Query 039226
Match_columns 121
No_of_seqs 104 out of 286
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 07:35:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039226.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039226hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03226 Yippee-Mis18: Yippee 95.9 0.0084 1.8E-07 40.5 2.9 21 14-34 2-23 (96)
2 PF13240 zinc_ribbon_2: zinc-r 87.9 0.22 4.7E-06 25.8 0.5 8 82-89 2-9 (23)
3 PF09814 HECT_2: HECT-like Ubi 85.8 1.1 2.5E-05 36.2 4.0 30 77-117 191-220 (354)
4 smart00714 LITAF Possible memb 85.1 0.47 1E-05 30.0 1.1 19 75-93 48-66 (67)
5 PF10601 zf-LITAF-like: LITAF- 82.3 0.8 1.7E-05 29.4 1.3 67 10-93 3-72 (73)
6 PF01641 SelR: SelR domain; I 81.5 1.7 3.6E-05 31.4 2.9 66 10-96 33-103 (124)
7 PF10122 Mu-like_Com: Mu-like 81.3 0.57 1.2E-05 29.0 0.4 17 14-30 4-20 (51)
8 PF10571 UPF0547: Uncharacteri 79.4 1.1 2.4E-05 23.8 1.1 20 81-103 2-22 (26)
9 PF11648 RIG-I_C-RD: C-termina 77.2 2.2 4.8E-05 30.4 2.4 68 12-98 2-80 (123)
10 PF12773 DZR: Double zinc ribb 75.5 1 2.2E-05 26.5 0.3 32 77-108 10-42 (50)
11 PF13453 zf-TFIIB: Transcripti 74.7 2.2 4.7E-05 24.5 1.5 23 81-103 1-27 (41)
12 PF13408 Zn_ribbon_recom: Reco 74.2 2.2 4.7E-05 25.4 1.5 21 76-96 2-22 (58)
13 PF09538 FYDLN_acid: Protein o 74.0 1.7 3.7E-05 30.6 1.1 33 76-108 6-39 (108)
14 PRK00222 methionine sulfoxide 73.2 5.8 0.00013 29.3 3.8 21 10-30 39-59 (142)
15 TIGR02300 FYDLN_acid conserved 72.3 2.1 4.5E-05 31.3 1.2 35 76-110 6-41 (129)
16 KOG3399 Predicted Yippee-type 69.0 2.2 4.8E-05 30.8 0.8 24 12-35 13-36 (122)
17 PF13248 zf-ribbon_3: zinc-rib 68.7 1.7 3.8E-05 22.7 0.1 13 77-89 14-26 (26)
18 PF13717 zinc_ribbon_4: zinc-r 68.4 3.4 7.3E-05 23.3 1.3 25 79-103 2-33 (36)
19 PF02591 DUF164: Putative zinc 67.7 4.4 9.6E-05 24.6 1.9 33 54-88 22-55 (56)
20 PF08996 zf-DNA_Pol: DNA Polym 67.5 1.9 4.2E-05 32.6 0.2 29 79-107 18-57 (188)
21 PF03119 DNA_ligase_ZBD: NAD-d 64.1 2.8 6E-05 22.5 0.4 10 81-90 1-10 (28)
22 TIGR02098 MJ0042_CXXC MJ0042 f 64.0 4.7 0.0001 22.4 1.4 13 77-89 23-35 (38)
23 PF07282 OrfB_Zn_ribbon: Putat 61.0 5.5 0.00012 24.8 1.4 25 81-105 30-56 (69)
24 PF09297 zf-NADH-PPase: NADH p 60.9 4.1 8.9E-05 22.1 0.7 9 81-89 5-13 (32)
25 PRK14018 trifunctional thiored 59.7 14 0.00031 32.5 4.1 20 10-29 414-433 (521)
26 PF03966 Trm112p: Trm112p-like 59.2 4.9 0.00011 25.4 1.0 14 74-87 48-61 (68)
27 PRK11823 DNA repair protein Ra 59.0 5.7 0.00012 33.9 1.6 24 79-105 7-31 (446)
28 PRK03681 hypA hydrogenase nick 58.9 9.1 0.0002 26.8 2.3 30 75-104 66-96 (114)
29 PF13719 zinc_ribbon_5: zinc-r 58.6 6.6 0.00014 22.1 1.3 11 79-89 2-12 (37)
30 smart00531 TFIIE Transcription 58.4 5.4 0.00012 28.9 1.2 17 76-92 120-136 (147)
31 PF03604 DNA_RNApol_7kD: DNA d 57.5 5.4 0.00012 22.2 0.8 24 82-105 3-27 (32)
32 smart00659 RPOLCX RNA polymera 56.5 6.4 0.00014 23.3 1.1 13 77-89 17-29 (44)
33 COG2888 Predicted Zn-ribbon RN 55.4 3.7 8.1E-05 26.3 -0.1 12 12-23 36-47 (61)
34 COG2093 DNA-directed RNA polym 55.3 5.3 0.00012 25.8 0.6 19 79-97 18-36 (64)
35 PRK12380 hydrogenase nickel in 55.2 12 0.00026 26.2 2.5 28 75-103 66-94 (113)
36 PRK00420 hypothetical protein; 54.4 7.9 0.00017 27.5 1.4 25 80-105 24-50 (112)
37 PRK00398 rpoP DNA-directed RNA 53.5 7.8 0.00017 22.6 1.1 12 79-90 21-32 (46)
38 PF00096 zf-C2H2: Zinc finger, 51.8 1.8 3.8E-05 21.2 -1.7 19 15-33 1-19 (23)
39 PF09082 DUF1922: Domain of un 51.4 7 0.00015 25.5 0.7 20 13-33 2-21 (68)
40 COG5629 Predicted metal-bindin 50.8 7.7 0.00017 31.9 1.0 37 76-112 166-212 (321)
41 PRK14890 putative Zn-ribbon RN 49.9 6.1 0.00013 25.1 0.2 11 13-23 35-45 (59)
42 COG1066 Sms Predicted ATP-depe 49.0 12 0.00027 32.5 2.0 25 78-105 6-31 (456)
43 TIGR00416 sms DNA repair prote 49.0 9.8 0.00021 32.6 1.4 24 79-105 7-31 (454)
44 TIGR00622 ssl1 transcription f 48.5 9.1 0.0002 27.2 1.0 31 81-114 3-34 (112)
45 TIGR00100 hypA hydrogenase nic 46.3 16 0.00034 25.6 1.9 29 75-104 66-95 (115)
46 PF01096 TFIIS_C: Transcriptio 46.2 12 0.00026 21.3 1.1 21 3-23 17-37 (39)
47 KOG4784 Uncharacterized conser 46.1 12 0.00027 31.4 1.5 85 9-96 98-201 (348)
48 PF07295 DUF1451: Protein of u 45.6 17 0.00038 26.7 2.1 27 76-103 109-138 (146)
49 PRK08351 DNA-directed RNA poly 44.9 11 0.00023 24.1 0.8 17 81-97 17-33 (61)
50 PF06750 DiS_P_DiS: Bacterial 44.7 14 0.00031 24.9 1.4 31 77-107 31-70 (92)
51 PF11781 RRN7: RNA polymerase 44.2 14 0.00031 20.9 1.2 23 80-104 9-34 (36)
52 COG4416 Com Mu-like prophage p 44.0 5.8 0.00013 25.0 -0.5 15 14-28 4-18 (60)
53 COG1645 Uncharacterized Zn-fin 44.0 13 0.00028 27.2 1.2 13 76-88 41-53 (131)
54 PRK14714 DNA polymerase II lar 43.8 18 0.0004 35.3 2.4 27 78-109 666-693 (1337)
55 COG3809 Uncharacterized protei 42.8 15 0.00033 24.9 1.3 35 80-119 2-40 (88)
56 PRK05508 methionine sulfoxide 41.9 21 0.00045 25.7 2.0 21 10-30 29-49 (119)
57 smart00834 CxxC_CXXC_SSSS Puta 41.5 18 0.00039 20.0 1.3 13 12-24 3-15 (41)
58 TIGR00354 polC DNA polymerase, 41.2 19 0.00041 34.3 2.1 37 77-116 1010-1047(1095)
59 PRK06835 DNA replication prote 40.9 14 0.00031 30.3 1.2 25 76-103 95-119 (329)
60 PF14599 zinc_ribbon_6: Zinc-r 40.8 16 0.00034 23.2 1.1 30 77-106 28-59 (61)
61 PF14205 Cys_rich_KTR: Cystein 40.8 16 0.00036 22.9 1.1 9 80-88 5-13 (55)
62 PF13790 DUF4182: Domain of un 40.7 17 0.00037 21.1 1.1 17 78-94 2-18 (38)
63 PHA02325 hypothetical protein 40.3 17 0.00037 23.7 1.2 16 81-96 5-22 (72)
64 PF09723 Zn-ribbon_8: Zinc rib 40.1 19 0.00041 20.7 1.3 12 12-23 3-14 (42)
65 PRK11032 hypothetical protein; 39.8 25 0.00053 26.4 2.2 27 76-103 121-150 (160)
66 TIGR00357 methionine-R-sulfoxi 39.1 24 0.00052 25.8 2.0 21 10-30 36-56 (134)
67 TIGR02605 CxxC_CxxC_SSSS putat 39.0 20 0.00042 21.1 1.3 11 12-22 3-13 (52)
68 PF08271 TF_Zn_Ribbon: TFIIB z 38.8 17 0.00037 20.8 0.9 17 75-91 15-31 (43)
69 PRK11827 hypothetical protein; 38.4 18 0.00039 22.9 1.1 12 78-89 7-18 (60)
70 COG4307 Uncharacterized protei 38.2 12 0.00025 31.0 0.2 23 80-105 4-27 (349)
71 PF13912 zf-C2H2_6: C2H2-type 38.2 4 8.7E-05 20.7 -1.7 20 15-34 2-21 (27)
72 PRK00564 hypA hydrogenase nick 38.0 34 0.00075 24.0 2.6 29 75-104 67-97 (117)
73 PF08772 NOB1_Zn_bind: Nin one 37.5 11 0.00024 24.7 0.0 12 77-88 22-33 (73)
74 COG1933 Archaeal DNA polymeras 37.1 19 0.00042 29.0 1.3 38 76-116 164-202 (253)
75 PRK14559 putative protein seri 37.0 18 0.0004 32.7 1.3 10 82-91 44-53 (645)
76 PF10955 DUF2757: Protein of u 36.3 19 0.00042 23.9 1.0 15 13-27 3-17 (76)
77 PF13894 zf-C2H2_4: C2H2-type 35.7 4.5 9.7E-05 19.2 -1.7 19 15-33 1-19 (24)
78 PF12760 Zn_Tnp_IS1595: Transp 35.5 20 0.00044 20.9 0.9 11 12-22 35-45 (46)
79 PRK14714 DNA polymerase II lar 35.3 26 0.00056 34.3 2.1 33 77-110 1251-1284(1337)
80 COG1996 RPC10 DNA-directed RNA 35.1 21 0.00046 21.8 1.0 10 80-89 25-34 (49)
81 PF06677 Auto_anti-p27: Sjogre 34.7 22 0.00047 20.8 1.0 11 76-86 31-41 (41)
82 PRK03824 hypA hydrogenase nick 34.5 47 0.001 23.8 2.9 12 76-87 67-78 (135)
83 COG3478 Predicted nucleic-acid 34.4 18 0.0004 23.5 0.7 11 78-88 3-13 (68)
84 smart00355 ZnF_C2H2 zinc finge 34.2 4.3 9.2E-05 19.4 -1.9 19 15-33 1-19 (26)
85 PF04438 zf-HIT: HIT zinc fing 34.0 22 0.00047 19.3 0.8 13 77-89 11-23 (30)
86 PRK04023 DNA polymerase II lar 33.7 28 0.00062 33.4 2.0 37 77-116 1035-1072(1121)
87 COG1571 Predicted DNA-binding 33.5 21 0.00045 30.8 1.0 30 76-105 347-377 (421)
88 smart00440 ZnF_C2C2 C2C2 Zinc 32.7 38 0.00083 19.3 1.8 20 3-22 17-36 (40)
89 PF14803 Nudix_N_2: Nudix N-te 31.7 19 0.00041 20.2 0.4 9 81-89 2-10 (34)
90 PF06044 DRP: Dam-replacing fa 31.6 12 0.00026 30.2 -0.6 24 73-96 25-49 (254)
91 PRK05638 threonine synthase; V 31.4 35 0.00075 28.9 2.0 28 79-108 1-28 (442)
92 PF00130 C1_1: Phorbol esters/ 31.2 23 0.00049 20.7 0.7 29 77-105 9-38 (53)
93 COG0143 MetG Methionyl-tRNA sy 31.1 24 0.00051 31.4 1.0 27 78-108 141-168 (558)
94 PF07754 DUF1610: Domain of un 30.9 31 0.00067 18.0 1.1 10 77-86 14-23 (24)
95 COG2816 NPY1 NTP pyrophosphohy 30.4 43 0.00092 27.4 2.3 43 75-118 107-156 (279)
96 PF01396 zf-C4_Topoisom: Topoi 30.2 24 0.00052 20.1 0.6 9 81-89 3-11 (39)
97 KOG3092 Casein kinase II, beta 29.9 30 0.00065 27.2 1.3 34 54-87 106-142 (216)
98 PF14471 DUF4428: Domain of un 29.9 23 0.0005 21.5 0.5 31 82-112 2-37 (51)
99 PF04810 zf-Sec23_Sec24: Sec23 29.9 22 0.00047 20.3 0.4 10 15-24 3-12 (40)
100 PF03811 Zn_Tnp_IS1: InsA N-te 29.4 42 0.00092 19.0 1.6 11 11-21 26-36 (36)
101 PF12992 DUF3876: Domain of un 29.3 24 0.00052 24.2 0.6 15 101-115 16-34 (95)
102 PF04606 Ogr_Delta: Ogr/Delta- 29.1 23 0.00051 20.8 0.5 9 81-89 1-9 (47)
103 PF07191 zinc-ribbons_6: zinc- 28.7 31 0.00068 22.6 1.0 14 80-96 2-15 (70)
104 PF12172 DUF35_N: Rubredoxin-l 28.6 42 0.0009 18.4 1.4 23 12-34 9-31 (37)
105 PF02943 FeThRed_B: Ferredoxin 27.7 7.8 0.00017 27.3 -2.1 29 78-109 62-91 (108)
106 cd04476 RPA1_DBD_C RPA1_DBD_C: 27.7 38 0.00083 24.5 1.5 26 80-105 35-61 (166)
107 PRK06393 rpoE DNA-directed RNA 27.6 29 0.00063 22.4 0.7 17 81-97 19-35 (64)
108 COG3877 Uncharacterized protei 26.8 58 0.0012 23.3 2.2 28 81-111 8-36 (122)
109 PF06174 DUF987: Protein of un 26.7 29 0.00063 22.4 0.6 11 90-100 27-37 (66)
110 PRK14715 DNA polymerase II lar 26.1 47 0.001 33.1 2.1 37 77-117 1540-1577(1627)
111 KOG2691 RNA polymerase II subu 25.8 1.6E+02 0.0034 21.0 4.2 26 10-35 22-47 (113)
112 PRK11088 rrmA 23S rRNA methylt 25.7 33 0.00072 26.7 0.9 25 80-105 3-27 (272)
113 PRK00241 nudC NADH pyrophospha 25.6 45 0.00097 26.4 1.6 30 75-105 95-127 (256)
114 PF15135 UPF0515: Uncharacteri 25.5 47 0.001 27.1 1.7 39 75-113 151-192 (278)
115 cd00065 FYVE FYVE domain; Zinc 25.5 41 0.00088 19.8 1.1 24 81-105 4-28 (57)
116 smart00109 C1 Protein kinase C 25.4 30 0.00066 19.2 0.5 25 80-105 12-37 (49)
117 PF09855 DUF2082: Nucleic-acid 25.3 34 0.00074 21.9 0.7 8 81-88 2-9 (64)
118 PRK08329 threonine synthase; V 23.1 53 0.0011 26.8 1.7 28 79-108 1-28 (347)
119 TIGR00319 desulf_FeS4 desulfof 22.8 47 0.001 18.0 0.9 13 12-24 5-17 (34)
120 KOG4487 Uncharacterized conser 22.3 53 0.0011 23.2 1.3 55 61-119 11-83 (110)
121 PHA01769 hypothetical protein 22.1 41 0.00089 23.0 0.7 13 13-25 5-18 (98)
122 KOG1088 Uncharacterized conser 21.9 51 0.0011 23.9 1.2 16 74-89 93-108 (124)
123 PF10272 Tmpp129: Putative tra 21.9 42 0.00091 28.3 0.9 36 54-89 303-350 (358)
124 PRK04136 rpl40e 50S ribosomal 21.8 48 0.001 20.2 0.9 26 75-103 10-36 (48)
125 cd01411 SIR2H SIR2H: Uncharact 21.8 1E+02 0.0023 23.6 3.0 38 77-117 116-158 (225)
126 PF13695 zf-3CxxC: Zinc-bindin 21.8 1.1E+02 0.0024 20.6 2.8 34 77-110 3-53 (98)
127 TIGR01053 LSD1 zinc finger dom 21.6 39 0.00085 18.5 0.4 13 15-27 2-14 (31)
128 PF02318 FYVE_2: FYVE-type zin 21.4 31 0.00067 24.0 -0.0 28 80-107 55-83 (118)
129 PF08600 Rsm1: Rsm1-like; Int 21.1 62 0.0013 21.7 1.4 20 77-96 17-36 (91)
130 PF13005 zf-IS66: zinc-finger 21.0 44 0.00096 19.1 0.6 10 81-90 4-13 (47)
131 PF11571 Med27: Mediator compl 20.5 25 0.00054 23.5 -0.6 18 14-32 54-71 (90)
132 PRK00481 NAD-dependent deacety 20.4 84 0.0018 24.3 2.2 38 77-117 120-164 (242)
133 PF10058 DUF2296: Predicted in 20.2 74 0.0016 19.5 1.5 14 9-22 39-52 (54)
134 cd00029 C1 Protein kinase C co 20.1 41 0.00089 18.9 0.3 26 80-105 12-38 (50)
No 1
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=95.87 E-value=0.0084 Score=40.51 Aligned_cols=21 Identities=29% Similarity=0.960 Sum_probs=19.2
Q ss_pred eEecccccccccCCCCeee-CC
Q 039226 14 IYRCKKCRRLVASEENIVP-HE 34 (121)
Q Consensus 14 ~yrCrKCR~~Lf~~~~ii~-H~ 34 (121)
.|.|++|+..|+.+.+|+. |.
