Query 034400
Match_columns 95
No_of_seqs 107 out of 262
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 02:27:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034400.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034400hhsearch_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 1.8E-59 4E-64 322.7 1.9 92 1-92 1-92 (92)
2 PTZ00073 60S ribosomal protein 100.0 1.5E-58 3.2E-63 318.4 3.5 90 1-90 1-90 (91)
3 PRK04179 rpl37e 50S ribosomal 100.0 1.9E-36 4.2E-41 196.7 2.3 57 1-57 1-59 (62)
4 PF01907 Ribosomal_L37e: Ribos 100.0 2.1E-36 4.5E-41 192.7 0.0 54 2-55 1-55 (55)
5 COG2126 RPL37A Ribosomal prote 100.0 3.4E-35 7.4E-40 190.3 2.3 60 1-60 1-61 (61)
6 COG1998 RPS31 Ribosomal protei 93.5 0.03 6.5E-07 35.6 0.7 26 15-40 18-46 (51)
7 PF14599 zinc_ribbon_6: Zinc-r 90.2 0.099 2.1E-06 33.7 0.3 27 12-38 26-55 (61)
8 PRK00432 30S ribosomal protein 90.0 0.17 3.7E-06 31.1 1.2 26 15-40 19-46 (50)
9 PF01783 Ribosomal_L32p: Ribos 88.4 0.28 6E-06 30.5 1.4 24 14-39 24-47 (56)
10 PF13248 zf-ribbon_3: zinc-rib 88.3 0.26 5.6E-06 26.3 1.0 23 17-40 3-25 (26)
11 PF01599 Ribosomal_S27: Riboso 82.9 0.6 1.3E-05 29.0 0.9 26 14-39 16-46 (47)
12 smart00661 RPOL9 RNA polymeras 82.2 0.75 1.6E-05 26.8 1.1 23 18-40 2-29 (52)
13 TIGR01031 rpmF_bact ribosomal 81.5 0.72 1.6E-05 28.9 0.9 24 14-39 24-47 (55)
14 COG0675 Transposase and inacti 80.6 0.79 1.7E-05 33.5 1.0 25 14-40 307-331 (364)
15 PF12773 DZR: Double zinc ribb 79.8 1.8 3.9E-05 25.1 2.2 32 9-40 5-38 (50)
16 PF09297 zf-NADH-PPase: NADH p 76.1 1.1 2.5E-05 24.6 0.5 25 15-39 2-29 (32)
17 PRK12286 rpmF 50S ribosomal pr 73.5 1.8 3.9E-05 27.3 1.0 24 14-39 25-48 (57)
18 PHA00626 hypothetical protein 73.3 1.9 4.2E-05 28.1 1.1 23 18-40 2-32 (59)
19 PRK05978 hypothetical protein; 73.1 2 4.4E-05 31.8 1.4 29 17-45 34-66 (148)
20 PRK14892 putative transcriptio 72.9 2.1 4.5E-05 29.8 1.3 59 13-89 18-84 (99)
21 PF13240 zinc_ribbon_2: zinc-r 72.2 2.2 4.8E-05 22.4 1.0 21 19-40 2-22 (23)
22 COG1571 Predicted DNA-binding 71.0 3 6.5E-05 35.7 2.1 26 16-41 350-377 (421)
23 PF09538 FYDLN_acid: Protein o 68.3 3 6.5E-05 29.2 1.3 24 16-39 9-34 (108)
24 PRK12496 hypothetical protein; 67.7 3.1 6.7E-05 30.5 1.3 29 17-46 128-158 (164)
25 PF12760 Zn_Tnp_IS1595: Transp 66.1 4 8.6E-05 23.9 1.3 24 16-39 18-45 (46)
26 TIGR02300 FYDLN_acid conserved 64.9 4 8.8E-05 30.1 1.5 24 16-39 9-34 (129)
27 PRK00420 hypothetical protein; 63.0 4.1 8.9E-05 29.0 1.2 24 17-40 24-49 (112)
28 PRK05508 methionine sulfoxide 62.5 4.7 0.0001 29.2 1.4 29 13-41 30-58 (119)
29 KOG3362 Predicted BBOX Zn-fing 61.9 3.9 8.4E-05 31.1 0.9 21 22-42 109-129 (156)
30 PF04060 FeS: Putative Fe-S cl 61.7 3.9 8.5E-05 23.3 0.7 13 29-41 2-14 (35)
31 KOG0856 Predicted pilin-like t 61.3 6.5 0.00014 29.6 2.0 39 3-41 36-79 (146)
32 PF09855 DUF2082: Nucleic-acid 60.5 4.7 0.0001 26.1 1.0 8 33-40 38-45 (64)
33 COG0333 RpmF Ribosomal protein 59.8 5.2 0.00011 25.7 1.1 23 16-40 27-49 (57)
34 PRK13130 H/ACA RNA-protein com 58.3 5.8 0.00013 25.2 1.1 20 18-40 7-26 (56)
35 TIGR00357 methionine-R-sulfoxi 55.5 12 0.00025 27.5 2.5 29 13-41 37-65 (134)
36 PF10571 UPF0547: Uncharacteri 55.1 7.4 0.00016 21.1 1.1 22 18-40 2-23 (26)
37 PF08271 TF_Zn_Ribbon: TFIIB z 53.0 7.6 0.00016 22.4 1.0 22 18-39 2-27 (43)
38 PF12172 DUF35_N: Rubredoxin-l 52.9 6 0.00013 22.0 0.5 22 16-38 11-32 (37)
39 COG5349 Uncharacterized protei 50.8 7.3 0.00016 28.7 0.8 26 15-40 20-49 (126)
40 TIGR02098 MJ0042_CXXC MJ0042 f 49.5 7.6 0.00016 21.5 0.6 24 16-40 2-34 (38)
41 PF13824 zf-Mss51: Zinc-finger 48.9 12 0.00026 23.9 1.4 24 18-41 1-24 (55)
42 COG0229 Conserved domain frequ 47.9 11 0.00023 28.3 1.3 27 15-41 41-67 (140)
43 TIGR00269 conserved hypothetic 47.3 9.4 0.0002 25.8 0.9 12 31-42 80-91 (104)
44 PRK05580 primosome assembly pr 46.8 13 0.00027 32.6 1.7 28 14-41 379-418 (679)
45 PF12387 Peptidase_C74: Pestiv 46.2 11 0.00024 29.7 1.2 26 12-39 158-183 (200)
46 PRK00241 nudC NADH pyrophospha 45.8 11 0.00024 29.3 1.1 26 14-39 97-125 (256)
47 PF10555 MraY_sig1: Phospho-N- 45.4 10 0.00022 18.2 0.6 7 3-9 2-8 (13)
48 COG1439 Predicted nucleic acid 45.1 11 0.00024 28.9 1.1 32 14-46 137-168 (177)
49 PF01641 SelR: SelR domain; I 45.1 15 0.00033 26.5 1.7 32 10-41 31-62 (124)
50 PHA02942 putative transposase; 44.8 12 0.00026 30.8 1.3 26 15-40 324-351 (383)
51 PRK00222 methionine sulfoxide 44.4 21 0.00046 26.5 2.4 29 13-41 40-68 (142)
52 PRK00398 rpoP DNA-directed RNA 43.6 14 0.00031 21.4 1.1 24 17-40 4-30 (46)
53 PRK01110 rpmF 50S ribosomal pr 43.5 12 0.00027 23.7 0.9 21 16-39 27-47 (60)
54 TIGR00311 aIF-2beta translatio 43.0 10 0.00023 27.4 0.6 25 15-39 96-126 (133)
55 COG1545 Predicted nucleic-acid 42.5 14 0.0003 26.5 1.2 27 14-41 27-53 (140)
56 PRK08329 threonine synthase; V 42.2 23 0.00049 28.2 2.4 66 17-87 2-69 (347)
57 PF09082 DUF1922: Domain of un 41.6 9.7 0.00021 25.3 0.2 22 17-40 4-28 (68)
58 PRK06450 threonine synthase; V 41.0 15 0.00033 29.4 1.3 24 16-40 3-27 (338)
59 KOG4192 Uncharacterized conser 40.9 12 0.00027 27.8 0.7 24 8-32 66-89 (134)
60 PRK14018 trifunctional thiored 40.4 16 0.00034 31.8 1.4 29 13-41 415-443 (521)
61 PF03604 DNA_RNApol_7kD: DNA d 40.4 23 0.00049 20.1 1.6 23 18-40 2-26 (32)
62 PF07282 OrfB_Zn_ribbon: Putat 40.2 16 0.00035 22.3 1.1 25 15-39 27-54 (69)
63 PF05191 ADK_lid: Adenylate ki 40.0 16 0.00035 21.0 1.0 21 18-39 3-29 (36)
64 COG1592 Rubrerythrin [Energy p 40.0 16 0.00034 27.6 1.1 28 16-43 134-161 (166)
65 COG1594 RPB9 DNA-directed RNA 39.4 15 0.00032 25.7 0.9 23 17-39 3-30 (113)
66 smart00834 CxxC_CXXC_SSSS Puta 39.4 22 0.00048 19.4 1.5 24 17-40 6-35 (41)
67 PRK14559 putative protein seri 39.2 22 0.00048 31.6 2.1 29 9-40 8-36 (645)
68 PRK11823 DNA repair protein Ra 39.1 18 0.00038 30.2 1.4 26 13-39 4-29 (446)
69 PRK12336 translation initiatio 38.9 15 0.00033 27.8 1.0 34 15-48 97-138 (201)
70 PRK04136 rpl40e 50S ribosomal 38.8 18 0.00039 22.7 1.1 22 17-39 15-36 (48)
71 PRK03681 hypA hydrogenase nick 38.0 17 0.00037 25.1 1.0 37 3-40 53-96 (114)
72 COG2816 NPY1 NTP pyrophosphohy 36.4 18 0.00038 29.5 1.0 27 13-39 108-137 (279)
73 COG3677 Transposase and inacti 36.2 21 0.00047 25.4 1.3 25 14-40 28-62 (129)
74 TIGR00515 accD acetyl-CoA carb 36.0 16 0.00036 29.2 0.8 26 15-40 25-54 (285)
75 PRK12380 hydrogenase nickel in 35.8 20 0.00043 24.8 1.1 26 14-40 68-95 (113)
76 PF10892 DUF2688: Protein of u 35.6 13 0.00027 24.4 0.0 16 14-29 8-23 (60)
