Query psy7895
Match_columns 108
No_of_seqs 102 out of 163
Neff 5.2
Searched_HMMs 46136
Date Fri Aug 16 21:35:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7895.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7895hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3463|consensus 100.0 8.7E-54 1.9E-58 297.7 11.9 105 1-106 1-107 (109)
2 COG5123 TOA2 Transcription ini 100.0 3.5E-42 7.5E-47 238.7 11.4 101 3-104 5-112 (113)
3 PF02751 TFIIA_gamma_C: Transc 100.0 9E-29 1.9E-33 153.6 6.0 50 51-101 1-52 (52)
4 PF02268 TFIIA_gamma_N: Transc 99.9 1.3E-26 2.9E-31 142.3 5.6 49 1-49 1-49 (49)
5 PF10925 DUF2680: Protein of u 92.7 0.37 8E-06 30.4 4.9 32 16-47 21-52 (59)
6 cd01709 RT_like_1 RT_like_1: A 88.6 0.7 1.5E-05 38.4 4.2 65 25-102 87-162 (346)
7 PF09925 DUF2157: Predicted me 87.2 0.6 1.3E-05 33.2 2.7 23 19-41 1-23 (145)
8 cd03487 RT_Bac_retron_II RT_Ba 87.1 1.9 4.1E-05 32.1 5.5 46 25-81 107-152 (214)
9 cd01646 RT_Bac_retron_I RT_Bac 86.9 1.4 2.9E-05 31.3 4.4 40 25-76 57-96 (158)
10 PF11848 DUF3368: Domain of un 86.0 2.3 5E-05 25.2 4.4 35 4-39 11-46 (48)
11 cd01651 RT_G2_intron RT_G2_int 79.5 3.7 8E-05 29.7 4.2 52 24-76 129-180 (226)
12 COG3937 Uncharacterized conser 79.5 8.1 0.00018 27.3 5.7 35 10-44 21-55 (108)
13 cd04437 DEP_Epac DEP (Dishevel 78.0 3.7 8E-05 29.4 3.7 61 4-71 25-87 (125)
14 cd04440 DEP_2_P-Rex DEP (Dishe 76.3 5.5 0.00012 27.2 4.1 62 4-71 32-93 (93)
15 PF00349 Hexokinase_1: Hexokin 71.9 7.8 0.00017 29.5 4.4 46 14-59 2-47 (206)
16 PF09677 TrbI_Ftype: Type-F co 71.3 14 0.0003 25.9 5.2 40 14-53 37-79 (111)
17 cd00304 RT_like RT_like: Rever 68.8 14 0.0003 23.3 4.5 41 24-76 14-54 (98)
18 PF00078 RVT_1: Reverse transc 67.3 13 0.00029 26.1 4.6 42 24-76 128-169 (214)
19 TIGR02744 TrbI_Ftype type-F co 63.9 21 0.00044 25.3 4.9 37 15-51 39-78 (112)
20 PF15606 Toxin_55: Putative to 61.8 9.4 0.0002 25.4 2.6 22 14-35 40-61 (77)
21 PF06702 DUF1193: Protein of u 59.9 7.9 0.00017 30.4 2.4 46 5-50 150-204 (221)
22 cd08332 CARD_CASP2 Caspase act 57.6 17 0.00036 24.2 3.4 25 15-39 22-46 (90)
23 PRK10753 transcriptional regul 57.6 29 0.00063 22.8 4.5 41 17-59 5-45 (90)
24 PF15658 Latrotoxin_C: Latroto 57.5 16 0.00034 26.6 3.4 42 8-49 85-126 (127)
25 smart00411 BHL bacterial (prok 57.5 30 0.00066 22.0 4.5 35 16-50 4-38 (90)
26 PF00619 CARD: Caspase recruit 56.3 20 0.00042 22.5 3.4 25 14-38 17-41 (85)
27 cd01648 TERT TERT: Telomerase 55.8 19 0.00042 24.4 3.6 68 24-100 22-102 (119)
28 cd04446 DEP_DEPDC4 DEP (Dishev 55.5 19 0.00041 24.7 3.4 50 3-55 21-76 (95)
29 PRK10664 transcriptional regul 55.1 34 0.00074 22.6 4.6 40 18-59 6-45 (90)
30 PRK00285 ihfA integration host 52.4 29 0.00064 22.9 3.9 37 14-50 4-40 (99)
31 KOG0037|consensus 51.6 17 0.00037 28.6 3.0 33 9-43 139-172 (221)
32 cd08330 CARD_ASC_NALP1 Caspase 50.7 22 0.00048 23.2 3.1 25 14-38 16-40 (82)
33 PF04719 TAFII28: hTAFII28-lik 50.6 37 0.0008 23.0 4.2 40 3-43 16-56 (90)
34 PF09851 SHOCT: Short C-termin 50.3 40 0.00086 18.2 3.6 22 16-37 5-26 (31)
35 PF05388 Carbpep_Y_N: Carboxyp 50.3 24 0.00053 24.7 3.4 49 28-82 59-108 (113)
36 PF14277 DUF4364: Domain of un 48.1 14 0.00029 27.4 1.9 38 14-51 35-85 (163)
37 PF14848 HU-DNA_bdg: DNA-bindi 47.6 53 0.0011 22.8 4.8 37 14-50 30-67 (124)
38 cd00591 HU_IHF Integration hos 46.8 56 0.0012 20.5 4.5 34 17-50 4-37 (87)
39 PF09693 Phage_XkdX: Phage unc 46.7 22 0.00048 20.4 2.3 21 16-36 15-35 (40)
40 PF03512 Glyco_hydro_52: Glyco 46.0 18 0.00039 31.0 2.5 59 13-72 274-367 (428)
41 PF00610 DEP: Domain found in 45.8 21 0.00046 21.9 2.3 62 4-68 12-74 (74)
42 TIGR01837 PHA_granule_1 poly(h 45.6 83 0.0018 21.9 5.5 33 13-45 22-54 (118)
43 cd08325 CARD_CASP1-like Caspas 44.1 62 0.0013 21.1 4.4 26 14-39 17-42 (83)
44 PF14490 HHH_4: Helix-hairpin- 43.1 45 0.00097 21.9 3.7 36 15-51 8-43 (94)
45 PRK00199 ihfB integration host 42.8 85 0.0018 20.4 5.0 41 17-59 5-46 (94)
46 KOG3219|consensus 42.8 18 0.00039 28.0 1.9 31 3-33 105-135 (195)
47 TIGR01669 phage_XkdX phage unc 42.6 27 0.00059 20.7 2.3 22 16-37 20-41 (45)
48 KOG1369|consensus 42.1 68 0.0015 27.9 5.5 71 12-83 24-99 (474)
49 cd04441 DEP_2_DEP6 DEP (Dishev 41.8 42 0.00092 22.4 3.4 58 4-68 27-85 (85)
50 smart00049 DEP Domain found in 41.5 32 0.00069 21.3 2.6 60 4-69 15-76 (77)
51 cd08048 TAF11 TATA Binding Pro 40.3 49 0.0011 22.0 3.5 33 3-35 9-41 (85)
52 TIGR03319 YmdA_YtgF conserved 39.1 59 0.0013 28.2 4.7 44 3-50 252-295 (514)
53 PF08638 Med14: Mediator compl 38.8 1E+02 0.0022 23.2 5.4 53 22-79 131-183 (195)
54 PF10051 DUF2286: Uncharacteri 38.3 95 0.0021 22.9 5.0 50 27-98 59-109 (141)
55 smart00114 CARD Caspase recrui 38.2 43 0.00094 21.5 3.0 23 16-38 23-45 (88)
56 PF13833 EF-hand_8: EF-hand do 37.8 65 0.0014 18.2 3.4 29 14-43 9-37 (54)
57 TIGR00987 himA integration hos 37.8 69 0.0015 21.1 3.9 35 16-50 5-39 (96)
58 PF12960 DUF3849: Protein of u 36.6 93 0.002 22.6 4.7 49 4-52 17-71 (133)
59 PF02982 Scytalone_dh: Scytalo 36.6 57 0.0012 24.6 3.7 31 54-85 110-145 (160)
60 PF03492 Methyltransf_7: SAM d 36.4 29 0.00062 28.2 2.3 24 10-33 198-221 (334)
61 PF14476 Chloroplast_duf: Peta 36.2 24 0.00053 29.0 1.8 21 1-21 260-285 (313)
62 PF00216 Bac_DNA_binding: Bact 36.0 76 0.0016 20.0 3.8 31 20-50 8-38 (90)
63 cd08323 CARD_APAF1 Caspase act 35.8 48 0.001 22.1 2.9 29 15-43 16-47 (86)
64 PF05186 Dpy-30: Dpy-30 motif; 35.3 46 0.00099 19.3 2.4 27 5-31 4-30 (42)
65 PF10335 DUF294_C: Putative nu 35.2 93 0.002 22.0 4.5 36 17-52 66-101 (145)
66 cd01671 CARD Caspase activatio 35.0 66 0.0014 19.8 3.4 26 14-39 14-39 (80)
67 TIGR00988 hip integration host 34.5 1.3E+02 0.0028 19.4 5.0 41 17-59 5-46 (94)
68 PF07527 Hairy_orange: Hairy O 34.5 91 0.002 17.7 4.6 35 12-46 8-42 (43)
69 PF14929 TAF1_subA: TAF RNA Po 34.0 38 0.00082 29.8 2.7 41 10-50 320-365 (547)
70 PF00681 Plectin: Plectin repe 34.0 72 0.0016 18.3 3.2 20 19-38 24-43 (45)
71 cd08329 CARD_BIRC2_BIRC3 Caspa 33.7 61 0.0013 21.7 3.2 22 17-38 27-48 (94)
72 PF12713 DUF3806: Domain of un 33.7 72 0.0016 21.0 3.5 39 17-56 4-43 (87)
73 COG5026 Hexokinase [Carbohydra 33.3 1.2E+02 0.0025 26.6 5.4 51 1-51 1-53 (466)
74 cd08326 CARD_CASP9 Caspase act 32.8 69 0.0015 21.1 3.3 24 15-38 18-41 (84)
75 TIGR02742 TrbC_Ftype type-F co 32.4 68 0.0015 22.9 3.4 27 13-39 102-128 (130)
76 PF12297 EVC2_like: Ellis van 31.5 1.7E+02 0.0038 25.2 6.2 43 3-45 297-339 (429)
77 COG3093 VapI Plasmid maintenan 30.5 56 0.0012 22.9 2.6 32 17-48 38-70 (104)
78 PF11429 Colicin_D: Colicin D; 30.3 43 0.00093 22.9 2.0 34 36-76 23-56 (92)
79 PF01756 ACOX: Acyl-CoA oxidas 30.2 1.5E+02 0.0034 21.4 5.1 36 14-49 92-127 (187)
80 COG2306 Predicted RNA-binding 29.5 1.4E+02 0.003 22.9 4.8 31 17-47 126-156 (183)
81 PF14793 DUF4478: Domain of un 29.4 32 0.00069 24.5 1.2 10 3-12 31-40 (112)
82 PF07565 Band_3_cyto: Band 3 c 28.1 67 0.0015 25.4 3.0 31 9-39 41-71 (257)
83 PF02885 Glycos_trans_3N: Glyc 27.8 1.1E+02 0.0024 18.7 3.5 25 15-39 2-26 (66)
84 cd01130 VirB11-like_ATPase Typ 27.7 68 0.0015 23.1 2.8 22 19-40 1-22 (186)
85 TIGR02009 PGMB-YQAB-SF beta-ph 27.6 1.3E+02 0.0029 20.7 4.3 44 5-48 37-82 (185)
86 PF09862 DUF2089: Protein of u 27.5 61 0.0013 22.9 2.4 22 16-38 92-113 (113)
87 PF13742 tRNA_anti_2: OB-fold 27.5 1.8E+02 0.0038 19.3 4.6 42 39-81 6-49 (99)
88 TIGR01425 SRP54_euk signal rec 27.3 1.5E+02 0.0032 25.3 5.1 38 10-47 4-41 (429)
89 PF03048 Herpes_UL92: UL92 fam 27.3 1.3E+02 0.0028 23.2 4.4 32 15-46 104-135 (192)
90 cd01650 RT_nLTR_like RT_nLTR: 27.2 1.2E+02 0.0027 21.6 4.1 71 24-101 109-192 (220)
91 PF06256 Nucleo_LEF-12: Nucleo 27.2 95 0.0021 23.9 3.6 43 7-49 11-90 (185)
92 PF10815 ComZ: ComZ; InterPro 26.8 1.7E+02 0.0037 18.4 5.2 35 14-48 13-48 (56)
93 PTZ00107 hexokinase; Provision 26.7 1.7E+02 0.0037 25.1 5.4 38 14-51 6-43 (464)
94 PLN02668 indole-3-acetate carb 26.2 75 0.0016 26.7 3.1 22 13-34 257-278 (386)
95 cd04371 DEP DEP domain, named 26.1 75 0.0016 19.5 2.5 51 4-59 23-74 (81)
96 cd04443 DEP_GPR155 DEP (Dishev 26.1 1.9E+02 0.0041 19.0 4.5 59 4-68 25-83 (83)
97 cd08324 CARD_NOD1_CARD4 Caspas 26.1 65 0.0014 21.9 2.2 22 16-37 18-39 (85)
98 TIGR01201 HU_rel DNA-binding p 25.4 1.5E+02 0.0033 21.2 4.2 38 13-50 31-68 (145)
99 PRK00106 hypothetical protein; 25.3 1.4E+02 0.003 26.3 4.7 44 3-50 273-316 (535)
100 COG0776 HimA Bacterial nucleoi 25.2 2E+02 0.0044 19.5 4.6 31 20-50 9-39 (94)
101 PF11630 DUF3254: Protein of u 25.2 1.5E+02 0.0032 20.7 3.9 31 7-37 69-99 (100)
102 cd08785 CARD_CARD9-like Caspas 25.1 1.1E+02 0.0024 20.4 3.2 23 16-38 19-41 (86)
103 TIGR02148 Fibro_Slime fibro-sl 25.1 63 0.0014 22.1 2.1 29 57-85 15-43 (90)
104 PF08784 RPA_C: Replication pr 24.8 62 0.0014 21.2 2.0 16 13-28 80-95 (102)
105 PRK10449 heat-inducible protei 24.3 1.7E+02 0.0036 20.7 4.3 42 37-81 98-139 (140)
106 COG3877 Uncharacterized protei 24.2 83 0.0018 22.5 2.6 20 19-38 102-121 (122)
107 PF14237 DUF4339: Domain of un 24.1 49 0.0011 18.8 1.2 16 16-31 16-31 (45)
108 PF12550 GCR1_C: Transcription 24.0 1.6E+02 0.0034 18.9 3.8 29 12-40 52-80 (81)
109 COG2405 Predicted nucleic acid 23.8 96 0.0021 23.2 3.0 25 17-41 130-155 (157)
110 COG0541 Ffh Signal recognition 23.8 1.9E+02 0.0041 25.2 5.1 39 9-47 3-41 (451)
111 PF08535 KorB: KorB domain; I 23.7 2.1E+02 0.0045 18.5 4.4 30 14-43 28-57 (93)
112 PLN02596 hexokinase-like 23.7 2.9E+02 0.0063 24.0 6.3 40 12-51 35-74 (490)
113 cd01733 LSm10 The eukaryotic S 23.6 1.8E+02 0.0038 18.8 4.0 30 52-85 26-55 (78)
114 PF10664 NdhM: Cyanobacterial 23.5 24 0.00052 24.9 -0.2 29 10-38 70-98 (108)
115 TIGR03573 WbuX N-acetyl sugar 23.3 84 0.0018 25.4 2.9 41 3-44 279-319 (343)
116 cd03715 RT_ZFREV_like RT_ZFREV 23.2 58 0.0012 23.9 1.7 20 12-31 14-33 (210)
117 PF10689 DUF2496: Protein of u 22.8 1.8E+02 0.004 17.4 3.9 27 13-39 9-35 (44)
118 PF05609 LAP1C: Lamina-associa 22.7 88 0.0019 27.2 2.9 44 28-71 331-380 (465)
119 PF08004 DUF1699: Protein of u 22.5 54 0.0012 23.9 1.4 27 12-38 104-130 (131)
120 cd07367 CarBb CarBb is the B s 22.5 36 0.00079 26.6 0.6 44 7-50 151-207 (268)
121 TIGR01420 pilT_fam pilus retra 22.4 98 0.0021 24.9 3.0 26 12-37 313-338 (343)
122 PRK03195 hypothetical protein; 22.4 1.2E+02 0.0026 23.1 3.4 59 13-74 73-133 (186)
123 KOG3438|consensus 22.2 1.9E+02 0.0042 20.3 4.1 30 10-46 69-98 (105)
124 PRK13717 conjugal transfer pro 22.1 3.2E+02 0.0069 19.9 5.5 37 16-52 53-92 (128)
125 PF14076 DUF4258: Domain of un 22.1 1.4E+02 0.003 17.7 3.1 23 16-39 4-26 (73)
126 TIGR02525 plasmid_TraJ plasmid 21.8 85 0.0018 26.1 2.6 26 12-37 342-367 (372)
127 KOG3456|consensus 21.7 64 0.0014 23.1 1.6 11 94-104 78-88 (120)
128 PF09687 PRESAN: Plasmodium RE 21.6 2.4E+02 0.0053 18.3 4.9 40 11-50 45-84 (129)
129 COG2257 Uncharacterized homolo 21.3 1.4E+02 0.003 20.6 3.1 27 14-40 53-79 (92)
130 KOG3618|consensus 21.1 1.5E+02 0.0034 28.2 4.3 50 25-74 1153-1215(1318)
131 PF05258 DUF721: Protein of un 20.9 1.7E+02 0.0036 17.9 3.3 39 15-53 2-42 (89)
132 PRK08132 FAD-dependent oxidore 20.9 3.5E+02 0.0077 22.8 6.2 39 61-104 147-185 (547)
133 PRK13358 protocatechuate 4,5-d 20.4 54 0.0012 25.4 1.1 41 10-50 154-207 (269)
134 COG4003 Uncharacterized protei 20.0 2.6E+02 0.0057 19.2 4.3 27 10-37 46-72 (98)
No 1
>KOG3463|consensus
Probab=100.00 E-value=8.7e-54 Score=297.74 Aligned_cols=105 Identities=70% Similarity=1.094 Sum_probs=101.7
Q ss_pred Ch-hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcC
Q psy7895 1 MS-YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTD 79 (108)
Q Consensus 1 m~-y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd 79 (108)
|+ |||||+||||.+|++|||||+++|.|||+||++||++||+||+++|+++|+++++|| |+|.|||||||||||+++|
T Consensus 1 m~~YelYR~ttlG~~L~~tLDe~v~~g~itp~la~~VL~~FDKSi~~al~~~vk~kmsfk-g~L~tYr~CDnVWTFil~~ 79 (109)
T KOG3463|consen 1 MSYYELYRRTTLGNALQKTLDELVSDGVITPSLAKKVLEQFDKSINEALNDKVKNKMSFK-GKLDTYRFCDNVWTFILKD 79 (109)
T ss_pred CcHHHHHHHhhHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHhcccceeee-eccceeeeccceeeEEEcC
Confidence 66 999999999999999999999999999999999999999999999999999999999 9999999999999999999
Q ss_pred eEEEecceEee-cCcEEEEEecCCCCCC
Q psy7895 80 VEFREVAEIAR-VNKLKIVACDGKSSDD 106 (108)
Q Consensus 80 ~~f~~~~~~~~-~~~lKIVAcd~~~~~~ 106 (108)
++|+.+++..+ +|+||||||||+.++.