T Consensus 2 vf~C~~C~t~l~ds~~lvs~~g 23 (96)
T PF03226_consen 2 VFQCKNCKTILADSNELVSFHG 23 (96)
T ss_pred EEECCCCCCCcCCHHHheecCC
Confidence 6999999999999999999 53
No 2
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=87.87 E-value=0.22 Score=25.77 Aligned_cols=8 Identities=38% Similarity=1.061 Sum_probs=5.0
Q ss_pred CCCCCCcc
Q 039226 82 CMGCKARL 89 (121)
Q Consensus 82 CPkC~~kL 89 (121)
||+|+++|
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 66666665
No 3
>PF09814 HECT_2: HECT-like Ubiquitin-conjugating enzyme (E2)-binding; InterPro: IPR019193 This entry consists of E3 ubiquitin-protein ligases which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfer it to substrates, generally promoting their degradation by the proteasome [].
Probab=85.83 E-value=1.1 Score=36.24 Aligned_cols=30 Identities=23% Similarity=0.513 Sum_probs=21.6
Q ss_pred ceeEECCCCCCccceeeeecccCCCCCeeeceEEEecCCcc
Q 039226 77 GEKLQCMGCKARLGSFNWAGLQCSCGAWATPAFQLHKSRLD 117 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w~G~qCsCG~wv~Paf~l~kskVD 117 (121)
+..+.|.+|++-||. ..-.-++.|+|..|.
T Consensus 191 ~~~v~C~~C~~~LG~-----------~~~~~~~rL~K~~l~ 220 (354)
T PF09814_consen 191 ERIVRCKRCSSQLGE-----------KFSDNTVRLYKWALS 220 (354)
T ss_pred CcEEEeCCCCceeCC-----------CccCCeEEEEeeeEE
Confidence 468999999999997 222346677766665
No 4
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=85.09 E-value=0.47 Score=30.01 Aligned_cols=19 Identities=37% Similarity=0.716 Sum_probs=15.9
Q ss_pred ccceeEECCCCCCccceee
Q 039226 75 FVGEKLQCMGCKARLGSFN 93 (121)
Q Consensus 75 ~~~GKL~CPkC~~kLG~f~ 93 (121)
-.+..-+||+|++.||.|+
T Consensus 48 ~kd~~H~Cp~C~~~lg~~~ 66 (67)
T smart00714 48 FKDVNHYCPNCGAFLGTYN 66 (67)
T ss_pred ccCccEECCCCCCEeEEec
Confidence 3456789999999999985
No 5
>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=82.29 E-value=0.8 Score=29.38 Aligned_cols=67 Identities=16% Similarity=0.202 Sum_probs=35.8
Q ss_pred CCCeeEecccccccccCCCCeeeCCCCCcchhhhhhccccCCCCCCCCceeEe---cccchhhhhhccccceeEECCCCC
Q 039226 10 NPQAIYRCKKCRRLVASEENIVPHEQGKGEQCFKRKKRSEMENEPAECSSLFV---ESMKWMQSVQEGFVGEKLQCMGCK 86 (121)
Q Consensus 10 ~~~~~yrCrKCR~~Lf~~~~ii~H~~~~~~~~~~~~~~~~~~~~~~~C~~~Fi---ep~~Wm~~~~~~~~~GKL~CPkC~ 86 (121)
+.+....|..|+...-+ .++|.++..... .+-.+|+ =|.-|+--..+.-.+-.-+||+|+
T Consensus 3 ~~p~~~~CP~C~~~~~T---~v~~~~g~~t~~--------------~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~ 65 (73)
T PF10601_consen 3 PEPVRIYCPYCQQQVQT---RVEYKSGTMTYI--------------CAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCG 65 (73)
T ss_pred CCceeeECCCCCCEEEE---EEEEEeChHHHH--------------HHHHHHHHHHHHHhhHhhccccccCceEECCCCC
Confidence 35667889999886632 345555432110 0111111 122222222222334568999999
Q ss_pred Cccceee
Q 039226 87 ARLGSFN 93 (121)
Q Consensus 87 ~kLG~f~ 93 (121)
+.||.|.
T Consensus 66 ~~lg~~~ 72 (73)
T PF10601_consen 66 AFLGTYK 72 (73)
T ss_pred CEeEEEe
Confidence 9999885
No 6
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=81.51 E-value=1.7 Score=31.42 Aligned_cols=66 Identities=23% Similarity=0.461 Sum_probs=37.0
Q ss_pred CCCeeEecccccccccCCCCeeeCCCCCcchhhhhhccccCCCCCCCCceeEecccch--hhhhh---ccccceeEECCC
Q 039226 10 NPQAIYRCKKCRRLVASEENIVPHEQGKGEQCFKRKKRSEMENEPAECSSLFVESMKW--MQSVQ---EGFVGEKLQCMG 84 (121)
Q Consensus 10 ~~~~~yrCrKCR~~Lf~~~~ii~H~~~~~~~~~~~~~~~~~~~~~~~C~~~Fiep~~W--m~~~~---~~~~~GKL~CPk 84 (121)
...-.|.|..|...||.+++=... +.|=.+ |-+|++- +.... -+..---+.|.+
T Consensus 33 ~~~G~Y~C~~Cg~pLF~S~~Kf~S--g~GWPS-------------------F~~~i~~~~v~~~~D~s~g~~R~Ev~C~~ 91 (124)
T PF01641_consen 33 KEEGIYVCAVCGTPLFSSDTKFDS--GCGWPS-------------------FWQPIPGDAVKEREDFSHGMVRTEVRCAR 91 (124)
T ss_dssp TSSEEEEETTTS-EEEEGGGEETS--SSSSSE-------------------ESSCSSTTSEEEEEEECTSSEEEEEEETT
T ss_pred CCCEEEEcCCCCCccccCcccccC--CcCCcc-------------------ccCcCChHHEEEeccccCCceEEEEEecC
Confidence 356799999999999988743321 111111 2222211 11110 122334689999
Q ss_pred CCCccceeeeec
Q 039226 85 CKARLGSFNWAG 96 (121)
Q Consensus 85 C~~kLG~f~w~G 96 (121)
|++.||.-=-.|
T Consensus 92 Cg~HLGHVF~DG 103 (124)
T PF01641_consen 92 CGSHLGHVFDDG 103 (124)
T ss_dssp TCCEEEEEESTS
T ss_pred CCCccccEeCCC
Confidence 999999754455
No 7
>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=81.27 E-value=0.57 Score=29.00 Aligned_cols=17 Identities=29% Similarity=0.751 Sum_probs=14.4
Q ss_pred eEecccccccccCCCCe
Q 039226 14 IYRCKKCRRLVASEENI 30 (121)
Q Consensus 14 ~yrCrKCR~~Lf~~~~i 30 (121)
.+||+.|.+.||...++
T Consensus 4 eiRC~~CnklLa~~g~~ 20 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEV 20 (51)
T ss_pred ceeccchhHHHhhhcCc
Confidence 68999999999996544
No 8
>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=79.44 E-value=1.1 Score=23.83 Aligned_cols=20 Identities=30% Similarity=0.714 Sum_probs=14.4
Q ss_pred ECCCCCCccceeeeecccCC-CCC
Q 039226 81 QCMGCKARLGSFNWAGLQCS-CGA 103 (121)
Q Consensus 81 ~CPkC~~kLG~f~w~G~qCs-CG~ 103 (121)
.||.|++.| .-+-..|+ ||.
T Consensus 2 ~CP~C~~~V---~~~~~~Cp~CG~ 22 (26)
T PF10571_consen 2 TCPECGAEV---PESAKFCPHCGY 22 (26)
T ss_pred cCCCCcCCc---hhhcCcCCCCCC
Confidence 489999888 33345787 886
No 9
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=77.17 E-value=2.2 Score=30.38 Aligned_cols=68 Identities=18% Similarity=0.362 Sum_probs=40.1
Q ss_pred CeeEecccccccccCCCCeeeCCCCCcc----hhhhhhccccCCCCCCCCceeEe-cc--c---chhhhhhccccceeEE
Q 039226 12 QAIYRCKKCRRLVASEENIVPHEQGKGE----QCFKRKKRSEMENEPAECSSLFV-ES--M---KWMQSVQEGFVGEKLQ 81 (121)
Q Consensus 12 ~~~yrCrKCR~~Lf~~~~ii~H~~~~~~----~~~~~~~~~~~~~~~~~C~~~Fi-ep--~---~Wm~~~~~~~~~GKL~ 81 (121)
...+-||||...+.++++|-. ..++.- .+|.. +|+ ++ . .... +-...|+|.
T Consensus 2 ~v~llC~kC~~~~C~~~DIr~-ie~~hhv~v~p~F~~---------------~~~~~~~~~~~~~~~~---d~~~~~~I~ 62 (123)
T PF11648_consen 2 NVKLLCRKCKKFACSGSDIRK-IENSHHVVVDPEFWE---------------RYIVRPHPKPLQKSFG---DWEPNGKIH 62 (123)
T ss_dssp GEEEEETTTTCEEEEGGGEEE-ETTTEEEE-SHHHHC---------------TEEEEECSSCTSEEES---SSEEEEEEE
T ss_pred ceEEECCCCCceeEchhheEE-ecCCcEEEcCcccee---------------eEEeccCCccccceec---ceEeCCEEE
Confidence 457899999999999999843 222110 11211 121 11 0 1111 224689999
Q ss_pred CCCCCCccceeee-eccc
Q 039226 82 CMGCKARLGSFNW-AGLQ 98 (121)
Q Consensus 82 CPkC~~kLG~f~w-~G~q 98 (121)
|-+|+..+|..-= .|..
T Consensus 63 C~~C~~~wG~~m~yk~~~ 80 (123)
T PF11648_consen 63 CKNCGQDWGIMMKYKGVE 80 (123)
T ss_dssp ETSTSBEEEEEEEETTEE
T ss_pred cCCCChHhhhheEECCcc
Confidence 9999999997533 4544
No 10
>PF12773 DZR: Double zinc ribbon
Probab=75.52 E-value=1 Score=26.54 Aligned_cols=32 Identities=25% Similarity=0.472 Sum_probs=20.3
Q ss_pred ceeEECCCCCCccceeeeecccCC-CCCeeece
Q 039226 77 GEKLQCMGCKARLGSFNWAGLQCS-CGAWATPA 108 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w~G~qCs-CG~wv~Pa 108 (121)
.+-..||.|+++|....=....|+ ||+-+.+.
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGAENPPN 42 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcCCCcCC
Confidence 445778888888873332335684 88876553
No 11
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=74.69 E-value=2.2 Score=24.49 Aligned_cols=23 Identities=26% Similarity=0.807 Sum_probs=17.0
Q ss_pred ECCCCCCccceeeeecc---cCC-CCC
Q 039226 81 QCMGCKARLGSFNWAGL---QCS-CGA 103 (121)
Q Consensus 81 ~CPkC~~kLG~f~w~G~---qCs-CG~ 103 (121)
+||+|+..|-.....+. .|+ ||-
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGG 27 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCe
Confidence 49999999988888663 463 653
No 12
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=74.20 E-value=2.2 Score=25.37 Aligned_cols=21 Identities=19% Similarity=0.466 Sum_probs=18.3
Q ss_pred cceeEECCCCCCccceeeeec
Q 039226 76 VGEKLQCMGCKARLGSFNWAG 96 (121)
Q Consensus 76 ~~GKL~CPkC~~kLG~f~w~G 96 (121)
+.|+|.|+.|+.++-...+.|
T Consensus 2 l~g~l~C~~CG~~m~~~~~~~ 22 (58)
T PF13408_consen 2 LSGLLRCGHCGSKMTRRKRKG 22 (58)
T ss_pred CCCcEEcccCCcEeEEEECCC
Confidence 478999999999999888864
No 13
>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=74.04 E-value=1.7 Score=30.56 Aligned_cols=33 Identities=30% Similarity=0.669 Sum_probs=23.2
Q ss_pred cceeEECCCCCCccceeeeecccCC-CCCeeece
Q 039226 76 VGEKLQCMGCKARLGSFNWAGLQCS-CGAWATPA 108 (121)
Q Consensus 76 ~~GKL~CPkC~~kLG~f~w~G~qCs-CG~wv~Pa 108 (121)
+--|-.||+|++|.=-.|=.=..|+ ||+-+.|.
