-.= -...|.-.+.-......+++.|.+|++-..|
T Consensus 32 ~tl~~l~~~L~~~~~~H~~~-C~~~p~F~v~~~~~~~~L~~~C~~Cd~~~vV 82 (82)
T PF14768_consen 32 LTLEELRQLLEEAVTEHSDR-CSSTPQFSVEPGFGESSLYMSCEACDFLEVV 82 (82)
T ss_pred CCHHHHHHHHHHHHHHHHHh-CCCCCEEEEecCCCchhheeECCCCCcceeC
Confidence 78889999998877765443 1668887777533334799999999986543
No 153
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=26.53 E-value=43 Score=26.33 Aligned_cols=25 Identities=32% Similarity=0.953 Sum_probs=17.6
Q ss_pred hhcccCCCCCCCCceEEEeccCCeEeeecccccCc
Q psy15553 95 RKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFH 129 (489)
Q Consensus 95 ~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~ 129 (489)
-.+|.|+.|+.+- +-...|..||.-
T Consensus 24 p~l~~C~~cG~~~----------~~H~vc~~cG~Y 48 (55)
T TIGR01031 24 PTLVVCPNCGEFK----------LPHRVCPSCGYY 48 (55)
T ss_pred CcceECCCCCCcc----------cCeeECCccCeE
Confidence 3468899999752 346678888853
No 154
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=26.42 E-value=54 Score=29.74 Aligned_cols=49 Identities=12% Similarity=0.218 Sum_probs=27.3
Q ss_pred HHHhhcCceeeecCCCeEEEEec-------cchHHHHHHHHHHHhhcccCCCCCCCCceEEE
Q psy15553 58 FGCELGAQTKLDHKNDRFIVNGS-------HDVVKLQDLLDGFIRKFVLCPECDNPETDLVV 112 (489)
Q Consensus 58 f~~ELGa~~~~d~~~~r~iinG~-------~~~~~lq~~L~~fI~~yVlC~~C~~PeT~l~~ 112 (489)
|.++.-+.|++- .+-+++|.=. .-..-++...-. ++||.|+|+...++-
T Consensus 46 FaFev~~egT~a-ega~l~Ie~~p~~~~C~~C~~~~~~e~~~-----~~CP~C~s~~~~i~~ 101 (115)
T COG0375 46 FAFEVVAEGTIA-EGAELHIEEEPAECWCLDCGQEVELEELD-----YRCPKCGSINLRIIG 101 (115)
T ss_pred HHHHHHhccCcc-cCCEEEEEEeccEEEeccCCCeecchhhe-----eECCCCCCCceEEec
Confidence 677777888876 4667776311 111111111112 228888888877764
No 155
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=26.22 E-value=38 Score=37.06 Aligned_cols=27 Identities=22% Similarity=0.508 Sum_probs=22.8
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
.|..|+. ....|+-+|.+||+..++..
T Consensus 9 ~C~~Cg~---------~~~~~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 9 VCQHCGA---------DSPKWQGKCPACHAWNTITE 35 (454)
T ss_pred ECCcCCC---------CCccccEECcCCCCccccch
Confidence 5999996 35578899999999999875
No 156
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=26.17 E-value=54 Score=34.42 Aligned_cols=36 Identities=19% Similarity=0.426 Sum_probs=25.5
Q ss_pred cccCCCCCCCC-ceEEE-eccCCeEeeecccccCcccc
Q psy15553 97 FVLCPECDNPE-TDLVV-SAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 97 yVlC~~C~~Pe-T~l~~-~~k~~~~~l~C~ACG~~~~v 132 (489)
--.||.|+++= ..++. ..+.+.-++.|.-||..-..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~ 224 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHV 224 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccc
Confidence 37899999875 34432 22456789999999987655
No 157
>PRK00378 nucleoid-associated protein NdpA; Validated
Probab=25.80 E-value=1.7e+02 Score=30.46 Aligned_cols=50 Identities=24% Similarity=0.405 Sum_probs=37.3
Q ss_pred EEEeccCCCeeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHHHHHHHh
Q psy15553 24 AKVEGKGNGIKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDLLDGFIR 95 (489)
Q Consensus 24 ~kieGkgngiKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~L~~fI~ 95 (489)
+++-|+++||...|. . -.||-...||+.++.++|+| .+..|.+.|.++++
T Consensus 283 ~k~~~~~~gi~Isf~-------------~-------~~~~~~i~yd~~~~~ltI~~--~p~~l~~ql~r~~~ 332 (334)
