Query 013311
Match_columns 445
No_of_seqs 282 out of 735
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 02:34:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013311.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013311hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2767 Translation initiation 100.0 2E-107 5E-112 801.6 25.3 388 2-445 1-396 (400)
2 smart00653 eIF2B_5 domain pres 100.0 8.4E-45 1.8E-49 313.1 13.2 110 15-129 1-110 (110)
3 PF01873 eIF-5_eIF-2B: Domain 100.0 5.8E-45 1.2E-49 320.8 11.3 121 3-130 4-124 (125)
4 TIGR00311 aIF-2beta translatio 100.0 2.1E-43 4.5E-48 313.7 13.1 113 15-134 20-132 (133)
5 PRK03988 translation initiatio 100.0 7.6E-43 1.7E-47 311.9 13.7 115 13-134 23-137 (138)
6 PRK12336 translation initiatio 100.0 2.6E-41 5.7E-46 320.5 13.5 118 11-135 17-134 (201)
7 KOG2768 Translation initiation 100.0 5.9E-32 1.3E-36 252.5 6.4 116 15-136 103-218 (231)
8 COG1601 GCD7 Translation initi 100.0 7.6E-30 1.7E-34 230.5 5.5 111 17-133 29-139 (151)
9 KOG2297 Predicted translation 99.9 3.3E-22 7.2E-27 196.9 12.1 134 295-443 270-412 (412)
10 PF02020 W2: eIF4-gamma/eIF5/e 99.9 1.2E-21 2.6E-26 161.6 7.5 79 365-445 2-83 (84)
11 smart00515 eIF5C Domain at the 99.8 1.8E-20 4E-25 154.0 8.0 83 354-438 1-83 (83)
12 KOG1461 Translation initiation 99.8 1.6E-18 3.4E-23 183.8 14.2 148 297-445 510-672 (673)
13 PF09090 MIF4G_like_2: MIF4G l 96.7 0.034 7.3E-07 54.9 13.8 118 293-414 7-136 (253)
14 COG1326 Uncharacterized archae 94.9 0.0081 1.8E-07 56.9 0.4 36 97-132 5-42 (201)
15 PF12677 DUF3797: Domain of un 94.6 0.033 7.1E-07 41.4 2.7 32 95-128 10-46 (49)
16 TIGR02443 conserved hypothetic 93.2 0.096 2.1E-06 40.6 3.1 40 93-133 5-44 (59)
17 PF09526 DUF2387: Probable met 92.8 0.075 1.6E-06 42.8 2.2 40 93-133 4-43 (71)
18 PF01253 SUI1: Translation ini 91.5 0.43 9.3E-06 39.2 5.3 73 19-95 3-79 (83)
19 PRK00464 nrdR transcriptional 91.2 0.18 3.9E-06 46.5 3.1 33 100-132 2-40 (154)
20 smart00440 ZnF_C2C2 C2C2 Zinc 90.2 0.35 7.6E-06 34.5 3.2 30 100-129 2-37 (40)
21 PF01096 TFIIS_C: Transcriptio 89.0 0.28 6.2E-06 34.8 1.9 31 99-129 1-37 (39)
22 PF01921 tRNA-synt_1f: tRNA sy 88.1 0.5 1.1E-05 49.2 3.8 54 83-136 150-215 (360)
23 PF14354 Lar_restr_allev: Rest 87.9 0.48 1E-05 36.3 2.7 29 99-128 4-37 (61)
24 TIGR00244 transcriptional regu 87.6 0.48 1E-05 43.3 3.0 32 100-131 2-39 (147)
25 PRK09710 lar restriction allev 86.9 0.93 2E-05 35.8 3.8 34 100-134 8-41 (64)
26 TIGR03655 anti_R_Lar restricti 86.4 0.78 1.7E-05 34.5 3.1 33 100-132 3-38 (53)
27 TIGR01159 DRP1 density-regulat 83.7 3 6.5E-05 39.3 6.3 72 19-94 87-162 (173)
28 PHA02998 RNA polymerase subuni 83.1 1.2 2.6E-05 42.0 3.3 82 41-131 87-182 (195)
29 PF14803 Nudix_N_2: Nudix N-te 81.9 0.76 1.6E-05 31.8 1.2 30 100-129 2-31 (34)
30 COG1384 LysS Lysyl-tRNA synthe 81.0 2.1 4.5E-05 46.5 4.7 50 85-135 149-209 (521)
31 PRK14892 putative transcriptio 81.0 1.1 2.3E-05 38.6 2.0 37 96-133 19-55 (99)
32 cd00674 LysRS_core_class_I cat 81.0 1.6 3.5E-05 45.4 3.8 93 41-135 89-207 (353)
33 cd00474 SUI1_eIF1 The SUI1/eIF 80.9 3.9 8.5E-05 33.4 5.3 59 24-88 3-62 (77)
34 PF14205 Cys_rich_KTR: Cystein 80.9 0.54 1.2E-05 35.9 0.2 48 97-146 3-53 (55)
35 PF08271 TF_Zn_Ribbon: TFIIB z 80.6 1.1 2.5E-05 32.1 1.8 28 100-130 2-29 (43)
36 PF13719 zinc_ribbon_5: zinc-r 80.1 0.9 2E-05 31.8 1.1 31 98-131 2-36 (37)
37 PRK00750 lysK lysyl-tRNA synth 78.3 2.6 5.6E-05 46.0 4.4 51 85-136 153-215 (510)
38 PF12760 Zn_Tnp_IS1595: Transp 78.1 2.1 4.6E-05 31.2 2.6 30 96-129 17-46 (46)
39 COG2051 RPS27A Ribosomal prote 77.8 1.3 2.8E-05 35.2 1.5 29 98-129 19-47 (67)
40 PRK00415 rps27e 30S ribosomal 75.3 2.1 4.5E-05 33.4 1.9 30 98-130 11-40 (59)
41 PF11331 DUF3133: Protein of u 75.0 1.2 2.7E-05 32.9 0.6 34 98-132 6-43 (46)
42 TIGR00467 lysS_arch lysyl-tRNA 75.0 3.5 7.6E-05 45.1 4.3 51 84-135 145-205 (515)
43 smart00661 RPOL9 RNA polymeras 72.9 2.5 5.5E-05 31.0 1.9 32 100-134 2-34 (52)
44 PF05129 Elf1: Transcription e 71.5 2.9 6.4E-05 34.4 2.1 39 95-133 19-59 (81)
45 PRK00939 translation initiatio 71.0 10 0.00022 32.5 5.4 64 23-93 26-90 (99)
46 TIGR01384 TFS_arch transcripti 68.5 4.6 9.9E-05 34.2 2.8 33 98-130 62-100 (104)
47 KOG1104 Nuclear cap-binding co 68.4 64 0.0014 36.8 12.1 113 299-415 502-623 (759)
48 TIGR01385 TFSII transcription 67.9 4.9 0.00011 41.0 3.3 55 75-129 206-295 (299)
49 cd00202 ZnF_GATA Zinc finger D 67.5 1.9 4.2E-05 32.8 0.2 32 100-132 1-33 (54)
50 PF04216 FdhE: Protein involve 67.4 3 6.4E-05 42.0 1.6 35 99-133 173-210 (290)
51 PF10474 DUF2451: Protein of u 66.7 54 0.0012 32.2 10.2 82 328-418 119-205 (234)
52 smart00401 ZnF_GATA zinc finge 66.3 3.2 6.9E-05 31.3 1.2 33 99-132 4-37 (52)
53 TIGR01158 SUI1_rel translation 65.3 16 0.00035 31.3 5.5 63 23-92 26-90 (101)
54 PF13453 zf-TFIIB: Transcripti 65.1 7.6 0.00017 27.5 2.9 28 100-129 1-28 (41)
55 PF02150 RNA_POL_M_15KD: RNA p 65.1 4.6 9.9E-05 28.0 1.7 29 100-133 3-33 (35)
56 COG1327 Predicted transcriptio 64.7 4.6 0.0001 37.2 2.1 32 100-131 2-39 (156)
57 PRK08665 ribonucleotide-diphos 64.6 7.2 0.00016 44.7 4.1 41 84-130 688-750 (752)
58 TIGR00340 zpr1_rel ZPR1-relate 64.3 5.9 0.00013 36.9 2.8 31 101-131 1-39 (163)
59 smart00531 TFIIE Transcription 64.2 15 0.00032 33.3 5.4 94 40-133 17-136 (147)
60 PHA00626 hypothetical protein 63.7 5.5 0.00012 30.8 2.0 34 100-133 2-36 (59)
61 TIGR02159 PA_CoA_Oxy4 phenylac 63.3 3.2 6.9E-05 38.0 0.8 31 99-129 106-139 (146)
62 PF09855 DUF2082: Nucleic-acid 62.5 8 0.00017 30.6 2.8 32 100-131 2-47 (64)
63 COG1997 RPL43A Ribosomal prote 62.2 6.9 0.00015 32.8 2.5 44 84-132 22-65 (89)
64 PRK00241 nudC NADH pyrophospha 61.8 6.9 0.00015 38.9 3.0 41 89-133 90-130 (256)
65 COG4888 Uncharacterized Zn rib 61.4 6.7 0.00014 33.8 2.3 38 95-133 19-59 (104)
66 KOG2906 RNA polymerase III sub 61.0 8.7 0.00019 33.0 3.0 31 100-133 3-34 (105)
67 PF03367 zf-ZPR1: ZPR1 zinc-fi 60.9 6 0.00013 36.7 2.2 33 99-131 2-41 (161)
68 TIGR00310 ZPR1_znf ZPR1 zinc f 60.4 8.4 0.00018 36.9 3.2 32 100-131 2-41 (192)
69 smart00709 Zpr1 Duplicated dom 59.9 8.5 0.00018 35.7 3.0 32 100-131 2-40 (160)
70 PF13717 zinc_ribbon_4: zinc-r 59.7 4.1 8.9E-05 28.4 0.7 29 98-129 2-34 (36)
71 PLN00209 ribosomal protein S27 59.4 7.1 0.00015 32.7 2.1 30 98-130 36-65 (86)
72 COG1779 C4-type Zn-finger prot 58.6 8.1 0.00017 37.1 2.7 33 98-131 14-54 (201)
73 COG3478 Predicted nucleic-acid 58.3 9.2 0.0002 30.4 2.5 36 98-133 4-53 (68)
74 PRK00398 rpoP DNA-directed RNA 58.3 8.9 0.00019 27.8 2.3 35 99-137 4-38 (46)
75 PRK03954 ribonuclease P protei 57.1 9.3 0.0002 34.0 2.6 39 93-133 60-106 (121)
76 COG2835 Uncharacterized conser 56.9 6.6 0.00014 30.7 1.5 33 97-133 7-39 (60)
77 COG1594 RPB9 DNA-directed RNA 56.9 9.4 0.0002 33.4 2.6 33 98-130 72-110 (113)
78 TIGR00100 hypA hydrogenase nic 56.3 9 0.0002 33.5 2.4 28 49-79 38-65 (115)
79 COG3529 Predicted nucleic-acid 56.2 2.1 4.5E-05 33.5 -1.4 38 92-130 5-42 (66)
80 PRK03564 formate dehydrogenase 55.5 8.9 0.00019 39.3 2.6 36 98-133 187-225 (309)
81 COG3058 FdhE Uncharacterized p 55.2 5.9 0.00013 40.0 1.2 31 98-128 185-219 (308)
82 TIGR01562 FdhE formate dehydro 54.8 6.8 0.00015 40.1 1.6 36 98-133 184-223 (305)
83 PTZ00083 40S ribosomal protein 54.3 10 0.00022 31.7 2.2 30 98-130 35-64 (85)
84 PF00320 GATA: GATA zinc finge 53.8 3.3 7.1E-05 28.8 -0.6 29 101-129 1-29 (36)
85 PRK07451 translation initiatio 53.6 31 0.00068 30.4 5.3 59 24-88 43-101 (115)
86 PF01927 Mut7-C: Mut7-C RNAse 52.1 21 0.00046 32.3 4.2 58 76-133 63-137 (147)
87 cd04762 HTH_MerR-trunc Helix-T 51.9 38 0.00083 23.3 4.8 46 40-91 2-47 (49)
88 PF05379 Peptidase_C23: Carlav 51.9 12 0.00025 31.5 2.3 66 41-116 7-73 (89)
89 PRK00564 hypA hydrogenase nick 51.8 12 0.00026 32.8 2.5 28 49-79 38-66 (117)
90 PF09297 zf-NADH-PPase: NADH p 51.8 3.9 8.4E-05 27.5 -0.5 28 98-129 3-30 (32)
91 PF14353 CpXC: CpXC protein 51.0 14 0.0003 32.4 2.8 35 99-133 2-51 (128)
92 PRK00420 hypothetical protein; 49.9 19 0.00041 31.6 3.4 41 91-136 16-56 (112)
93 PRK03824 hypA hydrogenase nick 49.7 13 0.00028 33.5 2.4 49 41-106 30-78 (135)
94 COG1645 Uncharacterized Zn-fin 49.0 12 0.00027 33.6 2.1 24 100-129 30-53 (131)
95 PF01396 zf-C4_Topoisom: Topoi 48.6 21 0.00046 25.2 2.9 33 99-133 2-37 (39)
96 PRK03681 hypA hydrogenase nick 48.6 13 0.00029 32.4 2.3 28 49-79 38-65 (114)
97 KOG2703 C4-type Zn-finger prot 48.4 11 0.00025 39.7 2.0 32 100-131 260-298 (460)
98 PRK00423 tfb transcription ini 48.3 12 0.00026 38.1 2.3 29 98-129 11-39 (310)
99 TIGR01391 dnaG DNA primase, ca 46.4 21 0.00045 38.0 3.7 33 99-132 35-67 (415)
100 PF10058 DUF2296: Predicted in 46.3 15 0.00033 28.0 1.9 31 99-129 23-53 (54)
101 PRK12380 hydrogenase nickel in 46.2 16 0.00034 31.9 2.3 28 49-79 38-65 (113)
102 PRK05580 primosome assembly pr 46.0 17 0.00037 41.1 3.1 50 98-148 381-452 (679)
103 KOG2907 RNA polymerase I trans 45.8 12 0.00026 32.8 1.5 33 100-132 76-114 (116)
104 smart00834 CxxC_CXXC_SSSS Puta 45.8 14 0.00029 25.6 1.5 28 100-128 7-34 (41)
105 PF01667 Ribosomal_S27e: Ribos 45.8 5.6 0.00012 30.6 -0.5 30 98-130 7-36 (55)
106 PRK00762 hypA hydrogenase nick 45.6 17 0.00038 32.1 2.6 28 49-79 38-65 (124)
107 PRK11827 hypothetical protein; 45.4 14 0.0003 29.0 1.6 36 94-133 4-39 (60)
108 PF05315 ICEA: ICEA Protein; 45.2 9.2 0.0002 36.9 0.8 67 48-114 44-117 (230)
109 PRK00432 30S ribosomal protein 45.1 14 0.00031 27.7 1.6 28 98-130 20-47 (50)
110 PRK05667 dnaG DNA primase; Val 45.0 31 0.00067 38.4 4.9 32 100-132 38-69 (580)
111 smart00778 Prim_Zn_Ribbon Zinc 43.4 17 0.00036 25.7 1.7 31 98-128 3-33 (37)
112 COG0023 SUI1 Translation initi 42.2 1E+02 0.0022 26.8 6.6 74 12-91 11-92 (104)
113 TIGR01206 lysW lysine biosynth 41.9 22 0.00047 27.2 2.2 31 100-133 4-35 (54)
114 COG1096 Predicted RNA-binding 41.5 18 0.00039 34.5 2.1 27 98-130 149-175 (188)
115 COG3741 HutG N-formylglutamate 40.2 6.8 0.00015 39.2 -1.0 108 33-143 62-172 (272)
116 TIGR02098 MJ0042_CXXC MJ0042 f 39.8 14 0.0003 25.5 0.8 30 98-130 2-35 (38)
117 PRK12286 rpmF 50S ribosomal pr 39.2 22 0.00049 27.4 1.9 27 94-129 23-49 (57)
118 PF06107 DUF951: Bacterial pro 39.2 37 0.0008 26.4 3.1 35 103-139 15-49 (57)
119 PF04760 IF2_N: Translation in 38.8 29 0.00063 25.8 2.5 26 41-66 6-31 (54)
120 COG1594 RPB9 DNA-directed RNA 38.5 16 0.00035 31.9 1.2 45 100-147 4-49 (113)
121 KOG3221 Glycolipid transfer pr 38.1 2E+02 0.0044 27.7 8.5 45 332-380 133-177 (199)
122 PF08535 KorB: KorB domain; I 37.9 24 0.00051 29.3 2.1 21 41-61 6-26 (93)
123 COG1499 NMD3 NMD protein affec 37.8 23 0.0005 37.0 2.4 33 100-132 23-55 (355)
124 COG0777 AccD Acetyl-CoA carbox 37.7 13 0.00028 37.6 0.5 44 98-144 28-71 (294)
125 PRK08332 ribonucleotide-diphos 37.2 29 0.00063 43.3 3.4 42 88-132 1695-1738(1740)
126 PF04032 Rpr2: RNAse P Rpr2/Rp 36.6 32 0.0007 27.6 2.7 30 99-128 47-85 (85)
127 PF13936 HTH_38: Helix-turn-he 36.6 30 0.00066 24.8 2.2 22 39-60 21-42 (44)
128 PF09723 Zn-ribbon_8: Zinc rib 36.3 22 0.00048 25.4 1.4 29 100-129 7-35 (42)
129 PF06044 DRP: Dam-replacing fa 36.1 26 0.00056 34.8 2.3 55 82-136 14-69 (254)
130 PRK07562 ribonucleotide-diphos 36.0 27 0.00058 42.0 2.8 40 86-132 1180-1219(1220)
131 PF07282 OrfB_Zn_ribbon: Putat 35.9 23 0.00049 27.5 1.6 31 99-133 29-59 (69)
132 PF06677 Auto_anti-p27: Sjogre 35.5 66 0.0014 23.2 3.7 35 88-127 7-41 (41)
133 PF08274 PhnA_Zn_Ribbon: PhnA 35.2 14 0.00031 24.9 0.2 27 98-129 2-28 (30)
134 TIGR03826 YvyF flagellar opero 35.0 27 0.00059 31.7 2.1 44 39-107 47-90 (137)
135 TIGR01160 SUI1_MOF2 translatio 34.8 58 0.0012 28.5 4.0 65 23-93 28-97 (110)
136 PRK11823 DNA repair protein Ra 34.6 22 0.00048 38.1 1.7 27 100-134 9-35 (446)
137 COG0375 HybF Zn finger protein 34.4 32 0.0007 30.3 2.4 49 59-113 46-101 (115)
138 PF00165 HTH_AraC: Bacterial r 34.4 48 0.001 23.0 2.9 28 39-66 9-36 (42)
139 PF14599 zinc_ribbon_6: Zinc-r 34.0 20 0.00044 28.1 1.0 31 97-131 29-59 (61)
140 PRK14973 DNA topoisomerase I; 33.8 25 0.00054 41.4 2.1 33 100-132 637-669 (936)
141 cd03031 GRX_GRX_like Glutaredo 33.5 35 0.00076 31.2 2.6 50 82-132 81-145 (147)
142 COG1198 PriA Primosomal protei 33.4 30 0.00066 39.6 2.6 36 98-134 435-476 (730)
143 PF03966 Trm112p: Trm112p-like 33.1 32 0.00068 27.0 2.0 14 120-133 53-66 (68)
144 PF03811 Zn_Tnp_IS1: InsA N-te 32.8 41 0.0009 23.5 2.3 29 98-126 5-35 (36)
145 KOG3507 DNA-directed RNA polym 32.4 13 0.00028 29.0 -0.3 32 99-135 21-52 (62)
146 PRK06319 DNA topoisomerase I/S 32.3 49 0.0011 38.6 4.1 33 100-133 594-629 (860)
147 TIGR00416 sms DNA repair prote 32.2 26 0.00057 37.7 1.8 27 100-134 9-35 (454)
148 PF09862 DUF2089: Protein of u 31.9 38 0.00082 29.8 2.4 21 101-129 1-21 (113)
149 PRK09019 translation initiatio 31.9 95 0.0021 27.1 4.9 57 26-88 38-94 (108)
150 PRK05654 acetyl-CoA carboxylas 31.6 13 0.00028 37.9 -0.6 43 98-143 27-69 (292)
151 COG2093 DNA-directed RNA polym 31.3 23 0.00049 28.0 0.9 11 100-110 20-30 (64)
152 TIGR00515 accD acetyl-CoA carb 31.2 12 0.00027 37.8 -0.8 43 98-143 26-68 (285)
153 PF06573 Churchill: Churchill 31.1 42 0.0009 29.3 2.5 36 94-129 23-67 (112)
154 PF01807 zf-CHC2: CHC2 zinc fi 30.9 29 0.00062 29.2 1.5 32 99-132 34-66 (97)
155 PF15494 SRCR_2: Scavenger rec 30.8 31 0.00067 28.9 1.7 15 116-130 84-98 (98)
156 PF03604 DNA_RNApol_7kD: DNA d 30.7 20 0.00044 24.5 0.4 28 100-132 2-29 (32)
157 cd01121 Sms Sms (bacterial rad 30.3 29 0.00064 36.4 1.8 27 100-134 2-28 (372)
158 COG1996 RPC10 DNA-directed RNA 30.0 19 0.00041 27.1 0.2 35 100-138 8-42 (49)
159 cd02983 P5_C P5 family, C-term 29.9 61 0.0013 28.7 3.5 57 41-97 46-117 (130)
160 COG1405 SUA7 Transcription ini 29.9 32 0.0007 34.9 1.9 28 100-130 3-30 (285)
161 TIGR03830 CxxCG_CxxCG_HTH puta 29.8 48 0.001 28.5 2.8 32 101-132 1-43 (127)
162 PF12898 Stc1: Stc1 domain; I 29.8 54 0.0012 27.1 2.9 51 74-133 6-63 (84)
163 COG1149 MinD superfamily P-loo 29.5 64 0.0014 32.8 3.9 104 24-144 4-128 (284)
164 COG1571 Predicted DNA-binding 29.5 24 0.00053 37.6 1.0 37 94-135 346-382 (421)
165 PHA02540 61 DNA primase; Provi 29.4 45 0.00097 34.7 2.9 34 99-132 28-67 (337)
166 smart00400 ZnF_CHCC zinc finge 29.3 54 0.0012 24.5 2.6 32 100-132 4-35 (55)
167 cd04761 HTH_MerR-SF Helix-Turn 29.3 1.3E+02 0.0027 21.1 4.5 45 40-90 2-46 (49)
168 PF11781 RRN7: RNA polymerase 29.3 42 0.00091 23.4 1.8 26 100-130 10-35 (36)
169 smart00659 RPOLCX RNA polymera 29.2 40 0.00086 24.6 1.8 31 100-135 4-34 (44)
170 TIGR00595 priA primosomal prot 28.8 37 0.0008 37.0 2.3 44 101-148 225-284 (505)
171 smart00647 IBR In Between Ring 28.8 76 0.0016 23.6 3.4 40 89-131 6-51 (64)
172 PF02847 MA3: MA3 domain; Int 28.5 3.4E+02 0.0075 22.5 10.4 96 302-402 8-112 (113)
173 PF00123 Hormone_2: Peptide ho 28.4 38 0.00082 22.5 1.4 11 426-436 17-27 (28)
174 PF01155 HypA: Hydrogenase exp 28.1 52 0.0011 28.6 2.6 50 51-113 40-101 (113)
175 PF12172 DUF35_N: Rubredoxin-l 27.8 36 0.00078 23.4 1.3 17 115-131 6-22 (37)
176 PF05876 Terminase_GpA: Phage 27.7 47 0.001 36.7 2.9 49 98-146 200-258 (557)
177 TIGR02609 doc_partner putative 27.7 81 0.0018 25.3 3.5 47 52-98 15-65 (74)
178 PF05046 Img2: Mitochondrial l 27.6 2.2E+02 0.0049 23.5 6.3 67 20-91 14-82 (87)
179 COG1066 Sms Predicted ATP-depe 27.5 32 0.00069 36.9 1.4 28 98-133 7-34 (456)
180 TIGR01031 rpmF_bact ribosomal 27.3 43 0.00092 25.6 1.7 25 96-129 24-48 (55)
181 PF04502 DUF572: Family of unk 27.2 27 0.00058 36.0 0.8 25 119-143 76-100 (324)
182 PF08792 A2L_zn_ribbon: A2L zi 27.0 56 0.0012 22.4 2.1 30 98-131 3-32 (33)
183 CHL00174 accD acetyl-CoA carbo 26.8 17 0.00037 37.1 -0.6 43 98-144 38-81 (296)
184 TIGR03831 YgiT_finger YgiT-typ 26.4 71 0.0015 22.3 2.7 10 121-130 33-42 (46)
185 PRK03824 hypA hydrogenase nick 26.3 28 0.0006 31.3 0.6 43 84-133 41-83 (135)
186 PF05180 zf-DNL: DNL zinc fing 26.1 31 0.00068 27.5 0.8 39 100-138 6-47 (66)
187 PRK00378 nucleoid-associated p 26.0 1.4E+02 0.003 30.6 5.8 50 25-96 283-332 (334)
188 KOG3084 NADH pyrophosphatase I 25.3 57 0.0012 33.8 2.7 25 88-113 140-164 (345)
189 PRK02935 hypothetical protein; 25.2 44 0.00095 29.1 1.6 31 99-135 71-101 (110)
190 smart00419 HTH_CRP helix_turn_ 25.2 1.6E+02 0.0034 20.3 4.4 39 39-78 9-47 (48)
191 PRK06556 vitamin B12-dependent 25.2 60 0.0013 38.4 3.2 46 81-132 907-952 (953)
192 PRK06824 translation initiatio 25.0 1.6E+02 0.0035 26.1 5.2 55 28-88 50-104 (118)
193 KOG1603 Copper chaperone [Inor 24.9 1.3E+02 0.0027 23.8 4.2 41 53-93 20-61 (73)
194 PHA02942 putative transposase; 24.8 35 0.00076 36.0 1.2 30 99-133 326-355 (383)
195 TIGR03829 YokU_near_AblA uncha 24.6 51 0.0011 27.8 1.9 24 117-140 32-56 (89)
196 PF13597 NRDD: Anaerobic ribon 24.6 40 0.00087 37.2 1.6 53 81-143 463-526 (546)
197 COG2023 RPR2 RNase P subunit R 24.5 74 0.0016 27.7 2.8 34 100-133 58-95 (105)
198 PRK07220 DNA topoisomerase I; 23.9 54 0.0012 37.6 2.5 30 99-128 636-665 (740)
199 COG2956 Predicted N-acetylgluc 23.5 1.9E+02 0.0042 30.3 6.1 76 44-136 305-384 (389)
200 PF04423 Rad50_zn_hook: Rad50 23.3 43 0.00094 25.0 1.1 17 91-107 9-29 (54)
201 PF15288 zf-CCHC_6: Zinc knuck 23.3 32 0.0007 24.8 0.4 13 121-133 2-14 (40)
202 PRK06393 rpoE DNA-directed RNA 23.2 41 0.00089 26.7 1.0 39 97-148 4-42 (64)
203 PF09851 SHOCT: Short C-termin 23.0 84 0.0018 21.0 2.3 18 391-408 6-23 (31)
204 COG0675 Transposase and inacti 23.0 46 0.001 32.8 1.6 25 99-132 310-334 (364)
205 PF04981 NMD3: NMD3 family ; 22.9 41 0.00088 32.9 1.1 34 99-132 14-47 (236)
206 TIGR01464 hemE uroporphyrinoge 22.9 58 0.0012 33.2 2.3 56 50-111 264-326 (338)
207 PF14255 Cys_rich_CPXG: Cystei 22.8 74 0.0016 24.1 2.3 35 99-133 1-37 (52)
208 TIGR02494 PFLE_PFLC glycyl-rad 22.8 37 0.00081 33.7 0.9 36 94-131 20-58 (295)
209 PRK07111 anaerobic ribonucleos 22.6 81 0.0018 36.2 3.6 51 82-142 654-714 (735)
210 KOG1824 TATA-binding protein-i 22.6 3.2E+02 0.007 32.6 8.1 50 347-396 249-303 (1233)
211 smart00497 IENR1 Intron encode 22.6 1.9E+02 0.004 20.7 4.4 25 37-61 16-40 (53)
212 smart00070 GLUCA Glucagon like 22.5 54 0.0012 21.6 1.3 11 426-436 17-27 (27)
213 PRK06266 transcription initiat 22.4 56 0.0012 30.8 1.9 90 39-131 37-147 (178)
214 TIGR01566 ZF_HD_prot_N ZF-HD h 22.4 37 0.00081 25.8 0.6 17 117-133 33-49 (53)
215 KOG1597 Transcription initiati 22.3 54 0.0012 33.5 1.9 41 100-141 2-45 (308)
216 PTZ00255 60S ribosomal protein 22.3 74 0.0016 26.9 2.4 44 85-133 24-67 (90)
217 TIGR00373 conserved hypothetic 22.2 56 0.0012 30.1 1.8 89 39-130 29-138 (158)
218 PF07191 zinc-ribbons_6: zinc- 22.1 61 0.0013 26.2 1.8 25 99-129 2-26 (70)
219 PF02591 DUF164: Putative zinc 22.0 58 0.0012 24.5 1.6 23 82-106 32-54 (56)
220 PF11023 DUF2614: Protein of u 22.0 37 0.0008 29.9 0.6 31 98-134 69-99 (114)
221 smart00422 HTH_MERR helix_turn 21.7 2E+02 0.0044 21.6 4.7 46 40-90 2-47 (70)
222 PRK11788 tetratricopeptide rep 21.5 62 0.0013 32.6 2.2 45 85-137 339-385 (389)
223 PF04810 zf-Sec23_Sec24: Sec23 21.5 48 0.0011 23.4 1.0 33 99-134 3-38 (40)
224 PF04161 Arv1: Arv1-like famil 21.2 51 0.0011 31.6 1.4 31 100-130 2-34 (208)
225 KOG2989 Uncharacterized conser 21.1 43 0.00094 33.2 0.9 46 98-144 40-101 (253)
226 PF09733 VEFS-Box: VEFS-Box of 21.1 4.7E+02 0.01 23.8 7.5 40 370-409 90-135 (140)
227 TIGR01051 topA_bact DNA topois 20.9 92 0.002 34.9 3.5 54 77-132 537-609 (610)
228 TIGR00280 L37a ribosomal prote 20.8 78 0.0017 26.9 2.2 44 85-133 23-66 (91)
229 cd01106 HTH_TipAL-Mta Helix-Tu 20.5 1.9E+02 0.0042 24.1 4.7 47 40-91 2-48 (103)
230 PF13240 zinc_ribbon_2: zinc-r 20.4 53 0.0012 20.6 0.9 7 101-107 2-8 (23)
231 PRK09678 DNA-binding transcrip 20.1 1E+02 0.0022 25.0 2.7 33 100-133 3-42 (72)
232 PRK08402 replication factor A; 20.0 72 0.0016 33.4 2.3 45 76-131 197-241 (355)
No 1
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-107 Score=801.59 Aligned_cols=388 Identities=48% Similarity=0.734 Sum_probs=311.7
Q ss_pred ceeccCCCCCCCCcccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEee
Q 013311 2 ALQNIGASNSDDAFYRYKMPKMITKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGA 81 (445)
Q Consensus 2 a~ini~~~~~~d~~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~ 81 (445)
|+||| +|++.|||||||||++++|+||+||||||+|+||.+||+||+|||.|++|||||||||||+||.++|||||||+
T Consensus 1 a~iNI-nrsn~D~FYRYKMPrl~aKvEGKGNGIKTvIvNm~eIakAL~RPp~Y~tKyFGcELGAQT~fd~kn~ryiVNG~ 79 (400)
T KOG2767|consen 1 ASINI-NRSNRDPFYRYKMPRLQAKVEGKGNGIKTVIVNMVEIAKALGRPPLYPTKYFGCELGAQTKFDVKNGRYIVNGA 79 (400)
T ss_pred Ccccc-cccccchhhhhccchhhhhccccCCCeeeeeecHHHHHHHhCCCCCcccccceeeccccccccccCCeeeeccc
Confidence 58999 88999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCHHHHHHHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCcccccchhhhhHHHhcCCCCccccchhhHHHHH
Q 013311 82 HDTAKLAGLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDKLTTFILKNPPVQKKTSKDKKSLRR 161 (445)
Q Consensus 82 ~~~~~l~~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~k~pP~~~~~~k~~k~~~~ 161 (445)
|++.+||++|++||++|||||+|+||||.|+++++++|.++|+|||.++.+++||||++||+||||++.+++|++|+.+
T Consensus 80 Hd~~KLqdlLdgFIkKFVlC~~C~NPETel~itk~q~i~~~CkACG~r~~~d~rhKLs~fIlKNPP~~~~~s~~kk~~~- 158 (400)
T KOG2767|consen 80 HEASKLQDLLDGFIKKFVLCPSCENPETELIITKKQTISLKCKACGFRSDMDLRHKLSTFILKNPPEQKDSSKDKKKAE- 158 (400)
T ss_pred ccHHHHHHHHHHHHHHheeCcCCCCCceeEEecccchhhhHHHHcCCcccccchhhhcceeecCCcccccchhhhHHHH-
Confidence 9999999999999999999999999999999987899999999999999999999999999999999888888776543
Q ss_pred HHHHHhhhchhhhHHHHHHHhhhccccCCCCCCcchhcccccccccCCCCCCCCCCCc-cccCCCCCCCCCCCCCccccc
Q 013311 162 AEKERLKEGEAADEELKKIKKEAGKKKGSSANSKDVTAKGASTKKKAHSSDDDHSPSR-SQADENEPAIDDADDDDDIQW 240 (445)
Q Consensus 162 ~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~d~~~~~-~~~~~~~~~~~~~~~dddv~W 240 (445)
+++|.+ |.+ . +++|. +. .++..+.+ +..++. ..++..+.+ .+++||| |
T Consensus 159 -~k~R~~----------K~k-~--k~~g~----~s--------~~~~~~~~-~~~~~~i~~~a~~~t~--e~~DDdd--W 207 (400)
T KOG2767|consen 159 -KKERKG----------KSK-D--KKDGS----KS--------SKNETSPD-DSLSREIDPAAPLETA--EEDDDDD--W 207 (400)
T ss_pred -HHHhhh----------hcc-c--ccccc----cC--------CccCCCcc-cccccccccccCcccc--ccccccc--c
Confidence 222211 000 0 11221 00 00111121 222211 222222221 2334444 9
Q ss_pred cccCcHHHHHHHHHHhhhhhhhhhhhccchhHhhhcCCCCCCcccCCCCCCCCCChhHHHHHHHHHHhcCC---ChHHHH
Q 013311 241 QTDTSLEAAKQRIQEQLSSVTADMVMLSTTEEKKKSGKKSPDRESKGHENGASGPNTHLADQMKDFLKKGA---SASQFK 317 (445)
Q Consensus 241 ~~DtSeeAvk~R~~e~ls~~~~~~~~~~~~e~ek~~~~~~~~~e~~~~~~~~~~~~~e~v~~lk~~l~~~~---s~~ei~ 317 (445)
++|||+||+++||+ +|++.+++|+|+++.+.. ++++ .+.+.+.+....+++. +..+|.