77 TIGR01384 TFS_arch transcripti 35.6 20 0.00044 23.6 1.0 23 18-40 2-25 (104)
78 PF02150 RNA_POL_M_15KD: RNA p 35.2 20 0.00044 20.3 0.9 23 17-39 2-28 (35)
79 smart00547 ZnF_RBZ Zinc finger 34.8 24 0.00052 17.9 1.1 22 18-40 4-25 (26)
80 PRK05550 bifunctional methioni 34.5 33 0.00072 27.8 2.3 29 13-41 33-61 (283)
81 PF10217 DUF2039: Uncharacteri 34.4 8 0.00017 26.9 -1.1 12 30-41 80-91 (92)
82 cd00729 rubredoxin_SM Rubredox 33.4 25 0.00055 19.7 1.1 27 17-43 3-30 (34)
83 PRK14873 primosome assembly pr 33.2 24 0.00051 31.4 1.4 16 25-40 402-419 (665)
84 PF10013 DUF2256: Uncharacteri 33.1 15 0.00032 22.5 0.0 20 28-53 5-24 (42)
85 PRK04351 hypothetical protein; 33.1 23 0.00049 25.9 1.1 22 17-38 113-139 (149)
86 PF04216 FdhE: Protein involve 33.1 22 0.00048 27.6 1.0 59 14-73 195-254 (290)
87 cd07153 Fur_like Ferric uptake 32.0 20 0.00043 23.4 0.5 12 14-25 71-82 (116)
88 COG2260 Predicted Zn-ribbon RN 31.6 25 0.00053 23.0 0.9 20 17-39 6-25 (59)
89 CHL00174 accD acetyl-CoA carbo 31.4 17 0.00037 29.7 0.2 31 15-45 37-74 (296)
90 TIGR00100 hypA hydrogenase nic 31.1 27 0.00058 24.2 1.1 38 3-41 53-96 (115)
91 smart00653 eIF2B_5 domain pres 31.1 19 0.00042 25.2 0.4 25 15-39 79-109 (110)
92 smart00659 RPOLCX RNA polymera 30.9 29 0.00062 20.7 1.1 23 18-40 4-28 (44)
93 PF14787 zf-CCHC_5: GAG-polypr 30.4 27 0.00058 20.8 0.8 13 16-28 2-14 (36)
94 PRK05654 acetyl-CoA carboxylas 30.4 18 0.00039 29.1 0.2 26 15-40 26-55 (292)
95 PF14803 Nudix_N_2: Nudix N-te 30.2 20 0.00043 20.6 0.3 9 31-39 22-30 (34)
96 PF07503 zf-HYPF: HypF finger; 30.0 28 0.00061 20.0 0.9 15 24-38 14-28 (35)
97 PRK14714 DNA polymerase II lar 27.7 31 0.00068 33.7 1.2 21 17-40 668-688 (1337)
98 TIGR00375 conserved hypothetic 27.7 35 0.00076 28.6 1.4 30 6-40 233-267 (374)
99 COG1645 Uncharacterized Zn-fin 27.6 31 0.00068 25.4 1.0 26 15-40 27-53 (131)
100 PRK09462 fur ferric uptake reg 27.4 26 0.00056 24.4 0.5 12 15-26 89-100 (148)
101 PF03858 Crust_neuro_H: Crusta 26.9 17 0.00037 22.2 -0.4 17 56-72 1-17 (41)
102 TIGR00416 sms DNA repair prote 26.6 37 0.0008 28.5 1.4 26 13-39 4-29 (454)
103 PRK03988 translation initiatio 26.3 27 0.00059 25.4 0.5 25 15-39 101-131 (138)
104 PF06221 zf-C2HC5: Putative zi 26.2 53 0.0012 20.9 1.7 33 8-40 8-44 (57)
105 PRK14890 putative Zn-ribbon RN 26.0 40 0.00087 21.9 1.2 27 14-40 23-57 (59)
106 PF01873 eIF-5_eIF-2B: Domain 25.9 27 0.00058 24.9 0.4 25 15-39 92-122 (125)
107 PRK08764 ferredoxin; Provision 25.6 35 0.00075 23.9 0.9 13 28-40 14-26 (135)
108 PF14653 IGFL: Insulin growth 25.1 35 0.00075 23.7 0.8 32 16-47 10-45 (89)
109 KOG3241 Uncharacterized conser 24.7 11 0.00023 30.0 -2.0 20 15-39 82-101 (227)
110 PTZ00255 60S ribosomal protein 24.5 38 0.00083 23.4 0.9 23 17-39 37-62 (90)
111 PF08772 NOB1_Zn_bind: Nin one 24.0 37 0.00081 22.5 0.8 24 18-41 11-34 (73)
112 PRK00564 hypA hydrogenase nick 23.9 50 0.0011 22.9 1.4 28 13-41 68-98 (117)
113 PF01475 FUR: Ferric uptake re 23.7 31 0.00068 22.9 0.3 13 13-25 77-89 (120)
114 PRK06260 threonine synthase; V 23.6 45 0.00099 26.9 1.3 24 16-40 3-28 (397)
115 PF09862 DUF2089: Protein of u 23.5 35 0.00075 24.4 0.6 20 19-39 1-20 (113)
116 TIGR00280 L37a ribosomal prote 22.9 41 0.00089 23.4 0.8 23 17-39 36-61 (91)
117 COG2888 Predicted Zn-ribbon RN 22.8 40 0.00086 22.2 0.7 28 13-40 24-59 (61)
118 COG4888 Uncharacterized Zn rib 22.4 40 0.00087 24.2 0.7 26 14-39 20-54 (104)
119 PF03367 zf-ZPR1: ZPR1 zinc-fi 22.2 35 0.00076 25.1 0.4 29 17-45 2-44 (161)
120 PRK06991 ferredoxin; Provision 22.1 44 0.00095 26.6 1.0 12 29-40 15-26 (270)
121 PRK07218 replication factor A; 22.1 46 0.00099 28.3 1.1 23 15-40 296-318 (423)
122 PF06869 DUF1258: Protein of u 21.9 35 0.00076 27.7 0.4 24 12-37 14-37 (258)
123 TIGR00340 zpr1_rel ZPR1-relate 21.7 43 0.00094 24.9 0.8 14 31-44 28-41 (163)
124 PF08536 Whirly: Whirly transc 21.6 37 0.00081 25.3 0.5 14 40-53 40-53 (139)
125 PRK14873 primosome assembly pr 21.2 56 0.0012 29.1 1.5 23 15-40 409-431 (665)
126 COG0777 AccD Acetyl-CoA carbox 21.1 38 0.00082 28.1 0.4 69 14-82 26-137 (294)
127 KOG2767 Translation initiation 20.8 43 0.00093 28.8 0.7 25 16-40 96-127 (400)
128 PRK04165 acetyl-CoA decarbonyl 20.8 47 0.001 28.4 0.9 12 29-40 12-23 (450)
129 PRK03976 rpl37ae 50S ribosomal 20.5 49 0.0011 22.9 0.8 23 17-39 37-62 (90)
130 PF14149 YhfH: YhfH-like prote 20.3 34 0.00074 20.4 0.0 12 28-39 10-21 (37)
131 PRK00423 tfb transcription ini 20.1 50 0.0011 26.2 0.9 36 16-51 11-58 (310)
No 1
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.8e-59 Score=322.65 Aligned_cols=92 Identities=71% Similarity=1.242 Sum_probs=89.7
Q ss_pred CCCCCCCCCCCCCCcccccccCCCccccccccccccccCcccccccCCccccccccccccccccccccccchhcccCcCc
Q 034400 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHLQKSRCAACAYPAARKRTYNWSVKAIRRKTTGTGRMRYLRHVPRRFKSGFRE 80 (95)
Q Consensus 1 MtKGT~SfGKr~~ktH~lCrRCG~~syH~qKk~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 034400 81 GTQAAPRKKGAA 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 999999977653
No 2
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=100.00 E-value=1.5e-58 Score=318.35 Aligned_cols=90 Identities=71% Similarity=1.243 Sum_probs=88.4
Q ss_pred CCCCCCCCCCCCCCcccccccCCCccccccccccccccCcccccccCCccccccccccccccccccccccchhcccCcCc
Q 034400 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHLQKSRCAACAYPAARKRTYNWSVKAIRRKTTGTGRMRYLRHVPRRFKSGFRE 80 (95)
Q Consensus 1 MtKGT~SfGKr~~ktH~lCrRCG~~syH~qKk~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 034400 81 GTQAAPRKKG 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=1.9e-36 Score=196.73 Aligned_cols=57 Identities=47% Similarity=0.934 Sum_probs=54.7
Q ss_pred CCCCCCCCCCCCCC-cccccccCCCccccccccccccccC-cccccccCCccccccccc
Q 034400 1 MGKGTGSFGKRRNK-THTLCVRCGRRSFHLQKSRCAACAY-PAARKRTYNWSVKAIRRK 57 (95)
Q Consensus 1 MtKGT~SfGKr~~k-tH~lCrRCG~~syH~qKk~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 999999999999997654
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=2.1e-36 Score=192.66 Aligned_cols=54 Identities=74% Similarity=1.329 Sum_probs=46.0
Q ss_pred CCCCCCCCCCCCCcccccccCCCccccccccccccccCcccccc-cCCccccccc
Q 034400 2 GKGTGSFGKRRNKTHTLCVRCGRRSFHLQKSRCAACAYPAARKR-TYNWSVKAIR 55 (95)
Q Consensus 2 tKGT~SfGKr~~ktH~lCrRCG~~syH~qKk~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=3.4e-35 Score=190.35 Aligned_cols=60 Identities=62% Similarity=1.119 Sum_probs=58.3
