Query 013781
Match_columns 436
No_of_seqs 276 out of 733
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 07:20:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013781.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013781hhsearch_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-108 5E-113 807.1 25.1 386 2-436 1-395 (400)
2 smart00653 eIF2B_5 domain pres 100.0 1.1E-44 2.5E-49 311.6 13.1 110 15-129 1-110 (110)
3 PF01873 eIF-5_eIF-2B: Domain 100.0 5.6E-45 1.2E-49 320.2 11.4 121 3-130 4-124 (125)
4 TIGR00311 aIF-2beta translatio 100.0 3.6E-43 7.7E-48 311.6 13.0 113 15-134 20-132 (133)
5 PRK03988 translation initiatio 100.0 1.5E-42 3.3E-47 309.3 13.6 115 13-134 23-137 (138)
6 PRK12336 translation initiatio 100.0 4E-41 8.6E-46 318.5 13.4 117 11-134 17-133 (201)
7 KOG2768 Translation initiation 100.0 7E-32 1.5E-36 251.6 6.4 114 15-134 103-216 (231)
8 COG1601 GCD7 Translation initi 100.0 2.2E-29 4.8E-34 227.0 5.5 111 17-133 29-139 (151)
9 KOG2297 Predicted translation 99.8 6.2E-21 1.4E-25 187.7 12.6 134 286-435 270-412 (412)
10 PF02020 W2: eIF4-gamma/eIF5/e 99.8 4E-21 8.7E-26 158.1 7.8 79 356-436 1-82 (84)
11 smart00515 eIF5C Domain at the 99.8 2.8E-20 6.1E-25 152.5 8.2 82 346-430 2-83 (83)
12 KOG1461 Translation initiation 99.7 1.2E-17 2.7E-22 176.7 14.7 130 305-436 531-671 (673)
13 PF09090 MIF4G_like_2: MIF4G l 96.6 0.053 1.1E-06 53.4 13.8 118 285-407 8-137 (253)
14 COG1326 Uncharacterized archae 94.5 0.012 2.5E-07 55.7 0.4 36 97-132 5-42 (201)
15 TIGR02443 conserved hypothetic 94.0 0.035 7.6E-07 43.0 2.0 40 93-133 5-44 (59)
16 PF09526 DUF2387: Probable met 93.7 0.041 8.8E-07 44.3 1.9 41 93-134 4-44 (71)
17 PRK00464 nrdR transcriptional 91.2 0.18 3.8E-06 46.5 3.0 33 100-132 2-40 (154)
18 PF01253 SUI1: Translation ini 89.8 0.73 1.6E-05 37.7 5.2 72 19-94 3-78 (83)
19 smart00440 ZnF_C2C2 C2C2 Zinc 89.7 0.42 9E-06 34.1 3.2 30 100-129 2-37 (40)
20 PF01096 TFIIS_C: Transcriptio 88.7 0.33 7.1E-06 34.4 2.1 31 99-129 1-37 (39)
21 PF01921 tRNA-synt_1f: tRNA sy 88.1 0.52 1.1E-05 49.0 3.9 53 83-135 150-214 (360)
22 PF14354 Lar_restr_allev: Rest 86.7 0.6 1.3E-05 35.6 2.7 28 100-128 5-37 (61)
23 PRK09710 lar restriction allev 86.3 0.88 1.9E-05 35.9 3.3 34 100-134 8-41 (64)
24 TIGR00244 transcriptional regu 85.8 0.68 1.5E-05 42.3 2.9 32 100-131 2-39 (147)
25 TIGR03655 anti_R_Lar restricti 85.6 0.9 1.9E-05 34.1 3.0 33 100-132 3-38 (53)
26 PF12677 DUF3797: Domain of un 85.5 0.83 1.8E-05 34.1 2.7 32 95-128 10-46 (49)
27 PHA02998 RNA polymerase subuni 83.3 1.1 2.5E-05 42.1 3.3 84 41-131 87-182 (195)
28 PF14803 Nudix_N_2: Nudix N-te 82.5 0.71 1.5E-05 31.9 1.2 30 100-129 2-31 (34)
29 TIGR01159 DRP1 density-regulat 82.3 3.7 8E-05 38.6 6.3 73 18-94 86-162 (173)
30 cd00674 LysRS_core_class_I cat 79.7 1.8 4E-05 44.9 3.7 93 41-135 89-207 (353)
31 PRK14892 putative transcriptio 79.5 1.2 2.6E-05 38.2 1.8 38 95-133 18-55 (99)
32 PF08271 TF_Zn_Ribbon: TFIIB z 79.4 1.4 3E-05 31.6 1.9 27 100-129 2-28 (43)
33 COG2051 RPS27A Ribosomal prote 79.0 0.85 1.8E-05 36.2 0.7 43 98-143 19-63 (67)
34 PF14205 Cys_rich_KTR: Cystein 78.5 0.78 1.7E-05 35.0 0.4 48 97-146 3-53 (55)
35 PF12760 Zn_Tnp_IS1595: Transp 78.2 2.1 4.5E-05 31.2 2.6 30 96-129 17-46 (46)
36 PRK00415 rps27e 30S ribosomal 76.2 2.1 4.6E-05 33.3 2.2 30 98-130 11-40 (59)
37 cd00474 SUI1_eIF1 The SUI1/eIF 76.0 6.9 0.00015 31.9 5.3 58 24-87 3-61 (77)
38 PF13719 zinc_ribbon_5: zinc-r 75.9 1.5 3.2E-05 30.7 1.2 32 98-132 2-37 (37)
39 PF11331 DUF3133: Protein of u 75.1 1.2 2.6E-05 33.0 0.6 33 98-131 6-42 (46)
40 smart00661 RPOL9 RNA polymeras 73.6 2.3 5.1E-05 31.1 1.8 32 100-134 2-34 (52)
41 TIGR00467 lysS_arch lysyl-tRNA 72.9 4 8.7E-05 44.5 4.2 51 84-135 145-205 (515)
42 PRK00939 translation initiatio 72.0 9.2 0.0002 32.7 5.3 63 23-92 26-89 (99)
43 COG1384 LysS Lysyl-tRNA synthe 71.6 5.1 0.00011 43.5 4.5 51 84-135 148-209 (521)
44 KOG1104 Nuclear cap-binding co 71.0 53 0.0011 37.4 12.2 103 301-407 513-623 (759)
45 PRK00750 lysK lysyl-tRNA synth 70.5 3.5 7.6E-05 44.9 3.1 51 85-136 153-215 (510)
46 COG1997 RPL43A Ribosomal prote 68.5 6.6 0.00014 32.9 3.5 48 81-133 19-66 (89)
47 TIGR01384 TFS_arch transcripti 66.2 5.5 0.00012 33.6 2.8 33 98-130 62-100 (104)
48 TIGR01385 TFSII transcription 66.1 5.5 0.00012 40.5 3.2 55 75-129 206-295 (299)
49 PF04216 FdhE: Protein involve 66.0 3.4 7.5E-05 41.4 1.7 35 99-133 173-210 (290)
50 PRK08665 ribonucleotide-diphos 65.7 6.7 0.00015 44.8 4.2 42 84-131 688-751 (752)
51 PF05129 Elf1: Transcription e 65.7 4.6 9.9E-05 33.2 2.1 39 95-133 19-59 (81)
52 PHA00626 hypothetical protein 65.6 4.9 0.00011 31.0 2.0 35 100-134 2-37 (59)
53 PF02150 RNA_POL_M_15KD: RNA p 65.1 4.8 0.0001 27.9 1.8 29 100-133 3-33 (35)
54 cd00202 ZnF_GATA Zinc finger D 63.7 2.6 5.6E-05 32.1 0.3 32 100-132 1-33 (54)
55 PF09855 DUF2082: Nucleic-acid 63.6 7.4 0.00016 30.7 2.8 32 100-131 2-47 (64)
56 PF13453 zf-TFIIB: Transcripti 63.6 8.3 0.00018 27.3 2.9 28 100-129 1-28 (41)
57 COG3529 Predicted nucleic-acid 62.3 1.4 3E-05 34.4 -1.5 38 92-130 5-42 (66)
58 smart00531 TFIIE Transcription 62.2 18 0.00039 32.7 5.5 95 39-133 16-136 (147)
59 TIGR01158 SUI1_rel translation 62.0 20 0.00044 30.7 5.5 59 23-87 26-86 (101)
60 COG4888 Uncharacterized Zn rib 61.5 6.4 0.00014 33.8 2.3 38 95-133 19-59 (104)
61 smart00401 ZnF_GATA zinc finge 61.4 4.3 9.3E-05 30.5 1.1 33 99-132 4-37 (52)
62 TIGR00340 zpr1_rel ZPR1-relate 60.6 7.6 0.00016 36.1 2.8 31 101-131 1-39 (163)
63 TIGR02159 PA_CoA_Oxy4 phenylac 60.5 3.9 8.4E-05 37.3 0.9 32 98-129 105-139 (146)
64 COG3478 Predicted nucleic-acid 60.1 7.8 0.00017 30.7 2.3 35 98-132 4-52 (68)
65 KOG2906 RNA polymerase III sub 59.5 9.2 0.0002 32.8 2.9 31 100-133 3-34 (105)
66 COG1327 Predicted transcriptio 59.3 6.6 0.00014 36.2 2.1 32 100-131 2-39 (156)
67 PLN00209 ribosomal protein S27 59.1 7.2 0.00016 32.6 2.1 30 98-130 36-65 (86)
68 PRK00398 rpoP DNA-directed RNA 58.4 8.8 0.00019 27.8 2.3 36 99-138 4-39 (46)
69 PRK00241 nudC NADH pyrophospha 57.6 9.8 0.00021 37.7 3.2 42 89-134 90-131 (256)
70 PF03367 zf-ZPR1: ZPR1 zinc-fi 56.6 7.8 0.00017 35.9 2.2 33 99-131 2-41 (161)
71 COG2835 Uncharacterized conser 56.1 6.8 0.00015 30.6 1.4 33 97-133 7-39 (60)
72 PRK03954 ribonuclease P protei 55.9 9.8 0.00021 33.8 2.6 35 99-133 65-106 (121)
73 COG1594 RPB9 DNA-directed RNA 55.6 10 0.00022 33.1 2.7 33 98-130 72-110 (113)
74 TIGR00100 hypA hydrogenase nic 55.5 9.6 0.00021 33.2 2.4 28 49-79 38-65 (115)
75 TIGR00310 ZPR1_znf ZPR1 zinc f 55.4 11 0.00024 35.9 3.1 32 100-131 2-41 (192)
76 smart00709 Zpr1 Duplicated dom 55.3 13 0.00027 34.5 3.3 32 100-131 2-40 (160)
77 PTZ00083 40S ribosomal protein 54.5 9.6 0.00021 31.8 2.1 30 98-130 35-64 (85)
78 PRK03564 formate dehydrogenase 53.4 9.9 0.00021 38.9 2.5 36 98-133 187-225 (309)
79 COG1779 C4-type Zn-finger prot 53.4 10 0.00022 36.4 2.4 33 98-131 14-54 (201)
80 KOG3221 Glycolipid transfer pr 53.2 89 0.0019 30.1 8.6 67 301-372 111-177 (199)
81 COG3058 FdhE Uncharacterized p 52.7 6.9 0.00015 39.4 1.2 31 98-128 185-219 (308)
82 PF05379 Peptidase_C23: Carlav 51.7 14 0.0003 30.9 2.7 65 41-115 7-72 (89)
83 PF00320 GATA: GATA zinc finge 51.6 6 0.00013 27.4 0.4 29 101-129 1-29 (36)
84 TIGR01562 FdhE formate dehydro 51.6 8 0.00017 39.5 1.5 36 98-133 184-223 (305)
85 COG1198 PriA Primosomal protei 51.4 10 0.00022 43.2 2.4 36 98-134 435-476 (730)
86 PRK00564 hypA hydrogenase nick 51.1 12 0.00027 32.7 2.4 28 49-79 38-66 (117)
87 PRK00420 hypothetical protein; 50.9 15 0.00032 32.2 2.9 40 90-134 15-54 (112)
88 PF09297 zf-NADH-PPase: NADH p 50.7 4.3 9.3E-05 27.2 -0.4 28 98-129 3-30 (32)
89 PF13717 zinc_ribbon_4: zinc-r 50.6 6.7 0.00015 27.2 0.6 29 98-129 2-34 (36)
90 PF04760 IF2_N: Translation in 49.9 15 0.00032 27.3 2.4 27 40-66 5-31 (54)
91 cd04762 HTH_MerR-trunc Helix-T 49.7 44 0.00096 22.9 4.8 46 40-91 2-47 (49)
92 PF10474 DUF2451: Protein of u 48.6 2.2E+02 0.0048 27.8 11.0 83 319-411 119-206 (234)
93 PRK00423 tfb transcription ini 47.6 12 0.00025 38.1 2.0 29 98-129 11-39 (310)
94 PF10058 DUF2296: Predicted in 47.5 13 0.00028 28.4 1.7 31 99-129 23-53 (54)
95 PRK03681 hypA hydrogenase nick 47.5 14 0.00031 32.1 2.3 28 49-79 38-65 (114)
96 PF14353 CpXC: CpXC protein 47.3 17 0.00038 31.7 2.8 35 99-133 2-51 (128)
97 PRK11827 hypothetical protein; 47.0 13 0.00028 29.1 1.7 36 94-133 4-39 (60)
98 PRK03824 hypA hydrogenase nick 45.9 15 0.00033 32.9 2.3 49 41-106 30-78 (135)
99 KOG2703 C4-type Zn-finger prot 45.9 13 0.00028 39.3 2.0 32 100-131 260-298 (460)
100 PF02847 MA3: MA3 domain; Int 45.7 1.8E+02 0.0038 24.2 8.7 88 303-394 17-112 (113)
101 PF01667 Ribosomal_S27e: Ribos 45.6 5.5 0.00012 30.6 -0.5 29 98-129 7-35 (55)
102 PF01396 zf-C4_Topoisom: Topoi 45.5 26 0.00056 24.7 2.9 32 99-133 2-37 (39)
103 COG0023 SUI1 Translation initi 45.4 66 0.0014 27.9 5.9 74 12-91 11-92 (104)
104 PRK07451 translation initiatio 45.4 50 0.0011 29.1 5.3 58 24-87 43-100 (115)
105 PRK12380 hydrogenase nickel in 45.3 17 0.00036 31.7 2.3 29 48-79 37-65 (113)
106 PRK00762 hypA hydrogenase nick 45.0 18 0.00039 32.0 2.5 28 49-79 38-65 (124)
107 PF01927 Mut7-C: Mut7-C RNAse 44.4 32 0.00068 31.1 4.1 59 75-133 62-137 (147)
108 KOG2907 RNA polymerase I trans 43.9 13 0.00029 32.5 1.5 34 100-133 76-115 (116)
109 COG1645 Uncharacterized Zn-fin 43.7 16 0.00036 32.8 2.1 25 99-129 29-53 (131)
110 PRK05667 dnaG DNA primase; Val 43.6 34 0.00074 38.0 5.0 32 100-132 38-69 (580)
111 TIGR03826 YvyF flagellar opero 43.2 25 0.00054 31.9 3.2 44 39-107 47-90 (137)
112 TIGR00595 priA primosomal prot 43.0 16 0.00034 39.8 2.2 44 101-148 225-284 (505)
113 smart00834 CxxC_CXXC_SSSS Puta 42.7 16 0.00035 25.2 1.5 28 100-128 7-34 (41)
114 COG0777 AccD Acetyl-CoA carbox 42.5 9.2 0.0002 38.5 0.3 44 97-143 27-70 (294)
115 PF08535 KorB: KorB domain; I 41.4 20 0.00043 29.7 2.1 21 41-61 6-26 (93)
116 COG1594 RPB9 DNA-directed RNA 41.3 16 0.00036 31.8 1.7 45 100-147 4-49 (113)
117 PF06107 DUF951: Bacterial pro 41.1 25 0.00054 27.3 2.4 34 104-139 16-49 (57)
118 PRK08332 ribonucleotide-diphos 41.1 23 0.0005 44.0 3.4 44 88-132 1695-1738(1740)
119 PRK00432 30S ribosomal protein 41.1 18 0.00039 27.0 1.7 28 98-130 20-47 (50)
120 PF05315 ICEA: ICEA Protein; 41.0 13 0.00028 35.9 1.1 67 48-114 44-117 (230)
121 PF14599 zinc_ribbon_6: Zinc-r 40.0 14 0.00031 28.9 1.0 30 97-130 29-58 (61)
122 PF00165 HTH_AraC: Bacterial r 39.6 35 0.00077 23.7 2.9 28 39-66 9-36 (42)
123 smart00778 Prim_Zn_Ribbon Zinc 38.7 21 0.00046 25.2 1.6 31 98-128 3-33 (37)
124 TIGR01391 dnaG DNA primase, ca 38.6 44 0.00095 35.4 4.7 33 99-132 35-67 (415)
125 PRK05580 primosome assembly pr 37.8 19 0.00042 40.6 2.0 50 98-148 381-452 (679)
126 PF04032 Rpr2: RNAse P Rpr2/Rp 37.5 31 0.00066 27.7 2.6 30 99-128 47-85 (85)
127 PRK12286 rpmF 50S ribosomal pr 36.9 25 0.00054 27.1 1.9 27 94-129 23-49 (57)
128 COG3741 HutG N-formylglutamate 36.2 8.8 0.00019 38.4 -0.9 109 32-143 61-172 (272)
129 PRK05654 acetyl-CoA carboxylas 35.7 9.2 0.0002 38.8 -0.9 43 98-143 27-69 (292)
130 PF06677 Auto_anti-p27: Sjogre 35.6 67 0.0015 23.1 3.8 35 88-127 7-41 (41)
131 PF13936 HTH_38: Helix-turn-he 35.6 33 0.00071 24.6 2.2 22 39-60 21-42 (44)
132 PF09723 Zn-ribbon_8: Zinc rib 35.4 24 0.00051 25.2 1.5 29 100-129 7-35 (42)
133 PF06322 Phage_NinH: Phage Nin 35.4 40 0.00086 26.6 2.7 37 39-83 17-53 (64)
134 PRK07562 ribonucleotide-diphos 35.2 28 0.00061 41.8 2.8 40 86-132 1180-1219(1220)
135 PF07282 OrfB_Zn_ribbon: Putat 35.1 23 0.0005 27.4 1.5 31 99-133 29-59 (69)
136 TIGR00515 accD acetyl-CoA carb 35.0 9.3 0.0002 38.6 -1.0 43 98-143 26-68 (285)
137 PF12898 Stc1: Stc1 domain; I 34.8 41 0.00089 27.7 3.0 51 74-133 6-63 (84)
138 TIGR01206 lysW lysine biosynth 34.7 27 0.00058 26.7 1.7 31 100-133 4-35 (54)
139 COG1096 Predicted RNA-binding 34.3 27 0.00058 33.3 2.0 27 98-130 149-175 (188)
140 PF08274 PhnA_Zn_Ribbon: PhnA 33.7 15 0.00033 24.7 0.2 27 98-129 2-28 (30)
141 PRK03824 hypA hydrogenase nick 33.5 42 0.00091 30.1 3.1 42 85-133 42-83 (135)
142 COG0375 HybF Zn finger protein 32.9 36 0.00077 30.0 2.4 20 59-79 46-65 (115)
143 TIGR01160 SUI1_MOF2 translatio 32.7 62 0.0014 28.3 3.9 65 23-93 28-97 (110)
144 PF04502 DUF572: Family of unk 32.6 22 0.00047 36.5 1.2 25 119-143 76-100 (324)
145 PF01807 zf-CHC2: CHC2 zinc fi 32.3 25 0.00055 29.5 1.4 33 99-132 34-66 (97)
146 PF03811 Zn_Tnp_IS1: InsA N-te 32.0 42 0.00092 23.5 2.2 29 98-126 5-35 (36)
147 KOG3507 DNA-directed RNA polym 31.6 12 0.00027 29.1 -0.6 31 100-135 22-52 (62)
148 PRK06319 DNA topoisomerase I/S 31.5 52 0.0011 38.3 4.1 34 99-133 593-629 (860)
149 COG1405 SUA7 Transcription ini 31.5 29 0.00062 35.2 1.9 39 100-141 3-44 (285)
150 PF09862 DUF2089: Protein of u 31.2 36 0.00078 29.9 2.2 18 230-247 59-76 (113)
151 cd02983 P5_C P5 family, C-term 30.8 59 0.0013 28.7 3.5 45 53-97 69-117 (130)
152 PHA02540 61 DNA primase; Provi 30.6 44 0.00095 34.7 3.0 34 99-132 28-67 (337)
153 TIGR02098 MJ0042_CXXC MJ0042 f 30.4 22 0.00048 24.4 0.6 30 98-130 2-35 (38)
154 cd04761 HTH_MerR-SF Helix-Turn 30.1 1.2E+02 0.0026 21.1 4.5 45 40-90 2-46 (49)
155 TIGR02609 doc_partner putative 30.1 73 0.0016 25.5 3.6 47 52-98 15-65 (74)
156 COG1996 RPC10 DNA-directed RNA 29.6 19 0.00041 27.1 0.1 35 100-138 8-42 (49)
157 CHL00174 accD acetyl-CoA carbo 29.4 13 0.00028 37.9 -1.0 43 98-143 38-80 (296)
158 COG2093 DNA-directed RNA polym 29.3 26 0.00056 27.7 0.9 11 100-110 20-30 (64)
159 PRK14973 DNA topoisomerase I; 29.2 33 0.00072 40.3 2.1 22 381-402 886-907 (936)
160 smart00400 ZnF_CHCC zinc finge 29.1 53 0.0012 24.5 2.5 32 100-132 4-35 (55)
161 PF06573 Churchill: Churchill 29.1 46 0.001 29.0 2.4 36 94-129 23-67 (112)
162 cd03031 GRX_GRX_like Glutaredo 28.7 46 0.00099 30.4 2.5 50 82-132 81-145 (147)
163 PF06044 DRP: Dam-replacing fa 28.6 43 0.00092 33.3 2.4 57 80-136 12-69 (254)
164 PF03604 DNA_RNApol_7kD: DNA d 28.5 23 0.0005 24.2 0.4 28 100-132 2-29 (32)
165 TIGR03830 CxxCG_CxxCG_HTH puta 28.5 51 0.0011 28.2 2.7 31 101-131 1-42 (127)
166 PF08792 A2L_zn_ribbon: A2L zi 28.3 47 0.001 22.7 1.9 30 98-131 3-32 (33)
167 PF09733 VEFS-Box: VEFS-Box of 27.9 2.5E+02 0.0055 25.4 7.1 27 374-400 108-134 (140)
168 smart00762 Cog4 COG4 transport 27.6 6.6E+02 0.014 25.6 11.0 61 322-391 76-136 (324)
169 COG1571 Predicted DNA-binding 27.5 28 0.00062 37.1 1.1 36 94-134 346-381 (421)
170 smart00659 RPOLCX RNA polymera 27.4 43 0.00092 24.4 1.7 31 100-135 4-34 (44)
171 PF12172 DUF35_N: Rubredoxin-l 27.4 36 0.00079 23.3 1.3 17 115-131 6-22 (37)
172 PF09851 SHOCT: Short C-termin 27.3 69 0.0015 21.4 2.6 18 383-400 6-23 (31)
173 TIGR03831 YgiT_finger YgiT-typ 27.1 70 0.0015 22.3 2.8 9 121-129 33-41 (46)
174 PF00123 Hormone_2: Peptide ho 27.1 40 0.00087 22.4 1.3 11 418-428 17-27 (28)
175 PF03966 Trm112p: Trm112p-like 26.9 42 0.00091 26.3 1.7 14 120-133 53-66 (68)
176 PF01155 HypA: Hydrogenase exp 26.8 56 0.0012 28.2 2.6 26 51-79 40-65 (113)
177 PF11781 RRN7: RNA polymerase 26.8 49 0.0011 23.1 1.8 26 100-130 10-35 (36)
178 PF05876 Terminase_GpA: Phage 26.6 50 0.0011 36.4 2.8 49 98-146 200-258 (557)
179 smart00647 IBR In Between Ring 26.4 1E+02 0.0022 22.8 3.7 41 88-131 5-51 (64)
180 PRK00378 nucleoid-associated p 26.0 1.4E+02 0.003 30.4 5.8 50 25-96 283-332 (334)
181 smart00419 HTH_CRP helix_turn_ 25.8 1.5E+02 0.0033 20.3 4.4 39 39-78 9-47 (48)
182 KOG4218 Nuclear hormone recept 25.7 3E+02 0.0065 28.9 7.9 72 306-389 367-438 (475)
183 KOG1824 TATA-binding protein-i 25.5 3.5E+02 0.0076 32.2 9.1 52 337-388 248-303 (1233)
184 KOG1597 Transcription initiati 25.5 44 0.00096 34.0 1.9 41 100-141 2-45 (308)
185 TIGR01566 ZF_HD_prot_N ZF-HD h 25.4 30 0.00065 26.3 0.6 16 118-133 34-49 (53)
186 TIGR01031 rpmF_bact ribosomal 25.4 48 0.001 25.3 1.7 24 96-128 24-47 (55)
187 PRK09019 translation initiatio 25.3 1.4E+02 0.003 26.1 4.7 56 27-88 39-94 (108)
188 COG2023 RPR2 RNase P subunit R 24.9 69 0.0015 27.8 2.8 34 100-133 58-95 (105)
189 PF05046 Img2: Mitochondrial l 24.5 2.8E+02 0.006 22.9 6.3 65 23-91 16-82 (87)
190 PF15494 SRCR_2: Scavenger rec 24.5 46 0.00099 27.8 1.6 15 116-130 84-98 (98)
191 PF05180 zf-DNL: DNL zinc fing 24.3 39 0.00085 26.9 1.1 39 100-138 6-47 (66)
192 smart00497 IENR1 Intron encode 24.3 1.7E+02 0.0036 20.9 4.5 25 37-61 16-40 (53)
193 PHA02942 putative transposase; 24.2 35 0.00076 35.9 1.0 31 99-134 326-356 (383)
194 COG3677 Transposase and inacti 24.1 97 0.0021 27.6 3.7 47 93-140 25-73 (129)
195 KOG1603 Copper chaperone [Inor 24.0 1.3E+02 0.0029 23.6 4.1 42 52-93 19-61 (73)
196 TIGR03829 YokU_near_AblA uncha 24.0 54 0.0012 27.6 1.9 24 117-140 32-56 (89)
197 KOG3084 NADH pyrophosphatase I 23.9 64 0.0014 33.3 2.8 24 89-113 141-164 (345)
198 PF08318 COG4: COG4 transport 23.5 6.9E+02 0.015 25.5 10.3 72 323-403 77-150 (331)
199 PF14255 Cys_rich_CPXG: Cystei 23.5 74 0.0016 24.1 2.4 34 99-132 1-36 (52)
200 PF04810 zf-Sec23_Sec24: Sec23 23.2 41 0.00089 23.7 0.9 33 99-134 3-38 (40)
201 smart00422 HTH_MERR helix_turn 23.2 1.8E+02 0.004 21.8 4.7 46 40-90 2-47 (70)
202 PF15288 zf-CCHC_6: Zinc knuck 22.8 38 0.00082 24.4 0.6 27 121-147 2-30 (40)
203 PF13597 NRDD: Anaerobic ribon 22.7 47 0.001 36.6 1.7 53 81-143 463-526 (546)
204 cd01106 HTH_TipAL-Mta Helix-Tu 22.5 1.7E+02 0.0036 24.5 4.7 48 40-92 2-49 (103)
205 TIGR02494 PFLE_PFLC glycyl-rad 22.4 39 0.00084 33.5 0.9 39 94-132 20-59 (295)
206 TIGR01464 hemE uroporphyrinoge 22.2 61 0.0013 32.9 2.3 56 50-111 264-326 (338)
207 PF04161 Arv1: Arv1-like famil 22.1 47 0.001 31.8 1.4 31 100-130 2-34 (208)
208 PF04981 NMD3: NMD3 family ; 22.1 42 0.00091 32.7 1.0 34 99-132 14-47 (236)
209 PRK06556 vitamin B12-dependent 22.0 74 0.0016 37.6 3.1 46 81-132 907-952 (953)