T Consensus 6 lGtKR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCcccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 3457889999999733333335797 99988776
No 14
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=73.16 E-value=5.8 Score=29.33 Aligned_cols=21 Identities=24% Similarity=0.499 Sum_probs=17.3
Q ss_pred CCCeeEecccccccccCCCCe
Q 039226 10 NPQAIYRCKKCRRLVASEENI 30 (121)
Q Consensus 10 ~~~~~yrCrKCR~~Lf~~~~i 30 (121)
...-.|.|+.|...||.+.+=
T Consensus 39 ~~~G~Y~C~~Cg~pLF~S~~K 59 (142)
T PRK00222 39 KEKGIYVCIVCGEPLFSSDTK 59 (142)
T ss_pred CCCeEEEecCCCchhcCCccc
Confidence 355699999999999998643
No 15
>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=72.25 E-value=2.1 Score=31.26 Aligned_cols=35 Identities=17% Similarity=0.212 Sum_probs=24.8
Q ss_pred cceeEECCCCCCccceeeeecccCC-CCCeeeceEE
Q 039226 76 VGEKLQCMGCKARLGSFNWAGLQCS-CGAWATPAFQ 110 (121)
Q Consensus 76 ~~GKL~CPkC~~kLG~f~w~G~qCs-CG~wv~Paf~ 110 (121)
+-.|-.||+|++|.=-.|=.=..|+ ||+-+.|+..
T Consensus 6 lGtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 6 LGTKRICPNTGSKFYDLNRRPAVSPYTGEQFPPEEA 41 (129)
T ss_pred hCccccCCCcCccccccCCCCccCCCcCCccCcchh
Confidence 3457889999999733333346796 9998877733
No 16
>KOG3399 consensus Predicted Yippee-type zinc-binding protein [General function prediction only]
Probab=69.03 E-value=2.2 Score=30.81 Aligned_cols=24 Identities=17% Similarity=0.675 Sum_probs=21.3
Q ss_pred CeeEecccccccccCCCCeeeCCC
Q 039226 12 QAIYRCKKCRRLVASEENIVPHEQ 35 (121)
Q Consensus 12 ~~~yrCrKCR~~Lf~~~~ii~H~~ 35 (121)
...|+|+.|+.-|+..++|+.+.-
T Consensus 13 ~~~y~C~~C~thla~~~dliSksf 36 (122)
T KOG3399|consen 13 HRLYSCAHCKTHLARHDDLISKSF 36 (122)
T ss_pred CceEeccCCcccccchhhcccccc
Confidence 458999999999999999998854
No 17
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=68.74 E-value=1.7 Score=22.71 Aligned_cols=13 Identities=31% Similarity=0.641 Sum_probs=9.6
Q ss_pred ceeEECCCCCCcc
Q 039226 77 GEKLQCMGCKARL 89 (121)
Q Consensus 77 ~GKL~CPkC~~kL 89 (121)
.+--.||+|+++|
T Consensus 14 ~~~~fC~~CG~~L 26 (26)
T PF13248_consen 14 PDAKFCPNCGAKL 26 (26)
T ss_pred cccccChhhCCCC
Confidence 4456799998876
No 18
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=68.43 E-value=3.4 Score=23.33 Aligned_cols=25 Identities=32% Similarity=0.794 Sum_probs=16.2
Q ss_pred eEECCCCCCccceeee----ec--ccCC-CCC
Q 039226 79 KLQCMGCKARLGSFNW----AG--LQCS-CGA 103 (121)
Q Consensus 79 KL~CPkC~~kLG~f~w----~G--~qCs-CG~ 103 (121)
+|.||+|+++---=+. .| .+|+ ||.
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 5899999987532222 23 4786 776
No 19
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=67.73 E-value=4.4 Score=24.63 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=23.5
Q ss_pred CCCCceeEec-ccchhhhhhccccceeEECCCCCCc
Q 039226 54 PAECSSLFVE-SMKWMQSVQEGFVGEKLQCMGCKAR 88 (121)
Q Consensus 54 ~~~C~~~Fie-p~~Wm~~~~~~~~~GKL~CPkC~~k 88 (121)
...|+.-|++ |++.+..+..+ ++-+.||.|+.-
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~--~~i~~Cp~CgRi 55 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKG--DEIVFCPNCGRI 55 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcC--CCeEECcCCCcc
Confidence 4579877776 66777765333 678999999864
No 20
>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=67.49 E-value=1.9 Score=32.55 Aligned_cols=29 Identities=41% Similarity=0.922 Sum_probs=11.2
Q ss_pred eEECCCCCCcc---ceee-------eecccCC-CCCeeec
Q 039226 79 KLQCMGCKARL---GSFN-------WAGLQCS-CGAWATP 107 (121)
Q Consensus 79 KL~CPkC~~kL---G~f~-------w~G~qCs-CG~wv~P 107 (121)
++.||+|+... |.|. ++|..|+ |++.+.|
T Consensus 18 ~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~~~ 57 (188)
T PF08996_consen 18 KLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPLSP 57 (188)
T ss_dssp EEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B--H
T ss_pred EeECCCCCCCccccccccCCccccccCcCcCCCCCCcCCH
Confidence 56666666543 2222 4566665 6665444
No 21
>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=64.07 E-value=2.8 Score=22.52 Aligned_cols=10 Identities=30% Similarity=0.690 Sum_probs=5.6
Q ss_pred ECCCCCCccc
Q 039226 81 QCMGCKARLG 90 (121)
Q Consensus 81 ~CPkC~~kLG 90 (121)
+||.|+++|=
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4999999984
No 22
>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=63.95 E-value=4.7 Score=22.39 Aligned_cols=13 Identities=31% Similarity=0.670 Sum_probs=10.8
Q ss_pred ceeEECCCCCCcc
Q 039226 77 GEKLQCMGCKARL 89 (121)
Q Consensus 77 ~GKL~CPkC~~kL 89 (121)
.+++.||+|+..+
T Consensus 23 ~~~v~C~~C~~~~ 35 (38)
T TIGR02098 23 GGKVRCGKCGHVW 35 (38)
T ss_pred CCEEECCCCCCEE
Confidence 4589999999875
No 23
>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=61.04 E-value=5.5 Score=24.83 Aligned_cols=25 Identities=24% Similarity=0.440 Sum_probs=15.9
Q ss_pred ECCCCCCccce-eeeecccCC-CCCee
Q 039226 81 QCMGCKARLGS-FNWAGLQCS-CGAWA 105 (121)
Q Consensus 81 ~CPkC~~kLG~-f~w~G~qCs-CG~wv 105 (121)
.||.|+.++.. -+.....|+ ||...
T Consensus 30 ~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 30 TCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCcccccccccccceEEcCCCCCEE
Confidence 47888877776 333445676 77643
No 24
>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=60.94 E-value=4.1 Score=22.11 Aligned_cols=9 Identities=33% Similarity=0.556 Sum_probs=3.7
Q ss_pred ECCCCCCcc
Q 039226 81 QCMGCKARL 89 (121)
Q Consensus 81 ~CPkC~~kL 89 (121)
.||+|++.+
T Consensus 5 fC~~CG~~t 13 (32)
T PF09297_consen 5 FCGRCGAPT 13 (32)
T ss_dssp B-TTT--BE
T ss_pred ccCcCCccc
Confidence 466666666
No 25
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=59.72 E-value=14 Score=32.52 Aligned_cols=20 Identities=15% Similarity=0.021 Sum_probs=17.0
Q ss_pred CCCeeEecccccccccCCCC
Q 039226 10 NPQAIYRCKKCRRLVASEEN 29 (121)
Q Consensus 10 ~~~~~yrCrKCR~~Lf~~~~ 29 (121)
...-.|.|+.|...||.+.+
T Consensus 414 ~~~G~y~c~~c~~pLf~s~~ 433 (521)
T PRK14018 414 FKPGIYVDVVSGEPLFSSAD 433 (521)
T ss_pred CCCEEEEecCCCCccccCcc
Confidence 35679999999999999864
No 26
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=59.23 E-value=4.9 Score=25.40 Aligned_cols=14 Identities=29% Similarity=0.558 Sum_probs=11.7
Q ss_pred cccceeEECCCCCC
Q 039226 74 GFVGEKLQCMGCKA 87 (121)
Q Consensus 74 ~~~~GKL~CPkC~~ 87 (121)
...+|.|.||+|+-
T Consensus 48 ~i~eg~L~Cp~c~r 61 (68)
T PF03966_consen 48 EIVEGELICPECGR 61 (68)
T ss_dssp ETTTTEEEETTTTE
T ss_pred cccCCEEEcCCCCC
Confidence 45799999999974
No 27
>PRK11823 DNA repair protein RadA; Provisional
Probab=58.97 E-value=5.7 Score=33.88 Aligned_cols=24 Identities=42% Similarity=1.186 Sum_probs=18.4
Q ss_pred eEECCCCCCccceeeeecccCC-CCCee
Q 039226 79 KLQCMGCKARLGSFNWAGLQCS-CGAWA 105 (121)
Q Consensus 79 KL~CPkC~~kLG~f~w~G~qCs-CG~wv 105 (121)
.-.|..|+..-. .|.| +|+ ||+|=
T Consensus 7 ~y~C~~Cg~~~~--~~~g-~Cp~C~~w~ 31 (446)
T PRK11823 7 AYVCQECGAESP--KWLG-RCPECGAWN 31 (446)
T ss_pred eEECCcCCCCCc--ccCe-eCcCCCCcc
Confidence 467999999876 5555 785 99986
No 28
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=58.89 E-value=9.1 Score=26.81 Aligned_cols=30 Identities=13% Similarity=0.238 Sum_probs=19.4
Q ss_pred ccceeEECCCCCCccceeeeecccCC-CCCe
Q 039226 75 FVGEKLQCMGCKARLGSFNWAGLQCS-CGAW 104 (121)
Q Consensus 75 ~~~GKL~CPkC~~kLG~f~w~G~qCs-CG~w 104 (121)
...+++.|+.|+...-.-.+.-..|+ ||..
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 66 EQEAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eeCcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 46788999999964432233325697 9853
No 29
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=58.60 E-value=6.6 Score=22.15 Aligned_cols=11 Identities=27% Similarity=0.923 Sum_probs=8.8
Q ss_pred eEECCCCCCcc
Q 039226 79 KLQCMGCKARL 89 (121)
Q Consensus 79 KL~CPkC~~kL 89 (121)
+|.||+|+++.
T Consensus 2 ~i~CP~C~~~f 12 (37)
T PF13719_consen 2 IITCPNCQTRF 12 (37)
T ss_pred EEECCCCCceE
Confidence 58899999854
No 30
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.36 E-value=5.4 Score=28.89 Aligned_cols=17 Identities=18% Similarity=0.409 Sum_probs=13.6
Q ss_pred cceeEECCCCCCcccee
Q 039226 76 VGEKLQCMGCKARLGSF 92 (121)
Q Consensus 76 ~~GKL~CPkC~~kLG~f 92 (121)
.+|++.||.|++.|=.+
T Consensus 120 ~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 120 MDGTFTCPRCGEELEED 136 (147)
T ss_pred CCCcEECCCCCCEEEEc
Confidence 37889999999988544
No 31
>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=57.51 E-value=5.4 Score=22.19 Aligned_cols=24 Identities=25% Similarity=0.560 Sum_probs=10.0
Q ss_pred CCCCCCccceeeeecccCC-CCCee
Q 039226 82 CMGCKARLGSFNWAGLQCS-CGAWA 105 (121)
Q Consensus 82 CPkC~~kLG~f~w~G~qCs-CG~wv 105 (121)
|..|++.+.--.-...+|. ||..|
T Consensus 3 C~~Cg~~~~~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 3 CGECGAEVELKPGDPIRCPECGHRI 27 (32)
T ss_dssp ESSSSSSE-BSTSSTSSBSSSS-SE
T ss_pred CCcCCCeeEcCCCCcEECCcCCCeE
Confidence 5555555541111234554 66554
No 32
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=56.54 E-value=6.4 Score=23.30 Aligned_cols=13 Identities=23% Similarity=0.716 Sum_probs=10.5
Q ss_pred ceeEECCCCCCcc
Q 039226 77 GEKLQCMGCKARL 89 (121)
Q Consensus 77 ~GKL~CPkC~~kL 89 (121)
.+.+.||.|+.||
T Consensus 17 ~~~irC~~CG~rI 29 (44)
T smart00659 17 KDVVRCRECGYRI 29 (44)
T ss_pred CCceECCCCCceE
Confidence 3568999999987
No 33
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.43 E-value=3.7 Score=26.25 Aligned_cols=12 Identities=67% Similarity=1.448 Sum_probs=8.7
Q ss_pred CeeEeccccccc
Q 039226 12 QAIYRCKKCRRL 23 (121)
Q Consensus 12 ~~~yrCrKCR~~ 23 (121)
...|||.+||+.
T Consensus 36 ~~I~Rc~~CRk~ 47 (61)
T COG2888 36 VEIYRCAKCRKL 47 (61)
T ss_pred eeeehhhhHHHc
Confidence 357888888874
No 34
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=55.25 E-value=5.3 Score=25.76 Aligned_cols=19 Identities=26% Similarity=0.441 Sum_probs=16.0
Q ss_pred eEECCCCCCccceeeeecc
Q 039226 79 KLQCMGCKARLGSFNWAGL 97 (121)
Q Consensus 79 KL~CPkC~~kLG~f~w~G~ 97 (121)
.-.||.|++.==+.+|.|+
T Consensus 18 ~e~CP~Cgs~~~te~W~G~ 36 (64)
T COG2093 18 TEICPVCGSTDLTEEWFGL 36 (64)
T ss_pred CccCCCCCCcccchhhccE
Confidence 3469999999779999995
No 35
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=55.23 E-value=12 Score=26.16 Aligned_cols=28 Identities=18% Similarity=0.507 Sum_probs=17.9
Q ss_pred ccceeEECCCCCCccceeeeecccCC-CCC
Q 039226 75 FVGEKLQCMGCKARLGSFNWAGLQCS-CGA 103 (121)
Q Consensus 75 ~~~GKL~CPkC~~kLG~f~w~G~qCs-CG~ 103 (121)
...+++.|+.|+.....-. ....|+ ||.
