Query 004163
Match_columns 771
No_of_seqs 168 out of 214
Neff 4.8
Searched_HMMs 46136
Date Thu Mar 28 18:38:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004163.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004163hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00423 tfb transcription ini 98.7 4.6E-06 9.9E-11 90.6 23.1 146 170-408 128-273 (310)
2 PF11781 RRN7: RNA polymerase 98.6 3E-08 6.5E-13 75.3 2.3 31 8-39 4-36 (36)
3 COG1405 SUA7 Transcription ini 98.1 0.00025 5.4E-09 76.6 20.4 107 259-408 142-248 (285)
4 PF08271 TF_Zn_Ribbon: TFIIB z 95.6 0.0089 1.9E-07 46.9 2.6 30 12-41 2-32 (43)
5 KOG1598 Transcription initiati 94.4 0.22 4.7E-06 57.8 10.3 108 262-408 114-223 (521)
6 smart00778 Prim_Zn_Ribbon Zinc 92.2 0.098 2.1E-06 40.5 2.0 27 9-36 2-33 (37)
7 PF12760 Zn_Tnp_IS1595: Transp 90.6 0.2 4.4E-06 39.9 2.5 29 9-37 17-46 (46)
8 PF08274 PhnA_Zn_Ribbon: PhnA 90.5 0.19 4.2E-06 37.2 2.0 28 11-39 3-30 (30)
9 PRK00420 hypothetical protein; 90.3 0.2 4.3E-06 47.6 2.5 29 10-39 23-51 (112)
10 PF08273 Prim_Zn_Ribbon: Zinc- 89.9 0.24 5.2E-06 38.9 2.2 28 9-36 2-34 (40)
11 KOG1597 Transcription initiati 88.9 42 0.00091 37.2 19.3 78 260-375 150-229 (308)
12 PF13248 zf-ribbon_3: zinc-rib 88.7 0.19 4E-06 35.7 0.8 24 11-38 3-26 (26)
13 PRK00432 30S ribosomal protein 85.6 0.54 1.2E-05 38.6 2.0 28 9-37 19-46 (50)
14 COG2824 PhnA Uncharacterized Z 84.3 0.76 1.6E-05 43.3 2.5 30 10-40 3-32 (112)
15 smart00661 RPOL9 RNA polymeras 83.2 0.86 1.9E-05 36.5 2.2 27 12-38 2-30 (52)
16 PF09538 FYDLN_acid: Protein o 81.9 0.92 2E-05 42.9 2.2 38 1-40 1-38 (108)
17 PF08792 A2L_zn_ribbon: A2L zi 80.0 1.6 3.5E-05 33.0 2.4 29 11-39 4-32 (33)
18 PF13240 zinc_ribbon_2: zinc-r 79.4 0.94 2E-05 31.5 1.0 23 12-38 1-23 (23)
19 PRK10220 hypothetical protein; 78.1 1.5 3.2E-05 41.5 2.2 29 11-40 4-32 (111)
20 PF06677 Auto_anti-p27: Sjogre 77.6 1.9 4E-05 34.2 2.2 26 9-35 16-41 (41)
21 TIGR00686 phnA alkylphosphonat 77.1 1.7 3.6E-05 41.2 2.2 29 11-40 3-31 (109)
22 COG1645 Uncharacterized Zn-fin 76.5 1.5 3.3E-05 42.7 1.9 29 10-40 28-56 (131)
23 TIGR02300 FYDLN_acid conserved 73.8 2.1 4.6E-05 41.6 2.0 31 8-39 7-37 (129)
24 smart00440 ZnF_C2C2 C2C2 Zinc 73.7 2.7 5.7E-05 32.9 2.2 27 12-38 2-38 (40)
25 PF01780 Ribosomal_L37ae: Ribo 73.3 2.4 5.3E-05 39.0 2.2 31 10-40 35-65 (90)
26 COG1997 RPL43A Ribosomal prote 73.3 2.7 5.9E-05 38.4 2.5 32 9-40 34-65 (89)
27 PF02150 RNA_POL_M_15KD: RNA p 73.3 3 6.4E-05 31.8 2.3 29 12-40 3-32 (35)
28 PRK00398 rpoP DNA-directed RNA 71.6 3 6.5E-05 33.1 2.1 29 11-39 4-32 (46)
29 smart00531 TFIIE Transcription 69.9 2.8 6.1E-05 41.2 2.0 33 8-40 97-135 (147)
30 PF07282 OrfB_Zn_ribbon: Putat 69.6 3.7 8E-05 34.9 2.4 33 9-41 27-59 (69)
31 PF10080 DUF2318: Predicted me 68.4 3.4 7.3E-05 38.8 2.0 28 11-39 36-63 (102)
32 PF01096 TFIIS_C: Transcriptio 65.3 6 0.00013 30.7 2.6 26 12-37 2-37 (39)
33 COG0675 Transposase and inacti 63.1 4 8.6E-05 43.3 1.7 28 9-41 308-335 (364)
34 PHA00626 hypothetical protein 59.7 7.1 0.00015 33.1 2.2 29 12-40 2-35 (59)
35 smart00659 RPOLCX RNA polymera 59.1 7.9 0.00017 31.0 2.3 27 12-39 4-30 (44)
36 TIGR02098 MJ0042_CXXC MJ0042 f 59.1 6.1 0.00013 29.9 1.6 29 11-39 3-36 (38)
37 PF14803 Nudix_N_2: Nudix N-te 58.1 8.2 0.00018 29.5 2.1 26 13-38 3-32 (34)
38 PF09862 DUF2089: Protein of u 57.6 7.6 0.00017 37.2 2.3 26 13-42 1-26 (113)
39 TIGR00373 conserved hypothetic 54.2 4.3 9.2E-05 40.6 0.0 35 6-40 105-140 (158)
40 KOG2907 RNA polymerase I trans 53.5 9.6 0.00021 36.5 2.2 33 6-38 70-112 (116)
41 cd00043 CYCLIN Cyclin box fold 53.4 34 0.00075 28.3 5.5 54 349-408 6-59 (88)
42 PHA02942 putative transposase; 52.9 9.5 0.00021 43.3 2.5 32 9-41 324-355 (383)
43 PF00382 TFIIB: Transcription 52.6 87 0.0019 26.6 7.8 26 259-284 39-64 (71)
44 PTZ00255 60S ribosomal protein 51.9 11 0.00023 34.9 2.2 30 11-40 37-66 (90)
45 PRK06266 transcription initiat 51.9 4.6 0.0001 41.2 -0.1 34 7-40 114-148 (178)
46 TIGR00280 L37a ribosomal prote 51.5 11 0.00023 35.0 2.1 30 11-40 36-65 (91)
47 TIGR01384 TFS_arch transcripti 51.4 9.3 0.0002 35.1 1.8 26 12-39 2-27 (104)
48 PF09526 DUF2387: Probable met 50.8 13 0.00028 32.8 2.5 35 7-41 5-43 (71)
49 PF09297 zf-NADH-PPase: NADH p 50.3 13 0.00029 27.3 2.2 29 10-38 3-31 (32)
50 PF00382 TFIIB: Transcription 48.4 25 0.00053 30.0 3.8 51 352-408 1-51 (71)
51 PF03966 Trm112p: Trm112p-like 48.1 14 0.0003 31.7 2.2 17 21-38 47-63 (68)
52 PRK03976 rpl37ae 50S ribosomal 47.8 13 0.00028 34.4 2.0 30 11-40 37-66 (90)
53 COG1998 RPS31 Ribosomal protei 47.0 12 0.00026 31.1 1.5 29 7-36 16-45 (51)
54 COG1594 RPB9 DNA-directed RNA 45.6 14 0.0003 35.2 2.1 29 10-38 72-110 (113)
55 PF08646 Rep_fac-A_C: Replicat 45.3 16 0.00036 35.3 2.6 29 10-39 18-48 (146)
56 smart00385 CYCLIN domain prese 44.2 39 0.00084 27.8 4.3 52 351-408 2-53 (83)
57 smart00401 ZnF_GATA zinc finge 42.0 17 0.00036 30.0 1.7 29 10-38 3-35 (52)
58 PF06827 zf-FPG_IleRS: Zinc fi 41.5 19 0.00042 26.0 1.8 27 10-36 1-29 (30)
59 PF12172 DUF35_N: Rubredoxin-l 41.0 11 0.00023 28.6 0.4 29 4-36 5-33 (37)
60 PF06107 DUF951: Bacterial pro 40.8 19 0.00041 30.7 1.9 26 14-39 14-42 (57)
61 TIGR00155 pqiA_fam integral me 39.0 21 0.00045 40.9 2.5 32 9-40 12-45 (403)
62 TIGR02443 conserved hypothetic 38.7 25 0.00054 30.2 2.3 34 7-40 6-43 (59)
63 PF10571 UPF0547: Uncharacteri 38.6 16 0.00035 26.3 1.0 24 12-39 2-25 (26)
64 COG1996 RPC10 DNA-directed RNA 38.5 18 0.00038 30.0 1.3 28 11-38 7-34 (49)
65 PF04161 Arv1: Arv1-like famil 38.4 15 0.00033 38.1 1.2 35 12-46 2-42 (208)
66 KOG0835 Cyclin L [General func 38.4 1.5E+02 0.0033 33.5 8.8 72 333-409 126-198 (367)
67 TIGR01384 TFS_arch transcripti 37.7 29 0.00062 31.9 2.8 30 10-39 62-101 (104)
68 PF12773 DZR: Double zinc ribb 36.8 15 0.00033 29.2 0.7 23 13-39 1-23 (50)
69 PRK12495 hypothetical protein; 36.7 23 0.0005 37.6 2.2 29 10-40 42-70 (226)
70 PF14353 CpXC: CpXC protein 36.4 23 0.00051 33.6 2.0 28 11-39 2-49 (128)
71 TIGR03655 anti_R_Lar restricti 35.7 27 0.00058 28.7 2.0 29 12-40 3-38 (53)
72 COG3529 Predicted nucleic-acid 35.3 13 0.00028 32.1 0.1 37 4-40 4-44 (66)
73 COG2835 Uncharacterized conser 34.7 28 0.00062 29.9 2.0 27 11-37 9-35 (60)
74 PF13719 zinc_ribbon_5: zinc-r 34.5 25 0.00055 26.9 1.6 27 11-38 3-35 (37)
75 TIGR00515 accD acetyl-CoA carb 34.2 13 0.00028 40.8 -0.2 29 11-39 27-56 (285)
76 PF03604 DNA_RNApol_7kD: DNA d 33.9 27 0.00058 26.4 1.5 26 12-38 2-27 (32)
77 PF13113 DUF3970: Protein of u 33.7 34 0.00073 29.4 2.3 33 480-514 12-55 (60)
78 PRK00564 hypA hydrogenase nick 33.4 19 0.00041 34.4 0.8 27 11-38 72-98 (117)
79 COG1594 RPB9 DNA-directed RNA 32.8 28 0.00061 33.2 1.9 29 12-40 4-34 (113)
80 cd04476 RPA1_DBD_C RPA1_DBD_C: 32.4 28 0.0006 34.5 1.9 28 10-38 34-61 (166)
81 PF14951 DUF4503: Domain of un 32.3 25 0.00055 39.8 1.7 38 3-40 267-306 (389)
82 COG4640 Predicted membrane pro 32.2 22 0.00047 40.7 1.2 26 12-41 3-28 (465)
83 PRK14559 putative protein seri 32.1 23 0.00049 43.1 1.5 24 12-39 3-26 (645)
84 PF07295 DUF1451: Protein of u 31.4 22 0.00048 35.4 1.0 16 24-39 108-123 (146)
85 PF14567 SUKH_5: SMI1-KNR4 cel 31.0 25 0.00055 34.5 1.3 42 477-525 19-60 (132)
86 PRK11827 hypothetical protein; 30.8 37 0.00081 29.2 2.1 30 10-39 8-37 (60)
87 PRK12366 replication factor A; 30.8 24 0.00052 42.8 1.4 28 8-37 530-557 (637)
88 COG1545 Predicted nucleic-acid 30.0 22 0.00047 35.0 0.7 32 3-38 22-53 (140)
89 PRK03824 hypA hydrogenase nick 29.7 28 0.0006 34.0 1.4 27 10-37 70-116 (135)
90 PF00320 GATA: GATA zinc finge 29.0 21 0.00046 27.2 0.3 24 13-36 1-28 (36)
91 cd00202 ZnF_GATA Zinc finger D 28.6 20 0.00044 29.9 0.2 27 12-38 1-31 (54)
92 PF15135 UPF0515: Uncharacteri 28.4 30 0.00064 37.5 1.4 36 11-49 133-176 (278)
93 COG4643 Uncharacterized protei 27.6 33 0.00071 38.6 1.6 28 9-36 31-62 (366)
94 PRK08402 replication factor A; 27.5 36 0.00078 38.5 1.9 27 11-37 213-239 (355)
95 CHL00174 accD acetyl-CoA carbo 27.0 19 0.00042 39.7 -0.3 29 11-39 39-68 (296)
96 PF13717 zinc_ribbon_4: zinc-r 26.6 40 0.00087 25.8 1.5 28 11-38 3-35 (36)
97 PRK05654 acetyl-CoA carboxylas 26.3 21 0.00045 39.3 -0.2 29 11-39 28-57 (292)
98 PRK12380 hydrogenase nickel in 26.0 35 0.00076 32.4 1.3 24 11-36 71-94 (113)
99 PRK15103 paraquat-inducible me 25.9 50 0.0011 38.2 2.7 32 9-40 9-42 (419)
100 KOG3507 DNA-directed RNA polym 25.5 31 0.00066 29.7 0.7 27 11-38 21-47 (62)
101 cd00674 LysRS_core_class_I cat 24.9 48 0.001 37.5 2.3 31 7-40 166-204 (353)
102 PF06044 DRP: Dam-replacing fa 24.7 43 0.00092 36.2 1.7 30 10-39 31-64 (254)
103 PRK04023 DNA polymerase II lar 24.7 42 0.00091 42.6 1.9 25 11-40 639-663 (1121)
104 PRK00750 lysK lysyl-tRNA synth 24.7 49 0.0011 39.1 2.4 34 7-41 172-212 (510)
105 PRK00464 nrdR transcriptional 24.1 47 0.001 33.4 1.8 29 12-41 2-41 (154)
106 cd00059 FH Forkhead (FH), also 23.7 78 0.0017 28.3 3.0 44 259-306 5-49 (78)
107 COG2517 Predicted RNA-binding 23.3 41 0.00089 35.0 1.3 72 640-715 39-110 (219)
108 PF05876 Terminase_GpA: Phage 23.0 42 0.00091 40.0 1.5 38 4-41 194-242 (557)
109 PF03833 PolC_DP2: DNA polymer 22.9 28 0.0006 43.3 0.0 33 8-40 653-692 (900)
110 KOG2463 Predicted RNA-binding 22.7 26 0.00057 39.2 -0.3 39 7-48 239-277 (376)
111 TIGR00100 hypA hydrogenase nic 22.6 45 0.00098 31.7 1.3 26 11-38 71-96 (115)
112 COG4481 Uncharacterized protei 22.0 65 0.0014 27.4 1.9 26 14-39 17-45 (60)
113 PRK14559 putative protein seri 21.7 44 0.00095 40.7 1.3 25 12-40 29-53 (645)
114 COG1656 Uncharacterized conser 20.8 44 0.00095 34.1 0.9 31 8-38 95-140 (165)
115 PF10058 DUF2296: Predicted in 20.6 68 0.0015 26.9 1.8 32 6-37 18-53 (54)
116 COG4530 Uncharacterized protei 20.5 52 0.0011 31.6 1.3 31 8-39 7-37 (129)
117 TIGR02605 CxxC_CxxC_SSSS putat 20.4 54 0.0012 26.3 1.2 26 11-36 6-34 (52)
118 TIGR01562 FdhE formate dehydro 20.2 75 0.0016 35.4 2.6 27 7-37 207-233 (305)
119 TIGR00155 pqiA_fam integral me 20.2 68 0.0015 36.8 2.4 26 12-40 217-242 (403)
120 PRK03681 hypA hydrogenase nick 20.0 54 0.0012 31.2 1.3 26 11-37 71-96 (114)
No 1
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=98.65 E-value=4.6e-06 Score=90.57 Aligned_cols=146 Identities=15% Similarity=0.207 Sum_probs=103.5
Q ss_pred HHHHHHHhcCCChhHHHHHHHHHHHHHhhcCcCCCCcccccccccccccccccCCCCcccCCCCCCccccchhhHHHHHH
Q 004163 170 QCEALVDKFNVCPLICGVAASIWFRFLASTGLLSQGWADEAIVQSESQELAESKDFQPRAKYRDEPHTLHGQRAVMIWYK 249 (771)
Q Consensus 170 Q~~aLV~~~G~ppELe~VVrdLWlRyL~~s~v~~~~~a~~~l~~Se~~sE~e~~ssq~~as~~~e~~~~~~kRk~~~wpr 249 (771)
.+..+...+|+|+.+.+....|-.++....- + .|++..
