Query 032503
Match_columns 139
No_of_seqs 182 out of 1084
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 14:56:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032503.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032503hhsearch_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 8.8E-73 1.9E-77 431.0 11.3 126 8-135 2-131 (140)
2 TIGR00357 methionine-R-sulfoxi 100.0 1.7E-71 3.8E-76 422.9 12.0 125 10-136 2-129 (134)
3 PRK00222 methionine sulfoxide 100.0 6.1E-71 1.3E-75 423.3 12.8 127 7-135 2-131 (142)
4 PF01641 SelR: SelR domain; I 100.0 1.1E-70 2.3E-75 413.9 10.2 121 12-133 1-124 (124)
5 PRK05508 methionine sulfoxide 100.0 1.5E-69 3.2E-74 405.3 11.9 117 17-134 2-118 (119)
6 KOG0856 Predicted pilin-like t 100.0 8.6E-69 1.9E-73 410.3 11.4 136 1-136 7-145 (146)
7 PRK05550 bifunctional methioni 100.0 6.8E-62 1.5E-66 406.9 10.2 122 13-135 1-122 (283)
8 PRK14018 trifunctional thiored 100.0 6.3E-61 1.4E-65 427.0 12.9 127 8-135 378-507 (521)
9 PF03226 Yippee-Mis18: Yippee 93.6 0.037 8.1E-07 38.9 1.4 78 48-129 2-93 (96)
10 TIGR01384 TFS_arch transcripti 75.9 3 6.6E-05 29.5 2.8 60 46-108 14-76 (104)
11 COG1645 Uncharacterized Zn-fin 75.3 0.95 2E-05 34.9 0.1 23 49-71 29-52 (131)
12 PF09855 DUF2082: Nucleic-acid 73.3 2.2 4.7E-05 29.0 1.4 43 49-101 1-43 (64)
13 PF01352 KRAB: KRAB box; Inte 72.3 4.3 9.3E-05 25.1 2.5 27 1-28 1-27 (41)
14 PF11781 RRN7: RNA polymerase 64.8 3.9 8.4E-05 24.6 1.1 21 37-57 14-34 (36)
15 PF06677 Auto_anti-p27: Sjogre 64.1 3.1 6.6E-05 25.9 0.6 14 50-63 19-32 (41)
16 PRK00420 hypothetical protein; 59.4 4.9 0.00011 30.1 1.1 22 50-71 25-48 (112)
17 PF04828 GFA: Glutathione-depe 55.1 19 0.00041 23.6 3.4 44 81-130 35-78 (92)
18 PF03811 Zn_Tnp_IS1: InsA N-te 54.7 18 0.00039 21.8 2.8 29 90-121 1-30 (36)
19 PF08271 TF_Zn_Ribbon: TFIIB z 54.4 8.3 0.00018 23.4 1.4 15 44-58 15-29 (43)
20 PF09965 DUF2199: Uncharacteri 49.0 5.6 0.00012 31.0 -0.0 27 49-85 1-27 (148)
21 smart00778 Prim_Zn_Ribbon Zinc 48.5 15 0.00032 22.4 1.8 20 35-56 14-33 (37)
22 PF06170 DUF983: Protein of un 47.0 10 0.00022 26.9 1.0 21 93-113 7-27 (86)
23 COG3791 Uncharacterized conser 45.6 8.7 0.00019 28.7 0.5 23 40-62 61-83 (133)
24 PF07295 DUF1451: Protein of u 45.5 11 0.00024 29.2 1.1 14 45-58 109-122 (146)
25 PF11682 DUF3279: Protein of u 43.9 30 0.00064 26.5 3.2 18 46-68 26-43 (128)
26 PRK00398 rpoP DNA-directed RNA 42.0 33 0.00072 20.9 2.7 11 48-58 3-13 (46)
27 PRK04351 hypothetical protein; 41.0 21 0.00045 27.6 2.0 15 93-107 131-145 (149)
28 PF03119 DNA_ligase_ZBD: NAD-d 38.5 21 0.00045 20.3 1.2 23 96-125 1-23 (28)
29 PRK12495 hypothetical protein; 37.6 12 0.00026 31.4 0.2 13 47-59 41-53 (226)
30 PF10058 DUF2296: Predicted in 36.8 17 0.00037 23.7 0.8 20 90-109 18-37 (54)
31 PRK03824 hypA hydrogenase nick 36.4 50 0.0011 24.9 3.4 75 21-109 41-122 (135)
32 PF15288 zf-CCHC_6: Zinc knuck 36.4 14 0.0003 23.2 0.3 14 95-109 2-15 (40)
33 PRK00423 tfb transcription ini 36.0 32 0.00069 29.1 2.6 31 44-76 26-56 (310)
34 PHA02540 61 DNA primase; Provi 35.0 21 0.00047 31.2 1.4 18 40-57 45-64 (337)
35 cd04984 IgV_L_lambda Immunoglo 34.8 25 0.00054 23.7 1.5 11 44-54 73-83 (98)
36 cd04980 IgV_L_kappa Immunoglob 34.2 23 0.0005 24.3 1.2 12 43-54 80-91 (106)
37 TIGR03655 anti_R_Lar restricti 33.6 35 0.00076 21.5 1.9 18 40-57 18-35 (53)
38 PF14206 Cys_rich_CPCC: Cystei 33.4 25 0.00054 24.7 1.3 24 49-72 2-29 (78)
39 KOG2292 Oligosaccharyltransfer 32.7 36 0.00078 32.5 2.5 92 14-109 288-430 (751)
40 PF06397 Desulfoferrod_N: Desu 31.3 32 0.00069 20.9 1.3 13 45-57 3-15 (36)
41 cd05862 Ig1_VEGFR First immuno 31.1 30 0.00066 23.2 1.4 23 42-64 58-81 (86)
42 COG1405 SUA7 Transcription ini 30.6 47 0.001 28.3 2.7 29 44-74 16-44 (285)
43 PRK13130 H/ACA RNA-protein com 30.3 28 0.0006 23.1 1.0 17 50-66 19-36 (56)
44 PF00047 ig: Immunoglobulin do 29.2 31 0.00067 20.9 1.1 10 44-53 55-64 (64)
45 COG1996 RPC10 DNA-directed RNA 28.2 29 0.00064 22.5 0.8 12 47-58 5-16 (49)
46 PF10367 Vps39_2: Vacuolar sor 27.9 28 0.0006 23.7 0.7 12 50-61 80-91 (109)
47 KOG2691 RNA polymerase II subu 27.8 53 0.0011 24.8 2.2 60 46-109 24-88 (113)
48 TIGR03831 YgiT_finger YgiT-typ 27.5 29 0.00063 20.3 0.7 16 47-62 31-46 (46)
49 PF08273 Prim_Zn_Ribbon: Zinc- 27.5 30 0.00065 21.4 0.7 17 40-56 18-34 (40)
50 PF13101 DUF3945: Protein of u 26.7 29 0.00063 22.7 0.6 25 8-32 24-48 (59)
51 PRK04179 rpl37e 50S ribosomal 26.6 35 0.00076 23.3 1.0 26 48-73 17-43 (62)
52 PF14392 zf-CCHC_4: Zinc knuck 26.2 36 0.00078 21.2 1.0 19 90-109 27-45 (49)
53 PHA03351 tegument protein UL16 25.9 43 0.00094 27.5 1.6 40 18-57 104-149 (235)
54 PRK11032 hypothetical protein; 25.7 38 0.00083 26.8 1.2 21 38-58 112-134 (160)
55 PF12760 Zn_Tnp_IS1595: Transp 25.7 46 0.00099 20.4 1.4 26 31-56 18-45 (46)
56 COG1885 Uncharacterized protei 25.7 26 0.00056 26.4 0.3 14 45-58 46-59 (115)
57 cd05861 Ig1_PDGFR-alphabeta Fr 25.1 43 0.00093 22.3 1.3 13 42-54 54-66 (84)
58 smart00408 IGc2 Immunoglobulin 25.0 42 0.00092 19.0 1.1 11 43-53 48-58 (63)
59 PRK08624 hypothetical protein; 24.6 29 0.00062 31.0 0.4 20 43-62 54-76 (373)
60 cd02181 GH16_fungal_Lam16A_glu 24.4 26 0.00056 30.2 0.1 20 58-77 82-103 (293)
61 PF02945 Endonuclease_7: Recom 24.3 29 0.00063 24.3 0.3 42 50-108 24-66 (81)
62 PTZ00073 60S ribosomal protein 24.3 40 0.00088 24.6 1.0 27 48-74 16-42 (91)
63 cd05895 Ig_Pro_neuregulin-1 Im 24.2 45 0.00098 21.2 1.2 14 42-55 52-65 (76)
64 KOG3507 DNA-directed RNA polym 24.0 44 0.00096 22.8 1.1 14 45-58 17-30 (62)
65 cd04983 IgV_TCR_alpha_like Imm 23.8 43 0.00093 22.6 1.1 13 43-55 79-91 (109)
66 PRK15450 signal transduction p 23.7 25 0.00055 25.3 -0.1 23 106-128 39-61 (85)
67 TIGR02098 MJ0042_CXXC MJ0042 f 23.6 45 0.00098 19.3 1.0 12 93-104 24-35 (38)
68 smart00406 IGv Immunoglobulin 23.6 43 0.00092 20.8 1.0 10 44-53 72-81 (81)
69 PF14066 DUF4256: Protein of u 23.5 53 0.0012 26.5 1.7 16 17-32 105-120 (173)
70 cd05742 Ig1_VEGFR_like First i 23.1 41 0.0009 21.9 0.9 13 43-55 58-70 (84)
71 cd04974 Ig3_FGFR Third immunog 23.1 42 0.00092 22.4 0.9 13 43-55 64-76 (90)
72 smart00531 TFIIE Transcription 23.0 45 0.00098 25.1 1.2 15 46-60 121-135 (147)
73 PF10601 zf-LITAF-like: LITAF- 22.9 43 0.00094 22.2 1.0 15 93-107 57-71 (73)
74 PF08792 A2L_zn_ribbon: A2L zi 22.6 51 0.0011 19.4 1.1 14 44-57 17-30 (33)
75 cd04981 IgV_H Immunoglobulin ( 22.5 45 0.00097 23.8 1.0 11 44-54 86-96 (117)
76 PF01907 Ribosomal_L37e: Ribos 22.3 54 0.0012 21.8 1.3 27 48-74 15-41 (55)
77 cd05734 Ig7_DSCAM Seventh immu 22.0 50 0.0011 21.2 1.1 14 42-55 52-65 (79)
78 PRK03954 ribonuclease P protei 21.8 1E+02 0.0022 23.3 2.9 44 49-109 65-108 (121)
79 PF05924 SAMP: SAMP Motif; In 21.7 12 0.00027 20.2 -1.5 9 119-127 6-14 (20)
80 cd05765 Ig_3 Subgroup of the i 21.6 49 0.0011 20.9 1.0 14 42-55 55-68 (81)
81 PF13240 zinc_ribbon_2: zinc-r 21.2 55 0.0012 17.7 1.0 19 51-70 2-20 (23)
82 PF10955 DUF2757: Protein of u 21.1 56 0.0012 23.0 1.2 55 47-102 3-60 (76)
83 PF03117 Herpes_UL49_1: UL49 f 21.0 1.2E+02 0.0025 25.8 3.3 50 48-103 105-161 (245)
84 PRK14810 formamidopyrimidine-D 20.5 71 0.0015 26.6 2.0 12 9-20 192-203 (272)
85 PRK00432 30S ribosomal protein 20.5 66 0.0014 20.5 1.4 14 47-60 36-49 (50)
86 cd07693 Ig1_Robo First immunog 20.5 61 0.0013 20.9 1.3 13 43-55 73-85 (100)
87 cd05725 Ig3_Robo Third immunog 20.4 51 0.0011 20.5 0.9 12 43-54 44-55 (69)
88 smart00659 RPOLCX RNA polymera 20.3 61 0.0013 20.2 1.2 11 48-58 2-12 (44)
89 PF09889 DUF2116: Uncharacteri 20.2 41 0.0009 22.5 0.4 9 50-58 5-13 (59)
90 cd05881 Ig1_Necl-2 First (N-te 20.0 15 0.00033 26.0 -1.9 35 21-55 49-83 (95)
No 1
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.8e-73 Score=431.00 Aligned_cols=126 Identities=45% Similarity=0.893 Sum_probs=120.7
Q ss_pred CCCCHHHHHhcCCHHHHHHhhhCCCCCCCccCCCccccceEEEeccCCcccccCCccccCCCCCccCCccc-CCCeEEcc
Q 032503 8 VQKTEEEWRAILSPEQFRILRQKGTEPRGTGEYNKLYADGFYNCAGCGTALYKSVTKFDSGCGWPAFYEGL-PGAINRSP 86 (139)
Q Consensus 8 ~~~~~~ewr~~Ltp~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i-~~~v~~~~ 86 (139)
+.+++++||+.|||+||+|||++|||+||+|+||+++++|||+|++||+|||+|.+|||||||||||++|| +++|++++
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 56799999999999999999999999999999999999999999999999999999999999999999999 55999999
Q ss_pred CCC--cceeEEEecCCCCCcccccCCCCCCCCCC-ceeeeccceeeeeeCCC
Q 032503 87 DPD--GRRTEITCAACGGHMGHVFKGEGFKTPTD-ERHCVNSVSIKFIPGDA 135 (139)
Q Consensus 87 D~s--m~RtEv~C~~Cg~HLGHVF~~DG~p~ptg-~RyCINs~sL~F~p~~~ 135 (139)
|.| |.||||+|++|++||||||+ || |.|+| +|||||||||+|+|.++
T Consensus 82 D~S~gM~RtEVrc~~c~sHLGHVF~-DG-P~~tgglRYCINSasL~Fip~~~ 131 (140)
T COG0229 82 DRSHGMVRTEVRCANCDSHLGHVFP-DG-PPPTGGLRYCINSASLRFIPKEE 131 (140)
T ss_pred ccCCCcEEEEEEecCCCCccccccC-CC-CCCCCCeeEeecchheeecchhh
Confidence 999 99999999999999999999 88 66777 99999999999999864
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=1.7e-71 Score=422.89 Aligned_cols=125 Identities=41% Similarity=0.801 Sum_probs=120.7
Q ss_pred CCHHHHHhcCCHHHHHHhhhCCCCCCCccCCCccccceEEEeccCCcccccCCccccCCCCCccCCccc-CCCeEEccCC
Q 032503 10 KTEEEWRAILSPEQFRILRQKGTEPRGTGEYNKLYADGFYNCAGCGTALYKSVTKFDSGCGWPAFYEGL-PGAINRSPDP 88 (139)
Q Consensus 10 ~~~~ewr~~Ltp~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i-~~~v~~~~D~ 88 (139)
++++|||+.|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|++||+||||||||+++| +++|+++.|.