210 PRK06393 rpoE DNA-directed RNA 21.9 44 0.00095 26.5 0.9 38 97-147 4-41 (64)
211 smart00070 GLUCA Glucagon like 21.2 58 0.0013 21.4 1.2 11 418-428 17-27 (27)
212 PF09788 Tmemb_55A: Transmembr 21.1 77 0.0017 31.7 2.6 39 98-150 65-104 (256)
213 PRK07220 DNA topoisomerase I; 21.0 66 0.0014 36.8 2.5 30 99-128 636-665 (740)
214 PRK09678 DNA-binding transcrip 21.0 93 0.002 25.2 2.6 32 100-132 3-41 (72)
215 KOG2989 Uncharacterized conser 20.6 45 0.00098 33.0 0.9 45 98-143 40-100 (253)
216 PRK02935 hypothetical protein; 20.3 63 0.0014 28.1 1.6 30 99-134 71-100 (110)
217 PF08064 UME: UME (NUC010) dom 20.3 5.2E+02 0.011 21.9 7.3 50 355-404 28-80 (107)
No 1
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.4e-108 Score=807.05 Aligned_cols=386 Identities=48% Similarity=0.734 Sum_probs=314.5
Q ss_pred ceeccCCCCCCCCcccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEec
Q 013781 2 ALLNIGADNRGDAFYRYKMPKMITKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGS 81 (436)
Q Consensus 2 a~ini~~~~~~D~~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~ 81 (436)
|+||| +|++.|||||||||++++|+||+||||||+|+||.|||+||+|||.|++|||||||||||+||.++|||||||+
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 57999 78888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCHHHHHHHHHHHHhhccccCCCCCCCceEEEecCceeeeeccccCcccccCchhhhhhhhhcCCCcccccchhhHHHHH
Q 013781 82 HDTAKLAGLLENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMRDKLNTFILKNPPESKKASKGKKAMRR 161 (436)
Q Consensus 82 ~~~~~l~~~l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~k~pp~~~~~~k~~k~~~~ 161 (436)
|++.+||++|++||++|||||+|+||||.|++++++++.++|+|||.++.+++||||++|||||||++.+++|++|+++
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 9999999999999999999999999999999987899999999999999999999999999999999888888877543
Q ss_pred HHHHHhhccchhhHHHHHHHHHhhhhcCCCCCCCccccccccccCCCCCCCC------CCCCCCCCCCccccccccccHH
Q 013781 162 AEKERLKEGEAADEELKKIKKEVKKKASSSKDGTTKATSSRRKANVSDEDHS------SPPHGKEEVDDDVQWQTDTSLE 235 (436)
Q Consensus 162 ~~~~~~~~~~~~d~~~kk~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~dddv~W~~DtSee 235 (436)
+++|.+ |.+ . +++|+ ++. ......+++.+ +|.+..+ ++||.+|++|||+|
T Consensus 159 -~k~R~~----------K~k-~-k~~g~--~s~--------~~~~~~~~~~~~~i~~~a~~~t~e-~~DDddW~~Dtsee 214 (400)
T KOG2767|consen 159 -KKERKG----------KSK-D-KKDGS--KSS--------KNETSPDDSLSREIDPAAPLETAE-EDDDDDWAVDTSEE 214 (400)
T ss_pred -HHHhhh----------hcc-c-ccccc--cCC--------ccCCCcccccccccccccCccccc-ccccccccccchHH
Confidence 222211 000 0 01110 000 00011111111 1122222 23333499999999
Q ss_pred HHHHHHHHHhHHHhhhhhhcccchhhhHhhhhccccCCCCCCCCCCCCCcchHHHHHHHHHHHhcCCChhHHHHHHHhcC
Q 013781 236 AARQRIQEQLSAATADMVMLSTDESENKAKATSKAVSSPKGSHAENGNSQSHENLVDELKANLQKSITGMQLQTILGSLS 315 (436)
Q Consensus 236 AvkaR~~e~ls~~~~~~~~~~~de~e~~~~~~~~~~~~~~e~~~~~~~~~~~~e~v~~l~~~~~~~~s~~ei~~~~~~l~ 315 (436)
|+++||+ +|+++++.|||++|.+..++++. . .-++.+..|+.+... +.+..||..++.+++
T Consensus 215 a~r~R~~-~Ls~~~~~~~~~sd~e~~E~~~~--------------~---~~~d~~~~~~~en~~-~~~~kEi~~~a~~l~ 275 (400)
T KOG2767|consen 215 AIRARMQ-ELSANAKEMLLLSDLEKSEEERE--------------D---ILYDFVKKKKEENVP-DKSDKEIVKEAERLD 275 (400)
T ss_pred HHHHHHH-HHhhhhhhhhhhhhhhhhHHHHH--------------H---HHHHhhhhcccccCC-CccHHHHHHHHHHHh
Confidence 9999995 69999999998877432211111 0 123333333333322 136679999999999
Q ss_pred CChHHHHHHHHHHHHhhhhhhHHHHHHhhHHHHHHHhcCChHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHhhccccc
Q 013781 316 GSAQEKMTALFEALFDGVEKGFSKEVVKKKNFLGAAVAEDEGLQLLLLRAIEAFCGKSSSYATKEVALVLKALYDSDVLE 395 (436)
Q Consensus 316 ls~~~~~~vl~eaLf~~v~~~i~k~I~k~~~lL~r~~~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYd~DIle 395 (436)
+. ++...+|.++||+. .|+++|.++++||.+|+.+++++|++||++||+||..++..+++.+|.||+.|||+|||+
T Consensus 276 i~-~k~p~vl~~~Lf~e---~ivkei~k~~~~l~k~~~~~~k~qr~LLggiE~~~~~~~~el~~kva~ilk~lYd~DI~~ 351 (400)
T KOG2767|consen 276 IK-NKAPLVLAEVLFDE---KIVKEILKHRALLLKFCTNNEKAQRYLLGGIERFVEKHEAELISKVAGILKELYDEDILE 351 (400)
T ss_pred hc-ccchHHHHHHHhhh---HHHHHHHHHHHHHHHHHhccHHHHHHHHhHHHHHHHhhHHHHHHHHHHHHHHHHhhhhhh
Confidence 84 48899999999998 999999999999999999669999999999999999988999999999999999999999
Q ss_pred hHHHHHHhhccCCCCc---chhHHHHhhhHHHHHhcccccccCC
Q 013781 396 EEYIVQWYQEGLKGGS---KNSQIWKNAKPFIEWLQSAESESEE 436 (436)
Q Consensus 396 EE~Il~W~~k~s~~~~---~~~~vrk~a~pFI~WLeEAEEEsee 436 (436)
|++|+.||++++++|| ..+++++.++|||+||++||+|++|
T Consensus 352 e~vi~~w~~K~skk~vsk~~sk~i~e~a~Pfi~WL~~AESe~ee 395 (400)
T KOG2767|consen 352 EEVIIKWGEKPSKKYVSKEKSKKIRENAKPFIEWLKNAESEDEE 395 (400)
T ss_pred HHHHHHHHhcccccccchhhhhhhHhhhhHHHHHHHhccccccc
Confidence 9999999999999998 3479999999999999999876653
No 2
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=100.00 E-value=1.1e-44 Score=311.62 Aligned_cols=110 Identities=49% Similarity=0.833 Sum_probs=106.9
Q ss_pred cccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHHHH
Q 013781 15 FYRYKMPKMITKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLENF 94 (436)
Q Consensus 15 ~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~f 94 (436)
||||+||+|++++||+| ||+|+||.|||++|||+|+||+|||++||||+|++|++ +++||||+|++.+||++|++|
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---KTVIVNFADIAKALNRPPDHVLKFLLAELGTQGSIDGK-GRLIVNGRFTPKKLQDLLRRY 76 (110)
T ss_pred CCccccCCCeEEEEcCC---eEEEEcHHHHHHHHCCCHHHHHHHHHHHhCCceeECCC-CeEEEEEeeCHHHHHHHHHHH
Confidence 79999999999999986 99999999999999999999999999999999999974 999999999999999999999
Q ss_pred HhhccccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 95 IKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 95 i~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
|++||+|++|+||||.|++ ++++++++|.|||++
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=5.6e-45 Score=320.23 Aligned_cols=121 Identities=48% Similarity=0.793 Sum_probs=111.4
Q ss_pred eeccCCCCCCCCcccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEecc
Q 013781 3 LLNIGADNRGDAFYRYKMPKMITKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSH 82 (436)
Q Consensus 3 ~ini~~~~~~D~~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~ 82 (436)
..|+ ++..+|.+ ||+||+|+++++|+ +||+|+||.|||++|||+|+||+|||++||||+|+||++ ++|||||+|
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 66677766 99999999999997 699999999999999999999999999999999999974 999999999
Q ss_pred CHHHHHHHHHHHHhhccccCCCCCCCceEEEecCceeeeeccccCccc
Q 013781 83 DTAKLAGLLENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVS 130 (436)
Q Consensus 83 ~~~~l~~~l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (436)
++++||++|++||++||+|++|+||||.|++ ++++++++|.|||+++
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 7899999999999986
No 4
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=100.00 E-value=3.6e-43 Score=311.58 Aligned_cols=113 Identities=34% Similarity=0.589 Sum_probs=109.6
Q ss_pred cccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHHHH
Q 013781 15 FYRYKMPKMITKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLENF 94 (436)
Q Consensus 15 ~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~f 94 (436)
-+||+||+|++++||+ ||+|+||.+||++|||+|+||+|||++||||+|++| ++++||||+|++.+||++|++|
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 013781 95 IKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 95 i~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
|++||+|+.|+||||.|++ ++++++++|.|||++++|.+
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=1.5e-42 Score=309.29 Aligned_cols=115 Identities=30% Similarity=0.563 Sum_probs=110.7
Q ss_pred CCcccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHH
Q 013781 13 DAFYRYKMPKMITKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLE 92 (436)
Q Consensus 13 D~~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~ 92 (436)
..-+||+||+|++++||+ ||+|+||.+||++|||+|+|++|||++||||+|+++ +|++||||+|++.+|+++|+
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 013781 93 NFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 93 ~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
+||++||+|+.|+||||.|++ ++++++++|.|||++++|++
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 78999999999999999974
No 6
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=100.00 E-value=4e-41 Score=318.47 Aligned_cols=117 Identities=28% Similarity=0.569 Sum_probs=112.5
Q ss_pred CCCCcccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHH
Q 013781 11 RGDAFYRYKMPKMITKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGL 90 (436)
Q Consensus 11 ~~D~~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~ 90 (436)
..+..|||+||+|++++||+ ||+|+||.+||++|||+|+||+|||++||||++++| ++++||||+|++.+||++
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 35668999999999999998 999999999999999999999999999999999997 589999999999999999
Q ss_pred HHHHHhhccccCCCCCCCceEEEecCceeeeeccccCcccccCc
Q 013781 91 LENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 91 l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
|++||++||+|++|+||||.|++ ++++++++|.|||++++|+.
T Consensus 91 l~~yi~~yV~C~~C~~pdT~l~k-~~~~~~l~C~aCGa~~~v~~ 133 (201)
T PRK12336 91 IDAYVDEYVICSECGLPDTRLVK-EDRVLMLRCDACGAHRPVKK 133 (201)
T ss_pred HHHHHHheEECCCCCCCCcEEEE-cCCeEEEEcccCCCCccccc
Confidence 99999999999999999999999 78999999999999999994
No 7
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=7e-32 Score=251.57 Aligned_cols=114 Identities=26% Similarity=0.514 Sum_probs=109.4
Q ss_pred cccccCCCceEEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHHHH
Q 013781 15 FYRYKMPKMITKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLENF 94 (436)
Q Consensus 15 ~~Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~f 94 (436)
..||.|++||+.+||+ ||+++||.|||+.|||.|+||++|+..||||.|++|+ ++||+|.|+|.+.++|++|++|
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 9999999999999999999999999999999999996 8999999999999999999999
Q ss_pred HhhccccCCCCCCCceEEEecCceeeeeccccCcccccCc
Q 013781 95 IKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 95 i~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
|..||.|..|+||||.|.+ ++|++||+|..||...+|..
T Consensus 178 I~eyV~C~~CkSpdt~L~k-enRLfFL~C~~cgs~~sv~~ 216 (231)
T KOG2768|consen 178 IKEYVTCKTCKSPDTILQK-ENRLFFLRCEKCGSRCSVAS 216 (231)
T ss_pred HHHheEeeecCChhHHhhh-hcceEEEEecCCCCeeeeee
Confidence 9999999999999999999 79999999999999988764
No 8
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=2.2e-29 Score=227.03 Aligned_cols=111 Identities=35% Similarity=0.684 Sum_probs=108.6
Q ss_pred cccCCCceEEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHHHHHh
Q 013781 17 RYKMPKMITKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLENFIK 96 (436)
Q Consensus 17 Rykmp~~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~ 96 (436)
||.||.|.+.++|+ +|+|.||.+||++|+|+|+|+++||..|||+.+++|++ ++++++|.|+...|++.|+.||.
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 99999999999999 99999999999999999999999999999999999974 99999999999999999999999
Q ss_pred hccccCCCCCCCceEEEecCceeeeeccccCcccccC
Q 013781 97 KYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 97 ~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (436)
.||.|+.|++|||.|++ .+|.++++|.|||+.+||.
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 6899999999999999997
No 9
>KOG2297 consensus Predicted translation factor, contains W2 domain [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=6.2e-21 Score=187.69 Aligned_cols=134 Identities=25% Similarity=0.431 Sum_probs=119.4
Q ss_pred chHHHHHHHHHHHhcCCChhHHHHHHHhcCCChHHHHHHHHHHHHhhhhh---------hHHHHHHhhHHHHHHHhcCCh
Q 013781 286 SHENLVDELKANLQKSITGMQLQTILGSLSGSAQEKMTALFEALFDGVEK---------GFSKEVVKKKNFLGAAVAEDE 356 (436)
Q Consensus 286 ~~~e~v~~l~~~~~~~~s~~ei~~~~~~l~ls~~~~~~vl~eaLf~~v~~---------~i~k~I~k~~~lL~r~~~~~~ 356 (436)
|+++++..+++.++++ +++.+.+++++|..+|+.+.| .++++++.|.|||..||+ ..
T Consensus 270 p~~evi~~VKee~k~~-------------nlPe~eVi~ivWs~iMsaveWnKkeelva~qalrhlK~yaPLL~af~s-~g 335 (412)
T KOG2297|consen 270 PVKEVILYVKEEMKRN-------------NLPETEVIGIVWSGIMSAVEWNKKEELVAEQALRHLKQYAPLLAAFCS-QG 335 (412)
T ss_pred CHHHHHHHHHHHHHhc-------------CCCCceEEeeeHhhhhHHHhhchHHHHHHHHHHHHHHhhhHHHHHHhc-CC
Confidence 6777777777766544 788889999999999999887 467899999999999999 88
Q ss_pred HHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHhhccccchHHHHHHhhccCCCCcchhHHHHhhhHHHHHhcccccccC
Q 013781 357 GLQLLLLRAIEAFCGKSSSYATKEVALVLKALYDSDVLEEEYIVQWYQEGLKGGSKNSQIWKNAKPFIEWLQSAESESE 435 (436)
Q Consensus 357 ~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYd~DIleEE~Il~W~~k~s~~~~~~~~vrk~a~pFI~WLeEAEEEse 435 (436)
.+++.||..+|.||+. +..+|+.|+.|+..||..|||+||.||+||.++.... +.+.+.++++|||+||++|||||+
T Consensus 336 ~sEL~Ll~KvQe~CYe-n~~fMKaFqkiV~lfYk~dVLsEe~IL~Wyk~gh~~K-Gk~~FleqmkkFVeWL~~AEEEsE 412 (412)
T KOG2297|consen 336 QSELELLLKVQEYCYE-NIHFMKAFQKIVVLFYKADVLSEETILKWYKEGHVAK-GKSVFLEQMKKFVEWLQNAEEESE 412 (412)
T ss_pred hHHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhccccc-cHHHHHHHHHHHHHHHHhhhhccC
Confidence 9999999999999998 7899999999999999999999999999998876544 257899999999999999999975
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=99.84 E-value=4e-21 Score=158.08 Aligned_cols=79 Identities=43% Similarity=0.762 Sum_probs=64.6
Q ss_pred hHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHhhccccchHHHHHHhhccCCCCc---chhHHHHhhhHHHHHhccccc
Q 013781 356 EGLQLLLLRAIEAFCGKSSSYATKEVALVLKALYDSDVLEEEYIVQWYQEGLKGGS---KNSQIWKNAKPFIEWLQSAES 432 (436)
Q Consensus 356 ~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYd~DIleEE~Il~W~~k~s~~~~---~~~~vrk~a~pFI~WLeEAEE 432 (436)
+..|+++|.+||.||.. ++.+++.|++||+.|||.|||+|++|++||+. +++.+ ...++|++++|||+||++|||
T Consensus 1 ~~~Q~~~L~ale~~~~~-~~~~~~~~~~il~~LYd~Dil~Eeail~W~~~-~~~~~~~~~~~~~r~~~~~fi~WL~eaee 78 (84)
T PF02020_consen 1 EDDQVDLLNALEEFCAE-NPNLMPLFPKILQQLYDEDILEEEAILEWYED-SKPAVDGEGRAKVRKQAQPFIEWLEEAEE 78 (84)
T ss_dssp HHHHHHHHHHHHHHHHH-TCGHGGHHHHHHHHHHHTTSS-HHHHHHHHHC--SSSSCHHHHHHHHHHHHHHHHHHHHCC-
T ss_pred CHHHHHHHHHHHHHHHh-CccHHHHHHHHHHHHhhhhhccHHHHHHHHHc-CCccccchhHHHHHHHHHHHHHHHhccCc
Confidence 36899999999999976 68889999999999999999999999999999 44432 346899999999999999999
Q ss_pred ccCC
Q 013781 433 ESEE 436 (436)
Q Consensus 433 Esee 436 (436)
|||+
T Consensus 79 E~~e 82 (84)
T PF02020_consen 79 ESDE 82 (84)
T ss_dssp ----
T ss_pred cCCC
Confidence 8874
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=2.8e-20 Score=152.49 Aligned_cols=82 Identities=43% Similarity=0.716 Sum_probs=73.5
Q ss_pred HHHHHHhcCChHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHhhccccchHHHHHHhhccCCCCcchhHHHHhhhHHHH
Q 013781 346 NFLGAAVAEDEGLQLLLLRAIEAFCGKSSSYATKEVALVLKALYDSDVLEEEYIVQWYQEGLKGGSKNSQIWKNAKPFIE 425 (436)
Q Consensus 346 ~lL~r~~~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYd~DIleEE~Il~W~~k~s~~~~~~~~vrk~a~pFI~ 425 (436)
+||.+|+. +..+|+++|++||.||..+++ ..+.|+.||+.|||+|||+||+|++||++.+... ..++++++++|||+
T Consensus 2 ~ll~~~~~-~~~~q~~~L~ale~~~~~~~~-~~~~~~~il~~LYd~dileEe~il~W~~~~~~~~-~~~~~~~~~~~fv~ 78 (83)
T smart00515 2 PLLKFLAK-DEEEQIDLLYAIEEFCVELEK-LIKLLPKILKSLYDADILEEEAILKWYEKAVSAE-GKKKVRKNAKPFVT 78 (83)
T ss_pred hHHHHHHC-ChHHHHHHHHHHHHHHHHcch-HHHHHHHHHHHHhhhccccHHHHHHHHHcCCChH-HHHHHHHHHhHHHH
Confidence 78999999 899999999999999987544 7899999999999999999999999999876422 35789999999999
Q ss_pred Hhccc
Q 013781 426 WLQSA 430 (436)
Q Consensus 426 WLeEA 430 (436)
||+||
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=99.75 E-value=1.2e-17 Score=176.70 Aligned_cols=130 Identities=25% Similarity=0.392 Sum_probs=114.1
Q ss_pred hHHHHHHHhcCCChHHHHHHHHHHHHhhh-----------hhhHHHHHHhhHHHHHHHhcCChHHHHHHHHHHHHHHhcC
Q 013781 305 MQLQTILGSLSGSAQEKMTALFEALFDGV-----------EKGFSKEVVKKKNFLGAAVAEDEGLQLLLLRAIEAFCGKS 373 (436)
Q Consensus 305 ~ei~~~~~~l~ls~~~~~~vl~eaLf~~v-----------~~~i~k~I~k~~~lL~r~~~~~~~~Q~~lL~alE~~~~~~ 373 (436)
.||+.++.++|++.++++.++|.++|.-+ .+++++.++.|+++|.+|+. +++.|+++|.+||.+|.++
T Consensus 531 lEINslRla~N~s~~ev~~av~~all~~~~~~~~~~~~~~~~~~~~~~~~w~~l~~~y~k-s~deqid~l~~led~~~e~ 609 (673)
T KOG1461|consen 531 LEINSLRLAYNVSLKEVAGAVFMALLKLILHQDHSSMNEVKRAALKVFTQWGPLLGNYIK-SEDEQIDLLLALEDKCVES 609 (673)
T ss_pred HHHhhhHHhhcCCHHHHHHHHHHHHHHHHhcCCCccchhHHHHHHHHHHHhhHHhhhhhh-hHHHHHHHHHHHHHHHHhc
Confidence 69999999999999999999999998653 23678889999999999999 9999999999999999885
Q ss_pred ChhhHHHHHHHHHHHhhccccchHHHHHHhhccCCCCcchhHHHHhhhHHHHHhcccccccCC
Q 013781 374 SSYATKEVALVLKALYDSDVLEEEYIVQWYQEGLKGGSKNSQIWKNAKPFIEWLQSAESESEE 436 (436)
Q Consensus 374 ~~~l~~~~~~ILk~LYd~DIleEE~Il~W~~k~s~~~~~~~~vrk~a~pFI~WLeEAEEEsee 436 (436)
..+.+.+..+++.||+.|||+|++|++||...+......+..++++++||+||+||+||||+
T Consensus 610 -~~~~~~~~~~v~~lY~~dil~EdaI~~W~~~~~~~~~~~~~~~~~~k~fv~WL~easeE~~~ 671 (673)
T KOG1461|consen 610 -EELGPKAAKLVHYLYDYDILQEDAILSWSSQKAGDDEEDAVYNQQLKKFVDWLKEASEEEES 671 (673)
T ss_pred -ccchHHHHHHHHHHHHHhHhhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHhhccccccc
Confidence 67788999999999999999999999999883332222357888999999999999988774
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=96.55 E-value=0.053 Score=53.42 Aligned_cols=118 Identities=15% Similarity=0.209 Sum_probs=89.2
Q ss_pred cchHHHHHHHHHHHhcCCChhHHHHHHHhcCCCh--------HHHHHHHHHHHHhhhhh---hHHHHHHhhHHHHHHH-h
Q 013781 285 QSHENLVDELKANLQKSITGMQLQTILGSLSGSA--------QEKMTALFEALFDGVEK---GFSKEVVKKKNFLGAA-V 352 (436)
Q Consensus 285 ~~~~e~v~~l~~~~~~~~s~~ei~~~~~~l~ls~--------~~~~~vl~eaLf~~v~~---~i~k~I~k~~~lL~r~-~ 352 (436)
.|+...+..|.+++....++.+|..+.....-.. ..++.+++++++....+ .+...|.+|+..|+.+ .
