Query 034472
Match_columns 93
No_of_seqs 95 out of 97
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 03:14:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034472.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034472hhsearch_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 2.6E-37 5.7E-42 196.8 6.8 57 19-75 1-57 (57)
2 PF09713 A_thal_3526: Plant pr 100.0 2.7E-36 5.8E-41 190.2 6.4 54 22-75 1-54 (54)
3 smart00411 BHL bacterial (prok 86.7 1.7 3.6E-05 27.6 4.3 31 34-64 1-31 (90)
4 PF03918 CcmH: Cytochrome C bi 81.7 2.9 6.2E-05 30.4 4.2 42 7-48 40-88 (148)
5 PF00216 Bac_DNA_binding: Bact 80.0 3.5 7.7E-05 25.9 3.7 32 34-65 1-32 (90)
6 PF13565 HTH_32: Homeodomain-l 79.4 7.8 0.00017 23.5 5.1 43 18-60 32-76 (77)
7 PF08986 DUF1889: Domain of un 78.5 3.2 6.9E-05 30.0 3.5 36 39-74 68-112 (119)
8 COG1725 Predicted transcriptio 77.8 5.1 0.00011 28.8 4.4 48 18-65 13-63 (125)
9 TIGR00988 hip integration host 75.6 7.3 0.00016 25.2 4.3 31 34-64 1-32 (94)
10 TIGR03147 cyt_nit_nrfF cytochr 74.7 7.7 0.00017 28.0 4.6 52 7-58 40-105 (126)
11 TIGR00987 himA integration hos 74.1 8 0.00017 25.4 4.3 32 34-65 2-33 (96)
12 PRK00285 ihfA integration host 71.6 9.7 0.00021 25.0 4.2 32 33-64 2-33 (99)
13 PRK00199 ihfB integration host 71.6 10 0.00022 24.6 4.3 31 34-64 1-32 (94)
14 PRK10664 transcriptional regul 71.4 10 0.00022 25.0 4.3 26 34-59 1-26 (90)
15 PRK10144 formate-dependent nit 67.6 14 0.00031 26.7 4.7 52 7-58 40-105 (126)
16 PRK10753 transcriptional regul 66.4 15 0.00032 24.1 4.3 27 34-60 1-27 (90)
17 COG2169 Ada Adenosine deaminas 66.4 23 0.00049 27.3 5.8 53 6-58 64-133 (187)
18 PF08145 BOP1NT: BOP1NT (NUC16 65.2 4.9 0.00011 32.3 2.1 32 17-52 213-244 (260)
19 PF08004 DUF1699: Protein of u 65.1 22 0.00047 26.3 5.3 52 4-59 79-130 (131)
20 PF14420 Clr5: Clr5 domain 61.8 33 0.00072 20.7 5.0 36 17-52 3-39 (54)
21 smart00139 MyTH4 Domain in Myo 60.6 28 0.00061 24.7 5.1 49 14-62 40-90 (144)
22 TIGR01201 HU_rel DNA-binding p 60.5 19 0.00041 25.6 4.3 34 34-67 31-64 (145)
23 PF05402 PqqD: Coenzyme PQQ sy 58.7 36 0.00078 20.2 4.7 34 28-61 24-58 (68)
24 PF00784 MyTH4: MyTH4 domain; 55.1 51 0.0011 22.0 5.4 45 18-62 2-48 (114)
25 PRK15435 bifunctional DNA-bind 53.8 20 0.00044 29.0 3.8 54 6-65 65-127 (353)
26 PF02082 Rrf2: Transcriptional 52.2 24 0.00051 22.3 3.3 27 39-65 27-53 (83)
27 PRK08091 ribulose-phosphate 3- 51.2 8.6 0.00019 29.8 1.3 36 34-70 1-36 (228)
28 TIGR01795 CM_mono_cladeE monof 50.4 31 0.00068 23.1 3.8 26 40-65 57-82 (94)
29 cd00591 HU_IHF Integration hos 49.4 44 0.00095 20.7 4.1 31 35-65 1-31 (87)
30 PRK10963 hypothetical protein; 47.5 15 0.00032 27.7 2.0 23 34-75 3-25 (223)
31 PF03979 Sigma70_r1_1: Sigma-7 46.9 55 0.0012 21.0 4.4 50 18-68 5-55 (82)
32 COG4359 Uncharacterized conser 46.2 23 0.00049 28.2 2.9 27 31-57 56-82 (220)
33 PF07527 Hairy_orange: Hairy O 43.5 50 0.0011 18.9 3.5 27 37-63 12-38 (43)
34 smart00345 HTH_GNTR helix_turn 42.5 48 0.001 18.3 3.3 26 40-65 23-48 (60)
35 PF05066 HARE-HTH: HB1, ASXL, 40.8 50 0.0011 20.2 3.4 29 34-63 1-29 (72)
36 PF05295 Luciferase_N: Lucifer 40.8 48 0.001 22.8 3.5 38 38-75 4-41 (82)
37 COG0776 HimA Bacterial nucleoi 40.4 66 0.0014 22.0 4.2 18 34-51 2-19 (94)
38 PF04433 SWIRM: SWIRM domain; 39.9 94 0.002 19.7 4.7 48 14-64 31-81 (86)
39 PRK05617 3-hydroxyisobutyryl-C 38.8 85 0.0018 25.1 5.2 49 14-66 220-268 (342)
40 PF14164 YqzH: YqzH-like prote 37.1 42 0.00092 21.9 2.7 14 20-33 4-17 (64)
41 KOG3973 Uncharacterized conser 37.1 22 0.00048 30.7 1.7 56 22-77 141-219 (465)
42 PF00325 Crp: Bacterial regula 36.9 78 0.0017 17.8 3.4 29 33-65 2-30 (32)
43 COG1725 Predicted transcriptio 36.3 67 0.0015 23.1 3.9 29 18-46 91-119 (125)
44 PF09280 XPC-binding: XPC-bind 35.9 41 0.00089 21.1 2.4 32 41-72 11-42 (59)
45 PF14769 CLAMP: Flagellar C1a 35.7 91 0.002 20.6 4.2 45 18-62 20-73 (101)
46 PRK09239 chorismate mutase; Pr 34.4 76 0.0016 21.7 3.8 26 40-65 64-89 (104)
47 PLN02849 beta-glucosidase 34.2 16 0.00034 31.2 0.4 37 37-74 122-169 (503)
48 smart00760 Bac_DnaA_C Bacteria 34.1 46 0.00099 20.0 2.4 18 35-52 1-18 (60)
49 PF10045 DUF2280: Uncharacteri 34.0 1.7E+02 0.0038 20.8 6.4 56 20-75 6-69 (104)
50 PRK13710 plasmid maintenance p 33.6 1.1E+02 0.0023 20.1 4.2 46 32-82 20-65 (72)
51 smart00511 ORANGE Orange domai 33.6 80 0.0017 18.0 3.3 27 37-63 12-38 (45)
52 TIGR03342 dsrC_tusE_dsvC sulfu 33.3 64 0.0014 22.6 3.3 35 37-74 24-58 (108)
53 PF13592 HTH_33: Winged helix- 33.1 35 0.00075 20.6 1.7 39 18-57 6-44 (60)
54 TIGR02010 IscR iron-sulfur clu 33.1 62 0.0013 22.1 3.2 27 39-65 27-53 (135)
55 PF11417 Inhibitor_G39P: Loade 32.8 47 0.001 21.5 2.4 31 34-64 1-42 (71)
56 PF14490 HHH_4: Helix-hairpin- 32.7 68 0.0015 20.9 3.2 31 32-63 4-34 (94)
57 COG3415 Transposase and inacti 32.7 1E+02 0.0022 22.4 4.4 50 18-68 65-114 (138)
58 KOG2211 Predicted Golgi transp 32.3 52 0.0011 30.5 3.3 18 47-64 360-377 (797)
59 cd07377 WHTH_GntR Winged helix 32.2 86 0.0019 17.6 3.3 26 40-65 28-53 (66)
60 PLN02998 beta-glucosidase 31.9 18 0.00039 30.7 0.4 37 37-74 125-172 (497)
61 PF01316 Arg_repressor: Argini 31.8 94 0.002 20.0 3.7 30 33-64 19-48 (70)
62 PF04358 DsrC: DsrC like prote 31.7 56 0.0012 22.8 2.8 34 37-73 25-58 (109)
63 smart00830 CM_2 Chorismate mut 31.7 60 0.0013 19.8 2.7 23 43-65 52-74 (79)
64 smart00543 MIF4G Middle domain 31.4 1.7E+02 0.0037 19.9 6.3 51 21-71 15-72 (200)
65 TIGR00269 conserved hypothetic 31.4 1.2E+02 0.0027 20.2 4.4 36 33-69 9-57 (104)
66 PF03965 Penicillinase_R: Peni 30.9 42 0.00092 22.3 2.0 31 34-64 18-48 (115)
67 TIGR01803 CM-like chorismate m 30.5 73 0.0016 20.3 3.0 39 15-64 39-77 (82)
68 PF09012 FeoC: FeoC like trans 30.5 65 0.0014 19.7 2.7 25 40-64 17-41 (69)
69 TIGR02173 cyt_kin_arch cytidyl 30.4 1.7E+02 0.0036 19.5 5.0 42 34-75 100-141 (171)
70 PF13720 Acetyltransf_11: Udp 30.4 1.6E+02 0.0034 19.2 5.4 42 16-57 30-71 (83)
71 PLN02814 beta-glucosidase 29.1 23 0.0005 30.2 0.6 38 37-75 120-168 (504)
72 cd05094 PTKc_TrkC Catalytic do 28.7 88 0.0019 22.5 3.5 30 19-48 251-284 (291)
73 PF04340 DUF484: Protein of un 28.5 19 0.00041 26.7 0.0 12 63-74 16-27 (225)
74 PF13936 HTH_38: Helix-turn-he 28.4 82 0.0018 18.0 2.7 32 25-63 12-43 (44)
75 PTZ00398 phosphoenolpyruvate c 28.4 55 0.0012 30.6 2.9 32 22-54 155-186 (974)
76 cd05062 PTKc_IGF-1R Catalytic 28.0 53 0.0011 23.3 2.2 25 20-44 248-276 (277)
77 PRK14552 C/D box methylation g 28.0 90 0.0019 26.3 3.9 45 15-59 227-272 (414)
78 PRK05066 arginine repressor; P 27.6 92 0.002 22.8 3.4 30 33-63 23-52 (156)
79 PF00232 Glyco_hydro_1: Glycos 27.6 8.2 0.00018 31.7 -2.3 38 37-75 102-149 (455)
80 smart00352 POU Found in Pit-Oc 27.6 1.9E+02 0.0042 19.3 4.8 53 19-73 10-62 (75)
81 PF13867 SAP30_Sin3_bdg: Sin3 27.5 53 0.0012 19.9 1.9 19 33-51 20-38 (53)
82 PRK00009 phosphoenolpyruvate c 27.4 61 0.0013 30.1 2.9 33 21-54 108-140 (911)
83 KOG1199 Short-chain alcohol de 27.2 43 0.00094 26.8 1.8 21 8-28 222-242 (260)
84 COG1412 Uncharacterized protei 27.1 1.5E+02 0.0032 21.5 4.4 41 25-66 19-59 (136)
85 KOG2049 Translational represso 27.0 1.1E+02 0.0025 26.9 4.4 70 23-92 449-529 (536)
86 PF11399 DUF3192: Protein of u 26.5 44 0.00096 23.5 1.6 22 30-56 31-52 (102)
87 PF11333 DUF3135: Protein of u 26.5 69 0.0015 21.4 2.4 26 51-78 4-29 (83)
88 PF08914 Myb_DNA-bind_2: Rap1 26.4 74 0.0016 20.2 2.4 41 39-79 13-60 (65)
89 PF07531 TAFH: NHR1 homology t 26.3 1.7E+02 0.0036 20.4 4.4 38 14-51 21-58 (96)
90 PF12415 rpo132: Poxvirus DNA 26.1 65 0.0014 18.6 1.9 15 14-28 11-25 (33)
91 PF00538 Linker_histone: linke 26.1 1.4E+02 0.0031 18.6 3.7 47 17-63 4-54 (77)
92 PF01799 Fer2_2: [2Fe-2S] bind 25.8 76 0.0017 20.6 2.5 39 4-45 20-58 (75)
93 PRK10857 DNA-binding transcrip 25.7 93 0.002 22.6 3.2 27 39-65 27-53 (164)
94 PRK11508 sulfur transfer prote 25.6 1E+02 0.0023 21.6 3.3 35 37-74 25-59 (109)
95 PF13625 Helicase_C_3: Helicas 25.4 1E+02 0.0022 21.0 3.1 32 24-55 45-78 (129)
96 PF14039 YusW: YusW-like prote 25.1 68 0.0015 21.7 2.2 36 19-54 46-82 (92)
97 cd00896 PI3Kc_III Phosphoinosi 24.8 1.1E+02 0.0024 25.0 3.8 38 5-46 290-327 (350)
98 PRK11675 LexA regulated protei 24.8 1.6E+02 0.0034 20.3 4.0 28 18-45 58-85 (90)
99 PRK14137 recX recombination re 24.4 3.1E+02 0.0068 20.6 6.2 60 12-72 29-96 (195)
100 PF05157 T2SE_Nter: Type II se 24.3 67 0.0015 19.9 2.0 20 32-51 5-24 (109)
101 TIGR02849 spore_III_AD stage I 24.3 1E+02 0.0022 21.5 3.0 24 38-61 26-49 (101)
102 TIGR02698 CopY_TcrY copper tra 24.2 1.4E+02 0.0031 20.7 3.8 31 34-64 19-49 (130)
103 cd07765 KRAB_A-box KRAB (Krupp 23.9 29 0.00063 14.9 0.2 24 49-72 6-29 (40)
104 PF14775 NYD-SP28_assoc: Sperm 23.8 67 0.0014 20.2 1.9 32 45-80 5-36 (60)
105 cd05093 PTKc_TrkB Catalytic do 23.7 90 0.002 22.4 2.8 32 20-51 249-284 (288)
106 KOG1684 Enoyl-CoA hydratase [L 23.2 1.4E+02 0.0031 25.7 4.2 25 22-47 265-289 (401)
107 COG1438 ArgR Arginine represso 23.1 1E+02 0.0022 22.9 3.0 32 31-64 18-49 (150)
108 COG4399 Uncharacterized protei 22.9 1.4E+02 0.0031 25.5 4.1 57 18-74 84-143 (376)
109 cd05049 PTKc_Trk Catalytic dom 22.6 96 0.0021 21.8 2.7 25 20-44 251-279 (280)
110 PRK07075 isochorismate-pyruvat 22.4 2E+02 0.0044 19.3 4.1 23 41-63 62-84 (101)
111 KOG3779 Homeobox transcription 22.3 92 0.002 28.1 3.0 37 35-71 688-727 (737)
112 TIGR01791 CM_archaeal chorisma 22.2 1.9E+02 0.0041 18.2 3.8 23 44-66 57-79 (83)
113 COG2080 CoxS Aerobic-type carb 22.1 95 0.0021 23.3 2.7 38 4-44 94-131 (156)
114 TIGR03198 pucE xanthine dehydr 22.0 88 0.0019 22.9 2.5 39 4-45 92-130 (151)
115 PF07954 DUF1689: Protein of u 21.9 42 0.00091 24.9 0.8 28 53-80 107-134 (152)
116 cd01784 rasfadin_RA Ubiquitin- 21.8 86 0.0019 21.6 2.2 29 33-74 22-50 (87)
117 PRK14135 recX recombination re 21.7 2.4E+02 0.0052 21.2 4.8 47 17-64 105-152 (263)
118 PF00392 GntR: Bacterial regul 21.7 1.6E+02 0.0036 17.4 3.3 26 40-65 27-52 (64)
119 PF04355 SmpA_OmlA: SmpA / Oml 21.7 54 0.0012 19.9 1.1 14 30-43 12-25 (71)
120 PF14076 DUF4258: Domain of un 21.2 1.4E+02 0.0031 17.4 2.9 23 23-45 4-26 (73)
121 TIGR01797 CM_P_1 chorismate mu 21.1 2E+02 0.0042 18.4 3.7 22 45-66 58-79 (83)
122 TIGR00738 rrf2_super rrf2 fami 21.1 1.5E+02 0.0032 19.6 3.2 26 39-64 27-52 (132)
123 PF12980 DUF3864: Domain of Un 20.7 27 0.00058 23.9 -0.4 32 45-76 49-80 (82)
124 PF05960 DUF885: Bacterial pro 20.5 3.7E+02 0.0079 22.1 6.0 60 14-74 433-501 (549)
125 PF13545 HTH_Crp_2: Crp-like h 20.5 1.8E+02 0.0038 17.2 3.2 31 31-65 26-56 (76)
126 PLN02951 Molybderin biosynthes 20.5 86 0.0019 25.4 2.3 12 6-17 68-79 (373)
127 PF04814 HNF-1_N: Hepatocyte n 20.4 1.2E+02 0.0025 23.4 2.9 30 23-53 10-39 (180)
128 PRK11145 pflA pyruvate formate 20.3 45 0.00097 24.5 0.6 12 6-17 30-41 (246)
129 cd06622 PKc_MAPKK_PBS2_like Ca 20.3 1.9E+02 0.0041 20.5 3.8 45 19-63 235-285 (286)
130 PF06711 DUF1198: Protein of u 20.2 2E+02 0.0044 21.7 4.0 38 38-75 26-63 (148)
131 PF02022 Integrase_Zn: Integra 20.1 1.4E+02 0.003 17.4 2.6 21 40-60 12-32 (40)
132 cd05116 PTKc_Syk Catalytic dom 20.1 1.2E+02 0.0027 21.1 2.8 26 20-45 225-254 (257)
133 TIGR03356 BGL beta-galactosida 20.0 56 0.0012 26.9 1.2 37 38-75 98-144 (427)
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=2.6e-37 Score=196.80 Aligned_cols=57 Identities=46% Similarity=0.695 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhhc
Q 034472 19 IRMVQHLIERCLLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFHS 75 (93)
Q Consensus 19 I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~r 75 (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=2.7e-36 Score=190.17 Aligned_cols=54 Identities=54% Similarity=1.040 Sum_probs=53.0
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhhc
Q 034472 22 VQHLIERCLLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFHS 75 (93)
Q Consensus 22 VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~r 75 (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 799999999999999999999999999999999999999999999999999976
No 3
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=86.72 E-value=1.7 Score=27.56 Aligned_cols=31 Identities=23% Similarity=0.289 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
||++|+++.++++.++...-...|++.|.+.