T PRK00378 283 TKFSGSGGGLTISFD-------------A-------HLLGERIFYDPATDTLTIKG--TPPNLRDQLQRRLK 332 (334)
T ss_pred EEEEecCCCEEEEee-------------H-------HHCCCceEEcCCCCEEEEeC--CCHHHHHHHHHHhc
Confidence 466699999988875 1 12367889999999999999 46666666666653
No 158
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=25.73 E-value=48 Score=35.41 Aligned_cols=33 Identities=27% Similarity=0.555 Sum_probs=21.1
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
||+.|---.|.++. ...+.-...|.-||+..+-
T Consensus 23 lC~dC~~~~~~~~~-ip~~~~v~~C~~Cga~~~~ 55 (355)
T COG1499 23 LCGDCYVETTPLIE-IPDEVNVEVCRHCGAYRIR 55 (355)
T ss_pred ccHHHHhccCcccc-CCCceEEEECCcCCCccCC
Confidence 34444433366654 3467889999999966543
No 159
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=25.36 E-value=35 Score=35.70 Aligned_cols=25 Identities=12% Similarity=0.292 Sum_probs=19.3
Q ss_pred EeeecccccCcccccchhhhhhhhh
Q psy15553 119 IQQVCKACGFHGMLQFNHKLNTFIL 143 (489)
Q Consensus 119 ~~l~C~ACG~~~~v~~~~kl~~~i~ 143 (489)
+.++|..|++.-.+.+--|=+.|++
T Consensus 76 F~~kC~~C~~~i~~kTDPkn~dY~~ 100 (324)
T PF04502_consen 76 FYIKCPRCSNEIEFKTDPKNTDYVV 100 (324)
T ss_pred EEEEcCCCCCEEeeecCCCCCCeee
Confidence 6899999999888777555566655
No 160
>cd02983 P5_C P5 family, C-terminal redox inactive TRX-like domain; P5 is a protein disulfide isomerase (PDI)-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. The C-terminal domain is likely involved in substrate binding, similar to the b and b' domains of PDI.
Probab=25.32 E-value=82 Score=28.44 Aligned_cols=44 Identities=14% Similarity=0.248 Sum_probs=29.7
Q ss_pred hhhhHHHH-hhc--CceeeecCCCeEE-EEeccchHHHHHHHHHHHhh
Q psy15553 53 YPTKYFGC-ELG--AQTKLDHKNDRFI-VNGSHDVVKLQDLLDGFIRK 96 (489)
Q Consensus 53 ~~~kyf~~-ELG--a~~~~d~~~~r~i-inG~~~~~~lq~~L~~fI~~ 96 (489)
++..|||. +-+ +-.-++.++++|. ..|.++.+.|..-+..|++.
T Consensus 70 ~~~~~fgl~~~~~P~v~i~~~~~~KY~~~~~~~t~e~i~~Fv~~~l~G 117 (130)
T cd02983 70 DLEEALNIGGFGYPAMVAINFRKMKFATLKGSFSEDGINEFLRELSYG 117 (130)
T ss_pred HHHHHcCCCccCCCEEEEEecccCccccccCccCHHHHHHHHHHHHcC
Confidence 37777774 223 2334555455888 88999999888877777654
No 161
>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=25.09 E-value=62 Score=28.20 Aligned_cols=32 Identities=31% Similarity=0.465 Sum_probs=17.5
Q ss_pred CCCCCCCCceEEEe-----ccCCe-----EeeecccccCccc
Q psy15553 100 CPECDNPETDLVVS-----AKKGT-----IQQVCKACGFHGM 131 (489)
Q Consensus 100 C~~C~~PeT~l~~~-----~k~~~-----~~l~C~ACG~~~~ 131 (489)
||.|++.++.-.+. -++.. -...|..||..-.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~~ 42 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEELL 42 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEEE
Confidence 99998765542220 01221 2457888887643
No 162
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=25.04 E-value=47 Score=28.34 Aligned_cols=15 Identities=20% Similarity=0.558 Sum_probs=12.8
Q ss_pred CCeEeeecccccCcc
Q psy15553 116 KGTIQQVCKACGFHG 130 (489)
Q Consensus 116 ~~~~~l~C~ACG~~~ 130 (489)
++.+.|+|.+||.++
T Consensus 84 ~~vVsL~C~~CG~r~ 98 (98)
T PF15494_consen 84 GSVVSLQCSDCGKRT 98 (98)
T ss_pred CCEEEEECcccCCcC
Confidence 567899999999874
No 163
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=24.86 E-value=35 Score=27.83 Aligned_cols=11 Identities=27% Similarity=1.029 Sum_probs=7.2
Q ss_pred cCCCCCCCCce
Q psy15553 99 LCPECDNPETD 109 (489)
Q Consensus 99 lC~~C~~PeT~ 109 (489)
+||.|+++++.
