Query 034486
Match_columns 93
No_of_seqs 87 out of 103
Neff 3.5
Searched_HMMs 46136
Date Fri Mar 29 03:22:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034486.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034486hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01589 A_thal_3526 uncharac 100.0 2.4E-37 5.2E-42 196.8 6.7 57 9-65 1-57 (57)
2 PF09713 A_thal_3526: Plant pr 100.0 2.1E-36 4.5E-41 190.5 6.3 54 12-65 1-54 (54)
3 PF13565 HTH_32: Homeodomain-l 83.3 3.8 8.2E-05 24.9 4.6 42 9-50 33-76 (77)
4 COG1725 Predicted transcriptio 82.6 2.6 5.7E-05 30.3 4.2 51 5-55 10-63 (125)
5 smart00411 BHL bacterial (prok 81.4 3.4 7.3E-05 26.1 4.0 30 24-53 1-30 (90)
6 PF08986 DUF1889: Domain of un 76.5 2.8 6.1E-05 30.2 2.7 35 30-64 69-112 (119)
7 PF08145 BOP1NT: BOP1NT (NUC16 74.7 2.5 5.3E-05 34.0 2.3 32 7-42 213-244 (260)
8 PF14420 Clr5: Clr5 domain 72.9 9.6 0.00021 23.1 4.1 36 7-42 3-39 (54)
9 PF00216 Bac_DNA_binding: Bact 72.3 6.9 0.00015 24.5 3.5 30 24-53 1-30 (90)
10 smart00139 MyTH4 Domain in Myo 70.9 14 0.00029 26.4 5.1 52 1-52 33-90 (144)
11 TIGR00988 hip integration host 66.1 14 0.00031 23.8 4.1 30 24-53 1-31 (94)
12 TIGR00987 himA integration hos 64.7 14 0.00031 24.1 4.0 29 24-52 2-30 (96)
13 PRK10664 transcriptional regul 60.9 19 0.00041 23.7 4.0 24 24-47 1-24 (90)
14 PRK00285 ihfA integration host 60.5 19 0.00041 23.6 3.9 31 23-53 2-32 (99)
15 PRK00199 ihfB integration host 60.3 21 0.00046 23.1 4.1 29 24-52 1-30 (94)
16 PF14775 NYD-SP28_assoc: Sperm 58.2 44 0.00095 21.0 5.3 30 35-68 5-34 (60)
17 PRK14552 C/D box methylation g 56.7 20 0.00043 30.2 4.3 47 1-47 222-270 (414)
18 PF04340 DUF484: Protein of un 54.5 4.1 8.9E-05 30.3 0.0 11 53-63 16-26 (225)
19 PRK10753 transcriptional regul 54.5 28 0.00061 22.8 4.0 24 24-47 1-24 (90)
20 PF03918 CcmH: Cytochrome C bi 53.7 29 0.00062 25.2 4.3 37 2-38 52-88 (148)
21 PF03979 Sigma70_r1_1: Sigma-7 53.6 44 0.00095 21.4 4.7 53 7-60 4-57 (82)
22 PRK10963 hypothetical protein; 53.3 11 0.00024 28.4 2.1 22 23-63 2-23 (223)
23 COG3415 Transposase and inacti 52.9 31 0.00067 25.0 4.3 55 3-58 60-114 (138)
24 PF05402 PqqD: Coenzyme PQQ sy 52.8 46 0.00099 19.8 4.5 25 18-42 24-48 (68)
25 PF02082 Rrf2: Transcriptional 49.0 25 0.00054 22.2 3.0 27 29-55 27-53 (83)
26 TIGR01201 HU_rel DNA-binding p 49.0 34 0.00073 24.3 4.0 31 24-54 31-61 (145)
27 PF09280 XPC-binding: XPC-bind 48.1 35 0.00075 21.4 3.5 36 31-66 11-46 (59)
28 KOG3973 Uncharacterized conser 48.1 25 0.00054 30.4 3.6 57 12-68 141-220 (465)
29 TIGR03147 cyt_nit_nrfF cytochr 47.4 41 0.00088 24.3 4.2 37 3-39 53-89 (126)
30 COG4359 Uncharacterized conser 46.9 22 0.00048 28.2 3.0 27 21-47 56-82 (220)
31 TIGR01795 CM_mono_cladeE monof 45.6 37 0.00081 22.7 3.6 25 31-55 58-82 (94)
32 PRK05686 fliG flagellar motor 45.1 1.3E+02 0.0028 24.0 7.1 60 1-62 171-237 (339)
33 KOG2211 Predicted Golgi transp 44.1 30 0.00064 31.9 3.7 22 38-59 361-382 (797)
34 PF13720 Acetyltransf_11: Udp 43.9 90 0.0019 20.3 5.4 43 5-47 29-71 (83)
35 PLN02814 beta-glucosidase 43.1 18 0.00038 30.9 2.0 45 5-64 112-167 (504)
36 COG1725 Predicted transcriptio 43.0 44 0.00095 24.0 3.8 29 7-35 90-118 (125)
37 PF05295 Luciferase_N: Lucifer 42.8 49 0.0011 22.7 3.8 41 28-68 4-44 (82)
38 PF14164 YqzH: YqzH-like prote 41.7 33 0.00071 22.4 2.7 14 10-23 4-17 (64)
39 PF07527 Hairy_orange: Hairy O 41.7 56 0.0012 18.6 3.5 27 27-53 12-38 (43)
40 PF08006 DUF1700: Protein of u 41.6 60 0.0013 23.2 4.3 37 24-67 1-37 (181)
41 PF00784 MyTH4: MyTH4 domain; 41.4 96 0.0021 20.6 5.1 45 8-52 2-48 (114)
42 PF14769 CLAMP: Flagellar C1a 39.4 79 0.0017 20.9 4.4 47 6-52 18-73 (101)
43 smart00345 HTH_GNTR helix_turn 38.6 53 0.0011 18.2 3.0 27 29-55 22-48 (60)
44 PF06570 DUF1129: Protein of u 38.6 26 0.00057 25.8 2.2 34 50-83 1-35 (206)
45 PLN02849 beta-glucosidase 38.5 22 0.00047 30.3 1.9 35 29-64 124-169 (503)
46 PRK10144 formate-dependent nit 38.4 68 0.0015 23.2 4.2 46 3-48 53-105 (126)
47 PF05960 DUF885: Bacterial pro 37.6 2.3E+02 0.005 23.3 8.8 62 3-65 432-502 (549)
48 cd00591 HU_IHF Integration hos 37.3 75 0.0016 19.7 3.9 29 25-53 1-29 (87)
49 TIGR00207 fliG flagellar motor 37.3 2.1E+02 0.0046 23.0 7.3 59 2-62 170-234 (338)
50 PF10045 DUF2280: Uncharacteri 37.0 1.5E+02 0.0033 21.0 6.2 54 11-64 7-68 (104)
51 PRK05617 3-hydroxyisobutyryl-C 37.0 2.1E+02 0.0046 22.8 7.2 53 6-62 222-274 (342)
52 PLN02998 beta-glucosidase 36.6 24 0.00052 30.0 1.9 35 29-64 127-172 (497)
53 COG2920 DsrC Dissimilatory sul 35.5 1.2E+02 0.0026 21.8 5.0 50 27-79 27-76 (111)
54 PRK08091 ribulose-phosphate 3- 34.8 25 0.00053 27.3 1.5 34 24-58 1-34 (228)
55 smart00511 ORANGE Orange domai 34.8 78 0.0017 18.1 3.3 27 27-53 12-38 (45)
56 PF08004 DUF1699: Protein of u 34.4 95 0.0021 22.9 4.4 36 14-49 95-130 (131)
57 PF03965 Penicillinase_R: Peni 34.1 48 0.001 22.0 2.7 32 24-55 18-49 (115)
58 COG0776 HimA Bacterial nucleoi 34.1 54 0.0012 22.5 3.0 18 24-41 2-19 (94)
59 smart00760 Bac_DnaA_C Bacteria 33.2 43 0.00093 20.1 2.1 18 25-42 1-18 (60)
60 PRK14137 recX recombination re 32.9 1.3E+02 0.0028 22.7 5.1 53 10-63 37-97 (195)
61 PF04358 DsrC: DsrC like prote 32.7 1.7E+02 0.0037 20.3 5.3 34 27-63 25-58 (109)
62 TIGR03356 BGL beta-galactosida 32.5 42 0.0009 27.7 2.6 36 28-64 98-143 (427)
63 PF14278 TetR_C_8: Transcripti 32.1 77 0.0017 18.3 3.1 16 53-68 12-27 (77)
64 PF11417 Inhibitor_G39P: Loade 32.0 50 0.0011 21.4 2.4 31 24-54 1-42 (71)
65 PF09012 FeoC: FeoC like trans 32.0 54 0.0012 20.1 2.5 24 30-53 17-40 (69)
66 KOG1924 RhoA GTPase effector D 31.8 1.6E+02 0.0035 28.1 6.4 58 14-80 426-502 (1102)
67 PF00232 Glyco_hydro_1: Glycos 31.8 13 0.00027 30.6 -0.5 45 5-64 94-148 (455)
68 PF05066 HARE-HTH: HB1, ASXL, 31.3 79 0.0017 19.3 3.2 30 24-54 1-30 (72)
69 PRK07194 fliG flagellar motor 31.2 2.8E+02 0.006 22.3 7.2 57 2-61 167-230 (334)
70 PRK00117 recX recombination re 30.9 1.8E+02 0.004 20.1 5.6 65 1-66 1-71 (157)
71 smart00543 MIF4G Middle domain 30.9 1.7E+02 0.0038 19.8 6.1 52 11-62 15-73 (200)
72 TIGR02173 cyt_kin_arch cytidyl 30.8 1.5E+02 0.0033 19.7 4.8 41 25-65 101-141 (171)
73 TIGR00269 conserved hypothetic 30.8 1.4E+02 0.0031 19.9 4.6 40 22-62 8-60 (104)
74 cd02433 Nodulin-21_like_2 Nodu 30.6 93 0.002 24.0 4.1 52 10-65 86-137 (234)
75 smart00830 CM_2 Chorismate mut 30.5 66 0.0014 19.6 2.7 15 37-51 56-70 (79)
76 cd07377 WHTH_GntR Winged helix 29.8 87 0.0019 17.6 3.0 26 30-55 28-53 (66)
77 PRK12461 UDP-N-acetylglucosami 29.7 2.2E+02 0.0048 21.9 6.0 43 5-47 201-243 (255)
78 cd05062 PTKc_IGF-1R Catalytic 29.4 60 0.0013 23.0 2.7 25 10-34 248-276 (277)
79 PRK09239 chorismate mutase; Pr 29.3 95 0.0021 21.2 3.6 19 34-52 68-86 (104)
80 PRK05289 UDP-N-acetylglucosami 29.2 2.3E+02 0.005 21.6 6.0 43 5-47 205-247 (262)
81 cd08637 DNA_pol_A_pol_I_C Poly 29.0 3E+02 0.0065 22.4 6.9 43 25-68 35-85 (377)
82 TIGR02010 IscR iron-sulfur clu 29.0 71 0.0015 21.8 2.9 27 29-55 27-53 (135)
83 TIGR01803 CM-like chorismate m 28.2 77 0.0017 20.2 2.8 20 34-53 57-76 (82)
84 PF07531 TAFH: NHR1 homology t 27.4 1.1E+02 0.0024 21.2 3.7 37 5-41 22-58 (96)
85 PTZ00398 phosphoenolpyruvate c 27.4 62 0.0013 30.2 3.0 33 12-45 155-187 (974)
86 PF09278 MerR-DNA-bind: MerR, 27.2 1.4E+02 0.003 17.5 4.9 36 14-51 5-40 (65)
87 COG1412 Uncharacterized protei 27.2 1.5E+02 0.0034 21.4 4.5 41 15-56 19-59 (136)
88 PF12383 SARS_3b: Severe acute 27.1 62 0.0014 23.9 2.5 34 14-47 114-147 (153)
89 PRK14135 recX recombination re 26.7 2.8E+02 0.006 20.8 7.2 47 7-54 105-152 (263)
90 PF01466 Skp1: Skp1 family, di 26.7 76 0.0016 20.1 2.6 24 33-56 51-74 (78)
91 cd05094 PTKc_TrkC Catalytic do 26.6 80 0.0017 22.7 3.0 29 10-38 252-284 (291)
92 PRK00009 phosphoenolpyruvate c 25.8 70 0.0015 29.7 3.1 34 11-45 108-141 (911)
93 PF08970 Sda: Sporulation inhi 25.6 1.7E+02 0.0036 17.9 3.8 33 23-55 3-37 (46)
94 PF14039 YusW: YusW-like prote 25.6 61 0.0013 21.9 2.1 38 7-44 44-82 (92)
95 KOG1684 Enoyl-CoA hydratase [L 25.4 91 0.002 26.8 3.5 45 12-57 265-311 (401)
96 PF13625 Helicase_C_3: Helicas 25.1 96 0.0021 21.0 3.0 34 14-47 45-80 (129)
97 KOG1199 Short-chain alcohol de 24.9 55 0.0012 26.2 2.0 15 5-19 229-243 (260)
98 PF12685 SpoIIIAH: SpoIIIAH-li 24.8 75 0.0016 23.4 2.6 34 53-88 82-115 (196)
99 PF13936 HTH_38: Helix-turn-he 24.8 1.3E+02 0.0028 17.1 3.1 33 14-53 11-43 (44)
100 PF11626 Rap1_C: TRF2-interact 24.8 90 0.0019 20.2 2.7 38 16-53 1-38 (87)
101 PF03081 Exo70: Exo70 exocyst 24.6 2.8E+02 0.0062 21.5 5.9 75 7-81 248-329 (371)
102 KOG3779 Homeobox transcription 24.2 85 0.0018 28.3 3.2 37 26-62 689-728 (737)
103 cd04763 HTH_MlrA-like Helix-Tu 24.1 1.7E+02 0.0036 17.4 3.7 29 5-34 40-68 (68)
104 PLN02350 phosphogluconate dehy 24.0 1.7E+02 0.0037 25.1 4.9 45 1-47 178-223 (493)
105 PRK10857 DNA-binding transcrip 24.0 94 0.002 22.6 2.9 27 29-55 27-53 (164)
106 COG1498 SIK1 Protein implicate 23.7 1.3E+02 0.0028 25.7 4.1 51 1-51 200-252 (395)
107 PF10239 DUF2465: Protein of u 23.2 77 0.0017 25.7 2.5 27 42-68 184-210 (318)
108 PF14076 DUF4258: Domain of un 22.8 1.3E+02 0.0028 17.6 2.9 23 13-35 4-26 (73)
109 PF12980 DUF3864: Domain of Un 22.7 22 0.00047 24.3 -0.6 29 36-64 50-78 (82)
110 cd07765 KRAB_A-box KRAB (Krupp 22.5 34 0.00073 14.7 0.2 25 38-62 5-29 (40)
111 PF00538 Linker_histone: linke 22.5 1.8E+02 0.0039 18.2 3.7 47 7-53 4-54 (77)
112 cd05049 PTKc_Trk Catalytic dom 22.3 98 0.0021 21.8 2.7 25 10-34 251-279 (280)
113 TIGR03342 dsrC_tusE_dsvC sulfu 22.3 2.5E+02 0.0054 19.6 4.7 36 27-65 24-59 (108)
114 COG2963 Transposase and inacti 22.3 1.1E+02 0.0023 20.2 2.7 41 19-59 16-57 (116)
115 PF10474 DUF2451: Protein of u 21.8 1.5E+02 0.0033 22.7 3.8 51 10-64 92-143 (234)
116 PF14123 DUF4290: Domain of un 21.6 2.2E+02 0.0049 21.8 4.6 46 6-52 13-68 (176)
117 PF12415 rpo132: Poxvirus DNA 21.5 1E+02 0.0023 17.7 2.2 15 5-19 12-26 (33)
118 PF10364 NKWYS: Putative capsu 21.5 81 0.0018 23.2 2.2 33 3-35 7-39 (141)
119 PF08020 DUF1706: Protein of u 21.2 1.4E+02 0.0031 22.0 3.5 30 36-65 68-99 (166)
120 cd05116 PTKc_Syk Catalytic dom 21.1 1.2E+02 0.0026 21.2 2.9 26 10-35 225-254 (257)
121 PF13518 HTH_28: Helix-turn-he 21.1 1.5E+02 0.0033 16.2 2.9 27 29-55 14-40 (52)
122 TIGR01797 CM_P_1 chorismate mu 21.1 1.4E+02 0.003 19.1 3.0 19 36-54 59-77 (83)
123 KOG2431 1, 2-alpha-mannosidase 21.0 1E+02 0.0022 27.4 3.0 21 5-25 390-411 (546)
124 cd05093 PTKc_TrkB Catalytic do 21.0 99 0.0021 22.2 2.5 29 11-39 250-282 (288)
125 KOG2939 Uncharacterized conser 20.9 1.2E+02 0.0027 26.7 3.4 40 28-67 122-165 (502)
126 PRK11675 LexA regulated protei 20.7 1.9E+02 0.0041 19.9 3.7 26 10-35 60-85 (90)
127 PF04814 HNF-1_N: Hepatocyte n 20.7 1.1E+02 0.0025 23.4 2.9 23 14-36 11-33 (180)
128 PF15637 Tox-HNH-HHH: HNH/Endo 20.7 58 0.0013 23.6 1.2 24 45-68 38-61 (116)
129 PF13592 HTH_33: Winged helix- 20.7 1.6E+02 0.0035 17.6 3.1 38 9-47 7-44 (60)
130 PF00452 Bcl-2: Apoptosis regu 20.6 1.4E+02 0.003 19.0 3.0 37 49-85 6-45 (101)
131 TIGR02698 CopY_TcrY copper tra 20.3 1.9E+02 0.0041 20.0 3.7 32 24-55 19-50 (130)
132 PF02022 Integrase_Zn: Integra 20.2 1.1E+02 0.0025 17.8 2.2 21 30-50 12-32 (40)
133 PF12096 DUF3572: Protein of u 20.0 1.3E+02 0.0028 20.6 2.8 34 18-51 50-83 (88)
134 PF08914 Myb_DNA-bind_2: Rap1 20.0 69 0.0015 20.3 1.4 28 29-56 13-41 (65)
No 1
>TIGR01589 A_thal_3526 uncharacterized plant-specific domain TIGR01589. This model represents an uncharacterized plant-specific domain 57 residues in length. It is found toward the N-terminus of most proteins that contain it. Examples include at least 10 proteins from Arabidopsis thaliana and at least one from Oryza sativa.