T Consensus 8 ~P~~~~a~~l~~~ir~k~~~eei~~~l~~i~~~~~~~~~~~~~~~i~v~~q~ll~~GSkS~SH~~~~lery~~~Lk~l~~ 87 (253)
T PF09090_consen 8 LPFHALAQKLLDLIRKKAPPEEISELLEEIEEPAEEHGSDFDKFVIDVFVQCLLHIGSKSFSHVLSALERYKEVLKELEA 87 (253)
T ss_dssp STTHHHHHHHHHHHHTT--HHHHHHHHTTS------------HHHHHHHHHHHHHHTTTSHHHHHHHHHHTHHHHHHH-T
T ss_pred CccHHHHHHHHHHHHcCCCHHHHHHHHHhccccccccccchhhHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHhcc
Confidence 5788899999998877778888888888766322 24677788888865333 4667899999999999 6
Q ss_pred cCChHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHhhccccchHHHHHHhhccC
Q 013781 353 AEDEGLQLLLLRAIEAFCGKSSSYATKEVALVLKALYDSDVLEEEYIVQWYQEGL 407 (436)
Q Consensus 353 ~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYd~DIleEE~Il~W~~k~s 407 (436)
. ++..|..+|.++=+|... +|. ....|+..|-..+||+-.+|+.|.=...
T Consensus 88 ~-~~~~q~~il~~v~~~W~~-~~q---~~~li~dkll~~~ii~~~~Vv~w~f~~~ 137 (253)
T PF09090_consen 88 E-SEEAQFWILDAVFRFWKN-NPQ---MGFLIIDKLLNYGIISPSAVVNWVFSPE 137 (253)
T ss_dssp S-SHHHHHHHHHHHHHHHTT--HH---HHHHHHHHHHHTTSS-HHHHHHHHTSGG
T ss_pred C-ChHHHHHHHHHHHHHHhc-CCc---eehHHHHHHHhcCCCCHHHHHHHHcCcc
Confidence 6 889999999999999864 666 3566889999999999999999985543
No 14
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=94.50 E-value=0.012 Score=55.73 Aligned_cols=36 Identities=31% Similarity=0.753 Sum_probs=31.1
Q ss_pred hccccCCCCCCCc--eEEEecCceeeeeccccCccccc
Q 013781 97 KYVQCYGCGNPET--EIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 97 ~yVlC~~C~~peT--~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
.|..||+|++-|| ++++.+++...++|..||...+.
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 4789999999999 88885567789999999999865
No 15
>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=93.99 E-value=0.035 Score=42.96 Aligned_cols=40 Identities=20% Similarity=0.568 Sum_probs=32.9
Q ss_pred HHHhhccccCCCCCCCceEEEecCceeeeeccccCcccccC
Q 013781 93 NFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 93 ~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (436)
+||-- ..||.|+..||-.....++.-+..|-.||++-..+
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 45554 67999999999988867788899999999986543
No 16
>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=93.69 E-value=0.041 Score=44.28 Aligned_cols=41 Identities=20% Similarity=0.484 Sum_probs=34.0
Q ss_pred HHHhhccccCCCCCCCceEEEecCceeeeeccccCcccccCc
Q 013781 93 NFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 93 ~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
+||-- ..||.|+.-||-.....++.-++.|-+||++-..+.
T Consensus 4 rFIAG-a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~ 44 (71)
T PF09526_consen 4 RFIAG-AVCPKCQAMDTIMMWRENGVEYVECVECGYTERQPD 44 (71)
T ss_pred eEecC-ccCCCCcCccEEEEEEeCCceEEEecCCCCeeccCC
Confidence 45554 689999999998887677889999999999876663
No 17
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.20 E-value=0.18 Score=46.48 Aligned_cols=33 Identities=33% Similarity=0.709 Sum_probs=24.8
Q ss_pred ccCCCCCCCceEEEec---Cc-ee--eeeccccCccccc
Q 013781 100 QCYGCGNPETEIIITK---TQ-MI--QLKCAACGFVSDV 132 (436)
Q Consensus 100 lC~~C~~peT~l~~~k---~~-~~--~~~C~aCG~~~~v 132 (436)
.||.|++|+|.++-.. .+ .+ +..|..||.+..-
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 6999999999998742 21 22 3899999998543
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=89.83 E-value=0.73 Score=37.71 Aligned_cols=72 Identities=15% Similarity=0.144 Sum_probs=49.1
Q ss_pred cCCCceEEEeccC-CCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccC---CCCeEEEEeccCHHHHHHHHHHH
Q 013781 19 KMPKMITKIEGRG-NGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDE---KTGTSLVNGSHDTAKLAGLLENF 94 (436)
Q Consensus 19 kmp~~~~k~eG~g-ng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~---~~~~~ii~G~~~~~~l~~~l~~f 94 (436)
..|.+.+.++-|+ |=.=|+|.||. .-.=++.-+.+.|...+|+.+++.. ++..+.|+|.|...-.+=|+..|
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 3678888888442 22336778887 4555788999999999999999943 24569999999887666555555
No 19
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.72 E-value=0.42 Score=34.10 Aligned_cols=30 Identities=27% Similarity=0.636 Sum_probs=24.7
Q ss_pred ccCCCCCCCceEEEe------cCceeeeeccccCcc
Q 013781 100 QCYGCGNPETEIIIT------KTQMIQLKCAACGFV 129 (436)
Q Consensus 100 lC~~C~~peT~l~~~------k~~~~~~~C~aCG~~ 129 (436)
.||.|++.+..+... +.-++|..|..||++
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 699999999988642 235889999999975
No 20
>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=88.71 E-value=0.33 Score=34.42 Aligned_cols=31 Identities=23% Similarity=0.624 Sum_probs=22.6
Q ss_pred cccCCCCCCCceEEEe------cCceeeeeccccCcc
Q 013781 99 VQCYGCGNPETEIIIT------KTQMIQLKCAACGFV 129 (436)
Q Consensus 99 VlC~~C~~peT~l~~~------k~~~~~~~C~aCG~~ 129 (436)
+.||.|++.++...-. +.-++|..|..||++
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 4699999999988842 235889999999975
No 21
>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=88.14 E-value=0.52 Score=49.02 Aligned_cols=53 Identities=19% Similarity=0.549 Sum_probs=35.4
Q ss_pred CHHHHHHHHHHHHhh---------ccccCCCCCCCceEEEe---cCceeeeeccccCcccccCch
Q 013781 83 DTAKLAGLLENFIKK---------YVQCYGCGNPETEIIIT---KTQMIQLKCAACGFVSDVDMR 135 (436)
Q Consensus 83 ~~~~l~~~l~~fi~~---------yVlC~~C~~peT~l~~~---k~~~~~~~C~aCG~~~~v~~~ 135 (436)
....|.++|..|..+ .++|+.|+.-+|+-+.. +...+.-+|..||+...++.+
T Consensus 150 ~~~~I~~Il~~~~~~~~~~~y~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~ 214 (360)
T PF01921_consen 150 NRDEIREILNEYRGRERPETYSPFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDIT 214 (360)
T ss_dssp THHHHHHHHHHHHHHT--TT--SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETT
T ss_pred hHHHHHHHHHHhcCcCCCCCeeeeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecC
Confidence 456788888887544 48999999966655543 478999999999999999854
No 22
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=86.72 E-value=0.6 Score=35.62 Aligned_cols=28 Identities=25% Similarity=0.609 Sum_probs=21.6
Q ss_pred ccCCCCCCCceEEEecCce-----eeeeccccCc
Q 013781 100 QCYGCGNPETEIIITKTQM-----IQLKCAACGF 128 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~-----~~~~C~aCG~ 128 (436)
-||-|+++...+.. .... ++..|..||+
T Consensus 5 PCPFCG~~~~~~~~-~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQ-DEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeec-ccCCCCCCEEEEEcCCCCC
Confidence 49999777777765 3222 8899999999
No 23
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=86.26 E-value=0.88 Score=35.88 Aligned_cols=34 Identities=21% Similarity=0.422 Sum_probs=28.0
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCcccccCc
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
-||-|+-..-.+.- .++.++..|..||+..+...
T Consensus 8 PCPFCG~~~~~v~~-~~g~~~v~C~~CgA~~~~~~ 41 (64)
T PRK09710 8 PCPFCGCPSVTVKA-ISGYYRAKCNGCESRTGYGG 41 (64)
T ss_pred CCCCCCCceeEEEe-cCceEEEEcCCCCcCccccc
Confidence 49999998877776 67888899999999866653
No 24
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=85.85 E-value=0.68 Score=42.29 Aligned_cols=32 Identities=19% Similarity=0.395 Sum_probs=23.9
Q ss_pred ccCCCCCCCceEEEe---cCce-e--eeeccccCcccc
Q 013781 100 QCYGCGNPETEIIIT---KTQM-I--QLKCAACGFVSD 131 (436)
Q Consensus 100 lC~~C~~peT~l~~~---k~~~-~--~~~C~aCG~~~~ 131 (436)
.||-|+++||.++-. +++. | -..|.+||.+.+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 599999999999853 2232 3 267999998754
No 25
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=85.57 E-value=0.9 Score=34.14 Aligned_cols=33 Identities=21% Similarity=0.457 Sum_probs=23.4
Q ss_pred ccCCCCCCCceEEE---ecCceeeeeccccCccccc
Q 013781 100 QCYGCGNPETEIII---TKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 100 lC~~C~~peT~l~~---~k~~~~~~~C~aCG~~~~v 132 (436)
-||-|++.+-.+.. +++...+..|..||+..++
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 49999996665552 1233334499999999987
No 26
>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=85.48 E-value=0.83 Score=34.08 Aligned_cols=32 Identities=38% Similarity=0.931 Sum_probs=25.1
Q ss_pred HhhccccCCCCC-----CCceEEEecCceeeeeccccCc
Q 013781 95 IKKYVQCYGCGN-----PETEIIITKTQMIQLKCAACGF 128 (436)
Q Consensus 95 i~~yVlC~~C~~-----peT~l~~~k~~~~~~~C~aCG~ 128 (436)
..+|+.||.|+| -|-.|++ ...++...|+ ||.
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 566999999987 5778888 6678888886 664
No 27
>PHA02998 RNA polymerase subunit; Provisional
Probab=83.35 E-value=1.1 Score=42.06 Aligned_cols=84 Identities=13% Similarity=0.262 Sum_probs=48.8
Q ss_pred hHHHHHHhC---CCchhHHHHHHhhhc---ccccccCCCCeEEEEeccCHHHHHHHHHHHHhhccccCCCCCCCceEEEe
Q 013781 41 MVDIAKALA---RPASYTTKYFGCELG---AQSKFDEKTGTSLVNGSHDTAKLAGLLENFIKKYVQCYGCGNPETEIIIT 114 (436)
Q Consensus 41 ~~~ia~~L~---R~p~~~~ky~~~ELg---~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~yVlC~~C~~peT~l~~~ 114 (436)
..+||..+. --...+++|+++-+- +...||- +.+. .|+...-=++++. +.-|.||.|++.++....-
T Consensus 87 y~~lc~~ir~tng~eke~lry~lfgikcv~~~veydi--d~~~---d~~y~~yfnvlpk--kt~v~CPkCg~~~A~f~ql 159 (195)
T PHA02998 87 YKDLCDMIRGTNGTEKEILRYLLFGIKCIKKGVEYDI--DKIP---DVDYDDYFNVLDE--KYNTPCPNCKSKNTTPMMI 159 (195)
T ss_pred HHHHHHHHHhcCCchHHHHHHHHHHHHHHhcCCccch--hhcc---cccchhheeccCc--ccCCCCCCCCCCceEEEEE
Confidence 677887664 345567888876542 2233332 0110 1111111122222 1358999999999986541
Q ss_pred ------cCceeeeeccccCcccc
Q 013781 115 ------KTQMIQLKCAACGFVSD 131 (436)
Q Consensus 115 ------k~~~~~~~C~aCG~~~~ 131 (436)
+..+.|.+|..||++-.
T Consensus 160 QTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 160 QTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred eeccCCCCceEEEEcCCCCCccC
Confidence 23689999999999843
No 28
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=82.51 E-value=0.71 Score=31.94 Aligned_cols=30 Identities=37% Similarity=0.765 Sum_probs=16.4
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
-||.|+.|=+..+...+...-+.|.+||..
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 499999994333333456678899999975
No 29
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=82.27 E-value=3.7 Score=38.61 Aligned_cols=73 Identities=14% Similarity=0.074 Sum_probs=54.1
Q ss_pred ccCCCceEEEeccCCCc-eEEEechHHHHHHhCCCchhHHHHHHhhhcccccccC---CCCeEEEEeccCHHHHHHHHHH
Q 013781 18 YKMPKMITKIEGRGNGI-KTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDE---KTGTSLVNGSHDTAKLAGLLEN 93 (436)
Q Consensus 18 ykmp~~~~k~eG~gng~-kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~---~~~~~ii~G~~~~~~l~~~l~~ 93 (436)
=..+++.|+++-|+.|+ =|+|.+|.. .+-++.-+.|+|...+++.+++.. +++.++|+|.|...-.+=|++.
T Consensus 86 ~~~~~V~I~~~~R~krK~VT~V~GLe~----f~idlk~laK~lkkkfacG~SV~k~~~~~~eI~IQGD~~~~v~e~L~~~ 161 (173)
T TIGR01159 86 KLPQKVTIKREPRTKRKFVTVIKGLET----FDIDLKKASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEK 161 (173)
T ss_pred CCCCeEEEEEEecCCCceEEEEeCCcC----CCcCHHHHHHHHHHHhCCCCccccCCCCCCEEEecCCHHHHHHHHHHHH
Confidence 35677788888885333 378888874 345789999999999999976621 4678999999987776555555
Q ss_pred H
Q 013781 94 F 94 (436)
Q Consensus 94 f 94 (436)
|
T Consensus 162 ~ 162 (173)
T TIGR01159 162 W 162 (173)
T ss_pred c
Confidence 5
No 30
>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=79.67 E-value=1.8 Score=44.92 Aligned_cols=93 Identities=22% Similarity=0.451 Sum_probs=55.4
Q ss_pred hHHHHHHhCCCchhHHHHHH------hhhcccccccCCCCeEEEEeccCH---------HHHHHHHHHHHhh--------
Q 013781 41 MVDIAKALARPASYTTKYFG------CELGAQSKFDEKTGTSLVNGSHDT---------AKLAGLLENFIKK-------- 97 (436)
Q Consensus 41 ~~~ia~~L~R~p~~~~ky~~------~ELg~~~~~~~~~~~~ii~G~~~~---------~~l~~~l~~fi~~-------- 97 (436)
+..|+.-.+.+|+|.-.|.. ..||..--+=. .-...-+|.++. ..|.++|..|...
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 34455555555666665532 34454322211 122334555543 4677778777765
Q ss_pred -ccccCCCCCCCceEE-Ee-cCceeeeeccccCcccccCch
Q 013781 98 -YVQCYGCGNPETEII-IT-KTQMIQLKCAACGFVSDVDMR 135 (436)
Q Consensus 98 -yVlC~~C~~peT~l~-~~-k~~~~~~~C~aCG~~~~v~~~ 135 (436)
.++|+.|+.-.|.++ .+ +.+.+.-+|. ||+...++.+
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 3466777995 9999999853
No 31
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=79.46 E-value=1.2 Score=38.17 Aligned_cols=38 Identities=24% Similarity=0.704 Sum_probs=27.6
Q ss_pred HhhccccCCCCCCCceEEEecCceeeeeccccCcccccC
Q 013781 95 IKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 95 i~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (436)
+..++.||.|+++--.+.+ +++...+.|..||....-.
T Consensus 18 lpt~f~CP~Cge~~v~v~~-~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 18 LPKIFECPRCGKVSISVKI-KKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred CCcEeECCCCCCeEeeeec-CCCcceEECCCCCCccCEE
Confidence 3468999999975333344 4477899999999985543
No 32
>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=79.40 E-value=1.4 Score=31.61 Aligned_cols=27 Identities=37% Similarity=0.925 Sum_probs=18.8
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
.||.|++.. ++.+ ...-.+.|..||..
T Consensus 2 ~Cp~Cg~~~--~~~D-~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKE--IVFD-PERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSE--EEEE-TTTTEEEETTT-BB
T ss_pred CCcCCcCCc--eEEc-CCCCeEECCCCCCE
Confidence 599999966 4553 33446699999976
No 33
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=78.99 E-value=0.85 Score=36.21 Aligned_cols=43 Identities=23% Similarity=0.475 Sum_probs=28.9
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCcc--cccCchhhhhhhhh
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFV--SDVDMRDKLNTFIL 143 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~--~~v~~~~kl~~~i~ 143 (436)
+|.||.|+|--|.+-. -.....|..||.. .|-..+-++..-|+
T Consensus 19 ~VkCpdC~N~q~vFsh---ast~V~C~~CG~~l~~PTGGka~i~~~i~ 63 (67)
T COG2051 19 RVKCPDCGNEQVVFSH---ASTVVTCLICGTTLAEPTGGKAKISGKII 63 (67)
T ss_pred EEECCCCCCEEEEecc---CceEEEecccccEEEecCCCeEEeeeeeE
Confidence 6999999997665543 5668899999987 33333444444433
No 34
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=78.55 E-value=0.78 Score=35.02 Aligned_cols=48 Identities=27% Similarity=0.630 Sum_probs=32.5
Q ss_pred hccccCCCCCCCceEEEecC---ceeeeeccccCcccccCchhhhhhhhhcCC
Q 013781 97 KYVQCYGCGNPETEIIITKT---QMIQLKCAACGFVSDVDMRDKLNTFILKNP 146 (436)
Q Consensus 97 ~yVlC~~C~~peT~l~~~k~---~~~~~~C~aCG~~~~v~~~~kl~~~i~k~p 146 (436)
+.++||.|+|. |.+.+..+ ..+-+-|.-|-..+-++.. .|.--++|.|
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 33333111 4567999999999999854 4444455555
No 35
>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=78.23 E-value=2.1 Score=31.18 Aligned_cols=30 Identities=27% Similarity=0.607 Sum_probs=21.7
Q ss_pred hhccccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 96 KKYVQCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 96 ~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
+.|| ||.|++. ....+ . .....+|++|+++
T Consensus 17 ~g~~-CP~Cg~~-~~~~~-~-~~~~~~C~~C~~q 46 (46)
T PF12760_consen 17 DGFV-CPHCGST-KHYRL-K-TRGRYRCKACRKQ 46 (46)
T ss_pred CCCC-CCCCCCe-eeEEe-C-CCCeEECCCCCCc
Confidence 4444 9999998 55555 3 3567899999974
No 36
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=76.18 E-value=2.1 Score=33.28 Aligned_cols=30 Identities=27% Similarity=0.594 Sum_probs=24.0
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCccc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFVS 130 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (436)
-|.||.|+|.-|.+-. -.....|..||..=
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 4899999998776655 45678999999873
No 37
>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=76.04 E-value=6.9 Score=31.85 Aligned_cols=58 Identities=10% Similarity=0.023 Sum_probs=42.9
Q ss_pred eEEEeccCCCc-eEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHH
Q 013781 24 ITKIEGRGNGI-KTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKL 87 (436)
Q Consensus 24 ~~k~eG~gng~-kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l 87 (436)
.++++-|+.|+ =|+|.+|..-. -++.-+.+.|...+|+.|++. ++...|+|.|...-.
T Consensus 3 ~I~~e~R~~~K~VT~I~Gl~~~~----~dlk~l~k~lKk~~~cggtv~--~~~I~lQGD~r~~v~ 61 (77)
T cd00474 3 RIRIQQRNGGKTVTTVQGLDLEY----ADLKKLAKELKKKCACGGTVK--DEVIELQGDQRKKIK 61 (77)
T ss_pred EEEEEECCCCccEEEEECCCCch----HhHHHHHHHHHHHcCCCcEEe--cCEEEEeCcHHHHHH
Confidence 45556554443 37788886322 168889999999999999996 488999999976544
No 38
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=75.91 E-value=1.5 Score=30.69 Aligned_cols=32 Identities=25% Similarity=0.679 Sum_probs=22.5
Q ss_pred ccccCCCCC----CCceEEEecCceeeeeccccCccccc
Q 013781 98 YVQCYGCGN----PETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 98 yVlC~~C~~----peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
.+.||.|+. |++.|-. . ...++|..||+.-.|
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~-~--~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPA-G--GRKVRCPKCGHVFRV 37 (37)
T ss_pred EEECCCCCceEEcCHHHccc-C--CcEEECCCCCcEeeC
Confidence 478999985 5555543 2 348999999987543
No 39
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=75.08 E-value=1.2 Score=32.96 Aligned_cols=33 Identities=30% Similarity=0.613 Sum_probs=26.1
Q ss_pred ccccCCCCC----CCceEEEecCceeeeeccccCcccc
Q 013781 98 YVQCYGCGN----PETEIIITKTQMIQLKCAACGFVSD 131 (436)
Q Consensus 98 yVlC~~C~~----peT~l~~~k~~~~~~~C~aCG~~~~ 131 (436)
||.|++|.. |...... +++...++|-+|...-.
T Consensus 6 Fv~C~~C~~lLqlP~~~~~~-~k~~~klrCGaCs~vl~ 42 (46)
T PF11331_consen 6 FVVCSSCFELLQLPAKFSLS-KKNQQKLRCGACSEVLS 42 (46)
T ss_pred EeECccHHHHHcCCCccCCC-ccceeEEeCCCCceeEE
Confidence 899999975 7777776 55688899999987543
No 40
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=73.59 E-value=2.3 Score=31.14 Aligned_cols=32 Identities=25% Similarity=0.675 Sum_probs=20.8
Q ss_pred ccCCCCCCCceEEEecC-ceeeeeccccCcccccCc
Q 013781 100 QCYGCGNPETEIIITKT-QMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~-~~~~~~C~aCG~~~~v~~ 134 (436)
.||.|++ -|..... +.....|..||+...+..
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 223678999998866653
No 41
>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=72.92 E-value=4 Score=44.53 Aligned_cols=51 Identities=24% Similarity=0.515 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHHhh---------ccccCCCCCCCceEEE-ecCceeeeeccccCcccccCch
Q 013781 84 TAKLAGLLENFIKK---------YVQCYGCGNPETEIII-TKTQMIQLKCAACGFVSDVDMR 135 (436)
Q Consensus 84 ~~~l~~~l~~fi~~---------yVlC~~C~~peT~l~~-~k~~~~~~~C~aCG~~~~v~~~ 135 (436)
..+|.++|..|... .++|+.|+.-.|.++- +....+.-+|. ||+.+.++.+
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 35677888887743 4799999998876653 22235767996 9999998754
No 42
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=71.96 E-value=9.2 Score=32.70 Aligned_cols=63 Identities=19% Similarity=0.154 Sum_probs=43.2
Q ss_pred ceEEEeccCCC-ceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHH
Q 013781 23 MITKIEGRGNG-IKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLE 92 (436)
Q Consensus 23 ~~~k~eG~gng-~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~ 92 (436)
+.++++-|..| .=|+|.||.. -.=++.-+.+.|...+|+.|++. ++.+.|+|.|...-. ++|.
