Query 032751
Match_columns 134
No_of_seqs 126 out of 472
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 05:29:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032751.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032751hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10601 zf-LITAF-like: LITAF- 99.9 8.6E-26 1.9E-30 151.5 7.9 70 44-113 1-73 (73)
2 smart00714 LITAF Possible memb 99.9 4.3E-24 9.3E-29 141.2 6.6 66 48-113 1-67 (67)
3 PF10164 DUF2367: Uncharacteri 97.7 0.00016 3.4E-09 51.6 6.4 50 49-107 48-97 (98)
4 PF14353 CpXC: CpXC protein 90.1 0.53 1.2E-05 33.9 4.1 48 50-110 1-50 (128)
5 KOG4440 NMDA selective glutama 89.6 0.14 3E-06 47.6 0.8 56 44-108 929-984 (993)
6 PF14205 Cys_rich_KTR: Cystein 80.0 1.7 3.7E-05 28.0 2.2 21 49-69 3-23 (55)
7 PRK14892 putative transcriptio 77.4 3.7 8.1E-05 29.2 3.6 38 46-110 17-54 (99)
8 PF14255 Cys_rich_CPXG: Cystei 76.3 1.1 2.4E-05 28.4 0.5 24 51-74 1-24 (52)
9 PRK02935 hypothetical protein; 75.1 1.8 3.8E-05 31.6 1.4 28 91-118 63-90 (110)
10 PRK00464 nrdR transcriptional 73.0 4.1 8.8E-05 31.1 3.1 17 99-115 29-45 (154)
11 PF11023 DUF2614: Protein of u 69.7 2.7 5.8E-05 30.9 1.3 28 91-118 62-89 (114)
12 PF04606 Ogr_Delta: Ogr/Delta- 67.9 4.8 0.0001 24.5 2.0 34 52-107 1-36 (47)
13 PF02591 DUF164: Putative zinc 64.8 3.9 8.4E-05 25.5 1.2 13 96-108 44-56 (56)
14 PF08209 Sgf11: Sgf11 (transcr 63.9 6.4 0.00014 22.7 1.9 15 96-110 2-16 (33)
15 PRK14890 putative Zn-ribbon RN 63.3 6 0.00013 25.8 1.9 16 95-110 22-38 (59)
16 COG2888 Predicted Zn-ribbon RN 62.4 4.7 0.0001 26.5 1.3 16 95-110 24-40 (61)
17 PRK08351 DNA-directed RNA poly 61.2 5.5 0.00012 26.1 1.4 24 100-123 17-40 (61)
18 PF06906 DUF1272: Protein of u 60.7 1.8 4E-05 28.1 -0.9 23 90-112 31-55 (57)
19 PF07754 DUF1610: Domain of un 60.3 6 0.00013 21.3 1.3 12 95-106 13-24 (24)
20 PF13248 zf-ribbon_3: zinc-rib 59.8 3.4 7.3E-05 22.2 0.2 10 98-107 16-25 (26)
21 PF01927 Mut7-C: Mut7-C RNAse 56.8 13 0.00027 27.6 3.0 49 45-108 86-134 (147)
22 PRK09678 DNA-binding transcrip 55.7 18 0.00038 24.4 3.2 42 51-114 2-45 (72)
23 smart00709 Zpr1 Duplicated dom 55.1 13 0.00028 28.4 2.9 15 52-66 2-16 (160)
24 PF13240 zinc_ribbon_2: zinc-r 54.6 6 0.00013 20.8 0.7 14 94-107 9-22 (23)
25 TIGR00310 ZPR1_znf ZPR1 zinc f 53.4 13 0.00028 29.3 2.7 16 51-66 1-16 (192)
26 PF06573 Churchill: Churchill 50.9 12 0.00025 27.4 1.8 17 97-113 57-73 (112)
27 TIGR02098 MJ0042_CXXC MJ0042 f 50.1 19 0.00041 20.4 2.4 18 44-61 19-36 (38)
28 PF03119 DNA_ligase_ZBD: NAD-d 49.4 17 0.00038 19.9 2.0 15 100-114 1-15 (28)
29 COG2051 RPS27A Ribosomal prote 49.2 17 0.00038 24.3 2.3 22 41-62 29-50 (67)
30 PRK01103 formamidopyrimidine/5 48.0 21 0.00046 29.1 3.2 14 51-64 246-259 (274)
31 PRK10445 endonuclease VIII; Pr 46.8 22 0.00048 28.9 3.2 14 52-65 237-250 (263)
32 PF09723 Zn-ribbon_8: Zinc rib 46.8 24 0.00051 20.8 2.5 26 37-64 15-40 (42)
33 PF12773 DZR: Double zinc ribb 46.8 5.1 0.00011 24.0 -0.5 12 98-109 29-40 (50)
34 PRK14810 formamidopyrimidine-D 46.6 22 0.00048 29.0 3.1 14 52-65 246-259 (272)
35 TIGR00340 zpr1_rel ZPR1-relate 46.2 22 0.00048 27.3 2.9 14 53-66 1-14 (163)
36 COG0266 Nei Formamidopyrimidin 45.5 23 0.0005 29.5 3.1 24 44-69 241-264 (273)
37 smart00659 RPOLCX RNA polymera 45.4 18 0.00038 22.0 1.8 19 48-66 17-35 (44)
38 PRK13945 formamidopyrimidine-D 43.5 19 0.00041 29.6 2.3 15 51-65 255-269 (282)
39 PF11672 DUF3268: Protein of u 43.1 19 0.00041 25.8 1.9 17 99-115 32-48 (102)
40 PF10955 DUF2757: Protein of u 42.9 24 0.00052 24.1 2.3 19 96-114 2-20 (76)
41 PF04216 FdhE: Protein involve 42.8 16 0.00034 29.9 1.7 65 50-115 172-255 (290)
42 COG1631 RPL42A Ribosomal prote 42.7 29 0.00064 24.6 2.8 28 47-74 5-36 (94)
43 PF04828 GFA: Glutathione-depe 42.5 27 0.00059 22.5 2.5 33 92-124 42-75 (92)
44 PF14577 SEO_C: Sieve element 42.1 16 0.00035 29.9 1.6 24 44-67 208-231 (235)
45 PRK00398 rpoP DNA-directed RNA 41.6 28 0.00061 20.7 2.3 19 98-116 21-39 (46)
46 PF02150 RNA_POL_M_15KD: RNA p 41.6 21 0.00046 20.5 1.6 17 99-115 2-18 (35)
47 PRK06393 rpoE DNA-directed RNA 41.0 15 0.00032 24.3 1.0 24 100-123 19-42 (64)
48 PF10122 Mu-like_Com: Mu-like 40.8 13 0.00027 23.7 0.6 13 98-110 4-16 (51)
49 COG2093 DNA-directed RNA polym 40.4 20 0.00044 23.7 1.6 25 99-123 19-43 (64)
50 PRK12286 rpmF 50S ribosomal pr 40.3 20 0.00044 22.9 1.6 20 91-110 33-52 (57)
51 PF09862 DUF2089: Protein of u 40.0 24 0.00053 25.7 2.1 25 89-113 2-28 (113)
52 PF08772 NOB1_Zn_bind: Nin one 38.4 17 0.00038 24.5 1.1 24 45-68 19-42 (73)
53 PRK14811 formamidopyrimidine-D 37.8 35 0.00077 27.8 3.0 14 52-65 237-250 (269)
54 COG5415 Predicted integral mem 37.8 16 0.00035 29.9 1.0 33 98-130 214-247 (251)
55 TIGR00577 fpg formamidopyrimid 37.4 37 0.0008 27.7 3.1 15 51-65 246-260 (272)
56 PF03811 Zn_Tnp_IS1: InsA N-te 37.3 24 0.00051 20.6 1.4 13 48-60 3-15 (36)
57 PF10571 UPF0547: Uncharacteri 37.1 15 0.00033 19.9 0.5 10 100-109 2-11 (26)
58 PF05876 Terminase_GpA: Phage 36.9 17 0.00038 32.7 1.2 47 47-115 197-246 (557)
59 PF06170 DUF983: Protein of un 36.7 15 0.00034 25.3 0.6 24 92-115 2-25 (86)
60 PRK00420 hypothetical protein; 36.2 23 0.0005 25.8 1.5 19 95-113 37-55 (112)
61 PF14803 Nudix_N_2: Nudix N-te 36.1 21 0.00046 20.5 1.1 13 94-106 18-30 (34)
62 PRK00415 rps27e 30S ribosomal 34.8 27 0.00058 22.8 1.5 20 41-60 21-40 (59)
63 PF09151 DUF1936: Domain of un 34.8 49 0.0011 19.1 2.4 22 98-119 1-24 (36)
64 TIGR01031 rpmF_bact ribosomal 34.7 27 0.00058 22.1 1.5 20 91-110 32-51 (55)
65 KOG1311 DHHC-type Zn-finger pr 34.6 18 0.00039 29.5 0.8 15 50-64 113-127 (299)
66 PF04981 NMD3: NMD3 family ; 34.4 27 0.00058 27.8 1.8 42 53-109 1-46 (236)
67 COG2995 PqiA Uncharacterized p 34.2 31 0.00067 30.5 2.2 38 46-83 34-71 (418)
68 PF10238 Eapp_C: E2F-associate 33.9 31 0.00068 25.9 2.0 16 100-115 111-126 (136)
69 PF13719 zinc_ribbon_5: zinc-r 32.8 40 0.00086 19.4 1.9 17 44-60 19-35 (37)
70 PF08271 TF_Zn_Ribbon: TFIIB z 32.1 27 0.00058 20.5 1.1 16 97-112 18-33 (43)
71 COG1645 Uncharacterized Zn-fin 32.0 34 0.00073 25.7 1.8 26 88-115 36-62 (131)
72 smart00661 RPOL9 RNA polymeras 31.7 19 0.00041 21.5 0.4 12 100-111 2-13 (52)
73 KOG4517 Uncharacterized conser 31.4 20 0.00043 26.3 0.5 12 97-108 105-116 (117)
74 PF02132 RecR: RecR protein; 31.3 16 0.00036 21.5 0.1 16 92-107 11-26 (41)
75 PF05129 Elf1: Transcription e 30.0 28 0.00061 23.6 1.1 22 46-67 18-41 (81)
76 COG1996 RPC10 DNA-directed RNA 29.5 40 0.00087 21.1 1.6 18 48-65 22-39 (49)
77 PRK03824 hypA hydrogenase nick 29.2 53 0.0011 24.2 2.5 19 44-62 64-82 (135)
78 PF13717 zinc_ribbon_4: zinc-r 29.0 51 0.0011 18.9 1.9 16 44-59 19-34 (36)
79 PF08882 Acetone_carb_G: Aceto 29.0 34 0.00073 25.1 1.4 19 92-110 68-86 (112)
80 cd07973 Spt4 Transcription elo 28.9 32 0.00069 24.4 1.2 25 99-123 21-57 (98)
81 PF09889 DUF2116: Uncharacteri 28.6 23 0.00049 23.0 0.4 13 98-110 3-15 (59)
82 PF13453 zf-TFIIB: Transcripti 28.5 36 0.00078 19.8 1.2 16 100-115 1-16 (41)
83 PF03604 DNA_RNApol_7kD: DNA d 28.2 26 0.00057 19.9 0.5 14 50-63 17-30 (32)
84 PF01155 HypA: Hydrogenase exp 27.2 40 0.00087 24.0 1.5 17 45-61 65-81 (113)
85 PF03884 DUF329: Domain of unk 27.0 46 0.001 21.4 1.6 13 50-62 2-14 (57)
86 COG4888 Uncharacterized Zn rib 26.9 58 0.0013 23.5 2.2 23 47-69 19-43 (104)
87 PF09788 Tmemb_55A: Transmembr 26.6 52 0.0011 27.3 2.2 10 49-58 176-185 (256)
88 PF01307 Plant_vir_prot: Plant 26.5 78 0.0017 22.6 2.9 34 69-105 70-104 (104)
89 PF04423 Rad50_zn_hook: Rad50 25.6 41 0.0009 20.6 1.2 22 92-113 14-35 (54)
90 PF01096 TFIIS_C: Transcriptio 25.6 61 0.0013 18.8 1.8 18 51-68 1-18 (39)
91 PF12760 Zn_Tnp_IS1595: Transp 25.5 45 0.00098 19.8 1.3 16 51-66 19-34 (46)
92 PRK14559 putative protein seri 25.4 11 0.00025 34.8 -2.0 17 95-111 38-54 (645)
93 PF01667 Ribosomal_S27e: Ribos 25.2 81 0.0018 20.2 2.5 21 41-61 17-37 (55)
94 smart00834 CxxC_CXXC_SSSS Puta 25.0 35 0.00076 19.2 0.7 13 48-60 24-36 (41)
95 PRK09710 lar restriction allev 24.8 48 0.001 22.0 1.4 15 51-65 7-21 (64)
96 PRK00432 30S ribosomal protein 24.8 28 0.0006 21.6 0.3 13 99-111 21-34 (50)
97 PF11697 DUF3293: Protein of u 24.3 41 0.00088 22.2 1.0 16 118-133 38-54 (73)
98 TIGR02605 CxxC_CxxC_SSSS putat 23.9 54 0.0012 19.6 1.4 21 48-68 24-44 (52)
99 PF01363 FYVE: FYVE zinc finge 23.9 57 0.0012 20.5 1.6 15 95-109 22-36 (69)
100 PF10083 DUF2321: Uncharacteri 23.9 19 0.00042 27.8 -0.7 21 95-115 36-57 (158)
101 PF10276 zf-CHCC: Zinc-finger 23.7 48 0.001 19.8 1.2 25 31-59 14-38 (40)
102 PF14446 Prok-RING_1: Prokaryo 23.3 76 0.0016 20.3 2.1 34 92-125 13-53 (54)
103 TIGR01206 lysW lysine biosynth 23.3 1.2E+02 0.0025 19.2 2.9 25 98-122 22-46 (54)
104 PRK05978 hypothetical protein; 23.2 33 0.00072 26.1 0.5 24 92-115 46-69 (148)
105 KOG2907 RNA polymerase I trans 22.6 36 0.00078 25.1 0.5 16 96-111 72-87 (116)
106 PF14471 DUF4428: Domain of un 22.6 36 0.00079 21.1 0.5 14 100-113 1-14 (51)
107 PRK00418 DNA gyrase inhibitor; 22.1 46 0.001 21.8 0.9 14 48-61 4-17 (62)