T Consensus 128 ~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~-~------------------------------------rgrs~~----- 165 (310)
T PRK00423 128 ELDRIASQLGLPRSVREEAAVIYRKAVEKGL-I------------------------------------RGRSIE----- 165 (310)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHhcCc-c------------------------------------cCCCHH-----
Confidence 3566777889999999888888766654311 0 011111
Q ss_pred HHhhcCCccchHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHH
Q 004163 250 LLRQKIPLSSSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLE 329 (771)
Q Consensus 250 llr~~Lp~~~TLAI~YLAcl~LR~PV~lsDLiRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~ 329 (771)
. ...|.+|+||..-+.|.++-||..... + +.+.|.
T Consensus 166 -~-------i~AAclYiACR~~~~prtl~eI~~~~~---v----------------------------------~~k~i~ 200 (310)
T PRK00423 166 -G-------VVAAALYAACRRCKVPRTLDEIAEVSR---V----------------------------------SRKEIG 200 (310)
T ss_pred -H-------HHHHHHHHHHHHcCCCcCHHHHHHHhC---C----------------------------------CHHHHH
Confidence 1 567899999999999999999976532 0 113455
Q ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004163 330 SFAASIAESIGLHLPPVNFYALASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 408 (771)
Q Consensus 330 ~la~~la~~~gL~fPpiN~~lLl~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~s~~~~~~Pe~V~LmA~IIVAlKLL 408 (771)
+.-..+.+.+++.+|+++..-++.||+..|+||.+ +...+.+|++......+ ...+-|. ..++|+|.+|.++.
T Consensus 201 ~~~~~l~k~L~~~~~~~~p~~~i~r~~~~L~L~~~-v~~~A~~i~~~a~~~~l----~~Gr~P~-sIAAAaIYlA~~~~ 273 (310)
T PRK00423 201 RCYRFLLRELNLKLPPTDPIDYVPRFASELGLSGE-VQKKAIEILQKAKEKGL----TSGKGPT-GLAAAAIYIASLLL 273 (310)
T ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHhcCc----ccCCCHH-HHHHHHHHHHHHHh
Confidence 55666777788889999999999999999999999 77888888863322211 1225577 88888888888874
No 2
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=98.57 E-value=3e-08 Score=75.34 Aligned_cols=31 Identities=32% Similarity=0.866 Sum_probs=26.2
Q ss_pred ccccc--cCCCCCCceeecCCcceecccCCeeec
Q 004163 8 IRRLK--CKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 8 ~r~~~--C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
.++++ |++|+++ |..++||+|||.+||||+|
T Consensus 4 ~~~~~~~C~~C~~~-~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 4 MRGPNEPCPVCGSR-WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred cccCCCcCCCCCCe-EeEccCCEEEhhhCceEcC
Confidence 35555 9999999 6555999999999999986
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=98.12 E-value=0.00025 Score=76.56 Aligned_cols=107 Identities=16% Similarity=0.199 Sum_probs=77.5
Q ss_pred chHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHHH
Q 004163 259 SSLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAES 338 (771)
Q Consensus 259 ~TLAI~YLAcl~LR~PV~lsDLiRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~la~~ 338 (771)
.+-|-+|.||...+.|.++.+|..-..-.. ..|.+.-..+.+.
T Consensus 142 v~AA~iY~acR~~~~prtl~eIa~a~~V~~-------------------------------------kei~rtyr~~~~~ 184 (285)
T COG1405 142 VAAACIYAACRINGVPRTLDEIAKALGVSK-------------------------------------KEIGRTYRLLVRE 184 (285)
T ss_pred HHHHHHHHHHHHcCCCccHHHHHHHHCCCH-------------------------------------HHHHHHHHHHHHh
Confidence 567889999999999999999986544111 3455555577888
Q ss_pred hCCCCCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004163 339 IGLHLPPVNFYALASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 408 (771)
Q Consensus 339 ~gL~fPpiN~~lLl~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~s~~~~~~Pe~V~LmA~IIVAlKLL 408 (771)
+++.+||......+-||+.+|+||++ +...+..|++-.--.. .....-|. ..+.|.|.+|.+|.
T Consensus 185 L~l~~~~~~p~~yi~rf~s~L~l~~~-v~~~a~ei~~~~~~~g----~~~Gk~P~-glAaaaiy~as~l~ 248 (285)
T COG1405 185 LKLKIPPVDPSDYIPRFASKLGLSDE-VRRKAIEIVKKAKRAG----LTAGKSPA-GLAAAAIYLASLLL 248 (285)
T ss_pred cCCCCCCCCHHHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHhC----cccCCCch-hHHHHHHHHHHHHh
Confidence 89999999999999999999999998 7777777776211100 01134577 67777777777664
No 4
>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=95.64 E-value=0.0089 Score=46.92 Aligned_cols=30 Identities=23% Similarity=0.473 Sum_probs=23.9
Q ss_pred ccCCCCCCce-eecCCcceecccCCeeeccc
Q 004163 12 KCKKCDNVGF-ECAYDGFYYCTHCNALDDEI 41 (771)
Q Consensus 12 ~C~~C~S~~w-~~~ddG~~yC~~CGhv~Eg~ 41 (771)
+|++|++... .+...|.++|..||.|++..
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVLEEN 32 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBEE-T
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEeecc
Confidence 6999999974 44579999999999999864
No 5
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=94.43 E-value=0.22 Score=57.84 Aligned_cols=108 Identities=16% Similarity=0.211 Sum_probs=62.3
Q ss_pred HHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHHHhCC
Q 004163 262 AISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAESIGL 341 (771)
Q Consensus 262 AI~YLAcl~LR~PV~lsDLiRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~la~~~gL 341 (771)
+-||+.|...+.++.+-||--... .....+- ..+..++..+.-.-+
T Consensus 114 sClY~vcR~e~t~hlliDfS~~Lq-------------------------------v~Vy~LG--~~~l~l~~~L~i~en- 159 (521)
T KOG1598|consen 114 ACLYLVCRLEKTDHLLIDFSSYLQ-------------------------------VSVYDLG--SNFLEVTDSLSIGEN- 159 (521)
T ss_pred HHHHHHHHhhCCceEEEEeccceE-------------------------------Eehhhhh--HHHHHHHHHhccccc-
Confidence 457999999999988887643211 0000111 234555555532222
Q ss_pred CCCCCCHHHHHHHHHHHcCC-Chh-hhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004163 342 HLPPVNFYALASRYLKQLCL-PLG-KILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 408 (771)
Q Consensus 342 ~fPpiN~~lLl~Ryl~eL~L-P~E-~iy~~v~RL~~fs~p~~l~~s~~~~~~Pe~V~LmA~IIVAlKLL 408 (771)
.+|-+...+.+.||.-.|-. |.. .+...+.+|++ .|. ..|. ...+-|. ..+-|+|++|.++.
T Consensus 160 ~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~-rMk-rdwm--~tGRRPs-glcGAaLliAar~h 223 (521)
T KOG1598|consen 160 VSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQ-RMK-RDWM--QTGRRPS-GLCGAALLIAARMH 223 (521)
T ss_pred cccccCcceeeechhHhhhcCCchHHHHHHHHHHHH-HHH-HHHH--HhCCCcc-chhHHHHHHHHHHc
Confidence 37778878888888887755 433 24444555554 000 1121 1235587 78888888888873
No 6
>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=92.19 E-value=0.098 Score=40.45 Aligned_cols=27 Identities=33% Similarity=0.870 Sum_probs=22.2
Q ss_pred cccccCCCCCCc-eeecCC----cceecccCCe
Q 004163 9 RRLKCKKCDNVG-FECAYD----GFYYCTHCNA 36 (771)
Q Consensus 9 r~~~C~~C~S~~-w~~~dd----G~~yC~~CGh 36 (771)
+..+|+.|+++. |+. +| |-|+|..||+
T Consensus 2 ~~~pCP~CGG~DrFr~-~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 2 RHGPCPNCGGSDRFRF-DDKDGRGTWFCSVCGA 33 (37)
T ss_pred CccCCCCCCCcccccc-ccCCCCcCEEeCCCCC
Confidence 567899999984 766 55 9999999985
No 7
>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=90.62 E-value=0.2 Score=39.89 Aligned_cols=29 Identities=21% Similarity=0.613 Sum_probs=24.3
Q ss_pred cccccCCCCCCc-eeecCCcceecccCCee
Q 004163 9 RRLKCKKCDNVG-FECAYDGFYYCTHCNAL 37 (771)
Q Consensus 9 r~~~C~~C~S~~-w~~~ddG~~yC~~CGhv 37 (771)
-|.+|+.||+.. +.+...+.|-|..|++|
T Consensus 17 ~g~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 17 DGFVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 358899999975 57766799999999986
No 8
>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=90.51 E-value=0.19 Score=37.17 Aligned_cols=28 Identities=18% Similarity=0.277 Sum_probs=16.6
Q ss_pred cccCCCCCCceeecCCcceecccCCeeec
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
+.|+.|+|.-=+. |...+.|..|||+.+
T Consensus 3 p~Cp~C~se~~y~-D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTYE-DGELLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----EE--SSSEEETTTTEEE-
T ss_pred CCCCCCCCcceec-cCCEEeCCcccccCC
Confidence 6899999998676 899999999999863
No 9
>PRK00420 hypothetical protein; Validated
Probab=90.30 E-value=0.2 Score=47.64 Aligned_cols=29 Identities=24% Similarity=0.296 Sum_probs=26.4
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeec
Q 004163 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 10 ~~~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
...|+.||+..|++ .+|..||..||.+..
