Query psy8716
Match_columns 141
No_of_seqs 92 out of 94
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 17:26:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8716.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8716hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1957|consensus 100.0 2.4E-30 5.3E-35 228.0 3.5 134 1-139 300-471 (555)
2 PRK07219 DNA topoisomerase I; 97.9 6.1E-05 1.3E-09 71.2 8.9 100 15-138 641-744 (822)
3 PF01396 zf-C4_Topoisom: Topoi 96.5 0.0049 1.1E-07 37.7 3.7 36 82-119 1-39 (39)
4 KOG2906|consensus 94.7 0.05 1.1E-06 40.3 4.0 33 84-118 3-35 (105)
5 COG0551 TopA Zn-finger domain 92.1 1.4 3E-05 32.9 8.2 78 21-118 16-99 (140)
6 PRK07220 DNA topoisomerase I; 91.6 0.29 6.2E-06 46.3 4.9 54 82-138 589-646 (740)
7 PRK07219 DNA topoisomerase I; 90.8 0.33 7.1E-06 46.4 4.5 55 81-138 601-659 (822)
8 PRK06319 DNA topoisomerase I/S 90.8 1.4 2.9E-05 42.6 8.6 34 83-117 694-732 (860)
9 PF02150 RNA_POL_M_15KD: RNA p 90.4 0.43 9.2E-06 28.5 3.1 31 84-117 3-33 (35)
10 smart00661 RPOL9 RNA polymeras 89.8 0.67 1.4E-05 28.7 3.9 34 84-119 2-35 (52)
11 PF14206 Cys_rich_CPCC: Cystei 87.3 0.4 8.7E-06 33.7 1.8 26 23-51 2-27 (78)
12 COG0551 TopA Zn-finger domain 87.1 0.92 2E-05 33.9 3.8 51 79-135 14-68 (140)
13 PF14803 Nudix_N_2: Nudix N-te 86.6 1.1 2.3E-05 26.8 3.1 29 85-114 3-32 (34)
14 PRK14973 DNA topoisomerase I; 86.1 0.72 1.5E-05 45.1 3.4 51 82-135 588-643 (936)
15 PF05502 Dynactin_p62: Dynacti 83.7 2.1 4.6E-05 38.8 5.1 55 44-113 26-95 (483)
16 PRK07220 DNA topoisomerase I; 83.4 4.1 8.9E-05 38.7 7.0 31 83-113 636-666 (740)
17 COG2835 Uncharacterized conser 79.5 3.5 7.5E-05 27.9 3.7 42 80-125 6-47 (60)
18 PF06827 zf-FPG_IleRS: Zinc fi 79.3 3.6 7.7E-05 23.1 3.3 29 22-52 1-29 (30)
19 PRK00398 rpoP DNA-directed RNA 78.0 5.2 0.00011 24.6 4.0 39 82-124 3-41 (46)
20 PF08271 TF_Zn_Ribbon: TFIIB z 76.3 5.3 0.00011 24.2 3.6 29 84-115 2-30 (43)
21 PRK09710 lar restriction allev 74.9 3.9 8.5E-05 27.9 3.0 38 80-118 4-41 (64)
22 PF07191 zinc-ribbons_6: zinc- 74.8 5.9 0.00013 27.5 3.9 34 80-115 28-61 (70)
23 PRK11827 hypothetical protein; 72.4 4.3 9.3E-05 27.3 2.7 38 80-121 6-43 (60)
24 COG1198 PriA Primosomal protei 72.0 4.1 8.9E-05 39.0 3.5 51 62-138 435-486 (730)
25 TIGR00595 priA primosomal prot 71.5 4.8 0.00011 36.4 3.7 51 62-138 213-264 (505)
26 TIGR01053 LSD1 zinc finger dom 71.2 3.7 7.9E-05 24.1 1.9 20 105-124 2-21 (31)
27 PF14354 Lar_restr_allev: Rest 68.8 8.2 0.00018 24.6 3.4 31 82-112 3-37 (61)
28 COG3809 Uncharacterized protei 65.8 7.1 0.00015 28.0 2.8 27 23-51 2-28 (88)
29 PRK14973 DNA topoisomerase I; 65.1 11 0.00025 36.9 5.0 35 83-118 636-671 (936)
30 PRK06319 DNA topoisomerase I/S 64.5 6.8 0.00015 37.9 3.3 55 82-138 592-656 (860)
31 COG1996 RPC10 DNA-directed RNA 61.5 6 0.00013 25.7 1.6 16 21-36 23-38 (49)
32 PRK00432 30S ribosomal protein 61.2 8.7 0.00019 24.6 2.4 27 84-115 22-48 (50)
33 PRK00420 hypothetical protein; 59.9 6 0.00013 29.6 1.7 26 22-52 23-48 (112)
34 PF05191 ADK_lid: Adenylate ki 59.3 13 0.00029 22.2 2.8 33 104-140 1-34 (36)
35 smart00834 CxxC_CXXC_SSSS Puta 59.1 9 0.0002 22.3 2.0 30 22-52 5-34 (41)
36 PF13248 zf-ribbon_3: zinc-rib 58.6 4.6 9.9E-05 22.3 0.6 22 22-51 2-23 (26)
37 PRK06599 DNA topoisomerase I; 56.8 12 0.00026 35.1 3.5 36 82-118 585-623 (675)
38 PF08792 A2L_zn_ribbon: A2L zi 56.5 13 0.00028 21.9 2.4 27 22-52 3-29 (33)
39 TIGR02098 MJ0042_CXXC MJ0042 f 56.5 4.9 0.00011 23.5 0.6 31 83-114 3-35 (38)
40 TIGR01562 FdhE formate dehydro 56.3 9.3 0.0002 33.0 2.4 44 23-70 185-232 (305)
41 PRK14873 primosome assembly pr 54.4 16 0.00035 34.5 3.8 41 82-138 392-433 (665)
42 PRK03564 formate dehydrogenase 54.4 21 0.00045 31.0 4.2 46 21-70 186-234 (309)
43 KOG1779|consensus 50.9 15 0.00031 26.4 2.3 44 64-112 36-79 (84)
44 PF13719 zinc_ribbon_5: zinc-r 50.7 7.6 0.00016 23.1 0.7 30 84-114 4-35 (37)
45 PRK14811 formamidopyrimidine-D 50.0 24 0.00053 29.4 3.9 35 21-57 234-268 (269)
46 PF10571 UPF0547: Uncharacteri 49.1 8.5 0.00018 21.6 0.7 12 21-32 13-24 (26)
47 PF09723 Zn-ribbon_8: Zinc rib 49.0 16 0.00034 22.2 2.0 28 22-52 5-34 (42)
48 TIGR02605 CxxC_CxxC_SSSS putat 48.6 15 0.00033 22.7 1.9 29 22-53 5-35 (52)
49 COG1439 Predicted nucleic acid 48.5 12 0.00027 30.1 1.8 29 100-138 135-164 (177)
50 cd02336 ZZ_RSC8 Zinc finger, Z 47.3 8.7 0.00019 24.2 0.7 24 33-57 13-36 (45)
51 PF11331 DUF3133: Protein of u 47.1 5.1 0.00011 25.6 -0.4 33 104-137 6-41 (46)
52 PF13717 zinc_ribbon_4: zinc-r 45.8 10 0.00022 22.6 0.7 16 104-119 2-17 (36)
53 TIGR00577 fpg formamidopyrimid 45.6 24 0.00052 29.4 3.2 28 21-50 244-271 (272)
54 PRK05580 primosome assembly pr 44.9 26 0.00057 32.9 3.7 42 82-138 390-432 (679)
55 PF04216 FdhE: Protein involve 44.8 32 0.0007 28.6 3.9 45 22-70 172-219 (290)
56 PF12773 DZR: Double zinc ribb 44.5 13 0.00027 22.8 1.1 27 22-53 12-38 (50)
57 COG1594 RPB9 DNA-directed RNA 44.5 35 0.00075 25.2 3.6 33 83-117 3-35 (113)
58 PRK01103 formamidopyrimidine/5 44.3 26 0.00056 29.1 3.2 29 21-51 244-272 (274)
59 PF14255 Cys_rich_CPXG: Cystei 43.9 70 0.0015 20.7 4.5 42 84-125 2-49 (52)
60 PRK10445 endonuclease VIII; Pr 43.8 27 0.00058 29.0 3.2 29 21-51 234-262 (263)
61 KOG4080|consensus 43.6 6.2 0.00013 31.8 -0.6 23 22-53 93-115 (176)
62 PRK06599 DNA topoisomerase I; 43.5 77 0.0017 29.8 6.5 34 83-118 638-674 (675)
63 COG1140 NarY Nitrate reductase 42.9 12 0.00026 34.1 1.1 42 63-112 181-228 (513)
64 PF10263 SprT-like: SprT-like 42.7 18 0.00039 26.8 1.8 38 99-140 118-156 (157)
65 PRK05582 DNA topoisomerase I; 42.5 75 0.0016 29.7 6.2 30 83-113 612-644 (650)
66 PF09862 DUF2089: Protein of u 42.4 34 0.00074 25.6 3.3 22 85-114 1-22 (113)
67 PF06943 zf-LSD1: LSD1 zinc fi 41.7 25 0.00054 19.8 1.9 18 107-124 1-18 (25)
68 PF09297 zf-NADH-PPase: NADH p 40.8 41 0.00088 19.1 2.8 26 85-114 6-31 (32)
69 PRK14890 putative Zn-ribbon RN 40.0 13 0.00029 25.0 0.7 13 19-31 45-57 (59)
70 PRK14892 putative transcriptio 39.5 30 0.00065 25.3 2.5 30 21-51 20-49 (99)
71 PRK14810 formamidopyrimidine-D 39.1 35 0.00075 28.4 3.2 29 21-51 243-271 (272)
72 PRK00423 tfb transcription ini 38.4 29 0.00064 29.3 2.7 10 80-89 28-37 (310)
73 PF07649 C1_3: C1-like domain; 37.3 24 0.00052 19.7 1.4 15 102-116 13-27 (30)
74 PF08274 PhnA_Zn_Ribbon: PhnA 37.2 13 0.00027 21.7 0.2 24 23-51 3-26 (30)
75 PRK09710 lar restriction allev 36.6 63 0.0014 22.1 3.6 35 23-58 7-41 (64)
76 PRK13945 formamidopyrimidine-D 35.9 40 0.00088 28.2 3.1 29 21-51 253-281 (282)
77 PF01873 eIF-5_eIF-2B: Domain 35.1 49 0.0011 24.9 3.2 29 83-112 94-122 (125)
78 COG0266 Nei Formamidopyrimidin 35.0 35 0.00076 29.1 2.7 29 21-51 244-272 (273)
79 COG2888 Predicted Zn-ribbon RN 34.1 18 0.00039 24.5 0.6 11 21-31 49-59 (61)
80 TIGR01384 TFS_arch transcripti 33.1 38 0.00082 23.8 2.2 25 85-115 3-27 (104)
81 COG1998 RPS31 Ribosomal protei 32.5 36 0.00079 22.3 1.8 28 84-115 21-48 (51)
82 PF14353 CpXC: CpXC protein 32.3 53 0.0011 23.9 2.9 16 22-37 1-18 (128)
83 PF13453 zf-TFIIB: Transcripti 31.7 41 0.00089 20.0 1.9 15 78-93 15-29 (41)
84 PRK08351 DNA-directed RNA poly 31.5 24 0.00051 23.8 0.9 23 106-140 5-28 (61)
85 TIGR03278 methan_mark_10 putat 31.1 40 0.00086 30.0 2.4 28 40-69 5-33 (404)
86 KOG2691|consensus 29.3 30 0.00066 26.0 1.2 33 80-113 2-35 (113)
87 PF01927 Mut7-C: Mut7-C RNAse 29.2 46 0.00099 25.1 2.2 15 23-37 92-106 (147)
88 COG1656 Uncharacterized conser 29.1 26 0.00057 27.9 0.9 30 22-51 97-137 (165)
89 PF13909 zf-H2C2_5: C2H2-type 28.2 21 0.00046 18.5 0.1 8 24-31 2-9 (24)
90 PF03604 DNA_RNApol_7kD: DNA d 27.6 35 0.00077 20.0 1.0 14 21-34 16-29 (32)
91 PF11238 DUF3039: Protein of u 27.4 27 0.00059 23.4 0.6 11 40-50 40-50 (58)
92 smart00659 RPOLCX RNA polymera 27.3 71 0.0015 19.8 2.5 17 21-37 18-34 (44)
93 PF15616 TerY-C: TerY-C metal 27.0 1.5E+02 0.0032 22.8 4.6 49 71-125 78-126 (131)
94 TIGR03831 YgiT_finger YgiT-typ 26.5 69 0.0015 18.6 2.3 15 126-141 31-46 (46)
95 PF03470 zf-XS: XS zinc finger 26.4 34 0.00074 21.6 0.9 8 47-54 1-8 (43)
96 PRK05582 DNA topoisomerase I; 26.3 83 0.0018 29.4 3.8 47 83-138 572-622 (650)
97 PF08063 PADR1: PADR1 (NUC008) 26.1 51 0.0011 21.4 1.7 23 81-108 13-35 (55)
98 PRK12496 hypothetical protein; 25.9 44 0.00094 26.0 1.6 29 101-137 124-153 (164)
99 PRK14559 putative protein seri 25.2 70 0.0015 30.3 3.1 47 23-89 2-48 (645)
100 PF07754 DUF1610: Domain of un 25.2 39 0.00084 18.8 0.9 10 21-30 15-24 (24)
101 PF14471 DUF4428: Domain of un 24.7 14 0.00031 23.6 -1.1 27 24-53 1-29 (51)
102 PF09706 Cas_CXXC_CXXC: CRISPR 24.7 21 0.00045 24.1 -0.4 27 3-30 25-59 (69)
103 smart00653 eIF2B_5 domain pres 24.7 75 0.0016 23.4 2.6 27 83-112 81-109 (110)
104 PF14311 DUF4379: Domain of un 24.1 39 0.00084 21.3 0.9 27 23-50 29-55 (55)
105 PF04759 DUF617: Protein of un 23.5 51 0.0011 26.4 1.6 18 99-116 71-90 (166)
106 PF11023 DUF2614: Protein of u 23.2 26 0.00056 26.5 -0.1 36 62-102 69-104 (114)
107 PF13408 Zn_ribbon_recom: Reco 22.2 1.7E+02 0.0038 17.6 3.6 36 18-54 1-36 (58)
108 PF07282 OrfB_Zn_ribbon: Putat 22.0 67 0.0015 20.7 1.7 13 22-34 28-40 (69)
109 TIGR03655 anti_R_Lar restricti 21.8 1.2E+02 0.0025 19.1 2.7 33 24-56 3-38 (53)
110 PF13894 zf-C2H2_4: C2H2-type 21.6 42 0.00092 16.4 0.6 9 24-32 2-10 (24)
111 cd02972 DsbA_family DsbA famil 21.3 25 0.00055 22.3 -0.5 11 45-55 7-17 (98)
112 smart00647 IBR In Between Ring 21.2 70 0.0015 19.7 1.6 8 104-111 40-47 (64)
113 TIGR00622 ssl1 transcription f 20.7 1.3E+02 0.0027 22.6 3.1 66 23-95 16-93 (112)