T Consensus 80 ~~~r~~~e~~~~vdkvkIVACdg~~~~~ 107 (109)
T KOG3463|consen 80 VEFREDNESFKTVDKVKIVACDGKDSGA 107 (109)
T ss_pred eEEecccccccccceEEEEEecCccccc
Confidence 99999999986 9999999999987653
No 2
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=100.00 E-value=3.5e-42 Score=238.72 Aligned_cols=101 Identities=50% Similarity=0.859 Sum_probs=96.5
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCeEE
Q psy7895 3 YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEF 82 (108)
Q Consensus 3 y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~f 82 (108)
|||||+|+||..|.|+|||+|++|.|+|+||++||+.||+++.++|++.|+|+++|| |+|++|+|||+||||+++|+.|
T Consensus 5 YElYRrs~ig~~L~dalD~lis~g~isp~lam~vLetFDksv~e~l~~~v~s~ltfK-G~lDtY~fcD~VWtFi~kn~~~ 83 (113)
T COG5123 5 YELYRRSMIGKVLEDALDELISAGVISPNLAMHVLETFDKSVPEVLNKSVTSSLTFK-GKLDTYNFCDGVWTFITKNFVM 83 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCcCHHHHHHHHHHhhhHHHHHHHhhhheeeEEe-ecccccccccceeEEEecCeEE
Confidence 999999999999999999999999999999999999999999999999999999999 9999999999999999999999
Q ss_pred Eecc------eE-eecCcEEEEEecCCCC
Q psy7895 83 REVA------EI-ARVNKLKIVACDGKSS 104 (108)
Q Consensus 83 ~~~~------~~-~~~~~lKIVAcd~~~~ 104 (108)
++++ +. |.+++++||||.++..
T Consensus 84 s~~n~~~~a~e~~i~~~k~rIvaca~r~s 112 (113)
T COG5123 84 SLNNEYFNAGEVNIVACKARIVACAGRRS 112 (113)
T ss_pred EeccccccccccceEeeeeeEEeeccccC
Confidence 9986 43 7889999999998764
No 3
>PF02751 TFIIA_gamma_C: Transcription initiation factor IIA, gamma subunit; InterPro: IPR015871 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the beta-barrel domain found at the C-terminal of the gamma subunit of transcription factor TFIIA. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=99.95 E-value=9e-29 Score=153.55 Aligned_cols=50 Identities=64% Similarity=1.193 Sum_probs=45.1
Q ss_pred hccCceeEeccccceeeeeCcEEEEEEcCeEEEe--cceEeecCcEEEEEecC
Q psy7895 51 KVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFRE--VAEIARVNKLKIVACDG 101 (108)
Q Consensus 51 ~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~f~~--~~~~~~~~~lKIVAcd~ 101 (108)
+|++|++|| |||+|||||||||||+++|++|++ +++.+++|+||||||||
T Consensus 1 ~vk~k~~fK-G~L~tYrfcDnVWTFi~kn~~fk~~~~~~~~~~dkvKIVACd~ 52 (52)
T PF02751_consen 1 KVKNKLSFK-GHLDTYRFCDNVWTFILKNVEFKMEDNNETVKVDKVKIVACDS 52 (52)
T ss_dssp T---EEEEE-EEEEEEEEETTEEEEEEEEEEEEEE-SSEEEEEEEEEEEEEES
T ss_pred CcceeEEEE-EeeeEEEeeCcEEEEEEcCEEEEEecCCcEEEcCeEEEEEcCC
Confidence 489999999 999999999999999999999999 58899999999999996
No 4
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=99.93 E-value=1.3e-26 Score=142.31 Aligned_cols=49 Identities=69% Similarity=0.969 Sum_probs=44.3
Q ss_pred ChhHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy7895 1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALP 49 (108)
Q Consensus 1 m~y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~ 49 (108)
|+|||||+||||.||+|||||||++|.|+|+||++||++||++|+++|+
T Consensus 1 ~~yelYR~stlG~aL~dtLDeli~~~~I~p~La~kVL~~FDksi~~~L~ 49 (49)
T PF02268_consen 1 MYYELYRRSTLGIALTDTLDELIQEGKITPQLAMKVLEQFDKSINEALS 49 (49)
T ss_dssp ---CGGGCSHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHH
T ss_pred CcHHHHHcchHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHhC
Confidence 8999999999999999999999999999999999999999999999985
No 5
>PF10925 DUF2680: Protein of unknown function (DUF2680); InterPro: IPR024485 Members in this family of proteins are annotated as YckD however currently no function is known.
Probab=92.74 E-value=0.37 Score=30.36 Aligned_cols=32 Identities=19% Similarity=0.255 Sum_probs=28.4
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHh
Q psy7895 16 QESLDELIQYGTITPTLAMKVLLQFDKSINGA 47 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~ 47 (108)
...+|..++.|.||+++|..+.+.+|.-....
T Consensus 21 K~~idk~Ve~G~iTqeqAd~ik~~id~~~~~~ 52 (59)
T PF10925_consen 21 KQIIDKYVEAGVITQEQADAIKKHIDQRQEYM 52 (59)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999877654
No 6
>cd01709 RT_like_1 RT_like_1: A subfamily of reverse transcriptases (RTs). An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=88.60 E-value=0.7 Score=38.39 Aligned_cols=65 Identities=18% Similarity=0.163 Sum_probs=46.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCeE-E----Eec------ceEeecCc
Q psy7895 25 YGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVE-F----REV------AEIARVNK 93 (108)
Q Consensus 25 ~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~-f----~~~------~~~~~~~~ 93 (108)
.|.|||=+|+-+|..||..|++... | ..-||+.|++|-+ -..-+ . .+. +=.++.+|
T Consensus 87 GgviSplLaNiyL~~lD~~v~~~~~-----------g-~~l~RYaDD~vi~-~~~~~a~~aw~~i~~fl~~lGLelN~eK 153 (346)
T cd01709 87 SHALSDVFGELVLFCLDFAVNQATD-----------G-GLLYRLHDDLWFW-GQPETCAKAWKAIQEFAKVMGLELNKEK 153 (346)
T ss_pred CchhhHHHHHHHHHHHHHHHHhcCC-----------C-ceEEEEcCeEEEE-cCHHHHHHHHHHHHHHHHHcCceecccc
Confidence 4689999999999999999998642 3 4789999999988 32100 0 000 22466688
Q ss_pred EEEEEecCC
Q psy7895 94 LKIVACDGK 102 (108)
Q Consensus 94 lKIVAcd~~ 102 (108)
=+||-|...
T Consensus 154 T~iV~~~~~ 162 (346)
T cd01709 154 TGSVYLSDD 162 (346)
T ss_pred ceEEEeccC
Confidence 888887654
No 7
>PF09925 DUF2157: Predicted membrane protein (DUF2157); InterPro: IPR018677 This family of various hypothetical prokaryotic proteins has no known function.
Probab=87.17 E-value=0.6 Score=33.24 Aligned_cols=23 Identities=35% Similarity=0.547 Sum_probs=22.0
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHH
Q psy7895 19 LDELIQYGTITPTLAMKVLLQFD 41 (108)
Q Consensus 19 Ldeli~~~~Is~~la~kVl~~FD 41 (108)
|++++++|.|+|+++.++++.++
T Consensus 1 l~~w~~~GlI~~~q~~~i~~~~~ 23 (145)
T PF09925_consen 1 LDRWVEQGLITPEQAEAILAFYG 23 (145)
T ss_pred CHhHHHCCCCCHHHHHHHHHHhh
Confidence 68999999999999999999998
No 8
>cd03487 RT_Bac_retron_II RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=87.07 E-value=1.9 Score=32.08 Aligned_cols=46 Identities=22% Similarity=0.322 Sum_probs=35.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCeE
Q psy7895 25 YGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVE 81 (108)
Q Consensus 25 ~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~ 81 (108)
...+||-|++-+|..||..+.+.... . .+..+||+||+ +|..++..
T Consensus 107 G~~lSp~Lanl~l~~~d~~l~~~~~~--------~--~~~~~RYaDD~-~i~~~~~~ 152 (214)
T cd03487 107 GAPTSPALSNLVFRKLDERLSKLAKS--------N--GLTYTRYADDI-TFSSNKKL 152 (214)
T ss_pred CCcccHHHHHHHHHHHHHHHHHHHHH--------c--CCeEEEEeccE-EEEccccc
Confidence 35899999999999999999876432 1 24567999996 67777765
No 9
>cd01646 RT_Bac_retron_I RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Probab=86.89 E-value=1.4 Score=31.34 Aligned_cols=40 Identities=18% Similarity=0.205 Sum_probs=34.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEE
Q psy7895 25 YGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFV 76 (108)
Q Consensus 25 ~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~ 76 (108)
...+||=+++.+|..||..+.+. . +.+...||+||++-+.
T Consensus 57 G~~lS~~L~~~~l~~~d~~i~~~-----------~-~~~~~~RY~DD~~i~~ 96 (158)
T cd01646 57 GPLTSRFLANIYLNDVDHELKSK-----------L-KGVDYVRYVDDIRIFA 96 (158)
T ss_pred CcchHHHHHHHHHHHHHHHHHhc-----------c-CCceEEEecCcEEEEc
Confidence 34899999999999999999876 4 5678999999999877
No 10
>PF11848 DUF3368: Domain of unknown function (DUF3368); InterPro: IPR021799 This domain is functionally uncharacterised. This domain is found in bacteria and archaea. This presumed domain is about 50 amino acids in length.
Probab=85.97 E-value=2.3 Score=25.23 Aligned_cols=35 Identities=29% Similarity=0.397 Sum_probs=28.2
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCC-CCCHHHHHHHHHH
Q psy7895 4 QLYRNTTLGNTLQESLDELIQYG-TITPTLAMKVLLQ 39 (108)
Q Consensus 4 ~lYR~stlG~aL~dtLdeli~~~-~Is~~la~kVl~~ 39 (108)
+.+|+.-|- .....|++|.+.| .|+|++..++|+.
T Consensus 11 ~Ak~~GlI~-~~~~~l~~l~~~g~~is~~l~~~~L~~ 46 (48)
T PF11848_consen 11 LAKRRGLIS-EVKPLLDRLQQAGFRISPKLIEEILRR 46 (48)
T ss_pred HHHHcCChh-hHHHHHHHHHHcCcccCHHHHHHHHHH
Confidence 345555565 7888999999988 8999999999874
No 11
>cd01651 RT_G2_intron RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).
Probab=79.52 E-value=3.7 Score=29.67 Aligned_cols=52 Identities=27% Similarity=0.250 Sum_probs=37.8
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEE
Q psy7895 24 QYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFV 76 (108)
Q Consensus 24 ~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~ 76 (108)
+...+||-|++-++..+|+.+.+.+.+.-.....-. +.+...||.||+.-+.
T Consensus 129 qG~~lSp~L~~~~l~~ld~~l~~~~~~~~~~~~~~~-~~~~~~rY~DD~~i~~ 180 (226)
T cd01651 129 QGGVISPLLANIYLHELDKFVEEKLKEYYDTSDPKF-RRLRYVRYADDFVIGV 180 (226)
T ss_pred CCccHHHHHHHHHHHHHHHHHHHhhhhccccccccc-CceEEEEecCceEEec
Confidence 345678999999999999999998865321122222 4578899999987763
No 12
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=79.45 E-value=8.1 Score=27.32 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=29.0
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Q psy7895 10 TLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSI 44 (108)
Q Consensus 10 tlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i 44 (108)
-++.-+++..|||+..|.||++.|-+++..-=+.+
T Consensus 21 ~~~ek~~klvDelVkkGeln~eEak~~vddl~~q~ 55 (108)
T COG3937 21 ETAEKVQKLVDELVKKGELNAEEAKRFVDDLLRQA 55 (108)
T ss_pred HHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHH
Confidence 46778899999999999999999999887654443
No 13
>cd04437 DEP_Epac DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in Epac-like proteins. Epac (exchange proteins directly activated by cAMP) proteins are GEFs (guanine-nucleotide-exchange factors) for the small GTPases, Rap1 and Rap2. They are directly regulated by cyclic AMP, a second messenger that plays a role in the control of diverse cellular processes, such as cell adhesion and insulin secretion. Epac-like proteins share a common domain architecture, containing RasGEF, DEP and CAP-effector (cAMP binding) domains. The DEP domain is involved in membrane localization.
Probab=78.00 E-value=3.7 Score=29.42 Aligned_cols=61 Identities=23% Similarity=0.401 Sum_probs=47.3
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCc
Q psy7895 4 QLYRNTTLGNTLQESLDELIQYGT--ITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDN 71 (108)
Q Consensus 4 ~lYR~stlG~aL~dtLdeli~~~~--Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDn 71 (108)
..||++-+|..|.|= |++.+. .+.+.|-.+.+.. +..-+-.+|..+..|++|. .-|||.++
T Consensus 25 ~~y~~cF~GsElVdW---Ll~~~~~v~sR~eAv~lgq~L---l~~gvi~HV~~~h~F~D~~-~fYrF~~d 87 (125)
T cd04437 25 RTYRQCCVGTELVDW---LLQQSPCVQSRSQAVGMWQVL---LEEGVLLHVDQELHFQDKY-QFYRFSDD 87 (125)
T ss_pred EECCcccccHHHHHH---HHHcCCCCCCHHHHHHHHHHH---HhCCCeEEeCCcCccccCC-eeEEECCc
Confidence 569999999876654 566654 4889998887654 6666777899999999666 88999776
No 14
>cd04440 DEP_2_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity.
Probab=76.26 E-value=5.5 Score=27.23 Aligned_cols=62 Identities=18% Similarity=0.162 Sum_probs=45.6
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCc
Q psy7895 4 QLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDN 71 (108)
Q Consensus 4 ~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDn 71 (108)
..|+++-+|..|.+=|-+- ....|.+.|-.+.+. -+..-+-.+|..+-.||+|. .-|||+.+
T Consensus 32 ~~y~~cFvGsElVdWLi~~--g~~~tR~eAv~~gq~---Ll~~gii~HV~~~h~F~D~~-lfYrF~~d 93 (93)
T cd04440 32 KTYKSVVPASKLVDWLLAQ--GDCRTREEAVILGVG---LCNNGFMHHVLEKSEFKDEP-LLFRFYAD 93 (93)
T ss_pred EEcccccchhHHHHHHHHc--CCCCCHHHHHHHHHH---HHhCCCEEecCCCcCcCCcC-eEEEEecC
Confidence 5699999999887765433 335688888777653 34555666899999999665 78999864
No 15
>PF00349 Hexokinase_1: Hexokinase; InterPro: IPR022672 Hexokinase is an important enzyme that catalyses the ATP-dependent conversion of aldo- and keto-hexose sugars to the hexose-6-phosphate (H6P). The enzyme can catalyse this reaction on glucose, fructose, sorbitol and glucosamine, and as such is the first step in a number of metabolic pathways []. The addition of a phosphate group to the sugar acts to trap it in a cell, since the negatively charged phosphate cannot easily traverse the plasma membrane. The enzyme is widely distributed in eukaryotes. There are three isozymes of hexokinase in yeast (PI, PII and glucokinase): isozymes PI and PII phosphorylate both aldo- and keto-sugars; glucokinase is specific for aldo-hexoses. All three isozymes contain two domains []. Structural studies of yeast hexokinase reveal a well-defined catalytic pocket that binds ATP and hexose, allowing easy transfer of the phosphate from ATP to the sugar []. Vertebrates contain four hexokinase isozymes, designated I to IV, where types I to III contain a duplication of the two-domain yeast-type hexokinases. Both the N- and C-terminal halves bind hexose and H6P, though in types I an III only the C-terminal half supports catalysis, while both halves support catalysis in type II. The N-terminal half is the regulatory region. Type IV hexokinase is similar to the yeast enzyme in containing only the two domains, and is sometimes incorrectly referred to as glucokinase. The different vertebrate isozymes differ in their catalysis, localisation and regulation, thereby contributing to the different patterns of glucose metabolism in different tissues []. Whereas types I to III can phosphorylate a variety of hexose sugars and are inhibited by glucose-6-phosphate (G6P), type IV is specific for glucose and shows no G6P inhibition. Type I enzyme may have a catabolic function, producing H6P for energy production in glycolysis; it is bound to the mitochondrial membrane, which enables the coordination of glycolysis with the TCA cycle. Types II and III enzyme may have anabolic functions, providing H6P for glycogen or lipid synthesis. Type IV enzyme is found in the liver and pancreatic beta-cells, where it is controlled by insulin (activation) and glucagon (inhibition). In pancreatic beta-cells, type IV enzyme acts as a glucose sensor to modify insulin secretion. Mutations in type IV hexokinase have been associated with diabetes mellitus. Hexokinase (2.7.1.1 from EC), a fructose and glucose phosphorylating enzyme, contains two structurally similar domains represented by this family and PF03727 from PFAM. Some hexokinases have two copies of each of these domains. This entry represents the N-terminal domain.; GO: 0005524 ATP binding, 0016773 phosphotransferase activity, alcohol group as acceptor, 0005975 carbohydrate metabolic process; PDB: 3O1W_A 3O6W_A 3O4W_B 3O08_B 3O80_A 3O5B_A 3O8M_A 3O1B_A 1BG3_A 4DHY_A ....
Probab=71.88 E-value=7.8 Score=29.46 Aligned_cols=46 Identities=20% Similarity=0.247 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEe
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFK 59 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K 59 (108)
-++++++++.+.-.++++....|...|-..|...|++.-.+...++
T Consensus 2 ~~~~~v~~~~~~f~~s~~~L~~i~~~f~~em~~gL~~~~~~~~~l~ 47 (206)
T PF00349_consen 2 DLQQAVQKLLQQFTLSDEQLQEISDRFLEEMEKGLAKSSSSMSSLK 47 (206)
T ss_dssp HHHHHHHHHHGGGS--HHHHHHHHHHHHHHHHHHHSTTTGCG-SS-
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHccCCCCceeee
Confidence 4788999999999999999999999999999999998766644444
No 16
>PF09677 TrbI_Ftype: Type-F conjugative transfer system protein (TrbI_Ftype); InterPro: IPR014115 This entry represents TrbI, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm [, ].
Probab=71.34 E-value=14 Score=25.87 Aligned_cols=40 Identities=20% Similarity=0.384 Sum_probs=34.1
Q ss_pred HHHHHHHHHHH---CCCCCHHHHHHHHHHHHHHHHHhhchhcc
Q psy7895 14 TLQESLDELIQ---YGTITPTLAMKVLLQFDKSINGALPSKVK 53 (108)
Q Consensus 14 aL~dtLdeli~---~~~Is~~la~kVl~~FDk~i~~~L~~~vk 53 (108)
-|..+++++++ ...++|++...-...|.++++..|.+.-.
T Consensus 37 dl~~tv~~f~~~~a~~~lt~~q~~a~t~~F~~aL~~~L~~~~~ 79 (111)
T PF09677_consen 37 DLKGTVDEFVQQLARSSLTPEQVEALTQRFMQALEASLAEYQA 79 (111)
T ss_pred eHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46778888776 45899999999999999999999999643
No 17
>cd00304 RT_like RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Probab=68.83 E-value=14 Score=23.35 Aligned_cols=41 Identities=17% Similarity=0.253 Sum_probs=32.7
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEE
Q psy7895 24 QYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFV 76 (108)
Q Consensus 24 ~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~ 76 (108)
+...+||-+++..+..+|..+.+. . +.....|+.|+++.+.
T Consensus 14 qG~~~Sp~l~~~~~~~l~~~~~~~-----------~-~~~~~~~Y~DD~~i~~ 54 (98)
T cd00304 14 QGSPLSPALANLYMEKLEAPILKQ-----------L-LDITLIRYVDDLVVIA 54 (98)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHh-----------c-CCceEEEeeCcEEEEe
Confidence 455789999999999999888871 2 3467889999998664
No 18
>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....
Probab=67.30 E-value=13 Score=26.08 Aligned_cols=42 Identities=19% Similarity=0.347 Sum_probs=34.7
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEE
Q psy7895 24 QYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFV 76 (108)
Q Consensus 24 ~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~ 76 (108)
+...+||-++...|..+|+.+...+ . +.....|++||+..+.