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~-~~~~CP~Cgs 94 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQ-HDAQCPHCHG 94 (113)
T ss_pred eeCcEEEcccCCCEEecCC-cCccCcCCCC
Confidence 4678999999995332211 224597 995
No 36
>PRK00420 hypothetical protein; Validated
Probab=54.43 E-value=7.9 Score=27.48 Aligned_cols=25 Identities=24% Similarity=0.392 Sum_probs=13.1
Q ss_pred EECCCCCCccceeeeec-ccCC-CCCee
Q 039226 80 LQCMGCKARLGSFNWAG-LQCS-CGAWA 105 (121)
Q Consensus 80 L~CPkC~~kLG~f~w~G-~qCs-CG~wv 105 (121)
-+||.|++.|=.+ -.| ..|+ ||..+
T Consensus 24 ~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLFEL-KDGEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCcceec-CCCceECCCCCCee
Confidence 4577777666322 234 4564 66633
No 37
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=53.50 E-value=7.8 Score=22.58 Aligned_cols=12 Identities=25% Similarity=0.517 Sum_probs=10.2
Q ss_pred eEECCCCCCccc
Q 039226 79 KLQCMGCKARLG 90 (121)
Q Consensus 79 KL~CPkC~~kLG 90 (121)
.+.||.|++++=
T Consensus 21 ~~~Cp~CG~~~~ 32 (46)
T PRK00398 21 GVRCPYCGYRIL 32 (46)
T ss_pred ceECCCCCCeEE
Confidence 689999998873
No 38
>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=51.77 E-value=1.8 Score=21.23 Aligned_cols=19 Identities=32% Similarity=0.793 Sum_probs=14.0
Q ss_pred EecccccccccCCCCeeeC
Q 039226 15 YRCKKCRRLVASEENIVPH 33 (121)
Q Consensus 15 yrCrKCR~~Lf~~~~ii~H 33 (121)
|.|..|.+...+..++..|
T Consensus 1 y~C~~C~~~f~~~~~l~~H 19 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRH 19 (23)
T ss_dssp EEETTTTEEESSHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHH
Confidence 7889998877666666555
No 39
>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=51.44 E-value=7 Score=25.53 Aligned_cols=20 Identities=30% Similarity=0.732 Sum_probs=12.4
Q ss_pred eeEecccccccccCCCCeeeC
Q 039226 13 AIYRCKKCRRLVASEENIVPH 33 (121)
Q Consensus 13 ~~yrCrKCR~~Lf~~~~ii~H 33 (121)
..||| +|+|.|...+..-.|
T Consensus 2 lifrC-~Cgr~lya~e~~kTk 21 (68)
T PF09082_consen 2 LIFRC-DCGRYLYAKEGAKTK 21 (68)
T ss_dssp EEEEE-TTS--EEEETT-SEE
T ss_pred EEEEe-cCCCEEEecCCccee
Confidence 47999 799999877655433
No 40
>COG5629 Predicted metal-binding protein [Function unknown]
Probab=50.81 E-value=7.7 Score=31.91 Aligned_cols=37 Identities=30% Similarity=0.322 Sum_probs=23.6
Q ss_pred cceeEECCCCCCccceee---------ee-cccCCCCCeeeceEEEe
Q 039226 76 VGEKLQCMGCKARLGSFN---------WA-GLQCSCGAWATPAFQLH 112 (121)
Q Consensus 76 ~~GKL~CPkC~~kLG~f~---------w~-G~qCsCG~wv~Paf~l~ 112 (121)
-+-||+|-+|+|+||--| |. ..-|+=.+.+-|.+-|.
T Consensus 166 pNfklhCsfCnA~lGlpn~~s~~kl~r~~k~~I~~g~tKihP~~dia 212 (321)
T COG5629 166 PNFKLHCSFCNARLGLPNDSSIRKLFRYNKEVIPNGCTKIHPHEDLA 212 (321)
T ss_pred CCcceeeehhhhhhCCCCchhhhhhhhcchheecCCCcccCchHHHH
Confidence 367999999999998644 43 23455334556655443
No 41
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=49.87 E-value=6.1 Score=25.13 Aligned_cols=11 Identities=64% Similarity=1.479 Sum_probs=8.5
Q ss_pred eeEeccccccc
Q 039226 13 AIYRCKKCRRL 23 (121)
Q Consensus 13 ~~yrCrKCR~~ 23 (121)
..+||.|||+.
T Consensus 35 ~I~RC~~CRk~ 45 (59)
T PRK14890 35 IIYRCEKCRKQ 45 (59)
T ss_pred eEeechhHHhc
Confidence 47888888874
No 42
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=49.04 E-value=12 Score=32.45 Aligned_cols=25 Identities=36% Similarity=1.042 Sum_probs=19.5
Q ss_pred eeEECCCCCCccceeeeecccCC-CCCee
Q 039226 78 EKLQCMGCKARLGSFNWAGLQCS-CGAWA 105 (121)
Q Consensus 78 GKL~CPkC~~kLG~f~w~G~qCs-CG~wv 105 (121)
-...|-.|+..- =.|.| ||+ ||+|-
T Consensus 6 t~f~C~~CG~~s--~KW~G-kCp~Cg~Wn 31 (456)
T COG1066 6 TAFVCQECGYVS--PKWLG-KCPACGAWN 31 (456)
T ss_pred cEEEcccCCCCC--ccccc-cCCCCCCcc
Confidence 357898998874 47888 896 99985
No 43
>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=49.04 E-value=9.8 Score=32.60 Aligned_cols=24 Identities=42% Similarity=1.149 Sum_probs=18.3
Q ss_pred eEECCCCCCccceeeeecccCC-CCCee
Q 039226 79 KLQCMGCKARLGSFNWAGLQCS-CGAWA 105 (121)
Q Consensus 79 KL~CPkC~~kLG~f~w~G~qCs-CG~wv 105 (121)
.-.|..|+..-- .|.| ||+ ||+|=
T Consensus 7 ~y~C~~Cg~~~~--~~~g-~Cp~C~~w~ 31 (454)
T TIGR00416 7 KFVCQHCGADSP--KWQG-KCPACHAWN 31 (454)
T ss_pred eEECCcCCCCCc--cccE-ECcCCCCcc
Confidence 467999998865 5565 785 99985
No 44
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=48.51 E-value=9.1 Score=27.24 Aligned_cols=31 Identities=26% Similarity=0.625 Sum_probs=21.1
Q ss_pred ECCCCCCccceeeeecccCC-CCCeeeceEEEecC
Q 039226 81 QCMGCKARLGSFNWAGLQCS-CGAWATPAFQLHKS 114 (121)
Q Consensus 81 ~CPkC~~kLG~f~w~G~qCs-CG~wv~Paf~l~ks 114 (121)
.||.|++|+=+. =..|+ ||-.+.=+-+|.||
T Consensus 3 ~CPrC~skvC~L---P~~CpiCgLtLVss~HLARS 34 (112)
T TIGR00622 3 FCPQCRAKVCEL---PVECPICGLTLILSTHLARS 34 (112)
T ss_pred cCCCCCCCccCC---CCcCCcCCCEEeccchHHHh
Confidence 599999998321 25775 88887655555554
No 45
>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=46.30 E-value=16 Score=25.60 Aligned_cols=29 Identities=14% Similarity=0.324 Sum_probs=18.5
Q ss_pred ccceeEECCCCCCccceeeeecccCC-CCCe
Q 039226 75 FVGEKLQCMGCKARLGSFNWAGLQCS-CGAW 104 (121)
Q Consensus 75 ~~~GKL~CPkC~~kLG~f~w~G~qCs-CG~w 104 (121)
...+++.|+.|+.... .......|+ ||..
T Consensus 66 ~~p~~~~C~~Cg~~~~-~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVS-PEIDLYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEe-cCCcCccCcCCcCC
Confidence 3578899999994432 222245795 8863
No 46
>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=46.21 E-value=12 Score=21.31 Aligned_cols=21 Identities=19% Similarity=0.325 Sum_probs=15.9
Q ss_pred ccccCCCCCCeeEeccccccc
Q 039226 3 QVHKHVANPQAIYRCKKCRRL 23 (121)
Q Consensus 3 ~~~~~~~~~~~~yrCrKCR~~ 23 (121)
|+-+.++.....|+|.+|+..
T Consensus 17 Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 17 QTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp SSSSSSSSSEEEEEESSSTEE
T ss_pred eccCCCCCCeEEEEeCCCCCe
Confidence 556666667789999999753
No 47
>KOG4784 consensus Uncharacterized conserved protein [Function unknown]
Probab=46.07 E-value=12 Score=31.41 Aligned_cols=85 Identities=15% Similarity=0.349 Sum_probs=46.2
Q ss_pred CCCCeeEecccccccccCCCCeeeC--CCCCc----chhh-------hhhccccCCCCCCCC---ceeEe---cccchhh
Q 039226 9 ANPQAIYRCKKCRRLVASEENIVPH--EQGKG----EQCF-------KRKKRSEMENEPAEC---SSLFV---ESMKWMQ 69 (121)
Q Consensus 9 ~~~~~~yrCrKCR~~Lf~~~~ii~H--~~~~~----~~~~-------~~~~~~~~~~~~~~C---~~~Fi---ep~~Wm~ 69 (121)
++.+..++|.+|+..|-...++..= -|.++ ...+ +.+....-.-..+++ .+||+ +..+|..
T Consensus 98 ~~~~~s~~C~~C~e~ii~~r~~~~l~~lPSe~W~el~d~w~CH~~~p~~~s~~tl~PsE~~l~lG~sY~lin~~t~e~~~ 177 (348)
T KOG4784|consen 98 EDEPCSFHCLNCKEEIIGQRSYRSLNELPSENWTELPDCWSCHNDEPKNKSSLTLYPSENELYLGDSYLLINLATGEGVK 177 (348)
T ss_pred cCCCceeEeccCcceEeccchhhhhhhcChhhhhhcCceecccCCccccccccccccCcCceEeeccEEEEEccccccee
Confidence 4557899999999988755544311 11110 0000 000000000012223 35675 2356766
Q ss_pred hhhccccceeEECCCCCCccceeeeec
Q 039226 70 SVQEGFVGEKLQCMGCKARLGSFNWAG 96 (121)
Q Consensus 70 ~~~~~~~~GKL~CPkC~~kLG~f~w~G 96 (121)
.. ....++.|-+|.+-||.+...+
T Consensus 178 ~~---~~~d~~~C~rC~~~lg~~~~~~ 201 (348)
T KOG4784|consen 178 TI---AGNDRVLCSRCKRCLGLFITKD 201 (348)
T ss_pred cc---CCCCchhhhhhHhhcCcccccc
Confidence 53 2467899999999999997643
No 48
>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=45.62 E-value=17 Score=26.73 Aligned_cols=27 Identities=22% Similarity=0.577 Sum_probs=20.7
Q ss_pred cceeEECCCCCCccceeeeec--ccCC-CCC
Q 039226 76 VGEKLQCMGCKARLGSFNWAG--LQCS-CGA 103 (121)
Q Consensus 76 ~~GKL~CPkC~~kLG~f~w~G--~qCs-CG~ 103 (121)
..|.+.|-+|+.++ .|+-.+ ..|+ ||.
T Consensus 109 g~G~l~C~~Cg~~~-~~~~~~~l~~Cp~C~~ 138 (146)
T PF07295_consen 109 GPGTLVCENCGHEV-ELTHPERLPPCPKCGH 138 (146)
T ss_pred cCceEecccCCCEE-EecCCCcCCCCCCCCC
Confidence 37899999999999 555566 4786 775
No 49
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=44.90 E-value=11 Score=24.09 Aligned_cols=17 Identities=35% Similarity=0.583 Sum_probs=15.0
Q ss_pred ECCCCCCccceeeeecc
Q 039226 81 QCMGCKARLGSFNWAGL 97 (121)
Q Consensus 81 ~CPkC~~kLG~f~w~G~ 97 (121)
.||.|++..=+-+|.|.
T Consensus 17 ~CP~Cgs~~~T~~W~G~ 33 (61)
T PRK08351 17 RCPVCGSRDLSDEWFDL 33 (61)
T ss_pred cCCCCcCCccccccccE
Confidence 49999999889999984
No 50
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=44.70 E-value=14 Score=24.95 Aligned_cols=31 Identities=26% Similarity=0.509 Sum_probs=19.4
Q ss_pred ceeEECCCCCCccceeee--------ecccCC-CCCeeec
Q 039226 77 GEKLQCMGCKARLGSFNW--------AGLQCS-CGAWATP 107 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w--------~G~qCs-CG~wv~P 107 (121)
.++=.||.|+.+|.-++. ..-+|. |++-+.+
T Consensus 31 ~~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 31 FPRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CCCCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCCh
Confidence 445678888888876654 223774 6666543
No 51
>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=44.21 E-value=14 Score=20.87 Aligned_cols=23 Identities=35% Similarity=0.703 Sum_probs=15.6
Q ss_pred EECCCCCCccceeee-ec-ccC-CCCCe
Q 039226 80 LQCMGCKARLGSFNW-AG-LQC-SCGAW 104 (121)
Q Consensus 80 L~CPkC~~kLG~f~w-~G-~qC-sCG~w 104 (121)
+.|+.|+++ .|.. .| .-| +||+-
T Consensus 9 ~~C~~C~~~--~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSR--WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCe--EeEccCCEEEhhhCceE
Confidence 568888888 3444 46 468 88864
No 52
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=43.98 E-value=5.8 Score=25.03 Aligned_cols=15 Identities=47% Similarity=0.981 Sum_probs=12.9
Q ss_pred eEecccccccccCCC
Q 039226 14 IYRCKKCRRLVASEE 28 (121)
Q Consensus 14 ~yrCrKCR~~Lf~~~ 28 (121)
.+||++|.++|+..+
T Consensus 4 tiRC~~CnKlLa~a~ 18 (60)
T COG4416 4 TIRCAKCNKLLAEAE 18 (60)
T ss_pred eeehHHHhHHHHhcc
Confidence 589999999998665
No 53
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=43.97 E-value=13 Score=27.16 Aligned_cols=13 Identities=23% Similarity=0.429 Sum_probs=10.9
Q ss_pred cceeEECCCCCCc
Q 039226 76 VGEKLQCMGCKAR 88 (121)
Q Consensus 76 ~~GKL~CPkC~~k 88 (121)
-.|+++||.|+.+
T Consensus 41 KdG~v~CPvC~~~ 53 (131)
T COG1645 41 KDGEVFCPVCGYR 53 (131)
T ss_pred eCCeEECCCCCce
Confidence 5889999999854
No 54
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=43.82 E-value=18 Score=35.29 Aligned_cols=27 Identities=22% Similarity=0.724 Sum_probs=17.7
Q ss_pred eeEECCCCCCccceeeeecccCC-CCCeeeceE
Q 039226 78 EKLQCMGCKARLGSFNWAGLQCS-CGAWATPAF 109 (121)
Q Consensus 78 GKL~CPkC~~kLG~f~w~G~qCs-CG~wv~Paf 109 (121)
|...||+|++-.-. ..|+ ||+...|.+
T Consensus 666 ~~rkCPkCG~~t~~-----~fCP~CGs~te~vy 693 (1337)
T PRK14714 666 GRRRCPSCGTETYE-----NRCPDCGTHTEPVY 693 (1337)
T ss_pred EEEECCCCCCcccc-----ccCcccCCcCCCce
Confidence 56889999986521 2776 777665433
No 55
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.76 E-value=15 Score=24.89 Aligned_cols=35 Identities=31% Similarity=0.488 Sum_probs=21.8
Q ss_pred EECCCCCCccceeeeec---ccCC-CCCeeeceEEEecCCcccc
Q 039226 80 LQCMGCKARLGSFNWAG---LQCS-CGAWATPAFQLHKSRLDKC 119 (121)
Q Consensus 80 L~CPkC~~kLG~f~w~G---~qCs-CG~wv~Paf~l~kskVD~~ 119 (121)
+.||.|+.-|=.-.=+| -+|+ |+ +++|.+.-.|++
T Consensus 2 llCP~C~v~l~~~~rs~vEiD~CPrCr-----GVWLDrGELdKl 40 (88)
T COG3809 2 LLCPICGVELVMSVRSGVEIDYCPRCR-----GVWLDRGELDKL 40 (88)
T ss_pred cccCcCCceeeeeeecCceeeeCCccc-----cEeecchhHHHH
Confidence 56888888886655566 2565 54 455566555543
No 56
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=41.90 E-value=21 Score=25.69 Aligned_cols=21 Identities=24% Similarity=0.488 Sum_probs=17.6
Q ss_pred CCCeeEecccccccccCCCCe
Q 039226 10 NPQAIYRCKKCRRLVASEENI 30 (121)
Q Consensus 10 ~~~~~yrCrKCR~~Lf~~~~i 30 (121)
...-.|.|+-|...||.+++=
T Consensus 29 ~~~G~Y~C~~Cg~pLF~S~~K 49 (119)
T PRK05508 29 FEKGTYVCKQCGAPLYRSEDK 49 (119)
T ss_pred CCCeEEEecCCCCcccccccc
Confidence 355699999999999998754
No 57
>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=41.48 E-value=18 Score=19.97 Aligned_cols=13 Identities=31% Similarity=0.738 Sum_probs=8.7
Q ss_pred CeeEecccccccc
Q 039226 12 QAIYRCKKCRRLV 24 (121)
Q Consensus 12 ~~~yrCrKCR~~L 24 (121)
.+.|+|.+|+...