114 PF05715 zf-piccolo: Piccolo Z 20.6 46 0.00099 22.6 0.7 26 23-50 3-28 (61)
115 PF06839 zf-GRF: GRF zinc fing 20.6 1.4E+02 0.003 18.1 2.8 28 24-52 2-33 (45)
No 1
>KOG1957|consensus
Probab=99.96 E-value=2.4e-30 Score=227.96 Aligned_cols=134 Identities=34% Similarity=0.697 Sum_probs=127.4
Q ss_pred CCcccccccccccccCcCCC-------------------------------------CCCcCcCCCceEEEEEeCCCCee
Q psy8716 1 MDQLFEVSFSPLAATGKAMS-------------------------------------QELKCPIDDFELLCWSMGNKGKS 43 (141)
Q Consensus 1 md~Lfe~~Fs~l~~sgkp~s-------------------------------------~e~~CPLd~FeLl~~s~g~~gks 43 (141)
+|.|||++|+++|+.|+||| +..+|||++||+++|.+|...++
T Consensus 300 ~D~L~~~s~gtdAgdgpPitpmr~~~R~m~~~dtkRLY~~vCqhf~~tp~~~~~k~it~~k~slgdeqf~lw~~Gk~~~~ 379 (555)
T KOG1957|consen 300 GDTLFEASFGTDAGDGPPITPMRKCNRYMKSGDTKRLYCYVCQHFYATPQFKCKKVITTVKCSLGDEQFILWCTGKRLRE 379 (555)
T ss_pred ccccccccccCcCCCCCCcCcccccccccccccceeecchhhhhheeccCcCceEEEeeeeeccCCeeEEeccCcceecc
Confidence 68999999999999999999 77999999999999999999999
Q ss_pred eecCccCCCCCCcCCCCCCcccccccCCCCccccccceeecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCCCeeE
Q psy8716 44 YILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKV 123 (141)
Q Consensus 44 y~lCP~CyN~PPf~~~~~~~~C~~C~hptC~~S~~~~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~a~kv 123 (141)
|.+||+||||| +|+.+++|++|+||.|+|||..+||++|.||++++|++|+++ |||+|.||+|+++++-.+.++++
T Consensus 380 ~gft~fm~n~p---~m~wgagcdECthPScq~slSmlgiG~~vEc~~v~Lv~~qTs-PkwylTcnkcisvme~hgigtda 455 (555)
T KOG1957|consen 380 FGFTPFMPNNP---KMPWGAGCDECTHPSCQQSLSMLGIGQCVECESVELVLDQTS-PKWYLTCNKCISVMEKHGIGTDA 455 (555)
T ss_pred CCccccccCCC---ccccccCCCccCCchHHhhhhcccceeEEEeccEEEEecCCC-CCceeehhhhHHHHHhhccccee
Confidence 99999999999 899999999999999999999999999999998999998877 99999999999999999999999
Q ss_pred ecCCCCce-eeccceec
Q psy8716 124 QVCTENNC-DCVQFTSN 139 (141)
Q Consensus 124 ~v~~~~~C-~C~a~ll~ 139 (141)
+|.-+. | -|++.+++
T Consensus 456 sI~Vhi-nsiceRnYv~ 471 (555)
T KOG1957|consen 456 SIPVHI-NSICERNYVT 471 (555)
T ss_pred eEEEee-cchhhhheEe
Confidence 998887 8 89887764
No 2
>PRK07219 DNA topoisomerase I; Validated
Probab=97.88 E-value=6.1e-05 Score=71.21 Aligned_cols=100 Identities=21% Similarity=0.376 Sum_probs=70.7
Q ss_pred cCcCCCCCCcCcCCCceEEEEEeCCCCeeeecCccCCCCCCcCCCCCCcccccccCCCCccccccceeecCCCCCCceEE
Q psy8716 15 TGKAMSQELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLV 94 (141)
Q Consensus 15 sgkp~s~e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN~PPf~~~~~~~~C~~C~hptC~~S~~~~~V~~C~~C~~G~Lv 94 (141)
.|+....+..||.||..++.+..+ ++..|..||.|.++.+++.- ...+..||+|+ |.|+
T Consensus 641 ~~~~~~~~~~Cp~CG~~lvk~~~~-r~~~~~~CP~C~~~~~~~~~-------------------~~~~~~CP~Cg-~~l~ 699 (822)
T PRK07219 641 TGRIKVLDEVCEKCGLPVIKILRG-KQTFVVGCPDCEAEKEEEDP-------------------DEVIGPCPKCG-GELA 699 (822)
T ss_pred CCccccccCCCCCCCcceEEEecc-CccccccCCCCCCCcccccc-------------------ccccccCCCCC-CeeE
Confidence 344333467899999999888653 45667889999998875421 11245899998 7888
Q ss_pred EecCCCCceEEEcCC---CCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716 95 LDLSSAPKWKICCNK---CDIIIHVFPDAQKVQVCTENNC-DCVQFTS 138 (141)
Q Consensus 95 Ldp~s~pkw~l~Cn~---C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll 138 (141)
+......+ ++.|++ |.+...+++.. .+.+++.. | +|+..++
T Consensus 700 ~k~gr~G~-F~~Cs~yp~C~~~~~l~~~~-~~~~~~~~-CpkCg~~l~ 744 (822)
T PRK07219 700 IKQLKYGS-FLGCTNYPKCKYTLPLPRRG-KITVTDEK-CPECGLPLL 744 (822)
T ss_pred EEcCCCCC-eeeCCCCCCCCceeeccccc-ccccccCC-CCCCCCeEE
Confidence 86544444 999985 99999999753 33345666 9 9998765
No 3
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=96.46 E-value=0.0049 Score=37.69 Aligned_cols=36 Identities=22% Similarity=0.485 Sum_probs=29.5
Q ss_pred eecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccCC
Q psy8716 82 IASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFPD 119 (141)
Q Consensus 82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~~ 119 (141)
|..||.|+ +.|++- .+..+.+++|+. |.++++++++
T Consensus 1 ~~~CP~Cg-~~lv~r-~~k~g~F~~Cs~yP~C~~~~~~~~n 39 (39)
T PF01396_consen 1 VEKCPKCG-GPLVLR-RGKKGKFLGCSNYPECKYTEPLPKN 39 (39)
T ss_pred CcCCCCCC-ceeEEE-ECCCCCEEECCCCCCcCCeEeCCCC
Confidence 35799999 999994 555669999995 9999999874
No 4
>KOG2906|consensus
Probab=94.72 E-value=0.05 Score=40.25 Aligned_cols=33 Identities=18% Similarity=0.561 Sum_probs=26.7
Q ss_pred cCCCCCCceEEEecCCCCceEEEcCCCCeEEEccC
Q psy8716 84 SCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFP 118 (141)
Q Consensus 84 ~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~ 118 (141)
-||.|+ .+|++. ..+.-.+++|+.|+++..+-.
T Consensus 3 FCP~Cg-n~Live-~g~~~~rf~C~tCpY~~~I~~ 35 (105)
T KOG2906|consen 3 FCPTCG-NMLIVE-SGESCNRFSCRTCPYVFPISR 35 (105)
T ss_pred ccCCCC-CEEEEe-cCCeEeeEEcCCCCceeeEee
Confidence 489999 899996 344479999999999887754
No 5
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=92.06 E-value=1.4 Score=32.91 Aligned_cols=78 Identities=24% Similarity=0.399 Sum_probs=50.0
Q ss_pred CCCcCcCCCceEEEEEeCCCCeeeecC---ccCCCCCCcCCCCCCcccccccCCCCccccccceeecCCCCCCceEEEec
Q psy8716 21 QELKCPIDDFELLCWSMGNKGKSYILC---PYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDL 97 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s~g~~gksy~lC---P~CyN~PPf~~~~~~~~C~~C~hptC~~S~~~~~V~~C~~C~~G~LvLdp 97 (141)
...+||.||=+++++.. ..| .|..| |-|..+|+. -.........||+|+.+.|++-.
T Consensus 16 ~~~~Cp~Cg~~m~~~~~-~~g-~f~gCs~yP~C~~~~~~------------------~~~~~~~~~~Cp~C~~~~~~~k~ 75 (140)
T COG0551 16 TGQICPKCGKNMVKKFG-KYG-IFLGCSNYPKCDYYEPE------------------KAIAEKTGVKCPKCGKGLLVLKK 75 (140)
T ss_pred cCccCCcCCCeeEEEEc-cCC-eEEEeCCCCCCCCCccc------------------ccccccCceeCCCCCCCceEEEe
Confidence 45789999999999974 446 66666 333322221 11223456789999988888865
Q ss_pred CCCCceEEEcC---CCCeEEEccC
Q psy8716 98 SSAPKWKICCN---KCDIIIHVFP 118 (141)
Q Consensus 98 ~s~pkw~l~Cn---~C~~~v~l~~ 118 (141)
+...+-++.|+ .|.++.+...
T Consensus 76 ~~~~~~f~~~~~~Pkc~~~~~~~~ 99 (140)
T COG0551 76 GRFGKNFLGCSNYPKCRFTEKPKP 99 (140)
T ss_pred ccCCceEEeecCCCcCceeecCCc
Confidence 55555677777 4666665444
No 6
>PRK07220 DNA topoisomerase I; Validated
Probab=91.65 E-value=0.29 Score=46.31 Aligned_cols=54 Identities=19% Similarity=0.295 Sum_probs=39.9
Q ss_pred eecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716 82 IASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFPDAQKVQVCTENNC-DCVQFTS 138 (141)
Q Consensus 82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll 138 (141)
+..||.|+ +.|++......++++.|+. |.+..++|+. .++.+++.. | +||..++
T Consensus 589 ~~~CP~Cg-~~l~~r~~r~g~~f~gCs~yp~C~~~~~l~~~-g~~~~~~~~-Cp~Cg~~~~ 646 (740)
T PRK07220 589 IGKCPLCG-SDLMVRRSKRGSRFIGCEGYPECTFSLPLPKS-GQIIVTDKV-CEAHGLNHI 646 (740)
T ss_pred ccccccCC-CeeeEEecCCCceEEEcCCCCCCCceeeCCCC-CccccCCCC-CCCCCCceE
Confidence 45899998 6677654444478899985 9999999974 345677777 9 9996444
No 7
>PRK07219 DNA topoisomerase I; Validated
Probab=90.83 E-value=0.33 Score=46.39 Aligned_cols=55 Identities=20% Similarity=0.428 Sum_probs=38.7
Q ss_pred eeecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716 81 GIASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFPDAQKVQVCTENNC-DCVQFTS 138 (141)
Q Consensus 81 ~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll 138 (141)
.+..||.|+ +.|++......++++.|.. |.+.++||+.. ++.+.... | .|+..++
T Consensus 601 ~~~~CP~Cg-~~l~~r~~~~g~~F~gCs~yp~C~~t~~lp~~~-~~~~~~~~-Cp~CG~~lv 659 (822)
T PRK07219 601 TIGKCPECG-GDLIIIRTDKGSRFVGCSGYPDCRNTFPLPSTG-RIKVLDEV-CEKCGLPVI 659 (822)
T ss_pred ccCcCCCCC-CcceeeeccCCceeeecCCCcCCCCeeecCCCC-ccccccCC-CCCCCcceE
Confidence 356799998 5555543333338999976 99999999854 35666666 8 8887654
No 8
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=90.80 E-value=1.4 Score=42.59 Aligned_cols=34 Identities=26% Similarity=0.526 Sum_probs=23.3
Q ss_pred ecCCC--CCCceEEEecCCCCceEEEcCC---CCeEEEcc
Q psy8716 83 ASCLQ--CEGGVLVLDLSSAPKWKICCNK---CDIIIHVF 117 (141)
Q Consensus 83 ~~C~~--C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~ 117 (141)
-.||+ |+ |-|++....-.+|++.|++ |.++++..
T Consensus 694 ~~CP~~~C~-g~l~~r~gr~G~~f~~Cs~yp~C~~~~~~~ 732 (860)
T PRK06319 694 VPCPAIGCT-GHIVKRRSRFNKMFYSCSEYPACSVIGNSI 732 (860)
T ss_pred CCCCCcCCC-CcEEEEecCCCCeeeccCCCCCCceeeccC
Confidence 37996 67 6677754444578899985 99775433
No 9
>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=90.37 E-value=0.43 Score=28.51 Aligned_cols=31 Identities=19% Similarity=0.387 Sum_probs=21.6
Q ss_pred cCCCCCCceEEEecCCCCceEEEcCCCCeEEEcc
Q psy8716 84 SCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVF 117 (141)
Q Consensus 84 ~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~ 117 (141)
-||+|+ ++|+... ...+.+ .|+.|+++..+-
T Consensus 3 FCp~C~-nlL~p~~-~~~~~~-~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 3 FCPECG-NLLYPKE-DKEKRV-ACRTCGYEEPIS 33 (35)
T ss_dssp BETTTT-SBEEEEE-ETTTTE-EESSSS-EEE-S
T ss_pred eCCCCC-ccceEcC-CCccCc-CCCCCCCccCCC
Confidence 389999 8888753 445555 999999987653
No 10
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=89.82 E-value=0.67 Score=28.70 Aligned_cols=34 Identities=21% Similarity=0.489 Sum_probs=24.5
Q ss_pred cCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCC
Q psy8716 84 SCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPD 119 (141)
Q Consensus 84 ~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~ 119 (141)
-||+|+ .+|... ....+.++.|..|.+...+.+.
