Query psy12346
Match_columns 107
No_of_seqs 141 out of 1070
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 16:41:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12346.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12346hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0229 Conserved domain frequ 100.0 3.2E-54 6.9E-59 314.0 9.8 97 10-106 2-98 (140)
2 TIGR00357 methionine-R-sulfoxi 100.0 8.6E-53 1.9E-57 305.6 10.7 96 11-106 1-96 (134)
3 PRK00222 methionine sulfoxide 100.0 3.3E-52 7.2E-57 304.9 10.7 97 10-106 3-99 (142)
4 PF01641 SelR: SelR domain; I 100.0 2.8E-52 6E-57 299.6 8.3 93 14-106 1-93 (124)
5 KOG0856|consensus 100.0 3E-50 6.6E-55 294.1 8.6 102 5-106 9-110 (146)
6 PRK05508 methionine sulfoxide 100.0 2E-47 4.4E-52 272.8 9.1 85 19-106 2-86 (119)
7 PRK14018 trifunctional thiored 100.0 4E-45 8.7E-50 309.8 10.6 96 11-106 379-474 (521)
8 PRK05550 bifunctional methioni 100.0 1.4E-42 3.1E-47 276.7 8.7 89 15-106 1-89 (283)
9 PF09855 DUF2082: Nucleic-acid 81.2 1.1 2.5E-05 28.9 1.8 43 51-106 1-43 (64)
10 COG1645 Uncharacterized Zn-fin 81.2 0.49 1.1E-05 34.7 0.0 23 51-73 29-52 (131)
11 TIGR01384 TFS_arch transcripti 80.5 2.9 6.3E-05 28.1 3.7 56 48-107 14-70 (104)
12 PRK00420 hypothetical protein; 75.6 1.4 3.1E-05 31.3 1.1 23 51-73 24-48 (112)
13 PF10122 Mu-like_Com: Mu-like 70.7 3.3 7.2E-05 25.9 1.7 11 97-107 22-32 (51)
14 PF06677 Auto_anti-p27: Sjogre 69.9 1.9 4.1E-05 25.5 0.5 13 52-64 19-31 (41)
15 PF03226 Yippee-Mis18: Yippee 67.3 4.2 9E-05 27.0 1.8 27 50-76 2-29 (96)
16 PRK08624 hypothetical protein; 66.5 7.7 0.00017 32.8 3.6 54 13-66 3-78 (373)
17 PF08271 TF_Zn_Ribbon: TFIIB z 65.6 4.1 8.8E-05 23.6 1.3 30 45-76 14-43 (43)
18 PRK00423 tfb transcription ini 58.3 9.6 0.00021 30.6 2.7 32 45-78 25-56 (310)
19 smart00778 Prim_Zn_Ribbon Zinc 53.6 13 0.00029 21.5 2.1 19 37-57 14-32 (37)
20 PF11781 RRN7: RNA polymerase 52.3 6.6 0.00014 22.4 0.6 21 39-59 14-34 (36)
21 COG1405 SUA7 Transcription ini 50.2 13 0.00027 30.2 2.1 31 44-76 14-44 (285)
22 COG3791 Uncharacterized conser 49.7 7.2 0.00016 27.7 0.6 21 43-63 62-82 (133)
23 PF07295 DUF1451: Protein of u 48.8 8.7 0.00019 28.3 1.0 14 47-60 109-122 (146)
24 PF13719 zinc_ribbon_5: zinc-r 46.9 12 0.00026 21.2 1.1 19 88-106 14-32 (37)
25 PF01352 KRAB: KRAB box; Inte 46.3 24 0.00053 20.6 2.4 21 9-30 7-27 (41)
26 PRK12495 hypothetical protein; 45.8 7.6 0.00017 30.9 0.3 16 46-61 38-53 (226)
27 PF13248 zf-ribbon_3: zinc-rib 45.8 9.6 0.00021 19.9 0.6 21 52-73 4-24 (26)
28 cd02181 GH16_fungal_Lam16A_glu 45.6 6.9 0.00015 32.0 -0.0 19 60-78 82-102 (293)
29 PHA02540 61 DNA primase; Provi 42.8 13 0.00028 30.9 1.2 10 49-58 54-63 (337)
30 cd04984 IgV_L_lambda Immunoglo 42.5 16 0.00035 23.5 1.4 12 45-56 72-83 (98)
31 PRK04179 rpl37e 50S ribosomal 42.4 14 0.0003 24.0 1.0 27 49-75 16-43 (62)
32 TIGR02098 MJ0042_CXXC MJ0042 f 42.2 17 0.00038 20.0 1.3 10 98-107 24-33 (38)
33 PF04828 GFA: Glutathione-depe 42.1 11 0.00024 23.6 0.6 20 44-63 42-61 (92)
34 KOG2292|consensus 41.8 22 0.00048 32.3 2.5 59 16-78 288-365 (751)
35 TIGR03655 anti_R_Lar restricti 41.1 23 0.00049 21.3 1.8 18 42-59 18-35 (53)
36 cd04980 IgV_L_kappa Immunoglob 40.4 15 0.00033 23.9 1.1 12 45-56 80-91 (106)
37 PTZ00073 60S ribosomal protein 39.7 16 0.00034 25.4 1.1 28 48-75 14-41 (91)
38 cd02178 GH16_beta_agarase Beta 38.9 9.6 0.00021 29.5 -0.1 19 60-78 100-118 (258)
39 cd04983 IgV_TCR_alpha_like Imm 38.6 22 0.00048 22.9 1.6 14 45-58 79-92 (109)
40 cd05862 Ig1_VEGFR First immuno 38.2 20 0.00044 22.9 1.4 23 44-66 58-81 (86)
41 PF01907 Ribosomal_L37e: Ribos 37.4 18 0.00039 22.9 1.0 27 49-75 14-40 (55)
42 PF09965 DUF2199: Uncharacteri 37.4 13 0.00029 27.4 0.4 19 51-79 1-19 (148)
43 PF13717 zinc_ribbon_4: zinc-r 37.1 24 0.00051 19.9 1.4 20 88-107 14-33 (36)
44 cd05861 Ig1_PDGFR-alphabeta Fr 36.9 24 0.00051 22.4 1.5 13 44-56 54-66 (84)
45 COG2126 RPL37A Ribosomal prote 35.9 18 0.0004 23.3 0.8 27 48-74 14-40 (61)
46 cd05895 Ig_Pro_neuregulin-1 Im 35.7 25 0.00054 21.3 1.4 14 44-57 52-65 (76)
47 smart00408 IGc2 Immunoglobulin 35.6 27 0.00058 18.9 1.4 11 45-55 48-58 (63)
48 PF14066 DUF4256: Protein of u 33.7 28 0.0006 26.7 1.6 16 19-34 105-120 (173)
49 PF00047 ig: Immunoglobulin do 33.4 23 0.0005 20.4 1.0 10 46-55 55-64 (64)
50 PF10367 Vps39_2: Vacuolar sor 33.1 21 0.00046 23.1 0.8 12 52-63 80-91 (109)
51 PHA03351 tegument protein UL16 33.1 33 0.00071 26.8 2.0 39 20-58 104-148 (235)
52 cd04974 Ig3_FGFR Third immunog 33.0 27 0.00058 22.2 1.3 13 45-57 64-76 (90)
53 COG1996 RPC10 DNA-directed RNA 33.0 22 0.00047 21.9 0.8 12 49-60 5-16 (49)
54 cd05742 Ig1_VEGFR_like First i 32.2 25 0.00053 21.9 1.0 13 45-57 58-70 (84)
55 cd05720 Ig_CD8_alpha Immunoglo 31.7 30 0.00064 22.9 1.4 26 45-76 78-103 (104)
56 PRK00398 rpoP DNA-directed RNA 31.1 26 0.00057 20.3 0.9 29 50-78 3-34 (46)
57 cd05734 Ig7_DSCAM Seventh immu 30.8 34 0.00074 20.9 1.5 14 44-57 52-65 (79)
58 PF03811 Zn_Tnp_IS1: InsA N-te 30.7 34 0.00075 19.5 1.3 12 95-106 1-12 (36)
59 PF06397 Desulfoferrod_N: Desu 30.4 35 0.00075 19.7 1.3 13 47-59 3-15 (36)
60 cd05765 Ig_3 Subgroup of the i 30.3 33 0.00072 20.6 1.3 14 44-57 55-68 (81)
61 PF13240 zinc_ribbon_2: zinc-r 30.2 31 0.00067 17.7 1.0 19 53-72 2-20 (23)
62 cd07693 Ig1_Robo First immunog 30.1 36 0.00079 20.9 1.5 13 45-57 73-85 (100)
63 PF08273 Prim_Zn_Ribbon: Zinc- 29.1 28 0.00061 20.4 0.8 16 42-57 18-33 (40)
64 PF09889 DUF2116: Uncharacteri 28.7 23 0.0005 22.5 0.4 10 52-61 5-14 (59)
65 cd04977 Ig1_NCAM-1_like First 28.6 37 0.00079 21.8 1.4 15 44-58 65-79 (92)
66 PF13101 DUF3945: Protein of u 28.5 32 0.00069 21.3 1.0 23 12-34 26-48 (59)
67 cd05725 Ig3_Robo Third immunog 28.4 30 0.00066 20.5 0.9 12 45-56 44-55 (69)
68 cd05763 Ig_1 Subgroup of the i 27.6 41 0.0009 20.3 1.4 14 44-57 48-61 (75)
69 KOG3507|consensus 27.6 37 0.0008 22.0 1.2 15 46-60 16-30 (62)
70 TIGR03831 YgiT_finger YgiT-typ 27.3 28 0.00061 19.4 0.6 17 48-64 30-46 (46)
71 COG1885 Uncharacterized protei 26.9 24 0.00053 25.3 0.3 14 47-60 46-59 (115)
72 smart00406 IGv Immunoglobulin 26.8 32 0.0007 20.3 0.8 10 46-55 72-81 (81)
73 COG0358 DnaG DNA primase (bact 26.6 53 0.0012 28.5 2.4 45 15-59 8-64 (568)
74 KOG3549|consensus 26.4 99 0.0021 26.9 3.9 59 23-81 119-191 (505)
75 smart00531 TFIIE Transcription 25.9 34 0.00073 24.5 0.9 16 48-63 121-136 (147)
76 cd05735 Ig8_DSCAM Eight immuno 25.3 45 0.00096 21.3 1.3 12 45-56 56-67 (88)
77 cd05899 IgV_TCR_beta Immunoglo 25.3 48 0.001 21.7 1.5 13 45-57 81-93 (110)
78 cd05871 Ig_Semaphorin_classIII 25.1 37 0.00081 22.0 0.9 14 44-57 61-74 (91)
79 PF12760 Zn_Tnp_IS1595: Transp 25.0 47 0.001 19.3 1.3 23 36-58 21-45 (46)
80 KOG3141|consensus 24.9 25 0.00054 29.2 0.1 32 24-56 142-173 (310)
81 PF12773 DZR: Double zinc ribb 24.8 47 0.001 19.1 1.3 24 50-73 12-37 (50)
82 cd07700 IgV_CD8_beta Immunoglo 24.7 42 0.00092 22.0 1.2 13 44-56 80-92 (107)
83 cd05738 Ig2_RPTP_IIa_LAR_like 24.6 44 0.00096 20.3 1.2 13 44-56 46-58 (74)
84 cd05726 Ig4_Robo Fhird immunog 24.6 40 0.00088 21.2 1.0 14 44-57 55-68 (90)
85 cd05874 Ig6_NrCAM Sixth immuno 24.6 45 0.00098 20.7 1.2 11 47-57 54-64 (77)
86 cd05723 Ig4_Neogenin Fourth im 24.6 48 0.001 20.0 1.3 14 44-57 45-58 (71)
87 cd04967 Ig1_Contactin First Ig 24.5 47 0.001 20.9 1.3 11 46-56 69-79 (91)
88 cd07701 Ig1_Necl-3 First (N-te 24.5 49 0.0011 21.5 1.4 14 44-57 70-83 (95)
89 cd04981 IgV_H Immunoglobulin ( 24.4 34 0.00073 23.2 0.7 12 46-57 86-97 (117)
90 cd05764 Ig_2 Subgroup of the i 24.3 41 0.00089 20.1 1.0 14 45-58 49-62 (74)
91 cd05750 Ig_Pro_neuregulin Immu 24.3 52 0.0011 19.4 1.4 13 44-56 51-63 (75)
92 cd05731 Ig3_L1-CAM_like Third 24.2 36 0.00079 19.9 0.7 13 45-57 45-57 (71)
93 cd05854 Ig6_Contactin-2 Sixth 24.0 42 0.00092 21.3 1.0 14 44-57 55-68 (85)
94 cd05746 Ig4_Peroxidasin Fourth 24.0 43 0.00093 20.0 1.0 14 44-57 44-57 (69)
95 PF12368 DUF3650: Protein of u 23.8 40 0.00086 18.6 0.7 12 11-22 15-26 (28)
96 cd05724 Ig2_Robo Second immuno 23.4 53 0.0011 19.9 1.4 14 44-57 59-72 (86)
97 cd04970 Ig6_Contactin_like Six 23.4 41 0.0009 20.8 0.9 13 45-57 56-68 (85)
98 cd05870 Ig5_NCAM-2 Fifth immun 23.2 56 0.0012 20.9 1.5 14 44-57 72-85 (98)
99 cd05753 Ig2_FcgammaR_like Seco 23.2 43 0.00092 21.2 0.9 13 45-57 57-69 (83)
100 PF10880 DUF2673: Protein of u 23.2 34 0.00073 22.1 0.4 15 15-29 44-58 (65)
101 PF13408 Zn_ribbon_recom: Reco 23.2 38 0.00082 19.7 0.6 19 48-66 3-21 (58)
102 KOG4397|consensus 23.1 22 0.00049 27.9 -0.5 12 51-62 89-100 (213)
103 cd05732 Ig5_NCAM-1_like Fifth 22.9 57 0.0012 20.4 1.5 14 45-58 71-84 (96)
104 cd05760 Ig2_PTK7 Second immuno 22.7 59 0.0013 19.9 1.5 13 45-57 47-59 (77)
105 COG2174 RPL34A Ribosomal prote 22.7 33 0.00071 23.9 0.3 48 46-105 30-77 (93)
106 PF08792 A2L_zn_ribbon: A2L zi 22.5 47 0.001 18.6 0.9 14 46-59 17-30 (33)
107 cd05852 Ig5_Contactin-1 Fifth 22.5 46 0.001 20.6 1.0 15 44-58 47-61 (73)
108 cd04971 Ig_TrKABC_d5 Fifth dom 22.4 57 0.0012 20.7 1.4 14 44-57 54-67 (81)
109 cd05857 Ig2_FGFR Second immuno 22.4 59 0.0013 19.8 1.4 14 44-57 59-72 (85)
110 PRK04860 hypothetical protein; 22.3 67 0.0015 23.8 1.9 37 14-58 87-126 (160)
111 PF13487 HD_5: HD domain; PDB: 22.3 56 0.0012 20.0 1.3 13 20-32 2-14 (64)
112 cd05856 Ig2_FGFRL1-like Second 22.3 48 0.001 19.8 1.0 13 45-57 57-69 (82)
113 cd05848 Ig1_Contactin-5 First 22.1 54 0.0012 21.1 1.3 12 46-57 69-80 (94)
114 cd00233 VIP2 VIP2; A family of 22.1 76 0.0016 23.9 2.2 18 14-31 20-37 (201)
115 cd05865 Ig1_NCAM-1 First immun 22.0 53 0.0012 21.6 1.2 15 44-58 68-82 (96)
116 cd04973 Ig1_FGFR First immunog 21.9 51 0.0011 20.3 1.1 14 44-57 53-66 (79)
117 cd05717 Ig1_Necl-1-3_like Firs 21.8 59 0.0013 20.6 1.4 14 44-57 70-83 (95)
118 COG4068 Uncharacterized protei 21.8 38 0.00082 22.0 0.4 9 52-60 10-18 (64)
119 cd05855 Ig_TrkB_d5 Fifth domai 21.2 56 0.0012 21.0 1.2 12 46-57 54-65 (79)
120 PF13842 Tnp_zf-ribbon_2: DDE_ 21.1 61 0.0013 17.8 1.2 12 49-60 15-26 (32)
121 cd05876 Ig3_L1-CAM Third immun 21.0 54 0.0012 19.8 1.0 13 45-57 45-57 (71)
122 cd05867 Ig4_L1-CAM_like Fourth 21.0 55 0.0012 19.9 1.1 14 44-57 49-62 (76)
123 smart00659 RPOLCX RNA polymera 20.9 55 0.0012 19.4 1.0 11 50-60 2-12 (44)
124 cd05729 Ig2_FGFR_like Second i 20.9 63 0.0014 19.2 1.3 13 44-56 59-71 (85)
125 cd04982 IgV_TCR_gamma Immunogl 20.8 49 0.0011 21.7 0.9 11 46-56 87-97 (116)
126 cd05866 Ig1_NCAM-2 First immun 20.7 45 0.00098 21.8 0.7 15 44-58 64-78 (92)
127 cd05754 Ig3_Perlecan_like Thir 20.5 51 0.0011 20.3 0.9 14 44-57 60-73 (85)
128 cd05740 Ig_CEACAM_D4 Fourth im 20.2 57 0.0012 21.0 1.1 14 44-57 63-76 (91)
129 smart00410 IG_like Immunoglobu 20.0 67 0.0015 18.1 1.3 12 45-56 60-71 (86)
130 smart00409 IG Immunoglobulin. 20.0 67 0.0015 18.1 1.3 12 45-56 60-71 (86)
No 1
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.2e-54 Score=313.98 Aligned_cols=97 Identities=49% Similarity=0.945 Sum_probs=94.9
Q ss_pred ccCCHHHHHhcCCHHHHHHHhhcCCCCCCCCCCCCCCCCeEEEeccCCCccccCCCcccCCCCCcccccccCCCCeEEee
Q psy12346 10 CKINKEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGKVKLTK 89 (107)
Q Consensus 10 ~~~sd~ewk~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~~v~~~~ 89 (107)
.+++|++||++|||+||+|||++|||+||+|+|++++++|||+|++||+|||+|++|||||||||||++||++++|.++.