T Consensus 208 ~~Dtseea~r~R~~-~Ls~~~~~~~~~sd~e~~--------E~~~----------~~~~~d~~~~~~~en~~~~~~kEi~ 268 (400)
T KOG2767|consen 208 AVDTSEEAIRARMQ-ELSANAKEMLLLSDLEKS--------EEER----------EDILYDFVKKKKEENVPDKSDKEIV 268 (400)
T ss_pred cccchHHHHHHHHH-HHhhhhhhhhhhhhhhhh--------HHHH----------HHHHHHhhhhcccccCCCccHHHHH
Confidence 99999999999995 699999999987653111 0111 1222222333333442 345677
Q ss_pred HHhhhcCCChhhHHHHHHHHHHhhhhhhHHHHHHhhHHHHHHhccC-chhHHHHHHHHHHHhcccChhhHHHHHHHHHHH
Q 013311 318 SFLGSLSGTPQEVMDALFVALFDGIEKGFAKEVTKKKNYLAAATQE-EGSQMVLLHSLESFCGKARPAAVKEVALVLKAL 396 (445)
Q Consensus 318 ~el~~~~l~~~~v~~vl~eaLf~~i~~~i~k~i~k~~~lL~~~~~~-~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~L 396 (445)
.++..+.+. +....+|.++||+. .++++|.++++||.+|+.. +++|++||++||+||..++..+++.+|.||+.|
T Consensus 269 ~~a~~l~i~-~k~p~vl~~~Lf~e---~ivkei~k~~~~l~k~~~~~~k~qr~LLggiE~~~~~~~~el~~kva~ilk~l 344 (400)
T KOG2767|consen 269 KEAERLDIK-NKAPLVLAEVLFDE---KIVKEILKHRALLLKFCTNNEKAQRYLLGGIERFVEKHEAELISKVAGILKEL 344 (400)
T ss_pred HHHHHHhhc-ccchHHHHHHHhhh---HHHHHHHHHHHHHHHHHhccHHHHHHHHhHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 777777664 38888999999998 9999999999999999985 899999999999999998899999999999999
Q ss_pred hhCCcchhHHHHHHhhcCCCCCc---chhHHHHhhhHHHHHhccCccCccCC
Q 013311 397 YDNDLLEEEFILDWYQKGLGGAN---KNSQVWKNAKPVIEWLQNAESETEED 445 (445)
Q Consensus 397 YD~DIleEE~Il~W~~k~s~~~~---~~~~vrk~a~pFI~WLeEAEEEsdeE 445 (445)
||+|||+|++|+.||++++++|| ..+++++.++|||+||++||+|+++|
T Consensus 345 Yd~DI~~e~vi~~w~~K~skk~vsk~~sk~i~e~a~Pfi~WL~~AESe~eeE 396 (400)
T KOG2767|consen 345 YDEDILEEEVIIKWGEKPSKKYVSKEKSKKIRENAKPFIEWLKNAESEDEEE 396 (400)
T ss_pred HhhhhhhHHHHHHHHhcccccccchhhhhhhHhhhhHHHHHHHhcccccccc
Confidence 99999999999999999999998 35699999999999999998776654
No 2
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=100.00 E-value=8.4e-45 Score=313.05 Aligned_cols=110 Identities=47% Similarity=0.832 Sum_probs=107.0
Q ss_pred cccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHH
Q 013311 15 FYRYKMPKMITKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENF 94 (445)
Q Consensus 15 ~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~f 94 (445)
||||+||+|++++||+| ||+|+||.+||++|||+|+||+|||++||||+|++|+ +|++||||+|++.+||++|++|
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 79999999999999986 9999999999999999999999999999999999997 4999999999999999999999
Q ss_pred HhhccccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 95 IKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 95 i~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
|++||+|++|+||||.|++ ++++++++|.||||+
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 789999999999985
No 3
>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=5.8e-45 Score=320.83 Aligned_cols=121 Identities=46% Similarity=0.826 Sum_probs=111.8
Q ss_pred eeccCCCCCCCCcccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeec
Q 013311 3 LQNIGASNSDDAFYRYKMPKMITKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAH 82 (445)
Q Consensus 3 ~ini~~~~~~d~~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~ 82 (445)
..|+ ++..+|.+ ||+||+|+++++|+ +||+|+||.|||++|||+|+||+|||++||||+|+||++ ++|||||+|
T Consensus 4 ~~np-~~~~~~~~-R~kmP~~~v~~eG~---~KTvi~Nf~dI~~~L~R~p~~~~ky~~~ELgt~~~id~~-~~lii~G~~ 77 (125)
T PF01873_consen 4 EKNP-ERSNSDKF-RYKMPPPQVKIEGK---KKTVIVNFVDICKALNRDPEHVLKYFGKELGTQGSIDGK-GRLIINGRF 77 (125)
T ss_dssp CSST-TTSCSSSS-S-CCCT--EEEETS---TEEEETTHHHHHHHHTSSHHHHHHHHHHHSSSEEEEETT-TEEEEESSS
T ss_pred HhCc-CcccCCCc-ceecCCCeEEEEcc---ceeeeecHHHHHHHHCCCHHHHHHHHHHHHCCceEECCC-CEEEEEEec
Confidence 3677 66778876 99999999999996 699999999999999999999999999999999999974 999999999
Q ss_pred CHHHHHHHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 83 DTAKLAGLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 83 ~~~~l~~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
++++||++|++||++||+|++|+||||.|++ ++++++++|.|||+.+
T Consensus 78 ~~~~i~~~L~~fI~~yVlC~~C~spdT~l~k-~~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 78 SSKQIQDLLDKFIKEYVLCPECGSPDTELIK-EGRLIFLKCKACGASR 124 (125)
T ss_dssp SCCHHHHHHHHHHCHHSSCTSTSSSSEEEEE-ETTCCEEEETTTSCEE
T ss_pred CHHHHHHHHHHHHHHEEEcCCCCCCccEEEE-cCCEEEEEecccCCcC
Confidence 9999999999999999999999999999999 7999999999999986
No 4
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=100.00 E-value=2.1e-43 Score=313.69 Aligned_cols=113 Identities=33% Similarity=0.590 Sum_probs=109.6
Q ss_pred cccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHH
Q 013311 15 FYRYKMPKMITKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENF 94 (445)
Q Consensus 15 ~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~f 94 (445)
-+||+||+|++++||+ ||+|+||.+||++|||+|+||+|||++||||+|++| +|++||||+|++.+||++|++|
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 5999999999999998 999999999999999999999999999999999997 5899999999999999999999
Q ss_pred HhhccccCCCCCCCceEEEecCCeeeeeccccCCcccccc
Q 013311 95 IKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDM 134 (445)
Q Consensus 95 i~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (445)
|++||+|++|+||||.|++ ++++++++|.||||+++|.+
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 78999999999999999964
No 5
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=100.00 E-value=7.6e-43 Score=311.88 Aligned_cols=115 Identities=30% Similarity=0.585 Sum_probs=110.8
Q ss_pred CCcccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHH
Q 013311 13 DAFYRYKMPKMITKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLE 92 (445)
Q Consensus 13 d~~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~ 92 (445)
..-+||+||+|++++||+ ||+|+||.+||++|||+|+||+|||++||||+|+++ +|++||||+|++.+|+++|+
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 446999999999999998 999999999999999999999999999999999994 69999999999999999999
Q ss_pred HHHhhccccCCCCCCCceEEEecCCeeeeeccccCCcccccc
Q 013311 93 NFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDM 134 (445)
Q Consensus 93 ~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (445)
+||++||+|++|+||||.|++ ++++++++|.||||+++|++
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 88999999999999999974
No 6
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=100.00 E-value=2.6e-41 Score=320.48 Aligned_cols=118 Identities=30% Similarity=0.600 Sum_probs=113.0
Q ss_pred CCCCcccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHH
Q 013311 11 SDDAFYRYKMPKMITKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGL 90 (445)
Q Consensus 11 ~~d~~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~ 90 (445)
..+..|||+||+|++++||+ ||+|+||.+||++|||+|+||+|||++||||+|++| ++++||||+|++.+||++
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 45678999999999999998 999999999999999999999999999999999997 589999999999999999
Q ss_pred HHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCcccccch
Q 013311 91 LENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMR 135 (445)
Q Consensus 91 l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~ 135 (445)
|++||++||+|++|+||||.|++ ++++++++|.|||++++|+.+
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 789999999999999999943
No 7
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=5.9e-32 Score=252.46 Aligned_cols=116 Identities=27% Similarity=0.506 Sum_probs=110.6
Q ss_pred cccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHH
Q 013311 15 FYRYKMPKMITKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENF 94 (445)
Q Consensus 15 ~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~f 94 (445)
-.||-|++|||..||+ ||+++||.|||+.|||.|+||++|+..||||.|++|+ ++||+|.|+|++.+||++|++|
T Consensus 103 ~~k~v~~PPqvlRegk----kT~f~Nf~Dick~mhR~pdHv~~FLlAELgTsGSidg-~~rLviKGrfq~kq~e~VLRrY 177 (231)
T KOG2768|consen 103 KRKFVMKPPQVLREGK----KTVFVNFADICKTMHRSPDHVMQFLLAELGTSGSIDG-QQRLVIKGRFQQKQFENVLRRY 177 (231)
T ss_pred ccceeeCCHHHHhhcc----ceeeeeHHHHHHHhccChHHHHHHHHHHhccccccCC-CceEEEeccccHHHHHHHHHHH
Confidence 3579999999999997 9999999999999999999999999999999999997 8999999999999999999999
Q ss_pred HhhccccCCCCCCCceEEEecCCeeeeeccccCCcccccchh
Q 013311 95 IKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRD 136 (445)
Q Consensus 95 i~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~ 136 (445)
|..||.|..|+||||.|.+ ++|++||+|..||.+..|....
T Consensus 178 I~eyV~C~~CkSpdt~L~k-enRLfFL~C~~cgs~~sv~~Ik 218 (231)
T KOG2768|consen 178 IKEYVTCKTCKSPDTILQK-ENRLFFLRCEKCGSRCSVASIK 218 (231)
T ss_pred HHHheEeeecCChhHHhhh-hcceEEEEecCCCCeeeeeeee
Confidence 9999999999999999999 7999999999999998887543
No 8
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=7.6e-30 Score=230.45 Aligned_cols=111 Identities=34% Similarity=0.706 Sum_probs=108.6
Q ss_pred cccCCCceEEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHHHh
Q 013311 17 RYKMPKMITKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENFIK 96 (445)
Q Consensus 17 Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~ 96 (445)
||.||.|.+.++|+ +|+|.||.+||++|+|+|+|+.+||..|||+.|++|++ +|+|++|.|+...|++.|+.||.
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----RTIIRNFGDIAEALNRDPEHLVKFLKKELGTAGSIDGK-GRLVLQGKFSDSEIVNEIERYIA 103 (151)
T ss_pred ceecCCcceecccc----hhHHHhHHHHHHHhcCCHHHHHHHHHHHhccccccCCc-ceEEEEecccHHHHHHHHHHHHH
Confidence 99999999999998 99999999999999999999999999999999999974 99999999999999999999999
Q ss_pred hccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 97 KYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 97 ~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
.||.|+.|++|||.|++ .+|.++++|.|||+.+||.
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 6999999999999999997
No 9
>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]
Probab=99.87 E-value=3.3e-22 Score=196.92 Aligned_cols=134 Identities=26% Similarity=0.428 Sum_probs=119.1
Q ss_pred ChhHHHHHHHHHHhcCCChHHHHHHhhhcCCChhhHHHHHHHHHHhhhhh---------hHHHHHHhhHHHHHHhccCch
Q 013311 295 PNTHLADQMKDFLKKGASASQFKSFLGSLSGTPQEVMDALFVALFDGIEK---------GFAKEVTKKKNYLAAATQEEG 365 (445)
Q Consensus 295 ~~~e~v~~lk~~l~~~~s~~ei~~el~~~~l~~~~v~~vl~eaLf~~i~~---------~i~k~i~k~~~lL~~~~~~~~ 365 (445)
|+++++..++++++. .++|.+.++.++|..+|+.+.| .++++++.|+|||..||+...
T Consensus 270 p~~evi~~VKee~k~-------------~nlPe~eVi~ivWs~iMsaveWnKkeelva~qalrhlK~yaPLL~af~s~g~ 336 (412)
T KOG2297|consen 270 PVKEVILYVKEEMKR-------------NNLPETEVIGIVWSGIMSAVEWNKKEELVAEQALRHLKQYAPLLAAFCSQGQ 336 (412)
T ss_pred CHHHHHHHHHHHHHh-------------cCCCCceEEeeeHhhhhHHHhhchHHHHHHHHHHHHHHhhhHHHHHHhcCCh
Confidence 566666666555543 4888999999999999999987 467889999999999999999
Q ss_pred hHHHHHHHHHHHhcccChhhHHHHHHHHHHHhhCCcchhHHHHHHhhcCCCCCcchhHHHHhhhHHHHHhccCccCcc
Q 013311 366 SQMVLLHSLESFCGKARPAAVKEVALVLKALYDNDLLEEEFILDWYQKGLGGANKNSQVWKNAKPVIEWLQNAESETE 443 (445)
Q Consensus 366 ~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DIleEE~Il~W~~k~s~~~~~~~~vrk~a~pFI~WLeEAEEEsd 443 (445)
+++.||..+|.||+. +..+|+.|+.|+..||..|||+||.||+||.++.... +.+.+.++++|||+||++|||||+
T Consensus 337 sEL~Ll~KvQe~CYe-n~~fMKaFqkiV~lfYk~dVLsEe~IL~Wyk~gh~~K-Gk~~FleqmkkFVeWL~~AEEEsE 412 (412)
T KOG2297|consen 337 SELELLLKVQEYCYE-NIHFMKAFQKIVVLFYKADVLSEETILKWYKEGHVAK-GKSVFLEQMKKFVEWLQNAEEESE 412 (412)
T ss_pred HHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccccc-cHHHHHHHHHHHHHHHHhhhhccC
Confidence 999999999999998 7999999999999999999999999999999877655 468999999999999999999975
No 10
>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=99.85 E-value=1.2e-21 Score=161.58 Aligned_cols=79 Identities=43% Similarity=0.789 Sum_probs=64.5
Q ss_pred hhHHHHHHHHHHHhcccChhhHHHHHHHHHHHhhCCcchhHHHHHHhhcCCCCCc---chhHHHHhhhHHHHHhccCccC
Q 013311 365 GSQMVLLHSLESFCGKARPAAVKEVALVLKALYDNDLLEEEFILDWYQKGLGGAN---KNSQVWKNAKPVIEWLQNAESE 441 (445)
Q Consensus 365 ~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DIleEE~Il~W~~k~s~~~~---~~~~vrk~a~pFI~WLeEAEEE 441 (445)
+.|+++|.+||.||.. ++.+++.|++||+.|||.|||+|++|++||+. +++.. ...++|++++|||+||++||||
T Consensus 2 ~~Q~~~L~ale~~~~~-~~~~~~~~~~il~~LYd~Dil~Eeail~W~~~-~~~~~~~~~~~~~r~~~~~fi~WL~eaeeE 79 (84)
T PF02020_consen 2 DDQVDLLNALEEFCAE-NPNLMPLFPKILQQLYDEDILEEEAILEWYED-SKPAVDGEGRAKVRKQAQPFIEWLEEAEEE 79 (84)
T ss_dssp HHHHHHHHHHHHHHHH-TCGHGGHHHHHHHHHHHTTSS-HHHHHHHHHC--SSSSCHHHHHHHHHHHHHHHHHHHHCC--
T ss_pred HHHHHHHHHHHHHHHh-CccHHHHHHHHHHHHhhhhhccHHHHHHHHHc-CCccccchhHHHHHHHHHHHHHHHhccCcc
Confidence 6899999999999976 78999999999999999999999999999999 44432 3568999999999999999999
Q ss_pred ccCC
Q 013311 442 TEED 445 (445)
Q Consensus 442 sdeE 445 (445)
||+|
T Consensus 80 ~~ee 83 (84)
T PF02020_consen 80 SDEE 83 (84)
T ss_dssp ----
T ss_pred CCCC
Confidence 8875
No 11
>smart00515 eIF5C Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5.
Probab=99.82 E-value=1.8e-20 Score=153.98 Aligned_cols=83 Identities=41% Similarity=0.706 Sum_probs=74.3
Q ss_pred HHHHHHhccCchhHHHHHHHHHHHhcccChhhHHHHHHHHHHHhhCCcchhHHHHHHhhcCCCCCcchhHHHHhhhHHHH
Q 013311 354 KNYLAAATQEEGSQMVLLHSLESFCGKARPAAVKEVALVLKALYDNDLLEEEFILDWYQKGLGGANKNSQVWKNAKPVIE 433 (445)
Q Consensus 354 ~~lL~~~~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DIleEE~Il~W~~k~s~~~~~~~~vrk~a~pFI~ 433 (445)
++||.+++++.++|+++|++||.||...++ ..+.|+.||+.|||+|||+||+|++||++.+... ...+++++++|||+
T Consensus 1 ~~ll~~~~~~~~~q~~~L~ale~~~~~~~~-~~~~~~~il~~LYd~dileEe~il~W~~~~~~~~-~~~~~~~~~~~fv~ 78 (83)
T smart00515 1 GPLLKFLAKDEEEQIDLLYAIEEFCVELEK-LIKLLPKILKSLYDADILEEEAILKWYEKAVSAE-GKKKVRKNAKPFVT 78 (83)
T ss_pred ChHHHHHHCChHHHHHHHHHHHHHHHHcch-HHHHHHHHHHHHhhhccccHHHHHHHHHcCCChH-HHHHHHHHHhHHHH
Confidence 378999999999999999999999987544 7899999999999999999999999999876432 45799999999999
Q ss_pred HhccC
Q 013311 434 WLQNA 438 (445)
Q Consensus 434 WLeEA 438 (445)
||+||
T Consensus 79 WL~eA 83 (83)
T smart00515 79 WLQEA 83 (83)
T ss_pred HHHcC
Confidence 99987
No 12
>KOG1461 consensus Translation initiation factor 2B, epsilon subunit (eIF-2Bepsilon/GCD6) [Translation, ribosomal structure and biogenesis]
Probab=99.78 E-value=1.6e-18 Score=183.82 Aligned_cols=148 Identities=24% Similarity=0.367 Sum_probs=127.2
Q ss_pred hHHHHHHHHHHhcCCCh----HHHHHHhhhcCCChhhHHHHHHHHHHhhhh-----------hhHHHHHHhhHHHHHHhc
Q 013311 297 THLADQMKDFLKKGASA----SQFKSFLGSLSGTPQEVMDALFVALFDGIE-----------KGFAKEVTKKKNYLAAAT 361 (445)
Q Consensus 297 ~e~v~~lk~~l~~~~s~----~ei~~el~~~~l~~~~v~~vl~eaLf~~i~-----------~~i~k~i~k~~~lL~~~~ 361 (445)
.|.+..+.+.+++++.. -+|+.++.++|++.++++.++|.++|..+. +++++.++.|+++|.+++
T Consensus 510 ~Ev~~s~~ra~Een~~~D~~vlEINslRla~N~s~~ev~~av~~all~~~~~~~~~~~~~~~~~~~~~~~~w~~l~~~y~ 589 (673)
T KOG1461|consen 510 KEVLGSLQRAFEENSDMDNLVLEINSLRLAYNVSLKEVAGAVFMALLKLILHQDHSSMNEVKRAALKVFTQWGPLLGNYI 589 (673)
T ss_pred HHHHHHHHHHHHhccchHHHHHHHhhhHHhhcCCHHHHHHHHHHHHHHHHhcCCCccchhHHHHHHHHHHHhhHHhhhhh
Confidence 36677777888888754 478888999999999999999999997643 367788999999999999
Q ss_pred cCchhHHHHHHHHHHHhcccChhhHHHHHHHHHHHhhCCcchhHHHHHHhhcCCCCCcchhHHHHhhhHHHHHhccCccC
Q 013311 362 QEEGSQMVLLHSLESFCGKARPAAVKEVALVLKALYDNDLLEEEFILDWYQKGLGGANKNSQVWKNAKPVIEWLQNAESE 441 (445)
Q Consensus 362 ~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DIleEE~Il~W~~k~s~~~~~~~~vrk~a~pFI~WLeEAEEE 441 (445)
++++.|+++|.+||.+|.+. ..+-+.+..+++.||+.|||+|++|++||...+......+..++++++||+||+||+||
T Consensus 590 ks~deqid~l~~led~~~e~-~~~~~~~~~~v~~lY~~dil~EdaI~~W~~~~~~~~~~~~~~~~~~k~fv~WL~easeE 668 (673)
T KOG1461|consen 590 KSEDEQIDLLLALEDKCVES-EELGPKAAKLVHYLYDYDILQEDAILSWSSQKAGDDEEDAVYNQQLKKFVDWLKEASEE 668 (673)
T ss_pred hhHHHHHHHHHHHHHHHHhc-ccchHHHHHHHHHHHHHhHhhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHhhcccc
Confidence 99999999999999999884 77778999999999999999999999999884333223467889999999999999999
Q ss_pred ccCC
Q 013311 442 TEED 445 (445)
Q Consensus 442 sdeE 445 (445)
||+|
T Consensus 669 ~~~e 672 (673)
T KOG1461|consen 669 EESE 672 (673)
T ss_pred cccC
Confidence 8875
No 13
>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=96.73 E-value=0.034 Score=54.92 Aligned_cols=118 Identities=19% Similarity=0.313 Sum_probs=89.9
Q ss_pred CCChhHHHHHHHHHHhcCCChHHHHHHhhhcCCCh--------hhHHHHHHHHHHhhhhh---hHHHHHHhhHHHHHHh-
Q 013311 293 SGPNTHLADQMKDFLKKGASASQFKSFLGSLSGTP--------QEVMDALFVALFDGIEK---GFAKEVTKKKNYLAAA- 360 (445)
Q Consensus 293 ~~~~~e~v~~lk~~l~~~~s~~ei~~el~~~~l~~--------~~v~~vl~eaLf~~i~~---~i~k~i~k~~~lL~~~- 360 (445)
+.|+......|.+++....++.++...+....-.. ..++.+++++++..-.. -+...|.+|...|+.+
T Consensus 7 ~~P~~~~a~~l~~~ir~k~~~eei~~~l~~i~~~~~~~~~~~~~~~i~v~~q~ll~~GSkS~SH~~~~lery~~~Lk~l~ 86 (253)
T PF09090_consen 7 SLPFHALAQKLLDLIRKKAPPEEISELLEEIEEPAEEHGSDFDKFVIDVFVQCLLHIGSKSFSHVLSALERYKEVLKELE 86 (253)
T ss_dssp TSTTHHHHHHHHHHHHTT--HHHHHHHHTTS------------HHHHHHHHHHHHHHTTTSHHHHHHHHHHTHHHHHHH-
T ss_pred CCccHHHHHHHHHHHHcCCCHHHHHHHHHhccccccccccchhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHhc
Confidence 35889999999999987778888888887653221 24677888888765333 4567799999999999
Q ss_pred ccCchhHHHHHHHHHHHhcccChhhHHHHHHHHHHHhhCCcchhHHHHHHhhcC
Q 013311 361 TQEEGSQMVLLHSLESFCGKARPAAVKEVALVLKALYDNDLLEEEFILDWYQKG 414 (445)
Q Consensus 361 ~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DIleEE~Il~W~~k~ 414 (445)
..++..|..+|.++=+|... +|.. ...|+..|=...||+-.+|+.|.=..