T Consensus 2 FCp~Cg-~~l~~~-~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCG-NMLIPK-EGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCC-Cccccc-cCCCCCEEECCcCCCeEECCCc
Confidence 388998 666553 2333468999999999888665
No 11
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=87.32 E-value=0.4 Score=33.74 Aligned_cols=26 Identities=27% Similarity=0.664 Sum_probs=21.1
Q ss_pred CcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716 23 LKCPIDDFELLCWSMGNKGKSYILCPYCY 51 (141)
Q Consensus 23 ~~CPLd~FeLl~~s~g~~gksy~lCP~Cy 51 (141)
++||-|||..+.-. .+.+|-+||-||
T Consensus 2 ~~CPCCg~~Tl~~~---~~~~ydIC~VC~ 27 (78)
T PF14206_consen 2 YPCPCCGYYTLEER---GEGTYDICPVCF 27 (78)
T ss_pred ccCCCCCcEEeccC---CCcCceECCCCC
Confidence 57999999887653 345699999998
No 12
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=87.06 E-value=0.92 Score=33.90 Aligned_cols=51 Identities=20% Similarity=0.358 Sum_probs=34.8
Q ss_pred cceeecCCCCCCceEEEecCCCCceEEEcC---CCCeEEEccCCCeeEecCCCCce-eecc
Q psy8716 79 STGIASCLQCEGGVLVLDLSSAPKWKICCN---KCDIIIHVFPDAQKVQVCTENNC-DCVQ 135 (141)
Q Consensus 79 ~~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn---~C~~~v~l~~~a~kv~v~~~~~C-~C~a 135 (141)
......||.|. +.|++- .+..+|++.|. .|.+ ++.....+..+..+ | +|+.
T Consensus 14 ~~~~~~Cp~Cg-~~m~~~-~~~~g~f~gCs~yP~C~~---~~~~~~~~~~~~~~-Cp~C~~ 68 (140)
T COG0551 14 LKTGQICPKCG-KNMVKK-FGKYGIFLGCSNYPKCDY---YEPEKAIAEKTGVK-CPKCGK 68 (140)
T ss_pred cccCccCCcCC-CeeEEE-EccCCeEEEeCCCCCCCC---CcccccccccCcee-CCCCCC
Confidence 35677899999 888884 45555999998 4998 33223333445565 9 8995
No 13
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=86.55 E-value=1.1 Score=26.83 Aligned_cols=29 Identities=28% Similarity=0.567 Sum_probs=17.3
Q ss_pred CCCCCCceEEE-ecCCCCceEEEcCCCCeEE
Q psy8716 85 CLQCEGGVLVL-DLSSAPKWKICCNKCDIII 114 (141)
Q Consensus 85 C~~C~~G~LvL-dp~s~pkw~l~Cn~C~~~v 114 (141)
|+.|. +.|.+ -|......|+.|..|.+|-
T Consensus 3 C~~CG-~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 3 CPQCG-GPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -TTT---B-EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccc-ChhhhhcCCCCCccceECCCCCCEE
Confidence 88898 54544 3567889999999999874
No 14
>PRK14973 DNA topoisomerase I; Provisional
Probab=86.10 E-value=0.72 Score=45.06 Aligned_cols=51 Identities=20% Similarity=0.223 Sum_probs=36.6
Q ss_pred eecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccCCC-eeEecCCCCce-eecc
Q psy8716 82 IASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFPDA-QKVQVCTENNC-DCVQ 135 (141)
Q Consensus 82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~~a-~kv~v~~~~~C-~C~a 135 (141)
...||.|+ +.|++... ..+-++.|++ |.+.+.|++.. .++.++++. | +||+
T Consensus 588 ~~~CP~CG-~~l~ik~~-k~gkFigCS~Yp~Ck~t~~L~~~~~g~~~~~~~~-Cp~CG~ 643 (936)
T PRK14973 588 IGPCPVCG-KDLRIKHI-GSSQFIGCSGYPDCTFNIGLPGTTWGWAIRTDEV-CPIHHL 643 (936)
T ss_pred cccCCccc-ccceeecc-cCceeEECCCCCCCCccccCCccccccCCCCCCC-CCCCCC
Confidence 46799998 66776533 3344789986 99999998543 345556676 9 9998
No 15
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=83.67 E-value=2.1 Score=38.78 Aligned_cols=55 Identities=22% Similarity=0.556 Sum_probs=35.1
Q ss_pred eecCccCCCCCCcCCC-CCCcccc-cccCCCCccccccceeecCCCCCCceEEEec-------------CCCCceEEEcC
Q psy8716 44 YILCPYCYNNPPYRDM-KKGSGCN-VCTHPTCGQALLSTGIASCLQCEGGVLVLDL-------------SSAPKWKICCN 108 (141)
Q Consensus 44 y~lCP~CyN~PPf~~~-~~~~~C~-~C~hptC~~S~~~~~V~~C~~C~~G~LvLdp-------------~s~pkw~l~Cn 108 (141)
+-.||.|--+-|-... .++.+|. .|. .||.|. +.|.+-. ..+..|.|.|+
T Consensus 26 ~~yCp~CL~~~p~~e~~~~~nrC~r~Cf--------------~CP~C~-~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~ 90 (483)
T PF05502_consen 26 SYYCPNCLFEVPSSEARSEKNRCSRNCF--------------DCPICF-SPLSVRASDTPPSPPDPSSDSGGKPYYLSCS 90 (483)
T ss_pred eeECccccccCChhhheeccceeccccc--------------cCCCCC-CcceeEecccccccccccccCCCCCEEEECC
Confidence 3489999988885432 3455665 555 255666 4333321 23468999999
Q ss_pred CCCeE
Q psy8716 109 KCDII 113 (141)
Q Consensus 109 ~C~~~ 113 (141)
.|.+.
T Consensus 91 ~C~Ws 95 (483)
T PF05502_consen 91 YCRWS 95 (483)
T ss_pred Cceee
Confidence 99874
No 16
>PRK07220 DNA topoisomerase I; Validated
Probab=83.39 E-value=4.1 Score=38.68 Aligned_cols=31 Identities=16% Similarity=0.442 Sum_probs=23.5
Q ss_pred ecCCCCCCceEEEecCCCCceEEEcCCCCeE
Q psy8716 83 ASCLQCEGGVLVLDLSSAPKWKICCNKCDII 113 (141)
Q Consensus 83 ~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~ 113 (141)
..||.|+.+.+.....+...|++.|..|++.
T Consensus 636 ~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~~ 666 (740)
T PRK07220 636 KVCEAHGLNHIRIINGGKRPWDLGCPQCNFI 666 (740)
T ss_pred CCCCCCCCceEEEEecCCccceeeCCCCCCc
Confidence 4699998677766655545699999889974
No 17
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=79.46 E-value=3.5 Score=27.86 Aligned_cols=42 Identities=21% Similarity=0.476 Sum_probs=33.0
Q ss_pred ceeecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCCCeeEec
Q psy8716 80 TGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQV 125 (141)
Q Consensus 80 ~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~a~kv~v 125 (141)
+.|-.||.|+ |-|.+|...+ .|.|..|...+.+-+++-..-+
T Consensus 6 LeiLaCP~~k-g~L~~~~~~~---~L~c~~~~~aYpI~dGIPvlL~ 47 (60)
T COG2835 6 LEILACPVCK-GPLVYDEEKQ---ELICPRCKLAYPIRDGIPVLLP 47 (60)
T ss_pred heeeeccCcC-CcceEeccCC---EEEecccCceeecccCccccCc
Confidence 4678899999 8899987554 9999999988887776654433
No 18
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=79.29 E-value=3.6 Score=23.15 Aligned_cols=29 Identities=31% Similarity=0.479 Sum_probs=19.5
Q ss_pred CCcCcCCCceEEEEEeCCCCeeeecCccCCC
Q psy8716 22 ELKCPIDDFELLCWSMGNKGKSYILCPYCYN 52 (141)
Q Consensus 22 e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN 52 (141)
+.+||-|+=-+..+.. .+++..+||.|..
T Consensus 1 G~~C~rC~~~~~~~~~--~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 1 GEKCPRCWNYIEDIGI--NGRSTYLCPRCQK 29 (30)
T ss_dssp TSB-TTT--BBEEEEE--TTEEEEE-TTTCC
T ss_pred CCcCccCCCcceEeEe--cCCCCeECcCCcC
Confidence 3679999877766664 5899999999975
No 19
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=77.97 E-value=5.2 Score=24.56 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=26.9
Q ss_pred eecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCCCeeEe
Q psy8716 82 IASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQ 124 (141)
Q Consensus 82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~a~kv~ 124 (141)
+..|+.|+ ..+.+|+... .+.|..|..-+-+.+.-..|+
T Consensus 3 ~y~C~~CG-~~~~~~~~~~---~~~Cp~CG~~~~~~~~~~~v~ 41 (46)
T PRK00398 3 EYKCARCG-REVELDEYGT---GVRCPYCGYRILFKERPPVVK 41 (46)
T ss_pred EEECCCCC-CEEEECCCCC---ceECCCCCCeEEEccCCCcce
Confidence 45688888 7888876554 578888887666655544443
No 20
>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=76.30 E-value=5.3 Score=24.24 Aligned_cols=29 Identities=21% Similarity=0.699 Sum_probs=21.2
Q ss_pred cCCCCCCceEEEecCCCCceEEEcCCCCeEEE
Q psy8716 84 SCLQCEGGVLVLDLSSAPKWKICCNKCDIIIH 115 (141)
Q Consensus 84 ~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~ 115 (141)
.||.|++..++.|... -.+.|..|-.+|.
T Consensus 2 ~Cp~Cg~~~~~~D~~~---g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPER---GELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSSEEEEETTT---TEEEETTT-BBEE
T ss_pred CCcCCcCCceEEcCCC---CeEECCCCCCEee
Confidence 5899987778888533 3569999998875
No 21
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=74.86 E-value=3.9 Score=27.92 Aligned_cols=38 Identities=13% Similarity=0.304 Sum_probs=27.7
Q ss_pred ceeecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccC
Q psy8716 80 TGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFP 118 (141)
Q Consensus 80 ~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~ 118 (141)
-++-+||.|...++... .+++-|+..|..|....-...
T Consensus 4 d~lKPCPFCG~~~~~v~-~~~g~~~v~C~~CgA~~~~~~ 41 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVK-AISGYYRAKCNGCESRTGYGG 41 (64)
T ss_pred ccccCCCCCCCceeEEE-ecCceEEEEcCCCCcCccccc
Confidence 46789999986666664 456777799999988654433
No 22
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=74.80 E-value=5.9 Score=27.46 Aligned_cols=34 Identities=29% Similarity=0.489 Sum_probs=18.8
Q ss_pred ceeecCCCCCCceEEEecCCCCceEEEcCCCCeEEE
Q psy8716 80 TGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIH 115 (141)
Q Consensus 80 ~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~ 115 (141)
.-++.||+|+...=+|-.-++- -..||+|+=+|.
T Consensus 28 ~~~a~CPdC~~~Le~LkACGAv--dYFC~~c~gLiS 61 (70)
T PF07191_consen 28 KKEAFCPDCGQPLEVLKACGAV--DYFCNHCHGLIS 61 (70)
T ss_dssp EEEEE-TTT-SB-EEEEETTEE--EEE-TTTT-EE-
T ss_pred eecccCCCcccHHHHHHHhccc--ceeeccCCceee
Confidence 4467799998778888544433 346888887664
No 23
>PRK11827 hypothetical protein; Provisional
Probab=72.41 E-value=4.3 Score=27.25 Aligned_cols=38 Identities=18% Similarity=0.360 Sum_probs=28.8
Q ss_pred ceeecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCCCe
Q psy8716 80 TGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQ 121 (141)
Q Consensus 80 ~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~a~ 121 (141)
+.|-.||.|+ |-|.+|.. +-.|.|..|...+-+-+++-
T Consensus 6 LeILaCP~ck-g~L~~~~~---~~~Lic~~~~laYPI~dgIP 43 (60)
T PRK11827 6 LEIIACPVCN-GKLWYNQE---KQELICKLDNLAFPLRDGIP 43 (60)
T ss_pred HhheECCCCC-CcCeEcCC---CCeEECCccCeeccccCCcc
Confidence 4577899999 99999752 23699999998877666543
No 24
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=72.00 E-value=4.1 Score=39.01 Aligned_cols=51 Identities=24% Similarity=0.486 Sum_probs=36.4
Q ss_pred CcccccccCCCCccccccceeecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716 62 GSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNC-DCVQFTS 138 (141)
Q Consensus 62 ~~~C~~C~hptC~~S~~~~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll 138 (141)
-..|..|-| |..||.|+ ..|++-. .+-.|-|..|...-.+| .. | +||+..|
T Consensus 435 ~l~C~~Cg~-----------v~~Cp~Cd-~~lt~H~---~~~~L~CH~Cg~~~~~p----------~~-Cp~Cgs~~L 486 (730)
T COG1198 435 LLLCRDCGY-----------IAECPNCD-SPLTLHK---ATGQLRCHYCGYQEPIP----------QS-CPECGSEHL 486 (730)
T ss_pred eeecccCCC-----------cccCCCCC-cceEEec---CCCeeEeCCCCCCCCCC----------CC-CCCCCCCee
Confidence 445666664 77899999 8888842 23689999998764444 34 9 9998755
No 25
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=71.51 E-value=4.8 Score=36.38 Aligned_cols=51 Identities=22% Similarity=0.451 Sum_probs=36.4
Q ss_pred CcccccccCCCCccccccceeecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716 62 GSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNC-DCVQFTS 138 (141)
Q Consensus 62 ~~~C~~C~hptC~~S~~~~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll 138 (141)
...|..|-+ +..||.|+ +-|++... .-+|.|..|.+...+|+ . | +||+.-+
T Consensus 213 ~~~C~~Cg~-----------~~~C~~C~-~~l~~h~~---~~~l~Ch~Cg~~~~~~~----------~-Cp~C~s~~l 264 (505)
T TIGR00595 213 NLLCRSCGY-----------ILCCPNCD-VSLTYHKK---EGKLRCHYCGYQEPIPK----------T-CPQCGSEDL 264 (505)
T ss_pred eeEhhhCcC-----------ccCCCCCC-CceEEecC---CCeEEcCCCcCcCCCCC----------C-CCCCCCCee
Confidence 345666664 67799999 88888532 22899999998766655 4 8 8988644
No 26
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=71.21 E-value=3.7 Score=24.06 Aligned_cols=20 Identities=20% Similarity=0.512 Sum_probs=15.9
Q ss_pred EEcCCCCeEEEccCCCeeEe
Q psy8716 105 ICCNKCDIIIHVFPDAQKVQ 124 (141)
Q Consensus 105 l~Cn~C~~~v~l~~~a~kv~ 124 (141)
+.|..|..++..|.+|.+|+
T Consensus 2 ~~C~~C~t~L~yP~gA~~vr 21 (31)
T TIGR01053 2 VVCGGCRTLLMYPRGASSVR 21 (31)
T ss_pred cCcCCCCcEeecCCCCCeEE
Confidence 56888888888888888764
No 27
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=68.80 E-value=8.2 Score=24.58 Aligned_cols=31 Identities=13% Similarity=0.494 Sum_probs=21.0
Q ss_pred eecCCCCCCceEEEecCCCCc----eEEEcCCCCe
Q psy8716 82 IASCLQCEGGVLVLDLSSAPK----WKICCNKCDI 112 (141)
Q Consensus 82 V~~C~~C~~G~LvLdp~s~pk----w~l~Cn~C~~ 112 (141)
+-+||.|+...+.++...... +.+.|..|..