T Consensus 1 mtk~eli~~ia~~~~~~~~~v~~vl~~l~~~ 31 (90)
T smart00411 1 MTKSELIDAIAEKAGLSKKDAKAAVDAFLEI 31 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 8999999999999999999999998877654
No 4
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=81.75 E-value=2.9 Score=30.43 Aligned_cols=42 Identities=24% Similarity=0.319 Sum_probs=32.2
Q ss_pred Ccccccccchh-------hHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC
Q 034472 7 FFPCLHCHPHS-------YIRMVQHLIERCLLLHMSRDQCIKALAEHAG 48 (93)
Q Consensus 7 ~~~c~~~~p~s-------~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~ 48 (93)
.+-|..|+..+ ...-..+.|.+=|+..+|++||++.+-.+.|
T Consensus 40 ~LrCp~Cq~qsi~~s~a~~A~dmR~~I~~~l~~G~s~~eI~~~~v~rYG 88 (148)
T PF03918_consen 40 ELRCPVCQNQSIADSNAPIARDMRREIREMLAEGKSDEEIIDYFVERYG 88 (148)
T ss_dssp CCE-TTTTS-CTTT--SHHHHHHHHHHHHHHHHT--HHHHHHHHHHHHT
T ss_pred cccCCCCCCCchhhcCcHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcC
Confidence 47799998655 5566778899999999999999999999987
No 5
>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=79.99 E-value=3.5 Score=25.87 Aligned_cols=32 Identities=25% Similarity=0.281 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
||++|+++.++++.++...-...|-+.|.+.=
T Consensus 1 Mtk~eli~~ia~~~~~s~~~v~~vl~~~~~~i 32 (90)
T PF00216_consen 1 MTKKELIKRIAEKTGLSKKDVEAVLDALFDVI 32 (90)
T ss_dssp EBHHHHHHHHHHHHTSSHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCCCHHHHHHHHHHHHHHH
Confidence 89999999999999999988888777665543
No 6
>PF13565 HTH_32: Homeodomain-like domain
Probab=79.40 E-value=7.8 Score=23.50 Aligned_cols=43 Identities=19% Similarity=0.109 Sum_probs=29.0
Q ss_pred hHHHHHHHHHHHHHh-cCCHHHHHHHHHHhcCCCh-hhHHHHHHH
Q 034472 18 YIRMVQHLIERCLLL-HMSRDQCIKALAEHAGIRP-LVTLTVWRE 60 (93)
Q Consensus 18 ~I~~VQ~LIErCLql-yMsk~Evv~~L~~~a~I~P-~fT~~VW~~ 60 (93)
+-++.+.+++-.... .+|.+++...|.+++||.. .=-++||+-
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 334445555544444 7999999999999999864 334567654
No 7
>PF08986 DUF1889: Domain of unknown function (DUF1889); InterPro: IPR015079 This family consist of hypothetical bacterial proteins. ; PDB: 2JN8_A 2ES9_A.
Probab=78.48 E-value=3.2 Score=30.01 Aligned_cols=36 Identities=31% Similarity=0.589 Sum_probs=23.1
Q ss_pred HHHHHHHhcCCChhhHHHH--HHH-------HHHhCHHHHHHHhh
Q 034472 39 CIKALAEHAGIRPLVTLTV--WRE-------LQKENKDFFRAYFH 74 (93)
Q Consensus 39 vv~~L~~~a~I~P~fT~~V--W~~-------LEkeNpeFFkaY~~ 74 (93)
-|.+=-+|-|-+|+||..| |.+ +-=.|||||..|..
T Consensus 68 dv~aRg~qeGWn~gFT~k~agwaeki~sG~rivIKnPEyFs~YMr 112 (119)
T PF08986_consen 68 DVTARGEQEGWNPGFTEKVAGWAEKIASGERIVIKNPEYFSSYMR 112 (119)
T ss_dssp HHHHHHHHCT--HHHHHHHHHHHHHHHCT-----SSGGGS-HHHH
T ss_pred HHHHhcccccCChhHHHHHHHHHHHHhcCCeeeecChHHHHHHHH
Confidence 3445568899999999987 543 22369999999964
No 8
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=77.82 E-value=5.1 Score=28.83 Aligned_cols=48 Identities=19% Similarity=0.409 Sum_probs=43.0
Q ss_pred hHHHHHHHHHHHHHhcCCHHH---HHHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 18 YIRMVQHLIERCLLLHMSRDQ---CIKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 18 ~I~~VQ~LIErCLqlyMsk~E---vv~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
|.+.++.+.+....--+...| -|+.|..+.+|+|..++-++++||++.
T Consensus 13 Y~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG 63 (125)
T COG1725 13 YEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREG 63 (125)
T ss_pred HHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 778888899999998888877 479999999999999999999999874
No 9
>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=75.58 E-value=7.3 Score=25.19 Aligned_cols=31 Identities=10% Similarity=0.186 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHh-cCCChhhHHHHHHHHHHh
Q 034472 34 MSRDQCIKALAEH-AGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 34 Msk~Evv~~L~~~-a~I~P~fT~~VW~~LEke 64 (93)
||++|+++.+.++ .++.+.-...|++.+-++
T Consensus 1 m~k~eli~~i~~~~~~~s~~~v~~vv~~~~~~ 32 (94)
T TIGR00988 1 MTKSELIERIATQQSHLPAKDVEDAVKTMLEH 32 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 8999999999875 579999888888766543
No 10
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=74.74 E-value=7.7 Score=28.04 Aligned_cols=52 Identities=21% Similarity=0.337 Sum_probs=39.9
Q ss_pred Ccccccccchh-------hHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC----Chh---hHHHHH
Q 034472 7 FFPCLHCHPHS-------YIRMVQHLIERCLLLHMSRDQCIKALAEHAGI----RPL---VTLTVW 58 (93)
Q Consensus 7 ~~~c~~~~p~s-------~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I----~P~---fT~~VW 58 (93)
.+-|..|+..| ..+-..+.|-+=+.-.+|++||++++.++.|- +|- .|-.+|
T Consensus 40 ~LRC~vCqnqsiadS~a~iA~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~~Vly~Pp~~~~t~~LW 105 (126)
T TIGR03147 40 SLRCPQCQNQNLVESNSPIAYDLRHEVYSMVNEGKSNQQIIDFMTARFGDFVLYNPPFKWQTLLLW 105 (126)
T ss_pred hCCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCCCCcchHHHH
Confidence 47799999877 34456677888889999999999999999873 443 355555
No 11
>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=74.12 E-value=8 Score=25.38 Aligned_cols=32 Identities=9% Similarity=0.100 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
||++|+++.++++.++...-...|-+.+.+.=
T Consensus 2 mtk~eli~~ia~~~~~s~~~v~~vv~~~~~~i 33 (96)
T TIGR00987 2 LTKAEMSEYLFDELGLSKREAKELVELFFEEI 33 (96)
T ss_pred CCHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 89999999999999999988888776665443
No 12
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=71.60 E-value=9.7 Score=24.97 Aligned_cols=32 Identities=16% Similarity=0.195 Sum_probs=27.2
Q ss_pred cCCHHHHHHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 33 HMSRDQCIKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 33 yMsk~Evv~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
.||++|+++.++++.++...-...|++.+.+.
T Consensus 2 tmtk~el~~~ia~~~~~s~~~v~~vl~~~~~~ 33 (99)
T PRK00285 2 TLTKADLAEALFEKVGLSKREAKELVELFFEE 33 (99)
T ss_pred CcCHHHHHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 48999999999999999999888888766543
No 13
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=71.59 E-value=10 Score=24.61 Aligned_cols=31 Identities=19% Similarity=0.272 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHh-cCCChhhHHHHHHHHHHh
Q 034472 34 MSRDQCIKALAEH-AGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 34 Msk~Evv~~L~~~-a~I~P~fT~~VW~~LEke 64 (93)
||+.|.++.+.++ .++...-...|++.+.+.
T Consensus 1 mtk~eli~~ia~~~~~~s~~~~~~vv~~~~~~ 32 (94)
T PRK00199 1 MTKSELIERLAARNPHLSAKDVENAVKEILEE 32 (94)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 8999999999875 688888888888766543
No 14
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=71.44 E-value=10 Score=25.05 Aligned_cols=26 Identities=23% Similarity=0.222 Sum_probs=21.5
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHH
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWR 59 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~ 59 (93)
|||.|+++.|++..++...-...+-+
T Consensus 1 MtK~eli~~ia~~~~~s~~~~~~~v~ 26 (90)
T PRK10664 1 MNKSQLIDKIAAGADISKAAAGRALD 26 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHHHH
Confidence 89999999999999988876665543
No 15
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=67.61 E-value=14 Score=26.73 Aligned_cols=52 Identities=21% Similarity=0.346 Sum_probs=39.7
Q ss_pred Ccccccccchh-------hHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCC----Chh---hHHHHH
Q 034472 7 FFPCLHCHPHS-------YIRMVQHLIERCLLLHMSRDQCIKALAEHAGI----RPL---VTLTVW 58 (93)
Q Consensus 7 ~~~c~~~~p~s-------~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I----~P~---fT~~VW 58 (93)
.+-|.-|+..+ -.+-..+.|-+=+.-.+|++||++++-++.|= +|- .|-.+|
T Consensus 40 ~LRC~vCqnqsiadSna~iA~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~~Pp~~~~t~~LW 105 (126)
T PRK10144 40 QLRCPQCQNQNLLESNAPVAVSMRHQVYSMVAEGKSEVEIIGWMTERYGDFVRYNPPLTGQTLVLW 105 (126)
T ss_pred cCCCCCCCCCChhhcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCCCCcchHHHH
Confidence 47799999877 34455667788889999999999999999873 444 355566
No 16
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=66.43 E-value=15 Score=24.11 Aligned_cols=27 Identities=19% Similarity=0.275 Sum_probs=21.1
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHH
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRE 60 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~ 60 (93)
|||.|+++.+.++.++...-...+-+.
T Consensus 1 M~K~eli~~ia~~~~~s~~~~~~~v~~ 27 (90)
T PRK10753 1 MNKTQLIDVIADKAELSKTQAKAALES 27 (90)
T ss_pred CCHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 899999999999988877666555443
No 17
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=66.38 E-value=23 Score=27.26 Aligned_cols=53 Identities=23% Similarity=0.357 Sum_probs=38.8
Q ss_pred CCcccccccchh-------hHHHHHHHHHH----------HHHhcCCHHHHHHHHHHhcCCChhhHHHHH
Q 034472 6 HFFPCLHCHPHS-------YIRMVQHLIER----------CLLLHMSRDQCIKALAEHAGIRPLVTLTVW 58 (93)
Q Consensus 6 ~~~~c~~~~p~s-------~I~~VQ~LIEr----------CLqlyMsk~Evv~~L~~~a~I~P~fT~~VW 58 (93)
+.-||+.|+|-. -+...-.+||+ +=++.+|.--.-++..++.|+.|.=...-|
T Consensus 64 GfRPCkRC~P~~~~~~~~~~V~~a~~~ie~~~~~~~le~la~~lg~sp~~~~R~FK~~~G~Tp~~ya~a~ 133 (187)
T COG2169 64 GFRPCKRCRPDLAAAGRSGLVATACRLIEQNPEKRWLEELADELGVSPSTLHRLFKAITGMTPKEYARAR 133 (187)
T ss_pred CCCcccccCcccccccccHHHHHHHHHHHcCCCcccHHHHHHHhCCChHHHHHHHHHHhCCCHHHHHHHH
Confidence 456999999966 56666777877 556777777777777788888776555444
No 18
>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=65.17 E-value=4.9 Score=32.30 Aligned_cols=32 Identities=25% Similarity=0.441 Sum_probs=26.1
Q ss_pred hhHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCChh
Q 034472 17 SYIRMVQHLIERCLLLHMSRDQCIKALAEHAGIRPL 52 (93)
Q Consensus 17 s~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~ 52 (93)
.|=+.|+..-||||.|||-.. +.....||+|.
T Consensus 213 ~Y~~~i~ErFeRCLDLYLcPR----~~k~rlnidPe 244 (260)
T PF08145_consen 213 AYENFIKERFERCLDLYLCPR----VRKKRLNIDPE 244 (260)
T ss_pred hHHHHHHHHHHHhhhhhcCcH----hhcccCCCCHH
Confidence 378899999999999999654 45567888884
No 19
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=65.05 E-value=22 Score=26.29 Aligned_cols=52 Identities=12% Similarity=0.111 Sum_probs=39.6
Q ss_pred CCCCcccccccchhhHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHHHH
Q 034472 4 NHHFFPCLHCHPHSYIRMVQHLIERCLLLHMSRDQCIKALAEHAGIRPLVTLTVWR 59 (93)
Q Consensus 4 ~~~~~~c~~~~p~s~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~ 59 (93)
.|....=++-=|.+-|..+..|+ .-.+|.+|+++.+++..+++|.+-..+.+
T Consensus 79 HRKDinEYy~i~~~vi~~I~el~----~eG~s~eei~~ki~~e~kl~pd~i~yi~~ 130 (131)
T PF08004_consen 79 HRKDINEYYEIPESVIERIKELK----SEGKSEEEIAEKISRETKLSPDMIKYILK 130 (131)
T ss_pred ccCCCcccccCCHHHHHHHHHHH----HcCCCHHHHHHHHHHhhcCCHHHHHHHhc
Confidence 34444555666777777776665 46899999999999999999999877653
No 20
>PF14420 Clr5: Clr5 domain
Probab=61.80 E-value=33 Score=20.68 Aligned_cols=36 Identities=14% Similarity=0.176 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHHH-HHhcCCHHHHHHHHHHhcCCChh
Q 034472 17 SYIRMVQHLIERC-LLLHMSRDQCIKALAEHAGIRPL 52 (93)
Q Consensus 17 s~I~~VQ~LIErC-LqlyMsk~Evv~~L~~~a~I~P~ 52 (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 3455667777754 46788999999999999998886
No 21
>smart00139 MyTH4 Domain in Myosin and Kinesin Tails. Domain present twice in myosin-VIIa, and also present in 3 other myosins.
