Query 034411
Match_columns 95
No_of_seqs 109 out of 267
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 02:34:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034411.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034411hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3475 60S ribosomal protein 100.0 1.4E-59 2.9E-64 323.5 2.2 92 1-92 1-92 (92)
2 PTZ00073 60S ribosomal protein 100.0 2.2E-58 4.7E-63 317.6 3.8 90 1-90 1-90 (91)
3 PRK04179 rpl37e 50S ribosomal 100.0 2.7E-36 6E-41 196.1 2.3 57 1-57 1-59 (62)
4 PF01907 Ribosomal_L37e: Ribos 100.0 2.6E-36 5.7E-41 192.3 -0.1 54 2-55 1-55 (55)
5 COG2126 RPL37A Ribosomal prote 100.0 4.7E-35 1E-39 189.8 2.2 60 1-60 1-61 (61)
6 COG1998 RPS31 Ribosomal protei 93.5 0.029 6.4E-07 35.7 0.6 26 15-40 18-46 (51)
7 PF14599 zinc_ribbon_6: Zinc-r 90.9 0.083 1.8E-06 34.1 0.4 27 12-38 26-55 (61)
8 PRK00432 30S ribosomal protein 89.6 0.18 3.9E-06 31.0 1.1 26 15-40 19-46 (50)
9 PF01783 Ribosomal_L32p: Ribos 87.9 0.33 7.1E-06 30.1 1.5 23 15-39 25-47 (56)
10 PF13248 zf-ribbon_3: zinc-rib 87.6 0.31 6.6E-06 26.0 1.0 23 17-40 3-25 (26)
11 PF01599 Ribosomal_S27: Riboso 83.0 0.48 1E-05 29.4 0.5 26 14-39 16-46 (47)
12 COG0675 Transposase and inacti 80.6 0.77 1.7E-05 33.6 0.9 25 14-40 307-331 (364)
13 smart00661 RPOL9 RNA polymeras 80.6 0.87 1.9E-05 26.5 1.0 23 18-40 2-29 (52)
14 TIGR01031 rpmF_bact ribosomal 79.5 0.9 1.9E-05 28.4 0.8 24 14-39 24-47 (55)
15 PF12773 DZR: Double zinc ribb 76.4 2.6 5.7E-05 24.4 2.2 32 9-40 5-38 (50)
16 PHA00626 hypothetical protein 72.6 2 4.4E-05 28.1 1.1 23 18-40 2-32 (59)
17 PF09297 zf-NADH-PPase: NADH p 72.5 1.4 3.1E-05 24.1 0.4 25 15-39 2-29 (32)
18 PRK12286 rpmF 50S ribosomal pr 71.0 2.2 4.7E-05 27.0 0.9 24 14-39 25-48 (57)
19 PRK05978 hypothetical protein; 70.0 2.7 5.9E-05 31.2 1.4 29 17-45 34-66 (148)
20 PF09538 FYDLN_acid: Protein o 69.8 2.6 5.6E-05 29.6 1.2 24 16-39 9-34 (108)
21 PF13240 zinc_ribbon_2: zinc-r 69.4 2.7 5.9E-05 22.1 1.0 21 19-40 2-22 (23)
22 PRK14892 putative transcriptio 69.3 2.7 6E-05 29.2 1.3 59 14-90 19-85 (99)
23 COG1571 Predicted DNA-binding 68.2 3.7 8E-05 35.2 2.0 26 16-41 350-377 (421)
24 PRK12496 hypothetical protein; 66.0 3.6 7.8E-05 30.2 1.4 29 17-46 128-158 (164)
25 TIGR02300 FYDLN_acid conserved 65.2 3.9 8.4E-05 30.2 1.4 24 16-39 9-34 (129)
26 PF12760 Zn_Tnp_IS1595: Transp 64.7 4.3 9.2E-05 23.8 1.3 24 16-39 18-45 (46)
27 PRK05508 methionine sulfoxide 62.1 4.9 0.00011 29.1 1.5 28 14-41 31-58 (119)
28 PF04060 FeS: Putative Fe-S cl 62.0 3.8 8.2E-05 23.4 0.7 13 29-41 2-14 (35)
29 PRK00420 hypothetical protein; 60.5 4.7 0.0001 28.7 1.1 25 16-40 23-49 (112)
30 KOG0856 Predicted pilin-like t 57.9 8.2 0.00018 29.1 2.1 39 3-41 36-79 (146)
31 PF08271 TF_Zn_Ribbon: TFIIB z 57.9 5.6 0.00012 22.9 1.0 22 18-39 2-27 (43)
32 KOG3362 Predicted BBOX Zn-fing 57.5 5 0.00011 30.5 0.9 21 22-42 109-129 (156)
33 PRK13130 H/ACA RNA-protein com 57.2 6.3 0.00014 25.1 1.2 20 18-40 7-26 (56)
34 COG0333 RpmF Ribosomal protein 56.3 6.4 0.00014 25.3 1.1 23 16-40 27-49 (57)
35 PF09855 DUF2082: Nucleic-acid 56.0 5.9 0.00013 25.6 0.9 8 33-40 38-45 (64)
36 PF10571 UPF0547: Uncharacteri 53.1 8.8 0.00019 20.8 1.2 22 18-40 2-23 (26)
37 TIGR00357 methionine-R-sulfoxi 51.8 15 0.00032 27.0 2.5 28 14-41 38-65 (134)
38 PF12172 DUF35_N: Rubredoxin-l 51.5 6.5 0.00014 21.9 0.5 22 16-38 11-32 (37)
39 COG0229 Conserved domain frequ 47.5 11 0.00024 28.2 1.3 26 16-41 42-67 (140)
40 PRK05580 primosome assembly pr 47.1 12 0.00027 32.7 1.8 27 14-40 379-417 (679)
41 TIGR00269 conserved hypothetic 47.0 9.8 0.00021 25.6 0.9 12 31-42 80-91 (104)
42 PF10555 MraY_sig1: Phospho-N- 46.7 9.4 0.0002 18.4 0.6 7 3-9 2-8 (13)
43 TIGR02098 MJ0042_CXXC MJ0042 f 46.5 8.7 0.00019 21.2 0.5 24 16-40 2-34 (38)
44 COG5349 Uncharacterized protei 46.2 9.3 0.0002 28.2 0.7 25 15-39 20-48 (126)
45 COG1545 Predicted nucleic-acid 46.1 11 0.00024 27.0 1.1 27 14-41 27-53 (140)
46 COG1439 Predicted nucleic acid 45.3 12 0.00025 28.8 1.2 33 14-47 137-169 (177)
47 PF12387 Peptidase_C74: Pestiv 45.1 12 0.00026 29.4 1.2 26 12-39 158-183 (200)
48 PHA02942 putative transposase; 44.2 12 0.00026 30.8 1.2 26 15-40 324-351 (383)
49 PF13824 zf-Mss51: Zinc-finger 43.9 16 0.00034 23.4 1.5 24 18-41 1-24 (55)
50 PRK00241 nudC NADH pyrophospha 43.3 12 0.00027 29.0 1.1 26 14-39 97-125 (256)
51 TIGR00311 aIF-2beta translatio 42.9 10 0.00022 27.4 0.6 26 15-40 96-127 (133)
52 PF01641 SelR: SelR domain; I 42.2 18 0.00039 26.2 1.7 31 11-41 32-62 (124)
53 PF03604 DNA_RNApol_7kD: DNA d 41.7 22 0.00047 20.2 1.7 23 18-40 2-26 (32)
54 PRK00222 methionine sulfoxide 41.4 26 0.00056 26.0 2.5 28 14-41 41-68 (142)
55 PRK08329 threonine synthase; V 41.4 22 0.00047 28.3 2.2 66 17-87 2-69 (347)
56 PRK06450 threonine synthase; V 40.5 16 0.00034 29.3 1.3 24 16-40 3-27 (338)
57 PRK00398 rpoP DNA-directed RNA 40.3 17 0.00036 21.1 1.1 24 17-40 4-30 (46)
58 PRK11823 DNA repair protein Ra 39.8 17 0.00036 30.3 1.4 26 13-39 4-29 (446)
59 PRK01110 rpmF 50S ribosomal pr 39.7 15 0.00032 23.3 0.9 21 16-39 27-47 (60)
60 PF05191 ADK_lid: Adenylate ki 39.7 17 0.00037 20.9 1.0 21 18-39 3-29 (36)
61 PRK14018 trifunctional thiored 39.2 17 0.00037 31.6 1.4 29 13-41 415-443 (521)
62 KOG4192 Uncharacterized conser 39.0 14 0.0003 27.5 0.7 24 8-32 66-89 (134)
63 PF07282 OrfB_Zn_ribbon: Putat 38.6 17 0.00037 22.1 1.0 25 15-39 27-54 (69)
64 PF10892 DUF2688: Protein of u 38.1 11 0.00023 24.8 0.0 16 14-29 8-23 (60)
65 COG1592 Rubrerythrin [Energy p 37.8 19 0.0004 27.3 1.3 28 16-43 134-161 (166)
66 PF10217 DUF2039: Uncharacteri 37.6 6.8 0.00015 27.3 -1.0 26 16-41 55-91 (92)
67 PRK03681 hypA hydrogenase nick 37.6 18 0.00039 25.1 1.1 37 3-40 53-96 (114)
68 COG1594 RPB9 DNA-directed RNA 37.6 16 0.00034 25.6 0.8 23 17-39 3-30 (113)
69 smart00834 CxxC_CXXC_SSSS Puta 37.5 26 0.00057 19.1 1.6 24 17-40 6-35 (41)
70 PRK14559 putative protein seri 36.7 27 0.00058 31.2 2.2 29 9-40 8-36 (645)
71 PF09082 DUF1922: Domain of un 36.5 12 0.00025 25.0 0.0 22 17-40 4-28 (68)
72 COG3677 Transposase and inacti 36.0 22 0.00049 25.3 1.4 24 14-39 28-61 (129)
73 CHL00174 accD acetyl-CoA carbo 35.9 13 0.00028 30.4 0.1 31 15-45 37-74 (296)
74 PF10013 DUF2256: Uncharacteri 35.8 13 0.00028 22.8 0.1 21 28-54 5-25 (42)
75 TIGR00515 accD acetyl-CoA carb 35.2 19 0.0004 28.9 1.0 26 15-40 25-54 (285)
76 PRK12380 hydrogenase nickel in 35.0 21 0.00046 24.6 1.1 37 3-40 53-95 (113)
77 PRK12336 translation initiatio 34.9 16 0.00035 27.6 0.5 33 15-47 97-137 (201)
78 PF02150 RNA_POL_M_15KD: RNA p 34.5 22 0.00048 20.1 1.0 23 17-39 2-28 (35)
79 PRK14873 primosome assembly pr 34.2 23 0.0005 31.4 1.4 24 12-38 405-429 (665)
80 TIGR01384 TFS_arch transcripti 34.2 21 0.00045 23.5 0.9 23 18-40 2-25 (104)
81 PRK04136 rpl40e 50S ribosomal 34.1 24 0.00051 22.2 1.1 22 17-39 15-36 (48)
82 cd07153 Fur_like Ferric uptake 32.5 19 0.00042 23.4 0.5 14 13-26 70-83 (116)
83 cd00729 rubredoxin_SM Rubredox 32.2 30 0.00066 19.4 1.3 27 17-43 3-30 (34)
84 COG2816 NPY1 NTP pyrophosphohy 32.2 23 0.00049 28.9 1.0 27 13-39 108-137 (279)
85 PRK05550 bifunctional methioni 32.0 39 0.00085 27.4 2.3 29 13-41 33-61 (283)
86 PRK04351 hypothetical protein; 31.8 24 0.00052 25.8 1.0 22 17-38 113-139 (149)
87 COG2260 Predicted Zn-ribbon RN 31.7 25 0.00055 22.9 1.0 20 17-39 6-25 (59)
88 smart00653 eIF2B_5 domain pres 30.9 19 0.00041 25.2 0.3 25 15-39 79-109 (110)
89 smart00547 ZnF_RBZ Zinc finger 30.8 31 0.00068 17.5 1.1 22 18-40 4-25 (26)
90 PRK05654 acetyl-CoA carboxylas 30.8 19 0.00042 28.9 0.4 26 15-40 26-55 (292)
91 TIGR00100 hypA hydrogenase nic 30.6 29 0.00062 24.0 1.2 38 3-41 53-96 (115)
92 smart00659 RPOLCX RNA polymera 30.1 30 0.00065 20.6 1.1 23 18-40 4-28 (44)
93 PF07503 zf-HYPF: HypF finger; 30.0 29 0.00062 20.0 0.9 15 24-38 14-28 (35)
94 PF04216 FdhE: Protein involve 29.3 27 0.00059 27.1 1.0 58 15-73 196-254 (290)
95 PF14787 zf-CCHC_5: GAG-polypr 29.0 28 0.00061 20.7 0.8 12 16-27 2-13 (36)
96 PF06869 DUF1258: Protein of u 28.2 21 0.00045 29.0 0.1 23 13-37 15-37 (258)
97 PRK09462 fur ferric uptake reg 28.0 25 0.00054 24.5 0.5 13 14-26 88-100 (148)
98 TIGR00375 conserved hypothetic 27.8 35 0.00077 28.5 1.5 30 6-40 233-267 (374)
99 PF14653 IGFL: Insulin growth 27.7 30 0.00064 24.1 0.8 32 16-47 10-45 (89)