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 468999965555554433322 8899999987
No 28
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.76 E-value=7.1 Score=28.04 Aligned_cols=27 Identities=37% Similarity=0.645 Sum_probs=22.5
Q ss_pred CcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716 23 LKCPIDDFELLCWSMGNKGKSYILCPYCY 51 (141)
Q Consensus 23 ~~CPLd~FeLl~~s~g~~gksy~lCP~Cy 51 (141)
+-||+||-+|+.... .|.-+-.||.|-
T Consensus 2 llCP~C~v~l~~~~r--s~vEiD~CPrCr 28 (88)
T COG3809 2 LLCPICGVELVMSVR--SGVEIDYCPRCR 28 (88)
T ss_pred cccCcCCceeeeeee--cCceeeeCCccc
Confidence 469999999998764 478888999995
No 29
>PRK14973 DNA topoisomerase I; Provisional
Probab=65.11 E-value=11 Score=36.95 Aligned_cols=35 Identities=23% Similarity=0.359 Sum_probs=26.0
Q ss_pred ecCCCCCCc-eEEEecCCCCceEEEcCCCCeEEEccC
Q psy8716 83 ASCLQCEGG-VLVLDLSSAPKWKICCNKCDIIIHVFP 118 (141)
Q Consensus 83 ~~C~~C~~G-~LvLdp~s~pkw~l~Cn~C~~~v~l~~ 118 (141)
..||+|+.+ ++++ ..+.-+|+|.|-.|..+-..-+
T Consensus 636 ~~Cp~CG~p~~~~~-r~Gr~g~fl~CP~C~~~~~~~~ 671 (936)
T PRK14973 636 EVCPIHHLNHVRLI-RKGARPWDIGCPLCSHIESNTE 671 (936)
T ss_pred CCCCCCCCCceEEe-ecCCCcccccCccccchhhccc
Confidence 369999954 5555 6788899999988887655433
No 30
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=64.53 E-value=6.8 Score=37.90 Aligned_cols=55 Identities=18% Similarity=0.258 Sum_probs=36.2
Q ss_pred eecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccCCC-----eeEe-cCCCCce-eecccee
Q psy8716 82 IASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFPDA-----QKVQ-VCTENNC-DCVQFTS 138 (141)
Q Consensus 82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~~a-----~kv~-v~~~~~C-~C~a~ll 138 (141)
-..||.|++|.|++. .+..+.++.|.+ |.+.-.+.+.. ..+. ..... | +||..|+
T Consensus 592 ~~~CP~Cg~~~L~~k-~gr~G~Fl~Cs~yP~C~~t~~~~~~~~~~~~~~~~~~~~~~-CP~Cg~~m~ 656 (860)
T PRK06319 592 EIDCPKCHKGKLVKI-WAKNRYFYGCSEYPECDYKTSEEELTFNKEDYAEDTPWDSP-CPLCGGEMK 656 (860)
T ss_pred CcccCCCCCcceeEE-ecCCCceeeccCCccccccCCcccccccccccccccccCCc-CccCCCeeE
Confidence 356999987899885 455678999985 98876666421 0011 12344 9 9997655
No 31
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=61.50 E-value=6 Score=25.66 Aligned_cols=16 Identities=19% Similarity=0.472 Sum_probs=12.5
Q ss_pred CCCcCcCCCceEEEEE
Q psy8716 21 QELKCPIDDFELLCWS 36 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s 36 (141)
.+.+||.|||-+|+=-
T Consensus 23 ~~irCp~Cg~rIl~K~ 38 (49)
T COG1996 23 RGIRCPYCGSRILVKE 38 (49)
T ss_pred CceeCCCCCcEEEEec
Confidence 6688999999887643
No 32
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=61.18 E-value=8.7 Score=24.59 Aligned_cols=27 Identities=22% Similarity=0.561 Sum_probs=17.5
Q ss_pred cCCCCCCceEEEecCCCCceEEEcCCCCeEEE
Q psy8716 84 SCLQCEGGVLVLDLSSAPKWKICCNKCDIIIH 115 (141)
Q Consensus 84 ~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~ 115 (141)
-||.|..+ ++.+ .. =++.|.+|.+...
T Consensus 22 fCP~Cg~~-~m~~-~~---~r~~C~~Cgyt~~ 48 (50)
T PRK00432 22 FCPRCGSG-FMAE-HL---DRWHCGKCGYTEF 48 (50)
T ss_pred cCcCCCcc-hhec-cC---CcEECCCcCCEEe
Confidence 58888756 4442 22 3778999987653
No 33
>PRK00420 hypothetical protein; Validated
Probab=59.88 E-value=6 Score=29.56 Aligned_cols=26 Identities=23% Similarity=0.576 Sum_probs=19.5
Q ss_pred CCcCcCCCceEEEEEeCCCCeeeecCccCCC
Q psy8716 22 ELKCPIDDFELLCWSMGNKGKSYILCPYCYN 52 (141)
Q Consensus 22 e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN 52 (141)
+..||.||+.|....+ |+ .+||.|-.
T Consensus 23 ~~~CP~Cg~pLf~lk~---g~--~~Cp~Cg~ 48 (112)
T PRK00420 23 SKHCPVCGLPLFELKD---GE--VVCPVHGK 48 (112)
T ss_pred cCCCCCCCCcceecCC---Cc--eECCCCCC
Confidence 3679999999887643 44 38999876
No 34
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=59.28 E-value=13 Score=22.23 Aligned_cols=33 Identities=21% Similarity=0.400 Sum_probs=23.3
Q ss_pred EEEcCCCCeEEEccCCCeeEecCCCCce-eeccceecC
Q psy8716 104 KICCNKCDIIIHVFPDAQKVQVCTENNC-DCVQFTSND 140 (141)
Q Consensus 104 ~l~Cn~C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll~~ 140 (141)
|..|..|.-++++.-+- ...+.. | .||+.|++-
T Consensus 1 Rr~C~~Cg~~Yh~~~~p---P~~~~~-Cd~cg~~L~qR 34 (36)
T PF05191_consen 1 RRICPKCGRIYHIEFNP---PKVEGV-CDNCGGELVQR 34 (36)
T ss_dssp EEEETTTTEEEETTTB-----SSTTB-CTTTTEBEBEE
T ss_pred CcCcCCCCCccccccCC---CCCCCc-cCCCCCeeEeC
Confidence 57899999999985432 333455 9 899988763
No 35
>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=59.09 E-value=9 Score=22.29 Aligned_cols=30 Identities=17% Similarity=0.307 Sum_probs=18.5
Q ss_pred CCcCcCCCceEEEEEeCCCCeeeecCccCCC
Q psy8716 22 ELKCPIDDFELLCWSMGNKGKSYILCPYCYN 52 (141)
Q Consensus 22 e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN 52 (141)
+++|+-||-+.-++..... .....||.|=.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~-~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD-DPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCC-CCCCCCCCCCC
Confidence 4678888865544443222 45567888865
No 36
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=58.56 E-value=4.6 Score=22.28 Aligned_cols=22 Identities=32% Similarity=0.656 Sum_probs=12.8
Q ss_pred CCcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716 22 ELKCPIDDFELLCWSMGNKGKSYILCPYCY 51 (141)
Q Consensus 22 e~~CPLd~FeLl~~s~g~~gksy~lCP~Cy 51 (141)
+.+||-||.++ .....+||+|=
T Consensus 2 ~~~Cp~Cg~~~--------~~~~~fC~~CG 23 (26)
T PF13248_consen 2 EMFCPNCGAEI--------DPDAKFCPNCG 23 (26)
T ss_pred cCCCcccCCcC--------CcccccChhhC
Confidence 35677777743 22344777773
No 37
>PRK06599 DNA topoisomerase I; Validated
Probab=56.81 E-value=12 Score=35.08 Aligned_cols=36 Identities=31% Similarity=0.619 Sum_probs=25.1
Q ss_pred eecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccC
Q psy8716 82 IASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFP 118 (141)
Q Consensus 82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~ 118 (141)
...||+|++|.|++......+ ++.|++ |.+..++++
T Consensus 585 ~~~CP~C~~~~l~~k~~k~g~-F~~Cs~~p~C~~~~~~~~ 623 (675)
T PRK06599 585 DETCPKCGGGPLVLKLGKNGK-FLGCSGYPECKYTKNITR 623 (675)
T ss_pred CccccccCCCcceEEecCCCc-eeeCCCCCccCCCCCCcc
Confidence 468999964677775444344 588974 998887775
No 38
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=56.54 E-value=13 Score=21.94 Aligned_cols=27 Identities=19% Similarity=0.311 Sum_probs=21.8
Q ss_pred CCcCcCCCceEEEEEeCCCCeeeecCccCCC
Q psy8716 22 ELKCPIDDFELLCWSMGNKGKSYILCPYCYN 52 (141)
Q Consensus 22 e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN 52 (141)
..+|+.|+=++|+++ .++|-+|+.|=.
T Consensus 3 ~~~C~~C~~~~i~~~----~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNK----EDDYEVCIFCGS 29 (33)
T ss_pred ceEcCCCCCCeEEEe----cCCeEEcccCCc
Confidence 468999999999885 467889999854
No 39
>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=56.45 E-value=4.9 Score=23.48 Aligned_cols=31 Identities=26% Similarity=0.471 Sum_probs=14.9
Q ss_pred ecCCCCCCceEEEecC--CCCceEEEcCCCCeEE
Q psy8716 83 ASCLQCEGGVLVLDLS--SAPKWKICCNKCDIII 114 (141)
Q Consensus 83 ~~C~~C~~G~LvLdp~--s~pkw~l~Cn~C~~~v 114 (141)
..||.|+ -...++.. .+.+-++.|.+|...+
T Consensus 3 ~~CP~C~-~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCK-TSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCC-CEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 3466666 44555431 1222355666665544
No 40
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=56.28 E-value=9.3 Score=32.97 Aligned_cols=44 Identities=20% Similarity=0.446 Sum_probs=31.1
Q ss_pred CcCcCCCceEEE--EEe--CCCCeeeecCccCCCCCCcCCCCCCcccccccC
Q psy8716 23 LKCPIDDFELLC--WSM--GNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTH 70 (141)
Q Consensus 23 ~~CPLd~FeLl~--~s~--g~~gksy~lCP~CyN~PPf~~~~~~~~C~~C~h 70 (141)
..||+||=.=+. +.. +..|..|-.|..|-..=.|. ...|-.|-+
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~----R~~C~~Cg~ 232 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYV----RVKCSHCEE 232 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCccccc----CccCCCCCC
Confidence 489999977431 222 24789999999998887763 556766665
No 41
>PRK14873 primosome assembly protein PriA; Provisional
Probab=54.42 E-value=16 Score=34.54 Aligned_cols=41 Identities=24% Similarity=0.340 Sum_probs=29.2
Q ss_pred eecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716 82 IASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNC-DCVQFTS 138 (141)
Q Consensus 82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll 138 (141)
+..|+.|+ +-|++.. .+-+|.|..|.+.. . ... | +||+.-+
T Consensus 392 ~~~C~~C~-~~L~~h~---~~~~l~Ch~CG~~~-~----------p~~-Cp~Cgs~~l 433 (665)
T PRK14873 392 PARCRHCT-GPLGLPS---AGGTPRCRWCGRAA-P----------DWR-CPRCGSDRL 433 (665)
T ss_pred eeECCCCC-CceeEec---CCCeeECCCCcCCC-c----------Ccc-CCCCcCCcc
Confidence 67799999 8899842 23479999998632 1 245 9 9998644
No 42
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=54.35 E-value=21 Score=30.96 Aligned_cols=46 Identities=20% Similarity=0.376 Sum_probs=32.7
Q ss_pred CCCcCcCCCceEE--EEE-eCCCCeeeecCccCCCCCCcCCCCCCcccccccC
Q psy8716 21 QELKCPIDDFELL--CWS-MGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTH 70 (141)
Q Consensus 21 ~e~~CPLd~FeLl--~~s-~g~~gksy~lCP~CyN~PPf~~~~~~~~C~~C~h 70 (141)
....||.||-.=+ ++. .+..|..|-.|..|-..=.|. ...|-.|-+
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~----R~~C~~Cg~ 234 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVV----RVKCSNCEQ 234 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCccccc----CccCCCCCC
Confidence 3578999998732 112 235799999999999887763 556777664
No 43
>KOG1779|consensus
Probab=50.88 E-value=15 Score=26.35 Aligned_cols=44 Identities=20% Similarity=0.393 Sum_probs=30.6
Q ss_pred ccccccCCCCccccccceeecCCCCCCceEEEecCCCCceEEEcCCCCe
Q psy8716 64 GCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDI 112 (141)
Q Consensus 64 ~C~~C~hptC~~S~~~~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~ 112 (141)
.|.-|.|-|+=+|- +.+|..|+.|. -+|+. .++.|.+++++ |++
T Consensus 36 kC~gc~~iT~vfSH-aqtvVvc~~c~-~il~~--~tggra~ls~~-csf 79 (84)
T KOG1779|consen 36 KCPGCFKITTVFSH-AQTVVVCEGCS-TILCQ--PTGGKAKLSEG-CSF 79 (84)
T ss_pred EcCCceEEEEEeec-CceEEEcCCCc-eEEEE--ecCCcEEecCC-Ccc
Confidence 57777777777776 45566788887 33333 47789999998 654
No 44
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=50.69 E-value=7.6 Score=23.11 Aligned_cols=30 Identities=23% Similarity=0.545 Sum_probs=13.8
Q ss_pred cCCCCCCceEEEecC--CCCceEEEcCCCCeEE
Q psy8716 84 SCLQCEGGVLVLDLS--SAPKWKICCNKCDIII 114 (141)
Q Consensus 84 ~C~~C~~G~LvLdp~--s~pkw~l~Cn~C~~~v 114 (141)
.||.|. -...|+.. ...+-++-|.+|.-++
T Consensus 4 ~CP~C~-~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQ-TRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCC-ceEEcCHHHcccCCcEEECCCCCcEe
Confidence 455555 44444332 1223355555555443
No 45
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=50.03 E-value=24 Score=29.36 Aligned_cols=35 Identities=26% Similarity=0.520 Sum_probs=29.5
Q ss_pred CCCcCcCCCceEEEEEeCCCCeeeecCccCCCCCCcC
Q psy8716 21 QELKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYR 57 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN~PPf~ 57 (141)
.+..||-||=.+.....+ |++.-.||.|-.-||..