Q ss_pred CCCCCCCCCCCCCCcccccccCCCccccccccccccccCc-ccccccCCcccccccccccc
Q 034400 1 MGKGTGSFGKRRNKTHTLCVRCGRRSFHLQKSRCAACAYP-AARKRTYNWSVKAIRRKTTG 60 (95)
Q Consensus 1 MtKGT~SfGKr~~ktH~lCrRCG~~syH~qKk~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=93.52 E-value=0.03 Score=35.62 Aligned_cols=26 Identities=31% Similarity=0.829 Sum_probs=21.9
Q ss_pred cccccccCCC---ccccccccccccccCc
Q 034400 15 THTLCVRCGR---RSFHLQKSRCAACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~---~syH~qKk~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 4669999999999995
No 7
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=90.22 E-value=0.099 Score=33.69 Aligned_cols=27 Identities=33% Similarity=0.872 Sum_probs=15.6
Q ss_pred CCCcccccccCCCcc---cccccccccccc
Q 034400 12 RNKTHTLCVRCGRRS---FHLQKSRCAACA 38 (95)
Q Consensus 12 ~~ktH~lCrRCG~~s---yH~qKk~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 346899999999876 999999999999
No 8
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=89.98 E-value=0.17 Score=31.13 Aligned_cols=26 Identities=35% Similarity=0.943 Sum_probs=20.9
Q ss_pred cccccccCCC--ccccccccccccccCc
Q 034400 15 THTLCVRCGR--RSFHLQKSRCAACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~--~syH~qKk~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 4456668899999984
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=88.40 E-value=0.28 Score=30.45 Aligned_cols=24 Identities=29% Similarity=0.776 Sum_probs=21.1
Q ss_pred CcccccccCCCccccccccccccccC
Q 034400 14 KTHTLCVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qKk~Ca~CGy 39 (95)
..-+.|.-|| .+++.+..|.+|||
T Consensus 24 ~~l~~c~~cg--~~~~~H~vc~~cG~ 47 (56)
T PF01783_consen 24 PNLVKCPNCG--EPKLPHRVCPSCGY 47 (56)
T ss_dssp TSEEESSSSS--SEESTTSBCTTTBB
T ss_pred cceeeeccCC--CEecccEeeCCCCe
Confidence 3557899999 79999999999997
No 10
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=88.32 E-value=0.26 Score=26.31 Aligned_cols=23 Identities=22% Similarity=0.671 Sum_probs=19.1
Q ss_pred cccccCCCccccccccccccccCc
Q 034400 17 TLCVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~syH~qKk~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 677888999999964
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=82.90 E-value=0.6 Score=28.95 Aligned_cols=26 Identities=31% Similarity=0.815 Sum_probs=20.6
Q ss_pred Ccccccc--cCCC---ccccccccccccccC
Q 034400 14 KTHTLCV--RCGR---RSFHLQKSRCAACAY 39 (95)
Q Consensus 14 ktH~lCr--RCG~---~syH~qKk~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 477999999999997
No 12
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=82.18 E-value=0.75 Score=26.77 Aligned_cols=23 Identities=26% Similarity=0.814 Sum_probs=18.9
Q ss_pred ccccCCCcccccc-----ccccccccCc
Q 034400 18 LCVRCGRRSFHLQ-----KSRCAACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~q-----Kk~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 4679999994
No 13
>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=81.46 E-value=0.72 Score=28.85 Aligned_cols=24 Identities=38% Similarity=1.010 Sum_probs=20.9
Q ss_pred CcccccccCCCccccccccccccccC
Q 034400 14 KTHTLCVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qKk~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 45567999997 8999999999997
No 14
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=80.63 E-value=0.79 Score=33.51 Aligned_cols=25 Identities=24% Similarity=0.646 Sum_probs=21.1
Q ss_pred CcccccccCCCccccccccccccccCc
Q 034400 14 KTHTLCVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qKk~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 45678999999 77788899999983
No 15
>PF12773 DZR: Double zinc ribbon
Probab=79.78 E-value=1.8 Score=25.13 Aligned_cols=32 Identities=22% Similarity=0.512 Sum_probs=25.1
Q ss_pred CCCCCCcccccccCCCccc--cccccccccccCc
Q 034400 9 GKRRNKTHTLCVRCGRRSF--HLQKSRCAACAYP 40 (95)
Q Consensus 9 GKr~~ktH~lCrRCG~~sy--H~qKk~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 4445566778999999988 7778889999985
No 16
>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=76.13 E-value=1.1 Score=24.55 Aligned_cols=25 Identities=32% Similarity=0.794 Sum_probs=13.7
Q ss_pred cccccccCCCccccccc---cccccccC
Q 034400 15 THTLCVRCGRRSFHLQK---SRCAACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK---k~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 56778888887766554 56777764
No 17
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=73.48 E-value=1.8 Score=27.34 Aligned_cols=24 Identities=29% Similarity=0.747 Sum_probs=19.9
Q ss_pred CcccccccCCCccccccccccccccC
Q 034400 14 KTHTLCVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qKk~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 44567999995 7888999999998
No 18
>PHA00626 hypothetical protein
Probab=73.31 E-value=1.9 Score=28.15 Aligned_cols=23 Identities=26% Similarity=0.787 Sum_probs=17.5
Q ss_pred ccccCCCccccc--------cccccccccCc
Q 034400 18 LCVRCGRRSFHL--------QKSRCAACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~--------qKk~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 689999864433 67789999984
No 19
>PRK05978 hypothetical protein; Provisional
Probab=73.13 E-value=2 Score=31.78 Aligned_cols=29 Identities=31% Similarity=0.641 Sum_probs=22.4
Q ss_pred cccccCCCc----cccccccccccccCcccccc
Q 034400 17 TLCVRCGRR----SFHLQKSRCAACAYPAARKR 45 (95)
Q Consensus 17 ~lCrRCG~~----syH~qKk~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 56889999999997643333
No 20
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=72.89 E-value=2.1 Score=29.82 Aligned_cols=59 Identities=19% Similarity=0.312 Sum_probs=37.0
Q ss_pred CCcccccccCCCcccccc--------ccccccccCcccccccCCccccccccccccccccccccccchhcccCcCcCCCC
Q 034400 13 NKTHTLCVRCGRRSFHLQ--------KSRCAACAYPAARKRTYNWSVKAIRRKTTGTGRMRYLRHVPRRFKSGFREGTQA 84 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~q--------Kk~Ca~CGyps~k~R~YnWs~Ka~rr~ttGTGRmr~lk~v~rrfkngFreGt~~ 84 (95)
..+.+.|..||. ..+. +-.|..|||--.+ ..+ .++-- =+||..|-.-|.||-..
T Consensus 18 lpt~f~CP~Cge--~~v~v~~~k~~~h~~C~~CG~y~~~--~V~----------~l~ep----IDVY~~wiD~~~eg~i~ 79 (99)
T PRK14892 18 LPKIFECPRCGK--VSISVKIKKNIAIITCGNCGLYTEF--EVP----------SVYDE----VDVYNKFIDLYLEGKIE 79 (99)
T ss_pred CCcEeECCCCCC--eEeeeecCCCcceEECCCCCCccCE--ECC----------ccccc----hhhHHHHHHHHHhcCCC
Confidence 357788999994 5554 8899999973111 111 11111 25788888888888766
Q ss_pred Ccccc
Q 034400 85 APRKK 89 (95)
Q Consensus 85 ~~~~~ 89 (95)
.|-..