T Consensus 23 ~~~CP~Cg~pLf~l-k~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCGLPLFEL-KDGEVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCCCcceec-CCCceECCCCCCeee
Confidence 46899999999999 999999999999765
No 10
>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=89.87 E-value=0.24 Score=38.93 Aligned_cols=28 Identities=25% Similarity=0.668 Sum_probs=18.7
Q ss_pred cccccCCCCCCc-eeecCC----cceecccCCe
Q 004163 9 RRLKCKKCDNVG-FECAYD----GFYYCTHCNA 36 (771)
Q Consensus 9 r~~~C~~C~S~~-w~~~dd----G~~yC~~CGh 36 (771)
+..+|+.|+++. |++=+| |.|+|..|+.
T Consensus 2 ~h~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 2 KHGPCPICGGKDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp EEE--TTTT-TTTEEEETT----S-EEETTTTB
T ss_pred CCCCCCCCcCccccccCcCcccCCCEECCCCCC
Confidence 567899999985 774356 9999999954
No 11
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=88.90 E-value=42 Score=37.16 Aligned_cols=78 Identities=18% Similarity=0.205 Sum_probs=52.2
Q ss_pred hHHHHHHHHHHhhcccChhHHHHHHhcCCcccccchhhhHHHhcccCCCCCCCCCccCCCCCCCchHHHHHHHHHHHHHh
Q 004163 260 SLAISFLACHVVREAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTSVACSLSPSFMFRPSKSVPSQKLESFAASIAESI 339 (771)
Q Consensus 260 TLAI~YLAcl~LR~PV~lsDLiRWI~eg~IPY~~A~~~LPkeMk~rLP~~~L~~~~~f~p~~l~s~~~I~~la~~la~~~ 339 (771)
.-|-+|+||....+|=|+-.|-..+.-. -+.|-+....+.+.+
T Consensus 150 ~AAclyiACRq~~~pRT~kEI~~~anv~-------------------------------------kKEIgr~~K~i~~~l 192 (308)
T KOG1597|consen 150 AAACLYIACRQEDVPRTFKEISAVANVS-------------------------------------KKEIGRCVKLIGEAL 192 (308)
T ss_pred HHHHHHHHHHhcCCCchHHHHHHHHcCC-------------------------------------HHHHHHHHHHHHHHH
Confidence 3467899999999988877776554311 133444444444444
Q ss_pred CCC--CCCCCHHHHHHHHHHHcCCChhhhHHHHHHhhh
Q 004163 340 GLH--LPPVNFYALASRYLKQLCLPLGKILPRALKIQE 375 (771)
Q Consensus 340 gL~--fPpiN~~lLl~Ryl~eL~LP~E~iy~~v~RL~~ 375 (771)
+.- +-.++..-+.-|||..|+||.. +..++..+.+
T Consensus 193 ~~s~~~~s~~t~~~m~RFCs~L~L~~~-~q~aA~e~a~ 229 (308)
T KOG1597|consen 193 ETSVDLISISTGDFMPRFCSNLGLPKS-AQEAATEIAE 229 (308)
T ss_pred hccchhhhhhHHHHHHHHHHhcCCCHH-HHHHHHHHHH
Confidence 433 2245567889999999999998 6667776665
No 12
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=88.69 E-value=0.19 Score=35.68 Aligned_cols=24 Identities=21% Similarity=0.526 Sum_probs=19.7
Q ss_pred cccCCCCCCceeecCCcceecccCCeee
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALD 38 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~ 38 (771)
-.|++||.. + +++..||.+||+.+
T Consensus 3 ~~Cp~Cg~~---~-~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 3 MFCPNCGAE---I-DPDAKFCPNCGAKL 26 (26)
T ss_pred CCCcccCCc---C-CcccccChhhCCCC
Confidence 469999993 4 78899999999853
No 13
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=85.59 E-value=0.54 Score=38.56 Aligned_cols=28 Identities=18% Similarity=0.452 Sum_probs=23.0
Q ss_pred cccccCCCCCCceeecCCcceecccCCee
Q 004163 9 RRLKCKKCDNVGFECAYDGFYYCTHCNAL 37 (771)
Q Consensus 9 r~~~C~~C~S~~w~~~ddG~~yC~~CGhv 37 (771)
...-|++||+. +-....++++|..||..
T Consensus 19 ~~~fCP~Cg~~-~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 19 KNKFCPRCGSG-FMAEHLDRWHCGKCGYT 46 (50)
T ss_pred ccCcCcCCCcc-hheccCCcEECCCcCCE
Confidence 35689999998 75557899999999964
No 14
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=84.26 E-value=0.76 Score=43.29 Aligned_cols=30 Identities=23% Similarity=0.341 Sum_probs=27.2
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeecc
Q 004163 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 10 ~~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
.|.|+.|.+.-|+. +.|.++|..|+|.--.
T Consensus 3 lp~cp~c~sEytYe-d~~~~~cpec~~ew~~ 32 (112)
T COG2824 3 LPPCPKCNSEYTYE-DGGQLICPECAHEWNE 32 (112)
T ss_pred CCCCCccCCceEEe-cCceEeCchhcccccc
Confidence 47899999999999 8889999999998764
No 15
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=83.23 E-value=0.86 Score=36.52 Aligned_cols=27 Identities=22% Similarity=0.484 Sum_probs=21.2
Q ss_pred ccCCCCCCceeecCCc--ceecccCCeee
Q 004163 12 KCKKCDNVGFECAYDG--FYYCTHCNALD 38 (771)
Q Consensus 12 ~C~~C~S~~w~~~ddG--~~yC~~CGhv~ 38 (771)
-|+.||+..+....++ +++|..||+..
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeE
Confidence 4999999998553433 89999999865
No 16
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=81.95 E-value=0.92 Score=42.87 Aligned_cols=38 Identities=18% Similarity=0.284 Sum_probs=29.1
Q ss_pred CCCccccccccccCCCCCCceeecCCcceecccCCeeecc
Q 004163 1 MADGEGDIRRLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 1 m~~~~~~~r~~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
|+..+- +.+.+|+.||.|-|.+ +--=-+|.+||+.+.-
T Consensus 1 Makpel-GtKR~Cp~CG~kFYDL-nk~PivCP~CG~~~~~ 38 (108)
T PF09538_consen 1 MAKPEL-GTKRTCPSCGAKFYDL-NKDPIVCPKCGTEFPP 38 (108)
T ss_pred CCcccc-CCcccCCCCcchhccC-CCCCccCCCCCCccCc
Confidence 444443 3456799999999998 6577889999998874
No 17
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=80.01 E-value=1.6 Score=32.98 Aligned_cols=29 Identities=28% Similarity=0.565 Sum_probs=24.7
Q ss_pred cccCCCCCCceeecCCcceecccCCeeec
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
.+|..|++..-..+++|.++|..||.+.+
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEee
Confidence 36999999997656999999999998754
No 18
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=79.35 E-value=0.94 Score=31.49 Aligned_cols=23 Identities=22% Similarity=0.527 Sum_probs=17.7
Q ss_pred ccCCCCCCceeecCCcceecccCCeee
Q 004163 12 KCKKCDNVGFECAYDGFYYCTHCNALD 38 (771)
Q Consensus 12 ~C~~C~S~~w~~~ddG~~yC~~CGhv~ 38 (771)
.|++||+.. .++-.||.+||+.+
T Consensus 1 ~Cp~CG~~~----~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEI----EDDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCC----CCcCcchhhhCCcC
Confidence 388888864 56778899999853
No 19
>PRK10220 hypothetical protein; Provisional
Probab=78.06 E-value=1.5 Score=41.55 Aligned_cols=29 Identities=24% Similarity=0.543 Sum_probs=25.9
Q ss_pred cccCCCCCCceeecCCcceecccCCeeecc
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
|.|++|.+.--|. +...|.|..|||.-..
T Consensus 4 P~CP~C~seytY~-d~~~~vCpeC~hEW~~ 32 (111)
T PRK10220 4 PHCPKCNSEYTYE-DNGMYICPECAHEWND 32 (111)
T ss_pred CcCCCCCCcceEc-CCCeEECCcccCcCCc
Confidence 7899999998787 8889999999998764
No 20
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=77.56 E-value=1.9 Score=34.22 Aligned_cols=26 Identities=27% Similarity=0.611 Sum_probs=22.9
Q ss_pred cccccCCCCCCceeecCCcceecccCC
Q 004163 9 RRLKCKKCDNVGFECAYDGFYYCTHCN 35 (771)
Q Consensus 9 r~~~C~~C~S~~w~~~ddG~~yC~~CG 35 (771)
-+..|+.|+...++. -+|..||-.|+
T Consensus 16 L~~~Cp~C~~PL~~~-k~g~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCGTPLMRD-KDGKIYCVSCG 41 (41)
T ss_pred hcCccCCCCCeeEEe-cCCCEECCCCC
Confidence 357899999999997 89999999986
No 21
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=77.06 E-value=1.7 Score=41.17 Aligned_cols=29 Identities=21% Similarity=0.256 Sum_probs=25.6
Q ss_pred cccCCCCCCceeecCCcceecccCCeeecc
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
|.|++|.|.--|. +...|.|..|||.-..
T Consensus 3 p~CP~C~seytY~-dg~~~iCpeC~~EW~~ 31 (109)
T TIGR00686 3 PPCPKCNSEYTYH-DGTQLICPSCLYEWNE 31 (109)
T ss_pred CcCCcCCCcceEe-cCCeeECccccccccc
Confidence 7899999998887 8889999999998754
No 22
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=76.50 E-value=1.5 Score=42.75 Aligned_cols=29 Identities=28% Similarity=0.571 Sum_probs=24.9
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeecc
Q 004163 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 10 ~~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
.-.|+.||...|+ -||.-||..||+....
T Consensus 28 ~~hCp~Cg~PLF~--KdG~v~CPvC~~~~~~ 56 (131)
T COG1645 28 AKHCPKCGTPLFR--KDGEVFCPVCGYREVV 56 (131)
T ss_pred HhhCcccCCccee--eCCeEECCCCCceEEE
Confidence 3569999999999 7999999999985543
No 23
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=73.78 E-value=2.1 Score=41.59 Aligned_cols=31 Identities=3% Similarity=-0.141 Sum_probs=26.2
Q ss_pred ccccccCCCCCCceeecCCcceecccCCeeec
Q 004163 8 IRRLKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 8 ~r~~~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
+.+.+|++||.+-|.+ +----+|.+||++.+
T Consensus 7 GtKr~Cp~cg~kFYDL-nk~p~vcP~cg~~~~ 37 (129)
T TIGR02300 7 GTKRICPNTGSKFYDL-NRRPAVSPYTGEQFP 37 (129)
T ss_pred CccccCCCcCcccccc-CCCCccCCCcCCccC
Confidence 3456799999999988 667889999999865
No 24
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=73.70 E-value=2.7 Score=32.90 Aligned_cols=27 Identities=41% Similarity=0.818 Sum_probs=21.1
Q ss_pred ccCCCCCCc--e-----eecCCc---ceecccCCeee
Q 004163 12 KCKKCDNVG--F-----ECAYDG---FYYCTHCNALD 38 (771)
Q Consensus 12 ~C~~C~S~~--w-----~~~ddG---~~yC~~CGhv~ 38 (771)
.|+.|++.. | +.+|+| ||.|..|||+-
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 699999886 2 235677 99999999974
No 25
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=73.35 E-value=2.4 Score=38.97 Aligned_cols=31 Identities=16% Similarity=0.493 Sum_probs=25.9
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeecc
Q 004163 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 10 ~~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
.-.|+.|+.....-..-|-|.|..||.++-|
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEEE-
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEEeC
Confidence 3579999999985558999999999999887
No 26
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.33 E-value=2.7 Score=38.45 Aligned_cols=32 Identities=19% Similarity=0.429 Sum_probs=27.3
Q ss_pred cccccCCCCCCceeecCCcceecccCCeeecc
Q 004163 9 RRLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 9 r~~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
-...|+.|+...-.-...|-|.|..||+..-|
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCeecc
Confidence 34679999999885549999999999999876
No 27
>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=73.31 E-value=3 Score=31.80 Aligned_cols=29 Identities=17% Similarity=0.401 Sum_probs=21.2
Q ss_pred ccCCCCCCce-eecCCcceecccCCeeecc
Q 004163 12 KCKKCDNVGF-ECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 12 ~C~~C~S~~w-~~~ddG~~yC~~CGhv~Eg 40 (771)
-|+.|++-.. .....+...|+.||.+.+-
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~ 32 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEEPI 32 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EEE-
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCccCC
Confidence 3999999998 4445666689999998763
No 28
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=71.65 E-value=3 Score=33.13 Aligned_cols=29 Identities=21% Similarity=0.250 Sum_probs=21.9
Q ss_pred cccCCCCCCceeecCCcceecccCCeeec
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
-+|++||...=.....+...|.+||+.+.
