Query psy836
Match_columns 122
No_of_seqs 128 out of 296
Neff 3.4
Searched_HMMs 46136
Date Fri Aug 16 16:40:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy836.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/836hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0402|consensus 100.0 2.8E-46 6.1E-51 266.3 6.0 92 6-122 1-92 (92)
2 PF01780 Ribosomal_L37ae: Ribo 100.0 1.4E-45 3E-50 262.5 8.2 90 7-121 1-90 (90)
3 PTZ00255 60S ribosomal protein 100.0 2E-45 4.3E-50 261.7 8.8 90 6-120 1-90 (90)
4 TIGR00280 L37a ribosomal prote 100.0 4.8E-45 1E-49 260.2 9.3 91 6-122 1-91 (91)
5 PRK03976 rpl37ae 50S ribosomal 100.0 1.5E-44 3.3E-49 257.2 8.7 89 6-119 1-89 (90)
6 COG1997 RPL43A Ribosomal prote 100.0 2.6E-38 5.6E-43 225.2 7.4 88 6-119 1-88 (89)
7 PRK03976 rpl37ae 50S ribosomal 97.2 4E-05 8.7E-10 55.1 -1.2 25 65-89 60-84 (90)
8 TIGR00280 L37a ribosomal prote 97.2 3.6E-05 7.7E-10 55.5 -1.6 25 65-89 59-83 (91)
9 PTZ00255 60S ribosomal protein 97.2 4.1E-05 8.9E-10 55.0 -1.5 25 65-89 60-84 (90)
10 PF01780 Ribosomal_L37ae: Ribo 97.2 3E-05 6.6E-10 55.7 -2.3 27 63-89 57-83 (90)
11 KOG0402|consensus 96.8 0.00019 4.1E-09 52.0 -1.4 25 65-89 60-84 (92)
12 PF12760 Zn_Tnp_IS1595: Transp 95.8 0.007 1.5E-07 37.4 2.1 27 41-67 18-45 (46)
13 TIGR03655 anti_R_Lar restricti 94.7 0.027 5.9E-07 35.7 2.3 25 43-67 3-34 (53)
14 PRK00398 rpoP DNA-directed RNA 94.4 0.023 5.1E-07 34.9 1.4 29 40-68 2-30 (46)
15 PF08271 TF_Zn_Ribbon: TFIIB z 94.3 0.028 6.1E-07 34.1 1.6 33 42-74 1-34 (43)
16 PRK00432 30S ribosomal protein 93.9 0.028 6E-07 36.1 1.1 26 42-68 21-46 (50)
17 PHA00626 hypothetical protein 93.1 0.055 1.2E-06 36.6 1.5 33 43-75 2-39 (59)
18 PF07282 OrfB_Zn_ribbon: Putat 93.1 0.063 1.4E-06 34.6 1.8 28 41-68 28-55 (69)
19 PRK00464 nrdR transcriptional 92.2 0.091 2E-06 40.5 1.9 24 42-69 1-38 (154)
20 PF14354 Lar_restr_allev: Rest 91.8 0.037 8E-07 35.1 -0.5 15 42-56 4-18 (61)
21 PF08273 Prim_Zn_Ribbon: Zinc- 91.7 0.12 2.7E-06 32.0 1.7 30 42-72 4-38 (40)
22 COG4888 Uncharacterized Zn rib 91.5 0.073 1.6E-06 39.5 0.7 25 28-52 9-33 (104)
23 COG1997 RPL43A Ribosomal prote 91.4 0.022 4.9E-07 41.2 -2.1 22 65-86 59-80 (89)
24 PRK04023 DNA polymerase II lar 90.8 0.16 3.4E-06 49.6 2.4 67 39-119 624-697 (1121)
25 smart00661 RPOL9 RNA polymeras 90.4 0.23 5E-06 30.2 2.1 32 43-74 2-35 (52)
26 COG0675 Transposase and inacti 90.3 0.17 3.7E-06 38.9 1.7 22 42-68 310-331 (364)
27 PRK09710 lar restriction allev 88.5 0.12 2.7E-06 35.3 -0.2 19 43-61 8-26 (64)
28 COG1998 RPS31 Ribosomal protei 88.5 0.22 4.9E-06 32.9 1.0 30 39-68 17-46 (51)
29 COG2956 Predicted N-acetylgluc 88.3 0.52 1.1E-05 41.6 3.4 37 26-67 340-376 (389)
30 PF08646 Rep_fac-A_C: Replicat 87.8 0.61 1.3E-05 34.0 3.1 33 43-76 20-54 (146)
31 PF11781 RRN7: RNA polymerase 87.8 0.3 6.4E-06 29.5 1.2 27 41-68 8-34 (36)
32 PRK14892 putative transcriptio 87.5 0.17 3.7E-06 36.7 -0.0 34 33-67 13-50 (99)
33 PRK14890 putative Zn-ribbon RN 87.2 0.34 7.4E-06 32.7 1.3 14 39-52 23-36 (59)
34 PRK00423 tfb transcription ini 86.9 0.4 8.7E-06 39.6 1.9 39 34-72 4-43 (310)
35 PF04981 NMD3: NMD3 family ; 86.8 0.72 1.6E-05 36.7 3.2 53 44-102 1-53 (236)
36 PRK14714 DNA polymerase II lar 86.6 0.52 1.1E-05 47.0 2.7 32 87-119 712-743 (1337)
37 PF05129 Elf1: Transcription e 85.7 1 2.3E-05 31.2 3.2 18 34-51 15-33 (81)
38 smart00834 CxxC_CXXC_SSSS Puta 85.5 0.62 1.3E-05 27.0 1.7 27 41-67 5-34 (41)
39 smart00531 TFIIE Transcription 85.4 0.45 9.8E-06 35.4 1.3 32 38-69 96-133 (147)
40 PF03833 PolC_DP2: DNA polymer 85.3 0.26 5.6E-06 47.3 0.0 66 39-118 653-725 (900)
41 PRK11823 DNA repair protein Ra 84.5 0.42 9.1E-06 41.5 0.9 32 38-79 4-35 (446)
42 PF05605 zf-Di19: Drought indu 83.3 0.57 1.2E-05 29.4 0.9 12 41-53 2-13 (54)
43 PF08772 NOB1_Zn_bind: Nin one 83.3 0.75 1.6E-05 31.8 1.6 22 39-60 22-43 (73)
44 TIGR00416 sms DNA repair prote 82.5 0.58 1.2E-05 40.8 1.0 32 38-79 4-35 (454)
45 PRK12366 replication factor A; 82.4 0.86 1.9E-05 41.5 2.1 23 44-68 535-557 (637)
46 PF07191 zinc-ribbons_6: zinc- 82.2 1.5 3.3E-05 30.4 2.8 26 43-70 3-28 (70)
47 PHA02942 putative transposase; 81.9 0.72 1.6E-05 39.6 1.3 26 42-68 326-351 (383)
48 PF10571 UPF0547: Uncharacteri 81.8 0.4 8.7E-06 27.2 -0.2 13 82-94 12-24 (26)
49 cd04476 RPA1_DBD_C RPA1_DBD_C: 80.5 1.3 2.9E-05 32.7 2.1 33 43-76 36-68 (166)
50 PF13465 zf-H2C2_2: Zinc-finge 80.3 1 2.3E-05 24.7 1.2 15 36-50 9-23 (26)
51 smart00659 RPOLCX RNA polymera 80.1 1.1 2.4E-05 28.0 1.4 27 41-69 2-29 (44)
52 PF12773 DZR: Double zinc ribb 79.2 0.47 1E-05 28.9 -0.5 27 42-69 13-39 (50)
53 COG1405 SUA7 Transcription ini 79.1 1.7 3.7E-05 36.4 2.6 35 42-76 2-37 (285)
54 COG1592 Rubrerythrin [Energy p 79.1 0.96 2.1E-05 35.6 1.1 23 26-50 121-143 (166)
55 TIGR03831 YgiT_finger YgiT-typ 78.5 4.8 0.0001 23.4 3.8 43 44-95 1-43 (46)
56 COG1645 Uncharacterized Zn-fin 78.3 1.5 3.3E-05 33.5 1.9 26 41-68 28-53 (131)
57 KOG2462|consensus 77.1 1.2 2.6E-05 37.9 1.1 68 32-99 177-258 (279)
58 cd01121 Sms Sms (bacterial rad 76.5 1.3 2.8E-05 37.9 1.2 28 42-79 1-28 (372)
59 PF07754 DUF1610: Domain of un 76.4 1.5 3.3E-05 24.8 1.1 9 40-48 15-23 (24)
60 PF13453 zf-TFIIB: Transcripti 76.2 3.6 7.8E-05 24.6 2.8 23 43-66 1-26 (41)
61 PRK14890 putative Zn-ribbon RN 75.9 1 2.3E-05 30.4 0.4 31 38-68 4-34 (59)
62 PF09855 DUF2082: Nucleic-acid 75.4 7 0.00015 26.3 4.3 41 42-93 1-45 (64)
63 COG2888 Predicted Zn-ribbon RN 75.3 0.78 1.7E-05 31.3 -0.3 13 39-51 25-37 (61)
64 PRK04023 DNA polymerase II lar 74.8 1.7 3.6E-05 42.9 1.6 14 55-68 622-635 (1121)
65 TIGR01384 TFS_arch transcripti 74.3 1.6 3.5E-05 30.2 1.0 27 43-71 2-28 (104)
66 PF09986 DUF2225: Uncharacteri 74.3 5.8 0.00013 31.4 4.3 60 40-103 4-67 (214)
67 COG3677 Transposase and inacti 73.3 0.62 1.3E-05 34.7 -1.3 65 38-105 27-96 (129)
68 PRK14714 DNA polymerase II lar 72.2 1.7 3.7E-05 43.6 1.0 39 41-97 667-705 (1337)
69 cd00350 rubredoxin_like Rubred 72.2 1.5 3.3E-05 25.4 0.4 24 42-67 2-25 (33)
70 smart00440 ZnF_C2C2 C2C2 Zinc 71.9 9.1 0.0002 23.1 3.8 12 42-53 1-12 (40)
71 PF08792 A2L_zn_ribbon: A2L zi 71.6 5 0.00011 23.7 2.6 28 41-68 3-30 (33)
72 smart00778 Prim_Zn_Ribbon Zinc 70.8 2.9 6.2E-05 25.5 1.4 27 41-67 3-33 (37)
73 PF03604 DNA_RNApol_7kD: DNA d 70.0 1.1 2.3E-05 26.6 -0.6 9 42-50 1-9 (32)
74 PF00641 zf-RanBP: Zn-finger i 69.7 2.2 4.8E-05 23.9 0.7 23 58-91 3-25 (30)
75 PRK00420 hypothetical protein; 69.5 6.4 0.00014 29.2 3.3 28 40-68 22-49 (112)
76 TIGR02605 CxxC_CxxC_SSSS putat 68.9 3.5 7.5E-05 25.2 1.5 27 41-67 5-34 (52)
77 PF13894 zf-C2H2_4: C2H2-type 68.2 2.2 4.7E-05 21.2 0.4 9 42-50 1-9 (24)
78 PF09538 FYDLN_acid: Protein o 67.6 2.2 4.7E-05 31.2 0.5 26 40-68 8-35 (108)
79 PF08790 zf-LYAR: LYAR-type C2 67.1 5.2 0.00011 23.4 1.9 18 86-103 2-19 (28)
80 PF13240 zinc_ribbon_2: zinc-r 66.8 1.9 4.2E-05 23.6 0.1 7 44-50 2-8 (23)
81 PF06044 DRP: Dam-replacing fa 66.0 4.3 9.3E-05 34.2 2.0 54 35-100 25-82 (254)
82 TIGR02098 MJ0042_CXXC MJ0042 f 66.0 3.5 7.6E-05 23.9 1.1 9 42-50 3-11 (38)
83 PRK00464 nrdR transcriptional 65.3 4.3 9.3E-05 31.3 1.8 36 61-96 2-40 (154)
84 PF14353 CpXC: CpXC protein 65.2 4.9 0.00011 28.7 1.9 9 43-51 3-11 (128)
85 PRK00241 nudC NADH pyrophospha 65.0 5.9 0.00013 32.2 2.6 29 40-68 98-126 (256)
86 COG1996 RPC10 DNA-directed RNA 64.8 3.2 6.9E-05 27.0 0.8 29 40-68 5-33 (49)
87 TIGR03830 CxxCG_CxxCG_HTH puta 64.8 15 0.00032 25.5 4.2 43 44-96 1-43 (127)
88 COG1571 Predicted DNA-binding 64.5 2.3 5.1E-05 37.9 0.2 30 41-72 350-380 (421)
89 PF09862 DUF2089: Protein of u 64.2 7.2 0.00016 29.0 2.7 25 44-72 1-25 (113)
90 PF09297 zf-NADH-PPase: NADH p 63.9 4.9 0.00011 22.9 1.4 26 42-67 4-29 (32)
91 PF00096 zf-C2H2: Zinc finger, 63.6 2.4 5.2E-05 21.7 0.1 8 42-49 1-8 (23)
92 PF11023 DUF2614: Protein of u 63.1 2.6 5.6E-05 31.8 0.2 27 38-68 66-94 (114)
93 PF13248 zf-ribbon_3: zinc-rib 63.1 2.5 5.5E-05 23.3 0.1 22 42-67 3-24 (26)
94 PF04216 FdhE: Protein involve 62.8 3.5 7.6E-05 33.5 0.9 53 40-92 171-246 (290)
95 PF09723 Zn-ribbon_8: Zinc rib 62.7 5.2 0.00011 24.2 1.5 17 39-55 24-40 (42)
96 PF11672 DUF3268: Protein of u 62.5 7 0.00015 28.6 2.3 64 41-119 2-65 (102)
97 KOG2593|consensus 62.4 6.4 0.00014 35.4 2.5 41 27-67 112-161 (436)
98 TIGR02300 FYDLN_acid conserved 62.3 3.5 7.5E-05 31.7 0.7 26 40-68 8-35 (129)
99 PHA00616 hypothetical protein 61.9 2.6 5.7E-05 26.8 0.0 11 41-51 1-11 (44)
100 COG1594 RPB9 DNA-directed RNA 61.4 6.7 0.00015 28.6 2.1 30 43-72 4-35 (113)
101 PF03119 DNA_ligase_ZBD: NAD-d 61.0 3.9 8.4E-05 23.3 0.6 20 43-62 1-20 (28)
102 PRK12366 replication factor A; 60.8 5.3 0.00012 36.5 1.8 53 28-93 504-557 (637)
103 PF01599 Ribosomal_S27: Riboso 60.2 7.8 0.00017 24.9 2.0 29 40-68 17-47 (47)
104 PRK14559 putative protein seri 60.2 3.4 7.4E-05 38.2 0.5 45 42-103 16-60 (645)
105 PF04606 Ogr_Delta: Ogr/Delta- 60.1 6.4 0.00014 24.3 1.6 16 43-58 1-16 (47)
106 PF06689 zf-C4_ClpX: ClpX C4-t 59.7 4 8.7E-05 24.8 0.6 25 41-65 1-30 (41)
107 PRK08402 replication factor A; 58.3 5.4 0.00012 34.4 1.3 26 42-67 213-238 (355)
108 COG3809 Uncharacterized protei 57.7 9.6 0.00021 27.6 2.3 29 43-71 3-33 (88)
109 PF14803 Nudix_N_2: Nudix N-te 56.5 9.3 0.0002 22.8 1.8 26 43-68 2-31 (34)
110 TIGR00340 zpr1_rel ZPR1-relate 56.3 13 0.00027 28.9 2.9 25 44-68 1-37 (163)
111 PRK08665 ribonucleotide-diphos 55.6 12 0.00027 35.1 3.3 24 43-68 726-749 (752)
112 PF08274 PhnA_Zn_Ribbon: PhnA 55.6 9.2 0.0002 22.4 1.6 25 43-68 4-28 (30)
113 PF02150 RNA_POL_M_15KD: RNA p 55.3 8.6 0.00019 22.8 1.5 26 43-68 3-29 (35)
114 PF04423 Rad50_zn_hook: Rad50 55.2 8.2 0.00018 24.1 1.5 11 40-50 19-29 (54)
115 PRK14559 putative protein seri 55.0 3.9 8.4E-05 37.9 -0.1 42 43-101 3-45 (645)
116 PF06677 Auto_anti-p27: Sjogre 55.0 9.2 0.0002 23.7 1.6 24 42-66 18-41 (41)
117 PF01927 Mut7-C: Mut7-C RNAse 54.1 9.6 0.00021 28.2 1.9 9 43-51 93-101 (147)
118 PF08646 Rep_fac-A_C: Replicat 53.6 8.2 0.00018 28.0 1.4 33 61-101 20-54 (146)
119 PF03811 Zn_Tnp_IS1: InsA N-te 53.1 7.7 0.00017 23.4 1.0 24 42-65 6-35 (36)
120 PRK06266 transcription initiat 52.8 4.2 9E-05 31.6 -0.2 30 87-119 139-168 (178)
121 COG1198 PriA Primosomal protei 52.6 8.8 0.00019 36.3 1.8 40 42-93 445-484 (730)
122 PF14319 Zn_Tnp_IS91: Transpos 52.0 7.3 0.00016 28.1 1.0 41 27-67 23-68 (111)
123 smart00547 ZnF_RBZ Zinc finger 51.8 4.7 0.0001 21.6 -0.1 11 58-68 1-11 (26)
124 KOG3214|consensus 51.6 9 0.0002 28.7 1.4 54 36-108 18-71 (109)
125 PF01096 TFIIS_C: Transcriptio 51.1 31 0.00067 20.6 3.5 9 43-51 2-10 (39)
126 PRK03681 hypA hydrogenase nick 50.4 7 0.00015 28.3 0.6 12 57-68 68-79 (114)
127 PRK07218 replication factor A; 50.2 6.9 0.00015 34.6 0.7 27 42-76 298-324 (423)
128 TIGR00595 priA primosomal prot 49.3 10 0.00022 33.5 1.6 38 43-92 224-261 (505)
129 PF04641 Rtf2: Rtf2 RING-finge 48.8 18 0.00039 29.2 2.8 57 38-101 110-167 (260)
130 PRK08173 DNA topoisomerase III 48.5 17 0.00036 34.7 3.0 26 42-69 625-650 (862)
131 PF04438 zf-HIT: HIT zinc fing 48.5 6.8 0.00015 22.7 0.3 12 39-50 11-22 (30)
132 PRK12495 hypothetical protein; 48.4 15 0.00033 30.5 2.4 30 40-71 41-70 (226)
133 PF03367 zf-ZPR1: ZPR1 zinc-fi 48.1 19 0.00042 27.6 2.8 26 43-68 3-39 (161)
134 COG3478 Predicted nucleic-acid 47.3 16 0.00034 25.5 2.0 12 82-93 38-49 (68)
135 PF01807 zf-CHC2: CHC2 zinc fi 47.0 16 0.00034 25.5 2.0 31 87-119 57-88 (97)
136 COG1592 Rubrerythrin [Energy p 46.7 12 0.00026 29.5 1.4 23 59-91 134-156 (166)
137 PRK11788 tetratricopeptide rep 46.4 21 0.00046 28.2 2.8 28 36-67 349-376 (389)
138 PF10263 SprT-like: SprT-like 46.3 13 0.00028 26.8 1.5 19 18-36 79-97 (157)
139 PF02977 CarbpepA_inh: Carboxy 46.2 4.4 9.6E-05 26.3 -0.8 34 46-79 7-42 (46)
140 TIGR01385 TFSII transcription 45.1 28 0.0006 29.5 3.5 20 37-56 254-273 (299)
141 TIGR01391 dnaG DNA primase, ca 45.0 10 0.00022 32.7 0.9 33 42-76 35-70 (415)
142 COG2051 RPS27A Ribosomal prote 44.9 26 0.00055 24.3 2.7 14 82-95 36-49 (67)
143 PF02945 Endonuclease_7: Recom 44.2 8.2 0.00018 26.9 0.2 47 18-67 2-49 (81)
144 PF05766 NinG: Bacteriophage L 43.7 19 0.00041 28.9 2.2 59 36-101 82-140 (189)
145 PRK04351 hypothetical protein; 43.6 17 0.00038 27.7 1.9 29 40-68 111-141 (149)
146 PLN03086 PRLI-interacting fact 43.5 5.9 0.00013 36.5 -0.8 28 43-70 435-464 (567)
147 TIGR00373 conserved hypothetic 43.5 7.8 0.00017 29.4 -0.0 12 39-50 107-118 (158)
148 COG3058 FdhE Uncharacterized p 42.3 6.1 0.00013 34.2 -0.8 59 33-91 173-259 (308)
149 PRK14873 primosome assembly pr 42.0 16 0.00034 33.9 1.7 39 42-93 393-431 (665)
150 PF13597 NRDD: Anaerobic ribon 41.8 23 0.0005 31.9 2.7 39 25-68 467-513 (546)
151 PRK06450 threonine synthase; V 41.7 9.6 0.00021 31.9 0.3 25 41-68 3-27 (338)
152 PF03107 C1_2: C1 domain; Int 41.6 25 0.00055 19.8 1.9 21 43-66 2-22 (30)
153 PRK03824 hypA hydrogenase nick 41.6 20 0.00043 26.6 1.9 14 57-70 68-81 (135)
154 TIGR00310 ZPR1_znf ZPR1 zinc f 40.9 30 0.00066 27.5 3.0 26 43-68 2-39 (192)
155 smart00355 ZnF_C2H2 zinc finge 40.8 14 0.0003 18.0 0.7 9 42-50 1-9 (26)
156 smart00507 HNHc HNH nucleases. 40.5 22 0.00048 20.0 1.6 14 37-51 7-20 (52)
157 COG2158 Uncharacterized protei 40.4 18 0.00039 27.3 1.5 23 83-112 61-83 (112)
158 TIGR01562 FdhE formate dehydro 40.4 23 0.0005 30.1 2.3 31 61-92 226-260 (305)
159 PF09082 DUF1922: Domain of un 40.1 17 0.00037 25.2 1.2 25 42-68 4-28 (68)
160 COG1779 C4-type Zn-finger prot 39.8 25 0.00053 28.8 2.3 30 40-69 13-53 (201)
161 PF01396 zf-C4_Topoisom: Topoi 39.7 21 0.00046 21.4 1.5 14 43-56 3-16 (39)
162 PRK09678 DNA-binding transcrip 39.3 20 0.00043 24.7 1.5 15 42-56 2-16 (72)
163 PF10122 Mu-like_Com: Mu-like 38.7 14 0.0003 24.4 0.6 13 41-53 4-16 (51)
164 PRK06386 replication factor A; 38.5 13 0.00028 32.3 0.6 20 42-67 237-256 (358)
165 PF14471 DUF4428: Domain of un 38.5 4.2 9E-05 26.0 -1.8 26 43-69 1-30 (51)
166 COG1499 NMD3 NMD protein affec 38.4 14 0.0003 32.1 0.8 54 41-101 6-60 (355)
167 COG4640 Predicted membrane pro 38.2 14 0.0003 33.6 0.7 27 43-73 3-29 (465)
168 smart00400 ZnF_CHCC zinc finge 38.1 32 0.0007 21.3 2.2 26 42-67 3-31 (55)
169 TIGR00686 phnA alkylphosphonat 38.1 23 0.00049 26.6 1.7 30 43-73 4-33 (109)
170 TIGR00617 rpa1 replication fac 38.0 20 0.00044 32.7 1.8 13 26-38 436-448 (608)
171 PF14690 zf-ISL3: zinc-finger 38.0 20 0.00043 21.2 1.2 14 41-54 2-15 (47)
172 PF00412 LIM: LIM domain; Int 38.0 19 0.00041 21.6 1.1 12 87-98 29-40 (58)
173 PRK03564 formate dehydrogenase 37.9 27 0.00058 29.9 2.4 52 40-92 186-260 (309)
174 PRK05667 dnaG DNA primase; Val 37.5 16 0.00036 33.1 1.1 33 42-76 37-72 (580)
175 PF14206 Cys_rich_CPCC: Cystei 37.5 19 0.0004 25.2 1.1 21 41-61 1-21 (78)
176 PHA02768 hypothetical protein; 37.3 14 0.00029 24.5 0.4 16 41-56 5-20 (55)
177 PF07295 DUF1451: Protein of u 37.1 18 0.0004 27.6 1.1 54 30-93 86-139 (146)
178 PRK07220 DNA topoisomerase I; 37.0 29 0.00064 32.4 2.6 27 41-67 635-665 (740)
179 PF06827 zf-FPG_IleRS: Zinc fi 36.8 29 0.00063 19.2 1.7 23 43-65 3-27 (30)
180 smart00731 SprT SprT homologue 36.7 24 0.00051 25.9 1.7 16 22-37 80-95 (146)
181 PHA00732 hypothetical protein 36.5 17 0.00037 25.0 0.8 13 106-118 65-77 (79)
182 PF13912 zf-C2H2_6: C2H2-type 36.5 13 0.00027 19.6 0.1 9 42-50 2-10 (27)
183 PF05741 zf-nanos: Nanos RNA b 36.3 15 0.00032 24.3 0.4 12 39-50 31-42 (55)
184 TIGR01206 lysW lysine biosynth 36.3 26 0.00056 22.9 1.6 28 41-68 2-31 (54)
185 KOG1986|consensus 36.2 18 0.00039 34.6 1.1 35 34-68 46-84 (745)
186 PRK08270 anaerobic ribonucleos 36.0 27 0.00059 32.4 2.2 39 25-68 602-648 (656)
187 PRK01103 formamidopyrimidine/5 35.7 34 0.00073 27.8 2.6 27 40-67 244-273 (274)
188 TIGR00382 clpX endopeptidase C 35.5 13 0.00028 32.6 0.1 26 42-67 8-37 (413)
189 PF04071 zf-like: Cysteine-ric 35.0 26 0.00056 25.0 1.6 19 72-91 40-58 (86)
190 PRK07111 anaerobic ribonucleos 34.7 17 0.00036 34.2 0.7 37 25-67 657-701 (735)
191 PRK10445 endonuclease VIII; Pr 34.4 27 0.00059 28.3 1.8 26 39-65 233-261 (263)
192 KOG4623|consensus 34.3 15 0.00033 34.2 0.4 43 24-66 10-54 (611)
193 TIGR02827 RNR_anaer_Bdell anae 34.2 28 0.00061 32.1 2.1 36 25-67 509-554 (586)
194 COG1066 Sms Predicted ATP-depe 34.2 17 0.00038 32.9 0.7 23 40-66 6-28 (456)
195 COG3091 SprT Zn-dependent meta 34.1 21 0.00045 28.3 1.0 48 19-68 96-149 (156)
196 PF06054 CoiA: Competence prot 34.0 24 0.00052 30.2 1.5 24 39-62 28-52 (375)
197 PF09779 Ima1_N: Ima1 N-termin 33.9 15 0.00033 27.2 0.2 25 43-67 2-28 (131)
198 PF02318 FYVE_2: FYVE-type zin 33.8 41 0.00089 24.1 2.5 29 40-69 53-81 (118)
199 PF06676 DUF1178: Protein of u 33.6 35 0.00076 26.4 2.2 22 35-56 26-47 (148)
200 COG4643 Uncharacterized protei 33.5 15 0.00033 32.4 0.2 29 38-66 29-61 (366)
201 PRK05580 primosome assembly pr 33.4 24 0.00053 32.3 1.5 40 42-93 391-430 (679)
202 PRK05452 anaerobic nitric oxid 33.3 16 0.00035 32.1 0.4 13 56-68 422-434 (479)
203 COG1656 Uncharacterized conser 33.2 18 0.00039 28.7 0.6 27 42-68 98-139 (165)
204 TIGR00311 aIF-2beta translatio 33.0 61 0.0013 24.4 3.4 40 28-68 83-127 (133)
205 PF05876 Terminase_GpA: Phage 33.0 58 0.0013 29.3 3.8 73 41-115 200-289 (557)
206 PF13909 zf-H2C2_5: C2H2-type 32.8 19 0.00041 18.7 0.4 8 42-49 1-8 (24)
207 PHA00733 hypothetical protein 32.6 12 0.00026 27.6 -0.5 12 39-50 71-82 (128)
208 PRK00564 hypA hydrogenase nick 32.3 14 0.00031 26.8 -0.1 7 42-48 72-78 (117)
209 PRK14811 formamidopyrimidine-D 32.1 30 0.00066 28.2 1.7 26 41-67 235-263 (269)
210 KOG1311|consensus 31.6 18 0.00039 29.2 0.3 24 40-67 112-135 (299)
211 KOG2463|consensus 31.3 35 0.00077 30.3 2.1 22 40-61 256-277 (376)
212 TIGR00354 polC DNA polymerase, 30.9 23 0.0005 35.2 1.0 17 102-118 656-672 (1095)
213 PF14447 Prok-RING_4: Prokaryo 30.7 23 0.0005 23.6 0.7 7 44-50 42-48 (55)
214 PF13717 zinc_ribbon_4: zinc-r 30.4 24 0.00051 20.9 0.6 8 87-94 28-35 (36)
215 PRK02935 hypothetical protein; 30.3 29 0.00063 26.1 1.2 29 36-68 65-95 (110)
216 PF14255 Cys_rich_CPXG: Cystei 30.3 24 0.00052 22.9 0.7 9 42-50 1-9 (52)
217 PRK07591 threonine synthase; V 30.3 18 0.00039 31.1 0.2 25 41-68 18-42 (421)
218 KOG4198|consensus 30.2 22 0.00048 30.2 0.7 52 43-105 117-175 (280)
219 PRK13945 formamidopyrimidine-D 30.2 45 0.00097 27.3 2.4 26 40-66 253-281 (282)
220 PRK14810 formamidopyrimidine-D 29.7 36 0.00078 27.8 1.8 25 40-65 243-270 (272)
221 PF08996 zf-DNA_Pol: DNA Polym 29.4 27 0.00059 26.9 1.0 11 41-51 18-28 (188)
222 PF13824 zf-Mss51: Zinc-finger 29.3 27 0.00058 23.2 0.8 13 38-50 11-23 (55)
223 PF10058 DUF2296: Predicted in 29.2 19 0.0004 23.4 0.0 15 35-49 38-52 (54)
224 PF13913 zf-C2HC_2: zinc-finge 29.2 28 0.0006 19.1 0.7 8 43-50 4-11 (25)
225 TIGR02159 PA_CoA_Oxy4 phenylac 29.1 15 0.00032 28.0 -0.5 16 41-56 105-120 (146)
226 PF09180 ProRS-C_1: Prolyl-tRN 28.9 37 0.00081 22.4 1.5 21 38-58 45-65 (68)
227 PF02891 zf-MIZ: MIZ/SP-RING z 28.6 31 0.00067 21.6 1.0 10 40-49 40-49 (50)
228 TIGR03844 cysteate_syn cysteat 28.6 22 0.00048 30.6 0.4 23 41-66 2-24 (398)
229 PF12874 zf-met: Zinc-finger o 28.4 43 0.00094 17.1 1.4 9 60-68 1-9 (25)
230 PRK03988 translation initiatio 28.3 75 0.0016 24.1 3.2 39 29-67 89-131 (138)
231 COG2995 PqiA Uncharacterized p 28.1 45 0.00098 30.1 2.2 26 87-112 41-67 (418)
232 PF13719 zinc_ribbon_5: zinc-r 28.0 54 0.0012 19.3 1.9 8 43-50 4-11 (37)
233 PRK05978 hypothetical protein; 27.9 27 0.00058 27.0 0.7 19 36-54 28-46 (148)
234 PF00569 ZZ: Zinc finger, ZZ t 27.9 45 0.00098 20.3 1.6 25 39-66 2-26 (46)
235 smart00132 LIM Zinc-binding do 27.5 37 0.00081 18.2 1.1 8 87-94 30-37 (39)
236 PF02892 zf-BED: BED zinc fing 27.4 42 0.00091 19.6 1.4 25 73-97 3-29 (45)
237 PF01155 HypA: Hydrogenase exp 27.3 42 0.0009 24.0 1.6 26 40-68 69-95 (113)
238 PRK08271 anaerobic ribonucleos 27.3 25 0.00053 32.7 0.5 38 25-67 543-588 (623)
239 TIGR00155 pqiA_fam integral me 27.0 35 0.00075 29.7 1.3 25 44-68 16-42 (403)
240 PRK14704 anaerobic ribonucleos 26.9 27 0.00059 32.2 0.7 39 25-68 536-581 (618)
241 cd06956 NR_DBD_RXR DNA-binding 26.9 35 0.00076 23.0 1.1 25 42-67 1-25 (77)
242 PHA02998 RNA polymerase subuni 26.8 65 0.0014 26.4 2.7 12 41-52 143-154 (195)
243 PF14205 Cys_rich_KTR: Cystein 26.7 33 0.00072 23.0 0.9 9 42-50 5-13 (55)
244 PRK04860 hypothetical protein; 26.6 17 0.00037 28.0 -0.5 29 40-69 118-153 (160)
245 smart00709 Zpr1 Duplicated dom 26.4 66 0.0014 24.8 2.7 26 43-68 2-38 (160)
246 PF05191 ADK_lid: Adenylate ki 26.4 45 0.00097 19.9 1.3 9 60-68 2-10 (36)
247 PRK05342 clpX ATP-dependent pr 26.0 22 0.00048 30.9 -0.0 27 40-66 8-38 (412)
248 PRK00415 rps27e 30S ribosomal 26.0 49 0.0011 22.3 1.6 13 82-94 28-40 (59)
249 PRK12380 hydrogenase nickel in 25.9 47 0.001 23.9 1.6 14 55-68 66-79 (113)
250 PF10588 NADH-G_4Fe-4S_3: NADH 25.7 56 0.0012 19.7 1.7 22 28-50 1-22 (41)
251 PF01363 FYVE: FYVE zinc finge 25.4 46 0.00099 21.1 1.4 26 40-69 8-35 (69)
252 cd00085 HNHc HNH nucleases; HN 25.3 50 0.0011 18.8 1.5 10 42-51 12-21 (57)
253 PF00301 Rubredoxin: Rubredoxi 25.1 38 0.00082 21.4 0.9 13 39-51 32-44 (47)
254 PRK06260 threonine synthase; V 25.0 27 0.00058 29.6 0.3 25 41-67 3-27 (397)
255 PF09151 DUF1936: Domain of un 25.0 32 0.0007 21.1 0.6 10 41-50 1-10 (36)
256 PF13901 DUF4206: Domain of un 24.9 53 0.0011 25.8 1.9 57 28-92 139-197 (202)
257 cd00730 rubredoxin Rubredoxin; 24.8 36 0.00079 21.7 0.8 14 38-51 31-44 (50)
258 TIGR00577 fpg formamidopyrimid 24.8 49 0.0011 27.0 1.7 25 40-65 244-271 (272)
259 TIGR00100 hypA hydrogenase nic 24.5 50 0.0011 23.8 1.6 25 48-72 59-83 (115)
260 PRK13130 H/ACA RNA-protein com 24.1 42 0.00092 22.1 1.0 11 42-52 6-16 (56)
261 smart00714 LITAF Possible memb 23.7 38 0.00082 21.8 0.8 16 35-50 46-61 (67)
262 COG2260 Predicted Zn-ribbon RN 23.7 46 0.00099 22.6 1.1 21 42-68 6-26 (59)
263 PRK12336 translation initiatio 23.4 1E+02 0.0022 24.3 3.3 41 28-68 84-128 (201)
264 PF01667 Ribosomal_S27e: Ribos 23.4 81 0.0017 20.8 2.3 15 81-95 23-37 (55)
265 PF09526 DUF2387: Probable met 23.3 1.3E+02 0.0027 20.6 3.3 14 82-95 28-41 (71)
266 cd06968 NR_DBD_ROR DNA-binding 23.2 44 0.00094 23.6 1.0 27 40-67 4-30 (95)
267 cd03031 GRX_GRX_like Glutaredo 23.2 1.2E+02 0.0025 23.0 3.4 53 27-92 86-141 (147)
268 PRK00762 hypA hydrogenase nick 23.2 46 0.001 24.3 1.2 11 42-52 93-103 (124)
269 COG1379 PHP family phosphoeste 22.8 15 0.00033 32.7 -1.6 30 43-72 248-278 (403)
270 PHA02540 61 DNA primase; Provi 22.7 71 0.0015 27.6 2.4 34 41-76 27-70 (337)
271 PF12171 zf-C2H2_jaz: Zinc-fin 22.5 44 0.00096 17.8 0.8 8 42-49 2-9 (27)
272 cd00729 rubredoxin_SM Rubredox 22.5 64 0.0014 18.8 1.5 14 59-72 2-15 (34)
273 PLN00209 ribosomal protein S27 22.4 91 0.002 22.5 2.5 14 81-94 52-65 (86)
274 PF00105 zf-C4: Zinc finger, C 22.4 45 0.00098 21.5 0.9 24 43-67 2-25 (70)
275 smart00647 IBR In Between Ring 22.3 1.9E+02 0.0041 17.3 3.7 26 43-68 20-49 (64)
276 cd00065 FYVE FYVE domain; Zinc 22.1 30 0.00065 21.0 0.0 32 43-76 4-35 (57)
277 KOG4317|consensus 22.1 36 0.00079 30.2 0.5 11 109-119 68-78 (383)
278 PF01529 zf-DHHC: DHHC palmito 22.1 37 0.00081 24.5 0.5 33 34-70 41-73 (174)
279 PF10601 zf-LITAF-like: LITAF- 22.0 41 0.00089 22.0 0.7 14 37-50 54-67 (73)
280 PRK05638 threonine synthase; V 22.0 37 0.0008 29.2 0.5 24 41-68 1-24 (442)
281 smart00249 PHD PHD zinc finger 22.0 51 0.0011 18.2 1.0 7 44-50 2-8 (47)
282 PF08209 Sgf11: Sgf11 (transcr 21.9 54 0.0012 19.5 1.1 16 86-101 6-21 (33)
283 PF01873 eIF-5_eIF-2B: Domain 21.7 80 0.0017 23.5 2.2 39 28-67 79-122 (125)
284 cd01675 RNR_III Class III ribo 21.7 38 0.00082 30.5 0.6 40 25-68 495-541 (555)
285 TIGR02487 NrdD anaerobic ribon 21.4 35 0.00075 31.0 0.3 40 25-68 501-547 (579)
286 COG2075 RPL24A Ribosomal prote 21.3 37 0.00081 23.4 0.4 21 42-62 4-32 (66)
287 PF02591 DUF164: Putative zinc 21.0 59 0.0013 20.3 1.2 11 39-49 44-54 (56)
288 COG1675 TFA1 Transcription ini 20.9 26 0.00057 27.8 -0.5 64 29-120 100-165 (176)
289 PF03884 DUF329: Domain of unk 20.7 44 0.00095 22.2 0.6 25 41-67 2-26 (57)
290 PF05899 Cupin_3: Protein of u 20.6 1.1E+02 0.0024 20.0 2.5 20 54-73 6-25 (74)
291 PRK11032 hypothetical protein; 20.3 54 0.0012 25.7 1.1 14 43-56 144-157 (160)
292 PF06397 Desulfoferrod_N: Desu 20.3 65 0.0014 19.6 1.2 12 58-69 5-16 (36)
293 PTZ00083 40S ribosomal protein 20.1 1.1E+02 0.0024 22.1 2.5 14 81-94 51-64 (85)
294 PRK14724 DNA topoisomerase III 20.1 78 0.0017 30.9 2.3 21 41-64 755-776 (987)
295 COG1439 Predicted nucleic acid 20.0 73 0.0016 25.5 1.8 13 39-51 151-163 (177)
No 1
>KOG0402|consensus
Probab=100.00 E-value=2.8e-46 Score=266.32 Aligned_cols=92 Identities=73% Similarity=1.192 Sum_probs=89.8
Q ss_pred hhhcceeeeeccccccccChhhhHhHHHHHHHhhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeee
Q psy836 6 QAKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIW 85 (122)
Q Consensus 6 M~krtkkvgi~gkyG~RYG~slRK~v~kie~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~ 85 (122)
|+||||||||+|+||+|||+||||++++||++||++|+|+||||..|||.|||||.
