Query 034819
Match_columns 82
No_of_seqs 107 out of 350
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 06:44:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034819.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034819hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2923 Uncharacterized conser 100.0 1.5E-28 3.2E-33 152.5 5.4 65 1-65 2-66 (67)
2 PF05207 zf-CSL: CSL zinc fing 99.9 3.9E-27 8.4E-32 141.1 6.6 55 4-58 1-55 (55)
3 COG5216 Uncharacterized conser 99.9 1E-24 2.2E-29 134.4 5.6 64 2-65 3-66 (67)
4 TIGR02098 MJ0042_CXXC MJ0042 f 96.9 0.0019 4E-08 35.0 3.9 35 21-55 2-37 (38)
5 PF13719 zinc_ribbon_5: zinc-r 95.9 0.012 2.6E-07 32.2 3.0 33 22-54 3-36 (37)
6 smart00834 CxxC_CXXC_SSSS Puta 95.8 0.0064 1.4E-07 32.8 1.7 33 19-53 3-36 (41)
7 PF05180 zf-DNL: DNL zinc fing 95.6 0.019 4.1E-07 35.7 3.6 37 20-56 3-42 (66)
8 PF09723 Zn-ribbon_8: Zinc rib 95.0 0.012 2.7E-07 32.9 1.2 31 19-51 3-34 (42)
9 PF13717 zinc_ribbon_4: zinc-r 95.0 0.029 6.3E-07 30.6 2.7 32 22-53 3-35 (36)
10 COG1996 RPC10 DNA-directed RNA 94.4 0.069 1.5E-06 31.5 3.3 34 18-56 3-37 (49)
11 TIGR01206 lysW lysine biosynth 94.1 0.11 2.4E-06 31.0 4.0 32 22-56 3-35 (54)
12 KOG3277 Uncharacterized conser 93.7 0.087 1.9E-06 37.9 3.4 45 11-55 69-116 (165)
13 TIGR02605 CxxC_CxxC_SSSS putat 92.8 0.12 2.6E-06 29.3 2.5 34 19-54 3-38 (52)
14 PF14354 Lar_restr_allev: Rest 85.9 0.69 1.5E-05 26.8 2.0 30 22-51 4-37 (61)
15 PRK00398 rpoP DNA-directed RNA 84.7 0.88 1.9E-05 25.4 2.0 29 21-54 3-32 (46)
16 PRK00464 nrdR transcriptional 84.2 0.72 1.6E-05 32.6 1.8 32 22-53 1-38 (154)
17 smart00659 RPOLCX RNA polymera 82.8 2.8 6.1E-05 23.8 3.6 29 21-55 2-31 (44)
18 PF12662 cEGF: Complement Clr- 81.6 0.48 1E-05 24.0 0.1 15 21-35 1-15 (24)
19 PF05280 FlhC: Flagellar trans 80.5 0.83 1.8E-05 32.8 1.0 33 17-52 130-163 (175)
20 PF08271 TF_Zn_Ribbon: TFIIB z 79.1 2.3 4.9E-05 23.4 2.3 30 22-55 1-31 (43)
21 smart00531 TFIIE Transcription 77.7 3 6.6E-05 28.5 3.1 38 18-55 96-135 (147)
22 PF05876 Terminase_GpA: Phage 76.8 2.2 4.7E-05 35.2 2.5 38 16-53 195-239 (557)
23 PRK12722 transcriptional activ 76.3 1.4 3E-05 32.2 1.2 31 18-51 131-162 (187)
24 PF10955 DUF2757: Protein of u 76.2 2.6 5.6E-05 26.9 2.2 8 20-27 3-11 (76)
25 PRK12860 transcriptional activ 75.1 1.5 3.4E-05 32.1 1.1 30 18-50 131-161 (189)
26 PF13831 PHD_2: PHD-finger; PD 74.8 3 6.5E-05 22.6 2.0 15 41-55 2-16 (36)
27 TIGR03655 anti_R_Lar restricti 74.8 2.8 6E-05 24.1 2.0 34 22-55 2-38 (53)
28 PF05605 zf-Di19: Drought indu 74.6 1.5 3.3E-05 25.1 0.8 29 21-51 2-39 (54)
29 PF09845 DUF2072: Zn-ribbon co 71.2 2 4.4E-05 29.9 0.9 24 22-50 2-26 (131)
30 PRK03824 hypA hydrogenase nick 70.6 3.5 7.6E-05 28.1 2.0 37 20-56 69-121 (135)
31 PF14446 Prok-RING_1: Prokaryo 69.7 3.5 7.6E-05 24.7 1.6 23 22-51 6-29 (54)
32 PF13451 zf-trcl: Probable zin 68.0 4.5 9.8E-05 23.7 1.8 29 21-49 4-39 (49)
33 PF08273 Prim_Zn_Ribbon: Zinc- 67.7 4.2 9.2E-05 22.8 1.6 28 20-49 2-32 (40)
34 PRK00762 hypA hydrogenase nick 67.1 2.9 6.3E-05 28.1 1.0 37 20-56 69-106 (124)
35 PF00628 PHD: PHD-finger; Int 67.0 6.4 0.00014 21.6 2.3 19 40-58 11-29 (51)
36 smart00249 PHD PHD zinc finger 66.4 4.1 8.8E-05 21.1 1.3 21 39-59 10-30 (47)
37 smart00778 Prim_Zn_Ribbon Zinc 64.9 4.4 9.5E-05 22.4 1.3 25 22-49 4-31 (37)
38 COG1579 Zn-ribbon protein, pos 64.8 3.6 7.8E-05 31.1 1.2 28 25-52 199-230 (239)
39 PF14353 CpXC: CpXC protein 63.3 5.1 0.00011 26.3 1.6 43 23-65 3-60 (128)
40 COG2331 Uncharacterized protei 62.9 2.1 4.5E-05 27.7 -0.3 35 18-54 9-44 (82)
41 COG5525 Bacteriophage tail ass 62.7 4.4 9.6E-05 34.5 1.5 39 17-55 223-271 (611)
42 PF04216 FdhE: Protein involve 61.3 11 0.00023 28.3 3.2 18 40-57 235-252 (290)
43 PF01831 Peptidase_C16: Peptid 59.9 7.6 0.00017 29.4 2.2 33 6-38 122-155 (249)
44 COG3364 Zn-ribbon containing p 59.5 4.6 9.9E-05 27.5 0.8 29 22-55 3-34 (112)
45 PF08274 PhnA_Zn_Ribbon: PhnA 57.8 5.2 0.00011 21.2 0.8 23 23-51 4-27 (30)
46 COG1110 Reverse gyrase [DNA re 57.7 3.8 8.2E-05 37.2 0.3 28 18-50 5-33 (1187)
47 PF09862 DUF2089: Protein of u 57.6 15 0.00033 24.8 3.2 32 24-64 1-33 (113)
48 KOG1779 40s ribosomal protein 56.7 14 0.0003 24.0 2.7 39 16-55 27-65 (84)
49 KOG3173 Predicted Zn-finger pr 56.3 4.5 9.7E-05 28.8 0.4 16 20-35 118-133 (167)
50 KOG3053 Uncharacterized conser 55.8 5.7 0.00012 31.0 0.9 45 14-58 30-86 (293)
51 PF02591 DUF164: Putative zinc 53.2 14 0.0003 21.2 2.1 26 25-50 24-53 (56)
52 PF14369 zf-RING_3: zinc-finge 52.4 7.8 0.00017 20.9 0.9 9 23-31 23-32 (35)
53 PF11331 DUF3133: Protein of u 51.8 13 0.00028 21.5 1.8 17 41-57 29-45 (46)
54 PF13913 zf-C2HC_2: zinc-finge 51.1 7.7 0.00017 19.3 0.7 10 22-31 3-13 (25)
55 PRK09710 lar restriction allev 48.6 17 0.00037 22.5 2.1 30 21-52 6-36 (64)
56 PRK09401 reverse gyrase; Revie 48.3 7.6 0.00017 35.0 0.7 29 18-51 4-33 (1176)
57 PF01155 HypA: Hydrogenase exp 47.3 8.2 0.00018 25.4 0.6 27 19-52 68-95 (113)
58 PF00096 zf-C2H2: Zinc finger, 46.6 7.8 0.00017 17.9 0.3 10 22-31 1-11 (23)
59 PF09064 Tme5_EGF_like: Thromb 46.2 8.4 0.00018 21.2 0.4 16 21-36 17-32 (34)
60 PRK06260 threonine synthase; V 45.7 21 0.00044 27.8 2.6 34 20-60 2-36 (397)
61 PRK12380 hydrogenase nickel in 45.3 12 0.00026 24.7 1.1 25 20-51 69-94 (113)
62 PF14311 DUF4379: Domain of un 44.8 25 0.00055 20.0 2.3 30 18-49 25-55 (55)
63 PF04071 zf-like: Cysteine-ric 43.7 25 0.00055 22.7 2.4 28 21-52 31-60 (86)
64 TIGR00100 hypA hydrogenase nic 43.0 12 0.00027 24.7 0.9 25 20-51 69-94 (115)
65 TIGR00373 conserved hypothetic 42.9 13 0.00027 25.9 1.0 33 17-53 105-138 (158)
66 COG1326 Uncharacterized archae 42.6 31 0.00066 25.7 3.0 34 19-53 4-40 (201)
67 PF13894 zf-C2H2_4: C2H2-type 41.6 15 0.00033 16.3 0.9 10 22-31 1-11 (24)
68 cd00498 Hsp33 Heat shock prote 41.0 16 0.00034 27.5 1.3 35 18-52 226-271 (275)
69 PRK06266 transcription initiat 40.7 17 0.00036 25.9 1.3 32 18-53 114-146 (178)
70 PF07754 DUF1610: Domain of un 39.9 17 0.00038 18.4 1.0 9 19-27 14-23 (24)
71 TIGR01562 FdhE formate dehydro 39.5 18 0.0004 28.1 1.5 20 40-59 249-268 (305)
72 PF04606 Ogr_Delta: Ogr/Delta- 39.3 70 0.0015 17.8 3.7 34 24-57 2-41 (47)
73 PF08996 zf-DNA_Pol: DNA Polym 39.1 26 0.00056 24.8 2.1 36 18-53 15-55 (188)
74 COG2888 Predicted Zn-ribbon RN 38.5 48 0.001 20.4 2.9 34 17-50 23-57 (61)
75 PRK03681 hypA hydrogenase nick 38.5 19 0.0004 23.8 1.2 25 20-50 69-94 (114)
76 PF14803 Nudix_N_2: Nudix N-te 38.4 41 0.00088 18.1 2.4 29 23-52 2-31 (34)
77 COG1281 Disulfide bond chapero 38.2 23 0.00049 27.6 1.8 35 19-53 231-276 (286)
78 PF03604 DNA_RNApol_7kD: DNA d 37.8 13 0.00027 19.9 0.3 27 22-54 1-28 (32)
79 PRK03564 formate dehydrogenase 37.5 31 0.00067 27.0 2.5 21 40-60 249-269 (309)
80 PRK09678 DNA-binding transcrip 37.3 1E+02 0.0022 19.2 4.5 35 22-56 2-42 (72)
81 PHA00616 hypothetical protein 37.3 7.9 0.00017 22.2 -0.6 15 22-37 2-17 (44)
82 PF13465 zf-H2C2_2: Zinc-finge 36.5 13 0.00029 18.3 0.2 11 21-31 14-25 (26)
83 PF13453 zf-TFIIB: Transcripti 35.8 33 0.00072 18.5 1.8 21 17-38 15-36 (41)
84 smart00744 RINGv The RING-vari 35.6 29 0.00063 19.6 1.6 16 14-29 9-24 (49)
85 COG5175 MOT2 Transcriptional r 35.6 18 0.00038 29.6 0.9 19 6-27 19-37 (480)
86 PLN03086 PRLI-interacting fact 35.3 31 0.00067 29.2 2.3 36 20-55 503-553 (567)
87 PF01363 FYVE: FYVE zinc finge 35.1 19 0.00042 21.0 0.8 23 19-56 23-46 (69)
88 PF01430 HSP33: Hsp33 protein; 35.0 18 0.00039 27.1 0.8 36 18-53 230-276 (280)
89 PF02150 RNA_POL_M_15KD: RNA p 34.8 19 0.00042 19.2 0.7 26 23-52 3-29 (35)
90 PHA02768 hypothetical protein; 34.3 17 0.00036 21.8 0.4 17 20-36 4-21 (55)
91 PRK00114 hslO Hsp33-like chape 34.1 29 0.00063 26.3 1.8 39 17-55 231-280 (293)
92 PRK07591 threonine synthase; V 34.1 46 0.00099 26.3 3.0 35 18-60 15-50 (421)
93 PF09855 DUF2082: Nucleic-acid 34.0 32 0.00069 21.0 1.7 11 42-52 35-45 (64)
94 cd01475 vWA_Matrilin VWA_Matri 33.8 15 0.00032 26.0 0.2 15 21-35 207-221 (224)
95 smart00661 RPOL9 RNA polymeras 33.8 43 0.00093 18.3 2.1 30 23-55 2-32 (52)
96 KOG2824 Glutaredoxin-related p 33.7 36 0.00079 26.5 2.3 34 18-51 237-281 (281)
97 PF09297 zf-NADH-PPase: NADH p 33.3 29 0.00063 17.8 1.2 25 23-52 5-30 (32)
98 COG2956 Predicted N-acetylgluc 31.8 32 0.0007 27.9 1.8 29 18-55 351-380 (389)
99 PF05129 Elf1: Transcription e 31.8 43 0.00093 21.0 2.0 37 21-58 22-61 (81)
100 PF02810 SEC-C: SEC-C motif; 31.6 25 0.00054 17.1 0.7 7 23-29 4-10 (21)
101 TIGR03844 cysteate_syn cysteat 31.6 35 0.00075 27.0 1.9 33 20-60 1-34 (398)
102 PF14670 FXa_inhibition: Coagu 31.3 22 0.00048 19.2 0.6 16 21-36 18-33 (36)
103 COG1594 RPB9 DNA-directed RNA 30.9 37 0.00079 22.6 1.7 31 23-56 4-35 (113)
104 TIGR02443 conserved hypothetic 30.8 50 0.0011 20.1 2.1 26 23-51 11-39 (59)
105 PF12906 RINGv: RING-variant d 30.6 39 0.00085 18.9 1.6 12 18-29 12-23 (47)
106 TIGR00244 transcriptional regu 30.2 39 0.00086 23.9 1.8 29 23-51 2-36 (147)
107 PHA02540 61 DNA primase; Provi 30.1 51 0.0011 26.0 2.6 39 9-50 15-62 (337)
108 PF05988 DUF899: Bacterial pro 29.9 14 0.0003 27.6 -0.6 12 43-54 82-93 (211)
109 PF10071 DUF2310: Zn-ribbon-co 29.8 27 0.00059 26.8 1.0 37 19-57 218-255 (258)
110 PF12760 Zn_Tnp_IS1595: Transp 29.6 26 0.00057 19.3 0.7 32 8-50 10-44 (46)
111 COG5595 Zn-ribbon-containing, 29.4 32 0.0007 26.1 1.4 35 21-57 218-253 (256)
112 PF02754 CCG: Cysteine-rich do 28.8 16 0.00034 21.0 -0.4 14 41-54 72-85 (85)
113 PF06906 DUF1272: Protein of u 28.6 26 0.00055 21.3 0.6 13 19-31 39-52 (57)
114 PRK00564 hypA hydrogenase nick 28.6 22 0.00048 23.6 0.3 26 20-51 70-96 (117)
115 PF14255 Cys_rich_CPXG: Cystei 27.9 69 0.0015 18.7 2.3 38 23-60 2-41 (52)
116 PRK00420 hypothetical protein; 27.9 56 0.0012 22.0 2.2 32 20-57 22-54 (112)
117 PRK00432 30S ribosomal protein 27.4 40 0.00086 19.4 1.2 27 21-53 20-47 (50)
118 smart00508 PostSET Cysteine-ri 27.3 25 0.00055 18.1 0.3 6 22-27 3-8 (26)
119 KOG1818 Membrane trafficking a 27.3 21 0.00046 30.6 0.1 34 21-54 181-223 (634)
120 PF07645 EGF_CA: Calcium-bindi 27.2 27 0.00059 18.7 0.5 13 21-33 24-36 (42)
121 PRK14701 reverse gyrase; Provi 27.0 24 0.00053 33.1 0.4 27 19-50 4-31 (1638)
122 PF12677 DUF3797: Domain of un 26.4 36 0.00077 20.1 0.9 11 17-27 35-45 (49)
123 TIGR00143 hypF [NiFe] hydrogen 26.3 15 0.00033 31.4 -1.0 44 13-56 79-153 (711)
124 TIGR01384 TFS_arch transcripti 26.2 39 0.00086 21.3 1.2 25 23-54 2-27 (104)
125 TIGR00416 sms DNA repair prote 26.0 50 0.0011 26.6 2.0 29 20-57 6-35 (454)
126 PF13948 DUF4215: Domain of un 26.0 36 0.00079 19.1 0.9 28 22-50 15-44 (47)
127 PF13005 zf-IS66: zinc-finger 25.7 51 0.0011 17.8 1.4 10 18-27 37-47 (47)
128 PF06007 PhnJ: Phosphonate met 25.3 41 0.00088 26.2 1.3 41 6-48 222-265 (277)
129 COG3877 Uncharacterized protei 24.5 80 0.0017 21.7 2.5 38 21-67 6-44 (122)
130 PRK12496 hypothetical protein; 24.3 50 0.0011 23.1 1.5 15 18-32 124-139 (164)
131 TIGR01054 rgy reverse gyrase. 24.1 33 0.00071 31.1 0.7 28 18-50 4-32 (1171)
132 PRK00750 lysK lysyl-tRNA synth 23.6 85 0.0018 25.7 2.9 25 12-36 191-215 (510)
133 PRK11823 DNA repair protein Ra 23.6 58 0.0012 26.1 1.9 28 20-56 6-34 (446)
134 PF01799 Fer2_2: [2Fe-2S] bind 23.4 35 0.00075 21.2 0.5 11 22-32 59-69 (75)
135 PRK04860 hypothetical protein; 22.4 1.7E+02 0.0036 20.6 3.8 37 18-55 116-155 (160)
136 PF06676 DUF1178: Protein of u 22.3 67 0.0015 22.6 1.8 34 18-51 2-40 (148)
137 TIGR01997 sufA_proteo FeS asse 22.1 75 0.0016 20.3 1.9 11 22-32 97-107 (107)
138 smart00064 FYVE Protein presen 20.4 44 0.00096 19.3 0.5 10 21-30 26-36 (68)
139 PF13912 zf-C2H2_6: C2H2-type 20.2 41 0.00089 15.9 0.3 10 22-31 2-12 (27)
No 1
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.95 E-value=1.5e-28 Score=152.48 Aligned_cols=65 Identities=63% Similarity=1.162 Sum_probs=62.3
Q ss_pred CccceeecCCceeccCCceEEEeCCCCCceeeehhhhhcCceEEEcCCCcceEEEEeeccccccc
Q 034819 1 MSYDDVEIEDMEWNEELQAYTYPCPCGDLFQITKDELRIGEEIARCPSCSLYITVIYNIEDFLDN 65 (82)
Q Consensus 1 ~~~d~v~LdDm~~~e~~~~y~y~CRCGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~~~~~~~e~ 65 (82)
++||+|.|+||+|+++++.|+|||||||.|+|++++|+.|+.+++|+||||.|+|+|+.+++++.