Probab=100.00 E-value=2.4e-37 Score=196.80 Aligned_cols=57 Identities=46% Similarity=0.673 Sum_probs=55.6
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHHhc
Q 034486 9 IHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 9 I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~ 65 (93)
|++|||||||||++|||++|||++|++||||+|+||++||++||+||||||+|||.+
T Consensus 1 i~~Vq~lIE~Cl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~LekeN~eFF~aY~~~ 57 (57)
T TIGR01589 1 IDLVQNRIETCIQGYMSKEETVSFLFENAGISPKFTRFVWYLLEKENADFFRCYKTH 57 (57)
T ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHcCCCchhHHHHHHHHHHHHHHHHHHHhcC
Confidence 689999999999999999999999999999999999999999999999999999975
No 2
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=100.00 E-value=2.1e-36 Score=190.51 Aligned_cols=54 Identities=65% Similarity=1.058 Sum_probs=52.9
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHHhc
Q 034486 12 VHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 12 VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~ 65 (93)
||+||||||++|||++|||++|++||||+|+||.+||++||+||||||+||++|
T Consensus 1 Vq~lIErCl~~yMsk~E~v~~L~~~a~I~P~~T~~VW~~Le~eN~eFF~aY~~r 54 (54)
T PF09713_consen 1 VQNLIERCLQLYMSKEECVRALQKQANIEPVFTSTVWQKLEKENPEFFKAYYTR 54 (54)
T ss_pred CchHHHHHHHHcCCHHHHHHHHHHHcCCChHHHHHHHHHHHHHCHHHHHHhhcC
Confidence 799999999999999999999999999999999999999999999999999975
No 3
>PF13565 HTH_32: Homeodomain-like domain
Probab=83.34 E-value=3.8 Score=24.95 Aligned_cols=42 Identities=21% Similarity=0.136 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHh-hCCHHHHHHHHHhhcCCCc-hhHHHHHHH
Q 034486 9 IHLVHHLIEECLVF-NMSKEECMEALSKHANIKP-VITSTVWKE 50 (93)
Q Consensus 9 I~~VQ~LIErCLql-yMsk~E~v~~L~~~a~I~P-~~T~~VW~~ 50 (93)
-.+.+.+++-.... .+|..++...|..++||.. .=-++||+-
T Consensus 33 ~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 33 PEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 34445555554444 7999999999999999864 334567653
No 4
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=82.59 E-value=2.6 Score=30.26 Aligned_cols=51 Identities=18% Similarity=0.361 Sum_probs=45.9
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHH---HHHHHHhhcCCCchhHHHHHHHHHHhC
Q 034486 5 SASYIHLVHHLIEECLVFNMSKEE---CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E---~v~~L~~~a~I~P~~T~~VW~~LEkeN 55 (93)
..-|.+.++.+.+.++.--+...| -|+.|..+.+|+|..++-++++||++.
T Consensus 10 ~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG 63 (125)
T COG1725 10 KPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREG 63 (125)
T ss_pred CCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 466889999999999999998887 579999999999999999999999874
No 5
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=81.37 E-value=3.4 Score=26.13 Aligned_cols=30 Identities=17% Similarity=0.267 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034486 24 MSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~VW~~LEk 53 (93)
||++|+++.++++.++.+.-...|++.|..
T Consensus 1 mtk~eli~~ia~~~~~~~~~v~~vl~~l~~ 30 (90)
T smart00411 1 MTKSELIDAIAEKAGLSKKDAKAAVDAFLE 30 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 899999999999999998888888776654
No 6
>PF08986 DUF1889: Domain of unknown function (DUF1889); InterPro: IPR015079 This family consist of hypothetical bacterial proteins. ; PDB: 2JN8_A 2ES9_A.
Probab=76.50 E-value=2.8 Score=30.22 Aligned_cols=35 Identities=31% Similarity=0.618 Sum_probs=22.0
Q ss_pred HHHHHhhcCCCchhHHHH--HHH-------HHHhCHHHHHHHHh
Q 034486 30 MEALSKHANIKPVITSTV--WKE-------LEKENKEFFEAYAR 64 (93)
Q Consensus 30 v~~L~~~a~I~P~~T~~V--W~~-------LEkeNpeFFkaY~~ 64 (93)
|.+=-++-|-+|.||..| |.+ +-=.|||||..|..
T Consensus 69 v~aRg~qeGWn~gFT~k~agwaeki~sG~rivIKnPEyFs~YMr 112 (119)
T PF08986_consen 69 VTARGEQEGWNPGFTEKVAGWAEKIASGERIVIKNPEYFSSYMR 112 (119)
T ss_dssp HHHHHHHCT--HHHHHHHHHHHHHHHCT-----SSGGGS-HHHH
T ss_pred HHHhcccccCChhHHHHHHHHHHHHhcCCeeeecChHHHHHHHH
Confidence 344455679999999987 543 23379999999975
No 7
>PF08145 BOP1NT: BOP1NT (NUC169) domain; InterPro: IPR012953 WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed beta-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised beta-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins. The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a beta-propeller), TAFII transcription factor, and E3 ubiquitin ligase [, ]. In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events. This N-terminal domain is found in BOP1-like WD40 proteins. Bop1 is a nucleolar protein involved in rRNA processing, thereby controlling the cell cycle []. It is required for the maturation of the 25S and 5.8S ribosomal RNAs. It may serve as an essential factor in ribosome formation that coordinates processing of the spacer regions in pre-rRNA. The Pes1-Bop1 complex has several components: BOP1, GRWD1, PES1, ORC6L, and RPL3 and is involved in ribosome biogenesis and altered chromosome segregation. The overexpression of BOP1 increases the percentage of multipolar spindles in human cells. Deregulation of the BOP1 pathway may contribute to colorectal tumourigenesis in humans []. Elevated levels of Bop1 induces Bop1/WDR12 and Bop1/Pes1 subcomplexes and the assembly and integrity of the PeBoW complex is highly sensitive to changes in Bop1 protein levels []. Nop7p-Erb1p-Ytm1p, found in yeast, is potentially the homologous complex of Pes1-Bop1-WDR12 as it is involved in the control of ribosome biogenesis and S phase entry. The integrity of the PeBoW complex is required for ribosome biogenesis and cell proliferation in mammalian cells []. In Giardia, the species specific cytoskeleton protein, beta-giardin, interacts with Bop1 []. ; GO: 0006364 rRNA processing, 0005634 nucleus
Probab=74.72 E-value=2.5 Score=33.96 Aligned_cols=32 Identities=25% Similarity=0.488 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCch
Q 034486 7 SYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPV 42 (93)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~ 42 (93)
.|=..|+..-||||.|||-. ++.....||+|.
T Consensus 213 ~Y~~~i~ErFeRCLDLYLcP----R~~k~rlnidPe 244 (260)
T PF08145_consen 213 AYENFIKERFERCLDLYLCP----RVRKKRLNIDPE 244 (260)
T ss_pred hHHHHHHHHHHHhhhhhcCc----HhhcccCCCCHH
Confidence 45678999999999999955 455667899884
No 8
>PF14420 Clr5: Clr5 domain
Probab=72.85 E-value=9.6 Score=23.06 Aligned_cols=36 Identities=22% Similarity=0.134 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHH-HhhCCHHHHHHHHHhhcCCCch
Q 034486 7 SYIHLVHHLIEECL-VFNMSKEECMEALSKHANIKPV 42 (93)
Q Consensus 7 ~~I~~VQ~LIErCL-qlyMsk~E~v~~L~~~a~I~P~ 42 (93)
++-...+..|.+.- ...+|.+||++.|..++|..+.
T Consensus 3 ~~We~~K~~I~~LY~~e~~tl~~v~~~M~~~~~F~at 39 (54)
T PF14420_consen 3 EDWEPHKEEIERLYIDENKTLEEVMEIMKEEHGFKAT 39 (54)
T ss_pred chHHHHHHHHHHHHHhCCCcHHHHHHHHHHHhCCCcC
Confidence 44556677777644 6789999999999999999886
No 9
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=72.27 E-value=6.9 Score=24.55 Aligned_cols=30 Identities=17% Similarity=0.263 Sum_probs=24.0
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034486 24 MSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~VW~~LEk 53 (93)
||++|+++.+++..++...-...|...|.+
T Consensus 1 Mtk~eli~~ia~~~~~s~~~v~~vl~~~~~ 30 (90)
T PF00216_consen 1 MTKKELIKRIAEKTGLSKKDVEAVLDALFD 30 (90)
T ss_dssp EBHHHHHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 899999999999999888777766555443
No 10
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=70.89 E-value=14 Score=26.35 Aligned_cols=52 Identities=23% Similarity=0.319 Sum_probs=39.9
Q ss_pred CCC-c---hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCch--hHHHHHHHHH
Q 034486 1 MDD-S---SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPV--ITSTVWKELE 52 (93)
Q Consensus 1 ~~~-~---s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~--~T~~VW~~LE 52 (93)
||| + +...++.+|++++.|+..--=++|+.-.|-+|-.=+|. -..-.|+-|-
T Consensus 33 mgd~~~~~~~~~~~l~~~i~~~~~~~~~LrDEiy~QLiKQtt~Np~~~s~~rgW~Ll~ 90 (144)
T smart00139 33 MGDLPLPKPDSHLDLVQFILQKGLAHPELRDEIYCQLIKQLTDNPSRQSEERGWELLY 90 (144)
T ss_pred hcCCCCCCcchHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHH
Confidence 788 2 35678999999999999888899998888887655554 4455677663
No 11
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=66.10 E-value=14 Score=23.82 Aligned_cols=30 Identities=17% Similarity=0.261 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHhh-cCCCchhHHHHHHHHHH
Q 034486 24 MSKEECMEALSKH-ANIKPVITSTVWKELEK 53 (93)
Q Consensus 24 Msk~E~v~~L~~~-a~I~P~~T~~VW~~LEk 53 (93)
||++|+++.+.++ .++.+.-...|++.+-.
T Consensus 1 m~k~eli~~i~~~~~~~s~~~v~~vv~~~~~ 31 (94)
T TIGR00988 1 MTKSELIERIATQQSHLPAKDVEDAVKTMLE 31 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 8999999999975 47888888877765543
No 12
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=64.67 E-value=14 Score=24.13 Aligned_cols=29 Identities=14% Similarity=0.064 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHH
Q 034486 24 MSKEECMEALSKHANIKPVITSTVWKELE 52 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~VW~~LE 52 (93)
||+.|+++.++++.++...-...|.+.+.
T Consensus 2 mtk~eli~~ia~~~~~s~~~v~~vv~~~~ 30 (96)
T TIGR00987 2 LTKAEMSEYLFDELGLSKREAKELVELFF 30 (96)
T ss_pred CCHHHHHHHHHHHhCcCHHHHHHHHHHHH
Confidence 89999999999999988877777665543
No 13
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=60.93 E-value=19 Score=23.73 Aligned_cols=24 Identities=17% Similarity=0.335 Sum_probs=19.1
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHH
Q 034486 24 MSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~V 47 (93)
|||.|+++.|.+..++...-...+
T Consensus 1 MtK~eli~~ia~~~~~s~~~~~~~ 24 (90)
T PRK10664 1 MNKSQLIDKIAAGADISKAAAGRA 24 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHH
Confidence 899999999999888776655444
No 14
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=60.46 E-value=19 Score=23.58 Aligned_cols=31 Identities=13% Similarity=0.143 Sum_probs=25.0
Q ss_pred hCCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034486 23 NMSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 23 yMsk~E~v~~L~~~a~I~P~~T~~VW~~LEk 53 (93)
.||++|+++.+..+.++...-...|++.+.+
T Consensus 2 tmtk~el~~~ia~~~~~s~~~v~~vl~~~~~ 32 (99)
T PRK00285 2 TLTKADLAEALFEKVGLSKREAKELVELFFE 32 (99)
T ss_pred CcCHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4899999999999988888877777765543
No 15
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=60.26 E-value=21 Score=23.13 Aligned_cols=29 Identities=24% Similarity=0.304 Sum_probs=21.8
Q ss_pred CCHHHHHHHHHhh-cCCCchhHHHHHHHHH
Q 034486 24 MSKEECMEALSKH-ANIKPVITSTVWKELE 52 (93)
Q Consensus 24 Msk~E~v~~L~~~-a~I~P~~T~~VW~~LE 52 (93)
||+.|+++.+.++ .++...-...|++.+.
T Consensus 1 mtk~eli~~ia~~~~~~s~~~~~~vv~~~~ 30 (94)
T PRK00199 1 MTKSELIERLAARNPHLSAKDVENAVKEIL 30 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 8999999999874 5777777776665543
No 16
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=58.23 E-value=44 Score=20.97 Aligned_cols=30 Identities=27% Similarity=0.552 Sum_probs=24.0
Q ss_pred hhcCCCchhHHHHHHHHHHhCHHHHHHHHhcHHH
Q 034486 35 KHANIKPVITSTVWKELEKENKEFFEAYARKNAE 68 (93)
Q Consensus 35 ~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~~~~ 68 (93)
+-++|=|.=+.-+|+-|+. |++.|+.-..+
T Consensus 5 ~~~~vip~~~~~~W~~L~~----~l~rY~~vL~~ 34 (60)
T PF14775_consen 5 RLANVIPDEKIRLWDALEN----FLKRYNKVLLD 34 (60)
T ss_pred HHhhcCChHHHHHHHHHHH----HHHHHHHHHHH
Confidence 3468889999999999984 88999885444
No 17
>PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional
Probab=56.72 E-value=20 Score=30.17 Aligned_cols=47 Identities=23% Similarity=0.273 Sum_probs=40.1
Q ss_pred CCCc-hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcC-CCchhHHHH
Q 034486 1 MDDS-SASYIHLVHHLIEECLVFNMSKEECMEALSKHAN-IKPVITSTV 47 (93)
Q Consensus 1 ~~~~-s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~-I~P~~T~~V 47 (93)
||-. |..++..|++++++-+.++=.++++.++|...++ |.|.+|..|
T Consensus 222 ~G~~lse~dl~~I~~~a~~I~~L~e~R~~L~~yI~~~M~~iAPNLtaLV 270 (414)
T PRK14552 222 MGADLSEFDLEAIKKLANEILDLYKLREELEDYLETVMKEVAPNLTALV 270 (414)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHH
Confidence 4543 7788999999999999999999999999998765 489888875
No 18
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=54.54 E-value=4.1 Score=30.28 Aligned_cols=11 Identities=27% Similarity=0.691 Sum_probs=0.0
Q ss_pred HhCHHHHHHHH
Q 034486 53 KENKEFFEAYA 63 (93)
Q Consensus 53 keNpeFFkaY~ 63 (93)
.+|||||..|-
T Consensus 16 ~~~PdFf~~~~ 26 (225)
T PF04340_consen 16 RQHPDFFERHP 26 (225)
T ss_dssp -----------
T ss_pred HhCcHHHHhCH
Confidence 35788888775
No 19
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=54.52 E-value=28 Score=22.77 Aligned_cols=24 Identities=13% Similarity=0.333 Sum_probs=18.2
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHH
Q 034486 24 MSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~V 47 (93)
||+.|+++.|.++.++...-...|
T Consensus 1 M~K~eli~~ia~~~~~s~~~~~~~ 24 (90)
T PRK10753 1 MNKTQLIDVIADKAELSKTQAKAA 24 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHH
Confidence 899999999998877766544444
No 20
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=53.73 E-value=29 Score=25.21 Aligned_cols=37 Identities=24% Similarity=0.223 Sum_probs=28.1
Q ss_pred CCchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcC
Q 034486 2 DDSSASYIHLVHHLIEECLVFNMSKEECMEALSKHAN 38 (93)
Q Consensus 2 ~~~s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~ 38 (93)
+||.+..-.-..+.|.+=|.-.+|++||++++-.++|
T Consensus 52 ~~s~a~~A~dmR~~I~~~l~~G~s~~eI~~~~v~rYG 88 (148)
T PF03918_consen 52 ADSNAPIARDMRREIREMLAEGKSDEEIIDYFVERYG 88 (148)
T ss_dssp TT--SHHHHHHHHHHHHHHHHT--HHHHHHHHHHHHT
T ss_pred hhcCcHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcC
Confidence 3455666677888899999999999999999999888
No 21
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=53.57 E-value=44 Score=21.43 Aligned_cols=53 Identities=23% Similarity=0.361 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHH-HHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHH
Q 034486 7 SYIHLVHHLIEEC-LVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFE 60 (93)
Q Consensus 7 ~~I~~VQ~LIErC-LqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFk 60 (93)
.+...|+.||++- =+.|+|-+|+.++|. ...+.|.--..|...|+..+=+...
T Consensus 4 ~~~~~i~~Li~~gK~~G~lT~~eI~~~L~-~~~~~~e~id~i~~~L~~~gI~Vvd 57 (82)
T PF03979_consen 4 QYEEAIKKLIEKGKKKGYLTYDEINDALP-EDDLDPEQIDEIYDTLEDEGIEVVD 57 (82)
T ss_dssp HHHHHHHHHHHHHHHHSS-BHHHHHHH-S--S---HHHHHHHHHHHHTT----B-
T ss_pred hhHHHHHHHHHHHhhcCcCCHHHHHHHcC-ccCCCHHHHHHHHHHHHHCCCEEec
Confidence 3557788899865 478999999999999 5679999999998888887655443
No 22
>PRK10963 hypothetical protein; Provisional
Probab=53.26 E-value=11 Score=28.40 Aligned_cols=22 Identities=23% Similarity=0.431 Sum_probs=15.6
Q ss_pred hCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHH
Q 034486 23 NMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYA 63 (93)
Q Consensus 23 yMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~ 63 (93)
.||.++|+.+|. +|||||..+-
T Consensus 2 ~l~~~~V~~yL~-------------------~~PdFf~~h~ 23 (223)
T PRK10963 2 ELDDRAVVDYLL-------------------QNPDFFIRNA 23 (223)
T ss_pred CCCHHHHHHHHH-------------------HCchHHhhCH
Confidence 367777777776 5788887663
No 23
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.85 E-value=31 Score=25.04 Aligned_cols=55 Identities=13% Similarity=0.047 Sum_probs=43.4
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHH
Q 034486 3 DSSASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEF 58 (93)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeF 58 (93)
.|+.-.-..++-+.|.|=+.+.+..+++..|..++||.=+-. .||.-|.+.-=.|
T Consensus 60 rP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~-~v~~~l~~~Glsy 114 (138)
T COG3415 60 RPRKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHAS-AVRRLLHELGLSY 114 (138)
T ss_pred CCcccCHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHH-HHHHHHHHcCCCc
Confidence 344444567788889999999999999999999999987665 8999888764333
No 24
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=52.78 E-value=46 Score=19.76 Aligned_cols=25 Identities=28% Similarity=0.321 Sum_probs=17.5
Q ss_pred HHHHhhCCHHHHHHHHHhhcCCCch
Q 034486 18 ECLVFNMSKEECMEALSKHANIKPV 42 (93)
Q Consensus 18 rCLqlyMsk~E~v~~L~~~a~I~P~ 42 (93)
+++.--.|.+|+++.|.++++++|.