T Consensus 20 ~CP~Cgs~~~t 30 (64)
T COG2093 20 ICPVCGSTDLT 30 (64)
T ss_pred cCCCCCCcccc
Confidence 47777777654
No 164
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=24.69 E-value=53 Score=23.87 Aligned_cols=33 Identities=27% Similarity=0.497 Sum_probs=18.6
Q ss_pred ccCCCCC---CCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 98 VLCPECD---NPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 98 VlC~~C~---~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
|.|..|+ ||=..+.. .++ .-.|.-||....++.
T Consensus 3 ~rC~~C~aylNp~~~~~~--~~~--~w~C~~C~~~N~lp~ 38 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDD--GGK--TWICNFCGTKNPLPP 38 (40)
T ss_dssp -B-TTT--BS-TTSEEET--TTT--EEEETTT--EEE--G
T ss_pred cccCCCCCEECCcceEcC--CCC--EEECcCCCCcCCCCC
Confidence 6799998 77777753 334 578999999988864
No 165
>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=24.65 E-value=53 Score=23.97 Aligned_cols=31 Identities=26% Similarity=0.546 Sum_probs=21.9
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccC
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGF 128 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~ 128 (489)
-+-||.|++-|.-=..+ +++.=.-.|..||+
T Consensus 3 ~~pCP~CGG~DrFr~~d-~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDD-KDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCcccccccc-CCCCcCEEeCCCCC
Confidence 46799999988766432 34445667888986
No 166
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=24.28 E-value=39 Score=24.91 Aligned_cols=22 Identities=18% Similarity=0.440 Sum_probs=16.1
Q ss_pred echHHHHHHhCCCCChhhhHHH
Q psy15553 38 VNMADVAKAIGRPPTYPTKYFG 59 (489)
Q Consensus 38 ~N~~dIakaL~R~p~~~~kyf~ 59 (489)
..+.+||+.|+|+|.-|.+++-
T Consensus 21 ~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 21 MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --HHHHHHHTT--HHHHHHHHH
T ss_pred CCHHHHHHHHCcCcHHHHHHHh
Confidence 3688999999999999988764
No 167
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=24.19 E-value=44 Score=35.70 Aligned_cols=27 Identities=26% Similarity=0.507 Sum_probs=22.1
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
.|..|+. ....|+-+|.+||+..++..
T Consensus 2 ~c~~cg~---------~~~~~~g~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGY---------VSPKWLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCC---------CCCCccEECcCCCCceeeee
Confidence 5999996 34567889999999999864
No 168
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=24.11 E-value=63 Score=38.86 Aligned_cols=46 Identities=30% Similarity=0.520 Sum_probs=29.5
Q ss_pred ccchHHHHHHHHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 80 SHDVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 80 ~~~~~~lq~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
.|++..+-....++--.--+|+.|+ |.++. .+ -...|..||..+-.
T Consensus 907 ~~~~~~~~~~~~~~~~~~~~c~~c~---~~~~~--~g--~c~~c~~cg~t~gc 952 (953)
T PRK06556 907 AHSSTELLELQLGEAADAPLCPTCG---TKMVR--NG--SCYVCEGCGSTSGC 952 (953)
T ss_pred CCccHHHHHHhhcccccCCcCCCcc---CeeeE--CC--ceEeccCCCCCCCC
Confidence 3444555455555555556778885 77766 23 47789999998653
No 169
>PRK09019 translation initiation factor Sui1; Validated
Probab=24.05 E-value=2.2e+02 Score=25.49 Aligned_cols=49 Identities=6% Similarity=-0.033 Sum_probs=35.3
Q ss_pred eeEEEechHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHH
Q psy15553 33 IKTVIVNMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQ 87 (489)
Q Consensus 33 iKTvi~N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq 87 (489)
.=|+|..|.--... -.-+.|+|-..+|+-|++- ++.+.|+|.|.....+
T Consensus 46 ~VTiI~Gl~~~~~d----lk~l~K~lKkk~gcGGtvk--~~~IelQGD~r~~v~~ 94 (108)
T PRK09019 46 GVCLITGLDLDDAE----LKKLAAELKKKCGCGGAVK--DGVIEIQGDKRDLLKS 94 (108)
T ss_pred eEEEEeCCcCCHHH----HHHHHHHHHHHhcCCCeEE--cCEEEEcCcHHHHHHH
Confidence 45778877511111 2457889999999999994 7899999999765444
No 170
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=23.78 E-value=53 Score=29.49 Aligned_cols=37 Identities=30% Similarity=0.702 Sum_probs=19.2
Q ss_pred HHhhcccCCCCCCCCceEEEecc----CC----eEeeecccccCc
Q psy15553 93 FIRKFVLCPECDNPETDLVVSAK----KG----TIQQVCKACGFH 129 (489)
Q Consensus 93 fI~~yVlC~~C~~PeT~l~~~~k----~~----~~~l~C~ACG~~ 129 (489)
|+-.|+-|..|+.-+-.++.+.. ++ ++...|+.|++.