T Consensus 234 ~g~pC~~Cg~~I~~~~~~--gR~ty~Cp~CQ~~~~~~ 268 (269)
T PRK14811 234 EGQPCPRCGTPIEKIVVG--GRGTHFCPQCQPLRPLR 268 (269)
T ss_pred CcCCCCcCCCeeEEEEEC--CCCcEECCCCcCCCCCC
Confidence 456799999999888774 78888999999999864
No 46
>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=49.08 E-value=8.5 Score=21.58 Aligned_cols=12 Identities=17% Similarity=0.512 Sum_probs=9.6
Q ss_pred CCCcCcCCCceE
Q psy8716 21 QELKCPIDDFEL 32 (141)
Q Consensus 21 ~e~~CPLd~FeL 32 (141)
...+||+|||+.
T Consensus 13 ~~~~Cp~CG~~F 24 (26)
T PF10571_consen 13 SAKFCPHCGYDF 24 (26)
T ss_pred hcCcCCCCCCCC
Confidence 457899999975
No 47
>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=48.98 E-value=16 Score=22.23 Aligned_cols=28 Identities=29% Similarity=0.539 Sum_probs=18.7
Q ss_pred CCcCcCCC--ceEEEEEeCCCCeeeecCccCCC
Q psy8716 22 ELKCPIDD--FELLCWSMGNKGKSYILCPYCYN 52 (141)
Q Consensus 22 e~~CPLd~--FeLl~~s~g~~gksy~lCP~CyN 52 (141)
|++|+-|| ||++. .... ..-..||.|-+
T Consensus 5 ey~C~~Cg~~fe~~~--~~~~-~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ--SISE-DDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEE--EcCC-CCCCcCCCCCC
Confidence 57888888 55553 3333 56678988866
No 48
>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=48.63 E-value=15 Score=22.66 Aligned_cols=29 Identities=31% Similarity=0.678 Sum_probs=16.5
Q ss_pred CCcCcCCC--ceEEEEEeCCCCeeeecCccCCCC
Q psy8716 22 ELKCPIDD--FELLCWSMGNKGKSYILCPYCYNN 53 (141)
Q Consensus 22 e~~CPLd~--FeLl~~s~g~~gksy~lCP~CyN~ 53 (141)
|++|+-|| ||++. +... ...+.||.|=..
T Consensus 5 ey~C~~Cg~~fe~~~-~~~~--~~~~~CP~Cg~~ 35 (52)
T TIGR02605 5 EYRCTACGHRFEVLQ-KMSD--DPLATCPECGGE 35 (52)
T ss_pred EEEeCCCCCEeEEEE-ecCC--CCCCCCCCCCCC
Confidence 46788776 45442 2122 345678888764
No 49
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=48.53 E-value=12 Score=30.10 Aligned_cols=29 Identities=24% Similarity=0.584 Sum_probs=22.1
Q ss_pred CCceEEEcCCCCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716 100 APKWKICCNKCDIIIHVFPDAQKVQVCTENNC-DCVQFTS 138 (141)
Q Consensus 100 ~pkw~l~Cn~C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll 138 (141)
--+|++.|..|--++. -..+. | .||++++
T Consensus 135 v~~w~~rC~GC~~~f~---------~~~~~-Cp~CG~~~~ 164 (177)
T COG1439 135 VRKWRLRCHGCKRIFP---------EPKDF-CPICGSPLK 164 (177)
T ss_pred EeeeeEEEecCceecC---------CCCCc-CCCCCCceE
Confidence 3489999999988776 22465 9 9999764
No 50
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=47.34 E-value=8.7 Score=24.16 Aligned_cols=24 Identities=33% Similarity=0.737 Sum_probs=18.3
Q ss_pred EEEEeCCCCeeeecCccCCCCCCcC
Q psy8716 33 LCWSMGNKGKSYILCPYCYNNPPYR 57 (141)
Q Consensus 33 l~~s~g~~gksy~lCP~CyN~PPf~ 57 (141)
|.+.+ .+.+.|-|||-||..-=|.
T Consensus 13 vryh~-~~~~~~dLC~~CF~~G~f~ 36 (45)
T cd02336 13 VRYHN-LKAKKYDLCPSCYQEGRFP 36 (45)
T ss_pred eEEEe-cCCCccccChHHHhCcCCC
Confidence 55655 4677899999999987664
No 51
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=47.11 E-value=5.1 Score=25.59 Aligned_cols=33 Identities=12% Similarity=0.349 Sum_probs=20.1
Q ss_pred EEEcCCCCeEEEccCCCeeEe--cCCCCce-eeccce
Q psy8716 104 KICCNKCDIIIHVFPDAQKVQ--VCTENNC-DCVQFT 137 (141)
Q Consensus 104 ~l~Cn~C~~~v~l~~~a~kv~--v~~~~~C-~C~a~l 137 (141)
++.|++|.-++.||++..-.+ ...=+ | +|+..+
T Consensus 6 Fv~C~~C~~lLqlP~~~~~~~k~~~klr-CGaCs~vl 41 (46)
T PF11331_consen 6 FVVCSSCFELLQLPAKFSLSKKNQQKLR-CGACSEVL 41 (46)
T ss_pred EeECccHHHHHcCCCccCCCccceeEEe-CCCCceeE
Confidence 577888888888888632221 22333 7 776654
No 52
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=45.81 E-value=10 Score=22.56 Aligned_cols=16 Identities=19% Similarity=0.472 Sum_probs=11.2
Q ss_pred EEEcCCCCeEEEccCC
Q psy8716 104 KICCNKCDIIIHVFPD 119 (141)
Q Consensus 104 ~l~Cn~C~~~v~l~~~ 119 (141)
++.|.+|...+.++++
T Consensus 2 ~i~Cp~C~~~y~i~d~ 17 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDE 17 (36)
T ss_pred EEECCCCCCEEeCCHH
Confidence 4567777777777765
No 53
>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=45.57 E-value=24 Score=29.39 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=23.9
Q ss_pred CCCcCcCCCceEEEEEeCCCCeeeecCccC
Q psy8716 21 QELKCPIDDFELLCWSMGNKGKSYILCPYC 50 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s~g~~gksy~lCP~C 50 (141)
.+..||.||=++.....+ |++.-.||.|
T Consensus 244 ~g~pC~~Cg~~I~~~~~~--gR~t~~CP~C 271 (272)
T TIGR00577 244 KGEPCRRCGTPIEKIKVG--GRGTHFCPQC 271 (272)
T ss_pred CCCCCCCCCCeeEEEEEC--CCCCEECCCC
Confidence 457899999999888764 7888899998
No 54
>PRK05580 primosome assembly protein PriA; Validated
Probab=44.90 E-value=26 Score=32.88 Aligned_cols=42 Identities=21% Similarity=0.561 Sum_probs=29.5
Q ss_pred eecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716 82 IASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQVCTENNC-DCVQFTS 138 (141)
Q Consensus 82 V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll 138 (141)
+..||.|+ +-|++.. .+=.|.|..|.+...+|+ . | +||+..+
T Consensus 390 ~~~C~~C~-~~l~~h~---~~~~l~Ch~Cg~~~~~~~----------~-Cp~Cg~~~l 432 (679)
T PRK05580 390 VAECPHCD-ASLTLHR---FQRRLRCHHCGYQEPIPK----------A-CPECGSTDL 432 (679)
T ss_pred ccCCCCCC-CceeEEC---CCCeEECCCCcCCCCCCC----------C-CCCCcCCee
Confidence 66788998 7888753 244688998987665554 3 8 8877544
No 55
>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=44.83 E-value=32 Score=28.61 Aligned_cols=45 Identities=24% Similarity=0.526 Sum_probs=21.1
Q ss_pred CCcCcCCCce-EEEEEeCCC--CeeeecCccCCCCCCcCCCCCCcccccccC
Q psy8716 22 ELKCPIDDFE-LLCWSMGNK--GKSYILCPYCYNNPPYRDMKKGSGCNVCTH 70 (141)
Q Consensus 22 e~~CPLd~Fe-Ll~~s~g~~--gksy~lCP~CyN~PPf~~~~~~~~C~~C~h 70 (141)
...||+||=. ++.+-.++. |+.|-.|..|-..=+|. ..+|-.|-+
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~----R~~Cp~Cg~ 219 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFV----RIKCPYCGN 219 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE------TTS-TTT--
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeec----CCCCcCCCC
Confidence 3689999977 444433444 89999999998877763 445655553
No 56
>PF12773 DZR: Double zinc ribbon
Probab=44.51 E-value=13 Score=22.78 Aligned_cols=27 Identities=26% Similarity=0.422 Sum_probs=15.6
Q ss_pred CCcCcCCCceEEEEEeCCCCeeeecCccCCCC
Q psy8716 22 ELKCPIDDFELLCWSMGNKGKSYILCPYCYNN 53 (141)
Q Consensus 22 e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN~ 53 (141)
...||.||..|. ....+..+||.|-..
T Consensus 12 ~~fC~~CG~~l~-----~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 12 AKFCPHCGTPLP-----PPDQSKKICPNCGAE 38 (50)
T ss_pred ccCChhhcCChh-----hccCCCCCCcCCcCC
Confidence 456777777666 123344566666554
No 57
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=44.46 E-value=35 Score=25.18 Aligned_cols=33 Identities=21% Similarity=0.407 Sum_probs=23.0
Q ss_pred ecCCCCCCceEEEecCCCCceEEEcCCCCeEEEcc
Q psy8716 83 ASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVF 117 (141)
Q Consensus 83 ~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~ 117 (141)
--||.|+ ++|+-. ...-+-+|.|.+|.+...+.
T Consensus 3 ~FCp~Cg-sll~p~-~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 3 RFCPKCG-SLLYPK-KDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred cccCCcc-CeeEEe-EcCCCcEEECCCCCcchhcc
Confidence 3588998 777763 33233399999998776665
No 58
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=44.28 E-value=26 Score=29.10 Aligned_cols=29 Identities=24% Similarity=0.469 Sum_probs=24.0
Q ss_pred CCCcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716 21 QELKCPIDDFELLCWSMGNKGKSYILCPYCY 51 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s~g~~gksy~lCP~Cy 51 (141)
.+..||.||=.+.....+ |++.-.||.|-
T Consensus 244 ~g~pC~~Cg~~I~~~~~~--gR~t~~CP~CQ 272 (274)
T PRK01103 244 EGEPCRRCGTPIEKIKQG--GRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCCeeEEEEEC--CCCcEECcCCC
Confidence 456799999998887764 78888999994
No 59
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=43.85 E-value=70 Score=20.72 Aligned_cols=42 Identities=26% Similarity=0.438 Sum_probs=27.6
Q ss_pred cCCCCCC-ceEEEecCCCC-ceEEEcCCCC--e--EEEccCCCeeEec
Q psy8716 84 SCLQCEG-GVLVLDLSSAP-KWKICCNKCD--I--IIHVFPDAQKVQV 125 (141)
Q Consensus 84 ~C~~C~~-G~LvLdp~s~p-kw~l~Cn~C~--~--~v~l~~~a~kv~v 125 (141)
.||.|+. -.|.+|++.+. .|--.|..|= + .|.+-++..+|.|
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~~d~~~~~v~v 49 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVTVDEDEPSVSV 49 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEEECCCCCEEEE
Confidence 5889974 57888987764 6888898752 3 3444444455554
No 60
>PRK10445 endonuclease VIII; Provisional
Probab=43.83 E-value=27 Score=28.97 Aligned_cols=29 Identities=14% Similarity=0.289 Sum_probs=24.1
Q ss_pred CCCcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716 21 QELKCPIDDFELLCWSMGNKGKSYILCPYCY 51 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s~g~~gksy~lCP~Cy 51 (141)
.+..||-||=.+.....+ |++.-.||.|-
T Consensus 234 ~g~~Cp~Cg~~I~~~~~~--gR~t~~CP~CQ 262 (263)
T PRK10445 234 DGEACERCGGIIEKTTLS--SRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCCEeEEEEEC--CCCcEECCCCc
Confidence 467899999999888874 68888999984
No 61
>KOG4080|consensus
Probab=43.63 E-value=6.2 Score=31.76 Aligned_cols=23 Identities=30% Similarity=0.671 Sum_probs=17.0
Q ss_pred CCcCcCCCceEEEEEeCCCCeeeecCccCCCC
Q psy8716 22 ELKCPIDDFELLCWSMGNKGKSYILCPYCYNN 53 (141)
Q Consensus 22 e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN~ 53 (141)
=.+||.||= --.+.+||+|||.+
T Consensus 93 l~~CP~CGh---------~k~a~~LC~~Cy~k 115 (176)
T KOG4080|consen 93 LNTCPACGH---------IKPAHTLCDYCYAK 115 (176)
T ss_pred cccCcccCc---------cccccccHHHHHHH
Confidence 467999872 34567899999965
No 62
>PRK06599 DNA topoisomerase I; Validated
Probab=43.48 E-value=77 Score=29.84 Aligned_cols=34 Identities=26% Similarity=0.464 Sum_probs=24.0
Q ss_pred ecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccC
Q psy8716 83 ASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFP 118 (141)
Q Consensus 83 ~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~ 118 (141)
..||+|+.+ +++ ..+.-+.++.|++ |.++-.||+
T Consensus 638 ~~Cp~C~~~-~~~-kkgk~g~f~~Cs~yp~ck~~~~~~~ 674 (675)
T PRK06599 638 EKCPKCGGP-LVL-KKGRYGKFLACSGYPECKHIKPLEK 674 (675)
T ss_pred CCCCCCCCe-eEE-EeCCCCceeeCCCCCCCCceeeCCC
Confidence 379999955 555 3444455778974 998888875
No 63
>COG1140 NarY Nitrate reductase beta subunit [Energy production and conversion]
Probab=42.88 E-value=12 Score=34.09 Aligned_cols=42 Identities=31% Similarity=0.910 Sum_probs=34.5
Q ss_pred cccccccCCCCccccccceeecCCC------CCCceEEEecCCCCceEEEcCCCCe
Q psy8716 63 SGCNVCTHPTCGQALLSTGIASCLQ------CEGGVLVLDLSSAPKWKICCNKCDI 112 (141)
Q Consensus 63 ~~C~~C~hptC~~S~~~~~V~~C~~------C~~G~LvLdp~s~pkw~l~Cn~C~~ 112 (141)
..|.+|.||+| |+.||. =+.|++++|-..-.+||+.=..|++
T Consensus 181 RiCeHCLNPsC--------vasCPsgaiYKReEDGIVLiDQd~CRGwR~CvsgCPY 228 (513)
T COG1140 181 RLCEHCLNPSC--------VASCPSGAIYKREEDGIVLIDQDKCRGWRMCVSGCPY 228 (513)
T ss_pred HHHhhcCCcHH--------hhcCCcccccccccCceEEeecccccchhhhhcCCCc
Confidence 37999999999 566774 1359999998888999998889996
No 64
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=42.67 E-value=18 Score=26.76 Aligned_cols=38 Identities=13% Similarity=0.193 Sum_probs=26.2
Q ss_pred CCCceEEEcCCCCeEEEccCCCeeEecCCCCce-eeccceecC
Q psy8716 99 SAPKWKICCNKCDIIIHVFPDAQKVQVCTENNC-DCVQFTSND 140 (141)
Q Consensus 99 s~pkw~l~Cn~C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll~~ 140 (141)
..++|...|..|...+.- -.++...... | .|++.|..-
T Consensus 118 ~~~~~~~~C~~C~~~~~r---~~~~~~~~~~-C~~C~~~l~~~ 156 (157)
T PF10263_consen 118 EYKKYVYRCPSCGREYKR---HRRSKRKRYR-CGRCGGPLVQV 156 (157)
T ss_pred cccceEEEcCCCCCEeee---ecccchhhEE-CCCCCCEEEEc
Confidence 347899999999977622 2344444455 9 999988654
No 65
>PRK05582 DNA topoisomerase I; Validated
Probab=42.47 E-value=75 Score=29.73 Aligned_cols=30 Identities=27% Similarity=0.629 Sum_probs=18.2
Q ss_pred ecCCCCCCceEEEecCCCCceEEEcCC---CCeE
Q psy8716 83 ASCLQCEGGVLVLDLSSAPKWKICCNK---CDII 113 (141)
Q Consensus 83 ~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~ 113 (141)
..||.|+ +.+++-.....++++.|.+ |.+.