T Consensus 1 m~krtKKVgI~gkyGtrYGaSLrk~vKkiei~Qhaky~CsfCGK~~vKR~AvGiW~------------------------ 56 (92)
T KOG0402|consen 1 MAKRTKKVGIVGKYGTRYGASLRKMVKKIEIQQHAKYTCSFCGKKTVKRKAVGIWK------------------------ 56 (92)
T ss_pred CCcccceeeeeecccchhhHHHHHHHHHHHHHHhhhhhhhhcchhhhhhhceeEEe------------------------
Confidence 89999999999999999999999999999999999999999999999999999999
Q ss_pred eecCcCeEEeccccccCchHHHHHHHHHHHHHHhhhC
Q psy836 86 SCKRCKRIVAGGAWVYNTTAATSVRSAIRRLREVNEL 122 (122)
Q Consensus 86 s~~rC~~~~AGGAy~~~T~~~~~~~~~i~rl~e~~~~ 122 (122)
|..|++++|||||+++|+++.+++++||||||+.|+
T Consensus 57 -C~~C~kv~agga~~~~t~aa~t~rs~irrlre~~e~ 92 (92)
T KOG0402|consen 57 -CGSCKKVVAGGAYTVTTAAAATVRSTIRRLRELVEQ 92 (92)
T ss_pred -cCCccceeccceEEeccchhHHHHHHHHHHHHHhcC
Confidence 788999999999999999999999999999999885
No 2
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=100.00 E-value=1.4e-45 Score=262.48 Aligned_cols=90 Identities=70% Similarity=1.163 Sum_probs=82.5
Q ss_pred hhcceeeeeccccccccChhhhHhHHHHHHHhhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeee
Q psy836 7 AKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWS 86 (122)
Q Consensus 7 ~krtkkvgi~gkyG~RYG~slRK~v~kie~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s 86 (122)
++|||||||+||||+|||++|||+|++||++||++|+|||||++.|+|.++|||+
T Consensus 1 a~rtkkvgi~GkyG~RYG~slRK~vkkie~~q~~ky~Cp~Cgk~~vkR~a~GIW~------------------------- 55 (90)
T PF01780_consen 1 AKRTKKVGIAGKYGTRYGASLRKRVKKIEISQHAKYTCPFCGKTSVKRVATGIWK------------------------- 55 (90)
T ss_dssp -S-SSS-TTGGGGTTSSTHHHHHHHHHHHHHHHS-BEESSSSSSEEEEEETTEEE-------------------------
T ss_pred CCCCceeeecCcCcCCcCHHHHHHHHHHHHHHhCCCcCCCCCCceeEEeeeEEee-------------------------
Confidence 5899999999999999999999999999999999999999999999999999999
Q ss_pred ecCcCeEEeccccccCchHHHHHHHHHHHHHHhhh
Q psy836 87 CKRCKRIVAGGAWVYNTTAATSVRSAIRRLREVNE 121 (122)
Q Consensus 87 ~~rC~~~~AGGAy~~~T~~~~~~~~~i~rl~e~~~ 121 (122)
|.+|+++||||||+|+||++.+++++|+||+|++|
T Consensus 56 C~~C~~~~AGGAy~~~T~~~~t~~~~i~rl~e~~e 90 (90)
T PF01780_consen 56 CKKCGKKFAGGAYTPSTPAAKTVKRAIRRLRELKE 90 (90)
T ss_dssp ETTTTEEEE-BSSSSS-HHHHHHHHHHHHHHHHHH
T ss_pred cCCCCCEEeCCCccccchHHHHHHHHHHHHHHhcC
Confidence 78999999999999999999999999999999987
No 3
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=100.00 E-value=2e-45 Score=261.68 Aligned_cols=90 Identities=71% Similarity=1.225 Sum_probs=87.5
Q ss_pred hhhcceeeeeccccccccChhhhHhHHHHHHHhhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeee
Q psy836 6 QAKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIW 85 (122)
Q Consensus 6 M~krtkkvgi~gkyG~RYG~slRK~v~kie~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~ 85 (122)
|++|||||||+||||+|||++|||+|++||++||++|+|||||++.|+|.++|||+
T Consensus 1 MakrtkkvG~~GrfG~RYG~slRK~v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~------------------------ 56 (90)
T PTZ00255 1 MAKRTKKVGITGKYGTRYGASLRKQIKKIEISQHAKYFCPFCGKHAVKRQAVGIWR------------------------ 56 (90)
T ss_pred CCCcCceeeecCCCcCccCHHHHHHHHHHHHHHhCCccCCCCCCCceeeeeeEEEE------------------------
Confidence 89999999999999999999999999999999999999999999999999999999
Q ss_pred eecCcCeEEeccccccCchHHHHHHHHHHHHHHhh
Q psy836 86 SCKRCKRIVAGGAWVYNTTAATSVRSAIRRLREVN 120 (122)
Q Consensus 86 s~~rC~~~~AGGAy~~~T~~~~~~~~~i~rl~e~~ 120 (122)
|..|+++||||||+|+||++.++.++|+||+|++
T Consensus 57 -C~~C~~~~AGGAy~~~T~~~~t~~~~irr~~e~~ 90 (90)
T PTZ00255 57 -CKGCKKTVAGGAWTLSTPAASTVRSTIRRLRKLK 90 (90)
T ss_pred -cCCCCCEEeCCccccccchhHHHHHHHHHHHhcC
Confidence 7888999999999999999999999999999974
No 4
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=100.00 E-value=4.8e-45 Score=260.25 Aligned_cols=91 Identities=54% Similarity=1.000 Sum_probs=87.7
Q ss_pred hhhcceeeeeccccccccChhhhHhHHHHHHHhhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeee
Q psy836 6 QAKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIW 85 (122)
Q Consensus 6 M~krtkkvgi~gkyG~RYG~slRK~v~kie~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~ 85 (122)
|+ |||||||+||||+|||++|||+|++||++||++|+|||||++.|+|.++|||+
T Consensus 1 ma-rtkkvG~~GrfG~RYG~slRK~v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~------------------------ 55 (91)
T TIGR00280 1 MK-RTKKVGITGRFGPRYGLKLRRQVKKIEIQQKAKYVCPFCGKKTVKRGSTGIWT------------------------ 55 (91)
T ss_pred CC-CCceeeecCCCcCccCHHHHHHHHHHHHHHhcCccCCCCCCCceEEEeeEEEE------------------------
Confidence 66 89999999999999999999999999999999999999999999999999999
Q ss_pred eecCcCeEEeccccccCchHHHHHHHHHHHHHHhhhC
Q psy836 86 SCKRCKRIVAGGAWVYNTTAATSVRSAIRRLREVNEL 122 (122)
Q Consensus 86 s~~rC~~~~AGGAy~~~T~~~~~~~~~i~rl~e~~~~ 122 (122)
|..|+++||||||+|+||++.++.++|+||+|++|.
T Consensus 56 -C~~C~~~~AGGAy~p~T~~~~t~~~~irrl~e~~~~ 91 (91)
T TIGR00280 56 -CRKCGAKFAGGAYTPVTPAGKTVRKTIRRIVEMKEA 91 (91)
T ss_pred -cCCCCCEEeCCccccccchhHHHHHHHHHHHHhhcC
Confidence 788899999999999999999999999999999873
No 5
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=100.00 E-value=1.5e-44 Score=257.15 Aligned_cols=89 Identities=44% Similarity=0.796 Sum_probs=86.1
Q ss_pred hhhcceeeeeccccccccChhhhHhHHHHHHHhhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeee
Q psy836 6 QAKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIW 85 (122)
Q Consensus 6 M~krtkkvgi~gkyG~RYG~slRK~v~kie~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~ 85 (122)
|++|||||||+||||+|||++|||+|++||++||++|+|||||+++|+|.++|||+
T Consensus 1 m~~rtkkvGi~Gr~G~RYG~slRK~v~kie~~q~a~y~CpfCgk~~vkR~a~GIW~------------------------ 56 (90)
T PRK03976 1 MMSRTKKVGSAGRFGARYGRKIRKRVADIEEKMRAKHVCPVCGRPKVKRVGTGIWE------------------------ 56 (90)
T ss_pred CCCcCceEeecCCCcCccCHHHHHHHHHHHHHHhcCccCCCCCCCceEEEEEEEEE------------------------
Confidence 67799999999999999999999999999999999999999999999999999999
Q ss_pred eecCcCeEEeccccccCchHHHHHHHHHHHHHHh
Q psy836 86 SCKRCKRIVAGGAWVYNTTAATSVRSAIRRLREV 119 (122)
Q Consensus 86 s~~rC~~~~AGGAy~~~T~~~~~~~~~i~rl~e~ 119 (122)
|.+|+++||||||+|+||++.++.++|+||+|.
T Consensus 57 -C~~C~~~~AGGAy~~~T~~~~t~~~~irr~~~~ 89 (90)
T PRK03976 57 -CRKCGAKFAGGAYTPETPAGKTVTRAIRRAVEE 89 (90)
T ss_pred -cCCCCCEEeCCccccccchhhhHHHHHHHHhhc
Confidence 788889999999999999999999999999985
No 6
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.6e-38 Score=225.21 Aligned_cols=88 Identities=49% Similarity=0.915 Sum_probs=85.6
Q ss_pred hhhcceeeeeccccccccChhhhHhHHHHHHHhhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeee
Q psy836 6 QAKRTKKVGITGKYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIW 85 (122)
Q Consensus 6 M~krtkkvgi~gkyG~RYG~slRK~v~kie~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~ 85 (122)
|++ ||||||+|+||+|||++||++|++||++|+++|.||+||++.++|.++|||.
T Consensus 1 M~~-TkkvG~aGrfGpRYG~~~Rrrv~~ie~~~~~~~~Cp~C~~~~VkR~a~GIW~------------------------ 55 (89)
T COG1997 1 MAK-TKKVGIAGRFGPRYGSKLRRRVKEIEAQQRAKHVCPFCGRTTVKRIATGIWK------------------------ 55 (89)
T ss_pred CCc-cceeccCcccccccchHHHHHHHHHHHHHhcCCcCCCCCCcceeeeccCeEE------------------------
Confidence 777 9999999999999999999999999999999999999999999999999999
Q ss_pred eecCcCeEEeccccccCchHHHHHHHHHHHHHHh
Q psy836 86 SCKRCKRIVAGGAWVYNTTAATSVRSAIRRLREV 119 (122)
Q Consensus 86 s~~rC~~~~AGGAy~~~T~~~~~~~~~i~rl~e~ 119 (122)
|.+||.+||||||+|.|+++.++.++|+|+.|.
T Consensus 56 -C~kCg~~fAGgay~P~t~~~k~~~~~i~r~~e~ 88 (89)
T COG1997 56 -CRKCGAKFAGGAYTPVTPAGKAVKRTIRREVEM 88 (89)
T ss_pred -cCCCCCeeccccccccchHHHHHHHHHHHHhcc
Confidence 789999999999999999999999999999985
No 7
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=97.25 E-value=4e-05 Score=55.07 Aligned_cols=25 Identities=24% Similarity=0.352 Sum_probs=22.6
Q ss_pred cceeeecceeeeeccceeeeeeecC
Q psy836 65 CKRIVAGGAWDSMKRSCVGIWSCKR 89 (122)
Q Consensus 65 C~~~vAggAy~~~t~~AvtV~s~~r 89 (122)
|+++||||||+|+|.+++++.+.|+
T Consensus 60 C~~~~AGGAy~~~T~~~~t~~~~ir 84 (90)
T PRK03976 60 CGAKFAGGAYTPETPAGKTVTRAIR 84 (90)
T ss_pred CCCEEeCCccccccchhhhHHHHHH
Confidence 8999999999999999999877665
No 8
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=97.23 E-value=3.6e-05 Score=55.48 Aligned_cols=25 Identities=24% Similarity=0.416 Sum_probs=22.6
Q ss_pred cceeeecceeeeeccceeeeeeecC
Q psy836 65 CKRIVAGGAWDSMKRSCVGIWSCKR 89 (122)
Q Consensus 65 C~~~vAggAy~~~t~~AvtV~s~~r 89 (122)
|+++||||||+|+|.+++++.+.|+
T Consensus 59 C~~~~AGGAy~p~T~~~~t~~~~ir 83 (91)
T TIGR00280 59 CGAKFAGGAYTPVTPAGKTVRKTIR 83 (91)
T ss_pred CCCEEeCCccccccchhHHHHHHHH
Confidence 8999999999999999999877665
No 9
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=97.20 E-value=4.1e-05 Score=55.02 Aligned_cols=25 Identities=40% Similarity=0.712 Sum_probs=22.7
Q ss_pred cceeeecceeeeeccceeeeeeecC
Q psy836 65 CKRIVAGGAWDSMKRSCVGIWSCKR 89 (122)
Q Consensus 65 C~~~vAggAy~~~t~~AvtV~s~~r 89 (122)
|+++||||||+|+|.+++++.+.++
T Consensus 60 C~~~~AGGAy~~~T~~~~t~~~~ir 84 (90)
T PTZ00255 60 CKKTVAGGAWTLSTPAASTVRSTIR 84 (90)
T ss_pred CCCEEeCCccccccchhHHHHHHHH
Confidence 8999999999999999999877665
No 10
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=97.19 E-value=3e-05 Score=55.69 Aligned_cols=27 Identities=26% Similarity=0.478 Sum_probs=21.3
Q ss_pred cCcceeeecceeeeeccceeeeeeecC
Q psy836 63 KRCKRIVAGGAWDSMKRSCVGIWSCKR 89 (122)
Q Consensus 63 ~~C~~~vAggAy~~~t~~AvtV~s~~r 89 (122)
++|+++||||||+|+|.+++++++.++
T Consensus 57 ~~C~~~~AGGAy~~~T~~~~t~~~~i~ 83 (90)
T PF01780_consen 57 KKCGKKFAGGAYTPSTPAAKTVKRAIR 83 (90)
T ss_dssp TTTTEEEE-BSSSSS-HHHHHHHHHHH
T ss_pred CCCCCEEeCCCccccchHHHHHHHHHH
Confidence 048999999999999999999987664
No 11
>KOG0402|consensus
Probab=96.76 E-value=0.00019 Score=51.96 Aligned_cols=25 Identities=36% Similarity=0.671 Sum_probs=23.0
Q ss_pred cceeeecceeeeeccceeeeeeecC
Q psy836 65 CKRIVAGGAWDSMKRSCVGIWSCKR 89 (122)
Q Consensus 65 C~~~vAggAy~~~t~~AvtV~s~~r 89 (122)
|++++|||||+++|.+|++++|.++
T Consensus 60 C~kv~agga~~~~t~aa~t~rs~ir 84 (92)
T KOG0402|consen 60 CKKVVAGGAYTVTTAAAATVRSTIR 84 (92)
T ss_pred ccceeccceEEeccchhHHHHHHHH
Confidence 7889999999999999999988775
No 12
>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=95.83 E-value=0.007 Score=37.39 Aligned_cols=27 Identities=30% Similarity=0.859 Sum_probs=22.6
Q ss_pred cccCCCCCCceeEeEEe-eeeeecCcce
Q psy836 41 KYTCSFCGKDSMKRSCV-GIWSCKRCKR 67 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~av-GIW~C~~C~~ 67 (122)
-+.||.||.....+... +.|.|+.|.+
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 46799999987777766 9999999875
No 13
>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=94.72 E-value=0.027 Score=35.68 Aligned_cols=25 Identities=28% Similarity=0.817 Sum_probs=15.7
Q ss_pred cCCCCCCcee-Ee------EEeeeeeecCcce
Q psy836 43 TCSFCGKDSM-KR------SCVGIWSCKRCKR 67 (122)
Q Consensus 43 ~Cp~Cgk~~m-kR------~avGIW~C~~C~~ 67 (122)
.|||||.... -| ...|+|.|..|+-
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCC
Confidence 6999998754 44 2445566555554
No 14
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=94.39 E-value=0.023 Score=34.85 Aligned_cols=29 Identities=24% Similarity=0.487 Sum_probs=22.3
Q ss_pred ccccCCCCCCceeEeEEeeeeeecCccee
Q psy836 40 AKYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
..|.||.||.....-...+.++|+.||..
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCe
Confidence 36899999998655555558899999875
No 15
>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=94.29 E-value=0.028 Score=34.11 Aligned_cols=33 Identities=18% Similarity=0.451 Sum_probs=23.8
Q ss_pred ccCCCCCCce-eEeEEeeeeeecCcceeeeccee
Q psy836 42 YTCSFCGKDS-MKRSCVGIWSCKRCKRIVAGGAW 74 (122)
Q Consensus 42 y~Cp~Cgk~~-mkR~avGIW~C~~C~~~vAggAy 74 (122)
|.||.||... +-=.+.|-..|+.||.++....-
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~~i 34 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEENII 34 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-TTB
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeecccc
Confidence 6899999986 34457789999999888765543
No 16
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=93.93 E-value=0.028 Score=36.05 Aligned_cols=26 Identities=23% Similarity=0.715 Sum_probs=21.4
Q ss_pred ccCCCCCCceeEeEEeeeeeecCccee
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
-.||.||.. +-....+.|+|++|+.+
T Consensus 21 ~fCP~Cg~~-~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 21 KFCPRCGSG-FMAEHLDRWHCGKCGYT 46 (50)
T ss_pred CcCcCCCcc-hheccCCcEECCCcCCE
Confidence 379999997 66666799999888876
No 17
>PHA00626 hypothetical protein
Probab=93.10 E-value=0.055 Score=36.63 Aligned_cols=33 Identities=18% Similarity=0.500 Sum_probs=25.0
Q ss_pred cCCCCCCceeEe-----EEeeeeeecCcceeeecceee
Q psy836 43 TCSFCGKDSMKR-----SCVGIWSCKRCKRIVAGGAWD 75 (122)
Q Consensus 43 ~Cp~Cgk~~mkR-----~avGIW~C~~C~~~vAggAy~ 75 (122)
.||.||+..+-| .....+.|+.||..+.-+|+.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~ 39 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFG 39 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhhhh
Confidence 599999975555 556789988888887766654
No 18
>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=93.10 E-value=0.063 Score=34.65 Aligned_cols=28 Identities=29% Similarity=0.654 Sum_probs=23.9
Q ss_pred cccCCCCCCceeEeEEeeeeeecCccee
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
.-+||.||...-++...-.|.|+.||..
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred ccCccCcccccccccccceEEcCCCCCE
Confidence 3469999999877888889999999886
No 19
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=92.17 E-value=0.091 Score=40.49 Aligned_cols=24 Identities=29% Similarity=0.901 Sum_probs=16.9
Q ss_pred ccCCCCCCce--------------eEeEEeeeeeecCcceee
Q psy836 42 YTCSFCGKDS--------------MKRSCVGIWSCKRCKRIV 69 (122)
Q Consensus 42 y~Cp~Cgk~~--------------mkR~avGIW~C~~C~~~v 69 (122)
+.||+||.+. ++|. .+|+.||+++
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~----~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRR----RECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeee----eeccccCCcc
Confidence 4799999654 3333 7888888874
No 20
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=91.84 E-value=0.037 Score=35.06 Aligned_cols=15 Identities=27% Similarity=0.662 Sum_probs=10.9
Q ss_pred ccCCCCCCceeEeEE
Q psy836 42 YTCSFCGKDSMKRSC 56 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~a 56 (122)
..|||||...+.-..
T Consensus 4 kPCPFCG~~~~~~~~ 18 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQ 18 (61)
T ss_pred cCCCCCCCcceEeec
Confidence 569999988655444
No 21
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=91.71 E-value=0.12 Score=32.02 Aligned_cols=30 Identities=30% Similarity=0.883 Sum_probs=14.7
Q ss_pred ccCCCCCCc-eeE----eEEeeeeeecCcceeeecc
Q psy836 42 YTCSFCGKD-SMK----RSCVGIWSCKRCKRIVAGG 72 (122)
Q Consensus 42 y~Cp~Cgk~-~mk----R~avGIW~C~~C~~~vAgg 72 (122)
-.||.||-. +++ ....|-|.|..|+. ++|.
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~-~~GD 38 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQCGG-DAGD 38 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTTTB-E---
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCCCC-cCCC
Confidence 469999654 666 33459999999955 4543
No 22
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=91.52 E-value=0.073 Score=39.50 Aligned_cols=25 Identities=28% Similarity=0.690 Sum_probs=17.2
Q ss_pred hHhHHHHHHHhhccccCCCCCCcee
Q psy836 28 RKMVKKMEITQHAKYTCSFCGKDSM 52 (122)
Q Consensus 28 RK~v~kie~~~~aky~Cp~Cgk~~m 52 (122)
|+.++..-......|+|||||...+
T Consensus 9 r~~ik~~~~~L~k~FtCp~Cghe~v 33 (104)
T COG4888 9 RKIIKRRPQVLPKTFTCPRCGHEKV 33 (104)
T ss_pred cccCcccCccCCceEecCccCCeee
Confidence 4444444444667899999999864
No 23
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=91.42 E-value=0.022 Score=41.16 Aligned_cols=22 Identities=23% Similarity=0.432 Sum_probs=18.0
Q ss_pred cceeeecceeeeeccceeeeee
Q psy836 65 CKRIVAGGAWDSMKRSCVGIWS 86 (122)
Q Consensus 65 C~~~vAggAy~~~t~~AvtV~s 86 (122)
||.++|||||++.|.++.++.+
T Consensus 59 Cg~~fAGgay~P~t~~~k~~~~ 80 (89)
T COG1997 59 CGAKFAGGAYTPVTPAGKAVKR 80 (89)
T ss_pred CCCeeccccccccchHHHHHHH
Confidence 7889999999998887766543
No 24
>PRK04023 DNA polymerase II large subunit; Validated
Probab=90.84 E-value=0.16 Score=49.65 Aligned_cols=67 Identities=24% Similarity=0.456 Sum_probs=37.8
Q ss_pred hccccCCCCCCceeEeEE-------eeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccccccCchHHHHHHH
Q psy836 39 HAKYTCSFCGKDSMKRSC-------VGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTAATSVRS 111 (122)
Q Consensus 39 ~aky~Cp~Cgk~~mkR~a-------vGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~~T~~~~~~~~ 111 (122)
-....||.||.......+ ..+|.|+.|+.... -..|.+||.....+.+. .-+....+++
T Consensus 624 Vg~RfCpsCG~~t~~frCP~CG~~Te~i~fCP~CG~~~~-------------~y~CPKCG~El~~~s~~-~i~l~~~~~~ 689 (1121)
T PRK04023 624 IGRRKCPSCGKETFYRRCPFCGTHTEPVYRCPRCGIEVE-------------EDECEKCGREPTPYSKR-KIDLKELYDR 689 (1121)
T ss_pred ccCccCCCCCCcCCcccCCCCCCCCCcceeCccccCcCC-------------CCcCCCCCCCCCccceE-EecHHHHHHH
Confidence 356678888777432211 23445555544311 12277777777666543 3456667777
Q ss_pred HHHHHHHh
Q psy836 112 AIRRLREV 119 (122)
Q Consensus 112 ~i~rl~e~ 119 (122)
|+.+|.+-
T Consensus 690 A~~~lg~~ 697 (1121)
T PRK04023 690 ALENLGER 697 (1121)
T ss_pred HHHHhCCc
Confidence 88877653
No 25
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=90.39 E-value=0.23 Score=30.23 Aligned_cols=32 Identities=16% Similarity=0.344 Sum_probs=23.6
Q ss_pred cCCCCCCceeEeEEee--eeeecCcceeeeccee
Q psy836 43 TCSFCGKDSMKRSCVG--IWSCKRCKRIVAGGAW 74 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avG--IW~C~~C~~~vAggAy 74 (122)
.||.||........-+ .|.|+.|+....-+++
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEECCCc
Confidence 6999999875554432 7999999887666665
No 26
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=90.34 E-value=0.17 Score=38.86 Aligned_cols=22 Identities=32% Similarity=0.853 Sum_probs=18.7
Q ss_pred ccCCCCCCceeEeEEeeeeeecCccee
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
=.||.||. ...+.|.|+.||.+
T Consensus 310 ~~C~~cg~-----~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH-----LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC-----ccceeEECCCCCCe
Confidence 35999999 66889999999986
No 27
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=88.52 E-value=0.12 Score=35.32 Aligned_cols=19 Identities=26% Similarity=0.655 Sum_probs=14.3
Q ss_pred cCCCCCCceeEeEEeeeee
Q psy836 43 TCSFCGKDSMKRSCVGIWS 61 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~ 61 (122)
.|||||...+.-.+.+-|-
T Consensus 8 PCPFCG~~~~~v~~~~g~~ 26 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYY 26 (64)
T ss_pred CCCCCCCceeEEEecCceE
Confidence 5999999987666656554
No 28
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=88.52 E-value=0.22 Score=32.85 Aligned_cols=30 Identities=20% Similarity=0.595 Sum_probs=18.1
Q ss_pred hccccCCCCCCceeEeEEeeeeeecCccee
Q psy836 39 HAKYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 39 ~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
..+-.||.||--.+==.----|+|.+||.+
T Consensus 17 rk~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 17 RKNRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred EccccCCCCCCcchhhhcCceeEeccccce
Confidence 356679999953211111125998888875
No 29
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=88.27 E-value=0.52 Score=41.56 Aligned_cols=37 Identities=30% Similarity=0.795 Sum_probs=28.3
Q ss_pred hhhHhHHHHHHHhhccccCCCCCCceeEeEEeeeeeecCcce
Q psy836 26 SLRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 26 slRK~v~kie~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
.||++|.+ .+.+...|.|..||-.+ -+=-|+||+|+.