108 PF01529 zf-DHHC: DHHC palmito 21.5 31 0.00068 25.2 0.0 48 44-112 42-90 (174)
109 PF03367 zf-ZPR1: ZPR1 zinc-fi 21.3 66 0.0014 24.5 1.8 15 51-65 2-16 (161)
110 COG4416 Com Mu-like prophage p 21.2 65 0.0014 20.9 1.4 27 48-74 22-48 (60)
111 PF06044 DRP: Dam-replacing fa 21.0 43 0.00093 27.8 0.7 19 98-116 31-50 (254)
112 TIGR00244 transcriptional regu 20.7 51 0.0011 25.2 1.0 18 98-115 28-45 (147)
113 PF03226 Yippee-Mis18: Yippee 20.5 30 0.00065 23.5 -0.2 18 94-111 53-70 (96)
114 PF09538 FYDLN_acid: Protein o 20.4 57 0.0012 23.4 1.2 18 44-63 22-39 (108)
115 PF10058 DUF2296: Predicted in 20.1 72 0.0016 20.1 1.5 16 92-107 38-53 (54)
116 PF06677 Auto_anti-p27: Sjogre 20.1 51 0.0011 19.7 0.8 11 100-110 19-29 (41)
No 1
>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=99.93 E-value=8.6e-26 Score=151.50 Aligned_cols=70 Identities=24% Similarity=0.601 Sum_probs=64.1
Q ss_pred cCCcCeeEECCCCCCeEEeEEEEccChhHHHHHHHHhhhhh--hccccc-ccccCCceeECCCcCceeEEEec
Q 032751 44 YRDTPAPFSCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGI--CFLCPS-MDCLWHKYHYCPSCNEKVANFEK 113 (134)
Q Consensus 44 ~~~~P~~~~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~--C~l~p~-~d~ckDv~H~Cp~C~~~lG~~~r 113 (134)
|+++|+.++||+||++++|+|++++|..||+++++|+++++ |+++|| +|++||++|+||+||++||+|+|
T Consensus 1 ~~~~p~~~~CP~C~~~~~T~v~~~~g~~t~~~~~~l~~~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~~r 73 (73)
T PF10601_consen 1 FGPEPVRIYCPYCQQQVQTRVEYKSGTMTYICAALLCLFGCWPCCCIPFCCDSCKDVYHYCPNCGAFLGTYKR 73 (73)
T ss_pred CCCCceeeECCCCCCEEEEEEEEEeChHHHHHHHHHHHHHHHHHhhHhhccccccCceEECCCCCCEeEEEeC
Confidence 68999999999999999999999999999999999999864 445555 69999999999999999999987
No 2
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=99.90 E-value=4.3e-24 Score=141.25 Aligned_cols=66 Identities=27% Similarity=0.645 Sum_probs=58.9
Q ss_pred CeeEECCCCCCeEEeEEEEccChhHHHHHHHHhhhhhhcccc-cccccCCceeECCCcCceeEEEec
Q 032751 48 PAPFSCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGICFLCP-SMDCLWHKYHYCPSCNEKVANFEK 113 (134)
Q Consensus 48 P~~~~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~C~l~p-~~d~ckDv~H~Cp~C~~~lG~~~r 113 (134)
|+.+.||+||++++|+|++++|.+||+++++++++++|+++| ++|++||++|+||+||++||+|+|
T Consensus 1 p~~i~Cp~C~~~~~T~v~~~~g~~t~~~~~ll~~~~~~~~iP~~~~~~kd~~H~Cp~C~~~lg~~~r 67 (67)
T smart00714 1 PYQLFCPRCQNNVTTRVETETGVCAWLICCLLFLLCFCCCLPCCLDSFKDVNHYCPNCGAFLGTYNR 67 (67)
T ss_pred CcceECCCCCCEEEEEEEEEeChHHHHHHHHHHHHHHHHHHHHhcccccCccEECCCCCCEeEEecC
Confidence 678999999999999999999999999999888765455555 469999999999999999999986
No 3
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=97.69 E-value=0.00016 Score=51.58 Aligned_cols=50 Identities=16% Similarity=0.316 Sum_probs=34.6
Q ss_pred eeEECCCCCCeEEeEEEEccChhHHHHHHHHhhhhhhcccccccccCCceeECCCcCce
Q 032751 49 APFSCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGICFLCPSMDCLWHKYHYCPSCNEK 107 (134)
Q Consensus 49 ~~~~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~C~l~p~~d~ckDv~H~Cp~C~~~ 107 (134)
+.--||.|+.-++ +.+-+...|++|+++|=+|+.|+ +.+.+-+|+||+..
T Consensus 48 vvggCp~CrvG~l---e~~ft~~Gi~~AI~fFPiGilcc------~~~r~~rC~nCG~~ 97 (98)
T PF10164_consen 48 VVGGCPACRVGVL---EDSFTCCGILCAIFFFPIGILCC------LAMRERRCSNCGAT 97 (98)
T ss_pred EecCCCCCceeee---cccccHHHHHHHHHHHhhHHHHh------hhcCccccCCCCcc
Confidence 3346999987665 56678888888877766775211 12466799999974
No 4
>PF14353 CpXC: CpXC protein
Probab=90.09 E-value=0.53 Score=33.93 Aligned_cols=48 Identities=21% Similarity=0.286 Sum_probs=28.6
Q ss_pred eEECCCCCCeEEeEEEEccChhHH--HHHHHHhhhhhhcccccccccCCceeECCCcCceeEE
Q 032751 50 PFSCVYCGNSGVTQVRSKPSSAAV--VGCMMPFFLGICFLCPSMDCLWHKYHYCPSCNEKVAN 110 (134)
Q Consensus 50 ~~~CP~C~~~v~T~V~~~~g~~t~--i~~~~lcl~g~C~l~p~~d~ckDv~H~Cp~C~~~lG~ 110 (134)
++.||+|++.....+........- +---+| =| .=-.|.||+||+..-.
T Consensus 1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il--~g-----------~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTSINADEDPELKEKIL--DG-----------SLFSFTCPSCGHKFRL 50 (128)
T ss_pred CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHH--cC-----------CcCEEECCCCCCceec
Confidence 378999999988888775432211 111222 11 1114589999987643
No 5
>KOG4440 consensus NMDA selective glutamate-gated ion channel receptor subunit GRIN1 [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=89.59 E-value=0.14 Score=47.58 Aligned_cols=56 Identities=20% Similarity=0.350 Sum_probs=48.0
Q ss_pred cCCcCeeEECCCCCCeEEeEEEEccChhHHHHHHHHhhhhhhcccccccccCCceeECCCcCcee
Q 032751 44 YRDTPAPFSCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGICFLCPSMDCLWHKYHYCPSCNEKV 108 (134)
Q Consensus 44 ~~~~P~~~~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~C~l~p~~d~ckDv~H~Cp~C~~~l 108 (134)
-++.|..+.|-.|...+.+.+.+|. +|++++|--+|+|.+++.|..|.||.|....
T Consensus 929 p~d~~~vl~csR~re~vesdvhret---------ilflwPcsPlPcflssfsdfvhicPlcShim 984 (993)
T KOG4440|consen 929 PKDKPLVLFCSRCREIVESDVHRET---------ILFLWPCSPLPCFLSSFSDFVHICPLCSHIM 984 (993)
T ss_pred CCCcceEEEeechhhcCCCCcChhh---------heecCCCCCccccccccccceeeCCccCcce
Confidence 3789999999999999999999986 6666775456777899999999999998765
No 6
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=80.04 E-value=1.7 Score=28.03 Aligned_cols=21 Identities=24% Similarity=0.471 Sum_probs=16.3
Q ss_pred eeEECCCCCCeEEeEEEEccC
Q 032751 49 APFSCVYCGNSGVTQVRSKPS 69 (134)
Q Consensus 49 ~~~~CP~C~~~v~T~V~~~~g 69 (134)
..+.||.|+.....+|+...-
T Consensus 3 ~Wi~CP~CgnKTR~kir~DT~ 23 (55)
T PF14205_consen 3 EWILCPICGNKTRLKIREDTV 23 (55)
T ss_pred eEEECCCCCCccceeeecCce
Confidence 467899999888888877543
No 7
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=77.43 E-value=3.7 Score=29.25 Aligned_cols=38 Identities=21% Similarity=0.420 Sum_probs=25.4
Q ss_pred CcCeeEECCCCCCeEEeEEEEccChhHHHHHHHHhhhhhhcccccccccCCceeECCCcCceeEE
Q 032751 46 DTPAPFSCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGICFLCPSMDCLWHKYHYCPSCNEKVAN 110 (134)
Q Consensus 46 ~~P~~~~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~C~l~p~~d~ckDv~H~Cp~C~~~lG~ 110 (134)
..|..+.||+|+...++.-..+ | -.++.|++|+.+-|+
T Consensus 17 klpt~f~CP~Cge~~v~v~~~k-~--------------------------~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 17 KLPKIFECPRCGKVSISVKIKK-N--------------------------IAIITCGNCGLYTEF 54 (99)
T ss_pred CCCcEeECCCCCCeEeeeecCC-C--------------------------cceEECCCCCCccCE
Confidence 4567889999996433322222 1 346799999988776
No 8
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=76.26 E-value=1.1 Score=28.43 Aligned_cols=24 Identities=17% Similarity=0.498 Sum_probs=19.3
Q ss_pred EECCCCCCeEEeEEEEccChhHHH
Q 032751 51 FSCVYCGNSGVTQVRSKPSSAAVV 74 (134)
Q Consensus 51 ~~CP~C~~~v~T~V~~~~g~~t~i 74 (134)
+.||+|+..+.+.|....|...|+
T Consensus 1 i~CPyCge~~~~~iD~s~~~Q~yi 24 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAGDQEYI 24 (52)
T ss_pred CCCCCCCCeeEEEEecCCCCeeEE
Confidence 469999999999998887766554
No 9
>PRK02935 hypothetical protein; Provisional
Probab=75.10 E-value=1.8 Score=31.55 Aligned_cols=28 Identities=25% Similarity=0.442 Sum_probs=22.3
Q ss_pred ccccCCceeECCCcCceeEEEecCCceE
Q 032751 91 MDCLWHKYHYCPSCNEKVANFEKRDICA 118 (134)
Q Consensus 91 ~d~ckDv~H~Cp~C~~~lG~~~r~~~~~ 118 (134)
+-+.|-+.-.||||++.--.--|.|.|+
T Consensus 63 mlStkavqV~CP~C~K~TKmLGrvD~CM 90 (110)
T PRK02935 63 MLSTKAVQVICPSCEKPTKMLGRVDACM 90 (110)
T ss_pred hhcccceeeECCCCCchhhhccceeecC
Confidence 4889999999999998766555666665
No 10
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=72.97 E-value=4.1 Score=31.12 Aligned_cols=17 Identities=24% Similarity=0.769 Sum_probs=13.9
Q ss_pred eECCCcCceeEEEecCC
Q 032751 99 HYCPSCNEKVANFEKRD 115 (134)
Q Consensus 99 H~Cp~C~~~lG~~~r~~ 115 (134)
+.|++|+...++|.+-+
T Consensus 29 ~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 29 RECLACGKRFTTFERVE 45 (154)
T ss_pred eeccccCCcceEeEecc
Confidence 89999999988876543
No 11
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=69.66 E-value=2.7 Score=30.87 Aligned_cols=28 Identities=21% Similarity=0.421 Sum_probs=21.6
Q ss_pred ccccCCceeECCCcCceeEEEecCCceE
Q 032751 91 MDCLWHKYHYCPSCNEKVANFEKRDICA 118 (134)
Q Consensus 91 ~d~ckDv~H~Cp~C~~~lG~~~r~~~~~ 118 (134)
+.+.|-+.-.||||++.--.-.|.|.|+
T Consensus 62 mlStkav~V~CP~C~K~TKmLGr~D~CM 89 (114)
T PF11023_consen 62 MLSTKAVQVECPNCGKQTKMLGRVDACM 89 (114)
T ss_pred hhcccceeeECCCCCChHhhhchhhccC
Confidence 4788889999999998865555556665
No 12
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=67.92 E-value=4.8 Score=24.45 Aligned_cols=34 Identities=21% Similarity=0.488 Sum_probs=23.4
Q ss_pred ECCCCCCeEEeEEEEccChhHHHHHHHHhhhhhhcccccccccCCceeECCC--cCce
Q 032751 52 SCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGICFLCPSMDCLWHKYHYCPS--CNEK 107 (134)
Q Consensus 52 ~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~C~l~p~~d~ckDv~H~Cp~--C~~~ 107 (134)
+||+|+.....+.....+ +..++.++.|.| |+..