T Consensus 3 ~Y~y~C~~Cg~~f 15 (41)
T smart00834 3 IYEYRCEDCGHTF 15 (41)
T ss_pred CEEEEcCCCCCEE
Confidence 4577888877643
No 58
>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=41.24 E-value=19 Score=34.35 Aligned_cols=37 Identities=22% Similarity=0.589 Sum_probs=28.1
Q ss_pred ceeEECCCCCCccceeeeecccCC-CCCeeeceEEEecCCc
Q 039226 77 GEKLQCMGCKARLGSFNWAGLQCS-CGAWATPAFQLHKSRL 116 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w~G~qCs-CG~wv~Paf~l~kskV 116 (121)
.-+.-|.||++|-=.-=.+| +|. ||..|.+.+ ++.-|
T Consensus 1010 rQ~fRC~kC~~kYRR~PL~G-~C~kCGg~lilTV--~~GsV 1047 (1095)
T TIGR00354 1010 RQEVRCTKCNTKYRRIPLVG-KCLKCGNNLTLTV--SKGSV 1047 (1095)
T ss_pred ccceeecccCCccccCCCCC-cccccCCeEEEEE--ecchh
Confidence 44789999999987666677 896 999996655 44444
No 59
>PRK06835 DNA replication protein DnaC; Validated
Probab=40.91 E-value=14 Score=30.31 Aligned_cols=25 Identities=36% Similarity=0.743 Sum_probs=19.4
Q ss_pred cceeEECCCCCCccceeeeecccCCCCC
Q 039226 76 VGEKLQCMGCKARLGSFNWAGLQCSCGA 103 (121)
Q Consensus 76 ~~GKL~CPkC~~kLG~f~w~G~qCsCG~ 103 (121)
++-.-.||+|+.. |-+ .|.+|+|=.
T Consensus 95 l~~~y~Cp~C~dt-G~i--~~~~C~C~~ 119 (329)
T PRK06835 95 LEMKYTCPKCKDT-GFI--NGKKCSCYK 119 (329)
T ss_pred cCCCCCCCCCCCC-CCc--CCccccchh
Confidence 3556689999998 766 467999975
No 60
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=40.84 E-value=16 Score=23.23 Aligned_cols=30 Identities=33% Similarity=0.833 Sum_probs=13.9
Q ss_pred ceeEECCCCCCccc-eeeeecccCC-CCCeee
Q 039226 77 GEKLQCMGCKARLG-SFNWAGLQCS-CGAWAT 106 (121)
Q Consensus 77 ~GKL~CPkC~~kLG-~f~w~G~qCs-CG~wv~ 106 (121)
...|.|-.|++|-= .|.|-|.||+ ||.+-|
T Consensus 28 ~v~IlCNDC~~~s~v~fH~lg~KC~~C~SYNT 59 (61)
T PF14599_consen 28 KVWILCNDCNAKSEVPFHFLGHKCSHCGSYNT 59 (61)
T ss_dssp EEEEEESSS--EEEEE--TT----TTTS---E
T ss_pred EEEEECCCCCCccceeeeHhhhcCCCCCCccc
Confidence 56799988998752 4677899996 998643
No 61
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=40.78 E-value=16 Score=22.87 Aligned_cols=9 Identities=22% Similarity=0.689 Sum_probs=7.2
Q ss_pred EECCCCCCc
Q 039226 80 LQCMGCKAR 88 (121)
Q Consensus 80 L~CPkC~~k 88 (121)
|.||.|+.|
T Consensus 5 i~CP~CgnK 13 (55)
T PF14205_consen 5 ILCPICGNK 13 (55)
T ss_pred EECCCCCCc
Confidence 788888865
No 62
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=40.72 E-value=17 Score=21.15 Aligned_cols=17 Identities=18% Similarity=0.567 Sum_probs=15.5
Q ss_pred eeEECCCCCCccceeee
Q 039226 78 EKLQCMGCKARLGSFNW 94 (121)
Q Consensus 78 GKL~CPkC~~kLG~f~w 94 (121)
|.|.|..|++-|++|.=
T Consensus 2 GtIvCq~C~~~Id~~e~ 18 (38)
T PF13790_consen 2 GTIVCQHCNETIDHFET 18 (38)
T ss_pred CEEEeccccceeeeecC
Confidence 78999999999999974
No 63
>PHA02325 hypothetical protein
Probab=40.31 E-value=17 Score=23.68 Aligned_cols=16 Identities=44% Similarity=1.043 Sum_probs=12.6
Q ss_pred ECCCCCCcc--ceeeeec
Q 039226 81 QCMGCKARL--GSFNWAG 96 (121)
Q Consensus 81 ~CPkC~~kL--G~f~w~G 96 (121)
.||+|+|+- |.--|+|
T Consensus 5 ~CPkC~A~WldgqhYWsg 22 (72)
T PHA02325 5 ICPKCGARWLDGQHYWSG 22 (72)
T ss_pred ccCccCCEeEcceeeecc
Confidence 499999984 7777875
No 64
>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=40.11 E-value=19 Score=20.72 Aligned_cols=12 Identities=33% Similarity=0.775 Sum_probs=8.1
Q ss_pred CeeEeccccccc
Q 039226 12 QAIYRCKKCRRL 23 (121)
Q Consensus 12 ~~~yrCrKCR~~ 23 (121)
.+.|+|.+|...
T Consensus 3 ~Yey~C~~Cg~~ 14 (42)
T PF09723_consen 3 IYEYRCEECGHE 14 (42)
T ss_pred CEEEEeCCCCCE
Confidence 457778777753
No 65
>PRK11032 hypothetical protein; Provisional
Probab=39.84 E-value=25 Score=26.45 Aligned_cols=27 Identities=30% Similarity=0.582 Sum_probs=22.1
Q ss_pred cceeEECCCCCCccceeeeec--ccCC-CCC
Q 039226 76 VGEKLQCMGCKARLGSFNWAG--LQCS-CGA 103 (121)
Q Consensus 76 ~~GKL~CPkC~~kLG~f~w~G--~qCs-CG~ 103 (121)
.-|.|.|-+|+.++ .|.-.| ..|+ ||.
T Consensus 121 g~G~LvC~~Cg~~~-~~~~p~~i~pCp~C~~ 150 (160)
T PRK11032 121 GLGNLVCEKCHHHL-AFYTPEVLPLCPKCGH 150 (160)
T ss_pred ecceEEecCCCCEE-EecCCCcCCCCCCCCC
Confidence 36899999999999 777777 4786 876
No 66
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=39.10 E-value=24 Score=25.81 Aligned_cols=21 Identities=24% Similarity=0.339 Sum_probs=17.4
Q ss_pred CCCeeEecccccccccCCCCe
Q 039226 10 NPQAIYRCKKCRRLVASEENI 30 (121)
Q Consensus 10 ~~~~~yrCrKCR~~Lf~~~~i 30 (121)
.+.-.|.|+.|...||.+++=
T Consensus 36 ~~~G~Y~C~~Cg~pLF~S~~K 56 (134)
T TIGR00357 36 KEEGIYVDITCGEPLFSSEDK 56 (134)
T ss_pred CCCeEEEccCCCCccccccch
Confidence 355689999999999998754
No 67
>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=38.97 E-value=20 Score=21.09 Aligned_cols=11 Identities=36% Similarity=0.848 Sum_probs=8.0
Q ss_pred CeeEecccccc
Q 039226 12 QAIYRCKKCRR 22 (121)
Q Consensus 12 ~~~yrCrKCR~ 22 (121)
.+.|+|.+|..
T Consensus 3 ~Yey~C~~Cg~ 13 (52)
T TIGR02605 3 IYEYRCTACGH 13 (52)
T ss_pred CEEEEeCCCCC
Confidence 46788888875
No 68
>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=38.77 E-value=17 Score=20.85 Aligned_cols=17 Identities=24% Similarity=0.321 Sum_probs=12.4
Q ss_pred ccceeEECCCCCCccce
Q 039226 75 FVGEKLQCMGCKARLGS 91 (121)
Q Consensus 75 ~~~GKL~CPkC~~kLG~ 91 (121)
...|.+.|+.|+.-|..
T Consensus 15 ~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 15 PERGELVCPNCGLVLEE 31 (43)
T ss_dssp TTTTEEEETTT-BBEE-
T ss_pred CCCCeEECCCCCCEeec
Confidence 35789999999988754
No 69
>PRK11827 hypothetical protein; Provisional
Probab=38.39 E-value=18 Score=22.93 Aligned_cols=12 Identities=33% Similarity=0.816 Sum_probs=10.4
Q ss_pred eeEECCCCCCcc
Q 039226 78 EKLQCMGCKARL 89 (121)
Q Consensus 78 GKL~CPkC~~kL 89 (121)
.-|.||.|+.+|
T Consensus 7 eILaCP~ckg~L 18 (60)
T PRK11827 7 EIIACPVCNGKL 18 (60)
T ss_pred hheECCCCCCcC
Confidence 358999999999
No 70
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.23 E-value=12 Score=31.02 Aligned_cols=23 Identities=30% Similarity=0.853 Sum_probs=16.1
Q ss_pred EECCCCCCccceeeeecccC-CCCCee
Q 039226 80 LQCMGCKARLGSFNWAGLQC-SCGAWA 105 (121)
Q Consensus 80 L~CPkC~~kLG~f~w~G~qC-sCG~wv 105 (121)
.+||+|+++| .|..+.| +||..+
T Consensus 4 FhC~~CgQ~v---~FeN~~C~~Cg~~L 27 (349)
T COG4307 4 FHCPNCGQRV---AFENSACLSCGSAL 27 (349)
T ss_pred ccCCCCCCee---eecchHHHhhhhHh
Confidence 5788888888 4555667 677644
No 71
>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=38.18 E-value=4 Score=20.72 Aligned_cols=20 Identities=20% Similarity=0.644 Sum_probs=15.4
Q ss_pred EecccccccccCCCCeeeCC
Q 039226 15 YRCKKCRRLVASEENIVPHE 34 (121)
Q Consensus 15 yrCrKCR~~Lf~~~~ii~H~ 34 (121)
|.|..|.+..-+...++.|.
T Consensus 2 ~~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 2 FECDECGKTFSSLSALREHK 21 (27)
T ss_dssp EEETTTTEEESSHHHHHHHH
T ss_pred CCCCccCCccCChhHHHHHh
Confidence 78999988777777777763
No 72
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.04 E-value=34 Score=23.95 Aligned_cols=29 Identities=21% Similarity=0.316 Sum_probs=17.9
Q ss_pred ccceeEECCCCCCccceeeeec-ccCC-CCCe
Q 039226 75 FVGEKLQCMGCKARLGSFNWAG-LQCS-CGAW 104 (121)
Q Consensus 75 ~~~GKL~CPkC~~kLG~f~w~G-~qCs-CG~w 104 (121)
...+++.|+.|+... .....+ ..|+ ||..
T Consensus 67 ~vp~~~~C~~Cg~~~-~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHVF-KPNALDYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCcc-ccCCccCCcCcCCCCC
Confidence 357889999998443 332222 3586 8853
No 73
>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=37.49 E-value=11 Score=24.73 Aligned_cols=12 Identities=25% Similarity=0.360 Sum_probs=5.9
Q ss_pred ceeEECCCCCCc
Q 039226 77 GEKLQCMGCKAR 88 (121)
Q Consensus 77 ~GKL~CPkC~~k 88 (121)
..|+.||+|+.+
T Consensus 22 ~~k~FCp~CGn~ 33 (73)
T PF08772_consen 22 MTKQFCPKCGNA 33 (73)
T ss_dssp SS--S-SSS--S
T ss_pred CCceeCcccCCC
Confidence 578999999875
No 74
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=37.13 E-value=19 Score=28.99 Aligned_cols=38 Identities=18% Similarity=0.631 Sum_probs=29.4
Q ss_pred cceeEECCCCCCccceeeeecccCC-CCCeeeceEEEecCCc
Q 039226 76 VGEKLQCMGCKARLGSFNWAGLQCS-CGAWATPAFQLHKSRL 116 (121)
Q Consensus 76 ~~GKL~CPkC~~kLG~f~w~G~qCs-CG~wv~Paf~l~kskV 116 (121)
.--+..|-+|++|+|.---+| .|. ||..+ ..-+++.+|
T Consensus 164 ~rq~~rc~~c~~k~rr~pl~g-~c~kcg~~~--~ltv~~g~v 202 (253)
T COG1933 164 TRQEFRCVKCNTKFRRPPLDG-KCPICGGKI--VLTVSKGAI 202 (253)
T ss_pred hhheeehHhhhhhhcCCCccc-cccccCCeE--EEEEeccHH
Confidence 344688999999999999998 887 99965 455566555
No 75
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=37.03 E-value=18 Score=32.65 Aligned_cols=10 Identities=40% Similarity=0.982 Sum_probs=3.7
Q ss_pred CCCCCCccce
Q 039226 82 CMGCKARLGS 91 (121)
Q Consensus 82 CPkC~~kLG~ 91 (121)
||+|++++|.