T Consensus 2 ~~~~ewr~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~~D~ 81 (134)
T TIGR00357 2 PSDEELKKKLTPLQYEVTQNAGTEPPFTNEYWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERDE 81 (134)
T ss_pred CCHHHHHHhCCHHHHHHHHHhCCCCCCCCCCCCCCCCeEEEccCCCCccccccchhcCCCCCcCcCcccCCCceEEeecC
Confidence 689999999999999999999999999999999999999999999999999999999999999999999 6799999999
Q ss_pred C--cceeEEEecCCCCCcccccCCCCCCCCCCceeeeccceeeeeeCCCC
Q 032503 89 D--GRRTEITCAACGGHMGHVFKGEGFKTPTDERHCVNSVSIKFIPGDAP 136 (139)
Q Consensus 89 s--m~RtEv~C~~Cg~HLGHVF~~DG~p~ptg~RyCINs~sL~F~p~~~~ 136 (139)
+ |+||||+|++||+||||||+ || |+|||+||||||+||+|+|.++.
T Consensus 82 s~gm~RtEv~C~~Cg~HLGHVF~-DG-P~ptg~RyCINs~sL~F~p~~~~ 129 (134)
T TIGR00357 82 SHGMIRTEVRCRNCDAHLGHVFD-DG-PEPTGLRYCINSAALKFIPLEEM 129 (134)
T ss_pred CCCcEEEEEEecCCCCccCcccC-CC-CCCCCceEeecceeEecccchhh
Confidence 8 99999999999999999998 88 78999999999999999998643
No 3
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=6.1e-71 Score=423.26 Aligned_cols=127 Identities=48% Similarity=0.923 Sum_probs=122.4
Q ss_pred CCCCCHHHHHhcCCHHHHHHhhhCCCCCCCccCCCccccceEEEeccCCcccccCCccccCCCCCccCCccc-CCCeEEc
Q 032503 7 SVQKTEEEWRAILSPEQFRILRQKGTEPRGTGEYNKLYADGFYNCAGCGTALYKSVTKFDSGCGWPAFYEGL-PGAINRS 85 (139)
Q Consensus 7 ~~~~~~~ewr~~Ltp~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i-~~~v~~~ 85 (139)
++.++++|||+.|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|++||+||||||||+++| +++|+++
T Consensus 2 ~~~~~~~ew~~~Lt~~qy~V~r~~gTE~pftg~~~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~V~~~ 81 (142)
T PRK00222 2 KIEKSKEEWKKQLTPEQYRVTQEHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKPIDEEAIREL 81 (142)
T ss_pred CccCCHHHHHhhCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcccCCCceEEe
Confidence 567899999999999999999999999999999999999999999999999999999999999999999999 5699999
Q ss_pred cCCC--cceeEEEecCCCCCcccccCCCCCCCCCCceeeeccceeeeeeCCC
Q 032503 86 PDPD--GRRTEITCAACGGHMGHVFKGEGFKTPTDERHCVNSVSIKFIPGDA 135 (139)
Q Consensus 86 ~D~s--m~RtEv~C~~Cg~HLGHVF~~DG~p~ptg~RyCINs~sL~F~p~~~ 135 (139)
+|.+ |.||||+|++||+||||||+ || |+|||+||||||+||+|+|+++
T Consensus 82 ~D~s~gm~RtEv~C~~Cg~HLGHVF~-DG-P~ptg~RyCINs~sL~F~p~~~ 131 (142)
T PRK00222 82 RDTSHGMVRTEVRCANCDSHLGHVFP-DG-PKPTGLRYCINSASLKFIPKDG 131 (142)
T ss_pred eccCCCceEEEEEeCCCCCccCcccC-CC-CCCCCCEeeeceeeEEeeccch
Confidence 9998 99999999999999999998 88 7899999999999999999864
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=1.1e-70 Score=413.91 Aligned_cols=121 Identities=55% Similarity=1.052 Sum_probs=113.7
Q ss_pred HHHHHhcCCHHHHHHhhhCCCCCCCccCCCccccceEEEeccCCcccccCCccccCCCCCccCCcccCC-CeEEccCCC-
Q 032503 12 EEEWRAILSPEQFRILRQKGTEPRGTGEYNKLYADGFYNCAGCGTALYKSVTKFDSGCGWPAFYEGLPG-AINRSPDPD- 89 (139)
Q Consensus 12 ~~ewr~~Ltp~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~-~v~~~~D~s- 89 (139)
|+|||++|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|++||+||||||||++||++ +|+++.|.+
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 689999999999999999999999999999999999999999999999999999999999999999977 999999999
Q ss_pred -cceeEEEecCCCCCcccccCCCCCCCCCCceeeeccceeeeeeC
Q 032503 90 -GRRTEITCAACGGHMGHVFKGEGFKTPTDERHCVNSVSIKFIPG 133 (139)
Q Consensus 90 -m~RtEv~C~~Cg~HLGHVF~~DG~p~ptg~RyCINs~sL~F~p~ 133 (139)
|+||||+|++||+||||||+ |||++|||+||||||+||+|+|+
T Consensus 81 g~~R~Ev~C~~Cg~HLGHVF~-DGp~~~tg~RyCINS~sL~F~p~ 124 (124)
T PF01641_consen 81 GMVRTEVRCARCGSHLGHVFD-DGPPPPTGLRYCINSASLKFIPK 124 (124)
T ss_dssp SSEEEEEEETTTCCEEEEEES-TSSTTCTSCEEEE-GGGEEEEE-
T ss_pred CceEEEEEecCCCCccccEeC-CCCCCCCCcEEEeeeeeEEEecC
Confidence 99999999999999999999 99655689999999999999995
No 5
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=1.5e-69 Score=405.32 Aligned_cols=117 Identities=54% Similarity=1.086 Sum_probs=112.8
Q ss_pred hcCCHHHHHHhhhCCCCCCCccCCCccccceEEEeccCCcccccCCccccCCCCCccCCcccCCCeEEccCCCcceeEEE
Q 032503 17 AILSPEQFRILRQKGTEPRGTGEYNKLYADGFYNCAGCGTALYKSVTKFDSGCGWPAFYEGLPGAINRSPDPDGRRTEIT 96 (139)
Q Consensus 17 ~~Ltp~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~v~~~~D~sm~RtEv~ 96 (139)
++|||+||+|||++||||||+|+||+++++|+|+|++||+|||+|++|||||||||||++||+++|++++|.+|.||||+
T Consensus 2 ~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~v~~~~D~~~~RtEv~ 81 (119)
T PRK05508 2 NELTPEEEAVILRKGTEPPFSGEYNDFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDEIKGAVKRIPDADGRRTEIV 81 (119)
T ss_pred CcCCHHHHHHHHhcCCCCCCCCCCcCcCCCeEEEecCCCCccccccccccCCCCCcccCcccccceEEEecCCCcEEEEE
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCCcccccCCCCCCCCCCceeeeccceeeeeeCC
Q 032503 97 CAACGGHMGHVFKGEGFKTPTDERHCVNSVSIKFIPGD 134 (139)
Q Consensus 97 C~~Cg~HLGHVF~~DG~p~ptg~RyCINs~sL~F~p~~ 134 (139)
|++||+||||||+ ||+|+|||+|||||||||+|+|+.