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEE
Confidence 47999999764443445899999998765
No 29
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=69.88 E-value=2.8 Score=41.19 Aligned_cols=33 Identities=27% Similarity=0.605 Sum_probs=23.6
Q ss_pred ccccccCCCCCCc-e----ee-cCCcceecccCCeeecc
Q 004163 8 IRRLKCKKCDNVG-F----EC-AYDGFYYCTHCNALDDE 40 (771)
Q Consensus 8 ~r~~~C~~C~S~~-w----~~-~ddG~~yC~~CGhv~Eg 40 (771)
.-.-+|++|+.+- + .. ..+|.|.|..||.+++-
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 3456899998652 1 11 24788999999999974
No 30
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=69.63 E-value=3.7 Score=34.88 Aligned_cols=33 Identities=15% Similarity=0.369 Sum_probs=27.7
Q ss_pred cccccCCCCCCceeecCCcceecccCCeeeccc
Q 004163 9 RRLKCKKCDNVGFECAYDGFYYCTHCNALDDEI 41 (771)
Q Consensus 9 r~~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg~ 41 (771)
....|+.||.+.=.......|+|..||+.+..+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEECcH
Confidence 577899999998774478899999999997654
No 31
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=68.39 E-value=3.4 Score=38.82 Aligned_cols=28 Identities=18% Similarity=0.428 Sum_probs=25.7
Q ss_pred cccCCCCCCceeecCCcceecccCCeeec
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
-.|+.|+.+.|+. ..+...|..||..+-
T Consensus 36 daCeiC~~~GY~q-~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 36 DACEICGPKGYYQ-EGDQLVCKNCGVRFN 63 (102)
T ss_pred EeccccCCCceEE-ECCEEEEecCCCEEe
Confidence 4699999999998 999999999999885
No 32
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=65.27 E-value=6 Score=30.72 Aligned_cols=26 Identities=35% Similarity=0.779 Sum_probs=17.4
Q ss_pred ccCCCCCCce-------eecCCc---ceecccCCee
Q 004163 12 KCKKCDNVGF-------ECAYDG---FYYCTHCNAL 37 (771)
Q Consensus 12 ~C~~C~S~~w-------~~~ddG---~~yC~~CGhv 37 (771)
.|++|++... +.+|+| ||.|..|||+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 5999999872 124555 8999999996
No 33
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=63.14 E-value=4 Score=43.32 Aligned_cols=28 Identities=18% Similarity=0.530 Sum_probs=23.4
Q ss_pred cccccCCCCCCceeecCCcceecccCCeeeccc
Q 004163 9 RRLKCKKCDNVGFECAYDGFYYCTHCNALDDEI 41 (771)
Q Consensus 9 r~~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg~ 41 (771)
..-.|..||. + ..+.|.|..||+++..+
T Consensus 308 tS~~C~~cg~----~-~~r~~~C~~cg~~~~rD 335 (364)
T COG0675 308 TSKTCPCCGH----L-SGRLFKCPRCGFVHDRD 335 (364)
T ss_pred CcccccccCC----c-cceeEECCCCCCeehhh
Confidence 3467999999 4 67889999999998764
No 34
>PHA00626 hypothetical protein
Probab=59.72 E-value=7.1 Score=33.11 Aligned_cols=29 Identities=24% Similarity=0.620 Sum_probs=22.1
Q ss_pred ccCCCCCCceee-----cCCcceecccCCeeecc
Q 004163 12 KCKKCDNVGFEC-----AYDGFYYCTHCNALDDE 40 (771)
Q Consensus 12 ~C~~C~S~~w~~-----~ddG~~yC~~CGhv~Eg 40 (771)
.|++|+|..-.. .-..+|.|..||+....
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 599999975422 12589999999998765
No 35
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=59.09 E-value=7.9 Score=31.04 Aligned_cols=27 Identities=19% Similarity=0.320 Sum_probs=20.9
Q ss_pred ccCCCCCCceeecCCcceecccCCeeec
Q 004163 12 KCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 12 ~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
+|..||.. +.+...+-..|.+|||.+-
T Consensus 4 ~C~~Cg~~-~~~~~~~~irC~~CG~rIl 30 (44)
T smart00659 4 ICGECGRE-NEIKSKDVVRCRECGYRIL 30 (44)
T ss_pred ECCCCCCE-eecCCCCceECCCCCceEE
Confidence 68899985 5454677889999998775
No 36
>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=59.08 E-value=6.1 Score=29.92 Aligned_cols=29 Identities=17% Similarity=0.377 Sum_probs=20.7
Q ss_pred cccCCCCCCceee----c-CCcceecccCCeeec
Q 004163 11 LKCKKCDNVGFEC----A-YDGFYYCTHCNALDD 39 (771)
Q Consensus 11 ~~C~~C~S~~w~~----~-ddG~~yC~~CGhv~E 39 (771)
..|++|++.-.-. . ..+...|.+||+...
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 4699999974322 1 234789999999874
No 37
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=58.07 E-value=8.2 Score=29.46 Aligned_cols=26 Identities=15% Similarity=0.386 Sum_probs=14.3
Q ss_pred cCCCCCCc-eeec---CCcceecccCCeee
Q 004163 13 CKKCDNVG-FECA---YDGFYYCTHCNALD 38 (771)
Q Consensus 13 C~~C~S~~-w~~~---ddG~~yC~~CGhv~ 38 (771)
|++||+.. +.+. +-=+++|..||.+.
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred cccccChhhhhcCCCCCccceECCCCCCEE
Confidence 88999886 4542 23378999999874
No 38
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=57.64 E-value=7.6 Score=37.17 Aligned_cols=26 Identities=15% Similarity=0.308 Sum_probs=21.8
Q ss_pred cCCCCCCceeecCCcceecccCCeeecccc
Q 004163 13 CKKCDNVGFECAYDGFYYCTHCNALDDEIV 42 (771)
Q Consensus 13 C~~C~S~~w~~~ddG~~yC~~CGhv~Eg~v 42 (771)
|+.|++..--- ++.|..||+.++|..
T Consensus 1 CPvCg~~l~vt----~l~C~~C~t~i~G~F 26 (113)
T PF09862_consen 1 CPVCGGELVVT----RLKCPSCGTEIEGEF 26 (113)
T ss_pred CCCCCCceEEE----EEEcCCCCCEEEeee
Confidence 99999887543 679999999999954
No 39
>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=54.18 E-value=4.3 Score=40.60 Aligned_cols=35 Identities=20% Similarity=0.233 Sum_probs=25.4
Q ss_pred ccccccccCCCCCCc-eeecCCcceecccCCeeecc
Q 004163 6 GDIRRLKCKKCDNVG-FECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 6 ~~~r~~~C~~C~S~~-w~~~ddG~~yC~~CGhv~Eg 40 (771)
+..-.-+|++|+.+- +.++-+.-|.|..||.+++-
T Consensus 105 ~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 105 TNNMFFICPNMCVRFTFNEAMELNFTCPRCGAMLDY 140 (158)
T ss_pred cCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCEeee
Confidence 334556899999553 44445667999999999874
No 40
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=53.47 E-value=9.6 Score=36.48 Aligned_cols=33 Identities=33% Similarity=0.759 Sum_probs=26.5
Q ss_pred ccccccccCCCCCCc-------eeecCCc---ceecccCCeee
Q 004163 6 GDIRRLKCKKCDNVG-------FECAYDG---FYYCTHCNALD 38 (771)
Q Consensus 6 ~~~r~~~C~~C~S~~-------w~~~ddG---~~yC~~CGhv~ 38 (771)
+.....+|+.||... -+-+|+| ||+|..|+++.
T Consensus 70 ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~ 112 (116)
T KOG2907|consen 70 GAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKF 112 (116)
T ss_pred ccchhccCcccCCchhhhhhhhcccccCCceEEEEcCccceee
Confidence 456678999999874 4667777 79999999875
No 41
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=53.42 E-value=34 Score=28.34 Aligned_cols=54 Identities=19% Similarity=0.187 Sum_probs=38.2
Q ss_pred HHHHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004163 349 YALASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 408 (771)
Q Consensus 349 ~lLl~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~s~~~~~~Pe~V~LmA~IIVAlKLL 408 (771)
.-.+.+++..+++|++ +...+..+++..+...... ..-|. ..++|+|.+|.|+.
T Consensus 6 ~~~l~~~~~~~~~~~~-~~~~A~~~~~~~~~~~~~~----~~~~~-~ia~a~l~lA~k~~ 59 (88)
T cd00043 6 LDFLRRVAKALGLSPE-TLTLAVNLLDRFLLDYSVL----GRSPS-LVAAAALYLAAKVE 59 (88)
T ss_pred HHHHHHHHHHcCCCHH-HHHHHHHHHHHHHHhcccc----cCChH-HHHHHHHHHHHHHc
Confidence 3568899999999999 7777777776332221111 23455 88999999999974
No 42
>PHA02942 putative transposase; Provisional
Probab=52.89 E-value=9.5 Score=43.31 Aligned_cols=32 Identities=22% Similarity=0.551 Sum_probs=24.9
Q ss_pred cccccCCCCCCceeecCCcceecccCCeeeccc
Q 004163 9 RRLKCKKCDNVGFECAYDGFYYCTHCNALDDEI 41 (771)
Q Consensus 9 r~~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg~ 41 (771)
....|+.||...-.. .+..|.|..||++...+
T Consensus 324 TSq~Cs~CG~~~~~l-~~r~f~C~~CG~~~drD 355 (383)
T PHA02942 324 SSVSCPKCGHKMVEI-AHRYFHCPSCGYENDRD 355 (383)
T ss_pred CCccCCCCCCccCcC-CCCEEECCCCCCEeCcH
Confidence 467899999976444 45679999999988543
No 43
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=52.57 E-value=87 Score=26.64 Aligned_cols=26 Identities=19% Similarity=0.230 Sum_probs=22.3
Q ss_pred chHHHHHHHHHHhhcccChhHHHHHH
Q 004163 259 SSLAISFLACHVVREAILPTDIVKWS 284 (771)
Q Consensus 259 ~TLAI~YLAcl~LR~PV~lsDLiRWI 284 (771)
-.-|.+|+||...+.|+++.||-.-+
T Consensus 39 iaAA~iY~acr~~~~~~t~~eIa~~~ 64 (71)
T PF00382_consen 39 IAAACIYLACRLNGVPRTLKEIAEAA 64 (71)
T ss_dssp HHHHHHHHHHHHTTSSSSHHHHHHHC
T ss_pred HHHHHHHHHHHHcCCCcCHHHHHHHh
Confidence 46789999999999999999987543
No 44
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=51.95 E-value=11 Score=34.89 Aligned_cols=30 Identities=17% Similarity=0.398 Sum_probs=25.4
Q ss_pred cccCCCCCCceeecCCcceecccCCeeecc
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
-.|+.|+.....-..-|-|.|..||.++-|
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 37 YFCPFCGKHAVKRQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred ccCCCCCCCceeeeeeEEEEcCCCCCEEeC
Confidence 479999988764447899999999999887
No 45
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.94 E-value=4.6 Score=41.20 Aligned_cols=34 Identities=21% Similarity=0.416 Sum_probs=26.3
Q ss_pred cccccccCCCCCCc-eeecCCcceecccCCeeecc
Q 004163 7 DIRRLKCKKCDNVG-FECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 7 ~~r~~~C~~C~S~~-w~~~ddG~~yC~~CGhv~Eg 40 (771)
..-.-+|++|+.+- +.++.+.-|.|..||.+++-
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 33456899999663 46666788999999999974
No 46
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=51.49 E-value=11 Score=34.99 Aligned_cols=30 Identities=20% Similarity=0.462 Sum_probs=25.6
Q ss_pred cccCCCCCCceeecCCcceecccCCeeecc
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
-.|+.|+.....-..-|-|.|..||.++-|
T Consensus 36 y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 65 (91)
T TIGR00280 36 YVCPFCGKKTVKRGSTGIWTCRKCGAKFAG 65 (91)
T ss_pred ccCCCCCCCceEEEeeEEEEcCCCCCEEeC
Confidence 479999988774448899999999999887
No 47
>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=51.37 E-value=9.3 Score=35.11 Aligned_cols=26 Identities=27% Similarity=0.691 Sum_probs=21.8
Q ss_pred ccCCCCCCceeecCCcceecccCCeeec
Q 004163 12 KCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 12 ~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
-|+.||+.... ..|.++|..||++.+
T Consensus 2 fC~~Cg~~l~~--~~~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTP--KNGVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCccccc--CCCeEECcCCCCccc
Confidence 59999999964 468999999998755
No 48
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=50.85 E-value=13 Score=32.83 Aligned_cols=35 Identities=17% Similarity=0.373 Sum_probs=28.2
Q ss_pred cccccccCCCCCCc----eeecCCcceecccCCeeeccc
Q 004163 7 DIRRLKCKKCDNVG----FECAYDGFYYCTHCNALDDEI 41 (771)
Q Consensus 7 ~~r~~~C~~C~S~~----w~~~ddG~~yC~~CGhv~Eg~ 41 (771)
.|-|-+|+.|.+.. |...+.=.+-|-.|||...-.
T Consensus 5 FIAGa~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~ 43 (71)
T PF09526_consen 5 FIAGAVCPKCQAMDTIMMWRENGVEYVECVECGYTERQP 43 (71)
T ss_pred EecCccCCCCcCccEEEEEEeCCceEEEecCCCCeeccC
Confidence 46688999999985 777566678899999998753
No 49
>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=50.27 E-value=13 Score=27.35 Aligned_cols=29 Identities=14% Similarity=0.230 Sum_probs=17.5
Q ss_pred ccccCCCCCCceeecCCcceecccCCeee
Q 004163 10 RLKCKKCDNVGFECAYDGFYYCTHCNALD 38 (771)
Q Consensus 10 ~~~C~~C~S~~w~~~ddG~~yC~~CGhv~ 38 (771)
..-|..||+..-.....-.+.|..||+..
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCEe
Confidence 34689999998776566678999999864
No 50
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=48.36 E-value=25 Score=30.01 Aligned_cols=51 Identities=22% Similarity=0.248 Sum_probs=33.6
Q ss_pred HHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004163 352 ASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 408 (771)
Q Consensus 352 l~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~s~~~~~~Pe~V~LmA~IIVAlKLL 408 (771)
+.|++..|+||.+ +...+..|++......+. ..+-|. ..+.|+|.+|.++.