T Consensus 26 i~I~~ekr~~gK~VTiI~Gl~~----~~~~lk~l~k~lKk~~gcGgsvk--~~~I~iQGD~r~~v~-~~L~ 89 (99)
T PRK00939 26 IKIKVDKRRYGKEVTIIEGIDP----KDIDLKELAKKLKSKLACGGTVK--DGRIELQGDHRERVK-ELLI 89 (99)
T ss_pred EEEEEEecCCCceEEEEeCCCC----cchhHHHHHHHHHHHhCCCceEE--CCEEEEeCcHHHHHH-HHHH
Confidence 44555543222 3477888863 11247788999999999999995 578999999975543 4444
No 43
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=71.56 E-value=5.1 Score=43.48 Aligned_cols=51 Identities=24% Similarity=0.587 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHhh---------ccccCCCCCCCceEEEe-cC-ceeeeeccccCcccccCch
Q 013781 84 TAKLAGLLENFIKK---------YVQCYGCGNPETEIIIT-KT-QMIQLKCAACGFVSDVDMR 135 (436)
Q Consensus 84 ~~~l~~~l~~fi~~---------yVlC~~C~~peT~l~~~-k~-~~~~~~C~aCG~~~~v~~~ 135 (436)
...|+++|..|-.. -++|+.|+...|+=+++ +. ..+.-+|. ||+.+.|+.+
T Consensus 148 rdeI~~il~~~~~~~~~e~~~P~~piC~kcGri~~t~v~~~d~~~~v~Y~Ce-~Gh~g~v~ir 209 (521)
T COG1384 148 RDEIMEILNEYRGRELEEDWSPFMPICEKCGRILTTPVIEWDGEGTVEYRCE-CGHEGEVDIR 209 (521)
T ss_pred HHHHHHHHHHhcCCcccCCceeccccccccCCcceeEEEEecCCceEEEEec-CCccceeecc
Confidence 46788888888777 37999999955555543 33 58889996 7999999975
No 44
>KOG1104 consensus Nuclear cap-binding complex, subunit NCBP1/CBP80 [RNA processing and modification]
Probab=71.02 E-value=53 Score=37.35 Aligned_cols=103 Identities=17% Similarity=0.219 Sum_probs=74.4
Q ss_pred CCChhHHHHHHH----hcCCC-hHHHHHHHHHHHHhhhhh---hHHHHHHhhHHHHHHHhcCChHHHHHHHHHHHHHHhc
Q 013781 301 SITGMQLQTILG----SLSGS-AQEKMTALFEALFDGVEK---GFSKEVVKKKNFLGAAVAEDEGLQLLLLRAIEAFCGK 372 (436)
Q Consensus 301 ~~s~~ei~~~~~----~l~ls-~~~~~~vl~eaLf~~v~~---~i~k~I~k~~~lL~r~~~~~~~~Q~~lL~alE~~~~~ 372 (436)
-.++.++...++ ...++ ..-.+.+++|++++...+ .....+.+|+..|+.++.+++..|..+|.++=.|...
T Consensus 513 k~~~e~~~~iLk~~~~~~~~~~n~~~i~lfvq~~l~lGSKSfSH~f~~lek~~~vfk~l~~~~e~~q~~vl~~vft~Wk~ 592 (759)
T KOG1104|consen 513 KATAEEIVNILKSEDESEIGSFNRLKIILFVQTLLDLGSKSFSHAFSALEKYHTVFKKLCEDSETKQIIVLEAVFTFWKA 592 (759)
T ss_pred cCCHHHHHHHHhcCccccccCCcceehhhHHHHHHHhccchhhhHHHHHHHHHHHHHHHhcCCchhHHHHHHHHHHHHhc
Confidence 456777877777 22222 345577889999987544 3455688999999999986677799999999888865
Q ss_pred CChhhHHHHHHHHHHHhhccccchHHHHHHhhccC
Q 013781 373 SSSYATKEVALVLKALYDSDVLEEEYIVQWYQEGL 407 (436)
Q Consensus 373 ~~~~l~~~~~~ILk~LYd~DIleEE~Il~W~~k~s 407 (436)
+|.. ...++-.|-..-||+--+|..|-=+..
T Consensus 593 -n~Qm---~~v~~Dkml~~~ii~~~aVv~WiF~~~ 623 (759)
T KOG1104|consen 593 -NPQM---GFVLTDKMLKYQIIDCSAVVRWIFSEE 623 (759)
T ss_pred -Cchh---hHHHHHHHhccccccHHHHHHHhcCHH
Confidence 4552 334556666788999999999985443
No 45
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=70.47 E-value=3.5 Score=44.85 Aligned_cols=51 Identities=20% Similarity=0.513 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHhh---------ccccCCCCCCCceEEEe---cCceeeeeccccCcccccCchh
Q 013781 85 AKLAGLLENFIKK---------YVQCYGCGNPETEIIIT---KTQMIQLKCAACGFVSDVDMRD 136 (436)
Q Consensus 85 ~~l~~~l~~fi~~---------yVlC~~C~~peT~l~~~---k~~~~~~~C~aCG~~~~v~~~~ 136 (436)
..|.++|..|... .++|+.|+.-.|..++. ..+.+.-.|. ||+...++.+.
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 4566666666433 47899999999887742 3456666887 99999998653
No 46
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=68.52 E-value=6.6 Score=32.92 Aligned_cols=48 Identities=25% Similarity=0.265 Sum_probs=30.4
Q ss_pred ccCHHHHHHHHHHHHhhccccCCCCCCCceEEEecCceeeeeccccCcccccC
Q 013781 81 SHDTAKLAGLLENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 81 ~~~~~~l~~~l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (436)
.--.....++...-...| .||.|+.+ |.-.+ ..+ +-.|.-||+...-.
T Consensus 19 ~~~Rrrv~~ie~~~~~~~-~Cp~C~~~-~VkR~-a~G--IW~C~kCg~~fAGg 66 (89)
T COG1997 19 SKLRRRVKEIEAQQRAKH-VCPFCGRT-TVKRI-ATG--IWKCRKCGAKFAGG 66 (89)
T ss_pred hHHHHHHHHHHHHHhcCC-cCCCCCCc-ceeee-ccC--eEEcCCCCCeeccc
Confidence 333455556655545554 69999999 43333 334 56799999886544
No 47
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=66.19 E-value=5.5 Score=33.64 Aligned_cols=33 Identities=30% Similarity=0.674 Sum_probs=26.4
Q ss_pred ccccCCCCCCCceEEE------ecCceeeeeccccCccc
Q 013781 98 YVQCYGCGNPETEIII------TKTQMIQLKCAACGFVS 130 (436)
Q Consensus 98 yVlC~~C~~peT~l~~------~k~~~~~~~C~aCG~~~ 130 (436)
.+.||.|++.+..+.. ++.-++|..|..||++-
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 5899999999976653 13478999999999863
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=66.09 E-value=5.5 Score=40.54 Aligned_cols=55 Identities=18% Similarity=0.337 Sum_probs=39.1
Q ss_pred eEEEEeccCHHHH-------------HHHHHHHHhh----------------ccccCCCCCCCceEEEe------cCcee
Q 013781 75 TSLVNGSHDTAKL-------------AGLLENFIKK----------------YVQCYGCGNPETEIIIT------KTQMI 119 (436)
Q Consensus 75 ~~ii~G~~~~~~l-------------~~~l~~fi~~----------------yVlC~~C~~peT~l~~~------k~~~~ 119 (436)
+-|++|.+++.+| +....++.++ -+.|+.|++.++.+.-- ..-+.
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 4578999988765 3333333332 47999999999987652 12478
Q ss_pred eeeccccCcc
Q 013781 120 QLKCAACGFV 129 (436)
Q Consensus 120 ~~~C~aCG~~ 129 (436)
|..|..||++
T Consensus 286 f~~C~~Cg~~ 295 (299)
T TIGR01385 286 FVTCEECGNR 295 (299)
T ss_pred EEEcCCCCCe
Confidence 9999999985
No 49
>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=65.99 E-value=3.4 Score=41.41 Aligned_cols=35 Identities=23% Similarity=0.401 Sum_probs=18.9
Q ss_pred cccCCCCC-CCceEEEecC--ceeeeeccccCcccccC
Q 013781 99 VQCYGCGN-PETEIIITKT--QMIQLKCAACGFVSDVD 133 (436)
Q Consensus 99 VlC~~C~~-peT~l~~~k~--~~~~~~C~aCG~~~~v~ 133 (436)
-.||.|++ |-..++..+. +.-++.|.-||..-...
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 56899999999986554
No 50
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=65.72 E-value=6.7 Score=44.76 Aligned_cols=42 Identities=21% Similarity=0.436 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhhc----------------------cccCCCCCCCceEEEecCceeeeeccccCcccc
Q 013781 84 TAKLAGLLENFIKKY----------------------VQCYGCGNPETEIIITKTQMIQLKCAACGFVSD 131 (436)
Q Consensus 84 ~~~l~~~l~~fi~~y----------------------VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~ 131 (436)
+..|-..|..|+..- ..||+|+. | |+. ..+ ...|..||++..
T Consensus 688 pDaI~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~--~-l~~-~~G--C~~C~~CG~skC 751 (752)
T PRK08665 688 PDAIAKVLEKHYLGGGKDVGAGNGTGSAGIEAPAPERGACPECGS--I-LEH-EEG--CVVCHSCGYSKC 751 (752)
T ss_pred HHHHHHHHHHHHHhccccccccccccccccccccCCCCCCCCCCc--c-cEE-CCC--CCcCCCCCCCCC
Confidence 567777777776530 35999984 3 666 444 679999999753
No 51
>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=65.66 E-value=4.6 Score=33.25 Aligned_cols=39 Identities=21% Similarity=0.396 Sum_probs=22.2
Q ss_pred HhhccccCCCCCCCceEEE-e-cCceeeeeccccCcccccC
Q 013781 95 IKKYVQCYGCGNPETEIII-T-KTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 95 i~~yVlC~~C~~peT~l~~-~-k~~~~~~~C~aCG~~~~v~ 133 (436)
+.++-.||.|+...|.-+. + +.+.-.+.|..||......
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 4466789999998887666 3 4578899999999886554
No 52
>PHA00626 hypothetical protein
Probab=65.56 E-value=4.9 Score=31.01 Aligned_cols=35 Identities=23% Similarity=0.474 Sum_probs=23.1
Q ss_pred ccCCCCCCCceEEEe-cCceeeeeccccCcccccCc
Q 013781 100 QCYGCGNPETEIIIT-KTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 100 lC~~C~~peT~l~~~-k~~~~~~~C~aCG~~~~v~~ 134 (436)
.||.|++-+-..-.. .+..---+|..||+..+-|.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhh
Confidence 699999865443211 22234568999999987663
No 53
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=65.12 E-value=4.8 Score=27.89 Aligned_cols=29 Identities=28% Similarity=0.755 Sum_probs=18.2
Q ss_pred ccCCCCCCCceEEEe--cCceeeeeccccCcccccC
Q 013781 100 QCYGCGNPETEIIIT--KTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 100 lC~~C~~peT~l~~~--k~~~~~~~C~aCG~~~~v~ 133 (436)
-||.|+|. |... +.... .|..||+..+++
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 54
>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=63.72 E-value=2.6 Score=32.06 Aligned_cols=32 Identities=25% Similarity=0.493 Sum_probs=24.8
Q ss_pred ccCCCCCCCceEEEecCc-eeeeeccccCccccc
Q 013781 100 QCYGCGNPETEIIITKTQ-MIQLKCAACGFVSDV 132 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~-~~~~~C~aCG~~~~v 132 (436)
.|..|+..+|-+-. ++. .-..-|.|||-....
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 432 456789999965443
No 55
>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=63.59 E-value=7.4 Score=30.74 Aligned_cols=32 Identities=28% Similarity=0.712 Sum_probs=22.1
Q ss_pred ccCCCCCCCceEE--------------EecCceeeeeccccCcccc
Q 013781 100 QCYGCGNPETEII--------------ITKTQMIQLKCAACGFVSD 131 (436)
Q Consensus 100 lC~~C~~peT~l~--------------~~k~~~~~~~C~aCG~~~~ 131 (436)
.||.|++-+.+.- +..++.+...|..||++-.
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 4999999766432 1123566789999999743
No 56
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=63.59 E-value=8.3 Score=27.28 Aligned_cols=28 Identities=21% Similarity=0.561 Sum_probs=20.8
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
.||.|+.+=..... ..+..-.|.+||-.
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 56888899999965
No 57
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=62.27 E-value=1.4 Score=34.44 Aligned_cols=38 Identities=21% Similarity=0.517 Sum_probs=30.7
Q ss_pred HHHHhhccccCCCCCCCceEEEecCceeeeeccccCccc
Q 013781 92 ENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVS 130 (436)
Q Consensus 92 ~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (436)
.+||-- -.||.|.--||--.-.+++.-...|-+||+.-
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 467776 56999999999655447888899999999875
No 58
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=62.22 E-value=18 Score=32.71 Aligned_cols=95 Identities=19% Similarity=0.169 Sum_probs=50.4
Q ss_pred echHHHHHHhCCCchhHHHHHH--hh--hcccc---cccCCCC-----eEEEEeccCHHHHHHHHHHH------------
Q 013781 39 VNMVDIAKALARPASYTTKYFG--CE--LGAQS---KFDEKTG-----TSLVNGSHDTAKLAGLLENF------------ 94 (436)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~--~E--Lg~~~---~~~~~~~-----~~ii~G~~~~~~l~~~l~~f------------ 94 (436)
+-=.+||+.|+-++..|-+.+. .+ ++... ..++.++ .|.|+-.+-...|.--|..-
T Consensus 16 ~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~~~~~L~~~l~~e~ 95 (147)
T smart00531 16 VTEEDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDKMRKRLEDKLEDET 95 (147)
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 3457999999999999988654 45 44222 2343233 23355433322222111111
Q ss_pred HhhccccCCCCCCCceEEEe--cCceeeeeccccCcccccC
Q 013781 95 IKKYVQCYGCGNPETEIIIT--KTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 95 i~~yVlC~~C~~peT~l~~~--k~~~~~~~C~aCG~~~~v~ 133 (436)
-..|..||.|+.-=|.+... .+..-...|.-||+.=...
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 12478899998532221110 0111228999999875444
No 59
>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=62.04 E-value=20 Score=30.68 Aligned_cols=59 Identities=15% Similarity=0.047 Sum_probs=42.6
Q ss_pred ceEEEecc--CCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHH
Q 013781 23 MITKIEGR--GNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKL 87 (436)
Q Consensus 23 ~~~k~eG~--gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l 87 (436)
+.+.++-+ |+=.=|+|.||..-. -++.-+.++|...+|+.+++. ++.+.|+|.|...-.
T Consensus 26 i~i~~e~rgr~gK~VTvV~Gl~~~~----~~l~~l~k~LKk~~gcGgtvk--~~~IeiQGD~~~~v~ 86 (101)
T TIGR01158 26 VRIQRETRGRKGKGVTIIEGLDLSD----IDLKELAKELKSKCGCGGTVK--DGVIEIQGDHRDRVK 86 (101)
T ss_pred EEEEEEEecCCCCEEEEEeCCcCch----hhHHHHHHHHHHHhcCCeeEe--CCEEEEeCcHHHHHH
Confidence 34555544 444558888985221 246788999999999999994 689999999975543
No 60
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=61.52 E-value=6.4 Score=33.82 Aligned_cols=38 Identities=18% Similarity=0.522 Sum_probs=29.1
Q ss_pred HhhccccCCCCCCCce---EEEecCceeeeeccccCcccccC
Q 013781 95 IKKYVQCYGCGNPETE---IIITKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 95 i~~yVlC~~C~~peT~---l~~~k~~~~~~~C~aCG~~~~v~ 133 (436)
+.++--||.|+.---. +.+ +....++.|..||.+....
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 3456789999875444 554 6678899999999998776
No 61
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=61.36 E-value=4.3 Score=30.50 Aligned_cols=33 Identities=27% Similarity=0.548 Sum_probs=24.5
Q ss_pred cccCCCCCCCceEEEecCcee-eeeccccCccccc
Q 013781 99 VQCYGCGNPETEIIITKTQMI-QLKCAACGFVSDV 132 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~-~~~C~aCG~~~~v 132 (436)
..|..|+..+|.+-. .+..- .+-|.|||-....
T Consensus 4 ~~C~~C~~~~T~~WR-~g~~g~~~LCnaCgl~~~k 37 (52)
T smart00401 4 RSCSNCGTTETPLWR-RGPSGNKTLCNACGLYYKK 37 (52)
T ss_pred CCcCCCCCCCCCccc-cCCCCCCcEeecccHHHHH
Confidence 369999999999987 33222 4889999976444
No 62
>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=60.60 E-value=7.6 Score=36.15 Aligned_cols=31 Identities=23% Similarity=0.585 Sum_probs=19.8
Q ss_pred cCCCCCC-CceEEE-ec----Cce--eeeeccccCcccc
Q 013781 101 CYGCGNP-ETEIII-TK----TQM--IQLKCAACGFVSD 131 (436)
Q Consensus 101 C~~C~~p-eT~l~~-~k----~~~--~~~~C~aCG~~~~ 131 (436)
||.|+.+ .+.+.. .+ +.. ....|..||++..
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 333221 11 122 2578999999854
No 63
>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=60.53 E-value=3.9 Score=37.33 Aligned_cols=32 Identities=31% Similarity=0.523 Sum_probs=23.2
Q ss_pred ccccCCCCCCCceEEEecCce---eeeeccccCcc
Q 013781 98 YVQCYGCGNPETEIIITKTQM---IQLKCAACGFV 129 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~---~~~~C~aCG~~ 129 (436)
-|-||.|+|.+|.++-.=+.+ -..+|.+|...
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~ep 139 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKEP 139 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCc
Confidence 389999999999999631211 24678888753
No 64
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=60.12 E-value=7.8 Score=30.73 Aligned_cols=35 Identities=29% Similarity=0.724 Sum_probs=23.4
Q ss_pred ccccCCCCCCCce---EE-----------EecCceeeeeccccCccccc
Q 013781 98 YVQCYGCGNPETE---II-----------ITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 98 yVlC~~C~~peT~---l~-----------~~k~~~~~~~C~aCG~~~~v 132 (436)
+-.||.|+|-+-. |. +.-++.+...|+-||++-.-
T Consensus 4 ~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY 52 (68)
T COG3478 4 AFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFY 52 (68)
T ss_pred cccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhhe
Confidence 3459999996522 11 11346778999999997543
No 65
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=59.51 E-value=9.2 Score=32.77 Aligned_cols=31 Identities=26% Similarity=0.683 Sum_probs=24.5
Q ss_pred ccCCCCCCCceEEEecC-ceeeeeccccCcccccC
Q 013781 100 QCYGCGNPETEIIITKT-QMIQLKCAACGFVSDVD 133 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~-~~~~~~C~aCG~~~~v~ 133 (436)
.||.|+| -|++.++ ...-+.|..|++..++.
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 34779999999999887
No 66
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=59.34 E-value=6.6 Score=36.17 Aligned_cols=32 Identities=28% Similarity=0.615 Sum_probs=23.0
Q ss_pred ccCCCCCCCceEEEe----cCcee--eeeccccCcccc
Q 013781 100 QCYGCGNPETEIIIT----KTQMI--QLKCAACGFVSD 131 (436)
Q Consensus 100 lC~~C~~peT~l~~~----k~~~~--~~~C~aCG~~~~ 131 (436)
.||.|+.++|.++-. ++..| -..|..||.+.+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccc
Confidence 599999999999852 11122 367999997743
No 67
>PLN00209 ribosomal protein S27; Provisional
Probab=59.06 E-value=7.2 Score=32.57 Aligned_cols=30 Identities=30% Similarity=0.483 Sum_probs=23.9
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCccc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFVS 130 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (436)
-|.||.|.+.-|.+-. -.....|..||..=
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 4999999998776654 45678999999763
No 68
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=58.37 E-value=8.8 Score=27.78 Aligned_cols=36 Identities=22% Similarity=0.559 Sum_probs=24.1
Q ss_pred cccCCCCCCCceEEEecCceeeeeccccCcccccCchhhh
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMRDKL 138 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl 138 (436)
..|+.|+. .+..+ ...-..+|.-||+.-....+.++
T Consensus 4 y~C~~CG~---~~~~~-~~~~~~~Cp~CG~~~~~~~~~~~ 39 (46)
T PRK00398 4 YKCARCGR---EVELD-EYGTGVRCPYCGYRILFKERPPV 39 (46)
T ss_pred EECCCCCC---EEEEC-CCCCceECCCCCCeEEEccCCCc
Confidence 46999987 44442 22227899999988776655444
No 69
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=57.60 E-value=9.8 Score=37.70 Aligned_cols=42 Identities=19% Similarity=0.289 Sum_probs=31.2
Q ss_pred HHHHHHHhhccccCCCCCCCceEEEecCceeeeeccccCcccccCc
Q 013781 89 GLLENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 89 ~~l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
..|-.|-..+-.|+.|+.| |.+. .....+.|.+||.......
T Consensus 90 ~~l~~w~~~~~fC~~CG~~-~~~~---~~~~~~~C~~c~~~~yp~~ 131 (256)
T PRK00241 90 VQLAEFYRSHRFCGYCGHP-MHPS---KTEWAMLCPHCRERYYPRI 131 (256)
T ss_pred HHHHHHhhcCccccccCCC-Ceec---CCceeEECCCCCCEECCCC
Confidence 3466888999999999998 4433 2345689999998766543
No 70
>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=56.65 E-value=7.8 Score=35.86 Aligned_cols=33 Identities=27% Similarity=0.844 Sum_probs=17.5
Q ss_pred cccCCCCCCCc-eEEEec----Cce--eeeeccccCcccc
Q 013781 99 VQCYGCGNPET-EIIITK----TQM--IQLKCAACGFVSD 131 (436)
Q Consensus 99 VlC~~C~~peT-~l~~~k----~~~--~~~~C~aCG~~~~ 131 (436)
.+||.|+.+-+ .+...+ +.. ....|..||+++.
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 47999999754 333321 122 2468999999853
No 71
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=56.10 E-value=6.8 Score=30.61 Aligned_cols=33 Identities=18% Similarity=0.572 Sum_probs=25.1
Q ss_pred hccccCCCCCCCceEEEecCceeeeeccccCcccccC
Q 013781 97 KYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 97 ~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (436)
.-+-||.|+.| |... ...-.+.|..||-..++.
T Consensus 7 eiLaCP~~kg~---L~~~-~~~~~L~c~~~~~aYpI~ 39 (60)
T COG2835 7 EILACPVCKGP---LVYD-EEKQELICPRCKLAYPIR 39 (60)
T ss_pred eeeeccCcCCc---ceEe-ccCCEEEecccCceeecc
Confidence 45789999999 5552 223389999999998875
No 72
>PRK03954 ribonuclease P protein component 4; Validated
Probab=55.90 E-value=9.8 Score=33.78 Aligned_cols=35 Identities=14% Similarity=0.473 Sum_probs=24.1
Q ss_pred cccCCCCCC-----CceEEEecC--ceeeeeccccCcccccC
Q 013781 99 VQCYGCGNP-----ETEIIITKT--QMIQLKCAACGFVSDVD 133 (436)
Q Consensus 99 VlC~~C~~p-----eT~l~~~k~--~~~~~~C~aCG~~~~v~ 133 (436)
-+|..|.+| ...+.+..+ ..+...|..||+..-.+
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P 106 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYP 106 (121)
T ss_pred HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEeec
Confidence 469999886 344444222 25789999999986544
No 73
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=55.65 E-value=10 Score=33.10 Aligned_cols=33 Identities=27% Similarity=0.525 Sum_probs=25.6
Q ss_pred ccccCCCCCCCceEEEe------cCceeeeeccccCccc
Q 013781 98 YVQCYGCGNPETEIIIT------KTQMIQLKCAACGFVS 130 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~------k~~~~~~~C~aCG~~~ 130 (436)
-+.||.|++-+-.+..- ..-+.|-+|..||++-
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 47899999988776652 2257799999999863
No 74
>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=55.45 E-value=9.6 Score=33.23 Aligned_cols=28 Identities=14% Similarity=0.051 Sum_probs=17.1
Q ss_pred CCCchhHHHHHHhhhcccccccCCCCeEEEE
Q 013781 49 ARPASYTTKYFGCELGAQSKFDEKTGTSLVN 79 (436)
Q Consensus 49 ~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~ 79 (436)
+-.|+.+.-.| ++-+.+++-+ +-++.|.
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 44577776555 4456666654 5677764
No 75
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=55.40 E-value=11 Score=35.90 Aligned_cols=32 Identities=28% Similarity=0.700 Sum_probs=21.0
Q ss_pred ccCCCCCC-CceEEEec-----Cce--eeeeccccCcccc
Q 013781 100 QCYGCGNP-ETEIIITK-----TQM--IQLKCAACGFVSD 131 (436)
Q Consensus 100 lC~~C~~p-eT~l~~~k-----~~~--~~~~C~aCG~~~~ 131 (436)
-||.|+.+ .|.+...+ +.. ....|..||++..
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 41 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSN 41 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccc
Confidence 49999975 44454423 122 2579999999853
No 76
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=55.27 E-value=13 Score=34.55 Aligned_cols=32 Identities=25% Similarity=0.876 Sum_probs=20.6
Q ss_pred ccCCCCCCCc-eEEEec----Cce--eeeeccccCcccc
Q 013781 100 QCYGCGNPET-EIIITK----TQM--IQLKCAACGFVSD 131 (436)
Q Consensus 100 lC~~C~~peT-~l~~~k----~~~--~~~~C~aCG~~~~ 131 (436)
+||.|+.+=| .+...+ +.. ....|..||++..
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 2579999999843
No 77
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=54.52 E-value=9.6 Score=31.75 Aligned_cols=30 Identities=23% Similarity=0.434 Sum_probs=23.9
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCccc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFVS 130 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (436)
-|.|+.|.+.-|.+.. -.....|..||..=
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 4999999998776665 45678999999763
No 78
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=53.40 E-value=9.9 Score=38.92 Aligned_cols=36 Identities=22% Similarity=0.420 Sum_probs=26.0
Q ss_pred ccccCCCCC-CCceEEEe--cCceeeeeccccCcccccC
Q 013781 98 YVQCYGCGN-PETEIIIT--KTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 98 yVlC~~C~~-peT~l~~~--k~~~~~~~C~aCG~~~~v~ 133 (436)
--.||.|++ |-..++.. +.+.-++.|.-||..-...