T Consensus 1 ~CP~Cg~~a~ir~S~~~s----------------------~~~~~~Y~qC~N~~Cg~t 36 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLS----------------------PLTRELYCQCTNPECGHT 36 (47)
T ss_pred CcCCCCCeeEEEEchhhC----------------------cceEEEEEEECCCcCCCE
Confidence 599999988766555322 445777888877 8764
No 13
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=64.79 E-value=3.9 Score=25.54 Aligned_cols=13 Identities=23% Similarity=0.922 Sum_probs=11.3
Q ss_pred CceeECCCcCcee
Q 032751 96 HKYHYCPSCNEKV 108 (134)
Q Consensus 96 Dv~H~Cp~C~~~l 108 (134)
|...+||+|+..|
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 6789999999875
No 14
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=63.90 E-value=6.4 Score=22.70 Aligned_cols=15 Identities=40% Similarity=0.877 Sum_probs=10.8
Q ss_pred CceeECCCcCceeEE
Q 032751 96 HKYHYCPSCNEKVAN 110 (134)
Q Consensus 96 Dv~H~Cp~C~~~lG~ 110 (134)
..+..|+||+..|+.
T Consensus 2 ~~~~~C~nC~R~v~a 16 (33)
T PF08209_consen 2 SPYVECPNCGRPVAA 16 (33)
T ss_dssp S-EEE-TTTSSEEEG
T ss_pred CCeEECCCCcCCcch
Confidence 457899999999874
No 15
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=63.33 E-value=6 Score=25.85 Aligned_cols=16 Identities=25% Similarity=0.559 Sum_probs=12.1
Q ss_pred CCceeECCCcCce-eEE
Q 032751 95 WHKYHYCPSCNEK-VAN 110 (134)
Q Consensus 95 kDv~H~Cp~C~~~-lG~ 110 (134)
+-+...|||||+. |++
T Consensus 22 ~~~~F~CPnCG~~~I~R 38 (59)
T PRK14890 22 KAVKFLCPNCGEVIIYR 38 (59)
T ss_pred ccCEeeCCCCCCeeEee
Confidence 4567788999888 776
No 16
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=62.40 E-value=4.7 Score=26.48 Aligned_cols=16 Identities=19% Similarity=0.441 Sum_probs=12.2
Q ss_pred CCceeECCCcC-ceeEE
Q 032751 95 WHKYHYCPSCN-EKVAN 110 (134)
Q Consensus 95 kDv~H~Cp~C~-~~lG~ 110 (134)
+-+.+.||||| ..|++
T Consensus 24 ~~v~F~CPnCGe~~I~R 40 (61)
T COG2888 24 TAVKFPCPNCGEVEIYR 40 (61)
T ss_pred ceeEeeCCCCCceeeeh
Confidence 45667999999 66776
No 17
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=61.19 E-value=5.5 Score=26.11 Aligned_cols=24 Identities=25% Similarity=0.487 Sum_probs=21.7
Q ss_pred ECCCcCceeEEEecCCceEEeCCC
Q 032751 100 YCPSCNEKVANFEKRDICAVMDPP 123 (134)
Q Consensus 100 ~Cp~C~~~lG~~~r~~~~~~~~p~ 123 (134)
.||+|+..-=+.+..+..++.||.
T Consensus 17 ~CP~Cgs~~~T~~W~G~viI~dPe 40 (61)
T PRK08351 17 RCPVCGSRDLSDEWFDLVIIIDVE 40 (61)
T ss_pred cCCCCcCCccccccccEEEEeCCc
Confidence 699999988788999999999996
No 18
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=60.75 E-value=1.8 Score=28.06 Aligned_cols=23 Identities=13% Similarity=0.189 Sum_probs=14.7
Q ss_pred cccccC-Cc-eeECCCcCceeEEEe
Q 032751 90 SMDCLW-HK-YHYCPSCNEKVANFE 112 (134)
Q Consensus 90 ~~d~ck-Dv-~H~Cp~C~~~lG~~~ 112 (134)
||..|- +. .+.|||||-.|-.+.
T Consensus 31 FC~~C~e~~l~~~CPNCgGelv~RP 55 (57)
T PF06906_consen 31 FCADCAETMLNGVCPNCGGELVRRP 55 (57)
T ss_pred ccHHHHHHHhcCcCcCCCCccccCC
Confidence 453333 33 589999998776543
No 19
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=60.28 E-value=6 Score=21.33 Aligned_cols=12 Identities=25% Similarity=0.459 Sum_probs=9.7
Q ss_pred CCceeECCCcCc
Q 032751 95 WHKYHYCPSCNE 106 (134)
Q Consensus 95 kDv~H~Cp~C~~ 106 (134)
+-+...|||||.
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 468889999984
No 20
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=59.76 E-value=3.4 Score=22.16 Aligned_cols=10 Identities=40% Similarity=1.285 Sum_probs=5.2
Q ss_pred eeECCCcCce
Q 032751 98 YHYCPSCNEK 107 (134)
Q Consensus 98 ~H~Cp~C~~~ 107 (134)
..+||+||+.
T Consensus 16 ~~fC~~CG~~ 25 (26)
T PF13248_consen 16 AKFCPNCGAK 25 (26)
T ss_pred cccChhhCCC
Confidence 3455555554
No 21
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=56.80 E-value=13 Score=27.61 Aligned_cols=49 Identities=16% Similarity=0.331 Sum_probs=32.9
Q ss_pred CCcCeeEECCCCCCeEEeEEEEccChhHHHHHHHHhhhhhhcccccccccCCceeECCCcCcee
Q 032751 45 RDTPAPFSCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGICFLCPSMDCLWHKYHYCPSCNEKV 108 (134)
Q Consensus 45 ~~~P~~~~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~C~l~p~~d~ckDv~H~Cp~C~~~l 108 (134)
...+....|+.||......-+.+.-. -+++..-.-.|.-..|+.|++.-
T Consensus 86 ~~~~~~sRC~~CN~~L~~v~~~~v~~---------------~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 86 RLDPIFSRCPKCNGPLRPVSKEEVKD---------------RVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred ccCCCCCccCCCCcEeeechhhcccc---------------ccCccccccCCeEEECCCCCCEe
Confidence 45677789999999665543332211 14566666667799999999874
No 22
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=55.70 E-value=18 Score=24.38 Aligned_cols=42 Identities=21% Similarity=0.574 Sum_probs=29.9
Q ss_pred EECCCCCCeEEeEEEEccChhHHHHHHHHhhhhhhcccccccccCCceeECC--CcCceeEEEecC
Q 032751 51 FSCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGICFLCPSMDCLWHKYHYCP--SCNEKVANFEKR 114 (134)
Q Consensus 51 ~~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~C~l~p~~d~ckDv~H~Cp--~C~~~lG~~~r~ 114 (134)
|.||+|+..-.++..+..+ +..++.++.|. +|+.-.-++..-
T Consensus 2 m~CP~Cg~~a~irtSr~~s----------------------~~~~~~Y~qC~N~eCg~tF~t~es~ 45 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYIT----------------------DTTKERYHQCQNVNCSATFITYESV 45 (72)
T ss_pred ccCCCCCCccEEEEChhcC----------------------hhhheeeeecCCCCCCCEEEEEEEE
Confidence 6899999988555444222 55789999997 999876665443
No 23
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=55.13 E-value=13 Score=28.40 Aligned_cols=15 Identities=33% Similarity=0.791 Sum_probs=12.0
Q ss_pred ECCCCCCeEEeEEEE
Q 032751 52 SCVYCGNSGVTQVRS 66 (134)
Q Consensus 52 ~CP~C~~~v~T~V~~ 66 (134)
.||+|+..+.|+...
T Consensus 2 ~Cp~C~~~~~~~~~~ 16 (160)
T smart00709 2 DCPSCGGNGTTRMLL 16 (160)
T ss_pred cCCCCCCCCEEEEEE
Confidence 599999998877653
No 24
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=54.55 E-value=6 Score=20.79 Aligned_cols=14 Identities=21% Similarity=0.812 Sum_probs=7.5
Q ss_pred cCCceeECCCcCce
Q 032751 94 LWHKYHYCPSCNEK 107 (134)
Q Consensus 94 ckDv~H~Cp~C~~~ 107 (134)
..|...+|++||+.
T Consensus 9 ~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 9 IEDDAKFCPNCGTP 22 (23)
T ss_pred CCCcCcchhhhCCc
Confidence 34455556666654
No 25
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=53.42 E-value=13 Score=29.31 Aligned_cols=16 Identities=25% Similarity=0.644 Sum_probs=13.1
Q ss_pred EECCCCCCeEEeEEEE
Q 032751 51 FSCVYCGNSGVTQVRS 66 (134)
Q Consensus 51 ~~CP~C~~~v~T~V~~ 66 (134)
+.||+|++.+.|++..
T Consensus 1 ~~Cp~C~~~~~~~~~~ 16 (192)
T TIGR00310 1 IDCPSCGGECETVMKT 16 (192)
T ss_pred CcCCCCCCCCEEEEEE
Confidence 3699999998888763
No 26
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=50.86 E-value=12 Score=27.42 Aligned_cols=17 Identities=29% Similarity=0.596 Sum_probs=12.4
Q ss_pred ceeECCCcCceeEEEec
Q 032751 97 KYHYCPSCNEKVANFEK 113 (134)
Q Consensus 97 v~H~Cp~C~~~lG~~~r 113 (134)
..|.|.||+.+|+++..
T Consensus 57 Y~HvC~nC~HvIA~HEY 73 (112)
T PF06573_consen 57 YDHVCKNCHHVIARHEY 73 (112)
T ss_dssp EEEEETTT--EEEEEEE
T ss_pred eeeccCccceEEEeeeE
Confidence 46999999999998654
No 27
>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=50.08 E-value=19 Score=20.38 Aligned_cols=18 Identities=17% Similarity=0.311 Sum_probs=13.2
Q ss_pred cCCcCeeEECCCCCCeEE
Q 032751 44 YRDTPAPFSCVYCGNSGV 61 (134)
Q Consensus 44 ~~~~P~~~~CP~C~~~v~ 61 (134)
+.+....+.||+|+....