T Consensus 128 qG~~~S~~l~~~~l~~l~~~~~~~~----------~-~~~~~~rY~DD~~i~~ 169 (214)
T PF00078_consen 128 QGSPLSPLLFNIYLDDLDRELQQEL----------N-PDISYLRYADDILIIS 169 (214)
T ss_dssp TTSTCHHHHHHHHHHHHHHHHHHHS------------TTSEEEEETTEEEEEE
T ss_pred ccccccchhhccccccccccccccc----------c-ccccceEeccccEEEE
Confidence 4458999999999999999999888 4 6677899999987554
No 19
>TIGR02744 TrbI_Ftype type-F conjugative transfer system protein TrbI. This protein is an essential component of the F-type conjugative transfer sytem for plasmid DNA transfer and has been shown to be localized to the periplasm.
Probab=63.91 E-value=21 Score=25.31 Aligned_cols=37 Identities=14% Similarity=0.302 Sum_probs=31.4
Q ss_pred HHHHHHHHHH---CCCCCHHHHHHHHHHHHHHHHHhhchh
Q psy7895 15 LQESLDELIQ---YGTITPTLAMKVLLQFDKSINGALPSK 51 (108)
Q Consensus 15 L~dtLdeli~---~~~Is~~la~kVl~~FDk~i~~~L~~~ 51 (108)
+..|||++++ +..+|+++..+.+..|..+++.+|...
T Consensus 39 mk~tld~F~~q~~~~~lte~q~~~~~~rF~~~L~~~L~~y 78 (112)
T TIGR02744 39 MKQTLDAFFDSASQKKLSEAQQKALLGRFNALLEAELQAW 78 (112)
T ss_pred cHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666655 679999999999999999999999985
No 20
>PF15606 Toxin_55: Putative toxin 55
Probab=61.84 E-value=9.4 Score=25.44 Aligned_cols=22 Identities=32% Similarity=0.395 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHCCCCCHHHHHH
Q psy7895 14 TLQESLDELIQYGTITPTLAMK 35 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~k 35 (108)
--=|.|+|||..|.|++.++.+
T Consensus 40 drCd~Lqelid~g~~~~k~~K~ 61 (77)
T PF15606_consen 40 DRCDVLQELIDCGDISAKQAKS 61 (77)
T ss_pred cHHHHHHHHHHccCcCHHHHHH
Confidence 3458899999999999988643
No 21
>PF06702 DUF1193: Protein of unknown function (DUF1193); InterPro: IPR009581 This family is baesd on the C terminus of several hypothetical eukaryotic proteins of unknown function. Proteins in this entry contain two conserved motifs: DRHHYE and QCC, as well as a number of conserved cysteine residues.
Probab=59.94 E-value=7.9 Score=30.42 Aligned_cols=46 Identities=22% Similarity=0.366 Sum_probs=41.3
Q ss_pred HHHhhhH---------HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 5 LYRNTTL---------GNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 5 lYR~stl---------G~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
+.|+||. |-.|.++|.|......+.|-|.+.-+.--|+-+..+|+.
T Consensus 150 ~iRrST~~rL~~l~~~~~~Ls~~m~~s~~~D~l~PvL~e~Hl~AldrRL~~Vl~~ 204 (221)
T PF06702_consen 150 RIRRSTWERLQLLSKGGYRLSDLMRESLSRDPLAPVLTEPHLEALDRRLDKVLRT 204 (221)
T ss_pred hccccHHHHHHHhccCCCcHHHHHHHHhccCccCccCcHHHHHHHHHHHHHHHHH
Confidence 5688888 888999999999999999999999999999998888865
No 22
>cd08332 CARD_CASP2 Caspase activation and recruitment domain of Caspase-2. Caspase activation and recruitment domain (CARD) similar to that found in caspase-2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Caspase-2 (also known as ICH1, NEDD2, or CASP2) is one of the most evolutionarily conserved caspases, and plays a role in apoptosis, DNA damage response, cell cycle regulation, and tumor suppression. It is localized in the nucleus and exhibits properties of both an initiator and an effector caspase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and
Probab=57.60 E-value=17 Score=24.19 Aligned_cols=25 Identities=28% Similarity=0.395 Sum_probs=21.6
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHH
Q psy7895 15 LQESLDELIQYGTITPTLAMKVLLQ 39 (108)
Q Consensus 15 L~dtLdeli~~~~Is~~la~kVl~~ 39 (108)
..+.+|+|++.|.||++....|...
T Consensus 22 ~~~v~~~L~~~gvlt~~~~~~I~~~ 46 (90)
T cd08332 22 LDELLIHLLQKDILTDSMAESIMAK 46 (90)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHcC
Confidence 4578999999999999999988653
No 23
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=57.58 E-value=29 Score=22.84 Aligned_cols=41 Identities=15% Similarity=0.139 Sum_probs=31.2
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEe
Q psy7895 17 ESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFK 59 (108)
Q Consensus 17 dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K 59 (108)
|.++++-+...+|...+..+++.|-..|.++|.+. .++.|.
T Consensus 5 eli~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~g--~~V~i~ 45 (90)
T PRK10753 5 QLIDVIADKAELSKTQAKAALESTLAAITESLKEG--DAVQLV 45 (90)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHcC--CeEEEc
Confidence 34455555667999999999999999999999763 245555
No 24
>PF15658 Latrotoxin_C: Latrotoxin C-terminal domain
Probab=57.49 E-value=16 Score=26.56 Aligned_cols=42 Identities=14% Similarity=0.194 Sum_probs=34.2
Q ss_pred hhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy7895 8 NTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALP 49 (108)
Q Consensus 8 ~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~ 49 (108)
.+.|-.-|-..+++-..+|.++|.+..+.|..|-..+..+|+
T Consensus 85 ~neIs~~L~Sy~e~a~p~~~Ls~kq~~kfl~~f~~~~~~~ln 126 (127)
T PF15658_consen 85 FNEISKILCSYAEKACPGSKLSPKQFDKFLAEFNSHLDVVLN 126 (127)
T ss_pred chHHHHHHHHHHHHhCcccCCCHHHHHHHHHHHHhccccccc
Confidence 345666777888888888999999999999999888777664
No 25
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=57.48 E-value=30 Score=22.00 Aligned_cols=35 Identities=20% Similarity=0.195 Sum_probs=30.0
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 16 QESLDELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
.|..+++-+...+++..+..+++.|-..|.+.|.+
T Consensus 4 ~eli~~ia~~~~~~~~~v~~vl~~l~~~i~~~L~~ 38 (90)
T smart00411 4 SELIDAIAEKAGLSKKDAKAAVDAFLEIITEALKK 38 (90)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 45566666677899999999999999999999987
No 26
>PF00619 CARD: Caspase recruitment domain; InterPro: IPR001315 The caspase recruitment domain domain (CARD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. CARD is related in sequence and structure to the death domain (DD, see IPR000488 from INTERPRO) and the death effector domain (DED, see IPR001875 from INTERPRO), which work in similar pathways and show similar interaction properties []. The CARD domain typically associates with other CARD-containing proteins, forming either dimers or trimers. CARD domains can be found in isolation, or in combination with other domains. Domains associated with CARD include: NACHT (IPR007111 from INTERPRO) (in Nal1 and Bir1), NB-ARC (IPR002182 from INTERPRO) (in Apaf-1), pyrin/dapin domains (IPR004020 from INTERPRO) (in Nal1), leucine-rich repeats () (in Nal1), WD repeats (IPR001680 from INTERPRO) (in Apaf1), Src homology domains (IPR001452 from INTERPRO), PDZ (IPR001478 from INTERPRO), RING, kinase and DD domains []. CARD-containing proteins are involved in apoptosis through their regulation of caspases that contain CARDs in their N-terminal pro-domains, including human caspases 1, 2, 9, 11 and 12 []. CARD-containing proteins are also involved in inflammation through their regulation of NF-kappaB []. The mechanisms by which CARDs activate caspases and NF-kappaB involve the assembly of multi-protein complexes, which can facilitate dimerisation or serve as scaffolds on which proteases and kinases are assembled and activated.; GO: 0005515 protein binding, 0042981 regulation of apoptosis, 0005622 intracellular; PDB: 2NSN_A 2NZ7_B 2DBD_A 4E9M_C 2B1W_A 3YGS_P 2KN6_A 3CRD_A 1DGN_A 3KAT_A ....
Probab=56.29 E-value=20 Score=22.50 Aligned_cols=25 Identities=24% Similarity=0.327 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHH
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~ 38 (108)
.+...||.|++.|.||++-...|..
T Consensus 17 ~~~~ild~L~~~~vlt~~e~e~I~~ 41 (85)
T PF00619_consen 17 DLDDILDHLLSRGVLTEEEYEEIRS 41 (85)
T ss_dssp HHHHHHHHHHHTTSSSHHHHHHHHT
T ss_pred cHHHHHHHHHHCCCCCHHHHHHHHc
Confidence 4889999999999999999999887
No 27
>cd01648 TERT TERT: Telomerase reverse transcriptase (TERT). Telomerase is a ribonucleoprotein (RNP) that synthesizes telomeric DNA repeats. The telomerase RNA subunit provides the template for synthesis of these repeats. The catalytic subunit of RNP is known as telomerase reverse transcriptase (TERT). The reverse transcriptase (RT) domain is located in the C-terminal region of the TERT polypeptide. Single amino acid substitutions in this region lead to telomere shortening and senescence. Telomerase is an enzyme that, in certain cells, maintains the physical ends of chromosomes (telomeres) during replication. In somatic cells, replication of the lagging strand requires the continual presence of an RNA primer approximately 200 nucleotides upstream, which is complementary to the template strand. Since there is a region of DNA less than 200 base pairs from the end of the chromosome where this is not possible, the chromosome is continually shortened. However, a surplus of repetitive DNA at
Probab=55.82 E-value=19 Score=24.43 Aligned_cols=68 Identities=12% Similarity=0.073 Sum_probs=43.5
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCeEEE----------e-c--ceEee
Q psy7895 24 QYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFR----------E-V--AEIAR 90 (108)
Q Consensus 24 ~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~f~----------~-~--~~~~~ 90 (108)
|...+||-|++-++..+|+.+.+.+.. .. +.....||.|++ .+...+..=- . . +=.++
T Consensus 22 QG~~lSp~L~nl~l~~l~~~~~~~~~~-------~~-~~~~~~rYaDD~-li~~~~~~~~~~~~~~l~~~l~~~~gl~iN 92 (119)
T cd01648 22 QGSPLSSLLCSLYYADLENKYLSFLDV-------ID-KDSLLLRLVDDF-LLITTSLDKAIKFLNLLLRGFINQYKTFVN 92 (119)
T ss_pred CCcchHHHHHHHHHHHHHHHHHhhccc-------CC-CCceEEEEeCcE-EEEeCCHHHHHHHHHHHHHhhHHhhCeEEC
Confidence 456899999999999999988776511 11 334567999995 5555442100 0 1 12455
Q ss_pred cCcEEEEEec
Q psy7895 91 VNKLKIVACD 100 (108)
Q Consensus 91 ~~~lKIVAcd 100 (108)
.+|-+++.+.
T Consensus 93 ~~Kt~~~~~~ 102 (119)
T cd01648 93 FDKTQINFSF 102 (119)
T ss_pred cccceeeccc
Confidence 6777777664
No 28
>cd04446 DEP_DEPDC4 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC4-like proteins. DEPDC4 is a DEP domain containing protein of unknown function.
Probab=55.52 E-value=19 Score=24.66 Aligned_cols=50 Identities=10% Similarity=0.192 Sum_probs=38.3
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCC------CCCHHHHHHHHHHHHHHHHHhhchhccCc
Q psy7895 3 YQLYRNTTLGNTLQESLDELIQYG------TITPTLAMKVLLQFDKSINGALPSKVKSR 55 (108)
Q Consensus 3 y~lYR~stlG~aL~dtLdeli~~~------~Is~~la~kVl~~FDk~i~~~L~~~vksk 55 (108)
+..|+.+-+|..+.|=|-+.+..+ .+|-+.|-++++.+ |.+-+-.+|+.+
T Consensus 21 lk~y~~CF~GsEaVDwL~~~l~~n~~f~~~~~tR~~Av~l~q~L---l~~gvi~~V~~~ 76 (95)
T cd04446 21 LKSYHDCFLGSEAVDVVLAHLMQNKYFGDVDVPRAKAVRLCQAL---MDCRVFEAVGTK 76 (95)
T ss_pred ceecccccchHHHHHHHHHHHhhccccCcccCCHHHHHHHHHHH---HHcCCeeeccch
Confidence 467999999999999887766444 78999999998877 555555667544
No 29
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=55.10 E-value=34 Score=22.60 Aligned_cols=40 Identities=15% Similarity=0.160 Sum_probs=30.3
Q ss_pred HHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEe
Q psy7895 18 SLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFK 59 (108)
Q Consensus 18 tLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K 59 (108)
.++++-+...+|...+..+++.|=.+|.++|.+. .++.|.
T Consensus 6 li~~ia~~~~~s~~~~~~~v~~~~~~i~~~L~~~--~~v~l~ 45 (90)
T PRK10664 6 LIDKIAAGADISKAAAGRALDAIIASVTESLKEG--DDVALV 45 (90)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhCC--CEEEEC
Confidence 3444444567999999999999999999999773 235555
No 30
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=52.38 E-value=29 Score=22.90 Aligned_cols=37 Identities=19% Similarity=0.179 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
...+.++++-....+|...+..+++.|=..|.+.|++
T Consensus 4 tk~el~~~ia~~~~~s~~~v~~vl~~~~~~i~~~L~~ 40 (99)
T PRK00285 4 TKADLAEALFEKVGLSKREAKELVELFFEEIRDALEN 40 (99)
T ss_pred CHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHc
Confidence 4556677777778899999999999999999999977
No 31
>KOG0037|consensus
Probab=51.59 E-value=17 Score=28.64 Aligned_cols=33 Identities=18% Similarity=0.354 Sum_probs=27.8
Q ss_pred hhHHH-HHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q psy7895 9 TTLGN-TLQESLDELIQYGTITPTLAMKVLLQFDKS 43 (108)
Q Consensus 9 stlG~-aL~dtLdeli~~~~Is~~la~kVl~~FDk~ 43 (108)
-+|.. .|.+||.+| ..+|||++.+.++.+||+.
T Consensus 139 G~I~~sEL~~Al~~~--Gy~Lspq~~~~lv~kyd~~ 172 (221)
T KOG0037|consen 139 GTIDSSELRQALTQL--GYRLSPQFYNLLVRKYDRF 172 (221)
T ss_pred CcccHHHHHHHHHHc--CcCCCHHHHHHHHHHhccc
Confidence 34443 599999999 8899999999999999965
No 32
>cd08330 CARD_ASC_NALP1 Caspase activation and recruitment domain found in Human ASC, NALP1, and similar proteins. Caspase activation and recruitment domain (CARD) similar to those found in human ASC (Apoptosis-associated speck-like protein containing a CARD) and NALP1 (CARD7, NLRP1). ASC, an adaptor molecule, and NALP1, a member of the Nod-like receptor (NLR) family, are involved in the assembly of the 'inflammasome', a multiprotein platform, which is responsible for caspase-1 activation and regulation of IL-1beta maturation. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They se
Probab=50.71 E-value=22 Score=23.19 Aligned_cols=25 Identities=24% Similarity=0.143 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHH
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~ 38 (108)
.....||.|++.|.||++....|..
T Consensus 16 ~v~~ilD~L~~~~Vit~e~~~~I~a 40 (82)
T cd08330 16 NVDPILDKLHGKKVITQEQYSEVRA 40 (82)
T ss_pred hHHHHHHHHHHCCCCCHHHHHHHHc
Confidence 3577899999999999999988875
No 33
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=50.64 E-value=37 Score=23.00 Aligned_cols=40 Identities=8% Similarity=0.417 Sum_probs=18.7
Q ss_pred hHHHHhhhHHHH-HHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q psy7895 3 YQLYRNTTLGNT-LQESLDELIQYGTITPTLAMKVLLQFDKS 43 (108)
Q Consensus 3 y~lYR~stlG~a-L~dtLdeli~~~~Is~~la~kVl~~FDk~ 43 (108)
|+.||+|.+-.+ ..........++.+++..+. ++.-+=|.
T Consensus 16 ye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i-~v~g~aKv 56 (90)
T PF04719_consen 16 YEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVI-AVAGIAKV 56 (90)
T ss_dssp HHHHHH----HHHHHHHHHHHHS-S---HHHHH-HHHHHHHH
T ss_pred HHHHHHccCCHHHHHHHHHHHcCCCCCChhHHH-HHHHHHHH
Confidence 999999998764 44444444433777777663 44444443
No 34
>PF09851 SHOCT: Short C-terminal domain; InterPro: IPR018649 This family of hypothetical prokaryotic proteins has no known function.
Probab=50.27 E-value=40 Score=18.17 Aligned_cols=22 Identities=27% Similarity=0.220 Sum_probs=17.5
Q ss_pred HHHHHHHHHCCCCCHHHHHHHH
Q psy7895 16 QESLDELIQYGTITPTLAMKVL 37 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kVl 37 (108)
-..|++|..+|.||++-..+..
T Consensus 5 L~~L~~l~~~G~IseeEy~~~k 26 (31)
T PF09851_consen 5 LEKLKELYDKGEISEEEYEQKK 26 (31)
T ss_pred HHHHHHHHHcCCCCHHHHHHHH
Confidence 3579999999999998766543
No 35
>PF05388 Carbpep_Y_N: Carboxypeptidase Y pro-peptide; InterPro: IPR008442 This signature is found at the N terminus of carboxypeptidase Y, which belong to MEROPS peptidase family S10. This region contains the signal peptide and pro-peptide regions [,].; GO: 0004185 serine-type carboxypeptidase activity, 0005773 vacuole
Probab=50.26 E-value=24 Score=24.74 Aligned_cols=49 Identities=20% Similarity=0.212 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHHHHHHHhhchh-ccCceeEeccccceeeeeCcEEEEEEcCeEE
Q psy7895 28 ITPTLAMKVLLQFDKSINGALPSK-VKSRLTFKSGKLNTYRFCDNVWTFVLTDVEF 82 (108)
Q Consensus 28 Is~~la~kVl~~FDk~i~~~L~~~-vksk~~~K~G~L~tYr~cDnVWtF~lkd~~f 82 (108)
||++ +..+|.+.=.-..+++.+. ..++..+| +=|.-|.-|-|+++|..+
T Consensus 59 Lt~e-~k~~W~E~~~~fP~~~~~l~~~s~PK~k-----~~~~~~~~wDf~V~~a~v 108 (113)
T PF05388_consen 59 LTSE-AKALWDEMMLLFPDAVSQLKFFSKPKKK-----HTRKPDSHWDFVVKGADV 108 (113)
T ss_pred ccHH-HHHHHHHHHHHCcHHHHhCcccCCCCCC-----CCCCCcCcCCeeeCCCcC
Confidence 4433 4567777666666666442 33333333 335667789999999765
No 36
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=48.09 E-value=14 Score=27.39 Aligned_cols=38 Identities=32% Similarity=0.435 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHCCCCCHH-------------HHHHHHHHHHHHHHHhhchh
Q psy7895 14 TLQESLDELIQYGTITPT-------------LAMKVLLQFDKSINGALPSK 51 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~-------------la~kVl~~FDk~i~~~L~~~ 51 (108)
.|+.+|+||+++|.|..+ ...++++.|..-|+...++.