T Consensus 24 ~~~~g~~t~~ei~~~l~~~y~~~~~ 48 (68)
T PF05402_consen 24 ELLDGPRTVEEIVDALAEEYDVDPE 48 (68)
T ss_dssp HH--SSS-HHHHHHHHHHHTT--HH
T ss_pred HHccCCCCHHHHHHHHHHHcCCCHH
Confidence 3346778999999999999999998
No 25
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=49.05 E-value=25 Score=22.16 Aligned_cols=27 Identities=15% Similarity=0.339 Sum_probs=22.5
Q ss_pred HHHHHHhhcCCCchhHHHHHHHHHHhC
Q 034486 29 CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 29 ~v~~L~~~a~I~P~~T~~VW~~LEkeN 55 (93)
.++.|.+..+|.|.+..-|-+.|++.+
T Consensus 27 s~~eiA~~~~i~~~~l~kil~~L~~~G 53 (83)
T PF02082_consen 27 SSKEIAERLGISPSYLRKILQKLKKAG 53 (83)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHhhCC
Confidence 467788889999999999999999864
No 26
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=48.98 E-value=34 Score=24.35 Aligned_cols=31 Identities=16% Similarity=0.213 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHHh
Q 034486 24 MSKEECMEALSKHANIKPVITSTVWKELEKE 54 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~VW~~LEke 54 (93)
||++|+++.++++.++.+.-...|+..|...
T Consensus 31 mt~~el~~~Ia~~s~~s~~dv~~vl~~l~~~ 61 (145)
T TIGR01201 31 IDFEEIAELIAEESSLSPGDVKGIIDRLAYV 61 (145)
T ss_pred cCHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 8999999999999999999999888877654
No 27
>PF09280 XPC-binding: XPC-binding domain; InterPro: IPR015360 Members of this entry adopt a structure consisting of four alpha helices, arranged in an array. They bind specifically and directly to the xeroderma pigmentosum group C protein (XPC) to initiate nucleotide excision repair []. ; GO: 0003684 damaged DNA binding, 0006289 nucleotide-excision repair, 0043161 proteasomal ubiquitin-dependent protein catabolic process; PDB: 1PVE_A 1QZE_A 1OQY_A 1TP4_A 1X3W_B 3ESW_B 2QSG_X 2QSF_X 1X3Z_B 2QSH_X ....
Probab=48.12 E-value=35 Score=21.41 Aligned_cols=36 Identities=11% Similarity=0.296 Sum_probs=26.6
Q ss_pred HHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHHhcH
Q 034486 31 EALSKHANIKPVITSTVWKELEKENKEFFEAYARKN 66 (93)
Q Consensus 31 ~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~~ 66 (93)
..|.....=+|..-..|.++|.+.||+.|+.-....
T Consensus 11 ~~lR~~vq~NP~lL~~lLqql~~~nP~l~q~I~~n~ 46 (59)
T PF09280_consen 11 QQLRQLVQQNPQLLPPLLQQLGQSNPQLLQLIQQNP 46 (59)
T ss_dssp HHHHHHHHC-GGGHHHHHHHHHCCSHHHHHHHHHTH
T ss_pred HHHHHHHHHCHHHHHHHHHHHhccCHHHHHHHHHCH
Confidence 334444455799999999999999999998765543
No 28
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=48.07 E-value=25 Score=30.39 Aligned_cols=57 Identities=23% Similarity=0.458 Sum_probs=39.3
Q ss_pred HHHHHH-HHHHhhCCHH-------HHHHHHHh-----hcCCCchh----------HHHHHHHHHHhCHHHHHHHHhcHHH
Q 034486 12 VHHLIE-ECLVFNMSKE-------ECMEALSK-----HANIKPVI----------TSTVWKELEKENKEFFEAYARKNAE 68 (93)
Q Consensus 12 VQ~LIE-rCLqlyMsk~-------E~v~~L~~-----~a~I~P~~----------T~~VW~~LEkeNpeFFkaY~~~~~~ 68 (93)
|+.+|+ -|..+.|++- ...+++.. -+++.|.. +..-|.++|++|.+|=+.||.||-.
T Consensus 141 v~q~i~~~~~~L~~~k~p~Nin~~~lfe~i~~kl~~ai~kv~p~~~~~PLlKkpl~~a~w~~iE~~~~~~~~ey~~Rr~l 220 (465)
T KOG3973|consen 141 VTQLIDSALRTLNFPKQPGNINEWKLFETIRQKLDGAIKKVSPSQRSHPLLKKPLDEATWPEIEKQCESFSREYYNRRLL 220 (465)
T ss_pred HHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHHhHHhcCCHhhcCCchhcCcCChhhHHHHHHHHHHHHHHHHHHHHH
Confidence 566666 5778887752 22333322 13555543 4678999999999999999998765
No 29
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=47.39 E-value=41 Score=24.31 Aligned_cols=37 Identities=8% Similarity=0.062 Sum_probs=31.2
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCC
Q 034486 3 DSSASYIHLVHHLIEECLVFNMSKEECMEALSKHANI 39 (93)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I 39 (93)
||.+..-.-..+.|-+=+.-.+|.+||++++-++.|-
T Consensus 53 dS~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~ 89 (126)
T TIGR03147 53 ESNSPIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGD 89 (126)
T ss_pred hcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCC
Confidence 5666666777888888899999999999999999883
No 30
>COG4359 Uncharacterized conserved protein [Function unknown]
Probab=46.94 E-value=22 Score=28.19 Aligned_cols=27 Identities=33% Similarity=0.334 Sum_probs=23.5
Q ss_pred HhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034486 21 VFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 21 qlyMsk~E~v~~L~~~a~I~P~~T~~V 47 (93)
..+.|-+||.+.|.+.+.|+|.|-..|
T Consensus 56 ~i~~s~~Eile~llk~i~Idp~fKef~ 82 (220)
T COG4359 56 SIHSSLEEILEFLLKDIKIDPGFKEFV 82 (220)
T ss_pred hcCCCHHHHHHHHHhhcccCccHHHHH
Confidence 346788999999999999999998766
No 31
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=45.56 E-value=37 Score=22.74 Aligned_cols=25 Identities=16% Similarity=0.210 Sum_probs=19.4
Q ss_pred HHHHhhcCCCchhHHHHHHHHHHhC
Q 034486 31 EALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 31 ~~L~~~a~I~P~~T~~VW~~LEkeN 55 (93)
..+..+.|++|.|...+|+-+-.+.
T Consensus 58 ~~~a~~~gl~p~~~e~i~~~i~~es 82 (94)
T TIGR01795 58 RRLAIDAGLDPEFAEKFLNFIVTEV 82 (94)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHH
Confidence 3445678999999999998876653
No 32
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=45.13 E-value=1.3e+02 Score=23.96 Aligned_cols=60 Identities=18% Similarity=0.257 Sum_probs=43.4
Q ss_pred CCCchHHHHHHHHHHHHHHHHhhC-C------HHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHH
Q 034486 1 MDDSSASYIHLVHHLIEECLVFNM-S------KEECMEALSKHANIKPVITSTVWKELEKENKEFFEAY 62 (93)
Q Consensus 1 ~~~~s~~~I~~VQ~LIErCLqlyM-s------k~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY 62 (93)
||.-+.+-++.|-..+++||..-. + --+.|-.+.+ ++++.-...|...|++.+|++.+.=
T Consensus 171 l~~v~~~~~~~i~~~L~~~l~~~~~~~~~~~~g~~~~a~Iln--~~~~~~~~~il~~L~~~d~~~a~~I 237 (339)
T PRK05686 171 LEGVSPEALKEVEEVLEKKLSSMANADRTKMGGVKTVAEILN--NLDRQTEKTILESLEEEDPELAEKI 237 (339)
T ss_pred cCCCCHHHHHHHHHHHHHHHhhcccccccccCcHHHHHHHHh--cCCchHHHHHHHHHHhhCHHHHHHH
Confidence 455678888889899999997522 1 1133434443 5777778899999999999998764
No 33
>KOG2211 consensus Predicted Golgi transport complex 1 protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=44.08 E-value=30 Score=31.93 Aligned_cols=22 Identities=32% Similarity=0.505 Sum_probs=18.0
Q ss_pred CCCchhHHHHHHHHHHhCHHHH
Q 034486 38 NIKPVITSTVWKELEKENKEFF 59 (93)
Q Consensus 38 ~I~P~~T~~VW~~LEkeNpeFF 59 (93)
+++|.++..+|++|++.=--=|
T Consensus 361 ~gd~cI~~rfw~~l~qal~sqf 382 (797)
T KOG2211|consen 361 NGDKCIPERFWKKLEQALHSQF 382 (797)
T ss_pred ccchhHHHHHHHHHHHHHHHHH
Confidence 8999999999999998644333
No 34
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=43.85 E-value=90 Score=20.33 Aligned_cols=43 Identities=19% Similarity=0.186 Sum_probs=34.4
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034486 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~V 47 (93)
|.++|..++.....=+...++.+|.++.|.+...=.|.+...|
T Consensus 29 s~~~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~~~~~v~~~~ 71 (83)
T PF13720_consen 29 SKEEISALRRAYRILFRSGLTLEEALEELEEEYPDSPEVREIV 71 (83)
T ss_dssp -HHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTTSCHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhccCCHHHHHHH
Confidence 5778888888888878788899999999998777788887766
No 35
>PLN02814 beta-glucosidase
Probab=43.11 E-value=18 Score=30.87 Aligned_cols=45 Identities=27% Similarity=0.342 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHH---HHH--------HhCHHHHHHHHh
Q 034486 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWK---ELE--------KENKEFFEAYAR 64 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~---~LE--------keNpeFFkaY~~ 64 (93)
..+-|+.=.++|..|+. +||+|.+|..=|. -|+ ++..++|..|-.
T Consensus 112 N~~Gl~fY~~lId~l~~---------------~GI~P~VTL~H~dlP~~L~~~yGGW~n~~~i~~F~~YA~ 167 (504)
T PLN02814 112 NPKGLLFYKNLIKELRS---------------HGIEPHVTLYHYDLPQSLEDEYGGWINRKIIEDFTAFAD 167 (504)
T ss_pred CHHHHHHHHHHHHHHHH---------------cCCceEEEecCCCCCHHHHHhcCCcCChhHHHHHHHHHH
Confidence 34555666666666664 4999999987662 333 466778888854
No 36
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=43.02 E-value=44 Score=24.00 Aligned_cols=29 Identities=28% Similarity=0.310 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 034486 7 SYIHLVHHLIEECLVFNMSKEECMEALSK 35 (93)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk~E~v~~L~~ 35 (93)
.....++++|+.|..+.+|++|+.+.|.+
T Consensus 90 ~~~~~l~~~I~~~~~~G~s~eei~~~~~~ 118 (125)
T COG1725 90 LAEEELEEFIEEAKALGLSLEEILELLKE 118 (125)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 34567899999999999999999998875
No 37
>PF05295 Luciferase_N: Luciferase/LBP N-terminal domain; InterPro: IPR007959 Proteins in this entry belong to a family of dinoflagellate luciferase and luciferin binding proteins. Luciferase is involved in catalysing the light emitting reaction in bioluminescence and luciferin binding protein (LBP) is known to bind to luciferin (the substrate for luciferase) to stop it reacting with the enzyme and therefore switching off the bioluminescence function. The expression of these two proteins is controlled by a circadian clock at the translational level, with synthesis and degradation occurring on a daily basis []. This entry consists of a presumed N-terminal domain that is conserved between dinoflagellate luciferase and luciferin binding proteins. This domain is not, however, the catalytic part of the protein. It has been suggested that this region may mediate an interaction between LBP and Luciferase or their association with the vacuolar membrane []. More information about these proteins can be found at Protein of the Month: Luciferase [].
Probab=42.83 E-value=49 Score=22.69 Aligned_cols=41 Identities=20% Similarity=0.274 Sum_probs=36.2
Q ss_pred HHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHHhcHHH
Q 034486 28 ECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARKNAE 68 (93)
Q Consensus 28 E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~~~~ 68 (93)
|....|.+.++++|.+-..+=+.|.-++-.=|.-|.++-+-
T Consensus 4 ql~~FLt~dakvD~~vv~ymTk~L~lesvsDFAn~WTs~ey 44 (82)
T PF05295_consen 4 QLAQFLTNDAKVDPKVVAYMTKQLQLESVSDFANYWTSAEY 44 (82)
T ss_pred HHHHHHhcccccCHHHHHHHHhhcchhhHHHHHhhhhHHHH
Confidence 67888999999999999999999999999889888876443
No 38
>PF14164 YqzH: YqzH-like protein
Probab=41.73 E-value=33 Score=22.44 Aligned_cols=14 Identities=29% Similarity=0.553 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHhh
Q 034486 10 HLVHHLIEECLVFN 23 (93)
Q Consensus 10 ~~VQ~LIErCLqly 23 (93)
.+++.+|-+||+.|
T Consensus 4 k~I~Kmi~~~l~QY 17 (64)
T PF14164_consen 4 KLIEKMIINCLRQY 17 (64)
T ss_pred HHHHHHHHHHHHHh
Confidence 56888999999999
No 39
>PF07527 Hairy_orange: Hairy Orange; InterPro: IPR003650 This domain confers specificity among members of the Hairy/E(SPL) family. HES-2 (hairy and enhancer of split 2) is a transcription factor, and the hairy protein is a pair-rule protein that regulates embryonic segmentation and adult bristle patterning. These proteins are transcriptional repressors of genes that require the BHLH protein for their transcription.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DB7_A.
Probab=41.68 E-value=56 Score=18.63 Aligned_cols=27 Identities=19% Similarity=0.310 Sum_probs=20.3
Q ss_pred HHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034486 27 EECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 27 ~E~v~~L~~~a~I~P~~T~~VW~~LEk 53 (93)
.|+.++|....+++|.+..-+-+.|..
T Consensus 12 ~Ev~~fL~~~~~~~~~~~~rLl~HL~~ 38 (43)
T PF07527_consen 12 NEVSRFLSSVEGVDPGVRARLLSHLQS 38 (43)
T ss_dssp HHHHHHHHHTS---THHHHHHHHHHHH
T ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHH
Confidence 589999999999999998888887765
No 40
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=41.62 E-value=60 Score=23.21 Aligned_cols=37 Identities=27% Similarity=0.388 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHHhcHH
Q 034486 24 MSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARKNA 67 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~~~ 67 (93)
|||+|-++.|.++.+-=|.=. .++.=+||+.|...+.
T Consensus 1 M~k~efL~~L~~~L~~lp~~e-------~~e~l~~Y~e~f~d~~ 37 (181)
T PF08006_consen 1 MNKNEFLNELEKYLKKLPEEE-------REEILEYYEEYFDDAG 37 (181)
T ss_pred CCHHHHHHHHHHHHHcCCHHH-------HHHHHHHHHHHHHHhh
Confidence 899999999988765333222 1445567777755433
No 41
>PF00784 MyTH4: MyTH4 domain; InterPro: IPR000857 The microtubule-based kinesin motors and actin-based myosin motors generate movements required for intracellular trafficking, cell division, and muscle contraction. In general, these proteins consist of a motor domain that generates movement and a tail region that varies widely from class to class and is thought to mediate many of the regulatory or cargo binding functions specific to each class of motor []. The Myosin Tail Homology 4 (MyTH4) domain has been identified as a conserved domain in the tail domains of several different unconventional myosins [] and a plant kinesin-like protein [], but has more recently been found in several non-motor proteins []. Although the function is not yet fully understood, there is an evidence that the MyTH4 domain of Myosin-X (Myo10) binds to microtubules and thus could provide a link between an actin-based motor protein and the microtubule cytoskeleton []. The MyTH4 domain is found in one or two copies associated with other domains, such as myosin head, kinesin motor, FERM, PH, SH3 and IQ. The domain is predicted to be largely alpha-helical, interrupted by three or four turns. The MyTH4 domain contains four highly conserved regions designated MGD (consensus sequence L(K/R)(F/Y)MGDhP, LRDE (consensus LRDEhYCQhhKQHxxxN), RGW (consensus RGWxLh), and ELEA (RxxPPSxhELEA), where h indicates a hydrophobic residue and x is any residue [].; GO: 0005856 cytoskeleton; PDB: 3AU5_A 3AU4_A 3PZD_A 3PVL_A.