T Consensus 87 ~~~~~~q~~il~~v~~~W~~-~~q~---~~li~dkll~~~ii~~~~Vv~w~f~~ 136 (253)
T PF09090_consen 87 AESEEAQFWILDAVFRFWKN-NPQM---GFLIIDKLLNYGIISPSAVVNWVFSP 136 (253)
T ss_dssp TSSHHHHHHHHHHHHHHHTT--HHH---HHHHHHHHHHTTSS-HHHHHHHHTSG
T ss_pred cCChHHHHHHHHHHHHHHhc-CCce---ehHHHHHHHhcCCCCHHHHHHHHcCc
Confidence 88899999999999999865 6763 55688999999999999999998543
No 14
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=94.94 E-value=0.0081 Score=56.86 Aligned_cols=36 Identities=28% Similarity=0.741 Sum_probs=31.1
Q ss_pred hccccCCCCCCCc--eEEEecCCeeeeeccccCCcccc
Q 013311 97 KYVQCYGCGNPET--DIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 97 ~fVlC~~C~~peT--~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
.|..||+|++-+| .+++.+++...++|..||...+.
T Consensus 5 iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 5 IYIECPSCGSEEVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EEEECCCCCcchhhHHHHHhcCCceEEEccCCCcEeec
Confidence 4889999999999 88885577789999999999855
No 15
>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=94.57 E-value=0.033 Score=41.43 Aligned_cols=32 Identities=38% Similarity=0.915 Sum_probs=26.4
Q ss_pred HhhccccCCCCC-----CCceEEEecCCeeeeeccccCC
Q 013311 95 IKKYVQCYGCGN-----PETDIIITKTQMVNLKCAACGF 128 (445)
Q Consensus 95 i~~fVlC~~C~~-----peT~l~~~k~~~~~~~C~aCG~ 128 (445)
..+|+.||.|+| -|-.|++ ...++...|+ ||.
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 456999999987 5778888 6788999998 885
No 16
>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=93.16 E-value=0.096 Score=40.61 Aligned_cols=40 Identities=20% Similarity=0.560 Sum_probs=32.4
Q ss_pred HHHhhccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 93 NFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 93 ~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
+||-- ..||.|+..||......++.-...|-.||++-..+
T Consensus 5 RFIAG-A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~ 44 (59)
T TIGR02443 5 RFIAG-AVCPACSAQDTLAMWKENNIELVECVECGYQEQQK 44 (59)
T ss_pred eEecc-ccCCCCcCccEEEEEEeCCceEEEeccCCCccccC
Confidence 34444 67999999999988767788899999999986543
No 17
>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=92.77 E-value=0.075 Score=42.84 Aligned_cols=40 Identities=20% Similarity=0.527 Sum_probs=33.1
Q ss_pred HHHhhccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 93 NFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 93 ~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
+||-- ..||.|+.-||......++.-++.|-+||+.-..+
T Consensus 4 rFIAG-a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~ 43 (71)
T PF09526_consen 4 RFIAG-AVCPKCQAMDTIMMWRENGVEYVECVECGYTERQP 43 (71)
T ss_pred eEecC-ccCCCCcCccEEEEEEeCCceEEEecCCCCeeccC
Confidence 34544 67999999999988767788999999999987665
No 18
>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=91.48 E-value=0.43 Score=39.19 Aligned_cols=73 Identities=16% Similarity=0.131 Sum_probs=50.1
Q ss_pred cCCCceEEEeccC-CCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccC---CCCeEEEEeecCHHHHHHHHHHH
Q 013311 19 KMPKMITKIEGRG-NGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDE---KTGTSLVNGAHDTAKLAGLLENF 94 (445)
Q Consensus 19 kmp~~~~k~eG~g-ng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~---~~~~~ii~G~~~~~~l~~~l~~f 94 (445)
..|.+.+.++-|. |=.=|+|.||. .-.=++.-+.+.|...+|+.+++.. ++..+.|+|.|...-.+-|+..|
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 3678888888543 22336788887 3455788999999999999999942 24569999999888666666665
Q ss_pred H
Q 013311 95 I 95 (445)
Q Consensus 95 i 95 (445)
+
T Consensus 79 ~ 79 (83)
T PF01253_consen 79 G 79 (83)
T ss_dssp S
T ss_pred C
Confidence 4
No 19
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.18 E-value=0.18 Score=46.50 Aligned_cols=33 Identities=30% Similarity=0.680 Sum_probs=24.7
Q ss_pred ccCCCCCCCceEEEec---CC-ee--eeeccccCCcccc
Q 013311 100 QCYGCGNPETDIIITK---TQ-MV--NLKCAACGFVSEV 132 (445)
Q Consensus 100 lC~~C~~peT~l~~~k---~~-~~--~~~C~aCG~~~~v 132 (445)
.||.|++|+|.++-.. .+ .+ +..|..||.+-.-
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 6999999999998732 21 22 3899999998543
No 20
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=90.20 E-value=0.35 Score=34.52 Aligned_cols=30 Identities=30% Similarity=0.635 Sum_probs=24.8
Q ss_pred ccCCCCCCCceEEEe------cCCeeeeeccccCCc
Q 013311 100 QCYGCGNPETDIIIT------KTQMVNLKCAACGFV 129 (445)
Q Consensus 100 lC~~C~~peT~l~~~------k~~~~~~~C~aCG~~ 129 (445)
.||.|++.+..+... +.-++|..|..||++
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 699999999998642 235889999999975
No 21
>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=88.95 E-value=0.28 Score=34.78 Aligned_cols=31 Identities=23% Similarity=0.597 Sum_probs=22.6
Q ss_pred cccCCCCCCCceEEEe------cCCeeeeeccccCCc
Q 013311 99 VQCYGCGNPETDIIIT------KTQMVNLKCAACGFV 129 (445)
Q Consensus 99 VlC~~C~~peT~l~~~------k~~~~~~~C~aCG~~ 129 (445)
+.||.|++.++..... +.-+++..|..||++
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 4699999999988852 235889999999975
No 22
>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=88.13 E-value=0.5 Score=49.24 Aligned_cols=54 Identities=22% Similarity=0.551 Sum_probs=35.9
Q ss_pred CHHHHHHHHHHHHhh---------ccccCCCCCCCceEEEe---cCCeeeeeccccCCcccccchh
Q 013311 83 DTAKLAGLLENFIKK---------YVQCYGCGNPETDIIIT---KTQMVNLKCAACGFVSEVDMRD 136 (445)
Q Consensus 83 ~~~~l~~~l~~fi~~---------fVlC~~C~~peT~l~~~---k~~~~~~~C~aCG~~~~v~~~~ 136 (445)
....|.++|..|..+ .++|+.|+.-+|+-+.. +...+.-+|..||+...++.+.
T Consensus 150 ~~~~I~~Il~~~~~~~~~~~y~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~~ 215 (360)
T PF01921_consen 150 NRDEIREILNEYRGRERPETYSPFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDITG 215 (360)
T ss_dssp THHHHHHHHHHHHHHT--TT--SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETTT
T ss_pred hHHHHHHHHHHhcCcCCCCCeeeeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecCC
Confidence 456788888888544 48999999966655442 4789999999999999998654
No 23
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=87.88 E-value=0.48 Score=36.26 Aligned_cols=29 Identities=24% Similarity=0.553 Sum_probs=22.0
Q ss_pred cccCCCCCCCceEEEecCCe-----eeeeccccCC
Q 013311 99 VQCYGCGNPETDIIITKTQM-----VNLKCAACGF 128 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~-----~~~~C~aCG~ 128 (445)
--||-|+.+...+.. .... ++..|..||+
T Consensus 4 kPCPFCG~~~~~~~~-~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQ-DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeec-ccCCCCCCEEEEEcCCCCC
Confidence 359999777777765 3222 8899999999
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=87.63 E-value=0.48 Score=43.33 Aligned_cols=32 Identities=16% Similarity=0.290 Sum_probs=24.0
Q ss_pred ccCCCCCCCceEEEe---cCCeee---eeccccCCccc
Q 013311 100 QCYGCGNPETDIIIT---KTQMVN---LKCAACGFVSE 131 (445)
Q Consensus 100 lC~~C~~peT~l~~~---k~~~~~---~~C~aCG~~~~ 131 (445)
.||-|+++||.++-. +++..+ ..|.+||.+-+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 599999999999853 233333 67999998744
No 25
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=86.87 E-value=0.93 Score=35.80 Aligned_cols=34 Identities=21% Similarity=0.398 Sum_probs=28.1
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccccc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDM 134 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (445)
-||.|+-..-.+.. .++.++..|..||+..+...
T Consensus 8 PCPFCG~~~~~v~~-~~g~~~v~C~~CgA~~~~~~ 41 (64)
T PRK09710 8 PCPFCGCPSVTVKA-ISGYYRAKCNGCESRTGYGG 41 (64)
T ss_pred CCCCCCCceeEEEe-cCceEEEEcCCCCcCccccc
Confidence 59999998877776 67888899999999866653
No 26
>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=86.39 E-value=0.78 Score=34.54 Aligned_cols=33 Identities=21% Similarity=0.464 Sum_probs=23.3
Q ss_pred ccCCCCCCCceEEE---ecCCeeeeeccccCCcccc
Q 013311 100 QCYGCGNPETDIII---TKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 100 lC~~C~~peT~l~~---~k~~~~~~~C~aCG~~~~v 132 (445)
-||-|++.+-.+.. +.+...+..|..||+..++
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 49999996665542 1233334499999999987
No 27
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=83.67 E-value=3 Score=39.29 Aligned_cols=72 Identities=13% Similarity=0.086 Sum_probs=54.5
Q ss_pred cCCCceEEEeccCCCc-eEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccC---CCCeEEEEeecCHHHHHHHHHHH
Q 013311 19 KMPKMITKIEGRGNGI-KTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDE---KTGTSLVNGAHDTAKLAGLLENF 94 (445)
Q Consensus 19 kmp~~~~k~eG~gng~-kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~---~~~~~ii~G~~~~~~l~~~l~~f 94 (445)
..+++.++++-|+.|+ =|+|.+|.. ..-++.-+.|+|...+++.+++.. +++.++|+|.|...-.+=|++.|
T Consensus 87 ~~~~V~I~~~~R~krK~VT~V~GLe~----f~idlk~laK~lkkkfacG~SV~k~~~~~~eI~IQGD~~~~v~e~L~~~~ 162 (173)
T TIGR01159 87 LPQKVTIKREPRTKRKFVTVIKGLET----FDIDLKKASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEKW 162 (173)
T ss_pred CCCeEEEEEEecCCCceEEEEeCCcC----CCcCHHHHHHHHHHHhCCCCccccCCCCCCEEEecCCHHHHHHHHHHHHc
Confidence 4677888888886444 378888874 245788999999999999976621 35789999999887776666665
No 28
>PHA02998 RNA polymerase subunit; Provisional
Probab=83.08 E-value=1.2 Score=42.01 Aligned_cols=82 Identities=16% Similarity=0.289 Sum_probs=49.5
Q ss_pred hHHHHHHhC---CCchHHHHHHHHhh-----cCcccccCCCCeEEEEeecCHHHHHHHHHHHHhhccccCCCCCCCceEE
Q 013311 41 MVDIAKALA---RPPSYTTKYFGNEL-----GAQSKFDEKTGTSLVNGAHDTAKLAGLLENFIKKYVQCYGCGNPETDII 112 (445)
Q Consensus 41 ~~~ia~~L~---R~p~~~~ky~~~EL-----g~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~fVlC~~C~~peT~l~ 112 (445)
..+||..++ --...+++||++-+ |+.-.||. +. .|+-..-=+++.. +.-|.||.|++.++...
T Consensus 87 y~~lc~~ir~tng~eke~lry~lfgikcv~~~veydid~----~~---d~~y~~yfnvlpk--kt~v~CPkCg~~~A~f~ 157 (195)
T PHA02998 87 YKDLCDMIRGTNGTEKEILRYLLFGIKCIKKGVEYDIDK----IP---DVDYDDYFNVLDE--KYNTPCPNCKSKNTTPM 157 (195)
T ss_pred HHHHHHHHHhcCCchHHHHHHHHHHHHHHhcCCccchhh----cc---cccchhheeccCc--ccCCCCCCCCCCceEEE
Confidence 567777664 44567889988754 33333332 10 1111222222222 13589999999999865
Q ss_pred Ee------cCCeeeeeccccCCccc
Q 013311 113 IT------KTQMVNLKCAACGFVSE 131 (445)
Q Consensus 113 ~~------k~~~~~~~C~aCG~~~~ 131 (445)
.- +..+.|.+|..||.+-.
T Consensus 158 qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 158 MIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred EEeeccCCCCceEEEEcCCCCCccC
Confidence 41 23689999999998743
No 29
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=81.87 E-value=0.76 Score=31.84 Aligned_cols=30 Identities=37% Similarity=0.753 Sum_probs=16.4
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
-||.|+.|=+..+...+...-+.|.+||..
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCE
Confidence 499999994444443356678899999975
No 30
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=81.03 E-value=2.1 Score=46.51 Aligned_cols=50 Identities=28% Similarity=0.604 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHhh---------ccccCCCCCCCceEEEe-cC-CeeeeeccccCCcccccch
Q 013311 85 AKLAGLLENFIKK---------YVQCYGCGNPETDIIIT-KT-QMVNLKCAACGFVSEVDMR 135 (445)
Q Consensus 85 ~~l~~~l~~fi~~---------fVlC~~C~~peT~l~~~-k~-~~~~~~C~aCG~~~~v~~~ 135 (445)
..|+++|..|-.+ -++|+.|+.-.|+=+++ +. ..+.-+|. ||+.+.|+.+
T Consensus 149 deI~~il~~~~~~~~~e~~~P~~piC~kcGri~~t~v~~~d~~~~v~Y~Ce-~Gh~g~v~ir 209 (521)
T COG1384 149 DEIMEILNEYRGRELEEDWSPFMPICEKCGRILTTPVIEWDGEGTVEYRCE-CGHEGEVDIR 209 (521)
T ss_pred HHHHHHHHHhcCCcccCCceeccccccccCCcceeEEEEecCCceEEEEec-CCccceeecc
Confidence 5788888888877 37899999955544443 33 58999998 9999999986
No 31
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=80.99 E-value=1.1 Score=38.55 Aligned_cols=37 Identities=27% Similarity=0.708 Sum_probs=27.0
Q ss_pred hhccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 96 KKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 96 ~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
..++.||.|+++--.+.+ +++...+.|..||....-.
T Consensus 19 pt~f~CP~Cge~~v~v~~-~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 19 PKIFECPRCGKVSISVKI-KKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred CcEeECCCCCCeEeeeec-CCCcceEECCCCCCccCEE
Confidence 467899999975333344 4477899999999985543
No 32
>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=80.98 E-value=1.6 Score=45.43 Aligned_cols=93 Identities=23% Similarity=0.469 Sum_probs=57.2
Q ss_pred hHHHHHHhCCCchHHHHHHH------HhhcCcccccCCCCeEEEEeecCH---------HHHHHHHHHHHhh--------
Q 013311 41 MVDIAKALARPPSYTTKYFG------NELGAQSKFDEKTGTSLVNGAHDT---------AKLAGLLENFIKK-------- 97 (445)
Q Consensus 41 ~~~ia~~L~R~p~~~~ky~~------~ELg~~~~~~~~~~~~ii~G~~~~---------~~l~~~l~~fi~~-------- 97 (445)
+..|++-.+.+|+|...|.. ..||..--+=. .-...-+|.+.. ..|.++|..|...
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 LSSVPDPFGCCESYAEHFERPFEESLEKLGIEVEFIS-QSQMYKSGLYDENILIALEKRDEIMAILNEYRGRELQETWYP 167 (353)
T ss_pred chhchhhcCCCHHHHHHHHHHHHHHHHHcCCeeeeee-cCCchhhchHHHHHHHHHHHCChHHHHHHHhcCCccCCCcee
Confidence 34555555666776666632 34555432211 122334565543 4567778877765
Q ss_pred -ccccCCCCCCCceEE-Ee-cCCeeeeeccccCCcccccch
Q 013311 98 -YVQCYGCGNPETDII-IT-KTQMVNLKCAACGFVSEVDMR 135 (445)
Q Consensus 98 -fVlC~~C~~peT~l~-~~-k~~~~~~~C~aCG~~~~v~~~ 135 (445)
.++|+.|+.-.|.++ .+ +.+.+.-+|. ||+...++.+
T Consensus 168 ~~p~c~~cg~~~~~v~~~d~~~~~v~y~c~-cG~~g~~~~~ 207 (353)
T cd00674 168 FMPYCEKCGKDTTTVEAYDAKAGTVTYKCE-CGHEETVDIR 207 (353)
T ss_pred eeeecCCcCcceeEEEEEeCCCCeEEEEcC-CCCEEEEeec
Confidence 479999997655554 33 3466777996 9999999854
No 33
>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=80.95 E-value=3.9 Score=33.37 Aligned_cols=59 Identities=12% Similarity=0.035 Sum_probs=43.7
Q ss_pred eEEEeccCCCc-eEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHH
Q 013311 24 ITKIEGRGNGI-KTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLA 88 (445)
Q Consensus 24 ~~k~eG~gng~-kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~ 88 (445)
.++++-|+.|+ =|+|.+|..-.. ++.-+.+.|...+|+.|++. ++.+.|+|.|...-.+
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 45566555443 477888863221 68889999999999999996 4789999998765543
No 34
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=80.89 E-value=0.54 Score=35.91 Aligned_cols=48 Identities=27% Similarity=0.617 Sum_probs=31.5
Q ss_pred hccccCCCCCCCceEEEecC---CeeeeeccccCCcccccchhhhhHHHhcCC
Q 013311 97 KYVQCYGCGNPETDIIITKT---QMVNLKCAACGFVSEVDMRDKLTTFILKNP 146 (445)
Q Consensus 97 ~fVlC~~C~~peT~l~~~k~---~~~~~~C~aCG~~~~v~~~~kl~~~i~k~p 146 (445)
+.++||.|+|. |.+.+..+ ..+-+-|.-|-..+-++.. .|.--++|.|
T Consensus 3 ~Wi~CP~CgnK-TR~kir~DT~LkNfPlyCpKCK~EtlI~v~-~~~i~vikep 53 (55)
T PF14205_consen 3 EWILCPICGNK-TRLKIREDTVLKNFPLYCPKCKQETLIDVK-QLKITVIKEP 53 (55)
T ss_pred eEEECCCCCCc-cceeeecCceeccccccCCCCCceEEEEee-ccEEEEEeCC
Confidence 57999999985 33333122 4577999999999998854 3333344444
No 35
>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=80.56 E-value=1.1 Score=32.12 Aligned_cols=28 Identities=36% Similarity=0.872 Sum_probs=19.1
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
.||.|++.. ++.+ ...-.+.|..||..-
T Consensus 2 ~Cp~Cg~~~--~~~D-~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKE--IVFD-PERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSE--EEEE-TTTTEEEETTT-BBE
T ss_pred CCcCCcCCc--eEEc-CCCCeEECCCCCCEe
Confidence 599999966 4543 333466999999863
No 36
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=80.15 E-value=0.9 Score=31.80 Aligned_cols=31 Identities=23% Similarity=0.661 Sum_probs=22.3
Q ss_pred ccccCCCCC----CCceEEEecCCeeeeeccccCCccc
Q 013311 98 YVQCYGCGN----PETDIIITKTQMVNLKCAACGFVSE 131 (445)
Q Consensus 98 fVlC~~C~~----peT~l~~~k~~~~~~~C~aCG~~~~ 131 (445)
.+.||+|+. |++.|-. . ...++|..||+.-.
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~-~--~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPA-G--GRKVRCPKCGHVFR 36 (37)
T ss_pred EEECCCCCceEEcCHHHccc-C--CcEEECCCCCcEee
Confidence 478999985 5555544 3 34899999998754
No 37
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=78.27 E-value=2.6 Score=46.00 Aligned_cols=51 Identities=24% Similarity=0.514 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHhh---------ccccCCCCCCCceEEE--e-cCCeeeeeccccCCcccccchh
Q 013311 85 AKLAGLLENFIKK---------YVQCYGCGNPETDIII--T-KTQMVNLKCAACGFVSEVDMRD 136 (445)
Q Consensus 85 ~~l~~~l~~fi~~---------fVlC~~C~~peT~l~~--~-k~~~~~~~C~aCG~~~~v~~~~ 136 (445)
..|.++|..|... .++|+.|+.-.|..++ + ..+.+.-.|. ||+...++.+.
T Consensus 153 ~~i~~il~~~~~~~~~~~~~P~~pic~~cg~~~~~~~~~~d~~~~~v~y~~~-cG~~~~~~~~~ 215 (510)
T PRK00750 153 DEIMEILLPYLGEERQATYSPFLPICPKCGKVLTTPVISYDAEAGTVTYDCE-CGHEGEVPVTG 215 (510)
T ss_pred HHHHHHHHHhcCCccCCCeeeeeeeCCCCCccceEEEEEEeCCCCEEEEEcC-CCCEEEEecCC
Confidence 4566666666443 4789999999987774 2 3456777897 99999998764
No 38
>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=78.05 E-value=2.1 Score=31.18 Aligned_cols=30 Identities=30% Similarity=0.635 Sum_probs=21.7
Q ss_pred hhccccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 96 KKYVQCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 96 ~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
+.|| ||.|++. ....+ ++ ....+|.+|+++
T Consensus 17 ~g~~-CP~Cg~~-~~~~~-~~-~~~~~C~~C~~q 46 (46)
T PF12760_consen 17 DGFV-CPHCGST-KHYRL-KT-RGRYRCKACRKQ 46 (46)
T ss_pred CCCC-CCCCCCe-eeEEe-CC-CCeEECCCCCCc
Confidence 4444 9999998 55555 33 567899999974
No 39
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=77.82 E-value=1.3 Score=35.19 Aligned_cols=29 Identities=28% Similarity=0.602 Sum_probs=23.4
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
+|.||.|+|--|.+-. -.....|..||..
T Consensus 19 ~VkCpdC~N~q~vFsh---ast~V~C~~CG~~ 47 (67)
T COG2051 19 RVKCPDCGNEQVVFSH---ASTVVTCLICGTT 47 (67)
T ss_pred EEECCCCCCEEEEecc---CceEEEecccccE
Confidence 7999999997665544 5668899999986
No 40
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=75.25 E-value=2.1 Score=33.40 Aligned_cols=30 Identities=27% Similarity=0.582 Sum_probs=24.1
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
-|.||.|+|.-|.+-. -.....|..||..=
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 4899999998776665 45678999999863
No 41
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=74.99 E-value=1.2 Score=32.95 Aligned_cols=34 Identities=29% Similarity=0.585 Sum_probs=26.9
Q ss_pred ccccCCCCC----CCceEEEecCCeeeeeccccCCcccc
Q 013311 98 YVQCYGCGN----PETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 98 fVlC~~C~~----peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
||.|++|.. |...... +++...++|-+|...-.+
T Consensus 6 Fv~C~~C~~lLqlP~~~~~~-~k~~~klrCGaCs~vl~~ 43 (46)
T PF11331_consen 6 FVVCSSCFELLQLPAKFSLS-KKNQQKLRCGACSEVLSF 43 (46)
T ss_pred EeECccHHHHHcCCCccCCC-ccceeEEeCCCCceeEEE
Confidence 899999975 7777776 556889999999876443
No 42
>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=74.97 E-value=3.5 Score=45.11 Aligned_cols=51 Identities=22% Similarity=0.503 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhh---------ccccCCCCCCCceEEE-ecCCeeeeeccccCCcccccch
Q 013311 84 TAKLAGLLENFIKK---------YVQCYGCGNPETDIII-TKTQMVNLKCAACGFVSEVDMR 135 (445)
Q Consensus 84 ~~~l~~~l~~fi~~---------fVlC~~C~~peT~l~~-~k~~~~~~~C~aCG~~~~v~~~ 135 (445)
...|.++|..|... .++|+.|+.-.|.++- +....+.-+|. ||+.+.++.+
T Consensus 145 ~~~I~~il~~~~~~~~~~~~~P~~pic~~cGrv~~~~~~~~~~~~v~Y~c~-cG~~g~~~~~ 205 (515)
T TIGR00467 145 RKEISEILNEYRTSKLEENWYPISVFCENCGRDTTTVNNYDNEYSIEYSCE-CGNQESVDIY 205 (515)
T ss_pred HHHHHHHHHHhcCCccCCCceeeeeecCCcCccCceEEEecCCceEEEEcC-CCCEEEEeec
Confidence 35677888888753 4799999998876553 22235777997 9999999764
No 43
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=72.93 E-value=2.5 Score=31.02 Aligned_cols=32 Identities=25% Similarity=0.659 Sum_probs=20.8
Q ss_pred ccCCCCCCCceEEEecC-CeeeeeccccCCcccccc
Q 013311 100 QCYGCGNPETDIIITKT-QMVNLKCAACGFVSEVDM 134 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~-~~~~~~C~aCG~~~~v~~ 134 (445)
.||.|++ .|..... +.....|..||+...+..
T Consensus 2 FCp~Cg~---~l~~~~~~~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 2 FCPKCGN---MLIPKEGKEKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCC---ccccccCCCCCEEECCcCCCeEECCC
Confidence 4999998 2333111 223678999998766653
No 44
>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=71.48 E-value=2.9 Score=34.45 Aligned_cols=39 Identities=21% Similarity=0.397 Sum_probs=22.5
Q ss_pred HhhccccCCCCCCCceEEE-e-cCCeeeeeccccCCccccc
Q 013311 95 IKKYVQCYGCGNPETDIII-T-KTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 95 i~~fVlC~~C~~peT~l~~-~-k~~~~~~~C~aCG~~~~v~ 133 (445)
+.++-.||.|+...|.-+. + +.+.-.+.|..||......
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 3456689999998887776 3 4578899999999986554
No 45
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=71.02 E-value=10 Score=32.46 Aligned_cols=64 Identities=16% Similarity=0.100 Sum_probs=43.7
Q ss_pred ceEEEecc-CCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHH
Q 013311 23 MITKIEGR-GNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLEN 93 (445)
Q Consensus 23 ~~~k~eG~-gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~ 93 (445)
+.++++-| ||=.=|+|.||..- .=++.-+.+.|...+|+.|++. ++.+.|+|.|...-. ++|..
T Consensus 26 i~I~~ekr~~gK~VTiI~Gl~~~----~~~lk~l~k~lKk~~gcGgsvk--~~~I~iQGD~r~~v~-~~L~~ 90 (99)
T PRK00939 26 IKIKVDKRRYGKEVTIIEGIDPK----DIDLKELAKKLKSKLACGGTVK--DGRIELQGDHRERVK-ELLIK 90 (99)
T ss_pred EEEEEEecCCCceEEEEeCCCCc----chhHHHHHHHHHHHhCCCceEE--CCEEEEeCcHHHHHH-HHHHH
Confidence 34455543 23344778888631 1246788999999999999995 578999999976544 44443
No 46
>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=68.48 E-value=4.6 Score=34.22 Aligned_cols=33 Identities=30% Similarity=0.672 Sum_probs=26.6
Q ss_pred ccccCCCCCCCceEEE------ecCCeeeeeccccCCcc
Q 013311 98 YVQCYGCGNPETDIII------TKTQMVNLKCAACGFVS 130 (445)
Q Consensus 98 fVlC~~C~~peT~l~~------~k~~~~~~~C~aCG~~~ 130 (445)
.+.||.|++.+..+.. ++.-++|..|..||++-
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 5899999999987663 13478999999999863
No 47
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=68.44 E-value=64 Score=36.82 Aligned_cols=113 Identities=14% Similarity=0.179 Sum_probs=78.3
Q ss_pred HHHHHHHHHhcCCChHHHHHHhh----hcCC-ChhhHHHHHHHHHHhhhhh---hHHHHHHhhHHHHHHhccCc-hhHHH
Q 013311 299 LADQMKDFLKKGASASQFKSFLG----SLSG-TPQEVMDALFVALFDGIEK---GFAKEVTKKKNYLAAATQEE-GSQMV 369 (445)
Q Consensus 299 ~v~~lk~~l~~~~s~~ei~~el~----~~~l-~~~~v~~vl~eaLf~~i~~---~i~k~i~k~~~lL~~~~~~~-~~Q~~ 369 (445)
+...+-..+....+++++...++ .... ...-++.++++++++.... .....+.+|...|++++.+. ..|..