T Consensus 23 yllN~~~Ca~C~krdfv~i~nk~~~eedgeEivTY~HvC~nC~Hv 67 (112)
T PF06573_consen 23 YLLNFVGCASCQKRDFVLISNKSIEEEDGEEIVTYDHVCKNCHHV 67 (112)
T ss_dssp -TTTB---SSS--SS-EEEEEEEEEEETTEEEEEEEEEETTT--E
T ss_pred eeeechhhhccCCCCcEEEecccccccCCcEEEEeeeccCccceE
Confidence 56679999999999987776421 11 256788888874
No 171
>smart00400 ZnF_CHCC zinc finger.
Probab=23.66 E-value=72 Score=24.37 Aligned_cols=32 Identities=31% Similarity=0.527 Sum_probs=23.3
Q ss_pred cCCCCCCCCceEEEeccCCeEeeecccccCcccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKACGFHGML 132 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v 132 (489)
+||-|.--.-.+.++++++ .-.|-+||..+.+
T Consensus 4 ~cPfh~d~~pSf~v~~~kn--~~~Cf~cg~gGd~ 35 (55)
T smart00400 4 LCPFHGEKTPSFSVSPDKQ--FFHCFGCGAGGNV 35 (55)
T ss_pred cCcCCCCCCCCEEEECCCC--EEEEeCCCCCCCH
Confidence 5999987777788854444 5789999977643
No 172
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=23.59 E-value=42 Score=37.65 Aligned_cols=53 Identities=17% Similarity=0.493 Sum_probs=30.6
Q ss_pred ccchHHHHHHHHHHHh-----------hcccCCCCCCCCceEEEeccCCeEeeecccccCcccccchhhhhhhhh
Q psy15553 80 SHDVVKLQDLLDGFIR-----------KFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQFNHKLNTFIL 143 (489)
Q Consensus 80 ~~~~~~lq~~L~~fI~-----------~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~~~kl~~~i~ 143 (489)
+.+.+.|.++++.=.+ .+-.|+.|+.-. +. .-.|..||... ++.-.+.+.|+-
T Consensus 463 ~~n~~al~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~---------~~-~~~CP~CGs~~-~~~~~Rv~GYl~ 526 (546)
T PF13597_consen 463 KPNPEALEKLVRYAMENTGIPYFTINPPIDICPDCGYIG---------GE-GDKCPKCGSEN-IEVYSRVTGYLR 526 (546)
T ss_dssp -T-HHHHHHHHHHHHH--H-SEEEEE--EEEETTT---S------------EEE-CCC-----EEEEB-SSSS-B
T ss_pred CCCHHHHHHHHHHHHHhCCCCeEEEecCcccccCCCcCC---------CC-CCCCCCCCCcc-cceEEEeecccc
Confidence 4577888888887776 245799999522 12 67799999987 667899999998
No 173
>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=22.76 E-value=60 Score=28.20 Aligned_cols=24 Identities=17% Similarity=0.284 Sum_probs=14.4
Q ss_pred CeEeeecccccCccccc-chhhhhh
Q psy15553 117 GTIQQVCKACGFHGMLQ-FNHKLNT 140 (489)
Q Consensus 117 ~~~~l~C~ACG~~~~v~-~~~kl~~ 140 (489)
.+-.+.|..||....-+ ..+++-.
T Consensus 32 nVPa~~C~~CGe~y~~dev~~eIE~ 56 (89)
T TIGR03829 32 ETPSISCSHCGMEYQDDTTVKEIED 56 (89)
T ss_pred cCCcccccCCCcEeecHHHHHHHHh
Confidence 44567899999875432 3455443
No 174
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=22.52 E-value=38 Score=26.62 Aligned_cols=17 Identities=29% Similarity=0.645 Sum_probs=13.2
Q ss_pred CeEeeecccccCccccc
Q psy15553 117 GTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 117 ~~~~l~C~ACG~~~~v~ 133 (489)
..-.|+|.|||..+...