Probab=41.37 E-value=96 Score=20.65 Aligned_cols=45 Identities=20% Similarity=0.282 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCch--hHHHHHHHHH
Q 034486 8 YIHLVHHLIEECLVFNMSKEECMEALSKHANIKPV--ITSTVWKELE 52 (93)
Q Consensus 8 ~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~--~T~~VW~~LE 52 (93)
.++.+|++|..|+..--=++|+.-.|-+|-+=+|. ...-.|+-|-
T Consensus 2 ~~~l~~~Il~~~l~~~~LrDEiy~QliKQtt~np~~~s~~r~W~Ll~ 48 (114)
T PF00784_consen 2 EIDLIQNILQKGLENPELRDEIYCQLIKQTTNNPSPDSCIRGWQLLA 48 (114)
T ss_dssp HHHHHHHHHHHHHH-CCHHHHHHHHHHHHTSS-SSCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcchhhHHHHHHHHHHHHHCCCchhhHHHHHHHHH
Confidence 46789999999999999999999999998776664 4567898774
No 42
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=39.37 E-value=79 Score=20.89 Aligned_cols=47 Identities=13% Similarity=0.306 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHHHhh---cCCC------chhHHHHHHHHH
Q 034486 6 ASYIHLVHHLIEECLVFNMSKEECMEALSKH---ANIK------PVITSTVWKELE 52 (93)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~---a~I~------P~~T~~VW~~LE 52 (93)
+.-...++.+.+.|+...||.+++++.+.+- .+|. |.|+..-.+.+-
T Consensus 18 s~~~~i~~~ll~~~i~~~~~~~~~~~~fk~~l~~~sv~rpp~~~~iFs~~~~~~i~ 73 (101)
T PF14769_consen 18 SAFLSILKELLEKNIEKGMSLEDSFKYFKELLLRHSVQRPPFSIGIFSVDQVKAII 73 (101)
T ss_pred HHHHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHhccCCCCcccCcCCHHHHHHHH
Confidence 3445678889999999999999999988763 3444 336665555544
No 43
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=38.62 E-value=53 Score=18.17 Aligned_cols=27 Identities=15% Similarity=0.201 Sum_probs=21.3
Q ss_pred HHHHHHhhcCCCchhHHHHHHHHHHhC
Q 034486 29 CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 29 ~v~~L~~~a~I~P~~T~~VW~~LEkeN 55 (93)
.+..|.++.+|.+..-.-..+.|++++
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~g 48 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAEG 48 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 367788888999888888888888754
No 44
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=38.57 E-value=26 Score=25.81 Aligned_cols=34 Identities=26% Similarity=0.351 Sum_probs=20.1
Q ss_pred HHHHhCHHHHHHHHhcH-HHHHhHHHHHHHHHHHH
Q 034486 50 ELEKENKEFFEAYARKN-AERATVMETRERIEKIL 83 (93)
Q Consensus 50 ~LEkeNpeFFkaY~~~~-~~~~~~~~~~~~iq~~~ 83 (93)
+|-++|.||...-.+.. ....++++..+++..|+
T Consensus 1 ~LTkkN~~y~~~l~~~L~~~~~~e~~~e~~L~eil 35 (206)
T PF06570_consen 1 KLTKKNQEYIFDLRKYLRSSGVSEEEIEELLEEIL 35 (206)
T ss_pred CCchHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 46789999987665433 22334555555555544
No 45
>PLN02849 beta-glucosidase
Probab=38.47 E-value=22 Score=30.35 Aligned_cols=35 Identities=31% Similarity=0.398 Sum_probs=21.7
Q ss_pred HHHHHHhhcCCCchhHHHHH---HHHHH--------hCHHHHHHHHh
Q 034486 29 CMEALSKHANIKPVITSTVW---KELEK--------ENKEFFEAYAR 64 (93)
Q Consensus 29 ~v~~L~~~a~I~P~~T~~VW---~~LEk--------eNpeFFkaY~~ 64 (93)
+++.|.+ +||+|.+|..=| ..|++ +..++|..|-.
T Consensus 124 lid~l~~-~GI~P~VTL~H~dlP~~L~~~yGGW~nr~~v~~F~~YA~ 169 (503)
T PLN02849 124 FIQELVK-HGIEPHVTLFHYDHPQYLEDDYGGWINRRIIKDFTAYAD 169 (503)
T ss_pred HHHHHHH-cCCeEEEeecCCCCcHHHHHhcCCcCCchHHHHHHHHHH
Confidence 3444443 499999998655 22443 45677888854
No 46
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=38.41 E-value=68 Score=23.20 Aligned_cols=46 Identities=17% Similarity=0.216 Sum_probs=35.4
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCC----Cch---hHHHHH
Q 034486 3 DSSASYIHLVHHLIEECLVFNMSKEECMEALSKHANI----KPV---ITSTVW 48 (93)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I----~P~---~T~~VW 48 (93)
||.+....-..+.|-+=+.-.+|++||+++|-+..|= +|- .|..+|
T Consensus 53 dSna~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~~Pp~~~~t~~LW 105 (126)
T PRK10144 53 ESNAPVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGDFVRYNPPLTGQTLVLW 105 (126)
T ss_pred hcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCCCCcchHHHH
Confidence 5556666677788888899999999999999998883 454 355555
No 47
>PF05960 DUF885: Bacterial protein of unknown function (DUF885); InterPro: IPR010281 This family consists of hypothetical bacterial proteins.; PDB: 3O0Y_B 3U24_A 3IUK_A.
Probab=37.63 E-value=2.3e+02 Score=23.27 Aligned_cols=62 Identities=6% Similarity=0.055 Sum_probs=49.4
Q ss_pred CchHHHHHHHHHHHHHHHHh---------hCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHHhc
Q 034486 3 DSSASYIHLVHHLIEECLVF---------NMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLql---------yMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~ 65 (93)
+.+...+-+.+..+-||+.+ -||.+|+++.|.++.+..+.....-|...-. +|..+-+|+.-
T Consensus 432 ~~p~~~lg~l~~~l~ra~r~vvD~glH~~~wt~e~a~~~l~~~~~~~~~~a~~ev~ry~~-~Pgq~~sY~~G 502 (549)
T PF05960_consen 432 DDPLDRLGQLNDELWRAARLVVDTGLHYGGWTREQAIDYLVENTGFSEEEAESEVDRYIS-SPGQALSYKVG 502 (549)
T ss_dssp CSHHHHHHHHHHHHHHHHHHHHHHHHHCCB--HHHHHHHHHHHS-S-HHHHHHHHHHHHH-STTGGGHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHh-CcHHHHHHHHH
Confidence 45677788888888888875 5899999999999999999888888877776 99999999874
No 48
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=37.34 E-value=75 Score=19.65 Aligned_cols=29 Identities=14% Similarity=0.210 Sum_probs=22.0
Q ss_pred CHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034486 25 SKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 25 sk~E~v~~L~~~a~I~P~~T~~VW~~LEk 53 (93)
||+|+++.|+...++.+.-...|...|..
T Consensus 1 ~K~~l~~~ia~~~~~~~~~v~~vl~~~~~ 29 (87)
T cd00591 1 TKSELIEAIAEKTGLSKKDAEAAVDAFLD 29 (87)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 68889999999888888777766555443
No 49
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=37.27 E-value=2.1e+02 Score=23.00 Aligned_cols=59 Identities=17% Similarity=0.133 Sum_probs=41.5
Q ss_pred CCchHHHHHHHHHHHHHHHHhhCCH------HHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHH
Q 034486 2 DDSSASYIHLVHHLIEECLVFNMSK------EECMEALSKHANIKPVITSTVWKELEKENKEFFEAY 62 (93)
Q Consensus 2 ~~~s~~~I~~VQ~LIErCLqlyMsk------~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY 62 (93)
|..|.+.+..|-..+++|+..+-+. -+.+..+.+ .+++.-...|...|++.+|++...=
T Consensus 170 ~~vs~~~i~~ie~~L~~~~~~~~~~~~~~gG~~~~a~ILN--~~~~~~~~~il~~L~~~dp~la~~I 234 (338)
T TIGR00207 170 GRTSPEVVAEVERVLEGKLDSLNSDYTKMGGVRAVAEIIN--LMDRKTEKTIITSLEEFDPELAEEI 234 (338)
T ss_pred CCCCHHHHHHHHHHHHHHHHhhccccccCChHHHHHHHHH--hCCchHHHHHHHHHHHhCHHHHHHH
Confidence 4457788888888999998865431 133333333 4566666799999999999998754
No 50
>PF10045 DUF2280: Uncharacterized conserved protein (DUF2280); InterPro: IPR018738 This entry is represented by Burkholderia phage Bups phi1, Orf2.36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=37.03 E-value=1.5e+02 Score=21.03 Aligned_cols=54 Identities=22% Similarity=0.218 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHhhcCCCc--------hhHHHHHHHHHHhCHHHHHHHHh
Q 034486 11 LVHHLIEECLVFNMSKEECMEALSKHANIKP--------VITSTVWKELEKENKEFFEAYAR 64 (93)
Q Consensus 11 ~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P--------~~T~~VW~~LEkeNpeFFkaY~~ 64 (93)
-|+--|=+-|--|.|+.|++++..+.+||+= .=|...=+.|-++-.+.|+....
T Consensus 7 ~vK~FIVQ~LAcfdTPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG~~Ls~k~~~lF~~TR~ 68 (104)
T PF10045_consen 7 EVKAFIVQSLACFDTPSEVAEAVKEEFGIDVSRQQVESYDPTKRAGRDLSKKWVDLFEETRK 68 (104)
T ss_pred HHHHHHHHHHHhhCCHHHHHHHHHHHhCCccCHHHHHHcCchHHHHHHHHHHHHHHHHHHHH
Confidence 4667777888889999999999999998863 34667777888888888877654
No 51
>PRK05617 3-hydroxyisobutyryl-CoA hydrolase; Provisional
Probab=37.02 E-value=2.1e+02 Score=22.80 Aligned_cols=53 Identities=17% Similarity=0.183 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHH
Q 034486 6 ASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAY 62 (93)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY 62 (93)
...++.....|.+|+.. -+.++++++|..+ .+.+....-++|.+..|.=.++.
T Consensus 222 ~~~~~~~~~~i~~~~~~-~~~~~~~~~l~~~---~~~~a~~~a~~i~~~sp~a~~~~ 274 (342)
T PRK05617 222 ASELAAQRAWIDECFAG-DTVEDIIAALEAD---GGEFAAKTADTLRSRSPTSLKVT 274 (342)
T ss_pred cchhHHHHHHHHHHhCC-CCHHHHHHHHHhc---cHHHHHHHHHHHHhCCcHHHHHH
Confidence 34667888999999977 5999999999987 45777777788888777644443
No 52
>PLN02998 beta-glucosidase
Probab=36.59 E-value=24 Score=30.03 Aligned_cols=35 Identities=29% Similarity=0.400 Sum_probs=22.2
Q ss_pred HHHHHHhhcCCCchhHHHHHH---H--------HHHhCHHHHHHHHh
Q 034486 29 CMEALSKHANIKPVITSTVWK---E--------LEKENKEFFEAYAR 64 (93)
Q Consensus 29 ~v~~L~~~a~I~P~~T~~VW~---~--------LEkeNpeFFkaY~~ 64 (93)
+++.|.+ .||+|.+|..=|. - |-++..++|..|-.
T Consensus 127 lid~L~~-~GIeP~VTL~H~dlP~~L~~~yGGW~n~~~v~~F~~YA~ 172 (497)
T PLN02998 127 LIDELIT-HGIQPHVTLHHFDLPQALEDEYGGWLSQEIVRDFTAYAD 172 (497)
T ss_pred HHHHHHH-cCCceEEEecCCCCCHHHHHhhCCcCCchHHHHHHHHHH
Confidence 3334443 4999999986652 2 33456778888854
No 53
>COG2920 DsrC Dissimilatory sulfite reductase (desulfoviridin), gamma subunit [Inorganic ion transport and metabolism]
Probab=35.45 E-value=1.2e+02 Score=21.84 Aligned_cols=50 Identities=26% Similarity=0.471 Sum_probs=39.8
Q ss_pred HHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHHhcHHHHHhHHHHHHHH
Q 034486 27 EECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARKNAERATVMETRERI 79 (93)
Q Consensus 27 ~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~~~~~~~~~~~~~~i 79 (93)
+.+.++|.++-+| ..|..=|+-+ .==.+||..|.++-..||..+...+.+
T Consensus 27 E~vAe~lA~~e~i--~LT~eHWevv-~fvR~fy~ef~tsPaiRMLvK~~~~~~ 76 (111)
T COG2920 27 EKVAEALAEREGI--ELTEEHWEVV-RFVREFYEEFNTSPAIRMLVKAMAKKL 76 (111)
T ss_pred HHHHHHHHHHhcc--CccHHHHHHH-HHHHHHHHHHCCCchHHHHHHHHHHHh
Confidence 6788999999999 7899999755 445789999988888888777766544
No 54
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=34.82 E-value=25 Score=27.31 Aligned_cols=34 Identities=21% Similarity=0.317 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHH
Q 034486 24 MSKEECMEALSKHANIKPVITSTVWKELEKENKEF 58 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeF 58 (93)
||+.+||..|. +.-|.|.+-..=|-+|+++=...
T Consensus 1 ~~~~~~~~~~~-~~~I~pSil~ad~~~l~~el~~l 34 (228)
T PRK08091 1 MSKLSLIQQLK-QQPISVGILASNWLKFNETLTTL 34 (228)
T ss_pred CCHHHHHHHhc-CCeEEeehhhcCHHHHHHHHHHH
Confidence 89999998887 57999999887777777664443
No 55
>smart00511 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family.
Probab=34.76 E-value=78 Score=18.05 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=23.0
Q ss_pred HHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034486 27 EECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 27 ~E~v~~L~~~a~I~P~~T~~VW~~LEk 53 (93)
.|++++|...-+++|.+...+.+.|..
T Consensus 12 ~Ev~~fLs~~~~~~~~~~~~Ll~HL~~ 38 (45)
T smart00511 12 NEVSRFLSQLPGTDPDVRARLLSHLQT 38 (45)
T ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHH
Confidence 589999998888999998888888764
No 56
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=34.43 E-value=95 Score=22.95 Aligned_cols=36 Identities=25% Similarity=0.301 Sum_probs=28.6
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHH
Q 034486 14 HLIEECLVFNMSKEECMEALSKHANIKPVITSTVWK 49 (93)
Q Consensus 14 ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~ 49 (93)
+-|+.-..-.+|.+|+++.+.+..++.|.+-..+.+
T Consensus 95 ~~I~el~~eG~s~eei~~ki~~e~kl~pd~i~yi~~ 130 (131)
T PF08004_consen 95 ERIKELKSEGKSEEEIAEKISRETKLSPDMIKYILK 130 (131)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhhcCCHHHHHHHhc
Confidence 334444567899999999999999999999877643
No 57
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=34.13 E-value=48 Score=22.03 Aligned_cols=32 Identities=19% Similarity=0.169 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHHhC
Q 034486 24 MSKEECMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~VW~~LEkeN 55 (93)
++-.||++.|.+..++.|.-+.++.+.|.+.+
T Consensus 18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg 49 (115)
T PF03965_consen 18 ATVREIHEALPEERSWAYSTVQTLLNRLVEKG 49 (115)
T ss_dssp EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTT
T ss_pred CCHHHHHHHHHhccccchhHHHHHHHHHHhCC
Confidence 78899999999988999999999999999853
No 58
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=34.08 E-value=54 Score=22.47 Aligned_cols=18 Identities=28% Similarity=0.551 Sum_probs=16.0
Q ss_pred CCHHHHHHHHHhhcCCCc
Q 034486 24 MSKEECMEALSKHANIKP 41 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P 41 (93)
|||.|+++.|.+++++..
T Consensus 2 mtKseli~~ia~~~~l~k 19 (94)
T COG0776 2 MTKSELIDAIAEKAGLSK 19 (94)
T ss_pred CCHHHHHHHHHHHcCCCH
Confidence 899999999999988655
No 59
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=33.22 E-value=43 Score=20.08 Aligned_cols=18 Identities=33% Similarity=0.482 Sum_probs=15.0
Q ss_pred CHHHHHHHHHhhcCCCch
Q 034486 25 SKEECMEALSKHANIKPV 42 (93)
Q Consensus 25 sk~E~v~~L~~~a~I~P~ 42 (93)
|.+++++...+.+||+|.
T Consensus 1 ~~~~I~~~Va~~~~i~~~ 18 (60)
T smart00760 1 TIEEIIEAVAEYFGVKPE 18 (60)
T ss_pred CHHHHHHHHHHHhCCCHH
Confidence 467889999999999875
No 60
>PRK14137 recX recombination regulator RecX; Provisional
Probab=32.87 E-value=1.3e+02 Score=22.71 Aligned_cols=53 Identities=11% Similarity=0.126 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHh----hCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhC----HHHHHHHH
Q 034486 10 HLVHHLIEECLVF----NMSKEECMEALSKHANIKPVITSTVWKELEKEN----KEFFEAYA 63 (93)
Q Consensus 10 ~~VQ~LIErCLql----yMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeN----peFFkaY~ 63 (93)
..-+.+...||.+ -.|..|+-+-|.++ +++|.+-..|-..|.+.| ..|=++|.
T Consensus 37 e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~k-g~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~ 97 (195)
T PRK14137 37 EAREALLAYAFRALAARAMTAAELRAKLERR-SEDEALVTEVLERVQELGYQDDAQVARAEN 97 (195)
T ss_pred HHHHHHHHHHHHHHhcchhhHHHHHHHHHhc-CCCHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 5567888899988 88999999999986 999999999999999976 34444543
No 61
>PF04358 DsrC: DsrC like protein; InterPro: IPR007453 DsrC (P45573 from SWISSPROT) has been observed to co-purify with Desulphovibrio vulgaris dissimilatory sulphite reductase []. However, DsrC appears to be only loosely associated to the sulphite reductase, which suggests that it may not be an integral part of the dissimilatory sulphite reductase. Many proteins in this entry are found in organisms such as Escherichia coli and Haemophilus influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins []. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds []. Also included in this entry is TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Many proteins in this entry are annotated as the third (gamma) subunit of dissimilatory sulphite reductase ; PDB: 2V4J_F 2A5W_C 1SAU_A 1JI8_A 1YX3_A.
Probab=32.70 E-value=1.7e+02 Score=20.31 Aligned_cols=34 Identities=29% Similarity=0.652 Sum_probs=23.1
Q ss_pred HHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHH
Q 034486 27 EECMEALSKHANIKPVITSTVWKELEKENKEFFEAYA 63 (93)
Q Consensus 27 ~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~ 63 (93)
+|+..+|.+.-||+ +|..-|+-+.- =.+||..|.
T Consensus 25 eevA~~lA~~egI~--Ltd~HW~vI~f-lR~~y~~~~ 58 (109)
T PF04358_consen 25 EEVAEALAKEEGIE--LTDEHWEVIRF-LRDYYQEYG 58 (109)
T ss_dssp HHHHHHHHHCTT-S----HHHHHHHHH-HHHHHHHHS
T ss_pred HHHHHHHHHHcCCC--CCHHHHHHHHH-HHHHHHHHC
Confidence 68999999999999 99999998752 234444443
No 62
>TIGR03356 BGL beta-galactosidase.
Probab=32.49 E-value=42 Score=27.69 Aligned_cols=36 Identities=33% Similarity=0.678 Sum_probs=22.5
Q ss_pred HHHHHHHhhcCCCchhHHHHHH---HHH-------HhCHHHHHHHHh
Q 034486 28 ECMEALSKHANIKPVITSTVWK---ELE-------KENKEFFEAYAR 64 (93)
Q Consensus 28 E~v~~L~~~a~I~P~~T~~VW~---~LE-------keNpeFFkaY~~ 64 (93)
++++.|.+ .||+|.+|..=|. .|+ .+..+.|..|-.