T Consensus 502 ~~~~l~~~~~~k~~~e~~~~iLk~~~~~~~~~~n~~~i~lfvq~~l~lGSKSfSH~f~~lek~~~vfk~l~~~~e~~q~~ 581 (759)
T KOG1104|consen 502 VAVQLIVAFREKATAEEIVNILKSEDESEIGSFNRLKIILFVQTLLDLGSKSFSHAFSALEKYHTVFKKLCEDSETKQII 581 (759)
T ss_pred HHHHHHHHHhccCCHHHHHHHHhcCccccccCCcceehhhHHHHHHHhccchhhhHHHHHHHHHHHHHHHhcCCchhHHH
Confidence 34444455555567888888888 2222 2344577888999886443 34556889999999999755 45999
Q ss_pred HHHHHHHHhcccChhhHHHHHHHHHHHhhCCcchhHHHHHHhhcCC
Q 013311 370 LLHSLESFCGKARPAAVKEVALVLKALYDNDLLEEEFILDWYQKGL 415 (445)
Q Consensus 370 lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DIleEE~Il~W~~k~s 415 (445)
+|.++=.|... +|.. ...++-.|-..-||+--+|..|-=+..
T Consensus 582 vl~~vft~Wk~-n~Qm---~~v~~Dkml~~~ii~~~aVv~WiF~~~ 623 (759)
T KOG1104|consen 582 VLEAVFTFWKA-NPQM---GFVLTDKMLKYQIIDCSAVVRWIFSEE 623 (759)
T ss_pred HHHHHHHHHhc-Cchh---hHHHHHHHhccccccHHHHHHHhcCHH
Confidence 99999888865 5653 233556666688999999999985433
No 48
>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=67.87 E-value=4.9 Score=41.01 Aligned_cols=55 Identities=20% Similarity=0.354 Sum_probs=39.5
Q ss_pred eEEEEeecCHHHHH-------------HHHHHHHhh----------------ccccCCCCCCCceEEEe------cCCee
Q 013311 75 TSLVNGAHDTAKLA-------------GLLENFIKK----------------YVQCYGCGNPETDIIIT------KTQMV 119 (445)
Q Consensus 75 ~~ii~G~~~~~~l~-------------~~l~~fi~~----------------fVlC~~C~~peT~l~~~------k~~~~ 119 (445)
+-|++|.+++.+|- ....++.++ -+.|+.|+..++.+... +.-++
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 45789999887652 333333332 57999999999988752 12478
Q ss_pred eeeccccCCc
Q 013311 120 NLKCAACGFV 129 (445)
Q Consensus 120 ~~~C~aCG~~ 129 (445)
|..|..||++
T Consensus 286 f~~C~~Cg~~ 295 (299)
T TIGR01385 286 FVTCEECGNR 295 (299)
T ss_pred EEEcCCCCCe
Confidence 9999999986
No 49
>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=67.46 E-value=1.9 Score=32.79 Aligned_cols=32 Identities=25% Similarity=0.518 Sum_probs=24.8
Q ss_pred ccCCCCCCCceEEEecCC-eeeeeccccCCcccc
Q 013311 100 QCYGCGNPETDIIITKTQ-MVNLKCAACGFVSEV 132 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~-~~~~~C~aCG~~~~v 132 (445)
.|..|+..+|-+-+ ++. .-..-|+|||-....
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 49999999999998 442 456789999965433
No 50
>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=67.45 E-value=3 Score=41.99 Aligned_cols=35 Identities=23% Similarity=0.417 Sum_probs=19.1
Q ss_pred cccCCCCC-CCceEEEecC--CeeeeeccccCCccccc
Q 013311 99 VQCYGCGN-PETDIIITKT--QMVNLKCAACGFVSEVD 133 (445)
Q Consensus 99 VlC~~C~~-peT~l~~~k~--~~~~~~C~aCG~~~~v~ 133 (445)
-.||.||+ |-..+++.+. +.-++.|.-||..-...
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 48999999 5666665333 57899999999987665
No 51
>PF10474 DUF2451: Protein of unknown function C-terminus (DUF2451); InterPro: IPR019514 This protein is found in eukaryotes but its function is not known. The N-terminal domain of some members is PF10475 from PFAM (DUF2450).
Probab=66.66 E-value=54 Score=32.21 Aligned_cols=82 Identities=22% Similarity=0.235 Sum_probs=50.9
Q ss_pred hhHHHHHHHHHHhhhhhhHHHHHHhhHHHHHHhccCchhHH-----HHHHHHHHHhcccChhhHHHHHHHHHHHhhCCcc
Q 013311 328 QEVMDALFVALFDGIEKGFAKEVTKKKNYLAAATQEEGSQM-----VLLHSLESFCGKARPAAVKEVALVLKALYDNDLL 402 (445)
Q Consensus 328 ~~v~~vl~eaLf~~i~~~i~k~i~k~~~lL~~~~~~~~~Q~-----~lL~alE~~~~~~~~~l~~~~~~ILk~LYD~DIl 402 (445)
.++..++|+.+...+...++.-+ +. +++.....++++ .++..||.+.....+.-...+-..++++| +
T Consensus 119 ~~~~~~lw~~~i~~~~~~Lveg~---s~-vkKCs~eGRalM~lD~q~~~~~le~l~~~~~~p~~~~Ve~YIKAyY----l 190 (234)
T PF10474_consen 119 PEVQNVLWDRLIFFAFETLVEGY---SR-VKKCSNEGRALMQLDFQQLQNKLEKLSGIRPIPNREYVENYIKAYY----L 190 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH---Hh-ccCCChhhHHHHHHHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHc----C
Confidence 44677777777665433333222 22 233333444443 67788888876543334567778899999 7
Q ss_pred hhHHHHHHhhcCCCCC
Q 013311 403 EEEFILDWYQKGLGGA 418 (445)
Q Consensus 403 eEE~Il~W~~k~s~~~ 418 (445)
.|+.+.+|.... ..|
T Consensus 191 ~e~e~~~W~~~h-~eY 205 (234)
T PF10474_consen 191 PEEELEEWIRTH-TEY 205 (234)
T ss_pred CHHHHHHHHHhC-ccc
Confidence 788999999775 444
No 52
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=66.27 E-value=3.2 Score=31.29 Aligned_cols=33 Identities=27% Similarity=0.558 Sum_probs=24.6
Q ss_pred cccCCCCCCCceEEEecCCee-eeeccccCCcccc
Q 013311 99 VQCYGCGNPETDIIITKTQMV-NLKCAACGFVSEV 132 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~-~~~C~aCG~~~~v 132 (445)
..|..|+..+|.+-+ ++..- .+-|.|||-....
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 369999999999998 43222 4889999966443
No 53
>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=65.34 E-value=16 Score=31.30 Aligned_cols=63 Identities=17% Similarity=0.095 Sum_probs=44.6
Q ss_pred ceEEEecc--CCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHH
Q 013311 23 MITKIEGR--GNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLE 92 (445)
Q Consensus 23 ~~~k~eG~--gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~ 92 (445)
+.+.++-+ |+=.=|+|.||..-. -++.-+.++|...+|+.|++. ++.+.|+|.|...-. ++|.
T Consensus 26 i~i~~e~rgr~gK~VTvV~Gl~~~~----~~l~~l~k~LKk~~gcGgtvk--~~~IeiQGD~~~~v~-~~L~ 90 (101)
T TIGR01158 26 VRIQRETRGRKGKGVTIIEGLDLSD----IDLKELAKELKSKCGCGGTVK--DGVIEIQGDHRDRVK-DLLE 90 (101)
T ss_pred EEEEEEEecCCCCEEEEEeCCcCch----hhHHHHHHHHHHHhcCCeeEe--CCEEEEeCcHHHHHH-HHHH
Confidence 34555544 444558899996322 246788999999999999994 689999999976544 4443
No 54
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=65.14 E-value=7.6 Score=27.52 Aligned_cols=28 Identities=21% Similarity=0.558 Sum_probs=20.9
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
.||.|+.+=..... ..+..-.|.+||-.
T Consensus 1 ~CP~C~~~l~~~~~--~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRL--GDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEE--CCEEEEECCCCCeE
Confidence 49999995444443 56888999999965
No 55
>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=65.08 E-value=4.6 Score=28.02 Aligned_cols=29 Identities=31% Similarity=0.761 Sum_probs=18.2
Q ss_pred ccCCCCCCCceEEEe--cCCeeeeeccccCCccccc
Q 013311 100 QCYGCGNPETDIIIT--KTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 100 lC~~C~~peT~l~~~--k~~~~~~~C~aCG~~~~v~ 133 (445)
-||.|+|. |... +...+ .|..||+..+++
T Consensus 3 FCp~C~nl---L~p~~~~~~~~--~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 3 FCPECGNL---LYPKEDKEKRV--ACRTCGYEEPIS 33 (35)
T ss_dssp BETTTTSB---EEEEEETTTTE--EESSSS-EEE-S
T ss_pred eCCCCCcc---ceEcCCCccCc--CCCCCCCccCCC
Confidence 59999984 3332 22323 999999988765
No 56
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=64.67 E-value=4.6 Score=37.18 Aligned_cols=32 Identities=25% Similarity=0.578 Sum_probs=22.9
Q ss_pred ccCCCCCCCceEEEe---cCC-ee--eeeccccCCccc
Q 013311 100 QCYGCGNPETDIIIT---KTQ-MV--NLKCAACGFVSE 131 (445)
Q Consensus 100 lC~~C~~peT~l~~~---k~~-~~--~~~C~aCG~~~~ 131 (445)
.||.|+.++|.++-. .++ .| -..|..||.+-+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccc
Confidence 599999999999852 112 22 267999997643
No 57
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=64.61 E-value=7.2 Score=44.66 Aligned_cols=41 Identities=22% Similarity=0.477 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhhc----------------------cccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 84 TAKLAGLLENFIKKY----------------------VQCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 84 ~~~l~~~l~~fi~~f----------------------VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
+..|-..|..|+..- ..||+|+. | |+. ..+ ...|..||+..
T Consensus 688 pDaI~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~--~-l~~-~~G--C~~C~~CG~sk 750 (752)
T PRK08665 688 PDAIAKVLEKHYLGGGKDVGAGNGTGSAGIEAPAPERGACPECGS--I-LEH-EEG--CVVCHSCGYSK 750 (752)
T ss_pred HHHHHHHHHHHHHhccccccccccccccccccccCCCCCCCCCCc--c-cEE-CCC--CCcCCCCCCCC
Confidence 567777777776540 35999984 3 666 444 66999999865
No 58
>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=64.25 E-value=5.9 Score=36.92 Aligned_cols=31 Identities=23% Similarity=0.595 Sum_probs=19.9
Q ss_pred cCCCCCC-CceEEE-ec----CCe--eeeeccccCCccc
Q 013311 101 CYGCGNP-ETDIII-TK----TQM--VNLKCAACGFVSE 131 (445)
Q Consensus 101 C~~C~~p-eT~l~~-~k----~~~--~~~~C~aCG~~~~ 131 (445)
||.|+.+ .+.+.. .+ +.+ +...|..||++..
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 343222 11 123 3579999999854
No 59
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=64.17 E-value=15 Score=33.34 Aligned_cols=94 Identities=19% Similarity=0.160 Sum_probs=49.4
Q ss_pred chHHHHHHhCCCchHHHHHHH--Hh--hcCcc---cccCCCC-----eEEEEeecCHHHHHHHHHHH------------H
Q 013311 40 NMVDIAKALARPPSYTTKYFG--NE--LGAQS---KFDEKTG-----TSLVNGAHDTAKLAGLLENF------------I 95 (445)
Q Consensus 40 N~~~ia~~L~R~p~~~~ky~~--~E--Lg~~~---~~~~~~~-----~~ii~G~~~~~~l~~~l~~f------------i 95 (445)
-=.+||..|+-++..|-+.+. .+ ++... ..++.++ .|.|+-.+-...|.-.|..- -
T Consensus 17 ~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~~~~~L~~~l~~e~~ 96 (147)
T smart00531 17 TEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDKMRKRLEDKLEDETN 96 (147)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHHHHHHHHHHHhcccC
Confidence 357899999999999888654 45 44222 2344233 13344333222221111111 2
Q ss_pred hhccccCCCCCCCceEEEe--cCCeeeeeccccCCccccc
Q 013311 96 KKYVQCYGCGNPETDIIIT--KTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 96 ~~fVlC~~C~~peT~l~~~--k~~~~~~~C~aCG~~~~v~ 133 (445)
..|..||.|+.-=|.+... .+..-...|.-||+.=...
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 3478899998532221110 0111228999999875444
No 60
>PHA00626 hypothetical protein
Probab=63.69 E-value=5.5 Score=30.76 Aligned_cols=34 Identities=24% Similarity=0.511 Sum_probs=22.7
Q ss_pred ccCCCCCCCceEEEe-cCCeeeeeccccCCccccc
Q 013311 100 QCYGCGNPETDIIIT-KTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 100 lC~~C~~peT~l~~~-k~~~~~~~C~aCG~~~~v~ 133 (445)
.||.|++-+-..-.. .+..---+|.-||+.-+-+
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechh
Confidence 699999965443211 2223456899999998776
No 61
>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=63.31 E-value=3.2 Score=37.98 Aligned_cols=31 Identities=32% Similarity=0.547 Sum_probs=22.8
Q ss_pred cccCCCCCCCceEEEecCC---eeeeeccccCCc
Q 013311 99 VQCYGCGNPETDIIITKTQ---MVNLKCAACGFV 129 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~---~~~~~C~aCG~~ 129 (445)
|.||.|+|.+|.++-.=+. .-..+|.+|...
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~ep 139 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEP 139 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCc
Confidence 8999999999999962121 134688888753
No 62
>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=62.51 E-value=8 Score=30.61 Aligned_cols=32 Identities=25% Similarity=0.720 Sum_probs=22.0
Q ss_pred ccCCCCCCCceEE--------------EecCCeeeeeccccCCccc
Q 013311 100 QCYGCGNPETDII--------------ITKTQMVNLKCAACGFVSE 131 (445)
Q Consensus 100 lC~~C~~peT~l~--------------~~k~~~~~~~C~aCG~~~~ 131 (445)
.||.|++-+...- +..++.+...|..||+.-.
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~ 47 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEF 47 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEE
Confidence 4999999765431 1123566789999999743
No 63
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=62.22 E-value=6.9 Score=32.85 Aligned_cols=44 Identities=25% Similarity=0.285 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 84 TAKLAGLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 84 ~~~l~~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
.....++...-...| .||.|+.+ |.--+ ..+ +-.|.-||+...-
T Consensus 22 Rrrv~~ie~~~~~~~-~Cp~C~~~-~VkR~-a~G--IW~C~kCg~~fAG 65 (89)
T COG1997 22 RRRVKEIEAQQRAKH-VCPFCGRT-TVKRI-ATG--IWKCRKCGAKFAG 65 (89)
T ss_pred HHHHHHHHHHHhcCC-cCCCCCCc-ceeee-ccC--eEEcCCCCCeecc
Confidence 345555555555554 59999999 43333 434 5579999987543
No 64
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=61.75 E-value=6.9 Score=38.88 Aligned_cols=41 Identities=20% Similarity=0.269 Sum_probs=30.8
Q ss_pred HHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 89 GLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 89 ~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
..|-.|-..+-.|+.|+.| |.+. ...+.+.|.+||......
T Consensus 90 ~~l~~w~~~~~fC~~CG~~-~~~~---~~~~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 90 VQLAEFYRSHRFCGYCGHP-MHPS---KTEWAMLCPHCRERYYPR 130 (256)
T ss_pred HHHHHHhhcCccccccCCC-Ceec---CCceeEECCCCCCEECCC
Confidence 3467888999999999998 4433 234678999999876544
No 65
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=61.35 E-value=6.7 Score=33.76 Aligned_cols=38 Identities=21% Similarity=0.547 Sum_probs=29.1
Q ss_pred HhhccccCCCCCCCce---EEEecCCeeeeeccccCCccccc
Q 013311 95 IKKYVQCYGCGNPETD---IIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 95 i~~fVlC~~C~~peT~---l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
+.++--||.|+.---. +.+ +....++.|..||.+..+.
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 3456789999985444 555 5678899999999988776
No 66
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=61.00 E-value=8.7 Score=32.97 Aligned_cols=31 Identities=26% Similarity=0.668 Sum_probs=24.5
Q ss_pred ccCCCCCCCceEEEecC-CeeeeeccccCCccccc
Q 013311 100 QCYGCGNPETDIIITKT-QMVNLKCAACGFVSEVD 133 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~-~~~~~~C~aCG~~~~v~ 133 (445)
.||.|+| .|++.++ ...-+.|..|++..++.
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 4666433 34679999999999887
No 67
>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=60.86 E-value=6 Score=36.72 Aligned_cols=33 Identities=27% Similarity=0.822 Sum_probs=17.7
Q ss_pred cccCCCCCCC-ceEEEec----CCe--eeeeccccCCccc
Q 013311 99 VQCYGCGNPE-TDIIITK----TQM--VNLKCAACGFVSE 131 (445)
Q Consensus 99 VlC~~C~~pe-T~l~~~k----~~~--~~~~C~aCG~~~~ 131 (445)
.+||.|+.+- |.+...+ +.+ ....|..||++..
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ 41 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNN 41 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEE
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEee
Confidence 4799999985 4443321 122 3468999999854
No 68
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=60.42 E-value=8.4 Score=36.86 Aligned_cols=32 Identities=28% Similarity=0.690 Sum_probs=21.2
Q ss_pred ccCCCCCC-CceEEEec-----CCe--eeeeccccCCccc
Q 013311 100 QCYGCGNP-ETDIIITK-----TQM--VNLKCAACGFVSE 131 (445)
Q Consensus 100 lC~~C~~p-eT~l~~~k-----~~~--~~~~C~aCG~~~~ 131 (445)
-||.|+.+ .|.+...+ +.+ ....|..||++..
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSN 41 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccc
Confidence 49999976 44444423 122 3579999999854
No 69
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=59.88 E-value=8.5 Score=35.73 Aligned_cols=32 Identities=25% Similarity=0.853 Sum_probs=20.7
Q ss_pred ccCCCCCCCc-eEEEec----CCe--eeeeccccCCccc
Q 013311 100 QCYGCGNPET-DIIITK----TQM--VNLKCAACGFVSE 131 (445)
Q Consensus 100 lC~~C~~peT-~l~~~k----~~~--~~~~C~aCG~~~~ 131 (445)
+||.|+.+=| .+...+ +.+ ....|..||++..
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ 40 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNN 40 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccc
Confidence 6999987544 333321 122 3579999999853
No 70
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=59.73 E-value=4.1 Score=28.38 Aligned_cols=29 Identities=24% Similarity=0.692 Sum_probs=19.7
Q ss_pred ccccCCCCC----CCceEEEecCCeeeeeccccCCc
Q 013311 98 YVQCYGCGN----PETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 98 fVlC~~C~~----peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
.+.||.|+. ||..|- .+...++|..||+.
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 478999975 333322 24458999999975
No 71
>PLN00209 ribosomal protein S27; Provisional
Probab=59.45 E-value=7.1 Score=32.66 Aligned_cols=30 Identities=30% Similarity=0.471 Sum_probs=24.1
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
-|.||.|.+.-|.+-. -.....|..||..=
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 5999999998776665 45678999999764
No 72
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=58.61 E-value=8.1 Score=37.14 Aligned_cols=33 Identities=21% Similarity=0.534 Sum_probs=21.1
Q ss_pred ccccCCCCCCCceEEEe--c----CCe--eeeeccccCCccc
Q 013311 98 YVQCYGCGNPETDIIIT--K----TQM--VNLKCAACGFVSE 131 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~--k----~~~--~~~~C~aCG~~~~ 131 (445)
-+-||.|+. .-.++-. + +++ ....|..||++..
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 467999999 2222220 1 233 3589999999954
No 73
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=58.33 E-value=9.2 Score=30.37 Aligned_cols=36 Identities=22% Similarity=0.691 Sum_probs=23.8
Q ss_pred ccccCCCCCCCce---EE-----------EecCCeeeeeccccCCccccc
Q 013311 98 YVQCYGCGNPETD---II-----------ITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 98 fVlC~~C~~peT~---l~-----------~~k~~~~~~~C~aCG~~~~v~ 133 (445)
+-.||.|+|-+-. |. +.-++.+...|+.||+.-.-+
T Consensus 4 ~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY~ 53 (68)
T COG3478 4 AFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFYS 53 (68)
T ss_pred cccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhhee
Confidence 4459999985421 11 113577889999999975443
No 74
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=58.32 E-value=8.9 Score=27.80 Aligned_cols=35 Identities=20% Similarity=0.584 Sum_probs=23.3
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCCcccccchhh
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDK 137 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~k 137 (445)
..|+.|+. .+.. .......+|..||+.-....+.+
T Consensus 4 y~C~~CG~---~~~~-~~~~~~~~Cp~CG~~~~~~~~~~ 38 (46)
T PRK00398 4 YKCARCGR---EVEL-DEYGTGVRCPYCGYRILFKERPP 38 (46)
T ss_pred EECCCCCC---EEEE-CCCCCceECCCCCCeEEEccCCC
Confidence 46999997 3444 22222789999998776665443
No 75
>PRK03954 ribonuclease P protein component 4; Validated
Probab=57.12 E-value=9.3 Score=33.98 Aligned_cols=39 Identities=18% Similarity=0.456 Sum_probs=25.9
Q ss_pred HHHhhccccCCCCCC-----CceEEEecCC---eeeeeccccCCccccc
Q 013311 93 NFIKKYVQCYGCGNP-----ETDIIITKTQ---MVNLKCAACGFVSEVD 133 (445)
Q Consensus 93 ~fi~~fVlC~~C~~p-----eT~l~~~k~~---~~~~~C~aCG~~~~v~ 133 (445)
..|+. -+|..|.+| ...+-+ .++ .+...|..||+..-.+
T Consensus 60 ~~~KR-~~CK~C~t~LiPG~n~~vRi-~~~~~~~vvitCl~CG~~kR~P 106 (121)
T PRK03954 60 RKWKR-RYCKRCHSFLVPGVNARVRL-RQKRMPHVVITCLECGHIMRYP 106 (121)
T ss_pred HHHHH-HHhhcCCCeeecCCceEEEE-ecCCcceEEEECccCCCEEeec
Confidence 33443 479999886 334444 332 6889999999986544
No 76
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=56.89 E-value=6.6 Score=30.70 Aligned_cols=33 Identities=18% Similarity=0.583 Sum_probs=24.9
Q ss_pred hccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 97 KYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 97 ~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
.-+-||.|+.| |...+ ..-.+.|..||-..++.
T Consensus 7 eiLaCP~~kg~---L~~~~-~~~~L~c~~~~~aYpI~ 39 (60)
T COG2835 7 EILACPVCKGP---LVYDE-EKQELICPRCKLAYPIR 39 (60)
T ss_pred eeeeccCcCCc---ceEec-cCCEEEecccCceeecc
Confidence 45789999999 55422 22389999999998875
No 77
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=56.88 E-value=9.4 Score=33.41 Aligned_cols=33 Identities=27% Similarity=0.523 Sum_probs=25.5
Q ss_pred ccccCCCCCCCceEEEe------cCCeeeeeccccCCcc
Q 013311 98 YVQCYGCGNPETDIIIT------KTQMVNLKCAACGFVS 130 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~------k~~~~~~~C~aCG~~~ 130 (445)
-+.||.|++-+-.+..- ..-+.|-+|..||++-
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 37899999988776652 2357899999999863
No 78
>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=56.34 E-value=9 Score=33.47 Aligned_cols=28 Identities=18% Similarity=0.138 Sum_probs=17.0
Q ss_pred CCCchHHHHHHHHhhcCcccccCCCCeEEEE
Q 013311 49 ARPPSYTTKYFGNELGAQSKFDEKTGTSLVN 79 (445)
Q Consensus 49 ~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~ 79 (445)
+-.|+.+.-.| ++-+.+++-+ +-+|.|.
T Consensus 38 ~V~p~~L~faf--~~~~~~t~~e-ga~L~I~ 65 (115)
T TIGR00100 38 CVNPSQLQFAF--EVVREGTVAE-GAKLNIE 65 (115)
T ss_pred ccCHHHHHHHH--HHHhCCCccC-CCEEEEE
Confidence 34577776555 4456666654 5677764
No 79
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=56.17 E-value=2.1 Score=33.48 Aligned_cols=38 Identities=21% Similarity=0.505 Sum_probs=30.4
Q ss_pred HHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 92 ENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 92 ~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
.+||-- -.||.|.--||--.-.++++-...|-+||+.-
T Consensus 5 KRFIAG-A~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 5 KRFIAG-AVCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred hhhhcc-CCCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 456665 46999999999655447889999999999874
No 80
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=55.50 E-value=8.9 Score=39.34 Aligned_cols=36 Identities=22% Similarity=0.430 Sum_probs=26.7
Q ss_pred ccccCCCCC-CCceEEEe--cCCeeeeeccccCCccccc
Q 013311 98 YVQCYGCGN-PETDIIIT--KTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 98 fVlC~~C~~-peT~l~~~--k~~~~~~~C~aCG~~~~v~ 133 (445)
--.||.|++ |-..+++. +++.-+++|.-||..-.+.
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~ 225 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVV 225 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccccc
Confidence 478999999 55555532 3577899999999886654
No 81
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=55.24 E-value=5.9 Score=39.95 Aligned_cols=31 Identities=23% Similarity=0.547 Sum_probs=24.7
Q ss_pred ccccCCCCC-CCceEEEec---CCeeeeeccccCC
Q 013311 98 YVQCYGCGN-PETDIIITK---TQMVNLKCAACGF 128 (445)
Q Consensus 98 fVlC~~C~~-peT~l~~~k---~~~~~~~C~aCG~ 128 (445)
--.||.|++ |=+.++... .++-+++|.-|-.
T Consensus 185 ~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~t 219 (308)
T COG3058 185 RQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCET 219 (308)
T ss_pred cccCCCcCCCCcceeeeecCccccchhhhhhhHHH
Confidence 348999999 899999842 3778999998853
No 82
>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=54.79 E-value=6.8 Score=40.12 Aligned_cols=36 Identities=22% Similarity=0.492 Sum_probs=26.3
Q ss_pred ccccCCCCC-CCceEEEe---cCCeeeeeccccCCccccc
Q 013311 98 YVQCYGCGN-PETDIIIT---KTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 98 fVlC~~C~~-peT~l~~~---k~~~~~~~C~aCG~~~~v~ 133 (445)
.-.||.|++ |-..+++. +.+.-++.|.-|+..-.+.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~ 223 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV 223 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccccc
Confidence 448999999 44455542 3577899999999886665
No 83
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=54.35 E-value=10 Score=31.69 Aligned_cols=30 Identities=23% Similarity=0.422 Sum_probs=24.0
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
-|.||.|.+.-|.+-. -.....|..||..=
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 5999999998776665 45678999999763
No 84
>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=53.82 E-value=3.3 Score=28.78 Aligned_cols=29 Identities=31% Similarity=0.590 Sum_probs=16.8
Q ss_pred cCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 101 CYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 101 C~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
|..|+..+|.+-+.....-..-|+|||-.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLY 29 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHH
Confidence 88999999999983222223389999853
No 85
>PRK07451 translation initiation factor Sui1; Validated
Probab=53.64 E-value=31 Score=30.42 Aligned_cols=59 Identities=15% Similarity=0.164 Sum_probs=41.4
Q ss_pred eEEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHH
Q 013311 24 ITKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLA 88 (445)
Q Consensus 24 ~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~ 88 (445)
++...||++=.=|+|.+|..-... -.-+.|.|-..+|+.|++- ++.+.|+|.|...-.+
T Consensus 43 ~~~r~gR~GK~VTvV~Gl~~~~~d----lk~LaK~LK~k~gcGGtvk--d~~IelQGD~r~~v~~ 101 (115)
T PRK07451 43 QATRSGRKGKTVTVITGFQHKPET----LAKLLKQLKTQCGSGGTVK--DNTIEIQGDHRQKILE 101 (115)
T ss_pred EEEecCCCCCeEEEEeCCCCCHHH----HHHHHHHHHHHhcCCceEc--CCEEEEcCcHHHHHHH
Confidence 334557754456888888632222 3567889999999999994 6789999999754433
No 86
>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=52.12 E-value=21 Score=32.29 Aligned_cols=58 Identities=21% Similarity=0.391 Sum_probs=39.5
Q ss_pred EEEEeecCHHHHHHHHHHHH-----hh-ccccCCCCCCCceEEEe-----------cCCeeeeeccccCCccccc
Q 013311 76 SLVNGAHDTAKLAGLLENFI-----KK-YVQCYGCGNPETDIIIT-----------KTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 76 ~ii~G~~~~~~l~~~l~~fi-----~~-fVlC~~C~~peT~l~~~-----------k~~~~~~~C~aCG~~~~v~ 133 (445)
+.|......++|..++..|= +. |-.|+.|+.|=..+.++ ....-|-.|..||...=..