T Consensus 44 C~~CG~~~~~ 53 (645)
T PRK14559 44 CPNCGAETGT 53 (645)
T ss_pred ccccCCcccc
Confidence 3333333333
No 76
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=36.27 E-value=19 Score=23.89 Aligned_cols=15 Identities=20% Similarity=0.631 Sum_probs=12.3
Q ss_pred eeEecccccccccCC
Q 039226 13 AIYRCKKCRRLVASE 27 (121)
Q Consensus 13 ~~yrCrKCR~~Lf~~ 27 (121)
+.|.||.|+..+-+-
T Consensus 3 i~Y~CRHCg~~IG~i 17 (76)
T PF10955_consen 3 IHYYCRHCGTKIGTI 17 (76)
T ss_pred eEEEecCCCCEEEEe
Confidence 579999999998543
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=35.70 E-value=4.5 Score=19.24 Aligned_cols=19 Identities=21% Similarity=0.651 Sum_probs=11.3
Q ss_pred EecccccccccCCCCeeeC
Q 039226 15 YRCKKCRRLVASEENIVPH 33 (121)
Q Consensus 15 yrCrKCR~~Lf~~~~ii~H 33 (121)
|.|..|.....+..++..|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H 19 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQH 19 (24)
T ss_dssp EE-SSTS-EESSHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHH
Confidence 6788888777666555544
No 78
>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=35.48 E-value=20 Score=20.85 Aligned_cols=11 Identities=55% Similarity=1.370 Sum_probs=9.3
Q ss_pred CeeEecccccc
Q 039226 12 QAIYRCKKCRR 22 (121)
Q Consensus 12 ~~~yrCrKCR~ 22 (121)
...|+|+.||+
T Consensus 35 ~~~~~C~~C~~ 45 (46)
T PF12760_consen 35 RGRYRCKACRK 45 (46)
T ss_pred CCeEECCCCCC
Confidence 46899999986
No 79
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=35.33 E-value=26 Score=34.30 Aligned_cols=33 Identities=21% Similarity=0.688 Sum_probs=26.2
Q ss_pred ceeEECCCCCCccceeeeecccCC-CCCeeeceEE
Q 039226 77 GEKLQCMGCKARLGSFNWAGLQCS-CGAWATPAFQ 110 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w~G~qCs-CG~wv~Paf~ 110 (121)
.-+.-|.||++|-=.-=.+| +|. ||..|.+.++
T Consensus 1251 rQ~~RC~kC~~kyRR~PL~G-~C~kCGg~iilTv~ 1284 (1337)
T PRK14714 1251 RQEFRCLKCGTKYRRMPLAG-KCRKCGGRIILTVH 1284 (1337)
T ss_pred ccceeecccCcccccCCCCC-cccccCCeEEEEEe
Confidence 44788999999977666677 896 9999976653
No 80
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=35.14 E-value=21 Score=21.79 Aligned_cols=10 Identities=30% Similarity=0.946 Sum_probs=8.4
Q ss_pred EECCCCCCcc
Q 039226 80 LQCMGCKARL 89 (121)
Q Consensus 80 L~CPkC~~kL 89 (121)
+-||.|+.||
T Consensus 25 irCp~Cg~rI 34 (49)
T COG1996 25 IRCPYCGSRI 34 (49)
T ss_pred eeCCCCCcEE
Confidence 7798898886
No 81
>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=34.69 E-value=22 Score=20.78 Aligned_cols=11 Identities=27% Similarity=0.782 Sum_probs=9.0
Q ss_pred cceeEECCCCC
Q 039226 76 VGEKLQCMGCK 86 (121)
Q Consensus 76 ~~GKL~CPkC~ 86 (121)
-+|++.||.|+
T Consensus 31 k~g~~~Cv~C~ 41 (41)
T PF06677_consen 31 KDGKIYCVSCG 41 (41)
T ss_pred cCCCEECCCCC
Confidence 47889999985
No 82
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.46 E-value=47 Score=23.85 Aligned_cols=12 Identities=25% Similarity=0.595 Sum_probs=8.3
Q ss_pred cceeEECCCCCC
Q 039226 76 VGEKLQCMGCKA 87 (121)
Q Consensus 76 ~~GKL~CPkC~~ 87 (121)
...+..|+.|+.
T Consensus 67 ~p~~~~C~~CG~ 78 (135)
T PRK03824 67 EEAVLKCRNCGN 78 (135)
T ss_pred cceEEECCCCCC
Confidence 456777888873
No 83
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=34.35 E-value=18 Score=23.51 Aligned_cols=11 Identities=18% Similarity=0.664 Sum_probs=7.8
Q ss_pred eeEECCCCCCc
Q 039226 78 EKLQCMGCKAR 88 (121)
Q Consensus 78 GKL~CPkC~~k 88 (121)
+...||||+.+
T Consensus 3 ~~~kCpKCgn~ 13 (68)
T COG3478 3 NAFKCPKCGNT 13 (68)
T ss_pred ccccCCCcCCc
Confidence 34459999865
No 84
>smart00355 ZnF_C2H2 zinc finger.
Probab=34.25 E-value=4.3 Score=19.43 Aligned_cols=19 Identities=32% Similarity=0.863 Sum_probs=13.3
Q ss_pred EecccccccccCCCCeeeC
Q 039226 15 YRCKKCRRLVASEENIVPH 33 (121)
Q Consensus 15 yrCrKCR~~Lf~~~~ii~H 33 (121)
|.|..|.....+..++..|
T Consensus 1 ~~C~~C~~~f~~~~~l~~H 19 (26)
T smart00355 1 YRCPECGKVFKSKSALKEH 19 (26)
T ss_pred CCCCCCcchhCCHHHHHHH
Confidence 5788888777666666555
No 85
>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=34.01 E-value=22 Score=19.31 Aligned_cols=13 Identities=38% Similarity=0.736 Sum_probs=8.6
Q ss_pred ceeEECCCCCCcc
Q 039226 77 GEKLQCMGCKARL 89 (121)
Q Consensus 77 ~GKL~CPkC~~kL 89 (121)
.+|-.||+|+.+.
T Consensus 11 ~~kY~Cp~C~~~~ 23 (30)
T PF04438_consen 11 PAKYRCPRCGARY 23 (30)
T ss_dssp EESEE-TTT--EE
T ss_pred CCEEECCCcCCce
Confidence 7899999999875
No 86
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.67 E-value=28 Score=33.36 Aligned_cols=37 Identities=24% Similarity=0.613 Sum_probs=27.6
Q ss_pred ceeEECCCCCCccceeeeecccCC-CCCeeeceEEEecCCc
Q 039226 77 GEKLQCMGCKARLGSFNWAGLQCS-CGAWATPAFQLHKSRL 116 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w~G~qCs-CG~wv~Paf~l~kskV 116 (121)
.-+.-|.||++|-=.-=.+| +|. ||..|.+.+ |+.-|
T Consensus 1035 rQ~fRC~kC~~kYRR~PL~G-~C~kCGg~lilTV--h~GsV 1072 (1121)
T PRK04023 1035 RQEFRCTKCGAKYRRPPLSG-KCPKCGGNLILTV--HKGSV 1072 (1121)
T ss_pred ccceeecccCcccccCCCCC-cCccCCCeEEEEE--ecchH
Confidence 44688999999976666677 895 999996655 44444
No 87
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=33.50 E-value=21 Score=30.82 Aligned_cols=30 Identities=30% Similarity=0.636 Sum_probs=22.3
Q ss_pred cceeEECCCCCCccceeeeecccCC-CCCee
Q 039226 76 VGEKLQCMGCKARLGSFNWAGLQCS-CGAWA 105 (121)
Q Consensus 76 ~~GKL~CPkC~~kLG~f~w~G~qCs-CG~wv 105 (121)
..-+-.||.|+.+.=|--=.|-+|+ ||+-.
T Consensus 347 ~~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~ 377 (421)
T COG1571 347 ERVNPVCPRCGGRMKSAGRNGFRCKKCGTRA 377 (421)
T ss_pred EEcCCCCCccCCchhhcCCCCcccccccccC
Confidence 3445579999999865544578998 99865
No 88
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=32.73 E-value=38 Score=19.32 Aligned_cols=20 Identities=25% Similarity=0.487 Sum_probs=14.5
Q ss_pred ccccCCCCCCeeEecccccc
Q 039226 3 QVHKHVANPQAIYRCKKCRR 22 (121)
Q Consensus 3 ~~~~~~~~~~~~yrCrKCR~ 22 (121)
|+-+.++...+.|.|.+|+.
T Consensus 17 Q~RsaDE~mT~fy~C~~C~~ 36 (40)
T smart00440 17 QTRSADEPMTVFYVCTKCGH 36 (40)
T ss_pred cccCCCCCCeEEEEeCCCCC
Confidence 44455566668999999975
No 89
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=31.73 E-value=19 Score=20.18 Aligned_cols=9 Identities=33% Similarity=0.722 Sum_probs=4.2
Q ss_pred ECCCCCCcc
Q 039226 81 QCMGCKARL 89 (121)
Q Consensus 81 ~CPkC~~kL 89 (121)
+||.|++.|
T Consensus 2 fC~~CG~~l 10 (34)
T PF14803_consen 2 FCPQCGGPL 10 (34)
T ss_dssp B-TTT--B-
T ss_pred ccccccChh
Confidence 589999988
No 90
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=31.61 E-value=12 Score=30.17 Aligned_cols=24 Identities=29% Similarity=0.666 Sum_probs=10.6
Q ss_pred ccccceeEECCCCCCc-cceeeeec
Q 039226 73 EGFVGEKLQCMGCKAR-LGSFNWAG 96 (121)
Q Consensus 73 ~~~~~GKL~CPkC~~k-LG~f~w~G 96 (121)
+.|+....+||.|+++ |-.|.=..
T Consensus 25 E~Wv~~n~yCP~Cg~~~L~~f~NN~ 49 (254)
T PF06044_consen 25 EDWVAENMYCPNCGSKPLSKFENNR 49 (254)
T ss_dssp HHHHHHH---TTT--SS-EE-----
T ss_pred HHHHHHCCcCCCCCChhHhhccCCC
Confidence 4577778999999999 88886644
No 91
>PRK05638 threonine synthase; Validated
Probab=31.41 E-value=35 Score=28.87 Aligned_cols=28 Identities=25% Similarity=0.512 Sum_probs=20.7
Q ss_pred eEECCCCCCccceeeeecccCCCCCeeece
Q 039226 79 KLQCMGCKARLGSFNWAGLQCSCGAWATPA 108 (121)
Q Consensus 79 KL~CPkC~~kLG~f~w~G~qCsCG~wv~Pa 108 (121)
||.|++|+..... ++. ..|.||..+...
T Consensus 1 ~l~C~~Cg~~~~~-~~~-~~C~c~~~l~~~ 28 (442)
T PRK05638 1 KMKCPKCGREYNS-YIP-PFCICGELLEII 28 (442)
T ss_pred CeEeCCCCCCCCC-CCc-eecCCCCcEEEE
Confidence 6899999999863 333 678999876444
No 92
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=31.17 E-value=23 Score=20.68 Aligned_cols=29 Identities=24% Similarity=0.512 Sum_probs=19.1
Q ss_pred ceeEECCCCCCccceeeeecccCC-CCCee
Q 039226 77 GEKLQCMGCKARLGSFNWAGLQCS-CGAWA 105 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w~G~qCs-CG~wv 105 (121)
..--.|-.|+..|..+.-.|.+|+ |+..+
T Consensus 9 ~~~~~C~~C~~~i~g~~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWGLGKQGYRCSWCGLVC 38 (53)
T ss_dssp SSTEB-TTSSSBECSSSSCEEEETTTT-EE
T ss_pred CCCCCCcccCcccCCCCCCeEEECCCCChH
Confidence 344578889999944555788997 77654
No 93
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=31.09 E-value=24 Score=31.43 Aligned_cols=27 Identities=30% Similarity=0.603 Sum_probs=20.0
Q ss_pred eeEECCCCCCccceeeeecccC-CCCCeeece
Q 039226 78 EKLQCMGCKARLGSFNWAGLQC-SCGAWATPA 108 (121)
Q Consensus 78 GKL~CPkC~~kLG~f~w~G~qC-sCG~wv~Pa 108 (121)
.+-.||+|+...+ .|.|| .||....|.
T Consensus 141 v~g~cp~cg~~~a----rGD~Ce~Cg~~~~P~ 168 (558)
T COG0143 141 VEGTCPKCGGEDA----RGDQCENCGRTLDPT 168 (558)
T ss_pred eeccCCCcCcccc----CcchhhhccCcCCch
Confidence 3456999986654 48899 599988774
No 94
>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=30.95 E-value=31 Score=18.03 Aligned_cols=10 Identities=20% Similarity=0.657 Sum_probs=7.6
Q ss_pred ceeEECCCCC
Q 039226 77 GEKLQCMGCK 86 (121)
Q Consensus 77 ~GKL~CPkC~ 86 (121)
.-...||+|+
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 3467899997
No 95
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=30.44 E-value=43 Score=27.41 Aligned_cols=43 Identities=21% Similarity=0.337 Sum_probs=27.3
Q ss_pred ccceeEECCCCCCccceeeeec--ccCC-CCCee----eceEEEecCCccc
Q 039226 75 FVGEKLQCMGCKARLGSFNWAG--LQCS-CGAWA----TPAFQLHKSRLDK 118 (121)
Q Consensus 75 ~~~GKL~CPkC~~kLG~f~w~G--~qCs-CG~wv----~Paf~l~kskVD~ 118 (121)
|...-=.||+|++|.=.. =.| ++|+ ||.-. .|++-+.-.|-|+
T Consensus 107 w~~~~RFCg~CG~~~~~~-~~g~~~~C~~cg~~~fPR~dP~vIv~v~~~~~ 156 (279)
T COG2816 107 WYRSHRFCGRCGTKTYPR-EGGWARVCPKCGHEHFPRIDPCVIVAVIRGDE 156 (279)
T ss_pred HHhhCcCCCCCCCcCccc-cCceeeeCCCCCCccCCCCCCeEEEEEecCCc
Confidence 445566799999998222 223 6896 99855 6666555444444
No 96
>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=30.22 E-value=24 Score=20.08 Aligned_cols=9 Identities=33% Similarity=0.870 Sum_probs=7.0
Q ss_pred ECCCCCCcc
Q 039226 81 QCMGCKARL 89 (121)
Q Consensus 81 ~CPkC~~kL 89 (121)
.||+|++.|
T Consensus 3 ~CP~Cg~~l 11 (39)
T PF01396_consen 3 KCPKCGGPL 11 (39)
T ss_pred CCCCCCcee
Confidence 599999755
No 97
>KOG3092 consensus Casein kinase II, beta subunit [Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Transcription]
Probab=29.94 E-value=30 Score=27.21 Aligned_cols=34 Identities=18% Similarity=0.314 Sum_probs=19.9
Q ss_pred CCCCceeEecccchhhh---hhccccceeEECCCCCC
Q 039226 54 PAECSSLFVESMKWMQS---VQEGFVGEKLQCMGCKA 87 (121)
Q Consensus 54 ~~~C~~~Fiep~~Wm~~---~~~~~~~GKL~CPkC~~ 87 (121)
-..|--+|-+-+.=+-. +.-|...-||+||+|..