T Consensus 2 ~~ydeVeiedfe~~~e~~~y~yPCpCGDrf~It~edL~~ge~Va~CpsCSL~I~ViYd~edf~~~ 66 (67)
T KOG2923|consen 2 SFYDEVEIEDFEFDEENQTYYYPCPCGDRFQITLEDLENGEDVARCPSCSLIIRVIYDKEDFAEY 66 (67)
T ss_pred cccceEEeecceeccCCCeEEcCCCCCCeeeecHHHHhCCCeeecCCCceEEEEEEeCHHHhhcc
Confidence 57999999999999999999999999999999999999999999999999999999999988764
No 2
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=99.94 E-value=3.9e-27 Score=141.15 Aligned_cols=55 Identities=49% Similarity=1.058 Sum_probs=49.2
Q ss_pred ceeecCCceeccCCceEEEeCCCCCceeeehhhhhcCceEEEcCCCcceEEEEee
Q 034819 4 DDVEIEDMEWNEELQAYTYPCPCGDLFQITKDELRIGEEIARCPSCSLYITVIYN 58 (82)
Q Consensus 4 d~v~LdDm~~~e~~~~y~y~CRCGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~~ 58 (82)
|+|+|+||+|+++++.|+|+|||||.|.|++++|++++.+++|++|||||||+|+
T Consensus 1 dev~l~d~~~~~~~~~~~y~CRCG~~f~i~e~~l~~~~~iv~C~sCSL~I~V~~~ 55 (55)
T PF05207_consen 1 DEVSLDDMEFDEEEGVYSYPCRCGGEFEISEEDLEEGEVIVQCDSCSLWIRVNYD 55 (55)
T ss_dssp -EEETTTSEEETTTTEEEEEETTSSEEEEEHHHHHCT--EEEETTTTEEEEEE--
T ss_pred CeEEhhhceecCCCCEEEEcCCCCCEEEEcchhccCcCEEEECCCCccEEEEEeC
Confidence 6899999999999999999999999999999999999999999999999999985
No 3
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=99.91 E-value=1e-24 Score=134.44 Aligned_cols=64 Identities=52% Similarity=1.096 Sum_probs=61.9
Q ss_pred ccceeecCCceeccCCceEEEeCCCCCceeeehhhhhcCceEEEcCCCcceEEEEeeccccccc
Q 034819 2 SYDDVEIEDMEWNEELQAYTYPCPCGDLFQITKDELRIGEEIARCPSCSLYITVIYNIEDFLDN 65 (82)
Q Consensus 2 ~~d~v~LdDm~~~e~~~~y~y~CRCGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~~~~~~~e~ 65 (82)
+||+|.++||+|+.+++.|+||||||+.|+|+.++|.+|+.++.|+||||.|.|+|+.+++.+.
T Consensus 3 fYDEieiedftf~~e~~~ftyPCPCGDRFeIsLeDl~~GE~VArCPSCSLiv~vvyd~edl~ey 66 (67)
T COG5216 3 FYDEIEIEDFTFSREEKTFTYPCPCGDRFEISLEDLRNGEVVARCPSCSLIVCVVYDAEDLEEY 66 (67)
T ss_pred ccceeEeeeeEEcCCCceEEecCCCCCEeEEEHHHhhCCceEEEcCCceEEEEEEecHHHHhhh
Confidence 7999999999999999999999999999999999999999999999999999999999998764
No 4
>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=96.94 E-value=0.0019 Score=34.96 Aligned_cols=35 Identities=23% Similarity=0.568 Sum_probs=29.9
Q ss_pred EEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEE
Q 034819 21 TYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITV 55 (82)
Q Consensus 21 ~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V 55 (82)
...|+ ||..|.|..+.+......+.|+.|...+.+
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 35796 999999999999765568999999998876
No 5
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=95.87 E-value=0.012 Score=32.22 Aligned_cols=33 Identities=33% Similarity=0.858 Sum_probs=28.7
Q ss_pred EeCC-CCCceeeehhhhhcCceEEEcCCCcceEE
Q 034819 22 YPCP-CGDLFQITKDELRIGEEIARCPSCSLYIT 54 (82)
Q Consensus 22 y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~ 54 (82)
-.|| |+-.|.|+.+.|..+...+.|+.|.-...
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 3697 99999999999988778999999986654
No 6
>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=95.79 E-value=0.0064 Score=32.82 Aligned_cols=33 Identities=30% Similarity=0.845 Sum_probs=25.2
Q ss_pred eEEEeCC-CCCceeeehhhhhcCceEEEcCCCcceE
Q 034819 19 AYTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYI 53 (82)
Q Consensus 19 ~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I 53 (82)
.|.|.|+ ||..|.+....-+ ...+.|+.|.--+
T Consensus 3 ~Y~y~C~~Cg~~fe~~~~~~~--~~~~~CP~Cg~~~ 36 (41)
T smart00834 3 IYEYRCEDCGHTFEVLQKISD--DPLATCPECGGDV 36 (41)
T ss_pred CEEEEcCCCCCEEEEEEecCC--CCCCCCCCCCCcc
Confidence 5899998 9999987765332 4677899998743
No 7
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=95.64 E-value=0.019 Score=35.72 Aligned_cols=37 Identities=27% Similarity=0.631 Sum_probs=28.2
Q ss_pred EEEeCC-CC--CceeeehhhhhcCceEEEcCCCcceEEEE
Q 034819 20 YTYPCP-CG--DLFQITKDELRIGEEIARCPSCSLYITVI 56 (82)
Q Consensus 20 y~y~CR-CG--g~f~i~~~~Le~g~~iv~C~sCSL~I~V~ 56 (82)
..|.|. || ..-.|++...+.|.++++|++|.-+=.|-
T Consensus 3 l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlIa 42 (66)
T PF05180_consen 3 LTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLIA 42 (66)
T ss_dssp EEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES-
T ss_pred EEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeeeh
Confidence 578896 99 56789999999999999999998775553
No 8
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=95.03 E-value=0.012 Score=32.88 Aligned_cols=31 Identities=29% Similarity=0.857 Sum_probs=24.5
Q ss_pred eEEEeCC-CCCceeeehhhhhcCceEEEcCCCcc
Q 034819 19 AYTYPCP-CGDLFQITKDELRIGEEIARCPSCSL 51 (82)
Q Consensus 19 ~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL 51 (82)
.|.|.|+ ||..|++...--+ ...+.|+.|.-
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~--~~~~~CP~Cg~ 34 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISE--DDPVPCPECGS 34 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCC--CCCCcCCCCCC
Confidence 5899998 9999998764333 57789999976
No 9
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.03 E-value=0.029 Score=30.64 Aligned_cols=32 Identities=22% Similarity=0.669 Sum_probs=27.5
Q ss_pred EeCC-CCCceeeehhhhhcCceEEEcCCCcceE
Q 034819 22 YPCP-CGDLFQITKDELRIGEEIARCPSCSLYI 53 (82)
Q Consensus 22 y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I 53 (82)
-.|+ |+-.|.|.++.+-..-..++|+.|+-..
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 3686 9999999999998877899999998643
No 10
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=94.37 E-value=0.069 Score=31.54 Aligned_cols=34 Identities=35% Similarity=0.639 Sum_probs=25.5
Q ss_pred ceEEEeC-CCCCceeeehhhhhcCceEEEcCCCcceEEEE
Q 034819 18 QAYTYPC-PCGDLFQITKDELRIGEEIARCPSCSLYITVI 56 (82)
Q Consensus 18 ~~y~y~C-RCGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~ 56 (82)
....|-| |||..| ++......+.|+-|+..|-+.
T Consensus 3 ~~~~Y~C~~Cg~~~-----~~~~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 3 AMMEYKCARCGREV-----ELDQETRGIRCPYCGSRILVK 37 (49)
T ss_pred ceEEEEhhhcCCee-----ehhhccCceeCCCCCcEEEEe
Confidence 4578999 799988 222234668999999988774
No 11
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=94.14 E-value=0.11 Score=30.99 Aligned_cols=32 Identities=34% Similarity=0.944 Sum_probs=25.7
Q ss_pred EeCC-CCCceeeehhhhhcCceEEEcCCCcceEEEE
Q 034819 22 YPCP-CGDLFQITKDELRIGEEIARCPSCSLYITVI 56 (82)
Q Consensus 22 y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~ 56 (82)
..|+ ||..+.+....+ | .++.|+.|..-+.|.
T Consensus 3 ~~CP~CG~~iev~~~~~--G-eiV~Cp~CGaeleVv 35 (54)
T TIGR01206 3 FECPDCGAEIELENPEL--G-ELVICDECGAELEVV 35 (54)
T ss_pred cCCCCCCCEEecCCCcc--C-CEEeCCCCCCEEEEE
Confidence 4697 999998865544 4 477999999999995
No 12
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.67 E-value=0.087 Score=37.95 Aligned_cols=45 Identities=22% Similarity=0.487 Sum_probs=36.0
Q ss_pred ceeccCCceEEEeCC-CC--CceeeehhhhhcCceEEEcCCCcceEEE
Q 034819 11 MEWNEELQAYTYPCP-CG--DLFQITKDELRIGEEIARCPSCSLYITV 55 (82)
Q Consensus 11 m~~~e~~~~y~y~CR-CG--g~f~i~~~~Le~g~~iv~C~sCSL~I~V 55 (82)
|....-.....|.|- || ..-.|++...+.|.++|+|++|...=.|
T Consensus 69 ~~~~kp~m~l~yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~Hli 116 (165)
T KOG3277|consen 69 FKVPKPRMQLAYTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHHLI 116 (165)
T ss_pred ccCCCcceEEEEEeeccCCccccccChhhhhCceEEEECCCCccceee
Confidence 333444467899997 99 5678999999999999999999976555
No 13
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=92.76 E-value=0.12 Score=29.31 Aligned_cols=34 Identities=29% Similarity=0.857 Sum_probs=24.8
Q ss_pred eEEEeCC-CCCceeeehhhhhcCceEEEcCCCcc-eEE
Q 034819 19 AYTYPCP-CGDLFQITKDELRIGEEIARCPSCSL-YIT 54 (82)
Q Consensus 19 ~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL-~I~ 54 (82)
.|.|.|+ ||..|++... +.+ ...+.|+.|.- .++
T Consensus 3 ~Yey~C~~Cg~~fe~~~~-~~~-~~~~~CP~Cg~~~~~ 38 (52)
T TIGR02605 3 IYEYRCTACGHRFEVLQK-MSD-DPLATCPECGGEKLR 38 (52)
T ss_pred CEEEEeCCCCCEeEEEEe-cCC-CCCCCCCCCCCCcee
Confidence 5899998 9999998743 222 35678999986 553
No 14
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=85.89 E-value=0.69 Score=26.82 Aligned_cols=30 Identities=27% Similarity=0.736 Sum_probs=18.7
Q ss_pred EeCC-CCCceeeehhhhhc--Cc-eEEEcCCCcc
Q 034819 22 YPCP-CGDLFQITKDELRI--GE-EIARCPSCSL 51 (82)
Q Consensus 22 y~CR-CGg~f~i~~~~Le~--g~-~iv~C~sCSL 51 (82)
+||| ||..-......... +. ..|.|..|-.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 6899 98444433332221 21 7889999977
No 15
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=84.69 E-value=0.88 Score=25.42 Aligned_cols=29 Identities=31% Similarity=0.748 Sum_probs=21.5
Q ss_pred EEeCC-CCCceeeehhhhhcCceEEEcCCCcceEE
Q 034819 21 TYPCP-CGDLFQITKDELRIGEEIARCPSCSLYIT 54 (82)
Q Consensus 21 ~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~ 54 (82)
.|.|+ ||..|.+.+... .+.|+.|.-.+-
T Consensus 3 ~y~C~~CG~~~~~~~~~~-----~~~Cp~CG~~~~ 32 (46)
T PRK00398 3 EYKCARCGREVELDEYGT-----GVRCPYCGYRIL 32 (46)
T ss_pred EEECCCCCCEEEECCCCC-----ceECCCCCCeEE
Confidence 58896 999998864432 579999986554
No 16
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=84.25 E-value=0.72 Score=32.56 Aligned_cols=32 Identities=28% Similarity=0.599 Sum_probs=21.0
Q ss_pred EeCC-CCCce--eeehhhhhcCceE---EEcCCCcceE
Q 034819 22 YPCP-CGDLF--QITKDELRIGEEI---ARCPSCSLYI 53 (82)
Q Consensus 22 y~CR-CGg~f--~i~~~~Le~g~~i---v~C~sCSL~I 53 (82)
+.|| ||+.+ .++...+.+|+.+ .+|+.|+-.-
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 3588 88544 5666666666433 6899888643
No 17
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.77 E-value=2.8 Score=23.76 Aligned_cols=29 Identities=31% Similarity=0.769 Sum_probs=22.3
Q ss_pred EEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEE
Q 034819 21 TYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITV 55 (82)
Q Consensus 21 ~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V 55 (82)
.|-|. ||..|.+. ....+.|+.|.-.|-.