T Consensus 80 ~~~~~ 84 (99)
T PRK14892 80 IKERK 84 (99)
T ss_pred ccccC
Confidence 55443
No 21
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=72.19 E-value=2.2 Score=22.44 Aligned_cols=21 Identities=29% Similarity=0.711 Sum_probs=14.0
Q ss_pred cccCCCccccccccccccccCc
Q 034400 19 CVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 19 CrRCG~~syH~qKk~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 777777653 445668888864
No 22
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=71.02 E-value=3 Score=35.71 Aligned_cols=26 Identities=35% Similarity=0.758 Sum_probs=18.6
Q ss_pred ccccccCCCccccccc--cccccccCcc
Q 034400 16 HTLCVRCGRRSFHLQK--SRCAACAYPA 41 (95)
Q Consensus 16 H~lCrRCG~~syH~qK--k~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 23
>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=68.27 E-value=3 Score=29.25 Aligned_cols=24 Identities=29% Similarity=0.825 Sum_probs=20.5
Q ss_pred ccccccCCCcccccccc--ccccccC
Q 034400 16 HTLCVRCGRRSFHLQKS--RCAACAY 39 (95)
Q Consensus 16 H~lCrRCG~~syH~qKk--~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 24
>PRK12496 hypothetical protein; Provisional
Probab=67.65 E-value=3.1 Score=30.55 Aligned_cols=29 Identities=24% Similarity=0.701 Sum_probs=21.9
Q ss_pred cccccCCCcccc--ccccccccccCccccccc
Q 034400 17 TLCVRCGRRSFH--LQKSRCAACAYPAARKRT 46 (95)
Q Consensus 17 ~lCrRCG~~syH--~qKk~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 5699999 4565 455789999998766654
No 25
>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=66.09 E-value=4 Score=23.94 Aligned_cols=24 Identities=33% Similarity=0.866 Sum_probs=16.5
Q ss_pred ccccccCCCc-cccccc---cccccccC
Q 034400 16 HTLCVRCGRR-SFHLQK---SRCAACAY 39 (95)
Q Consensus 16 H~lCrRCG~~-syH~qK---k~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 454433 57888875
No 26
>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=64.92 E-value=4 Score=30.08 Aligned_cols=24 Identities=13% Similarity=0.369 Sum_probs=20.8
Q ss_pred ccccccCCCccccccc--cccccccC
Q 034400 16 HTLCVRCGRRSFHLQK--SRCAACAY 39 (95)
Q Consensus 16 H~lCrRCG~~syH~qK--k~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 27
>PRK00420 hypothetical protein; Validated
Probab=63.00 E-value=4.1 Score=29.01 Aligned_cols=24 Identities=21% Similarity=0.373 Sum_probs=20.9
Q ss_pred cccccCCCccc--cccccccccccCc
Q 034400 17 TLCVRCGRRSF--HLQKSRCAACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~sy--H~qKk~Ca~CGyp 40 (95)
..|+.||..-| +-.+..|..||-+
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 57999999999 5778899999975
No 28
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=62.50 E-value=4.7 Score=29.19 Aligned_cols=29 Identities=21% Similarity=0.629 Sum_probs=25.8
Q ss_pred CCcccccccCCCccccccccccccccCcc
Q 034400 13 NKTHTLCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qKk~Ca~CGyps 41 (95)
..-.-.|..||..-|.-+.|.-+.||+||
T Consensus 30 ~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPS 58 (119)
T PRK05508 30 EKGTYVCKQCGAPLYRSEDKFKSGCGWPS 58 (119)
T ss_pred CCeEEEecCCCCccccccccccCCCCCcc
Confidence 34556899999999999999999999995
No 29
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=61.89 E-value=3.9 Score=31.11 Aligned_cols=21 Identities=29% Similarity=0.653 Sum_probs=16.7
Q ss_pred CCCccccccccccccccCccc
Q 034400 22 CGRRSFHLQKSRCAACAYPAA 42 (95)
Q Consensus 22 CG~~syH~qKk~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 566788888899999998753
No 30
>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=61.66 E-value=3.9 Score=23.30 Aligned_cols=13 Identities=46% Similarity=1.201 Sum_probs=6.0
Q ss_pred ccccccccccCcc
Q 034400 29 LQKSRCAACAYPA 41 (95)
Q Consensus 29 ~qKk~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 31
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=61.29 E-value=6.5 Score=29.62 Aligned_cols=39 Identities=26% Similarity=0.523 Sum_probs=31.3
Q ss_pred CCCCCCCC-----CCCCcccccccCCCccccccccccccccCcc
Q 034400 3 KGTGSFGK-----RRNKTHTLCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 3 KGT~SfGK-----r~~ktH~lCrRCG~~syH~qKk~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 67766665 2234456799999999999999999999994
No 32
>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=60.52 E-value=4.7 Score=26.11 Aligned_cols=8 Identities=38% Similarity=1.310 Sum_probs=5.7
Q ss_pred ccccccCc
Q 034400 33 RCAACAYP 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 33
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=59.77 E-value=5.2 Score=25.65 Aligned_cols=23 Identities=30% Similarity=0.933 Sum_probs=19.8
Q ss_pred ccccccCCCccccccccccccccCc
Q 034400 16 HTLCVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~syH~qKk~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 34
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=58.29 E-value=5.8 Score=25.23 Aligned_cols=20 Identities=30% Similarity=0.806 Sum_probs=17.1
Q ss_pred ccccCCCccccccccccccccCc
Q 034400 18 LCVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~qKk~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 35
>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=55.45 E-value=12 Score=27.55 Aligned_cols=29 Identities=17% Similarity=0.471 Sum_probs=25.7
Q ss_pred CCcccccccCCCccccccccccccccCcc
Q 034400 13 NKTHTLCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qKk~Ca~CGyps 41 (95)
..-.-.|..||...|--+.|.-+.||+||
T Consensus 37 ~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPS 65 (134)
T TIGR00357 37 EEGIYVDITCGEPLFSSEDKFDSGCGWPS 65 (134)
T ss_pred CCeEEEccCCCCccccccchhcCCCCCcC
Confidence 34456799999999999999999999995
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=55.14 E-value=7.4 Score=21.12 Aligned_cols=22 Identities=27% Similarity=0.736 Sum_probs=15.7
Q ss_pred ccccCCCccccccccccccccCc
Q 034400 18 LCVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~qKk~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 4556789999983
No 37
>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=52.98 E-value=7.6 Score=22.36 Aligned_cols=22 Identities=23% Similarity=0.720 Sum_probs=15.4
Q ss_pred ccccCCCccc----cccccccccccC
Q 034400 18 LCVRCGRRSF----HLQKSRCAACAY 39 (95)
Q Consensus 18 lCrRCG~~sy----H~qKk~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 5899999863 233458999997
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=52.90 E-value=6 Score=22.03 Aligned_cols=22 Identities=32% Similarity=0.804 Sum_probs=12.9
Q ss_pred ccccccCCCcccccccccccccc
Q 034400 16 HTLCVRCGRRSFHLQKSRCAACA 38 (95)
Q Consensus 16 H~lCrRCG~~syH~qKk~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 356889998755444 8999997
No 39
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.79 E-value=7.3 Score=28.73 Aligned_cols=26 Identities=35% Similarity=0.754 Sum_probs=21.4
Q ss_pred cccccccCCC----ccccccccccccccCc
Q 034400 15 THTLCVRCGR----RSFHLQKSRCAACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~----~syH~qKk~Ca~CGyp 40 (95)
.+-+|.|||. +.|=.-...|.+||..
T Consensus 20 l~grCP~CGeGrLF~gFLK~~p~C~aCG~d 49 (126)
T COG5349 20 LRGRCPRCGEGRLFRGFLKVVPACEACGLD 49 (126)
T ss_pred hcCCCCCCCCchhhhhhcccCchhhhcccc
Confidence 3568999997 6788889999999963
No 40
>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=49.48 E-value=7.6 Score=21.47 Aligned_cols=24 Identities=29% Similarity=0.733 Sum_probs=15.2
Q ss_pred ccccccCCCcccccc---------ccccccccCc
Q 034400 16 HTLCVRCGRRSFHLQ---------KSRCAACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~syH~q---------Kk~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 3478888853
No 41
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=48.93 E-value=12 Score=23.92 Aligned_cols=24 Identities=25% Similarity=0.609 Sum_probs=15.1
Q ss_pred ccccCCCccccccccccccccCcc
Q 034400 18 LCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 18 lCrRCG~~syH~qKk~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 42
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=47.88 E-value=11 Score=28.28 Aligned_cols=27 Identities=22% Similarity=0.639 Sum_probs=24.2
Q ss_pred cccccccCCCccccccccccccccCcc
Q 034400 15 THTLCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 15 tH~lCrRCG~~syH~qKk~Ca~CGyps 41 (95)
---.|.-||..-|.-.-|.-+-||.||
T Consensus 41 GiY~c~~cg~pLF~S~~KfdSgcGWPS 67 (140)
T COG0229 41 GIYVCIVCGEPLFSSEDKFDSGCGWPS 67 (140)
T ss_pred ceEEeecCCCccccccccccCCCCCcc
Confidence 345799999999999999999999994
No 43
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=47.33 E-value=9.4 Score=25.75 Aligned_cols=12 Identities=33% Similarity=0.886 Sum_probs=7.9
Q ss_pred ccccccccCccc
Q 034400 31 KSRCAACAYPAA 42 (95)
Q Consensus 31 Kk~Ca~CGyps~ 42 (95)
...|..||||+.
T Consensus 80 ~~~C~~CG~pss 91 (104)
T TIGR00269 80 LRRCERCGEPTS 91 (104)
T ss_pred CCcCCcCcCcCC
Confidence 356777777754
No 44
>PRK05580 primosome assembly protein PriA; Validated
Probab=46.77 E-value=13 Score=32.64 Aligned_cols=28 Identities=32% Similarity=0.788 Sum_probs=19.3
Q ss_pred CcccccccCCCc----------ccccccc--ccccccCcc
Q 034400 14 KTHTLCVRCGRR----------SFHLQKS--RCAACAYPA 41 (95)
Q Consensus 14 ktH~lCrRCG~~----------syH~qKk--~Ca~CGyps 41 (95)
...+.|+.||.. .||.... .|--|||..
T Consensus 379 ~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 379 APFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQE 418 (679)
T ss_pred CCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCC
Confidence 356778888855 5886554 488888853
No 45
>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=46.24 E-value=11 Score=29.66 Aligned_cols=26 Identities=27% Similarity=0.756 Sum_probs=22.8
Q ss_pred CCCcccccccCCCccccccccccccccC
Q 034400 12 RNKTHTLCVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 12 ~~ktH~lCrRCG~~syH~qKk~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 7788999995
No 46
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=45.75 E-value=11 Score=29.30 Aligned_cols=26 Identities=23% Similarity=0.556 Sum_probs=19.8
Q ss_pred CcccccccCCCcccc---ccccccccccC
Q 034400 14 KTHTLCVRCGRRSFH---LQKSRCAACAY 39 (95)
Q Consensus 14 ktH~lCrRCG~~syH---~qKk~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 34567999985
No 47
>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=45.39 E-value=10 Score=18.23 Aligned_cols=7 Identities=43% Similarity=0.824 Sum_probs=6.0
Q ss_pred CCCCCCC
Q 034400 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 48
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=45.14 E-value=11 Score=28.88 Aligned_cols=32 Identities=38% Similarity=0.637 Sum_probs=25.4
Q ss_pred CcccccccCCCccccccccccccccCccccccc
Q 034400 14 KTHTLCVRCGRRSFHLQKSRCAACAYPAARKRT 46 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qKk~Ca~CGyps~k~R~ 46 (95)
+--..|..|++. |+..+..|..||-|..+++.