T Consensus 106 FG~CPRV~C~~q~~LPvGLsDipg~~~VklYCP~C~d 142 (216)
T KOG3092|consen 106 FGRCPRVYCCGQPVLPVGLSDIPGKSTVKLYCPSCED 142 (216)
T ss_pred CCcCCcccccCCccccccccCCCCcceEEEeCCCccc
Confidence 35677777642222211 12355678999999963
No 98
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=29.91 E-value=23 Score=21.48 Aligned_cols=31 Identities=26% Similarity=0.533 Sum_probs=22.2
Q ss_pred CCCCCCccceee---e-ecccC-CCCCeeeceEEEe
Q 039226 82 CMGCKARLGSFN---W-AGLQC-SCGAWATPAFQLH 112 (121)
Q Consensus 82 CPkC~~kLG~f~---w-~G~qC-sCG~wv~Paf~l~ 112 (121)
|+-|+.++|-|. . +|--| +|-.-++|.+.-.
T Consensus 2 C~iCg~kigl~~~~k~~DG~iC~~C~~Kl~~~~~~~ 37 (51)
T PF14471_consen 2 CAICGKKIGLFKRFKIKDGYICKDCLKKLSGFFSDV 37 (51)
T ss_pred CCccccccccccceeccCccchHHHHHHhcCcccch
Confidence 889999999998 3 47667 4666655655443
No 99
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=29.86 E-value=22 Score=20.28 Aligned_cols=10 Identities=40% Similarity=1.261 Sum_probs=4.7
Q ss_pred Eecccccccc
Q 039226 15 YRCKKCRRLV 24 (121)
Q Consensus 15 yrCrKCR~~L 24 (121)
.||++||..|
T Consensus 3 ~rC~~C~ayl 12 (40)
T PF04810_consen 3 VRCRRCRAYL 12 (40)
T ss_dssp -B-TTT--BS
T ss_pred cccCCCCCEE
Confidence 5788888766
No 100
>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=29.38 E-value=42 Score=18.96 Aligned_cols=11 Identities=55% Similarity=1.238 Sum_probs=8.7
Q ss_pred CCeeEeccccc
Q 039226 11 PQAIYRCKKCR 21 (121)
Q Consensus 11 ~~~~yrCrKCR 21 (121)
..-.|||+.||
T Consensus 26 G~qryrC~~C~ 36 (36)
T PF03811_consen 26 GHQRYRCKDCR 36 (36)
T ss_pred CCEeEecCcCC
Confidence 34589999997
No 101
>PF12992 DUF3876: Domain of unknown function, B. Theta Gene description (DUF3876); InterPro: IPR024452 This bacterial family of conserved proteins has no known function.
Probab=29.30 E-value=24 Score=24.19 Aligned_cols=15 Identities=27% Similarity=0.955 Sum_probs=12.0
Q ss_pred CCCee----eceEEEecCC
Q 039226 101 CGAWA----TPAFQLHKSR 115 (121)
Q Consensus 101 CG~wv----~Paf~l~ksk 115 (121)
||.|+ .|+|.|.++.
T Consensus 16 ~G~W~Sv~~~P~v~I~r~g 34 (95)
T PF12992_consen 16 CGEWESVNGKPDVTIYRNG 34 (95)
T ss_pred EEEeEccCCCCCEEEEECC
Confidence 67777 6999998874
No 102
>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=29.09 E-value=23 Score=20.80 Aligned_cols=9 Identities=22% Similarity=0.822 Sum_probs=7.0
Q ss_pred ECCCCCCcc
Q 039226 81 QCMGCKARL 89 (121)
Q Consensus 81 ~CPkC~~kL 89 (121)
.||.|+++.
T Consensus 1 ~CP~Cg~~a 9 (47)
T PF04606_consen 1 RCPHCGSKA 9 (47)
T ss_pred CcCCCCCee
Confidence 489998865
No 103
>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=28.70 E-value=31 Score=22.58 Aligned_cols=14 Identities=36% Similarity=1.039 Sum_probs=8.6
Q ss_pred EECCCCCCccceeeeec
Q 039226 80 LQCMGCKARLGSFNWAG 96 (121)
Q Consensus 80 L~CPkC~~kLG~f~w~G 96 (121)
+.||.|.+-| .|.|
T Consensus 2 ~~CP~C~~~L---~~~~ 15 (70)
T PF07191_consen 2 NTCPKCQQEL---EWQG 15 (70)
T ss_dssp -B-SSS-SBE---EEET
T ss_pred CcCCCCCCcc---EEeC
Confidence 5788888887 7765
No 104
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=28.56 E-value=42 Score=18.45 Aligned_cols=23 Identities=26% Similarity=0.533 Sum_probs=13.6
Q ss_pred CeeEecccccccccCCCCeeeCC
Q 039226 12 QAIYRCKKCRRLVASEENIVPHE 34 (121)
Q Consensus 12 ~~~yrCrKCR~~Lf~~~~ii~H~ 34 (121)
-..-||+.|.+..|-...+-+|=
T Consensus 9 l~~~rC~~Cg~~~~pPr~~Cp~C 31 (37)
T PF12172_consen 9 LLGQRCRDCGRVQFPPRPVCPHC 31 (37)
T ss_dssp EEEEE-TTT--EEES--SEETTT
T ss_pred EEEEEcCCCCCEecCCCcCCCCc
Confidence 35779999999999888777653
No 105
>PF02943 FeThRed_B: Ferredoxin thioredoxin reductase catalytic beta chain; InterPro: IPR004209 Ferredoxin thioredoxin reductase is a [4FE-4S] protein present in organisms performing oxygenic photosynthesis, and plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit alpha and subunit beta. Subunit alpha is the variable subunit, and beta is the catalytic chain []. The structure of the beta subunit has been determined and found to fold around the FeS cluster [].; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0055114 oxidation-reduction process; PDB: 2PUK_E 2PVD_A 2PVG_A 2PUO_A 2PU9_A 1DJ7_A 2PVO_A.
Probab=27.75 E-value=7.8 Score=27.29 Aligned_cols=29 Identities=28% Similarity=0.798 Sum_probs=13.8
Q ss_pred eeEECCCCC-CccceeeeecccCCCCCeeeceE
Q 039226 78 EKLQCMGCK-ARLGSFNWAGLQCSCGAWATPAF 109 (121)
Q Consensus 78 GKL~CPkC~-~kLG~f~w~G~qCsCG~wv~Paf 109 (121)
.++.|| |. .+--.+ -.| .|-||-+|+|.+
T Consensus 62 ~~iiCP-C~~~r~~~~-~~G-~ChC~Lf~~~e~ 91 (108)
T PF02943_consen 62 RDIICP-CVPYREDDI-EYG-HCHCGLFVSPEY 91 (108)
T ss_dssp -TTBSS--HHHHHH---------TTSSSB-TTS
T ss_pred CCeecC-CHHHHhhcc-ccc-cceEeeeECccc
Confidence 456666 66 555555 445 799999999876
No 106
>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=27.72 E-value=38 Score=24.46 Aligned_cols=26 Identities=19% Similarity=0.517 Sum_probs=15.3
Q ss_pred EECCCCCCccceeeeecccCC-CCCee
Q 039226 80 LQCMGCKARLGSFNWAGLQCS-CGAWA 105 (121)
Q Consensus 80 L~CPkC~~kLG~f~w~G~qCs-CG~wv 105 (121)
..||+|+.||=..+-....|. |+..+
T Consensus 35 ~aC~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 35 PACPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred ccccccCcccEeCCCCcEECCCCCCcC
Confidence 458888888822211225675 77754
No 107
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=27.56 E-value=29 Score=22.36 Aligned_cols=17 Identities=18% Similarity=0.413 Sum_probs=14.7
Q ss_pred ECCCCCCccceeeeecc
Q 039226 81 QCMGCKARLGSFNWAGL 97 (121)
Q Consensus 81 ~CPkC~~kLG~f~w~G~ 97 (121)
.||.|++.==+-+|.|+
T Consensus 19 ~Cp~Cgs~~~S~~w~G~ 35 (64)
T PRK06393 19 TCPVHGDEKTTTEWFGF 35 (64)
T ss_pred cCCCCCCCcCCcCcceE
Confidence 69999998768899994
No 108
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.82 E-value=58 Score=23.32 Aligned_cols=28 Identities=29% Similarity=0.649 Sum_probs=16.8
Q ss_pred ECCCCCCccceeeeecccCC-CCCeeeceEEE
Q 039226 81 QCMGCKARLGSFNWAGLQCS-CGAWATPAFQL 111 (121)
Q Consensus 81 ~CPkC~~kLG~f~w~G~qCs-CG~wv~Paf~l 111 (121)
-||.|+.++ --.-.+|| |++-|.--|.+
T Consensus 8 ~cPvcg~~~---iVTeL~c~~~etTVrg~F~~ 36 (122)
T COG3877 8 RCPVCGRKL---IVTELKCSNCETTVRGNFKM 36 (122)
T ss_pred CCCcccccc---eeEEEecCCCCceEecceec
Confidence 477777666 22345675 77766665554
No 109
>PF06174 DUF987: Protein of unknown function (DUF987); InterPro: IPR009329 This is a family of bacterial proteins that are related to the hypothetical protein YeeT.
Probab=26.67 E-value=29 Score=22.38 Aligned_cols=11 Identities=36% Similarity=1.217 Sum_probs=9.7
Q ss_pred ceeeeecccCC
Q 039226 90 GSFNWAGLQCS 100 (121)
Q Consensus 90 G~f~w~G~qCs 100 (121)
|.|.|.|+.|.
T Consensus 27 GkY~W~Gs~~h 37 (66)
T PF06174_consen 27 GKYQWHGSVCH 37 (66)
T ss_pred ccceeeccccc
Confidence 78999999985
No 110
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=26.13 E-value=47 Score=33.06 Aligned_cols=37 Identities=22% Similarity=0.611 Sum_probs=27.2
Q ss_pred ceeEECCCCCCccceeeeecccCC-CCCeeeceEEEecCCcc
Q 039226 77 GEKLQCMGCKARLGSFNWAGLQCS-CGAWATPAFQLHKSRLD 117 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w~G~qCs-CG~wv~Paf~l~kskVD 117 (121)
.-+.-| ||++|-=.--.+| +|. ||..+.+.+ ++.-|.
T Consensus 1540 rQ~~RC-kC~~kyRR~PL~G-~C~kCGg~~ilTV--~kGsv~ 1577 (1627)
T PRK14715 1540 RQEFRC-KCGAKYRRVPLKG-KCPKCGSKLILTV--SKGAVE 1577 (1627)
T ss_pred ccceee-cCCCccccCCCCC-cCcccCCeEEEEE--ecchHH
Confidence 446889 9999987766777 897 999996654 444443
No 111
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=25.83 E-value=1.6e+02 Score=21.03 Aligned_cols=26 Identities=12% Similarity=0.362 Sum_probs=16.6
Q ss_pred CCCeeEecccccccccCCCCeeeCCC
Q 039226 10 NPQAIYRCKKCRRLVASEENIVPHEQ 35 (121)
Q Consensus 10 ~~~~~yrCrKCR~~Lf~~~~ii~H~~ 35 (121)
+....|.||.|..+-+..+.-+.-.+
T Consensus 22 d~~L~laCrnCd~ve~A~s~~vY~~~ 47 (113)
T KOG2691|consen 22 DRILLLACRNCDYVEEADSSRVYVNE 47 (113)
T ss_pred ccEEEEEecCCcceEecCCcceEcCC
Confidence 35568889999766655555544333
No 112
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=25.69 E-value=33 Score=26.70 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=17.6
Q ss_pred EECCCCCCccceeeeecccCCCCCee
Q 039226 80 LQCMGCKARLGSFNWAGLQCSCGAWA 105 (121)
Q Consensus 80 L~CPkC~~kLG~f~w~G~qCsCG~wv 105 (121)
+.||.|++.| ...=.+..|..|.-.
T Consensus 3 ~~CP~C~~~l-~~~~~~~~C~~~h~f 27 (272)
T PRK11088 3 YQCPLCHQPL-TLEENSWICPQNHQF 27 (272)
T ss_pred ccCCCCCcch-hcCCCEEEcCCCCCC
Confidence 6799999999 333355788877643
No 113
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=25.63 E-value=45 Score=26.41 Aligned_cols=30 Identities=17% Similarity=0.368 Sum_probs=21.7
Q ss_pred ccceeEECCCCCCccceeeeec--ccCC-CCCee
Q 039226 75 FVGEKLQCMGCKARLGSFNWAG--LQCS-CGAWA 105 (121)
Q Consensus 75 ~~~GKL~CPkC~~kLG~f~w~G--~qCs-CG~wv 105 (121)
|....-+||.|++++-... .| ..|+ ||...
T Consensus 95 w~~~~~fC~~CG~~~~~~~-~~~~~~C~~c~~~~ 127 (256)
T PRK00241 95 FYRSHRFCGYCGHPMHPSK-TEWAMLCPHCRERY 127 (256)
T ss_pred HhhcCccccccCCCCeecC-CceeEECCCCCCEE
Confidence 5566779999999985433 23 5795 99865
No 114
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=25.50 E-value=47 Score=27.07 Aligned_cols=39 Identities=23% Similarity=0.491 Sum_probs=29.5
Q ss_pred ccceeEECCCCCCccceeeeec--ccCC-CCCeeeceEEEec
Q 039226 75 FVGEKLQCMGCKARLGSFNWAG--LQCS-CGAWATPAFQLHK 113 (121)
Q Consensus 75 ~~~GKL~CPkC~~kLG~f~w~G--~qCs-CG~wv~Paf~l~k 113 (121)
|--|..+||+|+-..-.|.=-| +.|. ||.-|.|.--|.+
T Consensus 151 wG~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~v~P~~IlPP 192 (278)
T PF15135_consen 151 WGIAEFHCPKCRHNFRGFAQMGVPSPCYGCGNPVYPSRILPP 192 (278)
T ss_pred cceeeeecccccccchhhhhcCCCCCccCCCCccCcccccCC
Confidence 4467899999998877665544 5784 9999999876653
No 115
>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=25.47 E-value=41 Score=19.76 Aligned_cols=24 Identities=29% Similarity=0.715 Sum_probs=15.8
Q ss_pred ECCCCCCccceeeeecccC-CCCCee
Q 039226 81 QCMGCKARLGSFNWAGLQC-SCGAWA 105 (121)
Q Consensus 81 ~CPkC~~kLG~f~w~G~qC-sCG~wv 105 (121)
.|+.|+.++|.|... -.| .||..+
T Consensus 4 ~C~~C~~~F~~~~rk-~~Cr~Cg~~~ 28 (57)
T cd00065 4 SCMGCGKPFTLTRRR-HHCRNCGRIF 28 (57)
T ss_pred cCcccCccccCCccc-cccCcCcCCc
Confidence 577888888876654 355 366654
No 116
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=25.43 E-value=30 Score=19.23 Aligned_cols=25 Identities=28% Similarity=0.634 Sum_probs=16.9
Q ss_pred EECCCCCCccceeeeecccCC-CCCee
Q 039226 80 LQCMGCKARLGSFNWAGLQCS-CGAWA 105 (121)
Q Consensus 80 L~CPkC~~kLG~f~w~G~qCs-CG~wv 105 (121)
..|--|+..|..+. .|.+|+ |+..+
T Consensus 12 ~~C~~C~~~i~~~~-~~~~C~~C~~~~ 37 (49)
T smart00109 12 TKCCVCRKSIWGSF-QGLRCSWCKVKC 37 (49)
T ss_pred CCccccccccCcCC-CCcCCCCCCchH
Confidence 35777888887654 688886 66543
No 117
>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=25.29 E-value=34 Score=21.85 Aligned_cols=8 Identities=25% Similarity=0.833 Sum_probs=6.3
Q ss_pred ECCCCCCc
Q 039226 81 QCMGCKAR 88 (121)
Q Consensus 81 ~CPkC~~k 88 (121)
.||||+.+
T Consensus 2 ~C~KCg~~ 9 (64)
T PF09855_consen 2 KCPKCGNE 9 (64)
T ss_pred CCCCCCCc
Confidence 49999875
No 118
>PRK08329 threonine synthase; Validated
Probab=23.10 E-value=53 Score=26.85 Aligned_cols=28 Identities=25% Similarity=0.657 Sum_probs=19.9
Q ss_pred eEECCCCCCccceeeeecccCCCCCeeece
Q 039226 79 KLQCMGCKARLGSFNWAGLQCSCGAWATPA 108 (121)
Q Consensus 79 KL~CPkC~~kLG~f~w~G~qCsCG~wv~Pa 108 (121)
+|.|++|+..... ++. ..|.||..+...