T Consensus 19 ~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 19 LGANGGKVRCGKCGHVWY 36 (38)
T ss_pred cCCCCCEEECCCCCCEEE
Confidence 444556899999998754
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=49.37 E-value=17 Score=19.88 Aligned_cols=15 Identities=33% Similarity=0.727 Sum_probs=7.7
Q ss_pred ECCCcCceeEEEecC
Q 032751 100 YCPSCNEKVANFEKR 114 (134)
Q Consensus 100 ~Cp~C~~~lG~~~r~ 114 (134)
+||.|+..|-+.+.+
T Consensus 1 ~CP~C~s~l~~~~~e 15 (28)
T PF03119_consen 1 TCPVCGSKLVREEGE 15 (28)
T ss_dssp B-TTT--BEEE-CCT
T ss_pred CcCCCCCEeEcCCCC
Confidence 589999998754443
No 29
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=49.23 E-value=17 Score=24.27 Aligned_cols=22 Identities=18% Similarity=0.619 Sum_probs=15.7
Q ss_pred ecccCCcCeeEECCCCCCeEEe
Q 032751 41 QTIYRDTPAPFSCVYCGNSGVT 62 (134)
Q Consensus 41 q~~~~~~P~~~~CP~C~~~v~T 62 (134)
|.+|+.....+.|..|+..+.+
T Consensus 29 q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 29 QVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred EEEeccCceEEEecccccEEEe
Confidence 4557888888888888876543
No 30
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=47.97 E-value=21 Score=29.07 Aligned_cols=14 Identities=21% Similarity=0.318 Sum_probs=10.3
Q ss_pred EECCCCCCeEEeEE
Q 032751 51 FSCVYCGNSGVTQV 64 (134)
Q Consensus 51 ~~CP~C~~~v~T~V 64 (134)
.-||.|+..+....
T Consensus 246 ~pC~~Cg~~I~~~~ 259 (274)
T PRK01103 246 EPCRRCGTPIEKIK 259 (274)
T ss_pred CCCCCCCCeeEEEE
Confidence 35999998876533
No 31
>PRK10445 endonuclease VIII; Provisional
Probab=46.84 E-value=22 Score=28.88 Aligned_cols=14 Identities=21% Similarity=0.408 Sum_probs=10.8
Q ss_pred ECCCCCCeEEeEEE
Q 032751 52 SCVYCGNSGVTQVR 65 (134)
Q Consensus 52 ~CP~C~~~v~T~V~ 65 (134)
.||.|+..+.....
T Consensus 237 ~Cp~Cg~~I~~~~~ 250 (263)
T PRK10445 237 ACERCGGIIEKTTL 250 (263)
T ss_pred CCCCCCCEeEEEEE
Confidence 59999988765554
No 32
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=46.83 E-value=24 Score=20.84 Aligned_cols=26 Identities=27% Similarity=0.640 Sum_probs=16.5
Q ss_pred eeEeecccCCcCeeEECCCCCCeEEeEE
Q 032751 37 IPIQQTIYRDTPAPFSCVYCGNSGVTQV 64 (134)
Q Consensus 37 v~vqq~~~~~~P~~~~CP~C~~~v~T~V 64 (134)
+.+.+. .++ .....||.|+..-..++
T Consensus 15 fe~~~~-~~~-~~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 15 FEVLQS-ISE-DDPVPCPECGSTEVRRV 40 (42)
T ss_pred EEEEEE-cCC-CCCCcCCCCCCCceEEe
Confidence 334444 344 77789999999544444
No 33
>PF12773 DZR: Double zinc ribbon
Probab=46.78 E-value=5.1 Score=24.04 Aligned_cols=12 Identities=25% Similarity=0.805 Sum_probs=6.8
Q ss_pred eeECCCcCceeE
Q 032751 98 YHYCPSCNEKVA 109 (134)
Q Consensus 98 ~H~Cp~C~~~lG 109 (134)
..+|++|++.+.
T Consensus 29 ~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 29 KKICPNCGAENP 40 (50)
T ss_pred CCCCcCCcCCCc
Confidence 446666666543
No 34
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=46.56 E-value=22 Score=29.03 Aligned_cols=14 Identities=21% Similarity=0.401 Sum_probs=10.3
Q ss_pred ECCCCCCeEEeEEE
Q 032751 52 SCVYCGNSGVTQVR 65 (134)
Q Consensus 52 ~CP~C~~~v~T~V~ 65 (134)
-||.|+..+...+.
T Consensus 246 pCprCG~~I~~~~~ 259 (272)
T PRK14810 246 PCLNCKTPIRRVVV 259 (272)
T ss_pred cCCCCCCeeEEEEE
Confidence 69999988755433
No 35
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=46.25 E-value=22 Score=27.31 Aligned_cols=14 Identities=29% Similarity=0.698 Sum_probs=10.0
Q ss_pred CCCCCCeEEeEEEE
Q 032751 53 CVYCGNSGVTQVRS 66 (134)
Q Consensus 53 CP~C~~~v~T~V~~ 66 (134)
||.|+....+.+.+
T Consensus 1 CP~Cg~~~~~~~~~ 14 (163)
T TIGR00340 1 CPVCGSRTLKAVTY 14 (163)
T ss_pred CCCCCCcceEeeeE
Confidence 99999875555444
No 36
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=45.51 E-value=23 Score=29.54 Aligned_cols=24 Identities=21% Similarity=0.295 Sum_probs=17.2
Q ss_pred cCCcCeeEECCCCCCeEEeEEEEccC
Q 032751 44 YRDTPAPFSCVYCGNSGVTQVRSKPS 69 (134)
Q Consensus 44 ~~~~P~~~~CP~C~~~v~T~V~~~~g 69 (134)
|+++=. -|+.|+..+...+....|
T Consensus 241 YgR~Ge--pC~~CGt~I~k~~~~gR~ 264 (273)
T COG0266 241 YGRAGE--PCRRCGTPIEKIKLGGRS 264 (273)
T ss_pred ecCCCC--CCCccCCEeEEEEEcCCc
Confidence 555444 599999999888776444
No 37
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=45.41 E-value=18 Score=21.96 Aligned_cols=19 Identities=21% Similarity=0.385 Sum_probs=14.9
Q ss_pred CeeEECCCCCCeEEeEEEE
Q 032751 48 PAPFSCVYCGNSGVTQVRS 66 (134)
Q Consensus 48 P~~~~CP~C~~~v~T~V~~ 66 (134)
...+.||+|+..++-+...
T Consensus 17 ~~~irC~~CG~rIlyK~R~ 35 (44)
T smart00659 17 KDVVRCRECGYRILYKKRT 35 (44)
T ss_pred CCceECCCCCceEEEEeCC
Confidence 4568999999999866544
No 38
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=43.48 E-value=19 Score=29.56 Aligned_cols=15 Identities=20% Similarity=0.248 Sum_probs=11.0
Q ss_pred EECCCCCCeEEeEEE
Q 032751 51 FSCVYCGNSGVTQVR 65 (134)
Q Consensus 51 ~~CP~C~~~v~T~V~ 65 (134)
.-||.|+..+.....
T Consensus 255 ~pC~~Cg~~I~~~~~ 269 (282)
T PRK13945 255 KPCRKCGTPIERIKL 269 (282)
T ss_pred CCCCcCCCeeEEEEE
Confidence 369999988875443
No 39
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=43.13 E-value=19 Score=25.83 Aligned_cols=17 Identities=24% Similarity=0.495 Sum_probs=14.7
Q ss_pred eECCCcCceeEEEecCC
Q 032751 99 HYCPSCNEKVANFEKRD 115 (134)
Q Consensus 99 H~Cp~C~~~lG~~~r~~ 115 (134)
..|++|++.||.+++.+
T Consensus 32 y~C~~C~AyVG~H~~t~ 48 (102)
T PF11672_consen 32 YVCTPCDAYVGCHPGTD 48 (102)
T ss_pred EECCCCCceeeeeCCCC
Confidence 68999999999988664
No 40
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=42.92 E-value=24 Score=24.08 Aligned_cols=19 Identities=21% Similarity=0.581 Sum_probs=16.1
Q ss_pred CceeECCCcCceeEEEecC
Q 032751 96 HKYHYCPSCNEKVANFEKR 114 (134)
Q Consensus 96 Dv~H~Cp~C~~~lG~~~r~ 114 (134)
-++.+|..|+..||+.+.+
T Consensus 2 ai~Y~CRHCg~~IG~i~~~ 20 (76)
T PF10955_consen 2 AIHYYCRHCGTKIGTIDAS 20 (76)
T ss_pred ceEEEecCCCCEEEEeecc
Confidence 3678999999999997765
No 41
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=42.84 E-value=16 Score=29.91 Aligned_cols=65 Identities=15% Similarity=0.304 Sum_probs=28.5
Q ss_pred eEECCCCCCe-EEeEEEEcc--ChhHHHHHHHHhh-hhh-hcccccc--------------cccCCceeECCCcCceeEE
Q 032751 50 PFSCVYCGNS-GVTQVRSKP--SSAAVVGCMMPFF-LGI-CFLCPSM--------------DCLWHKYHYCPSCNEKVAN 110 (134)
Q Consensus 50 ~~~CP~C~~~-v~T~V~~~~--g~~t~i~~~~lcl-~g~-C~l~p~~--------------d~ckDv~H~Cp~C~~~lG~ 110 (134)
.-+||-||.. +.+.|+.+. |. =|+.|.++-. |-+ =.-+++| +.-.-..+.|-.|+.++-+
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~-R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~ 250 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGK-RYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKT 250 (290)
T ss_dssp -SS-TTT---EEEEEEE------E-EEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEE
T ss_pred CCcCCCCCCcCceEEEecCCCCcc-EEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHH
Confidence 4589999988 666676665 44 3332222111 110 0002222 2223346789999999999
Q ss_pred EecCC
Q 032751 111 FEKRD 115 (134)
Q Consensus 111 ~~r~~ 115 (134)
.+++.
T Consensus 251 vd~~~ 255 (290)
T PF04216_consen 251 VDREK 255 (290)
T ss_dssp EETTT
T ss_pred Hhhhh
Confidence 88553
No 42
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=42.74 E-value=29 Score=24.62 Aligned_cols=28 Identities=21% Similarity=0.305 Sum_probs=19.8
Q ss_pred cCeeEECCCCCCeEEeEEEEc----cChhHHH
Q 032751 47 TPAPFSCVYCGNSGVTQVRSK----PSSAAVV 74 (134)
Q Consensus 47 ~P~~~~CP~C~~~v~T~V~~~----~g~~t~i 74 (134)
.....+||+|++...-.|+.. ++.++|.
T Consensus 5 K~~~tyCp~CkkhT~H~V~~~kkgk~s~l~~g 36 (94)
T COG1631 5 KKRRTYCPYCKKHTIHKVERVKKGKASELAWG 36 (94)
T ss_pred cceeecCcccccceeeeeeehhcCCcchhhHH
Confidence 345789999999877777763 4455554
No 43
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=42.47 E-value=27 Score=22.52 Aligned_cols=33 Identities=12% Similarity=0.207 Sum_probs=19.4
Q ss_pred cccCCceeECCCcCceeEEE-ecCCceEEeCCCC
Q 032751 92 DCLWHKYHYCPSCNEKVANF-EKRDICAVMDPPH 124 (134)
Q Consensus 92 d~ckDv~H~Cp~C~~~lG~~-~r~~~~~~~~p~~ 124 (134)
.+-.-..++|++||..|..+ .+....+.+.-.-
T Consensus 42 s~~~~~r~FC~~CGs~l~~~~~~~~~~~~V~~g~ 75 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFSEDERDPDLVGVNAGT 75 (92)
T ss_dssp TTSSCEEEEETTT--EEEEEESSTTTEEEEEGGG
T ss_pred CCCcCcCcccCCCCCeeecccCCCCCEEEEEeEe
Confidence 34455678999999999964 3444455444333
No 44
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=42.12 E-value=16 Score=29.88 Aligned_cols=24 Identities=25% Similarity=0.342 Sum_probs=21.5
Q ss_pred cCCcCeeEECCCCCCeEEeEEEEc
Q 032751 44 YRDTPAPFSCVYCGNSGVTQVRSK 67 (134)
Q Consensus 44 ~~~~P~~~~CP~C~~~v~T~V~~~ 67 (134)
-++-|..+.||.|+..+.+.|.|+
T Consensus 208 ~g~ipe~i~CpeC~R~MEk~v~Yk 231 (235)
T PF14577_consen 208 AGRIPETIVCPECGRPMEKFVMYK 231 (235)
T ss_pred ccCCCceeECCCCCCchhhceeee
Confidence 488999999999999999888875
No 45
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=41.63 E-value=28 Score=20.66 Aligned_cols=19 Identities=21% Similarity=0.433 Sum_probs=14.5
Q ss_pred eeECCCcCceeEEEecCCc
Q 032751 98 YHYCPSCNEKVANFEKRDI 116 (134)
Q Consensus 98 ~H~Cp~C~~~lG~~~r~~~ 116 (134)
...||+||..+-.++|.+.