T Consensus 340 ~lr~mvge-~l~~~~~YRC~~CGF~a----~~l~W~CPsC~~ 376 (389)
T COG2956 340 LLRDMVGE-QLRRKPRYRCQNCGFTA----HTLYWHCPSCRA 376 (389)
T ss_pred HHHHHHHH-HHhhcCCceecccCCcc----eeeeeeCCCccc
Confidence 36666665 35678899999999875 345699999986
No 30
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=87.84 E-value=0.61 Score=33.95 Aligned_cols=33 Identities=21% Similarity=0.633 Sum_probs=21.7
Q ss_pred cCC--CCCCceeEeEEeeeeeecCcceeeecceeee
Q psy836 43 TCS--FCGKDSMKRSCVGIWSCKRCKRIVAGGAWDS 76 (122)
Q Consensus 43 ~Cp--~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~ 76 (122)
-|| .|+|.-.. ..-|.|.|++|++.+..--|-+
T Consensus 20 aC~~~~C~kKv~~-~~~~~y~C~~C~~~~~~~~~ry 54 (146)
T PF08646_consen 20 ACPNEKCNKKVTE-NGDGSYRCEKCNKTVENPKYRY 54 (146)
T ss_dssp E-TSTTTS-B-EE-ETTTEEEETTTTEEESS-EEEE
T ss_pred CCCCccCCCEeec-CCCcEEECCCCCCcCCCeeEEE
Confidence 499 99986433 3668999999999876555555
No 31
>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=87.83 E-value=0.3 Score=29.45 Aligned_cols=27 Identities=30% Similarity=0.663 Sum_probs=22.7
Q ss_pred cccCCCCCCceeEeEEeeeeeecCccee
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
...|+.|+.. .-...-|.|.|.+||-+
T Consensus 8 ~~~C~~C~~~-~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR-WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe-EeEccCCEEEhhhCceE
Confidence 3459999999 88899999998888764
No 32
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=87.52 E-value=0.17 Score=36.73 Aligned_cols=34 Identities=26% Similarity=0.598 Sum_probs=21.3
Q ss_pred HHHHHhhccccCCCCCCcee----EeEEeeeeeecCcce
Q psy836 33 KMEITQHAKYTCSFCGKDSM----KRSCVGIWSCKRCKR 67 (122)
Q Consensus 33 kie~~~~aky~Cp~Cgk~~m----kR~avGIW~C~~C~~ 67 (122)
+...+...-+.||+||...+ .| ..+.-.|+.||.
T Consensus 13 k~k~klpt~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~ 50 (99)
T PRK14892 13 RPKPKLPKIFECPRCGKVSISVKIKK-NIAIITCGNCGL 50 (99)
T ss_pred ccccCCCcEeECCCCCCeEeeeecCC-CcceEECCCCCC
Confidence 33445567789999996544 23 445566666654
No 33
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.25 E-value=0.34 Score=32.69 Aligned_cols=14 Identities=29% Similarity=0.767 Sum_probs=8.6
Q ss_pred hccccCCCCCCcee
Q psy836 39 HAKYTCSFCGKDSM 52 (122)
Q Consensus 39 ~aky~Cp~Cgk~~m 52 (122)
..+|.||.||...+
T Consensus 23 ~~~F~CPnCG~~~I 36 (59)
T PRK14890 23 AVKFLCPNCGEVII 36 (59)
T ss_pred cCEeeCCCCCCeeE
Confidence 35667777776533
No 34
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=86.94 E-value=0.4 Score=39.63 Aligned_cols=39 Identities=21% Similarity=0.505 Sum_probs=31.0
Q ss_pred HHHHhhccccCCCCCCce-eEeEEeeeeeecCcceeeecc
Q psy836 34 MEITQHAKYTCSFCGKDS-MKRSCVGIWSCKRCKRIVAGG 72 (122)
Q Consensus 34 ie~~~~aky~Cp~Cgk~~-mkR~avGIW~C~~C~~~vAgg 72 (122)
.+........||.||.+. +.-...|..-|..||.++...
T Consensus 4 ~~~~~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e~ 43 (310)
T PRK00423 4 LVLEEEEKLVCPECGSDKLIYDYERGEIVCADCGLVIEEN 43 (310)
T ss_pred hhhhcccCCcCcCCCCCCeeEECCCCeEeecccCCccccc
Confidence 345556677899999854 566789999999999998765
No 35
>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=86.81 E-value=0.72 Score=36.66 Aligned_cols=53 Identities=25% Similarity=0.474 Sum_probs=38.2
Q ss_pred CCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccccccC
Q psy836 44 CSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYN 102 (122)
Q Consensus 44 Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~~ 102 (122)
||.||++.-. .--| -|+.|=..-.+=+- ....+.|--|..||..+-+|.|...
T Consensus 1 C~~CG~~~~~-~~~~--lC~~C~~~~~~i~e---i~~~i~v~~C~~Cg~~~~~~~W~~~ 53 (236)
T PF04981_consen 1 CPRCGREIEP-LIDG--LCPDCYLKRFDIIE---IPDRIEVTICPKCGRYRIGGRWVDP 53 (236)
T ss_pred CCCCCCCCCC-cccc--cChHHhcccCCeee---cCCccCceECCCCCCEECCCEeeec
Confidence 9999996533 2223 79999776554333 3344577779999999999999987
No 36
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=86.61 E-value=0.52 Score=47.03 Aligned_cols=32 Identities=22% Similarity=0.316 Sum_probs=17.1
Q ss_pred ecCcCeEEeccccccCchHHHHHHHHHHHHHHh
Q psy836 87 CKRCKRIVAGGAWVYNTTAATSVRSAIRRLREV 119 (122)
Q Consensus 87 ~~rC~~~~AGGAy~~~T~~~~~~~~~i~rl~e~ 119 (122)
|.+|+...-.-.+. .-+....+++|+.+|.+-
T Consensus 712 CP~CGtplv~~~~~-~i~~~~~~~~A~~~~g~~ 743 (1337)
T PRK14714 712 CPRCDVELTPYQRR-TINVKEEYRSALENVGER 743 (1337)
T ss_pred CCCCCCcccccceE-EecHHHHHHHHHHHhCcc
Confidence 66665433322221 334566777788777553
No 37
>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=85.73 E-value=1 Score=31.20 Aligned_cols=18 Identities=22% Similarity=0.599 Sum_probs=5.4
Q ss_pred HHHHhhccccCCCCC-Cce
Q psy836 34 MEITQHAKYTCSFCG-KDS 51 (122)
Q Consensus 34 ie~~~~aky~Cp~Cg-k~~ 51 (122)
-.......+.||||+ ..+
T Consensus 15 ~~~~l~~~F~CPfC~~~~s 33 (81)
T PF05129_consen 15 KKPKLPKVFDCPFCNHEKS 33 (81)
T ss_dssp -----SS----TTT--SS-
T ss_pred cCCCCCceEcCCcCCCCCe
Confidence 334555789999999 544
No 38
>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=85.49 E-value=0.62 Score=27.00 Aligned_cols=27 Identities=22% Similarity=0.498 Sum_probs=17.3
Q ss_pred cccCCCCCCceeEeEE---eeeeeecCcce
Q psy836 41 KYTCSFCGKDSMKRSC---VGIWSCKRCKR 67 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~a---vGIW~C~~C~~ 67 (122)
.|.|+.||..--.... -..-.|+.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 5789999985322222 33667888876
No 39
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=85.41 E-value=0.45 Score=35.38 Aligned_cols=32 Identities=25% Similarity=0.573 Sum_probs=18.8
Q ss_pred hhccccCCCCCCceeEeE------EeeeeeecCcceee
Q psy836 38 QHAKYTCSFCGKDSMKRS------CVGIWSCKRCKRIV 69 (122)
Q Consensus 38 ~~aky~Cp~Cgk~~mkR~------avGIW~C~~C~~~v 69 (122)
...-|.||.||..---=. -.|.-.||.||..+
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 345789999986521101 13447777777653
No 40
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=85.31 E-value=0.26 Score=47.32 Aligned_cols=66 Identities=23% Similarity=0.528 Sum_probs=0.0
Q ss_pred hccccCCCCCCceeEeEE--ee-----eeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccccccCchHHHHHHH
Q psy836 39 HAKYTCSFCGKDSMKRSC--VG-----IWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTAATSVRS 111 (122)
Q Consensus 39 ~aky~Cp~Cgk~~mkR~a--vG-----IW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~~T~~~~~~~~ 111 (122)
-..+.||.||+.++...+ -| +|.|+.|+..+-.+ .|.+|+.....-.+ .+-+....+++
T Consensus 653 i~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~-------------~C~~C~~~~~~~~~-~~i~l~~~~~~ 718 (900)
T PF03833_consen 653 IGRRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVEED-------------ECPKCGRETTSYSK-QKIDLKEEYDR 718 (900)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred eecccCcccCCcchhhcCcccCCccccceeccccccccCcc-------------ccccccccCcccce-eecCHHHHHHH
Confidence 367789999999887766 23 56788888875554 58888876433222 23445555666
Q ss_pred HHHHHHH
Q psy836 112 AIRRLRE 118 (122)
Q Consensus 112 ~i~rl~e 118 (122)
|+.+|-+
T Consensus 719 A~e~lg~ 725 (900)
T PF03833_consen 719 ALENLGE 725 (900)
T ss_dssp -------
T ss_pred HHHhhcc
Confidence 6666654
No 41
>PRK11823 DNA repair protein RadA; Provisional
Probab=84.46 E-value=0.42 Score=41.45 Aligned_cols=32 Identities=31% Similarity=0.801 Sum_probs=25.1
Q ss_pred hhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeecc
Q psy836 38 QHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKR 79 (122)
Q Consensus 38 ~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~ 79 (122)
.+..|.|..||...-+.. |+||.|+ +|....-
T Consensus 4 ~~~~y~C~~Cg~~~~~~~----g~Cp~C~------~w~t~~e 35 (446)
T PRK11823 4 KKTAYVCQECGAESPKWL----GRCPECG------AWNTLVE 35 (446)
T ss_pred CCCeEECCcCCCCCcccC----eeCcCCC------Cccceee
Confidence 356799999999988875 9999995 4655544
No 42
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=83.28 E-value=0.57 Score=29.39 Aligned_cols=12 Identities=42% Similarity=1.334 Sum_probs=9.6
Q ss_pred cccCCCCCCceeE
Q psy836 41 KYTCSFCGKDSMK 53 (122)
Q Consensus 41 ky~Cp~Cgk~~mk 53 (122)
.|+|||||+ .+-
T Consensus 2 ~f~CP~C~~-~~~ 13 (54)
T PF05605_consen 2 SFTCPYCGK-GFS 13 (54)
T ss_pred CcCCCCCCC-ccC
Confidence 689999999 444
No 43
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=83.26 E-value=0.75 Score=31.82 Aligned_cols=22 Identities=32% Similarity=0.588 Sum_probs=10.5
Q ss_pred hccccCCCCCCceeEeEEeeee
Q psy836 39 HAKYTCSFCGKDSMKRSCVGIW 60 (122)
Q Consensus 39 ~aky~Cp~Cgk~~mkR~avGIW 60 (122)
-.+..||.||-..+.|.++.+=
T Consensus 22 ~~k~FCp~CGn~TL~rvsvsv~ 43 (73)
T PF08772_consen 22 MTKQFCPKCGNATLKRVSVSVD 43 (73)
T ss_dssp SS--S-SSS--S--EEEE-B--
T ss_pred CCceeCcccCCCcceEEEEEEC
Confidence 3678999999999999998753
No 44
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=82.54 E-value=0.58 Score=40.85 Aligned_cols=32 Identities=34% Similarity=0.908 Sum_probs=25.1
Q ss_pred hhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeecc
Q psy836 38 QHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKR 79 (122)
Q Consensus 38 ~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~ 79 (122)
.+..|.|..||-..-+.. |+||.|+ +|.....
T Consensus 4 ~~~~y~C~~Cg~~~~~~~----g~Cp~C~------~w~t~~~ 35 (454)
T TIGR00416 4 AKSKFVCQHCGADSPKWQ----GKCPACH------AWNTITE 35 (454)
T ss_pred CCCeEECCcCCCCCcccc----EECcCCC------Cccccch
Confidence 356799999999988875 9999995 4665554
No 45
>PRK12366 replication factor A; Reviewed
Probab=82.44 E-value=0.86 Score=41.52 Aligned_cols=23 Identities=26% Similarity=0.683 Sum_probs=10.1
Q ss_pred CCCCCCceeEeEEeeeeeecCccee
Q psy836 44 CSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 44 Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
||.|.|.-.. .-|.|.|++|+++
T Consensus 535 Cp~CnkKv~~--~~g~~~C~~c~~~ 557 (637)
T PRK12366 535 CPNCRKRVEE--VDGEYICEFCGEV 557 (637)
T ss_pred ccccCeEeEc--CCCcEECCCCCCC
Confidence 5555443321 2344555555544
No 46
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=82.19 E-value=1.5 Score=30.36 Aligned_cols=26 Identities=23% Similarity=0.733 Sum_probs=17.5
Q ss_pred cCCCCCCceeEeEEeeeeeecCcceeee
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKRIVA 70 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~~vA 70 (122)
.||.|+.. |.+.. |.++|..|.+-+.
T Consensus 3 ~CP~C~~~-L~~~~-~~~~C~~C~~~~~ 28 (70)
T PF07191_consen 3 TCPKCQQE-LEWQG-GHYHCEACQKDYK 28 (70)
T ss_dssp B-SSS-SB-EEEET-TEEEETTT--EEE
T ss_pred cCCCCCCc-cEEeC-CEEECccccccce
Confidence 69999988 77666 8999999998643
No 47
>PHA02942 putative transposase; Provisional
Probab=81.85 E-value=0.72 Score=39.56 Aligned_cols=26 Identities=19% Similarity=0.520 Sum_probs=18.4
Q ss_pred ccCCCCCCceeEeEEeeeeeecCccee
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
-+||.||... ++.+...|.|+.||..
T Consensus 326 q~Cs~CG~~~-~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 326 VSCPKCGHKM-VEIAHRYFHCPSCGYE 351 (383)
T ss_pred ccCCCCCCcc-CcCCCCEEECCCCCCE
Confidence 4599999754 3445568998888875
No 48
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=81.77 E-value=0.4 Score=27.19 Aligned_cols=13 Identities=15% Similarity=0.202 Sum_probs=7.1
Q ss_pred eeeeeecCcCeEE
Q psy836 82 VGIWSCKRCKRIV 94 (122)
Q Consensus 82 vtV~s~~rC~~~~ 94 (122)
+..+.|..||+.|
T Consensus 12 ~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 12 ESAKFCPHCGYDF 24 (26)
T ss_pred hhcCcCCCCCCCC
Confidence 3344466666654
No 49
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=80.48 E-value=1.3 Score=32.75 Aligned_cols=33 Identities=21% Similarity=0.635 Sum_probs=22.3
Q ss_pred cCCCCCCceeEeEEeeeeeecCcceeeecceeee
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDS 76 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~ 76 (122)
-||.|.|... -...|.|.|.+|+..+.---|-|
T Consensus 36 aC~~C~kkv~-~~~~~~~~C~~C~~~~~~~~~ry 68 (166)
T cd04476 36 ACPGCNKKVV-EEGNGTYRCEKCNKSVPNPEYRY 68 (166)
T ss_pred cccccCcccE-eCCCCcEECCCCCCcCCCccEEE
Confidence 4999988643 22238899999998875444444
No 50
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=80.26 E-value=1 Score=24.67 Aligned_cols=15 Identities=40% Similarity=1.008 Sum_probs=11.3
Q ss_pred HHhhccccCCCCCCc
Q psy836 36 ITQHAKYTCSFCGKD 50 (122)
Q Consensus 36 ~~~~aky~Cp~Cgk~ 50 (122)
-+...+|.||.|++.
T Consensus 9 H~~~k~~~C~~C~k~ 23 (26)
T PF13465_consen 9 HTGEKPYKCPYCGKS 23 (26)
T ss_dssp HSSSSSEEESSSSEE
T ss_pred cCCCCCCCCCCCcCe
Confidence 345578999999875
No 51
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=80.12 E-value=1.1 Score=28.03 Aligned_cols=27 Identities=26% Similarity=0.813 Sum_probs=17.8
Q ss_pred cccCCCCCCce-eEeEEeeeeeecCcceee
Q psy836 41 KYTCSFCGKDS-MKRSCVGIWSCKRCKRIV 69 (122)
Q Consensus 41 ky~Cp~Cgk~~-mkR~avGIW~C~~C~~~v 69 (122)
.|.|..||..- ++ ..+.=.|+.||..|
T Consensus 2 ~Y~C~~Cg~~~~~~--~~~~irC~~CG~rI 29 (44)
T smart00659 2 IYICGECGRENEIK--SKDVVRCRECGYRI 29 (44)
T ss_pred EEECCCCCCEeecC--CCCceECCCCCceE
Confidence 48888888863 43 23445788887764
No 52
>PF12773 DZR: Double zinc ribbon
Probab=79.16 E-value=0.47 Score=28.87 Aligned_cols=27 Identities=19% Similarity=0.303 Sum_probs=15.0
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcceee
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRIV 69 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~v 69 (122)
..||.||.... ......+.|+.|+..+
T Consensus 13 ~fC~~CG~~l~-~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 13 KFCPHCGTPLP-PPDQSKKICPNCGAEN 39 (50)
T ss_pred cCChhhcCChh-hccCCCCCCcCCcCCC
Confidence 45666766654 3333445666666653
No 53
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=79.14 E-value=1.7 Score=36.42 Aligned_cols=35 Identities=20% Similarity=0.470 Sum_probs=29.0
Q ss_pred ccCCCCCCceeEe-EEeeeeeecCcceeeecceeee
Q psy836 42 YTCSFCGKDSMKR-SCVGIWSCKRCKRIVAGGAWDS 76 (122)
Q Consensus 42 y~Cp~Cgk~~mkR-~avGIW~C~~C~~~vAggAy~~ 76 (122)
+.||.||.+.+-. ...|-|-|..||-++-+...++
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~~~id~ 37 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLVLEDSLIDP 37 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCEEeccccccC
Confidence 5799999996555 4789999999999998876654
No 54
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=79.07 E-value=0.96 Score=35.56 Aligned_cols=23 Identities=22% Similarity=0.684 Sum_probs=10.7
Q ss_pred hhhHhHHHHHHHhhccccCCCCCCc
Q psy836 26 SLRKMVKKMEITQHAKYTCSFCGKD 50 (122)
Q Consensus 26 slRK~v~kie~~~~aky~Cp~Cgk~ 50 (122)
-+|+-++.++..+ -|.||.||-+
T Consensus 121 ~~~~~Le~~~~~~--~~vC~vCGy~ 143 (166)
T COG1592 121 MFRGLLERLEEGK--VWVCPVCGYT 143 (166)
T ss_pred HHHHHHHhhhcCC--EEEcCCCCCc
Confidence 3455555555444 3444444433
No 55
>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=78.49 E-value=4.8 Score=23.40 Aligned_cols=43 Identities=19% Similarity=0.390 Sum_probs=24.1
Q ss_pred CCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEe
Q psy836 44 CSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVA 95 (122)
Q Consensus 44 Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~A 95 (122)
||+||...+.+...-.+-- . || ....-..+-.|.|..||+.+-
T Consensus 1 C~~C~~~~~~~~~~~~~~~------~-~~--~~~~i~~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYE------Y-GG--ELIVIENVPALVCPQCGEEYL 43 (46)
T ss_pred CCCCCCceecceEEEEEEE------e-CC--EEEEEeCCCccccccCCCEee
Confidence 8999777766666444331 1 11 112223445566888887764
No 56
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=78.32 E-value=1.5 Score=33.50 Aligned_cols=26 Identities=23% Similarity=0.429 Sum_probs=22.4
Q ss_pred cccCCCCCCceeEeEEeeeeeecCccee
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
.+.||.||.+.++ -.|-=.||-|+.+
T Consensus 28 ~~hCp~Cg~PLF~--KdG~v~CPvC~~~ 53 (131)
T COG1645 28 AKHCPKCGTPLFR--KDGEVFCPVCGYR 53 (131)
T ss_pred HhhCcccCCccee--eCCeEECCCCCce
Confidence 4679999999999 7888899988854
No 57
>KOG2462|consensus
Probab=77.08 E-value=1.2 Score=37.88 Aligned_cols=68 Identities=29% Similarity=0.501 Sum_probs=47.1
Q ss_pred HHHHHHhhc-cccCCCCCCcee--------EeEEeee--eeecCcceeeecceee---eeccceeeeeeecCcCeEEecc
Q psy836 32 KKMEITQHA-KYTCSFCGKDSM--------KRSCVGI--WSCKRCKRIVAGGAWD---SMKRSCVGIWSCKRCKRIVAGG 97 (122)
Q Consensus 32 ~kie~~~~a-ky~Cp~Cgk~~m--------kR~avGI--W~C~~C~~~vAggAy~---~~t~~AvtV~s~~rC~~~~AGG 97 (122)
.++++.-|. .+.|++|||.-- -|+-+|. ..|++|+|.+||--=- .-|-+.+-=-.|.+|+++||==
T Consensus 177 LkMHirTH~l~c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~ 256 (279)
T KOG2462|consen 177 LKMHIRTHTLPCECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALK 256 (279)
T ss_pred HhhHhhccCCCcccccccccccchHHhhcccccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHH
Confidence 356666676 899999999743 5777774 7899999999885321 1233344445699999988743
Q ss_pred cc
Q psy836 98 AW 99 (122)
Q Consensus 98 Ay 99 (122)
.|
T Consensus 257 Sy 258 (279)
T KOG2462|consen 257 SY 258 (279)
T ss_pred HH
Confidence 33
No 58
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=76.45 E-value=1.3 Score=37.85 Aligned_cols=28 Identities=36% Similarity=0.800 Sum_probs=22.4
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcceeeecceeeeecc
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKR 79 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~ 79 (122)
|.|..||....+.. |+||.|+ +|....-
T Consensus 1 ~~c~~cg~~~~~~~----g~cp~c~------~w~~~~e 28 (372)
T cd01121 1 YVCSECGYVSPKWL----GKCPECG------EWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCCcc----EECcCCC------Cceeeee
Confidence 78999999998875 8999996 4665544
No 59
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=76.40 E-value=1.5 Score=24.75 Aligned_cols=9 Identities=33% Similarity=1.169 Sum_probs=4.2
Q ss_pred ccccCCCCC
Q psy836 40 AKYTCSFCG 48 (122)
Q Consensus 40 aky~Cp~Cg 48 (122)
..|.||.||
T Consensus 15 v~f~CPnCG 23 (24)
T PF07754_consen 15 VPFPCPNCG 23 (24)
T ss_pred ceEeCCCCC
Confidence 344444444
No 60
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=76.15 E-value=3.6 Score=24.59 Aligned_cols=23 Identities=30% Similarity=0.741 Sum_probs=12.2
Q ss_pred cCCCCCCceeEeEE---eeeeeecCcc
Q psy836 43 TCSFCGKDSMKRSC---VGIWSCKRCK 66 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~a---vGIW~C~~C~ 66 (122)
+||.|+.. |.... +-|..|+.|+
T Consensus 1 ~CP~C~~~-l~~~~~~~~~id~C~~C~ 26 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRLGDVEIDVCPSCG 26 (41)
T ss_pred CcCCCCcc-cceEEECCEEEEECCCCC
Confidence 48888774 44333 2345544443
No 61
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=75.86 E-value=1 Score=30.38 Aligned_cols=31 Identities=19% Similarity=0.466 Sum_probs=23.1
Q ss_pred hhccccCCCCCCceeEeEEeeeeeecCccee
Q psy836 38 QHAKYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 38 ~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
+..+..|..||....-+.-.-...|+.||..
T Consensus 4 ~~~~~~CtSCg~~i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 4 MMEPPKCTSCGIEIAPREKAVKFLCPNCGEV 34 (59)
T ss_pred cccCccccCCCCcccCCCccCEeeCCCCCCe
Confidence 4466789999999877774456778888775
No 62
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=75.45 E-value=7 Score=26.34 Aligned_cols=41 Identities=27% Similarity=0.613 Sum_probs=22.2
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcceeeeccee----eeeccceeeeeeecCcCeE
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAW----DSMKRSCVGIWSCKRCKRI 93 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy----~~~t~~AvtV~s~~rC~~~ 93 (122)
|.||.||.....=..+ ...||.| +..... ..+-+|.+||++
T Consensus 1 y~C~KCg~~~~e~~~v----------~~tgg~~skiFdvq~~~-f~~v~C~~CGYT 45 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEV----------RATGGGLSKIFDVQNKK-FTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCCcceecceE----------EccCCeeEEEEEecCcE-EEEEECCCCCCE
Confidence 6788888764222111 1233333 223333 445589999987
No 63
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=75.31 E-value=0.78 Score=31.27 Aligned_cols=13 Identities=31% Similarity=0.848 Sum_probs=8.3
Q ss_pred hccccCCCCCCce
Q psy836 39 HAKYTCSFCGKDS 51 (122)
Q Consensus 39 ~aky~Cp~Cgk~~ 51 (122)
..+|.||.||...
T Consensus 25 ~v~F~CPnCGe~~ 37 (61)
T COG2888 25 AVKFPCPNCGEVE 37 (61)
T ss_pred eeEeeCCCCCcee
Confidence 3567777777543
No 64
>PRK04023 DNA polymerase II large subunit; Validated
Probab=74.83 E-value=1.7 Score=42.88 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=8.0
Q ss_pred EEeeeeeecCccee
Q psy836 55 SCVGIWSCKRCKRI 68 (122)
Q Consensus 55 ~avGIW~C~~C~~~ 68 (122)
..+|.-.|+.||..
T Consensus 622 VEVg~RfCpsCG~~ 635 (1121)
T PRK04023 622 VEIGRRKCPSCGKE 635 (1121)
T ss_pred ecccCccCCCCCCc
Confidence 34555566666654
No 65
>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=74.31 E-value=1.6 Score=30.23 Aligned_cols=27 Identities=22% Similarity=0.557 Sum_probs=20.5
Q ss_pred cCCCCCCceeEeEEeeeeeecCcceeeec
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKRIVAG 71 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~~vAg 71 (122)
.||.||...... .+.+.|+.|+.+..-
T Consensus 2 fC~~Cg~~l~~~--~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMTPK--NGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccccC--CCeEECcCCCCcccc
Confidence 599999887654 368999999976553
No 66
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=74.29 E-value=5.8 Score=31.41 Aligned_cols=60 Identities=18% Similarity=0.362 Sum_probs=34.8
Q ss_pred ccccCCCCCCc-eeEeEEeeeeee---cCcceeeecceeeeeccceeeeeeecCcCeEEeccccccCc
Q psy836 40 AKYTCSFCGKD-SMKRSCVGIWSC---KRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNT 103 (122)
Q Consensus 40 aky~Cp~Cgk~-~mkR~avGIW~C---~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~~T 103 (122)
.+.+||+|++. ..++.-+|--.- -.=-. --|.-..+---.||.|..||+.+.-.-|..-+
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~----~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F~~l~ 67 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFC----PRYKGVNPLFYEVWVCPHCGYAAFEEDFEKLS 67 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCc----cccCCCCCeeeeEEECCCCCCcccccccccCC
Confidence 57899999987 344433322110 00000 01223455667788899999988877776433
No 67
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=73.33 E-value=0.62 Score=34.70 Aligned_cols=65 Identities=14% Similarity=0.193 Sum_probs=44.7
Q ss_pred hhccccCCCCCCceeEeE-----EeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccccccCchH
Q psy836 38 QHAKYTCSFCGKDSMKRS-----CVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTA 105 (122)
Q Consensus 38 ~~aky~Cp~Cgk~~mkR~-----avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~~T~~ 105 (122)
++-+=.||+|+...+.+. ..--|.|+.|++++..---++... ....+..|..+++.+.+.+.-.+
T Consensus 27 ~~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~~~~~~~---~~~~~~~~~~~~~~~~~~i~~~a 96 (129)
T COG3677 27 QITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVETGSPLSK---ALYKIKLQAVTLYMLGLGIRDIA 96 (129)
T ss_pred hcccCcCCCCCccceeeECCccccccccccCCcCcceeeeccCcccc---cchHHHHHHHHHHHcCCCcccHH
Confidence 445578999998873332 355689999999866544444333 66778888888888877665443
No 68
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=72.22 E-value=1.7 Score=43.57 Aligned_cols=39 Identities=21% Similarity=0.604 Sum_probs=29.0
Q ss_pred cccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEecc
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGG 97 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGG 97 (122)
.+.||.||..... ..|+.||... ..+..|..||..+...
T Consensus 667 ~rkCPkCG~~t~~------~fCP~CGs~t------------e~vy~CPsCGaev~~d 705 (1337)
T PRK14714 667 RRRCPSCGTETYE------NRCPDCGTHT------------EPVYVCPDCGAEVPPD 705 (1337)
T ss_pred EEECCCCCCcccc------ccCcccCCcC------------CCceeCccCCCccCCC
Confidence 4899999997543 3999999862 1245799999987544
No 69
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=72.20 E-value=1.5 Score=25.38 Aligned_cols=24 Identities=29% Similarity=0.707 Sum_probs=12.2
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcce
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
|.|+.||-.-.. ...-|.|+-|+.
T Consensus 2 ~~C~~CGy~y~~--~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGYIYDG--EEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCCEECC--CcCCCcCcCCCC
Confidence 556666654221 125566666653
No 70
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=71.90 E-value=9.1 Score=23.15 Aligned_cols=12 Identities=25% Similarity=0.686 Sum_probs=7.9
Q ss_pred ccCCCCCCceeE
Q psy836 42 YTCSFCGKDSMK 53 (122)
Q Consensus 42 y~Cp~Cgk~~mk 53 (122)
+.||.||....-
T Consensus 1 ~~Cp~C~~~~a~ 12 (40)
T smart00440 1 APCPKCGNREAT 12 (40)
T ss_pred CcCCCCCCCeEE
Confidence 468888876433
No 71
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=71.60 E-value=5 Score=23.75 Aligned_cols=28 Identities=21% Similarity=0.357 Sum_probs=20.5
Q ss_pred cccCCCCCCceeEeEEeeeeeecCccee
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
...|+.||...+--..-++..|..|+.+
T Consensus 3 ~~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 3568888888776677777887777765
No 72
>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=70.85 E-value=2.9 Score=25.55 Aligned_cols=27 Identities=26% Similarity=0.779 Sum_probs=18.3
Q ss_pred cccCCCCCCc-eeE---eEEeeeeeecCcce
Q psy836 41 KYTCSFCGKD-SMK---RSCVGIWSCKRCKR 67 (122)
Q Consensus 41 ky~Cp~Cgk~-~mk---R~avGIW~C~~C~~ 67 (122)
.-.||.||.. +++ +...|-|.|..|+.