T Consensus 1 I~r~~~~L~L~~~-v~~~A~~i~~~~~~~~~~----~Gr~~~-~iaAA~iY~acr~~ 51 (71)
T PF00382_consen 1 IPRICSKLGLPED-VRERAKEIYKKAQERGLL----KGRSPE-SIAAACIYLACRLN 51 (71)
T ss_dssp HHHHHHHTT--HH-HHHHHHHHHHHHHHTTTS----TTS-HH-HHHHHHHHHHHHHT
T ss_pred ChHHHhHcCCCHH-HHHHHHHHHHHHHHcCCc----ccCCHH-HHHHHHHHHHHHHc
Confidence 4689999999999 888888887632222111 123476 88889999999874
No 51
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=48.07 E-value=14 Score=31.73 Aligned_cols=17 Identities=24% Similarity=0.469 Sum_probs=14.5
Q ss_pred eeecCCcceecccCCeee
Q 004163 21 FECAYDGFYYCTHCNALD 38 (771)
Q Consensus 21 w~~~ddG~~yC~~CGhv~ 38 (771)
+.+ .+|..+|..||+.-
T Consensus 47 ~~i-~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 47 VEI-VEGELICPECGREY 63 (68)
T ss_dssp EET-TTTEEEETTTTEEE
T ss_pred ccc-cCCEEEcCCCCCEE
Confidence 556 89999999999875
No 52
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=47.76 E-value=13 Score=34.39 Aligned_cols=30 Identities=20% Similarity=0.416 Sum_probs=25.7
Q ss_pred cccCCCCCCceeecCCcceecccCCeeecc
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
-.|+.|+.....-..-|-|-|..||.++-|
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 37 HVCPVCGRPKVKRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred ccCCCCCCCceEEEEEEEEEcCCCCCEEeC
Confidence 479999888875548899999999999887
No 53
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=46.97 E-value=12 Score=31.08 Aligned_cols=29 Identities=17% Similarity=0.402 Sum_probs=21.5
Q ss_pred cccccccCCCCCCce-eecCCcceecccCCe
Q 004163 7 DIRRLKCKKCDNVGF-ECAYDGFYYCTHCNA 36 (771)
Q Consensus 7 ~~r~~~C~~C~S~~w-~~~ddG~~yC~~CGh 36 (771)
...+..|++||.-.| .. -.-+|+|-+||-
T Consensus 16 ~rk~~~CPrCG~gvfmA~-H~dR~~CGkCgy 45 (51)
T COG1998 16 KRKNRFCPRCGPGVFMAD-HKDRWACGKCGY 45 (51)
T ss_pred EEccccCCCCCCcchhhh-cCceeEeccccc
Confidence 345678999998776 33 333999999984
No 54
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=45.55 E-value=14 Score=35.19 Aligned_cols=29 Identities=38% Similarity=0.676 Sum_probs=21.4
Q ss_pred ccccCCCCCCc--eee-----cCCc---ceecccCCeee
Q 004163 10 RLKCKKCDNVG--FEC-----AYDG---FYYCTHCNALD 38 (771)
Q Consensus 10 ~~~C~~C~S~~--w~~-----~ddG---~~yC~~CGhv~ 38 (771)
...|+.|++.. |.. +|++ ||.|.+|||+-
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~w 110 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRW 110 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEe
Confidence 35799999986 332 3333 89999999974
No 55
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=45.29 E-value=16 Score=35.34 Aligned_cols=29 Identities=34% Similarity=0.628 Sum_probs=21.0
Q ss_pred ccccC--CCCCCceeecCCcceecccCCeeec
Q 004163 10 RLKCK--KCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 10 ~~~C~--~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
=+.|+ .|+.+-=.. .+|.|+|..||...+
T Consensus 18 Y~aC~~~~C~kKv~~~-~~~~y~C~~C~~~~~ 48 (146)
T PF08646_consen 18 YPACPNEKCNKKVTEN-GDGSYRCEKCNKTVE 48 (146)
T ss_dssp EEE-TSTTTS-B-EEE-TTTEEEETTTTEEES
T ss_pred ECCCCCccCCCEeecC-CCcEEECCCCCCcCC
Confidence 36799 999865455 789999999998864
No 56
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=44.24 E-value=39 Score=27.78 Aligned_cols=52 Identities=17% Similarity=0.162 Sum_probs=36.2
Q ss_pred HHHHHHHHcCCChhhhHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHh
Q 004163 351 LASRYLKQLCLPLGKILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRIL 408 (771)
Q Consensus 351 Ll~Ryl~eL~LP~E~iy~~v~RL~~fs~p~~l~~s~~~~~~Pe~V~LmA~IIVAlKLL 408 (771)
.+.|++..+++|.+ +...+..+++-.+...... ..-|. ..++|+|.+|.|+.
T Consensus 2 ~l~~~~~~~~~~~~-~~~~a~~~~~~~l~~~~~~----~~~~~-~ia~a~l~lA~k~~ 53 (83)
T smart00385 2 FLRRVCKALNLDPE-TLNLAVNLLDRFLSDYKFL----KYSPS-LIAAAALYLAAKTE 53 (83)
T ss_pred HHHHHHHHcCCCHH-HHHHHHHHHHHHHHHhhcc----cCCHH-HHHHHHHHHHHHHh
Confidence 46789999999999 7777777776322211110 13455 88999999999986
No 57
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=41.97 E-value=17 Score=29.98 Aligned_cols=29 Identities=17% Similarity=0.472 Sum_probs=23.3
Q ss_pred ccccCCCCCCc---eeecCCcc-eecccCCeee
Q 004163 10 RLKCKKCDNVG---FECAYDGF-YYCTHCNALD 38 (771)
Q Consensus 10 ~~~C~~C~S~~---w~~~ddG~-~yC~~CGhv~ 38 (771)
..+|.+|+... |+.+..|. ..|..||--.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 46899999775 98878886 9999998544
No 58
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=41.48 E-value=19 Score=26.03 Aligned_cols=27 Identities=26% Similarity=0.502 Sum_probs=15.7
Q ss_pred ccccCCCCCCceee--cCCcceecccCCe
Q 004163 10 RLKCKKCDNVGFEC--AYDGFYYCTHCNA 36 (771)
Q Consensus 10 ~~~C~~C~S~~w~~--~ddG~~yC~~CGh 36 (771)
|.+|+.|+...=.+ ...+-++|.+|=+
T Consensus 1 G~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 1 GEKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp TSB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CCcCccCCCcceEeEecCCCCeECcCCcC
Confidence 57899999986544 3355689998854
No 59
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=40.96 E-value=11 Score=28.59 Aligned_cols=29 Identities=31% Similarity=0.766 Sum_probs=18.6
Q ss_pred ccccccccccCCCCCCceeecCCcceecccCCe
Q 004163 4 GEGDIRRLKCKKCDNVGFECAYDGFYYCTHCNA 36 (771)
Q Consensus 4 ~~~~~r~~~C~~C~S~~w~~~ddG~~yC~~CGh 36 (771)
.++.....+|..||...|.- +.+|..||.
T Consensus 5 ~~~~l~~~rC~~Cg~~~~pP----r~~Cp~C~s 33 (37)
T PF12172_consen 5 AEGRLLGQRCRDCGRVQFPP----RPVCPHCGS 33 (37)
T ss_dssp HTT-EEEEE-TTT--EEES------SEETTTT-
T ss_pred cCCEEEEEEcCCCCCEecCC----CcCCCCcCc
Confidence 45677889999999999966 478999983
No 60
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=40.83 E-value=19 Score=30.66 Aligned_cols=26 Identities=19% Similarity=0.254 Sum_probs=21.0
Q ss_pred CCCCCCcee---ecCCcceecccCCeeec
Q 004163 14 KKCDNVGFE---CAYDGFYYCTHCNALDD 39 (771)
Q Consensus 14 ~~C~S~~w~---~~ddG~~yC~~CGhv~E 39 (771)
.-||+..|. .+-|=+.-|..|||++.
T Consensus 14 HPCG~~~Wei~R~GaDikikC~gCg~~im 42 (57)
T PF06107_consen 14 HPCGSNEWEIIRIGADIKIKCLGCGRQIM 42 (57)
T ss_pred CCCCCCEEEEEEccCcEEEEECCCCCEEE
Confidence 359999994 46677788999999875
No 61
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=38.96 E-value=21 Score=40.93 Aligned_cols=32 Identities=16% Similarity=0.351 Sum_probs=23.9
Q ss_pred cccccCCCCCCce--eecCCcceecccCCeeecc
Q 004163 9 RRLKCKKCDNVGF--ECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 9 r~~~C~~C~S~~w--~~~ddG~~yC~~CGhv~Eg 40 (771)
.-..|+.|+..-= .+...+.-.|.||||+...
T Consensus 12 ~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 12 KHILCSQCDMLVALPRIESGQKAACPRCGTTLTV 45 (403)
T ss_pred CeeeCCCCCCcccccCCCCCCeeECCCCCCCCcC
Confidence 3446999998742 4445677899999999965
No 62
>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=38.69 E-value=25 Score=30.17 Aligned_cols=34 Identities=15% Similarity=0.343 Sum_probs=26.4
Q ss_pred cccccccCCCCCCc----eeecCCcceecccCCeeecc
Q 004163 7 DIRRLKCKKCDNVG----FECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 7 ~~r~~~C~~C~S~~----w~~~ddG~~yC~~CGhv~Eg 40 (771)
+|-|-+|+.|.+-. |...+.-..-|-.|||....
T Consensus 6 FIAGA~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 6 FIAGAVCPACSAQDTLAMWKENNIELVECVECGYQEQQ 43 (59)
T ss_pred EeccccCCCCcCccEEEEEEeCCceEEEeccCCCcccc
Confidence 46688999999975 66545556899999998754
No 63
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=38.56 E-value=16 Score=26.26 Aligned_cols=24 Identities=21% Similarity=0.563 Sum_probs=18.3
Q ss_pred ccCCCCCCceeecCCcceecccCCeeec
Q 004163 12 KCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 12 ~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
.|++|++.- ...-.+|..|||..+
T Consensus 2 ~CP~C~~~V----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEV----PESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCc----hhhcCcCCCCCCCCc
Confidence 589998875 344678999999764
No 64
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=38.53 E-value=18 Score=29.97 Aligned_cols=28 Identities=18% Similarity=0.223 Sum_probs=19.4
Q ss_pred cccCCCCCCceeecCCcceecccCCeee
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALD 38 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~ 38 (771)
=+|..||..-=.+......-|.+|||.+
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCcEE
Confidence 3688888776334456667788888866
No 65
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=38.39 E-value=15 Score=38.12 Aligned_cols=35 Identities=17% Similarity=0.432 Sum_probs=26.0
Q ss_pred ccCCCCCCc---eee---cCCcceecccCCeeecccccccc
Q 004163 12 KCKKCDNVG---FEC---AYDGFYYCTHCNALDDEIVETGV 46 (771)
Q Consensus 12 ~C~~C~S~~---w~~---~ddG~~yC~~CGhv~Eg~ve~~v 46 (771)
+|.+||..- |.. +.--.--|.+||++.+.++|.|.
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDkYiE~d~ 42 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADKYIEYDN 42 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCCcccceecccc
Confidence 699999984 422 22234689999999999997665
No 66
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=38.38 E-value=1.5e+02 Score=33.49 Aligned_cols=72 Identities=21% Similarity=0.251 Sum_probs=43.8
Q ss_pred HHHHHHhCCCCCCCCHHHHHHHHHHHcCCChhh-hHHHHHHhhhccCCccCccCCCCCCCChHHHHHHHHHHHHHHhh
Q 004163 333 ASIAESIGLHLPPVNFYALASRYLKQLCLPLGK-ILPRALKIQEWSMPPDLWLSTNECRFPTRVCVMSILIVSIRILY 409 (771)
Q Consensus 333 ~~la~~~gL~fPpiN~~lLl~Ryl~eL~LP~E~-iy~~v~RL~~fs~p~~l~~s~~~~~~Pe~V~LmA~IIVAlKLLf 409 (771)
..+.+.+|+..----...|+.-|+..|+||+.+ +...+-..++-+.-.+++- ..-|+ +.+.|+|-+|.+-+=
T Consensus 126 ~~ILr~LGF~~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~v----ry~pe-~iACaciyLaAR~~e 198 (367)
T KOG0835|consen 126 RRILRELGFDVHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFV----RYSPE-SIACACIYLAARNLE 198 (367)
T ss_pred HHHHHHhCCeeeeeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceee----ecCHH-HHHHHHHHHHHhhhc
Confidence 345566776544445568999999999999983 3333333333222222221 22355 888888888888653
No 67
>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=37.72 E-value=29 Score=31.89 Aligned_cols=30 Identities=33% Similarity=0.719 Sum_probs=22.8
Q ss_pred ccccCCCCCCc--ee-----ecCCc---ceecccCCeeec
Q 004163 10 RLKCKKCDNVG--FE-----CAYDG---FYYCTHCNALDD 39 (771)
Q Consensus 10 ~~~C~~C~S~~--w~-----~~ddG---~~yC~~CGhv~E 39 (771)
...|+.||+.. |. -+|+| ||.|..|||+--
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeE
Confidence 57899999998 42 23444 899999999753
No 68
>PF12773 DZR: Double zinc ribbon
Probab=36.78 E-value=15 Score=29.22 Aligned_cols=23 Identities=26% Similarity=0.660 Sum_probs=12.1
Q ss_pred cCCCCCCceeecCCcceecccCCeeec
Q 004163 13 CKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 13 C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
|+.|+.. + .++..||..||+.+.