T Consensus 63 ~li~~~~~~~QL~ev~~~~~l~~~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~G 137 (147)
T PF01927_consen 63 ILIRSDDPEEQLREVLERFGLKLRLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEG 137 (147)
T ss_pred EEEcCCCHHHHHHHHHHHcCCccccCCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEeccc
Confidence 55677777899999998873 33 78999999944333221 0012389999999875444
No 87
>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=51.93 E-value=38 Score=23.28 Aligned_cols=46 Identities=17% Similarity=0.161 Sum_probs=32.9
Q ss_pred chHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHH
Q 013311 40 NMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLL 91 (445)
Q Consensus 40 N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l 91 (445)
++.++|+.|+.++..+.+|............ ++++. |+...|..++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~~~~~~~~--~~~~~----~~~~ei~~~~ 47 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRTP--GGHRR----FPEEDLERLL 47 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCceeCC--CCcee----cCHHHHHHHH
Confidence 5789999999999999999987664433221 34443 6777777665
No 88
>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=51.88 E-value=12 Score=31.49 Aligned_cols=66 Identities=20% Similarity=0.286 Sum_probs=47.5
Q ss_pred hHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEee-cCHHHHHHHHHHHHhhccccCCCCCCCceEEEecC
Q 013311 41 MVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGA-HDTAKLAGLLENFIKKYVQCYGCGNPETDIIITKT 116 (445)
Q Consensus 41 ~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~-~~~~~l~~~l~~fi~~fVlC~~C~~peT~l~~~k~ 116 (445)
+.-||++|+|++..|.+.+....+..- + ..+..|. ++-..|+.++. -|=+|..|.-....++.+..
T Consensus 7 i~AiA~aL~R~~~dVl~Vl~~~~~~~~-~-----~~l~~G~Gl~l~~le~~f~----~F~I~A~v~~~g~~~~lN~~ 73 (89)
T PF05379_consen 7 IRAIAEALGRREQDVLAVLSRKCGEEL-L-----EELWSGEGLDLEDLEELFE----LFDICAHVNFGGETFVLNEE 73 (89)
T ss_pred hHHHHHHhCCCHHHHHHHHHhccCHHH-H-----HHHHcCCCcCHHHHHHHHH----HcCeEEEEEECCEEEEECCC
Confidence 357999999999999999999887432 2 2344454 56666666654 46899999877777777533
No 89
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=51.85 E-value=12 Score=32.78 Aligned_cols=28 Identities=11% Similarity=-0.072 Sum_probs=16.7
Q ss_pred CCCchHHHHHHHHhhcCccc-ccCCCCeEEEE
Q 013311 49 ARPPSYTTKYFGNELGAQSK-FDEKTGTSLVN 79 (445)
Q Consensus 49 ~R~p~~~~ky~~~ELg~~~~-~~~~~~~~ii~ 79 (445)
.-.|+.+.-.| ++-++++ +-+ +-++.|.
T Consensus 38 ~V~pe~L~faf--~~~~~~T~~~e-ga~L~Ie 66 (117)
T PRK00564 38 GMDKSLFVSAF--ETFREESLVCK-DAILDIV 66 (117)
T ss_pred CcCHHHHHHHH--HHHhcCCcccC-CCEEEEE
Confidence 34577776555 4456666 543 6677775
No 90
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=51.76 E-value=3.9 Score=27.50 Aligned_cols=28 Identities=25% Similarity=0.496 Sum_probs=15.4
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
.-.|+.|+.|- .+.. .-+.+.|.+||..
T Consensus 3 ~rfC~~CG~~t-~~~~---~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPT-KPAP---GGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BE-EE-S---SSS-EEESSSS-E
T ss_pred CcccCcCCccc-cCCC---CcCEeECCCCcCE
Confidence 34699999983 3332 3578999999975
No 91
>PF14353 CpXC: CpXC protein
Probab=50.98 E-value=14 Score=32.41 Aligned_cols=35 Identities=20% Similarity=0.552 Sum_probs=0.0
Q ss_pred cccCCCCCCCceEEEec---------------CCeeeeeccccCCccccc
Q 013311 99 VQCYGCGNPETDIIITK---------------TQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k---------------~~~~~~~C~aCG~~~~v~ 133 (445)
+.||.|+.+-+.-+-+- +.+....|..||+...++
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
No 92
>PRK00420 hypothetical protein; Validated
Probab=49.93 E-value=19 Score=31.62 Aligned_cols=41 Identities=22% Similarity=0.323 Sum_probs=28.0
Q ss_pred HHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCcccccchh
Q 013311 91 LENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRD 136 (445)
Q Consensus 91 l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~ 136 (445)
|.++-=.--.||.|+.|=+.+ + . + ...|..||..-.|...+
T Consensus 16 l~Ga~ml~~~CP~Cg~pLf~l-k-~-g--~~~Cp~Cg~~~~v~~~e 56 (112)
T PRK00420 16 LKGAKMLSKHCPVCGLPLFEL-K-D-G--EVVCPVHGKVYIVKSDE 56 (112)
T ss_pred HhHHHHccCCCCCCCCcceec-C-C-C--ceECCCCCCeeeeccHH
Confidence 333333346899999998777 3 2 3 56799999977776444
No 93
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=49.72 E-value=13 Score=33.48 Aligned_cols=49 Identities=14% Similarity=0.224 Sum_probs=28.1
Q ss_pred hHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHHHhhccccCCCCC
Q 013311 41 MVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENFIKKYVQCYGCGN 106 (445)
Q Consensus 41 ~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~fVlC~~C~~ 106 (445)
+-.|...=.-.|+.+...|.. + +++++-. +-++.|.- +.-...|+.|+.
T Consensus 30 ~l~IG~ls~V~pe~L~fafe~-l-~~gt~~e-ga~L~i~~--------------~p~~~~C~~CG~ 78 (135)
T PRK03824 30 KVVLGELQDVDKEIVEFALNE-L-LKGTILE-GAEIIFEE--------------EEAVLKCRNCGN 78 (135)
T ss_pred HhhHhhhhhhhHHHHHHHHHH-H-HcCCccc-CCEEEEEe--------------cceEEECCCCCC
Confidence 345555555667777777754 4 4444432 45666653 223577777773
No 94
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=49.03 E-value=12 Score=33.64 Aligned_cols=24 Identities=33% Similarity=0.982 Sum_probs=18.5
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
-||.|+.| |.+ +++ -..|.-||++
T Consensus 30 hCp~Cg~P---LF~-KdG--~v~CPvC~~~ 53 (131)
T COG1645 30 HCPKCGTP---LFR-KDG--EVFCPVCGYR 53 (131)
T ss_pred hCcccCCc---cee-eCC--eEECCCCCce
Confidence 59999998 555 555 4569999984
No 95
>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=48.62 E-value=21 Score=25.20 Aligned_cols=33 Identities=21% Similarity=0.566 Sum_probs=21.1
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccc---cCCccccc
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAA---CGFVSEVD 133 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~a---CG~~~~v~ 133 (445)
+.||.|+++ -+++..+...|+-|.. |.+..++.
T Consensus 2 ~~CP~Cg~~--lv~r~~k~g~F~~Cs~yP~C~~~~~~~ 37 (39)
T PF01396_consen 2 EKCPKCGGP--LVLRRGKKGKFLGCSNYPECKYTEPLP 37 (39)
T ss_pred cCCCCCCce--eEEEECCCCCEEECCCCCCcCCeEeCC
Confidence 579999942 2233222338899987 87776654
No 96
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=48.62 E-value=13 Score=32.39 Aligned_cols=28 Identities=14% Similarity=0.042 Sum_probs=17.2
Q ss_pred CCCchHHHHHHHHhhcCcccccCCCCeEEEE
Q 013311 49 ARPPSYTTKYFGNELGAQSKFDEKTGTSLVN 79 (445)
Q Consensus 49 ~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~ 79 (445)
+-.|+.+.-.|. +-+++++-+ +-++.|.
T Consensus 38 ~V~p~~L~f~f~--~~~~~t~~e-gA~L~i~ 65 (114)
T PRK03681 38 CVETSSLAFCFD--LVCRGTVAE-GCKLHLE 65 (114)
T ss_pred ccCHHHHHHHHH--HHhCCCccC-CCEEEEE
Confidence 445777776664 445666653 6677774
No 97
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=48.43 E-value=11 Score=39.74 Aligned_cols=32 Identities=31% Similarity=0.839 Sum_probs=23.4
Q ss_pred ccCCCCCC-CceEEEec----CCee--eeeccccCCccc
Q 013311 100 QCYGCGNP-ETDIIITK----TQMV--NLKCAACGFVSE 131 (445)
Q Consensus 100 lC~~C~~p-eT~l~~~k----~~~~--~~~C~aCG~~~~ 131 (445)
-||+|.-| ||.|...+ +.+| ...|.+||+++.
T Consensus 260 ~Cp~C~~pcet~Mk~~~IPhFkeVIiMst~Cd~CGyksn 298 (460)
T KOG2703|consen 260 TCPSCTAPCETNMKLTDIPHFKEVIIMSTVCDRCGYKSN 298 (460)
T ss_pred CCCCCCCchhccceeccCCcceeEEEEeecccccCCccc
Confidence 59999996 78887632 2333 478999999864
No 98
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=48.29 E-value=12 Score=38.09 Aligned_cols=29 Identities=31% Similarity=0.751 Sum_probs=21.6
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
-..||.|++ |.++.+ ...-.+.|.-||..
T Consensus 11 ~~~Cp~Cg~--~~iv~d-~~~Ge~vC~~CG~V 39 (310)
T PRK00423 11 KLVCPECGS--DKLIYD-YERGEIVCADCGLV 39 (310)
T ss_pred CCcCcCCCC--CCeeEE-CCCCeEeecccCCc
Confidence 357999997 467663 34557899999985
No 99
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=46.36 E-value=21 Score=37.95 Aligned_cols=33 Identities=12% Similarity=0.217 Sum_probs=23.7
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
.+||-|.--...+.++. ..-+-+|-+||..+.+
T Consensus 35 ~~CPfh~ek~pSf~v~~-~k~~~~Cf~Cg~~Gd~ 67 (415)
T TIGR01391 35 GLCPFHHEKTPSFSVSP-EKQFYHCFGCGAGGDA 67 (415)
T ss_pred eeCCCCCCCCCeEEEEc-CCCcEEECCCCCCCCH
Confidence 48999976555777742 2336789999997654
No 100
>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=46.29 E-value=15 Score=28.01 Aligned_cols=31 Identities=16% Similarity=0.400 Sum_probs=23.2
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
++|+.|..-.=-.-+.+...+.-+|..||+.
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 6899999866555333557779999999975
No 101
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=46.20 E-value=16 Score=31.91 Aligned_cols=28 Identities=11% Similarity=-0.001 Sum_probs=17.4
Q ss_pred CCCchHHHHHHHHhhcCcccccCCCCeEEEE
Q 013311 49 ARPPSYTTKYFGNELGAQSKFDEKTGTSLVN 79 (445)
Q Consensus 49 ~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~ 79 (445)
.-.|+.+.-+| ++-+++++-+ +-+|.|.
T Consensus 38 ~v~pe~L~f~f--~~~~~~T~~e-gA~L~I~ 65 (113)
T PRK12380 38 CVEESAVRFSF--EIVCHGTVAQ-GCDLHIV 65 (113)
T ss_pred ccCHHHHHHHH--HHHhCCCccC-CCEEEEE
Confidence 44577777666 4556666543 5677774
No 102
>PRK05580 primosome assembly protein PriA; Validated
Probab=46.03 E-value=17 Score=41.12 Aligned_cols=50 Identities=18% Similarity=0.517 Sum_probs=30.9
Q ss_pred ccccCCCCCC------CceEEEecCCeeeeeccccCCccccc----------------chhhhhHHHhcCCCC
Q 013311 98 YVQCYGCGNP------ETDIIITKTQMVNLKCAACGFVSEVD----------------MRDKLTTFILKNPPV 148 (445)
Q Consensus 98 fVlC~~C~~p------eT~l~~~k~~~~~~~C~aCG~~~~v~----------------~~~kl~~~i~k~pP~ 148 (445)
||.|..|+.+ +..|...+ ..-.+.|.-||+..+++ ...|+...+-++-|.
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 FLLCRDCGWVAECPHCDASLTLHR-FQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEEELAELFPE 452 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEEC-CCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHHHHHHHHhCCC
Confidence 5666666643 23344311 22367888888876542 357888888888775
No 103
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=45.82 E-value=12 Score=32.82 Aligned_cols=33 Identities=24% Similarity=0.494 Sum_probs=26.4
Q ss_pred ccCCCCCCCceEE----E--ecCCeeeeeccccCCcccc
Q 013311 100 QCYGCGNPETDII----I--TKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 100 lC~~C~~peT~l~----~--~k~~~~~~~C~aCG~~~~v 132 (445)
.||.|++++-.+. + +++++.|-.|..||++-..
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 6999999886554 2 3679999999999998654
No 104
>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=45.78 E-value=14 Score=25.64 Aligned_cols=28 Identities=21% Similarity=0.451 Sum_probs=20.2
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCC
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGF 128 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~ 128 (445)
.|+.|+..=+.+.. -...-...|-.||+
T Consensus 7 ~C~~Cg~~fe~~~~-~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQK-ISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEe-cCCCCCCCCCCCCC
Confidence 69999996655554 22245778999998
No 105
>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=45.77 E-value=5.6 Score=30.58 Aligned_cols=30 Identities=37% Similarity=0.649 Sum_probs=18.1
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
-|.||.|.+.-|.+ ..-.....|..||..=
T Consensus 7 ~VkCp~C~~~q~vF---Sha~t~V~C~~Cg~~L 36 (55)
T PF01667_consen 7 DVKCPGCYNIQTVF---SHAQTVVKCVVCGTVL 36 (55)
T ss_dssp EEE-TTT-SEEEEE---TT-SS-EE-SSSTSEE
T ss_pred EEECCCCCCeeEEE---ecCCeEEEcccCCCEe
Confidence 48999999865543 3355678999999863
No 106
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.62 E-value=17 Score=32.13 Aligned_cols=28 Identities=14% Similarity=0.135 Sum_probs=17.0
Q ss_pred CCCchHHHHHHHHhhcCcccccCCCCeEEEE
Q 013311 49 ARPPSYTTKYFGNELGAQSKFDEKTGTSLVN 79 (445)
Q Consensus 49 ~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~ 79 (445)
.-.|+.|.-+|. +-+.+++-+ +-.|.|.
T Consensus 38 ~V~pe~L~faf~--~~~~gT~~e-gA~L~I~ 65 (124)
T PRK00762 38 MLNPEQLRFMLD--VLAEGTIAE-DADLIVE 65 (124)
T ss_pred ccCHHHHHHHHH--HHhCCCCcC-CCEEEEE
Confidence 335777776664 455666654 5567664
No 107
>PRK11827 hypothetical protein; Provisional
Probab=45.43 E-value=14 Score=28.96 Aligned_cols=36 Identities=11% Similarity=0.136 Sum_probs=24.4
Q ss_pred HHhhccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 94 FIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 94 fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
.+-+.+-||.|+.|=. +.. . .-.+.|.+||-..||.
T Consensus 4 ~LLeILaCP~ckg~L~-~~~-~--~~~Lic~~~~laYPI~ 39 (60)
T PRK11827 4 RLLEIIACPVCNGKLW-YNQ-E--KQELICKLDNLAFPLR 39 (60)
T ss_pred HHHhheECCCCCCcCe-EcC-C--CCeEECCccCeecccc
Confidence 3445688999998633 222 2 2257799999998885
No 108
>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=45.18 E-value=9.2 Score=36.92 Aligned_cols=67 Identities=25% Similarity=0.263 Sum_probs=48.8
Q ss_pred hCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHHHhhc------cccCCCCCCC-ceEEEe
Q 013311 48 LARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENFIKKY------VQCYGCGNPE-TDIIIT 114 (445)
Q Consensus 48 L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~f------VlC~~C~~pe-T~l~~~ 114 (445)
-.|...++.|+|..|++-.-+-..+=+++.+||--+...+..-|+.=|+.| |+|..|++.+ |.|.++
T Consensus 44 WcR~~SsLak~y~lEfdk~~~~gnsId~IRLnG~n~~~~fnq~Ir~dIk~~yk~q~Cvm~g~~g~sent~ieiD 117 (230)
T PF05315_consen 44 WCRSSSSLAKEYILEFDKRQTSGNSIDRIRLNGFNTEKVFNQNIRQDIKNYYKQQCCVMCGVRGNSENTKIEID 117 (230)
T ss_pred ccCCchHHHHHhhcccccccCCCccHHHHHHcCcCchhhhhhHHHHHHHHHHHhcCeeeecccCCCccceeeec
Confidence 358889999999999875432211124788999888888888888777776 7888888854 556653
No 109
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=45.08 E-value=14 Score=27.67 Aligned_cols=28 Identities=21% Similarity=0.539 Sum_probs=19.5
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
+-.||.|++- -|.. .. -.+.|..||..-
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 5689999984 4443 22 356899999864
No 110
>PRK05667 dnaG DNA primase; Validated
Probab=44.96 E-value=31 Score=38.42 Aligned_cols=32 Identities=16% Similarity=0.319 Sum_probs=23.6
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
+||-|.--..++.++ ...-+-+|-+||+.+.+
T Consensus 38 ~CPfH~ektpSf~V~-~~k~~~~CF~Cg~~Gd~ 69 (580)
T PRK05667 38 LCPFHDEKTPSFTVS-PDKQFYHCFGCGAGGDV 69 (580)
T ss_pred cCCCCCCCCCceEEE-CCCCeEEECCCCCCCCH
Confidence 799998655578874 23346799999997755
No 111
>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=43.35 E-value=17 Score=25.71 Aligned_cols=31 Identities=23% Similarity=0.399 Sum_probs=22.3
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCC
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGF 128 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~ 128 (445)
-+-||.|+.-|.--..+++..=.-.|..||+
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 4679999998877654444445567888886
No 112
>COG0023 SUI1 Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=42.17 E-value=1e+02 Score=26.79 Aligned_cols=74 Identities=12% Similarity=0.004 Sum_probs=49.3
Q ss_pred CCCcccc---cCCC----ceEEEeccCCC-ceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecC
Q 013311 12 DDAFYRY---KMPK----MITKIEGRGNG-IKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHD 83 (445)
Q Consensus 12 ~d~~~Ry---kmp~----~~~k~eG~gng-~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~ 83 (445)
.+|+..+ .+|. +.++++-|.-| --|+|.+|..- .-++.-+.++|-..+|+.|++- ++...|+|.|.
T Consensus 11 ~~p~e~~~~~~~k~~~~~V~I~~e~rr~gK~VTiI~Gld~~----~~dlk~Lak~LKk~cacGGtvk--~~~IeiQGdhr 84 (104)
T COG0023 11 GLPKELTCEEVAKEGDQIVRIRRETRRKGKTVTIIEGLDLK----DIDLKKLAKELKKKCACGGTVK--DGEIEIQGDHR 84 (104)
T ss_pred CCchHHhhhhcccccCCeEEEEEEeecCCcEEEEEeCcccc----hhhHHHHHHHHHHHcCCCceec--CCEEEEeChHH
Confidence 5566555 5555 34555544222 24777888752 2346678889999999999994 68999999998
Q ss_pred HHHHHHHH
Q 013311 84 TAKLAGLL 91 (445)
Q Consensus 84 ~~~l~~~l 91 (445)
..-..=|+
T Consensus 85 ~~v~~~L~ 92 (104)
T COG0023 85 DKVKELLI 92 (104)
T ss_pred HHHHHHHH
Confidence 65544433
No 113
>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=41.86 E-value=22 Score=27.24 Aligned_cols=31 Identities=29% Similarity=0.562 Sum_probs=21.5
Q ss_pred ccCCCCCCCceEEEec-CCeeeeeccccCCccccc
Q 013311 100 QCYGCGNPETDIIITK-TQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 100 lC~~C~~peT~l~~~k-~~~~~~~C~aCG~~~~v~ 133 (445)
.||.|+. .|.+.. -.-..+.|..||+.--|-
T Consensus 4 ~CP~CG~---~iev~~~~~GeiV~Cp~CGaeleVv 35 (54)
T TIGR01206 4 ECPDCGA---EIELENPELGELVICDECGAELEVV 35 (54)
T ss_pred CCCCCCC---EEecCCCccCCEEeCCCCCCEEEEE
Confidence 7999998 444421 123467999999987664
No 114
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=41.53 E-value=18 Score=34.49 Aligned_cols=27 Identities=33% Similarity=0.828 Sum_probs=20.6
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
|-+|+.|+.| |++ +-..|+|.-||+.-
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 6689999865 666 34589999999864
No 115
>COG3741 HutG N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=40.21 E-value=6.8 Score=39.24 Aligned_cols=108 Identities=19% Similarity=0.210 Sum_probs=75.5
Q ss_pred CceEEEechHHHHHHhCCCchHHHHH---HHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHHHhhccccCCCCCCCc
Q 013311 33 GIKTNVVNMVDIAKALARPPSYTTKY---FGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENFIKKYVQCYGCGNPET 109 (445)
Q Consensus 33 g~kT~i~N~~~ia~~L~R~p~~~~ky---~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~fVlC~~C~~peT 109 (445)
|--++..||+-.+=.+||+|.+..-| --..||+++.||. .+.|+--|+.+...+...|..|-+=|--|-.=..--|
T Consensus 62 GA~~l~A~fsR~~vDvNR~p~~~~l~~~~~ttGL~~~~~fdg-e~l~~~g~~~~~~e~~~Rle~~~~PYHaaL~~el~r~ 140 (272)
T COG3741 62 GATLLRANFSRAVVDVNREPDGASLYPGRVTTGLGPVTTFDG-EPLYIYGGAPTPAEALARLETLWKPYHAALRRELERL 140 (272)
T ss_pred cchhhhccccceeEecCCCCCCCcCccccccCCccccccccC-ccccccCCCCCHHHHHHHHHHhhccHHHHHHHHHHHH
Confidence 56788889999999999999999988 4567999999997 6789989999999999999999887765533222212
Q ss_pred eEEEecCCeeeeeccccCCcccccchhhhhHHHh
Q 013311 110 DIIITKTQMVNLKCAACGFVSEVDMRDKLTTFIL 143 (445)
Q Consensus 110 ~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (445)
.-+- +-.+...|..=-+..+.--.-++..|++
T Consensus 141 ~a~~--G~avLiDcHSm~s~ip~l~~G~lPdfni 172 (272)
T COG3741 141 RAIF--GAAVLIDCHSMRSHIPRLFEGPLPDFNI 172 (272)
T ss_pred Hhhc--CeEEEEeccccccccccccCCCCCceee
Confidence 2111 3445667765444444433344444544
No 116
>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=39.78 E-value=14 Score=25.50 Aligned_cols=30 Identities=23% Similarity=0.621 Sum_probs=18.6
Q ss_pred ccccCCCCCCCceEEEec----CCeeeeeccccCCcc
Q 013311 98 YVQCYGCGNPETDIIITK----TQMVNLKCAACGFVS 130 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k----~~~~~~~C~aCG~~~ 130 (445)
.+.||.|+. .+.+.. ......+|..||+.-
T Consensus 2 ~~~CP~C~~---~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKT---SFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCC---EEEeCHHHcCCCCCEEECCCCCCEE
Confidence 478999986 222211 112368899999764
No 117
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=39.19 E-value=22 Score=27.39 Aligned_cols=27 Identities=30% Similarity=0.854 Sum_probs=19.8
Q ss_pred HHhhccccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 94 FIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 94 fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
.+-.++.|+.|+++- +-...|..||.-
T Consensus 23 ~~~~l~~C~~CG~~~---------~~H~vC~~CG~Y 49 (57)
T PRK12286 23 KAPGLVECPNCGEPK---------LPHRVCPSCGYY 49 (57)
T ss_pred cCCcceECCCCCCcc---------CCeEECCCCCcC
Confidence 345679999999863 336779999964
No 118
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=39.17 E-value=37 Score=26.36 Aligned_cols=35 Identities=31% Similarity=0.574 Sum_probs=28.2
Q ss_pred CCCCCCceEEEecCCeeeeeccccCCcccccchhhhh
Q 013311 103 GCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDKLT 139 (445)
Q Consensus 103 ~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~ 139 (445)
-|++-+=.+++ =+-.|-++|..||..-.++ |.+|-
T Consensus 15 PCG~~~Wei~R-~GaDikikC~gCg~~imlp-R~~fe 49 (57)
T PF06107_consen 15 PCGSNEWEIIR-IGADIKIKCLGCGRQIMLP-RSKFE 49 (57)
T ss_pred CCCCCEEEEEE-ccCcEEEEECCCCCEEEEe-HHHHH
Confidence 38888888887 5677889999999998887 66654
No 119
>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=38.81 E-value=29 Score=25.78 Aligned_cols=26 Identities=31% Similarity=0.379 Sum_probs=22.6
Q ss_pred hHHHHHHhCCCchHHHHHHHHhhcCc
Q 013311 41 MVDIAKALARPPSYTTKYFGNELGAQ 66 (445)
Q Consensus 41 ~~~ia~~L~R~p~~~~ky~~~ELg~~ 66 (445)
..++|+.|+.++.-|.+.+..++|..
T Consensus 6 V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 6 VSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred HHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 56999999999999999999999988
No 120
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=38.45 E-value=16 Score=31.93 Aligned_cols=45 Identities=18% Similarity=0.369 Sum_probs=28.3
Q ss_pred ccCCCCCCCceEEEe-cCCeeeeeccccCCcccccchhhhhHHHhcCCC
Q 013311 100 QCYGCGNPETDIIIT-KTQMVNLKCAACGFVSEVDMRDKLTTFILKNPP 147 (445)
Q Consensus 100 lC~~C~~peT~l~~~-k~~~~~~~C~aCG~~~~v~~~~kl~~~i~k~pP 147 (445)
-||.|+|- |+.. ++....+.|..||+.-++.+...-..++..+-|
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 3331 223349999999999999864333333443333
No 121
>KOG3221 consensus Glycolipid transfer protein [Carbohydrate transport and metabolism]
Probab=38.14 E-value=2e+02 Score=27.73 Aligned_cols=45 Identities=18% Similarity=0.204 Sum_probs=29.0
Q ss_pred HHHHHHHHhhhhhhHHHHHHhhHHHHHHhccCchhHHHHHHHHHHHhcc
Q 013311 332 DALFVALFDGIEKGFAKEVTKKKNYLAAATQEEGSQMVLLHSLESFCGK 380 (445)
Q Consensus 332 ~vl~eaLf~~i~~~i~k~i~k~~~lL~~~~~~~~~Q~~lL~alE~~~~~ 380 (445)
+.+++..|. -+++.++.++.++......+..+..++.-|+.|+..
T Consensus 133 GwI~q~~Fk----vaLklvP~r~~Fl~als~~d~t~~~~~edi~~fl~~ 177 (199)
T KOG3221|consen 133 GWIVQSTFK----VALKLVPDRKTFLKALSAGDETYDECIEDITSFLSL 177 (199)
T ss_pred hHHHHHHHH----HHHHHcCcHHHHHHHHhcccchHHHHHHHHHHHHHH
Confidence 344444444 345556667777777655566777888888888865
No 122
>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=37.92 E-value=24 Score=29.28 Aligned_cols=21 Identities=24% Similarity=0.341 Sum_probs=15.8
Q ss_pred hHHHHHHhCCCchHHHHHHHH
Q 013311 41 MVDIAKALARPPSYTTKYFGN 61 (445)
Q Consensus 41 ~~~ia~~L~R~p~~~~ky~~~ 61 (445)
-.+||+.|+|++.||.+|+..