T Consensus 2 ~Y~C~~Cg~~~~~~------~~~~irC~~CG~rIly 31 (44)
T smart00659 2 IYICGECGRENEIK------SKDVVRCRECGYRILY 31 (44)
T ss_pred EEECCCCCCEeecC------CCCceECCCCCceEEE
Confidence 58895 99998876 2356899999987653
No 18
>PF12662 cEGF: Complement Clr-like EGF-like
Probab=81.58 E-value=0.48 Score=24.02 Aligned_cols=15 Identities=33% Similarity=0.939 Sum_probs=12.7
Q ss_pred EEeCCCCCceeeehh
Q 034819 21 TYPCPCGDLFQITKD 35 (82)
Q Consensus 21 ~y~CRCGg~f~i~~~ 35 (82)
+|.|.|..+|.++.+
T Consensus 1 sy~C~C~~Gy~l~~d 15 (24)
T PF12662_consen 1 SYTCSCPPGYQLSPD 15 (24)
T ss_pred CEEeeCCCCCcCCCC
Confidence 588999999998764
No 19
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=80.46 E-value=0.83 Score=32.78 Aligned_cols=33 Identities=27% Similarity=0.473 Sum_probs=15.2
Q ss_pred CceEEEeCC-CCCceeeehhhhhcCceEEEcCCCcce
Q 034819 17 LQAYTYPCP-CGDLFQITKDELRIGEEIARCPSCSLY 52 (82)
Q Consensus 17 ~~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~ 52 (82)
+..-..+|+ ||+.|+....++.. -+.|+-|++-
T Consensus 130 g~l~l~~C~~C~~~fv~~~~~~~~---~~~Cp~C~~p 163 (175)
T PF05280_consen 130 GMLQLAPCRRCGGHFVTHAHDPRH---SFVCPFCQPP 163 (175)
T ss_dssp TSEEEEE-TTT--EEEEESS--SS-------TT----
T ss_pred CCccccCCCCCCCCeECcCCCCCc---CcCCCCCCCc
Confidence 345677897 99999998776543 3689999863
No 20
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=79.07 E-value=2.3 Score=23.43 Aligned_cols=30 Identities=33% Similarity=0.763 Sum_probs=18.2
Q ss_pred EeCC-CCCceeeehhhhhcCceEEEcCCCcceEEE
Q 034819 22 YPCP-CGDLFQITKDELRIGEEIARCPSCSLYITV 55 (82)
Q Consensus 22 y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V 55 (82)
|.|| ||....+.. -..|+ +-|..|=++|.=
T Consensus 1 m~Cp~Cg~~~~~~D--~~~g~--~vC~~CG~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKEIVFD--PERGE--LVCPNCGLVLEE 31 (43)
T ss_dssp ESBTTTSSSEEEEE--TTTTE--EEETTT-BBEE-
T ss_pred CCCcCCcCCceEEc--CCCCe--EECCCCCCEeec
Confidence 5697 998774333 22232 479999888753
No 21
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=77.71 E-value=3 Score=28.45 Aligned_cols=38 Identities=18% Similarity=0.456 Sum_probs=27.1
Q ss_pred ceEEEeCC-CCCceeeehhhhh-cCceEEEcCCCcceEEE
Q 034819 18 QAYTYPCP-CGDLFQITKDELR-IGEEIARCPSCSLYITV 55 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le-~g~~iv~C~sCSL~I~V 55 (82)
+.-.|-|| ||..|.+.+.... +....+.|+.|.-.+..
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 45689997 9999997655322 22334999999987765
No 22
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=76.79 E-value=2.2 Score=35.16 Aligned_cols=38 Identities=29% Similarity=0.679 Sum_probs=27.8
Q ss_pred CCceEEEeCC-CCCceeeehhhhh------cCceEEEcCCCcceE
Q 034819 16 ELQAYTYPCP-CGDLFQITKDELR------IGEEIARCPSCSLYI 53 (82)
Q Consensus 16 ~~~~y~y~CR-CGg~f~i~~~~Le------~g~~iv~C~sCSL~I 53 (82)
+...|.-+|| ||..+.+.=+.|. .......|+.|--.|
T Consensus 195 dqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i 239 (557)
T PF05876_consen 195 DQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEI 239 (557)
T ss_pred CceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCC
Confidence 3468999998 9988888755552 234688999996554
No 23
>PRK12722 transcriptional activator FlhC; Provisional
Probab=76.33 E-value=1.4 Score=32.24 Aligned_cols=31 Identities=19% Similarity=0.322 Sum_probs=23.9
Q ss_pred ceEEEeCC-CCCceeeehhhhhcCceEEEcCCCcc
Q 034819 18 QAYTYPCP-CGDLFQITKDELRIGEEIARCPSCSL 51 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL 51 (82)
..=.-+|| |||.|+....++.. -..|+-|..
T Consensus 131 ~L~l~~C~~Cgg~fv~~~~e~~~---~f~CplC~~ 162 (187)
T PRK12722 131 MLQLSSCNCCGGHFVTHAHDPVG---SFVCGLCQP 162 (187)
T ss_pred cEeeccCCCCCCCeeccccccCC---CCcCCCCCC
Confidence 34456798 99999988876643 368999988
No 24
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=76.23 E-value=2.6 Score=26.86 Aligned_cols=8 Identities=50% Similarity=1.348 Sum_probs=7.0
Q ss_pred EEEeCC-CC
Q 034819 20 YTYPCP-CG 27 (82)
Q Consensus 20 y~y~CR-CG 27 (82)
..|.|| ||
T Consensus 3 i~Y~CRHCg 11 (76)
T PF10955_consen 3 IHYYCRHCG 11 (76)
T ss_pred eEEEecCCC
Confidence 579999 99
No 25
>PRK12860 transcriptional activator FlhC; Provisional
Probab=75.09 E-value=1.5 Score=32.06 Aligned_cols=30 Identities=27% Similarity=0.472 Sum_probs=22.8
Q ss_pred ceEEEeCC-CCCceeeehhhhhcCceEEEcCCCc
Q 034819 18 QAYTYPCP-CGDLFQITKDELRIGEEIARCPSCS 50 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCS 50 (82)
..=.-+|| |||.|+..-.++.. -..|+-|.
T Consensus 131 ~L~l~~C~~Cgg~fv~~~~e~~~---~f~CplC~ 161 (189)
T PRK12860 131 MLQLARCCRCGGKFVTHAHDLRH---NFVCGLCQ 161 (189)
T ss_pred CeeeccCCCCCCCeeccccccCC---CCcCCCCC
Confidence 45567898 99999988775543 36899998
No 26
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=74.82 E-value=3 Score=22.59 Aligned_cols=15 Identities=13% Similarity=0.530 Sum_probs=9.9
Q ss_pred ceEEEcCCCcceEEE
Q 034819 41 EEIARCPSCSLYITV 55 (82)
Q Consensus 41 ~~iv~C~sCSL~I~V 55 (82)
+.++.|++|++.|+-
T Consensus 2 n~ll~C~~C~v~VH~ 16 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQ 16 (36)
T ss_dssp CEEEE-SSS--EEEH
T ss_pred CceEEeCCCCCcCCh
Confidence 468999999999975
No 27
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=74.81 E-value=2.8 Score=24.13 Aligned_cols=34 Identities=24% Similarity=0.448 Sum_probs=17.9
Q ss_pred EeCC-CCCcee-eeh-hhhhcCceEEEcCCCcceEEE
Q 034819 22 YPCP-CGDLFQ-ITK-DELRIGEEIARCPSCSLYITV 55 (82)
Q Consensus 22 y~CR-CGg~f~-i~~-~~Le~g~~iv~C~sCSL~I~V 55 (82)
.||| ||+.=. +.. .+-.++.-++.|..|--...+
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 4788 985422 221 111122345578888776554
No 28
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=74.58 E-value=1.5 Score=25.11 Aligned_cols=29 Identities=31% Similarity=0.787 Sum_probs=21.1
Q ss_pred EEeCC-CCCceeeehhhhhc--------CceEEEcCCCcc
Q 034819 21 TYPCP-CGDLFQITKDELRI--------GEEIARCPSCSL 51 (82)
Q Consensus 21 ~y~CR-CGg~f~i~~~~Le~--------g~~iv~C~sCSL 51 (82)
+|.|| ||.. ++...|.. ....+.|+=|+-
T Consensus 2 ~f~CP~C~~~--~~~~~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 2 SFTCPYCGKG--FSESSLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred CcCCCCCCCc--cCHHHHHHHHHhHCcCCCCCccCCCchh
Confidence 57899 9983 66777754 124689999985
No 29
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=71.25 E-value=2 Score=29.94 Aligned_cols=24 Identities=33% Similarity=0.904 Sum_probs=17.0
Q ss_pred EeC-CCCCceeeehhhhhcCceEEEcCCCc
Q 034819 22 YPC-PCGDLFQITKDELRIGEEIARCPSCS 50 (82)
Q Consensus 22 y~C-RCGg~f~i~~~~Le~g~~iv~C~sCS 50 (82)
|.| +||..|.=-..++.. +|+.|-
T Consensus 2 H~Ct~Cg~~f~dgs~eil~-----GCP~CG 26 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILS-----GCPECG 26 (131)
T ss_pred cccCcCCCCcCCCcHHHHc-----cCcccC
Confidence 568 599888855556655 688775
No 30
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=70.62 E-value=3.5 Score=28.12 Aligned_cols=37 Identities=19% Similarity=0.664 Sum_probs=23.0
Q ss_pred EEEeCC-CCCceeeeh--hhhhc----C--------ceEEEcCCCc-ceEEEE
Q 034819 20 YTYPCP-CGDLFQITK--DELRI----G--------EEIARCPSCS-LYITVI 56 (82)
Q Consensus 20 y~y~CR-CGg~f~i~~--~~Le~----g--------~~iv~C~sCS-L~I~V~ 56 (82)
-.+.|+ ||..|.+.. ..|.. . .....|+.|- .-++|.
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 121 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIV 121 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEe
Confidence 578898 998888762 22221 1 2346799994 445553
No 31
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=69.69 E-value=3.5 Score=24.71 Aligned_cols=23 Identities=43% Similarity=1.206 Sum_probs=16.9
Q ss_pred EeCC-CCCceeeehhhhhcCceEEEcCCCcc
Q 034819 22 YPCP-CGDLFQITKDELRIGEEIARCPSCSL 51 (82)
Q Consensus 22 y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL 51 (82)
..|. ||+.|. .+.++|.|+.|.-
T Consensus 6 ~~C~~Cg~~~~-------~~dDiVvCp~Cga 29 (54)
T PF14446_consen 6 CKCPVCGKKFK-------DGDDIVVCPECGA 29 (54)
T ss_pred ccChhhCCccc-------CCCCEEECCCCCC
Confidence 4576 887664 4678999999963
No 32
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=67.97 E-value=4.5 Score=23.74 Aligned_cols=29 Identities=48% Similarity=0.981 Sum_probs=19.9
Q ss_pred EEeCC-CCCceeeehhhhh----cC--ceEEEcCCC
Q 034819 21 TYPCP-CGDLFQITKDELR----IG--EEIARCPSC 49 (82)
Q Consensus 21 ~y~CR-CGg~f~i~~~~Le----~g--~~iv~C~sC 49 (82)
...|+ ||..|++|..+-+ .| +.-..|.+|
T Consensus 4 ~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~C 39 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSC 39 (49)
T ss_pred eEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHH
Confidence 46797 9999999987643 23 234566666
No 33
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=67.69 E-value=4.2 Score=22.77 Aligned_cols=28 Identities=43% Similarity=0.869 Sum_probs=13.9
Q ss_pred EEEeCC-CC--CceeeehhhhhcCceEEEcCCC
Q 034819 20 YTYPCP-CG--DLFQITKDELRIGEEIARCPSC 49 (82)
Q Consensus 20 y~y~CR-CG--g~f~i~~~~Le~g~~iv~C~sC 49 (82)
+--||| || |.|.|..+.-..|. .-|.+|
T Consensus 2 ~h~pCP~CGG~DrFri~~d~~~~G~--~~C~~C 32 (40)
T PF08273_consen 2 KHGPCPICGGKDRFRIFDDKDGRGT--WICRQC 32 (40)
T ss_dssp EEE--TTTT-TTTEEEETT----S---EEETTT
T ss_pred CCCCCCCCcCccccccCcCcccCCC--EECCCC
Confidence 346898 99 78996665433333 346666
No 34
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=67.05 E-value=2.9 Score=28.11 Aligned_cols=37 Identities=22% Similarity=0.518 Sum_probs=22.8
Q ss_pred EEEeCCCCCceeeehhhhhcCceEEEcCCC-cceEEEE
Q 034819 20 YTYPCPCGDLFQITKDELRIGEEIARCPSC-SLYITVI 56 (82)
Q Consensus 20 y~y~CRCGg~f~i~~~~Le~g~~iv~C~sC-SL~I~V~ 56 (82)
-...|.||..|.+....+..-.....|+.| |..++|.
T Consensus 69 ~~~~C~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~ 106 (124)
T PRK00762 69 VEIECECGYEGVVDEDEIDHYAAVIECPVCGNKRAHIL 106 (124)
T ss_pred eeEEeeCcCcccccccchhccccCCcCcCCCCCCCEEe
Confidence 455679998888765443321223579999 4566553
No 35
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=67.02 E-value=6.4 Score=21.62 Aligned_cols=19 Identities=16% Similarity=0.433 Sum_probs=15.2
Q ss_pred CceEEEcCCCcceEEEEee
Q 034819 40 GEEIARCPSCSLYITVIYN 58 (82)
Q Consensus 40 g~~iv~C~sCSL~I~V~~~ 58 (82)
+..++.|++|..|.+..-.
T Consensus 11 ~~~~i~C~~C~~~~H~~C~ 29 (51)
T PF00628_consen 11 DGDMIQCDSCNRWYHQECV 29 (51)
T ss_dssp TSSEEEBSTTSCEEETTTS
T ss_pred CCCeEEcCCCChhhCcccC
Confidence 4689999999999887433
No 36
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=64.93 E-value=4.4 Score=22.38 Aligned_cols=25 Identities=40% Similarity=1.035 Sum_probs=14.6
Q ss_pred EeCC-CC--CceeeehhhhhcCceEEEcCCC
Q 034819 22 YPCP-CG--DLFQITKDELRIGEEIARCPSC 49 (82)
Q Consensus 22 y~CR-CG--g~f~i~~~~Le~g~~iv~C~sC 49 (82)
-||| || |.|.++..+ +.-..-|..|
T Consensus 4 ~pCP~CGG~DrFr~~d~~---g~G~~~C~~C 31 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKD---GRGTWFCSVC 31 (37)
T ss_pred cCCCCCCCccccccccCC---CCcCEEeCCC
Confidence 4798 98 578854422 2233456666
No 38
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=64.79 E-value=3.6 Score=31.08 Aligned_cols=28 Identities=29% Similarity=0.543 Sum_probs=18.8
Q ss_pred CCCCceeeehhhh----hcCceEEEcCCCcce
Q 034819 25 PCGDLFQITKDEL----RIGEEIARCPSCSLY 52 (82)
Q Consensus 25 RCGg~f~i~~~~L----e~g~~iv~C~sCSL~ 52 (82)
+|||=+.+-.... ..++.+|.|+.||=+
T Consensus 199 ~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 199 VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred cccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 5887655444333 346789999999943
No 39
>PF14353 CpXC: CpXC protein
Probab=63.28 E-value=5.1 Score=26.32 Aligned_cols=43 Identities=26% Similarity=0.445 Sum_probs=28.1
Q ss_pred eCC-CCCceeeehhhh-------------hcCc-eEEEcCCCcceEEEEeeccccccc
Q 034819 23 PCP-CGDLFQITKDEL-------------RIGE-EIARCPSCSLYITVIYNIEDFLDN 65 (82)
Q Consensus 23 ~CR-CGg~f~i~~~~L-------------e~g~-~iv~C~sCSL~I~V~~~~~~~~e~ 65 (82)
.|| ||..|.+..-.+ .+|+ ..+.|++|--..++.|...-.+..