100 PRK08764 ferredoxin; Provision 27.5 31 0.00068 24.1 1.0 13 28-40 14-26 (135)
101 TIGR00595 priA primosomal prot 27.3 30 0.00065 29.3 0.9 24 16-39 213-248 (505)
102 PF06221 zf-C2HC5: Putative zi 26.7 54 0.0012 20.9 1.8 33 8-40 8-44 (57)
103 TIGR00416 sms DNA repair prote 26.5 36 0.00078 28.6 1.3 26 13-39 4-29 (454)
104 PRK03988 translation initiatio 26.4 29 0.00062 25.2 0.6 26 15-40 101-132 (138)
105 PF14803 Nudix_N_2: Nudix N-te 26.2 24 0.00053 20.2 0.2 8 32-39 23-30 (34)
106 PRK14714 DNA polymerase II lar 25.8 36 0.00078 33.3 1.3 21 17-40 668-688 (1337)
107 PF01873 eIF-5_eIF-2B: Domain 25.8 26 0.00055 25.0 0.2 25 15-39 92-122 (125)
108 TIGR01562 FdhE formate dehydro 25.7 62 0.0013 26.4 2.5 58 12-73 206-268 (305)
109 PRK00564 hypA hydrogenase nick 25.7 40 0.00088 23.4 1.2 28 13-41 68-98 (117)
110 COG1645 Uncharacterized Zn-fin 25.6 35 0.00075 25.1 0.9 26 15-40 27-53 (131)
111 PRK06991 ferredoxin; Provision 25.3 36 0.00078 27.1 1.0 12 29-40 15-26 (270)
112 PF01475 FUR: Ferric uptake re 24.5 29 0.00064 23.0 0.3 13 13-25 77-89 (120)
113 KOG3241 Uncharacterized conser 24.3 9.9 0.00022 30.2 -2.2 20 15-39 82-101 (227)
114 COG2878 Predicted NADH:ubiquin 24.2 37 0.00081 26.7 0.9 12 30-41 45-56 (198)
115 PF03858 Crust_neuro_H: Crusta 23.7 21 0.00046 21.9 -0.4 17 56-72 1-17 (41)
116 PRK06260 threonine synthase; V 23.1 48 0.001 26.8 1.4 24 16-40 3-28 (397)
117 PF08772 NOB1_Zn_bind: Nin one 23.0 42 0.00091 22.2 0.9 24 18-41 11-34 (73)
118 PTZ00255 60S ribosomal protein 23.0 42 0.0009 23.3 0.9 23 17-39 37-62 (90)
119 KOG2767 Translation initiation 22.0 39 0.00084 29.1 0.7 25 16-40 96-127 (400)
120 PRK04165 acetyl-CoA decarbonyl 21.9 45 0.00097 28.6 1.0 12 29-40 12-23 (450)
121 TIGR00280 L37a ribosomal prote 21.7 44 0.00095 23.2 0.8 23 17-39 36-61 (91)
122 COG0777 AccD Acetyl-CoA carbox 21.0 40 0.00087 28.0 0.6 26 14-39 26-55 (294)
123 PF08536 Whirly: Whirly transc 20.8 39 0.00084 25.2 0.4 14 40-53 40-53 (139)
124 PRK07218 replication factor A; 20.7 52 0.0011 28.0 1.2 23 15-40 296-318 (423)
125 PF03367 zf-ZPR1: ZPR1 zinc-fi 20.6 38 0.00083 24.9 0.3 29 17-45 2-44 (161)
126 PF09862 DUF2089: Protein of u 20.4 44 0.00095 23.9 0.6 20 19-39 1-20 (113)
127 COG4888 Uncharacterized Zn rib 20.3 45 0.00098 23.9 0.6 25 15-39 21-54 (104)
No 1
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.4e-59 Score=323.47 Aligned_cols=92 Identities=70% Similarity=1.194 Sum_probs=89.8
Q ss_pred CCCCCCCCCCCCCCcccccccCCCcccccccCccccccccccccccCCccccccccccccccccccccchhhhhccCcCc
Q 034411 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKYNWSVKAIRRKTTGTGRMRYLRHVPRRFKSNFRE 80 (95)
Q Consensus 1 MtKGT~SfGKr~~ktH~lCrRCG~~syH~qK~~Ca~CGyps~k~R~YnWs~Ka~rr~ttGTGrmr~lk~v~rrfkngfre 80 (95)
|+|||+||||+|+|+|+||+|||++||||||++|++||||++++|+||||+||+||+|||||||||||+|+|||+|||||
T Consensus 1 MtKGT~sFGKr~nkshtlC~RCG~~syH~QKstC~~CGYpaak~R~ynws~KAkRR~TtGTGrMr~lk~v~rrfrnGfre 80 (92)
T KOG3475|consen 1 MTKGTSSFGKRHNKSHTLCRRCGRRSYHIQKSTCSSCGYPAAKKRSYNWSAKAKRRRTTGTGRMRYLKIVYRRFRNGFRE 80 (92)
T ss_pred CCCcccchhhccccchHHHHHhCchhhhhhcccccccCCcchhccCCCcchhhhhccccccchhHHHHHHHHHHhccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCccccccc
Q 034411 81 GTEAAPRKKNVA 92 (95)
Q Consensus 81 Gt~~~~~~~~~~ 92 (95)
|++|+|+.++++
T Consensus 81 gt~~k~k~a~~~ 92 (92)
T KOG3475|consen 81 GTTAKPKAAAAA 92 (92)
T ss_pred CCccCccccccC
Confidence 999999987653
No 2
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=100.00 E-value=2.2e-58 Score=317.63 Aligned_cols=90 Identities=69% Similarity=1.238 Sum_probs=88.4
Q ss_pred CCCCCCCCCCCCCCcccccccCCCcccccccCccccccccccccccCCccccccccccccccccccccchhhhhccCcCc
Q 034411 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKYNWSVKAIRRKTTGTGRMRYLRHVPRRFKSNFRE 80 (95)
Q Consensus 1 MtKGT~SfGKr~~ktH~lCrRCG~~syH~qK~~Ca~CGyps~k~R~YnWs~Ka~rr~ttGTGrmr~lk~v~rrfkngfre 80 (95)
|+|||+||||+|+||||||+|||++|||+||++||+||||++++|+|||+.||++|+|||||||||||+|+|||+|||||
T Consensus 1 MtKGT~SfGKr~~ktHtlCrRCG~~syH~qK~~CasCGypsak~R~YnWs~Ka~rr~ttGtGrmr~lk~v~rrf~ngfre 80 (91)
T PTZ00073 1 MTKGTGSFGKRHGKTHTLCRRCGKRSFHVQKKRCASCGYPSAKMRRYNWSVKAKRRRTTGTGRCRYLKTVARRAKNGFRE 80 (91)
T ss_pred CCCCCcccccccCcCcchhcccCccccccccccchhcCCchhhccccchhhhhccccCCccchhHHHHHHHHHHhcCccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCccccc
Q 034411 81 GTEAAPRKKN 90 (95)
Q Consensus 81 Gt~~~~~~~~ 90 (95)
||+|+|++++
T Consensus 81 gt~~~~~~~~ 90 (91)
T PTZ00073 81 GTKAKPKVKA 90 (91)
T ss_pred CCccccccCC
Confidence 9999998765
No 3
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=100.00 E-value=2.7e-36 Score=196.08 Aligned_cols=57 Identities=46% Similarity=0.982 Sum_probs=54.7
Q ss_pred CCCCCCCCCCCCCC-cccccccCCCcccccccCccccccc-cccccccCCccccccccc
Q 034411 1 MGKGTGSFGKRRNK-THTLCVRCGRRSFHIQKSRCSACAY-PAARVRKYNWSVKAIRRK 57 (95)
Q Consensus 1 MtKGT~SfGKr~~k-tH~lCrRCG~~syH~qK~~Ca~CGy-ps~k~R~YnWs~Ka~rr~ 57 (95)
|+|||+||||||++ |||+|||||++|||+||++|++||| |++++|+|||+.||+.+.
T Consensus 1 MtKGT~SfGKr~~k~tHt~CrRCG~~syh~qK~~CasCGygps~k~R~YnWs~Ka~~~~ 59 (62)
T PRK04179 1 MSKGTPSMGKRNKGKTHIRCRRCGRHSYNVRKKYCAACGFGRSKRIRRYSWQNKKVNGK 59 (62)
T ss_pred CCCCCcccccccCCcccchhcccCcccccccccchhhcCCCcccccccccHHHHhhccc
Confidence 99999999999997 9999999999999999999999999 999999999999997653
No 4
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=100.00 E-value=2.6e-36 Score=192.28 Aligned_cols=54 Identities=74% Similarity=1.318 Sum_probs=46.0
Q ss_pred CCCCCCCCCCCCCcccccccCCCcccccccCccccccccccccc-cCCccccccc
Q 034411 2 GKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVR-KYNWSVKAIR 55 (95)
Q Consensus 2 tKGT~SfGKr~~ktH~lCrRCG~~syH~qK~~Ca~CGyps~k~R-~YnWs~Ka~r 55 (95)
|||||||||+|++|||||+|||++|||+||++||+||||++++| +|||+.||+|
T Consensus 1 tKGT~S~Gkr~~ktH~~CrRCG~~syH~qK~~CasCGyp~~kkrr~ynWs~Ka~r 55 (55)
T PF01907_consen 1 TKGTSSFGKRHNKTHTLCRRCGRRSYHIQKKTCASCGYPAAKKRRKYNWSAKAKR 55 (55)
T ss_dssp -TTHHHHTTS-S-SEEE-TTTSSEEEETTTTEETTTBTTTSSS----SSSSHHHH
T ss_pred CCCCCCccccCCccEeeecccCCeeeecCCCcccccCCCcccccccccchhhhcC
Confidence 69999999999999999999999999999999999999999999 9999999975
No 5
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.7e-35 Score=189.80 Aligned_cols=60 Identities=60% Similarity=1.128 Sum_probs=58.3
Q ss_pred CCCCCCCCCCCCCCcccccccCCCcccccccCcccccccc-ccccccCCcccccccccccc
Q 034411 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHIQKSRCSACAYP-AARVRKYNWSVKAIRRKTTG 60 (95)
Q Consensus 1 MtKGT~SfGKr~~ktH~lCrRCG~~syH~qK~~Ca~CGyp-s~k~R~YnWs~Ka~rr~ttG 60 (95)
|+||||||||+|+++||+|||||++|||+||++|++|||| ++++|+|+|+.|+++++++|
T Consensus 1 MskGT~S~GKrnk~tH~~CRRCGr~syhv~k~~CaaCGfgrs~r~R~y~W~~K~~~r~~~~ 61 (61)
T COG2126 1 MSKGTPSFGKRNKKTHIRCRRCGRRSYHVRKKYCAACGFGRSARMRSYNWQAKKKRRKTIG 61 (61)
T ss_pred CCCCCccccccCCcceehhhhccchheeeccceecccCCCCccccccchhhhhhhcCeecC
Confidence 9999999999999999999999999999999999999998 99999999999999998865
No 6
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=93.48 E-value=0.029 Score=35.69 Aligned_cols=26 Identities=31% Similarity=0.828 Sum_probs=21.9
Q ss_pred cccccccCCC---cccccccCcccccccc
Q 034411 15 THTLCVRCGR---RSFHIQKSRCSACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~---~syH~qK~~Ca~CGyp 40 (95)
-.-.|.|||- -+.|.....|+.|||-
T Consensus 18 k~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 18 KNRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred ccccCCCCCCcchhhhcCceeEeccccce
Confidence 4568999996 5679999999999995
No 7
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=90.86 E-value=0.083 Score=34.06 Aligned_cols=27 Identities=37% Similarity=0.874 Sum_probs=15.6
Q ss_pred CCCcccccccCCCcc---cccccCcccccc
Q 034411 12 RNKTHTLCVRCGRRS---FHIQKSRCSACA 38 (95)
Q Consensus 12 ~~ktH~lCrRCG~~s---yH~qK~~Ca~CG 38 (95)
+.+..|+|.-|+.+| ||+=-..|..||
T Consensus 26 ~~~v~IlCNDC~~~s~v~fH~lg~KC~~C~ 55 (61)
T PF14599_consen 26 NKKVWILCNDCNAKSEVPFHFLGHKCSHCG 55 (61)
T ss_dssp --EEEEEESSS--EEEEE--TT----TTTS
T ss_pred CCEEEEECCCCCCccceeeeHhhhcCCCCC
Confidence 346899999999875 999999999999
No 8
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=89.63 E-value=0.18 Score=31.03 Aligned_cols=26 Identities=31% Similarity=0.926 Sum_probs=20.8
Q ss_pred cccccccCCC--cccccccCcccccccc
Q 034411 15 THTLCVRCGR--RSFHIQKSRCSACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~--~syH~qK~~Ca~CGyp 40 (95)
+...|++||+ -+-|.....|++|||.