T Consensus 2 ~~~sd~e~~~~Lt~~qy~Vtq~~gTE~pft~~y~~~~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~pi~~~~I~~~~ 81 (140)
T COG0229 2 IKPSDEELKEKLTPEQYRVTQNHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTKPISPDAITYKE 81 (140)
T ss_pred CccchHHHHHhcCHHHHHHHHhcCCCCCCCChhhcccCCceEEeecCCCccccccccccCCCCCccccccCCcccceEee
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCceeeEEeCCCCC
Q psy12346 90 DTSHGKLYGDLVSSHPK 106 (107)
Q Consensus 90 D~s~gm~RtEV~C~~c~ 106 (107)
|.||||.||||+|++|+
T Consensus 82 D~S~gM~RtEVrc~~c~ 98 (140)
T COG0229 82 DRSHGMVRTEVRCANCD 98 (140)
T ss_pred ccCCCcEEEEEEecCCC
Confidence 99999999999999996
No 2
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=100.00 E-value=8.6e-53 Score=305.56 Aligned_cols=96 Identities=48% Similarity=0.868 Sum_probs=94.2
Q ss_pred cCCHHHHHhcCCHHHHHHHhhcCCCCCCCCCCCCCCCCeEEEeccCCCccccCCCcccCCCCCcccccccCCCCeEEeec
Q psy12346 11 KINKEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGKVKLTKD 90 (107)
Q Consensus 11 ~~sd~ewk~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~~v~~~~D 90 (107)
.++++|||++|||+||+|||++||||||||+|++++++|+|+|++||+|||+|++||+||||||||++||++++|.++.|
T Consensus 1 ~~~~~ewr~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~~D 80 (134)
T TIGR00357 1 KPSDEELKKKLTPLQYEVTQNAGTEPPFTNEYWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERD 80 (134)
T ss_pred CCCHHHHHHhCCHHHHHHHHHhCCCCCCCCCCCCCCCCeEEEccCCCCccccccchhcCCCCCcCcCcccCCCceEEeec
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceeeEEeCCCCC
Q psy12346 91 TSHGKLYGDLVSSHPK 106 (107)
Q Consensus 91 ~s~gm~RtEV~C~~c~ 106 (107)
.++||+||||+|++|+
T Consensus 81 ~s~gm~RtEv~C~~Cg 96 (134)
T TIGR00357 81 ESHGMIRTEVRCRNCD 96 (134)
T ss_pred CCCCcEEEEEEecCCC
Confidence 9999999999999997
No 3
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=3.3e-52 Score=304.92 Aligned_cols=97 Identities=54% Similarity=0.977 Sum_probs=95.1
Q ss_pred ccCCHHHHHhcCCHHHHHHHhhcCCCCCCCCCCCCCCCCeEEEeccCCCccccCCCcccCCCCCcccccccCCCCeEEee
Q psy12346 10 CKINKEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGKVKLTK 89 (107)
Q Consensus 10 ~~~sd~ewk~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~~v~~~~ 89 (107)
++++|+|||++|||+||+|||++||||||||+|++++++|+|+|++||+|||+|++||+||||||||++||.+++|.++.
T Consensus 3 ~~~~~~ew~~~Lt~~qy~V~r~~gTE~pftg~~~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~V~~~~ 82 (142)
T PRK00222 3 IEKSKEEWKKQLTPEQYRVTQEHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKPIDEEAIRELR 82 (142)
T ss_pred ccCCHHHHHhhCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcccCCCceEEee
Confidence 45799999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCceeeEEeCCCCC
Q psy12346 90 DTSHGKLYGDLVSSHPK 106 (107)
Q Consensus 90 D~s~gm~RtEV~C~~c~ 106 (107)
|.++||.||||+|++|+
T Consensus 83 D~s~gm~RtEv~C~~Cg 99 (142)
T PRK00222 83 DTSHGMVRTEVRCANCD 99 (142)
T ss_pred ccCCCceEEEEEeCCCC
Confidence 99999999999999997
No 4
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=100.00 E-value=2.8e-52 Score=299.55 Aligned_cols=93 Identities=53% Similarity=0.921 Sum_probs=90.2
Q ss_pred HHHHHhcCCHHHHHHHhhcCCCCCCCCCCCCCCCCeEEEeccCCCccccCCCcccCCCCCcccccccCCCCeEEeecCCC
Q psy12346 14 KEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGKVKLTKDTSH 93 (107)
Q Consensus 14 d~ewk~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~~v~~~~D~s~ 93 (107)
|+|||++|||+||+|||++||||||||+|++++++|+|+|++||+|||+|++||+||||||||++||.+++|.++.|.++
T Consensus 1 d~ew~~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~v~~~~D~s~ 80 (124)
T PF01641_consen 1 DEEWRKRLTPEQYRVLREKGTERPFSGEYWDHKEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQPIPGDAVKEREDFSH 80 (124)
T ss_dssp -HHHHHHSCHHHHHHHHHTTSSSTTSSGGCCTTSSEEEEETTTS-EEEEGGGEETSSSSSSEESSCSSTTSEEEEEEECT
T ss_pred CHHHHhhCCHHHHHHHHhcCCCCCCccCCcCCCCCEEEEcCCCCCccccCcccccCCcCCccccCcCChHHEEEeccccC
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeeEEeCCCCC
Q psy12346 94 GKLYGDLVSSHPK 106 (107)
Q Consensus 94 gm~RtEV~C~~c~ 106 (107)
||+||||+|++|+
T Consensus 81 g~~R~Ev~C~~Cg 93 (124)
T PF01641_consen 81 GMVRTEVRCARCG 93 (124)
T ss_dssp SSEEEEEEETTTC
T ss_pred CceEEEEEecCCC
Confidence 9999999999997
No 5
>KOG0856|consensus
Probab=100.00 E-value=3e-50 Score=294.05 Aligned_cols=102 Identities=43% Similarity=0.795 Sum_probs=99.2
Q ss_pred CCCCCccCCHHHHHhcCCHHHHHHHhhcCCCCCCCCCCCCCCCCeEEEeccCCCccccCCCcccCCCCCcccccccCCCC
Q psy12346 5 NNAGGCKINKEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGK 84 (107)
Q Consensus 5 ~~~~~~~~sd~ewk~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~~ 84 (107)
+.+.+++++++|||++||||||+|||++|||+||+|+|++++++|+|+|++|+.|||+|.+|||||||||||+++|.+++
T Consensus 9 ~~~~~v~k~~~EWr~~LsPeQ~~v~RekgTE~p~tGey~~~~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~i~~ga 88 (146)
T KOG0856|consen 9 PKTGSVQKNDEEWRKVLSPEQFRVLREKGTERPGTGEYTKHFEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEAIGPGA 88 (146)
T ss_pred CCCcccccCHHHHHhhcCHHHhhhhHhhcccCCCCcccccccCCceEEEeecCCccccccccccCCCCCchhhhccCCCc
Confidence 45678899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeecCCCCceeeEEeCCCCC
Q psy12346 85 VKLTKDTSHGKLYGDLVSSHPK 106 (107)
Q Consensus 85 v~~~~D~s~gm~RtEV~C~~c~ 106 (107)
|..+.|+|+||.|+||.|++|+
T Consensus 89 I~r~~d~s~~~~R~Ev~Ca~C~ 110 (146)
T KOG0856|consen 89 ITRTPDNSRGGRRTEVSCATCG 110 (146)
T ss_pred eeeccccCCCCcceEEEEeecC
Confidence 9999999999999999999997
No 6
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=2e-47 Score=272.80 Aligned_cols=85 Identities=45% Similarity=0.831 Sum_probs=82.0
Q ss_pred hcCCHHHHHHHhhcCCCCCCCCCCCCCCCCeEEEeccCCCccccCCCcccCCCCCcccccccCCCCeEEeecCCCCceee
Q psy12346 19 KRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGKVKLTKDTSHGKLYG 98 (107)
Q Consensus 19 ~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~~v~~~~D~s~gm~Rt 98 (107)
++|||+||+|||++||||||+|+|++++++|+|+|++||+|||+|++|||||||||||++||. ++|.++.|.+ |+||
T Consensus 2 ~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~-~~v~~~~D~~--~~Rt 78 (119)
T PRK05508 2 NELTPEEEAVILRKGTEPPFSGEYNDFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDEIK-GAVKRIPDAD--GRRT 78 (119)
T ss_pred CcCCHHHHHHHHhcCCCCCCCCCCcCcCCCeEEEecCCCCccccccccccCCCCCcccCcccc-cceEEEecCC--CcEE
Confidence 579999999999999999999999999999999999999999999999999999999999995 8999999988 5799
Q ss_pred EEeCCCCC
Q psy12346 99 DLVSSHPK 106 (107)
Q Consensus 99 EV~C~~c~ 106 (107)
||+|++|+
T Consensus 79 Ev~C~~C~ 86 (119)
T PRK05508 79 EIVCANCG 86 (119)
T ss_pred EEEeCCCC
Confidence 99999997
No 7
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=4e-45 Score=309.83 Aligned_cols=96 Identities=40% Similarity=0.640 Sum_probs=94.3
Q ss_pred cCCHHHHHhcCCHHHHHHHhhcCCCCCCCCCCCCCCCCeEEEeccCCCccccCCCcccCCCCCcccccccCCCCeEEeec
Q psy12346 11 KINKEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGKVKLTKD 90 (107)
Q Consensus 11 ~~sd~ewk~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~~v~~~~D 90 (107)
.+|++|||++|||+||+|||++||||||||+|++++++|+|+|++||+|||+|.+||+||||||||++||++++|.++.|
T Consensus 379 ~~~~~~~~~~Lt~~~y~v~~~~gtE~~f~~~~~~~~~~G~y~c~~c~~pLf~s~~Kf~sg~GWPsF~~~i~~~~v~~~~d 458 (521)
T PRK14018 379 KPSDAELKRTLTEEQYQITQNAATERAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKVVTEHDD 458 (521)
T ss_pred CCChHHHhccCCHHHHHHHHhcCCCCCCCCCCcCCCCCEEEEecCCCCccccCcccccCCCCCcccCcccCcCceEEeec
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceeeEEeCCCCC
Q psy12346 91 TSHGKLYGDLVSSHPK 106 (107)
Q Consensus 91 ~s~gm~RtEV~C~~c~ 106 (107)
.|+||.||||+|++|+
T Consensus 459 ~s~g~~R~Ev~c~~c~ 474 (521)
T PRK14018 459 FSYNMRRTEVRSRAAD 474 (521)
T ss_pred cCCCceEEEEEECCCC
Confidence 9999999999999997
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=100.00 E-value=1.4e-42 Score=276.73 Aligned_cols=89 Identities=46% Similarity=0.931 Sum_probs=84.7
Q ss_pred HHHHhcCCHHHHHHHhhcCCCCCCCCCCCCCCCCeEEEeccCCCccccCCCcccCCCCCcccccccCCCCeEEeecCCCC
Q psy12346 15 EELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGKVKLTKDTSHG 94 (107)
Q Consensus 15 ~ewk~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~~v~~~~D~s~g 94 (107)
+.||++|||+||+|||++||||||+|+||+++++|+|+|++||+|||+|++||+||||||||++||. ++|+++.|.+ |
T Consensus 1 ~~~~~~Lt~~~y~v~r~~gTE~pf~g~~~~~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~~~~-~~~~~~~d~~-~ 78 (283)
T PRK05550 1 MDKMKSLTPFEYRVIEDKGTERPFSGEYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEIP-GAVKRLPDAD-G 78 (283)
T ss_pred ChhhhhCCHHHHHHHHhcCCCCCCCCcCcCCCCCcEEEcCCCCchhcCChhhccCCCCCcCcCcccC-CccEEEEcCC-C
Confidence 3699999999999999999999999999999999999999999999999999999999999999995 6888888887 6
Q ss_pred ceeeEEeCCCCC
Q psy12346 95 KLYGDLVSSHPK 106 (107)
Q Consensus 95 m~RtEV~C~~c~ 106 (107)
| ||||+|++|+
T Consensus 79 ~-R~Ev~c~~c~ 89 (283)
T PRK05550 79 R-RTEIVCANCG 89 (283)
T ss_pred c-eEEEEecCCC
Confidence 6 9999999997
No 9
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=81.22 E-value=1.1 Score=28.86 Aligned_cols=43 Identities=19% Similarity=0.383 Sum_probs=33.4
Q ss_pred EEeccCCCccccCCCcccCCCCCcccccccCCCCeEEeecCCCCceeeEEeCCCCC
Q psy12346 51 YTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGKVKLTKDTSHGKLYGDLVSSHPK 106 (107)
Q Consensus 51 Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~~v~~~~D~s~gm~RtEV~C~~c~ 106 (107)
|.|.-||..-|.+..--.+|.||-.+++ |..+. =+=|.|.+||
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFd-vq~~~------------f~~v~C~~CG 43 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFD-VQNKK------------FTTVSCTNCG 43 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEE-ecCcE------------EEEEECCCCC
Confidence 7899999999999999999999987665 32211 1457899997
No 10
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=81.16 E-value=0.49 Score=34.69 Aligned_cols=23 Identities=35% Similarity=0.860 Sum_probs=16.6
Q ss_pred EEeccCCCccccCCCc-ccCCCCC
Q psy12346 51 YTCIVCAQPLFSSQTK-FDSGCGW 73 (107)
Q Consensus 51 Y~C~~Cg~pLF~S~~K-FdSg~GW 73 (107)
+||..||.|||.=+-+ |=+-||-
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGY 52 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCc
Confidence 6899999999983332 5555554
No 11
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=80.54 E-value=2.9 Score=28.10 Aligned_cols=56 Identities=9% Similarity=0.198 Sum_probs=31.4
Q ss_pred CeEEEeccCCCccccC-CCcccCCCCCcccccccCCCCeEEeecCCCCceeeEEeCCCCCC
Q psy12346 48 SGTYTCIVCAQPLFSS-QTKFDSGCGWPAFNDVLDQGKVKLTKDTSHGKLYGDLVSSHPKR 107 (107)
Q Consensus 48 ~G~Y~C~~Cg~pLF~S-~~KFdSg~GWPSF~~pi~~~~v~~~~D~s~gm~RtEV~C~~c~~ 107 (107)
.+.|+|..|+.....+ +.++..- -.+...+. +.+....|...+..+|++.|.+||.
T Consensus 14 ~~~~~C~~C~~~~~~~~~~~~v~~---~~~~~~~~-~~~~~~~~~~~~~~~~~~~Cp~Cg~ 70 (104)
T TIGR01384 14 NGVYVCPSCGYEKEKKPEDDYKVT---EKVKHKIK-ETIIIREEDSETLPTTRVECPKCGH 70 (104)
T ss_pred CCeEECcCCCCccccccccccEEE---EEeccccc-cceeeccccccCCCcccCCCCCCCC
Confidence 5799999999875543 1122110 01111111 2233344444567789999999983
No 12
>PRK00420 hypothetical protein; Validated
Probab=75.56 E-value=1.4 Score=31.31 Aligned_cols=23 Identities=30% Similarity=0.473 Sum_probs=16.5
Q ss_pred EEeccCCCcccc--CCCcccCCCCC
Q psy12346 51 YTCIVCAQPLFS--SQTKFDSGCGW 73 (107)
Q Consensus 51 Y~C~~Cg~pLF~--S~~KFdSg~GW 73 (107)
-+|..||.|||. ....|=+.||=
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCC
Confidence 468888888885 66667766664
No 13
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=70.65 E-value=3.3 Score=25.89 Aligned_cols=11 Identities=9% Similarity=-0.067 Sum_probs=8.7
Q ss_pred eeEEeCCCCCC
Q psy12346 97 YGDLVSSHPKR 107 (107)
Q Consensus 97 RtEV~C~~c~~ 107 (107)
.+||.|.+||.