T Consensus 612 ~~CP~C~-~~l~l~k~k~gk~f~~Cs~~p~C~~~ 644 (650)
T PRK05582 612 VKCPKCG-GQIVERKSKKGRKFYGCSRYPECDFV 644 (650)
T ss_pred CCCCCCC-CceEEEcCCCCceeeccCCCCCCCcc
Confidence 5699998 5455533334456778864 6643
No 66
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=42.37 E-value=34 Score=25.59 Aligned_cols=22 Identities=36% Similarity=0.878 Sum_probs=17.6
Q ss_pred CCCCCCceEEEecCCCCceEEEcCCCCeEE
Q psy8716 85 CLQCEGGVLVLDLSSAPKWKICCNKCDIII 114 (141)
Q Consensus 85 C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v 114 (141)
||.|+ +-|++- +|.|++|++.|
T Consensus 1 CPvCg-~~l~vt-------~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCG-GELVVT-------RLKCPSCGTEI 22 (113)
T ss_pred CCCCC-CceEEE-------EEEcCCCCCEE
Confidence 78898 777663 68999999877
No 67
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=41.72 E-value=25 Score=19.77 Aligned_cols=18 Identities=22% Similarity=0.504 Sum_probs=13.7
Q ss_pred cCCCCeEEEccCCCeeEe
Q psy8716 107 CNKCDIIIHVFPDAQKVQ 124 (141)
Q Consensus 107 Cn~C~~~v~l~~~a~kv~ 124 (141)
|++|..++..|.+|..|+
T Consensus 1 C~~Cr~~L~yp~GA~sVr 18 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVR 18 (25)
T ss_pred CCCCCceEEcCCCCCCeE
Confidence 667888888888887653
No 68
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=40.78 E-value=41 Score=19.07 Aligned_cols=26 Identities=19% Similarity=0.409 Sum_probs=14.8
Q ss_pred CCCCCCceEEEecCCCCceEEEcCCCCeEE
Q psy8716 85 CLQCEGGVLVLDLSSAPKWKICCNKCDIII 114 (141)
Q Consensus 85 C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v 114 (141)
|+.|. +-+.+.+ ..|.+.|..|...+
T Consensus 6 C~~CG-~~t~~~~---~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 6 CGRCG-APTKPAP---GGWARRCPSCGHEH 31 (32)
T ss_dssp -TTT---BEEE-S---SSS-EEESSSS-EE
T ss_pred cCcCC-ccccCCC---CcCEeECCCCcCEe
Confidence 77787 6666643 37999999998654
No 69
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=39.95 E-value=13 Score=24.95 Aligned_cols=13 Identities=38% Similarity=0.667 Sum_probs=10.4
Q ss_pred CCCCCcCcCCCce
Q psy8716 19 MSQELKCPIDDFE 31 (141)
Q Consensus 19 ~s~e~~CPLd~Fe 31 (141)
+|..++||-|||+
T Consensus 45 ~~~~Y~CP~CGF~ 57 (59)
T PRK14890 45 QSNPYTCPKCGFE 57 (59)
T ss_pred cCCceECCCCCCc
Confidence 3377899999996
No 70
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=39.50 E-value=30 Score=25.26 Aligned_cols=30 Identities=20% Similarity=0.363 Sum_probs=22.2
Q ss_pred CCCcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716 21 QELKCPIDDFELLCWSMGNKGKSYILCPYCY 51 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s~g~~gksy~lCP~Cy 51 (141)
+-..||.||=..|.+.. .+++.+..||.|=
T Consensus 20 t~f~CP~Cge~~v~v~~-~k~~~h~~C~~CG 49 (99)
T PRK14892 20 KIFECPRCGKVSISVKI-KKNIAIITCGNCG 49 (99)
T ss_pred cEeECCCCCCeEeeeec-CCCcceEECCCCC
Confidence 55789999944455554 4589999999994
No 71
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.07 E-value=35 Score=28.45 Aligned_cols=29 Identities=21% Similarity=0.321 Sum_probs=24.2
Q ss_pred CCCcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716 21 QELKCPIDDFELLCWSMGNKGKSYILCPYCY 51 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s~g~~gksy~lCP~Cy 51 (141)
....||.||=.+.....+ |++.-.||.|-
T Consensus 243 ~g~pCprCG~~I~~~~~~--gR~t~~CP~CQ 271 (272)
T PRK14810 243 TGEPCLNCKTPIRRVVVA--GRSSHYCPHCQ 271 (272)
T ss_pred CCCcCCCCCCeeEEEEEC--CCccEECcCCc
Confidence 467899999999888764 78888999994
No 72
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=38.36 E-value=29 Score=29.34 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=4.7
Q ss_pred ceeecCCCCC
Q psy8716 80 TGIASCLQCE 89 (141)
Q Consensus 80 ~~V~~C~~C~ 89 (141)
.|-.-|.+|+
T Consensus 28 ~Ge~vC~~CG 37 (310)
T PRK00423 28 RGEIVCADCG 37 (310)
T ss_pred CCeEeecccC
Confidence 3444455554
No 73
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=37.29 E-value=24 Score=19.69 Aligned_cols=15 Identities=33% Similarity=0.906 Sum_probs=6.1
Q ss_pred ceEEEcCCCCeEEEc
Q psy8716 102 KWKICCNKCDIIIHV 116 (141)
Q Consensus 102 kw~l~Cn~C~~~v~l 116 (141)
.|...|..|++.+++
T Consensus 13 ~~~Y~C~~Cdf~lH~ 27 (30)
T PF07649_consen 13 GWFYRCSECDFDLHE 27 (30)
T ss_dssp --EEE-TTT-----H
T ss_pred CceEECccCCCccCh
Confidence 699999999998874
No 74
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=37.25 E-value=13 Score=21.71 Aligned_cols=24 Identities=29% Similarity=0.591 Sum_probs=8.8
Q ss_pred CcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716 23 LKCPIDDFELLCWSMGNKGKSYILCPYCY 51 (141)
Q Consensus 23 ~~CPLd~FeLl~~s~g~~gksy~lCP~Cy 51 (141)
-+||+|+-|-.+.. ..--+||-|.
T Consensus 3 p~Cp~C~se~~y~D-----~~~~vCp~C~ 26 (30)
T PF08274_consen 3 PKCPLCGSEYTYED-----GELLVCPECG 26 (30)
T ss_dssp ---TTT-----EE------SSSEEETTTT
T ss_pred CCCCCCCCcceecc-----CCEEeCCccc
Confidence 36888887776632 2334666664
No 75
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=36.62 E-value=63 Score=22.07 Aligned_cols=35 Identities=17% Similarity=0.251 Sum_probs=27.9
Q ss_pred CcCcCCCceEEEEEeCCCCeeeecCccCCCCCCcCC
Q psy8716 23 LKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRD 58 (141)
Q Consensus 23 ~~CPLd~FeLl~~s~g~~gksy~lCP~CyN~PPf~~ 58 (141)
.-||.||-+.+.+.. ..+--+.+|.-|-..-|+..
T Consensus 7 KPCPFCG~~~~~v~~-~~g~~~v~C~~CgA~~~~~~ 41 (64)
T PRK09710 7 KPCPFCGCPSVTVKA-ISGYYRAKCNGCESRTGYGG 41 (64)
T ss_pred cCCCCCCCceeEEEe-cCceEEEEcCCCCcCccccc
Confidence 349999999999986 34555699999998888754
No 76
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=35.87 E-value=40 Score=28.17 Aligned_cols=29 Identities=21% Similarity=0.368 Sum_probs=23.9
Q ss_pred CCCcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716 21 QELKCPIDDFELLCWSMGNKGKSYILCPYCY 51 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s~g~~gksy~lCP~Cy 51 (141)
.+..||.||=.+..... .|++.-.||.|-
T Consensus 253 ~g~pC~~Cg~~I~~~~~--~gR~t~~CP~CQ 281 (282)
T PRK13945 253 TGKPCRKCGTPIERIKL--AGRSTHWCPNCQ 281 (282)
T ss_pred CcCCCCcCCCeeEEEEE--CCCccEECCCCc
Confidence 45789999998888776 478888999994
No 77
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=35.07 E-value=49 Score=24.88 Aligned_cols=29 Identities=17% Similarity=0.297 Sum_probs=20.5
Q ss_pred ecCCCCCCceEEEecCCCCceEEEcCCCCe
Q psy8716 83 ASCLQCEGGVLVLDLSSAPKWKICCNKCDI 112 (141)
Q Consensus 83 ~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~ 112 (141)
..|++|++..-.|... +..|.|.|+.|..
T Consensus 94 VlC~~C~spdT~l~k~-~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE-GRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEE-TTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEc-CCEEEEEecccCC
Confidence 4699998654444222 6889999999974
No 78
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=35.03 E-value=35 Score=29.12 Aligned_cols=29 Identities=21% Similarity=0.387 Sum_probs=24.1
Q ss_pred CCCcCcCCCceEEEEEeCCCCeeeecCccCC
Q psy8716 21 QELKCPIDDFELLCWSMGNKGKSYILCPYCY 51 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s~g~~gksy~lCP~Cy 51 (141)
++.-|+.||=-+..... .||+...||.|-
T Consensus 244 ~GepC~~CGt~I~k~~~--~gR~t~~CP~CQ 272 (273)
T COG0266 244 AGEPCRRCGTPIEKIKL--GGRSTFYCPVCQ 272 (273)
T ss_pred CCCCCCccCCEeEEEEE--cCCcCEeCCCCC
Confidence 66789999988887775 588999999994
No 79
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=34.14 E-value=18 Score=24.55 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=9.8
Q ss_pred CCCcCcCCCce
Q psy8716 21 QELKCPIDDFE 31 (141)
Q Consensus 21 ~e~~CPLd~Fe 31 (141)
..++||-||||
T Consensus 49 ~~Y~Cp~CGF~ 59 (61)
T COG2888 49 NPYRCPKCGFE 59 (61)
T ss_pred CceECCCcCcc
Confidence 77899999997
No 80
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=33.12 E-value=38 Score=23.78 Aligned_cols=25 Identities=16% Similarity=0.539 Sum_probs=14.1
Q ss_pred CCCCCCceEEEecCCCCceEEEcCCCCeEEE
Q psy8716 85 CLQCEGGVLVLDLSSAPKWKICCNKCDIIIH 115 (141)
Q Consensus 85 C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~ 115 (141)
||.|+ ++|.. .++ .+.|..|.+...
T Consensus 3 C~~Cg-~~l~~--~~~---~~~C~~C~~~~~ 27 (104)
T TIGR01384 3 CPKCG-SLMTP--KNG---VYVCPSCGYEKE 27 (104)
T ss_pred CcccC-ccccc--CCC---eEECcCCCCccc
Confidence 66776 55543 221 577777775433
No 81
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=32.46 E-value=36 Score=22.28 Aligned_cols=28 Identities=32% Similarity=0.646 Sum_probs=20.8
Q ss_pred cCCCCCCceEEEecCCCCceEEEcCCCCeEEE
Q psy8716 84 SCLQCEGGVLVLDLSSAPKWKICCNKCDIIIH 115 (141)
Q Consensus 84 ~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~ 115 (141)
-||.|..|+.+-|- +=|++|-+|.+.-+
T Consensus 21 ~CPrCG~gvfmA~H----~dR~~CGkCgyTe~ 48 (51)
T COG1998 21 FCPRCGPGVFMADH----KDRWACGKCGYTEF 48 (51)
T ss_pred cCCCCCCcchhhhc----CceeEeccccceEe
Confidence 48889878887752 23899999987654
No 82
>PF14353 CpXC: CpXC protein
Probab=32.30 E-value=53 Score=23.86 Aligned_cols=16 Identities=31% Similarity=0.777 Sum_probs=8.2
Q ss_pred CCcCcCCCc--eEEEEEe
Q psy8716 22 ELKCPIDDF--ELLCWSM 37 (141)
Q Consensus 22 e~~CPLd~F--eLl~~s~ 37 (141)
+.+||-|+- +.-+|+.