T Consensus 19 ~~~fCP~Cg~~~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 19 KNKFCPRCGSGFMAEHLDRWHCGKCGYT 46 (50)
T ss_pred ccCcCcCCCcchheccCCcEECCCcCCE
Confidence 5668999998 4456667899999984
No 9
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=87.88 E-value=0.33 Score=30.13 Aligned_cols=23 Identities=26% Similarity=0.803 Sum_probs=20.8
Q ss_pred cccccccCCCcccccccCccccccc
Q 034411 15 THTLCVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK~~Ca~CGy 39 (95)
.-+.|.-|| .+++.+..|.+|||
T Consensus 25 ~l~~c~~cg--~~~~~H~vc~~cG~ 47 (56)
T PF01783_consen 25 NLVKCPNCG--EPKLPHRVCPSCGY 47 (56)
T ss_dssp SEEESSSSS--SEESTTSBCTTTBB
T ss_pred ceeeeccCC--CEecccEeeCCCCe
Confidence 557899999 79999999999997
No 10
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=87.55 E-value=0.31 Score=26.04 Aligned_cols=23 Identities=22% Similarity=0.668 Sum_probs=19.1
Q ss_pred cccccCCCcccccccCcccccccc
Q 034411 17 TLCVRCGRRSFHIQKSRCSACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~syH~qK~~Ca~CGyp 40 (95)
+.|..||. .-...-..|..||.+
T Consensus 3 ~~Cp~Cg~-~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGA-EIDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCC-cCCcccccChhhCCC
Confidence 57999999 677888899999964
No 11
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=83.03 E-value=0.48 Score=29.42 Aligned_cols=26 Identities=31% Similarity=0.814 Sum_probs=20.7
Q ss_pred Ccccccc--cCCC---cccccccCccccccc
Q 034411 14 KTHTLCV--RCGR---RSFHIQKSRCSACAY 39 (95)
Q Consensus 14 ktH~lCr--RCG~---~syH~qK~~Ca~CGy 39 (95)
..+-.|. +||. -+-|.....|++|||
T Consensus 16 r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 16 RLRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp ESSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred EhhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 4677899 9999 478999999999997
No 12
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=80.64 E-value=0.77 Score=33.55 Aligned_cols=25 Identities=24% Similarity=0.646 Sum_probs=20.9
Q ss_pred CcccccccCCCcccccccCcccccccc
Q 034411 14 KTHTLCVRCGRRSFHIQKSRCSACAYP 40 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qK~~Ca~CGyp 40 (95)
-|-..|..||. .+.+.-.|..||+-
T Consensus 307 ~tS~~C~~cg~--~~~r~~~C~~cg~~ 331 (364)
T COG0675 307 YTSKTCPCCGH--LSGRLFKCPRCGFV 331 (364)
T ss_pred CCcccccccCC--ccceeEECCCCCCe
Confidence 35678999999 77778899999983
No 13
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=80.63 E-value=0.87 Score=26.48 Aligned_cols=23 Identities=26% Similarity=0.820 Sum_probs=18.8
Q ss_pred ccccCCCcccccc-----cCcccccccc
Q 034411 18 LCVRCGRRSFHIQ-----KSRCSACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~q-----K~~Ca~CGyp 40 (95)
.|..||...|... ...|..|||-
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCe
Confidence 5899999998874 3579999984
No 14
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=79.52 E-value=0.9 Score=28.42 Aligned_cols=24 Identities=33% Similarity=0.995 Sum_probs=20.8
Q ss_pred CcccccccCCCcccccccCccccccc
Q 034411 14 KTHTLCVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qK~~Ca~CGy 39 (95)
...+.|.-||. +++....|..|||
T Consensus 24 p~l~~C~~cG~--~~~~H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGE--FKLPHRVCPSCGY 47 (55)
T ss_pred CcceECCCCCC--cccCeeECCccCe
Confidence 34567999997 8999999999997
No 15
>PF12773 DZR: Double zinc ribbon
Probab=76.36 E-value=2.6 Score=24.44 Aligned_cols=32 Identities=22% Similarity=0.510 Sum_probs=24.3
Q ss_pred CCCCCCcccccccCCCccc--ccccCcccccccc
Q 034411 9 GKRRNKTHTLCVRCGRRSF--HIQKSRCSACAYP 40 (95)
Q Consensus 9 GKr~~ktH~lCrRCG~~sy--H~qK~~Ca~CGyp 40 (95)
|..+...-..|..||.... ......|..||.+
T Consensus 5 g~~~~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 5 GTPNPDDAKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred CCcCCccccCChhhcCChhhccCCCCCCcCCcCC
Confidence 3444555678889999888 7777889999985
No 16
>PHA00626 hypothetical protein
Probab=72.61 E-value=2 Score=28.07 Aligned_cols=23 Identities=26% Similarity=0.781 Sum_probs=17.5
Q ss_pred ccccCCCccccc--------ccCcccccccc
Q 034411 18 LCVRCGRRSFHI--------QKSRCSACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~--------qK~~Ca~CGyp 40 (95)
+|+.||+..... |--.|-.|||-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ 32 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYN 32 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCe
Confidence 689999964433 66789999984
No 17
>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=72.54 E-value=1.4 Score=24.15 Aligned_cols=25 Identities=32% Similarity=0.801 Sum_probs=13.0
Q ss_pred cccccccCCCccccccc---Cccccccc
Q 034411 15 THTLCVRCGRRSFHIQK---SRCSACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK---~~Ca~CGy 39 (95)
+|-.|-+||....-.+. .+|.+||.
T Consensus 2 ~~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 2 NHRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TTSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CCcccCcCCccccCCCCcCEeECCCCcC
Confidence 56677888877665554 45666663
No 18
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=70.97 E-value=2.2 Score=26.97 Aligned_cols=24 Identities=25% Similarity=0.732 Sum_probs=19.8
Q ss_pred CcccccccCCCcccccccCccccccc
Q 034411 14 KTHTLCVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qK~~Ca~CGy 39 (95)
..-+.|..||. +++....|..|||
T Consensus 25 ~~l~~C~~CG~--~~~~H~vC~~CG~ 48 (57)
T PRK12286 25 PGLVECPNCGE--PKLPHRVCPSCGY 48 (57)
T ss_pred CcceECCCCCC--ccCCeEECCCCCc
Confidence 34567999995 7888999999998
No 19
>PRK05978 hypothetical protein; Provisional
Probab=69.95 E-value=2.7 Score=31.15 Aligned_cols=29 Identities=28% Similarity=0.596 Sum_probs=22.4
Q ss_pred cccccCCCc----ccccccCccccccccccccc
Q 034411 17 TLCVRCGRR----SFHIQKSRCSACAYPAARVR 45 (95)
Q Consensus 17 ~lCrRCG~~----syH~qK~~Ca~CGyps~k~R 45 (95)
-.|.+||+- .|-.-...|+.||.+=..-|
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDFTHHR 66 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCccccCC
Confidence 479999984 56889999999997644333
No 20
>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=69.77 E-value=2.6 Score=29.58 Aligned_cols=24 Identities=25% Similarity=0.809 Sum_probs=20.5
Q ss_pred ccccccCCCcccccccC--ccccccc
Q 034411 16 HTLCVRCGRRSFHIQKS--RCSACAY 39 (95)
Q Consensus 16 H~lCrRCG~~syH~qK~--~Ca~CGy 39 (95)
--+|.-||.+-|-|+|. +|..||.
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~ 34 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGT 34 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCC
Confidence 34799999999999884 6999996
No 21
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=69.44 E-value=2.7 Score=22.12 Aligned_cols=21 Identities=29% Similarity=0.716 Sum_probs=13.8
Q ss_pred cccCCCcccccccCcccccccc
Q 034411 19 CVRCGRRSFHIQKSRCSACAYP 40 (95)
Q Consensus 19 CrRCG~~syH~qK~~Ca~CGyp 40 (95)
|..||...= ..-..|..||.|
T Consensus 2 Cp~CG~~~~-~~~~fC~~CG~~ 22 (23)
T PF13240_consen 2 CPNCGAEIE-DDAKFCPNCGTP 22 (23)
T ss_pred CcccCCCCC-CcCcchhhhCCc
Confidence 677777653 445568888864
No 22
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=69.31 E-value=2.7 Score=29.23 Aligned_cols=59 Identities=22% Similarity=0.357 Sum_probs=38.0
Q ss_pred CcccccccCCCcccccc--------cCccccccccccccccCCccccccccccccccccccccchhhhhccCcCcCCCCC
Q 034411 14 KTHTLCVRCGRRSFHIQ--------KSRCSACAYPAARVRKYNWSVKAIRRKTTGTGRMRYLRHVPRRFKSNFREGTEAA 85 (95)
Q Consensus 14 ktH~lCrRCG~~syH~q--------K~~Ca~CGyps~k~R~YnWs~Ka~rr~ttGTGrmr~lk~v~rrfkngfreGt~~~ 85 (95)
.+.+.|..||. ..+. .-.|..|||--.+ ..+=-..+ =+||..|-.-|.||-...
T Consensus 19 pt~f~CP~Cge--~~v~v~~~k~~~h~~C~~CG~y~~~--~V~~l~ep--------------IDVY~~wiD~~~eg~i~~ 80 (99)
T PRK14892 19 PKIFECPRCGK--VSISVKIKKNIAIITCGNCGLYTEF--EVPSVYDE--------------VDVYNKFIDLYLEGKIEI 80 (99)
T ss_pred CcEeECCCCCC--eEeeeecCCCcceEECCCCCCccCE--ECCccccc--------------hhhHHHHHHHHHhcCCCc
Confidence 46788999994 4554 8899999973111 11111111 268888888888887665
Q ss_pred ccccc
Q 034411 86 PRKKN 90 (95)
Q Consensus 86 ~~~~~ 90 (95)
|-..+
T Consensus 81 ~~~~~ 85 (99)
T PRK14892 81 KERKN 85 (99)
T ss_pred cccCc
Confidence 55443
No 23
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=68.23 E-value=3.7 Score=35.17 Aligned_cols=26 Identities=35% Similarity=0.769 Sum_probs=18.4
Q ss_pred ccccccCCCccccccc--Cccccccccc
Q 034411 16 HTLCVRCGRRSFHIQK--SRCSACAYPA 41 (95)
Q Consensus 16 H~lCrRCG~~syH~qK--~~Ca~CGyps 41 (95)
-.+|.+||.+-=-.-+ -+|-+||+.+
T Consensus 350 ~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~ 377 (421)
T COG1571 350 NPVCPRCGGRMKSAGRNGFRCKKCGTRA 377 (421)
T ss_pred CCCCCccCCchhhcCCCCcccccccccC
Confidence 3489999987544433 5799999853
No 24
>PRK12496 hypothetical protein; Provisional
Probab=65.97 E-value=3.6 Score=30.22 Aligned_cols=29 Identities=21% Similarity=0.620 Sum_probs=21.8
Q ss_pred cccccCCCcccc--cccCcccccccccccccc
Q 034411 17 TLCVRCGRRSFH--IQKSRCSACAYPAARVRK 46 (95)
Q Consensus 17 ~lCrRCG~~syH--~qK~~Ca~CGyps~k~R~ 46 (95)
-.|..|| +.|. .....|..||.|-++++.
T Consensus 128 ~~C~gC~-~~~~~~~~~~~C~~CG~~~~r~~~ 158 (164)
T PRK12496 128 KVCKGCK-KKYPEDYPDDVCEICGSPVKRKMV 158 (164)
T ss_pred EECCCCC-ccccCCCCCCcCCCCCChhhhcch
Confidence 4699999 4565 455789999998766654
No 25
>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=65.17 E-value=3.9 Score=30.20 Aligned_cols=24 Identities=8% Similarity=0.354 Sum_probs=20.7
Q ss_pred ccccccCCCccccccc--Cccccccc
Q 034411 16 HTLCVRCGRRSFHIQK--SRCSACAY 39 (95)
Q Consensus 16 H~lCrRCG~~syH~qK--~~Ca~CGy 39 (95)
--+|.-||.+-|-|.| -+|.+||.
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~ 34 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGE 34 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCC
Confidence 3479999999999987 47999996
No 26
>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=64.68 E-value=4.3 Score=23.81 Aligned_cols=24 Identities=29% Similarity=0.856 Sum_probs=16.5
Q ss_pred ccccccCCCc-cccccc---Cccccccc
Q 034411 16 HTLCVRCGRR-SFHIQK---SRCSACAY 39 (95)
Q Consensus 16 H~lCrRCG~~-syH~qK---~~Ca~CGy 39 (95)
...|.+||+. .|.+.. -.|.+|++
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 3679999984 555443 56888875
No 27
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=62.07 E-value=4.9 Score=29.09 Aligned_cols=28 Identities=25% Similarity=0.657 Sum_probs=25.3
Q ss_pred CcccccccCCCcccccccCccccccccc
Q 034411 14 KTHTLCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
.=.-.|..||...|.-+.|.-+.||.||
T Consensus 31 ~G~Y~C~~Cg~pLF~S~~KfdSg~GWPS 58 (119)
T PRK05508 31 KGTYVCKQCGAPLYRSEDKFKSGCGWPS 58 (119)
T ss_pred CeEEEecCCCCccccccccccCCCCCcc
Confidence 4456899999999999999999999995
No 28
>PF04060 FeS: Putative Fe-S cluster; InterPro: IPR007202 These proteins contain a domain with four conserved cysteines that probably form an Fe-S redox cluster.; GO: 0051536 iron-sulfur cluster binding; PDB: 2YCL_A 4DJF_E 4DJD_C 4DJE_C.
Probab=62.02 E-value=3.8 Score=23.36 Aligned_cols=13 Identities=38% Similarity=1.168 Sum_probs=6.1
Q ss_pred cccCccccccccc
Q 034411 29 IQKSRCSACAYPA 41 (95)
Q Consensus 29 ~qK~~Ca~CGyps 41 (95)
+.+.-|+.|||++
T Consensus 2 LP~~nCg~CG~~~ 14 (35)
T PF04060_consen 2 LPGTNCGACGYPT 14 (35)
T ss_dssp S-S----TTSSSS
T ss_pred CCCCcCCCCCCcc
Confidence 3456799999983
No 29
>PRK00420 hypothetical protein; Validated
Probab=60.49 E-value=4.7 Score=28.70 Aligned_cols=25 Identities=20% Similarity=0.360 Sum_probs=21.2
Q ss_pred ccccccCCCccc--ccccCcccccccc
Q 034411 16 HTLCVRCGRRSF--HIQKSRCSACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~sy--H~qK~~Ca~CGyp 40 (95)
-..|..||...| +-.+-.|..||-+
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceecCCCceECCCCCCe
Confidence 367999999999 5778899999975
No 30
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=57.93 E-value=8.2 Score=29.11 Aligned_cols=39 Identities=28% Similarity=0.521 Sum_probs=31.0
Q ss_pred CCCCCCCCC-----CCCcccccccCCCcccccccCccccccccc
Q 034411 3 KGTGSFGKR-----RNKTHTLCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 3 KGT~SfGKr-----~~ktH~lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
|||-+.|.- ...---.|-.||...|--..+.++.||.||
T Consensus 36 kgTE~p~tGey~~~~e~GvY~C~~C~~pLykS~tKfdsgcGWPA 79 (146)
T KOG0856|consen 36 KGTERPGTGEYTKHFEEGVYVCAGCGTPLYKSTTKFDSGCGWPA 79 (146)
T ss_pred hcccCCCCcccccccCCceEEEeecCCccccccccccCCCCCch
Confidence 677666652 233445799999999999999999999994
No 31
>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=57.85 E-value=5.6 Score=22.91 Aligned_cols=22 Identities=23% Similarity=0.682 Sum_probs=15.2
Q ss_pred ccccCCCcccc----cccCccccccc
Q 034411 18 LCVRCGRRSFH----IQKSRCSACAY 39 (95)
Q Consensus 18 lCrRCG~~syH----~qK~~Ca~CGy 39 (95)
.|..||+...- .-.-.|..||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 58999997632 23448999997
No 32
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=57.48 E-value=5 Score=30.53 Aligned_cols=21 Identities=24% Similarity=0.627 Sum_probs=16.5
Q ss_pred CCCcccccccCcccccccccc
Q 034411 22 CGRRSFHIQKSRCSACAYPAA 42 (95)
Q Consensus 22 CG~~syH~qK~~Ca~CGyps~ 42 (95)
|-..+|-.+.+.|+.|||+|.