T Consensus 22 ~leIKCpRC~t 32 (51)
T PF10122_consen 22 ELEIKCPRCKT 32 (51)
T ss_pred EEEEECCCCCc
Confidence 48888988873
No 14
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=69.90 E-value=1.9 Score=25.54 Aligned_cols=13 Identities=31% Similarity=0.838 Sum_probs=10.8
Q ss_pred EeccCCCccccCC
Q psy12346 52 TCIVCAQPLFSSQ 64 (107)
Q Consensus 52 ~C~~Cg~pLF~S~ 64 (107)
+|..|+.|||.+.
T Consensus 19 ~Cp~C~~PL~~~k 31 (41)
T PF06677_consen 19 HCPDCGTPLMRDK 31 (41)
T ss_pred ccCCCCCeeEEec
Confidence 6888999999844
No 15
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=67.27 E-value=4.2 Score=26.99 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=20.7
Q ss_pred EEEeccCCCccccCCCccc-CCCCCccc
Q psy12346 50 TYTCIVCAQPLFSSQTKFD-SGCGWPAF 76 (107)
Q Consensus 50 ~Y~C~~Cg~pLF~S~~KFd-Sg~GWPSF 76 (107)
+|.|+.|.++|=+|..=.. +|..=++|
T Consensus 2 vf~C~~C~t~l~ds~~lvs~~g~~~~a~ 29 (96)
T PF03226_consen 2 VFQCKNCKTILADSNELVSFHGREGKAY 29 (96)
T ss_pred EEECCCCCCCcCCHHHheecCCCCccEE
Confidence 7999999999988888777 55333444
No 16
>PRK08624 hypothetical protein; Provisional
Probab=66.46 E-value=7.7 Score=32.84 Aligned_cols=54 Identities=28% Similarity=0.465 Sum_probs=32.0
Q ss_pred CHHHHHhcCCHHHHH----------HHhhcCCCC-----CC--CCCCC--CCCCCeEEEec-cCCC--ccccCCCc
Q psy12346 13 NKEELKKRLTPMQYH----------VTQEKGTER-----PF--SGKYN--KNTESGTYTCI-VCAQ--PLFSSQTK 66 (107)
Q Consensus 13 sd~ewk~~Lt~~qy~----------V~r~~gTE~-----pf--sg~y~--~~~~~G~Y~C~-~Cg~--pLF~S~~K 66 (107)
+.+++++.||+++-. ++...|+.- ++ +..+. -+.+.++|+|- +||. -.|.=-.+
T Consensus 3 ~~~~~~~~l~~~~i~~il~~~g~~~~l~k~G~~~y~~~CH~e~~pS~sv~v~pekq~yhCF~GCGa~GDVf~Fv~~ 78 (373)
T PRK08624 3 DKDELKESLTPEDIIKILEEVGCENVRGKDGNTIAETACHNDGGGSTKLYYYIENDNFHCYTRCGDIFDVFELLCK 78 (373)
T ss_pred chHHHHhhcCHHHHHHHHHHhcccceeccCCcchhheecCCCCCCCceEEEcCCCCEEEEeCCCCCCCceeeehhh
Confidence 567888889988754 333333320 00 11121 14578999999 9998 66655544
No 17
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=65.63 E-value=4.1 Score=23.56 Aligned_cols=30 Identities=30% Similarity=0.675 Sum_probs=18.4
Q ss_pred CCCCeEEEeccCCCccccCCCcccCCCCCccc
Q psy12346 45 NTESGTYTCIVCAQPLFSSQTKFDSGCGWPAF 76 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF 76 (107)
....|.++|..||.-| .+...+++--|-+|
T Consensus 14 D~~~g~~vC~~CG~Vl--~e~~i~~~~e~r~f 43 (43)
T PF08271_consen 14 DPERGELVCPNCGLVL--EENIIDEGPEWREF 43 (43)
T ss_dssp ETTTTEEEETTT-BBE--E-TTBSCCCSCCHC
T ss_pred cCCCCeEECCCCCCEe--ecccccCCcccccC
Confidence 3678999999999877 23334444444433
No 18
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=58.33 E-value=9.6 Score=30.63 Aligned_cols=32 Identities=28% Similarity=0.644 Sum_probs=27.1
Q ss_pred CCCCeEEEeccCCCccccCCCcccCCCCCccccc
Q psy12346 45 NTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFND 78 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~ 78 (107)
..+.|.++|..||.-| .+.-.|.|.-|.+|..
T Consensus 25 d~~~Ge~vC~~CG~Vl--~e~~iD~g~EWR~f~~ 56 (310)
T PRK00423 25 DYERGEIVCADCGLVI--EENIIDQGPEWRAFDP 56 (310)
T ss_pred ECCCCeEeecccCCcc--cccccccCCCccCCCc
Confidence 3579999999999987 5667889999999975
No 19
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=53.59 E-value=13 Score=21.46 Aligned_cols=19 Identities=32% Similarity=0.870 Sum_probs=15.4
Q ss_pred CCCCCCCCCCCCeEEEeccCC
Q psy12346 37 PFSGKYNKNTESGTYTCIVCA 57 (107)
Q Consensus 37 pfsg~y~~~~~~G~Y~C~~Cg 57 (107)
.|+ |.+-+..|.|+|..|+
T Consensus 14 rFr--~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 14 RFR--FDDKDGRGTWFCSVCG 32 (37)
T ss_pred ccc--cccCCCCcCEEeCCCC
Confidence 455 7777788999999996
No 20
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=52.30 E-value=6.6 Score=22.44 Aligned_cols=21 Identities=24% Similarity=0.483 Sum_probs=15.2
Q ss_pred CCCCCCCCCCeEEEeccCCCc
Q psy12346 39 SGKYNKNTESGTYTCIVCAQP 59 (107)
Q Consensus 39 sg~y~~~~~~G~Y~C~~Cg~p 59 (107)
.|..+.....|.|.|+.||..
T Consensus 14 C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 14 CGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCeEeEccCCEEEhhhCceE
Confidence 444556668899999888864
No 21
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=50.19 E-value=13 Score=30.19 Aligned_cols=31 Identities=32% Similarity=0.667 Sum_probs=25.8
Q ss_pred CCCCCeEEEeccCCCccccCCCcccCCCCCccc
Q psy12346 44 KNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAF 76 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF 76 (107)
...+.|.++|+.||.-| -+.-+|.|..|=+|
T Consensus 14 ~d~~~ge~VC~~CG~Vi--~~~~id~gpewr~f 44 (285)
T COG1405 14 TDYERGEIVCADCGLVL--EDSLIDPGPEWRAF 44 (285)
T ss_pred eeccCCeEEeccCCEEe--ccccccCCCCcccc
Confidence 34468999999999887 45568999999999
No 22
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=49.71 E-value=7.2 Score=27.70 Aligned_cols=21 Identities=29% Similarity=0.548 Sum_probs=16.9
Q ss_pred CCCCCCeEEEeccCCCccccC
Q psy12346 43 NKNTESGTYTCIVCAQPLFSS 63 (107)
Q Consensus 43 ~~~~~~G~Y~C~~Cg~pLF~S 63 (107)
......+.+.|..||.+||..
T Consensus 62 ~~s~~~~r~FC~~CGs~l~~~ 82 (133)
T COG3791 62 FSSGSAGRGFCPTCGSPLFWR 82 (133)
T ss_pred eecCCCCCeecccCCCceEEe
Confidence 355567777999999999975
No 23
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=48.77 E-value=8.7 Score=28.29 Aligned_cols=14 Identities=29% Similarity=0.710 Sum_probs=12.5
Q ss_pred CCeEEEeccCCCcc
Q psy12346 47 ESGTYTCIVCAQPL 60 (107)
Q Consensus 47 ~~G~Y~C~~Cg~pL 60 (107)
.+|+|+|..||..+
T Consensus 109 g~G~l~C~~Cg~~~ 122 (146)
T PF07295_consen 109 GPGTLVCENCGHEV 122 (146)
T ss_pred cCceEecccCCCEE
Confidence 78999999999865
No 24
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=46.93 E-value=12 Score=21.16 Aligned_cols=19 Identities=5% Similarity=-0.206 Sum_probs=13.0
Q ss_pred eecCCCCceeeEEeCCCCC
Q psy12346 88 TKDTSHGKLYGDLVSSHPK 106 (107)
Q Consensus 88 ~~D~s~gm~RtEV~C~~c~ 106 (107)
..|...+.....|+|++|+
T Consensus 14 v~~~~l~~~~~~vrC~~C~ 32 (37)
T PF13719_consen 14 VPDDKLPAGGRKVRCPKCG 32 (37)
T ss_pred cCHHHcccCCcEEECCCCC
Confidence 3444455556789999997
No 25
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=46.34 E-value=24 Score=20.55 Aligned_cols=21 Identities=24% Similarity=0.341 Sum_probs=12.6
Q ss_pred CccCCHHHHHhcCCHHHHHHHh
Q psy12346 9 GCKINKEELKKRLTPMQYHVTQ 30 (107)
Q Consensus 9 ~~~~sd~ewk~~Lt~~qy~V~r 30 (107)
.+.+|.+||. .|.|.|...-|
T Consensus 7 av~fs~eEW~-~L~~~Qk~ly~ 27 (41)
T PF01352_consen 7 AVYFSQEEWE-LLDPAQKNLYR 27 (41)
T ss_dssp TT---HHHHH-TS-HHHHHHHH
T ss_pred EEEcChhhcc-cccceecccch
Confidence 3468999995 69999977544
No 26
>PRK12495 hypothetical protein; Provisional
Probab=45.83 E-value=7.6 Score=30.88 Aligned_cols=16 Identities=25% Similarity=0.669 Sum_probs=13.5
Q ss_pred CCCeEEEeccCCCccc
Q psy12346 46 TESGTYTCIVCAQPLF 61 (107)
Q Consensus 46 ~~~G~Y~C~~Cg~pLF 61 (107)
-...-++|..||.|||
T Consensus 38 atmsa~hC~~CG~PIp 53 (226)
T PRK12495 38 ATMTNAHCDECGDPIF 53 (226)
T ss_pred cccchhhcccccCccc
Confidence 3456789999999999
No 27
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=45.80 E-value=9.6 Score=19.95 Aligned_cols=21 Identities=29% Similarity=0.687 Sum_probs=14.8
Q ss_pred EeccCCCccccCCCcccCCCCC
Q psy12346 52 TCIVCAQPLFSSQTKFDSGCGW 73 (107)
Q Consensus 52 ~C~~Cg~pLF~S~~KFdSg~GW 73 (107)
.|..||+++ .++++|=+.||=
T Consensus 4 ~Cp~Cg~~~-~~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGAEI-DPDAKFCPNCGA 24 (26)
T ss_pred CCcccCCcC-CcccccChhhCC
Confidence 577788853 777777777763
No 28
>cd02181 GH16_fungal_Lam16A_glucanase fungal 1,3(4)-beta-D-glucanases, similar to Phanerochaete chrysosporium laminarinase 16A. Group of fungal 1,3(4)-beta-D-glucanases, similar to Phanerochaete chrysosporium laminarinase 16A. Lam16A belongs to the 'nonspecific' 1,3(4)-beta-glucanase subfamily, although beta-1,6 branching and beta-1,4 bonds specifically define where Lam16A hydrolyzes its substrates, like curdlan (beta-1,3-glucan), lichenin (beta-1,3-1,4-mixed linkage glucan), and laminarin (beta-1,6-branched-1,3-glucan).
Probab=45.58 E-value=6.9 Score=32.04 Aligned_cols=19 Identities=47% Similarity=1.136 Sum_probs=15.3
Q ss_pred cccCCC-cccCCCC-Cccccc
Q psy12346 60 LFSSQT-KFDSGCG-WPAFND 78 (107)
Q Consensus 60 LF~S~~-KFdSg~G-WPSF~~ 78 (107)
||..+. |+-.||| ||+||-
T Consensus 82 ~~~~~~~~~P~g~G~WPAfW~ 102 (293)
T cd02181 82 LFIADIAHMPGGCGTWPAFWT 102 (293)
T ss_pred eEEEEhhhCCCCCCccchhhh
Confidence 666663 8888999 999997
No 29
>PHA02540 61 DNA primase; Provisional
Probab=42.81 E-value=13 Score=30.87 Aligned_cols=10 Identities=30% Similarity=0.972 Sum_probs=8.9
Q ss_pred eEEEeccCCC
Q psy12346 49 GTYTCIVCAQ 58 (107)
Q Consensus 49 G~Y~C~~Cg~ 58 (107)
++|+|=+||.
T Consensus 54 ~~yhCFgCGa 63 (337)
T PHA02540 54 GVFKCHNCGY 63 (337)
T ss_pred eEEEecCCCC
Confidence 4999999996
No 30
>cd04984 IgV_L_lambda Immunoglobulin (Ig) lambda light chain variable (V) domain. IgV_L_lambda: Immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.
Probab=42.54 E-value=16 Score=23.46 Aligned_cols=12 Identities=25% Similarity=0.603 Sum_probs=9.5
Q ss_pred CCCCeEEEeccC
Q psy12346 45 NTESGTYTCIVC 56 (107)
Q Consensus 45 ~~~~G~Y~C~~C 56 (107)
..+.|+|.|++-
T Consensus 72 ~~Dsg~Y~C~~~ 83 (98)
T cd04984 72 TEDEADYYCQVW 83 (98)
T ss_pred hhhCEEEEEEEc
Confidence 346899999874
No 31
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=42.45 E-value=14 Score=23.99 Aligned_cols=27 Identities=19% Similarity=0.621 Sum_probs=24.2
Q ss_pred eEEEeccCCCccccCCCcccCCCCC-cc
Q psy12346 49 GTYTCIVCAQPLFSSQTKFDSGCGW-PA 75 (107)
Q Consensus 49 G~Y~C~~Cg~pLF~S~~KFdSg~GW-PS 75 (107)
=.-.|..||.--|....|.=+.||. ||
T Consensus 16 tHt~CrRCG~~syh~qK~~CasCGygps 43 (62)
T PRK04179 16 THIRCRRCGRHSYNVRKKYCAACGFGRS 43 (62)
T ss_pred ccchhcccCcccccccccchhhcCCCcc
Confidence 4457999999999999999999999 76
No 32
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=42.21 E-value=17 Score=20.02 Aligned_cols=10 Identities=10% Similarity=0.149 Sum_probs=8.0
Q ss_pred eEEeCCCCCC
Q psy12346 98 GDLVSSHPKR 107 (107)
Q Consensus 98 tEV~C~~c~~ 107 (107)
.+|+|.+|+.
T Consensus 24 ~~v~C~~C~~ 33 (38)
T TIGR02098 24 GKVRCGKCGH 33 (38)
T ss_pred CEEECCCCCC
Confidence 4799999973
No 33
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=42.10 E-value=11 Score=23.55 Aligned_cols=20 Identities=35% Similarity=0.758 Sum_probs=14.1
Q ss_pred CCCCCeEEEeccCCCccccC
Q psy12346 44 KNTESGTYTCIVCAQPLFSS 63 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg~pLF~S 63 (107)
..+..=.+.|..||.+||..