T Consensus 137 ~w~~rC~GC~~~-f~~~~~~Cp~CG~~~~~~~~ 168 (177)
T COG1439 137 KWRLRCHGCKRI-FPEPKDFCPICGSPLKRKRV 168 (177)
T ss_pred eeeEEEecCcee-cCCCCCcCCCCCCceEEeee
Confidence 345689999864 77999999999998666554
No 49
>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=45.05 E-value=15 Score=26.48 Aligned_cols=32 Identities=19% Similarity=0.551 Sum_probs=26.4
Q ss_pred CCCCCcccccccCCCccccccccccccccCcc
Q 034400 10 KRRNKTHTLCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 10 Kr~~ktH~lCrRCG~~syH~qKk~Ca~CGyps 41 (95)
.....-.-.|..||..-|.-..|.-+.||+||
T Consensus 31 ~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPS 62 (124)
T PF01641_consen 31 DHKEEGIYVCAVCGTPLFSSDTKFDSGCGWPS 62 (124)
T ss_dssp CTTSSEEEEETTTS-EEEEGGGEETSSSSSSE
T ss_pred CCCCCEEEEcCCCCCccccCcccccCCcCCcc
Confidence 33455667899999999999999999999995
No 50
>PHA02942 putative transposase; Provisional
Probab=44.75 E-value=12 Score=30.76 Aligned_cols=26 Identities=23% Similarity=0.749 Sum_probs=18.9
Q ss_pred cccccccCCCccc--cccccccccccCc
Q 034400 15 THTLCVRCGRRSF--HLQKSRCAACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~sy--H~qKk~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 5567999997643 2345689999995
No 51
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=44.42 E-value=21 Score=26.45 Aligned_cols=29 Identities=24% Similarity=0.628 Sum_probs=25.9
Q ss_pred CCcccccccCCCccccccccccccccCcc
Q 034400 13 NKTHTLCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qKk~Ca~CGyps 41 (95)
..-.-.|..||...|--..|.-+.||+||
T Consensus 40 ~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPS 68 (142)
T PRK00222 40 EKGIYVCIVCGEPLFSSDTKFDSGCGWPS 68 (142)
T ss_pred CCeEEEecCCCchhcCCcccccCCCCCcC
Confidence 34556999999999999999999999996
No 52
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=43.55 E-value=14 Score=21.43 Aligned_cols=24 Identities=38% Similarity=0.847 Sum_probs=15.1
Q ss_pred cccccCCCcc-c--cccccccccccCc
Q 034400 17 TLCVRCGRRS-F--HLQKSRCAACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~s-y--H~qKk~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 4677888752 2 1225778888875
No 53
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=43.45 E-value=12 Score=23.69 Aligned_cols=21 Identities=19% Similarity=0.351 Sum_probs=16.9
Q ss_pred ccccccCCCccccccccccccccC
Q 034400 16 HTLCVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 16 H~lCrRCG~~syH~qKk~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 54
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=42.96 E-value=10 Score=27.36 Aligned_cols=25 Identities=28% Similarity=0.715 Sum_probs=20.8
Q ss_pred cccccccCCCccccccc------cccccccC
Q 034400 15 THTLCVRCGRRSFHLQK------SRCAACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK------k~Ca~CGy 39 (95)
...+|.-||+.--.+.| ..|.+||.
T Consensus 96 ~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa 126 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKEGRVSLLKCEACGA 126 (133)
T ss_pred heEECCCCCCCCcEEEEeCCeEEEecccCCC
Confidence 45799999998877776 58999997
No 55
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=42.52 E-value=14 Score=26.46 Aligned_cols=27 Identities=26% Similarity=0.679 Sum_probs=21.3
Q ss_pred CcccccccCCCccccccccccccccCcc
Q 034400 14 KTHTLCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qKk~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 367889999975 556678999999764
No 56
>PRK08329 threonine synthase; Validated
Probab=42.23 E-value=23 Score=28.19 Aligned_cols=66 Identities=20% Similarity=0.341 Sum_probs=32.7
Q ss_pred cccccCCCccccccccccccccCcccccccCCccccccccccccccccccccccc--hhcccCcCcCCCCCcc
Q 034400 17 TLCVRCGRRSFHLQKSRCAACAYPAARKRTYNWSVKAIRRKTTGTGRMRYLRHVP--RRFKSGFREGTQAAPR 87 (95)
Q Consensus 17 ~lCrRCG~~syH~qKk~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--VEREYGSFDSPREYL--DMRRYIDYLPVDEEFLPHLTPPITPTVK 69 (347)
T ss_pred cCcCCCCCCcCCCCceec-CCCCcEE--EEecccccccccccc--chhhhHHhCCCCCCCCCcCCCCCCcccc
Confidence 469999976422223579 7986532 234444221122222 3334433333 2222356688777543
No 57
>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=41.57 E-value=9.7 Score=25.34 Aligned_cols=22 Identities=27% Similarity=0.819 Sum_probs=15.6
Q ss_pred cccccCCCcccccc---ccccccccCc
Q 034400 17 TLCVRCGRRSFHLQ---KSRCAACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~syH~q---Kk~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 5789 99983
No 58
>PRK06450 threonine synthase; Validated
Probab=41.02 E-value=15 Score=29.41 Aligned_cols=24 Identities=29% Similarity=0.873 Sum_probs=18.0
Q ss_pred ccccccCCCcccccc-ccccccccCc
Q 034400 16 HTLCVRCGRRSFHLQ-KSRCAACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~syH~q-Kk~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 59
>KOG4192 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.91 E-value=12 Score=27.78 Aligned_cols=24 Identities=46% Similarity=0.927 Sum_probs=18.4
Q ss_pred CCCCCCCcccccccCCCcccccccc
Q 034400 8 FGKRRNKTHTLCVRCGRRSFHLQKS 32 (95)
Q Consensus 8 fGKr~~ktH~lCrRCG~~syH~qKk 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 46799999999999997543
No 60
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=40.42 E-value=16 Score=31.79 Aligned_cols=29 Identities=17% Similarity=0.296 Sum_probs=25.9
Q ss_pred CCcccccccCCCccccccccccccccCcc
Q 034400 13 NKTHTLCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qKk~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 34566899999999999999999999995
No 61
>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=40.35 E-value=23 Score=20.09 Aligned_cols=23 Identities=26% Similarity=0.642 Sum_probs=11.1
Q ss_pred ccccCCCccccc--cccccccccCc
Q 034400 18 LCVRCGRRSFHL--QKSRCAACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~--qKk~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 466666654421 22367777763
No 62
>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=40.19 E-value=16 Score=22.26 Aligned_cols=25 Identities=32% Similarity=0.773 Sum_probs=15.7
Q ss_pred cccccccCCCcccc---ccccccccccC
Q 034400 15 THTLCVRCGRRSFH---LQKSRCAACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH---~qKk~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 44566777776
No 63
>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=39.97 E-value=16 Score=20.98 Aligned_cols=21 Identities=33% Similarity=1.115 Sum_probs=14.4
Q ss_pred ccccCCCcccccc------ccccccccC
Q 034400 18 LCVRCGRRSFHLQ------KSRCAACAY 39 (95)
Q Consensus 18 lCrRCG~~syH~q------Kk~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 67873 356888874
No 64
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=39.95 E-value=16 Score=27.64 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=23.1
Q ss_pred ccccccCCCccccccccccccccCcccc
Q 034400 16 HTLCVRCGRRSFHLQKSRCAACAYPAAR 43 (95)
Q Consensus 16 H~lCrRCG~~syH~qKk~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 4579999998888888999999977543
No 65
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=39.37 E-value=15 Score=25.70 Aligned_cols=23 Identities=30% Similarity=0.842 Sum_probs=18.8
Q ss_pred cccccCCCccccc-----cccccccccC
Q 034400 17 TLCVRCGRRSFHL-----QKSRCAACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~-----qKk~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 4699999988873 3678999999
No 66
>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=39.36 E-value=22 Score=19.39 Aligned_cols=24 Identities=21% Similarity=0.400 Sum_probs=15.8
Q ss_pred cccccCCCcccc------ccccccccccCc
Q 034400 17 TLCVRCGRRSFH------LQKSRCAACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~syH------~qKk~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 468888883322 335679999964
No 67
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=39.20 E-value=22 Score=31.63 Aligned_cols=29 Identities=17% Similarity=0.565 Sum_probs=19.3
Q ss_pred CCCCCCcccccccCCCccccccccccccccCc
Q 034400 9 GKRRNKTHTLCVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 9 GKr~~ktH~lCrRCG~~syH~qKk~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 445556677888888864 23567777774
No 68
>PRK11823 DNA repair protein RadA; Provisional
Probab=39.07 E-value=18 Score=30.18 Aligned_cols=26 Identities=35% Similarity=0.735 Sum_probs=20.7
Q ss_pred CCcccccccCCCccccccccccccccC
Q 034400 13 NKTHTLCVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qKk~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 378899999998775444 78999985
No 69
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=38.95 E-value=15 Score=27.75 Aligned_cols=34 Identities=29% Similarity=0.706 Sum_probs=24.9
Q ss_pred cccccccCCCccccccc------cccccccC--cccccccCC
Q 034400 15 THTLCVRCGRRSFHLQK------SRCAACAY--PAARKRTYN 48 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK------k~Ca~CGy--ps~k~R~Yn 48 (95)
...+|.-|++.--.+.+ ..|.+||. |-.....-|
T Consensus 97 ~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~~~~~~~ 138 (201)
T PRK12336 97 EYVICSECGLPDTRLVKEDRVLMLRCDACGAHRPVKKRKASS 138 (201)
T ss_pred heEECCCCCCCCcEEEEcCCeEEEEcccCCCCcccccccccc
Confidence 46799999998887776 47999999 544444333
No 70
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=38.83 E-value=18 Score=22.73 Aligned_cols=22 Identities=32% Similarity=1.081 Sum_probs=16.5
Q ss_pred cccccCCCccccccccccccccC
Q 034400 17 TLCVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qKk~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 4788888764 566677888887