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCC
Confidence 588 997776554332 2232 488999998888887765554444
No 40
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.87 E-value=2.1 Score=27.74 Aligned_cols=35 Identities=23% Similarity=0.801 Sum_probs=25.1
Q ss_pred ceEEEeCC-CCCceeeehhhhhcCceEEEcCCCcceEE
Q 034819 18 QAYTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYIT 54 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~ 54 (82)
-+|.|.|- ||..|.+-..-- ...+..|..|+-.+|
T Consensus 9 PtY~Y~c~~cg~~~dvvq~~~--ddplt~ce~c~a~~k 44 (82)
T COG2331 9 PTYSYECTECGNRFDVVQAMT--DDPLTTCEECGARLK 44 (82)
T ss_pred cceEEeecccchHHHHHHhcc--cCccccChhhChHHH
Confidence 47999996 998886543322 247889999996543
No 41
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=62.65 E-value=4.4 Score=34.47 Aligned_cols=39 Identities=28% Similarity=0.625 Sum_probs=30.1
Q ss_pred CceEEEeCC-CCCceeeehhhhhc--C-------ceEEEcCCCcceEEE
Q 034819 17 LQAYTYPCP-CGDLFQITKDELRI--G-------EEIARCPSCSLYITV 55 (82)
Q Consensus 17 ~~~y~y~CR-CGg~f~i~~~~Le~--g-------~~iv~C~sCSL~I~V 55 (82)
...|+-+|| ||..|.+.-++... | ...++|..|...|+=
T Consensus 223 ~rr~yvpCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~ 271 (611)
T COG5525 223 QRRFYVPCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRP 271 (611)
T ss_pred ceeEEeeCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeee
Confidence 467999998 99988887765542 1 246799999999986
No 42
>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=61.33 E-value=11 Score=28.27 Aligned_cols=18 Identities=22% Similarity=0.617 Sum_probs=16.3
Q ss_pred CceEEEcCCCcceEEEEe
Q 034819 40 GEEIARCPSCSLYITVIY 57 (82)
Q Consensus 40 g~~iv~C~sCSL~I~V~~ 57 (82)
+.-+-.|.+|.-.+|+++
T Consensus 235 ~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 235 AYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp SEEEEEETTTTEEEEEEE
T ss_pred cEEEEECCcccchHHHHh
Confidence 467889999999999998
No 43
>PF01831 Peptidase_C16: Peptidase C16 family; InterPro: IPR002705 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This entry contains coronavirus cysteine endopeptidases that belong to MEROPS peptidase families C30 (clan PA) and C16 (subfamiles C16A and C16B, clan CA). These peptidase are involved in viral polyprotein processing. All coronaviruses encodes between one and two accessory cysteine proteinases that recognise and process one or two sites in the amino-terminal half of the replicase polyprotein during assembly of the viral replication complex. MHV, HCoV and TGEV encode two accesssory proteinases, called coronavirus papain-like proteinase 1 and 2 (PL1-PRO and PL2-PRO). IBV and SARS encodes only one called PL-PRO []. Coronavirus papain-like proteinases 1 and 2 have restricted specificities, cleaving respectively two and one bond(s)in the polyprotein. This restricted activity may be due to extended specificity sites: Arg or Lys at the cleavage site position P5 are required for PL1-PRO [], and Phe at the cleavage site position P6 is required for PL2-PRO []. PL1-PRO releases p28 and p65 from the N terminus of the polyprotein; PL2-PRO cleaves between p210 and p150. ; GO: 0003968 RNA-directed RNA polymerase activity, 0008234 cysteine-type peptidase activity, 0006508 proteolysis
Probab=59.95 E-value=7.6 Score=29.36 Aligned_cols=33 Identities=9% Similarity=0.270 Sum_probs=21.9
Q ss_pred eecCCcee-ccCCceEEEeCCCCCceeeehhhhh
Q 034819 6 VEIEDMEW-NEELQAYTYPCPCGDLFQITKDELR 38 (82)
Q Consensus 6 v~LdDm~~-~e~~~~y~y~CRCGg~f~i~~~~Le 38 (82)
+.|.+|+- -..+..+++.||||....+-..++-
T Consensus 122 l~lngLDa~ffyGDivshvCKcG~sm~l~~~d~p 155 (249)
T PF01831_consen 122 LRLNGLDAMFFYGDIVSHVCKCGNSMTLISADVP 155 (249)
T ss_pred eeeccchheeeeccEEEEEeccCCceEEEecCCc
Confidence 44444431 1234689999999998887776653
No 44
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=59.49 E-value=4.6 Score=27.51 Aligned_cols=29 Identities=31% Similarity=0.883 Sum_probs=18.3
Q ss_pred EeC-CCCCceeeehhhhhcCceEEEcCCC--cceEEE
Q 034819 22 YPC-PCGDLFQITKDELRIGEEIARCPSC--SLYITV 55 (82)
Q Consensus 22 y~C-RCGg~f~i~~~~Le~g~~iv~C~sC--SL~I~V 55 (82)
|.| |||-.|.=-.+.+.. +|+.| ..+..|
T Consensus 3 H~CtrCG~vf~~g~~~il~-----GCp~CG~nkF~yv 34 (112)
T COG3364 3 HQCTRCGEVFDDGSEEILS-----GCPKCGCNKFLYV 34 (112)
T ss_pred ceecccccccccccHHHHc-----cCccccchheEec
Confidence 678 799988754444444 67655 444444
No 45
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=57.84 E-value=5.2 Score=21.16 Aligned_cols=23 Identities=35% Similarity=0.970 Sum_probs=10.3
Q ss_pred eCC-CCCceeeehhhhhcCceEEEcCCCcc
Q 034819 23 PCP-CGDLFQITKDELRIGEEIARCPSCSL 51 (82)
Q Consensus 23 ~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL 51 (82)
.|+ ||..|.. .+ ..+.-|+.|.-
T Consensus 4 ~Cp~C~se~~y-----~D-~~~~vCp~C~~ 27 (30)
T PF08274_consen 4 KCPLCGSEYTY-----ED-GELLVCPECGH 27 (30)
T ss_dssp --TTT-----E-----E--SSSEEETTTTE
T ss_pred CCCCCCCccee-----cc-CCEEeCCcccc
Confidence 587 8877776 33 35667888864
No 46
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=57.66 E-value=3.8 Score=37.16 Aligned_cols=28 Identities=36% Similarity=0.871 Sum_probs=22.5
Q ss_pred ceEEEeCC-CCCceeeehhhhhcCceEEEcCCCc
Q 034819 18 QAYTYPCP-CGDLFQITKDELRIGEEIARCPSCS 50 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCS 50 (82)
..|.+.|| |||. ||.+-|+.| .+|..|=
T Consensus 5 ~iY~~~CpNCGG~--isseRL~~g---lpCe~CL 33 (1187)
T COG1110 5 AIYGSSCPNCGGD--ISSERLEKG---LPCERCL 33 (1187)
T ss_pred hhhhccCCCCCCc--CcHHHHhcC---CCchhcc
Confidence 46889999 9996 568889887 5698883
No 47
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=57.55 E-value=15 Score=24.82 Aligned_cols=32 Identities=34% Similarity=0.838 Sum_probs=24.8
Q ss_pred CC-CCCceeeehhhhhcCceEEEcCCCcceEEEEeecccccc
Q 034819 24 CP-CGDLFQITKDELRIGEEIARCPSCSLYITVIYNIEDFLD 64 (82)
Q Consensus 24 CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~~~~~~~e 64 (82)
|| ||+...|++ ..|++|.-.|+=.|....+.-
T Consensus 1 CPvCg~~l~vt~---------l~C~~C~t~i~G~F~l~~~~~ 33 (113)
T PF09862_consen 1 CPVCGGELVVTR---------LKCPSCGTEIEGEFELPWFAR 33 (113)
T ss_pred CCCCCCceEEEE---------EEcCCCCCEEEeeeccchhhc
Confidence 77 988888764 689999999988887665443
No 48
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=56.74 E-value=14 Score=24.04 Aligned_cols=39 Identities=21% Similarity=0.397 Sum_probs=30.4
Q ss_pred CCceEEEeCCCCCceeeehhhhhcCceEEEcCCCcceEEE
Q 034819 16 ELQAYTYPCPCGDLFQITKDELRIGEEIARCPSCSLYITV 55 (82)
Q Consensus 16 ~~~~y~y~CRCGg~f~i~~~~Le~g~~iv~C~sCSL~I~V 55 (82)
..+.|+..=+|+|-|.||----. ..-+|.|.+|++.+-.
T Consensus 27 ~~nsyFm~VkC~gc~~iT~vfSH-aqtvVvc~~c~~il~~ 65 (84)
T KOG1779|consen 27 SPNSYFMDVKCPGCFKITTVFSH-AQTVVVCEGCSTILCQ 65 (84)
T ss_pred CCCceEEEEEcCCceEEEEEeec-CceEEEcCCCceEEEE
Confidence 34678999999999998854333 3678999999998754
No 49
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=56.29 E-value=4.5 Score=28.80 Aligned_cols=16 Identities=31% Similarity=0.708 Sum_probs=11.8
Q ss_pred EEEeCCCCCceeeehh
Q 034819 20 YTYPCPCGDLFQITKD 35 (82)
Q Consensus 20 y~y~CRCGg~f~i~~~ 35 (82)
-.|.||||..|-..--
T Consensus 118 tgf~CrCG~~fC~~HR 133 (167)
T KOG3173|consen 118 TGFKCRCGNTFCGTHR 133 (167)
T ss_pred cccccccCCccccccc
Confidence 3489999998875443
No 50
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=55.83 E-value=5.7 Score=30.98 Aligned_cols=45 Identities=20% Similarity=0.492 Sum_probs=29.6
Q ss_pred ccCC--ceEEEeCCCCCce----------eeehhhhhcCceEEEcCCCcceEEEEee
Q 034819 14 NEEL--QAYTYPCPCGDLF----------QITKDELRIGEEIARCPSCSLYITVIYN 58 (82)
Q Consensus 14 ~e~~--~~y~y~CRCGg~f----------~i~~~~Le~g~~iv~C~sCSL~I~V~~~ 58 (82)
++|+ ..|-+||||-|.- .|+|.+..+...-|.|+.|----.+.|.
T Consensus 30 deDn~~a~WV~PCrCRGt~KWVHqsCL~rWiDEK~~~n~~q~V~C~QCqTEYiiv~P 86 (293)
T KOG3053|consen 30 DEDNRLAAWVHPCRCRGTTKWVHQSCLSRWIDEKQRGNPLQTVSCPQCQTEYIIVFP 86 (293)
T ss_pred CcccchhhhcccccccCccHHHHHHHHHHHHhHHhcCCCCceeechhhcchheeecc
Confidence 4444 3599999998753 4666666444568899999654444443
No 51
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=53.17 E-value=14 Score=21.20 Aligned_cols=26 Identities=35% Similarity=0.866 Sum_probs=18.3
Q ss_pred CCCC-ceeeehhhhhc---CceEEEcCCCc
Q 034819 25 PCGD-LFQITKDELRI---GEEIARCPSCS 50 (82)
Q Consensus 25 RCGg-~f~i~~~~Le~---g~~iv~C~sCS 50 (82)
+|+| .+.|+...+.+ +..++.|++|.
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~Cg 53 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCG 53 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCC
Confidence 3543 56777776553 56899999996
No 52
>PF14369 zf-RING_3: zinc-finger
Probab=52.36 E-value=7.8 Score=20.88 Aligned_cols=9 Identities=44% Similarity=1.136 Sum_probs=7.7
Q ss_pred eCC-CCCcee
Q 034819 23 PCP-CGDLFQ 31 (82)
Q Consensus 23 ~CR-CGg~f~ 31 (82)
.|| |+++|+
T Consensus 23 ~CP~C~~gFv 32 (35)
T PF14369_consen 23 ACPRCHGGFV 32 (35)
T ss_pred CCcCCCCcEe
Confidence 597 999996
No 53
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=51.75 E-value=13 Score=21.50 Aligned_cols=17 Identities=24% Similarity=0.554 Sum_probs=14.5
Q ss_pred ceEEEcCCCcceEEEEe
Q 034819 41 EEIARCPSCSLYITVIY 57 (82)
Q Consensus 41 ~~iv~C~sCSL~I~V~~ 57 (82)
...++|.+||-.|.+.+
T Consensus 29 ~~klrCGaCs~vl~~s~ 45 (46)
T PF11331_consen 29 QQKLRCGACSEVLSFSL 45 (46)
T ss_pred eeEEeCCCCceeEEEec
Confidence 56889999999998865
No 54
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=51.07 E-value=7.7 Score=19.28 Aligned_cols=10 Identities=60% Similarity=1.630 Sum_probs=8.1
Q ss_pred EeCC-CCCcee
Q 034819 22 YPCP-CGDLFQ 31 (82)
Q Consensus 22 y~CR-CGg~f~ 31 (82)
.+|+ ||..|.
T Consensus 3 ~~C~~CgR~F~ 13 (25)
T PF13913_consen 3 VPCPICGRKFN 13 (25)
T ss_pred CcCCCCCCEEC
Confidence 4798 999994
No 55
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=48.55 E-value=17 Score=22.49 Aligned_cols=30 Identities=33% Similarity=0.594 Sum_probs=17.9
Q ss_pred EEeCC-CCCceeeehhhhhcCceEEEcCCCcce
Q 034819 21 TYPCP-CGDLFQITKDELRIGEEIARCPSCSLY 52 (82)
Q Consensus 21 ~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~ 52 (82)
..||| ||..=..-+.. .+--.+.|.+|--.
T Consensus 6 lKPCPFCG~~~~~v~~~--~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAI--SGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCCCCCceeEEEec--CceEEEEcCCCCcC
Confidence 46898 98443332322 34457888888653
No 56
>PRK09401 reverse gyrase; Reviewed
Probab=48.30 E-value=7.6 Score=35.01 Aligned_cols=29 Identities=31% Similarity=0.808 Sum_probs=23.4
Q ss_pred ceEEEeCC-CCCceeeehhhhhcCceEEEcCCCcc
Q 034819 18 QAYTYPCP-CGDLFQITKDELRIGEEIARCPSCSL 51 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL 51 (82)
..|.+.|| |||.. |.+-|..| .+|..|--
T Consensus 4 ~~y~~~cpnc~g~i--~~~rl~~g---~~c~~cl~ 33 (1176)
T PRK09401 4 AIYKNSCPNCGGDI--SDERLEKG---LPCEKCLP 33 (1176)
T ss_pred hhhcccCCCCCCcC--cHhHHhcC---CcChhhCC
Confidence 36889999 99964 58888877 69999975
No 57
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=47.28 E-value=8.2 Score=25.37 Aligned_cols=27 Identities=26% Similarity=0.667 Sum_probs=16.9
Q ss_pred eEEEeCC-CCCceeeehhhhhcCceEEEcCCCcce
Q 034819 19 AYTYPCP-CGDLFQITKDELRIGEEIARCPSCSLY 52 (82)
Q Consensus 19 ~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~ 52 (82)
-....|+ ||..|.+..... .|+.|.-.
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~-------~CP~Cgs~ 95 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFDF-------SCPRCGSP 95 (113)
T ss_dssp --EEEETTTS-EEECHHCCH-------H-SSSSSS
T ss_pred CCcEECCCCCCEEecCCCCC-------CCcCCcCC
Confidence 3567796 999998776653 38988765
No 58
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=46.63 E-value=7.8 Score=17.89 Aligned_cols=10 Identities=60% Similarity=1.663 Sum_probs=7.0
Q ss_pred EeCC-CCCcee
Q 034819 22 YPCP-CGDLFQ 31 (82)
Q Consensus 22 y~CR-CGg~f~ 31 (82)
|.|+ ||-.|.
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 5676 877765
No 59
>PF09064 Tme5_EGF_like: Thrombomodulin like fifth domain, EGF-like; InterPro: IPR015149 This domain adopts a fold similar to other EGF domains, with a flat major and a twisted minor beta sheet. Disulphide pairing, however, is not of the usual 1-3, 2-4, 5-6 type; rather 1-2, 3-4, 5-6 pairing is found. Its extended major sheet (strands beta-2 and beta-3 and the connecting loop) projects into thrombin's active site groove. This domain is required for interaction of thrombomodulin with thrombin, and subsequent activation of protein-C []. ; GO: 0004888 transmembrane signaling receptor activity, 0016021 integral to membrane
Probab=46.23 E-value=8.4 Score=21.17 Aligned_cols=16 Identities=13% Similarity=0.403 Sum_probs=12.9
Q ss_pred EEeCCCCCceeeehhh
Q 034819 21 TYPCPCGDLFQITKDE 36 (82)
Q Consensus 21 ~y~CRCGg~f~i~~~~ 36 (82)
...|.|.++|++.+..
T Consensus 17 ~~~C~CPeGyIlde~~ 32 (34)
T PF09064_consen 17 PGQCFCPEGYILDEGS 32 (34)
T ss_pred CCceeCCCceEecCCc
Confidence 3489999999998754
No 60
>PRK06260 threonine synthase; Validated
Probab=45.66 E-value=21 Score=27.85 Aligned_cols=34 Identities=35% Similarity=0.870 Sum_probs=24.5
Q ss_pred EEEeC-CCCCceeeehhhhhcCceEEEcCCCcceEEEEeecc
Q 034819 20 YTYPC-PCGDLFQITKDELRIGEEIARCPSCSLYITVIYNIE 60 (82)
Q Consensus 20 y~y~C-RCGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~~~~ 60 (82)
|.+.| +||..|..+ .....|+.|.-.+.+.|+..