T Consensus 1 Cp~Cg~~---~-~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTP---N-PDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCc---C-CccccCChhhcCChh
Confidence 4445444 3 455556666665554
No 69
>PRK12495 hypothetical protein; Provisional
Probab=36.68 E-value=23 Score=37.61 Aligned_cols=29 Identities=28% Similarity=0.682 Sum_probs=25.2
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeecc
Q 004163 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 10 ~~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
...|+.||.-.|.+ .|..+|-.|+.....
T Consensus 42 a~hC~~CG~PIpa~--pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 42 NAHCDECGDPIFRH--DGQEFCPTCQQPVTE 70 (226)
T ss_pred hhhcccccCcccCC--CCeeECCCCCCcccc
Confidence 45799999999965 999999999988764
No 70
>PF14353 CpXC: CpXC protein
Probab=36.42 E-value=23 Score=33.64 Aligned_cols=28 Identities=14% Similarity=0.497 Sum_probs=20.4
Q ss_pred cccCCCCCCc----eeecCCc----------------ceecccCCeeec
Q 004163 11 LKCKKCDNVG----FECAYDG----------------FYYCTHCNALDD 39 (771)
Q Consensus 11 ~~C~~C~S~~----w~~~ddG----------------~~yC~~CGhv~E 39 (771)
.+|+.|+... |.. .|. .++|.+||+...
T Consensus 2 itCP~C~~~~~~~v~~~-I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTS-INADEDPELKEKILDGSLFSFTCPSCGHKFR 49 (128)
T ss_pred cCCCCCCCeeEEEEEeE-EcCcCCHHHHHHHHcCCcCEEECCCCCCcee
Confidence 4799999875 533 332 689999998774
No 71
>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=35.74 E-value=27 Score=28.67 Aligned_cols=29 Identities=17% Similarity=0.521 Sum_probs=20.0
Q ss_pred ccCCCCCCce--e----e-cCCcceecccCCeeecc
Q 004163 12 KCKKCDNVGF--E----C-AYDGFYYCTHCNALDDE 40 (771)
Q Consensus 12 ~C~~C~S~~w--~----~-~ddG~~yC~~CGhv~Eg 40 (771)
.|+-||+..- . . ...|.+.|..||+...-
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 6999999863 2 1 13345569999998763
No 72
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=35.30 E-value=13 Score=32.06 Aligned_cols=37 Identities=16% Similarity=0.270 Sum_probs=29.4
Q ss_pred ccccccccccCCCCCCc----eeecCCcceecccCCeeecc
Q 004163 4 GEGDIRRLKCKKCDNVG----FECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 4 ~~~~~r~~~C~~C~S~~----w~~~ddG~~yC~~CGhv~Eg 40 (771)
-.-+|-|-+|++|.... |+...=-..-|-.|||.++.
T Consensus 4 rKRFIAGA~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~ 44 (66)
T COG3529 4 RKRFIAGAVCPACQAQDTLAMWRENNVEIVECVKCGHHMRE 44 (66)
T ss_pred hhhhhccCCCcccchhhHHHHHHhcCCceEehhhcchHhhh
Confidence 34467789999999885 87755567899999999864
No 73
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=34.72 E-value=28 Score=29.94 Aligned_cols=27 Identities=19% Similarity=0.341 Sum_probs=24.2
Q ss_pred cccCCCCCCceeecCCcceecccCCee
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNAL 37 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv 37 (771)
..|+.|....+.+.+.+..||..|+-.
T Consensus 9 LaCP~~kg~L~~~~~~~~L~c~~~~~a 35 (60)
T COG2835 9 LACPVCKGPLVYDEEKQELICPRCKLA 35 (60)
T ss_pred eeccCcCCcceEeccCCEEEecccCce
Confidence 679999999999989999999998843
No 74
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=34.54 E-value=25 Score=26.93 Aligned_cols=27 Identities=15% Similarity=0.378 Sum_probs=19.4
Q ss_pred cccCCCCCCceeec------CCcceecccCCeee
Q 004163 11 LKCKKCDNVGFECA------YDGFYYCTHCNALD 38 (771)
Q Consensus 11 ~~C~~C~S~~w~~~------ddG~~yC~~CGhv~ 38 (771)
-+|++|.++- .++ ..|..-|.+|||+.
T Consensus 3 i~CP~C~~~f-~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRF-RVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceE-EcCHHHcccCCcEEECCCCCcEe
Confidence 3699998764 221 35678899999985
No 75
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=34.22 E-value=13 Score=40.85 Aligned_cols=29 Identities=24% Similarity=0.504 Sum_probs=23.0
Q ss_pred cccCCCCCCceee-cCCcceecccCCeeec
Q 004163 11 LKCKKCDNVGFEC-AYDGFYYCTHCNALDD 39 (771)
Q Consensus 11 ~~C~~C~S~~w~~-~ddG~~yC~~CGhv~E 39 (771)
-.|++|+...|.. -...+++|..|||-+-
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCCCCCCcCc
Confidence 4799999999942 2677899999998543
No 76
>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=33.90 E-value=27 Score=26.40 Aligned_cols=26 Identities=15% Similarity=0.229 Sum_probs=15.8
Q ss_pred ccCCCCCCceeecCCcceecccCCeee
Q 004163 12 KCKKCDNVGFECAYDGFYYCTHCNALD 38 (771)
Q Consensus 12 ~C~~C~S~~w~~~ddG~~yC~~CGhv~ 38 (771)
+|..|++..- +....---|.+|||.+
T Consensus 2 ~C~~Cg~~~~-~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVE-LKPGDPIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE--BSTSSTSSBSSSS-SE
T ss_pred CCCcCCCeeE-cCCCCcEECCcCCCeE
Confidence 4778887764 3234456788888765
No 77
>PF13113 DUF3970: Protein of unknown function (DUF3970)
Probab=33.66 E-value=34 Score=29.41 Aligned_cols=33 Identities=30% Similarity=0.573 Sum_probs=25.8
Q ss_pred CHHHHHHHHHh--h---------hcccccccccccccChhHHHhhc
Q 004163 480 DAEALLYDLEA--R---------YNDIHDSVTYEYSKDLPTYLKYC 514 (771)
Q Consensus 480 ~~~ell~~~~~--~---------~~~~~~~~~~~~~kdl~~YL~y~ 514 (771)
+-+++|+.+++ . |..-++ -|+||||...||.+=
T Consensus 12 Ei~~fi~~~~~~~~~ei~h~sk~~~~nNP--KY~~sKdv~~Yl~~K 55 (60)
T PF13113_consen 12 EIEEFIKSFEKLKGFEITHTSKPYKKNNP--KYKYSKDVRVYLSLK 55 (60)
T ss_pred HHHHHHHhhhhcCCceEEEecccccCCCc--ccccchhhHHHHHhh
Confidence 55667777777 2 555588 899999999999874
No 78
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.41 E-value=19 Score=34.39 Aligned_cols=27 Identities=26% Similarity=0.639 Sum_probs=18.6
Q ss_pred cccCCCCCCceeecCCcceecccCCeee
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALD 38 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~ 38 (771)
.+|..|+ ..|.....+++.|.+||...
T Consensus 72 ~~C~~Cg-~~~~~~~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 72 LECKDCS-HVFKPNALDYGVCEKCHSKN 98 (117)
T ss_pred EEhhhCC-CccccCCccCCcCcCCCCCc
Confidence 5699999 55666334555699999643
No 79
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=32.83 E-value=28 Score=33.19 Aligned_cols=29 Identities=21% Similarity=0.525 Sum_probs=23.8
Q ss_pred ccCCCCCCcee--ecCCcceecccCCeeecc
Q 004163 12 KCKKCDNVGFE--CAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 12 ~C~~C~S~~w~--~~ddG~~yC~~CGhv~Eg 40 (771)
-|+.|++-..- ..+++.+.|+.||+..+-
T Consensus 4 FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~ 34 (113)
T COG1594 4 FCPKCGSLLYPKKDDEGGKLVCRKCGYEEEA 34 (113)
T ss_pred ccCCccCeeEEeEcCCCcEEECCCCCcchhc
Confidence 49999999983 336889999999988763
No 80
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=32.44 E-value=28 Score=34.46 Aligned_cols=28 Identities=29% Similarity=0.548 Sum_probs=21.7
Q ss_pred ccccCCCCCCceeecCCcceecccCCeee
Q 004163 10 RLKCKKCDNVGFECAYDGFYYCTHCNALD 38 (771)
Q Consensus 10 ~~~C~~C~S~~w~~~ddG~~yC~~CGhv~ 38 (771)
=..|+.|..+--.. .+|.|+|..|+...
T Consensus 34 Y~aC~~C~kkv~~~-~~~~~~C~~C~~~~ 61 (166)
T cd04476 34 YPACPGCNKKVVEE-GNGTYRCEKCNKSV 61 (166)
T ss_pred EccccccCcccEeC-CCCcEECCCCCCcC
Confidence 35799998886544 55999999998765
No 81
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=32.32 E-value=25 Score=39.77 Aligned_cols=38 Identities=21% Similarity=0.460 Sum_probs=30.6
Q ss_pred CccccccccccCCCCCCcee--ecCCcceecccCCeeecc
Q 004163 3 DGEGDIRRLKCKKCDNVGFE--CAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 3 ~~~~~~r~~~C~~C~S~~w~--~~ddG~~yC~~CGhv~Eg 40 (771)
+|+|.-.=|+|+.||+-+-. -.+.|-|+|-.|.++...
T Consensus 267 dE~TAfSWPvCd~CGn~rLe~~pe~rg~~~C~~Cs~~V~s 306 (389)
T PF14951_consen 267 DESTAFSWPVCDRCGNGRLEQSPEDRGAFSCGDCSRVVTS 306 (389)
T ss_pred cCcccccCccccccCCccceeCccCCCceeccchhhhccC
Confidence 56777778999999999974 246888999999987653
No 82
>COG4640 Predicted membrane protein [Function unknown]
Probab=32.18 E-value=22 Score=40.68 Aligned_cols=26 Identities=27% Similarity=0.415 Sum_probs=19.1
Q ss_pred ccCCCCCCceeecCCcceecccCCeeeccc
Q 004163 12 KCKKCDNVGFECAYDGFYYCTHCNALDDEI 41 (771)
Q Consensus 12 ~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg~ 41 (771)
-|+.||+..-. |-+.|.+|||-..+.
T Consensus 3 fC~kcG~qk~E----d~~qC~qCG~~~t~~ 28 (465)
T COG4640 3 FCPKCGSQKAE----DDVQCTQCGHKFTSR 28 (465)
T ss_pred ccccccccccc----ccccccccCCcCCch
Confidence 49999987643 334599999988763
No 83
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=32.12 E-value=23 Score=43.10 Aligned_cols=24 Identities=17% Similarity=0.505 Sum_probs=17.4
Q ss_pred ccCCCCCCceeecCCcceecccCCeeec
Q 004163 12 KCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 12 ~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
+|++|+... .+|-.||.+||+.+.
T Consensus 3 ~Cp~Cg~~n----~~~akFC~~CG~~l~ 26 (645)
T PRK14559 3 ICPQCQFEN----PNNNRFCQKCGTSLT 26 (645)
T ss_pred cCCCCCCcC----CCCCccccccCCCCC
Confidence 688888762 567778888887764
No 84
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=31.41 E-value=22 Score=35.41 Aligned_cols=16 Identities=19% Similarity=0.405 Sum_probs=14.1
Q ss_pred cCCcceecccCCeeec
Q 004163 24 AYDGFYYCTHCNALDD 39 (771)
Q Consensus 24 ~ddG~~yC~~CGhv~E 39 (771)
..-|.|+|..|||.+.
T Consensus 108 ~g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 108 VGPGTLVCENCGHEVE 123 (146)
T ss_pred ecCceEecccCCCEEE
Confidence 3579999999999987
No 85
>PF14567 SUKH_5: SMI1-KNR4 cell-wall; PDB: 2PAG_A.
Probab=31.00 E-value=25 Score=34.51 Aligned_cols=42 Identities=24% Similarity=0.480 Sum_probs=26.1
Q ss_pred cccCHHHHHHHHHhhhcccccccccccccChhHHHhhccceeecCCCCC
Q 004163 477 SELDAEALLYDLEARYNDIHDSVTYEYSKDLPTYLKYCKDVVFAGLEPP 525 (771)
Q Consensus 477 ~~~~~~ell~~~~~~~~~~~~~~~~~~~kdl~~YL~y~k~~vfag~~~~ 525 (771)
-++-++|.|..+|.. + .-.+.+|...||++|.+++|+++++-
T Consensus 19 l~lpd~e~I~~~Ee~---L----~i~lP~eyk~fL~~~s~v~~G~~E~~ 60 (132)
T PF14567_consen 19 LELPDDEQIVEAEEQ---L----GISLPEEYKEFLLEASDVIYGGLEPV 60 (132)
T ss_dssp -----HHHHHHHHHH---H----T----HHHHHHHHHHTT--BTTB-B-
T ss_pred CCCCCHHHHHHHHHH---H----CCCCCHHHHHHHHHCCCeeecceEEE
Confidence 456678888888888 5 55677999999999999999999884
No 86
>PRK11827 hypothetical protein; Provisional
Probab=30.84 E-value=37 Score=29.16 Aligned_cols=30 Identities=13% Similarity=0.124 Sum_probs=23.6
Q ss_pred ccccCCCCCCceeecCCcceecccCCeeec
Q 004163 10 RLKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 10 ~~~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
-.+|+.|.+...+..+....+|+.||-.-.