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 55555432 4577899999999875543
No 79
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=53.38 E-value=10 Score=36.40 Aligned_cols=33 Identities=21% Similarity=0.529 Sum_probs=20.8
Q ss_pred ccccCCCCCCCceEEEe--c----Cce--eeeeccccCcccc
Q 013781 98 YVQCYGCGNPETEIIIT--K----TQM--IQLKCAACGFVSD 131 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~--k----~~~--~~~~C~aCG~~~~ 131 (436)
-+-||.|+. .-.++-. + ++. ....|..||+++.
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 2222221 1 222 3589999999954
No 80
>KOG3221 consensus Glycolipid transfer protein [Carbohydrate transport and metabolism]
Probab=53.16 E-value=89 Score=30.06 Aligned_cols=67 Identities=16% Similarity=0.141 Sum_probs=41.5
Q ss_pred CCChhHHHHHHHhcCCChHHHHHHHHHHHHhhhhhhHHHHHHhhHHHHHHHhcCChHHHHHHHHHHHHHHhc
Q 013781 301 SITGMQLQTILGSLSGSAQEKMTALFEALFDGVEKGFSKEVVKKKNFLGAAVAEDEGLQLLLLRAIEAFCGK 372 (436)
Q Consensus 301 ~~s~~ei~~~~~~l~ls~~~~~~vl~eaLf~~v~~~i~k~I~k~~~lL~r~~~~~~~~Q~~lL~alE~~~~~ 372 (436)
+.+..=....+.+|+.+-..--+.+.+..|. -+++.++.++.++..... ....+..++.-|+.|+..
T Consensus 111 ~~~~~l~~av~daY~kTLK~~HGwI~q~~Fk----vaLklvP~r~~Fl~als~-~d~t~~~~~edi~~fl~~ 177 (199)
T KOG3221|consen 111 GESDCLIQAVADAYEKTLKKYHGWIVQSTFK----VALKLVPDRKTFLKALSA-GDETYDECIEDITSFLSL 177 (199)
T ss_pred chhhHHHHHHHHHHHHHHHHHHhHHHHHHHH----HHHHHcCcHHHHHHHHhc-ccchHHHHHHHHHHHHHH
Confidence 3333334455566665444444566666666 345667777777777765 456677888888888854
No 81
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=52.67 E-value=6.9 Score=39.42 Aligned_cols=31 Identities=23% Similarity=0.536 Sum_probs=24.6
Q ss_pred ccccCCCCC-CCceEEEec---CceeeeeccccCc
Q 013781 98 YVQCYGCGN-PETEIIITK---TQMIQLKCAACGF 128 (436)
Q Consensus 98 yVlC~~C~~-peT~l~~~k---~~~~~~~C~aCG~ 128 (436)
--.||.|++ |=+.++... .++-|++|.-|-.
T Consensus 185 ~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~t 219 (308)
T COG3058 185 RQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCET 219 (308)
T ss_pred cccCCCcCCCCcceeeeecCccccchhhhhhhHHH
Confidence 348999999 899998842 3778999998854
No 82
>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=51.72 E-value=14 Score=30.95 Aligned_cols=65 Identities=20% Similarity=0.282 Sum_probs=47.1
Q ss_pred hHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEec-cCHHHHHHHHHHHHhhccccCCCCCCCceEEEec
Q 013781 41 MVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGS-HDTAKLAGLLENFIKKYVQCYGCGNPETEIIITK 115 (436)
Q Consensus 41 ~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~-~~~~~l~~~l~~fi~~yVlC~~C~~peT~l~~~k 115 (436)
+.-||++|+|++..|.+.+....+..- + ..+..|. .+...|+.++. -|=+|..|.-....++.+.
T Consensus 7 i~AiA~aL~R~~~dVl~Vl~~~~~~~~-~-----~~l~~G~Gl~l~~le~~f~----~F~I~A~v~~~g~~~~lN~ 72 (89)
T PF05379_consen 7 IRAIAEALGRREQDVLAVLSRKCGEEL-L-----EELWSGEGLDLEDLEELFE----LFDICAHVNFGGETFVLNE 72 (89)
T ss_pred hHHHHHHhCCCHHHHHHHHHhccCHHH-H-----HHHHcCCCcCHHHHHHHHH----HcCeEEEEEECCEEEEECC
Confidence 467999999999999999998877332 1 1334444 56666665554 4799999988877777753
No 83
>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=51.63 E-value=6 Score=27.41 Aligned_cols=29 Identities=31% Similarity=0.599 Sum_probs=16.9
Q ss_pred cCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 101 CYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 101 C~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
|..|+..+|.+-+.....-..-|.|||-.
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 88999999999983222233389999953
No 84
>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=51.57 E-value=8 Score=39.50 Aligned_cols=36 Identities=22% Similarity=0.483 Sum_probs=25.6
Q ss_pred ccccCCCCC-CCceEEEe---cCceeeeeccccCcccccC
Q 013781 98 YVQCYGCGN-PETEIIIT---KTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 98 yVlC~~C~~-peT~l~~~---k~~~~~~~C~aCG~~~~v~ 133 (436)
--.||.|++ |-..+++. +.+.-++.|.-|+..-.+.
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 3567899999999875554
No 85
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=51.42 E-value=10 Score=43.16 Aligned_cols=36 Identities=25% Similarity=0.731 Sum_probs=24.6
Q ss_pred ccccCCCCC----C--CceEEEecCceeeeeccccCcccccCc
Q 013781 98 YVQCYGCGN----P--ETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 98 yVlC~~C~~----p--eT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
||+|..|+- | +..|+. -...-.+.|.-||++.++..
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 788887775 2 233444 23446899999999988774
No 86
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=51.07 E-value=12 Score=32.69 Aligned_cols=28 Identities=11% Similarity=-0.070 Sum_probs=16.9
Q ss_pred CCCchhHHHHHHhhhccccc-ccCCCCeEEEE
Q 013781 49 ARPASYTTKYFGCELGAQSK-FDEKTGTSLVN 79 (436)
Q Consensus 49 ~R~p~~~~ky~~~ELg~~~~-~~~~~~~~ii~ 79 (436)
+-.|+.+.-.| ++-++++ +-+ +-++.|.
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 44577776555 4456666 543 6677775
No 87
>PRK00420 hypothetical protein; Validated
Probab=50.92 E-value=15 Score=32.21 Aligned_cols=40 Identities=28% Similarity=0.350 Sum_probs=27.9
Q ss_pred HHHHHHhhccccCCCCCCCceEEEecCceeeeeccccCcccccCc
Q 013781 90 LLENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 90 ~l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
+|.++--.--.||.|+.|=+.+ + . + ...|..||..-.|..
T Consensus 15 Ll~Ga~ml~~~CP~Cg~pLf~l-k-~-g--~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 15 LLKGAKMLSKHCPVCGLPLFEL-K-D-G--EVVCPVHGKVYIVKS 54 (112)
T ss_pred HHhHHHHccCCCCCCCCcceec-C-C-C--ceECCCCCCeeeecc
Confidence 4444444456899999998777 3 2 2 567999999766653
No 88
>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=50.68 E-value=4.3 Score=27.23 Aligned_cols=28 Identities=25% Similarity=0.502 Sum_probs=15.4
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
.=.|+.|++|-+ +.. .-+.+.|.+||..
T Consensus 3 ~rfC~~CG~~t~-~~~---~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTK-PAP---GGWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEE-E-S---SSS-EEESSSS-E
T ss_pred CcccCcCCcccc-CCC---CcCEeECCCCcCE
Confidence 346999999833 332 3578999999975
No 89
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=50.61 E-value=6.7 Score=27.25 Aligned_cols=29 Identities=24% Similarity=0.703 Sum_probs=19.4
Q ss_pred ccccCCCCC----CCceEEEecCceeeeeccccCcc
Q 013781 98 YVQCYGCGN----PETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 98 yVlC~~C~~----peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
.+.||.|+. ||..|- .+...++|..||+.
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 478999974 333322 24458999999985
No 90
>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=49.88 E-value=15 Score=27.29 Aligned_cols=27 Identities=30% Similarity=0.334 Sum_probs=22.7
Q ss_pred chHHHHHHhCCCchhHHHHHHhhhccc
Q 013781 40 NMVDIAKALARPASYTTKYFGCELGAQ 66 (436)
Q Consensus 40 N~~~ia~~L~R~p~~~~ky~~~ELg~~ 66 (436)
-..++|+.|+.++..+.+.+..++|..
T Consensus 5 ~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred EHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 367999999999999999999999988
No 91
>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=49.71 E-value=44 Score=22.89 Aligned_cols=46 Identities=15% Similarity=0.082 Sum_probs=32.5
Q ss_pred chHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHH
Q 013781 40 NMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLL 91 (436)
Q Consensus 40 N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l 91 (436)
++.++|+.|+.++..+-+|........... + ++++. |+...|..++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~~~~~~~-~-~~~~~----~~~~ei~~~~ 47 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRT-P-GGHRR----FPEEDLERLL 47 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCceeC-C-CCcee----cCHHHHHHHH
Confidence 678999999999999999988765433322 1 34443 6777776655
No 92
>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=48.63 E-value=2.2e+02 Score=27.83 Aligned_cols=83 Identities=19% Similarity=0.192 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHHhhhhhhHHHHHHhhHHHHHHHhcCChHHHH-----HHHHHHHHHHhcCChhhHHHHHHHHHHHhhccc
Q 013781 319 QEKMTALFEALFDGVEKGFSKEVVKKKNFLGAAVAEDEGLQL-----LLLRAIEAFCGKSSSYATKEVALVLKALYDSDV 393 (436)
Q Consensus 319 ~~~~~vl~eaLf~~v~~~i~k~I~k~~~lL~r~~~~~~~~Q~-----~lL~alE~~~~~~~~~l~~~~~~ILk~LYd~DI 393 (436)
.++..++|+.+...+...+ |..|+. +++... ..++++ .++..+|.+.....+.-...+-..++++|
T Consensus 119 ~~~~~~lw~~~i~~~~~~L---veg~s~-vkKCs~-eGRalM~lD~q~~~~~le~l~~~~~~p~~~~Ve~YIKAyY---- 189 (234)
T PF10474_consen 119 PEVQNVLWDRLIFFAFETL---VEGYSR-VKKCSN-EGRALMQLDFQQLQNKLEKLSGIRPIPNREYVENYIKAYY---- 189 (234)
T ss_pred HHHHHHHHHHHHHHHHHHH---HHHHHh-ccCCCh-hhHHHHHHHHHHHHHHHHHHcCCCCCccHHHHHHHHHHHc----
Confidence 3466677777666533323 223332 122222 333333 57778887776533334557778899999
Q ss_pred cchHHHHHHhhccCCCCc
Q 013781 394 LEEEYIVQWYQEGLKGGS 411 (436)
Q Consensus 394 leEE~Il~W~~k~s~~~~ 411 (436)
+.|+.+.+|-... ..|.
T Consensus 190 l~e~e~~~W~~~h-~eYs 206 (234)
T PF10474_consen 190 LPEEELEEWIRTH-TEYS 206 (234)
T ss_pred CCHHHHHHHHHhC-cccC
Confidence 7788999999876 5554
No 93
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=47.56 E-value=12 Score=38.14 Aligned_cols=29 Identities=31% Similarity=0.754 Sum_probs=21.8
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
-..||.|++ |.++.+ ...-.+.|.-||..
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 467763 34557899999984
No 94
>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=47.53 E-value=13 Score=28.36 Aligned_cols=31 Identities=23% Similarity=0.444 Sum_probs=23.1
Q ss_pred cccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
++|+.|....=-.-+.....+.-+|..||+.
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 6799999866555333556778899999974
No 95
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=47.50 E-value=14 Score=32.14 Aligned_cols=28 Identities=14% Similarity=0.048 Sum_probs=17.3
Q ss_pred CCCchhHHHHHHhhhcccccccCCCCeEEEE
Q 013781 49 ARPASYTTKYFGCELGAQSKFDEKTGTSLVN 79 (436)
Q Consensus 49 ~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~ 79 (436)
+-.|+.+.-.|. +-+++++-+ +-++.|.
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 445888776664 345565543 6677764
No 96
>PF14353 CpXC: CpXC protein
Probab=47.27 E-value=17 Score=31.71 Aligned_cols=35 Identities=20% Similarity=0.553 Sum_probs=0.0
Q ss_pred cccCCCCCCCceEEEec---------------CceeeeeccccCcccccC
Q 013781 99 VQCYGCGNPETEIIITK---------------TQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k---------------~~~~~~~C~aCG~~~~v~ 133 (436)
+.||.|+.+-+.-+-+- +.+....|..||+...++
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 97
>PRK11827 hypothetical protein; Provisional
Probab=47.00 E-value=13 Score=29.08 Aligned_cols=36 Identities=11% Similarity=0.138 Sum_probs=24.7
Q ss_pred HHhhccccCCCCCCCceEEEecCceeeeeccccCcccccC
Q 013781 94 FIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 94 fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (436)
.+-...-||.|+.|=. +.. . .-.+.|.+||-..+|.
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 2257799999999885
No 98
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=45.90 E-value=15 Score=32.88 Aligned_cols=49 Identities=14% Similarity=0.177 Sum_probs=29.8
Q ss_pred hHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHHHHHhhccccCCCCC
Q 013781 41 MVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLENFIKKYVQCYGCGN 106 (436)
Q Consensus 41 ~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~yVlC~~C~~ 106 (436)
+..|.+.=+-.|+.+...|.. +. ++++-+ +-++.|.- +.-...|+.|+.
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-LL-KGTILE-GAEIIFEE--------------EEAVLKCRNCGN 78 (135)
T ss_pred HhhHhhhhhhhHHHHHHHHHH-HH-cCCccc-CCEEEEEe--------------cceEEECCCCCC
Confidence 455666666678888877754 44 444332 45666643 335677888873
No 99
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=45.88 E-value=13 Score=39.26 Aligned_cols=32 Identities=34% Similarity=0.841 Sum_probs=23.3
Q ss_pred ccCCCCCC-CceEEEec----Ccee--eeeccccCcccc
Q 013781 100 QCYGCGNP-ETEIIITK----TQMI--QLKCAACGFVSD 131 (436)
Q Consensus 100 lC~~C~~p-eT~l~~~k----~~~~--~~~C~aCG~~~~ 131 (436)
-||+|..| ||.|...+ +..| ...|.+||+++.
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 88887632 1333 468999999863
No 100
>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=45.68 E-value=1.8e+02 Score=24.24 Aligned_cols=88 Identities=13% Similarity=0.038 Sum_probs=45.7
Q ss_pred ChhHHHHHHHhcCCC--hHHHHHHHHHHHHhhhhhhHHHHHHhhHHHHHHHhcCChHHHHHHHHHHHHHHhc------CC
Q 013781 303 TGMQLQTILGSLSGS--AQEKMTALFEALFDGVEKGFSKEVVKKKNFLGAAVAEDEGLQLLLLRAIEAFCGK------SS 374 (436)
Q Consensus 303 s~~ei~~~~~~l~ls--~~~~~~vl~eaLf~~v~~~i~k~I~k~~~lL~r~~~~~~~~Q~~lL~alE~~~~~------~~ 374 (436)
+..|.....+.++++ .+.++..++...|+. -...-..+..+|.+++..+--.+.++..|++.+... .-
T Consensus 17 d~~ea~~~l~el~~~~~~~~vv~~~l~~~le~----~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~l~Dl~~D~ 92 (113)
T PF02847_consen 17 DVDEAVECLKELKLPSQHHEVVKVILECALEE----KKSYREYYSKLLSHLCKRKLISKEQFQEGFEDLLESLEDLELDI 92 (113)
T ss_dssp -HHHHHHHHHHTT-GGGHHHHHHHHHHHHHTS----SHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHS
T ss_pred CHHHHHHHHHHhCCCccHHHHHHHHHHHHhhc----cHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhHhhhccccc
Confidence 344555666666665 122233333333332 111233445667777642333444455555554432 14
Q ss_pred hhhHHHHHHHHHHHhhcccc
Q 013781 375 SYATKEVALVLKALYDSDVL 394 (436)
Q Consensus 375 ~~l~~~~~~ILk~LYd~DIl 394 (436)
|.....++.++-.++..|+|
T Consensus 93 P~~~~~la~~~~~~i~~~~l 112 (113)
T PF02847_consen 93 PKAPEYLAKFLARLIADGIL 112 (113)
T ss_dssp TTHHHHHHHHHHHHHHTTSS
T ss_pred hHHHHHHHHHHHHHHHcCCc
Confidence 67777888899888888876
No 101
>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=45.63 E-value=5.5 Score=30.59 Aligned_cols=29 Identities=38% Similarity=0.686 Sum_probs=17.7
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
-|.||.|.+.-|... .-.....|..||..
T Consensus 7 ~VkCp~C~~~q~vFS---ha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFS---HAQTVVKCVVCGTV 35 (55)
T ss_dssp EEE-TTT-SEEEEET---T-SS-EE-SSSTSE
T ss_pred EEECCCCCCeeEEEe---cCCeEEEcccCCCE
Confidence 389999998655433 35567899999986
No 102
>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=45.49 E-value=26 Score=24.74 Aligned_cols=32 Identities=22% Similarity=0.678 Sum_probs=20.9
Q ss_pred cccCCCCCCCceEEE-ecCceeeeeccc---cCcccccC
Q 013781 99 VQCYGCGNPETEIII-TKTQMIQLKCAA---CGFVSDVD 133 (436)
Q Consensus 99 VlC~~C~~peT~l~~-~k~~~~~~~C~a---CG~~~~v~ 133 (436)
+.||.|+++ |++ ..+...|+-|.. |.+...+.
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 333 222338899987 87776654
No 103
>COG0023 SUI1 Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=45.43 E-value=66 Score=27.91 Aligned_cols=74 Identities=15% Similarity=0.030 Sum_probs=49.3
Q ss_pred CCCcccc---cCCC----ceEEEeccCCC-ceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccC
Q 013781 12 GDAFYRY---KMPK----MITKIEGRGNG-IKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHD 83 (436)
Q Consensus 12 ~D~~~Ry---kmp~----~~~k~eG~gng-~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~ 83 (436)
.+|+..+ .+|. +.++++-+.-| --|+|.+|.. -.-++.-+.+.|-..+|+.|++- ++...|+|.|.
T Consensus 11 ~~p~e~~~~~~~k~~~~~V~I~~e~rr~gK~VTiI~Gld~----~~~dlk~Lak~LKk~cacGGtvk--~~~IeiQGdhr 84 (104)
T COG0023 11 GLPKELTCEEVAKEGDQIVRIRRETRRKGKTVTIIEGLDL----KDIDLKKLAKELKKKCACGGTVK--DGEIEIQGDHR 84 (104)
T ss_pred CCchHHhhhhcccccCCeEEEEEEeecCCcEEEEEeCccc----chhhHHHHHHHHHHHcCCCceec--CCEEEEeChHH
Confidence 5565555 5555 34555554222 2467778775 23346778888999999999994 68999999998
Q ss_pred HHHHHHHH
Q 013781 84 TAKLAGLL 91 (436)
Q Consensus 84 ~~~l~~~l 91 (436)
..-..-|+
T Consensus 85 ~~v~~~L~ 92 (104)
T COG0023 85 DKVKELLI 92 (104)
T ss_pred HHHHHHHH
Confidence 65544333
No 104
>PRK07451 translation initiation factor Sui1; Validated
Probab=45.38 E-value=50 Score=29.10 Aligned_cols=58 Identities=19% Similarity=0.193 Sum_probs=40.5
Q ss_pred eEEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHH
Q 013781 24 ITKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKL 87 (436)
Q Consensus 24 ~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l 87 (436)
++...||++=.=|+|.+|..-... -.-+.|.|-..+|+.+++ +++.+.|+|.|...-.
T Consensus 43 ~~~r~gR~GK~VTvV~Gl~~~~~d----lk~LaK~LK~k~gcGGtv--kd~~IelQGD~r~~v~ 100 (115)
T PRK07451 43 QATRSGRKGKTVTVITGFQHKPET----LAKLLKQLKTQCGSGGTV--KDNTIEIQGDHRQKIL 100 (115)
T ss_pred EEEecCCCCCeEEEEeCCCCCHHH----HHHHHHHHHHHhcCCceE--cCCEEEEcCcHHHHHH
Confidence 344567754455788888622222 356788999999999999 4678999999975433
No 105
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=45.31 E-value=17 Score=31.67 Aligned_cols=29 Identities=10% Similarity=-0.019 Sum_probs=17.8
Q ss_pred hCCCchhHHHHHHhhhcccccccCCCCeEEEE
Q 013781 48 LARPASYTTKYFGCELGAQSKFDEKTGTSLVN 79 (436)
Q Consensus 48 L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~ 79 (436)
-+-.|+.+.=+| ++-+++++-+ +-++.|.
T Consensus 37 s~v~pe~L~f~f--~~~~~~T~~e-gA~L~I~ 65 (113)
T PRK12380 37 SCVEESAVRFSF--EIVCHGTVAQ-GCDLHIV 65 (113)
T ss_pred cccCHHHHHHHH--HHHhCCCccC-CCEEEEE
Confidence 345688877666 4455555543 5677774
No 106
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.99 E-value=18 Score=31.96 Aligned_cols=28 Identities=11% Similarity=0.049 Sum_probs=17.1
Q ss_pred CCCchhHHHHHHhhhcccccccCCCCeEEEE
Q 013781 49 ARPASYTTKYFGCELGAQSKFDEKTGTSLVN 79 (436)
Q Consensus 49 ~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~ 79 (436)
+-.|+.|.-+|. +-+.+++-+ +-.+.|.
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 445888876664 445666653 5667664
No 107
>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=44.42 E-value=32 Score=31.07 Aligned_cols=59 Identities=20% Similarity=0.384 Sum_probs=40.0
Q ss_pred eEEEEeccCHHHHHHHHHHHH-----hh-ccccCCCCCCCceEEEe-----------cCceeeeeccccCcccccC
Q 013781 75 TSLVNGSHDTAKLAGLLENFI-----KK-YVQCYGCGNPETEIIIT-----------KTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 75 ~~ii~G~~~~~~l~~~l~~fi-----~~-yVlC~~C~~peT~l~~~-----------k~~~~~~~C~aCG~~~~v~ 133 (436)
.+.|......++|..++..|= +. |-.|+.|..|=..+.++ ....-|..|..||...=..
T Consensus 62 ~~li~~~~~~~QL~ev~~~~~l~~~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~G 137 (147)
T PF01927_consen 62 VILIRSDDPEEQLREVLERFGLKLRLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEG 137 (147)
T ss_pred EEEEcCCCHHHHHHHHHHHcCCccccCCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEeccc
Confidence 355677778899999998873 33 78999999954333321 0112389999999875443
No 108
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=43.89 E-value=13 Score=32.51 Aligned_cols=34 Identities=21% Similarity=0.518 Sum_probs=26.9
Q ss_pred ccCCCCCCCceEEE------ecCceeeeeccccCcccccC
Q 013781 100 QCYGCGNPETEIII------TKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 100 lC~~C~~peT~l~~------~k~~~~~~~C~aCG~~~~v~ 133 (436)
.||.|++++-.+.- +++++.|--|..||++-..+
T Consensus 76 kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e~ 115 (116)
T KOG2907|consen 76 KCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTEN 115 (116)
T ss_pred cCcccCCchhhhhhhhcccccCCceEEEEcCccceeeecc
Confidence 79999999865542 36799999999999986543
No 109
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=43.73 E-value=16 Score=32.81 Aligned_cols=25 Identities=32% Similarity=0.931 Sum_probs=18.6
Q ss_pred cccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
--||.|+.| |.. +++ -..|.-||++
T Consensus 29 ~hCp~Cg~P---LF~-KdG--~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGTP---LFR-KDG--EVFCPVCGYR 53 (131)
T ss_pred hhCcccCCc---cee-eCC--eEECCCCCce
Confidence 369999998 444 455 4569999984
No 110
>PRK05667 dnaG DNA primase; Validated
Probab=43.63 E-value=34 Score=37.97 Aligned_cols=32 Identities=19% Similarity=0.338 Sum_probs=23.5
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCccccc
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
+||-|.--..++.++ ...-+-+|-+||..+.+
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 799998655578884 23346789999997755
No 111
>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=43.18 E-value=25 Score=31.87 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=31.4
Q ss_pred echHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHHHHHhhccccCCCCCC
Q 013781 39 VNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLENFIKKYVQCYGCGNP 107 (436)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~yVlC~~C~~p 107 (436)
.|+.+|+++++-++.+|.+|+- .||+.|.+. =+-+..|..|+.|
T Consensus 47 ati~eV~e~tgVs~~~I~~~Ir------------eGRL~~~~~-------------~nl~~~CE~CG~~ 90 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIR------------EGRLQLKHF-------------PNLGYPCERCGTS 90 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH------------cCCeeccCC-------------CCCcCcccccCCc
Confidence 4788899999999999988872 467775441 1335777777765
No 112
>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=42.98 E-value=16 Score=39.77 Aligned_cols=44 Identities=23% Similarity=0.413 Sum_probs=26.1
Q ss_pred cCCCCCCCceEEEecCceeeeeccccCcccccCc----------------hhhhhhhhhcCCCc
Q 013781 101 CYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM----------------RDKLNTFILKNPPE 148 (436)
Q Consensus 101 C~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~----------------~~kl~~~i~k~pp~ 148 (436)
||.|..|=|. ++ . .-.+.|.-||++.+++. ..++..++-++=|.