No 71
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=38.00 E-value=17 Score=25.14 Aligned_cols=37 Identities=24% Similarity=0.486 Sum_probs=22.4
Q ss_pred CCCCCCCCCC----CCcccccccCCCcccccc---ccccccccCc
Q 034400 3 KGTGSFGKRR----NKTHTLCVRCGRRSFHLQ---KSRCAACAYP 40 (95)
Q Consensus 3 KGT~SfGKr~----~ktH~lCrRCG~~syH~q---Kk~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 4555444321 355678999995 44332 2559999954
No 72
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=36.44 E-value=18 Score=29.54 Aligned_cols=27 Identities=26% Similarity=0.835 Sum_probs=22.5
Q ss_pred CCcccccccCCCcccccc---ccccccccC
Q 034400 13 NKTHTLCVRCGRRSFHLQ---KSRCAACAY 39 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~q---Kk~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 468999999999988554 678999996
No 73
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.25 E-value=21 Score=25.38 Aligned_cols=25 Identities=28% Similarity=0.636 Sum_probs=19.6
Q ss_pred CcccccccCCCcccc----------ccccccccccCc
Q 034400 14 KTHTLCVRCGRRSFH----------LQKSRCAACAYP 40 (95)
Q Consensus 14 ktH~lCrRCG~~syH----------~qKk~Ca~CGyp 40 (95)
+++.-|++|+. || .|.-.|.+|++-
T Consensus 28 ~~~~~cP~C~s--~~~~k~g~~~~~~qRyrC~~C~~t 62 (129)
T COG3677 28 ITKVNCPRCKS--SNVVKIGGIRRGHQRYKCKSCGST 62 (129)
T ss_pred cccCcCCCCCc--cceeeECCccccccccccCCcCcc
Confidence 46678999875 44 788999999973
No 74
>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=36.00 E-value=16 Score=29.25 Aligned_cols=26 Identities=23% Similarity=0.594 Sum_probs=21.9
Q ss_pred cccccccCCCccccc----cccccccccCc
Q 034400 15 THTLCVRCGRRSFHL----QKSRCAACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~----qKk~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 75
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=35.79 E-value=20 Score=24.78 Aligned_cols=26 Identities=15% Similarity=0.589 Sum_probs=17.3
Q ss_pred CcccccccCCCccccc--cccccccccCc
Q 034400 14 KTHTLCVRCGRRSFHL--QKSRCAACAYP 40 (95)
Q Consensus 14 ktH~lCrRCG~~syH~--qKk~Ca~CGyp 40 (95)
+.-..|+.||.. |-+ ....|..||-+
T Consensus 68 p~~~~C~~Cg~~-~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 68 PAQAWCWDCSQV-VEIHQHDAQCPHCHGE 95 (113)
T ss_pred CcEEEcccCCCE-EecCCcCccCcCCCCC
Confidence 455789999943 333 33459999944
No 76
>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=35.57 E-value=13 Score=24.44 Aligned_cols=16 Identities=38% Similarity=0.667 Sum_probs=11.1
Q ss_pred CcccccccCCCccccc
Q 034400 14 KTHTLCVRCGRRSFHL 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 3557899999865433
No 77
>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=35.57 E-value=20 Score=23.60 Aligned_cols=23 Identities=26% Similarity=0.709 Sum_probs=18.2
Q ss_pred ccccCCCccccc-cccccccccCc
Q 034400 18 LCVRCGRRSFHL-QKSRCAACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~-qKk~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 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=35.24 E-value=20 Score=20.31 Aligned_cols=23 Identities=26% Similarity=0.882 Sum_probs=14.6
Q ss_pred cccccCCCcccccccc----ccccccC
Q 034400 17 TLCVRCGRRSFHLQKS----RCAACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qKk----~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 3588888877643321 4899999
No 79
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=34.84 E-value=24 Score=17.93 Aligned_cols=22 Identities=32% Similarity=0.751 Sum_probs=14.5
Q ss_pred ccccCCCccccccccccccccCc
Q 034400 18 LCVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~qKk~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 46667766666655 77777754
No 80
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=34.53 E-value=33 Score=27.82 Aligned_cols=29 Identities=31% Similarity=0.701 Sum_probs=26.1
Q ss_pred CCcccccccCCCccccccccccccccCcc
Q 034400 13 NKTHTLCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qKk~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 45566799999999999999999999996
No 81
>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=34.40 E-value=8 Score=26.90 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=9.4
Q ss_pred cccccccccCcc
Q 034400 30 QKSRCAACAYPA 41 (95)
Q Consensus 30 qKk~Ca~CGyps 41 (95)
+...||.||-|.
T Consensus 80 ~~~vCaKC~k~~ 91 (92)
T PF10217_consen 80 ELKVCAKCGKPP 91 (92)
T ss_pred hhccCcccCCCC
Confidence 568899999753
No 82
>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=33.43 E-value=25 Score=19.73 Aligned_cols=27 Identities=22% Similarity=0.549 Sum_probs=16.4
Q ss_pred cccccCCCccccc-cccccccccCcccc
Q 034400 17 TLCVRCGRRSFHL-QKSRCAACAYPAAR 43 (95)
Q Consensus 17 ~lCrRCG~~syH~-qKk~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 83
>PRK14873 primosome assembly protein PriA; Provisional
Probab=33.20 E-value=24 Score=31.37 Aligned_cols=16 Identities=19% Similarity=0.414 Sum_probs=8.0
Q ss_pred cccccc--ccccccccCc
Q 034400 25 RSFHLQ--KSRCAACAYP 40 (95)
Q Consensus 25 ~syH~q--Kk~Ca~CGyp 40 (95)
-.||.. .-.|--|||.
T Consensus 402 L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 402 LGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred eeEecCCCeeECCCCcCC
Confidence 345543 3446666653
No 84
>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=33.13 E-value=15 Score=22.53 Aligned_cols=20 Identities=30% Similarity=0.833 Sum_probs=14.2
Q ss_pred cccccccccccCcccccccCCccccc
Q 034400 28 HLQKSRCAACAYPAARKRTYNWSVKA 53 (95)
Q Consensus 28 H~qKk~Ca~CGyps~k~R~YnWs~Ka 53 (95)
|+-.+.|+.||-| |.|-.|.
T Consensus 5 ~lp~K~C~~C~rp------f~WRKKW 24 (42)
T PF10013_consen 5 NLPSKICPVCGRP------FTWRKKW 24 (42)
T ss_pred cCCCCcCcccCCc------chHHHHH
Confidence 6777999999965 5555443
No 85
>PRK04351 hypothetical protein; Provisional
Probab=33.08 E-value=23 Score=25.88 Aligned_cols=22 Identities=32% Similarity=0.902 Sum_probs=13.1
Q ss_pred cccccCCC-----cccccccccccccc
Q 034400 17 TLCVRCGR-----RSFHLQKSRCAACA 38 (95)
Q Consensus 17 ~lCrRCG~-----~syH~qKk~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 44555666666665
No 86
>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=33.06 E-value=22 Score=27.62 Aligned_cols=59 Identities=19% Similarity=0.380 Sum_probs=27.3
Q ss_pred CcccccccCCCccccccccccccccCc-ccccccCCccccccccccccccccccccccchh
Q 034400 14 KTHTLCVRCGRRSFHLQKSRCAACAYP-AARKRTYNWSVKAIRRKTTGTGRMRYLRHVPRR 73 (95)
Q Consensus 14 ktH~lCrRCG~~syH~qKk~Ca~CGyp-s~k~R~YnWs~Ka~rr~ttGTGRmr~lk~v~rr 73 (95)
+-+-.|-.||. .||.....|..||-. ..++..+.......-|=-+=----.|||+|++.
T Consensus 195 ~R~L~Cs~C~t-~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd~~ 254 (290)
T PF04216_consen 195 KRYLHCSLCGT-EWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVDRE 254 (290)
T ss_dssp EEEEEETTT---EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEETT
T ss_pred cEEEEcCCCCC-eeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHhhh
Confidence 34567777875 578888899999984 355555544444434433334455799999843
No 87
>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=32.00 E-value=20 Score=23.39 Aligned_cols=12 Identities=33% Similarity=1.132 Sum_probs=10.2
Q ss_pred CcccccccCCCc
Q 034400 14 KTHTLCVRCGRR 25 (95)
Q Consensus 14 ktH~lCrRCG~~ 25 (95)
.-|+.|..||+.
T Consensus 71 h~H~~C~~Cg~i 82 (116)
T cd07153 71 HHHLICTKCGKV 82 (116)
T ss_pred CCceEeCCCCCE
Confidence 469999999975
No 88
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=31.64 E-value=25 Score=22.97 Aligned_cols=20 Identities=35% Similarity=1.099 Sum_probs=14.9
Q ss_pred cccccCCCccccccccccccccC
Q 034400 17 TLCVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qKk~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 46888875 5555 89999995
No 89
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=31.42 E-value=17 Score=29.69 Aligned_cols=31 Identities=19% Similarity=0.503 Sum_probs=24.2
Q ss_pred cccccccCCCcccccc----ccccccccCc---ccccc
Q 034400 15 THTLCVRCGRRSFHLQ----KSRCAACAYP---AARKR 45 (95)
Q Consensus 15 tH~lCrRCG~~syH~q----Kk~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 4678999999999865 4799999993 44444
No 90
>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=31.11 E-value=27 Score=24.16 Aligned_cols=38 Identities=21% Similarity=0.382 Sum_probs=23.2
Q ss_pred CCCCCCCCC----CCCcccccccCCCccccc-c-ccccccccCcc
Q 034400 3 KGTGSFGKR----RNKTHTLCVRCGRRSFHL-Q-KSRCAACAYPA 41 (95)
Q Consensus 3 KGT~SfGKr----~~ktH~lCrRCG~~syH~-q-Kk~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 455544432 13556789999944 433 2 56699999553
No 91
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=31.07 E-value=19 Score=25.15 Aligned_cols=25 Identities=36% Similarity=0.761 Sum_probs=19.2
Q ss_pred cccccccCCCccccccc------cccccccC
Q 034400 15 THTLCVRCGRRSFHLQK------SRCAACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK------k~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 35789999998877776 35888884
No 92
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=30.90 E-value=29 Score=20.72 Aligned_cols=23 Identities=35% Similarity=0.869 Sum_probs=14.5
Q ss_pred ccccCCCccccc--cccccccccCc
Q 034400 18 LCVRCGRRSFHL--QKSRCAACAYP 40 (95)
Q Consensus 18 lCrRCG~~syH~--qKk~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
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=30.42 E-value=27 Score=20.81 Aligned_cols=13 Identities=38% Similarity=0.828 Sum_probs=6.8
Q ss_pred ccccccCCCcccc
Q 034400 16 HTLCVRCGRRSFH 28 (95)
Q Consensus 16 H~lCrRCG~~syH 28 (95)
-++|.|||+-...