T Consensus 109 ~a~p~~KP~r~fCaVCG~~S~ 129 (156)
T KOG3362|consen 109 YAKPSFKPLRKFCAVCGYDSK 129 (156)
T ss_pred ccCCCCCCcchhhhhcCCCch
Confidence 556778888889999998753
No 33
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=57.24 E-value=6.3 Score=25.08 Aligned_cols=20 Identities=30% Similarity=0.808 Sum_probs=17.1
Q ss_pred ccccCCCcccccccCcccccccc
Q 034411 18 LCVRCGRRSFHIQKSRCSACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~qK~~Ca~CGyp 40 (95)
.|..||.-.+ +.+|..||-+
T Consensus 7 ~C~~CgvYTL---k~~CP~CG~~ 26 (56)
T PRK13130 7 KCPKCGVYTL---KEICPVCGGK 26 (56)
T ss_pred ECCCCCCEEc---cccCcCCCCC
Confidence 5889998777 9999999975
No 34
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=56.26 E-value=6.4 Score=25.25 Aligned_cols=23 Identities=26% Similarity=0.902 Sum_probs=19.8
Q ss_pred ccccccCCCcccccccCcccccccc
Q 034411 16 HTLCVRCGRRSFHIQKSRCSACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~syH~qK~~Ca~CGyp 40 (95)
-..|.-||. |++....|..|||.
T Consensus 27 ~~~c~~cG~--~~l~Hrvc~~cg~Y 49 (57)
T COG0333 27 LSVCPNCGE--YKLPHRVCLKCGYY 49 (57)
T ss_pred ceeccCCCC--cccCceEcCCCCCc
Confidence 367999995 89999999999984
No 35
>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=56.05 E-value=5.9 Score=25.65 Aligned_cols=8 Identities=38% Similarity=1.348 Sum_probs=5.5
Q ss_pred cccccccc
Q 034411 33 RCSACAYP 40 (95)
Q Consensus 33 ~Ca~CGyp 40 (95)
+|..|||-
T Consensus 38 ~C~~CGYT 45 (64)
T PF09855_consen 38 SCTNCGYT 45 (64)
T ss_pred ECCCCCCE
Confidence 57777773
No 36
>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=53.10 E-value=8.8 Score=20.83 Aligned_cols=22 Identities=27% Similarity=0.739 Sum_probs=15.7
Q ss_pred ccccCCCcccccccCcccccccc
Q 034411 18 LCVRCGRRSFHIQKSRCSACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~qK~~Ca~CGyp 40 (95)
.|..|+... -+.-+.|..|||-
T Consensus 2 ~CP~C~~~V-~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEV-PESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCc-hhhcCcCCCCCCC
Confidence 377777765 5566789999973
No 37
>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=51.82 E-value=15 Score=27.05 Aligned_cols=28 Identities=21% Similarity=0.494 Sum_probs=25.2
Q ss_pred CcccccccCCCcccccccCccccccccc
Q 034411 14 KTHTLCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
.=.-.|..||...|--+.+.-+.||+||
T Consensus 38 ~G~Y~C~~Cg~pLF~S~~KfdSg~GWPS 65 (134)
T TIGR00357 38 EGIYVDITCGEPLFSSEDKFDSGCGWPS 65 (134)
T ss_pred CeEEEccCCCCccccccchhcCCCCCcC
Confidence 4456799999999999999999999995
No 38
>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=51.52 E-value=6.5 Score=21.90 Aligned_cols=22 Identities=32% Similarity=0.801 Sum_probs=13.0
Q ss_pred ccccccCCCcccccccCcccccc
Q 034411 16 HTLCVRCGRRSFHIQKSRCSACA 38 (95)
Q Consensus 16 H~lCrRCG~~syH~qK~~Ca~CG 38 (95)
-..|..||...|=.+ ..|..||
T Consensus 11 ~~rC~~Cg~~~~pPr-~~Cp~C~ 32 (37)
T PF12172_consen 11 GQRCRDCGRVQFPPR-PVCPHCG 32 (37)
T ss_dssp EEE-TTT--EEES---SEETTTT
T ss_pred EEEcCCCCCEecCCC-cCCCCcC
Confidence 457889998755444 8999997
No 39
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=47.53 E-value=11 Score=28.20 Aligned_cols=26 Identities=27% Similarity=0.695 Sum_probs=23.7
Q ss_pred ccccccCCCcccccccCccccccccc
Q 034411 16 HTLCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 16 H~lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
--.|.-||...|.-..|.-+-||.||
T Consensus 42 iY~c~~cg~pLF~S~~KfdSgcGWPS 67 (140)
T COG0229 42 IYVCIVCGEPLFSSEDKFDSGCGWPS 67 (140)
T ss_pred eEEeecCCCccccccccccCCCCCcc
Confidence 34799999999999999999999994
No 40
>PRK05580 primosome assembly protein PriA; Validated
Probab=47.10 E-value=12 Score=32.66 Aligned_cols=27 Identities=33% Similarity=0.822 Sum_probs=18.8
Q ss_pred CcccccccCCCc----------ccccccC--cccccccc
Q 034411 14 KTHTLCVRCGRR----------SFHIQKS--RCSACAYP 40 (95)
Q Consensus 14 ktH~lCrRCG~~----------syH~qK~--~Ca~CGyp 40 (95)
...+.|+.||.. .||.... .|--|||.
T Consensus 379 ~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 379 APFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred CCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCC
Confidence 356778888855 4886554 48888885
No 41
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=47.01 E-value=9.8 Score=25.65 Aligned_cols=12 Identities=33% Similarity=0.891 Sum_probs=8.0
Q ss_pred cCcccccccccc
Q 034411 31 KSRCSACAYPAA 42 (95)
Q Consensus 31 K~~Ca~CGyps~ 42 (95)
...|..||||+.
T Consensus 80 ~~~C~~CG~pss 91 (104)
T TIGR00269 80 LRRCERCGEPTS 91 (104)
T ss_pred CCcCCcCcCcCC
Confidence 456777777754
No 42
>PF10555 MraY_sig1: Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 ; InterPro: IPR018480 Phospho-N-acetylmuramoyl-pentapeptide-transferase (2.7.8.13 from EC) (MraY) is a bacterial enzyme responsible for the formation of the first lipid intermediate of the cell wall peptidoglycan synthesis []. It catalyses the formation of undecaprenyl-pyrophosphoryl-N-acetylmuramoyl-pentapeptide from UDP-MurNAc-pentapeptide and undecaprenyl-phosphate. MraY is an integral membrane protein with probably ten transmembrane domains. It belongs to family 4 of glycosyl transferases. Homologues of MraY have been found in archaebacteria Methanobacterium thermoautotrophicum and in Arabidopsis thaliana (Mouse-ear cress). This entry represents two conserved sites found in these proteins. The first site is located at the end of the first cytoplasmic loop and the beginning of the second transmembrane domain. The second site is located in the third cytoplasmic loop.
Probab=46.66 E-value=9.4 Score=18.36 Aligned_cols=7 Identities=43% Similarity=0.824 Sum_probs=6.1
Q ss_pred CCCCCCC
Q 034411 3 KGTGSFG 9 (95)
Q Consensus 3 KGT~SfG 9 (95)
+|||.||
T Consensus 2 ~gTPTMG 8 (13)
T PF10555_consen 2 SGTPTMG 8 (13)
T ss_pred CCCccce
Confidence 6899998
No 43
>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=46.51 E-value=8.7 Score=21.23 Aligned_cols=24 Identities=29% Similarity=0.750 Sum_probs=14.9
Q ss_pred ccccccCCCcccccc---------cCcccccccc
Q 034411 16 HTLCVRCGRRSFHIQ---------KSRCSACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~syH~q---------K~~Ca~CGyp 40 (95)
.+.|..||.. |-++ +-+|+.||.+
T Consensus 2 ~~~CP~C~~~-~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 2 RIQCPNCKTS-FRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCE-EEeCHHHcCCCCCEEECCCCCCE
Confidence 4678888874 2221 2478888853
No 44
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.19 E-value=9.3 Score=28.20 Aligned_cols=25 Identities=36% Similarity=0.796 Sum_probs=21.1
Q ss_pred cccccccCCC----cccccccCccccccc
Q 034411 15 THTLCVRCGR----RSFHIQKSRCSACAY 39 (95)
Q Consensus 15 tH~lCrRCG~----~syH~qK~~Ca~CGy 39 (95)
.+-+|.+||. +.|=.-...|.+||.
T Consensus 20 l~grCP~CGeGrLF~gFLK~~p~C~aCG~ 48 (126)
T COG5349 20 LRGRCPRCGEGRLFRGFLKVVPACEACGL 48 (126)
T ss_pred hcCCCCCCCCchhhhhhcccCchhhhccc
Confidence 4568999997 578888899999996
No 45
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=46.09 E-value=11 Score=26.99 Aligned_cols=27 Identities=26% Similarity=0.677 Sum_probs=21.4
Q ss_pred CcccccccCCCcccccccCccccccccc
Q 034411 14 KTHTLCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
-.-+.|..||+. |+.-...|..||.+.
T Consensus 27 l~g~kC~~CG~v-~~PPr~~Cp~C~~~~ 53 (140)
T COG1545 27 LLGTKCKKCGRV-YFPPRAYCPKCGSET 53 (140)
T ss_pred EEEEEcCCCCeE-EcCCcccCCCCCCCC
Confidence 367899999986 556668999999764
No 46
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=45.35 E-value=12 Score=28.83 Aligned_cols=33 Identities=33% Similarity=0.532 Sum_probs=25.8
Q ss_pred CcccccccCCCcccccccCccccccccccccccC
Q 034411 14 KTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKY 47 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qK~~Ca~CGyps~k~R~Y 47 (95)
+--..|..|++. |+..+..|..||-|..+++.-
T Consensus 137 ~w~~rC~GC~~~-f~~~~~~Cp~CG~~~~~~~~~ 169 (177)
T COG1439 137 KWRLRCHGCKRI-FPEPKDFCPICGSPLKRKRVK 169 (177)
T ss_pred eeeEEEecCcee-cCCCCCcCCCCCCceEEeeec
Confidence 345689999875 679999999999986666543
No 47
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=45.07 E-value=12 Score=29.43 Aligned_cols=26 Identities=27% Similarity=0.758 Sum_probs=22.8
Q ss_pred CCCcccccccCCCcccccccCccccccc
Q 034411 12 RNKTHTLCVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 12 ~~ktH~lCrRCG~~syH~qK~~Ca~CGy 39 (95)
.++.+++|--|-.+.+ +..+|.+||-
T Consensus 158 k~~hcilCtvCe~r~w--~g~~CPKCGr 183 (200)
T PF12387_consen 158 KSKHCILCTVCEGREW--KGGNCPKCGR 183 (200)
T ss_pred CCCceEEEeeeecCcc--CCCCCCcccC
Confidence 3678999999999999 7788999996
No 48
>PHA02942 putative transposase; Provisional
Probab=44.19 E-value=12 Score=30.79 Aligned_cols=26 Identities=23% Similarity=0.761 Sum_probs=18.8
Q ss_pred cccccccCCCcccc--cccCcccccccc
Q 034411 15 THTLCVRCGRRSFH--IQKSRCSACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH--~qK~~Ca~CGyp 40 (95)
|--.|..||...-- .+.-.|..|||-
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCCE
Confidence 55689999976432 345689999995
No 49
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=43.93 E-value=16 Score=23.35 Aligned_cols=24 Identities=25% Similarity=0.606 Sum_probs=14.9
Q ss_pred ccccCCCcccccccCccccccccc
Q 034411 18 LCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 18 lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
+|.-|+...=.-+.-.|..||+|.
T Consensus 1 ~Cpv~~~~~~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDLPAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCccccccccCCcCCCCCCcC
Confidence 355555544445566788888873
No 50
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=43.29 E-value=12 Score=29.01 Aligned_cols=26 Identities=23% Similarity=0.558 Sum_probs=19.7
Q ss_pred CcccccccCCCcccc---cccCccccccc
Q 034411 14 KTHTLCVRCGRRSFH---IQKSRCSACAY 39 (95)
Q Consensus 14 ktH~lCrRCG~~syH---~qK~~Ca~CGy 39 (95)
.+|-.|.+||..... -....|.+||.