T Consensus 42 s~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp TTSSCEEEEETTT--EEEEE
T ss_pred CCCcCcCcccCCCCCeeecc
Confidence 44556679999999999965
No 34
>KOG2292|consensus
Probab=41.84 E-value=22 Score=32.26 Aligned_cols=59 Identities=25% Similarity=0.468 Sum_probs=47.0
Q ss_pred HHHhcCCHHHHHHHhh-------------------cCCCCCCCCCCCCCCCCeEEEeccCCCccccCCCcccCCCCCccc
Q psy12346 16 ELKKRLTPMQYHVTQE-------------------KGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAF 76 (107)
Q Consensus 16 ewk~~Lt~~qy~V~r~-------------------~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF 76 (107)
-.|.+|++.||+|+.. .|--.|+||++....++|. |.=..|+-.|-+...+ +-||||
T Consensus 288 y~k~~ls~~~F~~l~~~~v~~~~~~~~vv~~~Lt~~g~iaPWtGRfySL~D~~Y---AK~hIPIIASVSEHQP-ttW~Sf 363 (751)
T KOG2292|consen 288 YLKGRLSPKQFQVLFRLVVSLVGVVVFVVVAALTATGYIAPWTGRFYSLWDTGY---AKIHIPIIASVSEHQP-TTWSSF 363 (751)
T ss_pred HHHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcceecccccceeeccCCcc---hhcccceEEeccccCC-CchHHH
Confidence 3678899999986543 4778999999987777764 5567899999888887 789999
Q ss_pred cc
Q psy12346 77 ND 78 (107)
Q Consensus 77 ~~ 78 (107)
+=
T Consensus 364 ff 365 (751)
T KOG2292|consen 364 FF 365 (751)
T ss_pred HH
Confidence 64
No 35
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=41.10 E-value=23 Score=21.31 Aligned_cols=18 Identities=17% Similarity=0.495 Sum_probs=13.9
Q ss_pred CCCCCCCeEEEeccCCCc
Q psy12346 42 YNKNTESGTYTCIVCAQP 59 (107)
Q Consensus 42 y~~~~~~G~Y~C~~Cg~p 59 (107)
+.+....|+|.|..||.-
T Consensus 18 ~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 18 FDPLDLSHYFECSTCGAS 35 (53)
T ss_pred cCCCCCEEEEECCCCCCC
Confidence 445667889999999865
No 36
>cd04980 IgV_L_kappa Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. IgV_L_kappa: Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.
Probab=40.37 E-value=15 Score=23.93 Aligned_cols=12 Identities=17% Similarity=0.468 Sum_probs=9.4
Q ss_pred CCCCeEEEeccC
Q psy12346 45 NTESGTYTCIVC 56 (107)
Q Consensus 45 ~~~~G~Y~C~~C 56 (107)
..+.|+|.|+.-
T Consensus 80 ~~Dsg~Y~Ca~~ 91 (106)
T cd04980 80 PEDAAVYYCQQY 91 (106)
T ss_pred hHHCEEEEEEEe
Confidence 346899999873
No 37
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=39.74 E-value=16 Score=25.37 Aligned_cols=28 Identities=29% Similarity=0.606 Sum_probs=25.0
Q ss_pred CeEEEeccCCCccccCCCcccCCCCCcc
Q psy12346 48 SGTYTCIVCAQPLFSSQTKFDSGCGWPA 75 (107)
Q Consensus 48 ~G~Y~C~~Cg~pLF~S~~KFdSg~GWPS 75 (107)
.=.-.|..||.--|.-..|.=+.||.||
T Consensus 14 ktHtlCrRCG~~syH~qK~~CasCGyps 41 (91)
T PTZ00073 14 KTHTLCRRCGKRSFHVQKKRCASCGYPS 41 (91)
T ss_pred cCcchhcccCccccccccccchhcCCch
Confidence 3445799999999999999999999997
No 38
>cd02178 GH16_beta_agarase Beta-agarase, member of glycosyl hydrolase family 16. Beta-agarase is a glycosyl hydrolase family 16 (GH16) member that hydrolyzes the internal beta-1,4-linkage of agarose, a hydrophilic polysaccharide found in the cell wall of Rhodophyceaea, marine red algae. Agarose is a linear chain of galactose units linked by alternating L-alpha-1,3- and D-beta-1,4-linkages that are additionally modified by a 3,6-anhydro-bridge. Agarose forms thermo-reversible gels that are widely used in the food industry or as a laboratory medium. While beta-agarases are also found in two other families derived from the sequence-based classification of glycosyl hydrolases (GH50, and GH86) the GH16 members are most abundant. This domain adopts a curved beta-sandwich conformation, with a tunnel-shaped active site cavity, referred to as a jellyroll fold.
Probab=38.87 E-value=9.6 Score=29.47 Aligned_cols=19 Identities=21% Similarity=0.013 Sum_probs=16.7
Q ss_pred cccCCCcccCCCCCccccc
Q psy12346 60 LFSSQTKFDSGCGWPAFND 78 (107)
Q Consensus 60 LF~S~~KFdSg~GWPSF~~ 78 (107)
-|....|+..+.||||||-
T Consensus 100 ~~EaR~K~p~~~~~pAfW~ 118 (258)
T cd02178 100 YFEARAKASNLPMSSAFWL 118 (258)
T ss_pred EEEEEEEcCCCCccceEEE
Confidence 4778899998899999997
No 39
>cd04983 IgV_TCR_alpha_like Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins. IgV_TCR_alpha: immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens; they recognize proteins antigens directly and without antigen processing, and MHC independently of the bound peptide.
Probab=38.64 E-value=22 Score=22.88 Aligned_cols=14 Identities=21% Similarity=0.532 Sum_probs=10.6
Q ss_pred CCCCeEEEeccCCC
Q psy12346 45 NTESGTYTCIVCAQ 58 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg~ 58 (107)
..+.|+|.|++-..
T Consensus 79 ~~DsG~Y~C~~~~~ 92 (109)
T cd04983 79 LSDSAVYFCALSES 92 (109)
T ss_pred HHHCEEEEEEEecC
Confidence 34689999997643
No 40
>cd05862 Ig1_VEGFR First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R). IG1_VEGFR: first immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R). The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family consists of three members, VEGFR-1 (Flt-1), VEGFR-2 (KDR/Flk-1) and VEGFR-3 (Flt-4). VEGF_A interacts with both VEGFR-1 and VEGFR-2. VEGFR-1 binds strongest to VEGF, VEGF-2 binds more weakly. VEGFR-3 appears not to bind VEGF, but binds other members of the VEGF family (VEGF-C and -D). VEGFRs bind VEGFs with high affinity with the IG-like domains. VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGFR-2 is a major mediator of the mitogenic, angioge
Probab=38.25 E-value=20 Score=22.91 Aligned_cols=23 Identities=26% Similarity=0.443 Sum_probs=14.2
Q ss_pred CCCCCeEEEeccCC-CccccCCCc
Q psy12346 44 KNTESGTYTCIVCA-QPLFSSQTK 66 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg-~pLF~S~~K 66 (107)
...+.|.|.|++-. .-++.+.++
T Consensus 58 ~~~DsG~Y~C~a~n~~~~~~~~t~ 81 (86)
T cd05862 58 TLSDLGRYTCTASSGQMIAKNSTI 81 (86)
T ss_pred CcccCEEEEEEEeecceEecccEE
Confidence 35689999996533 334444443
No 41
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=37.44 E-value=18 Score=22.90 Aligned_cols=27 Identities=30% Similarity=0.623 Sum_probs=23.1
Q ss_pred eEEEeccCCCccccCCCcccCCCCCcc
Q psy12346 49 GTYTCIVCAQPLFSSQTKFDSGCGWPA 75 (107)
Q Consensus 49 G~Y~C~~Cg~pLF~S~~KFdSg~GWPS 75 (107)
=.-.|..||.--|.-+.|-=+.||+|+
T Consensus 14 tH~~CrRCG~~syH~qK~~CasCGyp~ 40 (55)
T PF01907_consen 14 THTLCRRCGRRSYHIQKKTCASCGYPA 40 (55)
T ss_dssp SEEE-TTTSSEEEETTTTEETTTBTTT
T ss_pred cEeeecccCCeeeecCCCcccccCCCc
Confidence 345799999999999999999999997
No 42
>PF09965 DUF2199: Uncharacterized protein conserved in bacteria (DUF2199); InterPro: IPR018697 This domain has no known function.
Probab=37.37 E-value=13 Score=27.39 Aligned_cols=19 Identities=32% Similarity=0.665 Sum_probs=14.7
Q ss_pred EEeccCCCccccCCCcccCCCCCcccccc
Q psy12346 51 YTCIVCAQPLFSSQTKFDSGCGWPAFNDV 79 (107)
Q Consensus 51 Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~p 79 (107)
|.|.+||..- -|||||.-.
T Consensus 1 y~C~~Cg~~h----------~~~P~~~~~ 19 (148)
T PF09965_consen 1 YTCSCCGEEH----------EGLPSLGFD 19 (148)
T ss_pred CCCCcCCccC----------CCCcccccC
Confidence 7899999865 588887653
No 43
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=37.13 E-value=24 Score=19.92 Aligned_cols=20 Identities=10% Similarity=-0.119 Sum_probs=13.2
Q ss_pred eecCCCCceeeEEeCCCCCC
Q psy12346 88 TKDTSHGKLYGDLVSSHPKR 107 (107)
Q Consensus 88 ~~D~s~gm~RtEV~C~~c~~ 107 (107)
..|....-....|+|++|+.
T Consensus 14 i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 14 IDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred CCHHHCCCCCcEEECCCCCC
Confidence 34444444556899999973
No 44
>cd05861 Ig1_PDGFR-alphabeta Frst immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b). Ig1_PDGFR-alphabeta: The first immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b). PDGF is a potent mitogen for connective tissue cells. PDGF-stimulated processes are mediated by three different PDGFs (PDGF-A,-B, and C). PDGFRalpha binds to all three PDGFs, whereas the PDGFRbeta binds only to PDGF-B. PDGFRs alpha and beta have similar organization: an extracellular component with five Ig-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. In mice, PDGFRalpha and PDGFRbeta are essential for normal development.
Probab=36.88 E-value=24 Score=22.37 Aligned_cols=13 Identities=38% Similarity=0.744 Sum_probs=10.6
Q ss_pred CCCCCeEEEeccC
Q psy12346 44 KNTESGTYTCIVC 56 (107)
Q Consensus 44 ~~~~~G~Y~C~~C 56 (107)
...+.|+|.|++-
T Consensus 54 ~~~DsG~Y~C~a~ 66 (84)
T cd05861 54 TVEDSGTYECAAH 66 (84)
T ss_pred CcCCCEEEEEEEE
Confidence 4568999999984
No 45
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=35.93 E-value=18 Score=23.34 Aligned_cols=27 Identities=19% Similarity=0.589 Sum_probs=24.3
Q ss_pred CeEEEeccCCCccccCCCcccCCCCCc
Q psy12346 48 SGTYTCIVCAQPLFSSQTKFDSGCGWP 74 (107)
Q Consensus 48 ~G~Y~C~~Cg~pLF~S~~KFdSg~GWP 74 (107)
.-.-.|.-||.--|.-..|+-+.||.|
T Consensus 14 ~tH~~CRRCGr~syhv~k~~CaaCGfg 40 (61)
T COG2126 14 KTHIRCRRCGRRSYHVRKKYCAACGFG 40 (61)
T ss_pred cceehhhhccchheeeccceecccCCC
Confidence 445579999999999999999999999
No 46
>cd05895 Ig_Pro_neuregulin-1 Immunoglobulin (Ig)-like domain found in neuregulin (NRG)-1. Ig_Pro_neuregulin-1: immunoglobulin (Ig)-like domain found in neuregulin (NRG)-1. There are many NRG-1 isoforms which arise from the alternative splicing of mRNA. NRG-1 belongs to the neuregulin gene family, which is comprised of four genes. This group represents NRG-1. NRGs are signaling molecules, which participate in cell-cell interactions in the nervous system, breast, and heart, and other organ systems, and are implicated in the pathology of diseases including schizophrenia, multiple sclerosis, and breast cancer. The NRG-1 protein binds to and activates the tyrosine kinases receptors ErbB3 and ErbB4, initiating signaling cascades. NRG-1 has multiple functions; for example, in the brain it regulates various processes such as radial glia formation and neuronal migration, dendritic development, and expression of neurotransmitters receptors; in the peripheral nervous system NRG-1 regulates process
Probab=35.71 E-value=25 Score=21.33 Aligned_cols=14 Identities=29% Similarity=0.816 Sum_probs=11.0
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|.|.|++-.
T Consensus 52 ~~~DsG~Y~C~a~N 65 (76)
T cd05895 52 SLADNGEYKCMVSS 65 (76)
T ss_pred CcccCEEEEEEEEe
Confidence 45689999998754
No 47
>smart00408 IGc2 Immunoglobulin C-2 Type.
Probab=35.55 E-value=27 Score=18.89 Aligned_cols=11 Identities=45% Similarity=1.008 Sum_probs=8.9
Q ss_pred CCCCeEEEecc
Q psy12346 45 NTESGTYTCIV 55 (107)
Q Consensus 45 ~~~~G~Y~C~~ 55 (107)
....|.|.|.+
T Consensus 48 ~~d~G~Y~C~~ 58 (63)
T smart00408 48 LEDSGEYTCVA 58 (63)
T ss_pred cccCEEEEEEE
Confidence 45789999976
No 48
>PF14066 DUF4256: Protein of unknown function (DUF4256)
Probab=33.73 E-value=28 Score=26.70 Aligned_cols=16 Identities=38% Similarity=0.401 Sum_probs=14.1
Q ss_pred hcCCHHHHHHHhhcCC
Q psy12346 19 KRLTPMQYHVTQEKGT 34 (107)
Q Consensus 19 ~~Lt~~qy~V~r~~gT 34 (107)
+.||++||+-||+-|.
T Consensus 105 eLLtEeqYr~LQ~lg~ 120 (173)
T PF14066_consen 105 ELLTEEQYRELQKLGE 120 (173)
T ss_pred HhcCHHHHHHHHHhCC
Confidence 5799999999999874
No 49
>PF00047 ig: Immunoglobulin domain The Prosite family only concerns antibodies and MHCs.; InterPro: IPR013151 Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The Pfam alignments do not include the first and last strand of the immunoglobulin-like domain.; PDB: 1B6U_A 3O4O_C 3VH8_H 1BIH_A 2C9A_A 2V5Y_A 1BQH_K 2ATP_A 3B9K_A 1NEZ_H ....
Probab=33.44 E-value=23 Score=20.42 Aligned_cols=10 Identities=70% Similarity=1.404 Sum_probs=8.0
Q ss_pred CCCeEEEecc
Q psy12346 46 TESGTYTCIV 55 (107)
Q Consensus 46 ~~~G~Y~C~~ 55 (107)
...|+|.|.+
T Consensus 55 ~d~G~Y~C~v 64 (64)
T PF00047_consen 55 EDSGTYTCVV 64 (64)
T ss_dssp GGTEEEEEEE
T ss_pred HHCEEEEEEC
Confidence 3789999964
No 50
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=33.09 E-value=21 Score=23.11 Aligned_cols=12 Identities=50% Similarity=1.004 Sum_probs=10.2
Q ss_pred EeccCCCccccC
Q psy12346 52 TCIVCAQPLFSS 63 (107)
Q Consensus 52 ~C~~Cg~pLF~S 63 (107)
.|..|+.+|+.+
T Consensus 80 ~C~vC~k~l~~~ 91 (109)
T PF10367_consen 80 KCSVCGKPLGNS 91 (109)
T ss_pred CccCcCCcCCCc
Confidence 399999999774
No 51
>PHA03351 tegument protein UL16; Provisional
Probab=33.08 E-value=33 Score=26.84 Aligned_cols=39 Identities=21% Similarity=0.510 Sum_probs=30.6
Q ss_pred cCCHHHHHHHhhcCCC--CC----CCCCCCCCCCCeEEEeccCCC
Q psy12346 20 RLTPMQYHVTQEKGTE--RP----FSGKYNKNTESGTYTCIVCAQ 58 (107)
Q Consensus 20 ~Lt~~qy~V~r~~gTE--~p----fsg~y~~~~~~G~Y~C~~Cg~ 58 (107)
..|..|+.|+|.+--- -| |+....+++..|.|-|-.|..
T Consensus 104 nfs~i~~nilqdglkmr~vp~tklyt~rii~n~t~grydc~rcen 148 (235)
T PHA03351 104 NFSDIQTNILQDGLKMRHVPVTKLYTHRIINNHTAGRYDCFRCEN 148 (235)
T ss_pred chhHHHHHHHhccceeeecchhhheehhhhccccccceeeEEecC
Confidence 5789999999876432 24 566667899999999999975
No 52
>cd04974 Ig3_FGFR Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Ig3_FGFR: third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for FGFs.
Probab=33.03 E-value=27 Score=22.23 Aligned_cols=13 Identities=31% Similarity=0.759 Sum_probs=10.7
Q ss_pred CCCCeEEEeccCC
Q psy12346 45 NTESGTYTCIVCA 57 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg 57 (107)
..+.|.|.|.+-.