T Consensus 2 ~~~~C~~cg~~~~~~-------~~~~~Cp~cg~~l~~~y~~~ 36 (397)
T PRK06260 2 YWLKCIECGKEYDPD-------EIIYTCPECGGLLEVIYDLD 36 (397)
T ss_pred CEEEECCCCCCCCCC-------CccccCCCCCCeEEEEecch
Confidence 56789 499887532 12357999988899998844
No 61
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=45.30 E-value=12 Score=24.74 Aligned_cols=25 Identities=28% Similarity=0.600 Sum_probs=15.8
Q ss_pred EEEeCC-CCCceeeehhhhhcCceEEEcCCCcc
Q 034819 20 YTYPCP-CGDLFQITKDELRIGEEIARCPSCSL 51 (82)
Q Consensus 20 y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL 51 (82)
-...|+ ||..|.+.. ....|+.|--
T Consensus 69 ~~~~C~~Cg~~~~~~~-------~~~~CP~Cgs 94 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ-------HDAQCPHCHG 94 (113)
T ss_pred cEEEcccCCCEEecCC-------cCccCcCCCC
Confidence 456787 887776543 2235888863
No 62
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=44.77 E-value=25 Score=19.96 Aligned_cols=30 Identities=23% Similarity=0.691 Sum_probs=21.4
Q ss_pred ceEEEeCC-CCCceeeehhhhhcCceEEEcCCC
Q 034819 18 QAYTYPCP-CGDLFQITKDELRIGEEIARCPSC 49 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sC 49 (82)
......|+ ||..|.-+..+... .-.+|+-|
T Consensus 25 ~~v~W~C~~Cgh~w~~~v~~R~~--~~~~CP~C 55 (55)
T PF14311_consen 25 KKVWWKCPKCGHEWKASVNDRTR--RGKGCPYC 55 (55)
T ss_pred CEEEEECCCCCCeeEccHhhhcc--CCCCCCCC
Confidence 45667997 99999988887652 33467766
No 63
>PF04071 zf-like: Cysteine-rich small domain; InterPro: IPR007212 This is a probable metal-binding domain. It is found in a probable precorrin-3B C17-methyltransferase from Methanobacterium thermoautotrophicum, that catalyses the methylation of C-17 in precorrin-3B to form precorrin-4.
Probab=43.75 E-value=25 Score=22.74 Aligned_cols=28 Identities=43% Similarity=0.965 Sum_probs=20.8
Q ss_pred EEeC--CCCCceeeehhhhhcCceEEEcCCCcce
Q 034819 21 TYPC--PCGDLFQITKDELRIGEEIARCPSCSLY 52 (82)
Q Consensus 21 ~y~C--RCGg~f~i~~~~Le~g~~iv~C~sCSL~ 52 (82)
.|+| .|||.|+.++ .|..+-.|..|.|.
T Consensus 31 lY~c~d~~~G~~~~~~----~G~~vw~C~~C~~~ 60 (86)
T PF04071_consen 31 LYPCGDECGGNFIYTK----NGSKVWDCSDCTLP 60 (86)
T ss_pred cccccCCCCccEEEcC----CCCeeeECccCCCc
Confidence 4666 4888888755 45678899999874
No 64
>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=43.02 E-value=12 Score=24.71 Aligned_cols=25 Identities=28% Similarity=0.696 Sum_probs=16.9
Q ss_pred EEEeCC-CCCceeeehhhhhcCceEEEcCCCcc
Q 034819 20 YTYPCP-CGDLFQITKDELRIGEEIARCPSCSL 51 (82)
Q Consensus 20 y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL 51 (82)
-...|+ ||..|.+..- ...|+.|.-
T Consensus 69 ~~~~C~~Cg~~~~~~~~-------~~~CP~Cgs 94 (115)
T TIGR00100 69 VECECEDCSEEVSPEID-------LYRCPKCHG 94 (115)
T ss_pred cEEEcccCCCEEecCCc-------CccCcCCcC
Confidence 456796 9977776532 357999874
No 65
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=42.93 E-value=13 Score=25.94 Aligned_cols=33 Identities=18% Similarity=0.532 Sum_probs=22.8
Q ss_pred CceEEEeCC-CCCceeeehhhhhcCceEEEcCCCcceE
Q 034819 17 LQAYTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYI 53 (82)
Q Consensus 17 ~~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I 53 (82)
.+.-.|-|+ ||-.|.+.+. ++. -..|+.|.-.+
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA-~~~---~F~Cp~Cg~~L 138 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEA-MEL---NFTCPRCGAML 138 (158)
T ss_pred cCCCeEECCCCCcEeeHHHH-HHc---CCcCCCCCCEe
Confidence 345678896 9988885444 332 48999998653
No 66
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=42.59 E-value=31 Score=25.74 Aligned_cols=34 Identities=26% Similarity=0.723 Sum_probs=21.8
Q ss_pred eEEEeCC-CCCceeeehhhhhc-C-ceEEEcCCCcceE
Q 034819 19 AYTYPCP-CGDLFQITKDELRI-G-EEIARCPSCSLYI 53 (82)
Q Consensus 19 ~y~y~CR-CGg~f~i~~~~Le~-g-~~iv~C~sCSL~I 53 (82)
..++.|+ || .=.++-+-|.+ | +.++.|..|-..=
T Consensus 4 ~iy~~Cp~Cg-~eev~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 4 EIYIECPSCG-SEEVSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred eEEEECCCCC-cchhhHHHHHhcCCceEEEccCCCcEe
Confidence 4678998 99 22222233333 3 5799999998754
No 67
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=41.60 E-value=15 Score=16.35 Aligned_cols=10 Identities=50% Similarity=1.630 Sum_probs=4.8
Q ss_pred EeCC-CCCcee
Q 034819 22 YPCP-CGDLFQ 31 (82)
Q Consensus 22 y~CR-CGg~f~ 31 (82)
|.|+ ||-.|.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 4676 776554
No 68
>cd00498 Hsp33 Heat shock protein 33 (Hsp33): Cytosolic protein that acts as a molecular chaperone under oxidative conditions. In normal (reducing) cytosolic conditions, four conserved Cys residues are coordinated by a Zn ion. Under oxidative stress (such as heat shock), the Cys are reversibly oxidized to disulfide bonds, which causes the chaperone activity to be turned on. Hsp33 is homodimeric in its functional form.
Probab=41.00 E-value=16 Score=27.47 Aligned_cols=35 Identities=29% Similarity=0.578 Sum_probs=25.6
Q ss_pred ceEEEeCCCC------Cceeeehhhhhc-----CceEEEcCCCcce
Q 034819 18 QAYTYPCPCG------DLFQITKDELRI-----GEEIARCPSCSLY 52 (82)
Q Consensus 18 ~~y~y~CRCG------g~f~i~~~~Le~-----g~~iv~C~sCSL~ 52 (82)
....|.|||. -.-.+.++++++ |..-+.|.-|.-.
T Consensus 226 ~~v~f~C~CS~er~~~~L~~Lg~~El~~i~~e~g~iev~C~FC~~~ 271 (275)
T cd00498 226 QPVRFRCDCSRERVAAALLTLGKEELADMIEEDGGIEVTCEFCGEK 271 (275)
T ss_pred CCcCeeCCCCHHHHHHHHHhCCHHHHHHHHHcCCCEEEEEeCCCCE
Confidence 4578999998 235566777653 4678999999754
No 69
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=40.70 E-value=17 Score=25.93 Aligned_cols=32 Identities=25% Similarity=0.634 Sum_probs=22.8
Q ss_pred ceEEEeCC-CCCceeeehhhhhcCceEEEcCCCcceE
Q 034819 18 QAYTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYI 53 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I 53 (82)
+.-+|-|+ ||-.|.+.+. ++ .-..|+.|.-.+
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA-~~---~~F~Cp~Cg~~L 146 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEA-ME---YGFRCPQCGEML 146 (178)
T ss_pred CCCEEECCCCCcEEeHHHH-hh---cCCcCCCCCCCC
Confidence 34678896 9999986654 33 348999997654
No 70
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=39.86 E-value=17 Score=18.35 Aligned_cols=9 Identities=67% Similarity=1.896 Sum_probs=7.1
Q ss_pred eEEEeCC-CC
Q 034819 19 AYTYPCP-CG 27 (82)
Q Consensus 19 ~y~y~CR-CG 27 (82)
.-.|+|| ||
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 4578998 98
No 71
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=39.54 E-value=18 Score=28.10 Aligned_cols=20 Identities=25% Similarity=0.614 Sum_probs=16.6
Q ss_pred CceEEEcCCCcceEEEEeec
Q 034819 40 GEEIARCPSCSLYITVIYNI 59 (82)
Q Consensus 40 g~~iv~C~sCSL~I~V~~~~ 59 (82)
+.-+-.|.+|.-++|++|..
T Consensus 249 ~~r~e~C~~C~~YlK~~~~~ 268 (305)
T TIGR01562 249 VLKAETCDSCQGYLKILYQE 268 (305)
T ss_pred ceEEeeccccccchhhhccc
Confidence 34677999999999999764
No 72
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=39.26 E-value=70 Score=17.78 Aligned_cols=34 Identities=24% Similarity=0.530 Sum_probs=20.7
Q ss_pred CC-CCCceeeehhhhhc---CceEEEcCC--CcceEEEEe
Q 034819 24 CP-CGDLFQITKDELRI---GEEIARCPS--CSLYITVIY 57 (82)
Q Consensus 24 CR-CGg~f~i~~~~Le~---g~~iv~C~s--CSL~I~V~~ 57 (82)
|| ||..-.|....-.. .+.+.+|.. |+-......
T Consensus 2 CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~~ 41 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVANL 41 (47)
T ss_pred cCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEEE
Confidence 76 88766665554332 256888887 776555443
No 73
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=39.08 E-value=26 Score=24.84 Aligned_cols=36 Identities=28% Similarity=0.616 Sum_probs=17.7
Q ss_pred ceEEEeCC-CCCceeeehhhhhcC----ceEEEcCCCcceE
Q 034819 18 QAYTYPCP-CGDLFQITKDELRIG----EEIARCPSCSLYI 53 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~g----~~iv~C~sCSL~I 53 (82)
.-+...|| ||..|.+..---..+ .....|+.|+-.+
T Consensus 15 ~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~ 55 (188)
T PF08996_consen 15 EPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPL 55 (188)
T ss_dssp --EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B-
T ss_pred CceEeECCCCCCCccccccccCCccccccCcCcCCCCCCcC
Confidence 57899997 998888754322222 3478999998733
No 74
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=38.55 E-value=48 Score=20.37 Aligned_cols=34 Identities=32% Similarity=0.708 Sum_probs=16.2
Q ss_pred CceEEEeCC-CCCceeeehhhhhcCceEEEcCCCc
Q 034819 17 LQAYTYPCP-CGDLFQITKDELRIGEEIARCPSCS 50 (82)
Q Consensus 17 ~~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCS 50 (82)
+..-.++|| ||..-+.--.--..-.....|+.|-
T Consensus 23 e~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 23 ETAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred CceeEeeCCCCCceeeehhhhHHHcCCceECCCcC
Confidence 345567787 8744332222211112445666664
No 75
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=38.50 E-value=19 Score=23.83 Aligned_cols=25 Identities=24% Similarity=0.739 Sum_probs=15.1
Q ss_pred EEEeCC-CCCceeeehhhhhcCceEEEcCCCc
Q 034819 20 YTYPCP-CGDLFQITKDELRIGEEIARCPSCS 50 (82)
Q Consensus 20 y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCS 50 (82)
-...|+ ||..|.+... ....|+.|-
T Consensus 69 ~~~~C~~Cg~~~~~~~~------~~~~CP~Cg 94 (114)
T PRK03681 69 AECWCETCQQYVTLLTQ------RVRRCPQCH 94 (114)
T ss_pred cEEEcccCCCeeecCCc------cCCcCcCcC
Confidence 456687 8866654322 124688885
No 76
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=38.41 E-value=41 Score=18.06 Aligned_cols=29 Identities=31% Similarity=0.693 Sum_probs=12.8
Q ss_pred eCC-CCCceeeehhhhhcCceEEEcCCCcce
Q 034819 23 PCP-CGDLFQITKDELRIGEEIARCPSCSLY 52 (82)
Q Consensus 23 ~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~ 52 (82)
.|+ ||+.-+...-+-+ +..-.-|++|..+
T Consensus 2 fC~~CG~~l~~~ip~gd-~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGD-DRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT--SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCC-CccceECCCCCCE
Confidence 587 9977444333222 2456789999753
No 77
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=38.23 E-value=23 Score=27.56 Aligned_cols=35 Identities=26% Similarity=0.582 Sum_probs=27.1
Q ss_pred eEEEeCCCC------Cceeeehhhhhc-----CceEEEcCCCcceE
Q 034819 19 AYTYPCPCG------DLFQITKDELRI-----GEEIARCPSCSLYI 53 (82)
Q Consensus 19 ~y~y~CRCG------g~f~i~~~~Le~-----g~~iv~C~sCSL~I 53 (82)
...|.|+|. ....++.+++++ |..-+.|.-|+-+=
T Consensus 231 ~v~f~C~CSrEr~~~aL~~lg~eEi~~m~eedg~iev~C~FC~~~Y 276 (286)
T COG1281 231 PVEFRCSCSRERVAAALLSLGKEELEDMLEEDGGIEVTCEFCGTKY 276 (286)
T ss_pred cceEEcCCCHHHHHHHHHhcCHHHHHHHHhcCCCeEEEeeccCCEE
Confidence 478999998 356778888763 56789999999754
No 78
>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=37.77 E-value=13 Score=19.86 Aligned_cols=27 Identities=33% Similarity=0.859 Sum_probs=16.7
Q ss_pred EeC-CCCCceeeehhhhhcCceEEEcCCCcceEE
Q 034819 22 YPC-PCGDLFQITKDELRIGEEIARCPSCSLYIT 54 (82)
Q Consensus 22 y~C-RCGg~f~i~~~~Le~g~~iv~C~sCSL~I~ 54 (82)
|-| +||..+.|... ..+.|..|.-.|.
T Consensus 1 Y~C~~Cg~~~~~~~~------~~irC~~CG~RIl 28 (32)
T PF03604_consen 1 YICGECGAEVELKPG------DPIRCPECGHRIL 28 (32)
T ss_dssp EBESSSSSSE-BSTS------STSSBSSSS-SEE
T ss_pred CCCCcCCCeeEcCCC------CcEECCcCCCeEE
Confidence 567 49988775432 3468999987664
No 79
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=37.53 E-value=31 Score=26.96 Aligned_cols=21 Identities=19% Similarity=0.689 Sum_probs=16.9
Q ss_pred CceEEEcCCCcceEEEEeecc
Q 034819 40 GEEIARCPSCSLYITVIYNIE 60 (82)
Q Consensus 40 g~~iv~C~sCSL~I~V~~~~~ 60 (82)
+.-+-.|.+|.-.+|++|...
T Consensus 249 ~~r~e~C~~C~~YlK~~~~~~ 269 (309)
T PRK03564 249 AVKAESCGDCGTYLKILYQEK 269 (309)
T ss_pred ceEeeecccccccceeccccc
Confidence 346789999999999986643
No 80
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=37.33 E-value=1e+02 Score=19.16 Aligned_cols=35 Identities=20% Similarity=0.504 Sum_probs=22.1
Q ss_pred EeCC-CCCceeeehh-hhhcC--ceEEEcC--CCcceEEEE
Q 034819 22 YPCP-CGDLFQITKD-ELRIG--EEIARCP--SCSLYITVI 56 (82)
Q Consensus 22 y~CR-CGg~f~i~~~-~Le~g--~~iv~C~--sCSL~I~V~ 56 (82)
+.|| ||..-.|-.. .+.++ +.+.+|. .|+-.-..+
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITY 42 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEE
Confidence 4698 9955444444 44433 5789999 887665443
No 81
>PHA00616 hypothetical protein
Probab=37.27 E-value=7.9 Score=22.22 Aligned_cols=15 Identities=47% Similarity=1.263 Sum_probs=10.0
Q ss_pred EeC-CCCCceeeehhhh
Q 034819 22 YPC-PCGDLFQITKDEL 37 (82)
Q Consensus 22 y~C-RCGg~f~i~~~~L 37 (82)
|.| |||..|. ...+|
T Consensus 2 YqC~~CG~~F~-~~s~l 17 (44)
T PHA00616 2 YQCLRCGGIFR-KKKEV 17 (44)
T ss_pred CccchhhHHHh-hHHHH
Confidence 679 4998887 33343
No 82
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=36.53 E-value=13 Score=18.25 Aligned_cols=11 Identities=55% Similarity=1.515 Sum_probs=8.0
Q ss_pred EEeCC-CCCcee
Q 034819 21 TYPCP-CGDLFQ 31 (82)
Q Consensus 21 ~y~CR-CGg~f~ 31 (82)
.|.|+ ||..|.