T Consensus 6 q~eIA~~lGks~s~Vs~~l~L 26 (93)
T PF08535_consen 6 QEEIAKRLGKSRSWVSNHLAL 26 (93)
T ss_dssp HHHHHHHTT--HHHHHHHHGG
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 468999999999999998874
No 123
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=37.84 E-value=23 Score=37.04 Aligned_cols=33 Identities=21% Similarity=0.301 Sum_probs=22.2
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
||+.|---.|.++....++-...|.-||+..+-
T Consensus 23 lC~dC~~~~~~~~~ip~~~~v~~C~~Cga~~~~ 55 (355)
T COG1499 23 LCGDCYVETTPLIEIPDEVNVEVCRHCGAYRIR 55 (355)
T ss_pred ccHHHHhccCccccCCCceEEEECCcCCCccCC
Confidence 444444444666654568889999999966544
No 124
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=37.67 E-value=13 Score=37.60 Aligned_cols=44 Identities=18% Similarity=0.461 Sum_probs=31.7
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcccccchhhhhHHHhc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDKLTTFILK 144 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~k 144 (445)
++.||+|+. +.+.+ +=+.-...|..||+...+..+.+|-.++=.
T Consensus 28 w~KCp~c~~--~~y~~-eL~~n~~vcp~c~~h~ri~A~~Ri~~llD~ 71 (294)
T COG0777 28 WTKCPSCGE--MLYRK-ELESNLKVCPKCGHHMRISARERLEALLDE 71 (294)
T ss_pred eeECCCccc--eeeHH-HHHhhhhcccccCcccccCHHHHHHHhhCC
Confidence 789999984 22222 113446789999999999999888766643
No 125
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=37.24 E-value=29 Score=43.28 Aligned_cols=42 Identities=19% Similarity=0.439 Sum_probs=27.6
Q ss_pred HHHHHHHHhhccccCCCCCCCceEEEe--cCCeeeeeccccCCcccc
Q 013311 88 AGLLENFIKKYVQCYGCGNPETDIIIT--KTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 88 ~~~l~~fi~~fVlC~~C~~peT~l~~~--k~~~~~~~C~aCG~~~~v 132 (445)
..+|..++ .-+-||.|+.++-.|+-- ..+ ...|..||....+
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 44444444 234599999997655431 334 6799999987654
No 126
>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=36.64 E-value=32 Score=27.61 Aligned_cols=30 Identities=30% Similarity=0.789 Sum_probs=17.4
Q ss_pred cccCCCCC---CC-c-eEEEe----cCCeeeeeccccCC
Q 013311 99 VQCYGCGN---PE-T-DIIIT----KTQMVNLKCAACGF 128 (445)
Q Consensus 99 VlC~~C~~---pe-T-~l~~~----k~~~~~~~C~aCG~ 128 (445)
-+|..|++ |- | .+.+. ..+.+...|..||+
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 58999998 43 2 22221 15889999999995
No 127
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=36.58 E-value=30 Score=24.80 Aligned_cols=22 Identities=27% Similarity=0.397 Sum_probs=16.2
Q ss_pred echHHHHHHhCCCchHHHHHHH
Q 013311 39 VNMVDIAKALARPPSYTTKYFG 60 (445)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~ 60 (445)
..+.+||+.|+|++.-|.+++-
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 3578999999999999998874
No 128
>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=36.26 E-value=22 Score=25.40 Aligned_cols=29 Identities=21% Similarity=0.497 Sum_probs=21.6
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
.|..|+..-..+..-. ..-...|.+||..
T Consensus 7 ~C~~Cg~~fe~~~~~~-~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 7 RCEECGHEFEVLQSIS-EDDPVPCPECGST 35 (42)
T ss_pred EeCCCCCEEEEEEEcC-CCCCCcCCCCCCC
Confidence 5999998777776523 3668899999983
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=36.11 E-value=26 Score=34.84 Aligned_cols=55 Identities=16% Similarity=0.430 Sum_probs=27.1
Q ss_pred cCHHHHH-HHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCcccccchh
Q 013311 82 HDTAKLA-GLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRD 136 (445)
Q Consensus 82 ~~~~~l~-~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~ 136 (445)
++..++. -+-..|+.+-+.||.|++.-..=.-+...+--..|.-|+...-+..+.
T Consensus 14 kS~sQ~aRVltE~Wv~~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKSk~ 69 (254)
T PF06044_consen 14 KSNSQIARVLTEDWVAENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKSKK 69 (254)
T ss_dssp TT-TTHHHHHHHHHHHHH---TTT--SS-EE--------EEE-TTT--EEEEEEEE
T ss_pred cChhhhhHHHHHHHHHHCCcCCCCCChhHhhccCCCccceeECCCCchHHhhhhhc
Confidence 3444444 445789999999999999755544435577789999999998887443
No 130
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=35.96 E-value=27 Score=42.03 Aligned_cols=40 Identities=23% Similarity=0.554 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 86 KLAGLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 86 ~l~~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
..+..+.+| +=..|+.|+| ++|++ . --.++|..||..+-.
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 455666667 5567999997 67877 3 348999999998753
No 131
>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=35.93 E-value=23 Score=27.52 Aligned_cols=31 Identities=26% Similarity=0.584 Sum_probs=22.0
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
-.||.|+.+.-. .. ..-...|..||....-|
T Consensus 29 q~C~~CG~~~~~-~~---~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 29 QTCPRCGHRNKK-RR---SGRVFTCPNCGFEMDRD 59 (69)
T ss_pred cCccCccccccc-cc---ccceEEcCCCCCEECcH
Confidence 359999998766 11 23378899999985444
No 132
>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=35.46 E-value=66 Score=23.21 Aligned_cols=35 Identities=29% Similarity=0.707 Sum_probs=22.2
Q ss_pred HHHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccC
Q 013311 88 AGLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACG 127 (445)
Q Consensus 88 ~~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG 127 (445)
+-+|.+|-=---.||.|+.| |.+++++ ...|-+|+
T Consensus 7 ~~LL~G~~ML~~~Cp~C~~P---L~~~k~g--~~~Cv~C~ 41 (41)
T PF06677_consen 7 EYLLQGWTMLDEHCPDCGTP---LMRDKDG--KIYCVSCG 41 (41)
T ss_pred HHHHHhHhHhcCccCCCCCe---eEEecCC--CEECCCCC
Confidence 34566665556679999766 4543444 34688886
No 133
>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=35.18 E-value=14 Score=24.90 Aligned_cols=27 Identities=30% Similarity=0.509 Sum_probs=13.1
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
+-.||.|++..|- . ++ ..+.|.-||+.
T Consensus 2 ~p~Cp~C~se~~y--~-D~--~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSEYTY--E-DG--ELLVCPECGHE 28 (30)
T ss_dssp S---TTT-----E--E--S--SSEEETTTTEE
T ss_pred CCCCCCCCCccee--c-cC--CEEeCCccccc
Confidence 3469999999887 3 22 36789999974
No 134
>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=35.01 E-value=27 Score=31.68 Aligned_cols=44 Identities=14% Similarity=0.258 Sum_probs=32.7
Q ss_pred echHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHHHhhccccCCCCCC
Q 013311 39 VNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENFIKKYVQCYGCGNP 107 (445)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~fVlC~~C~~p 107 (445)
.|+.+|+.++.-++.+|.+|+- .|||.|.+. + +-+..|..||.|
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 4788999999999999999973 578876541 1 336778888865
No 135
>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=34.81 E-value=58 Score=28.54 Aligned_cols=65 Identities=17% Similarity=0.173 Sum_probs=44.5
Q ss_pred ceEEEeccCCC--ceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCC---CCeEEEEeecCHHHHHHHHHH
Q 013311 23 MITKIEGRGNG--IKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEK---TGTSLVNGAHDTAKLAGLLEN 93 (445)
Q Consensus 23 ~~~k~eG~gng--~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~---~~~~ii~G~~~~~~l~~~l~~ 93 (445)
+.++++-| || .=|+|.+|.+ .=+-.-++|+|...+|+.|++-.. ++.+.|+|.|...-.+-|...
T Consensus 28 I~Iri~qR-~grK~VTiI~Gl~~-----~~dlk~l~K~lKkk~~cGGsVk~~~~~~~~IelQGD~re~v~~~L~~~ 97 (110)
T TIGR01160 28 IHIRIQQR-NGRKTLTTVQGLPK-----EYDLKKIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEFLISQ 97 (110)
T ss_pred EEEEEEEc-cCCccEEEEeccCC-----hHHHHHHHHHHHHHhCCCceEEeCCCCCCEEEEeCcHHHHHHHHHHHc
Confidence 56777733 44 3467788862 223457889999999999999531 247889999987665555544
No 136
>PRK11823 DNA repair protein RadA; Provisional
Probab=34.55 E-value=22 Score=38.10 Aligned_cols=27 Identities=22% Similarity=0.517 Sum_probs=22.9
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccccc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDM 134 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (445)
.|.+|+. ....|+-+|.+||+..++..
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 45678999999999998875
No 137
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=34.41 E-value=32 Score=30.35 Aligned_cols=49 Identities=18% Similarity=0.154 Sum_probs=26.9
Q ss_pred HHHhhcCcccccCCCCeEEEEee-----c--CHHHHHHHHHHHHhhccccCCCCCCCceEEE
Q 013311 59 FGNELGAQSKFDEKTGTSLVNGA-----H--DTAKLAGLLENFIKKYVQCYGCGNPETDIII 113 (445)
Q Consensus 59 ~~~ELg~~~~~~~~~~~~ii~G~-----~--~~~~l~~~l~~fi~~fVlC~~C~~peT~l~~ 113 (445)
|.++.-+.|++-+ +-+++|-=. - =..-++-..- .++||.|+++...++-
T Consensus 46 FaFev~~egT~ae-ga~l~Ie~~p~~~~C~~C~~~~~~e~~-----~~~CP~C~s~~~~i~~ 101 (115)
T COG0375 46 FAFEVVAEGTIAE-GAELHIEEEPAECWCLDCGQEVELEEL-----DYRCPKCGSINLRIIG 101 (115)
T ss_pred HHHHHHhccCccc-CCEEEEEEeccEEEeccCCCeecchhh-----eeECCCCCCCceEEec
Confidence 6777888888865 667776311 0 0001111111 1238888888877775
No 138
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=34.35 E-value=48 Score=23.05 Aligned_cols=28 Identities=32% Similarity=0.552 Sum_probs=23.1
Q ss_pred echHHHHHHhCCCchHHHHHHHHhhcCc
Q 013311 39 VNMVDIAKALARPPSYTTKYFGNELGAQ 66 (445)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~~ELg~~ 66 (445)
..+.+||..++=.+.|+.+-|..++|..
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 4588999999999999999999999975
No 139
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=34.03 E-value=20 Score=28.07 Aligned_cols=31 Identities=19% Similarity=0.592 Sum_probs=13.5
Q ss_pred hccccCCCCCCCceEEEecCCeeeeeccccCCccc
Q 013311 97 KYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSE 131 (445)
Q Consensus 97 ~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~ 131 (445)
-.++|.-|+. |.-+. =-.+.++|..||+-.+
T Consensus 29 v~IlCNDC~~--~s~v~--fH~lg~KC~~C~SYNT 59 (61)
T PF14599_consen 29 VWILCNDCNA--KSEVP--FHFLGHKCSHCGSYNT 59 (61)
T ss_dssp EEEEESSS----EEEEE----TT----TTTS---E
T ss_pred EEEECCCCCC--cccee--eeHhhhcCCCCCCccc
Confidence 3689999998 33222 3577899999997543
No 140
>PRK14973 DNA topoisomerase I; Provisional
Probab=33.81 E-value=25 Score=41.38 Aligned_cols=33 Identities=12% Similarity=0.244 Sum_probs=23.9
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
.||.|+.|--.+++....-+++-|..|.+..+.
T Consensus 637 ~Cp~CG~p~~~~~r~Gr~g~fl~CP~C~~~~~~ 669 (936)
T PRK14973 637 VCPIHHLNHVRLIRKGARPWDIGCPLCSHIESN 669 (936)
T ss_pred CCCCCCCCceEEeecCCCcccccCccccchhhc
Confidence 699999995444442335679999999887763
No 141
>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=33.49 E-value=35 Score=31.17 Aligned_cols=50 Identities=20% Similarity=0.388 Sum_probs=33.9
Q ss_pred cCHHHHHHHHHHHH-------------hhccccCCCCCCCceEEEec--CCeeeeeccccCCcccc
Q 013311 82 HDTAKLAGLLENFI-------------KKYVQCYGCGNPETDIIITK--TQMVNLKCAACGFVSEV 132 (445)
Q Consensus 82 ~~~~~l~~~l~~fi-------------~~fVlC~~C~~peT~l~~~k--~~~~~~~C~aCG~~~~v 132 (445)
|...+|+.+|..+- -.||.|+.|+.---.+.. . +...+++|.+|..-+-|
T Consensus 81 ~e~G~L~~lL~~~~~~~~~~~C~~Cgg~rfv~C~~C~Gs~k~~~~-~~~~~~~~~rC~~Cnengl~ 145 (147)
T cd03031 81 NESGELRKLLKGIRARAGGGVCEGCGGARFVPCSECNGSCKVFAE-NATAAGGFLRCPECNENGLV 145 (147)
T ss_pred HHcCCHHHHHhhcccccCCCCCCCCCCcCeEECCCCCCcceEEec-cCcccccEEECCCCCccccc
Confidence 44556677777651 258999999876555544 3 24678999999876544
No 142
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=33.39 E-value=30 Score=39.57 Aligned_cols=36 Identities=22% Similarity=0.723 Sum_probs=23.6
Q ss_pred ccccCCCCC----C--CceEEEecCCeeeeeccccCCcccccc
Q 013311 98 YVQCYGCGN----P--ETDIIITKTQMVNLKCAACGFVSEVDM 134 (445)
Q Consensus 98 fVlC~~C~~----p--eT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (445)
||+|+.|+- | +..|.. -...-.+.|.-||+..+++.
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 688887775 2 223433 22335889999999977763
No 143
>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=33.10 E-value=32 Score=27.03 Aligned_cols=14 Identities=29% Similarity=0.667 Sum_probs=12.2
Q ss_pred eeeccccCCccccc
Q 013311 120 NLKCAACGFVSEVD 133 (445)
Q Consensus 120 ~~~C~aCG~~~~v~ 133 (445)
.|.|..||...||.
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 144
>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=32.80 E-value=41 Score=23.54 Aligned_cols=29 Identities=21% Similarity=0.399 Sum_probs=18.6
Q ss_pred ccccCCCCCCCceEEEe--cCCeeeeecccc
Q 013311 98 YVQCYGCGNPETDIIIT--KTQMVNLKCAAC 126 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~--k~~~~~~~C~aC 126 (445)
.|.||.|++.+-.+.-- .++.--.+|..|
T Consensus 5 ~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 48899999876433321 235556778877
No 145
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=32.41 E-value=13 Score=29.01 Aligned_cols=32 Identities=25% Similarity=0.580 Sum_probs=22.3
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCCcccccch
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMR 135 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~ 135 (445)
-+|..|+.-.| |. +.-..+|.-||++-....|
T Consensus 21 YiCgdC~~en~-lk----~~D~irCReCG~RIlyKkR 52 (62)
T KOG3507|consen 21 YICGDCGQENT-LK----RGDVIRCRECGYRILYKKR 52 (62)
T ss_pred EEecccccccc-cc----CCCcEehhhcchHHHHHHH
Confidence 36999997554 22 2346789999998766554
No 146
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=32.29 E-value=49 Score=38.64 Aligned_cols=33 Identities=15% Similarity=0.386 Sum_probs=24.8
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccc---cCCccccc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAA---CGFVSEVD 133 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~a---CG~~~~v~ 133 (445)
.||.|+.+...+.. .+...|+.|.. |.+..++.
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 59999998777665 33446888976 88877766
No 147
>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=32.18 E-value=26 Score=37.67 Aligned_cols=27 Identities=26% Similarity=0.535 Sum_probs=23.2
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccccc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDM 134 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (445)
.|..|+. ....|+-+|.+||+..++..
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 35678999999999999885
No 148
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=31.87 E-value=38 Score=29.82 Aligned_cols=21 Identities=38% Similarity=1.054 Sum_probs=15.8
Q ss_pred cCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 101 CYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 101 C~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
||.|+.+ |++ --++|..||-.
T Consensus 1 CPvCg~~---l~v-----t~l~C~~C~t~ 21 (113)
T PF09862_consen 1 CPVCGGE---LVV-----TRLKCPSCGTE 21 (113)
T ss_pred CCCCCCc---eEE-----EEEEcCCCCCE
Confidence 9999965 444 25899999854
No 149
>PRK09019 translation initiation factor Sui1; Validated
Probab=31.87 E-value=95 Score=27.13 Aligned_cols=57 Identities=9% Similarity=0.025 Sum_probs=39.3
Q ss_pred EEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHH
Q 013311 26 KIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLA 88 (445)
Q Consensus 26 k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~ 88 (445)
...||++=.=|+|..|..-... -.-+.|+|-..+|+-|++- ++.+.|+|.|...-.+
T Consensus 38 ~r~gRkGK~VTiI~Gl~~~~~d----lk~l~K~lKkk~gcGGtvk--~~~IelQGD~r~~v~~ 94 (108)
T PRK09019 38 QTSGRKGKGVCLITGLDLDDAE----LKKLAAELKKKCGCGGAVK--DGVIEIQGDKRDLLKS 94 (108)
T ss_pred ecCCCCCCeEEEEeCCcCCHHH----HHHHHHHHHHHhcCCCeEE--cCEEEEcCcHHHHHHH
Confidence 3345533345888887511111 3568899999999999995 6899999999765443
No 150
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=31.57 E-value=13 Score=37.86 Aligned_cols=43 Identities=19% Similarity=0.450 Sum_probs=30.7
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcccccchhhhhHHHh
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDKLTTFIL 143 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (445)
++.||.|+..=..-.. + .-...|..||+...+..+.+|...+=
T Consensus 27 ~~~c~~c~~~~~~~~l-~--~~~~vc~~c~~h~rl~areRi~~L~D 69 (292)
T PRK05654 27 WTKCPSCGQVLYRKEL-E--ANLNVCPKCGHHMRISARERLDLLLD 69 (292)
T ss_pred eeECCCccchhhHHHH-H--hcCCCCCCCCCCeeCCHHHHHHHHcc
Confidence 7999999973221111 1 12469999999999999988876554
No 151
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=31.35 E-value=23 Score=28.01 Aligned_cols=11 Identities=27% Similarity=0.718 Sum_probs=8.0
Q ss_pred ccCCCCCCCce
Q 013311 100 QCYGCGNPETD 110 (445)
Q Consensus 100 lC~~C~~peT~ 110 (445)
+||.|+++++.
T Consensus 20 ~CP~Cgs~~~t 30 (64)
T COG2093 20 ICPVCGSTDLT 30 (64)
T ss_pred cCCCCCCcccc
Confidence 48888887765
No 152
>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=31.21 E-value=12 Score=37.85 Aligned_cols=43 Identities=16% Similarity=0.417 Sum_probs=30.3
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcccccchhhhhHHHh
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDKLTTFIL 143 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (445)
++.||.|+..=..-.. . .-+..|..||+...+..+.+|...+=
T Consensus 26 ~~~c~~c~~~~~~~~l-~--~~~~vc~~c~~h~rl~areRi~~L~D 68 (285)
T TIGR00515 26 WTKCPKCGQVLYTKEL-E--RNLEVCPKCDHHMRMDARERIESLLD 68 (285)
T ss_pred eeECCCCcchhhHHHH-H--hhCCCCCCCCCcCcCCHHHHHHHcee
Confidence 7999999974221111 1 12479999999999999988875554
No 153
>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=31.07 E-value=42 Score=29.31 Aligned_cols=36 Identities=22% Similarity=0.587 Sum_probs=18.7
Q ss_pred HHhhccccCCCCCCCceEEEec-----C--C--eeeeeccccCCc
Q 013311 94 FIKKYVQCYGCGNPETDIIITK-----T--Q--MVNLKCAACGFV 129 (445)
Q Consensus 94 fi~~fVlC~~C~~peT~l~~~k-----~--~--~~~~~C~aCG~~ 129 (445)
|+=.|+-|..|+.-+-.++.++ + . ++...|+.|++.
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 6667999999999997777642 1 1 345788888874
No 154
>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=30.87 E-value=29 Score=29.24 Aligned_cols=32 Identities=22% Similarity=0.425 Sum_probs=15.8
Q ss_pred cccCCCCCCCceEEEe-cCCeeeeeccccCCcccc
Q 013311 99 VQCYGCGNPETDIIIT-KTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 99 VlC~~C~~peT~l~~~-k~~~~~~~C~aCG~~~~v 132 (445)
.+||-|.--.-.+.++ .++ .-+|-+||+.+.+
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 6799998644466664 223 6789999988744
No 155
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=30.83 E-value=31 Score=28.87 Aligned_cols=15 Identities=33% Similarity=0.824 Sum_probs=12.8
Q ss_pred CCeeeeeccccCCcc
Q 013311 116 TQMVNLKCAACGFVS 130 (445)
Q Consensus 116 ~~~~~~~C~aCG~~~ 130 (445)
++++.|+|.+||.++
T Consensus 84 ~~vVsL~C~~CG~r~ 98 (98)
T PF15494_consen 84 GSVVSLQCSDCGKRT 98 (98)
T ss_pred CCEEEEECcccCCcC
Confidence 478899999999874
No 156
>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=30.66 E-value=20 Score=24.48 Aligned_cols=28 Identities=21% Similarity=0.488 Sum_probs=17.7
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
+|..|+..-. |.. . -.++|.-||++-..
T Consensus 2 ~C~~Cg~~~~-~~~--~--~~irC~~CG~RIly 29 (32)
T PF03604_consen 2 ICGECGAEVE-LKP--G--DPIRCPECGHRILY 29 (32)
T ss_dssp BESSSSSSE--BST--S--STSSBSSSS-SEEB
T ss_pred CCCcCCCeeE-cCC--C--CcEECCcCCCeEEE
Confidence 5899998655 222 2 24699999998544
No 157
>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=30.30 E-value=29 Score=36.37 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=22.4
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccccc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDM 134 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (445)
.|..|+. ....|+-+|.+||+..++..
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 5999985 34678999999999998874
No 158
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=30.00 E-value=19 Score=27.07 Aligned_cols=35 Identities=26% Similarity=0.437 Sum_probs=26.5
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccccchhhh
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDKL 138 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl 138 (445)
.|..|+..=..+.. .-..+|.-||++--+.++++.
T Consensus 8 ~C~~Cg~~~~~~~~----~~~irCp~Cg~rIl~K~R~~~ 42 (49)
T COG1996 8 KCARCGREVELDQE----TRGIRCPYCGSRILVKERPKV 42 (49)
T ss_pred EhhhcCCeeehhhc----cCceeCCCCCcEEEEeccCCc
Confidence 69999986633333 447899999999999888764
No 159
>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=29.92 E-value=61 Score=28.68 Aligned_cols=57 Identities=9% Similarity=0.151 Sum_probs=37.6
Q ss_pred hHHHHHHhCCCc-----------hHHHHHHHH-hhcCc--ccccCCCCeEE-EEeecCHHHHHHHHHHHHhh
Q 013311 41 MVDIAKALARPP-----------SYTTKYFGN-ELGAQ--SKFDEKTGTSL-VNGAHDTAKLAGLLENFIKK 97 (445)
Q Consensus 41 ~~~ia~~L~R~p-----------~~~~ky~~~-ELg~~--~~~~~~~~~~i-i~G~~~~~~l~~~l~~fi~~ 97 (445)
|.+||+.++..| .++..||+. +-+.+ .-++.++++|. ..|.++.+.|..-+..|++.
T Consensus 46 l~~vAk~~kgk~i~Fv~vd~~~~~~~~~~fgl~~~~~P~v~i~~~~~~KY~~~~~~~t~e~i~~Fv~~~l~G 117 (130)
T cd02983 46 LKSVAEKFKKKPWGWLWTEAGAQLDLEEALNIGGFGYPAMVAINFRKMKFATLKGSFSEDGINEFLRELSYG 117 (130)
T ss_pred HHHHHHHhcCCcEEEEEEeCcccHHHHHHcCCCccCCCEEEEEecccCccccccCccCHHHHHHHHHHHHcC
Confidence 455555555553 347888874 22333 33455445888 88999999998888888764
No 160
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=29.86 E-value=32 Score=34.89 Aligned_cols=28 Identities=36% Similarity=0.813 Sum_probs=19.8
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
.||.|++. .++.+ -..-...|..||..-
T Consensus 3 ~CpeCg~~--~~~~d-~~~ge~VC~~CG~Vi 30 (285)
T COG1405 3 SCPECGST--NIITD-YERGEIVCADCGLVL 30 (285)
T ss_pred CCCCCCCc--cceee-ccCCeEEeccCCEEe
Confidence 59999998 55552 123367899999864
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=29.80 E-value=48 Score=28.46 Aligned_cols=32 Identities=31% Similarity=0.387 Sum_probs=18.8
Q ss_pred cCCCCCCCceEEE-----e-cCCe-----eeeeccccCCcccc
Q 013311 101 CYGCGNPETDIII-----T-KTQM-----VNLKCAACGFVSEV 132 (445)
Q Consensus 101 C~~C~~peT~l~~-----~-k~~~-----~~~~C~aCG~~~~v 132 (445)
||.|++.++.-.+ + ++.. -...|..||..-..
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEELLD 43 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEEEc
Confidence 9999975543222 0 2322 23689999986443
No 162
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=29.77 E-value=54 Score=27.07 Aligned_cols=51 Identities=25% Similarity=0.470 Sum_probs=37.8
Q ss_pred CeEEEEeecCHHHHHHHHHHHHhh-------ccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 74 GTSLVNGAHDTAKLAGLLENFIKK-------YVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 74 ~~~ii~G~~~~~~l~~~l~~fi~~-------fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
+.+.-.+.|+..+|+.+-..-... ++.|..|-.. ...-+.|..||...+++
T Consensus 6 ~~~k~~~~FS~~Ql~~~~~~~~~~~~~~~~~~i~C~~ct~~---------q~~El~C~~C~~~k~ld 63 (84)
T PF12898_consen 6 GKWKPLSAFSKNQLEKLRKQIRANRVDPANSGIRCRECTGG---------QVVELTCSPCGKTKPLD 63 (84)
T ss_pred ceECChHHcCHHHHHHHHHHHhhccCccCCCCCCCccCCCC---------CcCcCEeccCCCCcCHH
Confidence 456667789999988776655444 7999999754 33345899999888876
No 163
>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]
Probab=29.54 E-value=64 Score=32.77 Aligned_cols=104 Identities=16% Similarity=0.264 Sum_probs=52.6
Q ss_pred eEEEeccCC-CceEEEechHHHHHHhCCCchHHHHHHHHh---hcCcccccCCCCeEEEEeecCHHHHHHHHHH---HH-
Q 013311 24 ITKIEGRGN-GIKTNVVNMVDIAKALARPPSYTTKYFGNE---LGAQSKFDEKTGTSLVNGAHDTAKLAGLLEN---FI- 95 (445)
Q Consensus 24 ~~k~eG~gn-g~kT~i~N~~~ia~~L~R~p~~~~ky~~~E---Lg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~---fi- 95 (445)
.+.+-|||+ |+.|+-+|| ..+|+.+ +-+..-++.-|..+++.+... .+.+.+.. .|
T Consensus 4 vAV~sGKGGtGKTTva~~l--------------a~~l~~~~~~~l~DcDVe~PNl~l~l~~e~~--~~~e~~~~~~p~i~ 67 (284)
T COG1149 4 VAVASGKGGTGKTTVAANL--------------AVLLGDKYKLVLADCDVEAPNLHLLLGVEVL--EEEEVIRGEIPEID 67 (284)
T ss_pred EEEeecCCCCChhhHHHHH--------------HHHhccccceEEEecCCCCCCcceEeccchh--hhhHHHHhhccccC
Confidence 345567766 777775544 4556655 233455565577888877642 22222221 11
Q ss_pred -hhccccCCCCC---CCceEEEecCCeee---eeccccC---Cccccc---chhhhhHHHhc
Q 013311 96 -KKYVQCYGCGN---PETDIIITKTQMVN---LKCAACG---FVSEVD---MRDKLTTFILK 144 (445)
Q Consensus 96 -~~fVlC~~C~~---peT~l~~~k~~~~~---~~C~aCG---~~~~v~---~~~kl~~~i~k 144 (445)
+++..|..|.. ++--+.. +++.+. ..|..|| -..|++ ...+.+++|.+
T Consensus 68 ~e~C~~CG~C~~vC~f~Ai~~~-~~~~~~~~~~lC~GCgaC~~~CP~~AI~~~~~~~G~i~~ 128 (284)
T COG1149 68 PEKCIRCGKCAEVCRFGAIVVL-PGGKPVLNPDLCEGCGACSIVCPEPAIEEEPVVIGKIYE 128 (284)
T ss_pred hhhccccCcHHHhCCCCeEEEc-CCCceecCcccccCcccceeeCCCcccccccceeeEEEE
Confidence 23566666665 3433333 443333 3455555 455554 33444555544
No 164
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=29.50 E-value=24 Score=37.64 Aligned_cols=37 Identities=16% Similarity=0.455 Sum_probs=27.7
Q ss_pred HHhhccccCCCCCCCceEEEecCCeeeeeccccCCcccccch
Q 013311 94 FIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMR 135 (445)
Q Consensus 94 fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~ 135 (445)
|...--+||.|+. .+.- +++. ..+|+-||.+.+-..+
T Consensus 346 ~~~~~p~Cp~Cg~---~m~S-~G~~-g~rC~kCg~~~~~~~~ 382 (421)
T COG1571 346 YERVNPVCPRCGG---RMKS-AGRN-GFRCKKCGTRARETLI 382 (421)
T ss_pred eEEcCCCCCccCC---chhh-cCCC-CcccccccccCCcccc
Confidence 5555568999984 5554 6677 9999999998766533
No 165
>PHA02540 61 DNA primase; Provisional
Probab=29.39 E-value=45 Score=34.73 Aligned_cols=34 Identities=26% Similarity=0.544 Sum_probs=24.6
Q ss_pred cccCCCCCCC-----ceEEEe-cCCeeeeeccccCCcccc
Q 013311 99 VQCYGCGNPE-----TDIIIT-KTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 99 VlC~~C~~pe-----T~l~~~-k~~~~~~~C~aCG~~~~v 132 (445)
-+||-|+=-. +...+. .++..+-+|-.||+.+++
T Consensus 28 ~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~Gd~ 67 (337)
T PHA02540 28 FRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYHRPF 67 (337)
T ss_pred ecCCCCCCccccCcCCcEEEeccCCceEEEecCCCCCCCH
Confidence 4799998632 245553 345578899999999976
No 166
>smart00400 ZnF_CHCC zinc finger.