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 3469999654 554 22349999988863
No 73
>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=70.01 E-value=1.1 Score=26.62 Aligned_cols=9 Identities=44% Similarity=1.316 Sum_probs=5.3
Q ss_pred ccCCCCCCc
Q psy836 42 YTCSFCGKD 50 (122)
Q Consensus 42 y~Cp~Cgk~ 50 (122)
|.|..||..
T Consensus 1 Y~C~~Cg~~ 9 (32)
T PF03604_consen 1 YICGECGAE 9 (32)
T ss_dssp EBESSSSSS
T ss_pred CCCCcCCCe
Confidence 456666655
No 74
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=69.70 E-value=2.2 Score=23.90 Aligned_cols=23 Identities=26% Similarity=0.739 Sum_probs=14.6
Q ss_pred eeeeecCcceeeecceeeeeccceeeeeeecCcC
Q psy836 58 GIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCK 91 (122)
Q Consensus 58 GIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~ 91 (122)
|.|.|..|... +...-..|..|+
T Consensus 3 g~W~C~~C~~~-----------N~~~~~~C~~C~ 25 (30)
T PF00641_consen 3 GDWKCPSCTFM-----------NPASRSKCVACG 25 (30)
T ss_dssp SSEEETTTTEE-----------EESSSSB-TTT-
T ss_pred cCccCCCCcCC-----------chHHhhhhhCcC
Confidence 67999999875 344444577775
No 75
>PRK00420 hypothetical protein; Validated
Probab=69.54 E-value=6.4 Score=29.20 Aligned_cols=28 Identities=18% Similarity=0.349 Sum_probs=20.0
Q ss_pred ccccCCCCCCceeEeEEeeeeeecCccee
Q psy836 40 AKYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
....||.||.+.++= -.|--.|+.|+..
T Consensus 22 l~~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~ 49 (112)
T PRK00420 22 LSKHCPVCGLPLFEL-KDGEVVCPVHGKV 49 (112)
T ss_pred ccCCCCCCCCcceec-CCCceECCCCCCe
Confidence 346799999887762 4566787777764
No 76
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=68.89 E-value=3.5 Score=25.24 Aligned_cols=27 Identities=22% Similarity=0.657 Sum_probs=16.2
Q ss_pred cccCCCCCCce-eEeE-E-eeeeeecCcce
Q psy836 41 KYTCSFCGKDS-MKRS-C-VGIWSCKRCKR 67 (122)
Q Consensus 41 ky~Cp~Cgk~~-mkR~-a-vGIW~C~~C~~ 67 (122)
.|.|+.||..- +-+. + -..-.|+.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 57888888742 2221 1 13456888886
No 77
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=68.16 E-value=2.2 Score=21.16 Aligned_cols=9 Identities=44% Similarity=1.471 Sum_probs=3.7
Q ss_pred ccCCCCCCc
Q psy836 42 YTCSFCGKD 50 (122)
Q Consensus 42 y~Cp~Cgk~ 50 (122)
|.||.|++.
T Consensus 1 ~~C~~C~~~ 9 (24)
T PF13894_consen 1 FQCPICGKS 9 (24)
T ss_dssp EE-SSTS-E
T ss_pred CCCcCCCCc
Confidence 456666543
No 78
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=67.64 E-value=2.2 Score=31.24 Aligned_cols=26 Identities=27% Similarity=0.654 Sum_probs=15.0
Q ss_pred ccccCCCCCCce--eEeEEeeeeeecCccee
Q psy836 40 AKYTCSFCGKDS--MKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 40 aky~Cp~Cgk~~--mkR~avGIW~C~~C~~~ 68 (122)
.|++||.||+.- |.|.- =.|++||..
T Consensus 8 tKR~Cp~CG~kFYDLnk~P---ivCP~CG~~ 35 (108)
T PF09538_consen 8 TKRTCPSCGAKFYDLNKDP---IVCPKCGTE 35 (108)
T ss_pred CcccCCCCcchhccCCCCC---ccCCCCCCc
Confidence 467777777662 44422 146666654
No 79
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=67.10 E-value=5.2 Score=23.39 Aligned_cols=18 Identities=28% Similarity=0.623 Sum_probs=14.2
Q ss_pred eecCcCeEEeccccccCc
Q psy836 86 SCKRCKRIVAGGAWVYNT 103 (122)
Q Consensus 86 s~~rC~~~~AGGAy~~~T 103 (122)
+|+-|++.|.|..|.-.|
T Consensus 2 sCiDC~~~F~~~~y~~Ht 19 (28)
T PF08790_consen 2 SCIDCSKDFDGDSYKSHT 19 (28)
T ss_dssp EETTTTEEEEGGGTTT--
T ss_pred eeecCCCCcCcCCcCCCC
Confidence 699999999999887654
No 80
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=66.82 E-value=1.9 Score=23.57 Aligned_cols=7 Identities=43% Similarity=1.388 Sum_probs=3.4
Q ss_pred CCCCCCc
Q psy836 44 CSFCGKD 50 (122)
Q Consensus 44 Cp~Cgk~ 50 (122)
||.||+.
T Consensus 2 Cp~CG~~ 8 (23)
T PF13240_consen 2 CPNCGAE 8 (23)
T ss_pred CcccCCC
Confidence 4555444
No 81
>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=66.00 E-value=4.3 Score=34.22 Aligned_cols=54 Identities=19% Similarity=0.392 Sum_probs=24.7
Q ss_pred HHHhhccccCCCCCCceeEeE----EeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccccc
Q psy836 35 EITQHAKYTCSFCGKDSMKRS----CVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWV 100 (122)
Q Consensus 35 e~~~~aky~Cp~Cgk~~mkR~----avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~ 100 (122)
|.=-.....||-||...+... -|....|+.|+-. |++--. ...=+.++++|||.
T Consensus 25 E~Wv~~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~ee-----yELKSk-------~~~l~~~I~dGAY~ 82 (254)
T PF06044_consen 25 EDWVAENMYCPNCGSKPLSKFENNRPVADFYCPNCNEE-----YELKSK-------KKKLSNKINDGAYH 82 (254)
T ss_dssp HHHHHHH---TTT--SS-EE--------EEE-TTT--E-----EEEEEE-------ESS--SEEEEEEHH
T ss_pred HHHHHHCCcCCCCCChhHhhccCCCccceeECCCCchH-----Hhhhhh-------ccccCCcccCccHH
Confidence 344456788999999976654 5788999999864 333111 13334678888883
No 82
>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=65.98 E-value=3.5 Score=23.85 Aligned_cols=9 Identities=22% Similarity=0.708 Sum_probs=6.4
Q ss_pred ccCCCCCCc
Q psy836 42 YTCSFCGKD 50 (122)
Q Consensus 42 y~Cp~Cgk~ 50 (122)
..||.|+..
T Consensus 3 ~~CP~C~~~ 11 (38)
T TIGR02098 3 IQCPNCKTS 11 (38)
T ss_pred EECCCCCCE
Confidence 568888774
No 83
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=65.33 E-value=4.3 Score=31.32 Aligned_cols=36 Identities=11% Similarity=0.259 Sum_probs=23.5
Q ss_pred eecCcce--eeecceeeeeccceee-eeeecCcCeEEec
Q psy836 61 SCKRCKR--IVAGGAWDSMKRSCVG-IWSCKRCKRIVAG 96 (122)
Q Consensus 61 ~C~~C~~--~vAggAy~~~t~~Avt-V~s~~rC~~~~AG 96 (122)
+||+|+. +-+=..|..+-.+.+. -..|..||++|.+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~ 40 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTT 40 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceE
Confidence 6999994 2233334334455554 5889999999864
No 84
>PF14353 CpXC: CpXC protein
Probab=65.17 E-value=4.9 Score=28.69 Aligned_cols=9 Identities=44% Similarity=1.217 Sum_probs=5.9
Q ss_pred cCCCCCCce
Q psy836 43 TCSFCGKDS 51 (122)
Q Consensus 43 ~Cp~Cgk~~ 51 (122)
+||.||...
T Consensus 3 tCP~C~~~~ 11 (128)
T PF14353_consen 3 TCPHCGHEF 11 (128)
T ss_pred CCCCCCCee
Confidence 577777653
No 85
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=65.05 E-value=5.9 Score=32.18 Aligned_cols=29 Identities=17% Similarity=0.492 Sum_probs=21.8
Q ss_pred ccccCCCCCCceeEeEEeeeeeecCccee
Q psy836 40 AKYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
..-.||.||.....+..--...|+.|+..
T Consensus 98 ~~~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 98 SHRFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred cCccccccCCCCeecCCceeEECCCCCCE
Confidence 34469999998766655556789999865
No 86
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=64.84 E-value=3.2 Score=27.00 Aligned_cols=29 Identities=21% Similarity=0.489 Sum_probs=15.4
Q ss_pred ccccCCCCCCceeEeEEeeeeeecCccee
Q psy836 40 AKYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
..|.|..||+.--.=....--.|+.||..
T Consensus 5 ~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 5 MEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 35677777766521223333466666655
No 87
>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=64.83 E-value=15 Score=25.46 Aligned_cols=43 Identities=23% Similarity=0.454 Sum_probs=23.4
Q ss_pred CCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEec
Q psy836 44 CSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAG 96 (122)
Q Consensus 44 Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AG 96 (122)
||.||+..+.+. +..-+ .++-|-..++ -+..+.|..||..+..
T Consensus 1 C~~C~~~~~~~~-~~~~~-----~~~~G~~~~v----~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 1 CPICGSGELVRD-VKDEP-----YTYKGESITI----GVPGWYCPACGEELLD 43 (127)
T ss_pred CCCCCCccceee-eecce-----EEEcCEEEEE----eeeeeECCCCCCEEEc
Confidence 999997655422 22222 1222322222 5566679999887643
No 88
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=64.55 E-value=2.3 Score=37.86 Aligned_cols=30 Identities=20% Similarity=0.447 Sum_probs=19.8
Q ss_pred cccCCCCCCc-eeEeEEeeeeeecCcceeeecc
Q psy836 41 KYTCSFCGKD-SMKRSCVGIWSCKRCKRIVAGG 72 (122)
Q Consensus 41 ky~Cp~Cgk~-~mkR~avGIW~C~~C~~~vAgg 72 (122)
+=.||+||.. .-+-.. -|.|++|+.....-
T Consensus 350 ~p~Cp~Cg~~m~S~G~~--g~rC~kCg~~~~~~ 380 (421)
T COG1571 350 NPVCPRCGGRMKSAGRN--GFRCKKCGTRARET 380 (421)
T ss_pred CCCCCccCCchhhcCCC--CcccccccccCCcc
Confidence 4479999976 222222 59999999875443
No 89
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=64.24 E-value=7.2 Score=29.01 Aligned_cols=25 Identities=28% Similarity=0.747 Sum_probs=16.0
Q ss_pred CCCCCCceeEeEEeeeeeecCcceeeecc
Q psy836 44 CSFCGKDSMKRSCVGIWSCKRCKRIVAGG 72 (122)
Q Consensus 44 Cp~Cgk~~mkR~avGIW~C~~C~~~vAgg 72 (122)
||.||..- .|---+|+.|+-+|-|.
T Consensus 1 CPvCg~~l----~vt~l~C~~C~t~i~G~ 25 (113)
T PF09862_consen 1 CPVCGGEL----VVTRLKCPSCGTEIEGE 25 (113)
T ss_pred CCCCCCce----EEEEEEcCCCCCEEEee
Confidence 99999763 22335777777666553
No 90
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=63.86 E-value=4.9 Score=22.88 Aligned_cols=26 Identities=19% Similarity=0.396 Sum_probs=12.9
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcce
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
-.||.||.+...-.+--.-.|+.|+.
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred cccCcCCccccCCCCcCEeECCCCcC
Confidence 35999998876655543446666654
No 91
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=63.61 E-value=2.4 Score=21.69 Aligned_cols=8 Identities=63% Similarity=1.751 Sum_probs=3.8
Q ss_pred ccCCCCCC
Q psy836 42 YTCSFCGK 49 (122)
Q Consensus 42 y~Cp~Cgk 49 (122)
|.||.|++
T Consensus 1 y~C~~C~~ 8 (23)
T PF00096_consen 1 YKCPICGK 8 (23)
T ss_dssp EEETTTTE
T ss_pred CCCCCCCC
Confidence 34555544
No 92
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=63.14 E-value=2.6 Score=31.80 Aligned_cols=27 Identities=30% Similarity=0.742 Sum_probs=20.2
Q ss_pred hhccccCCCCCCce--eEeEEeeeeeecCccee
Q psy836 38 QHAKYTCSFCGKDS--MKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 38 ~~aky~Cp~Cgk~~--mkR~avGIW~C~~C~~~ 68 (122)
+-...+||.|||.. +.|+. .|.+|+..
T Consensus 66 kav~V~CP~C~K~TKmLGr~D----~CM~C~~p 94 (114)
T PF11023_consen 66 KAVQVECPNCGKQTKMLGRVD----ACMHCKEP 94 (114)
T ss_pred cceeeECCCCCChHhhhchhh----ccCcCCCc
Confidence 33456799999996 77773 78888764
No 93
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=63.13 E-value=2.5 Score=23.33 Aligned_cols=22 Identities=23% Similarity=0.581 Sum_probs=11.5
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcce
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
..||.||+. + ..+.=.|+.||.
T Consensus 3 ~~Cp~Cg~~-~---~~~~~fC~~CG~ 24 (26)
T PF13248_consen 3 MFCPNCGAE-I---DPDAKFCPNCGA 24 (26)
T ss_pred CCCcccCCc-C---CcccccChhhCC
Confidence 357777763 2 233345555554
No 94
>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=62.84 E-value=3.5 Score=33.51 Aligned_cols=53 Identities=17% Similarity=0.356 Sum_probs=21.1
Q ss_pred ccccCCCCCCc-eeEeEEe----ee-----------e-----eecCcceeeecceeee--eccceeeeeeecCcCe
Q psy836 40 AKYTCSFCGKD-SMKRSCV----GI-----------W-----SCKRCKRIVAGGAWDS--MKRSCVGIWSCKRCKR 92 (122)
Q Consensus 40 aky~Cp~Cgk~-~mkR~av----GI-----------W-----~C~~C~~~vAggAy~~--~t~~AvtV~s~~rC~~ 92 (122)
.+-.||.||.. .+-...- |. | .|+.||..=...-+.+ ....+.-|-.|..|+-
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~ 246 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGS 246 (290)
T ss_dssp T-SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTE
T ss_pred cCCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccc
Confidence 34689999887 3333222 21 2 3666666644444443 3566778888888874
No 95
>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=62.69 E-value=5.2 Score=24.23 Aligned_cols=17 Identities=24% Similarity=0.645 Sum_probs=13.6
Q ss_pred hccccCCCCCCceeEeE
Q psy836 39 HAKYTCSFCGKDSMKRS 55 (122)
Q Consensus 39 ~aky~Cp~Cgk~~mkR~ 55 (122)
...-.||.||...++|.
T Consensus 24 ~~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 24 DDPVPCPECGSTEVRRV 40 (42)
T ss_pred CCCCcCCCCCCCceEEe
Confidence 45678999999888875
No 96
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=62.50 E-value=7 Score=28.58 Aligned_cols=64 Identities=17% Similarity=0.340 Sum_probs=31.4
Q ss_pred cccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccccccCchHHHHHHHHHHHHHHh
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTAATSVRSAIRRLREV 119 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~~T~~~~~~~~~i~rl~e~ 119 (122)
+-.||+||.+..-+.+.-|+- . .++-.. -+|-|..|+-=|-==. .-+.|+++-+...+|++|..
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg-~-----------~~~~~~--~~y~C~~C~AyVG~H~-~t~~PlGtLAd~~lR~~R~~ 65 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYG-H-----------RYDDGP--YLYVCTPCDAYVGCHP-GTDIPLGTLADAELRRARKA 65 (102)
T ss_pred CcccCCCCCeeEEcccchhcC-c-----------cCCCCc--eeEECCCCCceeeeeC-CCCCcCcccCCHHHHHHHHH
Confidence 346999999876655433332 0 000001 1255666642211000 01456777777777766643
No 97
>KOG2593|consensus
Probab=62.36 E-value=6.4 Score=35.42 Aligned_cols=41 Identities=27% Similarity=0.546 Sum_probs=25.5
Q ss_pred hhHhHHHHHH--HhhccccCCCCCCc-------eeEeEEeeeeeecCcce
Q psy836 27 LRKMVKKMEI--TQHAKYTCSFCGKD-------SMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 27 lRK~v~kie~--~~~aky~Cp~Cgk~-------~mkR~avGIW~C~~C~~ 67 (122)
+||+++.-+. ...+-|.||+|.+. .+-=-..|-.+|..|+-
T Consensus 112 m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~g 161 (436)
T KOG2593|consen 112 MRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGG 161 (436)
T ss_pred HHHHHHHHhhhccccccccCCccccchhhhHHHHhhcccCceEEEecCCC
Confidence 4555555433 35688999999987 11112357788766654
No 98
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=62.29 E-value=3.5 Score=31.66 Aligned_cols=26 Identities=15% Similarity=0.119 Sum_probs=16.2
Q ss_pred ccccCCCCCCce--eEeEEeeeeeecCccee
Q psy836 40 AKYTCSFCGKDS--MKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 40 aky~Cp~Cgk~~--mkR~avGIW~C~~C~~~ 68 (122)
.|++||.||+.- +.|.- =.|++||..
T Consensus 8 tKr~Cp~cg~kFYDLnk~p---~vcP~cg~~ 35 (129)
T TIGR02300 8 TKRICPNTGSKFYDLNRRP---AVSPYTGEQ 35 (129)
T ss_pred ccccCCCcCccccccCCCC---ccCCCcCCc
Confidence 577888888763 44432 256666665
No 99
>PHA00616 hypothetical protein
Probab=61.88 E-value=2.6 Score=26.77 Aligned_cols=11 Identities=36% Similarity=0.697 Sum_probs=8.4
Q ss_pred cccCCCCCCce
Q psy836 41 KYTCSFCGKDS 51 (122)
Q Consensus 41 ky~Cp~Cgk~~ 51 (122)
+|+||.||+.-
T Consensus 1 pYqC~~CG~~F 11 (44)
T PHA00616 1 MYQCLRCGGIF 11 (44)
T ss_pred CCccchhhHHH
Confidence 48899998753
No 100
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=61.42 E-value=6.7 Score=28.62 Aligned_cols=30 Identities=20% Similarity=0.432 Sum_probs=24.0
Q ss_pred cCCCCCCceeEeE--EeeeeeecCcceeeecc
Q psy836 43 TCSFCGKDSMKRS--CVGIWSCKRCKRIVAGG 72 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~--avGIW~C~~C~~~vAgg 72 (122)
.||.||..-.-+. ..+.+.|++|+...--.
T Consensus 4 FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 4 FCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 6999999987776 46799999999765433
No 101
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=60.95 E-value=3.9 Score=23.31 Aligned_cols=20 Identities=25% Similarity=0.576 Sum_probs=11.1
Q ss_pred cCCCCCCceeEeEEeeeeee
Q psy836 43 TCSFCGKDSMKRSCVGIWSC 62 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C 62 (122)
.||.||...++-..--+|.|
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C 20 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRC 20 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE
T ss_pred CcCCCCCEeEcCCCCEeEEC
Confidence 59999999886555446665
No 102
>PRK12366 replication factor A; Reviewed
Probab=60.79 E-value=5.3 Score=36.53 Aligned_cols=53 Identities=21% Similarity=0.432 Sum_probs=34.3
Q ss_pred hHhHHHHHHHhhccccCCCCCCceeEeE-EeeeeeecCcceeeecceeeeeccceeeeeeecCcCeE
Q psy836 28 RKMVKKMEITQHAKYTCSFCGKDSMKRS-CVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRI 93 (122)
Q Consensus 28 RK~v~kie~~~~aky~Cp~Cgk~~mkR~-avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~ 93 (122)
||.+.+|+. ..+ -...|.....+. ..=+..||.|+|+|..+ -+.|.|.+|+++
T Consensus 504 ~~~I~~i~~---~~~-~~v~g~i~~i~~~~~~y~aCp~CnkKv~~~---------~g~~~C~~c~~~ 557 (637)
T PRK12366 504 RKFIADLEE---DDT-VEIRGTVVDIRKQKIILYLCPNCRKRVEEV---------DGEYICEFCGEV 557 (637)
T ss_pred ccCHHHccc---CCe-EEEEEEEEEEeCCCEEEecccccCeEeEcC---------CCcEECCCCCCC
Confidence 455555544 444 455565543333 33356899999998743 278899999987
No 103
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=60.24 E-value=7.8 Score=24.95 Aligned_cols=29 Identities=17% Similarity=0.434 Sum_probs=17.6
Q ss_pred ccccCC--CCCCceeEeEEeeeeeecCccee
Q psy836 40 AKYTCS--FCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 40 aky~Cp--~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
..-.|| .||.-.+==.-..-|+|.+|+.|
T Consensus 17 ~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 17 LRKECPSPRCGAGVFMAEHKDRHYCGKCGYT 47 (47)
T ss_dssp SSEE-TSTTTTSSSEEEE-SSEEEETTTSS-
T ss_pred hhhcCCCcccCCceEeeecCCCccCCCcccC
Confidence 455799 99986433333467898888753
No 104
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=60.22 E-value=3.4 Score=38.23 Aligned_cols=45 Identities=20% Similarity=0.392 Sum_probs=26.8
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccccccCc
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNT 103 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~~T 103 (122)
..||.||..... =.|+.||..+.. +.+.|..||.....=.|.+-+
T Consensus 16 kFC~~CG~~l~~------~~Cp~CG~~~~~-----------~~~fC~~CG~~~~~~~~~~~~ 60 (645)
T PRK14559 16 RFCQKCGTSLTH------KPCPQCGTEVPV-----------DEAHCPNCGAETGTIWWAIIA 60 (645)
T ss_pred ccccccCCCCCC------CcCCCCCCCCCc-----------ccccccccCCcccchhhhhcc
Confidence 357777776421 158888776433 334588888776555554443
No 105
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=60.14 E-value=6.4 Score=24.31 Aligned_cols=16 Identities=25% Similarity=0.644 Sum_probs=12.6
Q ss_pred cCCCCCCceeEeEEee
Q psy836 43 TCSFCGKDSMKRSCVG 58 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avG 58 (122)
.||.||.....|.+..
T Consensus 1 ~CP~Cg~~a~ir~S~~ 16 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQ 16 (47)
T ss_pred CcCCCCCeeEEEEchh
Confidence 5999999987776643
No 106
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=59.67 E-value=4 Score=24.84 Aligned_cols=25 Identities=36% Similarity=0.971 Sum_probs=11.4
Q ss_pred cccCCCCCCce--eEeEEe---eeeeecCc
Q psy836 41 KYTCSFCGKDS--MKRSCV---GIWSCKRC 65 (122)
Q Consensus 41 ky~Cp~Cgk~~--mkR~av---GIW~C~~C 65 (122)
+..|+|||+.. +.+.-. |.+-|..|
T Consensus 1 ~~~CSFCgr~~~~v~~li~g~~~~~IC~~C 30 (41)
T PF06689_consen 1 EKRCSFCGRPESEVGRLISGPNGAYICDEC 30 (41)
T ss_dssp --B-TTT--BTTTSSSEEEES-SEEEEHHH
T ss_pred CCCccCCCCCHHHHhceecCCCCcEECHHH
Confidence 35799999984 344333 44565555
No 107
>PRK08402 replication factor A; Reviewed
Probab=58.27 E-value=5.4 Score=34.35 Aligned_cols=26 Identities=15% Similarity=0.452 Sum_probs=16.1
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcce
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
..||.|.|.-..-..-|.|.|..|+.
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGE 238 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCC
Confidence 35777766443334457777777775
No 108
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.68 E-value=9.6 Score=27.60 Aligned_cols=29 Identities=34% Similarity=0.668 Sum_probs=19.5
Q ss_pred cCCCCCCce--eEeEEeeeeeecCcceeeec
Q psy836 43 TCSFCGKDS--MKRSCVGIWSCKRCKRIVAG 71 (122)
Q Consensus 43 ~Cp~Cgk~~--mkR~avGIW~C~~C~~~vAg 71 (122)
.||.|+-.. .-|..|-|=.||.|.=+|-+
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrGVWLD 33 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRGVWLD 33 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCccccEeec
Confidence 589998774 45666777777666655443
No 109
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=56.55 E-value=9.3 Score=22.83 Aligned_cols=26 Identities=31% Similarity=0.563 Sum_probs=13.3
Q ss_pred cCCCCCCceeEeEEee----eeeecCccee
Q psy836 43 TCSFCGKDSMKRSCVG----IWSCKRCKRI 68 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avG----IW~C~~C~~~ 68 (122)
.||.||.....+.-.| -+-|+.|+.+
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 4999999876665544 3677777654
No 110
>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=56.26 E-value=13 Score=28.95 Aligned_cols=25 Identities=24% Similarity=0.805 Sum_probs=17.4
Q ss_pred CCCCCCceeEeE------------EeeeeeecCccee
Q psy836 44 CSFCGKDSMKRS------------CVGIWSCKRCKRI 68 (122)
Q Consensus 44 Cp~Cgk~~mkR~------------avGIW~C~~C~~~ 68 (122)
||.||...++.. -.=-+.|++||.+
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr 37 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYR 37 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCc
Confidence 999998755552 2334788888875
No 111
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=55.61 E-value=12 Score=35.08 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=17.6
Q ss_pred cCCCCCCceeEeEEeeeeeecCccee
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
.||.||. .+.+. -|=..|+.||..
T Consensus 726 ~Cp~Cg~-~l~~~-~GC~~C~~CG~s 749 (752)
T PRK08665 726 ACPECGS-ILEHE-EGCVVCHSCGYS 749 (752)
T ss_pred CCCCCCc-ccEEC-CCCCcCCCCCCC
Confidence 5999994 45444 388898888874
No 112
>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=55.59 E-value=9.2 Score=22.40 Aligned_cols=25 Identities=20% Similarity=0.586 Sum_probs=9.6
Q ss_pred cCCCCCCceeEeEEeeeeeecCccee
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
.||.|+..-.- .--.++-|+.|+.-
T Consensus 4 ~Cp~C~se~~y-~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY-EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E-E-SSSEEETTTTEE
T ss_pred CCCCCCCccee-ccCCEEeCCccccc
Confidence 47777766433 34445666655543
No 113
>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=55.32 E-value=8.6 Score=22.77 Aligned_cols=26 Identities=19% Similarity=0.415 Sum_probs=15.1
Q ss_pred cCCCCCCceeEeEEeeee-eecCccee
Q psy836 43 TCSFCGKDSMKRSCVGIW-SCKRCKRI 68 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW-~C~~C~~~ 68 (122)
.||.||....-+...... .|+.|+..
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~ 29 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYE 29 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-E
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCc
Confidence 699999886554443322 46666554
No 114
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=55.21 E-value=8.2 Score=24.11 Aligned_cols=11 Identities=45% Similarity=1.062 Sum_probs=5.4
Q ss_pred ccccCCCCCCc
Q psy836 40 AKYTCSFCGKD 50 (122)
Q Consensus 40 aky~Cp~Cgk~ 50 (122)
++-.||.|+++
T Consensus 19 ~~~~CPlC~r~ 29 (54)
T PF04423_consen 19 AKGCCPLCGRP 29 (54)
T ss_dssp -SEE-TTT--E
T ss_pred CCCcCCCCCCC
Confidence 44489999976
No 115
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=55.04 E-value=3.9 Score=37.89 Aligned_cols=42 Identities=17% Similarity=0.359 Sum_probs=30.3
Q ss_pred cCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccc-ccc
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGA-WVY 101 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGA-y~~ 101 (122)
.||.||..- .-|--.|+.||..+. ...|..||..+..|+ |++
T Consensus 3 ~Cp~Cg~~n----~~~akFC~~CG~~l~-------------~~~Cp~CG~~~~~~~~fC~ 45 (645)
T PRK14559 3 ICPQCQFEN----PNNNRFCQKCGTSLT-------------HKPCPQCGTEVPVDEAHCP 45 (645)
T ss_pred cCCCCCCcC----CCCCccccccCCCCC-------------CCcCCCCCCCCCccccccc
Confidence 699999874 344458999998752 146999999876654 555
No 116
>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=55.01 E-value=9.2 Score=23.73 Aligned_cols=24 Identities=29% Similarity=0.589 Sum_probs=17.3
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcc
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCK 66 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~ 66 (122)
-.||.||-+.|+ .--|.-.|..|+
T Consensus 18 ~~Cp~C~~PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMR-DKDGKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEE-ecCCCEECCCCC
Confidence 469999999998 335556776663
No 117
>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=54.06 E-value=9.6 Score=28.24 Aligned_cols=9 Identities=22% Similarity=0.608 Sum_probs=7.4
Q ss_pred cCCCCCCce
Q psy836 43 TCSFCGKDS 51 (122)
Q Consensus 43 ~Cp~Cgk~~ 51 (122)
.|+.|+..-
T Consensus 93 RC~~CN~~L 101 (147)
T PF01927_consen 93 RCPKCNGPL 101 (147)
T ss_pred ccCCCCcEe
Confidence 699998864
No 118
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=53.56 E-value=8.2 Score=28.01 Aligned_cols=33 Identities=24% Similarity=0.775 Sum_probs=20.0
Q ss_pred eec--CcceeeecceeeeeccceeeeeeecCcCeEEecccccc
Q psy836 61 SCK--RCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVY 101 (122)
Q Consensus 61 ~C~--~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~ 101 (122)
.|+ .|+++|..+.- +.|.|.+|++.+..-.|.+
T Consensus 20 aC~~~~C~kKv~~~~~--------~~y~C~~C~~~~~~~~~ry 54 (146)
T PF08646_consen 20 ACPNEKCNKKVTENGD--------GSYRCEKCNKTVENPKYRY 54 (146)
T ss_dssp E-TSTTTS-B-EEETT--------TEEEETTTTEEESS-EEEE
T ss_pred CCCCccCCCEeecCCC--------cEEECCCCCCcCCCeeEEE
Confidence 699 99998764321 4478999999975544433
No 119
>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=53.07 E-value=7.7 Score=23.40 Aligned_cols=24 Identities=25% Similarity=0.703 Sum_probs=16.7
Q ss_pred ccCCCCCCce-eEeEEee-----eeeecCc
Q psy836 42 YTCSFCGKDS-MKRSCVG-----IWSCKRC 65 (122)
Q Consensus 42 y~Cp~Cgk~~-mkR~avG-----IW~C~~C 65 (122)
-.||+|+.+. ++|-..+ .|.|+.|
T Consensus 6 v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 3699999998 8875432 4666555
No 120
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=52.80 E-value=4.2 Score=31.65 Aligned_cols=30 Identities=20% Similarity=0.451 Sum_probs=19.0
Q ss_pred ecCcCeEEeccccccCchHHHHHHHHHHHHHHh
Q psy836 87 CKRCKRIVAGGAWVYNTTAATSVRSAIRRLREV 119 (122)
Q Consensus 87 ~~rC~~~~AGGAy~~~T~~~~~~~~~i~rl~e~ 119 (122)
|..||...- +.-|+.....++.-|..|.+.