T Consensus 2 ~~~CprC~kg~Hw 14 (36)
T PF14787_consen 2 PGLCPRCGKGFHW 14 (36)
T ss_dssp --C-TTTSSSCS-
T ss_pred CccCcccCCCcch
Confidence 3689999875433
No 94
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=30.41 E-value=18 Score=29.07 Aligned_cols=26 Identities=23% Similarity=0.584 Sum_probs=21.8
Q ss_pred cccccccCCCcccccc----ccccccccCc
Q 034400 15 THTLCVRCGRRSFHLQ----KSRCAACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~q----Kk~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 4689999999999864 3699999993
No 95
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=30.20 E-value=20 Score=20.55 Aligned_cols=9 Identities=33% Similarity=1.106 Sum_probs=4.9
Q ss_pred ccccccccC
Q 034400 31 KSRCAACAY 39 (95)
Q Consensus 31 Kk~Ca~CGy 39 (95)
..+|.+|||
T Consensus 22 R~vC~~Cg~ 30 (34)
T PF14803_consen 22 RLVCPACGF 30 (34)
T ss_dssp EEEETTTTE
T ss_pred ceECCCCCC
Confidence 345666654
No 96
>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=30.01 E-value=28 Score=20.02 Aligned_cols=15 Identities=40% Similarity=0.866 Sum_probs=10.2
Q ss_pred Ccccccccccccccc
Q 034400 24 RRSFHLQKSRCAACA 38 (95)
Q Consensus 24 ~~syH~qKk~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 97
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=27.74 E-value=31 Score=33.71 Aligned_cols=21 Identities=29% Similarity=0.928 Sum_probs=11.3
Q ss_pred cccccCCCccccccccccccccCc
Q 034400 17 TLCVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 17 ~lCrRCG~~syH~qKk~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 456666665442 255555544
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=27.67 E-value=35 Score=28.55 Aligned_cols=30 Identities=27% Similarity=0.579 Sum_probs=19.4
Q ss_pred CCCCCCCCCcccccccCCCccccccc-----cccccccCc
Q 034400 6 GSFGKRRNKTHTLCVRCGRRSFHLQK-----SRCAACAYP 40 (95)
Q Consensus 6 ~SfGKr~~ktH~lCrRCG~~syH~qK-----k~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 6799 9976
No 99
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=27.58 E-value=31 Score=25.36 Aligned_cols=26 Identities=27% Similarity=0.738 Sum_probs=20.3
Q ss_pred cccccccCCCcccccc-ccccccccCc
Q 034400 15 THTLCVRCGRRSFHLQ-KSRCAACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~q-Kk~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 3456999999999744 4579999974
No 100
>PRK09462 fur ferric uptake regulator; Provisional
Probab=27.44 E-value=26 Score=24.44 Aligned_cols=12 Identities=33% Similarity=1.041 Sum_probs=10.0
Q ss_pred cccccccCCCcc
Q 034400 15 THTLCVRCGRRS 26 (95)
Q Consensus 15 tH~lCrRCG~~s 26 (95)
-|..|..||+..
T Consensus 89 ~H~iC~~Cg~i~ 100 (148)
T PRK09462 89 DHLICLDCGKVI 100 (148)
T ss_pred CceEECCCCCEE
Confidence 689999999753
No 101
>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=26.94 E-value=17 Score=22.25 Aligned_cols=17 Identities=41% Similarity=0.516 Sum_probs=12.3
Q ss_pred cccccccccccccccch
Q 034400 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 56789999987755443
No 102
>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=26.61 E-value=37 Score=28.50 Aligned_cols=26 Identities=31% Similarity=0.744 Sum_probs=20.2
Q ss_pred CCcccccccCCCccccccccccccccC
Q 034400 13 NKTHTLCVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~qKk~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 46888999999876433 378999985
No 103
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=26.34 E-value=27 Score=25.37 Aligned_cols=25 Identities=32% Similarity=0.748 Sum_probs=20.2
Q ss_pred cccccccCCCccccccc------cccccccC
Q 034400 15 THTLCVRCGRRSFHLQK------SRCAACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qK------k~Ca~CGy 39 (95)
...+|.-||+.--.+.| ..|.+||.
T Consensus 101 ~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa 131 (138)
T PRK03988 101 EYVICPECGSPDTKLIKEGRIWVLKCEACGA 131 (138)
T ss_pred hcEECCCCCCCCcEEEEcCCeEEEEcccCCC
Confidence 45789999998877776 36999997
No 104
>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=26.15 E-value=53 Score=20.88 Aligned_cols=33 Identities=21% Similarity=0.534 Sum_probs=24.9
Q ss_pred CCCCCCC--cccccccCCCccccccc--cccccccCc
Q 034400 8 FGKRRNK--THTLCVRCGRRSFHLQK--SRCAACAYP 40 (95)
Q Consensus 8 fGKr~~k--tH~lCrRCG~~syH~qK--k~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 3555532 36679999999988887 899999975
No 105
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=25.99 E-value=40 Score=21.87 Aligned_cols=27 Identities=22% Similarity=0.695 Sum_probs=17.1
Q ss_pred CcccccccCCCc-ccc-------ccccccccccCc
Q 034400 14 KTHTLCVRCGRR-SFH-------LQKSRCAACAYP 40 (95)
Q Consensus 14 ktH~lCrRCG~~-syH-------~qKk~Ca~CGyp 40 (95)
-++..|.-||.. .+- -.--+|.+|||-
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhcCCceECCCCCCc
Confidence 477888888876 221 123467788873
No 106
>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=25.89 E-value=27 Score=24.91 Aligned_cols=25 Identities=36% Similarity=0.786 Sum_probs=19.0
Q ss_pred cccccccCCCcccccccc------ccccccC
Q 034400 15 THTLCVRCGRRSFHLQKS------RCAACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qKk------~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 357899999887777664 6888885
No 107
>PRK08764 ferredoxin; Provisional
Probab=25.55 E-value=35 Score=23.87 Aligned_cols=13 Identities=23% Similarity=0.887 Sum_probs=10.4
Q ss_pred cccccccccccCc
Q 034400 28 HLQKSRCAACAYP 40 (95)
Q Consensus 28 H~qKk~Ca~CGyp 40 (95)
.+-+.-|+.||||
T Consensus 14 ~lp~~ncg~cg~~ 26 (135)
T PRK08764 14 LLPQTQCGQCGFD 26 (135)
T ss_pred hCCCCCCccCCCc
Confidence 3556789999998
No 108
>PF14653 IGFL: Insulin growth factor-like family
Probab=25.07 E-value=35 Score=23.73 Aligned_cols=32 Identities=25% Similarity=0.567 Sum_probs=23.5
Q ss_pred ccccc---cCCCccccccccccccccC-cccccccC
Q 034400 16 HTLCV---RCGRRSFHLQKSRCAACAY-PAARKRTY 47 (95)
Q Consensus 16 H~lCr---RCG~~syH~qKk~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 45675 8999999999999976655 44555544
No 109
>KOG3241 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.68 E-value=11 Score=30.02 Aligned_cols=20 Identities=35% Similarity=0.913 Sum_probs=15.9
Q ss_pred cccccccCCCccccccccccccccC
Q 034400 15 THTLCVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 15 tH~lCrRCG~~syH~qKk~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 58888888654 489999986
No 110
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=24.48 E-value=38 Score=23.44 Aligned_cols=23 Identities=30% Similarity=0.752 Sum_probs=16.1
Q ss_pred cccccCCCccccccc---cccccccC
Q 034400 17 TLCVRCGRRSFHLQK---SRCAACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qK---k~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 458888877765444 67888886
No 111
>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=23.99 E-value=37 Score=22.47 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=12.0
Q ss_pred ccccCCCccccccccccccccCcc
Q 034400 18 LCVRCGRRSFHLQKSRCAACAYPA 41 (95)
Q Consensus 18 lCrRCG~~syH~qKk~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 588888888888899999999873
No 112
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.93 E-value=50 Score=22.92 Aligned_cols=28 Identities=21% Similarity=0.497 Sum_probs=18.8
Q ss_pred CCcccccccCCCcccccc---ccccccccCcc
Q 034400 13 NKTHTLCVRCGRRSFHLQ---KSRCAACAYPA 41 (95)
Q Consensus 13 ~ktH~lCrRCG~~syH~q---Kk~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 3567889999944 4332 23599999654
No 113
>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=23.68 E-value=31 Score=22.86 Aligned_cols=13 Identities=31% Similarity=1.022 Sum_probs=9.9
Q ss_pred CCcccccccCCCc
Q 034400 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 4579999999964
No 114
>PRK06260 threonine synthase; Validated
Probab=23.63 E-value=45 Score=26.93 Aligned_cols=24 Identities=21% Similarity=0.686 Sum_probs=17.5
Q ss_pred ccccccCCCcccccc--ccccccccCc
Q 034400 16 HTLCVRCGRRSFHLQ--KSRCAACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~syH~q--Kk~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 5433 2579999864
No 115
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=23.50 E-value=35 Score=24.39 Aligned_cols=20 Identities=25% Similarity=0.884 Sum_probs=16.3