T Consensus 64 ~~D~G~Y~C~A~N 76 (90)
T cd04974 64 FDDAGEYTCLAGN 76 (90)
T ss_pred cccCcEEEEEeec
Confidence 4689999998765
No 53
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=32.96 E-value=22 Score=21.95 Aligned_cols=12 Identities=25% Similarity=0.772 Sum_probs=10.5
Q ss_pred eEEEeccCCCcc
Q psy12346 49 GTYTCIVCAQPL 60 (107)
Q Consensus 49 G~Y~C~~Cg~pL 60 (107)
=+|.|+-||..+
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 479999999987
No 54
>cd05742 Ig1_VEGFR_like First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor (R) and similar proteins. Ig1_VEGFR_like: first immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R) related proteins. The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family consists of three members, VEGFR-1 (Flt-1), VEGFR-2 (KDR/Flk-1) and VEGFR-3 (Flt-4). VEGF-A interacts with both VEGFR-1 and VEGFR-2. VEGFR-1 binds strongest to VEGF, VEGF-2 binds more weakly. VEGFR-3 appears not to bind VEGF, but binds other members of the VEGF family (VEGF-C and -D). VEGFRs bind VEGFs with high affinity with the IG-like domains. VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGF
Probab=32.17 E-value=25 Score=21.86 Aligned_cols=13 Identities=46% Similarity=0.856 Sum_probs=10.3
Q ss_pred CCCCeEEEeccCC
Q psy12346 45 NTESGTYTCIVCA 57 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg 57 (107)
..+.|+|.|++-.
T Consensus 58 ~~DsG~Y~C~a~n 70 (84)
T cd05742 58 LKDSGTYTCAASS 70 (84)
T ss_pred hhhCEEEEEEEcc
Confidence 4578999998854
No 55
>cd05720 Ig_CD8_alpha Immunoglobulin (Ig) like domain of CD8 alpha chain. Ig_CD8_alpha: immunoglobulin (Ig)-like domain in CD8 alpha. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alphaalpha or alphabeta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners etc. Each CD8 subunit is comprised of an extracellular domain containing a v-type Ig-like domain, a single pass transmembrane portion and a short intracellular domain. The Ig domain of CD8 alpha binds to antibodies.
Probab=31.72 E-value=30 Score=22.86 Aligned_cols=26 Identities=31% Similarity=0.503 Sum_probs=16.1
Q ss_pred CCCCeEEEeccCCCccccCCCcccCCCCCccc
Q psy12346 45 NTESGTYTCIVCAQPLFSSQTKFDSGCGWPAF 76 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF 76 (107)
..+.|+|.|+.... ..-.| |.|=|.|
T Consensus 78 ~sDsgtY~Ca~~~~----~~~~F--g~~~~~~ 103 (104)
T cd05720 78 KENEGYYFCSVASN----SVLYF--SSFVPVF 103 (104)
T ss_pred HHHCEEEEEEEccC----CceEE--cCceecc
Confidence 34689999997632 23334 4466666
No 56
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=31.06 E-value=26 Score=20.28 Aligned_cols=29 Identities=17% Similarity=0.532 Sum_probs=17.9
Q ss_pred EEEeccCCCcc-ccCCC-ccc-CCCCCccccc
Q psy12346 50 TYTCIVCAQPL-FSSQT-KFD-SGCGWPAFND 78 (107)
Q Consensus 50 ~Y~C~~Cg~pL-F~S~~-KFd-Sg~GWPSF~~ 78 (107)
.|.|..||..+ |.... .+. +-||=|-++.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~ 34 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRILFK 34 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEEEc
Confidence 69999999965 33332 222 3377666665
No 57
>cd05734 Ig7_DSCAM Seventh immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM). Ig7_DSCAM: the seventh immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM). DSCAM is a cell adhesion molecule expressed largely in the developing nervous system. The gene encoding DSCAM is located at human chromosome 21q22, the locus associated with the mental retardation phenotype of Down Syndrome. DSCAM is predicted to be the largest member of the IG superfamily. It has been demonstrated that DSCAM can mediate cation-independent homophilic intercellular adhesion.
Probab=30.79 E-value=34 Score=20.92 Aligned_cols=14 Identities=36% Similarity=0.653 Sum_probs=10.9
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|+|.|++-.
T Consensus 52 ~~~D~G~Y~C~a~N 65 (79)
T cd05734 52 LEEDSGYYLCKVSN 65 (79)
T ss_pred CcccCEEEEEEEEe
Confidence 34678999998864
No 58
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=30.75 E-value=34 Score=19.52 Aligned_cols=12 Identities=8% Similarity=-0.142 Sum_probs=9.9
Q ss_pred ceeeEEeCCCCC
Q psy12346 95 KLYGDLVSSHPK 106 (107)
Q Consensus 95 m~RtEV~C~~c~ 106 (107)
|.-|+|+|.+|.
T Consensus 1 Ma~i~v~CP~C~ 12 (36)
T PF03811_consen 1 MAKIDVHCPRCQ 12 (36)
T ss_pred CCcEeeeCCCCC
Confidence 566899999986
No 59
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=30.39 E-value=35 Score=19.71 Aligned_cols=13 Identities=23% Similarity=0.600 Sum_probs=7.7
Q ss_pred CCeEEEeccCCCc
Q psy12346 47 ESGTYTCIVCAQP 59 (107)
Q Consensus 47 ~~G~Y~C~~Cg~p 59 (107)
.-.+|.|..||+-
T Consensus 3 ~~~~YkC~~CGni 15 (36)
T PF06397_consen 3 KGEFYKCEHCGNI 15 (36)
T ss_dssp TTEEEE-TTT--E
T ss_pred cccEEEccCCCCE
Confidence 4568999999864
No 60
>cd05765 Ig_3 Subgroup of the immunoglobulin (Ig) superfamily. Ig_3: subgroup of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of the Ig superfamily are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond.
Probab=30.31 E-value=33 Score=20.64 Aligned_cols=14 Identities=29% Similarity=0.679 Sum_probs=10.9
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|+|.|++-.
T Consensus 55 ~~~D~G~Y~C~a~N 68 (81)
T cd05765 55 QPQDAGLYTCTARN 68 (81)
T ss_pred CcccCEEEEEEEec
Confidence 44679999998764
No 61
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=30.24 E-value=31 Score=17.72 Aligned_cols=19 Identities=32% Similarity=0.857 Sum_probs=11.3
Q ss_pred eccCCCccccCCCcccCCCC
Q psy12346 53 CIVCAQPLFSSQTKFDSGCG 72 (107)
Q Consensus 53 C~~Cg~pLF~S~~KFdSg~G 72 (107)
|..||.+| ..+++|=+.||
T Consensus 2 Cp~CG~~~-~~~~~fC~~CG 20 (23)
T PF13240_consen 2 CPNCGAEI-EDDAKFCPNCG 20 (23)
T ss_pred CcccCCCC-CCcCcchhhhC
Confidence 55566666 45566655555
No 62
>cd07693 Ig1_Robo First immunoglobulin (Ig)-like domain in Robo (roundabout) receptors and similar proteins. Ig1_Robo: domain similar to the first immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit res
Probab=30.12 E-value=36 Score=20.92 Aligned_cols=13 Identities=23% Similarity=0.825 Sum_probs=10.5
Q ss_pred CCCCeEEEeccCC
Q psy12346 45 NTESGTYTCIVCA 57 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg 57 (107)
..+.|.|.|++-.
T Consensus 73 ~~D~G~Y~C~a~N 85 (100)
T cd07693 73 RSDEGVYVCVAHN 85 (100)
T ss_pred cCcCEEEEEEEEc
Confidence 5689999998753
No 63
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=29.12 E-value=28 Score=20.39 Aligned_cols=16 Identities=25% Similarity=0.829 Sum_probs=8.7
Q ss_pred CCCCCCCeEEEeccCC
Q psy12346 42 YNKNTESGTYTCIVCA 57 (107)
Q Consensus 42 y~~~~~~G~Y~C~~Cg 57 (107)
|.+....|.|+|..|+
T Consensus 18 ~~d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 18 FDDKDGRGTWICRQCG 33 (40)
T ss_dssp ETT----S-EEETTTT
T ss_pred CcCcccCCCEECCCCC
Confidence 3455667999999994
No 64
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=28.66 E-value=23 Score=22.48 Aligned_cols=10 Identities=40% Similarity=1.069 Sum_probs=8.3
Q ss_pred EeccCCCccc
Q psy12346 52 TCIVCAQPLF 61 (107)
Q Consensus 52 ~C~~Cg~pLF 61 (107)
||..||.|+=
T Consensus 5 HC~~CG~~Ip 14 (59)
T PF09889_consen 5 HCPVCGKPIP 14 (59)
T ss_pred cCCcCCCcCC
Confidence 7999999874
No 65
>cd04977 Ig1_NCAM-1_like First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1 and similar proteins. Ig1_NCAM-1 like: first immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1. NCAM-1 plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-nonNCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves the Ig1, Ig2, and Ig3 domains. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the s
Probab=28.60 E-value=37 Score=21.79 Aligned_cols=15 Identities=20% Similarity=0.651 Sum_probs=11.6
Q ss_pred CCCCCeEEEeccCCC
Q psy12346 44 KNTESGTYTCIVCAQ 58 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg~ 58 (107)
...+.|+|.|.+-..
T Consensus 65 ~~~D~G~Y~C~A~N~ 79 (92)
T cd04977 65 NIEDAGIYKCVATDA 79 (92)
T ss_pred CcccCEEEEEEEEcC
Confidence 456899999988653
No 66
>PF13101 DUF3945: Protein of unknown function (DUF3945)
Probab=28.49 E-value=32 Score=21.32 Aligned_cols=23 Identities=22% Similarity=0.125 Sum_probs=16.5
Q ss_pred CCHHHHHhcCCHHHHHHHhhcCC
Q psy12346 12 INKEELKKRLTPMQYHVTQEKGT 34 (107)
Q Consensus 12 ~sd~ewk~~Lt~~qy~V~r~~gT 34 (107)
+++.-.-..||++|.+.|+++.+
T Consensus 26 ip~~i~g~~Ls~~q~~~L~~G~~ 48 (59)
T PF13101_consen 26 IPDKIKGVELSPEQKEDLREGKP 48 (59)
T ss_pred ccceecCccCCHHHHHHHHCCCe
Confidence 34333445799999999998764
No 67
>cd05725 Ig3_Robo Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Ig3_Robo: domain similar to the third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit responsiveness, antagoni
Probab=28.41 E-value=30 Score=20.52 Aligned_cols=12 Identities=33% Similarity=0.717 Sum_probs=9.6
Q ss_pred CCCCeEEEeccC
Q psy12346 45 NTESGTYTCIVC 56 (107)
Q Consensus 45 ~~~~G~Y~C~~C 56 (107)
..+.|.|.|.+-
T Consensus 44 ~~D~G~Y~C~a~ 55 (69)
T cd05725 44 AGDEGSYTCEAE 55 (69)
T ss_pred hhHCEEEEEEEE
Confidence 457899999874
No 68
>cd05763 Ig_1 Subgroup of the immunoglobulin (Ig) superfamily. Ig_1: subgroup of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of the Ig superfamily are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond.
Probab=27.65 E-value=41 Score=20.26 Aligned_cols=14 Identities=29% Similarity=0.684 Sum_probs=10.7
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|.|.|.+..
T Consensus 48 ~~~D~G~Y~C~A~N 61 (75)
T cd05763 48 KIEDTGVYSCTAQN 61 (75)
T ss_pred CcccCEEEEEEEEc
Confidence 34579999998843
No 69
>KOG3507|consensus
Probab=27.55 E-value=37 Score=22.00 Aligned_cols=15 Identities=33% Similarity=0.499 Sum_probs=12.1
Q ss_pred CCCeEEEeccCCCcc
Q psy12346 46 TESGTYTCIVCAQPL 60 (107)
Q Consensus 46 ~~~G~Y~C~~Cg~pL 60 (107)
...=+|+|+-||+.+
T Consensus 16 ~~~miYiCgdC~~en 30 (62)
T KOG3507|consen 16 TATMIYICGDCGQEN 30 (62)
T ss_pred cccEEEEeccccccc
Confidence 356799999999764
No 70
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=27.30 E-value=28 Score=19.36 Aligned_cols=17 Identities=12% Similarity=0.470 Sum_probs=13.1
Q ss_pred CeEEEeccCCCccccCC
Q psy12346 48 SGTYTCIVCAQPLFSSQ 64 (107)
Q Consensus 48 ~G~Y~C~~Cg~pLF~S~ 64 (107)
--.++|..||..+|+.+
T Consensus 30 vp~~~C~~CGE~~~~~~ 46 (46)
T TIGR03831 30 VPALVCPQCGEEYLDAE 46 (46)
T ss_pred CCccccccCCCEeeCCC
Confidence 34567999999999753
No 71
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.95 E-value=24 Score=25.31 Aligned_cols=14 Identities=36% Similarity=0.971 Sum_probs=12.7
Q ss_pred CCeEEEeccCCCcc
Q psy12346 47 ESGTYTCIVCAQPL 60 (107)
Q Consensus 47 ~~G~Y~C~~Cg~pL 60 (107)
+-|.+.|..||+++
T Consensus 46 e~G~t~CP~Cg~~~ 59 (115)
T COG1885 46 EVGSTSCPKCGEPF 59 (115)
T ss_pred ecccccCCCCCCcc
Confidence 68999999999986
No 72
>smart00406 IGv Immunoglobulin V-Type.
Probab=26.79 E-value=32 Score=20.27 Aligned_cols=10 Identities=50% Similarity=1.105 Sum_probs=7.8
Q ss_pred CCCeEEEecc
Q psy12346 46 TESGTYTCIV 55 (107)
Q Consensus 46 ~~~G~Y~C~~ 55 (107)
.+.|+|.|+.
T Consensus 72 ~D~G~Y~C~v 81 (81)
T smart00406 72 EDTGTYYCAV 81 (81)
T ss_pred HHCEEEEEcC
Confidence 3689999963
No 73
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=26.59 E-value=53 Score=28.53 Aligned_cols=45 Identities=27% Similarity=0.617 Sum_probs=26.2
Q ss_pred HHHHhcCCHHH----HHHHhhcCCC----CCCCCCCC----CCCCCeEEEeccCCCc
Q psy12346 15 EELKKRLTPMQ----YHVTQEKGTE----RPFSGKYN----KNTESGTYTCIVCAQP 59 (107)
Q Consensus 15 ~ewk~~Lt~~q----y~V~r~~gTE----~pfsg~y~----~~~~~G~Y~C~~Cg~p 59 (107)
+++|+++...+ |--|+..|-. =||-++-. -+...|+|+|-+||.-
T Consensus 8 ~~l~~~~dIvdvI~~~v~Lkk~G~~y~~lCPFH~EktPSf~V~~~k~~yhCFGCg~~ 64 (568)
T COG0358 8 DELRERIDIVDVIGEYVKLKKQGANYTGLCPFHAEKTPSFTVSPEKGFYHCFGCGAG 64 (568)
T ss_pred HHHHHcCCHHHHHhhheEeeecCCCceeECcCCCCCCCCceEeCCCCeEecCCCCCC
Confidence 45666666443 3345555533 23433332 2346899999999975
No 74
>KOG3549|consensus
Probab=26.43 E-value=99 Score=26.87 Aligned_cols=59 Identities=15% Similarity=0.172 Sum_probs=39.0
Q ss_pred HHHHHHHhhcCCCCCCCCCCC-----------CCCCCeEEEeccCCCccccCCCc--ccCCCCCccccc-ccC
Q psy12346 23 PMQYHVTQEKGTERPFSGKYN-----------KNTESGTYTCIVCAQPLFSSQTK--FDSGCGWPAFND-VLD 81 (107)
Q Consensus 23 ~~qy~V~r~~gTE~pfsg~y~-----------~~~~~G~Y~C~~Cg~pLF~S~~K--FdSg~GWPSF~~-pi~ 81 (107)
++.-+|||++|-|--.+=+|. ....+-.=+..+|..|||+|.-+ ++|||-=||=.. |+.
T Consensus 119 eevV~iLRNAGdeVtlTV~~lr~ApaFLklpL~~~~p~SD~ssg~sspl~DsGlhln~ns~T~s~Scss~P~s 191 (505)
T KOG3549|consen 119 EEVVNILRNAGDEVTLTVKHLRAAPAFLKLPLTKDTPDSDNSSGCSSPLADSGLHLNVNSGTISRSCSSSPMS 191 (505)
T ss_pred HHHHHHHHhcCCEEEEEeHhhhcCcHHhcCccCCCCCCccccccccccccccceeecccCCCccCCCCCCCCC
Confidence 567789999998854444332 33334455668999999999877 556665555544 443
No 75
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=25.90 E-value=34 Score=24.54 Aligned_cols=16 Identities=38% Similarity=0.794 Sum_probs=10.1
Q ss_pred CeEEEeccCCCccccC
Q psy12346 48 SGTYTCIVCAQPLFSS 63 (107)
Q Consensus 48 ~G~Y~C~~Cg~pLF~S 63 (107)
.|.|.|..||.+|..-
T Consensus 121 ~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 121 DGTFTCPRCGEELEED 136 (147)
T ss_pred CCcEECCCCCCEEEEc
Confidence 5667777777766543
No 76
>cd05735 Ig8_DSCAM Eight immunoglobulin (Ig) domain of Down Syndrome Cell Adhesion molecule (DSCAM). Ig8_DSCAM: the eight immunoglobulin (Ig) domain of Down Syndrome Cell Adhesion molecule (DSCAM). DSCAM is a cell adhesion molecule expressed largely in the developing nervous system. The gene encoding DSCAM is located at human chromosome 21q22, the locus associated with the mental retardation phenotype of Down Syndrome. DSCAM is predicted to be the largest member of the IG superfamily. It has been demonstrated that DSCAM can mediate cation-independent homophilic intercellular adhesion.