T Consensus 1 ~l~C~~Cg~~~~~-~~~-~~C~c~~~l~~~ 28 (347)
T PRK08329 1 MLRCTKCGRTYEE-KFK-LRCDCGGTLLVE 28 (347)
T ss_pred CcCcCCCCCCcCC-CCc-eecCCCCcEEEE
Confidence 3789999998863 333 678998765444
No 119
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=22.84 E-value=47 Score=17.98 Aligned_cols=13 Identities=31% Similarity=1.035 Sum_probs=11.0
Q ss_pred CeeEecccccccc
Q 039226 12 QAIYRCKKCRRLV 24 (121)
Q Consensus 12 ~~~yrCrKCR~~L 24 (121)
...|+|..|+.++
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4589999999877
No 120
>KOG4487 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.35 E-value=53 Score=23.17 Aligned_cols=55 Identities=16% Similarity=0.142 Sum_probs=28.3
Q ss_pred Eecccchhhhhhcccc------ceeEECCCCCCccceeeee-cccC-----------CCCCeeeceEEEecCCcccc
Q 039226 61 FVESMKWMQSVQEGFV------GEKLQCMGCKARLGSFNWA-GLQC-----------SCGAWATPAFQLHKSRLDKC 119 (121)
Q Consensus 61 Fiep~~Wm~~~~~~~~------~GKL~CPkC~~kLG~f~w~-G~qC-----------sCG~wv~Paf~l~kskVD~~ 119 (121)
-++|+.||.....|++ .|.+. +-.+|.|+|+ |.|= +=|+.-.|-.-|.|+-+|.+
T Consensus 11 ~~~~~~~m~~ElqG~~e~q~~f~gs~d----s~~~Gr~c~~D~~q~~~~~G~~~l~G~v~k~~rpLlvv~Kld~~h~ 83 (110)
T KOG4487|consen 11 VITPLGMMMLELQGELELQKDFLGSRD----SPNEGRFCEQDGEQTLIRFGSLQLDGEVGKKQRPLLVVTKLDVMHF 83 (110)
T ss_pred cccchHhhhhhhccccccchhhccccc----CccccceeccCCCeEEEEEeeEEEeeeeeeecceeEEEEeehhhhh
Confidence 5789999986322321 22222 3356777773 4430 12333355556666655543
No 121
>PHA01769 hypothetical protein
Probab=22.12 E-value=41 Score=22.97 Aligned_cols=13 Identities=38% Similarity=0.876 Sum_probs=9.3
Q ss_pred eeEecccc-ccccc
Q 039226 13 AIYRCKKC-RRLVA 25 (121)
Q Consensus 13 ~~yrCrKC-R~~Lf 25 (121)
...|||+| |+..|
T Consensus 5 ~h~rcr~c~rrr~~ 18 (98)
T PHA01769 5 QHVRCRECTRRRAL 18 (98)
T ss_pred eeeeecccchhhcc
Confidence 46899999 45554
No 122
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.91 E-value=51 Score=23.86 Aligned_cols=16 Identities=13% Similarity=0.241 Sum_probs=12.8
Q ss_pred cccceeEECCCCCCcc
Q 039226 74 GFVGEKLQCMGCKARL 89 (121)
Q Consensus 74 ~~~~GKL~CPkC~~kL 89 (121)
...+|.+.||.|+..-
T Consensus 93 ~v~EG~l~CpetG~vf 108 (124)
T KOG1088|consen 93 DVIEGELVCPETGRVF 108 (124)
T ss_pred hhccceEecCCCCcEe
Confidence 3579999999998653
No 123
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=21.87 E-value=42 Score=28.32 Aligned_cols=36 Identities=31% Similarity=0.740 Sum_probs=26.5
Q ss_pred CCCCceeEeccc-------chhhhhh-----ccccceeEECCCCCCcc
Q 039226 54 PAECSSLFVESM-------KWMQSVQ-----EGFVGEKLQCMGCKARL 89 (121)
Q Consensus 54 ~~~C~~~Fiep~-------~Wm~~~~-----~~~~~GKL~CPkC~~kL 89 (121)
...|..-|-.|| .|-..-+ +.|+.||-.||-|.+|-
T Consensus 303 ~~~C~~C~CRPmWC~~Cm~kwFasrQd~~~~~~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 303 EPPCQQCYCRPMWCLECMGKWFASRQDQQHPETWLSGKCPCPTCRAKF 350 (358)
T ss_pred CCCCccccccchHHHHHHHHHhhhcCCCCChhhhhcCCCCCCCCcccc
Confidence 357888888887 5554421 24789999999999873
No 124
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=21.85 E-value=48 Score=20.21 Aligned_cols=26 Identities=42% Similarity=0.857 Sum_probs=19.3
Q ss_pred ccceeEECCCCCCccceeeeecccCC-CCC
Q 039226 75 FVGEKLQCMGCKARLGSFNWAGLQCS-CGA 103 (121)
Q Consensus 75 ~~~GKL~CPkC~~kLG~f~w~G~qCs-CG~ 103 (121)
....|..|-+|+|++ .|.-..|- ||.
T Consensus 10 ~~~~k~ICrkC~ARn---p~~A~~CRKCg~ 36 (48)
T PRK04136 10 RVFNKKICMRCNARN---PWRATKCRKCGY 36 (48)
T ss_pred HhhcccchhcccCCC---CccccccccCCC
Confidence 345678899999999 56556674 886
No 125
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=21.81 E-value=1e+02 Score=23.64 Aligned_cols=38 Identities=21% Similarity=0.495 Sum_probs=27.0
Q ss_pred ceeEECCCCCCccceeeee----cccCC-CCCeeeceEEEecCCcc
Q 039226 77 GEKLQCMGCKARLGSFNWA----GLQCS-CGAWATPAFQLHKSRLD 117 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w~----G~qCs-CG~wv~Paf~l~kskVD 117 (121)
-.++.|.+|+.. |+|. .-.|+ ||..+.|.+-+.-..++
T Consensus 116 ~~~~~C~~C~~~---~~~~~~~~~p~C~~Cgg~lrP~vv~fge~~~ 158 (225)
T cd01411 116 LYRIYCTVCGKT---VDWEEYLKSPYHAKCGGVIRPDIVLYEEMLN 158 (225)
T ss_pred cCeeEeCCCCCc---cchhhcCCCCCCCCCCCEeCCCEEEcCCCCC
Confidence 346889999653 4442 35796 99999999987665554
No 126
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=21.76 E-value=1.1e+02 Score=20.59 Aligned_cols=34 Identities=29% Similarity=0.678 Sum_probs=22.8
Q ss_pred ceeEECCCCCCcc--------------ceeee--ecccC-CCCCeeeceEE
Q 039226 77 GEKLQCMGCKARL--------------GSFNW--AGLQC-SCGAWATPAFQ 110 (121)
Q Consensus 77 ~GKL~CPkC~~kL--------------G~f~w--~G~qC-sCG~wv~Paf~ 110 (121)
.|++.|++|+..= |.++- -|.+| +|+....|-|.
T Consensus 3 ~grF~C~~C~~~W~S~~v~i~f~~~~~g~v~~rv~~Q~C~~C~~~~~P~~~ 53 (98)
T PF13695_consen 3 FGRFQCSKCSRGWTSAKVWILFHMYRGGQVNMRVFGQRCKKCNPLERPYFS 53 (98)
T ss_pred EEEEECCCCCCCCccCEEEEEEEEcCCCeEEEEEECCCCCCCCCCCCccCc
Confidence 5677777775432 33333 47788 59999999885
No 127
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=21.60 E-value=39 Score=18.51 Aligned_cols=13 Identities=31% Similarity=0.639 Sum_probs=9.7
Q ss_pred EecccccccccCC
Q 039226 15 YRCKKCRRLVASE 27 (121)
Q Consensus 15 yrCrKCR~~Lf~~ 27 (121)
..|..||..|...
T Consensus 2 ~~C~~C~t~L~yP 14 (31)
T TIGR01053 2 VVCGGCRTLLMYP 14 (31)
T ss_pred cCcCCCCcEeecC
Confidence 4688999888544
No 128
>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=21.36 E-value=31 Score=24.00 Aligned_cols=28 Identities=21% Similarity=0.463 Sum_probs=18.1
Q ss_pred EECCCCCCccceeeeecccCC-CCCeeec
Q 039226 80 LQCMGCKARLGSFNWAGLQCS-CGAWATP 107 (121)
Q Consensus 80 L~CPkC~~kLG~f~w~G~qCs-CG~wv~P 107 (121)
=.|..|...+|-..-.|..|. |+..|-.
T Consensus 55 ~~C~~C~~~fg~l~~~~~~C~~C~~~VC~ 83 (118)
T PF02318_consen 55 RHCARCGKPFGFLFNRGRVCVDCKHRVCK 83 (118)
T ss_dssp SB-TTTS-BCSCTSTTCEEETTTTEEEET
T ss_pred cchhhhCCcccccCCCCCcCCcCCccccC
Confidence 378889998886655688884 6666644
No 129
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=21.11 E-value=62 Score=21.66 Aligned_cols=20 Identities=30% Similarity=0.481 Sum_probs=17.7
Q ss_pred ceeEECCCCCCccceeeeec
Q 039226 77 GEKLQCMGCKARLGSFNWAG 96 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w~G 96 (121)
.|-|.|--|.-|||-|++..
T Consensus 17 ~~~~~C~~C~Rr~GLW~f~~ 36 (91)
T PF08600_consen 17 LGLLSCSYCFRRLGLWMFKS 36 (91)
T ss_pred cCeEEccccCcEeeeeeccc
Confidence 46899999999999999964
No 130
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=21.05 E-value=44 Score=19.06 Aligned_cols=10 Identities=30% Similarity=0.773 Sum_probs=8.1
Q ss_pred ECCCCCCccc
Q 039226 81 QCMGCKARLG 90 (121)
Q Consensus 81 ~CPkC~~kLG 90 (121)
.||.|++.|.
T Consensus 4 ~C~~Cg~~l~ 13 (47)
T PF13005_consen 4 ACPDCGGELK 13 (47)
T ss_pred cCCCCCceee
Confidence 5888998885
No 131
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=20.51 E-value=25 Score=23.50 Aligned_cols=18 Identities=39% Similarity=0.851 Sum_probs=12.3
Q ss_pred eEecccccccccCCCCeee
Q 039226 14 IYRCKKCRRLVASEENIVP 32 (121)
Q Consensus 14 ~yrCrKCR~~Lf~~~~ii~ 32 (121)
.=+|+||.+.| .....+|
T Consensus 54 s~pC~~C~klL-~~~~~LP 71 (90)
T PF11571_consen 54 STPCKKCGKLL-SSKAFLP 71 (90)
T ss_pred cchhhHHHhHh-hhcccCC
Confidence 34799999999 4344444
No 132
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=20.43 E-value=84 Score=24.30 Aligned_cols=38 Identities=21% Similarity=0.510 Sum_probs=27.1
Q ss_pred ceeEECCCCCCccceeeeec------ccCC-CCCeeeceEEEecCCcc
Q 039226 77 GEKLQCMGCKARLGSFNWAG------LQCS-CGAWATPAFQLHKSRLD 117 (121)
Q Consensus 77 ~GKL~CPkC~~kLG~f~w~G------~qCs-CG~wv~Paf~l~kskVD 117 (121)
-.++.|.+|+.. |.+.. ..|+ ||..+.|.+-+.-.-++
T Consensus 120 ~~~~~C~~C~~~---~~~~~~~~~~~p~C~~Cgg~lrP~Vv~fge~~~ 164 (242)
T PRK00481 120 LLRARCTKCGQT---YDLDEYLKPEPPRCPKCGGILRPDVVLFGEMLP 164 (242)
T ss_pred cCceeeCCCCCC---cChhhhccCCCCCCCCCCCccCCCeEECCCCCC
Confidence 457889999654 44431 3596 99999999988766553
No 133
>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=20.17 E-value=74 Score=19.49 Aligned_cols=14 Identities=29% Similarity=0.634 Sum_probs=9.3
Q ss_pred CCCCeeEecccccc
Q 039226 9 ANPQAIYRCKKCRR 22 (121)
Q Consensus 9 ~~~~~~yrCrKCR~ 22 (121)
+-+.+.|+|..|+.
T Consensus 39 ~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 39 EFEEIQYRCPYCGA 52 (54)
T ss_pred cCCceEEEcCCCCC
Confidence 34556788887764
No 134
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=20.13 E-value=41 Score=18.92 Aligned_cols=26 Identities=27% Similarity=0.547 Sum_probs=16.9
Q ss_pred EECCCCCCccceeeeecccCC-CCCee
Q 039226 80 LQCMGCKARLGSFNWAGLQCS-CGAWA 105 (121)
Q Consensus 80 L~CPkC~~kLG~f~w~G~qCs-CG~wv 105 (121)
..|--|+..|....-.|.+|+ |+..+
T Consensus 12 ~~C~~C~~~i~~~~~~~~~C~~C~~~~ 38 (50)
T cd00029 12 TFCDVCRKSIWGLFKQGLRCSWCKVKC 38 (50)
T ss_pred CChhhcchhhhccccceeEcCCCCCch
Confidence 346668887766544677886 66544
Done!