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-K--EGKLRCHYCGYQEPIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPG 284 (505)
T ss_pred CCCCCCceEE-ec-C--CCeEEcCCCcCcCCCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCC
Confidence 6666555332 22 2 22678988888876542 36666666666553
No 113
>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=42.74 E-value=16 Score=25.18 Aligned_cols=28 Identities=21% Similarity=0.470 Sum_probs=20.0
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCc
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGF 128 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~ 128 (436)
.|+.|+..=+.+.. -...-...|-.||+
T Consensus 7 ~C~~Cg~~fe~~~~-~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQK-ISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEe-cCCCCCCCCCCCCC
Confidence 69999986555554 22245778999998
No 114
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=42.49 E-value=9.2 Score=38.54 Aligned_cols=44 Identities=18% Similarity=0.453 Sum_probs=31.7
Q ss_pred hccccCCCCCCCceEEEecCceeeeeccccCcccccCchhhhhhhhh
Q 013781 97 KYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMRDKLNTFIL 143 (436)
Q Consensus 97 ~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (436)
-++.||+|+. +.+.+ +=+.-...|..||++..+..+.++-..+=
T Consensus 27 lw~KCp~c~~--~~y~~-eL~~n~~vcp~c~~h~ri~A~~Ri~~llD 70 (294)
T COG0777 27 LWTKCPSCGE--MLYRK-ELESNLKVCPKCGHHMRISARERLEALLD 70 (294)
T ss_pred ceeECCCccc--eeeHH-HHHhhhhcccccCcccccCHHHHHHHhhC
Confidence 3789999984 22222 11344789999999999999988876653
No 115
>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=41.37 E-value=20 Score=29.69 Aligned_cols=21 Identities=24% Similarity=0.369 Sum_probs=16.3
Q ss_pred hHHHHHHhCCCchhHHHHHHh
Q 013781 41 MVDIAKALARPASYTTKYFGC 61 (436)
Q Consensus 41 ~~~ia~~L~R~p~~~~ky~~~ 61 (436)
-.+||+.|+|++.||.+|+..
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 468999999999999999874
No 116
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=41.29 E-value=16 Score=31.83 Aligned_cols=45 Identities=16% Similarity=0.363 Sum_probs=28.0
Q ss_pred ccCCCCCCCceEEEe-cCceeeeeccccCcccccCchhhhhhhhhcCCC
Q 013781 100 QCYGCGNPETEIIIT-KTQMIQLKCAACGFVSDVDMRDKLNTFILKNPP 147 (436)
Q Consensus 100 lC~~C~~peT~l~~~-k~~~~~~~C~aCG~~~~v~~~~kl~~~i~k~pp 147 (436)
-||.|+|- |+.. ++....+.|..||+.-++.+...-..++..+-|
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 3332 223349999999999998864333333333333
No 117
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=41.10 E-value=25 Score=27.26 Aligned_cols=34 Identities=38% Similarity=0.631 Sum_probs=27.1
Q ss_pred CCCCCceEEEecCceeeeeccccCcccccCchhhhh
Q 013781 104 CGNPETEIIITKTQMIQLKCAACGFVSDVDMRDKLN 139 (436)
Q Consensus 104 C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~ 139 (436)
|++-+=++++ -+-.+-++|..||..-.++ |++|-
T Consensus 16 CG~~~Wei~R-~GaDikikC~gCg~~imlp-R~~fe 49 (57)
T PF06107_consen 16 CGSNEWEIIR-IGADIKIKCLGCGRQIMLP-RSKFE 49 (57)
T ss_pred CCCCEEEEEE-ccCcEEEEECCCCCEEEEe-HHHHH
Confidence 8887777877 5667889999999998887 66554
No 118
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=41.09 E-value=23 Score=43.99 Aligned_cols=44 Identities=18% Similarity=0.390 Sum_probs=27.9
Q ss_pred HHHHHHHHhhccccCCCCCCCceEEEecCceeeeeccccCccccc
Q 013781 88 AGLLENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 88 ~~~l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
..++..++ .-+-||.|+.++-.|+--.-.--...|..||.+..+
T Consensus 1695 ~~~~~~~~-~~~~cp~c~~~~~~~~~~~~~~gc~~c~~cg~s~c~ 1738 (1740)
T PRK08332 1695 EEKIRELL-GVVYCPVCYEKEGKLVELRMESGCATCPVCGWSKCV 1738 (1740)
T ss_pred HHHHHHHh-ccCCCCCCCCCCCcceeeEecCCceeCCCCCCcccc
Confidence 44444444 335599999998655531112236799999998654
No 119
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=41.06 E-value=18 Score=27.05 Aligned_cols=28 Identities=21% Similarity=0.549 Sum_probs=19.4
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCccc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFVS 130 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (436)
+-.||.|++- -|.. .. -.+.|..||.+-
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 5579999983 4443 22 367899999864
No 120
>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=41.02 E-value=13 Score=35.87 Aligned_cols=67 Identities=24% Similarity=0.262 Sum_probs=48.8
Q ss_pred hCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHHHHHhhc------cccCCCCCC-CceEEEe
Q 013781 48 LARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLENFIKKY------VQCYGCGNP-ETEIIIT 114 (436)
Q Consensus 48 L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~y------VlC~~C~~p-eT~l~~~ 114 (436)
-.|..++|.|+|-.|++-.-+-..+=+++-+||--+...+..-|+.=|+.| |.|..|++. .|.|.++
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 358899999999999885432211234788999888888888888777776 778888875 4556664
No 121
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=39.96 E-value=14 Score=28.86 Aligned_cols=30 Identities=20% Similarity=0.605 Sum_probs=13.5
Q ss_pred hccccCCCCCCCceEEEecCceeeeeccccCccc
Q 013781 97 KYVQCYGCGNPETEIIITKTQMIQLKCAACGFVS 130 (436)
Q Consensus 97 ~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (436)
-.++|.-|+. |.-+. =..+.++|..||+-.
T Consensus 29 v~IlCNDC~~--~s~v~--fH~lg~KC~~C~SYN 58 (61)
T PF14599_consen 29 VWILCNDCNA--KSEVP--FHFLGHKCSHCGSYN 58 (61)
T ss_dssp EEEEESSS----EEEEE----TT----TTTS---
T ss_pred EEEECCCCCC--cccee--eeHhhhcCCCCCCcc
Confidence 4689999998 33222 357889999999754
No 122
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=39.56 E-value=35 Score=23.70 Aligned_cols=28 Identities=29% Similarity=0.423 Sum_probs=23.1
Q ss_pred echHHHHHHhCCCchhHHHHHHhhhccc
Q 013781 39 VNMVDIAKALARPASYTTKYFGCELGAQ 66 (436)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~~ELg~~ 66 (436)
..+.+||..++=+|.|+.+-|..++|..
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 4589999999999999999999999964
No 123
>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=38.67 E-value=21 Score=25.18 Aligned_cols=31 Identities=23% Similarity=0.387 Sum_probs=22.1
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGF 128 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~ 128 (436)
-+-||.|+.-|.-=..+++..=.-.|..||+
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 4679999998877644344445567888886
No 124
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=38.64 E-value=44 Score=35.41 Aligned_cols=33 Identities=15% Similarity=0.235 Sum_probs=23.7
Q ss_pred cccCCCCCCCceEEEecCceeeeeccccCccccc
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
.+||-|.--...+.++. ..-+-+|-+||..+.+
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 125
>PRK05580 primosome assembly protein PriA; Validated
Probab=37.81 E-value=19 Score=40.55 Aligned_cols=50 Identities=20% Similarity=0.543 Sum_probs=29.7
Q ss_pred ccccCCCCCC------CceEEEecCceeeeeccccCcccccC----------------chhhhhhhhhcCCCc
Q 013781 98 YVQCYGCGNP------ETEIIITKTQMIQLKCAACGFVSDVD----------------MRDKLNTFILKNPPE 148 (436)
Q Consensus 98 yVlC~~C~~p------eT~l~~~k~~~~~~~C~aCG~~~~v~----------------~~~kl~~~i~k~pp~ 148 (436)
||.|..|+.+ +..|... ...-.+.|.-||++.+++ ..+++..++-++-|.
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h-~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~~~g~G~e~~~e~l~~~fp~ 452 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLH-RFQRRLRCHHCGYQEPIPKACPECGSTDLVPVGPGTERLEEELAELFPE 452 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEE-CCCCeEECCCCcCCCCCCCCCCCCcCCeeEEeeccHHHHHHHHHHhCCC
Confidence 5666666643 3344431 123467888888876643 346777777777554
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=37.54 E-value=31 Score=27.69 Aligned_cols=30 Identities=30% Similarity=0.793 Sum_probs=17.6
Q ss_pred cccCCCCC---CC--ceEEEe----cCceeeeeccccCc
Q 013781 99 VQCYGCGN---PE--TEIIIT----KTQMIQLKCAACGF 128 (436)
Q Consensus 99 VlC~~C~~---pe--T~l~~~----k~~~~~~~C~aCG~ 128 (436)
-+|..|++ |- ..+.+. ..+.+...|..||+
T Consensus 47 ~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 47 TICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp TB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred ccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 57999998 43 223331 15889999999995
No 127
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=36.89 E-value=25 Score=27.08 Aligned_cols=27 Identities=30% Similarity=0.844 Sum_probs=20.0
Q ss_pred HHhhccccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 94 FIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 94 fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
.+..+|.|+.|+++- +-...|..||.-
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 356779999999863 336779999954
No 128
>COG3741 HutG N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=36.16 E-value=8.8 Score=38.38 Aligned_cols=109 Identities=17% Similarity=0.171 Sum_probs=75.9
Q ss_pred CCceEEEechHHHHHHhCCCchhHHHH---HHhhhcccccccCCCCeEEEEeccCHHHHHHHHHHHHhhccccCCCCCCC
Q 013781 32 NGIKTNIVNMVDIAKALARPASYTTKY---FGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLENFIKKYVQCYGCGNPE 108 (436)
Q Consensus 32 ng~kT~i~N~~~ia~~L~R~p~~~~ky---~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~yVlC~~C~~pe 108 (436)
.|--++..||+-.+=.+||+|.+..-| -...||.++.||+ .+.|+--|+.+...+..-|..|-+=|--|-.=..--
T Consensus 61 lGA~~l~A~fsR~~vDvNR~p~~~~l~~~~~ttGL~~~~~fdg-e~l~~~g~~~~~~e~~~Rle~~~~PYHaaL~~el~r 139 (272)
T COG3741 61 LGATLLRANFSRAVVDVNREPDGASLYPGRVTTGLGPVTTFDG-EPLYIYGGAPTPAEALARLETLWKPYHAALRRELER 139 (272)
T ss_pred ccchhhhccccceeEecCCCCCCCcCccccccCCccccccccC-ccccccCCCCCHHHHHHHHHHhhccHHHHHHHHHHH
Confidence 356788889999999999999999998 4567999999997 788888888999999999988877765543222111
Q ss_pred ceEEEecCceeeeeccccCcccccCchhhhhhhhh
Q 013781 109 TEIIITKTQMIQLKCAACGFVSDVDMRDKLNTFIL 143 (436)
Q Consensus 109 T~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (436)
|.-+- +-.+...|..=-+.-+.--.-++..|+|
T Consensus 140 ~~a~~--G~avLiDcHSm~s~ip~l~~G~lPdfni 172 (272)
T COG3741 140 LRAIF--GAAVLIDCHSMRSHIPRLFEGPLPDFNI 172 (272)
T ss_pred HHhhc--CeEEEEeccccccccccccCCCCCceee
Confidence 11111 3445566765544444444455555555
No 129
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=35.67 E-value=9.2 Score=38.80 Aligned_cols=43 Identities=19% Similarity=0.473 Sum_probs=30.7
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCcccccCchhhhhhhhh
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMRDKLNTFIL 143 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (436)
++.||.|+..=..-.. + ..+..|..||++..+..|.+|...+=
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 7999999974221111 1 12579999999999998888876554
No 130
>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=35.58 E-value=67 Score=23.13 Aligned_cols=35 Identities=29% Similarity=0.713 Sum_probs=23.1
Q ss_pred HHHHHHHHhhccccCCCCCCCceEEEecCceeeeeccccC
Q 013781 88 AGLLENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACG 127 (436)
Q Consensus 88 ~~~l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG 127 (436)
+-+|.+|-=---.||.|+.| |..++++ ...|.+|+
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 45677777667789999766 4443333 34688886
No 131
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=35.56 E-value=33 Score=24.60 Aligned_cols=22 Identities=27% Similarity=0.401 Sum_probs=16.1
Q ss_pred echHHHHHHhCCCchhHHHHHH
Q 013781 39 VNMVDIAKALARPASYTTKYFG 60 (436)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~ 60 (436)
..+.+||+.|+|+|+-|.+++-
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 3578999999999999988764
No 132
>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=35.43 E-value=24 Score=25.21 Aligned_cols=29 Identities=21% Similarity=0.507 Sum_probs=21.5
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
.|..|+..-..+..-. ..-...|.+||..
T Consensus 7 ~C~~Cg~~fe~~~~~~-~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 7 RCEECGHEFEVLQSIS-EDDPVPCPECGST 35 (42)
T ss_pred EeCCCCCEEEEEEEcC-CCCCCcCCCCCCC
Confidence 5899998777776522 3667899999983
No 133
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=35.38 E-value=40 Score=26.58 Aligned_cols=37 Identities=24% Similarity=0.273 Sum_probs=28.8
Q ss_pred echHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccC
Q 013781 39 VNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHD 83 (436)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~ 83 (436)
-|+.++|+.|+-.-.-+.||..-- +. ....||||.+.
T Consensus 17 GnqtEvaR~l~c~R~TVrKY~~D~-------~a-~~HaIvNgvLM 53 (64)
T PF06322_consen 17 GNQTEVARRLGCNRATVRKYSRDK-------DA-KRHAIVNGVLM 53 (64)
T ss_pred CcHHHHHHHhcccHHHHHHHhccc-------cc-ceEEEEcCEEE
Confidence 589999999999999999997632 22 34678888653
No 134
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=35.24 E-value=28 Score=41.76 Aligned_cols=40 Identities=23% Similarity=0.551 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhhccccCCCCCCCceEEEecCceeeeeccccCccccc
Q 013781 86 KLAGLLENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 86 ~l~~~l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
..+..+.+| +=..|+.|+| ++|++ . --.++|..||.++..
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 455666666 5567999997 67776 2 348999999998753
No 135
>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=35.08 E-value=23 Score=27.41 Aligned_cols=31 Identities=29% Similarity=0.640 Sum_probs=22.0
Q ss_pred cccCCCCCCCceEEEecCceeeeeccccCcccccC
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (436)
-.||.|+.+.-. . ...-...|..||....-|
T Consensus 29 q~C~~CG~~~~~-~---~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 29 QTCPRCGHRNKK-R---RSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred cCccCccccccc-c---cccceEEcCCCCCEECcH
Confidence 459999997766 1 123378899999985544
No 136
>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=35.01 E-value=9.3 Score=38.65 Aligned_cols=43 Identities=16% Similarity=0.424 Sum_probs=30.2
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCcccccCchhhhhhhhh
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMRDKLNTFIL 143 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (436)
++.||.|+..=..-.. . .-+..|..||++..+..|.++...+=
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 8999999974221111 1 12479999999999998888875543
No 137
>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=34.85 E-value=41 Score=27.72 Aligned_cols=51 Identities=22% Similarity=0.464 Sum_probs=37.0
Q ss_pred CeEEEEeccCHHHHHHHHHHHHhh-------ccccCCCCCCCceEEEecCceeeeeccccCcccccC
Q 013781 74 GTSLVNGSHDTAKLAGLLENFIKK-------YVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 74 ~~~ii~G~~~~~~l~~~l~~fi~~-------yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (436)
+.+.-.+.|+..+|+.+-..-... ++.|..|-.. ...-+.|..||...+++
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 455566788989888776654444 6999999764 23345899999888877
No 138
>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=34.69 E-value=27 Score=26.68 Aligned_cols=31 Identities=29% Similarity=0.568 Sum_probs=21.9
Q ss_pred ccCCCCCCCceEEEec-CceeeeeccccCcccccC
Q 013781 100 QCYGCGNPETEIIITK-TQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 100 lC~~C~~peT~l~~~k-~~~~~~~C~aCG~~~~v~ 133 (436)
.||.|+. .|.+.. -.-..+.|..||+.--|-
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 455421 123466999999997775
No 139
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=34.27 E-value=27 Score=33.29 Aligned_cols=27 Identities=33% Similarity=0.835 Sum_probs=20.0
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCccc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFVS 130 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (436)
|-+|+.|+.| |++ +-..|+|.-||+.-
T Consensus 149 ~A~CsrC~~~---L~~---~~~~l~Cp~Cg~tE 175 (188)
T COG1096 149 YARCSRCRAP---LVK---KGNMLKCPNCGNTE 175 (188)
T ss_pred EEEccCCCcc---eEE---cCcEEECCCCCCEE
Confidence 5678888865 665 34588999999863
No 140
>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=33.72 E-value=15 Score=24.74 Aligned_cols=27 Identities=30% Similarity=0.518 Sum_probs=13.1
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCcc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFV 129 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~ 129 (436)
+-.||.|++..|- . ++ ..+.|..||+.
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 141
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.48 E-value=42 Score=30.07 Aligned_cols=42 Identities=24% Similarity=0.301 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhhccccCCCCCCCceEEEecCceeeeeccccCcccccC
Q 013781 85 AKLAGLLENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 85 ~~l~~~l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~ 133 (436)
+.|+..++.+.+ =.-|. ...|.+ ...-....|..||+..++.
T Consensus 42 e~L~fafe~l~~----gt~~e--ga~L~i-~~~p~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 42 EIVEFALNELLK----GTILE--GAEIIF-EEEEAVLKCRNCGNEWSLK 83 (135)
T ss_pred HHHHHHHHHHHc----CCccc--CCEEEE-EecceEEECCCCCCEEecc
Confidence 555555554332 22233 345666 3345678899999887775
No 142
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=32.85 E-value=36 Score=30.03 Aligned_cols=20 Identities=20% Similarity=0.285 Sum_probs=14.8
Q ss_pred HHhhhcccccccCCCCeEEEE
Q 013781 59 FGCELGAQSKFDEKTGTSLVN 79 (436)
Q Consensus 59 ~~~ELg~~~~~~~~~~~~ii~ 79 (436)
|.++.-+.+++-+ +.+++|-
T Consensus 46 FaFev~~egT~ae-ga~l~Ie 65 (115)
T COG0375 46 FAFEVVAEGTIAE-GAELHIE 65 (115)
T ss_pred HHHHHHhccCccc-CCEEEEE
Confidence 6778888888875 6777763
No 143
>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=32.67 E-value=62 Score=28.27 Aligned_cols=65 Identities=15% Similarity=0.164 Sum_probs=44.1
Q ss_pred ceEEEeccCCCce--EEEechHHHHHHhCCCchhHHHHHHhhhcccccccCC---CCeEEEEeccCHHHHHHHHHH
Q 013781 23 MITKIEGRGNGIK--TNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEK---TGTSLVNGSHDTAKLAGLLEN 93 (436)
Q Consensus 23 ~~~k~eG~gng~k--T~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~---~~~~ii~G~~~~~~l~~~l~~ 93 (436)
+.++++ ..||-| |+|.+|.+ .=+-.-+.|.|...+|+.|++-.. ++.+.|+|-|...-.+-|...
T Consensus 28 I~Iri~-qR~grK~VTiI~Gl~~-----~~dlk~l~K~lKkk~~cGGsVk~~~~~~~~IelQGD~re~v~~~L~~~ 97 (110)
T TIGR01160 28 IHIRIQ-QRNGRKTLTTVQGLPK-----EYDLKKIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEFLISQ 97 (110)
T ss_pred EEEEEE-EccCCccEEEEeccCC-----hHHHHHHHHHHHHHhCCCceEEeCCCCCCEEEEeCcHHHHHHHHHHHc
Confidence 567777 445534 66777762 223466889999999999999532 247889999986655544443
No 144
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=32.59 E-value=22 Score=36.53 Aligned_cols=25 Identities=16% Similarity=0.454 Sum_probs=20.7
Q ss_pred eeeeccccCcccccCchhhhhhhhh
Q 013781 119 IQLKCAACGFVSDVDMRDKLNTFIL 143 (436)
Q Consensus 119 ~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (436)
++++|..|++.-.+.+-.|=+.|++
T Consensus 76 F~~kC~~C~~~i~~kTDPkn~dY~~ 100 (324)
T PF04502_consen 76 FYIKCPRCSNEIEFKTDPKNTDYVV 100 (324)
T ss_pred EEEEcCCCCCEEeeecCCCCCCeee
Confidence 5699999999988887777777776
No 145
>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=32.31 E-value=25 Score=29.50 Aligned_cols=33 Identities=24% Similarity=0.380 Sum_probs=15.9
Q ss_pred cccCCCCCCCceEEEecCceeeeeccccCccccc
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
.+||-|.--.-.+.++.+ .-.-+|-+||+.+.+
T Consensus 34 ~~CPfH~d~~pS~~i~~~-k~~~~Cf~Cg~~Gd~ 66 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPD-KNRFKCFGCGKGGDV 66 (97)
T ss_dssp E--SSS--SS--EEEETT-TTEEEETTT--EE-H
T ss_pred EECcCCCCCCCceEEECC-CCeEEECCCCCCCcH
Confidence 679999864446776422 226789999988744
No 146
>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=31.97 E-value=42 Score=23.45 Aligned_cols=29 Identities=21% Similarity=0.419 Sum_probs=18.3
Q ss_pred ccccCCCCCCCceEEEe--cCceeeeecccc
Q 013781 98 YVQCYGCGNPETEIIIT--KTQMIQLKCAAC 126 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~--k~~~~~~~C~aC 126 (436)
.|.||.|.+.+-.+.-- .++.--.+|..|
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 48899999876333321 235556778877
No 147
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=31.59 E-value=12 Score=29.09 Aligned_cols=31 Identities=29% Similarity=0.652 Sum_probs=21.2
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCcccccCch
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMR 135 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~ 135 (436)
+|..|+.-.| + + +.-..+|.-||++-....|
T Consensus 22 iCgdC~~en~---l-k-~~D~irCReCG~RIlyKkR 52 (62)
T KOG3507|consen 22 ICGDCGQENT---L-K-RGDVIRCRECGYRILYKKR 52 (62)
T ss_pred Eecccccccc---c-c-CCCcEehhhcchHHHHHHH
Confidence 6999987554 2 1 2346789999998655544
No 148
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=31.52 E-value=52 Score=38.32 Aligned_cols=34 Identities=15% Similarity=0.427 Sum_probs=25.0
Q ss_pred cccCCCCCCCceEEEecCceeeeeccc---cCcccccC
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAA---CGFVSDVD 133 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~a---CG~~~~v~ 133 (436)
..||.|+.+...+.. .+...|+.|.. |.+..++.
T Consensus 593 ~~CP~Cg~~~L~~k~-gr~G~Fl~Cs~yP~C~~t~~~~ 629 (860)
T PRK06319 593 IDCPKCHKGKLVKIW-AKNRYFYGCSEYPECDYKTSEE 629 (860)
T ss_pred cccCCCCCcceeEEe-cCCCceeeccCCccccccCCcc
Confidence 359999998777665 34446888866 88877765
No 149
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=31.50 E-value=29 Score=35.16 Aligned_cols=39 Identities=31% Similarity=0.639 Sum_probs=24.6
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCccc---ccCchhhhhhh
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFVS---DVDMRDKLNTF 141 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~---~v~~~~kl~~~ 141 (436)
.||.|++. .++.+ -..-...|..||..- .+|...-.-+|
T Consensus 3 ~CpeCg~~--~~~~d-~~~ge~VC~~CG~Vi~~~~id~gpewr~f 44 (285)
T COG1405 3 SCPECGST--NIITD-YERGEIVCADCGLVLEDSLIDPGPEWRAF 44 (285)
T ss_pred CCCCCCCc--cceee-ccCCeEEeccCCEEeccccccCCCCcccc
Confidence 59999998 55552 123367899999873 44444333344
No 150
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=31.23 E-value=36 Score=29.90 Aligned_cols=18 Identities=17% Similarity=0.303 Sum_probs=14.1
Q ss_pred ccccHHHHHHHHHHHhHH
Q 013781 230 TDTSLEAARQRIQEQLSA 247 (436)
Q Consensus 230 ~DtSeeAvkaR~~e~ls~ 247 (436)
...|-..||.|+.+.+..
T Consensus 59 lgiSYPTvR~rLd~ii~~ 76 (113)
T PF09862_consen 59 LGISYPTVRNRLDKIIEK 76 (113)
T ss_pred HCCCcHHHHHHHHHHHHH
Confidence 467889999999886643
No 151
>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=30.82 E-value=59 Score=28.71 Aligned_cols=45 Identities=9% Similarity=0.063 Sum_probs=31.0
Q ss_pred hhHHHHHHh-hhcc--cccccCCCCeEE-EEeccCHHHHHHHHHHHHhh
Q 013781 53 SYTTKYFGC-ELGA--QSKFDEKTGTSL-VNGSHDTAKLAGLLENFIKK 97 (436)
Q Consensus 53 ~~~~ky~~~-ELg~--~~~~~~~~~~~i-i~G~~~~~~l~~~l~~fi~~ 97 (436)
.++..|||. +-+. -.-++.++++|. ..|.++.+.|..-+..|++.