Probab=25.31 E-value=45 Score=21.25 Aligned_cols=12 Identities=25% Similarity=0.678 Sum_probs=9.8
Q ss_pred CCCCeEEEeccC
Q psy12346 45 NTESGTYTCIVC 56 (107)
Q Consensus 45 ~~~~G~Y~C~~C 56 (107)
..+.|.|.|.+=
T Consensus 56 ~~D~G~YtC~A~ 67 (88)
T cd05735 56 REDSGFFSCHAI 67 (88)
T ss_pred cccCEEEEEEEE
Confidence 568899999873
No 77
>cd05899 IgV_TCR_beta Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) bet a chain. IgV_TCR_beta: immunoglobulin (Ig) variable domain of the beta chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the alpha chain of alpha/beta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens; they recognize proteins antigens directly and without antigen processing, and MHC independently of the bound peptide.
Probab=25.26 E-value=48 Score=21.67 Aligned_cols=13 Identities=23% Similarity=0.501 Sum_probs=9.9
Q ss_pred CCCCeEEEeccCC
Q psy12346 45 NTESGTYTCIVCA 57 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg 57 (107)
..+.|+|.|++-.
T Consensus 81 ~~Dsg~Y~Ca~~~ 93 (110)
T cd05899 81 PEDSAVYLCASSL 93 (110)
T ss_pred hhhCEEEEEEeeC
Confidence 3478999998753
No 78
>cd05871 Ig_Semaphorin_classIII Immunoglobulin (Ig)-like domain of class III semaphorin. Ig_Semaphorin_class III; Immunoglobulin (Ig)-like domain of class III semaphorins. Semaphorins are classified into various classes on the basis of structural features additional to the Sema domain. Class III semaphorins are a vertebrate class having a Sema domain, an Ig domain, a short basic domain, and are secreted. They have been shown to be axonal guidance cues and have a part in the regulation of the cardiovascular, immune and respiratory systems. Sema3A, the prototype member of this class III subfamily, induces growth cone collapse and is an inhibitor of axonal sprouting. In perinatal rat cortex as a chemoattractant, it functions to direct, for pyramidal neurons, the orientated extension of apical dendrites. It may play a role, prior to the development of apical dendrites, in signaling the radial migration of newborn cortical neurons towards the upper layers. Sema3A selectively inhibits vascula
Probab=25.15 E-value=37 Score=22.04 Aligned_cols=14 Identities=29% Similarity=0.833 Sum_probs=10.6
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|+|.|++-+
T Consensus 61 ~~~DsG~Y~C~a~~ 74 (91)
T cd05871 61 QRSDAGVYTCTAVE 74 (91)
T ss_pred ChhHCEEEEEEEEc
Confidence 34578999998854
No 79
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=25.04 E-value=47 Score=19.28 Aligned_cols=23 Identities=30% Similarity=0.681 Sum_probs=14.9
Q ss_pred CCCCC--CCCCCCCCeEEEeccCCC
Q psy12346 36 RPFSG--KYNKNTESGTYTCIVCAQ 58 (107)
Q Consensus 36 ~pfsg--~y~~~~~~G~Y~C~~Cg~ 58 (107)
=|+-| ++......+.|.|..|+.
T Consensus 21 CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 21 CPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCeeeEEeCCCCeEECCCCCC
Confidence 34544 344445589999999874
No 80
>KOG3141|consensus
Probab=24.93 E-value=25 Score=29.19 Aligned_cols=32 Identities=19% Similarity=0.340 Sum_probs=27.6
Q ss_pred HHHHHHhhcCCCCCCCCCCCCCCCCeEEEeccC
Q psy12346 24 MQYHVTQEKGTERPFSGKYNKNTESGTYTCIVC 56 (107)
Q Consensus 24 ~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~C 56 (107)
.+|+|+ +.|=++|.+--+.+++.+|-|+.+.-
T Consensus 142 ~eF~Vt-~~al~~pGt~l~~~hFk~GqyVDV~g 173 (310)
T KOG3141|consen 142 REFRVT-EEALLPPGTPLFARHFKPGQYVDVTG 173 (310)
T ss_pred heEeec-hhccCCCCcccchhhcCCCceEEEEe
Confidence 356777 88999999999999999999998753
No 81
>PF12773 DZR: Double zinc ribbon
Probab=24.84 E-value=47 Score=19.14 Aligned_cols=24 Identities=29% Similarity=0.560 Sum_probs=14.9
Q ss_pred EEEeccCCCccc--cCCCcccCCCCC
Q psy12346 50 TYTCIVCAQPLF--SSQTKFDSGCGW 73 (107)
Q Consensus 50 ~Y~C~~Cg~pLF--~S~~KFdSg~GW 73 (107)
.=.|..||.+|. ....++=+.||.
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcC
Confidence 345677777777 444556666665
No 82
>cd07700 IgV_CD8_beta Immunoglobulin (Ig) like domain of CD8 beta chain. IgV_CD8_beta: immunoglobulin (Ig)-like domain in CD8 beta. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion and a short intracellular domain.
Probab=24.73 E-value=42 Score=22.04 Aligned_cols=13 Identities=46% Similarity=0.917 Sum_probs=10.0
Q ss_pred CCCCCeEEEeccC
Q psy12346 44 KNTESGTYTCIVC 56 (107)
Q Consensus 44 ~~~~~G~Y~C~~C 56 (107)
...+.|+|.|+.-
T Consensus 80 ~~~Dsg~YyCa~~ 92 (107)
T cd07700 80 KPEDSGTYFCMTV 92 (107)
T ss_pred CHHHCEEEEEeEc
Confidence 3457899999974
No 83
>cd05738 Ig2_RPTP_IIa_LAR_like Second immunoglobulin (Ig)-like domain of the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR. Ig2_RPTP_IIa_LAR_like: domain similar to the second immunoglobulin (Ig)-like domain found in the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR. LAR belongs to the RPTP type IIa subfamily. Members of this subfamily are cell adhesion molecule-like proteins involved in central nervous system (CNS) development. They have large extracellular portions, comprised of multiple Ig-like domains and two to nine fibronectin type III (FNIII) domains, and a cytoplasmic portion having two tandem phosphatase domains.
Probab=24.63 E-value=44 Score=20.32 Aligned_cols=13 Identities=23% Similarity=0.900 Sum_probs=10.5
Q ss_pred CCCCCeEEEeccC
Q psy12346 44 KNTESGTYTCIVC 56 (107)
Q Consensus 44 ~~~~~G~Y~C~~C 56 (107)
...+.|.|.|++.
T Consensus 46 ~~~D~G~Y~C~a~ 58 (74)
T cd05738 46 EESDQGKYECVAT 58 (74)
T ss_pred ChhhCEEEEEEEE
Confidence 3457899999887
No 84
>cd05726 Ig4_Robo Fhird immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Ig4_Robo: domain similar to the fhird immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit responsiveness, antagoni
Probab=24.62 E-value=40 Score=21.19 Aligned_cols=14 Identities=21% Similarity=0.589 Sum_probs=10.8
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|+|.|++..
T Consensus 55 ~~~D~G~Y~C~a~N 68 (90)
T cd05726 55 QRSDVGYYICQTLN 68 (90)
T ss_pred ChhhCEEEEEEEEc
Confidence 34578999999854
No 85
>cd05874 Ig6_NrCAM Sixth immunoglobulin (Ig)-like domain of NrCAM (Ng (neuronglia) CAM-related cell adhesion molecule). Ig6_NrCAM: sixth immunoglobulin (Ig)-like domain of NrCAM (Ng (neuronglia) CAM-related cell adhesion molecule). NrCAM belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region, and an intracellular domain. NrCAM is primarily expressed in the nervous system.
Probab=24.60 E-value=45 Score=20.73 Aligned_cols=11 Identities=27% Similarity=0.619 Sum_probs=8.8
Q ss_pred CCeEEEeccCC
Q psy12346 47 ESGTYTCIVCA 57 (107)
Q Consensus 47 ~~G~Y~C~~Cg 57 (107)
+.|+|.|.+-.
T Consensus 54 d~G~Y~C~A~N 64 (77)
T cd05874 54 YEGVYQCTARN 64 (77)
T ss_pred CCEEEEEEEEc
Confidence 57999998754
No 86
>cd05723 Ig4_Neogenin Fourth immunoglobulin (Ig)-like domain in neogenin and similar proteins. Ig4_Neogenin: fourth immunoglobulin (Ig)-like domain in neogenin and related proteins. Neogenin is a cell surface protein which is expressed in the developing nervous system of vertebrate embryos in the growing nerve cells. It is also expressed in other embryonic tissues, and may play a general role in developmental processes such as cell migration, cell-cell recognition, and tissue growth regulation. Included in this group is the tumor suppressor protein DCC, which is deleted in colorectal carcinoma . DCC and neogenin each have four Ig-like domains followed by six fibronectin type III domains, a transmembrane domain, and an intracellular domain.
Probab=24.58 E-value=48 Score=19.97 Aligned_cols=14 Identities=29% Similarity=0.667 Sum_probs=10.5
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|.|.|.+-.
T Consensus 45 ~~~D~G~Y~C~A~N 58 (71)
T cd05723 45 VKSDEGFYQCIAEN 58 (71)
T ss_pred CcccCEEEEEEEEc
Confidence 34578999998754
No 87
>cd04967 Ig1_Contactin First Ig domain of contactin. Ig1_Contactin: First Ig domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III(FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 weeks postnata
Probab=24.49 E-value=47 Score=20.91 Aligned_cols=11 Identities=27% Similarity=0.987 Sum_probs=9.2
Q ss_pred CCCeEEEeccC
Q psy12346 46 TESGTYTCIVC 56 (107)
Q Consensus 46 ~~~G~Y~C~~C 56 (107)
...|.|.|.+-
T Consensus 69 ~d~G~Y~C~a~ 79 (91)
T cd04967 69 KDAGRYQCLAS 79 (91)
T ss_pred CCCEEEEEEEE
Confidence 57999999874
No 88
>cd07701 Ig1_Necl-3 First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3, also known as cell adhesion molecule 2 (CADM2)). Ig1_Necl-3: domain similar to the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-3, Necl-3 (also known as cell adhesion molecule 2 (CADM2), SynCAM2, IGSF4D). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region, belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-3 accumulates in central and peripheral nervous system tissue, and has been shown to selectively interact with oligodendrocytes.
Probab=24.48 E-value=49 Score=21.55 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=10.7
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|+|.|++=.
T Consensus 70 ~~~DsG~Y~C~~~t 83 (95)
T cd07701 70 SLSDEGQYTCSLFT 83 (95)
T ss_pred CcccCEEEEEEeEe
Confidence 44578999998754
No 89
>cd04981 IgV_H Immunoglobulin (Ig) heavy chain (H), variable (V) domain. IgV_H: Immunoglobulin (Ig) heavy chain (H), variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.
Probab=24.44 E-value=34 Score=23.19 Aligned_cols=12 Identities=17% Similarity=0.446 Sum_probs=9.3
Q ss_pred CCCeEEEeccCC
Q psy12346 46 TESGTYTCIVCA 57 (107)
Q Consensus 46 ~~~G~Y~C~~Cg 57 (107)
.+.|+|.|+.-.
T Consensus 86 ~Dsa~YyCa~~~ 97 (117)
T cd04981 86 EDTAVYYCARGL 97 (117)
T ss_pred HHCEEEEEEEEc
Confidence 368999998743
No 90
>cd05764 Ig_2 Subgroup of the immunoglobulin (Ig) superfamily. Ig_2: subgroup of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of the Ig superfamily are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond.
Probab=24.34 E-value=41 Score=20.09 Aligned_cols=14 Identities=29% Similarity=0.786 Sum_probs=11.1
Q ss_pred CCCCeEEEeccCCC
Q psy12346 45 NTESGTYTCIVCAQ 58 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg~ 58 (107)
..+.|.|.|.+-..
T Consensus 49 ~~D~G~Y~C~a~N~ 62 (74)
T cd05764 49 VKDTGSFTCIASNA 62 (74)
T ss_pred hhhCEEEEEEEECC
Confidence 45789999988754
No 91
>cd05750 Ig_Pro_neuregulin Immunoglobulin (Ig)-like domain in neuregulins (NRGs). Ig_Pro_neuregulin: immunoglobulin (Ig)-like domain in neuregulins (NRGs). NRGs are signaling molecules, which participate in cell-cell interactions in the nervous system, breast, heart, and other organ systems, and are implicated in the pathology of diseases including schizophrenia, multiple sclerosis, and breast cancer. There are four members of the neuregulin gene family (NRG1, -2, -3, and -4). The NRG-1 protein, binds to and activates the tyrosine kinases receptors ErbB3 and ErbB4, initiating signaling cascades. The other NRGs proteins bind one or the other or both of these ErbBs. NRG-1 has multiple functions; for example, in the brain it regulates various processes such as radial glia formation and neuronal migration, dendritic development, and expression of neurotransmitters receptors; in the peripheral nervous system NRG-1 regulates processes such as target cell differentiation, and Schwann cell surv
Probab=24.29 E-value=52 Score=19.42 Aligned_cols=13 Identities=54% Similarity=0.961 Sum_probs=10.0
Q ss_pred CCCCCeEEEeccC
Q psy12346 44 KNTESGTYTCIVC 56 (107)
Q Consensus 44 ~~~~~G~Y~C~~C 56 (107)
...+.|.|.|.+-
T Consensus 51 ~~~D~G~Y~C~a~ 63 (75)
T cd05750 51 KLADSGEYTCVVE 63 (75)
T ss_pred CcccCeEEEEEEE
Confidence 3467899999864
No 92
>cd05731 Ig3_L1-CAM_like Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). Ig3_L1-CAM_like: domain similar to the third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM and human neurofascin.
Probab=24.25 E-value=36 Score=19.90 Aligned_cols=13 Identities=23% Similarity=0.741 Sum_probs=9.8
Q ss_pred CCCCeEEEeccCC
Q psy12346 45 NTESGTYTCIVCA 57 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg 57 (107)
..+.|.|.|.+-.
T Consensus 45 ~~D~G~Y~C~a~N 57 (71)
T cd05731 45 EEDDGEYRCTASN 57 (71)
T ss_pred HHHCEEEEEEEEe
Confidence 3568999998754
No 93
>cd05854 Ig6_Contactin-2 Sixth Ig domain of contactin-2. Ig6_Contactin-2: Sixth Ig domain of the neural cell adhesion molecule contactin-2-like. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-2 (TAG-1, axonin-1) facilitates cell adhesion by homophilic binding between molecules in apposed membranes. It may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module by contacts between IG domains 1 and 4, and domains 2 and 3. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-2 is also expressed in retinal amacrine cells in the developing c
Probab=24.02 E-value=42 Score=21.27 Aligned_cols=14 Identities=36% Similarity=0.717 Sum_probs=10.3
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|.|.|.+=.
T Consensus 55 ~~~D~G~YtC~A~n 68 (85)
T cd05854 55 QLSHAGTYTCTAQT 68 (85)
T ss_pred ChhhCeEEEEEEec
Confidence 44578999997643
No 94
>cd05746 Ig4_Peroxidasin Fourth immunoglobulin (Ig)-like domain of peroxidasin. Ig4_Peroxidasin: the fourth immunoglobulin (Ig)-like domain in peroxidasin. Peroxidasin has a peroxidase domain and interacting extracellular motifs containing four Ig-like domains. It has been suggested that peroxidasin is secreted, and has functions related to the stabilization of the extracellular matrix. It may play a part in various other important processes such as removal and destruction of cells, which have undergone programmed cell death, and protection of the organism against non-self.
Probab=23.96 E-value=43 Score=20.03 Aligned_cols=14 Identities=21% Similarity=0.631 Sum_probs=10.6
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|.|.|.+-.