Probab=60.64 E-value=28 Score=24.72 Aligned_cols=49 Identities=22% Similarity=0.290 Sum_probs=39.0
Q ss_pred cchhhHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCCh--hhHHHHHHHHH
Q 034472 14 HPHSYIRMVQHLIERCLLLHMSRDQCIKALAEHAGIRP--LVTLTVWRELQ 62 (93)
Q Consensus 14 ~p~s~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P--~fT~~VW~~LE 62 (93)
.|.+.++.+|++++.|+..=-=+||+.-.|-+|-.=+| .-..-.|+-|-
T Consensus 40 ~~~~~~~l~~~i~~~~~~~~~LrDEiy~QLiKQtt~Np~~~s~~rgW~Ll~ 90 (144)
T smart00139 40 KPDSHLDLVQFILQKGLAHPELRDEIYCQLIKQLTDNPSRQSEERGWELLY 90 (144)
T ss_pred CcchHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHH
Confidence 35678999999999999988889999988888854444 45566788765
No 22
>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=60.52 E-value=19 Score=25.62 Aligned_cols=34 Identities=12% Similarity=0.133 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHH
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRELQKENKD 67 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpe 67 (93)
||++|+++.++++.++.+.-...|++.|.+.=.+
T Consensus 31 mt~~el~~~Ia~~s~~s~~dv~~vl~~l~~~i~~ 64 (145)
T TIGR01201 31 IDFEEIAELIAEESSLSPGDVKGIIDRLAYVLRR 64 (145)
T ss_pred cCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999888765443
No 23
>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=58.66 E-value=36 Score=20.22 Aligned_cols=34 Identities=24% Similarity=0.132 Sum_probs=22.0
Q ss_pred HHHHhcCCHHHHHHHHHHhcCCChh-hHHHHHHHH
Q 034472 28 RCLLLHMSRDQCIKALAEHAGIRPL-VTLTVWREL 61 (93)
Q Consensus 28 rCLqlyMsk~Evv~~L~~~a~I~P~-fT~~VW~~L 61 (93)
+.+..-.|.+|+++.|.++++++|. ...-|..-|
T Consensus 24 ~~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl 58 (68)
T PF05402_consen 24 ELLDGPRTVEEIVDALAEEYDVDPEEAEEDVEEFL 58 (68)
T ss_dssp HH--SSS-HHHHHHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3346778999999999999999998 445554433
No 24
>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=55.08 E-value=51 Score=22.00 Aligned_cols=45 Identities=20% Similarity=0.289 Sum_probs=36.3
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCCh--hhHHHHHHHHH
Q 034472 18 YIRMVQHLIERCLLLHMSRDQCIKALAEHAGIRP--LVTLTVWRELQ 62 (93)
Q Consensus 18 ~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P--~fT~~VW~~LE 62 (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 4688999999999999999999999999966555 45568898875
No 25
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=53.80 E-value=20 Score=28.99 Aligned_cols=54 Identities=22% Similarity=0.474 Sum_probs=28.7
Q ss_pred CCcccccccchhh---------HHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 6 HFFPCLHCHPHSY---------IRMVQHLIERCLLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 6 ~~~~c~~~~p~s~---------I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
+.-||..|+|... |..+..+|+. +.+--++.|.++.|++|.--.-++++.--..
T Consensus 65 GfRpC~rCrP~~~~~~~~~~~~i~~a~~~I~~------~~~lsl~eLA~~lG~S~~~L~R~Fkk~~G~T 127 (353)
T PRK15435 65 GFRPCKRCQPDKANPQQHRLDKITHACRLLEQ------ETPVTLEALADQVAMSPFHLHRLFKATTGMT 127 (353)
T ss_pred CCCchhccCCcccchhhhHHHHHHHHHHHHHh------CCCCCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 4469999999531 3333344444 1222355566666666655555554443333
No 26
>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=52.25 E-value=24 Score=22.27 Aligned_cols=27 Identities=30% Similarity=0.437 Sum_probs=22.6
Q ss_pred HHHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 39 CIKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 39 vv~~L~~~a~I~P~fT~~VW~~LEkeN 65 (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 467788889999999999999999865
No 27
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=51.15 E-value=8.6 Score=29.82 Aligned_cols=36 Identities=17% Similarity=0.233 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHH
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDFFR 70 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFk 70 (93)
||+++||..| ++.-|.|++-..=|-+|+++=...=+
T Consensus 1 ~~~~~~~~~~-~~~~I~pSil~ad~~~l~~el~~l~~ 36 (228)
T PRK08091 1 MSKLSLIQQL-KQQPISVGILASNWLKFNETLTTLSE 36 (228)
T ss_pred CCHHHHHHHh-cCCeEEeehhhcCHHHHHHHHHHHHH
Confidence 8999999988 66779999998888888776555444
No 28
>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=50.43 E-value=31 Score=23.14 Aligned_cols=26 Identities=23% Similarity=0.282 Sum_probs=21.1
Q ss_pred HHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 40 IKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 40 v~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
+..+..+.|++|.|...+|+.+-++.
T Consensus 57 ~~~~a~~~gl~p~~~e~i~~~i~~es 82 (94)
T TIGR01795 57 LRRLAIDAGLDPEFAEKFLNFIVTEV 82 (94)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHH
Confidence 34566889999999999999887654
No 29
>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=49.40 E-value=44 Score=20.74 Aligned_cols=31 Identities=16% Similarity=0.194 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 35 SRDQCIKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 35 sk~Evv~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
||+|+++.+++..++.+.-...|-+.|.+.-
T Consensus 1 ~K~~l~~~ia~~~~~~~~~v~~vl~~~~~~i 31 (87)
T cd00591 1 TKSELIEAIAEKTGLSKKDAEAAVDAFLDVI 31 (87)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 6899999999999999988888776665543
No 30
>PRK10963 hypothetical protein; Provisional
Probab=47.46 E-value=15 Score=27.72 Aligned_cols=23 Identities=22% Similarity=0.309 Sum_probs=16.5
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhhc
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFHS 75 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~r 75 (93)
||.++|+++| ++|||||..+-.-
T Consensus 3 l~~~~V~~yL-------------------~~~PdFf~~h~~L 25 (223)
T PRK10963 3 LDDRAVVDYL-------------------LQNPDFFIRNARL 25 (223)
T ss_pred CCHHHHHHHH-------------------HHCchHHhhCHHH
Confidence 5667777776 3799999887443
No 31
>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=46.91 E-value=55 Score=20.99 Aligned_cols=50 Identities=20% Similarity=0.286 Sum_probs=33.4
Q ss_pred hHHHHHHHHHHH-HHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHH
Q 034472 18 YIRMVQHLIERC-LLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDF 68 (93)
Q Consensus 18 ~I~~VQ~LIErC-LqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeF 68 (93)
+...|+.||++= =+.|+|-+|+.++|. ...++|.--..|...|++.+=+.
T Consensus 5 ~~~~i~~Li~~gK~~G~lT~~eI~~~L~-~~~~~~e~id~i~~~L~~~gI~V 55 (82)
T PF03979_consen 5 YEEAIKKLIEKGKKKGYLTYDEINDALP-EDDLDPEQIDEIYDTLEDEGIEV 55 (82)
T ss_dssp HHHHHHHHHHHHHHHSS-BHHHHHHH-S--S---HHHHHHHHHHHHTT----
T ss_pred hHHHHHHHHHHHhhcCcCCHHHHHHHcC-ccCCCHHHHHHHHHHHHHCCCEE
Confidence 456788899854 478999999999997 56699999999998888766443
No 32
>COG4359 Uncharacterized conserved protein [Function unknown]
Probab=46.18 E-value=23 Score=28.16 Aligned_cols=27 Identities=22% Similarity=0.228 Sum_probs=23.5
Q ss_pred HhcCCHHHHHHHHHHhcCCChhhHHHH
Q 034472 31 LLHMSRDQCIKALAEHAGIRPLVTLTV 57 (93)
Q Consensus 31 qlyMsk~Evv~~L~~~a~I~P~fT~~V 57 (93)
....|-+|+.+.|.+.++|+|+|-..|
T Consensus 56 ~i~~s~~Eile~llk~i~Idp~fKef~ 82 (220)
T COG4359 56 SIHSSLEEILEFLLKDIKIDPGFKEFV 82 (220)
T ss_pred hcCCCHHHHHHHHHhhcccCccHHHHH
Confidence 346788999999999999999998775
No 33
>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=43.50 E-value=50 Score=18.87 Aligned_cols=27 Identities=22% Similarity=0.351 Sum_probs=20.8
Q ss_pred HHHHHHHHHhcCCChhhHHHHHHHHHH
Q 034472 37 DQCIKALAEHAGIRPLVTLTVWRELQK 63 (93)
Q Consensus 37 ~Evv~~L~~~a~I~P~fT~~VW~~LEk 63 (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 589999999999999999888888765
No 34
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=42.55 E-value=48 Score=18.32 Aligned_cols=26 Identities=19% Similarity=0.262 Sum_probs=21.1
Q ss_pred HHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 40 IKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 40 v~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
++.|.++.+|.+..-.-..+.|++++
T Consensus 23 ~~~la~~~~vs~~tv~~~l~~L~~~g 48 (60)
T smart00345 23 ERELAAQLGVSRTTVREALSRLEAEG 48 (60)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 66788888999988888888888754
No 35
>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=40.78 E-value=50 Score=20.25 Aligned_cols=29 Identities=31% Similarity=0.629 Sum_probs=18.4
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHHHHH
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRELQK 63 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~LEk 63 (93)
||--|.+..+.+++| .|-=..-+|++..+
T Consensus 1 mt~~eaa~~vL~~~~-~pm~~~eI~~~i~~ 29 (72)
T PF05066_consen 1 MTFKEAAYEVLEEAG-RPMTFKEIWEEIQE 29 (72)
T ss_dssp S-HHHHHHHHHHHH--S-EEHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcC-CCcCHHHHHHHHHH
Confidence 566677766667777 77777777777764
No 36
>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=40.76 E-value=48 Score=22.80 Aligned_cols=38 Identities=29% Similarity=0.358 Sum_probs=32.0
Q ss_pred HHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhhc
Q 034472 38 QCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFHS 75 (93)
Q Consensus 38 Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~r 75 (93)
|....|.+.|+++|.+-..+=+.|.-|+-.=|-.|.+.
T Consensus 4 ql~~FLt~dakvD~~vv~ymTk~L~lesvsDFAn~WTs 41 (82)
T PF05295_consen 4 QLAQFLTNDAKVDPKVVAYMTKQLQLESVSDFANYWTS 41 (82)
T ss_pred HHHHHHhcccccCHHHHHHHHhhcchhhHHHHHhhhhH
Confidence 77888999999999999999999998887666666443
No 37
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=40.40 E-value=66 Score=22.05 Aligned_cols=18 Identities=39% Similarity=0.676 Sum_probs=16.8
Q ss_pred CCHHHHHHHHHHhcCCCh
Q 034472 34 MSRDQCIKALAEHAGIRP 51 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P 51 (93)
|||.|+++.|.+++++..
T Consensus 2 mtKseli~~ia~~~~l~k 19 (94)
T COG0776 2 MTKSELIDAIAEKAGLSK 19 (94)
T ss_pred CCHHHHHHHHHHHcCCCH
Confidence 899999999999999776
No 38
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=39.89 E-value=94 Score=19.71 Aligned_cols=48 Identities=13% Similarity=0.238 Sum_probs=31.7
Q ss_pred cchhhHHHHHHHHHH--H-HHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 14 HPHSYIRMVQHLIER--C-LLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 14 ~p~s~I~~VQ~LIEr--C-LqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
.|..|+..=-.+|.. + -..|++++++-+.+. |+++..+.-||.-|+..
T Consensus 31 ~p~~Yl~iRn~il~~w~~n~~~~lt~~~~~~~i~---~~d~~~~~ri~~FL~~~ 81 (86)
T PF04433_consen 31 TPEQYLKIRNTILAEWRKNPNKYLTKTDARKLIK---GIDVNKIRRIYDFLERW 81 (86)
T ss_dssp HHHHHHHHHHHHHHHHHHHTTS---HHHHHHHTT---SSSHHHHHHHHHHHHHT
T ss_pred ChHHHHHHHHHHHHHHHHCCCCcccHHHHHHHcc---ccCHHHHHHHHHHHHHc
Confidence 456666544444444 3 267999999977774 79999999999888753
No 39
>PRK05617 3-hydroxyisobutyryl-CoA hydrolase; Provisional
Probab=38.84 E-value=85 Score=25.06 Aligned_cols=49 Identities=16% Similarity=0.182 Sum_probs=33.9
Q ss_pred cchhhHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCH
Q 034472 14 HPHSYIRMVQHLIERCLLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKENK 66 (93)
Q Consensus 14 ~p~s~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNp 66 (93)
-|++.++.....|.+|+.. -|.++++++|..+ .+.+....-+++.+..|
T Consensus 220 ~~~~~~~~~~~~i~~~~~~-~~~~~~~~~l~~~---~~~~a~~~a~~i~~~sp 268 (342)
T PRK05617 220 APASELAAQRAWIDECFAG-DTVEDIIAALEAD---GGEFAAKTADTLRSRSP 268 (342)
T ss_pred CCcchhHHHHHHHHHHhCC-CCHHHHHHHHHhc---cHHHHHHHHHHHHhCCc
Confidence 3556888999999999987 5999999998765 23444444444444333
No 40
>PF14164 YqzH: YqzH-like protein
Probab=37.10 E-value=42 Score=21.95 Aligned_cols=14 Identities=21% Similarity=0.591 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHhc
Q 034472 20 RMVQHLIERCLLLH 33 (93)
Q Consensus 20 ~~VQ~LIErCLqly 33 (93)
.+++.+|-+||+.|
T Consensus 4 k~I~Kmi~~~l~QY 17 (64)
T PF14164_consen 4 KLIEKMIINCLRQY 17 (64)
T ss_pred HHHHHHHHHHHHHh
Confidence 46788999999999
No 41
>KOG3973 consensus Uncharacterized conserved glycine-rich protein [Function unknown]
Probab=37.05 E-value=22 Score=30.72 Aligned_cols=56 Identities=20% Similarity=0.439 Sum_probs=38.2
Q ss_pred HHHHHH-HHHHhcCCHH-------HHHHHHHH---h--cCCChhh----------HHHHHHHHHHhCHHHHHHHhhccC
Q 034472 22 VQHLIE-RCLLLHMSRD-------QCIKALAE---H--AGIRPLV----------TLTVWRELQKENKDFFRAYFHSIS 77 (93)
Q Consensus 22 VQ~LIE-rCLqlyMsk~-------Evv~~L~~---~--a~I~P~f----------T~~VW~~LEkeNpeFFkaY~~rl~ 77 (93)
|+.+|+ -|..+.|+|- ...+++.. . +++.|.. +..-|.++|++|.+|=+.||.|+.
T Consensus 141 v~q~i~~~~~~L~~~k~p~Nin~~~lfe~i~~kl~~ai~kv~p~~~~~PLlKkpl~~a~w~~iE~~~~~~~~ey~~Rr~ 219 (465)
T KOG3973|consen 141 VTQLIDSALRTLNFPKQPGNINEWKLFETIRQKLDGAIKKVSPSQRSHPLLKKPLDEATWPEIEKQCESFSREYYNRRL 219 (465)
T ss_pred HHHHHHHHHHHcCCCCCCCCchHHHHHHHHHHHHHhHHhcCCHhhcCCchhcCcCChhhHHHHHHHHHHHHHHHHHHHH
Confidence 556666 5778888752 22233222 2 4566653 477899999999999999998853
No 42
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=36.85 E-value=78 Score=17.81 Aligned_cols=29 Identities=17% Similarity=0.365 Sum_probs=19.9
Q ss_pred cCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 33 HMSRDQCIKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 33 yMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
-||.+|+.+.| |..|..-+-+..+|+++.