T Consensus 33 ~~~al~CaACgCHRnFH 49 (53)
T TIGR01566 33 DPESLTCAACGCHRNFH 49 (53)
T ss_pred CCcceeeeecCcccccc
Confidence 34489999999988654
No 175
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=22.35 E-value=55 Score=36.78 Aligned_cols=50 Identities=24% Similarity=0.518 Sum_probs=34.5
Q ss_pred cccCCCCCCCCce----EEEec--cCCeEeeecccccCcccccchhhh---hhhhhcCC
Q psy15553 97 FVLCPECDNPETD----LVVSA--KKGTIQQVCKACGFHGMLQFNHKL---NTFILKNP 146 (489)
Q Consensus 97 yVlC~~C~~PeT~----l~~~~--k~~~~~l~C~ACG~~~~v~~~~kl---~~~i~kn~ 146 (489)
||-||.|+-.-.- |.-+. ........|..||+.-.-..++.+ ..||-.||
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~~~~ 258 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVATNP 258 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEeccc
Confidence 9999999965432 33321 135689999999998665545554 56788888
No 176
>PRK14973 DNA topoisomerase I; Provisional
Probab=22.35 E-value=53 Score=39.35 Aligned_cols=22 Identities=14% Similarity=0.169 Sum_probs=20.2
Q ss_pred HHHHHHHHhhccCcchHHHHHH
Q psy15553 374 VPGILKLFYDYDILEEKVLLEW 395 (489)
Q Consensus 374 ~~~ILk~LYD~DILeEE~Il~W 395 (489)
=+..|..||-.+|.+=|.+..|
T Consensus 886 ge~t~~~l~~ag~~~~e~l~~~ 907 (936)
T PRK14973 886 GETTLEKLYLAGVYDGDLLVSA 907 (936)
T ss_pred CHHHHHHHHHcCCCCHHHhccC
Confidence 3778899999999999999999
No 177
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=22.30 E-value=45 Score=36.59 Aligned_cols=29 Identities=28% Similarity=0.485 Sum_probs=22.5
Q ss_pred cccCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 97 FVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 97 yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
+-.|.+|+.- .-.|.-+|.+||+.+++..
T Consensus 7 ~f~C~~CG~~---------s~KW~GkCp~Cg~Wns~vE 35 (456)
T COG1066 7 AFVCQECGYV---------SPKWLGKCPACGAWNTLVE 35 (456)
T ss_pred EEEcccCCCC---------CccccccCCCCCCccceEE
Confidence 3469999963 3358899999999988753
No 178
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.29 E-value=49 Score=32.92 Aligned_cols=24 Identities=33% Similarity=0.708 Sum_probs=18.0
Q ss_pred ccCCCCCCCCceEEEeccCCeEeeecccccCccc
Q psy15553 98 VLCPECDNPETDLVVSAKKGTIQQVCKACGFHGM 131 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~ 131 (489)
..||.|+. + ..+ ...|..||..-.
T Consensus 310 ~~C~~cg~----~----~~r--~~~C~~cg~~~~ 333 (364)
T COG0675 310 KTCPCCGH----L----SGR--LFKCPRCGFVHD 333 (364)
T ss_pred ccccccCC----c----cce--eEECCCCCCeeh
Confidence 68999999 2 233 568999999733
No 179
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.26 E-value=34 Score=31.40 Aligned_cols=43 Identities=12% Similarity=0.276 Sum_probs=25.8
Q ss_pred hHHHHHHHHHHHhhcccCCCCCCCCceEEEeccCCeEeeecccccCccccc
Q psy15553 83 VVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 83 ~~~lq~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~ 133 (489)
++.|+..++.+.+ =.-|. ...|.+ +..-...+|..||+..++.
T Consensus 41 pe~L~fafe~l~~----gt~~e--ga~L~i--~~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 41 KEIVEFALNELLK----GTILE--GAEIIF--EEEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred HHHHHHHHHHHHc----CCccc--CCEEEE--EecceEEECCCCCCEEecc
Confidence 4455555544332 22333 446666 4555788999999888775
No 180
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=22.22 E-value=57 Score=28.04 Aligned_cols=69 Identities=17% Similarity=0.319 Sum_probs=48.9
Q ss_pred hHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEec-cchHHHHHHHHHHHhhcccCCCCCCCCceEEEeccCCe
Q psy15553 40 MADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGS-HDVVKLQDLLDGFIRKFVLCPECDNPETDLVVSAKKGT 118 (489)
Q Consensus 40 ~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~-~~~~~lq~~L~~fI~~yVlC~~C~~PeT~l~~~~k~~~ 118 (489)
+.-||++|+|++..|++.+....+..-. +.+..|. .+-..|+.++. -|=+|..|.-....++.+.++++
T Consensus 7 i~AiA~aL~R~~~dVl~Vl~~~~~~~~~------~~l~~G~Gl~l~~le~~f~----~F~I~A~v~~~g~~~~lN~~G~i 76 (89)