T Consensus 8 ILaCP~ckg~L~~~~~~~~Lic~~~~laYP 37 (60)
T PRK11827 8 IIACPVCNGKLWYNQEKQELICKLDNLAFP 37 (60)
T ss_pred heECCCCCCcCeEcCCCCeEECCccCeecc
Confidence 468999999987665667789999986543
No 87
>PRK12366 replication factor A; Reviewed
Probab=30.79 E-value=24 Score=42.77 Aligned_cols=28 Identities=29% Similarity=0.562 Sum_probs=22.1
Q ss_pred ccccccCCCCCCceeecCCcceecccCCee
Q 004163 8 IRRLKCKKCDNVGFECAYDGFYYCTHCNAL 37 (771)
Q Consensus 8 ~r~~~C~~C~S~~w~~~ddG~~yC~~CGhv 37 (771)
..=+.|++|.-+-- . .+|.|+|..||.+
T Consensus 530 ~~y~aCp~CnkKv~-~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 530 IILYLCPNCRKRVE-E-VDGEYICEFCGEV 557 (637)
T ss_pred EEEecccccCeEeE-c-CCCcEECCCCCCC
Confidence 34488999976653 3 6899999999987
No 88
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=30.03 E-value=22 Score=34.98 Aligned_cols=32 Identities=38% Similarity=0.672 Sum_probs=26.4
Q ss_pred CccccccccccCCCCCCceeecCCcceecccCCeee
Q 004163 3 DGEGDIRRLKCKKCDNVGFECAYDGFYYCTHCNALD 38 (771)
Q Consensus 3 ~~~~~~r~~~C~~C~S~~w~~~ddG~~yC~~CGhv~ 38 (771)
..++++.+-+|.+||+.-+-- +-+|..||...
T Consensus 22 l~~~kl~g~kC~~CG~v~~PP----r~~Cp~C~~~~ 53 (140)
T COG1545 22 LKEGKLLGTKCKKCGRVYFPP----RAYCPKCGSET 53 (140)
T ss_pred hhhCcEEEEEcCCCCeEEcCC----cccCCCCCCCC
Confidence 346788999999999999854 56899999874
No 89
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.72 E-value=28 Score=34.04 Aligned_cols=27 Identities=30% Similarity=0.775 Sum_probs=18.0
Q ss_pred ccccCCCCCCceeecC--------------------CcceecccCCee
Q 004163 10 RLKCKKCDNVGFECAY--------------------DGFYYCTHCNAL 37 (771)
Q Consensus 10 ~~~C~~C~S~~w~~~d--------------------dG~~yC~~CGhv 37 (771)
..+|.+||. .|...+ ..++.|.+||..
T Consensus 70 ~~~C~~CG~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 70 VLKCRNCGN-EWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred EEECCCCCC-EEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 357899984 465532 456679999854
No 90
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=29.01 E-value=21 Score=27.18 Aligned_cols=24 Identities=21% Similarity=0.674 Sum_probs=17.7
Q ss_pred cCCCCCC---ceeecCCcce-ecccCCe
Q 004163 13 CKKCDNV---GFECAYDGFY-YCTHCNA 36 (771)
Q Consensus 13 C~~C~S~---~w~~~ddG~~-yC~~CGh 36 (771)
|.+|+.. .|+.+.+|.. .|..||-
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGL 28 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHH
Confidence 7788876 4988889999 9999984
No 91
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=28.63 E-value=20 Score=29.86 Aligned_cols=27 Identities=19% Similarity=0.506 Sum_probs=21.2
Q ss_pred ccCCCCCCc---eeecC-CcceecccCCeee
Q 004163 12 KCKKCDNVG---FECAY-DGFYYCTHCNALD 38 (771)
Q Consensus 12 ~C~~C~S~~---w~~~d-dG~~yC~~CGhv~ 38 (771)
+|.+|+... |+-+. .|...|..||--.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~ 31 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYW 31 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHH
Confidence 599999875 87644 8889999999544
No 92
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=28.43 E-value=30 Score=37.47 Aligned_cols=36 Identities=19% Similarity=0.490 Sum_probs=28.3
Q ss_pred cccCCCCCC--------ceeecCCcceecccCCeeeccccccccccc
Q 004163 11 LKCKKCDNV--------GFECAYDGFYYCTHCNALDDEIVETGVADE 49 (771)
Q Consensus 11 ~~C~~C~S~--------~w~~~ddG~~yC~~CGhv~Eg~ve~~vDde 49 (771)
-+|..|.-+ -|++ |.|-|..|||..-|+-+.++---
T Consensus 133 SRCr~C~~rYDPVP~dkmwG~---aef~C~~C~h~F~G~~qm~v~sP 176 (278)
T PF15135_consen 133 SRCRKCRKRYDPVPCDKMWGI---AEFHCPKCRHNFRGFAQMGVPSP 176 (278)
T ss_pred ccccccccccCCCccccccce---eeeecccccccchhhhhcCCCCC
Confidence 468888755 5888 89999999999999876666443
No 93
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.65 E-value=33 Score=38.65 Aligned_cols=28 Identities=21% Similarity=0.637 Sum_probs=21.3
Q ss_pred cccccCCCCCCc-eeec--C-CcceecccCCe
Q 004163 9 RRLKCKKCDNVG-FECA--Y-DGFYYCTHCNA 36 (771)
Q Consensus 9 r~~~C~~C~S~~-w~~~--d-dG~~yC~~CGh 36 (771)
++..|+.|+.+. |+.. . -|-|+|-+|||
T Consensus 31 ~~~~cpvcg~k~RFr~dD~kGrGtw~c~y~~~ 62 (366)
T COG4643 31 GGHPCPVCGGKDRFRFDDRKGRGTWFCNYCGH 62 (366)
T ss_pred CCCCCCccCCccccccCCccCCccEEEEeecc
Confidence 445899999985 5442 2 58899999995
No 94
>PRK08402 replication factor A; Reviewed
Probab=27.52 E-value=36 Score=38.52 Aligned_cols=27 Identities=11% Similarity=0.201 Sum_probs=21.5
Q ss_pred cccCCCCCCceeecCCcceecccCCee
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNAL 37 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv 37 (771)
+.|++|.-+-=....+|.|.|..||.+
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGEV 239 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCCc
Confidence 789999765554557899999999853
No 95
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=26.97 E-value=19 Score=39.72 Aligned_cols=29 Identities=14% Similarity=0.508 Sum_probs=22.5
Q ss_pred cccCCCCCCceee-cCCcceecccCCeeec
Q 004163 11 LKCKKCDNVGFEC-AYDGFYYCTHCNALDD 39 (771)
Q Consensus 11 ~~C~~C~S~~w~~-~ddG~~yC~~CGhv~E 39 (771)
-+|++|+...+.. -...+++|..|||-+-
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCcC
Confidence 4799999999832 2577899999998543
No 96
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=26.62 E-value=40 Score=25.80 Aligned_cols=28 Identities=14% Similarity=0.355 Sum_probs=18.0
Q ss_pred cccCCCCCCc----eeecCC-cceecccCCeee
Q 004163 11 LKCKKCDNVG----FECAYD-GFYYCTHCNALD 38 (771)
Q Consensus 11 ~~C~~C~S~~----w~~~dd-G~~yC~~CGhv~ 38 (771)
-+|++|.++- ..++.. ...-|..|||+.
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 3688898763 223333 346799999874
No 97
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=26.26 E-value=21 Score=39.33 Aligned_cols=29 Identities=21% Similarity=0.469 Sum_probs=22.3
Q ss_pred cccCCCCCCceee-cCCcceecccCCeeec
Q 004163 11 LKCKKCDNVGFEC-AYDGFYYCTHCNALDD 39 (771)
Q Consensus 11 ~~C~~C~S~~w~~-~ddG~~yC~~CGhv~E 39 (771)
-.|+.|+...|.. -....++|..|||-+.
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHHMR 57 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCCee
Confidence 5799999999832 2455789999998654
No 98
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=26.01 E-value=35 Score=32.37 Aligned_cols=24 Identities=25% Similarity=0.464 Sum_probs=17.2
Q ss_pred cccCCCCCCceeecCCcceecccCCe
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNA 36 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGh 36 (771)
.+|..|+ ..|.. .+-++.|..||.
T Consensus 71 ~~C~~Cg-~~~~~-~~~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCS-QVVEI-HQHDAQCPHCHG 94 (113)
T ss_pred EEcccCC-CEEec-CCcCccCcCCCC
Confidence 4689999 45655 455666999994
No 99
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=25.89 E-value=50 Score=38.17 Aligned_cols=32 Identities=16% Similarity=0.337 Sum_probs=23.6
Q ss_pred cccccCCCCCCce--eecCCcceecccCCeeecc
Q 004163 9 RRLKCKKCDNVGF--ECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 9 r~~~C~~C~S~~w--~~~ddG~~yC~~CGhv~Eg 40 (771)
..-.|+.|+..-= .+...+.-.|.||||+...
T Consensus 9 ~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 9 KHILCPQCDMLVALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred CcccCCCCCceeecCCCCCCCeeECCCCCCCCcC
Confidence 3456999998732 3334667889999999965
No 100
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=25.52 E-value=31 Score=29.69 Aligned_cols=27 Identities=15% Similarity=0.288 Sum_probs=18.3
Q ss_pred cccCCCCCCceeecCCcceecccCCeee
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALD 38 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~ 38 (771)
-+|..|++..--- .---.-|+.|||.+
T Consensus 21 YiCgdC~~en~lk-~~D~irCReCG~RI 47 (62)
T KOG3507|consen 21 YICGDCGQENTLK-RGDVIRCRECGYRI 47 (62)
T ss_pred EEecccccccccc-CCCcEehhhcchHH
Confidence 4688888887533 23356788888865
No 101
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=24.93 E-value=48 Score=37.47 Aligned_cols=31 Identities=23% Similarity=0.519 Sum_probs=21.2
Q ss_pred cccccccCCCCCCc------eeecCCc--ceecccCCeeecc
Q 004163 7 DIRRLKCKKCDNVG------FECAYDG--FYYCTHCNALDDE 40 (771)
Q Consensus 7 ~~r~~~C~~C~S~~------w~~~ddG--~~yC~~CGhv~Eg 40 (771)
.-..|+|++|| +. |.. +.| .|.| .|||.-+=
T Consensus 166 ~P~~p~c~~cg-~~~~~v~~~d~-~~~~v~y~c-~cG~~g~~ 204 (353)
T cd00674 166 YPFMPYCEKCG-KDTTTVEAYDA-KAGTVTYKC-ECGHEETV 204 (353)
T ss_pred eeeeeecCCcC-cceeEEEEEeC-CCCeEEEEc-CCCCEEEE
Confidence 34789999999 43 322 444 7889 58987663
No 102
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=24.73 E-value=43 Score=36.22 Aligned_cols=30 Identities=20% Similarity=0.601 Sum_probs=12.9
Q ss_pred ccccCCCCCCce-eecC---CcceecccCCeeec
Q 004163 10 RLKCKKCDNVGF-ECAY---DGFYYCTHCNALDD 39 (771)
Q Consensus 10 ~~~C~~C~S~~w-~~~d---dG~~yC~~CGhv~E 39 (771)
.--|++||+..- ..++ -.-|||..|+++-|
T Consensus 31 n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp H---TTT--SS-EE--------EEE-TTT--EEE
T ss_pred CCcCCCCCChhHhhccCCCccceeECCCCchHHh
Confidence 456999999942 2212 24599999999887
No 103
>PRK04023 DNA polymerase II large subunit; Validated
Probab=24.70 E-value=42 Score=42.62 Aligned_cols=25 Identities=24% Similarity=0.632 Sum_probs=13.7
Q ss_pred cccCCCCCCceeecCCcceecccCCeeecc
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
.+|++||+. ...-++|..||++...
T Consensus 639 frCP~CG~~-----Te~i~fCP~CG~~~~~ 663 (1121)
T PRK04023 639 RRCPFCGTH-----TEPVYRCPRCGIEVEE 663 (1121)
T ss_pred ccCCCCCCC-----CCcceeCccccCcCCC
Confidence 345555554 2344667777666553
No 104
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=24.65 E-value=49 Score=39.08 Aligned_cols=34 Identities=26% Similarity=0.323 Sum_probs=23.0
Q ss_pred cccccccCCCCCCce-----eecCCc--ceecccCCeeeccc
Q 004163 7 DIRRLKCKKCDNVGF-----ECAYDG--FYYCTHCNALDDEI 41 (771)
Q Consensus 7 ~~r~~~C~~C~S~~w-----~~~ddG--~~yC~~CGhv~Eg~ 41 (771)
.-..++|++||-..- .+.+.| .|.| .|||.-+=.