T Consensus 98 ~~i~~l~~-~gi~pivtL~Hfd~P~~l~~~gGw~~~~~~~~f~~ya~ 143 (427)
T TIGR03356 98 RLVDELLE-AGIEPFVTLYHWDLPQALEDRGGWLNRDTAEWFAEYAA 143 (427)
T ss_pred HHHHHHHH-cCCeeEEeeccCCccHHHHhcCCCCChHHHHHHHHHHH
Confidence 44444443 4999998874443 333 556688888854
No 63
>PF14278 TetR_C_8: Transcriptional regulator C-terminal region
Probab=32.05 E-value=77 Score=18.25 Aligned_cols=16 Identities=25% Similarity=0.588 Sum_probs=9.4
Q ss_pred HhCHHHHHHHHhcHHH
Q 034486 53 KENKEFFEAYARKNAE 68 (93)
Q Consensus 53 keNpeFFkaY~~~~~~ 68 (93)
.+|.+||++.......
T Consensus 12 ~~n~~~~~~ll~~~~~ 27 (77)
T PF14278_consen 12 YENRDFYKILLSPNGD 27 (77)
T ss_pred HHhHHHHHHHHCCCCC
Confidence 5666666666654433
No 64
>PF11417 Inhibitor_G39P: Loader and inhibitor of phage G40P; InterPro: IPR024424 G39P inhibits the initiation of DNA replication by blocking G40P replicative helicase. G39P has a bipartite stricture consisting of a folded N-terminal domain and an unfolded C-terminal domain. The C-terminal is essential for helicase interaction [].; PDB: 1NO1_B.
Probab=31.98 E-value=50 Score=21.41 Aligned_cols=31 Identities=29% Similarity=0.409 Sum_probs=19.2
Q ss_pred CCHHHHHHHHHhhcCCCc----h-------hHHHHHHHHHHh
Q 034486 24 MSKEECMEALSKHANIKP----V-------ITSTVWKELEKE 54 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P----~-------~T~~VW~~LEke 54 (93)
|+++|+++-|.--...=| . -+-.+|-.+-+.
T Consensus 1 Mtk~E~~~ll~~I~~aYP~~~~~f~~~~~k~~v~~W~~~L~d 42 (71)
T PF11417_consen 1 MTKEETAKLLKLIKAAYPQWAGNFKPTDSKETVDLWYDMLKD 42 (71)
T ss_dssp --HHHHHHHHHHHHHHST---TT---STHHHHHHHHHHHHTT
T ss_pred CCHHHHHHHHHHHHHHCCcchhccchhhHHHHHHHHHHHHHh
Confidence 899999999887655555 2 234666665544
No 65
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=31.97 E-value=54 Score=20.06 Aligned_cols=24 Identities=17% Similarity=0.372 Sum_probs=18.0
Q ss_pred HHHHHhhcCCCchhHHHHHHHHHH
Q 034486 30 MEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 30 v~~L~~~a~I~P~~T~~VW~~LEk 53 (93)
+..|+.+++++|..-..+...|++
T Consensus 17 ~~eLa~~~~~s~~~ve~mL~~l~~ 40 (69)
T PF09012_consen 17 LAELAREFGISPEAVEAMLEQLIR 40 (69)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHC
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHH
Confidence 356788999999999988888875
No 66
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=31.84 E-value=1.6e+02 Score=28.13 Aligned_cols=58 Identities=19% Similarity=0.303 Sum_probs=33.3
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHH------------------HHHHHHHhCHHHHHHHHhcHHH-HHhHHH
Q 034486 14 HLIEECLVFNMSKEECMEALSKHANIKPVITST------------------VWKELEKENKEFFEAYARKNAE-RATVME 74 (93)
Q Consensus 14 ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~------------------VW~~LEkeNpeFFkaY~~~~~~-~~~~~~ 74 (93)
.|||.|+.. .+...-+++|.|+.- --++-+++-.||-+.|.+-..+ ...+++
T Consensus 426 kLIEecISq---------IvlHr~~~DPdf~yr~~l~id~~~liD~~vdkak~eeseqkA~e~~kk~~ke~ta~qe~qae 496 (1102)
T KOG1924|consen 426 KLIEECISQ---------IVLHRTGMDPDFKYRFRLDIDLTELIDKMVDKAKAEESEQKAAELEKKFDKELTARQEAQAE 496 (1102)
T ss_pred HHHHHHHHH---------HHHhcCCCCCCcchhhcccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Confidence 467777653 345567888887652 2345555667777777665444 223444
Q ss_pred HHHHHH
Q 034486 75 TRERIE 80 (93)
Q Consensus 75 ~~~~iq 80 (93)
..-+++
T Consensus 497 l~k~e~ 502 (1102)
T KOG1924|consen 497 LQKHEE 502 (1102)
T ss_pred HHHhhh
Confidence 444443
No 67
>PF00232 Glyco_hydro_1: Glycosyl hydrolase family 1; InterPro: IPR001360 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 1 GH1 from CAZY comprises enzymes with a number of known activities; beta-glucosidase (3.2.1.21 from EC); beta-galactosidase (3.2.1.23 from EC); 6-phospho-beta-galactosidase (3.2.1.85 from EC); 6-phospho-beta-glucosidase (3.2.1.86 from EC); lactase-phlorizin hydrolase (3.2.1.62 from EC), (3.2.1.108 from EC); beta-mannosidase (3.2.1.25 from EC); myrosinase (3.2.1.147 from EC). ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 1QVB_A 3AHY_D 2E9L_A 2ZOX_A 2JFE_X 2E9M_A 3FIZ_A 3FIY_A 3CMJ_A 3FJ0_A ....
Probab=31.79 E-value=13 Score=30.63 Aligned_cols=45 Identities=31% Similarity=0.634 Sum_probs=26.9
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHH-----HHHH-----HHHhCHHHHHHHHh
Q 034486 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITST-----VWKE-----LEKENKEFFEAYAR 64 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~-----VW~~-----LEkeNpeFFkaY~~ 64 (93)
..+-++.=.++|+.|+. +||+|.+|.. .|-. +-++++++|..|-.
T Consensus 94 n~~~~~~Y~~~i~~l~~---------------~gi~P~vtL~H~~~P~~l~~~ggw~~~~~~~~F~~Ya~ 148 (455)
T PF00232_consen 94 NEEGLDFYRDLIDELLE---------------NGIEPIVTLYHFDLPLWLEDYGGWLNRETVDWFARYAE 148 (455)
T ss_dssp -HHHHHHHHHHHHHHHH---------------TT-EEEEEEESS--BHHHHHHTGGGSTHHHHHHHHHHH
T ss_pred CHhHhhhhHHHHHHHHh---------------hccceeeeeeecccccceeecccccCHHHHHHHHHHHH
Confidence 34445555555555543 5999988764 3332 33677899999854
No 68
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 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. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=31.33 E-value=79 Score=19.34 Aligned_cols=30 Identities=20% Similarity=0.510 Sum_probs=20.9
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHHh
Q 034486 24 MSKEECMEALSKHANIKPVITSTVWKELEKE 54 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~VW~~LEke 54 (93)
||--|.+..+.+++| .|.=..-+|++..+.
T Consensus 1 mt~~eaa~~vL~~~~-~pm~~~eI~~~i~~~ 30 (72)
T PF05066_consen 1 MTFKEAAYEVLEEAG-RPMTFKEIWEEIQER 30 (72)
T ss_dssp S-HHHHHHHHHHHH--S-EEHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcC-CCcCHHHHHHHHHHh
Confidence 667777777777778 888888888888764
No 69
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=31.15 E-value=2.8e+02 Score=22.26 Aligned_cols=57 Identities=16% Similarity=0.223 Sum_probs=40.6
Q ss_pred CCchHHHHHHHHHHHHHHHHhhC-------CHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHH
Q 034486 2 DDSSASYIHLVHHLIEECLVFNM-------SKEECMEALSKHANIKPVITSTVWKELEKENKEFFEA 61 (93)
Q Consensus 2 ~~~s~~~I~~VQ~LIErCLqlyM-------sk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFka 61 (93)
|.-|.+.+..|-..+++|+..+. .-.+.+..+.++.. ... ..+|..|++.+|++...
T Consensus 167 ~~Vs~e~~~~V~e~l~~~~~~~~~~~~~~~~G~~~aa~ILn~l~-~~~--~~il~~L~~~dp~~a~~ 230 (334)
T PRK07194 167 DDVDRDVVDELDELIERCLAVLSEQSHTKVIGVKQAADIINRFP-GDR--QQLMEMLKEHDEEVVNE 230 (334)
T ss_pred CCCCHHHHHHHHHHHHHHHHhhhhcccccCCCHHHHHHHHHhCc-hhH--HHHHHHHHhhCHHHHHH
Confidence 44577888888788899987643 22345666665544 222 58999999999999877
No 70
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=30.92 E-value=1.8e+02 Score=20.09 Aligned_cols=65 Identities=15% Similarity=0.198 Sum_probs=42.7
Q ss_pred CCCc-hHHHHHHHHHHHH-HHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhC----HHHHHHHHhcH
Q 034486 1 MDDS-SASYIHLVHHLIE-ECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKEN----KEFFEAYARKN 66 (93)
Q Consensus 1 ~~~~-s~~~I~~VQ~LIE-rCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeN----peFFkaY~~~~ 66 (93)
|||. +.+.+..+.+..= -|=..-.|..|+...|.+. |++|.+...|-..|.+.+ ..|-+.|-..+
T Consensus 1 ~~~~~~~~~~~~a~~~al~~L~~r~~s~~el~~kL~~k-g~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~ 71 (157)
T PRK00117 1 LEDTARRRMYASARARALRLLARREHSRAELRRKLAAK-GFSEEVIEAVLDRLKEEGLLDDERFAESFVRSR 71 (157)
T ss_pred CCCcccccHHHHHHHHHHHHHccchhHHHHHHHHHHhc-CCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 3552 3333343333333 3334456889999999976 999999999999999843 46666664443
No 71
>smart00543 MIF4G Middle domain of eukaryotic initiation factor 4G (eIF4G). Also occurs in NMD2p and CBP80. The domain is rich in alpha-helices and may contain multiple alpha-helical repeats. In eIF4G, this domain binds eIF4A, eIF3, RNA and DNA. Ponting (TiBS) "Novel eIF4G domain homologues (in press)
Probab=30.89 E-value=1.7e+02 Score=19.82 Aligned_cols=52 Identities=21% Similarity=0.245 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHhhCC----HHHHHHHHHhhcCCCchhH---HHHHHHHHHhCHHHHHHH
Q 034486 11 LVHHLIEECLVFNMS----KEECMEALSKHANIKPVIT---STVWKELEKENKEFFEAY 62 (93)
Q Consensus 11 ~VQ~LIErCLqlyMs----k~E~v~~L~~~a~I~P~~T---~~VW~~LEkeNpeFFkaY 62 (93)
.+...++.....+++ .+++++.+.+.+..+|.+. ..+...|...+|+|...-
T Consensus 15 n~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~~~f~~~l 73 (200)
T smart00543 15 NFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSLL 73 (200)
T ss_pred HHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555566665 5678888899999999877 456777777778776544
No 72
>TIGR02173 cyt_kin_arch cytidylate kinase, putative. Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by TIGR00017.
Probab=30.84 E-value=1.5e+02 Score=19.70 Aligned_cols=41 Identities=12% Similarity=0.064 Sum_probs=30.3
Q ss_pred CHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHHhc
Q 034486 25 SKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 25 sk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~ 65 (93)
+.+.+++-+.+..++++.-...-|.+-.+....||+.|+..
T Consensus 101 ~~~~r~~R~~~R~~~s~~~a~~~~~~~d~~~~~~~~~~~~~ 141 (171)
T TIGR02173 101 PLEVRARRIAKREGKSLTVARSETIEREESEKRRYLKFYGI 141 (171)
T ss_pred CHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 55667777777778887777766777777778888887764
No 73
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=30.82 E-value=1.4e+02 Score=19.87 Aligned_cols=40 Identities=10% Similarity=-0.027 Sum_probs=27.3
Q ss_pred hhCCHHHHHHHHHhhcCCCch-------------hHHHHHHHHHHhCHHHHHHH
Q 034486 22 FNMSKEECMEALSKHANIKPV-------------ITSTVWKELEKENKEFFEAY 62 (93)
Q Consensus 22 lyMsk~E~v~~L~~~a~I~P~-------------~T~~VW~~LEkeNpeFFkaY 62 (93)
.|.+.+|++.+-. ..||... ....+.++||+.||.+....
T Consensus 8 ~~v~E~ei~~ya~-~~~lp~~~~~CP~~~~a~R~~~k~~L~~LE~~~P~~k~~i 60 (104)
T TIGR00269 8 RYIPEKEVVLYAF-LNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVKFSV 60 (104)
T ss_pred ccCCHHHHHHHHH-HcCCCcCCCCCCCCCCCchHHHHHHHHHHHHHCcChHHHH
Confidence 3566777775444 4577643 55678999999999875444
No 74
>cd02433 Nodulin-21_like_2 Nodulin-21 and CCC1-related protein family. Nodulin-21_like_2: This is a family of proteins closely related to nodulin-21, a plant nodule-specific protein that may be involved in symbiotic nitrogen fixation. This family is also related to CCC1, a yeast vacuole transmembrane protein that functions as an iron and manganese transporter.
Probab=30.61 E-value=93 Score=24.01 Aligned_cols=52 Identities=8% Similarity=-0.066 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHHhc
Q 034486 10 HLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 10 ~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~ 65 (93)
+.-+..|+.|.. .-++|+++.+.++ |++|.--..|=+.|.+ ||++|-....+
T Consensus 86 ~re~~~i~~~p~--~e~~el~~iy~~~-G~~~~~a~~~~~~l~~-~~~~~~~~~~~ 137 (234)
T cd02433 86 PDERRELRKHPL--EEAAELALIYRAK-GLDEEEAKRVASQLMN-DPEQALDTLAR 137 (234)
T ss_pred HHHHHHhhhCcH--HHHHHHHHHHHHc-CCCHHHHHHHHHHHHh-CcchhHHHHHH
Confidence 344555666655 4568888888766 9999999999999965 78888766554
No 75
>smart00830 CM_2 Chorismate mutase type II. Chorismate mutase, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine PUBMED:9642265, PUBMED:9497350.
Probab=30.55 E-value=66 Score=19.61 Aligned_cols=15 Identities=13% Similarity=0.629 Sum_probs=7.0
Q ss_pred cCCCchhHHHHHHHH
Q 034486 37 ANIKPVITSTVWKEL 51 (93)
Q Consensus 37 a~I~P~~T~~VW~~L 51 (93)
.+++|.+...||+.+
T Consensus 56 ~~l~~~~~~~if~~i 70 (79)
T smart00830 56 PGLDPELVERIFREI 70 (79)
T ss_pred CCcCHHHHHHHHHHH
Confidence 344444444444444
No 76
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=29.79 E-value=87 Score=17.59 Aligned_cols=26 Identities=19% Similarity=0.291 Sum_probs=20.1
Q ss_pred HHHHHhhcCCCchhHHHHHHHHHHhC
Q 034486 30 MEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 30 v~~L~~~a~I~P~~T~~VW~~LEkeN 55 (93)
+..|.++++|.+.--.-+.++|++++
T Consensus 28 ~~~la~~~~is~~~v~~~l~~L~~~G 53 (66)
T cd07377 28 ERELAEELGVSRTTVREALRELEAEG 53 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 67788899999877677777777654
No 77
>PRK12461 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=29.73 E-value=2.2e+02 Score=21.89 Aligned_cols=43 Identities=12% Similarity=0.121 Sum_probs=34.8
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034486 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~V 47 (93)
|.+.|+.++.....-+..-++.+|.++.|.++..-.|.+-..+
T Consensus 201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 243 (255)
T PRK12461 201 SSRAIRALKRAYKIIYRSGLSVQQAVAELELQQFESPEVEELI 243 (255)
T ss_pred CHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhccCCHHHHHHH
Confidence 5678888888888888888899999999988777777766554
No 78
>cd05062 PTKc_IGF-1R Catalytic domain of the Protein Tyrosine Kinase, Insulin-like Growth Factor-1 Receptor. Protein Tyrosine Kinase (PTK) family; Insulin-like Growth Factor-1 Receptor (IGF-1R); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. IGF-1R is a receptor tyr kinases (RTK) that is composed of two alphabeta heterodimers. Binding of the ligand (IGF-1 or IGF-2) to the extracellular alpha subunit activates the intracellular tyr kinase domain of the transmembrane beta subunit. Receptor activation leads to autophosphorylation, which stimulates downstream kinase activities and biological function. IGF-1R signaling is important in the differentiation, growth, and survival of normal cells. In cancer cells, wh
Probab=29.37 E-value=60 Score=23.04 Aligned_cols=25 Identities=20% Similarity=0.418 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHhh----CCHHHHHHHHH
Q 034486 10 HLVHHLIEECLVFN----MSKEECMEALS 34 (93)
Q Consensus 10 ~~VQ~LIErCLqly----Msk~E~v~~L~ 34 (93)
..++++|.+||+.. .|-.|++..|.
T Consensus 248 ~~~~~li~~~l~~~p~~Rps~~e~l~~l~ 276 (277)
T cd05062 248 DMLFELMRMCWQYNPKMRPSFLEIISSIK 276 (277)
T ss_pred HHHHHHHHHHcCCChhhCcCHHHHHHHhh
Confidence 35788999999875 56666666553
No 79
>PRK09239 chorismate mutase; Provisional
Probab=29.25 E-value=95 Score=21.19 Aligned_cols=19 Identities=21% Similarity=0.303 Sum_probs=10.2
Q ss_pred HhhcCCCchhHHHHHHHHH
Q 034486 34 SKHANIKPVITSTVWKELE 52 (93)
Q Consensus 34 ~~~a~I~P~~T~~VW~~LE 52 (93)
....|++|.|...+|+.+-
T Consensus 68 a~~~gl~p~~~~~i~~~ii 86 (104)
T PRK09239 68 AKDANLDPDFAEKFLNFII 86 (104)
T ss_pred HHHCCCCHHHHHHHHHHHH
Confidence 3445666666655554443
No 80
>PRK05289 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=29.22 E-value=2.3e+02 Score=21.56 Aligned_cols=43 Identities=19% Similarity=0.219 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034486 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~V 47 (93)
+.+.+..++....-.|..-.+.+|.++.|.+...-.|.+...+
T Consensus 205 ~~~~~~~i~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 247 (262)
T PRK05289 205 SREEIHALRRAYKLLYRSGLTLEEALEELAEEYPDSPEVKEIL 247 (262)
T ss_pred CHHHHHHHHHHHHHHHHcCccHHHHHHHHHhhccCCHHHHHHH
Confidence 5677788888887777777888888888887766667655444
No 81
>cd08637 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuc
Probab=29.02 E-value=3e+02 Score=22.36 Aligned_cols=43 Identities=16% Similarity=0.111 Sum_probs=30.0
Q ss_pred CHHHHHHHHHhhcCCCch--------hHHHHHHHHHHhCHHHHHHHHhcHHH
Q 034486 25 SKEECMEALSKHANIKPV--------ITSTVWKELEKENKEFFEAYARKNAE 68 (93)
Q Consensus 25 sk~E~v~~L~~~a~I~P~--------~T~~VW~~LEkeNpeFFkaY~~~~~~ 68 (93)
|..++.+.|.++.|++|. .+..+++.|.+.+| |.+..-..|..