T PF05379_consen 7 IRAIAEALGRREQDVLAVLSRKCGEELL------EELWSGEGLDLEDLEELFE----LFDICAHVNFGGETFVLNEEGRI 76 (89)
T ss_pred hHHHHHHhCCCHHHHHHHHHhccCHHHH------HHHHcCCCcCHHHHHHHHH----HcCeEEEEEECCEEEEECCCCcE
Confidence 3579999999999999999988774322 1233343 46666666654 47999999877777777655543
No 181
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=22.03 E-value=71 Score=24.98 Aligned_cols=34 Identities=21% Similarity=0.477 Sum_probs=25.1
Q ss_pred ccCCCCCCCCceEEEecc--CCeEeeecccccCcccc
Q psy15553 98 VLCPECDNPETDLVVSAK--KGTIQQVCKACGFHGML 132 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k--~~~~~l~C~ACG~~~~v 132 (489)
|.||-|+-+-+.++ |+. ++.+.-.|..|...-.+
T Consensus 1 i~CPyCge~~~~~i-D~s~~~Q~yiEDC~vCC~PI~~ 36 (52)
T PF14255_consen 1 IQCPYCGEPIEILI-DPSAGDQEYIEDCQVCCRPIEV 36 (52)
T ss_pred CCCCCCCCeeEEEE-ecCCCCeeEEeehhhcCCccEE
Confidence 58999998865544 433 46789999999876544
No 182
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=21.95 E-value=54 Score=23.13 Aligned_cols=17 Identities=24% Similarity=0.544 Sum_probs=10.6
Q ss_pred cCCeEeeecccccCccc
Q psy15553 115 KKGTIQQVCKACGFHGM 131 (489)
Q Consensus 115 k~~~~~l~C~ACG~~~~ 131 (489)
+.+++..+|.+||....
T Consensus 6 ~~~l~~~rC~~Cg~~~~ 22 (37)
T PF12172_consen 6 EGRLLGQRCRDCGRVQF 22 (37)
T ss_dssp TT-EEEEE-TTT--EEE
T ss_pred CCEEEEEEcCCCCCEec
Confidence 57889999999998743
No 183
>PF00123 Hormone_2: Peptide hormone; InterPro: IPR000532 A number of polypeptidic hormones, mainly expressed in the intestine or the pancreas, belong to a group of structurally related peptides [, ]. Once such hormone, glucagon is widely distributed and produced in the alpha-cells of pancreatic islets []. It affects glucose metabolism in the liver [] by inhibiting glycogen synthesis, stimulating glycogenolysis and enchancing gluconeogenesis. It also increases mobilisation of glucose, free fatty acids and ketone bodies, which are metabolites produced in excess in diabetes mellitus. Glucagon is produced, like other peptide hormones, as part of a larger precursor (preproglucagon), which is cleaved to produce glucagon, glucagon-like protein I and glucagon-like protein II []. The structure of glucagon itself is fully conserved in all known mammalian species []. Other members of the structurally similar group include glicentin precursor, secretin, gastric inhibitory protein, vasoactive intestinal peptide (VIP), prealbumin, peptide HI-27 and growth hormone releasing factor.; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1T5Q_A 2OBU_A 2QKH_B 2L70_A 2L71_A 2B4N_A 1GCN_A 1D0R_A 3IOL_B 2RRI_A ....
Probab=21.86 E-value=63 Score=22.21 Aligned_cols=11 Identities=36% Similarity=0.851 Sum_probs=9.0
Q ss_pred HHHHHHHHHHc
Q psy15553 414 SRAEPFIKWLR 424 (489)
Q Consensus 414 k~a~pFIeWLk 424 (489)
..|+.||.||-
T Consensus 17 ~aak~fl~~L~ 27 (28)
T PF00123_consen 17 LAAKKFLQWLM 27 (28)
T ss_dssp HHHHHHHHHHC
T ss_pred HHHHHHHHHHh
Confidence 35889999995
No 184
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=21.62 E-value=86 Score=35.67 Aligned_cols=30 Identities=30% Similarity=0.619 Sum_probs=16.1
Q ss_pred cCCCCCCCCceEEEeccCCeEeeeccc---ccCccc
Q psy15553 99 LCPECDNPETDLVVSAKKGTIQQVCKA---CGFHGM 131 (489)
Q Consensus 99 lC~~C~~PeT~l~~~~k~~~~~l~C~A---CG~~~~ 131 (489)
.||.|+.+ .+.+..+.+ -+..|.. |++..+
T Consensus 576 ~CP~Cg~~--~~~~~~~~g-kf~gCs~y~~C~~~~~ 608 (610)
T TIGR01051 576 DCPLCGRP--MVVKLGKYG-PFLACSNFPECKYTKS 608 (610)
T ss_pred CCCCCCCe--eEEEecCCC-ceeeCCCCCCCCCCCC
Confidence 49999874 222211222 3567766 665544
No 185
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=21.59 E-value=49 Score=34.41 Aligned_cols=32 Identities=25% Similarity=0.605 Sum_probs=24.7
Q ss_pred ccCCCCCC-CCceEEEec--cCCeEeeecccccCc
Q psy15553 98 VLCPECDN-PETDLVVSA--KKGTIQQVCKACGFH 129 (489)
Q Consensus 98 VlC~~C~~-PeT~l~~~~--k~~~~~l~C~ACG~~ 129 (489)
-.||.|+| |=+.++... ..++-+++|.-|-..