T Consensus 35 ~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~F~~~Ip~~i~~~ 85 (163)
T PF14277_consen 35 TLQQALSELVESGLITLETDSDNKTRYSITEKGKETLEFFENRIPESIRED 85 (163)
T ss_pred HHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHHHHHhCCHHHHHH
Confidence 689999999999998854 35789999988887776664
No 37
>PF14848 HU-DNA_bdg: DNA-binding domain
Probab=47.60 E-value=53 Score=22.83 Aligned_cols=37 Identities=24% Similarity=0.244 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 14 TLQESLDELIQY-GTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 14 aL~dtLdeli~~-~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
.|.+..+++... ..+++.-..-||..|...|.+.|.+
T Consensus 30 tl~~Ia~~i~~~~s~~t~~di~~vl~~~~~~~~~~l~~ 67 (124)
T PF14848_consen 30 TLEDIAEEIAKEGSTLTRADIEAVLNALKDEMIEALMN 67 (124)
T ss_pred CHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 567888889864 6999999999999999999999987
No 38
>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=46.81 E-value=56 Score=20.54 Aligned_cols=34 Identities=18% Similarity=0.168 Sum_probs=28.2
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 17 ESLDELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 17 dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
|..+++-+..-+++..+..+++.|-..|.+.|.+
T Consensus 4 ~l~~~ia~~~~~~~~~v~~vl~~~~~~i~~~L~~ 37 (87)
T cd00591 4 ELIEAIAEKTGLSKKDAEAAVDAFLDVITEALAK 37 (87)
T ss_pred HHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHhC
Confidence 3445555666799999999999999999999986
No 39
>PF09693 Phage_XkdX: Phage uncharacterised protein (Phage_XkdX); InterPro: IPR010022 This entry is represented by Bacteriophage 69, Orf86. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry identifies a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=46.68 E-value=22 Score=20.35 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=18.2
Q ss_pred HHHHHHHHHCCCCCHHHHHHH
Q psy7895 16 QESLDELIQYGTITPTLAMKV 36 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kV 36 (108)
.+-+..++..|.|||++...|
T Consensus 15 ~~~v~~~V~~g~IT~eey~eI 35 (40)
T PF09693_consen 15 KEDVKNFVEAGWITKEEYKEI 35 (40)
T ss_pred HHHHHHHhhcCeECHHHHHHh
Confidence 456889999999999998876
No 40
>PF03512 Glyco_hydro_52: Glycosyl hydrolase family 52; InterPro: IPR000852 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 52 GH52 from CAZY comprises enzymes with only one known activity; beta-xylosidase (3.2.1.37 from EC). Proteins harboring beta-xylosidase and xylanase activities []have been identified in the Gram-positive, facultative thermophilic aerobe Bacillus stearothermophilus 21 []. This microbe, which functions in xylan degradation, can utilise xylan as a sole source of carbon. The enzyme hydrolyses 1,4-beta-D-xylans, removing successive D-xylose residues from the non-reducing termini. It also hydrolyses xylobiose.; GO: 0009044 xylan 1,4-beta-xylosidase activity, 0005975 carbohydrate metabolic process
Probab=46.05 E-value=18 Score=31.03 Aligned_cols=59 Identities=17% Similarity=0.269 Sum_probs=48.5
Q ss_pred HHHHHHHHHHHHCCCCCHHHHH-------------------------------HHHHHHHHHHHHhhchhccCceeEecc
Q psy7895 13 NTLQESLDELIQYGTITPTLAM-------------------------------KVLLQFDKSINGALPSKVKSRLTFKSG 61 (108)
Q Consensus 13 ~aL~dtLdeli~~~~Is~~la~-------------------------------kVl~~FDk~i~~~L~~~vksk~~~K~G 61 (108)
.+...+.|+.+.+-.+|+++.. ++++.||-.+.+.+=+..-+.+++| -
T Consensus 274 ~a~a~~~d~~l~~s~LsedqkFmlAhA~hSYYgSTqLL~~~G~PlWVVNEGEYrMmNTfDLTvDqlFfEL~~nPWTVr-N 352 (428)
T PF03512_consen 274 LALAAERDEELESSGLSEDQKFMLAHATHSYYGSTQLLDDDGKPLWVVNEGEYRMMNTFDLTVDQLFFELKFNPWTVR-N 352 (428)
T ss_pred HHHHHHHhHHHhhcCCChhHHHHHHHHHHhhhcchhhhhcCCceEEEEecceeEEeehhhhhHHHhhhheecCcceeh-h
Confidence 4567788999999999998865 6788999999999999889999999 5
Q ss_pred cc----ceeeeeCcE
Q psy7895 62 KL----NTYRFCDNV 72 (108)
Q Consensus 62 ~L----~tYr~cDnV 72 (108)
-| .-|.+-|.|
T Consensus 353 ~Ld~fv~rYSY~D~V 367 (428)
T PF03512_consen 353 VLDLFVERYSYRDEV 367 (428)
T ss_pred hHHHHhhhceecccc
Confidence 55 567777765
No 41
>PF00610 DEP: Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP); InterPro: IPR000591 This entry represents the DEP (Dishevelled, Egl-10 and Pleckstrin) domain, a globular domain of about 80 residues that is found in over 50 proteins involved in G-protein signalling pathways. It was named after the three proteins it was initially found in: Dishevelled (Dsh and Dvl), which play a key role in the transduction of the Wg/Wnt signal from the cell surface to the nucleus; it is a segment polarity protein required to establish coherent arrays of polarized cells and segments in embryos, and plays a role in wingless signalling. Egl-10, which regulates G-protein signalling in the central nervous system. Pleckstrin, the major substrate of protein kinase C in platelets; Pleckstrin contains two PH domains flanking the DEP domain. Mammalian regulators of G-protein signalling also contain these domains, and regulate signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving them into their inactive GDP-bound form. It has been proposed that the DEP domain could play a selective role in targeting DEP domain-containing proteins to specific subcellular membranous sites, perhaps even to specific G protein-coupled signaling pathways [, ]. Nuclear magnetic resonance spectroscopy has revealed that the DEP domain comprises a three-helix bundle, a beta-hairpin 'arm' composed of two beta-strands and two short beta-strands in the C-terminal region [].; GO: 0035556 intracellular signal transduction; PDB: 1UHW_A 1V3F_A 2YSR_A 2CSO_A 1W4M_A 2PBI_C 1O7F_A 2BYV_E 1FSH_A 3ML6_D ....
Probab=45.82 E-value=21 Score=21.94 Aligned_cols=62 Identities=19% Similarity=0.234 Sum_probs=43.0
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCce-eEeccccceeee
Q psy7895 4 QLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRL-TFKSGKLNTYRF 68 (108)
Q Consensus 4 ~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~-~~K~G~L~tYr~ 68 (108)
..|+++-.|..+.+-|-+-.+.-..+++.|..+.+.+ +..-+-.+|..+. .|+++.-.-|||
T Consensus 12 ~~~~~~F~G~e~v~WL~~~~~~~~~~r~eA~~l~q~L---l~~g~i~~v~~~~~~F~d~~~~~Yrf 74 (74)
T PF00610_consen 12 KTYPNCFTGSEAVDWLMDNFEGFVRDREEAVQLGQEL---LDHGFIEHVSDKSKQFKDSKNSLYRF 74 (74)
T ss_dssp EEECCEEEHHHHHHHHHHTSCTSTSSHHHHHHHHHHH---HHCTSEEESSSSSHSS-SSSSSEEEE
T ss_pred EEcCCEeEhHHHHHHHHHhccccccCHHHHHHHHHHH---HHCCCEEECCCCCCCEECCCCcEEEC
Confidence 3578888998888777654444489999999988765 3455555677666 588554566765
No 42
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=45.57 E-value=83 Score=21.87 Aligned_cols=33 Identities=9% Similarity=0.089 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q psy7895 13 NTLQESLDELIQYGTITPTLAMKVLLQFDKSIN 45 (108)
Q Consensus 13 ~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~ 45 (108)
.-....+++|+..|.++++.+..+++..=..+.
T Consensus 22 ek~~k~~~~LVkkGe~~~ee~k~~~~e~~~~~~ 54 (118)
T TIGR01837 22 EEGSKFFNRLVKEGELAEKRGQKRFDESVDAAR 54 (118)
T ss_pred HHHHHHHHHHHHhccccHHHHHHHHHHHHHHHH
Confidence 345788999999999999999887655544443
No 43
>cd08325 CARD_CASP1-like Caspase activation and recruitment domain found in Caspase-1 and related proteins. Caspase activation and recruitment domain (CARD) similar to those found in Caspase-1 (CASP1, ICE) and related proteins, including CARD-only proteins such as ICEBERG or CARD18, INCA (CARD17), CARD16 (COP1, PSEUDO-ICE), CARD8 (DACAR, NDPP1, TUCAN), and CARD12 (NLRC4), as well as ICE-like caspases such as CASP12, CASP5 (ICH-3) and CASP4 (TX, ICH-2). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. CASP1 plays a central role in the cellular response to a wide variety of microbial and non-microbial stimuli, being activated by the inflammasome or the pyroptosome. CARD8 binds itself and the initiator caspase-9, interfering with the binding of APAF-1 and suppressing caspase-9 activation. CARD12 is a Nod-like receptor (NLR) that plays an important role in the innate immune response to Gram-negative bacteria. Caspase-4 (CASP4), -5 (CASP5),
Probab=44.10 E-value=62 Score=21.10 Aligned_cols=26 Identities=15% Similarity=0.247 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHH
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLLQ 39 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~~ 39 (108)
.+...||+|++.+.|+.+-.+.|...
T Consensus 17 ~i~~llD~Ll~~~Vl~~~E~e~i~~~ 42 (83)
T cd08325 17 VINGLLDDLLEKNVLNEEEMEKIKEE 42 (83)
T ss_pred hHHHHHHHHHHcCCCCHHHHHHHHhc
Confidence 57889999999999999999999884
No 44
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=43.13 E-value=45 Score=21.94 Aligned_cols=36 Identities=25% Similarity=0.342 Sum_probs=23.4
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchh
Q psy7895 15 LQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSK 51 (108)
Q Consensus 15 L~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~ 51 (108)
+.+++..|.+ --|++.++++|.+.|-....+.|++.
T Consensus 8 ~~~~~~~L~~-~gl~~~~a~kl~~~yg~~ai~~l~~n 43 (94)
T PF14490_consen 8 LRELMAFLQE-YGLSPKLAMKLYKKYGDDAIEILKEN 43 (94)
T ss_dssp -HHHHHHHHH-TT--HHHHHHHHHHH-TTHHHHHHH-
T ss_pred HHHHHHHHHH-cCCCHHHHHHHHHHHhHHHHHHHHHC
Confidence 4455555544 45999999999999988777777764
No 45
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=42.78 E-value=85 Score=20.43 Aligned_cols=41 Identities=12% Similarity=0.219 Sum_probs=30.5
Q ss_pred HHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHhhchhccCceeEe
Q psy7895 17 ESLDELIQY-GTITPTLAMKVLLQFDKSINGALPSKVKSRLTFK 59 (108)
Q Consensus 17 dtLdeli~~-~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K 59 (108)
|.++.+-+. ..+|...+.++++.|=..|.++|.+. .++++.
T Consensus 5 eli~~ia~~~~~~s~~~~~~vv~~~~~~i~~~L~~g--~~V~l~ 46 (94)
T PRK00199 5 ELIERLAARNPHLSAKDVENAVKEILEEMSDALARG--DRIEIR 46 (94)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHcC--CeEEEc
Confidence 344455443 57999999999999999999999763 344554
No 46
>KOG3219|consensus
Probab=42.76 E-value=18 Score=28.01 Aligned_cols=31 Identities=16% Similarity=0.340 Sum_probs=26.9
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHH
Q psy7895 3 YQLYRNTTLGNTLQESLDELIQYGTITPTLA 33 (108)
Q Consensus 3 y~lYR~stlG~aL~dtLdeli~~~~Is~~la 33 (108)
||.||+|.+-+|-..-|-.=|..+.+++..+
T Consensus 105 YEvfRrs~f~Ka~iKkL~~~itg~~v~~nv~ 135 (195)
T KOG3219|consen 105 YEVFRRSAFPKAQIKKLMSSITGQSVSENVA 135 (195)
T ss_pred HHHHHHhcCCHHHHHHHHHHHhCCccCccee
Confidence 9999999999999988888888888887654
No 47
>TIGR01669 phage_XkdX phage uncharacterized protein, XkdX family. This model represents a family of small (about 50 amino acid) phage proteins, found in at least 12 different phage and prophage regions of Gram-positive bacteria. In a number of these phage, the gene for this protein is found near the holin and endolysin genes.
Probab=42.61 E-value=27 Score=20.67 Aligned_cols=22 Identities=14% Similarity=0.194 Sum_probs=18.2
Q ss_pred HHHHHHHHHCCCCCHHHHHHHH
Q psy7895 16 QESLDELIQYGTITPTLAMKVL 37 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kVl 37 (108)
.+=+.+++..|.|||++...|-
T Consensus 20 ~e~v~~~V~~~~IT~eey~eIT 41 (45)
T TIGR01669 20 NEDVNKFVEKKLITREQYKVIT 41 (45)
T ss_pred HHHHHHHhhcCccCHHHHHHHh
Confidence 3457899999999999998773
No 48
>KOG1369|consensus
Probab=42.09 E-value=68 Score=27.89 Aligned_cols=71 Identities=18% Similarity=0.183 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhc-----cCceeEeccccceeeeeCcEEEEEEcCeEEE
Q psy7895 12 GNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKV-----KSRLTFKSGKLNTYRFCDNVWTFVLTDVEFR 83 (108)
Q Consensus 12 G~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~v-----ksk~~~K~G~L~tYr~cDnVWtF~lkd~~f~ 83 (108)
-.++...|+++.+...++.+...+|...|...|...|++.- +--.++. ..+++=+=-..+-.+-+-.-.|+
T Consensus 24 ~~~~~~~l~~~~~~f~l~~~~L~~v~~~~~~em~~gL~~~~~g~~~~mlpt~V-~~lP~G~E~G~~lalDLGGTn~R 99 (474)
T KOG1369|consen 24 LAAVSRQLEELLALFQLPDEQLREVVDAFREEMERGLAKKTHGSAVKMLPTYV-PDLPDGTEKGKFLALDLGGTNFR 99 (474)
T ss_pred hhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhhhhccCCCcccccchhhc-ccCCCCCcCCCEEEEecCCCceE
Confidence 35678899999999999999999999999999999998542 3334555 44554233334444444444444
No 49
>cd04441 DEP_2_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=41.76 E-value=42 Score=22.38 Aligned_cols=58 Identities=19% Similarity=0.319 Sum_probs=43.4
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeee
Q psy7895 4 QLYRNTTLGNTLQESLDELIQYGT-ITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRF 68 (108)
Q Consensus 4 ~lYR~stlG~aL~dtLdeli~~~~-Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~ 68 (108)
..|+++-+|..|.|=| ++.+. -|.+.|..+.+.+ +.+-+-.+|.++-.|++|. .-|||
T Consensus 27 ~~y~~cF~GsElVdWL---~~~~~~~sR~eAv~lgq~L---l~~gii~HV~~~h~F~D~~-~fYrF 85 (85)
T cd04441 27 VKYERTFVGSEFIDWL---LQEGEAESRREAVQLCRRL---LEHGIIQHVSNKHHFFDSN-LLYQF 85 (85)
T ss_pred EEcCCEeEchHHHHHH---HHcCCCCCHHHHHHHHHHH---HHCCCEEecCCCCCccCCC-eeeeC
Confidence 4689999998777654 55664 5899998888754 5566667899999999654 66775
No 50
>smart00049 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
Probab=41.51 E-value=32 Score=21.30 Aligned_cols=60 Identities=25% Similarity=0.352 Sum_probs=42.0
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhcc--CceeEeccccceeeee
Q psy7895 4 QLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVK--SRLTFKSGKLNTYRFC 69 (108)
Q Consensus 4 ~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vk--sk~~~K~G~L~tYr~c 69 (108)
..|+++-.|..+.+-|.+... ..+++.|..+.+.+ +..-|-.+|. ++..|+++ -.-|||.
T Consensus 15 ~~~~~~F~G~e~v~wL~~~~~--~~~r~eA~~l~~~l---l~~g~i~~v~~~~~~~F~d~-~~~Yrf~ 76 (77)
T smart00049 15 KTYPNCFTGSELVDWLMDNLE--IIDREEAVHLGQLL---LDEGLIHHVNGPNKHTFKDS-KALYRFT 76 (77)
T ss_pred EECcceeEcHHHHHHHHHcCC--cCCHHHHHHHHHHH---HHCCCEEEeCCCCcCccccC-CEEEEeC
Confidence 468888899888887777654 57899999888776 3344445566 67778854 3566664
No 51
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=40.32 E-value=49 Score=22.00 Aligned_cols=33 Identities=9% Similarity=0.339 Sum_probs=24.7
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHH
Q psy7895 3 YQLYRNTTLGNTLQESLDELIQYGTITPTLAMK 35 (108)
Q Consensus 3 y~lYR~stlG~aL~dtLdeli~~~~Is~~la~k 35 (108)
|+.||++++=.+=..-|-.-+.++.++++.+.-
T Consensus 9 ye~~Rra~f~k~~iKr~~~~~~~~~v~~~v~i~ 41 (85)
T cd08048 9 YEMFRRSSFPKAAIKRLIQSVTGQSVSQNVVIA 41 (85)
T ss_pred HHHHHHhhccHHHHHHHHHHHcCCCCCchHHHH
Confidence 899999987776666666666677888777653
No 52
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=39.08 E-value=59 Score=28.18 Aligned_cols=44 Identities=23% Similarity=0.380 Sum_probs=30.5
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 3 YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 3 y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
|.-+|+-.- .-||..|+.+|+|.|.-.+.+.++--+-|.+.+.+
T Consensus 252 fdp~rreia----~~~l~~li~dgrihp~riee~~~~~~~~~~~~i~~ 295 (514)
T TIGR03319 252 FDPVRREIA----RMALEKLIQDGRIHPARIEEMVEKATKEVDNAIRE 295 (514)
T ss_pred CchHHHHHH----HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 556666543 34778899999999998887776655555554433
No 53
>PF08638 Med14: Mediator complex subunit MED14; InterPro: IPR013947 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Saccharomyces cerevisiae (Baker's yeast) RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes, and sporulation. It is required for glucose repression, HO repression, RME1 repression and sporulation [, ]. This subunit is also found in higher eukaryotes and MED14 is the agreed unified nomenclature for this subunit []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=38.77 E-value=1e+02 Score=23.24 Aligned_cols=53 Identities=19% Similarity=0.263 Sum_probs=40.6
Q ss_pred HHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcC
Q psy7895 22 LIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTD 79 (108)
Q Consensus 22 li~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd 79 (108)
++....|+|+...+.|...+..|.--|.-. -.+- -.+..|+.-|+-=||.+.|
T Consensus 131 ~~~~~~l~~~e~l~~l~~ln~~i~~RL~~~----~~iP-~~~~~~~I~dGrv~f~V~~ 183 (195)
T PF08638_consen 131 FIPPPPLSPEEILKTLRRLNTLIRIRLALH----EDIP-KQFRNYSIKDGRVTFTVPG 183 (195)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHhc----ccCC-cccceEEEECCEEEEEECC
Confidence 455578999999999999999999887631 1222 3457888999988888876
No 54
>PF10051 DUF2286: Uncharacterized protein conserved in archaea (DUF2286); InterPro: IPR017006 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=38.33 E-value=95 Score=22.87 Aligned_cols=50 Identities=28% Similarity=0.474 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeee-eCcEEEEEEcCeEEEecceEeecCcEEEEE
Q psy7895 27 TITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRF-CDNVWTFVLTDVEFREVAEIARVNKLKIVA 98 (108)
Q Consensus 27 ~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~-cDnVWtF~lkd~~f~~~~~~~~~~~lKIVA 98 (108)
.|+|+|..++ .+| .-++.++++.++ |+.|-- .||-|. ++.++.+++=+||
T Consensus 59 PL~pElyeki-~~~-------~~~r~~~~a~v~---lPvy~Isf~n~W~-----------~e~~~d~kv~VV~ 109 (141)
T PF10051_consen 59 PLKPELYEKI-KKF-------SPKREGNEAEVT---LPVYEISFDNQWI-----------GENYQDKKVYVVA 109 (141)
T ss_pred CCCHHHHHHH-Hhh-------CccccCceEEEE---eeEEEEEECCEec-----------CCCcEeeeEEEEE
Confidence 6899999998 566 456788999888 888874 788887 4445555555554
No 55
>smart00114 CARD Caspase recruitment domain. Motif contained in proteins involved in apoptotic signalling. Mediates homodimerisation. Structure consists of six antiparallel helices arranged in a topology homologue to the DEATH and the DED domain.