T Consensus 44 ~~~D~G~Y~C~a~N 57 (69)
T cd05746 44 GVADQGRYECVARN 57 (69)
T ss_pred ChhhCEEEEEEEEC
Confidence 35678999998753
No 95
>PF12368 DUF3650: Protein of unknown function (DUF3650) ; InterPro: IPR022111 This domain family is found in bacteria, and is approximately 30 amino acids in length. The family is found in association with PF00581 from PFAM. There is a single completely conserved residue N that may be functionally important.
Probab=23.80 E-value=40 Score=18.62 Aligned_cols=12 Identities=33% Similarity=0.637 Sum_probs=9.6
Q ss_pred cCCHHHHHhcCC
Q psy12346 11 KINKEELKKRLT 22 (107)
Q Consensus 11 ~~sd~ewk~~Lt 22 (107)
.+|++||.++|.
T Consensus 15 ~ls~ee~~~RL~ 26 (28)
T PF12368_consen 15 GLSEEEVAERLA 26 (28)
T ss_pred CCCHHHHHHHHH
Confidence 588999988874
No 96
>cd05724 Ig2_Robo Second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Ig2_Robo: domain similar to the second immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit responsiveness, antago
Probab=23.43 E-value=53 Score=19.94 Aligned_cols=14 Identities=29% Similarity=0.923 Sum_probs=10.4
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
.....|.|.|.+-.
T Consensus 59 ~~~D~G~Y~C~a~N 72 (86)
T cd05724 59 RKSDEGTYKCVATN 72 (86)
T ss_pred CcccCEEEEEEEEe
Confidence 34578999998743
No 97
>cd04970 Ig6_Contactin_like Sixth Ig domain of contactin. Ig6_Contactin_like: Sixth Ig domain of contactins. Contactins are neural cell adhesion molecules and are comprised of six Ig domains followed by four fibronectin type III(FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. The first four Ig domains form the intermolecular binding fragment, which arranges as a compact U-shaped module via contacts between Ig domains 1 and 4, and between Ig domains 2 and 3. Contactin-2 (TAG-1, axonin-1) may play a part in the neuronal processes of neurite outgrowth, axon guidance and fasciculation, and neuronal migration. This group also includes contactin-1 and contactin-5. The different contactins show different expression patterns in the central nervous system. During development and in adulthood, contactin-2 is transiently expressed in subsets of central and peripheral neurons. Contactin-5 is expressed specifically in the rat postnatal nervous system, peaking at about 3 week
Probab=23.37 E-value=41 Score=20.84 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=10.2
Q ss_pred CCCCeEEEeccCC
Q psy12346 45 NTESGTYTCIVCA 57 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg 57 (107)
....|.|.|.+-.
T Consensus 56 ~~D~G~Y~C~a~n 68 (85)
T cd04970 56 LKHAGKYTCTAQT 68 (85)
T ss_pred HHhCeeeEEEEec
Confidence 4578999998754
No 98
>cd05870 Ig5_NCAM-2 Fifth immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule NCAM-2 (also known as OCAM/mamFas II and RNCAM). Ig5_NCAM-2: the fifth immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule NCAM-2 (also known as OCAM/mamFas II and RNCAM). NCAM-2 is organized similarly to NCAM , including five N-terminal Ig-like domains and two fibronectin type III domains. NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE), and may function like NCAM, as an adhesion molecule.
Probab=23.24 E-value=56 Score=20.91 Aligned_cols=14 Identities=36% Similarity=0.745 Sum_probs=10.8
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|.|.|.+-.
T Consensus 72 ~~~D~G~Y~C~A~N 85 (98)
T cd05870 72 KLSDSGRYDCEAAS 85 (98)
T ss_pred CcCCCEEEEEEEec
Confidence 34688999998754
No 99
>cd05753 Ig2_FcgammaR_like Second immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs) and similar proteins. Ig2_FcgammaR_like: domain similar to the second immunoglobulin (Ig)-like domain of Fcgamma-receptors (FcgammaRs). Interactions between IgG and FcgammaR are important to the initiation of cellular and humoral response. IgG binding to FcgammaR leads to a cascade of signals and ultimately to functions such as antibody-dependent-cellular-cytotoxicity (ADCC), endocytosis, phagocytosis, release of inflammatory mediators, etc. FcgammaR has two Ig-like domains. This group also contains FcepsilonRI, which binds IgE with high affinity.
Probab=23.23 E-value=43 Score=21.22 Aligned_cols=13 Identities=31% Similarity=0.603 Sum_probs=9.7
Q ss_pred CCCCeEEEeccCC
Q psy12346 45 NTESGTYTCIVCA 57 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg 57 (107)
....|.|.|.+=+
T Consensus 57 ~~dsG~Y~C~~~~ 69 (83)
T cd05753 57 LSDSGSYHCSGII 69 (83)
T ss_pred HHHCEEEEEEEEe
Confidence 3568999997643
No 100
>PF10880 DUF2673: Protein of unknown function (DUF2673); InterPro: IPR024247 This family of proteins with unknown function appears to be restricted to Rickettsiae spp.
Probab=23.20 E-value=34 Score=22.11 Aligned_cols=15 Identities=27% Similarity=0.324 Sum_probs=13.1
Q ss_pred HHHHhcCCHHHHHHH
Q psy12346 15 EELKKRLTPMQYHVT 29 (107)
Q Consensus 15 ~ewk~~Lt~~qy~V~ 29 (107)
..|.+.||..||..+
T Consensus 44 q~wvasltadqynml 58 (65)
T PF10880_consen 44 QAWVASLTADQYNML 58 (65)
T ss_pred HHHHHHhhhhhhccc
Confidence 569999999999876
No 101
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=23.17 E-value=38 Score=19.68 Aligned_cols=19 Identities=26% Similarity=0.502 Sum_probs=14.8
Q ss_pred CeEEEeccCCCccccCCCc
Q psy12346 48 SGTYTCIVCAQPLFSSQTK 66 (107)
Q Consensus 48 ~G~Y~C~~Cg~pLF~S~~K 66 (107)
.|+=.|..||.+|.....+
T Consensus 3 ~g~l~C~~CG~~m~~~~~~ 21 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKRK 21 (58)
T ss_pred CCcEEcccCCcEeEEEECC
Confidence 3677899999999885544
No 102
>KOG4397|consensus
Probab=23.10 E-value=22 Score=27.90 Aligned_cols=12 Identities=50% Similarity=1.096 Sum_probs=10.7
Q ss_pred EEeccCCCcccc
Q psy12346 51 YTCIVCAQPLFS 62 (107)
Q Consensus 51 Y~C~~Cg~pLF~ 62 (107)
|.|+.|+.|||=
T Consensus 89 ~~C~~C~Lpl~Y 100 (213)
T KOG4397|consen 89 KKCIKCSLPLFY 100 (213)
T ss_pred HhhhcCCceeEE
Confidence 789999999983
No 103
>cd05732 Ig5_NCAM-1_like Fifth immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule NCAM-1 (NCAM) and similar proteins. Ig5_NCAM-1 like: domain similar to the fifth immunoglobulin (Ig)-like domain of Neural Cell Adhesion Molecule NCAM-1 (NCAM). NCAM plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-non-NCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves Ig1, Ig2, and Ig3. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM mole
Probab=22.86 E-value=57 Score=20.36 Aligned_cols=14 Identities=29% Similarity=0.660 Sum_probs=10.8
Q ss_pred CCCCeEEEeccCCC
Q psy12346 45 NTESGTYTCIVCAQ 58 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg~ 58 (107)
..+.|.|.|.+-..
T Consensus 71 ~~D~G~Y~C~a~N~ 84 (96)
T cd05732 71 LTDAGRYDCEASNR 84 (96)
T ss_pred cCcCEEeEEEEEeC
Confidence 46789999987643
No 104
>cd05760 Ig2_PTK7 Second immunoglobulin (Ig)-like domain of protein tyrosine kinase (PTK) 7, also known as CCK4. Ig2_PTK7: domain similar to the second immunoglobulin (Ig)-like domain in protein tyrosine kinase (PTK) 7, also known as CCK4. PTK7 is a subfamily of the receptor protein tyrosine kinase family, and is referred to as an RPTK-like molecule. RPTKs transduce extracellular signals across the cell membrane, and play important roles in regulating cell proliferation, migration, and differentiation. PTK7 is organized as an extracellular portion having seven Ig-like domains, a single transmembrane region, and a cytoplasmic tyrosine kinase-like domain. PTK7 is considered a pseudokinase as it has several unusual residues in some of the highly conserved tyrosine kinase (TK) motifs; it is predicted to lack TK activity. PTK7 may function as a cell-adhesion molecule. PTK7 mRNA is expressed at high levels in placenta, melanocytes, liver, lung, pancreas, and kidney. PTK7 is overexpressed in s
Probab=22.73 E-value=59 Score=19.94 Aligned_cols=13 Identities=31% Similarity=0.618 Sum_probs=10.2
Q ss_pred CCCCeEEEeccCC
Q psy12346 45 NTESGTYTCIVCA 57 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg 57 (107)
..+.|.|.|.+-.
T Consensus 47 ~~D~G~Y~C~a~N 59 (77)
T cd05760 47 PDDSGLYYCCAHN 59 (77)
T ss_pred cccCEEEEEEEEe
Confidence 4578999998754
No 105
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=22.72 E-value=33 Score=23.91 Aligned_cols=48 Identities=19% Similarity=0.301 Sum_probs=30.3
Q ss_pred CCCeEEEeccCCCccccCCCcccCCCCCcccccccCCCCeEEeecCCCCceeeEEeCCCC
Q psy12346 46 TESGTYTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGKVKLTKDTSHGKLYGDLVSSHP 105 (107)
Q Consensus 46 ~~~G~Y~C~~Cg~pLF~S~~KFdSg~GWPSF~~pi~~~~v~~~~D~s~gm~RtEV~C~~c 105 (107)
+.+++=.|+.||.||=.=. .|=|.++.-+.. -...+..-||. ++|++|
T Consensus 30 K~~~~p~C~~cg~pL~Gi~------r~RP~e~~r~sk--t~krp~RpYGG----~lc~~c 77 (93)
T COG2174 30 KKPTIPKCAICGRPLGGIP------RGRPREFRRLSK--TKKRPERPYGG----YLCANC 77 (93)
T ss_pred ccCCCCcccccCCccCCcc------CCCcHHHHhccc--cccCcCCCcCc----eecHHH
Confidence 4678889999999995432 455655554421 22344455666 677776
No 106
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.53 E-value=47 Score=18.55 Aligned_cols=14 Identities=29% Similarity=0.665 Sum_probs=12.0
Q ss_pred CCCeEEEeccCCCc
Q psy12346 46 TESGTYTCIVCAQP 59 (107)
Q Consensus 46 ~~~G~Y~C~~Cg~p 59 (107)
++.+.|+|.-||.-
T Consensus 17 ~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 17 KEDDYEVCIFCGSS 30 (33)
T ss_pred ecCCeEEcccCCcE
Confidence 78899999999863
No 107
>cd05852 Ig5_Contactin-1 Fifth Ig domain of contactin-1. Ig5_Contactin-1: fifth Ig domain of the neural cell adhesion molecule contactin-1. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains anchored to the membrane by glycosylphosphatidylinositol. Contactin-1 is differentially expressed in tumor tissues and may through a RhoA mechanism, facilitate invasion and metastasis of human lung adenocarcinoma.
Probab=22.50 E-value=46 Score=20.57 Aligned_cols=15 Identities=27% Similarity=0.687 Sum_probs=11.2
Q ss_pred CCCCCeEEEeccCCC
Q psy12346 44 KNTESGTYTCIVCAQ 58 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg~ 58 (107)
...+.|.|.|.+-..
T Consensus 47 ~~~D~G~Y~C~A~N~ 61 (73)
T cd05852 47 TKLDEGSYTCFAENN 61 (73)
T ss_pred ChhHCEEEEEEEECC
Confidence 345789999987653
No 108
>cd04971 Ig_TrKABC_d5 Fifth domain (immunoglobulin-like) of Trk receptors TrkA, TrkB and TrkC. TrkABC_d5: the fifth domain of Trk receptors TrkA, TrkB and TrkC, this is an immunoglobulin (Ig)-like domain which binds to neurotrophin. The Trk family of receptors are tyrosine kinase receptors. They are activated by dimerization, leading to autophosphorylation of intracellular tyrosine residues, and triggering the signal transduction pathway. TrkA, TrkB, and TrkC share significant sequence homology and domain organization. The first three domains are leucine-rich domains. The fourth and fifth domains are Ig-like domains playing a part in ligand binding. TrkA, Band C mediate the trophic effects of the neurotrophin Nerve growth factor (NGF) family. TrkA is recognized by NGF. TrkB is recognized by brain-derived neurotrophic factor (BDNF) and neurotrophin (NT)-4. TrkC is recognized by NT-3. NT-3 is promiscuous as in some cell systems it activates TrkA and TrkB receptors. TrkA is a receptor foun
Probab=22.36 E-value=57 Score=20.67 Aligned_cols=14 Identities=21% Similarity=0.525 Sum_probs=10.6
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|.|.|.+-.
T Consensus 54 ~~~D~G~YtC~A~N 67 (81)
T cd04971 54 THVNNGNYTLVASN 67 (81)
T ss_pred CcccCeEEEEEEEe
Confidence 34578999998754
No 109
>cd05857 Ig2_FGFR Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor. Ig2_FGFR: second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor. FGF receptors bind FGF signaling polypeptides. FGFs participate in multiple processes such as morphogenesis, development, and angiogenesis. FGFs bind to four FGF receptor tyrosine kinases (FGFR1, -2, -3, -4). Receptor diversity is controlled by alternative splicing producing splice variants with different ligand binding characteristics and different expression patterns. FGFRs have an extracellular region comprised of three IG-like domains, a single transmembrane helix, and an intracellular tyrosine kinase domain. Ligand binding and specificity reside in the Ig-like domains 2 and 3, and the linker region that connects these two. FGFR activation and signaling depend on FGF-induced dimerization, a process involving cell surface heparin or heparin sulfate proteoglycans.
Probab=22.35 E-value=59 Score=19.81 Aligned_cols=14 Identities=36% Similarity=0.805 Sum_probs=10.3
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|.|.|.+-.
T Consensus 59 ~~~D~G~Y~C~a~N 72 (85)
T cd05857 59 VPSDKGNYTCVVEN 72 (85)
T ss_pred CcccCEEEEEEEEe
Confidence 34578999998653
No 110
>PRK04860 hypothetical protein; Provisional
Probab=22.34 E-value=67 Score=23.84 Aligned_cols=37 Identities=14% Similarity=0.278 Sum_probs=23.8
Q ss_pred HHHHHhcCCHHHHHHHhhcCCCCCCCCCCCCCCCC---eEEEeccCCC
Q psy12346 14 KEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTES---GTYTCIVCAQ 58 (107)
Q Consensus 14 d~ewk~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~---G~Y~C~~Cg~ 58 (107)
+.|||..|.. -.|-++-++..|.-.... =.|.|. |+.
T Consensus 87 g~ewk~lm~~-------v~g~~~r~~h~~~~~~~~~~~~~Y~C~-C~~ 126 (160)
T PRK04860 87 GKEWQWMMES-------VLGVPARRTHQFEVQSVRGKTFPYRCK-CQE 126 (160)
T ss_pred CHHHHHHHHH-------hcCCCCcccCCCcCCccccCEEEEEcC-CCC
Confidence 6788765432 256677788866544322 369998 876
No 111
>PF13487 HD_5: HD domain; PDB: 3TMD_A 3TM8_B 3TMC_A 3TMB_B.
Probab=22.33 E-value=56 Score=19.96 Aligned_cols=13 Identities=31% Similarity=0.580 Sum_probs=6.9
Q ss_pred cCCHHHHHHHhhc
Q psy12346 20 RLTPMQYHVTQEK 32 (107)
Q Consensus 20 ~Lt~~qy~V~r~~ 32 (107)
+||++|+++++.+
T Consensus 2 ~Lt~~e~~~~~~H 14 (64)
T PF13487_consen 2 KLTPEEREIIQQH 14 (64)
T ss_dssp GS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHH
Confidence 4666666665544
No 112
>cd05856 Ig2_FGFRL1-like Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor_like-1(FGFRL1). Ig2_FGFRL1-like: second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor_like-1(FGFRL1). FGFRL1 is comprised of a signal peptide, three extracellular Ig-like modules, a transmembrane segment, and a short intracellular domain. FGFRL1 is expressed preferentially in skeletal tissues. Similar to FGF receptors, the expressed protein interacts specifically with heparin and with FGF2. FGFRL1 does not have a protein tyrosine kinase domain at its C terminus; neither does its cytoplasmic domain appear to interact with a signaling partner. It has been suggested that FGFRL1 may not have any direct signaling function, but instead acts as a decoy receptor trapping FGFs and preventing them from binding other receptors.