T Consensus 82 C~~C~~HLGHVF~-d~gp~ptg~RyCINS~sL~F~p~~ 118 (119)
T PRK05508 82 CANCGGHLGHVFE-GEGFTPKNTRHCVNSISLKFVPDK 118 (119)
T ss_pred eCCCCCccCcccC-CCCCCCCCCEEeecceeEEeecCC
Confidence 9999999999999 445789999999999999999964
No 6
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=8.6e-69 Score=410.27 Aligned_cols=136 Identities=70% Similarity=1.335 Sum_probs=130.1
Q ss_pred CCCCCCCCCCCHHHHHhcCCHHHHHHhhhCCCCCCCccCCCccccceEEEeccCCcccccCCccccCCCCCccCCccc-C
Q 032503 1 MTAAADSVQKTEEEWRAILSPEQFRILRQKGTEPRGTGEYNKLYADGFYNCAGCGTALYKSVTKFDSGCGWPAFYEGL-P 79 (139)
Q Consensus 1 ~~~~~~~~~~~~~ewr~~Ltp~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i-~ 79 (139)
|+.+..+++++++|||++|||+||+|||++|||+||+|+|++++++|+|+|++|++|||+|.+|||||||||||++.| +
T Consensus 7 ~~~~~~~v~k~~~EWr~~LsPeQ~~v~RekgTE~p~tGey~~~~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~i~~ 86 (146)
T KOG0856|consen 7 VAPKTGSVQKNDEEWRKVLSPEQFRVLREKGTERPGTGEYTKHFEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEAIGP 86 (146)
T ss_pred ccCCCcccccCHHHHHhhcCHHHhhhhHhhcccCCCCcccccccCCceEEEeecCCccccccccccCCCCCchhhhccCC
Confidence 456677899999999999999999999999999999999999999999999999999999999999999999999999 8
Q ss_pred CCeEEccCCC--cceeEEEecCCCCCcccccCCCCCCCCCCceeeeccceeeeeeCCCC
Q 032503 80 GAINRSPDPD--GRRTEITCAACGGHMGHVFKGEGFKTPTDERHCVNSVSIKFIPGDAP 136 (139)
Q Consensus 80 ~~v~~~~D~s--m~RtEv~C~~Cg~HLGHVF~~DG~p~ptg~RyCINs~sL~F~p~~~~ 136 (139)
++|++++|.| |.|+||+|++||+||||||.|||+..||++|||||||||+|.|++.+
T Consensus 87 gaI~r~~d~s~~~~R~Ev~Ca~C~~HLGHVF~~eG~~~Pt~~R~CiNS~sL~F~~~~~s 145 (146)
T KOG0856|consen 87 GAITRTPDNSRGGRRTEVSCATCGGHLGHVFKGEGPKTPTDERHCINSVSLKFVPADSS 145 (146)
T ss_pred CceeeccccCCCCcceEEEEeecCCceeeeecCCCCCCCCCceeEeeeeeeeeccCCCC
Confidence 9999999988 89999999999999999999999666999999999999999998765
No 7
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=100.00 E-value=6.8e-62 Score=406.91 Aligned_cols=122 Identities=51% Similarity=1.051 Sum_probs=116.1
Q ss_pred HHHHhcCCHHHHHHhhhCCCCCCCccCCCccccceEEEeccCCcccccCCccccCCCCCccCCcccCCCeEEccCCCcce
Q 032503 13 EEWRAILSPEQFRILRQKGTEPRGTGEYNKLYADGFYNCAGCGTALYKSVTKFDSGCGWPAFYEGLPGAINRSPDPDGRR 92 (139)
Q Consensus 13 ~ewr~~Ltp~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~v~~~~D~sm~R 92 (139)
+.||++|||+||+|||++||||||+|+||+++++|+|+|++||+|||+|++||+||||||||++||+++|+++.|.++.|
T Consensus 1 ~~~~~~Lt~~~y~v~r~~gTE~pf~g~~~~~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~~~~~~~~~~~d~~~~R 80 (283)
T PRK05550 1 MDKMKSLTPFEYRVIEDKGTERPFSGEYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEIPGAVKRLPDADGRR 80 (283)
T ss_pred ChhhhhCCHHHHHHHHhcCCCCCCCCcCcCCCCCcEEEcCCCCchhcCChhhccCCCCCcCcCcccCCccEEEEcCCCce
Confidence 36999999999999999999999999999999999999999999999999999999999999999999999988888559
Q ss_pred eEEEecCCCCCcccccCCCCCCCCCCceeeeccceeeeeeCCC
Q 032503 93 TEITCAACGGHMGHVFKGEGFKTPTDERHCVNSVSIKFIPGDA 135 (139)
Q Consensus 93 tEv~C~~Cg~HLGHVF~~DG~p~ptg~RyCINs~sL~F~p~~~ 135 (139)
|||+|++||+||||||+||| |+|||+||||||+||+|+|.++
T Consensus 81 ~Ev~c~~c~~HLGHvF~ddg-p~ptg~RyCiNs~sL~f~p~~~ 122 (283)
T PRK05550 81 TEIVCANCGAHLGHVFEGEG-LTPKNTRHCVNSASLDFVPAEE 122 (283)
T ss_pred EEEEecCCCCccCcccCCCC-CCCCCccccccccccccCcccc
Confidence 99999999999999999565 7899999999999999999865
No 8
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=6.3e-61 Score=427.02 Aligned_cols=127 Identities=35% Similarity=0.654 Sum_probs=121.0
Q ss_pred CCCCHHHHHhcCCHHHHHHhhhCCCCCCCccCCCccccceEEEeccCCcccccCCccccCCCCCccCCcccC-CCeEEcc
Q 032503 8 VQKTEEEWRAILSPEQFRILRQKGTEPRGTGEYNKLYADGFYNCAGCGTALYKSVTKFDSGCGWPAFYEGLP-GAINRSP 86 (139)
Q Consensus 8 ~~~~~~ewr~~Ltp~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~-~~v~~~~ 86 (139)
..++++|||++|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|.+||+||||||||++||+ ++|.++.
T Consensus 378 ~~~~~~~~~~~Lt~~~y~v~~~~gtE~~f~~~~~~~~~~G~y~c~~c~~pLf~s~~Kf~sg~GWPsF~~~i~~~~v~~~~ 457 (521)
T PRK14018 378 KKPSDAELKRTLTEEQYQITQNAATERAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTRPIDAKVVTEHD 457 (521)
T ss_pred cCCChHHHhccCCHHHHHHHHhcCCCCCCCCCCcCCCCCEEEEecCCCCccccCcccccCCCCCcccCcccCcCceEEee
Confidence 346999999999999999999999999999999999999999999999999999999999999999999996 5899999
Q ss_pred CCC--cceeEEEecCCCCCcccccCCCCCCCCCCceeeeccceeeeeeCCC
Q 032503 87 DPD--GRRTEITCAACGGHMGHVFKGEGFKTPTDERHCVNSVSIKFIPGDA 135 (139)
Q Consensus 87 D~s--m~RtEv~C~~Cg~HLGHVF~~DG~p~ptg~RyCINs~sL~F~p~~~ 135 (139)
|.| |.||||+|++||+||||||+ |||++|||+||||||+||+|+|+++
T Consensus 458 d~s~g~~R~Ev~c~~c~~HLGHvf~-dgp~~~~g~RyCiNs~~l~f~~~~~ 507 (521)
T PRK14018 458 DFSYNMRRTEVRSRAADSHLGHVFP-DGPRDKGGLRYCINGASLKFIPLEQ 507 (521)
T ss_pred ccCCCceEEEEEECCCCCcCCcccC-CCCCCCCCCEeeeceeEEEeecchh
Confidence 998 99999999999999999998 8955679999999999999999864
No 9
>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=93.61 E-value=0.037 Score=38.89 Aligned_cols=78 Identities=18% Similarity=0.418 Sum_probs=45.8
Q ss_pred EEEeccCCcccccCCcccc-CCCCCccCCc-ccCCCeEEccCCC---c------ceeEEEecCCCCCcccccCCCCCCCC
Q 032503 48 FYNCAGCGTALYKSVTKFD-SGCGWPAFYE-GLPGAINRSPDPD---G------RRTEITCAACGGHMGHVFKGEGFKTP 116 (139)
Q Consensus 48 ~Y~C~~Cg~pLF~S~~Kf~-Sg~GWPSF~~-~i~~~v~~~~D~s---m------~RtEv~C~~Cg~HLGHVF~~DG~p~p 116 (139)
+|.|+.|.++|=+|..-.. .|..=++|-- -+...+. .|.. + .-..+.|++|+.+||-.+. .- |+.
T Consensus 2 vf~C~~C~t~l~ds~~lvs~~g~~~~a~l~~~v~~~~~--~~~~~~t~~~~~~~~~~~l~C~~C~~~lGwkY~-~a-~~~ 77 (96)
T PF03226_consen 2 VFQCKNCKTILADSNELVSFHGREGKAYLFNNVSNGVP--VDRELMTGETGGDHTVRDLFCSGCNTILGWKYE-SA-PEE 77 (96)
T ss_pred EEECCCCCCCcCCHHHheecCCCCccEEEEeeeeeccc--ccceEEEeeCCCCEEEEEeEcccCChhHCcEEE-Ec-CHh
Confidence 7999999999987776665 4432233321 2211111 1111 1 2457999999999999987 32 221
Q ss_pred ---CCceeeeccceee
Q 032503 117 ---TDERHCVNSVSIK 129 (139)
Q Consensus 117 ---tg~RyCINs~sL~ 129 (139)
.--+|++.-++|.
T Consensus 78 ~~~k~g~file~~~i~ 93 (96)
T PF03226_consen 78 QKYKEGKFILEKASIS 93 (96)
T ss_pred HhhhCCEEEEEhhHEE
Confidence 3345666555543
No 10
>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=75.94 E-value=3 Score=29.45 Aligned_cols=60 Identities=18% Similarity=0.392 Sum_probs=33.0
Q ss_pred ceEEEeccCCcccccC-CccccCCCCCccCCcccCCCeEEccCCC--cceeEEEecCCCCCccccc
Q 032503 46 DGFYNCAGCGTALYKS-VTKFDSGCGWPAFYEGLPGAINRSPDPD--GRRTEITCAACGGHMGHVF 108 (139)
Q Consensus 46 ~G~Y~C~~Cg~pLF~S-~~Kf~Sg~GWPSF~~~i~~~v~~~~D~s--m~RtEv~C~~Cg~HLGHVF 108 (139)
.+.|.|..|+...... +.++..- -.+...+.+.+....|.. ..++.+.|.+||.+-...|
T Consensus 14 ~~~~~C~~C~~~~~~~~~~~~v~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~~a~f~ 76 (104)
T TIGR01384 14 NGVYVCPSCGYEKEKKPEDDYKVT---EKVKHKIKETIIIREEDSETLPTTRVECPKCGHKEAYYW 76 (104)
T ss_pred CCeEECcCCCCccccccccccEEE---EEeccccccceeeccccccCCCcccCCCCCCCCCeeEEE
Confidence 4789999999875543 1222110 011111222232333332 6789999999986666555
No 11
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=75.26 E-value=0.95 Score=34.89 Aligned_cols=23 Identities=35% Similarity=0.869 Sum_probs=16.5
Q ss_pred EEeccCCcccccCCc-cccCCCCC
Q 032503 49 YNCAGCGTALYKSVT-KFDSGCGW 71 (139)
Q Consensus 49 Y~C~~Cg~pLF~S~~-Kf~Sg~GW 71 (139)
++|..||.|||.=+- -|=+-||.
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGY 52 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCc
Confidence 599999999998332 25555664
No 12
>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=73.33 E-value=2.2 Score=28.99 Aligned_cols=43 Identities=28% Similarity=0.682 Sum_probs=31.0
Q ss_pred EEeccCCcccccCCccccCCCCCccCCcccCCCeEEccCCCcceeEEEecCCC
Q 032503 49 YNCAGCGTALYKSVTKFDSGCGWPAFYEGLPGAINRSPDPDGRRTEITCAACG 101 (139)
Q Consensus 49 Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~v~~~~D~sm~RtEv~C~~Cg 101 (139)
|.|..||..-|.++.--.+|.||-.+++--.. .=+-|.|.+||
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~----------~f~~v~C~~CG 43 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNK----------KFTTVSCTNCG 43 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCc----------EEEEEECCCCC
Confidence 78999999999988887888888654321111 12458899997
No 13
>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=72.25 E-value=4.3 Score=25.05 Aligned_cols=27 Identities=33% Similarity=0.559 Sum_probs=13.8
Q ss_pred CCCCCCCCCCCHHHHHhcCCHHHHHHhh
Q 032503 1 MTAAADSVQKTEEEWRAILSPEQFRILR 28 (139)
Q Consensus 1 ~~~~~~~~~~~~~ewr~~Ltp~qy~V~r 28 (139)
+++.+-.+.+|.+||. .|.|.|...-|
T Consensus 1 Vtf~Dvav~fs~eEW~-~L~~~Qk~ly~ 27 (41)
T PF01352_consen 1 VTFEDVAVYFSQEEWE-LLDPAQKNLYR 27 (41)
T ss_dssp ------TT---HHHHH-TS-HHHHHHHH
T ss_pred CeEEEEEEEcChhhcc-cccceecccch
Confidence 4566778899999998 69999976544
No 14
>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=64.79 E-value=3.9 Score=24.65 Aligned_cols=21 Identities=38% Similarity=0.760 Sum_probs=16.6
Q ss_pred ccCCCccccceEEEeccCCcc
Q 032503 37 TGEYNKLYADGFYNCAGCGTA 57 (139)
Q Consensus 37 sg~y~~~~~~G~Y~C~~Cg~p 57 (139)
.|..+...+.|.|+|+.||..