Probab=38.17 E-value=43 Score=21.49 Aligned_cols=23 Identities=17% Similarity=0.144 Sum_probs=20.8
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHH
Q psy7895 16 QESLDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kVl~ 38 (108)
.+.||.|+++|.|+++..+.|-.
T Consensus 23 ~~vld~L~~~~Vlt~~e~e~i~~ 45 (88)
T smart00114 23 DGLLDYLVEKNVLTEKEIEAIKA 45 (88)
T ss_pred hHHHHHHHHcCCCCHHHHHHHHc
Confidence 47999999999999999998876
No 56
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=37.82 E-value=65 Score=18.23 Aligned_cols=29 Identities=10% Similarity=0.269 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLLQFDKS 43 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~~FDk~ 43 (108)
.|..+| .....+.++++.+..++..||..
T Consensus 9 ~~~~~l-~~~g~~~~s~~e~~~l~~~~D~~ 37 (54)
T PF13833_consen 9 EFRRAL-SKLGIKDLSEEEVDRLFREFDTD 37 (54)
T ss_dssp HHHHHH-HHTTSSSSCHHHHHHHHHHHTTS
T ss_pred HHHHHH-HHhCCCCCCHHHHHHHHHhcccC
Confidence 455666 33333339999999999999863
No 57
>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=37.76 E-value=69 Score=21.06 Aligned_cols=35 Identities=20% Similarity=0.133 Sum_probs=28.5
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 16 QESLDELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
.+..+++-....+|...+..+++.|=..|.+.|.+
T Consensus 5 ~eli~~ia~~~~~s~~~v~~vv~~~~~~i~~~L~~ 39 (96)
T TIGR00987 5 AEMSEYLFDELGLSKREAKELVELFFEEIRRALEN 39 (96)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHc
Confidence 34455555566799999999999999999999976
No 58
>PF12960 DUF3849: Protein of unknown function (DUF3849); InterPro: IPR024383 This domain is found in a family of uncharacterised proteins found by clustering human gut metagenomic sequences [].
Probab=36.62 E-value=93 Score=22.59 Aligned_cols=49 Identities=14% Similarity=0.316 Sum_probs=33.9
Q ss_pred HHHHhhh-----HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH-HHHHhhchhc
Q psy7895 4 QLYRNTT-----LGNTLQESLDELIQYGTITPTLAMKVLLQFDK-SINGALPSKV 52 (108)
Q Consensus 4 ~lYR~st-----lG~aL~dtLdeli~~~~Is~~la~kVl~~FDk-~i~~~L~~~v 52 (108)
.+||.|- +-.+..+++.+-..+..++++-+..|+++|-- -+.-+|++-|
T Consensus 17 ~~~raS~~aN~~Ck~aIE~aI~~~~~~~~L~~~a~~~vie~fG~eR~~~VLAnTI 71 (133)
T PF12960_consen 17 AQYRASRKANIACKEAIEQAIREHFDGNRLDPDAVKEVIEKFGYERVAYVLANTI 71 (133)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677763 45556666666666779999999999999953 3445566544
No 59
>PF02982 Scytalone_dh: Scytalone dehydratase; InterPro: IPR004235 Scytalone dehydratase is a member of the group of enzymes involved in fungal melanin biosynthesis. It was first identified in a phytopathogenic fungus, Magnaporthe grisea (Rice blast fungus), which causes rice blast disease. Scytalone dehydratase is a molecular target of inhibitor design efforts aimed at protecting rice plants from fungal disease [, ].; GO: 0030411 scytalone dehydratase activity, 0006582 melanin metabolic process; PDB: 4STD_A 3STD_A 6STD_A 7STD_C 1STD_A 5STD_C 1IDP_B 2STD_A.
Probab=36.59 E-value=57 Score=24.55 Aligned_cols=31 Identities=32% Similarity=0.456 Sum_probs=24.3
Q ss_pred CceeEeccc-----cceeeeeCcEEEEEEcCeEEEec
Q psy7895 54 SRLTFKSGK-----LNTYRFCDNVWTFVLTDVEFREV 85 (108)
Q Consensus 54 sk~~~K~G~-----L~tYr~cDnVWtF~lkd~~f~~~ 85 (108)
..+..| || -+.|+-.|+||.|---.|.++-.
T Consensus 110 ~~V~~k-Gh~h~~~~h~Y~KvdG~WK~agl~P~v~w~ 145 (160)
T PF02982_consen 110 TEVKAK-GHGHGTNTHWYRKVDGVWKFAGLKPEVRWN 145 (160)
T ss_dssp -SEEEE-EEEEEEEEEEEEEETTEEEEEEEEEEEEEE
T ss_pred cEEEee-eccceeEEEEEEEeCCEEEEeeeccceeEe
Confidence 446667 75 38899999999999988888753
No 60
>PF03492 Methyltransf_7: SAM dependent carboxyl methyltransferase; InterPro: IPR005299 This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine [].; GO: 0008168 methyltransferase activity; PDB: 2EFJ_A 1M6E_X 2EG5_C 3B5I_B.
Probab=36.41 E-value=29 Score=28.17 Aligned_cols=24 Identities=21% Similarity=0.355 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHH
Q psy7895 10 TLGNTLQESLDELIQYGTITPTLA 33 (108)
Q Consensus 10 tlG~aL~dtLdeli~~~~Is~~la 33 (108)
.+...|.++|.+|+.+|.|+++..
T Consensus 198 ~~~~~l~~~l~dMv~eGlI~~ek~ 221 (334)
T PF03492_consen 198 MLWDLLADALRDMVAEGLISEEKV 221 (334)
T ss_dssp CHHHHHHHHHHHHHHTTSS-HCCC
T ss_pred hHHHHHHHHHHHHHHcCCcCHHHh
Confidence 577899999999999999998754
No 61
>PF14476 Chloroplast_duf: Petal formation-expressed
Probab=36.18 E-value=24 Score=29.01 Aligned_cols=21 Identities=33% Similarity=0.813 Sum_probs=16.3
Q ss_pred ChhHHHHhhh-----HHHHHHHHHHH
Q psy7895 1 MSYQLYRNTT-----LGNTLQESLDE 21 (108)
Q Consensus 1 m~y~lYR~st-----lG~aL~dtLde 21 (108)
|-|||||++. +-++...+|+|
T Consensus 260 MvfEMyRn~aGff~l~eetIe~~l~E 285 (313)
T PF14476_consen 260 MVFEMYRNCAGFFKLMEETIESTLEE 285 (313)
T ss_pred eehHHHhcccHHHHHHHHHHHHHHhc
Confidence 7799999984 66777777773
No 62
>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=35.99 E-value=76 Score=19.98 Aligned_cols=31 Identities=16% Similarity=0.088 Sum_probs=25.3
Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 20 DELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 20 deli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
+++-+...+|+..+..|+..|-..|.+.|.+
T Consensus 8 ~~ia~~~~~s~~~v~~vl~~~~~~i~~~L~~ 38 (90)
T PF00216_consen 8 KRIAEKTGLSKKDVEAVLDALFDVIKEALKE 38 (90)
T ss_dssp HHHHHHHTSSHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHhcCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 3333444599999999999999999999976
No 63
>cd08323 CARD_APAF1 Caspase activation and recruitment domain similar to that found in Apoptotic Protease-Activating Factor 1. Caspase activation and recruitment domain (CARD) similar to that found in apoptotic protease-activating factor 1 (APAF-1), which is an activator of caspase-9. APAF-1 contains WD-40 repeats, a CARD, and an ATPase domain. Upon stimulation, APAF-1, together with caspase-9, forms the heptameric 'apoptosome', which leads to the processing and activation of caspase-9, starting a caspase cascade which leads to apoptosis. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effect
Probab=35.84 E-value=48 Score=22.05 Aligned_cols=29 Identities=24% Similarity=0.219 Sum_probs=23.4
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHH---HHHH
Q psy7895 15 LQESLDELIQYGTITPTLAMKVLLQ---FDKS 43 (108)
Q Consensus 15 L~dtLdeli~~~~Is~~la~kVl~~---FDk~ 43 (108)
..+.+|-|+++|.||++-.+.|..+ .|++
T Consensus 16 v~~ild~L~~~gvlt~~~~e~I~~~~t~~~qa 47 (86)
T cd08323 16 TSYIMDHMISDGVLTLDEEEKVKSKATQKEKA 47 (86)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHcCCChHHHH
Confidence 3568999999999999999888753 4554
No 64
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=35.35 E-value=46 Score=19.32 Aligned_cols=27 Identities=33% Similarity=0.438 Sum_probs=21.0
Q ss_pred HHHhhhHHHHHHHHHHHHHHCCCCCHH
Q psy7895 5 LYRNTTLGNTLQESLDELIQYGTITPT 31 (108)
Q Consensus 5 lYR~stlG~aL~dtLdeli~~~~Is~~ 31 (108)
-|=..++|..|.++|.|+....--.|-
T Consensus 4 ~YL~~~v~p~L~~gL~~l~~~rP~DPi 30 (42)
T PF05186_consen 4 QYLKETVGPVLTEGLAELAKERPEDPI 30 (42)
T ss_dssp HHHHHHTHHHHHHHHHHHHHH--SSHH
T ss_pred HHHHHHhHHHHHHHHHHHHHHCCCChH
Confidence 467789999999999999987766663
No 65
>PF10335 DUF294_C: Putative nucleotidyltransferase substrate binding domain; InterPro: IPR018821 This entry is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding domains.
Probab=35.22 E-value=93 Score=21.96 Aligned_cols=36 Identities=22% Similarity=0.358 Sum_probs=31.2
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhc
Q psy7895 17 ESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKV 52 (108)
Q Consensus 17 dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~v 52 (108)
+=|+.+.+.|.|+++.+..+.+-|+-.+.--|...+
T Consensus 66 eRl~~L~~~g~l~~~~~~~l~~A~~~l~~lRl~~q~ 101 (145)
T PF10335_consen 66 ERLEALAEAGVLSPDDAEDLIEAFEFLLGLRLRHQL 101 (145)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457889999999999999999999999888776653
No 66
>cd01671 CARD Caspase activation and recruitment domain: a protein-protein interaction domain. Caspase activation and recruitment domains (CARDs) are death domains (DDs) found associated with caspases. Caspases are aspartate-specific cysteine proteases with functions in apoptosis, immune signaling, inflammation, and host-defense mechanisms. In addition to caspases, proteins containing CARDs include adaptor proteins such as RAIDD, CARD9, and RIG-I-like helicases, which can form mutliprotein complexes and play important roles in mediating the signals to induce immune and inflammatory responses. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and DED (Death Effector Domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=35.00 E-value=66 Score=19.79 Aligned_cols=26 Identities=23% Similarity=0.341 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHH
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLLQ 39 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~~ 39 (108)
.....||.|++.|.||++....|...
T Consensus 14 ~~~~il~~L~~~~vlt~~e~~~i~~~ 39 (80)
T cd01671 14 DVEDVLDHLLSDGVLTEEEYEKIRSE 39 (80)
T ss_pred cHHHHHHHHHHcCCCCHHHHHHHHcC
Confidence 66789999999999999999887754
No 67
>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=34.50 E-value=1.3e+02 Score=19.44 Aligned_cols=41 Identities=10% Similarity=0.198 Sum_probs=29.9
Q ss_pred HHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHhhchhccCceeEe
Q psy7895 17 ESLDELIQY-GTITPTLAMKVLLQFDKSINGALPSKVKSRLTFK 59 (108)
Q Consensus 17 dtLdeli~~-~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K 59 (108)
|.++.+.+. ..+|+..+..+++.|=..|.+.|.+ ..++.|.
T Consensus 5 eli~~i~~~~~~~s~~~v~~vv~~~~~~i~~~L~~--g~~V~l~ 46 (94)
T TIGR00988 5 ELIERIATQQSHLPAKDVEDAVKTMLEHMASALAQ--GDRIEIR 46 (94)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHHHc--CCeEEEc
Confidence 334444443 4799999999999999999999976 2335554
No 68
>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=34.50 E-value=91 Score=17.67 Aligned_cols=35 Identities=17% Similarity=0.264 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q psy7895 12 GNTLQESLDELIQYGTITPTLAMKVLLQFDKSING 46 (108)
Q Consensus 12 G~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~ 46 (108)
..++.++..=|....-++|+...+++..+...+++
T Consensus 8 ~~C~~Ev~~fL~~~~~~~~~~~~rLl~HL~~~~~~ 42 (43)
T PF07527_consen 8 SECLNEVSRFLSSVEGVDPGVRARLLSHLQSCLNQ 42 (43)
T ss_dssp HHHHHHHHHHHHHTS---THHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhcC
Confidence 46788899999888889999999999999998875
No 69
>PF14929 TAF1_subA: TAF RNA Polymerase I subunit A
Probab=34.05 E-value=38 Score=29.84 Aligned_cols=41 Identities=29% Similarity=0.479 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHHHCC-----CCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 10 TLGNTLQESLDELIQYG-----TITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 10 tlG~aL~dtLdeli~~~-----~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
.+|--|.|+|+|+...+ .+.-.++-++|+.||+..+.+|.+
T Consensus 320 l~~~~l~eal~~~e~~c~~~~~~lpi~~~~~lle~~d~~~~~~l~~ 365 (547)
T PF14929_consen 320 LIGGRLKEALNELEKFCISSTCALPIRLRAHLLEYFDQNNSSVLSS 365 (547)
T ss_pred eccccHHHHHHHHHHhccCCCccchHHHHHHHHHHhCcccHHHHHH
Confidence 47889999999998843 678899999999999644444433
No 70
>PF00681 Plectin: Plectin repeat; InterPro: IPR001101 Plectin may have a role in cross-linking intermediate filaments, in inter-linking intermediate filaments with microtubules and microfilaments and in anchoring intermediate filaments to the plasma and nuclear membranes. Plectin is recruited into hemidesmosomes, multiprotein complexes that facilitate adhesion of epithelia to the basement membrane, thereby providing linkage between the intracellular keratin filaments to the laminins of the extracellular matrix. Plectin binds to hemidesmosomes through association of its actin-binding domain with the first pair of fibronectin type III repeats and a small part of the connecting segment of the integrin-beta4 subunit, the latter (integrin-alpha6,beta4) acting as a receptor for the extracellular matrix component laminin-5. The plectin repeat is also seen in the cell adhesion junction plaque proteins, desmoplakin, envoplakin, and bullous pemphigoid antigen. The domains in plakins show considerable sequence homology. The N terminus consists of a plakin domain containing a number of subdomains with high alpha-helical content, while the central coiled-coil domain is composed of heptad repeats involved in the dimerisation of plakin, and the C terminus contains one or more homologous repeat sequences referred to plectin repeats []. This entry represents the plectin repeats found in the C terminus of plakin proteins.; GO: 0005856 cytoskeleton; PDB: 1LM7_A 1LM5_A.
Probab=34.03 E-value=72 Score=18.30 Aligned_cols=20 Identities=40% Similarity=0.464 Sum_probs=16.3
Q ss_pred HHHHHHCCCCCHHHHHHHHH
Q psy7895 19 LDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 19 Ldeli~~~~Is~~la~kVl~ 38 (108)
++|=++.|.|+++.+.++++
T Consensus 24 v~~A~~~glId~~~~~~L~e 43 (45)
T PF00681_consen 24 VEEAIQRGLIDSDTAQKLLE 43 (45)
T ss_dssp HHHHHHTTSS-HHHHHHHHH
T ss_pred HHHHHHCCCcCHHHHHHHHc
Confidence 56778899999999999886
No 71
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=33.72 E-value=61 Score=21.71 Aligned_cols=22 Identities=23% Similarity=0.116 Sum_probs=19.3
Q ss_pred HHHHHHHHCCCCCHHHHHHHHH
Q psy7895 17 ESLDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 17 dtLdeli~~~~Is~~la~kVl~ 38 (108)
..||.|++.|.||++-...|-.
T Consensus 27 ~ilD~Ll~~~Vlt~ee~e~I~~ 48 (94)
T cd08329 27 PILDSLLSANVITEQEYDVIKQ 48 (94)
T ss_pred HHHHHHHHcCCCCHHHHHHHHc
Confidence 5799999999999998888764
No 72
>PF12713 DUF3806: Domain of unknown function (DUF3806); InterPro: IPR024266 This entry represents a domain found at the C terminus of a family of bacterial proteins, whose function is unknown. In two related Bacteroides species the gene for members of this family lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1ma7, whose C-terminal domain is a phage integrase.; PDB: 3HLZ_A.
Probab=33.66 E-value=72 Score=20.97 Aligned_cols=39 Identities=21% Similarity=0.300 Sum_probs=31.1
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhc-cCce
Q psy7895 17 ESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKV-KSRL 56 (108)
Q Consensus 17 dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~v-ksk~ 56 (108)
++|+.++.++.++|+..+. ++.|=-++-+.|.+.+ ...+
T Consensus 4 ~~lq~~id~~~~~~~d~~~-~~alGialG~~L~~e~~g~eW 43 (87)
T PF12713_consen 4 EKLQRVIDSGEISPDDKDE-WQALGIALGDLLANEVDGMEW 43 (87)
T ss_dssp HHHHHHHHTT-S-TT-HHH-HHHHHHHHHHHHHHHSTT-EE
T ss_pred HHHHHHHHhCCCCCCcHHH-HHHHHHHHHHHHHhhcCCCeE
Confidence 6899999999999999998 9999999999999877 4444
No 73
>COG5026 Hexokinase [Carbohydrate transport and metabolism]
Probab=33.32 E-value=1.2e+02 Score=26.55 Aligned_cols=51 Identities=22% Similarity=0.318 Sum_probs=42.4
Q ss_pred ChhHHHHhhhH--HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchh
Q psy7895 1 MSYQLYRNTTL--GNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSK 51 (108)
Q Consensus 1 m~y~lYR~stl--G~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~ 51 (108)
|++.=.|.-|+ -.+|+++++|+++.-.++.+..++|-..|+..+...|+.+
T Consensus 1 ~~~~~~~kgt~~~~~~l~~~~~~~~~~~~~p~e~l~~v~~~Fieel~kgL~~~ 53 (466)
T COG5026 1 PSFADFHKGTLGVEAALEQAVEELVESFTVPTEDLREVVKAFIEELEKGLQPK 53 (466)
T ss_pred CcchhhhhccccccHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHHhccCCC
Confidence 34444555554 4689999999999999999999999999999999999844
No 74
>cd08326 CARD_CASP9 Caspase activation and recruitment domain of Caspase-9. Caspase activation and recruitment domain (CARD) similar to that found in caspase-9 (CASP9, MCH6, APAF3), which interacts with the CARD of apoptotic protease-activating factor 1 (APAF-1). Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-9 is the initiator caspase associated with the intrinsic or mitochondrial pathway of apoptosis, induced by many pro-apoptotic signals. Together with APAF-1, it forms the heptameric 'apoptosome' in response to the release of cytochrome c from mitochondria. Activated caspase-9 cleaves and activates downstream effector caspases, like caspase-3, caspase-6, and caspase-7, resulting in apoptosis. In general, CARDs are death domains (DDs) associated with caspases. They are known to be important in the signaling pathways for apopt
Probab=32.84 E-value=69 Score=21.06 Aligned_cols=24 Identities=21% Similarity=0.324 Sum_probs=20.9
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHH
Q psy7895 15 LQESLDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 15 L~dtLdeli~~~~Is~~la~kVl~ 38 (108)
..+.++.|+++|.+|++..+.|..
T Consensus 18 ~~~v~~~L~~~~Vlt~~~~e~I~~ 41 (84)
T cd08326 18 PKYLWDHLLSRGVFTPDMIEEIQA 41 (84)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHc
Confidence 357899999999999999988875
No 75
>TIGR02742 TrbC_Ftype type-F conjugative transfer system pilin assembly protein TrbC. This protein is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA. The N-terminal portion of these proteins are heterogeneous and are not covered by this model.
Probab=32.42 E-value=68 Score=22.94 Aligned_cols=27 Identities=22% Similarity=0.349 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHH
Q psy7895 13 NTLQESLDELIQYGTITPTLAMKVLLQ 39 (108)
Q Consensus 13 ~aL~dtLdeli~~~~Is~~la~kVl~~ 39 (108)
.+|.++|+++-++|......|.+.|+.