T Consensus 2 ~mtr~diA~~l----G~t~ETVSR~l~~l~~~g 30 (32)
T PF00325_consen 2 PMTRQDIADYL----GLTRETVSRILKKLERQG 30 (32)
T ss_dssp E--HHHHHHHH----TS-HHHHHHHHHHHHHTT
T ss_pred CcCHHHHHHHh----CCcHHHHHHHHHHHHHcC
Confidence 47888887765 788888888888888763
No 43
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=36.30 E-value=67 Score=23.08 Aligned_cols=29 Identities=21% Similarity=0.244 Sum_probs=25.0
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHHHHh
Q 034472 18 YIRMVQHLIERCLLLHMSRDQCIKALAEH 46 (93)
Q Consensus 18 ~I~~VQ~LIErCLqlyMsk~Evv~~L~~~ 46 (93)
....++++|+.+..+.+|++|+.+.+.+-
T Consensus 91 ~~~~l~~~I~~~~~~G~s~eei~~~~~~~ 119 (125)
T COG1725 91 AEEELEEFIEEAKALGLSLEEILELLKEI 119 (125)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 45678999999999999999999988653
No 44
>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=35.86 E-value=41 Score=21.11 Aligned_cols=32 Identities=13% Similarity=0.241 Sum_probs=24.0
Q ss_pred HHHHHhcCCChhhHHHHHHHHHHhCHHHHHHH
Q 034472 41 KALAEHAGIRPLVTLTVWRELQKENKDFFRAY 72 (93)
Q Consensus 41 ~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY 72 (93)
..|.....=+|..-..|.++|.+.||+.++.-
T Consensus 11 ~~lR~~vq~NP~lL~~lLqql~~~nP~l~q~I 42 (59)
T PF09280_consen 11 QQLRQLVQQNPQLLPPLLQQLGQSNPQLLQLI 42 (59)
T ss_dssp HHHHHHHHC-GGGHHHHHHHHHCCSHHHHHHH
T ss_pred HHHHHHHHHCHHHHHHHHHHHhccCHHHHHHH
Confidence 34444444679999999999999999998764
No 45
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=35.69 E-value=91 Score=20.61 Aligned_cols=45 Identities=13% Similarity=0.256 Sum_probs=33.2
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHHHHh-cCCCh--------hhHHHHHHHHH
Q 034472 18 YIRMVQHLIERCLLLHMSRDQCIKALAEH-AGIRP--------LVTLTVWRELQ 62 (93)
Q Consensus 18 ~I~~VQ~LIErCLqlyMsk~Evv~~L~~~-a~I~P--------~fT~~VW~~LE 62 (93)
-...++.+.+.|+...||.+|+++.+.+- +++.+ .|+..-.+.+-
T Consensus 20 ~~~i~~~ll~~~i~~~~~~~~~~~~fk~~l~~~sv~rpp~~~~iFs~~~~~~i~ 73 (101)
T PF14769_consen 20 FLSILKELLEKNIEKGMSLEDSFKYFKELLLRHSVQRPPFSIGIFSVDQVKAII 73 (101)
T ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHhccCCCCcccCcCCHHHHHHHH
Confidence 56678899999999999999999988665 23333 37666555554
No 46
>PRK09239 chorismate mutase; Provisional
Probab=34.42 E-value=76 Score=21.68 Aligned_cols=26 Identities=23% Similarity=0.277 Sum_probs=19.8
Q ss_pred HHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 40 IKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 40 v~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
+..+..+.|++|.|...+|+.+-++.
T Consensus 64 ~~~~a~~~gl~p~~~~~i~~~ii~es 89 (104)
T PRK09239 64 LRQLAKDANLDPDFAEKFLNFIIKEV 89 (104)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHH
Confidence 34455778999999999998876553
No 47
>PLN02849 beta-glucosidase
Probab=34.19 E-value=16 Score=31.20 Aligned_cols=37 Identities=32% Similarity=0.418 Sum_probs=24.8
Q ss_pred HHHHHHHHHhcCCChhhHHHHHH---HHH--------HhCHHHHHHHhh
Q 034472 37 DQCIKALAEHAGIRPLVTLTVWR---ELQ--------KENKDFFRAYFH 74 (93)
Q Consensus 37 ~Evv~~L~~~a~I~P~fT~~VW~---~LE--------keNpeFFkaY~~ 74 (93)
++++++| ..+||+|.+|..=|. .|+ ++..++|..|-.
T Consensus 122 ~~lid~l-~~~GI~P~VTL~H~dlP~~L~~~yGGW~nr~~v~~F~~YA~ 169 (503)
T PLN02849 122 KNFIQEL-VKHGIEPHVTLFHYDHPQYLEDDYGGWINRRIIKDFTAYAD 169 (503)
T ss_pred HHHHHHH-HHcCCeEEEeecCCCCcHHHHHhcCCcCCchHHHHHHHHHH
Confidence 4667777 558999999976551 244 345677887744
No 48
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=34.07 E-value=46 Score=19.95 Aligned_cols=18 Identities=33% Similarity=0.565 Sum_probs=15.0
Q ss_pred CHHHHHHHHHHhcCCChh
Q 034472 35 SRDQCIKALAEHAGIRPL 52 (93)
Q Consensus 35 sk~Evv~~L~~~a~I~P~ 52 (93)
|.+++++...+.+||+|.
T Consensus 1 ~~~~I~~~Va~~~~i~~~ 18 (60)
T smart00760 1 TIEEIIEAVAEYFGVKPE 18 (60)
T ss_pred CHHHHHHHHHHHhCCCHH
Confidence 468889999999999875
No 49
>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=33.99 E-value=1.7e+02 Score=20.77 Aligned_cols=56 Identities=23% Similarity=0.219 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHhcCCCh--------hhHHHHHHHHHHhCHHHHHHHhhc
Q 034472 20 RMVQHLIERCLLLHMSRDQCIKALAEHAGIRP--------LVTLTVWRELQKENKDFFRAYFHS 75 (93)
Q Consensus 20 ~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P--------~fT~~VW~~LEkeNpeFFkaY~~r 75 (93)
.-|+--|=+-|--|.|..||+++..+.+||+= .=|...=+.|-++-.+.|+....+
T Consensus 6 ~~vK~FIVQ~LAcfdTPs~v~~aVk~eFgi~vsrQqve~yDPTK~aG~~Ls~k~~~lF~~TR~~ 69 (104)
T PF10045_consen 6 KEVKAFIVQSLACFDTPSEVAEAVKEEFGIDVSRQQVESYDPTKRAGRDLSKKWVDLFEETRKR 69 (104)
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHHHHHhCCccCHHHHHHcCchHHHHHHHHHHHHHHHHHHHHH
Confidence 34677777888889999999999999998863 346677778888888888766443
No 50
>PRK13710 plasmid maintenance protein CcdA; Provisional
Probab=33.65 E-value=1.1e+02 Score=20.06 Aligned_cols=46 Identities=7% Similarity=-0.018 Sum_probs=29.4
Q ss_pred hcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhhccCCCCCc
Q 034472 32 LHMSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFHSISPRPFM 82 (93)
Q Consensus 32 lyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~rl~~k~~~ 82 (93)
+..|....++++-.++ +...-.++..+||.|.+++|...+..-+..
T Consensus 20 ~giNlS~~~e~~L~~~-----~~~~~~~~W~~eN~eai~~~n~~ve~~G~~ 65 (72)
T PRK13710 20 ADVNISGLVNTAMQNE-----ARRLRAERWKAENREGMAEVARFIEMNGSF 65 (72)
T ss_pred cCCcHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Confidence 3444445555443333 555666677789999999998776654433
No 51
>smart00511 ORANGE Orange domain. This domain confers specificity among members of the Hairy/E(SPL) family.
Probab=33.60 E-value=80 Score=18.02 Aligned_cols=27 Identities=22% Similarity=0.334 Sum_probs=23.2
Q ss_pred HHHHHHHHHhcCCChhhHHHHHHHHHH
Q 034472 37 DQCIKALAEHAGIRPLVTLTVWRELQK 63 (93)
Q Consensus 37 ~Evv~~L~~~a~I~P~fT~~VW~~LEk 63 (93)
.||++.|...-+++|.+...+-+.|..
T Consensus 12 ~Ev~~fLs~~~~~~~~~~~~Ll~HL~~ 38 (45)
T smart00511 12 NEVSRFLSQLPGTDPDVRARLLSHLQT 38 (45)
T ss_pred HHHHHHHhcCCCCChHHHHHHHHHHHH
Confidence 699999998888999998888888864
No 52
>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=33.28 E-value=64 Score=22.58 Aligned_cols=35 Identities=31% Similarity=0.564 Sum_probs=25.1
Q ss_pred HHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhh
Q 034472 37 DQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFH 74 (93)
Q Consensus 37 ~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~ 74 (93)
+|+..+|.++-||+ +|..-|+-+.- =.+||+.|..
T Consensus 24 e~vA~~lA~~egie--LT~~Hw~vI~~-lR~~y~e~~~ 58 (108)
T TIGR03342 24 EDVAEALAEEEGIE--LTEAHWEVINF-LRDFYAEYNI 58 (108)
T ss_pred HHHHHHHHHHcCCC--CCHHHHHHHHH-HHHHHHHHCC
Confidence 68899999999994 99999976642 2335555543
No 53
>PF13592 HTH_33: Winged helix-turn helix
Probab=33.12 E-value=35 Score=20.61 Aligned_cols=39 Identities=13% Similarity=0.102 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHH
Q 034472 18 YIRMVQHLIERCLLLHMSRDQCIKALAEHAGIRPLVTLTV 57 (93)
Q Consensus 18 ~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~V 57 (93)
....|+.+|++.+---+|..-|-+.| ++.|..+.-...+
T Consensus 6 t~~~i~~~I~~~fgv~ys~~~v~~lL-~r~G~s~~kp~~~ 44 (60)
T PF13592_consen 6 TLKEIAAYIEEEFGVKYSPSGVYRLL-KRLGFSYQKPRPR 44 (60)
T ss_pred cHHHHHHHHHHHHCCEEcHHHHHHHH-HHcCCccccCCCC
Confidence 46788999999999888888877777 5677776655544
No 54
>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=33.10 E-value=62 Score=22.15 Aligned_cols=27 Identities=19% Similarity=0.315 Sum_probs=22.9
Q ss_pred HHHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 39 CIKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 39 vv~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
-++.|+++.+|.|.+..-|.++|.+.+
T Consensus 27 s~~~ia~~~~ip~~~l~kil~~L~~~g 53 (135)
T TIGR02010 27 TLADISERQGISLSYLEQLFAKLRKAG 53 (135)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 356778889999999999999998754
No 55
>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=32.77 E-value=47 Score=21.54 Aligned_cols=31 Identities=23% Similarity=0.439 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHHhcCCCh----h-------hHHHHHHHHHHh
Q 034472 34 MSRDQCIKALAEHAGIRP----L-------VTLTVWRELQKE 64 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P----~-------fT~~VW~~LEke 64 (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 899999999987666666 2 245788776643
No 56
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=32.73 E-value=68 Score=20.90 Aligned_cols=31 Identities=10% Similarity=0.280 Sum_probs=19.0
Q ss_pred hcCCHHHHHHHHHHhcCCChhhHHHHHHHHHH
Q 034472 32 LHMSRDQCIKALAEHAGIRPLVTLTVWRELQK 63 (93)
Q Consensus 32 lyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEk 63 (93)
.+.+..+++..|+ ..||.|.....+|+....
T Consensus 4 ~~~~~~~~~~~L~-~~gl~~~~a~kl~~~yg~ 34 (94)
T PF14490_consen 4 ENRGLRELMAFLQ-EYGLSPKLAMKLYKKYGD 34 (94)
T ss_dssp -----HHHHHHHH-HTT--HHHHHHHHHHH-T
T ss_pred HHHHHHHHHHHHH-HcCCCHHHHHHHHHHHhH
Confidence 3456678888884 588999999999988653
No 57
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=32.66 E-value=1e+02 Score=22.39 Aligned_cols=50 Identities=16% Similarity=0.153 Sum_probs=41.1
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHH
Q 034472 18 YIRMVQHLIERCLLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDF 68 (93)
Q Consensus 18 ~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeF 68 (93)
+-..++-+.|.|=+.+.|..+++..|..+.||.=+-. .||.-|.+.-=.+
T Consensus 65 ~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~-~v~~~l~~~Glsy 114 (138)
T COG3415 65 SEEQLEILLERLREKDWTLKELVEELGLEFGVWYHAS-AVRRLLHELGLSY 114 (138)
T ss_pred CHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHH-HHHHHHHHcCCCc
Confidence 4566788899999999999999999999999986654 8999988764333
No 58
>KOG2211 consensus Predicted Golgi transport complex 1 protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.28 E-value=52 Score=30.45 Aligned_cols=18 Identities=11% Similarity=0.348 Sum_probs=15.9
Q ss_pred cCCChhhHHHHHHHHHHh
Q 034472 47 AGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 47 a~I~P~fT~~VW~~LEke 64 (93)
-+++|.++..+|++|++.
T Consensus 360 k~gd~cI~~rfw~~l~qa 377 (797)
T KOG2211|consen 360 KNGDKCIPERFWKKLEQA 377 (797)
T ss_pred hccchhHHHHHHHHHHHH
Confidence 369999999999999965
No 59
>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=32.25 E-value=86 Score=17.61 Aligned_cols=26 Identities=31% Similarity=0.401 Sum_probs=20.0
Q ss_pred HHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 40 IKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 40 v~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
+..|.++.+|.+.--..+-++|++++
T Consensus 28 ~~~la~~~~is~~~v~~~l~~L~~~G 53 (66)
T cd07377 28 ERELAEELGVSRTTVREALRELEAEG 53 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 66788999999877777777777654
No 60
>PLN02998 beta-glucosidase
Probab=31.88 E-value=18 Score=30.74 Aligned_cols=37 Identities=35% Similarity=0.450 Sum_probs=25.3
Q ss_pred HHHHHHHHHhcCCChhhHHHHHH---HH--------HHhCHHHHHHHhh
Q 034472 37 DQCIKALAEHAGIRPLVTLTVWR---EL--------QKENKDFFRAYFH 74 (93)
Q Consensus 37 ~Evv~~L~~~a~I~P~fT~~VW~---~L--------EkeNpeFFkaY~~ 74 (93)
++++++| ..+||+|.+|..=|. -| -++..+.|..|-.
T Consensus 125 ~~lid~L-~~~GIeP~VTL~H~dlP~~L~~~yGGW~n~~~v~~F~~YA~ 172 (497)
T PLN02998 125 NNLIDEL-ITHGIQPHVTLHHFDLPQALEDEYGGWLSQEIVRDFTAYAD 172 (497)
T ss_pred HHHHHHH-HHcCCceEEEecCCCCCHHHHHhhCCcCCchHHHHHHHHHH
Confidence 4567777 558999999876551 23 3456778888843
No 61
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=31.81 E-value=94 Score=20.03 Aligned_cols=30 Identities=27% Similarity=0.438 Sum_probs=20.2
Q ss_pred cCCHHHHHHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 33 HMSRDQCIKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 33 yMsk~Evv~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
.-|++|+++.|.++ ||+ .--.+|.+-|.+=
T Consensus 19 i~sQ~eL~~~L~~~-Gi~-vTQaTiSRDLkeL 48 (70)
T PF01316_consen 19 ISSQEELVELLEEE-GIE-VTQATISRDLKEL 48 (70)
T ss_dssp --SHHHHHHHHHHT-T-T---HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHc-CCC-cchhHHHHHHHHc
Confidence 45999999999775 999 5556777777654
No 62
>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=31.70 E-value=56 Score=22.76 Aligned_cols=34 Identities=26% Similarity=0.557 Sum_probs=22.7
Q ss_pred HHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHh
Q 034472 37 DQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYF 73 (93)
Q Consensus 37 ~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~ 73 (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 99999977642 234555443
No 63
>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=31.69 E-value=60 Score=19.81 Aligned_cols=23 Identities=30% Similarity=0.575 Sum_probs=15.2
Q ss_pred HHHhcCCChhhHHHHHHHHHHhC
Q 034472 43 LAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 43 L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
.....|++|.+...+|+.+-+.+
T Consensus 52 ~a~~~~l~~~~~~~if~~ii~~s 74 (79)
T smart00830 52 LAEGPGLDPELVERIFREIIEAS 74 (79)
T ss_pred HcccCCcCHHHHHHHHHHHHHHH
Confidence 44456777777777777765544
No 64
>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=31.42 E-value=1.7e+02 Score=19.86 Aligned_cols=51 Identities=24% Similarity=0.224 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHhcCC----HHHHHHHHHHhcCCChhhH---HHHHHHHHHhCHHHHHH
Q 034472 21 MVQHLIERCLLLHMS----RDQCIKALAEHAGIRPLVT---LTVWRELQKENKDFFRA 71 (93)
Q Consensus 21 ~VQ~LIErCLqlyMs----k~Evv~~L~~~a~I~P~fT---~~VW~~LEkeNpeFFka 71 (93)
.+...++.-...+++ .+++++.+.+.+..+|.+. ..+...|...+++|...