T Consensus 172 ~P~~pic~~cg~~~~~~~~~~d~~~~~v~y~~-~cG~~~~~~ 212 (510)
T PRK00750 172 SPFLPICPKCGKVLTTPVISYDAEAGTVTYDC-ECGHEGEVP 212 (510)
T ss_pred eeeeeeCCCCCccceEEEEEEeCCCCEEEEEc-CCCCEEEEe
Confidence 356799999998863 233566 4555 599987643
No 105
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.10 E-value=47 Score=33.43 Aligned_cols=29 Identities=21% Similarity=0.394 Sum_probs=22.1
Q ss_pred ccCCCCCCc------eeecCCc-----ceecccCCeeeccc
Q 004163 12 KCKKCDNVG------FECAYDG-----FYYCTHCNALDDEI 41 (771)
Q Consensus 12 ~C~~C~S~~------w~~~ddG-----~~yC~~CGhv~Eg~ 41 (771)
.|+.||+.. |+. .+| +|-|+.||--...+
T Consensus 2 ~cp~c~~~~~~~~~s~~~-~~~~~~~~~~~c~~c~~~f~~~ 41 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPA-EDGNAIRRRRECLACGKRFTTF 41 (154)
T ss_pred cCCCCCCCCCEeEecccc-CCCCceeeeeeccccCCcceEe
Confidence 699999854 655 345 58899999887765
No 106
>cd00059 FH Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
Probab=23.66 E-value=78 Score=28.30 Aligned_cols=44 Identities=20% Similarity=0.356 Sum_probs=30.9
Q ss_pred chHHHHHHHHHHhh-cccChhHHHHHHhcCCcccccchhhhHHHhcccC
Q 004163 259 SSLAISFLACHVVR-EAILPTDIVKWSIEGKIPYFAAFVEIEKRFGQTS 306 (771)
Q Consensus 259 ~TLAI~YLAcl~LR-~PV~lsDLiRWI~eg~IPY~~A~~~LPkeMk~rL 306 (771)
+=.+++.+|+.-.. -.+++.+|.+||++. .||++.. ++.|+...
T Consensus 5 sY~~LI~~Ai~~sp~~~lTL~eIy~~I~~~-~pyyr~~---~~gWknSI 49 (78)
T cd00059 5 SYSALIAMAIQSSPEKRLTLSEIYKWISDN-FPYFRDA---PAGWQNSI 49 (78)
T ss_pred CHHHHHHHHHHhCCCCCeeHHHHHHHHHHh-CCccccC---CCCCccce
Confidence 44567777766653 369999999998765 5999864 56665533
No 107
>COG2517 Predicted RNA-binding protein containing a C-terminal EMAP domain [General function prediction only]
Probab=23.25 E-value=41 Score=34.99 Aligned_cols=72 Identities=15% Similarity=0.292 Sum_probs=39.1
Q ss_pred HHHHHHHhhcccCceEeeCCCcccccccceeeEeeccCCcceeehhhHHHHHHHHhhhhhhcchhHHHHHHHHHHH
Q 004163 640 SAVKRLKLDMENNRFCYISPRVQIKRLDYLQYVRKSDEGALTYAAHADYYILLRACATIAQVDIRSMHMAVLSFER 715 (771)
Q Consensus 640 ~a~~~~~~~m~~~~f~y~~p~~~~~~~~y~~y~~~~~~~~~~~~~h~~y~~ll~~~a~~~~v~~~~~h~~v~~~er 715 (771)
+|++.|.++++..+|||+||.--+..-.++.-+-|..+=-.+-.--.||- +.|+--| =++|.+-.-+++++|
T Consensus 39 e~lksi~s~lQ~lrY~Yl~peel~~~e~~~~l~~~a~~ive~l~~ekdw~---~~~l~~a-~ev~fflnt~~~ldR 110 (219)
T COG2517 39 EALKSIESELQALRYSYLEPEELVDTEQMKDLKEKAEGIVEALGGEKDWS---TKFLEQA-DEVRFFLNTILNLDR 110 (219)
T ss_pred HHHHHHHHHHHhheeeccCHHHhcccHHHHHHHHHHHHHHHhcCCcchHH---HHHHHHH-HHHHHHHhchhhccc
Confidence 77889999999999999988765533223333222110001111122332 2333333 236666666777777
No 108
>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=23.03 E-value=42 Score=40.05 Aligned_cols=38 Identities=18% Similarity=0.475 Sum_probs=28.2
Q ss_pred ccccccccccCCCCCCc--------ee---ecCCcceecccCCeeeccc
Q 004163 4 GEGDIRRLKCKKCDNVG--------FE---CAYDGFYYCTHCNALDDEI 41 (771)
Q Consensus 4 ~~~~~r~~~C~~C~S~~--------w~---~~ddG~~yC~~CGhv~Eg~ 41 (771)
++-+....+|+.||... |. .+..-+|.|..||+.++..
T Consensus 194 sdqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~ 242 (557)
T PF05876_consen 194 SDQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEH 242 (557)
T ss_pred CCceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHH
Confidence 34456678999999874 42 2345799999999999863
No 109
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=22.93 E-value=28 Score=43.34 Aligned_cols=33 Identities=30% Similarity=0.641 Sum_probs=0.0
Q ss_pred ccccccCCCCCCceee--cC-----CcceecccCCeeecc
Q 004163 8 IRRLKCKKCDNVGFEC--AY-----DGFYYCTHCNALDDE 40 (771)
Q Consensus 8 ~r~~~C~~C~S~~w~~--~d-----dG~~yC~~CGhv~Eg 40 (771)
+-..+|+.||...|.. +. +=.|+|..||+..++
T Consensus 653 i~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~ 692 (900)
T PF03833_consen 653 IGRRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVEE 692 (900)
T ss_dssp ----------------------------------------
T ss_pred eecccCcccCCcchhhcCcccCCccccceeccccccccCc
Confidence 4445677777766532 11 123788888887654
No 110
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=22.69 E-value=26 Score=39.23 Aligned_cols=39 Identities=15% Similarity=0.296 Sum_probs=27.8
Q ss_pred cccccccCCCCCCceeecCCcceecccCCeeecccccccccc
Q 004163 7 DIRRLKCKKCDNVGFECAYDGFYYCTHCNALDDEIVETGVAD 48 (771)
Q Consensus 7 ~~r~~~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg~ve~~vDd 48 (771)
..+-++|..|=++. ++-++-||..|||..---+-..+++
T Consensus 239 r~~iLRCh~Cfsit---~~m~k~FCp~CG~~TL~K~aVsv~~ 277 (376)
T KOG2463|consen 239 RSYILRCHGCFSIT---SEMPKDFCPSCGHKTLTKCAVSVDE 277 (376)
T ss_pred hhheeEeeeeeEec---CccchhcccccCCCeeeEEEEEecC
Confidence 34568999997776 4678999999999966444334433
No 111
>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=22.60 E-value=45 Score=31.69 Aligned_cols=26 Identities=19% Similarity=0.593 Sum_probs=17.9
Q ss_pred cccCCCCCCceeecCCcceecccCCeee
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNALD 38 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv~ 38 (771)
.+|..|+ ..|.. .+-.+.|.+||.-.
T Consensus 71 ~~C~~Cg-~~~~~-~~~~~~CP~Cgs~~ 96 (115)
T TIGR00100 71 CECEDCS-EEVSP-EIDLYRCPKCHGIM 96 (115)
T ss_pred EEcccCC-CEEec-CCcCccCcCCcCCC
Confidence 5689998 55655 44466799998543
No 112
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.98 E-value=65 Score=27.44 Aligned_cols=26 Identities=15% Similarity=0.270 Sum_probs=21.2
Q ss_pred CCCCCCceee---cCCcceecccCCeeec
Q 004163 14 KKCDNVGFEC---AYDGFYYCTHCNALDD 39 (771)
Q Consensus 14 ~~C~S~~w~~---~ddG~~yC~~CGhv~E 39 (771)
.-|+..+|.+ +-|=+.-|..|||++-
T Consensus 17 H~Cg~NrwkIiRvGaDIkikC~nC~h~vm 45 (60)
T COG4481 17 HACGTNRWKIIRVGADIKIKCENCGHSVM 45 (60)
T ss_pred CccccceEEEEEecCcEEEEecCCCcEEE
Confidence 4689999944 6688999999999864
No 113
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.73 E-value=44 Score=40.74 Aligned_cols=25 Identities=20% Similarity=0.429 Sum_probs=16.8
Q ss_pred ccCCCCCCceeecCCcceecccCCeeecc
Q 004163 12 KCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 12 ~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
.|++||.. . ..|-.||.+||+.+..
T Consensus 29 ~Cp~CG~~---~-~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 29 PCPQCGTE---V-PVDEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCC---C-CcccccccccCCcccc
Confidence 46666665 3 5667788888877654
No 114
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=20.81 E-value=44 Score=34.12 Aligned_cols=31 Identities=23% Similarity=0.644 Sum_probs=21.7
Q ss_pred ccccccCCCCCCceeec---------------CCcceecccCCeee
Q 004163 8 IRRLKCKKCDNVGFECA---------------YDGFYYCTHCNALD 38 (771)
Q Consensus 8 ~r~~~C~~C~S~~w~~~---------------ddG~~yC~~CGhv~ 38 (771)
...-+|+.|+...-..+ .+-||+|..||.+-
T Consensus 95 ~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 95 PEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 33568999998764332 34588899999764
No 115
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=20.62 E-value=68 Score=26.87 Aligned_cols=32 Identities=31% Similarity=0.453 Sum_probs=23.5
Q ss_pred ccccccccCCCCCCc--e--eecCCcceecccCCee
Q 004163 6 GDIRRLKCKKCDNVG--F--ECAYDGFYYCTHCNAL 37 (771)
Q Consensus 6 ~~~r~~~C~~C~S~~--w--~~~ddG~~yC~~CGhv 37 (771)
...+..+|.+|.+.. . .....=.|.|..||+.
T Consensus 18 ~~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred cCceeEECcccchhhcccccccCCceEEEcCCCCCc
Confidence 556778999998874 2 2234558999999974
No 116
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.50 E-value=52 Score=31.63 Aligned_cols=31 Identities=0% Similarity=-0.259 Sum_probs=26.1
Q ss_pred ccccccCCCCCCceeecCCcceecccCCeeec
Q 004163 8 IRRLKCKKCDNVGFECAYDGFYYCTHCNALDD 39 (771)
Q Consensus 8 ~r~~~C~~C~S~~w~~~ddG~~yC~~CGhv~E 39 (771)
..+.+|++|+++-|.+ +---.+|.+||.+.-
T Consensus 7 GtKridPetg~KFYDL-NrdPiVsPytG~s~P 37 (129)
T COG4530 7 GTKRIDPETGKKFYDL-NRDPIVSPYTGKSYP 37 (129)
T ss_pred cccccCccccchhhcc-CCCccccCcccccch
Confidence 3467899999998888 778889999998764
No 117
>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=20.39 E-value=54 Score=26.31 Aligned_cols=26 Identities=19% Similarity=0.584 Sum_probs=13.4
Q ss_pred cccCCCCCCc--e-eecCCcceecccCCe
Q 004163 11 LKCKKCDNVG--F-ECAYDGFYYCTHCNA 36 (771)
Q Consensus 11 ~~C~~C~S~~--w-~~~ddG~~yC~~CGh 36 (771)
-+|..|+.+- | ...+++.-.|..||+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 4566666532 3 222345555666665
No 118
>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=20.23 E-value=75 Score=35.38 Aligned_cols=27 Identities=26% Similarity=0.659 Sum_probs=16.4
Q ss_pred cccccccCCCCCCceeecCCcceecccCCee
Q 004163 7 DIRRLKCKKCDNVGFECAYDGFYYCTHCNAL 37 (771)
Q Consensus 7 ~~r~~~C~~C~S~~w~~~ddG~~yC~~CGhv 37 (771)
..|...|.-|++ .|.. -+--|.+||+.
T Consensus 207 G~RyL~CslC~t-eW~~---~R~~C~~Cg~~ 233 (305)
T TIGR01562 207 GLRYLSCSLCAT-EWHY---VRVKCSHCEES 233 (305)
T ss_pred CceEEEcCCCCC-cccc---cCccCCCCCCC
Confidence 356666777764 3544 26677777763
No 119
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=20.20 E-value=68 Score=36.85 Aligned_cols=26 Identities=15% Similarity=0.254 Sum_probs=20.0
Q ss_pred ccCCCCCCceeecCCcceecccCCeeecc
Q 004163 12 KCKKCDNVGFECAYDGFYYCTHCNALDDE 40 (771)
Q Consensus 12 ~C~~C~S~~w~~~ddG~~yC~~CGhv~Eg 40 (771)
.|++|+... ...+.-.|.||||+...
T Consensus 217 ~C~~Cd~~~---~~~~~a~CpRC~~~L~~ 242 (403)
T TIGR00155 217 SCSACHTTI---LPAQEPVCPRCSTPLYV 242 (403)
T ss_pred cCCCCCCcc---CCCCCcCCcCCCCcccC
Confidence 399999843 34667789999999843
No 120
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.04 E-value=54 Score=31.15 Aligned_cols=26 Identities=15% Similarity=0.395 Sum_probs=16.5
Q ss_pred cccCCCCCCceeecCCcceecccCCee
Q 004163 11 LKCKKCDNVGFECAYDGFYYCTHCNAL 37 (771)
Q Consensus 11 ~~C~~C~S~~w~~~ddG~~yC~~CGhv 37 (771)
..|..|+. .|......++.|..||..
T Consensus 71 ~~C~~Cg~-~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 71 CWCETCQQ-YVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred EEcccCCC-eeecCCccCCcCcCcCCC
Confidence 46888883 444423344669999844
Done!