T Consensus 102 vsl~~ALe~ia~~g~~~~~~A~~~L~~ 128 (130)
T TIGR02742 102 VSLKGALEKMAQDGDSPQIVAQQLLER 128 (130)
T ss_pred ccHHHHHHHHHHhCCCcHHHHHHHHHh
Confidence 479999999999998877788888864
No 76
>PF12297 EVC2_like: Ellis van Creveld protein 2 like protein; InterPro: IPR022076 This family of proteins is found in eukaryotes. Proteins in this family are typically between 571 and 1310 amino acids in length. There are two conserved sequence motifs: LPA and ELH. EVC2 is implicated in Ellis van Creveld chondrodysplastic dwarfism in humans. Mutations in this protein can give rise to this congenital condition. LIMBIN is a protein which shares around 80% sequence homology with EVC2 and it is implicated in a similar condition in bovine chondrodysplastic dwarfism.
Probab=31.53 E-value=1.7e+02 Score=25.22 Aligned_cols=43 Identities=21% Similarity=0.367 Sum_probs=37.5
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q psy7895 3 YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSIN 45 (108)
Q Consensus 3 y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~ 45 (108)
+.++|+..+-.-...-|++.+..|.+.|+.|..+++.|-+...
T Consensus 297 la~~~R~eLh~if~~qi~~ai~~GeL~~e~Ak~Ll~~y~~~Q~ 339 (429)
T PF12297_consen 297 LAVFRRVELHEIFFEQIKSAIFKGELKPEAAKSLLQDYSKIQE 339 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHH
Confidence 4577888888888999999999999999999999999876553
No 77
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=30.45 E-value=56 Score=22.89 Aligned_cols=32 Identities=28% Similarity=0.324 Sum_probs=26.5
Q ss_pred HHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHhh
Q psy7895 17 ESLDELIQYG-TITPTLAMKVLLQFDKSINGAL 48 (108)
Q Consensus 17 dtLdeli~~~-~Is~~la~kVl~~FDk~i~~~L 48 (108)
.++.++|+.. .||++.|.++=..|+.+..--|
T Consensus 38 ~~is~ling~~~iT~dmAlrL~k~fGtspefWl 70 (104)
T COG3093 38 NTISELINGRRAITADMALRLAKVFGTSPEFWL 70 (104)
T ss_pred HHHHHHHcCCcCCCHHHHHHHHHHhCCCHHHHH
Confidence 4678899888 8999999999998888766544
No 78
>PF11429 Colicin_D: Colicin D; InterPro: IPR024440 Colicin D is a bacteriocin that kills target cells by cleaving tRNA(Arg). This entry represents a domain found in the C terminus of colicin D, which is responsible for its catalytic activity []. The domain is also found in some S-type pyocins, which are also bacteriocins.; GO: 0004540 ribonuclease activity; PDB: 1TFO_A 1V74_A 1TFK_A.
Probab=30.33 E-value=43 Score=22.93 Aligned_cols=34 Identities=21% Similarity=0.324 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEE
Q psy7895 36 VLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFV 76 (108)
Q Consensus 36 Vl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~ 76 (108)
=+.+|-.+|.+-|.. ..++. ..|||+..++|.|+
T Consensus 23 t~~~F~~aI~~hi~~----~~tv~---~GtYr~~~~skV~~ 56 (92)
T PF11429_consen 23 TLEEFEDAIKEHIKN----PDTVE---KGTYRRVKDSKVYF 56 (92)
T ss_dssp HHHHHHHHHHHHHH-----TT-EE-----BETTSTT-EEEE
T ss_pred hHHHHHHHHHHHhCC----CCeEe---ccceecCCCcEEEE
Confidence 356777777665544 45555 47899999999996
No 79
>PF01756 ACOX: Acyl-CoA oxidase; InterPro: IPR002655 Acyl-CoA oxidase (ACO) acts on CoA derivatives of fatty acids with chain lengths from 8 to 18. It catalyses the first and rate-determining step of the peroxisomal beta-oxidation of fatty acids []. Acyl-CoA oxidase is a homodimer and the polypeptide chain of the subunit is folded into the N-terminal alpha-domain, beta-domain, and C-terminal alpha-domain []. Functional differences between the peroxisomal acyl-CoA oxidases and the mitochondrial acyl-CoA dehydrogenases are attributed to structural differences in the FAD environments []. Experimental data indicate that, in the pumpkin, the expression pattern of ACOX is very similar to that of the glyoxysomal enzyme 3-ketoacyl-CoA thiolase []. In humans, defects in ACOX1 are the cause of pseudoneonatal adrenoleukodystrophy, also known as peroxisomal acyl-CoA oxidase deficiency. Pseudo-NALD is a peroxisomal single-enzyme disorder. Clinical features include mental retardation, leukodystrophy, seizures, mild hepatomegaly and hearing deficit. Pseudo-NALD is characterised by increased plasma levels of very-long chain fatty acids due to a decrease in, or absence of, peroxisome acyl-CoA oxidase activity, despite the peroxisomes being intact and functioning. This entry represents the Acyl-CoA oxidase C-terminal.; GO: 0003997 acyl-CoA oxidase activity, 0006635 fatty acid beta-oxidation, 0055114 oxidation-reduction process, 0005777 peroxisome; PDB: 2FON_A 1IS2_B 2DDH_A 1W07_B.
Probab=30.17 E-value=1.5e+02 Score=21.44 Aligned_cols=36 Identities=11% Similarity=0.267 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhc
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLLQFDKSINGALP 49 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~ 49 (108)
.+.+-+.++++.|.|||+++..|-+..+..+.+.-.
T Consensus 92 ~i~~~~g~fl~~g~ls~~~~~~l~~~i~~l~~~lrp 127 (187)
T PF01756_consen 92 IIEENAGDFLEHGYLSPEQIKALRKAIEELCAELRP 127 (187)
T ss_dssp HHHHTHHHHHHTTSS-HHHHHHHHHHHHHHHHHHGG
T ss_pred HHHHHHHHHHhCCcCCHHHHHHHHHHHHHHHHHHHh
Confidence 445667889999999999999999988887766533
No 80
>COG2306 Predicted RNA-binding protein, associated with RNAses E/G family [General function prediction only]
Probab=29.52 E-value=1.4e+02 Score=22.93 Aligned_cols=31 Identities=23% Similarity=0.337 Sum_probs=23.1
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHHh
Q psy7895 17 ESLDELIQYGTITPTLAMKVLLQFDKSINGA 47 (108)
Q Consensus 17 dtLdeli~~~~Is~~la~kVl~~FDk~i~~~ 47 (108)
|-|..-++.|.|||.++++-...-+..+.++
T Consensus 126 DEL~~Al~~GlIT~~qf~~Ay~~a~aVe~el 156 (183)
T COG2306 126 DELEDALRYGLITPEQFEKAYRTANAVEAEL 156 (183)
T ss_pred HHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence 3344556799999999999888777666554
No 81
>PF14793 DUF4478: Domain of unknown function (DUF4478); PDB: 2PMB_D 3GH1_D 3BQ9_B.
Probab=29.38 E-value=32 Score=24.49 Aligned_cols=10 Identities=60% Similarity=1.119 Sum_probs=8.4
Q ss_pred hHHHHhhhHH
Q psy7895 3 YQLYRNTTLG 12 (108)
Q Consensus 3 y~lYR~stlG 12 (108)
|+|||+++|.
T Consensus 31 y~LfR~CsLA 40 (112)
T PF14793_consen 31 YQLFRNCSLA 40 (112)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHhhHHH
Confidence 8999998764
No 82
>PF07565 Band_3_cyto: Band 3 cytoplasmic domain; InterPro: IPR013769 Bicarbonate (HCO3 -) transport mechanisms are the principal regulators of pH in animal cells. Such transport also plays a vital role in acid-base movements in the stomach, pancreas, intestine, kidney, reproductive organs and the central nervous system. Functional studies have suggested four different HCO3 - transport modes. Anion exchanger proteins exchange HCO3 - for Cl- in a reversible, electroneutral manner []. Na+/HCO3 - co-transport proteins mediate the coupled movement of Na+ and HCO3 - across plasma membranes, often in an electrogenic manner []. Na- driven Cl-/HCO3 - exchange and K+/HCO3 - exchange activities have also been detected in certain cell types, although the molecular identities of the proteins responsible remain to be determined. Sequence analysis of the two families of HCO3 - transporters that have been cloned to date (the anion exchangers and Na+/HCO3 - co-transporters) reveals that they are homologous. This is not entirely unexpected, given that they both transport HCO3 - and are inhibited by a class of pharmacological agents called disulphonic stilbenes []. They share around ~25-30% sequence identity, which is distributed along their entire sequence length, and have similar predicted membrane topologies, suggesting they have ~10 transmembrane (TM) domains.; GO: 0008509 anion transmembrane transporter activity, 0006820 anion transport, 0016021 integral to membrane; PDB: 1HYN_Q.
Probab=28.08 E-value=67 Score=25.43 Aligned_cols=31 Identities=26% Similarity=0.368 Sum_probs=24.7
Q ss_pred hhHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q psy7895 9 TTLGNTLQESLDELIQYGTITPTLAMKVLLQ 39 (108)
Q Consensus 9 stlG~aL~dtLdeli~~~~Is~~la~kVl~~ 39 (108)
+++..-....+|+|+.++.|+|+...+|++-
T Consensus 41 ~tl~~I~~~vvd~~v~~~~l~~~~r~~V~~a 71 (257)
T PF07565_consen 41 KTLPEIADKVVDQMVSEGQLRPEDRDKVLRA 71 (257)
T ss_dssp -SHHHHHHHHHHHHHHTTSS-GGGHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhcCCCHHHHHHHHHH
Confidence 4677777789999999999999998887753
No 83
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=27.79 E-value=1.1e+02 Score=18.67 Aligned_cols=25 Identities=16% Similarity=0.115 Sum_probs=14.3
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHH
Q psy7895 15 LQESLDELIQYGTITPTLAMKVLLQ 39 (108)
Q Consensus 15 L~dtLdeli~~~~Is~~la~kVl~~ 39 (108)
+.+.|..+.+...+|++.+..++..
T Consensus 2 ~~~~l~~l~~g~~Ls~~e~~~~~~~ 26 (66)
T PF02885_consen 2 IKEILKKLRDGEDLSREEAKAAFDA 26 (66)
T ss_dssp HHHHHHHHHTT----HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 5667777777777777777666543
No 84
>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB. This alignment contains the C-terminal domain, which is the ATPase.
Probab=27.69 E-value=68 Score=23.12 Aligned_cols=22 Identities=41% Similarity=0.582 Sum_probs=17.9
Q ss_pred HHHHHHCCCCCHHHHHHHHHHH
Q psy7895 19 LDELIQYGTITPTLAMKVLLQF 40 (108)
Q Consensus 19 Ldeli~~~~Is~~la~kVl~~F 40 (108)
||+|++.|.++|+++..+....
T Consensus 1 ~~~l~~~g~~~~~~~~~l~~~v 22 (186)
T cd01130 1 LDDLIAQGTFSPLQAAYLWLAV 22 (186)
T ss_pred CHHHHHcCCCCHHHHHHHHHHH
Confidence 6899999999999877665543
No 85
>TIGR02009 PGMB-YQAB-SF beta-phosphoglucomutase family hydrolase. All of these are members of the larger Haloacid dehalogenase (HAD) subfamily IA and include the "variant 3" glu-asp version of the third conserved HAD domain (TIGR01509).
Probab=27.56 E-value=1.3e+02 Score=20.69 Aligned_cols=44 Identities=9% Similarity=0.123 Sum_probs=33.6
Q ss_pred HHHhhhHHHHHHHHHHHHHHCC--CCCHHHHHHHHHHHHHHHHHhh
Q psy7895 5 LYRNTTLGNTLQESLDELIQYG--TITPTLAMKVLLQFDKSINGAL 48 (108)
Q Consensus 5 lYR~stlG~aL~dtLdeli~~~--~Is~~la~kVl~~FDk~i~~~L 48 (108)
.|+....|....+.+.++.... .++++...++.+.|...+.+.+
T Consensus 37 ~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 82 (185)
T TIGR02009 37 QYNTSLGGLSREDILRAILKLRKPGLSLETIHQLAERKNELYRELL 82 (185)
T ss_pred HHHHHcCCCCHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 4566778888888888888764 5788888888888877666555
No 86
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=27.53 E-value=61 Score=22.89 Aligned_cols=22 Identities=32% Similarity=0.521 Sum_probs=16.3
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHH
Q psy7895 16 QESLDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kVl~ 38 (108)
.+.|+. +.+|.||++-|.++|.
T Consensus 92 ~~IL~~-L~~GeIs~eeA~~~Lk 113 (113)
T PF09862_consen 92 KEILDK-LEKGEISVEEALEILK 113 (113)
T ss_pred HHHHHH-HHcCCCCHHHHHHHhC
Confidence 344544 5599999999999873
No 87
>PF13742 tRNA_anti_2: OB-fold nucleic acid binding domain
Probab=27.50 E-value=1.8e+02 Score=19.30 Aligned_cols=42 Identities=17% Similarity=0.269 Sum_probs=31.7
Q ss_pred HHHHHHHHhhchhcc-CceeEeccccceeee-eCcEEEEEEcCeE
Q psy7895 39 QFDKSINGALPSKVK-SRLTFKSGKLNTYRF-CDNVWTFVLTDVE 81 (108)
Q Consensus 39 ~FDk~i~~~L~~~vk-sk~~~K~G~L~tYr~-cDnVWtF~lkd~~ 81 (108)
++-..|...|.+... ...-++ |.+..++. --+-|-|.|+|-.
T Consensus 6 ~l~~~ik~~le~~~~~~~vwV~-GEIs~~~~~~~gh~YftLkD~~ 49 (99)
T PF13742_consen 6 ELNNYIKDLLERDPPLPNVWVE-GEISNLKRHSSGHVYFTLKDEE 49 (99)
T ss_pred HHHHHHHHHHhcCCCcCCEEEE-EEEeecEECCCceEEEEEEcCC
Confidence 444555666655433 778999 99999998 7799999999954
No 88
>TIGR01425 SRP54_euk signal recognition particle protein SRP54. This model represents examples from the eukaryotic cytosol of the signal recognition particle protein component, SRP54. This GTP-binding protein is a component of the eukaryotic signal recognition particle, along with several other protein subunits and a 7S RNA. Some species, including Arabidopsis, have several closely related forms. The extreme C-terminal region is glycine-rich and lower in complexity, poorly conserved between species, and excluded from this model.
Probab=27.31 E-value=1.5e+02 Score=25.31 Aligned_cols=38 Identities=13% Similarity=0.222 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHh
Q psy7895 10 TLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGA 47 (108)
Q Consensus 10 tlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~ 47 (108)
.||..|..++.-+-..+.|+++-....|++.-.+.-++
T Consensus 4 ~L~~~l~~~~~~l~~~~~l~e~~i~~~l~ei~~aLlea 41 (429)
T TIGR01425 4 DLGSSITSALRSMSNATVIDEEVLNAMLKEICTALLES 41 (429)
T ss_pred HHHHHHHHHHHHHhCCCccCHHHHHHHHHHHHHHHHHC
Confidence 68999999999999999999999888888877665443
No 89
>PF03048 Herpes_UL92: UL92 family; InterPro: IPR004289 Members of this family are functionally uncharacterised proteins from herpesviruses. The N terminus of these proteins contain 6 conserved cysteines and histidines that might form a zinc binding domain.
Probab=27.31 E-value=1.3e+02 Score=23.17 Aligned_cols=32 Identities=13% Similarity=0.337 Sum_probs=29.5
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q psy7895 15 LQESLDELIQYGTITPTLAMKVLLQFDKSING 46 (108)
Q Consensus 15 L~dtLdeli~~~~Is~~la~kVl~~FDk~i~~ 46 (108)
+.+..++.+.+|.+.|+....|-..|.++...
T Consensus 104 ~~~V~~~i~~~g~l~~~i~~~I~~TF~~c~~~ 135 (192)
T PF03048_consen 104 YAEVKQAIFEDGELKPHIEDLIYFTFNHCFHV 135 (192)
T ss_pred HHHHHHHHHcCCcccHhHHHHHHHHHHHHHHh
Confidence 88999999999999999999999999988654
No 90
>cd01650 RT_nLTR_like RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.
Probab=27.20 E-value=1.2e+02 Score=21.62 Aligned_cols=71 Identities=13% Similarity=0.056 Sum_probs=46.1
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCeE--EEe--c---------ceEee
Q psy7895 24 QYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVE--FRE--V---------AEIAR 90 (108)
Q Consensus 24 ~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~--f~~--~---------~~~~~ 90 (108)
|...+||-++.-.+..+|..+..... ...-. ..+...+|.||+=. ..++.. +.. + +-.+.
T Consensus 109 QG~~lSp~l~~l~~~~l~~~~~~~~~-----~~~~~-~~~~~~~yaDD~~i-~~~~~~~~~~~~~~~~~~~~~~~gl~in 181 (220)
T cd01650 109 QGDPLSPLLFNLALDDLLRLLNKEEE-----IKLGG-PGITHLAYADDIVL-FSEGKSRKLQELLQRLQEWSKESGLKIN 181 (220)
T ss_pred cCCcccHHHHHHHHHHHHHHHHhhcc-----ccCCC-CccceEEeccceee-eccCCHHHHHHHHHHHHHHHHHcCCEEC
Confidence 45589999999999999999877665 11112 45678899999754 444443 110 0 22456
Q ss_pred cCcEEEEEecC
Q psy7895 91 VNKLKIVACDG 101 (108)
Q Consensus 91 ~~~lKIVAcd~ 101 (108)
.+|-+++....
T Consensus 182 ~~Kt~~~~~~~ 192 (220)
T cd01650 182 PSKSKVMLIGN 192 (220)
T ss_pred hhheEEEEecC
Confidence 67777776544
No 91
>PF06256 Nucleo_LEF-12: Nucleopolyhedrovirus LEF-12 protein; InterPro: IPR009365 This family consists of several Nucleopolyhedrovirus late expression factor-12 (LEF-12) proteins. The function of this family is unknown [,].
Probab=27.17 E-value=95 Score=23.88 Aligned_cols=43 Identities=26% Similarity=0.404 Sum_probs=35.6
Q ss_pred HhhhHHHHHHHHHHHHHHCCCCCHHHHH-----------------------------------HHHH--HHHHHHHHhhc
Q psy7895 7 RNTTLGNTLQESLDELIQYGTITPTLAM-----------------------------------KVLL--QFDKSINGALP 49 (108)
Q Consensus 7 R~stlG~aL~dtLdeli~~~~Is~~la~-----------------------------------kVl~--~FDk~i~~~L~ 49 (108)
+-.++-.-...|||+|++.|.|+++=+. ++|+ .|+.++.+.+.
T Consensus 11 ~v~~~~~~~~~~ld~M~~~geit~~Da~sLClaDDTAAWvCGRi~~cnfVSFRi~~~~F~~~~~~L~~f~FeEsl~Q~~~ 90 (185)
T PF06256_consen 11 YVQDFADMMKRTLDEMVEHGEITRADADSLCLADDTAAWVCGRIETCNFVSFRIKSAQFQHPSRALEHFGFEESLEQRLL 90 (185)
T ss_pred HHHHHHHHHHHHHHHHHHcCCcchhhhcceeecccchHHhcCCccCCceEEEEEEHhhhcCchHHHHHhCcHHHHHHHhc
Confidence 3445667788999999999999998665 7788 78999999985
No 92
>PF10815 ComZ: ComZ; InterPro: IPR024558 ComZ, which contains a leucine zipper motif, negatively regulates transcription of the ComG operon [].