T Consensus 14 ~~~C~~C~k~F~ 25 (26)
T PF13465_consen 14 PYKCPYCGKSFS 25 (26)
T ss_dssp SEEESSSSEEES
T ss_pred CCCCCCCcCeeC
Confidence 47897 987763
No 83
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=35.81 E-value=33 Score=18.46 Aligned_cols=21 Identities=29% Similarity=0.596 Sum_probs=13.3
Q ss_pred CceEEEeCC-CCCceeeehhhhh
Q 034819 17 LQAYTYPCP-CGDLFQITKDELR 38 (82)
Q Consensus 17 ~~~y~y~CR-CGg~f~i~~~~Le 38 (82)
.+.-.+.|+ |||.+. +..+++
T Consensus 15 ~~~~id~C~~C~G~W~-d~~el~ 36 (41)
T PF13453_consen 15 GDVEIDVCPSCGGIWF-DAGELE 36 (41)
T ss_pred CCEEEEECCCCCeEEc-cHHHHH
Confidence 346677786 887665 555554
No 84
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=35.65 E-value=29 Score=19.64 Aligned_cols=16 Identities=25% Similarity=0.588 Sum_probs=12.1
Q ss_pred ccCCceEEEeCCCCCc
Q 034819 14 NEELQAYTYPCPCGDL 29 (82)
Q Consensus 14 ~e~~~~y~y~CRCGg~ 29 (82)
.++++.+..||+|-|.
T Consensus 9 ~~~~~~l~~PC~C~G~ 24 (49)
T smart00744 9 GDEGDPLVSPCRCKGS 24 (49)
T ss_pred CCCCCeeEeccccCCc
Confidence 3455678999999875
No 85
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=35.58 E-value=18 Score=29.64 Aligned_cols=19 Identities=42% Similarity=1.052 Sum_probs=13.9
Q ss_pred eecCCceeccCCceEEEeCCCC
Q 034819 6 VEIEDMEWNEELQAYTYPCPCG 27 (82)
Q Consensus 6 v~LdDm~~~e~~~~y~y~CRCG 27 (82)
+.++.|++.+.+ ++||+||
T Consensus 19 lcie~mditdkn---f~pc~cg 37 (480)
T COG5175 19 LCIEPMDITDKN---FFPCPCG 37 (480)
T ss_pred ccccccccccCC---cccCCcc
Confidence 456667766554 8899998
No 86
>PLN03086 PRLI-interacting factor K; Provisional
Probab=35.29 E-value=31 Score=29.18 Aligned_cols=36 Identities=31% Similarity=0.668 Sum_probs=21.7
Q ss_pred EEEeCC-CCCcee--------------eehhhhhcCceEEEcCCCcceEEE
Q 034819 20 YTYPCP-CGDLFQ--------------ITKDELRIGEEIARCPSCSLYITV 55 (82)
Q Consensus 20 y~y~CR-CGg~f~--------------i~~~~Le~g~~iv~C~sCSL~I~V 55 (82)
-.+.|+ ||-.|. ++.-+...|.--+.|..|...|+.
T Consensus 503 Kpi~C~fC~~~v~~g~~~~d~~d~~s~Lt~HE~~CG~rt~~C~~Cgk~Vrl 553 (567)
T PLN03086 503 RLITCRFCGDMVQAGGSAMDVRDRLRGMSEHESICGSRTAPCDSCGRSVML 553 (567)
T ss_pred CceeCCCCCCccccCccccchhhhhhhHHHHHHhcCCcceEccccCCeeee
Confidence 446777 876552 222222335667888888877765
No 87
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=35.06 E-value=19 Score=20.96 Aligned_cols=23 Identities=30% Similarity=0.618 Sum_probs=11.3
Q ss_pred eEEEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEEE
Q 034819 19 AYTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITVI 56 (82)
Q Consensus 19 ~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~ 56 (82)
.--|.|| ||. +-|..||-.....
T Consensus 23 ~rrhhCr~CG~---------------~vC~~Cs~~~~~~ 46 (69)
T PF01363_consen 23 RRRHHCRNCGR---------------VVCSSCSSQRIPL 46 (69)
T ss_dssp S-EEE-TTT-----------------EEECCCS-EEEEE
T ss_pred eeeEccCCCCC---------------EECCchhCCEEcc
Confidence 3468898 985 4567777554443
No 88
>PF01430 HSP33: Hsp33 protein; InterPro: IPR000397 Hsp33 is a molecular chaperone, distinguished from all other known chaperones by its mode of functional regulation. Its activity is redox regulated. Hsp33 is a cytoplasmically localized protein with highly reactive cysteines that respond quickly to changes in the redox environment. Oxidizing conditions like H2O2 cause disulphide bonds to form in Hsp33, a process that leads to the activation of its chaperone function [].; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0005737 cytoplasm; PDB: 1VZY_B 1VQ0_A 1I7F_A 3M7M_X 1XJH_A 1HW7_A.
Probab=35.02 E-value=18 Score=27.09 Aligned_cols=36 Identities=22% Similarity=0.548 Sum_probs=18.9
Q ss_pred ceEEEeCCCC-C-----ceeeehhhhhc-----CceEEEcCCCcceE
Q 034819 18 QAYTYPCPCG-D-----LFQITKDELRI-----GEEIARCPSCSLYI 53 (82)
Q Consensus 18 ~~y~y~CRCG-g-----~f~i~~~~Le~-----g~~iv~C~sCSL~I 53 (82)
....|.|||. + .-.+.+++|++ |..-+.|.-|.=.-
T Consensus 230 ~~v~f~C~CS~er~~~~L~~L~~eel~~i~~e~~~iev~C~fC~~~Y 276 (280)
T PF01430_consen 230 KPVKFFCRCSRERVENALASLGREELEEILEENGKIEVTCEFCGKKY 276 (280)
T ss_dssp EE-EE--SS-HHHHHHHHHTS-HHHHHHHHHHCSEEEEE-TTT--EE
T ss_pred cccccCCCCCHHHHHHHHHhCCHHHHHHHHhcCCCEEEEeeCCCCEE
Confidence 4678899998 2 24556666653 56889999997543
No 89
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=34.83 E-value=19 Score=19.21 Aligned_cols=26 Identities=31% Similarity=0.779 Sum_probs=14.5
Q ss_pred eCC-CCCceeeehhhhhcCceEEEcCCCcce
Q 034819 23 PCP-CGDLFQITKDELRIGEEIARCPSCSLY 52 (82)
Q Consensus 23 ~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~ 52 (82)
.|| ||..-...++.... . .|.+|.-.
T Consensus 3 FCp~C~nlL~p~~~~~~~--~--~C~~C~Y~ 29 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKR--V--ACRTCGYE 29 (35)
T ss_dssp BETTTTSBEEEEEETTTT--E--EESSSS-E
T ss_pred eCCCCCccceEcCCCccC--c--CCCCCCCc
Confidence 476 77776655443332 1 77777644
No 90
>PHA02768 hypothetical protein; Provisional
Probab=34.27 E-value=17 Score=21.78 Aligned_cols=17 Identities=35% Similarity=1.009 Sum_probs=12.7
Q ss_pred EEEeCC-CCCceeeehhh
Q 034819 20 YTYPCP-CGDLFQITKDE 36 (82)
Q Consensus 20 y~y~CR-CGg~f~i~~~~ 36 (82)
.-|.|+ ||..|.....-
T Consensus 4 ~~y~C~~CGK~Fs~~~~L 21 (55)
T PHA02768 4 LGYECPICGEIYIKRKSM 21 (55)
T ss_pred cccCcchhCCeeccHHHH
Confidence 457997 99999865543
No 91
>PRK00114 hslO Hsp33-like chaperonin; Reviewed
Probab=34.09 E-value=29 Score=26.32 Aligned_cols=39 Identities=26% Similarity=0.472 Sum_probs=28.4
Q ss_pred CceEEEeCCCC------Cceeeehhhhhc-----CceEEEcCCCcceEEE
Q 034819 17 LQAYTYPCPCG------DLFQITKDELRI-----GEEIARCPSCSLYITV 55 (82)
Q Consensus 17 ~~~y~y~CRCG------g~f~i~~~~Le~-----g~~iv~C~sCSL~I~V 55 (82)
.....|.|||. -.-.+.++++++ |..-+.|.-|.-.=++
T Consensus 231 ~~~v~f~C~CS~er~~~~L~~Lg~~El~~i~~e~~~iev~C~FC~~~Y~f 280 (293)
T PRK00114 231 PQPVEFKCDCSRERSANALKSLGKEELQEMIAEDGGAEMVCQFCGNKYLF 280 (293)
T ss_pred CccCceeCCCCHHHHHHHHHhCCHHHHHHHHHcCCCEEEEEeCCCCEEEe
Confidence 35688999998 235667777653 5678999999976554
No 92
>PRK07591 threonine synthase; Validated
Probab=34.08 E-value=46 Score=26.33 Aligned_cols=35 Identities=23% Similarity=0.547 Sum_probs=26.2
Q ss_pred ceEEEeC-CCCCceeeehhhhhcCceEEEcCCCcceEEEEeecc
Q 034819 18 QAYTYPC-PCGDLFQITKDELRIGEEIARCPSCSLYITVIYNIE 60 (82)
Q Consensus 18 ~~y~y~C-RCGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~~~~ 60 (82)
-.+.+.| +||..|-+. .. ..|+.|--.+.|.|+..
T Consensus 15 ~~~~l~C~~Cg~~~~~~-------~~-~~C~~cg~~l~~~y~~~ 50 (421)
T PRK07591 15 PAVALKCRECGAEYPLG-------PI-HVCEECFGPLEVAYDYD 50 (421)
T ss_pred ceeEEEeCCCCCcCCCC-------CC-ccCCCCCCeEEEEechh
Confidence 3567999 599888643 12 57999988999999743
No 93
>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=34.03 E-value=32 Score=20.98 Aligned_cols=11 Identities=18% Similarity=0.658 Sum_probs=8.0
Q ss_pred eEEEcCCCcce
Q 034819 42 EIARCPSCSLY 52 (82)
Q Consensus 42 ~iv~C~sCSL~ 52 (82)
..+.|..|...
T Consensus 35 ~~v~C~~CGYT 45 (64)
T PF09855_consen 35 TTVSCTNCGYT 45 (64)
T ss_pred EEEECCCCCCE
Confidence 47778888765
No 94
>cd01475 vWA_Matrilin VWA_Matrilin: In cartilaginous plate, extracellular matrix molecules mediate cell-matrix and matrix-matrix interactions thereby providing tissue integrity. Some members of the matrilin family are expressed specifically in developing cartilage rudiments. The matrilin family consists of at least four members. All the members of the matrilin family contain VWA domains, EGF-like domains and a heptad repeat coiled-coiled domain at the carboxy terminus which is responsible for the oligomerization of the matrilins. The VWA domains have been shown to be essential for matrilin network formation by interacting with matrix ligands.
Probab=33.76 E-value=15 Score=25.95 Aligned_cols=15 Identities=27% Similarity=0.884 Sum_probs=12.1
Q ss_pred EEeCCCCCceeeehh
Q 034819 21 TYPCPCGDLFQITKD 35 (82)
Q Consensus 21 ~y~CRCGg~f~i~~~ 35 (82)
+|.|+|..+|.+..+
T Consensus 207 ~~~c~c~~g~~~~~~ 221 (224)
T cd01475 207 SYLCACTEGYALLED 221 (224)
T ss_pred CEEeECCCCccCCCC
Confidence 479999999987654
No 95
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=33.75 E-value=43 Score=18.30 Aligned_cols=30 Identities=23% Similarity=0.562 Sum_probs=17.6
Q ss_pred eCC-CCCceeeehhhhhcCceEEEcCCCcceEEE
Q 034819 23 PCP-CGDLFQITKDELRIGEEIARCPSCSLYITV 55 (82)
Q Consensus 23 ~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V 55 (82)
.|+ ||...... +++. .....|+.|-...++
T Consensus 2 FCp~Cg~~l~~~--~~~~-~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGNMLIPK--EGKE-KRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCccccc--cCCC-CCEEECCcCCCeEEC
Confidence 476 88744333 2222 236679999876655
No 96
>KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=33.68 E-value=36 Score=26.52 Aligned_cols=34 Identities=29% Similarity=0.636 Sum_probs=18.2
Q ss_pred ceEEEeCC-CCCceeeehhhhhc----------CceEEEcCCCcc
Q 034819 18 QAYTYPCP-CGDLFQITKDELRI----------GEEIARCPSCSL 51 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~----------g~~iv~C~sCSL 51 (82)
+.-+.||+ |+|.=.+-...-.+ .+-++.|+.||+
T Consensus 237 g~rFlpC~~C~GS~kv~~~~~~~~~~~rC~~CNENGLvrCp~Cs~ 281 (281)
T KOG2824|consen 237 GARFLPCSNCHGSCKVHEEEEDDGGVLRCLECNENGLVRCPVCSN 281 (281)
T ss_pred CcceEecCCCCCceeeeeeccCCCcEEECcccCCCCceeCCccCC
Confidence 45667775 77665544421111 134677777763
No 97
>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=33.26 E-value=29 Score=17.77 Aligned_cols=25 Identities=32% Similarity=0.613 Sum_probs=12.0
Q ss_pred eC-CCCCceeeehhhhhcCceEEEcCCCcce
Q 034819 23 PC-PCGDLFQITKDELRIGEEIARCPSCSLY 52 (82)
Q Consensus 23 ~C-RCGg~f~i~~~~Le~g~~iv~C~sCSL~ 52 (82)
.| |||+.-.+... +....|++|-..
T Consensus 5 fC~~CG~~t~~~~~-----g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPG-----GWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SS-----SS-EEESSSS-E
T ss_pred ccCcCCccccCCCC-----cCEeECCCCcCE
Confidence 47 58876665543 345588888654
No 98
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=31.82 E-value=32 Score=27.88 Aligned_cols=29 Identities=34% Similarity=0.812 Sum_probs=20.5
Q ss_pred ceEEEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEE
Q 034819 18 QAYTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITV 55 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V 55 (82)
....|.|+ || |. .....-.|+||--|=.|
T Consensus 351 ~~~~YRC~~CG--F~-------a~~l~W~CPsC~~W~Ti 380 (389)
T COG2956 351 RKPRYRCQNCG--FT-------AHTLYWHCPSCRAWETI 380 (389)
T ss_pred hcCCceecccC--Cc-------ceeeeeeCCCccccccc
Confidence 45789997 97 22 12356799999988655
No 99
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=31.76 E-value=43 Score=21.04 Aligned_cols=37 Identities=24% Similarity=0.591 Sum_probs=17.6
Q ss_pred EEeCC-CC--CceeeehhhhhcCceEEEcCCCcceEEEEee
Q 034819 21 TYPCP-CG--DLFQITKDELRIGEEIARCPSCSLYITVIYN 58 (82)
Q Consensus 21 ~y~CR-CG--g~f~i~~~~Le~g~~iv~C~sCSL~I~V~~~ 58 (82)
.+.|| || ..-.+..+- ..+.-.+.|..|.+.-+...+
T Consensus 22 ~F~CPfC~~~~sV~v~idk-k~~~~~~~C~~Cg~~~~~~i~ 61 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDK-KEGIGILSCRVCGESFQTKIN 61 (81)
T ss_dssp ----TTT--SS-EEEEEET-TTTEEEEEESSS--EEEEE--
T ss_pred eEcCCcCCCCCeEEEEEEc-cCCEEEEEecCCCCeEEEccC
Confidence 46787 88 445555433 245678899999777666543
No 100
>PF02810 SEC-C: SEC-C motif; InterPro: IPR004027 The SEC-C motif found in the C terminus of the SecA protein, in the middle of some SWI2 ATPases and also solo in several proteins. The motif is predicted to chelate zinc with the CXC and C[HC] pairs that constitute the most conserved feature of the motif. It is predicted to be a potential nucleic acid binding domain.; PDB: 1OZB_J 1TM6_A 2I9W_A 2JQ5_A.