T Consensus 14 C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 14 CGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCeEeEccCCEEEhhhCceE
Confidence 566677778999999999864
No 15
>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=64.13 E-value=3.1 Score=25.93 Aligned_cols=14 Identities=36% Similarity=0.935 Sum_probs=11.5
Q ss_pred EeccCCcccccCCc
Q 032503 50 NCAGCGTALYKSVT 63 (139)
Q Consensus 50 ~C~~Cg~pLF~S~~ 63 (139)
+|..||.|||.+.+
T Consensus 19 ~Cp~C~~PL~~~k~ 32 (41)
T PF06677_consen 19 HCPDCGTPLMRDKD 32 (41)
T ss_pred ccCCCCCeeEEecC
Confidence 79999999998543
No 16
>PRK00420 hypothetical protein; Validated
Probab=59.41 E-value=4.9 Score=30.06 Aligned_cols=22 Identities=23% Similarity=0.430 Sum_probs=15.0
Q ss_pred EeccCCccccc--CCccccCCCCC
Q 032503 50 NCAGCGTALYK--SVTKFDSGCGW 71 (139)
Q Consensus 50 ~C~~Cg~pLF~--S~~Kf~Sg~GW 71 (139)
+|..||.|||. ....|=+.||=
T Consensus 25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 25 HCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCcceecCCCceECCCCCC
Confidence 78888888885 44555566664
No 17
>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=55.13 E-value=19 Score=23.64 Aligned_cols=44 Identities=11% Similarity=0.113 Sum_probs=26.3
Q ss_pred CeEEccCCCcceeEEEecCCCCCcccccCCCCCCCCCCceeeeccceeee
Q 032503 81 AINRSPDPDGRRTEITCAACGGHMGHVFKGEGFKTPTDERHCVNSVSIKF 130 (139)
Q Consensus 81 ~v~~~~D~sm~RtEv~C~~Cg~HLGHVF~~DG~p~ptg~RyCINs~sL~F 130 (139)
.+......+....-..|++||++|..... .. | ..+-||..+|+-
T Consensus 35 ~l~~y~~s~~~~~r~FC~~CGs~l~~~~~-~~-~----~~~~V~~g~ld~ 78 (92)
T PF04828_consen 35 NLKEYQFSGKGVERYFCPTCGSPLFSEDE-RD-P----DLVGVNAGTLDD 78 (92)
T ss_dssp GEEEC--TTSSCEEEEETTT--EEEEEES-ST-T----TEEEEEGGGBTT
T ss_pred cceEEEeCCCcCcCcccCCCCCeeecccC-CC-C----CEEEEEeEeeCC
Confidence 44443323344455999999999997644 22 2 488888888864
No 18
>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=54.66 E-value=18 Score=21.82 Aligned_cols=29 Identities=24% Similarity=0.531 Sum_probs=20.2
Q ss_pred cceeEEEecCCCCCcccccCCCCCCCC-CCcee
Q 032503 90 GRRTEITCAACGGHMGHVFKGEGFKTP-TDERH 121 (139)
Q Consensus 90 m~RtEv~C~~Cg~HLGHVF~~DG~p~p-tg~Ry 121 (139)
|.-++|.|..|++..+=+=. | ..+ ...||
T Consensus 1 Ma~i~v~CP~C~s~~~v~k~--G-~~~~G~qry 30 (36)
T PF03811_consen 1 MAKIDVHCPRCQSTEGVKKN--G-KSPSGHQRY 30 (36)
T ss_pred CCcEeeeCCCCCCCCcceeC--C-CCCCCCEeE
Confidence 66789999999999854433 3 233 34777
No 19
>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=54.42 E-value=8.3 Score=23.38 Aligned_cols=15 Identities=33% Similarity=0.671 Sum_probs=12.4
Q ss_pred ccceEEEeccCCccc
Q 032503 44 YADGFYNCAGCGTAL 58 (139)
Q Consensus 44 ~~~G~Y~C~~Cg~pL 58 (139)
...|.++|..||.-|
T Consensus 15 ~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 15 PERGELVCPNCGLVL 29 (43)
T ss_dssp TTTTEEEETTT-BBE
T ss_pred CCCCeEECCCCCCEe
Confidence 578999999999877
No 20
>PF09965 DUF2199: Uncharacterized protein conserved in bacteria (DUF2199); InterPro: IPR018697 This domain has no known function.
Probab=49.03 E-value=5.6 Score=30.95 Aligned_cols=27 Identities=26% Similarity=0.511 Sum_probs=21.2
Q ss_pred EEeccCCcccccCCccccCCCCCccCCcccCCCeEEc
Q 032503 49 YNCAGCGTALYKSVTKFDSGCGWPAFYEGLPGAINRS 85 (139)
Q Consensus 49 Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~v~~~ 85 (139)
|.|.+||..- -|||||.-..|+.+..+
T Consensus 1 y~C~~Cg~~h----------~~~P~~~~~~Pd~~~~~ 27 (148)
T PF09965_consen 1 YTCSCCGEEH----------EGLPSLGFDAPDYYYEL 27 (148)
T ss_pred CCCCcCCccC----------CCCcccccCCChhhhhC
Confidence 7899999864 59999988888765443
No 21
>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=48.54 E-value=15 Score=22.42 Aligned_cols=20 Identities=25% Similarity=0.597 Sum_probs=15.8
Q ss_pred CCccCCCccccceEEEeccCCc
Q 032503 35 RGTGEYNKLYADGFYNCAGCGT 56 (139)
Q Consensus 35 pfsg~y~~~~~~G~Y~C~~Cg~ 56 (139)
-|+ |.+.+..|.|+|..|+.
T Consensus 14 rFr--~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 14 RFR--FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccc--cccCCCCcCEEeCCCCC
Confidence 455 77777889999999963
No 22
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=46.98 E-value=10 Score=26.91 Aligned_cols=21 Identities=24% Similarity=0.487 Sum_probs=17.3
Q ss_pred eEEEecCCCCCcccccCCCCC
Q 032503 93 TEITCAACGGHMGHVFKGEGF 113 (139)
Q Consensus 93 tEv~C~~Cg~HLGHVF~~DG~ 113 (139)
..-+|..||.-++|.=.||||
T Consensus 7 ~~~~C~~CG~d~~~~~adDgP 27 (86)
T PF06170_consen 7 VAPRCPHCGLDYSHARADDGP 27 (86)
T ss_pred CCCcccccCCccccCCcCccc
Confidence 345799999999999877883
No 23
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=45.62 E-value=8.7 Score=28.72 Aligned_cols=23 Identities=26% Similarity=0.414 Sum_probs=17.5
Q ss_pred CCccccceEEEeccCCcccccCC
Q 032503 40 YNKLYADGFYNCAGCGTALYKSV 62 (139)
Q Consensus 40 y~~~~~~G~Y~C~~Cg~pLF~S~ 62 (139)
|......+.+.|..||.+||-..
T Consensus 61 ~~~s~~~~r~FC~~CGs~l~~~~ 83 (133)
T COG3791 61 YFSSGSAGRGFCPTCGSPLFWRG 83 (133)
T ss_pred EeecCCCCCeecccCCCceEEec
Confidence 34555677789999999998653
No 24
>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=45.46 E-value=11 Score=29.19 Aligned_cols=14 Identities=29% Similarity=0.797 Sum_probs=12.7
Q ss_pred cceEEEeccCCccc
Q 032503 45 ADGFYNCAGCGTAL 58 (139)
Q Consensus 45 ~~G~Y~C~~Cg~pL 58 (139)
.+|+|+|..||..+
T Consensus 109 g~G~l~C~~Cg~~~ 122 (146)
T PF07295_consen 109 GPGTLVCENCGHEV 122 (146)
T ss_pred cCceEecccCCCEE
Confidence 78999999999876
No 25
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=43.86 E-value=30 Score=26.52 Aligned_cols=18 Identities=28% Similarity=0.779 Sum_probs=14.8
Q ss_pred ceEEEeccCCcccccCCccccCC
Q 032503 46 DGFYNCAGCGTALYKSVTKFDSG 68 (139)
Q Consensus 46 ~G~Y~C~~Cg~pLF~S~~Kf~Sg 68 (139)
...|.|..||-|| .|..+
T Consensus 26 ~~~~tC~~Cg~~L-----~lh~~ 43 (128)
T PF11682_consen 26 YDHWTCHSCGCPL-----ILHPG 43 (128)
T ss_pred CCeEEEecCCceE-----EEecC
Confidence 4699999999999 67644
No 26
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=41.99 E-value=33 Score=20.90 Aligned_cols=11 Identities=45% Similarity=1.129 Sum_probs=8.3
Q ss_pred EEEeccCCccc
Q 032503 48 FYNCAGCGTAL 58 (139)
Q Consensus 48 ~Y~C~~Cg~pL 58 (139)
.|.|..||..+
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 58888888764
No 27
>PRK04351 hypothetical protein; Provisional
Probab=40.98 E-value=21 Score=27.60 Aligned_cols=15 Identities=20% Similarity=0.707 Sum_probs=11.7
Q ss_pred eEEEecCCCCCcccc
Q 032503 93 TEITCAACGGHMGHV 107 (139)
Q Consensus 93 tEv~C~~Cg~HLGHV 107 (139)
..-+|.+|++.|-.+
T Consensus 131 ~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 131 KRYRCGKCRGKLKLI 145 (149)
T ss_pred CcEEeCCCCcEeeec
Confidence 458899999988544
No 28
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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 the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=38.49 E-value=21 Score=20.28 Aligned_cols=23 Identities=35% Similarity=0.778 Sum_probs=11.5
Q ss_pred EecCCCCCcccccCCCCCCCCCCceeeecc
Q 032503 96 TCAACGGHMGHVFKGEGFKTPTDERHCVNS 125 (139)
Q Consensus 96 ~C~~Cg~HLGHVF~~DG~p~ptg~RyCINs 125 (139)
.|..||+.|=+. +| .-..||+|+
T Consensus 1 ~CP~C~s~l~~~---~~----ev~~~C~N~ 23 (28)
T PF03119_consen 1 TCPVCGSKLVRE---EG----EVDIRCPNP 23 (28)
T ss_dssp B-TTT--BEEE----CC----TTCEEE--C
T ss_pred CcCCCCCEeEcC---CC----CEeEECCCC
Confidence 488999998753 22 126999998
No 29
>PRK12495 hypothetical protein; Provisional
Probab=37.61 E-value=12 Score=31.37 Aligned_cols=13 Identities=23% Similarity=0.807 Sum_probs=11.3
Q ss_pred eEEEeccCCcccc
Q 032503 47 GFYNCAGCGTALY 59 (139)
Q Consensus 47 G~Y~C~~Cg~pLF 59 (139)
.-++|..||.|||
T Consensus 41 sa~hC~~CG~PIp 53 (226)
T PRK12495 41 TNAHCDECGDPIF 53 (226)
T ss_pred chhhcccccCccc
Confidence 3569999999999
No 30
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=36.81 E-value=17 Score=23.67 Aligned_cols=20 Identities=30% Similarity=0.544 Sum_probs=18.3
Q ss_pred cceeEEEecCCCCCcccccC
Q 032503 90 GRRTEITCAACGGHMGHVFK 109 (139)
Q Consensus 90 m~RtEv~C~~Cg~HLGHVF~ 109 (139)
..|..+.|++|..|=|-+..