T Consensus 97 ~~~~fC~~CG~~~~~~~~~~~~~C~~c~~ 125 (256)
T PRK00241 97 RSHRFCGYCGHPMHPSKTEWAMLCPHCRE 125 (256)
T ss_pred hcCccccccCCCCeecCCceeEECCCCCC
Confidence 578899999998543 33567999985
No 51
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=42.91 E-value=10 Score=27.39 Aligned_cols=26 Identities=31% Similarity=0.698 Sum_probs=21.3
Q ss_pred cccccccCCCccccccc------Ccccccccc
Q 034411 15 THTLCVRCGRRSFHIQK------SRCSACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK------~~Ca~CGyp 40 (95)
..++|.-||+.--.+.| -.|.+||.-
T Consensus 96 ~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred heEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 45899999998877777 589999973
No 52
>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=42.24 E-value=18 Score=26.16 Aligned_cols=31 Identities=23% Similarity=0.578 Sum_probs=25.9
Q ss_pred CCCCcccccccCCCcccccccCccccccccc
Q 034411 11 RRNKTHTLCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 11 r~~ktH~lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
....-.-.|..||...|.-..|.-+.||.||
T Consensus 32 ~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPS 62 (124)
T PF01641_consen 32 HKEEGIYVCAVCGTPLFSSDTKFDSGCGWPS 62 (124)
T ss_dssp TTSSEEEEETTTS-EEEEGGGEETSSSSSSE
T ss_pred CCCCEEEEcCCCCCccccCcccccCCcCCcc
Confidence 3345667899999999999999999999996
No 53
>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=41.74 E-value=22 Score=20.17 Aligned_cols=23 Identities=26% Similarity=0.644 Sum_probs=11.6
Q ss_pred ccccCCCccccc--ccCcccccccc
Q 034411 18 LCVRCGRRSFHI--QKSRCSACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~--qK~~Ca~CGyp 40 (95)
+|-.||...--. ..-+|-.|||.
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-S
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCe
Confidence 466676654421 22367777764
No 54
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=41.40 E-value=26 Score=26.02 Aligned_cols=28 Identities=29% Similarity=0.656 Sum_probs=25.4
Q ss_pred CcccccccCCCcccccccCccccccccc
Q 034411 14 KTHTLCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
.-.-.|..||...|--..+.-+.||.||
T Consensus 41 ~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPS 68 (142)
T PRK00222 41 KGIYVCIVCGEPLFSSDTKFDSGCGWPS 68 (142)
T ss_pred CeEEEecCCCchhcCCcccccCCCCCcC
Confidence 4456899999999999999999999996
No 55
>PRK08329 threonine synthase; Validated
Probab=41.39 E-value=22 Score=28.29 Aligned_cols=66 Identities=20% Similarity=0.360 Sum_probs=32.5
Q ss_pred cccccCCCcccccccCccccccccccccccCCccccccccccccccccccccchh--hhhccCcCcCCCCCcc
Q 034411 17 TLCVRCGRRSFHIQKSRCSACAYPAARVRKYNWSVKAIRRKTTGTGRMRYLRHVP--RRFKSNFREGTEAAPR 87 (95)
Q Consensus 17 ~lCrRCG~~syH~qK~~Ca~CGyps~k~R~YnWs~Ka~rr~ttGTGrmr~lk~v~--rrfkngfreGt~~~~~ 87 (95)
..|.+||...=--..-.| .||-|=. ..|+++.....+.. .|--||-.-++ ....--.-||.+|.-+
T Consensus 2 l~C~~Cg~~~~~~~~~~C-~c~~~l~--~~~~~~~~~~~~~~--~~~wry~~~lP~~~~~~~sl~eg~Tpl~~ 69 (347)
T PRK08329 2 LRCTKCGRTYEEKFKLRC-DCGGTLL--VEREYGSFDSPREY--LDMRRYIDYLPVDEEFLPHLTPPITPTVK 69 (347)
T ss_pred cCcCCCCCCcCCCCceec-CCCCcEE--EEeccccccccccc--cchhhhHHhCCCCCCCCCcCCCCCCcccc
Confidence 469999976422223579 7986533 23444422112222 34344433333 1112355678777543
No 56
>PRK06450 threonine synthase; Validated
Probab=40.48 E-value=16 Score=29.29 Aligned_cols=24 Identities=29% Similarity=0.884 Sum_probs=18.0
Q ss_pred ccccccCCCcccccc-cCcccccccc
Q 034411 16 HTLCVRCGRRSFHIQ-KSRCSACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~syH~q-K~~Ca~CGyp 40 (95)
...|.+||+. |... ...|..||-|
T Consensus 3 ~~~C~~Cg~~-~~~~~~~~C~~cg~~ 27 (338)
T PRK06450 3 KEVCMKCGKE-RESIYEIRCKKCGGP 27 (338)
T ss_pred eeEECCcCCc-CCCcccccCCcCCCE
Confidence 3589999988 5543 4579999975
No 57
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=40.34 E-value=17 Score=21.13 Aligned_cols=24 Identities=38% Similarity=0.847 Sum_probs=14.8
Q ss_pred cccccCCCcc-c--ccccCcccccccc
Q 034411 17 TLCVRCGRRS-F--HIQKSRCSACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~s-y--H~qK~~Ca~CGyp 40 (95)
..|..||... | ..+..+|..||.+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCe
Confidence 4577787742 2 1225678888875
No 58
>PRK11823 DNA repair protein RadA; Provisional
Probab=39.76 E-value=17 Score=30.31 Aligned_cols=26 Identities=35% Similarity=0.722 Sum_probs=20.9
Q ss_pred CCcccccccCCCcccccccCccccccc
Q 034411 13 NKTHTLCVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qK~~Ca~CGy 39 (95)
.|+.-.|..||-.+--.+ ..|.+|+-
T Consensus 4 ~~~~y~C~~Cg~~~~~~~-g~Cp~C~~ 29 (446)
T PRK11823 4 KKTAYVCQECGAESPKWL-GRCPECGA 29 (446)
T ss_pred CCCeEECCcCCCCCcccC-eeCcCCCC
Confidence 378899999998875444 78999985
No 59
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=39.74 E-value=15 Score=23.32 Aligned_cols=21 Identities=14% Similarity=0.333 Sum_probs=16.8
Q ss_pred ccccccCCCcccccccCccccccc
Q 034411 16 HTLCVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 16 H~lCrRCG~~syH~qK~~Ca~CGy 39 (95)
-+.|..||. |++....|. |||
T Consensus 27 ~~~c~~cg~--~~~pH~vc~-cG~ 47 (60)
T PRK01110 27 LSVDKTTGE--YHLPHHVSP-KGY 47 (60)
T ss_pred eeEcCCCCc--eeccceecC-Ccc
Confidence 357888884 788888899 997
No 60
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=39.74 E-value=17 Score=20.91 Aligned_cols=21 Identities=38% Similarity=1.146 Sum_probs=14.5
Q ss_pred ccccCCCcccccc------cCccccccc
Q 034411 18 LCVRCGRRSFHIQ------KSRCSACAY 39 (95)
Q Consensus 18 lCrRCG~~syH~q------K~~Ca~CGy 39 (95)
+|.-||+ .||+. ...|-.||-
T Consensus 3 ~C~~Cg~-~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGR-IYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EETTTTE-EEETTTB--SSTTBCTTTTE
T ss_pred CcCCCCC-ccccccCCCCCCCccCCCCC
Confidence 5777875 68873 357888874
No 61
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=39.17 E-value=17 Score=31.58 Aligned_cols=29 Identities=21% Similarity=0.312 Sum_probs=25.7
Q ss_pred CCcccccccCCCcccccccCccccccccc
Q 034411 13 NKTHTLCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
..=.-.|..||..-|.-..+.-+.||.||
T Consensus 415 ~~G~y~c~~c~~pLf~s~~Kf~sg~GWPs 443 (521)
T PRK14018 415 KPGIYVDVVSGEPLFSSADKYDSGCGWPS 443 (521)
T ss_pred CCEEEEecCCCCccccCcccccCCCCCcc
Confidence 34556899999999999999999999995
No 62
>KOG4192 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.00 E-value=14 Score=27.54 Aligned_cols=24 Identities=46% Similarity=0.931 Sum_probs=18.4
Q ss_pred CCCCCCCcccccccCCCcccccccC
Q 034411 8 FGKRRNKTHTLCVRCGRRSFHIQKS 32 (95)
Q Consensus 8 fGKr~~ktH~lCrRCG~~syH~qK~ 32 (95)
||-+ .-.|+.|.+||=+||+...+
T Consensus 66 ~gth-~aqhtfck~cGV~sf~~~rs 89 (134)
T KOG4192|consen 66 FGTH-QAQHTFCKRCGVQSFYSPRS 89 (134)
T ss_pred eccc-hhheeeeccccceecccccc
Confidence 4443 45799999999999997544
No 63
>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=38.62 E-value=17 Score=22.15 Aligned_cols=25 Identities=32% Similarity=0.773 Sum_probs=15.4
Q ss_pred cccccccCCCcccc---cccCccccccc
Q 034411 15 THTLCVRCGRRSFH---IQKSRCSACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH---~qK~~Ca~CGy 39 (95)
|--.|..||...-. ...-.|..||+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~ 54 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGF 54 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCC
Confidence 44567777765433 44556777776
No 64
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=38.09 E-value=11 Score=24.76 Aligned_cols=16 Identities=31% Similarity=0.642 Sum_probs=11.4
Q ss_pred CcccccccCCCccccc
Q 034411 14 KTHTLCVRCGRRSFHI 29 (95)
Q Consensus 14 ktH~lCrRCG~~syH~ 29 (95)
-.-+-|||||+.---+
T Consensus 8 IV~t~CrRCGk~i~tl 23 (60)
T PF10892_consen 8 IVETPCRRCGKSIRTL 23 (60)
T ss_pred eeeehhhhhCccHHHH
Confidence 3567899999875443
No 65
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=37.84 E-value=19 Score=27.25 Aligned_cols=28 Identities=21% Similarity=0.478 Sum_probs=23.2
Q ss_pred ccccccCCCcccccccCccccccccccc
Q 034411 16 HTLCVRCGRRSFHIQKSRCSACAYPAAR 43 (95)
Q Consensus 16 H~lCrRCG~~syH~qK~~Ca~CGyps~k 43 (95)
--.|+-||--..=.--..|..||-|..+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~k~~ 161 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAPKEK 161 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCChHHH
Confidence 4579999998888888999999977544
No 66
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=37.64 E-value=6.8 Score=27.27 Aligned_cols=26 Identities=23% Similarity=0.827 Sum_probs=16.3
Q ss_pred ccccccCCC----ccccc-------ccCccccccccc
Q 034411 16 HTLCVRCGR----RSFHI-------QKSRCSACAYPA 41 (95)
Q Consensus 16 H~lCrRCG~----~syH~-------qK~~Ca~CGyps 41 (95)
.-.|..|+. .|||. +...|+.||-|.
T Consensus 55 p~kC~~C~qktVk~AYh~iC~~Ca~~~~vCaKC~k~~ 91 (92)
T PF10217_consen 55 PKKCNKCQQKTVKHAYHVICDPCAKELKVCAKCGKPP 91 (92)
T ss_pred CccccccccchHHHHHHHHHHHHHHhhccCcccCCCC
Confidence 344555553 35553 568999999763
No 67
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=37.62 E-value=18 Score=25.05 Aligned_cols=37 Identities=22% Similarity=0.476 Sum_probs=22.4
Q ss_pred CCCCCCCCCC----CCcccccccCCCcccccc---cCcccccccc
Q 034411 3 KGTGSFGKRR----NKTHTLCVRCGRRSFHIQ---KSRCSACAYP 40 (95)
Q Consensus 3 KGT~SfGKr~----~ktH~lCrRCG~~syH~q---K~~Ca~CGyp 40 (95)
+||..-|-.- -+.-..|+.||. -|-+. ...|..||-+
T Consensus 53 ~~t~~egA~L~i~~~p~~~~C~~Cg~-~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 53 RGTVAEGCKLHLEEQEAECWCETCQQ-YVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred CCCccCCCEEEEEeeCcEEEcccCCC-eeecCCccCCcCcCcCCC
Confidence 4555544431 345678999995 34332 2559999954
No 68
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=37.61 E-value=16 Score=25.59 Aligned_cols=23 Identities=30% Similarity=0.847 Sum_probs=18.7
Q ss_pred cccccCCCccccc-----ccCccccccc
Q 034411 17 TLCVRCGRRSFHI-----QKSRCSACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~-----qK~~Ca~CGy 39 (95)
..|..||+--|=. ....|.+|||
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgy 30 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGY 30 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCc
Confidence 4699999988874 3578999999
No 69
>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=37.54 E-value=26 Score=19.11 Aligned_cols=24 Identities=21% Similarity=0.404 Sum_probs=15.9
Q ss_pred cccccCCCcccc------cccCcccccccc
Q 034411 17 TLCVRCGRRSFH------IQKSRCSACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~syH------~qK~~Ca~CGyp 40 (95)
..|.-||..--- .....|..||-+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 468888884322 335679999964
No 70
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=36.74 E-value=27 Score=31.18 Aligned_cols=29 Identities=17% Similarity=0.566 Sum_probs=19.1
Q ss_pred CCCCCCcccccccCCCcccccccCcccccccc
Q 034411 9 GKRRNKTHTLCVRCGRRSFHIQKSRCSACAYP 40 (95)
Q Consensus 9 GKr~~ktH~lCrRCG~~syH~qK~~Ca~CGyp 40 (95)
|.-+....-.|..||..- ..+.|..||.+
T Consensus 8 g~~n~~~akFC~~CG~~l---~~~~Cp~CG~~ 36 (645)
T PRK14559 8 QFENPNNNRFCQKCGTSL---THKPCPQCGTE 36 (645)
T ss_pred CCcCCCCCccccccCCCC---CCCcCCCCCCC
Confidence 444556677788888764 23567777774
No 71
>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=36.48 E-value=12 Score=24.95 Aligned_cols=22 Identities=27% Similarity=0.819 Sum_probs=15.5
Q ss_pred cccccCCCcccccc---cCcccccccc
Q 034411 17 TLCVRCGRRSFHIQ---KSRCSACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~syH~q---K~~Ca~CGyp 40 (95)
+.| .||+.+|-.+ .+.| -||+.