Probab=31.62 E-value=25 Score=17.10 Aligned_cols=7 Identities=71% Similarity=1.943 Sum_probs=5.3
Q ss_pred eCCCCCc
Q 034819 23 PCPCGDL 29 (82)
Q Consensus 23 ~CRCGg~ 29 (82)
+|+||.+
T Consensus 4 ~CpCgSg 10 (21)
T PF02810_consen 4 PCPCGSG 10 (21)
T ss_dssp BTTTSCS
T ss_pred cCcCCCC
Confidence 6999943
No 101
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=31.56 E-value=35 Score=27.01 Aligned_cols=33 Identities=30% Similarity=0.714 Sum_probs=21.6
Q ss_pred EEEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEEEeecc
Q 034819 20 YTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITVIYNIE 60 (82)
Q Consensus 20 y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~~~~ 60 (82)
|++.|+ ||..|- +.. ...|+.|--.+.+.|+..
T Consensus 1 ~~l~C~~Cg~~~~---~~~-----~~~C~~c~g~l~~~y~~~ 34 (398)
T TIGR03844 1 YTLRCPGCGEVLP---DHY-----TLSCPLDCGLLRAEYAER 34 (398)
T ss_pred CEEEeCCCCCccC---Ccc-----ccCCCCCCCceEEeeccc
Confidence 678895 998873 111 246877655677777743
No 102
>PF14670 FXa_inhibition: Coagulation Factor Xa inhibitory site; PDB: 3Q3K_B 1NFY_B 1LQD_A 1G2L_B 1IQF_L 2UWP_B 2VH6_B 3KQC_L 2P93_L 2BQW_A ....
Probab=31.27 E-value=22 Score=19.18 Aligned_cols=16 Identities=25% Similarity=0.837 Sum_probs=11.5
Q ss_pred EEeCCCCCceeeehhh
Q 034819 21 TYPCPCGDLFQITKDE 36 (82)
Q Consensus 21 ~y~CRCGg~f~i~~~~ 36 (82)
.|.|.|..+|.|.++.
T Consensus 18 ~~~C~C~~Gy~L~~D~ 33 (36)
T PF14670_consen 18 SYRCSCPPGYKLAEDG 33 (36)
T ss_dssp SEEEE-STTEEE-TTS
T ss_pred ceEeECCCCCEECcCC
Confidence 5889999999998753
No 103
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=30.86 E-value=37 Score=22.59 Aligned_cols=31 Identities=29% Similarity=0.518 Sum_probs=19.1
Q ss_pred eCC-CCCceeeehhhhhcCceEEEcCCCcceEEEE
Q 034819 23 PCP-CGDLFQITKDELRIGEEIARCPSCSLYITVI 56 (82)
Q Consensus 23 ~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~ 56 (82)
.|+ ||+.....+++... ...|.+|--...+.
T Consensus 4 FCp~Cgsll~p~~~~~~~---~l~C~kCgye~~~~ 35 (113)
T COG1594 4 FCPKCGSLLYPKKDDEGG---KLVCRKCGYEEEAS 35 (113)
T ss_pred ccCCccCeeEEeEcCCCc---EEECCCCCcchhcc
Confidence 576 88776665544332 67788886555443
No 104
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=30.81 E-value=50 Score=20.10 Aligned_cols=26 Identities=31% Similarity=0.777 Sum_probs=15.1
Q ss_pred eCC-CC--CceeeehhhhhcCceEEEcCCCcc
Q 034819 23 PCP-CG--DLFQITKDELRIGEEIARCPSCSL 51 (82)
Q Consensus 23 ~CR-CG--g~f~i~~~~Le~g~~iv~C~sCSL 51 (82)
.|| |+ |...+.. +++..++.|-.|-.
T Consensus 11 ~CP~C~~~Dtl~~~~---e~~~e~vECv~Cg~ 39 (59)
T TIGR02443 11 VCPACSAQDTLAMWK---ENNIELVECVECGY 39 (59)
T ss_pred cCCCCcCccEEEEEE---eCCceEEEeccCCC
Confidence 475 77 4444442 23456788888864
No 105
>PF12906 RINGv: RING-variant domain; PDB: 2D8S_A 1VYX_A.
Probab=30.60 E-value=39 Score=18.93 Aligned_cols=12 Identities=25% Similarity=0.725 Sum_probs=7.2
Q ss_pred ceEEEeCCCCCc
Q 034819 18 QAYTYPCPCGDL 29 (82)
Q Consensus 18 ~~y~y~CRCGg~ 29 (82)
+.+..||+|.|.
T Consensus 12 ~~li~pC~C~Gs 23 (47)
T PF12906_consen 12 EPLISPCRCKGS 23 (47)
T ss_dssp S-EE-SSS-SSC
T ss_pred CceecccccCCC
Confidence 368999999973
No 106
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=30.23 E-value=39 Score=23.93 Aligned_cols=29 Identities=24% Similarity=0.611 Sum_probs=17.5
Q ss_pred eCC-CC--CceeeehhhhhcCceE---EEcCCCcc
Q 034819 23 PCP-CG--DLFQITKDELRIGEEI---ARCPSCSL 51 (82)
Q Consensus 23 ~CR-CG--g~f~i~~~~Le~g~~i---v~C~sCSL 51 (82)
.|| || +.=+|..-..++|..+ -.|.+|.-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~ 36 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHE 36 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCC
Confidence 466 76 5556655556666544 56777763
No 107
>PHA02540 61 DNA primase; Provisional
Probab=30.06 E-value=51 Score=26.00 Aligned_cols=39 Identities=23% Similarity=0.555 Sum_probs=25.7
Q ss_pred CCceeccCCceEEEeCC-CCC--------ceeeehhhhhcCceEEEcCCCc
Q 034819 9 EDMEWNEELQAYTYPCP-CGD--------LFQITKDELRIGEEIARCPSCS 50 (82)
Q Consensus 9 dDm~~~e~~~~y~y~CR-CGg--------~f~i~~~~Le~g~~iv~C~sCS 50 (82)
.+|..-...+.|...|| ||+ .|.|+.+.= ..+.-|-+|-
T Consensus 15 ~~f~~~~~~~~~~~~CPf~~ds~~~~~kpsF~V~p~k~---~~~yhCFgCG 62 (337)
T PHA02540 15 PKFKQVRRSSFYNFRCPICGDSQKDKNKARGWIYEKKD---GGVFKCHNCG 62 (337)
T ss_pred hhhheeccCceEEecCCCCCCccccCcCCcEEEeccCC---ceEEEecCCC
Confidence 34444444444889999 997 588876532 4577888884
No 108
>PF05988 DUF899: Bacterial protein of unknown function (DUF899); InterPro: IPR010296 This family consists of uncharacterised bacterial proteins of unknown function which are thioredoxin-like.
Probab=29.90 E-value=14 Score=27.62 Aligned_cols=12 Identities=33% Similarity=0.935 Sum_probs=9.9
Q ss_pred EEEcCCCcceEE
Q 034819 43 IARCPSCSLYIT 54 (82)
Q Consensus 43 iv~C~sCSL~I~ 54 (82)
--+|++||+++-
T Consensus 82 ~~~C~gCs~~~D 93 (211)
T PF05988_consen 82 DEGCPGCSFWAD 93 (211)
T ss_pred CCCCCchhhhHh
Confidence 458999999874
No 109
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=29.83 E-value=27 Score=26.76 Aligned_cols=37 Identities=19% Similarity=0.465 Sum_probs=26.6
Q ss_pred eEEEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEEEe
Q 034819 19 AYTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITVIY 57 (82)
Q Consensus 19 ~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~ 57 (82)
...++|| ||+...+.+.-.. .--..|+-|-|+=-+-+
T Consensus 218 e~~r~CP~Cg~~W~L~~plh~--iFdFKCD~CRLVSnlsw 255 (258)
T PF10071_consen 218 EQARKCPSCGGDWRLKEPLHD--IFDFKCDPCRLVSNLSW 255 (258)
T ss_pred hhCCCCCCCCCccccCCchhh--ceeccCCcceeeccccc
Confidence 4567898 9998887665433 35689999998755544
No 110
>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=29.65 E-value=26 Score=19.35 Aligned_cols=32 Identities=28% Similarity=1.029 Sum_probs=18.1
Q ss_pred cCCceeccCCceEEEeCC-CCC--ceeeehhhhhcCceEEEcCCCc
Q 034819 8 IEDMEWNEELQAYTYPCP-CGD--LFQITKDELRIGEEIARCPSCS 50 (82)
Q Consensus 8 LdDm~~~e~~~~y~y~CR-CGg--~f~i~~~~Le~g~~iv~C~sCS 50 (82)
|.++.|.++ .-|| ||. .|.|.. .....|..|.
T Consensus 10 l~~~RW~~g-----~~CP~Cg~~~~~~~~~------~~~~~C~~C~ 44 (46)
T PF12760_consen 10 LEEIRWPDG-----FVCPHCGSTKHYRLKT------RGRYRCKACR 44 (46)
T ss_pred HHHhcCCCC-----CCCCCCCCeeeEEeCC------CCeEECCCCC
Confidence 344555433 3486 994 455544 3566777774
No 111
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=29.37 E-value=32 Score=26.13 Aligned_cols=35 Identities=23% Similarity=0.560 Sum_probs=23.5
Q ss_pred EEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEEEe
Q 034819 21 TYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITVIY 57 (82)
Q Consensus 21 ~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~ 57 (82)
++.|| ||+...+...-.. .-...|+.|-|+-.+.+
T Consensus 218 ~r~CPsC~k~Wqlk~~i~d--~fhfkcd~crlvsnlsw 253 (256)
T COG5595 218 YRCCPSCGKDWQLKNPIFD--TFHFKCDTCRLVSNLSW 253 (256)
T ss_pred cCCCCcccccceeccchhh--heeeecccceeeccccc
Confidence 56788 9988776443222 35789999988755543
No 112
>PF02754 CCG: Cysteine-rich domain; InterPro: IPR004017 This domain is usually found in two copies per protein. It contains up to four conserved cysteines. The group includes proteins characterised as: heterodisulphide reductase, subunit B (HrdB); succinate dehydrogenase, subunit C (SdhC, 1.3.99.1 from EC); Fe-S oxidoreductase; glycerol-3-phosphate dehydrogenase subunit C (Anaerobic GlpC, 1.1.99.5 from EC); and glycolate oxidase iron-sulphur subunit (GlcF) [].
Probab=28.76 E-value=16 Score=20.97 Aligned_cols=14 Identities=29% Similarity=0.823 Sum_probs=11.6
Q ss_pred ceEEEcCCCcceEE
Q 034819 41 EEIARCPSCSLYIT 54 (82)
Q Consensus 41 ~~iv~C~sCSL~I~ 54 (82)
..++.|++|.+.+|
T Consensus 72 ~iv~~c~~C~~~lr 85 (85)
T PF02754_consen 72 TIVTPCPSCYMQLR 85 (85)
T ss_pred EEEEeChhHHHhhC
Confidence 47999999998764
No 113
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=28.63 E-value=26 Score=21.32 Aligned_cols=13 Identities=31% Similarity=0.744 Sum_probs=9.4
Q ss_pred eEEEeCC-CCCcee
Q 034819 19 AYTYPCP-CGDLFQ 31 (82)
Q Consensus 19 ~y~y~CR-CGg~f~ 31 (82)
.+...|| |||.|+
T Consensus 39 ~l~~~CPNCgGelv 52 (57)
T PF06906_consen 39 MLNGVCPNCGGELV 52 (57)
T ss_pred HhcCcCcCCCCccc
Confidence 3466788 998875
No 114
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=28.62 E-value=22 Score=23.58 Aligned_cols=26 Identities=19% Similarity=0.591 Sum_probs=16.0
Q ss_pred EEEeCC-CCCceeeehhhhhcCceEEEcCCCcc
Q 034819 20 YTYPCP-CGDLFQITKDELRIGEEIARCPSCSL 51 (82)
Q Consensus 20 y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL 51 (82)
....|+ ||..|.+... ....|+.|.-
T Consensus 70 ~~~~C~~Cg~~~~~~~~------~~~~CP~Cgs 96 (117)
T PRK00564 70 VELECKDCSHVFKPNAL------DYGVCEKCHS 96 (117)
T ss_pred CEEEhhhCCCccccCCc------cCCcCcCCCC
Confidence 456787 9877765422 2235888864
No 115
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=27.91 E-value=69 Score=18.74 Aligned_cols=38 Identities=29% Similarity=0.594 Sum_probs=24.9
Q ss_pred eCC-CCCceeeehhhhhcCc-eEEEcCCCcceEEEEeecc
Q 034819 23 PCP-CGDLFQITKDELRIGE-EIARCPSCSLYITVIYNIE 60 (82)
Q Consensus 23 ~CR-CGg~f~i~~~~Le~g~-~iv~C~sCSL~I~V~~~~~ 60 (82)
.|| ||-.+.+..+.-..++ -+--|.-|=--|.+....+
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d 41 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVTVD 41 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEEEC
Confidence 588 9988888777665543 3556777765555555443
No 116
>PRK00420 hypothetical protein; Validated
Probab=27.90 E-value=56 Score=22.01 Aligned_cols=32 Identities=25% Similarity=0.479 Sum_probs=20.8
Q ss_pred EEEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEEEe
Q 034819 20 YTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITVIY 57 (82)
Q Consensus 20 y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~ 57 (82)
....|| ||.-+. . +. ..-+.|+.|+-.+.|.-
T Consensus 22 l~~~CP~Cg~pLf--~--lk--~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 22 LSKHCPVCGLPLF--E--LK--DGEVVCPVHGKVYIVKS 54 (112)
T ss_pred ccCCCCCCCCcce--e--cC--CCceECCCCCCeeeecc
Confidence 567897 993222 1 12 23578999999877744
No 117
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=27.37 E-value=40 Score=19.43 Aligned_cols=27 Identities=26% Similarity=0.561 Sum_probs=17.0
Q ss_pred EEeCC-CCCceeeehhhhhcCceEEEcCCCcceE
Q 034819 21 TYPCP-CGDLFQITKDELRIGEEIARCPSCSLYI 53 (82)
Q Consensus 21 ~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I 53 (82)
...|| ||..|.... .....|..|.+..
T Consensus 20 ~~fCP~Cg~~~m~~~------~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEH------LDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchhecc------CCcEECCCcCCEE
Confidence 34797 996533322 2456899998753
No 118
>smart00508 PostSET Cysteine-rich motif following a subset of SET domains.
Probab=27.35 E-value=25 Score=18.07 Aligned_cols=6 Identities=67% Similarity=1.840 Sum_probs=5.0
Q ss_pred EeCCCC
Q 034819 22 YPCPCG 27 (82)
Q Consensus 22 y~CRCG 27 (82)
++|+||
T Consensus 3 ~~C~CG 8 (26)
T smart00508 3 QPCLCG 8 (26)
T ss_pred eeeeCC
Confidence 589998
No 119
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.31 E-value=21 Score=30.64 Aligned_cols=34 Identities=24% Similarity=0.540 Sum_probs=22.6
Q ss_pred EEeCC-CCCceeeehhhhhc-------CceEEEcCCC-cceEE
Q 034819 21 TYPCP-CGDLFQITKDELRI-------GEEIARCPSC-SLYIT 54 (82)
Q Consensus 21 ~y~CR-CGg~f~i~~~~Le~-------g~~iv~C~sC-SL~I~ 54 (82)
.|.|| ||+.|-..-....- ...+-.|++| .+..+
T Consensus 181 kHHCr~CG~vFC~qcss~s~~lP~~Gi~~~VRVCd~C~E~l~~ 223 (634)
T KOG1818|consen 181 KHHCRNCGQVFCGQCSSKSLTLPKLGIEKPVRVCDSCYELLTR 223 (634)
T ss_pred cccccccchhhccCccccccCcccccccccceehhhhHHHhhh
Confidence 57999 99988765554332 2356889999 44443
No 120
>PF07645 EGF_CA: Calcium-binding EGF domain; InterPro: IPR001881 A sequence of about forty amino-acid residues found in epidermal growth factor (EGF) has been shown [, , , , , ] to be present in a large number of membrane-bound and extracellular, mostly animal, proteins. Many of these proteins require calcium for their biological function and a calcium-binding site has been found at the N terminus of some EGF-like domains []. Calcium-binding may be crucial for numerous protein-protein interactions. For human coagulation factor IX it has been shown [] that the calcium-ligands form a pentagonal bipyramid. The first, third and fourth conserved negatively charged or polar residues are side chain ligands. The latter is possibly hydroxylated (see aspartic acid and asparagine hydroxylation site) []. A conserved aromatic residue, as well as the second conserved negative residue, are thought to be involved in stabilising the calcium-binding site. As in non-calcium binding EGF-like domains, there are six conserved cysteines and the structure of both types is very similar as calcium-binding induces only strictly local structural changes []. +------------------+ +---------+ | | | | nxnnC-x(3,14)-C-x(3,7)-CxxbxxxxaxC-x(1,6)-C-x(8,13)-Cx | | +------------------+ 'n': negatively charged or polar residue [DEQN] 'b': possibly beta-hydroxylated residue [DN] 'a': aromatic amino acid 'C': cysteine, involved in disulphide bond 'x': any amino acid. ; GO: 0005509 calcium ion binding; PDB: 2VJ3_A 1TOZ_A 1LMJ_A 1UZQ_A 1UZK_A 1UZJ_B 1UZP_A 1EMO_A 1EMN_A 2RR0_A ....