T Consensus 18 ~~r~aLIC~~C~~hNGla~~ 37 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAPK 37 (54)
T ss_pred cCceeEECcccchhhccccc
Confidence 68999999999999999975
No 31
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.44 E-value=50 Score=24.88 Aligned_cols=75 Identities=23% Similarity=0.337 Sum_probs=40.2
Q ss_pred HHHHHHhhh---CCCCCCCcc-CCCccccceEEEeccCCcccccCC---ccccCCCCCccCCcccCCCeEEccCCCccee
Q 032503 21 PEQFRILRQ---KGTEPRGTG-EYNKLYADGFYNCAGCGTALYKSV---TKFDSGCGWPAFYEGLPGAINRSPDPDGRRT 93 (139)
Q Consensus 21 p~qy~V~r~---~gTE~pfsg-~y~~~~~~G~Y~C~~Cg~pLF~S~---~Kf~Sg~GWPSF~~~i~~~v~~~~D~sm~Rt 93 (139)
|++++-..+ +|| ++.| ++.=...+..|.|..||. .|... .+.+...+ ..+...++.- +.
T Consensus 41 pe~L~fafe~l~~gt--~~ega~L~i~~~p~~~~C~~CG~-~~~~~~~~~~~~~~~~---------~~~~~~~~~~--~~ 106 (135)
T PRK03824 41 KEIVEFALNELLKGT--ILEGAEIIFEEEEAVLKCRNCGN-EWSLKEVKESLDEEIR---------EAIHFIPEVV--HA 106 (135)
T ss_pred HHHHHHHHHHHHcCC--cccCCEEEEEecceEEECCCCCC-EEeccccccccccccc---------cccccccccc--cc
Confidence 555544433 344 4444 333336789999999994 35553 22322222 2233333211 22
Q ss_pred EEEecCCCCCcccccC
Q 032503 94 EITCAACGGHMGHVFK 109 (139)
Q Consensus 94 Ev~C~~Cg~HLGHVF~ 109 (139)
-..|..||++--++-.
T Consensus 107 ~~~CP~Cgs~~~~i~~ 122 (135)
T PRK03824 107 FLKCPKCGSRDFEIVK 122 (135)
T ss_pred CcCCcCCCCCCcEEec
Confidence 2679999998766644
No 32
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=36.38 E-value=14 Score=23.15 Aligned_cols=14 Identities=36% Similarity=1.077 Sum_probs=11.3
Q ss_pred EEecCCCCCcccccC
Q 032503 95 ITCAACGGHMGHVFK 109 (139)
Q Consensus 95 v~C~~Cg~HLGHVF~ 109 (139)
|.|.+||+ +||.-.
T Consensus 2 ~kC~~CG~-~GH~~t 15 (40)
T PF15288_consen 2 VKCKNCGA-FGHMRT 15 (40)
T ss_pred cccccccc-cccccc
Confidence 68999997 688754
No 33
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=36.01 E-value=32 Score=29.10 Aligned_cols=31 Identities=35% Similarity=0.707 Sum_probs=26.0
Q ss_pred ccceEEEeccCCcccccCCccccCCCCCccCCc
Q 032503 44 YADGFYNCAGCGTALYKSVTKFDSGCGWPAFYE 76 (139)
Q Consensus 44 ~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~ 76 (139)
.+.|.++|..||.-| .+.-.|.|.-|-+|..
T Consensus 26 ~~~Ge~vC~~CG~Vl--~e~~iD~g~EWR~f~~ 56 (310)
T PRK00423 26 YERGEIVCADCGLVI--EENIIDQGPEWRAFDP 56 (310)
T ss_pred CCCCeEeecccCCcc--cccccccCCCccCCCc
Confidence 578999999999877 4556788889999986
No 34
>PHA02540 61 DNA primase; Provisional
Probab=34.96 E-value=21 Score=31.17 Aligned_cols=18 Identities=17% Similarity=0.377 Sum_probs=12.5
Q ss_pred CCccccce--EEEeccCCcc
Q 032503 40 YNKLYADG--FYNCAGCGTA 57 (139)
Q Consensus 40 y~~~~~~G--~Y~C~~Cg~p 57 (139)
++=..++| +|+|-+||.-
T Consensus 45 F~V~p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 45 GWIYEKKDGGVFKCHNCGYH 64 (337)
T ss_pred EEEeccCCceEEEecCCCCC
Confidence 44444455 9999999963
No 35
>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=34.85 E-value=25 Score=23.75 Aligned_cols=11 Identities=18% Similarity=0.277 Sum_probs=9.1
Q ss_pred ccceEEEeccC
Q 032503 44 YADGFYNCAGC 54 (139)
Q Consensus 44 ~~~G~Y~C~~C 54 (139)
.+.|+|.|++-
T Consensus 73 ~Dsg~Y~C~~~ 83 (98)
T cd04984 73 EDEADYYCQVW 83 (98)
T ss_pred hhCEEEEEEEc
Confidence 47899999874
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=34.16 E-value=23 Score=24.28 Aligned_cols=12 Identities=17% Similarity=0.313 Sum_probs=9.4
Q ss_pred cccceEEEeccC
Q 032503 43 LYADGFYNCAGC 54 (139)
Q Consensus 43 ~~~~G~Y~C~~C 54 (139)
..+.|+|.|+.-
T Consensus 80 ~~Dsg~Y~Ca~~ 91 (106)
T cd04980 80 PEDAAVYYCQQY 91 (106)
T ss_pred hHHCEEEEEEEe
Confidence 347899999873
No 37
>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=33.61 E-value=35 Score=21.53 Aligned_cols=18 Identities=22% Similarity=0.892 Sum_probs=13.7
Q ss_pred CCccccceEEEeccCCcc
Q 032503 40 YNKLYADGFYNCAGCGTA 57 (139)
Q Consensus 40 y~~~~~~G~Y~C~~Cg~p 57 (139)
+.+....|+|.|..||.-
T Consensus 18 ~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 18 FDPLDLSHYFECSTCGAS 35 (53)
T ss_pred cCCCCCEEEEECCCCCCC
Confidence 345567888999999875
No 38
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=33.41 E-value=25 Score=24.74 Aligned_cols=24 Identities=29% Similarity=0.775 Sum_probs=19.3
Q ss_pred EEeccCCcccccCCcc--cc--CCCCCc
Q 032503 49 YNCAGCGTALYKSVTK--FD--SGCGWP 72 (139)
Q Consensus 49 Y~C~~Cg~pLF~S~~K--f~--Sg~GWP 72 (139)
|.|.+||..-|....- |+ +=|+|=
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCCcc
Confidence 7899999999988876 76 567883
No 39
>KOG2292 consensus Oligosaccharyltransferase, STT3 subunit [Posttranslational modification, protein turnover, chaperones]
Probab=32.72 E-value=36 Score=32.53 Aligned_cols=92 Identities=25% Similarity=0.476 Sum_probs=68.5
Q ss_pred HHHhcCCHHHHHHhhh-------------------CCCCCCCccCCCccccceEEEeccCCcccccCCccccCCCCCccC
Q 032503 14 EWRAILSPEQFRILRQ-------------------KGTEPRGTGEYNKLYADGFYNCAGCGTALYKSVTKFDSGCGWPAF 74 (139)
Q Consensus 14 ewr~~Ltp~qy~V~r~-------------------~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF 74 (139)
-.|.+|++.||+|+.. .|--.|+||.+....++|. +.=..|+-.|-+..++ +-||||
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 3677999999988754 4778999999988888875 5667798888888775 679998
Q ss_pred Cccc-------CC----CeEEccCCC----------------cce-----eEEEecCCCCCcccccC
Q 032503 75 YEGL-------PG----AINRSPDPD----------------GRR-----TEITCAACGGHMGHVFK 109 (139)
Q Consensus 75 ~~~i-------~~----~v~~~~D~s----------------m~R-----tEv~C~~Cg~HLGHVF~ 109 (139)
+=.+ |- -++.+.|.. |+| |-+.|--.+.-+.++|+
T Consensus 364 ffDlhiLv~lfPaGl~~Cfk~l~De~vFiilY~v~~~YFaGVMVRLmLtLtP~vCils~ia~S~~~~ 430 (751)
T KOG2292|consen 364 FFDLHILVFLFPAGLYYCFKNLSDERVFIILYGVTSVYFAGVMVRLMLTLTPVVCILSGIAFSQLLD 430 (751)
T ss_pred HHHHHHHHHhhhhhHHHhhhhcCCceEEEEehHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 7542 21 234455531 777 57788888888888876
No 40
>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=31.27 E-value=32 Score=20.91 Aligned_cols=13 Identities=38% Similarity=1.086 Sum_probs=7.7
Q ss_pred cceEEEeccCCcc
Q 032503 45 ADGFYNCAGCGTA 57 (139)
Q Consensus 45 ~~G~Y~C~~Cg~p 57 (139)
.--+|.|..||+-
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 3468999999974
No 41
>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=31.14 E-value=30 Score=23.24 Aligned_cols=23 Identities=30% Similarity=0.469 Sum_probs=14.2
Q ss_pred ccccceEEEeccC-CcccccCCcc
Q 032503 42 KLYADGFYNCAGC-GTALYKSVTK 64 (139)
Q Consensus 42 ~~~~~G~Y~C~~C-g~pLF~S~~K 64 (139)
...+.|.|.|.+- +.-++.+.++
T Consensus 58 ~~~DsG~Y~C~a~n~~~~~~~~t~ 81 (86)
T cd05862 58 TLSDLGRYTCTASSGQMIAKNSTI 81 (86)
T ss_pred CcccCEEEEEEEeecceEecccEE
Confidence 3568999999653 3444544443
No 42
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=30.55 E-value=47 Score=28.31 Aligned_cols=29 Identities=41% Similarity=0.809 Sum_probs=24.0
Q ss_pred ccceEEEeccCCcccccCCccccCCCCCccC
Q 032503 44 YADGFYNCAGCGTALYKSVTKFDSGCGWPAF 74 (139)
Q Consensus 44 ~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF 74 (139)
.+.|-++|+.||.-| -+.-+|.|..|=.|
T Consensus 16 ~~~ge~VC~~CG~Vi--~~~~id~gpewr~f 44 (285)
T COG1405 16 YERGEIVCADCGLVL--EDSLIDPGPEWRAF 44 (285)
T ss_pred ccCCeEEeccCCEEe--ccccccCCCCcccc
Confidence 357999999999887 44557899999999
No 43
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=30.31 E-value=28 Score=23.10 Aligned_cols=17 Identities=24% Similarity=0.557 Sum_probs=11.3
Q ss_pred EeccCCcccccCC-cccc
Q 032503 50 NCAGCGTALYKSV-TKFD 66 (139)
Q Consensus 50 ~C~~Cg~pLF~S~-~Kf~ 66 (139)
+|..||.++.++- .+|.