T Consensus 35 S~~qv~~~L~~~lgl~~~~~t~~~~~t~~~~L~~l~~~~p-~~~~lle~r~l 85 (377)
T cd08637 35 SPKQLGEVLFEKLGLPVGKKTKTGYSTDAEVLEKLADEHP-IVELILEYREL 85 (377)
T ss_pred CHHHHHHHHHHhCCCCCCCcCCCCCCchHHHHHhhhhcCh-HHHHHHHHHHH
Confidence 568899999999999865 23458888887776 55555443444
No 82
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=28.96 E-value=71 Score=21.84 Aligned_cols=27 Identities=15% Similarity=0.276 Sum_probs=23.1
Q ss_pred HHHHHHhhcCCCchhHHHHHHHHHHhC
Q 034486 29 CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 29 ~v~~L~~~a~I~P~~T~~VW~~LEkeN 55 (93)
-++.|+++.+|.|.+..-|.++|.+.+
T Consensus 27 s~~~ia~~~~ip~~~l~kil~~L~~~g 53 (135)
T TIGR02010 27 TLADISERQGISLSYLEQLFAKLRKAG 53 (135)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 456778888999999999999998865
No 83
>TIGR01803 CM-like chorismate mutase related enzymes. This subfamily includes two enzymes which are variants on the mechanism of chorismate mutase and are likely to have evolved from an ancestral chorismate mutase enzyme. 4-amino-4-deoxy-chorismate mutase produces amino-deoxy-prephenate which is subsequently converted to para-dimethylamino-phenylalanine, a component of the natural product pristinamycin. Isochorismate-pyruvate lyase presumably catalyzes the same type of 2+2+2 cyclo-rearrangement as chorismate mutase, but acting on isochorismate, this results in two broken bonds instead of one broken and one made. The product of this reaction is salicylate (2-hydroxy-benzoate) which is also incorporated into various natural products.
Probab=28.19 E-value=77 Score=20.23 Aligned_cols=20 Identities=5% Similarity=0.325 Sum_probs=15.8
Q ss_pred HhhcCCCchhHHHHHHHHHH
Q 034486 34 SKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 34 ~~~a~I~P~~T~~VW~~LEk 53 (93)
..+.|++|.+...+|+.+-.
T Consensus 57 a~~~gl~~~~~~~if~~ii~ 76 (82)
T TIGR01803 57 AEENGLDPPFVEGLFAQIIH 76 (82)
T ss_pred HHHcCCCHHHHHHHHHHHHH
Confidence 34578999999999988754
No 84
>PF07531 TAFH: NHR1 homology to TAF; InterPro: IPR003894 The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. The transcription initiation TFIID complex is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). The TAFH/NHR1 domain is named after fruit fly TATA-box-associated factor 110 (TAF110), human TAF105 and TAF130, and the fruit fly protein Nervy, which is a homologue of human MTG8/ETO [, ]. The human eight twenty-one (ETO or MTG8) and related myeloid transforming gene products MTGR1 and MTG16 as well as the Nervy protein contain the NHR1-4 domains. The NHR1/TAFH domain occurs in the N-terminal part of these proteins, while a MYND-type zinc finger forms the NHR4 domain []. The TAFH/NHR1 domain can be involved in protein-protein interactions, e.g in MTG8/ETO with HSP90 and Gfi-1 []. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2P6V_A 2KNH_A 2PP4_A 2H7B_A.
Probab=27.41 E-value=1.1e+02 Score=21.21 Aligned_cols=37 Identities=22% Similarity=0.216 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCc
Q 034486 5 SASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKP 41 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P 41 (93)
|.+....|+.||..++..-++-||--..|++..|-.|
T Consensus 22 spev~~~Vr~LV~~L~~~~i~~EeF~~~Lq~~lns~p 58 (96)
T PF07531_consen 22 SPEVGENVRELVQNLVDGKIEAEEFTSKLQEELNSSP 58 (96)
T ss_dssp -CCHHHHHHHHHHHHHTTSS-HHHHHHHHHHHCTSS-
T ss_pred ChHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcCCC
Confidence 5677889999999999999999999999998666554
No 85
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=27.38 E-value=62 Score=30.23 Aligned_cols=33 Identities=30% Similarity=0.373 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHH
Q 034486 12 VHHLIEECLVFNMSKEECMEALSKHANIKPVITS 45 (93)
Q Consensus 12 VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~ 45 (93)
+.+.+.++.+..++++++.++|.+ ..|.|+||.
T Consensus 155 l~~~l~~L~~~g~~~e~i~~~L~~-~~i~pVlTA 187 (974)
T PTZ00398 155 LKNTIEMLLQAGFDKEEIYKQLCN-QEIDLVLTA 187 (974)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhc-Cceeeeecc
Confidence 567899999999999999999985 799999995
No 86
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=27.24 E-value=1.4e+02 Score=17.51 Aligned_cols=36 Identities=19% Similarity=0.090 Sum_probs=25.4
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHH
Q 034486 14 HLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKEL 51 (93)
Q Consensus 14 ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~L 51 (93)
+.|-+|=.+.||.+||-+.|.-..+ |.-+..-|..+
T Consensus 5 ~~I~~~r~lGfsL~eI~~~l~l~~~--~~~~~~~~~~~ 40 (65)
T PF09278_consen 5 QFIRRLRELGFSLEEIRELLELYDQ--GDPPCADRRAL 40 (65)
T ss_dssp HHHHHHHHTT--HHHHHHHHHHCCS--HCHHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHhccCC--CCCCHHHHHHH
Confidence 4788999999999999999954444 66666666543
No 87
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=27.22 E-value=1.5e+02 Score=21.45 Aligned_cols=41 Identities=34% Similarity=0.360 Sum_probs=28.5
Q ss_pred HHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHhCH
Q 034486 15 LIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKENK 56 (93)
Q Consensus 15 LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEkeNp 56 (93)
.|-=|.|.-.+..+-++.+. .++.+|.+|+.|-.+|++--+
T Consensus 19 fl~~~~q~~vdi~~~l~r~l-~~~~~~~Ip~~Vi~EL~~l~~ 59 (136)
T COG1412 19 FLLYPYQFKVDIFEELERLL-GAKYKPAIPSCVIRELEKLKR 59 (136)
T ss_pred HHHHHHHccCCHHHHHHHHh-cccccccchHHHHHHHHHHHH
Confidence 34446666666656555555 256899999999999987544
No 88
>PF12383 SARS_3b: Severe acute respiratory syndrome coronavirus 3b protein; InterPro: IPR022117 This family of proteins is found in viruses. Proteins in this family are typically between 32 and 154 amino acids in length. This family contains the SARS coronavirus 3b protein which is predominantly localized in the nucleolus, and induces G0/G1 arrest and apoptosis in transfected cells.
Probab=27.06 E-value=62 Score=23.93 Aligned_cols=34 Identities=26% Similarity=0.436 Sum_probs=28.9
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034486 14 HLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 14 ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~V 47 (93)
-||.+-+||-||+.....-|.+|-++....-+.-
T Consensus 114 lliqqwiqfmmsrrrllaclckhkkvstnlcshs 147 (153)
T PF12383_consen 114 LLIQQWIQFMMSRRRLLACLCKHKKVSTNLCSHS 147 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcccccccccchhh
Confidence 4688999999999999999999999887665543
No 89
>PRK14135 recX recombination regulator RecX; Provisional
Probab=26.70 E-value=2.8e+02 Score=20.81 Aligned_cols=47 Identities=11% Similarity=0.091 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHHh-hCCHHHHHHHHHhhcCCCchhHHHHHHHHHHh
Q 034486 7 SYIHLVHHLIEECLVF-NMSKEECMEALSKHANIKPVITSTVWKELEKE 54 (93)
Q Consensus 7 ~~I~~VQ~LIErCLql-yMsk~E~v~~L~~~a~I~P~~T~~VW~~LEke 54 (93)
+|.+.++..+...+.. ..++.++...|... ||++.+...|...|..+
T Consensus 105 dD~~~a~~~~~~~~~~~~~g~~~I~~kL~~k-Gi~~~~Ie~~l~~l~~~ 152 (263)
T PRK14135 105 DDKEYAESYVRTNINTGDKGPRVIKQKLLQK-GIEDEIIEEALSEYTEE 152 (263)
T ss_pred CHHHHHHHHHHHHHhccccchHHHHHHHHHc-CCCHHHHHHHHHhCChh
Confidence 4567788888877764 46889999999965 99999999999988443
No 90
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=26.66 E-value=76 Score=20.08 Aligned_cols=24 Identities=29% Similarity=0.311 Sum_probs=13.2
Q ss_pred HHhhcCCCchhHHHHHHHHHHhCH
Q 034486 33 LSKHANIKPVITSTVWKELEKENK 56 (93)
Q Consensus 33 L~~~a~I~P~~T~~VW~~LEkeNp 56 (93)
+.+-+||+-.+|.--=.+++++|+
T Consensus 51 ir~~fgi~~d~t~eee~~i~~e~~ 74 (78)
T PF01466_consen 51 IRKYFGIENDLTPEEEEEIRKENE 74 (78)
T ss_dssp HHHHHT---TSSHHHHHHHHHHCC
T ss_pred HHHHcCCCCCCCHHHHHHHHHHcc
Confidence 344457777777666666777775
No 91
>cd05094 PTKc_TrkC Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase C. Protein Tyrosine Kinase (PTK) family; Tropomyosin Related Kinase C (TrkC); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkC is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkC to its ligand, neurotrophin 3 (NT3), results in receptor oligomerization and activation of the catalytic domain. TrkC is broadly expressed in the nervous system and in some n
Probab=26.56 E-value=80 Score=22.71 Aligned_cols=29 Identities=14% Similarity=0.184 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHh----hCCHHHHHHHHHhhcC
Q 034486 10 HLVHHLIEECLVF----NMSKEECMEALSKHAN 38 (93)
Q Consensus 10 ~~VQ~LIErCLql----yMsk~E~v~~L~~~a~ 38 (93)
..++++|.+||+. ..|-+|+++.|.+-.+
T Consensus 252 ~~~~~li~~~l~~~P~~Rpt~~~v~~~l~~~~~ 284 (291)
T cd05094 252 KEVYDIMLGCWQREPQQRLNIKEIYKILHALGK 284 (291)
T ss_pred HHHHHHHHHHcccChhhCcCHHHHHHHHHHHHh
Confidence 4588999999985 5667888888876433
No 92
>PRK00009 phosphoenolpyruvate carboxylase; Reviewed
Probab=25.81 E-value=70 Score=29.68 Aligned_cols=34 Identities=26% Similarity=0.356 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHH
Q 034486 11 LVHHLIEECLVFNMSKEECMEALSKHANIKPVITS 45 (93)
Q Consensus 11 ~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~ 45 (93)
.+.+.+.++.+..++++++.+.|.+ ..|.|+||.
T Consensus 108 sl~~~~~~l~~~g~~~e~i~~~L~~-~~i~pVlTA 141 (911)
T PRK00009 108 SLAETLRRLKAAGVSPEELARALEE-LDIEPVLTA 141 (911)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHhh-Ccceeeeec
Confidence 3567888888888999999999985 799999995
No 93
>PF08970 Sda: Sporulation inhibitor A; InterPro: IPR015064 Members of this protein group contain two antiparallel alpha helices that are linked by a highly structured inter-helix loop to form a helical hairpin; the structure is stabilised by numerous hydrophobic and electrostatic interactions. These sporulation inhibitors are antikinases that bind to the histidine kinase KinA phosphotransfer domain and act as a molecular barricade that inhibit productive interaction between the ATP binding site and the phosphorylatable KinA His residue. This results in the inhibition of sporulation (by preventing phosphorylation of spo0A) []. ; PDB: 3FYR_B 1PV0_A.
Probab=25.64 E-value=1.7e+02 Score=17.92 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=20.8
Q ss_pred hCCHHHHHHHHHh--hcCCCchhHHHHHHHHHHhC
Q 034486 23 NMSKEECMEALSK--HANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 23 yMsk~E~v~~L~~--~a~I~P~~T~~VW~~LEkeN 55 (93)
+||.+-.+++-.+ .-|.+|.|..++-+++++-|
T Consensus 3 ~LSDe~LiesY~~A~el~L~~dFI~Ll~~Ei~rR~ 37 (46)
T PF08970_consen 3 KLSDELLIESYHKAIELNLDPDFIRLLEEEIQRRS 37 (46)
T ss_dssp TS-HHHHHHHHHHHHHTT--HHHHHHHHHHHHHCT
T ss_pred cccHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcC
Confidence 3555555555443 56899999999988887654
No 94
>PF14039 YusW: YusW-like protein
Probab=25.59 E-value=61 Score=21.90 Aligned_cols=38 Identities=21% Similarity=0.289 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHH-HHHhhCCHHHHHHHHHhhcCCCchhH
Q 034486 7 SYIHLVHHLIEE-CLVFNMSKEECMEALSKHANIKPVIT 44 (93)
Q Consensus 7 ~~I~~VQ~LIEr-CLqlyMsk~E~v~~L~~~a~I~P~~T 44 (93)
+-++.++.++.+ -|.-.|+.+++|..+.+.+|++|.+.
T Consensus 44 eA~~~l~~~l~~L~~~~~t~~~evi~~Vl~~f~Ld~dy~ 82 (92)
T PF14039_consen 44 EAFDELEPLLSELSFDSDTSEEEVIDQVLKAFNLDPDYQ 82 (92)
T ss_pred HHHHHHHHHHHhCCCCCCCChHHHHHHHHHHhCCCccce
Confidence 334555555543 45668999999999999999998653
No 95
>KOG1684 consensus Enoyl-CoA hydratase [Lipid transport and metabolism]
Probab=25.42 E-value=91 Score=26.81 Aligned_cols=45 Identities=24% Similarity=0.274 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhhCCHHHHHHHHHhhc--CCCchhHHHHHHHHHHhCHH
Q 034486 12 VHHLIEECLVFNMSKEECMEALSKHA--NIKPVITSTVWKELEKENKE 57 (93)
Q Consensus 12 VQ~LIErCLqlyMsk~E~v~~L~~~a--~I~P~~T~~VW~~LEkeNpe 57 (93)
+=++|+.|+... |-+|++++|.+.. +=--.+-....+.|++-.|-
T Consensus 265 ~~~~i~~~Fs~~-tVeeIie~lk~~q~~~~~~ewak~tlk~L~k~SPt 311 (401)
T KOG1684|consen 265 KLDVINKCFSAN-TVEEIIEALKNYQQSADGSEWAKETLKTLKKMSPT 311 (401)
T ss_pred hHHHHHHhhccc-cHHHHHHHHHHHhhhhhHHHHHHHHHHHHhhcCCc
Confidence 678999999888 9999999986543 22233444555666666664
No 96
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=25.08 E-value=96 Score=21.03 Aligned_cols=34 Identities=12% Similarity=0.185 Sum_probs=26.0
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhc--CCCchhHHHH
Q 034486 14 HLIEECLVFNMSKEECMEALSKHA--NIKPVITSTV 47 (93)
Q Consensus 14 ~LIErCLqlyMsk~E~v~~L~~~a--~I~P~~T~~V 47 (93)
.-+-+++...|+.+++++.|.+++ +|.+.+...+
T Consensus 45 ~Sl~~A~~~G~~~e~i~~~L~~~S~~~lP~~v~~~i 80 (129)
T PF13625_consen 45 ASLWRAASAGLTAEEIIEFLERYSKNPLPQNVEQSI 80 (129)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHcCCCCCHHHHHHH
Confidence 456789999999999999999976 3555555443
No 97
>KOG1199 consensus Short-chain alcohol dehydrogenase/3-hydroxyacyl-CoA dehydrogenase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=24.93 E-value=55 Score=26.23 Aligned_cols=15 Identities=40% Similarity=0.640 Sum_probs=13.1
Q ss_pred hHHHHHHHHHHHHHH
Q 034486 5 SASYIHLVHHLIEEC 19 (93)
Q Consensus 5 s~~~I~~VQ~LIErC 19 (93)
+++|-++||++||.-
T Consensus 229 p~eyahlvqaiienp 243 (260)
T KOG1199|consen 229 PHEYAHLVQAIIENP 243 (260)
T ss_pred hHHHHHHHHHHHhCc
Confidence 489999999999963
No 98
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=24.81 E-value=75 Score=23.40 Aligned_cols=34 Identities=12% Similarity=0.302 Sum_probs=19.3
Q ss_pred HhCHHHHHHHHhcHHHHHhHHHHHHHHHHHHhcccc
Q 034486 53 KENKEFFEAYARKNAERATVMETRERIEKILANSTT 88 (93)
Q Consensus 53 keNpeFFkaY~~~~~~~~~~~~~~~~iq~~~s~~~~ 88 (93)
....+||..|...|+... .+.-+.++.+|.+...
T Consensus 82 ~~~~~~f~~~rl~Re~~r--~~~~e~L~~ii~~~~~ 115 (196)
T PF12685_consen 82 SSGSDYFAEARLEREQSR--SKQIETLKEIINNENA 115 (196)
T ss_dssp -----HHHHHHHHHHHHH--HHHHHHHHHHHT-TTS
T ss_pred cchHHHHHHHHHHHHHHH--HHHHHHHHHHHhCCCC
Confidence 344579999987776643 3445677788866543
No 99
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=24.80 E-value=1.3e+02 Score=17.13 Aligned_cols=33 Identities=36% Similarity=0.335 Sum_probs=18.5
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034486 14 HLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 14 ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEk 53 (93)
..|+..+...||..|+.+.|- +.| ++|.++|..