T Consensus 139 Cp~Cg~~L~---~~dn~~~~~~l~~~I~~l~~~ 168 (178)
T PRK06266 139 CPQCGEMLE---EYDNSELIKELKEQIKELEEE 168 (178)
T ss_pred CCCCCCCCe---ecccHHHHHHHHHHHHHHHHH
Confidence 666654332 234777777788777777664
No 121
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=52.58 E-value=8.8 Score=36.27 Aligned_cols=40 Identities=20% Similarity=0.344 Sum_probs=29.7
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeE
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRI 93 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~ 93 (122)
..||+|+..-.-=...+.=.|..||.. --.-.+|..||-+
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~------------~~~p~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQ------------EPIPQSCPECGSE 484 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCC------------CCCCCCCCCCCCC
Confidence 469999888766666789999999985 1223459999765
No 122
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=52.00 E-value=7.3 Score=28.13 Aligned_cols=41 Identities=22% Similarity=0.511 Sum_probs=23.1
Q ss_pred hhHhHHHHHHH-----hhccccCCCCCCceeEeEEeeeeeecCcce
Q psy836 27 LRKMVKKMEIT-----QHAKYTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 27 lRK~v~kie~~-----~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
.+|-+.+|+.= -...|.|+.||....--.+-+--+||+|+.
T Consensus 23 ~~k~~~~il~Crt~~~G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 23 QRKAVEAILACRTEALGFHRYRCEDCGHEKIVYNSCKNRHCPSCQA 68 (111)
T ss_pred HHHHHHHHHhcCCccCCcceeecCCCCceEEecCcccCcCCCCCCC
Confidence 34445555432 234577888877765555555556666654
No 123
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=51.75 E-value=4.7 Score=21.57 Aligned_cols=11 Identities=36% Similarity=1.171 Sum_probs=7.9
Q ss_pred eeeeecCccee
Q psy836 58 GIWSCKRCKRI 68 (122)
Q Consensus 58 GIW~C~~C~~~ 68 (122)
|.|.|..|+..
T Consensus 1 g~W~C~~C~~~ 11 (26)
T smart00547 1 GDWECPACTFL 11 (26)
T ss_pred CcccCCCCCCc
Confidence 56888888653
No 124
>KOG3214|consensus
Probab=51.63 E-value=9 Score=28.73 Aligned_cols=54 Identities=19% Similarity=0.401 Sum_probs=36.2
Q ss_pred HHhhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccccccCchHHHH
Q psy836 36 ITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTAATS 108 (122)
Q Consensus 36 ~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~~T~~~~~ 108 (122)
...-..|.||||.-.+. =+| ++....-+|.-+|.-|+..|+.-+=.+++|.-.+
T Consensus 18 ~~ldt~FnClfcnHek~-------v~~------------~~Dk~~~iG~~sC~iC~esFqt~it~LsepIDVY 71 (109)
T KOG3214|consen 18 EPLDTQFNCLFCNHEKS-------VSC------------TLDKKHNIGKASCRICEESFQTTITALSEPIDVY 71 (109)
T ss_pred cchheeeccCccccccc-------eee------------eehhhcCcceeeeeehhhhhccchHhhccchHHH
Confidence 34456788999976641 111 2344555666778999999888887777776554
No 125
>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=51.10 E-value=31 Score=20.63 Aligned_cols=9 Identities=33% Similarity=1.102 Sum_probs=4.0
Q ss_pred cCCCCCCce
Q psy836 43 TCSFCGKDS 51 (122)
Q Consensus 43 ~Cp~Cgk~~ 51 (122)
+||.||...
T Consensus 2 ~Cp~Cg~~~ 10 (39)
T PF01096_consen 2 KCPKCGHNE 10 (39)
T ss_dssp --SSS-SSE
T ss_pred CCcCCCCCe
Confidence 577777664
No 126
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=50.40 E-value=7 Score=28.30 Aligned_cols=12 Identities=17% Similarity=0.498 Sum_probs=6.1
Q ss_pred eeeeeecCccee
Q psy836 57 VGIWSCKRCKRI 68 (122)
Q Consensus 57 vGIW~C~~C~~~ 68 (122)
-+...|+.|+..
T Consensus 68 p~~~~C~~Cg~~ 79 (114)
T PRK03681 68 EAECWCETCQQY 79 (114)
T ss_pred CcEEEcccCCCe
Confidence 344555555543
No 127
>PRK07218 replication factor A; Provisional
Probab=50.21 E-value=6.9 Score=34.56 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=19.6
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcceeeecceeee
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDS 76 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~ 76 (122)
..||.|++.- ..|.|+.||.+ .+-|++
T Consensus 298 ~rCP~C~r~v------~~~~C~~hG~v--e~~~dl 324 (423)
T PRK07218 298 ERCPECGRVI------QKGQCRSHGAV--EGEDDL 324 (423)
T ss_pred ecCcCccccc------cCCcCCCCCCc--CCeeee
Confidence 5799998765 33899999976 444544
No 128
>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=49.34 E-value=10 Score=33.53 Aligned_cols=38 Identities=18% Similarity=0.345 Sum_probs=23.9
Q ss_pred cCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCe
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKR 92 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~ 92 (122)
.||.|+-.-.--...+.=.|..||.+ +.--+.|..|+-
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~------------~~~~~~Cp~C~s 261 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQ------------EPIPKTCPQCGS 261 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCc------------CCCCCCCCCCCC
Confidence 47777765444345556678888875 222346888865
No 129
>PF04641 Rtf2: Rtf2 RING-finger
Probab=48.82 E-value=18 Score=29.24 Aligned_cols=57 Identities=18% Similarity=0.348 Sum_probs=40.1
Q ss_pred hhccccCCCCCCce-eEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEecccccc
Q psy836 38 QHAKYTCSFCGKDS-MKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVY 101 (122)
Q Consensus 38 ~~aky~Cp~Cgk~~-mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~ 101 (122)
....|.||..++.- -+-..|-||.| |-+++.-|..-.. .=+.|.-|+..|.---=.+
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~c---G~V~s~~alke~k----~~~~Cp~c~~~f~~~DiI~ 167 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPC---GCVFSEKALKELK----KSKKCPVCGKPFTEEDIIP 167 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCC---CCEeeHHHHHhhc----ccccccccCCccccCCEEE
Confidence 57889999999884 45678999985 5566666665553 1235999999887554333
No 130
>PRK08173 DNA topoisomerase III; Validated
Probab=48.55 E-value=17 Score=34.72 Aligned_cols=26 Identities=19% Similarity=0.575 Sum_probs=17.6
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcceee
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRIV 69 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~v 69 (122)
-.||.||+..+++ -+.|.|..|+.++
T Consensus 625 ~~CP~Cg~~~~~~--~~~~~Cs~C~f~~ 650 (862)
T PRK08173 625 TPCPNCGGVVKEN--YRRFACTKCDFSI 650 (862)
T ss_pred ccCCccccccccc--CceeEcCCCCccc
Confidence 4699999864322 3349998887653
No 131
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=48.52 E-value=6.8 Score=22.67 Aligned_cols=12 Identities=50% Similarity=1.060 Sum_probs=6.5
Q ss_pred hccccCCCCCCc
Q psy836 39 HAKYTCSFCGKD 50 (122)
Q Consensus 39 ~aky~Cp~Cgk~ 50 (122)
.++|+||.|+..
T Consensus 11 ~~kY~Cp~C~~~ 22 (30)
T PF04438_consen 11 PAKYRCPRCGAR 22 (30)
T ss_dssp EESEE-TTT--E
T ss_pred CCEEECCCcCCc
Confidence 467888888754
No 132
>PRK12495 hypothetical protein; Provisional
Probab=48.43 E-value=15 Score=30.50 Aligned_cols=30 Identities=23% Similarity=0.519 Sum_probs=22.5
Q ss_pred ccccCCCCCCceeEeEEeeeeeecCcceeeec
Q psy836 40 AKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAG 71 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAg 71 (122)
..+.|+.||.+.++ --|.=.|+.|...+..
T Consensus 41 sa~hC~~CG~PIpa--~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 41 TNAHCDECGDPIFR--HDGQEFCPTCQQPVTE 70 (226)
T ss_pred chhhcccccCcccC--CCCeeECCCCCCcccc
Confidence 35779999999882 2688888888776543
No 133
>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=48.11 E-value=19 Score=27.59 Aligned_cols=26 Identities=23% Similarity=0.620 Sum_probs=14.0
Q ss_pred cCCCCCCceeEe-EEe----------eeeeecCccee
Q psy836 43 TCSFCGKDSMKR-SCV----------GIWSCKRCKRI 68 (122)
Q Consensus 43 ~Cp~Cgk~~mkR-~av----------GIW~C~~C~~~ 68 (122)
.||.||+...-| .-+ =-+.|.+||.+
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk 39 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYK 39 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--E
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCE
Confidence 599999985333 233 33788888775
No 134
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=47.34 E-value=16 Score=25.47 Aligned_cols=12 Identities=25% Similarity=0.595 Sum_probs=8.5
Q ss_pred eeeeeecCcCeE
Q psy836 82 VGIWSCKRCKRI 93 (122)
Q Consensus 82 vtV~s~~rC~~~ 93 (122)
..+.+|.+||++
T Consensus 38 f~~itCk~CgYt 49 (68)
T COG3478 38 FIVITCKNCGYT 49 (68)
T ss_pred EEEEEeccCCch
Confidence 446678888875
No 135
>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=47.03 E-value=16 Score=25.45 Aligned_cols=31 Identities=23% Similarity=0.441 Sum_probs=13.6
Q ss_pred ecCcCeEEeccccccC-chHHHHHHHHHHHHHHh
Q psy836 87 CKRCKRIVAGGAWVYN-TTAATSVRSAIRRLREV 119 (122)
Q Consensus 87 ~~rC~~~~AGGAy~~~-T~~~~~~~~~i~rl~e~ 119 (122)
|-.||. .|.+..+- .--..+...|++.|.+.
T Consensus 57 Cf~Cg~--~Gd~i~~v~~~~~~~f~eAv~~l~~~ 88 (97)
T PF01807_consen 57 CFGCGK--GGDVIDFVMKYEGCSFKEAVKWLAEE 88 (97)
T ss_dssp ETTT----EE-HHHHHHHHHT--HHHHHHHHHHH
T ss_pred ECCCCC--CCcHHhHHHHHhCCCHHHHHHHHHHH
Confidence 556653 35554441 22344566677766653
No 136
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=46.66 E-value=12 Score=29.51 Aligned_cols=23 Identities=30% Similarity=0.731 Sum_probs=17.7
Q ss_pred eeeecCcceeeecceeeeeccceeeeeeecCcC
Q psy836 59 IWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCK 91 (122)
Q Consensus 59 IW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~ 91 (122)
+|.|+-||.++.|-| -+.|+.||
T Consensus 134 ~~vC~vCGy~~~ge~----------P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHEGEA----------PEVCPICG 156 (166)
T ss_pred EEEcCCCCCcccCCC----------CCcCCCCC
Confidence 899999999988733 12388887
No 137
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=46.39 E-value=21 Score=28.19 Aligned_cols=28 Identities=29% Similarity=0.866 Sum_probs=20.7
Q ss_pred HHhhccccCCCCCCceeEeEEeeeeeecCcce
Q psy836 36 ITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 36 ~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
+..-..|.|+.||-..-... |.||.|+.
T Consensus 349 ~~~~p~~~c~~cg~~~~~~~----~~c~~c~~ 376 (389)
T PRK11788 349 LKRKPRYRCRNCGFTARTLY----WHCPSCKA 376 (389)
T ss_pred HhCCCCEECCCCCCCCccce----eECcCCCC
Confidence 45566788999998876654 78888864
No 138
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=46.35 E-value=13 Score=26.77 Aligned_cols=19 Identities=5% Similarity=0.190 Sum_probs=10.0
Q ss_pred ccccccChhhhHhHHHHHH
Q psy836 18 KYGTRYGASLRKMVKKMEI 36 (122)
Q Consensus 18 kyG~RYG~slRK~v~kie~ 36 (122)
+-..-.|...++...++..
T Consensus 79 ~~~~~Hg~~fk~~~~~ig~ 97 (157)
T PF10263_consen 79 GRRRGHGKEFKQWARRIGA 97 (157)
T ss_pred CCCCCCCHHHHHHHHHHCC
Confidence 3334455655655555555
No 139
>PF02977 CarbpepA_inh: Carboxypeptidase A inhibitor; InterPro: IPR004231 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family is represented by the well-characterised metallocarboxypeptidase A inhibitor (MCPI) from potatoes, which belongs to the MEROPS inhibitor family I37, clan IE. It inhibits metallopeptidases belonging to MEROPS peptidase family M14, carboxypeptidase A. In Russet Burbank potatoes, it is a mixture of approximately equal amounts of two polypeptide chains containing 38 or 39 amino acid residues. The chains differ in their amino terminal sequence only [] and are resistant to fragmentation by proteases []. The structure of the complex between bovine carboxypeptidase A and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-A resolution []. The potato inhibitor is synthesised as a precursor, having a 29 residue N-terminal signal peptide, a 27 residue pro-peptide, the 39 residue mature inhibitor region and a 7 residue C-terminal extension. The 7 residue C-terminal extension is involved in inhibitor inactivation and may be required for targeting to the vacuole where the mature active inhibitor accumulates []. The N-terminal region and the mature inhibitor are weakly related to other solananaceous proteins found in this entry, from potato, tomato and henbane, which have been incorrectly described as metallocarboxipeptidase inhibitors [].; GO: 0008191 metalloendopeptidase inhibitor activity; PDB: 4CPA_I 1H20_A 2HLG_A.
Probab=46.21 E-value=4.4 Score=26.26 Aligned_cols=34 Identities=26% Similarity=0.495 Sum_probs=21.2
Q ss_pred CCCCc-eeEeEEeeeeeecCc-ceeeecceeeeecc
Q psy836 46 FCGKD-SMKRSCVGIWSCKRC-KRIVAGGAWDSMKR 79 (122)
Q Consensus 46 ~Cgk~-~mkR~avGIW~C~~C-~~~vAggAy~~~t~ 79 (122)
-|++. ...=...|+|-|.-| +++..++-|+.++-
T Consensus 7 tCn~~C~t~sDC~g~tlC~~C~k~~~t~~g~~~~~~ 42 (46)
T PF02977_consen 7 TCNKYCNTNSDCSGITLCQWCWKLKKTCGGYVGSAC 42 (46)
T ss_dssp TTT-B-SSSCCCTTSSSS-EE-CCCEBCC--EEEEE
T ss_pred ccCCccccCccccceeehHHHHhcccCCCCccccee
Confidence 34444 344457899999999 88888888877653
No 140
>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=45.06 E-value=28 Score=29.46 Aligned_cols=20 Identities=15% Similarity=0.305 Sum_probs=12.2
Q ss_pred HhhccccCCCCCCceeEeEE
Q psy836 37 TQHAKYTCSFCGKDSMKRSC 56 (122)
Q Consensus 37 ~~~aky~Cp~Cgk~~mkR~a 56 (122)
.....++||.||....--..
T Consensus 254 ~~t~~~~C~~C~~~~~~~~q 273 (299)
T TIGR01385 254 AVTDLFTCGKCKQKKCTYYQ 273 (299)
T ss_pred CCcccccCCCCCCccceEEE
Confidence 33446888888876543333
No 141
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=45.03 E-value=10 Score=32.67 Aligned_cols=33 Identities=24% Similarity=0.389 Sum_probs=22.4
Q ss_pred ccCCCCCCc--eeEeE-EeeeeeecCcceeeecceeee
Q psy836 42 YTCSFCGKD--SMKRS-CVGIWSCKRCKRIVAGGAWDS 76 (122)
Q Consensus 42 y~Cp~Cgk~--~mkR~-avGIW~C~~C~~~vAggAy~~ 76 (122)
..||||+.. ++.-. .-++|+|-.|+. .|++.++
T Consensus 35 ~~CPfh~ek~pSf~v~~~k~~~~Cf~Cg~--~Gd~i~f 70 (415)
T TIGR01391 35 GLCPFHHEKTPSFSVSPEKQFYHCFGCGA--GGDAIKF 70 (415)
T ss_pred eeCCCCCCCCCeEEEEcCCCcEEECCCCC--CCCHHHH
Confidence 469999754 33333 457899988886 4666655
No 142
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=44.92 E-value=26 Score=24.32 Aligned_cols=14 Identities=21% Similarity=0.494 Sum_probs=7.4
Q ss_pred eeeeeecCcCeEEe
Q psy836 82 VGIWSCKRCKRIVA 95 (122)
Q Consensus 82 vtV~s~~rC~~~~A 95 (122)
.++-.|..||.++|
T Consensus 36 st~V~C~~CG~~l~ 49 (67)
T COG2051 36 STVVTCLICGTTLA 49 (67)
T ss_pred ceEEEecccccEEE
Confidence 33344666666554
No 143
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=44.20 E-value=8.2 Score=26.87 Aligned_cols=47 Identities=17% Similarity=0.255 Sum_probs=20.3
Q ss_pred ccccccChhhhHhHHHHHHHhhccccCCCCCCce-eEeEEeeeeeecCcce
Q psy836 18 KYGTRYGASLRKMVKKMEITQHAKYTCSFCGKDS-MKRSCVGIWSCKRCKR 67 (122)
Q Consensus 18 kyG~RYG~slRK~v~kie~~~~aky~Cp~Cgk~~-mkR~avGIW~C~~C~~ 67 (122)
+...+||.+....- ++... ....|+.|+++. ......-+=||-.+|.
T Consensus 2 ~~~~~Ygit~~~~~-~l~~~--q~~~C~iC~~~~~~~~~~~~vDHdH~tG~ 49 (81)
T PF02945_consen 2 RLKRRYGITPEEYE-ALLEE--QGGRCAICGKPLPGESRKLVVDHDHKTGR 49 (81)
T ss_dssp -----H-HHHHHHH-CCHHH--TTTE-TTT-SEEETTCGGCEEEE-TTTTB
T ss_pred CcccccCCCHHHHH-HHHHH--hCCcCcCCCCCcccCCCcceecCCCCCCC
Confidence 35678999987665 33333 344899999832 1122223335555544
No 144
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=43.71 E-value=19 Score=28.93 Aligned_cols=59 Identities=22% Similarity=0.405 Sum_probs=40.8
Q ss_pred HHhhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEecccccc
Q psy836 36 ITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVY 101 (122)
Q Consensus 36 ~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~ 101 (122)
-..-+.+.|..||+ .-.|-|+|++.-.+=|--+--|.-.++-.- |..||.-..|+.-.+
T Consensus 82 R~RD~~~~CiSCG~-----~~~~~~dagHy~s~g~~~~lRF~~~N~~~q--C~~CN~~~sgn~~~Y 140 (189)
T PF05766_consen 82 RLRDAGKPCISCGR-----KHGGQWDAGHYRSRGAAPELRFNEDNIHAQ--CKHCNRHLSGNIVEY 140 (189)
T ss_pred HHHhcCCCcccCCC-----cCCCCcccccccccccCcccccChhhHhHc--CCccccccccCHHHH
Confidence 34446899999999 345889998887763444444444444444 999999988876543
No 145
>PRK04351 hypothetical protein; Provisional
Probab=43.59 E-value=17 Score=27.65 Aligned_cols=29 Identities=24% Similarity=0.685 Sum_probs=18.7
Q ss_pred ccccCCCCCCc--eeEeEEeeeeeecCccee
Q psy836 40 AKYTCSFCGKD--SMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 40 aky~Cp~Cgk~--~mkR~avGIW~C~~C~~~ 68 (122)
-.|.|..||.. +.+|...-.+.|..|+-.
T Consensus 111 y~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~ 141 (149)
T PRK04351 111 YLYECQSCGQQYLRKRRINTKRYRCGKCRGK 141 (149)
T ss_pred EEEECCCCCCEeeeeeecCCCcEEeCCCCcE
Confidence 45778888874 345555566777766644
No 146
>PLN03086 PRLI-interacting factor K; Provisional
Probab=43.49 E-value=5.9 Score=36.48 Aligned_cols=28 Identities=18% Similarity=0.484 Sum_probs=21.1
Q ss_pred cCCC--CCCceeEeEEeeeeeecCcceeee
Q psy836 43 TCSF--CGKDSMKRSCVGIWSCKRCKRIVA 70 (122)
Q Consensus 43 ~Cp~--Cgk~~mkR~avGIW~C~~C~~~vA 70 (122)
.||. ||..-.++.----|+|+.|++.+.
T Consensus 435 ~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~ 464 (567)
T PLN03086 435 VCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ 464 (567)
T ss_pred eCCcccccceeeccccccCccCCCCCCccc
Confidence 3653 888877777777888888888764
No 147
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=43.49 E-value=7.8 Score=29.42 Aligned_cols=12 Identities=8% Similarity=0.157 Sum_probs=8.8
Q ss_pred hccccCCCCCCc
Q psy836 39 HAKYTCSFCGKD 50 (122)
Q Consensus 39 ~aky~Cp~Cgk~ 50 (122)
..-|.||.|+..
T Consensus 107 ~~~Y~Cp~c~~r 118 (158)
T TIGR00373 107 NMFFICPNMCVR 118 (158)
T ss_pred CCeEECCCCCcE
Confidence 456889999854
No 148
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=42.28 E-value=6.1 Score=34.17 Aligned_cols=59 Identities=22% Similarity=0.522 Sum_probs=35.9
Q ss_pred HHHHHhhccc----cCCCCCCc---eeEeEE---eee-----------e-----eecCcceeeecceeeeec--cceeee
Q psy836 33 KMEITQHAKY----TCSFCGKD---SMKRSC---VGI-----------W-----SCKRCKRIVAGGAWDSMK--RSCVGI 84 (122)
Q Consensus 33 kie~~~~aky----~Cp~Cgk~---~mkR~a---vGI-----------W-----~C~~C~~~vAggAy~~~t--~~AvtV 84 (122)
.|+.+.+.++ .||.||.. +|-+.. .|. | +|..|+.+=--+=|.+.+ -++|-.
T Consensus 173 ~i~~~~~~e~e~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t~~l~y~sl~s~E~A~vkA 252 (308)
T COG3058 173 GIPGKARVENESRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQSKKLHYWSLESSELAAVKA 252 (308)
T ss_pred cCCccccccccccccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhccccccCCccceeccchhhhHhhh
Confidence 4455555555 89999987 344433 222 3 367777765555555544 566666
Q ss_pred eeecCcC
Q psy836 85 WSCKRCK 91 (122)
Q Consensus 85 ~s~~rC~ 91 (122)
-+|..|+
T Consensus 253 EtC~~C~ 259 (308)
T COG3058 253 ETCGDCN 259 (308)
T ss_pred hcCCcHH
Confidence 7777774
No 149
>PRK14873 primosome assembly protein PriA; Provisional
Probab=42.03 E-value=16 Score=33.90 Aligned_cols=39 Identities=28% Similarity=0.573 Sum_probs=23.4
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeE
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRI 93 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~ 93 (122)
..||.|+-.-.--...+.=.|..||.. + .-|.|..||-.
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~------------~-~p~~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRA------------A-PDWRCPRCGSD 431 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCC------------C-cCccCCCCcCC
Confidence 356777655433345566778888764 1 13558888653
No 150
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=41.85 E-value=23 Score=31.91 Aligned_cols=39 Identities=23% Similarity=0.362 Sum_probs=19.8
Q ss_pred hhhhHhHHHHHHHhhccc--------cCCCCCCceeEeEEeeeeeecCccee
Q psy836 25 ASLRKMVKKMEITQHAKY--------TCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 25 ~slRK~v~kie~~~~aky--------~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
..|++.|+++.....-.| .|+.||.... +.+.||.||..
T Consensus 467 ~al~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~~-----~~~~CP~CGs~ 513 (546)
T PF13597_consen 467 EALEKLVRYAMENTGIPYFTINPPIDICPDCGYIGG-----EGDKCPKCGSE 513 (546)
T ss_dssp HHHHHHHHHHHH--H-SEEEEE--EEEETTT---S-------EEE-CCC---
T ss_pred HHHHHHHHHHHHhCCCCeEEEecCcccccCCCcCCC-----CCCCCCCCCCc
Confidence 456777777777444444 4999997543 37899999987
No 151
>PRK06450 threonine synthase; Validated
Probab=41.66 E-value=9.6 Score=31.93 Aligned_cols=25 Identities=32% Similarity=0.638 Sum_probs=17.8
Q ss_pred cccCCCCCCceeEeEEeeeeeecCccee
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
++.|+.||+..- ..-.|.|+.|+-.
T Consensus 3 ~~~C~~Cg~~~~---~~~~~~C~~cg~~ 27 (338)
T PRK06450 3 KEVCMKCGKERE---SIYEIRCKKCGGP 27 (338)
T ss_pred eeEECCcCCcCC---CcccccCCcCCCE
Confidence 478999998852 1335899999743
No 152
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=41.59 E-value=25 Score=19.76 Aligned_cols=21 Identities=19% Similarity=0.586 Sum_probs=9.6
Q ss_pred cCCCCCCceeEeEEeeeeeecCcc
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCK 66 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~ 66 (122)
.|..|++..-.-. .++|..|+
T Consensus 2 ~C~~C~~~~~~~~---~Y~C~~c~ 22 (30)
T PF03107_consen 2 WCDVCRRKIDGFY---FYHCSECC 22 (30)
T ss_pred CCCCCCCCcCCCE---eEEeCCCC
Confidence 4555544432222 45555555
No 153
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.56 E-value=20 Score=26.64 Aligned_cols=14 Identities=14% Similarity=0.527 Sum_probs=8.4
Q ss_pred eeeeeecCcceeee
Q psy836 57 VGIWSCKRCKRIVA 70 (122)
Q Consensus 57 vGIW~C~~C~~~vA 70 (122)
-..|.|+.||..+.
T Consensus 68 p~~~~C~~CG~~~~ 81 (135)
T PRK03824 68 EAVLKCRNCGNEWS 81 (135)
T ss_pred ceEEECCCCCCEEe
Confidence 35667777765543
No 154
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=40.92 E-value=30 Score=27.47 Aligned_cols=26 Identities=23% Similarity=0.503 Sum_probs=15.4
Q ss_pred cCCCCCCce-eEeEEe-----------eeeeecCccee
Q psy836 43 TCSFCGKDS-MKRSCV-----------GIWSCKRCKRI 68 (122)
Q Consensus 43 ~Cp~Cgk~~-mkR~av-----------GIW~C~~C~~~ 68 (122)
.||.||... .+=.-+ =-+.|++||.+
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr 39 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYR 39 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCc
Confidence 599998652 222222 24778888764
No 155
>smart00355 ZnF_C2H2 zinc finger.
Probab=40.84 E-value=14 Score=18.03 Aligned_cols=9 Identities=56% Similarity=1.257 Sum_probs=5.7
Q ss_pred ccCCCCCCc
Q psy836 42 YTCSFCGKD 50 (122)
Q Consensus 42 y~Cp~Cgk~ 50 (122)
|.|+.|++.
T Consensus 1 ~~C~~C~~~ 9 (26)
T smart00355 1 YRCPECGKV 9 (26)
T ss_pred CCCCCCcch
Confidence 467777654
No 156
>smart00507 HNHc HNH nucleases.
Probab=40.46 E-value=22 Score=19.97 Aligned_cols=14 Identities=29% Similarity=0.847 Sum_probs=10.6
Q ss_pred HhhccccCCCCCCce
Q psy836 37 TQHAKYTCSFCGKDS 51 (122)
Q Consensus 37 ~~~aky~Cp~Cgk~~ 51 (122)
.++. +.|++||...
T Consensus 7 ~~r~-~~C~~C~~~~ 20 (52)
T smart00507 7 LHRD-GVCAYCGKPA 20 (52)
T ss_pred HHHC-CCCcCCcCCC
Confidence 3445 8999999875
No 157
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=40.39 E-value=18 Score=27.26 Aligned_cols=23 Identities=26% Similarity=0.862 Sum_probs=14.5
Q ss_pred eeeeecCcCeEEeccccccCchHHHHHHHH
Q psy836 83 GIWSCKRCKRIVAGGAWVYNTTAATSVRSA 112 (122)
Q Consensus 83 tV~s~~rC~~~~AGGAy~~~T~~~~~~~~~ 112 (122)
-||||..| -|.++-..+..+.+.
T Consensus 61 ~VwSC~dC-------~~iH~ke~~~~ilr~ 83 (112)
T COG2158 61 KVWSCSDC-------HWIHRKEGAEEILRE 83 (112)
T ss_pred EEeecccc-------ceecccchHHHHHHH
Confidence 37778888 466666666555433
No 158
>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=40.37 E-value=23 Score=30.13 Aligned_cols=31 Identities=16% Similarity=0.440 Sum_probs=17.7
Q ss_pred eecCcceeeecce-eeeec---cceeeeeeecCcCe
Q psy836 61 SCKRCKRIVAGGA-WDSMK---RSCVGIWSCKRCKR 92 (122)
Q Consensus 61 ~C~~C~~~vAggA-y~~~t---~~AvtV~s~~rC~~ 92 (122)
.|+.|+.. -+-. |++.. ..++-+-+|..|+-
T Consensus 226 ~C~~Cg~~-~~l~y~~~e~~~~~~~~r~e~C~~C~~ 260 (305)
T TIGR01562 226 KCSHCEES-KHLAYLSLEHDAEKAVLKAETCDSCQG 260 (305)
T ss_pred cCCCCCCC-CceeeEeecCCCCCcceEEeecccccc
Confidence 37777764 1222 33322 35677778999963
No 159
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=40.07 E-value=17 Score=25.16 Aligned_cols=25 Identities=20% Similarity=0.602 Sum_probs=12.3
Q ss_pred ccCCCCCCceeEeEEeeeeeecCccee
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
+.| .||....-+..+---+| .||++
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~ 28 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKT 28 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEE
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCe
Confidence 345 46666655555555565 55554
No 160
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=39.77 E-value=25 Score=28.83 Aligned_cols=30 Identities=20% Similarity=0.538 Sum_probs=17.8
Q ss_pred ccccCCCCCCce-----------eEeEEeeeeeecCcceee
Q psy836 40 AKYTCSFCGKDS-----------MKRSCVGIWSCKRCKRIV 69 (122)
Q Consensus 40 aky~Cp~Cgk~~-----------mkR~avGIW~C~~C~~~v 69 (122)
..-.||.||..- +.+.-.--|.|.+||..-
T Consensus 13 ~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~ 53 (201)
T COG1779 13 TRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRS 53 (201)
T ss_pred eeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcc
Confidence 345699999841 133444556666666653
No 161
>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=39.70 E-value=21 Score=21.40 Aligned_cols=14 Identities=29% Similarity=0.593 Sum_probs=10.3
Q ss_pred cCCCCCCceeEeEE
Q psy836 43 TCSFCGKDSMKRSC 56 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~a 56 (122)
.||.||..-+.|.+
T Consensus 3 ~CP~Cg~~lv~r~~ 16 (39)
T PF01396_consen 3 KCPKCGGPLVLRRG 16 (39)
T ss_pred CCCCCCceeEEEEC
Confidence 69999987655543
No 162
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=39.31 E-value=20 Score=24.70 Aligned_cols=15 Identities=20% Similarity=0.782 Sum_probs=11.2
Q ss_pred ccCCCCCCceeEeEE
Q psy836 42 YTCSFCGKDSMKRSC 56 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~a 56 (122)
..||+||....-|.+
T Consensus 2 m~CP~Cg~~a~irtS 16 (72)
T PRK09678 2 FHCPLCQHAAHARTS 16 (72)
T ss_pred ccCCCCCCccEEEEC
Confidence 479999999855544
No 163
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=38.69 E-value=14 Score=24.40 Aligned_cols=13 Identities=31% Similarity=0.606 Sum_probs=7.3
Q ss_pred cccCCCCCCceeE
Q psy836 41 KYTCSFCGKDSMK 53 (122)
Q Consensus 41 ky~Cp~Cgk~~mk 53 (122)
.+.|+.|++...+
T Consensus 4 eiRC~~CnklLa~ 16 (51)
T PF10122_consen 4 EIRCGHCNKLLAK 16 (51)
T ss_pred ceeccchhHHHhh
Confidence 4556666665444
No 164
>PRK06386 replication factor A; Reviewed
Probab=38.54 E-value=13 Score=32.33 Aligned_cols=20 Identities=30% Similarity=0.454 Sum_probs=13.8
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcce
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
..||.|++.--+ |.|+.||.