T Consensus 19 ~CP~CG~~t~~~~P~rfS 36 (56)
T PRK13130 19 ICPVCGGKTKNPHPPRFS 36 (56)
T ss_pred cCcCCCCCCCCCCCCCCC
Confidence 5888898886554 4443
No 44
>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=29.24 E-value=31 Score=20.89 Aligned_cols=10 Identities=30% Similarity=0.617 Sum_probs=8.1
Q ss_pred ccceEEEecc
Q 032503 44 YADGFYNCAG 53 (139)
Q Consensus 44 ~~~G~Y~C~~ 53 (139)
.+.|+|.|.+
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 4789999964
No 45
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.23 E-value=29 Score=22.50 Aligned_cols=12 Identities=42% Similarity=0.938 Sum_probs=10.3
Q ss_pred eEEEeccCCccc
Q 032503 47 GFYNCAGCGTAL 58 (139)
Q Consensus 47 G~Y~C~~Cg~pL 58 (139)
=+|.|+.||..+
T Consensus 5 ~~Y~C~~Cg~~~ 16 (49)
T COG1996 5 MEYKCARCGREV 16 (49)
T ss_pred EEEEhhhcCCee
Confidence 379999999887
No 46
>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=27.88 E-value=28 Score=23.73 Aligned_cols=12 Identities=42% Similarity=0.877 Sum_probs=10.5
Q ss_pred EeccCCcccccC
Q 032503 50 NCAGCGTALYKS 61 (139)
Q Consensus 50 ~C~~Cg~pLF~S 61 (139)
.|..|+++|+.+
T Consensus 80 ~C~vC~k~l~~~ 91 (109)
T PF10367_consen 80 KCSVCGKPLGNS 91 (109)
T ss_pred CccCcCCcCCCc
Confidence 599999999774
No 47
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=27.75 E-value=53 Score=24.84 Aligned_cols=60 Identities=17% Similarity=0.232 Sum_probs=34.3
Q ss_pred ceEEEeccCCcccccCCccccCCCCCccCCcccCC--CeE--EccCCCcce-eEEEecCCCCCcccccC
Q 032503 46 DGFYNCAGCGTALYKSVTKFDSGCGWPAFYEGLPG--AIN--RSPDPDGRR-TEITCAACGGHMGHVFK 109 (139)
Q Consensus 46 ~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~--~v~--~~~D~sm~R-tEv~C~~Cg~HLGHVF~ 109 (139)
.=.|.|..|..--|..+.++--.-+=++ +.+ .|. ...|..-.| ....|.+||.+-+=.|.
T Consensus 24 ~L~laCrnCd~ve~A~s~~vY~~~~~~e----~dE~t~ii~Dl~~DPTLPrts~~~C~~C~~~eavffQ 88 (113)
T KOG2691|consen 24 ILLLACRNCDYVEEADSSRVYVNELSHE----HDELTQIIMDLASDPTLPRTSDKHCPKCGHREAVFFQ 88 (113)
T ss_pred EEEEEecCCcceEecCCcceEcCCcccc----hhhHHHHHHhhccCCCcCccccccCCccCCcceEEEe
Confidence 3456666666655555555433222221 111 111 133444778 67899999999998887
No 48
>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=27.55 E-value=29 Score=20.32 Aligned_cols=16 Identities=19% Similarity=0.468 Sum_probs=12.9
Q ss_pred eEEEeccCCcccccCC
Q 032503 47 GFYNCAGCGTALYKSV 62 (139)
Q Consensus 47 G~Y~C~~Cg~pLF~S~ 62 (139)
-.++|..||..+|+.+
T Consensus 31 p~~~C~~CGE~~~~~~ 46 (46)
T TIGR03831 31 PALVCPQCGEEYLDAE 46 (46)
T ss_pred CccccccCCCEeeCCC
Confidence 4568999999999753
No 49
>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=27.47 E-value=30 Score=21.38 Aligned_cols=17 Identities=24% Similarity=0.700 Sum_probs=9.2
Q ss_pred CCccccceEEEeccCCc
Q 032503 40 YNKLYADGFYNCAGCGT 56 (139)
Q Consensus 40 y~~~~~~G~Y~C~~Cg~ 56 (139)
|.+....|.|+|..|+.
T Consensus 18 ~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 18 FDDKDGRGTWICRQCGG 34 (40)
T ss_dssp ETT----S-EEETTTTB
T ss_pred CcCcccCCCEECCCCCC
Confidence 44556679999999953
No 50
>PF13101 DUF3945: Protein of unknown function (DUF3945)
Probab=26.69 E-value=29 Score=22.65 Aligned_cols=25 Identities=28% Similarity=0.247 Sum_probs=17.7
Q ss_pred CCCCHHHHHhcCCHHHHHHhhhCCC
Q 032503 8 VQKTEEEWRAILSPEQFRILRQKGT 32 (139)
Q Consensus 8 ~~~~~~ewr~~Ltp~qy~V~r~~gT 32 (139)
+...+.-.-..||++|.+.|+++.+
T Consensus 24 i~ip~~i~g~~Ls~~q~~~L~~G~~ 48 (59)
T PF13101_consen 24 IRIPDKIKGVELSPEQKEDLREGKP 48 (59)
T ss_pred ccccceecCccCCHHHHHHHHCCCe
Confidence 3334333446899999999998764
No 51
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=26.63 E-value=35 Score=23.28 Aligned_cols=26 Identities=27% Similarity=0.752 Sum_probs=23.4
Q ss_pred EEEeccCCcccccCCccccCCCCC-cc
Q 032503 48 FYNCAGCGTALYKSVTKFDSGCGW-PA 73 (139)
Q Consensus 48 ~Y~C~~Cg~pLF~S~~Kf~Sg~GW-PS 73 (139)
.-.|..||.--|....|.=+.||+ ||
T Consensus 17 Ht~CrRCG~~syh~qK~~CasCGygps 43 (62)
T PRK04179 17 HIRCRRCGRHSYNVRKKYCAACGFGRS 43 (62)
T ss_pred cchhcccCcccccccccchhhcCCCcc
Confidence 348999999999999999999999 76
No 52
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=26.17 E-value=36 Score=21.19 Aligned_cols=19 Identities=37% Similarity=0.607 Sum_probs=14.3
Q ss_pred cceeEEEecCCCCCcccccC
Q 032503 90 GRRTEITCAACGGHMGHVFK 109 (139)
Q Consensus 90 m~RtEv~C~~Cg~HLGHVF~ 109 (139)
.+|.-..|..|| .+||.-.
T Consensus 27 YE~lp~~C~~C~-~~gH~~~ 45 (49)
T PF14392_consen 27 YERLPRFCFHCG-RIGHSDK 45 (49)
T ss_pred ECCcChhhcCCC-CcCcCHh
Confidence 566777899997 5888643
No 53
>PHA03351 tegument protein UL16; Provisional
Probab=25.86 E-value=43 Score=27.52 Aligned_cols=40 Identities=23% Similarity=0.188 Sum_probs=31.1
Q ss_pred cCCHHHHHHhhhCCCC--CC----CccCCCccccceEEEeccCCcc
Q 032503 18 ILSPEQFRILRQKGTE--PR----GTGEYNKLYADGFYNCAGCGTA 57 (139)
Q Consensus 18 ~Ltp~qy~V~r~~gTE--~p----fsg~y~~~~~~G~Y~C~~Cg~p 57 (139)
..|..||.|+|++--- -| |+....++...|.|-|-.|.+-
T Consensus 104 nfs~i~~nilqdglkmr~vp~tklyt~rii~n~t~grydc~rceng 149 (235)
T PHA03351 104 NFSDIQTNILQDGLKMRHVPVTKLYTHRIINNHTAGRYDCFRCENG 149 (235)
T ss_pred chhHHHHHHHhccceeeecchhhheehhhhccccccceeeEEecCC
Confidence 6889999999986433 34 4555568899999999999763
No 54
>PRK11032 hypothetical protein; Provisional
Probab=25.67 E-value=38 Score=26.75 Aligned_cols=21 Identities=29% Similarity=0.469 Sum_probs=16.2
Q ss_pred cCCCcc--ccceEEEeccCCccc
Q 032503 38 GEYNKL--YADGFYNCAGCGTAL 58 (139)
Q Consensus 38 g~y~~~--~~~G~Y~C~~Cg~pL 58 (139)
|.|--- -..|+++|..||..+
T Consensus 112 g~Y~sGEvvg~G~LvC~~Cg~~~ 134 (160)
T PRK11032 112 GVYHSGEVVGLGNLVCEKCHHHL 134 (160)
T ss_pred CeeecceeeecceEEecCCCCEE
Confidence 666433 378999999999876
No 55
>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=25.66 E-value=46 Score=20.37 Aligned_cols=26 Identities=27% Similarity=0.506 Sum_probs=16.5
Q ss_pred CCCCCCcc--CCCccccceEEEeccCCc
Q 032503 31 GTEPRGTG--EYNKLYADGFYNCAGCGT 56 (139)
Q Consensus 31 gTE~pfsg--~y~~~~~~G~Y~C~~Cg~ 56 (139)
|=.=|+.| .+......+.|.|..|+.
T Consensus 18 g~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 18 GFVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 33345555 344455678999998874
No 56
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.66 E-value=26 Score=26.45 Aligned_cols=14 Identities=29% Similarity=0.736 Sum_probs=12.8
Q ss_pred cceEEEeccCCccc
Q 032503 45 ADGFYNCAGCGTAL 58 (139)
Q Consensus 45 ~~G~Y~C~~Cg~pL 58 (139)
+-|.+.|..||+++
T Consensus 46 e~G~t~CP~Cg~~~ 59 (115)
T COG1885 46 EVGSTSCPKCGEPF 59 (115)
T ss_pred ecccccCCCCCCcc
Confidence 78999999999986
No 57
>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=25.09 E-value=43 Score=22.27 Aligned_cols=13 Identities=31% Similarity=0.657 Sum_probs=10.3
Q ss_pred ccccceEEEeccC
Q 032503 42 KLYADGFYNCAGC 54 (139)
Q Consensus 42 ~~~~~G~Y~C~~C 54 (139)
...+.|+|.|++-
T Consensus 54 ~~~DsG~Y~C~a~ 66 (84)
T cd05861 54 TVEDSGTYECAAH 66 (84)
T ss_pred CcCCCEEEEEEEE
Confidence 3468999999983
No 58
>smart00408 IGc2 Immunoglobulin C-2 Type.