T Consensus 15 n~~~~~~~l~~~~~~~~~~~~~l~~~i~~~~~~~~~~~~~ya~L~~~l~~~~~~f~~~ 72 (200)
T smart00543 15 NFESIIKELLKLNNSDKNLRKYILELIFEKAVEEPNFIPAYARLCALLNAKNPDFGSL 72 (200)
T ss_pred HHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555566666 5678888889999998776 45566677777776543
No 65
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=31.37 E-value=1.2e+02 Score=20.17 Aligned_cols=36 Identities=3% Similarity=-0.033 Sum_probs=24.5
Q ss_pred cCCHHHHHHHHHHhcCCChh-------------hHHHHHHHHHHhCHHHH
Q 034472 33 HMSRDQCIKALAEHAGIRPL-------------VTLTVWRELQKENKDFF 69 (93)
Q Consensus 33 yMsk~Evv~~L~~~a~I~P~-------------fT~~VW~~LEkeNpeFF 69 (93)
|.+.+|++.+- ...||... ....+.++||+.||++.
T Consensus 9 ~v~E~ei~~ya-~~~~lp~~~~~CP~~~~a~R~~~k~~L~~LE~~~P~~k 57 (104)
T TIGR00269 9 YIPEKEVVLYA-FLNELKVHLDECPYSSLSVRARIRDFLYDLENKKPGVK 57 (104)
T ss_pred cCCHHHHHHHH-HHcCCCcCCCCCCCCCCCchHHHHHHHHHHHHHCcChH
Confidence 56667776443 55667643 45678899999999753
No 66
>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=30.94 E-value=42 Score=22.29 Aligned_cols=31 Identities=16% Similarity=0.095 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
+|-.||++.|.+..++.+.-+.++.+.|++.
T Consensus 18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~K 48 (115)
T PF03965_consen 18 ATVREIHEALPEERSWAYSTVQTLLNRLVEK 48 (115)
T ss_dssp EEHHHHHHHHCTTSS--HHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHhccccchhHHHHHHHHHHhC
Confidence 7889999999888899999999999999874
No 67
>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=30.48 E-value=73 Score=20.34 Aligned_cols=39 Identities=13% Similarity=0.159 Sum_probs=25.3
Q ss_pred chhhHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 15 PHSYIRMVQHLIERCLLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 15 p~s~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
|.-+-...+.+|++. ..+..+.|++|.+...+|+.+=++
T Consensus 39 ~v~d~~Re~~vl~~~-----------~~~a~~~gl~~~~~~~if~~ii~~ 77 (82)
T TIGR01803 39 AIPAPERVAAVLPNA-----------ARWAEENGLDPPFVEGLFAQIIHW 77 (82)
T ss_pred CCCChHHHHHHHHHH-----------HHHHHHcCCCHHHHHHHHHHHHHH
Confidence 334445555555553 334455889999999999887543
No 68
>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=30.47 E-value=65 Score=19.69 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=18.9
Q ss_pred HHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 40 IKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 40 v~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
+..|+++++++|..-..+...|++.
T Consensus 17 ~~eLa~~~~~s~~~ve~mL~~l~~k 41 (69)
T PF09012_consen 17 LAELAREFGISPEAVEAMLEQLIRK 41 (69)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHCC
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3568899999999999999888753
No 69
>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=30.44 E-value=1.7e+02 Score=19.49 Aligned_cols=42 Identities=12% Similarity=0.126 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhhc
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFHS 75 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~r 75 (93)
-+.+..++-+.++.++++.-...-|.+-++....||+.|+..
T Consensus 100 a~~~~r~~R~~~R~~~s~~~a~~~~~~~d~~~~~~~~~~~~~ 141 (171)
T TIGR02173 100 APLEVRARRIAKREGKSLTVARSETIEREESEKRRYLKFYGI 141 (171)
T ss_pred CCHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 366677777777788888877777777778888889888754
No 70
>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=30.43 E-value=1.6e+02 Score=19.17 Aligned_cols=42 Identities=14% Similarity=0.123 Sum_probs=33.1
Q ss_pred hhhHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHH
Q 034472 16 HSYIRMVQHLIERCLLLHMSRDQCIKALAEHAGIRPLVTLTV 57 (93)
Q Consensus 16 ~s~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~V 57 (93)
.++|..++.....=+...++.+|.++.|.+...=.|.+...|
T Consensus 30 ~~~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~~~~~v~~~~ 71 (83)
T PF13720_consen 30 KEEISALRRAYRILFRSGLTLEEALEELEEEYPDSPEVREIV 71 (83)
T ss_dssp HHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTTSCHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhccCCHHHHHHH
Confidence 457888888887777788899999999988777788887664
No 71
>PLN02814 beta-glucosidase
Probab=29.13 E-value=23 Score=30.18 Aligned_cols=38 Identities=32% Similarity=0.451 Sum_probs=25.8
Q ss_pred HHHHHHHHHhcCCChhhHHHHHH---HHH--------HhCHHHHHHHhhc
Q 034472 37 DQCIKALAEHAGIRPLVTLTVWR---ELQ--------KENKDFFRAYFHS 75 (93)
Q Consensus 37 ~Evv~~L~~~a~I~P~fT~~VW~---~LE--------keNpeFFkaY~~r 75 (93)
+++++.| ..+||+|.+|..=|. -|+ ++..++|..|-..
T Consensus 120 ~~lId~l-~~~GI~P~VTL~H~dlP~~L~~~yGGW~n~~~i~~F~~YA~~ 168 (504)
T PLN02814 120 KNLIKEL-RSHGIEPHVTLYHYDLPQSLEDEYGGWINRKIIEDFTAFADV 168 (504)
T ss_pred HHHHHHH-HHcCCceEEEecCCCCCHHHHHhcCCcCChhHHHHHHHHHHH
Confidence 4566777 558999999976662 233 4666788888443
No 72
>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=28.67 E-value=88 Score=22.49 Aligned_cols=30 Identities=13% Similarity=0.159 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHh----cCCHHHHHHHHHHhcC
Q 034472 19 IRMVQHLIERCLLL----HMSRDQCIKALAEHAG 48 (93)
Q Consensus 19 I~~VQ~LIErCLql----yMsk~Evv~~L~~~a~ 48 (93)
-..++++|.+|++. ..|-+|+++.|.+-.+
T Consensus 251 ~~~~~~li~~~l~~~P~~Rpt~~~v~~~l~~~~~ 284 (291)
T cd05094 251 PKEVYDIMLGCWQREPQQRLNIKEIYKILHALGK 284 (291)
T ss_pred CHHHHHHHHHHcccChhhCcCHHHHHHHHHHHHh
Confidence 35689999999985 5677888888866544
No 73
>PF04340 DUF484: Protein of unknown function, DUF484; InterPro: IPR007435 This family consists of several proteins of uncharacterised function.; PDB: 3E98_B.
Probab=28.47 E-value=19 Score=26.72 Aligned_cols=12 Identities=25% Similarity=0.498 Sum_probs=0.0
Q ss_pred HhCHHHHHHHhh
Q 034472 63 KENKDFFRAYFH 74 (93)
Q Consensus 63 keNpeFFkaY~~ 74 (93)
.+|||||..+-.
T Consensus 16 ~~~PdFf~~~~~ 27 (225)
T PF04340_consen 16 RQHPDFFERHPE 27 (225)
T ss_dssp ------------
T ss_pred HhCcHHHHhCHH
Confidence 379999999853
No 74
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=28.45 E-value=82 Score=17.99 Aligned_cols=32 Identities=41% Similarity=0.339 Sum_probs=18.8
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHH
Q 034472 25 LIERCLLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQK 63 (93)
Q Consensus 25 LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEk 63 (93)
.|++-+...||..|+.+.| |+.| ++|.++|..
T Consensus 12 ~I~~l~~~G~s~~~IA~~l----g~s~---sTV~relkR 43 (44)
T PF13936_consen 12 QIEALLEQGMSIREIAKRL----GRSR---STVSRELKR 43 (44)
T ss_dssp HHHHHHCS---HHHHHHHT----T--H---HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHH----CcCc---HHHHHHHhc
Confidence 4777788888888877766 4443 577777653
No 75
>PTZ00398 phosphoenolpyruvate carboxylase; Provisional
Probab=28.43 E-value=55 Score=30.59 Aligned_cols=32 Identities=22% Similarity=0.278 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhH
Q 034472 22 VQHLIERCLLLHMSRDQCIKALAEHAGIRPLVT 54 (93)
Q Consensus 22 VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT 54 (93)
+.+.+++..+..++++++.++| .+..|+|+||
T Consensus 155 l~~~l~~L~~~g~~~e~i~~~L-~~~~i~pVlT 186 (974)
T PTZ00398 155 LKNTIEMLLQAGFDKEEIYKQL-CNQEIDLVLT 186 (974)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-hcCceeeeec
Confidence 5678888899999999999999 5577999999
No 76
>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=28.02 E-value=53 Score=23.32 Aligned_cols=25 Identities=20% Similarity=0.268 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHhc----CCHHHHHHHHH
Q 034472 20 RMVQHLIERCLLLH----MSRDQCIKALA 44 (93)
Q Consensus 20 ~~VQ~LIErCLqly----Msk~Evv~~L~ 44 (93)
..++++|.+||+.. .|-+|++..|.
T Consensus 248 ~~~~~li~~~l~~~p~~Rps~~e~l~~l~ 276 (277)
T cd05062 248 DMLFELMRMCWQYNPKMRPSFLEIISSIK 276 (277)
T ss_pred HHHHHHHHHHcCCChhhCcCHHHHHHHhh
Confidence 46899999999875 66677776653
No 77
>PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional
Probab=27.98 E-value=90 Score=26.32 Aligned_cols=45 Identities=18% Similarity=0.115 Sum_probs=38.3
Q ss_pred chhhHHHHHHHHHHHHHhcCCHHHHHHHHHHhcC-CChhhHHHHHH
Q 034472 15 PHSYIRMVQHLIERCLLLHMSRDQCIKALAEHAG-IRPLVTLTVWR 59 (93)
Q Consensus 15 p~s~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~-I~P~fT~~VW~ 59 (93)
+.+|+..|++++++-+.++=.++++.++|...++ |.|.+|..|=.
T Consensus 227 se~dl~~I~~~a~~I~~L~e~R~~L~~yI~~~M~~iAPNLtaLVG~ 272 (414)
T PRK14552 227 SEFDLEAIKKLANEILDLYKLREELEDYLETVMKEVAPNLTALVGP 272 (414)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHhh
Confidence 3458899999999999999999999999998854 58998887643
No 78
>PRK05066 arginine repressor; Provisional
Probab=27.61 E-value=92 Score=22.79 Aligned_cols=30 Identities=30% Similarity=0.319 Sum_probs=25.4
Q ss_pred cCCHHHHHHHHHHhcCCChhhHHHHHHHHHH
Q 034472 33 HMSRDQCIKALAEHAGIRPLVTLTVWRELQK 63 (93)
Q Consensus 33 yMsk~Evv~~L~~~a~I~P~fT~~VW~~LEk 63 (93)
.=|++|.++.|.+ .||++.--.||.+-|.+
T Consensus 23 I~tQeeL~~~L~~-~Gi~~vTQATiSRDike 52 (156)
T PRK05066 23 FGSQGEIVTALQE-QGFDNINQSKVSRMLTK 52 (156)
T ss_pred CCCHHHHHHHHHH-CCCCeecHHHHHHHHHH
Confidence 4689999999966 59999888899888875
No 79
>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=27.60 E-value=8.2 Score=31.69 Aligned_cols=38 Identities=39% Similarity=0.690 Sum_probs=25.0
Q ss_pred HHHHHHHHHhcCCChhhHHH-----HHHH-----HHHhCHHHHHHHhhc
Q 034472 37 DQCIKALAEHAGIRPLVTLT-----VWRE-----LQKENKDFFRAYFHS 75 (93)
Q Consensus 37 ~Evv~~L~~~a~I~P~fT~~-----VW~~-----LEkeNpeFFkaY~~r 75 (93)
++++++| +.+||+|.+|.. .|=. +-+++.++|..|-..
T Consensus 102 ~~~i~~l-~~~gi~P~vtL~H~~~P~~l~~~ggw~~~~~~~~F~~Ya~~ 149 (455)
T PF00232_consen 102 RDLIDEL-LENGIEPIVTLYHFDLPLWLEDYGGWLNRETVDWFARYAEF 149 (455)
T ss_dssp HHHHHHH-HHTT-EEEEEEESS--BHHHHHHTGGGSTHHHHHHHHHHHH
T ss_pred HHHHHHH-HhhccceeeeeeecccccceeecccccCHHHHHHHHHHHHH
Confidence 4667777 569999988754 4422 236778899988543
No 80
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=27.55 E-value=1.9e+02 Score=19.26 Aligned_cols=53 Identities=13% Similarity=0.043 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHh
Q 034472 19 IRMVQHLIERCLLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYF 73 (93)
Q Consensus 19 I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~ 73 (93)
=.....++++=+.+.||+.|+.+.+....|. .++..--.++|+-|=.|=.++.
T Consensus 10 e~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~--i~SQstISR~Es~~ls~~n~~k 62 (75)
T smart00352 10 EAFAKTFKQRRIKLGFTQADVGLALGALYGP--DFSQTTICRFEALQLSFKNMCK 62 (75)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhcccccC--cCCHHHHHHHHhcCccHHHHHH
Confidence 3567888999999999999999999776665 5776666677777766655543
No 81
>PF13867 SAP30_Sin3_bdg: Sin3 binding region of histone deacetylase complex subunit SAP30; PDB: 2LD7_A.
Probab=27.47 E-value=53 Score=19.88 Aligned_cols=19 Identities=26% Similarity=0.426 Sum_probs=13.6
Q ss_pred cCCHHHHHHHHHHhcCCCh
Q 034472 33 HMSRDQCIKALAEHAGIRP 51 (93)
Q Consensus 33 yMsk~Evv~~L~~~a~I~P 51 (93)
.+||+|.+.++.+|++=.|
T Consensus 20 ~~sK~qLa~~V~kHF~s~~ 38 (53)
T PF13867_consen 20 RSSKEQLANAVRKHFNSQP 38 (53)
T ss_dssp S--HHHHHHHHHHHHTT--
T ss_pred CCCHHHHHHHHHHHHhcCC
Confidence 4899999999999987665
No 82
>PRK00009 phosphoenolpyruvate carboxylase; Reviewed
Probab=27.39 E-value=61 Score=30.09 Aligned_cols=33 Identities=24% Similarity=0.354 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHhcCCChhhH
Q 034472 21 MVQHLIERCLLLHMSRDQCIKALAEHAGIRPLVT 54 (93)
Q Consensus 21 ~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P~fT 54 (93)
.+.+.+.+..+..++++++.+.| ++..|+|+||
T Consensus 108 sl~~~~~~l~~~g~~~e~i~~~L-~~~~i~pVlT 140 (911)
T PRK00009 108 SLAETLRRLKAAGVSPEELARAL-EELDIEPVLT 140 (911)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHH-hhCcceeeee
Confidence 35677888888889999999999 5578999999
No 83
>KOG1199 consensus Short-chain alcohol dehydrogenase/3-hydroxyacyl-CoA dehydrogenase [Secondary metabolites biosynthesis, transport and catabolism]
Probab=27.25 E-value=43 Score=26.84 Aligned_cols=21 Identities=48% Similarity=0.869 Sum_probs=18.4
Q ss_pred cccccccchhhHHHHHHHHHH
Q 034472 8 FPCLHCHPHSYIRMVQHLIER 28 (93)
Q Consensus 8 ~~c~~~~p~s~I~~VQ~LIEr 28 (93)
.|+--=||++|.++||++||.