T Consensus 237 ~rCP~C~R~l~~------g~C~~HG~ 256 (358)
T PRK06386 237 TKCSVCNKIIED------GVCKDHPD 256 (358)
T ss_pred ecCcCCCeEccC------CcCCCCCC
Confidence 568888765442 68888876
No 165
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=38.51 E-value=4.2 Score=26.03 Aligned_cols=26 Identities=38% Similarity=0.907 Sum_probs=17.4
Q ss_pred cCCCCCCce--eEe--EEeeeeeecCcceee
Q psy836 43 TCSFCGKDS--MKR--SCVGIWSCKRCKRIV 69 (122)
Q Consensus 43 ~Cp~Cgk~~--mkR--~avGIW~C~~C~~~v 69 (122)
.|+.||+.. +.| .+=| |-|+.|.+++
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 499998873 332 4456 7877777664
No 166
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=38.44 E-value=14 Score=32.09 Aligned_cols=54 Identities=20% Similarity=0.317 Sum_probs=39.9
Q ss_pred cccCCCCCCceeEeEEeeeeeecCcceeeecceeee-eccceeeeeeecCcCeEEecccccc
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDS-MKRSCVGIWSCKRCKRIVAGGAWVY 101 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~-~t~~AvtV~s~~rC~~~~AGGAy~~ 101 (122)
.-.||+||+.-- ..----|+.|-.. .+.. .+.-.+.|.-|..||..+-+|-|.-
T Consensus 6 ~~~C~~CGr~~~---~~~~~lC~dC~~~----~~~~~~ip~~~~v~~C~~Cga~~~~~~W~~ 60 (355)
T COG1499 6 TILCVRCGRSVD---PLIDGLCGDCYVE----TTPLIEIPDEVNVEVCRHCGAYRIRGRWVD 60 (355)
T ss_pred ccEeccCCCcCc---hhhccccHHHHhc----cCccccCCCceEEEECCcCCCccCCCccee
Confidence 457999999865 2222368899876 2333 3334788888999999999999988
No 167
>COG4640 Predicted membrane protein [Function unknown]
Probab=38.24 E-value=14 Score=33.55 Aligned_cols=27 Identities=19% Similarity=0.495 Sum_probs=18.5
Q ss_pred cCCCCCCceeEeEEeeeeeecCcceeeecce
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKRIVAGGA 73 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggA 73 (122)
.||-||+.. +-+--+|+.||..+.++-
T Consensus 3 fC~kcG~qk----~Ed~~qC~qCG~~~t~~~ 29 (465)
T COG4640 3 FCPKCGSQK----AEDDVQCTQCGHKFTSRQ 29 (465)
T ss_pred ccccccccc----ccccccccccCCcCCchh
Confidence 588888765 344556888888776653
No 168
>smart00400 ZnF_CHCC zinc finger.
Probab=38.12 E-value=32 Score=21.35 Aligned_cols=26 Identities=27% Similarity=0.516 Sum_probs=16.1
Q ss_pred ccCCCCCCc--eeEeE-EeeeeeecCcce
Q psy836 42 YTCSFCGKD--SMKRS-CVGIWSCKRCKR 67 (122)
Q Consensus 42 y~Cp~Cgk~--~mkR~-avGIW~C~~C~~ 67 (122)
..|||++.. ++.-. .-+.|+|-.|+.
T Consensus 3 ~~cPfh~d~~pSf~v~~~kn~~~Cf~cg~ 31 (55)
T smart00400 3 GLCPFHGEKTPSFSVSPDKQFFHCFGCGA 31 (55)
T ss_pred ccCcCCCCCCCCEEEECCCCEEEEeCCCC
Confidence 359999755 44333 347788766653
No 169
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=38.07 E-value=23 Score=26.58 Aligned_cols=30 Identities=13% Similarity=0.276 Sum_probs=17.9
Q ss_pred cCCCCCCceeEeEEeeeeeecCcceeeecce
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKRIVAGGA 73 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggA 73 (122)
.||.|+..-..-.. ..|-|+.|+.-|+..+
T Consensus 4 ~CP~C~seytY~dg-~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYTYHDG-TQLICPSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcceEecC-CeeECccccccccccc
Confidence 47777766444332 2577777776665543
No 170
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.04 E-value=20 Score=32.68 Aligned_cols=13 Identities=15% Similarity=0.348 Sum_probs=9.5
Q ss_pred hhhHhHHHHHHHh
Q psy836 26 SLRKMVKKMEITQ 38 (122)
Q Consensus 26 slRK~v~kie~~~ 38 (122)
.-||-+.+|...+
T Consensus 436 ~~~ktI~ei~~~~ 448 (608)
T TIGR00617 436 AERKTIAEIQAEN 448 (608)
T ss_pred cccccHHHHhhhc
Confidence 4688888887654
No 171
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=38.00 E-value=20 Score=21.17 Aligned_cols=14 Identities=36% Similarity=0.821 Sum_probs=10.5
Q ss_pred cccCCCCCCceeEe
Q psy836 41 KYTCSFCGKDSMKR 54 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR 54 (122)
+..||.||...+.+
T Consensus 2 ~~~Cp~Cg~~~~~~ 15 (47)
T PF14690_consen 2 PPRCPHCGSPSVHR 15 (47)
T ss_pred CccCCCcCCCceEC
Confidence 56799999887544
No 172
>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=37.99 E-value=19 Score=21.60 Aligned_cols=12 Identities=25% Similarity=0.908 Sum_probs=6.6
Q ss_pred ecCcCeEEeccc
Q psy836 87 CKRCKRIVAGGA 98 (122)
Q Consensus 87 ~~rC~~~~AGGA 98 (122)
|..|++.+.++.
T Consensus 29 C~~C~~~l~~~~ 40 (58)
T PF00412_consen 29 CSKCGKPLNDGD 40 (58)
T ss_dssp ETTTTCBTTTSS
T ss_pred cCCCCCccCCCe
Confidence 555555555554
No 173
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=37.85 E-value=27 Score=29.86 Aligned_cols=52 Identities=23% Similarity=0.572 Sum_probs=29.4
Q ss_pred ccccCCCCCCc---eeEeE--Eeee-----------e-----eecCcceeeeccee-eeecc-ceeeeeeecCcCe
Q psy836 40 AKYTCSFCGKD---SMKRS--CVGI-----------W-----SCKRCKRIVAGGAW-DSMKR-SCVGIWSCKRCKR 92 (122)
Q Consensus 40 aky~Cp~Cgk~---~mkR~--avGI-----------W-----~C~~C~~~vAggAy-~~~t~-~AvtV~s~~rC~~ 92 (122)
.+..||.||.. +|-+. ..|. | .|+.|+.. -+-.| ++..- .++-+-+|..|+-
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~-~~l~y~~~~~~~~~~r~e~C~~C~~ 260 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQS-GKLHYWSLDSEQAAVKAESCGDCGT 260 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCC-CceeeeeecCCCcceEeeecccccc
Confidence 46789999887 33221 1221 3 37777763 12222 22222 5778888999974
No 174
>PRK05667 dnaG DNA primase; Validated
Probab=37.53 E-value=16 Score=33.15 Aligned_cols=33 Identities=18% Similarity=0.379 Sum_probs=22.0
Q ss_pred ccCCCCCCc--eeE-eEEeeeeeecCcceeeecceeee
Q psy836 42 YTCSFCGKD--SMK-RSCVGIWSCKRCKRIVAGGAWDS 76 (122)
Q Consensus 42 y~Cp~Cgk~--~mk-R~avGIW~C~~C~~~vAggAy~~ 76 (122)
..||||+.. ++. -..-++|+|-.||. .|++.++
T Consensus 37 ~~CPfH~ektpSf~V~~~k~~~~CF~Cg~--~Gd~i~f 72 (580)
T PRK05667 37 GLCPFHDEKTPSFTVSPDKQFYHCFGCGA--GGDVIKF 72 (580)
T ss_pred ecCCCCCCCCCceEEECCCCeEEECCCCC--CCCHHHH
Confidence 359999854 332 23568999988886 3666555
No 175
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=37.46 E-value=19 Score=25.23 Aligned_cols=21 Identities=29% Similarity=0.759 Sum_probs=16.3
Q ss_pred cccCCCCCCceeEeEEeeeee
Q psy836 41 KYTCSFCGKDSMKRSCVGIWS 61 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~ 61 (122)
||.||-||...+....-|.+-
T Consensus 1 K~~CPCCg~~Tl~~~~~~~yd 21 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERGEGTYD 21 (78)
T ss_pred CccCCCCCcEEeccCCCcCce
Confidence 689999999988777655443
No 176
>PHA02768 hypothetical protein; Provisional
Probab=37.34 E-value=14 Score=24.49 Aligned_cols=16 Identities=38% Similarity=0.910 Sum_probs=11.7
Q ss_pred cccCCCCCCceeEeEE
Q psy836 41 KYTCSFCGKDSMKRSC 56 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~a 56 (122)
-|.||.||+.-..+.+
T Consensus 5 ~y~C~~CGK~Fs~~~~ 20 (55)
T PHA02768 5 GYECPICGEIYIKRKS 20 (55)
T ss_pred ccCcchhCCeeccHHH
Confidence 5899999998655443
No 177
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=37.10 E-value=18 Score=27.64 Aligned_cols=54 Identities=19% Similarity=0.288 Sum_probs=30.6
Q ss_pred hHHHHHHHhhccccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeE
Q psy836 30 MVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRI 93 (122)
Q Consensus 30 ~v~kie~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~ 93 (122)
+|.-.|..+..+|.=.+ .+=.-..-|...|..||..+. + +. +..|-.|++|+.+
T Consensus 86 qvEw~el~~d~~h~g~Y---~sGE~~g~G~l~C~~Cg~~~~-----~-~~-~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 86 QVEWAELAQDLEHHGVY---HSGEVVGPGTLVCENCGHEVE-----L-TH-PERLPPCPKCGHT 139 (146)
T ss_pred HHHHHHHHHHHHhcCCe---ecCcEecCceEecccCCCEEE-----e-cC-CCcCCCCCCCCCC
Confidence 44444444444444211 123345778888999988742 2 22 3457789999754
No 178
>PRK07220 DNA topoisomerase I; Validated
Probab=37.00 E-value=29 Score=32.36 Aligned_cols=27 Identities=19% Similarity=0.407 Sum_probs=18.2
Q ss_pred cccCCCCCCceeEeEEee----eeeecCcce
Q psy836 41 KYTCSFCGKDSMKRSCVG----IWSCKRCKR 67 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avG----IW~C~~C~~ 67 (122)
...||.||...++...-| .|.|+.|..
T Consensus 635 ~~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~ 665 (740)
T PRK07220 635 DKVCEAHGLNHIRIINGGKRPWDLGCPQCNF 665 (740)
T ss_pred CCCCCCCCCceEEEEecCCccceeeCCCCCC
Confidence 467999987655444434 578877775
No 179
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=36.80 E-value=29 Score=19.22 Aligned_cols=23 Identities=22% Similarity=0.541 Sum_probs=9.5
Q ss_pred cCCCCCCce--eEeEEeeeeeecCc
Q psy836 43 TCSFCGKDS--MKRSCVGIWSCKRC 65 (122)
Q Consensus 43 ~Cp~Cgk~~--mkR~avGIW~C~~C 65 (122)
.||.|+... +.-.+-...-|+.|
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rC 27 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRC 27 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTT
T ss_pred cCccCCCcceEeEecCCCCeECcCC
Confidence 588888773 22222344555555
No 180
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=36.66 E-value=24 Score=25.91 Aligned_cols=16 Identities=6% Similarity=0.200 Sum_probs=8.8
Q ss_pred ccChhhhHhHHHHHHH
Q psy836 22 RYGASLRKMVKKMEIT 37 (122)
Q Consensus 22 RYG~slRK~v~kie~~ 37 (122)
..|...+..+.++...
T Consensus 80 ~Hg~~f~~~~~~~~~~ 95 (146)
T smart00731 80 GHGDEWKRWMRQVNGL 95 (146)
T ss_pred CcCHHHHHHHHHHcCC
Confidence 4555566655555443
No 181
>PHA00732 hypothetical protein
Probab=36.51 E-value=17 Score=24.99 Aligned_cols=13 Identities=46% Similarity=0.445 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHH
Q psy836 106 ATSVRSAIRRLRE 118 (122)
Q Consensus 106 ~~~~~~~i~rl~e 118 (122)
.-.|+-+|.|--|
T Consensus 65 ~~~~~~~~~~~~~ 77 (79)
T PHA00732 65 PYHVRLAIKRKLE 77 (79)
T ss_pred hHHHHHHHHHHhc
Confidence 4456666766544
No 182
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=36.48 E-value=13 Score=19.62 Aligned_cols=9 Identities=44% Similarity=1.272 Sum_probs=4.7
Q ss_pred ccCCCCCCc
Q psy836 42 YTCSFCGKD 50 (122)
Q Consensus 42 y~Cp~Cgk~ 50 (122)
|+|+.|++.
T Consensus 2 ~~C~~C~~~ 10 (27)
T PF13912_consen 2 FECDECGKT 10 (27)
T ss_dssp EEETTTTEE
T ss_pred CCCCccCCc
Confidence 455555543
No 183
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=36.33 E-value=15 Score=24.34 Aligned_cols=12 Identities=42% Similarity=1.085 Sum_probs=4.5
Q ss_pred hccccCCCCCCc
Q psy836 39 HAKYTCSFCGKD 50 (122)
Q Consensus 39 ~aky~Cp~Cgk~ 50 (122)
..+|+||.||.+
T Consensus 31 Lr~y~Cp~CgAt 42 (55)
T PF05741_consen 31 LRKYVCPICGAT 42 (55)
T ss_dssp GGG---TTT---
T ss_pred HhcCcCCCCcCc
Confidence 356999999976
No 184
>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=36.31 E-value=26 Score=22.90 Aligned_cols=28 Identities=21% Similarity=0.720 Sum_probs=15.3
Q ss_pred cccCCCCCCce-eEeEEee-eeeecCccee
Q psy836 41 KYTCSFCGKDS-MKRSCVG-IWSCKRCKRI 68 (122)
Q Consensus 41 ky~Cp~Cgk~~-mkR~avG-IW~C~~C~~~ 68 (122)
.++||.||..- +.-...| |=.|+.||..
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGae 31 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAE 31 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCE
Confidence 35789998862 2221112 4566666653
No 185
>KOG1986|consensus
Probab=36.19 E-value=18 Score=34.64 Aligned_cols=35 Identities=23% Similarity=0.400 Sum_probs=28.2
Q ss_pred HHHHhhccccCCCCCCce----eEeEEeeeeeecCccee
Q psy836 34 MEITQHAKYTCSFCGKDS----MKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 34 ie~~~~aky~Cp~Cgk~~----mkR~avGIW~C~~C~~~ 68 (122)
+-..++++..|..|+... .-....++|.|+.|+..
T Consensus 46 ~~~~~y~P~~C~~C~AvlNPyc~vd~~a~~W~CpfC~qr 84 (745)
T KOG1986|consen 46 LPPIQYDPLRCSKCGAVLNPYCSVDFRAKSWICPFCNQR 84 (745)
T ss_pred CCccCCCCchhccchhhcCcceeecccCceEeccccccC
Confidence 346788999999999873 56677889999999864
No 186
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=35.97 E-value=27 Score=32.40 Aligned_cols=39 Identities=26% Similarity=0.330 Sum_probs=26.7
Q ss_pred hhhhHhHHHHHHHhhccc--------cCCCCCCceeEeEEeeeeeecCccee
Q psy836 25 ASLRKMVKKMEITQHAKY--------TCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 25 ~slRK~v~kie~~~~aky--------~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
..|++.|+.+-....-.| .|+.||... .. .|.||.||+.
T Consensus 602 ~a~~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~-g~----~~~CP~CG~~ 648 (656)
T PRK08270 602 EACKKLVKKALENYRLPYITITPTFSICPKHGYLS-GE----HEFCPKCGEE 648 (656)
T ss_pred HHHHHHHHHHHHhCCCceEEeCCCCcccCCCCCcC-CC----CCCCcCCcCc
Confidence 577888888865433333 599999742 22 4999999864
No 187
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=35.73 E-value=34 Score=27.79 Aligned_cols=27 Identities=22% Similarity=0.615 Sum_probs=17.3
Q ss_pred ccccCCCCCCceeEeEEe---eeeeecCcce
Q psy836 40 AKYTCSFCGKDSMKRSCV---GIWSCKRCKR 67 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~av---GIW~C~~C~~ 67 (122)
..-.||.||.+- .+..+ +.|-|+.|-+
T Consensus 244 ~g~pC~~Cg~~I-~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 244 EGEPCRRCGTPI-EKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCCCCee-EEEEECCCCcEECcCCCC
Confidence 445699999774 44444 3677777743
No 188
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=35.47 E-value=13 Score=32.61 Aligned_cols=26 Identities=35% Similarity=1.011 Sum_probs=18.4
Q ss_pred ccCCCCCCce--eEeEEee--eeeecCcce
Q psy836 42 YTCSFCGKDS--MKRSCVG--IWSCKRCKR 67 (122)
Q Consensus 42 y~Cp~Cgk~~--mkR~avG--IW~C~~C~~ 67 (122)
..|+|||+.. +.+.-.| .+-|..|-.
T Consensus 8 ~~c~fc~~~~~~~~~~~~~~~~~ic~~c~~ 37 (413)
T TIGR00382 8 LYCSFCGKSQDEVRKLIAGPGVYICDECIE 37 (413)
T ss_pred eecCCCCCChhhcccccCCCCCcCCCchHH
Confidence 3799999974 5555555 678888753
No 189
>PF04071 zf-like: Cysteine-rich small domain; InterPro: IPR007212 This is a probable metal-binding domain. It is found in a probable precorrin-3B C17-methyltransferase from Methanobacterium thermoautotrophicum, that catalyses the methylation of C-17 in precorrin-3B to form precorrin-4.
Probab=35.02 E-value=26 Score=25.02 Aligned_cols=19 Identities=26% Similarity=0.777 Sum_probs=11.7
Q ss_pred ceeeeeccceeeeeeecCcC
Q psy836 72 GAWDSMKRSCVGIWSCKRCK 91 (122)
Q Consensus 72 gAy~~~t~~AvtV~s~~rC~ 91 (122)
|-|.... +-..||+|..|.
T Consensus 40 G~~~~~~-~G~~vw~C~~C~ 58 (86)
T PF04071_consen 40 GNFIYTK-NGSKVWDCSDCT 58 (86)
T ss_pred ccEEEcC-CCCeeeECccCC
Confidence 5555533 223688899993
No 190
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=34.73 E-value=17 Score=34.18 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=22.9
Q ss_pred hhhhHhHHHHHHHhhccc--------cCCCCCCceeEeEEeeeeeecCcce
Q psy836 25 ASLRKMVKKMEITQHAKY--------TCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 25 ~slRK~v~kie~~~~aky--------~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
..+.+-|+.+.. ..-.| .|+.||-.... -|.||.||.
T Consensus 657 eal~~lvk~~~~-~~i~Y~sin~~~~~C~~CG~~~~~-----~~~CP~CG~ 701 (735)
T PRK07111 657 EAFEIIVKAMKN-TNIGYGSINHPVDRCPVCGYLGVI-----EDKCPKCGS 701 (735)
T ss_pred HHHHHHHHHHHh-CCCceEEeCCCCeecCCCCCCCCc-----CccCcCCCC
Confidence 355666665432 23334 69999964432 299999986
No 191
>PRK10445 endonuclease VIII; Provisional
Probab=34.42 E-value=27 Score=28.35 Aligned_cols=26 Identities=19% Similarity=0.581 Sum_probs=15.6
Q ss_pred hccccCCCCCCceeEeEEe---eeeeecCc
Q psy836 39 HAKYTCSFCGKDSMKRSCV---GIWSCKRC 65 (122)
Q Consensus 39 ~aky~Cp~Cgk~~mkR~av---GIW~C~~C 65 (122)
+..-.||.||..- .+..+ +.|-|+.|
T Consensus 233 r~g~~Cp~Cg~~I-~~~~~~gR~t~~CP~C 261 (263)
T PRK10445 233 RDGEACERCGGII-EKTTLSSRPFYWCPGC 261 (263)
T ss_pred CCCCCCCCCCCEe-EEEEECCCCcEECCCC
Confidence 3456799999663 33333 35666665
No 192
>KOG4623|consensus
Probab=34.35 E-value=15 Score=34.22 Aligned_cols=43 Identities=23% Similarity=0.600 Sum_probs=34.3
Q ss_pred ChhhhHhHHHHHHHhh-ccccCCCCCCc-eeEeEEeeeeeecCcc
Q psy836 24 GASLRKMVKKMEITQH-AKYTCSFCGKD-SMKRSCVGIWSCKRCK 66 (122)
Q Consensus 24 G~slRK~v~kie~~~~-aky~Cp~Cgk~-~mkR~avGIW~C~~C~ 66 (122)
|+.|=+-++-|..... +.-.|=||.+. .+.+..-.-|+|++|-
T Consensus 10 ~a~l~~ly~~Irsr~k~t~VnCwFCnk~t~vpyq~rNswTCpsCE 54 (611)
T KOG4623|consen 10 GAGLGNLYDGIRSRFKDTTVNCWFCNKKTEVPYQGRNSWTCPSCE 54 (611)
T ss_pred hhcchHHHHHHHhhcCCceEEEEEecCcceeccCCCCCCcCCcHH
Confidence 5666666777776666 77789999766 6999999999999994
No 193
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=34.25 E-value=28 Score=32.11 Aligned_cols=36 Identities=22% Similarity=0.436 Sum_probs=25.6
Q ss_pred hhhhHhHHHHHHHhhccc--------cCCCCCCceeEeEEee-e-eeecCcce
Q psy836 25 ASLRKMVKKMEITQHAKY--------TCSFCGKDSMKRSCVG-I-WSCKRCKR 67 (122)
Q Consensus 25 ~slRK~v~kie~~~~aky--------~Cp~Cgk~~mkR~avG-I-W~C~~C~~ 67 (122)
..+++.|+.+... +-.| .|+.||.. .| . +.||.||.
T Consensus 509 ea~~~lv~~~~~~-~i~Y~tin~~~siC~~CGy~------~g~~~~~CP~CGs 554 (586)
T TIGR02827 509 DGYRKLLRVAADT-GCNYFCFNIKITICNDCHHI------DKRTLHRCPVCGS 554 (586)
T ss_pred HHHHHHHHHHHhc-CCceEEeCCCCeecCCCCCc------CCCcCCcCcCCCC
Confidence 4688888888653 4444 49999972 23 2 99999986
No 194
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=34.18 E-value=17 Score=32.92 Aligned_cols=23 Identities=30% Similarity=0.642 Sum_probs=19.5
Q ss_pred ccccCCCCCCceeEeEEeeeeeecCcc
Q psy836 40 AKYTCSFCGKDSMKRSCVGIWSCKRCK 66 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avGIW~C~~C~ 66 (122)
..|.|..||...-|+.. +|+.|+
T Consensus 6 t~f~C~~CG~~s~KW~G----kCp~Cg 28 (456)
T COG1066 6 TAFVCQECGYVSPKWLG----KCPACG 28 (456)
T ss_pred cEEEcccCCCCCccccc----cCCCCC
Confidence 57999999999998764 788886
No 195
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=34.06 E-value=21 Score=28.28 Aligned_cols=48 Identities=19% Similarity=0.472 Sum_probs=32.1
Q ss_pred cccccChhhhHhHHHHHHHhhccccCCCCCCc--eeEeEEeee----eeecCccee
Q psy836 19 YGTRYGASLRKMVKKMEITQHAKYTCSFCGKD--SMKRSCVGI----WSCKRCKRI 68 (122)
Q Consensus 19 yG~RYG~slRK~v~kie~~~~aky~Cp~Cgk~--~mkR~avGI----W~C~~C~~~ 68 (122)
||.||-.++-.-++.+.. ..-.|.|. |+.. +.+|...-. +.|.+|+-+
T Consensus 96 ~~l~~~~~h~~~~~~v~~-~~~~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gk 149 (156)
T COG3091 96 LGLRFCRTHQFEVQSVRR-TTYPYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGK 149 (156)
T ss_pred CCCCCCccchHHHhhccc-cceeEEee-cCCccchhhhcccccccceEEeccCCce
Confidence 677777776665555433 34579999 9986 455555555 898888754
No 196
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=33.97 E-value=24 Score=30.22 Aligned_cols=24 Identities=29% Similarity=0.486 Sum_probs=19.7
Q ss_pred hccccCCCCCCc-eeEeEEeeeeee
Q psy836 39 HAKYTCSFCGKD-SMKRSCVGIWSC 62 (122)
Q Consensus 39 ~aky~Cp~Cgk~-~mkR~avGIW~C 62 (122)
..+|.||.|+.. .+|.-...+||=
T Consensus 28 ~~~~~CP~C~~~v~lk~G~~k~~HF 52 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKGKKKIPHF 52 (375)
T ss_pred CCcEECCCCCCeeEEEEcCccccee
Confidence 789999999888 577777778883
No 197
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=33.93 E-value=15 Score=27.16 Aligned_cols=25 Identities=32% Similarity=0.994 Sum_probs=17.4
Q ss_pred cCCCCCCce-eEeEEee-eeeecCcce
Q psy836 43 TCSFCGKDS-MKRSCVG-IWSCKRCKR 67 (122)
Q Consensus 43 ~Cp~Cgk~~-mkR~avG-IW~C~~C~~ 67 (122)
.|=|||+.+ +...... -|.|++|.-
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w~C~~C~q 28 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNWTCPHCEQ 28 (131)
T ss_pred eeccCCCCCCCCCCCCCCeeECCCCCC
Confidence 588999874 4444434 499999964
No 198
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=33.80 E-value=41 Score=24.08 Aligned_cols=29 Identities=31% Similarity=0.472 Sum_probs=16.1
Q ss_pred ccccCCCCCCceeEeEEeeeeeecCcceee
Q psy836 40 AKYTCSFCGKDSMKRSCVGIWSCKRCKRIV 69 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avGIW~C~~C~~~v 69 (122)
..+.|..|+++.--=...| =.|..|...|
T Consensus 53 ~~~~C~~C~~~fg~l~~~~-~~C~~C~~~V 81 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRG-RVCVDCKHRV 81 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTC-EEETTTTEEE
T ss_pred CCcchhhhCCcccccCCCC-CcCCcCCccc
Confidence 5678999988621111223 4788887764
No 199
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=33.63 E-value=35 Score=26.40 Aligned_cols=22 Identities=14% Similarity=0.487 Sum_probs=16.0
Q ss_pred HHHhhccccCCCCCCceeEeEE
Q psy836 35 EITQHAKYTCSFCGKDSMKRSC 56 (122)
Q Consensus 35 e~~~~aky~Cp~Cgk~~mkR~a 56 (122)
.+....--.||+||...+.|.-
T Consensus 26 ~Q~~~glv~CP~Cgs~~V~K~l 47 (148)
T PF06676_consen 26 RQQARGLVSCPVCGSTEVSKAL 47 (148)
T ss_pred HHHHcCCccCCCCCCCeEeeec
Confidence 3444455789999999988763
No 200
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.52 E-value=15 Score=32.44 Aligned_cols=29 Identities=28% Similarity=0.809 Sum_probs=22.0
Q ss_pred hhccccCCCCCCc-eeE---eEEeeeeeecCcc
Q psy836 38 QHAKYTCSFCGKD-SMK---RSCVGIWSCKRCK 66 (122)
Q Consensus 38 ~~aky~Cp~Cgk~-~mk---R~avGIW~C~~C~ 66 (122)
+-..|.||.||+. +++ |..-|-|.|..|+
T Consensus 29 ~~~~~~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 29 KPGGHPCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred cCCCCCCCccCCccccccCCccCCccEEEEeec
Confidence 3445699999866 443 6678999998888
No 201
>PRK05580 primosome assembly protein PriA; Validated
Probab=33.45 E-value=24 Score=32.32 Aligned_cols=40 Identities=15% Similarity=0.303 Sum_probs=23.2
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeE
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRI 93 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~ 93 (122)
..||.|+-.-.--...+.=.|..||.+ ...-+.|..||..
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~------------~~~~~~Cp~Cg~~ 430 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQ------------EPIPKACPECGST 430 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCC------------CCCCCCCCCCcCC
Confidence 357777665433334455678888875 1122458888654
No 202
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=33.30 E-value=16 Score=32.06 Aligned_cols=13 Identities=23% Similarity=0.396 Sum_probs=8.3
Q ss_pred EeeeeeecCccee
Q psy836 56 CVGIWSCKRCKRI 68 (122)
Q Consensus 56 avGIW~C~~C~~~ 68 (122)
....|.|.-|+..
T Consensus 422 ~~~~~~c~~c~~~ 434 (479)
T PRK05452 422 LGPRMQCSVCQWI 434 (479)
T ss_pred CCCeEEECCCCeE
Confidence 3456777777765
No 203
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=33.17 E-value=18 Score=28.72 Aligned_cols=27 Identities=22% Similarity=0.660 Sum_probs=16.8
Q ss_pred ccCCCCCCcee--Ee-------------EEeeeeeecCccee
Q psy836 42 YTCSFCGKDSM--KR-------------SCVGIWSCKRCKRI 68 (122)
Q Consensus 42 y~Cp~Cgk~~m--kR-------------~avGIW~C~~C~~~ 68 (122)
-.||.|+.... .+ .+.--|.|+.|++.
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccc
Confidence 45999987742 22 33337777666664
No 204
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=33.05 E-value=61 Score=24.44 Aligned_cols=40 Identities=15% Similarity=0.362 Sum_probs=23.3
Q ss_pred hHhHHHHHHHhhcccc-CCCCCCc--eeEeEEeeee--eecCccee
Q psy836 28 RKMVKKMEITQHAKYT-CSFCGKD--SMKRSCVGIW--SCKRCKRI 68 (122)
Q Consensus 28 RK~v~kie~~~~aky~-Cp~Cgk~--~mkR~avGIW--~C~~C~~~ 68 (122)
.+.+..+...=-.+|. ||.|+.+ .+.+. -.+| +|.-||..
T Consensus 83 ~~~i~~~L~~yI~~yVlC~~C~sPdT~l~k~-~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 83 HFLLNERIEDYVRKYVICRECNRPDTRIIKE-GRVSLLKCEACGAK 127 (133)
T ss_pred HHHHHHHHHHHHhheEECCCCCCCCcEEEEe-CCeEEEecccCCCC
Confidence 3445555544455564 9999998 34443 2344 67777653
No 205
>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=33.01 E-value=58 Score=29.35 Aligned_cols=73 Identities=15% Similarity=0.294 Sum_probs=43.6
Q ss_pred cccCCCCCCce-eE----------eEEeeeeeecCcceeeecceeeeeccceeeeeeecCc--CeEEec----cccccCc
Q psy836 41 KYTCSFCGKDS-MK----------RSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRC--KRIVAG----GAWVYNT 103 (122)
Q Consensus 41 ky~Cp~Cgk~~-mk----------R~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC--~~~~AG----GAy~~~T 103 (122)
-..||.||... ++ ....-.+.|++||-.|-..-..-+. +-+.|-+... ....+| +.|+|..