T Consensus 4 frC-~Cgr~lya~e~~kTkkC-~CG~~ 28 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGAKTKKC-VCGKT 28 (68)
T ss_dssp EEE-TTS--EEEETT-SEEEE-TTTEE
T ss_pred EEe-cCCCEEEecCCcceeEe-cCCCe
Confidence 578 7999999654 5689 99983
No 72
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=35.97 E-value=22 Score=25.28 Aligned_cols=24 Identities=29% Similarity=0.664 Sum_probs=19.3
Q ss_pred CcccccccCCCcccc----------cccCccccccc
Q 034411 14 KTHTLCVRCGRRSFH----------IQKSRCSACAY 39 (95)
Q Consensus 14 ktH~lCrRCG~~syH----------~qK~~Ca~CGy 39 (95)
+++.-|..|++ || .|.-.|.+|++
T Consensus 28 ~~~~~cP~C~s--~~~~k~g~~~~~~qRyrC~~C~~ 61 (129)
T COG3677 28 ITKVNCPRCKS--SNVVKIGGIRRGHQRYKCKSCGS 61 (129)
T ss_pred cccCcCCCCCc--cceeeECCccccccccccCCcCc
Confidence 46678999975 44 78899999997
No 73
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=35.85 E-value=13 Score=30.40 Aligned_cols=31 Identities=19% Similarity=0.461 Sum_probs=24.4
Q ss_pred cccccccCCCccccccc----Ccccccccc---ccccc
Q 034411 15 THTLCVRCGRRSFHIQK----SRCSACAYP---AARVR 45 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK----~~Ca~CGyp---s~k~R 45 (95)
.-+.|..|+...|+.+- .+|..|||. +++.|
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltAreR 74 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGYHLKMSSSDR 74 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCCCcCCCHHHH
Confidence 46789999999998653 799999993 44544
No 74
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=35.76 E-value=13 Score=22.81 Aligned_cols=21 Identities=24% Similarity=0.763 Sum_probs=14.9
Q ss_pred ccccCccccccccccccccCCcccccc
Q 034411 28 HIQKSRCSACAYPAARVRKYNWSVKAI 54 (95)
Q Consensus 28 H~qK~~Ca~CGyps~k~R~YnWs~Ka~ 54 (95)
|+-.+.|+.||-| |.|-.|..
T Consensus 5 ~lp~K~C~~C~rp------f~WRKKW~ 25 (42)
T PF10013_consen 5 NLPSKICPVCGRP------FTWRKKWA 25 (42)
T ss_pred cCCCCcCcccCCc------chHHHHHH
Confidence 6777999999965 56655543
No 75
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=35.17 E-value=19 Score=28.94 Aligned_cols=26 Identities=23% Similarity=0.595 Sum_probs=21.9
Q ss_pred cccccccCCCccccc----ccCcccccccc
Q 034411 15 THTLCVRCGRRSFHI----QKSRCSACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~----qK~~Ca~CGyp 40 (95)
.-+.|..|+..-|+. .-.+|..|||.
T Consensus 25 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred CeeECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence 468899999999986 34799999993
No 76
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=35.04 E-value=21 Score=24.63 Aligned_cols=37 Identities=22% Similarity=0.489 Sum_probs=21.7
Q ss_pred CCCCCCCCCC----CCcccccccCCCccccc--ccCcccccccc
Q 034411 3 KGTGSFGKRR----NKTHTLCVRCGRRSFHI--QKSRCSACAYP 40 (95)
Q Consensus 3 KGT~SfGKr~----~ktH~lCrRCG~~syH~--qK~~Ca~CGyp 40 (95)
+||..-|-.- -+.-..|+.||.. |-+ ....|..||-+
T Consensus 53 ~~T~~egA~L~I~~vp~~~~C~~Cg~~-~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 53 HGTVAQGCDLHIVYKPAQAWCWDCSQV-VEIHQHDAQCPHCHGE 95 (113)
T ss_pred CCCccCCCEEEEEeeCcEEEcccCCCE-EecCCcCccCcCCCCC
Confidence 4554444321 2455689999943 333 33459999944
No 77
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=34.87 E-value=16 Score=27.62 Aligned_cols=33 Identities=27% Similarity=0.657 Sum_probs=24.5
Q ss_pred cccccccCCCccccccc------Cccccccc--cccccccC
Q 034411 15 THTLCVRCGRRSFHIQK------SRCSACAY--PAARVRKY 47 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK------~~Ca~CGy--ps~k~R~Y 47 (95)
..++|.-|++.--.+.+ ..|.+||. |-.....-
T Consensus 97 ~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~~~~~~ 137 (201)
T PRK12336 97 EYVICSECGLPDTRLVKEDRVLMLRCDACGAHRPVKKRKAS 137 (201)
T ss_pred heEECCCCCCCCcEEEEcCCeEEEEcccCCCCccccccccc
Confidence 46899999998888776 47999999 44443333
No 78
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=34.45 E-value=22 Score=20.15 Aligned_cols=23 Identities=26% Similarity=0.888 Sum_probs=14.7
Q ss_pred cccccCCCcccccccC----ccccccc
Q 034411 17 TLCVRCGRRSFHIQKS----RCSACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qK~----~Ca~CGy 39 (95)
..|..||+--|-.... .|..|||
T Consensus 2 ~FCp~C~nlL~p~~~~~~~~~C~~C~Y 28 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKEKRVACRTCGY 28 (35)
T ss_dssp -BETTTTSBEEEEEETTTTEEESSSS-
T ss_pred eeCCCCCccceEcCCCccCcCCCCCCC
Confidence 3588888877654322 4899998
No 79
>PRK14873 primosome assembly protein PriA; Provisional
Probab=34.22 E-value=23 Score=31.45 Aligned_cols=24 Identities=33% Similarity=0.710 Sum_probs=0.0
Q ss_pred CCCcccc-cccCCCcccccccCcccccc
Q 034411 12 RNKTHTL-CVRCGRRSFHIQKSRCSACA 38 (95)
Q Consensus 12 ~~ktH~l-CrRCG~~syH~qK~~Ca~CG 38 (95)
|.....+ |+.||... . -..|..||
T Consensus 405 h~~~~~l~Ch~CG~~~--~-p~~Cp~Cg 429 (665)
T PRK14873 405 PSAGGTPRCRWCGRAA--P-DWRCPRCG 429 (665)
T ss_pred ecCCCeeECCCCcCCC--c-CccCCCCc
No 80
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=34.20 E-value=21 Score=23.52 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=18.1
Q ss_pred ccccCCCccccc-ccCcccccccc
Q 034411 18 LCVRCGRRSFHI-QKSRCSACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~-qK~~Ca~CGyp 40 (95)
.|..||..-+=. ..-.|..|||-
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCc
Confidence 589999887643 56789999985
No 81
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=34.09 E-value=24 Score=22.19 Aligned_cols=22 Identities=32% Similarity=1.070 Sum_probs=16.0
Q ss_pred cccccCCCcccccccCccccccc
Q 034411 17 TLCVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qK~~Ca~CGy 39 (95)
-+|++|+-+- ++.-..|-+|||
T Consensus 15 ~ICrkC~ARn-p~~A~~CRKCg~ 36 (48)
T PRK04136 15 KICMRCNARN-PWRATKCRKCGY 36 (48)
T ss_pred cchhcccCCC-CccccccccCCC
Confidence 4688888663 566677888887
No 82
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=32.47 E-value=19 Score=23.44 Aligned_cols=14 Identities=29% Similarity=0.956 Sum_probs=10.9
Q ss_pred CCcccccccCCCcc
Q 034411 13 NKTHTLCVRCGRRS 26 (95)
Q Consensus 13 ~ktH~lCrRCG~~s 26 (95)
..-|..|..||+..
T Consensus 70 ~h~H~~C~~Cg~i~ 83 (116)
T cd07153 70 HHHHLICTKCGKVI 83 (116)
T ss_pred CCCceEeCCCCCEE
Confidence 34699999999753
No 83
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=32.18 E-value=30 Score=19.41 Aligned_cols=27 Identities=22% Similarity=0.551 Sum_probs=16.6
Q ss_pred cccccCCCccccc-ccCccccccccccc
Q 034411 17 TLCVRCGRRSFHI-QKSRCSACAYPAAR 43 (95)
Q Consensus 17 ~lCrRCG~~syH~-qK~~Ca~CGyps~k 43 (95)
-+|.-||-.--=. .-..|..||.|...
T Consensus 3 ~~C~~CG~i~~g~~~p~~CP~Cg~~~~~ 30 (34)
T cd00729 3 WVCPVCGYIHEGEEAPEKCPICGAPKEK 30 (34)
T ss_pred EECCCCCCEeECCcCCCcCcCCCCchHH
Confidence 3688888542111 23689999987543
No 84
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=32.15 E-value=23 Score=28.92 Aligned_cols=27 Identities=26% Similarity=0.834 Sum_probs=22.3
Q ss_pred CCcccccccCCCcccccc---cCccccccc
Q 034411 13 NKTHTLCVRCGRRSFHIQ---KSRCSACAY 39 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~q---K~~Ca~CGy 39 (95)
..+|-.|-+||.+.+=.+ +..|.+||.
T Consensus 108 ~~~~RFCg~CG~~~~~~~~g~~~~C~~cg~ 137 (279)
T COG2816 108 YRSHRFCGRCGTKTYPREGGWARVCPKCGH 137 (279)
T ss_pred HhhCcCCCCCCCcCccccCceeeeCCCCCC
Confidence 468899999999988554 678999996
No 85
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=31.96 E-value=39 Score=27.40 Aligned_cols=29 Identities=34% Similarity=0.717 Sum_probs=25.9
Q ss_pred CCcccccccCCCcccccccCccccccccc
Q 034411 13 NKTHTLCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
..=.-.|..||...|.-+.|.-+.||.||
T Consensus 33 ~~G~y~c~~c~~~LF~s~~Kf~sg~GWPs 61 (283)
T PRK05550 33 EKGVYLCRRCGAPLFRSEDKFNSGCGWPS 61 (283)
T ss_pred CCcEEEcCCCCchhcCChhhccCCCCCcC
Confidence 44566799999999999999999999996
No 86
>PRK04351 hypothetical protein; Provisional
Probab=31.75 E-value=24 Score=25.78 Aligned_cols=22 Identities=32% Similarity=0.911 Sum_probs=13.0
Q ss_pred cccccCCC-----cccccccCcccccc
Q 034411 17 TLCVRCGR-----RSFHIQKSRCSACA 38 (95)
Q Consensus 17 ~lCrRCG~-----~syH~qK~~Ca~CG 38 (95)
-.|..||. ++.+..+-.|+.|+
T Consensus 113 Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~ 139 (149)
T PRK04351 113 YECQSCGQQYLRKRRINTKRYRCGKCR 139 (149)
T ss_pred EECCCCCCEeeeeeecCCCcEEeCCCC
Confidence 45666665 44555566666665
No 87
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=31.65 E-value=25 Score=22.91 Aligned_cols=20 Identities=30% Similarity=1.080 Sum_probs=15.0
Q ss_pred cccccCCCcccccccCccccccc
Q 034411 17 TLCVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qK~~Ca~CGy 39 (95)
-+|..||. |-++ ..|..||-
T Consensus 6 rkC~~cg~--YTLk-e~Cp~CG~ 25 (59)
T COG2260 6 RKCPKCGR--YTLK-EKCPVCGG 25 (59)
T ss_pred hcCcCCCc--eeec-ccCCCCCC
Confidence 46888775 5555 89999995
No 88
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=30.91 E-value=19 Score=25.21 Aligned_cols=25 Identities=32% Similarity=0.748 Sum_probs=19.5
Q ss_pred cccccccCCCccccccc------Cccccccc
Q 034411 15 THTLCVRCGRRSFHIQK------SRCSACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK------~~Ca~CGy 39 (95)
..++|.-|++.-=.+.+ ..|.+||.
T Consensus 79 ~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 79 EYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred hcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 35789999998888776 35888884
No 89
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=30.77 E-value=31 Score=17.48 Aligned_cols=22 Identities=32% Similarity=0.748 Sum_probs=14.1
Q ss_pred ccccCCCcccccccCcccccccc
Q 034411 18 LCVRCGRRSFHIQKSRCSACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~qK~~Ca~CGyp 40 (95)
.|..|+-.-|..+. .|..|+-|
T Consensus 4 ~C~~C~~~N~~~~~-~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNFASRS-KCFACGAP 25 (26)
T ss_pred cCCCCCCcChhhhc-cccccCCc
Confidence 46667666666554 67777754
No 90
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=30.76 E-value=19 Score=28.91 Aligned_cols=26 Identities=23% Similarity=0.585 Sum_probs=21.8
Q ss_pred cccccccCCCcccccc----cCcccccccc
Q 034411 15 THTLCVRCGRRSFHIQ----KSRCSACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~q----K~~Ca~CGyp 40 (95)
.-+.|..|+...|+.+ -.+|..|||-
T Consensus 26 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h 55 (292)
T PRK05654 26 LWTKCPSCGQVLYRKELEANLNVCPKCGHH 55 (292)
T ss_pred CeeECCCccchhhHHHHHhcCCCCCCCCCC
Confidence 4689999999999865 3699999993
No 91
>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=30.63 E-value=29 Score=24.02 Aligned_cols=38 Identities=21% Similarity=0.364 Sum_probs=23.2
Q ss_pred CCCCCCCCCC----CCcccccccCCCccccc-c-cCccccccccc
Q 034411 3 KGTGSFGKRR----NKTHTLCVRCGRRSFHI-Q-KSRCSACAYPA 41 (95)
Q Consensus 3 KGT~SfGKr~----~ktH~lCrRCG~~syH~-q-K~~Ca~CGyps 41 (95)
+||+.-|-.- -+.-..|+.||.. |-+ + ...|..||-+.