T Consensus 186 ~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~te 220 (308)
T COG3058 186 QYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETE 220 (308)
T ss_pred ccCCCcCCCCcceeeeecCccccchhhhhhhHHHH
Confidence 47999996 678888754 257789999999654
No 186
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.38 E-value=1.2e+02 Score=27.84 Aligned_cols=41 Identities=22% Similarity=0.479 Sum_probs=28.0
Q ss_pred HHhhcccCCCCCCCCceEEEecc-CCeEeeecccccCcccccc
Q psy15553 93 FIRKFVLCPECDNPETDLVVSAK-KGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 93 fI~~yVlC~~C~~PeT~l~~~~k-~~~~~l~C~ACG~~~~v~~ 134 (489)
+...-+-||-|++.. ....... .+.---+|+.||....+..
T Consensus 26 ~~~~~~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 26 MQITKVNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred hhcccCcCCCCCccc-eeeECCccccccccccCCcCcceeeec
Confidence 334448999999998 4443211 2244668999999988854
No 187
>KOG2691|consensus
Probab=21.12 E-value=91 Score=28.09 Aligned_cols=60 Identities=22% Similarity=0.427 Sum_probs=39.9
Q ss_pred CCCeEEE-EeccchHHHHHHHHHHHh-------hcccCCCCCCCCceEEEeccCC-----eEeeecccccCcc
Q psy15553 71 KNDRFIV-NGSHDVVKLQDLLDGFIR-------KFVLCPECDNPETDLVVSAKKG-----TIQQVCKACGFHG 130 (489)
Q Consensus 71 ~~~r~ii-nG~~~~~~lq~~L~~fI~-------~yVlC~~C~~PeT~l~~~~k~~-----~~~l~C~ACG~~~ 130 (489)
++.++-+ +|+|+...+..++..-+. .-.-||.|+.-+-...-...++ .++-.|-.||++-
T Consensus 39 ~s~~vY~~~~~~e~dE~t~ii~Dl~~DPTLPrts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h~w 111 (113)
T KOG2691|consen 39 DSSRVYVNELSHEHDELTQIIMDLASDPTLPRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGHRW 111 (113)
T ss_pred CCcceEcCCcccchhhHHHHHHhhccCCCcCccccccCCccCCcceEEEecccccccceEEEEEEeccccccc
Confidence 4555545 488888888777765442 2467999999988877531111 2567787899864
No 188
>PHA02942 putative transposase; Provisional
Probab=21.04 E-value=46 Score=35.69 Aligned_cols=31 Identities=23% Similarity=0.667 Sum_probs=21.7
Q ss_pred ccCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 98 VLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
-.||.|+.....+ .++ ...|..||+...-|.
T Consensus 326 q~Cs~CG~~~~~l----~~r--~f~C~~CG~~~drD~ 356 (383)
T PHA02942 326 VSCPKCGHKMVEI----AHR--YFHCPSCGYENDRDV 356 (383)
T ss_pred ccCCCCCCccCcC----CCC--EEECCCCCCEeCcHH
Confidence 4699999865432 234 578999999876553
No 189
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=20.95 E-value=52 Score=27.57 Aligned_cols=13 Identities=31% Similarity=0.567 Sum_probs=10.4
Q ss_pred CeEeeecccccCc
Q psy15553 117 GTIQQVCKACGFH 129 (489)
Q Consensus 117 ~~~~l~C~ACG~~ 129 (489)
+.-.|.|.|||..
T Consensus 54 ~~~tLsCsACGS~ 66 (74)
T PF05077_consen 54 KGNTLSCSACGSE 66 (74)
T ss_pred CCCeEeehhcccc
Confidence 3468999999975
No 190
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=20.86 E-value=69 Score=22.81 Aligned_cols=28 Identities=29% Similarity=0.571 Sum_probs=23.1
Q ss_pred echHHHHHHhCCCCChhhhHHHHhhcCc
Q psy15553 38 VNMADVAKAIGRPPTYPTKYFGCELGAQ 65 (489)
Q Consensus 38 ~N~~dIakaL~R~p~~~~kyf~~ELGa~ 65 (489)
..+.+||..++=.|.|+.+-|..++|..