T Consensus 21 ~~~Cp~CG~~~~~~~~~~~ 39 (46)
T PRK00398 21 GVRCPYCGYRILFKERPPV 39 (46)
T ss_pred ceECCCCCCeEEEccCCCc
Confidence 3489999998887777653
No 46
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=41.57 E-value=21 Score=20.48 Aligned_cols=17 Identities=24% Similarity=0.796 Sum_probs=12.1
Q ss_pred eECCCcCceeEEEecCC
Q 032751 99 HYCPSCNEKVANFEKRD 115 (134)
Q Consensus 99 H~Cp~C~~~lG~~~r~~ 115 (134)
++||.|+.+|-..+.++
T Consensus 2 ~FCp~C~nlL~p~~~~~ 18 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDKE 18 (35)
T ss_dssp -BETTTTSBEEEEEETT
T ss_pred eeCCCCCccceEcCCCc
Confidence 57999999997654443
No 47
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=41.03 E-value=15 Score=24.33 Aligned_cols=24 Identities=17% Similarity=0.340 Sum_probs=20.0
Q ss_pred ECCCcCceeEEEecCCceEEeCCC
Q 032751 100 YCPSCNEKVANFEKRDICAVMDPP 123 (134)
Q Consensus 100 ~Cp~C~~~lG~~~r~~~~~~~~p~ 123 (134)
.||+|+..==+-+.++..+++||.
T Consensus 19 ~Cp~Cgs~~~S~~w~G~v~i~dPe 42 (64)
T PRK06393 19 TCPVHGDEKTTTEWFGFLIITEPE 42 (64)
T ss_pred cCCCCCCCcCCcCcceEEEEECCc
Confidence 799999974466788899999996
No 48
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=40.82 E-value=13 Score=23.67 Aligned_cols=13 Identities=31% Similarity=0.575 Sum_probs=7.7
Q ss_pred eeECCCcCceeEE
Q 032751 98 YHYCPSCNEKVAN 110 (134)
Q Consensus 98 ~H~Cp~C~~~lG~ 110 (134)
+.+|++||++|++
T Consensus 4 eiRC~~CnklLa~ 16 (51)
T PF10122_consen 4 EIRCGHCNKLLAK 16 (51)
T ss_pred ceeccchhHHHhh
Confidence 3456666666654
No 49
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=40.39 E-value=20 Score=23.73 Aligned_cols=25 Identities=24% Similarity=0.499 Sum_probs=21.5
Q ss_pred eECCCcCceeEEEecCCceEEeCCC
Q 032751 99 HYCPSCNEKVANFEKRDICAVMDPP 123 (134)
Q Consensus 99 H~Cp~C~~~lG~~~r~~~~~~~~p~ 123 (134)
-.||+|+.-=-+.++++..++.||-
T Consensus 19 e~CP~Cgs~~~te~W~G~~iIidpe 43 (64)
T COG2093 19 EICPVCGSTDLTEEWFGLLIIIDPE 43 (64)
T ss_pred ccCCCCCCcccchhhccEEEEEcCc
Confidence 4699999987778999999999984
No 50
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=40.27 E-value=20 Score=22.92 Aligned_cols=20 Identities=20% Similarity=0.213 Sum_probs=14.3
Q ss_pred ccccCCceeECCCcCceeEE
Q 032751 91 MDCLWHKYHYCPSCNEKVAN 110 (134)
Q Consensus 91 ~d~ckDv~H~Cp~C~~~lG~ 110 (134)
|...+--+|.|++||.+-|+
T Consensus 33 CG~~~~~H~vC~~CG~Y~gr 52 (57)
T PRK12286 33 CGEPKLPHRVCPSCGYYKGR 52 (57)
T ss_pred CCCccCCeEECCCCCcCCCE
Confidence 34455568999999977665
No 51
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=40.04 E-value=24 Score=25.72 Aligned_cols=25 Identities=32% Similarity=0.584 Sum_probs=19.0
Q ss_pred ccc-cccCCceeECCCcCcee-EEEec
Q 032751 89 PSM-DCLWHKYHYCPSCNEKV-ANFEK 113 (134)
Q Consensus 89 p~~-d~ckDv~H~Cp~C~~~l-G~~~r 113 (134)
|.| ...+-+..+|++|+..| |.|.-
T Consensus 2 PvCg~~l~vt~l~C~~C~t~i~G~F~l 28 (113)
T PF09862_consen 2 PVCGGELVVTRLKCPSCGTEIEGEFEL 28 (113)
T ss_pred CCCCCceEEEEEEcCCCCCEEEeeecc
Confidence 445 66777888999999988 77654
No 52
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=38.41 E-value=17 Score=24.47 Aligned_cols=24 Identities=21% Similarity=0.361 Sum_probs=11.1
Q ss_pred CCcCeeEECCCCCCeEEeEEEEcc
Q 032751 45 RDTPAPFSCVYCGNSGVTQVRSKP 68 (134)
Q Consensus 45 ~~~P~~~~CP~C~~~v~T~V~~~~ 68 (134)
..+....+||+|++..+.+|....
T Consensus 19 t~~~~k~FCp~CGn~TL~rvsvsv 42 (73)
T PF08772_consen 19 TKDMTKQFCPKCGNATLKRVSVSV 42 (73)
T ss_dssp ES-SS--S-SSS--S--EEEE-B-
T ss_pred cCCCCceeCcccCCCcceEEEEEE
Confidence 346677899999999998887653
No 53
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=37.83 E-value=35 Score=27.84 Aligned_cols=14 Identities=29% Similarity=0.489 Sum_probs=10.4
Q ss_pred ECCCCCCeEEeEEE
Q 032751 52 SCVYCGNSGVTQVR 65 (134)
Q Consensus 52 ~CP~C~~~v~T~V~ 65 (134)
.||.|+..+...+.
T Consensus 237 pC~~Cg~~I~~~~~ 250 (269)
T PRK14811 237 PCPRCGTPIEKIVV 250 (269)
T ss_pred CCCcCCCeeEEEEE
Confidence 59999988766443
No 54
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=37.80 E-value=16 Score=29.87 Aligned_cols=33 Identities=27% Similarity=0.438 Sum_probs=25.3
Q ss_pred eeECCCcCceeEEE-ecCCceEEeCCCCcccccc
Q 032751 98 YHYCPSCNEKVANF-EKRDICAVMDPPHWTQLSF 130 (134)
Q Consensus 98 ~H~Cp~C~~~lG~~-~r~~~~~~~~p~~~~~~~~ 130 (134)
+.+|++|+...|.. +++|.--..+|.+=+|.-|
T Consensus 214 efiC~~Cn~~n~~~~~~~dsn~~~~p~~~s~~~k 247 (251)
T COG5415 214 EFICPHCNHKNDEVKEREDSNEAKQPAQPSQSEK 247 (251)
T ss_pred heecccchhhcCcccccccchhhcCCCCcccccc
Confidence 47999999999875 4457777888888776543
No 55
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.36 E-value=37 Score=27.70 Aligned_cols=15 Identities=20% Similarity=0.253 Sum_probs=11.1
Q ss_pred EECCCCCCeEEeEEE
Q 032751 51 FSCVYCGNSGVTQVR 65 (134)
Q Consensus 51 ~~CP~C~~~v~T~V~ 65 (134)
.-||.|+..+.....
T Consensus 246 ~pC~~Cg~~I~~~~~ 260 (272)
T TIGR00577 246 EPCRRCGTPIEKIKV 260 (272)
T ss_pred CCCCCCCCeeEEEEE
Confidence 359999988876443
No 56
>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=37.34 E-value=24 Score=20.57 Aligned_cols=13 Identities=15% Similarity=0.457 Sum_probs=10.1
Q ss_pred CeeEECCCCCCeE
Q 032751 48 PAPFSCVYCGNSG 60 (134)
Q Consensus 48 P~~~~CP~C~~~v 60 (134)
.+.+.||+|+..-
T Consensus 3 ~i~v~CP~C~s~~ 15 (36)
T PF03811_consen 3 KIDVHCPRCQSTE 15 (36)
T ss_pred cEeeeCCCCCCCC
Confidence 4678999999753
No 57
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=37.06 E-value=15 Score=19.92 Aligned_cols=10 Identities=40% Similarity=1.139 Sum_probs=7.8
Q ss_pred ECCCcCceeE
Q 032751 100 YCPSCNEKVA 109 (134)
Q Consensus 100 ~Cp~C~~~lG 109 (134)
.||+|++.|-
T Consensus 2 ~CP~C~~~V~ 11 (26)
T PF10571_consen 2 TCPECGAEVP 11 (26)
T ss_pred cCCCCcCCch
Confidence 5888888874
No 58
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=36.91 E-value=17 Score=32.72 Aligned_cols=47 Identities=23% Similarity=0.437 Sum_probs=31.3
Q ss_pred cCeeEECCCCCCeEEeEEEEccChhHHHHHHHHhhhhhhccccccc---ccCCceeECCCcCceeEEEecCC
Q 032751 47 TPAPFSCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGICFLCPSMD---CLWHKYHYCPSCNEKVANFEKRD 115 (134)
Q Consensus 47 ~P~~~~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~C~l~p~~d---~ckDv~H~Cp~C~~~lG~~~r~~ 115 (134)
.--.+.||+|+....-+-+. | -++ .-+.+...||.|+..|-..++..
T Consensus 197 r~~~vpCPhCg~~~~l~~~~---------------l-------~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~ 246 (557)
T PF05876_consen 197 RRYYVPCPHCGEEQVLEWEN---------------L-------KWDKGEAPETARYVCPHCGCEIEEHDKRR 246 (557)
T ss_pred eEEEccCCCCCCCccccccc---------------e-------eecCCCCccceEEECCCCcCCCCHHHHhh
Confidence 34567899999987633111 0 012 45778999999999998655444
No 59
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=36.69 E-value=15 Score=25.29 Aligned_cols=24 Identities=17% Similarity=0.315 Sum_probs=19.3
Q ss_pred cccCCceeECCCcCceeEEEecCC
Q 032751 92 DCLWHKYHYCPSCNEKVANFEKRD 115 (134)
Q Consensus 92 d~ckDv~H~Cp~C~~~lG~~~r~~ 115 (134)
+++-++.-+|++||.-++..+.+|
T Consensus 2 ~g~Lk~~~~C~~CG~d~~~~~adD 25 (86)
T PF06170_consen 2 RGYLKVAPRCPHCGLDYSHARADD 25 (86)
T ss_pred CccccCCCcccccCCccccCCcCc
Confidence 445567779999999999888776
No 60
>PRK00420 hypothetical protein; Validated
Probab=36.17 E-value=23 Score=25.77 Aligned_cols=19 Identities=11% Similarity=0.003 Sum_probs=15.5
Q ss_pred CCceeECCCcCceeEEEec
Q 032751 95 WHKYHYCPSCNEKVANFEK 113 (134)
Q Consensus 95 kDv~H~Cp~C~~~lG~~~r 113 (134)
+|-..+||+|+..+-..+.
T Consensus 37 k~g~~~Cp~Cg~~~~v~~~ 55 (112)
T PRK00420 37 KDGEVVCPVHGKVYIVKSD 55 (112)
T ss_pred CCCceECCCCCCeeeeccH
Confidence 8999999999998765443
No 61
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=36.15 E-value=21 Score=20.54 Aligned_cols=13 Identities=23% Similarity=0.411 Sum_probs=6.8
Q ss_pred cCCceeECCCcCc
Q 032751 94 LWHKYHYCPSCNE 106 (134)
Q Consensus 94 ckDv~H~Cp~C~~ 106 (134)
-....+.|++|+.
T Consensus 18 d~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 18 DDRERLVCPACGF 30 (34)
T ss_dssp -SS-EEEETTTTE
T ss_pred CCccceECCCCCC
Confidence 3455666777664
No 62
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=34.78 E-value=27 Score=22.78 Aligned_cols=20 Identities=20% Similarity=0.650 Sum_probs=14.4
Q ss_pred ecccCCcCeeEECCCCCCeE
Q 032751 41 QTIYRDTPAPFSCVYCGNSG 60 (134)
Q Consensus 41 q~~~~~~P~~~~CP~C~~~v 60 (134)
|.+|+.....+.|..|++..