Probab=29.33 E-value=54 Score=24.46 Aligned_cols=32 Identities=19% Similarity=0.376 Sum_probs=22.9
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
+||-|.--.-.+.++ .+.-.-.|-+||..+.+
T Consensus 4 ~cPfh~d~~pSf~v~-~~kn~~~Cf~cg~gGd~ 35 (55)
T smart00400 4 LCPFHGEKTPSFSVS-PDKQFFHCFGCGAGGNV 35 (55)
T ss_pred cCcCCCCCCCCEEEE-CCCCEEEEeCCCCCCCH
Confidence 599998766777773 33346789999977643
No 167
>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=29.30 E-value=1.3e+02 Score=21.08 Aligned_cols=45 Identities=27% Similarity=0.206 Sum_probs=32.0
Q ss_pred chHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHH
Q 013311 40 NMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGL 90 (445)
Q Consensus 40 N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~ 90 (445)
++.++|+.|+-++..|-.|....+.. ..... +++.. |+...|..+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g~l~-~~~~~-~~~~~----y~~~~v~~l 46 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIGLLS-PARTE-GGYRL----YSDADLERL 46 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCCCC-CCcCC-CCCEE----eCHHHHHHh
Confidence 47899999999999999998777766 33332 34333 667766654
No 168
>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=29.28 E-value=42 Score=23.43 Aligned_cols=26 Identities=27% Similarity=0.512 Sum_probs=18.0
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
.|+.|++- .... .++ +.-|..||+..
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 3333 344 56798899753
No 169
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=29.22 E-value=40 Score=24.60 Aligned_cols=31 Identities=29% Similarity=0.568 Sum_probs=21.7
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCcccccch
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMR 135 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~ 135 (445)
+|..|+.. +.. + ..-.++|.-||++--...|
T Consensus 4 ~C~~Cg~~---~~~-~-~~~~irC~~CG~rIlyK~R 34 (44)
T smart00659 4 ICGECGRE---NEI-K-SKDVVRCRECGYRILYKKR 34 (44)
T ss_pred ECCCCCCE---eec-C-CCCceECCCCCceEEEEeC
Confidence 69999984 223 2 3457899999998766544
No 170
>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=28.84 E-value=37 Score=37.05 Aligned_cols=44 Identities=23% Similarity=0.407 Sum_probs=27.4
Q ss_pred cCCCCCCCceEEEecCCeeeeeccccCCccccc----------------chhhhhHHHhcCCCC
Q 013311 101 CYGCGNPETDIIITKTQMVNLKCAACGFVSEVD----------------MRDKLTTFILKNPPV 148 (445)
Q Consensus 101 C~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~----------------~~~kl~~~i~k~pP~ 148 (445)
||.|..|=|. .+ ..+ .+.|.-||+..+++ ...++..++.++=|.
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 6666655333 22 222 67888888887643 247777777777664
No 171
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=28.83 E-value=76 Score=23.61 Aligned_cols=40 Identities=30% Similarity=0.634 Sum_probs=25.6
Q ss_pred HHHHHHHhh---ccccC--CCCCCCceEEEe-cCCeeeeeccccCCccc
Q 013311 89 GLLENFIKK---YVQCY--GCGNPETDIIIT-KTQMVNLKCAACGFVSE 131 (445)
Q Consensus 89 ~~l~~fi~~---fVlC~--~C~~peT~l~~~-k~~~~~~~C~aCG~~~~ 131 (445)
-+++.||+. +.-|| .|+.. +... ..+.....|..||...-
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 3331 12556788988987644
No 172
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=28.47 E-value=3.4e+02 Score=22.49 Aligned_cols=96 Identities=15% Similarity=0.166 Sum_probs=49.4
Q ss_pred HHHHHHhcCCChHHHHHHhhhcCCC--hhhHHHHHHHHHHhhhhhhHHHHHHhhHHHHHHhcc-CchhHHHHHHHHHHHh
Q 013311 302 QMKDFLKKGASASQFKSFLGSLSGT--PQEVMDALFVALFDGIEKGFAKEVTKKKNYLAAATQ-EEGSQMVLLHSLESFC 378 (445)
Q Consensus 302 ~lk~~l~~~~s~~ei~~el~~~~l~--~~~v~~vl~eaLf~~i~~~i~k~i~k~~~lL~~~~~-~~~~Q~~lL~alE~~~ 378 (445)
.|.+++..+ +..++...++.++++ .+.++..++...|+. -...-..+..||..++. +--.+-++..|++.++
T Consensus 8 ~l~ey~~~~-d~~ea~~~l~el~~~~~~~~vv~~~l~~~le~----~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l 82 (113)
T PF02847_consen 8 ILMEYFSSG-DVDEAVECLKELKLPSQHHEVVKVILECALEE----KKSYREYYSKLLSHLCKRKLISKEQFQEGFEDLL 82 (113)
T ss_dssp HHHHHHHHT--HHHHHHHHHHTT-GGGHHHHHHHHHHHHHTS----SHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHH
T ss_pred HHHHHhcCC-CHHHHHHHHHHhCCCccHHHHHHHHHHHHhhc----cHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 344444433 445666666666665 223333333333442 11223344566666664 3333444555555544
Q ss_pred cc------cChhhHHHHHHHHHHHhhCCcc
Q 013311 379 GK------ARPAAVKEVALVLKALYDNDLL 402 (445)
Q Consensus 379 ~~------~~~~l~~~~~~ILk~LYD~DIl 402 (445)
.. .-|.....+..++-.++..|+|
T Consensus 83 ~~l~Dl~~D~P~~~~~la~~~~~~i~~~~l 112 (113)
T PF02847_consen 83 ESLEDLELDIPKAPEYLAKFLARLIADGIL 112 (113)
T ss_dssp HHHHHHHHHSTTHHHHHHHHHHHHHHTTSS
T ss_pred hHhhhccccchHHHHHHHHHHHHHHHcCCc
Confidence 32 1477777888888888888776
No 173
>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=28.41 E-value=38 Score=22.51 Aligned_cols=11 Identities=36% Similarity=0.739 Sum_probs=9.0
Q ss_pred HhhhHHHHHhc
Q 013311 426 KNAKPVIEWLQ 436 (445)
Q Consensus 426 k~a~pFI~WLe 436 (445)
..++.||.||-
T Consensus 17 ~aak~fl~~L~ 27 (28)
T PF00123_consen 17 LAAKKFLQWLM 27 (28)
T ss_dssp HHHHHHHHHHC
T ss_pred HHHHHHHHHHh
Confidence 46889999995
No 174
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=28.06 E-value=52 Score=28.56 Aligned_cols=50 Identities=20% Similarity=0.356 Sum_probs=24.7
Q ss_pred CchHHHHHHHHhhcCcccccCCCCeEEEEe------------ecCHHHHHHHHHHHHhhccccCCCCCCCceEEE
Q 013311 51 PPSYTTKYFGNELGAQSKFDEKTGTSLVNG------------AHDTAKLAGLLENFIKKYVQCYGCGNPETDIII 113 (445)
Q Consensus 51 ~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G------------~~~~~~l~~~l~~fi~~fVlC~~C~~peT~l~~ 113 (445)
.|+.+.-+|. .-+.+++-+ +-+|.|.- .|+.... +..||.|++++..++.
T Consensus 40 ~pe~L~f~f~--~~~~~T~~e-~a~L~Ie~~p~~~~C~~Cg~~~~~~~~----------~~~CP~Cgs~~~~i~~ 101 (113)
T PF01155_consen 40 EPEALRFAFE--VLAEGTILE-GAELEIEEVPARARCRDCGHEFEPDEF----------DFSCPRCGSPDVEIIS 101 (113)
T ss_dssp -HHHHHHHHH--HHHCCSTTT-T-EEEEEEE--EEEETTTS-EEECHHC----------CHH-SSSSSS-EEEEE
T ss_pred CHHHHHHHHH--HHhCCCCcc-CCEEEEEecCCcEECCCCCCEEecCCC----------CCCCcCCcCCCcEEcc
Confidence 4777665554 445555554 56777742 1222221 1238888888777765
No 175
>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=27.81 E-value=36 Score=23.38 Aligned_cols=17 Identities=24% Similarity=0.645 Sum_probs=10.4
Q ss_pred cCCeeeeeccccCCccc
Q 013311 115 KTQMVNLKCAACGFVSE 131 (445)
Q Consensus 115 k~~~~~~~C~aCG~~~~ 131 (445)
+.+++..+|.+||....
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 46889999999998743
No 176
>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=27.70 E-value=47 Score=36.71 Aligned_cols=49 Identities=24% Similarity=0.569 Sum_probs=34.5
Q ss_pred ccccCCCCCCCce----EEEec---CCeeeeeccccCCcccccchhhh---hHHHhcCC
Q 013311 98 YVQCYGCGNPETD----IIITK---TQMVNLKCAACGFVSEVDMRDKL---TTFILKNP 146 (445)
Q Consensus 98 fVlC~~C~~peT~----l~~~k---~~~~~~~C~aCG~~~~v~~~~kl---~~~i~k~p 146 (445)
||-||.|+-.-.- |.-++ .....+.|..||..-.-..++.+ ..||-.+|
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 9999999985432 33321 35788999999998665544443 56888888
No 177
>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=27.66 E-value=81 Score=25.26 Aligned_cols=47 Identities=21% Similarity=0.285 Sum_probs=35.2
Q ss_pred chHHHHHHHHhhcCcccccCCCCeEEEEeecC----HHHHHHHHHHHHhhc
Q 013311 52 PSYTTKYFGNELGAQSKFDEKTGTSLVNGAHD----TAKLAGLLENFIKKY 98 (445)
Q Consensus 52 p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~----~~~l~~~l~~fi~~f 98 (445)
|..+..-++..-|....+...++.++|.=.-. ...+..+++.++++|
T Consensus 15 Pk~i~~~lgl~~Gd~v~v~~~~~~iii~~~~~~~~~~~~~~~~~~~~~~~y 65 (74)
T TIGR02609 15 PKEVLESLGLKEGDTLYVDEEEGGLKLKRFDEGKELEKKMQMAVERAMSKY 65 (74)
T ss_pred CHHHHHHcCcCCCCEEEEEEECCEEEEEECCCCccHHHHHHHHHHHHHHHH
Confidence 77788888888888888887788888875544 455556677777766
No 178
>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=27.64 E-value=2.2e+02 Score=23.52 Aligned_cols=67 Identities=22% Similarity=0.302 Sum_probs=46.7
Q ss_pred CCCceEEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhc--CcccccCCCCeEEEEeecCHHHHHHHH
Q 013311 20 MPKMITKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELG--AQSKFDEKTGTSLVNGAHDTAKLAGLL 91 (445)
Q Consensus 20 mp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg--~~~~~~~~~~~~ii~G~~~~~~l~~~l 91 (445)
+| +-.++...||-.-|+|.++.==..+|. +.|.+||+...+ -.+.+++-.+.++|+|.|. ..+...|
T Consensus 14 LP-VY~~~k~~g~~~~T~IrkI~GD~~aL~---~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~~-~~Vk~wL 82 (87)
T PF05046_consen 14 LP-VYLDIKNGGNRKITVIRKIEGDIWALK---KDLRKFLGEKPKKKIDVRVNELTGHIEIKGDHV-EEVKKWL 82 (87)
T ss_pred cc-EEEEEeCCCcEeEEEEEeecCCHHHHH---HHHHHHhhhhcCCCcceEEeecCCEEEEcCccH-HHHHHHH
Confidence 45 677788788889999998764444443 346667776666 4566677789999999994 4444433
No 179
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=27.46 E-value=32 Score=36.92 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=22.3
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
+-.|.+|+.- ...|.-+|.+||+..++.
T Consensus 7 ~f~C~~CG~~--------s~KW~GkCp~Cg~Wns~v 34 (456)
T COG1066 7 AFVCQECGYV--------SPKWLGKCPACGAWNTLV 34 (456)
T ss_pred EEEcccCCCC--------CccccccCCCCCCccceE
Confidence 4469999962 356899999999998775
No 180
>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=27.30 E-value=43 Score=25.62 Aligned_cols=25 Identities=28% Similarity=0.802 Sum_probs=17.8
Q ss_pred hhccccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 96 KKYVQCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 96 ~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
-.+|.|+.|+.+ .+-...|..||.-
T Consensus 24 p~l~~C~~cG~~---------~~~H~vc~~cG~Y 48 (55)
T TIGR01031 24 PTLVVCPNCGEF---------KLPHRVCPSCGYY 48 (55)
T ss_pred CcceECCCCCCc---------ccCeeECCccCeE
Confidence 346889999974 2346678888853
No 181
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=27.22 E-value=27 Score=35.97 Aligned_cols=25 Identities=24% Similarity=0.485 Sum_probs=19.3
Q ss_pred eeeeccccCCcccccchhhhhHHHh
Q 013311 119 VNLKCAACGFVSEVDMRDKLTTFIL 143 (445)
Q Consensus 119 ~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (445)
++++|..|++.-.+.+-.|=+.|++
T Consensus 76 F~~kC~~C~~~i~~kTDPkn~dY~~ 100 (324)
T PF04502_consen 76 FYIKCPRCSNEIEFKTDPKNTDYVV 100 (324)
T ss_pred EEEEcCCCCCEEeeecCCCCCCeee
Confidence 4689999999888766666677765
No 182
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=27.02 E-value=56 Score=22.41 Aligned_cols=30 Identities=23% Similarity=0.427 Sum_probs=21.0
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCccc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVSE 131 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~ 131 (445)
..+|+.|+.+- |+..+ .-.+.|.-||+..+
T Consensus 3 ~~~C~~C~~~~--i~~~~--~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 3 LKKCSKCGGNG--IVNKE--DDYEVCIFCGSSFP 32 (33)
T ss_pred ceEcCCCCCCe--EEEec--CCeEEcccCCcEee
Confidence 46899999986 33212 33778999998754
No 183
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=26.83 E-value=17 Score=37.07 Aligned_cols=43 Identities=23% Similarity=0.447 Sum_probs=30.9
Q ss_pred ccccCCCCCCCceEEEecC-CeeeeeccccCCcccccchhhhhHHHhc
Q 013311 98 YVQCYGCGNPETDIIITKT-QMVNLKCAACGFVSEVDMRDKLTTFILK 144 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~-~~~~~~C~aCG~~~~v~~~~kl~~~i~k 144 (445)
++.||.|+..= .. +. ..-...|..||+...+..+.+|...+=.
T Consensus 38 w~kc~~C~~~~---~~-~~l~~~~~vcp~c~~h~rltAreRI~~L~D~ 81 (296)
T CHL00174 38 WVQCENCYGLN---YK-KFLKSKMNICEQCGYHLKMSSSDRIELLIDP 81 (296)
T ss_pred eeECCCccchh---hH-HHHHHcCCCCCCCCCCcCCCHHHHHHHHccC
Confidence 79999998632 11 11 2235799999999999999888765543
No 184
>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=26.36 E-value=71 Score=22.29 Aligned_cols=10 Identities=40% Similarity=0.810 Sum_probs=7.4
Q ss_pred eeccccCCcc
Q 013311 121 LKCAACGFVS 130 (445)
Q Consensus 121 ~~C~aCG~~~ 130 (445)
..|..||..-
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3699999753
No 185
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.35 E-value=28 Score=31.33 Aligned_cols=43 Identities=21% Similarity=0.294 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 84 TAKLAGLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 84 ~~~l~~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
++.|+-.++.+.+. .-|. ...|.+ ...-...+|..||+..++.
T Consensus 41 pe~L~fafe~l~~g----t~~e--ga~L~i-~~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 41 KEIVEFALNELLKG----TILE--GAEIIF-EEEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred HHHHHHHHHHHHcC----Cccc--CCEEEE-EecceEEECCCCCCEEecc
Confidence 35566666554332 2233 446666 4445678999999888775
No 186
>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=26.08 E-value=31 Score=27.49 Aligned_cols=39 Identities=15% Similarity=0.377 Sum_probs=26.5
Q ss_pred ccCCCCCCCceEEEe---cCCeeeeeccccCCcccccchhhh
Q 013311 100 QCYGCGNPETDIIIT---KTQMVNLKCAACGFVSEVDMRDKL 138 (445)
Q Consensus 100 lC~~C~~peT~l~~~---k~~~~~~~C~aCG~~~~v~~~~kl 138 (445)
.|..|+...+..+-. .+++.+.+|..|....-+.-+.++
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 599999988888862 269999999999988777645443
No 187
>PRK00378 nucleoid-associated protein NdpA; Validated
Probab=26.00 E-value=1.4e+02 Score=30.56 Aligned_cols=50 Identities=28% Similarity=0.437 Sum_probs=37.5
Q ss_pred EEEeccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHHHh
Q 013311 25 TKIEGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENFIK 96 (445)
Q Consensus 25 ~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~ 96 (445)
+++-|+++||...|.. -.||-...||+.++.++|+| .+..|.+.|.++++
T Consensus 283 ~k~~~~~~gi~Isf~~--------------------~~~~~~i~yd~~~~~ltI~~--~p~~l~~ql~r~~~ 332 (334)
T PRK00378 283 TKFSGSGGGLTISFDA--------------------HLLGERIFYDPATDTLTIKG--TPPNLRDQLQRRLK 332 (334)
T ss_pred EEEEecCCCEEEEeeH--------------------HHCCCceEEcCCCCEEEEeC--CCHHHHHHHHHHhc
Confidence 4666999999988761 12467889999999999999 45666666666653
No 188
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=25.34 E-value=57 Score=33.75 Aligned_cols=25 Identities=40% Similarity=0.704 Sum_probs=19.5
Q ss_pred HHHHHHHHhhccccCCCCCCCceEEE
Q 013311 88 AGLLENFIKKYVQCYGCGNPETDIII 113 (445)
Q Consensus 88 ~~~l~~fi~~fVlC~~C~~peT~l~~ 113 (445)
-..+-+++.+|-.||.|++| |....
T Consensus 140 ars~l~W~skykFCp~CG~~-tkp~e 164 (345)
T KOG3084|consen 140 ARSLLDWVSKYKFCPGCGSP-TKPEE 164 (345)
T ss_pred HHHHHHHHHHhccCcccCCC-ccccc
Confidence 45667899999999999998 44443
No 189
>PRK02935 hypothetical protein; Provisional
Probab=25.19 E-value=44 Score=29.12 Aligned_cols=31 Identities=23% Similarity=0.384 Sum_probs=22.1
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCCcccccch
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMR 135 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~ 135 (445)
|.||+|+.|---|-+ .-.|--|+..=++|+.
T Consensus 71 V~CP~C~K~TKmLGr------vD~CM~C~~PLTLd~~ 101 (110)
T PRK02935 71 VICPSCEKPTKMLGR------VDACMHCNQPLTLDRS 101 (110)
T ss_pred eECCCCCchhhhccc------eeecCcCCCcCCcCcc
Confidence 799999987444333 2368889988777754
No 190
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=25.17 E-value=1.6e+02 Score=20.28 Aligned_cols=39 Identities=13% Similarity=0.223 Sum_probs=29.4
Q ss_pred echHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEE
Q 013311 39 VNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLV 78 (445)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii 78 (445)
....+||+.|+-++..+.+++. .|-.++-+....++|.|
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~-~L~~~g~l~~~~~~~~i 47 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLK-RLEKEGLISREGGRIVI 47 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHH-HHHHCCCEEEeCCEEEE
Confidence 6788999999999999988764 56666666544556655
No 191
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=25.16 E-value=60 Score=38.38 Aligned_cols=46 Identities=26% Similarity=0.413 Sum_probs=29.8
Q ss_pred ecCHHHHHHHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 81 AHDTAKLAGLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 81 ~~~~~~l~~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
.|....+-....++--.--+|++|+ |.++. + --...|..||..+-.
T Consensus 907 ~~~~~~~~~~~~~~~~~~~~c~~c~---~~~~~--~-g~c~~c~~cg~t~gc 952 (953)
T PRK06556 907 AHSSTELLELQLGEAADAPLCPTCG---TKMVR--N-GSCYVCEGCGSTSGC 952 (953)
T ss_pred CCccHHHHHHhhcccccCCcCCCcc---CeeeE--C-CceEeccCCCCCCCC
Confidence 3455555555555555556788885 77766 2 347789999998643
No 192
>PRK06824 translation initiation factor Sui1; Validated
Probab=25.04 E-value=1.6e+02 Score=26.07 Aligned_cols=55 Identities=22% Similarity=0.245 Sum_probs=37.7
Q ss_pred eccCCCceEEEechHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHH
Q 013311 28 EGRGNGIKTNVVNMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLA 88 (445)
Q Consensus 28 eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~ 88 (445)
.||++=.=|+|..|..-... -.-+.|.|...+|+.|++- ++.+.|+|.|...-.+
T Consensus 50 kgr~gK~VTvI~Gl~~~~~d----lk~l~K~LKkk~gcGGtvk--d~~IeiQGD~r~~v~~ 104 (118)
T PRK06824 50 KGRGGKTVTVITGVPLAEDA----LKELAKELKRRCGTGGTLK--DGVIEIQGDHVELLLA 104 (118)
T ss_pred ccCCCceEEEEeCCcCCHHH----HHHHHHHHHHHhcCCceEe--cCEEEEcCcHHHHHHH
Confidence 34433345677777521111 2467899999999999994 6899999999765444
No 193
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=24.94 E-value=1.3e+02 Score=23.79 Aligned_cols=41 Identities=22% Similarity=0.229 Sum_probs=35.8
Q ss_pred hHHHHHHHHhhc-CcccccCCCCeEEEEeecCHHHHHHHHHH
Q 013311 53 SYTTKYFGNELG-AQSKFDEKTGTSLVNGAHDTAKLAGLLEN 93 (445)
Q Consensus 53 ~~~~ky~~~ELg-~~~~~~~~~~~~ii~G~~~~~~l~~~l~~ 93 (445)
.++.+.|..--| -+..+|.+++++++.|.+++..|...|.+
T Consensus 20 ~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k 61 (73)
T KOG1603|consen 20 RKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKK 61 (73)
T ss_pred HHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHh
Confidence 478888888888 56778988999999999999999998887
No 194
>PHA02942 putative transposase; Provisional
Probab=24.82 E-value=35 Score=35.97 Aligned_cols=30 Identities=30% Similarity=0.853 Sum_probs=21.0
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
-.||.|+.....+ .++ ...|..||+...-|
T Consensus 326 q~Cs~CG~~~~~l---~~r--~f~C~~CG~~~drD 355 (383)
T PHA02942 326 VSCPKCGHKMVEI---AHR--YFHCPSCGYENDRD 355 (383)
T ss_pred ccCCCCCCccCcC---CCC--EEECCCCCCEeCcH
Confidence 4699999865432 223 57899999986655
No 195
>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=24.61 E-value=51 Score=27.83 Aligned_cols=24 Identities=13% Similarity=0.437 Sum_probs=14.3
Q ss_pred CeeeeeccccCCcccc-cchhhhhH
Q 013311 117 QMVNLKCAACGFVSEV-DMRDKLTT 140 (445)
Q Consensus 117 ~~~~~~C~aCG~~~~v-~~~~kl~~ 140 (445)
.+-.+.|.-||...-- +..++|-.
T Consensus 32 nVPa~~C~~CGe~y~~dev~~eIE~ 56 (89)
T TIGR03829 32 ETPSISCSHCGMEYQDDTTVKEIED 56 (89)
T ss_pred cCCcccccCCCcEeecHHHHHHHHh
Confidence 3445789999987433 33345443
No 196
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=24.60 E-value=40 Score=37.21 Aligned_cols=53 Identities=19% Similarity=0.411 Sum_probs=30.9
Q ss_pred ecCHHHHHHHHHHHHh-----------hccccCCCCCCCceEEEecCCeeeeeccccCCcccccchhhhhHHHh
Q 013311 81 AHDTAKLAGLLENFIK-----------KYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDKLTTFIL 143 (445)
Q Consensus 81 ~~~~~~l~~~l~~fi~-----------~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (445)
+.+++.|.++++.=.+ .+-.|+.|+.-. +. .-.|..||... ++.-.++++|+-
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 4678888888887777 245799999622 12 67799999987 777789999998
No 197
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=24.48 E-value=74 Score=27.71 Aligned_cols=34 Identities=21% Similarity=0.520 Sum_probs=24.5
Q ss_pred ccCCCCC---CCceEEE-ecCCeeeeeccccCCccccc
Q 013311 100 QCYGCGN---PETDIII-TKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 100 lC~~C~~---peT~l~~-~k~~~~~~~C~aCG~~~~v~ 133 (445)
.|+.|.+ |--...+ -+++.+...|.-||...-.+
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 4433333 25566899999999986655
No 198
>PRK07220 DNA topoisomerase I; Validated
Probab=23.86 E-value=54 Score=37.59 Aligned_cols=30 Identities=27% Similarity=0.470 Sum_probs=18.5
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCC
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGF 128 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~ 128 (445)
..||.|+.|...+...+++.+++.|..|.+
T Consensus 636 ~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~ 665 (740)
T PRK07220 636 KVCEAHGLNHIRIINGGKRPWDLGCPQCNF 665 (740)
T ss_pred CCCCCCCCceEEEEecCCccceeeCCCCCC
Confidence 369999887554443122345778877765
No 199
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=23.47 E-value=1.9e+02 Score=30.30 Aligned_cols=76 Identities=16% Similarity=0.416 Sum_probs=56.6
Q ss_pred HHHHhCCCchHH--HHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHHHhhcc--ccCCCCCCCceEEEecCCee
Q 013311 44 IAKALARPPSYT--TKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENFIKKYV--QCYGCGNPETDIIITKTQMV 119 (445)
Q Consensus 44 ia~~L~R~p~~~--~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~fV--lC~~C~~peT~l~~~k~~~~ 119 (445)
+-+.|+|.|+.. .+++...|. |.+.|+ ++-+...|++++..=|+.-+ .|..|+- ....+
T Consensus 305 l~~Ql~r~Pt~~gf~rl~~~~l~-----daeeg~----~k~sL~~lr~mvge~l~~~~~YRC~~CGF--------~a~~l 367 (389)
T COG2956 305 LTRQLRRKPTMRGFHRLMDYHLA-----DAEEGR----AKESLDLLRDMVGEQLRRKPRYRCQNCGF--------TAHTL 367 (389)
T ss_pred HHHHHhhCCcHHHHHHHHHhhhc-----cccccc----hhhhHHHHHHHHHHHHhhcCCceecccCC--------cceee
Confidence 457899999864 455555543 223455 67788889999998888755 6999984 35688
Q ss_pred eeeccccCCcccccchh
Q 013311 120 NLKCAACGFVSEVDMRD 136 (445)
Q Consensus 120 ~~~C~aCG~~~~v~~~~ 136 (445)
+-+|.+|.+..++.++.