T Consensus 69 ~~~~~~fgl~~~~~P~v~i~~~~~~KY~~~~~~~t~e~i~~Fv~~~l~G 117 (130)
T cd02983 69 LDLEEALNIGGFGYPAMVAINFRKMKFATLKGSFSEDGINEFLRELSYG 117 (130)
T ss_pred HHHHHHcCCCccCCCEEEEEecccCccccccCccCHHHHHHHHHHHHcC
Confidence 347888874 2233 334455445888 88999999998888888764
No 152
>PHA02540 61 DNA primase; Provisional
Probab=30.56 E-value=44 Score=34.70 Aligned_cols=34 Identities=26% Similarity=0.544 Sum_probs=24.4
Q ss_pred cccCCCCCCC-----ceEEEe-cCceeeeeccccCccccc
Q 013781 99 VQCYGCGNPE-----TEIIIT-KTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 99 VlC~~C~~pe-----T~l~~~-k~~~~~~~C~aCG~~~~v 132 (436)
-+||-|+=-. +...+. .++..+-+|-.||+.+.+
T Consensus 28 ~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~Gd~ 67 (337)
T PHA02540 28 FRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYHRPF 67 (337)
T ss_pred ecCCCCCCccccCcCCcEEEeccCCceEEEecCCCCCCCH
Confidence 3799998632 245553 345578899999999976
No 153
>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=30.44 E-value=22 Score=24.40 Aligned_cols=30 Identities=23% Similarity=0.612 Sum_probs=18.5
Q ss_pred ccccCCCCCCCceEEEec----CceeeeeccccCccc
Q 013781 98 YVQCYGCGNPETEIIITK----TQMIQLKCAACGFVS 130 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k----~~~~~~~C~aCG~~~ 130 (436)
.+.||.|+. .+.+.. .......|..||+.-
T Consensus 2 ~~~CP~C~~---~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKT---SFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCC---EEEeCHHHcCCCCCEEECCCCCCEE
Confidence 378999986 222211 112368899999864
No 154
>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=30.10 E-value=1.2e+02 Score=21.13 Aligned_cols=45 Identities=24% Similarity=0.164 Sum_probs=31.5
Q ss_pred chHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHH
Q 013781 40 NMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGL 90 (436)
Q Consensus 40 N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~ 90 (436)
++.++|+.|+-+|..|-.|...-+.. ...+. +++.. |+...|..+
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 47899999999999999998777765 33332 34332 666666654
No 155
>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=30.06 E-value=73 Score=25.48 Aligned_cols=47 Identities=19% Similarity=0.240 Sum_probs=35.1
Q ss_pred chhHHHHHHhhhcccccccCCCCeEEEEeccC----HHHHHHHHHHHHhhc
Q 013781 52 ASYTTKYFGCELGAQSKFDEKTGTSLVNGSHD----TAKLAGLLENFIKKY 98 (436)
Q Consensus 52 p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~----~~~l~~~l~~fi~~y 98 (436)
|..+..-++..-|....+...++.++|.=.-. ...+...++.++++|
T Consensus 15 Pk~i~~~lgl~~Gd~v~v~~~~~~iii~~~~~~~~~~~~~~~~~~~~~~~y 65 (74)
T TIGR02609 15 PKEVLESLGLKEGDTLYVDEEEGGLKLKRFDEGKELEKKMQMAVERAMSKY 65 (74)
T ss_pred CHHHHHHcCcCCCCEEEEEEECCEEEEEECCCCccHHHHHHHHHHHHHHHH
Confidence 77778888888888888877788888875544 456666677777766
No 156
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=29.62 E-value=19 Score=27.08 Aligned_cols=35 Identities=26% Similarity=0.462 Sum_probs=26.6
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCcccccCchhhh
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMRDKL 138 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl 138 (436)
.|..|+..=..+. ..-..+|.-||++-.+.+|++.
T Consensus 8 ~C~~Cg~~~~~~~----~~~~irCp~Cg~rIl~K~R~~~ 42 (49)
T COG1996 8 KCARCGREVELDQ----ETRGIRCPYCGSRILVKERPKV 42 (49)
T ss_pred EhhhcCCeeehhh----ccCceeCCCCCcEEEEeccCCc
Confidence 5899998663333 2457899999999999888765
No 157
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=29.40 E-value=13 Score=37.89 Aligned_cols=43 Identities=21% Similarity=0.481 Sum_probs=30.4
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCcccccCchhhhhhhhh
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMRDKLNTFIL 143 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (436)
++.||.|+..=..=.. ...+..|..||++..+..|.++...+=
T Consensus 38 w~kc~~C~~~~~~~~l---~~~~~vcp~c~~h~rltAreRI~~L~D 80 (296)
T CHL00174 38 WVQCENCYGLNYKKFL---KSKMNICEQCGYHLKMSSSDRIELLID 80 (296)
T ss_pred eeECCCccchhhHHHH---HHcCCCCCCCCCCcCCCHHHHHHHHcc
Confidence 7999999863211111 223589999999999998988876553
No 158
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=29.31 E-value=26 Score=27.67 Aligned_cols=11 Identities=27% Similarity=0.715 Sum_probs=8.0
Q ss_pred ccCCCCCCCce
Q 013781 100 QCYGCGNPETE 110 (436)
Q Consensus 100 lC~~C~~peT~ 110 (436)
+||.|++++++
T Consensus 20 ~CP~Cgs~~~t 30 (64)
T COG2093 20 ICPVCGSTDLT 30 (64)
T ss_pred cCCCCCCcccc
Confidence 48888887765
No 159
>PRK14973 DNA topoisomerase I; Provisional
Probab=29.24 E-value=33 Score=40.29 Aligned_cols=22 Identities=23% Similarity=0.305 Sum_probs=19.9
Q ss_pred HHHHHHHHhhccccchHHHHHH
Q 013781 381 VALVLKALYDSDVLEEEYIVQW 402 (436)
Q Consensus 381 ~~~ILk~LYd~DIleEE~Il~W 402 (436)
=+..|..||-.+|.+-|.+..|
T Consensus 886 ge~t~~~l~~ag~~~~e~l~~~ 907 (936)
T PRK14973 886 GETTLEKLYLAGVYDGDLLVSA 907 (936)
T ss_pred CHHHHHHHHHcCCCCHHHhccC
Confidence 3667899999999999999999
No 160
>smart00400 ZnF_CHCC zinc finger.
Probab=29.10 E-value=53 Score=24.46 Aligned_cols=32 Identities=19% Similarity=0.388 Sum_probs=22.9
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCccccc
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
+||-|.--.-.+.++ .+.-.-.|-+||..+.+
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 599998777777773 33346789999977643
No 161
>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=29.06 E-value=46 Score=29.00 Aligned_cols=36 Identities=22% Similarity=0.558 Sum_probs=18.4
Q ss_pred HHhhccccCCCCCCCceEEEec-----C----ceeeeeccccCcc
Q 013781 94 FIKKYVQCYGCGNPETEIIITK-----T----QMIQLKCAACGFV 129 (436)
Q Consensus 94 fi~~yVlC~~C~~peT~l~~~k-----~----~~~~~~C~aCG~~ 129 (436)
|+-.|+-|..|+.-+-.++.++ + =++...|+.|++.
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 6777999999999997776642 1 1345788888864
No 162
>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=28.73 E-value=46 Score=30.36 Aligned_cols=50 Identities=20% Similarity=0.382 Sum_probs=33.5
Q ss_pred cCHHHHHHHHHHHH-------------hhccccCCCCCCCceEEEec--CceeeeeccccCccccc
Q 013781 82 HDTAKLAGLLENFI-------------KKYVQCYGCGNPETEIIITK--TQMIQLKCAACGFVSDV 132 (436)
Q Consensus 82 ~~~~~l~~~l~~fi-------------~~yVlC~~C~~peT~l~~~k--~~~~~~~C~aCG~~~~v 132 (436)
|...+|+.+|..+- -.||.|+.|+.---.+.. . +...+++|.+|..-+-|
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 45556677777651 258999999876555544 3 24668999999876543
No 163
>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=28.62 E-value=43 Score=33.29 Aligned_cols=57 Identities=14% Similarity=0.423 Sum_probs=28.0
Q ss_pred eccCHHHHHHH-HHHHHhhccccCCCCCCCceEEEecCceeeeeccccCcccccCchh
Q 013781 80 GSHDTAKLAGL-LENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMRD 136 (436)
Q Consensus 80 G~~~~~~l~~~-l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~ 136 (436)
|-++..++..+ -..|+.+-+.||.|++.-..=.-+....--..|.-|+...-+..+.
T Consensus 12 ~YkS~sQ~aRVltE~Wv~~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKSk~ 69 (254)
T PF06044_consen 12 GYKSNSQIARVLTEDWVAENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKSKK 69 (254)
T ss_dssp HTTT-TTHHHHHHHHHHHHH---TTT--SS-EE--------EEE-TTT--EEEEEEEE
T ss_pred hccChhhhhHHHHHHHHHHCCcCCCCCChhHhhccCCCccceeECCCCchHHhhhhhc
Confidence 33444444444 4789999999999999755444434567788999999998887543
No 164
>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=28.55 E-value=23 Score=24.17 Aligned_cols=28 Identities=21% Similarity=0.443 Sum_probs=17.6
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCccccc
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
+|..|+..-. |.. .-.++|.-||++-..
T Consensus 2 ~C~~Cg~~~~-~~~----~~~irC~~CG~RIly 29 (32)
T PF03604_consen 2 ICGECGAEVE-LKP----GDPIRCPECGHRILY 29 (32)
T ss_dssp BESSSSSSE--BST----SSTSSBSSSS-SEEB
T ss_pred CCCcCCCeeE-cCC----CCcEECCcCCCeEEE
Confidence 6899988655 222 224699999987543
No 165
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=28.50 E-value=51 Score=28.19 Aligned_cols=31 Identities=32% Similarity=0.404 Sum_probs=18.2
Q ss_pred cCCCCCCCceEEE-----e-cCce-----eeeeccccCcccc
Q 013781 101 CYGCGNPETEIII-----T-KTQM-----IQLKCAACGFVSD 131 (436)
Q Consensus 101 C~~C~~peT~l~~-----~-k~~~-----~~~~C~aCG~~~~ 131 (436)
||.|++.++.-.+ + ++.. -...|..||..-.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~~ 42 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEELL 42 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEEE
Confidence 9999875543222 1 2221 2468999998643
No 166
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=28.34 E-value=47 Score=22.75 Aligned_cols=30 Identities=23% Similarity=0.411 Sum_probs=21.1
Q ss_pred ccccCCCCCCCceEEEecCceeeeeccccCcccc
Q 013781 98 YVQCYGCGNPETEIIITKTQMIQLKCAACGFVSD 131 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~ 131 (436)
...|+.|+.+- |+..+ .-++.|.-||+..+
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 33112 34788999998754
No 167
>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=27.89 E-value=2.5e+02 Score=25.45 Aligned_cols=27 Identities=26% Similarity=0.306 Sum_probs=22.8
Q ss_pred ChhhHHHHHHHHHHHhhccccchHHHH
Q 013781 374 SSYATKEVALVLKALYDSDVLEEEYIV 400 (436)
Q Consensus 374 ~~~l~~~~~~ILk~LYd~DIleEE~Il 400 (436)
.+.+...|..-|-.||+.++|+..+|.
T Consensus 108 ~~~l~~~f~lHl~~L~d~glLd~~~i~ 134 (140)
T PF09733_consen 108 KPNLRREFLLHLINLWDFGLLDARTID 134 (140)
T ss_pred ChhHHHHHHHHHHHHHHcCCCCHHHHH
Confidence 356777788889999999999999885
No 168
>smart00762 Cog4 COG4 transport protein. This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport.
Probab=27.62 E-value=6.6e+02 Score=25.64 Aligned_cols=61 Identities=5% Similarity=0.136 Sum_probs=41.8
Q ss_pred HHHHHHHHHhhhhhhHHHHHHhhHHHHHHHhcCChHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHhhc
Q 013781 322 MTALFEALFDGVEKGFSKEVVKKKNFLGAAVAEDEGLQLLLLRAIEAFCGKSSSYATKEVALVLKALYDS 391 (436)
Q Consensus 322 ~~vl~eaLf~~v~~~i~k~I~k~~~lL~r~~~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYd~ 391 (436)
..+.|-.+++.++++|+..|..+.+++.++.. +..-..++..||.=|-. ....||..+|+.
T Consensus 76 ~~~~~a~~lt~Lfe~ia~ii~~h~~~I~~~yG--~~~~~~vi~~Lq~E~D~-------q~~~Ild~f~~~ 136 (324)
T smart00762 76 AAVFYADTLTHLFENVATIIEQHQPVIEKYYG--PDGMLYVITKLQKEADL-------QGGIILDTFMDE 136 (324)
T ss_pred ccchHHHHHHHHHHHHHHHHHhccHHHHHHcC--chhHHHHHHHHHHHHHH-------HHHHHHHHHHHH
Confidence 34556666777777999999999999999885 45556677777765532 234456666643
No 169
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.51 E-value=28 Score=37.07 Aligned_cols=36 Identities=17% Similarity=0.477 Sum_probs=26.9
Q ss_pred HHhhccccCCCCCCCceEEEecCceeeeeccccCcccccCc
Q 013781 94 FIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 94 fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
|-..--+||.|+. .|.- +++. ..+|+-||.+.+-..
T Consensus 346 ~~~~~p~Cp~Cg~---~m~S-~G~~-g~rC~kCg~~~~~~~ 381 (421)
T COG1571 346 YERVNPVCPRCGG---RMKS-AGRN-GFRCKKCGTRARETL 381 (421)
T ss_pred eEEcCCCCCccCC---chhh-cCCC-CcccccccccCCccc
Confidence 5555568999984 5554 6666 999999999876653
No 170
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=27.43 E-value=43 Score=24.41 Aligned_cols=31 Identities=29% Similarity=0.553 Sum_probs=21.6
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCcccccCch
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMR 135 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~ 135 (436)
+|..|+.. +.. + ..-.++|.-||++-....|
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 3456899999998665544
No 171
>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=27.42 E-value=36 Score=23.31 Aligned_cols=17 Identities=24% Similarity=0.626 Sum_probs=10.3
Q ss_pred cCceeeeeccccCcccc
Q 013781 115 KTQMIQLKCAACGFVSD 131 (436)
Q Consensus 115 k~~~~~~~C~aCG~~~~ 131 (436)
+.+++..+|.+||....
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 172
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=27.27 E-value=69 Score=21.39 Aligned_cols=18 Identities=39% Similarity=0.416 Sum_probs=16.0
Q ss_pred HHHHHHhhccccchHHHH
Q 013781 383 LVLKALYDSDVLEEEYIV 400 (436)
Q Consensus 383 ~ILk~LYd~DIleEE~Il 400 (436)
..|+.||+.++|+++.+.
T Consensus 6 ~~L~~l~~~G~IseeEy~ 23 (31)
T PF09851_consen 6 EKLKELYDKGEISEEEYE 23 (31)
T ss_pred HHHHHHHHcCCCCHHHHH
Confidence 578999999999999875
No 173
>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=27.11 E-value=70 Score=22.30 Aligned_cols=9 Identities=44% Similarity=0.969 Sum_probs=7.1
Q ss_pred eeccccCcc
Q 013781 121 LKCAACGFV 129 (436)
Q Consensus 121 ~~C~aCG~~ 129 (436)
..|..||..
T Consensus 33 ~~C~~CGE~ 41 (46)
T TIGR03831 33 LVCPQCGEE 41 (46)
T ss_pred cccccCCCE
Confidence 469999975
No 174
>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=27.11 E-value=40 Score=22.37 Aligned_cols=11 Identities=45% Similarity=0.948 Sum_probs=8.9
Q ss_pred HhhhHHHHHhc
Q 013781 418 KNAKPFIEWLQ 428 (436)
Q Consensus 418 k~a~pFI~WLe 428 (436)
..++.||.||.
T Consensus 17 ~aak~fl~~L~ 27 (28)
T PF00123_consen 17 LAAKKFLQWLM 27 (28)
T ss_dssp HHHHHHHHHHC
T ss_pred HHHHHHHHHHh
Confidence 36889999995
No 175
>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=26.95 E-value=42 Score=26.25 Aligned_cols=14 Identities=29% Similarity=0.681 Sum_probs=12.1
Q ss_pred eeeccccCcccccC
Q 013781 120 QLKCAACGFVSDVD 133 (436)
Q Consensus 120 ~~~C~aCG~~~~v~ 133 (436)
.+.|..||...||.
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 78999999988874
No 176
>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=26.82 E-value=56 Score=28.25 Aligned_cols=26 Identities=12% Similarity=-0.023 Sum_probs=13.9
Q ss_pred CchhHHHHHHhhhcccccccCCCCeEEEE
Q 013781 51 PASYTTKYFGCELGAQSKFDEKTGTSLVN 79 (436)
Q Consensus 51 ~p~~~~ky~~~ELg~~~~~~~~~~~~ii~ 79 (436)
.|+.+.-+|. .-+++++-+ +-++.|.
T Consensus 40 ~pe~L~f~f~--~~~~~T~~e-~a~L~Ie 65 (113)
T PF01155_consen 40 EPEALRFAFE--VLAEGTILE-GAELEIE 65 (113)
T ss_dssp -HHHHHHHHH--HHHCCSTTT-T-EEEEE
T ss_pred CHHHHHHHHH--HHhCCCCcc-CCEEEEE
Confidence 4777765554 445555553 5677764
No 177
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=26.81 E-value=49 Score=23.06 Aligned_cols=26 Identities=27% Similarity=0.530 Sum_probs=17.9
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCccc
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFVS 130 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~~ 130 (436)
.|+.|++- .... .++ +..|..||+..
T Consensus 10 ~C~~C~~~--~~~~-~dG--~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSR--WFYS-DDG--FYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCe--EeEc-cCC--EEEhhhCceEc
Confidence 69999998 3332 334 66799999753
No 178
>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=26.57 E-value=50 Score=36.40 Aligned_cols=49 Identities=22% Similarity=0.583 Sum_probs=34.2
Q ss_pred ccccCCCCCCCce----EEEec---CceeeeeccccCcccccCchhhh---hhhhhcCC
Q 013781 98 YVQCYGCGNPETE----IIITK---TQMIQLKCAACGFVSDVDMRDKL---NTFILKNP 146 (436)
Q Consensus 98 yVlC~~C~~peT~----l~~~k---~~~~~~~C~aCG~~~~v~~~~kl---~~~i~k~p 146 (436)
||-||.|+-.-.- |.-++ .....+.|..||..-.-..++.+ ..||-.||
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 9999999984432 33321 35788999999998655444443 56888888
No 179
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=26.35 E-value=1e+02 Score=22.83 Aligned_cols=41 Identities=29% Similarity=0.617 Sum_probs=26.3
Q ss_pred HHHHHHHHhh---ccccC--CCCCCCceEEEe-cCceeeeeccccCcccc
Q 013781 88 AGLLENFIKK---YVQCY--GCGNPETEIIIT-KTQMIQLKCAACGFVSD 131 (436)
Q Consensus 88 ~~~l~~fi~~---yVlC~--~C~~peT~l~~~-k~~~~~~~C~aCG~~~~ 131 (436)
+-+++.||+. +.-|| .|+.. +... ..+...+.|..||...-
T Consensus 5 ~~~~~~~i~~~~~~~~CP~~~C~~~---~~~~~~~~~~~v~C~~C~~~fC 51 (64)
T smart00647 5 RLLLESYVESNPDLKWCPAPDCSAA---IIVTEEEGCNRVTCPKCGFSFC 51 (64)
T ss_pred HHHHHHHHhcCCCccCCCCCCCcce---EEecCCCCCCeeECCCCCCeEC
Confidence 3456677764 78899 99652 2321 12556788988987654
No 180
>PRK00378 nucleoid-associated protein NdpA; Validated
Probab=26.02 E-value=1.4e+02 Score=30.43 Aligned_cols=50 Identities=28% Similarity=0.426 Sum_probs=37.3
Q ss_pred EEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHHHHHh
Q 013781 25 TKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLENFIK 96 (436)
Q Consensus 25 ~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~ 96 (436)
.+.-|+++||...|.. -.||-...||+.++.++|+| .+..|.+.|.++++
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 4656999999988752 12467889999999999999 56666666666653
No 181
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=25.77 E-value=1.5e+02 Score=20.32 Aligned_cols=39 Identities=13% Similarity=0.226 Sum_probs=29.1
Q ss_pred echHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEE
Q 013781 39 VNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLV 78 (436)
Q Consensus 39 ~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii 78 (436)
....+||+.|+-++..+.+++. .|-.++-+....+.|.|
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 6789999999999999988875 46666666544456655
No 182
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=25.67 E-value=3e+02 Score=28.94 Aligned_cols=72 Identities=21% Similarity=0.074 Sum_probs=44.6
Q ss_pred HHHHHHHhcCCChHHHHHHHHHHHHhhhhhhHHHHHHhhHHHHHHHhcCChHHHHHHHHHHHHHHhcCChhhHHHHHHHH
Q 013781 306 QLQTILGSLSGSAQEKMTALFEALFDGVEKGFSKEVVKKKNFLGAAVAEDEGLQLLLLRAIEAFCGKSSSYATKEVALVL 385 (436)
Q Consensus 306 ei~~~~~~l~ls~~~~~~vl~eaLf~~v~~~i~k~I~k~~~lL~r~~~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~IL 385 (436)
|+..-+.+++....+.+...|-+||+. ++ .+|..|.. -.+.|-+.+.+|-.|-.-+.|.+-..|+.+|
T Consensus 367 elV~~Lr~lqfd~~efvclkFl~LFsl---d~--------kfLenf~l-v~~~qe~~naaLldyt~c~yp~~~~kF~qll 434 (475)
T KOG4218|consen 367 ELVIRLRNLQFDNFEFVCLKFLALFSL---DM--------KFLENFEL-VRRLQEDSNAALLDYTSCCYPNWEQKFPQLL 434 (475)
T ss_pred HHHHHHHhcCCccchhhHHHHHHHHhh---hH--------HHHHHHHH-HHHHHHHHHHHHHHhhccCCccHHHHHHHHH
Confidence 445555566665556666667777774 11 24444444 3466667777777775555677777888877
Q ss_pred HHHh
Q 013781 386 KALY 389 (436)
Q Consensus 386 k~LY 389 (436)
..|-
T Consensus 435 L~L~ 438 (475)
T KOG4218|consen 435 LVLE 438 (475)
T ss_pred HHHH
Confidence 6663
No 183
>KOG1824 consensus TATA-binding protein-interacting protein [General function prediction only]
Probab=25.54 E-value=3.5e+02 Score=32.22 Aligned_cols=52 Identities=17% Similarity=0.261 Sum_probs=35.8
Q ss_pred HHHHHHhhHHHHHHHhc----CChHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHH
Q 013781 337 FSKEVVKKKNFLGAAVA----EDEGLQLLLLRAIEAFCGKSSSYATKEVALVLKAL 388 (436)
Q Consensus 337 i~k~I~k~~~lL~r~~~----~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~L 388 (436)
+-..+.+--+++..||+ ++...--++|.|+|.|+.....+..|..|-|+..+
T Consensus 248 ~~~h~~~ivp~v~~y~~~~e~~dDELrE~~lQale~fl~rcp~ei~p~~pei~~l~ 303 (1233)
T KOG1824|consen 248 FGSHLDKIVPLVADYCNKIEEDDDELREYCLQALESFLRRCPKEILPHVPEIINLC 303 (1233)
T ss_pred hhcccchhhHHHHHHhcccccCcHHHHHHHHHHHHHHHHhChhhhcccchHHHHHH
Confidence 44455566688889994 12334459999999999876666777777776654
No 184
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=25.45 E-value=44 Score=34.04 Aligned_cols=41 Identities=22% Similarity=0.508 Sum_probs=31.0
Q ss_pred ccCCCCCCCceEEEecCceeeeeccccCcc---cccCchhhhhhh
Q 013781 100 QCYGCGNPETEIIITKTQMIQLKCAACGFV---SDVDMRDKLNTF 141 (436)
Q Consensus 100 lC~~C~~peT~l~~~k~~~~~~~C~aCG~~---~~v~~~~kl~~~ 141 (436)
.|+.|+.+--.++. +-+.-...|-.||-. +.++.+|-.=||
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 788888877777
No 185
>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=25.37 E-value=30 Score=26.26 Aligned_cols=16 Identities=38% Similarity=0.694 Sum_probs=12.5
Q ss_pred eeeeeccccCcccccC
Q 013781 118 MIQLKCAACGFVSDVD 133 (436)
Q Consensus 118 ~~~~~C~aCG~~~~v~ 133 (436)
.-.++|.|||..+.--
T Consensus 34 ~~al~CaACgCHRnFH 49 (53)
T TIGR01566 34 PESLTCAACGCHRNFH 49 (53)
T ss_pred CcceeeeecCcccccc
Confidence 3479999999987643
No 186
>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=25.37 E-value=48 Score=25.29 Aligned_cols=24 Identities=29% Similarity=0.840 Sum_probs=17.6
Q ss_pred hhccccCCCCCCCceEEEecCceeeeeccccCc
Q 013781 96 KKYVQCYGCGNPETEIIITKTQMIQLKCAACGF 128 (436)
Q Consensus 96 ~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~ 128 (436)
-.+|.|+.|+.+ .+-...|..||.