T Consensus 222 fpsrlg~p~eyahlvqaiien 242 (260)
T KOG1199|consen 222 FPSRLGHPHEYAHLVQAIIEN 242 (260)
T ss_pred CchhcCChHHHHHHHHHHHhC
Confidence 566677999999999999995
No 84
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=27.11 E-value=1.5e+02 Score=21.53 Aligned_cols=41 Identities=20% Similarity=0.205 Sum_probs=28.4
Q ss_pred HHHHHHHhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCH
Q 034472 25 LIERCLLLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKENK 66 (93)
Q Consensus 25 LIErCLqlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNp 66 (93)
.|==|.|.-.+-.|-++.+ -.++.+|.+|+.|-.+|++--+
T Consensus 19 fl~~~~q~~vdi~~~l~r~-l~~~~~~~Ip~~Vi~EL~~l~~ 59 (136)
T COG1412 19 FLLYPYQFKVDIFEELERL-LGAKYKPAIPSCVIRELEKLKR 59 (136)
T ss_pred HHHHHHHccCCHHHHHHHH-hcccccccchHHHHHHHHHHHH
Confidence 3444566666666666555 3355799999999999996543
No 85
>KOG2049 consensus Translational repressor MPT5/PUF4 and related RNA-binding proteins (Puf superfamily) [Translation, ribosomal structure and biogenesis]
Probab=27.01 E-value=1.1e+02 Score=26.89 Aligned_cols=70 Identities=21% Similarity=0.290 Sum_probs=47.1
Q ss_pred HHHHHHHHHhcCCH-HHHHHHHHHhcCCC--------hhhHHHHHHHHH-HhCHHHHHHHhhccCC-CCCcccccccccc
Q 034472 23 QHLIERCLLLHMSR-DQCIKALAEHAGIR--------PLVTLTVWRELQ-KENKDFFRAYFHSISP-RPFMSKTSSCFIN 91 (93)
Q Consensus 23 Q~LIErCLqlyMsk-~Evv~~L~~~a~I~--------P~fT~~VW~~LE-keNpeFFkaY~~rl~~-k~~~s~~~~~~~~ 91 (93)
-+.+|+||..+=+. +.+|..|...-+++ +-+-.+.|.--+ +-.+++|.-|-.++.+ -+-++.+-+|-++
T Consensus 449 S~vVEk~L~~~~~~~~~iV~ell~~~~~~~Ll~D~ygNyViq~AL~vtk~~~~~~~~~~lv~~~~~~~~~lr~~p~~~~~ 528 (536)
T KOG2049|consen 449 SHVVEKLLKVRESSRAQIVLELLSCDELDRLLRDPYGNYVIQTALRVTKVKLREDLFGLLVQKLMPRIRLLRNNPGGNIA 528 (536)
T ss_pred cHHHHHHHhcCcchhhHHHHHHHccccHHHHhhCccchHHHHHHHHHhhhcccchhhHHHHHHHhhhhHHhhcCccccee
Confidence 36799999999888 88887776642222 223355565555 4566899999777666 5567777777665
Q ss_pred c
Q 034472 92 L 92 (93)
Q Consensus 92 ~ 92 (93)
+
T Consensus 529 ~ 529 (536)
T KOG2049|consen 529 L 529 (536)
T ss_pred e
Confidence 4
No 86
>PF11399 DUF3192: Protein of unknown function (DUF3192); InterPro: IPR021534 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Probab=26.55 E-value=44 Score=23.50 Aligned_cols=22 Identities=41% Similarity=0.392 Sum_probs=17.9
Q ss_pred HHhcCCHHHHHHHHHHhcCCChhhHHH
Q 034472 30 LLLHMSRDQCIKALAEHAGIRPLVTLT 56 (93)
Q Consensus 30 LqlyMsk~Evv~~L~~~a~I~P~fT~~ 56 (93)
|++-||+++|+..| =.|.||++
T Consensus 31 L~lg~s~~~V~~~l-----G~pdfsEa 52 (102)
T PF11399_consen 31 LSLGMSKDQVIALL-----GTPDFSEA 52 (102)
T ss_pred cCCCCCHHHHHHHh-----CCCCchhh
Confidence 78999999999998 45666665
No 87
>PF11333 DUF3135: Protein of unknown function (DUF3135); InterPro: IPR021482 This family of proteins with unkown function appears to be restricted to Proteobacteria.
Probab=26.51 E-value=69 Score=21.40 Aligned_cols=26 Identities=15% Similarity=0.266 Sum_probs=19.0
Q ss_pred hhhHHHHHHHHHHhCHHHHHHHhhccCC
Q 034472 51 PLVTLTVWRELQKENKDFFRAYFHSISP 78 (93)
Q Consensus 51 P~fT~~VW~~LEkeNpeFFkaY~~rl~~ 78 (93)
|.|.. |..|-++|||=|++..+.+..
T Consensus 4 p~FD~--L~~LA~~dPe~fe~lr~~~~e 29 (83)
T PF11333_consen 4 PDFDE--LKELAQNDPEAFEQLRQELIE 29 (83)
T ss_pred CCHHH--HHHHHHhCHHHHHHHHHHHHH
Confidence 44544 556999999999998766543
No 88
>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=26.35 E-value=74 Score=20.21 Aligned_cols=41 Identities=15% Similarity=0.386 Sum_probs=21.7
Q ss_pred HHHHHHHhcCC-ChhhHHHHHHHHHHhCH------HHHHHHhhccCCC
Q 034472 39 CIKALAEHAGI-RPLVTLTVWRELQKENK------DFFRAYFHSISPR 79 (93)
Q Consensus 39 vv~~L~~~a~I-~P~fT~~VW~~LEkeNp------eFFkaY~~rl~~k 79 (93)
+++.+.+.+.- .+.--..+|++|++++| .-=.-|-+++..+
T Consensus 13 l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 13 LLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp HHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred HHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 44556444322 34556889999999998 4444444444443
No 89
>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=26.34 E-value=1.7e+02 Score=20.39 Aligned_cols=38 Identities=13% Similarity=0.156 Sum_probs=31.2
Q ss_pred cchhhHHHHHHHHHHHHHhcCCHHHHHHHHHHhcCCCh
Q 034472 14 HPHSYIRMVQHLIERCLLLHMSRDQCIKALAEHAGIRP 51 (93)
Q Consensus 14 ~p~s~I~~VQ~LIErCLqlyMsk~Evv~~L~~~a~I~P 51 (93)
.+.+..+.|+.||...+..-++-||--..|++.-|-.|
T Consensus 21 ~spev~~~Vr~LV~~L~~~~i~~EeF~~~Lq~~lns~p 58 (96)
T PF07531_consen 21 QSPEVGENVRELVQNLVDGKIEAEEFTSKLQEELNSSP 58 (96)
T ss_dssp C-CCHHHHHHHHHHHHHTTSS-HHHHHHHHHHHCTSS-
T ss_pred CChHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcCCC
Confidence 56678899999999999999999999999998876554
No 90
>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=26.13 E-value=65 Score=18.61 Aligned_cols=15 Identities=40% Similarity=0.543 Sum_probs=13.1
Q ss_pred cchhhHHHHHHHHHH
Q 034472 14 HPHSYIRMVQHLIER 28 (93)
Q Consensus 14 ~p~s~I~~VQ~LIEr 28 (93)
=|.+-+.+|+-+||.
T Consensus 11 mp~ei~ylvnalIes 25 (33)
T PF12415_consen 11 MPPEIIYLVNALIES 25 (33)
T ss_pred CCHHHHHHHHHHHHH
Confidence 478899999999995
No 91
>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=26.07 E-value=1.4e+02 Score=18.65 Aligned_cols=47 Identities=17% Similarity=0.140 Sum_probs=35.0
Q ss_pred hhHHHHHHHHHHHHH-hcCCHHHHHHHHHHhcC--CCh-hhHHHHHHHHHH
Q 034472 17 SYIRMVQHLIERCLL-LHMSRDQCIKALAEHAG--IRP-LVTLTVWRELQK 63 (93)
Q Consensus 17 s~I~~VQ~LIErCLq-lyMsk~Evv~~L~~~a~--I~P-~fT~~VW~~LEk 63 (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 467788888875422 45678899999999986 566 688888877764
No 92
>PF01799 Fer2_2: [2Fe-2S] binding domain; InterPro: IPR002888 The [2Fe-2S] binding domain is found in a range of enzymes including dehydrogenases, oxidases and oxidoreductases. The aldehyde oxido-reductase (Mop) from the sulphate reducing anaerobic Gram-negative bacterium Desulfovibrio gigas is a homodimer of 907 amino acid residues subunits and is a member of the xanthine oxidase family. The protein contains a molybdopterin cofactor (Mo-co) and two different [2Fe-2S] centres. It is folded into four domains of which the first two bind the iron sulphur centres and the last two are involved in Mo-co binding. Mo-co is a molybdenum molybdopterin cytosine dinucleotide. Molybdopterin forms a tricyclic system with the pterin bicycle annealed to a pyran ring. The molybdopterin dinucleotide is deeply buried in the protein. The cis-dithiolene group of the pyran ring binds the molybdenum, which is coordinated by three more (oxygen) ligands [].; GO: 0016491 oxidoreductase activity, 0046872 metal ion binding, 0055114 oxidation-reduction process; PDB: 2E3T_A 1WYG_A 3AN1_B 2E1Q_C 2CKJ_A 3B9J_I 3NVY_J 1FO4_B 3NRZ_J 3AM9_A ....
Probab=25.78 E-value=76 Score=20.63 Aligned_cols=39 Identities=23% Similarity=0.348 Sum_probs=26.1
Q ss_pred CCCCcccccccchhhHHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034472 4 NHHFFPCLHCHPHSYIRMVQHLIERCLLLHMSRDQCIKALAE 45 (93)
Q Consensus 4 ~~~~~~c~~~~p~s~I~~VQ~LIErCLqlyMsk~Evv~~L~~ 45 (93)
.||..+|-+|.|.- |-.+..|+++ .-.-|.+|+-++|.-
T Consensus 20 ~~~a~QCGfCtpG~-im~~~~ll~~--~~~p~~~ei~~al~g 58 (75)
T PF01799_consen 20 EHGAVQCGFCTPGM-IMAAYALLRR--NPDPTEEEIREALSG 58 (75)
T ss_dssp HTT--SSSSSHHHH-HHHHHHHHHH--SSS-CHHHHHHHTTT
T ss_pred HhCCCcCCcchHHH-HHHHHHHhhc--ccchhhHHHHHHHHc
Confidence 47889999999974 5556677776 335688888888753
No 93
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=25.65 E-value=93 Score=22.58 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=22.3
Q ss_pred HHHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 39 CIKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 39 vv~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
-++.|+++.||.+.+..-|+++|.+.+
T Consensus 27 s~~eIA~~~~ip~~~l~kIl~~L~~aG 53 (164)
T PRK10857 27 PLADISERQGISLSYLEQLFSRLRKNG 53 (164)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 345677888999999999999998753
No 94
>PRK11508 sulfur transfer protein TusE; Provisional
Probab=25.56 E-value=1e+02 Score=21.60 Aligned_cols=35 Identities=20% Similarity=0.452 Sum_probs=24.3
Q ss_pred HHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhh
Q 034472 37 DQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFH 74 (93)
Q Consensus 37 ~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~ 74 (93)
+|+...|.++-||+ +|..-|+-+.- =++||..|..
T Consensus 25 e~vA~~lA~~egie--LT~~HW~VI~~-lR~~y~e~~~ 59 (109)
T PRK11508 25 EPLAVVIAENEGIS--LSPEHWEVVRF-VRDFYLEFNT 59 (109)
T ss_pred HHHHHHHHHHhCCC--CCHHHHHHHHH-HHHHHHHHCC
Confidence 68889999998985 99999976642 2235555533
No 95
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=25.36 E-value=1e+02 Score=20.96 Aligned_cols=32 Identities=13% Similarity=0.079 Sum_probs=24.6
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHhcC--CChhhHH
Q 034472 24 HLIERCLLLHMSRDQCIKALAEHAG--IRPLVTL 55 (93)
Q Consensus 24 ~LIErCLqlyMsk~Evv~~L~~~a~--I~P~fT~ 55 (93)
.-+.+.+...|+.+|+++.|.+.++ |.+.+..
T Consensus 45 ~Sl~~A~~~G~~~e~i~~~L~~~S~~~lP~~v~~ 78 (129)
T PF13625_consen 45 ASLWRAASAGLTAEEIIEFLERYSKNPLPQNVEQ 78 (129)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHcCCCCCHHHHH
Confidence 4567889999999999999999873 4444443
No 96
>PF14039 YusW: YusW-like protein
Probab=25.13 E-value=68 Score=21.70 Aligned_cols=36 Identities=11% Similarity=0.184 Sum_probs=26.1
Q ss_pred HHHHHHHHHH-HHHhcCCHHHHHHHHHHhcCCChhhH
Q 034472 19 IRMVQHLIER-CLLLHMSRDQCIKALAEHAGIRPLVT 54 (93)
Q Consensus 19 I~~VQ~LIEr-CLqlyMsk~Evv~~L~~~a~I~P~fT 54 (93)
++.++.++.+ =+.--||.+++|+.+.+.+|++|.+.
T Consensus 46 ~~~l~~~l~~L~~~~~t~~~evi~~Vl~~f~Ld~dy~ 82 (92)
T PF14039_consen 46 FDELEPLLSELSFDSDTSEEEVIDQVLKAFNLDPDYQ 82 (92)
T ss_pred HHHHHHHHHhCCCCCCCChHHHHHHHHHHhCCCccce
Confidence 3344444432 35567999999999999999998654
No 97
>cd00896 PI3Kc_III Phosphoinositide 3-kinase (PI3K), class III, catalytic domain; The PI3K catalytic domain family is part of a larger superfamily that includes the catalytic domains of other kinases such as the typical serine/threonine/tyrosine protein kinases (PKs), aminoglycoside phosphotransferase, choline kinase, and RIO kinases. PI3Ks catalyze the transfer of the gamma-phosphoryl group from ATP to the 3-hydroxyl of the inositol ring of D-myo-phosphatidylinositol (PtdIns) or its derivatives. PI3Ks play an important role in a variety of fundamental cellular processes, including cell motility, the Ras pathway, vesicle trafficking and secretion, immune cell activation and apoptosis. They can be divided into three main classes (I, II, and III), defined by their substrate specificity, regulation, and domain structure. Class III PI3Ks, also called Vps34 (vacuolar protein sorting 34), contain an N-terminal lipid binding C2 domain, a PI3K homology domain of unknown function, and a C-termin
Probab=24.80 E-value=1.1e+02 Score=25.03 Aligned_cols=38 Identities=24% Similarity=0.298 Sum_probs=29.4
Q ss_pred CCCcccccccchhhHHHHHHHHHHHHHhcCCHHHHHHHHHHh
Q 034472 5 HHFFPCLHCHPHSYIRMVQHLIERCLLLHMSRDQCIKALAEH 46 (93)
Q Consensus 5 ~~~~~c~~~~p~s~I~~VQ~LIErCLqlyMsk~Evv~~L~~~ 46 (93)
+.++||....|..+|..|++ .|.+-||.+|..+.+.+.
T Consensus 290 ~~~ip~~~~~~~~~i~~l~~----rf~l~~s~~ea~~~~~~l 327 (350)
T cd00896 290 DANIPDIALDPDKAILKVQE----KFRLDLSDEEAIKHFQNL 327 (350)
T ss_pred CCCCcccccCHHHHHHHHHH----HhCCCCCHHHHHHHHHHH
Confidence 45689988777777776554 589999999999887663
No 98
>PRK11675 LexA regulated protein; Provisional
Probab=24.80 E-value=1.6e+02 Score=20.34 Aligned_cols=28 Identities=21% Similarity=0.202 Sum_probs=23.7
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034472 18 YIRMVQHLIERCLLLHMSRDQCIKALAE 45 (93)
Q Consensus 18 ~I~~VQ~LIErCLqlyMsk~Evv~~L~~ 45 (93)
+-+.++.|-+-|-+..||+.|+|+..-.
T Consensus 58 dedl~ekL~eyAe~~nitRSElIr~~I~ 85 (90)
T PRK11675 58 NADLVDALNELAEARNISRSELIEEILM 85 (90)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4578999999999999999999976533
No 99
>PRK14137 recX recombination regulator RecX; Provisional
Probab=24.40 E-value=3.1e+02 Score=20.63 Aligned_cols=60 Identities=13% Similarity=0.078 Sum_probs=47.2
Q ss_pred cccchhhHHHHHHHHHHHHHh----cCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhC----HHHHHHH
Q 034472 12 HCHPHSYIRMVQHLIERCLLL----HMSRDQCIKALAEHAGIRPLVTLTVWRELQKEN----KDFFRAY 72 (93)
Q Consensus 12 ~~~p~s~I~~VQ~LIErCLql----yMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeN----peFFkaY 72 (93)
.|.|.+.=..-+.+...||.+ -.|..|+-+-|.++ ++++.+-..|-..|.+.| ..|=++|
T Consensus 29 ~~~~~~~~e~~~~~~~~Al~~Ls~R~rS~~ELr~KL~~k-g~~~e~Ie~vI~rL~e~gyLDD~rfAe~~ 96 (195)
T PRK14137 29 RRTPPTPDEAREALLAYAFRALAARAMTAAELRAKLERR-SEDEALVTEVLERVQELGYQDDAQVARAE 96 (195)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHhcchhhHHHHHHHHHhc-CCCHHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 444445557778888999988 88999999999664 799999999999999875 3444555
No 100
>PF05157 T2SE_Nter: Type II secretion system (T2SS), protein E, N-terminal domain; InterPro: IPR007831 This domain is found at the N terminus of members of the general secretory system II protein E. Proteins in this subfamily are typically involved in Type IV pilus biogenesis (e.g. Q9X4G8 from SWISSPROT), though some are involved in other processes; for instance aggregation in Myxococcus xanthus (e.g. Q9RF11 from SWISSPROT) [].; GO: 0005524 ATP binding, 0006810 transport; PDB: 2D27_A 2D28_C.