T Consensus 21 q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 21 QVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEEEecCCcEEECcccCCCc
Confidence 44577777778888887765
No 63
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=34.78 E-value=49 Score=19.14 Aligned_cols=22 Identities=23% Similarity=0.563 Sum_probs=11.8
Q ss_pred eeECCCcCc--eeEEEecCCceEE
Q 032751 98 YHYCPSCNE--KVANFEKRDICAV 119 (134)
Q Consensus 98 ~H~Cp~C~~--~lG~~~r~~~~~~ 119 (134)
.|.||.|+- ++-.|+.+++.-|
T Consensus 1 ~hlcpkcgvgvl~pvy~~kgeikv 24 (36)
T PF09151_consen 1 QHLCPKCGVGVLEPVYNQKGEIKV 24 (36)
T ss_dssp --B-TTTSSSBEEEEE-TTS-EEE
T ss_pred CccCCccCceEEEEeecCCCcEEE
Confidence 489999974 4456887776654
No 64
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=34.71 E-value=27 Score=22.12 Aligned_cols=20 Identities=20% Similarity=0.285 Sum_probs=14.4
Q ss_pred ccccCCceeECCCcCceeEE
Q 032751 91 MDCLWHKYHYCPSCNEKVAN 110 (134)
Q Consensus 91 ~d~ckDv~H~Cp~C~~~lG~ 110 (134)
|...+--+|.|++||.+-|+
T Consensus 32 cG~~~~~H~vc~~cG~Y~gr 51 (55)
T TIGR01031 32 CGEFKLPHRVCPSCGYYKGR 51 (55)
T ss_pred CCCcccCeeECCccCeECCE
Confidence 45566778899999865553
No 65
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=34.56 E-value=18 Score=29.51 Aligned_cols=15 Identities=13% Similarity=0.000 Sum_probs=7.4
Q ss_pred eEECCCCCCeEEeEE
Q 032751 50 PFSCVYCGNSGVTQV 64 (134)
Q Consensus 50 ~~~CP~C~~~v~T~V 64 (134)
..+|..|+..+.-|-
T Consensus 113 ~~~C~~C~~~rPpRs 127 (299)
T KOG1311|consen 113 WKYCDTCQLYRPPRS 127 (299)
T ss_pred eEEcCcCcccCCCCc
Confidence 445555555544333
No 66
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=34.45 E-value=27 Score=27.82 Aligned_cols=42 Identities=19% Similarity=0.488 Sum_probs=24.6
Q ss_pred CCCCCCeEEeEEEEccChhHHHHHHHHhhhhhhcc--cccccccCC--ceeECCCcCceeE
Q 032751 53 CVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGICFL--CPSMDCLWH--KYHYCPSCNEKVA 109 (134)
Q Consensus 53 CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~C~l--~p~~d~ckD--v~H~Cp~C~~~lG 109 (134)
|+.||......+.. ||. - |++ ..+.+ ..+ ..-+|+.||++.=
T Consensus 1 C~~CG~~~~~~~~~------------lC~-~-C~~~~~~i~e-i~~~i~v~~C~~Cg~~~~ 46 (236)
T PF04981_consen 1 CPRCGREIEPLIDG------------LCP-D-CYLKRFDIIE-IPDRIEVTICPKCGRYRI 46 (236)
T ss_pred CCCCCCCCCCcccc------------cCh-H-HhcccCCeee-cCCccCceECCCCCCEEC
Confidence 89999866554441 211 1 332 33334 333 5679999998873
No 67
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=34.24 E-value=31 Score=30.49 Aligned_cols=38 Identities=13% Similarity=0.141 Sum_probs=23.1
Q ss_pred CcCeeEECCCCCCeEEeEEEEccChhHHHHHHHHhhhh
Q 032751 46 DTPAPFSCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLG 83 (134)
Q Consensus 46 ~~P~~~~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g 83 (134)
++-+.-+||.||+...+.-+..-...+=++...|+++.
T Consensus 34 ~~~q~A~CPRC~~~l~~~~~~sl~r~~a~A~s~LiLm~ 71 (418)
T COG2995 34 DSGQSAYCPRCGHTLTRGGDWSLQRPAAYALAALILMP 71 (418)
T ss_pred CCCCcccCCCCCCccccCCCCCccchHHHHHHHHHHHH
Confidence 34556799999998877666654444444433443433
No 68
>PF10238 Eapp_C: E2F-associated phosphoprotein; InterPro: IPR019370 This entry represents E2F binding proteins. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. E2F-associated phosphoprotein (EAPP)interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis [].
Probab=33.92 E-value=31 Score=25.86 Aligned_cols=16 Identities=31% Similarity=0.843 Sum_probs=14.1
Q ss_pred ECCCcCceeEEEecCC
Q 032751 100 YCPSCNEKVANFEKRD 115 (134)
Q Consensus 100 ~Cp~C~~~lG~~~r~~ 115 (134)
.|..|+..||.+++++
T Consensus 111 ~Cs~C~TeVaV~D~DE 126 (136)
T PF10238_consen 111 KCSECSTEVAVYDKDE 126 (136)
T ss_pred ecccCCCEEEEEeccC
Confidence 7999999999999554
No 69
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=32.79 E-value=40 Score=19.38 Aligned_cols=17 Identities=18% Similarity=0.305 Sum_probs=13.3
Q ss_pred cCCcCeeEECCCCCCeE
Q 032751 44 YRDTPAPFSCVYCGNSG 60 (134)
Q Consensus 44 ~~~~P~~~~CP~C~~~v 60 (134)
+......+.|++|++.-
T Consensus 19 l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 19 LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred cccCCcEEECCCCCcEe
Confidence 45677789999999753
No 70
>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=32.08 E-value=27 Score=20.52 Aligned_cols=16 Identities=19% Similarity=0.366 Sum_probs=10.2
Q ss_pred ceeECCCcCceeEEEe
Q 032751 97 KYHYCPSCNEKVANFE 112 (134)
Q Consensus 97 v~H~Cp~C~~~lG~~~ 112 (134)
-+-.|++||.+|....
T Consensus 18 g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 18 GELVCPNCGLVLEENI 33 (43)
T ss_dssp TEEEETTT-BBEE-TT
T ss_pred CeEECCCCCCEeeccc
Confidence 3448999999988643
No 71
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=31.99 E-value=34 Score=25.66 Aligned_cols=26 Identities=23% Similarity=0.506 Sum_probs=18.2
Q ss_pred cccccccCCceeECCCcC-ceeEEEecCC
Q 032751 88 CPSMDCLWHKYHYCPSCN-EKVANFEKRD 115 (134)
Q Consensus 88 ~p~~d~ckDv~H~Cp~C~-~~lG~~~r~~ 115 (134)
.|++. ||=.-+||+|+ ..........
T Consensus 36 ~PLF~--KdG~v~CPvC~~~~~~v~~e~~ 62 (131)
T COG1645 36 TPLFR--KDGEVFCPVCGYREVVVEEEEE 62 (131)
T ss_pred Cccee--eCCeEECCCCCceEEEeecccc
Confidence 45666 99999999999 5555544333
No 72
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=31.67 E-value=19 Score=21.48 Aligned_cols=12 Identities=25% Similarity=0.902 Sum_probs=8.5
Q ss_pred ECCCcCceeEEE
Q 032751 100 YCPSCNEKVANF 111 (134)
Q Consensus 100 ~Cp~C~~~lG~~ 111 (134)
+||+||..|-..
T Consensus 2 FCp~Cg~~l~~~ 13 (52)
T smart00661 2 FCPKCGNMLIPK 13 (52)
T ss_pred CCCCCCCccccc
Confidence 688888877443
No 73
>KOG4517 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.45 E-value=20 Score=26.33 Aligned_cols=12 Identities=25% Similarity=0.861 Sum_probs=9.0
Q ss_pred ceeECCCcCcee
Q 032751 97 KYHYCPSCNEKV 108 (134)
Q Consensus 97 v~H~Cp~C~~~l 108 (134)
.+-+|+||+..+
T Consensus 105 r~rrc~ncg~~f 116 (117)
T KOG4517|consen 105 RKRRCPNCGPTF 116 (117)
T ss_pred hhccCCCccccc
Confidence 455899998754
No 74
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=31.31 E-value=16 Score=21.47 Aligned_cols=16 Identities=13% Similarity=0.414 Sum_probs=9.4
Q ss_pred cccCCceeECCCcCce
Q 032751 92 DCLWHKYHYCPSCNEK 107 (134)
Q Consensus 92 d~ckDv~H~Cp~C~~~ 107 (134)
...|+..++|..|+.+
T Consensus 11 ~~~~~~i~~C~~C~nl 26 (41)
T PF02132_consen 11 KEAKENIKFCSICGNL 26 (41)
T ss_dssp HHHHHH-EE-SSS--E
T ss_pred HHHHHcCCccCCCCCc
Confidence 4567889999999875
No 75
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=30.00 E-value=28 Score=23.64 Aligned_cols=22 Identities=23% Similarity=0.659 Sum_probs=7.8
Q ss_pred CcCeeEECCCCCCe--EEeEEEEc
Q 032751 46 DTPAPFSCVYCGNS--GVTQVRSK 67 (134)
Q Consensus 46 ~~P~~~~CP~C~~~--v~T~V~~~ 67 (134)
.-+..+.||+|++. |.-++.++
T Consensus 18 ~l~~~F~CPfC~~~~sV~v~idkk 41 (81)
T PF05129_consen 18 KLPKVFDCPFCNHEKSVSVKIDKK 41 (81)
T ss_dssp --SS----TTT--SS-EEEEEETT
T ss_pred CCCceEcCCcCCCCCeEEEEEEcc
Confidence 34567899999943 44444443
No 76
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=29.47 E-value=40 Score=21.14 Aligned_cols=18 Identities=28% Similarity=0.678 Sum_probs=13.3
Q ss_pred CeeEECCCCCCeEEeEEE
Q 032751 48 PAPFSCVYCGNSGVTQVR 65 (134)
Q Consensus 48 P~~~~CP~C~~~v~T~V~ 65 (134)
-..+.||+|+..+.-+..
T Consensus 22 ~~~irCp~Cg~rIl~K~R 39 (49)
T COG1996 22 TRGIRCPYCGSRILVKER 39 (49)
T ss_pred cCceeCCCCCcEEEEecc
Confidence 345799999998875543
No 77
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=29.17 E-value=53 Score=24.19 Aligned_cols=19 Identities=26% Similarity=0.600 Sum_probs=14.9
Q ss_pred cCCcCeeEECCCCCCeEEe
Q 032751 44 YRDTPAPFSCVYCGNSGVT 62 (134)
Q Consensus 44 ~~~~P~~~~CP~C~~~v~T 62 (134)
+...|....|+.|+.....
T Consensus 64 i~~~p~~~~C~~CG~~~~~ 82 (135)
T PRK03824 64 FEEEEAVLKCRNCGNEWSL 82 (135)
T ss_pred EEecceEEECCCCCCEEec
Confidence 3467899999999977554
No 78
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=29.01 E-value=51 Score=18.90 Aligned_cols=16 Identities=19% Similarity=0.451 Sum_probs=12.7
Q ss_pred cCCcCeeEECCCCCCe
Q 032751 44 YRDTPAPFSCVYCGNS 59 (134)
Q Consensus 44 ~~~~P~~~~CP~C~~~ 59 (134)
+......+.|++|++.
T Consensus 19 ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 19 IPPKGRKVRCSKCGHV 34 (36)
T ss_pred CCCCCcEEECCCCCCE
Confidence 4567778999999975
No 79
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=28.98 E-value=34 Score=25.06 Aligned_cols=19 Identities=21% Similarity=0.585 Sum_probs=16.0
Q ss_pred cccCCceeECCCcCceeEE
Q 032751 92 DCLWHKYHYCPSCNEKVAN 110 (134)
Q Consensus 92 d~ckDv~H~Cp~C~~~lG~ 110 (134)
+++.-.+.|||+|+.+|-.
T Consensus 68 ~w~~irEyyCP~Cgt~lev 86 (112)
T PF08882_consen 68 EWQVIREYYCPGCGTQLEV 86 (112)
T ss_pred CcEEEEEEECCCCcceeEE
Confidence 6677788999999999864
No 80
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=28.91 E-value=32 Score=24.41 Aligned_cols=25 Identities=32% Similarity=0.577 Sum_probs=17.4
Q ss_pred eECCCcCceeEEE------------ecCCceEEeCCC
Q 032751 99 HYCPSCNEKVANF------------EKRDICAVMDPP 123 (134)
Q Consensus 99 H~Cp~C~~~lG~~------------~r~~~~~~~~p~ 123 (134)
.-||||+.+|... +.++..++++|.