Probab=24.99 E-value=42 Score=19.00 Aligned_cols=11 Identities=36% Similarity=0.745 Sum_probs=8.8
Q ss_pred cccceEEEecc
Q 032503 43 LYADGFYNCAG 53 (139)
Q Consensus 43 ~~~~G~Y~C~~ 53 (139)
..+.|.|.|.+
T Consensus 48 ~~d~G~Y~C~~ 58 (63)
T smart00408 48 LEDSGEYTCVA 58 (63)
T ss_pred cccCEEEEEEE
Confidence 35789999976
No 59
>PRK08624 hypothetical protein; Provisional
Probab=24.64 E-value=29 Score=31.01 Aligned_cols=20 Identities=15% Similarity=0.645 Sum_probs=14.3
Q ss_pred cccceEEEec-cCCc--ccccCC
Q 032503 43 LYADGFYNCA-GCGT--ALYKSV 62 (139)
Q Consensus 43 ~~~~G~Y~C~-~Cg~--pLF~S~ 62 (139)
+.+.++|+|- +||. -.|.==
T Consensus 54 ~pekq~yhCF~GCGa~GDVf~Fv 76 (373)
T PRK08624 54 YIENDNFHCYTRCGDIFDVFELL 76 (373)
T ss_pred cCCCCEEEEeCCCCCCCceeeeh
Confidence 3477899999 9998 444433
No 60
>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=24.37 E-value=26 Score=30.22 Aligned_cols=20 Identities=40% Similarity=1.071 Sum_probs=15.5
Q ss_pred cccCC-ccccCCCC-CccCCcc
Q 032503 58 LYKSV-TKFDSGCG-WPAFYEG 77 (139)
Q Consensus 58 LF~S~-~Kf~Sg~G-WPSF~~~ 77 (139)
||..+ .|+-.||| ||+||.-
T Consensus 82 ~~~~~~~~~P~g~G~WPAfW~~ 103 (293)
T cd02181 82 LFIADIAHMPGGCGTWPAFWTV 103 (293)
T ss_pred eEEEEhhhCCCCCCccchhhhc
Confidence 66666 38888997 9999963
No 61
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=24.32 E-value=29 Score=24.34 Aligned_cols=42 Identities=31% Similarity=0.626 Sum_probs=25.5
Q ss_pred EeccCCcccccCCccccCCCCCccCCcccCCCeEEccCCC-cceeEEEecCCCCCccccc
Q 032503 50 NCAGCGTALYKSVTKFDSGCGWPAFYEGLPGAINRSPDPD-GRRTEITCAACGGHMGHVF 108 (139)
Q Consensus 50 ~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~v~~~~D~s-m~RtEv~C~~Cg~HLGHVF 108 (139)
.|+.|+.|++....+. + .-.|.. ..--.+.|..|..=||++=
T Consensus 24 ~C~iC~~~~~~~~~~~----------------~-vDHdH~tG~vRGlLC~~CN~~lG~~~ 66 (81)
T PF02945_consen 24 RCAICGKPLPGESRKL----------------V-VDHDHKTGRVRGLLCRSCNTALGKVR 66 (81)
T ss_dssp E-TTT-SEEETTCGGC----------------E-EEE-TTTTBEEEEEEHHHHHHHHHCT
T ss_pred cCcCCCCCcccCCCcc----------------e-ecCCCCCCCchhhhhhHHhhhhcccc
Confidence 8999999887654332 1 111222 2233589999999999983
No 62
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=24.27 E-value=40 Score=24.58 Aligned_cols=27 Identities=26% Similarity=0.625 Sum_probs=24.3
Q ss_pred EEEeccCCcccccCCccccCCCCCccC
Q 032503 48 FYNCAGCGTALYKSVTKFDSGCGWPAF 74 (139)
Q Consensus 48 ~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF 74 (139)
.-.|..||.--|.-..+.=+.||+||=
T Consensus 16 HtlCrRCG~~syH~qK~~CasCGypsa 42 (91)
T PTZ00073 16 HTLCRRCGKRSFHVQKKRCASCGYPSA 42 (91)
T ss_pred cchhcccCccccccccccchhcCCchh
Confidence 448999999999999999999999864
No 63
>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=24.19 E-value=45 Score=21.21 Aligned_cols=14 Identities=29% Similarity=0.551 Sum_probs=10.8
Q ss_pred ccccceEEEeccCC
Q 032503 42 KLYADGFYNCAGCG 55 (139)
Q Consensus 42 ~~~~~G~Y~C~~Cg 55 (139)
...+.|.|.|++..
T Consensus 52 ~~~DsG~Y~C~a~N 65 (76)
T cd05895 52 SLADNGEYKCMVSS 65 (76)
T ss_pred CcccCEEEEEEEEe
Confidence 44688999998754
No 64
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=24.04 E-value=44 Score=22.76 Aligned_cols=14 Identities=36% Similarity=0.764 Sum_probs=11.6
Q ss_pred cceEEEeccCCccc
Q 032503 45 ADGFYNCAGCGTAL 58 (139)
Q Consensus 45 ~~G~Y~C~~Cg~pL 58 (139)
..=+|+|.-||+.+
T Consensus 17 ~~miYiCgdC~~en 30 (62)
T KOG3507|consen 17 ATMIYICGDCGQEN 30 (62)
T ss_pred ccEEEEeccccccc
Confidence 55699999999865
No 65
>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=23.84 E-value=43 Score=22.62 Aligned_cols=13 Identities=31% Similarity=0.422 Sum_probs=10.2
Q ss_pred cccceEEEeccCC
Q 032503 43 LYADGFYNCAGCG 55 (139)
Q Consensus 43 ~~~~G~Y~C~~Cg 55 (139)
..+.|+|.|++..
T Consensus 79 ~~DsG~Y~C~~~~ 91 (109)
T cd04983 79 LSDSAVYFCALSE 91 (109)
T ss_pred HHHCEEEEEEEec
Confidence 3478999999764
No 66
>PRK15450 signal transduction protein PmrD; Provisional
Probab=23.67 E-value=25 Score=25.29 Aligned_cols=23 Identities=13% Similarity=0.260 Sum_probs=14.1
Q ss_pred cccCCCCCCCCCCceeeecccee
Q 032503 106 HVFKGEGFKTPTDERHCVNSVSI 128 (139)
Q Consensus 106 HVF~~DG~p~ptg~RyCINs~sL 128 (139)
+++.||=--+-..-|||||--..
T Consensus 39 ~l~~gDlLsPL~dA~YciNr~~~ 61 (85)
T PRK15450 39 ALKVGDLLSPLQNALYCINREKL 61 (85)
T ss_pred ccCcccccccchhhhhhhcCCCC
Confidence 45565542223678999996543
No 67
>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=23.65 E-value=45 Score=19.26 Aligned_cols=12 Identities=25% Similarity=0.786 Sum_probs=9.2
Q ss_pred eEEEecCCCCCc
Q 032503 93 TEITCAACGGHM 104 (139)
Q Consensus 93 tEv~C~~Cg~HL 104 (139)
.+|+|.+|+.-+
T Consensus 24 ~~v~C~~C~~~~ 35 (38)
T TIGR02098 24 GKVRCGKCGHVW 35 (38)
T ss_pred CEEECCCCCCEE
Confidence 379999998654
No 68
>smart00406 IGv Immunoglobulin V-Type.
Probab=23.59 E-value=43 Score=20.78 Aligned_cols=10 Identities=40% Similarity=0.614 Sum_probs=8.0
Q ss_pred ccceEEEecc
Q 032503 44 YADGFYNCAG 53 (139)
Q Consensus 44 ~~~G~Y~C~~ 53 (139)
.+.|+|.|+.
T Consensus 72 ~D~G~Y~C~v 81 (81)
T smart00406 72 EDTGTYYCAV 81 (81)
T ss_pred HHCEEEEEcC
Confidence 4789999974
No 69
>PF14066 DUF4256: Protein of unknown function (DUF4256)
Probab=23.53 E-value=53 Score=26.48 Aligned_cols=16 Identities=38% Similarity=0.679 Sum_probs=14.1
Q ss_pred hcCCHHHHHHhhhCCC
Q 032503 17 AILSPEQFRILRQKGT 32 (139)
Q Consensus 17 ~~Ltp~qy~V~r~~gT 32 (139)
+.||.+||+-||+-|.
T Consensus 105 eLLtEeqYr~LQ~lg~ 120 (173)
T PF14066_consen 105 ELLTEEQYRELQKLGE 120 (173)
T ss_pred HhcCHHHHHHHHHhCC
Confidence 5899999999998774
No 70
>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=23.14 E-value=41 Score=21.90 Aligned_cols=13 Identities=38% Similarity=0.761 Sum_probs=10.1
Q ss_pred cccceEEEeccCC
Q 032503 43 LYADGFYNCAGCG 55 (139)
Q Consensus 43 ~~~~G~Y~C~~Cg 55 (139)
..+.|+|.|++-.
T Consensus 58 ~~DsG~Y~C~a~n 70 (84)
T cd05742 58 LKDSGTYTCAASS 70 (84)
T ss_pred hhhCEEEEEEEcc
Confidence 4578999998843
No 71
>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=23.13 E-value=42 Score=22.41 Aligned_cols=13 Identities=23% Similarity=0.483 Sum_probs=10.4
Q ss_pred cccceEEEeccCC
Q 032503 43 LYADGFYNCAGCG 55 (139)
Q Consensus 43 ~~~~G~Y~C~~Cg 55 (139)
..+.|.|.|.+-.
T Consensus 64 ~~D~G~Y~C~A~N 76 (90)
T cd04974 64 FDDAGEYTCLAGN 76 (90)
T ss_pred cccCcEEEEEeec
Confidence 3689999998754
No 72
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=22.96 E-value=45 Score=25.14 Aligned_cols=15 Identities=40% Similarity=1.021 Sum_probs=8.2
Q ss_pred ceEEEeccCCccccc
Q 032503 46 DGFYNCAGCGTALYK 60 (139)
Q Consensus 46 ~G~Y~C~~Cg~pLF~ 60 (139)
.|.|.|..||.+|..
T Consensus 121 ~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 121 DGTFTCPRCGEELEE 135 (147)
T ss_pred CCcEECCCCCCEEEE
Confidence 445566666655543
No 73
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=22.93 E-value=43 Score=22.19 Aligned_cols=15 Identities=27% Similarity=0.693 Sum_probs=12.7
Q ss_pred eEEEecCCCCCcccc
Q 032503 93 TEITCAACGGHMGHV 107 (139)
Q Consensus 93 tEv~C~~Cg~HLGHV 107 (139)
++-.|.+|+.+||..
T Consensus 57 ~~H~Cp~C~~~lg~~ 71 (73)
T PF10601_consen 57 VYHYCPNCGAFLGTY 71 (73)
T ss_pred ceEECCCCCCEeEEE
Confidence 558999999999963
No 74
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=22.57 E-value=51 Score=19.39 Aligned_cols=14 Identities=29% Similarity=0.693 Sum_probs=12.2
Q ss_pred ccceEEEeccCCcc
Q 032503 44 YADGFYNCAGCGTA 57 (139)
Q Consensus 44 ~~~G~Y~C~~Cg~p 57 (139)
++++.|+|.-||.-
T Consensus 17 ~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 17 KEDDYEVCIFCGSS 30 (33)
T ss_pred ecCCeEEcccCCcE
Confidence 78899999999963
No 75
>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=22.49 E-value=45 Score=23.77 Aligned_cols=11 Identities=27% Similarity=0.453 Sum_probs=9.0
Q ss_pred ccceEEEeccC
Q 032503 44 YADGFYNCAGC 54 (139)
Q Consensus 44 ~~~G~Y~C~~C 54 (139)
.+.|+|.|+.-
T Consensus 86 ~Dsa~YyCa~~ 96 (117)
T cd04981 86 EDTAVYYCARG 96 (117)
T ss_pred HHCEEEEEEEE
Confidence 47899999874
No 76
>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=22.28 E-value=54 Score=21.84 Aligned_cols=27 Identities=33% Similarity=0.673 Sum_probs=22.6
Q ss_pred EEEeccCCcccccCCccccCCCCCccC
Q 032503 48 FYNCAGCGTALYKSVTKFDSGCGWPAF 74 (139)
Q Consensus 48 ~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF 74 (139)
.-.|..||.--|.-..|.=+.||+|+=
T Consensus 15 H~~CrRCG~~syH~qK~~CasCGyp~~ 41 (55)
T PF01907_consen 15 HTLCRRCGRRSYHIQKKTCASCGYPAA 41 (55)
T ss_dssp EEE-TTTSSEEEETTTTEETTTBTTTS
T ss_pred EeeecccCCeeeecCCCcccccCCCcc
Confidence 447999999999999999999999963
No 77
>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=22.00 E-value=50 Score=21.24 Aligned_cols=14 Identities=21% Similarity=0.415 Sum_probs=10.7
Q ss_pred ccccceEEEeccCC
Q 032503 42 KLYADGFYNCAGCG 55 (139)
Q Consensus 42 ~~~~~G~Y~C~~Cg 55 (139)
...+.|+|.|.+..