Probab=24.34 E-value=67 Score=19.90 Aligned_cols=20 Identities=40% Similarity=0.431 Sum_probs=14.5
Q ss_pred hcCCHHHHHHHHHHhcCCCh
Q 034472 32 LHMSRDQCIKALAEHAGIRP 51 (93)
Q Consensus 32 lyMsk~Evv~~L~~~a~I~P 51 (93)
.++|.+++.++|+++.|++.
T Consensus 5 g~ise~~l~~~la~~~~l~~ 24 (109)
T PF05157_consen 5 GLISEDQLLEALAEQLGLPF 24 (109)
T ss_dssp T-S-HHHHHHHHHHHHT--B
T ss_pred CCCCHHHHHHHHHHHhCCCe
Confidence 57899999999999999875
No 101
>TIGR02849 spore_III_AD stage III sporulation protein AD. Members of this family are the uncharacterized protein SpoIIIAD, part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. Note that the start sites of members of this family as annotated tend to be variable; quite a few members have apparent homologous protein-coding regions continuing upstream of the first available start codon. The length of the alignment has been set to try to detect all valid members of the family, even if annotation of the start site begins too far downstream.
Probab=24.32 E-value=1e+02 Score=21.50 Aligned_cols=24 Identities=33% Similarity=0.501 Sum_probs=20.3
Q ss_pred HHHHHHHHhcCCChhhHHHHHHHH
Q 034472 38 QCIKALAEHAGIRPLVTLTVWREL 61 (93)
Q Consensus 38 Evv~~L~~~a~I~P~fT~~VW~~L 61 (93)
+.++.|..++||++..-.++|+-+
T Consensus 26 ~~l~~l~~~a~i~~~Yi~~llKii 49 (101)
T TIGR02849 26 EVIQSLARKAGLDSLYLATVLKII 49 (101)
T ss_pred HHHHHHHHHcCCChHHHHHHHHHH
Confidence 567889999999999999988754
No 102
>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=24.19 E-value=1.4e+02 Score=20.66 Aligned_cols=31 Identities=19% Similarity=0.175 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 34 MSRDQCIKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 34 Msk~Evv~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
.+-.||++.|.+..++.+.-+.++.+.|++.
T Consensus 19 ~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~K 49 (130)
T TIGR02698 19 TTSRDIIRILAEKKDWSDSTIKTLLGRLVDK 49 (130)
T ss_pred CCHHHHHHHHhhccCCcHHHHHHHHHHHHHC
Confidence 5788999999888889999999999999863
No 103
>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=23.92 E-value=29 Score=14.87 Aligned_cols=24 Identities=17% Similarity=0.463 Sum_probs=17.1
Q ss_pred CChhhHHHHHHHHHHhCHHHHHHH
Q 034472 49 IRPLVTLTVWRELQKENKDFFRAY 72 (93)
Q Consensus 49 I~P~fT~~VW~~LEkeNpeFFkaY 72 (93)
+...++..-|..++....++|+.-
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~ 29 (40)
T cd07765 6 VAVYFSQEEWELLDPAQRDLYRDV 29 (40)
T ss_pred eeeecCHHHHhcCCHHHHHHHHHH
Confidence 445577778888887777777653
No 104
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=23.76 E-value=67 Score=20.16 Aligned_cols=32 Identities=22% Similarity=0.511 Sum_probs=25.0
Q ss_pred HhcCCChhhHHHHHHHHHHhCHHHHHHHhhccCCCC
Q 034472 45 EHAGIRPLVTLTVWRELQKENKDFFRAYFHSISPRP 80 (93)
Q Consensus 45 ~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~rl~~k~ 80 (93)
+-++|=|.=+.-+|+-|+. |++.|+.-+..|.
T Consensus 5 ~~~~vip~~~~~~W~~L~~----~l~rY~~vL~~R~ 36 (60)
T PF14775_consen 5 RLANVIPDEKIRLWDALEN----FLKRYNKVLLDRA 36 (60)
T ss_pred HHhhcCChHHHHHHHHHHH----HHHHHHHHHHHHH
Confidence 3467889999999999974 8888887665543
No 105
>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=23.65 E-value=90 Score=22.40 Aligned_cols=32 Identities=19% Similarity=0.238 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhc----CCHHHHHHHHHHhcCCCh
Q 034472 20 RMVQHLIERCLLLH----MSRDQCIKALAEHAGIRP 51 (93)
Q Consensus 20 ~~VQ~LIErCLqly----Msk~Evv~~L~~~a~I~P 51 (93)
..+.++|.+||+.- .|-+|+...|++-++..+
T Consensus 249 ~~l~~li~~~l~~~p~~Rpt~~~v~~~l~~~~~~~~ 284 (288)
T cd05093 249 KEVYDLMLGCWQREPHMRLNIKEIHSLLQNLAKASP 284 (288)
T ss_pred HHHHHHHHHHccCChhhCCCHHHHHHHHHHHHHhcc
Confidence 35789999999864 788999888877555433
No 106
>KOG1684 consensus Enoyl-CoA hydratase [Lipid transport and metabolism]
Probab=23.19 E-value=1.4e+02 Score=25.68 Aligned_cols=25 Identities=20% Similarity=0.406 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhc
Q 034472 22 VQHLIERCLLLHMSRDQCIKALAEHA 47 (93)
Q Consensus 22 VQ~LIErCLqlyMsk~Evv~~L~~~a 47 (93)
+=++|+.|+... |-+|++++|.+..
T Consensus 265 ~~~~i~~~Fs~~-tVeeIie~lk~~q 289 (401)
T KOG1684|consen 265 KLDVINKCFSAN-TVEEIIEALKNYQ 289 (401)
T ss_pred hHHHHHHhhccc-cHHHHHHHHHHHh
Confidence 778999999888 9999999884443
No 107
>COG1438 ArgR Arginine repressor [Transcription]
Probab=23.07 E-value=1e+02 Score=22.89 Aligned_cols=32 Identities=25% Similarity=0.349 Sum_probs=25.5
Q ss_pred HhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 31 LLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 31 qlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
...-|++|+++.|++ .||+ .-..+|.+-|+|=
T Consensus 18 ~~i~TQ~Elv~~L~~-~Gi~-vTQaTvSRDlkel 49 (150)
T COG1438 18 EKISTQEELVELLQE-EGIE-VTQATVSRDLKEL 49 (150)
T ss_pred CCCCCHHHHHHHHHH-cCCe-EehHHHHHHHHHc
Confidence 356799999999965 7799 6667888888763
No 108
>COG4399 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.86 E-value=1.4e+02 Score=25.47 Aligned_cols=57 Identities=19% Similarity=0.127 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHHHHhcCCHHHHH-HHHHHh--cCCChhhHHHHHHHHHHhCHHHHHHHhh
Q 034472 18 YIRMVQHLIERCLLLHMSRDQCI-KALAEH--AGIRPLVTLTVWRELQKENKDFFRAYFH 74 (93)
Q Consensus 18 ~I~~VQ~LIErCLqlyMsk~Evv-~~L~~~--a~I~P~fT~~VW~~LEkeNpeFFkaY~~ 74 (93)
--+.|...|.+=||+.|..+-.. +.|..+ ++++-..-.-+-+-|++++.|+|..+.-
T Consensus 84 ~~~rv~~~i~~~lqk~lk~~~t~k~~l~~~~~~d~e~~~i~~~~~~l~~~l~e~f~e~qs 143 (376)
T COG4399 84 FQERVTEAIDQLLQKLLKSEVTDKEQLHQQIFADIEKDLIGNSERWLEKELAEKFTEAQS 143 (376)
T ss_pred HHHHHHHHHHHHHHHHHHhhcchHHHHHHHHHhhHHHHHHHhhHHHHHHHHHHHHHHHHh
Confidence 44678999999999999877663 444443 4555555566667899999999988753
No 109
>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=22.56 E-value=96 Score=21.80 Aligned_cols=25 Identities=12% Similarity=0.159 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHhc----CCHHHHHHHHH
Q 034472 20 RMVQHLIERCLLLH----MSRDQCIKALA 44 (93)
Q Consensus 20 ~~VQ~LIErCLqly----Msk~Evv~~L~ 44 (93)
..+.++|.+||+.- .|-+|+.+.|.
T Consensus 251 ~~~~~li~~~l~~~p~~Rp~~~eil~~l~ 279 (280)
T cd05049 251 SEVYDIMLGCWKRDPQQRINIKDIHERLQ 279 (280)
T ss_pred HHHHHHHHHHcCCCcccCCCHHHHHHHhh
Confidence 56889999999874 67777777763
No 110
>PRK07075 isochorismate-pyruvate lyase; Reviewed
Probab=22.45 E-value=2e+02 Score=19.34 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=17.5
Q ss_pred HHHHHhcCCChhhHHHHHHHHHH
Q 034472 41 KALAEHAGIRPLVTLTVWRELQK 63 (93)
Q Consensus 41 ~~L~~~a~I~P~fT~~VW~~LEk 63 (93)
..+....|++|.+...+|+.+=+
T Consensus 62 ~~~a~~~gl~~~~i~~if~~Ii~ 84 (101)
T PRK07075 62 RRWAEQAGLDADFVEKLFAQLIH 84 (101)
T ss_pred HHHhhcCCCCHHHHHHHHHHHHH
Confidence 34445578999999999987754
No 111
>KOG3779 consensus Homeobox transcription factor prospero [Transcription]
Probab=22.28 E-value=92 Score=28.15 Aligned_cols=37 Identities=14% Similarity=0.319 Sum_probs=28.2
Q ss_pred CHHHHHHHHHHhcCCChhhHHHHH---HHHHHhCHHHHHH
Q 034472 35 SRDQCIKALAEHAGIRPLVTLTVW---RELQKENKDFFRA 71 (93)
Q Consensus 35 sk~Evv~~L~~~a~I~P~fT~~VW---~~LEkeNpeFFka 71 (93)
+..|..+++..--.|+|....+++ .+|+.|=|||||.
T Consensus 688 TLREF~~AI~~GKDvdPSWKK~IYKVI~kLd~evPe~FK~ 727 (737)
T KOG3779|consen 688 TLREFFNAIIAGKDVDPSWKKAIYKVICKLDSEVPEIFKS 727 (737)
T ss_pred HHHHHHHHHhcCCcCCchHHHHHHHHHHhhhhhhhHhhcC
Confidence 345666666556679999887765 5899999999985
No 112
>TIGR01791 CM_archaeal chorismate mutase, archaeal type. This model represents a clade of archaeal chorismate mutases. Chorismate mutase catalyzes the conversion of chorismate into prephenate which is subsequently converted into either phenylalanine or tyrosine. In Sulfolobus this gene is found as a fusion with prephenate dehydrogenase (although the non-TIGR annotation contains a typographical error indicating it as a dehydratase) which is the next enzyme in the tyrosine biosynthesis pathway. The Archaeoglobus gene contains an N-terminal prephenate dehydrogenase domain and a C-terminal prephenate dehydratase domain followed by a regulatory amino acid-binding ACT domain. The Thermoplasma volcanium gene is adjacent to prephenate dehydratase.
Probab=22.23 E-value=1.9e+02 Score=18.22 Aligned_cols=23 Identities=22% Similarity=0.258 Sum_probs=16.7
Q ss_pred HHhcCCChhhHHHHHHHHHHhCH
Q 034472 44 AEHAGIRPLVTLTVWRELQKENK 66 (93)
Q Consensus 44 ~~~a~I~P~fT~~VW~~LEkeNp 66 (93)
....|++|.+...+|+.+-+.+.
T Consensus 57 ~~~~~l~~~~i~~if~~i~~~s~ 79 (83)
T TIGR01791 57 ARNLGLDVLKLKEIFEILMSLSK 79 (83)
T ss_pred HHhcCCCHHHHHHHHHHHHHHHH
Confidence 34467889888888887766543
No 113
>COG2080 CoxS Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs [Energy production and conversion]
Probab=22.05 E-value=95 Score=23.29 Aligned_cols=38 Identities=26% Similarity=0.440 Sum_probs=27.1
Q ss_pred CCCCcccccccchhhHHHHHHHHHHHHHhcCCHHHHHHHHH
Q 034472 4 NHHFFPCLHCHPHSYIRMVQHLIERCLLLHMSRDQCIKALA 44 (93)
Q Consensus 4 ~~~~~~c~~~~p~s~I~~VQ~LIErCLqlyMsk~Evv~~L~ 44 (93)
.|+..+|.||.|- .|.....|+++=-.- |++||-++|+
T Consensus 94 e~~~~QCGyCtpG-~Imsa~~lL~~~~~p--s~~eI~~~ls 131 (156)
T COG2080 94 EHDAFQCGYCTPG-QIMSATALLDRNPAP--TDEEIREALS 131 (156)
T ss_pred HcCCCcCCCCcHH-HHHHHHHHHHhCCCC--CHHHHHHHHh
Confidence 5788999999996 455555666553333 7888888875
No 114
>TIGR03198 pucE xanthine dehydrogenase E subunit. This gene has been characterized in B. subtilis as the Iron-sulfur cluster binding-subunit of xanthine dehydrogenase (pucE), acting in conjunction with pucC, the FAD-binding subunit and pucD, the molybdopterin binding subunit. The more common XDH complex (GenProp0640) includes the xdhA gene as the Fe-S cluster binding component.
Probab=22.00 E-value=88 Score=22.94 Aligned_cols=39 Identities=18% Similarity=0.301 Sum_probs=30.3
Q ss_pred CCCCcccccccchhhHHHHHHHHHHHHHhcCCHHHHHHHHHH
Q 034472 4 NHHFFPCLHCHPHSYIRMVQHLIERCLLLHMSRDQCIKALAE 45 (93)
Q Consensus 4 ~~~~~~c~~~~p~s~I~~VQ~LIErCLqlyMsk~Evv~~L~~ 45 (93)
.||..+|-+|.|-- |..+..|+++. -.-|.+|+-++|.-
T Consensus 92 ~~~a~QCGfCtpG~-im~~~~ll~~~--p~p~~~ei~~al~g 130 (151)
T TIGR03198 92 EEGGFQCGYCTPGM-VVALKALFRET--PQPSDEDMEEGLSG 130 (151)
T ss_pred HcCCCcCCCCCccH-HHHHHHHHHcC--CCCCHHHHHHHHcC
Confidence 57889999999974 55667888874 55688899888853
No 115
>PF07954 DUF1689: Protein of unknown function (DUF1689) ; InterPro: IPR012470 Family of fungal proteins with unknown function. A member of this family has been found to localise in the mitochondria [].
Probab=21.87 E-value=42 Score=24.89 Aligned_cols=28 Identities=18% Similarity=0.515 Sum_probs=23.9
Q ss_pred hHHHHHHHHHHhCHHHHHHHhhccCCCC
Q 034472 53 VTLTVWRELQKENKDFFRAYFHSISPRP 80 (93)
Q Consensus 53 fT~~VW~~LEkeNpeFFkaY~~rl~~k~ 80 (93)
=-.-||+-|+-.|+.+|-.||.+-+..|
T Consensus 107 ~q~~vwk~m~~~~~~~~~~Yy~~Ta~dP 134 (152)
T PF07954_consen 107 RQYEVWKLMDYGSASFWYLYYYKTAQDP 134 (152)
T ss_pred HHHHHHHhcccCCchHHHHHHHHHhhCh
Confidence 3457999999999999999999877655
No 116
>cd01784 rasfadin_RA Ubiquitin-like domain of Rasfadin. rasfadin_RA Rasfadin (RASSF2) belongs to a family of Ras effectors/tumor suppressors that includes RASSF1 and NORE1. RASSF2 binds directly to K-Ras in a GTP-dependent manner via its RA (RAS-associated) domain. RASSF2 promotes apoptosis and cell cycle arrest and is frequently down-regulated in lung tumor cell lines
Probab=21.75 E-value=86 Score=21.63 Aligned_cols=29 Identities=24% Similarity=0.342 Sum_probs=22.9
Q ss_pred cCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhh
Q 034472 33 HMSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFH 74 (93)
Q Consensus 33 yMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~ 74 (93)
-|+-.||+++|.++++|+ .||+=|.-|..