T Consensus 53 ~~t~~ega~L~I~~~p~~~~C~~Cg~~-~~~~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 53 EGTVAEGAKLNIEDEPVECECEDCSEE-VSPEIDLYRCPKCHGIM 96 (115)
T ss_pred CCCccCCCEEEEEeeCcEEEcccCCCE-EecCCcCccCcCCcCCC
Confidence 4555444321 3456789999944 433 2 46699999543
No 92
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=30.13 E-value=30 Score=20.63 Aligned_cols=23 Identities=35% Similarity=0.875 Sum_probs=14.5
Q ss_pred ccccCCCccccc--ccCcccccccc
Q 034411 18 LCVRCGRRSFHI--QKSRCSACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~--qK~~Ca~CGyp 40 (95)
+|..||..---. ..-.|..||+.
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCCce
Confidence 577777743322 45678888874
No 93
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=29.99 E-value=29 Score=20.01 Aligned_cols=15 Identities=40% Similarity=0.871 Sum_probs=10.3
Q ss_pred CcccccccCcccccc
Q 034411 24 RRSFHIQKSRCSACA 38 (95)
Q Consensus 24 ~~syH~qK~~Ca~CG 38 (95)
.+-||.|--.|..||
T Consensus 14 ~RR~~~~~isC~~CG 28 (35)
T PF07503_consen 14 NRRFHYQFISCTNCG 28 (35)
T ss_dssp STTTT-TT--BTTCC
T ss_pred CCcccCcCccCCCCC
Confidence 356999999999999
No 94
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=29.34 E-value=27 Score=27.10 Aligned_cols=58 Identities=17% Similarity=0.384 Sum_probs=26.8
Q ss_pred cccccccCCCcccccccCcccccccc-ccccccCCccccccccccccccccccccchhhh
Q 034411 15 THTLCVRCGRRSFHIQKSRCSACAYP-AARVRKYNWSVKAIRRKTTGTGRMRYLRHVPRR 73 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK~~Ca~CGyp-s~k~R~YnWs~Ka~rr~ttGTGrmr~lk~v~rr 73 (95)
-+-.|-.||. .||.....|..||-. ..+...+.......-|=-+=----.|||+|.+.
T Consensus 196 R~L~Cs~C~t-~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd~~ 254 (290)
T PF04216_consen 196 RYLHCSLCGT-EWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVDRE 254 (290)
T ss_dssp EEEEETTT---EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEETT
T ss_pred EEEEcCCCCC-eeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHhhh
Confidence 4566777875 478888899999984 355555544444444433334455799999843
No 95
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=29.02 E-value=28 Score=20.70 Aligned_cols=12 Identities=42% Similarity=0.919 Sum_probs=6.7
Q ss_pred ccccccCCCccc
Q 034411 16 HTLCVRCGRRSF 27 (95)
Q Consensus 16 H~lCrRCG~~sy 27 (95)
-++|.|||+-..
T Consensus 2 ~~~CprC~kg~H 13 (36)
T PF14787_consen 2 PGLCPRCGKGFH 13 (36)
T ss_dssp --C-TTTSSSCS
T ss_pred CccCcccCCCcc
Confidence 368999987543
No 96
>PF06869 DUF1258: Protein of unknown function (DUF1258); InterPro: IPR009667 This family represents a conserved region approximately 260 residues long within a number of hypothetical proteins of unknown function that seem to be specific to Caenorhabditis elegans. Note that this family contains a number of conserved cysteine and histidine residues.
Probab=28.18 E-value=21 Score=29.04 Aligned_cols=23 Identities=39% Similarity=0.821 Sum_probs=18.2
Q ss_pred CCcccccccCCCcccccccCccccc
Q 034411 13 NKTHTLCVRCGRRSFHIQKSRCSAC 37 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qK~~Ca~C 37 (95)
--+|.+|..||+...+.++ |.-|
T Consensus 15 ~S~h~~CN~CG~~~~~~~k--C~~c 37 (258)
T PF06869_consen 15 FSTHFICNSCGKVVESNEK--CSCC 37 (258)
T ss_pred ceeehhhhhhhhhhccCce--eecc
Confidence 4689999999998777764 6555
No 97
>PRK09462 fur ferric uptake regulator; Provisional
Probab=27.97 E-value=25 Score=24.52 Aligned_cols=13 Identities=31% Similarity=0.976 Sum_probs=10.5
Q ss_pred CcccccccCCCcc
Q 034411 14 KTHTLCVRCGRRS 26 (95)
Q Consensus 14 ktH~lCrRCG~~s 26 (95)
--|..|..||+..
T Consensus 88 H~H~iC~~Cg~i~ 100 (148)
T PRK09462 88 HDHLICLDCGKVI 100 (148)
T ss_pred CCceEECCCCCEE
Confidence 3689999999763
No 98
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=27.83 E-value=35 Score=28.52 Aligned_cols=30 Identities=27% Similarity=0.584 Sum_probs=19.4
Q ss_pred CCCCCCCCCcccccccCCCccccccc-----Ccccccccc
Q 034411 6 GSFGKRRNKTHTLCVRCGRRSFHIQK-----SRCSACAYP 40 (95)
Q Consensus 6 ~SfGKr~~ktH~lCrRCG~~syH~qK-----~~Ca~CGyp 40 (95)
|-.||-| .+-|++|+.. |...- ..|. ||-|
T Consensus 233 P~~GKYh---~~~c~~C~~~-~~~~~~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 233 PLLGKYH---QTACEACGEP-AVSEDAETACANCP-CGGR 267 (374)
T ss_pred cCCCccc---hhhhcccCCc-CCchhhhhcCCCCC-CCCc
Confidence 3456666 5678888754 33333 7799 9976
No 99
>PF14653 IGFL: Insulin growth factor-like family
Probab=27.67 E-value=30 Score=24.08 Aligned_cols=32 Identities=28% Similarity=0.591 Sum_probs=23.3
Q ss_pred ccccc---cCCCcccccccCccccccc-cccccccC
Q 034411 16 HTLCV---RCGRRSFHIQKSRCSACAY-PAARVRKY 47 (95)
Q Consensus 16 H~lCr---RCG~~syH~qK~~Ca~CGy-ps~k~R~Y 47 (95)
..+|. |||.+.|+.++..|..=.+ +-.|.|.+
T Consensus 10 l~~Cq~~~rCG~~~YNPl~~cC~~~~iv~l~kT~~C 45 (89)
T PF14653_consen 10 LWLCQPAPRCGDKFYNPLEHCCCDDTIVPLPKTRKC 45 (89)
T ss_pred cccccccCcccCcccChhhhcccCCcEEcCCCcccc
Confidence 34665 8999999999999976555 44555543
No 100
>PRK08764 ferredoxin; Provisional
Probab=27.50 E-value=31 Score=24.09 Aligned_cols=13 Identities=15% Similarity=0.853 Sum_probs=10.6
Q ss_pred ccccCcccccccc
Q 034411 28 HIQKSRCSACAYP 40 (95)
Q Consensus 28 H~qK~~Ca~CGyp 40 (95)
.|-+.-|+.||||
T Consensus 14 ~lp~~ncg~cg~~ 26 (135)
T PRK08764 14 LLPQTQCGQCGFD 26 (135)
T ss_pred hCCCCCCccCCCc
Confidence 4567789999998
No 101
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.30 E-value=30 Score=29.31 Aligned_cols=24 Identities=42% Similarity=1.024 Sum_probs=13.2
Q ss_pred ccccccCCCc----------ccccc--cCccccccc
Q 034411 16 HTLCVRCGRR----------SFHIQ--KSRCSACAY 39 (95)
Q Consensus 16 H~lCrRCG~~----------syH~q--K~~Ca~CGy 39 (95)
.+.|+.||.. .||.. .-.|--|||
T Consensus 213 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 213 NLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGY 248 (505)
T ss_pred eeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcC
Confidence 3456655544 46643 345666666
No 102
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=26.72 E-value=54 Score=20.88 Aligned_cols=33 Identities=21% Similarity=0.532 Sum_probs=25.0
Q ss_pred CCCCCCC--cccccccCCCccccccc--Ccccccccc
Q 034411 8 FGKRRNK--THTLCVRCGRRSFHIQK--SRCSACAYP 40 (95)
Q Consensus 8 fGKr~~k--tH~lCrRCG~~syH~qK--~~Ca~CGyp 40 (95)
+|.+|.- ....|..||+..--... ..|..||-|
T Consensus 8 ~a~~H~L~~~~~NCl~CGkIiC~~Eg~~~pC~fCg~~ 44 (57)
T PF06221_consen 8 QARRHPLFPYAPNCLNCGKIICEQEGPLGPCPFCGTP 44 (57)
T ss_pred ccccCCCccccccccccChhhcccccCcCcCCCCCCc
Confidence 3455532 36679999999988887 899999975
No 103
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=26.54 E-value=36 Score=28.55 Aligned_cols=26 Identities=31% Similarity=0.731 Sum_probs=20.3
Q ss_pred CCcccccccCCCcccccccCccccccc
Q 034411 13 NKTHTLCVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qK~~Ca~CGy 39 (95)
.|+.-.|..||-.+.-. -..|.+|+-
T Consensus 4 ~~~~y~C~~Cg~~~~~~-~g~Cp~C~~ 29 (454)
T TIGR00416 4 AKSKFVCQHCGADSPKW-QGKCPACHA 29 (454)
T ss_pred CCCeEECCcCCCCCccc-cEECcCCCC
Confidence 46888999999876543 378999985
No 104
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=26.38 E-value=29 Score=25.25 Aligned_cols=26 Identities=27% Similarity=0.700 Sum_probs=20.7
Q ss_pred cccccccCCCccccccc------Ccccccccc
Q 034411 15 THTLCVRCGRRSFHIQK------SRCSACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK------~~Ca~CGyp 40 (95)
..++|.-||+.-=.+.+ ..|.+||.-
T Consensus 101 ~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 101 EYVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred hcEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 46899999998887776 369999973
No 105
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=26.18 E-value=24 Score=20.17 Aligned_cols=8 Identities=38% Similarity=1.136 Sum_probs=4.2
Q ss_pred Cccccccc
Q 034411 32 SRCSACAY 39 (95)
Q Consensus 32 ~~Ca~CGy 39 (95)
..|.+|||
T Consensus 23 ~vC~~Cg~ 30 (34)
T PF14803_consen 23 LVCPACGF 30 (34)
T ss_dssp EEETTTTE
T ss_pred eECCCCCC
Confidence 45555554
No 106
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.79 E-value=36 Score=33.32 Aligned_cols=21 Identities=29% Similarity=0.929 Sum_probs=11.1
Q ss_pred cccccCCCcccccccCcccccccc
Q 034411 17 TLCVRCGRRSFHIQKSRCSACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~syH~qK~~Ca~CGyp 40 (95)
..|..||...|- ..|..||.+
T Consensus 668 rkCPkCG~~t~~---~fCP~CGs~ 688 (1337)
T PRK14714 668 RRCPSCGTETYE---NRCPDCGTH 688 (1337)
T ss_pred EECCCCCCcccc---ccCcccCCc
Confidence 456666665432 255555544
No 107
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=25.75 E-value=26 Score=25.02 Aligned_cols=25 Identities=32% Similarity=0.777 Sum_probs=19.1
Q ss_pred cccccccCCCcccccccC------ccccccc
Q 034411 15 THTLCVRCGRRSFHIQKS------RCSACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK~------~Ca~CGy 39 (95)
..++|.-|++.--.+.+. .|.+||.
T Consensus 92 ~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 92 EYVLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp HHSSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred HEEEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 457899999888777664 6888885
No 108
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=25.74 E-value=62 Score=26.42 Aligned_cols=58 Identities=19% Similarity=0.397 Sum_probs=37.6
Q ss_pred CCCcccccccCCCcccccccCccccccccccccccCCccccc-----cccccccccccccccchhhh
Q 034411 12 RNKTHTLCVRCGRRSFHIQKSRCSACAYPAARVRKYNWSVKA-----IRRKTTGTGRMRYLRHVPRR 73 (95)
Q Consensus 12 ~~ktH~lCrRCG~~syH~qK~~Ca~CGyps~k~R~YnWs~Ka-----~rr~ttGTGrmr~lk~v~rr 73 (95)
.+.-+-.|-.|+. .||.....|..||-. +.-.| |+... .-|=-+=-.--.|||+|+.+
T Consensus 206 ~G~RyL~CslC~t-eW~~~R~~C~~Cg~~--~~l~y-~~~e~~~~~~~~r~e~C~~C~~YlK~~~~~ 268 (305)
T TIGR01562 206 TGLRYLSCSLCAT-EWHYVRVKCSHCEES--KHLAY-LSLEHDAEKAVLKAETCDSCQGYLKILYQE 268 (305)
T ss_pred CCceEEEcCCCCC-cccccCccCCCCCCC--Cceee-EeecCCCCCcceEEeeccccccchhhhccc
Confidence 3445667777765 488888999999964 33345 77643 22333334456899999875
No 109
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=25.70 E-value=40 Score=23.38 Aligned_cols=28 Identities=21% Similarity=0.496 Sum_probs=18.7
Q ss_pred CCcccccccCCCcccccc---cCccccccccc
Q 034411 13 NKTHTLCVRCGRRSFHIQ---KSRCSACAYPA 41 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~q---K~~Ca~CGyps 41 (95)
-+....|+.||.. |-+. ...|..||-+.
T Consensus 68 vp~~~~C~~Cg~~-~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 68 EKVELECKDCSHV-FKPNALDYGVCEKCHSKN 98 (117)
T ss_pred cCCEEEhhhCCCc-cccCCccCCcCcCCCCCc
Confidence 3567789999944 4332 23599999654
No 110
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=25.56 E-value=35 Score=25.14 Aligned_cols=26 Identities=27% Similarity=0.740 Sum_probs=20.5
Q ss_pred cccccccCCCcccccc-cCcccccccc
Q 034411 15 THTLCVRCGRRSFHIQ-KSRCSACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~q-K~~Ca~CGyp 40 (95)
+-.-|..||..-|-.+ +-.|..|||.