Probab=26.76 E-value=1.7e+02 Score=18.37 Aligned_cols=35 Identities=23% Similarity=0.308 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHhh
Q psy7895 14 TLQESLDELIQYG-TITPTLAMKVLLQFDKSINGAL 48 (108)
Q Consensus 14 aL~dtLdeli~~~-~Is~~la~kVl~~FDk~i~~~L 48 (108)
.|-++=.+|-..| .+|++...-+++-|=++|+++-
T Consensus 13 ~lPEak~~L~k~GIeLsme~~qP~m~L~~~VM~eAY 48 (56)
T PF10815_consen 13 YLPEAKEELDKKGIELSMEMLQPLMQLLTKVMNEAY 48 (56)
T ss_pred HhHHHHHHHHHcCccCCHHHHHHHHHHHHHHHHHHH
Confidence 4567778888888 7999999999999999999984
No 93
>PTZ00107 hexokinase; Provisional
Probab=26.74 E-value=1.7e+02 Score=25.15 Aligned_cols=38 Identities=13% Similarity=0.086 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchh
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSK 51 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~ 51 (108)
.....++++++...++.+.-..|...|...|.+-|++.
T Consensus 6 ~~~~~~~~~~~~f~~~~~~L~~i~~~f~~em~~GL~~~ 43 (464)
T PTZ00107 6 KQRVRLASLVNQFTMSKEKLKELVDYFLYELVEGLEAH 43 (464)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhcc
Confidence 34678999999999999999999999999999999875
No 94
>PLN02668 indole-3-acetate carboxyl methyltransferase
Probab=26.21 E-value=75 Score=26.75 Aligned_cols=22 Identities=27% Similarity=0.425 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHCCCCCHHHHH
Q psy7895 13 NTLQESLDELIQYGTITPTLAM 34 (108)
Q Consensus 13 ~aL~dtLdeli~~~~Is~~la~ 34 (108)
..|.++|++|+.+|.|+++-..
T Consensus 257 ~~l~~al~dlv~eGlI~eek~d 278 (386)
T PLN02668 257 THFQDAWDDLVQEGLVTSEKRD 278 (386)
T ss_pred HHHHHHHHHHHHcCCCCHHHHh
Confidence 3489999999999999998654
No 95
>cd04371 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
Probab=26.09 E-value=75 Score=19.54 Aligned_cols=51 Identities=24% Similarity=0.253 Sum_probs=35.0
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccC-ceeEe
Q psy7895 4 QLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKS-RLTFK 59 (108)
Q Consensus 4 ~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vks-k~~~K 59 (108)
..|+++-.|..+.+-|-+.... .+.+.|..+.+.+= ..-+-.+|.. +..|.
T Consensus 23 ~~~~~~F~G~e~v~WL~~~~~~--~~r~ea~~~~~~ll---~~g~i~~v~~~~~~F~ 74 (81)
T cd04371 23 KTYPNCFTGSELVDWLLDNLEA--ITREEAVELGQALL---KHGLIHHVSDDKHTFR 74 (81)
T ss_pred EECCceeEcHHHHHHHHHhCCC--CCHHHHHHHHHHHH---HCCCEEEeCCCCCccc
Confidence 4578888899888888777544 89999998887763 2333344544 55555
No 96
>cd04443 DEP_GPR155 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in GPR155-like proteins. GRP155-like proteins, also known as PGR22, contain an N-terminal permease domain, a central transmembrane region and a C-terminal DEP domain. They are orphan receptors of the class B G protein-coupled receptors. Their function is unknown.
Probab=26.08 E-value=1.9e+02 Score=18.98 Aligned_cols=59 Identities=19% Similarity=0.222 Sum_probs=41.8
Q ss_pred HHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchhccCceeEeccccceeee
Q psy7895 4 QLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRF 68 (108)
Q Consensus 4 ~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~ 68 (108)
..|+++-+|..|.|=|-+. ....|.+.|..+.+.+ +..-+-.+|..+..||+|. .-|||
T Consensus 25 ~~y~~cF~GselVdWL~~~--~~~~sR~eAv~lg~~L---l~~G~i~HV~~~~~F~D~~-~~YrF 83 (83)
T cd04443 25 RTYKGVFCGCDLVSWLIEV--GLAQDRGEAVLYGRRL---LQGGVLQHITNEHHFRDEN-LLYRF 83 (83)
T ss_pred eeccccccHHHHHHHHHHc--CCCCCHHHHHHHHHHH---HHCCCEEecCCCcCEecCC-eeEeC
Confidence 5688899999888765542 3357888887776543 4555556788899999654 56775
No 97
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=26.07 E-value=65 Score=21.86 Aligned_cols=22 Identities=23% Similarity=0.135 Sum_probs=18.3
Q ss_pred HHHHHHHHHCCCCCHHHHHHHH
Q psy7895 16 QESLDELIQYGTITPTLAMKVL 37 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kVl 37 (108)
+-.||.|+++|.|+.+.+..|-
T Consensus 18 ~plLD~Ll~n~~it~E~y~~V~ 39 (85)
T cd08324 18 QCLVDNLLKNDYFSTEDAEIVC 39 (85)
T ss_pred HHHHHHHhccCCccHHHHHHHH
Confidence 4569999999999999887664
No 98
>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=25.42 E-value=1.5e+02 Score=21.16 Aligned_cols=38 Identities=8% Similarity=0.160 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 13 NTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 13 ~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
+.+.+..+.+-+...+|+..+..||+.+=..|.+.|++
T Consensus 31 mt~~el~~~Ia~~s~~s~~dv~~vl~~l~~~i~~~L~~ 68 (145)
T TIGR01201 31 IDFEEIAELIAEESSLSPGDVKGIIDRLAYVLRRELAN 68 (145)
T ss_pred cCHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhC
Confidence 34555555666667899999999999999999999977
No 99
>PRK00106 hypothetical protein; Provisional
Probab=25.28 E-value=1.4e+02 Score=26.34 Aligned_cols=44 Identities=16% Similarity=0.296 Sum_probs=29.6
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 3 YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 3 y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
|.-+|+-.- .-||..|+.+|+|.|.=.+.|.++--+-|.+.+.+
T Consensus 273 fdpvRReiA----r~~le~Li~dgrIhp~rIEe~v~k~~~e~~~~i~~ 316 (535)
T PRK00106 273 FDPIRREIA----RMTLESLIKDGRIHPARIEELVEKNRLEMDNRIRE 316 (535)
T ss_pred CChHHHHHH----HHHHHHHHHcCCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 555665433 45788999999999988777666555555544433
No 100
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=25.24 E-value=2e+02 Score=19.50 Aligned_cols=31 Identities=19% Similarity=0.214 Sum_probs=25.2
Q ss_pred HHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 20 DELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 20 deli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
+.+-+...|+...+..+++.|=..|.++|.+
T Consensus 9 ~~ia~~~~l~k~~a~~~v~~~~~~i~~aL~~ 39 (94)
T COG0776 9 DAIAEKAGLSKKDAEEAVDAFLEEITEALAK 39 (94)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHHHHc
Confidence 3333444499999999999999999999977
No 101
>PF11630 DUF3254: Protein of unknown function (DUF3254); InterPro: IPR024509 Anti-lipopolysaccharide factor binds to bacterial LPS and may specifically inhibit the LPS-mediated activation of the hemolymph coagulation. It has a strong antibacterial effect, especially on the growth of Gram-negative bacteria [,]. This entry also includes the antibacterial protein Scygonadin, which has antibacterial activity against the Gram-positive bacterium Micrococcus luteus [].; PDB: 2JOB_A.
Probab=25.16 E-value=1.5e+02 Score=20.72 Aligned_cols=31 Identities=23% Similarity=0.221 Sum_probs=23.4
Q ss_pred HhhhHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q psy7895 7 RNTTLGNTLQESLDELIQYGTITPTLAMKVL 37 (108)
Q Consensus 7 R~stlG~aL~dtLdeli~~~~Is~~la~kVl 37 (108)
|...++.|..|=...-++.|.||++.|..-|
T Consensus 69 ~sg~~~~a~rDFv~kA~~~gLiT~eeA~~wL 99 (100)
T PF11630_consen 69 RSGVVRKATRDFVRKAFQAGLITEEEAQPWL 99 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHT-S-HHHHHHHH
T ss_pred CcchhhHHHHHHHHHHHHcCCccHHHHHHhh
Confidence 4456788888888888899999999997654
No 102
>cd08785 CARD_CARD9-like Caspase activation and recruitment domain of CARD9 and related proteins. Caspase activation and recruitment domain (CARD) found in CARD9, CARD14 (CARMA2), CARD10 (CARMA3), CARD11 (CARMA1) and BCL10. BCL10 (B-cell lymphoma 10), together with Malt1 (mucosa-associated lymphoid tissue-lymphoma-translocation gene 1), are integral components of the CBM signalosome. They associate with CARD9 to form M-CBM (CBM complex in myeloid immune cells), and with CARD11 to form L-CBM (CBM complex in lymphoid immune cells), which mediates activation of NF-kB and MAPK by ITAM-coupled receptors expressed on immune cells. BCL10/Malt1 also associates with CARD10, which is more widely expressed and is not restricted to hematopoietic cells, to play a role in GPCR-induced NF-kB activation. CARD14 has also been shown to associate with BCL10. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inf
Probab=25.08 E-value=1.1e+02 Score=20.36 Aligned_cols=23 Identities=17% Similarity=-0.008 Sum_probs=20.7
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHH
Q psy7895 16 QESLDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kVl~ 38 (108)
.+.+|-|++.|.+|++-++.|..
T Consensus 19 ~~l~d~L~q~~VLt~~d~EeI~~ 41 (86)
T cd08785 19 SRLTPYLRQCKVLDEQDEEEVLS 41 (86)
T ss_pred HHHHHHHHhcCCCCHHHHHHHhC
Confidence 45789999999999999999987
No 103
>TIGR02148 Fibro_Slime fibro-slime domain. This model represents a conserved region of about 90 amino acids, shared in at least 4 distinct large putative proteins from the slime mold Dictyostelium discoideum and 10 proteins from the rumen bacterium Fibrobacter succinogenes, and in no other species so far. We propose here the name fibro-slime domain
Probab=25.08 E-value=63 Score=22.06 Aligned_cols=29 Identities=21% Similarity=0.421 Sum_probs=19.1
Q ss_pred eEeccccceeeeeCcEEEEEEcCeEEEec
Q psy7895 57 TFKSGKLNTYRFCDNVWTFVLTDVEFREV 85 (108)
Q Consensus 57 ~~K~G~L~tYr~cDnVWtF~lkd~~f~~~ 85 (108)
+.++|.--+++=-|+||.|+=.-..+.+.
T Consensus 15 ~Y~~~e~F~F~GDDDvWVFIn~kLv~DlG 43 (90)
T TIGR02148 15 KYVGGQYFEFRGDDDVWVFINNKLVVDIG 43 (90)
T ss_pred EEcCCcEEEEEcCCeEEEEECCEEEEEcc
Confidence 44544444555579999999666666655
No 104
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=24.76 E-value=62 Score=21.22 Aligned_cols=16 Identities=38% Similarity=0.513 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHCCCC
Q psy7895 13 NTLQESLDELIQYGTI 28 (108)
Q Consensus 13 ~aL~dtLdeli~~~~I 28 (108)
..+..+|++|+.+|.|
T Consensus 80 ~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 80 NEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhCCeE
Confidence 4578899999999986
No 105
>PRK10449 heat-inducible protein; Provisional
Probab=24.33 E-value=1.7e+02 Score=20.72 Aligned_cols=42 Identities=17% Similarity=0.267 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhhchhccCceeEeccccceeeeeCcEEEEEEcCeE
Q psy7895 37 LLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVE 81 (108)
Q Consensus 37 l~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDnVWtF~lkd~~ 81 (108)
+++.+..+.++|++. .+..+. |.--+.+--+..++|-.+|++
T Consensus 98 ~~~~E~~~~~~L~~~--~~~~~~-g~~L~L~~~~~~l~f~~~~~~ 139 (140)
T PRK10449 98 LNELDNTISEMLKKG--AQVDLT-ANQLTLATAKQTLMYKLADLV 139 (140)
T ss_pred HHHHHHHHHHHHhcC--ceEEEc-CCEEEEEcCCcEEEEEEhhhc
Confidence 457788888888774 444566 444455667889999988863
No 106
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.22 E-value=83 Score=22.53 Aligned_cols=20 Identities=30% Similarity=0.499 Sum_probs=16.0
Q ss_pred HHHHHHCCCCCHHHHHHHHH
Q psy7895 19 LDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 19 Ldeli~~~~Is~~la~kVl~ 38 (108)
+-.+++.|.|+|+-|.++|.
T Consensus 102 i~~qle~Gei~peeA~~~L~ 121 (122)
T COG3877 102 IIDQLEKGEISPEEAIKMLN 121 (122)
T ss_pred HHHHHHcCCCCHHHHHHHhc
Confidence 33456789999999999885
No 107
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=24.12 E-value=49 Score=18.82 Aligned_cols=16 Identities=44% Similarity=0.667 Sum_probs=12.8
Q ss_pred HHHHHHHHHCCCCCHH
Q psy7895 16 QESLDELIQYGTITPT 31 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~ 31 (108)
.+.|.+|+++|.|+++
T Consensus 16 ~~el~~l~~~g~i~~~ 31 (45)
T PF14237_consen 16 LEELRQLISSGEIDPD 31 (45)
T ss_pred HHHHHHHHHcCCCCCC
Confidence 4678889999999874
No 108
>PF12550 GCR1_C: Transcriptional activator of glycolytic enzymes; InterPro: IPR022210 This domain family is found in eukaryotes, and is approximately 80 amino acids in length. This family is activates the transcription of glycolytic enzymes.
Probab=24.05 E-value=1.6e+02 Score=18.88 Aligned_cols=29 Identities=14% Similarity=0.241 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q psy7895 12 GNTLQESLDELIQYGTITPTLAMKVLLQF 40 (108)
Q Consensus 12 G~aL~dtLdeli~~~~Is~~la~kVl~~F 40 (108)
-..+.+.+..+....-++++.|..+++.+
T Consensus 52 RK~Ii~~I~~l~~~~g~~~~~ai~~le~~ 80 (81)
T PF12550_consen 52 RKVIIDFIERLANERGISEEEAIEILEEI 80 (81)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 45778888888888889999999888765
No 109
>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=23.84 E-value=96 Score=23.24 Aligned_cols=25 Identities=32% Similarity=0.537 Sum_probs=21.4
Q ss_pred HHHHHHHHCC-CCCHHHHHHHHHHHH
Q psy7895 17 ESLDELIQYG-TITPTLAMKVLLQFD 41 (108)
Q Consensus 17 dtLdeli~~~-~Is~~la~kVl~~FD 41 (108)
-.||||++.| .+|.++.+.+|..-+
T Consensus 130 pild~LI~~GF~iS~~~~eeiL~~~~ 155 (157)
T COG2405 130 PILDELIEKGFRISRSILEEILRKLQ 155 (157)
T ss_pred HHHHHHHHhcCcccHHHHHHHHHHhc
Confidence 5799999988 899999999987654
No 110
>COG0541 Ffh Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=23.79 E-value=1.9e+02 Score=25.18 Aligned_cols=39 Identities=23% Similarity=0.310 Sum_probs=32.5
Q ss_pred hhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHh
Q psy7895 9 TTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGA 47 (108)
Q Consensus 9 stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~ 47 (108)
.+||..|+++|.-+...+.|+++....++.+-.+|.-++
T Consensus 3 e~L~~~l~~~l~kl~g~~~i~E~~i~e~~reir~ALLeA 41 (451)
T COG0541 3 ESLSDRLSNALKKLRGKGRITEKDVKEALREIRRALLEA 41 (451)
T ss_pred HHHHHHHHHHHHHhhCCCcCCHHHHHHHHHHHHHHHHhc
Confidence 368999999999999999999998888777766665544
No 111
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=23.69 E-value=2.1e+02 Score=18.49 Aligned_cols=30 Identities=27% Similarity=0.413 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLLQFDKS 43 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~~FDk~ 43 (108)
.|-+.+.+|+.+|.|+.-.+...|..+.+.
T Consensus 28 ~lP~~i~~~v~~g~~~~~~a~~~L~~~~~~ 57 (93)
T PF08535_consen 28 DLPEEIKELVRSGRISDIRALYELRKLAEK 57 (93)
T ss_dssp S--HHHHHHHHTTS---HHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHcCCCchHHHHHHHHHHHHh
Confidence 477889999999999877777556554433
No 112
>PLN02596 hexokinase-like
Probab=23.68 E-value=2.9e+02 Score=24.05 Aligned_cols=40 Identities=10% Similarity=0.042 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhchh
Q psy7895 12 GNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSK 51 (108)
Q Consensus 12 G~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~~ 51 (108)
=..+.++|+++.+...++.+.-.+|-..|-+.|..-|+..
T Consensus 35 ~~~~~~~l~~~~~~f~~~~~~L~~i~~~f~~em~~GL~~~ 74 (490)
T PLN02596 35 WKHTQRILRKFARECATPVSKLWEVADALVSDMTASLTAE 74 (490)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhccC
Confidence 3478889999999999999999999999999999999764
No 113
>cd01733 LSm10 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=23.63 E-value=1.8e+02 Score=18.78 Aligned_cols=30 Identities=17% Similarity=0.297 Sum_probs=23.1
Q ss_pred ccCceeEeccccceeeeeCcEEEEEEcCeEEEec
Q psy7895 52 VKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFREV 85 (108)
Q Consensus 52 vksk~~~K~G~L~tYr~cDnVWtF~lkd~~f~~~ 85 (108)
.|+...++ |.| ..||+-..+.|+|+++...
T Consensus 26 LKng~~~~-G~L---~~vD~~MNl~L~~~~~~~~ 55 (78)
T cd01733 26 LRNETTVT-GRI---ASVDAFMNIRLAKVTIIDR 55 (78)
T ss_pred ECCCCEEE-EEE---EEEcCCceeEEEEEEEEcC
Confidence 46666777 776 4689999999999998754
No 114
>PF10664 NdhM: Cyanobacterial and plastid NDH-1 subunit M; InterPro: IPR018922 The NADH dehydrogenase I complex shuttles electrons from an unknown electron donor, via FMN and iron-sulphur (Fe-S) centres, to quinones in the respiratory and/or the photosynthetic chain. The immediate electron acceptor for the enzyme in plants is believed to be plastoquinone. The NADH dehydrogenase I complex couples the redox reaction to proton translocation, and thus conserves the redox energy in a proton gradient. This entry represents subunit M of the NADH dehydrogenase I complex in cyanobacteria and plant chloroplasts []. ; GO: 0016655 oxidoreductase activity, acting on NADH or NADPH, quinone or similar compound as acceptor, 0055114 oxidation-reduction process
Probab=23.47 E-value=24 Score=24.87 Aligned_cols=29 Identities=31% Similarity=0.486 Sum_probs=24.4
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q psy7895 10 TLGNTLQESLDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 10 tlG~aL~dtLdeli~~~~Is~~la~kVl~ 38 (108)
-||.-|..-+-.|+++|.|+=.+.-+|++
T Consensus 70 rIGSdLE~~iR~LLq~GeisYNl~~RVlN 98 (108)
T PF10664_consen 70 RIGSDLEHFIRSLLQAGEISYNLDSRVLN 98 (108)
T ss_pred HhccHHHHHHHHHHHCCceeeCCCcceec
Confidence 48999999999999999998777666653
No 115
>TIGR03573 WbuX N-acetyl sugar amidotransferase. This enzyme has been implicated in the formation of the acetamido moiety (sugar-NC(=NH)CH3) which is found on some exopolysaccharides and is positively charged at neutral pH. The reaction involves ligation of ammonia with a sugar N-acetyl group, displacing water. In E. coli (O145 strain) and Pseudomonas aeruginosa (O12 strain) this gene is known as wbuX and ifnA respectively and likely acts on sialic acid. In Campylobacter jejuni, the gene is known as pseA and acts on pseudaminic acid in the process of flagellin glycosylation. In other Pseudomonas strains and various organisms it is unclear what the identity of the sugar substrate is, and in fact, the phylogenetic tree of this family sports a considerably deep branching suggestive of possible major differences in substrate structure. Nevertheless, the family is characterized by a conserved tetracysteine motif (CxxC.....[GN]xCxxC) possibly indicative of a metal binding site, as well as an
Probab=23.35 E-value=84 Score=25.40 Aligned_cols=41 Identities=22% Similarity=0.346 Sum_probs=32.0
Q ss_pred hHHHHhhhHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Q psy7895 3 YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSI 44 (108)
Q Consensus 3 y~lYR~stlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i 44 (108)
|-+|+..-.|.+- +-+-.+|..|+||.+.|.+.+++||--.