T Consensus 9 ~~l~~iA~~~g~S~~~f~r~Fk~~~g~t 36 (42)
T PF00165_consen 9 LTLEDIAEQAGFSPSYFSRLFKKETGMT 36 (42)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 3689999999999999999999999975
No 191
>PRK02935 hypothetical protein; Provisional
Probab=20.75 E-value=58 Score=29.21 Aligned_cols=30 Identities=30% Similarity=0.639 Sum_probs=20.9
Q ss_pred ccCCCCCCCCceEEEeccCCeEeeecccccCcccccc
Q psy15553 98 VLCPECDNPETDLVVSAKKGTIQQVCKACGFHGMLQF 134 (489)
Q Consensus 98 VlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~~~~v~~ 134 (489)
|.||+|+.|---|-+ .-.|--|+..=++|+
T Consensus 71 V~CP~C~K~TKmLGr-------vD~CM~C~~PLTLd~ 100 (110)
T PRK02935 71 VICPSCEKPTKMLGR-------VDACMHCNQPLTLDR 100 (110)
T ss_pred eECCCCCchhhhccc-------eeecCcCCCcCCcCc
Confidence 799999987443333 236888988777664
No 192
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=20.73 E-value=53 Score=34.39 Aligned_cols=37 Identities=24% Similarity=0.529 Sum_probs=26.0
Q ss_pred cccCCCCCCCCc-eEEEec--cCCeEeeecccccCccccc
Q psy15553 97 FVLCPECDNPET-DLVVSA--KKGTIQQVCKACGFHGMLQ 133 (489)
Q Consensus 97 yVlC~~C~~PeT-~l~~~~--k~~~~~l~C~ACG~~~~v~ 133 (489)
--.||.|+++=+ .+++.. +.+.-++.|.-|+..-.+.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~ 223 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV 223 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccccc
Confidence 348999998764 344321 3567799999999886553
No 193
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.63 E-value=1.4e+02 Score=21.32 Aligned_cols=45 Identities=18% Similarity=0.140 Sum_probs=31.4
Q ss_pred chHHHHHHhCCCCChhhhHHHHhhcCceeeecCCCeEEEEeccchHHHHHH
Q psy15553 39 NMADVAKAIGRPPTYPTKYFGCELGAQTKLDHKNDRFIVNGSHDVVKLQDL 89 (489)
Q Consensus 39 N~~dIakaL~R~p~~~~kyf~~ELGa~~~~d~~~~r~iinG~~~~~~lq~~ 89 (489)
++.++|+.|+-++..|-.|...-+.. .... .+++. .|+...|..+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g~l~-~~~~-~~~~~----~y~~~~v~~l 46 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIGLLS-PART-EGGYR----LYSDADLERL 46 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCCCC-CCcC-CCCCE----EeCHHHHHHh
Confidence 57899999999999999998777765 3333 23433 2666666654
No 194
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=20.50 E-value=50 Score=32.30 Aligned_cols=32 Identities=25% Similarity=0.552 Sum_probs=22.7
Q ss_pred cCCCCCCCCceEEEe-ccCCeEeeecccccCcc
Q psy15553 99 LCPECDNPETDLVVS-AKKGTIQQVCKACGFHG 130 (489)
Q Consensus 99 lC~~C~~PeT~l~~~-~k~~~~~l~C~ACG~~~ 130 (489)
.|-+|+.|=..|-+. +.+..-..+|..||+.-
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~va 34 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVA 34 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCCcc
Confidence 599999996555443 23445588999999653
No 195
>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=20.48 E-value=1.1e+02 Score=21.83 Aligned_cols=9 Identities=44% Similarity=0.914 Sum_probs=6.7
Q ss_pred ecccccCcc
Q psy15553 122 VCKACGFHG 130 (489)
Q Consensus 122 ~C~ACG~~~ 130 (489)
.|..||..-
T Consensus 34 ~C~~CGE~~ 42 (46)
T TIGR03831 34 VCPQCGEEY 42 (46)
T ss_pred ccccCCCEe
Confidence 599998753
No 196
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=20.45 E-value=47 Score=28.90 Aligned_cols=25 Identities=24% Similarity=0.778 Sum_probs=20.0
Q ss_pred hcccCCCCCCCCceEEEeccCCeEeeecccccC
Q psy15553 96 KFVLCPECDNPETDLVVSAKKGTIQQVCKACGF 128 (489)
Q Consensus 96 ~yVlC~~C~~PeT~l~~~~k~~~~~l~C~ACG~ 128 (489)
..+||.-|++---.+.+ ..|.+||+
T Consensus 15 tHtlCrRCG~~syH~qK--------~~CasCGy 39 (91)
T PTZ00073 15 THTLCRRCGKRSFHVQK--------KRCASCGY 39 (91)
T ss_pred CcchhcccCcccccccc--------ccchhcCC
Confidence 46899999988777765 24999999
Done!