T Consensus 368 ~W~CPsC~~W~TikPir 384 (389)
T COG2956 368 YWHCPSCRAWETIKPIR 384 (389)
T ss_pred eeeCCCcccccccCCcc
Confidence 99999999999998753
No 200
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=23.34 E-value=43 Score=24.98 Aligned_cols=17 Identities=35% Similarity=0.851 Sum_probs=7.7
Q ss_pred HHHHHhhcc----ccCCCCCC
Q 013311 91 LENFIKKYV----QCYGCGNP 107 (445)
Q Consensus 91 l~~fi~~fV----lC~~C~~p 107 (445)
|.+||+..- .||.|++|
T Consensus 9 ~~k~i~~l~~~~~~CPlC~r~ 29 (54)
T PF04423_consen 9 LKKYIEELKEAKGCCPLCGRP 29 (54)
T ss_dssp HHHHHHHHTT-SEE-TTT--E
T ss_pred HHHHHHHHhcCCCcCCCCCCC
Confidence 444555444 67777765
No 201
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=23.30 E-value=32 Score=24.80 Aligned_cols=13 Identities=31% Similarity=0.866 Sum_probs=11.0
Q ss_pred eeccccCCccccc
Q 013311 121 LKCAACGFVSEVD 133 (445)
Q Consensus 121 ~~C~aCG~~~~v~ 133 (445)
++|.+||+.+...
T Consensus 2 ~kC~~CG~~GH~~ 14 (40)
T PF15288_consen 2 VKCKNCGAFGHMR 14 (40)
T ss_pred ccccccccccccc
Confidence 5899999988775
No 202
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=23.21 E-value=41 Score=26.72 Aligned_cols=39 Identities=18% Similarity=0.429 Sum_probs=23.6
Q ss_pred hccccCCCCCCCceEEEecCCeeeeeccccCCcccccchhhhhHHHhcCCCC
Q 013311 97 KYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDKLTTFILKNPPV 148 (445)
Q Consensus 97 ~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~k~pP~ 148 (445)
.|.-|..|+.--+ . . .|..||... ....+.+||+=--|+
T Consensus 4 ~~~AC~~C~~i~~-----~-~----~Cp~Cgs~~---~S~~w~G~v~i~dPe 42 (64)
T PRK06393 4 QYRACKKCKRLTP-----E-K----TCPVHGDEK---TTTEWFGFLIITEPE 42 (64)
T ss_pred hhhhHhhCCcccC-----C-C----cCCCCCCCc---CCcCcceEEEEECCc
Confidence 4667888886321 1 1 788888863 344566666555553
No 203
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=22.98 E-value=84 Score=21.01 Aligned_cols=18 Identities=39% Similarity=0.373 Sum_probs=15.9
Q ss_pred HHHHHHhhCCcchhHHHH
Q 013311 391 LVLKALYDNDLLEEEFIL 408 (445)
Q Consensus 391 ~ILk~LYD~DIleEE~Il 408 (445)
..|+.||+.++|+++.+-
T Consensus 6 ~~L~~l~~~G~IseeEy~ 23 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYE 23 (31)
T ss_pred HHHHHHHHcCCCCHHHHH
Confidence 579999999999999875
No 204
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.95 E-value=46 Score=32.81 Aligned_cols=25 Identities=36% Similarity=0.929 Sum_probs=18.3
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
..|+.|+. . ..+ ...|..||..-.-
T Consensus 310 ~~C~~cg~------~-~~r--~~~C~~cg~~~~r 334 (364)
T COG0675 310 KTCPCCGH------L-SGR--LFKCPRCGFVHDR 334 (364)
T ss_pred ccccccCC------c-cce--eEECCCCCCeehh
Confidence 68999999 2 223 5789999997333
No 205
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=22.91 E-value=41 Score=32.87 Aligned_cols=34 Identities=24% Similarity=0.296 Sum_probs=27.1
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCCcccc
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGFVSEV 132 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (445)
-||+.|-.-.+.|..-.+++-...|.-||+...-
T Consensus 14 ~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 14 GLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIG 47 (236)
T ss_pred ccChHHhcccCCeeecCCccCceECCCCCCEECC
Confidence 4888888888888654567889999999997554
No 206
>TIGR01464 hemE uroporphyrinogen decarboxylase. This model represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products.
Probab=22.87 E-value=58 Score=33.18 Aligned_cols=56 Identities=18% Similarity=0.223 Sum_probs=39.3
Q ss_pred CCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHHHHHHhh------ccccCCCCCC-CceE
Q 013311 50 RPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLLENFIKK------YVQCYGCGNP-ETDI 111 (445)
Q Consensus 50 R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~------fVlC~~C~~p-eT~l 111 (445)
-+.....+.++.....+|++|+ .+ +.| +.+.+++...+.|+. |++.+.|+-| +|-+
T Consensus 264 ~dl~e~~~~~~~~~~i~Gni~p---~~-l~g--t~e~i~~~v~~~l~~~~~~~g~Il~~Gc~i~~~tp~ 326 (338)
T TIGR01464 264 VDLKEARKRVGPGVAIQGNLDP---AV-LYA--PEEALEEKVEKILEAFGGKSRYIFNLGHGILPDTPP 326 (338)
T ss_pred CCHHHHHHHhCCCeeEEeCCCh---HH-hcC--CHHHHHHHHHHHHHHhccCCCceecCCCcCCCCcCH
Confidence 3444556666666778899975 23 367 678888777777774 8999999975 6653
No 207
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=22.85 E-value=74 Score=24.14 Aligned_cols=35 Identities=31% Similarity=0.465 Sum_probs=26.5
Q ss_pred cccCCCCCCCceEEEe--cCCeeeeeccccCCccccc
Q 013311 99 VQCYGCGNPETDIIIT--KTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 99 VlC~~C~~peT~l~~~--k~~~~~~~C~aCG~~~~v~ 133 (445)
|.||-|+-+-+.++=. .++.++-.|..|...-.+.
T Consensus 1 i~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~ 37 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQ 37 (52)
T ss_pred CCCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEE
Confidence 5799999987665532 4578999999998765543
No 208
>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family. This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0
Probab=22.78 E-value=37 Score=33.71 Aligned_cols=36 Identities=31% Similarity=0.669 Sum_probs=21.5
Q ss_pred HHhh-ccccCCCCCCCceEEEecCCe--eeeeccccCCccc
Q 013311 94 FIKK-YVQCYGCGNPETDIIITKTQM--VNLKCAACGFVSE 131 (445)
Q Consensus 94 fi~~-fVlC~~C~~peT~l~~~k~~~--~~~~C~aCG~~~~ 131 (445)
|+.- -..|+.|.+|++.... ... ...+|..||.-..
T Consensus 20 f~~gc~~~C~~c~~p~~~~~~--~~~~~~~~~C~~C~~C~~ 58 (295)
T TIGR02494 20 FLKGCPLRCKWCSNPESQRKS--PELLFKENRCLGCGKCVE 58 (295)
T ss_pred HhhcCCccCcccCCccccCCC--ceEEEccccCCCCchhhh
Confidence 5555 5789999999976432 111 1245666665433
No 209
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.63 E-value=81 Score=36.24 Aligned_cols=51 Identities=16% Similarity=0.421 Sum_probs=37.6
Q ss_pred cCHHHHHHHHHHHHh----------hccccCCCCCCCceEEEecCCeeeeeccccCCcccccchhhhhHHH
Q 013311 82 HDTAKLAGLLENFIK----------KYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDKLTTFI 142 (445)
Q Consensus 82 ~~~~~l~~~l~~fi~----------~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i 142 (445)
.+++.+.++++.+-+ .+-.|+.|+. .+. +.-.|.-||. ..+....++++|+
T Consensus 654 ~n~eal~~lvk~~~~~~i~Y~sin~~~~~C~~CG~-~~~--------~~~~CP~CG~-~~~~~~~Ri~GYl 714 (735)
T PRK07111 654 KNVEAFEIIVKAMKNTNIGYGSINHPVDRCPVCGY-LGV--------IEDKCPKCGS-TNIQRIRRITGYL 714 (735)
T ss_pred CCHHHHHHHHHHHHhCCCceEEeCCCCeecCCCCC-CCC--------cCccCcCCCC-ccceeeehhhhhc
Confidence 578889999886443 1347999993 221 2378999998 4677789999999
No 210
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=22.61 E-value=3.2e+02 Score=32.56 Aligned_cols=50 Identities=18% Similarity=0.268 Sum_probs=35.2
Q ss_pred HHHHHhhHHHHHHhcc---CchhHH--HHHHHHHHHhcccChhhHHHHHHHHHHH
Q 013311 347 AKEVTKKKNYLAAATQ---EEGSQM--VLLHSLESFCGKARPAAVKEVALVLKAL 396 (445)
Q Consensus 347 ~k~i~k~~~lL~~~~~---~~~~Q~--~lL~alE~~~~~~~~~l~~~~~~ILk~L 396 (445)
-..+.+-.|++..||+ ...+++ ++|.|+|.|+.....+..|..|.|+..+
T Consensus 249 ~~h~~~ivp~v~~y~~~~e~~dDELrE~~lQale~fl~rcp~ei~p~~pei~~l~ 303 (1233)
T KOG1824|consen 249 GSHLDKIVPLVADYCNKIEEDDDELREYCLQALESFLRRCPKEILPHVPEIINLC 303 (1233)
T ss_pred hcccchhhHHHHHHhcccccCcHHHHHHHHHHHHHHHHhChhhhcccchHHHHHH
Confidence 3345566688889993 444443 9999999999875556667777776655
No 211
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=22.58 E-value=1.9e+02 Score=20.71 Aligned_cols=25 Identities=24% Similarity=0.311 Sum_probs=22.8
Q ss_pred EEechHHHHHHhCCCchHHHHHHHH
Q 013311 37 NVVNMVDIAKALARPPSYTTKYFGN 61 (445)
Q Consensus 37 ~i~N~~~ia~~L~R~p~~~~ky~~~ 61 (445)
.+..+.+.|+.|+.++.++.+++--
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHhC
Confidence 6899999999999999999999763
No 212
>smart00070 GLUCA Glucagon like hormones.
Probab=22.46 E-value=54 Score=21.59 Aligned_cols=11 Identities=36% Similarity=0.739 Sum_probs=8.7
Q ss_pred HhhhHHHHHhc
Q 013311 426 KNAKPVIEWLQ 436 (445)
Q Consensus 426 k~a~pFI~WLe 436 (445)
..|+.||.||-
T Consensus 17 ~~ar~fl~~L~ 27 (27)
T smart00070 17 LAAKKFLQWLM 27 (27)
T ss_pred HHHHHHHHHhC
Confidence 56788999983
No 213
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=22.37 E-value=56 Score=30.76 Aligned_cols=90 Identities=18% Similarity=0.159 Sum_probs=52.3
Q ss_pred echHHHHHHhCCCchHHHHHHH--HhhcCcc--c-ccCCCCeEEEEeecCHHHHHHHHHH---------------HH-hh
Q 013311 39 VNMVDIAKALARPPSYTTKYFG--NELGAQS--K-FDEKTGTSLVNGAHDTAKLAGLLEN---------------FI-KK 97 (445)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~--~ELg~~~--~-~~~~~~~~ii~G~~~~~~l~~~l~~---------------fi-~~ 97 (445)
..-.++|..|+-.+..|-+-+. .|-|.-+ . -++..|++..-=.++...+-++|.. .- ..
T Consensus 37 ~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~~~~~~klk~~l~~e~~~~ 116 (178)
T PRK06266 37 VTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKKKMEELKKLKEQLEEEENNM 116 (178)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHHHHHHHHHHHHHhhhccCCC
Confidence 4567899999999987776443 3444433 2 1223556555445555555444332 11 24
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCccc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVSE 131 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~ 131 (445)
|-.||.|+.-=|.+.- =.....|.-||..=.
T Consensus 117 ~Y~Cp~C~~rytf~eA---~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 117 FFFCPNCHIRFTFDEA---MEYGFRCPQCGEMLE 147 (178)
T ss_pred EEECCCCCcEEeHHHH---hhcCCcCCCCCCCCe
Confidence 7789999843332222 224688999998743
No 214
>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=22.36 E-value=37 Score=25.78 Aligned_cols=17 Identities=35% Similarity=0.675 Sum_probs=12.9
Q ss_pred CeeeeeccccCCccccc
Q 013311 117 QMVNLKCAACGFVSEVD 133 (445)
Q Consensus 117 ~~~~~~C~aCG~~~~v~ 133 (445)
..-.|+|.|||..+..-
T Consensus 33 ~~~al~CaACgCHRnFH 49 (53)
T TIGR01566 33 DPESLTCAACGCHRNFH 49 (53)
T ss_pred CCcceeeeecCcccccc
Confidence 34479999999987643
No 215
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=22.34 E-value=54 Score=33.53 Aligned_cols=41 Identities=22% Similarity=0.544 Sum_probs=30.5
Q ss_pred ccCCCCCCCceEEEecCCeeeeeccccCCc---ccccchhhhhHH
Q 013311 100 QCYGCGNPETDIIITKTQMVNLKCAACGFV---SEVDMRDKLTTF 141 (445)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~---~~v~~~~kl~~~ 141 (445)
.|+.|+.+--.++. +-+.-...|..||-. +.++.+|-.=||
T Consensus 2 ~c~~C~~~~~~~V~-d~~~gdtvC~~CGlVl~~r~Id~~sEwrtf 45 (308)
T KOG1597|consen 2 TCPDCKRHPENLVE-DHSAGDTVCSECGLVLEDRIIDEGSEWRTF 45 (308)
T ss_pred CCCCCCCCCCCeee-eccCCceecccCCeeecccccccccccccc
Confidence 49999994336666 445557899999976 778878777777
No 216
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=22.28 E-value=74 Score=26.94 Aligned_cols=44 Identities=16% Similarity=0.272 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 85 AKLAGLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 85 ~~l~~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
..+.++...=-.+| .||.|+. +.+.+ ...-+-.|..||..-.-.
T Consensus 24 K~v~kie~~q~a~y-~CpfCgk--~~vkR--~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 24 KQIKKIEISQHAKY-FCPFCGK--HAVKR--QAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred HHHHHHHHHHhCCc-cCCCCCC--Cceee--eeeEEEEcCCCCCEEeCC
Confidence 34444433333444 6999995 44555 345577899999875543
No 217
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=22.21 E-value=56 Score=30.11 Aligned_cols=89 Identities=17% Similarity=0.184 Sum_probs=49.1
Q ss_pred echHHHHHHhCCCchHHHHHH--HHhhcCcc--c-ccCCCCeEEEEeecCHHHHHHHH---------------HHHH-hh
Q 013311 39 VNMVDIAKALARPPSYTTKYF--GNELGAQS--K-FDEKTGTSLVNGAHDTAKLAGLL---------------ENFI-KK 97 (445)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~--~~ELg~~~--~-~~~~~~~~ii~G~~~~~~l~~~l---------------~~fi-~~ 97 (445)
..-.+||..|+-....|-+-+ +.|.|.-+ . -++.+|++..-=.++..++-+.| ...- ..
T Consensus 29 ~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~~~~~~~~lk~~l~~e~~~~ 108 (158)
T TIGR00373 29 FTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLKRKLEETAKKLREKLEFETNNM 108 (158)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHHHHHHHHHHHHHHHHhhccCCC
Confidence 456788888888888776643 44555542 1 13334443333233443333322 2221 35
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVS 130 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (445)
|-.||.|+. .+...+--.....|..||..=
T Consensus 109 ~Y~Cp~c~~---r~tf~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 109 FFICPNMCV---RFTFNEAMELNFTCPRCGAML 138 (158)
T ss_pred eEECCCCCc---EeeHHHHHHcCCcCCCCCCEe
Confidence 778999993 333321122468899999873
No 218
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=22.09 E-value=61 Score=26.22 Aligned_cols=25 Identities=20% Similarity=0.417 Sum_probs=12.5
Q ss_pred cccCCCCCCCceEEEecCCeeeeeccccCCc
Q 013311 99 VQCYGCGNPETDIIITKTQMVNLKCAACGFV 129 (445)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (445)
.+||.|+.| |.. .+ -...|.+|+..
T Consensus 2 ~~CP~C~~~---L~~-~~--~~~~C~~C~~~ 26 (70)
T PF07191_consen 2 NTCPKCQQE---LEW-QG--GHYHCEACQKD 26 (70)
T ss_dssp -B-SSS-SB---EEE-ET--TEEEETTT--E
T ss_pred CcCCCCCCc---cEE-eC--CEEECcccccc
Confidence 478999887 665 33 24556666654
No 219
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=22.04 E-value=58 Score=24.50 Aligned_cols=23 Identities=22% Similarity=0.473 Sum_probs=16.8
Q ss_pred cCHHHHHHHHHHHHhhccccCCCCC
Q 013311 82 HDTAKLAGLLENFIKKYVQCYGCGN 106 (445)
Q Consensus 82 ~~~~~l~~~l~~fi~~fVlC~~C~~ 106 (445)
.++..++++... ++.|.||+|+.
T Consensus 32 l~~~~~~~i~~~--~~i~~Cp~CgR 54 (56)
T PF02591_consen 32 LPPQELNEIRKG--DEIVFCPNCGR 54 (56)
T ss_pred cCHHHHHHHHcC--CCeEECcCCCc
Confidence 456777777666 77888888875
No 220
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=21.99 E-value=37 Score=29.88 Aligned_cols=31 Identities=26% Similarity=0.538 Sum_probs=22.0
Q ss_pred ccccCCCCCCCceEEEecCCeeeeeccccCCcccccc
Q 013311 98 YVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDM 134 (445)
Q Consensus 98 fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (445)
-|.||+|+.| |.+.- |. -.|--|+..=++|+
T Consensus 69 ~V~CP~C~K~-TKmLG---r~--D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 69 QVECPNCGKQ-TKMLG---RV--DACMHCKEPLTLDP 99 (114)
T ss_pred eeECCCCCCh-Hhhhc---hh--hccCcCCCcCccCc
Confidence 5889999987 33332 22 37999998888774
No 221
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=21.70 E-value=2e+02 Score=21.64 Aligned_cols=46 Identities=17% Similarity=0.044 Sum_probs=32.0
Q ss_pred chHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHH
Q 013311 40 NMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGL 90 (445)
Q Consensus 40 N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~ 90 (445)
++.++|+.++.+|..+..|....+-.+..-++ +|+. .|+...|..+
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~gli~~~~~~~-~g~r----~y~~~dl~~l 47 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERIGLLPPPIRTE-GGYR----LYSDEDLERL 47 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCCE----ecCHHHHHHH
Confidence 47899999999999999998766655432233 4443 3667777654
No 222
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=21.51 E-value=62 Score=32.62 Aligned_cols=45 Identities=18% Similarity=0.399 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhh--ccccCCCCCCCceEEEecCCeeeeeccccCCcccccchhh
Q 013311 85 AKLAGLLENFIKK--YVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVDMRDK 137 (445)
Q Consensus 85 ~~l~~~l~~fi~~--fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~k 137 (445)
..++.++.+.|.. .-.|..|+.- ...|+..|..||+..++.++.-
T Consensus 339 ~~~~~~~~~~~~~~p~~~c~~cg~~--------~~~~~~~c~~c~~~~~~~~~~~ 385 (389)
T PRK11788 339 LLLRDLVGEQLKRKPRYRCRNCGFT--------ARTLYWHCPSCKAWETIKPIRG 385 (389)
T ss_pred HHHHHHHHHHHhCCCCEECCCCCCC--------CccceeECcCCCCccCcCCccc
Confidence 3466666655542 2459999962 3568889999999999887643
No 223
>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=21.49 E-value=48 Score=23.40 Aligned_cols=33 Identities=21% Similarity=0.410 Sum_probs=18.0
Q ss_pred cccCCCCC---CCceEEEecCCeeeeeccccCCcccccc
Q 013311 99 VQCYGCGN---PETDIIITKTQMVNLKCAACGFVSEVDM 134 (445)
Q Consensus 99 VlC~~C~~---peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (445)
|.|..|+. |=..+.. .++ .-.|.-||...+++.
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 67999986 6666654 334 568999999988863
No 224
>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=21.18 E-value=51 Score=31.61 Aligned_cols=31 Identities=29% Similarity=0.673 Sum_probs=23.5
Q ss_pred ccCCCCCCCceEEEe--cCCeeeeeccccCCcc
Q 013311 100 QCYGCGNPETDIIIT--KTQMVNLKCAACGFVS 130 (445)
Q Consensus 100 lC~~C~~peT~l~~~--k~~~~~~~C~aCG~~~ 130 (445)
.|-+|+.|=..|.+. .+..-..+|..||+.-
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 599999997766663 3445578999999754
No 225
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.07 E-value=43 Score=33.22 Aligned_cols=46 Identities=24% Similarity=0.426 Sum_probs=32.3
Q ss_pred ccccCCCCCC----------------CceEEEecCCeeeeeccccCCcccccchhhhhHHHhc
Q 013311 98 YVQCYGCGNP----------------ETDIIITKTQMVNLKCAACGFVSEVDMRDKLTTFILK 144 (445)
Q Consensus 98 fVlC~~C~~p----------------eT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~k 144 (445)
-+.|.+|++. +|.|-+ +--.++.+|..|++.-+..+-.+=+.|++-
T Consensus 40 ~~rC~tCgeyi~kg~kfN~r~E~~~~e~yLgi-ki~Rf~i~Ct~cl~el~~rTDp~N~dY~~E 101 (253)
T KOG2989|consen 40 RLRCNTCGEYIYKGKKFNAREEDVIEETYLGI-KIFRFYIKCTRCLRELSFRTDPKNSDYVIE 101 (253)
T ss_pred eeecccccchhhcCCCcchhHHhhhccccccc-eeeeeeeeccchHhhhhhhcCCcchHHHHH
Confidence 4678888874 444544 446678999999998777666666667653
No 226
>PF09733 VEFS-Box: VEFS-Box of polycomb protein; InterPro: IPR019135 The VEFS-Box is found in the the C-terminal region of the VRN2, EMF2, FIS2, and Su(z)12 polycomb proteins. This domain is characterised by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain []. In some proteins the VEFS-Box is associated with a zinc-finger domain located roughly 100 residues towards the N terminus. These proteins are part of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression [].
Probab=21.06 E-value=4.7e+02 Score=23.76 Aligned_cols=40 Identities=28% Similarity=0.396 Sum_probs=28.5
Q ss_pred HHHHHHHHhccc------ChhhHHHHHHHHHHHhhCCcchhHHHHH
Q 013311 370 LLHSLESFCGKA------RPAAVKEVALVLKALYDNDLLEEEFILD 409 (445)
Q Consensus 370 lL~alE~~~~~~------~~~l~~~~~~ILk~LYD~DIleEE~Il~ 409 (445)
+=.+++.|+..+ .+.+...|..-|-.||+.++|+..+|..
T Consensus 90 ip~ac~~Fv~~~~~~L~~~~~l~~~f~lHl~~L~d~glLd~~~i~~ 135 (140)
T PF09733_consen 90 IPWACEAFVREHGQWLVEKPNLRREFLLHLINLWDFGLLDARTIDE 135 (140)
T ss_pred HHHHHHHHHHHhHHHHhhChhHHHHHHHHHHHHHHcCCCCHHHHHH
Confidence 334455555432 3567777888899999999999998864
No 227
>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=20.87 E-value=92 Score=34.86 Aligned_cols=54 Identities=17% Similarity=0.343 Sum_probs=27.7
Q ss_pred EEEeecCHHHHHHHHHHHHhhcc----------------ccCCCCCCCceEEEecCCeeeeeccc---cCCcccc
Q 013311 77 LVNGAHDTAKLAGLLENFIKKYV----------------QCYGCGNPETDIIITKTQMVNLKCAA---CGFVSEV 132 (445)
Q Consensus 77 ii~G~~~~~~l~~~l~~fi~~fV----------------lC~~C~~peT~l~~~k~~~~~~~C~a---CG~~~~v 132 (445)
|-.|..+...+-+-+..|+.+.| .||.|+.+ .+.+..+..-+..|.. |++..++
T Consensus 537 I~~G~~~~~~~l~~~~~~~~~~v~~~~~~~~~~~~~~~~~CP~Cg~~--~~~~~~~~gkf~gCs~y~~C~~~~~l 609 (610)
T TIGR01051 537 IAEGKAEWKPVLKNFYTGFSSKVKKLRNMRIIVDFKTSQDCPLCGRP--MVVKLGKYGPFLACSNFPECKYTKSI 609 (610)
T ss_pred HHcCCCCHHHHHHHHHHHHHHHHHHhhhcccccccccCCCCCCCCCe--eEEEecCCCceeeCCCCCCCCCCCCC
Confidence 34566665555444444443322 49999874 2222111223567876 6655443
No 228
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=20.78 E-value=78 Score=26.87 Aligned_cols=44 Identities=18% Similarity=0.259 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCccccc
Q 013311 85 AKLAGLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSEVD 133 (445)
Q Consensus 85 ~~l~~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (445)
..+.++...=-.+| .||.|+.+. +.+ ..+-+-+|..||..-.-.
T Consensus 23 K~v~kie~~q~a~y-~CpfCgk~~--vkR--~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 23 RQVKKIEIQQKAKY-VCPFCGKKT--VKR--GSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred HHHHHHHHHHhcCc-cCCCCCCCc--eEE--EeeEEEEcCCCCCEEeCC
Confidence 34444443333444 699999644 544 345577999999875543
No 229
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=20.49 E-value=1.9e+02 Score=24.15 Aligned_cols=47 Identities=19% Similarity=0.070 Sum_probs=35.1
Q ss_pred chHHHHHHhCCCchHHHHHHHHhhcCcccccCCCCeEEEEeecCHHHHHHHH
Q 013311 40 NMVDIAKALARPPSYTTKYFGNELGAQSKFDEKTGTSLVNGAHDTAKLAGLL 91 (445)
Q Consensus 40 N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l 91 (445)
++.++|+.++-+|..+-.|....+..+...++ +|+- .|+...|..+.
T Consensus 2 ti~eva~~~gvs~~tlR~ye~~Gll~~~~~~~-~g~R----~y~~~di~~l~ 48 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTE-NGYR----LYTEEDLERLQ 48 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCce----eeCHHHHHHHH
Confidence 57899999999999999998877766654443 4432 37888887763
No 230
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=20.43 E-value=53 Score=20.61 Aligned_cols=7 Identities=43% Similarity=1.241 Sum_probs=5.0
Q ss_pred cCCCCCC
Q 013311 101 CYGCGNP 107 (445)
Q Consensus 101 C~~C~~p 107 (445)
||.|+++
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 7777764
No 231
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=20.07 E-value=1e+02 Score=24.99 Aligned_cols=33 Identities=15% Similarity=0.289 Sum_probs=22.6
Q ss_pred ccCCCCCCCceEEEec-----CCeeeeecc--ccCCccccc
Q 013311 100 QCYGCGNPETDIIITK-----TQMVNLKCA--ACGFVSEVD 133 (445)
Q Consensus 100 lC~~C~~peT~l~~~k-----~~~~~~~C~--aCG~~~~v~ 133 (445)
.||.|+.+. .+.... -+..+..|. .||++....
T Consensus 3 ~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 3 HCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATFITY 42 (72)
T ss_pred cCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEEEEE
Confidence 599999999 333211 144678898 999986543
No 232
>PRK08402 replication factor A; Reviewed
Probab=20.04 E-value=72 Score=33.43 Aligned_cols=45 Identities=18% Similarity=0.293 Sum_probs=27.2
Q ss_pred EEEEeecCHHHHHHHHHHHHhhccccCCCCCCCceEEEecCCeeeeeccccCCccc
Q 013311 76 SLVNGAHDTAKLAGLLENFIKKYVQCYGCGNPETDIIITKTQMVNLKCAACGFVSE 131 (445)
Q Consensus 76 ~ii~G~~~~~~l~~~l~~fi~~fVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~ 131 (445)
+-|.|.... |.. +++ |-.||.|.. .+.. +...-.-+|..||...|
T Consensus 197 v~v~g~Iv~--i~~---~~~--y~aCp~CnK---kv~~-~~~~~~~~Ce~~~~v~p 241 (355)
T PRK08402 197 VEVRGTIAK--VYR---VLV--YDACPECRR---KVDY-DPATDTWICPEHGEVEP 241 (355)
T ss_pred EEEEEEEEE--Eec---Cee--EecCCCCCe---EEEE-ecCCCCEeCCCCCCcCc
Confidence 567776543 222 332 899999987 4442 22223458999997444
Done!