T Consensus 21 ~gCpnC~~~l~~~g~~~~v~~~tT~~f~G~i~i~dP~ 57 (98)
T cd07973 21 DGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPE 57 (98)
T ss_pred CCCCCCcchhccCCCccccccccCCCcceEEEEECCc
Confidence 5799998776432 344667778876
No 81
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=28.58 E-value=23 Score=22.98 Aligned_cols=13 Identities=23% Similarity=0.751 Sum_probs=10.5
Q ss_pred eeECCCcCceeEE
Q 032751 98 YHYCPSCNEKVAN 110 (134)
Q Consensus 98 ~H~Cp~C~~~lG~ 110 (134)
+.+|++||+-|-.
T Consensus 3 HkHC~~CG~~Ip~ 15 (59)
T PF09889_consen 3 HKHCPVCGKPIPP 15 (59)
T ss_pred CCcCCcCCCcCCc
Confidence 5789999988763
No 82
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=28.46 E-value=36 Score=19.77 Aligned_cols=16 Identities=25% Similarity=0.684 Sum_probs=11.9
Q ss_pred ECCCcCceeEEEecCC
Q 032751 100 YCPSCNEKVANFEKRD 115 (134)
Q Consensus 100 ~Cp~C~~~lG~~~r~~ 115 (134)
+||+|+..+-.++..+
T Consensus 1 ~CP~C~~~l~~~~~~~ 16 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGD 16 (41)
T ss_pred CcCCCCcccceEEECC
Confidence 5999999887666543
No 83
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=28.16 E-value=26 Score=19.90 Aligned_cols=14 Identities=29% Similarity=0.747 Sum_probs=10.5
Q ss_pred eEECCCCCCeEEeE
Q 032751 50 PFSCVYCGNSGVTQ 63 (134)
Q Consensus 50 ~~~CP~C~~~v~T~ 63 (134)
.+.|++|+..++-+
T Consensus 17 ~irC~~CG~RIlyK 30 (32)
T PF03604_consen 17 PIRCPECGHRILYK 30 (32)
T ss_dssp TSSBSSSS-SEEBE
T ss_pred cEECCcCCCeEEEe
Confidence 46999999988754
No 84
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=27.21 E-value=40 Score=23.96 Aligned_cols=17 Identities=29% Similarity=0.565 Sum_probs=10.2
Q ss_pred CCcCeeEECCCCCCeEE
Q 032751 45 RDTPAPFSCVYCGNSGV 61 (134)
Q Consensus 45 ~~~P~~~~CP~C~~~v~ 61 (134)
...|....|..|++...
T Consensus 65 e~~p~~~~C~~Cg~~~~ 81 (113)
T PF01155_consen 65 EEVPARARCRDCGHEFE 81 (113)
T ss_dssp EEE--EEEETTTS-EEE
T ss_pred EecCCcEECCCCCCEEe
Confidence 45678888888887654
No 85
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=26.97 E-value=46 Score=21.40 Aligned_cols=13 Identities=23% Similarity=0.511 Sum_probs=7.3
Q ss_pred eEECCCCCCeEEe
Q 032751 50 PFSCVYCGNSGVT 62 (134)
Q Consensus 50 ~~~CP~C~~~v~T 62 (134)
.+.||.|++.+..
T Consensus 2 ~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 2 TVKCPICGKPVEW 14 (57)
T ss_dssp EEE-TTT--EEE-
T ss_pred cccCCCCCCeecc
Confidence 5789999998765
No 86
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=26.94 E-value=58 Score=23.54 Aligned_cols=23 Identities=30% Similarity=0.741 Sum_probs=15.7
Q ss_pred cCeeEECCCCCCeEEe--EEEEccC
Q 032751 47 TPAPFSCVYCGNSGVT--QVRSKPS 69 (134)
Q Consensus 47 ~P~~~~CP~C~~~v~T--~V~~~~g 69 (134)
-+..+.||+|++.-.+ .|++..+
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~~ 43 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTVN 43 (104)
T ss_pred CCceEecCccCCeeeeEEEEEecCc
Confidence 4567899999998554 4554443
No 87
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=26.58 E-value=52 Score=27.34 Aligned_cols=10 Identities=20% Similarity=0.487 Sum_probs=6.5
Q ss_pred eeEECCCCCC
Q 032751 49 APFSCVYCGN 58 (134)
Q Consensus 49 ~~~~CP~C~~ 58 (134)
....||||+|
T Consensus 176 tlARCPHCrK 185 (256)
T PF09788_consen 176 TLARCPHCRK 185 (256)
T ss_pred ccccCCCCce
Confidence 4557777774
No 88
>PF01307 Plant_vir_prot: Plant viral movement protein; InterPro: IPR001896 This family of membrane/coat proteins are found in a number of different ssRNA plant virus families that include Potexvirus, Hordeivirus and Carlavirus.
Probab=26.51 E-value=78 Score=22.59 Aligned_cols=34 Identities=18% Similarity=0.201 Sum_probs=17.6
Q ss_pred ChhHHHHHHHHhhhhhhcccccccccCC-ceeECCCcC
Q 032751 69 SSAAVVGCMMPFFLGICFLCPSMDCLWH-KYHYCPSCN 105 (134)
Q Consensus 69 g~~t~i~~~~lcl~g~C~l~p~~d~ckD-v~H~Cp~C~ 105 (134)
+...+.+++++++.. +|.+...+.. ..|.|+.|+
T Consensus 70 ~~~~~~~~~vl~L~~---~I~~~~~~~~~~~~~C~~C~ 104 (104)
T PF01307_consen 70 SSKFQPFLLVLLLIL---LIYLSSRFSSRRRRRCPHCS 104 (104)
T ss_pred CccHHHHHHHHHHHH---HHHHhhcccCCCCCcCCCCC
Confidence 344455444444432 2333333322 789999986
No 89
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=25.58 E-value=41 Score=20.59 Aligned_cols=22 Identities=18% Similarity=0.403 Sum_probs=11.8
Q ss_pred cccCCceeECCCcCceeEEEec
Q 032751 92 DCLWHKYHYCPSCNEKVANFEK 113 (134)
Q Consensus 92 d~ckDv~H~Cp~C~~~lG~~~r 113 (134)
+..++....||.|++-|+.-++
T Consensus 14 ~~l~~~~~~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 14 EELKEAKGCCPLCGRPLDEEHR 35 (54)
T ss_dssp HHHTT-SEE-TTT--EE-HHHH
T ss_pred HHHhcCCCcCCCCCCCCCHHHH
Confidence 3456677799999999886444
No 90
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (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 eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=25.55 E-value=61 Score=18.82 Aligned_cols=18 Identities=17% Similarity=0.501 Sum_probs=10.8
Q ss_pred EECCCCCCeEEeEEEEcc
Q 032751 51 FSCVYCGNSGVTQVRSKP 68 (134)
Q Consensus 51 ~~CP~C~~~v~T~V~~~~ 68 (134)
+.||.|+......++...
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~ 18 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQT 18 (39)
T ss_dssp S--SSS-SSEEEEEEESS
T ss_pred CCCcCCCCCeEEEEEeec
Confidence 369999998777776643
No 91
>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=25.49 E-value=45 Score=19.84 Aligned_cols=16 Identities=25% Similarity=0.760 Sum_probs=11.2
Q ss_pred EECCCCCCeEEeEEEE
Q 032751 51 FSCVYCGNSGVTQVRS 66 (134)
Q Consensus 51 ~~CP~C~~~v~T~V~~ 66 (134)
+.||+|+..-...+..
T Consensus 19 ~~CP~Cg~~~~~~~~~ 34 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT 34 (46)
T ss_pred CCCCCCCCeeeEEeCC
Confidence 5699999985554443
No 92
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=25.38 E-value=11 Score=34.78 Aligned_cols=17 Identities=18% Similarity=0.450 Sum_probs=13.4
Q ss_pred CCceeECCCcCceeEEE
Q 032751 95 WHKYHYCPSCNEKVANF 111 (134)
Q Consensus 95 kDv~H~Cp~C~~~lG~~ 111 (134)
..-..+|++||+.+|+.
T Consensus 38 ~~~~~fC~~CG~~~~~~ 54 (645)
T PRK14559 38 PVDEAHCPNCGAETGTI 54 (645)
T ss_pred CcccccccccCCcccch
Confidence 34455999999999975
No 93
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 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 include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=25.19 E-value=81 Score=20.16 Aligned_cols=21 Identities=29% Similarity=0.637 Sum_probs=13.6
Q ss_pred ecccCCcCeeEECCCCCCeEE
Q 032751 41 QTIYRDTPAPFSCVYCGNSGV 61 (134)
Q Consensus 41 q~~~~~~P~~~~CP~C~~~v~ 61 (134)
|.+|+.....+.|..|+...-
T Consensus 17 q~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 17 QTVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp EEEETT-SS-EE-SSSTSEEE
T ss_pred eEEEecCCeEEEcccCCCEec
Confidence 455888888888888887654
No 94
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=24.99 E-value=35 Score=19.21 Aligned_cols=13 Identities=23% Similarity=0.493 Sum_probs=10.2
Q ss_pred CeeEECCCCCCeE
Q 032751 48 PAPFSCVYCGNSG 60 (134)
Q Consensus 48 P~~~~CP~C~~~v 60 (134)
.....||+|+..+
T Consensus 24 ~~~~~CP~Cg~~~ 36 (41)
T smart00834 24 DPLATCPECGGDV 36 (41)
T ss_pred CCCCCCCCCCCcc
Confidence 5667899999954
No 95
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=24.82 E-value=48 Score=21.97 Aligned_cols=15 Identities=33% Similarity=0.691 Sum_probs=12.1
Q ss_pred EECCCCCCeEEeEEE
Q 032751 51 FSCVYCGNSGVTQVR 65 (134)
Q Consensus 51 ~~CP~C~~~v~T~V~ 65 (134)
.-||+|+...++...
T Consensus 7 KPCPFCG~~~~~v~~ 21 (64)
T PRK09710 7 KPCPFCGCPSVTVKA 21 (64)
T ss_pred cCCCCCCCceeEEEe
Confidence 459999999887664
No 96
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=24.77 E-value=28 Score=21.62 Aligned_cols=13 Identities=31% Similarity=0.979 Sum_probs=8.3
Q ss_pred eECCCcCc-eeEEE
Q 032751 99 HYCPSCNE-KVANF 111 (134)
Q Consensus 99 H~Cp~C~~-~lG~~ 111 (134)
-+||+|+. ++...
T Consensus 21 ~fCP~Cg~~~m~~~ 34 (50)
T PRK00432 21 KFCPRCGSGFMAEH 34 (50)
T ss_pred CcCcCCCcchhecc
Confidence 37888877 55543
No 97
>PF11697 DUF3293: Protein of unknown function (DUF3293); InterPro: IPR021710 This bacterial family of proteins has no known function.
Probab=24.32 E-value=41 Score=22.20 Aligned_cols=16 Identities=38% Similarity=0.609 Sum_probs=11.8
Q ss_pred EEeCCC-CccccccccC
Q 032751 118 AVMDPP-HWTQLSFALP 133 (134)
Q Consensus 118 ~~~~p~-~~~~~~~~~~ 133 (134)
++.+|. .|.|+||+++
T Consensus 38 ~g~~~~~~W~E~s~~V~ 54 (73)
T PF11697_consen 38 VGGDPDGSWREPSFAVL 54 (73)
T ss_pred eccCCCCCccCCEeEEc
Confidence 345664 8999999874
No 98
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=23.90 E-value=54 Score=19.64 Aligned_cols=21 Identities=19% Similarity=0.379 Sum_probs=13.7
Q ss_pred CeeEECCCCCCeEEeEEEEcc
Q 032751 48 PAPFSCVYCGNSGVTQVRSKP 68 (134)
Q Consensus 48 P~~~~CP~C~~~v~T~V~~~~ 68 (134)
...+.||.|+..-..++...+
T Consensus 24 ~~~~~CP~Cg~~~~~r~~s~~ 44 (52)
T TIGR02605 24 DPLATCPECGGEKLRRLLSAV 44 (52)
T ss_pred CCCCCCCCCCCCceeEEeccc
Confidence 455789999985445554433
No 99
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=23.88 E-value=57 Score=20.52 Aligned_cols=15 Identities=27% Similarity=0.775 Sum_probs=8.9
Q ss_pred CCceeECCCcCceeE
Q 032751 95 WHKYHYCPSCNEKVA 109 (134)
Q Consensus 95 kDv~H~Cp~C~~~lG 109 (134)
-...|+|.+||..+=
T Consensus 22 ~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 22 FRRRHHCRNCGRVVC 36 (69)
T ss_dssp SS-EEE-TTT--EEE
T ss_pred ceeeEccCCCCCEEC
Confidence 478899999998874
No 100
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.87 E-value=19 Score=27.82 Aligned_cols=21 Identities=14% Similarity=0.572 Sum_probs=11.9
Q ss_pred CCceeECCCcCcee-EEEecCC
Q 032751 95 WHKYHYCPSCNEKV-ANFEKRD 115 (134)
Q Consensus 95 kDv~H~Cp~C~~~l-G~~~r~~ 115 (134)
..+.-.||+|+.-| |.|.-++
T Consensus 36 ~~tI~~Cp~C~~~IrG~y~v~g 57 (158)
T PF10083_consen 36 AKTITSCPNCSTPIRGDYHVEG 57 (158)
T ss_pred HHHHHHCcCCCCCCCCceecCC
Confidence 34444677777766 4554444
No 101
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=23.74 E-value=48 Score=19.78 Aligned_cols=25 Identities=40% Similarity=0.837 Sum_probs=16.3
Q ss_pred CCCCceeeEeecccCCcCeeEECCCCCCe
Q 032751 31 LGDPMGIPIQQTIYRDTPAPFSCVYCGNS 59 (134)
Q Consensus 31 ~~~p~~v~vqq~~~~~~P~~~~CP~C~~~ 59 (134)
.++|.+..- +.+++..+.||+|+..