T Consensus 27 L~~hCp~Cg~PLF~KdG~v~CPvC~~~ 53 (131)
T COG1645 27 LAKHCPKCGTPLFRKDGEVFCPVCGYR 53 (131)
T ss_pred HHhhCcccCCcceeeCCeEECCCCCce
Confidence 4567999999999744 4579999974
No 111
>PRK06991 ferredoxin; Provisional
Probab=25.29 E-value=36 Score=27.09 Aligned_cols=12 Identities=25% Similarity=1.077 Sum_probs=9.8
Q ss_pred cccCcccccccc
Q 034411 29 IQKSRCSACAYP 40 (95)
Q Consensus 29 ~qK~~Ca~CGyp 40 (95)
|-...|+.||||
T Consensus 15 LP~~nCg~CGy~ 26 (270)
T PRK06991 15 LPQTQCTKCGYD 26 (270)
T ss_pred CCCCCCccCCCC
Confidence 456789999998
No 112
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=24.47 E-value=29 Score=22.97 Aligned_cols=13 Identities=31% Similarity=1.022 Sum_probs=10.0
Q ss_pred CCcccccccCCCc
Q 034411 13 NKTHTLCVRCGRR 25 (95)
Q Consensus 13 ~ktH~lCrRCG~~ 25 (95)
.-.|..|..||+.
T Consensus 77 ~h~h~iC~~Cg~v 89 (120)
T PF01475_consen 77 HHHHFICTQCGKV 89 (120)
T ss_dssp SCEEEEETTTS-E
T ss_pred cceEEEECCCCCE
Confidence 4589999999974
No 113
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.35 E-value=9.9 Score=30.25 Aligned_cols=20 Identities=30% Similarity=0.891 Sum_probs=16.0
Q ss_pred cccccccCCCcccccccCccccccc
Q 034411 15 THTLCVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK~~Ca~CGy 39 (95)
-|++||-|-.. -+.||+|+-
T Consensus 82 YH~~Cr~CA~e-----~~vCAKC~k 101 (227)
T KOG3241|consen 82 YHKLCRGCAKE-----QKVCAKCCK 101 (227)
T ss_pred HHHhcccHHHH-----HHHHHHHhc
Confidence 58888888754 489999986
No 114
>COG2878 Predicted NADH:ubiquinone oxidoreductase, subunit RnfB [Energy production and conversion]
Probab=24.20 E-value=37 Score=26.75 Aligned_cols=12 Identities=33% Similarity=1.218 Sum_probs=9.5
Q ss_pred ccCccccccccc
Q 034411 30 QKSRCSACAYPA 41 (95)
Q Consensus 30 qK~~Ca~CGyps 41 (95)
--..|+.||||.
T Consensus 45 PqsqCgqCGy~G 56 (198)
T COG2878 45 PQTQCGQCGYPG 56 (198)
T ss_pred CccccccCCCCc
Confidence 347899999984
No 115
>PF03858 Crust_neuro_H: Crustacean neurohormone H; InterPro: IPR005558 Arthropod express a family of neuropeptides [] which so far consist of the following types of neurohormones: Crustacean hyperglycemic hormone (CHH). CHH is primarily involved in blood sugar regulation, but also plays a role in the control of molting and reproduction. Molt-inhibiting hormone (MIH). MIH inhibits Y-organs where molting hormone (ecdysteroid) is secreted. A molting cycle is initiated when MIH secretion diminishes or stops. Gonad-inhibiting hormone (GIH), also known as vitellogenesis-inhibiting hormone (VIH) because of its role in inhibiting vitellogenesis in female animals. Mandibular organ-inhibiting hormone (MOIH). MOIH represses the synthesis of methyl farnesoate, the precursor of insect juvenile hormone III in the mandibular organ. Ion transport peptide (ITP) from locust. ITP stimulates salt and water reabsorption and inhibits acid secretion in the ileum of the locust. Caenorhabditis elegans hypothetical protein ZC168.2. These neurohormones are peptides of 70 to 80 residues which are processed from larger size precursors. They contain six conserved cysteines that are involved in disulphide bonds, as shown in the following schematic representation. Crustacean neurohormone H proteins are referred to as precursor-related peptides as they are typically co-transcribed and translated with the CHH neurohormone (IPR001166 from INTERPRO). However, in some species this neuropeptide is synthesized as a separate protein. Furthermore, neurohormone H can undergo proteolysis to give rise to 5 different neuropeptides [].
Probab=23.73 E-value=21 Score=21.85 Aligned_cols=17 Identities=41% Similarity=0.516 Sum_probs=12.2
Q ss_pred cccccccccccccchhh
Q 034411 56 RKTTGTGRMRYLRHVPR 72 (95)
Q Consensus 56 r~ttGTGrmr~lk~v~r 72 (95)
|.+.|.|||..|-.-.+
T Consensus 1 RSaeG~GRMerLLaSlr 17 (41)
T PF03858_consen 1 RSAEGFGRMERLLASLR 17 (41)
T ss_pred CCccchhhHHHHHHHHh
Confidence 46789999987755444
No 116
>PRK06260 threonine synthase; Validated
Probab=23.12 E-value=48 Score=26.78 Aligned_cols=24 Identities=21% Similarity=0.684 Sum_probs=17.6
Q ss_pred ccccccCCCcccccc--cCcccccccc
Q 034411 16 HTLCVRCGRRSFHIQ--KSRCSACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~syH~q--K~~Ca~CGyp 40 (95)
+..|.+||.. |... -..|..||-+
T Consensus 3 ~~~C~~cg~~-~~~~~~~~~Cp~cg~~ 28 (397)
T PRK06260 3 WLKCIECGKE-YDPDEIIYTCPECGGL 28 (397)
T ss_pred EEEECCCCCC-CCCCCccccCCCCCCe
Confidence 4689999977 5543 2579999864
No 117
>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=23.02 E-value=42 Score=22.24 Aligned_cols=24 Identities=21% Similarity=0.523 Sum_probs=12.1
Q ss_pred ccccCCCcccccccCccccccccc
Q 034411 18 LCVRCGRRSFHIQKSRCSACAYPA 41 (95)
Q Consensus 18 lCrRCG~~syH~qK~~Ca~CGyps 41 (95)
.|.-|=...--..+.-|.+||.++
T Consensus 11 rC~aCf~~t~~~~k~FCp~CGn~T 34 (73)
T PF08772_consen 11 RCHACFKITKDMTKQFCPKCGNAT 34 (73)
T ss_dssp E-SSS--EES-SS--S-SSS--S-
T ss_pred EccccccCcCCCCceeCcccCCCc
Confidence 588888888888999999999873
No 118
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=22.97 E-value=42 Score=23.28 Aligned_cols=23 Identities=30% Similarity=0.756 Sum_probs=16.1
Q ss_pred cccccCCCccccccc---Cccccccc
Q 034411 17 TLCVRCGRRSFHIQK---SRCSACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qK---~~Ca~CGy 39 (95)
-.|..||+.+.--+- ..|.+||+
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~~ 62 (90)
T PTZ00255 37 YFCPFCGKHAVKRQAVGIWRCKGCKK 62 (90)
T ss_pred ccCCCCCCCceeeeeeEEEEcCCCCC
Confidence 468888877755443 67888886
No 119
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=22.03 E-value=39 Score=29.13 Aligned_cols=25 Identities=32% Similarity=0.820 Sum_probs=19.3
Q ss_pred ccccccCCCcc--ccccc-----Ccccccccc
Q 034411 16 HTLCVRCGRRS--FHIQK-----SRCSACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~s--yH~qK-----~~Ca~CGyp 40 (95)
-+||.-|+..- +++.+ ..|.+|||.
T Consensus 96 FVlC~~C~NPETel~itk~q~i~~~CkACG~r 127 (400)
T KOG2767|consen 96 FVLCPSCENPETELIITKKQTISLKCKACGFR 127 (400)
T ss_pred heeCcCCCCCceeEEecccchhhhHHHHcCCc
Confidence 46899999874 55554 469999995
No 120
>PRK04165 acetyl-CoA decarbonylase/synthase complex subunit gamma; Provisional
Probab=21.94 E-value=45 Score=28.60 Aligned_cols=12 Identities=33% Similarity=1.010 Sum_probs=9.7
Q ss_pred cccCcccccccc
Q 034411 29 IQKSRCSACAYP 40 (95)
Q Consensus 29 ~qK~~Ca~CGyp 40 (95)
+.+.-|+.||||
T Consensus 12 LP~~nCg~CG~~ 23 (450)
T PRK04165 12 LPKTNCGECGEP 23 (450)
T ss_pred CCCCCCCCCCCc
Confidence 456779999998
No 121
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=21.66 E-value=44 Score=23.25 Aligned_cols=23 Identities=22% Similarity=0.667 Sum_probs=16.1
Q ss_pred cccccCCCccccccc---Cccccccc
Q 034411 17 TLCVRCGRRSFHIQK---SRCSACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qK---~~Ca~CGy 39 (95)
-.|..||+.+.--+- ..|.+||+
T Consensus 36 y~CpfCgk~~vkR~a~GIW~C~~C~~ 61 (91)
T TIGR00280 36 YVCPFCGKKTVKRGSTGIWTCRKCGA 61 (91)
T ss_pred ccCCCCCCCceEEEeeEEEEcCCCCC
Confidence 458888877754433 67888886
No 122
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=20.98 E-value=40 Score=27.96 Aligned_cols=26 Identities=23% Similarity=0.565 Sum_probs=22.4
Q ss_pred CcccccccCCCcccccc----cCccccccc
Q 034411 14 KTHTLCVRCGRRSFHIQ----KSRCSACAY 39 (95)
Q Consensus 14 ktH~lCrRCG~~syH~q----K~~Ca~CGy 39 (95)
-.-+.|.-||.-.||.. ..+|.+|+|
T Consensus 26 ~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~ 55 (294)
T COG0777 26 GLWTKCPSCGEMLYRKELESNLKVCPKCGH 55 (294)
T ss_pred CceeECCCccceeeHHHHHhhhhcccccCc
Confidence 35689999999999975 578999999
No 123
>PF08536 Whirly: Whirly transcription factor; InterPro: IPR013742 This is a family of plant transcription factors. ; PDB: 3R9Y_A 3N1I_A 3N1K_A 3RA0_A 3N1H_A 3N1J_A 3N1L_A 3R9Z_A 1L3A_D.
Probab=20.77 E-value=39 Score=25.22 Aligned_cols=14 Identities=50% Similarity=0.980 Sum_probs=9.3
Q ss_pred cccccccCCccccc
Q 034411 40 PAARVRKYNWSVKA 53 (95)
Q Consensus 40 ps~k~R~YnWs~Ka 53 (95)
|+.--|.|+|+.|-
T Consensus 40 pa~g~r~YDW~kKq 53 (139)
T PF08536_consen 40 PAVGPRQYDWSKKQ 53 (139)
T ss_dssp EBCSTTEB-GGG-E
T ss_pred cccCCcccccccce
Confidence 56667999999885
No 124
>PRK07218 replication factor A; Provisional
Probab=20.75 E-value=52 Score=27.95 Aligned_cols=23 Identities=30% Similarity=0.562 Sum_probs=19.6
Q ss_pred cccccccCCCcccccccCcccccccc
Q 034411 15 THTLCVRCGRRSFHIQKSRCSACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK~~Ca~CGyp 40 (95)
.-.+|+-|++.- |+..|..||-.
T Consensus 296 li~rCP~C~r~v---~~~~C~~hG~v 318 (423)
T PRK07218 296 LIERCPECGRVI---QKGQCRSHGAV 318 (423)
T ss_pred ceecCcCccccc---cCCcCCCCCCc
Confidence 446899999997 88999999973
No 125
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=20.64 E-value=38 Score=24.85 Aligned_cols=29 Identities=31% Similarity=0.792 Sum_probs=16.1
Q ss_pred cccccCCCcccc--------------cccCccccccccccccc
Q 034411 17 TLCVRCGRRSFH--------------IQKSRCSACAYPAARVR 45 (95)
Q Consensus 17 ~lCrRCG~~syH--------------~qK~~Ca~CGyps~k~R 45 (95)
++|.-||..... +.--.|.+|||...-..
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~ 44 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNEVK 44 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEEEE
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeeeEE
Confidence 578889887643 12347999999755444
No 126
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=20.36 E-value=44 Score=23.88 Aligned_cols=20 Identities=25% Similarity=0.908 Sum_probs=16.0
Q ss_pred cccCCCcccccccCccccccc
Q 034411 19 CVRCGRRSFHIQKSRCSACAY 39 (95)
Q Consensus 19 CrRCG~~syH~qK~~Ca~CGy 39 (95)
|.-|| ...++.+-.|..|+-
T Consensus 1 CPvCg-~~l~vt~l~C~~C~t 20 (113)
T PF09862_consen 1 CPVCG-GELVVTRLKCPSCGT 20 (113)
T ss_pred CCCCC-CceEEEEEEcCCCCC
Confidence 77888 567888889999973
No 127
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=20.34 E-value=45 Score=23.92 Aligned_cols=25 Identities=24% Similarity=0.729 Sum_probs=18.1
Q ss_pred cccccccCCCcccc---c------ccCccccccc
Q 034411 15 THTLCVRCGRRSFH---I------QKSRCSACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH---~------qK~~Ca~CGy 39 (95)
+-+.|.+||+..-- + ---.|+.||-
T Consensus 21 k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGl 54 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGL 54 (104)
T ss_pred ceEecCccCCeeeeEEEEEecCceeEEEcccCcc
Confidence 45679999987654 3 3347999995
Done!