T Consensus 24 p~l~~C~~cG~~---------~~~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEF---------KLPHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCc---------ccCeeECCccCe
Confidence 456889999974 244677888885
No 187
>PRK09019 translation initiation factor Sui1; Validated
Probab=25.35 E-value=1.4e+02 Score=26.08 Aligned_cols=56 Identities=11% Similarity=0.012 Sum_probs=38.1
Q ss_pred EeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHH
Q 013781 27 IEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLA 88 (436)
Q Consensus 27 ~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~ 88 (436)
..||+.=.=|+|..|..-... -.-+.|+|-..+|+-+++- ++.+.|+|.|...-.+
T Consensus 39 r~gRkGK~VTiI~Gl~~~~~d----lk~l~K~lKkk~gcGGtvk--~~~IelQGD~r~~v~~ 94 (108)
T PRK09019 39 TSGRKGKGVCLITGLDLDDAE----LKKLAAELKKKCGCGGAVK--DGVIEIQGDKRDLLKS 94 (108)
T ss_pred cCCCCCCeEEEEeCCcCCHHH----HHHHHHHHHHHhcCCCeEE--cCEEEEcCcHHHHHHH
Confidence 344432245778887511111 3568899999999999995 6899999999755433
No 188
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=24.93 E-value=69 Score=27.81 Aligned_cols=34 Identities=18% Similarity=0.515 Sum_probs=24.7
Q ss_pred ccCCCCC---CCceEEEe-cCceeeeeccccCcccccC
Q 013781 100 QCYGCGN---PETEIIIT-KTQMIQLKCAACGFVSDVD 133 (436)
Q Consensus 100 lC~~C~~---peT~l~~~-k~~~~~~~C~aCG~~~~v~ 133 (436)
.|+.|.+ |--...+. +++.+...|.-||...-.+
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 5999999 44444432 5566899999999986554
No 189
>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=24.55 E-value=2.8e+02 Score=22.93 Aligned_cols=65 Identities=23% Similarity=0.247 Sum_probs=45.3
Q ss_pred ceEEEeccCCCceEEEechHHHHHHhCCCchhHHHHHHhhhc--ccccccCCCCeEEEEeccCHHHHHHHH
Q 013781 23 MITKIEGRGNGIKTNIVNMVDIAKALARPASYTTKYFGCELG--AQSKFDEKTGTSLVNGSHDTAKLAGLL 91 (436)
Q Consensus 23 ~~~k~eG~gng~kT~i~N~~~ia~~L~R~p~~~~ky~~~ELg--~~~~~~~~~~~~ii~G~~~~~~l~~~l 91 (436)
+-.++...||-.-|+|.++.==..+|. +.|.+||+...+ -.+.+.+-.+.++|+|.|. ..+...|
T Consensus 16 VY~~~k~~g~~~~T~IrkI~GD~~aL~---~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~~-~~Vk~wL 82 (87)
T PF05046_consen 16 VYLDIKNGGNRKITVIRKIEGDIWALK---KDLRKFLGEKPKKKIDVRVNELTGHIEIKGDHV-EEVKKWL 82 (87)
T ss_pred EEEEEeCCCcEeEEEEEeecCCHHHHH---HHHHHHhhhhcCCCcceEEeecCCEEEEcCccH-HHHHHHH
Confidence 566777778889999998864444453 346677776666 4566777789999999994 3444433
No 190
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=24.48 E-value=46 Score=27.76 Aligned_cols=15 Identities=27% Similarity=0.802 Sum_probs=12.6
Q ss_pred CceeeeeccccCccc
Q 013781 116 TQMIQLKCAACGFVS 130 (436)
Q Consensus 116 ~~~~~~~C~aCG~~~ 130 (436)
++.+.|+|.+||.++
T Consensus 84 ~~vVsL~C~~CG~r~ 98 (98)
T PF15494_consen 84 GSVVSLQCSDCGKRT 98 (98)
T ss_pred CCEEEEECcccCCcC
Confidence 478899999999874
No 191
>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=24.32 E-value=39 Score=26.91 Aligned_cols=39 Identities=13% Similarity=0.377 Sum_probs=26.4
Q ss_pred ccCCCCCCCceEEEe---cCceeeeeccccCcccccCchhhh
Q 013781 100 QCYGCGNPETEIIIT---KTQMIQLKCAACGFVSDVDMRDKL 138 (436)
Q Consensus 100 lC~~C~~peT~l~~~---k~~~~~~~C~aCG~~~~v~~~~kl 138 (436)
.|..|+...+..+-. .+++.+.+|..|....-+.-+-++
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 599999988888863 369999999999988776554444
No 192
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=24.31 E-value=1.7e+02 Score=20.91 Aligned_cols=25 Identities=24% Similarity=0.313 Sum_probs=22.7
Q ss_pred EEechHHHHHHhCCCchhHHHHHHh
Q 013781 37 NIVNMVDIAKALARPASYTTKYFGC 61 (436)
Q Consensus 37 ~i~N~~~ia~~L~R~p~~~~ky~~~ 61 (436)
.+..+.+.|+.|+.++.++.+++--
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHhC
Confidence 6899999999999999999998754
No 193
>PHA02942 putative transposase; Provisional
Probab=24.20 E-value=35 Score=35.85 Aligned_cols=31 Identities=35% Similarity=0.870 Sum_probs=21.4
Q ss_pred cccCCCCCCCceEEEecCceeeeeccccCcccccCc
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
-.||.|+.....+ .++ ...|..||+...-|.
T Consensus 326 q~Cs~CG~~~~~l---~~r--~f~C~~CG~~~drD~ 356 (383)
T PHA02942 326 VSCPKCGHKMVEI---AHR--YFHCPSCGYENDRDV 356 (383)
T ss_pred ccCCCCCCccCcC---CCC--EEECCCCCCEeCcHH
Confidence 4699999865432 223 578999999876553
No 194
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.07 E-value=97 Score=27.64 Aligned_cols=47 Identities=21% Similarity=0.393 Sum_probs=31.3
Q ss_pred HHHhhccccCCCCCCCceEEEec--CceeeeeccccCcccccCchhhhhh
Q 013781 93 NFIKKYVQCYGCGNPETEIIITK--TQMIQLKCAACGFVSDVDMRDKLNT 140 (436)
Q Consensus 93 ~fi~~yVlC~~C~~peT~l~~~k--~~~~~~~C~aCG~~~~v~~~~kl~~ 140 (436)
++...-+-||-|++.. ...... .+.---+|+.||....+.....++.
T Consensus 25 ~~~~~~~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~~~~~~~~ 73 (129)
T COG3677 25 RMQITKVNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVETGSPLSK 73 (129)
T ss_pred hhhcccCcCCCCCccc-eeeECCccccccccccCCcCcceeeeccCcccc
Confidence 3344458999999998 444421 1345578999999998875444433
No 195
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=24.03 E-value=1.3e+02 Score=23.63 Aligned_cols=42 Identities=24% Similarity=0.223 Sum_probs=36.0
Q ss_pred chhHHHHHHhhhc-ccccccCCCCeEEEEeccCHHHHHHHHHH
Q 013781 52 ASYTTKYFGCELG-AQSKFDEKTGTSLVNGSHDTAKLAGLLEN 93 (436)
Q Consensus 52 p~~~~ky~~~ELg-~~~~~~~~~~~~ii~G~~~~~~l~~~l~~ 93 (436)
..++.+.|..--| -...+|.++.+.++.|.+++..|...|.+
T Consensus 19 ~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k 61 (73)
T KOG1603|consen 19 ARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKK 61 (73)
T ss_pred HHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHh
Confidence 3478888888888 56778988999999999999999998887
No 196
>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=24.01 E-value=54 Score=27.63 Aligned_cols=24 Identities=13% Similarity=0.419 Sum_probs=14.0
Q ss_pred ceeeeeccccCccccc-Cchhhhhh
Q 013781 117 QMIQLKCAACGFVSDV-DMRDKLNT 140 (436)
Q Consensus 117 ~~~~~~C~aCG~~~~v-~~~~kl~~ 140 (436)
.+-.+.|.-||..-.- +..+++-.
T Consensus 32 nVPa~~C~~CGe~y~~dev~~eIE~ 56 (89)
T TIGR03829 32 ETPSISCSHCGMEYQDDTTVKEIED 56 (89)
T ss_pred cCCcccccCCCcEeecHHHHHHHHh
Confidence 3445789999987433 23344433
No 197
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=23.88 E-value=64 Score=33.29 Aligned_cols=24 Identities=38% Similarity=0.710 Sum_probs=18.5
Q ss_pred HHHHHHHhhccccCCCCCCCceEEE
Q 013781 89 GLLENFIKKYVQCYGCGNPETEIII 113 (436)
Q Consensus 89 ~~l~~fi~~yVlC~~C~~peT~l~~ 113 (436)
..+-.++.+|-.||.|++| |....
T Consensus 141 rs~l~W~skykFCp~CG~~-tkp~e 164 (345)
T KOG3084|consen 141 RSLLDWVSKYKFCPGCGSP-TKPEE 164 (345)
T ss_pred HHHHHHHHHhccCcccCCC-ccccc
Confidence 4566789999999999998 34443
No 198
>PF08318 COG4: COG4 transport protein; InterPro: IPR013167 This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport [].
Probab=23.50 E-value=6.9e+02 Score=25.50 Aligned_cols=72 Identities=8% Similarity=0.274 Sum_probs=47.6
Q ss_pred HHHHHHHHhhhhhhHHHHHHhhHHHHHHHhcCChHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHhhccccch--HHHH
Q 013781 323 TALFEALFDGVEKGFSKEVVKKKNFLGAAVAEDEGLQLLLLRAIEAFCGKSSSYATKEVALVLKALYDSDVLEE--EYIV 400 (436)
Q Consensus 323 ~vl~eaLf~~v~~~i~k~I~k~~~lL~r~~~~~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LYd~DIleE--E~Il 400 (436)
.+.|-.+++.+++.|+..|..+.+++.++.. +..-..++..||.-|-. ....||..+++.==|+. -.|.
T Consensus 77 ~~~~~~~lt~LFe~ia~ii~~h~~lI~~~yG--~~~~~~vi~~Lq~E~D~-------q~~~Ild~f~~~R~l~~~~~~i~ 147 (331)
T PF08318_consen 77 PVFYADALTKLFEHIATIIEQHQPLIEKYYG--PGYMVYVIEKLQKECDL-------QAGIILDTFMDERRLDRKLQDIQ 147 (331)
T ss_pred cccHHHHHHHHHHHHHHHHHHccHHHHHHcC--CcHHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcHHHHHHHHH
Confidence 3456666666777889999999999999885 34456777777776632 34457777776543322 2455
Q ss_pred HHh
Q 013781 401 QWY 403 (436)
Q Consensus 401 ~W~ 403 (436)
.|-
T Consensus 148 ~~~ 150 (331)
T PF08318_consen 148 SYN 150 (331)
T ss_pred hhh
Confidence 555
No 199
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=23.50 E-value=74 Score=24.12 Aligned_cols=34 Identities=29% Similarity=0.484 Sum_probs=25.7
Q ss_pred cccCCCCCCCceEEEe--cCceeeeeccccCccccc
Q 013781 99 VQCYGCGNPETEIIIT--KTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 99 VlC~~C~~peT~l~~~--k~~~~~~~C~aCG~~~~v 132 (436)
|.||-|+-+-+.++=. .++.++-.|..|...-.+
T Consensus 1 i~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~ 36 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEV 36 (52)
T ss_pred CCCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEE
Confidence 5799999986665532 457899999999876544
No 200
>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=23.19 E-value=41 Score=23.73 Aligned_cols=33 Identities=21% Similarity=0.411 Sum_probs=17.6
Q ss_pred cccCCCCC---CCceEEEecCceeeeeccccCcccccCc
Q 013781 99 VQCYGCGN---PETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 99 VlC~~C~~---peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
|.|..|+. |=..+.. .++ .-.|.-||...+++.
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 67899986 5555554 333 578999999988864
No 201
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.18 E-value=1.8e+02 Score=21.81 Aligned_cols=46 Identities=17% Similarity=0.064 Sum_probs=31.3
Q ss_pred chHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHH
Q 013781 40 NMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGL 90 (436)
Q Consensus 40 N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~ 90 (436)
++.++|+.++.+|..+..|...-+-.+..-++ +|+. .|+...|..+
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 47899999999999999997755544431232 4433 3666766654
No 202
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=22.77 E-value=38 Score=24.43 Aligned_cols=27 Identities=22% Similarity=0.456 Sum_probs=16.3
Q ss_pred eeccccCcccccCc--hhhhhhhhhcCCC
Q 013781 121 LKCAACGFVSDVDM--RDKLNTFILKNPP 147 (436)
Q Consensus 121 ~~C~aCG~~~~v~~--~~kl~~~i~k~pp 147 (436)
++|.+||+.+.... +=.|..+-.-.||
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~~~~a~~p 30 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYCWSGALAP 30 (40)
T ss_pred ccccccccccccccCccCCCCCCCCCCCC
Confidence 58999999877653 2334444433343
No 203
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=22.74 E-value=47 Score=36.61 Aligned_cols=53 Identities=17% Similarity=0.393 Sum_probs=30.7
Q ss_pred ccCHHHHHHHHHHHHh-----------hccccCCCCCCCceEEEecCceeeeeccccCcccccCchhhhhhhhh
Q 013781 81 SHDTAKLAGLLENFIK-----------KYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMRDKLNTFIL 143 (436)
Q Consensus 81 ~~~~~~l~~~l~~fi~-----------~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (436)
+++++.|.++++.=.+ .+-.|+.|+.-. +. .-.|..||.+. ++.-.+.+.|+-
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 4578888888888666 245799999622 12 67799999987 777789999988
No 204
>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=22.49 E-value=1.7e+02 Score=24.47 Aligned_cols=48 Identities=19% Similarity=0.099 Sum_probs=34.9
Q ss_pred chHHHHHHhCCCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHH
Q 013781 40 NMVDIAKALARPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLE 92 (436)
Q Consensus 40 N~~~ia~~L~R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~ 92 (436)
++.++|+.++-+|..+-.|....+..+...++ +|+- .|+...|..+..
T Consensus 2 ti~eva~~~gvs~~tlR~ye~~Gll~~~~~~~-~g~R----~y~~~di~~l~~ 49 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTE-NGYR----LYTEEDLERLQQ 49 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCccCC-CCce----eeCHHHHHHHHH
Confidence 57899999999999999998877765554443 3422 378888776643
No 205
>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=22.42 E-value=39 Score=33.50 Aligned_cols=39 Identities=28% Similarity=0.610 Sum_probs=22.6
Q ss_pred HHhh-ccccCCCCCCCceEEEecCceeeeeccccCccccc
Q 013781 94 FIKK-YVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 94 fi~~-yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
|+.- -..|+.|.+|+|......-.....+|..||.--.+
T Consensus 20 f~~gc~~~C~~c~~p~~~~~~~~~~~~~~~C~~C~~C~~~ 59 (295)
T TIGR02494 20 FLKGCPLRCKWCSNPESQRKSPELLFKENRCLGCGKCVEV 59 (295)
T ss_pred HhhcCCccCcccCCccccCCCceEEEccccCCCCchhhhh
Confidence 6666 58899999999764320001112466666654333
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=22.16 E-value=61 Score=32.87 Aligned_cols=56 Identities=18% Similarity=0.217 Sum_probs=39.1
Q ss_pred CCchhHHHHHHhhhcccccccCCCCeEEEEeccCHHHHHHHHHHHHhh------ccccCCCCCC-CceE
Q 013781 50 RPASYTTKYFGCELGAQSKFDEKTGTSLVNGSHDTAKLAGLLENFIKK------YVQCYGCGNP-ETEI 111 (436)
Q Consensus 50 R~p~~~~ky~~~ELg~~~~~~~~~~~~ii~G~~~~~~l~~~l~~fi~~------yVlC~~C~~p-eT~l 111 (436)
-+.....+.|+.....+|++|+ . + +.| +.+.+++...+.|+. |++.+.|+-| +|-+
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--A-V-LYA--PEEALEEKVEKILEAFGGKSRYIFNLGHGILPDTPP 326 (338)
T ss_pred CCHHHHHHHhCCCeeEEeCCCh--H-H-hcC--CHHHHHHHHHHHHHHhccCCCceecCCCcCCCCcCH
Confidence 3445566666666778888875 2 3 366 677787777777764 8999999975 6653
No 207
>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=22.09 E-value=47 Score=31.80 Aligned_cols=31 Identities=29% Similarity=0.681 Sum_probs=23.7
Q ss_pred ccCCCCCCCceEEEe--cCceeeeeccccCccc
Q 013781 100 QCYGCGNPETEIIIT--KTQMIQLKCAACGFVS 130 (436)
Q Consensus 100 lC~~C~~peT~l~~~--k~~~~~~~C~aCG~~~ 130 (436)
.|-+|+.|=..|-+. .+..-..+|..||+.-
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 599999997766664 3456679999999653
No 208
>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=22.09 E-value=42 Score=32.69 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=27.0
Q ss_pred cccCCCCCCCceEEEecCceeeeeccccCccccc
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
-+|+.|---++.|..-.+++....|.-||+...-
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 4888888888888653567889999999997554
No 209
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=21.99 E-value=74 Score=37.56 Aligned_cols=46 Identities=24% Similarity=0.405 Sum_probs=29.0
Q ss_pred ccCHHHHHHHHHHHHhhccccCCCCCCCceEEEecCceeeeeccccCccccc
Q 013781 81 SHDTAKLAGLLENFIKKYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDV 132 (436)
Q Consensus 81 ~~~~~~l~~~l~~fi~~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v 132 (436)
.|+...+.....++--.--+|+.|+ |.++. + --...|..||.++..
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 3444444444455544556777775 77766 2 247789999998753
No 210
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=21.93 E-value=44 Score=26.51 Aligned_cols=38 Identities=18% Similarity=0.453 Sum_probs=22.9
Q ss_pred hccccCCCCCCCceEEEecCceeeeeccccCcccccCchhhhhhhhhcCCC
Q 013781 97 KYVQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDMRDKLNTFILKNPP 147 (436)
Q Consensus 97 ~yVlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~k~pp 147 (436)
.|.-|..|+..-+ . . .|..||.. +....+..+|+=--|
T Consensus 4 ~~~AC~~C~~i~~-----~-~----~Cp~Cgs~---~~S~~w~G~v~i~dP 41 (64)
T PRK06393 4 QYRACKKCKRLTP-----E-K----TCPVHGDE---KTTTEWFGFLIITEP 41 (64)
T ss_pred hhhhHhhCCcccC-----C-C----cCCCCCCC---cCCcCcceEEEEECC
Confidence 4667888886431 1 1 78888886 334556666554444
No 211
>smart00070 GLUCA Glucagon like hormones.
Probab=21.17 E-value=58 Score=21.41 Aligned_cols=11 Identities=45% Similarity=0.948 Sum_probs=8.6
Q ss_pred HhhhHHHHHhc
Q 013781 418 KNAKPFIEWLQ 428 (436)
Q Consensus 418 k~a~pFI~WLe 428 (436)
..|+.||.||.
T Consensus 17 ~~ar~fl~~L~ 27 (27)
T smart00070 17 LAAKKFLQWLM 27 (27)
T ss_pred HHHHHHHHHhC
Confidence 35889999983
No 212
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=21.07 E-value=77 Score=31.66 Aligned_cols=39 Identities=31% Similarity=0.558 Sum_probs=30.1
Q ss_pred ccccCCCCCCCceEEEe-cCceeeeeccccCcccccCchhhhhhhhhcCCCccc
Q 013781 98 YVQCYGCGNPETEIIIT-KTQMIQLKCAACGFVSDVDMRDKLNTFILKNPPESK 150 (436)
Q Consensus 98 yVlC~~C~~peT~l~~~-k~~~~~~~C~aCG~~~~v~~~~kl~~~i~k~pp~~~ 150 (436)
.|.|..|++. |.+. +......+|..|...+++. |||..|
T Consensus 65 ~v~CrVCq~~---I~i~gk~~QhVVkC~~CnEATPIr-----------~aPpGK 104 (256)
T PF09788_consen 65 VVTCRVCQSL---IDIEGKMHQHVVKCSVCNEATPIR-----------NAPPGK 104 (256)
T ss_pred eEEeecCCce---ecccCccceeeEECCCCCcccccc-----------CCCCCC
Confidence 5899999873 3343 5577899999999999865 888644
No 213
>PRK07220 DNA topoisomerase I; Validated
Probab=21.03 E-value=66 Score=36.77 Aligned_cols=30 Identities=27% Similarity=0.472 Sum_probs=18.5
Q ss_pred cccCCCCCCCceEEEecCceeeeeccccCc
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAACGF 128 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~ 128 (436)
..||.|+.|...+...+++.+++.|..|.+
T Consensus 636 ~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~ 665 (740)
T PRK07220 636 KVCEAHGLNHIRIINGGKRPWDLGCPQCNF 665 (740)
T ss_pred CCCCCCCCceEEEEecCCccceeeCCCCCC
Confidence 369999887554443122345678877765
No 214
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=20.97 E-value=93 Score=25.17 Aligned_cols=32 Identities=16% Similarity=0.309 Sum_probs=22.6
Q ss_pred ccCCCCCCCceEEEec-----Cceeeeecc--ccCccccc
Q 013781 100 QCYGCGNPETEIIITK-----TQMIQLKCA--ACGFVSDV 132 (436)
Q Consensus 100 lC~~C~~peT~l~~~k-----~~~~~~~C~--aCG~~~~v 132 (436)
.||.|+.+. .+.... -+..+..|. .||++...
T Consensus 3 ~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 3 HCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATFIT 41 (72)
T ss_pred cCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEEEE
Confidence 599999999 333311 145678998 99998654
No 215
>KOG2989 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.64 E-value=45 Score=33.04 Aligned_cols=45 Identities=24% Similarity=0.430 Sum_probs=33.7
Q ss_pred ccccCCCCCC----------------CceEEEecCceeeeeccccCcccccCchhhhhhhhh
Q 013781 98 YVQCYGCGNP----------------ETEIIITKTQMIQLKCAACGFVSDVDMRDKLNTFIL 143 (436)
Q Consensus 98 yVlC~~C~~p----------------eT~l~~~k~~~~~~~C~aCG~~~~v~~~~kl~~~i~ 143 (436)
-+.|.+|++. +|.|-+ +--.++.+|.-|++.-+..+-.+=+.|++
T Consensus 40 ~~rC~tCgeyi~kg~kfN~r~E~~~~e~yLgi-ki~Rf~i~Ct~cl~el~~rTDp~N~dY~~ 100 (253)
T KOG2989|consen 40 RLRCNTCGEYIYKGKKFNAREEDVIEETYLGI-KIFRFYIKCTRCLRELSFRTDPKNSDYVI 100 (253)
T ss_pred eeecccccchhhcCCCcchhHHhhhccccccc-eeeeeeeeccchHhhhhhhcCCcchHHHH
Confidence 4678888874 455555 55678899999999888877667677776
No 216
>PRK02935 hypothetical protein; Provisional
Probab=20.35 E-value=63 Score=28.15 Aligned_cols=30 Identities=23% Similarity=0.419 Sum_probs=20.9
Q ss_pred cccCCCCCCCceEEEecCceeeeeccccCcccccCc
Q 013781 99 VQCYGCGNPETEIIITKTQMIQLKCAACGFVSDVDM 134 (436)
Q Consensus 99 VlC~~C~~peT~l~~~k~~~~~~~C~aCG~~~~v~~ 134 (436)
|.||+|+.|---|-+ .-.|--|+..=++|+
T Consensus 71 V~CP~C~K~TKmLGr------vD~CM~C~~PLTLd~ 100 (110)
T PRK02935 71 VICPSCEKPTKMLGR------VDACMHCNQPLTLDR 100 (110)
T ss_pred eECCCCCchhhhccc------eeecCcCCCcCCcCc
Confidence 799999987433333 236888888777764
No 217
>PF08064 UME: UME (NUC010) domain; InterPro: IPR012993 This domain is characteristic of UVSB PI-3 kinase, MEI-41 and ESR1 [].; GO: 0004674 protein serine/threonine kinase activity
Probab=20.31 E-value=5.2e+02 Score=21.93 Aligned_cols=50 Identities=20% Similarity=0.185 Sum_probs=34.7
Q ss_pred ChHHHHHHHHHHHHHHhcCChhhHHHHHHHHHHHh---hccccchHHHHHHhh
Q 013781 355 DEGLQLLLLRAIEAFCGKSSSYATKEVALVLKALY---DSDVLEEEYIVQWYQ 404 (436)
Q Consensus 355 ~~~~Q~~lL~alE~~~~~~~~~l~~~~~~ILk~LY---d~DIleEE~Il~W~~ 404 (436)
+...++..|.+|+.++....+.+....|+|.-.|. +.+=+.+.++-.|..
T Consensus 28 ~~~ek~~~l~si~~lI~~~~~~i~~~~pQI~a~L~sal~~~~l~~~al~~W~~ 80 (107)
T PF08064_consen 28 PIPEKKRALRSIEELIKLGGSHISSARPQIMACLQSALEIPELREEALSCWNC 80 (107)
T ss_pred CHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhCChhhHHHHHHHHHH
Confidence 44567789999999887544444445555544444 677788889999984
Done!