Probab=27.16 E-value=27 Score=18.73 Aligned_cols=13 Identities=23% Similarity=0.935 Sum_probs=10.4
Q ss_pred EEeCCCCCceeee
Q 034819 21 TYPCPCGDLFQIT 33 (82)
Q Consensus 21 ~y~CRCGg~f~i~ 33 (82)
+|.|.|..+|...
T Consensus 24 sy~C~C~~Gy~~~ 36 (42)
T PF07645_consen 24 SYSCSCPPGYELN 36 (42)
T ss_dssp EEEEEESTTEEEC
T ss_pred CEEeeCCCCcEEC
Confidence 5789999999844
No 121
>PRK14701 reverse gyrase; Provisional
Probab=26.96 E-value=24 Score=33.12 Aligned_cols=27 Identities=37% Similarity=0.790 Sum_probs=21.9
Q ss_pred eEEEeCC-CCCceeeehhhhhcCceEEEcCCCc
Q 034819 19 AYTYPCP-CGDLFQITKDELRIGEEIARCPSCS 50 (82)
Q Consensus 19 ~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCS 50 (82)
.|.+.|| |||. ||.+-|+.| .+|..|-
T Consensus 4 ~y~~~cpnc~g~--~~~~rl~~g---~~c~~cl 31 (1638)
T PRK14701 4 IYKEMCPNCGGD--ITDERLAEK---GVCEKCL 31 (1638)
T ss_pred hhcccCCCCCCc--cchhHHhcC---CCchhhc
Confidence 5888998 9996 568888877 6899995
No 122
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=26.39 E-value=36 Score=20.10 Aligned_cols=11 Identities=27% Similarity=0.945 Sum_probs=9.4
Q ss_pred CceEEEeCCCC
Q 034819 17 LQAYTYPCPCG 27 (82)
Q Consensus 17 ~~~y~y~CRCG 27 (82)
+.+|.+.|.||
T Consensus 35 edtfkRtCkCG 45 (49)
T PF12677_consen 35 EDTFKRTCKCG 45 (49)
T ss_pred ccceeeeeccc
Confidence 46799999997
No 123
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=26.30 E-value=15 Score=31.42 Aligned_cols=44 Identities=25% Similarity=0.668 Sum_probs=29.6
Q ss_pred eccCCceEEEe---CC-CCCceeeehh---hhhc------------------------CceEEEcCCCcceEEEE
Q 034819 13 WNEELQAYTYP---CP-CGDLFQITKD---ELRI------------------------GEEIARCPSCSLYITVI 56 (82)
Q Consensus 13 ~~e~~~~y~y~---CR-CGg~f~i~~~---~Le~------------------------g~~iv~C~sCSL~I~V~ 56 (82)
++..+..|-|| |- ||-.|.|.+. +... .-.-+.|+.|-=.++..
T Consensus 79 ~dp~~Rry~YpF~nCt~CGPr~~i~~~lpydr~~t~m~~f~~C~~C~~ey~~p~~rr~h~~~~~C~~Cgp~l~l~ 153 (711)
T TIGR00143 79 LDKNDRRYLYPFISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAKEYKDPLDRRFHAQPIACPRCGPQLNFV 153 (711)
T ss_pred cCCCcccccCCcccccCCCCCeEEeecCCCCCCCcCCCCCcCCHHHHHHhcCCccccCCCCCccCCCCCcEEEEE
Confidence 34455666665 85 9999999888 2221 01478899998777663
No 124
>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=26.23 E-value=39 Score=21.29 Aligned_cols=25 Identities=36% Similarity=0.857 Sum_probs=15.6
Q ss_pred eCC-CCCceeeehhhhhcCceEEEcCCCcceEE
Q 034819 23 PCP-CGDLFQITKDELRIGEEIARCPSCSLYIT 54 (82)
Q Consensus 23 ~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~ 54 (82)
.|+ ||+.+... .....|+.|.-...
T Consensus 2 fC~~Cg~~l~~~-------~~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPK-------NGVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccccC-------CCeEECcCCCCccc
Confidence 475 88777532 13567888885544
No 125
>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=26.03 E-value=50 Score=26.59 Aligned_cols=29 Identities=24% Similarity=0.625 Sum_probs=20.6
Q ss_pred EEEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEEEe
Q 034819 20 YTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITVIY 57 (82)
Q Consensus 20 y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~ 57 (82)
..|.|+ ||-.+ ....-+|++|.-|=.+.-
T Consensus 6 ~~y~C~~Cg~~~---------~~~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 6 SKFVCQHCGADS---------PKWQGKCPACHAWNTITE 35 (454)
T ss_pred CeEECCcCCCCC---------ccccEECcCCCCccccch
Confidence 368898 98432 235679999999977653
No 126
>PF13948 DUF4215: Domain of unknown function (DUF4215)
Probab=25.96 E-value=36 Score=19.11 Aligned_cols=28 Identities=21% Similarity=0.481 Sum_probs=20.3
Q ss_pred EeCC--CCCceeeehhhhhcCceEEEcCCCc
Q 034819 22 YPCP--CGDLFQITKDELRIGEEIARCPSCS 50 (82)
Q Consensus 22 y~CR--CGg~f~i~~~~Le~g~~iv~C~sCS 50 (82)
..|- ||++++...++=+++ ...+.++|+
T Consensus 15 ~~C~~~CGDgii~~~E~CDD~-N~~~~DGC~ 44 (47)
T PF13948_consen 15 NKCEPICGDGIIVGDEQCDDG-NSIPFDGCY 44 (47)
T ss_pred CccccccCCCeEECCcccCCC-CccCCCCcc
Confidence 4584 999999988887776 344566665
No 127
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=25.73 E-value=51 Score=17.80 Aligned_cols=10 Identities=50% Similarity=1.368 Sum_probs=7.1
Q ss_pred ceEEEeCC-CC
Q 034819 18 QAYTYPCP-CG 27 (82)
Q Consensus 18 ~~y~y~CR-CG 27 (82)
..+.|.|| ||
T Consensus 37 ~~~~y~C~~C~ 47 (47)
T PF13005_consen 37 VRHKYACPCCG 47 (47)
T ss_pred EeceEECCCCC
Confidence 46788888 64
No 128
>PF06007 PhnJ: Phosphonate metabolism protein PhnJ; InterPro: IPR010306 This family consists of several bacterial phosphonate metabolism (PhnJ) sequences. The exact role that PhnJ plays in phosphonate utilisation is unknown.; GO: 0042916 alkylphosphonate transport
Probab=25.28 E-value=41 Score=26.16 Aligned_cols=41 Identities=24% Similarity=0.524 Sum_probs=21.5
Q ss_pred eecCCceeccCCceEEEeCC-CC--CceeeehhhhhcCceEEEcCC
Q 034819 6 VEIEDMEWNEELQAYTYPCP-CG--DLFQITKDELRIGEEIARCPS 48 (82)
Q Consensus 6 v~LdDm~~~e~~~~y~y~CR-CG--g~f~i~~~~Le~g~~iv~C~s 48 (82)
++++|.-|.- +.|..+|+ || +.|.-..-.-..|.....|+.
T Consensus 222 L~FeD~pF~~--e~~~~~C~~CGs~~s~LdEvi~dd~G~~~~~CSD 265 (277)
T PF06007_consen 222 LDFEDHPFEV--ERFDGPCALCGSTDSFLDEVIDDDDGGRMFVCSD 265 (277)
T ss_pred cCccCCCCcc--ccccCcccccCCCceeceeeEEcCCCCEEEEECC
Confidence 4455555533 34777995 99 444311101123567777764
No 129
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.45 E-value=80 Score=21.72 Aligned_cols=38 Identities=24% Similarity=0.599 Sum_probs=29.1
Q ss_pred EEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEEEeeccccccccc
Q 034819 21 TYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITVIYNIEDFLDNKS 67 (82)
Q Consensus 21 ~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~~~~~~~~e~~~ 67 (82)
.-+|| ||...+||+ ..|+.|--.|+=+|....++=..+
T Consensus 6 ~~~cPvcg~~~iVTe---------L~c~~~etTVrg~F~~s~F~~Lt~ 44 (122)
T COG3877 6 INRCPVCGRKLIVTE---------LKCSNCETTVRGNFKMSKFEYLTS 44 (122)
T ss_pred CCCCCcccccceeEE---------EecCCCCceEecceecccccccCH
Confidence 34788 998888774 579999999999998877664443
No 130
>PRK12496 hypothetical protein; Provisional
Probab=24.32 E-value=50 Score=23.13 Aligned_cols=15 Identities=13% Similarity=0.437 Sum_probs=12.4
Q ss_pred ceEEEeCC-CCCceee
Q 034819 18 QAYTYPCP-CGDLFQI 32 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i 32 (82)
..|-|.|+ ||..|-.
T Consensus 124 ~~w~~~C~gC~~~~~~ 139 (164)
T PRK12496 124 IKWRKVCKGCKKKYPE 139 (164)
T ss_pred eeeeEECCCCCccccC
Confidence 56899999 9988853
No 131
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=24.10 E-value=33 Score=31.07 Aligned_cols=28 Identities=32% Similarity=0.875 Sum_probs=20.6
Q ss_pred ceEEEeCC-CCCceeeehhhhhcCceEEEcCCCc
Q 034819 18 QAYTYPCP-CGDLFQITKDELRIGEEIARCPSCS 50 (82)
Q Consensus 18 ~~y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCS 50 (82)
..|.+.|| |||.. +.+-|..| .+|.-|-
T Consensus 4 ~~y~~~CPnCgg~i--~~~rl~~~---~~c~~Cl 32 (1171)
T TIGR01054 4 AVYSNLCPNCGGEI--SSERLEKG---LPCARCL 32 (1171)
T ss_pred chhcCCCCCCCCcc--chhHhhcC---CCccccC
Confidence 46889999 99864 46666665 5788884
No 132
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=23.60 E-value=85 Score=25.72 Aligned_cols=25 Identities=24% Similarity=0.546 Sum_probs=17.5
Q ss_pred eeccCCceEEEeCCCCCceeeehhh
Q 034819 12 EWNEELQAYTYPCPCGDLFQITKDE 36 (82)
Q Consensus 12 ~~~e~~~~y~y~CRCGg~f~i~~~~ 36 (82)
+++.+.+...|.|.||...+++...
T Consensus 191 ~~d~~~~~v~y~~~cG~~~~~~~~~ 215 (510)
T PRK00750 191 SYDAEAGTVTYDCECGHEGEVPVTG 215 (510)
T ss_pred EEeCCCCEEEEEcCCCCEEEEecCC
Confidence 4555666778899999777666544
No 133
>PRK11823 DNA repair protein RadA; Provisional
Probab=23.59 E-value=58 Score=26.09 Aligned_cols=28 Identities=32% Similarity=0.852 Sum_probs=18.6
Q ss_pred EEEeCC-CCCceeeehhhhhcCceEEEcCCCcceEEEE
Q 034819 20 YTYPCP-CGDLFQITKDELRIGEEIARCPSCSLYITVI 56 (82)
Q Consensus 20 y~y~CR-CGg~f~i~~~~Le~g~~iv~C~sCSL~I~V~ 56 (82)
..|.|+ ||-.+. ...-+|++|.-|=.+.
T Consensus 6 ~~y~C~~Cg~~~~---------~~~g~Cp~C~~w~t~~ 34 (446)
T PRK11823 6 TAYVCQECGAESP---------KWLGRCPECGAWNTLV 34 (446)
T ss_pred CeEECCcCCCCCc---------ccCeeCcCCCCcccee
Confidence 367887 874322 3556899998886554
No 134
>PF01799 Fer2_2: [2Fe-2S] binding domain; InterPro: IPR002888 The [2Fe-2S] binding domain is found in a range of enzymes including dehydrogenases, oxidases and oxidoreductases. The aldehyde oxido-reductase (Mop) from the sulphate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas is a homodimer of 907 amino acid residues subunits and is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different [2Fe-2S] centres. It is folded into four domains of which the first two bind the iron sulphur centres and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands [].; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 2E3T_A 1WYG_A 3AN1_B 2E1Q_C 2CKJ_A 3B9J_I 3NVY_J 1FO4_B 3NRZ_J 3AM9_A ....
Probab=23.42 E-value=35 Score=21.22 Aligned_cols=11 Identities=27% Similarity=0.546 Sum_probs=6.0
Q ss_pred EeCCCCCceee
Q 034819 22 YPCPCGDLFQI 32 (82)
Q Consensus 22 y~CRCGg~f~i 32 (82)
.-|||+|.-.|
T Consensus 59 nlCRCTgY~~I 69 (75)
T PF01799_consen 59 NLCRCTGYRPI 69 (75)
T ss_dssp S--SSSTSHHH
T ss_pred CccCCCCcHHH
Confidence 34999986443
No 135
>PRK04860 hypothetical protein; Provisional
Probab=22.37 E-value=1.7e+02 Score=20.62 Aligned_cols=37 Identities=27% Similarity=0.672 Sum_probs=25.6
Q ss_pred ceEEEeCCCCCceeeehhhh---hcCceEEEcCCCcceEEE
Q 034819 18 QAYTYPCPCGDLFQITKDEL---RIGEEIARCPSCSLYITV 55 (82)
Q Consensus 18 ~~y~y~CRCGg~f~i~~~~L---e~g~~iv~C~sCSL~I~V 55 (82)
..|.|.|.||. ..++..-- ..|.....|..|.=.++-
T Consensus 116 ~~~~Y~C~C~~-~~~~~rrH~ri~~g~~~YrC~~C~~~l~~ 155 (160)
T PRK04860 116 KTFPYRCKCQE-HQLTVRRHNRVVRGEAVYRCRRCGETLVF 155 (160)
T ss_pred CEEEEEcCCCC-eeCHHHHHHHHhcCCccEECCCCCceeEE
Confidence 46999999997 44444332 235677899999866653
No 136
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=22.28 E-value=67 Score=22.61 Aligned_cols=34 Identities=21% Similarity=0.509 Sum_probs=22.9
Q ss_pred ceEEEeCCCCCce---eeehhhhhc--CceEEEcCCCcc
Q 034819 18 QAYTYPCPCGDLF---QITKDELRI--GEEIARCPSCSL 51 (82)
Q Consensus 18 ~~y~y~CRCGg~f---~i~~~~Le~--g~~iv~C~sCSL 51 (82)
..|...|.+|-.| .=+.++++. ..-++.|+-|--
T Consensus 2 I~y~L~C~~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs 40 (148)
T PF06676_consen 2 IVYDLRCENGHEFEGWFRSSAAFDRQQARGLVSCPVCGS 40 (148)
T ss_pred eeEEEecCCCCccceecCCHHHHHHHHHcCCccCCCCCC
Confidence 3689999999444 335555543 246889999943
No 137
>TIGR01997 sufA_proteo FeS assembly scaffold SufA. This model represents the SufA protein of the SUF system of iron-sulfur cluster biosynthesis. This system performs FeS biosynthesis even during oxidative stress and tends to be absent in obligate anaerobic and microaerophilic bacteria.
Probab=22.12 E-value=75 Score=20.27 Aligned_cols=11 Identities=36% Similarity=1.165 Sum_probs=8.5
Q ss_pred EeCCCCCceee
Q 034819 22 YPCPCGDLFQI 32 (82)
Q Consensus 22 y~CRCGg~f~i 32 (82)
..|-||..|.+
T Consensus 97 ~~CgCG~Sf~~ 107 (107)
T TIGR01997 97 SACGCGESFEL 107 (107)
T ss_pred CccCCCCCccC
Confidence 45999998864
No 138
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=20.22 E-value=41 Score=15.92 Aligned_cols=10 Identities=40% Similarity=1.328 Sum_probs=7.0
Q ss_pred EeCC-CCCcee
Q 034819 22 YPCP-CGDLFQ 31 (82)
Q Consensus 22 y~CR-CGg~f~ 31 (82)
|.|. |+..|.
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 5675 887775
Done!