T Consensus 11 ~~I~~l~~~G~s~~~IA~~lg----~s~---sTV~relkR 43 (44)
T PF13936_consen 11 NQIEALLEQGMSIREIAKRLG----RSR---STVSRELKR 43 (44)
T ss_dssp -HHHHHHCS---HHHHHHHTT------H---HHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHC----cCc---HHHHHHHhc
Confidence 347777788888888777664 444 477777653
No 100
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=24.76 E-value=90 Score=20.24 Aligned_cols=38 Identities=18% Similarity=0.096 Sum_probs=25.1
Q ss_pred HHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHH
Q 034486 16 IEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEK 53 (93)
Q Consensus 16 IErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEk 53 (93)
|.+|..+..++..|+.+|....+-.+.+...|-+.|..
T Consensus 1 i~~~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~l~~ 38 (87)
T PF11626_consen 1 IKHYEELGYSREFVTHALYATSGDPELARRFVLNFLQA 38 (87)
T ss_dssp -HHHHHHTB-HHHHHHHHHHTTTBHHHHHHHHHHCHCH
T ss_pred CchHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 67788899999999999988655444444446665543
No 101
>PF03081 Exo70: Exo70 exocyst complex subunit; InterPro: IPR004140 The Exo70 protein forms one subunit of the exocyst complex. First discovered in Saccharomyces cerevisiae [], Exo70 and other exocyst proteins have been observed in several other eukaryotes, including humans. In S. cerevisiae, the exocyst complex is involved in the late stages of exocytosis, and is localized at the tip of the bud, the major site of exocytosis in yeast []. Exo70 interacts with the Rho3 GTPase []. This interaction mediates one of the three known functions of Rho3 in cell polarity: vesicle docking and fusion with the plasma membrane (the other two functions are regulation of actin polarity and transport of exocytic vesicles from the mother cell to the bud) []. In humans, the functions of Exo70 and the exocyst complex are less well characterised: Exo70 is expressed in several tissues and is thought to also be involved in exocytosis [].; GO: 0006887 exocytosis, 0000145 exocyst; PDB: 2PFV_A 2B7M_B 2B1E_A 2PFT_A.
Probab=24.57 E-value=2.8e+02 Score=21.47 Aligned_cols=75 Identities=16% Similarity=0.223 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHHHHhhCCH--HHHHHHHHhh-----cCCCchhHHHHHHHHHHhCHHHHHHHHhcHHHHHhHHHHHHHH
Q 034486 7 SYIHLVHHLIEECLVFNMSK--EECMEALSKH-----ANIKPVITSTVWKELEKENKEFFEAYARKNAERATVMETRERI 79 (93)
Q Consensus 7 ~~I~~VQ~LIErCLqlyMsk--~E~v~~L~~~-----a~I~P~~T~~VW~~LEkeNpeFFkaY~~~~~~~~~~~~~~~~i 79 (93)
+-++.....|++|...||.- .-|+..|... .+....--..+=+++.+=|.+|=++|...+.-.-.+.+.++.+
T Consensus 248 ~~~~~~~~~~~~~~~~Y~~~sW~~v~~~L~~~~~~~~~~~~~~~~~~~ke~f~~Fn~~fee~~~~q~~~~vpD~~LR~~L 327 (371)
T PF03081_consen 248 DWEQRLSSKIEQYIKSYLRSSWGPVLSCLSDDSSSSGGKLSSKERELLKEKFKKFNSAFEEIYKAQKTWKVPDPELREEL 327 (371)
T ss_dssp CHHHHHHHHHHHHHHHHHCHHHHHHHCTCCHHCC-T-SSS-HHHHHHHHHHHHHHHHHHHHHHHHHTT---S-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccCCCCCccHHHHHHHHHHHHHHHHHHHHcCcceecCCHHHHHHH
Confidence 44567779999999999976 5566666652 3444445556666777778888888876544444444444444
Q ss_pred HH
Q 034486 80 EK 81 (93)
Q Consensus 80 q~ 81 (93)
.+
T Consensus 328 r~ 329 (371)
T PF03081_consen 328 RR 329 (371)
T ss_dssp HH
T ss_pred HH
Confidence 43
No 102
>KOG3779 consensus Homeobox transcription factor prospero [Transcription]
Probab=24.17 E-value=85 Score=28.33 Aligned_cols=37 Identities=19% Similarity=0.363 Sum_probs=27.7
Q ss_pred HHHHHHHHHhhcCCCchhHHHHH---HHHHHhCHHHHHHH
Q 034486 26 KEECMEALSKHANIKPVITSTVW---KELEKENKEFFEAY 62 (93)
Q Consensus 26 k~E~v~~L~~~a~I~P~~T~~VW---~~LEkeNpeFFkaY 62 (93)
..|..+++-.--.|+|..-.+++ ++|+.|=|||||.=
T Consensus 689 LREF~~AI~~GKDvdPSWKK~IYKVI~kLd~evPe~FK~P 728 (737)
T KOG3779|consen 689 LREFFNAIIAGKDVDPSWKKAIYKVICKLDSEVPEIFKSP 728 (737)
T ss_pred HHHHHHHHhcCCcCCchHHHHHHHHHHhhhhhhhHhhcCc
Confidence 34555666666679998877655 68999999999864
No 103
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=24.08 E-value=1.7e+02 Score=17.40 Aligned_cols=29 Identities=14% Similarity=0.126 Sum_probs=21.1
Q ss_pred hHHHHHHHHHHHHHHHHhhCCHHHHHHHHH
Q 034486 5 SASYIHLVHHLIEECLVFNMSKEECMEALS 34 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~ 34 (93)
+.++|..++. |-...+..||.+||...|+
T Consensus 40 t~~di~~l~~-i~~l~~~g~~l~~i~~~l~ 68 (68)
T cd04763 40 NDADIDRILE-IKRWIDNGVQVSKVKKLLS 68 (68)
T ss_pred CHHHHHHHHH-HHHHHHcCCCHHHHHHHhC
Confidence 4567776654 6666778999999988763
No 104
>PLN02350 phosphogluconate dehydrogenase (decarboxylating)
Probab=23.99 E-value=1.7e+02 Score=25.05 Aligned_cols=45 Identities=16% Similarity=0.200 Sum_probs=32.4
Q ss_pred CCC-chHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034486 1 MDD-SSASYIHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 1 ~~~-~s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~V 47 (93)
+|+ .+..++.+|+|.|+=+.-. ---|.+..+.+..|++|.--..|
T Consensus 178 vG~~GaG~~vKlv~N~i~~~~m~--~iaEA~~l~~~~~Gld~~~l~~v 223 (493)
T PLN02350 178 IGPGGAGNFVKMVHNGIEYGDMQ--LISEAYDVLKSVGGLSNEELAEV 223 (493)
T ss_pred eCCcCHHHHHHHHHHHHHHHHHH--HHHHHHHHHHhhCCCCHHHHHHH
Confidence 355 3788999999999965543 24577777776568988877666
No 105
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=23.98 E-value=94 Score=22.56 Aligned_cols=27 Identities=15% Similarity=0.251 Sum_probs=22.4
Q ss_pred HHHHHHhhcCCCchhHHHHHHHHHHhC
Q 034486 29 CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 29 ~v~~L~~~a~I~P~~T~~VW~~LEkeN 55 (93)
-++.|++..||.|.+..-|++.|.+.+
T Consensus 27 s~~eIA~~~~ip~~~l~kIl~~L~~aG 53 (164)
T PRK10857 27 PLADISERQGISLSYLEQLFSRLRKNG 53 (164)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 346677888999999999999998754
No 106
>COG1498 SIK1 Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]
Probab=23.66 E-value=1.3e+02 Score=25.68 Aligned_cols=51 Identities=25% Similarity=0.238 Sum_probs=43.0
Q ss_pred CCCc-hHHHHHHHHHHHHHHHHhhCCHHHHHHHHHhhc-CCCchhHHHHHHHH
Q 034486 1 MDDS-SASYIHLVHHLIEECLVFNMSKEECMEALSKHA-NIKPVITSTVWKEL 51 (93)
Q Consensus 1 ~~~~-s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~~a-~I~P~~T~~VW~~L 51 (93)
||.. +..||+.|+.+.|.-..+|==++++-+++.... .|-|.+|.+|=-.|
T Consensus 200 mG~~~~~~Di~~i~~~ae~i~~L~~~R~~l~~Yi~~~M~~vAPNlt~LVG~~l 252 (395)
T COG1498 200 MGADLSEEDIDNIRELAEIILELYELREQLEEYIESKMSEIAPNLTALVGPVL 252 (395)
T ss_pred cccCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCccHHHHHhHHH
Confidence 5553 789999999999999999999999999998854 58999999884433
No 107
>PF10239 DUF2465: Protein of unknown function (DUF2465); InterPro: IPR018797 FAM98A, B and C are glycine-rich proteins found from worms to humans whose function is unknown.
Probab=23.17 E-value=77 Score=25.75 Aligned_cols=27 Identities=26% Similarity=0.495 Sum_probs=23.2
Q ss_pred hhHHHHHHHHHHhCHHHHHHHHhcHHH
Q 034486 42 VITSTVWKELEKENKEFFEAYARKNAE 68 (93)
Q Consensus 42 ~~T~~VW~~LEkeNpeFFkaY~~~~~~ 68 (93)
.+|..=|.+|++-|....+.|..||.-
T Consensus 184 ~L~~~Qw~~Le~i~~~L~~EY~~RR~m 210 (318)
T PF10239_consen 184 SLTDEQWEKLEKINQALSKEYECRRQM 210 (318)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345788999999999999999998753
No 108
>PF14076 DUF4258: Domain of unknown function (DUF4258)
Probab=22.81 E-value=1.3e+02 Score=17.62 Aligned_cols=23 Identities=26% Similarity=0.277 Sum_probs=20.5
Q ss_pred HHHHHHHHHhhCCHHHHHHHHHh
Q 034486 13 HHLIEECLVFNMSKEECMEALSK 35 (93)
Q Consensus 13 Q~LIErCLqlyMsk~E~v~~L~~ 35 (93)
.|.++|..+-..|.+++..+|..
T Consensus 4 ~Ha~~rm~eR~Is~~~I~~~l~~ 26 (73)
T PF14076_consen 4 KHARERMQERGISEEDIEDALEN 26 (73)
T ss_pred HHHHHHHHhCCCCHHHHHHHHhc
Confidence 57889999999999999999975
No 109
>PF12980 DUF3864: Domain of Unknown Function with PDB structure (DUF3864); InterPro: IPR024335 This entry represents a functionally uncharacterised domain found in bacterial sequences. The structure of one of the sequences, A6LGL1 from SWISSPROT from Parabacteroides distasonis atcc 8503, has been determined.; PDB: 3LM3_A.
Probab=22.66 E-value=22 Score=24.30 Aligned_cols=29 Identities=17% Similarity=0.434 Sum_probs=19.6
Q ss_pred hcCCCchhHHHHHHHHHHhCHHHHHHHHh
Q 034486 36 HANIKPVITSTVWKELEKENKEFFEAYAR 64 (93)
Q Consensus 36 ~a~I~P~~T~~VW~~LEkeNpeFFkaY~~ 64 (93)
|-|..|.=+-.+..+|.++|.+|-++||-
T Consensus 50 qkglrpqd~pvll~~l~~~~q~li~kyyp 78 (82)
T PF12980_consen 50 QKGLRPQDKPVLLSELSQEDQDLIRKYYP 78 (82)
T ss_dssp TT--SGGGS-B-GGGS-HHHHHHHHHH-G
T ss_pred hccCCCcCcchHHHHHhHHHHHHHHHHhH
Confidence 45777777777889999999999999985
No 110
>cd07765 KRAB_A-box KRAB (Kruppel-associated box) domain -A box. The KRAB domain is a transcription repression module, found in a subgroup of the zinc finger proteins (ZFPs) of the C2H2 family, KRAB-ZFPs. KRAB-ZFPs comprise the largest group of transcriptional regulators in mammals, and are only found in tetrapods. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through
Probab=22.48 E-value=34 Score=14.66 Aligned_cols=25 Identities=8% Similarity=0.449 Sum_probs=17.1
Q ss_pred CCCchhHHHHHHHHHHhCHHHHHHH
Q 034486 38 NIKPVITSTVWKELEKENKEFFEAY 62 (93)
Q Consensus 38 ~I~P~~T~~VW~~LEkeNpeFFkaY 62 (93)
++...++..-|..++....++|+.-
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~ 29 (40)
T cd07765 5 DVAVYFSQEEWELLDPAQRDLYRDV 29 (40)
T ss_pred eeeeecCHHHHhcCCHHHHHHHHHH
Confidence 3445667778888887777777643
No 111
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=22.45 E-value=1.8e+02 Score=18.18 Aligned_cols=47 Identities=13% Similarity=0.189 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHH-hhCCHHHHHHHHHhhcC--CCc-hhHHHHHHHHHH
Q 034486 7 SYIHLVHHLIEECLV-FNMSKEECMEALSKHAN--IKP-VITSTVWKELEK 53 (93)
Q Consensus 7 ~~I~~VQ~LIErCLq-lyMsk~E~v~~L~~~a~--I~P-~~T~~VW~~LEk 53 (93)
.+.+||...|..+=. .--|...|..++..+.+ ++| .+...|..-|.+
T Consensus 4 ~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~ 54 (77)
T PF00538_consen 4 PYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKR 54 (77)
T ss_dssp CHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHH
Confidence 456777777765432 45678889999999886 556 677777776654
No 112
>cd05049 PTKc_Trk Catalytic domain of the Protein Tyrosine Kinases, Tropomyosin Related Kinases. Protein Tyrosine Kinase (PTK) family; Tropomyosin Related Kinase (Trk) subfamily; catalytic (c) domain. The Trk subfamily consists of TrkA, TrkB, TrkC, and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Trk subfamily members are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding to their ligands, the nerve growth factor (NGF) family of neutrotrophins, leads to Trk receptor oligomerization and activation of the catalyt
Probab=22.35 E-value=98 Score=21.76 Aligned_cols=25 Identities=16% Similarity=0.247 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHhh----CCHHHHHHHHH
Q 034486 10 HLVHHLIEECLVFN----MSKEECMEALS 34 (93)
Q Consensus 10 ~~VQ~LIErCLqly----Msk~E~v~~L~ 34 (93)
..+.++|.+||+.- .+-+|+.+.|.
T Consensus 251 ~~~~~li~~~l~~~p~~Rp~~~eil~~l~ 279 (280)
T cd05049 251 SEVYDIMLGCWKRDPQQRINIKDIHERLQ 279 (280)
T ss_pred HHHHHHHHHHcCCCcccCCCHHHHHHHhh
Confidence 46788999999774 66677766664
No 113
>TIGR03342 dsrC_tusE_dsvC sulfur relay protein, TusE/DsrC/DsvC family. Members of this protein family may be described as TusE, a partner to TusBCD in a sulfur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Other members are DsrC, a functionally similar protein in species where the sulfur relay system exists primarily for sulfur metabolism rather than tRNA base modification. Some members of this family are known explicitly as the gamma subunit of sulfite reductases.
Probab=22.34 E-value=2.5e+02 Score=19.63 Aligned_cols=36 Identities=25% Similarity=0.544 Sum_probs=26.4
Q ss_pred HHHHHHHHhhcCCCchhHHHHHHHHHHhCHHHHHHHHhc
Q 034486 27 EECMEALSKHANIKPVITSTVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 27 ~E~v~~L~~~a~I~P~~T~~VW~~LEkeNpeFFkaY~~~ 65 (93)
+|+..+|.++-|| .+|..-|+-+.-- .+||..|...
T Consensus 24 e~vA~~lA~~egi--eLT~~Hw~vI~~l-R~~y~e~~~~ 59 (108)
T TIGR03342 24 EDVAEALAEEEGI--ELTEAHWEVINFL-RDFYAEYNIS 59 (108)
T ss_pred HHHHHHHHHHcCC--CCCHHHHHHHHHH-HHHHHHHCCC
Confidence 6899999999999 4999999877422 3355555443
No 114
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.27 E-value=1.1e+02 Score=20.15 Aligned_cols=41 Identities=10% Similarity=0.131 Sum_probs=30.0
Q ss_pred HHHhhCCHHHHHHHHHhhcCC-CchhHHHHHHHHHHhCHHHH
Q 034486 19 CLVFNMSKEECMEALSKHANI-KPVITSTVWKELEKENKEFF 59 (93)
Q Consensus 19 CLqlyMsk~E~v~~L~~~a~I-~P~~T~~VW~~LEkeNpeFF 59 (93)
..++|......|..+..++|| .|..-..=|.++.+.....|
T Consensus 16 iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~ 57 (116)
T COG2963 16 AVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAF 57 (116)
T ss_pred HHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccc
Confidence 445566666688899999996 88888777788887664443
No 115
>PF10474 DUF2451: Protein of unknown function C-terminus (DUF2451); InterPro: IPR019514 This protein is found in eukaryotes but its function is not known. The N-terminal domain of some members is PF10475 from PFAM (DUF2450).
Probab=21.83 E-value=1.5e+02 Score=22.73 Aligned_cols=51 Identities=25% Similarity=0.436 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHHHHh-CHHHHHHHHh
Q 034486 10 HLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTVWKELEKE-NKEFFEAYAR 64 (93)
Q Consensus 10 ~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~LEke-NpeFFkaY~~ 64 (93)
..|..|+..|-.+.+..+++. .+..|.|.+...+|+.+-.- +.-+=+.|-.