Probab=22.29 E-value=48 Score=19.76 Aligned_cols=13 Identities=46% Similarity=0.856 Sum_probs=10.0
Q ss_pred CCCCeEEEeccCC
Q psy12346 45 NTESGTYTCIVCA 57 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg 57 (107)
..+.|.|.|.+-.
T Consensus 57 ~~D~G~Y~C~a~N 69 (82)
T cd05856 57 PEDSGKYTCHVSN 69 (82)
T ss_pred hhhCEEEEEEEEc
Confidence 4578999998754
No 113
>cd05848 Ig1_Contactin-5 First Ig domain of contactin-5. Ig1_Contactin-5: First Ig domain of the neural cell adhesion molecule contactin-5. Contactins are comprised of six Ig domains followed by four fibronectin type III (FnIII) domains, anchored to the membrane by glycosylphosphatidylinositol. The different contactins show different expression patterns in the central nervous system. In rats, a lack of contactin-5 (NB-2) results in an impairment of the neuronal activity in the auditory system. Contactin-5 is expressed specifically in the postnatal nervous system, peaking at about 3 weeks postnatal. Contactin-5 is highly expressed in the adult human brain in the occipital lobe and in the amygdala; lower levels of expression have been detected in the corpus callosum, caudate nucleus, and spinal cord.
Probab=22.14 E-value=54 Score=21.13 Aligned_cols=12 Identities=33% Similarity=0.911 Sum_probs=9.6
Q ss_pred CCCeEEEeccCC
Q psy12346 46 TESGTYTCIVCA 57 (107)
Q Consensus 46 ~~~G~Y~C~~Cg 57 (107)
.+.|.|.|.+-.
T Consensus 69 ~D~G~Y~C~A~N 80 (94)
T cd05848 69 KDSGRYQCLATN 80 (94)
T ss_pred CcCEEEEEEEEc
Confidence 578999998753
No 114
>cd00233 VIP2 VIP2; A family of actin-ADP-ribosylating toxin. A member of the Bacillus-prodiced vegetative insecticidal proteins (VIPs) possesses high specificity against the major insect pest, corn rootworms, and belongs to a classs of binary toxins and regulators of biological pathways distinct from classical A-B toxins. A novel family of insecticidal ADP-ribosyltransferses were isolated from Bacillus cereus during vegetative growth, where VIP1 likely targets insect cells and VIP2 ribosylates actin. VIP2 shares significant sequence similarity with enzymatic components of other binary toxins, Clostridium botulinum C2 toxin, C. perfringens iota toxin, C. piroforme toxin, C. piroforme toxin and C. difficile toxin.
Probab=22.05 E-value=76 Score=23.85 Aligned_cols=18 Identities=22% Similarity=0.366 Sum_probs=14.4
Q ss_pred HHHHHhcCCHHHHHHHhh
Q psy12346 14 KEELKKRLTPMQYHVTQE 31 (107)
Q Consensus 14 d~ewk~~Lt~~qy~V~r~ 31 (107)
-.+|++.||++|...++.
T Consensus 20 ~~~w~~~Lt~~e~~Ai~~ 37 (201)
T cd00233 20 YKKWLKKLSPSEKEAIRE 37 (201)
T ss_pred HHHHHhhCCHHHHHHHHH
Confidence 367999999999886654
No 115
>cd05865 Ig1_NCAM-1 First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1. Ig1_NCAM-1: first immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1. NCAM-1 plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-nonNCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves the Ig1, Ig2, and Ig3 domains. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the surface of opposing cells (trans
Probab=21.96 E-value=53 Score=21.56 Aligned_cols=15 Identities=27% Similarity=0.782 Sum_probs=11.4
Q ss_pred CCCCCeEEEeccCCC
Q psy12346 44 KNTESGTYTCIVCAQ 58 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg~ 58 (107)
...+.|.|.|.+-..
T Consensus 68 ~~~D~G~YtC~A~N~ 82 (96)
T cd05865 68 NIDDAGIYKCVVSNE 82 (96)
T ss_pred ChhhCEEEEEEEEcC
Confidence 455789999987654
No 116
>cd04973 Ig1_FGFR First immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Ig1_FGFR: The first immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for all FGFs.
Probab=21.88 E-value=51 Score=20.34 Aligned_cols=14 Identities=29% Similarity=0.752 Sum_probs=10.8
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|+|.|.+-+
T Consensus 53 ~~~DsG~Y~C~a~n 66 (79)
T cd04973 53 VPRDSGLYACVTSS 66 (79)
T ss_pred ChhhCEEEEEEEeC
Confidence 34578999999854
No 117
>cd05717 Ig1_Necl-1-3_like First (N-terminal) immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-3 (also known as cell adhesion molecules CADM3, CADM1, and CADM2 respectively). Ig1_Necl-1-3_like: N-terminal immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1), and Necl-3 (CADM2). At least five nectin-like molecules have been identified (Necl-1 - Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1, Necl-2, and Necl-3 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue, and is important to the form
Probab=21.81 E-value=59 Score=20.56 Aligned_cols=14 Identities=29% Similarity=0.710 Sum_probs=10.4
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|+|.|++=.
T Consensus 70 ~~~DsG~Y~C~~~~ 83 (95)
T cd05717 70 SLSDEGRYTCSLYT 83 (95)
T ss_pred CcccCEEEEEEEec
Confidence 34578999998653
No 118
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=21.76 E-value=38 Score=22.02 Aligned_cols=9 Identities=33% Similarity=1.268 Sum_probs=7.6
Q ss_pred EeccCCCcc
Q psy12346 52 TCIVCAQPL 60 (107)
Q Consensus 52 ~C~~Cg~pL 60 (107)
||++||+++
T Consensus 10 HC~VCg~aI 18 (64)
T COG4068 10 HCVVCGKAI 18 (64)
T ss_pred cccccCCcC
Confidence 799999875
No 119
>cd05855 Ig_TrkB_d5 Fifth domain (immunoglobulin-like) of Trk receptor TrkB. TrkB_d5: the fifth domain of Trk receptor TrkB, this is an immunoglobulin (Ig)-like domain which binds to neurotrophin. The Trk family of receptors are tyrosine kinase receptors, which mediate the trophic effects of the neurotrophin Nerve growth factor (NGF) family. The Trks are activated by dimerization, leading to autophosphorylation of intracellular tyrosine residues, and triggering the signal transduction pathway. TrkB shares significant sequence homology and domain organization with TrkA, and TrkC. The first three domains are leucine-rich domains. The fourth and fifth domains are Ig-like domains playing a part in ligand binding. TrKB is recognized by brain-derived neurotrophic factor (BDNF) and neurotrophin (NT)-4. In some cell systems NT-3 can activate TrkA and TrkB receptors. TrKB transcripts are found throughout multiple structures of the central and peripheral nervous systems.
Probab=21.22 E-value=56 Score=21.05 Aligned_cols=12 Identities=25% Similarity=0.429 Sum_probs=9.6
Q ss_pred CCCeEEEeccCC
Q psy12346 46 TESGTYTCIVCA 57 (107)
Q Consensus 46 ~~~G~Y~C~~Cg 57 (107)
.+.|.|.|++-.
T Consensus 54 ~D~G~YtC~A~N 65 (79)
T cd05855 54 LNNGIYTLVAKN 65 (79)
T ss_pred ccCEEEEEEEEc
Confidence 479999998753
No 120
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=21.12 E-value=61 Score=17.85 Aligned_cols=12 Identities=42% Similarity=0.977 Sum_probs=10.4
Q ss_pred eEEEeccCCCcc
Q psy12346 49 GTYTCIVCAQPL 60 (107)
Q Consensus 49 G~Y~C~~Cg~pL 60 (107)
=.|.|..|+.+|
T Consensus 15 T~~~C~~C~v~l 26 (32)
T PF13842_consen 15 TRYMCSKCDVPL 26 (32)
T ss_pred eEEEccCCCCcc
Confidence 689999998776
No 121
>cd05876 Ig3_L1-CAM Third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). Ig3_L1-CAM: third immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 belongs to the L1 subfamily of cell adhesion molecules (CAMs) and is comprised of an extracellular region having six Ig-like domains, five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM.
Probab=21.05 E-value=54 Score=19.76 Aligned_cols=13 Identities=23% Similarity=0.708 Sum_probs=10.0
Q ss_pred CCCCeEEEeccCC
Q psy12346 45 NTESGTYTCIVCA 57 (107)
Q Consensus 45 ~~~~G~Y~C~~Cg 57 (107)
..+.|.|.|.+..
T Consensus 45 ~~D~G~Y~C~a~N 57 (71)
T cd05876 45 ESDDGEYVCTAEN 57 (71)
T ss_pred HHhCEEEEEEEEc
Confidence 3578999998754
No 122
>cd05867 Ig4_L1-CAM_like Fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). Ig4_L1-CAM_like: fourth immunoglobulin (Ig)-like domain of the L1 cell adhesion molecule (CAM). L1 is comprised of an extracellular region having six Ig-like domains and five fibronectin type III domains, a transmembrane region and an intracellular domain. L1 is primarily expressed in the nervous system and is involved in its development and function. L1 is associated with an X-linked recessive disorder, X-linked hydrocephalus, MASA syndrome, or spastic paraplegia type 1, that involves abnormalities of axonal growth. This group also contains the chicken neuron-glia cell adhesion molecule, Ng-CAM.
Probab=20.97 E-value=55 Score=19.86 Aligned_cols=14 Identities=14% Similarity=0.501 Sum_probs=10.6
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|+|.|.+-.
T Consensus 49 ~~~D~G~Y~C~a~N 62 (76)
T cd05867 49 QPSDTAVYQCEARN 62 (76)
T ss_pred ChhhCEEEEEEEEC
Confidence 34578999998754
No 123
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=20.94 E-value=55 Score=19.35 Aligned_cols=11 Identities=27% Similarity=0.658 Sum_probs=9.2
Q ss_pred EEEeccCCCcc
Q psy12346 50 TYTCIVCAQPL 60 (107)
Q Consensus 50 ~Y~C~~Cg~pL 60 (107)
+|.|..||.+.
T Consensus 2 ~Y~C~~Cg~~~ 12 (44)
T smart00659 2 IYICGECGREN 12 (44)
T ss_pred EEECCCCCCEe
Confidence 69999999864
No 124
>cd05729 Ig2_FGFR_like Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor and similar proteins. Ig2_FGFR_like: domain similar to the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor. FGF receptors bind FGF signaling polypeptides. FGFs participate in multiple processes such as morphogenesis, development, and angiogenesis. FGFs bind to four FGF receptor tyrosine kinases (FGFR1, -2, -3, -4). Receptor diversity is controlled by alternative splicing producing splice variants with different ligand binding characteristics and different expression patterns. FGFRs have an extracellular region comprised of three Ig-like domains, a single transmembrane helix, and an intracellular tyrosine kinase domain. Ligand binding and specificity reside in the Ig-like domains 2 and 3, and the linker region that connects these two. FGFR activation and signaling depend on FGF-induced dimerization, a process involving cell surface heparin or heparin
Probab=20.85 E-value=63 Score=19.20 Aligned_cols=13 Identities=54% Similarity=0.940 Sum_probs=10.0
Q ss_pred CCCCCeEEEeccC
Q psy12346 44 KNTESGTYTCIVC 56 (107)
Q Consensus 44 ~~~~~G~Y~C~~C 56 (107)
...+.|+|.|.+=
T Consensus 59 ~~~d~g~Y~C~~~ 71 (85)
T cd05729 59 VPSDSGKYTCIVE 71 (85)
T ss_pred CcccCEEEEEEEE
Confidence 3568899999763
No 125
>cd04982 IgV_TCR_gamma Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain. IgV_TCR_gamma: immunoglobulin (Ig) variable (V) domain of the gamma chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is
Probab=20.76 E-value=49 Score=21.70 Aligned_cols=11 Identities=36% Similarity=0.676 Sum_probs=9.1
Q ss_pred CCCeEEEeccC
Q psy12346 46 TESGTYTCIVC 56 (107)
Q Consensus 46 ~~~G~Y~C~~C 56 (107)
.+.|+|.|+.-
T Consensus 87 ~Dsg~Y~C~~~ 97 (116)
T cd04982 87 EDSATYYCAYW 97 (116)
T ss_pred HHCEEEEEEEe
Confidence 46899999874
No 126
>cd05866 Ig1_NCAM-2 First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-2. Ig1_NCAM-2: first immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-2 (OCAM/mamFas II, RNCAM). NCAM-2 is organized similarly to NCAM , including five N-terminal Ig-like domains and two fibronectin type III domains. NCAM-2 is differentially expressed in the developing and mature olfactory epithelium (OE), and may function like NCAM, as an adhesion molecule.
Probab=20.69 E-value=45 Score=21.83 Aligned_cols=15 Identities=20% Similarity=0.534 Sum_probs=11.6
Q ss_pred CCCCCeEEEeccCCC
Q psy12346 44 KNTESGTYTCIVCAQ 58 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg~ 58 (107)
...+.|+|.|.+...
T Consensus 64 ~~~D~G~Y~C~A~N~ 78 (92)
T cd05866 64 NIEDAGIYRCQATDA 78 (92)
T ss_pred ChHHCEEEEEEEEcC
Confidence 445789999988754
No 127
>cd05754 Ig3_Perlecan_like Third immunoglobulin (Ig)-like domain found in Perlecan and similar proteins. Ig3_Perlecan_like: domain similar to the third immunoglobulin (Ig)-like domain found in Perlecan. Perlecan is a large multi-domain heparin sulfate proteoglycan, important in tissue development and organogenesis. Perlecan can be represented as 5 major portions; its fourth major portion (domain IV) is a tandem repeat of immunoglobulin-like domains (Ig2-Ig15), which can vary in size due to alternative splicing. Perlecan binds many cellular and extracellular ligands. Its domain IV region has many binding sites. Some of these have been mapped at the level of individual Ig-like domains, including a site restricted to the Ig5 domain for heparin/sulfatide, a site restricted to the Ig3 domain for nidogen-1 and nidogen-2, a site restricted to Ig4-5 for fibronectin, and sites restricted to Ig2 and to Ig13-15 for fibulin-2.
Probab=20.50 E-value=51 Score=20.34 Aligned_cols=14 Identities=29% Similarity=0.669 Sum_probs=10.6
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|+|.|++-.
T Consensus 60 ~~~DsG~Y~C~a~n 73 (85)
T cd05754 60 QLSDAGTYVCTGSN 73 (85)
T ss_pred CHHHCEEEEEEEec
Confidence 34578999999754
No 128
>cd05740 Ig_CEACAM_D4 Fourth immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM). Ig_CEACAM_D4: immunoglobulin (Ig)-like domain 4 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions, it is a cell adhesion molecule, and a signaling molecule that regulates the growth of tumor cells, it is an angiogenic factor, and is a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two [D1, D4] or four [D1-D4] Ig-like domains on the cell surface. This family corresponds to the
Probab=20.19 E-value=57 Score=21.02 Aligned_cols=14 Identities=21% Similarity=0.688 Sum_probs=10.4
Q ss_pred CCCCCeEEEeccCC
Q psy12346 44 KNTESGTYTCIVCA 57 (107)
Q Consensus 44 ~~~~~G~Y~C~~Cg 57 (107)
...+.|.|.|.+-.
T Consensus 63 ~~~D~G~Y~C~a~N 76 (91)
T cd05740 63 TRSDTGHYQCEASN 76 (91)
T ss_pred ChhhCEEEEEEEEc
Confidence 34578999998744
No 129
>smart00410 IG_like Immunoglobulin like. IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
Probab=20.00 E-value=67 Score=18.13 Aligned_cols=12 Identities=50% Similarity=0.933 Sum_probs=8.7
Q ss_pred CCCCeEEEeccC
Q psy12346 45 NTESGTYTCIVC 56 (107)
Q Consensus 45 ~~~~G~Y~C~~C 56 (107)
....|.|.|.+=
T Consensus 60 ~~d~G~Y~C~v~ 71 (86)
T smart00410 60 PEDSGTYTCAAT 71 (86)
T ss_pred cccCeEEEEEEE
Confidence 346799999654
No 130
>smart00409 IG Immunoglobulin.
Probab=20.00 E-value=67 Score=18.13 Aligned_cols=12 Identities=50% Similarity=0.933 Sum_probs=8.7
Q ss_pred CCCCeEEEeccC
Q psy12346 45 NTESGTYTCIVC 56 (107)
Q Consensus 45 ~~~~G~Y~C~~C 56 (107)
....|.|.|.+=
T Consensus 60 ~~d~G~Y~C~v~ 71 (86)
T smart00409 60 PEDSGTYTCAAT 71 (86)
T ss_pred cccCeEEEEEEE
Confidence 346799999654
Done!