T Consensus 1 ~itCP~C~~~~~~~v~~~ 18 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTS 18 (128)
T ss_pred CcCCCCCCCeeEEEEEeE
Confidence 356777663 3334443
No 83
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=31.67 E-value=41 Score=20.05 Aligned_cols=15 Identities=27% Similarity=0.603 Sum_probs=9.4
Q ss_pred ccceeecCCCCCCceE
Q psy8716 78 LSTGIASCLQCEGGVL 93 (141)
Q Consensus 78 ~~~~V~~C~~C~~G~L 93 (141)
..+.|-.|+.|. |+.
T Consensus 15 ~~~~id~C~~C~-G~W 29 (41)
T PF13453_consen 15 GDVEIDVCPSCG-GIW 29 (41)
T ss_pred CCEEEEECCCCC-eEE
Confidence 345667777777 554
No 84
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=31.48 E-value=24 Score=23.79 Aligned_cols=23 Identities=26% Similarity=0.684 Sum_probs=15.8
Q ss_pred EcCCCCeEEEccCCCeeEecCCCCce-eeccceecC
Q psy8716 106 CCNKCDIIIHVFPDAQKVQVCTENNC-DCVQFTSND 140 (141)
Q Consensus 106 ~Cn~C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll~~ 140 (141)
+|.+|.+++ +++. | .||+.-+++
T Consensus 5 AC~~C~~i~-----------~~~~-CP~Cgs~~~T~ 28 (61)
T PRK08351 5 ACRHCHYIT-----------TEDR-CPVCGSRDLSD 28 (61)
T ss_pred hhhhCCccc-----------CCCc-CCCCcCCcccc
Confidence 788888776 2345 8 888876554
No 85
>TIGR03278 methan_mark_10 putative methanogenesis marker protein 10. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The presence of motifs with seven invariant Cys residues in the N-terminal 50 residues, including three instances of CXXC, would be consistent with function as an oxidoreductase with FeS clusters. The exact function is unknown, but likely is linked to methanogenesis. In most genomes, the member of this family is encoded by a gene next to, and divergently transcribed from, the methyl coenzyme M reductase operon.
Probab=31.09 E-value=40 Score=30.03 Aligned_cols=28 Identities=32% Similarity=0.744 Sum_probs=16.8
Q ss_pred CCeee-ecCccCCCCCCcCCCCCCccccccc
Q psy8716 40 KGKSY-ILCPYCYNNPPYRDMKKGSGCNVCT 69 (141)
Q Consensus 40 ~gksy-~lCP~CyN~PPf~~~~~~~~C~~C~ 69 (141)
+|+.= -.|+||||.= ....+..+|..|.
T Consensus 5 ~~~gC~~~C~wC~~p~--~~~~~~~~c~~C~ 33 (404)
T TIGR03278 5 PGIDCRGFCRYCYFKK--VDDEQPFGCKNCP 33 (404)
T ss_pred CCCCCCCcCCCCCCCC--CCCCCCCCCCcCC
Confidence 34433 3699999842 1122347888885
No 86
>KOG2691|consensus
Probab=29.35 E-value=30 Score=26.03 Aligned_cols=33 Identities=24% Similarity=0.590 Sum_probs=25.4
Q ss_pred ceeecCCCCCCceEEEe-cCCCCceEEEcCCCCeE
Q psy8716 80 TGIASCLQCEGGVLVLD-LSSAPKWKICCNKCDII 113 (141)
Q Consensus 80 ~~V~~C~~C~~G~LvLd-p~s~pkw~l~Cn~C~~~ 113 (141)
+++--|+||+ ++|.-. ..-..+..|+|+.|+.+
T Consensus 2 ~~~rfC~eCN-NmLYPkEDked~~L~laCrnCd~v 35 (113)
T KOG2691|consen 2 VGIRFCRECN-NMLYPKEDKEDRILLLACRNCDYV 35 (113)
T ss_pred Cccchhhhhh-ccccccccccccEEEEEecCCcce
Confidence 4566799999 888762 13468899999999876
No 87
>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=29.20 E-value=46 Score=25.08 Aligned_cols=15 Identities=27% Similarity=0.175 Sum_probs=12.3
Q ss_pred CcCcCCCceEEEEEe
Q psy8716 23 LKCPIDDFELLCWSM 37 (141)
Q Consensus 23 ~~CPLd~FeLl~~s~ 37 (141)
-+|+.||=.|..++.
T Consensus 92 sRC~~CN~~L~~v~~ 106 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSK 106 (147)
T ss_pred CccCCCCcEeeechh
Confidence 589999998888754
No 88
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=29.14 E-value=26 Score=27.93 Aligned_cols=30 Identities=27% Similarity=0.355 Sum_probs=21.9
Q ss_pred CCcCcCCCceEEEEEeCC-----------CCeeeecCccCC
Q psy8716 22 ELKCPIDDFELLCWSMGN-----------KGKSYILCPYCY 51 (141)
Q Consensus 22 e~~CPLd~FeLl~~s~g~-----------~gksy~lCP~Cy 51 (141)
.-+||.||=+|+.++... ....|..||.|.
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~Cg 137 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCG 137 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCc
Confidence 468999999999987642 234566788885
No 89
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=28.17 E-value=21 Score=18.52 Aligned_cols=8 Identities=38% Similarity=0.945 Sum_probs=4.4
Q ss_pred cCcCCCce
Q psy8716 24 KCPIDDFE 31 (141)
Q Consensus 24 ~CPLd~Fe 31 (141)
+|++|+|.
T Consensus 2 ~C~~C~y~ 9 (24)
T PF13909_consen 2 KCPHCSYS 9 (24)
T ss_dssp E-SSSS-E
T ss_pred CCCCCCCc
Confidence 67888775
No 90
>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=27.61 E-value=35 Score=19.99 Aligned_cols=14 Identities=21% Similarity=0.615 Sum_probs=10.6
Q ss_pred CCCcCcCCCceEEE
Q psy8716 21 QELKCPIDDFELLC 34 (141)
Q Consensus 21 ~e~~CPLd~FeLl~ 34 (141)
...+||.|||-+|.
T Consensus 16 ~~irC~~CG~RIly 29 (32)
T PF03604_consen 16 DPIRCPECGHRILY 29 (32)
T ss_dssp STSSBSSSS-SEEB
T ss_pred CcEECCcCCCeEEE
Confidence 44799999999874
No 91
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=27.35 E-value=27 Score=23.43 Aligned_cols=11 Identities=36% Similarity=1.050 Sum_probs=8.4
Q ss_pred CCeeeecCccC
Q psy8716 40 KGKSYILCPYC 50 (141)
Q Consensus 40 ~gksy~lCP~C 50 (141)
..+.||+||-|
T Consensus 40 dp~~~PVCP~C 50 (58)
T PF11238_consen 40 DPKPFPVCPEC 50 (58)
T ss_pred CCCCCCCCcCH
Confidence 34449999988
No 92
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=27.30 E-value=71 Score=19.82 Aligned_cols=17 Identities=12% Similarity=0.296 Sum_probs=13.1
Q ss_pred CCCcCcCCCceEEEEEe
Q psy8716 21 QELKCPIDDFELLCWSM 37 (141)
Q Consensus 21 ~e~~CPLd~FeLl~~s~ 37 (141)
...+||-||+.+|+=..
T Consensus 18 ~~irC~~CG~rIlyK~R 34 (44)
T smart00659 18 DVVRCRECGYRILYKKR 34 (44)
T ss_pred CceECCCCCceEEEEeC
Confidence 55889999999886543
No 93
>PF15616 TerY-C: TerY-C metal binding domain
Probab=27.00 E-value=1.5e+02 Score=22.75 Aligned_cols=49 Identities=18% Similarity=0.320 Sum_probs=26.6
Q ss_pred CCCccccccceeecCCCCCCceEEEecCCCCceEEEcCCCCeEEEccCCCeeEec
Q psy8716 71 PTCGQALLSTGIASCLQCEGGVLVLDLSSAPKWKICCNKCDIIIHVFPDAQKVQV 125 (141)
Q Consensus 71 ptC~~S~~~~~V~~C~~C~~G~LvLdp~s~pkw~l~Cn~C~~~v~l~~~a~kv~v 125 (141)
|.|||==+..+++.| .|+ .++.+|- +. ...|.-|.-.+.+-.+...+.|
T Consensus 78 PgCP~CGn~~~fa~C-~CG-kl~Ci~g---~~-~~~CPwCg~~g~~~~~~~~fdv 126 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVC-GCG-KLFCIDG---EG-EVTCPWCGNEGSFGAGDGGFDV 126 (131)
T ss_pred CCCCCCcChhcEEEe-cCC-CEEEeCC---CC-CEECCCCCCeeeecccCCceEe
Confidence 444444444455556 566 6666642 22 5666666666665554444444
No 94
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=26.48 E-value=69 Score=18.64 Aligned_cols=15 Identities=13% Similarity=0.224 Sum_probs=10.6
Q ss_pred CCCCce-eeccceecCC
Q psy8716 126 CTENNC-DCVQFTSNDK 141 (141)
Q Consensus 126 ~~~~~C-~C~a~ll~~~ 141 (141)
.... | +||-..+++.
T Consensus 31 p~~~-C~~CGE~~~~~~ 46 (46)
T TIGR03831 31 PALV-CPQCGEEYLDAE 46 (46)
T ss_pred Cccc-cccCCCEeeCCC
Confidence 3355 9 9998887763
No 95
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=26.45 E-value=34 Score=21.59 Aligned_cols=8 Identities=38% Similarity=1.381 Sum_probs=6.8
Q ss_pred CccCCCCC
Q psy8716 47 CPYCYNNP 54 (141)
Q Consensus 47 CP~CyN~P 54 (141)
||||.+.+
T Consensus 1 CP~C~~kk 8 (43)
T PF03470_consen 1 CPFCPGKK 8 (43)
T ss_pred CCCCCCCC
Confidence 89998877
No 96
>PRK05582 DNA topoisomerase I; Validated
Probab=26.31 E-value=83 Score=29.43 Aligned_cols=47 Identities=17% Similarity=0.403 Sum_probs=28.3
Q ss_pred ecCCCCCCceEEEecCCCCceEEEcCC---CCeEEEccCCCeeEecCCCCce-eecccee
Q psy8716 83 ASCLQCEGGVLVLDLSSAPKWKICCNK---CDIIIHVFPDAQKVQVCTENNC-DCVQFTS 138 (141)
Q Consensus 83 ~~C~~C~~G~LvLdp~s~pkw~l~Cn~---C~~~v~l~~~a~kv~v~~~~~C-~C~a~ll 138 (141)
..||.|+ +-++..... .+.++.|+. |.+..++.+ ..... | +|+..++
T Consensus 572 ~~CP~Cg-~~l~~~~~k-~gkf~~Cs~~~~C~~~~~~~~------~~~~~-CP~C~~~l~ 622 (650)
T PRK05582 572 EDCPKCG-SPMVIKMGR-YGKFIACSNFPDCRNTKPIVK------EIGVK-CPKCGGQIV 622 (650)
T ss_pred CCCCCCC-CEeEEEecC-CCceeecCCccccccCCCccc------ccCCC-CCCCCCceE
Confidence 5799998 555554322 335788975 887654442 12344 8 8877543
No 97
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=26.11 E-value=51 Score=21.42 Aligned_cols=23 Identities=35% Similarity=0.777 Sum_probs=13.8
Q ss_pred eeecCCCCCCceEEEecCCCCceEEEcC
Q psy8716 81 GIASCLQCEGGVLVLDLSSAPKWKICCN 108 (141)
Q Consensus 81 ~V~~C~~C~~G~LvLdp~s~pkw~l~Cn 108 (141)
.+.+||+|++|.|+.|.. .-.|+
T Consensus 13 al~~Cp~C~~~~l~~~~~-----~Y~C~ 35 (55)
T PF08063_consen 13 ALEPCPKCKGGQLYFDGS-----GYKCT 35 (55)
T ss_dssp EE---SSSSE-EEEEETT-----EEEEE
T ss_pred CCCCCCCCCCCeEEecCC-----ccEeC
Confidence 456899999789999743 55565
No 98
>PRK12496 hypothetical protein; Provisional
Probab=25.93 E-value=44 Score=26.03 Aligned_cols=29 Identities=21% Similarity=0.401 Sum_probs=19.4
Q ss_pred CceEEEcCCCCeEEEccCCCeeEecCCCCce-eeccce
Q psy8716 101 PKWKICCNKCDIIIHVFPDAQKVQVCTENNC-DCVQFT 137 (141)
Q Consensus 101 pkw~l~Cn~C~~~v~l~~~a~kv~v~~~~~C-~C~a~l 137 (141)
-+|+..|..|.-.+... ...+. | .||+.+
T Consensus 124 ~~w~~~C~gC~~~~~~~-------~~~~~-C~~CG~~~ 153 (164)
T PRK12496 124 IKWRKVCKGCKKKYPED-------YPDDV-CEICGSPV 153 (164)
T ss_pred eeeeEECCCCCccccCC-------CCCCc-CCCCCChh
Confidence 47999999998433211 12355 9 999875
No 99
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=25.24 E-value=70 Score=30.35 Aligned_cols=47 Identities=26% Similarity=0.545 Sum_probs=29.4
Q ss_pred CcCcCCCceEEEEEeCCCCeeeecCccCCCCCCcCCCCCCcccccccCCCCccccccceeecCCCCC
Q psy8716 23 LKCPIDDFELLCWSMGNKGKSYILCPYCYNNPPYRDMKKGSGCNVCTHPTCGQALLSTGIASCLQCE 89 (141)
Q Consensus 23 ~~CPLd~FeLl~~s~g~~gksy~lCP~CyN~PPf~~~~~~~~C~~C~hptC~~S~~~~~V~~C~~C~ 89 (141)
.+||-||++. .....+||+|-..-+ ...|.+|-+. ...+..-|++|+
T Consensus 2 ~~Cp~Cg~~n--------~~~akFC~~CG~~l~------~~~Cp~CG~~------~~~~~~fC~~CG 48 (645)
T PRK14559 2 LICPQCQFEN--------PNNNRFCQKCGTSLT------HKPCPQCGTE------VPVDEAHCPNCG 48 (645)
T ss_pred CcCCCCCCcC--------CCCCccccccCCCCC------CCcCCCCCCC------CCcccccccccC
Confidence 4799999882 122338999955432 1357777643 345666788886
No 100
>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=25.17 E-value=39 Score=18.80 Aligned_cols=10 Identities=30% Similarity=0.653 Sum_probs=6.3
Q ss_pred CCCcCcCCCc
Q psy8716 21 QELKCPIDDF 30 (141)
Q Consensus 21 ~e~~CPLd~F 30 (141)
..++||-|||
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4466777665
No 101
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=24.71 E-value=14 Score=23.61 Aligned_cols=27 Identities=26% Similarity=0.583 Sum_probs=20.5
Q ss_pred cCcCCCceEEEEEeC--CCCeeeecCccCCCC
Q psy8716 24 KCPIDDFELLCWSMG--NKGKSYILCPYCYNN 53 (141)
Q Consensus 24 ~CPLd~FeLl~~s~g--~~gksy~lCP~CyN~ 53 (141)
+|++||=|+=++..- ..| | ||..|++.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG--~-iC~~C~~K 29 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG--Y-ICKDCLKK 29 (51)
T ss_pred CCCccccccccccceeccCc--c-chHHHHHH
Confidence 599999998777632 334 4 99999977
No 102
>PF09706 Cas_CXXC_CXXC: CRISPR-associated protein (Cas_CXXC_CXXC); InterPro: IPR019121 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved domain of about 65 amino acids found in otherwise highly divergent proteins encoded in CRISPR-associated regions. This domain features two CXXC motifs.