T Consensus 92 ~YVd~l~~~~~~f~~rL~~i~----~~~~i~~~~~~~lw~~~i~~~~~~Lveg~s~ 143 (234)
T PF10474_consen 92 SYVDQLVQEFQQFSERLDEIS----KQGPIPPEVQNVLWDRLIFFAFETLVEGYSR 143 (234)
T ss_pred HHHHHHHHHHHHHHHHHHHHH----hcCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356778888888876666665 67899999999999987543 3444455644
No 116
>PF14123 DUF4290: Domain of unknown function (DUF4290)
Probab=21.61 E-value=2.2e+02 Score=21.78 Aligned_cols=46 Identities=20% Similarity=0.382 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHHhhCCHHH----------HHHHHHhhcCCCchhHHHHHHHHH
Q 034486 6 ASYIHLVHHLIEECLVFNMSKEE----------CMEALSKHANIKPVITSTVWKELE 52 (93)
Q Consensus 6 ~~~I~~VQ~LIErCLqlyMsk~E----------~v~~L~~~a~I~P~~T~~VW~~LE 52 (93)
.+|=+-||++|+-|+.+ =+++| +|..|.=|..=.|.|..-+|..|-
T Consensus 13 pEYGR~IQ~MVd~~~ti-eDreeR~~~A~~II~iM~~l~P~lRd~~Df~hKLWDhL~ 68 (176)
T PF14123_consen 13 PEYGRNIQKMVDYAVTI-EDREERNRCAETIIEIMGNLNPHLRDVPDFKHKLWDHLF 68 (176)
T ss_pred chhhHHHHHHHHHHHhC-CCHHHHHHHHHHHHHHHHhcCCccCCChhHHHHHHHHHH
Confidence 46778999999999986 24433 455555566667889999999883
No 117
>PF12415 rpo132: Poxvirus DNA dependent RNA polymerase; InterPro: IPR024390 All three classes of poxvirus genes - early, intermediate and late - are transcribed by the viral RNA polymerase compex []. This complex is composed of nine distinct subunits which total more than 500kDa in mass. The two largest subunits (147 and 136kDa) are homologous to the largest subunits of eukaryotic and prokaryotic RNA polymerases and, like them, are thought to form a claw-shaped structure whose cleft is the site of template interaction and phosphodiester bond formation. While the smaller subunits of poxvirus RNA polymerase show much less similarity, if any, to the smaller subunits of the eukaryotic and prokaryotic enzymes, it is thought that they may play a similar role in interacting with transcription factors. The 132kDa subunit is the second largest subunit of the poxvirus DNA dependent RNA polymerase and shows structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
Probab=21.47 E-value=1e+02 Score=17.71 Aligned_cols=15 Identities=40% Similarity=0.470 Sum_probs=12.9
Q ss_pred hHHHHHHHHHHHHHH
Q 034486 5 SASYIHLVHHLIEEC 19 (93)
Q Consensus 5 s~~~I~~VQ~LIErC 19 (93)
|.+-+.+|+.+||.-
T Consensus 12 p~ei~ylvnalIest 26 (33)
T PF12415_consen 12 PPEIIYLVNALIEST 26 (33)
T ss_pred CHHHHHHHHHHHHHH
Confidence 688899999999963
No 118
>PF10364 NKWYS: Putative capsular polysaccharide synthesis protein; InterPro: IPR018831 This entry contains proteins of no known function. They are found predominantly in Vibrio and cyanobacterial species and are characterised by having a NKWYS sequence motif.
Probab=21.47 E-value=81 Score=23.22 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=28.3
Q ss_pred CchHHHHHHHHHHHHHHHHhhCCHHHHHHHHHh
Q 034486 3 DSSASYIHLVHHLIEECLVFNMSKEECMEALSK 35 (93)
Q Consensus 3 ~~s~~~I~~VQ~LIErCLqlyMsk~E~v~~L~~ 35 (93)
|+++.+|..-|.+.|.|+..+|+.+-...-+-+
T Consensus 7 d~~~~~~e~~~~l~e~~F~~~~~~~~~~~WFD~ 39 (141)
T PF10364_consen 7 DDIHIDIERTQLLLEHCFENHFNHNYPLNWFDN 39 (141)
T ss_pred hhhhhcchHHHHHHHHHHhccCCcchhhhHHHH
Confidence 567889999999999999999999988766554
No 119
>PF08020 DUF1706: Protein of unknown function (DUF1706) ; InterPro: IPR012550 This family contains many hypothetical proteins from bacteria and yeast.
Probab=21.20 E-value=1.4e+02 Score=21.98 Aligned_cols=30 Identities=23% Similarity=0.478 Sum_probs=24.3
Q ss_pred hcCCCchhHH--HHHHHHHHhCHHHHHHHHhc
Q 034486 36 HANIKPVITS--TVWKELEKENKEFFEAYARK 65 (93)
Q Consensus 36 ~a~I~P~~T~--~VW~~LEkeNpeFFkaY~~~ 65 (93)
.+|-.|.|-. .=|+.|-.=|..|++.|...
T Consensus 68 ~~G~~~~fp~~gykWn~lg~Ln~~f~~~y~~~ 99 (166)
T PF08020_consen 68 QAGEEVDFPAPGYKWNQLGELNQSFYEKYQDT 99 (166)
T ss_pred cCCCCCCCCCCCCChhhhhHHHHHHHHHHcCC
Confidence 5677777754 56999999999999999663
No 120
>cd05116 PTKc_Syk Catalytic domain of the Protein Tyrosine Kinase, Spleen tyrosine kinase. Protein Tyrosine Kinase (PTK) family; Spleen tyrosine kinase (Syk); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Syk, together with Zap-70, form the Syk subfamily of kinases which are cytoplasmic (or nonreceptor) tyr kinases containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. Syk was first cloned from the spleen, and its function in hematopoietic cells is well-established. Syk is involved in the signaling downstream of activated receptors (including B-cell and Fc receptors) that contain ITAMs (immunoreceptor tyr activation motifs), leading to processes such as cell proliferatio
Probab=21.11 E-value=1.2e+02 Score=21.22 Aligned_cols=26 Identities=12% Similarity=0.117 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHh----hCCHHHHHHHHHh
Q 034486 10 HLVHHLIEECLVF----NMSKEECMEALSK 35 (93)
Q Consensus 10 ~~VQ~LIErCLql----yMsk~E~v~~L~~ 35 (93)
..++++|.+|++. ..+-++|+..|.+
T Consensus 225 ~~l~~li~~~~~~~p~~Rp~~~~i~~~l~~ 254 (257)
T cd05116 225 PEMYDLMKLCWTYGVDERPGFAVVELRLRN 254 (257)
T ss_pred HHHHHHHHHHhccCchhCcCHHHHHHHHhc
Confidence 4567899999964 5677778777764
No 121
>PF13518 HTH_28: Helix-turn-helix domain
Probab=21.06 E-value=1.5e+02 Score=16.21 Aligned_cols=27 Identities=7% Similarity=0.090 Sum_probs=15.7
Q ss_pred HHHHHHhhcCCCchhHHHHHHHHHHhC
Q 034486 29 CMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 29 ~v~~L~~~a~I~P~~T~~VW~~LEkeN 55 (93)
-+..+.+++||.|.--...++..++.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 455577788997754444444444433
No 122
>TIGR01797 CM_P_1 chorismate mutase domain of proteobacterial P-protein, clade 1. This model represents the chorismate mutase domain of the gamma and beta proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain.
Probab=21.06 E-value=1.4e+02 Score=19.11 Aligned_cols=19 Identities=0% Similarity=0.141 Sum_probs=12.9
Q ss_pred hcCCCchhHHHHHHHHHHh
Q 034486 36 HANIKPVITSTVWKELEKE 54 (93)
Q Consensus 36 ~a~I~P~~T~~VW~~LEke 54 (93)
..+++|.+...+|+.+=+.
T Consensus 59 ~~~l~~~~i~~if~~ii~~ 77 (83)
T TIGR01797 59 AYHLDAHYITRLFQLIIED 77 (83)
T ss_pred hCCCCHHHHHHHHHHHHHH
Confidence 3567777777777766544
No 123
>KOG2431 consensus 1, 2-alpha-mannosidase [Carbohydrate transport and metabolism]
Probab=21.04 E-value=1e+02 Score=27.37 Aligned_cols=21 Identities=24% Similarity=0.464 Sum_probs=18.6
Q ss_pred hHHHHHHHHHHHHHHHHhh-CC
Q 034486 5 SASYIHLVHHLIEECLVFN-MS 25 (93)
Q Consensus 5 s~~~I~~VQ~LIErCLqly-Ms 25 (93)
+.++..+.|+|-+.|.|.| ||
T Consensus 390 ~~~hl~lA~~l~~TCyqMY~~~ 411 (546)
T KOG2431|consen 390 SEEHLELAQELMETCYQMYRQN 411 (546)
T ss_pred chHHHHHHHHHHHHHHHHHccC
Confidence 4679999999999999999 54
No 124
>cd05093 PTKc_TrkB Catalytic domain of the Protein Tyrosine Kinase, Tropomyosin Related Kinase B. Protein Tyrosine Kinase (PTK) family; Tropomyosin Related Kinase B (TrkB); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. TrkB is a member of the Trk subfamily of proteins, which are receptor tyr kinases (RTKs) containing an extracellular region with arrays of leucine-rich motifs flanked by two cysteine-rich clusters followed by two immunoglobulin-like domains, a transmembrane segment, and an intracellular catalytic domain. Binding of TrkB to its ligands, brain-derived neurotrophic factor (BDNF) or neurotrophin 4 (NT4), results in receptor oligomerization and activation of the catalytic domain. TrkB is broadly
Probab=21.00 E-value=99 Score=22.21 Aligned_cols=29 Identities=21% Similarity=0.200 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHhh----CCHHHHHHHHHhhcCC
Q 034486 11 LVHHLIEECLVFN----MSKEECMEALSKHANI 39 (93)
Q Consensus 11 ~VQ~LIErCLqly----Msk~E~v~~L~~~a~I 39 (93)
-+.++|.+||+.- .|-+|+...|.+-++.
T Consensus 250 ~l~~li~~~l~~~p~~Rpt~~~v~~~l~~~~~~ 282 (288)
T cd05093 250 EVYDLMLGCWQREPHMRLNIKEIHSLLQNLAKA 282 (288)
T ss_pred HHHHHHHHHccCChhhCCCHHHHHHHHHHHHHh
Confidence 4788999999764 7778888877764443
No 125
>KOG2939 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.86 E-value=1.2e+02 Score=26.74 Aligned_cols=40 Identities=18% Similarity=0.462 Sum_probs=27.0
Q ss_pred HHHHHHHhhcCCCchh----HHHHHHHHHHhCHHHHHHHHhcHH
Q 034486 28 ECMEALSKHANIKPVI----TSTVWKELEKENKEFFEAYARKNA 67 (93)
Q Consensus 28 E~v~~L~~~a~I~P~~----T~~VW~~LEkeNpeFFkaY~~~~~ 67 (93)
.+++++..--+|--.| +..+=..++++.++||++|+.-+-
T Consensus 122 qive~isrf~~vGeeFcg~ese~l~Esi~k~se~YFkrYH~q~m 165 (502)
T KOG2939|consen 122 QIVETISRFYYVGEEFCGFESEKLHESIKKQSEEYFKRYHRQRM 165 (502)
T ss_pred HHHHHHHHHHhhhhhhccchHHHHHHHHHhhhHHHHHHHHHHHH
Confidence 5666666544444333 345566789999999999987443
No 126
>PRK11675 LexA regulated protein; Provisional
Probab=20.74 E-value=1.9e+02 Score=19.90 Aligned_cols=26 Identities=31% Similarity=0.295 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHh
Q 034486 10 HLVHHLIEECLVFNMSKEECMEALSK 35 (93)
Q Consensus 10 ~~VQ~LIErCLqlyMsk~E~v~~L~~ 35 (93)
+.++.|-+-|-+..||+.|+|+..-+
T Consensus 60 dl~ekL~eyAe~~nitRSElIr~~I~ 85 (90)
T PRK11675 60 DLVDALNELAEARNISRSELIEEILM 85 (90)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 57889999999999999999976543
No 127
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=20.72 E-value=1.1e+02 Score=23.40 Aligned_cols=23 Identities=30% Similarity=0.349 Sum_probs=15.7
Q ss_pred HHHHHHHHhhCCHHHHHHHHHhh
Q 034486 14 HLIEECLVFNMSKEECMEALSKH 36 (93)
Q Consensus 14 ~LIErCLqlyMsk~E~v~~L~~~ 36 (93)
.|+-|=+.-.|||+++|.+|..-
T Consensus 11 eLLqrL~~SG~TK~~ii~ALe~l 33 (180)
T PF04814_consen 11 ELLQRLRRSGMTKEEIIHALETL 33 (180)
T ss_dssp HHHHHHHHCT--HHHHHHHHTT-
T ss_pred HHHHHHHHcCCCHHHHHHHHhcc
Confidence 34445577899999999999853
No 128
>PF15637 Tox-HNH-HHH: HNH/Endo VII superfamily nuclease toxin with a HHH motif
Probab=20.68 E-value=58 Score=23.57 Aligned_cols=24 Identities=29% Similarity=0.385 Sum_probs=17.5
Q ss_pred HHHHHHHHHhCHHHHHHHHhcHHH
Q 034486 45 STVWKELEKENKEFFEAYARKNAE 68 (93)
Q Consensus 45 ~~VW~~LEkeNpeFFkaY~~~~~~ 68 (93)
..-|++|.+-|||||..=...+-+
T Consensus 38 k~fw~~l~~~~pe~~S~~N~~~I~ 61 (116)
T PF15637_consen 38 KYFWDELLKLYPEMLSKENRARIE 61 (116)
T ss_pred HHHHHHHHHhChhhcCHhHHHHHH
Confidence 357999999999988766554444
No 129
>PF13592 HTH_33: Winged helix-turn helix
Probab=20.67 E-value=1.6e+02 Score=17.58 Aligned_cols=38 Identities=13% Similarity=0.055 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHhhCCHHHHHHHHHhhcCCCchhHHHH
Q 034486 9 IHLVHHLIEECLVFNMSKEECMEALSKHANIKPVITSTV 47 (93)
Q Consensus 9 I~~VQ~LIErCLqlyMsk~E~v~~L~~~a~I~P~~T~~V 47 (93)
...|+.+|++++---+|..-|-+.|. +.|..+.-...+
T Consensus 7 ~~~i~~~I~~~fgv~ys~~~v~~lL~-r~G~s~~kp~~~ 44 (60)
T PF13592_consen 7 LKEIAAYIEEEFGVKYSPSGVYRLLK-RLGFSYQKPRPR 44 (60)
T ss_pred HHHHHHHHHHHHCCEEcHHHHHHHHH-HcCCccccCCCC
Confidence 56789999999999888888877777 458776655544
No 130
>PF00452 Bcl-2: Apoptosis regulator proteins, Bcl-2 family; InterPro: IPR000712 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 2WH6_A 1K3K_A 1AF3_A 3PK1_B 2K7W_A 1F16_A 3PL7_C 2VM6_A 3I1H_A 3MQP_A ....
Probab=20.61 E-value=1.4e+02 Score=18.99 Aligned_cols=37 Identities=22% Similarity=0.337 Sum_probs=26.6
Q ss_pred HHHHHhCHHHHHHHHhcHHH---HHhHHHHHHHHHHHHhc
Q 034486 49 KELEKENKEFFEAYARKNAE---RATVMETRERIEKILAN 85 (93)
Q Consensus 49 ~~LEkeNpeFFkaY~~~~~~---~~~~~~~~~~iq~~~s~ 85 (93)
.++++.++++|+........ ......+.+....++++
T Consensus 6 ~~~e~~~~~~f~~~~~~l~~~~~~~~~~~f~~v~~~lf~d 45 (101)
T PF00452_consen 6 DELERKYEDFFENMLNQLNINTPDNAYETFNEVAEELFED 45 (101)
T ss_dssp HHHHHHHHHHHHHHHHHHCSSSTTTHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhcc
Confidence 57889999999998775433 33556677777777765
No 131
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=20.30 E-value=1.9e+02 Score=20.04 Aligned_cols=32 Identities=9% Similarity=0.173 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHhhcCCCchhHHHHHHHHHHhC
Q 034486 24 MSKEECMEALSKHANIKPVITSTVWKELEKEN 55 (93)
Q Consensus 24 Msk~E~v~~L~~~a~I~P~~T~~VW~~LEkeN 55 (93)
.+-.||++.|.+..++.+.-+.++.+.|++..
T Consensus 19 ~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG 50 (130)
T TIGR02698 19 TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKG 50 (130)
T ss_pred CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCC
Confidence 57889999998888899999999999998743
No 132
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=20.18 E-value=1.1e+02 Score=17.80 Aligned_cols=21 Identities=14% Similarity=0.273 Sum_probs=14.8
Q ss_pred HHHHHhhcCCCchhHHHHHHH
Q 034486 30 MEALSKHANIKPVITSTVWKE 50 (93)
Q Consensus 30 v~~L~~~a~I~P~~T~~VW~~ 50 (93)
..+|...+||.+.+..-+++.
T Consensus 12 ~~~L~~~f~ip~~vAk~IV~~ 32 (40)
T PF02022_consen 12 AKALRHKFGIPRLVAKQIVNQ 32 (40)
T ss_dssp HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHccCHHHHHHHHHH
Confidence 467888899999888877753
No 133
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=20.03 E-value=1.3e+02 Score=20.58 Aligned_cols=34 Identities=24% Similarity=0.301 Sum_probs=29.0
Q ss_pred HHHHhhCCHHHHHHHHHhhcCCCchhHHHHHHHH
Q 034486 18 ECLVFNMSKEECMEALSKHANIKPVITSTVWKEL 51 (93)
Q Consensus 18 rCLqlyMsk~E~v~~L~~~a~I~P~~T~~VW~~L 51 (93)
--|.|.|+.|..+-+..+..+|.|.---.-|+.|
T Consensus 50 ~VLdFl~~de~~l~af~~a~~~~p~~v~~Ar~~L 83 (88)
T PF12096_consen 50 AVLDFLLMDEAWLLAFCDAAGIPPEAVAAARQAL 83 (88)
T ss_pred HHHHHHHcchHHHHHHHHHcCcChhHHHHHHHHC
Confidence 3578899999999999999999998887777665
No 134
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=20.01 E-value=69 Score=20.33 Aligned_cols=28 Identities=21% Similarity=0.477 Sum_probs=16.4
Q ss_pred HHHHHHhhcCC-CchhHHHHHHHHHHhCH
Q 034486 29 CMEALSKHANI-KPVITSTVWKELEKENK 56 (93)
Q Consensus 29 ~v~~L~~~a~I-~P~~T~~VW~~LEkeNp 56 (93)
+++.+.+++.- .+.--..+|++|++++|
T Consensus 13 l~~~v~~~~~~~~~~~Gn~iwk~le~~~~ 41 (65)
T PF08914_consen 13 LLDYVKENERQGGSVSGNKIWKELEEKHP 41 (65)
T ss_dssp HHHHHHHT--STTTTTSSHHHHHHHHS-S
T ss_pred HHHHHHHhccCCCCCchHHHHHHHHHHcC
Confidence 34455433221 34455799999999998
Done!