T Consensus 52 ~~~D~G~Y~C~a~N 65 (79)
T cd05734 52 LEEDSGYYLCKVSN 65 (79)
T ss_pred CcccCEEEEEEEEe
Confidence 34578999998864
No 78
>PRK03954 ribonuclease P protein component 4; Validated
Probab=21.83 E-value=1e+02 Score=23.27 Aligned_cols=44 Identities=23% Similarity=0.388 Sum_probs=26.9
Q ss_pred EEeccCCcccccCCccccCCCCCccCCcccCCCeEEccCCCcceeEEEecCCCCCcccccC
Q 032503 49 YNCAGCGTALYKSVTKFDSGCGWPAFYEGLPGAINRSPDPDGRRTEITCAACGGHMGHVFK 109 (139)
Q Consensus 49 Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~v~~~~D~sm~RtEv~C~~Cg~HLGHVF~ 109 (139)
-.|..|+.+|-...+ ..|. +.+..+..+-|.|..||..-=+.+.
T Consensus 65 ~~CK~C~t~LiPG~n----------------~~vR-i~~~~~~~vvitCl~CG~~kR~P~~ 108 (121)
T PRK03954 65 RYCKRCHSFLVPGVN----------------ARVR-LRQKRMPHVVITCLECGHIMRYPYL 108 (121)
T ss_pred HHhhcCCCeeecCCc----------------eEEE-EecCCcceEEEECccCCCEEeeccc
Confidence 379999998843210 0122 2222345678999999987666554
No 79
>PF05924 SAMP: SAMP Motif; InterPro: IPR009224 This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin [].; GO: 0008013 beta-catenin binding, 0016055 Wnt receptor signaling pathway; PDB: 1EMU_B 2RQU_B.
Probab=21.72 E-value=12 Score=20.20 Aligned_cols=9 Identities=22% Similarity=0.556 Sum_probs=6.8
Q ss_pred ceeeeccce
Q 032503 119 ERHCVNSVS 127 (139)
Q Consensus 119 ~RyCINs~s 127 (139)
++=|||||-
T Consensus 6 L~~CI~sAm 14 (20)
T PF05924_consen 6 LQECIGSAM 14 (20)
T ss_dssp HHHHHHCTS
T ss_pred HHHHHHHhc
Confidence 567999984
No 80
>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=21.63 E-value=49 Score=20.91 Aligned_cols=14 Identities=21% Similarity=0.586 Sum_probs=10.7
Q ss_pred ccccceEEEeccCC
Q 032503 42 KLYADGFYNCAGCG 55 (139)
Q Consensus 42 ~~~~~G~Y~C~~Cg 55 (139)
...+.|+|.|.+-.
T Consensus 55 ~~~D~G~Y~C~a~N 68 (81)
T cd05765 55 QPQDAGLYTCTARN 68 (81)
T ss_pred CcccCEEEEEEEec
Confidence 44588999998754
No 81
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=21.21 E-value=55 Score=17.68 Aligned_cols=19 Identities=37% Similarity=1.034 Sum_probs=9.2
Q ss_pred eccCCcccccCCccccCCCC
Q 032503 51 CAGCGTALYKSVTKFDSGCG 70 (139)
Q Consensus 51 C~~Cg~pLF~S~~Kf~Sg~G 70 (139)
|..||.+| .-+++|=+.||
T Consensus 2 Cp~CG~~~-~~~~~fC~~CG 20 (23)
T PF13240_consen 2 CPNCGAEI-EDDAKFCPNCG 20 (23)
T ss_pred CcccCCCC-CCcCcchhhhC
Confidence 44555555 33455544444
No 82
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=21.10 E-value=56 Score=22.96 Aligned_cols=55 Identities=16% Similarity=0.319 Sum_probs=28.1
Q ss_pred eEEEeccCCcccccCCcc--ccCCCCCccCCccc-CCCeEEccCCCcceeEEEecCCCC
Q 032503 47 GFYNCAGCGTALYKSVTK--FDSGCGWPAFYEGL-PGAINRSPDPDGRRTEITCAACGG 102 (139)
Q Consensus 47 G~Y~C~~Cg~pLF~S~~K--f~Sg~GWPSF~~~i-~~~v~~~~D~sm~RtEv~C~~Cg~ 102 (139)
-.|+|+.||..+=+=+.. -..-=|-=..+..- .+-|....+. ...+.+.|-.|.-
T Consensus 3 i~Y~CRHCg~~IG~i~~~~v~~~~LGf~~Lt~eEr~dmI~~~~~G-~i~V~~iCe~C~e 60 (76)
T PF10955_consen 3 IHYYCRHCGTKIGTIDASAVDEEQLGFHHLTPEERQDMISYDENG-DIHVKVICEDCQE 60 (76)
T ss_pred eEEEecCCCCEEEEeeccccCHhhcCcccCCHHHHhhheEEcCCC-CEEEEEecHHHHH
Confidence 479999999988222211 11112332222221 1234444333 3577888888753
No 83
>PF03117 Herpes_UL49_1: UL49 family; InterPro: IPR004339 UL49 proteins are present in the viral tegument at the surface of the nucleocapsid []. Many of the nonconserved tegument proteins of alpha-herpes viruses play important roles during different steps of the viral replication cycle, such as the shutoff of host cell functions by the vhs protein encoded by UL41 and the transcriptional activation of viral immediate-early genes by the UL48 gene product, VP16. UL49 of Human herpesvirus 1 (HHV-1) has been shown to directly interact with VP16. The UL49 gene products of HHV-1 and Bovine herpesvirus 1 exhibit virus-independent intercellular trafficking of unknown biological function but are dispensable for productive viral replication. Envelope glycoprotein M (gM) and the complex formed by glycoproteins E (gE) and I (gI) are involved in the secondary envelopment of Suid herpesvirus 1 (Pseudorabies virus, PrV) particles in the cytoplasm of infected cells. In the absence of the gE-gI complex and gM, envelopment is blocked and capsids surrounded by tegument proteins accumulate in the cytoplasm. The cytoplasmic domains of gE and gM specifically interact with the C-terminal part of the UL49 gene product of PrV suggesting a role for the protein in secondary envelopment during herpesvirus virion maturation [].; GO: 0016032 viral reproduction, 0019033 viral tegument
Probab=20.99 E-value=1.2e+02 Score=25.80 Aligned_cols=50 Identities=26% Similarity=0.503 Sum_probs=37.6
Q ss_pred EEEeccCCcccccCCccccCCCCCccCCcccCCCeEEccCCC-------cceeEEEecCCCCC
Q 032503 48 FYNCAGCGTALYKSVTKFDSGCGWPAFYEGLPGAINRSPDPD-------GRRTEITCAACGGH 103 (139)
Q Consensus 48 ~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~v~~~~D~s-------m~RtEv~C~~Cg~H 103 (139)
+=+|..||-=|=--..||..+ .+|. +.+|=+-+|.. |.---|+|+.||+=
T Consensus 105 aVvC~~CGhCLN~GK~K~~~~---~~F~---pts~FY~RDqkEK~v~~c~~tgriyCS~CGS~ 161 (245)
T PF03117_consen 105 AVVCMECGHCLNFGKGKLKCG---QNFP---PTSMFYYRDQKEKQVIYCATTGRIYCSLCGSQ 161 (245)
T ss_pred EEEeccCCchhhccchhhccc---cCcC---CcceeEeccccceeEEEeccCCCEEEccCCCC
Confidence 558999999998899999876 4443 56776666754 44456899999973
No 84
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.49 E-value=71 Score=26.57 Aligned_cols=12 Identities=17% Similarity=0.252 Sum_probs=8.3
Q ss_pred CCCHHHHHhcCC
Q 032503 9 QKTEEEWRAILS 20 (139)
Q Consensus 9 ~~~~~ewr~~Lt 20 (139)
.+|+++|++...
T Consensus 192 ~l~~~~~~~l~~ 203 (272)
T PRK14810 192 SLSRERLRKLHD 203 (272)
T ss_pred cCCHHHHHHHHH
Confidence 467888876655
No 85
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.45 E-value=66 Score=20.52 Aligned_cols=14 Identities=29% Similarity=0.842 Sum_probs=9.9
Q ss_pred eEEEeccCCccccc
Q 032503 47 GFYNCAGCGTALYK 60 (139)
Q Consensus 47 G~Y~C~~Cg~pLF~ 60 (139)
+.++|..||...|.
T Consensus 36 ~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 36 DRWHCGKCGYTEFK 49 (50)
T ss_pred CcEECCCcCCEEec
Confidence 67777777777663
No 86
>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=20.45 E-value=61 Score=20.92 Aligned_cols=13 Identities=23% Similarity=0.560 Sum_probs=10.3
Q ss_pred cccceEEEeccCC
Q 032503 43 LYADGFYNCAGCG 55 (139)
Q Consensus 43 ~~~~G~Y~C~~Cg 55 (139)
..+.|.|.|.+-.
T Consensus 73 ~~D~G~Y~C~a~N 85 (100)
T cd07693 73 RSDEGVYVCVAHN 85 (100)
T ss_pred cCcCEEEEEEEEc
Confidence 4689999998743
No 87
>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=20.39 E-value=51 Score=20.54 Aligned_cols=12 Identities=25% Similarity=0.509 Sum_probs=9.6
Q ss_pred cccceEEEeccC
Q 032503 43 LYADGFYNCAGC 54 (139)
Q Consensus 43 ~~~~G~Y~C~~C 54 (139)
..+.|.|.|.+.
T Consensus 44 ~~D~G~Y~C~a~ 55 (69)
T cd05725 44 AGDEGSYTCEAE 55 (69)
T ss_pred hhHCEEEEEEEE
Confidence 357899999874
No 88
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=20.35 E-value=61 Score=20.17 Aligned_cols=11 Identities=36% Similarity=0.972 Sum_probs=8.9
Q ss_pred EEEeccCCccc
Q 032503 48 FYNCAGCGTAL 58 (139)
Q Consensus 48 ~Y~C~~Cg~pL 58 (139)
+|.|..||...
T Consensus 2 ~Y~C~~Cg~~~ 12 (44)
T smart00659 2 IYICGECGREN 12 (44)
T ss_pred EEECCCCCCEe
Confidence 68999999863
No 89
>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=20.24 E-value=41 Score=22.45 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=8.0
Q ss_pred EeccCCccc
Q 032503 50 NCAGCGTAL 58 (139)
Q Consensus 50 ~C~~Cg~pL 58 (139)
+|..||+|+
T Consensus 5 HC~~CG~~I 13 (59)
T PF09889_consen 5 HCPVCGKPI 13 (59)
T ss_pred cCCcCCCcC
Confidence 799999987
No 90
>cd05881 Ig1_Necl-2 First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2 (also known as cell adhesion molecule 1 (CADM1)). Ig1_Necl-2: domain similar to the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-2, Necl-2 (also known as cell adhesion molecule 1 (CADM1), SynCAM1, IGSF4A, Tslc1, sgIGSF, and RA175). 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-2 has Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-2 is expressed in a wide variety of tissues, and is a
Probab=20.01 E-value=15 Score=26.00 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=21.3
Q ss_pred HHHHHHhhhCCCCCCCccCCCccccceEEEeccCC
Q 032503 21 PEQFRILRQKGTEPRGTGEYNKLYADGFYNCAGCG 55 (139)
Q Consensus 21 p~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg 55 (139)
+..|.+....+.+--.+=......+.|.|.|.+=.
T Consensus 49 d~Rf~~~~~~~~~~tL~I~~vq~~D~G~Y~Cqv~t 83 (95)
T cd05881 49 DSRFQLVNFSSNELRVSLSNVSLSDEGRYFCQLYT 83 (95)
T ss_pred CcCEEEEeCCCCEEEEEECcCCcccCEEEEEEEEc
Confidence 44444443334444445555677899999997743
Done!