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~--~~G~Wv~~~~~~~~~~~gf~i~~l~Sp~~ 277 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMV--RRGRWVATNPDRRPRHVGFHINALYSPFV 277 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhcc--CCeEEEeccccCCCCEEEEEeeeeecccC
Confidence 34699999874 33 2234578899999887764444433 3355556655 444444 6677766
Q ss_pred hHHHHHHHHHHH
Q psy836 104 TAATSVRSAIRR 115 (122)
Q Consensus 104 ~~~~~~~~~i~r 115 (122)
+-+..++.-++-
T Consensus 278 sw~~ia~~~l~A 289 (557)
T PF05876_consen 278 SWAEIAREFLEA 289 (557)
T ss_pred CHHHHHHHHHhh
Confidence 666555554443
No 206
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=32.83 E-value=19 Score=18.65 Aligned_cols=8 Identities=38% Similarity=1.227 Sum_probs=3.7
Q ss_pred ccCCCCCC
Q psy836 42 YTCSFCGK 49 (122)
Q Consensus 42 y~Cp~Cgk 49 (122)
|.|++|.-
T Consensus 1 y~C~~C~y 8 (24)
T PF13909_consen 1 YKCPHCSY 8 (24)
T ss_dssp EE-SSSS-
T ss_pred CCCCCCCC
Confidence 55666653
No 207
>PHA00733 hypothetical protein
Probab=32.57 E-value=12 Score=27.62 Aligned_cols=12 Identities=25% Similarity=0.700 Sum_probs=8.5
Q ss_pred hccccCCCCCCc
Q psy836 39 HAKYTCSFCGKD 50 (122)
Q Consensus 39 ~aky~Cp~Cgk~ 50 (122)
..+|.|+.||+.
T Consensus 71 ~kPy~C~~Cgk~ 82 (128)
T PHA00733 71 VSPYVCPLCLMP 82 (128)
T ss_pred CCCccCCCCCCc
Confidence 456778888765
No 208
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=32.32 E-value=14 Score=26.76 Aligned_cols=7 Identities=29% Similarity=0.899 Sum_probs=3.3
Q ss_pred ccCCCCC
Q psy836 42 YTCSFCG 48 (122)
Q Consensus 42 y~Cp~Cg 48 (122)
..|+.||
T Consensus 72 ~~C~~Cg 78 (117)
T PRK00564 72 LECKDCS 78 (117)
T ss_pred EEhhhCC
Confidence 3455554
No 209
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=32.07 E-value=30 Score=28.22 Aligned_cols=26 Identities=27% Similarity=0.694 Sum_probs=16.5
Q ss_pred cccCCCCCCceeEeEEe---eeeeecCcce
Q psy836 41 KYTCSFCGKDSMKRSCV---GIWSCKRCKR 67 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~av---GIW~C~~C~~ 67 (122)
.-.||.||.+- .+..+ +.|-|+.|-+
T Consensus 235 g~pC~~Cg~~I-~~~~~~gR~ty~Cp~CQ~ 263 (269)
T PRK14811 235 GQPCPRCGTPI-EKIVVGGRGTHFCPQCQP 263 (269)
T ss_pred cCCCCcCCCee-EEEEECCCCcEECCCCcC
Confidence 44799999764 33433 3677776654
No 210
>KOG1311|consensus
Probab=31.58 E-value=18 Score=29.22 Aligned_cols=24 Identities=25% Similarity=0.422 Sum_probs=21.2
Q ss_pred ccccCCCCCCceeEeEEeeeeeecCcce
Q psy836 40 AKYTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
.-+.|+.|...+..|. |||+-|++
T Consensus 112 ~~~~C~~C~~~rPpRs----~HCsvC~~ 135 (299)
T KOG1311|consen 112 EWKYCDTCQLYRPPRS----SHCSVCNN 135 (299)
T ss_pred ceEEcCcCcccCCCCc----ccchhhcc
Confidence 4688999999999997 79999988
No 211
>KOG2463|consensus
Probab=31.27 E-value=35 Score=30.29 Aligned_cols=22 Identities=23% Similarity=0.552 Sum_probs=18.8
Q ss_pred ccccCCCCCCceeEeEEeeeee
Q psy836 40 AKYTCSFCGKDSMKRSCVGIWS 61 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avGIW~ 61 (122)
.+..||.||-..+.+.+|.|=.
T Consensus 256 ~k~FCp~CG~~TL~K~aVsv~~ 277 (376)
T KOG2463|consen 256 PKDFCPSCGHKTLTKCAVSVDE 277 (376)
T ss_pred chhcccccCCCeeeEEEEEecC
Confidence 4778999999999999997754
No 212
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=30.93 E-value=23 Score=35.23 Aligned_cols=17 Identities=24% Similarity=0.178 Sum_probs=11.6
Q ss_pred CchHHHHHHHHHHHHHH
Q psy836 102 NTTAATSVRSAIRRLRE 118 (122)
Q Consensus 102 ~T~~~~~~~~~i~rl~e 118 (122)
.-+....+++|+.+|.+
T Consensus 656 ~i~l~~~~~~A~~~lg~ 672 (1095)
T TIGR00354 656 KVDLRELYEEAIANLGE 672 (1095)
T ss_pred EecHHHHHHHHHHHhCC
Confidence 45666777778777744
No 213
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=30.66 E-value=23 Score=23.59 Aligned_cols=7 Identities=57% Similarity=1.730 Sum_probs=6.1
Q ss_pred CCCCCCc
Q psy836 44 CSFCGKD 50 (122)
Q Consensus 44 Cp~Cgk~ 50 (122)
|||||+.
T Consensus 42 CPfC~~~ 48 (55)
T PF14447_consen 42 CPFCGTP 48 (55)
T ss_pred CCCCCCc
Confidence 9999975
No 214
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=30.41 E-value=24 Score=20.88 Aligned_cols=8 Identities=25% Similarity=1.186 Sum_probs=4.2
Q ss_pred ecCcCeEE
Q psy836 87 CKRCKRIV 94 (122)
Q Consensus 87 ~~rC~~~~ 94 (122)
|.+|+.+|
T Consensus 28 C~~C~~~f 35 (36)
T PF13717_consen 28 CSKCGHVF 35 (36)
T ss_pred CCCCCCEe
Confidence 55555544
No 215
>PRK02935 hypothetical protein; Provisional
Probab=30.31 E-value=29 Score=26.13 Aligned_cols=29 Identities=24% Similarity=0.579 Sum_probs=18.9
Q ss_pred HHhhccccCCCCCCce--eEeEEeeeeeecCccee
Q psy836 36 ITQHAKYTCSFCGKDS--MKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 36 ~~~~aky~Cp~Cgk~~--mkR~avGIW~C~~C~~~ 68 (122)
+.+-..-.||.|+|.. +.|.- -|.+|+.-
T Consensus 65 StkavqV~CP~C~K~TKmLGrvD----~CM~C~~P 95 (110)
T PRK02935 65 STKAVQVICPSCEKPTKMLGRVD----ACMHCNQP 95 (110)
T ss_pred cccceeeECCCCCchhhhcccee----ecCcCCCc
Confidence 3444455899999984 45543 67777653
No 216
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=30.30 E-value=24 Score=22.89 Aligned_cols=9 Identities=33% Similarity=1.291 Sum_probs=7.1
Q ss_pred ccCCCCCCc
Q psy836 42 YTCSFCGKD 50 (122)
Q Consensus 42 y~Cp~Cgk~ 50 (122)
+.||+||..
T Consensus 1 i~CPyCge~ 9 (52)
T PF14255_consen 1 IQCPYCGEP 9 (52)
T ss_pred CCCCCCCCe
Confidence 468999876
No 217
>PRK07591 threonine synthase; Validated
Probab=30.25 E-value=18 Score=31.08 Aligned_cols=25 Identities=24% Similarity=0.513 Sum_probs=17.7
Q ss_pred cccCCCCCCceeEeEEeeeeeecCccee
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
.+.|+.||+..--- ..|.|+.|+--
T Consensus 18 ~l~C~~Cg~~~~~~---~~~~C~~cg~~ 42 (421)
T PRK07591 18 ALKCRECGAEYPLG---PIHVCEECFGP 42 (421)
T ss_pred EEEeCCCCCcCCCC---CCccCCCCCCe
Confidence 58899999875321 22999999743
No 218
>KOG4198|consensus
Probab=30.22 E-value=22 Score=30.20 Aligned_cols=52 Identities=25% Similarity=0.460 Sum_probs=36.9
Q ss_pred cCCCCCCceeEeE-------EeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccccccCchH
Q psy836 43 TCSFCGKDSMKRS-------CVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTA 105 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~-------avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~~T~~ 105 (122)
.||.|.-..+-|. -.|.|.|+.|+.. -|..+.+ |-+|+..-.=.|+.-++++
T Consensus 117 ~~~~~~g~~~~~n~~~~r~~~~GDW~Cp~C~fh------Nfarn~~-----C~rC~~~r~~~a~~~~~~s 175 (280)
T KOG4198|consen 117 LCPRCPGLGFSRNNKPKRPWRSGDWECPGCNFH------NFARNSE-----CFRCGAKRPLAALLGNQAS 175 (280)
T ss_pred CCCCCCCCcccccccccCCccccCcccCCCCce------eccccch-----hhhcCCcCccccccccccc
Confidence 4888877776665 7899999988874 3333322 9999988877777655554
No 219
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=30.21 E-value=45 Score=27.31 Aligned_cols=26 Identities=23% Similarity=0.528 Sum_probs=16.3
Q ss_pred ccccCCCCCCceeEeEEee---eeeecCcc
Q psy836 40 AKYTCSFCGKDSMKRSCVG---IWSCKRCK 66 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avG---IW~C~~C~ 66 (122)
..-.||.||.+-. +..+| .|-|+.|-
T Consensus 253 ~g~pC~~Cg~~I~-~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 253 TGKPCRKCGTPIE-RIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CcCCCCcCCCeeE-EEEECCCccEECCCCc
Confidence 3457999997643 34433 67776663
No 220
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.70 E-value=36 Score=27.79 Aligned_cols=25 Identities=24% Similarity=0.591 Sum_probs=15.6
Q ss_pred ccccCCCCCCceeEeEEee---eeeecCc
Q psy836 40 AKYTCSFCGKDSMKRSCVG---IWSCKRC 65 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avG---IW~C~~C 65 (122)
..-.||.||.. +.+..+| .|-|+.|
T Consensus 243 ~g~pCprCG~~-I~~~~~~gR~t~~CP~C 270 (272)
T PRK14810 243 TGEPCLNCKTP-IRRVVVAGRSSHYCPHC 270 (272)
T ss_pred CCCcCCCCCCe-eEEEEECCCccEECcCC
Confidence 34579999954 4555544 5666655
No 221
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=29.40 E-value=27 Score=26.95 Aligned_cols=11 Identities=45% Similarity=0.996 Sum_probs=5.2
Q ss_pred cccCCCCCCce
Q psy836 41 KYTCSFCGKDS 51 (122)
Q Consensus 41 ky~Cp~Cgk~~ 51 (122)
..+||.|+...
T Consensus 18 ~~~C~~C~~~~ 28 (188)
T PF08996_consen 18 KLTCPSCGTEF 28 (188)
T ss_dssp EEE-TTT--EE
T ss_pred EeECCCCCCCc
Confidence 45688887663
No 222
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=29.33 E-value=27 Score=23.18 Aligned_cols=13 Identities=31% Similarity=0.881 Sum_probs=9.5
Q ss_pred hhccccCCCCCCc
Q psy836 38 QHAKYTCSFCGKD 50 (122)
Q Consensus 38 ~~aky~Cp~Cgk~ 50 (122)
.+..|.||.||-+
T Consensus 11 ~~v~~~Cp~cGip 23 (55)
T PF13824_consen 11 AHVNFECPDCGIP 23 (55)
T ss_pred cccCCcCCCCCCc
Confidence 4567888888754
No 223
>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=29.21 E-value=19 Score=23.36 Aligned_cols=15 Identities=33% Similarity=0.972 Sum_probs=10.1
Q ss_pred HHHhhccccCCCCCC
Q psy836 35 EITQHAKYTCSFCGK 49 (122)
Q Consensus 35 e~~~~aky~Cp~Cgk 49 (122)
|+-..-.|.||+||.
T Consensus 38 ~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 38 EEFEEIQYRCPYCGA 52 (54)
T ss_pred ccCCceEEEcCCCCC
Confidence 334445788888875
No 224
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=29.20 E-value=28 Score=19.06 Aligned_cols=8 Identities=38% Similarity=1.427 Sum_probs=4.4
Q ss_pred cCCCCCCc
Q psy836 43 TCSFCGKD 50 (122)
Q Consensus 43 ~Cp~Cgk~ 50 (122)
.||.||+.
T Consensus 4 ~C~~CgR~ 11 (25)
T PF13913_consen 4 PCPICGRK 11 (25)
T ss_pred cCCCCCCE
Confidence 46666553
No 225
>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=29.08 E-value=15 Score=27.96 Aligned_cols=16 Identities=19% Similarity=0.517 Sum_probs=12.2
Q ss_pred cccCCCCCCceeEeEE
Q psy836 41 KYTCSFCGKDSMKRSC 56 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~a 56 (122)
.-.||.||+...++.+
T Consensus 105 ~~~cp~c~s~~t~~~s 120 (146)
T TIGR02159 105 SVQCPRCGSADTTITS 120 (146)
T ss_pred CCcCCCCCCCCcEeec
Confidence 3579999998766654
No 226
>PF09180 ProRS-C_1: Prolyl-tRNA synthetase, C-terminal; InterPro: IPR016061 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Prolyl tRNA synthetase (6.1.1.15 from EC) exists in two forms, which are loosely related. The first form is present in the majority of eubacteria species. The second one, present in some eubacteria, is essentially present in archaea and eukaryota. Prolyl-tRNA synthetase belongs to class IIa. This domain is found at the C-terminal in archaeal and eukaryotic enzymes, as well as in certain bacterial ones.; GO: 0000166 nucleotide binding, 0004827 proline-tRNA ligase activity, 0005524 ATP binding, 0006433 prolyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1NJ6_A 1NJ2_A 1NJ5_A 1NJ1_A 1H4T_C 1H4S_A 1HC7_C 1H4Q_B 3IAL_B.
Probab=28.93 E-value=37 Score=22.40 Aligned_cols=21 Identities=24% Similarity=0.404 Sum_probs=11.4
Q ss_pred hhccccCCCCCCceeEeEEee
Q psy836 38 QHAKYTCSFCGKDSMKRSCVG 58 (122)
Q Consensus 38 ~~aky~Cp~Cgk~~mkR~avG 58 (122)
....-+|++||+++..+.-.|
T Consensus 45 ~~~~~~Ci~cgk~a~~~~~fa 65 (68)
T PF09180_consen 45 EPEGGKCIVCGKPAKKWVLFA 65 (68)
T ss_dssp EBTT-B-TTT-SB-SCEEEEE
T ss_pred CCCCCeeecCCChhhEEEEEE
Confidence 345667999999987665443
No 227
>PF02891 zf-MIZ: MIZ/SP-RING zinc finger; InterPro: IPR004181 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MIZ-type zinc finger domains. Miz1 (Msx-interacting-zinc finger) is a zinc finger-containing protein with homology to the yeast protein, Nfi-1. Miz1 is a sequence specific DNA binding protein that can function as a positive-acting transcription factor. Miz1 binds to the homeobox protein Msx2, enhancing the specific DNA-binding ability of Msx2 []. Other proteins containing this domain include the human pias family (protein inhibitor of activated STAT protein). More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3I2D_A.
Probab=28.60 E-value=31 Score=21.65 Aligned_cols=10 Identities=40% Similarity=1.188 Sum_probs=2.8
Q ss_pred ccccCCCCCC
Q psy836 40 AKYTCSFCGK 49 (122)
Q Consensus 40 aky~Cp~Cgk 49 (122)
..+.||.|++
T Consensus 40 ~~W~CPiC~~ 49 (50)
T PF02891_consen 40 PKWKCPICNK 49 (50)
T ss_dssp ---B-TTT--
T ss_pred CCeECcCCcC
Confidence 3466777765
No 228
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=28.60 E-value=22 Score=30.62 Aligned_cols=23 Identities=22% Similarity=0.252 Sum_probs=16.9
Q ss_pred cccCCCCCCceeEeEEeeeeeecCcc
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCK 66 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~ 66 (122)
.+.|+.||+..- .. ..|.|+.|+
T Consensus 2 ~l~C~~Cg~~~~--~~-~~~~C~~c~ 24 (398)
T TIGR03844 2 TLRCPGCGEVLP--DH-YTLSCPLDC 24 (398)
T ss_pred EEEeCCCCCccC--Cc-cccCCCCCC
Confidence 468999998853 23 269998886
No 229
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=28.36 E-value=43 Score=17.13 Aligned_cols=9 Identities=22% Similarity=0.907 Sum_probs=4.9
Q ss_pred eeecCccee
Q psy836 60 WSCKRCKRI 68 (122)
Q Consensus 60 W~C~~C~~~ 68 (122)
|.|.-|+++
T Consensus 1 ~~C~~C~~~ 9 (25)
T PF12874_consen 1 FYCDICNKS 9 (25)
T ss_dssp EEETTTTEE
T ss_pred CCCCCCCCC
Confidence 555555554
No 230
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=28.29 E-value=75 Score=24.08 Aligned_cols=39 Identities=15% Similarity=0.485 Sum_probs=21.8
Q ss_pred HhHHHHHHHhhcccc-CCCCCCc--eeEeE-EeeeeeecCcce
Q psy836 29 KMVKKMEITQHAKYT-CSFCGKD--SMKRS-CVGIWSCKRCKR 67 (122)
Q Consensus 29 K~v~kie~~~~aky~-Cp~Cgk~--~mkR~-avGIW~C~~C~~ 67 (122)
+.+..+...=-..|. ||.||.+ .+.+. .+=.=+|..||.
T Consensus 89 ~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa 131 (138)
T PRK03988 89 RVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVLKCEACGA 131 (138)
T ss_pred HHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 445555544455554 9999998 34432 222345655554
No 231
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=28.09 E-value=45 Score=30.05 Aligned_cols=26 Identities=31% Similarity=0.756 Sum_probs=19.8
Q ss_pred ecCcCeEE-eccccccCchHHHHHHHH
Q psy836 87 CKRCKRIV-AGGAWVYNTTAATSVRSA 112 (122)
Q Consensus 87 ~~rC~~~~-AGGAy~~~T~~~~~~~~~ 112 (122)
|.|||.+. .||-|.++.+++-++..-
T Consensus 41 CPRC~~~l~~~~~~sl~r~~a~A~s~L 67 (418)
T COG2995 41 CPRCGHTLTRGGDWSLQRPAAYALAAL 67 (418)
T ss_pred CCCCCCccccCCCCCccchHHHHHHHH
Confidence 88888775 578888888888766543
No 232
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=28.02 E-value=54 Score=19.28 Aligned_cols=8 Identities=38% Similarity=0.899 Sum_probs=5.1
Q ss_pred cCCCCCCc
Q psy836 43 TCSFCGKD 50 (122)
Q Consensus 43 ~Cp~Cgk~ 50 (122)
+||.|+..
T Consensus 4 ~CP~C~~~ 11 (37)
T PF13719_consen 4 TCPNCQTR 11 (37)
T ss_pred ECCCCCce
Confidence 47777654
No 233
>PRK05978 hypothetical protein; Provisional
Probab=27.94 E-value=27 Score=27.01 Aligned_cols=19 Identities=21% Similarity=0.503 Sum_probs=13.8
Q ss_pred HHhhccccCCCCCCceeEe
Q psy836 36 ITQHAKYTCSFCGKDSMKR 54 (122)
Q Consensus 36 ~~~~aky~Cp~Cgk~~mkR 54 (122)
+..-..-.||.||+-.|=+
T Consensus 28 ~~rGl~grCP~CG~G~LF~ 46 (148)
T PRK05978 28 MWRGFRGRCPACGEGKLFR 46 (148)
T ss_pred HHHHHcCcCCCCCCCcccc
Confidence 3444567799999998754
No 234
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=27.89 E-value=45 Score=20.31 Aligned_cols=25 Identities=36% Similarity=0.836 Sum_probs=16.1
Q ss_pred hccccCCCCCCceeEeEEeeeeeecCcc
Q psy836 39 HAKYTCSFCGKDSMKRSCVGIWSCKRCK 66 (122)
Q Consensus 39 ~aky~Cp~Cgk~~mkR~avGIW~C~~C~ 66 (122)
|..+.|..|+...+... .|+|..|-
T Consensus 2 h~~~~C~~C~~~~i~g~---Ry~C~~C~ 26 (46)
T PF00569_consen 2 HHGYTCDGCGTDPIIGV---RYHCLVCP 26 (46)
T ss_dssp CSSCE-SSS-SSSEESS---EEEESSSS
T ss_pred CCCeECcCCCCCcCcCC---eEECCCCC
Confidence 67889999998544332 39988774
No 235
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=27.50 E-value=37 Score=18.24 Aligned_cols=8 Identities=25% Similarity=1.107 Sum_probs=3.9
Q ss_pred ecCcCeEE
Q psy836 87 CKRCKRIV 94 (122)
Q Consensus 87 ~~rC~~~~ 94 (122)
|..|+..+
T Consensus 30 C~~C~~~L 37 (39)
T smart00132 30 CSKCGKPL 37 (39)
T ss_pred CcccCCcC
Confidence 55555443
No 236
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=27.37 E-value=42 Score=19.60 Aligned_cols=25 Identities=16% Similarity=0.453 Sum_probs=12.1
Q ss_pred eeeeeccce--eeeeeecCcCeEEecc
Q psy836 73 AWDSMKRSC--VGIWSCKRCKRIVAGG 97 (122)
Q Consensus 73 Ay~~~t~~A--vtV~s~~rC~~~~AGG 97 (122)
.|.+++... ...-.|.-|++.+.++
T Consensus 3 vW~~F~~~~~~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 3 VWKHFTKIPGDKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CCCCCEE--GCSS-EEETTTTEE----
T ss_pred ccccEEEccCCcCeEEeCCCCeEEeeC
Confidence 355555555 5556688888888887
No 237
>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=27.35 E-value=42 Score=24.05 Aligned_cols=26 Identities=31% Similarity=0.636 Sum_probs=13.3
Q ss_pred ccccCCCCCCce-eEeEEeeeeeecCccee
Q psy836 40 AKYTCSFCGKDS-MKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 40 aky~Cp~Cgk~~-mkR~avGIW~C~~C~~~ 68 (122)
....|+.||... +.... ..||.|+..
T Consensus 69 ~~~~C~~Cg~~~~~~~~~---~~CP~Cgs~ 95 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDEFD---FSCPRCGSP 95 (113)
T ss_dssp -EEEETTTS-EEECHHCC---HH-SSSSSS
T ss_pred CcEECCCCCCEEecCCCC---CCCcCCcCC
Confidence 455677777763 22222 557777763
No 238
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.35 E-value=25 Score=32.68 Aligned_cols=38 Identities=24% Similarity=0.449 Sum_probs=24.1
Q ss_pred hhhhHhHHHHHHHhhccc--------cCCCCCCceeEeEEeeeeeecCcce
Q psy836 25 ASLRKMVKKMEITQHAKY--------TCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 25 ~slRK~v~kie~~~~aky--------~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
..+++.|+.+.. ..-.| .|+.||... .+. .|.||.||.
T Consensus 543 eal~~lv~~~~~-~~i~Yf~in~~~~iC~~CG~~~-~g~---~~~CP~CGs 588 (623)
T PRK08271 543 EGYRKLLNIAAK-TGCNYFAFNVKITICNDCHHID-KRT---GKRCPICGS 588 (623)
T ss_pred HHHHHHHHHHHH-cCCceEEeCCCCccCCCCCCcC-CCC---CcCCcCCCC
Confidence 467777777754 33333 489999751 111 488888875
No 239
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=26.99 E-value=35 Score=29.70 Aligned_cols=25 Identities=32% Similarity=0.598 Sum_probs=13.3
Q ss_pred CCCCCCce-eEeEEeee-eeecCccee
Q psy836 44 CSFCGKDS-MKRSCVGI-WSCKRCKRI 68 (122)
Q Consensus 44 Cp~Cgk~~-mkR~avGI-W~C~~C~~~ 68 (122)
||.||..- ..+.+.|- -+|++||.+
T Consensus 16 C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 42 (403)
T TIGR00155 16 CSQCDMLVALPRIESGQKAACPRCGTT 42 (403)
T ss_pred CCCCCCcccccCCCCCCeeECCCCCCC
Confidence 89998763 44434443 454444433
No 240
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.89 E-value=27 Score=32.22 Aligned_cols=39 Identities=21% Similarity=0.439 Sum_probs=22.1
Q ss_pred hhhhHhHHHHHHH-------hhccccCCCCCCceeEeEEeeeeeecCccee
Q psy836 25 ASLRKMVKKMEIT-------QHAKYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 25 ~slRK~v~kie~~-------~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
..|.+-|+.+... -+.--.|+.||....- .|.||.||..
T Consensus 536 ~Al~~lvk~~~~~~i~Y~sin~~~~~C~~CGy~g~~-----~~~CP~CG~~ 581 (618)
T PRK14704 536 KALKQIVQAMAEHGVGYGSINHPVDRCKCCSYHGVI-----GNECPSCGNE 581 (618)
T ss_pred HHHHHHHHHHHhcCCceEEeCCCCeecCCCCCCCCc-----CccCcCCCCC
Confidence 4556666665431 1122359999963221 1899998863
No 241
>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec
Probab=26.86 E-value=35 Score=22.96 Aligned_cols=25 Identities=32% Similarity=0.890 Sum_probs=18.6
Q ss_pred ccCCCCCCceeEeEEeeeeeecCcce
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
|.|..||.++.. .-.|.|+|..|.-
T Consensus 1 ~~C~VC~~~~~g-~hygv~sC~aC~~ 25 (77)
T cd06956 1 HICAICGDRASG-KHYGVYSCEGCKG 25 (77)
T ss_pred CCCcccCCcCcc-eEECceeehhHHH
Confidence 569999976543 5788888888763
No 242
>PHA02998 RNA polymerase subunit; Provisional
Probab=26.76 E-value=65 Score=26.40 Aligned_cols=12 Identities=17% Similarity=0.531 Sum_probs=7.7
Q ss_pred cccCCCCCCcee
Q psy836 41 KYTCSFCGKDSM 52 (122)
Q Consensus 41 ky~Cp~Cgk~~m 52 (122)
.-+||.||....
T Consensus 143 ~v~CPkCg~~~A 154 (195)
T PHA02998 143 NTPCPNCKSKNT 154 (195)
T ss_pred CCCCCCCCCCce
Confidence 346888876643
No 243
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=26.74 E-value=33 Score=22.96 Aligned_cols=9 Identities=33% Similarity=1.121 Sum_probs=6.9
Q ss_pred ccCCCCCCc
Q psy836 42 YTCSFCGKD 50 (122)
Q Consensus 42 y~Cp~Cgk~ 50 (122)
..||.||..
T Consensus 5 i~CP~CgnK 13 (55)
T PF14205_consen 5 ILCPICGNK 13 (55)
T ss_pred EECCCCCCc
Confidence 469999954
No 244
>PRK04860 hypothetical protein; Provisional
Probab=26.58 E-value=17 Score=28.03 Aligned_cols=29 Identities=24% Similarity=0.842 Sum_probs=17.3
Q ss_pred ccccCCCCCCcee--EeEE-----eeeeeecCcceee
Q psy836 40 AKYTCSFCGKDSM--KRSC-----VGIWSCKRCKRIV 69 (122)
Q Consensus 40 aky~Cp~Cgk~~m--kR~a-----vGIW~C~~C~~~v 69 (122)
-.|.|+ |++... +|-. ...+.|+.|+..+
T Consensus 118 ~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 118 FPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred EEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCcee
Confidence 468888 876432 3322 3457877777653
No 245
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=26.45 E-value=66 Score=24.76 Aligned_cols=26 Identities=23% Similarity=0.612 Sum_probs=15.4
Q ss_pred cCCCCCCce---eEe--------EEeeeeeecCccee
Q psy836 43 TCSFCGKDS---MKR--------SCVGIWSCKRCKRI 68 (122)
Q Consensus 43 ~Cp~Cgk~~---mkR--------~avGIW~C~~C~~~ 68 (122)
.||.||... |.- .-.=-..|++||.+
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk 38 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYR 38 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCc
Confidence 499997653 222 22234678888765
No 246
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=26.36 E-value=45 Score=19.93 Aligned_cols=9 Identities=44% Similarity=1.084 Sum_probs=6.2
Q ss_pred eeecCccee
Q psy836 60 WSCKRCKRI 68 (122)
Q Consensus 60 W~C~~C~~~ 68 (122)
|.|+.||++
T Consensus 2 r~C~~Cg~~ 10 (36)
T PF05191_consen 2 RICPKCGRI 10 (36)
T ss_dssp EEETTTTEE
T ss_pred cCcCCCCCc
Confidence 567777765
No 247
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=26.00 E-value=22 Score=30.91 Aligned_cols=27 Identities=33% Similarity=0.938 Sum_probs=17.4
Q ss_pred ccccCCCCCCce--eEeEEe--eeeeecCcc
Q psy836 40 AKYTCSFCGKDS--MKRSCV--GIWSCKRCK 66 (122)
Q Consensus 40 aky~Cp~Cgk~~--mkR~av--GIW~C~~C~ 66 (122)
....|+|||+.. +.+.-. +.+-|..|-
T Consensus 8 ~~~~CSFCGr~~~ev~~li~g~~~~IC~~Ci 38 (412)
T PRK05342 8 KLLYCSFCGKSQHEVRKLIAGPGVYICDECI 38 (412)
T ss_pred CccccCCCCCChhhccccccCCCCcccchHH
Confidence 345799999974 444322 457777773
No 248
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=25.96 E-value=49 Score=22.27 Aligned_cols=13 Identities=15% Similarity=0.511 Sum_probs=6.8
Q ss_pred eeeeeecCcCeEE
Q psy836 82 VGIWSCKRCKRIV 94 (122)
Q Consensus 82 vtV~s~~rC~~~~ 94 (122)
.++-.|..|+.+.
T Consensus 28 ~t~V~C~~Cg~~L 40 (59)
T PRK00415 28 STVVRCLVCGKTL 40 (59)
T ss_pred CcEEECcccCCCc
Confidence 3344466666554
No 249
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=25.92 E-value=47 Score=23.95 Aligned_cols=14 Identities=14% Similarity=0.218 Sum_probs=7.5
Q ss_pred EEeeeeeecCccee
Q psy836 55 SCVGIWSCKRCKRI 68 (122)
Q Consensus 55 ~avGIW~C~~C~~~ 68 (122)
.--+...|+.|+..
T Consensus 66 ~vp~~~~C~~Cg~~ 79 (113)
T PRK12380 66 YKPAQAWCWDCSQV 79 (113)
T ss_pred eeCcEEEcccCCCE
Confidence 33445566666644
No 250
>PF10588 NADH-G_4Fe-4S_3: NADH-ubiquinone oxidoreductase-G iron-sulfur binding region; InterPro: IPR019574 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This entry describes the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes. This entry represents the iron-sulphur binding domain of the G subunit.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3.
Probab=25.70 E-value=56 Score=19.74 Aligned_cols=22 Identities=27% Similarity=0.690 Sum_probs=11.2
Q ss_pred hHhHHHHHHHhhccccCCCCCCc
Q psy836 28 RKMVKKMEITQHAKYTCSFCGKD 50 (122)
Q Consensus 28 RK~v~kie~~~~aky~Cp~Cgk~ 50 (122)
||.+-+...+.| +..||.|.+.
T Consensus 1 Rr~~lelll~~H-~~dC~~C~~~ 22 (41)
T PF10588_consen 1 RRTVLELLLANH-PLDCPTCDKN 22 (41)
T ss_dssp -HHHHHHHHTT-----TTT-TTG
T ss_pred CHHHHHHHHhCC-CCcCcCCCCC
Confidence 556666666666 6779999864
No 251
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=25.39 E-value=46 Score=21.08 Aligned_cols=26 Identities=35% Similarity=0.925 Sum_probs=11.4
Q ss_pred ccccCCCCCCce--eEeEEeeeeeecCcceee
Q psy836 40 AKYTCSFCGKDS--MKRSCVGIWSCKRCKRIV 69 (122)
Q Consensus 40 aky~Cp~Cgk~~--mkR~avGIW~C~~C~~~v 69 (122)
..-.|+.|++.- ++|. .+|..||..|
T Consensus 8 ~~~~C~~C~~~F~~~~rr----hhCr~CG~~v 35 (69)
T PF01363_consen 8 EASNCMICGKKFSLFRRR----HHCRNCGRVV 35 (69)
T ss_dssp G-SB-TTT--B-BSSS-E----EE-TTT--EE
T ss_pred CCCcCcCcCCcCCCceee----EccCCCCCEE
Confidence 345688888873 3333 5888888875
No 252
>cd00085 HNHc HNH nucleases; HNH endonuclease signature which is found in viral, prokaryotic, and eukaryotic proteins. The alignment includes members of the large group of homing endonucleases, yeast intron 1 protein, MutS, as well as bacterial colicins, pyocins, and anaredoxins.