T Consensus 14 lgHPrVyl~----l~~~~~~~~CpYCg~~ 38 (40)
T PF10276_consen 14 LGHPRVYLN----LDDEPGPVVCPYCGTR 38 (40)
T ss_dssp SCCCCEEEE-----TTTTCEEEETTTTEE
T ss_pred CCCCeEEEe----cCCCCCeEECCCCCCE
Confidence 456655431 4565668999999875
No 102
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=23.33 E-value=76 Score=20.28 Aligned_cols=34 Identities=21% Similarity=0.407 Sum_probs=23.4
Q ss_pred ccc--CCceeECCCcCceeEE--EecCCceEE---eCCCCc
Q 032751 92 DCL--WHKYHYCPSCNEKVAN--FEKRDICAV---MDPPHW 125 (134)
Q Consensus 92 d~c--kDv~H~Cp~C~~~lG~--~~r~~~~~~---~~p~~~ 125 (134)
+.+ +|-.-.||.|++.--+ |++.+.|+. .+++.|
T Consensus 13 ~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~~~ 53 (54)
T PF14446_consen 13 KKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGFEW 53 (54)
T ss_pred CcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCccc
Confidence 555 6778889999887665 566677776 445555
No 103
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=23.33 E-value=1.2e+02 Score=19.24 Aligned_cols=25 Identities=12% Similarity=0.299 Sum_probs=18.7
Q ss_pred eeECCCcCceeEEEecCCceEEeCC
Q 032751 98 YHYCPSCNEKVANFEKRDICAVMDP 122 (134)
Q Consensus 98 ~H~Cp~C~~~lG~~~r~~~~~~~~p 122 (134)
.-.||.|+..|=....+...+-.+|
T Consensus 22 iV~Cp~CGaeleVv~~~p~~L~~ap 46 (54)
T TIGR01206 22 LVICDECGAELEVVSLDPLRLEAAP 46 (54)
T ss_pred EEeCCCCCCEEEEEeCCCCEEEeCc
Confidence 3389999999988777775555555
No 104
>PRK05978 hypothetical protein; Provisional
Probab=23.19 E-value=33 Score=26.07 Aligned_cols=24 Identities=17% Similarity=0.469 Sum_probs=19.3
Q ss_pred cccCCceeECCCcCceeEEEecCC
Q 032751 92 DCLWHKYHYCPSCNEKVANFEKRD 115 (134)
Q Consensus 92 d~ckDv~H~Cp~C~~~lG~~~r~~ 115 (134)
+++-+++.+|++|+..++..+..|
T Consensus 46 ~g~Lkv~~~C~~CG~~~~~~~a~D 69 (148)
T PRK05978 46 RAFLKPVDHCAACGEDFTHHRADD 69 (148)
T ss_pred ccccccCCCccccCCccccCCccc
Confidence 455678889999999999876665
No 105
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=22.61 E-value=36 Score=25.06 Aligned_cols=16 Identities=25% Similarity=0.704 Sum_probs=12.6
Q ss_pred CceeECCCcCceeEEE
Q 032751 96 HKYHYCPSCNEKVANF 111 (134)
Q Consensus 96 Dv~H~Cp~C~~~lG~~ 111 (134)
-+.|.||.||+.=-.|
T Consensus 72 ~I~~kCpkCghe~m~Y 87 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSY 87 (116)
T ss_pred chhccCcccCCchhhh
Confidence 4789999999865554
No 106
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=22.59 E-value=36 Score=21.13 Aligned_cols=14 Identities=29% Similarity=0.850 Sum_probs=11.8
Q ss_pred ECCCcCceeEEEec
Q 032751 100 YCPSCNEKVANFEK 113 (134)
Q Consensus 100 ~Cp~C~~~lG~~~r 113 (134)
.|+-||+.||.+.+
T Consensus 1 ~C~iCg~kigl~~~ 14 (51)
T PF14471_consen 1 KCAICGKKIGLFKR 14 (51)
T ss_pred CCCccccccccccc
Confidence 38999999998773
No 107
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=22.13 E-value=46 Score=21.85 Aligned_cols=14 Identities=21% Similarity=0.532 Sum_probs=11.1
Q ss_pred CeeEECCCCCCeEE
Q 032751 48 PAPFSCVYCGNSGV 61 (134)
Q Consensus 48 P~~~~CP~C~~~v~ 61 (134)
+..+.||.|++.+.
T Consensus 4 ~~~v~CP~C~k~~~ 17 (62)
T PRK00418 4 TITVNCPTCGKPVE 17 (62)
T ss_pred CccccCCCCCCccc
Confidence 45678999999765
No 108
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=21.49 E-value=31 Score=25.20 Aligned_cols=48 Identities=15% Similarity=0.260 Sum_probs=32.6
Q ss_pred cCCcCeeEECCCCCCeEEeEEEEccChhHHHHHHHHhhhhhhcccccc-cccCCceeECCCcCceeEEEe
Q 032751 44 YRDTPAPFSCVYCGNSGVTQVRSKPSSAAVVGCMMPFFLGICFLCPSM-DCLWHKYHYCPSCNEKVANFE 112 (134)
Q Consensus 44 ~~~~P~~~~CP~C~~~v~T~V~~~~g~~t~i~~~~lcl~g~C~l~p~~-d~ckDv~H~Cp~C~~~lG~~~ 112 (134)
.+.......|..|+....-|.++ ...| .+-.+-.|+|+==++-||...
T Consensus 42 ~~~~~~~~~C~~C~~~kp~Rs~H---------------------C~~C~~CV~~~DHHC~w~~~cIG~~N 90 (174)
T PF01529_consen 42 DDENGELKYCSTCKIIKPPRSHH---------------------CRVCNRCVLRFDHHCPWLGNCIGRRN 90 (174)
T ss_pred cccCCCCEECcccCCcCCCccee---------------------ccccccccccccccchhhcccccccc
Confidence 35566677899999887777776 1223 334566788887777777643
No 109
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=21.33 E-value=66 Score=24.47 Aligned_cols=15 Identities=33% Similarity=0.773 Sum_probs=11.8
Q ss_pred EECCCCCCeEEeEEE
Q 032751 51 FSCVYCGNSGVTQVR 65 (134)
Q Consensus 51 ~~CP~C~~~v~T~V~ 65 (134)
..||.|++...|++.
T Consensus 2 s~Cp~C~~~~~~~~~ 16 (161)
T PF03367_consen 2 SLCPNCGENGTTRIL 16 (161)
T ss_dssp EE-TTTSSCCEEEEE
T ss_pred CcCCCCCCCcEEEEE
Confidence 579999999988773
No 110
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=21.19 E-value=65 Score=20.90 Aligned_cols=27 Identities=7% Similarity=0.133 Sum_probs=21.2
Q ss_pred CeeEECCCCCCeEEeEEEEccChhHHH
Q 032751 48 PAPFSCVYCGNSGVTQVRSKPSSAAVV 74 (134)
Q Consensus 48 P~~~~CP~C~~~v~T~V~~~~g~~t~i 74 (134)
=..+.||.|+..-.+.+..|....++-
T Consensus 22 yle~KCPrCK~vN~~~~~~e~~t~~~k 48 (60)
T COG4416 22 YLEKKCPRCKEVNEFYIKEEATTQIHK 48 (60)
T ss_pred eeeecCCccceeeeeecccccchhhhh
Confidence 356899999999999988877666553
No 111
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=21.00 E-value=43 Score=27.76 Aligned_cols=19 Identities=37% Similarity=0.927 Sum_probs=5.5
Q ss_pred eeECCCcCce-eEEEecCCc
Q 032751 98 YHYCPSCNEK-VANFEKRDI 116 (134)
Q Consensus 98 ~H~Cp~C~~~-lG~~~r~~~ 116 (134)
+-|||+||.. |-.+..-.+
T Consensus 31 n~yCP~Cg~~~L~~f~NN~P 50 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNRP 50 (254)
T ss_dssp H---TTT--SS-EE------
T ss_pred CCcCCCCCChhHhhccCCCc
Confidence 4589999988 777655443
No 112
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=20.71 E-value=51 Score=25.19 Aligned_cols=18 Identities=28% Similarity=0.761 Sum_probs=14.8
Q ss_pred eeECCCcCceeEEEecCC
Q 032751 98 YHYCPSCNEKVANFEKRD 115 (134)
Q Consensus 98 ~H~Cp~C~~~lG~~~r~~ 115 (134)
.--|.+|+.-..+|.+-+
T Consensus 28 RReC~~C~~RFTTyErve 45 (147)
T TIGR00244 28 RRECLECHERFTTFERAE 45 (147)
T ss_pred cccCCccCCccceeeecc
Confidence 356999999999998875
No 113
>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=20.47 E-value=30 Score=23.48 Aligned_cols=18 Identities=17% Similarity=0.307 Sum_probs=13.7
Q ss_pred cCCceeECCCcCceeEEE
Q 032751 94 LWHKYHYCPSCNEKVANF 111 (134)
Q Consensus 94 ckDv~H~Cp~C~~~lG~~ 111 (134)
+.-..-+|.+|+..||..
T Consensus 53 ~~~~~l~C~~C~~~lGwk 70 (96)
T PF03226_consen 53 HTVRDLFCSGCNTILGWK 70 (96)
T ss_pred EEEEEeEcccCChhHCcE
Confidence 334456899999999964
No 114
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=20.38 E-value=57 Score=23.44 Aligned_cols=18 Identities=22% Similarity=0.549 Sum_probs=13.3
Q ss_pred cCCcCeeEECCCCCCeEEeE
Q 032751 44 YRDTPAPFSCVYCGNSGVTQ 63 (134)
Q Consensus 44 ~~~~P~~~~CP~C~~~v~T~ 63 (134)
|++.| +.||+|+......
T Consensus 22 Lnk~P--ivCP~CG~~~~~~ 39 (108)
T PF09538_consen 22 LNKDP--IVCPKCGTEFPPE 39 (108)
T ss_pred CCCCC--ccCCCCCCccCcc
Confidence 35555 5899999987665
No 115
>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=20.15 E-value=72 Score=20.07 Aligned_cols=16 Identities=19% Similarity=0.355 Sum_probs=10.4
Q ss_pred cccCCceeECCCcCce
Q 032751 92 DCLWHKYHYCPSCNEK 107 (134)
Q Consensus 92 d~ckDv~H~Cp~C~~~ 107 (134)
....++..+|++|+.+
T Consensus 38 ~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 38 EEFEEIQYRCPYCGAL 53 (54)
T ss_pred ccCCceEEEcCCCCCc
Confidence 4455666678888754
No 116
>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=20.11 E-value=51 Score=19.71 Aligned_cols=11 Identities=27% Similarity=0.908 Sum_probs=5.6
Q ss_pred ECCCcCceeEE
Q 032751 100 YCPSCNEKVAN 110 (134)
Q Consensus 100 ~Cp~C~~~lG~ 110 (134)
+||.|+.-|-+
T Consensus 19 ~Cp~C~~PL~~ 29 (41)
T PF06677_consen 19 HCPDCGTPLMR 29 (41)
T ss_pred ccCCCCCeeEE
Confidence 45555555444
Done!