Q ss_pred cccCCCccccccccccccccC
Q 034400 19 CVRCGRRSFHLQKSRCAACAY 39 (95)
Q Consensus 19 CrRCG~~syH~qKk~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 78888 567888899999983
No 116
>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=22.87 E-value=41 Score=23.39 Aligned_cols=23 Identities=22% Similarity=0.664 Sum_probs=16.2
Q ss_pred cccccCCCccccccc---cccccccC
Q 034400 17 TLCVRCGRRSFHLQK---SRCAACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qK---k~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 458888877754443 67888886
No 117
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=22.83 E-value=40 Score=22.16 Aligned_cols=28 Identities=21% Similarity=0.667 Sum_probs=17.5
Q ss_pred CCcccccccCCCc-cccc-------cccccccccCc
Q 034400 13 NKTHTLCVRCGRR-SFHL-------QKSRCAACAYP 40 (95)
Q Consensus 13 ~ktH~lCrRCG~~-syH~-------qKk~Ca~CGyp 40 (95)
+-++..|.-||.. -|-- .--+|.+|||-
T Consensus 24 ~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 24 TAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred ceeEeeCCCCCceeeehhhhHHHcCCceECCCcCcc
Confidence 4577889999932 2222 22468888884
No 118
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=22.36 E-value=40 Score=24.19 Aligned_cols=26 Identities=23% Similarity=0.710 Sum_probs=18.6
Q ss_pred CcccccccCCCcccc---cc------ccccccccC
Q 034400 14 KTHTLCVRCGRRSFH---LQ------KSRCAACAY 39 (95)
Q Consensus 14 ktH~lCrRCG~~syH---~q------Kk~Ca~CGy 39 (95)
++-+.|.+||...-- +. --.|+.||-
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGl 54 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGL 54 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcc
Confidence 345779999987654 33 347999995
No 119
>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=22.18 E-value=35 Score=25.05 Aligned_cols=29 Identities=24% Similarity=0.717 Sum_probs=16.0
Q ss_pred cccccCCCcccc--------------ccccccccccCcccccc
Q 034400 17 TLCVRCGRRSFH--------------LQKSRCAACAYPAARKR 45 (95)
Q Consensus 17 ~lCrRCG~~syH--------------~qKk~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 578889987643 12347999999754444
No 120
>PRK06991 ferredoxin; Provisional
Probab=22.14 E-value=44 Score=26.60 Aligned_cols=12 Identities=33% Similarity=1.085 Sum_probs=9.7
Q ss_pred ccccccccccCc
Q 034400 29 LQKSRCAACAYP 40 (95)
Q Consensus 29 ~qKk~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 121
>PRK07218 replication factor A; Provisional
Probab=22.07 E-value=46 Score=28.28 Aligned_cols=23 Identities=30% Similarity=0.556 Sum_probs=19.4
Q ss_pred cccccccCCCccccccccccccccCc
Q 034400 15 THTLCVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~qKk~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 346899999997 88999999973
No 122
>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=21.93 E-value=35 Score=27.71 Aligned_cols=24 Identities=33% Similarity=0.773 Sum_probs=18.6
Q ss_pred CCCcccccccCCCccccccccccccc
Q 034400 12 RNKTHTLCVRCGRRSFHLQKSRCAAC 37 (95)
Q Consensus 12 ~~ktH~lCrRCG~~syH~qKk~Ca~C 37 (95)
+--+|.+|..||+...+.++ |.-|
T Consensus 14 ~~S~h~~CN~CG~~~~~~~k--C~~c 37 (258)
T PF06869_consen 14 NFSTHFICNSCGKVVESNEK--CSCC 37 (258)
T ss_pred cceeehhhhhhhhhhccCce--eecc
Confidence 34689999999997777764 6555
No 123
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=21.68 E-value=43 Score=24.92 Aligned_cols=14 Identities=21% Similarity=0.608 Sum_probs=9.8
Q ss_pred ccccccccCccccc
Q 034400 31 KSRCAACAYPAARK 44 (95)
Q Consensus 31 Kk~Ca~CGyps~k~ 44 (95)
--.|..|||...-.
T Consensus 28 sf~C~~CGyr~~ev 41 (163)
T TIGR00340 28 TYICEKCGYRSTDV 41 (163)
T ss_pred EEECCCCCCchhhe
Confidence 34799999975443
No 124
>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=21.62 E-value=37 Score=25.29 Aligned_cols=14 Identities=50% Similarity=0.973 Sum_probs=9.3
Q ss_pred cccccccCCccccc
Q 034400 40 PAARKRTYNWSVKA 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 56667999999884
No 125
>PRK14873 primosome assembly protein PriA; Provisional
Probab=21.15 E-value=56 Score=29.08 Aligned_cols=23 Identities=30% Similarity=0.725 Sum_probs=17.4
Q ss_pred cccccccCCCccccccccccccccCc
Q 034400 15 THTLCVRCGRRSFHLQKSRCAACAYP 40 (95)
Q Consensus 15 tH~lCrRCG~~syH~qKk~Ca~CGyp 40 (95)
....|+.||... .-..|..||-+
T Consensus 409 ~~l~Ch~CG~~~---~p~~Cp~Cgs~ 431 (665)
T PRK14873 409 GTPRCRWCGRAA---PDWRCPRCGSD 431 (665)
T ss_pred CeeECCCCcCCC---cCccCCCCcCC
Confidence 345699999864 36799999954
No 126
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=21.15 E-value=38 Score=28.10 Aligned_cols=69 Identities=26% Similarity=0.449 Sum_probs=44.4
Q ss_pred CcccccccCCCcccccc----ccccccccCc---ccccc--------c---------------------CC-cccccccc
Q 034400 14 KTHTLCVRCGRRSFHLQ----KSRCAACAYP---AARKR--------T---------------------YN-WSVKAIRR 56 (95)
Q Consensus 14 ktH~lCrRCG~~syH~q----Kk~Ca~CGyp---s~k~R--------~---------------------Yn-Ws~Ka~rr 56 (95)
-.-+.|.-||.-.||.. ..+|.+|+|- +++.| + |. |-.++...
T Consensus 26 ~lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A~~Ri~~llD~gsf~el~~~l~~~dPL~F~d~k~Y~~rL~~a~~~ 105 (294)
T COG0777 26 GLWTKCPSCGEMLYRKELESNLKVCPKCGHHMRISARERLEALLDEGSFEELDSPLEPKDPLKFPDSKKYKDRLEAARKK 105 (294)
T ss_pred CceeECCCccceeeHHHHHhhhhcccccCcccccCHHHHHHHhhCCCcceecccCCCcCCcccCCcchhhHHHHHHHHhh
Confidence 45689999999999974 5789999992 34433 1 21 22222111
Q ss_pred c------cccccccccccccchhcccCcCcCC
Q 034400 57 K------TTGTGRMRYLRHVPRRFKSGFREGT 82 (95)
Q Consensus 57 ~------ttGTGRmr~lk~v~rrfkngFreGt 82 (95)
. -+|.|.+--++.|.-=+.-.|..|+
T Consensus 106 tg~~davvtg~g~i~G~pvv~av~df~FmgGS 137 (294)
T COG0777 106 TGLDDAVVTGEGTINGLPVVLAVMDFAFMGGS 137 (294)
T ss_pred cCCCcceEEEeeEECCeEEEEEEEeccccccc
Confidence 1 2577777777777777777776665
No 127
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=20.82 E-value=43 Score=28.85 Aligned_cols=25 Identities=28% Similarity=0.797 Sum_probs=19.2
Q ss_pred ccccccCCCcc--ccccc-----cccccccCc
Q 034400 16 HTLCVRCGRRS--FHLQK-----SRCAACAYP 40 (95)
Q Consensus 16 H~lCrRCG~~s--yH~qK-----k~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 36899999874 56665 469999995
No 128
>PRK04165 acetyl-CoA decarbonylase/synthase complex subunit gamma; Provisional
Probab=20.76 E-value=47 Score=28.44 Aligned_cols=12 Identities=42% Similarity=1.046 Sum_probs=9.6
Q ss_pred ccccccccccCc
Q 034400 29 LQKSRCAACAYP 40 (95)
Q Consensus 29 ~qKk~Ca~CGyp 40 (95)
+.+.-|+.||||
T Consensus 12 LP~~nCg~CG~~ 23 (450)
T PRK04165 12 LPKTNCGECGEP 23 (450)
T ss_pred CCCCCCCCCCCc
Confidence 456679999998
No 129
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=20.50 E-value=49 Score=22.94 Aligned_cols=23 Identities=26% Similarity=0.645 Sum_probs=16.0
Q ss_pred cccccCCCccccccc---cccccccC
Q 034400 17 TLCVRCGRRSFHLQK---SRCAACAY 39 (95)
Q Consensus 17 ~lCrRCG~~syH~qK---k~Ca~CGy 39 (95)
-.|..||+.++--+- ..|.+||+
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~~ 62 (90)
T PRK03976 37 HVCPVCGRPKVKRVGTGIWECRKCGA 62 (90)
T ss_pred ccCCCCCCCceEEEEEEEEEcCCCCC
Confidence 358888877765444 67888886
No 130
>PF14149 YhfH: YhfH-like protein
Probab=20.32 E-value=34 Score=20.35 Aligned_cols=12 Identities=25% Similarity=0.811 Sum_probs=10.0
Q ss_pred cccccccccccC
Q 034400 28 HLQKSRCAACAY 39 (95)
Q Consensus 28 H~qKk~Ca~CGy 39 (95)
++-.|.|+.||-
T Consensus 10 nLp~K~C~~CG~ 21 (37)
T PF14149_consen 10 NLPPKKCTECGK 21 (37)
T ss_pred hCCCcccHHHHH
Confidence 577899999995
No 131
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.10 E-value=50 Score=26.17 Aligned_cols=36 Identities=19% Similarity=0.494 Sum_probs=24.3
Q ss_pred ccccccCCCccc----cccccccccccCc--------ccccccCCccc
Q 034400 16 HTLCVRCGRRSF----HLQKSRCAACAYP--------AARKRTYNWSV 51 (95)
Q Consensus 16 H~lCrRCG~~sy----H~qKk~Ca~CGyp--------s~k~R~YnWs~ 51 (95)
...|+.||...+ -----.|+.||+= ..-+|.|+=..
T Consensus 11 ~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~ 58 (310)
T PRK00423 11 KLVCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ 58 (310)
T ss_pred CCcCcCCCCCCeeEECCCCeEeecccCCcccccccccCCCccCCCccc
Confidence 357999997432 3355789999992 45677776433
Done!