Probab=25.34 E-value=50 Score=18.81 Aligned_cols=10 Identities=40% Similarity=1.089 Sum_probs=8.3
Q ss_pred ccCCCCCCce
Q psy836 42 YTCSFCGKDS 51 (122)
Q Consensus 42 y~Cp~Cgk~~ 51 (122)
+.|++||...
T Consensus 12 ~~C~~c~~~~ 21 (57)
T cd00085 12 GLCPYCGKPG 21 (57)
T ss_pred CcCccCCCcC
Confidence 8899998864
No 253
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=25.13 E-value=38 Score=21.44 Aligned_cols=13 Identities=23% Similarity=0.828 Sum_probs=7.3
Q ss_pred hccccCCCCCCce
Q psy836 39 HAKYTCSFCGKDS 51 (122)
Q Consensus 39 ~aky~Cp~Cgk~~ 51 (122)
-..+.||.|+..+
T Consensus 32 p~~w~CP~C~a~K 44 (47)
T PF00301_consen 32 PDDWVCPVCGAPK 44 (47)
T ss_dssp -TT-B-TTTSSBG
T ss_pred CCCCcCcCCCCcc
Confidence 4678899998653
No 254
>PRK06260 threonine synthase; Validated
Probab=25.05 E-value=27 Score=29.56 Aligned_cols=25 Identities=28% Similarity=0.555 Sum_probs=16.4
Q ss_pred cccCCCCCCceeEeEEeeeeeecCcce
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
.+.|+.||+..-- ..-.|.|+.|+-
T Consensus 3 ~~~C~~cg~~~~~--~~~~~~Cp~cg~ 27 (397)
T PRK06260 3 WLKCIECGKEYDP--DEIIYTCPECGG 27 (397)
T ss_pred EEEECCCCCCCCC--CCccccCCCCCC
Confidence 4789999877421 112588988874
No 255
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=24.99 E-value=32 Score=21.09 Aligned_cols=10 Identities=30% Similarity=0.770 Sum_probs=4.8
Q ss_pred cccCCCCCCc
Q psy836 41 KYTCSFCGKD 50 (122)
Q Consensus 41 ky~Cp~Cgk~ 50 (122)
+|.||.||--
T Consensus 1 ~hlcpkcgvg 10 (36)
T PF09151_consen 1 QHLCPKCGVG 10 (36)
T ss_dssp --B-TTTSSS
T ss_pred CccCCccCce
Confidence 3678888754
No 256
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=24.92 E-value=53 Score=25.76 Aligned_cols=57 Identities=25% Similarity=0.573 Sum_probs=35.7
Q ss_pred hHhHHHHHHHhhccccCCCCCCce-eEeEEe-eeeeecCcceeeecceeeeeccceeeeeeecCcCe
Q psy836 28 RKMVKKMEITQHAKYTCSFCGKDS-MKRSCV-GIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKR 92 (122)
Q Consensus 28 RK~v~kie~~~~aky~Cp~Cgk~~-mkR~av-GIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~ 92 (122)
.+.|..-+.=+-.-|.|.+|..+. +-=... ..-.|+.|+...--.=|. . .+|.+|.+
T Consensus 139 ~~HV~~C~lC~~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~-------~-~~CpkC~R 197 (202)
T PF13901_consen 139 EKHVYSCELCQQKGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFR-------K-KSCPKCAR 197 (202)
T ss_pred HHHHHHhHHHHhCCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcC-------C-CCCCCcHh
Confidence 455566666677789999998653 222233 667899998864333333 2 45888754
No 257
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=24.81 E-value=36 Score=21.74 Aligned_cols=14 Identities=21% Similarity=0.750 Sum_probs=10.6
Q ss_pred hhccccCCCCCCce
Q psy836 38 QHAKYTCSFCGKDS 51 (122)
Q Consensus 38 ~~aky~Cp~Cgk~~ 51 (122)
.-..+.||.||..+
T Consensus 31 Lp~~w~CP~C~a~K 44 (50)
T cd00730 31 LPDDWVCPVCGAGK 44 (50)
T ss_pred CCCCCCCCCCCCcH
Confidence 45678999998764
No 258
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.80 E-value=49 Score=26.96 Aligned_cols=25 Identities=28% Similarity=0.650 Sum_probs=15.7
Q ss_pred ccccCCCCCCceeEeEEee---eeeecCc
Q psy836 40 AKYTCSFCGKDSMKRSCVG---IWSCKRC 65 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avG---IW~C~~C 65 (122)
+.-.||.||..- ++..+| .|-|+.|
T Consensus 244 ~g~pC~~Cg~~I-~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 244 KGEPCRRCGTPI-EKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCCee-EEEEECCCCCEECCCC
Confidence 345799999763 444444 5666666
No 259
>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=24.50 E-value=50 Score=23.83 Aligned_cols=25 Identities=16% Similarity=0.181 Sum_probs=12.7
Q ss_pred CCceeEeEEeeeeeecCcceeeecc
Q psy836 48 GKDSMKRSCVGIWSCKRCKRIVAGG 72 (122)
Q Consensus 48 gk~~mkR~avGIW~C~~C~~~vAgg 72 (122)
|....--..-+...|+.|+..+.-.
T Consensus 59 ga~L~I~~~p~~~~C~~Cg~~~~~~ 83 (115)
T TIGR00100 59 GAKLNIEDEPVECECEDCSEEVSPE 83 (115)
T ss_pred CCEEEEEeeCcEEEcccCCCEEecC
Confidence 4443333344556677777554443
No 260
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=24.11 E-value=42 Score=22.15 Aligned_cols=11 Identities=27% Similarity=0.751 Sum_probs=7.2
Q ss_pred ccCCCCCCcee
Q psy836 42 YTCSFCGKDSM 52 (122)
Q Consensus 42 y~Cp~Cgk~~m 52 (122)
.+|+.||...+
T Consensus 6 r~C~~CgvYTL 16 (56)
T PRK13130 6 RKCPKCGVYTL 16 (56)
T ss_pred eECCCCCCEEc
Confidence 35777776666
No 261
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=23.73 E-value=38 Score=21.85 Aligned_cols=16 Identities=19% Similarity=0.405 Sum_probs=11.9
Q ss_pred HHHhhccccCCCCCCc
Q psy836 35 EITQHAKYTCSFCGKD 50 (122)
Q Consensus 35 e~~~~aky~Cp~Cgk~ 50 (122)
..-+...|.||.||+.
T Consensus 46 ~~~kd~~H~Cp~C~~~ 61 (67)
T smart00714 46 DSFKDVNHYCPNCGAF 61 (67)
T ss_pred ccccCccEECCCCCCE
Confidence 3446678899999875
No 262
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=23.65 E-value=46 Score=22.57 Aligned_cols=21 Identities=29% Similarity=0.749 Sum_probs=12.9
Q ss_pred ccCCCCCCceeEeEEeeeeeecCccee
Q psy836 42 YTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 42 y~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
+.||.||...++ . .|+.||..
T Consensus 6 rkC~~cg~YTLk-e-----~Cp~CG~~ 26 (59)
T COG2260 6 RKCPKCGRYTLK-E-----KCPVCGGD 26 (59)
T ss_pred hcCcCCCceeec-c-----cCCCCCCc
Confidence 357777777766 2 46666553
No 263
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=23.44 E-value=1e+02 Score=24.34 Aligned_cols=41 Identities=20% Similarity=0.387 Sum_probs=24.8
Q ss_pred hHhHHHHHHHhhcccc-CCCCCCc--eeEeE-EeeeeeecCccee
Q psy836 28 RKMVKKMEITQHAKYT-CSFCGKD--SMKRS-CVGIWSCKRCKRI 68 (122)
Q Consensus 28 RK~v~kie~~~~aky~-Cp~Cgk~--~mkR~-avGIW~C~~C~~~ 68 (122)
.+.+..+...=-.+|. ||.|+.+ .+.+. .+=.=+|.-||..
T Consensus 84 ~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~ 128 (201)
T PRK12336 84 EEDIQAAIDAYVDEYVICSECGLPDTRLVKEDRVLMLRCDACGAH 128 (201)
T ss_pred HHHHHHHHHHHHHheEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 4555555555555664 9999998 34433 2223468888765
No 264
>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=23.36 E-value=81 Score=20.82 Aligned_cols=15 Identities=20% Similarity=0.530 Sum_probs=7.4
Q ss_pred eeeeeeecCcCeEEe
Q psy836 81 CVGIWSCKRCKRIVA 95 (122)
Q Consensus 81 AvtV~s~~rC~~~~A 95 (122)
|.++-.|..|+.+.+
T Consensus 23 a~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 23 AQTVVKCVVCGTVLA 37 (55)
T ss_dssp -SS-EE-SSSTSEEE
T ss_pred CCeEEEcccCCCEec
Confidence 444445777777663
No 265
>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=23.32 E-value=1.3e+02 Score=20.56 Aligned_cols=14 Identities=21% Similarity=0.363 Sum_probs=9.0
Q ss_pred eeeeeecCcCeEEe
Q psy836 82 VGIWSCKRCKRIVA 95 (122)
Q Consensus 82 vtV~s~~rC~~~~A 95 (122)
+-+..|..||+.-.
T Consensus 28 ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 28 VEYVECVECGYTER 41 (71)
T ss_pred ceEEEecCCCCeec
Confidence 45556888877643
No 266
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=23.21 E-value=44 Score=23.61 Aligned_cols=27 Identities=30% Similarity=0.737 Sum_probs=20.4
Q ss_pred ccccCCCCCCceeEeEEeeeeeecCcce
Q psy836 40 AKYTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 40 aky~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
....|..||.++.. .-.|.|+|..|.-
T Consensus 4 ~~~~C~VCg~~~~g-~hyGv~sC~aC~~ 30 (95)
T cd06968 4 EVIPCKICGDKSSG-IHYGVITCEGCKG 30 (95)
T ss_pred cccCCcccCCcCcc-eEECceeehhhHH
Confidence 44579999987644 4589999988874
No 267
>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=23.19 E-value=1.2e+02 Score=23.02 Aligned_cols=53 Identities=26% Similarity=0.634 Sum_probs=31.5
Q ss_pred hhHhHHHHHHHhhccccCCCCCCceeEeEEeeeeeecCcc---eeeecceeeeeccceeeeeeecCcCe
Q psy836 27 LRKMVKKMEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCK---RIVAGGAWDSMKRSCVGIWSCKRCKR 92 (122)
Q Consensus 27 lRK~v~kie~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~---~~vAggAy~~~t~~AvtV~s~~rC~~ 92 (122)
|++.++.+. .+.....|.-||-..+ =.|..|+ |.+..++. ....+..|..||+
T Consensus 86 L~~lL~~~~-~~~~~~~C~~Cgg~rf-------v~C~~C~Gs~k~~~~~~~-----~~~~~~rC~~Cne 141 (147)
T cd03031 86 LRKLLKGIR-ARAGGGVCEGCGGARF-------VPCSECNGSCKVFAENAT-----AAGGFLRCPECNE 141 (147)
T ss_pred HHHHHhhcc-cccCCCCCCCCCCcCe-------EECCCCCCcceEEeccCc-----ccccEEECCCCCc
Confidence 566666663 3445678999985432 3566554 44443322 3455677888886
No 268
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.18 E-value=46 Score=24.34 Aligned_cols=11 Identities=27% Similarity=0.899 Sum_probs=7.2
Q ss_pred ccCCCCCCcee
Q psy836 42 YTCSFCGKDSM 52 (122)
Q Consensus 42 y~Cp~Cgk~~m 52 (122)
+.||.||...+
T Consensus 93 ~~CP~Cgs~~~ 103 (124)
T PRK00762 93 IECPVCGNKRA 103 (124)
T ss_pred CcCcCCCCCCC
Confidence 46887776544
No 269
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=22.78 E-value=15 Score=32.69 Aligned_cols=30 Identities=27% Similarity=0.651 Sum_probs=19.4
Q ss_pred cCCCCCCc-eeEeEEeeeeeecCcceeeecc
Q psy836 43 TCSFCGKD-SMKRSCVGIWSCKRCKRIVAGG 72 (122)
Q Consensus 43 ~Cp~Cgk~-~mkR~avGIW~C~~C~~~vAgg 72 (122)
.|..|... ++.=.-.+-|.|++||.+|--|
T Consensus 248 AC~rC~t~y~le~A~~~~wrCpkCGg~ikKG 278 (403)
T COG1379 248 ACSRCYTRYSLEEAKSLRWRCPKCGGKIKKG 278 (403)
T ss_pred HHHHhhhccCcchhhhhcccCcccccchhhh
Confidence 48888744 3443344579998888765433
No 270
>PHA02540 61 DNA primase; Provisional
Probab=22.70 E-value=71 Score=27.58 Aligned_cols=34 Identities=21% Similarity=0.585 Sum_probs=20.4
Q ss_pred cccCCCCCCce----eEeEE------eeeeeecCcceeeecceeee
Q psy836 41 KYTCSFCGKDS----MKRSC------VGIWSCKRCKRIVAGGAWDS 76 (122)
Q Consensus 41 ky~Cp~Cgk~~----mkR~a------vGIW~C~~C~~~vAggAy~~ 76 (122)
+..|||||-.. --|-. .++|+|=.||.- |++-.|
T Consensus 27 ~~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~--Gd~i~F 70 (337)
T PHA02540 27 NFRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYH--RPFGNF 70 (337)
T ss_pred EecCCCCCCccccCcCCcEEEeccCCceEEEecCCCCC--CCHHHH
Confidence 56799998632 11222 349998888763 444443
No 271
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=22.53 E-value=44 Score=17.84 Aligned_cols=8 Identities=38% Similarity=1.153 Sum_probs=4.2
Q ss_pred ccCCCCCC
Q psy836 42 YTCSFCGK 49 (122)
Q Consensus 42 y~Cp~Cgk 49 (122)
|.|+.|++
T Consensus 2 ~~C~~C~k 9 (27)
T PF12171_consen 2 FYCDACDK 9 (27)
T ss_dssp CBBTTTTB
T ss_pred CCcccCCC
Confidence 45555554
No 272
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=22.46 E-value=64 Score=18.81 Aligned_cols=14 Identities=36% Similarity=0.990 Sum_probs=10.2
Q ss_pred eeeecCcceeeecc
Q psy836 59 IWSCKRCKRIVAGG 72 (122)
Q Consensus 59 IW~C~~C~~~vAgg 72 (122)
+|.|.-||.+.-|.
T Consensus 2 ~~~C~~CG~i~~g~ 15 (34)
T cd00729 2 VWVCPVCGYIHEGE 15 (34)
T ss_pred eEECCCCCCEeECC
Confidence 58888888776654
No 273
>PLN00209 ribosomal protein S27; Provisional
Probab=22.40 E-value=91 Score=22.51 Aligned_cols=14 Identities=14% Similarity=0.593 Sum_probs=8.2
Q ss_pred eeeeeeecCcCeEE
Q psy836 81 CVGIWSCKRCKRIV 94 (122)
Q Consensus 81 AvtV~s~~rC~~~~ 94 (122)
|.++-.|..|+.+.
T Consensus 52 A~t~V~C~~Cg~~L 65 (86)
T PLN00209 52 SQTVVVCGSCQTVL 65 (86)
T ss_pred CceEEEccccCCEe
Confidence 44444567776665
No 274
>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....
Probab=22.39 E-value=45 Score=21.48 Aligned_cols=24 Identities=33% Similarity=0.832 Sum_probs=18.1
Q ss_pred cCCCCCCceeEeEEeeeeeecCcce
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
.|..||..+.. ...|.++|..|..
T Consensus 2 ~C~VCg~~~~~-~~ygv~sC~~C~~ 25 (70)
T PF00105_consen 2 KCKVCGDPASG-YHYGVLSCNACKM 25 (70)
T ss_dssp BSTTTSSBESE-EETTEEEEHHHHH
T ss_pred CCeECCCccCc-cccccccccccee
Confidence 58999986533 4688999888864
No 275
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=22.26 E-value=1.9e+02 Score=17.33 Aligned_cols=26 Identities=15% Similarity=0.360 Sum_probs=15.8
Q ss_pred cCC--CCCCceeEeE--EeeeeeecCccee
Q psy836 43 TCS--FCGKDSMKRS--CVGIWSCKRCKRI 68 (122)
Q Consensus 43 ~Cp--~Cgk~~mkR~--avGIW~C~~C~~~ 68 (122)
.|| .|+.....=. ....=.|+.|+..
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~ 49 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCGFS 49 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCCCe
Confidence 499 9977654321 3445567777764
No 276
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=22.13 E-value=30 Score=20.97 Aligned_cols=32 Identities=25% Similarity=0.487 Sum_probs=17.4
Q ss_pred cCCCCCCceeEeEEeeeeeecCcceeeecceeee
Q psy836 43 TCSFCGKDSMKRSCVGIWSCKRCKRIVAGGAWDS 76 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~avGIW~C~~C~~~vAggAy~~ 76 (122)
.|+.|++.-.- ....-+|..||+.+=+.....
T Consensus 4 ~C~~C~~~F~~--~~rk~~Cr~Cg~~~C~~C~~~ 35 (57)
T cd00065 4 SCMGCGKPFTL--TRRRHHCRNCGRIFCSKCSSN 35 (57)
T ss_pred cCcccCccccC--CccccccCcCcCCcChHHcCC
Confidence 47777764211 223357777777765544433
No 277
>KOG4317|consensus
Probab=22.10 E-value=36 Score=30.19 Aligned_cols=11 Identities=9% Similarity=0.220 Sum_probs=6.3
Q ss_pred HHHHHHHHHHh
Q psy836 109 VRSAIRRLREV 119 (122)
Q Consensus 109 ~~~~i~rl~e~ 119 (122)
+-+.++|+++.
T Consensus 68 m~e~lkr~~q~ 78 (383)
T KOG4317|consen 68 MGEELKRKMQK 78 (383)
T ss_pred HHHHHHHHHhh
Confidence 34556666665
No 278
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=22.06 E-value=37 Score=24.47 Aligned_cols=33 Identities=27% Similarity=0.398 Sum_probs=24.5
Q ss_pred HHHHhhccccCCCCCCceeEeEEeeeeeecCcceeee
Q psy836 34 MEITQHAKYTCSFCGKDSMKRSCVGIWSCKRCKRIVA 70 (122)
Q Consensus 34 ie~~~~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~vA 70 (122)
-+........|+.|...+.-|. .||+.|++-|.
T Consensus 41 ~~~~~~~~~~C~~C~~~kp~Rs----~HC~~C~~CV~ 73 (174)
T PF01529_consen 41 EDDENGELKYCSTCKIIKPPRS----HHCRVCNRCVL 73 (174)
T ss_pred ccccCCCCEECcccCCcCCCcc----eeccccccccc
Confidence 3445566778999998888875 69998887543
No 279
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=22.01 E-value=41 Score=21.97 Aligned_cols=14 Identities=21% Similarity=0.413 Sum_probs=11.1
Q ss_pred HhhccccCCCCCCc
Q psy836 37 TQHAKYTCSFCGKD 50 (122)
Q Consensus 37 ~~~aky~Cp~Cgk~ 50 (122)
-+...|.||.|++.
T Consensus 54 ~kd~~H~Cp~C~~~ 67 (73)
T PF10601_consen 54 CKDVYHYCPNCGAF 67 (73)
T ss_pred ccCceEECCCCCCE
Confidence 45678899999875
No 280
>PRK05638 threonine synthase; Validated
Probab=21.99 E-value=37 Score=29.23 Aligned_cols=24 Identities=29% Similarity=0.564 Sum_probs=16.6
Q ss_pred cccCCCCCCceeEeEEeeeeeecCccee
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
|+.|+.||+..- .. -.|.| .|+-.
T Consensus 1 ~l~C~~Cg~~~~--~~-~~~~C-~c~~~ 24 (442)
T PRK05638 1 KMKCPKCGREYN--SY-IPPFC-ICGEL 24 (442)
T ss_pred CeEeCCCCCCCC--CC-Cceec-CCCCc
Confidence 578999998853 12 23899 89743
No 281
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=21.89 E-value=54 Score=19.54 Aligned_cols=16 Identities=31% Similarity=0.638 Sum_probs=10.4
Q ss_pred eecCcCeEEecccccc
Q psy836 86 SCKRCKRIVAGGAWVY 101 (122)
Q Consensus 86 s~~rC~~~~AGGAy~~ 101 (122)
.|..|++.|+.+-|-+
T Consensus 6 ~C~nC~R~v~a~RfA~ 21 (33)
T PF08209_consen 6 ECPNCGRPVAASRFAP 21 (33)
T ss_dssp E-TTTSSEEEGGGHHH
T ss_pred ECCCCcCCcchhhhHH
Confidence 3777777777776644
No 283
>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=21.73 E-value=80 Score=23.47 Aligned_cols=39 Identities=21% Similarity=0.492 Sum_probs=22.9
Q ss_pred hHhHHHHHHHhhcccc-CCCCCCce--eEeEEeeee--eecCcce
Q psy836 28 RKMVKKMEITQHAKYT-CSFCGKDS--MKRSCVGIW--SCKRCKR 67 (122)
Q Consensus 28 RK~v~kie~~~~aky~-Cp~Cgk~~--mkR~avGIW--~C~~C~~ 67 (122)
.+++.++...=-.+|. ||.|+.+- +.+. -++| +|..||.
T Consensus 79 ~~~i~~~L~~fI~~yVlC~~C~spdT~l~k~-~r~~~l~C~aCGa 122 (125)
T PF01873_consen 79 SKQIQDLLDKFIKEYVLCPECGSPDTELIKE-GRLIFLKCKACGA 122 (125)
T ss_dssp CCHHHHHHHHHHCHHSSCTSTSSSSEEEEEE-TTCCEEEETTTSC
T ss_pred HHHHHHHHHHHHHHEEEcCCCCCCccEEEEc-CCEEEEEecccCC
Confidence 3455555555556654 99999983 4443 3444 4555554
No 284
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=21.69 E-value=38 Score=30.54 Aligned_cols=40 Identities=23% Similarity=0.379 Sum_probs=24.8
Q ss_pred hhhhHhHHHHHHH--h-----hccccCCCCCCceeEeEEeeeeeecCccee
Q psy836 25 ASLRKMVKKMEIT--Q-----HAKYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 25 ~slRK~v~kie~~--~-----~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
..|.+.|+.+-.. . .....|+.||.... +. .|.||.||+.
T Consensus 495 ~al~~lv~~a~~~~~~y~~~~~p~~~C~~CG~~~~-~~---~~~CP~CGs~ 541 (555)
T cd01675 495 EALEALVKKAAKRGVIYFGINTPIDICNDCGYIGE-GE---GFKCPKCGSE 541 (555)
T ss_pred HHHHHHHHHHHHcCCceEEEecCCccCCCCCCCCc-CC---CCCCcCCCCc
Confidence 4566666666543 1 12348999997432 11 3999999975
No 285
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=21.39 E-value=35 Score=31.00 Aligned_cols=40 Identities=20% Similarity=0.319 Sum_probs=22.4
Q ss_pred hhhhHhHHHHHHHh-------hccccCCCCCCceeEeEEeeeeeecCccee
Q psy836 25 ASLRKMVKKMEITQ-------HAKYTCSFCGKDSMKRSCVGIWSCKRCKRI 68 (122)
Q Consensus 25 ~slRK~v~kie~~~-------~aky~Cp~Cgk~~mkR~avGIW~C~~C~~~ 68 (122)
..|++-|+.+...- +.--.|+.||.. -++. .|.||.||..
T Consensus 501 eal~~lv~~a~~~~i~Y~~~n~~~~~C~~CG~~-g~~~---~~~CP~Cgs~ 547 (579)
T TIGR02487 501 EALKDITKKAMKNGIGYFGINPPVDVCEDCGYT-GEGL---NDKCPKCGSH 547 (579)
T ss_pred HHHHHHHHHHHhcCCceEEeccCCccCCCCCCC-CCCC---CCcCcCCCCc
Confidence 34566666664431 122259999863 1111 2889999864
No 286
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=21.32 E-value=37 Score=23.44 Aligned_cols=21 Identities=33% Similarity=0.745 Sum_probs=14.1
Q ss_pred ccCCCCCCce--------eEeEEeeeeee
Q psy836 42 YTCSFCGKDS--------MKRSCVGIWSC 62 (122)
Q Consensus 42 y~Cp~Cgk~~--------mkR~avGIW~C 62 (122)
++|.|||+.- +++.+.=.|-|
T Consensus 4 ~~CsFcG~~I~PGtG~m~Vr~Dg~v~~Fc 32 (66)
T COG2075 4 RVCSFCGKKIEPGTGIMYVRNDGKVLRFC 32 (66)
T ss_pred eEecCcCCccCCCceEEEEecCCeEEEEe
Confidence 6799998863 45555556665
No 287
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.02 E-value=59 Score=20.32 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=8.5
Q ss_pred hccccCCCCCC
Q psy836 39 HAKYTCSFCGK 49 (122)
Q Consensus 39 ~aky~Cp~Cgk 49 (122)
..-..||.||+
T Consensus 44 ~~i~~Cp~CgR 54 (56)
T PF02591_consen 44 DEIVFCPNCGR 54 (56)
T ss_pred CCeEECcCCCc
Confidence 56678999886
No 288
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.91 E-value=26 Score=27.76 Aligned_cols=64 Identities=20% Similarity=0.354 Sum_probs=37.2
Q ss_pred HhHHHHH-HHhhccccCCCCCCc-eeEeEEeeeeeecCcceeeecceeeeeccceeeeeeecCcCeEEeccccccCchHH
Q psy836 29 KMVKKME-ITQHAKYTCSFCGKD-SMKRSCVGIWSCKRCKRIVAGGAWDSMKRSCVGIWSCKRCKRIVAGGAWVYNTTAA 106 (122)
Q Consensus 29 K~v~kie-~~~~aky~Cp~Cgk~-~mkR~avGIW~C~~C~~~vAggAy~~~t~~AvtV~s~~rC~~~~AGGAy~~~T~~~ 106 (122)
+-...+| ..+..-|.||.|.-. ++-..-.--.. |.+||... -|.=+++.-
T Consensus 100 ~Lk~~le~~~~~~~y~C~~~~~r~sfdeA~~~~F~-------------------------Cp~Cg~~L---~~~d~s~~i 151 (176)
T COG1675 100 KLKRKLEKETENNYYVCPNCHVKYSFDEAMELGFT-------------------------CPKCGEDL---EEYDSSEEI 151 (176)
T ss_pred HHHHHHHhhccCCceeCCCCCCcccHHHHHHhCCC-------------------------CCCCCchh---hhccchHHH
Confidence 3333444 567788999888644 22222222244 55665433 234467777
Q ss_pred HHHHHHHHHHHHhh
Q psy836 107 TSVRSAIRRLREVN 120 (122)
Q Consensus 107 ~~~~~~i~rl~e~~ 120 (122)
.-..+.|++|.+.-
T Consensus 152 ~~l~~~i~~l~~~l 165 (176)
T COG1675 152 EELESELDELEEEL 165 (176)
T ss_pred HHHHHHHHHHHHHH
Confidence 77888888888763
No 289
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=20.65 E-value=44 Score=22.16 Aligned_cols=25 Identities=20% Similarity=0.259 Sum_probs=10.4
Q ss_pred cccCCCCCCceeEeEEeeeeeecCcce
Q psy836 41 KYTCSFCGKDSMKRSCVGIWSCKRCKR 67 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGIW~C~~C~~ 67 (122)
+..||.||+...-...- =.-++|.+
T Consensus 2 ~v~CP~C~k~~~~~~~n--~~rPFCS~ 26 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPEN--PFRPFCSE 26 (57)
T ss_dssp EEE-TTT--EEE-SSSS--S--SSSSH
T ss_pred cccCCCCCCeecccCCC--CcCCcccH
Confidence 35799998876542221 13456654
No 290
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=20.59 E-value=1.1e+02 Score=20.02 Aligned_cols=20 Identities=20% Similarity=0.297 Sum_probs=14.9
Q ss_pred eEEeeeeeecCcceeeecce
Q psy836 54 RSCVGIWSCKRCKRIVAGGA 73 (122)
Q Consensus 54 R~avGIW~C~~C~~~vAggA 73 (122)
+..+|+|.|.+....+.-..
T Consensus 6 ~~~~g~w~~~pg~~~~~~~~ 25 (74)
T PF05899_consen 6 VFSAGVWECTPGKFPWPYPE 25 (74)
T ss_dssp SEEEEEEEEECEEEEEEESS
T ss_pred CEEEEEEEECCceeEeeCCC
Confidence 46899999999877655443
No 291
>PRK11032 hypothetical protein; Provisional
Probab=20.28 E-value=54 Score=25.65 Aligned_cols=14 Identities=36% Similarity=0.842 Sum_probs=11.4
Q ss_pred cCCCCCCceeEeEE
Q psy836 43 TCSFCGKDSMKRSC 56 (122)
Q Consensus 43 ~Cp~Cgk~~mkR~a 56 (122)
.||.||.+.+.|.+
T Consensus 144 pCp~C~~~~F~R~~ 157 (160)
T PRK11032 144 LCPKCGHDQFQRRP 157 (160)
T ss_pred CCCCCCCCeeeeCC
Confidence 58999988888864
No 292
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=20.27 E-value=65 Score=19.60 Aligned_cols=12 Identities=33% Similarity=0.994 Sum_probs=6.1
Q ss_pred eeeeecCcceee
Q psy836 58 GIWSCKRCKRIV 69 (122)
Q Consensus 58 GIW~C~~C~~~v 69 (122)
.++.|..||..|
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 367777777764
No 293
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=20.10 E-value=1.1e+02 Score=22.05 Aligned_cols=14 Identities=14% Similarity=0.406 Sum_probs=8.5
Q ss_pred eeeeeeecCcCeEE
Q psy836 81 CVGIWSCKRCKRIV 94 (122)
Q Consensus 81 AvtV~s~~rC~~~~ 94 (122)
|.++-.|..|+.+.
T Consensus 51 A~t~V~C~~Cg~~L 64 (85)
T PTZ00083 51 AQTVVLCGGCSSQL 64 (85)
T ss_pred CceEEEccccCCEe
Confidence 44455577777665
No 294
>PRK14724 DNA topoisomerase III; Provisional
Probab=20.08 E-value=78 Score=30.87 Aligned_cols=21 Identities=24% Similarity=0.678 Sum_probs=14.9
Q ss_pred cccCCCCCCceeEeEEeee-eeecC
Q psy836 41 KYTCSFCGKDSMKRSCVGI-WSCKR 64 (122)
Q Consensus 41 ky~Cp~Cgk~~mkR~avGI-W~C~~ 64 (122)
--.||.||...+. .|. |.|..
T Consensus 755 ~g~CPkCg~~v~e---~gk~y~Cs~ 776 (987)
T PRK14724 755 LGPCPKCGAPVFE---HGSNYVCEK 776 (987)
T ss_pred ccCCCCCCCceEe---ecceEEcCC
Confidence 4579999887554 455 88875
No 295
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=20.01 E-value=73 Score=25.54 Aligned_cols=13 Identities=31% Similarity=0.698 Sum_probs=10.3
Q ss_pred hccccCCCCCCce
Q psy836 39 HAKYTCSFCGKDS 51 (122)
Q Consensus 39 ~aky~Cp~Cgk~~ 51 (122)
.....||.||...
T Consensus 151 ~~~~~Cp~CG~~~ 163 (177)
T COG1439 151 EPKDFCPICGSPL 163 (177)
T ss_pred CCCCcCCCCCCce
Confidence 4677899999884
Done!