T Consensus 279 y~~~~KfG~~~~~-~~~s~~IR~G~itReeal~~v~~~d~~~ 319 (343)
T TIGR03573 279 YLKYLKFGFGRAT-DHASIDIRSGRITREEAIELVKEYDGEF 319 (343)
T ss_pred HHHHhhcCCCcCc-hHHHHHHHcCCCCHHHHHHHHHHhcccc
Confidence 5666666667554 3456789999999999999999997654
No 116
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=23.19 E-value=58 Score=23.94 Aligned_cols=20 Identities=20% Similarity=0.508 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHCCCCCHH
Q psy7895 12 GNTLQESLDELIQYGTITPT 31 (108)
Q Consensus 12 G~aL~dtLdeli~~~~Is~~ 31 (108)
=.++.+.++||++.|.|.|.
T Consensus 14 ~~~~~~~v~~ll~~G~I~~~ 33 (210)
T cd03715 14 REGITPHIQELLEAGILVPC 33 (210)
T ss_pred HHHHHHHHHHHHHCCCeECC
Confidence 46788999999999999875
No 117
>PF10689 DUF2496: Protein of unknown function (DUF2496); InterPro: IPR019630 This family consists of proteins from Gammaproteobacteria species. Many members are annotated as being like the Escherichia coli protein; YbaM.
Probab=22.80 E-value=1.8e+02 Score=17.39 Aligned_cols=27 Identities=26% Similarity=0.238 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHHH
Q psy7895 13 NTLQESLDELIQYGTITPTLAMKVLLQ 39 (108)
Q Consensus 13 ~aL~dtLdeli~~~~Is~~la~kVl~~ 39 (108)
..|.--|-.|++++.|.|+.+.+-|+.
T Consensus 9 vkLAVDLI~LLE~n~i~p~~aL~ALeI 35 (44)
T PF10689_consen 9 VKLAVDLIYLLESNEIDPETALAALEI 35 (44)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHH
Confidence 345556778999999999999877654
No 118
>PF05609 LAP1C: Lamina-associated polypeptide 1C (LAP1C); InterPro: IPR008662 This entry contains Rattus norvegicus LAP1C proteins and several uncharacterised highly related sequences from both Mus sp. and humans. Lamina-associated polypeptide 1s (LAP1s), also known as Torsin-1A-interacting protein 1, are type 2 integral membrane proteins with a single membrane-spanning region of the inner nuclear membrane []. LAP1s bind to both A- and B-type lamins and have a putative role in the membrane attachment and assembly of the nuclear lamina [].
Probab=22.68 E-value=88 Score=27.18 Aligned_cols=44 Identities=20% Similarity=0.438 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHHHHHHHhhchhccCce-----eEecc-ccceeeeeCc
Q psy7895 28 ITPTLAMKVLLQFDKSINGALPSKVKSRL-----TFKSG-KLNTYRFCDN 71 (108)
Q Consensus 28 Is~~la~kVl~~FDk~i~~~L~~~vksk~-----~~K~G-~L~tYr~cDn 71 (108)
-....+..|-..+|..+..+|.+-.+.-+ .+.+| .|..|+|||+
T Consensus 331 ~~~~dsd~vK~~vD~~l~~~f~~~~~aavv~~~e~lpp~stlify~YCD~ 380 (465)
T PF05609_consen 331 KAHQDSDQVKLEVDNELSSGFENGQKAAVVHRFESLPPGSTLIFYKYCDH 380 (465)
T ss_pred ccccChHHHHHHHHHHHHHHhhCCCeeEEeehhhhCCCchhHHHHHhccC
Confidence 34456678888999999999987322221 22233 4799999998
No 119
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=22.49 E-value=54 Score=23.92 Aligned_cols=27 Identities=15% Similarity=0.329 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHHH
Q psy7895 12 GNTLQESLDELIQYGTITPTLAMKVLL 38 (108)
Q Consensus 12 G~aL~dtLdeli~~~~Is~~la~kVl~ 38 (108)
|.+-.++.+++-.+.+++|++...|+.
T Consensus 104 G~s~eei~~ki~~e~kl~pd~i~yi~~ 130 (131)
T PF08004_consen 104 GKSEEEIAEKISRETKLSPDMIKYILK 130 (131)
T ss_pred CCCHHHHHHHHHHhhcCCHHHHHHHhc
Confidence 667777777788888888888777764
No 120
>cd07367 CarBb CarBb is the B subunit of the Class III Extradiol ring-cleavage dioxygenase, 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBb is the B subunit of 2-aminophenol 1,6-dioxygenase (CarB), which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. It is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, it has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=22.47 E-value=36 Score=26.64 Aligned_cols=44 Identities=25% Similarity=0.315 Sum_probs=33.4
Q ss_pred HhhhHHHHHHHHHHH---------HHHCCCCCHHH----HHHHHHHHHHHHHHhhch
Q psy7895 7 RNTTLGNTLQESLDE---------LIQYGTITPTL----AMKVLLQFDKSINGALPS 50 (108)
Q Consensus 7 R~stlG~aL~dtLde---------li~~~~Is~~l----a~kVl~~FDk~i~~~L~~ 50 (108)
|.-.+|.+|.+++++ +|-+|-+|-++ ...+-.+||+.+.+.|.+
T Consensus 151 ~~~~lG~al~~~i~~~~~~d~rV~iiaSGgLSH~l~~~~~~~~~~efD~~i~~~l~~ 207 (268)
T cd07367 151 RCWALGKVLAQYVEKRRPAGERVAVIAAGGLSHWLGVPRHGEVNEAFDRMFLDLLEG 207 (268)
T ss_pred HHHHHHHHHHHHHHhcCCCCCcEEEEEcccccCCCCCCcccccCHHHHHHHHHHHHc
Confidence 444699999999888 56677777666 223457999999999876
No 121
>TIGR01420 pilT_fam pilus retraction protein PilT. This model represents the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction. Members of this family may be found in some species that type IV pili but have related structures for DNA uptake and natural transformation.
Probab=22.42 E-value=98 Score=24.91 Aligned_cols=26 Identities=27% Similarity=0.295 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHH
Q psy7895 12 GNTLQESLDELIQYGTITPTLAMKVL 37 (108)
Q Consensus 12 G~aL~dtLdeli~~~~Is~~la~kVl 37 (108)
|.+|.+.+.+++.+|.|+++-+.++.
T Consensus 313 ~~t~~~~~~~~~~~g~~~~~~~~~~~ 338 (343)
T TIGR01420 313 MQTFDQHLAQLYRKGLITLEDALEAA 338 (343)
T ss_pred ChhHHHHHHHHHHcCCCCHHHHHHhc
Confidence 46889999999999999999887754
No 122
>PRK03195 hypothetical protein; Provisional
Probab=22.36 E-value=1.2e+02 Score=23.06 Aligned_cols=59 Identities=15% Similarity=0.288 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHCCCCCHHHHH-HHHHHHHHHHHHhhchhccCceeEeccccceeeeeCc-EEE
Q psy7895 13 NTLQESLDELIQYGTITPTLAM-KVLLQFDKSINGALPSKVKSRLTFKSGKLNTYRFCDN-VWT 74 (108)
Q Consensus 13 ~aL~dtLdeli~~~~Is~~la~-kVl~~FDk~i~~~L~~~vksk~~~K~G~L~tYr~cDn-VWt 74 (108)
.+|.++|++|+.+.-....++. .|+......+-+.++.+.+. ..|+.|.|.. .||+ +|.
T Consensus 73 q~Lg~il~~l~~~~gW~~~l~~~~V~~~W~~IVG~~IA~ht~P-~~i~~gvL~V--~~~SsaWA 133 (186)
T PRK03195 73 QPLGALARDLAKKRGWSAKVAEGTVLGQWSAVVGEQIAAHATP-TALNDGVLSV--SAESTAWA 133 (186)
T ss_pred ccHHHHHHHHHHhcCchhhhhHhHHHHHhHHHHCHHHHhhcce-eEEECCEEEE--EeCCHHHH
Confidence 4688899999988887766654 79999999999999886543 4556455432 3443 554
No 123
>KOG3438|consensus
Probab=22.24 E-value=1.9e+02 Score=20.31 Aligned_cols=30 Identities=30% Similarity=0.457 Sum_probs=24.4
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
Q psy7895 10 TLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSING 46 (108)
Q Consensus 10 tlG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~ 46 (108)
+--..|...|+||++ +-..|...|+++|.+
T Consensus 69 ~A~evl~kgl~el~~-------~c~~v~~kF~~~i~~ 98 (105)
T KOG3438|consen 69 PAVEVLKKGLEELMQ-------LCDHVRSKFEEEIEE 98 (105)
T ss_pred cchHHHHHHHHHHHH-------HHHHHHHHHHHHHHH
Confidence 344678999999975 788999999999875
No 124
>PRK13717 conjugal transfer protein TrbI; Provisional
Probab=22.14 E-value=3.2e+02 Score=19.87 Aligned_cols=37 Identities=8% Similarity=0.272 Sum_probs=30.3
Q ss_pred HHHHHHHHH---CCCCCHHHHHHHHHHHHHHHHHhhchhc
Q psy7895 16 QESLDELIQ---YGTITPTLAMKVLLQFDKSINGALPSKV 52 (108)
Q Consensus 16 ~dtLdeli~---~~~Is~~la~kVl~~FDk~i~~~L~~~v 52 (108)
..|||.+++ +..+|+++.+.....|..++...|...-
T Consensus 53 K~Tld~F~~Q~~~~~lte~q~e~lt~rF~~aL~~~L~~yq 92 (128)
T PRK13717 53 KQTVDAFFDSASQKQLSEAQSKALSARFNTALEASLQAWQ 92 (128)
T ss_pred HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555544 5689999999999999999999998864
No 125
>PF14076 DUF4258: Domain of unknown function (DUF4258)
Probab=22.08 E-value=1.4e+02 Score=17.69 Aligned_cols=23 Identities=13% Similarity=0.174 Sum_probs=17.9
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHHH
Q psy7895 16 QESLDELIQYGTITPTLAMKVLLQ 39 (108)
Q Consensus 16 ~dtLdeli~~~~Is~~la~kVl~~ 39 (108)
..|++.|.+.| |+.+....+|..
T Consensus 4 ~Ha~~rm~eR~-Is~~~I~~~l~~ 26 (73)
T PF14076_consen 4 KHARERMQERG-ISEEDIEDALEN 26 (73)
T ss_pred HHHHHHHHhCC-CCHHHHHHHHhc
Confidence 35788888777 999988888854
No 126
>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ. Members of this protein family are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase of a type-IV secretion-like system of obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii (TIGR02524).
Probab=21.77 E-value=85 Score=26.07 Aligned_cols=26 Identities=19% Similarity=0.192 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHH
Q psy7895 12 GNTLQESLDELIQYGTITPTLAMKVL 37 (108)
Q Consensus 12 G~aL~dtLdeli~~~~Is~~la~kVl 37 (108)
|.++.+.+.+|+.+|.|+++.+.+++
T Consensus 342 ~~~~~~~~~~l~~~g~i~~~~~~~~~ 367 (372)
T TIGR02525 342 QRRIADQAWAMHQEGRIDEREAAEVI 367 (372)
T ss_pred CCCHHHHHHHHHHcCCCCHHHHHHHh
Confidence 56777778999999999999999886
No 127
>KOG3456|consensus
Probab=21.71 E-value=64 Score=23.07 Aligned_cols=11 Identities=45% Similarity=0.933 Sum_probs=8.9
Q ss_pred EEEEEecCCCC
Q psy7895 94 LKIVACDGKSS 104 (108)
Q Consensus 94 lKIVAcd~~~~ 104 (108)
=+|||||+...
T Consensus 78 ~RVV~CdGg~~ 88 (120)
T KOG3456|consen 78 GRVVACDGGTP 88 (120)
T ss_pred ceEEEecCCCC
Confidence 47999999864
No 128
>PF09687 PRESAN: Plasmodium RESA N-terminal; InterPro: IPR019111 The short, four-helical domain first identified in the Plasmodium export proteins PHISTa and PHISTc [] has been extended to become this six-helical PRESAC domain identified in the P. falciparum-specific RESA-type (Ring-infected erythrocyte surface antigen) proteins in association with the DnaJ domain. Overall, at least 67 proteins have been detected in P. falciparum with complete copies of the PRESAC domain. No versions of this domain were detected in other apicomplexan genera, suggesting that the domain was 'invented' after the divergence of the lineage leading to the genus Plasmodium undergoing a dramatic proliferation only in P. falciparum. A secondary structure-prediction derived from the multiple alignment of the PRESAC family reveals that it is composed of an all-helical fold with six conserved helical segments. There is some evidence it might localise to membranes [].
Probab=21.58 E-value=2.4e+02 Score=18.32 Aligned_cols=40 Identities=20% Similarity=0.184 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHhhch
Q psy7895 11 LGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPS 50 (108)
Q Consensus 11 lG~aL~dtLdeli~~~~Is~~la~kVl~~FDk~i~~~L~~ 50 (108)
+-.-|-.-+++|.....|+++...++|.+.-..|...|.+
T Consensus 45 m~~~L~~~~~~la~~~~ip~~~~~k~W~~c~~~i~~~l~~ 84 (129)
T PF09687_consen 45 MINKLWKYFEELAKKYNIPEEYKKKIWKECYEEITKELKK 84 (129)
T ss_pred HHHHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHHHHH
Confidence 5567888999999999999999999999999999888775
No 129
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=21.32 E-value=1.4e+02 Score=20.60 Aligned_cols=27 Identities=30% Similarity=0.073 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHH
Q psy7895 14 TLQESLDELIQYGTITPTLAMKVLLQF 40 (108)
Q Consensus 14 aL~dtLdeli~~~~Is~~la~kVl~~F 40 (108)
.|.+.|-+|--...|+|++..-|-+-|
T Consensus 53 ~Lv~~L~~lelg~~IPeelY~vVAEif 79 (92)
T COG2257 53 LLVELLLKLELGDEIPEELYEVVAEIF 79 (92)
T ss_pred HHHHHHHhccccccCCHHHHHHHHHHH
Confidence 588888888889999999999888877
No 130
>KOG3618|consensus
Probab=21.08 E-value=1.5e+02 Score=28.23 Aligned_cols=50 Identities=20% Similarity=0.422 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHhhchhccCcee--Ee-----------ccccceeeeeCcEEE
Q psy7895 25 YGTITPTLAMKVLLQFDKSINGALPSKVKSRLT--FK-----------SGKLNTYRFCDNVWT 74 (108)
Q Consensus 25 ~~~Is~~la~kVl~~FDk~i~~~L~~~vksk~~--~K-----------~G~L~tYr~cDnVWt 74 (108)
.+-..|+--..+|-+|-++|.+++..--++=.. |+ ||-+.|-+..-++|-
T Consensus 1153 ~~~~hp~EHl~~l~eFa~amq~Vvd~FN~dlL~Fnf~lrvG~NiGpvTAGVIGTtKLyYDIWG 1215 (1318)
T KOG3618|consen 1153 QDGSHPQEHLQILFEFAKAMQRVVDDFNNDLLWFNFKLRVGFNIGPVTAGVIGTTKLYYDIWG 1215 (1318)
T ss_pred cCCCChHHHHHHHHHHHHHHHHHHHHhhhhhhheeeeEEeeccccCccccccccceeeehhhc
Confidence 344577777899999999999997653222222 22 888888888889995
No 131
>PF05258 DUF721: Protein of unknown function (DUF721); InterPro: IPR007922 This family contains several actinomycete proteins of unknown function, and related sequences from other species.
Probab=20.88 E-value=1.7e+02 Score=17.94 Aligned_cols=39 Identities=13% Similarity=0.242 Sum_probs=24.9
Q ss_pred HHHHHHHHHHCCC-C-CHHHHHHHHHHHHHHHHHhhchhcc
Q psy7895 15 LQESLDELIQYGT-I-TPTLAMKVLLQFDKSINGALPSKVK 53 (108)
Q Consensus 15 L~dtLdeli~~~~-I-s~~la~kVl~~FDk~i~~~L~~~vk 53 (108)
|.+.|++++.... . ......++...+...+...++++.+
T Consensus 2 l~~~L~~~~~~~~~~~~~~~~~~l~~~w~~ivg~~l~~~~~ 42 (89)
T PF05258_consen 2 LGDLLEELLKKSGLKKRALQLARLQQNWKQIVGPELAQHTR 42 (89)
T ss_pred HHHHHHHHHhhhhHHHhhHHHHHHHHHHHHHhCHHHHccEE
Confidence 5566777765433 3 3455567777788888777776543
No 132
>PRK08132 FAD-dependent oxidoreductase; Provisional
Probab=20.85 E-value=3.5e+02 Score=22.76 Aligned_cols=39 Identities=21% Similarity=0.282 Sum_probs=24.2
Q ss_pred cccceeeeeCcEEEEEEcCeEEEecceEeecCcEEEEEecCCCC
Q psy7895 61 GKLNTYRFCDNVWTFVLTDVEFREVAEIARVNKLKIVACDGKSS 104 (108)
Q Consensus 61 G~L~tYr~cDnVWtF~lkd~~f~~~~~~~~~~~lKIVAcd~~~~ 104 (108)
-++..+...++-|+..+++. .+.+.+.++.| |+|||..+
T Consensus 147 ~~v~~i~~~~~~v~v~~~~~---~g~~~i~ad~v--VgADG~~S 185 (547)
T PRK08132 147 NKVTGLEQHDDGVTLTVETP---DGPYTLEADWV--IACDGARS 185 (547)
T ss_pred CEEEEEEEcCCEEEEEEECC---CCcEEEEeCEE--EECCCCCc
Confidence 34566666677777655431 11236777764 99998754
No 133
>PRK13358 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=20.44 E-value=54 Score=25.43 Aligned_cols=41 Identities=27% Similarity=0.444 Sum_probs=30.3
Q ss_pred hHHHHHHHHHHH---------HHHCCCCCHHHH----HHHHHHHHHHHHHhhch
Q psy7895 10 TLGNTLQESLDE---------LIQYGTITPTLA----MKVLLQFDKSINGALPS 50 (108)
Q Consensus 10 tlG~aL~dtLde---------li~~~~Is~~la----~kVl~~FDk~i~~~L~~ 50 (108)
.+|.+|.+++++ +|-+|-+|-.+. .-.-++||+.+.+.+.+
T Consensus 154 ~lG~al~~~~~~~~~~~~rvlvIaSGdlSH~l~~~~~~~~~~~fD~~~~~~i~~ 207 (269)
T PRK13358 154 ALGEVIRQAVEKDRPADERVAVIGTGGLSHWLGVPEHGEVNEDFDRMVMDALVS 207 (269)
T ss_pred HHHHHHHHHHHhhCCCCCcEEEEecCCccCCCCCccccccHHHHHHHHHHHHHc
Confidence 499999999987 455665555443 33457999999998876
No 134
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.00 E-value=2.6e+02 Score=19.23 Aligned_cols=27 Identities=33% Similarity=0.409 Sum_probs=21.0
Q ss_pred hHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q psy7895 10 TLGNTLQESLDELIQYGTITPTLAMKVL 37 (108)
Q Consensus 10 tlG~aL~dtLdeli~~~~Is~~la~kVl 37 (108)
|.-+|| +.|+=|...|.|+|+.|..+-
T Consensus 46 T~EEAl-Eii~yleKrGEi~~E~A~~L~ 72 (98)
T COG4003 46 TEEEAL-EIINYLEKRGEITPEMAKALR 72 (98)
T ss_pred cHHHHH-HHHHHHHHhCCCCHHHHHHHH
Confidence 444454 789999999999999987653
Done!