T Consensus 22 ~~tt~eVI~~LL~KFkv~-------------~~p~~FALy~v 50 (87)
T cd01784 22 TMTTPQVLKLLLNKFKIE-------------NSAEEFALYIV 50 (87)
T ss_pred CCCHHHHHHHHHHhcccc-------------CCHHHeEEEEE
Confidence 478899999999999997 56666666643
No 117
>PRK14135 recX recombination regulator RecX; Provisional
Probab=21.73 E-value=2.4e+02 Score=21.17 Aligned_cols=47 Identities=11% Similarity=0.075 Sum_probs=37.8
Q ss_pred hhHHHHHHHHHHHHHh-cCCHHHHHHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 17 SYIRMVQHLIERCLLL-HMSRDQCIKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 17 s~I~~VQ~LIErCLql-yMsk~Evv~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
+|.+.++..+...+.. ..++.++...|. +-||++.+...|...+.++
T Consensus 105 dD~~~a~~~~~~~~~~~~~g~~~I~~kL~-~kGi~~~~Ie~~l~~l~~~ 152 (263)
T PRK14135 105 DDKEYAESYVRTNINTGDKGPRVIKQKLL-QKGIEDEIIEEALSEYTEE 152 (263)
T ss_pred CHHHHHHHHHHHHHhccccchHHHHHHHH-HcCCCHHHHHHHHHhCChh
Confidence 4778888888887764 468899999995 5699999999999888543
No 118
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=21.70 E-value=1.6e+02 Score=17.36 Aligned_cols=26 Identities=27% Similarity=0.350 Sum_probs=20.7
Q ss_pred HHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 40 IKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 40 v~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
...|.++.+|.+....-+++.|+++.
T Consensus 27 ~~~la~~~~vsr~tvr~al~~L~~~g 52 (64)
T PF00392_consen 27 ERELAERYGVSRTTVREALRRLEAEG 52 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHhccCCcHHHHHHHHHHHCC
Confidence 35677888999999999999998764
No 119
>PF04355 SmpA_OmlA: SmpA / OmlA family; InterPro: IPR007450 This is a bacterial outer membrane lipoprotein, possibly involved in maintaining the structural integrity of the cell envelope []. The lipid attachment site is a conserved N-terminal cysteine residue sometimes found adjacent to the OmpA domain (IPR006665 from INTERPRO).; GO: 0019867 outer membrane; PDB: 4DM5_C 2PXG_A 2YH9_B 2KXX_A 2KM7_A.
Probab=21.67 E-value=54 Score=19.91 Aligned_cols=14 Identities=29% Similarity=0.309 Sum_probs=11.2
Q ss_pred HHhcCCHHHHHHHH
Q 034472 30 LLLHMSRDQCIKAL 43 (93)
Q Consensus 30 LqlyMsk~Evv~~L 43 (93)
|+..||++||...|
T Consensus 12 i~~GmTk~qV~~lL 25 (71)
T PF04355_consen 12 IKPGMTKDQVRALL 25 (71)
T ss_dssp T-TTSBHHHHHHHH
T ss_pred hcCCCCHHHHHHhc
Confidence 34679999999988
No 120
>PF14076 DUF4258: Domain of unknown function (DUF4258)
Probab=21.17 E-value=1.4e+02 Score=17.40 Aligned_cols=23 Identities=26% Similarity=0.234 Sum_probs=19.9
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHH
Q 034472 23 QHLIERCLLLHMSRDQCIKALAE 45 (93)
Q Consensus 23 Q~LIErCLqlyMsk~Evv~~L~~ 45 (93)
.|.++|..+-..|.+++.++|..
T Consensus 4 ~Ha~~rm~eR~Is~~~I~~~l~~ 26 (73)
T PF14076_consen 4 KHARERMQERGISEEDIEDALEN 26 (73)
T ss_pred HHHHHHHHhCCCCHHHHHHHHhc
Confidence 57788999999999999999954
No 121
>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=21.10 E-value=2e+02 Score=18.42 Aligned_cols=22 Identities=0% Similarity=0.042 Sum_probs=16.6
Q ss_pred HhcCCChhhHHHHHHHHHHhCH
Q 034472 45 EHAGIRPLVTLTVWRELQKENK 66 (93)
Q Consensus 45 ~~a~I~P~fT~~VW~~LEkeNp 66 (93)
+..|++|.+...+|+.+=+...
T Consensus 58 ~~~~l~~~~i~~if~~ii~~S~ 79 (83)
T TIGR01797 58 KAYHLDAHYITRLFQLIIEDSV 79 (83)
T ss_pred hhCCCCHHHHHHHHHHHHHHHH
Confidence 3467999999999988766543
No 122
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=21.09 E-value=1.5e+02 Score=19.58 Aligned_cols=26 Identities=27% Similarity=0.425 Sum_probs=21.8
Q ss_pred HHHHHHHhcCCChhhHHHHHHHHHHh
Q 034472 39 CIKALAEHAGIRPLVTLTVWRELQKE 64 (93)
Q Consensus 39 vv~~L~~~a~I~P~fT~~VW~~LEke 64 (93)
-++.|++..+|.|.+..-+.+.|++.
T Consensus 27 s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 27 SVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45667788899999999999999874
No 123
>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=20.72 E-value=27 Score=23.88 Aligned_cols=32 Identities=28% Similarity=0.636 Sum_probs=20.6
Q ss_pred HhcCCChhhHHHHHHHHHHhCHHHHHHHhhcc
Q 034472 45 EHAGIRPLVTLTVWRELQKENKDFFRAYFHSI 76 (93)
Q Consensus 45 ~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~rl 76 (93)
+|-|..|.=+-.+..+|++++.+|-++||-.+
T Consensus 49 nqkglrpqd~pvll~~l~~~~q~li~kyyp~l 80 (82)
T PF12980_consen 49 NQKGLRPQDKPVLLSELSQEDQDLIRKYYPEL 80 (82)
T ss_dssp -TT--SGGGS-B-GGGS-HHHHHHHHHH-GGG
T ss_pred hhccCCCcCcchHHHHHhHHHHHHHHHHhHHh
Confidence 45567777777788999999999999998543
No 124
>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=20.53 E-value=3.7e+02 Score=22.11 Aligned_cols=60 Identities=17% Similarity=0.134 Sum_probs=44.5
Q ss_pred cchhhHHHHHHHHHHHHHh---------cCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhh
Q 034472 14 HPHSYIRMVQHLIERCLLL---------HMSRDQCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFH 74 (93)
Q Consensus 14 ~p~s~I~~VQ~LIErCLql---------yMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~ 74 (93)
.|...+-+.+.-+-||..+ -||.+|+++.|.++.+.++.....-|+.... +|..+-+|+.
T Consensus 433 ~p~~~lg~l~~~l~ra~r~vvD~glH~~~wt~e~a~~~l~~~~~~~~~~a~~ev~ry~~-~Pgq~~sY~~ 501 (549)
T PF05960_consen 433 DPLDRLGQLNDELWRAARLVVDTGLHYGGWTREQAIDYLVENTGFSEEEAESEVDRYIS-SPGQALSYKV 501 (549)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHCCB--HHHHHHHHHHHS-S-HHHHHHHHHHHHH-STTGGGHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcCCChHHHHHHHHHHHh-CcHHHHHHHH
Confidence 4666777778888888875 6999999999999999999888777776665 7887777754
No 125
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=20.49 E-value=1.8e+02 Score=17.22 Aligned_cols=31 Identities=13% Similarity=0.287 Sum_probs=25.1
Q ss_pred HhcCCHHHHHHHHHHhcCCChhhHHHHHHHHHHhC
Q 034472 31 LLHMSRDQCIKALAEHAGIRPLVTLTVWRELQKEN 65 (93)
Q Consensus 31 qlyMsk~Evv~~L~~~a~I~P~fT~~VW~~LEkeN 65 (93)
.+.+|++|+.+. +|+.+...+-+.++|++++
T Consensus 26 ~~~lt~~~iA~~----~g~sr~tv~r~l~~l~~~g 56 (76)
T PF13545_consen 26 PLPLTQEEIADM----LGVSRETVSRILKRLKDEG 56 (76)
T ss_dssp EEESSHHHHHHH----HTSCHHHHHHHHHHHHHTT
T ss_pred EecCCHHHHHHH----HCCCHHHHHHHHHHHHHCC
Confidence 467888876554 6899999999999999875
No 126
>PLN02951 Molybderin biosynthesis protein CNX2
Probab=20.46 E-value=86 Score=25.37 Aligned_cols=12 Identities=25% Similarity=0.634 Sum_probs=9.7
Q ss_pred CCcccccccchh
Q 034472 6 HFFPCLHCHPHS 17 (93)
Q Consensus 6 ~~~~c~~~~p~s 17 (93)
=|+-|.||.|.+
T Consensus 68 CNlrC~yC~~~~ 79 (373)
T PLN02951 68 CNLRCQYCMPEE 79 (373)
T ss_pred cCcCCCCCCCCc
Confidence 468899999865
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=20.41 E-value=1.2e+02 Score=23.41 Aligned_cols=30 Identities=23% Similarity=0.265 Sum_probs=16.9
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHhcCCChhh
Q 034472 23 QHLIERCLLLHMSRDQCIKALAEHAGIRPLV 53 (93)
Q Consensus 23 Q~LIErCLqlyMsk~Evv~~L~~~a~I~P~f 53 (93)
+.|+-|=+.--|||+|+|.+|..-. +.|.+
T Consensus 10 ieLLqrL~~SG~TK~~ii~ALe~l~-~~~~~ 39 (180)
T PF04814_consen 10 IELLQRLRRSGMTKEEIIHALETLD-PSPSP 39 (180)
T ss_dssp HHHHHHHHHCT--HHHHHHHHTT--------
T ss_pred HHHHHHHHHcCCCHHHHHHHHhccC-CCccc
Confidence 4566666788999999999997533 43443
No 128
>PRK11145 pflA pyruvate formate lyase-activating enzyme 1; Provisional
Probab=20.29 E-value=45 Score=24.49 Aligned_cols=12 Identities=33% Similarity=0.899 Sum_probs=9.5
Q ss_pred CCcccccccchh
Q 034472 6 HFFPCLHCHPHS 17 (93)
Q Consensus 6 ~~~~c~~~~p~s 17 (93)
=|+-|.+|++.+
T Consensus 30 Cnl~C~~C~~~~ 41 (246)
T PRK11145 30 CLMRCLYCHNRD 41 (246)
T ss_pred CCCcCCCCCCHH
Confidence 368899999754
No 129
>cd06622 PKc_MAPKK_PBS2_like Catalytic domain of fungal PBS2-like dual-specificity MAP kinase kinases. Protein kinases (PKs), MAP kinase kinase (MAPKK) subfamily, fungal PBS2-like proteins, catalytic (c) domain. PKs catalyze the transfer of the gamma-phosphoryl group from ATP to serine/threonine or tyrosine residues on protein substrates. The MAPKK subfamily is part of a larger superfamily that includes the catalytic domains of other protein serine/threonine kinases, protein tyrosine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase. The mitogen-activated protein (MAP) kinase signaling pathways are important mediators of cellular responses to extracellular signals. The pathways involve a triple kinase core cascade comprising of the MAP kinase (MAPK), which is phosphorylated and activated by a MAPK kinase (MAPKK or MKK), which itself is phosphorylated and activated by a MAPK kinase kinase (MAPKKK or MKKK). Members of this group include
Probab=20.28 E-value=1.9e+02 Score=20.50 Aligned_cols=45 Identities=16% Similarity=0.090 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHhc----CCHHHHHH--HHHHhcCCChhhHHHHHHHHHH
Q 034472 19 IRMVQHLIERCLLLH----MSRDQCIK--ALAEHAGIRPLVTLTVWRELQK 63 (93)
Q Consensus 19 I~~VQ~LIErCLqly----Msk~Evv~--~L~~~a~I~P~fT~~VW~~LEk 63 (93)
-..+..+|++||+.- .+-+|++. .+.+....+..+..-||..+++
T Consensus 235 ~~~~~~li~~~l~~~p~~Rp~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 (286)
T cd06622 235 SDDAQDFVAKCLNKIPNRRPTYAQLLEHPWLVKYKNADVDMAEWVTGALKR 285 (286)
T ss_pred CHHHHHHHHHHcccCcccCCCHHHHhcChhhhhccCCccchHHHHHHHHhc
Confidence 356778999999775 44456664 2334445566666667766654
No 130
>PF06711 DUF1198: Protein of unknown function (DUF1198); InterPro: IPR009587 This family consists of several bacterial proteins of around 150 residues in length which are specific to Escherichia coli, Salmonella species and Yersinia pestis. The function of this family is unknown.
Probab=20.15 E-value=2e+02 Score=21.67 Aligned_cols=38 Identities=21% Similarity=0.408 Sum_probs=33.1
Q ss_pred HHHHHHHHhcCCChhhHHHHHHHHHHhCHHHHHHHhhc
Q 034472 38 QCIKALAEHAGIRPLVTLTVWRELQKENKDFFRAYFHS 75 (93)
Q Consensus 38 Evv~~L~~~a~I~P~fT~~VW~~LEkeNpeFFkaY~~r 75 (93)
-.++.|++..||+|+--+.+-.++-|++.+=|-.|-.+
T Consensus 26 ~A~~~Ls~rL~I~Pv~iESMl~qMGk~~~~~Firyl~~ 63 (148)
T PF06711_consen 26 RAIRRLSERLNIKPVYIESMLDQMGKRAGQEFIRYLSR 63 (148)
T ss_pred HHHHHHHHHhCCCceeHHHHHHHHhHhHHHHHHHHHcC
Confidence 35789999999999999999999999998888777543
No 131
>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=20.11 E-value=1.4e+02 Score=17.44 Aligned_cols=21 Identities=33% Similarity=0.384 Sum_probs=15.3
Q ss_pred HHHHHHhcCCChhhHHHHHHH
Q 034472 40 IKALAEHAGIRPLVTLTVWRE 60 (93)
Q Consensus 40 v~~L~~~a~I~P~fT~~VW~~ 60 (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 468888999999988887763
No 132
>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=20.06 E-value=1.2e+02 Score=21.14 Aligned_cols=26 Identities=12% Similarity=0.065 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHh----cCCHHHHHHHHHH
Q 034472 20 RMVQHLIERCLLL----HMSRDQCIKALAE 45 (93)
Q Consensus 20 ~~VQ~LIErCLql----yMsk~Evv~~L~~ 45 (93)
..++++|++|++. ..|-++|+..|++
T Consensus 225 ~~l~~li~~~~~~~p~~Rp~~~~i~~~l~~ 254 (257)
T cd05116 225 PEMYDLMKLCWTYGVDERPGFAVVELRLRN 254 (257)
T ss_pred HHHHHHHHHHhccCchhCcCHHHHHHHHhc
Confidence 4578899999964 5778888888854
No 133
>TIGR03356 BGL beta-galactosidase.
Probab=20.01 E-value=56 Score=26.95 Aligned_cols=37 Identities=32% Similarity=0.682 Sum_probs=24.6
Q ss_pred HHHHHHHHhcCCChhhHHHHHH---HHH-------HhCHHHHHHHhhc
Q 034472 38 QCIKALAEHAGIRPLVTLTVWR---ELQ-------KENKDFFRAYFHS 75 (93)
Q Consensus 38 Evv~~L~~~a~I~P~fT~~VW~---~LE-------keNpeFFkaY~~r 75 (93)
++++.| ...||+|.+|..=|. .|+ .+..+.|..|-..
T Consensus 98 ~~i~~l-~~~gi~pivtL~Hfd~P~~l~~~gGw~~~~~~~~f~~ya~~ 144 (427)
T TIGR03356 98 RLVDEL-LEAGIEPFVTLYHWDLPQALEDRGGWLNRDTAEWFAEYAAV 144 (427)
T ss_pred HHHHHH-HHcCCeeEEeeccCCccHHHHhcCCCCChHHHHHHHHHHHH
Confidence 677777 458999998874332 233 5566888888544
Done!