Probab=24.67 E-value=21 Score=24.11 Aligned_cols=27 Identities=26% Similarity=0.592 Sum_probs=16.0
Q ss_pred ccccccccccccc-CcCCC-------CCCcCcCCCc
Q psy8716 3 QLFEVSFSPLAAT-GKAMS-------QELKCPIDDF 30 (141)
Q Consensus 3 ~Lfe~~Fs~l~~s-gkp~s-------~e~~CPLd~F 30 (141)
.+++..| ||..+ |+--+ .-.-||+|.|
T Consensus 25 ~~~~t~f-pl~g~~~~~~N~fwn~~~~~~iCp~C~~ 59 (69)
T PF09706_consen 25 FFNDTGF-PLSGSNGRKPNFFWNFNNDADICPICEL 59 (69)
T ss_pred hhhhccc-cccccCCCcccccccCcCCCccCHHHHH
Confidence 4556677 77766 55444 4455666654
No 103
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=24.65 E-value=75 Score=23.38 Aligned_cols=27 Identities=19% Similarity=0.544 Sum_probs=19.1
Q ss_pred ecCCCCCCc--eEEEecCCCCceEEEcCCCCe
Q psy8716 83 ASCLQCEGG--VLVLDLSSAPKWKICCNKCDI 112 (141)
Q Consensus 83 ~~C~~C~~G--~LvLdp~s~pkw~l~Cn~C~~ 112 (141)
..|++|++. .|+.| +.-|.|.|+.|..
T Consensus 81 VlC~~C~spdT~l~k~---~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKE---NRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEe---CCeEEEEccccCC
Confidence 458888765 44444 5789999998853
No 104
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=24.11 E-value=39 Score=21.27 Aligned_cols=27 Identities=30% Similarity=0.560 Sum_probs=11.9
Q ss_pred CcCcCCCceEEEEEeCCCCeeeecCccC
Q psy8716 23 LKCPIDDFELLCWSMGNKGKSYILCPYC 50 (141)
Q Consensus 23 ~~CPLd~FeLl~~s~g~~gksy~lCP~C 50 (141)
-+||-||.|--.-.+ ...+...-||||
T Consensus 29 W~C~~Cgh~w~~~v~-~R~~~~~~CP~C 55 (55)
T PF14311_consen 29 WKCPKCGHEWKASVN-DRTRRGKGCPYC 55 (55)
T ss_pred EECCCCCCeeEccHh-hhccCCCCCCCC
Confidence 356666654332111 111334466666
No 105
>PF04759 DUF617: Protein of unknown function, DUF617; InterPro: IPR006460 This family of hypothetical plant proteins are defined by a region of about 170 amino acids found at the C terminus. These proteins have highly divergent N-terminal regions rich in low complexity sequence. PSI-BLAST reveals no clear similarity to any characterised protein. At least 12 distinct members are found in Arabidopsis thaliana (Mouse-ear cress).
Probab=23.51 E-value=51 Score=26.39 Aligned_cols=18 Identities=28% Similarity=0.763 Sum_probs=14.5
Q ss_pred CCCceEEEcC--CCCeEEEc
Q psy8716 99 SAPKWKICCN--KCDIIIHV 116 (141)
Q Consensus 99 s~pkw~l~Cn--~C~~~v~l 116 (141)
+-|.|.++|| +|-+.|+=
T Consensus 71 ~ep~W~myCNGrK~GyAvRR 90 (166)
T PF04759_consen 71 EEPVWTMYCNGRKVGYAVRR 90 (166)
T ss_pred cceeEEEEECCceeeeeEEc
Confidence 4589999999 58887764
No 106
>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=23.22 E-value=26 Score=26.47 Aligned_cols=36 Identities=28% Similarity=0.472 Sum_probs=22.1
Q ss_pred CcccccccCCCCccccccceeecCCCCCCceEEEecCCCCc
Q psy8716 62 GSGCNVCTHPTCGQALLSTGIASCLQCEGGVLVLDLSSAPK 102 (141)
Q Consensus 62 ~~~C~~C~hptC~~S~~~~~V~~C~~C~~G~LvLdp~s~pk 102 (141)
+..|..|-++|=-+.. +..|+.|+ --|.|||+..+|
T Consensus 69 ~V~CP~C~K~TKmLGr----~D~CM~C~-~pLTLd~~legk 104 (114)
T PF11023_consen 69 QVECPNCGKQTKMLGR----VDACMHCK-EPLTLDPSLEGK 104 (114)
T ss_pred eeECCCCCChHhhhch----hhccCcCC-CcCccCchhhcc
Confidence 3455555544433332 35788888 788888876655
No 107
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=22.18 E-value=1.7e+02 Score=17.63 Aligned_cols=36 Identities=14% Similarity=0.122 Sum_probs=26.5
Q ss_pred CCCCCCcCcCCCceEEEEEeCCCCeeeecCccCCCCC
Q psy8716 18 AMSQELKCPIDDFELLCWSMGNKGKSYILCPYCYNNP 54 (141)
Q Consensus 18 p~s~e~~CPLd~FeLl~~s~g~~gksy~lCP~CyN~P 54 (141)
+|++=++|+.||--+..-.. .+++.|-.|....+..
T Consensus 1 ll~g~l~C~~CG~~m~~~~~-~~~~~yy~C~~~~~~~ 36 (58)
T PF13408_consen 1 LLSGLLRCGHCGSKMTRRKR-KGKYRYYRCSNRRRKG 36 (58)
T ss_pred CCCCcEEcccCCcEeEEEEC-CCCceEEEcCCCcCCC
Confidence 35566899999999888654 3667888888776554
No 108
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.01 E-value=67 Score=20.69 Aligned_cols=13 Identities=15% Similarity=0.123 Sum_probs=6.0
Q ss_pred CCcCcCCCceEEE
Q psy8716 22 ELKCPIDDFELLC 34 (141)
Q Consensus 22 e~~CPLd~FeLl~ 34 (141)
...||.||...-.
T Consensus 28 Sq~C~~CG~~~~~ 40 (69)
T PF07282_consen 28 SQTCPRCGHRNKK 40 (69)
T ss_pred ccCccCccccccc
Confidence 3445555544433
No 109
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=21.83 E-value=1.2e+02 Score=19.07 Aligned_cols=33 Identities=21% Similarity=0.371 Sum_probs=21.0
Q ss_pred cCcCCCceEEEEEeC--C-CCeeeecCccCCCCCCc
Q psy8716 24 KCPIDDFELLCWSMG--N-KGKSYILCPYCYNNPPY 56 (141)
Q Consensus 24 ~CPLd~FeLl~~s~g--~-~gksy~lCP~CyN~PPf 56 (141)
-||.||=+-.++..+ . .+..|..|..|=-.-|.
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 599999888866532 2 34445567777655554
No 110
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=21.62 E-value=42 Score=16.37 Aligned_cols=9 Identities=33% Similarity=0.755 Sum_probs=4.3
Q ss_pred cCcCCCceE
Q psy8716 24 KCPIDDFEL 32 (141)
Q Consensus 24 ~CPLd~FeL 32 (141)
+|++|++..
T Consensus 2 ~C~~C~~~~ 10 (24)
T PF13894_consen 2 QCPICGKSF 10 (24)
T ss_dssp E-SSTS-EE
T ss_pred CCcCCCCcC
Confidence 477777653
No 111
>cd02972 DsbA_family DsbA family; consists of DsbA and DsbA-like proteins, including DsbC, DsbG, glutathione (GSH) S-transferase kappa (GSTK), 2-hydroxychromene-2-carboxylate (HCCA) isomerase, an oxidoreductase (FrnE) presumed to be involved in frenolicin biosynthesis, a 27-kDa outer membrane protein, and similar proteins. Members of this family contain a redox active CXXC motif (except GSTK and HCCA isomerase) imbedded in a TRX fold, and an alpha helical insert of about 75 residues (shorter in DsbC and DsbG) relative to TRX. DsbA is involved in the oxidative protein folding pathway in prokaryotes, catalyzing disulfide bond formation of proteins secreted into the bacterial periplasm. DsbC and DsbG function as protein disulfide isomerases and chaperones to correct non-native disulfide bonds formed by DsbA and prevent aggregation of incorrectly folded proteins.
Probab=21.32 E-value=25 Score=22.31 Aligned_cols=11 Identities=64% Similarity=1.470 Sum_probs=8.0
Q ss_pred ecCccCCCCCC
Q psy8716 45 ILCPYCYNNPP 55 (141)
Q Consensus 45 ~lCP~CyN~PP 55 (141)
+.|||||.-=|
T Consensus 7 ~~Cp~C~~~~~ 17 (98)
T cd02972 7 PLCPYCYLFEP 17 (98)
T ss_pred CCCHhHHhhhH
Confidence 57888887654
No 112
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=21.18 E-value=70 Score=19.72 Aligned_cols=8 Identities=38% Similarity=1.277 Sum_probs=3.7
Q ss_pred EEEcCCCC
Q psy8716 104 KICCNKCD 111 (141)
Q Consensus 104 ~l~Cn~C~ 111 (141)
.+.|-.|.
T Consensus 40 ~v~C~~C~ 47 (64)
T smart00647 40 RVTCPKCG 47 (64)
T ss_pred eeECCCCC
Confidence 45554444
No 113
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.70 E-value=1.3e+02 Score=22.60 Aligned_cols=66 Identities=23% Similarity=0.457 Sum_probs=35.4
Q ss_pred CcCcCCCceEEEEEeCCCCeee-ecCccCCCCCCcCCC-----CCCcccccccCCC--Ccc----ccccceeecCCCCCC
Q psy8716 23 LKCPIDDFELLCWSMGNKGKSY-ILCPYCYNNPPYRDM-----KKGSGCNVCTHPT--CGQ----ALLSTGIASCLQCEG 90 (141)
Q Consensus 23 ~~CPLd~FeLl~~s~g~~gksy-~lCP~CyN~PPf~~~-----~~~~~C~~C~hpt--C~~----S~~~~~V~~C~~C~~ 90 (141)
..||+||-.||+- .--.||| .|-| -+||+.. .....|+-|.-+= =+- .+...++.+|+.|.
T Consensus 16 ~~CpiCgLtLVss--~HLARSyHHLfP----l~~f~ev~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~- 88 (112)
T TIGR00622 16 VECPICGLTLILS--THLARSYHHLFP----LKAFQEIPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCK- 88 (112)
T ss_pred CcCCcCCCEEecc--chHHHhhhccCC----CcccccccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCC-
Confidence 5799997666554 3568886 4444 3567533 1223477775321 000 03345566777776
Q ss_pred ceEEE
Q psy8716 91 GVLVL 95 (141)
Q Consensus 91 G~LvL 95 (141)
....+
T Consensus 89 ~~FC~ 93 (112)
T TIGR00622 89 NVFCV 93 (112)
T ss_pred Ccccc
Confidence 44433
No 114
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=20.64 E-value=46 Score=22.58 Aligned_cols=26 Identities=27% Similarity=0.462 Sum_probs=16.1
Q ss_pred CcCcCCCceEEEEEeCCCCeeeecCccC
Q psy8716 23 LKCPIDDFELLCWSMGNKGKSYILCPYC 50 (141)
Q Consensus 23 ~~CPLd~FeLl~~s~g~~gksy~lCP~C 50 (141)
..||||+-++.+-+ ...-.|..|--|
T Consensus 3 ~~CPlCkt~~n~gs--k~~pNyntCT~C 28 (61)
T PF05715_consen 3 SLCPLCKTTLNVGS--KDPPNYNTCTEC 28 (61)
T ss_pred ccCCcccchhhcCC--CCCCCccHHHHH
Confidence 46999999994443 234455555444
No 115
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=20.57 E-value=1.4e+02 Score=18.08 Aligned_cols=28 Identities=25% Similarity=0.501 Sum_probs=19.5
Q ss_pred cCcCCCceEEEEEe----CCCCeeeecCccCCC
Q psy8716 24 KCPIDDFELLCWSM----GNKGKSYILCPYCYN 52 (141)
Q Consensus 24 ~CPLd~FeLl~~s~----g~~gksy~lCP~CyN 52 (141)
.|+ ||=..++.++ .+.||.|--||+-..
T Consensus 2 ~C~-Cg~~~~~~~s~k~~~N~GR~Fy~C~~~~~ 33 (45)
T PF06839_consen 2 KCP-CGEPAVRRTSKKTGPNPGRRFYKCPNYKD 33 (45)
T ss_pred CCC-CCCEeEEEEEeCCCCCCCCcceECCCCCC
Confidence 477 8865554433 258999999998654
Done!